Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 77 of 198
Found at i:24064292 original size:30 final size:32
Alignment explanation
Indices: 24064257--24064343 Score: 97
Period size: 33 Copynumber: 2.7 Consensus size: 32
24064247 ATAATATGAG
* *
24064257 TCTTTAATTATGTCTTG-TTTATTAA-ATGCA
1 TCTTTAATTATGTCTTGCATTATTAATATACA
*
24064287 TCTTTAATTAATGTCTTGCATTATTAATCTACA
1 TCTTTAATT-ATGTCTTGCATTATTAATATACA
* *
24064320 TCTTTTAATTATGACATGCATTAT
1 TC-TTTAATTATGTCTTGCATTAT
24064344 GTGTTCTGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
30 9 0.19
31 8 0.17
32 7 0.15
33 17 0.35
34 7 0.15
ACGTcount: A:0.29, C:0.13, G:0.08, T:0.51
Consensus pattern (32 bp):
TCTTTAATTATGTCTTGCATTATTAATATACA
Found at i:24066080 original size:20 final size:22
Alignment explanation
Indices: 24066052--24066102 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
24066042 TTTATTCTTG
* *
24066052 ATATATTTAATTAG-TG-TTTA
1 ATATGTTTAATGAGTTGTTTTA
24066072 ATATGTTTAATGAGTTGTTTTA
1 ATATGTTTAATGAGTTGTTTTA
24066094 ATATGTTTA
1 ATATGTTTA
24066103 TTATAGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 12 0.44
21 2 0.07
22 13 0.48
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
ATATGTTTAATGAGTTGTTTTA
Found at i:24066810 original size:9 final size:9
Alignment explanation
Indices: 24066796--24066821 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
24066786 ATTCATTAAT
24066796 TTTTAGTTA
1 TTTTAGTTA
24066805 TTTTAGTTA
1 TTTTAGTTA
24066814 TTTTAGTT
1 TTTTAGTT
24066822 TGTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:24067347 original size:19 final size:19
Alignment explanation
Indices: 24067319--24067356 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
24067309 ACAAATTAAA
* *
24067319 TAAAGTGGCTGTTACAAAG
1 TAAAGAGGCTATTACAAAG
24067338 TAAAGAGGCTATTACAAAG
1 TAAAGAGGCTATTACAAAG
24067357 GAGGTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.24
Consensus pattern (19 bp):
TAAAGAGGCTATTACAAAG
Found at i:24068645 original size:447 final size:447
Alignment explanation
Indices: 24067805--24068659 Score: 1442
Period size: 447 Copynumber: 1.9 Consensus size: 447
24067795 GTCTCGAGTG
* * *
24067805 ACTTATCTAGTGAGCTAGTGGCGTCATCCTGAACTTGTTTCTGAACTTATCACCAACCTTGGTGT
1 ACTTAGCTAGTGAGCTAGTGGCGTCATCCTAAACTTGTTTCTGAACTTATCACCAACCCTGGTGT
*
24067870 GGCGTTCATCCATCTAAATATACCTTCGATTCCTACTTTGCTAAGTAACGGGTCGAGGTCCATCA
66 GGCGTTCATCCATCTAAATATAACTTCGATTCCTACTTTGCTAAGTAACGGGTCGAGGTCCATCA
* *
24067935 ACCTATTCCCAATTGTCACCTTAAACCATAAAAGATTTGGGGCGATACGCGTTATAGTATCGAAT
131 ACCTATTCCCAACTGTCACCTTAAACCATAAAAGATTTGGGGCGATACGCATTATAGTATCGAAT
*
24068000 CTTTCTTGATGTTTAAGTTCTATTATTCATCTCTATCACTTACTTTTTCTATCCTACTTCTTTGT
196 CTTTCTTGATGTGTAAGTTCTATTATTCATCTCTATCACTTACTTTTTCTATCCTACTTCTTTGT
* * * *
24068065 TAAACCAAGCTCATCCAACGATATTCCATTTAAAATCCATCTATCTATTAGCCACCTTGAACTTA
261 TAAACCAAGCCCATCCAAAGATATTCCATCTAAAATACATCTATCTATTAGCCACCTTGAACTTA
* * *
24068130 TTCCAATATACAATTCCATACTTAACCAAAATTCATCCATTTTTGAAACTGAACGAAACTTCCTC
326 TTCCAACATACAATTCCATACTTAACCAAAATTCATCCATTTTTGAAACCGAACAAAACTTCCTC
* *
24068195 GTCGATGGTCGGGCAACTCAAATACGACTCGACTCAACACTGAGGTGGATCGTATCA
391 GTCGACGATCGGGCAACTCAAATACGACTCGACTCAACACTGAGGTGGATCGTATCA
* *
24068252 ACTTAGCTAGTGAGTTAGTGGCGTCATCCTAAACTTGTTTTTGAACTTATCACCAACCCTGGTGT
1 ACTTAGCTAGTGAGCTAGTGGCGTCATCCTAAACTTGTTTCTGAACTTATCACCAACCCTGGTGT
* * *
24068317 GGCGTTCATCCATCTACATATAACTTTGGTTCCTACTTTGCTAAGTAACGGGTCGAGGTCCATCA
66 GGCGTTCATCCATCTAAATATAACTTCGATTCCTACTTTGCTAAGTAACGGGTCGAGGTCCATCA
* * *
24068382 ACGTATTCCCAGCTGTCACCTTAAACCATATAAGATTTGGGGCGATACGCATTATAGTATCGAAT
131 ACCTATTCCCAACTGTCACCTTAAACCATAAAAGATTTGGGGCGATACGCATTATAGTATCGAAT
*
24068447 CTTTCTTGATGTGTAAGTTCTATTATTCATCT-TCATCACTTATTTTTTCTATCCTACTTCTTTG
196 CTTTCTTGATGTGTAAGTTCTATTATTCATCTCT-ATCACTTACTTTTTCTATCCTACTTCTTTG
* * *
24068511 TTAAACCGAGCCCATCCAAAGTTATTCCATCTAAAATACATCTATCTTTTAGCCACCTTGAACTT
260 TTAAACCAAGCCCATCCAAAGATATTCCATCTAAAATACATCTATCTATTAGCCACCTTGAACTT
24068576 ATTCCAACATACAATTCCATACTTAACCAAAATTCATCCATTTTTGAAACCGAACAAAACTTCCT
325 ATTCCAACATACAATTCCATACTTAACCAAAATTCATCCATTTTTGAAACCGAACAAAACTTCCT
24068641 CGTCGACGATCGGGCAACT
390 CGTCGACGATCGGGCAACT
24068660 TGATGAGATC
Statistics
Matches: 379, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
446 1 0.00
447 378 1.00
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (447 bp):
ACTTAGCTAGTGAGCTAGTGGCGTCATCCTAAACTTGTTTCTGAACTTATCACCAACCCTGGTGT
GGCGTTCATCCATCTAAATATAACTTCGATTCCTACTTTGCTAAGTAACGGGTCGAGGTCCATCA
ACCTATTCCCAACTGTCACCTTAAACCATAAAAGATTTGGGGCGATACGCATTATAGTATCGAAT
CTTTCTTGATGTGTAAGTTCTATTATTCATCTCTATCACTTACTTTTTCTATCCTACTTCTTTGT
TAAACCAAGCCCATCCAAAGATATTCCATCTAAAATACATCTATCTATTAGCCACCTTGAACTTA
TTCCAACATACAATTCCATACTTAACCAAAATTCATCCATTTTTGAAACCGAACAAAACTTCCTC
GTCGACGATCGGGCAACTCAAATACGACTCGACTCAACACTGAGGTGGATCGTATCA
Found at i:24069870 original size:20 final size:20
Alignment explanation
Indices: 24069831--24069891 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
24069821 CCAATAAAAT
* *
24069831 AAATGAGTTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
24069851 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
24069872 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
24069892 GTCGGAGCTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.30
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:24080149 original size:18 final size:18
Alignment explanation
Indices: 24080126--24080160 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
24080116 ATACAACCTC
24080126 TTTTTTTT-ATGCACGAA
1 TTTTTTTTAATGCACGAA
*
24080143 TTTTTTTTAATTCACGAA
1 TTTTTTTTAATGCACGAA
24080161 CCTAATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (18 bp):
TTTTTTTTAATGCACGAA
Found at i:24103367 original size:19 final size:20
Alignment explanation
Indices: 24103330--24103369 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
24103320 ATATATGAAG
*
24103330 TAAAAAAAAGAGTTCGAATA
1 TAAAAAAAAGAATTCGAATA
24103350 TAAAAAAAAGAATT-GAATA
1 TAAAAAAAAGAATTCGAATA
24103369 T
1 T
24103370 TTTGTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.62, C:0.03, G:0.12, T:0.23
Consensus pattern (20 bp):
TAAAAAAAAGAATTCGAATA
Found at i:24104277 original size:15 final size:15
Alignment explanation
Indices: 24104257--24104298 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
24104247 CCAAATGAAA
* *
24104257 GAAAAAGAAAATATT
1 GAAAAAGAAAAAAAT
24104272 GAAAAAGAAAAAAAT
1 GAAAAAGAAAAAAAT
24104287 GAAAAAGAAAAA
1 GAAAAAGAAAAA
24104299 GAAAAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
GAAAAAGAAAAAAAT
Found at i:24106118 original size:14 final size:13
Alignment explanation
Indices: 24106095--24106136 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
24106085 TAGGTTCGTG
24106095 AATT-GAAAAAAA
1 AATTCGAAAAAAA
24106107 AAGTTCGAAAAAAA
1 AA-TTCGAAAAAAA
*
24106121 AATTTGAAAGAAAA
1 AATTCGAAA-AAAA
24106135 AA
1 AA
24106137 AACTTGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 8 0.31
14 16 0.62
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (13 bp):
AATTCGAAAAAAA
Found at i:24106134 original size:16 final size:16
Alignment explanation
Indices: 24106115--24106156 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
24106105 AAAAGTTCGA
24106115 AAAAAAAATTTGAAAG
1 AAAAAAAATTTGAAAG
*
24106131 AAAAAAAACTTGAAAG
1 AAAAAAAATTTGAAAG
24106147 AAAAAAAATT
1 AAAAAAAATT
24106157 GTATACGGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (16 bp):
AAAAAAAATTTGAAAG
Found at i:24107128 original size:18 final size:18
Alignment explanation
Indices: 24107107--24107141 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
24107097 AGAAAAGAAA
24107107 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
24107125 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
24107142 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:24132178 original size:20 final size:20
Alignment explanation
Indices: 24132153--24132198 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
24132143 GCTCGTTTCT
24132153 AGCTCACTCGAGCTCAAGTC
1 AGCTCACTCGAGCTCAAGTC
* * * *
24132173 AGCTCATTCGAGTTGAATTC
1 AGCTCACTCGAGCTCAAGTC
24132193 AGCTCA
1 AGCTCA
24132199 ACCTCAACCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (20 bp):
AGCTCACTCGAGCTCAAGTC
Found at i:24136392 original size:20 final size:20
Alignment explanation
Indices: 24136343--24136396 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
24136333 TCTCGCTTTC
* *
24136343 TTTTCATTTTCATTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
24136364 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
24136383 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
24136397 GTATTTTCGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 16 0.55
20 8 0.28
21 5 0.17
ACGTcount: A:0.09, C:0.13, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:24138076 original size:23 final size:23
Alignment explanation
Indices: 24138041--24138152 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
24138031 CGGTTTTGGG
* *
24138041 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
24138064 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
24138087 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
24138110 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
24138133 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
24138153 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:24138103 original size:46 final size:46
Alignment explanation
Indices: 24138041--24138152 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
24138031 CGGTTTTGGG
*
24138041 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
24138087 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
24138133 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
24138153 GTTCAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:24139813 original size:19 final size:20
Alignment explanation
Indices: 24139775--24139813 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
24139765 GCAAGCTGAT
* *
24139775 TTTAGCTTGCTTTTAGCTCC
1 TTTAGCTCGCTTTCAGCTCC
24139795 TTTAGCTCG-TTTCAGCTCC
1 TTTAGCTCGCTTTCAGCTCC
24139814 AACCAGCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.10, C:0.28, G:0.15, T:0.46
Consensus pattern (20 bp):
TTTAGCTCGCTTTCAGCTCC
Found at i:24140995 original size:34 final size:34
Alignment explanation
Indices: 24140956--24141025 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
24140946 CTTTAATTGA
24140956 AACTCCTTGTTCAGTTGAATAGTTTAGGAGCTTT
1 AACTCCTTGTTCAGTTGAATAGTTTAGGAGCTTT
24140990 AACTCCTTGTTCAGTTGAATAGTTTAGGAGCTTT
1 AACTCCTTGTTCAGTTGAATAGTTTAGGAGCTTT
24141024 AA
1 AA
24141026 TTGCTAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.26, C:0.14, G:0.20, T:0.40
Consensus pattern (34 bp):
AACTCCTTGTTCAGTTGAATAGTTTAGGAGCTTT
Found at i:24141307 original size:21 final size:21
Alignment explanation
Indices: 24141281--24141324 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
24141271 TTGGTATTTG
24141281 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24141302 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
24141323 GG
1 GG
24141325 TATTTGGNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.36, T:0.30
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24141312 original size:11 final size:11
Alignment explanation
Indices: 24141292--24141324 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
24141282 GAATTGGTAC
24141292 GAAATGGTATG
1 GAAATGGTATG
*
24141303 GAATTGGTAT-
1 GAAATGGTATG
24141313 GAAATGGTATG
1 GAAATGGTATG
24141324 G
1 G
24141325 TATTTGGNNN
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:24145800 original size:15 final size:14
Alignment explanation
Indices: 24145780--24145835 Score: 53
Period size: 15 Copynumber: 4.0 Consensus size: 14
24145770 AACCGTATAA
24145780 ATTTTTTTTTCTTTC
1 ATTTTTTTTT-TTTC
24145795 ATTTTTTTTTGTTT-
1 ATTTTTTTTT-TTTC
*
24145809 -TTGTTTTTTTTTC
1 ATTTTTTTTTTTTC
**
24145822 AAATTTTTTTTTTC
1 ATTTTTTTTTTTTC
24145836 GAACTTTTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
12 3 0.09
13 8 0.24
14 10 0.29
15 13 0.38
ACGTcount: A:0.09, C:0.07, G:0.04, T:0.80
Consensus pattern (14 bp):
ATTTTTTTTTTTTC
Found at i:24145829 original size:14 final size:15
Alignment explanation
Indices: 24145812--24145847 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
24145802 TTTGTTTTTG
24145812 TTTTTTTTTC-AAAT
1 TTTTTTTTTCGAAAT
*
24145826 TTTTTTTTTCGAACT
1 TTTTTTTTTCGAAAT
24145841 TTTTTTT
1 TTTTTTT
24145848 ACGTACCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.14, C:0.08, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTTTTTTCGAAAT
Found at i:24146172 original size:21 final size:21
Alignment explanation
Indices: 24146146--24146208 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24146136 TTGGTATTTG
24146146 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24146167 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24146188 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
24146209 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24147905 original size:21 final size:21
Alignment explanation
Indices: 24147881--24147944 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
24147871 AAGGCCCAAT
24147881 AAGATGATTCCAAGCCCAAAC
1 AAGATGATTCCAAGCCCAAAC
* * *
24147902 AAGAAGA---CAA-ACCATAAT
1 AAGATGATTCCAAGCCCA-AAC
24147920 AAGATGATTCCAAGCCCAAAC
1 AAGATGATTCCAAGCCCAAAC
24147941 AAGA
1 AAGA
24147945 AGACAAACCA
Statistics
Matches: 32, Mismatches: 6, Indels: 10
0.67 0.12 0.21
Matches are distributed among these distances:
17 3 0.09
18 11 0.34
21 15 0.47
22 3 0.09
ACGTcount: A:0.50, C:0.23, G:0.14, T:0.12
Consensus pattern (21 bp):
AAGATGATTCCAAGCCCAAAC
Found at i:24147922 original size:39 final size:39
Alignment explanation
Indices: 24147878--24147956 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
24147868 GGCAAGGCCC
24147878 AATAAGATGATTCCAAGCCCAAACAAGAAGACAAACCAT
1 AATAAGATGATTCCAAGCCCAAACAAGAAGACAAACCAT
24147917 AATAAGATGATTCCAAGCCCAAACAAGAAGACAAACCAT
1 AATAAGATGATTCCAAGCCCAAACAAGAAGACAAACCAT
24147956 A
1 A
24147957 CTTACTTGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.52, C:0.23, G:0.13, T:0.13
Consensus pattern (39 bp):
AATAAGATGATTCCAAGCCCAAACAAGAAGACAAACCAT
Found at i:24160652 original size:14 final size:14
Alignment explanation
Indices: 24160633--24160685 Score: 74
Period size: 13 Copynumber: 3.9 Consensus size: 14
24160623 TAGCTCTCTC
24160633 TTTTTTTTCACAAT
1 TTTTTTTTCACAAT
*
24160647 TTTTTTTTCA-AAA
1 TTTTTTTTCACAAT
*
24160660 TTTTTTTT-AAAAT
1 TTTTTTTTCACAAT
24160673 TTTTTTTTCACAA
1 TTTTTTTTCACAA
24160686 CTTGATATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 1 0.03
13 20 0.59
14 13 0.38
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTTTTTCACAAT
Found at i:24160679 original size:12 final size:13
Alignment explanation
Indices: 24160633--24160679 Score: 69
Period size: 12 Copynumber: 3.6 Consensus size: 13
24160623 TAGCTCTCTC
*
24160633 TTTTTTTTCACAAT
1 TTTTTTTTCA-AAA
24160647 TTTTTTTTCAAAA
1 TTTTTTTTCAAAA
24160660 TTTTTTTT-AAAA
1 TTTTTTTTCAAAA
24160672 TTTTTTTT
1 TTTTTTTT
24160680 TCACAACTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 12 0.38
13 10 0.31
14 10 0.31
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTTTTCAAAA
Found at i:24160759 original size:12 final size:12
Alignment explanation
Indices: 24160724--24160759 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
24160714 GGAAACTAGT
* *
24160724 TTTTTTTTTGAA
1 TTTTTTTTCGAG
24160736 TTTTTTTTCGAG
1 TTTTTTTTCGAG
24160748 TTTTTTTTCGAG
1 TTTTTTTTCGAG
24160760 AAACTACTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.11, C:0.06, G:0.14, T:0.69
Consensus pattern (12 bp):
TTTTTTTTCGAG
Found at i:24172964 original size:34 final size:34
Alignment explanation
Indices: 24172921--24172996 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
24172911 AGATTTAAGC
24172921 AAATTAATTACTAACACTTATTTAAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
24172955 AAATTAATTACTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
24172989 AAGTTAAT
1 AAATTAAT
24172997 AAACTAACTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:24173812 original size:17 final size:18
Alignment explanation
Indices: 24173780--24173815 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
24173770 TTTTGAGCTG
24173780 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
24173798 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
24173815 A
1 A
24173816 TGTTTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:24177251 original size:17 final size:15
Alignment explanation
Indices: 24177219--24177248 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
24177209 GTAATTGTAG
24177219 TTTCGAAGTAAAAAA
1 TTTCGAAGTAAAAAA
24177234 TTTCGAAGTAAAAAA
1 TTTCGAAGTAAAAAA
24177249 AATCTGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
TTTCGAAGTAAAAAA
Found at i:24186402 original size:15 final size:14
Alignment explanation
Indices: 24186376--24186427 Score: 68
Period size: 15 Copynumber: 3.5 Consensus size: 14
24186366 ATTTCCTCTC
*
24186376 TTTTTTTCTTTCGAA
1 TTTTTTT-TTTCAAA
24186391 TTATTTTTTTTCCAAA
1 TT-TTTTTTTT-CAAA
24186407 TTTTTTTTTTCAAA
1 TTTTTTTTTTCAAA
24186421 TTTTTTT
1 TTTTTTT
24186428 AATTCAATAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
14 11 0.32
15 13 0.38
16 10 0.29
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTTTTTTTCAAA
Found at i:24186413 original size:14 final size:14
Alignment explanation
Indices: 24186394--24186427 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
24186384 TTTCGAATTA
24186394 TTTTTTTTCCAAAT
1 TTTTTTTTCCAAAT
*
24186408 TTTTTTTTTCAAAT
1 TTTTTTTTCCAAAT
24186422 TTTTTT
1 TTTTTT
24186428 AATTCAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTTTTTCCAAAT
Found at i:24186433 original size:15 final size:14
Alignment explanation
Indices: 24186393--24186434 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
24186383 CTTTCGAATT
*
24186393 ATTTTTTT-TCCAA
1 ATTTTTTTATTCAA
*
24186406 ATTTTTTTTTTCAA
1 ATTTTTTTATTCAA
24186420 ATTTTTTTAATTCAA
1 ATTTTTTT-ATTCAA
24186435 TACAATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 8 0.32
14 12 0.48
15 5 0.20
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (14 bp):
ATTTTTTTATTCAA
Found at i:24186496 original size:12 final size:13
Alignment explanation
Indices: 24186475--24186499 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24186465 AAATTACACC
24186475 TTGAATTTTTTTT
1 TTGAATTTTTTTT
24186488 TTGAATTTTTTT
1 TTGAATTTTTTT
24186500 CACATTGACT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTGAATTTTTTTT
Found at i:24187321 original size:12 final size:12
Alignment explanation
Indices: 24187297--24187348 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
24187287 TCGTTTTCTC
24187297 TTCTTTCTTCAAT
1 TTCTTT-TTCAAT
24187310 TTCTTTTTCAATTT
1 TTCTTTTTCAA--T
*
24187324 TCTCTTTTTCACT
1 T-TCTTTTTCAAT
*
24187337 TCCTTTTTCAAT
1 TTCTTTTTCAAT
24187349 CTCAATTTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
12 14 0.42
13 8 0.24
14 2 0.06
15 9 0.27
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.63
Consensus pattern (12 bp):
TTCTTTTTCAAT
Found at i:24187382 original size:26 final size:27
Alignment explanation
Indices: 24187340--24187397 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
24187330 TTTCACTTCC
24187340 TTTT-TCAATCTCAA-TTTCTTTTTTCT
1 TTTTCTCAATCTCAATTTTC-TTTTTCT
*
24187366 TTTTCTCACTCTC-ATTTTCTTTTTCT
1 TTTTCTCAATCTCAATTTTCTTTTTCT
*
24187392 ATTTCT
1 TTTTCT
24187398 TGTTCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (27 bp):
TTTTCTCAATCTCAATTTTCTTTTTCT
Found at i:24187384 original size:27 final size:27
Alignment explanation
Indices: 24187340--24187422 Score: 75
Period size: 27 Copynumber: 3.1 Consensus size: 27
24187330 TTTCACTTCC
*
24187340 TTTT-TCAATCTCAATTTCTTTTTTCT
1 TTTTCTCAATCTCATTTTCTTTTTTCT
*
24187366 TTTTCTCACTCTCATTTTC-TTTTTCT
1 TTTTCTCAATCTCATTTTCTTTTTTCT
* **
24187392 ATTTCT-TGT-TCATTTTCTTTCATTTCT
1 TTTTCTCAATCTCATTTTCTTT--TTTCT
24187419 TTTT
1 TTTT
24187423 TTCGTTTCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 8 0.17
25 3 0.06
26 16 0.34
27 20 0.43
ACGTcount: A:0.11, C:0.20, G:0.01, T:0.67
Consensus pattern (27 bp):
TTTTCTCAATCTCATTTTCTTTTTTCT
Found at i:24187398 original size:12 final size:11
Alignment explanation
Indices: 24187381--24187422 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
24187371 TCACTCTCAT
24187381 TTTCTTTTTCTA
1 TTTCTTTTTC-A
*
24187393 TTTCTTGTTCA
1 TTTCTTTTTCA
*
24187404 TTT-TCTTTCA
1 TTTCTTTTTCA
24187414 TTTCTTTTT
1 TTTCTTTTT
24187423 TTCGTTTCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
10 8 0.32
11 8 0.32
12 9 0.36
ACGTcount: A:0.07, C:0.17, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTCTTTTTCA
Found at i:24192308 original size:19 final size:20
Alignment explanation
Indices: 24192284--24192321 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
24192274 TGAGCTGGTT
24192284 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
24192303 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
24192322 AATTAGCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:24195762 original size:17 final size:16
Alignment explanation
Indices: 24195740--24195773 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
24195730 AATTAAACTA
24195740 TAACTTAACTAATTAAC
1 TAACTTAACTAA-TAAC
*
24195757 TAACTTAATTAATAAC
1 TAACTTAACTAATAAC
24195773 T
1 T
24195774 TTATTCAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACTTAACTAATAAC
Found at i:24199701 original size:20 final size:19
Alignment explanation
Indices: 24199672--24199709 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
24199662 AGCTAATAAC
24199672 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
24199691 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
24199710 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:24202791 original size:6 final size:6
Alignment explanation
Indices: 24202774--24202803 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
24202764 TCAATTTTTT
*
24202774 TCTCAA TATCAA TCTCAA TCTCAA TCTCAA
1 TCTCAA TCTCAA TCTCAA TCTCAA TCTCAA
24202804 ATTCTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.30, G:0.00, T:0.33
Consensus pattern (6 bp):
TCTCAA
Found at i:24202839 original size:6 final size:6
Alignment explanation
Indices: 24202830--24202881 Score: 50
Period size: 6 Copynumber: 7.7 Consensus size: 6
24202820 CTCACTCTCA
24202830 TTTTCT TTTTCTTT TATTTCT TTTTCT TTTTCTTT TATTTCT TTTTCT
1 TTTTCT TTTTC--T T-TTTCT TTTTCT TTTTC--T T-TTTCT TTTTCT
24202878 TTTT
1 TTTT
24202882 TTCTTCTCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
6 24 0.60
7 4 0.10
8 4 0.10
9 8 0.20
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:24202849 original size:15 final size:15
Alignment explanation
Indices: 24202831--24202859 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24202821 TCACTCTCAT
24202831 TTTCTTTTTCTTTTA
1 TTTCTTTTTCTTTTA
24202846 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
24202860 TCTTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTTTTCTTTTA
Found at i:24202854 original size:21 final size:21
Alignment explanation
Indices: 24202830--24202881 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
24202820 CTCACTCTCA
24202830 TTTTCTTTTTCTTTTATTTCT
1 TTTTCTTTTTCTTTTATTTCT
24202851 TTTTCTTTTTCTTTTATTTCT
1 TTTTCTTTTTCTTTTATTTCT
24202872 TTTTCTTTTT
1 TTTTCTTTTT
24202882 TTCTTCTCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTCTTTTTCTTTTATTTCT
Found at i:24202870 original size:15 final size:14
Alignment explanation
Indices: 24202835--24202886 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
24202825 TCTCATTTTC
24202835 TTTTTCTTTTAT-TT
1 TTTTTCTTTT-TCTT
24202849 CTTTTTCTTTTTCTT
1 -TTTTTCTTTTTCTT
24202864 TTATTTCTTTTTCTT
1 TT-TTTCTTTTTCTT
24202879 TTTTTCTT
1 TTTTTCTT
24202887 CTCTCAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.26
15 26 0.74
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTTCTT
Found at i:24203850 original size:27 final size:28
Alignment explanation
Indices: 24203810--24203878 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
24203800 TCAATCACTC
*
24203810 TTTTTTTTTCAATTTCG-ATTTTTTTCT
1 TTTTTTTTTCAATTCCGAATTTTTTTCT
*
24203837 TTTTTTTTTTAATTCCGAATTTTTTTCT
1 TTTTTTTTTCAATTCCGAATTTTTTTCT
24203865 TTTTTTTCTTCAAT
1 TTTTTTT-TTCAAT
24203879 ACTAAATACA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 15 0.41
28 17 0.46
29 5 0.14
ACGTcount: A:0.13, C:0.12, G:0.03, T:0.72
Consensus pattern (28 bp):
TTTTTTTTTCAATTCCGAATTTTTTTCT
Found at i:24203933 original size:12 final size:12
Alignment explanation
Indices: 24203911--24203960 Score: 73
Period size: 12 Copynumber: 4.0 Consensus size: 12
24203901 AAATTGAATA
24203911 CAAACTTTTTTTT
1 CAAA-TTTTTTTT
*
24203924 CGAATTTTTTTT
1 CAAATTTTTTTT
24203936 CAAATTTTTTTTT
1 CAAA-TTTTTTTT
24203949 CAAATTTTTTTT
1 CAAATTTTTTTT
24203961 ACAACTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
12 19 0.56
13 15 0.44
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (12 bp):
CAAATTTTTTTT
Found at i:24203934 original size:13 final size:13
Alignment explanation
Indices: 24203911--24203960 Score: 75
Period size: 13 Copynumber: 3.9 Consensus size: 13
24203901 AAATTGAATA
*
24203911 CAAACTTTTTTTT
1 CAAATTTTTTTTT
*
24203924 CGAA-TTTTTTTT
1 CAAATTTTTTTTT
24203936 CAAATTTTTTTTT
1 CAAATTTTTTTTT
24203949 CAAATTTTTTTT
1 CAAATTTTTTTT
24203961 ACAACTCGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
12 11 0.32
13 23 0.68
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (13 bp):
CAAATTTTTTTTT
Found at i:24203939 original size:25 final size:25
Alignment explanation
Indices: 24203911--24203960 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
24203901 AAATTGAATA
*
24203911 CAAACTTTTTTTTCGAATTTTTTTT
1 CAAACTTTTTTTTCAAATTTTTTTT
*
24203936 CAAATTTTTTTTTCAAATTTTTTTT
1 CAAACTTTTTTTTCAAATTTTTTTT
24203961 ACAACTCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (25 bp):
CAAACTTTTTTTTCAAATTTTTTTT
Found at i:24205527 original size:10 final size:10
Alignment explanation
Indices: 24205512--24205553 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
24205502 TTTGCAAGTT
24205512 TTGAGCTAAA
1 TTGAGCTAAA
* *
24205522 TTGAGCTGAT
1 TTGAGCTAAA
*
24205532 TTGAGCT-CA
1 TTGAGCTAAA
24205541 TTGAGCTAAA
1 TTGAGCTAAA
24205551 TTG
1 TTG
24205554 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:24209307 original size:23 final size:23
Alignment explanation
Indices: 24209282--24209393 Score: 93
Period size: 23 Copynumber: 4.9 Consensus size: 23
24209272 TGGTTTTGGG
* *
24209282 TTTGTTACGAAATGGTAATGTGG
1 TTTGTTACGAAATGGTAATGCGA
* *
24209305 TTTGGTT-CAAAATGGTAATACGA
1 TTT-GTTACGAAATGGTAATGCGA
* * * *
24209328 TTTGGTACGAATTGGTAAGGTGA
1 TTTGTTACGAAATGGTAATGCGA
*
24209351 TTTGGTT-CGAAATGGTAATACGA
1 TTT-GTTACGAAATGGTAATGCGA
* *
24209374 TTTGGTACGAAATGTTAATG
1 TTTGTTACGAAATGGTAATG
24209394 GTTCAAAAAG
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
22 4 0.06
23 58 0.87
24 5 0.07
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.37
Consensus pattern (23 bp):
TTTGTTACGAAATGGTAATGCGA
Found at i:24209344 original size:46 final size:46
Alignment explanation
Indices: 24209282--24209393 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
24209272 TGGTTTTGGG
* *
24209282 TTTGTTACGAAATGGTAATGTGGTTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
24209328 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
24209374 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
24209394 GTTCAAAAAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.29, C:0.06, G:0.28, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:24215677 original size:14 final size:15
Alignment explanation
Indices: 24215646--24215679 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
24215636 TTTGCGAGAG
24215646 ATTGGTGAGGATTTCA
1 ATTGGTGAGGA-TTCA
24215662 ATTGGTGAGG-TTCA
1 ATTGGTGAGGATTCA
24215676 ATTG
1 ATTG
24215680 CTGTTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.44
16 10 0.56
ACGTcount: A:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (15 bp):
ATTGGTGAGGATTCA
Found at i:24218575 original size:20 final size:19
Alignment explanation
Indices: 24218539--24218599 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
24218529 TATAAACGCA
*
24218539 ATTGAGCTTAAAATGAGCTG
1 ATTGAGC-TAAAGTGAGCTG
24218559 ATTGAGCTAAGAGTGAGCTCG
1 ATTGAGCTAA-AGTGAGCT-G
24218580 A-TGAGCTAAAGTTGAGCTG
1 ATTGAGCTAAAG-TGAGCTG
24218599 A
1 A
24218600 ATGAACTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 7 0.19
20 28 0.76
21 2 0.05
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (19 bp):
ATTGAGCTAAAGTGAGCTG
Found at i:24220889 original size:17 final size:17
Alignment explanation
Indices: 24220856--24220889 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
24220846 AGACCGTATG
**
24220856 CAATTTTTTTTTCTTTT
1 CAATTTTTTTTGATTTT
24220873 CAATTTTTTTTGATTTT
1 CAATTTTTTTTGATTTT
24220890 TTTTTCGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.09, G:0.03, T:0.74
Consensus pattern (17 bp):
CAATTTTTTTTGATTTT
Found at i:24220901 original size:19 final size:19
Alignment explanation
Indices: 24220880--24220916 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24220870 TTTCAATTTT
24220880 TTTTG-ATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
24220898 TTTTGAATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
24220917 ACTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.14, C:0.05, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTTGAATTTTTTTTTCGA
Found at i:24233021 original size:21 final size:21
Alignment explanation
Indices: 24232995--24233057 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24232985 TTGGTATTTG
24232995 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24233016 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24233037 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
24233058 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24238745 original size:20 final size:20
Alignment explanation
Indices: 24238695--24238749 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
24238685 TTTCTCATTT
* *
24238695 TTTTTCATTCTCTTTTTTTGA
1 TTTTTC-TTTTCTTTTTTTCA
*
24238716 ATTTTC-TTTCTTTTTTTCA
1 TTTTTCTTTTCTTTTTTTCA
24238735 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
24238750 GTATTTTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.55
20 8 0.28
21 5 0.17
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTTTTCA
Found at i:24240919 original size:21 final size:21
Alignment explanation
Indices: 24240893--24240955 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24240883 TTGGTATTTG
24240893 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24240914 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24240935 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
24240956 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24242146 original size:30 final size:30
Alignment explanation
Indices: 24242088--24242146 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
24242078 TTGAAAAGGT
* *
24242088 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
24242118 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
24242147 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:24243710 original size:17 final size:16
Alignment explanation
Indices: 24243688--24243721 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
24243678 AATTAAACTA
24243688 TAACTTAACTAATTAAC
1 TAACTTAACTAA-TAAC
*
24243705 TAACTTAATTAATAAC
1 TAACTTAACTAATAAC
24243721 T
1 T
24243722 TTATTCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (16 bp):
TAACTTAACTAATAAC
Found at i:24249147 original size:17 final size:18
Alignment explanation
Indices: 24249115--24249151 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
24249105 TTTTGAGCTG
24249115 AACTTAATTAAATTAACT
1 AACTTAATTAAATTAACT
*
24249133 AACTT-ATTTAATTAACT
1 AACTTAATTAAATTAACT
24249150 AA
1 AA
24249152 GTTTATTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AACTTAATTAAATTAACT
Found at i:24250068 original size:19 final size:19
Alignment explanation
Indices: 24250046--24250084 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
24250036 ATATTAACTT
24250046 AGCCTATCTTTTGAACCCA
1 AGCCTATCTTTTGAACCCA
24250065 AGCCTATCTTTTGAACCCA
1 AGCCTATCTTTTGAACCCA
24250084 A
1 A
24250085 ATTACCGGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (19 bp):
AGCCTATCTTTTGAACCCA
Found at i:24253060 original size:18 final size:18
Alignment explanation
Indices: 24253039--24253082 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
24253029 AAAGGAAGAC
24253039 AGAAAAAGA-AATCGAAAA
1 AGAAAAAGAGAAT-GAAAA
24253057 AGAAAAAGAGAATGAAAA
1 AGAAAAAGAGAATGAAAA
24253075 AGAGAAAA
1 AGA-AAAA
24253083 AAGAGATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.05
Consensus pattern (18 bp):
AGAAAAAGAGAATGAAAA
Found at i:24253095 original size:19 final size:19
Alignment explanation
Indices: 24253041--24253101 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 19
24253031 AGGAAGACAG
* * *
24253041 AAAAAGAAATCGAAAAAG-
1 AAAAAGAGATTGAAAGAGA
*
24253059 AAAAAGAGAATGAAAAAGAGA
1 AAAAAGAGATTG--AAAGAGA
*
24253080 AAAAAGAGATTGAAAGTGA
1 AAAAAGAGATTGAAAGAGA
24253099 AAA
1 AAA
24253102 GGAATGTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 9 0.26
19 9 0.26
20 5 0.15
21 11 0.32
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.08
Consensus pattern (19 bp):
AAAAAGAGATTGAAAGAGA
Found at i:24255356 original size:29 final size:29
Alignment explanation
Indices: 24255319--24255391 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
24255309 TTAGATATTA
* *
24255319 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
24255348 TTAATTATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
*
24255377 CTAAATATGTCCTAA
1 TTAAATATGTCCTAA
24255392 ACTAATACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:24256001 original size:21 final size:21
Alignment explanation
Indices: 24255975--24256037 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
24255965 TTGGTATTTG
24255975 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
24255996 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
24256017 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
24256038 ATGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:24257243 original size:30 final size:30
Alignment explanation
Indices: 24257185--24257243 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
24257175 TTGAAAAGGT
* *
24257185 TTGAGCTAAAGTTGAGCTAATTCAAGCTCA
1 TTGAGCTAAAATGGAGCTAATTCAAGCTCA
*
24257215 TTGAGCTAAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTAAAATGG-AGCTAATTCAAGCTC
24257244 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (30 bp):
TTGAGCTAAAATGGAGCTAATTCAAGCTCA
Found at i:24260174 original size:39 final size:39
Alignment explanation
Indices: 24260120--24260299 Score: 218
Period size: 39 Copynumber: 4.6 Consensus size: 39
24260110 AACATGTTTT
* * *
24260120 TGAGTATTGTGATATATGTTTGAATGGTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * **
24260159 TGAGTAATGTGATATATGCTTGAACATTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
* * *
24260198 TCAGTATTGTGATATGTGCTTAAATGTTATGCGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
*
24260237 TGAGTATTGTGATATATGCTAAAAT-TATATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGT-TATGTGATTATA
* * *
24260276 TGTGTAATGTGATATGTGCTTAAA
1 TGAGTATTGTGATATATGCTTAAA
24260300 AGTGAATATG
Statistics
Matches: 120, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
38 1 0.01
39 119 0.99
ACGTcount: A:0.31, C:0.04, G:0.22, T:0.43
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
Found at i:24261322 original size:21 final size:22
Alignment explanation
Indices: 24261296--24261359 Score: 85
Period size: 21 Copynumber: 2.9 Consensus size: 22
24261286 TATTTGGGAA
24261296 TTGGTACGAAATGGTATGG-AG
1 TTGGTACGAAATGGTATGGTAG
* *
24261317 TTGGTATGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATGGTAG
*
24261339 TTGGTACGAATTGGTAATGGT
1 TTGGTACGAAATGGT-ATGGT
24261360 TCAAAGAGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 18 0.49
22 14 0.38
23 5 0.14
ACGTcount: A:0.27, C:0.03, G:0.34, T:0.36
Consensus pattern (22 bp):
TTGGTACGAAATGGTATGGTAG
Found at i:24263228 original size:62 final size:62
Alignment explanation
Indices: 24263162--24263329 Score: 237
Period size: 62 Copynumber: 2.7 Consensus size: 62
24263152 TGTGTCTCAG
* * * *
24263162 ATTCGAAGTCAATGAGTCACATGGCCTGGACACACGCCCGTGTGTCAGCATGTATGATTCAA
1 ATTCGAAGTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCAGCATGTATGATCCAA
* * * * * *
24263224 ATTCGAAGTCAGTGAGTTACACGACCTGGACACATGCCTGTGTGTTAGCCTGTGTGATCCAA
1 ATTCGAAGTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCAGCATGTATGATCCAA
*
24263286 ATTTGAAGTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTG
1 ATTCGAAGTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTG
24263330 ACCCAAATTC
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 92 1.00
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (62 bp):
ATTCGAAGTCAGTGAGTTACACGGCCTGGACACACGCCCGTGTGTCAGCATGTATGATCCAA
Found at i:24266774 original size:13 final size:13
Alignment explanation
Indices: 24266756--24266787 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
24266746 TAAAAAAAAT
24266756 AAAAAAATTCAAA
1 AAAAAAATTCAAA
24266769 AAAAAAATTCAAA
1 AAAAAAATTCAAA
24266782 AAAAAA
1 AAAAAA
24266788 GTTTGTATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAATTCAAA
Found at i:24266775 original size:14 final size:14
Alignment explanation
Indices: 24266751--24266787 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
24266741 GATTGTAAAA
24266751 AAAATAAAAAAATTC
1 AAAA-AAAAAAATTC
24266766 -AAAAAAAAAATTC
1 AAAAAAAAAAATTC
24266779 AAAAAAAAA
1 AAAAAAAAA
24266788 GTTTGTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAAATTC
Found at i:24270373 original size:14 final size:14
Alignment explanation
Indices: 24270354--24270408 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 14
24270344 TCTATTGAGC
24270354 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
24270368 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
* *
24270382 GAGTGAAAATAAAAA
1 GAG-AAAAAGAAAAA
*
24270397 GAAAGAAAAGAA
1 GAGA-AAAAGAA
24270409 TGATGAGAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 16 0.48
15 17 0.52
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:24270404 original size:15 final size:15
Alignment explanation
Indices: 24270354--24270405 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 15
24270344 TCTATTGAGC
*
24270354 GAGA-AAAAGAAAAA
1 GAGAGAAAACAAAAA
24270368 GAGA-AAAACAAAAA
1 GAGAGAAAACAAAAA
* *
24270382 GAGTGAAAATAAAAA
1 GAGAGAAAACAAAAA
*
24270397 GAAAGAAAA
1 GAGAGAAAA
24270406 GAATGATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (15 bp):
GAGAGAAAACAAAAA
Found at i:24271404 original size:22 final size:22
Alignment explanation
Indices: 24271352--24271416 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
24271342 TATTTGGGAA
* * *
24271352 TTGGTATGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
24271374 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
24271396 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
24271417 TTCAAAAAGG
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
22 23 0.68
23 11 0.32
ACGTcount: A:0.37, C:0.05, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:24283476 original size:20 final size:19
Alignment explanation
Indices: 24283447--24283484 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
24283437 AGCTAATAAC
24283447 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
24283466 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAGCTGAAT
24283485 CAAAAATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:24285528 original size:23 final size:22
Alignment explanation
Indices: 24285491--24285556 Score: 87
Period size: 23 Copynumber: 2.9 Consensus size: 22
24285481 ACCTTTTTGA
*
24285491 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
24285514 ACCATACCATTTTCGTACCAACT
1 ACCATACCA-TTTCGTACCAAAT
*
24285537 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
24285557 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
22 16 0.41
23 23 0.59
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.29
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:24290967 original size:19 final size:19
Alignment explanation
Indices: 24290946--24290982 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24290936 TTTAATTTTT
24290946 TTTTG-ATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
24290964 TTTTGAATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
24290983 ACTCTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.14, C:0.05, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTTGAATTTTTTTTTCGA
Found at i:24290979 original size:12 final size:11
Alignment explanation
Indices: 24290929--24290967 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
24290919 TATGCAATTT
*
24290929 TTTTTCTTTTAA
1 TTTTT-TTTTGA
24290941 TTTTTTTTTGA
1 TTTTTTTTTGA
24290952 TTTTTTTTTCGA
1 TTTTTTTTT-GA
24290964 TTTT
1 TTTT
24290968 GAATTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:24291295 original size:23 final size:23
Alignment explanation
Indices: 24291268--24291371 Score: 118
Period size: 23 Copynumber: 4.5 Consensus size: 23
24291258 GGTTTGTTAT
* *
24291268 GAAATGGTAATGTGATTTGGTTC
1 GAAATGGTAATGCGATTTGGTAC
* *
24291291 AAAATGGTAATACGATTTGGTAC
1 GAAATGGTAATGCGATTTGGTAC
* * * *
24291314 GAATTGGTAAGGTGATTTGGTTC
1 GAAATGGTAATGCGATTTGGTAC
*
24291337 GAAATGGTAATACGATTTGGTAC
1 GAAATGGTAATGCGATTTGGTAC
*
24291360 GAAATGTTAATG
1 GAAATGGTAATG
24291372 GTTCAAAAAG
Statistics
Matches: 64, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 64 1.00
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.35
Consensus pattern (23 bp):
GAAATGGTAATGCGATTTGGTAC
Found at i:24291329 original size:46 final size:46
Alignment explanation
Indices: 24291272--24291362 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
24291262 TGTTATGAAA
*
24291272 TGGTAATGTGATTTGGTTCAAAATGGTAATACGATTTGGTACGAAT
1 TGGTAAGGTGATTTGGTTCAAAATGGTAATACGATTTGGTACGAAT
*
24291318 TGGTAAGGTGATTTGGTTCGAAATGGTAATACGATTTGGTACGAA
1 TGGTAAGGTGATTTGGTTCAAAATGGTAATACGATTTGGTACGAA
24291363 ATGTTAATGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.30, C:0.07, G:0.29, T:0.35
Consensus pattern (46 bp):
TGGTAAGGTGATTTGGTTCAAAATGGTAATACGATTTGGTACGAAT
Found at i:24302877 original size:13 final size:13
Alignment explanation
Indices: 24302859--24302883 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24302849 GAATTCGAAA
24302859 TCAGCTAGCTAAC
1 TCAGCTAGCTAAC
24302872 TCAGCTAGCTAA
1 TCAGCTAGCTAA
24302884 ACTTAGACAT
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
TCAGCTAGCTAAC
Found at i:24309436 original size:20 final size:20
Alignment explanation
Indices: 24309413--24309459 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
24309403 GGGTTGAGGT
24309413 TGAGCTGAATTCAACTCGAA
1 TGAGCTGAATTCAACTCGAA
* * * *
24309433 TGAGCTGACTTGAGCTCGAG
1 TGAGCTGAATTCAACTCGAA
24309453 TGAGCTG
1 TGAGCTG
24309460 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (20 bp):
TGAGCTGAATTCAACTCGAA
Found at i:24324546 original size:20 final size:20
Alignment explanation
Indices: 24324518--24324576 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
24324508 GAGAAAAACG
* *
24324518 AAGACGAGCTGAATGAGCTA
1 AAGATGAGCTGAATGAACTA
*
24324538 AAGATGAGCTCAATGAACTA
1 AAGATGAGCTGAATGAACTA
** *
24324558 TGGTTGAGCTGAATGAACT
1 AAGATGAGCTGAATGAACT
24324577 TGAAGTAGGA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.22
Consensus pattern (20 bp):
AAGATGAGCTGAATGAACTA
Found at i:24330620 original size:16 final size:17
Alignment explanation
Indices: 24330599--24330632 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
24330589 CGAGACATAG
24330599 CCAACAT-TGTGGAACT
1 CCAACATATGTGGAACT
24330615 CCAACATCATGTGGAACT
1 CCAACAT-ATGTGGAACT
24330633 TGTTGACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
18 9 0.56
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (17 bp):
CCAACATATGTGGAACT
Found at i:24342638 original size:15 final size:15
Alignment explanation
Indices: 24342618--24342672 Score: 60
Period size: 15 Copynumber: 3.8 Consensus size: 15
24342608 GCTCTCATCA
*
24342618 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
24342633 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
24342648 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
*
24342662 TTATTTT-TCTC
1 TTCTTTTCTCTC
24342673 GCTCAATAGA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
14 16 0.46
15 19 0.54
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.75
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:24342659 original size:14 final size:14
Alignment explanation
Indices: 24342628--24342672 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
24342618 TTCTTTTCTT
* *
24342628 TCTTTTTCTTTTCAC
1 TCTTTTTATTTT-TC
*
24342643 TCTTTTTGTTTTTC
1 TCTTTTTATTTTTC
24342657 TCTTTTTATTTTTC
1 TCTTTTTATTTTTC
24342671 TC
1 TC
24342673 GCTCAATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.73
Consensus pattern (14 bp):
TCTTTTTATTTTTC
Found at i:24344238 original size:32 final size:32
Alignment explanation
Indices: 24344197--24344260 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
24344187 GCTTGCGATC
24344197 AAACAATCGCTCCATTTCTCGCATAATGGCTT
1 AAACAATCGCTCCATTTCTCGCATAATGGCTT
24344229 AAACAATCGCTCCATTTCTCGCATAATGGCTT
1 AAACAATCGCTCCATTTCTCGCATAATGGCTT
24344261 GCAAAGTGAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.31
Consensus pattern (32 bp):
AAACAATCGCTCCATTTCTCGCATAATGGCTT
Found at i:24344710 original size:19 final size:19
Alignment explanation
Indices: 24344686--24344723 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
24344676 TTTCAATCAC
*
24344686 TTTTTTTTT-AATTCTGAA
1 TTTTTTTTTCAATACTGAA
24344704 TTTTTTTTTCAATACTGAA
1 TTTTTTTTTCAATACTGAA
24344723 T
1 T
24344724 ACACAAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTTTTTTCAATACTGAA
Found at i:24344771 original size:11 final size:11
Alignment explanation
Indices: 24344755--24344794 Score: 57
Period size: 12 Copynumber: 3.7 Consensus size: 11
24344745 AATACAAACT
24344755 TTTTTTTTGAA
1 TTTTTTTTGAA
24344766 TTTTTTTTCGAA
1 TTTTTTTT-GAA
24344778 TTTTTTTT--A
1 TTTTTTTTGAA
24344787 TTTTTTTT
1 TTTTTTTT
24344795 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
11 8 0.29
12 11 0.39
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:24349259 original size:18 final size:19
Alignment explanation
Indices: 24349214--24349262 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
24349204 GAATATTTAC
*
24349214 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
24349234 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
24349252 ATAAAAATAAA
1 ATAAAAATAAA
24349263 AATAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:24360935 original size:13 final size:13
Alignment explanation
Indices: 24360917--24360941 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24360907 GAATTCGAAA
24360917 TCAGCTAGCTAAC
1 TCAGCTAGCTAAC
24360930 TCAGCTAGCTAA
1 TCAGCTAGCTAA
24360942 ACTTAGACAT
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
TCAGCTAGCTAAC
Found at i:24373305 original size:18 final size:17
Alignment explanation
Indices: 24373284--24373328 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
24373274 GAGTGACGAG
24373284 AGAAAAAGAAACTGAAAA
1 AGAAAAA-AAACTGAAAA
*
24373302 AGAAACAAAAATTGAAAA
1 AGAAA-AAAAACTGAAAA
24373320 AGAGAAAAA
1 AGA-AAAAA
24373329 GATTGGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.73, C:0.04, G:0.16, T:0.07
Consensus pattern (17 bp):
AGAAAAAAAACTGAAAA
Found at i:24373333 original size:18 final size:18
Alignment explanation
Indices: 24373282--24373333 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
24373272 AAGAGTGACG
*
24373282 AGAGAAAAAGAAACTGAAAA
1 AGAGAAAAAG--ATTGAAAA
*
24373302 AGA-AACAAAAATTGAAAA
1 AGAGAA-AAAGATTGAAAA
24373320 AGAGAAAAAGATTG
1 AGAGAAAAAGATTG
24373334 GAGAAAGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 17 0.63
19 4 0.15
20 6 0.22
ACGTcount: A:0.67, C:0.04, G:0.19, T:0.10
Consensus pattern (18 bp):
AGAGAAAAAGATTGAAAA
Found at i:24377877 original size:19 final size:20
Alignment explanation
Indices: 24377853--24377890 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
24377843 TGAGCTGATT
24377853 GGAGCTGAAA-TGAGCTAAG
1 GGAGCTGAAATTGAGCTAAG
24377872 GGAGCTGAAATTGAGCTAA
1 GGAGCTGAAATTGAGCTAA
24377891 AGTCAGCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.37, C:0.11, G:0.34, T:0.18
Consensus pattern (20 bp):
GGAGCTGAAATTGAGCTAAG
Found at i:24380781 original size:18 final size:18
Alignment explanation
Indices: 24380760--24380802 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
24380750 AAGAGACGAG
24380760 AGAAAAAGAAATTGAAAA
1 AGAAAAAGAAATTGAAAA
*
24380778 AGAAAAAGACATTGAAAA
1 AGAAAAAGAAATTGAAAA
24380796 AGAAAAA
1 AGAAAAA
24380803 AAGAGTGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.02, G:0.16, T:0.09
Consensus pattern (18 bp):
AGAAAAAGAAATTGAAAA
Found at i:24383619 original size:20 final size:21
Alignment explanation
Indices: 24383574--24383620 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
24383564 TTTAAATCTT
*
24383574 AATGTTTCTTGATGAATAAAG
1 AATGTTTCTTGATGAACAAAG
* *
24383595 GATGTTTCTTGATG-CCAAAG
1 AATGTTTCTTGATGAACAAAG
24383615 AATGTT
1 AATGTT
24383621 GAAAAATAGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (21 bp):
AATGTTTCTTGATGAACAAAG
Found at i:24427757 original size:12 final size:12
Alignment explanation
Indices: 24427740--24427770 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
24427730 CCACCCTTAA
24427740 ACACATTGAATT
1 ACACATTGAATT
24427752 ACACATTGAATT
1 ACACATTGAATT
24427764 ACACATT
1 ACACATT
24427771 AAATCAGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.42, C:0.19, G:0.06, T:0.32
Consensus pattern (12 bp):
ACACATTGAATT
Found at i:24443349 original size:13 final size:13
Alignment explanation
Indices: 24443331--24443355 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24443321 GAATTCGAAA
24443331 TCAGCTAGCTAAC
1 TCAGCTAGCTAAC
24443344 TCAGCTAGCTAA
1 TCAGCTAGCTAA
24443356 ACTTAGACAT
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:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (13 bp):
TCAGCTAGCTAAC
Found at i:24452620 original size:798 final size:776
Alignment explanation
Indices: 24451101--24452679 Score: 1997
Period size: 798 Copynumber: 2.0 Consensus size: 776
24451091 TAAAGTCCTA
* * *
24451101 AGAAGCCTTGAAATCGAGAAAGATTTCACAACTCCCTTCAAACGGCTCTAATCTCCCCTCCAATG
1 AGAAGCCTTGAAATCAAAAAAGATTTCACAACTCCCTTCAAACGGCTCTAATCTCACCTCCAATG
24451166 AAGAACAATGGCAAGAAGAAGGCTGAAGATGGCTCACACAATCAAAAAGATTGTTAAAACTACTT
66 AAGAACAATGGCAAGAAGAAGGCTGAAGATGGCTCACACAATCAAAAAGATTGTTAAAACTACTT
* *
24451231 CTAAAGAAAACTCAAGAGAAAATTCTTGAAGAACTGAAAGAGAATTTTCACTCAAAGCAAATCTG
131 CTAAAGAAAACTCAAGAGAAAATTCTTGAAAAACTCAAAGAGAATTTTCACTCAAA-CAAATCTG
* * * *
24451296 AAATTTTTAATGTAATTGTAATGTGTGTAACAAGGGTGGCCGGCTATGCCTATAAATAGGCCTTA
195 -AATTTTCAATGTAATTGTAATGTGTCT-A-AAGGGTGGCCGGCCAAGCCTATAAATAGGCCTTA
* *
24451361 TAACTATTTCCTAATCTCATTAGGAAAACATAAAAAAAACCTAATTAACATATTGAAGAGGGAAA
257 TAACTATTTCCTAATCTCAATAGGAAAACATAAAAAAAACCTAATTAACATATTAAAGAGGGAAA
* ** * * *
24451426 TTCGGGGAAGGCATTCTAATGGGCTACTTGGGCCGAATTTTTACATATAATACTCCTAAAGTCTA
322 TTCAGCCAAGGCATTCTAATGGGCTACTTGGACCGAATTTTTACATAAAATACTCATAAAGTCTA
*** *
24451491 AAAATTAAATTAAACAATTAAATTTTTTACAAATTAGGCCACTTTAACAATTTGGCCTGATTTTC
387 AAAATTAAATTAAACAATTAAATACATAACAAATTAGGCCACTTTAACAATTTGGCCTGATTTTC
* * * *
24451556 AACTAAGTATGGTTTGACTTCTTGGTTGGGCTTGGAATCCTATTATTGGGCCTTGCCTTCAAGAA
452 AACTAAGTATGATTTAACTTCTTGATTGGGCTTGGAATCATATTATTGGGCCTTGCCTTCAAGAA
* * * * *
24451621 CTTGGGCTTGTAGTCCATCTCCTATCGAAATTGGCTCGTTGATGCTCGTAACGGAGATCCAATGC
517 CTTGGGCTTGTAATCAATCTCCTACCGAAATTAGCTCGTTAATGCTCGTAACGGAGATCCAATGC
* * * * * *
24451686 GCTTTGGCTGTAAGATTCGGTTTCTTGGACCAATATTTCCAAGATTTGAAATCTTGATTTTATTG
582 GCCTTAGCTGCAAGATTCGGTTTCTTGGACCAAGAGTTCCAAGATTTGAAATCTTGATTTGATTG
* * *
24451751 ACTCTTGAAATCGCTCCAAACAGCAAAATTAGGCCGAGATTCGGTTTCTTGATTTTCTTGAAAAT
647 ACTCTTGAAATCGCTCAAAACAGCAAAATTAGGCCAAGATTCGGTTTCTTGATTTTCTTGAAAAC
* *
24451816 AAGAAAGTGAATCTTGATTTTCTCTTTCTTTCGTGTACGCATCTAAGGCCTTTGTGACTCGTATC
712 AAGAAAGTGAATCTTGATTTTCTCTTTCCTTCGTATACGCATCTAAGGCCTTTGTGACTCGTATC
24451881 AGAAGCCTTGAAATCAAAAAAGATTTCACAACTCCCTTCAAACGGCTCTAATCTCACCTCCAATG
1 AGAAGCCTTGAAATCAAAAAAGATTTCACAACTCCCTTCAAACGGCTCTAATCTCACCTCCAATG
*
24451946 TAAG-ACAATGGCAAGAAGAAGGCTGAAGATGGCTCCCACAATCAAAAAGATTGTTAAAACTACT
66 -AAGAACAATGGCAAGAAGAAGGCTGAAGATGGCTCACACAATCAAAAAGATTGTTAAAACTACT
* *
24452010 TCTAAAGAAAATTCAAGAGAGAATTCTTGGAGAAAACTCAAAGAGAATTTTTCACTCAATA-AAA
130 TCTAAAGAAAACTCAAGAGAAAATTCTT-GA-AAAACTCAAAGAGAA-TTTTCACTCAA-ACAAA
*
24452074 TCTG-A-TTTCAATGTATTATTCAAGTATAATGTGTCT-AAGGGTGGCTGGCCAAGCC-ATACAT
191 TCTGAATTTTCAATGTA--ATT---G--TAATGTGTCTAAAGGGTGGCCGGCCAAGCCTATA-A-
* * ****
24452135 ATAGGCCTTCTAACTATTTTCCTAGTC-CTAATAGGAAAAC-TAAAAAAAAACCTAATACTTTTT
247 ATAGGCCTTATAACTA-TTTCCTAATCTC-AATAGGAAAACAT-AAAAAAAACCTAAT--TAACA
*
24452198 TACTTTAAAG-GGGAAATTCAGCCAAGG-ACTT-TAAATGGGCGT-CTTGGACTGAATTTTTACA
307 TA--TTAAAGAGGGAAATTCAGCCAAGGCA-TTCT-AATGGGC-TACTTGGACCGAATTTTTACA
* * * *
24452259 TAGAAATTTATTCATAAATTCTAAAAATGAAAAGTAAGTATTTAAAGACTTAAA-ACATAACAAA
367 TA-AAA--TACTCATAAAGTCTAAAAAT------TAA--A-TTAAACAATTAAATACATAACAAA
* * * *
24452323 TTGGGCCACTTTGACAATTTGGCCTGATTTTCAACTAAGT-TTATTTAAATTTCTTGATTGGGCT
420 TTAGGCCACTTTAACAATTTGGCCTGATTTTCAACTAAGTATGATTT-AACTTCTTGATTGGGCT
* * *
24452387 TGGAA-CATCTTATTGGGCCTTGTCTTCAAGAACTTGGGCTTGTAAT-AAGT-TCTCTCCCGAAA
484 TGGAATCATATTATTGGGCCTTGCCTTCAAGAACTTGGGCTTGTAATCAA-TCTC-CTACCGAAA
* * * * *
24452449 TTAGCTTGTTAATGCTCGTAACTGAGATCCAATGCGCCTTAGTTGCAAGATTTGTTTTCTTGGAC
547 TTAGCTCGTTAATGCTCGTAACGGAGATCCAATGCGCCTTAGCTGCAAGATTCGGTTTCTTGGAC
* *
24452514 CAAGAGTTCCAAGATTTGAAATCTTGATTTGCTTGATTCTTGAAATCGCTCAAAACAGCAAAATT
612 CAAGAGTTCCAAGATTTGAAATCTTGATTTGATTGACTCTTGAAATCGCTCAAAACAGCAAAATT
*
24452579 -GGACCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCTTTTTCC
677 AGG-CCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATTTTCTCTTTCC
24452643 TTCGTATACGCATCTAAGGCCTTTGTGACTCGTATC
741 TTCGTATACGCATCTAAGGCCTTTGTGACTCGTATC
24452679 A
1 A
24452680 TTCCCCCCCT
Statistics
Matches: 688, Mismatches: 71, Indels: 62
0.84 0.09 0.08
Matches are distributed among these distances:
779 9 0.01
780 148 0.22
781 8 0.01
782 23 0.03
783 28 0.04
784 19 0.03
785 33 0.05
786 9 0.01
787 5 0.01
788 42 0.06
789 8 0.01
791 17 0.02
797 8 0.01
798 256 0.37
799 64 0.09
800 11 0.02
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (776 bp):
AGAAGCCTTGAAATCAAAAAAGATTTCACAACTCCCTTCAAACGGCTCTAATCTCACCTCCAATG
AAGAACAATGGCAAGAAGAAGGCTGAAGATGGCTCACACAATCAAAAAGATTGTTAAAACTACTT
CTAAAGAAAACTCAAGAGAAAATTCTTGAAAAACTCAAAGAGAATTTTCACTCAAACAAATCTGA
ATTTTCAATGTAATTGTAATGTGTCTAAAGGGTGGCCGGCCAAGCCTATAAATAGGCCTTATAAC
TATTTCCTAATCTCAATAGGAAAACATAAAAAAAACCTAATTAACATATTAAAGAGGGAAATTCA
GCCAAGGCATTCTAATGGGCTACTTGGACCGAATTTTTACATAAAATACTCATAAAGTCTAAAAA
TTAAATTAAACAATTAAATACATAACAAATTAGGCCACTTTAACAATTTGGCCTGATTTTCAACT
AAGTATGATTTAACTTCTTGATTGGGCTTGGAATCATATTATTGGGCCTTGCCTTCAAGAACTTG
GGCTTGTAATCAATCTCCTACCGAAATTAGCTCGTTAATGCTCGTAACGGAGATCCAATGCGCCT
TAGCTGCAAGATTCGGTTTCTTGGACCAAGAGTTCCAAGATTTGAAATCTTGATTTGATTGACTC
TTGAAATCGCTCAAAACAGCAAAATTAGGCCAAGATTCGGTTTCTTGATTTTCTTGAAAACAAGA
AAGTGAATCTTGATTTTCTCTTTCCTTCGTATACGCATCTAAGGCCTTTGTGACTCGTATC
Found at i:24457619 original size:20 final size:20
Alignment explanation
Indices: 24457591--24457666 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
24457581 GCTTATTTTG
*
24457591 TTAGTTCATTCGAGCTCAAA
1 TTAGCTCATTCGAGCTCAAA
*
24457611 TTAGCTCATTCGAGCTCAAG
1 TTAGCTCATTCGAGCTCAAA
*
24457631 TCAGCTCATTCGAGCTC-AA
1 TTAGCTCATTCGAGCTCAAA
*
24457650 TTCAACTCATT-GAGCTC
1 TT-AGCTCATTCGAGCTC
24457667 GTTATTAGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
19 8 0.16
20 41 0.84
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (20 bp):
TTAGCTCATTCGAGCTCAAA
Found at i:24457626 original size:10 final size:10
Alignment explanation
Indices: 24457596--24457666 Score: 53
Period size: 10 Copynumber: 7.2 Consensus size: 10
24457586 TTTTGTTAGT
24457596 TCATTCGAGC
1 TCATTCGAGC
24457606 TCAAATT--AGC
1 TC--ATTCGAGC
24457616 TCATTCGAGC
1 TCATTCGAGC
*
24457626 TCAAGTC-AGC
1 TC-ATTCGAGC
24457636 TCATTCGAGC
1 TCATTCGAGC
*
24457646 TCAATTC-AAC
1 TC-ATTCGAGC
24457656 TCATT-GAGC
1 TCATTCGAGC
24457665 TC
1 TC
24457667 GTTATTAGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 17
0.70 0.06 0.24
Matches are distributed among these distances:
8 3 0.06
9 10 0.20
10 26 0.53
11 7 0.14
12 3 0.06
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (10 bp):
TCATTCGAGC
Found at i:24457677 original size:40 final size:40
Alignment explanation
Indices: 24457590--24457666 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
24457580 AGCTTATTTT
* *
24457590 GTTAGTTCATTCGAGCTCAAATTAGCTCATTCGAGCTCAA
1 GTTAGCTCATTCGAGCTCAAATTAACTCATTCGAGCTCAA
*
24457630 GTCAGCTCATTCGAGCTC-AATTCAACTCATT-GAGCTC
1 GTTAGCTCATTCGAGCTCAAATT-AACTCATTCGAGCTC
24457667 GTTATTAGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 10 0.30
40 23 0.70
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (40 bp):
GTTAGCTCATTCGAGCTCAAATTAACTCATTCGAGCTCAA
Found at i:24460555 original size:27 final size:27
Alignment explanation
Indices: 24460522--24460580 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
24460512 AATTTTAATT
24460522 CTTTAAATACTTAGTTTCAATTTTAGA
1 CTTTAAATACTTAGTTTCAATTTTAGA
24460549 CTTTAAATACTTAGTTTCAATTTTAGA
1 CTTTAAATACTTAGTTTCAATTTTAGA
24460576 CTTTA
1 CTTTA
24460581 TAAATTAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.07, T:0.49
Consensus pattern (27 bp):
CTTTAAATACTTAGTTTCAATTTTAGA
Found at i:24463978 original size:20 final size:20
Alignment explanation
Indices: 24463953--24463997 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
24463943 GTCCAAACCG
24463953 AATTAATTAG-GTCTTAG-TTT
1 AATTAATT-GTGTCTT-GTTTT
24463973 AATTAATTGTGTCTTGTTTT
1 AATTAATTGTGTCTTGTTTT
24463993 AATTA
1 AATTA
24463998 TGTGAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.29, C:0.04, G:0.13, T:0.53
Consensus pattern (20 bp):
AATTAATTGTGTCTTGTTTT
Found at i:24465020 original size:24 final size:22
Alignment explanation
Indices: 24464992--24465039 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
24464982 TTAAAACTCC
24464992 TTCTAAAGAAAACTCAAGAGAGAA
1 TTCT-AAGAAAACTCAA-AGAGAA
* *
24465016 TTCTAGGAGAACTCAAAGAGAA
1 TTCTAAGAAAACTCAAAGAGAA
24465038 TT
1 TT
24465040 TCACTCAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 8 0.36
23 10 0.45
24 4 0.18
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (22 bp):
TTCTAAGAAAACTCAAAGAGAA
Found at i:24469693 original size:20 final size:19
Alignment explanation
Indices: 24469668--24469705 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
24469658 AACATTTTTG
24469668 ATTCAGCTCATTCGAGCTCA
1 ATTCAGCTCATT-GAGCTCA
24469688 ATTCAGCTCATTGAGCTC
1 ATTCAGCTCATTGAGCTC
24469706 GTTATTAGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTCAGCTCATTGAGCTCA
Found at i:24473113 original size:29 final size:29
Alignment explanation
Indices: 24473079--24473151 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
24473069 ATGTATTAGT
** *
24473079 TTAGGACATATTTAAAACATTTGAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
* *
24473108 TTAGGAAATAATTAAAACACCTAAACTAA
1 TTAGGACATATTTAAAACACCTAAACTAA
24473137 TTAGGACATATTTAA
1 TTAGGACATATTTAA
24473152 TAATATCTAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.48, C:0.11, G:0.10, T:0.32
Consensus pattern (29 bp):
TTAGGACATATTTAAAACACCTAAACTAA
Found at i:24477219 original size:19 final size:19
Alignment explanation
Indices: 24477192--24477304 Score: 108
Period size: 19 Copynumber: 6.1 Consensus size: 19
24477182 TGATTTAAGC
*
24477192 AACTAAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
24477211 AACTTAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
* * * * *
24477230 -A-GTAATTTATTCCAG--C
1 AACTTAATTAACT-AAGATG
*
24477246 AACTTATTTAACTAAGATG
1 AACTTAATTAACTAAGATG
24477265 CAACTTAATTAACTAAGATG
1 -AACTTAATTAACTAAGATG
*
24477285 AACTCAATTAACTAAGATG
1 AACTTAATTAACTAAGATG
24477304 A
1 A
24477305 GTAATTTATT
Statistics
Matches: 74, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
17 10 0.14
18 9 0.12
19 37 0.50
20 18 0.24
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.31
Consensus pattern (19 bp):
AACTTAATTAACTAAGATG
Found at i:24477269 original size:20 final size:20
Alignment explanation
Indices: 24477244--24477303 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
24477234 ATTTATTCCA
*
24477244 GCAACTTATTTAACTAAGAT
1 GCAACTTAATTAACTAAGAT
24477264 GCAACTTAATTAACTAAGAT
1 GCAACTTAATTAACTAAGAT
*
24477284 G-AACTCAATTAACTAAGAT
1 GCAACTTAATTAACTAAGAT
24477303 G
1 G
24477304 AGTAATTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
19 18 0.47
20 20 0.53
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
GCAACTTAATTAACTAAGAT
Found at i:24477602 original size:170 final size:170
Alignment explanation
Indices: 24477320--24477652 Score: 594
Period size: 170 Copynumber: 2.0 Consensus size: 170
24477310 TTATTCCAGT
*
24477320 AACTAAATACTTATTCCAACAAATTAAAAATGGGTTGAAGTTAAGCTAAATGAGCTTGGGTTGAA
1 AACTAAATACTTATTCCAACAAATTAAAAATGGGTTGAAATTAAGCTAAATGAGCTTGGGTTGAA
*
24477385 CTAGACGAGCTTGAAGAAGCTAGAATTGAGCTCATTGAGCTGAAATTAAGCTTCATTTTACACTT
66 CTAGACGAGCTTGAAGAAGCTAGAATTGAGCTCATTGAGATGAAATTAAGCTTCATTTTACACTT
*
24477450 GGGGCCCTCGAGCTTAGGCCAATTTTGAGGTCATTCCAAC
131 GGGGCCCTCAAGCTTAGGCCAATTTTGAGGTCATTCCAAC
* *
24477490 AACTAAATATTTATTCCAGCAAATTAAAAATGGGTTGAAATTAAGCTAAATGAGCTTGGGTTGAA
1 AACTAAATACTTATTCCAACAAATTAAAAATGGGTTGAAATTAAGCTAAATGAGCTTGGGTTGAA
* * *
24477555 CTAGACGAGCTTTAAGGAGCTAGAATTGAGCTCATTGAGATGAAATTAAGCTTCATTTTGCACTT
66 CTAGACGAGCTTGAAGAAGCTAGAATTGAGCTCATTGAGATGAAATTAAGCTTCATTTTACACTT
24477620 GGGGCCCTCAAGCTTAGGCCAATTTTGAGGTCA
131 GGGGCCCTCAAGCTTAGGCCAATTTTGAGGTCA
24477653 CCGAGTTGTA
Statistics
Matches: 155, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
170 155 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (170 bp):
AACTAAATACTTATTCCAACAAATTAAAAATGGGTTGAAATTAAGCTAAATGAGCTTGGGTTGAA
CTAGACGAGCTTGAAGAAGCTAGAATTGAGCTCATTGAGATGAAATTAAGCTTCATTTTACACTT
GGGGCCCTCAAGCTTAGGCCAATTTTGAGGTCATTCCAAC
Found at i:24481403 original size:10 final size:10
Alignment explanation
Indices: 24481380--24481428 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
24481370 CATCCTTTCA
*
24481380 AGCTCGATCT
1 AGCTCAATCT
*
24481390 AGCTCAATCG
1 AGCTCAATCT
*
24481400 AGCTCAATTT
1 AGCTCAATCT
24481410 AGCTCAATTCT
1 AGCTCAA-TCT
24481421 AGCTCAAT
1 AGCTCAAT
24481429 GATCTCGTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
10 24 0.73
11 9 0.27
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (10 bp):
AGCTCAATCT
Found at i:24485167 original size:19 final size:18
Alignment explanation
Indices: 24485131--24485170 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24485121 TTTCCATTCG
*
24485131 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
24485149 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
24485168 TTT
1 TTT
24485171 GTTTGTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:24490613 original size:17 final size:17
Alignment explanation
Indices: 24490589--24490621 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
24490579 GGTTTCATAT
24490589 TTTGCTTGGA-TTAGCA
1 TTTGCTTGGACTTAGCA
24490605 TTTGACTTGGACTTAGC
1 TTTG-CTTGGACTTAGC
24490622 TAAATCAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.18, C:0.15, G:0.24, T:0.42
Consensus pattern (17 bp):
TTTGCTTGGACTTAGCA
Found at i:24493587 original size:13 final size:13
Alignment explanation
Indices: 24493569--24493593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24493559 CCCTCTATCA
24493569 TTTGGTATCAAAT
1 TTTGGTATCAAAT
24493582 TTTGGTATCAAA
1 TTTGGTATCAAA
24493594 ATGCCACACA
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TTTGGTATCAAAT
Found at i:24495850 original size:19 final size:20
Alignment explanation
Indices: 24495818--24495855 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
24495808 CAAGCTGACT
24495818 TTAGCTCAATTTCAGCTCCC
1 TTAGCTCAATTTCAGCTCCC
24495838 TTAGCTC-ATTTCAGCTCC
1 TTAGCTCAATTTCAGCTCC
24495856 AATCAGCTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.18, C:0.34, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGCTCAATTTCAGCTCCC
Found at i:24495863 original size:20 final size:19
Alignment explanation
Indices: 24495820--24495865 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
24495810 AGCTGACTTT
* *
24495820 AGCTCAATTTCAGCTCCCTT
1 AGCTC-ATTTCAGCTCCATC
24495840 AGCTCATTTCAGCTCCAATC
1 AGCTCATTTCAGCTCC-ATC
24495860 AGCTCA
1 AGCTCA
24495866 CTTGAGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.24, C:0.35, G:0.11, T:0.30
Consensus pattern (19 bp):
AGCTCATTTCAGCTCCATC
Done.