Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 174 of 193
Found at i:54280010 original size:21 final size:21
Alignment explanation
Indices: 54279985--54280029 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
54279975 ATTATTGAAA
54279985 TAAAATA-TTATTATAAAAAAT
1 TAAAATATTTATTAT-AAAAAT
*
54280006 TAAAATATTTCTTATAAAAAT
1 TAAAATATTTATTATAAAAAT
54280027 TAA
1 TAA
54280030 TTAGTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAAATATTTATTATAAAAAT
Found at i:54295838 original size:81 final size:82
Alignment explanation
Indices: 54295745--54295906 Score: 256
Period size: 82 Copynumber: 2.0 Consensus size: 82
54295735 CTCGTAAAAA
54295745 TAATAAATTTTGGCCTTGT-T-TATATAAAATAATAATAATTTCAATAAACAAATTAAATTAAAA
1 TAATAAATTTTGGCCTTGTGTGTATA-AAAATAATAATAATTTCAATAAACAAATTAAATTAAAA
54295808 TAGAGACTAAATTATAAT
65 TAGAGACTAAATTATAAT
* * *
54295826 TAATAATTTTTGGTCTTGTGTGTATAAAAATAATAATAATTTCAATAAACAAATTAAATTCAAAT
1 TAATAAATTTTGGCCTTGTGTGTATAAAAATAATAATAATTTCAATAAACAAATTAAATTAAAAT
* *
54295891 AGGGACTACATTATAA
66 AGAGACTAAATTATAA
54295907 ATCTAACAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 17 0.23
82 53 0.72
83 4 0.05
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.37
Consensus pattern (82 bp):
TAATAAATTTTGGCCTTGTGTGTATAAAAATAATAATAATTTCAATAAACAAATTAAATTAAAAT
AGAGACTAAATTATAAT
Found at i:54296411 original size:34 final size:33
Alignment explanation
Indices: 54296346--54296411 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
54296336 CACTTTATGT
* * *
54296346 AAATTTTAATATCTGTATTTTTATTATTTAAAG
1 AAATTTTAATATCTGTATTATCATTAATTAAAG
*
54296379 AAATTTTTATATCTGTATTATCATTACATTAAA
1 AAATTTTAATATCTGTATTATCATTA-ATTAAA
54296412 TATAAATTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 23 0.82
34 5 0.18
ACGTcount: A:0.38, C:0.06, G:0.05, T:0.52
Consensus pattern (33 bp):
AAATTTTAATATCTGTATTATCATTAATTAAAG
Found at i:54296802 original size:16 final size:18
Alignment explanation
Indices: 54296778--54296810 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
54296768 ATTTAAGTCC
54296778 TTTATAATTTAT-AAAAT
1 TTTATAATTTATGAAAAT
54296795 TTTA-AATTTATGAAAA
1 TTTATAATTTATGAAAA
54296811 GTATAAGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (18 bp):
TTTATAATTTATGAAAAT
Found at i:54297480 original size:29 final size:29
Alignment explanation
Indices: 54297438--54297544 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 29
54297428 GAAAAATGTC
* *
54297438 AAGTTCAGGCACCAAATTGGGTCCAAAAA
1 AAGTTCAGGTACCAAATTGGGTCAAAAAA
* *
54297467 AAGTTTAGGTACCAAATTAGG--AAAAAA
1 AAGTTCAGGTACCAAATTGGGTCAAAAAA
* *
54297494 TCTCAAGTTCATGTACTAAATTGGGTCAAAAAA
1 ----AAGTTCAGGTACCAAATTGGGTCAAAAAA
*
54297527 AAGTTTAGGTACCAAATT
1 AAGTTCAGGTACCAAATT
54297545 AAGAAAAAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
27 5 0.08
29 33 0.54
31 17 0.28
33 6 0.10
ACGTcount: A:0.43, C:0.14, G:0.18, T:0.25
Consensus pattern (29 bp):
AAGTTCAGGTACCAAATTGGGTCAAAAAA
Found at i:54297502 original size:60 final size:60
Alignment explanation
Indices: 54297387--54297574 Score: 252
Period size: 60 Copynumber: 3.1 Consensus size: 60
54297377 ATACATTAAG
** * * * *
54297387 GTACCAAATTGAATCTAAAAAAAGCTTAGGTGCCAAATTAGG-AAAAATGTCAAGTTCAG
1 GTACCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
* * * *
54297446 GCACCAAATTGGGTCCAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATCTCAAGTTCAT
1 GTACCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
* * *
54297506 GTACTAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAAGAAAAAGTGTCAAGTTCAA
1 GTACCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
54297566 GTACCAAAT
1 GTACCAAAT
54297575 ATTATATTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 36 0.32
60 76 0.68
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (60 bp):
GTACCAAATTGGGTCAAAAAAAAGTTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAA
Found at i:54302327 original size:35 final size:34
Alignment explanation
Indices: 54302281--54302360 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 34
54302271 TAGCAATCAG
* *
54302281 AATCCAATCAAAATCGAA-ATAATCCTAAATCGAA
1 AATCCAATCAAAATCGAATA-AACCCTAAATCAAA
54302315 AATCCAAATCAAAATCGAATAAACCCTAAATCAAA
1 AATCC-AATCAAAATCGAATAAACCCTAAATCAAA
54302350 AATCACAATCA
1 AATC-CAATCA
54302361 GTATCGACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
34 5 0.12
35 34 0.83
36 2 0.05
ACGTcount: A:0.55, C:0.23, G:0.04, T:0.19
Consensus pattern (34 bp):
AATCCAATCAAAATCGAATAAACCCTAAATCAAA
Found at i:54303201 original size:21 final size:20
Alignment explanation
Indices: 54303155--54303202 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
54303145 AGTTTTAAAC
54303155 AATTTTTAATTTTAAAAATA
1 AATTTTTAATTTTAAAAATA
**
54303175 AATTTTTAATTTTGGAAATA
1 AATTTTTAATTTTAAAAATA
*
54303195 AAGTTTTA
1 AATTTTTA
54303203 GATAATGTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
AATTTTTAATTTTAAAAATA
Found at i:54303439 original size:83 final size:80
Alignment explanation
Indices: 54303342--54303509 Score: 212
Period size: 81 Copynumber: 2.0 Consensus size: 80
54303332 ATCTCGTAAA
* *
54303342 AAATAATAAATTTTGGCCTTGTTTATATAGAAAAAAAATAATAATTTCAATAAA-AATTAAAATT
1 AAATAATAAATTTTGGACTTGTTTATATAG---AAAAATAATAATTACAATAAACAATT-AAATT
54303406 AAAATAGGGAATAAATTAT
62 AAAATAGGGAATAAATTAT
* * * * *
54303425 AAATAATAATTTTTGGAGTTGTTTATTTAGTAAAATAATAATTACAATAAACTAATTAAATTCAA
1 AAATAATAAATTTTGGACTTGTTTATATAGAAAAATAATAATTACAATAAAC-AATTAAATTAAA
*
54303490 ATAGGGACTAAATTAT
65 ATAGGGAATAAATTAT
54303506 AAAT
1 AAAT
54303510 CTAACAAAGC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
80 19 0.25
81 26 0.35
82 4 0.05
83 26 0.35
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (80 bp):
AAATAATAAATTTTGGACTTGTTTATATAGAAAAATAATAATTACAATAAACAATTAAATTAAAA
TAGGGAATAAATTAT
Found at i:54303966 original size:2 final size:2
Alignment explanation
Indices: 54303959--54303987 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
54303949 CAATCAGCTA
54303959 AT AT AT AT AT -T 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
54303988 TGTTCAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:54306169 original size:14 final size:13
Alignment explanation
Indices: 54306125--54306171 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
54306115 ATCTATATGT
54306125 TTTATGTTTAAATA
1 TTTAT-TTTAAATA
*
54306139 TTT-TTTTGAATA
1 TTTATTTTAAATA
*
54306151 GTTATATTTAAATA
1 TTTAT-TTTAAATA
54306165 TTTATTT
1 TTTATTT
54306172 GCATTTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
12 9 0.33
13 4 0.15
14 14 0.52
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TTTATTTTAAATA
Found at i:54312646 original size:24 final size:24
Alignment explanation
Indices: 54312602--54312648 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
54312592 ACTTTTTAAC
54312602 CTTATTTTCCTATTTTCATTTTTT
1 CTTATTTTCCTATTTTCATTTTTT
*
54312626 CTTA-TTTCTTATTTT-ATATTTTT
1 CTTATTTTCCTATTTTCAT-TTTTT
54312649 AACTCTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 15 0.71
24 4 0.19
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (24 bp):
CTTATTTTCCTATTTTCATTTTTT
Found at i:54312882 original size:13 final size:14
Alignment explanation
Indices: 54312860--54312892 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
54312850 AAAGCTTGAA
*
54312860 CATTACGAAGATTT
1 CATTAAGAAGATTT
54312874 -ATTAAGAAGATTT
1 CATTAAGAAGATTT
54312887 CATTAA
1 CATTAA
54312893 TTTCAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.36
Consensus pattern (14 bp):
CATTAAGAAGATTT
Found at i:54322043 original size:27 final size:27
Alignment explanation
Indices: 54322013--54322092 Score: 79
Period size: 27 Copynumber: 3.0 Consensus size: 27
54322003 TGACATCATA
* *
54322013 GATAGTTCATTGGGACAATAAACATGG
1 GATAGTTCATCGGGACAATAAACACGG
* * * *
54322040 GATAATCCGTCGGGATAATAAACACGG
1 GATAGTTCATCGGGACAATAAACACGG
** *
54322067 GATAGTTTGTCGGTACAATAAACACG
1 GATAGTTCATCGGGACAATAAACACG
54322093 AAAAAATTTG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (27 bp):
GATAGTTCATCGGGACAATAAACACGG
Found at i:54323882 original size:3 final size:3
Alignment explanation
Indices: 54323867--54323916 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
54323857 TAGCACACAA
* *
54323867 CCT CCT -CT TCT CCT CCT CCT CCT CCTT CCT -CT TCT CCT CCT CCT
1 CCT CCT CCT CCT CCT CCT CCT CCT CC-T CCT CCT CCT CCT CCT CCT
54323911 CCT CCT
1 CCT CCT
54323917 TCCTTTAGCT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 35 0.83
4 3 0.07
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (3 bp):
CCT
Found at i:54323901 original size:24 final size:24
Alignment explanation
Indices: 54323869--54323920 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
54323859 GCACACAACC
54323869 TCCTCTTCTCCTCCTCCTCCTCCT
1 TCCTCTTCTCCTCCTCCTCCTCCT
54323893 TCCTCTTCTCCTCCTCCTCCTCCT
1 TCCTCTTCTCCTCCTCCTCCTCCT
54323917 TCCT
1 TCCT
54323921 TTAGCTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (24 bp):
TCCTCTTCTCCTCCTCCTCCTCCT
Found at i:54324244 original size:19 final size:20
Alignment explanation
Indices: 54324217--54324255 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
54324207 TAGAAAAAAC
54324217 TTTTAATAATTAT-TTTAAA
1 TTTTAATAATTATATTTAAA
*
54324236 TTTTTATAATTATATTTAAA
1 TTTTAATAATTATATTTAAA
54324256 CATAAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAATAATTATATTTAAA
Found at i:54324808 original size:20 final size:20
Alignment explanation
Indices: 54324783--54324829 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
54324773 CCTTCGCCCA
54324783 CTCTCTCACCATGTGGGCCT
1 CTCTCTCACCATGTGGGCCT
54324803 CTCTCTCACCATGTGGGCCT
1 CTCTCTCACCATGTGGGCCT
*
54324823 CTTTCTC
1 CTCTCTC
54324830 CCTTTCTCGT
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:0.09, C:0.40, G:0.17, T:0.34
Consensus pattern (20 bp):
CTCTCTCACCATGTGGGCCT
Found at i:54327663 original size:54 final size:54
Alignment explanation
Indices: 54327593--54327700 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
54327583 TTTTAGGGAT
*
54327593 TTTTAATTTGATTAATGTTAAATATGTATAGAGGGTAATTTCATAAATATTTCA
1 TTTTAATTTAATTAATGTTAAATATGTATAGAGGGTAATTTCATAAATATTTCA
54327647 TTTTAATTTAATTAATGTTAAATATGTATAGAGGGTAATTTCATAAATATTTCA
1 TTTTAATTTAATTAATGTTAAATATGTATAGAGGGTAATTTCATAAATATTTCA
54327701 GAACGAGGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (54 bp):
TTTTAATTTAATTAATGTTAAATATGTATAGAGGGTAATTTCATAAATATTTCA
Found at i:54340139 original size:18 final size:19
Alignment explanation
Indices: 54340100--54340141 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
54340090 TTAATTTTTT
*
54340100 AAAAATTATTAAAAATAGA
1 AAAAATTATTAAAAATACA
*
54340119 AAAAATTA-TAAAATTACA
1 AAAAATTATTAAAAATACA
54340137 AAAAA
1 AAAAA
54340142 AATTCTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAATTATTAAAAATACA
Found at i:54340142 original size:19 final size:19
Alignment explanation
Indices: 54340100--54340142 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
54340090 TTAATTTTTT
*
54340100 AAAAATTATTAAAAATAGA
1 AAAAATTATTAAAAATAAA
*
54340119 AAAAATTA-TAAAATTACAA
1 AAAAATTATTAAAAATA-AA
54340138 AAAAA
1 AAAAA
54340143 ATTCTAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATTATTAAAAATAAA
Found at i:54343227 original size:18 final size:17
Alignment explanation
Indices: 54343199--54343267 Score: 102
Period size: 17 Copynumber: 4.0 Consensus size: 17
54343189 TAAATTGATT
*
54343199 TTAAATTTAAATTTAAA
1 TTAATTTTAAATTTAAA
54343216 TTAATTTTTAAATTTAAA
1 TTAA-TTTTAAATTTAAA
*
54343234 TTTATTTTAAATTTAAA
1 TTAATTTTAAATTTAAA
*
54343251 ATAATTTTAAATTTAAA
1 TTAATTTTAAATTTAAA
54343268 AATAAATTTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
17 32 0.68
18 15 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TTAATTTTAAATTTAAA
Found at i:54343229 original size:24 final size:23
Alignment explanation
Indices: 54343187--54343263 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
54343177 TTATGTTTGG
*
54343187 TTTAAATTGATTTTAAATTTAAA
1 TTTAAATTAATTTTAAATTTAAA
54343210 TTTAAATTAATTTTTAAATTTAAA
1 TTTAAATTAA-TTTTAAATTTAAA
** * * *
54343234 TTTATTTTAAATTTAAA-ATAAT
1 TTTAAATTAATTTTAAATTTAAA
54343256 TTTAAATT
1 TTTAAATT
54343264 TAAAAATAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
22 9 0.20
23 15 0.33
24 21 0.47
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
TTTAAATTAATTTTAAATTTAAA
Found at i:54343252 original size:7 final size:6
Alignment explanation
Indices: 54343198--54343278 Score: 78
Period size: 6 Copynumber: 13.8 Consensus size: 6
54343188 TTAAATTGAT
* *
54343198 TTTAAA TTTAAA TTTAAA -TTAATT TTTAAA TTTAAA TTT-AT TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
* * **
54343245 TTTAAA -ATAAT TTTAAA TTTAAA AATAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
54343279 GAGTCCAAAT
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
5 11 0.19
6 44 0.75
7 4 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:54343269 original size:18 final size:17
Alignment explanation
Indices: 54343204--54343278 Score: 96
Period size: 18 Copynumber: 4.3 Consensus size: 17
54343194 TGATTTTAAA
*
54343204 TTTAAATTTAAATTAATT
1 TTTAAATTTAAAATAA-T
* *
54343222 TTTAAATTTAAATTTAT
1 TTTAAATTTAAAATAAT
54343239 TTTAAATTTAAAATAAT
1 TTTAAATTTAAAATAAT
*
54343256 TTTAAATTTAAAAATAAA
1 TTTAAATTT-AAAATAAT
54343274 TTTAA
1 TTTAA
54343279 GAGTCCAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
17 25 0.48
18 27 0.52
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAAAATAAT
Found at i:54344131 original size:3 final size:3
Alignment explanation
Indices: 54344123--54344165 Score: 50
Period size: 3 Copynumber: 13.7 Consensus size: 3
54344113 AGATTTTTAT
* *
54344123 TAA TAA TAAA TAA TAA TAT TAA TAA TAA TGA TAA TAA TTAA TA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
54344166 TTAAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:54344144 original size:19 final size:19
Alignment explanation
Indices: 54344120--54344170 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
54344110 AAGAGATTTT
54344120 TATTAATAATAAATAATAA
1 TATTAATAATAAATAATAA
*
54344139 TATTAATAAT-AATGATAA
1 TATTAATAATAAATAATAA
*
54344157 TAATTAATATTAAA
1 T-ATTAATAATAAA
54344171 AAAATAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.29
19 18 0.64
20 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TATTAATAATAAATAATAA
Found at i:54344639 original size:29 final size:28
Alignment explanation
Indices: 54344607--54344874 Score: 150
Period size: 29 Copynumber: 9.3 Consensus size: 28
54344597 AAAATCATAT
*
54344607 TTTTGACCCTAAAATTTCCAAAAATTTCA
1 TTTTGACCCTAAAATTT-CAAAAATTACA
* * *
54344636 TTTTTACTCCCAAACTTTCAAAAATTACA
1 TTTTGAC-CCTAAAATTTCAAAAATTACA
* * *
54344665 TTTTTACCTCT-AAATTCCCAAAAATTCCA
1 TTTTGACC-CTAAAATT-TCAAAAATTACA
* *
54344694 TTTTAACCCTAAAACTTTCAAGAATTACA
1 TTTTGACCCTAAAA-TTTCAAAAATTACA
* *** *
54344723 TTTTTACCCCCTAACTTCTAAAAATT-CA
1 TTTTGACCCTAAAATTTC-AAAAATTACA
* * * *
54344751 TTTTGACCTCGAAACTTTAAAAAATTACC
1 TTTTGACC-CTAAAATTTCAAAAATTACA
* * * *
54344780 TTTTTACCCTCGAACTTTCAAAAATTTA-T
1 TTTTGACCCT-AAAATTTCAAAAA-TTACA
* * *
54344809 TTTTGACCTTAAAACTTCCAAAAATTCCA
1 TTTTGACCCTAAAA-TTTCAAAAATTACA
* *
54344838 TTTTGACCTCGAAACTTTC-AAAATTACCA
1 TTTTGACC-CTAAAATTTCAAAAATTA-CA
54344867 TTTT-ACCC
1 TTTTGACCC
54344875 CGAATATCCA
Statistics
Matches: 182, Mismatches: 43, Indels: 30
0.71 0.17 0.12
Matches are distributed among these distances:
27 1 0.01
28 40 0.22
29 125 0.69
30 16 0.09
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.38
Consensus pattern (28 bp):
TTTTGACCCTAAAATTTCAAAAATTACA
Found at i:54344696 original size:58 final size:54
Alignment explanation
Indices: 54344596--54344841 Score: 186
Period size: 58 Copynumber: 4.3 Consensus size: 54
54344586 TCAACTATCT
* * * *
54344596 AAAAATCATATTTTTGACCCTAAAATTTCCAAAAATTTCATTTTTACTCCCAAACTTTC
1 AAAAATTACATTTTT-ACCCT-AAA-TTCCAAAAA-TTCATTTTAAC-CCAAAACTTTC
54344655 AAAAATTACATTTTTACCTCTAAATTCCCAAAAATTCCATTTTAACCCTAAAACTTTC
1 AAAAATTACATTTTTACC-CTAAATT-CCAAAAATT-CATTTTAACCC-AAAACTTTC
* * * * * *
54344713 AAGAATTACATTTTTACCCCCTAACTTCTAAAAATTCATTTTGACCTCGAAACTTTA
1 AAAAATTACATTTTTA--CCCTAAATTCCAAAAATTCATTTTAACC-CAAAACTTTC
* * * * * * *
54344770 AAAAATTACCTTTTTACCCTCGAACTTTCAAAAATTTATTTTTGACCTTAAAACTTCC
1 AAAAATTACATTTTTACCCT--AAATTCCAAAAATTCA-TTTTAACC-CAAAACTTTC
*
54344828 AAAAATTCCATTTT
1 AAAAATTACATTTT
54344842 GACCTCGAAA
Statistics
Matches: 156, Mismatches: 21, Indels: 21
0.79 0.11 0.11
Matches are distributed among these distances:
55 4 0.03
57 49 0.31
58 80 0.51
59 21 0.13
60 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.02, T:0.38
Consensus pattern (54 bp):
AAAAATTACATTTTTACCCTAAATTCCAAAAATTCATTTTAACCCAAAACTTTC
Found at i:54344854 original size:58 final size:57
Alignment explanation
Indices: 54344647--54344860 Score: 218
Period size: 58 Copynumber: 3.7 Consensus size: 57
54344637 TTTTACTCCC
* * * *
54344647 AAACTTTCAAAAATTACATTTTTACCTCTAAA-TTCCCAAAAATTCCATTTTAACCCTA
1 AAACTTTCAAAAATTACATTTTTACCTCGAAACTT-TCAAAAATT-CATTTTGACCTTA
* * ** **
54344705 AAACTTTCAAGAATTACATTTTTACCCCCTAAC-TTCTAAAAATTCATTTTGACCTCG
1 AAACTTTCAAAAATTACATTTTTACCTCGAAACTTTC-AAAAATTCATTTTGACCTTA
* * *
54344762 AAACTTTAAAAAATTACCTTTTTACCCTCG-AACTTTCAAAAATTTATTTTTGACCTTA
1 AAACTTTCAAAAATTACATTTTTA-CCTCGAAACTTTCAAAAATTCA-TTTTGACCTTA
* * *
54344820 AAACTTCCAAAAATTCCATTTTGACCTCGAAACTTTCAAAA
1 AAACTTTCAAAAATTACATTTTTACCTCGAAACTTTCAAAA
54344861 TTACCATTTT
Statistics
Matches: 128, Mismatches: 22, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
57 47 0.37
58 81 0.63
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.36
Consensus pattern (57 bp):
AAACTTTCAAAAATTACATTTTTACCTCGAAACTTTCAAAAATTCATTTTGACCTTA
Found at i:54344862 original size:57 final size:57
Alignment explanation
Indices: 54344683--54344860 Score: 150
Period size: 57 Copynumber: 3.1 Consensus size: 57
54344673 TCTAAATTCC
* * * * * *
54344683 CAAAAATTCCATTTTAACC-CTAAAACTTTC-AAGAATTACATTTTTACCCCCTAAC-TT
1 CAAAAATT-CATTTTGACCTC-AAAAC-TTCAAAAAATTACCTTTTGACCCTCGAACTTT
* * *
54344740 CTAAAAATTCATTTTGACCTCGAAACTTTAAAAAATTACCTTTTTACCCTCGAACTTT
1 C-AAAAATTCATTTTGACCTCAAAACTTCAAAAAATTACCTTTTGACCCTCGAACTTT
* * *
54344798 CAAAAATTTATTTTTGACCTTAAAACTTCCAAAAATT-CCATTTTGA-CCTCGAAACTTT
1 CAAAAATTCA-TTTTGACCTCAAAACTTCAAAAAATTACC-TTTTGACCCTCG-AACTTT
54344856 CAAAA
1 CAAAA
54344861 TTACCATTTT
Statistics
Matches: 101, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
56 2 0.02
57 50 0.50
58 49 0.49
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (57 bp):
CAAAAATTCATTTTGACCTCAAAACTTCAAAAAATTACCTTTTGACCCTCGAACTTT
Found at i:54349110 original size:6 final size:6
Alignment explanation
Indices: 54349085--54349127 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
54349075 ACAATTCATA
* * *
54349085 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT T
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT T
54349128 TGATCACAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.21, C:0.30, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:54356052 original size:11 final size:10
Alignment explanation
Indices: 54355988--54356129 Score: 52
Period size: 10 Copynumber: 14.4 Consensus size: 10
54355978 CAAATGTGAT
54355988 AAAAA-TATAA
1 AAAAATTAT-A
54355998 AAAAATTA-A
1 AAAAATTATA
*
54356007 TAAAAACTATA
1 -AAAAATTATA
54356018 AAAATATT-T-
1 AAAA-ATTATA
* *
54356027 AAAATTTATT
1 AAAAATTATA
*
54356037 GAAAATTATGA
1 AAAAATTAT-A
54356048 AAAAATTAT-
1 AAAAATTATA
*
54356057 -AAAATTGT-
1 AAAAATTATA
54356065 AAAAATATATA
1 AAAAAT-TATA
*
54356076 GAAATATTGA-A
1 -AAAAATT-ATA
54356087 AAAAATTAT-
1 AAAAATTATA
*
54356096 -AAAATTTTA
1 AAAAATTATA
* * *
54356105 TAAAGTCATA
1 AAAAATTATA
54356115 AGAAAATTATA
1 A-AAAATTATA
54356126 AAAA
1 AAAA
54356130 TGTAAAGAAA
Statistics
Matches: 98, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
8 16 0.16
9 12 0.12
10 41 0.42
11 23 0.23
12 6 0.06
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.31
Consensus pattern (10 bp):
AAAAATTATA
Found at i:54356129 original size:39 final size:38
Alignment explanation
Indices: 54355987--54356129 Score: 116
Period size: 39 Copynumber: 3.7 Consensus size: 38
54355977 TCAAATGTGA
* *
54355987 TAAAAATATA-AAAAAATTA-ATAAAAACTATAAAAATAT-
1 TAAAAATATATAGAAAATTATA-AAAAATTAT-AAAAT-TG
* * *
54356025 TTAAAATTTATTGAAAATTATGAAAAAATTATAAAATTG
1 TAAAAATATATAGAAAATTAT-AAAAAATTATAAAATTG
*
54356064 TAAAAATATATAGAAATATTGA-AAAAAATTATAAAATTT
1 TAAAAATATATAGAAA-ATT-ATAAAAAATTATAAAATTG
*
54356103 TATAAAGTCATA-AGAAAATTATAAAAA
1 TA-AAAAT-ATATAGAAAATTATAAAAA
54356130 TGTAAAGAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 17
0.76 0.09 0.15
Matches are distributed among these distances:
38 10 0.12
39 51 0.59
40 20 0.23
41 5 0.06
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (38 bp):
TAAAAATATATAGAAAATTATAAAAAATTATAAAATTG
Found at i:54356139 original size:20 final size:21
Alignment explanation
Indices: 54356114--54356170 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 21
54356104 ATAAAGTCAT
54356114 AAGAAAATTATAAAAAT-GTA
1 AAGAAAATTATAAAAATCGTA
*
54356134 AAG-AAA-TATAAAATTCGTA
1 AAGAAAATTATAAAAATCGTA
*
54356153 AAAACAAATTATAAAAAT
1 AAGA-AAATTATAAAAAT
54356171 ACTATACTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 8 0.27
19 8 0.27
20 3 0.10
21 3 0.10
22 8 0.27
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (21 bp):
AAGAAAATTATAAAAATCGTA
Found at i:54356144 original size:29 final size:29
Alignment explanation
Indices: 54355990--54356146 Score: 90
Period size: 29 Copynumber: 5.3 Consensus size: 29
54355980 AATGTGATAA
54355990 AAATATAAAAAAATTAATAAAAACTATA-A-
1 AAATATAAAAAAATT-ATAAAAA-TATATAG
** * *
54356019 AAATATTTAAAATTTATTGAAAAT-TAT-G
1 AAATATAAAAAAATTA-TAAAAATATATAG
* * * *
54356047 AAAAAATTATAAAATTGTAAAAATATATAG
1 -AAATATAAAAAAATTATAAAAATATATAG
* *
54356077 AAATATTGAAAAAAATTATAAAATTTTATA-
1 AAATA-T-AAAAAAATTATAAAAATATATAG
* * * *
54356107 AAGTCATAAGAAAATTATAAAAATGTAAAG
1 AAAT-ATAAAAAAATTATAAAAATATATAG
54356137 AAATATAAAA
1 AAATATAAAA
54356147 TTCGTAAAAA
Statistics
Matches: 95, Mismatches: 23, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
27 2 0.02
28 8 0.08
29 58 0.61
30 9 0.09
31 18 0.19
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (29 bp):
AAATATAAAAAAATTATAAAAATATATAG
Found at i:54356364 original size:9 final size:9
Alignment explanation
Indices: 54356350--54356489 Score: 55
Period size: 9 Copynumber: 14.4 Consensus size: 9
54356340 TTTTGATGCA
54356350 TTTTATAAT
1 TTTTATAAT
* *
54356359 TTTTATGAG
1 TTTTATAAT
*
54356368 TTTTATAAAA
1 TTTTAT-AAT
*
54356378 TTTTACAAT
1 TTTTATAAT
*
54356387 TTTGTACAATT
1 TTT-TATAA-T
*
54356398 TTTTATTAT
1 TTTTATAAT
54356407 TTTTATAATT
1 TTTTATAA-T
* *
54356417 ATTTTCTTAT
1 -TTTTATAAT
*
54356427 TTTTAATAAAA
1 TTTT-AT-AAT
*
54356438 TTTTAAATAT
1 TTTTATA-AT
*
54356448 TTTTATAAC
1 TTTTATAAT
* *
54356457 CTTTATTGAT
1 TTTTA-TAAT
**
54356467 TTTTATTTT
1 TTTTATAAT
54356476 TTTTATAAT
1 TTTTATAAT
54356485 ATTTT
1 -TTTT
54356490 TACCACATGT
Statistics
Matches: 95, Mismatches: 26, Indels: 19
0.68 0.19 0.14
Matches are distributed among these distances:
9 45 0.47
10 35 0.37
11 15 0.16
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:54356440 original size:20 final size:20
Alignment explanation
Indices: 54356350--54356455 Score: 69
Period size: 20 Copynumber: 5.4 Consensus size: 20
54356340 TTTTGATGCA
* *
54356350 TTTTATAAT--TTTTATGAG
1 TTTTATAATAATTTTATTAT
**
54356368 TTTTATAA-AATTTTACAAT
1 TTTTATAATAATTTTATTAT
* *
54356387 TTTGTACAAT-TTTTTATTAT
1 TTT-TATAATAATTTTATTAT
* *
54356407 TTTTATAATTATTTTCTTAT
1 TTTTATAATAATTTTATTAT
*
54356427 TTTTAATAA-AATTTTAAATAT
1 TTTT-ATAATAATTTT-ATTAT
54356448 TTTTATAA
1 TTTTATAA
54356456 CCTTTATTGA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
18 8 0.12
19 14 0.21
20 35 0.51
21 11 0.16
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTTATAATAATTTTATTAT
Found at i:54358205 original size:13 final size:13
Alignment explanation
Indices: 54358187--54358220 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
54358177 TCTTCTTTTG
54358187 AGGGTTTTAATTT
1 AGGGTTTTAATTT
54358200 AGGGTTTTAATTT
1 AGGGTTTTAATTT
54358213 AGGGTTTT
1 AGGGTTTT
54358221 TTTAGGAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (13 bp):
AGGGTTTTAATTT
Found at i:54358642 original size:9 final size:9
Alignment explanation
Indices: 54358616--54358653 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
54358606 TAATATAATT
*
54358616 TTATTCGAT
1 TTATTCGAA
54358625 TTATTCGAA
1 TTATTCGAA
54358634 TTATTCGAA
1 TTATTCGAA
*
54358643 TAATTCGAA
1 TTATTCGAA
54358652 TT
1 TT
54358654 CGAAAATTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.47
Consensus pattern (9 bp):
TTATTCGAA
Found at i:54358998 original size:17 final size:17
Alignment explanation
Indices: 54358973--54359018 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
54358963 GCTGGTATTC
*
54358973 CTAAATTATTGAACTTA
1 CTAAGTTATTGAACTTA
**
54358990 CTAAGTTATAAAACTTA
1 CTAAGTTATTGAACTTA
54359007 CTACAGTTATTG
1 CTA-AGTTATTG
54359019 TTGTTGTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (17 bp):
CTAAGTTATTGAACTTA
Found at i:54359463 original size:58 final size:58
Alignment explanation
Indices: 54359401--54359518 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
54359391 AGGGTAGGAG
54359401 AGAGGTTGTTCTCTGACTTGTATTGTATTGTATTGGTAGTTTAATTACAGGTATCGGT
1 AGAGGTTGTTCTCTGACTTGTATTGTATTGTATTGGTAGTTTAATTACAGGTATCGGT
54359459 AGAGGTTGTTCTCTGACTTGTATTGTATTGTATTGGTAGTTTAATTACAGGTATCGGT
1 AGAGGTTGTTCTCTGACTTGTATTGTATTGTATTGGTAGTTTAATTACAGGTATCGGT
54359517 AG
1 AG
54359519 TTCATAGTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.21, C:0.08, G:0.26, T:0.44
Consensus pattern (58 bp):
AGAGGTTGTTCTCTGACTTGTATTGTATTGTATTGGTAGTTTAATTACAGGTATCGGT
Found at i:54361511 original size:10 final size:10
Alignment explanation
Indices: 54361438--54361581 Score: 52
Period size: 10 Copynumber: 14.5 Consensus size: 10
54361428 AAATATGATA
*
54361438 AAAAAAATAT
1 AAAAAATTAT
54361448 AAAAAATTA-
1 AAAAAATTAT
*
54361457 ATAAAAACTAT
1 A-AAAAATTAT
54361468 AAAAATATT-T
1 AAAAA-ATTAT
*
54361478 -AAAATTTAT
1 AAAAAATTAT
** *
54361487 TGAAAATTAGG
1 AAAAAATTA-T
54361498 AAAAAATTAT
1 AAAAAATTAT
**
54361508 --AAAATCGT
1 AAAAAATTAT
54361516 -AAAAATATAT
1 AAAAAAT-TAT
*
54361526 AGAAATATTGA-
1 A-AAAAATT-AT
54361537 AAAAAATT-T
1 AAAAAATTAT
* *
54361546 ATAAAATTTT
1 AAAAAATTAT
* *
54361556 ATAAAATCAT
1 AAAAAATTAT
54361566 AAAAAAATTAT
1 -AAAAAATTAT
54361577 AAAAA
1 AAAAA
54361582 TGTAAAGAAA
Statistics
Matches: 99, Mismatches: 21, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
8 8 0.08
9 18 0.18
10 47 0.47
11 20 0.20
12 6 0.06
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:54361817 original size:9 final size:9
Alignment explanation
Indices: 54361803--54361939 Score: 60
Period size: 9 Copynumber: 14.4 Consensus size: 9
54361793 TTTTGATGCA
54361803 TTTTATAAT
1 TTTTATAAT
* *
54361812 TTTTATGAG
1 TTTTATAAT
*
54361821 TTTTATAAAA
1 TTTTAT-AAT
*
54361831 TTTTACAAT
1 TTTTATAAT
*
54361840 TTTGTACAATT
1 TTT-TATAA-T
*
54361851 TTTTATTAT
1 TTTTATAAT
*
54361860 TTTTGTAATT
1 TTTTATAA-T
*
54361870 ATTTTCTAAT
1 -TTTTATAAT
*
54361880 TTTTAATAAA
1 TTTT-ATAAT
*
54361890 TTTTAAATAT
1 TTTTATA-AT
*
54361900 TTTTATAAC
1 TTTTATAAT
* *
54361909 CTTTATTGAT
1 TTTTA-TAAT
* *
54361919 TTTCAT-TT
1 TTTTATAAT
54361927 TTTTATAAT
1 TTTTATAAT
54361936 TTTT
1 TTTT
54361940 TACCACATGT
Statistics
Matches: 94, Mismatches: 25, Indels: 18
0.69 0.18 0.13
Matches are distributed among these distances:
8 6 0.06
9 42 0.45
10 35 0.37
11 11 0.12
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:54362272 original size:90 final size:89
Alignment explanation
Indices: 54362043--54362272 Score: 252
Period size: 89 Copynumber: 2.6 Consensus size: 89
54362033 TTAAATAGCC
* * * ** *
54362043 TTTTTGATGCA-TTTAACAGTTCAAGTATCCAATTGAGTGCAAAAAGAATTAGGGGTTTAATTGC
1 TTTTTGATGCATTTTAAAAGTTCAAGTA-CCAAATGAGTGCAAAAAAAAAAAGGGGCTTAATTGC
*
54362107 TTTTTTTTGAAAAAATTTGAGAGCT
65 TTTTTTTTGAAAAAATTTGAGAACT
** ** *
54362132 TTTTTGATTAATTTTGGAAGTTCAAGTACCAAATTGAGTGCAAAAAAAAAAGGGGGCTTAATTGC
1 TTTTTGATGCATTTTAAAAGTTCAAGTACCAAA-TGAGTGCAAAAAAAAAAAGGGGCTTAATTGC
54362197 -TTTTTTTGAAAAAATTT-A-AACATT
65 TTTTTTTTGAAAAAATTTGAGAAC--T
* * *
54362221 TTTTTAATGCATTTTAAAAGTTTAAGTACCCAAATAAGTGCAAAAAAAAAAA
1 TTTTTGATGCATTTTAAAAGTTCAAGTA-CCAAATGAGTGCAAAAAAAAAAA
54362273 AAAAAACAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
87 2 0.02
88 1 0.01
89 69 0.59
90 44 0.38
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (89 bp):
TTTTTGATGCATTTTAAAAGTTCAAGTACCAAATGAGTGCAAAAAAAAAAAGGGGCTTAATTGCT
TTTTTTTGAAAAAATTTGAGAACT
Found at i:54366180 original size:42 final size:42
Alignment explanation
Indices: 54366133--54366215 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
54366123 AAAAGAAATT
* *
54366133 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGAGTTTA
*
54366175 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGAGTTT
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTT
54366216 TAAAATATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGAGTTTA
Found at i:54374173 original size:58 final size:58
Alignment explanation
Indices: 54374102--54374231 Score: 165
Period size: 58 Copynumber: 2.2 Consensus size: 58
54374092 ACTCGGGGGC
* * * *
54374102 AAAATGGTAATTTTAGTTAAAATTG-GGTCAAAACGGGAATTTTGGAAAGTTC-AGGAGT
1 AAAATGGTAATTTT-GGTAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCAAAG-GT
* * *
54374160 AAAATGGTAATTTTGGTGAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTTAAAGGT
1 AAAATGGTAATTTTGGTAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCAAAGGT
54374218 AAAATGGTAATTTT
1 AAAATGGTAATTTT
54374232 CAAAAAGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
57 7 0.11
58 54 0.86
59 2 0.03
ACGTcount: A:0.39, C:0.04, G:0.25, T:0.32
Consensus pattern (58 bp):
AAAATGGTAATTTTGGTAAAATCGAGGTCAAAAAGGGAATTTTGGAAAGTTCAAAGGT
Found at i:54374221 original size:29 final size:29
Alignment explanation
Indices: 54374190--54374300 Score: 98
Period size: 29 Copynumber: 3.8 Consensus size: 29
54374180 ATCGAGGTCA
*
54374190 AAAATGGAATTTTGGAAAGTTTAAAGG-T
1 AAAATGGAATTTTGAAAAGTTTAAAGGTT
* ***
54374218 AAAATGGTAATTTTCAAAAAGTTTTGGGGTT
1 AAAATGG-AATTTT-GAAAAGTTTAAAGGTT
** *
54374249 AAAATATAATTTTGAAAAGTTTAAGGGTT
1 AAAATGGAATTTTGAAAAGTTTAAAGGTT
* *
54374278 AAAATGTAATTTTTAAAAAGTTT
1 AAAATGGAA-TTTTGAAAAGTTT
54374301 TGGGGTTAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
28 7 0.10
29 27 0.40
30 27 0.40
31 6 0.09
ACGTcount: A:0.42, C:0.01, G:0.19, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTGAAAAGTTTAAAGGTT
Found at i:54374241 original size:30 final size:29
Alignment explanation
Indices: 54374190--54374320 Score: 129
Period size: 30 Copynumber: 4.4 Consensus size: 29
54374180 ATCGAGGTCA
* ** *
54374190 AAAATGGAATTTTGGAAAGTTTAAAGG-T
1 AAAATGTAATTTTAAAAAGTTTAAGGGTT
**
54374218 AAAATGGTAATTTTCAAAAAGTTTTGGGGTT
1 AAAAT-GTAATTTT-AAAAAGTTTAAGGGTT
* *
54374249 AAAATATAATTTTGAAAAGTTTAAGGGTT
1 AAAATGTAATTTTAAAAAGTTTAAGGGTT
**
54374278 AAAATGTAATTTTTAAAAAGTTTTGGGGTT
1 AAAATGTAA-TTTTAAAAAGTTTAAGGGTT
*
54374308 AAAATATAATTTT
1 AAAATGTAATTTT
54374321 TGGACAGTCG
Statistics
Matches: 84, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
28 5 0.06
29 32 0.38
30 41 0.49
31 6 0.07
ACGTcount: A:0.41, C:0.01, G:0.19, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTAAAAAGTTTAAGGGTT
Found at i:54374268 original size:59 final size:59
Alignment explanation
Indices: 54374197--54374320 Score: 205
Period size: 59 Copynumber: 2.1 Consensus size: 59
54374187 TCAAAAATGG
*
54374197 AATTTTGGAAAGTTTAAAGG-TAAAATGGTAATTTTCAAAAAGTTTTGGGGTTAAAATAT
1 AATTTTGAAAAGTTTAAAGGTTAAAAT-GTAATTTTCAAAAAGTTTTGGGGTTAAAATAT
* *
54374256 AATTTTGAAAAGTTTAAGGGTTAAAATGTAATTTTTAAAAAGTTTTGGGGTTAAAATAT
1 AATTTTGAAAAGTTTAAAGGTTAAAATGTAATTTTCAAAAAGTTTTGGGGTTAAAATAT
54374315 AATTTT
1 AATTTT
54374321 TGGACAGTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 55 0.90
60 6 0.10
ACGTcount: A:0.40, C:0.01, G:0.19, T:0.40
Consensus pattern (59 bp):
AATTTTGAAAAGTTTAAAGGTTAAAATGTAATTTTCAAAAAGTTTTGGGGTTAAAATAT
Found at i:54374321 original size:30 final size:30
Alignment explanation
Indices: 54374225--54374321 Score: 142
Period size: 30 Copynumber: 3.3 Consensus size: 30
54374215 GGTAAAATGG
*
54374225 TAATTTTCAAAAAGTTTTGGGGTTAAAATA
1 TAATTTTTAAAAAGTTTTGGGGTTAAAATA
* ** *
54374255 TAA-TTTTGAAAAGTTTAAGGGTTAAAATG
1 TAATTTTTAAAAAGTTTTGGGGTTAAAATA
54374284 TAATTTTTAAAAAGTTTTGGGGTTAAAATA
1 TAATTTTTAAAAAGTTTTGGGGTTAAAATA
54374314 TAATTTTT
1 TAATTTTT
54374322 GGACAGTCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
29 24 0.42
30 33 0.58
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.43
Consensus pattern (30 bp):
TAATTTTTAAAAAGTTTTGGGGTTAAAATA
Found at i:54375401 original size:26 final size:26
Alignment explanation
Indices: 54375352--54375401 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
54375342 ATTTTTTTTG
* **
54375352 AAATAATATTTATTATTATTATTATT
1 AAATAATATTTATTATAACAATTATT
*
54375378 AAATATTATTTATTATAACAATTA
1 AAATAATATTTATTATAACAATTA
54375402 ATATTATGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
AAATAATATTTATTATAACAATTATT
Found at i:54376073 original size:17 final size:17
Alignment explanation
Indices: 54376051--54376093 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
54376041 CTTCATTTAA
*
54376051 TTAAATTTATAATAATT
1 TTAAATTTATAATAAAT
*
54376068 TTAAATTTATATTAAAT
1 TTAAATTTATAATAAAT
54376085 TTAAATTTA
1 TTAAATTTA
54376094 AAGTGATTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAATTTATAATAAAT
Found at i:54376699 original size:6 final size:6
Alignment explanation
Indices: 54376679--54376737 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
54376669 TTAAATGAGT
* * *
54376679 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTCA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
54376727 TTTAAG TTTAA
1 TTTAAA TTTAA
54376738 TCAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:54376714 original size:14 final size:14
Alignment explanation
Indices: 54376695--54376721 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54376685 TTTATTTTAA
54376695 ATTTAAATTTACTC
1 ATTTAAATTTACTC
54376709 ATTTAAATTTACT
1 ATTTAAATTTACT
54376722 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATTTACTC
Found at i:54377453 original size:25 final size:24
Alignment explanation
Indices: 54377425--54377472 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
54377415 ATTGAATATT
54377425 TAATATT-ATAACAAATTAATAATAG
1 TAATATTGATAAC-AATT-ATAATAG
*
54377450 TAATATTGATAGCAATTATAATA
1 TAATATTGATAACAATTATAATA
54377473 TTTATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (24 bp):
TAATATTGATAACAATTATAATAG
Found at i:54377511 original size:14 final size:14
Alignment explanation
Indices: 54377475--54377517 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54377465 TTATAATATT
*
54377475 TATTAAT-ATTAAA
1 TATTAATAATAAAA
* *
54377488 TAATATTAATAAAA
1 TATTAATAATAAAA
54377502 TATTAATAATAAAA
1 TATTAATAATAAAA
54377516 TA
1 TA
54377518 GTAAAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATTAATAATAAAA
Found at i:54378644 original size:59 final size:59
Alignment explanation
Indices: 54378514--54378944 Score: 548
Period size: 59 Copynumber: 7.4 Consensus size: 59
54378504 GAACTGTCTG
* * * *
54378514 AAAATTACCATTTTACCCCTAAACTTTCTAAAACT-CAATTTTAACCCCGATTTTATCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
54378572 AAAATTACCATTTTA-CCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGGTTTCATCA
1 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
54378631 ATAATTACCATTTTACCTCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CC
1 AAAATTACCATTTTACC-CCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * ** *
54378689 AAAATTATCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCTAATTTCACCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* *
54378748 AAAATTACCA-TTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTAATCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
** * *
54378806 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTATTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* ** * * *
54378865 AAAATTACCATTTTACCCCTAAACTTTCTAAGCTTCCATTTTTAATCCCGATCTCACCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* *
54378924 AAAATTAACATTTTGCCCCTA
1 AAAATTACCATTTTACCCCTA
54378945 CGTGTCTAAA
Statistics
Matches: 323, Mismatches: 43, Indels: 13
0.85 0.11 0.03
Matches are distributed among these distances:
57 6 0.02
58 126 0.39
59 188 0.58
60 1 0.00
61 2 0.01
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:54378722 original size:117 final size:118
Alignment explanation
Indices: 54378514--54378943 Score: 555
Period size: 117 Copynumber: 3.7 Consensus size: 118
54378504 GAACTGTCTG
* * * * *
54378514 AAAATTACCATTTTACCCCTAAACTTTCTAAAACT-CAATTTTAACCCCGATTTTATCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTCATCAAAAATT
* *
54378578 ACCATTTTA-CCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGGTTTCATCA
66 ACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * *
54378631 ATAATTACCATTTTACCTCC-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CCAAAAT
1 AAAATTACCATTTTACC-CCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTCATCAAAAAT
* * * ** *
54378694 TATCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCTAATTTCACCA
65 TACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
*
54378748 AAAATTACCA-TTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTAATCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTCATCAAAAATT
* * *
54378812 ACCATTTTACCCCCGAACTTTCCAAAATTCCATTATTAACCTCGATTTCATCA
66 ACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* ** * *
54378865 AAAATTACCATTTTACCCCTAAACTTTCTAAGCTTCCATTTTTAATCCCGATCTCACCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTCATCAAAAATT
* *
54378930 AACATTTTGCCCCT
66 ACCATTTTACCCCT
54378944 ACGTGTCTAA
Statistics
Matches: 269, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
115 2 0.01
116 39 0.14
117 145 0.54
118 83 0.31
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (118 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATCTCATCAAAAATT
ACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:54391253 original size:38 final size:38
Alignment explanation
Indices: 54391211--54391489 Score: 213
Period size: 38 Copynumber: 7.3 Consensus size: 38
54391201 CCTATCCTCT
54391211 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
*** ** *
54391249 TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTATCCTC
1 TGAAATTGAAGT-AGAGTTGGATAACAAGTCTTTAT-CTC
* *
54391286 TTGAAATTGAAGTAGAGTCGGGTAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
* * * ** *
54391325 TGAAATGGAAGTAAAG--GCA-ACATCATTTC-CTATCCTC
1 TGAAATTGAAGTAGAGTTGGATA-A-CAAGTCTTTAT-CTC
54391362 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
** *
54391401 TGAAATTGAAGTA-AG--GGCA-AGATCATTTC-CTATCCTC
1 TGAAATTGAAGTAGAGTTGG-ATA-A-CAAGTCTTTAT-CTC
54391438 TTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
1 -TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
54391477 TGAAATTGAAGTA
1 TGAAATTGAAGTA
54391490 AGGGCAAGGT
Statistics
Matches: 185, Mismatches: 32, Indels: 48
0.70 0.12 0.18
Matches are distributed among these distances:
35 4 0.02
36 13 0.07
37 29 0.16
38 91 0.49
39 30 0.16
40 14 0.08
41 4 0.02
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (38 bp):
TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
Found at i:54391320 original size:76 final size:76
Alignment explanation
Indices: 54391194--54391750 Score: 697
Period size: 76 Copynumber: 7.0 Consensus size: 76
54391184 AAGCACCAAC
54391194 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
54391259 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
54391270 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTCGGGTAACAAGTCTTTATCTCTGAAATGGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
54391335 GTAA-AGGCAAC
66 GTAAGA-GCAAG
54391346 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
54391411 GTAAGGGCAAG
66 GTAAGAGCAAG
54391422 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
54391487 GTAAGGGCAAG
66 GTAAGAGCAAG
* * * * * *
54391498 GTCATTTCCTATCCTCTTGAAATTGAAGTATCCTATCCTCTTGAAATTGAAGTAGAGT-TGGATA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTA---GA----GTTG-GA-T-AA-CA-AGTCT--TTA
* * **
54391562 ACAAATCTTTATCTCTGAAATTGAAGTAAGAGCAAG
52 TC---TC-TGAAAT-TG-A-----AGTAAGAGCAAG
*
54391598 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTTGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
54391663 GTAAGAGCAAG
66 GTAAGAGCAAG
*
54391674 ATCATTTCCTATCCTCTTGAAATTGAAGCAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
54391739 -TAAGAGCAAG
66 GTAAGAGCAAG
54391749 AT
1 AT
54391751 GAAGCCTCAA
Statistics
Matches: 420, Mismatches: 33, Indels: 57
0.82 0.06 0.11
Matches are distributed among these distances:
75 13 0.03
76 320 0.76
79 1 0.00
81 1 0.00
82 2 0.00
83 6 0.01
84 3 0.01
85 1 0.00
86 2 0.00
87 5 0.01
88 6 0.01
89 5 0.01
90 2 0.00
91 1 0.00
92 3 0.01
93 5 0.01
94 2 0.00
95 1 0.00
97 1 0.00
100 40 0.10
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:54391519 original size:38 final size:38
Alignment explanation
Indices: 54391249--54391527 Score: 162
Period size: 38 Copynumber: 7.3 Consensus size: 38
54391239 TCTTTATCTC
* *
54391249 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCT
* * ** *
54391287 TGAAATTGAAGT-AGAGTC-GGGTAACAAGTCTTTAT-CTC-
1 TGAAATTGAAGTAAG-GGCAAGGT--CATTTC-CTATCCTCT
* * **
54391325 TGAAATGGAAGTAAAGGCAACATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCT
54391363 TGAAATTGAAGTAGAGTTGGATAACAA-GTC--TT--TAT-CTC-
1 TGAAATTGAAGTA-AG--GG----CAAGGTCATTTCCTATCCTCT
*
54391401 TGAAATTGAAGTAAGGGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCT
54391439 TGAAATTGAAGTAGAGTTGGATAACAA-GTC--TT--TAT-CTC-
1 TGAAATTGAAGTA-AG--GG----CAAGGTCATTTCCTATCCTCT
54391477 TGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCT
54391515 TGAAATTGAAGTA
1 TGAAATTGAAGTA
54391528 TCCTATCCTC
Statistics
Matches: 184, Mismatches: 21, Indels: 72
0.66 0.08 0.26
Matches are distributed among these distances:
31 6 0.03
32 5 0.03
34 4 0.02
35 4 0.02
36 9 0.05
37 21 0.11
38 90 0.49
39 18 0.10
40 9 0.05
41 4 0.02
42 4 0.02
44 4 0.02
45 6 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (38 bp):
TGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCT
Found at i:54391536 original size:24 final size:24
Alignment explanation
Indices: 54391504--54391551 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
54391494 CAAGGTCATT
54391504 TCCTATCCTCTTGAAATTGAAGTA
1 TCCTATCCTCTTGAAATTGAAGTA
54391528 TCCTATCCTCTTGAAATTGAAGTA
1 TCCTATCCTCTTGAAATTGAAGTA
54391552 GAGTTGGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (24 bp):
TCCTATCCTCTTGAAATTGAAGTA
Found at i:54391573 original size:252 final size:251
Alignment explanation
Indices: 54391276--54391748 Score: 840
Period size: 252 Copynumber: 1.9 Consensus size: 251
54391266 CAAGATCATT
* *
54391276 TCCTATCCTCTTGAAATTGAAGTAGAGTCGGGTAACAAGTCTTTATCTCTGAAATGGAAGTAA-A
1 TCCTATCCTCTTGAAATTGAAGTAGAGTCGGATAACAAATCTTTATCTCTGAAATGGAAGTAAGA
54391340 GGCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
66 -GCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAA
* *
54391405 ATTGAAGTAAGGGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCT
130 ATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGCAGAGTTGGATAACAAGTCT
*
54391470 TTATCTCTGAAATTGAAGTAAGGGCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTA
195 TTATCTCTGAAATTGAA-TAAGAGCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTA
* *
54391528 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
1 TCCTATCCTCTTGAAATTGAAGTAGAGTCGGATAACAAATCTTTATCTCTGAAATGGAAGTAAGA
* *
54391593 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTTGATAACAAGTCTTTATCTCTGAAA
66 GCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
54391658 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGCAGAGTTGGATAACAAGTCTT
131 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGCAGAGTTGGATAACAAGTCTT
54391723 TATCTCTGAAATTGAATAAGAGCAAG
196 TATCTCTGAAATTGAATAAGAGCAAG
54391749 ATGAAGCCTC
Statistics
Matches: 211, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
251 9 0.04
252 201 0.95
253 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (251 bp):
TCCTATCCTCTTGAAATTGAAGTAGAGTCGGATAACAAATCTTTATCTCTGAAATGGAAGTAAGA
GCAACATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGCAGAGTTGGATAACAAGTCTT
TATCTCTGAAATTGAATAAGAGCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTA
Found at i:54391603 original size:100 final size:100
Alignment explanation
Indices: 54391428--54391627 Score: 373
Period size: 100 Copynumber: 2.0 Consensus size: 100
54391418 CAAGATCATT
* *
54391428 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGG
1 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
*
54391493 GCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTA
66 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTA
54391528 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
1 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
54391593 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTA
66 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTA
54391628 GAGTTTGATA
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (100 bp):
TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTA
Found at i:54391619 original size:38 final size:38
Alignment explanation
Indices: 54391577--54391701 Score: 148
Period size: 38 Copynumber: 3.3 Consensus size: 38
54391567 TCTTTATCTC
54391577 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
*** ** *
54391615 TGAAATTGAAGT-AGAGTTTGATAACAAGTCTTTAT-CTC-
1 TGAAATTGAAGTAAGAGCAAGAT--CATTTC-CTATCCTCT
54391653 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
1 TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
54391691 TGAAATTGAAG
1 TGAAATTGAAG
54391702 CAGAGTTGGA
Statistics
Matches: 69, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
36 3 0.04
37 14 0.20
38 35 0.51
39 14 0.20
40 3 0.04
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (38 bp):
TGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCT
Found at i:54391646 original size:176 final size:176
Alignment explanation
Indices: 54391352--54391701 Score: 655
Period size: 176 Copynumber: 2.0 Consensus size: 176
54391342 CAACATCATT
* *
54391352 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGG
1 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
54391417 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
66 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
* *
54391482 TTGAAGTAAGGGCAAGGTCATTTCCTATCCTCTTGAAATTGAAGTA
131 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTA
54391528 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
1 TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
*
54391593 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTTGATAACAAGTCTTTATCTCTGAAA
66 GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
54391658 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAG
131 TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAG
54391702 CAGAGTTGGA
Statistics
Matches: 169, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 169 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (176 bp):
TCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAATCTTTATCTCTGAAATTGAAGTAAGA
GCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
TTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTA
Found at i:54392054 original size:6 final size:6
Alignment explanation
Indices: 54392034--54392092 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
54392024 TTAAATGGGT
* * *
54392034 TTTAAA TTT-AT TTTAAA TTTAAA TTTACTCA TTTAAA TTT-AC TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA
*
54392082 TTTAAG TTTAA
1 TTTAAA TTTAA
54392093 TAAAATTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:54392069 original size:14 final size:14
Alignment explanation
Indices: 54392050--54392076 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
54392040 TTTATTTTAA
54392050 ATTTAAATTTACTC
1 ATTTAAATTTACTC
54392064 ATTTAAATTTACT
1 ATTTAAATTTACT
54392077 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATTTACTC
Found at i:54392802 original size:25 final size:24
Alignment explanation
Indices: 54392774--54392821 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
54392764 ATTGAATATT
54392774 TAATATT-ATAACAAATTAATAATAG
1 TAATATTGATAAC-AATT-ATAATAG
*
54392799 TAATATTGATAGCAATTATAATA
1 TAATATTGATAACAATTATAATA
54392822 TTTATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (24 bp):
TAATATTGATAACAATTATAATAG
Found at i:54392860 original size:14 final size:14
Alignment explanation
Indices: 54392824--54392866 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
54392814 TTATAATATT
*
54392824 TATTAAT-ATTAAA
1 TATTAATAATAAAA
* *
54392837 TAATATTAATAAAA
1 TATTAATAATAAAA
54392851 TATTAATAATAAAA
1 TATTAATAATAAAA
54392865 TA
1 TA
54392867 GTAAAAAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 5 0.21
14 19 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATTAATAATAAAA
Found at i:54393913 original size:29 final size:29
Alignment explanation
Indices: 54393881--54394274 Score: 164
Period size: 29 Copynumber: 13.5 Consensus size: 29
54393871 TAAACTTTCC
*
54393881 AAAATT-CCTTTTTAACCCCGATTTCATAA
1 AAAATTACCATTTTAACCCCGATTTCAT-A
* * **
54393910 AAAATTATCATTTT-ACCCTCGAACTTC-CC
1 AAAATTACCATTTTAACCC-CG-ATTTCATA
54393939 AAAATT-CCATTTTTAACCCCGATTTCATA
1 AAAATTACCA-TTTTAACCCCGATTTCATA
* * **
54393968 AAAATTACCATTTTACCCCCGAACTTC-CC
1 AAAATTACCATTTTAACCCCG-ATTTCATA
* *
54393997 AAAATT-CCATTTTTAACCTCGGTTTCATCA
1 AAAATTACCA-TTTTAACCCCGATTTCAT-A
* *
54394027 ATAATTACCATTTT-ACCCTCGAACTTTC--C
1 AAAATTACCATTTTAACCC-CG-A-TTTCATA
** **
54394056 AAAATT-CCATTTTTAACCCTAATTTCACC
1 AAAATTACCA-TTTTAACCCCGATTTCATA
* * * *
54394085 AAAATTATCATTTTACCCCCAAACTTTC--C
1 AAAATTACCATTTTAACCCC-GA-TTTCATA
* *
54394114 AAAATT-CCATTTTTAACCCCGATTTTACCA
1 AAAATTACCA-TTTTAACCCCGATTTCA-TA
**
54394144 AAAATTACCATTTT-ACCCTTAAACTTTC--A
1 AAAATTACCATTTTAACCC--CGA-TTTCATA
*
54394173 AAAATT-CCATTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTAACCCCGATTTCAT-A
*
54394202 AAAATTACCATTTT-ACCCCTAAACTTTC-T-
1 AAAATTACCATTTTAACCCC--GA-TTTCATA
* *
54394231 AAAATT-CCATTTTTAACCCCGATCTCACCA
1 AAAATTACCA-TTTTAACCCCGATTTCA-TA
54394261 AAAATTACCATTTT
1 AAAATTACCATTTT
54394275 GCCCCCGCGT
Statistics
Matches: 276, Mismatches: 45, Indels: 87
0.68 0.11 0.21
Matches are distributed among these distances:
26 4 0.01
27 11 0.04
28 30 0.11
29 131 0.47
30 69 0.25
31 20 0.07
32 11 0.04
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCGATTTCATA
Found at i:54393942 original size:58 final size:59
Alignment explanation
Indices: 54393852--54394274 Score: 570
Period size: 58 Copynumber: 7.2 Consensus size: 59
54393842 GAACTGTCTG
*
54393852 AAAATTACCATTTTACCC-CTAAACTTTCCAAAATTCC-TTTTTAACCCCGATTTCATAA
1 AAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
54393910 AAAATTATCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGATTTCAT-A
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * * *
54393968 AAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTTAACCTCGGTTTCATCA
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * ** *
54394027 ATAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCTAATTTCA-CC
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * * *
54394085 AAAATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
54394144 AAAATTACCATTTTACCCTTAAACTTTCAAAAATTCCA-TTTTAACCTCGATTTCATCA
1 AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
* * *
54394202 AAAATTACCATTTTACCC-CTAAACTTTCTAAAATTCCATTTTTAACCCCGATCTCACCA
1 AAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
54394261 AAAATTACCATTTT
1 AAAATTACCATTTT
54394275 GCCCCCGCGT
Statistics
Matches: 324, Mismatches: 35, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
58 188 0.58
59 136 0.42
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (59 bp):
AAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCA
Found at i:54394058 original size:117 final size:117
Alignment explanation
Indices: 54393852--54394274 Score: 607
Period size: 117 Copynumber: 3.6 Consensus size: 117
54393842 GAACTGTCTG
* **
54393852 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC-TTTTTAACCCCGATTTCATAAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
* *
54393916 ATCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGATTTCATA
66 ACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATA
* * * * * *
54393968 AAAATTACCATTTTACCCCCGAACTTCCCAAAATTCCATTTTTAACCTCGGTTTCATCAATAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
** **
54394033 ACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACC
66 ACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATA
* *
54394085 AAAATTATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
** * *
54394150 ACCATTTTACCCTTAAACTTTCAAAAATTCCA-TTTTAACCTCGATTTCATCA
66 ACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAT-A
* * *
54394202 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATCTCACCAAAAATT
1 AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
54394267 ACCATTTT
66 ACCATTTT
54394275 GCCCCCGCGT
Statistics
Matches: 271, Mismatches: 34, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
116 48 0.18
117 223 0.82
ACGTcount: A:0.34, C:0.28, G:0.02, T:0.36
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATT
ACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATA
Found at i:54394188 original size:175 final size:175
Alignment explanation
Indices: 54393852--54394280 Score: 612
Period size: 175 Copynumber: 2.4 Consensus size: 175
54393842 GAACTGTCTG
**
54393852 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCC-TTTTTAACCCCGATTTCATAAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA-CCAAAATT
* * *
54393916 ATCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCCCGATTTCATAAAAATTACCATTT
65 ATCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTACCATTT
* * *
54393981 TACCCCCGAACTTCCCAAAATTCCATTTTTAACCTCGGTTTCATCA
130 TACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGATTTCATCA
* * **
54394027 ATAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCCTAATTTCACCAAAATT
1 AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATT
* *
54394091 ATCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATT
65 ATCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCA-CAAAAATTACCATT
** *
54394156 TTACCCTTAAACTTTCAAAAATTCCA-TTTTAACCTCGATTTCATCA
129 TTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGATTTCATCA
* *
54394202 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATCTCACCAAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC-AAAATT
* *
54394267 ACCATTTTGCCCCC
65 ATCATTTTACCCCC
54394281 GCGTCCAAAA
Statistics
Matches: 224, Mismatches: 25, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
174 4 0.02
175 148 0.66
176 72 0.32
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.36
Consensus pattern (175 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATTA
TCATTTTACCCCCAAACTTCCCAAAATTCCATTTTTAACCCCGATTTCACAAAAATTACCATTTT
ACCCCCAAACTTCCAAAAATTCCATTTTTAACCTCGATTTCATCA
Found at i:54395749 original size:58 final size:58
Alignment explanation
Indices: 54395685--54395799 Score: 194
Period size: 58 Copynumber: 2.0 Consensus size: 58
54395675 ATCCATCAAC
*
54395685 AAACTAACCCCAAATATTTTTAAACCCAAATATAATTTCATTCTTAAAAAACACTCAT
1 AAACTAACCCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
* * *
54395743 AAACTAATCCCAAATATTTTTAAACCCAAATATAATTTTATTCCTAAATAACACTCA
1 AAACTAACCCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCA
54395800 AACAATTCCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (58 bp):
AAACTAACCCCAAATATTTTTAAACCCAAATATAATTTCATTCCTAAAAAACACTCAT
Found at i:54399664 original size:20 final size:20
Alignment explanation
Indices: 54399641--54399678 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54399631 GAATTTTGAA
* *
54399641 TTTTTTTTTTCAATTTTTTC
1 TTTTTCTTTTAAATTTTTTC
54399661 TTTTTCTTTTAAATTTTT
1 TTTTTCTTTTAAATTTTT
54399679 AGAAACAATA
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:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTCTTTTAAATTTTTTC
Found at i:54400108 original size:56 final size:58
Alignment explanation
Indices: 54400039--54400166 Score: 206
Period size: 56 Copynumber: 2.2 Consensus size: 58
54400029 AATTATGGGT
54400039 AAATTTTCATTTTGGTCATTTAACTAAAAAAAGTTACAATTTGG-TT-AACTATTCAA
1 AAATTTTCATTTTGGTCATTTAACTAAAAAAAGTTACAATTTGGTTTGAACTATTCAA
*
54400095 AAATTTTCGTTTTGGTCATTTAACTAAAAAAAGTTACAATTTGGTTATTGAACTATTCAA
1 AAATTTTCATTTTGGTCATTTAACTAAAAAAAGTTACAATTTGG-T-TTGAACTATTCAA
*
54400155 AAATTTTTATTT
1 AAATTTTCATTT
54400167 AAGTTACTGA
Statistics
Matches: 65, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
56 43 0.66
59 2 0.03
60 20 0.31
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (58 bp):
AAATTTTCATTTTGGTCATTTAACTAAAAAAAGTTACAATTTGGTTTGAACTATTCAA
Found at i:54400125 original size:29 final size:29
Alignment explanation
Indices: 54400039--54400149 Score: 86
Period size: 29 Copynumber: 3.9 Consensus size: 29
54400029 AATTATGGGT
54400039 AAATTTTCATTTTGGTCATTTAACTAAAA
1 AAATTTTCATTTTGGTCATTTAACTAAAA
* * * *
54400068 AAAGTTACAATTTGG----TTAACTATTCAA
1 AAATTTTCATTTTGGTCATTTAACTA--AAA
*
54400095 AAATTTTCGTTTTGGTCATTTAACTAAAA
1 AAATTTTCATTTTGGTCATTTAACTAAAA
* * * * *
54400124 AAAGTTACAATTTGGTTATTGAACTA
1 AAATTTTCATTTTGGTCATTTAACTA
54400150 TTCAAAAATT
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
25 7 0.11
27 13 0.21
29 34 0.56
31 7 0.11
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (29 bp):
AAATTTTCATTTTGGTCATTTAACTAAAA
Found at i:54400517 original size:31 final size:31
Alignment explanation
Indices: 54400482--54400540 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
54400472 AATAGCCCAG
*
54400482 TGACTTAAATAAAAACTTTTAAATAATTCAA
1 TGACTTAAATAAAAACTTTCAAATAATTCAA
* *
54400513 TGACTTAAATGAAAACTTTCGAATAATT
1 TGACTTAAATAAAAACTTTCAAATAATT
54400541 TAATAATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAATTCAA
Found at i:54402680 original size:26 final size:27
Alignment explanation
Indices: 54402628--54402680 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
54402618 TATTAAATTT
*
54402628 AAAAGAAATCAAAATTTTTATTAAAAA
1 AAAAGAAATCAAAATTTTTAGTAAAAA
*
54402655 AAAAGAAAT-TAAATTTTTAGGTAAAA
1 AAAAGAAATCAAAATTTTTA-GTAAAA
54402681 GTTAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (27 bp):
AAAAGAAATCAAAATTTTTAGTAAAAA
Found at i:54404123 original size:3 final size:3
Alignment explanation
Indices: 54404115--54404160 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
54404105 TCATTCGCAA
54404115 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54404161 TGCATTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:54410433 original size:219 final size:221
Alignment explanation
Indices: 54409984--54410565 Score: 623
Period size: 219 Copynumber: 2.6 Consensus size: 221
54409974 TTATTTTTTC
* *
54409984 AAATATTTCTATAAGTTAATTTATTTAAATTAATATTTTCAAATTTAAATTAAATC-AATTCAAT
1 AAATATTTATATAAGTTAATTTATTTAAATTAAAATTTTCAAATTTAAATTAAA-CAAATTCAAT
* *
54410048 GAATAAAATATTTTATATTAAAAAAATTAGATAAATTTAAAATTTAAAAATTCATTTATCCATTC
65 GAATAAAATATTTTATATTAAAAAAATTAGATAAATATAAAATTAAAAAATTCATTTATCCATTC
54410113 AATTTAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATTTTTTTATAAGTTTAATTTATT
130 AATTTAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATTTTTTTATAAGTTTAATTTATT
* * * * * *
54410178 TATCGTAATTTTTTTACACATTAAATA
195 TACCATAATCTTTTCAAACACTAAATA
*
54410205 AAATATTTATATAAGTTAATTTATTTAAATTAAAATTTT-AAATTTTAAATTAAACAAATTAAAT
1 AAATATTTATATAAGTTAATTTATTTAAATTAAAATTTTCAAA-TTTAAATTAAACAAATTCAAT
* **
54410269 G-A-AAAATATTTTA-ATTAAAAATTATTAGATAAATATAAAATTGAAAAAGGATTTTTTTTAT-
65 GAATAAAATATTTTATATTAAAAA-AATTAGATAAATATAAAATT-AAAAA--A-TTCATTTATC
* *** * *** ** *
54410330 CATTCAATTTAATTTAATTTTTTTAAATTT-TTTTAAGTTTTTC-AATTATTTTTTTAAG-TTAA
125 CATTCAATTTAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATT-TTTTTATAAGTTTAA
* *
54410392 TTTATTTACCATAA-CTTTTCAAATACTAGATA
189 TTTATTTACCATAATCTTTTCAAACACTAAATA
* * * * *
54410424 AAATATTTATATAATTTAATTTATTTTAATTAAAATTTTCGAATTTATATTAAATAAATTCAATG
1 AAATATTTATATAAGTTAATTTATTTAAATTAAAATTTTCAAATTTAAATTAAACAAATTCAATG
** * * * *
54410489 GGTAAAATGTTTTTTAATAAAAAATATAATTACAT-AATATAAAATTAAAAAA-TCATTTATCCA
66 AATAAAATATTTTAT-AT-TAAAA-A-AATTAGATAAATATAAAATTAAAAAATTCATTTATCCA
54410552 TTCAA-TTAAATTAA
127 TTCAATTTAAATTAA
54410566 ATAAAGCCTT
Statistics
Matches: 303, Mismatches: 42, Indels: 34
0.80 0.11 0.09
Matches are distributed among these distances:
218 8 0.03
219 111 0.37
220 38 0.13
221 83 0.27
222 26 0.09
223 14 0.05
224 15 0.05
225 8 0.03
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.46
Consensus pattern (221 bp):
AAATATTTATATAAGTTAATTTATTTAAATTAAAATTTTCAAATTTAAATTAAACAAATTCAATG
AATAAAATATTTTATATTAAAAAAATTAGATAAATATAAAATTAAAAAATTCATTTATCCATTCA
ATTTAAATTAACCATTTCAAATTTAAAATAAAATTTTCAAATTTTTTTATAAGTTTAATTTATTT
ACCATAATCTTTTCAAACACTAAATA
Found at i:54413413 original size:19 final size:19
Alignment explanation
Indices: 54413391--54413427 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
54413381 TTTATTTATT
54413391 ATATGTTAT-TTTTAAATAA
1 ATAT-TTATATTTTAAATAA
54413410 ATATTTATATTTTAAATA
1 ATATTTATATTTTAAATA
54413428 CGTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (19 bp):
ATATTTATATTTTAAATAA
Found at i:54414690 original size:4 final size:4
Alignment explanation
Indices: 54414681--54414722 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
54414671 TCACTTGATA
* *
54414681 TATG TATG TATG TATG TATG TATG CATG CATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
54414723 GTCGTTCTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (4 bp):
TATG
Found at i:54417088 original size:2 final size:2
Alignment explanation
Indices: 54417081--54417106 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
54417071 CGCATACGGA
54417081 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
54417107 ATACTTTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:54418822 original size:12 final size:13
Alignment explanation
Indices: 54418804--54418833 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
54418794 TAATTATGAT
54418804 TATAAATATATAA
1 TATAAATATATAA
54418817 -ATAAATATATAA
1 TATAAATATATAA
54418829 TATAA
1 TATAA
54418834 TTAAACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TATAAATATATAA
Found at i:54429132 original size:29 final size:29
Alignment explanation
Indices: 54429099--54429154 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
54429089 TAAATGTTAA
54429099 AATTT-TAATATAGAATTT-TTTAGGTATTG
1 AATTTATAATATA-AATTTATTT-GGTATTG
*
54429128 AATTTATATTATAAATTTATTTGGTAT
1 AATTTATAATATAAATTTATTTGGTAT
54429155 ATTAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.54
Consensus pattern (29 bp):
AATTTATAATATAAATTTATTTGGTATTG
Found at i:54429884 original size:15 final size:15
Alignment explanation
Indices: 54429855--54429893 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
54429845 TGTCGTAGGA
*
54429855 AATTTCATAATTAAAT
1 AATTT-ATAAATAAAT
54429871 AATTTATAAATAAAT
1 AATTTATAAATAAAT
*
54429886 AATATATA
1 AATTTATA
54429894 TTTATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTATAAATAAAT
Found at i:54441201 original size:97 final size:97
Alignment explanation
Indices: 54441029--54441218 Score: 247
Period size: 97 Copynumber: 2.0 Consensus size: 97
54441019 ACAACAATCA
* * * *
54441029 CCATCAAACAATGCTGCTCCAAATACACTACCAATACTCGACCACGAATTCACATAATAAAATAA
1 CCATAAAACAATGCTGCTACAAATACAATACCAATACTCGACCACAAATTCACATAATAAAATAA
*
54441094 TAATCCTCCAACAATT-ATAAGATCCTGCAGTC
66 TAATACTCCAACAATTAATAA-ATCCTGCAGTC
* * * * * *
54441126 CCATAAAACAATGCTGCTACAGATACAATATCTATATTCGACCACAAATTCACATCATAAGATAA
1 CCATAAAACAATGCTGCTACAAATACAATACCAATACTCGACCACAAATTCACATAATAAAATAA
* *
54441191 TAATATTCCAACAGTTAATAAATCCTGC
66 TAATACTCCAACAATTAATAAATCCTGC
54441219 TGCACAAGGT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
97 75 0.95
98 4 0.05
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (97 bp):
CCATAAAACAATGCTGCTACAAATACAATACCAATACTCGACCACAAATTCACATAATAAAATAA
TAATACTCCAACAATTAATAAATCCTGCAGTC
Found at i:54444407 original size:14 final size:14
Alignment explanation
Indices: 54444388--54444417 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54444378 CAGGCACTGT
54444388 TGACCACCGACCAC
1 TGACCACCGACCAC
*
54444402 TGACCATCGACCAC
1 TGACCACCGACCAC
54444416 TG
1 TG
54444418 GCCTCCAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.43, G:0.17, T:0.13
Consensus pattern (14 bp):
TGACCACCGACCAC
Found at i:54445370 original size:20 final size:19
Alignment explanation
Indices: 54445347--54445386 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
54445337 AGAGCAAAAA
54445347 TTTCATTTATTCTTCCTTCT
1 TTTCATTTATTCTT-CTTCT
* *
54445367 TTTCTTTTCTTCTTCTTCT
1 TTTCATTTATTCTTCTTCT
54445386 T
1 T
54445387 CTTCTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTCATTTATTCTTCTTCT
Found at i:54445381 original size:3 final size:3
Alignment explanation
Indices: 54445356--54445395 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
54445346 ATTTCATTTA
54445356 TTC TTCC TTC TT- TTC TT- TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TT-C TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
54445396 TTTTTTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 27 0.79
4 3 0.09
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:54453628 original size:21 final size:21
Alignment explanation
Indices: 54453587--54453628 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
54453577 TAAATTTTTT
*
54453587 GAACAAAACAAAACAATAAAA
1 GAACAAAACAAAACAACAAAA
*
54453608 GAACAATACAACAAC-ACAAAA
1 GAACAAAACAA-AACAACAAAA
54453629 TGCTCCCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.71, C:0.19, G:0.05, T:0.05
Consensus pattern (21 bp):
GAACAAAACAAAACAACAAAA
Found at i:54455711 original size:9 final size:9
Alignment explanation
Indices: 54455697--54455721 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
54455687 TTCAGGTACG
54455697 CCCATTTCA
1 CCCATTTCA
54455706 CCCATTTCA
1 CCCATTTCA
54455715 CCCATTT
1 CCCATTT
54455722 TAACTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (9 bp):
CCCATTTCA
Found at i:54473637 original size:27 final size:26
Alignment explanation
Indices: 54473607--54473684 Score: 79
Period size: 26 Copynumber: 2.9 Consensus size: 26
54473597 TAATTATTAA
54473607 TTTTATTATATTAAAAATAAATATATT
1 TTTTA-TATATTAAAAATAAATATATT
*
54473634 TTTTGA-ATAGTAAAAATAAATATATT
1 TTTT-ATATATTAAAAATAAATATATT
* *
54473660 TTTAAATATTATTTAAAAT-AATATA
1 TTT-TATA-TATTAAAAATAAATATA
54473685 ATTTGTGAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
26 23 0.53
27 11 0.26
28 9 0.21
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (26 bp):
TTTTATATATTAAAAATAAATATATT
Found at i:54477879 original size:10 final size:11
Alignment explanation
Indices: 54477856--54477883 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54477846 AAGGTATAAT
54477856 AAAATATTTAA
1 AAAATATTTAA
54477867 AAAATATTTAA
1 AAAATATTTAA
54477878 AAAATA
1 AAAATA
54477884 GAGATAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATATTTAA
Found at i:54478904 original size:21 final size:22
Alignment explanation
Indices: 54478880--54478928 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
54478870 CATTCAAATT
54478880 TAAAAAAT-TTAAAAATTTAAA
1 TAAAAAATATTAAAAATTTAAA
*
54478901 T-AAAAATATTAAGAATTTAAA
1 TAAAAAATATTAAAAATTTAAA
54478922 TAAAAAA
1 TAAAAAA
54478929 ATAAATCGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
21 14 0.56
22 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAAAATATTAAAAATTTAAA
Found at i:54479615 original size:60 final size:61
Alignment explanation
Indices: 54479512--54479638 Score: 166
Period size: 60 Copynumber: 2.1 Consensus size: 61
54479502 ATTCTAAATA
* ** * * * *
54479512 TAAAAAATTCAACAAATTTAACTCTCATTATTTGCAAAGTTTATCATTTTAGTTCGAATTT
1 TAAAAAATTCAACAAATTTAACCCTCAACATTTACAAAATTTATCAATTTAATTCGAATTT
* *
54479573 TAAAAAA-TCAATAAATTTAACCCTCAACATTTACAAAATTTATCAATTTAATTCTAATTT
1 TAAAAAATTCAACAAATTTAACCCTCAACATTTACAAAATTTATCAATTTAATTCGAATTT
54479633 TAAAAA
1 TAAAAA
54479639 TTAAAAAAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
60 50 0.88
61 7 0.12
ACGTcount: A:0.44, C:0.13, G:0.03, T:0.39
Consensus pattern (61 bp):
TAAAAAATTCAACAAATTTAACCCTCAACATTTACAAAATTTATCAATTTAATTCGAATTT
Found at i:54481493 original size:12 final size:12
Alignment explanation
Indices: 54481478--54481557 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 12
54481468 ATAACATCAA
54481478 AACAACCAAAAT
1 AACAACCAAAAT
*
54481490 AACAACCAAAAC
1 AACAACCAAAAT
* * *
54481502 AGC-AGCAAAAC
1 AACAACCAAAAT
*
54481513 AACAACAAAAAT
1 AACAACCAAAAT
* *
54481525 AACAGCAAAAAT
1 AACAACCAAAAT
54481537 AACAA-CAAAAT
1 AACAACCAAAAT
54481548 AACAA-CAAAA
1 AACAACCAAAA
54481558 CAGCACCAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
11 24 0.42
12 33 0.58
ACGTcount: A:0.69, C:0.23, G:0.04, T:0.05
Consensus pattern (12 bp):
AACAACCAAAAT
Found at i:54481516 original size:23 final size:23
Alignment explanation
Indices: 54481475--54481571 Score: 85
Period size: 23 Copynumber: 4.3 Consensus size: 23
54481465 AAAATAACAT
*
54481475 CAAAACAAC--CAAAATAACAAC
1 CAAAACAACAGCAAAACAACAAC
*
54481496 CAAAACAGCAGCAAAACAACAAC
1 CAAAACAACAGCAAAACAACAAC
* * *
54481519 AAAAATAACAGCAAAAATAACAA-
1 CAAAACAACAGC-AAAACAACAAC
* * *
54481542 CAAAATAACAACAAAACAGC-AC
1 CAAAACAACAGCAAAACAACAAC
54481564 CAAAACAA
1 CAAAACAA
54481572 TAAAAAAAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
21 9 0.15
22 13 0.21
23 30 0.49
24 9 0.15
ACGTcount: A:0.67, C:0.25, G:0.04, T:0.04
Consensus pattern (23 bp):
CAAAACAACAGCAAAACAACAAC
Found at i:54481524 original size:35 final size:35
Alignment explanation
Indices: 54481478--54481557 Score: 97
Period size: 35 Copynumber: 2.3 Consensus size: 35
54481468 ATAACATCAA
* * * *
54481478 AACAACCAAAATAACAACCAAAACAGCAGCAAAAC
1 AACAACAAAAATAACAACAAAAACAACAACAAAAC
* * *
54481513 AACAACAAAAATAACAGCAAAAATAACAACAAAAT
1 AACAACAAAAATAACAACAAAAACAACAACAAAAC
54481548 AACAACAAAA
1 AACAACAAAA
54481558 CAGCACCAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.69, C:0.23, G:0.04, T:0.05
Consensus pattern (35 bp):
AACAACAAAAATAACAACAAAAACAACAACAAAAC
Found at i:54481579 original size:22 final size:21
Alignment explanation
Indices: 54481561--54481654 Score: 70
Period size: 22 Copynumber: 4.5 Consensus size: 21
54481551 AACAAAACAG
54481561 CACCAAAACAAT--AAAAAAA
1 CACCAAAACAATAAAAAAAAA
* *
54481580 -ATCAAAACAGTAAAAAAACAA
1 CACCAAAACAATAAAAAAA-AA
* **
54481601 CATCAAAACAGCAAAAAATAGAA
1 CACCAAAACAATAAAAAA-A-AA
* *
54481624 -ACCAAAATAGTAAAAAAAAA
1 CACCAAAACAATAAAAAAAAA
54481644 CACCAAAACAA
1 CACCAAAACAA
54481655 CAATATAATT
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
18 9 0.15
20 7 0.12
21 11 0.18
22 30 0.50
23 3 0.05
ACGTcount: A:0.70, C:0.18, G:0.04, T:0.07
Consensus pattern (21 bp):
CACCAAAACAATAAAAAAAAA
Found at i:54481597 original size:29 final size:30
Alignment explanation
Indices: 54481476--54481602 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 30
54481466 AAATAACATC
**
54481476 AAAACAACCAAAATAACAACCAAAACAGCAGC
1 AAAACAA-CAAAATAACAA-CAAAACAGCAAA
* *
54481508 AAAACAAC--AACAA-AA-ATAACAGCAAA
1 AAAACAACAAAATAACAACAAAACAGCAAA
**
54481534 AATAACAACAAAATAACAACAAAACAGCACC
1 AA-AACAACAAAATAACAACAAAACAGCAAA
* *
54481565 AAAACAATAAAA-AA-AATCAAAACAGTAAA
1 AAAACAACAAAATAACAA-CAAAACAGCAAA
54481594 AAAACAACA
1 AAAACAACA
54481603 TCAAAACAGC
Statistics
Matches: 76, Mismatches: 13, Indels: 15
0.73 0.12 0.14
Matches are distributed among these distances:
26 10 0.13
27 6 0.08
28 4 0.05
29 27 0.36
30 11 0.14
31 11 0.14
32 7 0.09
ACGTcount: A:0.69, C:0.21, G:0.04, T:0.06
Consensus pattern (30 bp):
AAAACAACAAAATAACAACAAAACAGCAAA
Found at i:54486765 original size:3 final size:3
Alignment explanation
Indices: 54486757--54486781 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54486747 TGCAAGGGTT
54486757 GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG G
54486782 ATCATGTGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:54495554 original size:18 final size:18
Alignment explanation
Indices: 54495527--54495717 Score: 166
Period size: 18 Copynumber: 10.6 Consensus size: 18
54495517 GCCTGCGAAG
* *
54495527 CCTAAGGAACCTGAAAAA
1 CCTAAAGAACCCGAAAAA
* * *
54495545 CCCAAAGAACCCGAGAAG
1 CCTAAAGAACCCGAAAAA
* *
54495563 CCTAAAGTACCAGAAAAA
1 CCTAAAGAACCCGAAAAA
* *
54495581 CCAAAAGAACCCGAAAAG
1 CCTAAAGAACCCGAAAAA
*
54495599 CCTAAGGAACCCGAAAAA
1 CCTAAAGAACCCGAAAAA
* *
54495617 CCCAAAGAACCCGAGAAA
1 CCTAAAGAACCCGAAAAA
* *
54495635 CCTAAACAACCCGAAAAG
1 CCTAAAGAACCCGAAAAA
* ** *
54495653 CCGAAAGAACCCGCGAAG
1 CCTAAAGAACCCGAAAAA
* *
54495671 CCTAAACAACCCGAAAAG
1 CCTAAAGAACCCGAAAAA
* * *
54495689 CCTAAGGAACCTGAGAAA
1 CCTAAAGAACCCGAAAAA
*
54495707 CCAAAAGAACC
1 CCTAAAGAACC
54495718 ACCACCGAAA
Statistics
Matches: 134, Mismatches: 39, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 134 1.00
ACGTcount: A:0.49, C:0.29, G:0.17, T:0.05
Consensus pattern (18 bp):
CCTAAAGAACCCGAAAAA
Found at i:54495563 original size:36 final size:36
Alignment explanation
Indices: 54495523--54495717 Score: 219
Period size: 36 Copynumber: 5.4 Consensus size: 36
54495513 AGGAGCCTGC
* *
54495523 GAAGCCTAAGGAACCTGAAAAACCCAAAGAACCCGA
1 GAAGCCTAAAGAACCCGAAAAACCCAAAGAACCCGA
* * *
54495559 GAAGCCTAAAGTACCAGAAAAACCAAAAGAACCCGA
1 GAAGCCTAAAGAACCCGAAAAACCCAAAGAACCCGA
* *
54495595 AAAGCCTAAGGAACCCGAAAAACCCAAAGAACCCGA
1 GAAGCCTAAAGAACCCGAAAAACCCAAAGAACCCGA
* * * * *
54495631 GAAACCTAAACAACCCGAAAAGCCGAAAGAACCCGC
1 GAAGCCTAAAGAACCCGAAAAACCCAAAGAACCCGA
* * * * *
54495667 GAAGCCTAAACAACCCGAAAAGCCTAAGGAACCTGA
1 GAAGCCTAAAGAACCCGAAAAACCCAAAGAACCCGA
* *
54495703 GAAACCAAAAGAACC
1 GAAGCCTAAAGAACC
54495718 ACCACCGAAA
Statistics
Matches: 135, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 135 1.00
ACGTcount: A:0.49, C:0.29, G:0.17, T:0.05
Consensus pattern (36 bp):
GAAGCCTAAAGAACCCGAAAAACCCAAAGAACCCGA
Found at i:54495744 original size:12 final size:12
Alignment explanation
Indices: 54495729--54495780 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
54495719 CCACCGAAAC
* *
54495729 CACCAGCTCCGG
1 CACCAGCACCAG
*
54495741 CACCCA-CACCCG
1 CA-CCAGCACCAG
54495753 CACCAGCACCAG
1 CACCAGCACCAG
54495765 CACCAGCACCAG
1 CACCAGCACCAG
54495777 CACC
1 CACC
54495781 GAAGGCTCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 3 0.09
12 29 0.83
13 3 0.09
ACGTcount: A:0.27, C:0.56, G:0.15, T:0.02
Consensus pattern (12 bp):
CACCAGCACCAG
Found at i:54495756 original size:6 final size:6
Alignment explanation
Indices: 54495747--54495780 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
54495737 CCGGCACCCA
*
54495747 CACCCG CACCAG CACCAG CACCAG CACCAG CACC
1 CACCAG CACCAG CACCAG CACCAG CACCAG CACC
54495781 GAAGGCTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.29, C:0.56, G:0.15, T:0.00
Consensus pattern (6 bp):
CACCAG
Found at i:54495761 original size:18 final size:19
Alignment explanation
Indices: 54495729--54495780 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
54495719 CCACCGAAAC
* *
54495729 CACCAGCTCCGGCACCCA-
1 CACCAGCACCAGCACCCAG
*
54495747 CACCCGCACCAGCA-CCAG
1 CACCAGCACCAGCACCCAG
54495765 CACCAGCACCAGCACC
1 CACCAGCACCAGCACC
54495781 GAAGGCTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 3 0.11
18 24 0.86
19 1 0.04
ACGTcount: A:0.27, C:0.56, G:0.15, T:0.02
Consensus pattern (19 bp):
CACCAGCACCAGCACCCAG
Found at i:54497138 original size:24 final size:24
Alignment explanation
Indices: 54497105--54497155 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
54497095 AGAAATAATC
* *
54497105 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTGTAATTG
*
54497129 TTTCAATTAAACTCTGTGTATTTG
1 TTTCAATTAAACTCTGTGTAATTG
54497153 TTT
1 TTT
54497156 GAGTCAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTGTAATTG
Found at i:54497164 original size:24 final size:24
Alignment explanation
Indices: 54497113--54497165 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
54497103 TCTTTCAGTT
* *
54497113 AAACTCTGTTTAATTGTTTCAATT
1 AAACTCTGTGTAATTGTTTCAATC
* * *
54497137 AAACTCTGTGTATTTGTTTGAGTC
1 AAACTCTGTGTAATTGTTTCAATC
54497161 AAACT
1 AAACT
54497166 TTTATTAGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.45
Consensus pattern (24 bp):
AAACTCTGTGTAATTGTTTCAATC
Found at i:54504823 original size:16 final size:16
Alignment explanation
Indices: 54504787--54504822 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
54504777 AAAAAAACAC
*
54504787 TTTTGAAATAAAAATA
1 TTTTTAAATAAAAATA
54504803 TTTTTAAAT-AAAATA
1 TTTTTAAATAAAAATA
54504818 TTTTT
1 TTTTT
54504823 TTTTAGGCTT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTTTTAAATAAAAATA
Found at i:54506378 original size:31 final size:31
Alignment explanation
Indices: 54506312--54506450 Score: 128
Period size: 31 Copynumber: 4.6 Consensus size: 31
54506302 TGAACCCCAA
* * *
54506312 AAAGTTTAAGTACCAAATTA-AAAAAAGTGT
1 AAAGTTTAGGTACCAAATTAGAAAAAAATAT
*
54506342 CAAGTTTAGGTACCAAATTAGAAAAAAATAT
1 AAAGTTTAGGTACCAAATTAGAAAAAAATAT
* * *
54506373 AAAGTTTAGGTACTAAATTAGGAAAAAATGT
1 AAAGTTTAGGTACCAAATTAGAAAAAAATAT
* * **
54506404 AAAGTTT-GAGTGCCAAATT-G-GACCAA-A-
1 AAAGTTTAG-GTACCAAATTAGAAAAAAATAT
54506431 AAAGTTTAGGTACCAAATTA
1 AAAGTTTAGGTACCAAATTA
54506451 AGGAAAAGTG
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
27 16 0.18
28 1 0.01
29 3 0.03
30 20 0.22
31 50 0.56
ACGTcount: A:0.48, C:0.09, G:0.17, T:0.27
Consensus pattern (31 bp):
AAAGTTTAGGTACCAAATTAGAAAAAAATAT
Found at i:54509255 original size:25 final size:23
Alignment explanation
Indices: 54509196--54509256 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 23
54509186 TAATTCATTA
*
54509196 TGCATAAAATATATGCTTTTTTT
1 TGCATAAAATATATGCTTTTTAT
**
54509219 TAAAATAAAAATATATGCTTTTTAAT
1 T-GCAT-AAAATATATGCTTTTT-AT
54509245 TGCATATAAATA
1 TGCATA-AAATA
54509257 AGTTTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
23 1 0.03
24 3 0.10
25 23 0.79
26 2 0.07
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Consensus pattern (23 bp):
TGCATAAAATATATGCTTTTTAT
Found at i:54510334 original size:3 final size:3
Alignment explanation
Indices: 54510326--54510359 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
54510316 GATGTTCTTA
54510326 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
54510360 TGCAGAGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54512195 original size:6 final size:6
Alignment explanation
Indices: 54512184--54512208 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
54512174 AGCTGGGGAC
54512184 GCACAA GCACAA GCACAA GCACAA G
1 GCACAA GCACAA GCACAA GCACAA G
54512209 AAGGCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.32, G:0.20, T:0.00
Consensus pattern (6 bp):
GCACAA
Found at i:54516052 original size:15 final size:15
Alignment explanation
Indices: 54516032--54516061 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
54516022 ATTAAAACTT
*
54516032 CTTAATTTTAGTTTC
1 CTTAATTGTAGTTTC
54516047 CTTAATTGTAGTTTC
1 CTTAATTGTAGTTTC
54516062 TTATTCTACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (15 bp):
CTTAATTGTAGTTTC
Found at i:54518988 original size:35 final size:35
Alignment explanation
Indices: 54518949--54519019 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
54518939 TAGCCTTGAT
*
54518949 GAGAAGAGAGCATATGCAGCGGGCACATTCTTGTG
1 GAGAAGAGAGCATATGCAACGGGCACATTCTTGTG
*
54518984 GAGAAGAGAGCATATGCAATGGGCACATTCTTGTG
1 GAGAAGAGAGCATATGCAACGGGCACATTCTTGTG
54519019 G
1 G
54519020 CCTCATCAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.15, G:0.34, T:0.21
Consensus pattern (35 bp):
GAGAAGAGAGCATATGCAACGGGCACATTCTTGTG
Found at i:54522737 original size:11 final size:11
Alignment explanation
Indices: 54522692--54522737 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
54522682 TTATAAAATT
54522692 TTAATTTAATA
1 TTAATTTAATA
*
54522703 ATAATCTTAATA
1 TTAAT-TTAATA
54522715 TT-ATTT--TA
1 TTAATTTAATA
54522723 TTAATTTAATA
1 TTAATTTAATA
54522734 TTAA
1 TTAA
54522738 AGTGATTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 2 0.07
11 12 0.41
12 7 0.24
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
TTAATTTAATA
Done.