Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 57 of 202
Found at i:16898811 original size:3 final size:3
Alignment explanation
Indices: 16898803--16898838 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16898793 TCAAAGAACA
16898803 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
16898839 TAGAGGGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:16899893 original size:2 final size:2
Alignment explanation
Indices: 16899882--16899923 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
16899872 AAGGAGGAAA
* **
16899882 AG AG -G AG AG AG AG TG AG TT AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16899923 A
1 A
16899924 TCCCTTTGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.48, T:0.07
Consensus pattern (2 bp):
AG
Found at i:16903302 original size:6 final size:6
Alignment explanation
Indices: 16903291--16903364 Score: 52
Period size: 6 Copynumber: 12.8 Consensus size: 6
16903281 TTCAGTTATT
* *
16903291 TAATTA TAATTAA TTAATTA TATTTA -AATAA TAATTCA -AATT- TAATTA
1 TAATTA TAATT-A -TAATTA TAATTA TAATTA TAATT-A TAATTA TAATTA
*
16903339 TAA-T- TAATTA TAATTA -AATAA TAATT
1 TAATTA TAATTA TAATTA TAATTA TAATT
16903365 CAAAGAACCT
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
4 3 0.06
5 13 0.25
6 29 0.55
7 3 0.06
8 5 0.09
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (6 bp):
TAATTA
Found at i:16903305 original size:10 final size:10
Alignment explanation
Indices: 16903301--16903355 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
16903291 TAATTATAAT
16903301 TAATTAATTA
1 TAATTAATTA
*
16903311 TATTTAA--A
1 TAATTAATTA
16903319 TAA-TAATTCA
1 TAATTAATT-A
16903329 -AATTTAATTA
1 TAA-TTAATTA
16903339 TAATTAATTA
1 TAATTAATTA
16903349 TAATTAA
1 TAATTAA
16903356 ATAATAATTC
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
7 3 0.08
8 3 0.08
9 2 0.05
10 22 0.59
11 7 0.19
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (10 bp):
TAATTAATTA
Found at i:16903309 original size:14 final size:14
Alignment explanation
Indices: 16903290--16903348 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
16903280 CTTCAGTTAT
16903290 TTAATTATAATTAA
1 TTAATTATAATTAA
16903304 TTAATTAT-ATT--
1 TTAATTATAATTAA
* *
16903315 TAAATAATAATTCAAA
1 TTAATTATAATT--AA
16903331 TTTAATTATAATTAA
1 -TTAATTATAATTAA
16903346 TTA
1 TTA
16903349 TAATTAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
11 6 0.17
12 3 0.09
13 3 0.09
14 11 0.31
15 2 0.06
17 10 0.29
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (14 bp):
TTAATTATAATTAA
Found at i:16926569 original size:41 final size:40
Alignment explanation
Indices: 16926470--16926570 Score: 100
Period size: 37 Copynumber: 2.6 Consensus size: 40
16926460 GGATAATTCA
* **
16926470 AAGTAATAAATTGACACCCAGTGTCTCATCTGCTAAACCG
1 AAGTAATAAATTGACACCCAGTGCCTCATCAACTAAACCG
* * * * *
16926510 AAG---TAAATTGGCAGCCAGTGCCTCATCAAATTAATCTG
1 AAGTAATAAATTGACACCCAGTGCCTCATC-AACTAAACCG
16926548 AAGTAATAAATTGACACCCAGTG
1 AAGTAATAAATTGACACCCAGTG
16926571 TCTTATCGAC
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
37 21 0.45
38 8 0.17
40 3 0.06
41 15 0.32
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (40 bp):
AAGTAATAAATTGACACCCAGTGCCTCATCAACTAAACCG
Found at i:16927474 original size:16 final size:17
Alignment explanation
Indices: 16927453--16927499 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
16927443 ACTTTTCTCC
16927453 TTCTTTCTTTCTCT-TT
1 TTCTTTCTTTCTCTGTT
* *
16927469 TTCTTTCCTTCTATGTT
1 TTCTTTCTTTCTCTGTT
**
16927486 TAGTTTCTTTCTCT
1 TTCTTTCTTTCTCT
16927500 CCTTTTTCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.04, C:0.23, G:0.04, T:0.68
Consensus pattern (17 bp):
TTCTTTCTTTCTCTGTT
Found at i:16927547 original size:5 final size:5
Alignment explanation
Indices: 16927537--16927686 Score: 291
Period size: 5 Copynumber: 30.0 Consensus size: 5
16927527 TAATTATTAT
*
16927537 ATATA ATATA ATATA ATATA ATATA ATATA ATACA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16927587 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16927637 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16927687 TACTTAACAT
Statistics
Matches: 143, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
5 143 1.00
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:16927715 original size:40 final size:39
Alignment explanation
Indices: 16927671--16927754 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 39
16927661 AATATAATAT
16927671 AATATAATATAATATATACTTAACATTTAAGTTTTAT-TAA
1 AATATAATATAATATAT-CTTAAC-TTTAAGTTTTATATAA
* * *
16927711 AATATTATATTATATATTTTAACTTTAAGTTTTATAATAA
1 AATATAATATAATATATCTTAACTTTAAGTTTTAT-ATAA
16927751 AATA
1 AATA
16927755 CACTATTCCG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
38 12 0.31
39 5 0.13
40 22 0.56
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (39 bp):
AATATAATATAATATATCTTAACTTTAAGTTTTATATAA
Found at i:16927726 original size:38 final size:39
Alignment explanation
Indices: 16927667--16927754 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 39
16927657 ATATAATATA
* *
16927667 ATATAATATAATATAATATATA-CTTAACATTTAAGTTTT
1 ATATAAAATATTATAATATATATCTTAAC-TTTAAGTTTT
* *
16927706 AT-TAAAATATTATATTATATATTTTAACTTTAAGTTTT
1 ATATAAAATATTATAATATATATCTTAACTTTAAGTTTT
16927744 ATAATAAAATA
1 AT-ATAAAATA
16927755 CACTATTCCG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 28 0.67
39 7 0.17
40 7 0.17
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (39 bp):
ATATAAAATATTATAATATATATCTTAACTTTAAGTTTT
Found at i:16929550 original size:21 final size:21
Alignment explanation
Indices: 16929524--16929614 Score: 128
Period size: 21 Copynumber: 4.3 Consensus size: 21
16929514 CACAGTTTGT
*
16929524 TCACACGGCCATTTGACCCAC
1 TCACACGGCCATGTGACCCAC
* *
16929545 TCACACGGTCATTTGACCCAC
1 TCACACGGCCATGTGACCCAC
16929566 TCACACGGCCATGTGACCCAC
1 TCACACGGCCATGTGACCCAC
* * *
16929587 TCAGACAGCCATGTGAACCAC
1 TCACACGGCCATGTGACCCAC
16929608 TCACACG
1 TCACACG
16929615 AACATGTGGC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.26, C:0.40, G:0.16, T:0.18
Consensus pattern (21 bp):
TCACACGGCCATGTGACCCAC
Found at i:16934031 original size:18 final size:18
Alignment explanation
Indices: 16934008--16934050 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16933998 CAGTGGCTGT
16934008 GACGACGGCGTCTTGGTG
1 GACGACGGCGTCTTGGTG
* *
16934026 GACGACAGTGTCTTGGTG
1 GACGACGGCGTCTTGGTG
*
16934044 GCCGACG
1 GACGACG
16934051 ACTGTTAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.23, G:0.42, T:0.21
Consensus pattern (18 bp):
GACGACGGCGTCTTGGTG
Found at i:16935705 original size:20 final size:20
Alignment explanation
Indices: 16935664--16935708 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
16935654 GAAAAAAATC
*
16935664 TTAAAAATAAATATAAATCA
1 TTAAAAATAAATATAAAACA
*
16935684 TTAAAAATATAT-TAAAAACA
1 TTAAAAATAAATAT-AAAACA
16935704 TTAAA
1 TTAAA
16935709 TCATCAATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (20 bp):
TTAAAAATAAATATAAAACA
Found at i:16935963 original size:21 final size:21
Alignment explanation
Indices: 16935937--16935992 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
16935927 AACAGCGGTG
*
16935937 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
16935958 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
16935979 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
16935993 AACAGCGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:16936121 original size:18 final size:19
Alignment explanation
Indices: 16936098--16936135 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
16936088 ACAATAGAAG
*
16936098 TTTTTT-AAATTATTTAAA
1 TTTTTTAAAATTATTAAAA
16936116 TTTTTTAAAATTATTAAAA
1 TTTTTTAAAATTATTAAAA
16936135 T
1 T
16936136 ATGTGAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTAAAATTATTAAAA
Found at i:16937519 original size:28 final size:28
Alignment explanation
Indices: 16937487--16937543 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
16937477 TATTTCCAAG
16937487 AATGTACAATGATAATGCTAACTTCTCC
1 AATGTACAATGATAATGCTAACTTCTCC
16937515 AATGTACAATGATAATGCTAACTTCTCC
1 AATGTACAATGATAATGCTAACTTCTCC
16937543 A
1 A
16937544 TCGCCGATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.21, G:0.11, T:0.32
Consensus pattern (28 bp):
AATGTACAATGATAATGCTAACTTCTCC
Found at i:16948055 original size:28 final size:28
Alignment explanation
Indices: 16948015--16948070 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
16948005 ATGTAGAACT
16948015 GTCGTCCGCTTTCGTACTTCTTGGGGGA
1 GTCGTCCGCTTTCGTACTTCTTGGGGGA
16948043 GTCGTCCGCTTTCGTACTTCTTGGGGGA
1 GTCGTCCGCTTTCGTACTTCTTGGGGGA
16948071 CAGTTACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.07, C:0.25, G:0.32, T:0.36
Consensus pattern (28 bp):
GTCGTCCGCTTTCGTACTTCTTGGGGGA
Found at i:16951436 original size:37 final size:39
Alignment explanation
Indices: 16951386--16951481 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 39
16951376 GATTAATTCA
**
16951386 ATGAGGCACTGGGTGCCAA-T-TTACTTTGGTTTAGCCG
1 ATGAGGCACTGGGTGCCAATTATTACTTTGAATTAGCCG
* * *
16951423 ATGAGACACTGGGTGTCAAATTATTACTTTGAATTATCCG
1 ATGAGGCACTGGGTG-CCAATTATTACTTTGAATTAGCCG
16951463 ATGAGGCACTGGGTGCCAA
1 ATGAGGCACTGGGTGCCAA
16951482 ACTGGTGTGT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
37 14 0.29
38 3 0.06
39 4 0.08
40 28 0.57
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (39 bp):
ATGAGGCACTGGGTGCCAATTATTACTTTGAATTAGCCG
Found at i:16951464 original size:40 final size:40
Alignment explanation
Indices: 16951345--16951482 Score: 122
Period size: 40 Copynumber: 3.5 Consensus size: 40
16951335 CTTTGAGTCA
* * * * *
16951345 ATGAGACACTGGGTGTCAATTTACTAC-TTCAGATTAATTCA
1 ATGAGACACTGGGTGTCAAATTATTACTTTGA-ATT-ATCCG
* * ** *
16951386 ATGAGGCACTGGGTG-CCAA-T-TTACTTTGGTTTAGCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTTGAATTATCCG
16951423 ATGAGACACTGGGTGTCAAATTATTACTTTGAATTATCCG
1 ATGAGACACTGGGTGTCAAATTATTACTTTGAATTATCCG
* *
16951463 ATGAGGCACTGGGTGCCAAA
1 ATGAGACACTGGGTGTCAAA
16951483 CTGGTGTGTT
Statistics
Matches: 76, Mismatches: 17, Indels: 9
0.75 0.17 0.09
Matches are distributed among these distances:
37 16 0.21
38 8 0.11
39 4 0.05
40 34 0.45
41 14 0.18
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (40 bp):
ATGAGACACTGGGTGTCAAATTATTACTTTGAATTATCCG
Found at i:16955781 original size:42 final size:42
Alignment explanation
Indices: 16955684--16955961 Score: 290
Period size: 42 Copynumber: 6.9 Consensus size: 42
16955674 TTTAAACAAA
* * * *
16955684 TTCACCGGCACTT-AGCCTGCTAGACATATAGTCTGA-AATGT
1 TTCACTGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* *
16955725 TTCACCGGCATTAAGCCTGCTAGATGTAAAGTCTGATATTGT
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* * * *
16955767 TTCATTGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATTAT
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
16955809 TTCACTGGC----A---T--TAGACGTAAAGTCTGATATTGT
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* * * * *
16955842 TTCACTGGCAATAAGCCTACTAGACGTAAAGTCTAAAATTAT
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
**
16955884 TTCACCAGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
* * *
16955926 TTCACTGGCAATAAGCCTGCGAGGCGTAAAGTCTGA
1 TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGA
16955962 AATCTCAATT
Statistics
Matches: 197, Mismatches: 29, Indels: 21
0.80 0.12 0.09
Matches are distributed among these distances:
33 28 0.14
35 1 0.01
37 1 0.01
38 1 0.01
40 3 0.02
41 30 0.15
42 133 0.68
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.31
Consensus pattern (42 bp):
TTCACTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
Found at i:16955829 original size:33 final size:33
Alignment explanation
Indices: 16955787--16955851 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
16955777 TTAAGCCTGC
16955787 TAGACGTAAAGTCTAAAATTATTTCACTGGCAT
1 TAGACGTAAAGTCTAAAATTATTTCACTGGCAT
* * *
16955820 TAGACGTAAAGTCTGATATTGTTTCACTGGCA
1 TAGACGTAAAGTCTAAAATTATTTCACTGGCA
16955852 ATAAGCCTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.34
Consensus pattern (33 bp):
TAGACGTAAAGTCTAAAATTATTTCACTGGCAT
Found at i:16955873 original size:75 final size:80
Alignment explanation
Indices: 16955744--16955964 Score: 290
Period size: 75 Copynumber: 2.8 Consensus size: 80
16955734 ATTAAGCCTG
* * *
16955744 CTAGATGTAAAGTCTGATATTGTTTCATTGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATTAT
1 CTAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTGCTAGACGTAAAGTCTAAAATTAT
*
16955809 TT-CA-C-T-GGCAT
66 TTCCAGCATAAGCAT
*
16955820 -TAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTACTAGACGTAAAGTCTAAAATTAT
1 CTAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTGCTAGACGTAAAGTCTAAAATTAT
*
16955884 TTCACCAGCATTAAGCCT
66 TT--CCAGCA-TAAGCAT
* * *
16955902 GCTAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTGCGAGGCGTAAAGTCTGAAAT
1 -CTAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTGCTAGACGTAAAGTCTAAAAT
16955965 CTCAATTTCA
Statistics
Matches: 126, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
75 62 0.49
78 2 0.02
79 1 0.01
81 1 0.01
82 3 0.02
84 57 0.45
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (80 bp):
CTAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTGCTAGACGTAAAGTCTAAAATTAT
TTCCAGCATAAGCAT
Found at i:16955929 original size:117 final size:116
Alignment explanation
Indices: 16955704--16955935 Score: 311
Period size: 117 Copynumber: 2.0 Consensus size: 116
16955694 CTTAGCCTGC
* * * * * * *
16955704 TAGACATATAGTCTGAAATGTTTCACCGGCATTAAGCCTGCTAGATGTAAAGTCTGATATTGTTT
1 TAGACATAAAGTCTGAAATGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTAAAATTATTT
***
16955769 CATTGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATTATTTCACTGGCAT
66 CACCAGCATTAAGCCTGCTAGACGTAAAGTCTAAAATTATTTCACTGGCAT
* * *
16955820 TAGACGTAAAGTCTGATATTGTTTCACTGGCAATAAGCCTACTAGACGTAAAGTCTAAAATTATT
1 TAGACATAAAGTCTGA-AATGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTAAAATTATT
* * *
16955885 TCACCAGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGTTTCACTGGCA
65 TCACCAGCATTAAGCCTGCTAGACGTAAAGTCTAAAATTATTTCACTGGCA
16955936 ATAAGCCTGC
Statistics
Matches: 99, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
116 14 0.14
117 85 0.86
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (116 bp):
TAGACATAAAGTCTGAAATGTTTCACCGGCAATAAGCCTACTAGACGTAAAGTCTAAAATTATTT
CACCAGCATTAAGCCTGCTAGACGTAAAGTCTAAAATTATTTCACTGGCAT
Found at i:16962081 original size:42 final size:42
Alignment explanation
Indices: 16961941--16962182 Score: 249
Period size: 42 Copynumber: 5.8 Consensus size: 42
16961931 TTTAAACAAA
* * * * * *
16961941 TTCATCGGCACTT-AGCCTGCTAGGCTTAAAGCCTGAT-TCAG
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATATTAT
* * * *
16961982 TACACCGGCACTT-AGCCTGCTAGACATATAGTCTGA-AATAT
1 TTCACCGGCA-TTAAGCCTGCTAGACGTAAAGTCTGATATTAT
* *
16962023 TTCACCAGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTAT
* *
16962065 TTCACCGGCATTAAGCCTGCTAGACGTGAAGTCTGAAATTAT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTAT
* * *
16962107 TTCGCTGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTGT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTAT
* * * *
16962149 TTCACTGGCAATAAGCCTGCTAGGCTTAAAGTCT
1 TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCT
16962183 TAAATCTCAA
Statistics
Matches: 170, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
40 2 0.01
41 60 0.35
42 108 0.64
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
TTCACCGGCATTAAGCCTGCTAGACGTAAAGTCTGATATTAT
Found at i:16962181 original size:84 final size:84
Alignment explanation
Indices: 16961984--16962187 Score: 284
Period size: 84 Copynumber: 2.4 Consensus size: 84
16961974 TGATTCAGTA
* * *
16961984 CACCGGCACTTAGCCTGCTAGACATATAGTCTGAAA-TATTTCACCAGCATTAAGCCTGCTAGAC
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCAGCATTAAGCCTGCTAGAC
16962048 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
* * * * **
16962067 CACCGGCATTAAGCCTGCTAGACGTGAAGTCTGAAATTATTTCGCTGGCATTAAGCCTGCTAGAC
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCAGCATTAAGCCTGCTAGAC
16962132 GTAAAGTCTGATATTGTTT
66 GTAAAGTCTGATATTGTTT
* * * *
16962151 CACTGGCAATAAGCCTGCTAGGCTTAAAGTCTTAAAT
1 CACCGGCAATAAGCCTGCTAGACATAAAGTCTGAAAT
16962188 CTCAATTTCA
Statistics
Matches: 106, Mismatches: 14, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
83 31 0.29
84 75 0.71
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (84 bp):
CACCGGCAATAAGCCTGCTAGACATAAAGTCTGAAATTATTTCACCAGCATTAAGCCTGCTAGAC
GTAAAGTCTGATATTGTTT
Found at i:16962921 original size:34 final size:34
Alignment explanation
Indices: 16962883--16962949 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
16962873 ACATATATAA
16962883 ATATTCGAACAATATATATATC-TATATACCATTC
1 ATATTCGAACAATATATATA-CATATATACCATTC
* * *
16962917 ATATTTGAACATTGTATATACATATATACCATT
1 ATATTCGAACAATATATATACATATATACCATT
16962950 TATACTTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 28 0.97
ACGTcount: A:0.40, C:0.15, G:0.04, T:0.40
Consensus pattern (34 bp):
ATATTCGAACAATATATATACATATATACCATTC
Found at i:16968513 original size:14 final size:14
Alignment explanation
Indices: 16968496--16968603 Score: 57
Period size: 14 Copynumber: 7.7 Consensus size: 14
16968486 GTAAATGTGA
16968496 ATTCATAGATATGC
1 ATTCATAGATATGC
*
16968510 ATTCATAGATACAG-
1 ATTCATAGATA-TGC
* *
16968524 ATTCATAAATACAG-
1 ATTCATAGATA-TGC
16968538 ATTCAT--ATATGC
1 ATTCATAGATATGC
16968550 GGATTCATAGATA--C
1 --ATTCATAGATATGC
* *
16968564 ATATCCATAGATGTGG
1 AT-T-CATAGATATGC
*
16968580 ATTCATAGATATGT
1 ATTCATAGATATGC
*
16968594 ACTCATAGAT
1 ATTCATAGAT
16968604 GCAGATTTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
11 1 0.01
12 5 0.07
13 1 0.01
14 62 0.82
15 2 0.03
16 5 0.07
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (14 bp):
ATTCATAGATATGC
Found at i:16968527 original size:28 final size:28
Alignment explanation
Indices: 16968496--16968610 Score: 101
Period size: 28 Copynumber: 4.1 Consensus size: 28
16968486 GTAAATGTGA
*
16968496 ATTCATAGATATGCATTCATAGATACAG
1 ATTCATAGATATGCATTCATAGATGCAG
* * * *
16968524 ATTCATAAATACAG-ATTCATATATGCGG
1 ATTCATAGATA-TGCATTCATAGATGCAG
**
16968552 ATTCATAGATA--CATATCCATAGATGTGG
1 ATTCATAGATATGCAT-T-CATAGATGCAG
* *
16968580 ATTCATAGATATGTACTCATAGATGCAG
1 ATTCATAGATATGCATTCATAGATGCAG
16968608 ATT
1 ATT
16968611 TATATACATG
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
26 2 0.03
27 1 0.01
28 63 0.91
29 2 0.03
30 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (28 bp):
ATTCATAGATATGCATTCATAGATGCAG
Found at i:16968542 original size:42 final size:42
Alignment explanation
Indices: 16968496--16968610 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 42
16968486 GTAAATGTGA
16968496 ATTCATAGATATGCATTCATAGATACAGATTCATAAATACAG
1 ATTCATAGATATGCATTCATAGATACAGATTCATAAATACAG
* * * ***
16968538 ATTCAT--ATATGCGGATTCATAGATACATATCCATAGATGTGG
1 ATTCATAGATATGC--ATTCATAGATACAGATTCATAAATACAG
* * *
16968580 ATTCATAGATATGTACTCATAGATGCAGATT
1 ATTCATAGATATGCATTCATAGATACAGATT
16968611 TATATACATG
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
40 6 0.10
42 47 0.81
44 5 0.09
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (42 bp):
ATTCATAGATATGCATTCATAGATACAGATTCATAAATACAG
Found at i:16969251 original size:98 final size:98
Alignment explanation
Indices: 16969077--16969271 Score: 336
Period size: 98 Copynumber: 2.0 Consensus size: 98
16969067 ATAATGAAAA
* *
16969077 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
16969142 CCTTTAGAATCCCAAACTCGGAATATTTCCTTC
66 CCTTTAAAATCCCAAACTCAGAAAATTTCCTTC
*
16969175 ACTTTAAAAGAACATCCGCTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
16969240 CCTTTAAAATCCCAAACTCAGAAAATTTCCTT
66 CCTTTAAAATCCCAAACTCAGAAAATTTCCTT
16969272 TATGATTTCA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 91 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCAGAAAATTTCCTTC
Found at i:16971182 original size:44 final size:44
Alignment explanation
Indices: 16971133--16971599 Score: 294
Period size: 44 Copynumber: 10.8 Consensus size: 44
16971123 TGCCATCTTC
16971133 AGTCTGC-CTCACTGCAACTTCA-GGAGGATAAGACCTGCTTATTT
1 AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGACCTGCTTATTT
* *
16971177 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTACTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTT
*
16971221 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAG---A-TG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCT-GCTTATTT
* * * * **
16971261 CGATCTGCT-CTCTGCAACTTCAGAGAGATAAGATCTGAGGT-TTT
1 AG-TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTG-CTTATTT
* * * * *
16971305 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-CT-ATCGACTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCT-TA-TTT
* * * * *
16971349 AATCTGGTCCACTGCTACTTCAGGGAGATAAGACTTGC-CATCTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTAT-TT
* * *
16971393 CAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTT
1 -AGTCTGCTCCACTGCAACTTCAGGGA-GATAAGACCTGCTTATTT
* *
16971438 AGTCTGCTCCACTGCAACTTCAGGGAGATTAGA-CTAG---A-TG
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCT-GCTTATTT
* ** * * **
16971478 CGATCTGCT-TTCTGCAACTTCAGAGAGATAAGATCTGAGGT-TTT
1 AG-TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTG-CTTATTT
* * * * *
16971522 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-CT-ATCGACTTT
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCT-TA-TTT
* * *
16971566 AATCTGGTCCACTGCTACTTCAGGGAGATAAGAC
1 AGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
16971600 TTGCCATCTT
Statistics
Matches: 335, Mismatches: 54, Indels: 67
0.73 0.12 0.15
Matches are distributed among these distances:
40 48 0.14
41 18 0.05
43 17 0.05
44 211 0.63
45 40 0.12
46 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTT
Found at i:16971552 original size:217 final size:217
Alignment explanation
Indices: 16971142--16971610 Score: 829
Period size: 217 Copynumber: 2.2 Consensus size: 217
16971132 CAGTCTGCCT
* * * *
16971142 CACTGCAACTTCA-GGAGGATAAGACCTGCTTAT-TT-AGTCTGCTCCACTGCAACTTCAGGGAG
1 CACTGCTACTTCAGGGA-GATAAGACTTGC-CATCTTCAGTCTGCCCCACTGCAACTTCAGGGAG
16971204 ATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGC
64 ATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGC
16971269 TCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
129 TCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGAT
16971334 AGGACTATCGACTTTAATCTGGTC
194 AGGACTATCGACTTTAATCTGGTC
16971358 CACTGCTACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCA-GGAGGA
1 CACTGCTACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGA-GA
*
16971422 TAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATTAGACTAGATGCGATCTGCT
65 TAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCT
*
16971487 TTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
130 CTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
16971552 GGACTATCGACTTTAATCTGGTC
195 GGACTATCGACTTTAATCTGGTC
16971575 CACTGCTACTTCAGGGAGATAAGACTTGCCATCTTC
1 CACTGCTACTTCAGGGAGATAAGACTTGCCATCTTC
16971611 GATCTGCTCC
Statistics
Matches: 243, Mismatches: 6, Indels: 7
0.95 0.02 0.03
Matches are distributed among these distances:
215 2 0.01
216 28 0.12
217 213 0.88
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (217 bp):
CACTGCTACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGAT
AAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTC
TCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
GACTATCGACTTTAATCTGGTC
Found at i:16978251 original size:98 final size:98
Alignment explanation
Indices: 16978077--16978271 Score: 309
Period size: 98 Copynumber: 2.0 Consensus size: 98
16978067 ATAATGAAAA
* * * *
16978077 ACTTTAAAGGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAAAATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* * *
16978142 CCTTTAGAATCCCAAACTCGGAATATTTCCTTC
66 CCTTTAAAATCCCAAACTCAGAAAATTTCCTTC
* *
16978175 ACTTTAAAAGAAAATCCGCTTATCCAAAATTTAAGAAATCACGCCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAAAATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
16978240 CCTTTAAAATCCCAAACTCAGAAAATTTCCTT
66 CCTTTAAAATCCCAAACTCAGAAAATTTCCTT
16978272 TATGATTTTA
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 88 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAAAATCCACTTATCCAAAATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTTTAAAATCCCAAACTCAGAAAATTTCCTTC
Found at i:16988448 original size:31 final size:32
Alignment explanation
Indices: 16988392--16988451 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
16988382 ACTTCAAATT
*
16988392 TTGAAAAGTAATAATAATTAAAATTGATCGAC
1 TTGAAAAGTAATAATAACTAAAATTGATCGAC
16988424 TTGAAAAGTACAT-A-AACTAAAATTGATC
1 TTGAAAAGTA-ATAATAACTAAAATTGATC
16988452 AAATTAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.50
32 11 0.42
33 2 0.08
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (32 bp):
TTGAAAAGTAATAATAACTAAAATTGATCGAC
Found at i:16988470 original size:29 final size:30
Alignment explanation
Indices: 16988395--16988474 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
16988385 TCAAATTTTG
* * * *
16988395 AAAAGTAATAATAATTAAAATTGATCGACTT
1 AAAAGT-ATAAAAACTAAAATTGATCAAATT
* *
16988426 GAAAAGTACATAAACTAAAATTGATCAAATT
1 -AAAAGTATAAAAACTAAAATTGATCAAATT
16988457 -AAAGTATAAAAACTAAAA
1 AAAAGTATAAAAACTAAAA
16988475 CAAAGTACAG
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 16 0.40
31 18 0.45
32 6 0.15
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.26
Consensus pattern (30 bp):
AAAAGTATAAAAACTAAAATTGATCAAATT
Found at i:16989524 original size:2 final size:2
Alignment explanation
Indices: 16989519--16989557 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
16989509 TGATTTTTTA
16989519 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16989558 AAATCAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16990802 original size:29 final size:31
Alignment explanation
Indices: 16990765--16990827 Score: 103
Period size: 29 Copynumber: 2.1 Consensus size: 31
16990755 CTCAAATCCA
16990765 TTTTTTAAAATAATTAT-AA-TTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
*
16990794 TTTTTTAAAATAATTTTAAATTTTTTTATAT
1 TTTTTTAAAATAATTATAAATTTTTTTATAT
16990825 TTT
1 TTT
16990828 CATCAATGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 16 0.52
30 2 0.06
31 13 0.42
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (31 bp):
TTTTTTAAAATAATTATAAATTTTTTTATAT
Found at i:16992893 original size:24 final size:24
Alignment explanation
Indices: 16992860--16992915 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
16992850 ATGCGGAATC
*
16992860 GGAAGAACCACAACCACCACCGGA
1 GGAAGAACCACAACCACCACCAGA
* * *
16992884 GGAAGGACCATAATCACCACCAGA
1 GGAAGAACCACAACCACCACCAGA
16992908 GGAAGAAC
1 GGAAGAAC
16992916 AACCGCCGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.30, G:0.23, T:0.04
Consensus pattern (24 bp):
GGAAGAACCACAACCACCACCAGA
Found at i:16993204 original size:28 final size:28
Alignment explanation
Indices: 16993144--16993421 Score: 358
Period size: 28 Copynumber: 9.4 Consensus size: 28
16993134 TAACCAAACA
*
16993144 CTAACCTAAATTAATTAAAAAAACCTAAT
1 CTAACCTAAATTAATT-AAAAACCCTAAT
*
16993173 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAATTAAAAACCCTAA--T
*
16993203 AACCCTAACCTAAATTAACTAAAAACCCTAAT
1 ----CTAACCTAAATTAATTAAAAACCCTAAT
16993235 CTAACCTAAATTAATTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
* *
16993263 CTAACCTAAATTAATTTAAAACCCTAACC
1 CTAACCTAAATTAATTAAAAACCCTAA-T
*
16993292 CTAACCTAAATTAATTAAAAAACCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
*
16993320 CTAACCTAAATTAACTAAAAACCCTAACCT
1 CTAACCTAAATTAATTAAAAACCCTAA--T
*
16993350 AACCCTAACCTAAATTAACTAAAAACCCTAAT
1 ----CTAACCTAAATTAATTAAAAACCCTAAT
16993382 CTAACCTAAATTAATTAAAAACCCTAAT
1 CTAACCTAAATTAATTAAAAACCCTAAT
16993410 CTAACCTAAATT
1 CTAACCTAAATT
16993422 TTTTTGGCTT
Statistics
Matches: 225, Mismatches: 11, Indels: 27
0.86 0.04 0.10
Matches are distributed among these distances:
28 127 0.56
29 40 0.18
30 2 0.01
32 2 0.01
34 54 0.24
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (28 bp):
CTAACCTAAATTAATTAAAAACCCTAAT
Found at i:16993255 original size:62 final size:60
Alignment explanation
Indices: 16993114--16993421 Score: 316
Period size: 62 Copynumber: 5.1 Consensus size: 60
16993104 AAATAAAAAC
* * * * *
16993114 CCTAATTTAATTGAAAACTCTAACCAAACACTAACCTAAATTAATTAAAAAAACCTAATCTAA
1 CCTAAATTAATTAAAAACCCTAACC-TA-ACTAACCTAAATTAATT-AAAAACCCTAATCTAA
* *
16993177 CCTAAATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAATCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAA--CTAACCTAAATTAATTAAAAACCCTAATCTAA
* *
16993239 CCTAAATTAATTAAAAACCCTAA--T--CTAACCTAAATTAATTTAAAACCCTAACCCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAACTAACCTAAATTAATTAAAAACCCTAA-TCTAA
* *
16993296 CCTAAATTAATTAAAAAACCTAA--T--CTAACCTAAATTAACTAAAAACCCTAACCTAACCCTA
1 CCTAAATTAATTAAAAACCCTAACCTAACTAACCTAAATTAATTAAAAACCCTAA--T----CTA
16993357 A
60 A
*
16993358 CCTAAATTAACTAAAAACCCTAA--T--CTAACCTAAATTAATTAAAAACCCTAATCTAA
1 CCTAAATTAATTAAAAACCCTAACCTAACTAACCTAAATTAATTAAAAACCCTAATCTAA
16993414 CCTAAATT
1 CCTAAATT
16993422 TTTTTGGCTT
Statistics
Matches: 219, Mismatches: 18, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
56 37 0.17
57 52 0.24
58 1 0.00
60 2 0.01
61 1 0.00
62 90 0.41
63 36 0.16
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (60 bp):
CCTAAATTAATTAAAAACCCTAACCTAACTAACCTAAATTAATTAAAAACCCTAATCTAA
Found at i:16993334 original size:147 final size:148
Alignment explanation
Indices: 16993144--16993421 Score: 549
Period size: 147 Copynumber: 1.9 Consensus size: 148
16993134 TAACCAAACA
16993144 CTAACCTAAATTAATTAAAAAAACCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCT
1 CTAACCTAAATTAATTAAAAAAACCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCT
16993209 AACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAAT
66 AACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAAT
16993274 TAATTTAAAACCCTAACC
131 TAATTTAAAACCCTAACC
16993292 CTAACCTAAATTAATT-AAAAAACCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCT
1 CTAACCTAAATTAATTAAAAAAACCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCT
16993356 AACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAAT
66 AACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAAT
16993421 T
131 T
16993422 TTTTTGGCTT
Statistics
Matches: 130, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 114 0.88
148 16 0.12
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (148 bp):
CTAACCTAAATTAATTAAAAAAACCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCT
AACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAAT
TAATTTAAAACCCTAACC
Found at i:16997869 original size:89 final size:90
Alignment explanation
Indices: 16997764--16997970 Score: 269
Period size: 94 Copynumber: 2.3 Consensus size: 90
16997754 TCAATTTTTT
* * *
16997764 TTTTAAAAAAAAGCAATTAATCCCCTAC-C-TTTTTTTGCACTTATTTGGGTACTTGAACTTTCA
1 TTTTCAAAAAAAGCAATTAATCCCCTACTCTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCA
* *
16997827 AAATGCATTAAAAA-TGCCCTCAAGCC
66 AAATGCATCAAAAAGT-CCCTCAA-AC
*
16997853 TTTTCAAAAAAAGCAATTAAGCCCCTACTCTTTTTTTTTTTGCACTCAATTGGGTACTTGAACTT
1 TTTTCAAAAAAAGCAATTAATCCCCTACTC---TTTTTTTTGCACTCAATTGGGTACTTGAACTT
*
16997918 TCAAAATGCATCAAAAAGTCCCTCAAAT
63 TCAAAATGCATCAAAAAGTCCCTCAAAC
*
16997946 TTTTCAAAAAAA-TAATTAATCCCCT
1 TTTTCAAAAAAAGCAATTAATCCCCT
16997971 GCTTTTGTTA
Statistics
Matches: 103, Mismatches: 9, Indels: 9
0.85 0.07 0.07
Matches are distributed among these distances:
89 26 0.25
90 1 0.01
92 11 0.11
93 12 0.12
94 52 0.50
95 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (90 bp):
TTTTCAAAAAAAGCAATTAATCCCCTACTCTTTTTTTTGCACTCAATTGGGTACTTGAACTTTCA
AAATGCATCAAAAAGTCCCTCAAAC
Found at i:16998133 original size:19 final size:18
Alignment explanation
Indices: 16998084--16998145 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 18
16998074 AAATTAGAAA
16998084 AAAAATCGTAAAAAATAT
1 AAAAATCGTAAAAAATAT
* * **
16998102 AAAAATTGGAAAATTTTAT
1 AAAAATCGTAAAA-AATAT
*
16998121 AAAAATCGTAAAAAAAAT
1 AAAAATCGTAAAAAATAT
16998139 ATAAAAT
1 A-AAAAT
16998146 ATATAGAAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
18 14 0.42
19 19 0.58
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (18 bp):
AAAAATCGTAAAAAATAT
Found at i:16998396 original size:10 final size:10
Alignment explanation
Indices: 16998381--16998501 Score: 52
Period size: 10 Copynumber: 12.3 Consensus size: 10
16998371 TAGGGGTCGT
16998381 TAATTTTTTA
1 TAATTTTTTA
16998391 TAA-TTTTTA
1 TAATTTTTTA
**
16998400 TAAAATTTTA
1 TAATTTTTTA
*
16998410 -CATTTTTTA
1 TAATTTTTTA
*
16998419 -AAGATTTTTA
1 TAA-TTTTTTA
**** *
16998429 TAAAAAATTC
1 TAATTTTTTA
*
16998439 TAATTTTTAA
1 TAATTTTTTA
16998449 TAATTTTTCTA
1 TAATTTTT-TA
*
16998460 AAATTTTTTA
1 TAATTTTTTA
* *
16998470 T-GTTTTATA
1 TAATTTTTTA
* *
16998479 TATTTTTTTC
1 TAATTTTTTA
*
16998489 TAATTTTTAA
1 TAATTTTTTA
16998499 TAA
1 TAA
16998502 GGGCAAGGGC
Statistics
Matches: 79, Mismatches: 27, Indels: 10
0.68 0.23 0.09
Matches are distributed among these distances:
9 23 0.29
10 46 0.58
11 10 0.13
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (10 bp):
TAATTTTTTA
Found at i:16998425 original size:29 final size:27
Alignment explanation
Indices: 16998380--16998466 Score: 95
Period size: 29 Copynumber: 3.1 Consensus size: 27
16998370 CTAGGGGTCG
*
16998380 TTAATTTTTTATAATTTTTATAAAATT
1 TTAATTTTTTAAAATTTTTATAAAATT
16998407 TTACATTTTTTAAAGATTTTTATAAAAAATT
1 TTA-ATTTTTTAAA-ATTTTTAT--AAAATT
* *
16998438 CTAA-TTTTTAATAATTTTTCTAAAATT
1 TTAATTTTTTAA-AATTTTTATAAAATT
16998465 TT
1 TT
16998467 TTATGTTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
27 10 0.20
28 9 0.18
29 22 0.43
30 2 0.04
31 8 0.16
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (27 bp):
TTAATTTTTTAAAATTTTTATAAAATT
Found at i:16998475 original size:29 final size:29
Alignment explanation
Indices: 16998380--16998499 Score: 88
Period size: 29 Copynumber: 4.2 Consensus size: 29
16998370 CTAGGGGTCG
*
16998380 TTAATTTTTTATA-ATTTTTATAAAA-TT
1 TTAATTTTTAATAGATTTTTATAAAATTT
*
16998407 TTACATTTTTTAA-AGATTTTTATAAAAAATT
1 TTA-A-TTTTTAATAGATTTTTAT-AAAATTT
* *
16998438 CTAATTTTTAATA-ATTTTTCTAAAATTT
1 TTAATTTTTAATAGATTTTTATAAAATTT
* * * **
16998466 TTTATGTTTT-ATATATTTTTTTCTAATTT
1 TTAAT-TTTTAATAGATTTTTATAAAATTT
16998495 TTAAT
1 TTAAT
16998500 AAGGGCAAGG
Statistics
Matches: 75, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.04
28 14 0.19
29 48 0.64
30 6 0.08
31 4 0.05
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (29 bp):
TTAATTTTTAATAGATTTTTATAAAATTT
Found at i:16998614 original size:90 final size:90
Alignment explanation
Indices: 16998509--16998706 Score: 244
Period size: 90 Copynumber: 2.2 Consensus size: 90
16998499 TAAGGGCAAG
* * *
16998509 GGCTTAATTGCTTTTTTTGAAAAAATTTTAGGGTCTTTTTGAT-GCTTTTGAAAGTTCAAGTAT-
1 GGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATCACTTTTGAAAGTTCAA--ATG
*
16998572 C-CAATTGAGTGGAAAA-AAAAAAGCAGA
64 CTCAATTGAGTGCAAAAGAAAAAAG--GA
* *
16998599 GGCTTAATTGCTTTTTTTGAAGAAGTTTGAGGGCCTTTTTGATCCACTTTTGAAAGTTCAAATGC
1 GGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGAT-CACTTTTGAAAGTTCAAATGC
*
16998664 TCAATTGAGTGCAAAAGAAAGAAGGA
65 TCAATTGAGTGCAAAAGAAAAAAGGA
*
16998690 -GCTTAATTGTTTTTTTT
1 GGCTTAATTGCTTTTTTT
16998707 TTTTTTGAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
90 57 0.60
91 3 0.03
92 29 0.31
93 6 0.06
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (90 bp):
GGCTTAATTGCTTTTTTTGAAAAAATTTGAGGGCCTTTTTGATCACTTTTGAAAGTTCAAATGCT
CAATTGAGTGCAAAAGAAAAAAGGA
Found at i:17006732 original size:37 final size:37
Alignment explanation
Indices: 17006651--17006745 Score: 100
Period size: 37 Copynumber: 2.6 Consensus size: 37
17006641 CTTAGTGCCA
* * * *
17006651 TGGCGTGTTATCGGATGGATTAGCTCTTACGAGCATT
1 TGGCATGTTTTCGGTTGGATTAGCTCTTACAAGCATT
** * *
17006688 TAACATGTTTTCGGTTGGATTAGCTCTTATAAGGATT
1 TGGCATGTTTTCGGTTGGATTAGCTCTTACAAGCATT
**
17006725 TGGCATGTTTTTAGTTGGATT
1 TGGCATGTTTTCGGTTGGATT
17006746 GCTTGTGTAC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.20, C:0.12, G:0.26, T:0.42
Consensus pattern (37 bp):
TGGCATGTTTTCGGTTGGATTAGCTCTTACAAGCATT
Found at i:17010066 original size:27 final size:26
Alignment explanation
Indices: 17010009--17010067 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
17009999 AAAGTACGTA
* *
17010009 AATTTTTAACAAAATTAAAAAAATCT
1 AATTTTAAACAAAATTAAAAAAATAT
* * *
17010035 TATTTTAAACAAAAATTTAAAAATTAT
1 AATTTTAAAC-AAAATTAAAAAAATAT
17010062 AATTTT
1 AATTTT
17010068 TTCAATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (26 bp):
AATTTTAAACAAAATTAAAAAAATAT
Found at i:17012368 original size:29 final size:29
Alignment explanation
Indices: 17012326--17012383 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
17012316 GATATTTAAC
17012326 CACTCAAACCTCGTTTCTAAGCTTAGAGT
1 CACTCAAACCTCGTTTCTAAGCTTAGAGT
17012355 CACTCAAACCTCGTTTCTAAGCTTAGAGT
1 CACTCAAACCTCGTTTCTAAGCTTAGAGT
17012384 TCAACTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (29 bp):
CACTCAAACCTCGTTTCTAAGCTTAGAGT
Found at i:17017183 original size:6 final size:6
Alignment explanation
Indices: 17017172--17017200 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17017162 CTCTACCCCA
17017172 CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
1 CCCTCT CCCTCT CCCTCT CCCTCT CCCTC
17017201 CCAACATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (6 bp):
CCCTCT
Found at i:17020039 original size:120 final size:120
Alignment explanation
Indices: 17019906--17020149 Score: 488
Period size: 120 Copynumber: 2.0 Consensus size: 120
17019896 ATAATTAAAT
17019906 TATTTGTTTCACTAATGATATTTTAGCACATTAAATATGTATTGCAGTTTAAAAATAATAAAGTA
1 TATTTGTTTCACTAATGATATTTTAGCACATTAAATATGTATTGCAGTTTAAAAATAATAAAGTA
17019971 GATTATAAAAAATATTTAATAATAATTATTTTAAATTATATTTTATAGTATCATA
66 GATTATAAAAAATATTTAATAATAATTATTTTAAATTATATTTTATAGTATCATA
17020026 TATTTGTTTCACTAATGATATTTTAGCACATTAAATATGTATTGCAGTTTAAAAATAATAAAGTA
1 TATTTGTTTCACTAATGATATTTTAGCACATTAAATATGTATTGCAGTTTAAAAATAATAAAGTA
17020091 GATTATAAAAAATATTTAATAATAATTATTTTAAATTATATTTTATAGTATCATA
66 GATTATAAAAAATATTTAATAATAATTATTTTAAATTATATTTTATAGTATCATA
17020146 TATT
1 TATT
17020150 ATTATTTTAG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 124 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (120 bp):
TATTTGTTTCACTAATGATATTTTAGCACATTAAATATGTATTGCAGTTTAAAAATAATAAAGTA
GATTATAAAAAATATTTAATAATAATTATTTTAAATTATATTTTATAGTATCATA
Found at i:17020196 original size:61 final size:60
Alignment explanation
Indices: 17020128--17020291 Score: 144
Period size: 57 Copynumber: 2.7 Consensus size: 60
17020118 ATTTTAAATT
* *
17020128 ATATTTTATAGTATCATATATTATTATTTTAGTAAATTCATATAAGAATATTTATTATTAA
1 ATATTTTATAGTATCATATATTATTATTTTAGTAAATTCATATAAGAATAATTATT-TCAA
* * * * *
17020189 GA-ATTTTATTA-AATTATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTATTTCAA
1 -ATATTTTA-TAGTATCATATATTATTATTTTAGTAAAT-TCATATAAGAATAATTATTTCAA
*
17020245 ATTATATTATATAGTATCATATATTATGATTTTAGTAAATTCATATA
1 A-TAT-TT-TATAGTATCATATATTATTATTTTAGTAAATTCATATA
17020292 TTTTATTAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 23
0.69 0.11 0.20
Matches are distributed among these distances:
55 1 0.01
56 3 0.04
57 20 0.26
58 5 0.06
59 14 0.18
60 5 0.06
61 18 0.23
62 4 0.05
63 8 0.10
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (60 bp):
ATATTTTATAGTATCATATATTATTATTTTAGTAAATTCATATAAGAATAATTATTTCAA
Found at i:17020198 original size:15 final size:16
Alignment explanation
Indices: 17020170--17020199 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17020160 TAAATTCATA
17020170 TAAGAATATTTATTAT
1 TAAGAATATTTATTAT
17020186 TAAGAAT-TTTATTA
1 TAAGAATATTTATTA
17020200 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (16 bp):
TAAGAATATTTATTAT
Found at i:17020513 original size:39 final size:41
Alignment explanation
Indices: 17020453--17020558 Score: 126
Period size: 44 Copynumber: 2.5 Consensus size: 41
17020443 TTTCCTTATG
* * *
17020453 CTATTACACCTCTATTACATTCAACCAAACACAAGAA-TAC
1 CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
17020493 C-ATTACGCCTCTATTCCATTCCATTCAACCAAACAAAAGAATTAC
1 CTATTACGCCTC---T--ATTCCATTCAACCAAACAAAAGAATTAC
17020538 CTATTACGCCTCTATTCCATT
1 CTATTACGCCTCTATTCCATT
17020559 ACGCATCTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
39 9 0.16
40 1 0.02
41 8 0.14
42 1 0.02
43 1 0.02
44 22 0.39
45 4 0.07
46 10 0.18
ACGTcount: A:0.36, C:0.31, G:0.04, T:0.29
Consensus pattern (41 bp):
CTATTACGCCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:17020533 original size:44 final size:46
Alignment explanation
Indices: 17020470--17020558 Score: 155
Period size: 44 Copynumber: 2.0 Consensus size: 46
17020460 ACCTCTATTA
*
17020470 CATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCCATTC
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTC
17020514 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
1 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATT
17020559 ACGCATCTAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
44 19 0.45
45 4 0.10
46 19 0.45
ACGTcount: A:0.37, C:0.31, G:0.04, T:0.27
Consensus pattern (46 bp):
CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTC
Found at i:17020561 original size:16 final size:16
Alignment explanation
Indices: 17020540--17020585 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
17020530 AGAATTACCT
17020540 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
17020556 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
17020572 ATTACACCTCTATT
1 ATTACGCCTCTATT
17020586 TCAATACAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.04, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:17020694 original size:39 final size:39
Alignment explanation
Indices: 17020612--17020798 Score: 315
Period size: 38 Copynumber: 4.8 Consensus size: 39
17020602 AACGTGCTGT
* *
17020612 TAGACTTTAGTTTTATTTTTATTGAGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
17020650 TAGACTTTAATTTTAGTTTTATTGGGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
17020689 TAGACTTTAGTTTTAGTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
17020727 TAGACTTTAATTTTAGTTTTATTGGGTTGGGTAATTGGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATT-GGG
17020767 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGT
17020799 GTAGTAACCA
Statistics
Matches: 140, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
38 62 0.44
39 44 0.31
40 34 0.24
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:17020739 original size:77 final size:78
Alignment explanation
Indices: 17020612--17020796 Score: 345
Period size: 77 Copynumber: 2.4 Consensus size: 78
17020602 AACGTGCTGT
* *
17020612 TAGACTTTAGTTTTATTTTTATTGAGTTGGTAATTGGGTAGACTTTAATTTTAGTTTTATTGGGT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTAGACTTTAATTTTAGTTTTATTGGGT
17020677 TGGGTAATT-GGG
66 TGGGTAATTGGGG
17020689 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTAGACTTTAATTTTAGTTTTATTGGGT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTAGACTTTAATTTTAGTTTTATTGGGT
17020754 TGGGTAATTGGGG
66 TGGGTAATTGGGG
17020767 TAGACTTTAGTTTTAGTTTTATTGGGTTGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGG
17020797 GTGTAGTAAC
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
77 72 0.69
78 33 0.31
ACGTcount: A:0.19, C:0.03, G:0.28, T:0.50
Consensus pattern (78 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGTAATTGGGTAGACTTTAATTTTAGTTTTATTGGGT
TGGGTAATTGGGG
Found at i:17021832 original size:3 final size:3
Alignment explanation
Indices: 17021824--17021866 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
17021814 ATTAGTTTGC
17021824 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17021867 GTTAATCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17022127 original size:2 final size:2
Alignment explanation
Indices: 17022117--17022158 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
17022107 ATTCATTTTC
*
17022117 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17022159 CTTTTAATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17023246 original size:30 final size:31
Alignment explanation
Indices: 17023210--17023267 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
17023200 GGTTTCGACA
17023210 TTGGGTAATTGGGTTGAGTTGG-TAATTGGG
1 TTGGGTAATTGGGTTGAGTTGGATAATTGGG
*
17023240 TTGGGTAATTGGGTTGGGTTGGATAATT
1 TTGGGTAATTGGGTTGAGTTGGATAATT
17023268 TTATTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.41
Consensus pattern (31 bp):
TTGGGTAATTGGGTTGAGTTGGATAATTGGG
Found at i:17023248 original size:13 final size:13
Alignment explanation
Indices: 17023210--17023258 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
17023200 GGTTTCGACA
17023210 TTGGGTAATTGGG
1 TTGGGTAATTGGG
17023223 TTGAGTTGGTAATTGGG
1 TT--G--GGTAATTGGG
17023240 TTGGGTAATTGGG
1 TTGGGTAATTGGG
17023253 TTGGGT
1 TTGGGT
17023259 TGGATAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 18 0.56
15 2 0.06
17 12 0.38
ACGTcount: A:0.14, C:0.00, G:0.45, T:0.41
Consensus pattern (13 bp):
TTGGGTAATTGGG
Found at i:17028173 original size:88 final size:85
Alignment explanation
Indices: 17028080--17028257 Score: 230
Period size: 88 Copynumber: 2.1 Consensus size: 85
17028070 TAAGCTCCTG
* * * * *
17028080 CTTTTTTTTCACTCATTTAGGTACTTAAACTTTTAAAATGTATCAAAAAGGCCCTCAAACCTTTT
1 CTTTTTTTGCACTCAATTAGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAA-C-TTT
* *
17028145 CAAAAAAAGCAATTAATCCCCTA
64 -AAAAAAAACAATTAAACCCCTA
* * * *
17028168 TTTTTTTTGCACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAATACCCTCAAACTTTAA
1 CTTTTTTTGCACTCAATTAGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTTAA
17028233 AAAAAACAATTAAACCCCTA
66 AAAAAACAATTAAACCCCTA
17028253 CTTTT
1 CTTTT
17028258 ATTAAAAATT
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
85 24 0.31
86 3 0.04
87 1 0.01
88 50 0.64
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.35
Consensus pattern (85 bp):
CTTTTTTTGCACTCAATTAGGTACTTAAACTTTCAAAATGCATCAAAAAGACCCTCAAACTTTAA
AAAAAACAATTAAACCCCTA
Found at i:17028364 original size:12 final size:11
Alignment explanation
Indices: 17028334--17028360 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17028324 TTCAAATATT
17028334 AAAAATTAGAA
1 AAAAATTAGAA
17028345 AAAAATTAGAA
1 AAAAATTAGAA
17028356 AAAAA
1 AAAAA
17028361 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:17028392 original size:20 final size:21
Alignment explanation
Indices: 17028369--17028416 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
17028359 AAATTATATA
* *
17028369 TATAAAAAATTG-TAAAATTT
1 TATAAAAAATTGCAAAAAATT
17028389 TATAAAAAATTGCAAAAAATT
1 TATAAAAAATTGCAAAAAATT
17028410 TATAAAA
1 TATAAAA
17028417 TATATAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
TATAAAAAATTGCAAAAAATT
Found at i:17028396 original size:38 final size:37
Alignment explanation
Indices: 17028307--17028397 Score: 87
Period size: 38 Copynumber: 2.4 Consensus size: 37
17028297 AAATATTATT
*
17028307 AAATTTTAATAAAAAAATTCAAATATTAAAAATTAGAA
1 AAATTTTAA-AAAAAAATTCAAATATAAAAAATTAGAA
** *
17028345 AAAAATTAGAAAAAAAATT-ATATATATAAAAAATT-GTA
1 AAATTTTA-AAAAAAAATTCA-A-ATATAAAAAATTAGAA
*
17028383 AAATTTTATAAAAAA
1 AAATTTTAAAAAAAA
17028398 TTGCAAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
37 7 0.16
38 24 0.56
39 12 0.28
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (37 bp):
AAATTTTAAAAAAAAATTCAAATATAAAAAATTAGAA
Found at i:17028680 original size:18 final size:18
Alignment explanation
Indices: 17028659--17028746 Score: 56
Period size: 18 Copynumber: 4.9 Consensus size: 18
17028649 TTTTTTTATG
17028659 ATTTTTATAAATTTTACA
1 ATTTTTATAAATTTTACA
**
17028677 ATTTTTA-ATTTTTTTACA
1 ATTTTTATA-AATTTTACA
* ** *
17028695 ATTGTTATAAAAAATTATA
1 ATTTTTAT-AAATTTTACA
*
17028714 ATTTTTAATAATTTTTA-A
1 ATTTTT-ATAAATTTTACA
*
17028732 ATTTTT-TATATTTTA
1 ATTTTTATAAATTTTA
17028747 TTAAAATTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
16 7 0.13
17 1 0.02
18 27 0.52
19 14 0.27
20 3 0.06
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (18 bp):
ATTTTTATAAATTTTACA
Found at i:17028724 original size:10 final size:10
Alignment explanation
Indices: 17028711--17028790 Score: 55
Period size: 10 Copynumber: 8.4 Consensus size: 10
17028701 ATAAAAAATT
17028711 ATAATTTTTA
1 ATAATTTTTA
17028721 ATAATTTTT-
1 ATAATTTTTA
*
17028730 A-AATTTTTT
1 ATAATTTTTA
*
17028739 ATATTTTATTA
1 ATAATTT-TTA
17028750 A-AA--TTTA
1 ATAATTTTTA
*
17028757 AT-ATTTTTT
1 ATAATTTTTA
*
17028766 ATAATTTTTTT
1 ATAA-TTTTTA
*
17028777 CTAATTTTTA
1 ATAATTTTTA
17028787 ATAA
1 ATAA
17028791 GAGCAGGGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
7 5 0.09
8 8 0.15
9 7 0.13
10 23 0.42
11 12 0.22
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:17028738 original size:20 final size:18
Alignment explanation
Indices: 17028713--17028787 Score: 62
Period size: 18 Copynumber: 4.1 Consensus size: 18
17028703 AAAAAATTAT
*
17028713 AATTTTTAATAATTTTTA
1 AATTTTTTATAATTTTTA
*
17028731 AATTTTTTATATTTTATTA
1 AATTTTTTATAATTT-TTA
* * *
17028750 AA-ATTTAATATTTTTTA
1 AATTTTTTATAATTTTTA
*
17028767 TAATTTTTTTCTAATTTTTA
1 -AA-TTTTTTATAATTTTTA
17028787 A
1 A
17028788 TAAGAGCAGG
Statistics
Matches: 45, Mismatches: 8, Indels: 7
0.75 0.13 0.12
Matches are distributed among these distances:
17 3 0.07
18 25 0.56
19 6 0.13
20 11 0.24
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTTTATAATTTTTA
Found at i:17028752 original size:46 final size:45
Alignment explanation
Indices: 17028663--17028774 Score: 120
Period size: 46 Copynumber: 2.4 Consensus size: 45
17028653 TTTATGATTT
* * *
17028663 TTATAAATTTTACAATTTTTAATTTTTTTACAATTGTTATAAAAAA
1 TTATAATTTTTATAATTTTTAAATTTTTTACAATTGTTAT-AAAAA
* *
17028709 TTATAATTTTTAATAATTTTTAAATTTTTTA-TATT-TTATTAAAAT
1 TTATAATTTTT-ATAATTTTTAAATTTTTTACAATTGTTA-TAAAAA
*
17028754 TTAATATTTTTTATAATTTTT
1 TT-ATAATTTTTATAATTTTT
17028775 TTCTAATTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
45 18 0.32
46 22 0.39
47 17 0.30
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (45 bp):
TTATAATTTTTATAATTTTTAAATTTTTTACAATTGTTATAAAAA
Found at i:17028947 original size:90 final size:88
Alignment explanation
Indices: 17028795--17028997 Score: 218
Period size: 90 Copynumber: 2.3 Consensus size: 88
17028785 TAATAAGAGC
* * *
17028795 AGGGGCTTAATTAC-TTTTTTGAAAAATGTTAAGGGTCTTTCTGATACATTTTGAAAGTTCAAGT
1 AGGGGCTTAATTGCTTTTTTTGAAAAATGTTAAGGGCCTTTCTGATACATTTTGAAAATTCAAGT
17028859 ACCT-AATTGAGTGAAAAAAAAAAG
66 -CCTCAATTGAGTG-AAAAAAAAAG
* * *
17028883 AAGGGGCTTAATTGCTTTTTTTGAAGAA-GTTTGAGGGCCTTTTTGATGA-ATTTTGAAAATTCA
1 -AGGGGCTTAATTGCTTTTTTTGAAAAATG-TTAAGGGCCTTTCTGAT-ACATTTTGAAAATTCA
** *
17028946 AGTGTTCAATTGAGTGCAAAAAAAAG
63 AGTCCTCAATTGAGTGAAAAAAAAAG
* *
17028972 GGGGGCTTAATTG-TGTTTTTTTAAAA
1 AGGGGCTTAATTGCT-TTTTTTGAAAA
17028998 TTTGAGAGCT
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
87 1 0.01
88 21 0.22
89 24 0.25
90 50 0.52
91 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.36
Consensus pattern (88 bp):
AGGGGCTTAATTGCTTTTTTTGAAAAATGTTAAGGGCCTTTCTGATACATTTTGAAAATTCAAGT
CCTCAATTGAGTGAAAAAAAAAG
Found at i:17038096 original size:26 final size:26
Alignment explanation
Indices: 17038065--17038126 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
17038055 ATAAAAAATA
* **
17038065 ACCAAAATGTTATCTTTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
17038091 ACCAAAATATTATAATTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
*
17038117 ACTAAAATAT
1 ACCAAAATAT
17038127 ACCAAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.52
Consensus pattern (26 bp):
ACCAAAATATTATAATTTTTTTATTT
Found at i:17040269 original size:27 final size:27
Alignment explanation
Indices: 17040215--17040276 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
17040205 TTTTTTTAGT
* * ***
17040215 ATATTTTGGTAAATAAAAGAATTTATA
1 ATATTTTGATAAATAAAAAAAAGGATA
17040242 ATATTTTGATAAATAAAAAAAAGGATA
1 ATATTTTGATAAATAAAAAAAAGGATA
*
17040269 ACATTTTG
1 ATATTTTG
17040277 GTTATTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (27 bp):
ATATTTTGATAAATAAAAAAAAGGATA
Found at i:17040818 original size:12 final size:12
Alignment explanation
Indices: 17040801--17040825 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17040791 GGTGTTCATT
17040801 CGGTTAACCGAC
1 CGGTTAACCGAC
17040813 CGGTTAACCGAC
1 CGGTTAACCGAC
17040825 C
1 C
17040826 CGAAATTGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:17041712 original size:8 final size:9
Alignment explanation
Indices: 17041683--17041880 Score: 61
Period size: 10 Copynumber: 21.0 Consensus size: 9
17041673 CATATGACAA
17041683 AAAAATTTAT
1 AAAAA-TTAT
17041693 AAAAA--AT
1 AAAAATTAT
17041700 AAAAATTAT
1 AAAAATTAT
17041709 AAAAATTATT
1 AAAAATTA-T
**
17041719 AAATTTTAAT
1 AAAAATT-AT
*
17041729 AAAAAATATT
1 AAAAATTA-T
*
17041739 AAATATTTATT
1 AAA-AATTA-T
17041750 AAAAATTA-
1 AAAAATTAT
17041758 AAAAATCGTA-
1 AAAAAT--TAT
*
17041768 AAAAATTGT
1 AAAAATTAT
17041777 -AAAATATAT
1 AAAAAT-TAT
* *
17041786 AGAAATATAG
1 AAAAAT-TAT
*
17041796 AAAAAATAT
1 AAAAATTAT
*
17041805 -AAAATTTT
1 AAAAATTAT
*
17041813 ATAAAGTCGTA-
1 A-AAAAT--TAT
17041824 AGAAAATTAT
1 A-AAAATTAT
*
17041834 AAAAAATAT
1 AAAAATTAT
*
17041843 AAAGAAATAT
1 AAA-AATTAT
*
17041853 -AAAATTCGT
1 AAAAATT-AT
17041862 AAAAAATTAT
1 -AAAAATTAT
*
17041872 GAAAATTAT
1 AAAAATTAT
17041881 CTACCAAAAG
Statistics
Matches: 142, Mismatches: 26, Indels: 41
0.68 0.12 0.20
Matches are distributed among these distances:
7 7 0.05
8 21 0.15
9 38 0.27
10 55 0.39
11 20 0.14
12 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:17041732 original size:20 final size:21
Alignment explanation
Indices: 17041707--17041757 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
17041697 AATAAAAATT
17041707 ATAAAAATTATTAAAT-TTTA
1 ATAAAAATTATTAAATATTTA
*
17041727 ATAAAAAATATTAAATATTTA
1 ATAAAAATTATTAAATATTTA
*
17041748 TTAAAAATTA
1 ATAAAAATTA
17041758 AAAAATCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAAAATTATTAAATATTTA
Found at i:17042071 original size:9 final size:9
Alignment explanation
Indices: 17042059--17042207 Score: 76
Period size: 10 Copynumber: 16.3 Consensus size: 9
17042049 TTTTATGCAA
17042059 TTTATAATT
1 TTTATAATT
17042068 TTTAATAATT
1 TTT-ATAATT
**
17042078 TTTATAAAAG
1 TTTAT-AATT
17042088 TTTATAATTT
1 TTTATAA-TT
*
17042098 TTTATATTTT
1 TTTATA-ATT
*
17042108 TTTATGA-T
1 TTTATAATT
17042116 TTTA-AATT
1 TTTATAATT
*
17042124 TTTTTAATT
1 TTTATAATT
*
17042133 TTAAT-ATT
1 TTTATAATT
*
17042141 TTAAT-ATT
1 TTTATAATT
*
17042149 TTTATTAAAAT
1 TTTA-T-AATT
*
17042160 TTAATAATTT
1 TTTATAA-TT
*
17042170 TTTATAAAT
1 TTTATAATT
*
17042179 TTTATTGA-T
1 TTTA-TAATT
*
17042188 TTTAT-TTT
1 TTTATAATT
17042196 TTTATAATT
1 TTTATAATT
17042205 TTT
1 TTT
17042208 TGCCACATGT
Statistics
Matches: 107, Mismatches: 20, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
7 1 0.01
8 30 0.28
9 32 0.30
10 39 0.36
11 5 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTATAATT
Found at i:17042124 original size:18 final size:16
Alignment explanation
Indices: 17042097--17042142 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
17042087 GTTTATAATT
*
17042097 TTTTATATTTTTTTATGA
1 TTTTAAATTTTTTTA--A
17042115 TTTTAAATTTTTTTAA
1 TTTTAAATTTTTTTAA
17042131 TTTTAATATTTT
1 TTTTAA-ATTTT
17042143 AATATTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 5 0.19
18 14 0.54
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTTAAATTTTTTTAA
Found at i:17042133 original size:72 final size:72
Alignment explanation
Indices: 17042046--17042206 Score: 197
Period size: 72 Copynumber: 2.2 Consensus size: 72
17042036 GTTAAATGAT
*
17042046 ATTTTTTATGCAATTTATAAT-TTTTAATAATTTTTA-TAAAAGTTT-ATAATTTTTTAT-ATTT
1 ATTTTTTAT--AATTT-TAATATTTTAAT-ATTTTTATTAAAA-TTTAATAATTTTTTATAAATT
*
17042107 TTTTATGATTTTAA
61 TTAT-TGATTTT-A
17042121 ATTTTTT-TAATTTTAATATTTTAATATTTTTATTAAAATTTAATAATTTTTTATAAATTTTATT
1 ATTTTTTATAATTTTAATATTTTAATATTTTTATTAAAATTTAATAATTTTTTATAAATTTTATT
17042185 GATTTTA
66 GATTTTA
*
17042192 TTTTTTTATAATTTT
1 ATTTTTTATAATTTT
17042207 TTGCCACATG
Statistics
Matches: 78, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
71 21 0.27
72 43 0.55
73 6 0.08
74 1 0.01
75 7 0.09
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (72 bp):
ATTTTTTATAATTTTAATATTTTAATATTTTTATTAAAATTTAATAATTTTTTATAAATTTTATT
GATTTTA
Found at i:17042405 original size:89 final size:88
Alignment explanation
Indices: 17042280--17042591 Score: 337
Period size: 89 Copynumber: 3.5 Consensus size: 88
17042270 GTCAAAGGGG
** * * *
17042280 TTTTTTTAATGCATTTTGGCAGTTTAAGTATC-CAATTGAGTGTAAAAAAAGTAGGGGCTTAATT
1 TTTTTTT-ATGCATTTTGAAAGTTCAAGTA-CACAATTGAGTGTAAAAAAAGTAGGGGATTAATG
*
17042344 TCTTTTCTTGAAAAAGTTTGAGGGCA
64 ACTTTT-TTGAAAAAGTTTGAGGGCA
* * *
17042370 TTTTTTTATGTATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAA-AAGGGGGATTAATGG
1 TTTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAAGTA-GGGGATTAATGA
***
17042434 CTTTTTT-TTTAAGTTTGAGGGC-
65 CTTTTTTGAAAAAGTTTGAGGGCA
* * * * *
17042456 TTTTTTTATGCATTTTGAAATTTTAAGTACACAATTGAGTGGAAAAAAAAGTAAGGGTTTAATGA
1 TTTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGT-GTAAAAAAAGTAGGGGATTAATGA
17042521 CTTTTTTTGAAAAAGTTTGAGGGCA
65 C-TTTTTTGAAAAAGTTTGAGGGCA
* ** * *
17042546 -TTTTTGATAAATTTTGAAAGTTCAAGTACTCAATTGAGTGCAAAAA
1 TTTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAA
17042592 CAAAAAACAA
Statistics
Matches: 186, Mismatches: 29, Indels: 16
0.81 0.13 0.07
Matches are distributed among these distances:
86 37 0.20
87 30 0.16
88 17 0.09
89 95 0.51
90 7 0.04
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.39
Consensus pattern (88 bp):
TTTTTTTATGCATTTTGAAAGTTCAAGTACACAATTGAGTGTAAAAAAAGTAGGGGATTAATGAC
TTTTTTGAAAAAGTTTGAGGGCA
Found at i:17042572 original size:175 final size:177
Alignment explanation
Indices: 17042275--17042596 Score: 463
Period size: 175 Copynumber: 1.8 Consensus size: 177
17042265 GGTAGGTCAA
* ** * *
17042275 AGGGGTTTTTTTAATGCATTTTGGCAGTTTAAGTATCCAATTGAGTGTAAAAAAAGTAGGGGCTT
1 AGGGCTTTTTTTAATGCATTTTGAAAGTTTAAGTATCCAATTGAGTGAAAAAAAAGTAAGGGCTT
** * **
17042340 AATTTCTTTTCTTGAAAAAGTTTGAGGGCATTTTTTTATGTATTTTGAAAGTTCAAGTACACAAT
66 AATGACTTTTCTTGAAAAAGTTTGAGGGCATTTTTTGATAAATTTTGAAAGTTCAAGTACACAAT
*
17042405 TGAGTGTAAAAA-AAAAGGGGGATTAATGGCTTTTTTTTTAAGTTTG
131 TGAGTGCAAAAACAAAAGGGGGATTAATGGCTTTTTTTTTAAGTTTG
* *
17042451 AGGGCTTTTTTT-ATGCATTTTGAAATTTTAAGTA-CACAATTGAGTGGAAAAAAAAGTAAGGGT
1 AGGGCTTTTTTTAATGCATTTTGAAAGTTTAAGTATC-CAATTGAGT-GAAAAAAAAGTAAGGGC
* *
17042514 TTAATGACTTTTTTTGAAAAAGTTTGAGGGCA-TTTTTGATAAATTTTGAAAGTTCAAGTACTCA
64 TTAATGACTTTTCTTGAAAAAGTTTGAGGGCATTTTTTGATAAATTTTGAAAGTTCAAGTACACA
17042578 ATTGAGTGCAAAAACAAAA
129 ATTGAGTGCAAAAACAAAA
17042597 AACAAAAAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
174 1 0.01
175 69 0.54
176 58 0.45
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (177 bp):
AGGGCTTTTTTTAATGCATTTTGAAAGTTTAAGTATCCAATTGAGTGAAAAAAAAGTAAGGGCTT
AATGACTTTTCTTGAAAAAGTTTGAGGGCATTTTTTGATAAATTTTGAAAGTTCAAGTACACAAT
TGAGTGCAAAAACAAAAGGGGGATTAATGGCTTTTTTTTTAAGTTTG
Found at i:17045432 original size:13 final size:13
Alignment explanation
Indices: 17045414--17045438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17045404 AAATTCAATG
17045414 TCAATTTCATATA
1 TCAATTTCATATA
17045427 TCAATTTCATAT
1 TCAATTTCATAT
17045439 CTAAACATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (13 bp):
TCAATTTCATATA
Found at i:17046296 original size:20 final size:19
Alignment explanation
Indices: 17046273--17046331 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
17046263 CATCAGTAAT
17046273 AACAGAAATTTATCCATATC
1 AACAG-AATTTATCCATATC
* * *
17046293 AACATTAACTTATACATATC
1 AACA-GAATTTATCCATATC
*
17046313 AACAGTATTTCATCCATAT
1 AACAGAATTT-ATCCATAT
17046332 AATTATATAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 3 0.10
20 27 0.90
ACGTcount: A:0.42, C:0.20, G:0.03, T:0.34
Consensus pattern (19 bp):
AACAGAATTTATCCATATC
Found at i:17046498 original size:22 final size:23
Alignment explanation
Indices: 17046468--17046558 Score: 100
Period size: 23 Copynumber: 4.0 Consensus size: 23
17046458 TTGAGCAGGT
*
17046468 AAACGGTAAGCTCTATCA-AGCTG
1 AAACAGTAAGCTCTAT-AGAGCTG
*
17046491 -AACAGTAAGCTCTGTAGAGCTG
1 AAACAGTAAGCTCTATAGAGCTG
17046513 AAACAGTAAGCTCGTA-AGAGCTG
1 AAACAGTAAGCTC-TATAGAGCTG
*
17046536 AAACGGTAAGCTC-ATACGAGCTG
1 AAACAGTAAGCTCTATA-GAGCTG
17046559 TGGTGAGTCC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
21 2 0.03
22 19 0.32
23 37 0.63
24 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (23 bp):
AAACAGTAAGCTCTATAGAGCTG
Found at i:17048611 original size:18 final size:18
Alignment explanation
Indices: 17048588--17048625 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17048578 AAATAAAAAA
17048588 AAACTAAAATGGAAGAAG
1 AAACTAAAATGGAAGAAG
* *
17048606 AAACTACAATGGAAGGAG
1 AAACTAAAATGGAAGAAG
17048624 AA
1 AA
17048626 GACCCAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.08, G:0.24, T:0.11
Consensus pattern (18 bp):
AAACTAAAATGGAAGAAG
Found at i:17059068 original size:4 final size:4
Alignment explanation
Indices: 17059051--17059094 Score: 72
Period size: 4 Copynumber: 11.2 Consensus size: 4
17059041 TCTGTCAAAA
*
17059051 AAAT AAAA AAAT AAAT -AAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
17059095 CTCCTCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 3 0.08
4 34 0.92
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:17066927 original size:10 final size:9
Alignment explanation
Indices: 17066894--17066966 Score: 67
Period size: 10 Copynumber: 7.8 Consensus size: 9
17066884 TTATAAAAAT
17066894 AAAATTATTA
1 AAAATTA-TA
* *
17066904 AAAATGATT
1 AAAATTATA
*
17066913 TAAATTCATA
1 AAAATT-ATA
17066923 AAAATTATA
1 AAAATTATA
17066932 AAAA-TATA
1 AAAATTATA
*
17066940 ATAAATTTTA
1 A-AAATTATA
17066950 ACAAATTATA
1 A-AAATTATA
17066960 AAAATTA
1 AAAATTA
17066967 CCAAAGTAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
8 5 0.10
9 21 0.41
10 25 0.49
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (9 bp):
AAAATTATA
Found at i:17066944 original size:28 final size:27
Alignment explanation
Indices: 17066894--17066964 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 27
17066884 TTATAAAAAT
*
17066894 AAAATTATTAAAAATGATTTAAATTCATA
1 AAAATTA-TAAAAATGATATAAATT-ATA
*
17066923 AAAATTATAAAAAT-ATAATAAATTTTA
1 AAAATTATAAAAATGAT-ATAAATTATA
17066950 ACAAATTATAAAAAT
1 A-AAATTATAAAAAT
17066965 TACCAAAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 5 0.13
28 26 0.68
29 7 0.18
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (27 bp):
AAAATTATAAAAATGATATAAATTATA
Found at i:17067529 original size:10 final size:9
Alignment explanation
Indices: 17067496--17067586 Score: 71
Period size: 10 Copynumber: 9.7 Consensus size: 9
17067486 CGTTTTTTTA
17067496 TTTTA-AAT
1 TTTTATAAT
17067504 ATTTTATTAA-
1 -TTTTA-TAAT
17067514 TTTTATAACT
1 TTTTATAA-T
17067524 TTTTATAAT
1 TTTTATAAT
* *
17067533 TTATTAGATT
1 TT-TTATAAT
17067543 TTTTAT-AT
1 TTTTATAAT
17067551 TTTTGATAAT
1 TTTT-ATAAT
*
17067561 TTTTATAGTT
1 TTTTATA-AT
17067571 TTTTATGAAT
1 TTTTAT-AAT
17067581 TTTTAT
1 TTTTAT
17067587 TTTTAATATT
Statistics
Matches: 67, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
8 8 0.12
9 21 0.31
10 35 0.52
11 3 0.04
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTATAAT
Found at i:17067554 original size:9 final size:9
Alignment explanation
Indices: 17067488--17067590 Score: 61
Period size: 9 Copynumber: 11.4 Consensus size: 9
17067478 TTCTAATACG
17067488 TTTTTT-TA
1 TTTTTTATA
**
17067496 TTTTAAATA
1 TTTTTTATA
17067505 TTTTATTA-A
1 TTTT-TTATA
*
17067514 TTTTATA-A
1 TTTTTTATA
*
17067522 CTTTTTATAA
1 TTTTTTAT-A
* *
17067532 TTTATTAGA
1 TTTTTTATA
17067541 TTTTTTATA
1 TTTTTTATA
*
17067550 TTTTTGATA
1 TTTTTTATA
*
17067559 ATTTTTATA
1 TTTTTTATA
17067568 GTTTTTTATGA
1 -TTTTTTAT-A
*
17067579 ATTTTTAT-
1 TTTTTTATA
17067587 TTTT
1 TTTT
17067591 AATATTAAAT
Statistics
Matches: 71, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
8 15 0.21
9 34 0.48
10 21 0.30
11 1 0.01
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (9 bp):
TTTTTTATA
Found at i:17067662 original size:24 final size:22
Alignment explanation
Indices: 17067618--17067669 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17067608 ATATTTTTTG
17067618 ATAATTTTTCTGATACCTTATT
1 ATAATTTTTCTGATACCTTATT
* *
17067640 ATAATTTTTTTGATATCTT-TT
1 ATAATTTTTCTGATACCTTATT
*
17067661 ATGATTTTT
1 ATAATTTTT
17067670 ATAATTGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 10 0.37
22 17 0.63
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.62
Consensus pattern (22 bp):
ATAATTTTTCTGATACCTTATT
Found at i:17073429 original size:27 final size:27
Alignment explanation
Indices: 17073399--17073450 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
17073389 GCCCAAAAAA
* * *
17073399 TTTAATTAATTATGTAAATGACCTATT
1 TTTAATAAAATATGTAAATAACCTATT
17073426 TTTAATAAAATATGTAAATAACCTA
1 TTTAATAAAATATGTAAATAACCTA
17073451 AAATCTAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (27 bp):
TTTAATAAAATATGTAAATAACCTATT
Found at i:17074607 original size:27 final size:26
Alignment explanation
Indices: 17074560--17074620 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
17074550 TAATGTGAAA
*
17074560 TAAA-AAAAAATTAAAGGGACATTTT
1 TAAAGAAAAAATTAAACGGACATTTT
*
17074585 TAAAGAAAGAATTATAACGGACATTTT
1 TAAAGAAAAAATTA-AACGGACATTTT
17074612 TAATAGAAA
1 TAA-AGAAA
17074621 TAAAAAAACG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.13
26 8 0.26
27 14 0.45
28 5 0.16
ACGTcount: A:0.54, C:0.05, G:0.13, T:0.28
Consensus pattern (26 bp):
TAAAGAAAAAATTAAACGGACATTTT
Found at i:17074630 original size:27 final size:27
Alignment explanation
Indices: 17074576--17074632 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
17074566 AAAATTAAAG
* *
17074576 GGACATTTTTAAAGAAAGAATTATAAC
1 GGACATTTTTAAAGAAAGAATAAAAAC
*
17074603 GGACATTTTTAATAGAAATAA-AAAAAC
1 GGACATTTTTAA-AGAAAGAATAAAAAC
17074630 GGA
1 GGA
17074633 TGACTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (27 bp):
GGACATTTTTAAAGAAAGAATAAAAAC
Found at i:17078689 original size:23 final size:23
Alignment explanation
Indices: 17078663--17078738 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
17078653 ATAAGTGCCA
17078663 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
17078686 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
17078709 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
17078732 CACTGAT
1 CACTGAT
17078739 CAATAACACT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:17078838 original size:8 final size:8
Alignment explanation
Indices: 17078825--17078853 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
17078815 ACCCGGGACT
17078825 CACTGTAA
1 CACTGTAA
17078833 CACTGTAA
1 CACTGTAA
17078841 CACTGTAA
1 CACTGTAA
17078849 CACTG
1 CACTG
17078854 GTCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:17078990 original size:17 final size:17
Alignment explanation
Indices: 17078958--17078995 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
17078948 ATTTTCCTTC
17078958 CACATTCAATATTAATT
1 CACATTCAATATTAATT
17078975 CACATATCAATA-TAATT
1 CACAT-TCAATATTAATT
17078992 CACA
1 CACA
17078996 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (17 bp):
CACATTCAATATTAATT
Found at i:17083486 original size:56 final size:56
Alignment explanation
Indices: 17083376--17083488 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 56
17083366 GATTGAGACA
* *** *
17083376 AATTTGATGAGATTTTATTTATTTCTTTGTTTAGGATGGAGTTGGCCCTTGATTAT
1 AATTTGATGAGATTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTCGATTAT
* * * *
17083432 AATTTGATGAGATTTTCTTTCTTTCTTTCTTTAGGATTGAGTCAATCCTCGATTAT
1 AATTTGATGAGATTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTCGATTAT
17083488 A
1 A
17083489 GGGATTCTTC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.22, C:0.11, G:0.18, T:0.50
Consensus pattern (56 bp):
AATTTGATGAGATTTTATTTATTTCTTTCTTTAGGATGGAGTCAACCCTCGATTAT
Found at i:17083877 original size:18 final size:17
Alignment explanation
Indices: 17083852--17083887 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
17083842 AAAAAAGTAT
*
17083852 AAAAATTTAAAATTTAA
1 AAAAATTTAAAATATAA
17083869 AAAATATTTAAAATATAA
1 AAAA-ATTTAAAATATAA
17083887 A
1 A
17083888 TTATCAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTTAAAATATAA
Found at i:17083918 original size:10 final size:9
Alignment explanation
Indices: 17083711--17083918 Score: 51
Period size: 10 Copynumber: 22.6 Consensus size: 9
17083701 TAAAAAATGA
*
17083711 AAAAAATAT
1 AAAAATTAT
17083720 AAAAATTAT
1 AAAAATTAT
* *
17083729 TAAAATCTTT
1 AAAAAT-TAT
* *
17083739 AAAGATGAT
1 AAAAATTAT
17083748 AGAAAATTATTTT
1 A-AAAATTA---T
17083761 AAAAA--AT
1 AAAAATTAT
*
17083768 -AAAATTTT
1 AAAAATTAT
*
17083776 AGAAATT-T
1 AAAAATTAT
*
17083784 CAAAATTTAT
1 -AAAAATTAT
*
17083794 AAAAAAATATT
1 -AAAAATTA-T
* *
17083805 AAAGATAAT
1 AAAAATTAT
*
17083814 ATAAAATTAC
1 A-AAAATTAT
17083824 AAAAATT-T
1 AAAAATTAT
*
17083832 AAAAATTGGAA
1 AAAAATT--AT
*
17083843 AAAAAGTAT
1 AAAAATTAT
17083852 AAAAATT-T
1 AAAAATTAT
17083860 -AAAATT-T
1 AAAAATTAT
*
17083867 AAAAAATATT
1 AAAAATTA-T
*
17083877 TAAAA-TAT
1 AAAAATTAT
17083885 --AAATTAT
1 AAAAATTAT
17083892 CAAAAAATTAT
1 --AAAAATTAT
17083903 ATAAAATTAT
1 A-AAAATTAT
17083913 GAAAAA
1 -AAAAA
17083919 GAGTTTGAAT
Statistics
Matches: 145, Mismatches: 29, Indels: 49
0.65 0.13 0.22
Matches are distributed among these distances:
6 7 0.05
7 11 0.08
8 16 0.11
9 43 0.30
10 47 0.32
11 15 0.10
12 4 0.03
13 2 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:17084179 original size:30 final size:30
Alignment explanation
Indices: 17084106--17084179 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
17084096 AAATATATAA
*
17084106 TTTGTTAT-ATTTTCATAATTTTCTATTAC
1 TTTGTTATAATTTTTATAATTTTCTATTAC
*
17084135 TTT-TTAATACTTTTTATAAATTTT-T-TTCAC
1 TTTGTT-ATAATTTTTAT-AATTTTCTATT-AC
17084165 TTTGTTATAATTTTT
1 TTTGTTATAATTTTT
17084180 CAAATTAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
28 2 0.05
29 7 0.19
30 20 0.54
31 8 0.22
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTGTTATAATTTTTATAATTTTCTATTAC
Found at i:17090490 original size:14 final size:14
Alignment explanation
Indices: 17090471--17090510 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
17090461 TTGATTGCCA
17090471 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
17090485 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
17090499 GGAAAATGTTTT
1 GTAAAATGTTTT
17090511 ACTTTTCTGT
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:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:17090519 original size:20 final size:20
Alignment explanation
Indices: 17090494--17090533 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
17090484 CGTAAAATGA
*
17090494 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
17090514 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
17090534 GAAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:17090523 original size:34 final size:35
Alignment explanation
Indices: 17090479--17090545 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
17090469 CAGTAAAATG
* *
17090479 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
*
17090513 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
17090546 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:0.09, G:0.12, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:17093240 original size:24 final size:24
Alignment explanation
Indices: 17093213--17093264 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17093203 TTAGTAAGTC
*
17093213 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17093237 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17093261 AAAT
1 AAAT
17093265 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:17095197 original size:24 final size:24
Alignment explanation
Indices: 17095170--17095221 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
17095160 TTAGTAAGTC
*
17095170 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17095194 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17095218 AAAT
1 AAAT
17095222 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:17097882 original size:18 final size:17
Alignment explanation
Indices: 17097854--17097887 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17097844 ATTGTGTTGA
17097854 GAAAATAATTTAATTAG
1 GAAAATAATTTAATTAG
17097871 GAAAATTAATTTAATTA
1 GAAAA-TAATTTAATTA
17097888 ATTAATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (17 bp):
GAAAATAATTTAATTAG
Found at i:17098534 original size:24 final size:24
Alignment explanation
Indices: 17098507--17098570 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
17098497 AAATTTAATG
17098507 TGCAGAATTAATGTGTTTTTATGC
1 TGCAGAATTAATGTGTTTTTATGC
17098531 TGCAGAATTAATGTGTTTTTATGC
1 TGCAGAATTAATGTGTTTTTATGC
* *
17098555 TACCGAATTAATGTGT
1 TGCAGAATTAATGTGT
17098571 CCAAAGGGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.27, C:0.09, G:0.20, T:0.44
Consensus pattern (24 bp):
TGCAGAATTAATGTGTTTTTATGC
Found at i:17102932 original size:26 final size:25
Alignment explanation
Indices: 17102885--17102970 Score: 104
Period size: 26 Copynumber: 3.4 Consensus size: 25
17102875 AGCCATATCG
*
17102885 GGAAGCTC-CATAGAGCCATTAATC
1 GGAAGCTCACAAAGAGCCATTAATC
*
17102909 AGGAAGCTCACAAAGAGCCTTTAATC
1 -GGAAGCTCACAAAGAGCCATTAATC
17102935 GAGAAGCTCACAAAGAGCCATATAA-C
1 G-GAAGCTCACAAAGAGCCAT-TAATC
17102961 GGAACGCTCA
1 GGAA-GCTCA
17102971 TAAGAGCTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
25 12 0.22
26 39 0.72
27 3 0.06
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.16
Consensus pattern (25 bp):
GGAAGCTCACAAAGAGCCATTAATC
Found at i:17104001 original size:7 final size:7
Alignment explanation
Indices: 17103989--17104020 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
17103979 TATTTTATTA
17103989 TTTCCAC
1 TTTCCAC
17103996 TTTCCAC
1 TTTCCAC
17104003 TTTCCAC
1 TTTCCAC
*
17104010 TTTCCAA
1 TTTCCAC
17104017 TTTC
1 TTTC
17104021 ATCATTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTCCAC
Found at i:17106824 original size:5 final size:5
Alignment explanation
Indices: 17106795--17106833 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
17106785 TAACTTTAGC
* *
17106795 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCA
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCA
17106834 CGTCCTAAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 24 0.83
6 5 0.17
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
TCAAT
Found at i:17120777 original size:12 final size:12
Alignment explanation
Indices: 17120760--17120791 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17120750 TTGGGATAAT
17120760 TCCCTTTTTTTC
1 TCCCTTTTTTTC
*
17120772 TCCCTTTTTTTT
1 TCCCTTTTTTTC
17120784 TCCCTTTT
1 TCCCTTTT
17120792 CTATTGGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (12 bp):
TCCCTTTTTTTC
Found at i:17121985 original size:49 final size:48
Alignment explanation
Indices: 17121929--17122022 Score: 118
Period size: 49 Copynumber: 1.9 Consensus size: 48
17121919 AGACTTATGG
*
17121929 AAGGTAAAATAATAAAATTGCT-TCTAGACGCATGGGAGAAGGCTTACAA
1 AAGGTAAAATAATAAAATTGCTCT-TAGACGCACGGG-GAAGGCTTACAA
* ** *
17121978 AAGGTAAAATACTAACCTTGCTCTTAGACGCACGGGGGAGGCTTA
1 AAGGTAAAATAATAAAATTGCTCTTAGACGCACGGGGAAGGCTTA
17122023 TGGAAGGCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
48 8 0.21
49 30 0.77
50 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.22
Consensus pattern (48 bp):
AAGGTAAAATAATAAAATTGCTCTTAGACGCACGGGGAAGGCTTACAA
Found at i:17122726 original size:23 final size:23
Alignment explanation
Indices: 17122696--17122746 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
17122686 ACTTAATAGC
*
17122696 GATCATATAACC-AGAACGAAATA
1 GATCATAT-ACCTAGAACGAAACA
*
17122719 GATCATATACCTAGAACGATACA
1 GATCATATACCTAGAACGAAACA
17122742 GATCA
1 GATCA
17122747 AAATATCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.47, C:0.20, G:0.14, T:0.20
Consensus pattern (23 bp):
GATCATATACCTAGAACGAAACA
Found at i:17124698 original size:25 final size:24
Alignment explanation
Indices: 17124650--17124715 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
17124640 GCCATATAAT
* *
17124650 AGGAAGTTC-CAACGAGCCATATC
1 AGGAAGCTCACAAAGAGCCATATC
17124673 AGGAAGCTCACAAAGAGCCTATATC
1 AGGAAGCTCACAAAGAGCC-ATATC
* * *
17124698 AAGACGCTCATAAAGAGC
1 AGGAAGCTCACAAAGAGC
17124716 TGCCGTATGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
23 8 0.22
24 8 0.22
25 20 0.56
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (24 bp):
AGGAAGCTCACAAAGAGCCATATC
Found at i:17126617 original size:12 final size:12
Alignment explanation
Indices: 17126600--17126642 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
17126590 TTGAAGAACT
17126600 AATAAATAAATG
1 AATAAATAAATG
*
17126612 AATAAATAAAATA
1 AATAAAT-AAATG
17126625 AATAAACT-AATG
1 AATAAA-TAAATG
17126637 AATAAA
1 AATAAA
17126643 ACAATTTACA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 16 0.59
13 10 0.37
14 1 0.04
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (12 bp):
AATAAATAAATG
Found at i:17126624 original size:21 final size:21
Alignment explanation
Indices: 17126600--17126643 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17126590 TTGAAGAACT
17126600 AATAAATAAA-TGAATAAATAA
1 AATAAATAAACT-AATAAATAA
*
17126621 AATAAATAAACTAATGAATAA
1 AATAAATAAACTAATAAATAA
17126642 AA
1 AA
17126644 CAATTTACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (21 bp):
AATAAATAAACTAATAAATAA
Found at i:17128359 original size:143 final size:142
Alignment explanation
Indices: 17128101--17128891 Score: 1083
Period size: 143 Copynumber: 5.5 Consensus size: 142
17128091 TCCGACCCGT
* * *
17128101 TGCAACTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTACAACTTCAAGAAGATAAGA
1 TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
*
17128166 TCGGCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTT
66 TC-TCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTT
*
17128231 CAGTCTGCTCCAC
130 CAGTCTGCTCCGC
17128244 TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCA-GAGAGATAAG
1 TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGA-AGATAAG
* * * *
17128308 ATTCTCCATAATTTGTAGCTTTAATCCGTTCCACTGCAACGCAATGGAAATAAGATTCGCTGTCT
65 A-TCTCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCT
* *
17128373 TCAGTCTACTTCGC
129 TCAGTCTGCTCCGC
*
17128387 TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAAT-TGCTCCACTGCAACTTTAGGAAGATAAGA
1 TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
* * *
17128451 TCTGCCATAACTTGTAGCTTTAATCTTGTTCCACTGCAATGCTAGGGAAATAAGATTCGTTGTCT
66 TCT-CCATAATTTGTAGCTTTAATC-TGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCT
*
17128516 TCAGTCTACTCCGC
129 TCAGTCTGCTCCGC
* * * *
17128530 TGTAAGTTCAGGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGTAACTTCAGGAAGATAAGA
1 TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
* * * * *
17128595 TC-CGCTATAACTTGTAGTTTTAATCTGTTCCACTGCAACGCTAGGAAAATAAGATTCGCTGTCT
66 TCTC-C-ATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCT
17128659 TCAGTCTGCTCCGC
129 TCAGTCTGCTCCGC
* * * *
17128673 CGTAACTTC-AGAGAGATAAAGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAG
1 TGCAACTTCAAG-GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAG
* * *
17128737 AT-TCGTCATAATTTGTAGCTTTAAT-TCGTTCCACTACAACGCCATGGAAATAAGATTTGTTGT
65 ATCTC--CATAATTTGTAGCTTTAATCT-GTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGT
*
17128800 CTTCAGTCTGCTCGGC
127 CTTCAGTCTGCTCCGC
* * * *
17128816 TACAACTT-TAGAGAGATAAGGCCGGTGGCTTCAATCTGCTTCACTGCAACTTCAGGAAGATAAG
1 TGCAACTTCAAG-GAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAG
17128880 ATCTACCATAAT
65 ATCT-CCATAAT
17128892 GACTTCAATC
Statistics
Matches: 582, Mismatches: 51, Indels: 30
0.88 0.08 0.05
Matches are distributed among these distances:
141 3 0.01
142 50 0.09
143 477 0.82
144 51 0.09
145 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (142 bp):
TGCAACTTCAAGGAGATAAGGCTGGTGGCTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGA
TCTCCATAATTTGTAGCTTTAATCTGTTCCACTGCAACGCCAGGGAAATAAGATTCGTTGTCTTC
AGTCTGCTCCGC
Found at i:17130864 original size:8 final size:8
Alignment explanation
Indices: 17130853--17130877 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17130843 TCTTTCATAA
17130853 TTTCACTT
1 TTTCACTT
17130861 TTTCACTT
1 TTTCACTT
17130869 TTTCACTT
1 TTTCACTT
17130877 T
1 T
17130878 CAATCACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCACTT
Done.