Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 10 of 189
Found at i:3319861 original size:18 final size:17
Alignment explanation
Indices: 3319825--3319868 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
3319815 AAATTAGTTG
*
3319825 TTGGGCCTGTTAATGGT
1 TTGGGCCCGTTAATGGT
*
3319842 TTGGGCCCGTTTATTGGT
1 TTGGGCCCG-TTAATGGT
*
3319860 TTAGGCCCG
1 TTGGGCCCG
3319869 GGCATTATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.09, C:0.18, G:0.34, T:0.39
Consensus pattern (17 bp):
TTGGGCCCGTTAATGGT
Found at i:3344309 original size:26 final size:27
Alignment explanation
Indices: 3344280--3344334 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
3344270 TTTTTCCTTA
*
3344280 ATTTTAATATACATATTT-AAATTTTT
1 ATTTTAATATAAATATTTAAAATTTTT
**
3344306 ATTTTTTTATAAATATTTAGAAATTTTT
1 ATTTTAATATAAATATTTA-AAATTTTT
3344334 A
1 A
3344335 GAAATATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (27 bp):
ATTTTAATATAAATATTTAAAATTTTT
Found at i:3354216 original size:33 final size:31
Alignment explanation
Indices: 3354142--3354216 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
3354132 GCTTAAAAAA
* *
3354142 ATATATATACCTATATATATAAAAAAATGCCC
1 ATATATATA-TTATATATAAAAAAAAATGCCC
* **
3354174 ATATGTATATTATATATAAAAAAAACTATGCGT
1 ATATATATATTATATATAAAAAAAA--ATGCCC
3354207 ATATATATAT
1 ATATATATAT
3354217 AGAAAATATG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
31 14 0.40
32 8 0.23
33 13 0.37
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.36
Consensus pattern (31 bp):
ATATATATATTATATATAAAAAAAAATGCCC
Found at i:3354267 original size:31 final size:32
Alignment explanation
Indices: 3354229--3354292 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
3354219 AAAATATGAT
3354229 AATAATTAA-TAATAATAA-ATAATATAATAAA
1 AATAATTAATTAATAATAACATAAT-TAATAAA
3354260 AATAATTAATTTTAATAATAACATAATTAATAA
1 AATAATTAA--TTAATAATAACATAATTAATAA
3354293 CAAGGGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 9 0.31
34 15 0.52
35 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (32 bp):
AATAATTAATTAATAATAACATAATTAATAAA
Found at i:3355749 original size:59 final size:60
Alignment explanation
Indices: 3355667--3355817 Score: 191
Period size: 59 Copynumber: 2.5 Consensus size: 60
3355657 TAAGGCTTGG
* * * ** *
3355667 GTGACTAAAATGAAAGCACCCTAAACTTTGGGTGACTAAATTG-AAAGGATTTAATTTTGA
1 GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGTGACTAAATTGCAAA-AATTTAATTTTGA
* *
3355727 -TGACAAAAATAAAAGCGTCCTAAAAGTTGGGTGATTAAATTGCAAAAATTTAATTTTGA
1 GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGTGACTAAATTGCAAAAATTTAATTTTGA
*
3355786 GTGACCAAAATAAAA-CGCCCTAAAAGTTGGGT
1 GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGT
3355818 AACCAACTAG
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
59 63 0.80
60 16 0.20
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (60 bp):
GTGACAAAAATAAAAGCGCCCTAAAAGTTGGGTGACTAAATTGCAAAAATTTAATTTTGA
Found at i:3356291 original size:20 final size:19
Alignment explanation
Indices: 3356256--3356298 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 19
3356246 AATATTAAAA
3356256 AAATATTTTTATAATTTTT
1 AAATATTTTTATAATTTTT
3356275 AAATAATTTTCTA-AATTTTT
1 AAAT-ATTTT-TATAATTTTT
3356295 AAAT
1 AAAT
3356299 TAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.18
20 16 0.73
21 2 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATATTTTTATAATTTTT
Found at i:3372795 original size:9 final size:9
Alignment explanation
Indices: 3372781--3372806 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3372771 TTTCTTCTCC
3372781 TCTCTCCCA
1 TCTCTCCCA
3372790 TCTCTCCCA
1 TCTCTCCCA
3372799 TCTCTCCC
1 TCTCTCCC
3372807 CGCTGCCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.58, G:0.00, T:0.35
Consensus pattern (9 bp):
TCTCTCCCA
Found at i:3379626 original size:28 final size:28
Alignment explanation
Indices: 3379586--3379646 Score: 95
Period size: 28 Copynumber: 2.2 Consensus size: 28
3379576 ATTCTTAGAG
*
3379586 CTTTAAACATACTCTAATACATTTTCAT
1 CTTTAAACATACTCTAACACATTTTCAT
**
3379614 CTTTAAACATACTCTAACATGTTTTCAT
1 CTTTAAACATACTCTAACACATTTTCAT
3379642 CTTTA
1 CTTTA
3379647 TTCTTCAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.02, T:0.44
Consensus pattern (28 bp):
CTTTAAACATACTCTAACACATTTTCAT
Found at i:3381415 original size:50 final size:50
Alignment explanation
Indices: 3381310--3381430 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 50
3381300 CAGACACACC
*
3381310 ATGGCTCTCACGAGCTTCCCGTTATTTAGCTCATATGAGTACCCTGATAT
1 ATGGCTCTCACGAGCTTCCCGATATTTAGCTCATATGAGTACCCTGATAT
* * * * * * *
3381360 TTGGCTCTCATGAGTTTCCCGATATTTGGCTCGTATGAGCTTCCC-GTTAT
1 ATGGCTCTCACGAGCTTCCCGATATTTAGCTCATATGAG-TACCCTGATAT
** *
3381410 ATGGCTCGGAAGAGCTTCCCG
1 ATGGCTCTCACGAGCTTCCCG
3381431 TTAACATGCT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
50 53 0.93
51 4 0.07
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (50 bp):
ATGGCTCTCACGAGCTTCCCGATATTTAGCTCATATGAGTACCCTGATAT
Found at i:3381417 original size:25 final size:25
Alignment explanation
Indices: 3381321--3381433 Score: 113
Period size: 25 Copynumber: 4.5 Consensus size: 25
3381311 TGGCTCTCAC
* *
3381321 GAGCTTCCCGTTATTTAGCTCATAT
1 GAGCTTCCCGTTATTTGGCTCGTAT
* *
3381346 GAG-TACCCTGATATTTGGCTC-TCAT
1 GAGCTTCCC-GTTATTTGGCTCGT-AT
* *
3381371 GAGTTTCCCGATATTTGGCTCGTAT
1 GAGCTTCCCGTTATTTGGCTCGTAT
* * *
3381396 GAGCTTCCCGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATTTGGCTCGTAT
3381421 GAGCTTCCCGTTA
1 GAGCTTCCCGTTA
3381434 ACATGCTCGT
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
24 5 0.07
25 65 0.87
26 5 0.07
ACGTcount: A:0.19, C:0.24, G:0.22, T:0.35
Consensus pattern (25 bp):
GAGCTTCCCGTTATTTGGCTCGTAT
Found at i:3381449 original size:25 final size:25
Alignment explanation
Indices: 3381386--3381449 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
3381376 TCCCGATATT
*
3381386 TGGCTCGTATGAGCTTCCCGTTATA
1 TGGCTCGTATGAGCTTCCCGTTACA
* *
3381411 TGGCTCGGAAGAGCTTCCCGTTAACA
1 TGGCTCGTATGAGCTTCCCGTT-ACA
3381437 T-GCTCGTATGAGC
1 TGGCTCGTATGAGC
3381450 ACATATGTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 30 0.91
26 3 0.09
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.30
Consensus pattern (25 bp):
TGGCTCGTATGAGCTTCCCGTTACA
Found at i:3381919 original size:29 final size:30
Alignment explanation
Indices: 3381884--3381941 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
3381874 ACAACAAGAC
*
3381884 CCAACCCAAACTCAAA-CCAACCAAAACCA
1 CCAACCCAAACCCAAACCCAACCAAAACCA
*
3381913 CCAACCCAAACCCAAACCCAACCTAAACC
1 CCAACCCAAACCCAAACCCAACCAAAACC
3381942 TAACCCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.48, C:0.48, G:0.00, T:0.03
Consensus pattern (30 bp):
CCAACCCAAACCCAAACCCAACCAAAACCA
Found at i:3381924 original size:6 final size:6
Alignment explanation
Indices: 3381866--3381933 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
3381856 CCGAGGCCCA
* * *
3381866 AAACCC AAACAAC AAGACCC -AACCC AAACTC AAA-CC -AACCA AAACCAC
1 AAACCC AAAC-CC AA-ACCC AAACCC AAACCC AAACCC AAACCC AAACC-C
*
3381914 CAACCC AAACCC AAACCC AA
1 AAACCC AAACCC AAACCC AA
3381934 CCTAAACCTA
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
4 2 0.04
5 6 0.12
6 30 0.62
7 8 0.17
8 2 0.04
ACGTcount: A:0.53, C:0.44, G:0.01, T:0.01
Consensus pattern (6 bp):
AAACCC
Found at i:3383232 original size:28 final size:28
Alignment explanation
Indices: 3383165--3383233 Score: 68
Period size: 28 Copynumber: 2.4 Consensus size: 28
3383155 TCGAATATGC
*
3383165 TATTCATTTATTTATTTTAAATCCTTTTCT
1 TATT-ATTTA-TTATTTTAAATCCTTTTAT
* **
3383195 CA-TATATTATTATTTTAAATTGTTTTAT
1 TATTAT-TTATTATTTTAAATCCTTTTAT
3383223 TATTATTTATT
1 TATTATTTATT
3383234 TCAAGTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 24 0.75
29 7 0.22
30 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (28 bp):
TATTATTTATTATTTTAAATCCTTTTAT
Found at i:3383388 original size:26 final size:27
Alignment explanation
Indices: 3383354--3383421 Score: 86
Period size: 26 Copynumber: 2.5 Consensus size: 27
3383344 TACACATCAT
3383354 TTATTTATTTTAAACTAT-TTTGT-ATA
1 TTATTTATTTTAAACT-TCTTTGTAATA
* *
3383380 TTATTTATTTGAAACTTCTTTTTACATA
1 TTATTTATTTTAAACTTCTTTGTA-ATA
3383408 TTATTTATTTTAAA
1 TTATTTATTTTAAA
3383422 TTTTTTACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 1 0.03
26 19 0.53
28 16 0.44
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (27 bp):
TTATTTATTTTAAACTTCTTTGTAATA
Found at i:3383435 original size:28 final size:27
Alignment explanation
Indices: 3383354--3383437 Score: 82
Period size: 28 Copynumber: 3.1 Consensus size: 27
3383344 TACACATCAT
* **
3383354 TTATTTATTTTAAACTATTTT-GTATA
1 TTATTTATTTTAAACTTTTTTCACATA
* *
3383380 TTATTTATTTGAAACTTCTTTTTACATA
1 TTATTTATTTTAAACTT-TTTTCACATA
3383408 TTATTTATTTTAAA-TTTTTTACATCATA
1 TTATTTATTTTAAACTTTTTT-CA-CATA
3383436 TT
1 TT
3383438 TTAAATTGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 19 0.40
27 7 0.15
28 22 0.46
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATTTATTTTAAACTTTTTTCACATA
Found at i:3383542 original size:27 final size:26
Alignment explanation
Indices: 3383485--3383565 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 26
3383475 TGTAGTTTGT
* *
3383485 ATATTATTTATTTTAATTTGTTTTAC
1 ATATTATTTACTTTAAATTGTTTTAC
*
3383511 ATATTATTTGCTTTAAATTGTTTT--
1 ATATTATTTACTTTAAATTGTTTTAC
* ** * *
3383535 ATACTATTTACTCCAAATTGTTCTAT
1 ATATTATTTACTTTAAATTGTTTTAC
3383561 ATATT
1 ATATT
3383566 TTTTTTTCGT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 19 0.43
26 25 0.57
ACGTcount: A:0.28, C:0.09, G:0.05, T:0.58
Consensus pattern (26 bp):
ATATTATTTACTTTAAATTGTTTTAC
Found at i:3386906 original size:22 final size:22
Alignment explanation
Indices: 3386878--3386921 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
3386868 TAGGGGGACA
3386878 AAGGGTCCCATGTCTCACTCCT
1 AAGGGTCCCATGTCTCACTCCT
3386900 AAGGGTCCCATGTCTCACTCCT
1 AAGGGTCCCATGTCTCACTCCT
3386922 TTTTCTCCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.36, G:0.18, T:0.27
Consensus pattern (22 bp):
AAGGGTCCCATGTCTCACTCCT
Found at i:3402452 original size:29 final size:29
Alignment explanation
Indices: 3402401--3402477 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
3402391 TTAACCTTTA
*
3402401 TCAAAGTGCTCAAATGAATGTCAAAC-ATT
1 TCAAAGTGCTCAAAT-AAAGTCAAACTATT
* *
3402430 TCAAAGTGCTTAAATAAGAGTCAAACTTTT
1 TCAAAGTGCTCAAATAA-AGTCAAACTATT
*
3402460 TGAAAGTGCTCAAATAAA
1 TCAAAGTGCTCAAATAAA
3402478 TTACGTCTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 2 0.05
29 22 0.54
30 17 0.41
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (29 bp):
TCAAAGTGCTCAAATAAAGTCAAACTATT
Found at i:3405814 original size:40 final size:40
Alignment explanation
Indices: 3405759--3405841 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
3405749 ATTTATAGAG
3405759 TTACAAATGTAATTTCTATCTAAAGGAAAATAGATATTAA
1 TTACAAATGTAATTTCTATCTAAAGGAAAATAGATATTAA
*
3405799 TTACACATGTAATTTCTATCTAAAGGAAAATAGATATTAA
1 TTACAAATGTAATTTCTATCTAAAGGAAAATAGATATTAA
3405839 TTA
1 TTA
3405842 TGAATAAATG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (40 bp):
TTACAAATGTAATTTCTATCTAAAGGAAAATAGATATTAA
Found at i:3409209 original size:15 final size:17
Alignment explanation
Indices: 3409172--3409215 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3409162 CTAATATCCT
3409172 AATCCAAAAATTATCAG
1 AATCCAAAAATTATCAG
*
3409189 AATCCAAAAGTTA-CA-
1 AATCCAAAAATTATCAG
3409204 AATCCAACAAAT
1 AATCCAA-AAAT
3409216 GATGTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 5 0.21
17 12 0.50
ACGTcount: A:0.55, C:0.20, G:0.05, T:0.20
Consensus pattern (17 bp):
AATCCAAAAATTATCAG
Found at i:3420621 original size:19 final size:18
Alignment explanation
Indices: 3420581--3420621 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
3420571 TTTATAATAT
3420581 TTTATTTTATTATTTCAG
1 TTTATTTTATTATTTCAG
3420599 TTTATTTTATAGTATTT-AG
1 TTTATTTTAT--TATTTCAG
3420618 TTTA
1 TTTA
3420622 AGTATTGGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.66
Consensus pattern (18 bp):
TTTATTTTATTATTTCAG
Found at i:3421854 original size:5 final size:5
Alignment explanation
Indices: 3421839--3421875 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
3421829 TTTTGCAGGT
3421839 TTTTCA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
3421876 AAATTTCGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:3427769 original size:15 final size:16
Alignment explanation
Indices: 3427745--3427777 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3427735 GCAATAAAAA
*
3427745 TTCAGTACTTA-ATTT
1 TTCAGCACTTAGATTT
3427760 TTCAGCACTTAGATTT
1 TTCAGCACTTAGATTT
3427776 TT
1 TT
3427778 AGTTTATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (16 bp):
TTCAGCACTTAGATTT
Found at i:3429460 original size:50 final size:50
Alignment explanation
Indices: 3429406--3429503 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 50
3429396 AAAAGATAAT
*
3429406 ATTAATATATTTAA-ATATTTTCAATAATTTTTATTATTA-CAAATATTTTA
1 ATTAA-ATATTTAATA-ATTTTCAATAATCTTTATTATTATCAAATATTTTA
*
3429456 ATTAAGTATTTAATAATTTTCAATAATCTTTATTATTATCAAATATTT
1 ATTAAATATTTAATAATTTTCAATAATCTTTATTATTATCAAATATTT
3429504 GAACTAACCA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
49 29 0.66
50 15 0.34
ACGTcount: A:0.41, C:0.05, G:0.01, T:0.53
Consensus pattern (50 bp):
ATTAAATATTTAATAATTTTCAATAATCTTTATTATTATCAAATATTTTA
Found at i:3429524 original size:49 final size:48
Alignment explanation
Indices: 3429419--3429524 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 48
3429409 AATATATTTA
* * * ** *
3429419 AATATTTTCAATAATTTTTATTATTACAAATATTTTAATTAAGTATTT
1 AATATTTTCAATAATCTTTATTATTACAAATATTTGAACTAACAATAT
3429467 AATAATTTTCAATAATCTTTATTATTATCAAATATTTGAACTAACCAATAT
1 AAT-ATTTTCAATAATCTTTATTATTA-CAAATATTTGAACTAA-CAATAT
3429518 -ATATTTT
1 AATATTTT
3429525 ATCCACAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.06
49 27 0.55
50 16 0.33
51 3 0.06
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50
Consensus pattern (48 bp):
AATATTTTCAATAATCTTTATTATTACAAATATTTGAACTAACAATAT
Found at i:3433769 original size:41 final size:41
Alignment explanation
Indices: 3433712--3433801 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
3433702 ACAAATTTGA
*
3433712 GGAAAATGTCTTACGCTTTTAAACTCGGTAAGACATTTTCC
1 GGAAAATGTCTTACGCTTTTAAACTCGATAAGACATTTTCC
3433753 GGAAAATGTCTTACGCTTTTAAACTCGATAAGACATTTTCC
1 GGAAAATGTCTTACGCTTTTAAACTCGATAAGACATTTTCC
*
3433794 GAAAAATG
1 GGAAAATG
3433802 ACGCCTTCTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (41 bp):
GGAAAATGTCTTACGCTTTTAAACTCGATAAGACATTTTCC
Found at i:3433850 original size:18 final size:17
Alignment explanation
Indices: 3433823--3433856 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3433813 TCCCCTTTAA
3433823 CCTTTCCCTTCCCCTTC
1 CCTTTCCCTTCCCCTTC
3433840 CCTTCTCCCTTCCCCTT
1 CCTT-TCCCTTCCCCTT
3433857 GTGTTGCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (17 bp):
CCTTTCCCTTCCCCTTC
Found at i:3433978 original size:25 final size:27
Alignment explanation
Indices: 3433916--3433978 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 27
3433906 CAGGTAAGGC
3433916 TCCTTCTTCTTCTTCTTCCATTCTTCAT
1 TCCTTC-TCTTCTTCTTCCATTCTTCAT
**
3433944 TCCTT-T-TTCTTCTTCTGTTCTTCA-
1 TCCTTCTCTTCTTCTTCCATTCTTCAT
3433968 T-CTTCTCTTCT
1 TCCTTCTCTTCT
3433979 CAACATATTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
23 3 0.10
24 2 0.06
25 20 0.65
26 1 0.03
28 5 0.16
ACGTcount: A:0.05, C:0.33, G:0.02, T:0.60
Consensus pattern (27 bp):
TCCTTCTCTTCTTCTTCCATTCTTCAT
Found at i:3436808 original size:20 final size:20
Alignment explanation
Indices: 3436783--3436822 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3436773 AATATTTTCC
*
3436783 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
3436803 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
3436823 TCATTTTACG
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:3436828 original size:34 final size:35
Alignment explanation
Indices: 3436771--3436837 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3436761 CAAACACTAG
*
3436771 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3436806 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
3436838 CATTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3436829 original size:14 final size:14
Alignment explanation
Indices: 3436806--3436845 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3436796 ACAGAAAAGT
*
3436806 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
3436820 AAATCATTTTACGG
1 AAAACATTTTACAG
3436834 AAAACATTTTAC
1 AAAACATTTTAC
3436846 TACCAATCAA
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:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:3439298 original size:20 final size:20
Alignment explanation
Indices: 3439277--3439329 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
3439267 TACTTAATAT
3439277 TTTAT-TTAATTATTTAAAA
1 TTTATATTAATTATTTAAAA
**
3439296 TTTATATTAATT-TATTAATT
1 TTTATATTAATTAT-TTAAAA
3439316 TTTATATTATATTA
1 TTTATATTA-ATTA
3439330 AAAAGAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATATTAATTATTTAAAA
Found at i:3442695 original size:18 final size:18
Alignment explanation
Indices: 3442670--3442744 Score: 87
Period size: 18 Copynumber: 4.2 Consensus size: 18
3442660 ACCGTTTACG
3442670 GTACTATTCACGTATACA
1 GTACTATTCACGTATACA
** * *
3442688 ACACTATTTACGTATACG
1 GTACTATTCACGTATACA
* *
3442706 GTACTATTTACGTATACG
1 GTACTATTCACGTATACA
*
3442724 GTACTGTTCACGTATACA
1 GTACTATTCACGTATACA
3442742 GTA
1 GTA
3442745 GTTGGGATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (18 bp):
GTACTATTCACGTATACA
Found at i:3442737 original size:36 final size:36
Alignment explanation
Indices: 3442666--3442740 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
3442656 TACGACCGTT
*
3442666 TACGGTACTATTCACGTATACAACACTATTTACGTA
1 TACGGTACTATTCACGTATACAACACTATTCACGTA
* *** *
3442702 TACGGTACTATTTACGTATACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTATACAACACTATTCACGTA
3442738 TAC
1 TAC
3442741 AGTAGTTGGG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (36 bp):
TACGGTACTATTCACGTATACAACACTATTCACGTA
Found at i:3450961 original size:3 final size:3
Alignment explanation
Indices: 3450953--3450995 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3450943 AAATGTTTTT
3450953 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3450996 GGAACAAAGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3453007 original size:33 final size:32
Alignment explanation
Indices: 3452935--3453010 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
3452925 ATGTTTAAAT
* * * *
3452935 GTAAGACCATAGCTAGGCTATGGCATTTTAAT
1 GTAAGACCATAACTAGGCTATGACATTTGAAC
* *
3452967 GAAAAGACCATAACTAGGTTATGACACTTTGAAC
1 G-TAAGACCATAACTAGGCTATGACA-TTTGAAC
3453001 GTAAGACCAT
1 GTAAGACCAT
3453011 GGTTAGATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
32 1 0.03
33 28 0.80
34 6 0.17
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAACTAGGCTATGACATTTGAAC
Found at i:3459194 original size:13 final size:13
Alignment explanation
Indices: 3459176--3459200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3459166 CCTCTCTCAC
3459176 TTCTTTTTTTCTT
1 TTCTTTTTTTCTT
3459189 TTCTTTTTTTCT
1 TTCTTTTTTTCT
3459201 AATGGAAATT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTTTTTTTCTT
Found at i:3465653 original size:15 final size:16
Alignment explanation
Indices: 3465633--3465665 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3465623 ATTAGTTAAA
3465633 ATTAACTACAA-ATAT
1 ATTAACTACAATATAT
*
3465648 ATTAACTATAATATAT
1 ATTAACTACAATATAT
3465664 AT
1 AT
3465666 ATACTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAACTACAATATAT
Found at i:3473456 original size:11 final size:11
Alignment explanation
Indices: 3473440--3473467 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
3473430 GTCGCCTCTT
3473440 CCTTCGTTCTA
1 CCTTCGTTCTA
3473451 CCTTCGTTCTA
1 CCTTCGTTCTA
3473462 CCTTCG
1 CCTTCG
3473468 CCTCTCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:3476861 original size:18 final size:17
Alignment explanation
Indices: 3476833--3476867 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3476823 ATTATTAAGA
*
3476833 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3476850 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3476868 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3476919 original size:120 final size:120
Alignment explanation
Indices: 3476783--3477004 Score: 435
Period size: 120 Copynumber: 1.9 Consensus size: 120
3476773 TTGGTCCAAT
*
3476783 TCATATATTATGATTTGAGTCAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
3476848 ATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA
66 ATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA
3476903 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
1 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
3476968 ATATTTTAATTAAAATATATTTAATAATAATTATGTT
66 ATATTTTAATTAAAATATATTTAATAATAATTATGTT
3477005 TAAATATGAT
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 101 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (120 bp):
TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
ATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTA
Found at i:3476981 original size:18 final size:17
Alignment explanation
Indices: 3476953--3476987 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3476943 ATTATTAAGA
*
3476953 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3476970 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3476988 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3477217 original size:44 final size:45
Alignment explanation
Indices: 3477152--3477242 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
3477142 ACCTCTATTC
* * *
3477152 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
3477196 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
3477241 CA
1 CA
3477243 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:3477244 original size:16 final size:16
Alignment explanation
Indices: 3477223--3477291 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
3477213 GATTAGCTAT
3477223 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3477239 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
3477256 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
3477272 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
3477288 TACA
1 TACA
3477292 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3477265 original size:33 final size:32
Alignment explanation
Indices: 3477223--3477291 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
3477213 GATTAGCTAT
3477223 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
3477256 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
3477288 TACA
1 TACA
3477292 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:3479005 original size:3 final size:3
Alignment explanation
Indices: 3478997--3479027 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3478987 TTTGGCTCCT
3478997 AAC AAC AAC AAC AAC AAC AAC AAC AA- AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
3479028 TTAAAAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.71, C:0.29, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:3483358 original size:20 final size:20
Alignment explanation
Indices: 3483333--3483375 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3483323 TGTAGCTTTG
3483333 GTTTCTTTTAAAGCAGTTTA
1 GTTTCTTTTAAAGCAGTTTA
3483353 GTTTCTTTTAAAGCAGTTTA
1 GTTTCTTTTAAAGCAGTTTA
3483373 GTT
1 GTT
3483376 AATCATTACA
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:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (20 bp):
GTTTCTTTTAAAGCAGTTTA
Found at i:3490590 original size:19 final size:19
Alignment explanation
Indices: 3490563--3490606 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
3490553 TACTATCTAT
*
3490563 CTAAGAAAAGAAAAGAAAA
1 CTAACAAAAGAAAAGAAAA
3490582 CTAACAAAAGAAAAGAAAA
1 CTAACAAAAGAAAAGAAAA
3490601 CTAACA
1 CTAACA
3490607 CCATGTTTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.70, C:0.11, G:0.11, T:0.07
Consensus pattern (19 bp):
CTAACAAAAGAAAAGAAAA
Found at i:3491150 original size:23 final size:23
Alignment explanation
Indices: 3491120--3491165 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3491110 TACTTTGCAG
3491120 TAATTGTAGAAGTTTGGGGTTTT
1 TAATTGTAGAAGTTTGGGGTTTT
3491143 TAATTGTAGAAGTTTGGGGTTTT
1 TAATTGTAGAAGTTTGGGGTTTT
3491166 ACTTGATCTC
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:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (23 bp):
TAATTGTAGAAGTTTGGGGTTTT
Found at i:3493269 original size:44 final size:43
Alignment explanation
Indices: 3493220--3493348 Score: 102
Period size: 47 Copynumber: 2.9 Consensus size: 43
3493210 AATAATAATT
3493220 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTAT-AAGA
* * * **
3493264 ATTTTATGAAATTATATATCATT-AT-TAA-ATTATATTTAATAATAATT
1 A-TTT-T-AAATTATATA-AATTCATATAAGA--AAATTT-ATTATAAGA
* *
3493311 ATTTAAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
3493349 GTTATAATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
43 6 0.09
44 17 0.26
45 7 0.11
46 8 0.12
47 20 0.31
48 7 0.11
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (43 bp):
ATTTTAAATTATATAAATTCATATAAGAAAATTTATTATAAGA
Found at i:3493513 original size:18 final size:17
Alignment explanation
Indices: 3493485--3493519 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3493475 ATTATTAAGA
*
3493485 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
3493502 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
3493520 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:3493764 original size:45 final size:40
Alignment explanation
Indices: 3493665--3493771 Score: 117
Period size: 45 Copynumber: 2.6 Consensus size: 40
3493655 TTTTCCATTA
3493665 TGCTATTACACCTCTATTCC-ATTCAACCAAATACAAGAT
1 TGCTATTACACCTCTATTCCAATTCAACCAAATACAAGAT
* * ***
3493704 TACTATTACGCCTCTATTCCATTATATTCAACCAAATAGTTGATT
1 TGCTATTACACCTCTATTCC---A-ATTCAACCAAATACAAGA-T
3493749 TGCTATTACACCTCTATTCCAAT
1 TGCTATTACACCTCTATTCCAAT
3493772 ACACCTCTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
39 18 0.33
41 2 0.04
42 1 0.02
44 15 0.27
45 19 0.35
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (40 bp):
TGCTATTACACCTCTATTCCAATTCAACCAAATACAAGAT
Found at i:3493776 original size:16 final size:16
Alignment explanation
Indices: 3493755--3493790 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
3493745 GATTTGCTAT
*
3493755 TACACCTCTATTCCAA
1 TACACCTCTAATCCAA
3493771 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3493787 TACA
1 TACA
3493791 GCGAACCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.28
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3496753 original size:15 final size:15
Alignment explanation
Indices: 3496733--3496761 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3496723 GAACTATTAG
3496733 TTTTTTCTATTAATC
1 TTTTTTCTATTAATC
3496748 TTTTTTCTATTAAT
1 TTTTTTCTATTAAT
3496762 TCCTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTCTATTAATC
Found at i:3500264 original size:27 final size:27
Alignment explanation
Indices: 3500192--3500264 Score: 110
Period size: 27 Copynumber: 2.7 Consensus size: 27
3500182 GTCGGGTGGC
*
3500192 GCCTCATAGGGAGGCACCATTAAAAGT
1 GCCTCATAGGGAGGCGCCATTAAAAGT
* *
3500219 GCCTCATAAGGAGGTGCCATTAAAAGT
1 GCCTCATAGGGAGGCGCCATTAAAAGT
*
3500246 GTCTCATAGGGAGGCGCCA
1 GCCTCATAGGGAGGCGCCA
3500265 ATGGGTAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.29, T:0.19
Consensus pattern (27 bp):
GCCTCATAGGGAGGCGCCATTAAAAGT
Found at i:3500400 original size:22 final size:22
Alignment explanation
Indices: 3500374--3500419 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3500364 TGGATTAGTA
3500374 TTTTGTATGAATAGTGTAATTT
1 TTTTGTATGAATAGTGTAATTT
*
3500396 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATAGTGTAATTT
3500418 TT
1 TT
3500420 ATGAATATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (22 bp):
TTTTGTATGAATAGTGTAATTT
Found at i:3500424 original size:18 final size:19
Alignment explanation
Indices: 3500269--3500805 Score: 128
Period size: 19 Copynumber: 26.3 Consensus size: 19
3500259 GCGCCAATGG
*
3500269 GTAATTTTGTATGTATATT
1 GTAATTTTGTATGAATATT
3500288 GTAACTTTTTGTATGAATATT
1 GTAA--TTTTGTATGAATATT
*
3500309 ATAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
* * *
3500328 GTAATTACTTTATAATTAATTTT
1 GTAA-T--TTTGT-ATGAATATT
* * *
3500351 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
*
3500371 GT-ATTTTGTATGAATAGT
1 GTAATTTTGTATGAATATT
3500389 GTAATTTTTTTGTATGAATATT
1 GTAA---TTTTGTATGAATATT
3500411 GTAATTTT-TATGAATATT
1 GTAATTTTGTATGAATATT
*
3500429 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * * *
3500452 GT-ATTTACAGTTTTTAAT-TA
1 GTAATTT--TG-TATGAATATT
3500472 GT-ATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
* *
3500490 GAAATTTTG--T-AATTTT
1 GTAATTTTGTATGAATATT
* *
3500506 GTATGAATATTG-A--AATTTT
1 G--T-AATTTTGTATGAATATT
3500525 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
3500544 GTAATTATTTTAT-AATTAATTAT
1 GTAATT-TTGTATGAA-T-A-T-T
***
3500567 GT-ATTTATAGT-TTTTTATT
1 GTAATTT-T-GTATGAATATT
3500586 AGT-ATTTTGTATGAATATT
1 -GTAATTTTGTATGAATATT
* *
3500605 ATAATGTTGTATGAATATT
1 GTAATTTTGTATGAATATT
*
3500624 GTAATTATTTTAT-AATTAATTTT
1 GTAATT-TTGTATGAA-T-A--TT
* * *
3500647 GT-ATTTATAGTTTTGGAT-TA
1 GTAATTT-T-G-TATGAATATT
3500667 GT-ATTTTGTATGAATATTGTAATTTT
1 GTAATTTTGTATG-A-A---T-A--TT
3500693 GTAATTTTGTATGAATATT
1 GTAATTTTGTATGAATATT
3500712 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
*
3500735 GTAATTTTGTATGGATATT
1 GTAATTTTGTATGAATATT
3500754 GTAGTATTGTTTGTATGAATATT
1 GTA--A-T-TTTGTATGAATATT
3500777 GTAATATTGTTTGTATGAATATT
1 GT-A-A-T-TTTGTATGAATATT
3500800 GTAATT
1 GTAATT
3500806 ATTTTATAAT
Statistics
Matches: 395, Mismatches: 51, Indels: 144
0.67 0.09 0.24
Matches are distributed among these distances:
16 12 0.03
17 16 0.04
18 26 0.07
19 117 0.30
20 49 0.12
21 33 0.08
22 44 0.11
23 73 0.18
24 7 0.02
25 4 0.01
26 4 0.01
27 10 0.03
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.55
Consensus pattern (19 bp):
GTAATTTTGTATGAATATT
Found at i:3500504 original size:27 final size:27
Alignment explanation
Indices: 3500474--3500549 Score: 143
Period size: 27 Copynumber: 2.8 Consensus size: 27
3500464 TTTAATTAGT
3500474 ATTTTGTATGAATATTGAAATTTTGTA
1 ATTTTGTATGAATATTGAAATTTTGTA
3500501 ATTTTGTATGAATATTGAAATTTTGTA
1 ATTTTGTATGAATATTGAAATTTTGTA
*
3500528 ATTTTGTATGAATATTGTAATT
1 ATTTTGTATGAATATTGAAATT
3500550 ATTTTATAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (27 bp):
ATTTTGTATGAATATTGAAATTTTGTA
Found at i:3500627 original size:80 final size:80
Alignment explanation
Indices: 3500526--3500695 Score: 295
Period size: 80 Copynumber: 2.1 Consensus size: 80
3500516 TGAAATTTTG
**
3500526 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTTTATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTGGATTAGTAT
3500591 TTTGTATGAATATTA
66 TTTGTATGAATATTA
* *
3500606 TAATGTTGTATGAATATTGTAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTAT
1 TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTGGATTAGTAT
*
3500671 TTTGTATGAATATTG
66 TTTGTATGAATATTA
3500686 TAATTTTGTA
1 TAATTTTGTA
3500696 ATTTTGTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
80 84 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (80 bp):
TAATTTTGTATGAATATTGTAATTATTTTATAATTAATTATGTATTTATAGTTTTGGATTAGTAT
TTTGTATGAATATTA
Found at i:3500699 original size:27 final size:27
Alignment explanation
Indices: 3500669--3500745 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
3500659 TTGGATTAGT
3500669 ATTTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
*
3500696 ATTTTGTATGAATATTGTAATATTG--
1 ATTTTGTATGAATATTGTAATTTTGTA
3500721 --TTTGTATGAATATTGTAATTTTGTA
1 ATTTTGTATGAATATTGTAATTTTGTA
3500746 TGGATATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 22 0.48
27 24 0.52
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATTTTGTA
Found at i:3500728 original size:23 final size:23
Alignment explanation
Indices: 3500671--3500804 Score: 177
Period size: 23 Copynumber: 5.8 Consensus size: 23
3500661 GGATTAGTAT
*
3500671 TTTGTATGAATATTGTAATTTTG
1 TTTGTATGAATATTGTAATATTG
3500694 TAATTTTGTATGAATATTGTAATATTG
1 ----TTTGTATGAATATTGTAATATTG
3500721 TTTGTATGAATATTGT-A-A-T-
1 TTTGTATGAATATTGTAATATTG
* *
3500740 TTTGTATGGATATTGTAGTATTG
1 TTTGTATGAATATTGTAATATTG
3500763 TTTGTATGAATATTGTAATATTG
1 TTTGTATGAATATTGTAATATTG
3500786 TTTGTATGAATATTGTAAT
1 TTTGTATGAATATTGTAAT
3500805 TATTTTATAA
Statistics
Matches: 98, Mismatches: 5, Indels: 12
0.85 0.04 0.10
Matches are distributed among these distances:
19 15 0.15
20 1 0.01
21 2 0.02
22 2 0.02
23 56 0.57
27 22 0.22
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (23 bp):
TTTGTATGAATATTGTAATATTG
Found at i:3500737 original size:42 final size:42
Alignment explanation
Indices: 3500691--3500804 Score: 174
Period size: 42 Copynumber: 2.6 Consensus size: 42
3500681 TATTGTAATT
3500691 TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
* *
3500733 TTGTAATTTTGTATGGATATTGTAGTATTGTTTGTATGAATA
1 TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
3500775 TTGTAATATTGTTTGTATGAATATTGTAAT
1 TTGT-A-A-T-TTTGTATGAATATTGTAAT
3500805 TATTTTATAA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
42 44 0.69
43 1 0.02
44 1 0.02
45 1 0.02
46 17 0.27
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (42 bp):
TTGTAATTTTGTATGAATATTGTAATATTGTTTGTATGAATA
Found at i:3500792 original size:195 final size:190
Alignment explanation
Indices: 3500370--3500805 Score: 567
Period size: 195 Copynumber: 2.3 Consensus size: 190
3500360 GTTTTGGATT
* * *
3500370 AGTAT-TTTGTATGAATAGTGTAATTTTTTTGTATGAATATTGTAATTTTTATGAATATTGTAAT
1 AGTATGTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATTTGTATGAATATTGTAAT
*
3500434 TATTTTATAATTAATTTTGTATTTACAGTTTTTAATTAGTATTTTGTATGAATATTGAAATTTTG
66 TATTTTATAATTAATTTTGTATTTACAGTTTTGAATTAGTATTTTGTATGAATATTGAAATTTTG
* *
3500499 TAATTTTGTATGAATATTGAAATTTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTA
131 TAATTTTGTATGAATATTGAAATATTG--A-TTTGTATGAATATTGTAATTATTGTATAATTA
* * * * * *
3500562 ATTATGTATT-TAT-AGTTTTTTATTAGTATTTTGTATGAATATTATAATGTTGTATGAATATTG
1 AGTATGT-TTGTATGAATATTGTAATA-T-TTTTGTATGAATATTGTAAT-TTGTATGAATATTG
* * *
3500625 TAATTATTTTATAATTAATTTTGTATTTATAGTTTTGGATTAGTATTTTGTATGAATATTGTAAT
62 TAATTATTTTATAATTAATTTTGTATTTACAGTTTTGAATTAGTATTTTGTATGAATATTGAAAT
*
3500690 TTTGTAATTTTGTATGAATATTGTAATATTG-TTTGTATGAATATTGTAATT-TTGTATGGATAT
127 TTTGTAATTTTGTATGAATATTGAAATATTGATTTGTATGAATATTGTAATTATTGTAT--A-AT
*
3500753 TGT
189 T-A
3500756 AGTATTGTTTGTATGAATATTGTAATATTGTTTGTATGAATATTGTAATT
1 AGTA-TGTTTGTATGAATATTGTAATATT-TTTGTATGAATATTGTAATT
3500806 ATTTTATAAT
Statistics
Matches: 208, Mismatches: 23, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
190 5 0.02
191 20 0.10
192 11 0.05
193 8 0.04
194 28 0.13
195 128 0.62
196 8 0.04
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (190 bp):
AGTATGTTTGTATGAATATTGTAATATTTTTGTATGAATATTGTAATTTGTATGAATATTGTAAT
TATTTTATAATTAATTTTGTATTTACAGTTTTGAATTAGTATTTTGTATGAATATTGAAATTTTG
TAATTTTGTATGAATATTGAAATATTGATTTGTATGAATATTGTAATTATTGTATAATTA
Found at i:3500855 original size:88 final size:86
Alignment explanation
Indices: 3500501--3500855 Score: 236
Period size: 88 Copynumber: 4.1 Consensus size: 86
3500491 AAATTTTGTA
* *
3500501 ATTTTGTATGAATATTGAAATTTTGTAATTTTGTATGAATATTGTAATTATTTTATAATTAATT-
1 ATTTTGTATGAATATTGTAATATTG--A-TTTGTATGAATATTGTAATTATTTTATAATTAATTG
* * * * *
3500565 ATGTATTTATAGTT-TTTTATTAGT
63 TTGTATTTAGA-TTATGTTATAAAT
*
3500589 ATTTTGTATGAATA-T-T-ATAATG--TTGTATGAATATTGTAATTATTTTATAATTAATT-TTG
1 ATTTTGTATGAATATTGTAATATTGATTTGTATGAATATTGTAATTATTTTATAATTAATTGTTG
* * * * *
3500648 TATTTATAGTTTTG-GATTAGT
66 TATTTAGA-TTATGTTATAAAT
* * *
3500669 ATTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATATTGTAA-TATTGTT-TGTATGAA-
1 ATTTTGTATGAATATTGTAATATTG--A-TTTGTATGAATATTGTAATTATT-TTAT-AATTAAT
* * * * * *
3500731 TATTGTAATTTTGTATGGATATTGT-AGT
61 TGTTGT-ATTTAG-AT-TATGTTATAAAT
3500759 ATTGTTTGTATGAATATTGTAATATTG-TTTGTATGAATATTGTAATTATTTTATAATTAATTTG
1 A-T-TTTGTATGAATATTGTAATATTGATTTGTATGAATATTGTAATTATTTTATAATTAA-TTG
3500823 TTAGTAATTTAGGATTATGTTATAAAT
63 TT-GT-ATTTA-GATTATGTTATAAAT
3500850 -TTTTGT
1 ATTTTGT
3500856 GTTTGTAATT
Statistics
Matches: 216, Mismatches: 26, Indels: 50
0.74 0.09 0.17
Matches are distributed among these distances:
80 67 0.31
81 2 0.01
82 1 0.00
83 4 0.02
85 4 0.02
87 7 0.03
88 70 0.32
89 11 0.05
90 14 0.06
91 13 0.06
92 23 0.11
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (86 bp):
ATTTTGTATGAATATTGTAATATTGATTTGTATGAATATTGTAATTATTTTATAATTAATTGTTG
TATTTAGATTATGTTATAAAT
Found at i:3500879 original size:60 final size:60
Alignment explanation
Indices: 3500798--3500919 Score: 174
Period size: 60 Copynumber: 2.0 Consensus size: 60
3500788 TGTATGAATA
* ** * * *
3500798 TTGTAATTATTTTATAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGT
1 TTGTAATTATTTTAAAATTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
3500858 TTGTAATTA-TTTAAAATTTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
1 TTGTAATTATTTTAAAA-TTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
3500918 TT
1 TT
3500920 AGTTTAGTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 6 0.11
60 49 0.89
ACGTcount: A:0.32, C:0.02, G:0.13, T:0.53
Consensus pattern (60 bp):
TTGTAATTATTTTAAAATTAATTTACTAGTAATTTAGGATTAAGCTATAAATTGTTGTGT
Found at i:3501073 original size:15 final size:16
Alignment explanation
Indices: 3501037--3501073 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3501027 CTCATTTAAT
3501037 TTTTATATAATGTAAC
1 TTTTATATAATGTAAC
*
3501053 TTTTATATTATGTAA-
1 TTTTATATAATGTAAC
3501068 TTTTAT
1 TTTTAT
3501074 TTGATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTTTATATAATGTAAC
Found at i:3504683 original size:18 final size:20
Alignment explanation
Indices: 3504635--3504688 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 20
3504625 AAATGAGTAC
3504635 ATTATAAAAAAAATTATAAA
1 ATTATAAAAAAAATTATAAA
* *
3504655 ATT-TCATAAAAATTA-AAA
1 ATTATAAAAAAAATTATAAA
3504673 ATTAT-AAAAAAATTAT
1 ATTATAAAAAAAATTAT
3504689 TTTAAGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 15 0.52
19 11 0.38
20 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTATAAAAAAAATTATAAA
Found at i:3506267 original size:9 final size:9
Alignment explanation
Indices: 3506249--3506289 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
3506239 TGGCTGAAGC
3506249 TCTTCCTCT
1 TCTTCCTCT
*
3506258 TCTTCATCT
1 TCTTCCTCT
*
3506267 TCTTCCTCC
1 TCTTCCTCT
3506276 TCTTCCTCT
1 TCTTCCTCT
3506285 TCTTC
1 TCTTC
3506290 TTCGCCTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:3506456 original size:21 final size:21
Alignment explanation
Indices: 3506432--3506471 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3506422 ATCTTCCTCC
3506432 TCACCTGCAT-CTTCATCTTGA
1 TCACCTGC-TGCTTCATCTTGA
3506453 TCACCTGCTGCTTCATCTT
1 TCACCTGCTGCTTCATCTT
3506472 CCTCATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (21 bp):
TCACCTGCTGCTTCATCTTGA
Found at i:3506479 original size:24 final size:24
Alignment explanation
Indices: 3506421--3506479 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
3506411 TCACCTGATC
*
3506421 CATCTTCCTCCTCACCTGCATCTT
1 CATCTTCCTCATCACCTGCATCTT
*
3506445 CATC-T--TGATCACCTGC-TGCTT
1 CATCTTCCTCATCACCTGCAT-CTT
3506466 CATCTTCCTCATCA
1 CATCTTCCTCATCA
3506480 TCATTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 1 0.04
23 1 0.04
24 9 0.32
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (24 bp):
CATCTTCCTCATCACCTGCATCTT
Found at i:3510261 original size:100 final size:101
Alignment explanation
Indices: 3510071--3510293 Score: 349
Period size: 100 Copynumber: 2.2 Consensus size: 101
3510061 TTCATAATGT
*
3510071 CATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGTCTTACATATAAACAT
1 CATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGTCTTACATATAAACAC
** *
3510136 TGTCATGGTCCAAATATGGTATTACGTACATAGTGC
66 TACCATGGTCCAAACATGGTATTACGTACATAGTGC
* *
3510172 CATAACCCAGTT-TGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGTCTTACATATAAACAC
1 CATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGTCTTACATATAAACAC
* * * *
3510236 TACCATGGTCCAACCATGGTCTTACGTTCATAGTGT
66 TACCATGGTCCAAACATGGTATTACGTACATAGTGC
3510272 CATAACCCAGTTATGGTCTTAT
1 CATAACCCAGTTATGGTCTTAT
3510294 TCGTCAATTC
Statistics
Matches: 111, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
100 90 0.81
101 21 0.19
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (101 bp):
CATAACCCAGTTATGGTCTTATCATCAGAACGCCATAGCCCAACTATGGTCTTACATATAAACAC
TACCATGGTCCAAACATGGTATTACGTACATAGTGC
Found at i:3516606 original size:18 final size:17
Alignment explanation
Indices: 3516562--3516606 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
3516552 TGTATATACT
3516562 AAATAAAATAATAATAA
1 AAATAAAATAATAATAA
*
3516579 ATAATAAAATAATATTTAA
1 A-AATAAAATAATA-ATAA
*
3516598 AAATTAAAT
1 AAATAAAAT
3516607 TAAAATATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 1 0.04
18 19 0.79
19 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAAAATAATAATAA
Found at i:3520726 original size:19 final size:19
Alignment explanation
Indices: 3520702--3520743 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
3520692 GAGGCAATAT
*
3520702 GAAGGCACAA-GAAAGAAAA
1 GAAGGCAAAAGGAAAG-AAA
3520721 GAAGGCAAAAGGAAAGAAA
1 GAAGGCAAAAGGAAAGAAA
3520740 GAAG
1 GAAG
3520744 TTTAGGCCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.62, C:0.07, G:0.31, T:0.00
Consensus pattern (19 bp):
GAAGGCAAAAGGAAAGAAA
Found at i:3534963 original size:22 final size:21
Alignment explanation
Indices: 3534927--3534980 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
3534917 GGCCCGGCCT
3534927 ATTT-TTTTAATAAATACAAAAA
1 ATTTATTTTAA-AAAT-CAAAAA
*
3534949 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAATCAAAAA
*
3534970 A-GTATTTTAAA
1 ATTTATTTTAAA
3534981 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 9 0.31
21 6 0.21
22 8 0.28
23 6 0.21
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTTATTTTAAAAATCAAAAA
Found at i:3535007 original size:38 final size:39
Alignment explanation
Indices: 3534963--3535038 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 39
3534953 ATTTTAAAAA
*
3534963 TTAAAAAAGTATTTT-AAATATTTTAAAATTAAAAAATT
1 TTAAAAAAGAATTTTAAAATATTTTAAAATTAAAAAATT
3535001 TTAAAAAAGAATTTTAAAAATATTTTAAAATTAAAAAA
1 TTAAAAAAGAATTTT-AAAATATTTTAAAATTAAAAAA
3535039 AATATTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 14 0.40
40 21 0.60
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (39 bp):
TTAAAAAAGAATTTTAAAATATTTTAAAATTAAAAAATT
Found at i:3535015 original size:13 final size:12
Alignment explanation
Indices: 3534993--3535030 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3534983 TTTTAAAATT
3534993 AAAAAATTTTAA
1 AAAAAATTTTAA
3535005 AAAAGAATTTT-A
1 AAAA-AATTTTAA
*
3535017 AAAATATTTTAA
1 AAAAAATTTTAA
3535029 AA
1 AA
3535031 TTAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 5 0.22
12 12 0.52
13 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
AAAAAATTTTAA
Found at i:3535041 original size:20 final size:21
Alignment explanation
Indices: 3535016--3535059 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
3535006 AAAGAATTTT
3535016 AAAAATATTTTAAAA-TTAAA
1 AAAAATATTTTAAAATTTAAA
3535036 AAAAATATTTTAAAATTTAAA
1 AAAAATATTTTAAAATTTAAA
3535057 AAA
1 AAA
3535060 TAAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAATATTTTAAAATTTAAA
Found at i:3538187 original size:75 final size:74
Alignment explanation
Indices: 3537975--3538272 Score: 315
Period size: 75 Copynumber: 4.0 Consensus size: 74
3537965 TGGGTATGAT
* * * * *
3537975 GTATGAATATGGA-G-GT-GAACACTGAATTGCTACCATATCTTATAGAAGATTCTACAAGTGCT
1 GTAT-AATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGCT
3538037 AAAGAGATGG
65 AAAGAGATGG
* * *
3538047 GTA-AGACTATGGA-GA-T-GAACATTGAATTGTTACCAAAGCCTTATAGAAGATTCTACAAGTC
1 GTATA-A-TATGGAGGAGTGGAACATTGAATTGATATCAAAG-CTTATAGAAGATTCTACAAGTG
3538108 CTAAAGAGATGG
63 CTAAAGAGATGG
* * *
3538120 GTCATAATATGGAGGAGTGGAGCATCGAATTGATATCAAAGCTTATAGAAGATTCTCCAAGTGCT
1 GT-ATAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGCT
*
3538185 AAAGAGATAG
65 AAAGAGATGG
* * * * * *
3538195 ATATGAATATTGAGGAG-GAGAACGTTGAATTGATGTCAAAGCTTATAGAAGATTCTTCAAATGC
1 GTAT-AATATGGAGGAGTG-GAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGC
3538259 TAAAGAGATGG
64 TAAAGAGATGG
3538270 GTA
1 GTA
3538273 AGGATGTGGC
Statistics
Matches: 193, Mismatches: 22, Indels: 19
0.82 0.09 0.08
Matches are distributed among these distances:
70 1 0.01
71 1 0.01
72 29 0.15
73 41 0.21
74 7 0.04
75 96 0.50
76 18 0.09
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (74 bp):
GTATAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTGCTA
AAGAGATGG
Found at i:3543263 original size:28 final size:29
Alignment explanation
Indices: 3543232--3543290 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
3543222 GTAAGTACTT
3543232 AATT-TTTTAAAAAATTAAAAATTA-TAAA
1 AATTGTTTTAAAAAATT-AAAATTATTAAA
**
3543260 AATTGTTTTGTAAAATTAAAATTATTAAA
1 AATTGTTTTAAAAAATTAAAATTATTAAA
3543289 AA
1 AA
3543291 GTATAAGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (29 bp):
AATTGTTTTAAAAAATTAAAATTATTAAA
Found at i:3544401 original size:2 final size:2
Alignment explanation
Indices: 3544394--3544422 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3544384 AATTCCCAAC
3544394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3544423 TTTCAGTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3546960 original size:26 final size:25
Alignment explanation
Indices: 3546930--3546981 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3546920 GTCAACTCTC
3546930 TTTTATAAGCAAATATAAAATATTAA
1 TTTTATAA-CAAATATAAAATATTAA
* * *
3546956 TTTTATAACTATTATAAAATTTTAA
1 TTTTATAACAAATATAAAATATTAA
3546981 T
1 T
3546982 AATTTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (25 bp):
TTTTATAACAAATATAAAATATTAA
Found at i:3548509 original size:30 final size:29
Alignment explanation
Indices: 3548468--3548524 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
3548458 ATAAAATTAT
*
3548468 ATATGAATTTTAATTTTATGTAATTTTAA
1 ATATGAATTTTAATTTGATGTAATTTTAA
*
3548497 ATATGAAATTTTAATTTGATTTAATTTT
1 ATATG-AATTTTAATTTGATGTAATTTT
3548525 TTTAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (29 bp):
ATATGAATTTTAATTTGATGTAATTTTAA
Found at i:3552993 original size:17 final size:16
Alignment explanation
Indices: 3552971--3553004 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
3552961 ATCAACAAAA
3552971 TTATTAAAGATATATTT
1 TTATTAAAGATAT-TTT
3552988 TTATTAAAGATATTTT
1 TTATTAAAGATATTTT
3553004 T
1 T
3553005 ACCCCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATTAAAGATATTTT
Found at i:3553002 original size:15 final size:16
Alignment explanation
Indices: 3552971--3553005 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
3552961 ATCAACAAAA
3552971 TTATTAAAGATATATTT
1 TTATTAAAGA-ATATTT
3552988 TTATTAAAG-ATATTT
1 TTATTAAAGAATATTT
3553003 TTA
1 TTA
3553006 CCCCAAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
17 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (16 bp):
TTATTAAAGAATATTT
Found at i:3556610 original size:12 final size:12
Alignment explanation
Indices: 3556593--3556618 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3556583 CTTGTAACCC
3556593 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3556605 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3556617 TG
1 TG
3556619 CCTCACACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (12 bp):
TGTTTGAGTTCA
Found at i:3557752 original size:15 final size:15
Alignment explanation
Indices: 3557732--3557769 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
3557722 ACCTCCTCCT
3557732 ACCGCAGCTGCTGCC
1 ACCGCAGCTGCTGCC
*
3557747 ACCGCATCTGCTGCC
1 ACCGCAGCTGCTGCC
*
3557762 GCCGCAGC
1 ACCGCAGC
3557770 CGCGTCGTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.13, C:0.47, G:0.26, T:0.13
Consensus pattern (15 bp):
ACCGCAGCTGCTGCC
Found at i:3558548 original size:3 final size:3
Alignment explanation
Indices: 3558540--3558583 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
3558530 GTGGGGGACC
3558540 ATT ATT ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
3558584 GGGTTGAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:3562424 original size:3 final size:3
Alignment explanation
Indices: 3562416--3562455 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3562406 AGTTTCATCC
3562416 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3562456 GGTGTTCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3589323 original size:17 final size:17
Alignment explanation
Indices: 3589294--3589327 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3589284 TTCTTTATTT
3589294 ATTTAAAATTATTAAAA
1 ATTTAAAATTATTAAAA
3589311 ATTTATAAA-TATTAAAA
1 ATTTA-AAATTATTAAAA
3589328 TAGAGACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTTAAAATTATTAAAA
Found at i:3607133 original size:17 final size:17
Alignment explanation
Indices: 3607099--3607154 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
3607089 AATATTACGA
*
3607099 ATTAAAAAATAGATATAT
1 ATTAAATAATA-ATATAT
*
3607117 ATTTAATAATAATATAT
1 ATTAAATAATAATATAT
* *
3607134 AATAAATAATAAAATAT
1 ATTAAATAATAATATAT
3607151 ATTA
1 ATTA
3607155 TTTTAAATTA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
17 23 0.72
18 9 0.28
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTAAATAATAATATAT
Found at i:3610505 original size:14 final size:15
Alignment explanation
Indices: 3610481--3610509 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3610471 CTAAGAAATT
3610481 AAAAAGTAAAAAAAA
1 AAAAAGTAAAAAAAA
3610496 AAAAAG-AAAAAAAA
1 AAAAAGTAAAAAAAA
3610510 GTCATCATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (15 bp):
AAAAAGTAAAAAAAA
Found at i:3614830 original size:2 final size:2
Alignment explanation
Indices: 3614823--3614852 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3614813 CTATTTGCTA
3614823 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3614853 TTCGTGTGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3615443 original size:2 final size:2
Alignment explanation
Indices: 3615436--3615463 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3615426 TGTCTTAAAC
3615436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3615464 GTCCCTAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3615590 original size:14 final size:14
Alignment explanation
Indices: 3615573--3615599 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3615563 TAGAAATGAG
3615573 TTTTTTTTTTTGTT
1 TTTTTTTTTTTGTT
3615587 TTTTTTTTTTTGT
1 TTTTTTTTTTTGT
3615600 AAATTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (14 bp):
TTTTTTTTTTTGTT
Found at i:3624806 original size:18 final size:17
Alignment explanation
Indices: 3624783--3624827 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
3624773 ATTTAAATTG
3624783 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCG-TTT
*
3624801 CGGTCGC-GCCGCGTTT
1 CGGTCGCGGTCGCGTTT
3624817 --GTCGCGGTCGC
1 CGGTCGCGGTCGC
3624828 AGACATAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
14 5 0.21
15 4 0.17
16 3 0.12
17 5 0.21
18 7 0.29
ACGTcount: A:0.00, C:0.33, G:0.40, T:0.27
Consensus pattern (17 bp):
CGGTCGCGGTCGCGTTT
Found at i:3625155 original size:27 final size:25
Alignment explanation
Indices: 3625101--3625155 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 25
3625091 CAGATGCCCA
* **
3625101 AAAGTAAAAAAATTTAGATATTTTT
1 AAAGTAAAAAAATCTAGATATTCCT
3625126 AAAGTAAAAAAATCTAGATATAATCCT
1 AAAGTAAAAAAATCTAGATAT--TCCT
3625153 AAA
1 AAA
3625156 AAAAGGCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.80
27 5 0.20
ACGTcount: A:0.56, C:0.05, G:0.07, T:0.31
Consensus pattern (25 bp):
AAAGTAAAAAAATCTAGATATTCCT
Found at i:3626184 original size:110 final size:108
Alignment explanation
Indices: 3626040--3626322 Score: 331
Period size: 109 Copynumber: 2.6 Consensus size: 108
3626030 AAATACGGAT
3626040 ATACGAAAAAAAAAATTTTTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAA
1 ATACGAAAAAAAAAA---TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAA
** * ** **
3626105 AGAAAAAAAAATTTTAATTTTTTTTTC-GTGTCAG-AATCAGAT-AAAAAA
63 AG---AAAAAATTTT--TTTTCGTGTCAGAATCAGAAAAAAGATGAAAAAA
* *
3626153 ATACGAAAAAAAAAATTTTGGGTGCTGGCCTGTTAATGGCCGGCACCCAGTCCACAGTACAAAGA
1 ATACGAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGA
*
3626218 AAAAATTTTTTTTCGTGTCAGAATCAGATAAAAAATATGAAAAAA
66 AAAAATTTTTTTTCGTGTCAGAATCAG--AAAAAAGATGAAAAAA
* * *
3626263 ATA-AAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTATACAATACA
1 ATACGAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACA
3626323 CAGCCTGCCA
Statistics
Matches: 150, Mismatches: 15, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
105 7 0.05
106 5 0.03
107 10 0.07
109 57 0.38
110 56 0.37
113 15 0.10
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.25
Consensus pattern (108 bp):
ATACGAAAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACACAGTACAAAGA
AAAAATTTTTTTTCGTGTCAGAATCAGAAAAAAGATGAAAAAA
Found at i:3626470 original size:117 final size:116
Alignment explanation
Indices: 3626332--3626821 Score: 738
Period size: 117 Copynumber: 4.2 Consensus size: 116
3626322 ACAGCCTGCC
* * *
3626332 AATTTTTTTTTTTATTTTTTTCGTATTTTTTATCTGATTCTGACATGAAAAAAAA-AAAAAATTT
1 AATTTTTTTTTTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGAAAAATTTT
3626396 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAAAA
66 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACC--AAA
* *
3626449 AATTTTTTTTCTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAATTAGAAAATTT
1 AATTTTTTTTTTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAA--AGAAAAATT
* * *
3626514 TTTTTTCTTTGTACTATGTACTAGGTGCCGGCCATTGACAGGCCAGCACCCAA
64 TTTTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAA
* *
3626567 AA-TTTTTTTTT-ATTTTTTTCGTATTTTTTATCTGATTCTGACACG-AAAAAAA-ATAATTTTT
1 AATTTTTTTTTTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGAAAAATTTT
3626628 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCCAAA
66 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCA-CCAAA
* **
3626680 ATTTTTTTTTTTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAATTAAAATTTT
1 AATTTTTTTTTTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGAAAAATTTT
* * *
3626745 TTTTCTTTATACTGTGTACTGGGTACCGGCCATTGACAGGCCAGCACCCAA
66 TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAA
**
3626796 AATTTTTTTTTTGTTTTTTTTCGTAT
1 AATTTTTTTTTTAATTTTTTTCGTAT
3626822 ATCCATATTT
Statistics
Matches: 342, Mismatches: 23, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
112 52 0.15
113 6 0.02
114 9 0.03
115 40 0.12
116 68 0.20
117 109 0.32
118 4 0.01
119 1 0.00
120 53 0.15
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.45
Consensus pattern (116 bp):
AATTTTTTTTTTAATTTTTTTCGTATTTTTTATCTGATTCTGACACGAAAAAAAAGAAAAATTTT
TTTTCTTTGTACTGTGTACTGGGTGCCGGCCATTGACAGGCCAGCACCAAA
Found at i:3627823 original size:16 final size:18
Alignment explanation
Indices: 3627802--3627839 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3627792 TTCTATAAAA
3627802 ATTTTACT-TT-TATTTT
1 ATTTTACTATTGTATTTT
3627818 ATTTTACTATTGTATTTT
1 ATTTTACTATTGTATTTT
3627836 ATTT
1 ATTT
3627840 AAATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.40
17 2 0.10
18 10 0.50
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (18 bp):
ATTTTACTATTGTATTTT
Found at i:3629922 original size:29 final size:30
Alignment explanation
Indices: 3629898--3629954 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
3629888 TCATGTGTAT
*
3629898 AATTGCAC-TAAATCAAAGTTCATGTAGCA
1 AATTGCACATAAACCAAAGTTCATGTAGCA
3629927 AATTGCACATTAAACCAAAGTTCATGTA
1 AATTGCACA-TAAACCAAAGTTCATGTA
3629955 CATATTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 8 0.32
31 17 0.68
ACGTcount: A:0.42, C:0.18, G:0.12, T:0.28
Consensus pattern (30 bp):
AATTGCACATAAACCAAAGTTCATGTAGCA
Found at i:3638941 original size:16 final size:17
Alignment explanation
Indices: 3638914--3638950 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
3638904 AATTAAGTCA
3638914 ATAATAATATAACATTT
1 ATAATAATATAACATTT
3638931 ATAAT-ATATAACATTT
1 ATAATAATATAACATTT
3638947 ATAA
1 ATAA
3638951 GTAAGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATATAACATTT
Found at i:3639715 original size:117 final size:118
Alignment explanation
Indices: 3639489--3639724 Score: 327
Period size: 117 Copynumber: 2.0 Consensus size: 118
3639479 ATGCCATTAT
* *
3639489 TGTGTAATTACATGCAATTAAATCCAAATCCAATTACTTGGTGGCTTTCCGAATACTATTGAATT
1 TGTGTAATTACATGCAATTAAATCCAAATCCAATTACTTGGTGACTTTCCAAATACTATTGAATT
* * *
3639554 CAAGAAAAAAGTAATTTAATATCATGTTCATTTTTATAACGGCATAATGATAA
66 CAAGAAAAAAGTAATTTAATATCATGTTCATTCTCATAAAGGCATAATGATAA
* * *
3639607 TGTGTAATTACATGCAATTACA-CCAAATCGAATTA-TTAGGTGACTTTCTAAATA-TATTGAAT
1 TGTGTAATTACATGCAATTAAATCCAAATCCAATTACTT-GGTGACTTTCCAAATACTATTGAAT
**
3639669 TCAAGAAAAAAAAGTAATTT-ATATCATGTTTGTTCTCATAAAGGCATAATGATAA
65 TCAAG--AAAAAAGTAATTTAATATCATGTTCATTCTCATAAAGGCATAATGATAA
3639724 T
1 T
3639725 TTTAACCTTC
Statistics
Matches: 105, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
116 15 0.14
117 56 0.53
118 34 0.32
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (118 bp):
TGTGTAATTACATGCAATTAAATCCAAATCCAATTACTTGGTGACTTTCCAAATACTATTGAATT
CAAGAAAAAAGTAATTTAATATCATGTTCATTCTCATAAAGGCATAATGATAA
Found at i:3639995 original size:13 final size:14
Alignment explanation
Indices: 3639977--3640005 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3639967 AAATAAAATT
3639977 AAAGTT-ATAAAAA
1 AAAGTTCATAAAAA
3639990 AAAGTTCATAAAAA
1 AAAGTTCATAAAAA
3640004 AA
1 AA
3640006 TTCAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (14 bp):
AAAGTTCATAAAAA
Found at i:3644346 original size:23 final size:22
Alignment explanation
Indices: 3644310--3644363 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
3644300 TTTTATATAT
3644310 ATATTATAAATAAATATAATAA-A
1 ATATTATAAATAAA-A-AATAACA
* *
3644333 ATATTATTACTAAAAAATAACA
1 ATATTATAAATAAAAAATAACA
3644355 ATAATTATA
1 AT-ATTATA
3644364 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 17 0.65
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (22 bp):
ATATTATAAATAAAAAATAACA
Found at i:3644357 original size:27 final size:27
Alignment explanation
Indices: 3644306--3644358 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3644296 GTGTTTTTAT
*
3644306 ATATATATTATAAATAAATATAATAAA
1 ATATATATTATAAATAAATACAATAAA
3644333 ATAT-TATTACTAAA-AAATAACAATAA
1 ATATATATTA-TAAATAAAT-ACAATAA
3644359 TTATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (27 bp):
ATATATATTATAAATAAATACAATAAA
Found at i:3646108 original size:3 final size:3
Alignment explanation
Indices: 3646100--3646152 Score: 52
Period size: 3 Copynumber: 17.7 Consensus size: 3
3646090 CCACTCATCT
* * * * * *
3646100 TAA TAA TAA TAA TAA AAA TAA TAA TAA TAC TAT TAC TAA TAC TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3646148 TAA TA
1 TAA TA
3646153 CTTACCTCAC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3646921 original size:19 final size:19
Alignment explanation
Indices: 3646876--3646915 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3646866 TTTGTTTTGT
*
3646876 TTTTATTT-CTTTACTTTC
1 TTTTATTTACTTTACTTTA
3646894 TTTTATTTACTTTACTTTA
1 TTTTATTTACTTTACTTTA
3646913 TTT
1 TTT
3646916 CTTTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTACTTTACTTTA
Found at i:3647073 original size:5 final size:5
Alignment explanation
Indices: 3647065--3647119 Score: 53
Period size: 5 Copynumber: 11.2 Consensus size: 5
3647055 TATTTAATTT
* *
3647065 ATATA ATATA ATACA ATATA ATATA TTATATT ATATA ATA-A A-ATA ATAT-
1 ATATA ATATA ATATA ATATA ATATA --ATATA ATATA ATATA ATATA ATATA
3647114 ATATA A
1 ATATA A
3647120 AACATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.20
5 28 0.68
7 4 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:3647094 original size:27 final size:25
Alignment explanation
Indices: 3647063--3647115 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
3647053 TCTATTTAAT
3647063 TTATATAATATAATACAATATAATATA
1 TTATATAATATAATA-AA-ATAATATA
*
3647090 TTATATTATATAATAAAATAATATA
1 TTATATAATATAATAAAATAATATA
3647115 T
1 T
3647116 ATAAAACATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 2 0.08
27 14 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (25 bp):
TTATATAATATAATAAAATAATATA
Found at i:3651704 original size:42 final size:43
Alignment explanation
Indices: 3651600--3651709 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 43
3651590 CAATGTCAAC
*** *
3651600 GTCCCAGACATGGTCTTACATGTAATCAAATAACGATGTCACT
1 GTCCCAGACATGGTCTTACATGTAATCAAATAACGACACCAAT
* * * *
3651643 GTCCCAGACAGGGTCTTACACGTAATCATAT-ATGACACCAAT
1 GTCCCAGACATGGTCTTACATGTAATCAAATAACGACACCAAT
*
3651685 GTTCCAGACATGGTCTTACATGTAA
1 GTCCCAGACATGGTCTTACATGTAA
3651710 ATCTTAAACC
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
42 28 0.50
43 28 0.50
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGTAATCAAATAACGACACCAAT
Found at i:3656366 original size:29 final size:29
Alignment explanation
Indices: 3656332--3656388 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
3656322 TTTTTTTTAC
3656332 TTTAGTATAGGTTTTACTTACTACTTTTT
1 TTTAGTATAGGTTTTACTTACTACTTTTT
*
3656361 TTTAGTATAGGTTTTTCTTACTACTTTT
1 TTTAGTATAGGTTTTACTTACTACTTTT
3656389 ACCCAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.60
Consensus pattern (29 bp):
TTTAGTATAGGTTTTACTTACTACTTTTT
Found at i:3657779 original size:18 final size:18
Alignment explanation
Indices: 3657718--3657781 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
3657708 TCTAATTTAA
3657718 AAAAATATAAATTA-TA-
1 AAAAATATAAATTATTAT
3657734 AAAACATA-AAGATTATTAT
1 AAAA-ATATAA-ATTATTAT
**
3657753 AAATTTATAAATTATTAT
1 AAAAATATAAATTATTAT
3657771 AAAAATATAAA
1 AAAAATATAAA
3657782 AAATAAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.15
17 7 0.18
18 21 0.54
19 5 0.13
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAAATATAAATTATTAT
Found at i:3658116 original size:17 final size:17
Alignment explanation
Indices: 3658091--3658150 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
3658081 ATTAAAAAGT
*
3658091 AATAAAAATATTATTTA
1 AATATAAATATTATTTA
*
3658108 AATATAAATATTAATATA
1 AATATAAATATT-ATTTA
* *
3658126 AA-ATTATTATT-TTTA
1 AATATAAATATTATTTA
3658141 AATAGTAAAT
1 AATA-TAAAT
3658151 CAAAGTGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 5 0.15
16 1 0.03
17 21 0.64
18 6 0.18
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATAAATATTATTTA
Found at i:3658359 original size:14 final size:14
Alignment explanation
Indices: 3658340--3658389 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
3658330 TTTTCTACAA
3658340 ATTTTAATATTTTT
1 ATTTTAATATTTTT
* *
3658354 ATTTTATAAACTTTT
1 ATTTTA-ATATTTTT
3658369 A--TTAATATTTTT
1 ATTTTAATATTTTT
3658381 ATTTTAATA
1 ATTTTAATA
3658390 ATATTCTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 7 0.24
13 3 0.10
14 12 0.41
15 7 0.24
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTAATATTTTT
Found at i:3658448 original size:20 final size:20
Alignment explanation
Indices: 3658423--3658478 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
3658413 TTTTTTTTGG
*
3658423 AATTTTTAATAATTTCTCAA
1 AATTTTTAATAATTTATCAA
*
3658443 AATTTTATAATAATTTATCAT
1 AATTTT-TAATAATTTATCAA
*
3658464 AATTTATAAT-ATTTA
1 AATTTTTAATAATTTA
3658479 ATGATGTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 10 0.31
21 17 0.53
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTTTTAATAATTTATCAA
Found at i:3658455 original size:21 final size:21
Alignment explanation
Indices: 3658423--3658478 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
3658413 TTTTTTTTGG
*
3658423 AATTTT-TAATAATTTCTCAA
1 AATTTTATAATAATTTATCAA
*
3658443 AATTTTATAATAATTTATCAT
1 AATTTTATAATAATTTATCAA
3658464 AA-TTTATAAT-ATTTA
1 AATTTTATAATAATTTA
3658479 ATGATGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 14 0.42
21 14 0.42
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTATAATAATTTATCAA
Found at i:3663237 original size:20 final size:19
Alignment explanation
Indices: 3663212--3663253 Score: 75
Period size: 20 Copynumber: 2.2 Consensus size: 19
3663202 AATATATTTA
3663212 TTTTTTAATTTTAAAATACT
1 TTTTTTAATTTTAAAATA-T
3663232 TTTTTTAATTTTAAAATAT
1 TTTTTTAATTTTAAAATAT
3663251 TTT
1 TTT
3663254 AAAATTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTTAATTTTAAAATAT
Found at i:3663254 original size:10 final size:10
Alignment explanation
Indices: 3663239--3663278 Score: 62
Period size: 10 Copynumber: 3.8 Consensus size: 10
3663229 ACTTTTTTTA
3663239 ATTTTAAAAT
1 ATTTTAAAAT
3663249 ATTTTAAAATT
1 ATTTTAAAA-T
3663260 ATTTTAAAAAT
1 ATTTT-AAAAT
3663271 ATTTTAAA
1 ATTTTAAA
3663279 TTTTTTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 12 0.43
11 12 0.43
12 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:3663264 original size:11 final size:11
Alignment explanation
Indices: 3663239--3663289 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
3663229 ACTTTTTTTA
3663239 ATTTTAAAA-T
1 ATTTTAAAATT
3663249 ATTTTAAAATT
1 ATTTTAAAATT
*
3663260 ATTTTAAAAAT
1 ATTTTAAAATT
*
3663271 ATTTTAAATTT
1 ATTTTAAAATT
*
3663282 TTTTTAAA
1 ATTTTAAA
3663290 TTTTTTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 9 0.25
11 27 0.75
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTTAAAATT
Done.