Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10
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: 48586650
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2183483 characters in sequence are not A, C, G, or T
File 115 of 145
Found at i:38580212 original size:42 final size:41
Alignment explanation
Indices: 38580076--38580207 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 41
38580066 ATTATTAGCA
38580076 ATTATTTGAATTAAATATTAAATAATAATGTTTTAATTATCC
1 ATTATTT-AATTAAATATTAAATAATAATGTTTTAATTATCC
* * * * *
38580118 ATTATGT-ATTTAATATTCACAAT-A-AAT-TTTATTATTAGCA
1 ATTATTTAATTAAATATT-A-AATAATAATGTTT-TAATTATCC
38580158 ATTATTTGAATTAAATATTAAATAATAATGTTTTAATTATCC
1 ATTATTT-AATTAAATATTAAATAATAATGTTTTAATTATCC
38580200 ATT-TTTAA
1 ATTATTTAA
38580208 AATTATCATT
Statistics
Matches: 72, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
39 3 0.04
40 29 0.40
41 7 0.10
42 30 0.42
43 3 0.04
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (41 bp):
ATTATTTAATTAAATATTAAATAATAATGTTTTAATTATCC
Found at i:38580611 original size:1 final size:1
Alignment explanation
Indices: 38580607--38580631 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
38580597 TTTCTATTGT
38580607 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
38580632 CCTACTTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38584958 original size:55 final size:55
Alignment explanation
Indices: 38584885--38584997 Score: 149
Period size: 55 Copynumber: 2.0 Consensus size: 55
38584875 AATAAAAATT
* *
38584885 AAAAATTAAATTTTTATAAAAATCGTAA-AAAATTAT-AAAATATATAGAAATATA
1 AAAAATTAAATTTTTAT-AAAATCATAAGAAAATTATAAAAATATAAAGAAATATA
* *
38584939 AAAAATATAAATTTTTATAAAGTCATAAGAAAATTATACAAAATGTAAAGAAATATA
1 AAAAAT-TAAATTTTTATAAAATCATAAGAAAATTATA-AAAATATAAAGAAATATA
38584996 AA
1 AA
38584998 TTTCGTAAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
54 14 0.27
55 19 0.37
57 18 0.35
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.31
Consensus pattern (55 bp):
AAAAATTAAATTTTTATAAAATCATAAGAAAATTATAAAAATATAAAGAAATATA
Found at i:38585205 original size:39 final size:38
Alignment explanation
Indices: 38585162--38585245 Score: 89
Period size: 39 Copynumber: 2.2 Consensus size: 38
38585152 TTTTACAAAT
*
38585162 TTTTTTATTTTTTTACAATTTTTATAAAAAAATTT-CTAA
1 TTTTTTATTTTTTT-CAATTTTT-TAAAAAAATTTAATAA
* * **
38585201 TTTTTAAATTTTTTTTAATTTTTTATTAAAATTTAATAA
1 TTTTT-TATTTTTTTCAATTTTTTAAAAAAATTTAATAA
38585240 TTTTTT
1 TTTTTT
38585246 TAAAATTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
38 9 0.24
39 20 0.54
40 8 0.22
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (38 bp):
TTTTTTATTTTTTTCAATTTTTTAAAAAAATTTAATAA
Found at i:38585245 original size:40 final size:39
Alignment explanation
Indices: 38585141--38585245 Score: 99
Period size: 40 Copynumber: 2.6 Consensus size: 39
38585131 TAATTTATGC
*
38585141 TTTTTATAAAATTTTACA-AATTTTTTTATTTTTTTACAAT
1 TTTTTATAAAA-TTTA-ATAATTTTTTAATTTTTTTACAAT
* * * *
38585181 TTTTATAAAAAAATTT-CTAATTTTTAAATTTTTTT-TAAT
1 TTTT-T-ATAAAATTTAATAATTTTTTAATTTTTTTACAAT
38585220 TTTTTATTAAAATTTAATAATTTTTT
1 TTTTTA-TAAAATTTAATAATTTTTT
38585246 TAAAATTTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
37 1 0.02
38 8 0.15
39 15 0.29
40 19 0.37
41 4 0.08
42 5 0.10
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTATAAAATTTAATAATTTTTTAATTTTTTTACAAT
Found at i:38585262 original size:19 final size:20
Alignment explanation
Indices: 38585218--38585265 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
38585208 ATTTTTTTTA
38585218 ATTTTTTATTAAAATTTAAT
1 ATTTTTTATTAAAATTTAAT
* *
38585238 AATTTTT-TTAAAATTTATT
1 ATTTTTTATTAAAATTTAAT
38585257 ATTTTTTAT
1 ATTTTTTAT
38585266 AATTTTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTTTTATTAAAATTTAAT
Found at i:38595411 original size:24 final size:24
Alignment explanation
Indices: 38595384--38595433 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
38595374 ATAAGGAAAG
38595384 TTTGATTTCCATTGGGAGCAAGCC
1 TTTGATTTCCATTGGGAGCAAGCC
38595408 TTTGATTTCCATTGGGAGCAAGCC
1 TTTGATTTCCATTGGGAGCAAGCC
38595432 TT
1 TT
38595434 GGAAATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.36
Consensus pattern (24 bp):
TTTGATTTCCATTGGGAGCAAGCC
Found at i:38599646 original size:21 final size:21
Alignment explanation
Indices: 38599620--38599663 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
38599610 TAGATTGGCG
38599620 GTGCGTTTACCTGCGGTTAGT
1 GTGCGTTTACCTGCGGTTAGT
*
38599641 GTGCGTTTACTTGCGGTTAGT
1 GTGCGTTTACCTGCGGTTAGT
38599662 GT
1 GT
38599664 AAAAGCAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.16, G:0.34, T:0.41
Consensus pattern (21 bp):
GTGCGTTTACCTGCGGTTAGT
Found at i:38605520 original size:18 final size:18
Alignment explanation
Indices: 38605499--38605535 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38605489 GAGTAATAAG
38605499 AGCAGTTAGAAGTCAGTT
1 AGCAGTTAGAAGTCAGTT
38605517 AGCAGTTAGAAGTCAGTT
1 AGCAGTTAGAAGTCAGTT
38605535 A
1 A
38605536 ACACAAACTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (18 bp):
AGCAGTTAGAAGTCAGTT
Found at i:38611969 original size:43 final size:43
Alignment explanation
Indices: 38611834--38611970 Score: 177
Period size: 43 Copynumber: 3.2 Consensus size: 43
38611824 TGTATTTTGT
* * * *
38611834 CAATGGGTGAATTGTTTAAAGTCTGCTTATGTATAGCATTCGC
1 CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
* * **
38611877 CAAT-GTCTGAATTGTATAAAGTATGCTTGCATATAGTATTCGC
1 CAATGGGC-GAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
*
38611920 CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTTGC
1 CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
38611963 CAATGGGC
1 CAATGGGC
38611971 AAACTATGTG
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 76 0.96
44 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (43 bp):
CAATGGGCGAATTGTATAAAGTCTGCTTGTGTATAGTATTCGC
Found at i:38612939 original size:10 final size:11
Alignment explanation
Indices: 38612909--38612938 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
38612899 TCAAACTTGT
*
38612909 AAATATTTTTA
1 AAATATTTTAA
38612920 AAATATTTTAA
1 AAATATTTTAA
38612931 AAATATTT
1 AAATATTT
38612939 ACAAAGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:38614006 original size:16 final size:17
Alignment explanation
Indices: 38613975--38614007 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38613965 ACTATTGTAC
38613975 TTTATAATTGAATTGAA
1 TTTATAATTGAATTGAA
*
38613992 TTTATAGTT-AATTGAA
1 TTTATAATTGAATTGAA
38614008 ATGGATTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (17 bp):
TTTATAATTGAATTGAA
Found at i:38614942 original size:26 final size:25
Alignment explanation
Indices: 38614888--38614942 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 25
38614878 AAATTGAGTT
* *
38614888 ATAAATATAATGTTGGTTTGAATAT
1 ATAAATATAATGTTGGTTTGAAGAC
*
38614913 ATAAATAT-ATGTTGGTGTTTGAAGCC
1 ATAAATATAATGTT-G-GTTTGAAGAC
38614939 ATAA
1 ATAA
38614943 TTTGGCATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 9 0.36
26 11 0.44
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (25 bp):
ATAAATATAATGTTGGTTTGAAGAC
Found at i:38621662 original size:43 final size:43
Alignment explanation
Indices: 38621614--38621754 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 43
38621604 AGTTTTGTAT
* * * *
38621614 TTCACCAATGGGCGAATTGTATAAAGTTTGCTTGTGTATACTA
1 TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
* * *
38621657 TTCACCAATTGGAAAATAGTATAAAGTCTGCTTGTGTATAGTA
1 TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
** * *
38621700 TTTGCCAATAGACAAATTGTATAAAGCCTGCTTGTGTATAGTA
1 TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
*
38621743 TTCGCCAATAGG
1 TTCACCAATAGG
38621755 TGAACTATGT
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 83 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (43 bp):
TTCACCAATAGGCAAATTGTATAAAGTCTGCTTGTGTATAGTA
Found at i:38627249 original size:13 final size:13
Alignment explanation
Indices: 38627231--38627275 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
38627221 AACATGGTTT
38627231 TTTATTTATTTTA
1 TTTATTTATTTTA
38627244 TTTATTTATTTTA
1 TTTATTTATTTTA
*
38627257 TCTTATCT-TTTTA
1 T-TTATTTATTTTA
38627270 TTTATT
1 TTTATT
38627276 ACCCTAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 4 0.14
13 20 0.69
14 5 0.17
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTA
Found at i:38628032 original size:61 final size:62
Alignment explanation
Indices: 38627916--38628034 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
38627906 AAGGATCGGC
* * * *
38627916 GGCGACTCCATTTTTATTTTTTAAAATAAAAGTCGATTTCAAAAAAAAGGTTTCGACAGCTT
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTTAAAAAAAAAAGTTTCGACAGCTT
* **
38627978 GGCGACTCCGTTTTCATTTTTTAAAATAAAAATTTA-TTAAAAAAAAAAGTTTCGACA
1 GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTTAAAAAAAAAAGTTTCGACA
38628035 ATCTCCTTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
61 19 0.38
62 31 0.62
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (62 bp):
GGCGACTCCATTTTCATTTTTTAAAATAAAAATCGATTTAAAAAAAAAAGTTTCGACAGCTT
Found at i:38643957 original size:15 final size:15
Alignment explanation
Indices: 38643937--38643967 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38643927 GCCCATATGG
38643937 ATCATCTTCATCTTC
1 ATCATCTTCATCTTC
*
38643952 ATCATCTTCTTCTTC
1 ATCATCTTCATCTTC
38643967 A
1 A
38643968 CTTTTAACTC
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:0.19, C:0.32, G:0.00, T:0.48
Consensus pattern (15 bp):
ATCATCTTCATCTTC
Found at i:38645110 original size:8 final size:8
Alignment explanation
Indices: 38645097--38645144 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
38645087 AATGTGTAAA
38645097 TTATATAT
1 TTATATAT
38645105 TTATATAT
1 TTATATAT
38645113 TTATA-A-
1 TTATATAT
*
38645119 ATATATAT
1 TTATATAT
*
38645127 ATATATAT
1 TTATATAT
*
38645135 TTATAAAT
1 TTATATAT
38645143 TT
1 TT
38645145 TCGTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
6 4 0.11
7 2 0.06
8 29 0.83
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
TTATATAT
Found at i:38645236 original size:77 final size:77
Alignment explanation
Indices: 38645149--38645303 Score: 292
Period size: 77 Copynumber: 2.0 Consensus size: 77
38645139 AAATTTTCGT
* *
38645149 TTATTTTTAAACTGGACAATCCTCAAATACATTACTTTTATTATACTTCAAATGACTAAGAACTT
1 TTATTATTAAACTAGACAATCCTCAAATACATTACTTTTATTATACTTCAAATGACTAAGAACTT
38645214 GATATCTCTCAA
66 GATATCTCTCAA
38645226 TTATTATTAAACTAGACAATCCTCAAATACATTACTTTTATTATACTTCAAATGACTAAGAACTT
1 TTATTATTAAACTAGACAATCCTCAAATACATTACTTTTATTATACTTCAAATGACTAAGAACTT
38645291 GATATCTCTCAA
66 GATATCTCTCAA
38645303 T
1 T
38645304 GATAACCAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (77 bp):
TTATTATTAAACTAGACAATCCTCAAATACATTACTTTTATTATACTTCAAATGACTAAGAACTT
GATATCTCTCAA
Found at i:38648897 original size:24 final size:24
Alignment explanation
Indices: 38648869--38648920 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
38648859 TTAGTAAGTC
* *
38648869 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
38648893 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
38648917 AAAT
1 AAAT
38648921 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:38651433 original size:2 final size:2
Alignment explanation
Indices: 38651426--38651450 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38651416 TTTATAAAAT
38651426 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 T
38651451 TAAAGCAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38652403 original size:23 final size:23
Alignment explanation
Indices: 38652373--38652419 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
38652363 ATTCTGAGTA
38652373 GGCGTCGGGCATGTTGAACACGT
1 GGCGTCGGGCATGTTGAACACGT
38652396 GGCGTCGGGCATGTTGAACACGT
1 GGCGTCGGGCATGTTGAACACGT
38652419 G
1 G
38652420 TACTGTTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.40, T:0.21
Consensus pattern (23 bp):
GGCGTCGGGCATGTTGAACACGT
Found at i:38655339 original size:346 final size:347
Alignment explanation
Indices: 38654696--38655392 Score: 1362
Period size: 346 Copynumber: 2.0 Consensus size: 347
38654686 CAATTTACTT
38654696 TCATTATCGACATTCAACTTTTACAATCATAATTATAGCTATAAATATTTGCATTATATATGTAT
1 TCATTATC-ACATTCAACTTTTACAATCATAATTATAGCTATAAATATTTGCATTATATATGTAT
38654761 TCTCGGAGGGGTCAGGTGCAGGACCCAATTGAACAAACTAAAGTAAAAGAAGTAACATGAATATA
65 TCTCGGAGGGGTCAGGTGCAGGACCCAATTGAACAAACTAAAGTAAAAGAAGTAACATGAATATA
38654826 TATATATATACATGTATGTTGTGTACGTATACAGAGAATTAAGATATGATGTTTGATGTGAGGAA
130 TATATATATACATGTATGTTGTGTACGTATACAGAGAATTAAGATATGATGTTTGATGTGAGGAA
38654891 TGGGCCTCCACCATTTGCCATTACCAATTCATTTCCAGTTAATTTTTATACCAACAAATCTTGTA
195 TGGGCCTCCACCATTTGCCATTACCAATTCATTTCCAGTTAATTTTTATACCAACAAATCTTGTA
38654956 TAATGAAAGATACCAACTTTATTAAGAAAAAGAAGAAATAAAAGTAGAATAATTTACAACTAGAC
260 TAATGAAAGATACCAACTTTATTAAGAAAAAGAAGAAATAAAAGTAGAATAATTTACAACTAGAC
38655021 AATGGTGTAATGTCGTTTGAGTG
325 AATGGTGTAATGTCGTTTGAGTG
38655044 TCATTATC-CATTCAACTTTTACAATCATAATTATAGCTATAAATATTTGCATTATATATGTATT
1 TCATTATCACATTCAACTTTTACAATCATAATTATAGCTATAAATATTTGCATTATATATGTATT
38655108 CAT-GGAGGGGTCAGGTGCAGGACCCAATTGAACAAACTAAAGTAAAAGAAGTAACATGAATATA
66 C-TCGGAGGGGTCAGGTGCAGGACCCAATTGAACAAACTAAAGTAAAAGAAGTAACATGAATATA
38655172 TATATATATACATGTATGTTGTGTACGTATACAGAGAATTAAGATATGATGTTTGATGTGAGGAA
130 TATATATATACATGTATGTTGTGTACGTATACAGAGAATTAAGATATGATGTTTGATGTGAGGAA
38655237 TGGGCCTCCACCATTTGCCATTACCAATTCATTTCCAGTTAATTTTTATACCAACAAATCTTGTA
195 TGGGCCTCCACCATTTGCCATTACCAATTCATTTCCAGTTAATTTTTATACCAACAAATCTTGTA
38655302 TAATGAAAGATACCAACTTTATTAAGAAAAAGAAGAAATAAAAGTAGAATAATTTACAACTAGAC
260 TAATGAAAGATACCAACTTTATTAAGAAAAAGAAGAAATAAAAGTAGAATAATTTACAACTAGAC
38655367 AATGGTGTAATGTCGTTTGAGTG
325 AATGGTGTAATGTCGTTTGAGTG
38655390 TCA
1 TCA
38655393 GTGACATGAG
Statistics
Matches: 348, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
346 339 0.97
347 1 0.00
348 8 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (347 bp):
TCATTATCACATTCAACTTTTACAATCATAATTATAGCTATAAATATTTGCATTATATATGTATT
CTCGGAGGGGTCAGGTGCAGGACCCAATTGAACAAACTAAAGTAAAAGAAGTAACATGAATATAT
ATATATATACATGTATGTTGTGTACGTATACAGAGAATTAAGATATGATGTTTGATGTGAGGAAT
GGGCCTCCACCATTTGCCATTACCAATTCATTTCCAGTTAATTTTTATACCAACAAATCTTGTAT
AATGAAAGATACCAACTTTATTAAGAAAAAGAAGAAATAAAAGTAGAATAATTTACAACTAGACA
ATGGTGTAATGTCGTTTGAGTG
Found at i:38667345 original size:73 final size:73
Alignment explanation
Indices: 38667256--38667409 Score: 238
Period size: 73 Copynumber: 2.1 Consensus size: 73
38667246 ACGAAACTTA
* * *
38667256 TAACATTT-TCATGTTATAAAACATATACAAGTAAACACATTAGACATATCATTTATTCAACATC
1 TAACATTTCACATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATC
*
38667320 TATTCATT
66 TATTAATT
* * *
38667328 TAACATTTCACATGTTATAAAACGTGTACAAGTAAACACATTAGATATACCATTCATTCAACATC
1 TAACATTTCACATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATC
38667393 TATTAATT
66 TATTAATT
38667401 TAACATTTC
1 TAACATTTC
38667410 CCATTTCCCA
Statistics
Matches: 74, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
72 8 0.11
73 66 0.89
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (73 bp):
TAACATTTCACATGTTATAAAACATATACAAGTAAACACATTAGACATACCATTCATTCAACATC
TATTAATT
Found at i:38667414 original size:7 final size:7
Alignment explanation
Indices: 38667404--38667430 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38667394 ATTAATTTAA
38667404 CATTTCC
1 CATTTCC
38667411 CATTTCC
1 CATTTCC
38667418 CATTTCC
1 CATTTCC
38667425 CATTTC
1 CATTTC
38667431 AAGCGTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (7 bp):
CATTTCC
Found at i:38667864 original size:45 final size:45
Alignment explanation
Indices: 38667815--38667913 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 45
38667805 ACAGTTACGG
*
38667815 TCTTACACACTTCCGAT-ATGAT-GTCATAGTGTCTTTCAACAATGA
1 TCTTACACACTTCCG-TCATGATAG-CATAATGTCTTTCAACAATGA
* * * *
38667860 TCTTATC-CATTTCCGTCATGTTAGCATAATGTCTTTCAACTATGG
1 TCTTA-CACACTTCCGTCATGATAGCATAATGTCTTTCAACAATGA
38667905 TCTTACACA
1 TCTTACACA
38667914 TTGAATCGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
44 2 0.04
45 41 0.91
46 2 0.04
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.38
Consensus pattern (45 bp):
TCTTACACACTTCCGTCATGATAGCATAATGTCTTTCAACAATGA
Found at i:38667976 original size:45 final size:44
Alignment explanation
Indices: 38667891--38668004 Score: 156
Period size: 45 Copynumber: 2.6 Consensus size: 44
38667881 TAGCATAATG
* * *
38667891 TCTTTCAACTATGGTCTTACACATTGAATCGTGATGCCATAGCA
1 TCTTTCAGCTATGGTCTTACTCATTGAATCATGATGCCATAGCA
* * *
38667935 TCTTTTAGCTATGGTCTTACTCGTTTGAATCATGATGCCATAGCG
1 TCTTTCAGCTATGGTCTTACTC-ATTGAATCATGATGCCATAGCA
*
38667980 TCTTTCAGCTATGATCTTACTCATT
1 TCTTTCAGCTATGGTCTTACTCATT
38668005 TCCAGTATAG
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
44 21 0.35
45 39 0.65
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (44 bp):
TCTTTCAGCTATGGTCTTACTCATTGAATCATGATGCCATAGCA
Found at i:38669798 original size:24 final size:27
Alignment explanation
Indices: 38669771--38669820 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
38669761 CAAATACTCA
38669771 TTTATA-TA-ATTAAAATAT-TCATAT
1 TTTATACTAGATTAAAATATGTCATAT
38669795 TTTATACTAGATTAAAATATGTCATA
1 TTTATACTAGATTAAAATATGTCATA
38669821 AGTCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 10 0.43
27 5 0.22
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TTTATACTAGATTAAAATATGTCATAT
Found at i:38670237 original size:23 final size:23
Alignment explanation
Indices: 38670196--38670239 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
38670186 CTATAAAAAA
*
38670196 TTATTATTAATATTGTAATATAT
1 TTATTATTAAAATTGTAATATAT
38670219 TTATTATTAAAATAT-TAATAT
1 TTATTATTAAAAT-TGTAATAT
38670240 TAATATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTATTAAAATTGTAATATAT
Found at i:38670240 original size:6 final size:6
Alignment explanation
Indices: 38670229--38670258 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
38670219 TTATTATTAA
38670229 AATATT AATATT AATATT AATATT ATATAT
1 AATATT AATATT AATATT AATATT A-ATAT
38670259 AAAAATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATATT
Found at i:38689133 original size:16 final size:17
Alignment explanation
Indices: 38689093--38689134 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
38689083 TTCTCCACAT
38689093 AGTTATTCCCAATATAG
1 AGTTATTCCCAATATAG
*
38689110 AGGTTATTCCGAATA-AG
1 A-GTTATTCCCAATATAG
38689127 AGTTATTC
1 AGTTATTC
38689135 TGTAATAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 4 0.17
18 12 0.52
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (17 bp):
AGTTATTCCCAATATAG
Found at i:38689198 original size:15 final size:16
Alignment explanation
Indices: 38689178--38689216 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
38689168 GAATAATGGC
*
38689178 TCTAAATAC-ATTTGT
1 TCTAAATACAAGTTGT
38689193 TCTAAATACAAGTTGT
1 TCTAAATACAAGTTGT
*
38689209 TCCAAATA
1 TCTAAATA
38689217 ATGGTTGGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (16 bp):
TCTAAATACAAGTTGT
Found at i:38689296 original size:26 final size:26
Alignment explanation
Indices: 38689260--38689312 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
38689250 CCATATTCTA
38689260 AACAAGAGTTATTTCGAACTTTAATC
1 AACAAGAGTTATTTCGAACTTTAATC
38689286 AACAAGAGTTATTTCGAACTTTAATC
1 AACAAGAGTTATTTCGAACTTTAATC
38689312 A
1 A
38689313 TTCTCAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (26 bp):
AACAAGAGTTATTTCGAACTTTAATC
Found at i:38696474 original size:2 final size:2
Alignment explanation
Indices: 38696467--38696498 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
38696457 GAGTGACCAA
38696467 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
38696499 TGGTATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38703742 original size:17 final size:16
Alignment explanation
Indices: 38703717--38703789 Score: 58
Period size: 17 Copynumber: 4.4 Consensus size: 16
38703707 TTTAAACTAC
*
38703717 AAAAGATTATAAAAATT
1 AAAAAATTAT-AAAATT
* * *
38703734 ACAAAATTAGT-TATTT
1 AAAAAATTA-TAAAATT
*
38703750 AAAAAATTATAATATT
1 AAAAAATTATAAAATT
38703766 AAACAAATTATAAAATT
1 AAA-AAATTATAAAATT
38703783 ACAAAAA
1 A-AAAAA
38703790 AGAATATATA
Statistics
Matches: 43, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
15 1 0.02
16 16 0.37
17 23 0.53
18 3 0.07
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.32
Consensus pattern (16 bp):
AAAAAATTATAAAATT
Found at i:38704174 original size:21 final size:21
Alignment explanation
Indices: 38704137--38704206 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
38704127 AAATTTTTTT
* *
38704137 ATTTTTATATTATTTTTTGTA
1 ATTTTTATAATATTTTTTGGA
38704158 ATTTTTA-AATATGTTTTTGGA
1 ATTTTTATAATAT-TTTTTGGA
*
38704179 ATTTTTTTATAA-CTTTTTTGGA
1 A--TTTTTATAATATTTTTTGGA
*
38704201 TTTTTT
1 ATTTTT
38704207 TCATTTAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
20 9 0.22
21 15 0.37
22 8 0.20
23 7 0.17
24 2 0.05
ACGTcount: A:0.23, C:0.01, G:0.09, T:0.67
Consensus pattern (21 bp):
ATTTTTATAATATTTTTTGGA
Found at i:38711353 original size:91 final size:91
Alignment explanation
Indices: 38711168--38711435 Score: 369
Period size: 92 Copynumber: 2.9 Consensus size: 91
38711158 TGCCAGATGC
* * * *
38711168 ACATAGTGCAAACCCGTAGGCTAAATATTCT-CCTCGATAACACGCCAGATTTCTTATAAGAGCT
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGCT
* * * *
38711232 ATTCTAATCAATAACATGCTAGATGC
66 ATTCTAATCAAGAACACGCTAAATGA
* * *
38711258 ACATAGTGCAAAGCCATAGGCTAAATATTCTCCCCCGATAACATGCCAGATTGCGCATAAGAGCT
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGCT
*
38711323 ATTCTAATCGAGAACACG-TCAAATGA
66 ATTCTAATCAAGAACACGCT-AAATGA
*
38711349 ACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCTGATAACACGCCAGATTGCTCATAAGAGC
1 ACATAGTGCAAAGCC-GTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGC
* *
38711414 TATTCCAATCTAGAACACGCTA
65 TATTCTAATCAAGAACACGCTA
38711436 GAATCTCTGA
Statistics
Matches: 156, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
90 30 0.19
91 62 0.40
92 63 0.40
93 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (91 bp):
ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCCGATAACACGCCAGATTGCTCATAAGAGCT
ATTCTAATCAAGAACACGCTAAATGA
Found at i:38711400 original size:92 final size:90
Alignment explanation
Indices: 38711168--38711435 Score: 367
Period size: 91 Copynumber: 2.9 Consensus size: 90
38711158 TGCCAGATGC
* * * *
38711168 ACATAGTGCAAACCCGTAGGCTAAATATTCTCCTCGATAACACGCCAGATTTCTTATAAGAGCTA
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCGATAACACGCCAGATTGCTCATAAGAGCTA
* * * *
38711233 TTCTAATCAATAACATGCTAGATGC
66 TTCTAATCAAGAACACGCTAAATGA
* * *
38711258 ACATAGTGCAAAGCCATAGGCTAAATATTCTCCCCCGATAACATGCCAGATTGCGCATAAGAGCT
1 ACATAGTGCAAAGCCGTAGGCTAAATATTCT-CCCCGATAACACGCCAGATTGCTCATAAGAGCT
*
38711323 ATTCTAATCGAGAACACG-TCAAATGA
65 ATTCTAATCAAGAACACGCT-AAATGA
38711349 ACATAGTGCAAAGCCTGTAGGCTAAATATTCTCCCCTGATAACACGCCAGATTGCTCATAAGAGC
1 ACATAGTGCAAAGCC-GTAGGCTAAATATTCTCCCC-GATAACACGCCAGATTGCTCATAAGAGC
* *
38711414 TATTCCAATCTAGAACACGCTA
64 TATTCTAATCAAGAACACGCTA
38711436 GAATCTCTGA
Statistics
Matches: 156, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
90 30 0.19
91 66 0.42
92 59 0.38
93 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (90 bp):
ACATAGTGCAAAGCCGTAGGCTAAATATTCTCCCCGATAACACGCCAGATTGCTCATAAGAGCTA
TTCTAATCAAGAACACGCTAAATGA
Found at i:38716010 original size:22 final size:24
Alignment explanation
Indices: 38715985--38716033 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
38715975 CTCTTGAAAG
* *
38715985 AATACCTAAAAGAGAGT-CA-CAA
1 AATAACTAAAAGAAAGTACACCAA
*
38716007 AATAACTACAAGAAAGTACACCAA
1 AATAACTAAAAGAAAGTACACCAA
38716031 AAT
1 AAT
38716034 TGTGAACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 14 0.64
23 2 0.09
24 6 0.27
ACGTcount: A:0.57, C:0.18, G:0.10, T:0.14
Consensus pattern (24 bp):
AATAACTAAAAGAAAGTACACCAA
Found at i:38717383 original size:109 final size:107
Alignment explanation
Indices: 38717265--38717498 Score: 330
Period size: 109 Copynumber: 2.2 Consensus size: 107
38717255 ATGTGAAAGG
*
38717265 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAATTCCACCG-AATCCTT
1 GGTTGCTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTAATTCCACCGTAAT--TT
*
38717329 -AATTGTAAAC-GGGGTTGCTAAGTGCTGATTCCCCGAATCAATAGT
64 GAA---TAAACAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATAGT
* * *
38717374 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGA
1 GGTTGCTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
* *
38717439 ATAAGCGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGT
66 ATAAAC-AGGGGTTGCTAAGTGCTGATTCCCCAAATCAATAGT
38717482 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
38717499 CCCATCGTAT
Statistics
Matches: 113, Mismatches: 8, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
106 4 0.04
108 51 0.45
109 55 0.49
110 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (107 bp):
GGTTGCTAAGTGCTGATTCCCCAAATCACTGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
ATAAACAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATAGT
Found at i:38717393 original size:76 final size:75
Alignment explanation
Indices: 38717144--38717385 Score: 373
Period size: 76 Copynumber: 3.2 Consensus size: 75
38717134 TGAATGTAAA
* * *
38717144 GGTGGTTGCTGAGTGCTGATTCCACCGAATCCTTAATTGTAAATGGGGTTGCTAAGTGTTGATTC
1 GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAA-GGGGTTGCTAAGTGCTGATTC
38717209 CCCGAATCAAT
65 CCCGAATCAAT
38717220 GGTGGTTGCTAAGTGCTAATTCCACCGTAAT--TTGAA-TGTGAAAGGGGTTGCTAAGTGCTGAT
1 GGTGGTTGCTAAGTGCTAATTCCACCG-AATCCTT-AATTGT-AAAGGGGTTGCTAAGTGCTGAT
*
38717282 TCCCCGAATCACT
63 TCCCCGAATCAAT
38717295 GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAACGGGGTTGCTAAGTGCTGATTC
1 GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAA-GGGGTTGCTAAGTGCTGATTC
38717360 CCCGAATCAAT
65 CCCGAATCAAT
*
38717371 AGTGGTTGCTAAGTG
1 GGTGGTTGCTAAGTG
38717386 TTGATTCCCC
Statistics
Matches: 153, Mismatches: 6, Indels: 14
0.88 0.03 0.08
Matches are distributed among these distances:
74 3 0.02
75 67 0.44
76 80 0.52
77 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (75 bp):
GGTGGTTGCTAAGTGCTAATTCCACCGAATCCTTAATTGTAAAGGGGTTGCTAAGTGCTGATTCC
CCGAATCAAT
Found at i:38717453 original size:151 final size:147
Alignment explanation
Indices: 38717339--38717731 Score: 487
Period size: 151 Copynumber: 2.7 Consensus size: 147
38717329 AATTGTAAAC
* * *
38717339 GGGGTTGCTAAGTGCTGATTCCC-CG-A-ATC-AA-T-AGTGGTTGCTAAGTGTTGATTCCCCAA
1 GGGGTTGCTAAGTGCTGA-TCCCACGTACATCGAAGTAAGGGGTTGATAAGTGCTGATTCCCCAA
* *
38717398 ATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAGTGCT
65 ATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAGTGCT
*
38717463 GATTCCCCAAAT-CAATG
130 GATTCCCCGAATCCAATG
* *
38717480 GTGGTTGCTAAGTGCTGATCCCATCGTATCTTCGAATGTGAAAGGGGTTGATAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATCCCA-CGTA-CATCGAA-GT--AAGGGGTTGATAAGTGCTGATTCC
*
38717545 CCGAATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAG
61 CCAAATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAG
38717610 TGCTGATTCCCCGAAT-CAATG
126 TGCTGATTCCCCGAATCCAATG
* * * *
38717631 GTGGTTGCTAAGTGCTGATCCCATCGTATCTTCAAATGTGAAAGGGGTTGCTAAGTGCTGATTCC
1 GGGGTTGCTAAGTGCTGATCCCA-CGTA-CATCGAA-GT--AAGGGGTTGATAAGTGCTGATTCC
* * *
38717696 CCGAATCACTGGTGGTTGCTAAGTGTTGAATCCACC
61 CCAAATCACTGGTGGTTGCTAAGTGCTGACTCCACC
38717732 AACTAACGGA
Statistics
Matches: 228, Mismatches: 13, Indels: 12
0.90 0.05 0.05
Matches are distributed among these distances:
140 4 0.02
141 17 0.07
142 2 0.01
143 1 0.00
145 2 0.01
146 2 0.01
148 1 0.00
151 199 0.87
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (147 bp):
GGGGTTGCTAAGTGCTGATCCCACGTACATCGAAGTAAGGGGTTGATAAGTGCTGATTCCCCAAA
TCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGCGAGGGGTTGCTAAGTGCTG
ATTCCCCGAATCCAATG
Found at i:38717497 original size:75 final size:75
Alignment explanation
Indices: 38717374--38717731 Score: 461
Period size: 75 Copynumber: 4.7 Consensus size: 75
38717364 AATCAATAGT
* * *
38717374 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAAT-TTG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGT-ATCTTG
38717438 AATAAGCGAGG
65 AATAAGCGAGG
* * * *
38717449 GGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTGATCCCATCGTATCTTCG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTT-G
** **
38717514 AATGTGAAAGG
65 AATAAGCGAGG
* *
38717525 GGTTGATAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGACTCCACCGTAAT-TTG
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGT-ATCTTG
38717589 AATAAGCGAGG
65 AATAAGCGAGG
* * * *
38717600 GGTTGCTAAGTGCTGATTCCCCGAATCAATGGTGGTTGCTAAGTGCTGATCCCATCGTATCTTCA
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTGA
* *
38717665 A-ATGTGAAAGG
66 ATAAGCG--AGG
* *
38717676 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGTTGAATCCACC
1 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACC
38717732 AACTAACGGA
Statistics
Matches: 245, Mismatches: 32, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
74 7 0.03
75 120 0.49
76 116 0.47
77 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (75 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTGA
ATAAGCGAGG
Found at i:38717529 original size:184 final size:184
Alignment explanation
Indices: 38717190--38717569 Score: 559
Period size: 184 Copynumber: 2.1 Consensus size: 184
38717180 TTGTAAATGG
*
38717190 GGTTGCTAAGTGTTGATTCCCCGAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
1 GGTTGCTAAGTGTTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
** * * *
38717255 ATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAATTCCAC
66 ATAAGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
*
38717320 CGAATCCTTAATTGTAAACGGGGTTGCTAAGTGCTGATTCCCCGAATCAATAGT
131 CGAATCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
* * *
38717374 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGA
1 GGTTGCTAAGTGTTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
** * *
38717439 ATAAGCGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTGATCCCAT
66 ATAAGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
* * *
38717504 CGTAT-CTTCGAA-TGTGAAA-GGGGTTGATAAGTGCTGATTCCCCGAATCACTGGT
131 CGAATCCTT--AATTGT-AAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
38717558 GGTTGCTAAGTG
1 GGTTGCTAAGTG
38717570 CTGACTCCAC
Statistics
Matches: 176, Mismatches: 17, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
183 3 0.02
184 168 0.95
185 5 0.03
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (184 bp):
GGTTGCTAAGTGTTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTGA
ATAAGAAAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
CGAATCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
Found at i:38717639 original size:184 final size:180
Alignment explanation
Indices: 38717190--38717649 Score: 445
Period size: 184 Copynumber: 2.5 Consensus size: 180
38717180 TTGTAAATGG
* * * * * *
38717190 GGTTGCTAAGTGTTGATTCCCCGAATCAA-TGGTGGTTGCTAAGTGCTAATTCCACCGTAATTTG
1 GGTTGCTAAGTGCTGACTCCCCAAAT-AACTGGGGGTTGCTAAGTGCTGATTCCACCGTAA-TTC
* * * *
38717254 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTAATTCCA
64 AA--T-AGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCA
*
38717319 CCGAATCCTTAATTGTAAACGGGGTTGCTAAGTGCTGATTCCCCGAATCAATAGT
126 CCGAATCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
* * * * * *
38717374 GGTTGCTAAGTGTTGATTCCCCAAATCACTGGTGGTTGGTAAGTGCTGATTCCACCGTAATTTGA
1 GGTTGCTAAGTGCTGACTCCCCAAATAACTGGGGGTTGCTAAGTGCTGATTCCACCGTAA-TTCA
* *
38717439 ATAAGCGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTGATCCCAT
65 AT-A--GAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCAC
* * *
38717504 CGTAT-CTTCGAA-TGTGAAA-GGGGTTGATAAGTGCTGATTCCCCGAATCACTGGT
127 CGAATCCTT--AATTGT-AAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
38717558 GGTTGCTAAGTGCTGACTCCACCGTAATTTGAATAAGC-GAGGGGTTGCTAAGTGCTGATTCC-C
1 GGTTGCTAAGTGCTGACTCC-CC---A----AATAA-CTG-GGGGTTGCTAAGTGCTGATTCCAC
*
38717621 CG-AA-TCAAT-G-GTGGTTGCTAAGTGCTGAT
56 CGTAATTCAATAGAGGGGTTGCTAAGTGCTGAT
38717650 CCCATCGTAT
Statistics
Matches: 238, Mismatches: 22, Indels: 32
0.82 0.08 0.11
Matches are distributed among these distances:
182 2 0.01
183 4 0.02
184 188 0.79
185 8 0.03
188 1 0.00
189 4 0.02
191 2 0.01
192 8 0.03
193 21 0.09
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (180 bp):
GGTTGCTAAGTGCTGACTCCCCAAATAACTGGGGGTTGCTAAGTGCTGATTCCACCGTAATTCAA
TAGAGGGGTTGCTAAGTGCTGATTCCCCAAATCAATGGTGGTTGCTAAGTGCTAATCCCACCGAA
TCCTTAATTGTAAACGGGGTTGATAAGTGCTGATTCCCCGAATCAATAGT
Found at i:38719009 original size:26 final size:26
Alignment explanation
Indices: 38718979--38719038 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
38718969 GTCAAAGCTA
*
38718979 CTGCAAAAAAATTTTTAGCACCACTG
1 CTGCAAAAAAAATTTTAGCACCACTG
38719005 CTGCAAAAAAAATTTTAGCACCACTG
1 CTGCAAAAAAAATTTTAGCACCACTG
*
38719031 CTCCAAAA
1 CTGCAAAA
38719039 TTTGTTCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (26 bp):
CTGCAAAAAAAATTTTAGCACCACTG
Found at i:38721060 original size:13 final size:13
Alignment explanation
Indices: 38721039--38721079 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
38721029 AAAAAATCAT
38721039 AAAAA-TTATAAA
1 AAAAATTTATAAA
*
38721051 CAAAATTTATAAA
1 AAAAATTTATAAA
38721064 AAAAATTTATAAA
1 AAAAATTTATAAA
38721077 AAA
1 AAA
38721080 TTAAAATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 4 0.15
13 22 0.85
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (13 bp):
AAAAATTTATAAA
Found at i:38721236 original size:13 final size:13
Alignment explanation
Indices: 38721220--38721260 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
38721210 ATAATTTTAA
38721220 TTTTTTATAAATT
1 TTTTTTATAAATT
38721233 TTTTTTATAAATT
1 TTTTTTATAAATT
*
38721246 TTGTTTAT-AATT
1 TTTTTTATAAATT
38721258 TTT
1 TTT
38721261 ATGATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTTTATAAATT
Found at i:38722656 original size:21 final size:22
Alignment explanation
Indices: 38722625--38722666 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
38722615 TAATTTTGGT
38722625 TTTGTTTTTCTTTTCTTCTTTC
1 TTTGTTTTTCTTTTCTTCTTTC
*
38722647 TTTG-TTTTCTTTTGTTCTTT
1 TTTGTTTTTCTTTTCTTCTTT
38722667 TGGTTCTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTGTTTTTCTTTTCTTCTTTC
Found at i:38726653 original size:30 final size:30
Alignment explanation
Indices: 38726595--38726650 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
38726585 ATACTTTTCT
* **
38726595 AATACTTTTAATCTTTTTTTTATTTTTAAA
1 AATAATTTTAATCTTTTTTGAATTTTTAAA
38726625 AATAATTTTAAT-TTTTTTGAATTTTT
1 AATAATTTTAATCTTTTTTGAATTTTT
38726651 TAATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 12 0.52
30 11 0.48
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (30 bp):
AATAATTTTAATCTTTTTTGAATTTTTAAA
Found at i:38727189 original size:20 final size:19
Alignment explanation
Indices: 38727166--38727207 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
38727156 AAAAAGAACT
38727166 TATAAATGAAAATTAAAATA
1 TATAAATGAAAATTAAAA-A
**
38727186 TATATTTGAAAATTAAAAA
1 TATAAATGAAAATTAAAAA
38727205 TAT
1 TAT
38727208 TAAAAAAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (19 bp):
TATAAATGAAAATTAAAAA
Found at i:38727854 original size:2 final size:2
Alignment explanation
Indices: 38727847--38727880 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38727837 GCCATGGGAG
38727847 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
38727881 AGTGTGTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38727918 original size:2 final size:2
Alignment explanation
Indices: 38727911--38727940 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38727901 CAATACTCTG
38727911 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
38727941 AGTGTGTGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38730180 original size:19 final size:21
Alignment explanation
Indices: 38730153--38730191 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
38730143 TTCTACCAAA
*
38730153 ATTCTTCAAT-ATAT-TTACT
1 ATTCCTCAATCATATCTTACT
38730172 ATTCCTCAATCATATCTTAC
1 ATTCCTCAATCATATCTTAC
38730192 ATCATATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTCCTCAATCATATCTTACT
Found at i:38732533 original size:17 final size:17
Alignment explanation
Indices: 38732511--38732545 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38732501 AAATAGGAAA
*
38732511 GTAATTTTAAAAGATTT
1 GTAATTTGAAAAGATTT
*
38732528 GTAATTTGATAAGATTT
1 GTAATTTGAAAAGATTT
38732545 G
1 G
38732546 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
GTAATTTGAAAAGATTT
Found at i:38740813 original size:6 final size:6
Alignment explanation
Indices: 38740802--38740832 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
38740792 AACGCACATG
38740802 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC C
1 CTGTTC CTGTTC CTGTTC CTGTTC CTGTTC C
38740833 AGCACTGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.35, G:0.16, T:0.48
Consensus pattern (6 bp):
CTGTTC
Found at i:38742334 original size:101 final size:104
Alignment explanation
Indices: 38742143--38742342 Score: 280
Period size: 101 Copynumber: 1.9 Consensus size: 104
38742133 AAAAGGAAAA
* * *
38742143 TTTTGGGTGTTGGCCTGTCAATGGCCGACACCCAGTACAATTTAAAAAAAATTTCTTTTTTTTCG
1 TTTTGGGTGCTGGCATGTCAATGGCCGACACCCAATACAATTT---AAAAA-TTCTTTTTTTTCG
*
38742208 TGTCAGAATCAGATATCAGTATACGAAAAAAATAATAAATTTT
62 TGTCAGAATCAAATATCAGTATACGAAAAAAATAATAAATTTT
*
38742251 TTTTGGGTGCTGGCATGTCAATGGCCGGCACCCAATACAATTT-AAAA-T-TTTTTTTTCGTGTC
1 TTTTGGGTGCTGGCATGTCAATGGCCGACACCCAATACAATTTAAAAATTCTTTTTTTTCGTGTC
* *
38742313 TGAATCAAATATCTGTATACGAAAAAAATA
66 AGAATCAAATATCAGTATACGAAAAAAATA
38742343 TTGTTTTCTC
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
101 41 0.48
102 1 0.01
104 4 0.05
108 39 0.46
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (104 bp):
TTTTGGGTGCTGGCATGTCAATGGCCGACACCCAATACAATTTAAAAATTCTTTTTTTTCGTGTC
AGAATCAAATATCAGTATACGAAAAAAATAATAAATTTT
Found at i:38745222 original size:23 final size:21
Alignment explanation
Indices: 38745180--38745223 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
38745170 AATGCCACAT
* *
38745180 AATATATATTTTTTATTTAAA
1 AATATATATTTTTAAATTAAA
38745201 AATATATATTTATTAAAATTAAA
1 AATATATATTT-TT-AAATTAAA
38745224 TTGAATTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 2 0.11
23 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATATATTTTTAAATTAAA
Found at i:38745307 original size:26 final size:26
Alignment explanation
Indices: 38745278--38745327 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
38745268 CAAATAAACC
38745278 TAGCCCAATACACCACAACCCAAAAA
1 TAGCCCAATACACCACAACCCAAAAA
* *
38745304 TAGCCCAATACACTACAACTCAAA
1 TAGCCCAATACACCACAACCCAAA
38745328 TCAGAAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.48, C:0.36, G:0.04, T:0.12
Consensus pattern (26 bp):
TAGCCCAATACACCACAACCCAAAAA
Found at i:38745827 original size:36 final size:36
Alignment explanation
Indices: 38745779--38745849 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
38745769 ATCAAAGGCT
*
38745779 ATAATTAAAAGCTGTATACAATTAGAACTCTAAGAC
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
*
38745815 ATAATTAGAAGCTGTATACAATTAAAACTCTAAGA
1 ATAATTAAAAGCTGTATACAATTAAAACTCTAAGA
38745850 TTAAATAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (36 bp):
ATAATTAAAAGCTGTATACAATTAAAACTCTAAGAC
Found at i:38751756 original size:36 final size:36
Alignment explanation
Indices: 38751686--38751756 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
38751676 TATAATTAAA
* *
38751686 AGCTGTATACAATTAGAACTCTAAGAAGACATAATT
1 AGCTGTATACAATTAAAACTCTAAGAAGAAATAATT
**
38751722 AGCTGTATACAATTAAAACTCTAAGATTAAATAAT
1 AGCTGTATACAATTAAAACTCTAAGAAGAAATAAT
38751757 CATATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (36 bp):
AGCTGTATACAATTAAAACTCTAAGAAGAAATAATT
Found at i:38755985 original size:18 final size:17
Alignment explanation
Indices: 38755952--38755990 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
38755942 TTGTATAAAT
38755952 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
38755970 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
38755987 TGTG
1 TGTG
38755991 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:38756108 original size:8 final size:8
Alignment explanation
Indices: 38756095--38756123 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
38756085 CACTAGAGAC
38756095 CAGTGTTA
1 CAGTGTTA
38756103 CAGTGTTA
1 CAGTGTTA
38756111 CAGTGTTA
1 CAGTGTTA
38756119 CAGTG
1 CAGTG
38756124 AGTCCCGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:38756237 original size:23 final size:23
Alignment explanation
Indices: 38756211--38756285 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
38756201 GTGTTATTGA
*
38756211 TCAGTGGTAGCTTCGGCTACGTT
1 TCAGTGGTAGCTTCGGCTACATT
*
38756234 TCAGTGTTAGCTTCGGCTACATT
1 TCAGTGGTAGCTTCGGCTACATT
*
38756257 TCAGTGGTAGCTTCGGCTACATA
1 TCAGTGGTAGCTTCGGCTACATT
38756280 TCAGTG
1 TCAGTG
38756286 TTGCACTTAT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (23 bp):
TCAGTGGTAGCTTCGGCTACATT
Found at i:38770952 original size:41 final size:41
Alignment explanation
Indices: 38770907--38771019 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 41
38770897 TTGTATATAA
* * *
38770907 CACCGGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTT
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
* * * * *
38770948 CACCGGCACAAAGCCTGCTAGACATAAAGTCTGATATAATT
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
*
38770989 CACCGGCACAAAGCCTGCTAGGCATAAAGCC
1 CACCGGCACAAAGCCTGCTAGGCACAAAGCC
38771020 TGAACTTACA
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (41 bp):
CACCGGCACAAAGCCTGCTAGGCACAAAGCCCGATACAATT
Found at i:38772203 original size:16 final size:17
Alignment explanation
Indices: 38772182--38772213 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
38772172 AAATATGCAA
38772182 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
38772198 TCACATAACTTCATAT
1 TCACATAACTTCATAT
38772214 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:38773398 original size:28 final size:31
Alignment explanation
Indices: 38773366--38773424 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
38773356 CCTTTCCTTT
38773366 TTATTATAATAAC-ATTAT-AATA-TATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
* *
38773394 TTATTATTATAACTTTTATAAATAGTATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
38773425 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 4 0.15
30 4 0.15
31 6 0.23
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTATTATAATAACTATTATAAATAGTATAAA
Found at i:38773992 original size:26 final size:25
Alignment explanation
Indices: 38773963--38774012 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 25
38773953 CAAATAAACC
38773963 TAGCCCAATACACTACAACCCAAAAA
1 TAGCCCAATACACTACAA-CCAAAAA
38773989 TAGCCCAATACACTACAACCAAAA
1 TAGCCCAATACACTACAACCAAAA
38774013 TCAGAAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.50, C:0.34, G:0.04, T:0.12
Consensus pattern (25 bp):
TAGCCCAATACACTACAACCAAAAA
Found at i:38775641 original size:7 final size:7
Alignment explanation
Indices: 38775629--38775654 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38775619 TCAATATTAT
38775629 TTTATGC
1 TTTATGC
38775636 TTTATGC
1 TTTATGC
38775643 TTTATGC
1 TTTATGC
38775650 TTTAT
1 TTTAT
38775655 TATTTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.62
Consensus pattern (7 bp):
TTTATGC
Found at i:38775660 original size:14 final size:14
Alignment explanation
Indices: 38775623--38775661 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
38775613 ATTATGTCAA
38775623 TATTATTTTATGCTT
1 TATTA-TTTATGCTT
**
38775638 TATGCTTTATGCTT
1 TATTATTTATGCTT
38775652 TATTATTTAT
1 TATTATTTAT
38775662 TTTTATATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (14 bp):
TATTATTTATGCTT
Found at i:38779476 original size:40 final size:40
Alignment explanation
Indices: 38779408--38779531 Score: 117
Period size: 40 Copynumber: 3.1 Consensus size: 40
38779398 GCGTTTGGAT
*
38779408 AAAAAACGCCGCTTAAAATTAAGCATTAGCGGCGCTTTTA
1 AAAAAACGCCACTTAAAATTAAGCATTAGCGGCGCTTTTA
* * *
38779448 AAAAAACGCCAC-TAAAGATTGAGTATTAGCGGCGCTTTTT
1 AAAAAACGCCACTTAAA-ATTAAGCATTAGCGGCGCTTTTA
** * * * * * *
38779488 GGAAAATGCCGCTAAAAATT-AGCATTAGCAGCGATTTTC
1 AAAAAACGCCACTTAAAATTAAGCATTAGCGGCGCTTTTA
38779527 AAAAA
1 AAAAA
38779532 GCGCTGCAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
39 22 0.33
40 42 0.63
41 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (40 bp):
AAAAAACGCCACTTAAAATTAAGCATTAGCGGCGCTTTTA
Found at i:38779613 original size:13 final size:13
Alignment explanation
Indices: 38779597--38779625 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38779587 TGGCGTTTTT
38779597 TAAAAAGCGCCGC
1 TAAAAAGCGCCGC
38779610 TAAAAAGCGCCGC
1 TAAAAAGCGCCGC
38779623 TAA
1 TAA
38779626 TACTCGGGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (13 bp):
TAAAAAGCGCCGC
Found at i:38779669 original size:41 final size:40
Alignment explanation
Indices: 38779611--38779721 Score: 177
Period size: 41 Copynumber: 2.7 Consensus size: 40
38779601 AAGCGCCGCT
38779611 AAAAAGCGCCGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
1 AAAAAGCG-CGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
*
38779652 GAAAAGCGACGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
1 AAAAAGCG-CGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
*
38779693 AAAAAGCGCTGCTAAAACTCGGGGCTTTA
1 AAAAAGCGC-GCTAATACTCGGGGCTTTA
38779722 ACGGTATTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
40 1 0.02
41 64 0.98
ACGTcount: A:0.25, C:0.23, G:0.29, T:0.23
Consensus pattern (40 bp):
AAAAAGCGCGCTAATACTCGGGGCTTTAGCGGCGTTTCTG
Found at i:38783976 original size:43 final size:43
Alignment explanation
Indices: 38783909--38784001 Score: 132
Period size: 43 Copynumber: 2.2 Consensus size: 43
38783899 AGGTTATGTT
* * *
38783909 TTTAGCGGCGTTTTTGCGAGAAGCGCCGCTAAAGATCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
* * *
38783952 TTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATTGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
38783995 TTTAGCG
1 TTTAGCG
38784002 CCGCTAAAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGGTC
Found at i:38784001 original size:25 final size:25
Alignment explanation
Indices: 38783973--38784026 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
38783963 TTGTGAGAAA
* *
38783973 AGCGTCGCTAAAGGTCATTGTCTTT
1 AGCGCCGCTAAAGGTCATAGTCTTT
38783998 AGCGCCGCTAAAGGTCATAGTCTTT
1 AGCGCCGCTAAAGGTCATAGTCTTT
38784023 AGCG
1 AGCG
38784027 GCGTTTGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (25 bp):
AGCGCCGCTAAAGGTCATAGTCTTT
Found at i:38784042 original size:68 final size:68
Alignment explanation
Indices: 38783930--38784069 Score: 228
Period size: 68 Copynumber: 2.1 Consensus size: 68
38783920 TTTTGCGAGA
* * *
38783930 AGCGCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGAGAAAAGCGTCGCTAAAGGTCATTG-T
1 AGCGCCGCTAAAGATCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTC-TTGTT
38783994 CTTT
65 CTTT
*
38783998 AGCGCCGCTAAAGGTCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGTTC
1 AGCGCCGCTAAAGATCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGTTC
38784063 TTT
66 TTT
38784066 AGCG
1 AGCG
38784070 GCGTTTATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
67 3 0.04
68 64 0.96
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (68 bp):
AGCGCCGCTAAAGATCATAGTCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCTTGTTC
TTT
Found at i:38784197 original size:22 final size:22
Alignment explanation
Indices: 38784169--38784211 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
38784159 TAGTGACGCT
*
38784169 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
38784191 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
38784212 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:38785457 original size:30 final size:31
Alignment explanation
Indices: 38785421--38785487 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
38785411 ATACATGAAT
38785421 TTTAATT-TGATGC-AATTATACATATGAAAC
1 TTTAATTGTGATGCAAATT-TACATATGAAAC
* * *
38785451 TTTAATTGTGGTTCAAATTTATATATGAAAC
1 TTTAATTGTGATGCAAATTTACATATGAAAC
38785482 TTTAAT
1 TTTAAT
38785488 CTTAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 21 0.66
32 4 0.12
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (31 bp):
TTTAATTGTGATGCAAATTTACATATGAAAC
Found at i:38786215 original size:16 final size:16
Alignment explanation
Indices: 38786186--38786219 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
38786176 AAATTAAAGC
38786186 TAATTGTTATTAAAAT
1 TAATTGTTATTAAAAT
38786202 TAATTGTT-TGTAAAAT
1 TAATTGTTAT-TAAAAT
38786218 TA
1 TA
38786220 TCAAATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (16 bp):
TAATTGTTATTAAAAT
Found at i:38787099 original size:95 final size:95
Alignment explanation
Indices: 38786964--38787269 Score: 355
Period size: 95 Copynumber: 3.0 Consensus size: 95
38786954 GGAAAAAGAA
* *
38786964 GAAAAAGAAAAAAAAAATTTGGGTGTTGGCCTGTCAATGGCCGGCACCCAGTACAA-TTAAAAAA
1 GAAAAAGTAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAA
* * *
38787028 AATTTCGTGTTAGAATTAGATATCAGTATAT
66 AATTT-GTGTCAAAATCAGATATCAGTATAT
*
38787059 GAAAACAGTAAAAAAAAA-TTGGATGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAGAAA
1 GAAAA-AGTAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTT----A
*
38787123 AAAAATTAATTTTTTTGTGTCAAAATCAGATATCAGTATAC
61 AAAAA--AA----TTTGTGTCAAAATCAGATATCAGTATAT
*
38787164 GAAAAAAATAAAAAAAATAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATT
1 G-AAAAAGT----AAAA-AAAAA-TTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATT
38787229 TAAAAAAAATTTGTGTCAAAATCAGATATCAGTATAT
59 TAAAAAAAATTTGTGTCAAAATCAGATATCAGTATAT
38787266 GAAA
1 GAAA
38787270 TTTTTTTATT
Statistics
Matches: 181, Mismatches: 10, Indels: 34
0.80 0.04 0.15
Matches are distributed among these distances:
95 41 0.23
96 13 0.07
100 6 0.03
101 3 0.02
102 30 0.17
105 24 0.13
106 9 0.05
108 6 0.03
109 4 0.02
110 5 0.03
112 40 0.22
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (95 bp):
GAAAAAGTAAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAGTACAATTTAAAAAA
AATTTGTGTCAAAATCAGATATCAGTATAT
Found at i:38787352 original size:48 final size:46
Alignment explanation
Indices: 38787278--38787378 Score: 166
Period size: 48 Copynumber: 2.2 Consensus size: 46
38787268 AATTTTTTTA
38787278 TTTTTTTCGTATACTGATATCCGATTCTGACACGAAAAAAAAAGAACT
1 TTTTTTTCGTATACTGATATCCGATTCTGACACG-AAAAAAAAGAA-T
* *
38787326 TTTTTTTCGTATATTGATATCTGATTCTGACACGAAAAAAAAGAAT
1 TTTTTTTCGTATACTGATATCCGATTCTGACACGAAAAAAAAGAAT
38787372 TTTTTTT
1 TTTTTTT
38787379 AAATTGTACT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
46 8 0.16
47 11 0.22
48 32 0.63
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (46 bp):
TTTTTTTCGTATACTGATATCCGATTCTGACACGAAAAAAAAGAAT
Found at i:38788134 original size:19 final size:19
Alignment explanation
Indices: 38788112--38788153 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38788102 CATGCAAATT
*
38788112 TATTACCAAAAATAAAACG
1 TATTACCAAAAAGAAAACG
* *
38788131 TATTTCCAAAAAGAAAACT
1 TATTACCAAAAAGAAAACG
38788150 TATT
1 TATT
38788154 GCCATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.52, C:0.14, G:0.05, T:0.29
Consensus pattern (19 bp):
TATTACCAAAAAGAAAACG
Found at i:38789165 original size:39 final size:39
Alignment explanation
Indices: 38789037--38789166 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
38789027 CGTTAGGACA
* * *
38789037 AAAAACGCCACTAAAAATCAAGCATTAGCGGTGCTTTTAC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTT-C
* * *
38789077 AAAAACGCCGCTAAAGATCGAGCATTAGCGGCGGATTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGC-GATTTTC
*
38789117 GAAAACGCCGCTAAAAAT-AAGCATTAGCGGCG-TTTTCC
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTT-C
38789155 AAAAAGCGCCGC
1 AAAAA-CGCCGC
38789167 ACAAAACCTA
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 4 0.05
38 5 0.07
39 18 0.24
40 44 0.58
41 5 0.07
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (39 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGATTTTC
Found at i:38789286 original size:41 final size:42
Alignment explanation
Indices: 38789211--38789367 Score: 248
Period size: 41 Copynumber: 3.8 Consensus size: 42
38789201 TTTTTGGGGT
*
38789211 CTTTAGTGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
* * *
38789253 CTTTAGCGGCGTTTTGT-AATAAGCGCCGCTAATGCTCCTAC
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
*
38789294 CTTTAGCGGCG-TTTTTGAAGAAGCGCCGCTAATGCTCGTAC
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
38789335 CTTTAGCGGCGTTTTTT-AAAAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAAT
38789368 AATAAAATCT
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 4 0.04
41 81 0.77
42 20 0.19
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTTGAAAAAGCGCCGCTAATGCTCGTAC
Found at i:38790688 original size:20 final size:20
Alignment explanation
Indices: 38790666--38790728 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
38790656 TTCGTGATTT
38790666 AAAATTTTAAAATGAATTTTA
1 AAAATTTTAAAATG-ATTTTA
**
38790687 AAAGATTTT-AAATTTTTTTA
1 AAA-ATTTTAAAATGATTTTA
*
38790707 AAAATTTTAAAAAGATTTTA
1 AAAATTTTAAAATGATTTTA
38790727 AA
1 AA
38790729 CTTTTATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.14
20 18 0.51
21 7 0.20
22 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
AAAATTTTAAAATGATTTTA
Found at i:38790696 original size:10 final size:10
Alignment explanation
Indices: 38790669--38790728 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
38790659 GTGATTTAAA
38790669 ATTTTAAAATG
1 ATTTTAAAA-G
38790680 AATTTTAAAAG
1 -ATTTTAAAAG
**
38790691 ATTTTAAATT
1 ATTTTAAAAG
*
38790701 TTTTTAAAA-
1 ATTTTAAAAG
38790710 ATTTTAAAAAG
1 ATTTT-AAAAG
38790721 ATTTTAAA
1 ATTTTAAA
38790729 CTTTTATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
9 4 0.10
10 22 0.54
11 6 0.15
12 9 0.22
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (10 bp):
ATTTTAAAAG
Found at i:38795602 original size:43 final size:43
Alignment explanation
Indices: 38795486--38795800 Score: 290
Period size: 43 Copynumber: 7.3 Consensus size: 43
38795476 ATGATATGTT
* * * * * * *
38795486 TTTAGCGGTGTTTTTGTGAGAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
38795528 TATAGCGGTGTTTGTGATAAAAAGTGCCGCTAAAGGTCATGCTC
1 TTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
38795572 TATAGCGGCGTTTGTGACAAATGCGTCGCTAAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCT-AAAGGTCATGGTC
* * *
38795616 TTTATCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * *
38795659 TATAGCGGTGTTTGTGACAAAAGCGCAGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
38795702 TTTAGCGACGTTTGTGGGAAAAGCACCGCTAAAGGTCCTAGTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
* * * ** **
38795745 TTTAGCGGCGTTTGTGGGAAAAGTGTCGCTAAAGACCATGACC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
38795788 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
38795801 ATTTCTAAAA
Statistics
Matches: 222, Mismatches: 48, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
42 14 0.06
43 153 0.69
44 55 0.25
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:38795891 original size:22 final size:22
Alignment explanation
Indices: 38795865--38795906 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
38795855 GGTGCTTCTC
*
38795865 AAAAGCGCAGCTAAAGGCCTAA
1 AAAAGCGCAGCTAAAAGCCTAA
*
38795887 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCAGCTAAAAGCCT
38795907 GTTTTGGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.26, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCAGCTAAAAGCCTAA
Found at i:38809843 original size:18 final size:18
Alignment explanation
Indices: 38809820--38809854 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38809810 CTTAGCAATG
38809820 TTTTTATCTCAAAAGTGT
1 TTTTTATCTCAAAAGTGT
* *
38809838 TTTTTATTTTAAAAGTG
1 TTTTTATCTCAAAAGTG
38809855 CTTCTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.11, T:0.54
Consensus pattern (18 bp):
TTTTTATCTCAAAAGTGT
Found at i:38810442 original size:59 final size:59
Alignment explanation
Indices: 38810334--38810458 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
38810324 TTTTTAAAAC
* *
38810334 TTTTAGAATTAGAATTAAGTTGAAAAATTTTGTAAATGTTCAAGATAAATTTATTGAAT
1 TTTTAGAATTAGAATTAAGATGAAAAATTTTGTAAATATTCAAGATAAATTTATTGAAT
* * * * * * *
38810393 TTTTAGAATTAGAATTAA-ATGACAAATTTTGTAGATATTGAGGGCTAAATTTGTTTAAT
1 TTTTAGAATTAGAATTAAGATGAAAAATTTTGTAAATATTCA-AGATAAATTTATTGAAT
38810452 TTTTAGA
1 TTTTAGA
38810459 TTTAAGATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 18 0.32
59 38 0.68
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.43
Consensus pattern (59 bp):
TTTTAGAATTAGAATTAAGATGAAAAATTTTGTAAATATTCAAGATAAATTTATTGAAT
Found at i:38816915 original size:17 final size:17
Alignment explanation
Indices: 38816893--38816943 Score: 84
Period size: 17 Copynumber: 3.0 Consensus size: 17
38816883 GACTAATCCC
*
38816893 TATACATCACTTAGGTA
1 TATACATTACTTAGGTA
38816910 TATACATTACTTAGGTA
1 TATACATTACTTAGGTA
*
38816927 TGTACATTACTTAGGTA
1 TATACATTACTTAGGTA
38816944 CATGCCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (17 bp):
TATACATTACTTAGGTA
Found at i:38817759 original size:23 final size:23
Alignment explanation
Indices: 38817689--38817773 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 23
38817679 CCTGATCAGT
38817689 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
38817710 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
38817730 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
38817753 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
38817774 GTCGGCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:38817771 original size:44 final size:41
Alignment explanation
Indices: 38817689--38817773 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
38817679 CCTGATCAGT
* *
38817689 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
38817730 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
38817774 GTCGGCAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
43 1 0.03
44 16 0.42
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:38819236 original size:18 final size:18
Alignment explanation
Indices: 38819200--38819247 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
38819190 ATCTACCATT
*
38819200 TCATATTCCACTTCACATC
1 TCAT-TTCCATTTCACATC
*
38819219 TCATTTCCATTTCTCATC
1 TCATTTCCATTTCACATC
*
38819237 -CTTTTCCATTT
1 TCATTTCCATTT
38819248 TAATATCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 10 0.38
18 12 0.46
19 4 0.15
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (18 bp):
TCATTTCCATTTCACATC
Found at i:38819629 original size:24 final size:25
Alignment explanation
Indices: 38819586--38819634 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
38819576 AATTTCATAA
38819586 ATGTATATTATCACATATTCAATTT
1 ATGTATATTATCACATATTCAATTT
38819611 ATGTATATTATCACA-ATTCAATTT
1 ATGTATATTATCACATATTCAATTT
38819635 GATAGCAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.37, C:0.12, G:0.04, T:0.47
Consensus pattern (25 bp):
ATGTATATTATCACATATTCAATTT
Found at i:38821186 original size:2 final size:2
Alignment explanation
Indices: 38821179--38821212 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
38821169 ACTTTAGATA
* *
38821179 AT AT AT AT AT AT AT AT AC AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38821213 GATTTTGTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:38822385 original size:14 final size:14
Alignment explanation
Indices: 38822366--38822399 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
38822356 TAATGCACAT
*
38822366 ACAAATTTTATTAA
1 ACAAATTTTAATAA
38822380 ACAAATTTTAATAA
1 ACAAATTTTAATAA
*
38822394 GCAAAT
1 ACAAAT
38822400 GTGCTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (14 bp):
ACAAATTTTAATAA
Found at i:38823606 original size:2 final size:2
Alignment explanation
Indices: 38823599--38823637 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
38823589 TATCAAAATT
*
38823599 TC TC TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
38823638 TTTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:38826897 original size:37 final size:37
Alignment explanation
Indices: 38826835--38826933 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 37
38826825 TTCGAAGTAA
* * * *
38826835 TAAAATGACACCCAGTGTCTCATCGGCTAAACCGAAG
1 TAAATTGACACACAGTGCCTCATCGGCTAAACCAAAG
* *
38826872 TAAATTGGCACACAGTGCCTAATCGGCTAAACCAAAG
1 TAAATTGACACACAGTGCCTCATCGGCTAAACCAAAG
* *
38826909 TAAATTGACACCCAATGCCTCATCG
1 TAAATTGACACACAGTGCCTCATCG
38826934 AATTAATCCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.20
Consensus pattern (37 bp):
TAAATTGACACACAGTGCCTCATCGGCTAAACCAAAG
Found at i:38835337 original size:17 final size:16
Alignment explanation
Indices: 38835300--38835338 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
38835290 AATAAATAAT
38835300 TAAA-TAAATTGGAAA
1 TAAATTAAATTGGAAA
38835315 TAAAATTAAATTGGGAAA
1 T-AAATTAAATT-GGAAA
38835333 TAAATT
1 TAAATT
38835339 TGAATTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 1 0.05
16 3 0.14
17 11 0.52
18 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (16 bp):
TAAATTAAATTGGAAA
Found at i:38838639 original size:212 final size:213
Alignment explanation
Indices: 38838262--38838652 Score: 730
Period size: 212 Copynumber: 1.8 Consensus size: 213
38838252 TTCAATTAAC
38838262 ACCAAGTGCTTTCTTTTACACAACAAATCAATAAGAACAACAGAAGAACACATGCAACCCCAAAT
1 ACCAAGTGCTTTCTTTTACACAACAAATCAATAAGAACAACAGAAGAACACATGCAACCCCAAAT
*
38838327 CCCCCTTAAAAACGCTTCTTTTCCTTTGATTAATTAATGCTTTTAACAATTTAAACCCAAAATGA
66 CCCCCTTAAAAACGCTTCTTTTCCTTTGATTAATTAATGCTTTTAACAATTTAAACCCAAAATAA
*
38838392 AACAACTTCCAATTCCCTGTTAGAACGAACCAACAAAGCCTATATACTTCAGTAAATGAATGATG
131 AACAACTTCCAATTCCCTGTTAGAACAAACCAACAAAGCCTATATACTTCAGTAAATGAATGATG
38838457 CAATATAAAACCAAAAGA
196 CAATATAAAACCAAAAGA
38838475 ACCAAGTGC-TTCTTTTACACAACAAATCAATAAGAACAACAGAAGAACACATGCAACCCCAAAT
1 ACCAAGTGCTTTCTTTTACACAACAAATCAATAAGAACAACAGAAGAACACATGCAACCCCAAAT
*
38838539 CCCCCTTAAAAACGCTTCTTTTCCTTTGATTAATTAATGCTTTTCACAATTTAAACCCAAAATAA
66 CCCCCTTAAAAACGCTTCTTTTCCTTTGATTAATTAATGCTTTTAACAATTTAAACCCAAAATAA
* *
38838604 AACAGCTTCCAATTTCCTGTTAGAACAAACCAACAAAGCCTATATACTT
131 AACAACTTCCAATTCCCTGTTAGAACAAACCAACAAAGCCTATATACTT
38838653 AATGATGAAG
Statistics
Matches: 173, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
212 164 0.95
213 9 0.05
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (213 bp):
ACCAAGTGCTTTCTTTTACACAACAAATCAATAAGAACAACAGAAGAACACATGCAACCCCAAAT
CCCCCTTAAAAACGCTTCTTTTCCTTTGATTAATTAATGCTTTTAACAATTTAAACCCAAAATAA
AACAACTTCCAATTCCCTGTTAGAACAAACCAACAAAGCCTATATACTTCAGTAAATGAATGATG
CAATATAAAACCAAAAGA
Found at i:38839157 original size:33 final size:32
Alignment explanation
Indices: 38839100--38839171 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 32
38839090 GTTGAGTGAG
*
38839100 GAAGGCTAGTGGCCGAAGGCGAAGCAAGCAAT
1 GAAGGCTAGGGGCCGAAGGCGAAGCAAGCAAT
* *
38839132 GAAGGCTAAGGGGCCGGAGGTGAAGCAAGCAAT
1 GAAGGCT-AGGGGCCGAAGGCGAAGCAAGCAAT
*
38839165 GGAGGCT
1 GAAGGCT
38839172 GGATAAGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.32, C:0.17, G:0.42, T:0.10
Consensus pattern (32 bp):
GAAGGCTAGGGGCCGAAGGCGAAGCAAGCAAT
Found at i:38844887 original size:27 final size:26
Alignment explanation
Indices: 38844831--38844897 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 26
38844821 TGGGTTAATG
*
38844831 ATTTAATATAAATAA-AATATATATT
1 ATTTAATATATATAATAATATATATT
38844856 ATTTAATATATATAATTAATATGAT-TT
1 ATTTAATATATATAA-TAATAT-ATATT
*
38844883 -TTTTATA-ATATAATA
1 ATTTAATATATATAATA
38844898 CATTCGAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
24 2 0.05
25 20 0.54
26 6 0.16
27 7 0.19
28 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (26 bp):
ATTTAATATATATAATAATATATATT
Found at i:38851148 original size:24 final size:24
Alignment explanation
Indices: 38851133--38851184 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38851123 AATCAAAGTC
38851133 AAATATATTATGCTAATAAATGCT
1 AAATATATTATGCTAATAAATGCT
* * *
38851157 AAATATATTATACTCATAAATACT
1 AAATATATTATGCTAATAAATGCT
38851181 AAAT
1 AAAT
38851185 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATGCTAATAAATGCT
Found at i:38855566 original size:24 final size:24
Alignment explanation
Indices: 38855539--38855592 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
38855529 AATCAAAGTC
* *
38855539 AAATATATTATGCT-ACTAAATGTT
1 AAATATATTATACTCA-TAAATATT
38855563 AAATATATTATACTCATAAATATT
1 AAATATATTATACTCATAAATATT
38855587 AAATAT
1 AAATAT
38855593 TCTAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (24 bp):
AAATATATTATACTCATAAATATT
Found at i:38855790 original size:19 final size:20
Alignment explanation
Indices: 38855748--38855791 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
38855738 TTCAAAAAAT
38855748 AATTTCTGGTAAATAGATTA
1 AATTTCTGGTAAATAGATTA
*
38855768 AATTTTTGGTATAAT-GA-TA
1 AATTTCTGGTA-AATAGATTA
38855787 AATTT
1 AATTT
38855792 AGCTCTCAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 12 0.55
21 3 0.14
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.45
Consensus pattern (20 bp):
AATTTCTGGTAAATAGATTA
Found at i:38857177 original size:67 final size:66
Alignment explanation
Indices: 38857106--38857238 Score: 185
Period size: 67 Copynumber: 2.0 Consensus size: 66
38857096 CAAATTTTCC
* * ** *
38857106 CTATATTTTATGCTTAGAGTTCTATTCAACTAATAAATTTATTTTAAAATTAGCACAACTTTTTT
1 CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAA-TTTTTT
38857171 TT
65 TT
* * *
38857173 CTATATTTTATACTTAGAATTCTATTCAAGTAATAAACATACTTTAAAATTTGTACAATTTTTTT
1 CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAATTTTTTT
38857238 T
66 T
38857239 ACATTAAACT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
66 8 0.14
67 50 0.86
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (66 bp):
CTATATTTTATACTTAGAATTCTATTCAACTAATAAACATACTTTAAAATTAGCACAATTTTTTT
T
Found at i:38859557 original size:165 final size:163
Alignment explanation
Indices: 38859283--38859671 Score: 607
Period size: 165 Copynumber: 2.4 Consensus size: 163
38859273 GGTTTGTAGA
*
38859283 GAAAATTGAGAAGAAATACAGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
1 GAAAATTGAGAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
* *
38859348 AATTGTGCTAGGAAATGGTTTATTAGTTGGACTTTGGGAAAAAAATAAGGGTTGTTTGAAAACAA
66 AATTGTGCTAGGAAATGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGAAAACAA
38859413 ACCCTTTTTTAGCAGAAATCAAGGAAAAATTAAAG
131 ACCC--TTTTAGCAGAAATCAAGGAAAAATTAAAG
*
38859448 GAAAATTGATAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
1 GAAAATTGAGAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
* * * * **
38859513 ATTTGTGCTAGGGAGTGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGACAATTA
66 AATTGTGCTAGGAAATGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGAAAACAA
* * * * *
38859578 ACCCTTTTGGCCGGAATCAATGAAAAATTAAGG
131 ACCCTTTTAGCAGAAATCAAGGAAAAATTAAAG
**
38859611 GAAAATTGAGAAGAAATGGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAA
1 GAAAATTGAGAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAA
38859672 CTTTAAGAGA
Statistics
Matches: 206, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
163 82 0.40
165 124 0.60
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.28
Consensus pattern (163 bp):
GAAAATTGAGAAGAAATACGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGAAATCCT
AATTGTGCTAGGAAATGGTTTATTAGTTGCACTTTGGAAAAAAAATAAGGGTTGTTTGAAAACAA
ACCCTTTTAGCAGAAATCAAGGAAAAATTAAAG
Found at i:38860025 original size:230 final size:228
Alignment explanation
Indices: 38859605--38860062 Score: 729
Period size: 230 Copynumber: 2.0 Consensus size: 228
38859595 CAATGAAAAA
* *
38859605 TTAAGGGAAAATTGAGAAGAAATGGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGA
1 TTAAAGGAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGA
* *
38859670 AACTTTAAGAGAATTTTGCAAAAGAGGGTTTGTAGAGAAAATTGAGTAGAAATAGGGAGAATAGG
66 AACTTTAAGAGAATTTTACAAAAGAGGGTTTGTAGAGAAAATTGAGAAGAAATAGGGAGAATAGG
* * * * *
38859735 GGTGTCAATTTGGGTTAGAATCAAATAGGAAATCCCAATTTTACTAGGGAGTGGTTTATTAGTTG
131 GGTGTCAATTTGGATTAGAATCAAATAGGAAATCCCAATTGTACTAGGAAGTGATTTATTAATTG
*
38859800 GACTTTGGAAAAACAATAAGGGTTGTTTGACAATT
196 GACTTT-GAAAAA-AATAAGGATTGTTTGACAATT
*
38859835 TTAAAGGAAAATTGAGAAGAAATAGGGAGAATGGTGGTTTCAATTTGGGTTAGAATCAAATAGGA
1 TTAAAGGAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGA
* *
38859900 AACTTTGAGAGAATTTTATAAAAGAGGGTTTGTAGAGAAAATTGAGAAGAAATAGGGAGAAT-GG
66 AACTTTAAGAGAATTTTACAAAAGAGGGTTTGTAGAGAAAATTGAGAAGAAATAGGGAGAATAGG
* * *
38859964 AGGTTTCAATTTGGATTAGAATCAAATAGGAAATCCTAATTGTGCTAGGAAGTGATTTATTAATT
131 -GGTGTCAATTTGGATTAGAATCAAATAGGAAATCCCAATTGTACTAGGAAGTGATTTATTAATT
*
38860029 GGACTTTGAAAAAAGTAAGGATTGTTTGACAATT
195 GGACTTTGAAAAAAATAAGGATTGTTTGACAATT
38860063 AACCCTTTTT
Statistics
Matches: 210, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
228 19 0.09
229 8 0.04
230 183 0.87
ACGTcount: A:0.38, C:0.05, G:0.27, T:0.29
Consensus pattern (228 bp):
TTAAAGGAAAATTGAGAAGAAATAGGGAGAATGGGGGTTTCAATTTGGGTTAGAATCAAATAGGA
AACTTTAAGAGAATTTTACAAAAGAGGGTTTGTAGAGAAAATTGAGAAGAAATAGGGAGAATAGG
GGTGTCAATTTGGATTAGAATCAAATAGGAAATCCCAATTGTACTAGGAAGTGATTTATTAATTG
GACTTTGAAAAAAATAAGGATTGTTTGACAATT
Found at i:38860632 original size:86 final size:86
Alignment explanation
Indices: 38860525--38860709 Score: 352
Period size: 86 Copynumber: 2.1 Consensus size: 86
38860515 AATTCAATTA
*
38860525 TTTAAATCTATATATATTTTAAAAAATATAAGATATTCAATTAAAAGTAAAAAAAATTGATCAAT
1 TTTAAATATA-ATATATTTTAAAAAATATAAGATATTCAATTAAAAGTAAAAAAAATTGATCAAT
38860590 AATAATTAGAGTACGTAAGAGT
65 AATAATTAGAGTACGTAAGAGT
38860612 TTTAAATATAATATATTTTAAAAAATATAAGATATTCAATTAAAAGTAAAAAAAATTGATCAATA
1 TTTAAATATAATATATTTTAAAAAATATAAGATATTCAATTAAAAGTAAAAAAAATTGATCAATA
38860677 ATAATTAGAGTACGTAAGAGT
66 ATAATTAGAGTACGTAAGAGT
38860698 TTTAAATATAAT
1 TTTAAATATAAT
38860710 TTTACATTTC
Statistics
Matches: 97, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
86 88 0.91
87 9 0.09
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (86 bp):
TTTAAATATAATATATTTTAAAAAATATAAGATATTCAATTAAAAGTAAAAAAAATTGATCAATA
ATAATTAGAGTACGTAAGAGT
Found at i:38865764 original size:6 final size:6
Alignment explanation
Indices: 38865753--38865780 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
38865743 GCAGCTTGGG
38865753 TTCACT TTCACT TTCACT TTCACT TTCA
1 TTCACT TTCACT TTCACT TTCACT TTCA
38865781 ACTTGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCACT
Found at i:38869347 original size:19 final size:20
Alignment explanation
Indices: 38869305--38869347 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
38869295 TCATGCTTTC
*
38869305 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
38869325 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
38869343 TATTC
1 TATTC
38869348 TACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:38869586 original size:45 final size:45
Alignment explanation
Indices: 38869513--38869622 Score: 166
Period size: 45 Copynumber: 2.4 Consensus size: 45
38869503 CCTAAACAGT
* * *
38869513 AATCAGTAACGGTAGCAGTAACAATATTCAACACACAAAGTGCCA
1 AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
* * *
38869558 AATCGGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCG
1 AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
38869603 AATCGGTAACAGTAACAGTA
1 AATCGGTAACAGTAACAGTA
38869623 GTCGGCATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 59 1.00
ACGTcount: A:0.43, C:0.21, G:0.18, T:0.18
Consensus pattern (45 bp):
AATCGGTAACAGTAACAGTAACAATATTCAACACACAAAGTGCCA
Found at i:38872047 original size:23 final size:23
Alignment explanation
Indices: 38872021--38872069 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
38872011 TTTTCAGAAG
38872021 TTTAATTAAATTAGAAGTTTGTT
1 TTTAATTAAATTAGAAGTTTGTT
*
38872044 TTTAATTAAATTAGAATTTTGTT
1 TTTAATTAAATTAGAAGTTTGTT
38872067 TTT
1 TTT
38872070 CATTTTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (23 bp):
TTTAATTAAATTAGAAGTTTGTT
Found at i:38873988 original size:3 final size:3
Alignment explanation
Indices: 38873980--38874031 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
38873970 TTGCACCATG
38873980 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
38874028 TAT T
1 TAT T
38874032 CATTCACCAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:38876803 original size:24 final size:24
Alignment explanation
Indices: 38876755--38876801 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
38876745 ACTGGTCATA
*
38876755 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
38876779 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
38876802 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:38877514 original size:27 final size:27
Alignment explanation
Indices: 38877475--38877586 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
38877465 AGAGGTCGAT
* ** *
38877475 AAATGATCAAAATACCCTTACAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
*
38877502 AAATGATCGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
* *
38877529 AAATGATTGAAATACCCCCGTAGGGTA
1 AAATGATCGAAATACCCCCATAGGGTA
38877556 AAATGA-CTGAAATACCCCCATAGGGTA
1 AAATGATC-GAAATACCCCCATAGGGTA
38877583 AAAT
1 AAAT
38877587 AACTGTTATA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.21
Consensus pattern (27 bp):
AAATGATCGAAATACCCCCATAGGGTA
Found at i:38877591 original size:27 final size:27
Alignment explanation
Indices: 38877496--38877600 Score: 149
Period size: 27 Copynumber: 3.9 Consensus size: 27
38877486 ATACCCTTAC
38877496 AGGGTAAAATGA-TCGAAATACCCCCGT
1 AGGGTAAAATGACT-GAAATACCCCCGT
*
38877523 AGGGTAAAATGATTGAAATACCCCCGT
1 AGGGTAAAATGACTGAAATACCCCCGT
*
38877550 AGGGTAAAATGACTGAAATACCCCCAT
1 AGGGTAAAATGACTGAAATACCCCCGT
* **
38877577 AGGGTAAAATAACTGTTATACCCC
1 AGGGTAAAATGACTGAAATACCCC
38877601 TAGGAGATGA
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
27 71 0.99
28 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (27 bp):
AGGGTAAAATGACTGAAATACCCCCGT
Found at i:38880542 original size:26 final size:26
Alignment explanation
Indices: 38880502--38880560 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
38880492 AGTTTGACAG
*
38880502 AATCATTTTAGACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
38880528 AATCATTTTACACCAATCTAGTCCTT
1 AATCATTTTACACCAATCTAGTCCTT
38880554 AATCATT
1 AATCATT
38880561 AACATGTCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (26 bp):
AATCATTTTACACCAATCTAGTCCTT
Found at i:38884173 original size:20 final size:21
Alignment explanation
Indices: 38884128--38884175 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
38884118 TCCAAATCAG
* **
38884128 TTTCCCGAAATCCCTTATTTT
1 TTTCCCCAAATCCCTTATAAT
38884149 TTTCCCCAAATCCCTTA-AAT
1 TTTCCCCAAATCCCTTATAAT
38884169 TTTCCCC
1 TTTCCCC
38884176 GATCGTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.21, C:0.35, G:0.02, T:0.42
Consensus pattern (21 bp):
TTTCCCCAAATCCCTTATAAT
Done.