Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008374.1 Hibiscus syriacus cultivar Beakdansim tig00111131_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: 1731758
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:367112 original size:50 final size:50
Alignment explanation
Indices: 367037--367277 Score: 482
Period size: 50 Copynumber: 4.8 Consensus size: 50
367027 TGAATTTGCC
367037 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
367087 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
367137 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
367187 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
367237 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
367278 TTTTGGTAAG
Statistics
Matches: 191, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 191 1.00
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (50 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAG
Found at i:368161 original size:114 final size:114
Alignment explanation
Indices: 367961--368709 Score: 1444
Period size: 114 Copynumber: 6.5 Consensus size: 114
367951 TGCAAGGTAG
*
367961 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
368026 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
368075 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
368140 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
368189 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
368254 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
368303 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
368368 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
368417 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
368482 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
368531 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
368596 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGGAA
66 AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGA-GAA
368646 GAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
1 -AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
368710 CATCAAGAGC
Statistics
Matches: 629, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
114 566 0.90
115 3 0.00
116 18 0.03
118 1 0.00
119 41 0.07
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (114 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTGAATTCATCACTTGATGGATCATTCTTTTCCAGAGAA
Found at i:368964 original size:3 final size:3
Alignment explanation
Indices: 368956--369037 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
368946 TTTTTATCCA
*
368956 TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
369003 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
369038 ATTTATATTA
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 74 0.97
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:370496 original size:22 final size:20
Alignment explanation
Indices: 370455--370499 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
370445 ATAGAATTAT
**
370455 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
370475 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
370497 TAT
1 TAT
370500 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:374175 original size:29 final size:29
Alignment explanation
Indices: 374117--374175 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
374107 TAATAAACCT
* *
374117 AATTTAAAAAAATAAAATAGCAAATAAAA
1 AATTAAAAAAAATAAAATAACAAATAAAA
374146 AATTAAAAAACAATAAAA-AACAACATAAAA
1 AATTAAAAAA-AATAAAATAACAA-ATAAAA
374176 TAACAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.17
Consensus pattern (29 bp):
AATTAAAAAAAATAAAATAACAAATAAAA
Found at i:374177 original size:17 final size:17
Alignment explanation
Indices: 374123--374197 Score: 53
Period size: 17 Copynumber: 4.2 Consensus size: 17
374113 ACCTAATTTA
*
374123 AAAAAATAAAATAGCAAAT
1 AAAAAACAAAATA--AAAT
*
374142 AAAAAATTAAAA-AACAAT
1 AAAAAA-CAAAATAA-AAT
*
374160 AAAAAACAACATAAAAT
1 AAAAAACAAAATAAAAT
* *
374177 AACAAATAAAATAAACAT
1 AAAAAACAAAATAAA-AT
374195 AAA
1 AAA
374198 TACAATGACC
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
17 19 0.41
18 15 0.33
19 7 0.15
20 5 0.11
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.15
Consensus pattern (17 bp):
AAAAAACAAAATAAAAT
Found at i:374187 original size:23 final size:22
Alignment explanation
Indices: 374122--374197 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 22
374112 AACCTAATTT
*
374122 AAAAAA-ATAAAATAGCAAAT-
1 AAAAAACATAAAATAACAAATA
*
374142 AAAAAA-TTAAAA-AAC-AATAA
1 AAAAAACATAAAATAACAAAT-A
374162 AAAACAACATAAAATAACAAATA
1 AAAA-AACATAAAATAACAAATA
374185 AAATAAACATAAA
1 AAA-AAACATAAA
374198 TACAATGACC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.07
19 2 0.04
20 15 0.33
21 2 0.04
22 5 0.11
23 15 0.33
24 4 0.09
ACGTcount: A:0.76, C:0.08, G:0.01, T:0.14
Consensus pattern (22 bp):
AAAAAACATAAAATAACAAATA
Found at i:374188 original size:12 final size:12
Alignment explanation
Indices: 374138--374190 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
374128 ATAAAATAGC
*
374138 AAATAAAAAATTA
1 AAATAACAAA-TA
374151 AAA-AAC-AATA
1 AAATAACAAATA
374161 AAA-AACAACATA
1 AAATAACAA-ATA
374173 AAATAACAAATA
1 AAATAACAAATA
374185 AAATAA
1 AAATAA
374191 ACATAAATAC
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
10 8 0.22
11 3 0.08
12 17 0.47
13 8 0.22
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAATAACAAATA
Found at i:377653 original size:13 final size:13
Alignment explanation
Indices: 377635--377661 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
377625 TAGACCAAGT
377635 GTATCACCTTGGG
1 GTATCACCTTGGG
377648 GTATCACCTTGGG
1 GTATCACCTTGGG
377661 G
1 G
377662 AGCTCCTGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.22, G:0.33, T:0.30
Consensus pattern (13 bp):
GTATCACCTTGGG
Found at i:381256 original size:64 final size:64
Alignment explanation
Indices: 381107--381264 Score: 169
Period size: 64 Copynumber: 2.5 Consensus size: 64
381097 TTGAAGGTGT
* *** *
381107 ATCGATGCACATGTAGTGCATCGATGCACTCTTTTTAAAATAAAAAGATCGAATACAATTAGTGC
1 ATCGATGCACAAGTAGTGCATCGATGCA-TCCCATTAAAATAAAAACATCGAATACAATTAGTGC
* * * * *
381172 ATCGATGCATAAGGCA-TGCATCGATGCATCCCATTAATAAT-AAATCATCGAATGCATTTTA-T
1 ATCGATGCACAA-GTAGTGCATCGATGCATCCCATTAA-AATAAAAACATCGAATACA-ATTAGT
381234 GC
63 GC
381236 ATCGATGCACAAGTAGTGCATCGATGCAT
1 ATCGATGCACAAGTAGTGCATCGATGCAT
381265 ACCTTCATTA
Statistics
Matches: 77, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
63 2 0.03
64 45 0.58
65 28 0.36
66 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (64 bp):
ATCGATGCACAAGTAGTGCATCGATGCATCCCATTAAAATAAAAACATCGAATACAATTAGTGC
Found at i:382007 original size:42 final size:42
Alignment explanation
Indices: 381929--382008 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
381919 CTTATCATCT
* * * *
381929 TGCTCGAAAGACTTATAGATGACTCGAAGGATTTAAGCACCA
1 TGCTCGAAAGACTTATAGATGACCCAAAAGACTTAAGCACCA
*
381971 TGCTCGAAAGACTTACT-GATGGCCCAAAAGACTTAAGC
1 TGCTCGAAAGACTTA-TAGATGACCCAAAAGACTTAAGC
382009 TGATTCAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
42 31 0.97
43 1 0.03
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (42 bp):
TGCTCGAAAGACTTATAGATGACCCAAAAGACTTAAGCACCA
Found at i:383018 original size:21 final size:22
Alignment explanation
Indices: 382994--383039 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
382984 ACAAGAAACG
*
382994 AAATTATGC-ATGTAAGAATGT
1 AAATTATGCAATGTAAGAATGA
383015 AAA-TATGCAATGTAAGAATGA
1 AAATTATGCAATGTAAGAATGA
383036 AAAT
1 AAAT
383040 AACAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.28
Consensus pattern (22 bp):
AAATTATGCAATGTAAGAATGA
Found at i:383817 original size:15 final size:15
Alignment explanation
Indices: 383785--383854 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
383775 TAATATTTTC
*
383785 ATAATATAATAATATA
1 ATAATAT-ATATTATA
*
383801 ATCAAT-TCTATTATA
1 AT-AATATATATTATA
383816 ATAATATATATTATA
1 ATAATATATATTATA
* *
383831 AT-ATTTTTAATT-TA
1 ATAATATAT-ATTATA
383845 ATAATATATA
1 ATAATATATA
383855 ATAAATTATT
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
14 12 0.28
15 25 0.58
16 3 0.07
17 3 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATATATATTATA
Found at i:383865 original size:52 final size:53
Alignment explanation
Indices: 383764--383968 Score: 132
Period size: 52 Copynumber: 3.9 Consensus size: 53
383754 TTAATTATTA
*
383764 AATATATTTATTAATATTTTCATAATATAATAATATAATCAATTCTATTATAAT
1 AATATATTTATTAATATTTT-ATAATATAATAATATAATCAAATCTATTATAAT
*
383818 AATATATATTA-TAATATTTT-TAATTTAATAATATATAAT-AAAT-TATTAATAAATT
1 AATATAT-TTATTAATATTTTATAATATAAT-A-ATATAATCAAATCTATT-AT-AA-T
* * * *
383873 TATATTATTTATTAAT-TTTTATAA-A-AATAATGTTATTAAA-CTATTAGTAAT
1 AATA-TATTTATTAATATTTTATAATATAATAATATAATCAAATCTATTA-TAAT
* * *
383924 GAATGATA-TTATTTATGTATT-TAATAT--TAATATAAT--AATCTATTA
1 -AAT-ATATTTATTAATATTTTATAATATAATAATATAATCAAATCTATTA
383969 ATATTTTTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 40
0.71 0.06 0.23
Matches are distributed among these distances:
49 2 0.02
50 6 0.05
51 18 0.15
52 28 0.23
53 16 0.13
54 28 0.23
55 14 0.11
56 10 0.08
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (53 bp):
AATATATTTATTAATATTTTATAATATAATAATATAATCAAATCTATTATAAT
Found at i:387382 original size:30 final size:30
Alignment explanation
Indices: 387347--387406 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
387337 CAAACGAGAC
* *
387347 AAAAAGTCAACGA-TGGGTACTAAAATGAAA
1 AAAAAGTCAAC-ATTAGATACTAAAATGAAA
*
387377 AAAAAGTTAACATTAGATACTAAAATGAAA
1 AAAAAGTCAACATTAGATACTAAAATGAAA
387407 TAAAGAGTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 1 0.04
30 25 0.96
ACGTcount: A:0.57, C:0.08, G:0.15, T:0.20
Consensus pattern (30 bp):
AAAAAGTCAACATTAGATACTAAAATGAAA
Found at i:390202 original size:35 final size:35
Alignment explanation
Indices: 390149--390247 Score: 94
Period size: 44 Copynumber: 2.6 Consensus size: 35
390139 CTTAGATTTG
*
390149 ATGTTGAAGC-ATT-CCAACTTATTTTATAAAACT
1 ATGTTGGAGCTATTACCAACTTATTTTATAAAACT
390182 ATGTTGGAGCTATTACCAACTTTTCCAACTTATTTTATAAAACT
1 ATGTTGGAGCTATT----A-----CCAACTTATTTTATAAAACT
390226 ATGTTGGAGCTATTACCAACTT
1 ATGTTGGAGCTATTACCAACTT
390248 TTCCAACTTA
Statistics
Matches: 54, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
33 9 0.17
34 3 0.06
35 7 0.13
40 1 0.02
44 34 0.63
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (35 bp):
ATGTTGGAGCTATTACCAACTTATTTTATAAAACT
Found at i:390223 original size:44 final size:44
Alignment explanation
Indices: 390160--390260 Score: 202
Period size: 44 Copynumber: 2.3 Consensus size: 44
390150 TGTTGAAGCA
390160 TTCCAACTTATTTTATAAAACTATGTTGGAGCTATTACCAACTT
1 TTCCAACTTATTTTATAAAACTATGTTGGAGCTATTACCAACTT
390204 TTCCAACTTATTTTATAAAACTATGTTGGAGCTATTACCAACTT
1 TTCCAACTTATTTTATAAAACTATGTTGGAGCTATTACCAACTT
390248 TTCCAACTTATTT
1 TTCCAACTTATTT
390261 GTATTTTTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.31, C:0.19, G:0.08, T:0.43
Consensus pattern (44 bp):
TTCCAACTTATTTTATAAAACTATGTTGGAGCTATTACCAACTT
Found at i:397394 original size:2 final size:2
Alignment explanation
Indices: 397387--397453 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
397377 CTTATAAATA
397387 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
397429 AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
397454 TTTAATAAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:397739 original size:16 final size:15
Alignment explanation
Indices: 397709--397760 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
397699 AAAATATGTT
397709 TATAAAAGTAATTTA
1 TATAAAAGTAATTTA
*
397724 TATAAAATTAAATTTA
1 TATAAAAGT-AATTTA
* * *
397740 T-TAATAGGATTTTA
1 TATAAAAGTAATTTA
397754 TATAAAA
1 TATAAAA
397761 AATAAATAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 6 0.21
15 16 0.55
16 7 0.24
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
TATAAAAGTAATTTA
Found at i:399186 original size:3 final size:3
Alignment explanation
Indices: 399178--399300 Score: 130
Period size: 3 Copynumber: 41.0 Consensus size: 3
399168 TTTGGGCATG
* * *
399178 TAA TAA TAA T-T TAA TTAA TAA TAA TAA TTAA TTAA TAA T-T TAA TTA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA
*
399224 -AA TAA T-A TAA TAAA TAA TAAA TAA TAA TAA TAA TAG TAA T-A TAA
1 TAA TAA TAA TAA T-AA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
399268 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
399301 ACCAAATGAA
Statistics
Matches: 103, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
2 7 0.07
3 80 0.78
4 16 0.16
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:399214 original size:29 final size:27
Alignment explanation
Indices: 399181--399299 Score: 127
Period size: 29 Copynumber: 4.3 Consensus size: 27
399171 GGGCATGTAA
*
399181 TAATAATTTAATTAATAATAATAATTAAT
1 TAATAATATAA-TAATAATAATAA-TAAT
* *
399210 TAATAATTTAATTAAATAAT-ATAATAAA
1 TAATAATATAA-T-AATAATAATAATAAT
*
399238 TAATAA-ATAATAATAATAATAGTAAT
1 TAATAATATAATAATAATAATAATAAT
399264 ATAATAATAATAATAATAATAATAATAA-
1 -TAATAAT-ATAATAATAATAATAATAAT
399292 TAATAATA
1 TAATAATA
399300 AACCAAATGA
Statistics
Matches: 80, Mismatches: 5, Indels: 13
0.82 0.05 0.13
Matches are distributed among these distances:
25 6 0.08
26 8 0.10
27 16 0.20
28 9 0.11
29 35 0.44
30 6 0.08
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
TAATAATATAATAATAATAATAATAAT
Found at i:400976 original size:54 final size:54
Alignment explanation
Indices: 400889--401050 Score: 236
Period size: 54 Copynumber: 3.0 Consensus size: 54
400879 ATAATTACTG
* * * *
400889 GTTCATAAAACATTTGACAACACATTTATCCTTTCTTGTGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGATTCTGCACAGAT
*
400943 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGT-GATTCATGCACATAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGATTC-TGCACAGAT
* * *
400997 GTTCGTAAAACATTTGACAACGCATTCATCCTTTCCTGTGGTTTTTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGATTCTGCACAGAT
401051 TTTTTCTCTG
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 4 0.04
54 90 0.93
55 3 0.03
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGATTCTGCACAGAT
Found at i:412904 original size:23 final size:23
Alignment explanation
Indices: 412866--412933 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
412856 TTTTAAGAAA
*
412866 ATATA-TTAAATTTTATAAATAT
1 ATATATTTATATTTTATAAATAT
412888 ATATATTTATATTTTATAAATA-
1 ATATATTTATATTTTATAAATAT
*
412910 AGATATTTAT-TTACTTATAAATAT
1 ATATATTTATATT--TTATAAATAT
412934 CAGAAAAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
21 2 0.05
22 14 0.35
23 24 0.60
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
ATATATTTATATTTTATAAATAT
Found at i:414645 original size:3 final size:3
Alignment explanation
Indices: 414637--414729 Score: 97
Period size: 3 Copynumber: 32.0 Consensus size: 3
414627 TTTGTACCTG
* *
414637 TAA TAA TAA T-T TAA TTAT TAA TAA TAA TAA -AA -AA TATA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
* *
414681 TAA -AA AAA TAA TAG TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
414727 TAA
1 TAA
414730 ACCAAATGAA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
2 9 0.12
3 63 0.82
4 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:414679 original size:17 final size:16
Alignment explanation
Indices: 414655--414729 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
414645 ATTTAATTAT
414655 TAATAATAATAAAAAA
1 TAATAATAATAAAAAA
414671 TATATAATAATAAAAAAA
1 TA-ATAATAAT-AAAAAA
* *
414689 TAATAGTAATATAATAA
1 TAATAATAATA-AAAAA
*
414706 TAATAATAAT-AATAA
1 TAATAATAATAAAAAA
414721 TAATAATAA
1 TAATAATAA
414730 ACCAAATGAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.26
16 3 0.06
17 28 0.53
18 8 0.15
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (16 bp):
TAATAATAATAAAAAA
Found at i:419937 original size:466 final size:464
Alignment explanation
Indices: 418968--420108 Score: 1842
Period size: 466 Copynumber: 2.5 Consensus size: 464
418958 ACAAGTAAGA
** * ** ** *
418968 TAAAGCCTTTGCTCGAAGTACATTTTACAAAAAATACTGAAACAAAAAGAAATAAAACACAAACT
1 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAA-AAAGGGAAATGCAATACAAACT
* * * * *
419033 TCAAAGCCAAAAACGGAGCTCTATTTTTTAACAATAGAACAGAGAAACTTGTCCTCTG-TTTTAA
65 TCAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGAAACTTCTCCTTTGTTTTTAA
* *
419097 ACAACAAAGTACATTTTAAAATCAACCATAAAGGATAAAAGAACTAAAAG-A-AAAAAATAGTAG
130 ACAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAG
* *
419160 AATAGATAGAGACTCAAGGAAAAAAGTGAAGGCGACAGCGTTAAGGTTTAAAGAGAGTGCGAAGG
195 AATAGAT--AGACTCAAGGAAAAAAGTAAAGGCGACAGCGTTAAGATTTAAAGAGAGTGCGAAGG
*
419225 TGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGGGATAGCTTATTTTTAG
258 TGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTATTTTTAG
*
419290 TCAGTGTTGTCAAGGGCACCAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATAT
323 TCAGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATAT
*
419355 GGAGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATGCATATAAAAATATTTATAATGCATG
388 GGAGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCATG
419420 TAGACGTAAAAT
453 TAGACGTAAAAT
*
419432 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAAGGCAATACAAACTT
1 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAATGCAATACAAACTT
* *
419497 CAAAGCCAAAAACCGAGCTCTATTTTTTAACGCTAAAACAGAAAAACTTCTCCTTTGTTTTTTAA
66 CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGAAACTTCTCCTTTG-TTTTTAA
419562 ACAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAG
130 ACAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAG
* *
419627 AATAGATAGACTCAAGGAAAAAAAAAGTAAAGGTGACAGCGTTAAGATTTAAAGAGGGTGCGAAG
195 AATAGATAGACTCAAGG---AAAAAAGTAAAGGCGACAGCGTTAAGATTTAAAGAGAGTGCGAAG
419692 GTGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTA-TTTTA
257 GTGAGTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTATTTTTA
* ** *
419756 GTCCGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGAGTTCTATATAGCCTGAGGCATA
322 GTCAGTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATA
* * *
419821 TGG-TCAAAAAAGCGCTTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCAT
387 TGGAGCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCAT
419885 GTAGACGTAAAAT
452 GTAGACGTAAAAT
* *
419898 TAAAGTCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGTAAATGCAATACAAACTT
1 TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAATGCAATACAAACTT
* *
419963 CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAATAGAGCAACTTCTCCTTTGTTTTTAAA
66 CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGAAACTTCTCCTTTGTTTTTAAA
*
420028 CAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAATTAGTAGA
131 CAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAGA
*
420093 ATAGGTAGACTCAAGG
196 ATAGATAGACTCAAGG
420109 GGGAAAAAGT
Statistics
Matches: 629, Mismatches: 41, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
463 67 0.11
464 39 0.06
465 151 0.24
466 186 0.30
467 87 0.14
468 99 0.16
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (464 bp):
TAAAGCCTTTGCTCGAAGTACATTTTAGGAAAAATAATGAAAAAAGGGAAATGCAATACAAACTT
CAAAGCCAAAAACCGAGCTCTATTTTTTAACACTAAAACAGAGAAACTTCTCCTTTGTTTTTAAA
CAACAAAGTACACTTTAAAATCAACCATAAAGGAGAAAAGAACTAAAAGAAGAAAAAATAGTAGA
ATAGATAGACTCAAGGAAAAAAGTAAAGGCGACAGCGTTAAGATTTAAAGAGAGTGCGAAGGTGA
GTTAAATATTTTAATTTATTAGAACTTAGTATTGTTATTTCATTGAGATAGCTTATTTTTAGTCA
GTGTTGTCAAGGGCAACAGGTGCACTAGAGGCGCTAAGACCTCTAAATAGCCTGAGGCATATGGA
GCAAAAAAGCACGTGCCCGGTTGAAATAAGGTGCATACATATAAAAATATTTATAATGCATGTAG
ACGTAAAAT
Found at i:426083 original size:18 final size:18
Alignment explanation
Indices: 426060--426115 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
426050 TAATCATATT
426060 CCTGGTAATCTTACATTC
1 CCTGGTAATCTTACATTC
426078 CCTGGTAATC-TACATTC
1 CCTGGTAATCTTACATTC
*
426095 ACACTGGTAATCTCACATTC
1 -C-CTGGTAATCTTACATTC
426115 C
1 C
426116 GTGAACCAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
17 7 0.21
18 11 0.32
19 10 0.29
20 6 0.18
ACGTcount: A:0.25, C:0.30, G:0.11, T:0.34
Consensus pattern (18 bp):
CCTGGTAATCTTACATTC
Found at i:426541 original size:11 final size:10
Alignment explanation
Indices: 426527--426602 Score: 53
Period size: 11 Copynumber: 7.0 Consensus size: 10
426517 GGAAAATTAG
426527 AAAAAAATACA
1 AAAAAAATA-A
426538 AAAAAAATAA
1 AAAAAAATAA
* *
426548 ATAAAAATATT
1 AAAAAAATA-A
* *
426559 AAATAAACAA
1 AAAAAAATAA
426569 AAAATAAATGCAA
1 AAAA-AAAT--AA
426582 AATAAAAATAA
1 AA-AAAAATAA
*
426593 AAAATAATAA
1 AAAAAAATAA
426603 GAAGTAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
10 19 0.37
11 22 0.43
13 8 0.16
14 2 0.04
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.17
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:426553 original size:13 final size:14
Alignment explanation
Indices: 426527--426602 Score: 59
Period size: 13 Copynumber: 5.5 Consensus size: 14
426517 GGAAAATTAG
426527 AAAA-AAATACAAAA
1 AAAATAAATA-AAAA
426541 AAAATAAAT-AAAA
1 AAAATAAATAAAAA
* *
426554 ATATTAAATAAACAA
1 AAAATAAATAAA-AA
**
426569 AAAATAAATGCAAA
1 AAAATAAATAAAAA
*
426583 ATAA-AAATAAAAA
1 AAAATAAATAAAAA
*
426596 ATAATAA
1 AAAATAA
426603 GAAGTAAATA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
13 22 0.45
14 13 0.27
15 14 0.29
ACGTcount: A:0.78, C:0.04, G:0.01, T:0.17
Consensus pattern (14 bp):
AAAATAAATAAAAA
Found at i:426563 original size:28 final size:27
Alignment explanation
Indices: 426529--426602 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
426519 AAAATTAGAA
426529 AAAAATACAAAAAAAATAAAT-AAAAAT
1 AAAAATA-AAAAAAAATAAATGAAAAAT
* *
426556 ATTAAATAAACAAAAAATAAATGCAAAAT
1 A-AAAATAAA-AAAAAATAAATGAAAAAT
*
426585 AAAAATAAAAAATAATAA
1 AAAAATAAAAAAAAATAA
426603 GAAGTAAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 11 0.28
28 23 0.57
29 6 0.15
ACGTcount: A:0.77, C:0.04, G:0.01, T:0.18
Consensus pattern (27 bp):
AAAAATAAAAAAAAATAAATGAAAAAT
Found at i:431395 original size:162 final size:162
Alignment explanation
Indices: 431129--431455 Score: 613
Period size: 162 Copynumber: 2.0 Consensus size: 162
431119 AGAACCATGC
431129 TTTGTGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCAAAATACCGCTTGTTATGTTGTAA
1 TTTGTGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCAAAATACCGCTTGTTATGTTGTAA
431194 ATCAAGTAATGATTAGGCCAATTTTAAAGAAACTCCATATAAAATTTTCAAAACTAAAAAGCCTA
66 ATCAAGTAATGATTAGGCCAATTTTAAAGAAACTCCATATAAAATTTTCAAAACTAAAAAGCCTA
*
431259 ACAGTA-TTTTTTCATCCTTTTGGATGT-AATG
131 ACA-TAGTTATTTCATCCTTTTGGATGTAAATG
431290 TTTGTGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCAAAAATACCGCTTGTTATGTTGTA
1 TTTGTGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCC-AAAATACCGCTTGTTATGTTGTA
431355 AATCAAGTAATGATTAGGCCAATTTTAAAGAAACTCCATATAAAATTTTCAAAACTAAAAAGCCT
65 AATCAAGTAATGATTAGGCCAATTTTAAAGAAACTCCATATAAAATTTTCAAAACTAAAAAGCCT
431420 AACATAGTTATTTCATCCTTTTGGATGTAAATG
130 AACATAGTTATTTCATCCTTTTGGATGTAAATG
431453 TTT
1 TTT
431456 TGTTTTAAAC
Statistics
Matches: 162, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
161 43 0.27
162 112 0.69
163 7 0.04
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (162 bp):
TTTGTGAAAATAATTTGCCAAAATATTTTTGGGCTGAAGCCAAAATACCGCTTGTTATGTTGTAA
ATCAAGTAATGATTAGGCCAATTTTAAAGAAACTCCATATAAAATTTTCAAAACTAAAAAGCCTA
ACATAGTTATTTCATCCTTTTGGATGTAAATG
Found at i:431808 original size:19 final size:20
Alignment explanation
Indices: 431771--431809 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
431761 GCATAGAGCT
431771 CTAAGATTATTATAAGAAAC
1 CTAAGATTATTATAAGAAAC
431791 CTAAGATTATTA-AAGAAAC
1 CTAAGATTATTATAAGAAAC
431810 ATTAAATGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.28
Consensus pattern (20 bp):
CTAAGATTATTATAAGAAAC
Found at i:433588 original size:20 final size:21
Alignment explanation
Indices: 433563--433601 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
433553 TTTTGGTGCA
*
433563 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGAGTCCCCCCTT
433583 GAGGGAACCGAGTCCCCCC
1 GAGGGAACCGAGTCCCCCC
433602 ACAGGGGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.28, T:0.13
Consensus pattern (21 bp):
GAGGGAACCGAGTCCCCCCTT
Found at i:440038 original size:36 final size:34
Alignment explanation
Indices: 439985--440328 Score: 268
Period size: 36 Copynumber: 9.6 Consensus size: 34
439975 TATTTAATAA
* * *
439985 AAAAACTCTATATTATATGTTTTCAAAATGTTTTTT
1 AAAAACTATATAATATATATTTTCAAAATG--TTTT
*
440021 AAAAACTATATAATATATATATATAT-ATATATGTTTT
1 AAAAACTATATAATATATAT-T-T-TCA-AAATGTTTT
* * * *
440058 CAAAA-TGT-T--T-TAAATTTTTAAAATGTTTT
1 AAAAACTATATAATATATATTTTCAAAATGTTTT
440087 AAAAACTATATAATATATATATGTTTTCAAAAATGTTTT
1 AAAAACTATAT-A-ATATATA--TTTTC-AAAATGTTTT
*
440126 AAAAACTATATATTATATATACTTTCAAAATGTTTT
1 AAAAACTATATA--ATATATATTTTCAAAATGTTTT
440162 AAAAACTATATAATATATATATGTTTTCAAAATGTTTT
1 AAAAACTATAT-A-ATATATA--TTTTCAAAATGTTTT
* * * *
440200 AAAAACTATATATTATATATTTTTAAATTTTTTT
1 AAAAACTATATAATATATATTTTCAAAATGTTTT
*
440234 ATAAACTATATATTATATATATTTTCAAAATGTTTT
1 AAAAACTATATA--ATATATATTTTCAAAATGTTTT
**
440270 AAAAAACTATATAATATATATATATTTCAAAAATCATTT
1 -AAAAACTATAT-A-ATATATAT-TTTC-AAAATGTTTT
**
440309 GCAAACTATATAATATATAT
1 AAAAACTATATAATATATAT
440329 AAATGTTTTT
Statistics
Matches: 255, Mismatches: 28, Indels: 50
0.77 0.08 0.15
Matches are distributed among these distances:
29 13 0.05
30 4 0.02
31 2 0.01
32 4 0.02
33 1 0.00
34 23 0.09
35 2 0.01
36 83 0.33
37 35 0.14
38 46 0.18
39 42 0.16
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (34 bp):
AAAAACTATATAATATATATTTTCAAAATGTTTT
Found at i:440078 original size:56 final size:57
Alignment explanation
Indices: 440016--440128 Score: 151
Period size: 56 Copynumber: 2.0 Consensus size: 57
440006 TTCAAAATGT
*
440016 TTTTTAAAAAC-TATATAATA-TATATATATATATATATGTTTTC-AAAATGTTTTAAA
1 TTTTTAAAAACTTATA-AAAACTATATA-ATATATATATGTTTTCAAAAATGTTTTAAA
** *
440072 TTTTTAAAATGTTTTAAAAACTATATAATATATATATGTTTTCAAAAATGTTTTAAA
1 TTTTTAAAAACTTATAAAAACTATATAATATATATATGTTTTCAAAAATGTTTTAAA
440129 AACTATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
56 28 0.56
57 22 0.44
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (57 bp):
TTTTTAAAAACTTATAAAAACTATATAATATATATATGTTTTCAAAAATGTTTTAAA
Found at i:440080 original size:18 final size:18
Alignment explanation
Indices: 440054--440089 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
440044 TATATATATG
440054 TTTTCAAAATGTTTTAAA
1 TTTTCAAAATGTTTTAAA
*
440072 TTTTTAAAATGTTTTAAA
1 TTTTCAAAATGTTTTAAA
440090 AACTATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.06, T:0.53
Consensus pattern (18 bp):
TTTTCAAAATGTTTTAAA
Found at i:440091 original size:11 final size:10
Alignment explanation
Indices: 440051--440090 Score: 57
Period size: 9 Copynumber: 4.1 Consensus size: 10
440041 ATATATATAT
440051 ATGTTTTCAAA
1 ATGTTTT-AAA
440062 ATGTTTT-AA
1 ATGTTTTAAA
440071 AT-TTTTAAA
1 ATGTTTTAAA
440080 ATGTTTTAAA
1 ATGTTTTAAA
440090 A
1 A
440091 ACTATATAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 4 0.15
9 8 0.30
10 8 0.30
11 7 0.26
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (10 bp):
ATGTTTTAAA
Found at i:440102 original size:66 final size:74
Alignment explanation
Indices: 439985--440329 Score: 340
Period size: 75 Copynumber: 4.8 Consensus size: 74
439975 TATTTAATAA
* *
439985 AAAAACTCTATATTATATGT-TTTCAAAATGTTTTTTAAAAACTATATAATATATATAT-ATAT-
1 AAAAACTATATATTATATATATTTCAAAATG--TTTTAAAAACTATATAATATATATATGATATC
* *
440047 ATATATGTTTT
64 AAAAATGTTTT
* * * * *
440058 CAAAA-TGT-T-TTA-A-AT-TTTTAAAATGTTTTAAAAACTATATAATATATATATGTTTTCAA
1 AAAAACTATATATTATATATATTTCAAAATGTTTTAAAAACTATATAATATATATATGATATCAA
440117 AAATGTTTT
66 AAATGTTTT
* *
440126 AAAAACTATATATTATATATACTTTCAAAATGTTTTAAAAACTATATAATATATATATGTTTTC-
1 AAAAACTATATATTATATATA-TTTCAAAATGTTTTAAAAACTATATAATATATATATGATATCA
440190 AAAATGTTTT
65 AAAATGTTTT
* * * * * *
440200 AAAAACTATATATTATATAT-TTTTAAATTTTTTTATAAACTATATATTATATATAT--TTTC-A
1 AAAAACTATATATTATATATATTTCAAAATGTTTTAAAAACTATATAATATATATATGATATCAA
440261 AAATGTTTT
66 AAATGTTTT
** **
440270 AAAAAACTATATAATATATATATATTTCAAAAATCATTTGCAAACTATATAATATATATA
1 -AAAAACTATAT-AT-TATATATATTTC-AAAATGTTTTAAAAACTATATAATATATATA
440330 AATGTTTTTA
Statistics
Matches: 235, Mismatches: 23, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
66 26 0.11
67 2 0.01
68 23 0.10
69 3 0.01
70 18 0.08
71 15 0.06
72 36 0.15
73 13 0.06
74 33 0.14
75 66 0.28
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (74 bp):
AAAAACTATATATTATATATATTTCAAAATGTTTTAAAAACTATATAATATATATATGATATCAA
AAATGTTTT
Found at i:440190 original size:38 final size:37
Alignment explanation
Indices: 440071--440329 Score: 332
Period size: 36 Copynumber: 7.0 Consensus size: 37
440061 AATGTTTTAA
440071 ATTTTT-AAAATGTTTTAAAAACTATATAATATATAT
1 ATTTTTCAAAATGTTTTAAAAACTATATAATATATAT
*
440107 ATGTTTTCAAAAATGTTTTAAAAACTATATATTATATAT
1 AT-TTTTC-AAAATGTTTTAAAAACTATATAATATATAT
*
440146 A-CTTTCAAAATGTTTTAAAAACTATATAATATATAT
1 ATTTTTCAAAATGTTTTAAAAACTATATAATATATAT
440182 ATGTTTTCAAAATGTTTTAAAAACTATAT-AT-TATAT
1 AT-TTTTCAAAATGTTTTAAAAACTATATAATATATAT
* * * *
440218 ATTTTT-AAATTTTTTTATAAACTATATATTATATAT
1 ATTTTTCAAAATGTTTTAAAAACTATATAATATATAT
440254 A-TTTTCAAAATGTTTTAAAAAACTATATAATATATAT
1 ATTTTTCAAAATGTTTT-AAAAACTATATAATATATAT
* ** **
440291 ATATTTCAAAAATCATTTGCAAACTATATAATATATAT
1 ATTTTTC-AAAATGTTTTAAAAACTATATAATATATAT
440329 A
1 A
440330 AATGTTTTTA
Statistics
Matches: 195, Mismatches: 17, Indels: 20
0.84 0.07 0.09
Matches are distributed among these distances:
34 18 0.09
35 9 0.05
36 53 0.27
37 29 0.15
38 48 0.25
39 38 0.19
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
ATTTTTCAAAATGTTTTAAAAACTATATAATATATAT
Found at i:440909 original size:80 final size:80
Alignment explanation
Indices: 440748--442124 Score: 1756
Period size: 80 Copynumber: 17.0 Consensus size: 80
440738 TTTATTGGTA
* * * * *
440748 GATG-GCC-TTGAGCTGAATGTAATCGAACTCGAATGTATTTGTTGACAGATAATCCTTCTCGCC
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTTGCC
* *
440811 TTGAGTTATGCTGTAAAT
63 TTGAGCTATGCTGCAAAT
* *
440829 GATGTGCCTTTGTGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
* *
440894 AGCTATACTACAAAT
66 AGCTATGCTGCAAAT
* * * *
440909 GATGTGCCTCTGAGCTGAATGTAATCGAACTCGAAGGTATTTGGCAGATAACCCTTCTTTCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
* *
440974 AGTTATGCTGAAAAT
66 AGCTATGCTGCAAAT
* * * * *
440989 TATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGGCAGATAACCATTCTTGCCTTA
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
441054 AGCTATGCTGCAAAT
66 AGCTATGCTGCAAAT
* * * * *
441069 GATGTGTCTCTAAGTTGAGTGTTAATCGAACTCGAAGGTCTTTGGTAGATAACCCTTCTTGCCTT
1 GATGTGCCTTTGAGCTGAGTG-TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTT
441134 GAGCTATGCTGCAAAT
65 GAGCTATGCTGCAAAT
* * * *
441150 GATATGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTGGCAGATAACCCTTCTTTCCTTA
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
* *
441215 AGTTATGCTGTAAAT
66 AGCTATGCTGCAAAT
* ** * * * *
441230 GTTGTGTTTTTGAGCTGAGTGTAATCAAACTCGAAGGTCATTGGCAGGTAGCCCTTCTTGCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
*
441295 AGCTATGCTGTAAAT
66 AGCTATGCTGCAAAT
* * *
441310 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGATGGTCTTTGGCAAATAACCCATCTTGCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
*
441375 AGCTATGCTACAAAT
66 AGCTATGCTGCAAAT
* * * * * *
441390 GACGTGCCTCTGAGCTGAGTGTTAATTGAACTTGAAGGTCTTTGGCAGATAACCATTCTTGCATT
1 GATGTGCCTTTGAGCTGAGTG-TAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTT
*
441455 GAGCTATGTTGCAAAT
65 GAGCTATGCTGCAAAT
* * * *
441471 GATGTGCCTTTGAGCTAAGTGTAATCAAACTCAAAGGTCTTTGGCAGATAACCCTTATTGCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
*
441536 AGTTATGCTGCAAAT
66 AGCTATGCTGCAAAT
* *
441551 GATGTACCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCATG-TAGCCCTTCTTGCCTT
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCA-GATAACCCTTCTTGCCTT
*
441615 GAGCTATACTGCAAAT
65 GAGCTATGCTGCAAAT
* * *
441631 GATGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGCAGATATCCCTTCTTGCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
*
441696 AGTTATGCTGCAAAT
66 AGCTATGCTGCAAAT
* * * * *
441711 GATGTACCTTTGAGCTGAGTATAATCGAACTCGAAGGTGTTTGGCAGATAGCCCTTATTGCCTTG
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
* *
441776 AGTTATTCTGCAAAT
66 AGCTATGCTGCAAAT
*
441791 GATGTGCATTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGTCAGATAACCCTT-TTAGC
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTT-GC
* *
441855 CTTGAGTTATGCTGTAAAT
62 CTTGAGCTATGCTGCAAAT
* *
441874 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGC
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGC
441939 CTTGAGCTATGCTGCAAAT
62 CTTGAGCTATGCTGCAAAT
* *
441958 GAGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACTCTT-TTAGC
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACCCTTCTT-GC
* * *
442022 CTTGAGTTATGTTGTAAAT
62 CTTGAGCTATGCTGCAAAT
** *
442041 GATACGCCTTTGAGCTGAGTGTAATCGAACTCGAATGTCTTTTGTTGGCAGATAACCCTTCTTGC
1 GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC---T-TTGGCAGATAACCCTTCTTGC
*
442106 CTTGAGCTATACTGCAAAT
62 CTTGAGCTATGCTGCAAAT
442125 ACAAAAAAAA
Statistics
Matches: 1126, Mismatches: 146, Indels: 45
0.85 0.11 0.03
Matches are distributed among these distances:
79 1 0.00
80 702 0.62
81 145 0.13
82 9 0.01
83 160 0.14
84 95 0.08
85 6 0.01
86 2 0.00
87 6 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (80 bp):
GATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTG
AGCTATGCTGCAAAT
Found at i:441391 original size:321 final size:321
Alignment explanation
Indices: 440793--442124 Score: 1742
Period size: 321 Copynumber: 4.1 Consensus size: 321
440783 TATTTGTTGA
* * * * *
440793 CAGATAATCCTTCTCGCCTTGAGTTATGCTGTAAATGATGTGCCTTTGTGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * * *
440858 CTCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTTGAGCTATACTACAAATGATGTGCCTCTGAG
66 CTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAG
* * * * *
440923 CTGAATGTAATCGAACTCGAAGGT-ATTTGGCAGATAACCCTTCTTTCCTTGAGTTATGCTGAAA
131 CTGAGTGTAATCGAACTCGAAGGTCA-TTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAA
* * *
440987 ATTATGTGCCTTTGAGCTGAGTGTAATCAAACTCAAAGGTCTTTGGCAGATAA-CCATTCTTGCC
195 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCA-TCTTGCC
* * * *
441051 TTAAGCTATGCTGCAAATGATGTGTCTCTAAGTTGAGTGTTAATCGAACTCGAAGGTCTTTGG
259 TTGAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTTAATCGAACTCGAAGGTCTTTGG
* *
441114 TAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATATGCCTTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * * * * **
441179 CTCGAATGTCTTTGGCAGATAACCCTTCTTTCCTTAAGTTATGCTGTAAATGTTGTGTTTTTGAG
66 CTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAG
* * *
441244 CTGAGTGTAATCAAACTCGAAGGTCATTGGCAGGTAGCCCTTCTTGCCTTGAGCTATGCTGTAAA
131 CTGAGTGTAATCGAACTCGAAGGTCATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA
* *
441309 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGATGGTCTTTGGCAAATAACCCATCTTGCCTT
196 TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCATCTTGCCTT
* * * *
441374 GAGCTATGCTACAAATGACGTGCCTCTGAGCTGAGTGTTAATTGAACTTGAAGGTCTTTGG
261 GAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTTAATCGAACTCGAAGGTCTTTGG
* * * * *
441435 CAGATAACCATTCTTGCATTGAGCTATGTTGCAAATGATGTGCCTTTGAGCTAAGTGTAATCAAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* * *
441500 CTCAAAGGTCTTTGGCAGATAACCCTTATTGCCTTGAGTTATGCTGCAAATGATGTACCTTTGAG
66 CTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAG
* *
441565 CTGAGTGTAATCGAACTCGAAGGTCTTTGGCATG-TAGCCCTTCTTGCCTTGAGCTATACTGCAA
131 CTGAGTGTAATCGAACTCGAAGGTCATTGGCA-GATAGCCCTTCTTGCCTTGAGCTATGCTGCAA
* * * *
441629 ATGATGTACCTTTGAGCTGAGTGTAATCGAACTTGAAGGTCTTTGGCAGATATCCCTTCTTGCCT
195 ATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCATCTTGCCT
* * * * *
441694 TGAGTTATGCTGCAAATGATGTACCTTTGAGCTGAGT-ATAATCGAACTCGAAGGTGTTTGG
260 TGAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTTAATCGAACTCGAAGGTCTTTGG
* * * * *
441755 CAGATAGCCCTTATTGCCTTGAGTTATTCTGCAAATGATGTGCATTTGAGCTGAGTGTAATCGAA
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
*
441820 CTCGAAGGTCTTTGTTGTCAGATAACCCTT-TTAGCCTTGAGTTATGCTGTAAATGATGTGCCTT
66 CTCGAAGGTCTTTG--G-CAGATAACCCTTCTT-GCCTTGAGTTATGCTGCAAATGATGTGCCTT
* *
441884 TGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGGCATATAGCCCTTCTTGCCTTGAGCTAT
127 TGAGCTGAGTGTAATCGAACTCGAAGGTC----ATTGGCAGATAGCCCTTCTTGCCTTGAGCTAT
* *
441949 GCTGCAAATGAGGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACT
188 GCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG--G-CAGATAACC
* * * * ** * *
442014 C-TTTTAGCCTTGAGTTATGTTGTAAATGATACGCCTTTGAGCTGAGTG-TAATCGAACTCGAAT
250 CATCTT-GCCTTGAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTTAATCGAACTCGAAG
442077 GTCTTTTGTTGG
314 GTC---T-TTGG
*
442089 CAGATAACCCTTCTTGCCTTGAGCTATACTGCAAAT
1 CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAAT
442125 ACAAAAAAAA
Statistics
Matches: 882, Mismatches: 108, Indels: 29
0.87 0.11 0.03
Matches are distributed among these distances:
320 88 0.10
321 538 0.61
322 8 0.01
323 70 0.08
327 77 0.09
329 4 0.00
330 60 0.07
333 1 0.00
334 36 0.04
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (321 bp):
CAGATAACCCTTCTTGCCTTGAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
CTCGAAGGTCTTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATGATGTGCCTTTGAG
CTGAGTGTAATCGAACTCGAAGGTCATTGGCAGATAGCCCTTCTTGCCTTGAGCTATGCTGCAAA
TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCAGATAACCCATCTTGCCTT
GAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGTGTTAATCGAACTCGAAGGTCTTTGG
Found at i:444483 original size:3 final size:3
Alignment explanation
Indices: 444477--444545 Score: 86
Period size: 3 Copynumber: 23.0 Consensus size: 3
444467 ATTTTTTTAT
* *
444477 TAA TAA TAA TAA TAG TAA TAA TAA TAG TAA TAAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* *
444522 TAA CAA TAA TAA TAA TAA AAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
444546 ATGGATGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:444999 original size:121 final size:113
Alignment explanation
Indices: 444874--445552 Score: 747
Period size: 113 Copynumber: 5.9 Consensus size: 113
444864 GAATCAAATT
* *
444874 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTTAGATGAGTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* **
444938 TGAA-TAT-CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCAAAC-A
66 TGAACT-TCCTCTGGAAAAGTTGAT-C----C-A--T-C--GAGTGAT-GAATTCAAACAA
* * ** *
444995 AAGGTTGAACAAGTTCTTCTCATTAAGAACAACTTCTTCC-TCTTCAGATGATTTCTTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * **
445059 TGAACAT-CTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAA-TCAAAC-A
66 TGAACTTCCTCTGGAAAAGTTGAT-C----C-A--T-C--GAGTGAT-GAATTCAAACAA
* * *
445116 AAGGTTGAACAAGTTCTTCTCATTATGAACCTCTTCTTCC-TCTTCAGATGAGTTCTTATCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
445180 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
66 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
*
445228 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
445293 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
66 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
* * *
445341 AAGGTTAAACAATTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTATCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
*
445406 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGCAA
66 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
* *
445454 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTC-T--TTCTTTAGATGAGTTATTCTCATTA
1 AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
* * * * *
445516 TGAACTCTAC-CTGGCAATGCTGATCCATTGAGTGATG
66 TGAACT-TCCTCTGGAAAAGTTGATCCATCGAGTGATG
445553 GATTTGAATC
Statistics
Matches: 517, Mismatches: 34, Indels: 25
0.90 0.06 0.04
Matches are distributed among these distances:
110 53 0.10
111 12 0.02
112 40 0.08
113 215 0.42
114 1 0.00
116 1 0.00
117 1 0.00
121 176 0.34
122 18 0.03
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTA
TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAACAA
Found at i:446747 original size:18 final size:18
Alignment explanation
Indices: 446710--446747 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
446700 TATGTGAAAG
**
446710 AATAAATTGAATTTTGAA
1 AATAAATTGAATTTCAAA
446728 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
446746 AA
1 AA
446748 GATAATCTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Found at i:447079 original size:10 final size:10
Alignment explanation
Indices: 447066--447098 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
447056 TTCATTTCAT
447066 TTTTTTCTTC
1 TTTTTTCTTC
447076 TTTTCTTCTTC
1 TTTT-TTCTTC
447087 TTTTTTCTTC
1 TTTTTTCTTC
447097 TT
1 TT
447099 CTTTAAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:447079 original size:11 final size:11
Alignment explanation
Indices: 447065--447098 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
447055 TTTCATTTCA
447065 TTTTTTTCTTC
1 TTTTTTTCTTC
*
447076 TTTTCTTCTTC
1 TTTTTTTCTTC
447087 -TTTTTTCTTC
1 TTTTTTTCTTC
447097 TT
1 TT
447099 CTTTAAGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:447094 original size:13 final size:13
Alignment explanation
Indices: 447070--447102 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
447060 TTTCATTTTT
447070 TTCTTCTTTTCTTC
1 TTCTT-TTTTCTTC
447084 TTCTTTTTTCTTC
1 TTCTTTTTTCTTC
447097 TTCTTT
1 TTCTTT
447103 AAGCATAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (13 bp):
TTCTTTTTTCTTC
Found at i:459377 original size:21 final size:21
Alignment explanation
Indices: 459351--459404 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
459341 TGGAGGTTTT
459351 TGGTGAGTCACCAAACTATTG
1 TGGTGAGTCACCAAACTATTG
459372 TGGTGAGTCACCAAACTATTG
1 TGGTGAGTCACCAAACTATTG
*
459393 TGGTGAATCACC
1 TGGTGAGTCACC
459405 TTGTAGCTTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (21 bp):
TGGTGAGTCACCAAACTATTG
Found at i:460718 original size:97 final size:95
Alignment explanation
Indices: 460527--460791 Score: 327
Period size: 97 Copynumber: 2.7 Consensus size: 95
460517 GGCTAGCTGG
* * *
460527 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTTAATACCATTGTATAG-AT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAAC-TCA-AGC-TT-TATTGTAT
* *
460591 ATTATAATCGCTTTTATCAGGCTAGTTGAATATT
62 ATTATAATCACTTTTATCAGGCTAGCTGAATATT
* * * *
460625 ATCCATAAAGCTGGGGTGTTTAACCAATTTCTCTCTTGAGGGACAACTCAAGCTTTATTGTATTT
1 ATCCATAAAGCTGGGGCGTTTAACCAATTGCT-T-TAGAGGGACAACTCAAGCTTTATTGTATAT
*
460690 TATAATCACTTTTATCAGGCTAGCTGAATCTT
64 TATAATCACTTTTATCAGGCTAGCTGAATATT
* * *
460722 ATCCATAAAG-TCAGGGCGTTTAACCAATTGCTTTAGAGGGATAACTCAAGCTTTATTGTACATA
1 ATCCATAAAGCT-GGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAT-
460786 TATAAT
64 TATAAT
460792 ATTATAATCT
Statistics
Matches: 145, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
95 26 0.18
96 12 0.08
97 61 0.42
98 32 0.22
99 3 0.02
100 11 0.08
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (95 bp):
ATCCATAAAGCTGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATTA
TAATCACTTTTATCAGGCTAGCTGAATATT
Found at i:464814 original size:26 final size:26
Alignment explanation
Indices: 464785--464874 Score: 78
Period size: 28 Copynumber: 3.4 Consensus size: 26
464775 AAACCTATAT
464785 AATATATATTTTCAAAAATATTTAAA
1 AATATATATTTTCAAAAATATTTAAA
*
464811 AATAT-T-TTTCTTAAAAGA-ATTTCAAA
1 AATATATATTT-TCAAAA-ATATTT-AAA
* *
464837 ATTATATAGTTTTCAAAAATGTTTTAAA
1 AATATATA-TTTTCAAAAAT-ATTTAAA
*
464865 ACTATATATT
1 AATATATATT
464875 AATTATATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
24 3 0.06
25 10 0.20
26 13 0.25
27 4 0.08
28 15 0.29
29 6 0.12
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (26 bp):
AATATATATTTTCAAAAATATTTAAA
Found at i:464879 original size:39 final size:39
Alignment explanation
Indices: 464836--464912 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 39
464826 AGAATTTCAA
464836 AATTATATAGTTTTCAAAAATG-TTTT-AAAACTATATATT
1 AATTATAT-GTTTTC-AAAATGTTTTTAAAAACTATATATT
464875 AATTATATGTTTTCAAAATGTTTTTTAAAAACTATATA
1 AATTATATGTTTTCAAAATG-TTTTTAAAAACTATATA
464913 ATATATATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
37 6 0.17
38 6 0.17
39 12 0.34
40 11 0.31
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (39 bp):
AATTATATGTTTTCAAAATGTTTTTAAAAACTATATATT
Found at i:464956 original size:2 final size:2
Alignment explanation
Indices: 464907--464942 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
464897 TTTTAAAAAC
464907 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
464943 GTTTTCATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:464981 original size:70 final size:68
Alignment explanation
Indices: 464878--465150 Score: 210
Period size: 70 Copynumber: 3.9 Consensus size: 68
464868 ATATATTAAT
* *
464878 TATATGTTTTCAAAATGTTTTTTAAAAACTATATAATATATATATATATATATATATATATATAT
1 TATATATTTTCAAAATG--TTTTAAAAACTATATAATATATATATATATATATATATATAAATAT
464943 GTTTTCA
64 -TTTT-A
* * * * * * *
464950 TATATATTTTTAAAATGTTTTAAAAACTATATATTATGTATAT-TTTCATAATGTTTTAAAAACT
1 TATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATATAT-AT-AT-ATATATAAA-T
**
465014 ATATAATA
62 AT-TTTTA
* * * * * * * *
465022 TATATGTTTTCAAAATGTTTTAAAAACTATATATTGTATAT-TTTCA-AAATGTTTTAAAAACTA
1 TATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATAT-ATATAT-ATATATAAA-TA
*
465085 TATATTA
63 T-TTTTA
*
465092 TATATATTTTCAAAATATTTTAAAAAACTATATAATATATATATATATATATATATATA
1 TATATATTTTCAAAATGTTTT-AAAAACTATATAATATATATATATATATATATATATA
465151 TTTCAAAAAT
Statistics
Matches: 164, Mismatches: 28, Indels: 19
0.78 0.13 0.09
Matches are distributed among these distances:
69 2 0.01
70 66 0.40
71 27 0.16
72 64 0.39
73 5 0.03
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (68 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATAATATATATATATATATATATATATAAATATTT
TTA
Found at i:464994 original size:36 final size:36
Alignment explanation
Indices: 464949--465135 Score: 279
Period size: 36 Copynumber: 5.2 Consensus size: 36
464939 ATATGTTTTC
* *
464949 ATATATATTTTTAAAATGTTTTAAAAACTATATATT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATAAT
* *
464985 ATGTATATTTTCATAATGTTTTAAAAACTATATAAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATAAT
*
465021 ATATATGTTTTCAAAATGTTTTAAAAACTATAT-AT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATAAT
* *
465056 -TGTATATTTTCAAAATGTTTTAAAAACTATATATT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATAAT
*
465091 ATATATATTTTCAAAATATTTTAAAAAACTATATAAT
1 ATATATATTTTCAAAATGTTTT-AAAAACTATATAAT
465128 ATATATAT
1 ATATATAT
465136 ATATATATAT
Statistics
Matches: 135, Mismatches: 13, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
34 30 0.22
35 3 0.02
36 81 0.60
37 21 0.16
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAACTATATAAT
Found at i:465125 original size:2 final size:2
Alignment explanation
Indices: 465120--465151 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
465110 TTTAAAAAAC
465120 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
465152 TTCAAAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:465172 original size:52 final size:48
Alignment explanation
Indices: 465083--465188 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 48
465073 TTTTAAAAAC
465083 TATATATTATATATATTTTCAAAATATTTTAAAAAACTATATAATATATA
1 TATATATTATATATATTTTCAAAATATTTTAAAAAAC--TATAATATATA
**
465133 TATATATATATATATATATTTCAAAA-ATCATTT-CCAAACTATAATATATA
1 TATATAT-TATATATAT-TTTCAAAATAT--TTTAAAAAACTATAATATATA
465183 TATATA
1 TATATA
465189 AATAAAAAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
50 24 0.48
51 11 0.22
52 12 0.24
53 3 0.06
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (48 bp):
TATATATTATATATATTTTCAAAATATTTTAAAAAACTATAATATATA
Found at i:465961 original size:14 final size:14
Alignment explanation
Indices: 465942--465973 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
465932 GACGCTTATT
465942 TATTATCATGCTAA
1 TATTATCATGCTAA
465956 TATTATCATGCTAA
1 TATTATCATGCTAA
465970 TATT
1 TATT
465974 TCCTGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (14 bp):
TATTATCATGCTAA
Found at i:466246 original size:36 final size:36
Alignment explanation
Indices: 466206--466279 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
466196 ATGTTTACGG
466206 TTATACTTGTAAATCTTTATTGTAATTATGAATATT
1 TTATACTTGTAAATCTTTATTGTAATTATGAATATT
*
466242 TTATACTTGTAAATCTTTGTTGTAATTATGAATATT
1 TTATACTTGTAAATCTTTATTGTAATTATGAATATT
466278 TT
1 TT
466280 CTATTATTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.54
Consensus pattern (36 bp):
TTATACTTGTAAATCTTTATTGTAATTATGAATATT
Found at i:473811 original size:21 final size:20
Alignment explanation
Indices: 473781--473820 Score: 55
Period size: 19 Copynumber: 1.9 Consensus size: 20
473771 TATGTTTTTT
473781 AATTTAATATTTAAATATTTAC
1 AATTTAATA-TTAAA-ATTTAC
473803 AATTT-ATATTAAAATTTA
1 AATTTAATATTAAAATTTA
473821 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 3 0.17
22 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTAATATTAAAATTTAC
Found at i:473830 original size:15 final size:15
Alignment explanation
Indices: 473810--473840 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
473800 TACAATTTAT
*
473810 ATTAAAATTTAAAAA
1 ATTAAAAATTAAAAA
473825 ATTAAAAATTAAAAA
1 ATTAAAAATTAAAAA
473840 A
1 A
473841 ATTTAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAAATTAAAAA
Found at i:473834 original size:16 final size:16
Alignment explanation
Indices: 473813--473861 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
473803 AATTTATATT
*
473813 AAAATTTAAAAAATTA
1 AAAATTAAAAAAATTA
473829 AAAATTAAAAAAATT-
1 AAAATTAAAAAAATTA
* **
473844 TAAATTAATCAAATTA
1 AAAATTAAAAAAATTA
473860 AA
1 AA
473862 TTACATATAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTAAAAAAATTA
Found at i:474503 original size:34 final size:33
Alignment explanation
Indices: 474438--474510 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
474428 TTACCCTAAT
*
474438 TTTTATGATATTATTAACAAAATGTGTTTATTA
1 TTTTATGATATTATTAACAAAATGTGATTATTA
*
474471 TTTTATGATATTATTAACAAAATTTTGATTATTA
1 TTTTATGATATTATTAACAAAA-TGTGATTATTA
474505 TATTTA
1 T-TTTA
474511 ATTGAGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 22 0.61
34 10 0.28
35 4 0.11
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (33 bp):
TTTTATGATATTATTAACAAAATGTGATTATTA
Found at i:476268 original size:2 final size:2
Alignment explanation
Indices: 476257--476304 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
476247 AAGAATTTAG
476257 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
476298 TA TA TA T
1 TA TA TA T
476305 TATTTAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:489890 original size:24 final size:26
Alignment explanation
Indices: 489840--489890 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
489830 CGTTCGTGAA
*
489840 CGTTCGATTATATATTCGTTTATGTT
1 CGTTCGATTATATATTCATTTATGTT
*
489866 CGTTC-ATT-TATTTTCATTTATGTT
1 CGTTCGATTATATATTCATTTATGTT
489890 C
1 C
489891 ATTTATGTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.18, C:0.14, G:0.12, T:0.57
Consensus pattern (26 bp):
CGTTCGATTATATATTCATTTATGTT
Found at i:489915 original size:10 final size:10
Alignment explanation
Indices: 489867--489900 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
489857 GTTTATGTTC
489867 GTTCATTTAT
1 GTTCATTTAT
*
489877 TTTCATTTAT
1 GTTCATTTAT
489887 GTTCATTTAT
1 GTTCATTTAT
489897 GTTC
1 GTTC
489901 GTTCATTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.62
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:490329 original size:16 final size:16
Alignment explanation
Indices: 490308--490340 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
490298 CAAATTTTTT
490308 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
490324 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
490340 T
1 T
490341 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:497587 original size:32 final size:32
Alignment explanation
Indices: 497524--497587 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
497514 GGCAGAAACA
* * *
497524 CCGTAATAGGTTTGATATTTATAGGCGTTTTT
1 CCGTAACAGGTTTGATATTTAGAGGCATTTTT
* *
497556 CCGTAACAGGTTTGCTATTTAGCGGCATTTTT
1 CCGTAACAGGTTTGATATTTAGAGGCATTTTT
497588 AGTCACAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (32 bp):
CCGTAACAGGTTTGATATTTAGAGGCATTTTT
Found at i:502267 original size:18 final size:19
Alignment explanation
Indices: 502246--502286 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
502236 TATTTATTAT
*
502246 TTTATTATT-TCCCTTTTA
1 TTTATTATTATCCATTTTA
*
502264 TTTATTATTATCTATTTTA
1 TTTATTATTATCCATTTTA
502283 TTTA
1 TTTA
502287 ATTAAATCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTATTATTATCCATTTTA
Found at i:502281 original size:19 final size:19
Alignment explanation
Indices: 502220--502286 Score: 66
Period size: 18 Copynumber: 3.6 Consensus size: 19
502210 CCTTTTTTTA
* *
502220 TATTTATATTTATTACTATT
1 TATTT-TATTTATTATTATC
*
502240 TATTAT-TTTATTATT-TC
1 TATTTTATTTATTATTATC
**
502257 CCTTTTATTTATTATTATC
1 TATTTTATTTATTATTATC
502276 TATTTTATTTA
1 TATTTTATTTA
502287 ATTAAATCTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
17 4 0.11
18 17 0.46
19 12 0.32
20 4 0.11
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTATTTATTATTATC
Found at i:504690 original size:15 final size:17
Alignment explanation
Indices: 504664--504697 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
504654 ACATGATACG
504664 TGTGATTACATG-TATA
1 TGTGATTACATGTTATA
504680 TGTGA-TACATGTTATA
1 TGTGATTACATGTTATA
504696 TG
1 TG
504698 ATATGAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGATTACATGTTATA
Found at i:504861 original size:30 final size:30
Alignment explanation
Indices: 504825--504882 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
504815 AGAGTCGAGG
*
504825 GTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTACCTATGTTCTCTCGA-ACATATGGACA
*
504855 GTTACCTATGTTCTCTGGAACATATGGA
1 GTTACCTATGTTCTCTCGAACATATGGA
504883 TAGGTCATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (30 bp):
GTTACCTATGTTCTCTCGAACATATGGACA
Found at i:505682 original size:2 final size:2
Alignment explanation
Indices: 505677--505703 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
505667 TATATATATA
505677 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
505704 AACATCCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:507174 original size:15 final size:15
Alignment explanation
Indices: 507156--507205 Score: 100
Period size: 15 Copynumber: 3.3 Consensus size: 15
507146 CGAGGGTATT
507156 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
507171 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
507186 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
507201 GTAGT
1 GTAGT
507206 GGTCCTACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.34, T:0.28
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:508124 original size:18 final size:18
Alignment explanation
Indices: 508101--508141 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
508091 TTATATGTGT
508101 GCATGAGTATACGTGATA
1 GCATGAGTATACGTGATA
508119 GCATGAGTATACGTGATA
1 GCATGAGTATACGTGATA
*
508137 ACATG
1 GCATG
508142 TTACTACGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.34, C:0.12, G:0.27, T:0.27
Consensus pattern (18 bp):
GCATGAGTATACGTGATA
Found at i:508808 original size:15 final size:17
Alignment explanation
Indices: 508782--508815 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
508772 ACATGATACG
508782 TGTGATTACATG-TATA
1 TGTGATTACATGTTATA
508798 TGTGA-TACATGTTATA
1 TGTGATTACATGTTATA
508814 TG
1 TG
508816 ATATGAGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.29, C:0.06, G:0.21, T:0.44
Consensus pattern (17 bp):
TGTGATTACATGTTATA
Found at i:508979 original size:30 final size:30
Alignment explanation
Indices: 508943--509000 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
508933 AGAGTCGAGG
*
508943 GTTACCTATG-TCTTTCGAGACATATGGACA
1 GTTACCTATGTTCTCTCGA-ACATATGGACA
*
508973 GTTACCTATGTTCTCTGGAACATATGGA
1 GTTACCTATGTTCTCTCGAACATATGGA
509001 TAGGTCATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (30 bp):
GTTACCTATGTTCTCTCGAACATATGGACA
Found at i:510763 original size:23 final size:23
Alignment explanation
Indices: 510737--510800 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
510727 CAGCTCGTAT
510737 AATTGCACCGAAGTGCCAAGTAG
1 AATTGCACCGAAGTGCCAAGTAG
* * **
510760 AATTGCACCGGAGTGTCGCGTAG
1 AATTGCACCGAAGTGCCAAGTAG
* *
510783 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
510801 TCTAATAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCAAGTAG
Found at i:511046 original size:30 final size:30
Alignment explanation
Indices: 511003--511080 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
510993 TCACAATTCA
* * * *
511003 CATAATTTGTATCACGTAGACATATTATTTT
1 CATAACTT-TATCACATAGACATATCATTTC
511034 CATAACTTTATCACATAGACATATCATTTC
1 CATAACTTTATCACATAGACATATCATTTC
511064 CAT-ACTTTTATCACATA
1 CATAAC-TTTATCACATA
511081 ACTCATATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.05
30 33 0.79
31 7 0.17
ACGTcount: A:0.35, C:0.19, G:0.05, T:0.41
Consensus pattern (30 bp):
CATAACTTTATCACATAGACATATCATTTC
Found at i:511479 original size:19 final size:19
Alignment explanation
Indices: 511455--511504 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
511445 TTTAAGGGGG
511455 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
511474 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
511493 TGCATCGATGCA
1 TGCATCGATGCA
511505 TTGATGGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:511545 original size:83 final size:83
Alignment explanation
Indices: 511389--511565 Score: 207
Period size: 83 Copynumber: 2.1 Consensus size: 83
511379 TTAATGGAGG
** *
511389 TATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTATATTTAAGGGG
1 TATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTATATTTAAAAGA
*
511454 GTGCATCGATGCACTCCT
66 GTGCATCGATGCACTCCA
* ** * *
511472 TATGCATCGATGCACT-C-CTTATGCATCGATGCATTGATGGC-ATTCGATGTTTGTATTTTAAA
1 TATGCATCGATGCACTACAC-CATGCATCGATGCATAAAT-CCTATTCGATGTTTATA-TTTAAA
*
511534 AGAGTGCATCGATGCACTTCA
63 AGAGTGCATCGATGCACTCCA
*
511555 TGTGCATCGAT
1 TATGCATCGAT
511566 ACACCTTGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
81 1 0.01
82 30 0.38
83 49 0.61
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.33
Consensus pattern (83 bp):
TATGCATCGATGCACTACACCATGCATCGATGCATAAATCCTATTCGATGTTTATATTTAAAAGA
GTGCATCGATGCACTCCA
Found at i:513788 original size:19 final size:20
Alignment explanation
Indices: 513760--513815 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 20
513750 TAAGGTAAAA
* *
513760 ATATTTTATGAATAGTAT-T
1 ATATTGTATGAATAGTATCG
513779 ATATTGTATGAATAGTATCG
1 ATATTGTATGAATAGTATCG
* *
513799 ATATTGTTTAAATAGTA
1 ATATTGTATGAATAGTA
513816 CCGTAAACAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (20 bp):
ATATTGTATGAATAGTATCG
Found at i:513861 original size:21 final size:21
Alignment explanation
Indices: 513836--513877 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
513826 TAATGAATAG
*
513836 TGCTACAGTGTATCGATGCAC
1 TGCTACAGTGTATCAATGCAC
513857 TGCTACAGTGTATCAATGCAC
1 TGCTACAGTGTATCAATGCAC
513878 AAAAACATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTATCAATGCAC
Found at i:514477 original size:23 final size:23
Alignment explanation
Indices: 514451--514538 Score: 63
Period size: 23 Copynumber: 3.8 Consensus size: 23
514441 AGCTCGTATA
514451 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
514474 AATT-TATCCCGAAAG-ACCGCGTAG
1 AATTGCA--CCG-AAGTGCCACGTAG
* *
514498 AGTTGCACCGAAGTGCCTCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* * *
514521 AAATGCATCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
514539 TATAAGATTT
Statistics
Matches: 48, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
22 4 0.08
23 27 0.56
24 13 0.27
25 4 0.08
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:521022 original size:21 final size:21
Alignment explanation
Indices: 520998--521044 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
520988 ATGAACATTG
520998 CTACAGTGTA-TCGATGCACTA
1 CTACAGTGTACT-GATGCACTA
*
521019 CTACAGTGTACTGATGCACTG
1 CTACAGTGTACTGATGCACTA
521040 CTACA
1 CTACA
521045 ATAAATTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (21 bp):
CTACAGTGTACTGATGCACTA
Found at i:521798 original size:23 final size:23
Alignment explanation
Indices: 521755--521798 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
521745 AATACATATA
**
521755 TGTCCCGAAGGACCATGTAGAAT
1 TGTCCCGAAGGACCACATAGAAT
*
521778 TGTCCCGAAGGACCGCATAGA
1 TGTCCCGAAGGACCACATAGA
521799 CCCTCTACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (23 bp):
TGTCCCGAAGGACCACATAGAAT
Found at i:523492 original size:12 final size:12
Alignment explanation
Indices: 523455--523492 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
523445 AGGCAACCCA
*
523455 TTTCGTTATATT
1 TTTCGTTTTATT
*
523467 TTT-GTTTTAAT
1 TTTCGTTTTATT
523478 TTTCGTTTTATT
1 TTTCGTTTTATT
523490 TTT
1 TTT
523493 AGCGAACTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (12 bp):
TTTCGTTTTATT
Found at i:523642 original size:52 final size:54
Alignment explanation
Indices: 523585--523691 Score: 164
Period size: 53 Copynumber: 2.0 Consensus size: 54
523575 TAACGAAAAA
* * *
523585 AACAGTGCAG-AAAAACTGACTTGGTTCGAACTGTGCAGAAAAATTCA-AACAT
1 AACAGTGCAGAAAAAAATGACTTGGTTCGAACAGTGCAGAAAAATACACAACAT
*
523637 AACAGTGCAGAAAAAAATGATTTGGTTCGAACAGTGCAGAAAAATACACAACAT
1 AACAGTGCAGAAAAAAATGACTTGGTTCGAACAGTGCAGAAAAATACACAACAT
523691 A
1 A
523692 TTCGAACAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 10 0.20
53 33 0.67
54 6 0.12
ACGTcount: A:0.46, C:0.16, G:0.19, T:0.20
Consensus pattern (54 bp):
AACAGTGCAGAAAAAAATGACTTGGTTCGAACAGTGCAGAAAAATACACAACAT
Found at i:523869 original size:16 final size:16
Alignment explanation
Indices: 523848--523897 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
523838 GCAAATCCGA
*
523848 GTACCCGAATTTTCAG
1 GTACCCGAATTTCCAG
*
523864 GTACCC-AATTTCCGG
1 GTACCCGAATTTCCAG
*
523879 GTACCCGAAACTTCCAG
1 GTACCCG-AATTTCCAG
523896 GT
1 GT
523898 CGACAATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 13 0.46
16 6 0.21
17 9 0.32
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (16 bp):
GTACCCGAATTTCCAG
Found at i:523881 original size:15 final size:16
Alignment explanation
Indices: 523843--523887 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
523833 GGTATGCAAA
*
523843 TCCGAGTACCCGAATT
1 TCCGGGTACCCGAATT
* *
523859 TTCAGGTACCC-AATT
1 TCCGGGTACCCGAATT
523874 TCCGGGTACCCGAA
1 TCCGGGTACCCGAA
523888 ACTTCCAGGT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (16 bp):
TCCGGGTACCCGAATT
Found at i:523968 original size:32 final size:32
Alignment explanation
Indices: 523923--523991 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
523913 CCGTGTCCCG
* *
523923 ACCCGGATGTTACGGGTACCTGGTAATCGGGT
1 ACCCGGATGTTACGGGTACCCGATAATCGGGT
*
523955 ACCCGGATTTTACGGGTACCCGATAATCGGGT
1 ACCCGGATGTTACGGGTACCCGATAATCGGGT
523987 ACCCG
1 ACCCG
523992 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.23
Consensus pattern (32 bp):
ACCCGGATGTTACGGGTACCCGATAATCGGGT
Found at i:523972 original size:17 final size:17
Alignment explanation
Indices: 523923--523991 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 17
523913 CCGTGTCCCG
*
523923 ACCCGGATGTTACGGGT
1 ACCCGGATATTACGGGT
* *
523940 ACCTGG-TAAT-CGGGT
1 ACCCGGATATTACGGGT
*
523955 ACCCGGATTTTACGGGT
1 ACCCGGATATTACGGGT
*
523972 ACCC-GATAAT-CGGGT
1 ACCCGGATATTACGGGT
523987 ACCCG
1 ACCCG
523992 ATACCCGGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
15 19 0.46
16 8 0.20
17 14 0.34
ACGTcount: A:0.20, C:0.26, G:0.30, T:0.23
Consensus pattern (17 bp):
ACCCGGATATTACGGGT
Found at i:523992 original size:15 final size:15
Alignment explanation
Indices: 523935--523994 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
523925 CCGGATGTTA
* *
523935 CGGGTACCTGGTAAT
1 CGGGTACCCGATAAT
**
523950 CGGGTACCCGGATTTT
1 CGGGTACCC-GATAAT
523966 ACGGGTACCCGATAAT
1 -CGGGTACCCGATAAT
523982 CGGGTACCCGATA
1 CGGGTACCCGATA
523995 CCCGGTTTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
15 21 0.57
16 7 0.19
17 9 0.24
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGATAAT
Found at i:526067 original size:41 final size:41
Alignment explanation
Indices: 526012--526116 Score: 124
Period size: 41 Copynumber: 2.5 Consensus size: 41
526002 TTTTATCTTT
*
526012 GTATTTTAGTTTAAATAAGTTTTTATTTCA-ATTAGGTTTTAG
1 GTATATTAGTTTAAAT-AGTTTTTATTTCATATT-GGTTTTAG
* * *
526054 G-ATATTATTTTAAATAGTATTTTATTTTATATTTGTTTTAG
1 GTATATTAGTTTAAATAGT-TTTTATTTCATATTGGTTTTAG
*
526095 GTATTTTAGTTTAAATAGTTTT
1 GTATATTAGTTTAAATAGTTTT
526117 AAGAGTTTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
40 3 0.06
41 32 0.59
42 19 0.35
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.58
Consensus pattern (41 bp):
GTATATTAGTTTAAATAGTTTTTATTTCATATTGGTTTTAG
Found at i:526781 original size:17 final size:17
Alignment explanation
Indices: 526756--526789 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
526746 CTTTATCCCA
*
526756 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
526773 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
526790 TTATCTCATT
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:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:527922 original size:12 final size:12
Alignment explanation
Indices: 527901--527937 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
527891 ATGTCGCGAC
527901 AAACGCCGCTAT
1 AAACGCCGCTAT
*
527913 AAACGTCGCTAT
1 AAACGCCGCTAT
527925 AAACGCCGCTAT
1 AAACGCCGCTAT
527937 A
1 A
527938 TACCTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.35, C:0.30, G:0.16, T:0.19
Consensus pattern (12 bp):
AAACGCCGCTAT
Found at i:529999 original size:21 final size:21
Alignment explanation
Indices: 529975--530014 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
529965 TAAAGCACCC
529975 AATAATAACATTTCCGGTAGA
1 AATAATAACATTTCCGGTAGA
*
529996 AATAATAATATTTCCGGTA
1 AATAATAACATTTCCGGTA
530015 ATTTTTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
AATAATAACATTTCCGGTAGA
Found at i:533247 original size:14 final size:14
Alignment explanation
Indices: 533230--533265 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
533220 ATTTTATGGC
*
533230 TTAAGGTTTAGGAT
1 TTAAGATTTAGGAT
533244 TTAAGATTTAGGAT
1 TTAAGATTTAGGAT
*
533258 TTGAGATT
1 TTAAGATT
533266 GAGGTAAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TTAAGATTTAGGAT
Found at i:538110 original size:36 final size:36
Alignment explanation
Indices: 538063--538134 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
538053 CATGTTAACA
538063 GAAGATGGTAAATCAAATTCTTCAGCAAGAAACTAC
1 GAAGATGGTAAATCAAATTCTTCAGCAAGAAACTAC
538099 GAAGATGGTAAATCAAATTCTTCAGCAAGAAACTAC
1 GAAGATGGTAAATCAAATTCTTCAGCAAGAAACTAC
538135 TTACTCTAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (36 bp):
GAAGATGGTAAATCAAATTCTTCAGCAAGAAACTAC
Found at i:541736 original size:15 final size:15
Alignment explanation
Indices: 541716--541744 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
541706 GCCATAAACC
541716 TCATCGTCATCGTCT
1 TCATCGTCATCGTCT
541731 TCATCGTCATCGTC
1 TCATCGTCATCGTC
541745 GGCCAAGTCA
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:0.14, C:0.34, G:0.14, T:0.38
Consensus pattern (15 bp):
TCATCGTCATCGTCT
Found at i:543135 original size:15 final size:15
Alignment explanation
Indices: 543115--543166 Score: 86
Period size: 15 Copynumber: 3.4 Consensus size: 15
543105 TAATTTACTT
543115 TATATAGTTTATATA
1 TATATAGTTTATATA
*
543130 TATATAGGTTATATA
1 TATATAGTTTATATA
543145 TATATAGTTTATATA
1 TATATAGTTTATATA
543160 TACTATA
1 TA-TATA
543167 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
15 30 0.88
16 4 0.12
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:543545 original size:7 final size:7
Alignment explanation
Indices: 543524--543595 Score: 101
Period size: 7 Copynumber: 10.3 Consensus size: 7
543514 TCCATTTATA
543524 TTAGGGT
1 TTAGGGT
543531 TT-GTGGT
1 TTAG-GGT
543538 TTAGGGT
1 TTAGGGT
543545 TTAGGGT
1 TTAGGGT
*
543552 TTAGTGT
1 TTAGGGT
543559 TTAGGGT
1 TTAGGGT
543566 TTAGGGT
1 TTAGGGT
543573 TTAGGGT
1 TTAGGGT
* *
543580 TTATGAT
1 TTAGGGT
543587 TTAGGGT
1 TTAGGGT
543594 TT
1 TT
543596 CTATAAACTA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
6 1 0.02
7 55 0.96
8 1 0.02
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.49
Consensus pattern (7 bp):
TTAGGGT
Found at i:543672 original size:20 final size:19
Alignment explanation
Indices: 543633--543683 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
543623 ATATAGTTTA
*
543633 TATATATATATATATAGTT
1 TATATATATATACATAGTT
*
543652 TATATATACTATACATGGTT
1 TATATATA-TATACATAGTT
*
543672 TATACATATATA
1 TATATATATATA
543684 TACTATAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (19 bp):
TATATATATATACATAGTT
Found at i:543934 original size:4 final size:4
Alignment explanation
Indices: 543925--546240 Score: 4397
Period size: 4 Copynumber: 586.8 Consensus size: 4
543915 TATATAGTTT
543925 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
543973 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
544021 ATAC AGAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544069 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544117 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A-AC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544164 ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544210 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544258 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544306 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544354 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-C ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544401 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544449 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544497 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544545 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544593 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544641 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544689 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544737 ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544783 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544829 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544877 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544925 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
544973 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545021 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545069 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545117 ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545163 -TAC -TAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC ATAC AT--
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545206 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545254 ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545300 ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
545346 CTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545394 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545440 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA- ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545487 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545535 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545583 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545631 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545679 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545727 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545775 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545823 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545871 ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545916 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
545964 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
546012 ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
546058 ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
546104 ATAC AT-- ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
546150 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
546198 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
546241 ATTAAAAGTA
Statistics
Matches: 2278, Mismatches: 4, Indels: 60
0.97 0.00 0.03
Matches are distributed among these distances:
2 24 0.01
3 21 0.01
4 2233 0.98
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:546595 original size:2 final size:2
Alignment explanation
Indices: 546588--546668 Score: 85
Period size: 2 Copynumber: 40.5 Consensus size: 2
546578 ACTTTGAATA
* *
546588 AT AT AT AT AT AT AT AT AT AT AT A- AGT AT AT AC AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT
* * *
546630 AT AT AT AT A- AGT AT AT AC AT AA AT TT AT AT AT AT AT AT A
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
546669 AATAAACATA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
1 2 0.03
2 61 0.94
3 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:546636 original size:28 final size:28
Alignment explanation
Indices: 546596--546666 Score: 133
Period size: 28 Copynumber: 2.5 Consensus size: 28
546586 TAATATATAT
546596 ATATATATATATATAAGTATATACATAA
1 ATATATATATATATAAGTATATACATAA
546624 ATATATATATATATAAGTATATACATAA
1 ATATATATATATATAAGTATATACATAA
*
546652 ATTTATATATATATA
1 ATATATATATATATA
546667 TAAATAAACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (28 bp):
ATATATATATATATAAGTATATACATAA
Found at i:546677 original size:28 final size:27
Alignment explanation
Indices: 546596--546679 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 27
546586 TAATATATAT
546596 ATATATATATATATAAGTATATACATAA
1 ATATATATATATATAAG-ATATACATAA
546624 ATATATATATATATAAGTATATACATAA
1 ATATATATATATATAAG-ATATACATAA
*
546652 ATTTATATATATATATAA-ATAAACATAA
1 A--TATATATATATATAAGATATACATAA
546680 GTGACTAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
28 38 0.72
30 15 0.28
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (27 bp):
ATATATATATATATAAGATATACATAA
Found at i:547058 original size:22 final size:22
Alignment explanation
Indices: 547000--547059 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
546990 CTCAAAAATT
*
547000 TTCCCACCTCTAAATTTGCCAA
1 TTCCCACCTTTAAATTTGCCAA
*** ** *
547022 TTATAAGATTAAAATTTGCCAA
1 TTCCCACCTTTAAATTTGCCAA
547044 TTCCCACCTTTAAATT
1 TTCCCACCTTTAAATT
547060 CCTACCACTC
Statistics
Matches: 25, Mismatches: 13, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (22 bp):
TTCCCACCTTTAAATTTGCCAA
Found at i:547174 original size:15 final size:15
Alignment explanation
Indices: 547151--547184 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
547141 TTAAATTTTT
547151 TATAATTTATACATA
1 TATAATTTATACATA
* *
547166 TATAGTTTATATATA
1 TATAATTTATACATA
547181 TATA
1 TATA
547185 TTAACATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (15 bp):
TATAATTTATACATA
Found at i:547248 original size:26 final size:26
Alignment explanation
Indices: 547166--547272 Score: 67
Period size: 26 Copynumber: 4.0 Consensus size: 26
547156 TTTATACATA
**
547166 TATAGTTTATATATATATATTAACATAAAT
1 TATAGTTTATATATATATA-T---ATAGTT
* * *
547196 TAAAGTTTATAAACTATATA-AT-TTT
1 TATAGTTTATATA-TATATATATAGTT
547221 TATAGTTTATATATATATATATAGTT
1 TATAGTTTATATATATATATATAGTT
* * *
547247 TACA-TATATAATTTATATATATAGTT
1 TATAGTTTAT-ATATATATATATAGTT
547273 CATATAAACA
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
24 6 0.10
25 18 0.29
26 22 0.35
30 11 0.17
31 6 0.10
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (26 bp):
TATAGTTTATATATATATATATAGTT
Found at i:547277 original size:13 final size:13
Alignment explanation
Indices: 547234--547278 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
547224 AGTTTATATA
547234 TATATATATAGTT
1 TATATATATAGTT
* *
547247 TACATATATAATT
1 TATATATATAGTT
547260 TATATATATAGTT
1 TATATATATAGTT
*
547273 CATATA
1 TATATA
547279 AACATAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (13 bp):
TATATATATAGTT
Found at i:549044 original size:216 final size:215
Alignment explanation
Indices: 548595--549291 Score: 1191
Period size: 216 Copynumber: 3.2 Consensus size: 215
548585 TCCCTTCGTA
* *
548595 TTGTTTAATTTACTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAAATTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
548660 ATTTGCATCTAAAATTGACCCATACTT-TTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
548724 TAAATGGGTATAATTTAGTACTTTTTGTATTAATTTCAACCTCACAATTTAAAGTTATTTCGATT
131 TAAATGGGTATAATTTAGTATTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATT
548789 TGATCCCTCATCAATGTGTG
196 TGATCCCTCATCAATGTGTG
548809 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
* * * * * *
548874 ATTTGCTTCTGAAATTGACCTATACTTATTATTTATTTCTATTTTTAAATTGGACCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
* *
548939 TAAATGGATATAATTTAGTATTTTTTTGTATTAATTTCAACCTCA-ATTTTTAAAATTATTTCGA
131 TAAATGGGTATAATTTAGTA-TTTTTTGTATTAATTTCAACCTCACA-ATTTAAAATTATTTCGA
*
549003 TTTGACCCCTCATCAATGTGTG
194 TTTGATCCCTCATCAATGTGTG
* * *
549025 TTGTTTAATTTATTTAAATTTTTATTTGAAATTTCATATTTATTCAAGTTAGTCCTCCAAATTTT
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
549090 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
66 ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
549155 TAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
131 TAAATGGGTATAATTTAGTA-TTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGAT
549220 TTGATCCCTCATCAATGTGTG
195 TTGATCCCTCATCAATGTGTG
* *
549241 TTGTTTAATTTATTTAAATTTTTATTTGTAACTCCATATTTGTTCAATTTA
1 TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTA
549292 ATTCTTAAAT
Statistics
Matches: 448, Mismatches: 31, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
214 87 0.19
215 54 0.12
216 306 0.68
217 1 0.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.50
Consensus pattern (215 bp):
TTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTT
ATTTGCATCTAAAATTGACCCATACTTATTACTTATTTCTATTTTTTAATTGGCCCATAACTTTT
TAAATGGGTATAATTTAGTATTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATTTCGATT
TGATCCCTCATCAATGTGTG
Found at i:549997 original size:50 final size:50
Alignment explanation
Indices: 549906--550004 Score: 128
Period size: 50 Copynumber: 2.0 Consensus size: 50
549896 AGTATTTAAG
** * ** *
549906 AAACTCGTCATGTTGAGGTGATAAGTTCGTTCAAATAATATTTTTTATTC
1 AAACTCGTCACCTTGAGGTGACAAGTTCAATAAAATAATATTTTTTATTC
549956 AAACTCGTCACCTTGAGGTGACAAGTTCCAATAAAAT-ATATTTTTTATT
1 AAACTCGTCACCTTGAGGTGACAAGTT-CAATAAAATAATATTTTTTATT
550005 AATTTTCTCA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 36 0.86
51 6 0.14
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (50 bp):
AAACTCGTCACCTTGAGGTGACAAGTTCAATAAAATAATATTTTTTATTC
Found at i:550670 original size:2 final size:2
Alignment explanation
Indices: 550663--550713 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
550653 ATTGTCATTA
550663 AT AT AT AT AT AT AT AT AT A- 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
550704 AT AT AT AT AT
1 AT AT AT AT AT
550714 TTAAGGCCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:567586 original size:20 final size:20
Alignment explanation
Indices: 567522--567594 Score: 71
Period size: 20 Copynumber: 3.6 Consensus size: 20
567512 CAACTTAATT
567522 TCGAATTCGCAACAC-GAAAG
1 TCGAATTCGCAACACAG-AAG
* **
567542 -CTAATTTCGCAACACAG-TT
1 TCGAA-TTCGCAACACAGAAG
567561 TCCGAATTCGCAACACAGAAG
1 T-CGAATTCGCAACACAGAAG
567582 TCGAATTCGCAAC
1 TCGAATTCGCAAC
567595 TCGAAATTGA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
19 3 0.07
20 34 0.81
21 5 0.12
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (20 bp):
TCGAATTCGCAACACAGAAG
Found at i:567615 original size:22 final size:21
Alignment explanation
Indices: 567587--567640 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
567577 AGAAGTCGAA
567587 TTCGCAACTCGAAATTGACATT
1 TTCGCAACTCGAAATT-ACATT
* * *
567609 TTCGCAACACG-AATTTCTTT
1 TTCGCAACTCGAAATTACATT
567629 TTCGCAACTCGA
1 TTCGCAACTCGA
567641 TTTTTAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 13 0.48
21 4 0.15
22 10 0.37
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (21 bp):
TTCGCAACTCGAAATTACATT
Found at i:567633 original size:42 final size:40
Alignment explanation
Indices: 567587--567716 Score: 116
Period size: 40 Copynumber: 3.2 Consensus size: 40
567577 AGAAGTCGAA
* *
567587 TTCGCAACTCGAAATTGACATTTTCGCAACACGAATTTCTTT
1 TTCGCAACTCGAAATTGA-A-ATTCGCAACACGAATTTCATT
** * *
567629 TTCGCAACTCGATTTTTAAATTCGCAACACGAGTTTCATT
1 TTCGCAACTCGAAATTGAAATTCGCAACACGAATTTCATT
* ** ** * * *
567669 TTCACAACTCGATTTTCTAATTCGCAACGCGAGTTTCGTT
1 TTCGCAACTCGAAATTGAAATTCGCAACACGAATTTCATT
567709 TTCGCAAC
1 TTCGCAAC
567717 GCAAATTTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
40 60 0.79
41 1 0.01
42 15 0.20
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (40 bp):
TTCGCAACTCGAAATTGAAATTCGCAACACGAATTTCATT
Found at i:567660 original size:40 final size:39
Alignment explanation
Indices: 567609--567736 Score: 157
Period size: 40 Copynumber: 3.2 Consensus size: 39
567599 AATTGACATT
* *
567609 TTCGCAACACGAATTTCTTTTTCGCAACTCGATTTTTAAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTT-AA
*
567649 TTCGCAACACGAGTTTCATTTTCACAACTCGATTTTCTAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTT-TAA
* * * * *
567689 TTCGCAACGCGAGTTTCGTTTTCGCAACGCAAATTTTGAA
1 TTCGCAACACGAGTTTCATTTTCGCAACTC-GATTTTTAA
567729 TTCGCAAC
1 TTCGCAAC
567737 CCATCCTGCT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
40 71 0.92
41 6 0.08
ACGTcount: A:0.27, C:0.24, G:0.13, T:0.36
Consensus pattern (39 bp):
TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTTAA
Found at i:567718 original size:20 final size:20
Alignment explanation
Indices: 567605--567716 Score: 91
Period size: 20 Copynumber: 5.6 Consensus size: 20
567595 TCGAAATTGA
*
567605 CATTTTCGCAACACGAATTT
1 CATTTTCGCAACACGAGTTT
* * *
567625 CTTTTTCGCAACTCGATTTT
1 CATTTTCGCAACACGAGTTT
* **
567645 TAAATTCGCAACACGAGTTT
1 CATTTTCGCAACACGAGTTT
* * *
567665 CATTTTCACAACTCGATTTT
1 CATTTTCGCAACACGAGTTT
* *
567685 C-TAATTCGCAACGCGAGTTT
1 CAT-TTTCGCAACACGAGTTT
*
567705 CGTTTTCGCAAC
1 CATTTTCGCAAC
567717 GCAAATTTTG
Statistics
Matches: 70, Mismatches: 20, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
19 1 0.01
20 68 0.97
21 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (20 bp):
CATTTTCGCAACACGAGTTT
Found at i:568187 original size:17 final size:17
Alignment explanation
Indices: 568156--568206 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
568146 GCTTTATGAT
568156 TCTTCTCTCTCTCTTTTG
1 TCTTCTCT-TCTCTTTTG
*
568174 TCTTTTCTTCTCTTTTG
1 TCTTCTCTTCTCTTTTG
568191 TCTTCTCTTCTCTTTT
1 TCTTCTCTTCTCTTTT
568207 TCATTGAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 24 0.77
18 7 0.23
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (17 bp):
TCTTCTCTTCTCTTTTG
Found at i:568403 original size:22 final size:20
Alignment explanation
Indices: 568354--568408 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
568344 GTGAATTTAA
568354 AAATATCGAGTTGCGAAAAAG
1 AAAT-TCGAGTTGCGAAAAAG
* *
568375 AAATTCGTGTTGCGAAAATG
1 AAATTCGAGTTGCGAAAAAG
568395 TCAAATTCGAGTTG
1 --AAATTCGAGTTG
568409 TGAATTCGAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 14 0.48
21 4 0.14
22 11 0.38
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AAATTCGAGTTGCGAAAAAG
Done.