Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397270.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_55.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4719911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 90628 characters in sequence are not A, C, G, or T
File 8 of 10
Found at i:3065157 original size:28 final size:28
Alignment explanation
Indices: 3065125--3065180 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
3065115 ACCAAGTTAC
*
3065125 AAAAAAAAAATTTATTACATATCATGTTG
1 AAAAAAAAAA-TTATTACAGATCATGTTG
3065154 AAAAAAAAAATTATTACAGATCATGTT
1 AAAAAAAAAATTATTACAGATCATGTT
3065181 TAAGTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAAAAAAATTATTACAGATCATGTTG
Found at i:3065903 original size:17 final size:18
Alignment explanation
Indices: 3065881--3065914 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3065871 GCCTTTTATA
3065881 TAAATTAACATA-ATAAC
1 TAAATTAACATATATAAC
*
3065898 TAAATTATCATATATAA
1 TAAATTAACATATATAA
3065915 GTATGTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAATTAACATATATAAC
Found at i:3074215 original size:29 final size:29
Alignment explanation
Indices: 3074140--3074216 Score: 68
Period size: 29 Copynumber: 2.6 Consensus size: 29
3074130 AACCGTTATT
*
3074140 AATAAAAATTTATTTAATTCAAAATAAAAG
1 AATAAAAATTTATTTAA-ACAAAATAAAAG
* * * *
3074170 TACAAAAACTTCA-TTAAACATAATAGAAA-
1 AATAAAAA-TTTATTTAAACAAAATA-AAAG
3074199 AATAAAAATTTATTTAAA
1 AATAAAAATTTATTTAAA
3074217 TTTTCTTGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
28 3 0.08
29 17 0.47
30 13 0.36
31 3 0.08
ACGTcount: A:0.60, C:0.06, G:0.03, T:0.31
Consensus pattern (29 bp):
AATAAAAATTTATTTAAACAAAATAAAAG
Found at i:3078321 original size:2 final size:2
Alignment explanation
Indices: 3078314--3078354 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
3078304 GGAGGTCACT
3078314 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
3078355 GCCACATACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3086454 original size:29 final size:29
Alignment explanation
Indices: 3086421--3086476 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
3086411 AAATATTTAT
*
3086421 AATATCCACTATAACAAAACAAGATATGC
1 AATATCCACAATAACAAAACAAGATATGC
* * *
3086450 AATATCCACAATAGCTAAGCAAGATAT
1 AATATCCACAATAACAAAACAAGATAT
3086477 ATTGAATATC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (29 bp):
AATATCCACAATAACAAAACAAGATATGC
Found at i:3092274 original size:21 final size:20
Alignment explanation
Indices: 3092249--3092308 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 20
3092239 GCAAAAAAAG
3092249 AAAAATTATTTATAAATTAT
1 AAAAATTATTTATAAATTAT
3092269 AAAAAATAATATTT-TAAATT-T
1 -AAAAAT--TATTTATAAATTAT
* *
3092290 GAAAATTAATTA-AAATTAT
1 AAAAATTATTTATAAATTAT
3092309 TAATATTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
18 9 0.27
19 1 0.03
20 5 0.15
21 7 0.21
22 6 0.18
23 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAAATTATTTATAAATTAT
Found at i:3094305 original size:25 final size:25
Alignment explanation
Indices: 3094277--3094353 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
3094267 TTACAACAAT
3094277 TTAAAATATTAATAATTAAATTATA
1 TTAAAATATTAATAATTAAATTATA
* *
3094302 TTAAAATGTTAATATTTAAATTATCAA
1 TTAAAATATTAATAATTAAATTAT--A
* *
3094329 TTATTAATATT-TTAATTAAATTATA
1 TTA-AAATATTAATAATTAAATTATA
3094354 AATTATCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
25 23 0.53
27 15 0.35
28 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TTAAAATATTAATAATTAAATTATA
Found at i:3096410 original size:17 final size:18
Alignment explanation
Indices: 3096385--3096418 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3096375 AACATACATG
*
3096385 GCATTTAAT-AATTAAAT
1 GCATGTAATAAATTAAAT
3096402 GCATGTAATAAATTAAA
1 GCATGTAATAAATTAAA
3096419 CAAGCTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (18 bp):
GCATGTAATAAATTAAAT
Found at i:3098461 original size:20 final size:21
Alignment explanation
Indices: 3098432--3098479 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
3098422 AAATAAATAA
* *
3098432 AAAGACAAAAGAGA-AGAGAT
1 AAAGAAAAAAGAGAGAGAGAG
3098452 AAAGAAAAAAGAGAGAGAGAG
1 AAAGAAAAAAGAGAGAGAGAG
3098473 AAAGAAA
1 AAAGAAA
3098480 GATATGTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAGAGAGAGAGAG
Found at i:3114193 original size:35 final size:35
Alignment explanation
Indices: 3114154--3114237 Score: 159
Period size: 35 Copynumber: 2.4 Consensus size: 35
3114144 GTTTAATCTT
3114154 GTGAAAAAGCTATTGTAAGGATTTCACTTGATCCC
1 GTGAAAAAGCTATTGTAAGGATTTCACTTGATCCC
3114189 GTGAAAAAGCTATTGTAAGGATTTCACTTGATCCC
1 GTGAAAAAGCTATTGTAAGGATTTCACTTGATCCC
*
3114224 GTGAAAAAGTTATT
1 GTGAAAAAGCTATT
3114238 ATAATAGTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.32
Consensus pattern (35 bp):
GTGAAAAAGCTATTGTAAGGATTTCACTTGATCCC
Found at i:3115763 original size:27 final size:25
Alignment explanation
Indices: 3115733--3115783 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
3115723 GATTATACTA
*
3115733 ATTGATTCTTTTAAATACATTATTAAG
1 ATTGATTATTTTAAATA-ATT-TTAAG
*
3115760 ATTGATTATTTTGAATAATTTTAA
1 ATTGATTATTTTAAATAATTTTAA
3115784 AAATTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 3 0.14
27 15 0.68
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (25 bp):
ATTGATTATTTTAAATAATTTTAAG
Found at i:3115801 original size:22 final size:23
Alignment explanation
Indices: 3115774--3115818 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3115764 ATTATTTTGA
3115774 ATAATTTTA-A-AAATTTATTTAT
1 ATAATTTTATATAAATTT-TTTAT
3115796 ATAATTTTATATAAATTTTTTAT
1 ATAATTTTATATAAATTTTTTAT
3115819 CTAAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (23 bp):
ATAATTTTATATAAATTTTTTAT
Found at i:3115832 original size:14 final size:14
Alignment explanation
Indices: 3115799--3115834 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
3115789 TATTTATATA
3115799 ATTTTATATAAATT
1 ATTTTATATAAATT
*
3115813 -TTTTATCTAAATT
1 ATTTTATATAAATT
3115826 ATTTTATAT
1 ATTTTATAT
3115835 TATTATCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (14 bp):
ATTTTATATAAATT
Found at i:3125154 original size:30 final size:30
Alignment explanation
Indices: 3125108--3125174 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
3125098 ATATTCAATA
3125108 AAACCC-TTATACTTTTATTTTGAACTAAAT
1 AAACCCTTTATACTTTTATTTTGAAC-AAAT
* *
3125138 -AACCCTTTATATTTTTATTTTGATCAAAT
1 AAACCCTTTATACTTTTATTTTGAACAAAT
3125167 AAACCCTT
1 AAACCCTT
3125175 ACTATTAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (30 bp):
AAACCCTTTATACTTTTATTTTGAACAAAT
Found at i:3127892 original size:52 final size:52
Alignment explanation
Indices: 3127835--3127963 Score: 188
Period size: 52 Copynumber: 2.5 Consensus size: 52
3127825 AAAAGAACAT
* *
3127835 ATAATAAATCAAGGAAAAATATTTTCCTAA-CTCAAAGGTAAGCAAAGCATAA
1 ATAATAAATCAAGGTAAAATATTTTCCTAAGCT-AAAGGCAAGCAAAGCATAA
* *
3127887 ATAATAAATTAAGGTAAAATATTTTCCTAAGCTAAATGCAAGCAAAGCATAA
1 ATAATAAATCAAGGTAAAATATTTTCCTAAGCTAAAGGCAAGCAAAGCATAA
* *
3127939 ATAACAAATGAAGGTAAAATATTTT
1 ATAATAAATCAAGGTAAAATATTTT
3127964 TCTAGAGGCA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
52 68 0.97
53 2 0.03
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (52 bp):
ATAATAAATCAAGGTAAAATATTTTCCTAAGCTAAAGGCAAGCAAAGCATAA
Found at i:3128706 original size:20 final size:20
Alignment explanation
Indices: 3128681--3128727 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
3128671 AAAAGCAGTA
3128681 ATGTATCGATACATCCATTC
1 ATGTATCGATACATCCATTC
*
3128701 ATGTATCGATACTTCCATTC
1 ATGTATCGATACATCCATTC
3128721 ATGTATC
1 ATGTATC
3128728 AATATAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATCCATTC
Found at i:3137056 original size:12 final size:12
Alignment explanation
Indices: 3137039--3137091 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 12
3137029 GGTGTATATC
3137039 TAACTAATAAAT
1 TAACTAATAAAT
3137051 TAACTAATATATATAT
1 TAACT-A-ATA-A-AT
3137067 GTATACTAATAAAT
1 -TA-ACTAATAAAT
3137081 TAACTAATAAA
1 TAACTAATAAA
3137092 GATTTGATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 14 0.40
13 3 0.09
14 5 0.14
15 2 0.06
16 5 0.14
17 3 0.09
18 3 0.09
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.36
Consensus pattern (12 bp):
TAACTAATAAAT
Found at i:3137075 original size:30 final size:29
Alignment explanation
Indices: 3137033--3137089 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 29
3137023 AGTCATGGTG
3137033 TATATCTAACTAATAAATTAACTAATATA
1 TATATCTAACTAATAAATTAACTAATATA
*
3137062 TATATGTATACTAATAAATTAACTAATA
1 TATATCTA-ACTAATAAATTAACTAATA
3137090 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 7 0.27
30 19 0.73
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.39
Consensus pattern (29 bp):
TATATCTAACTAATAAATTAACTAATATA
Found at i:3139406 original size:17 final size:18
Alignment explanation
Indices: 3139384--3139436 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
3139374 GACAATTAAC
3139384 TTTATATTTCAAAA-ATA
1 TTTATATTTCAAAAGATA
*
3139401 TTTATATCTTATAAATAGATA
1 TTTATAT-TT-CAAA-AGATA
3139422 TTTATTATTTCAAAA
1 TTTA-TATTTCAAAA
3139437 TAAATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 7 0.24
18 2 0.07
19 4 0.14
20 4 0.14
21 9 0.31
22 3 0.10
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (18 bp):
TTTATATTTCAAAAGATA
Found at i:3139506 original size:3 final size:3
Alignment explanation
Indices: 3139498--3139540 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
3139488 AGTATCAGTA
* *
3139498 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TGT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3139541 GTTACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3143095 original size:18 final size:18
Alignment explanation
Indices: 3143072--3143128 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
3143062 CTACCACCGG
3143072 TTCTGGTACAATTATTGA
1 TTCTGGTACAATTATTGA
* *
3143090 TTCTGGTA-ATGCTTATTGC
1 TTCTGGTACA--ATTATTGA
*
3143109 TTCTGGTACCATTATTGA
1 TTCTGGTACAATTATTGA
3143127 TT
1 TT
3143129 AGGTTGAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 1 0.03
18 16 0.52
19 14 0.45
ACGTcount: A:0.21, C:0.14, G:0.18, T:0.47
Consensus pattern (18 bp):
TTCTGGTACAATTATTGA
Found at i:3158386 original size:30 final size:28
Alignment explanation
Indices: 3158345--3158402 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
3158335 ATAAGAACAT
3158345 ATTTAATT--ATA-AATAAAAATATAAAA
1 ATTTAATTAAATATAATAAAAA-ATAAAA
*
3158371 ATTTAATTAAATATAATAAAAAATAATA
1 ATTTAATTAAATATAATAAAAAATAAAA
3158399 ATTT
1 ATTT
3158403 TTTATAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 8 0.29
28 12 0.43
29 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTTAATTAAATATAATAAAAAATAAAA
Found at i:3165176 original size:21 final size:18
Alignment explanation
Indices: 3165163--3165197 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3165153 TCTTTCTTAG
3165163 CTTTTTTCTTTTC-TTCCA
1 CTTTTTT-TTTTCTTTCCA
3165181 CTTTTTTTTTTCTTTCC
1 CTTTTTTTTTTCTTTCC
3165198 TACCAAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (18 bp):
CTTTTTTTTTTCTTTCCA
Found at i:3172778 original size:19 final size:19
Alignment explanation
Indices: 3172730--3172792 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
3172720 CTTACATAAG
* *
3172730 AAAGAGAAAAGTAAAAATAA
1 AAAGAGAAAA-AAAAAAGAA
*
3172750 AAA-A-ATAAAAAAGAAGAA
1 AAAGAGA-AAAAAAAAAGAA
*
3172768 AAAGAGAAAAAAAAAAGAG
1 AAAGAGAAAAAAAAAAGAA
3172787 AAAGAG
1 AAAGAG
3172793 GTGTGAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 10 0.29
19 21 0.60
20 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAGAGAAAAAAAAAAGAA
Found at i:3176824 original size:23 final size:21
Alignment explanation
Indices: 3176780--3176830 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
3176770 TTCTTGATAT
*
3176780 AATATTTTAAAAAATCTCTAA
1 AATATTTTAAAAAATCTATAA
*
3176801 ATTATTTTAAAAAATTCATATAA
1 AATATTTTAAAAAA-TC-TATAA
3176824 AATATTT
1 AATATTT
3176831 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 10 0.40
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
AATATTTTAAAAAATCTATAA
Found at i:3196502 original size:3 final size:3
Alignment explanation
Indices: 3196494--3196535 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
3196484 GTCTAGAACT
*
3196494 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3196536 TGCAGAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:3205271 original size:36 final size:36
Alignment explanation
Indices: 3205231--3205498 Score: 268
Period size: 36 Copynumber: 7.4 Consensus size: 36
3205221 ACTGCGGTGG
*
3205231 TGGTGGTGGTTGAGGCAATGGAGGTTGAGGAAGAGC
1 TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
*
3205267 TGGTGGTGGTTGAGGCAATGGTGGTTGAGG-CG-G-
1 TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
* ** *
3205300 TGGAGGCTGAG--GAAGAGCTGGTGGTGGTTGAGGAAGTGC
1 TGGTGG-TG-GTTG-AG-GC-AATGGTGGTTGAGGAAGAGC
*
3205339 TGGTGGTGGTTGAGGCAATGGTGGTTGAGG-CG-G-
1 TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
* * ** *
3205372 TGGAGGAGGCGGGAAGAGC-GTGGTGGTTGAAGGAAGAGC
1 TGGTGGTGG-TTG-AG-GCAATGGTGGTTG-AGGAAGAGC
3205411 TGGTGGTGG-TGAGGCAATGGTGGTTGAGGAAGAGC
1 TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
3205446 TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
1 TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
3205482 TGGTGGTGGGTTGAGGC
1 TGGTGGT-GGTTGAGGC
3205499 GGCGATGGTT
Statistics
Matches: 192, Mismatches: 20, Indels: 39
0.76 0.08 0.16
Matches are distributed among these distances:
33 13 0.07
34 7 0.04
35 36 0.19
36 102 0.53
37 15 0.08
38 6 0.03
39 13 0.07
ACGTcount: A:0.18, C:0.06, G:0.53, T:0.23
Consensus pattern (36 bp):
TGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGC
Found at i:3205290 original size:51 final size:51
Alignment explanation
Indices: 3205234--3205332 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
3205224 GCGGTGGTGG
*
3205234 TGGTGGTTGAGGCAATGGAGGTTGAGGAAGAGCTGGTGGTGGTTGAGGCAA
1 TGGTGGTTGAGGCAATGGAGGCTGAGGAAGAGCTGGTGGTGGTTGAGGCAA
**
3205285 TGGTGGTTGAGGCGGTGGAGGCTGAGGAAGAGCTGGTGGTGGTTGAGG
1 TGGTGGTTGAGGCAATGGAGGCTGAGGAAGAGCTGGTGGTGGTTGAGG
3205333 AAGTGCTGGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.18, C:0.06, G:0.53, T:0.23
Consensus pattern (51 bp):
TGGTGGTTGAGGCAATGGAGGCTGAGGAAGAGCTGGTGGTGGTTGAGGCAA
Found at i:3205300 original size:72 final size:72
Alignment explanation
Indices: 3205224--3205498 Score: 310
Period size: 72 Copynumber: 3.8 Consensus size: 72
3205214 CAATCAGACT
* *
3205224 GCGGTGGTGGTGGTGGTTGAGGCAATGGAGGTTGAGGAAGAGCTGGTGGTGGTTGAGGCAATGGT
1 GCGGTGGAGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGCTGGTGGTGGTTGAGGCAATGGT
3205289 GGTTGAG
66 GGTTGAG
* ** ** *
3205296 GCGGTGGAGGCT-GAGGAAGA-GCTGGTGGTGGTTGAGGAAGTGCTGGTGGTGGTTGAGGCAATG
1 GCGGTGGAGG-TGGTGGTTGAGGC-AATGGTGGTTGAGGAAGAGCTGGTGGTGGTTGAGGCAATG
3205359 GTGGTTGAG
64 GTGGTTGAG
* * *
3205368 GCGGTGGAGGAGGCGG--GAAGAGC-GTGGTGGTTGAAGGAAGAGCTGGTGGTGG-TGAGGCAAT
1 GCGGTGGAGGTGGTGGTTG-AG-GCAATGGTGGTTG-AGGAAGAGCTGGTGGTGGTTGAGGCAAT
3205429 GGTGGTTGAG
63 GGTGGTTGAG
** * **
3205439 GAAGAGCTGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGCTGGTGGTGGGTTGAGGC
1 GCGGTGGAGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGCTGGTGGT-GGTTGAGGC
3205499 GGCGATGGTT
Statistics
Matches: 172, Mismatches: 19, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
70 1 0.01
71 59 0.34
72 102 0.59
73 10 0.06
ACGTcount: A:0.18, C:0.07, G:0.53, T:0.23
Consensus pattern (72 bp):
GCGGTGGAGGTGGTGGTTGAGGCAATGGTGGTTGAGGAAGAGCTGGTGGTGGTTGAGGCAATGGT
GGTTGAG
Found at i:3205323 original size:21 final size:21
Alignment explanation
Indices: 3205298--3205497 Score: 92
Period size: 21 Copynumber: 9.7 Consensus size: 21
3205288 TGGTTGAGGC
* *
3205298 GGTGGAGGCTGAGGAAGAGCT
1 GGTGGTGGTTGAGGAAGAGCT
*
3205319 GGTGGTGGTTGAGGAAGTGCT
1 GGTGGTGGTTGAGGAAGAGCT
3205340 GGTGGTGGTTGAGGCAATG-G-T
1 GGTGGTGGTTGAGG-AA-GAGCT
* *
3205361 GGTTGAGGCGGTGGAGGAGGCGGGAAGAGC-
1 GG-T--GGTGGTTGA-G------GAAGAGCT
3205391 -GTGGTGGTTGAAGGAAGAGCT
1 GGTGGTGGTTG-AGGAAGAGCT
*
3205412 GGTGGTGG-TGAGGCA-A---
1 GGTGGTGGTTGAGGAAGAGCT
3205428 --TGGTGGTTGAGGAAGAGCT
1 GGTGGTGGTTGAGGAAGAGCT
*
3205447 GGTGGTGGTTGAGGCA-A---
1 GGTGGTGGTTGAGGAAGAGCT
3205464 --TGGTGGTTGAGGAAGAGCT
1 GGTGGTGGTTGAGGAAGAGCT
3205483 GGTGGTGGGTTGAGG
1 GGTGGT-GGTTGAGG
3205498 CGGCGATGGT
Statistics
Matches: 137, Mismatches: 11, Indels: 61
0.66 0.05 0.29
Matches are distributed among these distances:
14 6 0.04
15 19 0.14
16 2 0.01
19 1 0.01
20 12 0.09
21 54 0.39
22 19 0.14
23 1 0.01
24 7 0.05
25 1 0.01
26 7 0.05
27 1 0.01
28 1 0.01
29 2 0.01
30 3 0.02
31 1 0.01
ACGTcount: A:0.18, C:0.06, G:0.54, T:0.22
Consensus pattern (21 bp):
GGTGGTGGTTGAGGAAGAGCT
Found at i:3205582 original size:15 final size:15
Alignment explanation
Indices: 3205562--3205721 Score: 79
Period size: 15 Copynumber: 10.2 Consensus size: 15
3205552 GGTGGAGCTT
3205562 AGGTTGAGGTGGTGG
1 AGGTTGAGGTGGTGG
***
3205577 AGGTTGAGGCAATGG
1 AGGTTGAGGTGGTGG
* * *
3205592 TGGTTGAGGAGATGG
1 AGGTTGAGGTGGTGG
*
3205607 TGGTTGAGGTGGTGG
1 AGGTTGAGGTGGTGG
* **
3205622 AGGCTGAGACGGTGG
1 AGGTTGAGGTGGTGG
* *
3205637 AGGCTGAGATGGTGG
1 AGGTTGAGGTGGTGG
3205652 AGGCTT-AGGTTGAGGAGATGG
1 AGG-TTGAGG-T---G-G-TGG
*
3205673 TGGTTGAGGTGGTGG
1 AGGTTGAGGTGGTGG
* **
3205688 AGGCTGAGACGGTGG
1 AGGTTGAGGTGGTGG
* *
3205703 AGGCTGAGAATGGTGG
1 AGGTTGAG-GTGGTGG
3205719 AGG
1 AGG
3205722 CTTAGGTTGA
Statistics
Matches: 115, Mismatches: 21, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
15 89 0.77
16 12 0.10
17 1 0.01
19 1 0.01
20 4 0.03
21 8 0.07
ACGTcount: A:0.19, C:0.05, G:0.54, T:0.23
Consensus pattern (15 bp):
AGGTTGAGGTGGTGG
Found at i:3205674 original size:66 final size:67
Alignment explanation
Indices: 3205593--3205757 Score: 305
Period size: 66 Copynumber: 2.5 Consensus size: 67
3205583 AGGCAATGGT
3205593 GGTTGAGGAGATGGTGGTTGAGGTGGTGGAGGCTGAGACGGTGGAGGCTGAG-ATGGTGGAGGCT
1 GGTTGAGGAGATGGTGGTTGAGGTGGTGGAGGCTGAGACGGTGGAGGCTGAGAATGGTGGAGGCT
3205657 TA
66 TA
3205659 GGTTGAGGAGATGGTGGTTGAGGTGGTGGAGGCTGAGACGGTGGAGGCTGAGAATGGTGGAGGCT
1 GGTTGAGGAGATGGTGGTTGAGGTGGTGGAGGCTGAGACGGTGGAGGCTGAGAATGGTGGAGGCT
3205724 TA
66 TA
* *
3205726 GGTTGAGGAGATGGTGGTTGAAGCGGTGGAGG
1 GGTTGAGGAGATGGTGGTTGAGGTGGTGGAGG
3205758 TTGTGGTTGA
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
66 52 0.54
67 44 0.46
ACGTcount: A:0.19, C:0.05, G:0.53, T:0.22
Consensus pattern (67 bp):
GGTTGAGGAGATGGTGGTTGAGGTGGTGGAGGCTGAGACGGTGGAGGCTGAGAATGGTGGAGGCT
TA
Found at i:3205763 original size:21 final size:21
Alignment explanation
Indices: 3205739--3205778 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3205729 TGAGGAGATG
3205739 GTGGTTGAAGCGGTGGAGGTT
1 GTGGTTGAAGCGGTGGAGGTT
*
3205760 GTGGTTGAGGCGGTGGAGG
1 GTGGTTGAAGCGGTGGAGG
3205779 CTTAGGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.57, T:0.25
Consensus pattern (21 bp):
GTGGTTGAAGCGGTGGAGGTT
Found at i:3205786 original size:21 final size:21
Alignment explanation
Indices: 3205741--3205791 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3205731 AGGAGATGGT
* *
3205741 GGTTGAAGCGGTGGAGGTTGT
1 GGTTGAGGCGGTGGAGGTTGA
3205762 GGTTGAGGCGGTGGAGGCTT-A
1 GGTTGAGGCGGTGGAGG-TTGA
3205783 GGTTGAGGC
1 GGTTGAGGC
3205792 AATGGTGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 25 0.93
22 2 0.07
ACGTcount: A:0.14, C:0.08, G:0.53, T:0.25
Consensus pattern (21 bp):
GGTTGAGGCGGTGGAGGTTGA
Found at i:3205841 original size:36 final size:36
Alignment explanation
Indices: 3205800--3205897 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
3205790 GCAATGGTGG
* *
3205800 TGAGGCACTGGAGGTTGAGACGGTGGCGGTGGAGGT
1 TGAGGCAATGGTGGTTGAGACGGTGGCGGTGGAGGT
*
3205836 TGAGGCAATGGTGGTTGAGACGGTGGTGGTGGAGGT
1 TGAGGCAATGGTGGTTGAGACGGTGGCGGTGGAGGT
*
3205872 TGAGGCAATGGTGGTTGAGGCGGTGG
1 TGAGGCAATGGTGGTTGAGACGGTGG
3205898 AGGCTGAGAC
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.16, C:0.08, G:0.53, T:0.22
Consensus pattern (36 bp):
TGAGGCAATGGTGGTTGAGACGGTGGCGGTGGAGGT
Found at i:3205874 original size:21 final size:21
Alignment explanation
Indices: 3205808--3205875 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
3205798 GGTGAGGCAC
*
3205808 TGGAGGTTGAGACGGTGGCGG
1 TGGAGGTTGAGACGGTGGTGG
***
3205829 TGGAGGTT--GA-GGCAATGG
1 TGGAGGTTGAGACGGTGGTGG
3205847 T---GGTTGAGACGGTGGTGG
1 TGGAGGTTGAGACGGTGGTGG
3205865 TGGAGGTTGAG
1 TGGAGGTTGAG
3205876 GCAATGGTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
15 4 0.12
17 2 0.06
18 11 0.32
19 2 0.06
21 15 0.44
ACGTcount: A:0.16, C:0.06, G:0.54, T:0.24
Consensus pattern (21 bp):
TGGAGGTTGAGACGGTGGTGG
Found at i:3205906 original size:51 final size:52
Alignment explanation
Indices: 3205824--3206258 Score: 260
Period size: 51 Copynumber: 8.5 Consensus size: 52
3205814 TTGAGACGGT
* * ** * *
3205824 GGCGGTGGAGGTTGAGGCAATGGTGGTTGAGACGGTGGTGG-TGGAGGTTGA
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCTGGAGGTTGA
* *
3205875 GGCAATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCT-TAGGTTGA
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCTGGAGGTTGA
* * * *
3205926 GGTGATGGTGG-TGAGGCGGTAGAGGCTGAGACGGTGGTGGCTGAGATGGTGGT
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCTG-GA-GGTTGA
* * * *
3205979 GGC--T--TAGGTTGAGGCGATGGTGGTTGAG-C-------GCATGGAGGCTGA
1 GGCGATGGT-GGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGC-TGGAGGTTGA
* ** * * *
3206021 GACGATGGTGGTTGAGATGGTGGAGGTTGAGACGATGGTGGAGGCT-TAGGTTGA
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGAC---GGTGGTGGCTGGAGGTTGA
* * * * * * * * * *
3206075 GGTGATGGAGGCTGAGACGATGGTGGTTGAGATGGTGGAGGCT-TAGGTTGA
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCTGGAGGTTGA
** * *
3206126 GGCGATGGTGGTTGAGATGGTGGAGGCTGAGACGATGGTGGAGGCT-TAGGTTGA
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGAC---GGTGGTGGCTGGAGGTTGA
* * * *
3206180 GGCGATGGAGGTTGAGGCGATGGAGGCTGAGACGGTGGAGGCT-TAGGTTGA
1 GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCTGGAGGTTGA
* * *
3206231 GGCGATGGAGGCTGAGACGGTGGAGGCT
1 GGCGATGGTGGTTGAGGCGGTGGAGGCT
3206259 TAGTTGAGGC
Statistics
Matches: 307, Mismatches: 52, Indels: 50
0.75 0.13 0.12
Matches are distributed among these distances:
42 5 0.02
43 4 0.01
44 3 0.01
45 18 0.06
46 2 0.01
49 1 0.00
50 33 0.11
51 152 0.50
52 2 0.01
53 6 0.02
54 78 0.25
55 1 0.00
56 2 0.01
ACGTcount: A:0.18, C:0.08, G:0.51, T:0.23
Consensus pattern (52 bp):
GGCGATGGTGGTTGAGGCGGTGGAGGCTGAGACGGTGGTGGCTGGAGGTTGA
Found at i:3205976 original size:15 final size:15
Alignment explanation
Indices: 3205880--3205982 Score: 64
Period size: 15 Copynumber: 6.5 Consensus size: 15
3205870 GTTGAGGCAA
* *
3205880 TGGTGGTTGAGGCGG
1 TGGTGGCTGAGACGG
*
3205895 TGGAGGCTGAGACGG
1 TGGTGGCTGAGACGG
* *
3205910 TGGTGGCTTAGGTTGAGGTG
1 TGGTGGC-T--G-AGACG-G
*
3205930 ATGGTGG-TGAGGCGG
1 -TGGTGGCTGAGACGG
* *
3205945 TAGAGGCTGAGACGG
1 TGGTGGCTGAGACGG
*
3205960 TGGTGGCTGAGATGG
1 TGGTGGCTGAGACGG
3205975 TGGTGGCT
1 TGGTGGCT
3205983 TAGGTTGAGG
Statistics
Matches: 66, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
14 4 0.06
15 46 0.70
16 3 0.05
17 1 0.02
18 1 0.02
19 4 0.06
20 1 0.02
21 6 0.09
ACGTcount: A:0.14, C:0.09, G:0.53, T:0.24
Consensus pattern (15 bp):
TGGTGGCTGAGACGG
Found at i:3206005 original size:15 final size:15
Alignment explanation
Indices: 3205985--3206061 Score: 84
Period size: 15 Copynumber: 5.1 Consensus size: 15
3205975 TGGTGGCTTA
*
3205985 GGTTGAGGCGATGGT
1 GGTTGAGACGATGGT
*
3206000 GGTTGAG-CGCATGGA
1 GGTTGAGACG-ATGGT
*
3206015 GGCTGAGACGATGGT
1 GGTTGAGACGATGGT
* * *
3206030 GGTTGAGATGGTGGA
1 GGTTGAGACGATGGT
3206045 GGTTGAGACGATGGT
1 GGTTGAGACGATGGT
3206060 GG
1 GG
3206062 AGGCTTAGGT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
14 2 0.04
15 46 0.92
16 2 0.04
ACGTcount: A:0.18, C:0.08, G:0.51, T:0.23
Consensus pattern (15 bp):
GGTTGAGACGATGGT
Found at i:3206139 original size:36 final size:36
Alignment explanation
Indices: 3206087--3206433 Score: 296
Period size: 36 Copynumber: 9.5 Consensus size: 36
3206077 TGATGGAGGC
* *
3206087 TGAGACGATGGTGGTTGAGATGGTGGAGGCTTAGGT
1 TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
*
3206123 TGAGGCGATGGTGGTTGAGATGGTGGAGGC------
1 TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
* ** ** * *
3206153 TGAGACGATGGTGGAGGCTTA-GGTTGAGGCGATGGAGGT
1 TGAGGCGATGGTGGTTG-AGACGGTGGAGGC--T-TAGGT
* *
3206192 TGAGGCGATGGAGGCTGAGACGGTGGAGGCTTAGGT
1 TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
* *
3206228 TGAGGCGATGGAGGCTGAGACGGTGGAGGCTTA-GT
1 TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
* *
3206263 TGAGGCGATGGTGGTTGAGGCGATGGAGGCTTAGGT
1 TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
* * *
3206299 TGAGGGGATGGAGGTTGAGACGGTGGAGCCTTAGGT
1 TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
* * * *
3206335 TGAGGTGATGGTGGTTGAGGTGATGGAGGTAGAGAGTTTAGGT
1 TGAGGCGATGGTGGTTGA---GA---CGGTGGAG-GCTTAGGT
* *
3206378 TGAGGCGATGGAGGTTGAGACGCGTGGAGGCTAAGGT
1 TGAGGCGATGGTGGTTGAGACG-GTGGAGGCTTAGGT
*
3206415 TGAGGTGATGGTGGTTGAG
1 TGAGGCGATGGTGGTTGAG
3206434 GTGATGGAGG
Statistics
Matches: 253, Mismatches: 38, Indels: 39
0.77 0.12 0.12
Matches are distributed among these distances:
30 22 0.09
31 1 0.00
35 31 0.12
36 115 0.45
37 25 0.10
38 6 0.02
39 23 0.09
40 2 0.01
42 6 0.02
43 22 0.09
ACGTcount: A:0.19, C:0.07, G:0.50, T:0.24
Consensus pattern (36 bp):
TGAGGCGATGGTGGTTGAGACGGTGGAGGCTTAGGT
Found at i:3206157 original size:105 final size:105
Alignment explanation
Indices: 3206018--3206363 Score: 396
Period size: 105 Copynumber: 3.3 Consensus size: 105
3206008 GCATGGAGGC
* * *
3206018 TGAGACGATGGTGGTTGAGATGGTGGAGGTTGAGACGATGGTGGAGGCTTAGGTTGAGGTGATGG
1 TGAGGCGATGGTGGTTGAGATGGTGGAGGCTGAGACGATGGTGGAGGCTTAGGTTGAGGCGATGG
* * *
3206083 AGGCTGAGACGATGGTGGTTGAGATGGTGGAGGCTTAGGT
66 AGGCTGAGACGATGGAGGCTGAGACGGTGGAGGCTTAGGT
3206123 TGAGGCGATGGTGGTTGAGATGGTGGAGGCTGAGACGATGGTGGAGGCTTAGGTTGAGGCGATGG
1 TGAGGCGATGGTGGTTGAGATGGTGGAGGCTGAGACGATGGTGGAGGCTTAGGTTGAGGCGATGG
* *
3206188 AGGTTGAGGCGATGGAGGCTGAGACGGTGGAGGCTTAGGT
66 AGGCTGAGACGATGGAGGCTGAGACGGTGGAGGCTTAGGT
* * * * ** *
3206228 TGAGGCGATGGAGGCTGAGACGGTGGAGGCTTAGTTGA-GG-CGATGG--T-GGTTGAGGCGATG
1 TGAGGCGATGGTGGTTGAGATGGTGGAGGCTGAGACGATGGTGGA-GGCTTAGGTTGAGGCGATG
** * *
3206288 GAGGCTTAGGTTGAGGGGATGGAGGTTGAGACGGTGGAGCCTTAGGT
65 GAGGC------TGAGACGATGGAGGCTGAGACGGTGGAGGCTTAGGT
* * *
3206335 TGAGGTGATGGTGGTTGAGGTGATGGAGG
1 TGAGGCGATGGTGGTTGAGATGGTGGAGG
3206364 TAGAGAGTTT
Statistics
Matches: 209, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
101 17 0.08
102 1 0.00
103 2 0.01
104 4 0.02
105 129 0.62
107 56 0.27
ACGTcount: A:0.19, C:0.07, G:0.50, T:0.24
Consensus pattern (105 bp):
TGAGGCGATGGTGGTTGAGATGGTGGAGGCTGAGACGATGGTGGAGGCTTAGGTTGAGGCGATGG
AGGCTGAGACGATGGAGGCTGAGACGGTGGAGGCTTAGGT
Found at i:3206290 original size:71 final size:72
Alignment explanation
Indices: 3206087--3206443 Score: 325
Period size: 71 Copynumber: 4.9 Consensus size: 72
3206077 TGATGGAGGC
* * * ** *
3206087 TGAGACGATGGTGGTTGAGATGGTGGAGGCTTAGGTTGAGGCGATGGTGGTTGAGATGGTGGAGG
1 TGAGGCGATGGAGGTTGAGACGGTGGAGGCTTAGGTTGAGGCGATGGTGGTTGAGGCGATGGAGG
* *
3206152 CTGA-GA
66 CTTAGGT
* * * * * * * *
3206158 CGATG-G-TGGAGGCTT---A-GGTTGAGGCGATGGAGGTTGAGGCGATGGAGGCTGAGACGGTG
1 TGAGGCGATGGAGG-TTGAGACGGTGGAGGC--T-TAGGTTGAGGCGATGGTGGTTGAGGCGATG
3206217 GAGGCTTAGGT
62 GAGGCTTAGGT
*
3206228 TGAGGCGATGGAGGCTGAGACGGTGGAGGCTTA-GTTGAGGCGATGGTGGTTGAGGCGATGGAGG
1 TGAGGCGATGGAGGTTGAGACGGTGGAGGCTTAGGTTGAGGCGATGGTGGTTGAGGCGATGGAGG
3206292 CTTAGGT
66 CTTAGGT
* * * *
3206299 TGAGGGGATGGAGGTTGAGACGGTGGAGCCTTAGGTTGAGGTGATGGTGGTTGAGGTGATGGAGG
1 TGAGGCGATGGAGGTTGAGACGGTGGAGGCTTAGGTTGAGGCGATGGTGGTTGAGGCGAT----G
*
3206364 TAGAGAGTTTAGGT
62 --GAG-GCTTAGGT
* * *
3206378 TGAGGCGATGGAGGTTGAGACGCGTGGAGGCTAAGGTTGAGGTGATGGTGGTTGAGGTGATGGAG
1 TGAGGCGATGGAGGTTGAGACG-GTGGAGGCTTAGGTTGAGGCGATGGTGGTTGAGGCGATGGAG
3206443 G
65 G
3206444 TTGAGGAGGT
Statistics
Matches: 237, Mismatches: 29, Indels: 38
0.78 0.10 0.12
Matches are distributed among these distances:
66 8 0.03
67 1 0.00
68 1 0.00
69 38 0.16
70 7 0.03
71 68 0.29
72 31 0.13
73 2 0.01
74 4 0.02
75 8 0.03
76 2 0.01
78 3 0.01
79 28 0.12
80 36 0.15
ACGTcount: A:0.19, C:0.07, G:0.50, T:0.24
Consensus pattern (72 bp):
TGAGGCGATGGAGGTTGAGACGGTGGAGGCTTAGGTTGAGGCGATGGTGGTTGAGGCGATGGAGG
CTTAGGT
Found at i:3206352 original size:15 final size:15
Alignment explanation
Indices: 3206332--3206360 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3206322 TGGAGCCTTA
3206332 GGTTGAGGTGATGGT
1 GGTTGAGGTGATGGT
3206347 GGTTGAGGTGATGG
1 GGTTGAGGTGATGG
3206361 AGGTAGAGAG
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:0.14, C:0.00, G:0.55, T:0.31
Consensus pattern (15 bp):
GGTTGAGGTGATGGT
Found at i:3206407 original size:16 final size:15
Alignment explanation
Indices: 3205984--3206291 Score: 77
Period size: 15 Copynumber: 20.2 Consensus size: 15
3205974 GTGGTGGCTT
3205984 AGGTTGAGGCGATGG
1 AGGTTGAGGCGATGG
*
3205999 TGGTTGA-GCGCATGG
1 AGGTTGAGGCG-ATGG
* *
3206014 AGGCTGAGACGATGG
1 AGGTTGAGGCGATGG
* ** *
3206029 TGGTTGAGATGGTGG
1 AGGTTGAGGCGATGG
*
3206044 AGGTTGAGACGAT--
1 AGGTTGAGGCGATGG
* *
3206057 -GGTGGAGGC--T-T
1 AGGTTGAGGCGATGG
*
3206068 AGGTTGAGGTGATGG
1 AGGTTGAGGCGATGG
* *
3206083 AGGCTGAGACGATGG
1 AGGTTGAGGCGATGG
* *
3206098 TGGTTGAGATGGTGGA-GG
1 AGGTT--GA-GG-CGATGG
3206116 CTTAGGTTGAGGCGATGG
1 ---AGGTTGAGGCGATGG
* ** *
3206134 TGGTTGAGATGGTGG
1 AGGTTGAGGCGATGG
* *
3206149 AGGCTGAGACGAT--
1 AGGTTGAGGCGATGG
* *
3206162 -GGTGGAGGC--T-T
1 AGGTTGAGGCGATGG
3206173 AGGTTGAGGCGATGG
1 AGGTTGAGGCGATGG
3206188 AGGTTGAGGCGATGG
1 AGGTTGAGGCGATGG
* * *
3206203 AGGCTGAGACGGTGGAGG
1 AGGTTGAGGCGAT---GG
3206221 CTTAGGTTGAGGCGATGG
1 ---AGGTTGAGGCGATGG
* * *
3206239 AGGCTGAGACGGTGG
1 AGGTTGAGGCGATGG
3206254 AGGCTTAGTTGAGGCGATGG
1 A-G----GTTGAGGCGATGG
*
3206274 TGGTTGAGGCGATGG
1 AGGTTGAGGCGATGG
3206289 AGG
1 AGG
3206292 CTTAGGTTGA
Statistics
Matches: 210, Mismatches: 52, Indels: 62
0.65 0.16 0.19
Matches are distributed among these distances:
10 2 0.01
12 28 0.13
14 5 0.02
15 128 0.61
16 3 0.01
17 4 0.02
18 11 0.05
19 5 0.02
20 10 0.05
21 14 0.07
ACGTcount: A:0.19, C:0.08, G:0.50, T:0.23
Consensus pattern (15 bp):
AGGTTGAGGCGATGG
Found at i:3206431 original size:80 final size:81
Alignment explanation
Indices: 3206287--3206464 Score: 288
Period size: 80 Copynumber: 2.2 Consensus size: 81
3206277 TTGAGGCGAT
* * *
3206287 GGAGGCTTAGGTTGAGGGGATGGAGGTTGAGACGGTGGAGCCTTAGGTTGAGGTGATGGTGGTTG
1 GGAGGTTTAGGTTGAGGCGATGGAGGTTGAGACGGTGGAGCCTAAGGTTGAGGTGATGGTGGTTG
3206352 AGGTGATGGAGGTAGA
66 AGGTGATGGAGGTAGA
*
3206368 -GA-GTTTAGGTTGAGGCGATGGAGGTTGAGACGCGTGGAGGCTAAGGTTGAGGTGATGGTGGTT
1 GGAGGTTTAGGTTGAGGCGATGGAGGTTGAGACG-GTGGAGCCTAAGGTTGAGGTGATGGTGGTT
*
3206431 GAGGTGATGGAGGTTGA
65 GAGGTGATGGAGGTAGA
3206448 GGAGGTTTAGGTTGAGG
1 GGAGGTTTAGGTTGAGG
3206465 TTGAAGCGAT
Statistics
Matches: 89, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
79 28 0.31
80 46 0.52
81 2 0.02
82 13 0.15
ACGTcount: A:0.20, C:0.04, G:0.50, T:0.26
Consensus pattern (81 bp):
GGAGGTTTAGGTTGAGGCGATGGAGGTTGAGACGGTGGAGCCTAAGGTTGAGGTGATGGTGGTTG
AGGTGATGGAGGTAGA
Found at i:3206432 original size:15 final size:15
Alignment explanation
Indices: 3206411--3206449 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
3206401 GTGGAGGCTA
3206411 AGGTTGAGGTGATGG
1 AGGTTGAGGTGATGG
*
3206426 TGGTTGAGGTGATGG
1 AGGTTGAGGTGATGG
3206441 AGGTTGAGG
1 AGGTTGAGG
3206450 AGGTTTAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.54, T:0.28
Consensus pattern (15 bp):
AGGTTGAGGTGATGG
Found at i:3214565 original size:44 final size:44
Alignment explanation
Indices: 3214500--3214584 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
3214490 TATGACACTT
*
3214500 GACATGACATTTGATTTAAAAAC-CGAAAAACATGTGTGAAAATA
1 GACATGACATTTGATTGAAAAACTC-AAAAACATGTGTGAAAATA
* *
3214544 GACATGACATTTGATTGAAAAACTCAAATACGTGTGTGAAA
1 GACATGACATTTGATTGAAAAACTCAAAAACATGTGTGAAA
3214585 TAAGACTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 36 0.97
45 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.26
Consensus pattern (44 bp):
GACATGACATTTGATTGAAAAACTCAAAAACATGTGTGAAAATA
Found at i:3223097 original size:5 final size:5
Alignment explanation
Indices: 3223087--3223139 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
3223077 CGTAATATAG
* **
3223087 AAATA AAATA AAATA CCAAT- AAATA ATGTAA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA -AAATA AAATA AAAT-A AAATA AAATA AAATA AAATA
3223138 AA
1 AA
3223140 CTACAAGGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.08
5 30 0.77
6 6 0.15
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:3224937 original size:17 final size:16
Alignment explanation
Indices: 3224915--3224963 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
3224905 AAAAAAAGGG
*
3224915 AAAAAAATAACTAAAAT
1 AAAAAAATAA-AAAAAT
*
3224932 AAAAAATTAAAAAAATT
1 AAAAAAATAAAAAAA-T
*
3224949 AAAAAATTAAAAAAA
1 AAAAAAATAAAAAAA
3224964 AGAAGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (16 bp):
AAAAAAATAAAAAAAT
Found at i:3224944 original size:8 final size:8
Alignment explanation
Indices: 3224927--3224962 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
3224917 AAAAATAACT
3224927 AAAA-TAA
1 AAAATTAA
3224934 AAAATTAAA
1 AAAATT-AA
3224943 AAAATTAA
1 AAAATTAA
3224951 AAAATTAA
1 AAAATTAA
3224959 AAAA
1 AAAA
3224963 AAGAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 15 0.56
9 8 0.30
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (8 bp):
AAAATTAA
Found at i:3224944 original size:9 final size:9
Alignment explanation
Indices: 3224932--3224963 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
3224922 TAACTAAAAT
3224932 AAAAAATTA
1 AAAAAATTA
3224941 AAAAAATT-
1 AAAAAATTA
3224949 AAAAAATTA
1 AAAAAATTA
3224958 AAAAAA
1 AAAAAA
3224964 AGAAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAAAATTA
Found at i:3230417 original size:28 final size:28
Alignment explanation
Indices: 3230385--3230441 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
3230375 ACAAAAGACT
3230385 TAGTCTCCTATACAATTCTACCTTGTCA
1 TAGTCTCCTATACAATTCTACCTTGTCA
*
3230413 TAGTCTCTTATACAATTCTACCTTGTCA
1 TAGTCTCCTATACAATTCTACCTTGTCA
3230441 T
1 T
3230442 GGCCCCATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.26, G:0.07, T:0.42
Consensus pattern (28 bp):
TAGTCTCCTATACAATTCTACCTTGTCA
Found at i:3232274 original size:17 final size:17
Alignment explanation
Indices: 3232252--3232300 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
3232242 AATAGAAAGT
3232252 AAGTATATTTATATTAA
1 AAGTATATTTATATTAA
*
3232269 AAGTATATATATA-TAA
1 AAGTATATTTATATTAA
*
3232285 AA-TAGTAATTATATTA
1 AAGTA-TATTTATATTA
3232301 TTTATAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.07
16 11 0.41
17 14 0.52
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (17 bp):
AAGTATATTTATATTAA
Found at i:3233341 original size:50 final size:50
Alignment explanation
Indices: 3233233--3233401 Score: 257
Period size: 50 Copynumber: 3.4 Consensus size: 50
3233223 AGATTTCTGA
* * * *
3233233 CTTTAGTTTGGTACGTGTAAATGACGAGCACTAACTTGGTTAGTTATAAGT
1 CTTTAGTTTGGTACGTGTAAACGACAAGCAC-CACTTGGTTAGCTATAAGT
3233284 CTTTAGTTTGGTACGTGTAAACGACAAGCACCACTTGGTTAGCTATAAGT
1 CTTTAGTTTGGTACGTGTAAACGACAAGCACCACTTGGTTAGCTATAAGT
* * * *
3233334 CTTTAGTTTTGTACGTGTAAACGACAAGCACCGCTTGGCTAGCTCTAAGT
1 CTTTAGTTTGGTACGTGTAAACGACAAGCACCACTTGGTTAGCTATAAGT
3233384 CTTTAGTTTGGTACGTGT
1 CTTTAGTTTGGTACGTGT
3233402 CATCAATCTG
Statistics
Matches: 109, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
50 80 0.73
51 29 0.27
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (50 bp):
CTTTAGTTTGGTACGTGTAAACGACAAGCACCACTTGGTTAGCTATAAGT
Found at i:3236056 original size:2 final size:2
Alignment explanation
Indices: 3236049--3236078 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3236039 CATTTGGATC
3236049 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
3236079 TGAAGTTGTT
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:3236592 original size:14 final size:15
Alignment explanation
Indices: 3236562--3236594 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3236552 AAAAATTTTA
*
3236562 AAAAGACATACTTAT
1 AAAAGAAATACTTAT
3236577 AAAAGAAATA-TTAT
1 AAAAGAAATACTTAT
3236591 AAAA
1 AAAA
3236595 TAATAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAGAAATACTTAT
Found at i:3236844 original size:2 final size:2
Alignment explanation
Indices: 3236796--3236825 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3236786 TTATCTTTCA
3236796 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
3236826 GCATGCATGT
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:3243548 original size:35 final size:35
Alignment explanation
Indices: 3243509--3243588 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 35
3243499 GTCTTAGTAG
*
3243509 AAGTTACACCTAG-TCTTG-CAAAAGGCATGTTGTGA
1 AAGTTACACC-AGATATTGTCAAAAGGCATGTTGT-A
* *
3243544 AAGTTACACCCGATATTGTTAAAAGGCATGTTGTA
1 AAGTTACACCAGATATTGTCAAAAGGCATGTTGTA
3243579 AAGGTTACAC
1 AA-GTTACAC
3243589 TTGATCTTAG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
34 1 0.03
35 17 0.44
36 21 0.54
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (35 bp):
AAGTTACACCAGATATTGTCAAAAGGCATGTTGTA
Found at i:3247556 original size:15 final size:14
Alignment explanation
Indices: 3247532--3247565 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
3247522 AATTTTTTCA
3247532 AATTTTTATTTTTT
1 AATTTTTATTTTTT
*
3247546 TATTTTCTATTTTTT
1 AATTTT-TATTTTTT
3247561 AATTT
1 AATTT
3247566 ATTTTCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (14 bp):
AATTTTTATTTTTT
Found at i:3247568 original size:19 final size:19
Alignment explanation
Indices: 3247544--3247580 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3247534 TTTTTATTTT
*
3247544 TTTATTTTCTATTTTTTAA
1 TTTATTTTCAATTTTTTAA
3247563 TTTATTTTCAATTTTTTA
1 TTTATTTTCAATTTTTTA
3247581 CTTATCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTTCAATTTTTTAA
Found at i:3247585 original size:18 final size:19
Alignment explanation
Indices: 3247545--3247585 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3247535 TTTTATTTTT
* *
3247545 TTATTTTCTATTTTTTAAT
1 TTATTTTCAATTTTTTAAC
3247564 TTATTTTCAATTTTTT-AC
1 TTATTTTCAATTTTTTAAC
3247582 TTAT
1 TTAT
3247586 CTTATTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTCAATTTTTTAAC
Found at i:3248005 original size:48 final size:49
Alignment explanation
Indices: 3247913--3248287 Score: 282
Period size: 48 Copynumber: 7.6 Consensus size: 49
3247903 CTTATACAAT
* ** * * * * *
3247913 ATTGGAAAAAACTCCCCATCTTTAAATGAAGTTACACAAC-TTAAAATG
1 ATTGGAAAAAGCTCTTCATCTCTAAACGAGGTCACGCAACTTTAAAATG
* * *
3247961 ATTGGAAAAA-CTCTTCATCTTTAACCGAGGTCATGCAACTTTAAAATG
1 ATTGGAAAAAGCTCTTCATCTCTAAACGAGGTCACGCAACTTTAAAATG
* * **
3248009 ATTGGAAAATTAAGCTCCTCATCGT-TAAACGAGGCCACAAAACTTTAAAATG
1 ATTGG-AAA--AAGCTCTTCATC-TCTAAACGAGGTCACGCAACTTTAAAATG
* * * * *
3248061 ATTGG-AAAAGCTTTTCATCCCTAAACGA-GACTATGTAACTTTAAAATG
1 ATTGGAAAAAGCTCTTCATCTCTAAACGAGGTC-ACGCAACTTTAAAATG
* * * * *
3248109 ATTGGAAAAA-CTC-CCTATCTCTAAACAAAGTCACACAACTTGAAAATG
1 ATTGGAAAAAGCTCTTC-ATCTCTAAACGAGGTCACGCAACTTTAAAATG
* * **
3248157 ACTGAAAAAAGCTCTTCATCTCTAAACGAGG-CTACATAACTTTAAATAAATG
1 ATTGGAAAAAGCTCTTCATCTCTAAACGAGGTC-ACGCAACTTT--A-AAATG
* * **
3248209 ATTGAAAAAAGCTCCTT-ATCTCCAAACGAGGTTGCGCAACTTTAAAATG
1 ATTGGAAAAAGCT-CTTCATCTCTAAACGAGGTCACGCAACTTTAAAATG
*
3248258 ATTGGAAAAAGCTCCTCATCTCTAAACGAG
1 ATTGGAAAAAGCTCTTCATCTCTAAACGAG
3248288 TCTTCTTAAC
Statistics
Matches: 261, Mismatches: 46, Indels: 39
0.75 0.13 0.11
Matches are distributed among these distances:
47 24 0.09
48 93 0.36
49 61 0.23
50 4 0.02
51 3 0.01
52 72 0.28
53 4 0.02
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (49 bp):
ATTGGAAAAAGCTCTTCATCTCTAAACGAGGTCACGCAACTTTAAAATG
Found at i:3248101 original size:100 final size:97
Alignment explanation
Indices: 3247913--3248287 Score: 350
Period size: 100 Copynumber: 3.8 Consensus size: 97
3247903 CTTATACAAT
* * * * * *
3247913 ATTGGAAAAAA-CTCCCCATCTTTAAATGAAGTTACACAAC-TTAAAATGATTGGAAAAACTCTT
1 ATTGGAAAAAAGCTCCTCATCTCTAAACGAGGTCACACAACTTTAAAATGATTGGAAAAGCTCTT
* * * *
3247976 CATCTTTAACCGAGGTCATGCAACTTTAAAATG
66 CATCTCTAAACGAGCT-ATGTAACTTTAAAATG
* *
3248009 ATTGGAAAATTAAGCTCCTCATCGT-TAAACGAGGCCACAAAACTTTAAAATGATTGGAAAAGCT
1 ATTGGAAAA--AAGCTCCTCATC-TCTAAACGAGGTCACACAACTTTAAAATGATTGGAAAAGCT
* *
3248073 TTTCATCCCTAAACGAGACTATGTAACTTTAAAATG
63 CTTCATCTCTAAACGAG-CTATGTAACTTTAAAATG
* * * * *
3248109 ATTGG-AAAAA-CTCC-CTATCTCTAAACAAAGTCACACAACTTGAAAATGACTGAAAAAAGCTC
1 ATTGGAAAAAAGCTCCTC-ATCTCTAAACGAGGTCACACAACTTTAAAATGATTG-GAAAAGCTC
**
3248171 TTCATCTCTAAACGAGGCTACATAACTTTAAATAAATG
64 TTCATCTCTAAACGA-GCTATGTAACTTT--A-AAATG
* * ** * *
3248209 ATT-GAAAAAAGCTCCTTATCTCCAAACGAGGTTGCGCAACTTTAAAATGATTGGAAAAAGCTCC
1 ATTGGAAAAAAGCTCCTCATCTCTAAACGAGGTCACACAACTTTAAAATGATTGG-AAAAGCTCT
3248273 TCATCTCTAAACGAG
65 TCATCTCTAAACGAG
3248288 TCTTCTTAAC
Statistics
Matches: 227, Mismatches: 35, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
95 2 0.01
96 41 0.18
97 33 0.15
98 3 0.01
99 26 0.11
100 67 0.30
101 55 0.24
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (97 bp):
ATTGGAAAAAAGCTCCTCATCTCTAAACGAGGTCACACAACTTTAAAATGATTGGAAAAGCTCTT
CATCTCTAAACGAGCTATGTAACTTTAAAATG
Found at i:3248252 original size:197 final size:195
Alignment explanation
Indices: 3247913--3248287 Score: 447
Period size: 197 Copynumber: 1.9 Consensus size: 195
3247903 CTTATACAAT
* ** * * *
3247913 ATTGGAAAAAACTCCCCATCTTTAAATGAAGTTACACAACTTAAAATGATTGGAAAAACTCTTCA
1 ATTGGAAAAAACTCCCCATCTCTAAACAAAGTCACACAACTTAAAATGACTGAAAAAACTCTTCA
* * *
3247978 TCTTTAACCGAGGTCATGCAACTTTAAAATGATTGGAAAATTAAGCTCCTCATCGTTAAACGAGG
66 TCTCTAAACGAGGTCAT-CAACTTTAAAATGATTGGAAAA-TAAGCTCCTCATCGTCAAACGAGG
**
3248043 CCACAAAACTTTAAAATGATTGG-AAAAGCTTTTCATCCCTAAACGAGACTATGTAACTTTAAAA
129 CCACAAAACTTTAAAATGATTGGAAAAAGCTCCTCATCCCTAAACGAGACTATGTAACTTTAAAA
3248107 TG
194 TG
*
3248109 ATTGG-AAAAACTCCCTATCTCTAAACAAAGTCACACAACTTGAAAATGACTGAAAAAAGCTCTT
1 ATTGGAAAAAACTCCCCATCTCTAAACAAAGTCACACAACTT-AAAATGACTGAAAAAA-CTCTT
*
3248173 CATCTCTAAACGAGGCTACAT-AACTTTAAATAAATGATT-GAAAA-AAGCTCCTTATC-TCCAA
64 CATCTCTAAACGAGG-T-CATCAACTTT--A-AAATGATTGGAAAATAAGCTCCTCATCGT-CAA
*** ** *
3248234 ACGAGGTTGCGCAACTTTAAAATGATTGGAAAAAGCTCCTCATCTCTAAACGAG
123 ACGAGGCCACAAAACTTTAAAATGATTGGAAAAAGCTCCTCATCCCTAAACGAG
3248288 TCTTCTTAAC
Statistics
Matches: 151, Mismatches: 19, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
195 31 0.21
196 20 0.13
197 61 0.40
198 22 0.15
199 9 0.06
200 8 0.05
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.27
Consensus pattern (195 bp):
ATTGGAAAAAACTCCCCATCTCTAAACAAAGTCACACAACTTAAAATGACTGAAAAAACTCTTCA
TCTCTAAACGAGGTCATCAACTTTAAAATGATTGGAAAATAAGCTCCTCATCGTCAAACGAGGCC
ACAAAACTTTAAAATGATTGGAAAAAGCTCCTCATCCCTAAACGAGACTATGTAACTTTAAAATG
Found at i:3249043 original size:8 final size:8
Alignment explanation
Indices: 3249026--3249055 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
3249016 TCTTTAAACT
3249026 TTTTTCTTC
1 TTTTT-TTC
3249035 TTTTTTTC
1 TTTTTTTC
3249043 TTTTTTTC
1 TTTTTTTC
3249051 TTTTT
1 TTTTT
3249056 GTTATTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:3253356 original size:8 final size:8
Alignment explanation
Indices: 3253345--3253383 Score: 60
Period size: 9 Copynumber: 4.6 Consensus size: 8
3253335 TTTTTTCAAA
3253345 TTTTTATT
1 TTTTTATT
3253353 TTTTTATT
1 TTTTTATT
3253361 TTGTTTATT
1 TT-TTTATT
3253370 TTTTTAATT
1 TTTTT-ATT
3253379 TTTTT
1 TTTTT
3253384 CAATGTTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.45
9 16 0.55
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (8 bp):
TTTTTATT
Found at i:3253367 original size:17 final size:18
Alignment explanation
Indices: 3253347--3253380 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3253337 TTTTCAAATT
3253347 TTTATTTTTTT-ATTTTG
1 TTTATTTTTTTAATTTTG
3253364 TTTATTTTTTTAATTTT
1 TTTATTTTTTTAATTTT
3253381 TTTCAATGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (18 bp):
TTTATTTTTTTAATTTTG
Found at i:3254037 original size:14 final size:13
Alignment explanation
Indices: 3253995--3254046 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3253985 TAATTATATT
*
3253995 TTATTTATAATAA
1 TTATTTATAAAAA
3254008 TTATTTATAAATAAA
1 TTATTTAT-AA-AAA
*
3254023 TCTTTTTATAAAAA
1 T-TATTTATAAAAA
*
3254037 TAATTTATAA
1 TTATTTATAA
3254047 GATTCCGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
13 15 0.47
14 6 0.19
15 5 0.16
16 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
TTATTTATAAAAA
Found at i:3254900 original size:95 final size:95
Alignment explanation
Indices: 3254733--3254966 Score: 308
Period size: 95 Copynumber: 2.5 Consensus size: 95
3254723 TAAAGAATAA
* *** *
3254733 TGAATTTATTCTTTAATCAGTCTTTGTTTGTAATATGAGTTTGGGCAAAGAAAGTGAATTTATTC
1 TGAATTTATTCTTTAGTCAGTCTTTGTTTGTAATATGAGTTCACGCAAAGAAAGTGAATTTATTA
* * **
3254798 TTTAGTCAGTTGTATTGTGGGTAAAAAATG
66 TTGAGTCAGTTGCATTGTGCATAAAAAATG
* * * *
3254828 TGAATTTATTCTTTAGTTAGTCTTTATTTGTAACATGAGTTCACGTAAAGAAAGTGAATTTATTA
1 TGAATTTATTCTTTAGTCAGTCTTTGTTTGTAATATGAGTTCACGCAAAGAAAGTGAATTTATTA
*
3254893 TTGAGTCAGTTGCATTGTGCATAAAGAATG
66 TTGAGTCAGTTGCATTGTGCATAAAAAATG
* *
3254923 TGAATTTATTTTTTAGTCCG-CTTTTGTTTGTAATATGAGTTCAC
1 TGAATTTATTCTTTAGTCAGTC-TTTGTTTGTAATATGAGTTCAC
3254967 TAGCTAGGTC
Statistics
Matches: 119, Mismatches: 19, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
94 1 0.01
95 118 0.99
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.44
Consensus pattern (95 bp):
TGAATTTATTCTTTAGTCAGTCTTTGTTTGTAATATGAGTTCACGCAAAGAAAGTGAATTTATTA
TTGAGTCAGTTGCATTGTGCATAAAAAATG
Found at i:3264536 original size:62 final size:60
Alignment explanation
Indices: 3264418--3264536 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 60
3264408 TGTTAAAATA
* * *
3264418 TTTTAAGCATTTTGGAGTAATTTTTGATATACGAAGAAAACTTTTGAACGTTTTGAGTAT
1 TTTTAAGCATTTTGGAATAATTTTTGATATACGAAAAAAACTTTTGAACATTTTGAGTAT
* * *
3264478 TTTTAAGCATTTTTGGAATAATTTTTTATATATGAACAAAAATTTTTGAACATTTTGAG
1 TTTTAAGCA-TTTTGGAATAATTTTTGATATACGAA-AAAAACTTTTGAACATTTTGAG
3264537 CATTCTTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
60 9 0.18
61 23 0.45
62 19 0.37
ACGTcount: A:0.34, C:0.06, G:0.15, T:0.45
Consensus pattern (60 bp):
TTTTAAGCATTTTGGAATAATTTTTGATATACGAAAAAAACTTTTGAACATTTTGAGTAT
Found at i:3264676 original size:21 final size:21
Alignment explanation
Indices: 3264643--3264770 Score: 64
Period size: 21 Copynumber: 6.0 Consensus size: 21
3264633 ATTTTGGTGG
*
3264643 TTTTTGAGCATTACGTGACTA
1 TTTTTAAGCATTACGTGACTA
*
3264664 TTTTTAAGTATTACGTGACTTA
1 TTTTTAAGCATTACGTGAC-TA
* *
3264686 CTTTGT-A-CATTATGTGACTGA
1 -TTTTTAAGCATTACGTGACT-A
* * *
3264707 -CTTTAGGCATTGCGTGACTTA
1 TTTTTAAGCATTACGTGAC-TA
* * **
3264728 TTTTTAGGTATTGTGTGACTA
1 TTTTTAAGCATTACGTGACTA
** *
3264749 GTTGGTAAGCATTGCGTGACTA
1 -TTTTTAAGCATTACGTGACTA
3264771 GTTAGTAAGG
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
19 2 0.02
20 1 0.01
21 39 0.48
22 35 0.43
23 4 0.05
ACGTcount: A:0.23, C:0.12, G:0.22, T:0.43
Consensus pattern (21 bp):
TTTTTAAGCATTACGTGACTA
Found at i:3264740 original size:22 final size:24
Alignment explanation
Indices: 3264709--3264818 Score: 88
Period size: 23 Copynumber: 4.8 Consensus size: 24
3264699 GTGACTGACT
* *
3264709 TTAGGCATTGCGTGACTTA-TT-T
1 TTAGGTATTGCGTGACTTAGTTAG
*
3264731 TTAGGTATTGTGTGAC-TAGTT-G
1 TTAGGTATTGCGTGACTTAGTTAG
* * *
3264753 GTAAGCATTGCGTGAC-TAGTTAG
1 TTAGGTATTGCGTGACTTAGTTAG
* *
3264776 TAAGGTATTGCGTGAC-TAATTAG
1 TTAGGTATTGCGTGACTTAGTTAG
* *
3264799 TAAGGTATTGTGTGACTTAG
1 TTAGGTATTGCGTGACTTAG
3264819 GCATTGCTTA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
21 2 0.03
22 33 0.46
23 34 0.48
24 2 0.03
ACGTcount: A:0.24, C:0.09, G:0.28, T:0.39
Consensus pattern (24 bp):
TTAGGTATTGCGTGACTTAGTTAG
Found at i:3264789 original size:23 final size:23
Alignment explanation
Indices: 3264733--3264815 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
3264723 ACTTATTTTT
* *
3264733 AGGTATTGTGTGACTAGTTGGTA
1 AGGTATTGCGTGACTAGTTAGTA
*
3264756 A-GCATTGCGTGACTAGTTAGTA
1 AGGTATTGCGTGACTAGTTAGTA
*
3264778 AGGTATTGCGTGACTAATTAGTA
1 AGGTATTGCGTGACTAGTTAGTA
*
3264801 AGGTATTGTGTGACT
1 AGGTATTGCGTGACT
3264816 TAGGCATTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
22 19 0.36
23 34 0.64
ACGTcount: A:0.25, C:0.08, G:0.30, T:0.36
Consensus pattern (23 bp):
AGGTATTGCGTGACTAGTTAGTA
Found at i:3267670 original size:583 final size:580
Alignment explanation
Indices: 3266445--3268501 Score: 2088
Period size: 583 Copynumber: 3.5 Consensus size: 580
3266435 NNNNNNNNNN
* * * *
3266445 GTTTGTAATATGAGTTCACTAGCTAGGGTAAAGAATGTGAATTTATTGTGGAAAG-AAAAATCTT
1 GTTTGTAATATGAGTTCACTAGCTAGCGTAAA-AATGTGAATTTATTGTGGAAGGAAAAAAGCCT
* * * * * * *
3266509 AGCACATGTTTATTTCTCGTTAAAGAAAAAAGTTACGCAATTGATAATATTCATT-TGGGAATAT
65 AGCACATGCTAATTTCTCGCTAAAGAAAAAAGCTACGAAACTGATAATATTCATTATGAGAATA-
* ** * ** * * * * *
3266573 TTC-AAGGTATTTTAGATGAAAAATCACAATAGTCTCATTCGTCAAGTTATTATGATATCATTCA
129 TTCAAAGGTATTTTAGACGAAAAATCATGACAGTCTTGTACATCAAGTTACTATGACATCATACA
* * * * *
3266637 TTGCAAATAAACAAAATGAAAGATTGGCAGTTAGTCTAGTATTTCATCTTCAAGAAAGAAGATAT
194 TTACAAAT-----AAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGATAT
* * * * *
3266702 TTTTCACATTCCGTAGCTGCACGTCAAGACTTTGATACAAACTTTTGGATTTTAAAATTTAATTT
254 TTTTCACATTCCTTAGCTGCACGTCAAGACTGTGATACATATTTTTGGATTTTAAAATTTTATTT
* * *
3266767 TCATTAACTCATTTTA-AATGGAAAATTGTATGAACTTGACTTTGAATTTGGAATGAAATTGCAT
319 TTATT---TCTTTTTATAA--GAAAATTGTACGAACTTGACTTTGAATTTGGAATGAAATTGCAT
* * * * * * *
3266831 TGTATGCCACGATTAAGTTGTAG-TTTTTTATTTCTTTAGTGGGCATGGCATTTGCTCATATGTT
379 TGTATGTCAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTAT-GCATCTGCTCATATGTT
* * *
3266895 GCCCCTATTTATAGCCAACTTACGATAAGCCAAAAGAAAGAAAGAATAAAAAATTATGAACAAAA
443 GTCCCTATTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAAC-AAA
* *
3266960 TTCCTTTGTTGGTCTTTGTTTGTG-ATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGA
507 TTCTTTTGTCGGTCTTTGTTTG-GAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGA
*
3267024 ATTAATCTTT
571 ATCAATCTTT
* * * * * *
3267034 CTTTTTAATATAAGTTCACTAGCTAGCATGAAAATGTGAATTTATTATGGAAGGAAAAAAAGCCT
1 GTTTGTAATATGAGTTCACTAGCTAGCGTAAAAATGTGAATTTATTGTGGAAGG-AAAAAAGCCT
* * * * * *
3267099 AGCACATGCTAATTTCTTGCTAAAGAAAAACGCTACTAAATTGATAATATTCGTTACGAGAATAT
65 AGCACATGCTAATTTCTCGCTAAAGAAAAAAGCTACGAAACTGATAATATTCATTATGAGAATAT
* * ** *
3267164 TCAAAGGTATTTTAGACGAAAAAGCAGGACAAACTTGTACATCAAGTTACTATAACATCATACAT
130 TCAAAGGTATTTTAGACGAAAAATCATGACAGTCTTGTACATCAAGTTACTATGACATCATACAT
* * * *
3267229 TACAAATAAATGAAAGATTTACATTTAGTTTAGTATTTTATTTTCAAGAAAGAAGATTATTATTT
195 TACAAATAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGA-TATT-TTT
* ** *
3267294 -ACATTCCTTGAGTTATACGTCAAGACTGTGATACATATTTTTGAATTTTAAAAATTTTATTTTT
258 CACATTCCTT-AGCTGCACGTCAAGACTGTGATACATATTTTTGGATTTT-AAAATTTTATTTTT
* * *
3267358 ATTT-TTTTTATAA-AAAATTGTACGAACTTGATTTTGAATTTGGAATAAAATTGCATTGTAAGT
321 ATTTCTTTTTATAAGAAAATTGTACGAACTTGACTTTGAATTTGGAATGAAATTGCATTGTATGT
* * * *
3267421 CAAGATCAAGCTGTAGCTTCTTAATTACTTTGGTGGGTATGACATCTGTTCATATGTTGTCCCTA
386 CAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTATG-CATCTGCTCATATGTTGTCCCTA
* * ********** * * *
3267486 TTTATAGCGAACTTATGAGAANNNNNNNNNNACAAAGAATCAAAGATTATGAACATA-TCTTTTG
450 TTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAACAAATTCTTTTG
* * *********
3267550 ACGGTCTTTGTTTGGAATATGAGTTCATTAGTTAGGTCTTGTATTGTGCCTAAAGANNNNNNNNN
515 TCGGTCTTTGTTTGGAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGAATCAATCTT
*
3267615 N
580 T
* *
3267616 GTTTGTAATATGAGTTCACTAGCTACCGTAAAGAATGTGAATTTATTGTGGAAGGAAGAAAGCCT
1 GTTTGTAATATGAGTTCACTAGCTAGCGTAAA-AATGTGAATTTATTGTGGAAGGAAAAAAGCCT
* * ** *
3267681 AGCACATGCTAATTTCTCGCTAAAGAAAAAAAGTTACGCAACTGATAATATTTGTCATGAGAATA
65 AGCACATGCTAATTTCTCGCTAAAG-AAAAAAGCTACGAAACTGATAATATTCATTATGAGAATA
* *
3267746 TTCAAAGGTATTTTAGACGAAAAATCATGACACTCTCATG-A-ATCAAGTTACTATGACATCATT
129 TTCAAAGGTATTTTAGACGAAAAATCATGACAGTCT--TGTACATCAAGTTACTATGACATCATA
* * *
3267809 CATTACAAACAAACAAAACGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGCAGAT
192 CATT----ACAAA-TAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGAT
* * * *
3267874 ATTTTTGACATTCC-TAGCTGCACATCAAGACT-TCGGTACATATTTTTGGATTTGAAAATTTTA
252 ATTTTTCACATTCCTTAGCTGCACGTCAAGACTGT-GATACATATTTTTGGATTTTAAAATTTT-
* * *
3267937 ATTTTTATTTACTCATTTT-TGAACGAAAATAGTAGGAACTTGACTTTGAATTTGGAATGAAACT
315 ATTTTTATTT-CT--TTTTAT-AA-GAAAATTGTACGAACTTGACTTTGAATTTGGAATGAAATT
* * * *
3268001 GCATTCTATGTCATGATTAAGCTATAGCTTCTTAATTTCTTTCGTGGGTATGCATCTGCTCATAT
375 GCATTGTATGTCAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTATGCATCTGCTCATAT
** * * * *
3268066 ACTATCCCTATTTATAGCCAACTTACAAGAAGCCAAAAGAAAGAAAGAATTAAAGATAATGAACA
440 GTTGTCCCTATTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAACA
* * * * ** *
3268131 GAATTCTTTAGTCGGTTTTTGTTTGTAATATGAGTTCATTAGCTAAGTGATGTATTGTG-CTATA
505 -AATTCTTTTGTCGGTCTTTGTTTGGAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAA
*
3268195 GAATCAGTCTTT
569 GAATCAATCTTT
** * * ** * *
3268207 GGCTGTAATATGAGTTCACAAGTTATTGTGAAAACTGTGAATTTATTGTGGAAGGAAAAAAGTCT
1 GTTTGTAATATGAGTTCACTAGCTAGCGT-AAAAATGTGAATTTATTGTGGAAGGAAAAAAGCCT
* * *
3268272 AGCACAAGTTAATTTCTAG-TAAAAGAAAAAAGCTAC-ACAACTGATAATATTCATTATGAGAAT
65 AGCACATGCTAATTTCTCGCT-AAAGAAAAAAGCTACGA-AACTGATAATATTCATTATGAGAAT
** * * *
3268335 ATTCAAAGGTGGTTTAGAC-AACAAATCATGTCAGTTTTGT-CAATCAAGTTACTCTGACATCAT
128 ATTCAAAGGTATTTTAGACGAA-AAATCATGACAGTCTTGTAC-ATCAAGTTACTATGACATCAT
* *
3268398 ACAATACAAATAAA--AAAAATTGACATTTAGTCTAGTATTTCATTTTCAAAAAAGAAGATATTT
191 ACATTACAAATAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGATATTT
* *
3268461 TTCATATTCCTTAAGCTGCACGTCAAGACTGTGATATATAT
256 TTCACATTCCTT-AGCTGCACGTCAAGACTGTGATACATAT
3268502 ATATATATTT
Statistics
Matches: 1202, Mismatches: 223, Indels: 90
0.79 0.15 0.06
Matches are distributed among these distances:
581 1 0.00
582 116 0.10
583 224 0.19
584 87 0.07
585 73 0.06
586 56 0.05
587 29 0.02
588 101 0.08
589 49 0.04
590 199 0.17
591 217 0.18
592 50 0.04
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (580 bp):
GTTTGTAATATGAGTTCACTAGCTAGCGTAAAAATGTGAATTTATTGTGGAAGGAAAAAAGCCTA
GCACATGCTAATTTCTCGCTAAAGAAAAAAGCTACGAAACTGATAATATTCATTATGAGAATATT
CAAAGGTATTTTAGACGAAAAATCATGACAGTCTTGTACATCAAGTTACTATGACATCATACATT
ACAAATAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGATATTTTTCAC
ATTCCTTAGCTGCACGTCAAGACTGTGATACATATTTTTGGATTTTAAAATTTTATTTTTATTTC
TTTTTATAAGAAAATTGTACGAACTTGACTTTGAATTTGGAATGAAATTGCATTGTATGTCAAGA
TTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTATGCATCTGCTCATATGTTGTCCCTATTTATA
GCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAACAAATTCTTTTGTCGGTC
TTTGTTTGGAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGAATCAATCTTT
Found at i:3268252 original size:591 final size:589
Alignment explanation
Indices: 3266445--3268582 Score: 2163
Period size: 591 Copynumber: 3.6 Consensus size: 589
3266435 NNNNNNNNNN
* * * *
3266445 GTTTGTAATATGAGTTCACTAGCTAGGGTAAAGAATGTGAATTTATTGTGGAAAG-AAAAATCTT
1 GTTTGTAATATGAGTTCACTAGCTAGCGTAAAGAATGTGAATTTATTGTGGAAGGAAAAAAGCCT
* * * * * *
3266509 AGCACATGTTTATTTCTCGTTAAAGAAAAAAGTTACGCAATTGATAATATTCATT-TGGGAATAT
66 AGCACATGCTAATTTCTCGCTAAAGAAAAAAGCTACGCAACTGATAATATTCATTATGAGAATA-
* ** * *** * *
3266573 TTC-AAGGTATTTTAGATGAAAAATCACAATAGTCTCATTCGTCAAGTTATTATGATATCATTCA
130 TTCAAAGGTATTTTAGACGAAAAATCATGACAGTCTCATGAATCAAGTTACTATGACATCATTCA
* * * * * *
3266637 TTGCAAATAAACAAAATGAAAGATTGGCAGTTAGTCTAGTATTTCATCTTCAAGAAAGAAGATAT
195 TTACAAACAAA-AAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGATAT
* * * *
3266702 TTTTCACATTCCGT-AGCTGCACGTCAAGACTTTGATACAAACTTTTGGATTTT-AAAATTTAAT
259 TTTTCACATTCCTTAAGCTGCACGTCAAGACTGTGATACATATTTTTGGATTTTGAAAATTTAAT
* * * * *
3266765 TTTCATTAACTCATTTTAAATGGAAAATTGTATGAACTTGACTTTGAATTTGGAATGAAATTGCA
324 TTTTATTTACTCATTTTTAA-GGAAAATAGTAGGAACTTGACTTTGAATTTGGAATGAAATTGCA
* * * * * * *
3266830 TTGTATGCCACGATTAAGTTGTAG-TTTTTTATTTCTTTAGTGGGCATGGCATTTGCTCATATGT
388 TTGTATGTCAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTAT-GCATCTGCTCATATGT
* * *
3266894 TGCCCCTATTTATAGCCAACTTACGATAAGCCAAAAGAAAGAAAGAATAAAAAATTATGAACAAA
452 TGTCCCTATTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAAC-AA
* *
3266959 ATTCCTTTGTTGGTCTTTGTTTGTGATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGA
516 ATT-CTTTGTCGGTCTTTGTTTGTAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGA
*
3267024 ATTAATCTTT
580 ATCAATCTTT
* * * * * *
3267034 CTTTTTAATATAAGTTCACTAGCTAGCATGAA-AATGTGAATTTATTATGGAAGGAAAAAAAGCC
1 GTTTGTAATATGAGTTCACTAGCTAGCGTAAAGAATGTGAATTTATTGTGGAAGG-AAAAAAGCC
* * ** * * *
3267098 TAGCACATGCTAATTTCTTGCTAAAGAAAAACGCTACTAAATTGATAATATTCGTTACGAGAATA
65 TAGCACATGCTAATTTCTCGCTAAAGAAAAAAGCTACGCAACTGATAATATTCATTATGAGAATA
* * ** * *
3267163 TTCAAAGGTATTTTAGACGAAAAAGCAGGACAAACT--TGTACATCAAGTTACTATAACATCATA
130 TTCAAAGGTATTTTAGACGAAAAATCATGACAGTCTCATG-A-ATCAAGTTACTATGACATCATT
* * * * *
3267226 CATT----ACAAATAAATGAAAGATTTACATTTAGTTTAGTATTTTATTTTCAAGAAAGAAGATT
193 CATTACAAACAAAAAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGA-T
* * ** * *
3267287 ATTATTT-ACATTCCTTGAGTTATACGTCAAGACTGTGATACATATTTTTGAATTTTAAAAATTT
257 ATT-TTTCACATTCCTTAAGCTGCACGTCAAGACTGTGATACATATTTTTGGATTTTGAAAATTT
* * * * *
3267351 TATTTTTATTT--T--TTTTATAA--AAAATTGTACGAACTTGATTTTGAATTTGGAATAAAATT
321 AATTTTTATTTACTCATTTT-TAAGGAAAATAGTAGGAACTTGACTTTGAATTTGGAATGAAATT
* * * * *
3267410 GCATTGTAAGTCAAGATCAAGCTGTAGCTTCTTAATTACTTTGGTGGGTATGACATCTGTTCATA
385 GCATTGTATGTCAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTATG-CATCTGCTCATA
* * ********** * *
3267475 TGTTGTCCCTATTTATAGCGAACTTATGAGAANNNNNNNNNNACAAAGAATCAAAGATTATGAAC
449 TGTTGTCCCTATTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAAC
* * * *
3267540 ATA-TCTTTTGACGGTCTTTGTTTGGAATATGAGTTCATTAGTTAGGTCTTGTATTGTGCCTAAA
514 AAATTC-TTTGTCGGTCTTTGTTTGTAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAA
**********
3267604 GANNNNNNNNNN
578 GAATCAATCTTT
* *
3267616 GTTTGTAATATGAGTTCACTAGCTACCGTAAAGAATGTGAATTTATTGTGGAAGGAAGAAAGCCT
1 GTTTGTAATATGAGTTCACTAGCTAGCGTAAAGAATGTGAATTTATTGTGGAAGGAAAAAAGCCT
* ** *
3267681 AGCACATGCTAATTTCTCGCTAAAGAAAAAAAGTTACGCAACTGATAATATTTGTCATGAGAATA
66 AGCACATGCTAATTTCTCGCTAAAG-AAAAAAGCTACGCAACTGATAATATTCATTATGAGAATA
*
3267746 TTCAAAGGTATTTTAGACGAAAAATCATGACACTCTCATGAATCAAGTTACTATGACATCATTCA
130 TTCAAAGGTATTTTAGACGAAAAATCATGACAGTCTCATGAATCAAGTTACTATGACATCATTCA
* *
3267811 TTACAAACAAACAAAACGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGCAGATAT
195 TTACAAACAAA-AAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGATAT
* * *
3267876 TTTTGACATTCC-T-AGCTGCACATCAAGACT-TCGGTACATATTTTTGGA-TTTGAAAATTTTA
259 TTTTCACATTCCTTAAGCTGCACGTCAAGACTGT-GATACATATTTTTGGATTTTGAAAA-TTTA
* *
3267937 ATTTTTATTTACTCATTTTTGAACGAAAATAGTAGGAACTTGACTTTGAATTTGGAATGAAACTG
322 ATTTTTATTTACTCATTTTT-AAGGAAAATAGTAGGAACTTGACTTTGAATTTGGAATGAAATTG
* * * * *
3268002 CATTCTATGTCATGATTAAGCTATAGCTTCTTAATTTCTTTCGTGGGTATGCATCTGCTCATATA
386 CATTGTATGTCAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTATGCATCTGCTCATATG
* * * * *
3268067 CTATCCCTATTTATAGCCAACTTACAAGAAGCCAAAAGAAAGAAAGAATTAAAGATAATGAACAG
451 TTGTCCCTATTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAACA-
* * ** *
3268132 AATTCTTTAGTCGGTTTTTGTTTGTAATATGAGTTCATTAGCTAAGTGATGTATTGTG-CTATAG
515 AATTCTTT-GTCGGTCTTTGTTTGTAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAG
*
3268196 AATCAGTCTTT
579 AATCAATCTTT
** * * ** * *
3268207 GGCTGTAATATGAGTTCACAAGTTATTGTGAAA-ACTGTGAATTTATTGTGGAAGGAAAAAAGTC
1 GTTTGTAATATGAGTTCACTAGCTAGCGT-AAAGAATGTGAATTTATTGTGGAAGGAAAAAAGCC
* * * *
3268271 TAGCACAAGTTAATTTCTAG-TAAAAGAAAAAAGCTACACAACTGATAATATTCATTATGAGAAT
65 TAGCACATGCTAATTTCTCGCT-AAAGAAAAAAGCTACGCAACTGATAATATTCATTATGAGAAT
** * * ** * *
3268335 ATTCAAAGGTGGTTTAGAC-AACAAATCATGTCAGTTTTGTCAATCAAGTTACTCTG--A-CA-T
129 ATTCAAAGGTATTTTAGACGAA-AAATCATGACAGTCTCATGAATCAAGTTACTATGACATCATT
* *
3268395 CA-TACAATACAAATAAA--AAAAATTGACATTTAGTCTAGTATTTCATTTTCAAAAAAGAAGAT
193 CATTACAA-ACAAAAAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGAT
* *
3268457 ATTTTTCATATTCCTTAAGCTGCACGTCAAGACTGTGATATATATATATATATTTGGATTTTGAA
257 ATTTTTCACATTCCTTAAGCTGCACGTCAAGACTGTG----ATACATAT-T-TTTGGATTTTGAA
* * * *
3268522 AACTTAATCTTTATTTACTCATTTTTAGTGGAAAATTA-TAGGAACTTGACTTTAAATTTGG
316 AATTTAATTTTTATTTACTCATTTTTA-AGGAAAA-TAGTAGGAACTTGACTTTGAATTTGG
3268583 GACATAATTA
Statistics
Matches: 1266, Mismatches: 231, Indels: 102
0.79 0.14 0.06
Matches are distributed among these distances:
581 1 0.00
582 115 0.09
583 224 0.18
584 86 0.07
585 71 0.06
586 58 0.05
587 36 0.03
588 100 0.08
589 56 0.04
590 194 0.15
591 268 0.21
592 57 0.05
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (589 bp):
GTTTGTAATATGAGTTCACTAGCTAGCGTAAAGAATGTGAATTTATTGTGGAAGGAAAAAAGCCT
AGCACATGCTAATTTCTCGCTAAAGAAAAAAGCTACGCAACTGATAATATTCATTATGAGAATAT
TCAAAGGTATTTTAGACGAAAAATCATGACAGTCTCATGAATCAAGTTACTATGACATCATTCAT
TACAAACAAAAAAATGAAAAATTGACATTTAGTCTAGTATTTCATTTTCAAGAAAGAAGATATTT
TTCACATTCCTTAAGCTGCACGTCAAGACTGTGATACATATTTTTGGATTTTGAAAATTTAATTT
TTATTTACTCATTTTTAAGGAAAATAGTAGGAACTTGACTTTGAATTTGGAATGAAATTGCATTG
TATGTCAAGATTAAGCTGTAGCTTCTTAATTTCTTTAGTGGGTATGCATCTGCTCATATGTTGTC
CCTATTTATAGCCAACTTACGAGAAGCCAAAAGAAAGAAAGAATAAAAGATTATGAACAAATTCT
TTGTCGGTCTTTGTTTGTAATATGAGTTCATTAGCTAGGTCTTGTATTGTGCCTAAAGAATCAAT
CTTT
Found at i:3272720 original size:2 final size:2
Alignment explanation
Indices: 3272713--3272742 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3272703 TAATGTCTTC
*
3272713 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3272743 GGTCAGCTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:3272925 original size:106 final size:106
Alignment explanation
Indices: 3272731--3272925 Score: 284
Period size: 106 Copynumber: 1.8 Consensus size: 106
3272721 ATATATATAT
* *
3272731 ATATTTATATATGGTCAGCTCATGTCTTCATATATACATATATGTATGCATGTATGTATGTATGA
1 ATATTTATATATGGTCAGCTCATGTCTTCATATATACATATATGTATGCATGTATGTATATATCA
* * * * *
3272796 TATATACACACACATATATACACAAATAGACACACACACAC
66 CAAATACACACACACACACACACAAATAGACACACACACAC
*
3272837 ATATTTATATATGGTCAGCTCATGTCTTCATATATACATATATGTATGTATGTATG-ATATATAC
1 ATATTTATATATGGTCAGCTCATGTCTTCATATATACATATATGTATGCATGTATGTATATAT-C
* *
3272901 ACAAATAGATACACACACACACACA
65 ACAAATACACACACACACACACACA
3272926 CATATTCATA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
105 5 0.06
106 73 0.94
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.33
Consensus pattern (106 bp):
ATATTTATATATGGTCAGCTCATGTCTTCATATATACATATATGTATGCATGTATGTATATATCA
CAAATACACACACACACACACACAAATAGACACACACACAC
Found at i:3275170 original size:21 final size:24
Alignment explanation
Indices: 3275146--3275196 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 24
3275136 AACTTAGATA
3275146 ATTTTTAAAT-TTATTT-A-TTTT
1 ATTTTTAAATGTTATTTAATTTTT
3275167 A-TTTTAAATGTTATTTAATTTTT
1 ATTTTTAAATGTTATTTAATTTTT
3275190 ATTTTTA
1 ATTTTTA
3275197 TTATATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.31
21 7 0.27
22 1 0.04
23 5 0.19
24 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (24 bp):
ATTTTTAAATGTTATTTAATTTTT
Found at i:3275915 original size:253 final size:250
Alignment explanation
Indices: 3275408--3276548 Score: 1034
Period size: 253 Copynumber: 4.5 Consensus size: 250
3275398 CTATAATTAT
* ** * *
3275408 TTTTATTC-TTTCATAGATTAAAATTTATAAGATG-TAAGATACTTTAAACTCAAAAATACAAAT
1 TTTTATTCATTT-ATAGATTAAAATTTGTAAGCCGTTAA-ATACTTTAAACTCGAGAATA-AAAT
* * *
3275471 TTAAA-ATTTTAATTTTTTCAAAAATTA-AGTTTATTTGACATAATTAACTTATTACGTTAAATC
63 TTAAATA-TTTAATTTTTTTAAAAATTATA-TTTATTTGACATAA-TGACTTATTACATTAAATC
** * * * * * *
3275534 TTATTCATTTACATCAATATTTTGACAATTATTGTTCCACTTTTATAATTTTTTTTCATTAATTT
125 TTACACATTTACGTCAATATTTTGACAATTCTTATTCCACCTTTATAA-TTTTTTACATTAATTC
* * * * *
3275599 TTATAACTTTACATCAATG-TTTTTCAACTACTAACTTTCACTATAATTATTCTTATCCTTAC
189 TTATTACTTTACGTCAA-GATTTTTCAACTACTAATTTTCACTATAATTATTTTTATTCTTAC
* * * *
3275661 TTTTATTCGTTTATAGATTAAAATTTGTAAGTCGTTACATACTTTAAACTCGTGAATATAAACTT
1 TTTTATTCATTTATAGATTAAAATTTGTAAGCCGTTAAATACTTTAAACTCGAGAATA-AAA-TT
* *
3275726 TAAATATTTAATTTTTTTAAAAATTATATTTATTTGACATAATCGACTTGTTGCATTAAATCTTA
64 TAAATATTTAATTTTTTTAAAAATTATATTTATTTGACATAAT-GACTTATTACATTAAATCTTA
* * * * * ** *
3275791 AACGTTTATGTCAATACTTTGACAATTCTTATTCCACCTCTATAATTTTTTACGCTAATTCGTAT
128 CACATTTACGTCAATATTTTGACAATTCTTATTCCACCTTTATAATTTTTTACATTAATTCTTAT
* * * * * *
3275856 TGCTTTATGTCGAGATTTTTAAACTACTAATTTTCACTACAATTATTTTTATGCTTAC
193 TACTTTACGTCAAGATTTTTCAACTACTAATTTTCACTATAATTATTTTTATTCTTAC
* * * *
3275914 TTTTATTCATTCT-TAAAATTAAAATTTGTAAGCTGTAAAATACTTTAAGA-TAGAGAATAAATA
1 TTTTATTCATT-TAT-AGATTAAAATTTGTAAGCCGTTAAATACTTTAA-ACTCGAGAATAAA-A
* * ** * * * *
3275977 TTTACATGTTTAATTTTCCTGAAAATTATGTTTGTTTGATC-TAAATGACTTATTACATTAAATG
62 TTTAAATATTTAATTTTTTTAAAAATTATATTTATTTGA-CAT-AATGACTTATTACATTAAATC
* * * * * * * **
3276041 TCACACACTTATGCCAATATTTTGACGATCCTTGTTCTGCCTTTATAATTTTTTACATTAATTCT
125 TTACACATTTACGTCAATATTTTGACAATTCTTATTCCACCTTTATAATTTTTTACATTAATTCT
* * * * * * * *
3276106 CACTACTTTAGGTCAATG-TTGTCCAAGTACTAATATTCACTATATTTATTTTTATTCTTAC
190 TATTACTTTACGTCAA-GATTTTTCAACTACTAATTTTCACTATAATTATTTTTATTCTTAC
* * **
3276167 TTTT-TTTATTTATATATTACAAATTTGTAAGCCGTTACTTACTTTAAACTCGAGAATAAAAATT
1 TTTTATTCATTTATAGATTA-AAATTTGTAAGCCGTTAAATACTTTAAACTCGAGAAT-AAAATT
* * * * * *
3276231 TAAATATTTAATTTTTCTAAAAAATATTTTTATTTGCCATAAATGACTTATTACGTT-AATGCCT
64 TAAATATTTAATTTTTTTAAAAATTATATTTATTTGACAT-AATGACTTATTACATTAAAT-CTT
* * * * * * *
3276295 -CACATTTACGTTAATATTTTGATAATTTTTATTCCACTTTTATAAATTTTTATATTAATTATTA
127 ACACATTTACGTCAATATTTTGACAATTCTTATTCCACCTTTATAATTTTTTACATTAATTCTTA
* * *
3276359 TTGCTTTACGTCAATATTTTTCAACTACTAATTTTCACTATAATTATTTTTATTCTTAT
192 TTACTTTACGTCAAGATTTTTCAACTACTAATTTTCACTATAATTATTTTTATTCTTAC
* ** * *
3276418 TTTTATTCATTTAT--ATTAAAATTCGTTGGCCATTAAATACTTTAAACTCAAGAATATAAATTT
1 TTTTATTCATTTATAGATTAAAATTTGTAAGCCGTTAAATACTTTAAACTCGAGAATA-AAATTT
* * * ** *
3276481 TAAT-TTTAATTTTTTTAAAAAAATCATATTTATTTGACATAATTGACTTCTTATGTTAAATCTC
65 AAATATTTAATTTTTTT--AAAAATTATATTTATTTGACATAA-TGACTTATTACATTAAATCTT
3276545 ACAC
127 ACAC
3276549 CATTGTTCAA
Statistics
Matches: 713, Mismatches: 147, Indels: 58
0.78 0.16 0.06
Matches are distributed among these distances:
248 12 0.02
249 41 0.06
250 35 0.05
251 117 0.16
252 94 0.13
253 273 0.38
254 138 0.19
255 3 0.00
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (250 bp):
TTTTATTCATTTATAGATTAAAATTTGTAAGCCGTTAAATACTTTAAACTCGAGAATAAAATTTA
AATATTTAATTTTTTTAAAAATTATATTTATTTGACATAATGACTTATTACATTAAATCTTACAC
ATTTACGTCAATATTTTGACAATTCTTATTCCACCTTTATAATTTTTTACATTAATTCTTATTAC
TTTACGTCAAGATTTTTCAACTACTAATTTTCACTATAATTATTTTTATTCTTAC
Found at i:3276717 original size:16 final size:16
Alignment explanation
Indices: 3276696--3276744 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3276686 ACTAATTATA
3276696 ATTAAAATAATTATTT
1 ATTAAAATAATTATTT
*
3276712 ATTAAACTAAATT-TTT
1 ATTAAAAT-AATTATTT
* *
3276728 ATTATAATATTTATTT
1 ATTAAAATAATTATTT
3276744 A
1 A
3276745 AAAATTTCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 3 0.11
16 20 0.74
17 4 0.15
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAAAATAATTATTT
Found at i:3277666 original size:41 final size:41
Alignment explanation
Indices: 3277621--3277701 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
3277611 ACATATTGGG
* * *
3277621 CTATTAGGCTGAA-TCGTTGAGATCTAATATGTTATGATAAA
1 CTATTAGGCTGAACT-GTTAAAATATAATATGTTATGATAAA
*
3277662 CTATTGGGCTGAACTGTTAAAATATAATATGTTATGATAA
1 CTATTAGGCTGAACTGTTAAAATATAATATGTTATGATAA
3277702 GCTTAAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.36, C:0.09, G:0.19, T:0.37
Consensus pattern (41 bp):
CTATTAGGCTGAACTGTTAAAATATAATATGTTATGATAAA
Found at i:3279455 original size:13 final size:13
Alignment explanation
Indices: 3279439--3279490 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 13
3279429 TCAGGTATTA
3279439 TTTCTTTTTTTTC
1 TTTCTTTTTTTTC
*
3279452 TTTCTATTTTGTT-
1 TTTCT-TTTTTTTC
3279465 TTTCATTTTATTTTC
1 TTTC-TTTT-TTTTC
*
3279480 TATCTTTTTTT
1 TTTCTTTTTTT
3279491 GTACTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 15 0.47
14 14 0.44
15 3 0.09
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTCTTTTTTTTC
Found at i:3279468 original size:17 final size:17
Alignment explanation
Indices: 3279446--3279478 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3279436 TTATTTCTTT
3279446 TTTTTC-TTTCTATTTTG
1 TTTTTCATTT-TATTTTG
3279463 TTTTTCATTTTATTTT
1 TTTTTCATTTTATTTT
3279479 CTATCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCATTTTATTTTG
Found at i:3282013 original size:16 final size:15
Alignment explanation
Indices: 3281994--3282050 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
3281984 TAGGCCGAAC
3281994 CTTCACTTTCTCTTTT
1 CTTC-CTTTCTCTTTT
* *
3282010 CTT-CTTCCTCCTTT
1 CTTCCTTTCTCTTTT
*
3282024 CTTCCGTTCTCTCTTT
1 CTTCCTTTCTCT-TTT
*
3282040 CTTTCTTTCTC
1 CTTCCTTTCTC
3282051 CCCTTCTCTT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
14 12 0.38
15 5 0.16
16 15 0.47
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (15 bp):
CTTCCTTTCTCTTTT
Found at i:3283951 original size:14 final size:15
Alignment explanation
Indices: 3283920--3283957 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
3283910 TTTCATTCTA
*
3283920 TTTTATTTTGGTATTT
1 TTTTATTTT-GTAGTT
3283936 TTTTATTTT-TAGTT
1 TTTTATTTTGTAGTT
3283950 TTTTATTT
1 TTTTATTT
3283958 GATAAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (15 bp):
TTTTATTTTGTAGTT
Found at i:3284220 original size:24 final size:25
Alignment explanation
Indices: 3284166--3284221 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
3284156 TTTCAAAATA
3284166 ATAAA-AAAATAAGTTTGAAATAAAC
1 ATAAATAAAATAAGTTT-AAATAAAC
*
3284191 AT--ATAAAATAAGTTT-AATATAC
1 ATAAATAAAATAAGTTTAAATAAAC
3284213 ATAAATAAA
1 ATAAATAAA
3284222 TGAGTAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 8 0.30
23 1 0.04
24 16 0.59
25 2 0.07
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.29
Consensus pattern (25 bp):
ATAAATAAAATAAGTTTAAATAAAC
Found at i:3290903 original size:41 final size:41
Alignment explanation
Indices: 3290827--3290904 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
3290817 AATTAAGTCT
* * * **
3290827 ATCATAACATATTATATCTTAATAGTTTAGGCTAATAGCCC
1 ATCATAACATATTATATCTAAATAATTCAACCTAATAGCCC
*
3290868 ATCATAATATATTATATCTAAATAATTCAACCTAATA
1 ATCATAACATATTATATCTAAATAATTCAACCTAATA
3290905 ACACAATATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.05, T:0.37
Consensus pattern (41 bp):
ATCATAACATATTATATCTAAATAATTCAACCTAATAGCCC
Found at i:3293088 original size:252 final size:251
Alignment explanation
Indices: 3292799--3294586 Score: 1055
Period size: 252 Copynumber: 7.2 Consensus size: 251
3292789 TATAATTAAT
* * * * * *
3292799 TTTTTTTAAAAAAATTAAAGATTTAAATTTGTATTCTCAAATTTAGACTATGTAATGGCTTCCGA
1 TTTTTTT--AAAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAA
* *
3292864 ATTT-TAATATATAAATGAATAAAAGTAAAGATAAAAATGATTATAATAAAAATTAGTAGCTGAA
64 ATTTGTAATATATAAATGAATAAAAGTAAAGATAAAAATAATTATAATAAAAATTAGTAGTTGAA
* * * * * * ** *
3292928 CAATG-GCAGTGTAAAGTAGTAAGAATTAACGTTAAAAATTATAAAAGTGGGACATTGATTGTCA
129 AAATGTG-ACT-TAAACTAGTAAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGATTGCCA
* **** * * * * *
3292992 AACTATTGGTGTAAATGTGTGACATGTAATGTAACAAGTCATTTATATCAAATAAACATAA
192 AAATATTCACAT-AATGTATAACATGTAACGTAACAAGTAAATTATATCAAATAAACATAA
* * *
3293053 TTTTTTTAAAAATTAAATATTTAAATTTTTATTCTCAAGTTTAAATTATATAATGGCTTACAAAT
1 TTTTTTTAAAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAAAT
* * * * * * *
3293118 TTGTAACATATAAATAAATAAAAGTAAGGAT-AAAATAAATTACAATGAAATTTAGTAGTTAAAA
66 TTGTAATATATAAATGAATAAAAGTAAAGATAAAAAT-AATTATAATAAAAATTAGTAGTTGAAA
*
3293182 AATGTTGACTTAAACTAGTTAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGATTGCCAAA
130 AATG-TGACTTAAACTAGTAAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGATTGCCAAA
* * *
3293247 ATATTCACATAATGTATAACATTTAACGTAATAAGTAAATTATGTCAAATAAACATAA
194 ATATTCACATAATGTATAACATGTAACGTAACAAGTAAATTATATCAAATAAACATAA
* * * * *
3293305 -TTGTTGAGAAAATTAAACATTTAAATTTTTATTTTCGAGTTTAAAGTATGTAATGGCTTACAAA
1 TTTTTTTA-AAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAAA
* * *
3293369 TTTGTAATATATAAATGAGTAAAAGTAAAGATAAAAATAATTATAGTAAAAATTATTAGTTGAAA
65 TTTGTAATATATAAATGAATAAAAGTAAAGATAAAAATAATTATAATAAAAATTAGTAGTTGAAA
* * * * * * * * * *
3293434 AACTTTGACATAAAGTACTAAGAACTAACAT-AGAGA--AT----GTCG---AAATATTG---AC
130 AA-TGTGACTTAAACTAGTAAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGATTGCCAAA
* * * * * ** * * * * * *
3293486 GTA---A-A-CATG--TGAGATTTAATATAAGAAGTCAATTATGTGAAATAAATATAT
194 ATATTCACATAATGTATAACATGTAACGTAACAAGTAAATTATATCAAATAAACATAA
** * * * ** **
3293537 TTTTTTTGAAAAATTAAA-ATCAAAATTTATATTCTCAAGTTTAAAGTATGCAATGGCCAATGAA
1 TTTTTTT-AAAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAAA
* * * *
3293601 TTT-T-A-ATATAAATGAATAAAAAT-AAGAATCAAAATAATTATAGTGAAAATTAGTAGTTGAA
65 TTTGTAATATATAAATGAATAAAAGTAAAG-ATAAAAATAATTATAATAAAAATTAGTAGTTGAA
* * * * * * *
3293662 AAATGTTGACGTAAAGC-AATAAGAATTAACGTAAAAATTTATAAAAGTAGAATAAGGATTGTCA
129 AAATG-TGACTTAAA-CTAGTAAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGATTGCCA
* **** * * * * * * ** *
3293726 AAATATTGACATAAATGTGGGGCATTTAACATGATAAGTCATTTATGCCAAATAAAAAT-A
192 AAATATTCACAT-AATGTATAACATGTAACGTAACAAGTAAATTATATCAAATAAACATAA
*** * ** * *
3293786 TTTCTTGGGAAAATTAAAGATTTCTATTTTTATTCTCAAGTTTAAAGTATGTAACGGCTTACAAA
1 TTT-TTTTAAAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAAA
* * *
3293851 TTTGTAATATATAAAT-AAAAAAAGT-AAGAATAAAAATAATTATAATGAATATTAGTAGTTGAA
65 TTTGTAATATATAAATGAATAAAAGTAAAG-ATAAAAATAATTATAATAAAAATTAGTAGTTG-A
* * * *
3293914 AAACAT-TGACCTAAAGTAGTAAGAATTAATGTAAAAAATTAT-AAAGGCAGAAC-AAGATT-CA
128 AAA-ATGTGACTTAAACTAGTAAGAATTAACGTAAAAAATTATAAAAGTC-GAACAAAGATTGC-
* * * * * * * * *
3293975 TTAAAATATTGACATAAATGTGTGACATTTAACGTAATAAAT-CATTAATATCAAGTAAACATAA
190 -CAAAATATTCACAT-AATGTATAACATGTAACGTAACAAGTAAATT-ATATCAAATAAACATAA
* *** * * * *
3294039 TCTTCAAAAAAATTAAACATGTAAATATTTT-TTCTCTA-TCTTAAAGTAAAT-TAA-AGCTTAC
1 TTTTTTTAAAAATTAAACATTTAAAT-TTTTATTCTCAAGT-TTAAACT--ATGTAATGGCTTAC
* * * *
3294100 AAATTT-TAAT-T-TAAGAGTGAATAAAAGT-AAGAATAAGAACAATTATAGTGAAAATTAGTAG
62 AAATTTGTAATATATAA-A-TGAATAAAAGTAAAG-ATAAAAATAATTATAATAAAAATTAGTAG
* * *
3294161 TTGAAAAATCTTGA-TGTAAAAC-AGTAAGAATTAACGTAAAAAATTATAAAGGTGGAACAAAGA
124 TTGAAAAAT-GTGACT-T-AAACTAGTAAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGA
* ** * * * ** * * ** * *
3294224 TTGTCAAAGCATTGACCTAAACGGGTAAAATTTAACGTAACAAGTCGATTATGTTAAATAAACAT
186 TTGCCAAAATATTCACAT-AATGTATAACATGTAACGTAACAAGTAAATTATATCAAATAAACAT
3294289 AA
250 AA
** * * * *
3294291 TTTTTGAAAAAATTAAACATTTAAATTTATATTCTCAAGTTTAAAGTATGTAACGACTTACAAAT
1 TTTTTTTAAAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAAAT
* * ** * * * * *
3294356 TT-TAATCTAAAAACAAATAAAAGTAAGGA-AAAAATAATTATAGTGAAAATTAATAGTTAAAAA
66 TTGTAATATATAAATGAATAAAAGTAAAGATAAAAATAATTATAATAAAAATTAGTAGTT-GAAA
* * * * * *
3294419 ACAT-TGACGTAAAGCTA-TAAAAATTAACGAAAAAAATTAT-AAAGACGGAACAATGATTGTCA
130 A-ATGTGACTTAAA-CTAGTAAGAATTAACGTAAAAAATTATAAAAGTC-GAACAAAGATTGCCA
* * * ** * *
3294481 AAATA-TCA-ATGTATATGTATGAGAT-TGAACTTAGTAAGTTAATTATGTCAAATAAACATAA
192 AAATATTCACA--TA-ATGTATAACATGT-AACGTAACAAGTAAATTATATCAAATAAACATAA
* * **
3294542 -TATTTGAGAAAATTAAA-ATTTTAAATTTTTATTCTTGAGTTTAAA
1 TTTTTTTA-AAAATTAAACA-TTTAAATTTTTATTCTCAAGTTTAAA
3294587 TTATTTTAAT
Statistics
Matches: 1210, Mismatches: 244, Indels: 163
0.75 0.15 0.10
Matches are distributed among these distances:
228 4 0.00
229 70 0.06
230 3 0.00
231 1 0.00
232 74 0.06
233 13 0.01
234 4 0.00
235 1 0.00
236 4 0.00
239 9 0.01
242 10 0.01
245 5 0.00
246 1 0.00
248 3 0.00
249 17 0.01
250 91 0.08
251 172 0.14
252 561 0.46
253 151 0.12
254 15 0.01
255 1 0.00
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (251 bp):
TTTTTTTAAAAATTAAACATTTAAATTTTTATTCTCAAGTTTAAACTATGTAATGGCTTACAAAT
TTGTAATATATAAATGAATAAAAGTAAAGATAAAAATAATTATAATAAAAATTAGTAGTTGAAAA
ATGTGACTTAAACTAGTAAGAATTAACGTAAAAAATTATAAAAGTCGAACAAAGATTGCCAAAAT
ATTCACATAATGTATAACATGTAACGTAACAAGTAAATTATATCAAATAAACATAA
Found at i:3294832 original size:25 final size:23
Alignment explanation
Indices: 3294786--3294886 Score: 61
Period size: 25 Copynumber: 4.4 Consensus size: 23
3294776 TACATTATTG
*
3294786 TTAAAATTAAAAATAATGAAATT
1 TTAAAATTAAAAATAATAAAATT
*
3294809 TTAATATTAAAAATATAATAAAATAT
1 TTAAAATT-AAAA-ATAATAAAAT-T
* *
3294835 AATAAAA-TAAAAATTAAATAACA-T
1 -TTAAAATTAAAAA-T-AATAAAATT
*
3294859 TT-AAAGT-AAAATAAT-AAA-T
1 TTAAAATTAAAAATAATAAAATT
3294878 TTAAAATTA
1 TTAAAATTA
3294887 TCTAAGTTGT
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
19 5 0.08
20 7 0.11
21 1 0.02
22 7 0.11
23 9 0.15
24 6 0.10
25 14 0.23
26 8 0.13
27 4 0.07
ACGTcount: A:0.63, C:0.01, G:0.02, T:0.34
Consensus pattern (23 bp):
TTAAAATTAAAAATAATAAAATT
Found at i:3294833 original size:10 final size:10
Alignment explanation
Indices: 3294818--3294843 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3294808 TTTAATATTA
3294818 AAAATATAAT
1 AAAATATAAT
3294828 AAAATATAAT
1 AAAATATAAT
3294838 AAAATA
1 AAAATA
3294844 AAAATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (10 bp):
AAAATATAAT
Found at i:3304053 original size:11 final size:11
Alignment explanation
Indices: 3304037--3304091 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
3304027 TTTTTAAAAT
*
3304037 TATTATTATTA
1 TATTTTTATTA
3304048 TATTATTT-TTA
1 TATT-TTTATTA
3304059 T-TTTTTATT-
1 TATTTTTATTA
3304068 TATTTTTGATTA
1 TATTTTT-ATTA
3304080 -ATTTTTATTA
1 TATTTTTATTA
3304090 TA
1 TA
3304092 AATATATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
9 4 0.11
10 13 0.35
11 18 0.49
12 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TATTTTTATTA
Found at i:3304067 original size:21 final size:21
Alignment explanation
Indices: 3304042--3304091 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
3304032 AAAATTATTA
*
3304042 TTATTATATTATTT-TTATTTT
1 TTATTATATT-TTTATTAATTT
3304063 TTATT-TATTTTTGATTAATTT
1 TTATTATATTTTT-ATTAATTT
3304084 TTATTATA
1 TTATTATA
3304092 AATATATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 4 0.16
21 16 0.64
22 2 0.08
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (21 bp):
TTATTATATTTTTATTAATTT
Found at i:3310726 original size:17 final size:17
Alignment explanation
Indices: 3310704--3310738 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3310694 TATTCGAACC
3310704 TCATCATGCACAACGTT
1 TCATCATGCACAACGTT
*
3310721 TCATCATGCACAATGTT
1 TCATCATGCACAACGTT
3310738 T
1 T
3310739 ACTGTCGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (17 bp):
TCATCATGCACAACGTT
Found at i:3316759 original size:15 final size:16
Alignment explanation
Indices: 3316741--3316773 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3316731 TTTTGTATTA
3316741 TTATTGTTATCAT-AT
1 TTATTGTTATCATCAT
3316756 TTATTGTTATCATCAT
1 TTATTGTTATCATCAT
3316772 TT
1 TT
3316774 CCTTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (16 bp):
TTATTGTTATCATCAT
Found at i:3317058 original size:2 final size:2
Alignment explanation
Indices: 3317051--3317102 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3317041 TATCTATTAT
3317051 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3317093 AC AC AC AC AC
1 AC AC AC AC AC
3317103 CTATGTGAAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3317400 original size:15 final size:16
Alignment explanation
Indices: 3317370--3317405 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3317360 CTGCTAAATG
*
3317370 TTTATTTTTATTATTT
1 TTTATTATTATTATTT
3317386 TTTATTATT-TTATTT
1 TTTATTATTATTATTT
3317401 TTTAT
1 TTTAT
3317406 CCTATATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTATTATTATTATTT
Found at i:3320199 original size:16 final size:16
Alignment explanation
Indices: 3320178--3320215 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
3320168 GAAAAAACTA
3320178 GAGTTGGTCTCAGACC
1 GAGTTGGTCTCAGACC
3320194 GAGTTGGTCTCAGACC
1 GAGTTGGTCTCAGACC
*
3320210 AAGTTG
1 GAGTTG
3320216 CAAACAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (16 bp):
GAGTTGGTCTCAGACC
Found at i:3320672 original size:41 final size:41
Alignment explanation
Indices: 3320594--3320674 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
3320584 AATCTAAATC
* * *
3320594 TATCATAACATATTATATCTTAATAATCTAGCCTAATAGCT
1 TATCATAACATATTATATCTCAACAATCTAACCTAATAGCT
* *
3320635 TATCATAATATATTATATCTCAACAAT-TCAACTTAATAGC
1 TATCATAACATATTATATCTCAACAATCT-AACCTAATAGC
3320675 ACAATATGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 33 0.97
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (41 bp):
TATCATAACATATTATATCTCAACAATCTAACCTAATAGCT
Found at i:3322503 original size:27 final size:26
Alignment explanation
Indices: 3322472--3322523 Score: 95
Period size: 27 Copynumber: 2.0 Consensus size: 26
3322462 ACAGAATAGA
3322472 TAAAAATAAAATAAAATAATTATTATG
1 TAAAAATAAAATAAAATAA-TATTATG
3322499 TAAAAATAAAATAAAATAATATTAT
1 TAAAAATAAAATAAAATAATATTAT
3322524 ATAATTTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
TAAAAATAAAATAAAATAATATTATG
Found at i:3322733 original size:22 final size:22
Alignment explanation
Indices: 3322658--3322735 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
3322648 TATATATGAT
* * *
3322658 TATTTTATTTTTTAAACATTAA
1 TATTTTATTTATAAAATATTAA
*
3322680 TATTTTATTTAT--AAT-CTAA
1 TATTTTATTTATAAAATATTAA
**
3322699 TCATTAGCA-TTATAAAATATTAA
1 T-ATT-TTATTTATAAAATATTAA
3322722 TATTTTATTTATAA
1 TATTTTATTTATAA
3322736 TTTAAATATT
Statistics
Matches: 42, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 4 0.10
20 9 0.21
21 2 0.05
22 23 0.55
23 4 0.10
ACGTcount: A:0.40, C:0.05, G:0.01, T:0.54
Consensus pattern (22 bp):
TATTTTATTTATAAAATATTAA
Found at i:3322741 original size:27 final size:26
Alignment explanation
Indices: 3322711--3322798 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 26
3322701 ATTAGCATTA
3322711 TAAAATATTAATATTTTATTTATAATT
1 TAAAATATTAATATTTTATTTAT-ATT
* *
3322738 T-AAATATTATTATAATTATTTAT-TT
1 TAAAATATTAATAT-TTTATTTATATT
* *
3322763 TTAAATATTAATGATTTATAATT-TATT
1 TAAAATATTAAT-ATTT-TATTTATATT
3322790 TAAAATATT
1 TAAAATATT
3322799 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
25 3 0.06
26 22 0.44
27 25 0.50
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (26 bp):
TAAAATATTAATATTTTATTTATATT
Found at i:3322742 original size:26 final size:25
Alignment explanation
Indices: 3322713--3322798 Score: 84
Period size: 26 Copynumber: 3.3 Consensus size: 25
3322703 TAGCATTATA
3322713 AAATATTAATATTTTATTTATAATTT
1 AAATATTAATATTTTATTTAT-ATTT
* * *
3322739 AAATATTATTATAATTATTTATTTTT
1 AAATATTAATAT-TTTATTTATATTT
*
3322765 AAATATTAATGATTTATAATTTAT-TTA
1 AAATATTAAT-ATTT-T-ATTTATATTT
3322792 AAATATT
1 AAATATT
3322799 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 24 0.48
27 20 0.40
28 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (25 bp):
AAATATTAATATTTTATTTATATTT
Found at i:3322962 original size:27 final size:28
Alignment explanation
Indices: 3322906--3322963 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
3322896 ATTTATTTTC
* *
3322906 ATTTTATTTTATTTTTTAAATATCATTA
1 ATTTTATTTTATTTTATAAATATCAATA
*
3322934 ATTTATATTTTA-TTTAT-AATATTAATA
1 ATTT-TATTTTATTTTATAAATATCAATA
3322961 ATT
1 ATT
3322964 CATCATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 11 0.42
28 8 0.31
29 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
ATTTTATTTTATTTTATAAATATCAATA
Found at i:3324253 original size:16 final size:16
Alignment explanation
Indices: 3324232--3324262 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3324222 TTAGGGAGCT
3324232 TTTTCGTTTCTAACTA
1 TTTTCGTTTCTAACTA
3324248 TTTTCGTTTCTAACT
1 TTTTCGTTTCTAACT
3324263 GTCTTCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (16 bp):
TTTTCGTTTCTAACTA
Found at i:3325866 original size:30 final size:30
Alignment explanation
Indices: 3325832--3325896 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
3325822 TGACTTGGGT
* **
3325832 CTATGCTACTTTTGAATTTTGTGTATCAAG
1 CTATGATACTTTTGAATTTTGCCTATCAAG
3325862 CTATGATACTTTTGAATTTTGCCTATCAAG
1 CTATGATACTTTTGAATTTTGCCTATCAAG
3325892 C-ATGA
1 CTATGA
3325897 GAGAAATAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (30 bp):
CTATGATACTTTTGAATTTTGCCTATCAAG
Found at i:3331863 original size:26 final size:26
Alignment explanation
Indices: 3331834--3331904 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
3331824 AGGCTCGTAA
* *
3331834 GAAATACTTTCTACTGAAAATTT-ATT
1 GAAA-ACTTTCAACAGAAAATTTCATT
*
3331860 GAAAATTTTCAACAGAAAATTTCATT
1 GAAAACTTTCAACAGAAAATTTCATT
* * *
3331886 GAAAAATCTCATCAGAAAA
1 GAAAACTTTCAACAGAAAA
3331905 AGTACATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 15 0.39
26 23 0.61
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.32
Consensus pattern (26 bp):
GAAAACTTTCAACAGAAAATTTCATT
Found at i:3331869 original size:25 final size:26
Alignment explanation
Indices: 3331849--3331904 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
3331839 ACTTTCTACT
3331849 GAAAATTT-ATTGAAAATTTTCAACA
1 GAAAATTTCATTGAAAATTTTCAACA
* * *
3331874 GAAAATTTCATTGAAAAATCTCATCA
1 GAAAATTTCATTGAAAATTTTCAACA
3331900 GAAAA
1 GAAAA
3331905 AGTACATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (26 bp):
GAAAATTTCATTGAAAATTTTCAACA
Found at i:3354518 original size:14 final size:13
Alignment explanation
Indices: 3354502--3354526 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3354492 TATTATTTAT
3354502 TTTTAAATGGATA
1 TTTTAAATGGATA
3354515 TTTTAAATGGAT
1 TTTTAAATGGAT
3354527 CAAATTTAAG
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:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAAATGGATA
Found at i:3355577 original size:92 final size:93
Alignment explanation
Indices: 3355416--3355585 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
3355406 CTTGCCTTAG
* * *
3355416 GTAAGTTGGTTGTAATTTTTTTACTTACAAGGAAACCTAGGATTTACTTACCATGAATTAAAGTC
1 GTAAGTTGGCTGTAACTTTTTTACTTACAAGGAAACCCAGGATTTACTTACCATGAATTAAAGTC
3355481 TTACTCTTTTTGGCCCTTGCCTTATACA
66 TTACTCTTTTTGGCCCTTGCCTTATACA
* * *
3355509 GTAAGTTGGCTGTAACTTTTTT-CTTACAAGGAAACCCAGGATTTACTTACCATGAATTGATGTG
1 GTAAGTTGGCTGTAACTTTTTTACTTACAAGGAAACCCAGGATTTACTTACCATGAATTAAAGTC
3355573 TTACTCTTTTTGG
66 TTACTCTTTTTGG
3355586 ATTGCTAGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 51 0.72
93 20 0.28
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (93 bp):
GTAAGTTGGCTGTAACTTTTTTACTTACAAGGAAACCCAGGATTTACTTACCATGAATTAAAGTC
TTACTCTTTTTGGCCCTTGCCTTATACA
Found at i:3357281 original size:3 final size:3
Alignment explanation
Indices: 3357273--3357305 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
3357263 AATAATGCAG
3357273 TAA TAA TAA TACA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
3357306 ATACAAGAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.86
4 2 0.07
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3357292 original size:12 final size:13
Alignment explanation
Indices: 3357263--3357310 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
3357253 AACAAAAAGA
*
3357263 AATAATGCAGTAAT
1 AATAATACA-TAAT
3357277 AATAATACAT-AT
1 AATAATACATAAT
3357289 AATAATA-ATAAT
1 AATAATACATAAT
3357301 AATAAATACA
1 AAT-AATACA
3357311 AGAGGGAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 2 0.07
12 14 0.47
13 5 0.17
14 9 0.30
ACGTcount: A:0.60, C:0.06, G:0.04, T:0.29
Consensus pattern (13 bp):
AATAATACATAAT
Found at i:3357817 original size:2 final size:2
Alignment explanation
Indices: 3357810--3357838 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3357800 TTAAGAAATG
3357810 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 A
3357839 GATGGATGAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3361325 original size:30 final size:30
Alignment explanation
Indices: 3361281--3361347 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
3361271 TCAATCAAGC
*
3361281 CTTTT-TACTTTTATTTTGAACT-AAATAAA
1 CTTTTATATTTTTATTTTG-ACTCAAATAAA
* *
3361310 TTTTTATATTTTTATTTTGAGTCAAATAAA
1 CTTTTATATTTTTATTTTGACTCAAATAAA
3361340 CTTTTATA
1 CTTTTATA
3361348 ACTAATGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 6 0.19
30 26 0.81
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.55
Consensus pattern (30 bp):
CTTTTATATTTTTATTTTGACTCAAATAAA
Found at i:3371559 original size:18 final size:20
Alignment explanation
Indices: 3371526--3371563 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
3371516 AATGACATAA
3371526 TATTTAGAAAATTTTTAAAT
1 TATTTAGAAAATTTTTAAAT
3371546 TATTTA-AAAA-TTTTAAAT
1 TATTTAGAAAATTTTTAAAT
3371564 AAAATTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (20 bp):
TATTTAGAAAATTTTTAAAT
Found at i:3372892 original size:19 final size:18
Alignment explanation
Indices: 3372847--3372894 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
3372837 TATGAATTAA
3372847 AATTTGTAAATCAATAAAT
1 AATTT-TAAATCAATAAAT
* *
3372866 ACTTTTAACTCAATAACAT
1 AATTTTAAATCAATAA-AT
3372885 AATTTTAAAT
1 AATTTTAAAT
3372895 GTTTAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTTTAAATCAATAAAT
Found at i:3373194 original size:253 final size:250
Alignment explanation
Indices: 3372631--3373442 Score: 910
Period size: 253 Copynumber: 3.2 Consensus size: 250
3372621 TTGGCTTGGT
* *
3372631 AATATAAATTTAATTTTTTAATTTGCACAAAAATTATATTTATTTTGACTTAATTGACTTT-TTA
1 AATATAAATTTAAATTTTTATTTTGCACAAAAATTATATTTATTTTGACTTAATTGA-TTTGTTA
* * * *
3372695 TGTTAAATCTCACACATTT-AGT-AAGTATTTTAACAATGTTTGTTTCACCTTTATAATTTTTTA
65 TGTTAAATCTCACAAATTTAAGTCAA-TATTTTAACAATGATTGTTCCATCTTTATAATTTTTTA
* * *
3372758 CATTAACTT-TCACAAGTTTATGTTAAGGTTTTTCAATTGCTAATTTCAACTATATT-TTTAATC
129 CATTAA-TTCTTACAAGTTTATGTTAAGATTTTTCAATTGCTAATTTCAA-TATATTATTTTATC
* * * * * *
3372821 CCTATTTTTATTCATTTATGAATTAAAATTTGTAAATCAATAAATACTTTTAACTCAAT-
192 CTTATTATTATTCATTTATAAATTAAAATTTGTAAATC-ATAAATAATTTTAGCTCTATG
* * * *
3372880 AACATAATTTTAAATGTTTAATATT-CACAAAAATTATATTTATTTTGACTTAATTGATTTGTTA
1 AATATAAATTTAAAT-TTTTATTTTGCACAAAAATTATATTTATTTTGACTTAATTGATTTGTTA
*
3372944 TGTTATATCTCACAAATTTAAGTCAATATTTTAACAATGATTGTTCCATCTTTATAATTTTTTAC
65 TGTTAAATCTCACAAATTTAAGTCAATATTTTAACAATGATTGTTCCATCTTTATAATTTTTTAC
* * *
3373009 ATTAATTCTTACAGGTTTTTGTTAAGATTTTT-AACTTTCTAAGTTTGACAATA-ATTATCTTTA
130 ATTAATTCTTACAAGTTTATGTTAAGATTTTTCAA-TTGCTAA-TTT--CAATATATTAT-TTTA
* * * * *
3373072 TCCTTATTATTATTTATTTATAAATAAAAATTTATAAATCATCACATAAATTTAGCT-TATG
190 TCCTTATTATTATTCATTTATAAATTAAAATTTGTAAATCAT-AAATAATTTTAGCTCTATG
* * * *
3373133 AATATAAATTTAAATTTTTATTTTGCACAAAGATTAGATTCATTTTGATTTAATTGATTTGTTAT
1 AATATAAATTTAAATTTTTATTTTGCACAAAAATTATATTTATTTTGACTTAATTGATTTGTTAT
* * * * *
3373198 GTTAAATCTCATATATTTAAATCAATATTTTAACAATGCTTGTTCCATCTTTATAATTTTTTACG
66 GTTAAATCTCACAAATTTAAGTCAATATTTTAACAATGATTGTTCCATCTTTATAATTTTTTACA
* * * * ** * * *
3373263 TCACTCCTTATAAGTTTACATCAAGATTTTTCAATTGCTAATTTTCAATATGATTATTTTTGTTC
131 TTAATTCTTACAAGTTTATGTTAAGATTTTTCAATTGCTAA-TTTCAATAT-ATTA-TTTTATCC
* * *
3373328 TTATTATTATTCCTTTATAAATTAAAATTTGTAAATTATTAAATCATTTTAGCTCTA-G
193 TTATTATTATTCATTTATAAATTAAAATTTGTAAATCA-TAAATAATTTTAGCTCTATG
* * * *
3373386 AATATAAATAT-AATTGTTTATTTTTCATAAAAATTAAATTTATTTTGACTTAATTGA
1 AATATAAATTTAAATT-TTTATTTTGCACAAAAATTATATTTATTTTGACTTAATTGA
3373443 CTTTTTACTT
Statistics
Matches: 472, Mismatches: 70, Indels: 38
0.81 0.12 0.07
Matches are distributed among these distances:
248 3 0.01
249 68 0.14
250 76 0.16
251 13 0.03
252 18 0.04
253 288 0.61
254 6 0.01
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (250 bp):
AATATAAATTTAAATTTTTATTTTGCACAAAAATTATATTTATTTTGACTTAATTGATTTGTTAT
GTTAAATCTCACAAATTTAAGTCAATATTTTAACAATGATTGTTCCATCTTTATAATTTTTTACA
TTAATTCTTACAAGTTTATGTTAAGATTTTTCAATTGCTAATTTCAATATATTATTTTATCCTTA
TTATTATTCATTTATAAATTAAAATTTGTAAATCATAAATAATTTTAGCTCTATG
Found at i:3374035 original size:14 final size:13
Alignment explanation
Indices: 3373996--3374043 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
3373986 CGTATTTAAC
3373996 TATTTATATTTTA
1 TATTTATATTTTA
*
3374009 TAAATTATAATTTTA
1 T-ATTTAT-ATTTTA
3374024 TATTTAGTATTTTA
1 TATTTA-TATTTTA
*
3374038 AATTTA
1 TATTTA
3374044 AAGAGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.03
14 20 0.69
15 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATTTATATTTTA
Found at i:3387365 original size:18 final size:20
Alignment explanation
Indices: 3387342--3387380 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3387332 ATATGACCTG
3387342 TTTCATG-ATAAA-TAAATC
1 TTTCATGCATAAATTAAATC
3387360 TTTCATGCTATAAATTAAATC
1 TTTCATGC-ATAAATTAAATC
3387381 CAATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.39
20 5 0.28
21 6 0.33
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (20 bp):
TTTCATGCATAAATTAAATC
Found at i:3390262 original size:16 final size:16
Alignment explanation
Indices: 3390241--3390282 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
3390231 TTTGTCCTAT
3390241 TACCTTTAACGTATCC
1 TACCTTTAACGTATCC
3390257 TACCTTTAACGTATCC
1 TACCTTTAACGTATCC
*
3390273 TTCCTTTAAC
1 TACCTTTAAC
3390283 TGTACTATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.05, T:0.40
Consensus pattern (16 bp):
TACCTTTAACGTATCC
Found at i:3392397 original size:2 final size:2
Alignment explanation
Indices: 3392390--3392416 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3392380 AGCAATATGC
3392390 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 A
3392417 AACAAGCCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.