Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 51 of 163
Found at i:16410410 original size:21 final size:21
Alignment explanation
Indices: 16410376--16410415 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
16410366 CAATTTAACC
**
16410376 TAAGGTATTGATACATGGGGG
1 TAAGGTATCAATACATGGGGG
*
16410397 TAAGGTATCAATACCTGGG
1 TAAGGTATCAATACATGGG
16410416 CCCTAAAATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.10, G:0.33, T:0.28
Consensus pattern (21 bp):
TAAGGTATCAATACATGGGGG
Found at i:16413362 original size:25 final size:27
Alignment explanation
Indices: 16413332--16413390 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 27
16413322 TGAGAATGCA
16413332 AAAATAACA-TACAAACA-AAGC-ATAT
1 AAAATAACATTA-AAACACAAGCAATAT
* *
16413357 AAAATAATATTAAAACACAATCAATAT
1 AAAATAACATTAAAACACAAGCAATAT
16413384 AAAATAA
1 AAAATAA
16413391 AAAAGCTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 13 0.45
26 5 0.17
27 11 0.38
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.20
Consensus pattern (27 bp):
AAAATAACATTAAAACACAAGCAATAT
Found at i:16419471 original size:43 final size:43
Alignment explanation
Indices: 16419419--16419699 Score: 332
Period size: 43 Copynumber: 6.6 Consensus size: 43
16419409 GGCAAATCAA
* * *
16419419 ATGCACAACATATTTGCAAATAAAAATTGCCATTAGGTTGTGG
1 ATGCACAACATATTTGCAGATAAAAATTGTCACTAGGTTGTGG
* * * *
16419462 ATGTACAACATATTTGCAGATAAAAACTGTAACTGGGTTGTGG
1 ATGCACAACATATTTGCAGATAAAAATTGTCACTAGGTTGTGG
* * *
16419505 ATGCACAACATATTTGCAGAT--AAACTGCCACTGGGTTGTGG
1 ATGCACAACATATTTGCAGATAAAAATTGTCACTAGGTTGTGG
* * * *
16419546 ATGCACAACATATTTTCAAAAAAAAAATTGTCATTAGGTTGTGG
1 ATGCACAACATATTTGC-AGATAAAAATTGTCACTAGGTTGTGG
* * *
16419590 TTGCACAACATATTTGCAAATAAAAATTTTCACTAGGTTGTGG
1 ATGCACAACATATTTGCAGATAAAAATTGTCACTAGGTTGTGG
* * * * *
16419633 TTGCACAACATATTTGCAGCTAAAAATTGTCACTGGGCTATGG
1 ATGCACAACATATTTGCAGATAAAAATTGTCACTAGGTTGTGG
*
16419676 ATGCACAGCATATTTGCAGATAAA
1 ATGCACAACATATTTGCAGATAAA
16419700 CTGCCACTCT
Statistics
Matches: 204, Mismatches: 31, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
41 34 0.17
42 2 0.01
43 137 0.67
44 31 0.15
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (43 bp):
ATGCACAACATATTTGCAGATAAAAATTGTCACTAGGTTGTGG
Found at i:16419598 original size:128 final size:128
Alignment explanation
Indices: 16419419--16419693 Score: 372
Period size: 128 Copynumber: 2.1 Consensus size: 128
16419409 GGCAAATCAA
* * *
16419419 ATGCACAACATATTTGCAAATAAAAATTGCCATTAGGTTGTGGATGTACAACATATTTGCAGATA
1 ATGCACAACATATTTGCAAAAAAAAATTGCCATTAGGTTGTGGATGCACAACATATTTGCAAATA
* * * *
16419484 AAAACTGTAACTGGGTTGTGGATGCACAACATATTTGCAG-ATAAACTGCCACTGGGTTGTGG
66 AAAACTGTAACTAGGTTGTGGATGCACAACATATTTGCAGCAAAAACTGCCACTGGGCTATGG
* * *
16419546 ATGCACAACATATTTTCAAAAAAAAAATTGTCATTAGGTTGTGGTTGCACAACATATTTGCAAAT
1 ATGCACAACATATTTGC-AAAAAAAAATTGCCATTAGGTTGTGGATGCACAACATATTTGCAAAT
* * * * * *
16419611 AAAAATTTTCACTAGGTTGTGGTTGCACAACATATTTGCAGCTAAAAATTGTCACTGGGCTATGG
65 AAAAACTGTAACTAGGTTGTGGATGCACAACATATTTGCAGC-AAAAACTGCCACTGGGCTATGG
*
16419676 ATGCACAGCATATTTGCA
1 ATGCACAACATATTTGCA
16419694 GATAAACTGC
Statistics
Matches: 127, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
127 16 0.13
128 78 0.61
129 1 0.01
130 32 0.25
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.31
Consensus pattern (128 bp):
ATGCACAACATATTTGCAAAAAAAAATTGCCATTAGGTTGTGGATGCACAACATATTTGCAAATA
AAAACTGTAACTAGGTTGTGGATGCACAACATATTTGCAGCAAAAACTGCCACTGGGCTATGG
Found at i:16419818 original size:38 final size:38
Alignment explanation
Indices: 16419767--16419839 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
16419757 TGTAATAGAA
* *
16419767 CAATTTAACACTAGCAGTGGACATGCTTAACATGTATT
1 CAATTGAACACTAGCAGTAGACATGCTTAACATGTATT
* * *
16419805 CAATTGAACACTAGTAGTAGACATGTTTATCATGT
1 CAATTGAACACTAGCAGTAGACATGCTTAACATGT
16419840 GCGCAATAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (38 bp):
CAATTGAACACTAGCAGTAGACATGCTTAACATGTATT
Found at i:16426822 original size:22 final size:22
Alignment explanation
Indices: 16426760--16426826 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
16426750 AAGAATATAA
16426760 AAAAATAATTTTTTGAAAATTTA-
1 AAAAAT-ATTTTTT-AAAATTTAT
* ** *
16426783 ATATTTATTTTTT-GAATTTAT
1 AAAAATATTTTTTAAAATTTAT
16426804 AAAAATATTTTTTAAAA-TTAT
1 AAAAATATTTTTTAAAATTTAT
16426825 AA
1 AA
16426827 TTATGTAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
20 6 0.18
21 16 0.47
22 9 0.26
23 3 0.09
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (22 bp):
AAAAATATTTTTTAAAATTTAT
Found at i:16428066 original size:26 final size:24
Alignment explanation
Indices: 16428037--16428086 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
16428027 TTCTTGATTT
16428037 ATATTATAAAATATTATTTAATTAAA
1 ATATTATAAAATA-TA-TTAATTAAA
*
16428063 ATATTATAAATTATATTAATTAAA
1 ATATTATAAAATATATTAATTAAA
16428087 GTTAAGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.39
25 2 0.09
26 12 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATTATAAAATATATTAATTAAA
Found at i:16428103 original size:28 final size:26
Alignment explanation
Indices: 16428037--16428105 Score: 66
Period size: 28 Copynumber: 2.5 Consensus size: 26
16428027 TTCTTGATTT
** *
16428037 ATATTATAAAATATTATTTAATTAAA
1 ATATTATATTATATTATTAAATTAAA
*
16428063 ATATTATAAATTATATTAATTAAAGTTAAG
1 ATATTAT--ATTATATT-ATTAAA-TTAAA
16428093 ATATTATATTATA
1 ATATTATATTATA
16428106 GGAAATAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 7 0.20
28 12 0.34
29 5 0.14
30 11 0.31
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (26 bp):
ATATTATATTATATTATTAAATTAAA
Found at i:16429235 original size:23 final size:22
Alignment explanation
Indices: 16429204--16429289 Score: 106
Period size: 21 Copynumber: 4.0 Consensus size: 22
16429194 GCTTTGTCGA
16429204 TCAGGCACTTTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
*
16429226 CTCAAGCACTTTATGTGTCGTA-
1 -TCAGGCACTTTATGTGTCGTAT
* **
16429248 TCAGGCACCTCGTGTGTCGT-T
1 TCAGGCACTTTATGTGTCGTAT
16429269 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
16429290 ACTGATTAGA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 9 0.17
21 25 0.46
23 20 0.37
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.37
Consensus pattern (22 bp):
TCAGGCACTTTATGTGTCGTAT
Found at i:16431541 original size:18 final size:18
Alignment explanation
Indices: 16431514--16431548 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16431504 AAACTTTTAA
*
16431514 TTTTTGCTCAAAAATATT
1 TTTTTACTCAAAAATATT
16431532 TTTTTACTCAAAAATAT
1 TTTTTACTCAAAAATAT
16431549 ATTTGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (18 bp):
TTTTTACTCAAAAATATT
Found at i:16432850 original size:3 final size:3
Alignment explanation
Indices: 16432842--16432900 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
16432832 CCTATAGGTG
* * *
16432842 TAA TAA TAA TATA TAA T-A TAA TTA TAA TTA TAA TAA CAA TAA TTAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
16432888 TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TA
16432901 GTGAAAAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 4 0.09
3 36 0.78
4 6 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:16437280 original size:40 final size:40
Alignment explanation
Indices: 16437227--16437342 Score: 139
Period size: 40 Copynumber: 3.0 Consensus size: 40
16437217 AGTTTGGATA
16437227 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAT-
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTT-TG
** *
16437267 AAAAACGCCACTAAAGGTCGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTG
* * * *
16437307 GAAAATGCCGCTAAAAAT-AAGCATTACCGGCG-TTTT
1 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTT
16437343 CCAAAAAGCG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
38 4 0.06
39 13 0.20
40 48 0.74
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:16437466 original size:41 final size:41
Alignment explanation
Indices: 16437397--16437598 Score: 289
Period size: 41 Copynumber: 5.0 Consensus size: 41
16437387 TGAGTTTTTG
* *
16437397 GGGCCTTTAGCGGTGTTTTTGAAAAAGCGCCGCTAATTCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
16437438 GGGCCTTTAGCGGCGTTTGTGAAGAAGCGCAGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* ** *
16437479 GGGCCTTTAGTGGCGTTTTTGAATCAGCGCAGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
16437520 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGATT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
16437561 GGGCCTTTAGCGGCGTTTTTG-AAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
16437599 CCGCTTTTGA
Statistics
Matches: 143, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 16 0.11
41 127 0.89
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:16438074 original size:14 final size:15
Alignment explanation
Indices: 16438046--16438078 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
16438036 AAGATTTATA
16438046 GATTATGGAATTAGG
1 GATTATGGAATTAGG
16438061 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
16438075 GATT
1 GATT
16438079 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:16438327 original size:14 final size:14
Alignment explanation
Indices: 16438297--16438342 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
16438287 TAAATAAGAT
*
16438297 TTAGGGGTTAGTAG
1 TTAGGGGTTAGGAG
*
16438311 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
* *
16438325 TTAGAGGTTAAGAG
1 TTAGGGGTTAGGAG
16438339 TTAG
1 TTAG
16438343 TGATTTAAGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:16438341 original size:21 final size:21
Alignment explanation
Indices: 16438291--16438342 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
16438281 ATATATTAAA
*
16438291 TAAGATTTAGGGGTTAGTAGT
1 TAAGAGTTAGGGGTTAGTAGT
* *
16438312 TAGGGGTTAGGGGTTAG-AGGT
1 TAAGAGTTAGGGGTTAGTA-GT
16438333 TAAGAGTTAG
1 TAAGAGTTAG
16438343 TGATTTAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.27, C:0.00, G:0.40, T:0.33
Consensus pattern (21 bp):
TAAGAGTTAGGGGTTAGTAGT
Found at i:16443659 original size:43 final size:43
Alignment explanation
Indices: 16443599--16443689 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
16443589 CTTTGAGTTC
* * * *
16443599 ATTA-CAAGATTTCCTTGATTAAGTAAATGTATTATATCTTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
*
16443641 ATTACCAAGATTTACTTGATTAAGAAAATGCATTGTATATTTT
1 ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
16443684 ATTACC
1 ATTACC
16443690 TTGCATATGT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 4 0.09
43 39 0.91
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (43 bp):
ATTACCAAGATTTACTTGATTAAGAAAATGCATTATATATTTT
Found at i:16444084 original size:42 final size:42
Alignment explanation
Indices: 16443965--16444168 Score: 252
Period size: 42 Copynumber: 4.8 Consensus size: 42
16443955 AAGATATATT
** *
16443965 TTTAGCGGCGTTTGTGTTAAAAGCGTCGCTAAAGGTCTAT--TC
1 TTTAGCGGCGTTTGTG-GGAAAGCGCCGCTAAAGGTCT-TGGTC
* *
16444007 TATAGCGACGTTTGTGGGAAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGG--AAAGCGCCGCTAAAGGTCTTGGTC
*
16444051 TTTAGCGGCGTTTGTGGGGAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
* * *
16444093 TTTAGTGGCGTTTGTAGGG-AAGCGCCGCTAGAGGTCATGGTC
1 TTTAGCGGCGTTTGT-GGGAAAGCGCCGCTAAAGGTCTTGGTC
16444135 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGG-AAAGCGCCGCTAAAG
16444169 TTAGCGACGC
Statistics
Matches: 142, Mismatches: 13, Indels: 13
0.85 0.08 0.08
Matches are distributed among these distances:
41 3 0.02
42 87 0.61
43 34 0.24
44 18 0.13
ACGTcount: A:0.20, C:0.18, G:0.34, T:0.28
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTGGGAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:16446882 original size:17 final size:16
Alignment explanation
Indices: 16446839--16446890 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
16446829 AAAAGAATAG
16446839 AAGAAGAATAAAGCGAAA
1 AAGAAGAA-AAAG-GAAA
*
16446857 AAGAGGAAAAAGGAAA
1 AAGAAGAAAAAGGAAA
*
16446873 AAGAAAGAAAAATGAAA
1 AAG-AAGAAAAAGGAAA
16446890 A
1 A
16446891 GACGAAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.23
17 16 0.53
18 7 0.23
ACGTcount: A:0.71, C:0.02, G:0.23, T:0.04
Consensus pattern (16 bp):
AAGAAGAAAAAGGAAA
Found at i:16449431 original size:26 final size:25
Alignment explanation
Indices: 16449393--16449442 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
16449383 AATATTTAAA
*
16449393 AAGAGATATAGATATATATACATAAT
1 AAGAGATAAAGATATATATA-ATAAT
* *
16449419 AAGATATAAAGATATTTATAATAA
1 AAGAGATAAAGATATATATAATAA
16449443 GTTATATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.56, C:0.02, G:0.10, T:0.32
Consensus pattern (25 bp):
AAGAGATAAAGATATATATAATAAT
Found at i:16449455 original size:22 final size:22
Alignment explanation
Indices: 16449414--16449455 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16449404 ATATATATAC
*
16449414 ATAATAAGATATAAAGATATTT
1 ATAATAAGATATAAACATATTT
* *
16449436 ATAATAAGTTATATACATAT
1 ATAATAAGATATAAACATAT
16449456 GTATGTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (22 bp):
ATAATAAGATATAAACATATTT
Found at i:16452602 original size:23 final size:23
Alignment explanation
Indices: 16452546--16452602 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
16452536 TGTAGTGTAA
*
16452546 GTATGTTTATATTATTTTGTAGT
1 GTATGTTTATTTTATTTTGTAGT
*
16452569 ATATGTTTATTTTATTTTGTAGT
1 GTATGTTTATTTTATTTTGTAGT
16452592 GTATGTTTATT
1 GTATGTTTATT
16452603 AAGATAGGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.63
Consensus pattern (23 bp):
GTATGTTTATTTTATTTTGTAGT
Found at i:16458470 original size:2 final size:2
Alignment explanation
Indices: 16458463--16458489 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16458453 CTTCTAGAAT
16458463 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
16458490 AATTGACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16463254 original size:18 final size:18
Alignment explanation
Indices: 16463224--16463259 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
16463214 GCTGTTACGT
16463224 TTATAATATTATTTTTTA
1 TTATAATATTATTTTTTA
16463242 TTAT-ATATATATTTTTTA
1 TTATAATAT-TATTTTTTA
16463260 AAAAGAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATAATATTATTTTTTA
Found at i:16463329 original size:128 final size:127
Alignment explanation
Indices: 16463099--16463346 Score: 322
Period size: 128 Copynumber: 1.9 Consensus size: 127
16463089 TATAATATTC
* *
16463099 ATAATATTATTTTTATTATATATATACATTTAAACAGAAAGTAAAAGAAACTTATATATAAAATA
1 ATAATATTATTTTTATTATATATATACATTTAAAAAGAAAGTAAAAGAAACTTATAAATAAAATA
* * * * *
16463164 ATTGGGTGTTAGAACTCGGACCTGTGATCGACGGGTCACATCAGTGGCAGGCTGTTACGTTT
66 ATTGGGTATTAGAACCCAGACCCGTGATCGACAGGTCACATCAGTGGCAGGCTGTTACGTTT
** *
16463226 ATAATATTATTTTTTATTATATATATATTTTTTAAAAAGAAAGT-AAA-AAAGTTGATAAATAAA
1 ATAATATTA-TTTTTATTATATATATA-CATTTAAAAAGAAAGTAAAAGAAACTT-ATAAATAAA
* * *
16463289 ATAATTGGGTATTGGAACCCAGACCCGTG-GCTGACAGGTCACATCGGTGGCAGGCTGT
63 ATAATTGGGTATTAGAACCCAGACCCGTGATC-GACAGGTCACATCAGTGGCAGGCTGT
16463347 CAGGCTGGTG
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
127 15 0.14
128 76 0.73
129 13 0.12
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (127 bp):
ATAATATTATTTTTATTATATATATACATTTAAAAAGAAAGTAAAAGAAACTTATAAATAAAATA
ATTGGGTATTAGAACCCAGACCCGTGATCGACAGGTCACATCAGTGGCAGGCTGTTACGTTT
Found at i:16465731 original size:35 final size:35
Alignment explanation
Indices: 16465685--16465755 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
16465675 TAACATTTTA
* *
16465685 TAGGAGTTTAGAAGAGGTAAATATTGCACAAACTT
1 TAGGAGTTTAGAAGAGGTAAAAATTACACAAACTT
16465720 TAGGAGTTTAGAAGAGGTAAAAATTACACAAACTT
1 TAGGAGTTTAGAAGAGGTAAAAATTACACAAACTT
16465755 T
1 T
16465756 CTCATTTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.28
Consensus pattern (35 bp):
TAGGAGTTTAGAAGAGGTAAAAATTACACAAACTT
Found at i:16472186 original size:78 final size:78
Alignment explanation
Indices: 16472042--16472189 Score: 181
Period size: 78 Copynumber: 1.9 Consensus size: 78
16472032 TTATGTTTGT
* * * ** *
16472042 AAACAAAAATCAATTGAACAATTCTATTTCAGGATTTTATTCCTGTCGTTTAACAGGATTTGTTC
1 AAACAAAAATCAATTGAACAATTCTATTTCAGGATTTTATTACTATCGTTCAACAAAATTTATTC
16472107 GATTTTTTGTTTC
66 GATTTTTTGTTTC
* * * * *
16472120 AAACAGAAATCAATTGAATATTTCTGTTTCAGGATTCTT-TTATTATCGTTCAACAAAATTTATT
1 AAACAAAAATCAATTGAACAATTCTATTTCAGGATT-TTATTACTATCGTTCAACAAAATTTATT
16472184 CGATTT
65 CGATTT
16472190 CTGTTGTTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
78 56 0.97
79 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (78 bp):
AAACAAAAATCAATTGAACAATTCTATTTCAGGATTTTATTACTATCGTTCAACAAAATTTATTC
GATTTTTTGTTTC
Found at i:16481458 original size:26 final size:26
Alignment explanation
Indices: 16481427--16481478 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
16481417 AAAGTACAAG
*
16481427 TACTATTAACCGCTCTTTAGCGTACA
1 TACTATTAACCACTCTTTAGCGTACA
16481453 TACTATTAACCACTCTTTAGCGTACA
1 TACTATTAACCACTCTTTAGCGTACA
16481479 CACATCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.35
Consensus pattern (26 bp):
TACTATTAACCACTCTTTAGCGTACA
Found at i:16484905 original size:18 final size:17
Alignment explanation
Indices: 16484872--16484910 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
16484862 TTTTATAAAT
16484872 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
16484890 TGTGAATTACTA-TTGAA
1 TGTGAATTA-TATTTGAA
16484907 TGTG
1 TGTG
16484911 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 13 0.65
19 2 0.10
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:16485172 original size:23 final size:23
Alignment explanation
Indices: 16485135--16485226 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
16485125 TTGATTATTA
*
16485135 GTAGCTTCGGCTACATTTCAGTG
1 GTAGCTTCGGCTACATATCAGTG
* *
16485158 GTAGCTACGGTTACATATCAGTG
1 GTAGCTTCGGCTACATATCAGTG
* * *
16485181 ATAGCTTTGGCTACGTATCAGTG
1 GTAGCTTCGGCTACATATCAGTG
*
16485204 GTAGCTTCGACTACATATCAGTG
1 GTAGCTTCGGCTACATATCAGTG
16485227 TGGCACTTAT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
GTAGCTTCGGCTACATATCAGTG
Found at i:16487525 original size:48 final size:46
Alignment explanation
Indices: 16487461--16487576 Score: 117
Period size: 48 Copynumber: 2.4 Consensus size: 46
16487451 AGAATAAGTT
**
16487461 AATATGACTACATATGTGTTAT-ACATTAAGATATGAAAAGAGTAAACA
1 AATATGACTATGTATGTGTTATGACA-T-AGAT-TGAAAAGAGTAAACA
* * * *
16487509 AATATGACTCTGTATGTGCTATATGCCATATATTGAAAAGAGTAAGCA
1 AATATGACTATGTATGTG-T-TATGACATAGATTGAAAAGAGTAAACA
*
16487557 AATATGATTATGTATGTGTT
1 AATATGACTATGTATGTGTT
16487577 GTTATTATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
46 1 0.02
47 1 0.02
48 45 0.79
49 4 0.07
50 4 0.07
51 2 0.04
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.34
Consensus pattern (46 bp):
AATATGACTATGTATGTGTTATGACATAGATTGAAAAGAGTAAACA
Found at i:16497875 original size:16 final size:16
Alignment explanation
Indices: 16497854--16497892 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
16497844 TTTTAATAAA
16497854 ATTAAAACTAATTATT
1 ATTAAAACTAATTATT
* *
16497870 ATTAAAATTAATTGTT
1 ATTAAAACTAATTATT
*
16497886 AGTAAAA
1 ATTAAAA
16497893 TCATCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
ATTAAAACTAATTATT
Found at i:16497878 original size:22 final size:23
Alignment explanation
Indices: 16497825--16497880 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 23
16497815 TCCGTTTTTA
* *
16497825 ATTAAAATTAAAATTATATTTTT
1 ATTAAAATTAAAACTATATTATT
*
16497848 AATAAAATTAAAACTA-ATTATT
1 ATTAAAATTAAAACTATATTATT
16497870 ATTAAAATTAA
1 ATTAAAATTAA
16497881 TTGTTAGTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTATT
Found at i:16498789 original size:19 final size:21
Alignment explanation
Indices: 16498761--16498809 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
16498751 GTTTTTTTAC
*
16498761 TAAAATAATAC-AAAAGAA-A
1 TAAAAAAATACTAAAAGAATA
*
16498780 TAAAAAAATACTAAAATAATA
1 TAAAAAAATACTAAAAGAATA
16498801 TACAAAAAA
1 TA-AAAAAA
16498810 AATTATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.40
20 6 0.24
21 3 0.12
22 6 0.24
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAAAAAATACTAAAAGAATA
Found at i:16498893 original size:27 final size:27
Alignment explanation
Indices: 16498863--16498925 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
16498853 GGTAATGGAA
* * *
16498863 TGGCGGCACCGGTGGTGCCTTTCTCAT
1 TGGCGGCACCGGTGATGCCATTCCCAT
16498890 TGGCGGCACCGGTGATGCCATTCCCAT
1 TGGCGGCACCGGTGATGCCATTCCCAT
16498917 TGGCGGCAC
1 TGGCGGCAC
16498926 AAGACTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.11, C:0.32, G:0.33, T:0.24
Consensus pattern (27 bp):
TGGCGGCACCGGTGATGCCATTCCCAT
Found at i:16499771 original size:17 final size:16
Alignment explanation
Indices: 16499739--16499778 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
16499729 ATTTTTTTTG
16499739 TATTTTATTTTAGTAT
1 TATTTTATTTTAGTAT
* *
16499755 TTTTTTATTTTTTGTAT
1 TATTTTA-TTTTAGTAT
16499772 TATTTTA
1 TATTTTA
16499779 GTAAAAACCC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (16 bp):
TATTTTATTTTAGTAT
Found at i:16499775 original size:28 final size:27
Alignment explanation
Indices: 16499703--16499783 Score: 90
Period size: 29 Copynumber: 2.9 Consensus size: 27
16499693 TTCAGCCGTC
*
16499703 TTTTTTTTGTATTATTTTGGTAAATAA
1 TTTTTTTTGTATTATTTTAGTAAATAA
** **
16499730 TTTTTTTTGTATTTTATTTTAGTATTTTT
1 TTTTTTTTGTA--TTATTTTAGTAAATAA
16499759 TTATTTTTTGTATTATTTTAGTAAA
1 TT-TTTTTTGTATTATTTTAGTAAA
16499784 AACCCCGCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.25
28 11 0.25
29 13 0.30
30 9 0.20
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (27 bp):
TTTTTTTTGTATTATTTTAGTAAATAA
Found at i:16510471 original size:22 final size:23
Alignment explanation
Indices: 16510438--16510480 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
16510428 TTATTAAATC
16510438 TTTTATTATTTTCAAAATTTTCA
1 TTTTATTATTTTCAAAATTTTCA
*
16510461 TTTT-TTATTTTTAAAATTTT
1 TTTTATTATTTTCAAAATTTT
16510481 TATAGCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTATTTTCAAAATTTTCA
Found at i:16518782 original size:130 final size:130
Alignment explanation
Indices: 16518545--16518902 Score: 447
Period size: 130 Copynumber: 2.8 Consensus size: 130
16518535 GAAATATGTA
* * * * *
16518545 AAACAAATCACTGATTTAAAGTCACAACTGATATTATTAATGCTC-TCTAATTTACGATCACAAA
1 AAACAACTCACTGATTTAAAGTCACAACTGATATTATTAAGGTTCGT-TGATTTACGATCACAAC
* * * *
16518609 CTAAGTTCATTGATTTACTATCATGAAAAATCTTCTCTAAGTTAGTTGATTTACTATTGTTACTT
65 CTAAGTTCATTGATTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATCTACTATTGCTACTT
*
16518674 T
130 C
* * * *
16518675 AAACAGA-T-AGCTGATTTAAGGTCACAGCTGACATTATTAAGGTTCGTTGATTTATGATCACAA
1 AAACA-ACTCA-CTGATTTAAAGTCACAACTGATATTATTAAGGTTCGTTGATTTACGATCACAA
* * *
16518738 CCTAAATTCATTAATTTACTATCATGAACAATCTTCTCTGAGTTAGCTGATCTACTATTGCTACT
64 CCTAAGTTCATTGATTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATCTACTATTGCTACT
16518803 TC
129 TC
* * *
16518805 AAACAACTCACTGATTTAATA-TCACAATTGATGTTATTAAGGATT-GTTGATTTACGATCACAT
1 AAACAACTCACTGATTTAA-AGTCACAACTGATATTATTAAGG-TTCGTTGATTTACGATCACAA
*
16518868 CCTAAGTTTATTGATTTACTATCATGAACAATCTT
64 CCTAAGTTCATTGATTTACTATCATGAACAATCTT
16518903 TCCCAAGTTG
Statistics
Matches: 195, Mismatches: 26, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
129 2 0.01
130 188 0.96
131 5 0.03
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (130 bp):
AAACAACTCACTGATTTAAAGTCACAACTGATATTATTAAGGTTCGTTGATTTACGATCACAACC
TAAGTTCATTGATTTACTATCATGAACAATCTTCTCTAAGTTAGCTGATCTACTATTGCTACTTC
Found at i:16523983 original size:16 final size:16
Alignment explanation
Indices: 16523962--16523992 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16523952 AATATATTTT
*
16523962 TGTAAATGTGATAATG
1 TGTAAATATGATAATG
16523978 TGTAAATATGATAAT
1 TGTAAATATGATAAT
16523993 TGGATATTGG
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:0.42, C:0.00, G:0.19, T:0.39
Consensus pattern (16 bp):
TGTAAATATGATAATG
Found at i:16525682 original size:22 final size:22
Alignment explanation
Indices: 16525657--16525699 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
16525647 TAATAATCCC
16525657 AAATTAAATTAGA-TATAAATTG
1 AAATT-AATTAGATTATAAATTG
*
16525679 AAATTAATTATATTATAAATT
1 AAATTAATTAGATTATAAATT
16525700 AATACATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
AAATTAATTAGATTATAAATTG
Found at i:16527068 original size:19 final size:21
Alignment explanation
Indices: 16527044--16527086 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16527034 GCACCTAGGA
16527044 TGATTGT-TTTGA-CATGTTT
1 TGATTGTATTTGATCATGTTT
*
16527063 TGATTGTATTTGATCGTGTTT
1 TGATTGTATTTGATCATGTTT
16527084 TGA
1 TGA
16527087 ACTAGTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (21 bp):
TGATTGTATTTGATCATGTTT
Found at i:16528307 original size:15 final size:16
Alignment explanation
Indices: 16528287--16528316 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16528277 TTTATTTAAA
16528287 TTTTAATAA-GAAAAT
1 TTTTAATAATGAAAAT
16528302 TTTTAATAATGAAAA
1 TTTTAATAATGAAAA
16528317 ATGAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (16 bp):
TTTTAATAATGAAAAT
Found at i:16528448 original size:13 final size:13
Alignment explanation
Indices: 16528425--16528460 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
16528415 CAGAAAAAGG
*
16528425 AAAAAAATATTTT
1 AAAAGAATATTTT
*
16528438 ATAAGAATATTTT
1 AAAAGAATATTTT
16528451 AAAAGAATAT
1 AAAAGAATAT
16528461 AGAAAATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (13 bp):
AAAAGAATATTTT
Found at i:16529037 original size:14 final size:14
Alignment explanation
Indices: 16529014--16529055 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
16529004 TACAATATCC
16529014 AAATAATAACAATA
1 AAATAATAACAATA
*
16529028 AAATAGTAACAATA
1 AAATAATAACAATA
*
16529042 TAATAATAA-AATA
1 AAATAATAACAATA
16529055 A
1 A
16529056 CATCAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
13 4 0.17
14 20 0.83
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:16529066 original size:22 final size:22
Alignment explanation
Indices: 16529018--16529069 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
16529008 ATATCCAAAT
**
16529018 AATAACAATAAAATAGTAACAA
1 AATAACAATAAAATAACAACAA
* * *
16529040 TATAATAATAAAATAACATCAA
1 AATAACAATAAAATAACAACAA
16529062 AATAACAA
1 AATAACAA
16529070 ACAAAACAGT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (22 bp):
AATAACAATAAAATAACAACAA
Found at i:16529764 original size:134 final size:135
Alignment explanation
Indices: 16529509--16529852 Score: 356
Period size: 134 Copynumber: 2.5 Consensus size: 135
16529499 ATCATTATCC
* * * * * * * *
16529509 TTGTTGTTGATCTC-TGATATGCCATTTTTCTTTTCTTTCATCTCTCTGTCTGAATGTTAAAGAT
1 TTGTTGTCGACCTCTTGATAAGCCATTATACTTTTCTTTTATCTCTCTATATGAATGTTAAAGAT
* * * *
16529573 TTTTGTTCTTGTTCATTTCTCATACAAAGTCATTTCAAGGCATTGAAATTATCTGCTCAT-ATGC
66 TTTTGTTCTTATTCATGTCTCATACAAAGTCATTTCAAGGCACTGAAACTATCTGCTCATAATGC
16529637 TATTA
131 TATTA
* * * * *
16529642 TTGTTGTTGACCTTTTGATAAGCTATTATACTTTTCTTTTATCTCTCTATATGAATGTCAAAGCT
1 TTGTTGTCGACCTCTTGATAAGCCATTATACTTTTCTTTTATCTCTCTATATGAATGTTAAAGAT
* * *
16529707 TTTTGTTCTTATTCATGTCTCATGCAAAGTCATTTCAAGGTACT-ACAACTATTTGCTCATACAA
66 TTTTGTTCTTATTCATGTCTCATACAAAGTCATTTCAAGGCACTGA-AACTATCTGCTCAT--AA
* *
16529771 TGTTATTG
128 TGCTATTA
* * * * *
16529779 TTGTTGTCGATCTCTTGATATGCCATTATA-TTATTGTTTTATCTCAT-TATATGACTGTTGAAG
1 TTGTTGTCGACCTCTTGATAAGCCATTATACTT-TTCTTTTATCTC-TCTATATGAATGTTAAAG
*
16529842 TTTTTTGTTCT
64 ATTTTTGTTCT
16529853 CATTTCAAGG
Statistics
Matches: 174, Mismatches: 30, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
133 13 0.07
134 92 0.53
136 2 0.01
137 66 0.38
138 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.13, T:0.49
Consensus pattern (135 bp):
TTGTTGTCGACCTCTTGATAAGCCATTATACTTTTCTTTTATCTCTCTATATGAATGTTAAAGAT
TTTTGTTCTTATTCATGTCTCATACAAAGTCATTTCAAGGCACTGAAACTATCTGCTCATAATGC
TATTA
Found at i:16534674 original size:16 final size:17
Alignment explanation
Indices: 16534648--16534680 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16534638 ATAAATTTAA
16534648 CTCATTTCAATATAATC
1 CTCATTTCAATATAATC
*
16534665 CTCA-TTCAATTTAATC
1 CTCATTTCAATATAATC
16534681 TAACATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.42
Consensus pattern (17 bp):
CTCATTTCAATATAATC
Found at i:16545192 original size:13 final size:13
Alignment explanation
Indices: 16545176--16545223 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
16545166 CTCTCTACGC
*
16545176 GAGCCCTATGTGT
1 GAGCCCAATGTGT
* * *
16545189 GAGCTCAATATGC
1 GAGCCCAATGTGT
16545202 GAGCCCAATGTGT
1 GAGCCCAATGTGT
*
16545215 GAGCTCAAT
1 GAGCCCAAT
16545224 ACACAAGCCT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (13 bp):
GAGCCCAATGTGT
Found at i:16545193 original size:26 final size:26
Alignment explanation
Indices: 16545160--16545249 Score: 108
Period size: 26 Copynumber: 3.5 Consensus size: 26
16545150 TTTAGCGTCA
** *
16545160 TGTGAGCTCTCTACGCGAGCCCTATG
1 TGTGAGCTCAATACGCGAGCCCAATG
*
16545186 TGTGAGCTCAATATGCGAGCCCAATG
1 TGTGAGCTCAATACGCGAGCCCAATG
* * *
16545212 TGTGAGCTCAATACACAAGCCTAATG
1 TGTGAGCTCAATACGCGAGCCCAATG
*
16545238 TGCGAGCTCAAT
1 TGTGAGCTCAAT
16545250 GTGTGAACCA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (26 bp):
TGTGAGCTCAATACGCGAGCCCAATG
Found at i:16545252 original size:13 final size:13
Alignment explanation
Indices: 16545183--16545252 Score: 52
Period size: 13 Copynumber: 5.4 Consensus size: 13
16545173 CGCGAGCCCT
*
16545183 ATGTGTGAGCTCA
1 ATGTGCGAGCTCA
* *
16545196 ATATGCGAGCCCA
1 ATGTGCGAGCTCA
*
16545209 ATGTGTGAGCTCA
1 ATGTGCGAGCTCA
*** *
16545222 ATACACAAGC-CTA
1 ATGTGCGAGCTC-A
16545235 ATGTGCGAGCTCA
1 ATGTGCGAGCTCA
16545248 ATGTG
1 ATGTG
16545253 TGAACCATTT
Statistics
Matches: 40, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
12 1 0.03
13 38 0.95
14 1 0.03
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (13 bp):
ATGTGCGAGCTCA
Found at i:16545495 original size:20 final size:19
Alignment explanation
Indices: 16545466--16545526 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
16545456 TTTTTTAAAT
*
16545466 AAATACAAAAA-ATTTTAGA
1 AAATAAAAAAAGATTTTA-A
16545485 AAATTAAAAAAAGTATTTTAA
1 AAA-TAAAAAAAG-ATTTTAA
16545506 AAAT-AAAAAAGTATTTTAA
1 AAATAAAAAAAG-ATTTTAA
16545525 AA
1 AA
16545527 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 20 0.53
20 8 0.21
21 4 0.11
22 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATAAAAAAAGATTTTAA
Found at i:16545513 original size:19 final size:21
Alignment explanation
Indices: 16545477--16545526 Score: 77
Period size: 19 Copynumber: 2.4 Consensus size: 21
16545467 AATACAAAAA
16545477 ATTTTAGAAAATTAAAAAAAGT
1 ATTTTA-AAAATTAAAAAAAGT
16545499 ATTTTAAAAA-T-AAAAAAGT
1 ATTTTAAAAATTAAAAAAAGT
16545518 ATTTTAAAA
1 ATTTTAAAA
16545527 TATTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.61
20 1 0.04
21 4 0.14
22 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (21 bp):
ATTTTAAAAATTAAAAAAAGT
Found at i:16565482 original size:23 final size:23
Alignment explanation
Indices: 16565456--16565501 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
16565446 AGTTCTGTTC
16565456 TGATGAGTTTAATAAACTGTGCA
1 TGATGAGTTTAATAAACTGTGCA
16565479 TGATGAGTTTAATAAACTGTGCA
1 TGATGAGTTTAATAAACTGTGCA
16565502 AGTCGGAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.35
Consensus pattern (23 bp):
TGATGAGTTTAATAAACTGTGCA
Found at i:16567785 original size:5 final size:5
Alignment explanation
Indices: 16567775--16567804 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
16567765 ATTATACTTC
16567775 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
16567805 GAATAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:16568806 original size:29 final size:30
Alignment explanation
Indices: 16568752--16568820 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
16568742 GAGAGCTTTC
* *
16568752 AATAAAAAAAAGTAAAAAGAAGTC-AAAGA
1 AATAGAAAAAAGTAAAAAGAACTCAAAAGA
* *
16568781 AATAGAAAAAAGTAATCAA-AACTCAAAAGC
1 AATAGAAAAAAGTAA-AAAGAACTCAAAAGA
16568811 AATAGAAAAA
1 AATAGAAAAA
16568821 GAAATATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.12
Consensus pattern (30 bp):
AATAGAAAAAAGTAAAAAGAACTCAAAAGA
Found at i:16569640 original size:17 final size:18
Alignment explanation
Indices: 16569606--16569651 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
16569596 CCGTTATGTC
16569606 CGCGACCGCGA-C--AAA
1 CGCGACCGCGACCGAAAA
16569621 CGCGA-CGCGACCGAAAA
1 CGCGACCGCGACCGAAAA
16569638 CGCGACCGCGACCG
1 CGCGACCGCGACCG
16569652 CAATTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 6 0.22
17 8 0.30
18 8 0.30
ACGTcount: A:0.28, C:0.41, G:0.30, T:0.00
Consensus pattern (18 bp):
CGCGACCGCGACCGAAAA
Found at i:16570798 original size:14 final size:15
Alignment explanation
Indices: 16570778--16570818 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
16570768 TTTGTTTGCC
16570778 AGTAAAATGTTTTC-
1 AGTAAAATGTTTTCT
* *
16570792 GGTAAAATGATTTCT
1 AGTAAAATGTTTTCT
16570807 AG-AAAATGTTTT
1 AGTAAAATGTTTT
16570819 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.05, G:0.17, T:0.41
Consensus pattern (15 bp):
AGTAAAATGTTTTCT
Found at i:16570831 original size:34 final size:35
Alignment explanation
Indices: 16570787--16570853 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16570777 CAGTAAAATG
*
16570787 TTTTCGGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCGGTAAAATGATTTACTAGAAAATATTTTAC
* *
16570821 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCGGTAAAATGATTTACTAGAAAATATTTT
16570854 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCGGTAAAATGATTTACTAGAAAATATTTTAC
Found at i:16570918 original size:32 final size:32
Alignment explanation
Indices: 16570832--16570918 Score: 88
Period size: 33 Copynumber: 2.7 Consensus size: 32
16570822 TTTCTGTAAA
* *
16570832 ATGATTTACTGGAAAATATTTTCTGGTGTTTGG
1 ATGATTTCCT-GAAAATATTTTCTGCTGTTTGG
* *
16570865 ATGA-ATCTGTGTAAAATATTTTCTGCTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGCTGTTTGG
16570898 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
16570919 TCGGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
32 12 0.27
33 29 0.66
34 3 0.07
ACGTcount: A:0.26, C:0.09, G:0.20, T:0.45
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGCTGTTTGG
Found at i:16574779 original size:12 final size:12
Alignment explanation
Indices: 16574762--16574787 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16574752 CAAAACAGGC
16574762 TTTTAGCGGCGT
1 TTTTAGCGGCGT
16574774 TTTTAGCGGCGT
1 TTTTAGCGGCGT
16574786 TT
1 TT
16574788 GGATAAAAAA
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:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:16575119 original size:112 final size:114
Alignment explanation
Indices: 16574916--16575210 Score: 368
Period size: 112 Copynumber: 2.6 Consensus size: 114
16574906 GTTTTTAAGC
* * ** * *
16574916 TTTCTG-AGCTTTCGGGGATTT-GCGGCGCTTTTAAGAAAGCGCCGCTAATGTTCGGGGTTTTAG
1 TTTCTGAAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATCCT-AGGGCTTTAG
* * *
16574979 CGGCATTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGT
65 CGGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACGCCGT
* * *
16575029 TTT-T-AAGCTTTCGGGGATTTAGCGACATTTTTAAGTATGCGCCGCTAATCCTAGGGCTTTAGC
1 TTTCTGAAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATCCTAGGGCTTTAGC
*
16575092 GGCGTTTTTGATAAAGCGCCGCAAAAAAACCTAAGCCCAACAACGCCGT
66 GGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACGCCGT
* * * *
16575141 TTTCTGAA-CTTTCAGGGATTTAGCGGCGTTTTT-GGTAAAGCGCCACTAATGCCCAGGGCTTTA
1 TTTCTGAAGCTTTCGGGGATTTAGCGGCGTTTTTAAGT-AAGCGCCGCTAAT-CCTAGGGCTTTA
16575204 GCGGCGT
64 GCGGCGT
16575211 CGGCGTTTTT
Statistics
Matches: 156, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
112 75 0.48
113 61 0.39
114 20 0.13
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (114 bp):
TTTCTGAAGCTTTCGGGGATTTAGCGGCGTTTTTAAGTAAGCGCCGCTAATCCTAGGGCTTTAGC
GGCGTTTTTGAGAAAGCGCCGCAAAAAAACCTAAGCCCAACAACGCCGT
Found at i:16575488 original size:147 final size:146
Alignment explanation
Indices: 16575222--16576161 Score: 935
Period size: 147 Copynumber: 6.2 Consensus size: 146
16575212 GGCGTTTTTG
* *
16575222 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTAGAATAGCAAAACGAC
1 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGC
*
16575287 GTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCCGCTAAAGGTAAGCAA
66 GTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAA
16575352 TAGCGGCGTTTCCTAT
131 TAGCGGCGTTTCCTAT
* *
16575368 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAAATAAAAAATTTTTAAAATAGCAAAACGG
1 AAAAACGCCGCAAAAAATAAATCAACTTAT-AAAAAAATAAAAAAATTTTAGAATAGCAAAACGG
* *
16575433 CGTCATTTTGTTCAAAACGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCA
65 CGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCA
16575498 ATAGCGGCGTTTCCTAT
130 ATAGCGGCGTTTCCTAT
*
16575515 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGG
1 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAAT-AAAAAAATTTTAGAATAGCAAAACGG
*** ** * * * ** *
16575580 CGTCGTTTTGTTCAAAATGAAAAAATTTTGAAAACGCTGCAAAAAATAAATCAAT-TTATAA---
65 CGTCGTTTTGTTCAAAATGAAAAAATTTTG-CGGCGCT--TTATAA-GAAGCGCTGCTA-AAGGT
** ****** *
16575641 AAAAAATAAAAAATTTTTCTTTAT
125 AAGCAAT-AGCGGCGTTTC-CTAT
* ** * **
16575665 AAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCA
1 AA-AAACGCCGC-AAA---AAATAA-ATCAAC---T--TAT-------------AAAA-AAAT--
16575730 ATTTATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGC
39 A---A--AAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGC
16575795 GCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTAT
99 GCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTAT
* *
16575843 AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGG
1 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAAT-AAAAAAATTTTAGAATAGCAAAACGG
*
16575908 CGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGC--T-T--------CT--TATAGGTAAGCA
65 CGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCA
*
16575960 ATAGCGGCGTTTCATAT
130 ATAGCGGCGTTTCCTAT
*
16575977 AAAAACGCTGCAAAAAATAAATCAACTTATAAAAAAATTTTAAAAAAA-TTTAGAATAGCAAAAC
1 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAA---TAAAAAAATTTTAGAATAGCAAAAC
* * *
16576041 GGCGTCGTTTTGTTCAAAATGAAAAAAAATTTGCGGCGCTTTATAGGAAGCGCCGCTAAAGGTAA
63 GGCGTCGTTTTGTTCAAAATG-AAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAA
*
16576106 GCAATAGTGGCGTTTCCTAT
127 GCAATAGCGGCGTTTCCTAT
* *
16576126 AAAAACGCCGCAAAAAATAAATCAATTTATTAAAAA
1 AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAA
16576162 TTTCCCAAAA
Statistics
Matches: 653, Mismatches: 80, Indels: 119
0.77 0.09 0.14
Matches are distributed among these distances:
134 62 0.09
135 36 0.06
136 25 0.04
137 1 0.00
138 1 0.00
139 1 0.00
144 1 0.00
145 1 0.00
146 38 0.06
147 250 0.38
148 9 0.01
149 65 0.10
150 10 0.02
151 14 0.02
152 5 0.01
153 4 0.01
154 4 0.01
155 4 0.01
156 3 0.00
159 1 0.00
161 3 0.00
167 3 0.00
169 1 0.00
172 2 0.00
173 4 0.01
174 4 0.01
175 4 0.01
176 5 0.01
177 14 0.02
178 10 0.02
179 6 0.01
180 9 0.01
181 53 0.08
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (146 bp):
AAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAATTTTAGAATAGCAAAACGGC
GTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAA
TAGCGGCGTTTCCTAT
Found at i:16575816 original size:137 final size:140
Alignment explanation
Indices: 16575659--16576155 Score: 632
Period size: 137 Copynumber: 3.5 Consensus size: 140
16575649 AAAAATTTTT
16575659 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
1 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
16575724 AAATCAA-TT-T-ATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAA
66 AAATCAACTTATAATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAA
16575786 TTTTGCGGCG
131 TTTTGCGGCG
*
16575796 CTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
1 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
* *
16575861 AAATCAATTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGGCGTCGTTTTGTTCAAAAT
66 AAATCAACTTAT-----AAT--AAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAAT
16575926 GAAAAAATTTTGCGGCG
124 GAAAAAATTTTGCGGCG
* *
16575943 CTTCT-T----A-------T--AGGTAAGCAATAGCGGCGTTTCATATAAAAACGCTGCAAAAAA
1 CTT-TATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAA
*
16575994 TAAATCAACTTATAAAAAAATTTTAAAAAAATTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAA
65 TAAATCAACTTAT-----AA---TAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAA
*
16576059 ATGAAAAAAAATTTGCGGCG
122 ATG-AAAAAATTTTGCGGCG
* *
16576079 CTTTATAGGAAGCGCCGCTAAAGGTAAGCAATAGTGGCGTTTCCTATAAAAACGCCGCAAAAAAT
1 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
*
16576144 AAATCAATTTAT
66 AAATCAACTTAT
16576156 TAAAAATTTC
Statistics
Matches: 319, Mismatches: 12, Indels: 46
0.85 0.03 0.12
Matches are distributed among these distances:
134 60 0.19
135 43 0.13
136 20 0.06
137 72 0.23
138 2 0.01
139 1 0.00
140 1 0.00
143 1 0.00
145 2 0.01
147 64 0.20
148 1 0.00
149 52 0.16
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (140 bp):
CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
AAATCAACTTATAATAAAAAATTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAA
TTTTGCGGCG
Found at i:16575842 original size:328 final size:332
Alignment explanation
Indices: 16575321--16575937 Score: 1116
Period size: 328 Copynumber: 1.9 Consensus size: 332
16575311 TTTTGCGGCG
16575321 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
1 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
16575386 AAATCAACTTATAAAAAAAATAAAAAATTTTTAAAATAGCAAAACGGCGTCATTTTGTTCAAAAC
66 AAATCAACTTAT------AATAAAAAATTTTTAAAATAGCAAAACGGCGTCATTTTGTTCAAAAC
16575451 GAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTATA
125 GAAAAAATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTATA
16575516 AAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGGC
190 AAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGGC
16575581 GTCGTTTTGTTCAAAATGAAAAAATTTTGAAAACGCTGCAAAAAATAAATCAATTTATAAAAAAA
255 GTCGTTTTGTTCAAAATGAAAAAATTTTGAAAACGCTGCAAAAAATAAATCAATTTATAAAAAAA
16575646 ATAAAAAATTTTT
320 ATAAAAAATTTTT
16575659 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
1 CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
* * *
16575724 AAATCAA-TT-T-ATAAAAAA-TTTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAA
66 AAATCAACTTATAATAAAAAATTTTTAAAATAGCAAAACGGCGTCATTTTGTTCAAAACGAAAAA
16575785 ATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACG
131 ATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACG
*
16575850 CCGCAAAAAATAAATCAATTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGGCGTCGTT
196 CCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGGCGTCGTT
16575915 TTGTTCAAAATGAAAAAATTTTG
261 TTGTTCAAAATGAAAAAATTTTG
16575938 CGGCGCTTCT
Statistics
Matches: 275, Mismatches: 4, Indels: 10
0.95 0.01 0.03
Matches are distributed among these distances:
328 192 0.70
329 8 0.03
336 1 0.00
337 2 0.01
338 72 0.26
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.25
Consensus pattern (332 bp):
CTTTATAAGAAGCGCCGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAAT
AAATCAACTTATAATAAAAAATTTTTAAAATAGCAAAACGGCGTCATTTTGTTCAAAACGAAAAA
ATTTTGCGGCGCTTTATAAGAAGCGCTGCTAAAGGTAAGCAATAGCGGCGTTTCCTATAAAAACG
CCGCAAAAAATAAATCAACTTATAAAAAAATAAAAAAAATTTTAGAATAGCAAAAAGGCGTCGTT
TTGTTCAAAATGAAAAAATTTTGAAAACGCTGCAAAAAATAAATCAATTTATAAAAAAAATAAAA
AATTTTT
Found at i:16576087 original size:134 final size:134
Alignment explanation
Indices: 16575817--16576081 Score: 442
Period size: 134 Copynumber: 2.0 Consensus size: 134
16575807 GCGCTGCTAA
* *
16575817 AGGTAAGCAATAGCGGCGTTTCCTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATA
1 AGGTAAGCAATAGCGGCGTTTCATATAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATA
*
16575882 AAAAAAATTTTAGAATAGCAAAAAGGCGTCGTTTTGTTCAAAATGAAAAAATTTTGCGGCGCTTC
66 AAAAAAATTTTAGAATAGCAAAAAGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTC
16575947 TTAT
131 TTAT
*
16575951 AGGTAAGCAATAGCGGCGTTTCATATAAAAACGCTGCAAAAAATAAATCAACTTATAAAAAAATT
1 AGGTAAGCAATAGCGGCGTTTCATATAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAA--
* *
16576016 TTAAAAAAA-TTTAGAATAGCAAAACGGCGTCGTTTTGTTCAAAATGAAAAAAAATTTGCGGCGC
64 TAAAAAAAATTTTAGAATAGCAAAAAGGCGTCGTTTTGTTCAAAATG-AAAAAAATTTGCGGCGC
16576080 TT
128 TT
16576082 TATAGGAAGC
Statistics
Matches: 122, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
134 60 0.49
135 36 0.30
136 26 0.21
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (134 bp):
AGGTAAGCAATAGCGGCGTTTCATATAAAAACGCCGCAAAAAATAAATCAACTTATAAAAAAATA
AAAAAAATTTTAGAATAGCAAAAAGGCGTCGTTTTGTTCAAAATGAAAAAAATTTGCGGCGCTTC
TTAT
Found at i:16576924 original size:14 final size:14
Alignment explanation
Indices: 16576899--16576938 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16576889 ATATATTAAA
*
16576899 TAAGGTTTAGGGGT
1 TAAGGATTAGGGGT
*
16576913 TATGGATTAGGGGT
1 TAAGGATTAGGGGT
*
16576927 TAAGGGTTAGGG
1 TAAGGATTAGGG
16576939 ATTCAAGATC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.45, T:0.33
Consensus pattern (14 bp):
TAAGGATTAGGGGT
Found at i:16578786 original size:20 final size:20
Alignment explanation
Indices: 16578761--16578803 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
16578751 TATACAAAGT
16578761 TTGGGTTCAAGTATAAATTA
1 TTGGGTTCAAGTATAAATTA
16578781 TTGGGTTCAAGTATAAATTA
1 TTGGGTTCAAGTATAAATTA
16578801 TTG
1 TTG
16578804 AGGCTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (20 bp):
TTGGGTTCAAGTATAAATTA
Found at i:16578830 original size:13 final size:13
Alignment explanation
Indices: 16578812--16578841 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
16578802 TGAGGCTTAA
16578812 TTATATGCCTTGT
1 TTATATGCCTTGT
16578825 TTATATGCCTTGT
1 TTATATGCCTTGT
16578838 TTAT
1 TTAT
16578842 GCATTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.13, G:0.13, T:0.57
Consensus pattern (13 bp):
TTATATGCCTTGT
Found at i:16579895 original size:85 final size:84
Alignment explanation
Indices: 16579724--16579972 Score: 327
Period size: 85 Copynumber: 2.9 Consensus size: 84
16579714 TTTTTGCGAG
* * * *
16579724 AAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAACGCCGCTAAAGGTCGTAATC
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCTTGATC
* * * *
16579789 TATAGCAGCATTTTTTGAAA
66 TATAGCGGC-GTTTGTAAAA
* * * *
16579809 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCCTTTGTGGTATAAGCGCCGCTAATGGTCTTGAT
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCTTGAT
16579874 CTATAGCGGCGTTTGTAAAA
65 CTATAGCGGCGTTTGTAAAA
* * * *
16579894 AAGCACCGCTAAAGATCCTGATCTATAGCGGCGTTTGTTGAAAAAGCGCCGCTAAAGGTCTTGAT
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTG-TGAAAAAGCGCCGCTAAAGGTCTTGAT
16579959 CTATAGCGGCGTTT
65 CTATAGCGGCGTTT
16579973 ATTTATAAAA
Statistics
Matches: 142, Mismatches: 20, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
85 112 0.79
86 30 0.21
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (84 bp):
AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAGCGCCGCTAAAGGTCTTGATC
TATAGCGGCGTTTGTAAAA
Found at i:16579952 original size:128 final size:128
Alignment explanation
Indices: 16579724--16579968 Score: 375
Period size: 128 Copynumber: 1.9 Consensus size: 128
16579714 TTTTTGCGAG
* * * *
16579724 AAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAACGCCGCTAAAGGTCGTAATC
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAACACCGCTAAAGATCCTAATC
*
16579789 TATAGCAGCATTTTTTGAAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCCTTTGTGGTAT
66 TATAGCAGCATTTGTTGAAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCCTTTGTGGTAT
* * *
16579852 AAGCGCCGCTAATGGTCTTGATCTATAGCGGCGTTTGT-AAAAAAGCACCGCTAAAGATCCTGAT
1 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAA-CACCGCTAAAGATCCTAAT
* * *
16579916 CTATAGCGGCGTTTGTTGAAAAAGCGCCGCTAAAGGTCTTGATCTATAGCGGC
65 CTATAGCAGCATTTGTTGAAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGC
16579969 GTTTATTTAT
Statistics
Matches: 105, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
127 6 0.06
128 99 0.94
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (128 bp):
AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCGTTTGTGAAAAAACACCGCTAAAGATCCTAATC
TATAGCAGCATTTGTTGAAAAAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCCTTTGTGGTAT
Found at i:16579969 original size:43 final size:43
Alignment explanation
Indices: 16579724--16579972 Score: 322
Period size: 43 Copynumber: 5.8 Consensus size: 43
16579714 TTTTTGCGAG
* *
16579724 AAGCGTCGCTAAAGGTCTTGAGCTATAGCGGCGTTTG-TGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTTGAAA
* * * * * *
16579766 AAACGCCGCTAAAGGTCGTAATCTATAGCAGCATTTTTTGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTTGAAA
* * * * *
16579809 AAGCGCCGCTAAAGGTCTTGAGCTATAGCGGCCTTTGTGGTAT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTTGAAA
* *
16579852 AAGCGCCGCTAATGGTCTTGATCTATAGCGGCGTTTG-TAAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTTGAAA
* * *
16579894 AAGCACCGCTAAAGATCCTGATCTATAGCGGCGTTTGTTGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTTGAAA
16579937 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
16579973 ATTTATAAAA
Statistics
Matches: 172, Mismatches: 33, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
42 63 0.37
43 109 0.63
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTTGAAA
Found at i:16584453 original size:40 final size:40
Alignment explanation
Indices: 16584402--16584886 Score: 671
Period size: 40 Copynumber: 11.9 Consensus size: 40
16584392 GTTTATTTCG
16584402 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
*
16584442 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG-GTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGAG-GC-GA
16584484 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
*
16584524 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTG-GTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGAG-GC-GA
*
16584566 TCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
*
16584606 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
* *
16584646 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTG-GTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGAG-GC-GA
*
16584688 TCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
*
16584728 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
* *
16584768 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTG-GTTCTG-
1 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGAG-GC-GA
*
16584810 TCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGCGA
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
16584850 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGG
1 TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGG
16584887 TGGCTTAGGG
Statistics
Matches: 399, Mismatches: 22, Indels: 48
0.85 0.05 0.10
Matches are distributed among these distances:
39 4 0.01
40 242 0.61
41 24 0.06
42 125 0.31
43 4 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (40 bp):
TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
Found at i:16584490 original size:82 final size:82
Alignment explanation
Indices: 16584401--16584879 Score: 735
Period size: 82 Copynumber: 5.9 Consensus size: 82
16584391 GGTTTATTTC
16584401 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
16584466 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
16584483 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
16584548 ATAAGATCTGTGGTTCT
66 ATAAGATCTGTGGTTCT
*
16584565 GTCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
*
16584630 ATAAGA-CT-TGAG--GT
66 ATAAGATCTGTG-GTTCT
* *
16584644 GATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTG-GTTCTG-TCTGCTCCACTACTGCTTA
1 G-TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGAG-GC-GATCTGCTCCACTACTGCTTA
* *
16584707 GAGAGATAAGA-CT-TGAG-GC-
61 GGGAGATAAGATCTGTG-GTTCT
* *
16584726 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGATCTGCTCCACTACTACTTAGGGA
1 G-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGA
16584791 GATAAGATCTGTGGTTCT
65 GATAAGATCTGTGGTTCT
*
16584809 GTCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
1 GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
16584874 ATAAGA
66 ATAAGA
16584880 CTTGAGGTGG
Statistics
Matches: 368, Mismatches: 16, Indels: 26
0.90 0.04 0.06
Matches are distributed among these distances:
79 3 0.01
80 60 0.16
81 12 0.03
82 291 0.79
83 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (82 bp):
GTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAG
ATAAGATCTGTGGTTCT
Found at i:16584530 original size:122 final size:122
Alignment explanation
Indices: 16584402--16584986 Score: 879
Period size: 122 Copynumber: 4.9 Consensus size: 122
16584392 GTTTATTTCG
* * *
16584402 TCTGCTCCACTACTGCTTAGGGAGATAAGA-CT-TGAG-GC-GATCTGCTCCACTACTGCTTAGG
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTG-GTTCTG-TCTGCTCCACTACTGCTTAGA
* *
16584463 GAGATAAGATCTGTG-GTTCTG-TCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGA
64 GAGATAAGA-CT-TGAG-GC-GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
*
16584524 TCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
16584589 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
66 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
16584646 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
16584711 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
66 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
16584768 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
16584833 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTG-
66 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
* *
16584889 ---G-----------CTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGA
1 TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
* *
16584940 GATAAGAGTTGAGGCTATCTGCTCCACTACTGCTTAGGGAGATAAGA
66 GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGA
16584987 TATGTGGTTT
Statistics
Matches: 448, Mismatches: 9, Indels: 27
0.93 0.02 0.06
Matches are distributed among these distances:
107 93 0.21
118 1 0.00
121 1 0.00
122 314 0.70
123 6 0.01
124 32 0.07
125 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (122 bp):
TCTGCTCCACTACTACTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGA
GATAAGACTTGAGGCGATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGA
Found at i:16584969 original size:107 final size:107
Alignment explanation
Indices: 16584783--16584986 Score: 372
Period size: 107 Copynumber: 1.9 Consensus size: 107
16584773 TCCACTACTA
16584783 CTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGC
1 CTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGC
16584848 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGG
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGG
* * *
16584890 CTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACTGCTTAGGGAGATAAGAGTTGAGGC
1 CTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGC
*
16584955 TATCTGCTCCACTACTGCTTAGGGAGATAAGA
66 GATCTGCTCCACTACTGCTTAGGGAGATAAGA
16584987 TATGTGGTTT
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 93 1.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (107 bp):
CTTAGGGAGATAAGATCTGTGGTTCTGTCTGCTCCACTACTGCTTAGAGAGATAAGACTTGAGGC
GATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGTGG
Found at i:16585012 original size:40 final size:38
Alignment explanation
Indices: 16584889--16585012 Score: 90
Period size: 40 Copynumber: 3.1 Consensus size: 38
16584879 ACTTGAGGTG
* **
16584889 GCTTAGGGAGATAAGATCTGTGGTTTTGTCTGCTCCACTACT
1 GCTTAGGGAGATAAGAT-TGTGGTTTTATCCACT-C-C-ACT
* **
16584931 GCTTAGGGAGATAAGAGTTGAGGCTATCTGCTCCACT--ACT
1 GCTTAGGGAGATAAGA-TTGTGG-T-T-TTATCCACTCCACT
16584971 GCTTAGGGAGATAAGATATGTGGTTTTAATCCACTCCACT
1 GCTTAGGGAGATAAGAT-TGTGGTTTT-ATCCACTCCACT
16585011 GC
1 GC
16585013 AACTTCAGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
37 1 0.02
38 7 0.11
39 2 0.03
40 28 0.42
42 20 0.30
43 2 0.03
44 1 0.02
45 5 0.08
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
GCTTAGGGAGATAAGATTGTGGTTTTATCCACTCCACT
Found at i:16585777 original size:82 final size:82
Alignment explanation
Indices: 16585640--16586712 Score: 2137
Period size: 82 Copynumber: 13.1 Consensus size: 82
16585630 NNNNNNNNNN
16585640 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16585705 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16585722 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16585787 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16585804 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16585869 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16585886 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16585951 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16585968 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586033 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586050 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586115 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586132 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586197 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586214 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586279 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586296 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586361 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586378 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586443 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586460 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586525 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586542 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
16586607 CTTAGGGAGATAAGATC
66 CTTAGGGAGATAAGATC
16586624 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
1 TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
*
16586689 CTTAGGGAGATAAGATA
66 CTTAGGGAGATAAGATC
16586706 TGTGGTT
1 TGTGGTT
16586713 TTAATCCACT
Statistics
Matches: 990, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 990 1.00
ACGTcount: A:0.22, C:0.22, G:0.27, T:0.29
Consensus pattern (82 bp):
TGTGGTTCTGTCTGCTCCACTACTGCTTAGGGAGATAAGACTTGAGGCGATCTGCTCCACTACTG
CTTAGGGAGATAAGATC
Found at i:16586895 original size:100 final size:100
Alignment explanation
Indices: 16586766--16587632 Score: 1238
Period size: 100 Copynumber: 8.7 Consensus size: 100
16586756 TTTCAAATTG
** * * * *
16586766 ATTGCAATGTCGGGGAAATAAGATTCGTCGTTGTAGCTTCAATCTGTTCCACTGCACCGCCAAGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
*
16586831 AAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAA
66 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
16586866 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
*
16586931 AAGTAAGATTCGCTGTTGCGGCTTCAATCTTTTAA
66 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
** * * *
16586966 ATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCGTCAATCTGCTCCACTGCATTGCCATGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
* * *
16587031 AAGTAAGATTCACCTTTGTGGCTTCAATCTTTTAA
66 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
*
16587066 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATTGCCATGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
* *
16587131 AAGTAAGATTCGCCGTTACGGCCTCAATCTTTTAA
66 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
* * * * * *
16587166 ATTGCAATGTTGAGGAAGCAAGATTCGCCGTTGTAACTTTAATCTGC-CCTATTGCATTGCCATG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCC-ACTGCATCGCCATG
*
16587230 GAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTAA
65 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
* * * * * *
16587266 ATTGCAATGTCGGGGAAGGAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCATCACCATGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
* *
16587331 AAGTAAGATTCGCCGTTGTGGCCTCAATCTTTTAA
66 AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
*** *
16587366 ATTGCAATGTAAAGGAAGCAAGATTCG-CTGTTGTAGCTTTAATCTGCCCCACTGCATCGCCATG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTC-GTTGTAGCTTTAATCTGCTCCACTGCATCGCCATG
16587430 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
65 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
* *
16587466 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGTTCCACTGCATCACC-TGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCAT-G
* * *
16587530 GAAGTAAGATTCGTCGTTGTGGCTTCAATCCTTTAA
65 GAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
* * * * * *
16587566 ATTGCAATGTTGGGGAA-CAAGTTTCGTAGTTGTAGCTTCAATCTGCTCCACTGCATTGCCAGGG
1 ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
16587630 AAG
66 AAG
16587633 GTAACTTCAT
Statistics
Matches: 688, Mismatches: 73, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
99 46 0.07
100 639 0.93
101 3 0.00
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.31
Consensus pattern (100 bp):
ATTGCAATGTCGGGGAAGCAAGATTCGTCGTTGTAGCTTTAATCTGCTCCACTGCATCGCCATGG
AAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTAA
Found at i:16587945 original size:24 final size:24
Alignment explanation
Indices: 16587912--16587969 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
16587902 CCGGACTGCC
*
16587912 CCACTGTAATCTTCAAAGTTCAAT
1 CCACTATAATCTTCAAAGTTCAAT
* *
16587936 CCACTATAATCTTCAAGGTTCAGT
1 CCACTATAATCTTCAAAGTTCAAT
16587960 CCACTATAAT
1 CCACTATAAT
16587970 TTAGGGACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (24 bp):
CCACTATAATCTTCAAAGTTCAAT
Found at i:16588604 original size:97 final size:93
Alignment explanation
Indices: 16588442--16588623 Score: 258
Period size: 97 Copynumber: 1.9 Consensus size: 93
16588432 CAAAAATGCT
*
16588442 TGAAAAAGATTATCACAATGGATAAAAATTTATTGAGAACAAAGCCCGAAATGAATAAATTAATC
1 TGAAAAAGATTATCACAATGGATAAAAATTTATTGAGAACAAAGCCCGAAATGAATAAATCAATC
*
16588507 AAGATAGCAA-ATTTTGCTAAGATAAGA
66 AAGATAACAATATTTTGCTAAGATAAGA
** *
16588534 TGAAAAAGATTATCACAATGGATAAGGTGAAATTTTATTGAGAACAAAGCTTGAAATGAATGAAT
1 TGAAAAAGATTATCACAATGGATAA----AAA-TTTATTGAGAACAAAGCCCGAAATGAATAAAT
*
16588599 CAATCAAGATAACAATTTTTTGCTA
61 CAATCAAGATAACAATATTTTGCTA
16588624 GAATGAGAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
92 25 0.32
96 3 0.04
97 42 0.54
98 8 0.10
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.27
Consensus pattern (93 bp):
TGAAAAAGATTATCACAATGGATAAAAATTTATTGAGAACAAAGCCCGAAATGAATAAATCAATC
AAGATAACAATATTTTGCTAAGATAAGA
Found at i:16588992 original size:23 final size:22
Alignment explanation
Indices: 16588953--16588997 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
16588943 TGGCCTCTCC
*
16588953 TTTTTCTTTTTTGTTCTTCTTTT
1 TTTTTCTTTTGTGTTCTT-TTTT
16588976 TTTTTCTTTTCGT-TTCTTTTTT
1 TTTTTCTTTT-GTGTTCTTTTTT
16588998 CAAGTGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 15 0.75
24 1 0.05
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.82
Consensus pattern (22 bp):
TTTTTCTTTTGTGTTCTTTTTT
Found at i:16589446 original size:10 final size:10
Alignment explanation
Indices: 16589431--16589473 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
16589421 CTAGTAGAGG
16589431 TTTTTTTGTT
1 TTTTTTTGTT
16589441 TTTTTTTG-T
1 TTTTTTTGTT
* *
16589450 CTCTTTTGTT
1 TTTTTTTGTT
16589460 CTTTTTTTGTT
1 -TTTTTTTGTT
16589471 TTT
1 TTT
16589474 GTGTTTTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 7 0.26
10 12 0.44
11 8 0.30
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:16589458 original size:19 final size:17
Alignment explanation
Indices: 16589432--16589481 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 17
16589422 TAGTAGAGGT
16589432 TTTTTTGTTTTTTTTTG
1 TTTTTTGTTTTTTTTTG
16589449 TCTCTTTTGTTCTTTTTTTG
1 T-T-TTTTGTT-TTTTTTTG
16589469 TTTTTGTGTTTTT
1 TTTTT-TGTTTTT
16589482 GGTTTTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.03
18 7 0.24
19 12 0.41
20 9 0.31
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.82
Consensus pattern (17 bp):
TTTTTTGTTTTTTTTTG
Found at i:16589481 original size:25 final size:26
Alignment explanation
Indices: 16589432--16589493 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
16589422 TAGTAGAGGT
*
16589432 TTTTTTGTTTTTTTTTGTCTCTTTT-G
1 TTTTTT-TTTGTTTTTGTCTCTTTTGG
*
16589458 TTCTTTTTTTGTTTTTGTGT-TTTTGG
1 TT-TTTTTTTGTTTTTGTCTCTTTTGG
16589484 TTTTTTTTTG
1 TTTTTTTTTG
16589494 CCTTCACTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 12 0.38
26 16 0.50
27 4 0.12
ACGTcount: A:0.00, C:0.05, G:0.15, T:0.81
Consensus pattern (26 bp):
TTTTTTTTTGTTTTTGTCTCTTTTGG
Found at i:16592247 original size:19 final size:20
Alignment explanation
Indices: 16592223--16592267 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
16592213 TGTGAAAATC
16592223 TAATGCATATG-ATGCAATG
1 TAATGCATATGTATGCAATG
*
16592242 TAATGCATATGTATGGAATG
1 TAATGCATATGTATGCAATG
16592262 -AATGCA
1 TAATGCA
16592268 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (20 bp):
TAATGCATATGTATGCAATG
Found at i:16595072 original size:16 final size:17
Alignment explanation
Indices: 16595040--16595072 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16595030 ATTTTTGTGT
*
16595040 TAAAAAACATAATAAAA
1 TAAAAAACATAAAAAAA
16595057 TAAAAAA-ATAAAAAAA
1 TAAAAAACATAAAAAAA
16595073 CAATCGGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (17 bp):
TAAAAAACATAAAAAAA
Found at i:16596745 original size:334 final size:335
Alignment explanation
Indices: 16596125--16596794 Score: 1315
Period size: 334 Copynumber: 2.0 Consensus size: 335
16596115 GCATTTGTAG
16596125 TGTTTAGTAAGTTGGCACTGCTTGAGGTGTTTCAAGGTTTGCCACTACCTTATATGGATGTAACT
1 TGTTTAGTAAGTTGGCACTGCTTGAGGTGTTTCAAGGTTTGCCACTACCTTATATGGATGTAACT
* *
16596190 AATAAAGGCAAAATTCTATTTGTGCATATGGATGTGATTTCTTGACCTTTAACCCAATAACAATG
66 AATAAAGGCAAAATTCTATTTGTGCAAATGAATGTGATTTCTTGACCTTTAACCCAATAACAATG
16596255 GGTTGGATGAGAATTGACATTGCTAATTTGGTGATTTGCATTGTGCAGCATGTACCCAAAATTAA
131 GGTTGGATGAGAATTGACATTGCTAATTTGGTGATTTGCATTGTGCAGCATGTACCCAAAATTAA
16596320 TGGAGTAATACCATCAGTTGATGAAGAGACATCTGACCATCAAAGGCTGCATGATAGGTTTGGCT
196 TGGAGTAATACCATCAGTTGATGAAGAGACATCTGACCATCAAAGGCTGCATGATAGGTTTGGCT
16596385 TGAATTTTTCCTTTATATAGCTAATGGCATCTTGGTCTATTTTTTTATTCTGTTACTTTGTGGCA
261 TGAATTTTTCCTTTATATAGCTAATGGCATCTTGGTCTATTTTTTTATTCTGTTACTTTGTGGCA
16596450 ATTAACTTTA
326 ATTAACTTTA
16596460 TGTTTAGTAA-TTGGCACTGCTTGAGGTGTTTCAAGGTTTGCCACTACCTTATATGGATGTAACT
1 TGTTTAGTAAGTTGGCACTGCTTGAGGTGTTTCAAGGTTTGCCACTACCTTATATGGATGTAACT
16596524 AATAAAGGCAAAATTCTATTTGTGCAAATGAATGTGATTTCTTGACCTTTAACCCAATAACAATG
66 AATAAAGGCAAAATTCTATTTGTGCAAATGAATGTGATTTCTTGACCTTTAACCCAATAACAATG
16596589 GGTTGGATGAGAATTGACATTGCTAATTTGGTGATTTGCATTGTGCAGCATGTACCCAAAATTAA
131 GGTTGGATGAGAATTGACATTGCTAATTTGGTGATTTGCATTGTGCAGCATGTACCCAAAATTAA
16596654 TGGAGTAATACCATCAGTTGATGAAGAGACATCTGACCATCAAAGGCTGCATGATAGGTTTGGCT
196 TGGAGTAATACCATCAGTTGATGAAGAGACATCTGACCATCAAAGGCTGCATGATAGGTTTGGCT
16596719 TGAATTTTTCCTTTATATAGCTAATGGCATCTTGGTCTATTTTTTTATTCTGTTACTTTGTGGCA
261 TGAATTTTTCCTTTATATAGCTAATGGCATCTTGGTCTATTTTTTTATTCTGTTACTTTGTGGCA
16596784 ATTAACTTTA
326 ATTAACTTTA
16596794 T
1 T
16596795 CACCCTAGTT
Statistics
Matches: 333, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
334 323 0.97
335 10 0.03
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (335 bp):
TGTTTAGTAAGTTGGCACTGCTTGAGGTGTTTCAAGGTTTGCCACTACCTTATATGGATGTAACT
AATAAAGGCAAAATTCTATTTGTGCAAATGAATGTGATTTCTTGACCTTTAACCCAATAACAATG
GGTTGGATGAGAATTGACATTGCTAATTTGGTGATTTGCATTGTGCAGCATGTACCCAAAATTAA
TGGAGTAATACCATCAGTTGATGAAGAGACATCTGACCATCAAAGGCTGCATGATAGGTTTGGCT
TGAATTTTTCCTTTATATAGCTAATGGCATCTTGGTCTATTTTTTTATTCTGTTACTTTGTGGCA
ATTAACTTTA
Found at i:16596971 original size:38 final size:39
Alignment explanation
Indices: 16596929--16597006 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
16596919 ACTCTTGTAT
*
16596929 TGGGATCCATTTTGGTAAAGTAGTTGCT-CTTTTTTCCC
1 TGGGATCCATTTTGGTAAAGTAATTGCTGCTTTTTTCCC
*
16596967 TGGGATCCATTTTGGTAAAGTAATTGCTGTTTTTTTCCC
1 TGGGATCCATTTTGGTAAAGTAATTGCTGCTTTTTTCCC
16597006 T
1 T
16597007 TTTCTCAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 27 0.73
39 10 0.27
ACGTcount: A:0.17, C:0.17, G:0.21, T:0.46
Consensus pattern (39 bp):
TGGGATCCATTTTGGTAAAGTAATTGCTGCTTTTTTCCC
Found at i:16598175 original size:24 final size:24
Alignment explanation
Indices: 16598107--16598175 Score: 61
Period size: 24 Copynumber: 2.9 Consensus size: 24
16598097 GAGGATGAGT
* *
16598107 TTTATGCAAAATATAATTCTCAAG
1 TTTATGCAAAATATAATTATTAAG
* * *
16598131 -TTATGTTAATATATGAA-TATTATG
1 TTTATG-CAAAATAT-AATTATTAAG
16598155 TTTATGCAAAATATAATTATT
1 TTTATGCAAAATATAATTATT
16598176 TGCTAAGGGT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
23 7 0.21
24 20 0.59
25 7 0.21
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (24 bp):
TTTATGCAAAATATAATTATTAAG
Found at i:16598315 original size:45 final size:44
Alignment explanation
Indices: 16598228--16598320 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 44
16598218 ATTACAACAT
16598228 CATTCCATTCAACCAAACACAAAAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAAAATACTATTACAGTTCTATTC
* *
16598272 CATTCCATTTAACCAAACA-ATAGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-A-AAATACTATTACAGTTCTATTC
16598317 CATT
1 CATT
16598321 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 19 0.42
45 25 0.56
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAAAATACTATTACAGTTCTATTC
Found at i:16598323 original size:16 final size:16
Alignment explanation
Indices: 16598302--16598357 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
16598292 TAGAATTACT
*
16598302 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCC
*
16598318 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
*
16598334 ATTACTGCTCTATTCC
1 ATTACAGCTCTATTCC
16598350 ATTACAGC
1 ATTACAGC
16598358 GAACCAAACG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:16604417 original size:21 final size:21
Alignment explanation
Indices: 16604391--16604430 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16604381 TAGAATGAAT
16604391 TTGTATACTAGTCTTTCAATC
1 TTGTATACTAGTCTTTCAATC
16604412 TTGTATACTAGTCTTTCAA
1 TTGTATACTAGTCTTTCAA
16604431 ACTAGAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
TTGTATACTAGTCTTTCAATC
Found at i:16613496 original size:47 final size:47
Alignment explanation
Indices: 16613426--16613883 Score: 630
Period size: 47 Copynumber: 9.7 Consensus size: 47
16613416 NNNNNNNNNN
16613426 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
* *
16613473 CCCATTTTAATGTGTAATGCTGTCCAATTTTGAGTGTATTGATGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
*
16613520 TCCATTTTAATGTGTAATGCTGTCCAATTTTGAGTGTATTGATGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
*
16613567 CCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
*
16613614 TCCATTGTAATGTATAATATGCTGTCCAATTTTGAGTGTATTGATGCTG
1 TCCATTTTAATGTAT-A-ATGCTGTCCAATTTTGAGTGTATTGATGCTG
*
16613663 TCCATTTTAATGTGTAATGCTGTCCAATTTTGAGTGTATTGATGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
* * * * *
16613710 TCCATTTTAATATATAATGCTGTCCAATTGTGAGTATATTTAAGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
* * * * * * *
16613757 TCTAATTTGATGTATAATGCTGTCCAATTGTGAGTATATTTAAGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
* * * * * * * *
16613804 TCTAATTTGATGGATAATGCTGTCCAATTTTGGGTATATTTAAGCTG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
* * *
16613851 TCGAATTTGATGTATAATGCTGTCC-ATTTTGAG
1 TCCATTTTAATGTATAATGCTGTCCAATTTTGAG
16613884 CATGTTATTG
Statistics
Matches: 384, Mismatches: 25, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
46 7 0.02
47 331 0.86
48 2 0.01
49 44 0.11
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (47 bp):
TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
Found at i:16613772 original size:190 final size:187
Alignment explanation
Indices: 16613426--16613883 Score: 630
Period size: 190 Copynumber: 2.4 Consensus size: 187
16613416 NNNNNNNNNN
*
16613426 TCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTGCCCATTTTAATGTGTAAT
1 TCCA-TTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAAT
* * * *
16613491 GCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATGCTGTCCAATTTTGAGTG
65 GCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGCTGTCCAATTGTGAGTA
* * * * *
16613556 TATTGATGCTGCCCATTTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTG
130 TATTGAAGCTGCCCAATTTAATGTATAATGCTGTCCAATTGTGAGTATATTGAAGCTG
16613614 TCCATTGTAATGTATAATATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTA
1 TCCATT-TAATGTAT-A-ATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTA
16613679 ATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGCTGTCCAATTGTGAG
63 ATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGCTGTCCAATTGTGAG
* * * * *
16613744 TATATTTAAGCTGTCTAATTTGATGTATAATGCTGTCCAATTGTGAGTATATTTAAGCTG
128 TATATTGAAGCTGCCCAATTTAATGTATAATGCTGTCCAATTGTGAGTATATTGAAGCTG
* * * * * * * * * * *
16613804 TCTAATTTGATGGATAATGCTGTCCAATTTTGGGTATATTTAAGCTGTCGAATTTGATGTATAAT
1 TC-CATTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAAT
16613869 GCTGTCC-ATTTTGAG
65 GCTGTCCAATTTTGAG
16613884 CATGTTATTG
Statistics
Matches: 240, Mismatches: 26, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
187 10 0.04
188 60 0.25
189 2 0.01
190 165 0.69
191 3 0.01
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (187 bp):
TCCATTTAATGTATAATGCTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATGTGTAATG
CTGTCCAATTTTGAGTGTATTGATGCTGTCCATTTTAATATATAATGCTGTCCAATTGTGAGTAT
ATTGAAGCTGCCCAATTTAATGTATAATGCTGTCCAATTGTGAGTATATTGAAGCTG
Found at i:16616840 original size:18 final size:18
Alignment explanation
Indices: 16616817--16616853 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16616807 AAGCCGAGAT
16616817 TGATCCGATGGGTACTTC
1 TGATCCGATGGGTACTTC
16616835 TGATCCGATGGGTACTTC
1 TGATCCGATGGGTACTTC
16616853 T
1 T
16616854 ACTTTAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.35
Consensus pattern (18 bp):
TGATCCGATGGGTACTTC
Found at i:16618734 original size:16 final size:15
Alignment explanation
Indices: 16618707--16618740 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
16618697 ATAACAAGTA
*
16618707 TATAATTATATTTAT
1 TATAATTATATTAAT
16618722 TATAATATATATTAAT
1 TATAAT-TATATTAAT
16618738 TAT
1 TAT
16618741 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:16620264 original size:3 final size:3
Alignment explanation
Indices: 16620256--16620280 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16620246 GAGGATCCCA
16620256 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
16620281 TCCCATAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16624375 original size:17 final size:17
Alignment explanation
Indices: 16624353--16624396 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
16624343 TTTATAAACA
16624353 TATATCATTCATTTCAT-
1 TATATCATT-ATTTCATG
*
16624370 TATATCAATATTTCATG
1 TATATCATTATTTCATG
16624387 TATCATCATT
1 TAT-ATCATT
16624397 TTCATGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 7 0.30
17 11 0.48
18 5 0.22
ACGTcount: A:0.32, C:0.16, G:0.02, T:0.50
Consensus pattern (17 bp):
TATATCATTATTTCATG
Found at i:16624803 original size:24 final size:24
Alignment explanation
Indices: 16624776--16624854 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
16624766 ATATAACGAA
16624776 AAGCTCATAAGAGCCATAATCGGG
1 AAGCTCATAAGAGCCATAATCGGG
** *
16624800 AAGCTCATGTGAGCCAATAA-CAGG
1 AAGCTCATAAGAGCC-ATAATCGGG
* ** *
16624824 TAGCTCCGAAGAGCCATTAATCGAG
1 AAGCTCATAAGAGCCA-TAATCGGG
16624849 AAGCTC
1 AAGCTC
16624855 CAAATAACCA
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
23 1 0.02
24 29 0.71
25 11 0.27
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (24 bp):
AAGCTCATAAGAGCCATAATCGGG
Found at i:16630667 original size:24 final size:24
Alignment explanation
Indices: 16630620--16630667 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16630610 AATTCTAGGT
* * * *
16630620 ACATATAAGCTTGTGATGTGATAA
1 ACATATAAGCATGTAACGTAATAA
16630644 ACATATAAGCATGTAACGTAATAA
1 ACATATAAGCATGTAACGTAATAA
16630668 GTAAATTTAC
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:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (24 bp):
ACATATAAGCATGTAACGTAATAA
Found at i:16632299 original size:298 final size:297
Alignment explanation
Indices: 16631665--16632470 Score: 808
Period size: 298 Copynumber: 2.7 Consensus size: 297
16631655 CACCAATTTG
* * * * *
16631665 GTTAGGAAAATTTTATAAATGTCTTTCCGTAATTAAAATATGTTAAATTATTTGAGAGTATTTTA
1 GTTAGGAAAATTTCAAAAATGTCATTCCGTAATTAAAATAAGTTATATTATTTGAGAGTATTTTA
* * * * * * *
16631730 GTATTTTTATTTCTAAAAAATCAATAAAAAATTTATATGTAACTAGATTTGAACCTCTGCTATAT
66 GTCTTTTTATTTCTAAAAAACCAATAAAAAA-TTATATGTGATTAGATTT-AACTTATGCTATTT
* * * *
16631795 ATATTAATAAAACAATTTTACCACTAATCTAAAGCTTTATTTT-A-AT-AT-TTAAATTTTAATT
129 ACATTAATAAAACAATTTTA-CACTAA-CCAAAGATTTATTTTAATATAATATTACATTTTAATT
* * * *
16631856 ATATTATACATACTTTATTATCTCTATCAATTGTATATCTCTATCTATATCTATATACTATTATT
192 ATATTATGCATACTTTATAATCTCCATCAATTGTATA---CTATCTATATCTATATACTAGTATT
* * ***
16631921 TAAGCCCTTAAGTTGGTGTCATGAGTCAACCGGGCACCAACTTG
254 TAAGCCCTTAAGTTGGTGTCACGAGTCAACCGAGCACCAACCCA
* * ** * * *
16631965 GTTAGGGAAATTTCAAAAATGTTATTGTGTAATTAAAATAACTTATATTATTTGTGAATATTTTA
1 GTTAGGAAAATTTCAAAAATGTCATTCCGTAATTAAAATAAGTTATATTATTTGAGAGTATTTTA
* * *
16632030 GTCTTTTTATTTTTTAAAAACCAATAAAAAATTGTATGTGATTAGATTTAAACTTATGCTATTTA
66 GTCTTTTTATTTCTAAAAAACCAATAAAAAATTATATGTGATTAGATTT-AACTTATGCTATTTA
16632095 CATTAATAAAACAATTTTATCACTGAACCAAAGATTTATTTTAATATAATATCTACATTTTAATT
130 CATTAATAAAACAATTTTA-CACT-AACCAAAGATTTATTTTAATATAATAT-TACATTTTAATT
* * *
16632160 GTATTATGCATATTTTATAATCTCCATCAA-T-TATA-TAT-T-TAT-T-TATATTAGTATTTAA
192 ATATTATGCATACTTTATAATCTCCATCAATTGTATACTATCTATATCTATATACTAGTATTTAA
*
16632218 GCCCCTAACTAAGTTGGTGTTACGAGTCAACCGAGCACCAACCCA
257 G-CCCT---TAAGTTGGTGTCACGAGTCAACCGAGCACCAACCCA
* * * * * * *
16632263 GTTAAGAAAATTTCAAAAATATCATTCCATAATTAAAATTAGTTATATAATTCGAGAGTATTTTT
1 GTTAGGAAAATTTCAAAAATGTCATTCCGTAATTAAAATAAGTTATATTATTTGAGAGTATTTTA
* * * * * * * * * *
16632328 GTCTTTCTATTTCTGAAAAACAAATAGAAAATTATATATGATTGGATTTAACTCAAGTTATTGAC
66 GTCTTTTTATTTCTAAAAAACCAATAAAAAATTATATGTGATTAGATTTAACTTATGCTATTTAC
* * * * *
16632393 AATAATTAAACAATGTTACAACTAAACC-ATGACTTTAATTTAATATAATATTTACATTTTAATT
131 ATTAATAAAACAATTTTAC-ACT-AACCAAAGA-TTTATTTTAATATAATA-TTACATTTTAATT
16632457 ATATTATGCATACT
192 ATATTATGCATACT
16632471 CTAATGAGTT
Statistics
Matches: 418, Mismatches: 75, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
294 14 0.03
295 5 0.01
296 7 0.02
297 75 0.18
298 126 0.30
299 62 0.15
300 83 0.20
301 2 0.00
302 6 0.01
303 2 0.00
304 36 0.09
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.42
Consensus pattern (297 bp):
GTTAGGAAAATTTCAAAAATGTCATTCCGTAATTAAAATAAGTTATATTATTTGAGAGTATTTTA
GTCTTTTTATTTCTAAAAAACCAATAAAAAATTATATGTGATTAGATTTAACTTATGCTATTTAC
ATTAATAAAACAATTTTACACTAACCAAAGATTTATTTTAATATAATATTACATTTTAATTATAT
TATGCATACTTTATAATCTCCATCAATTGTATACTATCTATATCTATATACTAGTATTTAAGCCC
TTAAGTTGGTGTCACGAGTCAACCGAGCACCAACCCA
Found at i:16633904 original size:19 final size:19
Alignment explanation
Indices: 16633882--16633920 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
16633872 ATTAAAATTT
16633882 TAAAAAGAATT-TAAAAAAA
1 TAAAAA-AATTATAAAAAAA
*
16633901 TAAAAAATTTATAAAAAAA
1 TAAAAAAATTATAAAAAAA
16633920 T
1 T
16633921 TAATTAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (19 bp):
TAAAAAAATTATAAAAAAA
Found at i:16633911 original size:17 final size:19
Alignment explanation
Indices: 16633884--16633918 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
16633874 TAAAATTTTA
16633884 AAAAGAATTTA-AAAAAAT
1 AAAAGAATTTATAAAAAAT
16633902 AAAA-AATTTATAAAAAA
1 AAAAGAATTTATAAAAAA
16633919 ATTAATTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAAGAATTTATAAAAAAT
Found at i:16656848 original size:21 final size:22
Alignment explanation
Indices: 16656808--16656848 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16656798 ATTACCTGCC
*
16656808 AAGAAACCCAAAATGTTAATCA
1 AAGAAACCCAAAATGGTAATCA
*
16656830 AAGAAA-CCAGAATGGTAAT
1 AAGAAACCCAAAATGGTAAT
16656849 ATACTAAACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.17
Consensus pattern (22 bp):
AAGAAACCCAAAATGGTAATCA
Found at i:16657739 original size:16 final size:16
Alignment explanation
Indices: 16657715--16657747 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16657705 TTTGCTGTAA
16657715 ATAAAATTTTTTATTT
1 ATAAAATTTTTTATTT
*
16657731 ATAAGATTTTTTATTT
1 ATAAAATTTTTTATTT
16657747 A
1 A
16657748 AATCCTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATAAAATTTTTTATTT
Found at i:16659124 original size:22 final size:22
Alignment explanation
Indices: 16659099--16659162 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
16659089 GGAGAAGTAG
*
16659099 AAAAAAA-TGAAAATTAAAAGA
1 AAAAAAAGAGAAAATTAAAAGA
16659120 AAAAAAAGAGAAAATTAAAAGA
1 AAAAAAAGAGAAAATTAAAAGA
* *
16659142 ACATAAAAGAAAAGAATTAAA
1 A-AAAAAAGAGAA-AATTAAA
16659163 TTGCTCAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.19
22 14 0.38
23 9 0.24
24 7 0.19
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.12
Consensus pattern (22 bp):
AAAAAAAGAGAAAATTAAAAGA
Found at i:16659142 original size:11 final size:10
Alignment explanation
Indices: 16659097--16659154 Score: 55
Period size: 11 Copynumber: 5.6 Consensus size: 10
16659087 AGGGAGAAGT
16659097 AGAAAA-AAA
1 AGAAAATAAA
*
16659106 TGAAAATTAAA
1 AGAAAA-TAAA
*
16659117 AGAAAAAAAA
1 AGAAAATAAA
16659127 GAGAAAATTAAA
1 -AGAAAA-TAAA
*
16659139 AGAACATAAA
1 AGAAAATAAA
16659149 AGAAAA
1 AGAAAA
16659155 GAATTAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
9 5 0.13
10 12 0.31
11 19 0.49
12 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (10 bp):
AGAAAATAAA
Found at i:16670114 original size:31 final size:29
Alignment explanation
Indices: 16670076--16670145 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
16670066 ACTACCAAAA
* *
16670076 TAGTCACTTTTGTTTGACTCAGGTTACATTT
1 TAGTCACTTATGTTTGA--AAGGTTACATTT
* *
16670107 TAGTCACTTATGTTTGAAATGTTACGTTT
1 TAGTCACTTATGTTTGAAAGGTTACATTT
16670136 TAGTCACTTA
1 TAGTCACTTA
16670146 CGTTATCGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.47
Consensus pattern (29 bp):
TAGTCACTTATGTTTGAAAGGTTACATTT
Found at i:16670559 original size:11 final size:11
Alignment explanation
Indices: 16670543--16670567 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16670533 AATGGAAAAG
16670543 AAAGAAAGTTA
1 AAAGAAAGTTA
16670554 AAAGAAAGTTA
1 AAAGAAAGTTA
16670565 AAA
1 AAA
16670568 AACATAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (11 bp):
AAAGAAAGTTA
Found at i:16676069 original size:21 final size:21
Alignment explanation
Indices: 16676045--16676085 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16676035 TCCAAAGCAC
*
16676045 GGGAAATTGGCTTACATTTTA
1 GGGAAAATGGCTTACATTTTA
* *
16676066 GGGAAAATGTCTTACCTTTT
1 GGGAAAATGGCTTACATTTT
16676086 CAATTTCCGT
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:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (21 bp):
GGGAAAATGGCTTACATTTTA
Found at i:16677708 original size:17 final size:17
Alignment explanation
Indices: 16677686--16677720 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
16677676 ACTTTCAGAA
16677686 AACTTGACAACTATGCT
1 AACTTGACAACTATGCT
16677703 AACTTGACAACTATGCT
1 AACTTGACAACTATGCT
16677720 A
1 A
16677721 TTTAGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (17 bp):
AACTTGACAACTATGCT
Found at i:16679231 original size:12 final size:12
Alignment explanation
Indices: 16679214--16679262 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
16679204 ACACTCATCT
*
16679214 TAATAATAATAA
1 TAATAATAATAC
16679226 TAATAATAATAC
1 TAATAATAATAC
* *
16679238 TATTACTAATAC
1 TAATAATAATAC
*
16679250 TAATATTAATAC
1 TAATAATAATAC
16679262 T
1 T
16679263 TACCTCACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATAATAC
Found at i:16679984 original size:20 final size:20
Alignment explanation
Indices: 16679950--16679989 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
16679940 TGCTATTCTG
*
16679950 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
16679970 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
16679990 ATTTACTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:16681871 original size:20 final size:20
Alignment explanation
Indices: 16681846--16681885 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16681836 AATATTTTCC
*
16681846 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
16681866 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
16681886 TTATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:16682770 original size:2 final size:2
Alignment explanation
Indices: 16682765--16682801 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16682755 ATATATATAT
16682765 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
16682802 CCTCATCTGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16684801 original size:41 final size:41
Alignment explanation
Indices: 16684744--16684939 Score: 288
Period size: 41 Copynumber: 4.8 Consensus size: 41
16684734 TGAGCTTTCG
*
16684744 GGGCTTTAGCGGCGTTTTT-AGGAAAGCGCCGCTAATACTCA
1 GGGCTTTAGCGGCGTTTTTGA-GAAAGCGCCGCTAATGCTCA
*
16684785 GGGCTTTAGCGGCGTTTTT-AGGAAAGCGCCGCTAATTCTCA
1 GGGCTTTAGCGGCGTTTTTGA-GAAAGCGCCGCTAATGCTCA
* *
16684826 GGGCTTTAGCGGCGTTTTTGAGTAAGCGCTGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
16684867 GGGATTTAGCGGCGTTTTTGAGTAAGCGCCGCTAATGCTCA
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
* *
16684908 GGGCTTTAGCGGAGTTTTTGAGAAAGCACCGC
1 GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGC
16684940 AAAAAGTTGT
Statistics
Matches: 144, Mismatches: 10, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
41 143 0.99
42 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (41 bp):
GGGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCA
Found at i:16685338 original size:161 final size:158
Alignment explanation
Indices: 16685060--16685361 Score: 534
Period size: 161 Copynumber: 1.9 Consensus size: 158
16685050 ATAATTTTAG
*
16685060 GGTTTAGGTGTTATTATAATTTAAAGTTTATCATATATGGTTTAGGGTTTTAGGGTTCATTATAT
1 GGTTTAGGTGTTATTATAATTTAAAGTTTATCATATATGGTTTAAGGTTTTAGGGTTCATTATAT
16685125 AATGTTTATTATTTTGGGATTAGAGTTTTGAGTTTAAGGTTTATGATGTAGGTTTAGTGTTTTGG
66 AATGTTTATTATTTTGGGATTAGAGTTTTGAGTTTAAGGTTTATGATGTAGGTTTAGTGTTTTGG
16685190 GTTTAGGGTTTGGGAGTTTGGTGATTAA
131 GTTTAGGGTTTGGGAGTTTGGTGATTAA
*
16685218 GGTTTA-GTGATTATTATAATTTAAAGTTTATCGTATATGGTTTAAGGTTTTAGGGTTAATCATT
1 GGTTTAGGTG-TTATTATAATTTAAAGTTTATCATATATGGTTTAAGGTTTTAGGG-T--TCATT
16685282 ATATAATGTTTATTATTTTGGGATTAGAGTTTTGAGTTTAAGGTTTATGATGTAGGTTTAGTGTT
62 ATATAATGTTTATTATTTTGGGATTAGAGTTTTGAGTTTAAGGTTTATGATGTAGGTTTAGTGTT
*
16685347 TTTGGTTTAGGGTTT
127 TTGGGTTTAGGGTTT
16685362 AAGATTTGGG
Statistics
Matches: 137, Mismatches: 3, Indels: 5
0.94 0.02 0.03
Matches are distributed among these distances:
157 3 0.02
158 49 0.36
159 1 0.01
161 84 0.61
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.50
Consensus pattern (158 bp):
GGTTTAGGTGTTATTATAATTTAAAGTTTATCATATATGGTTTAAGGTTTTAGGGTTCATTATAT
AATGTTTATTATTTTGGGATTAGAGTTTTGAGTTTAAGGTTTATGATGTAGGTTTAGTGTTTTGG
GTTTAGGGTTTGGGAGTTTGGTGATTAA
Found at i:16685373 original size:14 final size:14
Alignment explanation
Indices: 16685356--16685387 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16685346 TTTTGGTTTA
16685356 GGGTTTAAGATTTG
1 GGGTTTAAGATTTG
16685370 GGGTTTAAGATTTG
1 GGGTTTAAGATTTG
16685384 GGGT
1 GGGT
16685388 GGGATTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.41, T:0.41
Consensus pattern (14 bp):
GGGTTTAAGATTTG
Found at i:16685923 original size:13 final size:13
Alignment explanation
Indices: 16685910--16685940 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
16685900 AAAATTTTTA
16685910 AATAATA-ATATT
1 AATAATATATATT
16685922 AATAATATATATT
1 AATAATATATATT
16685935 AATAAT
1 AATAAT
16685941 GTCATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAATATATATT
Done.