Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011701.1 Kokia drynarioides strain JFW-HI SEQ_126695, 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: 550108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 160 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:391734 original size:23 final size:23
Alignment explanation
Indices: 391686--391737 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
391676 TACAATATTC
* *
391686 AAATAATATTAAAAAAGACAACA
1 AAATAATAGTAAAAAAGACAAAA
*
391709 AAATAATAGTAAAAACG-CATAAA
1 AAATAATAGTAAAAAAGACA-AAA
391732 AAATAA
1 AAATAA
391738 CATCAAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (23 bp):
AAATAATAGTAAAAAAGACAAAA
Found at i:391756 original size:23 final size:23
Alignment explanation
Indices: 391730--391791 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
391720 AAAACGCATA
*
391730 AAAAATAACATCAAAACAACAAC
1 AAAAATAACAACAAAACAACAAC
* * * *
391753 AAAAATAACAGCAAGACAATAAT
1 AAAAATAACAACAAAACAACAAC
*
391776 AAAAACAACAACAAAA
1 AAAAATAACAACAAAA
391792 ATAATAATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08
Consensus pattern (23 bp):
AAAAATAACAACAAAACAACAAC
Found at i:391791 original size:12 final size:12
Alignment explanation
Indices: 391742--391809 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 12
391732 AAATAACATC
391742 AAAACAACAACA
1 AAAACAACAACA
* *
391754 AAAATAACAGC-
1 AAAACAACAACA
* * *
391765 AAGACAATAATA
1 AAAACAACAACA
391777 AAAACAACAACA
1 AAAACAACAACA
* * *
391789 AAAATAATAATA
1 AAAACAACAACA
391801 AAAACAACA
1 AAAACAACA
391810 CCAATCAATA
Statistics
Matches: 40, Mismatches: 15, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
11 6 0.15
12 34 0.85
ACGTcount: A:0.72, C:0.16, G:0.03, T:0.09
Consensus pattern (12 bp):
AAAACAACAACA
Found at i:391796 original size:21 final size:20
Alignment explanation
Indices: 391770--391824 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
391760 ACAGCAAGAC
391770 AATAATAAAAACAACAACAAA
1 AATAATAAAAA-AACAACAAA
**
391791 AATAATAATAAAAACAACACC
1 AATAATAA-AAAAACAACAAA
391812 AATCAATAAAAAA
1 AAT-AATAAAAAA
391825 CAGTAACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.13
Consensus pattern (20 bp):
AATAATAAAAAAACAACAAA
Found at i:391873 original size:21 final size:21
Alignment explanation
Indices: 391842--391881 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
391832 CAAATTAGTA
391842 AAAAAATAACAACCAAAACAGT
1 AAAAAATAAC-ACCAAAACAGT
*
391864 AAAAAA-AACATCAAAACA
1 AAAAAATAACACCAAAACA
391882 ATAATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.72, C:0.17, G:0.03, T:0.07
Consensus pattern (21 bp):
AAAAAATAACACCAAAACAGT
Found at i:399414 original size:15 final size:15
Alignment explanation
Indices: 399394--399430 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
399384 TAAATCTTAG
*
399394 ATTATATATTTAAAT
1 ATTATATATATAAAT
*
399409 ATTATAAATATAAAT
1 ATTATATATATAAAT
399424 ATTATAT
1 ATTATAT
399431 TTAAACATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATATATATAAAT
Found at i:401073 original size:27 final size:28
Alignment explanation
Indices: 401038--401093 Score: 96
Period size: 27 Copynumber: 2.0 Consensus size: 28
401028 ATCTACCGAT
*
401038 TAACGAATAATGCGATAAAGATCGCCAA
1 TAACGAATAACGCGATAAAGATCGCCAA
401066 TAAC-AATAACGCGATAAAGATCGCCAA
1 TAACGAATAACGCGATAAAGATCGCCAA
401093 T
1 T
401094 CCCCTCTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (28 bp):
TAACGAATAACGCGATAAAGATCGCCAA
Found at i:411394 original size:254 final size:254
Alignment explanation
Indices: 410945--411407 Score: 811
Period size: 254 Copynumber: 1.8 Consensus size: 254
410935 GTCATTTCAC
* * * *
410945 ACACTTCAATTTACAACATTAAAAAACCTCCACTCACATCAATTTAACACTTCATATTTATAACC
1 ACACTTCAATTGACAACATTAAAAAACCTCCACTCACAACAATTAAACACTTCAAATTTATAACC
411010 TTTAATCAACTCAATTTACAGCATTTAAACACCTCCATTTATAGCAACTAAACACTTCAATTTAT
66 TTTAATCAACTCAATTTACAGCATTTAAACACCTCCATTTATAGCAACTAAACACTTCAATTTAT
* *
411075 AGCCTTTAATCAACTCAATTTACAGCATTTATACACCTCAAGTTACAACACTTAAACTCTTCAAT
131 AGCCTTTAATCAACTCAATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCTTCAAT
411140 TTACAGCATTTAAAGACCTCCATTTACAGCGTTTAAACACCTCAAATTAAAGCACCTAA
196 TTACAGCATTTAAAGACCTCCATTTACAGCGTTTAAACACCTCAAATTAAAGCACCTAA
* * * *
411199 ACACTTCAATTGACAACATTTAAACACCTCCATTCACAACAATTAAACACTTCAAATTTATGGA-
1 ACACTTCAATTGACAACATTAAAAAACCTCCACTCACAACAATTAAACACTTCAAATTTAT-AAC
*
411263 CTTTAATCAACTCAATTTACAGCATTTAAACACCTCCATTTATAGGAACTAAACACTTCAATTTA
65 CTTTAATCAACTCAATTTACAGCATTTAAACACCTCCATTTATAGCAACTAAACACTTCAATTTA
411328 TAGCCTTTAATCAACTCAATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCTTCAA
130 TAGCCTTTAATCAACTCAATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCTTCAA
411393 TTTACAGCATTTAAA
195 TTTACAGCATTTAAA
411408 CACCATTTAC
Statistics
Matches: 197, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
254 196 0.99
255 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.32
Consensus pattern (254 bp):
ACACTTCAATTGACAACATTAAAAAACCTCCACTCACAACAATTAAACACTTCAAATTTATAACC
TTTAATCAACTCAATTTACAGCATTTAAACACCTCCATTTATAGCAACTAAACACTTCAATTTAT
AGCCTTTAATCAACTCAATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCTTCAAT
TTACAGCATTTAAAGACCTCCATTTACAGCGTTTAAACACCTCAAATTAAAGCACCTAA
Found at i:411436 original size:112 final size:113
Alignment explanation
Indices: 411274--411491 Score: 350
Period size: 112 Copynumber: 1.9 Consensus size: 113
411264 TTTAATCAAC
* * *
411274 TCAATTTACAGCATTTAAACACCTCCATTTATAGGAACTAAACACTTCAA-TTTATAGCCTTTAA
1 TCAATTTACAGCATTTAAACA-C-CCATTTACAGCAACTAAACACTTCAATTTTATAACCTTTAA
411338 TCAACTCAATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCT
64 TCAACTC-ATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCT
411389 TCAATTTACAGCATTTAAACA-CCATTTACAGCAACTAAACACTTCAATTTTATAACCTTTAATC
1 TCAATTTACAGCATTTAAACACCCATTTACAGCAACTAAACACTTCAATTTTATAACCTTTAATC
* *
411453 AACTCATTTACAGCATTTAAACACCTCCATTTACAACAA
66 AACTCATTTACAGCATTTAAACACCTCAAGTTACAACAA
411492 GGTTTAGCTA
Statistics
Matches: 97, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
112 56 0.58
113 20 0.21
115 21 0.22
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.32
Consensus pattern (113 bp):
TCAATTTACAGCATTTAAACACCCATTTACAGCAACTAAACACTTCAATTTTATAACCTTTAATC
AACTCATTTACAGCATTTAAACACCTCAAGTTACAACAATTAAACTCT
Found at i:411486 original size:23 final size:23
Alignment explanation
Indices: 411010--411487 Score: 354
Period size: 23 Copynumber: 20.9 Consensus size: 23
411000 ATTTATAACC
* *
411010 TTTAATCAACTCAATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
* *
411033 TTTAAACACCTCCATTTATAGCA
1 TTTAAACACCTCAATTTACAGCA
** * * *
411056 ACTAAACACTTCAATTTATAGCC
1 TTTAAACACCTCAATTTACAGCA
* *
411079 TTTAATCAACTCAATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
* * *
411102 TTTATACACCTCAAGTTACAACA
1 TTTAAACACCTCAATTTACAGCA
* * *
411125 CTTAAACTCTTCAATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
* * *
411148 TTTAAAGACCTCCATTTACAGCG
1 TTTAAACACCTCAATTTACAGCA
* *
411171 TTTAAACACCTCAAATTAAAGCA
1 TTTAAACACCTCAATTTACAGCA
** * * *
411194 CCTAAACACTTCAATTGACAACA
1 TTTAAACACCTCAATTTACAGCA
* * *
411217 TTTAAACACCTCCATTCACAACA
1 TTTAAACACCTCAATTTACAGCA
* * * *
411240 ATTAAACACTTCAAATTTA-TGGA
1 TTTAAACACCTC-AATTTACAGCA
* *
411263 CTTTAATCAACTCAATTTACAGCA
1 -TTTAAACACCTCAATTTACAGCA
* * *
411287 TTTAAACACCTCCATTTATAGGA
1 TTTAAACACCTCAATTTACAGCA
** * * *
411310 ACTAAACACTTCAATTTATAGCC
1 TTTAAACACCTCAATTTACAGCA
* *
411333 TTTAATCAACTCAATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
* *
411356 TTTAAACACCTCAAGTTACAACA
1 TTTAAACACCTCAATTTACAGCA
* * *
411379 ATTAAACTCTTCAATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
411402 TTTAAACA-C-C-ATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
** * * * *
411422 ACTAAACACTTCAATTTTATAACC
1 TTTAAACACCTCAA-TTTACAGCA
* *
411446 TTTAATCAACTC-ATTTACAGCA
1 TTTAAACACCTCAATTTACAGCA
*
411468 TTTAAACACCTCCATTTACA
1 TTTAAACACCTCAATTTACA
411488 ACAAGGTTTA
Statistics
Matches: 338, Mismatches: 109, Indels: 16
0.73 0.24 0.03
Matches are distributed among these distances:
20 16 0.05
21 1 0.00
22 17 0.05
23 277 0.82
24 27 0.08
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (23 bp):
TTTAAACACCTCAATTTACAGCA
Found at i:426610 original size:18 final size:18
Alignment explanation
Indices: 426599--426644 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
426589 CTATGTTGAT
426599 TCAAGTGTCTATTCTGAC
1 TCAAGTGTCTATTCTGAC
426617 TCAAGTGTCTATTCTGAC
1 TCAAGTGTCTATTCTGAC
426635 TCAAGTGTCT
1 TCAAGTGTCT
426645 CATACCAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (18 bp):
TCAAGTGTCTATTCTGAC
Found at i:429212 original size:46 final size:46
Alignment explanation
Indices: 429160--429283 Score: 203
Period size: 46 Copynumber: 2.7 Consensus size: 46
429150 TGGTATGAAT
*
429160 TGTATATATATTGCATGTGAACATATGTTATGCAAACCTTGATAAA
1 TGTATATATATTGCATGCGAACATATGTTATGCAAACCTTGATAAA
* * *
429206 TGTATATATATTGCATGCGAACATATGTTATGCGAACCTTGTTTAA
1 TGTATATATATTGCATGCGAACATATGTTATGCAAACCTTGATAAA
*
429252 TGTATATATATTGCATGCGAACATATATTATG
1 TGTATATATATTGCATGCGAACATATGTTATG
429284 TGCGAACACT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (46 bp):
TGTATATATATTGCATGCGAACATATGTTATGCAAACCTTGATAAA
Found at i:443868 original size:49 final size:49
Alignment explanation
Indices: 443761--443890 Score: 138
Period size: 49 Copynumber: 2.7 Consensus size: 49
443751 ACGGAGGAAG
* * * * *
443761 TATCTGGCCGTAAATCTGCACTATCTGGTGGCTTATCCACAATATTCTA
1 TATCTGGCAGTAAATTTGCACTATTTGGTGGCTAAACCACAATATTCTA
* * *
443810 TATCTGGCAGTAAATTTGCATTATTTGGTGGCTAAACCACAATATTTTG
1 TATCTGGCAGTAAATTTGCACTATTTGGTGGCTAAACCACAATATTCTA
* *
443859 T-TTTCGGCAGCTCAA-TTGCACTATTTGGTGGC
1 TATCT-GGCAG-TAAATTTGCACTATTTGGTGGC
443891 CGGTCCACAA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 2 0.03
49 63 0.93
50 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (49 bp):
TATCTGGCAGTAAATTTGCACTATTTGGTGGCTAAACCACAATATTCTA
Found at i:444214 original size:17 final size:16
Alignment explanation
Indices: 444190--444225 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
444180 ATAATCGAGG
444190 TTACGATGGGCTCGAC
1 TTACGATGGGCTCGAC
444206 TTACAGATGGGCTCGAC
1 TTAC-GATGGGCTCGAC
444223 TTA
1 TTA
444226 ATTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (16 bp):
TTACGATGGGCTCGAC
Found at i:445683 original size:85 final size:85
Alignment explanation
Indices: 445579--445747 Score: 284
Period size: 85 Copynumber: 2.0 Consensus size: 85
445569 ATTACTCACA
* * *
445579 TCCAAGTCAATTTTACTTTATAAGGTAATGGTTACATTTCAATTTTATCCCTCTATTCTTTTAAG
1 TCCAAGTCAATGTTACTTTATAAAGTAATGGTTACATTTCAATTTTATCCCTCTATCCTTTTAAG
445644 ATTATATAACAATGGTCAAG
66 ATTATATAACAATGGTCAAG
* *
445664 TCCAAGTCAATGTTACTTTATAAAGTAATGGTTACATTTTAATTTTATGCCTCTATCCTTTTAAG
1 TCCAAGTCAATGTTACTTTATAAAGTAATGGTTACATTTCAATTTTATCCCTCTATCCTTTTAAG
*
445729 ATTATATAATAATGGTCAA
66 ATTATATAACAATGGTCAA
445748 AATTTAGTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
85 78 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (85 bp):
TCCAAGTCAATGTTACTTTATAAAGTAATGGTTACATTTCAATTTTATCCCTCTATCCTTTTAAG
ATTATATAACAATGGTCAAG
Found at i:445862 original size:19 final size:19
Alignment explanation
Indices: 445838--445882 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
445828 AAATTTTTAC
445838 AATATTATTAGT-TAATCAA
1 AATATT-TTAGTCTAATCAA
* *
445857 AATATTTTATTCTAATTAA
1 AATATTTTAGTCTAATCAA
445876 AATATTT
1 AATATTT
445883 ATGTGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
AATATTTTAGTCTAATCAA
Found at i:446099 original size:29 final size:30
Alignment explanation
Indices: 446049--446116 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 30
446039 AACAACTAGA
* ** *
446049 ATTAAAATTTTAAATTTGAAAAGCA-AAGAG
1 ATTAAATTTTTAAAAATGAAAAACATAA-AG
*
446079 ATTAAATTTTTAAAAAT-AAAAATATAAAG
1 ATTAAATTTTTAAAAATGAAAAACATAAAG
446108 ATTAAATTT
1 ATTAAATTT
446117 CAAATATATG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.35
Consensus pattern (30 bp):
ATTAAATTTTTAAAAATGAAAAACATAAAG
Found at i:448379 original size:33 final size:33
Alignment explanation
Indices: 448337--448410 Score: 148
Period size: 33 Copynumber: 2.2 Consensus size: 33
448327 TGGTACACAT
448337 GGGAGAGAGGGAGATTGGCATCCAACAACATTA
1 GGGAGAGAGGGAGATTGGCATCCAACAACATTA
448370 GGGAGAGAGGGAGATTGGCATCCAACAACATTA
1 GGGAGAGAGGGAGATTGGCATCCAACAACATTA
448403 GGGAGAGA
1 GGGAGAGA
448411 CTAGATAGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.36, T:0.14
Consensus pattern (33 bp):
GGGAGAGAGGGAGATTGGCATCCAACAACATTA
Found at i:452744 original size:9 final size:9
Alignment explanation
Indices: 452726--452780 Score: 51
Period size: 9 Copynumber: 5.8 Consensus size: 9
452716 ACATGTGAAT
452726 AATT-TTAA
1 AATTATTAA
452734 AATTATTAA
1 AATTATTAA
452743 AATTAATTTTTAAA
1 AATT-A---TT-AA
452757 AATT-TTAA
1 AATTATTAA
452765 AATTATTAA
1 AATTATTAA
452774 AATTATT
1 AATTATT
452781 TTTTTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
8 10 0.25
9 21 0.52
10 1 0.03
13 2 0.05
14 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
AATTATTAA
Found at i:452756 original size:22 final size:22
Alignment explanation
Indices: 452728--452769 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
452718 ATGTGAATAA
452728 TTTT-AAAATTATTAAAATTAAT
1 TTTTAAAAATT-TTAAAATTAAT
452750 TTTTAAAAATTTTAAAATTA
1 TTTTAAAAATTTTAAAATTA
452770 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAAATTTTAAAATTAAT
Found at i:452761 original size:31 final size:31
Alignment explanation
Indices: 452726--452812 Score: 115
Period size: 31 Copynumber: 2.9 Consensus size: 31
452716 ACATGTGAAT
452726 AATTTTAAAATTATTAAAATTAATTTTTAAA
1 AATTTTAAAATTATTAAAATTAATTTTTAAA
* **
452757 AATTTTAAAATTATTAAAATTATTTTTTTGA
1 AATTTTAAAATTATTAAAATTAATTTTTAAA
**
452788 AATAATAAAATTATT-AAA-TAATTTT
1 AATTTTAAAATTATTAAAATTAATTTT
452813 GATTTTTAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
29 6 0.12
30 3 0.06
31 41 0.82
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
AATTTTAAAATTATTAAAATTAATTTTTAAA
Found at i:452784 original size:22 final size:22
Alignment explanation
Indices: 452759--452802 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
452749 TTTTTAAAAA
*
452759 TTTTAAAATTATTAAAATTATTT
1 TTTTAAAA-TAATAAAATTATTT
*
452782 TTTTGAAATAATAAAATTATT
1 TTTTAAAATAATAAAATTATT
452803 AAATAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTTAAAATAATAAAATTATTT
Found at i:453553 original size:18 final size:18
Alignment explanation
Indices: 453511--453552 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
453501 TTTTGTTTTG
*
453511 TTTTTTTAATTTTAATTA
1 TTTTTTTAACTTTAATTA
* *
453529 TGTTTTTCACTTTAATT-
1 TTTTTTTAACTTTAATTA
453546 TTTTTTT
1 TTTTTTT
453553 TTTGCTAACG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTTTTTAACTTTAATTA
Found at i:464098 original size:13 final size:13
Alignment explanation
Indices: 464080--464114 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
464070 ATACGTGTAA
464080 ATGATATTATTTG
1 ATGATATTATTTG
464093 ATGATATTATTTG
1 ATGATATTATTTG
464106 ATGATATTA
1 ATGATATTA
464115 CAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (13 bp):
ATGATATTATTTG
Found at i:464499 original size:3 final size:3
Alignment explanation
Indices: 464469--464523 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
464459 AAATGCATGG
464469 ATA ATA A-A ATA A-A ATA A-A ATA A-A ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
464513 ATA ATA ATA AT
1 ATA ATA ATA AT
464524 TATACAATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 8 0.17
3 40 0.83
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:466446 original size:41 final size:38
Alignment explanation
Indices: 466346--466449 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
466336 TTCGAAGCAA
* * *
466346 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCTAAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCAAAG
* * ** * *
466383 TAAAGTGATACCCAGTACCTCATCGAATCTATCCAAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCAAAG
466421 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
466450 CTCAAGGTCG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 22 0.42
38 9 0.17
40 2 0.04
41 19 0.37
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCAAAG
Found at i:466575 original size:18 final size:18
Alignment explanation
Indices: 466552--466588 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
466542 ACAATTCATA
466552 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
466570 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
466588 T
1 T
466589 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:472460 original size:17 final size:18
Alignment explanation
Indices: 472440--472473 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
472430 ATTTTTAAAA
*
472440 AATATTTAT-TTTATTTT
1 AATATTAATATTTATTTT
472457 AATATTAATATTTATTT
1 AATATTAATATTTATTT
472474 ATTTATTAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATATTAATATTTATTTT
Found at i:472480 original size:18 final size:17
Alignment explanation
Indices: 472459--472492 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
472449 TTTATTTTAA
*
472459 TATTAATATTTATTTATT
1 TATTAAAATTT-TTTATT
472477 TATTAAAATTTTTTAT
1 TATTAAAATTTTTTAT
472493 ATAGTCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTAAAATTTTTTATT
Found at i:472726 original size:20 final size:18
Alignment explanation
Indices: 472697--472735 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
472687 AATTTTTTAC
*
472697 CTAAATTTTTTTTTTAAAT
1 CTAAA-TTTTTATTTAAAT
472716 CTAATATTTTTATTTAAAT
1 CTAA-ATTTTTATTTAAAT
472735 C
1 C
472736 CGACCAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (18 bp):
CTAAATTTTTATTTAAAT
Found at i:482731 original size:24 final size:24
Alignment explanation
Indices: 482703--482785 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 24
482693 TAGACTAATA
* * *
482703 AGAGTTTGACTCAAATAAATAAAT
1 AGAGTTTAACTCAAACAAATAAAC
* *
482727 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* * *
482751 AGAGTTTAATTGAAACAATTAAAC
1 AGAGTTTAACTCAAACAAATAAAC
*
482775 AGAATTTAACT
1 AGAGTTTAACT
482786 GAAAGATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:482788 original size:24 final size:24
Alignment explanation
Indices: 482719--482789 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
482709 TGACTCAAAT
*
482719 AAATAAATAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAATTGAAAC
482743 AAATAAACAGAGTTTAATTGAAAC
1 AAATAAACAGAGTTTAATTGAAAC
* * *
482767 AATTAAACAGAATTTAACTGAAA
1 AAATAAACAGAGTTTAATTGAAA
482790 GATTATTTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (24 bp):
AAATAAACAGAGTTTAATTGAAAC
Found at i:487998 original size:41 final size:41
Alignment explanation
Indices: 487902--488238 Score: 297
Period size: 41 Copynumber: 8.2 Consensus size: 41
487892 TTTTCATTAA
* * * * *
487902 CGCCGCAAAAGGT-AAAGTATTAACGGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
* * * * *
487942 CGCCGTTAAAAGTTAGAGCATTAGCGGTGCTTGTGGAAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
* * *
487983 TGCCGCTAAAGGTTAGAGCATTAGTGGCGCTTAT-GACAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGA-AAAG
* * *
488024 CGCTGCTAAAGGTCAGAGCATTAGCGACGCTTGA-GGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTT-ATGGAAAAG
* ** * * *
488065 CACCGCTAAATATCAAAGCATTAGCGGTGCTTGA-GGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTT-ATGGAAAAG
* * * * * **
488106 CACCGCTAAATGTCAGAGCATTAGCGACACTTTTCCATAAA-
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGA-AAAG
* *
488147 CACCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGGAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
* * *
488188 CGCCACTAAAGGTCAAAGCATTAACGGCGCTTATGGAAAAG
1 CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
488229 CGCCGCTAAA
1 CGCCGCTAAA
488239 AGTGGATTTT
Statistics
Matches: 240, Mismatches: 50, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
40 15 0.06
41 220 0.92
42 5 0.02
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGGAAAAG
Found at i:488042 original size:82 final size:82
Alignment explanation
Indices: 487920--488238 Score: 327
Period size: 82 Copynumber: 3.9 Consensus size: 82
487910 AAGGTAAAGT
* * * * ** **
487920 ATTAACGGCGCTTATGGGAAAGCGCCGTTAAAAGTTAGAGCATTAGCGGTGCTTGTGGAAAAGTG
1 ATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTGTGGAAAAGCA
*
487985 CCGCTAAAGGTTAGAGC
66 CCGCTAAAGGTCAGAGC
* ** * * *
488002 ATTAGTGGCGCTTATGACAAAGCGCTGCTAAAGGTCAGAGCATTAGCGACGCTTGAGGGAAAGCA
1 ATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTGTGGAAAAGCA
** *
488067 CCGCTAAATATCAAAGC
66 CCGCTAAAGGTCAGAGC
* * * * * **
488084 ATTAGCGGTGCTTGA-GGGAAAGCACCGCTAAATGTCAGAGCATTAGCGACACTTTTCCATAAA-
1 ATTAGCGGCGCTT-ATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTGTGGA-AAAG
488147 CACCGCTAAAGGTCAGAGC
64 CACCGCTAAAGGTCAGAGC
* * * * * *
488166 ATTAGCGGCGCTTATGGGAAAGCGCCACTAAAGGTCAAAGCATTAACGGCGCTTATGGAAAAGCG
1 ATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTGTGGAAAAGCA
488231 CCGCTAAA
66 CCGCTAAA
488239 AGTGGATTTT
Statistics
Matches: 187, Mismatches: 46, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
81 4 0.02
82 179 0.96
83 4 0.02
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (82 bp):
ATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTGTGGAAAAGCA
CCGCTAAAGGTCAGAGC
Found at i:490589 original size:19 final size:19
Alignment explanation
Indices: 490561--490606 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
490551 ATATCGCTTC
*
490561 TGATTTACATTAGAAAGAG
1 TGATTAACATTAGAAAGAG
490580 TGATTAACATTAGAAAGAG
1 TGATTAACATTAGAAAGAG
490599 TGATTAAC
1 TGATTAAC
490607 CCTAAGTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (19 bp):
TGATTAACATTAGAAAGAG
Found at i:492179 original size:43 final size:43
Alignment explanation
Indices: 492113--492240 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 43
492103 TGTTAGTGGT
* * *
492113 GTTTGTG-GGAAAGCGTCGCTAAAGATCATATCCTTTATCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGATCATATCCTTTAGCGGC
* * * *
492155 GTTTGTGAGAAAAGTGCTGCTAAAGATCATGTTCTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGATCATATCCTTTAGCGGC
* * * *
492198 GTTTGTGGGGAAAGCGCCGCTAAAGACCATGGT-CTTTAGCGGC
1 GTTTGTGAGAAAAGCGCCGCTAAAGATCAT-ATCCTTTAGCGGC
492241 CTTTTTTCAC
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
42 7 0.10
43 63 0.88
44 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
GTTTGTGAGAAAAGCGCCGCTAAAGATCATATCCTTTAGCGGC
Found at i:493650 original size:148 final size:148
Alignment explanation
Indices: 493382--493676 Score: 500
Period size: 148 Copynumber: 2.0 Consensus size: 148
493372 TATAGTATCC
* *
493382 TAATAAAATGTTTTATACATGTGATGAAAAATTGCTTAGGTGATTTAGATAGAACCCATATCAAG
1 TAATAAAATCTTTTATACATGTGATGAAAAATTGCTTAGGTGATTTAGATAGAACCCATAGCAAG
* *
493447 ATTAGGGTTCCAAAAGTTGATAAACTTAGATATCGAACGTGAAAAGGTGACATAGCAACAAATAT
66 ATTAGGGTTCCAAAAGTTGATAAACCTAGATATCGAACGCGAAAAGGTGACATAGCAACAAATAT
*
493512 GTTAGGTGTTTGTACACT
131 GTCAGGTGTTTGTACACT
* * * *
493530 TAATAAAATCTTTTATTCATGTGATGAAGAATTGCTTAGGTGCTTTAGATGGAACCCATAGCAAG
1 TAATAAAATCTTTTATACATGTGATGAAAAATTGCTTAGGTGATTTAGATAGAACCCATAGCAAG
*
493595 ATTAGGGTTCCAAAAGTTGATAAACCTAGATATCGAATGCGAAAAGGTGACATAGCAACAAATAT
66 ATTAGGGTTCCAAAAGTTGATAAACCTAGATATCGAACGCGAAAAGGTGACATAGCAACAAATAT
493660 GTCAGGTGTTTGTACAC
131 GTCAGGTGTTTGTACAC
493677 CTGATATGCA
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
148 137 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (148 bp):
TAATAAAATCTTTTATACATGTGATGAAAAATTGCTTAGGTGATTTAGATAGAACCCATAGCAAG
ATTAGGGTTCCAAAAGTTGATAAACCTAGATATCGAACGCGAAAAGGTGACATAGCAACAAATAT
GTCAGGTGTTTGTACACT
Found at i:494959 original size:24 final size:23
Alignment explanation
Indices: 494910--494959 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
494900 TAAAGTAGGT
* *
494910 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
494933 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
494957 TAT
1 TAT
494960 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:495704 original size:19 final size:19
Alignment explanation
Indices: 495676--495714 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
495666 TTTATGGTTT
495676 TAAATAATTTTTGGGTAAAA
1 TAAATAA-TTTTGGGTAAAA
*
495696 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGTAAAA
495714 T
1 T
495715 TGGCATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 1 0.06
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TAAATAATTTTGGGTAAAA
Found at i:498820 original size:1 final size:1
Alignment explanation
Indices: 498816--498841 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
498806 AAACCTCAAA
498816 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
498842 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:500158 original size:40 final size:40
Alignment explanation
Indices: 500089--500302 Score: 186
Period size: 40 Copynumber: 5.4 Consensus size: 40
500079 ATAACTTTAG
* * *
500089 GGGTAAAAGATTGAATTGT-TTCAATCTGCCCCATGA-TC
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTA
* **
500127 GTGGTAAGAGATTGGATGGTCTTCAATCTGCCCTTTGATTA
1 G-GGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTA
* *
500168 GGGTAAAAGATTGGATGGTTTTCAATTTGCCCTC-TGATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGATTA
* * * * * **
500208 GGGTAAAAGATTGGATAGTTTTTAATTTGCCTCATGATCG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTA
* * *
500248 GGGTAAGAGATCGGATGATCTTCAATCTGCCCTC-T-AGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCC-CATGA-TTA
*
500288 GGGTAAGAGATTGGA
1 GGGTAAAAGATTGGA
500303 GGTTGTAACT
Statistics
Matches: 143, Mismatches: 26, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
38 1 0.01
39 17 0.12
40 122 0.85
41 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCCATGATTA
Found at i:500213 original size:80 final size:80
Alignment explanation
Indices: 500089--500302 Score: 213
Period size: 80 Copynumber: 2.7 Consensus size: 80
500079 ATAACTTTAG
* * * *
500089 GGGTAAAAGATTGAATTG-TTTCAATCTGCCC-CATGA-TCGTGGTAAGAGATTGGATGGTCTTC
1 GGGTAAAAGATTGGATGGTTTTCAATCTGCCCTC-TGATTAG-GGTAAGAGATTGGATAGTCTTC
* *
500151 AATCTGCC-CTTTGATTA
64 AATCTGCCTC-ATGATCA
* * * *
500168 GGGTAAAAGATTGGATGGTTTTCAATTTGCCCTCTGATTAGGGTAAAAGATTGGATAGTTTTTAA
1 GGGTAAAAGATTGGATGGTTTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGATAGTCTTCAA
* *
500233 TTTGCCTCATGATCG
66 TCTGCCTCATGATCA
* * * *
500248 GGGTAAGAGATCGGATGATCTTCAATCTGCCCTCT-AGTTAGGGTAAGAGATTGGA
1 GGGTAAAAGATTGGATGGTTTTCAATCTGCCCTCTGA-TTAGGGTAAGAGATTGGA
500303 GGTTGTAACT
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
79 17 0.15
80 91 0.81
81 4 0.04
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (80 bp):
GGGTAAAAGATTGGATGGTTTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGATAGTCTTCAA
TCTGCCTCATGATCA
Found at i:500299 original size:120 final size:118
Alignment explanation
Indices: 500089--500306 Score: 312
Period size: 120 Copynumber: 1.8 Consensus size: 118
500079 ATAACTTTAG
* * * *
500089 GGGTAAAAGATTGAATTGTTTCAATCTGCCCCATGATCGTGGTAAGAGATTGGATGGTCTTCAAT
1 GGGTAAAAGATTGAATAGTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAAT
*
500154 CTGCCCTTTGATTAGGGTAAAAGATTGGATGGTTTTCAATTTGCCCTCTGATTA
66 CTGCCCTTAGATTAGGGTAAAAGATTGGA-GGTTTTCAATTTGCCCTCTGATTA
* * * *
500208 GGGTAAAAGATTGGATAGTTTTTAATTTGCCTCATGATCGGGGTAAGAGATCGGATGATCTTCAA
1 GGGTAAAAGATTGAATAG-TTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAA
*
500273 TCTGCCCTCTAG-TTAGGGTAAGAGATTGGAGGTT
65 TCTGCCCT-TAGATTAGGGTAAAAGATTGGAGGTT
500307 GTAACTTCAC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
119 20 0.23
120 65 0.75
121 2 0.02
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.34
Consensus pattern (118 bp):
GGGTAAAAGATTGAATAGTTTCAATCTGCCCCATGATCGGGGTAAGAGATCGGATGATCTTCAAT
CTGCCCTTAGATTAGGGTAAAAGATTGGAGGTTTTCAATTTGCCCTCTGATTA
Found at i:500431 original size:50 final size:50
Alignment explanation
Indices: 500356--500483 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
500346 ATCCTGGTGA
* * * *
500356 CTTCAATCTGCCCCTTTATTGCTTTAGGTGAATGAGATTTGCCGTTGTGG
1 CTTCATTCTGCCCCTCTATAGCTTTAGGTGAATGAGATTTGCCATTGTGG
* *
500406 CTTCATTCTGCCCCTCTACAGCTTTAGGTGTATGAGATTTGCCATTGTGG
1 CTTCATTCTGCCCCTCTATAGCTTTAGGTGAATGAGATTTGCCATTGTGG
* * *
500456 TTTCAATT-TGCACCTCCATAGCTTTAGG
1 CTTC-ATTCTGCCCCTCTATAGCTTTAGG
500484 GGTAAAAGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
50 64 0.96
51 3 0.04
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.39
Consensus pattern (50 bp):
CTTCATTCTGCCCCTCTATAGCTTTAGGTGAATGAGATTTGCCATTGTGG
Found at i:500494 original size:50 final size:50
Alignment explanation
Indices: 500390--500496 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 50
500380 TAGGTGAATG
* * * * **
500390 AGATTTGCCGTTGTGGCTTCATTCTGCCCCTCTACAGCTTTAGGTGTATG
1 AGATTTGCCATTGTGGCTTCATTCTGCACCTCCACAGCTTTAGGGGTAAA
* *
500440 AGATTTGCCATTGTGGTTTCAATT-TGCACCTCCATAGCTTTAGGGGTAAA
1 AGATTTGCCATTGTGGCTTC-ATTCTGCACCTCCACAGCTTTAGGGGTAAA
500490 AGATTTG
1 AGATTTG
500497 TCGTTCTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 45 0.94
51 3 0.06
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (50 bp):
AGATTTGCCATTGTGGCTTCATTCTGCACCTCCACAGCTTTAGGGGTAAA
Found at i:511778 original size:51 final size:53
Alignment explanation
Indices: 511693--511806 Score: 144
Period size: 51 Copynumber: 2.2 Consensus size: 53
511683 ATATAAATAT
* * * *
511693 ACATACTATATATAAAGAGATTAACTATATATATACATAAGTTAGGGAGACAG
1 ACATACTATATATAAAGAGATAAACCATATATATACATAAGTTAAGGAAACAG
* * *
511746 TCATACTATATATAAA-AGA-AAACCATATATATATATATGTTAAGGAAACAG
1 ACATACTATATATAAAGAGATAAACCATATATATACATAAGTTAAGGAAACAG
511797 ACATA-TATAT
1 ACATACTATAT
511807 GAGGGAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
50 5 0.09
51 30 0.57
52 3 0.06
53 15 0.28
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (53 bp):
ACATACTATATATAAAGAGATAAACCATATATATACATAAGTTAAGGAAACAG
Found at i:515990 original size:22 final size:22
Alignment explanation
Indices: 515965--516009 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
515955 GTATGTATAC
515965 TTTTAAAATTAAAAAAAAATTA
1 TTTTAAAATTAAAAAAAAATTA
*** *
515987 TTTTATTTTTAAAAATAAATTA
1 TTTTAAAATTAAAAAAAAATTA
516009 T
1 T
516010 GACGTCAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TTTTAAAATTAAAAAAAAATTA
Found at i:520950 original size:18 final size:18
Alignment explanation
Indices: 520923--520964 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
520913 GGAGGTAATA
*
520923 AAAATGTATAATAAA-ATT
1 AAAATATATAA-AAATATT
520941 AAAATATATAAAAATATT
1 AAAATATATAAAAATATT
520959 AAAATA
1 AAAATA
520965 AAACTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAATATATAAAAATATT
Found at i:527342 original size:25 final size:26
Alignment explanation
Indices: 527294--527342 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
527284 AATTTAAAAA
*
527294 TAAAAATAAAAATTATTAACATTATT
1 TAAAAATAAAAATTATTAAAATTATT
527320 TAAAAATAAAAATTA-TAAAATTA
1 TAAAAATAAAAATTATTAAAATTA
527343 AATAATATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TAAAAATAAAAATTATTAAAATTATT
Found at i:527819 original size:18 final size:18
Alignment explanation
Indices: 527771--527836 Score: 57
Period size: 18 Copynumber: 3.8 Consensus size: 18
527761 ATTTCCCAAT
527771 ATTTTT-TAATTTT-ATA
1 ATTTTTGTAATTTTAATA
* * *
527787 ATCATTTCTATTTTTAATA
1 AT-TTTTGTAATTTTAATA
527806 ATTTTTGTAATTTTAAT-
1 ATTTTTGTAATTTTAATA
* *
527823 TTTTTTGCAATTTT
1 ATTTTTGTAATTTT
527837 TAAATATTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.05
17 15 0.38
18 18 0.45
19 5 0.12
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.65
Consensus pattern (18 bp):
ATTTTTGTAATTTTAATA
Found at i:528410 original size:9 final size:10
Alignment explanation
Indices: 528372--528420 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
528362 AATTTTTCAC
528372 AATTATAAAA
1 AATTATAAAA
*
528382 ATTTATAAAA
1 AATTATAAAA
528392 CAA-TATAAAA
1 -AATTATAAAA
*
528402 GATTA-AAAA
1 AATTATAAAA
528411 AATTATAAAA
1 AATTATAAAA
528421 TATATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 9 0.28
10 22 0.69
11 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (10 bp):
AATTATAAAA
Found at i:528412 original size:21 final size:21
Alignment explanation
Indices: 528370--528412 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
528360 ATAATTTTTC
* *
528370 ACAATTATAAAAATTTATAAA
1 ACAATTATAAAAATTAAAAAA
528391 ACAA-TATAAAAGATTAAAAAA
1 ACAATTATAAAA-ATTAAAAAA
528412 A
1 A
528413 TTATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (21 bp):
ACAATTATAAAAATTAAAAAA
Found at i:529018 original size:89 final size:91
Alignment explanation
Indices: 528923--529133 Score: 232
Period size: 90 Copynumber: 2.3 Consensus size: 91
528913 CTTAAAGGTG
* * *
528923 TAAAAAA-CCCTCAAACTTTTTCAAAAAATAAAGCAATTAAGCCCTTAC-CTTGTCTTGCACTCA
1 TAAAAAAGCCCTCAAACTTTTTCAAAAAA-AAAGCAATTAAGCCCCTACTCTTATCTTCCACTCA
* * *
528986 CTTGAGTATTTGAACTTTCAAAATATA
65 ATTGAGTACTTAAACTTTCAAAATATA
* * * * * *
529013 TAAAAAAGGCCCTTAAACTTTTTC--AAAAAGAGCAATTAAGCCCCTGCTTTTATTTTCCATTCA
1 TAAAAAA-GCCCTCAAACTTTTTCAAAAAAAAAGCAATTAAGCCCCTACTCTTATCTTCCACTCA
*
529076 ATTGGGTACTTAAACTTTCAAAATATA
65 ATTGAGTACTTAAACTTTCAAAATATA
* *
529103 TCAAAAAGGCCTTCAAACTTTTTCAAAAAAA
1 T-AAAAAAGCCCTCAAACTTTTTCAAAAAAA
529134 GCATTTAAGT
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
89 16 0.16
90 59 0.60
91 5 0.05
92 19 0.19
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (91 bp):
TAAAAAAGCCCTCAAACTTTTTCAAAAAAAAAGCAATTAAGCCCCTACTCTTATCTTCCACTCAA
TTGAGTACTTAAACTTTCAAAATATA
Found at i:529244 original size:20 final size:20
Alignment explanation
Indices: 529208--529245 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
529198 AAAAGACCCT
**
529208 TTGATCGTTAACTTTAACAA
1 TTGATCGTTAAAGTTAACAA
529228 TTGATCGTTAAAGTTAAC
1 TTGATCGTTAAAGTTAAC
529246 TGCCCCTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (20 bp):
TTGATCGTTAAAGTTAACAA
Found at i:529347 original size:27 final size:26
Alignment explanation
Indices: 529309--529382 Score: 82
Period size: 25 Copynumber: 2.8 Consensus size: 26
529299 GTGGCAAAAG
*
529309 AATTATAAAAAAATATTATAAATATTA
1 AATT-TAAAAAAATATTATAAAAATTA
529336 AATTTAATAAAAATA-TA-AAAAATTA
1 AATTTAA-AAAAATATTATAAAAATTA
*
529361 AAATTAGAAAAAAT-TTATAAAA
1 AATTTA-AAAAAATATTATAAAA
529383 TGCATAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 20 0.49
26 10 0.24
27 11 0.27
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (26 bp):
AATTTAAAAAAATATTATAAAAATTA
Found at i:529647 original size:90 final size:88
Alignment explanation
Indices: 529480--529722 Score: 264
Period size: 90 Copynumber: 2.7 Consensus size: 88
529470 GTTCAAGTAT
* * * *
529480 CCAATTGAGTGCAAAAAAAAAATCAGAGGCTTAATTGCTTTTTTGAAAAGGTTTG-AGGTTTTTT
1 CCAATTGAGTGC-AAAATAAAAGCAGAGGCTTAATTGCTTTTTTGAAAAAGTTTGAAGG---CTT
*
529544 TTTTATGCATTTTGAAAGTTT-AAAAAC
62 TTTTATACATTTTG-AAGTTTCAAAAAC
*
529571 CCAATTGAGTGCAAAATAAAAGCAGAGGCTTAATTGCTTTTCTTGAAAAAATTTGAAGGCCTTTT
1 CCAATTGAGTGCAAAATAAAAGCAGAGGCTTAATTGCTTTT-TTGAAAAAGTTTGAAGG-CTTTT
* * *
529636 TTATACATTTTGAATTTTCAAATAT
64 TTATACATTTTGAAGTTTCAAAAAC
* *
529661 CC-A---AGTGCAAAATAAAAGCAGAGACTTAATTGCTTTTTTTTGAAAAAGTTTAAAGGCTTTT
1 CCAATTGAGTGCAAAATAAAAGCAGAGGCTTAATTGC--TTTTTTGAAAAAGTTTGAAGGCTTTT
529722 T
64 T
529723 ACATCCTTAA
Statistics
Matches: 134, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
86 35 0.26
87 15 0.11
88 4 0.03
89 6 0.04
90 48 0.36
91 23 0.17
92 3 0.02
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (88 bp):
CCAATTGAGTGCAAAATAAAAGCAGAGGCTTAATTGCTTTTTTGAAAAAGTTTGAAGGCTTTTTT
ATACATTTTGAAGTTTCAAAAAC
Found at i:529907 original size:20 final size:20
Alignment explanation
Indices: 529852--529895 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
529842 AAGCAAAAAT
* **
529852 AACAACAAAAGCAGTACCAA
1 AACAACAAAAACAACACCAA
529872 AACAACAAAAACAACACCAA
1 AACAACAAAAACAACACCAA
529892 AACA
1 AACA
529896 CCAGGAACAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.66, C:0.27, G:0.05, T:0.02
Consensus pattern (20 bp):
AACAACAAAAACAACACCAA
Found at i:530512 original size:122 final size:121
Alignment explanation
Indices: 530276--531013 Score: 810
Period size: 122 Copynumber: 6.1 Consensus size: 121
530266 TGAAAATTTT
* * * * * *
530276 AAATTTTT-TGTGTTGGTCATGCCATGACCGACACCCCTATTTA-CTGATAAAAAAATTCAAATT
1 AAATTTTTAGGTGTTAGCCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAATTTAAATT
* * * * * *
530339 TTTTT-GTGTTAGCCATGCAATGGCCGACACCCCCTTTTTGTCAG-ATAAAAAATCC
66 TTTTTGGTGTTTGTCATGCCATGGCCGACACCCCTTTTTTATCTGAATAAAAAAT-C
* * * * ** * *
530394 AATTTTTTTGGTGTTAGTCGTGCCATGGTTGACGCCCCTATTTATCAAATAAAAAAATTTAAATA
1 AAATTTTTAGGTGTTAGCCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAATTTAAAT-
* * *
530459 TTTTTTGGTATTTGTCATGCCATGGCCTACACCCCTTTTTTATTTGAATAAAAAATC
65 TTTTTTGGTGTTTGTCATGCCATGGCCGACACCCCTTTTTTATCTGAATAAAAAATC
* ** * * * *
530516 AAATTTTTGGGTGTT-GACCATGCCATAACTGACACCCTTATTTATCAAATAAAAAAATTTCAAT
1 AAATTTTTAGGTGTTAG-CCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAATTTAAAT
* * * * * *
530580 TTTTTTTGTGTTAGTTATGCAATGACCGACACCTCCTTTTTTATCTAAATAAAAAATC
65 TTTTTTGGTGTTTGTCATGCCATGGCCGACACC-CCTTTTTTATCTGAATAAAAAATC
* * *
530638 AAATTTTTGGGTGTTAGCCATGCCATGACCGACACCCCTATTTATCTGATAAAAAAATTTTAAAT
1 AAATTTTTAGGTGTTAGCCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAA-TTTAAAT
* *
530703 TGTTTTTGGTG-TTGGCAATGCTATGGCCGACACCCCCTTTTTTATCTGAATAAAAAATC
65 T-TTTTTGGTGTTTGTC-ATGCCATGGCCGACA-CCCCTTTTTTATCTGAATAAAAAATC
* * * *
530762 AAAATTTTAGGTGTTGGCCATGCCATGGCCGACACCCCTATTTATCTGATAAAAAAA-TCAAA-T
1 AAATTTTTAGGTGTTAGCCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAATTTAAATT
*
530825 TTTTTGGTG-TTGATCATGCCATGGCCGACACCCTTTTTTTTTATCTGAATAAAAAATC
66 TTTTTGGTGTTTG-TCATGCCATGGCCGACACCC--CTTTTTTATCTGAATAAAAAATC
* * * * *
530883 AAAATTTTAAGTGTTGGCCATGCCATGGCCGACACCTCTATTTATCAGATAAAAAAATTTCAATT
1 AAATTTTTAGGTGTTAGCCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAATTTAAATT
* * *
530948 TTTTTGGTGTTGGTCATGACATGACCGACACCCCCCTTTTTTATCTGAATAAAAAATC
66 TTTTTGGTGTTTGTCATGCCATGGCCGACA--CCCCTTTTTTATCTGAATAAAAAATC
531006 AAATTTTT
1 AAATTTTT
531014 GCATGGCCGA
Statistics
Matches: 530, Mismatches: 70, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
118 7 0.01
119 31 0.06
120 42 0.08
121 111 0.21
122 162 0.31
123 73 0.14
124 99 0.19
125 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (121 bp):
AAATTTTTAGGTGTTAGCCATGCCATGGCCGACACCCCTATTTATCAGATAAAAAAATTTAAATT
TTTTTGGTGTTTGTCATGCCATGGCCGACACCCCTTTTTTATCTGAATAAAAAATC
Found at i:530652 original size:61 final size:60
Alignment explanation
Indices: 530276--531013 Score: 554
Period size: 61 Copynumber: 12.1 Consensus size: 60
530266 TGAAAATTTT
* * *
530276 AAATTTTTT-GTGTTGGTCATGCCATGACCGACACCCC-TATTTA-CTGATAA-AAAAATTC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCT-A-AATAAAAAATC
* * * * *
530334 AAATTTTTTTGTGTTAGCCATGCAATGGCCGACACCCCCTT-TTTGTC-AGATAAAAAATCC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACA-CCCCTTATTTATCTAAATAAAAAAT-C
* * * * ** * *
530394 AATTTTTTTGGTGTTAGTCGTGCCATGGTTGACGCCCC-TATTTATC-AAATAAAAAAATTTA
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCTAAAT-AAAAAA--TC
* * * * * * *
530455 AATATTTTTTGGTATTTGTCATGCCATGGCCTACACCCCTTTTTTATTTGAATAAAAAATC
1 AA-ATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCTAAATAAAAAATC
* * ** *
530516 AAATTTTTGGGTGTTGACCATGCCATAACTGACA-CCCTTATTTATC-AAATAAAAAAATTTC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCTAAAT-AAAAAA--TC
* * * ** * * *
530577 AATTTTTTTTGTGTTAGTTATGCAATGACCGACACCTCCTTTTTTATCTAAATAAAAAATC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACC-CCTTATTTATCTAAATAAAAAATC
* * * * *
530638 AAATTTTTGGGTGTTAGCCATGCCATGACCGACACCCC-TATTTATCTGATAA-AAAAATTTT
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCT-A-AATAAAAA-ATC
* * * *
530699 AAATTGTTTTTGGTGTTGGCAATGCTATGGCCGACACCCCCTTTTTTATCTGAATAAAAAATC
1 AAA-T-TTTTTGGTGTTGGCCATGCCATGGCCGACA-CCCCTTATTTATCTAAATAAAAAATC
* * *
530762 AAAATTTTAGGTGTTGGCCATGCCATGGCCGACACCCC-TATTTATCT-GATAAAAAAATC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCTAAAT-AAAAAATC
** * * *
530821 AAATTTTTTGGTGTTGATCATGCCATGGCCGACACCCTTTTTTTTTATCTGAATAAAAAATC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCC--CTTATTTATCTAAATAAAAAATC
* ** * *
530883 AAAATTTTAAGTGTTGGCCATGCCATGGCCGACACCTC-TATTTATC-AGATAAAAAAATTTC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCTAAAT-AAAAAA--TC
* * * * * *
530944 AATTTTTTTGGTGTTGGTCATGACATGACCGACACCCCCCTTTTTTATCTGAATAAAAAATC
1 AAATTTTTTGGTGTTGGCCATGCCATGGCCGACA--CCCCTTATTTATCTAAATAAAAAATC
531006 AAATTTTT
1 AAATTTTT
531014 GCATGGCCGA
Statistics
Matches: 535, Mismatches: 106, Indels: 74
0.75 0.15 0.10
Matches are distributed among these distances:
58 18 0.03
59 125 0.23
60 75 0.14
61 127 0.24
62 87 0.16
63 64 0.12
64 29 0.05
65 10 0.02
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (60 bp):
AAATTTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTATTTATCTAAATAAAAAATC
Found at i:531014 original size:61 final size:59
Alignment explanation
Indices: 530276--531014 Score: 525
Period size: 59 Copynumber: 12.2 Consensus size: 59
530266 TGAAAATTTT
* * * *
530276 AAATTTTTTGTGTTGGTCATGCCATGACCGACACCCC-TATTTA-CTG-ATAAAAAAATTC
1 AAATTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAAT-AAAAAA-TC
* * * * * *
530334 AAATTTTTTTGTGTTAGCCATGCAATGGCCGACACCCCCTTTTTGTCAG-ATAAAAAATCC
1 AAA-TTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAATAAAAAAT-C
* * * * ** * * * *
530394 AATTTTTTTGGTGTTAGTCGTGCCATGGTTGACGCCCC-TATTTATC-AAATAAAAAAATTTA
1 AA-ATTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAAT-AAAAAA--TC
* * * * *
530455 AATATTTTTTGGTATTTGTCATGCCATGGCCTACACCCCTTTTTTATTTGAATAAAAAATC
1 AA-A-TTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAATAAAAAATC
* ** * * *
530516 AAATTTTTGGGTGTTGACCATGCCATAACTGACA-CCCTTATTTATC-AAATAAAAAAATTTC
1 AAATTTTT-GGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAAT-AAAAAA--TC
* * * ** * * *
530577 AATTTTTTTTGTGTTAGTTATGCAATGACCGACACCTCCTTTTTTATCTAAATAAAAAATC
1 AA-ATTTTTGGTGTTGGCCATGCCATGGCCGACACC-CCTTTTTTATCTGAATAAAAAATC
* * * *
530638 AAATTTTTGGGTGTTAGCCATGCCATGACCGACACCCC-TATTTATCTG-ATAAAAAAATTTT
1 AAATTTTT-GGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAAT-AAAAAA--TC
* *
530699 AAATTGTTTTTGGTGTTGGCAATGCTATGGCCGACACCCCCTTTTTTATCTGAATAAAAAATC
1 AAA---TTTTTGGTGTTGGCCATGCCATGGCCGACA-CCCCTTTTTTATCTGAATAAAAAATC
* *
530762 AAAATTTTAGGTGTTGGCCATGCCATGGCCGACACCCC-TATTTATCTG-ATAAAAAAATC
1 -AAATTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAAT-AAAAAATC
** *
530821 AAATTTTTTGGTGTTGATCATGCCATGGCCGACACCCTTTTTTTTTATCTGAATAAAAAATC
1 AAA-TTTTTGGTGTTGGCCATGCCATGGCCGACACCC--CTTTTTTATCTGAATAAAAAATC
** * * *
530883 AAAATTTTAAGTGTTGGCCATGCCATGGCCGACACCTC-TATTTATCAG-ATAAAAAAATTTC
1 -AAATTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAAT-AAAAAA--TC
* * * *
530944 AATTTTTTTGGTGTTGGTCATGACATGACCGACACCCCCCTTTTTTATCTGAATAAAAAATC
1 AA-ATTTTTGGTGTTGGCCATGCCATGGCCGACA--CCCCTTTTTTATCTGAATAAAAAATC
531006 AAATTTTTG
1 AAATTTTTG
531015 CATGGCCGAC
Statistics
Matches: 542, Mismatches: 93, Indels: 89
0.75 0.13 0.12
Matches are distributed among these distances:
58 15 0.03
59 135 0.25
60 77 0.14
61 122 0.23
62 83 0.15
63 58 0.11
64 33 0.06
65 17 0.03
66 2 0.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (59 bp):
AAATTTTTGGTGTTGGCCATGCCATGGCCGACACCCCTTTTTTATCTGAATAAAAAATC
Found at i:531925 original size:17 final size:17
Alignment explanation
Indices: 531905--531959 Score: 64
Period size: 17 Copynumber: 3.5 Consensus size: 17
531895 AAAAAATAAT
531905 AATTAGAATATACAGGA
1 AATTAGAATATACAGGA
*
531922 AATTAGAA-AT-TA--A
1 AATTAGAATATACAGGA
*
531935 AATTAAAATATACAGGA
1 AATTAGAATATACAGGA
531952 AATTAGAA
1 AATTAGAA
531960 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
13 8 0.27
14 2 0.07
15 2 0.07
16 2 0.07
17 16 0.53
ACGTcount: A:0.58, C:0.04, G:0.13, T:0.25
Consensus pattern (17 bp):
AATTAGAATATACAGGA
Found at i:531939 original size:30 final size:30
Alignment explanation
Indices: 531905--532001 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
531895 AAAAAATAAT
*
531905 AATTAGAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
531935 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
* * * * *
531965 ATTTAAAA-AAAAAAGAAATTACAAATTAA
1 AATTAAAATATACAGGAAATTAGAAATTAA
*
531994 ATTTAAAA
1 AATTAAAA
532002 AGTAAACGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
29 25 0.41
30 36 0.59
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTAGAAATTAA
Found at i:531982 original size:29 final size:29
Alignment explanation
Indices: 531920--532002 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
531910 GAATATACAG
* * * *
531920 GAAATTAGAAATTAAAATTAAAATATACAG
1 GAAATTAGAAATTAAATTTAAAA-AAAAAA
531950 GAAATTAGAAATTAAATTTAAAAAAAAAA
1 GAAATTAGAAATTAAATTTAAAAAAAAAA
*
531979 GAAATTACAAATTAAATTTAAAAA
1 GAAATTAGAAATTAAATTTAAAAA
532003 GTAAACGAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 26 0.54
30 22 0.46
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (29 bp):
GAAATTAGAAATTAAATTTAAAAAAAAAA
Found at i:532618 original size:202 final size:202
Alignment explanation
Indices: 532265--532669 Score: 765
Period size: 202 Copynumber: 2.0 Consensus size: 202
532255 AAGCCAAAAA
* *
532265 TATCCTTCATTGTCGATGTACGTTCTTTCGGATGGATCTTCGGTTGATATGAGGAAGAACCAAAG
1 TATCCTCCATTGTCAATGTACGTTCTTTCGGATGGATCTTCGGTTGATATGAGGAAGAACCAAAG
* *
532330 TAACATGAGCGTTGAAAGTCGAGGTCGACGCCAAAAATCTCCTCTATGCAACGATGATAATAATT
66 TAACATGAACGTTGAAAATCGAGGTCGACGCCAAAAATCTCCTCTATGCAACGATGATAATAATT
532395 GTGTAGCAAAAAAGACGAAGAGCCAGATGTTTGATATTGGGGATCGGGTTGGTGCTCCGACTGGT
131 GTGTAGCAAAAAAGACGAAGAGCCAGATGTTTGATATTGGGGATCGGGTTGGTGCTCCGACTGGT
532460 ACTCGGG
196 ACTCGGG
*
532467 TATCCTCCATTGTCAATGTACGTTCTTTCGGATGGATCTTCGGTTGATATGAGGAAGAACCAGAG
1 TATCCTCCATTGTCAATGTACGTTCTTTCGGATGGATCTTCGGTTGATATGAGGAAGAACCAAAG
532532 TAACATGAACGTTGAAAATCGAGGTCGACGCCAAAAATCTCCTCTATGCAACGATGATAATAATT
66 TAACATGAACGTTGAAAATCGAGGTCGACGCCAAAAATCTCCTCTATGCAACGATGATAATAATT
532597 GTGTAGCAAAAAAGACGAAGAGCCAGATGTTTGATATTGGGGATCGGGTTGGTGCTCCGACTGGT
131 GTGTAGCAAAAAAGACGAAGAGCCAGATGTTTGATATTGGGGATCGGGTTGGTGCTCCGACTGGT
532662 ACTCGGG
196 ACTCGGG
532669 T
1 T
532670 TGGTCCTGAG
Statistics
Matches: 198, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
202 198 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.27
Consensus pattern (202 bp):
TATCCTCCATTGTCAATGTACGTTCTTTCGGATGGATCTTCGGTTGATATGAGGAAGAACCAAAG
TAACATGAACGTTGAAAATCGAGGTCGACGCCAAAAATCTCCTCTATGCAACGATGATAATAATT
GTGTAGCAAAAAAGACGAAGAGCCAGATGTTTGATATTGGGGATCGGGTTGGTGCTCCGACTGGT
ACTCGGG
Found at i:533582 original size:15 final size:16
Alignment explanation
Indices: 533552--533585 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
533542 TAAAAAATTG
533552 AAAAATAATTAGAATAA
1 AAAAATAATTA-AATAA
533569 AAAAATAATT-AATAA
1 AAAAATAATTAAATAA
533584 AA
1 AA
533586 TTTTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
17 10 0.59
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATAATTAAATAA
Found at i:534522 original size:22 final size:22
Alignment explanation
Indices: 534474--534524 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
534464 TGAGGTGCTA
* *
534474 GTGAGCTGAAATTTCAATTTTG
1 GTGAGCTAAAATTTCAATTTAG
* **
534496 ATGAGCTAAAATTTCGGTTTAG
1 GTGAGCTAAAATTTCAATTTAG
534518 GTGAGCT
1 GTGAGCT
534525 GGAATTTTGG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.37
Consensus pattern (22 bp):
GTGAGCTAAAATTTCAATTTAG
Found at i:534859 original size:84 final size:84
Alignment explanation
Indices: 534624--535340 Score: 1048
Period size: 84 Copynumber: 8.5 Consensus size: 84
534614 TAAATTTAAA
* *
534624 ATTTGATAAAAATTGTAATATAATAAT-ATTTTTTATTTAAATATTAAAATTTAGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
* *
534688 CTTGTCAAATCAACATATT
66 ATTGTCAAATCAACACATT
* *
534707 ATTTGATAAAAA-TATAATATAATAATAATATTTTTTTTATTTAAATATTAAAATTTAGTAAATA
1 ATTTGATAAAAATTGTAATATAATAAT-A-A--TTTTTTATTTAAATATTAAAATTTAATAAATA
**
534771 ATGTATTGTCAAATCGTCACATT
62 ATGTATTGTCAAATCAACACATT
*
534794 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTACATATTAAAATTTAATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
**
534859 ATTGTCAAATCAATTCATT
66 ATTGTCAAATCAACACATT
* *
534878 ATTTGAT-AAAATGGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
*
534942 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* * *
534961 ATTTGATAAAACTTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
*
535026 ATTGTCAAATCAACATATT
66 ATTGTCAAATCAACACATT
* *
535045 ATTTGATAAAAATTGTAATATAATAATAACTTTTTATTTACATATTAAAATTTAATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
*
535110 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* * *
535129 A-TTGATAAAAATTGTAATATAATAATAA-TTTTTATTTACATATTAAAATTTGATAAATAATGC
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
* *
535192 ATTGTCAACTCAATACATT
66 ATTGTCAAATCAACACATT
* ** *
535211 ATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATTCGAATTTAATAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
*
535276 ATTATCAAATCAACACATT
66 ATTGTCAAATCAACACATT
* *
535295 ATTTGATATAAATTGAAATATAATAATAATATTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATA
535341 ATGTTAAATT
Statistics
Matches: 574, Mismatches: 49, Indels: 19
0.89 0.08 0.03
Matches are distributed among these distances:
82 63 0.11
83 143 0.25
84 274 0.48
85 2 0.00
86 16 0.03
87 63 0.11
88 13 0.02
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (84 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATGT
ATTGTCAAATCAACACATT
Found at i:534983 original size:167 final size:168
Alignment explanation
Indices: 534624--535340 Score: 1068
Period size: 167 Copynumber: 4.3 Consensus size: 168
534614 TAAATTTAAA
*
534624 ATTTGATAAAAATTGTAATATAATAAT-ATTTTTTATTTAAATATTAAAATTTAGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATAT
* *
534688 CTTGTCAAATCAACATATTATTTGATAAAAA-TATAATATAATAATAATATTTTTTTTATTTAAA
66 ATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAAT-A-A--TTTTTTATTTAAA
* * **
534752 TATTAAAATTTAGTAAATAATGTATTGTCAAATCGTCACATT
127 TATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
* *
534794 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTACATATTAAAATTTAATAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATAT
* *
534859 ATTGTCAAATCAA-TTCATTATTTGAT-AAAATGGTAATATAATAATAATTTTTTATTTAAATAT
66 ATTGTCAAATCAACAT-ATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATAT
*
534922 TAAAATTTAGTAAATAATGTATTATCAAATCAACACATT
130 TAAAATTTAATAAATAATGTATTATCAAATCAACACATT
* *
534961 ATTTGATAAAACTTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATAT
* *
535026 ATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAACTTTTTATTTACATATT
66 ATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
535091 AAAATTTAATAAATAATGTATTATCAAATCAACACATT
131 AAAATTTAATAAATAATGTATTATCAAATCAACACATT
* * **
535129 A-TTGATAAAAATTGTAATATAATAATAA-TTTTTATTTACATATTAAAATTTGATAAATAATGC
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATAT
* * * *
535192 ATTGTCAACTCAATACATTATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATT
66 ATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
** *
535257 CGAATTTAATAAATAATATATTATCAAATCAACACATT
131 AAAATTTAATAAATAATGTATTATCAAATCAACACATT
* *
535295 ATTTGATATAAATTGAAATATAATAATAATATTTTTTATTTAAATA
1 ATTTGATAAAAATTGTAATATAATAAT-A-ATTTTTTATTTAAATA
535341 ATGTTAAATT
Statistics
Matches: 501, Mismatches: 37, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
166 125 0.25
167 185 0.37
168 75 0.15
169 2 0.00
170 46 0.09
171 68 0.14
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (168 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATAT
ATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
AAAATTTAATAAATAATGTATTATCAAATCAACACATT
Found at i:535070 original size:251 final size:251
Alignment explanation
Indices: 534624--535336 Score: 1076
Period size: 251 Copynumber: 2.8 Consensus size: 251
534614 TAAATTTAAA
*
534624 ATTTGATAAAAATTGTAATATAATAAT-ATTTTTTATTTAAATATTAAAATTTAGTAAATAATAT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATGT
* * * *
534688 CTTGTCAAATCAACATATTATTTGATAAAAATATAATATAATAATAATATTTTTTTTATTTAAAT
66 ATTGTCAAATCAACACATTATTTGATAAAATTGTAATATAATAAT-A-A--TTTTTTATTTAAAT
* **
534753 ATTAAAATTTAGTAAATAATGTATTGTCAAATCGTCACATTATTTGATAAAAATTGTAATATAAT
127 ATTAAAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAAT
* **
534818 AATAATTTTTTATTTACATATTAAAATTTAATAAATAATGTATTGTCAAATCAATTCATT
192 AATAATTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
*
534878 ATTTGAT-AAAATGGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATGT
*
534942 ATTATCAAATCAACACATTATTTGATAAAACTTGTAATATAATAATAATTTTTTATTTAAATATT
66 ATTGTCAAATCAACACATTATTTGATAAAA-TTGTAATATAATAATAATTTTTTATTTAAATATT
*
535007 AAAATTTAGTAAATAATATATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAAT
130 AAAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAAT
*
535072 AACTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
195 AATTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
*
535129 A-TTGATAAAAATTGTAATATAATAATAA-TTTTTATTTACATATTAAAATTT-GATAAATAATG
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAG-TAAATAATG
* * * *
535191 CATTGTCAACTCAATACATTATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATAT
65 TATTGTCAAATCAACACATTATTTGAT-AAAATTGTAATATAATAATAATTTTTTATTTAAATAT
** * * * *
535256 TCGAATTTAATAAATAATATATTATCAAATCAACACATTATTTGATATAAATTGAAATATAATAA
129 TAAAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAA
535321 TAATATTTTTTATTTA
194 T-A-ATTTTTTATTTA
535337 AATAATGTTA
Statistics
Matches: 422, Mismatches: 30, Indels: 16
0.90 0.06 0.03
Matches are distributed among these distances:
249 1 0.00
250 150 0.36
251 157 0.37
252 11 0.03
253 19 0.05
254 71 0.17
255 13 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (251 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATGT
ATTGTCAAATCAACACATTATTTGATAAAATTGTAATATAATAATAATTTTTTATTTAAATATTA
AAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATA
ATTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
Found at i:535287 original size:250 final size:251
Alignment explanation
Indices: 534624--535323 Score: 1068
Period size: 250 Copynumber: 2.8 Consensus size: 251
534614 TAAATTTAAA
* *
534624 ATTTGATAAAAATTGTAATATAATAATATTTTTTATTTAAATATTAAAATTTAGTAAATAATATC
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTAAAATTTAGTAAATAAT-GC
* *
534689 -TTGTCAAATCAACATATTATTTGATAAAAA-TATAATATAATAATAATATTTTTTTTATTTAAA
65 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAAT-A-A--TTTTTTATTTAAA
* **
534752 TATTAAAATTTAGTAAATAATGTATTGTCAAATCGTCACATTATTTGATAAAAATTGTAATATAA
126 TATTAAAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAA
* * **
534817 TAATAATTTTTTATTTACATATTAAAATTTAATAAATAATGTATTGTCAAATCAATTCATT
191 TAATAACTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
* *
534878 ATTTGAT-AAAATGGTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATGT
1 ATTTGATAAAAATTGTAATATAATAATAA-TTTTTATTTAAATATTAAAATTTAGTAAATAATGC
* *
534942 ATTATCAAATCAACACATTATTTGATAAAACTTGTAATATAATAATAATTTTTTATTTAAATATT
65 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
*
535007 AAAATTTAGTAAATAATATATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAAT
130 AAAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAAT
535072 AACTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
195 AACTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
*
535129 A-TTGATAAAAATTGTAATATAATAATAATTTTTATTTACATATTAAAATTT-GATAAATAATGC
1 ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTAAAATTTAG-TAAATAATGC
* * *
535192 ATTGTCAACTCAATACATTATTTGATAAAAATTGTAATATAATAATAATTTTTAATTTAAATATT
65 ATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATT
** * * * *
535257 CGAATTTAATAAATAATATATTATCAAATCAACACATTATTTGATATAAATTGAAATATAATAAT
130 AAAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAAT
535322 AA
195 AA
535324 TATTTTTTAT
Statistics
Matches: 410, Mismatches: 31, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
249 1 0.00
250 156 0.38
251 152 0.37
253 20 0.05
254 68 0.17
255 13 0.03
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (251 bp):
ATTTGATAAAAATTGTAATATAATAATAATTTTTATTTAAATATTAAAATTTAGTAAATAATGCA
TTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTA
AAATTTAGTAAATAATATATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATA
ACTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAACACATT
Found at i:535495 original size:28 final size:28
Alignment explanation
Indices: 535455--535511 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
535445 AACATGAACC
*
535455 TTAATTTTTAAATTAATTTCAACATAAA
1 TTAATTTTCAAATTAATTTCAACATAAA
**
535483 TTAATTTTCAAATTAATTTTTACATAAA
1 TTAATTTTCAAATTAATTTCAACATAAA
535511 T
1 T
535512 ATTCTTCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAATTTTCAAATTAATTTCAACATAAA
Found at i:535511 original size:16 final size:16
Alignment explanation
Indices: 535463--535511 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
535453 CCTTAATTTT
**
535463 TAAATTAATTTCAACA
1 TAAATTAATTTTTACA
535479 TAAATTAA-TTTT-C-
1 TAAATTAATTTTTACA
535492 -AAATTAATTTTTACA
1 TAAATTAATTTTTACA
535507 TAAAT
1 TAAAT
535512 ATTCTTCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 2 0.07
15 2 0.07
16 12 0.44
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAATTTTTACA
Found at i:539454 original size:60 final size:60
Alignment explanation
Indices: 539240--539741 Score: 419
Period size: 60 Copynumber: 8.3 Consensus size: 60
539230 AGGGAAAGTT
* * * * *
539240 GGTGTCGGCCATTGTATGGCCAACACCCAAAAATTTGA-TTTTTTATTCAGATAAAAAAGAG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGAT-AAAAAG-G
* * ** * ** *
539301 GGTTTCGGCCATGGCATGGTCAACACAAAAAAAAATTAAAATTTTTTTATT-AGATAAATAGG
1 GGTGTCGACCATGGCATGACCAACAC--CAAAAAATT-TGATTTTTTTATTCAGATAAAAAGG
* * *
539363 GGTGTCGGCCATGGCATGACCAACACCCAAAACTTTGATTTTTTTATTCAGATAAAAATGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
* * * * * *
539424 GAGTGTTGACCATGGCATGACCAACACAAAAAAAATTGAAATTTTTTATT-TGATAAATAGG
1 G-GTGTCGACCATGGCATGACCAACACCAAAAAATTTG-ATTTTTTTATTCAGATAAAAAGG
* * * * * *
539485 GGTGTCGATCATGGCATGGCCAACACCCAAAAATTCGA-TTTTTTATCCAAATAAAAAGGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
* * * *
539545 GGTGTCGACCATGGCATGACCAACACAAAAAAAATTGGA-TTTTTTA-TCTGAAAAAAAGGG
1 GGTGTCGACCATGGCATGACCAACAC-CAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
* * * * *
539605 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGCTTTTTTT-TATCA-ATAAATAGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTAT-TCAGATAAAAAGG
* * * * * * *
539664 AGTGTCGGCCATGGCATGACCAACACCAAAAAAATTGAATTTTTCA-TCTGAAAAAAAGGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
*
539724 GGTGTCGACCATTGCATG
1 GGTGTCGACCATGGCATG
539742 GCAAACACAC
Statistics
Matches: 355, Mismatches: 69, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
58 10 0.03
59 71 0.20
60 131 0.37
61 46 0.13
62 61 0.17
63 22 0.06
64 5 0.01
65 9 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (60 bp):
GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAAGG
Found at i:539750 original size:119 final size:120
Alignment explanation
Indices: 539240--539749 Score: 539
Period size: 119 Copynumber: 4.2 Consensus size: 120
539230 AGGGAAAGTT
* * * * *
539240 GGTGTCGGCCATTGTATGGCCAACACCCAAAAATTTGATTTTTTAT-TCAGATAAAAAAGAGGGT
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTATCAGATAAAAAAG-GAGT
* * ** * * *
539304 TTCGGCCATGGCATGGTCAACACAAAAAAAAATTAAAATTTTTTTAT-TAGATAAATAGG
65 GTCGACCATGGCATGACCAACAC-AAAAAAAATT-GAA-TTTTTTATCT-GAAAAAAAGG
* * * * * *
539363 GGTGTCGGCCATGGCATGACCAACACCCAAAACTTTG-ATTTTTTTATTCAGATAAAAATGGGAG
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTA-TCAGATAAAAA-AGGAG
* * * *
539427 TGTTGACCATGGCATGACCAACACAAAAAAAATTGAAATTTTTTATTTGATAAATAGG
64 TGTCGACCATGGCATGACCAACACAAAAAAAATTG-AATTTTTTATCTGAAAAAAAGG
* * ** * * *
539485 GGTGTCGATCATGGCATGGCCAACACCCAAAAA-TT-CGATTTTTTATCCAAATAAAAAGGGGGT
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTAT-CAGATAAAAAAGGAGT
*
539548 GTCGACCATGGCATGACCAACACAAAAAAAATTGGATTTTTTATCTGAAAAAAAGGG
65 GTCGACCATGGCATGACCAACACAAAAAAAATTGAATTTTTTATCTGAAAAAAA-GG
** *
539605 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGCTTTTTTTTATCA-AT-AAATAGGAGTG
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTATCAGATAAAAAAGGAGTG
* * *
539668 TCGGCCATGGCATGACCAACACCAAAAAAATTGAATTTTTCATCTGAAAAAAAGGG
66 TCGACCATGGCATGACCAACACAAAAAAAATTGAATTTTTTATCTGAAAAAAA-GG
*
539724 GGTGTCGACCATTGCATGGCAAACAC
1 GGTGTCGACCATTGCATGGCCAACAC
539750 ACATGGCCGA
Statistics
Matches: 336, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
119 101 0.30
120 72 0.21
121 22 0.07
122 62 0.18
123 46 0.14
124 32 0.10
125 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (120 bp):
GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTATCAGATAAAAAAGGAGTG
TCGACCATGGCATGACCAACACAAAAAAAATTGAATTTTTTATCTGAAAAAAAGG
Found at i:542641 original size:84 final size:84
Alignment explanation
Indices: 542547--542912 Score: 538
Period size: 84 Copynumber: 4.4 Consensus size: 84
542537 NNNNNNNNNN
* *
542547 GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATATATTGTCAAATCAAC
1 GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATATATTATCAAATCAAC
*
542612 ATATTATTTGATAAAAATT
66 ACATTATTTGATAAAAATT
* * *
542631 GTAATATAATAATAACTTTTTATTTACATATTAAAATTTAATAAATAATGTATTATCAAATCAAC
1 GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATATATTATCAAATCAAC
542696 ACATTA-TTGATAAAAATT
66 ACATTATTTGATAAAAATT
* * ** * * *
542714 GTAATATAATAATAA-TTTTTATTTACATATTAAAATTTGATAAATAATGCATTGTCAACTCAAT
1 GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATATATTATCAAATCAAC
542778 ACATTATTTGATAAAAATT
66 ACATTATTTGATAAAAATT
* **
542797 GTAATATAATAATAATTTTTAATTTAAATATTCGAATTTAATAAATAATATATTATCAAATCAAC
1 GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATATATTATCAAATCAAC
*
542862 ACATTATTTGATATAAATT
66 ACATTATTTGATAAAAATT
*
542881 GAAATATAATAATAATATTTTTTATTTAAATA
1 GTAATATAATAAT-A-ATTTTTTATTTAAATA
542913 ATGTTAAATT
Statistics
Matches: 254, Mismatches: 24, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
82 50 0.20
83 54 0.21
84 134 0.53
85 1 0.00
86 15 0.06
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (84 bp):
GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAATAAATAATATATTATCAAATCAAC
ACATTATTTGATAAAAATT
Found at i:542837 original size:166 final size:167
Alignment explanation
Indices: 542547--542912 Score: 549
Period size: 166 Copynumber: 2.2 Consensus size: 167
542537 NNNNNNNNNN
*
542547 GTAATATAATAATAATTTTTTATTTAAATATTAAAATTTAGTAAATAATATATTGTCAAATCAAC
1 GTAATATAATAATAA-TTTTTATTTAAATATTAAAATTTAGTAAATAATACATTGTCAAATCAAC
* *
542612 ATATTATTTGATAAAAATTGTAATATAATAATAACTTTTTATTTACATATTAAAATTTAATAAAT
65 ACATTATTTGATAAAAATTGTAATATAATAATAACTTTTTATTTAAATATTAAAATTTAATAAAT
*
542677 AATGTATTATCAAATCAACACATTA-TTGATAAAAATT
130 AATATATTATCAAATCAACACATTATTTGATAAAAATT
* * * *
542714 GTAATATAATAATAATTTTTATTTACATATTAAAATTT-GATAAATAATGCATTGTCAACTCAAT
1 GTAATATAATAATAATTTTTATTTAAATATTAAAATTTAG-TAAATAATACATTGTCAAATCAAC
**
542778 ACATTATTTGATAAAAATTGTAATATAATAATAA-TTTTTAATTTAAATATTCGAATTTAATAAA
65 ACATTATTTGATAAAAATTGTAATATAATAATAACTTTTT-ATTTAAATATTAAAATTTAATAAA
*
542842 TAATATATTATCAAATCAACACATTATTTGATATAAATT
129 TAATATATTATCAAATCAACACATTATTTGATAAAAATT
*
542881 GAAATATAATAATAATATTTTTTATTTAAATA
1 GTAATATAATAAT-A-A-TTTTTATTTAAATA
542913 ATGTTAAATT
Statistics
Matches: 180, Mismatches: 13, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
165 6 0.03
166 121 0.67
167 38 0.21
168 1 0.01
169 1 0.01
170 13 0.07
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (167 bp):
GTAATATAATAATAATTTTTATTTAAATATTAAAATTTAGTAAATAATACATTGTCAAATCAACA
CATTATTTGATAAAAATTGTAATATAATAATAACTTTTTATTTAAATATTAAAATTTAATAAATA
ATATATTATCAAATCAACACATTATTTGATAAAAATT
Found at i:543067 original size:28 final size:28
Alignment explanation
Indices: 543027--543083 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
543017 AACATGAACC
*
543027 TTAATTTTTAAATTAATTTCAACATAAA
1 TTAATTTTCAAATTAATTTCAACATAAA
**
543055 TTAATTTTCAAATTAATTTTTACATAAA
1 TTAATTTTCAAATTAATTTCAACATAAA
543083 T
1 T
543084 ATTCTTCATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAATTTTCAAATTAATTTCAACATAAA
Found at i:543083 original size:16 final size:16
Alignment explanation
Indices: 543035--543083 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
543025 CCTTAATTTT
**
543035 TAAATTAATTTCAACA
1 TAAATTAATTTTTACA
543051 TAAATTAA-TTTT-C-
1 TAAATTAATTTTTACA
543064 -AAATTAATTTTTACA
1 TAAATTAATTTTTACA
543079 TAAAT
1 TAAAT
543084 ATTCTTCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
12 7 0.26
13 4 0.15
14 2 0.07
15 2 0.07
16 12 0.44
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAATTAATTTTTACA
Found at i:547026 original size:60 final size:60
Alignment explanation
Indices: 546812--547313 Score: 419
Period size: 60 Copynumber: 8.3 Consensus size: 60
546802 AGGGAAAGTT
* * * * *
546812 GGTGTCGGCCATTGTATGGCCAACACCCAAAAATTTGA-TTTTTTATTCAGATAAAAAAGAG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGAT-AAAAAG-G
* * ** * ** *
546873 GGTTTCGGCCATGGCATGGTCAACACAAAAAAAAATTAAAATTTTTTTATT-AGATAAATAGG
1 GGTGTCGACCATGGCATGACCAACAC--CAAAAAATT-TGATTTTTTTATTCAGATAAAAAGG
* * *
546935 GGTGTCGGCCATGGCATGACCAACACCCAAAACTTTGATTTTTTTATTCAGATAAAAATGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
* * * * * *
546996 GAGTGTTGACCATGGCATGACCAACACAAAAAAAATTGAAATTTTTTATT-TGATAAATAGG
1 G-GTGTCGACCATGGCATGACCAACACCAAAAAATTTG-ATTTTTTTATTCAGATAAAAAGG
* * * * * *
547057 GGTGTCGATCATGGCATGGCCAACACCCAAAAATTCGA-TTTTTTATCCAAATAAAAAGGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
* * * *
547117 GGTGTCGACCATGGCATGACCAACACAAAAAAAATTGGA-TTTTTTA-TCTGAAAAAAAGGG
1 GGTGTCGACCATGGCATGACCAACAC-CAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
* * * * *
547177 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGCTTTTTTT-TATCA-ATAAATAGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTAT-TCAGATAAAAAGG
* * * * * * *
547236 AGTGTCGGCCATGGCATGACCAACACCAAAAAAATTGAATTTTTCA-TCTGAAAAAAAGGG
1 GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAA-GG
*
547296 GGTGTCGACCATTGCATG
1 GGTGTCGACCATGGCATG
547314 GCAAACACAC
Statistics
Matches: 355, Mismatches: 69, Indels: 35
0.77 0.15 0.08
Matches are distributed among these distances:
58 10 0.03
59 71 0.20
60 131 0.37
61 46 0.13
62 61 0.17
63 22 0.06
64 5 0.01
65 9 0.03
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (60 bp):
GGTGTCGACCATGGCATGACCAACACCAAAAAATTTGATTTTTTTATTCAGATAAAAAGG
Found at i:547322 original size:119 final size:120
Alignment explanation
Indices: 546812--547321 Score: 539
Period size: 119 Copynumber: 4.2 Consensus size: 120
546802 AGGGAAAGTT
* * * * *
546812 GGTGTCGGCCATTGTATGGCCAACACCCAAAAATTTGATTTTTTAT-TCAGATAAAAAAGAGGGT
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTATCAGATAAAAAAG-GAGT
* * ** * * *
546876 TTCGGCCATGGCATGGTCAACACAAAAAAAAATTAAAATTTTTTTAT-TAGATAAATAGG
65 GTCGACCATGGCATGACCAACAC-AAAAAAAATT-GAA-TTTTTTATCT-GAAAAAAAGG
* * * * * *
546935 GGTGTCGGCCATGGCATGACCAACACCCAAAACTTTG-ATTTTTTTATTCAGATAAAAATGGGAG
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTA-TCAGATAAAAA-AGGAG
* * * *
546999 TGTTGACCATGGCATGACCAACACAAAAAAAATTGAAATTTTTTATTTGATAAATAGG
64 TGTCGACCATGGCATGACCAACACAAAAAAAATTG-AATTTTTTATCTGAAAAAAAGG
* * ** * * *
547057 GGTGTCGATCATGGCATGGCCAACACCCAAAAA-TT-CGATTTTTTATCCAAATAAAAAGGGGGT
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTAT-CAGATAAAAAAGGAGT
*
547120 GTCGACCATGGCATGACCAACACAAAAAAAATTGGATTTTTTATCTGAAAAAAAGGG
65 GTCGACCATGGCATGACCAACACAAAAAAAATTGAATTTTTTATCTGAAAAAAA-GG
** *
547177 GGTGTCGACCATTGCATGGCCAACACAAAAAAATTTGCTTTTTTTTATCA-AT-AAATAGGAGTG
1 GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTATCAGATAAAAAAGGAGTG
* * *
547240 TCGGCCATGGCATGACCAACACCAAAAAAATTGAATTTTTCATCTGAAAAAAAGGG
66 TCGACCATGGCATGACCAACACAAAAAAAATTGAATTTTTTATCTGAAAAAAA-GG
*
547296 GGTGTCGACCATTGCATGGCAAACAC
1 GGTGTCGACCATTGCATGGCCAACAC
547322 ACATGGCCGA
Statistics
Matches: 336, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
119 101 0.30
120 72 0.21
121 22 0.07
122 62 0.18
123 46 0.14
124 32 0.10
125 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.27
Consensus pattern (120 bp):
GGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGCTTTTTTTTATCAGATAAAAAAGGAGTG
TCGACCATGGCATGACCAACACAAAAAAAATTGAATTTTTTATCTGAAAAAAAGG
Done.