Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000001.1 Hibiscus syriacus cultivar Beakdansim tig00000002_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2159989
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:176052 original size:22 final size:22
Alignment explanation
Indices: 175979--176052 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
175969 AAATTATTTA
175979 AAATAAATCAATTCATACAACTACA-
1 AAATAAATCAATTCAT--AA-TA-AT
**
176004 ATAATAAATCAATTCAT-ATTTT
1 A-AATAAATCAATTCATAATAAT
176026 AAAATAAATCAATTCATAATAAT
1 -AAATAAATCAATTCATAATAAT
176049 AAAT
1 AAAT
176053 TATTTAAAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
22 20 0.49
23 5 0.12
25 1 0.02
26 15 0.37
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.32
Consensus pattern (22 bp):
AAATAAATCAATTCATAATAAT
Found at i:176063 original size:14 final size:15
Alignment explanation
Indices: 176023--176070 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
176013 CAATTCATAT
176023 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
*
176038 TTCATAATAATAAAT-TA
1 TT--TAA-AATAAATCAA
176055 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
176070 T
1 T
176071 ACATACAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 7 0.26
15 7 0.26
17 6 0.22
18 7 0.26
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTAAAATAAATCAA
Found at i:176132 original size:22 final size:21
Alignment explanation
Indices: 176080--176132 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
176070 TACATACAAC
*
176080 TATAAT-AATAAATCAATTCA
1 TATAATAAATAAATCAATCCA
**
176100 TATTTTAAAATAAATCAATCCA
1 TATAAT-AAATAAATCAATCCA
176122 TACTAATAAAT
1 TA-TAATAAAT
176133 TATTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
TATAATAAATAAATCAATCCA
Found at i:176174 original size:15 final size:15
Alignment explanation
Indices: 176154--176228 Score: 132
Period size: 15 Copynumber: 5.0 Consensus size: 15
176144 AATCAATCCA
*
176154 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
176169 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
*
176184 TATTTTATAATAAAT
1 TATTTTAAAATAAAT
176199 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
176214 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
176229 AACCTTATTA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATTTTAAAATAAAT
Found at i:178031 original size:2 final size:2
Alignment explanation
Indices: 178024--178068 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
178014 GATTTTTAAA
*
178024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT -T AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
178066 AT A
1 AT A
178069 AAAAAAGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.92
3 2 0.05
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:180691 original size:2 final size:2
Alignment explanation
Indices: 180684--180708 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
180674 AAACAAAATA
180684 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
180709 AAAGAAAGTC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:183599 original size:19 final size:20
Alignment explanation
Indices: 183577--183618 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
183567 TAAATTAATC
183577 ATAATTCTTTAAATTT-TAA
1 ATAATTCTTTAAATTTATAA
* *
183596 ATAATTTTTTACATTTATAA
1 ATAATTCTTTAAATTTATAA
183616 ATA
1 ATA
183619 TTTGAATTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (20 bp):
ATAATTCTTTAAATTTATAA
Found at i:185258 original size:31 final size:31
Alignment explanation
Indices: 185220--185344 Score: 189
Period size: 31 Copynumber: 4.0 Consensus size: 31
185210 CCCGAAGGAC
* * *
185220 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
185251 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
185282 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
185313 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
185344 C
1 C
185345 CCTCGACCCT
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 85 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:186172 original size:21 final size:21
Alignment explanation
Indices: 186148--186192 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
186138 TGTTGTTCGT
* *
186148 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
186169 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
186190 TTG
1 TTG
186193 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:187938 original size:2 final size:2
Alignment explanation
Indices: 187931--187976 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
187921 ACATACATAC
187931 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187973 AT AT
1 AT AT
187977 GTACAATATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:188087 original size:24 final size:25
Alignment explanation
Indices: 188036--188087 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 25
188026 TAAAACATAT
188036 AAAAATTAATATAATATATATAGTCA
1 AAAAATTAATATAATATATATAG-CA
188062 AAAAATTAATATAATATATATA-CA
1 AAAAATTAATATAATATATATAGCA
188086 AA
1 AA
188088 TTTATGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 4 0.15
26 22 0.85
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAAATTAATATAATATATATAGCA
Found at i:188088 original size:21 final size:21
Alignment explanation
Indices: 188032--188089 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 21
188022 TCACTAAAAC
*
188032 ATATAAAAATTAATATAATAT
1 ATATACAAATTAATATAATAT
188053 ATATAGTCAAAAAATTAATATAATAT
1 ATATA--C---AAATTAATATAATAT
188079 ATATACAAATT
1 ATATACAAATT
188090 TATGATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
21 10 0.32
24 1 0.03
26 20 0.65
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATACAAATTAATATAATAT
Found at i:194740 original size:2 final size:2
Alignment explanation
Indices: 194733--194762 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
194723 AAGGATATGA
194733 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
194763 CTTTTATTAT
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):
AT
Found at i:197954 original size:2 final size:2
Alignment explanation
Indices: 197947--197988 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
197937 GGTTTTTGTG
197947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
197989 CAATGAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:201237 original size:151 final size:149
Alignment explanation
Indices: 200960--201265 Score: 513
Period size: 151 Copynumber: 2.0 Consensus size: 149
200950 CAAAGTGCCG
200960 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* * *
201025 CATATACATATGCTAGGGATCAAGTATGTGTCTCTCACGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTCCAAAG-A-ATA
*
201090 TATATATATCCCGAAGGACCA
129 TACATATATCCCGAAGGACCA
**
201111 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
201176 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTCCAAAGAATATA
* *
201241 CATATGTCCCGAAGGACCG
131 CATATATCCCGAAGGACCA
201260 CGTAGA
1 CGTAGA
201266 CCCTCGACTC
Statistics
Matches: 146, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
149 27 0.18
150 1 0.01
151 118 0.81
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTCCAAAGAATATA
CATATATCCCGAAGGACCA
Found at i:201385 original size:14 final size:14
Alignment explanation
Indices: 201366--201393 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
201356 AACTTGTAAT
201366 TCACGTATCACATA
1 TCACGTATCACATA
201380 TCACGTATCACATA
1 TCACGTATCACATA
201394 GCTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.29, G:0.07, T:0.29
Consensus pattern (14 bp):
TCACGTATCACATA
Found at i:202177 original size:18 final size:18
Alignment explanation
Indices: 202156--202190 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
202146 TCCCATCTAG
202156 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
202174 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
202191 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:202795 original size:21 final size:21
Alignment explanation
Indices: 202771--202815 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
202761 TGTTGTTCGT
* *
202771 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
202792 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
202813 TTG
1 TTG
202816 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:205017 original size:6 final size:6
Alignment explanation
Indices: 205006--205071 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
204996 ATTTGGACCT
* * * *
205006 TAAAAA TAAAAA AATAAAA TGAAAAA TAAATAA TAATAA TAATAA TAATAA
1 TAAAAA TAAAAA TA-AAAA T-AAAAA TAAA-AA TAAAAA TAAAAA TAAAAA
* *
205057 TAATAA TAAACA TAA
1 TAAAAA TAAAAA TAA
205072 TATATATATT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
6 37 0.71
7 14 0.27
8 1 0.02
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (6 bp):
TAAAAA
Found at i:205042 original size:3 final size:3
Alignment explanation
Indices: 205034--205065 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
205024 ATGAAAAATA
205034 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
205066 ACATAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:205134 original size:21 final size:22
Alignment explanation
Indices: 205100--205149 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
205090 ACTATATAAC
*
205100 ATAT-TATATTTTCAAA-ATCAT
1 ATATATATGTTTTCAAATAT-AT
205121 ATA-ATATGTTTTCAAATATAT
1 ATATATATGTTTTCAAATATAT
205142 ATATATAT
1 ATATATAT
205150 ATATATATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATATATGTTTTCAAATATAT
Found at i:205143 original size:2 final size:2
Alignment explanation
Indices: 205136--205169 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
205126 ATGTTTTCAA
205136 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205170 TACATATGTT
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):
AT
Found at i:205327 original size:23 final size:22
Alignment explanation
Indices: 205285--205328 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
205275 ATATAATATG
* *
205285 ATACTATATGTTTTTTAAAAACT
1 ATACTATAT-ATTTTCAAAAACT
205308 ATACTATATATTTTCAAAAAC
1 ATACTATATATTTTCAAAAAC
205329 AATAAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (22 bp):
ATACTATATATTTTCAAAAACT
Found at i:205356 original size:78 final size:78
Alignment explanation
Indices: 205212--205357 Score: 188
Period size: 78 Copynumber: 1.9 Consensus size: 78
205202 CTATATAATA
* * *** *
205212 ATATATTTTTTAAAAACTATACTATATATCTTCAAAAACTATATATTATATGTTTTTTTAATTAT
1 ATATATTTTTTAAAAACTATACTATATATCTTCAAAAACAATAAATTATATGTTTTAAAAACTAT
205277 ATAATATGATACT
66 ATAATATGATACT
* *
205290 ATATGTTTTTTAAAAACTATACTATATATTTTCAAAAACAATAAATTAT-T-TTTTGAAAAAACT
1 ATATATTTTTTAAAAACTATACTATATATCTTCAAAAACAATAAATTATATGTTTT--AAAAACT
205353 ATATA
64 ATATA
205358 CTATATATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
76 4 0.07
77 1 0.02
78 53 0.91
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (78 bp):
ATATATTTTTTAAAAACTATACTATATATCTTCAAAAACAATAAATTATATGTTTTAAAAACTAT
ATAATATGATACT
Found at i:212341 original size:57 final size:57
Alignment explanation
Indices: 212253--212366 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
212243 TTGAAACATA
212253 GTATATATATGTTCAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGG
1 GTATATATATGTTCAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGG
* * *
212310 GTATATGTGTGTTCAGATTGTGGATAAAACTATAGCTTATCGTTACTAATTGTGCGG
1 GTATATATATGTTCAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGG
212367 ATTTATTGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.38
Consensus pattern (57 bp):
GTATATATATGTTCAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGG
Found at i:212384 original size:57 final size:57
Alignment explanation
Indices: 212266--212384 Score: 168
Period size: 57 Copynumber: 2.1 Consensus size: 57
212256 TATATATGTT
* ** *
212266 CAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGGGTATATGTGTGTT
1 CAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGGATATATGTGAATA
* *
212323 CAGATTGTGGATAAAACTATAGCTTATCGTTACTAATTGTGCGGATTTAT-TGAATAA
1 CAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGGATATATGTGAAT-A
212380 CAGAT
1 CAGAT
212385 ATCAGCCTGA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
56 3 0.05
57 52 0.95
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (57 bp):
CAGATTGTGGATAAAACTATAGCTTATCGTTACTAATAGTGCGGATATATGTGAATA
Found at i:215606 original size:60 final size:60
Alignment explanation
Indices: 215513--215625 Score: 174
Period size: 60 Copynumber: 1.9 Consensus size: 60
215503 CACGATGTTG
* * *
215513 ACATTTAGGTCGAACAAGCTGGTAGTTGAATGCCTTCCCCTTG-AACTTGAAGGTATCTCA
1 ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCC-TCCCCTTGAAACTTGAAGGTATCTCA
*
215573 ACATTGAGGTCGAAGAAGCTCGCAGTTGAATGCCTCCCCTTGAAACTTGAAGG
1 ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCCCCTTGAAACTTGAAGG
215626 CATCGTGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 8 0.17
60 40 0.83
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (60 bp):
ACATTGAGGTCGAACAAGCTCGCAGTTGAATGCCTCCCCTTGAAACTTGAAGGTATCTCA
Found at i:217246 original size:15 final size:16
Alignment explanation
Indices: 217226--217257 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
217216 TGAAGTGGTA
217226 GTATCGATACC-ATGG
1 GTATCGATACCAATGG
217241 GTATCGATACCAATGG
1 GTATCGATACCAATGG
217257 G
1 G
217258 GAGGCATCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (16 bp):
GTATCGATACCAATGG
Found at i:218229 original size:42 final size:42
Alignment explanation
Indices: 218155--218234 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
218145 TCGAGGGTTC
* * *
218155 TATGTGGTTCTTCGGGATATATATGTAATCCTTTGGAACATG
1 TATGCGGTTCTTCGGGACACATATGTAATCCTTTGGAACATG
* * *
218197 TATGCGGTTTTTCGGGACACATATTTAGTCCTTTGGAA
1 TATGCGGTTCTTCGGGACACATATGTAATCCTTTGGAA
218235 TATATATGTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.14, G:0.24, T:0.40
Consensus pattern (42 bp):
TATGCGGTTCTTCGGGACACATATGTAATCCTTTGGAACATG
Found at i:221553 original size:12 final size:12
Alignment explanation
Indices: 221536--221562 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
221526 CTCTCTCATG
221536 CTTATCCTAATA
1 CTTATCCTAATA
221548 CTTATCCTAATA
1 CTTATCCTAATA
221560 CTT
1 CTT
221563 GTCTACACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.26, G:0.00, T:0.44
Consensus pattern (12 bp):
CTTATCCTAATA
Found at i:243217 original size:44 final size:44
Alignment explanation
Indices: 243154--243238 Score: 152
Period size: 44 Copynumber: 1.9 Consensus size: 44
243144 TAAGGAATCC
* *
243154 GAGTCATTTGTTCACGTAATAATATTTTGTTGGTTGAGTCATCT
1 GAGTCATTTGTTCAAGTAATAATATTTTGATGGTTGAGTCATCT
243198 GAGTCATTTGTTCAAGTAATAATATTTTGATGGTTGAGTCA
1 GAGTCATTTGTTCAAGTAATAATATTTTGATGGTTGAGTCA
243239 ACGGATTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (44 bp):
GAGTCATTTGTTCAAGTAATAATATTTTGATGGTTGAGTCATCT
Found at i:249490 original size:15 final size:15
Alignment explanation
Indices: 249451--249492 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
249441 ATTTTTATTA
*
249451 AATTATAATAAAGTT
1 AATTATAATATAGTT
*
249466 -ATTTTAAATATAGTT
1 AATTAT-AATATAGTT
249481 AATTATAATATA
1 AATTATAATATA
249493 ATAAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 4 0.18
15 14 0.64
16 4 0.18
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (15 bp):
AATTATAATATAGTT
Found at i:257362 original size:2 final size:2
Alignment explanation
Indices: 257355--257389 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
257345 CTTGAATGTG
257355 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
257390 TACATCTTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:259326 original size:12 final size:12
Alignment explanation
Indices: 259309--259335 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
259299 AACTATGTTC
259309 ATCAAAACAAGT
1 ATCAAAACAAGT
259321 ATCAAAACAAGT
1 ATCAAAACAAGT
259333 ATC
1 ATC
259336 CCCCAGGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.19, G:0.07, T:0.19
Consensus pattern (12 bp):
ATCAAAACAAGT
Found at i:264068 original size:31 final size:30
Alignment explanation
Indices: 263999--264068 Score: 70
Period size: 32 Copynumber: 2.2 Consensus size: 30
263989 ATGATTGTGC
*
263999 AACCAAGAGCAAGGAAAGAAAGAAACCAGAA
1 AACCAA-AGCAAGAAAAGAAAGAAACCAGAA
* *
264030 ACCCCAAAGCAAGAACAAGAAAGAAAGGC-GAA
1 A-ACCAAAGCAAGAA-AAGAAAGAAA-CCAGAA
264062 AACCAAA
1 AACCAAA
264069 CCAGGATTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
31 13 0.41
32 18 0.56
33 1 0.03
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (30 bp):
AACCAAAGCAAGAAAAGAAAGAAACCAGAA
Found at i:275059 original size:17 final size:17
Alignment explanation
Indices: 275037--275071 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
275027 AAGAAGCGCG
275037 GAGTAGAAGCTTGGGCA
1 GAGTAGAAGCTTGGGCA
275054 GAGTAGAAGCTTGGGCA
1 GAGTAGAAGCTTGGGCA
275071 G
1 G
275072 TGAGTGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.43, T:0.17
Consensus pattern (17 bp):
GAGTAGAAGCTTGGGCA
Found at i:278324 original size:21 final size:20
Alignment explanation
Indices: 278238--278395 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
278228 AAATGACCAA
**
278238 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
278257 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
278277 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
278297 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
278318 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
278339 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
278359 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
278380 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
278396 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:278427 original size:20 final size:20
Alignment explanation
Indices: 278362--278611 Score: 220
Period size: 20 Copynumber: 12.5 Consensus size: 20
278352 CGATTTTCCA
* ** *
278362 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
278382 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
278402 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
278422 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
278442 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
278462 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
*
278482 AAATCGCAACGAT-AATCCAT
1 AAATCGCAACG-TGAATCCGT
* *
278502 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
278522 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
278542 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
278562 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
278582 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
278602 AAATCACAAC
1 AAATCGCAAC
278612 ACTGAAAATT
Statistics
Matches: 193, Mismatches: 29, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
20 192 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:279333 original size:24 final size:24
Alignment explanation
Indices: 279294--279348 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
279284 AAATTTGGTC
279294 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
279318 TTGGTCAATA-CACGGATTTTGATA
1 TTGGTCAATATC-CGGACTTTGATA
279342 TTGGTCA
1 TTGGTCA
279349 GTATTCGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 1 0.03
24 28 0.97
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:280251 original size:19 final size:19
Alignment explanation
Indices: 280211--280308 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
280201 GATTCTCTCG
280211 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
280231 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
280250 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
280264 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
280283 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
280302 TTGCGAT
1 TTGCGAT
280309 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:280305 original size:52 final size:53
Alignment explanation
Indices: 280192--280308 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
280182 GAAATGAAAA
280192 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
280245 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
280297 TCGCATTGCGAT
1 TCGCATTGCGAT
280309 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:280419 original size:33 final size:33
Alignment explanation
Indices: 280367--280515 Score: 142
Period size: 33 Copynumber: 4.3 Consensus size: 33
280357 CCATTACATT
280367 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
280401 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
280433 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
280472 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
280505 TCGCAATGCGA
1 TCGCAATGCGA
280516 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 11, Indels: 23
0.73 0.09 0.18
Matches are distributed among these distances:
31 7 0.08
32 7 0.08
33 42 0.45
34 10 0.11
35 1 0.01
36 2 0.02
38 10 0.11
39 7 0.08
40 7 0.08
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:280423 original size:19 final size:19
Alignment explanation
Indices: 280367--280496 Score: 163
Period size: 19 Copynumber: 7.3 Consensus size: 19
280357 CCATTACATT
280367 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
280387 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
280401 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
280420 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
280439 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
280453 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
280472 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
280491 TCGCAA
1 TCGCAA
280497 CGAGAGAATC
Statistics
Matches: 96, Mismatches: 4, Indels: 21
0.79 0.03 0.17
Matches are distributed among these distances:
14 20 0.21
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 58 0.60
20 6 0.06
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:280533 original size:19 final size:19
Alignment explanation
Indices: 280505--280640 Score: 166
Period size: 19 Copynumber: 7.6 Consensus size: 19
280495 AACGAGAGAA
*
280505 TCGCAATGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
280524 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
*
280538 TCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
280557 TCCGCATTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
*
280577 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
280593 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
280610 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
280629 TCGCATTGCGAT
1 TCGCATTGCGAT
280641 AGTCAATTTT
Statistics
Matches: 101, Mismatches: 5, Indels: 22
0.79 0.04 0.17
Matches are distributed among these distances:
14 16 0.16
16 10 0.10
17 10 0.10
19 47 0.47
20 18 0.18
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:280534 original size:52 final size:52
Alignment explanation
Indices: 280367--280515 Score: 289
Period size: 52 Copynumber: 2.8 Consensus size: 52
280357 CCATTACATT
280367 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
280420 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
280472 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
280516 TTTTCATTTC
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 87 0.91
53 9 0.09
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.13
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:280548 original size:33 final size:33
Alignment explanation
Indices: 280505--280640 Score: 125
Period size: 33 Copynumber: 3.9 Consensus size: 33
280495 AACGAGAGAA
*
280505 TCGCAATGCGATTTTCATTTCGCATTGCGATTC
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTC
*
280538 TCCCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 TCGCATTGCGATTTTCATTT-CGCATTGCGA--TTC
* * *
280574 ATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-
1 ---TCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTC
280610 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
280641 AGTCAATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
31 9 0.11
32 4 0.05
33 31 0.37
34 10 0.12
36 3 0.04
37 2 0.02
39 14 0.17
40 6 0.07
41 4 0.05
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTC
Found at i:280573 original size:53 final size:52
Alignment explanation
Indices: 280505--280640 Score: 236
Period size: 53 Copynumber: 2.6 Consensus size: 52
280495 AACGAGAGAA
*
280505 TCGCAATGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
* *
280557 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
280610 TCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT
280641 AGTCAATTTT
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
52 31 0.39
53 49 0.61
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCCCATTGCGATTTTCATT
Found at i:282788 original size:14 final size:14
Alignment explanation
Indices: 282769--282825 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
282759 GCGAAATGAA
*
282769 AATCGCAACGACAG
1 AATCGCAACGAAAG
282783 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
282800 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
282816 AATCGCAACG
1 AATCGCAACG
282826 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:282796 original size:33 final size:33
Alignment explanation
Indices: 282712--282842 Score: 172
Period size: 33 Copynumber: 3.8 Consensus size: 33
282702 CGAAACTTAA
** *
282712 AATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATGAAAATCGCAA--CG-AA--AG
*
282750 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
282783 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
282816 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
282843 TGCGATTTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
33 58 0.67
35 1 0.01
36 2 0.02
38 25 0.29
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.09
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:282807 original size:19 final size:19
Alignment explanation
Indices: 282694--282847 Score: 148
Period size: 19 Copynumber: 8.6 Consensus size: 19
282684 TAGTTTACTT
* *
282694 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
282714 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
282733 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
282752 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
282771 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
282785 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
282804 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
282818 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
282837 TCGCAATGCGA
1 TCGCAACGCGA
282848 TTTTGGTTTC
Statistics
Matches: 116, Mismatches: 8, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
14 16 0.14
16 11 0.09
17 11 0.09
19 66 0.57
20 12 0.10
ACGTcount: A:0.46, C:0.25, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:282839 original size:52 final size:54
Alignment explanation
Indices: 282711--282847 Score: 144
Period size: 52 Copynumber: 2.6 Consensus size: 54
282701 ACGAAACTTA
* *
282711 AAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAA-GAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG
* **
282767 AAAATCGCAA--CGACAG--AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G
1 -AAATCGCAACGCGAAAGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATG
282816 -AATCGCAACGCGAAATGAAAATCGCAATGCGA
1 AAATCGCAACGCGAAA-GAAAATCGCAATGCGA
282848 TTTTGGTTTC
Statistics
Matches: 69, Mismatches: 6, Indels: 15
0.77 0.07 0.17
Matches are distributed among these distances:
47 8 0.12
49 5 0.07
50 6 0.09
52 37 0.54
55 4 0.06
57 9 0.13
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (54 bp):
AAATCGCAACGCGAAAGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATG
Found at i:282865 original size:19 final size:19
Alignment explanation
Indices: 282843--282971 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
282833 AAAATCGCAA
282843 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
282862 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
282876 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
282895 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
282909 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
282928 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
282947 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
282967 TGCGA
1 TGCGA
282972 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:282885 original size:33 final size:33
Alignment explanation
Indices: 282843--282934 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
282833 AAAATCGCAA
282843 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
282876 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
282909 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
282935 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:283176 original size:93 final size:93
Alignment explanation
Indices: 283017--283953 Score: 1829
Period size: 93 Copynumber: 10.1 Consensus size: 93
283007 GAATGGATAC
283017 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283082 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
*
283110 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283175 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
283203 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283268 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
*
283296 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283361 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
283389 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283454 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
*
283482 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283547 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
283575 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283640 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
*
283668 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283733 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
283761 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
283826 TTTAGCAGAATTGGCAGCAACCGAACAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
283854 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
1 ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
*
283919 TTTAGCAGAATTGGCAGCAACCGAATAA
66 TTTAGCAGAATTGGCAGCAACCGAACAA
283947 ATTTACT
1 ATTTACT
283954 AAGCAATCTA
Statistics
Matches: 835, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 835 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
ATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAG
TTTAGCAGAATTGGCAGCAACCGAACAA
Found at i:285679 original size:14 final size:14
Alignment explanation
Indices: 285660--285749 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
285650 TTGAAATAAA
285660 AATCGCAACGAGAG
1 AATCGCAACGAGAG
285674 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
285691 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
285707 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
285726 AATCGCAACGAGAG
1 AATCGCAACGAGAG
285740 AATCGCAACG
1 AATCGCAACG
285750 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:285697 original size:33 final size:33
Alignment explanation
Indices: 285652--285766 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
285642 TCTTTTGGTT
*
285652 GAAATAAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
285685 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
285718 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
285751 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
285767 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:285698 original size:19 final size:18
Alignment explanation
Indices: 285659--285771 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
285649 GTTGAAATAA
285659 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
285674 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
285691 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
285707 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
285724 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
285740 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
285757 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
285772 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:285802 original size:14 final size:14
Alignment explanation
Indices: 285783--285839 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
285773 TTTGGTTTCG
285783 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
285797 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
285816 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
285830 CGTTGCGATT
1 CGTTGCGATT
285840 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:285815 original size:33 final size:33
Alignment explanation
Indices: 285767--285847 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
285757 AAAATCGCAA
**
285767 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
285800 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
285833 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
285848 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:285881 original size:41 final size:41
Alignment explanation
Indices: 285823--285900 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
285813 TCGCGTTGCG
*
285823 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
*
285864 ATTCTCTCGTTGTGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
285901 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:285885 original size:20 final size:21
Alignment explanation
Indices: 285824--285899 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
285814 CGCGTTGCGA
285824 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
285845 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
*
285865 TTCTCTCGTTGTGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
285886 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
285900 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:286017 original size:33 final size:33
Alignment explanation
Indices: 285979--286049 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
285969 AATACTAACT
* *
285979 TGAAAATCGGAACAAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACAACAGAATAGCAACGCGAAA
* * *
286012 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACAACAGAATAGCAACGCGAAA
286045 TGAAA
1 TGAAA
286050 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.17, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACAACAGAATAGCAACGCGAAA
Found at i:286282 original size:22 final size:22
Alignment explanation
Indices: 286230--286284 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
286220 TGGTTGTGAG
**
286230 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
* **
286252 AGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
286274 GGATTTCTTCG
1 GGATTTCTTCG
286285 CCGTAGAGAG
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.38, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:286457 original size:20 final size:20
Alignment explanation
Indices: 286430--286623 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
286420 CTTTAAATAT
286430 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
286450 CACGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
286472 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
286491 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
286511 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
286531 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
286551 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
286571 CGCGTTGCAATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
286591 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
286611 CGCGTTGCGATTT
1 CGCGTTGCGATTT
286624 TGGAAAATCG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:286617 original size:60 final size:60
Alignment explanation
Indices: 286430--286623 Score: 226
Period size: 60 Copynumber: 3.2 Consensus size: 60
286420 CTTTAAATAT
* * **
286430 CGCGTTGCGATTTACGGATACACGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGC-AATTTATGTATTCGCGTTGCGATTTACGGATA
* * * *** *
286491 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCAATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
286551 CACGTTGCGATTTACGGATACGCGTTGCAATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCAATTTATGTATTCGCGTTGCGATTTACGGATA
286611 CGCGTTGCGATTT
1 CGCGTTGCGATTT
286624 TGGAAAATCG
Statistics
Matches: 108, Mismatches: 25, Indels: 1
0.81 0.19 0.01
Matches are distributed among these distances:
60 83 0.77
61 25 0.23
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCAATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:286640 original size:21 final size:21
Alignment explanation
Indices: 286610--286692 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
286600 ATTTTCATAT
*
286610 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
286631 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
286652 TCGCATTGTGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
286673 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
286693 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:295086 original size:23 final size:23
Alignment explanation
Indices: 295060--295110 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
295050 TTCTATGATT
295060 GAATTCAATTCTCTTGTTGGAGG
1 GAATTCAATTCTCTTGTTGGAGG
295083 GAATTCAATTCTCTTGTTGGAGG
1 GAATTCAATTCTCTTGTTGGAGG
295106 GAATT
1 GAATT
295111 GAAATTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (23 bp):
GAATTCAATTCTCTTGTTGGAGG
Found at i:295646 original size:253 final size:253
Alignment explanation
Indices: 295159--295765 Score: 900
Period size: 253 Copynumber: 2.4 Consensus size: 253
295149 CTTATTCATA
*
295159 TATTGAATAAAAAT-ATTTTTTTATTATTTCGGGTC--G--GG-TTTCTAATTCATATATTTGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
* * *
295218 TCGGGTGGGGTGAAACTTTATTTTGGTCGAGTCTGGTCGGTTTTTTTAAGTGTGATATTCGGGTC
66 TCGGGTCGGGTGAAACTTTATTTTGATCGAGTCGGGTCGGTTTTTTTAAGTGTGATATT---GTC
* *
295283 GGGTCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAGTTTTACCTTATAT
128 -GG-CGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAGTTTTACCTTATAT
295348 ATTTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCATTATTTT
191 ATTTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCATTATTTT
295411 TATTGAATAAAAATAAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGG
1 TATTGAATAAAAAT-AATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGG
* *
295476 GTCGGGTCAGGTGAAACTTTATTTTGATCTG-GTCGGGTTGGTTTTTTTTAAGTGTGATA-T-TC
65 GTCGGGTCGGGTGAAACTTTATTTTGATC-GAGTCGGGTCGG-TTTTTTTAAGTGTGATATTGTC
295538 -G-G-G-TCGGGTTTAGGGTGAAAAATACCCGACCCAACCCAAAAAATATATAGTTTTACCTTAT
128 GGCGAGTTCGGGTTTAGGGTGAAAAATACCCGA--C--CCCAAAAAATATATAGTTTTACCTTAT
* *
295599 ATATTTAGGAATAATTACAATAATATCCCTCTATATATAATTTTTTTCAATTAAGTCATTATTTT
189 ATATTTAGGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCATTATTTT
295664 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTC-GATTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
* *
295728 TCAGGTCGGGTGAAACTTTATTTTGGTCGAGTCGGGTC
66 TCGGGTCGGGTGAAACTTTATTTTGATCGAGTCGGGTC
295766 TTGGATGGAG
Statistics
Matches: 327, Mismatches: 14, Indels: 29
0.88 0.04 0.08
Matches are distributed among these distances:
249 26 0.08
250 2 0.01
251 57 0.17
252 41 0.13
253 103 0.31
254 21 0.06
255 2 0.01
256 1 0.00
258 2 0.01
259 54 0.17
260 18 0.06
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (253 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGG
TCGGGTCGGGTGAAACTTTATTTTGATCGAGTCGGGTCGGTTTTTTTAAGTGTGATATTGTCGGC
GAGTTCGGGTTTAGGGTGAAAAATACCCGACCCCAAAAAATATATAGTTTTACCTTATATATTTA
GGAATAATTACAATAATACCCCTATATATATAATTTTTTTCAATTAAGTCATTATTTT
Found at i:296139 original size:17 final size:18
Alignment explanation
Indices: 296117--296164 Score: 71
Period size: 18 Copynumber: 2.7 Consensus size: 18
296107 ATATGAAATT
*
296117 AGATTCTAATTCC-TGAC
1 AGATTCTAATTCCTTAAC
296134 AGATTCTAATTCCTTAAC
1 AGATTCTAATTCCTTAAC
*
296152 AGATTCCAATTCC
1 AGATTCTAATTCC
296165 CTCAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.35
Consensus pattern (18 bp):
AGATTCTAATTCCTTAAC
Found at i:297651 original size:24 final size:24
Alignment explanation
Indices: 297623--297691 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
297613 ATAAAACCGG
*
297623 ATAAACAAGCTTATAAACAGATAA
1 ATAAACAAGCTTATAAACAAATAA
* * *
297647 ATAAACAAACTTATAAATAAATCA
1 ATAAACAAGCTTATAAACAAATAA
*
297671 ATAAACGAGCTT-TCAAACAAA
1 ATAAACAAGCTTAT-AAACAAA
297692 CTTGTTTATA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
23 1 0.03
24 36 0.97
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (24 bp):
ATAAACAAGCTTATAAACAAATAA
Found at i:299692 original size:36 final size:36
Alignment explanation
Indices: 299573--299691 Score: 161
Period size: 35 Copynumber: 3.3 Consensus size: 36
299563 TGGTAACCAA
*
299573 CTTTGAAAAAATGATTTTCAAAGTTTAGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
299610 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
299645 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
299682 -GTTGAAAAAT
1 CTTTGAAAAAT
299692 AATAATGAGA
Statistics
Matches: 75, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
35 33 0.44
36 14 0.19
37 28 0.37
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:304217 original size:21 final size:20
Alignment explanation
Indices: 304193--304256 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
304183 AACTTTGAAA
304193 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
304214 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
304228 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
304249 AAATGTTT
1 AAATGTTT
304257 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:304231 original size:35 final size:36
Alignment explanation
Indices: 304185--304306 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
304175 TGGTAACCAA
304185 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
304222 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
304257 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
304294 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
304307 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:309972 original size:2 final size:2
Alignment explanation
Indices: 309965--309992 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
309955 TAAAATACTC
309965 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
309993 TGTACTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:310537 original size:2 final size:2
Alignment explanation
Indices: 310530--310557 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
310520 TTTATCTTCA
310530 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
310558 TAAGTGGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:311319 original size:2 final size:2
Alignment explanation
Indices: 311312--311341 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
311302 AATTTTCTAA
311312 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
311342 TTTATGAATT
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):
AT
Found at i:311554 original size:18 final size:19
Alignment explanation
Indices: 311531--311573 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
311521 CAGTAATCCT
311531 ATTCC-CTGATAATCTTAC
1 ATTCCACTGATAATCTTAC
*
311549 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGATAATCTTAC
311569 ATTCC
1 ATTCC
311574 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 4 0.18
20 15 0.68
ACGTcount: A:0.26, C:0.30, G:0.07, T:0.37
Consensus pattern (19 bp):
ATTCCACTGATAATCTTAC
Found at i:319053 original size:16 final size:16
Alignment explanation
Indices: 319032--319070 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
319022 TCCATATGAG
319032 GTGGCAATCGGCATTT
1 GTGGCAATCGGCATTT
319048 GTGGCAATCGGCATTT
1 GTGGCAATCGGCATTT
319064 GTGGCAA
1 GTGGCAA
319071 CCTGTCTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.28
Consensus pattern (16 bp):
GTGGCAATCGGCATTT
Found at i:322608 original size:37 final size:35
Alignment explanation
Indices: 322567--322635 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
322557 CTTTTTATAT
*
322567 TTTAATTTTGTAAAAAAAATTATATAAATTTTTTGAA
1 TTTAATTTT-TAAAAAAAA-TATATAAATATTTTGAA
**
322604 TTTAATTTTTTTAAAAAATATATAAATATTTT
1 TTTAATTTTTAAAAAAAATATATAAATATTTT
322636 CTAACTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 13 0.45
36 7 0.24
37 9 0.31
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (35 bp):
TTTAATTTTTAAAAAAAATATATAAATATTTTGAA
Found at i:322813 original size:18 final size:18
Alignment explanation
Indices: 322777--322860 Score: 91
Period size: 20 Copynumber: 4.6 Consensus size: 18
322767 AACATTCTCA
322777 GTAATCTTATT-CC-CTG
1 GTAATCTTATTCCCACTG
322793 GTAATCTTATTCCCACTG
1 GTAATCTTATTCCCACTG
*
322811 GTAATCTTATATTCTCACTG
1 GTAATC-T-TATTCCCACTG
*
322831 ATAATCTTACATTCCCACTG
1 GTAATCTT--ATTCCCACTG
*
322851 ATAATCTTAT
1 GTAATCTTAT
322861 ATTCTCACTA
Statistics
Matches: 59, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.19
17 2 0.03
18 12 0.20
19 2 0.03
20 32 0.54
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.42
Consensus pattern (18 bp):
GTAATCTTATTCCCACTG
Found at i:322829 original size:20 final size:20
Alignment explanation
Indices: 322800--322885 Score: 118
Period size: 20 Copynumber: 4.3 Consensus size: 20
322790 CTGGTAATCT
*
322800 TATTCCCACTGGTAATCTTA
1 TATTCCCACTGATAATCTTA
*
322820 TATTCTCACTGATAATCTTA
1 TATTCCCACTGATAATCTTA
*
322840 CATTCCCACTGATAATCTTA
1 TATTCCCACTGATAATCTTA
* *
322860 TATTCTCACTAATAATCTTA
1 TATTCCCACTGATAATCTTA
*
322880 CATTCC
1 TATTCC
322886 GTGAATTAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.29, C:0.26, G:0.05, T:0.41
Consensus pattern (20 bp):
TATTCCCACTGATAATCTTA
Found at i:322848 original size:40 final size:40
Alignment explanation
Indices: 322794--322885 Score: 152
Period size: 40 Copynumber: 2.4 Consensus size: 40
322784 TATTCCCTGG
* *
322794 TAATCTT--ATTCCCACTGGTAATCTTATATTCTCACTGA
1 TAATCTTACATTCCCACTGATAATCTTATATTCTCACTAA
322832 TAATCTTACATTCCCACTGATAATCTTATATTCTCACTAA
1 TAATCTTACATTCCCACTGATAATCTTATATTCTCACTAA
322872 TAATCTTACATTCC
1 TAATCTTACATTCC
322886 GTGAATTAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
38 7 0.14
40 43 0.86
ACGTcount: A:0.29, C:0.25, G:0.04, T:0.41
Consensus pattern (40 bp):
TAATCTTACATTCCCACTGATAATCTTATATTCTCACTAA
Found at i:323725 original size:23 final size:23
Alignment explanation
Indices: 323696--323790 Score: 88
Period size: 23 Copynumber: 4.3 Consensus size: 23
323686 TCATTTATCA
*
323696 TTCTTCTTCCATAAACTCGTTGC
1 TTCTTCTTCCATAAACTCATTGC
* * **
323719 TTCTTCTTCAATAAACTTATTTT
1 TTCTTCTTCCATAAACTCATTGC
*
323742 TTCTTCTTCCATAAACACATT-C
1 TTCTTCTTCCATAAACTCATTGC
* * *
323764 CT-TTCTTTCAT-AACTCATTTC
1 TTCTTCTTCCATAAACTCATTGC
323785 TTCTTC
1 TTCTTC
323791 CTCTTCCATA
Statistics
Matches: 57, Mismatches: 13, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.12
21 10 0.18
22 4 0.07
23 36 0.63
ACGTcount: A:0.21, C:0.27, G:0.02, T:0.49
Consensus pattern (23 bp):
TTCTTCTTCCATAAACTCATTGC
Found at i:326183 original size:34 final size:34
Alignment explanation
Indices: 326137--326428 Score: 94
Period size: 34 Copynumber: 8.5 Consensus size: 34
326127 TTTCAAAAAT
* *
326137 TATATATTATATAGTTTTTGAAAATATTTTTAAA
1 TATATATAATATAGTTTTTAAAAATATTTTTAAA
* * *
326171 TATATATAATATATAGTTTTGAAAACTA--TTGAAA
1 TATATAT-A-ATATAGTTTTTAAAAATATTTTTAAA
* * ** *
326205 CGTTTATATTATATAGTTTTT-AAACCA-TTTGAAA
1 --TATATATAATATAGTTTTTAAAAATATTTTTAAA
* *
326239 CATATAGT-ATATAG-TTTTAAAACATTTTTTGTGAAA
1 TATATA-TAATATAGTTTTTAAAA-ATATTTT-T-AAA
*
326275 T-TATATAATATA-TTTTTAAAAACTTTTTTTGAAA
1 TATATATAATATAGTTTTTAAAAA-TATTTTT-AAA
* ** *
326309 -A-ACT-T-ATATAATATTTT-AAAACGTTTTGAAA
1 TATA-TATAATATAGT-TTTTAAAAATATTTTTAAA
* * ** * *
326340 -ACTATGTAATATAGTTTTGGAAACTTTTTTTTAAG
1 TA-TATATAATATAGTTTT-TAAAAATATTTTTAAA
326375 TATA-AT-ATATAGTTTTCTAAAACATATTTTTGAAA
1 TATATATAATATAGTTTT-TAAAA-ATATTTTT-AAA
326410 TATATATATTATATAGTTT
1 TATATATA--ATATAGTTT
326429 ATCATAATTT
Statistics
Matches: 193, Mismatches: 34, Indels: 57
0.68 0.12 0.20
Matches are distributed among these distances:
31 8 0.04
32 23 0.12
33 31 0.16
34 56 0.29
35 39 0.20
36 27 0.14
39 9 0.05
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (34 bp):
TATATATAATATAGTTTTTAAAAATATTTTTAAA
Found at i:326184 original size:36 final size:36
Alignment explanation
Indices: 326100--326200 Score: 114
Period size: 36 Copynumber: 2.7 Consensus size: 36
326090 TTTTGACAAA
* *
326100 ATATAATATATAATTTTCAGAAATGATTTTCAAAAATT
1 ATATAATATATAGTTTTGA-AAAT-ATTTTCAAAAATT
* * *
326138 ATATATTATATAGTTTTTGAAAATATTTTTAAATA-T
1 ATATAATATATAG-TTTTGAAAATATTTTCAAAAATT
326174 ATATAATATATAGTTTTGAAAACTATT
1 ATATAATATATAGTTTTGAAAA-TATT
326201 GAAACGTTTA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
35 9 0.16
36 17 0.31
37 9 0.16
38 15 0.27
39 5 0.09
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.47
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAATATTTTCAAAAATT
Found at i:326255 original size:32 final size:33
Alignment explanation
Indices: 326138--326265 Score: 100
Period size: 34 Copynumber: 3.8 Consensus size: 33
326128 TTCAAAAATT
* * * **
326138 ATATATTATATAGTTTTTGAAAATATTTTTAAATAT
1 ATATAATATATAGTTTTT-AAAACA-TTTGAAA-CG
*
326174 ATATAATATATAGTTTTGAAAAC-TATTGAAACG
1 ATATAATATATAGTTTTTAAAACAT-TTGAAACG
* * *
326207 TTTATATTATATAGTTTTTAAACCATTTGAAAC-
1 -ATATAATATATAGTTTTTAAAACATTTGAAACG
*
326240 ATATAGTATATAG-TTTTAAAACATTT
1 ATATAATATATAGTTTTTAAAACATTT
326266 TTTGTGAAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
31 12 0.16
32 11 0.14
33 1 0.01
34 31 0.41
35 5 0.07
36 16 0.21
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (33 bp):
ATATAATATATAGTTTTTAAAACATTTGAAACG
Found at i:326281 original size:37 final size:34
Alignment explanation
Indices: 326247--326428 Score: 103
Period size: 35 Copynumber: 5.3 Consensus size: 34
326237 AACATATAGT
326247 ATATAGTTTT-AAAACATTTTTTGTGAAATTATATA
1 ATATAGTTTTAAAAAC-TTTTTT-TGAAATTATATA
*
326282 ATATATTTTTAAAAACTTTTTTTGAAAAACTTATAT-
1 ATATAGTTTTAAAAACTTTTTTTG--AAA-TTATATA
* * *
326318 A-ATA-TTTT-AAAAC--GTTTTGAAAACTATGTA
1 ATATAGTTTTAAAAACTTTTTTTG-AAATTATATA
** * *
326348 ATATAGTTTTGGAAACTTTTTTT-TAAGTATA-A
1 ATATAGTTTTAAAAACTTTTTTTGAAATTATATA
* *
326380 TATATAGTTTTCTAAAACATATTTTTGAAATATATATA
1 -ATATAGTTTT-AAAAAC-TTTTTTTGAAAT-TATATA
326418 TTATATAGTTT
1 --ATATAGTTT
326429 ATCATAATTT
Statistics
Matches: 116, Mismatches: 14, Indels: 30
0.73 0.09 0.19
Matches are distributed among these distances:
29 4 0.03
30 5 0.04
31 8 0.07
32 5 0.04
33 24 0.21
34 10 0.09
35 28 0.24
36 11 0.09
37 10 0.09
38 1 0.01
39 10 0.09
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (34 bp):
ATATAGTTTTAAAAACTTTTTTTGAAATTATATA
Found at i:326292 original size:35 final size:37
Alignment explanation
Indices: 326247--326322 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 37
326237 AACATATAGT
**
326247 ATATAGTTTT-AAAACATTTTTTGTGAAA-TTATATA
1 ATATAGTTTTAAAAACATTTTTTGAAAAACTTATATA
* *
326282 ATATATTTTTAAAAACTTTTTTTGAAAAACTTATATA
1 ATATAGTTTTAAAAACATTTTTTGAAAAACTTATATA
326319 ATAT
1 ATAT
326323 TTTAAAACGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 9 0.26
36 15 0.43
37 11 0.31
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (37 bp):
ATATAGTTTTAAAAACATTTTTTGAAAAACTTATATA
Found at i:327782 original size:22 final size:22
Alignment explanation
Indices: 327717--327783 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 22
327707 AAACTTAACC
*
327717 TTTTATTATTTCTTTCTTTCATTA
1 TTTTATTATTT-TTTATTT-ATTA
327741 TTATTATTATTTTTTA--TATT-
1 TT-TTATTATTTTTTATTTATTA
327761 TTTTATTCATTTTTTATTTATTA
1 TTTTATT-ATTTTTTATTTATTA
327784 GCATTTTGTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
19 5 0.14
20 10 0.27
21 3 0.08
22 5 0.14
24 5 0.14
25 9 0.24
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTATTATTTTTTATTTATTA
Found at i:331012 original size:2 final size:2
Alignment explanation
Indices: 331005--331061 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
330995 CTCAAGTCTA
*
331005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
331047 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
331062 ATACACTCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:333266 original size:23 final size:21
Alignment explanation
Indices: 333240--333296 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
333230 TTTACCCATT
333240 TAATTTTCAAACATTATTACACC
1 TAATTTT--AACATTATTACACC
* * *
333263 TAATTTTGACATTGTTGCACC
1 TAATTTTAACATTATTACACC
*
333284 TAATTTTGACATT
1 TAATTTTAACATT
333297 GCAATATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 24 0.77
23 7 0.23
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.44
Consensus pattern (21 bp):
TAATTTTAACATTATTACACC
Found at i:333283 original size:21 final size:21
Alignment explanation
Indices: 333250--333297 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
333240 TAATTTTCAA
*
333250 ACATTATTACACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
*
333271 ACATTGTTGCACCTAATTTTG
1 ACATTGTTACACCTAATTTTG
333292 ACATTG
1 ACATTG
333298 CAATATTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (21 bp):
ACATTGTTACACCTAATTTTG
Found at i:337939 original size:21 final size:21
Alignment explanation
Indices: 337909--337956 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
337899 TAATTTTCAA
*
337909 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
337930 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
337951 ACATTG
1 ACATTG
337957 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:352366 original size:27 final size:29
Alignment explanation
Indices: 352314--352373 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
352304 ATATGATATA
* *
352314 AAAATCTTAAATAAATATATATAAATCAT
1 AAAATCTTAAATAAATACATAAAAATCAT
*
352343 AAAA-CTTAAA-AAATACATAAAAATCTT
1 AAAATCTTAAATAAATACATAAAAATCAT
352370 AAAA
1 AAAA
352374 GTTCAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 18 0.64
28 6 0.21
29 4 0.14
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.28
Consensus pattern (29 bp):
AAAATCTTAAATAAATACATAAAAATCAT
Found at i:354856 original size:71 final size:71
Alignment explanation
Indices: 354740--354895 Score: 249
Period size: 71 Copynumber: 2.2 Consensus size: 71
354730 AAAAAATATA
354740 GTTCTTGTGGTAATAATGGCAGCTATATTTCTATTTGCATTCTGTTTCTTGTTGAATATTCAGTA
1 GTTCTTGTGGTAATAATGGCAGCTATATTTCTATTTGCATTCTGTTTCTTGTTGAATATTCAGTA
354805 ATTACG
66 ATTACG
* * * *
354811 GTTCTTGTGGTGATATTGGCAGCTCTATTTCTTTTTGCATTCTGTTTCTTGTTGAATATTCAGTA
1 GTTCTTGTGGTAATAATGGCAGCTATATTTCTATTTGCATTCTGTTTCTTGTTGAATATTCAGTA
**
354876 ATTATA
66 ATTACG
*
354882 GTTCGTGTGGTAAT
1 GTTCTTGTGGTAAT
354896 TCATATATTG
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 77 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (71 bp):
GTTCTTGTGGTAATAATGGCAGCTATATTTCTATTTGCATTCTGTTTCTTGTTGAATATTCAGTA
ATTACG
Found at i:362119 original size:153 final size:155
Alignment explanation
Indices: 361940--362249 Score: 606
Period size: 153 Copynumber: 2.0 Consensus size: 155
361930 AATTTAATTT
361940 TTTATTTATATTTATATTTCAACTAAAATATTAATGAAAAACTGTATTTACCTCTTAAGATAGAA
1 TTTATTTATATTTATATTTCAACTAAAATATTAATGAAAAACTGTATTTACCTCTTAAGATAGAA
362005 GAACACCAAACACATTGAAAATTATTTAATTTTTA-TTAATAGTATTAAATTAAAAGAGGTGATG
66 GAACACCAAACACATTGAAAATTATTTAATTTTTATTTAATAGTATTAAATTAAAAGAGGTGATG
362069 GTCCT-CCATGAGGGTTTCCCTCCC
131 GTCCTACCATGAGGGTTTCCCTCCC
362093 TTTATTTATATTTATATTTCAACTAAAATATTAATGAAAAACTGTATTTACCTCTTAAGATAGAA
1 TTTATTTATATTTATATTTCAACTAAAATATTAATGAAAAACTGTATTTACCTCTTAAGATAGAA
362158 GAACACCAAACACATTGAAAATTATTTAATTTTTATTTAATAGTATTAAATTAAAAGAGGTGATG
66 GAACACCAAACACATTGAAAATTATTTAATTTTTATTTAATAGTATTAAATTAAAAGAGGTGATG
362223 GTCCTACCATGAGGGTTTCCCTCCC
131 GTCCTACCATGAGGGTTTCCCTCCC
362248 TT
1 TT
362250 CCATGAAGGA
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
153 100 0.65
154 34 0.22
155 21 0.14
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (155 bp):
TTTATTTATATTTATATTTCAACTAAAATATTAATGAAAAACTGTATTTACCTCTTAAGATAGAA
GAACACCAAACACATTGAAAATTATTTAATTTTTATTTAATAGTATTAAATTAAAAGAGGTGATG
GTCCTACCATGAGGGTTTCCCTCCC
Found at i:362371 original size:3 final size:3
Alignment explanation
Indices: 362328--362353 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
362318 CTCATTTACC
362328 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
362354 CTACAACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:367204 original size:77 final size:77
Alignment explanation
Indices: 367077--367229 Score: 306
Period size: 77 Copynumber: 2.0 Consensus size: 77
367067 TCCCCCTAAG
367077 ATTTTATAAGTTAATCCCTCATAAAATCTTAGAAGTTCACCTCTTAACGTAAGATTTTGCATCTG
1 ATTTTATAAGTTAATCCCTCATAAAATCTTAGAAGTTCACCTCTTAACGTAAGATTTTGCATCTG
367142 TCCCTACATGTA
66 TCCCTACATGTA
367154 ATTTTATAAGTTAATCCCTCATAAAATCTTAGAAGTTCACCTCTTAACGTAAGATTTTGCATCTG
1 ATTTTATAAGTTAATCCCTCATAAAATCTTAGAAGTTCACCTCTTAACGTAAGATTTTGCATCTG
367219 TCCCTACATGT
66 TCCCTACATGT
367230 CTGATCACAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (77 bp):
ATTTTATAAGTTAATCCCTCATAAAATCTTAGAAGTTCACCTCTTAACGTAAGATTTTGCATCTG
TCCCTACATGTA
Found at i:374316 original size:64 final size:64
Alignment explanation
Indices: 374215--374334 Score: 222
Period size: 64 Copynumber: 1.9 Consensus size: 64
374205 GGGTATGGGC
* *
374215 GTATGGCAGTGTGGGACTGGAAAGCTACTTGTGGTGAACGGCAATTCATACCTCGATGAGTTGG
1 GTATGGCAGTGTGGGACTGGAAAGCAACTTGCGGTGAACGGCAATTCATACCTCGATGAGTTGG
374279 GTATGGCAGTGTGGGACTGGAAAGCAACTTGCGGTGAACGGCAATTCATACCTCGA
1 GTATGGCAGTGTGGGACTGGAAAGCAACTTGCGGTGAACGGCAATTCATACCTCGA
374335 GAATTAACCT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.24
Consensus pattern (64 bp):
GTATGGCAGTGTGGGACTGGAAAGCAACTTGCGGTGAACGGCAATTCATACCTCGATGAGTTGG
Found at i:383220 original size:22 final size:22
Alignment explanation
Indices: 383195--383243 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
383185 CTAACTATAC
*
383195 TATAATAA-TTAAGAAAATGTAT
1 TATAATAACATAA-AAAATGTAT
*
383217 TATAATAACATAAAAAATGTGT
1 TATAATAACATAAAAAATGTAT
383239 TATAA
1 TATAA
383244 GGATAGACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (22 bp):
TATAATAACATAAAAAATGTAT
Found at i:391915 original size:9 final size:9
Alignment explanation
Indices: 391901--391928 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
391891 CAAAACATAA
391901 ATCTGGCAC
1 ATCTGGCAC
391910 ATCTGGCAC
1 ATCTGGCAC
391919 ATCTGGCAC
1 ATCTGGCAC
391928 A
1 A
391929 AGGATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.21
Consensus pattern (9 bp):
ATCTGGCAC
Found at i:393340 original size:23 final size:23
Alignment explanation
Indices: 393310--393353 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
393300 TCCTTTTATT
393310 CTAAACGAACATGTTCGCGAACA
1 CTAAACGAACATGTTCGCGAACA
*
393333 CTAAACGAACATGTTTGCGAA
1 CTAAACGAACATGTTCGCGAA
393354 TTAACGAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (23 bp):
CTAAACGAACATGTTCGCGAACA
Found at i:399637 original size:20 final size:18
Alignment explanation
Indices: 399594--399642 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 18
399584 AATGACCAAT
**
399594 AAATCGCAACGCGATATC
1 AAATCGCAACGCGATAGA
399612 AAATCGCAACGCGATTTAGA
1 AAATCGCAACGCGA--TAGA
399632 AAATCGCAACG
1 AAATCGCAACG
399643 TTAAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 14 0.52
20 13 0.48
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.16
Consensus pattern (18 bp):
AAATCGCAACGCGATAGA
Found at i:400490 original size:22 final size:22
Alignment explanation
Indices: 400465--400517 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
400455 TTCAACGTTA
*
400465 AATGTTGAATTATTCAGTATTG
1 AATGTTGAATCATTCAGTATTG
*
400487 AATGTTGAATCGTTCAGTATTG
1 AATGTTGAATCATTCAGTATTG
400509 AATGTTGAA
1 AATGTTGAA
400518 CCGTTCAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.42
Consensus pattern (22 bp):
AATGTTGAATCATTCAGTATTG
Found at i:400522 original size:22 final size:22
Alignment explanation
Indices: 400477--400525 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
400467 TGTTGAATTA
*
400477 TTCAGTATTGAATGTTGAATCG
1 TTCAGTATTGAATGTTGAACCG
400499 TTCAGTATTGAATGTTGAACCG
1 TTCAGTATTGAATGTTGAACCG
400521 TTCAG
1 TTCAG
400526 CATTCAGCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.22, T:0.39
Consensus pattern (22 bp):
TTCAGTATTGAATGTTGAACCG
Found at i:400633 original size:27 final size:27
Alignment explanation
Indices: 400595--400655 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
400585 AGTGTTAAAT
*
400595 GATTCAGCACAGAAGTACATTTTGAAC
1 GATTCAGCACAGAAGTACATTCTGAAC
*
400622 GATTCAGCACAGAAGTACATTCTGAAT
1 GATTCAGCACAGAAGTACATTCTGAAC
400649 GATTCAG
1 GATTCAG
400656 AGCCAGTAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (27 bp):
GATTCAGCACAGAAGTACATTCTGAAC
Found at i:410005 original size:13 final size:14
Alignment explanation
Indices: 409982--410010 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
409972 AGTAATTCAG
409982 ATGAGAATGGAAGT
1 ATGAGAATGGAAGT
409996 ATGA-AATGGAAGT
1 ATGAGAATGGAAGT
410009 AT
1 AT
410011 TGAGTGCACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (14 bp):
ATGAGAATGGAAGT
Found at i:413258 original size:45 final size:45
Alignment explanation
Indices: 413194--413286 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
413184 TATGTATTTT
413194 CATCAGCCATTAACTGAAAGCACATAAGTTAAAATGGAGTAAATC
1 CATCAGCCATTAACTGAAAGCACATAAGTTAAAATGGAGTAAATC
413239 CATCAGCCATTAACTGAAAGCACATAAGTTAAAATGGAGTAAATC
1 CATCAGCCATTAACTGAAAGCACATAAGTTAAAATGGAGTAAATC
413284 CAT
1 CAT
413287 TAAAAGCTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (45 bp):
CATCAGCCATTAACTGAAAGCACATAAGTTAAAATGGAGTAAATC
Found at i:419961 original size:16 final size:16
Alignment explanation
Indices: 419940--419972 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
419930 TAACCACGTC
419940 ACTTTCCATGTTCTTT
1 ACTTTCCATGTTCTTT
419956 ACTTTCCATGTTCTTT
1 ACTTTCCATGTTCTTT
419972 A
1 A
419973 GCCCATGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.15, C:0.24, G:0.06, T:0.55
Consensus pattern (16 bp):
ACTTTCCATGTTCTTT
Found at i:423700 original size:14 final size:15
Alignment explanation
Indices: 423676--423705 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
423666 TCATGGGTTA
423676 TAGCTAAATGACTTG
1 TAGCTAAATGACTTG
423691 TAGC-AAATGACTTG
1 TAGCTAAATGACTTG
423705 T
1 T
423706 GTCCATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TAGCTAAATGACTTG
Found at i:425983 original size:15 final size:15
Alignment explanation
Indices: 425963--425997 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
425953 TAGCTTTCCA
425963 AACAGTCCAAATAAC
1 AACAGTCCAAATAAC
425978 AACAGTCCAAATAAC
1 AACAGTCCAAATAAC
425993 AACAG
1 AACAG
425998 CAGGAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.26, G:0.09, T:0.11
Consensus pattern (15 bp):
AACAGTCCAAATAAC
Found at i:426391 original size:221 final size:221
Alignment explanation
Indices: 426008--426450 Score: 886
Period size: 221 Copynumber: 2.0 Consensus size: 221
425998 CAGGAATTAG
426008 CTTCCAAATAGCAGAGTTATGATTTAGTTCTTCCCAAGCTTGGAGGAACTTCTGCGCATTCTCAT
1 CTTCCAAATAGCAGAGTTATGATTTAGTTCTTCCCAAGCTTGGAGGAACTTCTGCGCATTCTCAT
426073 GAAGAACCAAACTAAGACTCCAATATTGCTCAAATTTATTCCAAAGTGACCAAACCACAGCACAA
66 GAAGAACCAAACTAAGACTCCAATATTGCTCAAATTTATTCCAAAGTGACCAAACCACAGCACAA
426138 GAGAAAAATAAATGTGAAGAAGATTCATCAGCCAAATGACAAAGAGGACAAGACAAATCTGCAAT
131 GAGAAAAATAAATGTGAAGAAGATTCATCAGCCAAATGACAAAGAGGACAAGACAAATCTGCAAT
426203 ACCCGTAACCCCTCTTTTAACCAGTT
196 ACCCGTAACCCCTCTTTTAACCAGTT
426229 CTTCCAAATAGCAGAGTTATGATTTAGTTCTTCCCAAGCTTGGAGGAACTTCTGCGCATTCTCAT
1 CTTCCAAATAGCAGAGTTATGATTTAGTTCTTCCCAAGCTTGGAGGAACTTCTGCGCATTCTCAT
426294 GAAGAACCAAACTAAGACTCCAATATTGCTCAAATTTATTCCAAAGTGACCAAACCACAGCACAA
66 GAAGAACCAAACTAAGACTCCAATATTGCTCAAATTTATTCCAAAGTGACCAAACCACAGCACAA
426359 GAGAAAAATAAATGTGAAGAAGATTCATCAGCCAAATGACAAAGAGGACAAGACAAATCTGCAAT
131 GAGAAAAATAAATGTGAAGAAGATTCATCAGCCAAATGACAAAGAGGACAAGACAAATCTGCAAT
426424 ACCCGTAACCCCTCTTTTAACCAGTT
196 ACCCGTAACCCCTCTTTTAACCAGTT
426450 C
1 C
426451 AGTCCTCACT
Statistics
Matches: 222, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
221 222 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (221 bp):
CTTCCAAATAGCAGAGTTATGATTTAGTTCTTCCCAAGCTTGGAGGAACTTCTGCGCATTCTCAT
GAAGAACCAAACTAAGACTCCAATATTGCTCAAATTTATTCCAAAGTGACCAAACCACAGCACAA
GAGAAAAATAAATGTGAAGAAGATTCATCAGCCAAATGACAAAGAGGACAAGACAAATCTGCAAT
ACCCGTAACCCCTCTTTTAACCAGTT
Found at i:429596 original size:75 final size:76
Alignment explanation
Indices: 429456--429599 Score: 254
Period size: 75 Copynumber: 1.9 Consensus size: 76
429446 ATTGCTATAG
*
429456 TGCTAAGAGCACAATTTTTAAAATTATTTCTATAAAAATACAAATCATATAAACATTATATAGGC
1 TGCTAAGAGCACAATTTTTAAAATTATTTCTATAAAAATACAAATCATATAAACATTAAATAGGC
429521 TGGAATAATAC
66 TGGAATAATAC
* *
429532 TGCTAAGAGCACAGTTTTTAAAATTATTTCTA-CAAAATACAAATCATATAAACATTAAATAGGC
1 TGCTAAGAGCACAATTTTTAAAATTATTTCTATAAAAATACAAATCATATAAACATTAAATAGGC
429596 TGGA
66 TGGA
429600 TGCATGCACG
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
75 34 0.52
76 31 0.48
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.32
Consensus pattern (76 bp):
TGCTAAGAGCACAATTTTTAAAATTATTTCTATAAAAATACAAATCATATAAACATTAAATAGGC
TGGAATAATAC
Found at i:432314 original size:2 final size:2
Alignment explanation
Indices: 432307--432358 Score: 95
Period size: 2 Copynumber: 25.5 Consensus size: 2
432297 GTATAAATAC
432307 AT AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
432350 AT AT AT AT A
1 AT AT AT AT A
432359 GTTTTGAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 47 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:454066 original size:24 final size:24
Alignment explanation
Indices: 454026--454090 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 24
454016 GTTGTGGAAT
*
454026 ATATTTTTCTAAA-TTTTATACAA
1 ATATTTTTATAAATTTTTATACAA
454049 ATATTTTTATAAATTTTTATACAA
1 ATATTTTTATAAATTTTTATACAA
* * *
454073 ATAATTTAATATATTTTT
1 ATATTTTTATAAATTTTT
454091 CTACGGCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 12 0.32
24 25 0.68
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (24 bp):
ATATTTTTATAAATTTTTATACAA
Found at i:454074 original size:12 final size:13
Alignment explanation
Indices: 454038--454080 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 13
454028 ATTTTTCTAA
454038 ATTTTATACAAAT
1 ATTTTATACAAAT
*
454051 ATTTT-TATAAAT
1 ATTTTATACAAAT
454063 -TTTTATACAAAT
1 ATTTTATACAAAT
*
454075 AATTTA
1 ATTTTA
454081 ATATATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 4 0.16
12 12 0.48
13 9 0.36
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (13 bp):
ATTTTATACAAAT
Found at i:471115 original size:2 final size:2
Alignment explanation
Indices: 471108--471134 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
471098 ATAATAGATT
471108 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
471135 GAATCACGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:471890 original size:33 final size:34
Alignment explanation
Indices: 471848--471930 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
471838 CAAGAGATCC
471848 CCGTTAGATATGATAG-CGTTAGTTGAA-ATTGAG
1 CCGTTAGATATGATAGCCGTTAGTTGAATA-TGAG
*
471881 CCGTTAGATATGATAGCCGTTGGTTGAATATGAG
1 CCGTTAGATATGATAGCCGTTAGTTGAATATGAG
*
471915 CTGTTAGATATGATAG
1 CCGTTAGATATGATAG
471931 GCTCCTATGG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
33 16 0.35
34 29 0.63
35 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.34
Consensus pattern (34 bp):
CCGTTAGATATGATAGCCGTTAGTTGAATATGAG
Found at i:472700 original size:41 final size:41
Alignment explanation
Indices: 472644--472739 Score: 115
Period size: 41 Copynumber: 2.4 Consensus size: 41
472634 GTTGATTTGG
* * * *
472644 CGCCACGT-GGGGTATAGTGCGCCCCCTGA-TCCGCGCTATA
1 CGCCACGTAGGGGTATAGCGCG-CACCAGAGGCCGCGCTATA
* *
472684 CGCCACGTAGGGGTATAGCGCGGATCAGAGGCCGCGCTATA
1 CGCCACGTAGGGGTATAGCGCGCACCAGAGGCCGCGCTATA
472725 CGCCACGTAGGGGTA
1 CGCCACGTAGGGGTA
472740 ATTATATTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 11 0.23
41 37 0.77
ACGTcount: A:0.19, C:0.30, G:0.34, T:0.17
Consensus pattern (41 bp):
CGCCACGTAGGGGTATAGCGCGCACCAGAGGCCGCGCTATA
Found at i:476351 original size:35 final size:34
Alignment explanation
Indices: 476266--476352 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
476256 AATATAATTT
*
476266 TAAATACAACAAACTTACAATAAGTATTAAATGG
1 TAAATACAACAAAATTACAATAAGTATTAAATGG
* *
476300 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--G-TATTAAATGG
476338 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
476353 ACTAAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 4 0.09
38 11 0.24
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.28
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGTATTAAATGG
Done.