Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008349.1 Hibiscus syriacus cultivar Beakdansim tig00111081_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 333942
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:186955 original size:20 final size:20
Alignment explanation
Indices: 186918--186956 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
186908 TTTCCATATG
**
186918 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
186938 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
186957 CAGTAATTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:186969 original size:29 final size:30
Alignment explanation
Indices: 186930--187002 Score: 130
Period size: 30 Copynumber: 2.5 Consensus size: 30
186920 TTCCAGAAAT
186930 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
*
186959 GTAATTTATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
186989 GTAATTCATTTTCC
1 GTAATTCATTTTCC
187003 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 15 0.37
30 26 0.63
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:186972 original size:15 final size:15
Alignment explanation
Indices: 186930--187002 Score: 94
Period size: 15 Copynumber: 4.9 Consensus size: 15
186920 TTCCAGAAAT
186930 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
186945 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
186959 GTAATTTATTTTCCA
1 GTAATTCATTTTCCA
**
186974 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
186989 GTAATTCATTTTCC
1 GTAATTCATTTTCC
187003 GAAAAATCAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
14 12 0.26
15 35 0.74
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:192406 original size:21 final size:21
Alignment explanation
Indices: 192362--192408 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
192352 TTGTATTAAA
*
192362 TTTTATTCACTTTTAATTCTT
1 TTTTATTCACTTTTAATTCAT
*
192383 TTTTATTGCACTTTT-ATTGAT
1 TTTTATT-CACTTTTAATTCAT
192404 TTTTA
1 TTTTA
192409 AAAAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.19, C:0.11, G:0.04, T:0.66
Consensus pattern (21 bp):
TTTTATTCACTTTTAATTCAT
Found at i:192406 original size:22 final size:21
Alignment explanation
Indices: 192362--192407 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
192352 TTGTATTAAA
*
192362 TTTTATTCACTTTTAATTCTT
1 TTTTATTCACTTTTAATTATT
192383 TTTTATTGCACTTTT-ATTGATT
1 TTTTATT-CACTTTTAATT-ATT
192405 TTT
1 TTT
192408 AAAAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTTATTCACTTTTAATTATT
Found at i:192586 original size:21 final size:20
Alignment explanation
Indices: 192562--192618 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
192552 AAAGTTTACG
192562 TTTTTATTGAATTTTATT-CA
1 TTTTTATTG-ATTTTATTGCA
* **
192582 CTTTTAATTCTTTTTTATTGCA
1 -TTTTTATT-GATTTTATTGCA
192604 TTTTTATTGATTTTA
1 TTTTTATTGATTTTA
192619 AAAAAATGAA
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
20 5 0.18
21 21 0.75
22 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTATTGATTTTATTGCA
Found at i:192737 original size:209 final size:211
Alignment explanation
Indices: 192350--192739 Score: 454
Period size: 209 Copynumber: 1.9 Consensus size: 211
192340 TTTATATTCT
192350 TTTTGTATTAAATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTTAAAAAAA
1 TTTTGTATTAAATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTTAAAAAAA
** * ** **** *
192415 ATGAATAATAATTCATTTGATCTATCAATTGTAATTAAAATTTTATTTTAATATTTTTATATTTT
66 ATGAATAATAATTCATTTGATCTATCAATTGTAATTAAAATTAAAATGCAATATAAAAATATATT
* * * * * * * ***
192480 TAAATAATTAATATTAAAAGTCAATAAGCATTATTAGCTGTTAAAAAATAATATCACAAAAAAAA
131 AAAAGAAATAAAATTAAAAG-CAAAAAGAATTATAAGCTCAAAAAAAATAATATCACAAAAAAAA
192545 AATCAATAAAGTTTACG
195 AATCAATAAAGTTTACG
* *
192562 TTTT-TATTGAATTTTATTCACTTTTAATTCTTTTTTATTGCATTTTTATTGA-TTTT-AAAAAA
1 TTTTGTATTAAATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTTAAAAAAA
192624 ATGAATAATAATTCATTTGATCTATCAATTGTAATTAAAAGTATAAAAATGCAATA-AAAAATA-
66 ATGAATAATAATTCATTTGATCTATCAATTGTAATTAAAA-T-T-AAAATGCAATATAAAAATAT
*
192687 ATTAAAAGAGAATAAAATTCAATA-CAAAAAGAA-TATAAAG-TCAAAAAAAATAA
128 ATTAAAAGA-AATAAAATT-AAAAGCAAAAAGAATTAT-AAGCTCAAAAAAAATAA
192740 AAAATTTATA
Statistics
Matches: 149, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
209 59 0.40
210 20 0.13
211 57 0.38
212 13 0.09
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.43
Consensus pattern (211 bp):
TTTTGTATTAAATTTTATTCACTTTTAATTCTTTTTTATTGCACTTTTATTGATTTTTAAAAAAA
ATGAATAATAATTCATTTGATCTATCAATTGTAATTAAAATTAAAATGCAATATAAAAATATATT
AAAAGAAATAAAATTAAAAGCAAAAAGAATTATAAGCTCAAAAAAAATAATATCACAAAAAAAAA
ATCAATAAAGTTTACG
Found at i:193142 original size:17 final size:17
Alignment explanation
Indices: 193120--193159 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
193110 CGCTTCAGGG
193120 GGCGCCTTACCCCACGT
1 GGCGCCTTACCCCACGT
193137 GGCGCCTTACCCCACGT
1 GGCGCCTTACCCCACGT
*
193154 GACGCC
1 GGCGCC
193160 AGATCAGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.12, C:0.47, G:0.25, T:0.15
Consensus pattern (17 bp):
GGCGCCTTACCCCACGT
Found at i:198209 original size:104 final size:104
Alignment explanation
Indices: 198018--198224 Score: 342
Period size: 104 Copynumber: 2.0 Consensus size: 104
198008 TTTGGTAAAA
**
198018 TATACATTTTAATAATATTTTATTCCTTTAACCAAACATTTTAATCTTACATTCATGCTAAACCA
1 TATACATTCCAATAATATTTTATTCCTTTAACCAAACATTTTAATCTTACATTCATGCTAAACCA
* *
198083 ACCAAACACAAAATACAGCATTCTTAGTAATCATATTCC
66 ACCAAACACAAAATACAACATTCTCAGTAATCATATTCC
* * * *
198122 TATACATTCCAATAATTTTTTATTCCTTTAACCAAATATTTTAATCTTACATTCCTGTTAAACCA
1 TATACATTCCAATAATATTTTATTCCTTTAACCAAACATTTTAATCTTACATTCATGCTAAACCA
198187 ACCAAACACAAAATACAACATTCTCAGTAATCATATTC
66 ACCAAACACAAAATACAACATTCTCAGTAATCATATTC
198225 TTCGATAGTC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 95 1.00
ACGTcount: A:0.39, C:0.22, G:0.02, T:0.37
Consensus pattern (104 bp):
TATACATTCCAATAATATTTTATTCCTTTAACCAAACATTTTAATCTTACATTCATGCTAAACCA
ACCAAACACAAAATACAACATTCTCAGTAATCATATTCC
Found at i:204630 original size:47 final size:47
Alignment explanation
Indices: 204428--204641 Score: 241
Period size: 47 Copynumber: 4.6 Consensus size: 47
204418 ATGTACATTT
* * * *
204428 CTGATGCTATGTGACCCCGGGCCTCATTCGATGTAGAGTGTATTTTC
1 CTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAGTGTATGTTC
* * * * *
204475 CTGATGTTATGTTATCCCATGCCTTACTCGATGTC-AGGTGTATGTTC
1 CTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGA-GTGTATGTTC
* * * *
204522 CTGATGCTATGTGATCTCAAGCCTCACTCGATGTCGAGTGTACGTTC
1 CTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAGTGTATGTTC
* * *
204569 TTGATGCTATGTGACCCCAGGTCTCACTCGATGTCGAATGTATGTTC
1 CTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAGTGTATGTTC
* * *
204616 CTAATGCTATGTGACCCTAGGTCTCA
1 CTGATGCTATGTGACCCCAGGCCTCA
204642 TCCGAGGATA
Statistics
Matches: 140, Mismatches: 25, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
46 1 0.01
47 138 0.99
48 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.35
Consensus pattern (47 bp):
CTGATGCTATGTGACCCCAGGCCTCACTCGATGTCGAGTGTATGTTC
Found at i:206149 original size:11 final size:11
Alignment explanation
Indices: 206133--206180 Score: 60
Period size: 11 Copynumber: 4.4 Consensus size: 11
206123 AAAAGAAAGA
206133 TAAACAAACAC
1 TAAACAAACAC
*
206144 TAAACAAACGC
1 TAAACAAACAC
* *
206155 TACACGAACAC
1 TAAACAAACAC
*
206166 TAAATAAACAC
1 TAAACAAACAC
206177 TAAA
1 TAAA
206181 AGAATGCTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.58, C:0.25, G:0.04, T:0.12
Consensus pattern (11 bp):
TAAACAAACAC
Found at i:206180 original size:33 final size:33
Alignment explanation
Indices: 206133--206197 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
206123 AAAAGAAAGA
*
206133 TAAACAAACACTAAACA-AACGCTACACGAACAC
1 TAAACAAACACTAAA-AGAACGCTAAACGAACAC
* *
206166 TAAATAAACACTAAAAGAATGCTAAACGAACA
1 TAAACAAACACTAAAAGAACGCTAAACGAACA
206198 TGTTCGTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.04
33 27 0.96
ACGTcount: A:0.57, C:0.23, G:0.08, T:0.12
Consensus pattern (33 bp):
TAAACAAACACTAAAAGAACGCTAAACGAACAC
Found at i:206214 original size:23 final size:23
Alignment explanation
Indices: 206188--206247 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
206178 AAAAGAATGC
* **
206188 TAAACGAACATGTTCGTAAACAT
1 TAAACGAACATATTCACAAACAT
* * *
206211 TAAATGCACACATTCACAAACAT
1 TAAACGAACATATTCACAAACAT
206234 TAAACGAACATATT
1 TAAACGAACATATT
206248 TACTAACAAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.47, C:0.20, G:0.08, T:0.25
Consensus pattern (23 bp):
TAAACGAACATATTCACAAACAT
Found at i:206291 original size:30 final size:30
Alignment explanation
Indices: 206237--206319 Score: 85
Period size: 30 Copynumber: 2.6 Consensus size: 30
206227 CAAACATTAA
* *
206237 ACGAACATATTTACTAACAATAAATAAACGAGC
1 ACGAACACATTTA--AA-AATAAATAAACGAAC
*
206270 ACGAACACATTTAAAAATAAATAAATGAAC
1 ACGAACACATTTAAAAATAAATAAACGAAC
*
206300 GCGAACACAATATTAAAAAT
1 ACGAACAC-AT-TTAAAAAT
206320 TTAAACTGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 20 0.45
31 4 0.09
32 8 0.18
33 12 0.27
ACGTcount: A:0.55, C:0.16, G:0.08, T:0.20
Consensus pattern (30 bp):
ACGAACACATTTAAAAATAAATAAACGAAC
Found at i:207114 original size:4 final size:4
Alignment explanation
Indices: 207105--207129 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
207095 CCCACTGAAC
207105 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
207130 TCTTTTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:207732 original size:23 final size:22
Alignment explanation
Indices: 207673--207739 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
207663 CCAAACGACC
*
207673 GAAAATGTGCCATAAAAACAAA
1 GAAAATGTGCCATAAAGACAAA
**
207695 GAAAATGTGTTATAAAGACAGAA
1 GAAAATGTGCCATAAAGACA-AA
* *
207718 GAAGATGTGCCATAAAGTCAAA
1 GAAAATGTGCCATAAAGACAAA
207740 ATTATTAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.18
Consensus pattern (22 bp):
GAAAATGTGCCATAAAGACAAA
Found at i:208985 original size:23 final size:22
Alignment explanation
Indices: 208942--208986 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
208932 AAACATTATA
*
208942 TTAATTATAATAGAAATATTTT
1 TTAATTATAATAGAAAAATTTT
208964 TTAATTAATAATA-ATAAAATTTT
1 TTAATT-ATAATAGA-AAAATTTT
208987 AAAGCATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTATAATAGAAAAATTTT
Found at i:211999 original size:15 final size:15
Alignment explanation
Indices: 211979--212008 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
211969 CATGAACGTC
*
211979 TAATTATAATTTGTA
1 TAATTATAACTTGTA
211994 TAATTATAACTTGTA
1 TAATTATAACTTGTA
212009 ATTTTATAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (15 bp):
TAATTATAACTTGTA
Found at i:212536 original size:286 final size:285
Alignment explanation
Indices: 212011--212763 Score: 956
Period size: 286 Copynumber: 2.6 Consensus size: 285
212001 AACTTGTAAT
* *
212011 TTTATAGGGTTTGAAATAAATTATAAAATATAAAAATAATTATGGCCCAATTTAT-GAT-AAAAT
1 TTTATAGGG-TTGGAGTAAATTATAAAATATAAAAATAATTATGG-CCAATTT-TGGATAAAAAT
* ** * *
212074 ATAATGTTATCGACTAAATTGAACAAACATAAAATTACAAACTGAAATTTAATTAAATTGAAACA
63 ATAATTTTAAGGACTAAATT-AACAAACATGAAATTACAAACTGAAATTTAAATAAATT-AAACA
* * **
212139 ACACACAAGGAATAAATTGAAACAATTGTAAAATGTAAAGCTGAAACCAATATAAAAATGGACTA
126 ACACACAAGGATTAAATTGAAACAATTATAAAATGTAAAGCTGAAATTAATATAAAAATGGACTA
* * * * *
212204 AATTGCATTCATTTACAAAGTTGATGAACAAAAGTTTATAGGGTTTGGAGATTATGATATAATTT
191 AATTGCATTCAATTAAAAAGTTGACGAACAAAAATTTATAGGGTTTGGAGATTATGATACAATTT
* * *
212269 ATAAGATTTAAAATGAAGTTTATGATGTGA
256 ATAAGATTTAAAATAAAGTTTATGATATAA
* *
212299 TTTATAGGGTTGGAGTAAATTACAAAATATAGAAATAATTATGTGCCAATTTTGGATAAAAATAT
1 TTTATAGGGTTGGAGTAAATTATAAAATATAAAAATAATTATG-GCCAATTTTGGATAAAAATAT
* * *
212364 AATTTTAAGGACTAAATTAA-AATACATGAAATTACAAACTGAACTTTAAATAAATTAAATAACG
65 AATTTTAAGGACTAAATTAACAA-ACATGAAATTACAAACTGAAATTTAAATAAATTAAACAACA
* *
212428 C-CAAAGGATTAAATTGAAACAATCATAAAATGTAAAGCTGAAATTAATATAAAAATGGACTAAG
129 CAC-AAGGATTAAATTGAAACAATTATAAAATGTAAAGCTGAAATTAATATAAAAATGGACTAAA
*
212492 TTGCATTCAATTAAAAAGTTGACGAACAAAAATTTATGGGGTTTGGAGATTATGATACAATTTAT
193 TTGCATTCAATTAAAAAGTTGACGAACAAAAATTTATAGGGTTTGGAGATTATGATACAATTTAT
* * * *
212557 ATGGTTTGAAATAAATTTTATGATATAA
258 AAGATTTAAAATAAAGTTTATGATATAA
* * * *
212585 TTTATAGGATTTGGAGTAAATTATAAAAAATAAAAATAATTATAGGCCAATTTCGAATAAAAATA
1 TTTATAGG-GTTGGAGTAAATTATAAAATATAAAAATAATTAT-GGCCAATTTTGGATAAAAATA
* * * * * *
212650 TAACTTTAAGTACTAAACTGAACAAACATGAAATTACAAACTAAAATTTGAATAAACTAAACAAC
64 TAATTTTAAGGACTAAA-TTAACAAACATGAAATTACAAACTGAAATTTAAATAAATTAAACAAC
* * * * * *
212715 ACATATGGATCAAATTGAAATAATTATAAAATATAATGCTGAAATTAAT
128 ACACAAGGATTAAATTGAAACAATTATAAAATGTAAAGCTGAAATTAAT
212764 TGGACTAAAT
Statistics
Matches: 402, Mismatches: 53, Indels: 20
0.85 0.11 0.04
Matches are distributed among these distances:
285 1 0.00
286 153 0.38
287 135 0.34
288 111 0.28
289 2 0.00
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.31
Consensus pattern (285 bp):
TTTATAGGGTTGGAGTAAATTATAAAATATAAAAATAATTATGGCCAATTTTGGATAAAAATATA
ATTTTAAGGACTAAATTAACAAACATGAAATTACAAACTGAAATTTAAATAAATTAAACAACACA
CAAGGATTAAATTGAAACAATTATAAAATGTAAAGCTGAAATTAATATAAAAATGGACTAAATTG
CATTCAATTAAAAAGTTGACGAACAAAAATTTATAGGGTTTGGAGATTATGATACAATTTATAAG
ATTTAAAATAAAGTTTATGATATAA
Found at i:212860 original size:28 final size:27
Alignment explanation
Indices: 212825--212881 Score: 78
Period size: 28 Copynumber: 2.1 Consensus size: 27
212815 TTGTAGATTA
*
212825 TGAATTTATGATATATTTTATAGGGTT
1 TGAATTTATGATATAATTTATAGGGTT
* *
212852 TGAAGTTTATGATGTAATTTATATGGTT
1 TGAA-TTTATGATATAATTTATAGGGTT
212880 TG
1 TG
212882 GAGTAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 22 0.85
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (27 bp):
TGAATTTATGATATAATTTATAGGGTT
Found at i:213966 original size:4 final size:4
Alignment explanation
Indices: 212991--213959 Score: 1318
Period size: 4 Copynumber: 243.5 Consensus size: 4
212981 ATTATGCATG
* * * * * * *
212991 CATA CATG CATG CATA CATG CATGTA CATG CATG CATA CATG CATA CATG
1 CATA CATA CATA CATA CATA CA--TA CATA CATA CATA CATA CATA CATA
* * * *
213041 CATA CATA CATG CATA CATG CATA CATG CATA CATA CATA AATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
213089 CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
213135 CATG CATA CATA CATA CATG CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
213183 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
213231 CATA CATA CATA CATA CATA CATA CATA CATG CAATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA
* *
213280 CATG CATA CATA CATA CATA CATA CATA CATG CAATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA
* * * *
213329 CATA CATA CATG CATG CATG CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
213377 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
213425 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
213473 CATG CATG CATG CATG CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
213521 CATA CATA CATG CATG CATG CATA CATA CAT- -ATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
213567 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
213615 -ATA CATA C-TA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
213661 CATA CATA CATA CATA CATA CATG CATA CATG CATA CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
213709 CATA CATA CATA CATA CATA CATA CATG CATA CATA CACTA -ATA AATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA
* * * * * * *
213757 CAT- TATA CATG CATTA -ATGA -ATA -ATA AAT- TATG CATG CATA CATG
1 CATA CATA CATA CA-TA CAT-A CATA CATA CATA CATA CATA CATA CATA
* * * * * *
213802 CATG CATA CATG CATGTA CATG CATG CATA CATG CATA CATG CATA CATA
1 CATA CATA CATA CA--TA CATA CATA CATA CATA CATA CATA CATA CATA
213852 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
213900 CATA CATG CATA CATA C--A CATA CATG CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
213946 CATA CATG CATA CA
1 CATA CATA CATA CA
213960 CATACATGCA
Statistics
Matches: 876, Mismatches: 68, Indels: 42
0.89 0.07 0.04
Matches are distributed among these distances:
2 6 0.01
3 17 0.02
4 838 0.96
5 9 0.01
6 6 0.01
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:213985 original size:8 final size:8
Alignment explanation
Indices: 213972--214644 Score: 763
Period size: 8 Copynumber: 84.2 Consensus size: 8
213962 TACATGCATG
213972 CACACACA
1 CACACACA
213980 CACACACA
1 CACACACA
213988 CACACACA
1 CACACACA
213996 CACACACA
1 CACACACA
214004 CACACACA
1 CACACACA
214012 CACACACA
1 CACACACA
214020 CACACACA
1 CACACACA
214028 CACACACA
1 CACACACA
214036 CACACACA
1 CACACACA
214044 CACACACA
1 CACACACA
*
214052 CCCACACA
1 CACACACA
*
214060 CACACCCA
1 CACACACA
214068 CACACACA
1 CACACACA
*
214076 CCCACACA
1 CACACACA
*
214084 CACACCCA
1 CACACACA
*
214092 CACACACG
1 CACACACA
*
214100 CGCACACA
1 CACACACA
* *
214108 CACACGCG
1 CACACACA
214116 CACACACA
1 CACACACA
* *
214124 CACGCGCA
1 CACACACA
*
214132 CACGCACA
1 CACACACA
* *
214140 CGCGCACA
1 CACACACA
*
214148 CACGCACA
1 CACACACA
*
214156 CACGCACA
1 CACACACA
*
214164 CACGCACA
1 CACACACA
*
214172 CACGCACA
1 CACACACA
*
214180 CACGCACA
1 CACACACA
*
214188 CACGCACA
1 CACACACA
*
214196 CACGCACA
1 CACACACA
*
214204 CACGCACA
1 CACACACA
*
214212 CACGCACA
1 CACACACA
*
214220 CACGCACA
1 CACACACA
*
214228 CACGCACA
1 CACACACA
*
214236 CACGCACA
1 CACACACA
*
214244 CACGCACA
1 CACACACA
*
214252 CACGCACA
1 CACACACA
*
214260 CACGCACA
1 CACACACA
*
214268 CACGCACA
1 CACACACA
*
214276 CACGCACA
1 CACACACA
*
214284 CACGCACA
1 CACACACA
*
214292 CACGCACA
1 CACACACA
*
214300 CACGCACA
1 CACACACA
*
214308 CACGCACA
1 CACACACA
*
214316 C-CGCACA
1 CACACACA
*
214323 CACGCACA
1 CACACACA
*
214331 CACGCACA
1 CACACACA
*
214339 CACGCACA
1 CACACACA
* *
214347 CACGCACG
1 CACACACA
* *
214355 CATACACG
1 CACACACA
*
214363 CACACGCA
1 CACACACA
* *
214371 CACGCACG
1 CACACACA
*
214379 CACACGCA
1 CACACACA
* *
214387 CACGCACG
1 CACACACA
*
214395 CACACACG
1 CACACACA
*
214403 CACACACG
1 CACACACA
*
214411 CACACACG
1 CACACACA
*
214419 CACACACG
1 CACACACA
*
214427 CACACGCA
1 CACACACA
*
214435 CAAACACA
1 CACACACA
*
214443 CACACGCA
1 CACACACA
214451 CACACACA
1 CACACACA
*
214459 CACACGCA
1 CACACACA
214467 CACACACA
1 CACACACA
*
214475 CGCACACA
1 CACACACA
*
214483 CACACACG
1 CACACACA
*
214491 CACACGCA
1 CACACACA
*
214499 CACGCACA
1 CACACACA
* *
214507 CGCACACG
1 CACACACA
214515 CACACACA
1 CACACACA
*
214523 CACACCCA
1 CACACACA
*
214531 CACCCACA
1 CACACACA
214539 CACACACA
1 CACACACA
214547 CACACACA
1 CACACACA
214555 CACACACA
1 CACACACA
214563 CACACACA
1 CACACACA
214571 CACACACA
1 CACACACA
214579 CACACACA
1 CACACACA
214587 CACACACA
1 CACACACA
214595 CACACACA
1 CACACACA
214603 CACACACA
1 CACACACA
214611 CACACACA
1 CACACACA
214619 CACACACA
1 CACACACA
214627 CACACACA
1 CACACACA
214635 CACACACA
1 CACACACA
214643 CA
1 CA
214645 TATCGGTCCG
Statistics
Matches: 602, Mismatches: 62, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
7 7 0.01
8 595 0.99
ACGTcount: A:0.41, C:0.51, G:0.08, T:0.00
Consensus pattern (8 bp):
CACACACA
Found at i:216000 original size:25 final size:25
Alignment explanation
Indices: 215972--216026 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
215962 AAAATGAAAG
215972 TTAATTTAATTTAATTA-ATAATTAA
1 TTAATTTAATTTAATTATAT-ATTAA
* * *
215997 TTAAGTTAATTTCATTATATTTTAA
1 TTAATTTAATTTAATTATATATTAA
216022 TTAAT
1 TTAAT
216027 GAATATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 23 0.92
26 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTAATTTAATTTAATTATATATTAA
Found at i:217761 original size:139 final size:139
Alignment explanation
Indices: 217589--217899 Score: 396
Period size: 139 Copynumber: 2.2 Consensus size: 139
217579 GAATCTCGAG
* * *
217589 GCGATGACCAAATTAAGAATTCTTCTAATTTAAGGACTAAAGGTGAAATTAGGCCTAAGATGGAG
1 GCGAGGACCAAATTAAGAATTCTCCTAATTTAAGGACTAAAGATGAAATTAGGCCTAAGATGGAG
*
217654 GATCTAATATATTAATTCTAATCAACTTTAATCAATTAT-TGA-T-TCAAATAATTAAATT-GGA
66 GAT-TAA-ATATTAATCCTAATCAACTTTAATCAATTATGT-ACTATCAAATAATT-AATTCGGA
*
217715 ACCTCGAGCACAA
127 ACCTAGAGCACAA
* * *
217728 GCGAGGACCAAATTAAGAATTCACCTAATTTAAGGATTAAATATGAAATTAGGCCTAAGATGGAG
1 GCGAGGACCAAATTAAGAATTCTCCTAATTTAAGGACTAAAGATGAAATTAGGCCTAAGATGGAG
* * * * *
217793 GCTTTAATATTAATCCTAATTAATTTTAATCAATTATGTACTATCGAATAATTAATTCGGAACCT
66 GATTAAATATTAATCCTAATCAACTTTAATCAATTATGTACTATCAAATAATTAATTCGGAACCT
*
217858 AGAGCATAA
131 AGAGCACAA
* * * *
217867 GCAAGGACCAAATCAAAAATTCTCCTAAATTAA
1 GCGAGGACCAAATTAAGAATTCTCCTAATTTAA
217900 ACATTTAAGG
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
137 29 0.19
138 8 0.05
139 112 0.75
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.30
Consensus pattern (139 bp):
GCGAGGACCAAATTAAGAATTCTCCTAATTTAAGGACTAAAGATGAAATTAGGCCTAAGATGGAG
GATTAAATATTAATCCTAATCAACTTTAATCAATTATGTACTATCAAATAATTAATTCGGAACCT
AGAGCACAA
Found at i:220837 original size:203 final size:203
Alignment explanation
Indices: 220502--221265 Score: 1085
Period size: 203 Copynumber: 3.8 Consensus size: 203
220492 AACCAAGGTG
* * * * * *
220502 ATGTTGATCCAACTCCTTATT-TGATGG-A-CGAGCGAAA-TGACGTTGCTGATCTAACTCCTTA
1 ATGTTGATCCACCTCCTT-TTGTGATGGAATCGAAC-AAAGTGATGATGCTGATCCAACTCCATA
* * * *
220563 TACGATGGATGAGCCAAGGTA--GGTGTTGTTCCAACTCTTTATATGATGGAAATGAGCTAATGT
64 TGCGATGGATGAGCCAA-GTATTGGTGTTGTTCCAACTCCTTATGTGATGGAAATGAGCTAAGGT
* * * * *
220626 TGAACAAGTTCTTCTTATTATGTACTTCTTCTCCCTCATCGGATGAGTTATTCTAATTATGAACT
128 TGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACT
*
220691 CTCCGTTGGAA
193 CTCCATTGGAA
* *
220702 ATGTTGATCCACCTCCTTTTGTGATGGAATTGAACAAAGTGATTATGCTGATCCAACTCCATATG
1 ATGTTGATCCACCTCCTTTTGTGATGGAATCGAACAAAGTGATGATGCTGATCCAACTCCATATG
*
220767 CGATGGATGAGCCAAGTATTGGTGATGTTCCAACTCCTTATGTGATGGAAATGAGCTAAGGTTGA
66 CGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGGAAATGAGCTAAGGTTGA
*
220832 ACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTC
131 ACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTC
* * *
220897 TACTGGTA
196 CATTGGAA
*
220905 ATGTTGATCCACCT-CTTTCTGTGATGGAATCGAACAAAGTGATGATGTTGATCCAACTCCATAT
1 ATGTTGATCCACCTCCTTT-TGTGATGGAATCGAACAAAGTGATGATGCTGATCCAACTCCATAT
* * * * * *
220969 GCGATGGATGAGCCAAG-GTCGATGTTGTTCCACCTCCTTATGTGATGAAAATGAGATAAGGTTG
65 GCGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGGAAATGAGCTAAGGTTG
*
221033 AACAAGTTCTTCTCATTATGAACTTATTATCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
130 AACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCT
*
221098 ACATTGGAA
195 CCATTGGAA
* * * *
221107 ATATTGATCCACCTCCTTCTGTGATGGAATCAAACAAAGTGACGATGCTGATCCAACTCCATATG
1 ATGTTGATCCACCTCCTTTTGTGATGGAATCGAACAAAGTGATGATGCTGATCCAACTCCATATG
* *
221172 CGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTAATGGAAATGAGCTAAGGTTTA
66 CGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGGAAATGAGCTAAGGTTGA
*
221237 ACAAGTTCTTATCATTATGAACTTATTCT
131 ACAAGTTCTTCTCATTATGAACTTATTCT
221266 AGTAAAGGGT
Statistics
Matches: 502, Mismatches: 53, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
199 2 0.00
200 23 0.05
201 7 0.01
202 222 0.44
203 248 0.49
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (203 bp):
ATGTTGATCCACCTCCTTTTGTGATGGAATCGAACAAAGTGATGATGCTGATCCAACTCCATATG
CGATGGATGAGCCAAGTATTGGTGTTGTTCCAACTCCTTATGTGATGGAAATGAGCTAAGGTTGA
ACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATCGGATGAGTTCTTCTCATTATGAACTCTC
CATTGGAA
Found at i:226569 original size:18 final size:18
Alignment explanation
Indices: 226546--226596 Score: 93
Period size: 18 Copynumber: 2.8 Consensus size: 18
226536 CACACCGAAC
*
226546 TGAGTCAACTCGACTGGT
1 TGAGTCAACTTGACTGGT
226564 TGAGTCAACTTGACTGGT
1 TGAGTCAACTTGACTGGT
226582 TGAGTCAACTTGACT
1 TGAGTCAACTTGACT
226597 AAGTCAACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (18 bp):
TGAGTCAACTTGACTGGT
Found at i:229148 original size:21 final size:21
Alignment explanation
Indices: 229122--229168 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
229112 TAACATTTCC
229122 GGTAGAAAAAATAAAAAAACA
1 GGTAGAAAAAATAAAAAAACA
* *
229143 GGTAGAAAAAATAACAAAACC
1 GGTAGAAAAAATAAAAAAACA
229164 GGTAG
1 GGTAG
229169 CGCTTTACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.09, G:0.19, T:0.11
Consensus pattern (21 bp):
GGTAGAAAAAATAAAAAAACA
Found at i:230621 original size:17 final size:17
Alignment explanation
Indices: 230572--230622 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
230562 TTTTAAAAAA
230572 ATAT-AAAA-TTAAATT
1 ATATAAAAATTTAAATT
230587 ATCAATAAAAATATTTAAATT
1 AT--AT-AAAA-ATTTAAATT
230608 ATATAAAAATTTAAA
1 ATATAAAAATTTAAA
230623 AATTTCAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.07
17 9 0.30
18 4 0.13
19 5 0.17
20 1 0.03
21 9 0.30
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAAAAATTTAAATT
Found at i:232459 original size:6 final size:6
Alignment explanation
Indices: 232390--232459 Score: 68
Period size: 6 Copynumber: 11.3 Consensus size: 6
232380 TTAGTACTAC
* * * * *
232390 TTTATT TATTATT TTATGTT TTTAGT TTTAGT TTTAAT TTTATT TCTATT
1 TTTATT T-TTATT TT-TATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
232440 TTTATT TCTATT TTTATT TT
1 TTTATT TTTATT TTTATT TT
232460 CTTCGTCTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
6 42 0.79
7 11 0.21
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:242847 original size:17 final size:15
Alignment explanation
Indices: 242825--242859 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
242815 TCTTAAGTCG
*
242825 AAAAAAAGGAAAAAA
1 AAAAAAAAGAAAAAA
242840 CAAAAAAAAGAAAAAA
1 -AAAAAAAAGAAAAAA
242856 AAAA
1 AAAA
242860 CGTTTAGGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.89, C:0.03, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:242918 original size:72 final size:71
Alignment explanation
Indices: 242791--242925 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 71
242781 AGTACTTCAC
* * *
242791 TTAGGATGAAAACCCGAAAGGGCGTCTTAAGTCGAAAAAAAGGAAAAAACAAAAAAAAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCTTAAATCGAAAAAAAGAAAAAAAC-AAAAAAAGAAAAAA
242856 AAAACGT
65 AAAACGT
* * *
242863 TTAGGGTGAAGACCCGAAAGGGCGCCTTAAATTG-AAAAAAGAAAAAAGA-ACAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCGCCTTAAATCGAAAAAAAGAAAAAA-ACA-AAAAAAGAAAAA
242926 GAAAGATAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
70 1 0.02
71 24 0.44
72 30 0.55
ACGTcount: A:0.57, C:0.11, G:0.21, T:0.11
Consensus pattern (71 bp):
TTAGGATGAAAACCCGAAAGGGCGCCTTAAATCGAAAAAAAGAAAAAAACAAAAAAAGAAAAAAA
AAACGT
Found at i:244225 original size:100 final size:100
Alignment explanation
Indices: 244045--244226 Score: 283
Period size: 100 Copynumber: 1.8 Consensus size: 100
244035 ATTTCAGTGC
* * *
244045 CAATTTCAACTTCACAGCAAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACAAAAGATATTAGACCCAAGACAACACAAGCTCAACTTCACAACGAAG
*
244110 GGGCGACTGATTGTCAAATAAATTTCATTCATAGT
66 GGGCGACTGACTGTCAAATAAATTTCATTCATAGT
* * * *
244145 CAATTTCAACTTCACAACAAAAGATATTAGACTCGAGACAGCGCAAGCTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAACAAAAGATATTAGACCCAAGACAACACAAGCTCAACTTCACAACGAAG
*
244210 GGGCGACTGGCTGTCAA
66 GGGCGACTGACTGTCAA
244227 CAAACAATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
100 73 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (100 bp):
CAATTTCAACTTCACAACAAAAGATATTAGACCCAAGACAACACAAGCTCAACTTCACAACGAAG
GGGCGACTGACTGTCAAATAAATTTCATTCATAGT
Found at i:247723 original size:13 final size:14
Alignment explanation
Indices: 247673--247723 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
247663 ACATATGTTA
247673 ATAATATAAAATTTT
1 ATAA-ATAAAATTTT
* *
247688 -TAAATAAGATATAT
1 ATAAATAAAAT-TTT
247702 ATAAATAAAATTTT
1 ATAAATAAAATTTT
247716 AT-AATAAA
1 ATAAATAAA
247724 TATCATTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
13 12 0.40
14 9 0.30
15 9 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (14 bp):
ATAAATAAAATTTT
Found at i:247726 original size:27 final size:29
Alignment explanation
Indices: 247673--247738 Score: 79
Period size: 28 Copynumber: 2.4 Consensus size: 29
247663 ACATATGTTA
247673 ATAATATAAAATTTTTAAATAAGATAT-AT
1 ATAA-ATAAAATTTTTAAATAAGATATCAT
247702 ATAAATAAAA-TTTTATAATAA-ATATCAT
1 ATAAATAAAATTTTTA-AATAAGATATCAT
247730 -T-AATAAAAT
1 ATAAATAAAAT
247739 AATAATTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
26 7 0.21
27 10 0.29
28 13 0.38
29 4 0.12
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (29 bp):
ATAAATAAAATTTTTAAATAAGATATCAT
Found at i:248822 original size:30 final size:30
Alignment explanation
Indices: 248786--248881 Score: 165
Period size: 30 Copynumber: 3.2 Consensus size: 30
248776 TTTCAAAATT
*
248786 ACAAATCGGTCACTAATGTTATCGTTTGTG
1 ACAAATCGGTCACTAACGTTATCGTTTGTG
* *
248816 ACAAATCTGTCACTAACGTAATCGTTTGTG
1 ACAAATCGGTCACTAACGTTATCGTTTGTG
248846 ACAAATCGGTCACTAACGTTATCGTTTGTG
1 ACAAATCGGTCACTAACGTTATCGTTTGTG
248876 ACAAAT
1 ACAAAT
248882 TAGTCACTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (30 bp):
ACAAATCGGTCACTAACGTTATCGTTTGTG
Found at i:250559 original size:55 final size:55
Alignment explanation
Indices: 250498--250644 Score: 222
Period size: 55 Copynumber: 2.6 Consensus size: 55
250488 TTCACCTGCA
250498 TAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACAAAAATTCATACACT
1 TAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACAAAAATTCATACACT
* * **
250553 TGGTATGAATTTCCTAGTTTTGCACACATAGTGCCCATACGGAAATTCATACACT
1 TAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACAAAAATTCATACACT
* *
250608 TAGTACGAATTTCTTAGCTTTTTGCACACAAAGTGCC
1 TAGTATGAATTTCTTAG--TTTTGCACACATAGTGCC
250645 ATTTGATAAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
55 65 0.79
57 17 0.21
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (55 bp):
TAGTATGAATTTCTTAGTTTTGCACACATAGTGCCCATACAAAAATTCATACACT
Found at i:258431 original size:136 final size:138
Alignment explanation
Indices: 258163--258438 Score: 450
Period size: 136 Copynumber: 2.0 Consensus size: 138
258153 GGTAATGCTC
*
258163 ACTGTACAGATAATGATGCCAGGTTTTTTTAAAGCAAACACTATTGCTGCCAATTCTAAATCATG
1 ACTGTACAGATAATGATGCCAAGTTTTTTTAAAGCAAACACTATTGCTGCCAATTCTAAATCATG
* *
258228 TATTGGGTAATTTCACTCATGATTCTTTAGCTGTCGTGAGGCATAAGCCATAACTTTACCTTGTT
66 TATTGGGTAATTTCACTCATGATTCTTCAGCTGTCGTGAGGCATAAGCCACAACTTTACCTTGTT
258293 GCATCAGT
131 GCATCAGT
* *
258301 ACTGTACA-ATAATGATGCTAAG-TTTTTTAAAGCAAACACTATTGCTTCCAATTCTAAATCATG
1 ACTGTACAGATAATGATGCCAAGTTTTTTTAAAGCAAACACTATTGCTGCCAATTCTAAATCATG
* * *
258364 TGTTGGGTAATTTCTCTCATGATTCTTCAGCTGTCTTGAGGCATAAGCCACAACTTT-CTCTTGT
66 TATTGGGTAATTTCACTCATGATTCTTCAGCTGTCGTGAGGCATAAGCCACAACTTTAC-CTTGT
258428 TGCATCAGT
130 TGCATCAGT
258437 AC
1 AC
258439 ACAACCCAAC
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
135 1 0.01
136 108 0.84
137 12 0.09
138 8 0.06
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (138 bp):
ACTGTACAGATAATGATGCCAAGTTTTTTTAAAGCAAACACTATTGCTGCCAATTCTAAATCATG
TATTGGGTAATTTCACTCATGATTCTTCAGCTGTCGTGAGGCATAAGCCACAACTTTACCTTGTT
GCATCAGT
Found at i:261960 original size:55 final size:55
Alignment explanation
Indices: 261899--262300 Score: 608
Period size: 55 Copynumber: 7.3 Consensus size: 55
261889 ATTGCTTATG
** * * *
261899 TTTGCACATGTAGTTCCCATACGGAAATTCATACACGTAATATGAATTTCTTAGT
1 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
* * *
261954 TATGCACATATAGTGCCCATGCGGAAATTCATACACTTAGTATGAATTTCTTAGT
1 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
*
262009 TTTGCACACATAGTGCCCATAAGGAAATT-ATTACACTTAGTATGAATTTCTTAGT
1 TTTGCACACATAGTGCCCATACGGAAATTCA-TACACTTAGTATGAATTTCTTAGT
**
262064 TTTGCACACATAGTGCCCATATAGAAATTCATACACTTAGTATGAATTTCTTAGT
1 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
* * *
262119 TTTGTACATATAGTGTCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
1 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
* * *
262174 TTTGCACACATAGTGCCCATACGTACATTCATACACTTAGTATTAATTTCTTAGT
1 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
262229 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGCTT
1 TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAG--T
*
262286 TTTGCACACAAAGTG
1 TTTGCACACATAGTG
262301 TCATTTGGTA
Statistics
Matches: 316, Mismatches: 27, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
54 1 0.00
55 299 0.95
56 1 0.00
57 15 0.05
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.36
Consensus pattern (55 bp):
TTTGCACACATAGTGCCCATACGGAAATTCATACACTTAGTATGAATTTCTTAGT
Found at i:264240 original size:30 final size:30
Alignment explanation
Indices: 264200--264269 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
264190 GTGGTAGTTA
264200 TGAAACTGGTGATGTAGAAATGGATAATGC
1 TGAAACTGGTGATGTAGAAATGGATAATGC
* * *
264230 TGAAAGTGGTGGTGTAGAAATGGATACTGC
1 TGAAACTGGTGATGTAGAAATGGATAATGC
*
264260 TGAAATTGGT
1 TGAAACTGGT
264270 AGTGTTGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.29
Consensus pattern (30 bp):
TGAAACTGGTGATGTAGAAATGGATAATGC
Found at i:266893 original size:55 final size:54
Alignment explanation
Indices: 266834--267213 Score: 432
Period size: 55 Copynumber: 6.9 Consensus size: 54
266824 AATGACGAGC
* * *
266834 CTGCTCCCTATTCCTTCAGGAAGTATA-AGACTCGAACAATCTTCATAAAATGTGT
1 CTGCTCTCTATTCCTTCA-GAAGTATAGA-ACTCGAACAATCTTCATAAAACGGGT
* * *
266889 CTGCTCTCTATTCATTCAGAGAGTATA-AGACTCAAATAATCTTCA-ACAAACGGGT
1 CTGCTCTCTATTCCTTCAGA-AGTATAGA-ACTCGAACAATCTTCATA-AAACGGGT
266944 -TCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1 CT-GCTCTCTATTCCTTCAGA-AGTATAGAACTCGAACAATCTTCATAAAACGGGT
*
266999 CCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1 CTGCTCTCTATTCCTTCAGA-AGTATAGAACTCGAACAATCTTCATAAAACGGGT
*
267054 CCGCTCTCTATTCCTTCA-AAGTATAGAACTCGAACAATCTTCATAAAACGGGT
1 CTGCTCTCTATTCCTTCAGAAGTATAGAACTCGAACAATCTTCATAAAACGGGT
* * * * * *
267107 -TCACTCCCCATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGT
1 CT-GCTCTCTATTCCTTCA-GAAGTATAGAACTCGAACAATCTTCATAAAACGGGT
* * * * *
267162 -TCGCTCCCTATGCATTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACG
1 CT-GCTCTCTATTCCTTCA-GAAGTATAGAACTCGAACAATCTTCATAAAACG
267214 TATTTGCTTC
Statistics
Matches: 296, Mismatches: 20, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
53 46 0.16
54 5 0.02
55 243 0.82
56 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (54 bp):
CTGCTCTCTATTCCTTCAGAAGTATAGAACTCGAACAATCTTCATAAAACGGGT
Found at i:267005 original size:110 final size:110
Alignment explanation
Indices: 266836--267213 Score: 507
Period size: 110 Copynumber: 3.5 Consensus size: 110
266826 TGACGAGCCT
* * *
266836 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTA
* *
266899 TTCATTCAGAGAGTATA-AGACTCAAATAATCTTCAACAAACGGGTTC
64 TTCATTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTTC
*
266946 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
267011 CCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCC
66 CATTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTTC
* * * * *
267056 GCTCTCTATTCCTTCA-A-AGTATAGAACTCGAACAATCTTCATAAAACGGGTTCACTCCCCATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* *
267119 CATTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACGGGTTC
66 CATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTC
* * * *
267164 GCTCCCTATGCATTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACG
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACG
267214 TATTTGCTTC
Statistics
Matches: 240, Mismatches: 21, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
108 95 0.40
109 1 0.00
110 140 0.58
111 4 0.02
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
CATTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTTC
Found at i:267160 original size:163 final size:164
Alignment explanation
Indices: 266836--267213 Score: 514
Period size: 163 Copynumber: 2.3 Consensus size: 164
266826 TGACGAGCCT
* * *
266836 GCTCCCTATTCCTTCAGGAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTGCTCTCTAT
1 GCTCCCTATTCCTTCAGG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTAT
* * * * *
266900 TCATTCAGAGAGTATAAGACTCAAATAATCTTCAACAAACGGGTTCGCTCTCTATTCCTTCAGAG
64 TCATTCAGAGAGTATAAGACTCAAACAATCTTCAACAAACGGGTTCACTCCCCATTCATTCAGAG
266965 AGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
129 AGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
*
267001 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
1 GCTCCCTATTCCTTCAG-GAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATT
* * *
267066 CCTTCA-A-AGTAT-AGAACTCGAACAATCTTCATA-AAACGGGTTCACTCCCCATTCATTCAGG
65 CATTCAGAGAGTATAAG-ACTCAAACAATCTTCA-ACAAACGGGTTCACTCCCCATTCATTCAGA
* *
267127 GAGTATAGAACTCGAACAATCTTCATCAAACGGGTTC
128 GAGTATAGAACTCGAACAATCTTCATAAAACGGGTCC
* * *
267164 GCTCCCTATGCATTCAGGGAGTATAGAACTCGAACAATCTTCATCAAACG
1 GCTCCCTATTCCTTCA-GGAGTATAGAACTCGAACAATCTTCATAAAACG
267214 TATTTGCTTC
Statistics
Matches: 190, Mismatches: 18, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
162 2 0.01
163 121 0.64
164 3 0.02
165 62 0.33
166 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (164 bp):
GCTCCCTATTCCTTCAGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTC
ATTCAGAGAGTATAAGACTCAAACAATCTTCAACAAACGGGTTCACTCCCCATTCATTCAGAGAG
TATAGAACTCGAACAATCTTCATAAAACGGGTCC
Found at i:267277 original size:37 final size:37
Alignment explanation
Indices: 267215--267322 Score: 119
Period size: 37 Copynumber: 2.9 Consensus size: 37
267205 CATCAAACGT
* * *
267215 ATTTGCTTCACTATTCTTTCATGAAGGCTTATAG-ATG
1 ATTTGCTTCACAACTCTTTCGTGAAGGCTTA-AGTATG
* * *
267252 ATTTGCTTCACCACTCTTCCGTGAAGGCTTAAGTTTG
1 ATTTGCTTCACAACTCTTTCGTGAAGGCTTAAGTATG
* * *
267289 AATTGCTTCATAACTCTTTTGTGAAGGCTTAAGT
1 ATTTGCTTCACAACTCTTTCGTGAAGGCTTAAGT
267323 TTGACTTGTT
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
36 2 0.03
37 58 0.97
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.41
Consensus pattern (37 bp):
ATTTGCTTCACAACTCTTTCGTGAAGGCTTAAGTATG
Found at i:268621 original size:15 final size:15
Alignment explanation
Indices: 268601--268734 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
268591 TTTTTTCTTT
268601 ATTTTTTCATTTTTC
1 ATTTTTTCATTTTTC
*
268616 ATTTTTCTCTTTTTTC
1 ATTTTT-TCATTTTTC
* *
268632 ATTTTCTCTTTTTTC
1 ATTTTTTCATTTTTC
*
268647 -TTCTTTT-TTCTTTTC
1 ATT-TTTTCAT-TTTTC
*
268662 GTTTTTTCCATCATTTTC
1 ATTTTTT-CAT--TTTTC
268680 ATTTTTCTCA-TTTT-
1 ATTTTT-TCATTTTTC
268694 -TTTTTTC-TTCTTCTC
1 ATTTTTTCATT-TT-TC
*
268709 A-TTTTT-ATTATT-
1 ATTTTTTCATTTTTC
268721 ATTTTTTCATTTTT
1 ATTTTTTCATTTTT
268735 TTCTTTTATT
Statistics
Matches: 95, Mismatches: 8, Indels: 33
0.70 0.06 0.24
Matches are distributed among these distances:
12 4 0.04
13 13 0.14
14 11 0.12
15 38 0.40
16 15 0.16
17 1 0.01
18 12 0.13
19 1 0.01
ACGTcount: A:0.10, C:0.16, G:0.01, T:0.73
Consensus pattern (15 bp):
ATTTTTTCATTTTTC
Found at i:268648 original size:7 final size:7
Alignment explanation
Indices: 268602--268669 Score: 57
Period size: 8 Copynumber: 9.0 Consensus size: 7
268592 TTTTTCTTTA
268602 TTTTTTC
1 TTTTTTC
*
268609 ATTTTTC
1 TTTTTTC
268616 ATTTTTCTC
1 -TTTTT-TC
268625 TTTTTTC
1 TTTTTTC
*
268632 ATTTTCTC
1 -TTTTTTC
268640 TTTTTTC
1 TTTTTTC
268647 TTCTTTT-
1 TT-TTTTC
268654 TTCTTTTC
1 TT-TTTTC
268662 GTTTTTTC
1 -TTTTTTC
268670 CATCATTTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
7 23 0.45
8 24 0.47
9 4 0.08
ACGTcount: A:0.04, C:0.18, G:0.01, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:268660 original size:24 final size:25
Alignment explanation
Indices: 268591--268713 Score: 94
Period size: 24 Copynumber: 4.9 Consensus size: 25
268581 CATCCTTTTA
*
268591 TTTTTTCTTTATTTTTTCATTTT-TC
1 TTTTTTC-TTCTTTTTTCATTTTCTC
*
268616 ATTTTTC-TCTTTTTTCATTTTCTC
1 TTTTTTCTTCTTTTTTCATTTTCTC
268640 TTTTTTCTTCTTTTTTC-TTTTCGT-
1 TTTTTTCTTCTTTTTTCATTTTC-TC
* * *
268664 TTTTTCCATC-ATTTTCATTTTTCTC
1 TTTTTTCTTCTTTTTTCA-TTTTCTC
* *
268689 ATTTTTTTTTTCTTCTTCTCATTTT
1 --TTTTTTCTTCTT-TTTTCATTTT
268714 TATTATTATT
Statistics
Matches: 77, Mismatches: 11, Indels: 17
0.73 0.10 0.16
Matches are distributed among these distances:
23 18 0.23
24 22 0.29
25 21 0.27
27 7 0.09
28 4 0.05
29 5 0.06
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (25 bp):
TTTTTTCTTCTTTTTTCATTTTCTC
Found at i:268707 original size:20 final size:19
Alignment explanation
Indices: 268682--268736 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
268672 TCATTTTCAT
* *
268682 TTTTCTCATTTTTTTTTTC
1 TTTTCTCATTTTTTTATTA
268701 TTCTTCTCATTTTTATTATTA
1 TT-TTCTCATTTTT-TTATTA
*
268722 TTTTTTCATTTTTTT
1 TTTTCTCATTTTTTT
268737 CTTTTATTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 21 0.68
21 6 0.19
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTCTCATTTTTTTATTA
Found at i:280253 original size:17 final size:17
Alignment explanation
Indices: 280232--280270 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
280222 AACTAACACA
*
280232 AAAATTAGGAAAACTAC
1 AAAATCAGGAAAACTAC
* *
280249 GAAATCAGGACAACTAC
1 AAAATCAGGAAAACTAC
280266 AAAAT
1 AAAAT
280271 GGCAGAATTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (17 bp):
AAAATCAGGAAAACTAC
Found at i:283247 original size:10 final size:10
Alignment explanation
Indices: 283190--283269 Score: 54
Period size: 10 Copynumber: 7.5 Consensus size: 10
283180 TAATATTTTC
*
283190 GTTGATATAT
1 GTTGAAATAT
*
283200 GCTGAAATAT
1 GTTGAAATAT
283210 GCTATGAAATAT
1 G-T-TGAAATAT
283222 GTT-AAGATATGTT
1 GTTGAA-ATA---T
283235 GTTGAAATAT
1 GTTGAAATAT
*
283245 GTTGAGATAT
1 GTTGAAATAT
* *
283255 GCTGTAATAT
1 GTTGAAATAT
283265 GTTGA
1 GTTGA
283270 GACTATTTGA
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
9 2 0.04
10 33 0.61
11 1 0.02
12 9 0.17
13 7 0.13
14 2 0.04
ACGTcount: A:0.34, C:0.04, G:0.23, T:0.40
Consensus pattern (10 bp):
GTTGAAATAT
Found at i:283265 original size:20 final size:22
Alignment explanation
Indices: 283196--283271 Score: 75
Period size: 23 Copynumber: 3.5 Consensus size: 22
283186 TTTCGTTGAT
* * * *
283196 ATATGCTGAAATATGCTATGAA
1 ATATGTTGAGATATGCTGTTAA
* *
283218 ATATGTTAAGATATGTTGTTGAA
1 ATATGTTGAGATATGCTGTT-AA
283241 ATATGTTGAGATATGCTG-T-A
1 ATATGTTGAGATATGCTGTTAA
283261 ATATGTTGAGA
1 ATATGTTGAGA
283272 CTATTTGAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 12 0.27
22 15 0.33
23 18 0.40
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (22 bp):
ATATGTTGAGATATGCTGTTAA
Found at i:288161 original size:12 final size:12
Alignment explanation
Indices: 288134--288171 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
288124 TATGACTAAT
288134 ATAATAA-TAAA
1 ATAATAATTAAA
288145 ATAATAATTAAA
1 ATAATAATTAAA
* *
288157 GTAATAATTTAA
1 ATAATAATTAAA
288169 ATA
1 ATA
288172 TATTGGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
11 7 0.30
12 16 0.70
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (12 bp):
ATAATAATTAAA
Found at i:288261 original size:29 final size:30
Alignment explanation
Indices: 288207--288263 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
288197 ATTAAATTGC
288207 AATAGTGACTAAAACATATAAAATTAAAGT
1 AATAGTGACTAAAACATATAAAATTAAAGT
* *
288237 AATAGT-ATTAAAATATA-AAATATTAAA
1 AATAGTGACTAAAACATATAAA-ATTAAA
288264 ATTAACAGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 3 0.12
29 15 0.62
30 6 0.25
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.30
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAGT
Found at i:289082 original size:25 final size:24
Alignment explanation
Indices: 289046--289104 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
289036 CTTGGTTGTA
*
289046 TCTTGCTGTCGTGGTCTCCTCGGGT
1 TCTTGCTCTCGT-GTCTCCTCGGGT
*
289071 TTTTGCTCTC--GTCTCCTCGGGT
1 TCTTGCTCTCGTGTCTCCTCGGGT
289093 TCTTGCTCTCGT
1 TCTTGCTCTCGT
289105 CGTTCTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 21 0.72
25 8 0.28
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (24 bp):
TCTTGCTCTCGTGTCTCCTCGGGT
Found at i:289087 original size:22 final size:22
Alignment explanation
Indices: 289059--289105 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
289049 TGCTGTCGTG
*
289059 GTCTCCTCGGGTTTTTGCTCTC
1 GTCTCCTCGGGTTCTTGCTCTC
289081 GTCTCCTCGGGTTCTTGCTCTC
1 GTCTCCTCGGGTTCTTGCTCTC
289103 GTC
1 GTC
289106 GTTCTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.00, C:0.34, G:0.23, T:0.43
Consensus pattern (22 bp):
GTCTCCTCGGGTTCTTGCTCTC
Found at i:289603 original size:3 final size:3
Alignment explanation
Indices: 289595--289664 Score: 81
Period size: 3 Copynumber: 23.0 Consensus size: 3
289585 TTTATTTATT
*
289595 TAA TAA TAA AAA TAA -ATA TATA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
289640 TAA TATT TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA
289665 AATGAAAAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
2 3 0.05
3 49 0.83
4 7 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:289623 original size:22 final size:20
Alignment explanation
Indices: 289595--289664 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 20
289585 TTTATTTATT
289595 TAATAATAAAAATAAATATATA
1 TAATAATAAAAAT-AATA-ATA
*
289617 TAATAATAATAATAATAATA
1 TAATAATAAAAATAATAATA
**
289637 TAATAATATTTAATAATAATAA
1 TAATAATA-AAAATAATAAT-A
289659 TAATAA
1 TAATAA
289665 AATGAAAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.25
21 14 0.32
22 19 0.43
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAATAATAAAAATAATAATA
Found at i:289653 original size:30 final size:28
Alignment explanation
Indices: 289595--289664 Score: 104
Period size: 30 Copynumber: 2.4 Consensus size: 28
289585 TTTATTTATT
*
289595 TAATAATAAAAATAAATATATATAATAA
1 TAATAATAATAATAAATATATATAATAA
*
289623 TAATAATAATAATATAATAATATTTAATAA
1 TAATAATAATAATA-AAT-ATATATAATAA
289653 TAATAATAATAA
1 TAATAATAATAA
289665 AATGAAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 13 0.34
29 3 0.08
30 22 0.58
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (28 bp):
TAATAATAATAATAAATATATATAATAA
Found at i:290080 original size:74 final size:74
Alignment explanation
Indices: 289944--290780 Score: 1434
Period size: 74 Copynumber: 11.4 Consensus size: 74
289934 GAGGTCTTAT
* * *
289944 CATCTTGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCTGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290009 TTTTGAAAA
66 TTTTGAAAA
290018 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290083 TTTTGAAAA
66 TTTTGAAAA
* *
290092 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAA-ATCATAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290156 TTTTGAAAA
66 TTTTGAAAA
290165 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGC-
290230 TTTTTGAAAA
65 TTTTTGAAAA
* *
290240 CATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAA-ATCAAAAAGCTCCCAAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
290304 TTTTGAAAG
66 TTTTGAAAA
* * *
290313 CATCATGCACTGCAGGTCTTACAGATGACCATGAGGCTTTAAATATCAAAAAGCTCCCGAAGGTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGG-C
290378 TTTTTGAAAA
65 TTTTTGAAAA
*
290388 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTT-AA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290451 TTTTGAAAA
66 TTTTGAAAA
*
290460 CATCATGCACTGTAGGTCTTATAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
290525 TTTTAAAAA
66 TTTTGAAAA
290534 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290598 TTTTGAAAA
66 TTTTGAAAA
** *
290607 CATCATGCACTACAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290672 TTTTGAAAA
66 TTTTGAAAA
* *
290681 CATCATGCGCTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCGAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290745 TTTTGAAAA
66 TTTTGAAAA
*
290754 CATCATGCACTTTAGGTCTTACAGATG
1 CATCATGCACTGTAGGTCTTACAGATG
290781 TGGGAAATAA
Statistics
Matches: 724, Mismatches: 32, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
72 48 0.07
73 266 0.37
74 311 0.43
75 99 0.14
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (74 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAA
Found at i:290222 original size:147 final size:147
Alignment explanation
Indices: 289944--290780 Score: 1460
Period size: 147 Copynumber: 5.7 Consensus size: 147
289934 GAGGTCTTAT
* * *
289944 CATCTTGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCTGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCAAAAAGCTCCCGAAGGCT
290009 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
65 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
290074 CCGAAGGCTTTTTGAAAA
130 CCGAAGGCTTTTTGAAAA
* *
290092 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAAATCATAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
290157 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
66 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
290222 CGAAGGCTTTTTTGAAAA
131 CGAAGGC-TTTTTGAAAA
* *
290240 CATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCAAAAAGCTCCCAAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
* * *
290305 TTTGAAAGCATCATGCACTGCAGGTCTTACAGATGACCATGAGGCTTTAAATATCAAAAAGCTCC
66 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
*
290370 CGAAGGTTTTTTTGAAAA
131 CGAAGG-CTTTTTGAAAA
*
290388 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTT-AAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
*
290452 TTTGAAAACATCATGCACTGTAGGTCTTATAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
66 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
*
290517 CGAAGGCTTTTTAAAAA
131 CGAAGGCTTTTTGAAAA
290534 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
** *
290599 TTTGAAAACATCATGCACTACAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTTC
66 TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
290664 CGAAGGCTTTTTGAAAA
131 CGAAGGCTTTTTGAAAA
* *
290681 CATCATGCGCTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCGAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
*
290746 TTTGAAAACATCATGCACTTTAGGTCTTACAGATG
66 TTTGAAAACATCATGCACTGTAGGTCTTACAGATG
290781 TGGGAAATAA
Statistics
Matches: 656, Mismatches: 30, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
146 48 0.07
147 379 0.58
148 229 0.35
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (147 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCAAAAAGCTCCCGAAGGCTT
TTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCC
CGAAGGCTTTTTGAAAA
Found at i:290337 original size:221 final size:221
Alignment explanation
Indices: 289944--290780 Score: 1439
Period size: 221 Copynumber: 3.8 Consensus size: 221
289934 GAGGTCTTAT
* * *
289944 CATCTTGCATTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCTGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
290009 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
66 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
*
290074 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTTAAAATCA
131 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCA
*
290139 TAAAGCTCCCGAAGGCTTTTTGAAAA
196 AAAAGCTCCCGAAGGCTTTTTGAAAA
290165 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGC-
*
290230 TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAA-ATCAAAAAGCT
65 TTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCT
* * *
290294 CCCAAAGGCTTTTTGAAAGCATCATGCACTGCAGGTCTTACAGATGACCATGAGGCTTTAAATAT
130 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAA-AT
*
290359 CAAAAAGCTCCCGAAGGTTTTTTTGAAAA
194 CAAAAAGCTCCCGAAGG-CTTTTTGAAAA
*
290388 CATCATGCACTGTAGGTCTTACAGATGACCTTGAGGCTTT-AA-ATCAAAAAGCTCCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
*
290451 TTTTGAAAACATCATGCACTGTAGGTCTTATAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
66 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
* *
290516 CCGAAGGCTTTTTAAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAATCA
131 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCA
290581 AAAAGCTCCCGAAGGCTTTTTGAAAA
196 AAAAGCTCCCGAAGGCTTTTTGAAAA
** *
290607 CATCATGCACTACAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTTCCGAAGGCT
1 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
* *
290672 TTTTGAAAACATCATGCGCTGTAGGTCTTACAGATGACCCTGAGGCTTTAAA-ATCGAAAAGCTC
66 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
*
290736 CCGAAGGCTTTTTGAAAACATCATGCACTTTAGGTCTTACAGATG
131 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
290781 TGGGAAATAA
Statistics
Matches: 582, Mismatches: 28, Indels: 13
0.93 0.04 0.02
Matches are distributed among these distances:
219 47 0.08
220 126 0.22
221 288 0.49
222 72 0.12
223 49 0.08
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (221 bp):
CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTCCCGAAGGCT
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCATGAGGCTTTAAAATCA
AAAAGCTCCCGAAGGCTTTTTGAAAA
Found at i:295760 original size:20 final size:20
Alignment explanation
Indices: 295735--295779 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
295725 CTTGATTCAA
295735 TTTTTTCTTT-TTTCTTGTTCT
1 TTTTTTCTTTCTTT-TT-TTCT
295756 TTTTTTCTTTCTTTTTTTCT
1 TTTTTTCTTTCTTTTTTTCT
295776 TTTT
1 TTTT
295780 CTCTGATGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.35
21 12 0.52
22 3 0.13
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (20 bp):
TTTTTTCTTTCTTTTTTTCT
Found at i:295761 original size:14 final size:13
Alignment explanation
Indices: 295737--295778 Score: 61
Period size: 12 Copynumber: 3.3 Consensus size: 13
295727 TGATTCAATT
295737 TTTTC-TTTTTTC
1 TTTTCTTTTTTTC
295749 TTGTTCTTTTTTTC
1 TT-TTCTTTTTTTC
295763 -TTTCTTTTTTTC
1 TTTTCTTTTTTTC
295775 TTTT
1 TTTT
295779 TCTCTGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 13 0.48
13 7 0.26
14 7 0.26
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.83
Consensus pattern (13 bp):
TTTTCTTTTTTTC
Found at i:298265 original size:15 final size:17
Alignment explanation
Indices: 298247--298278 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
298237 AAAACAATGT
298247 AATGTA-AAC-GCAAAA
1 AATGTATAACTGCAAAA
298262 AATGTATAACTGCAAAA
1 AATGTATAACTGCAAAA
298279 TAAGAATGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 3 0.20
17 6 0.40
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.19
Consensus pattern (17 bp):
AATGTATAACTGCAAAA
Found at i:300236 original size:5 final size:5
Alignment explanation
Indices: 300226--300254 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
300216 ATTTATTCAG
300226 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAA
300255 TTAAAAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:303834 original size:59 final size:59
Alignment explanation
Indices: 303667--304021 Score: 511
Period size: 59 Copynumber: 6.1 Consensus size: 59
303657 GATTACAAAA
* ** * *
303667 AGGGCACTTCATGTGCTAA-ATGTTAAGAAATTCATACTAAGTGCATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * *
303725 AGGGCATTTTGTGTGCTAAC-TGAGAAAGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
303783 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
*
303842 AGGGCACTACGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * *
303901 AGGGCACTACGTGTGCTAACATGGGAAGGAATTCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * ** *
303960 -GAGGCACCTT-GTGTGCTAAAATGATAACAAATTCATCCTAAGTGTATGAATTTCCATAT
1 AG-GGCA-CTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
304019 AGG
1 AGG
304022 AAATATATAT
Statistics
Matches: 270, Mismatches: 22, Indels: 9
0.90 0.07 0.03
Matches are distributed among these distances:
58 68 0.25
59 199 0.74
60 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:304510 original size:56 final size:55
Alignment explanation
Indices: 304431--304572 Score: 153
Period size: 55 Copynumber: 2.5 Consensus size: 55
304421 TGAACATGAT
* **
304431 TTCATACTAAGTGTATGAATTTCCATATAGGGCACTACGTGTGCTAACATGGGAAGGAA
1 TTCATACTAA--GTATGAATTTCCATATAGGGCACT-CGTGTGCTAA-ATGAGAACAAA
* * *
304490 TTCATACTAA-TATGAATTTCCAGAT-GAGGCACTTGTGTGCTAAATGATAACAAA
1 TTCATACTAAGTATGAATTTCCATATAG-GGCACTCGTGTGCTAAATGAGAACAAA
* *
304544 TTCATCCTAAGTGTGAATTTCCATATAGG
1 TTCATACTAAGTATGAATTTCCATATAGG
304573 AAATATATGT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
54 16 0.23
55 24 0.34
56 21 0.30
59 10 0.14
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (55 bp):
TTCATACTAAGTATGAATTTCCATATAGGGCACTCGTGTGCTAAATGAGAACAAA
Found at i:304991 original size:68 final size:68
Alignment explanation
Indices: 304911--305515 Score: 1004
Period size: 68 Copynumber: 9.0 Consensus size: 68
304901 AAAAGATTTA
* * *
304911 AGGCCTAACTGTGCATTTGACAAAAAGGTGTTAATTATGCCAGTTAGATGAAAGGCTGAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
304976 TTG
66 TTG
*
304979 AGGCCTAACTGTGCATTTGACAGAAAGGTATCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305044 TTG
66 TTG
*
305047 AGGCCTAACTGTGCATTTGTCAGAAA--TGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305110 TTG
66 TTG
*
305113 AGGCCTAACTGTGCATTTGAC--AAAGGCGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305176 TTG
66 TTG
* *
305179 AGGCCTAACTGTGCATTTGACAGCAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305244 TTG
66 TTG
* * * *
305247 TGGCCTAACTTTGCA-TTGACAGAAAGGTGTTAATTATGCTAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305311 TTG
66 TTG
*
305314 AGGCCTAACTGTGCATTTGACAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305379 TTG
66 TTG
* * * *
305382 AGGCCTAACTATGCATTTGACATAAAGGTGTCAATTATACCAGTTACATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305447 TTG
66 TTG
**
305450 AGGCCTAGTTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
305515 T
66 T
305516 GAGTAAAAGA
Statistics
Matches: 499, Mismatches: 33, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
64 3 0.01
66 119 0.24
67 61 0.12
68 316 0.63
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TTG
Found at i:305603 original size:45 final size:45
Alignment explanation
Indices: 305539--305676 Score: 186
Period size: 45 Copynumber: 3.0 Consensus size: 45
305529 GATGTATAAC
* *
305539 AATGTATAATGATGTATAAAAGGCATGAAAGGATGCCATAAATGA
1 AATGTATAAAGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * * *
305584 AATGTATAACGGTGTATAAAAGACATGAAATGATGCCATAAATAA
1 AATGTATAAAGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
* * *
305629 AATGTATAAAAGTGTATAAAAAGGCATGAATGGTTGCCATAAATGA
1 AATGTATAAAGGTGTAT-AAAAGGCATGAAAGGATGCCATAAATGA
305675 AA
1 AA
305677 ATGCATAATG
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
45 55 0.69
46 25 0.31
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (45 bp):
AATGTATAAAGGTGTATAAAAGGCATGAAAGGATGCCATAAATGA
Found at i:306808 original size:19 final size:20
Alignment explanation
Indices: 306768--306816 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
306758 TAGAAAAATA
306768 ATATATATATAAACACTATT
1 ATATATATATAAACACTATT
*
306788 ATATATA-ATAACATACT-TT
1 ATATATATATAA-ACACTATT
306807 ATATATATAT
1 ATATATATAT
306817 TGAACCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (20 bp):
ATATATATATAAACACTATT
Found at i:307037 original size:27 final size:27
Alignment explanation
Indices: 307005--307060 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 27
306995 TAAGTTATGG
307005 AGCCAGAGAAGCAAGCAGCCGTGGAGA
1 AGCCAGAGAAGCAAGCAGCCGTGGAGA
* * *
307032 AGCCAGATAATCAGGCAGCCGTGGAGA
1 AGCCAGAGAAGCAAGCAGCCGTGGAGA
307059 AG
1 AG
307061 GGAAGTTGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.36, C:0.21, G:0.36, T:0.07
Consensus pattern (27 bp):
AGCCAGAGAAGCAAGCAGCCGTGGAGA
Found at i:310597 original size:17 final size:18
Alignment explanation
Indices: 310575--310608 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
310565 GAGGTAGGGA
*
310575 CTCTCGGTTTT-TGGGGG
1 CTCTCGATTTTGTGGGGG
310592 CTCTCGATTTTGTGGGG
1 CTCTCGATTTTGTGGGG
310609 TTCTCAGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.03, C:0.18, G:0.38, T:0.41
Consensus pattern (18 bp):
CTCTCGATTTTGTGGGGG
Found at i:310748 original size:2 final size:2
Alignment explanation
Indices: 310743--310770 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
310733 TAACACCTAG
310743 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
310771 TCGAACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:315883 original size:14 final size:14
Alignment explanation
Indices: 315860--315897 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
315850 TCTGTCTATA
*
315860 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
315873 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
315888 TGCAGGGATT
1 TGCAGGGATT
315898 ACTTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:318304 original size:36 final size:36
Alignment explanation
Indices: 318215--318361 Score: 138
Period size: 36 Copynumber: 4.0 Consensus size: 36
318205 ACAAAGTGTC
* * * *
318215 GTCTCGCTAGAGACATTTTTTCTTAAAAATAAATTTT
1 GTCTCGCTTGAGACAATTTTT-TTAAGAACAAATTTT
318252 GTCTCGCTTGA-A-AATTTTTTTAAGAACAAATTTT
1 GTCTCGCTTGAGACAATTTTTTTAAGAACAAATTTT
* * * *
318286 GTCTCACTTGAGACAATTTCTCTCAA-AACAAATTTC
1 GTCTCGCTTGAGACAATTT-TTTTAAGAACAAATTTT
* *
318322 GTCTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTT
1 GTCTCGCTTGAGACAATTTT--TTTAAGA-ACAAATTTT
318361 G
1 G
318362 AATTTAAACA
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
34 23 0.26
35 8 0.09
36 32 0.36
37 16 0.18
38 1 0.01
39 9 0.10
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (36 bp):
GTCTCGCTTGAGACAATTTTTTTAAGAACAAATTTT
Found at i:318642 original size:16 final size:16
Alignment explanation
Indices: 318621--318655 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
318611 CAAAATTTGG
318621 AAATTGTTTCACTTGA
1 AAATTGTTTCACTTGA
318637 AAATTGTTTCACTTGA
1 AAATTGTTTCACTTGA
318653 AAA
1 AAA
318656 AATATCTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.40
Consensus pattern (16 bp):
AAATTGTTTCACTTGA
Found at i:318711 original size:36 final size:35
Alignment explanation
Indices: 318663--318888 Score: 168
Period size: 36 Copynumber: 6.7 Consensus size: 35
318653 AAAAATATCT
* *
318663 TTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAAC-AATTTTATCTCTC
* * *
318699 TTGAGATAGTTTCTCTGGAAAC-A--TCAT-T-T-
1 TTGAGATAGTTTCCCTTGAAACAATTTTATCTCTC
* * *
318728 TTAAGATCGTTTCCCTTAAAACAAATTTTATCTCTC
1 TTGAGATAGTTTCCCTTGAAAC-AATTTTATCTCTC
* * **
318764 TTAAGATAGTTTCTCTTGAAA-AA--AAAT-TC-C
1 TTGAGATAGTTTCCCTTGAAACAATTTTATCTCTC
* * * *
318794 TTGAGTTTGTTTCCCTTGAAACAAGTTTTGTCTCCC
1 TTGAGATAGTTTCCCTTGAAACAA-TTTTATCTCTC
*
318830 TTGAGATAGTTTCCCTTGAAACAAGTTTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAACAA-TTTTATCTCTC
* *
318866 TTGAGACAGTTTCTCTTGAAACA
1 TTGAGATAGTTTCCCTTGAAACA
318889 TTATCCCTAA
Statistics
Matches: 149, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
29 17 0.11
30 19 0.13
31 6 0.04
32 4 0.03
33 3 0.02
34 5 0.03
35 3 0.02
36 92 0.62
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (35 bp):
TTGAGATAGTTTCCCTTGAAACAATTTTATCTCTC
Found at i:318742 original size:65 final size:65
Alignment explanation
Indices: 318666--318853 Score: 225
Period size: 65 Copynumber: 2.9 Consensus size: 65
318656 AATATCTTTG
* ** *
318666 AGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGATAGTTTCTCTGGAAACATCATT-TTT
1 AGATCGTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTCCTT
318730 A
65 A
* * * *
318731 AGATCGTTTCCCTTAAAACAAATTTTATCTCTCTTAAGATAGTTTCTCTTGAAAAAAAATTCCTT
1 AGATCGTTTCCCTTGAAAC-AATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTCCTT
*
318796 G
65 A
* * * *
318797 AGTTTGTTTCCCTTGAAACAAGTTTTGTCTCCCTTGAGATAGTTTCCCTTGAAACAA
1 AGATCGTTTCCCTTGAAACAA-TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAA
318854 GTTTTGTCTC
Statistics
Matches: 103, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
65 55 0.53
66 48 0.47
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (65 bp):
AGATCGTTTCCCTTGAAACAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAAATTCCTTA
Found at i:319383 original size:134 final size:133
Alignment explanation
Indices: 318912--319367 Score: 592
Period size: 134 Copynumber: 3.4 Consensus size: 133
318902 TTCCTAGCCG
* * *
318912 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACATAGGAGCCGCATAA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
** * *
318977 CCCCAAGATAACAAGCCGTCCTCATCGCGTAGGAACCGTGTTATCATCATCCCTAAAGATGGCCA
66 CCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCATCAT-CCTAAAGATGGCCA
319042 ACCA
130 ACCA
* * * *
319046 TCCTCATCATGTAGGAACCGTGTCATCCACCGACCAAATCTCCTCATCACGTAGAAGCCACGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
* * *
319111 CCCTTAGATAACCAGCTGTCCTCATCACGTAAGAACCGTGTTATCATC--CCTAAAGACGGCCAA
66 CCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCATCATCCTAAAGATGGCCAA
*
319174 TCA
131 CCA
* ** * * * *
319177 TCCTCATCACATAGGAATTGTGTCATCCCCCAACCAGATCTCCTCATCACGTAGGAGTCGCGCCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
* * * * *
319242 ACCTTAGATAACCAGCCATCCTCATCGCATAAGAATCGTGTTATCATCAATCCTAAAGATGGTCA
66 CCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCATC-ATCCTAAAGATGGCCA
*
319307 GCCA
130 ACCA
* * * *
319311 TCCTCATCGCGTAGAAACCGTGTCATCTACCGACCATATCTCCTCATCACGTAGGAG
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAG
319368 TTGTGTCATC
Statistics
Matches: 274, Mismatches: 45, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
131 112 0.41
134 162 0.59
ACGTcount: A:0.29, C:0.33, G:0.16, T:0.22
Consensus pattern (133 bp):
TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGAGCCGCGTCA
CCCTTAGATAACCAGCCGTCCTCATCGCGTAAGAACCGTGTTATCATCATCCTAAAGATGGCCAA
CCA
Found at i:324675 original size:17 final size:17
Alignment explanation
Indices: 324653--324686 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
324643 CCTTGCATCT
324653 TCAAATAAGC-CGATAGA
1 TCAAATAA-CTCGATAGA
324670 TCAAATAACTCGATAGA
1 TCAAATAACTCGATAGA
324687 ATAGATCCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (17 bp):
TCAAATAACTCGATAGA
Found at i:326176 original size:2 final size:2
Alignment explanation
Indices: 326169--326211 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
326159 TTACGTTCCA
326169 AT AT AT AT AT AT 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 AT AT AT AT AT AT
326211 A
1 A
326212 CGTGCCAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:327006 original size:12 final size:12
Alignment explanation
Indices: 326989--327015 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
326979 TGCATGATAC
326989 ATATAATATAAT
1 ATATAATATAAT
327001 ATATAATATAAT
1 ATATAATATAAT
327013 ATA
1 ATA
327016 GTTATACAAT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:330499 original size:55 final size:55
Alignment explanation
Indices: 330439--330814 Score: 478
Period size: 55 Copynumber: 6.9 Consensus size: 55
330429 AACGAGTTCA
* * *
330439 CTCCCTCTTTCTTCAGGGAGTAT-AGAACTCGAACAATCTTCATCAATCGTGTTTG
1 CTCCCTATTTCTTCAGAGAGTATAAG-ACTCGAACAATCTTCATCAATCGTGTCTG
* * * * * *
330494 TTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAACTCTTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAA-TCGTGTCTG
* *
330550 CTCCCTATTTCTTCAGAGAGTATAAGACCCGAACAATCTTCATCAACCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
330605 CTCCC-ATTCCTTCAGAGAG-ATAAGACTTGAATAATCTTCATCAATCGTGT-TG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
330657 --CCCTATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAACAGTCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* *
330710 CTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATTTTCATCAATCGTGTCTG
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
* * *
330765 CTCCCCATTCCTTCAGAGAGTATAAGACTCGATCAATCTTCAAT-AATCGT
1 CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC-ATCAATCGT
330815 TGGGAAATCT
Statistics
Matches: 279, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
50 3 0.01
51 12 0.04
52 29 0.10
53 29 0.10
54 13 0.05
55 140 0.50
56 53 0.19
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (55 bp):
CTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCATCAATCGTGTCTG
Found at i:330745 original size:160 final size:165
Alignment explanation
Indices: 330449--330814 Score: 525
Period size: 160 Copynumber: 2.2 Consensus size: 165
330439 CTCCCTCTTT
* *
330449 CTTCAGGGAGTAT-AGAACTCGAACAATCTTCATCAATCGTGTTTGTTCCCTATTTCCTCAGAGA
1 CTTCAGAGAGTATAAG-ACTCGATCAATCTTCATCAATCGTGTTTG-TCCCTATTTCCTCAGAGA
* *
330513 GTATAAGACCCAAACAATCTTCAACAACTCTTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGAC
64 GTATAAGACCCAAACAATCTTCAACAACTCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGAC
330578 CCGAACAATCTTCATCAACCGTGTCTGCT-CCCATTC
129 CCGAACAATCTTCATCAACCGTGTCTGCTCCCCATTC
*
330614 CTTCAGAGAG-ATAAGACTTGAAT-AATCTTCATCAATCGTG-TTG-CCCTATTT-CTGCAGAGA
1 CTTCAGAGAGTATAAGACTCG-ATCAATCTTCATCAATCGTGTTTGTCCCTATTTCCT-CAGAGA
* * *
330674 GTATAAGACTCGAACAATCTTCAAC-AGTCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGAC
64 GTATAAGACCCAAACAATCTTCAACAACTCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGAC
* * *
330738 TCGAACAATTTTCATCAATCGTGTCTGCTCCCCATTC
129 CCGAACAATCTTCATCAACCGTGTCTGCTCCCCATTC
330775 CTTCAGAGAGTATAAGACTCGATCAATCTTCAAT-AATCGT
1 CTTCAGAGAGTATAAGACTCGATCAATCTTC-ATCAATCGT
330815 TGGGAAATCT
Statistics
Matches: 182, Mismatches: 12, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
160 64 0.35
161 56 0.31
162 22 0.12
163 5 0.03
164 23 0.13
165 12 0.07
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (165 bp):
CTTCAGAGAGTATAAGACTCGATCAATCTTCATCAATCGTGTTTGTCCCTATTTCCTCAGAGAGT
ATAAGACCCAAACAATCTTCAACAACTCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACCC
GAACAATCTTCATCAACCGTGTCTGCTCCCCATTC
Done.