Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold89
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: 5168001
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 33045 characters in sequence are not A, C, G, or T
File 23 of 27
Found at i:3882965 original size:23 final size:23
Alignment explanation
Indices: 3882920--3882970 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
3882910 AAAATTTTAA
* *
3882920 ATAAAATTATTATTTTATTTAAT
1 ATAAAAATATTATTTTATATAAT
3882943 ATAAAAAT-TTATTTTAGTATAAT
1 ATAAAAATATTATTTTA-TATAAT
3882966 A-AAAA
1 ATAAAA
3882971 TATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATAAAAATATTATTTTATATAAT
Found at i:3885606 original size:13 final size:15
Alignment explanation
Indices: 3885574--3885604 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3885564 TGTTTTTAAA
3885574 ATAAAAAATTATTTT
1 ATAAAAAATTATTTT
3885589 ATAAAAAATTATTTT
1 ATAAAAAATTATTTT
3885604 A
1 A
3885605 AATAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAAAAATTATTTT
Found at i:3885906 original size:30 final size:29
Alignment explanation
Indices: 3885870--3885967 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 29
3885860 ATCAACTTTT
* *
3885870 AATTTTATAGTTTGTAATTTTATTTCAATA
1 AATTTTATA-TTTTTAATTTTATTTAAATA
*
3885900 AATTTTATATTTTTAATTTTTATTTGAATA
1 AATTTTATATTTTTAA-TTTTATTTAAATA
*
3885930 AATTTT-TAATTTTTAATGTATATTTAAATAA
1 AATTTTAT-ATTTTTAAT-TTTATTTAAAT-A
3885961 AATTTTA
1 AATTTTA
3885968 AATAAAATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.14
30 44 0.75
31 7 0.12
ACGTcount: A:0.37, C:0.01, G:0.04, T:0.58
Consensus pattern (29 bp):
AATTTTATATTTTTAATTTTATTTAAATA
Found at i:3885969 original size:12 final size:12
Alignment explanation
Indices: 3885952--3885976 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3885942 TTAATGTATA
3885952 TTTAAATAAAAT
1 TTTAAATAAAAT
3885964 TTTAAATAAAAT
1 TTTAAATAAAAT
3885976 T
1 T
3885977 ATTATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAATAAAAT
Found at i:3885988 original size:23 final size:22
Alignment explanation
Indices: 3885962--3886006 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3885952 TTTAAATAAA
* *
3885962 ATTTTAAATAAAATTATTATTTT
1 ATTTGAAATAAAAAT-TTATTTT
*
3885985 ATTTGATATAAAAATTTATTTT
1 ATTTGAAATAAAAATTTATTTT
3886007 GATAAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTGAAATAAAAATTTATTTT
Found at i:3886004 original size:17 final size:17
Alignment explanation
Indices: 3885982--3886014 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3885972 AAATTATTAT
3885982 TTTA-TTTGATATAAAAA
1 TTTATTTTGATA-AAAAA
3885999 TTTATTTTGATAAAAA
1 TTTATTTTGATAAAAA
3886015 TTAAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
TTTATTTTGATAAAAAA
Found at i:3887528 original size:24 final size:24
Alignment explanation
Indices: 3887496--3887556 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
3887486 TCCCGTGAAT
*
3887496 CCTCTTCTTCATCGTCATCATCAG
1 CCTCTTCTTCATCATCATCATCAG
* * *
3887520 CCTCCTCTTCATCATCATCGTCGG
1 CCTCTTCTTCATCATCATCATCAG
*
3887544 CTTCTTCTTCATC
1 CCTCTTCTTCATC
3887557 CAACAGCAGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.39, G:0.08, T:0.39
Consensus pattern (24 bp):
CCTCTTCTTCATCATCATCATCAG
Found at i:3888238 original size:82 final size:81
Alignment explanation
Indices: 3888137--3888307 Score: 306
Period size: 82 Copynumber: 2.1 Consensus size: 81
3888127 TTCTTACAAT
*
3888137 AATTTTTTGGAATATCTATCGGAATAGCTGCGGCTGCAATTCCCAGAATATACACGAAATAATTG
1 AATTTTTTGGAATATCTATCGGAATAGCTGCGCCTGCAATTCCCAGAATATACACGAAATAATTG
3888202 AATTGATCTTTGGTTG
66 AATTGATCTTTGGTTG
* *
3888218 AATTTTTCTGGAATATCTATCTGACTAGCTGCGCCTGCAATTCCCAGAATATACACGAAATAATT
1 AATTTTT-TGGAATATCTATCGGAATAGCTGCGCCTGCAATTCCCAGAATATACACGAAATAATT
3888283 GAATTGATCTTTGGTTG
65 GAATTGATCTTTGGTTG
3888300 AATTTTTT
1 AATTTTTT
3888308 TCTCCTGCTT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
81 8 0.09
82 78 0.91
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.37
Consensus pattern (81 bp):
AATTTTTTGGAATATCTATCGGAATAGCTGCGCCTGCAATTCCCAGAATATACACGAAATAATTG
AATTGATCTTTGGTTG
Found at i:3896777 original size:13 final size:13
Alignment explanation
Indices: 3896759--3896795 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
3896749 AAATATTGCC
3896759 TATACATGCGCGA
1 TATACATGCGCGA
*
3896772 TATACATGCGCGT
1 TATACATGCGCGA
3896785 TATACATGCGC
1 TATACATGCGC
3896796 AATAGTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (13 bp):
TATACATGCGCGA
Found at i:3897483 original size:53 final size:53
Alignment explanation
Indices: 3897401--3897512 Score: 147
Period size: 53 Copynumber: 2.1 Consensus size: 53
3897391 TGAAAATAGT
*
3897401 CAATGTAATTAAAAATGGAAAACACCAATGGCTC-A-TTCCTTGAATGGGACAGC
1 CAATGTAATTAAAAATGGAAAACAACAATGGC-CGACTT-CTTGAATGGGACAGC
* * *
3897454 CAATGTAATTAAAAGTGGTAAGCAACAATGGCCGACTTCTTGAATGGGACAGC
1 CAATGTAATTAAAAATGGAAAACAACAATGGCCGACTTCTTGAATGGGACAGC
3897507 CGAATG
1 C-AATG
3897513 CTGGAGAAGA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
52 1 0.02
53 45 0.87
54 6 0.12
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (53 bp):
CAATGTAATTAAAAATGGAAAACAACAATGGCCGACTTCTTGAATGGGACAGC
Found at i:3897926 original size:3 final size:3
Alignment explanation
Indices: 3897918--3897943 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3897908 AAAAATAAAA
3897918 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
3897944 GAAGATATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3898140 original size:2 final size:2
Alignment explanation
Indices: 3898133--3898171 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
3898123 ACCGATCTCT
*
3898133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3898172 TAAAATTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3898951 original size:16 final size:15
Alignment explanation
Indices: 3898912--3898970 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
3898902 GATACGATAT
3898912 TAACATAATATAAATA
1 TAACATAATA-AAATA
* *
3898928 AAAAATAATTAAAATA
1 TAACATAA-TAAAATA
*
3898944 TAACATAAAAATAATA
1 TAACATAATAA-AATA
3898960 TGAACATAATA
1 T-AACATAATA
3898971 TGAATTTGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 22 0.65
17 10 0.29
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (15 bp):
TAACATAATAAAATA
Found at i:3899094 original size:23 final size:23
Alignment explanation
Indices: 3899051--3899114 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
3899041 TATTTTAAAT
* * *
3899051 ATATAAAAAATAATATGAATATG
1 ATATAAAAATTAATATAAATATA
3899074 ATATAAAAATTAACTA-AAATATA
1 ATATAAAAATTAA-TATAAATATA
* *
3899097 ATACAAAAATAAATATAA
1 ATATAAAAATTAATATAA
3899115 CACAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.06
23 30 0.88
24 2 0.06
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (23 bp):
ATATAAAAATTAATATAAATATA
Found at i:3899131 original size:19 final size:18
Alignment explanation
Indices: 3899088--3899133 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
3899078 AAAAATTAAC
*
3899088 TAAAATATAATACAAAAA
1 TAAAATATAACACAAAAA
3899106 T-AAATATAACACAAAAA
1 TAAAATATAACACAAAAA
3899123 TAAAAATATAA
1 T-AAAATATAA
3899134 AATATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 16 0.64
18 1 0.04
19 8 0.32
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.22
Consensus pattern (18 bp):
TAAAATATAACACAAAAA
Found at i:3899206 original size:19 final size:19
Alignment explanation
Indices: 3899161--3899207 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3899151 TTGGCAGCTT
**
3899161 AAGAAGTTAATTTTTTTCA
1 AAGAAGTTAATAATTTTCA
*
3899180 ATA-TAGTTAATAATTTTCA
1 A-AGAAGTTAATAATTTTCA
3899199 AAGAAGTTA
1 AAGAAGTTA
3899208 GAGTAGTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 1 0.05
19 20 0.91
20 1 0.05
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (19 bp):
AAGAAGTTAATAATTTTCA
Found at i:3899485 original size:30 final size:31
Alignment explanation
Indices: 3899423--3899486 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
3899413 AAAAATTATT
* * * *
3899423 TAATTATTATTTTAAAAATATTTTATATTAA
1 TAATTATTATTTTAAAAAAATTTAAAAATAA
3899454 TAATTATT-TTTTAAAAAAATTTAAAAATAA
1 TAATTATTATTTTAAAAAAATTTAAAAATAA
3899484 TAA
1 TAA
3899487 CATATTAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TAATTATTATTTTAAAAAAATTTAAAAATAA
Found at i:3899916 original size:26 final size:25
Alignment explanation
Indices: 3899873--3899944 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 25
3899863 TACAATATAC
*
3899873 TAAAAATATAAAAAAATATAAAATATT
1 TAAAAA-ATAAAATAA-ATAAAATATT
*
3899900 TTAAAAATAAAAT-AAT--AAT-TT
1 TAAAAAATAAAATAAATAAAATATT
3899921 TAAAAAATAAAATAAAATAAAATA
1 TAAAAAATAAAAT-AAATAAAATA
3899945 AATCAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
21 14 0.38
22 3 0.08
23 3 0.08
24 2 0.05
25 4 0.11
26 6 0.16
27 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (25 bp):
TAAAAAATAAAATAAATAAAATATT
Found at i:3900285 original size:23 final size:23
Alignment explanation
Indices: 3900241--3900306 Score: 82
Period size: 23 Copynumber: 2.8 Consensus size: 23
3900231 GGTAAATTAA
3900241 AATAT-AATATAGAGTATAAAAAAT
1 AATATAAATATA-A-TATAAAAAAT
*
3900265 AAT-TAAAATATTATATAAAAAAT
1 AATAT-AAATATAATATAAAAAAT
3900288 AATATAAATATAATATAAA
1 AATATAAATATAATATAAA
3900307 TATATAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
23 27 0.73
24 5 0.14
25 5 0.14
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (23 bp):
AATATAAATATAATATAAAAAAT
Found at i:3900302 original size:11 final size:11
Alignment explanation
Indices: 3900240--3900310 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
3900230 AGGTAAATTA
3900240 AAATATAATAT
1 AAATATAATAT
*
3900251 AGAGTATAA-A-
1 A-AATATAATAT
*
3900261 AAATA-ATTA-
1 AAATATAATAT
*
3900270 AAATATTATAT
1 AAATATAATAT
*
3900281 AAAAAATAATAT
1 -AAATATAATAT
3900293 AAATATAATAT
1 AAATATAATAT
3900304 AAATATA
1 AAATATA
3900311 TAAATATATT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 9 0.19
10 3 0.06
11 19 0.40
12 15 0.32
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (11 bp):
AAATATAATAT
Found at i:3900313 original size:19 final size:19
Alignment explanation
Indices: 3900223--3900318 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 19
3900213 AAATTATGTA
**
3900223 AAATATAAGGTAAAT-TA-
1 AAATATAATATAAATATAT
*
3900240 AAATATAATATAGAGTATA-
1 AAATATAATATA-AATATAT
*
3900259 AAAAATAAT-TAAA-ATAT
1 AAATATAATATAAATATAT
*
3900276 -TATATAA-A-AAATAATAT
1 AAATATAATATAAAT-ATAT
3900293 AAATATAATATAAATATAT
1 AAATATAATATAAATATAT
3900312 AAATATA
1 AAATATA
3900319 TTCGAATATA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
15 3 0.05
16 8 0.13
17 15 0.24
18 10 0.16
19 22 0.35
20 4 0.06
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (19 bp):
AAATATAATATAAATATAT
Found at i:3900606 original size:16 final size:15
Alignment explanation
Indices: 3900567--3900625 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
3900557 GATACGATAT
3900567 TAACATAATATAAATA
1 TAACATAATA-AAATA
* *
3900583 AAAAATAATTAAAATA
1 TAACATAA-TAAAATA
*
3900599 TAACATAAAAATAATA
1 TAACATAATAA-AATA
3900615 TGAACATAATA
1 T-AACATAATA
3900626 TGAATTTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 22 0.65
17 10 0.29
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (15 bp):
TAACATAATAAAATA
Found at i:3908090 original size:12 final size:12
Alignment explanation
Indices: 3908073--3908099 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3908063 GAACAAAAGC
3908073 AAGGGGAAGGGA
1 AAGGGGAAGGGA
3908085 AAGGGGAAGGGA
1 AAGGGGAAGGGA
3908097 AAG
1 AAG
3908100 AGGCAGGCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (12 bp):
AAGGGGAAGGGA
Found at i:3908790 original size:2 final size:2
Alignment explanation
Indices: 3908783--3908812 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3908773 ATATTATGAA
3908783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3908813 TAATATAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3910617 original size:3 final size:3
Alignment explanation
Indices: 3910611--3910635 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3910601 GCAGCAGTAG
3910611 CAA CAA CAA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA C
3910636 CCATCATCAT
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:0.64, C:0.36, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:3918330 original size:28 final size:27
Alignment explanation
Indices: 3918278--3918338 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 27
3918268 AAGTATTTAT
*
3918278 TAAAAA-TAAAATATTTATATTTAAAC
1 TAAAAATTAAAATATTTATATATAAAC
* *
3918304 TAAAAATTAAAATTATTTATGTATAAAT
1 TAAAAATTAAAA-TATTTATATATAAAC
3918332 TAAAAAT
1 TAAAAAT
3918339 CAAATAACTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 6 0.20
27 5 0.17
28 19 0.63
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAAAATTAAAATATTTATATATAAAC
Found at i:3925273 original size:19 final size:18
Alignment explanation
Indices: 3925235--3925274 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3925225 TAATATTTTA
* *
3925235 TTATTTTTTAAAATTATT
1 TTATTTATTAAAAATATT
3925253 TTATTTATTAAATAATATT
1 TTATTTATTAAA-AATATT
3925272 TTA
1 TTA
3925275 AGTTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTATTAAAAATATT
Found at i:3928801 original size:31 final size:31
Alignment explanation
Indices: 3928763--3928824 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3928753 CTAGTAAGAT
3928763 AGATTCTTTCCTGGATGACTGAAGAACTGGC
1 AGATTCTTTCCTGGATGACTGAAGAACTGGC
*
3928794 AGATTCTTTCCTGGATGACTGAATAACTGGC
1 AGATTCTTTCCTGGATGACTGAAGAACTGGC
3928825 CCCAATTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (31 bp):
AGATTCTTTCCTGGATGACTGAAGAACTGGC
Found at i:3937142 original size:56 final size:56
Alignment explanation
Indices: 3937055--3937169 Score: 187
Period size: 56 Copynumber: 2.1 Consensus size: 56
3937045 TTTAGAATGC
3937055 CTGTAAACTGTCCTGCCAAACTCAACGTCCTAAATGCTGTTTTAGCAGGCAGAAGCA
1 CTGTAAACTGTCCTGCCAAACTCAACGTCCTAAATGCT-TTTTAGCAGGCAGAAGCA
* * *
3937112 CTGTAGACTGT-CTGCCAAACTCAATGTCCTAAATGCTTTTTAGTAGGCAGAAGCA
1 CTGTAAACTGTCCTGCCAAACTCAACGTCCTAAATGCTTTTTAGCAGGCAGAAGCA
3937167 CTG
1 CTG
3937170 CAATAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
55 20 0.36
56 25 0.45
57 10 0.18
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (56 bp):
CTGTAAACTGTCCTGCCAAACTCAACGTCCTAAATGCTTTTTAGCAGGCAGAAGCA
Found at i:3938146 original size:19 final size:18
Alignment explanation
Indices: 3938122--3938167 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
3938112 TGCAGATTTC
3938122 CAGATTTCCTGAATTCTAG
1 CAGATTTCCTGAATTCT-G
*
3938141 CAGATTTCCTGATTTCTG
1 CAGATTTCCTGAATTCTG
*
3938159 CATATTTCC
1 CAGATTTCC
3938168 AGATCTGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (18 bp):
CAGATTTCCTGAATTCTG
Found at i:3938195 original size:16 final size:16
Alignment explanation
Indices: 3938176--3938206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3938166 CCAGATCTGC
3938176 AAATTTACTGATTTTG
1 AAATTTACTGATTTTG
*
3938192 AAATTTCCTGATTTT
1 AAATTTACTGATTTT
3938207 TTAAGATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (16 bp):
AAATTTACTGATTTTG
Found at i:3941929 original size:18 final size:18
Alignment explanation
Indices: 3941895--3941939 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
3941885 TGCAGATTTC
3941895 CAGATTTCCTGCATTCTAG
1 CAGATTTCCTGCATTCT-G
3941914 CA-ATTTCCTG-ATTTCTG
1 CAGATTTCCTGCA-TTCTG
3941931 CAGATTTCC
1 CAGATTTCC
3941940 AGATCTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 4 0.17
18 18 0.75
19 2 0.08
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (18 bp):
CAGATTTCCTGCATTCTG
Found at i:3958485 original size:103 final size:103
Alignment explanation
Indices: 3958306--3958512 Score: 342
Period size: 103 Copynumber: 2.0 Consensus size: 103
3958296 GGTGCTCCCG
* * *
3958306 TTGTTTAGAGAAACTCCAAACAAAACTAGTTACACTTGAAAAGACGAAGAATATTTTAGCAAACT
1 TTGTTCAGAGAAACTCCAAACAAAACTAGTTACACTTGAAAAGACAAAGAATATTGTAGCAAACT
3958371 TGAACAACACATCCACAAATATAACAAATGAAGAATTT
66 TGAACAACACATCCACAAATATAACAAATGAAGAATTT
* * *
3958409 TTGTTCAGAGAAACTCCAAACAAAACTAGTTGCACTTGAAAAGACAAAGGATATTGTAGCAAGCT
1 TTGTTCAGAGAAACTCCAAACAAAACTAGTTACACTTGAAAAGACAAAGAATATTGTAGCAAACT
* *
3958474 TGAGCAACACATCCACAAATCTAACAAATGAAGAATTT
66 TGAACAACACATCCACAAATATAACAAATGAAGAATTT
3958512 T
1 T
3958513 CTTTGCAAGG
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (103 bp):
TTGTTCAGAGAAACTCCAAACAAAACTAGTTACACTTGAAAAGACAAAGAATATTGTAGCAAACT
TGAACAACACATCCACAAATATAACAAATGAAGAATTT
Found at i:3970133 original size:21 final size:21
Alignment explanation
Indices: 3970090--3970135 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3970080 TAATTTATTG
* *
3970090 TTTAAAAATATTCATATATTA
1 TTTAAAAAAATTCATATAATA
3970111 TTTAAAAAAATT-ATAATAATA
1 TTTAAAAAAATTCAT-ATAATA
3970132 TTTA
1 TTTA
3970136 TATTTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAAAAAAATTCATATAATA
Found at i:3973835 original size:18 final size:19
Alignment explanation
Indices: 3973812--3973860 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
3973802 AGAAAATGTT
3973812 ATATTAATATAA-TTTTAA
1 ATATTAATATAAGTTTTAA
3973830 ATATTAATATAAGTTTTAA
1 ATATTAATATAAGTTTTAA
* *
3973849 TTATTTATATAA
1 ATATTAATATAA
3973861 AAGGTAACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATATTAATATAAGTTTTAA
Found at i:3974635 original size:24 final size:24
Alignment explanation
Indices: 3974588--3974632 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
3974578 TCAATTAATT
3974588 TATTAATTACATAAAGTAAAAATA
1 TATTAATTACATAAAGTAAAAATA
* *
3974612 TATTATTTA-ATAAATTAAAAA
1 TATTAATTACATAAAGTAAAAA
3974633 ATAAATAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TATTAATTACATAAAGTAAAAATA
Found at i:3975387 original size:18 final size:20
Alignment explanation
Indices: 3975359--3975401 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
3975349 ATGTATATTT
*
3975359 AATATAAAATATTATT-ATA
1 AATATAAAATATAATTAATA
3975378 AATA-AAAATATAATTAATA
1 AATATAAAATATAATTAATA
3975397 AATAT
1 AATAT
3975402 CTTAAAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATAAAATATAATTAATA
Found at i:3977050 original size:15 final size:16
Alignment explanation
Indices: 3977030--3977063 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3977020 TGAAACGATG
3977030 ATAAAATAA-AATATT
1 ATAAAATAATAATATT
*
3977045 ATAAAATAATTATATT
1 ATAAAATAATAATATT
3977061 ATA
1 ATA
3977064 GTATGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAATAATAATATT
Found at i:3977394 original size:24 final size:23
Alignment explanation
Indices: 3977345--3977394 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3977335 ATGTAACCAA
*
3977345 TTCCTTTTTAATAAATAATCAGTT
1 TTCCTTTTTAATAAAAAATCA-TT
3977369 TTCCTTTTATACATAAAAAATC-TT
1 TTCCTTTT-TA-ATAAAAAATCATT
3977393 TT
1 TT
3977395 AGAATATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 12 0.52
25 2 0.09
26 9 0.39
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (23 bp):
TTCCTTTTTAATAAAAAATCATT
Found at i:3977498 original size:22 final size:20
Alignment explanation
Indices: 3977458--3977493 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3977448 AAATATATCT
3977458 TATTT-TTT-ATTTTTAAAA
1 TATTTATTTAATTTTTAAAA
3977476 TATTTATTTAATTTTTAA
1 TATTTATTTAATTTTTAA
3977494 TAAATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.31
19 3 0.19
20 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTATTTAATTTTTAAAA
Found at i:3977502 original size:21 final size:20
Alignment explanation
Indices: 3977466--3977508 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
3977456 CTTATTTTTT
*
3977466 ATTTTTAAAATATTTATTTA
1 ATTTTTAAAATATTTAATTA
3977486 ATTTTTAATAA-ATTTTAATTA
1 ATTTTTAA-AATA-TTTAATTA
3977507 AT
1 AT
3977509 ATAATATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATTTTTAAAATATTTAATTA
Found at i:3977625 original size:19 final size:20
Alignment explanation
Indices: 3977594--3977643 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
3977584 ACCTATTATA
3977594 TTAAATAAAATATAT-A-TTT
1 TTAAA-AAAATATATAATTTT
3977613 TTAAAAAATATATATAATTTT
1 TTAAAAAA-ATATATAATTTT
3977634 TTAAAAAAAT
1 TTAAAAAAAT
3977644 TTTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.11
19 11 0.39
20 3 0.11
21 11 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAAAAATATATAATTTT
Found at i:3988871 original size:24 final size:25
Alignment explanation
Indices: 3988825--3988870 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
3988815 TTAAATCAAT
3988825 TTTTAATTTTTATAATATAAAAATA
1 TTTTAATTTTTATAATATAAAAATA
*
3988850 TTTT-ATTTTTA-AATTTAAAAA
1 TTTTAATTTTTATAATATAAAAA
3988871 AAAATTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 7 0.35
25 4 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTAATTTTTATAATATAAAAATA
Found at i:3989508 original size:67 final size:67
Alignment explanation
Indices: 3989400--3989533 Score: 250
Period size: 67 Copynumber: 2.0 Consensus size: 67
3989390 GATTATTGAA
*
3989400 GACTTAATTAAATTGACTATTTTGATTTTAAATAGAGATTTATAAAACCAATGTTTTCATCAAAA
1 GACTTAATTAAATTGACTATTTTGATTTTAAATAGAAATTTATAAAACCAATGTTTTCATCAAAA
3989465 TC
66 TC
*
3989467 GACTTAATTAAATTGACTATTTTGATTTTAAATAGAAATTTATAAAACCAATGTTTTCATGAAAA
1 GACTTAATTAAATTGACTATTTTGATTTTAAATAGAAATTTATAAAACCAATGTTTTCATCAAAA
3989532 TC
66 TC
3989534 AAATTACCCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (67 bp):
GACTTAATTAAATTGACTATTTTGATTTTAAATAGAAATTTATAAAACCAATGTTTTCATCAAAA
TC
Found at i:3990528 original size:22 final size:23
Alignment explanation
Indices: 3990493--3990537 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
3990483 AAATAATGTA
3990493 ATTTTTGAAATAAT-AATAAAAT
1 ATTTTTGAAATAATAAATAAAAT
* *
3990515 ATTTTTTAACTAATCAAATAAAA
1 ATTTTTGAAATAAT-AAATAAAA
3990538 AAAATCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 12 0.63
24 7 0.37
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (23 bp):
ATTTTTGAAATAATAAATAAAAT
Found at i:3990547 original size:26 final size:27
Alignment explanation
Indices: 3990504--3990554 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3990494 TTTTTGAAAT
* *
3990504 AATAATAAAATATTTTTTAACTAATCA
1 AATAATAAAAAATCTTTTAACTAATCA
*
3990531 AATAA-AAAAAATCTTTTATCTAAT
1 AATAATAAAAAATCTTTTAACTAAT
3990555 GCATCATTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (27 bp):
AATAATAAAAAATCTTTTAACTAATCA
Found at i:3990680 original size:2 final size:2
Alignment explanation
Indices: 3990673--3990699 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3990663 TAACGTCTTA
3990673 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3990700 AATACTTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3994466 original size:25 final size:27
Alignment explanation
Indices: 3994432--3994492 Score: 90
Period size: 25 Copynumber: 2.3 Consensus size: 27
3994422 TTAATTTTAA
3994432 AATAAATATTATTATA-AT-TAATTAT
1 AATAAATATTATTATATATATAATTAT
* *
3994457 AATAATTATTATTATATTTATAATTAT
1 AATAAATATTATTATATATATAATTAT
3994484 AATAAATAT
1 AATAAATAT
3994493 AAAACACTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 15 0.48
26 1 0.03
27 15 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (27 bp):
AATAAATATTATTATATATATAATTAT
Found at i:3997292 original size:107 final size:107
Alignment explanation
Indices: 3997153--3997366 Score: 428
Period size: 107 Copynumber: 2.0 Consensus size: 107
3997143 AGAGATTGCC
3997153 TATGTCCCACACACATAAATAATTAAAAATAATATGTAAGTATGTGATTTGAAAAAGTTATAATT
1 TATGTCCCACACACATAAATAATTAAAAATAATATGTAAGTATGTGATTTGAAAAAGTTATAATT
3997218 AAATTTAAAATTTAATTTAATTAATTTATATAATTATTTTTT
66 AAATTTAAAATTTAATTTAATTAATTTATATAATTATTTTTT
3997260 TATGTCCCACACACATAAATAATTAAAAATAATATGTAAGTATGTGATTTGAAAAAGTTATAATT
1 TATGTCCCACACACATAAATAATTAAAAATAATATGTAAGTATGTGATTTGAAAAAGTTATAATT
3997325 AAATTTAAAATTTAATTTAATTAATTTATATAATTATTTTTT
66 AAATTTAAAATTTAATTTAATTAATTTATATAATTATTTTTT
3997367 AAAAAAATAA
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.43
Consensus pattern (107 bp):
TATGTCCCACACACATAAATAATTAAAAATAATATGTAAGTATGTGATTTGAAAAAGTTATAATT
AAATTTAAAATTTAATTTAATTAATTTATATAATTATTTTTT
Found at i:3999525 original size:3 final size:3
Alignment explanation
Indices: 3999517--3999553 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
3999507 TAATTATACA
3999517 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 T
3999554 GCCTTTTCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4001755 original size:2 final size:2
Alignment explanation
Indices: 4001748--4001772 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4001738 TAAAGGGGGA
4001748 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4001773 AGTAAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4004833 original size:19 final size:20
Alignment explanation
Indices: 4004793--4004839 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
4004783 TAATTACAAT
4004793 TAATATATATTTAATGATTA
1 TAATATATATTTAATGATTA
* *
4004813 TATTATATATTT-ATTATTA
1 TAATATATATTTAATGATTA
4004832 TAATATAT
1 TAATATAT
4004840 GTAATAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TAATATATATTTAATGATTA
Found at i:4005556 original size:22 final size:23
Alignment explanation
Indices: 4005522--4005574 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
4005512 TATAATATTT
4005522 TTAATATATTAAAATTAAT-TAAA
1 TTAAT-TATTAAAATTAATGTAAA
*
4005545 TTAATTATTAAATTTAATGTAAA
1 TTAATTATTAAAATTAATGTAAA
4005568 --AATTATT
1 TTAATTATT
4005575 TTTTATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 7 0.25
22 12 0.43
23 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTAATTATTAAAATTAATGTAAA
Found at i:4005939 original size:14 final size:14
Alignment explanation
Indices: 4005920--4005947 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4005910 TAATTACTAA
4005920 AATAAAATAATTAT
1 AATAAAATAATTAT
4005934 AATAAAATAATTAT
1 AATAAAATAATTAT
4005948 TTTATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAAATAATTAT
Found at i:4006572 original size:14 final size:13
Alignment explanation
Indices: 4006553--4006619 Score: 55
Period size: 14 Copynumber: 4.8 Consensus size: 13
4006543 TAGAGTTTTT
4006553 TTAAAAAGAAATAA
1 TTAAAAA-AAATAA
4006567 TTAAAAAAATATAA
1 TTAAAAAAA-ATAA
**
4006581 TTTTAAAAAATAA
1 TTAAAAAAAATAA
*
4006594 TTTATAAATATAAT-A
1 -TTA-AAA-AAAATAA
4006609 TTAAAAAAAAT
1 TTAAAAAAAAT
4006620 TATTTTTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.09
13 9 0.21
14 23 0.53
15 3 0.07
16 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (13 bp):
TTAAAAAAAATAA
Found at i:4006586 original size:16 final size:15
Alignment explanation
Indices: 4006551--4006625 Score: 54
Period size: 14 Copynumber: 5.3 Consensus size: 15
4006541 GTTAGAGTTT
4006551 TTTTAAAAAGAAATAA
1 TTTTAAAAA-AAATAA
4006567 --TTAAAAAAATATAA
1 TTTTAAAAAAA-ATAA
4006581 TTTT--AAAAAATAA
1 TTTTAAAAAAAATAA
* *
4006594 -TTT-ATAAATATAA
1 TTTTAAAAAAAATAA
* *
4006607 TATTAAAAAAAATTA
1 TTTTAAAAAAAATAA
4006622 TTTT
1 TTTT
4006626 TATTATTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
12 3 0.07
13 13 0.28
14 18 0.39
15 10 0.22
16 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (15 bp):
TTTTAAAAAAAATAA
Found at i:4006588 original size:13 final size:13
Alignment explanation
Indices: 4006572--4006614 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
4006562 AATAATTAAA
4006572 AAAATATAATTTT
1 AAAATATAATTTT
*
4006585 AAAAAATAA-TTT
1 AAAATATAATTTT
*
4006597 ATAAATATAATATT
1 A-AAATATAATTTT
4006611 AAAA
1 AAAA
4006615 AAAATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
12 4 0.16
13 18 0.72
14 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATATAATTTT
Found at i:4014494 original size:14 final size:14
Alignment explanation
Indices: 4014475--4014517 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
4014465 ACGTATTTTT
*
4014475 TATATTTATATTTA
1 TATATTTATATATA
4014489 TATATTTATATATA
1 TATATTTATATATA
* *
4014503 TATATATATGTATA
1 TATATTTATATATA
4014517 T
1 T
4014518 TACATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (14 bp):
TATATTTATATATA
Found at i:4014510 original size:8 final size:8
Alignment explanation
Indices: 4014475--4014517 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
4014465 ACGTATTTTT
*
4014475 TATATTTA
1 TATATATA
*
4014483 TATTTATA
1 TATATATA
*
4014491 TATTTATA
1 TATATATA
4014499 TATATATA
1 TATATATA
*
4014507 TATATGTA
1 TATATATA
4014515 TAT
1 TAT
4014518 TACATTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (8 bp):
TATATATA
Found at i:4024283 original size:1 final size:1
Alignment explanation
Indices: 4024247--4024271 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
4024237 ATTTTTTTTT
4024247 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
4024272 AAGGAGTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:4028010 original size:17 final size:17
Alignment explanation
Indices: 4027988--4028023 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4027978 TGGTCCCAAA
4027988 AAACAATTTTGGAAAGT
1 AAACAATTTTGGAAAGT
4028005 AAACAATTTTGGAAAGT
1 AAACAATTTTGGAAAGT
4028022 AA
1 AA
4028024 TGGCTTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.28
Consensus pattern (17 bp):
AAACAATTTTGGAAAGT
Found at i:4033876 original size:31 final size:33
Alignment explanation
Indices: 4033814--4033887 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 33
4033804 TTTTGTTTAG
*
4033814 TTTTAATAAATAATTTTTTTATTCTATTTTTAAT
1 TTTTAA-AAATAATTTTATTATTCTATTTTTAAT
*
4033848 TTTTAAAGATAATTTTATT-TT-TATTTTTAAT
1 TTTTAAAAATAATTTTATTATTCTATTTTTAAT
*
4033879 TTATAAAAA
1 TTTTAAAAA
4033888 ATGTATTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 17 0.47
32 2 0.06
33 11 0.31
34 6 0.17
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
TTTTAAAAATAATTTTATTATTCTATTTTTAAT
Found at i:4034414 original size:13 final size:13
Alignment explanation
Indices: 4034396--4034420 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4034386 TATATATTTT
4034396 ATTATTTAATATC
1 ATTATTTAATATC
4034409 ATTATTTAATAT
1 ATTATTTAATAT
4034421 AAGTTTCTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (13 bp):
ATTATTTAATATC
Found at i:4034589 original size:24 final size:24
Alignment explanation
Indices: 4034534--4034598 Score: 87
Period size: 25 Copynumber: 2.7 Consensus size: 24
4034524 CGTGAATAAT
* * *
4034534 TTTTTAATTGAAAAATAAAGAGTA
1 TTTTTAAGTGAAAAATGAACAGTA
4034558 TTTCTTAAGTGAAAAATGAACAGTA
1 TTT-TTAAGTGAAAAATGAACAGTA
4034583 TTTTTAAGT-AAAAATG
1 TTTTTAAGTGAAAAATG
4034599 TGGTTTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.19
24 9 0.24
25 21 0.57
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (24 bp):
TTTTTAAGTGAAAAATGAACAGTA
Found at i:4035002 original size:15 final size:15
Alignment explanation
Indices: 4034981--4035033 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
4034971 TATTTTATTT
*
4034981 ATATTTTTATTTAAT
1 ATATTTTTATTTAAA
*
4034996 TTATTTTTATTTAAA
1 ATATTTTTATTTAAA
*
4035011 ATATTTTTATAT-AA
1 ATATTTTTATTTAAA
4035025 AT-TTTTTAT
1 ATATTTTTAT
4035034 AATTAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 23 0.68
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
ATATTTTTATTTAAA
Found at i:4035093 original size:21 final size:21
Alignment explanation
Indices: 4035067--4035106 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4035057 AGTAAAATAA
4035067 TTTTATAATATATTATATTAT
1 TTTTATAATATATTATATTAT
* *
4035088 TTTTATATTTTATTATATT
1 TTTTATAATATATTATATT
4035107 TTTATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATAATATATTATATTAT
Found at i:4035096 original size:16 final size:15
Alignment explanation
Indices: 4035075--4035141 Score: 57
Period size: 16 Copynumber: 4.3 Consensus size: 15
4035065 AATTTTATAA
4035075 TATATTATATTATTTT
1 TATATT-TATTATTTT
4035091 TATATTTTATTATATTT
1 TATA-TTTATTAT-TTT
4035108 T-TATTT-TTATTTT
1 TATATTTATTATTTT
* * *
4035121 AATTATTTTTTATATT
1 TA-TATTTATTATTTT
4035137 TATAT
1 TATAT
4035142 AATATTCTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 11
0.75 0.05 0.19
Matches are distributed among these distances:
13 3 0.07
14 4 0.09
15 11 0.26
16 19 0.44
17 6 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATATTTATTATTTT
Found at i:4035100 original size:18 final size:18
Alignment explanation
Indices: 4035085--4035118 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4035075 TATATTATAT
4035085 TATTTTTATATTTTATTA
1 TATTTTTATATTTTATTA
4035103 TATTTTTAT-TTTTATT
1 TATTTTTATATTTTATT
4035119 TTAATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
TATTTTTATATTTTATTA
Found at i:4035121 original size:22 final size:22
Alignment explanation
Indices: 4035077--4035139 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
4035067 TTTTATAATA
* *
4035077 TATTATATTATT-TTTATATTT
1 TATTATATTTTTATTTTTATTT
4035098 TATTATATTTTTATTTTTATTT
1 TATTATATTTTTATTTTTATTT
*
4035120 TAATTAT-TTTTTATATTTAT
1 T-ATTATATTTTTATTTTTAT
4035140 ATAATATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.30
22 21 0.57
23 5 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTATATTTTTATTTTTATTT
Found at i:4043156 original size:202 final size:202
Alignment explanation
Indices: 4042810--4043202 Score: 786
Period size: 202 Copynumber: 1.9 Consensus size: 202
4042800 TATTTTATTC
4042810 TATAGATTAAACTCTTAGCTGTCAATATATACATACCAGTGTGATATTATATTGCTGTGAAATGA
1 TATAGATTAAACTCTTAGCTGTCAATATATACATACCAGTGTGATATTATATTGCTGTGAAATGA
4042875 ATCTTAAGAATTAGAATGATTCACAAGGGAAAAAGATGAGGTAGTTGGTTAATGAAATTATAATT
66 ATCTTAAGAATTAGAATGATTCACAAGGGAAAAAGATGAGGTAGTTGGTTAATGAAATTATAATT
4042940 AATCTCTCCATCCTTAGGTATTTCAAAGAGTTCTCAAAGCCTATGCTACAAAGCTTTTCGCCTAT
131 AATCTCTCCATCCTTAGGTATTTCAAAGAGTTCTCAAAGCCTATGCTACAAAGCTTTTCGCCTAT
4043005 CCTTAGG
196 CCTTAGG
4043012 TATAGATTAAACTCTTAGCTGTCAATATATACATACCAGTGTGATATTATATTGCTGTGAAATGA
1 TATAGATTAAACTCTTAGCTGTCAATATATACATACCAGTGTGATATTATATTGCTGTGAAATGA
4043077 ATCTTAAGAATTAGAATGATTCACAAGGGAAAAAGATGAGGTAGTTGGTTAATGAAATTATAATT
66 ATCTTAAGAATTAGAATGATTCACAAGGGAAAAAGATGAGGTAGTTGGTTAATGAAATTATAATT
4043142 AATCTCTCCATCCTTAGGTATTTCAAAGAGTTCTCAAAGCCTATGCTACAAAGCTTTTCGC
131 AATCTCTCCATCCTTAGGTATTTCAAAGAGTTCTCAAAGCCTATGCTACAAAGCTTTTCGC
4043203 AAGACTGCCT
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 191 1.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (202 bp):
TATAGATTAAACTCTTAGCTGTCAATATATACATACCAGTGTGATATTATATTGCTGTGAAATGA
ATCTTAAGAATTAGAATGATTCACAAGGGAAAAAGATGAGGTAGTTGGTTAATGAAATTATAATT
AATCTCTCCATCCTTAGGTATTTCAAAGAGTTCTCAAAGCCTATGCTACAAAGCTTTTCGCCTAT
CCTTAGG
Found at i:4045500 original size:13 final size:13
Alignment explanation
Indices: 4045482--4045507 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4045472 TTTGATGCCG
4045482 CAGTTGGCTCTCA
1 CAGTTGGCTCTCA
4045495 CAGTTGGCTCTCA
1 CAGTTGGCTCTCA
4045508 AACTTTACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.23, T:0.31
Consensus pattern (13 bp):
CAGTTGGCTCTCA
Found at i:4059911 original size:14 final size:16
Alignment explanation
Indices: 4059888--4059925 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
4059878 CATTACTATG
*
4059888 TAACTAAATAAAAA-C
1 TAACTTAATAAAAATC
4059903 -AACTTAATAAAAATC
1 TAACTTAATAAAAATC
4059918 TAACTTAA
1 TAACTTAA
4059926 ACGAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 12 0.60
15 1 0.05
16 7 0.35
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
TAACTTAATAAAAATC
Found at i:4060354 original size:34 final size:33
Alignment explanation
Indices: 4060306--4060526 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 33
4060296 TGGTAAAAAC
*
4060306 CACCATTTAATCAACAATGGCAACCTACCAAAT
1 CACCATTTAATCAACAATGGTAACCTACCAAAT
*
4060339 CTACCATTTAGTCAACAATGGTAAGCC-ACCAAAT
1 C-ACCATTTAATCAACAATGGTAA-CCTACCAAAT
* * *
4060373 CACCCATTTAATCAATAATAGTAAGCTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
** *
4060407 TTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CAC-CATTTAATCAACAATGGTAACCTACCAAAT
* * *
4060441 CTCCCATTTAGTCAACAATGGCAAACC-ACCAAAT
1 C-ACCATTTAATCAACAATGG-TAACCTACCAAAT
*
4060475 CACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CA-CCATTTAATCAACAATGGTAACCTACCAAAT
4060509 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
4060527 TCTCCCACTT
Statistics
Matches: 160, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
33 23 0.14
34 131 0.82
35 6 0.04
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (33 bp):
CACCATTTAATCAACAATGGTAACCTACCAAAT
Found at i:4060422 original size:68 final size:67
Alignment explanation
Indices: 4060308--4060526 Score: 287
Period size: 68 Copynumber: 3.2 Consensus size: 67
4060298 GTAAAAACCA
* * *
4060308 CCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAAT-TACCATTTAATCAACAATGGTAAGCTACCAAAT
4060373 CAC
65 CAC
* * * * *
4060376 CCATTTAATCAATAATAGTAAGCTACCAAATTTCTCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTAC-CATTTAATCAACAATGGTAAGCTACCAAAT
*
4060441 CTC
65 CAC
* * * *
4060444 CCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAACAATGGTAAACTACCAAAT
1 CCATTTAATCAACAATGGCAAACTACCAAATTA-CCATTTAATCAACAATGGTAAGCTACCAAAT
4060509 CA-
65 CAC
4060511 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
4060527 TCTCCCACTT
Statistics
Matches: 130, Mismatches: 19, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
67 17 0.13
68 112 0.86
69 1 0.01
ACGTcount: A:0.41, C:0.26, G:0.07, T:0.25
Consensus pattern (67 bp):
CCATTTAATCAACAATGGCAAACTACCAAATTACCATTTAATCAACAATGGTAAGCTACCAAATC
AC
Found at i:4060485 original size:102 final size:101
Alignment explanation
Indices: 4060306--4060526 Score: 343
Period size: 102 Copynumber: 2.2 Consensus size: 101
4060296 TGGTAAAAAC
* *
4060306 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
* *
4060371 ATCACCCATTTAATCAATAATAGTAAGCTACCAAAT
66 ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
** * * *
4060407 TTCTCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAGTCAACAATGGCAAACCACCA
1 CAC-CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCA
*
4060472 AATCACCCATTTAATCAACAATGGTAAACTACCAAAT
65 AATCACCCATTTAATCAACAATAGTAAACTACCAAAT
4060509 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
4060527 TCTCCCACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 91 0.85
ACGTcount: A:0.41, C:0.27, G:0.07, T:0.25
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATAGTAAACTACCAAAT
Found at i:4065005 original size:34 final size:34
Alignment explanation
Indices: 4064942--4065059 Score: 132
Period size: 34 Copynumber: 3.5 Consensus size: 34
4064932 AGTAAAAACC
** *
4064942 ACCATTTAATCAACAATGGCAACCTACCAAATCT
1 ACCATTTAATCAACAATGATAAGCTACCAAATCT
*
4064976 ACCATTTAGTCAACAATGATAAG-TCACCAAATC-
1 ACCATTTAATCAACAATGATAAGCT-ACCAAATCT
* *
4065009 ACCCATTTAATCAATAATGATAAGCTACCAAATTT
1 A-CCATTTAATCAACAATGATAAGCTACCAAATCT
**
4065044 TTCATTTAATCAACAA
1 ACCATTTAATCAACAA
4065060 AACCAATTTA
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
33 2 0.03
34 67 0.96
35 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (34 bp):
ACCATTTAATCAACAATGATAAGCTACCAAATCT
Found at i:4069137 original size:34 final size:33
Alignment explanation
Indices: 4069094--4069159 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
4069084 TTATCAAAAC
*
4069094 TATTATAAGTATTTATAAAATTA-TTAAAAATTTA
1 TATTATAAGT-TAT-TAAAATTATTTAAAAATTTA
*
4069128 TATTTTAAGTTATTAAAATTATTTTAAAAATT
1 TATTATAAGTTATTAAAATTA-TTTAAAAATT
4069160 ATTAAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 8 0.29
33 2 0.07
34 18 0.64
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (33 bp):
TATTATAAGTTATTAAAATTATTTAAAAATTTA
Found at i:4069161 original size:21 final size:23
Alignment explanation
Indices: 4069103--4069165 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 23
4069093 CTATTATAAG
4069103 TATTTATAAAATTATTAAAAATTTA
1 TATTTA-AAAATTATT-AAAATTTA
* *
4069128 TATTT-TAAGTTATTAAAA-TTA
1 TATTTAAAAATTATTAAAATTTA
4069149 T-TTTAAAAATTATTAAA
1 TATTTAAAAATTATTAAA
4069166 CTTAAAATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.09
21 14 0.42
22 4 0.12
23 7 0.21
25 5 0.15
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTTAAAAATTATTAAAATTTA
Found at i:4069368 original size:17 final size:17
Alignment explanation
Indices: 4069348--4069398 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
4069338 TTTAAAAATT
4069348 AATATTATTTATTTTAA
1 AATATTATTTATTTTAA
*
4069365 AATATAATTTATTATTAA
1 AATATTATTTATT-TTAA
4069383 AA-ATT-TTTATTTTAA
1 AATATTATTTATTTTAA
4069398 A
1 A
4069399 TTTATATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 5 0.16
16 6 0.19
17 14 0.45
18 6 0.19
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
AATATTATTTATTTTAA
Found at i:4069372 original size:22 final size:20
Alignment explanation
Indices: 4069337--4069387 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
4069327 CACGTCAATA
4069337 ATTTAAAAATTAATATTATTT
1 ATTTAAAAATTAAT-TTATTT
*
4069358 ATTTTAAAATATAATTTA-TT
1 ATTTAAAAAT-TAATTTATTT
4069378 A-TTAAAAATT
1 ATTTAAAAATT
4069388 TTTATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 1 0.04
19 7 0.26
20 3 0.11
21 12 0.44
22 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAAAATTAATTTATTT
Found at i:4069422 original size:29 final size:27
Alignment explanation
Indices: 4069370--4069426 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
4069360 TTTAAAATAT
4069370 AATTTATTATTAAAAATTTTTATTTTA
1 AATTTATTATTAAAAATTTTTATTTTA
* *
4069397 AATTTATATATTAGATATATTTTATTTTA
1 AATTTAT-TATTAAAAAT-TTTTATTTTA
4069426 A
1 A
4069427 TATAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 7 0.27
28 8 0.31
29 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
AATTTATTATTAAAAATTTTTATTTTA
Found at i:4070268 original size:16 final size:16
Alignment explanation
Indices: 4070247--4070280 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4070237 AATTTAAAAA
* *
4070247 AAAATATTAAAATTTT
1 AAAATATAAAAAATTT
4070263 AAAATATAAAAAATTT
1 AAAATATAAAAAATTT
4070279 AA
1 AA
4070281 TACATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATATAAAAAATTT
Found at i:4070642 original size:28 final size:27
Alignment explanation
Indices: 4070583--4070646 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
4070573 CACCCATTTG
* *
4070583 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
4070610 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
4070638 TTTGTCAAA
1 TTTGTCAAA
4070647 TATAGAGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 1 0.03
27 19 0.58
28 13 0.39
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:4071241 original size:15 final size:15
Alignment explanation
Indices: 4071189--4071241 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
4071179 TATACTTTTA
*
4071189 TATATACATTATAATAT
1 TATATATATT-TAA-AT
* *
4071206 TATATATACTTAATT
1 TATATATATTTAAAT
*
4071221 TTTATATATTTAAAT
1 TATATATATTTAAAT
4071236 TATATA
1 TATATA
4071242 ATATATATAA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
15 18 0.62
16 3 0.10
17 8 0.28
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATATATTTAAAT
Found at i:4071499 original size:30 final size:30
Alignment explanation
Indices: 4071453--4071531 Score: 99
Period size: 30 Copynumber: 2.6 Consensus size: 30
4071443 AATAAAAAAG
4071453 ATTTATAATATCAAATAAATTCTTATT-TTTT
1 ATTTAT-AT-TCAAATAAATTCTTATTATTTT
4071484 AATTTATATTCAAATAAATTCTTATTATTTT
1 -ATTTATATTCAAATAAATTCTTATTATTTT
*
4071515 ATTTGTATT-AACATAAA
1 ATTTATATTCAA-ATAAA
4071532 CTTTTACATT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 2 0.05
30 30 0.68
31 6 0.14
32 6 0.14
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (30 bp):
ATTTATATTCAAATAAATTCTTATTATTTT
Found at i:4072622 original size:28 final size:27
Alignment explanation
Indices: 4072563--4072652 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
4072553 CATCTATTTG
* *
4072563 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
4072590 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
4072618 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
4072643 TTTGTCAAAA
1 TTTGTCAAAA
4072653 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:4077195 original size:28 final size:27
Alignment explanation
Indices: 4077136--4077225 Score: 87
Period size: 28 Copynumber: 3.4 Consensus size: 27
4077126 CACCTATTTG
* *
4077136 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTATA
4077163 TTTGTCAAAAATGGTGGTT-TCCTTTATA
1 TTTGTCAAAAATGGTGGTTAT--TTTATA
* * * *
4077191 TTTGTCAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTATA
4077216 TTTGTCAAAA
1 TTTGTCAAAA
4077226 TTTGTGGCTA
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
25 11 0.20
26 3 0.06
27 19 0.35
28 21 0.39
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTATA
Found at i:4078541 original size:2 final size:2
Alignment explanation
Indices: 4078524--4078561 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
4078514 AAACACACAC
* *
4078524 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4078562 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:4081581 original size:2 final size:2
Alignment explanation
Indices: 4081574--4081612 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4081564 AAAATAAACA
4081574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4081613 AAGAAACTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4082212 original size:33 final size:34
Alignment explanation
Indices: 4082169--4082259 Score: 103
Period size: 33 Copynumber: 2.7 Consensus size: 34
4082159 GTTTAAGATG
* ** *
4082169 TTTAATATTTAGTGTTTAGAGTTTAAGATTAA-A
1 TTTAAAATTTAGAATTTAGAATTTAAGATTAAGA
*
4082202 TTTAAAATTTAGAATTTAGAATTTAAGTTTAAGA
1 TTTAAAATTTAGAATTTAGAATTTAAGATTAAGA
* *
4082236 TTTAAGAGTTTAAAATTTAGAATT
1 TTTAA-AATTTAGAATTTAGAATT
4082260 AACTAAAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 27 0.55
34 6 0.12
35 16 0.33
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
TTTAAAATTTAGAATTTAGAATTTAAGATTAAGA
Found at i:4082238 original size:13 final size:13
Alignment explanation
Indices: 4082183--4082241 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
4082173 ATATTTAGTG
4082183 TTTAGAGTTTAAGA
1 TTTA-AGTTTAAGA
* *
4082197 -TTAAATTTAAAA
1 TTTAAGTTTAAGA
*
4082209 TTTAGAATTT-AGAA
1 TTTA-AGTTTAAG-A
4082223 TTTAAGTTTAAGA
1 TTTAAGTTTAAGA
4082236 TTTAAG
1 TTTAAG
4082242 AGTTTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
12 7 0.19
13 18 0.49
14 12 0.32
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (13 bp):
TTTAAGTTTAAGA
Found at i:4082320 original size:7 final size:7
Alignment explanation
Indices: 4082190--4082320 Score: 73
Period size: 7 Copynumber: 18.9 Consensus size: 7
4082180 GTGTTTAGAG
4082190 TTTAAGA
1 TTTAAGA
4082197 -TTAA-A
1 TTTAAGA
*
4082202 TTTAAAA
1 TTTAAGA
4082209 TTT-AGAA
1 TTTAAG-A
4082216 TTT-AGAA
1 TTTAAG-A
4082223 TTTAAG-
1 TTTAAGA
4082229 TTTAAGA
1 TTTAAGA
4082236 TTTAAGA
1 TTTAAGA
*
4082243 GTTTAAAA
1 -TTTAAGA
4082251 TTT-AGAA
1 TTTAAG-A
*
4082258 TTAACTAAAA
1 TT---TAAGA
*
4082268 TTTAATA
1 TTTAAGA
4082275 -TTAA-A
1 TTTAAGA
4082280 TTTATA-A
1 TTTA-AGA
*
4082287 TTTATGA
1 TTTAAGA
*
4082294 TTTCAGA
1 TTTAAGA
4082301 TTTAAGA
1 TTTAAGA
4082308 TTTAAGA
1 TTTAAGA
4082315 TTTAAG
1 TTTAAG
4082321 CTTAACATTT
Statistics
Matches: 101, Mismatches: 9, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
5 2 0.02
6 23 0.23
7 63 0.62
8 8 0.08
10 4 0.04
11 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (7 bp):
TTTAAGA
Found at i:4084338 original size:18 final size:18
Alignment explanation
Indices: 4084317--4084355 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
4084307 TTTTTTTCAA
* *
4084317 TTTAATCAATTTTTAATT
1 TTTAATCAATTATAAATT
*
4084335 TTTAATTAATTATAAATT
1 TTTAATCAATTATAAATT
4084353 TTT
1 TTT
4084356 GTAAATTTCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTAATCAATTATAAATT
Found at i:4084798 original size:21 final size:21
Alignment explanation
Indices: 4084765--4084811 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4084755 TCTATCATAG
*
4084765 TATTGGACCTCGTATTAGTAC
1 TATTAGACCTCGTATTAGTAC
* *
4084786 TATTAGACGTCGTATTGGTAC
1 TATTAGACCTCGTATTAGTAC
4084807 TATTA
1 TATTA
4084812 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (21 bp):
TATTAGACCTCGTATTAGTAC
Found at i:4084909 original size:27 final size:27
Alignment explanation
Indices: 4084879--4084937 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
4084869 TTATTACAAA
4084879 ATTTTAATTTTTTAAA-AATTTTAATTT
1 ATTTTAA-TTTTTAAATAATTTTAATTT
*
4084906 A-TTTGATTTTTAAATTAATTTTAATTT
1 ATTTTAATTTTTAAA-TAATTTTAATTT
*
4084933 TTTTT
1 ATTTT
4084938 GATAACTTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
25 8 0.30
26 4 0.15
27 12 0.44
28 3 0.11
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
ATTTTAATTTTTAAATAATTTTAATTT
Found at i:4085047 original size:33 final size:33
Alignment explanation
Indices: 4085000--4085082 Score: 127
Period size: 33 Copynumber: 2.6 Consensus size: 33
4084990 GCTAATAATA
*
4085000 ATTTAC-TA-TATTTTAAAAATATTTGAAACTT
1 ATTTACTTAGTATTTTAAAAATATTTGAAAATT
*
4085031 ATTTACTTAGTATTTTAAAAATATTTTAAAATT
1 ATTTACTTAGTATTTTAAAAATATTTGAAAATT
4085064 ATTTACTTAGTA-TTTAAAA
1 ATTTACTTAGTATTTTAAAA
4085083 TTTAAAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
31 6 0.12
32 9 0.19
33 33 0.69
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (33 bp):
ATTTACTTAGTATTTTAAAAATATTTGAAAATT
Found at i:4085149 original size:2 final size:2
Alignment explanation
Indices: 4085144--4085169 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4085134 GCACTTGATC
4085144 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4085170 CTTATTAAAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4086140 original size:44 final size:44
Alignment explanation
Indices: 4086090--4086181 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 44
4086080 TGTTATTTTA
*
4086090 GTTTAATTAAGAATT-GGACTTATTAGCATAATAAAT-TCATTAGG
1 GTTTAATTAAGAATTAGG-CTTATTAGCATAATAAGTCT-ATTAGG
* *
4086134 GTTTAATTAAGAATTAGGCTTGTTAGTATAATAAGTCTATTAGG
1 GTTTAATTAAGAATTAGGCTTATTAGCATAATAAGTCTATTAGG
4086178 GTTT
1 GTTT
4086182 GTGTTATGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
44 40 0.93
45 3 0.07
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (44 bp):
GTTTAATTAAGAATTAGGCTTATTAGCATAATAAGTCTATTAGG
Found at i:4087413 original size:22 final size:22
Alignment explanation
Indices: 4087382--4087444 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
4087372 CTCAAAGGGA
*
4087382 AAGAAGAGAGATGAGGGATGAT
1 AAGAAAAGAGATGAGGGATGAT
*
4087404 AAGAAAAGAGAT-ATGAGA-GAT
1 AAGAAAAGAGATGA-GGGATGAT
* *
4087425 AATAAAA-AGATGAAGGATGA
1 AAGAAAAGAGATGAGGGATGA
4087445 CAGAAGGAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.18
21 13 0.39
22 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.32, T:0.14
Consensus pattern (22 bp):
AAGAAAAGAGATGAGGGATGAT
Found at i:4089076 original size:44 final size:44
Alignment explanation
Indices: 4088972--4089063 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
4088962 TGTTATTTTA
** * *
4088972 GTTTAATTAAGAATTATGCTTGTTAGTACAATAAGTCCATTAGG
1 GTTTAATTAAGAATTGGGCTTATTAGCACAATAAGTCCATTAGG
*
4089016 GTTTAATTAAGAATTGGGCTTATTAGCACAATAAGTTCATTAGG
1 GTTTAATTAAGAATTGGGCTTATTAGCACAATAAGTCCATTAGG
4089060 GTTT
1 GTTT
4089064 GTGTTAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.39
Consensus pattern (44 bp):
GTTTAATTAAGAATTGGGCTTATTAGCACAATAAGTCCATTAGG
Found at i:4091822 original size:53 final size:54
Alignment explanation
Indices: 4091723--4091825 Score: 129
Period size: 53 Copynumber: 1.9 Consensus size: 54
4091713 CTAAATCTAA
* * *
4091723 AATGACTTGAACCCGATTTAACTCGAATATTAAACTCAATTAACTCGAATCCAG
1 AATGACCTGAACCCGATTTAACTCGAACATTAAACCCAATTAACTCGAATCCAG
* * *
4091777 AATGACCTGAACCCGA-TTAAC-CTAAGCATTAAACCCGATTGACTCGAAT
1 AATGACCTGAACCCGATTTAACTCGAA-CATTAAACCCAATTAACTCGAAT
4091826 TCGAAATGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 3 0.07
53 24 0.57
54 15 0.36
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.25
Consensus pattern (54 bp):
AATGACCTGAACCCGATTTAACTCGAACATTAAACCCAATTAACTCGAATCCAG
Found at i:4091841 original size:53 final size:53
Alignment explanation
Indices: 4091722--4091841 Score: 127
Period size: 53 Copynumber: 2.2 Consensus size: 53
4091712 TCTAAATCTA
* *
4091722 AAATGACTTGAACCCGATTTAACTCGAATATTAAACTCAATTAACTCGAATCC
1 AAATGACTTGAACCCGATTTAACTCGAACATTAAACCCAATTAACTCGAATCC
* * * * *
4091775 AGAATGACCTGAACCCGA-TTAAC-CTAAGCATTAAACCCGATTGACTCGAATTCG
1 A-AATGACTTGAACCCGATTTAACTCGAA-CATTAAACCCAATTAACTCGAA-TCC
*
4091829 AAATGATTTGAAC
1 AAATGACTTGAAC
4091842 TCGAAATAAC
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
52 3 0.05
53 34 0.62
54 18 0.33
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (53 bp):
AAATGACTTGAACCCGATTTAACTCGAACATTAAACCCAATTAACTCGAATCC
Found at i:4094466 original size:30 final size:29
Alignment explanation
Indices: 4094432--4094536 Score: 95
Period size: 30 Copynumber: 3.6 Consensus size: 29
4094422 TATGTTAAGT
4094432 ATTTATTTAAGTATAAATTAAATATTAAAA
1 ATTTATTTAA-TATAAATTAAATATTAAAA
* **
4094462 ATTTATTTATATATAAATTAAAAATTAATG
1 ATTTATTTA-ATATAAATTAAATATTAAAA
* * * *
4094492 ATATATATAAATCTAAATTAAATATTAAGA
1 ATTTAT-TTAATATAAATTAAATATTAAAA
* *
4094522 GTTTA-TTAAAATAAA
1 ATTTATTTAATATAAA
4094537 ATAATTACAG
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
28 7 0.12
30 49 0.83
31 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (29 bp):
ATTTATTTAATATAAATTAAATATTAAAA
Found at i:4094485 original size:23 final size:24
Alignment explanation
Indices: 4094455--4094508 Score: 74
Period size: 23 Copynumber: 2.2 Consensus size: 24
4094445 TAAATTAAAT
* *
4094455 ATTAAAAATTTAT-TTATATATAA
1 ATTAAAAATTAATGATATATATAA
4094478 ATTAAAAATTAATGATATATATAA
1 ATTAAAAATTAATGATATATATAA
4094502 ATCTAAA
1 AT-TAAA
4094509 TTAAATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 12 0.44
24 11 0.41
25 4 0.15
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (24 bp):
ATTAAAAATTAATGATATATATAA
Found at i:4094495 original size:22 final size:23
Alignment explanation
Indices: 4094455--4094498 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
4094445 TAAATTAAAT
* *
4094455 ATTAAAAATTTATTTATATATAA
1 ATTAAAAATTTAATGATATATAA
4094478 ATTAAAAA-TTAATGATATATA
1 ATTAAAAATTTAATGATATATA
4094499 TAAATCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATTAAAAATTTAATGATATATAA
Found at i:4096116 original size:16 final size:17
Alignment explanation
Indices: 4096095--4096128 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4096085 ATGAGAATCC
4096095 AAGAAGA-GAAAAAGAG
1 AAGAAGAGGAAAAAGAG
*
4096111 AAGAAGAGGTAAAAGAG
1 AAGAAGAGGAAAAAGAG
4096128 A
1 A
4096129 GAATTGGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (17 bp):
AAGAAGAGGAAAAAGAG
Found at i:4098133 original size:7 final size:7
Alignment explanation
Indices: 4098121--4098239 Score: 64
Period size: 7 Copynumber: 16.9 Consensus size: 7
4098111 CTTTAATATT
4098121 AAATTTA
1 AAATTTA
4098128 AAATTTA
1 AAATTTA
* *
4098135 GAGTTTA
1 AAATTTA
4098142 AAATTT-
1 AAATTTA
4098148 AAA--TA
1 AAATTTA
4098153 AAGATTTA
1 AA-ATTTA
**
4098161 AGAGCTTA
1 A-AATTTA
4098169 AAATTTA
1 AAATTTA
*
4098176 AATTAATTA
1 AA--ATTTA
4098185 AAATTTA
1 AAATTTA
*
4098192 ATATTTA
1 AAATTTA
*
4098199 AAATTTT
1 AAATTTA
*
4098206 TAATTTA
1 AAATTTA
* *
4098213 TAATTTC
1 AAATTTA
*
4098220 AAATTCA
1 AAATTTA
*
4098227 AGATTTA
1 AAATTTA
*
4098234 AGATTT
1 AAATTT
4098240 CAACTTAACA
Statistics
Matches: 84, Mismatches: 21, Indels: 14
0.71 0.18 0.12
Matches are distributed among these distances:
4 1 0.01
5 2 0.02
6 4 0.05
7 63 0.75
8 7 0.08
9 7 0.08
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (7 bp):
AAATTTA
Found at i:4098164 original size:27 final size:25
Alignment explanation
Indices: 4098126--4098178 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
4098116 ATATTAAATT
*
4098126 TAAAATTTAGAGTTTAAAATTTAAA
1 TAAAATTTAGAGCTTAAAATTTAAA
4098151 TAAAGATTTAAGAGCTTAAAATTTAAA
1 TAAA-ATTT-AGAGCTTAAAATTTAAA
4098178 T
1 T
4098179 TAATTAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.16
26 4 0.16
27 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (25 bp):
TAAAATTTAGAGCTTAAAATTTAAA
Found at i:4099213 original size:16 final size:16
Alignment explanation
Indices: 4099203--4099234 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4099193 GTTATCATTA
4099203 AAATTATTTATAAATT
1 AAATTATTTATAAATT
*
4099219 AAATTATTTATTAATT
1 AAATTATTTATAAATT
4099235 TTATAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTATTTATAAATT
Found at i:4100863 original size:18 final size:19
Alignment explanation
Indices: 4100832--4100869 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
4100822 AATTTTAAAA
* *
4100832 TTTTTCTGTTATTTTTATT
1 TTTTTCTGTAATTTATATT
4100851 TTTTTC-GTAATTTATATT
1 TTTTTCTGTAATTTATATT
4100869 T
1 T
4100870 AAAAATAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTTCTGTAATTTATATT
Found at i:4101033 original size:2 final size:2
Alignment explanation
Indices: 4101028--4101058 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4101018 TGCACGTGAT
4101028 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4101059 CTTATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4102956 original size:27 final size:26
Alignment explanation
Indices: 4102914--4102984 Score: 97
Period size: 27 Copynumber: 2.7 Consensus size: 26
4102904 CAAAAATCAC
*
4102914 TCTTTGTGTTTATCAAAAATAGTGAT
1 TCTTTTTGTTTATCAAAAATAGTGAT
* *
4102940 TCTTTTTTGTTTTTCAAAAATGGTGAT
1 TC-TTTTTGTTTATCAAAAATAGTGAT
*
4102967 TCTTTTTGTTTATTAAAA
1 TCTTTTTGTTTATCAAAA
4102985 TTGGTGGCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.41
27 23 0.59
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.54
Consensus pattern (26 bp):
TCTTTTTGTTTATCAAAAATAGTGAT
Found at i:4103065 original size:13 final size:13
Alignment explanation
Indices: 4103047--4103080 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4103037 GGCTCCATCT
*
4103047 TCCCTCTTATGTA
1 TCCCTCTTATGGA
*
4103060 TCCCTCTCATGGA
1 TCCCTCTTATGGA
4103073 TCCCTCTT
1 TCCCTCTT
4103081 CAATTCATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.12, C:0.38, G:0.09, T:0.41
Consensus pattern (13 bp):
TCCCTCTTATGGA
Found at i:4107485 original size:27 final size:26
Alignment explanation
Indices: 4107440--4107511 Score: 83
Period size: 26 Copynumber: 2.7 Consensus size: 26
4107430 ACAAAAGCCA
*
4107440 CTTTTTGTATTTGTTAAAAATGGT-AGTT
1 CTTTTTG--TTTGTCAAAAATGGTGA-TT
*
4107468 CCTTTTTGTTTGTCAAAAATTGTGATT
1 -CTTTTTGTTTGTCAAAAATGGTGATT
4107495 CTTTTTGTTTGTCAAAA
1 CTTTTTGTTTGTCAAAA
4107512 TTGATAACTA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 17 0.43
27 15 0.38
28 1 0.03
29 7 0.17
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (26 bp):
CTTTTTGTTTGTCAAAAATGGTGATT
Found at i:4107526 original size:26 final size:26
Alignment explanation
Indices: 4107471--4107526 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
4107461 GGTAGTTCCT
* * **
4107471 TTTTGTTTGTCAAAAATTGTGATTCT
1 TTTTGTTTGTCAAAAATTGTAACTAA
4107497 TTTTGTTTGTC-AAAATTGATAACTAA
1 TTTTGTTTGTCAAAAATTG-TAACTAA
4107523 TTTT
1 TTTT
4107527 TATTACAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.27, C:0.07, G:0.12, T:0.54
Consensus pattern (26 bp):
TTTTGTTTGTCAAAAATTGTAACTAA
Found at i:4108985 original size:20 final size:20
Alignment explanation
Indices: 4108933--4108985 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
4108923 AATCTATTTC
* *
4108933 TATTGATTAATTTTAATTAA
1 TATTGATTAATATTAAGTAA
*
4108953 TATT-AGTATATATTAAGTAA
1 TATTGATTA-ATATTAAGTAA
4108973 TATTGATTAATAT
1 TATTGATTAATAT
4108986 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 3 0.11
20 21 0.78
21 3 0.11
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TATTGATTAATATTAAGTAA
Found at i:4109172 original size:7 final size:7
Alignment explanation
Indices: 4109162--4109205 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
4109152 TTTATTTATT
4109162 TATTTAA
1 TATTTAA
4109169 TATTTAA
1 TATTTAA
*
4109176 AATTTTAAA
1 TA-TTT-AA
*
4109185 TATTAAA
1 TATTTAA
4109192 TATTTAA
1 TATTTAA
4109199 TATTTAA
1 TATTTAA
4109206 AACTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
7 23 0.74
8 5 0.16
9 3 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
TATTTAA
Found at i:4109182 original size:15 final size:16
Alignment explanation
Indices: 4109162--4109207 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
4109152 TTTATTTATT
4109162 TATTTAATATTTAAAA
1 TATTTAATATTTAAAA
4109178 T-TTTAA-ATATT-AAA
1 TATTTAATAT-TTAAAA
4109192 TATTTAATATTTAAAA
1 TATTTAATATTTAAAA
4109208 CTTATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 6 0.23
15 14 0.54
16 6 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATTTAATATTTAAAA
Found at i:4113736 original size:19 final size:19
Alignment explanation
Indices: 4113712--4113772 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
4113702 TTAATAAAAA
4113712 ATTAAAATATAAATTAAAT
1 ATTAAAATATAAATTAAAT
* * *
4113731 ATTAAAA-ATTAATGATAT
1 ATTAAAATATAAATTAAAT
*
4113749 ATTTAAATATAAATTAAAT
1 ATTAAAATATAAATTAAAT
*
4113768 GTTAA
1 ATTAA
4113773 GAGTTTATTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 14 0.44
19 18 0.56
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
ATTAAAATATAAATTAAAT
Found at i:4113742 original size:37 final size:37
Alignment explanation
Indices: 4113701--4113772 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
4113691 AAACTTTTAC
4113701 ATTAATAAAAAATTAAAATATAAATTAAATATTAAAA
1 ATTAATAAAAAATTAAAATATAAATTAAATATTAAAA
* * * * *
4113738 ATTAATGATATATTTAAATATAAATTAAATGTTAA
1 ATTAATAAAAAATTAAAATATAAATTAAATATTAA
4113773 GAGTTTATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (37 bp):
ATTAATAAAAAATTAAAATATAAATTAAATATTAAAA
Done.