Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 117 of 207
Found at i:35218293 original size:28 final size:28
Alignment explanation
Indices: 35218247--35218327 Score: 117
Period size: 28 Copynumber: 2.9 Consensus size: 28
35218237 ACTGTACTGG
*
35218247 TTACTATATTGGGCTAAGGCCCACATTA
1 TTACTGTATTGGGCTAAGGCCCACATTA
* *
35218275 TTATTGTATTGGGCTAAGGCCCACATTG
1 TTACTGTATTGGGCTAAGGCCCACATTA
* *
35218303 TTACTGTTTTGGGCTAAGGCTCACA
1 TTACTGTATTGGGCTAAGGCCCACA
35218328 CTGTACTGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 47 1.00
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACATTA
Found at i:35218536 original size:6 final size:6
Alignment explanation
Indices: 35218521--35218549 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35218511 TCACACTTGC
35218521 TTTT-A TTTTAA TTTTAA TTTTAA TTTTAA
1 TTTTAA TTTTAA TTTTAA TTTTAA TTTTAA
35218550 GTTGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:35221553 original size:50 final size:50
Alignment explanation
Indices: 35221478--35221718 Score: 320
Period size: 50 Copynumber: 4.8 Consensus size: 50
35221468 ATTTGGGTAA
* *
35221478 AGAGGTCTCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* *
35221528 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* **
35221578 AGAGGTCCCATGTAAGACCGTGTCTGGGACATGGCGTTGGCACTAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
35221628 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * *
35221678 AGAACATCCCATTTAAGACCATGTCTGGGGCATGGCTTTGG
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGG
35221719 TATGTTATTA
Statistics
Matches: 167, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 137 0.82
51 30 0.18
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:35223154 original size:20 final size:20
Alignment explanation
Indices: 35223131--35223196 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
35223121 GAGGCACCGT
*
35223131 AGTGTAAACAGGGACACCGA
1 AGTGTAAACAGGGACACCAA
*
35223151 AGTGTATACAGAGG-CACCAA
1 AGTGTAAACAG-GGACACCAA
* * *
35223171 AGTGCAAACAGAGACATCAA
1 AGTGTAAACAGGGACACCAA
35223191 AGTGTA
1 AGTGTA
35223197 TACATAGGCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.03
20 34 0.92
21 2 0.05
ACGTcount: A:0.42, C:0.18, G:0.26, T:0.14
Consensus pattern (20 bp):
AGTGTAAACAGGGACACCAA
Found at i:35223163 original size:40 final size:40
Alignment explanation
Indices: 35223119--35223211 Score: 123
Period size: 40 Copynumber: 2.3 Consensus size: 40
35223109 ATTGAGCAAG
* * * *
35223119 CAGAGGCACCGTAGTGTAAACAGGGACACCGAAGTGTATA
1 CAGAGGCACCGAAGTGCAAACAGAGACACCAAAGTGTATA
* *
35223159 CAGAGGCACCAAAGTGCAAACAGAGACATCAAAGTGTATA
1 CAGAGGCACCGAAGTGCAAACAGAGACACCAAAGTGTATA
*
35223199 CATAGGCACCGAA
1 CAGAGGCACCGAA
35223212 CTACAAATCC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.40, C:0.22, G:0.26, T:0.13
Consensus pattern (40 bp):
CAGAGGCACCGAAGTGCAAACAGAGACACCAAAGTGTATA
Found at i:35230725 original size:21 final size:22
Alignment explanation
Indices: 35230683--35230725 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
35230673 AAATTACATG
* *
35230683 AAATAATATAAATTATGTACAA
1 AAATAATATAAATTAAGCACAA
*
35230705 AAATAATGT-AATTAAGCACAA
1 AAATAATATAAATTAAGCACAA
35230726 TTTCACATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.58, C:0.07, G:0.07, T:0.28
Consensus pattern (22 bp):
AAATAATATAAATTAAGCACAA
Found at i:35236315 original size:25 final size:25
Alignment explanation
Indices: 35236287--35236337 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
35236277 CAAACTTATC
35236287 TAATTTGAAACTTAAATTAGAGATT
1 TAATTTGAAACTTAAATTAGAGATT
35236312 TAATTTGAAACTTAAATTAGAGATT
1 TAATTTGAAACTTAAATTAGAGATT
35236337 T
1 T
35236338 TTACTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (25 bp):
TAATTTGAAACTTAAATTAGAGATT
Found at i:35237196 original size:21 final size:21
Alignment explanation
Indices: 35237170--35237220 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
35237160 GGGAATGTGT
35237170 AATAAAAA-AAACATGAA-AATA
1 AATAAAAATAAA-AT-AAGAATA
*
35237191 AATAAAAATGAAATAAGAATA
1 AATAAAAATAAAATAAGAATA
35237212 AATAAAAAT
1 AATAAAAAT
35237221 TATACAAGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (21 bp):
AATAAAAATAAAATAAGAATA
Found at i:35237198 original size:10 final size:10
Alignment explanation
Indices: 35237170--35237220 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
35237160 GGGAATGTGT
*
35237170 AATAAAAAAA
1 AATAAAAATA
*
35237180 ACATGAAAATA
1 A-ATAAAAATA
35237191 AATAAAAATGA
1 AATAAAAAT-A
*
35237202 AATAAGAATA
1 AATAAAAATA
35237212 AATAAAAAT
1 AATAAAAAT
35237221 TATACAAGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 17 0.50
11 17 0.50
ACGTcount: A:0.75, C:0.02, G:0.06, T:0.18
Consensus pattern (10 bp):
AATAAAAATA
Found at i:35237203 original size:16 final size:17
Alignment explanation
Indices: 35237170--35237203 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
35237160 GGGAATGTGT
35237170 AATAAAAAAAACATGAA
1 AATAAAAAAAACATGAA
*
35237187 AATAAATAAAA-ATGAA
1 AATAAAAAAAACATGAA
35237203 A
1 A
35237204 TAAGAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
AATAAAAAAAACATGAA
Found at i:35238085 original size:138 final size:140
Alignment explanation
Indices: 35237831--35238223 Score: 447
Period size: 138 Copynumber: 2.7 Consensus size: 140
35237821 CGAAATAGTT
* * * *
35237831 AAAAAAATAAAAAATTTGTTTTAAAATTTTAAAATTTCCTTTAAAATGACTTAAAAAAACATATT
1 AAAAAAATCAAAATTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGAC-T---AAAATATATT
*
35237896 TTTATTTTTCAAAATCTAAACTTTTTCATTCTTT-AAAAAAACACTATTTTTCTTAAAAATTAAA
62 TTTATTTTTCAAAATCTAAACTTTCTC-TT-TTTAAAAAAAACACTATTTTTCTTAAAAATTAAA
35237960 GCTTTTA-TT-T-TTG
125 GCTTTTACTTATATTG
* * *
35237973 AAAAAAAATCAAATTTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACT-AAATTTTTTTTT
1 -AAAAAAATCAAAATTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAAATATATTTTT
*
35238037 ATTTTTCAAAATCTAAACTTTCTCTTTTTAAAAAAAAACACTATTTTTCTTAAAGATTAAAGCTT
65 ATTTTTCAAAATCTAAACTTTCTCTTTTT-AAAAAAAACACTATTTTTCTTAAAAATTAAAGCTT
35238102 TTACTTTGAAATAGTTG
129 TTAC-TT---ATA-TTG
* * * * *
35238119 AAAAAAATCAAAATTTTGTTTTAAAAATTTAAACTTTTCTTTATAATAACTAAAAAAATAGATTT
1 AAAAAAATCAAAATTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACT---AAAATATATTT
*
35238184 TTATTTGTT-AAAATCTAAATTTTCTCTTTTTTAAAAAAAA
63 TTATTT-TTCAAAATCTAAACTTTCTC-TTTTTAAAAAAAA
35238224 TCAAAAATTT
Statistics
Matches: 216, Mismatches: 18, Indels: 26
0.83 0.07 0.10
Matches are distributed among these distances:
136 3 0.01
137 2 0.01
138 68 0.31
140 2 0.01
142 1 0.00
143 46 0.21
144 1 0.00
145 46 0.21
146 3 0.01
149 37 0.17
150 7 0.03
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (140 bp):
AAAAAAATCAAAATTTTGTTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAAATATATTTTTA
TTTTTCAAAATCTAAACTTTCTCTTTTTAAAAAAAACACTATTTTTCTTAAAAATTAAAGCTTTT
ACTTATATTG
Found at i:35238844 original size:16 final size:16
Alignment explanation
Indices: 35238823--35238853 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35238813 TGGGCCTCTA
35238823 AATGCAATGAAAAGTC
1 AATGCAATGAAAAGTC
35238839 AATGCAATGAAAAGT
1 AATGCAATGAAAAGT
35238854 AAACTAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.19, T:0.19
Consensus pattern (16 bp):
AATGCAATGAAAAGTC
Found at i:35238958 original size:42 final size:42
Alignment explanation
Indices: 35238860--35239111 Score: 312
Period size: 42 Copynumber: 6.1 Consensus size: 42
35238850 AAGTAAACTA
* * * * *
35238860 GAAAAGTAAACGGGCCTCCACACCTGGGTCTTTAAA--CTA-
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
*** * * *
35238899 GAAAAGTAAACAAACCTCCACACTTGGGTCTCTAAATGTAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
35238941 GAAAAGTGAATGGACCTCCACACCTGGGTCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* * *
35238983 GAAAAGTGAATGGACCTCCGCACCTGGGACTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
*
35239025 GAAAAGTAAATGGACCTCCACACCTGAGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
* *
35239067 GAAAAGTAAATGGAGCTCGACACCTGGGCCTCTAAATGCAAT
1 GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
35239109 GAA
1 GAA
35239112 TGTTTTCCTT
Statistics
Matches: 188, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
39 31 0.16
41 1 0.01
42 156 0.83
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.20
Consensus pattern (42 bp):
GAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAAT
Found at i:35249527 original size:332 final size:333
Alignment explanation
Indices: 35248921--35249579 Score: 1275
Period size: 332 Copynumber: 2.0 Consensus size: 333
35248911 GCCATACTTG
*
35248921 TCATAGAAGTACCTTTTTTTTAGCATCATTACTTGATTGCCATATTCCTTTTAACTCATCTTCAC
1 TCATAGAAGTACCTTTTTTTTAGCATCATTACTTGATTGCCATATTCCCTTTAACTCATCTTCAC
35248986 AATTCCTCCTACAATCCATGCGAACTATCTAAGGTAGGCGCAAGCCAAAATAAGCTATCTAGCAA
66 AATTCCTCCTACAATCCATGCGAACTATCTAAGGTAGGCGCAAGCCAAAATAAGCTATCTAGCAA
35249051 TCACCTTCTCTGCTTTGAGTATCCTTTGACATTCTCGCTATTATCCCTATATTTTCTACCCCATG
131 TCACCTTCTCTGCTTTGAGTATCCTTTGACATTCTCGCTATTATCCCTATATTTTCTACCCCATG
35249116 CCGAACAACTAAATCTTTTTGAAGTATGTTCATGTGAATATAGATGCGACACCGTGCCCCAGGTA
196 CCGAACAACTAAATCTTTTTGAAGTATGTTCATGTGAATATAGATGCGACACCGTGCCCCAGGTA
35249181 TTTAAATGATGCATGAATTATGCCAAGGAGAGACACAGACAC-AAAAAAAACAAAGTCAGCAAAA
261 TTTAAATGATGCATGAATTATGCCAAGGAGAGACACAGACACAAAAAAAAACAAAGTCAGCAAAA
35249245 AAAAACAA
326 AAAAACAA
*
35249253 TCATAGAAGTACCTTTTTTTTAGCATCATTACTTGATTGCCATATTCCCTTTAACTCATCTTCGC
1 TCATAGAAGTACCTTTTTTTTAGCATCATTACTTGATTGCCATATTCCCTTTAACTCATCTTCAC
*
35249318 AATTCCTCCTACAATCCATGCGAACTATCTAAGGTAGGCTCAAGCCAAAATAAGCTATCTAGCAA
66 AATTCCTCCTACAATCCATGCGAACTATCTAAGGTAGGCGCAAGCCAAAATAAGCTATCTAGCAA
35249383 TCACCTTCTCTGCTTTGAGTATCCTTTGACATTCTCGCTATTATCCCTATATTTTCTACCCCATG
131 TCACCTTCTCTGCTTTGAGTATCCTTTGACATTCTCGCTATTATCCCTATATTTTCTACCCCATG
*
35249448 CCGAACAACTAAATCTTTTTGAAGTATGTTCATGTGAATATAGATGCGACACTGTGCCCCAGGTA
196 CCGAACAACTAAATCTTTTTGAAGTATGTTCATGTGAATATAGATGCGACACCGTGCCCCAGGTA
35249513 TTTAAATGATGCATGAATTATGCCAAGGAGAGACACAGACACAAAAAAAAACAAAGTCAGCAAAA
261 TTTAAATGATGCATGAATTATGCCAAGGAGAGACACAGACACAAAAAAAAACAAAGTCAGCAAAA
35249578 AA
326 AA
35249580 TAATAATAAA
Statistics
Matches: 322, Mismatches: 4, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
332 298 0.93
333 24 0.07
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (333 bp):
TCATAGAAGTACCTTTTTTTTAGCATCATTACTTGATTGCCATATTCCCTTTAACTCATCTTCAC
AATTCCTCCTACAATCCATGCGAACTATCTAAGGTAGGCGCAAGCCAAAATAAGCTATCTAGCAA
TCACCTTCTCTGCTTTGAGTATCCTTTGACATTCTCGCTATTATCCCTATATTTTCTACCCCATG
CCGAACAACTAAATCTTTTTGAAGTATGTTCATGTGAATATAGATGCGACACCGTGCCCCAGGTA
TTTAAATGATGCATGAATTATGCCAAGGAGAGACACAGACACAAAAAAAAACAAAGTCAGCAAAA
AAAAACAA
Found at i:35254102 original size:27 final size:27
Alignment explanation
Indices: 35254058--35254211 Score: 146
Period size: 27 Copynumber: 5.7 Consensus size: 27
35254048 CACGACAGCT
35254058 AAGAATAGCCTTTGTGGTGAACTCTGA
1 AAGAATAGCCTTTGTGGTGAACTCTGA
* * * *
35254085 TAGATTAGCCTTTATGGTGAACACTGA
1 AAGAATAGCCTTTGTGGTGAACTCTGA
* * * *
35254112 AAAAATAGCCTTGGTGGCGAACTCCGA
1 AAGAATAGCCTTTGTGGTGAACTCTGA
* * *
35254139 AAGAATAGCCTTTTTGGTAAACTCTAA
1 AAGAATAGCCTTTGTGGTGAACTCTGA
** * ** *
35254166 AAGAATAGTATTTGTTGCAAACTCTAA
1 AAGAATAGCCTTTGTGGTGAACTCTGA
*
35254193 AAGAATAGTCTTTGTGGTG
1 AAGAATAGCCTTTGTGGTG
35254212 TGTTTTATAT
Statistics
Matches: 99, Mismatches: 28, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 99 1.00
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (27 bp):
AAGAATAGCCTTTGTGGTGAACTCTGA
Found at i:35257987 original size:18 final size:18
Alignment explanation
Indices: 35257957--35257995 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
35257947 TAATTAATTC
35257957 TTTATTATTATTC-TTAT
1 TTTATTATTATTCTTTAT
35257974 TTTATTATTTATTCTTTAT
1 TTTATTA-TTATTCTTTAT
35257993 TTT
1 TTT
35257996 TTAGTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 6 0.30
19 7 0.35
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTATTATTCTTTAT
Found at i:35261836 original size:27 final size:27
Alignment explanation
Indices: 35261798--35261849 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
35261788 ATGGTGGGGG
35261798 TAAGGCAATATTAGCATGAAATTTATT
1 TAAGGCAATATTAGCATGAAATTTATT
* * *
35261825 TAAGGGAATATTTGCATGAATTTTA
1 TAAGGCAATATTAGCATGAAATTTA
35261850 AATTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (27 bp):
TAAGGCAATATTAGCATGAAATTTATT
Found at i:35261978 original size:18 final size:19
Alignment explanation
Indices: 35261955--35261992 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
35261945 GCAAGCATGA
35261955 TTTTTAT-TTAATC-TAAGT
1 TTTTTATGTT-ATCTTAAGT
35261973 TTTTTATGTTATCTTAAGT
1 TTTTTATGTTATCTTAAGT
35261992 T
1 T
35261993 ATGAAATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (19 bp):
TTTTTATGTTATCTTAAGT
Found at i:35263672 original size:23 final size:23
Alignment explanation
Indices: 35263645--35263720 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
35263635 AGTGTTATTG
35263645 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35263668 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35263691 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35263714 ATCAGTG
1 ATCAGTG
35263721 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35270744 original size:18 final size:17
Alignment explanation
Indices: 35270711--35270749 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
35270701 TTGTATAAAT
35270711 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
35270729 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
35270746 TGTG
1 TGTG
35270750 GAAGGAAATT
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:35271001 original size:23 final size:23
Alignment explanation
Indices: 35270974--35271049 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
35270964 AGTGTTATTG
35270974 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35270997 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35271020 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35271043 ATCAGTG
1 ATCAGTG
35271050 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35274811 original size:27 final size:27
Alignment explanation
Indices: 35274767--35274936 Score: 205
Period size: 27 Copynumber: 6.3 Consensus size: 27
35274757 CACGACAACT
* * *
35274767 AAGAATAACCTTTCTGGTGAACTCTAA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
*
35274794 AAGAATAGCATTTTTGGTGAACTCTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
* ** *
35274821 AATAATAGTGTTTTTGGTGAACTTTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
* * *
35274848 AAGAATAGCCATTGTGGCGAACTCTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
*
35274875 AAGAATAGCCTTTTTGGTGAACTTTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
* * *
35274902 AAGAATGGCCTTTATGGCGAACTCTGA
1 AAGAATAGCCTTTTTGGTGAACTCTGA
35274929 AAGAATAG
1 AAGAATAG
35274937 TCTATGTGGT
Statistics
Matches: 119, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 119 1.00
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (27 bp):
AAGAATAGCCTTTTTGGTGAACTCTGA
Found at i:35275988 original size:22 final size:22
Alignment explanation
Indices: 35275940--35275988 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
35275930 ATAAACCTCA
*
35275940 TTTTTTTTCATTTTGTTACACC
1 TTTTTTTTCATTTTCTTACACC
* *
35275962 ATTTTTTTC-TTTTCTCTACTCC
1 TTTTTTTTCATTTTCT-TACACC
35275984 TTTTT
1 TTTTT
35275989 CATTCACTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.10, C:0.20, G:0.02, T:0.67
Consensus pattern (22 bp):
TTTTTTTTCATTTTCTTACACC
Found at i:35302437 original size:4 final size:4
Alignment explanation
Indices: 35302428--35302456 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
35302418 AATGTCATAT
35302428 TATC TATC TATC TATC TATC TATC TATC T
1 TATC TATC TATC TATC TATC TATC TATC T
35302457 CTATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TATC
Found at i:35306805 original size:42 final size:40
Alignment explanation
Indices: 35306746--35306882 Score: 126
Period size: 42 Copynumber: 3.5 Consensus size: 40
35306736 AATCATTGGT
*
35306746 GGTTGCTAGGTGCTGATTCCACCATATTTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACC-TATTTTAAATGTG-AAGG
* * * * *
35306788 GGTTGCTAAGTGTTGATTCC-CCGA--CT-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCTATTTTAAATGTGAAGG
*
35306821 GGTTGCTAAATGCTGATTCCACCGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACC-TATTTTAAATGTGAA-GG
35306863 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
35306883 CCCAAGGGGT
Statistics
Matches: 73, Mismatches: 13, Indels: 18
0.70 0.12 0.17
Matches are distributed among these distances:
33 19 0.26
34 2 0.03
35 1 0.01
36 2 0.03
37 3 0.04
38 3 0.04
39 2 0.03
40 1 0.01
41 2 0.03
42 38 0.52
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.34
Consensus pattern (40 bp):
GGTTGCTAAGTGCTGATTCCACCTATTTTAAATGTGAAGG
Found at i:35306835 original size:75 final size:75
Alignment explanation
Indices: 35306709--35306884 Score: 289
Period size: 75 Copynumber: 2.3 Consensus size: 75
35306699 TGATTCCCCC
* **
35306709 AAGGGGTTGCTAAGTGCTAATTCCCCGAATCATTGGTGGTTGCTAGGTGCTGATTCCACCATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATT
35306774 TTAAATGTGA
66 TTAAATGTGA
* * *
35306784 AAGGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAATGCTGATTCCACCGTATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATT
35306849 TTAAATGTGA
66 TTAAATGTGA
*
35306859 AGGGGGTTGCTAAGTGCTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
35306885 CAAGGGGTTG
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 93 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCATATT
TTAAATGTGA
Found at i:35306897 original size:27 final size:27
Alignment explanation
Indices: 35306861--35306937 Score: 145
Period size: 27 Copynumber: 2.9 Consensus size: 27
35306851 AAATGTGAAG
35306861 GGGGTTGCTAAGTGCTGATTCCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
*
35306888 GGGGTTGCTAAGTGCTGATTTCCCCAA
1 GGGGTTGCTAAGTGCTGATTCCCCCAA
35306915 GGGGTTGCTAAGTGCTGATTCCC
1 GGGGTTGCTAAGTGCTGATTCCC
35306938 TAACTCATTG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (27 bp):
GGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:35309117 original size:25 final size:26
Alignment explanation
Indices: 35309089--35309138 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 26
35309079 CGCTGAATCG
*
35309089 GGGAATCAGCACTTAGC-ACCCCCTC
1 GGGAATCAGCACATAGCAACCCCCTC
35309114 GGGAATCAGCACATAGCAACCCCCT
1 GGGAATCAGCACATAGCAACCCCCT
35309139 TTCACATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.28, C:0.38, G:0.20, T:0.14
Consensus pattern (26 bp):
GGGAATCAGCACATAGCAACCCCCTC
Found at i:35309369 original size:100 final size:89
Alignment explanation
Indices: 35309191--35309386 Score: 257
Period size: 100 Copynumber: 2.1 Consensus size: 89
35309181 AACGGGGAAT
*
35309191 GCAACCCCTCGGGGGATCACAATACAACCCACATTTCAAAGATATGGTGGCGCACATAGCACCAC
1 GCAACCCCTCGGGGAATCACAATACAACCCACATTTCAAAGATATGGTGGCGCACATAGCACCAC
**
35309256 AATGAATCGGGGAATCAGCACTTA
66 AATGAATCGGGGAATCAGCACACA
*
35309280 GCAACCCCTCGGGGAATCAGCACATACACCCCCTTTACATTTCAAAGATATGGTGGATCACGCAC
1 GCAACCCCTCGGGGAATCA-CA-ATACA-ACCC---ACATTTCAAAGATATGGTGG----CGCAC
35309345 ATAGCACCACCAATGAATCGGGGAATCAGCACACA
56 ATAGCACCA-CAATGAATCGGGGAATCAGCACACA
35309380 GCAACCC
1 GCAACCC
35309387 TTTATATACA
Statistics
Matches: 92, Mismatches: 4, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
89 18 0.20
90 2 0.02
91 5 0.05
92 3 0.03
95 20 0.22
99 14 0.15
100 30 0.33
ACGTcount: A:0.33, C:0.31, G:0.20, T:0.16
Consensus pattern (89 bp):
GCAACCCCTCGGGGAATCACAATACAACCCACATTTCAAAGATATGGTGGCGCACATAGCACCAC
AATGAATCGGGGAATCAGCACACA
Found at i:35321303 original size:21 final size:20
Alignment explanation
Indices: 35321273--35321313 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
35321263 ATTTTTTATT
*
35321273 TTGAAAACTTGTATTAATTTA
1 TTGAAAACTTAT-TTAATTTA
*
35321294 TTGAATACTTATTTAATTTA
1 TTGAAAACTTATTTAATTTA
35321314 ACTTTGTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (20 bp):
TTGAAAACTTATTTAATTTA
Found at i:35324850 original size:42 final size:42
Alignment explanation
Indices: 35324803--35324940 Score: 134
Period size: 42 Copynumber: 3.5 Consensus size: 42
35324793 AACCCCTTGG
35324803 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGT
* * * *
35324845 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-GAGT-CGG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGT
*
35324878 GGAAATCAACACTTAGC-ACCCCCTTCACATTTAAAATATGGT
1 GG-AATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGT
*
35324920 GGAGATCAGCACCTAGCAACC
1 GGA-ATCAGCACTTAGCAACC
35324941 ACCAATAATT
Statistics
Matches: 73, Mismatches: 11, Indels: 23
0.68 0.10 0.21
Matches are distributed among these distances:
33 3 0.04
34 18 0.25
35 2 0.03
36 3 0.04
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.03
41 6 0.08
42 31 0.42
43 3 0.04
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGT
Found at i:35324854 original size:100 final size:102
Alignment explanation
Indices: 35324704--35324902 Score: 303
Period size: 100 Copynumber: 2.0 Consensus size: 102
35324694 GTGATTCGGA
* * * *
35324704 GAATCAACACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGATCAGCACTTAGCAATCACCA
1 GAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCA
* *
35324769 ATGAGTC-GGG-AATCAGCACTTAGGAACCCCTTGGG
66 ATGAGTCGGGGAAATCAACACTTAGCAACCCCTTGGG
* *
35324804 GAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACTTAGCAACCACCA
1 GAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCA
*
35324869 ATGAGTCGGGGAAATCAACACTTAGCACCCCCTT
66 ATGAGTCGGGGAAATCAACACTTAGCAACCCCTT
35324903 CACATTTAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
100 66 0.75
101 3 0.03
102 19 0.22
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.22
Consensus pattern (102 bp):
GAATCAACACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCA
ATGAGTCGGGGAAATCAACACTTAGCAACCCCTTGGG
Found at i:35324937 original size:76 final size:76
Alignment explanation
Indices: 35324801--35324957 Score: 255
Period size: 76 Copynumber: 2.1 Consensus size: 76
35324791 GGAACCCCTT
* *
35324801 GGGG-AATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACTTAGCAACC
1 GGGGAAATCAACACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACCTAGCAACC
*
35324865 ACCAATGAGTC
66 ACCAATAAGTC
35324876 GGGGAAATCAACACTTAGC-ACCCCCTTCACATTTAAAATATGGTGGAGATCAGCACCTAGCAAC
1 GGGGAAATCAACACTTAGCAACCCCCTTCACATTTAAAATATGGTGGA-ATCAGCACCTAGCAAC
*
35324940 CACCAATAATTC
65 CACCAATAAGTC
35324952 GGGGAA
1 GGGGAA
35324958 TAAGCACTTG
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
75 32 0.42
76 44 0.58
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (76 bp):
GGGGAAATCAACACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACCTAGCAACC
ACCAATAAGTC
Found at i:35324966 original size:75 final size:75
Alignment explanation
Indices: 35324801--35324970 Score: 256
Period size: 75 Copynumber: 2.3 Consensus size: 75
35324791 GGAACCCCTT
* *
35324801 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATAAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACCTAGCAACCA
*
35324866 CCAATGAGTC
66 CCAATAAGTC
35324876 GGGGAAATCAA-CACTTAGC-ACCCCCTTCACATTTAAAATATGGTGGAGATCAGCACCTAGCAA
1 GGGG-AAT-AAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGA-ATCAGCACCTAGCAA
*
35324939 CCACCAATAATTC
63 CCACCAATAAGTC
35324952 GGGGAATAAGCACTT-GCAA
1 GGGGAATAAGCACTTAGCAA
35324971 ACCCATTGGG
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
74 4 0.05
75 41 0.48
76 40 0.47
77 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (75 bp):
GGGGAATAAGCACTTAGCAACCCCCTTCACATTTAAAATATGGTGGAATCAGCACCTAGCAACCA
CCAATAAGTC
Found at i:35332164 original size:26 final size:26
Alignment explanation
Indices: 35332129--35332180 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
35332119 TGGTAAAAAG
*
35332129 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
35332155 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
35332181 TTCATTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:35332273 original size:27 final size:27
Alignment explanation
Indices: 35332232--35332283 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
35332222 AATGTGAAAA
*
35332232 GGGGGTGCTATGTGCTGATTCCCCGAC
1 GGGGGTGCTAAGTGCTGATTCCCCGAC
*
35332259 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGGTGCTAAGTGCTGATTCCCCG
35332284 GTTCATTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.37, T:0.27
Consensus pattern (27 bp):
GGGGGTGCTAAGTGCTGATTCCCCGAC
Found at i:35332383 original size:104 final size:108
Alignment explanation
Indices: 35332066--35332383 Score: 372
Period size: 104 Copynumber: 3.0 Consensus size: 108
35332056 GCGGTTTGCT
* *
35332066 GATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTTGAAATGGTAAAAAGGG
1 GATTCCCCG-TTCATTGGT-GTGCTAAGTGCGTGATCCACCATATCTTTGAAAT-GT-GAAA-GG
35332131 GGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
61 GGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
35332179 GA-------TTCATTGTGTGTGGCT-AGTGCGTGATCCACCATATCTTTGAAATGTGAAAAGGGG
1 GATTCCCCGTTCATTG-GTGT-GCTAAGTGCGTGATCCACCATATCTTTGAAATGTG-AAAGGGG
*
35332236 GTGCTATGTGCTGATTCCCCGACGGGGTTGCTAAGTGCTGATTCCCC
63 TTGCTATGTGCTGATTCCCCGA-GGGGTTGCTAAGTGCTGATTCCCC
35332283 G-------GTTCATTGGTGTGCTAAG-GCGAT-ATCCACCATATCTTTG-AATGTGAAA-GGGTT
1 GATTCCCCGTTCATTGGTGTGCTAAGTGCG-TGATCCACCATATCTTTGAAATGTGAAAGGGGTT
35332337 GCTATGT-CTGATTCCCCGAGGGGTTG-TAAGTGCTGATTCCCC
65 GCTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
35332379 GATTC
1 GATTC
35332384 AGCGGTGTGC
Statistics
Matches: 190, Mismatches: 4, Indels: 35
0.83 0.02 0.15
Matches are distributed among these distances:
96 17 0.09
97 7 0.04
98 12 0.06
99 11 0.06
100 3 0.02
101 6 0.03
102 22 0.12
103 32 0.17
104 37 0.19
105 36 0.19
106 5 0.03
113 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.31
Consensus pattern (108 bp):
GATTCCCCGTTCATTGGTGTGCTAAGTGCGTGATCCACCATATCTTTGAAATGTGAAAGGGGTTG
CTATGTGCTGATTCCCCGAGGGGTTGCTAAGTGCTGATTCCCC
Found at i:35332391 original size:96 final size:101
Alignment explanation
Indices: 35332062--35332411 Score: 507
Period size: 105 Copynumber: 3.4 Consensus size: 101
35332052 GGTTGCGGTT
* *
35332062 TGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTTTGAAATGGTAAAA
1 TGCTGATTCCCCGATTCATTGGT-GTGCTAAGTGCGTGATCCACCATATCTTTGAAAT-GT-GAA
35332127 AGGGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAG
63 A-GGGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAG
35332167 TGCTGATTCCCCGATTCATTGTGTGTGGCT-AGTGCGTGATCCACCATATCTTTGAAATGTGAAA
1 TGCTGATTCCCCGATTCATTG-GTGT-GCTAAGTGCGTGATCCACCATATCTTTGAAATGTG-AA
*
35332231 AGGGGGTGCTATGTGCTGATTCCCCGACGGGGTTGCTAAG
63 AGGGGTTGCTATGTGCTGATTCCCCGA-GGGGTTGCTAAG
*
35332271 TGCTGATTCCCCGGTTCATTGGTGTGCTAAG-GCGAT-ATCCACCATATCTTTG-AATGTGAAA-
1 TGCTGATTCCCCGATTCATTGGTGTGCTAAGTGCG-TGATCCACCATATCTTTGAAATGTGAAAG
35332332 GGGTTGCTATGT-CTGATTCCCCGAGGGGTTG-TAAG
65 GGGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAG
** *
35332367 TGCTGATTCCCCGATTCAGCGGTGTGCTAAGTGCGAGATCCACCA
1 TGCTGATTCCCCGATTCATTGGTGTGCTAAGTGCGTGATCCACCA
35332412 ATAACGGTTA
Statistics
Matches: 228, Mismatches: 9, Indels: 24
0.87 0.03 0.09
Matches are distributed among these distances:
96 32 0.14
97 18 0.08
98 12 0.05
99 11 0.05
100 3 0.01
101 6 0.03
102 22 0.10
103 32 0.14
104 37 0.16
105 50 0.22
106 5 0.02
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.31
Consensus pattern (101 bp):
TGCTGATTCCCCGATTCATTGGTGTGCTAAGTGCGTGATCCACCATATCTTTGAAATGTGAAAGG
GGTTGCTATGTGCTGATTCCCCGAGGGGTTGCTAAG
Found at i:35339091 original size:25 final size:25
Alignment explanation
Indices: 35339058--35339107 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
35339048 ATGTAAAAAG
*
35339058 GGGTTGCTATGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
35339083 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTTGCTAAGTGCTGATTCCCCGA
35339108 TTCATTGGTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.14, C:0.24, G:0.32, T:0.30
Consensus pattern (25 bp):
GGGTTGCTAAGTGCTGATTCCCCGA
Found at i:35339167 original size:103 final size:100
Alignment explanation
Indices: 35338984--35339189 Score: 310
Period size: 103 Copynumber: 2.0 Consensus size: 100
35338974 GTATATAAAG
**
35338984 GGGTTGCTGTGTGCTGATTCCGATTCATGGTGTGGTGCTATGTGCGTGATCACCATATTTTGAAA
1 GGGTTGCTAAGTGCTGATTCCGATTCATGGTGTGGTGCTATGTGCGTGATCACCATATTTTGAAA
35339049 TGTAAAAAGGGGTTGCTATGTGCTGATT-CCCCGA
66 TGTAAAAAGGGGTTGCTATGTGCTGATTCCCCCGA
35339083 GGGTTGCTAAGTGCTGATTCCCCGATTCATTGGT-TGCGTGCTATGTGCGTGATCCACCATATCT
1 GGGTTGCTAAGTGCTGATT--CCGATTCA-TGGTGTG-GTGCTATGTGCGTGAT-CACCATAT-T
*
35339147 TTGAAATGT-GAAAGGGGTTGCTATGTGCTGATTCCCCCGA
60 TTGAAATGTAAAAAGGGGTTGCTATGTGCTGATTCCCCCGA
35339187 GGG
1 GGG
35339190 GTTGATCTCT
Statistics
Matches: 97, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
99 17 0.18
101 10 0.10
102 20 0.21
103 31 0.32
104 19 0.20
ACGTcount: A:0.18, C:0.18, G:0.30, T:0.33
Consensus pattern (100 bp):
GGGTTGCTAAGTGCTGATTCCGATTCATGGTGTGGTGCTATGTGCGTGATCACCATATTTTGAAA
TGTAAAAAGGGGTTGCTATGTGCTGATTCCCCCGA
Found at i:35345534 original size:42 final size:42
Alignment explanation
Indices: 35345475--35345611 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
35345465 AATTATTGGT
*
35345475 GGTTGCTAGGTGCTGATTCCACCATATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
* * * * *
35345517 GGTTGCTAAGTGTTGATTCC-CC-GA--CT-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
35345550 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
35345592 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
35345612 CCCAAGGGGT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
33 21 0.28
34 2 0.03
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 1 0.01
40 1 0.01
41 2 0.03
42 40 0.53
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
Found at i:35345564 original size:75 final size:75
Alignment explanation
Indices: 35345441--35345613 Score: 294
Period size: 75 Copynumber: 2.3 Consensus size: 75
35345431 TTCCCCCAAT
* *
35345441 GGGTTGCTAAGTGCTT-ATTCCCCGAATTATTGGTGGTTGCTAGGTGCTGATTCCACCATATTTT
1 GGGTTGCTAAGTG-TTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
35345505 AAATGTGAAGG
65 AAATGTGAAGG
*
35345516 GGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTTA
1 GGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTTA
35345581 AATGTGAAGG
66 AATGTGAAGG
*
35345591 GGGTTGCTAAGTGCTGATTCCCC
1 GGGTTGCTAAGTGTTGATTCCCC
35345614 CAAGGGGTTC
Statistics
Matches: 93, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
74 2 0.02
75 91 0.98
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (75 bp):
GGGTTGCTAAGTGTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTTA
AATGTGAAGG
Found at i:35345621 original size:102 final size:102
Alignment explanation
Indices: 35345515--35345712 Score: 324
Period size: 102 Copynumber: 1.9 Consensus size: 102
35345505 AAATGTGAAG
* * * * *
35345515 GGGGTTGCTAAGTGTTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTT
1 GGGGTTCCTAAGTGCTGATTCCCCGACTCATTGGTGATTGCTAAGTGCTGATCCCACCATATCTT
*
35345580 AAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
*
35345617 GGGGTTCCTAAGTGCTGATTCCCCGACTCATTGGTGATTGCTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTCCTAAGTGCTGATTCCCCGACTCATTGGTGATTGCTAAGTGCTGATCCCACCATATCTT
*
35345682 AAATGTGAAAGGGGTTGCTAAGTGTTGATTC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTC
35345713 TCCGAATCAC
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 88 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (102 bp):
GGGGTTCCTAAGTGCTGATTCCCCGACTCATTGGTGATTGCTAAGTGCTGATCCCACCATATCTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:35345712 original size:177 final size:177
Alignment explanation
Indices: 35345410--35345749 Score: 518
Period size: 177 Copynumber: 1.9 Consensus size: 177
35345400 ATTGAATATA
* * * * *
35345410 AAGGGAGTTGCTAAGTTCTGATTCCCCCAATGGGTTGCTAAGTGCTTATTCCCCGAATTATTGGT
1 AAGGGAGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
* * * * *
35345475 GGTTGCTAGGTGCTGATTCCACCATATTTTAAATGTGAAGGGGGTTGCTAAGTGTTGATTCCCCG
66 GATTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCG
* * * *
35345540 ACTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTG
131 AATCACTGGTGGTTCCTAAGTGCTGAATCCACCATATTTTAAATGTG
* *
35345587 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGACTCATTGGT
1 AAGGGAGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
* *
35345652 GATTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCTCCG
66 GATTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCG
35345717 AATCACTGGTGGTTCCTAAGTGCTGAATCCACC
131 AATCACTGGTGGTTCCTAAGTGCTGAATCCACC
35345750 GATAACGGAC
Statistics
Matches: 145, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
177 145 1.00
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.32
Consensus pattern (177 bp):
AAGGGAGTTGCTAAGTGCTGATTCCCCCAAGGGGTTCCTAAGTGCTGATTCCCCGAATCATTGGT
GATTGCTAAGTGCTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCG
AATCACTGGTGGTTCCTAAGTGCTGAATCCACCATATTTTAAATGTG
Found at i:35349181 original size:20 final size:19
Alignment explanation
Indices: 35349143--35349199 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 19
35349133 CTACAAAGTT
*
35349143 AAAATTAAATAAGTATTCA
1 AAAATTAAACAAGTATTCA
*
35349162 AAAATTAATACAAGTTTTCA
1 AAAATTAA-ACAAGTATTCA
*
35349182 AAAA-TAAA-AAATATTCA
1 AAAATTAAACAAGTATTCA
35349199 A
1 A
35349200 TCATCCTCTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 8 0.24
18 1 0.03
19 11 0.33
20 13 0.39
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.30
Consensus pattern (19 bp):
AAAATTAAACAAGTATTCA
Found at i:35357903 original size:14 final size:14
Alignment explanation
Indices: 35357884--35357910 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35357874 CATTTCTTGG
35357884 TCGGTTCAGTTCAC
1 TCGGTTCAGTTCAC
35357898 TCGGTTCAGTTCA
1 TCGGTTCAGTTCA
35357911 ACTGGACCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.22, T:0.37
Consensus pattern (14 bp):
TCGGTTCAGTTCAC
Found at i:35366468 original size:87 final size:88
Alignment explanation
Indices: 35366310--35366509 Score: 241
Period size: 87 Copynumber: 2.3 Consensus size: 88
35366300 CAAACATAAA
*
35366310 AAAAAAAGCAATTAAGCCTCTCCT-TTTTTGTTTGCACTCAATTGAGCACTTCAACCTTTAAAAT
1 AAAAAAAGCAATTAAG--TC-CCTGCTTTTGTTTGCACTCAATTGAGCACTTCAACCTTTAAAAT
*
35366374 GCATC-AAAAAGGCCCTCAAAATTCTTC
63 GCATCAAAAAAAG-CCTCAAAATT-TTC
* * *
35366401 AAAAAAAGCAATTAAGTCCCTGCTTTT-TTT-CACTCAATTGGGTACTTGAA-CTTTCAAAATGC
1 AAAAAAAGCAATTAAGTCCCTGCTTTTGTTTGCACTCAATTGAGCACTTCAACCTTT-AAAATGC
35366463 ATCAAAAAAAGCCTCAAAATTTTC
65 ATCAAAAAAAGCCTCAAAATTTTC
* *
35366487 -AAAACAGCAATTAAGCCCCTGCT
1 AAAAAAAGCAATTAAGTCCCTGCT
35366510 CTTATTAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
85 21 0.21
86 7 0.07
87 37 0.37
88 12 0.12
89 6 0.06
91 16 0.16
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.29
Consensus pattern (88 bp):
AAAAAAAGCAATTAAGTCCCTGCTTTTGTTTGCACTCAATTGAGCACTTCAACCTTTAAAATGCA
TCAAAAAAAGCCTCAAAATTTTC
Found at i:35366778 original size:11 final size:11
Alignment explanation
Indices: 35366752--35366784 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
35366742 GATAAAAAAA
35366752 ATAAAAATTA-
1 ATAAAAATTAT
*
35366762 ATAAAAGTTAT
1 ATAAAAATTAT
35366773 ATAAAAATTAT
1 ATAAAAATTAT
35366784 A
1 A
35366785 AAATGCTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (11 bp):
ATAAAAATTAT
Found at i:35366885 original size:10 final size:10
Alignment explanation
Indices: 35366870--35366932 Score: 64
Period size: 10 Copynumber: 6.7 Consensus size: 10
35366860 TTCTTACAAC
35366870 TTTATAAAAT
1 TTTATAAAAT
35366880 TTTATAAAAT
1 TTTATAAAAT
35366890 TTTAT---AT
1 TTTATAAAAT
*
35366897 TTCTAT-ATAT
1 TT-TATAAAAT
*
35366907 TTT-TAATAT
1 TTTATAAAAT
35366916 TTTATAAAAT
1 TTTATAAAAT
35366926 TTTATAA
1 TTTATAA
35366933 TTTTTTTATT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
7 4 0.09
8 4 0.09
9 8 0.17
10 31 0.66
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTATAAAAT
Found at i:35366910 original size:18 final size:17
Alignment explanation
Indices: 35366878--35366936 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 17
35366868 ACTTTATAAA
35366878 ATTTTATAAAATTTTAT
1 ATTTTATAAAATTTTAT
* *
35366895 ATTTCTATATATTTTTAAT
1 ATTT-TATAAAATTTT-AT
35366914 ATTTTATAAAATTTTAT
1 ATTTTATAAAATTTTAT
35366931 AATTTT
1 -ATTTT
35366937 TTTATTTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.17
18 23 0.66
19 6 0.17
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTTATAAAATTTTAT
Found at i:35366967 original size:8 final size:8
Alignment explanation
Indices: 35366956--35366989 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
35366946 TTACAAATTT
35366956 TTTTTTAA
1 TTTTTTAA
35366964 TTTTTCTAA
1 TTTTT-TAA
35366973 TTTTTTAA
1 TTTTTTAA
*
35366981 TATTTTAA
1 TTTTTTAA
35366989 T
1 T
35366990 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTTAA
Found at i:35366967 original size:20 final size:20
Alignment explanation
Indices: 35366931--35366987 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
35366921 AAAATTTTAT
*
35366931 AATTTTTTTATTTTTTTACA
1 AATTTTTTTATTATTTTACA
* *
35366951 AATTTTTTT-TTAATTTTTCT
1 AATTTTTTTATT-ATTTTACA
*
35366971 AA-TTTTTTAATATTTTA
1 AATTTTTTTATTATTTTA
35366988 ATATTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 13 0.43
20 17 0.57
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (20 bp):
AATTTTTTTATTATTTTACA
Found at i:35366967 original size:21 final size:21
Alignment explanation
Indices: 35366933--35366978 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
35366923 AATTTTATAA
*
35366933 TTTTTTTATTTTTTTACAAATT
1 TTTTTTTATATTTTT-CAAATT
*
35366955 TTTTTTTA-ATTTTTCTAATT
1 TTTTTTTATATTTTTCAAATT
35366975 TTTT
1 TTTT
35366979 AATATTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 5 0.23
22 8 0.36
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTTATATTTTTCAAATT
Found at i:35367033 original size:9 final size:10
Alignment explanation
Indices: 35367014--35367038 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35367004 ATATTATTGC
35367014 TTTTAATTTT
1 TTTTAATTTT
35367024 TTTTAATTTT
1 TTTTAATTTT
35367034 TTTTA
1 TTTTA
35367039 TAAATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:35367273 original size:87 final size:90
Alignment explanation
Indices: 35367058--35367266 Score: 318
Period size: 87 Copynumber: 2.4 Consensus size: 90
35367048 ATAAAAGCAT
*
35367058 GGGCTTAATTTCTTTTTCTGAAAAAGTTTGAGGGTTTTTTTTATGCATCTTGAAAGTTCAAGTAC
1 GGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGGGTTTTTTTTATGCATCTTGAAAGTTCAAGTAC
* **
35367123 CCAATTGAGTGCAAAAAAAAAGGGG
66 CCAAATGAGTGCAAAAAAAAAGGAA
* * *
35367148 GGGCTTAATTG-TTTTT-T-TAAAGGTTTGAGGGTTTTTTTTATGCATTTTGAAAGTTCAAGTAC
1 GGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGGGTTTTTTTTATGCATCTTGAAAGTTCAAGTAC
*
35367210 CCAAATGAGTGC-AAAAAAAAGTAA
66 CCAAATGAGTGCAAAAAAAAAGGAA
35367234 GGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGG
1 GGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGG
35367267 ACTTTTTGCA
Statistics
Matches: 106, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
86 20 0.19
87 58 0.55
88 2 0.02
89 16 0.15
90 10 0.09
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (90 bp):
GGGCTTAATTGCTTTTTCTGAAAAAGTTTGAGGGTTTTTTTTATGCATCTTGAAAGTTCAAGTAC
CCAAATGAGTGCAAAAAAAAAGGAA
Found at i:35371803 original size:24 final size:24
Alignment explanation
Indices: 35371776--35371870 Score: 77
Period size: 25 Copynumber: 3.9 Consensus size: 24
35371766 TGGCTCTTCG
*
35371776 GAGCTACCCGTTATAGGCTCGCAT
1 GAGCTTCCCGTTATAGGCTCGCAT
* * **
35371800 GAGCTTCCTGATTAT-GACTCTTAT
1 GAGCTTCCCG-TTATAGGCTCGCAT
*
35371824 GAGCTTCCCGTTACATA-GCTCACAT
1 GAGCTTCCCGTT--ATAGGCTCGCAT
*
35371849 GGGCTTCCCGTTATATGGCTCG
1 GAGCTTCCCGTTATA-GGCTCG
35371871 AGAGAGTGCT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
23 5 0.09
24 23 0.43
25 26 0.48
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (24 bp):
GAGCTTCCCGTTATAGGCTCGCAT
Found at i:35371869 original size:25 final size:25
Alignment explanation
Indices: 35371776--35371869 Score: 84
Period size: 24 Copynumber: 3.8 Consensus size: 25
35371766 TGGCTCTTCG
* *
35371776 GAGCTACCCGTTATA-GGCTCGCAT
1 GAGCTTCCCGTTATATGGCTCACAT
* * * **
35371800 GAGCTTCCTGAT-TATGACTCTTAT
1 GAGCTTCCCGTTATATGGCTCACAT
* *
35371824 GAGCTTCCCGTTACATAGCTCACAT
1 GAGCTTCCCGTTATATGGCTCACAT
*
35371849 GGGCTTCCCGTTATATGGCTC
1 GAGCTTCCCGTTATATGGCTC
35371870 GAGAGAGTGC
Statistics
Matches: 52, Mismatches: 16, Indels: 3
0.73 0.23 0.04
Matches are distributed among these distances:
23 2 0.04
24 25 0.48
25 25 0.48
ACGTcount: A:0.19, C:0.28, G:0.21, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCACAT
Found at i:35379155 original size:21 final size:23
Alignment explanation
Indices: 35379105--35379149 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35379095 TTAATGCGCC
* *
35379105 AATTATATTACTTTTTTTAGATA
1 AATTATATTACTTTTTTAAAATA
35379128 AATTATATTAC-TTTTTAAAATA
1 AATTATATTACTTTTTTAAAATA
35379150 TATATAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTATATTACTTTTTTAAAATA
Found at i:35379348 original size:16 final size:18
Alignment explanation
Indices: 35379315--35379349 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35379305 TTAAAATCTT
35379315 TATATACAAAGTTAAAAA
1 TATATACAAAGTTAAAAA
*
35379333 TATATA-AATGTTAAAAA
1 TATATACAAAGTTAAAAA
35379350 GTAAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
TATATACAAAGTTAAAAA
Found at i:35380511 original size:30 final size:30
Alignment explanation
Indices: 35380471--35380530 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
35380461 GGATTGAGAG
* *
35380471 GGGAGGGAGTAAAAGTTTTGGGGGAAAAGT
1 GGGAAGGAGTAAAAGTTTTGAGGGAAAAGT
35380501 GGGAAGGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGGAGTAAAAGTTTTGAGGGAAAAGT
35380531 AAAAAGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (30 bp):
GGGAAGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:35380602 original size:18 final size:18
Alignment explanation
Indices: 35380579--35380615 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
35380569 TATACTTTGA
35380579 TATTTGAATTATTCGAAT
1 TATTTGAATTATTCGAAT
*
35380597 TATTTGAGTTATTCGAAT
1 TATTTGAATTATTCGAAT
35380615 T
1 T
35380616 CGAAAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (18 bp):
TATTTGAATTATTCGAAT
Found at i:35380686 original size:9 final size:9
Alignment explanation
Indices: 35380669--35380699 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
35380659 TCAAGTTGAT
35380669 TCGAATAAC
1 TCGAATAAC
*
35380678 TCGATTAAC
1 TCGAATAAC
35380687 TCGAATAAC
1 TCGAATAAC
35380696 TCGA
1 TCGA
35380700 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:35382842 original size:199 final size:199
Alignment explanation
Indices: 35382332--35382927 Score: 1061
Period size: 198 Copynumber: 3.0 Consensus size: 199
35382322 CTAATTATCA
* *
35382332 ACAAGAAAAAACTTGAAAAAGGCATCCTAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
1 ACAAGAAAAAACTTGAAAAGGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
* *
35382397 TCCATATTAAGGCTTTTCTAGGGACAAAGGACAGGAAAAGAGTGAGAATGGAAAATTTGTTAATC
66 TCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAATC
*
35382462 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTCGCTTAAGCATTAGATTGACAAATTTTTA
131 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
35382527 ATCC
196 ATCC
35382531 ACAAG-AAAAACTTGAAAAGGGCA-CCCTAAAAGAGATTATGTTCACCGACACATTATCTTACAA
1 ACAAGAAAAAACTTGAAAAGGGCATCCC-AAAAGAGATTATGTTCACCGACACATTATCTTACAA
35382594 TTCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAAT
65 TTCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAAT
35382659 CAAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTT
130 CAAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTT
35382724 AATCC
195 AATCC
* *
35382729 ACAAGAAAAAACTTGGAAAGGGCATCCCAAAAGAGATTATGTTCACTGACACATTATCTTACAAT
1 ACAAGAAAAAACTTGAAAAGGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
* * * *
35382794 TCCATATTAAGGCTTTTCTATGTACAAAGGATAGGAAAAGAATGAGGATGGAAAATTTGTTAACC
66 TCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAATC
*
35382859 AAAAAGTTCAGATTCATAACCACTTTCTTACCTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
131 AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
35382924 ATCC
196 ATCC
35382928 TCCCCTTTTT
Statistics
Matches: 382, Mismatches: 12, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
197 2 0.01
198 190 0.50
199 187 0.49
200 3 0.01
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (199 bp):
ACAAGAAAAAACTTGAAAAGGGCATCCCAAAAGAGATTATGTTCACCGACACATTATCTTACAAT
TCCATATTAAGGCTTTTCTAGGTACAAAGGACAGGAAAAGAGTGAGGATGGAAAATTTGTTAATC
AAAAAGTTCAGATTCATAACCACTTTCTTACTTTGTAGCTTAAGCATTAGATTGACAAATTTTTA
ATCC
Found at i:35389169 original size:9 final size:9
Alignment explanation
Indices: 35389151--35389196 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
35389141 CACTTAAATC
35389151 CAACTCTCT
1 CAACTCTCT
*
35389160 CAATTCTCT
1 CAACTCTCT
*
35389169 CAACTCTTT
1 CAACTCTCT
* *
35389178 CAATTCTTT
1 CAACTCTCT
35389187 CAACTCTCT
1 CAACTCTCT
35389196 C
1 C
35389197 TAGTTTTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (9 bp):
CAACTCTCT
Found at i:35389174 original size:18 final size:18
Alignment explanation
Indices: 35389151--35389196 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
35389141 CACTTAAATC
35389151 CAACTCTCTCAATTCTCT
1 CAACTCTCTCAATTCTCT
* *
35389169 CAACTCTTTCAATTCTTT
1 CAACTCTCTCAATTCTCT
35389187 CAACTCTCTC
1 CAACTCTCTC
35389197 TAGTTTTGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.22, C:0.37, G:0.00, T:0.41
Consensus pattern (18 bp):
CAACTCTCTCAATTCTCT
Found at i:35389423 original size:10 final size:10
Alignment explanation
Indices: 35389408--35389433 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
35389398 AGTTTTTAAA
35389408 ATTTTAAATT
1 ATTTTAAATT
35389418 ATTTTAAATT
1 ATTTTAAATT
35389428 ATTTTA
1 ATTTTA
35389434 TTTTGTCGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTAAATT
Found at i:35394138 original size:12 final size:12
Alignment explanation
Indices: 35394123--35394155 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
35394113 TGTTGTCATT
35394123 AATGCCAACATC
1 AATGCCAACATC
*
35394135 AATGCCCACATC
1 AATGCCAACATC
35394147 AATGCCAAC
1 AATGCCAAC
35394156 GTATCCAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.39, C:0.36, G:0.09, T:0.15
Consensus pattern (12 bp):
AATGCCAACATC
Found at i:35394362 original size:6 final size:6
Alignment explanation
Indices: 35394351--35394403 Score: 79
Period size: 6 Copynumber: 8.8 Consensus size: 6
35394341 ACTGGGGTGG
* * *
35394351 AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA GGGTGG AGATGA
1 AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA AGATGA
35394399 AGATG
1 AGATG
35394404 GGTACGAGGG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.43, C:0.00, G:0.40, T:0.17
Consensus pattern (6 bp):
AGATGA
Found at i:35395507 original size:8 final size:8
Alignment explanation
Indices: 35395494--35395518 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35395484 TTATCAGCTC
35395494 TTATTATT
1 TTATTATT
35395502 TTATTATT
1 TTATTATT
35395510 TTATTATT
1 TTATTATT
35395518 T
1 T
35395519 GAAATTCTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTATT
Found at i:35395760 original size:27 final size:25
Alignment explanation
Indices: 35395730--35395780 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
35395720 TTGTTTTAAC
35395730 TTAATAAATTT-TCTTTGAGTTTTTCTT
1 TTAA-AAATTTCTC-TTGA-TTTTTCTT
*
35395757 TTAAGAATTTCTCTTGATTTTTCT
1 TTAAAAATTTCTCTTGATTTTTCT
35395781 CTTGCCAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 9 0.41
27 6 0.27
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.61
Consensus pattern (25 bp):
TTAAAAATTTCTCTTGATTTTTCTT
Found at i:35402738 original size:21 final size:21
Alignment explanation
Indices: 35402712--35402775 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
35402702 GGAACATGCC
**
35402712 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
* *
35402733 AACAGAAGCACAAAAGAGCTA
1 AACAGAAGCTCAAAAGAGCTG
*
35402754 AACAAAAGCTCAAAAGAGCTG
1 AACAGAAGCTCAAAAGAGCTG
35402775 A
1 A
35402776 TCCACCCAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.50, C:0.19, G:0.22, T:0.09
Consensus pattern (21 bp):
AACAGAAGCTCAAAAGAGCTG
Found at i:35405256 original size:14 final size:14
Alignment explanation
Indices: 35405213--35405257 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 14
35405203 AATTAACTAC
35405213 ACATTAGTCTTAAT
1 ACATTAGTCTTAAT
*
35405227 GCATTATTGTTCTTAAT
1 ACATTA--G-TCTTAAT
35405244 ACATTAGTCTTAAT
1 ACATTAGTCTTAAT
35405258 GTATTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 1 0.04
17 12 0.46
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (14 bp):
ACATTAGTCTTAAT
Found at i:35410319 original size:18 final size:18
Alignment explanation
Indices: 35410298--35410341 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
35410288 AAAATATATT
35410298 AAATCAATGTTTTCAAGA
1 AAATCAATGTTTTCAAGA
* *
35410316 AAATCAGTGTTTTTAAGA
1 AAATCAATGTTTTCAAGA
35410334 AAATCAAT
1 AAATCAAT
35410342 TTCATAGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (18 bp):
AAATCAATGTTTTCAAGA
Found at i:35416395 original size:17 final size:17
Alignment explanation
Indices: 35416373--35416406 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
35416363 TACTAACATT
* *
35416373 AAAATGTAATGACAATA
1 AAAATGCAATGAAAATA
35416390 AAAATGCAATGAAAATA
1 AAAATGCAATGAAAATA
35416407 TGCACTAACA
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:0.62, C:0.06, G:0.12, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGAAAATA
Found at i:35420319 original size:50 final size:50
Alignment explanation
Indices: 35420217--35420458 Score: 198
Period size: 50 Copynumber: 4.7 Consensus size: 50
35420207 GGGGATGATA
* * **
35420217 TCCCATGTAAGACCATGTTTGGGACATGACATTGGCATTATTGAGGTTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA---A---TATGAGAGG
*
35420273 TCCCATGTAAGACCATGTCTGGGACATGGCCTTGGCACCAATATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAGG
** * * * **
35420323 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAGG
* * * * ** * * * **
35420373 TCCCATGTAAGCCCATATCTGGGATATGACATTGGCA-GTACAGGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAGG
* *
35420422 TCCCATGTAAGACCATGTCTGGGACATGCCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35420459 TGTTATTATT
Statistics
Matches: 153, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
49 37 0.24
50 80 0.52
53 1 0.01
56 35 0.23
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAATATGAGAGG
Found at i:35425650 original size:11 final size:11
Alignment explanation
Indices: 35425634--35425659 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35425624 TCCAATGCCC
35425634 GAATAGAAGAT
1 GAATAGAAGAT
35425645 GAATAGAAGAT
1 GAATAGAAGAT
35425656 GAAT
1 GAAT
35425660 TATCCTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.27, T:0.19
Consensus pattern (11 bp):
GAATAGAAGAT
Found at i:35425818 original size:16 final size:17
Alignment explanation
Indices: 35425797--35425831 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
35425787 AAATATTAAG
35425797 AAATAAA-AACAAACAA
1 AAATAAACAACAAACAA
*
35425813 AAATAAACATCAAACAA
1 AAATAAACAACAAACAA
35425830 AA
1 AA
35425832 GTCGTTCCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (17 bp):
AAATAAACAACAAACAA
Found at i:35428356 original size:31 final size:31
Alignment explanation
Indices: 35428318--35428380 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
35428308 ACTATACTAG
35428318 TCAAATGTTCAACTCGTATTCATACTTATGA
1 TCAAATGTTCAACTCGTATTCATACTTATGA
35428349 TCAAATGTTCAACTCGTATTCATACTTATGA
1 TCAAATGTTCAACTCGTATTCATACTTATGA
35428380 T
1 T
35428381 ATATACCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.40
Consensus pattern (31 bp):
TCAAATGTTCAACTCGTATTCATACTTATGA
Found at i:35428549 original size:46 final size:46
Alignment explanation
Indices: 35428436--35428688 Score: 296
Period size: 46 Copynumber: 5.5 Consensus size: 46
35428426 TGATGTCATC
* * ** * * *
35428436 GTGTCTTTCAACCATGTTCTTATTCATTCGC-GACTTGGTGCCATA
1 GTGTCTTTCAACTATGGTCTTATTCATTTTCTGTCATGTTGCCATA
* ** ** * *
35428481 GTGTCTTTCAACCATGACCTTATTCATTTT-TCGTTGTGTTTCCATT
1 GTGTCTTTCAACTATGGTCTTATTCATTTTCT-GTCATGTTGCCATA
**
35428527 GTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATA
1 GTGTCTTTCAACTATGGTCTTATTCATTTTCTGTCATGTTGCCATA
*
35428573 GTGTCTTTCAACTATGGTGC-TATTCATTTTCTGTCATGATGCCATA
1 GTGTCTTTCAACTATGGT-CTTATTCATTTTCTGTCATGTTGCCATA
* *
35428619 GTTTCTTTCAACTATGGTCATATTCATTTTCTGTCATGTTGCCATA
1 GTGTCTTTCAACTATGGTCTTATTCATTTTCTGTCATGTTGCCATA
35428665 GTGTCTTTCAACTATGGTCTTATT
1 GTGTCTTTCAACTATGGTCTTATT
35428689 TGTTTGATTC
Statistics
Matches: 177, Mismatches: 26, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
45 27 0.15
46 149 0.84
47 1 0.01
ACGTcount: A:0.18, C:0.21, G:0.15, T:0.46
Consensus pattern (46 bp):
GTGTCTTTCAACTATGGTCTTATTCATTTTCTGTCATGTTGCCATA
Found at i:35428597 original size:92 final size:93
Alignment explanation
Indices: 35428425--35428731 Score: 302
Period size: 92 Copynumber: 3.4 Consensus size: 93
35428415 AAATGATCGA
* * * * ** * * *
35428425 ATGATGTCATCGTGTCTTTCAACCATGTTCTTATTCATTCGCGA-CTTGGTGCCATAGTGTCTTT
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
* * *
35428489 CAACCAT-GACCTTATTCATTTT-TCGTT
66 CAACTATGGTCCTTATTCATTTTCT-GTC
* * * *
35428516 GTGTTTCCATTGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
*
35428581 CAACTATGGTGC-TATTCATTTTCTGTC
66 CAACTATGGTCCTTATTCATTTTCTGTC
* * **
35428608 ATGATGCCATAGTTTCTTTCAACTATGGTCATATTCATTTTCTGTCATGTTGCCATAGTGTCTTT
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
** **
35428673 CAACTATGGT-CTTATTTGTTTGAT-TC
66 CAACTATGGTCCTTATTCATTTTCTGTC
* * * *
35428699 GTGATGCCATAGCGTCTTTCAGCTATGATCTTA
1 ATGATGCCATAGTGTCTTTCAACTATGGTCTTA
35428732 CTCGATAGAA
Statistics
Matches: 178, Mismatches: 34, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
91 64 0.36
92 111 0.62
93 3 0.02
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.45
Consensus pattern (93 bp):
ATGATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCATCATGTTGCCATAGTGTCTTT
CAACTATGGTCCTTATTCATTTTCTGTC
Found at i:35428874 original size:45 final size:45
Alignment explanation
Indices: 35428768--35428874 Score: 142
Period size: 45 Copynumber: 2.4 Consensus size: 45
35428758 TCTTTTAGCC
* * *
35428768 ATGGTCTTACTCATTTCTGGTATAGTGCCATAGTGTCTTTCATCT
1 ATGGTCTTAATCATTTCTGGTATAGTGCCATAGTGTCTTTAAACT
* * * *
35428813 CTGGTGTTATTTATTTCTGGTATAGTGCCATAGTGTCTTTAAACT
1 ATGGTCTTAATCATTTCTGGTATAGTGCCATAGTGTCTTTAAACT
*
35428858 ATGGTCTAAATCATTTC
1 ATGGTCTTAATCATTTC
35428875 CTTCAAGCCA
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.45
Consensus pattern (45 bp):
ATGGTCTTAATCATTTCTGGTATAGTGCCATAGTGTCTTTAAACT
Found at i:35430535 original size:15 final size:14
Alignment explanation
Indices: 35430506--35430539 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
35430496 AATTAAGTTG
*
35430506 ATAAAGAAAATAAA
1 ATAAACAAAATAAA
35430520 ATAAACAAACATAAA
1 ATAAACAAA-ATAAA
35430535 ATAAA
1 ATAAA
35430540 ATAAAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (14 bp):
ATAAACAAAATAAA
Found at i:35433493 original size:27 final size:27
Alignment explanation
Indices: 35433463--35433640 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
35433453 ATATTAAGTC
* * *
35433463 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* *
35433490 CGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
35433518 CGCACACTTAGTGCTACATAGTCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
** * *
35433545 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
35433572 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
* *
35433599 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
35433626 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35433641 GTACAATTTA
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 105 0.80
28 26 0.20
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:35433547 original size:55 final size:54
Alignment explanation
Indices: 35433463--35433640 Score: 232
Period size: 54 Copynumber: 3.3 Consensus size: 54
35433453 ATATTAAGTC
* * *
35433463 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCCACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAA-T
* * * *
35433518 CGCACACTTAGTGCTACATAGTCAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
* ** *
35433572 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
35433626 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
35433641 GTACAATTTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.01
54 60 0.56
55 46 0.43
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:35433629 original size:81 final size:82
Alignment explanation
Indices: 35433484--35433639 Score: 235
Period size: 81 Copynumber: 1.9 Consensus size: 82
35433474 TGCTATATAA
* *
35433484 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCTACATAGTCAACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
35433549 CACTTAGTGCCGCATGG
66 CACTTAGTGCCGCATGG
* * **
35433566 TCAATTCGCACACTTAGTG-CATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAATCGC
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGC
35433629 ACACTTAGTGC
65 ACACTTAGTGC
35433640 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 43 0.64
82 24 0.36
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (82 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAACTCGCACACTTAGTGCAACATAGTCAAATCGCA
CACTTAGTGCCGCATGG
Found at i:35454311 original size:16 final size:16
Alignment explanation
Indices: 35454290--35454320 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35454280 GATAATTATG
35454290 GTGAAATGATATGCGT
1 GTGAAATGATATGCGT
35454306 GTGAAATGATATGCG
1 GTGAAATGATATGCG
35454321 AATGTGTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.29
Consensus pattern (16 bp):
GTGAAATGATATGCGT
Found at i:35456648 original size:28 final size:28
Alignment explanation
Indices: 35456602--35456697 Score: 131
Period size: 28 Copynumber: 3.4 Consensus size: 28
35456592 GAGCCCTATA
*
35456602 CAATAACAGT-ACAGTGTGGGCCTTAGCC
1 CAAT-ACAGTAACAATGTGGGCCTTAGCC
* *
35456630 CAAAATAGTAACAATGTGGGCCTTAGCC
1 CAATACAGTAACAATGTGGGCCTTAGCC
* *
35456658 CAATACAGTAATAGTGTGGGCCTTAGCC
1 CAATACAGTAACAATGTGGGCCTTAGCC
35456686 CAATACAGTAAC
1 CAATACAGTAAC
35456698 CATTACAGTG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
27 4 0.07
28 55 0.93
ACGTcount: A:0.33, C:0.23, G:0.22, T:0.22
Consensus pattern (28 bp):
CAATACAGTAACAATGTGGGCCTTAGCC
Found at i:35456664 original size:61 final size:56
Alignment explanation
Indices: 35456585--35456697 Score: 136
Period size: 56 Copynumber: 1.9 Consensus size: 56
35456575 AGTATCAGTC
* *
35456585 TGGGCCTGAGCCCTATACAATAACAGTACAGTGTGGGCCTTAGCCCAAAATAGTAACAATG
1 TGGGCCTGAGCCCAATACAAT-A-A-T--AGTGTGGGCCTTAGCCCAAAACAGTAACAATG
* * *
35456646 TGGGCCTTAGCCCAATACAGTAATAGTGTGGGCCTTAGCCCAATACAGTAAC
1 TGGGCCTGAGCCCAATACAATAATAGTGTGGGCCTTAGCCCAAAACAGTAAC
35456698 CATTACAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 26 0.55
58 1 0.02
59 1 0.02
60 1 0.02
61 18 0.38
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (56 bp):
TGGGCCTGAGCCCAATACAATAATAGTGTGGGCCTTAGCCCAAAACAGTAACAATG
Found at i:35457084 original size:27 final size:27
Alignment explanation
Indices: 35457054--35457291 Score: 284
Period size: 27 Copynumber: 8.8 Consensus size: 27
35457044 TATAACAGTT
* *
35457054 ATTTTA-CCTTATGAGGGTATTTCAATC
1 ATTTTACCCTT-TGGGGGTATTTCGATC
*
35457081 ATTTTACCCTTTGGGGGTATTTCAATC
1 ATTTTACCCTTTGGGGGTATTTCGATC
35457108 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGGTATTTCGATC
* *
35457135 ATTTTACCCTTTGGGGGTACTTCGGTC
1 ATTTTACCCTTTGGGGGTATTTCGATC
35457162 ATTTTACCCTTTGGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGGTATTTCGATC
**
35457189 ATTTTACCCTTCAGGGGTATTTCGATC
1 ATTTTACCCTTTGGGGGTATTTCGATC
* * * * *
35457216 ATTTTAACCTCTGAGGGTATTTTGGTC
1 ATTTTACCCTTTGGGGGTATTTCGATC
** *
35457243 ATTTTA-CCTTCCAGGGGTATTTCGGTC
1 ATTTTACCCTT-TGGGGGTATTTCGATC
*
35457270 ATTTTA-CCTTCTAGGGGTATTT
1 ATTTTACCCTT-TGGGGGTATTT
35457292 TAGTCATTTT
Statistics
Matches: 188, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 3 0.02
27 181 0.96
28 4 0.02
ACGTcount: A:0.17, C:0.18, G:0.21, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTTGGGGGTATTTCGATC
Found at i:35458003 original size:5 final size:5
Alignment explanation
Indices: 35457983--35458021 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
35457973 GCACTGGAAT
*
35457983 GAAGA GGAGAA GAAGA GAAGA GAAGA GAAGA GAAGA GAA
1 GAAGA GAAG-A GAAGA GAAGA GAAGA GAAGA GAAGA GAA
35458022 AAGAGAGGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:35468241 original size:45 final size:45
Alignment explanation
Indices: 35468177--35468271 Score: 172
Period size: 45 Copynumber: 2.1 Consensus size: 45
35468167 TAACAGATAC
* *
35468177 TCGGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
35468222 TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
35468267 TCGGT
1 TCGGT
35468272 TCACATAGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (45 bp):
TCGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
Found at i:35468335 original size:51 final size:50
Alignment explanation
Indices: 35468268--35468453 Score: 212
Period size: 51 Copynumber: 3.7 Consensus size: 50
35468258 CAATGATGTT
* * *
35468268 CGGTTCACATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCA-TACCATC
* * * * *
35468319 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGA-CCATACCATC
* * * *
35468370 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCA-TC
* *
35468420 TGGTACACGTAGTAGCCTTCACATAGTACTACAC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACAC
35468454 TAACGTGATC
Statistics
Matches: 112, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 2 0.02
50 33 0.29
51 75 0.67
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACATGTGACCATACCATC
Found at i:35468452 original size:101 final size:102
Alignment explanation
Indices: 35468275--35468463 Score: 283
Period size: 101 Copynumber: 1.8 Consensus size: 102
35468265 GTTCGGTTCA
*
35468275 CATAGTAGCCTGCACATAGTACTACACATATGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATACGACCA-TACCATCCGATACACGTAGTAGCCTGCA
35468340 CATAGTACTACAC-ACGTGATCGAAACTATCCGGTACG
65 CATAGTACTACACAACGTGATCGAAACTATCCGGTACG
* * * * *
35468377 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTCTGGTACACGTAGTAGCCTTCA
1 CATAGTAGCCTGCACATAGTACTACACATACGACCATACCA-TCCGATACACGTAGTAGCCTGCA
35468441 CATAGTACTACACTAACGTGATC
65 CATAGTACTACAC-AACGTGATC
35468464 CGGCTCAGTT
Statistics
Matches: 78, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
100 4 0.05
101 33 0.42
102 33 0.42
103 8 0.10
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATACGACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACAACGTGATCGAAACTATCCGGTACG
Found at i:35471816 original size:15 final size:15
Alignment explanation
Indices: 35471781--35471809 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35471771 ATTCTTCAAA
35471781 AACATGAGGAGAAAC
1 AACATGAGGAGAAAC
35471796 AACATGAGGA-AAAC
1 AACATGAGGAGAAAC
35471810 TCACATGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.55, C:0.14, G:0.24, T:0.07
Consensus pattern (15 bp):
AACATGAGGAGAAAC
Found at i:35471918 original size:18 final size:18
Alignment explanation
Indices: 35471897--35471935 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
35471887 TCTTTTTATT
35471897 TTTCAATTT-TTTTCTCAA
1 TTTCAATTTCTTTT-TCAA
35471915 TTTCAATTTCTTTTTCAA
1 TTTCAATTTCTTTTTCAA
35471933 TTT
1 TTT
35471936 TCTTTTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTCAATTTCTTTTTCAA
Found at i:35471939 original size:13 final size:12
Alignment explanation
Indices: 35471915--35471980 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
35471905 TTTTTCTCAA
35471915 TTTCAATTTCTT
1 TTTCAATTTCTT
35471927 TTTCAATTTTCTTT
1 TTTCAA-TTTC-TT
*
35471941 TCTTCGATTTCTT
1 T-TTCAATTTCTT
* **
35471954 TTTCTATCACTT
1 TTTCAATTTCTT
*
35471966 TTT-GATTTCTT
1 TTTCAATTTCTT
35471977 TTTC
1 TTTC
35471981 TTTTGCAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.19
12 17 0.40
13 7 0.16
14 7 0.16
15 4 0.09
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:35472002 original size:5 final size:6
Alignment explanation
Indices: 35471971--35472010 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
35471961 CACTTTTTGA
* **
35471971 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCTT TTTC
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC
35472011 ACATGCTGTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.05, C:0.17, G:0.03, T:0.75
Consensus pattern (6 bp):
TTTCTT
Found at i:35472022 original size:24 final size:24
Alignment explanation
Indices: 35471971--35472022 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
35471961 CACTTTTTGA
* *
35471971 TTTCTTTTTCTTTTGCAATTTCTT
1 TTTCTTTTTCTTTTGCAATTGCTG
*
35471995 TTTCTTTTTCTTTTTCACA-TGCTG
1 TTTCTTTTTCTTTTGCA-ATTGCTG
35472019 TTTC
1 TTTC
35472023 GATTTCATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.08, C:0.19, G:0.06, T:0.67
Consensus pattern (24 bp):
TTTCTTTTTCTTTTGCAATTGCTG
Found at i:35476540 original size:23 final size:24
Alignment explanation
Indices: 35476514--35476558 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
35476504 TGGTCTTGGA
* *
35476514 AGGA-ATTGTGGAGCAAATCAATG
1 AGGAGATTGGGGAGAAAATCAATG
35476537 AGGAGATTGGGGAGAAAATCAA
1 AGGAGATTGGGGAGAAAATCAA
35476559 GGAAATTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.42, C:0.07, G:0.33, T:0.18
Consensus pattern (24 bp):
AGGAGATTGGGGAGAAAATCAATG
Found at i:35487642 original size:50 final size:50
Alignment explanation
Indices: 35487500--35487785 Score: 207
Period size: 50 Copynumber: 5.6 Consensus size: 50
35487490 GACAATAACA
* * ** * *
35487500 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCT-CGG
* * * * * * ** * **
35487549 TACCAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATTAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * *
35487599 TGCCCATGCCATGTCCTAGACATAGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * * * *
35487649 TGCTAACGCCATGTCCCAGACATGGTATTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* *** *
35487699 TGCCAATTCCATGTCCCAGACATGGTCTTACATTAGACCTCTCATGATCCCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATCTC--GG
*
35487754 ATGCCAATGCCATGCCCCAGACATGGTCTTAC
1 -TGCCAATGCCATGTCCCAGACATGGTCTTAC
35487786 GTGGTGATAG
Statistics
Matches: 184, Mismatches: 45, Indels: 9
0.77 0.19 0.04
Matches are distributed among these distances:
49 37 0.20
50 113 0.61
53 3 0.02
55 2 0.01
56 29 0.16
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:35499714 original size:56 final size:50
Alignment explanation
Indices: 35499488--35499730 Score: 315
Period size: 50 Copynumber: 4.7 Consensus size: 50
35499478 GATAATAACA
* * * ** *
35499488 TGCCAAAGCCATGTCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ***
35499538 TGCCCATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
35499588 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
35499638 TGCCAATTCCATGTCCCAGACATGGTCTTACATTGGACCTCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
35499693 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
35499731 TCTTTTTACC
Statistics
Matches: 167, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
50 125 0.75
53 5 0.03
55 2 0.01
56 35 0.21
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:35500101 original size:29 final size:30
Alignment explanation
Indices: 35500069--35500128 Score: 68
Period size: 30 Copynumber: 2.0 Consensus size: 30
35500059 GCCCTCGACT
*
35500069 CTAACCTTGGA-AAAATTACAATTTTGCCC
1 CTAAACTTGGACAAAATTACAATTTTGCCC
** * *
35500098 CTAAACTTTTACATAATTACACTTTTGCCC
1 CTAAACTTGGACAAAATTACAATTTTGCCC
35500128 C
1 C
35500129 AAAGCTCAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.35
Consensus pattern (30 bp):
CTAAACTTGGACAAAATTACAATTTTGCCC
Found at i:35504190 original size:28 final size:27
Alignment explanation
Indices: 35504104--35504431 Score: 138
Period size: 27 Copynumber: 12.4 Consensus size: 27
35504094 GATAGATGAT
* *
35504104 TGAAATA-CCCTAT-AGGATAAAATGAC
1 TGAAATACCCCCATAAGG-TAAAATAAC
*
35504130 CGAAATACCCCCATAAGGTAAAATAA-
1 TGAAATACCCCCATAAGGTAAAATAAC
* * *
35504156 TCAAAATTCCCCCCATAGGGTAAAATAAC
1 T-GAAA-TACCCCCATAAGGTAAAATAAC
* *
35504185 TGAAATACCCCCGTAAGGTAAAATAAT
1 TGAAATACCCCCATAAGGTAAAATAAC
* *
35504212 TGAAAT---TCC--AGGGTAAAATAAC
1 TGAAATACCCCCATAAGGTAAAATAAC
* ***** *
35504234 CGAAAT--GGGGGTAAGGTAAAATGAC
1 TGAAATACCCCCATAAGGTAAAATAAC
* * *
35504259 CGAAACACCCCTATAAGGTAAAATAAC
1 TGAAATACCCCCATAAGGTAAAATAAC
* * * * *
35504286 CGAAATACCCCTATAGGGTAGAATGAC
1 TGAAATACCCCCATAAGGTAAAATAAC
* ** *
35504313 CGAAATACCCTTATAAGGTAAAATTAC
1 TGAAATACCCCCATAAGGTAAAATAAC
* * *
35504340 CGAAATACCCCCGTATA-GTAAAATGAC
1 TGAAATACCCCCATA-AGGTAAAATAAC
* * * * *
35504367 CGAAATACTCTCATAGGGTAAAATGAC
1 TGAAATACCCCCATAAGGTAAAATAAC
** ** * *
35504394 CAAAATACCCTTATAGGGTAAAATGAC
1 TGAAATACCCCCATAAGGTAAAATAAC
**
35504421 TGTTATACCCC
1 TGAAATACCCC
35504432 TAGGAGATGA
Statistics
Matches: 238, Mismatches: 52, Indels: 23
0.76 0.17 0.07
Matches are distributed among these distances:
22 16 0.07
24 2 0.01
25 16 0.07
26 6 0.03
27 171 0.72
28 26 0.11
29 1 0.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (27 bp):
TGAAATACCCCCATAAGGTAAAATAAC
Found at i:35504202 original size:55 final size:55
Alignment explanation
Indices: 35504115--35504220 Score: 158
Period size: 55 Copynumber: 1.9 Consensus size: 55
35504105 GAAATACCCT
*
35504115 ATAGGATAAAATGACCGAAATACCCCCATAAGGTAAAATAATCAAAATTCCCCCC
1 ATAGGATAAAATAACCGAAATACCCCCATAAGGTAAAATAATCAAAATTCCCCCC
* * * **
35504170 ATAGGGTAAAATAACTGAAATACCCCCGTAAGGTAAAATAATTGAAATTCC
1 ATAGGATAAAATAACCGAAATACCCCCATAAGGTAAAATAATCAAAATTCC
35504221 AGGGTAAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.45, C:0.21, G:0.13, T:0.21
Consensus pattern (55 bp):
ATAGGATAAAATAACCGAAATACCCCCATAAGGTAAAATAATCAAAATTCCCCCC
Found at i:35504430 original size:27 final size:27
Alignment explanation
Indices: 35504248--35504420 Score: 206
Period size: 27 Copynumber: 6.4 Consensus size: 27
35504238 ATGGGGGTAA
* * *
35504248 GGTAAAATGACCGAAACACCCCTATAA
1 GGTAAAATGACCGAAATACCCTTATAG
* *
35504275 GGTAAAATAACCGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCTTATAG
* *
35504302 GGTAGAATGACCGAAATACCCTTATAA
1 GGTAAAATGACCGAAATACCCTTATAG
* *
35504329 GGTAAAATTACCGAAATACCCCCGTATA-
1 GGTAAAATGACCGAAATA--CCCTTATAG
* *
35504357 -GTAAAATGACCGAAATACTCTCATAG
1 GGTAAAATGACCGAAATACCCTTATAG
*
35504383 GGTAAAATGACCAAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCTTATAG
35504410 GGTAAAATGAC
1 GGTAAAATGAC
35504421 TGTTATACCC
Statistics
Matches: 125, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
25 5 0.04
27 113 0.90
29 7 0.06
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCTTATAG
Found at i:35504431 original size:81 final size:81
Alignment explanation
Indices: 35504245--35504420 Score: 241
Period size: 81 Copynumber: 2.2 Consensus size: 81
35504235 GAAATGGGGG
* *
35504245 TAAGGTAAAATGACCGAAACA-CCCC-TATAAGGTAAAATAACCGAAATACCCCTATAGGGTAGA
1 TAAGGTAAAATGACCGAAATACCCCCGTAT-A-GTAAAATAACCGAAATACCCCTATAGGGTAAA
*
35504308 ATGACCGAAATACCCTTA
64 ATGACCAAAATACCCTTA
* * *
35504326 TAAGGTAAAATTACCGAAATACCCCCGTATAGTAAAATGACCGAAATA-CTCTCATAGGGTAAAA
1 TAAGGTAAAATGACCGAAATACCCCCGTATAGTAAAATAACCGAAATACCCCT-ATAGGGTAAAA
35504390 TGACCAAAATACCCTTA
65 TGACCAAAATACCCTTA
*
35504407 TAGGGTAAAATGAC
1 TAAGGTAAAATGAC
35504421 TGTTATACCC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
80 3 0.04
81 73 0.87
82 5 0.06
83 3 0.04
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (81 bp):
TAAGGTAAAATGACCGAAATACCCCCGTATAGTAAAATAACCGAAATACCCCTATAGGGTAAAAT
GACCAAAATACCCTTA
Found at i:35504696 original size:26 final size:26
Alignment explanation
Indices: 35504659--35504733 Score: 89
Period size: 26 Copynumber: 2.9 Consensus size: 26
35504649 ACATATATTG
* *
35504659 TTACTGGTAGCTTTGCTCCGATACTGA
1 TTACTGGCAGCTTTGCTGCGATACT-A
* *
35504686 -TACTGGCAGCTCTGCTGCGATGCTA
1 TTACTGGCAGCTTTGCTGCGATACTA
*
35504711 TTACTGGCCGCTTTGCTGCGATA
1 TTACTGGCAGCTTTGCTGCGATA
35504734 TTGGTGTGTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 39 0.98
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.33
Consensus pattern (26 bp):
TTACTGGCAGCTTTGCTGCGATACTA
Found at i:35504875 original size:28 final size:28
Alignment explanation
Indices: 35504835--35504984 Score: 167
Period size: 28 Copynumber: 5.2 Consensus size: 28
35504825 TATTGCACTG
35504835 CACT-ATTACTGTATTGGGCTAAGGCCCA
1 CACTGATT-CTGTATTGGGCTAAGGCCCA
*
35504863 CACTGATTCTGTATTGGGATAAGGCCCA
1 CACTGATTCTGTATTGGGCTAAGGCCCA
** * *
35504891 CACCAATTCTGCAATGGGCTAAGGCCCA
1 CACTGATTCTGTATTGGGCTAAGGCCCA
*
35504919 CATTGATTCTGTATTGGGCTAAGGCCCA
1 CACTGATTCTGTATTGGGCTAAGGCCCA
* *
35504947 CACTGTACTATTACTATATTGGGCTGAGGCCCA
1 CACTG----ATT-CTGTATTGGGCTAAGGCCCA
35504980 CACTG
1 CACTG
35504985 TATTGTCACT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
28 73 0.72
29 3 0.03
32 3 0.03
33 23 0.23
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (28 bp):
CACTGATTCTGTATTGGGCTAAGGCCCA
Found at i:35506518 original size:36 final size:36
Alignment explanation
Indices: 35506415--35506524 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 36
35506405 ACAGCAAGTA
35506415 GAAGATCCCACAGAGATCGAGCTAGTGCAATCGGCT
1 GAAGATCCCACAGAGATCGAGCTAGTGCAATCGGCT
*
35506451 GAAG-TCCCTGGTA-AGGTGCAATCGAGCTAGTGCAATCGGCT
1 GAAGATCCC----ACA-GAG--ATCGAGCTAGTGCAATCGGCT
35506492 GAAGATCCCACAGAGATCGAGCTAGTGCAATCG
1 GAAGATCCCACAGAGATCGAGCTAGTGCAATCG
35506525 AGACTTCAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 18
0.76 0.02 0.22
Matches are distributed among these distances:
35 4 0.06
36 22 0.35
38 4 0.06
39 4 0.06
41 25 0.40
42 4 0.06
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (36 bp):
GAAGATCCCACAGAGATCGAGCTAGTGCAATCGGCT
Found at i:35510377 original size:14 final size:15
Alignment explanation
Indices: 35510345--35510378 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
35510335 TTTATTATAT
*
35510345 TTTATTTTACTTTTG
1 TTTATTTTACTTTTC
35510360 TTTATTTTA-TTTTC
1 TTTATTTTACTTTTC
35510374 TTTAT
1 TTTAT
35510379 CAACTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTATTTTACTTTTC
Found at i:35519408 original size:30 final size:26
Alignment explanation
Indices: 35519346--35519402 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
35519336 CTGGTCCTGA
*
35519346 GTATTAAAGACTTTGAAATGGTGTAT
1 GTATGAAAGACTTTGAAATGGTGTAT
35519372 GTATGAAAGACTTTGAAATGGTGTAT
1 GTATGAAAGACTTTGAAATGGTGTAT
35519398 GTATG
1 GTATG
35519403 TATGAATACA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.04, G:0.26, T:0.37
Consensus pattern (26 bp):
GTATGAAAGACTTTGAAATGGTGTAT
Found at i:35519455 original size:20 final size:20
Alignment explanation
Indices: 35519430--35519492 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
35519420 TGGTGCTCAA
35519430 TATGAACCAAGATATGTATG
1 TATGAACCAAGATATGTATG
* *
35519450 TATGAA--ATAG-TGT-TCA-A
1 TATGAACCA-AGATATGT-ATG
35519467 TATGAACCAAGATATGTATG
1 TATGAACCAAGATATGTATG
35519487 TATGAA
1 TATGAA
35519493 AGACTTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
17 7 0.22
18 6 0.19
19 6 0.19
20 13 0.41
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.32
Consensus pattern (20 bp):
TATGAACCAAGATATGTATG
Found at i:35519468 original size:37 final size:37
Alignment explanation
Indices: 35519417--35519493 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
35519407 AATACATGAA
*
35519417 AAATGGTGCTCAATATGAACCAAGATATGTATGTATG
1 AAATAGTGCTCAATATGAACCAAGATATGTATGTATG
*
35519454 AAATAGTGTTCAATATGAACCAAGATATGTATGTATG
1 AAATAGTGCTCAATATGAACCAAGATATGTATGTATG
35519491 AAA
1 AAA
35519494 GACTTTGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.30
Consensus pattern (37 bp):
AAATAGTGCTCAATATGAACCAAGATATGTATGTATG
Found at i:35543804 original size:20 final size:20
Alignment explanation
Indices: 35543779--35543818 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
35543769 CGGAAAATGA
*
35543779 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
35543799 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
35543819 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:35543834 original size:14 final size:15
Alignment explanation
Indices: 35543758--35543834 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 15
35543748 GATTGGCAGT
*
35543758 AAAATG-TTTTCCGG
1 AAAATGATTTTCTGG
35543772 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
35543786 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
35543806 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
35543821 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
35543835 TGTTTGATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
14 26 0.51
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:35545197 original size:35 final size:36
Alignment explanation
Indices: 35545150--35545226 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 36
35545140 ATTGTCATTG
* *
35545150 TCAATAATTTCAATATCCAACAAGCTTAAAACATAA
1 TCAATAAATTCAATATCCAACAAGATTAAAACATAA
35545186 T-AATAAATTCAATATCCAACAAGATTAAAACATAA
1 TCAATAAATTCAATATCCAACAAGATTAAAACATAA
35545221 TCAATA
1 TCAATA
35545227 TCTAACAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (36 bp):
TCAATAAATTCAATATCCAACAAGATTAAAACATAA
Found at i:35545224 original size:27 final size:28
Alignment explanation
Indices: 35545194--35545262 Score: 88
Period size: 27 Copynumber: 2.5 Consensus size: 28
35545184 AATAATAAAT
35545194 TCAATATCCAACAAGATT-AAAACATA-A
1 TCAATATCCAACAA-ATTCAAAACATATA
* *
35545221 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAACAAATTCAAAACATATA
*
35545249 TCAAAATCCAACAA
1 TCAATATCCAACAA
35545263 TCTAAAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 3 0.08
27 20 0.56
28 13 0.36
ACGTcount: A:0.54, C:0.20, G:0.03, T:0.23
Consensus pattern (28 bp):
TCAATATCCAACAAATTCAAAACATATA
Found at i:35547400 original size:29 final size:31
Alignment explanation
Indices: 35547359--35547418 Score: 70
Period size: 29 Copynumber: 2.0 Consensus size: 31
35547349 TAATATAGAG
*
35547359 ATTAAATTAATTC-ATTTC-ATAATAAAAAA
1 ATTAAATTAATTCGATTCCTATAATAAAAAA
* * *
35547388 ATTAATTTGATTCGATTCCTATAATAGAAAA
1 ATTAAATTAATTCGATTCCTATAATAAAAAA
35547419 CCTCCCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
29 11 0.44
30 4 0.16
31 10 0.40
ACGTcount: A:0.48, C:0.08, G:0.05, T:0.38
Consensus pattern (31 bp):
ATTAAATTAATTCGATTCCTATAATAAAAAA
Found at i:35550649 original size:54 final size:54
Alignment explanation
Indices: 35550567--35550676 Score: 177
Period size: 54 Copynumber: 2.0 Consensus size: 54
35550557 TTTCTAATGT
*
35550567 TATAATAAACATGAATTTTAATTAACTATACTAAT-AAAATTCCTCCTAGAAAGA
1 TATAATAAACACGAATTTTAATTAACTATACTAATCAAAA-TCCTCCTAGAAAGA
* *
35550621 TATAATAAACACGAATTTTAATTAACTATACTAATCGAAATCCTCTTAGAAAGA
1 TATAATAAACACGAATTTTAATTAACTATACTAATCAAAATCCTCCTAGAAAGA
35550675 TA
1 TA
35550677 CCTTACCAGA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
54 49 0.94
55 3 0.06
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (54 bp):
TATAATAAACACGAATTTTAATTAACTATACTAATCAAAATCCTCCTAGAAAGA
Found at i:35554745 original size:27 final size:27
Alignment explanation
Indices: 35554714--35554811 Score: 124
Period size: 27 Copynumber: 3.6 Consensus size: 27
35554704 TGACAGATAC
35554714 TTTTGGTGAACTATGTTTGCAGATGTG
1 TTTTGGTGAACTATGTTTGCAGATGTG
* * *
35554741 TTTTGGTGAACTAAGTTTGCAGGTCTG
1 TTTTGGTGAACTATGTTTGCAGATGTG
** *
35554768 ACTTGGTGAACTATGTTCGCAGATGTG
1 TTTTGGTGAACTATGTTTGCAGATGTG
* *
35554795 TTTTGGAGAACTGTGTT
1 TTTTGGTGAACTATGTT
35554812 CGCAAATAAG
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.19, C:0.10, G:0.30, T:0.41
Consensus pattern (27 bp):
TTTTGGTGAACTATGTTTGCAGATGTG
Done.