Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1301
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1559340
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 165545 characters in sequence are not A, C, G, or T
File 3 of 4
Found at i:396930 original size:45 final size:44
Alignment explanation
Indices: 396878--396969 Score: 166
Period size: 45 Copynumber: 2.1 Consensus size: 44
396868 AAAATGCACC
396878 TTTATAGTCCAGAGACAAGCAACCTGCAATCTAAAATGCATGCGA
1 TTTATAGTCCAGAGACAAGCAACCTGCAATCTAAAATGCATGC-A
*
396923 TTTATAGTCCAGAGACAAGCAACCTGCAGTCTAAAATGCATGCA
1 TTTATAGTCCAGAGACAAGCAACCTGCAATCTAAAATGCATGCA
396967 TTT
1 TTT
396970 TTTTAATGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
44 4 0.09
45 42 0.91
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (44 bp):
TTTATAGTCCAGAGACAAGCAACCTGCAATCTAAAATGCATGCA
Found at i:409846 original size:38 final size:39
Alignment explanation
Indices: 409802--409877 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 39
409792 ATGTAGTCCC
409802 TCCGTTA-TTTATTTTTCAATCAGAAAATGTCTAGTCAG
1 TCCGTTATTTTATTTTTCAATCAGAAAATGTCTAGTCAG
* *
409840 TCCGTTATTTTTTTTTTTCAATCAGAATATGTCTAGTC
1 TCCGTTA-TTTTATTTTTCAATCAGAAAATGTCTAGTC
409878 TTTTCGTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 7 0.21
40 27 0.79
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (39 bp):
TCCGTTATTTTATTTTTCAATCAGAAAATGTCTAGTCAG
Found at i:409893 original size:40 final size:40
Alignment explanation
Indices: 409813--409893 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
409803 CCGTTATTTA
* **
409813 TTTTTCAATCAGAAAATGTCTAGTCAGTCCGTTATTTTTT
1 TTTTTCAATCAGAAAATGTCTAGTCAGTCCGTCAGCTTTT
* ** *
409853 TTTTTCAATCAGAATATGTCTAGTCTTTTCGTCAGCTTTT
1 TTTTTCAATCAGAAAATGTCTAGTCAGTCCGTCAGCTTTT
409893 T
1 T
409894 GTAATCAGAC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.49
Consensus pattern (40 bp):
TTTTTCAATCAGAAAATGTCTAGTCAGTCCGTCAGCTTTT
Found at i:419429 original size:170 final size:175
Alignment explanation
Indices: 419078--419437 Score: 518
Period size: 170 Copynumber: 2.1 Consensus size: 175
419068 GTGAAATGGA
*
419078 GTACCCTATATGCAATGTCTTGCCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATGA
1 GTACCCTATATGCAATATCTTGCCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATGA
419143 ATTATCAGAAATCAAAATTCTAGCAATATGCACACCTCTGATATATGTTCAATTGATCTGCAAAA
66 ATTATCAGAAATC--AA---TA-CAATATGCACACCTCTGATATATGTTCAATTGATCTGCAAAA
* * *
419208 GAAAAACTTCCTTTCTTGAAAACTGTAGGAGGAGTTATCCGTACGATAAGG
125 GAAAAACTCCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATAAGG
* *
419259 GTACCCTATATGCAATATTTTG-CCAAAAAATGACTAAGTTTAAAAGCTGGTA-TTTTTTCAT-A
1 GTACCCTATATGCAATATCTTGCCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATGA
* *
419321 AGTTATCAGAAATC-A-A-AATATGCACACCTCTGATGTAT-TTACAATTGATCTGCAAAAGAAC
66 A-TTATCAGAAATCAATACAATATGCACACCTCTGATATATGTT-CAATTGATCTGCAAAAGAAA
*
419382 AACTCCCTATCTTGAAAACTGTAGGAGGAGTTATCCTTACAATAAGG
129 AACTCCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATAAGG
419429 GTACCCTAT
1 GTACCCTAT
419438 TGGCAGCCGC
Statistics
Matches: 168, Mismatches: 9, Indels: 15
0.88 0.05 0.08
Matches are distributed among these distances:
169 2 0.01
170 92 0.55
172 1 0.01
176 1 0.01
178 2 0.01
179 21 0.12
180 29 0.17
181 20 0.12
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (175 bp):
GTACCCTATATGCAATATCTTGCCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTTCATGA
ATTATCAGAAATCAATACAATATGCACACCTCTGATATATGTTCAATTGATCTGCAAAAGAAAAA
CTCCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATAAGG
Found at i:430251 original size:2 final size:2
Alignment explanation
Indices: 430244--430277 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
430234 GCAGTTAATG
430244 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
430278 TAGTGTCGGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:431980 original size:2 final size:2
Alignment explanation
Indices: 431973--432011 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
431963 CATTAAAATG
431973 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
432012 ATATATATAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:432124 original size:2 final size:2
Alignment explanation
Indices: 432119--432161 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
432109 ATTCAGTCAG
432119 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
432161 T
1 T
432162 AACATATACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:432165 original size:98 final size:94
Alignment explanation
Indices: 432047--432252 Score: 367
Period size: 98 Copynumber: 2.1 Consensus size: 94
432037 CTATACTTAA
*
432047 TCTCTCTCTCTCTCTCTAACATATACAGAAACCAACTATACTTAATTTCTCTCTCTCTCCTCATT
1 TCTCTCTCTCTCTCTCTAACATATACAGAAACCAACTATACTTAA-TT-TCTCTCTCTCCTCACT
432112 CAGTCAGTCTCTCTCTCTCTCTCTCTCTCTCTC
64 CAGTC--TCTCTCTCTCTCTCTCTCTCTCTCTC
432145 TCTCTCTCTCTCTCTCTAACATATACAGAAACCAACTATACTTAATTTCTCTCTCTCCTCACTCA
1 TCTCTCTCTCTCTCTCTAACATATACAGAAACCAACTATACTTAATTTCTCTCTCTCCTCACTCA
432210 GTCTCTCTCTCTCTCTCTCTCTCTCTCTC
66 GTCTCTCTCTCTCTCTCTCTCTCTCTCTC
432239 TCTCTCTCTCTCTC
1 TCTCTCTCTCTCTC
432253 NNNNNNNNNN
Statistics
Matches: 107, Mismatches: 1, Indels: 4
0.96 0.01 0.04
Matches are distributed among these distances:
94 40 0.37
96 20 0.19
97 2 0.02
98 45 0.42
ACGTcount: A:0.17, C:0.39, G:0.02, T:0.41
Consensus pattern (94 bp):
TCTCTCTCTCTCTCTCTAACATATACAGAAACCAACTATACTTAATTTCTCTCTCTCCTCACTCA
GTCTCTCTCTCTCTCTCTCTCTCTCTCTC
Found at i:432199 original size:2 final size:2
Alignment explanation
Indices: 432192--432252 Score: 88
Period size: 2 Copynumber: 31.0 Consensus size: 2
432182 ATACTTAATT
* **
432192 TC TC TC TC TC -C TC AC TC AG TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
432233 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
432253 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.03, C:0.49, G:0.02, T:0.46
Consensus pattern (2 bp):
TC
Found at i:436499 original size:2 final size:2
Alignment explanation
Indices: 436494--436531 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
436484 ATTTTGTATC
436494 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
436532 GTTATATACT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:439793 original size:21 final size:21
Alignment explanation
Indices: 439738--439793 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
439728 ATCTGCCACC
*
439738 ACTTGTCAGATAATT-ATGTCG
1 ACTTGTCAGAT-CTTGATGTCG
439759 ACTTGTCAGATCTTGATGTCG
1 ACTTGTCAGATCTTGATGTCG
*
439780 ACTTGTCAGTTCTT
1 ACTTGTCAGATCTT
439794 TAAGCCGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (21 bp):
ACTTGTCAGATCTTGATGTCG
Found at i:439912 original size:21 final size:21
Alignment explanation
Indices: 439885--440044 Score: 178
Period size: 21 Copynumber: 7.7 Consensus size: 21
439875 AATAATATTT
**
439885 TCTGACAAGTCGACATAAGGA
1 TCTGACAAGTCGACATAATTA
* *
439906 TCAGACAAGTCGACATAATAA
1 TCTGACAAGTCGACATAATTA
*** *
439927 TCTTTTAAGTCGATATAATTA
1 TCTGACAAGTCGACATAATTA
*
439948 TTTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
439969 TCTGACAAGTCGACATAATTA
1 TCTGACAAGTCGACATAATTA
* * *
439990 TTTGACAAGACGACATAA-CA
1 TCTGACAAGTCGACATAATTA
* * *
440010 TCTGACAAGACAACATCATTA
1 TCTGACAAGTCGACATAATTA
440031 TCTGACAAGTCGAC
1 TCTGACAAGTCGAC
440045 TTACAATATG
Statistics
Matches: 114, Mismatches: 24, Indels: 2
0.81 0.17 0.01
Matches are distributed among these distances:
20 16 0.14
21 98 0.86
ACGTcount: A:0.39, C:0.19, G:0.15, T:0.27
Consensus pattern (21 bp):
TCTGACAAGTCGACATAATTA
Found at i:440105 original size:21 final size:21
Alignment explanation
Indices: 440075--440145 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
440065 TTCTTGACAG
*
440075 ACTTGACAGATAATTATGTTA
1 ACTTGTCAGATAATTATGTTA
** *
440096 ACTTGTCAGATCTTTATGTTG
1 ACTTGTCAGATAATTATGTTA
* *
440117 ACTTGTCAGATGATTATGTAA
1 ACTTGTCAGATAATTATGTTA
440138 ACTTGTCA
1 ACTTGTCA
440146 AATATTGTCA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (21 bp):
ACTTGTCAGATAATTATGTTA
Found at i:445101 original size:8 final size:7
Alignment explanation
Indices: 445087--445132 Score: 51
Period size: 8 Copynumber: 6.4 Consensus size: 7
445077 GCGAGGGCGA
445087 AAGTGCG
1 AAGTGCG
445094 AAGTTGCG
1 AAG-TGCG
445102 AA-TGCG
1 AAGTGCG
445108 AGAGTGCG
1 A-AGTGCG
445116 AAGTTGCG
1 AAG-TGCG
445124 AA-TGCG
1 AAGTGCG
445130 AAG
1 AAG
445133 AAGCGATAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
6 11 0.32
7 6 0.18
8 17 0.50
ACGTcount: A:0.30, C:0.13, G:0.39, T:0.17
Consensus pattern (7 bp):
AAGTGCG
Found at i:445108 original size:22 final size:22
Alignment explanation
Indices: 445083--445131 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
445073 AAAGGCGAGG
445083 GCGAAAGTGCGAAGTTGCGAAT
1 GCGAAAGTGCGAAGTTGCGAAT
*
445105 GCGAGAGTGCGAAGTTGCGAAT
1 GCGAAAGTGCGAAGTTGCGAAT
445127 GCGAA
1 GCGAA
445132 GAAGCGATAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.31, C:0.14, G:0.39, T:0.16
Consensus pattern (22 bp):
GCGAAAGTGCGAAGTTGCGAAT
Found at i:445138 original size:22 final size:22
Alignment explanation
Indices: 445091--445138 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
445081 GGGCGAAAGT
*
445091 GCGAAGTTGCGAATGCGAGAGT
1 GCGAAGTTGCGAATGCGAGAGA
445113 GCGAAGTTGCGAATGCGA-AGAA
1 GCGAAGTTGCGAATGCGAGAG-A
445135 GCGA
1 GCGA
445139 TAGTAGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.31, C:0.15, G:0.40, T:0.15
Consensus pattern (22 bp):
GCGAAGTTGCGAATGCGAGAGA
Found at i:448047 original size:167 final size:165
Alignment explanation
Indices: 447765--448561 Score: 1058
Period size: 166 Copynumber: 4.8 Consensus size: 165
447755 GTCGCATTTA
* * *
447765 TCTCAGCAACTATTTATCGCAGATGCTTAAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
** *
447830 CGTAAGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTA-TTT
*
447895 TTAACCAACATTTTCAAACAAATTTTCGTCAAAGATT
129 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
447932 TCTCATCAACTATTTATCGCAGATGCTTGAAATTTTTACACAATATTTGTATAGGCATGTCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGT-TAGGCATGCCATAT
* * * *
447997 CGTGGAATATATTTTTGTACCAATCAGACGTTAACTTCCTATTAAATGACGACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* * *
448062 TAGCCAAAAATTTCAAACAAATTTTTGTCAAAGATT
130 TAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* **
448098 TCTCAGCAACTGTTTATCGCAGATGC-TGAAATTTTAACACAGTATTTGTATAGGCATGCTTTAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGT-TAGGCATGCCATAT
* *
448162 CGTGGGATGTATTTTTGTACCAATCGGACGTCAACTTCCTGTTTAATGA-GTATACTTTGTTTAT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG---ACTTTGTTTAT
*
448226 TTTTAAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATT
127 TTTTAA-CCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * * *
448266 TCTCAGCAACTAATAATCGCAGATGCTTGAAATTTTAACATACTATTTGTTTAGGCATGTCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTG-TTAGGCATGCCATAT
* * * * *
448331 TGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCAGTTAAATAATGACTTTGTTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
* *
448396 TAGCCAAAACTTTCAAACAAATTTTCGTCAAAGATT
130 TAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
448432 TCTCAGCAGCTATTCATCGCAGATGCTTGAAATTTTAACACAGTGTTCGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTT-AGGCATGCCATAT
* * * * * * * *
448497 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
65 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTT
448562 GCATATTCTC
Statistics
Matches: 552, Mismatches: 69, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
164 1 0.00
165 78 0.14
166 199 0.36
167 144 0.26
168 54 0.10
169 74 0.13
170 2 0.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (165 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTAGGCATGCCATATC
GTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTTTT
AACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:448401 original size:334 final size:333
Alignment explanation
Indices: 447765--448561 Score: 1154
Period size: 334 Copynumber: 2.4 Consensus size: 333
447755 GTCGCATTTA
* *
447765 TCTCAGCAACTATTTATCGCAGATGCTTAAAATTTTTACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
**
447830 CGTAAGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
* * * * *
447895 TTAACCAACATTTTCAAACAAATTTTCGTCAAAGATTTCTCATCAACTATTTATCGCAGATGCTT
131 TTAACCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTAATAATCGCAGATGCTT
*
447960 GAAATTTTTACACAATATTTGTATAGGCATGTCATATCGTGGAATATATTTTTGTACCAATCAGA
196 GAAATTTTAACACAATATTTGTATAGGCATGTCATATCGTGGAATATATTTTTGTACCAATCAGA
* * *
448025 CGTTAACTTCCTATTAAATGACGACTTTGTTTATTTTTAGCCAAAAATTTCAAACAAATTTTTGT
261 CGTCAACTTCCTATTAAATAACGACTTTGTTTATTTTTAGCCAAAAATTTCAAACAAATTTTCGT
448090 CAAAGATT
326 CAAAGATT
* * **
448098 TCTCAGCAACTGTTTATCGCAGATGC-TGAAATTTTAACACAGTATTTG-TATAGGCATGCTTTA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTA-AGGCATGCCATA
* * *
448161 TCGTGGGATGTATTTTTGTACCAATCGGACGTCAACTTCCTGTTTAATGA-GTATACTTTGTTTA
65 TCGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACG---ACTTTGCTTA
448225 -TTTTTAAGCCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTAATAATCGCAGA
127 TTTTTTAA-CCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTAATAATCGCAGA
* * * * * *
448289 TGCTTGAAATTTTAACATACTATTTGTTTAGGCATGTCATATTGTGGGATATATTTTTGTATCAA
191 TGCTTGAAATTTTAACACAATATTTGTATAGGCATGTCATATCGTGGAATATATTTTTGTACCAA
* * *
448354 TCGGACGTCAACTTCC-AGTTAAATAATGACTTTGTTTATTTTTAGCCAAAACTTTCAAACAAAT
256 TCAGACGTCAACTTCCTA-TTAAATAACGACTTTGTTTATTTTTAGCCAAAAATTTCAAACAAAT
448418 TTTCGTCAAAGATT
320 TTTCGTCAAAGATT
* * *
448432 TCTCAGCAGCTATTCATCGCAGATGCTTGAAATTTTAACACAGTGTTCGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
* * * * * * *
448497 TGTGGGATATATTTCTGTACCAATCGGATGCCAGCTTTCTGTTAAATGTCGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
448562 GCATATTCTC
Statistics
Matches: 408, Mismatches: 46, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
331 3 0.01
332 75 0.18
333 42 0.10
334 214 0.52
335 71 0.17
336 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (333 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCGGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTCCGTCAAAGATTTCTCAGCAACTAATAATCGCAGATGCTT
GAAATTTTAACACAATATTTGTATAGGCATGTCATATCGTGGAATATATTTTTGTACCAATCAGA
CGTCAACTTCCTATTAAATAACGACTTTGTTTATTTTTAGCCAAAAATTTCAAACAAATTTTCGT
CAAAGATT
Found at i:449356 original size:2 final size:2
Alignment explanation
Indices: 449349--449412 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
449339 AGGGACCGGG
449349 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
449391 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
449413 GACCCGGATG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:455695 original size:145 final size:134
Alignment explanation
Indices: 455459--455723 Score: 422
Period size: 145 Copynumber: 1.9 Consensus size: 134
455449 GTGAATTTGA
455459 TTAAGTTTAATTTCTTATTTTTCTCAGAAAAGGTTCGGACCCCCCCCCCTTTAAAAAAAAAGGCA
1 TTAAGTTTAATTTCTTATTTTTCTCAGAAAAGGTTCGGACCCCCCCCCCTTTAAAAAAAAAGGCA
455524 AAATCCGCTTATGCTGGCTATATCAAATTATGAGTAATTTGTAGAGCTCGGTGTTAATTTCTGTT
66 AAATCCGCTTATGCTGGCTATATCAAATTATGAGTAATTTGTAGAGCTCGGTGTTAATTTCTGTT
455589 TAAT
131 TAAT
455593 TTAAGTTTAATTTCTTATTTTTCTCAGAAAAGGTTCGGACCTCCCCCCCCCCTTTTTTTTTTAAA
1 TTAAGTTTAATTTCTTATTTTTCTCAGAAAAGGTTCGGA---CCCCCCCCCC-------TTT-AA
*
455658 AAAAAAAGGCAAAATCCGCTTATGCTGGCTTTATCAAATTATGAGTAATTTGTAGAGCTCGGTGT
55 AAAAAAAGGCAAAATCCGCTTATGCTGGCTATATCAAATTATGAGTAATTTGTAGAGCTCGGTGT
455723 T
120 T
455724 TGTAATCAGT
Statistics
Matches: 119, Mismatches: 1, Indels: 11
0.91 0.01 0.08
Matches are distributed among these distances:
134 39 0.33
137 10 0.08
144 3 0.03
145 67 0.56
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.37
Consensus pattern (134 bp):
TTAAGTTTAATTTCTTATTTTTCTCAGAAAAGGTTCGGACCCCCCCCCCTTTAAAAAAAAAGGCA
AAATCCGCTTATGCTGGCTATATCAAATTATGAGTAATTTGTAGAGCTCGGTGTTAATTTCTGTT
TAAT
Found at i:457182 original size:17 final size:17
Alignment explanation
Indices: 457148--457185 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
457138 TTACTTTATG
*
457148 AAAGTGACAGATTGTCA
1 AAAGTGACAGATTATCA
457165 AAAGTGACA-ATTAATCA
1 AAAGTGACAGATT-ATCA
457182 AAAG
1 AAAG
457186 ACATTTCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (17 bp):
AAAGTGACAGATTATCA
Found at i:460883 original size:34 final size:34
Alignment explanation
Indices: 460845--461054 Score: 115
Period size: 34 Copynumber: 6.2 Consensus size: 34
460835 AGGTCAAAAG
* * *
460845 GTGAGTCAGA-AAGGTCATTGAGATATGTCAGTTT
1 GTGAGTCA-ATAAGGTCATTGAGATAGGTCAGGTA
*
460879 GTGAGTCAATACGGTCATTGAGATAGGTCAGGTA
1 GTGAGTCAATAAGGTCATTGAGATAGGTCAGGTA
* * ** *
460913 GTGAGTTACAAT--GGTCAGTAAGATAGAACAGATA
1 GTGAG-T-CAATAAGGTCATTGAGATAGGTCAGGTA
* * * * *
460947 GTGAGTTACTACGGTCAGTGAGAAAGGTCAAAGG-A
1 GTGAGTCAATAAGGTCATTGAGATAGGTC--AGGTA
* * * *
460982 -TGAGTTAATATGGTCAGTGAGATAGGTCAGATA
1 GTGAGTCAATAAGGTCATTGAGATAGGTCAGGTA
* * ** * * *
461015 GTGAGTTACTATTGTCAGTGAGATAGTTCAGATA
1 GTGAGTCAATAAGGTCATTGAGATAGGTCAGGTA
461049 GTGAGT
1 GTGAGT
461055 TACTATGGTT
Statistics
Matches: 144, Mismatches: 23, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
32 4 0.03
33 3 0.02
34 129 0.90
35 2 0.01
36 6 0.04
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.28
Consensus pattern (34 bp):
GTGAGTCAATAAGGTCATTGAGATAGGTCAGGTA
Found at i:461055 original size:34 final size:34
Alignment explanation
Indices: 460891--461810 Score: 1005
Period size: 34 Copynumber: 27.4 Consensus size: 34
460881 GAGTCAATAC
* * * *
460891 GGTCATTGAGATAGGTCAGGTAGTGAGTTACAAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* ** *
460925 GGTCAGTAAGATAGAACAGATAGTGAGTTACTAC
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * *
460959 GGTCAGTGAGAAAGGTCA-A-AGGATGAGTTAATAT
1 GGTCAGTGAGATAGTTCAGATA-G-TGAGTTACTAT
*
460993 GGTCAGTGAGATAGGTCAGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461027 TGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * * * *
461061 GGTTAGTGAAATAGGTCAAATTGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * * **
461095 GGTTAGTGAGATAGGTCAGATTGTGAGTTGTTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461129 GGTTAGTGAGATAG-TCAGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461162 GGTCAGTGAGTTAGTT-AG--A-T-AGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * *
461191 TGTCAGTGAGATAGGTCAGATAGTGAGTTACTAC
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * * *
461225 GGTCAGTGAGGTAGGTCAGATTGTGAGTTACAAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461259 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* ** * * *
461292 AGTCAGTGAGATAGGACAGATGGTTAGTTCCTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * **
461326 AGTCAGTGAGAAAGCACAGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* * * *
461360 GATCAGTGAGATAGGTCAGATTGTGAATTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461394 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461427 GGTCAGTGAGATA-TGTCAGATTGTGAGTTACTAT
1 GGTCAGTGAGATAGT-TCAGATAGTGAGTTACTAT
*
461461 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461494 GGTCAGTGAGATA-TGTCAGATTGTGAGTTACTAT
1 GGTCAGTGAGATAGT-TCAGATAGTGAGTTACTAT
*
461528 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* ** * * *
461561 GGTCAGTGAGATGGGACAGATGGTTAGTTCCTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461595 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* *
461628 GGTCAGTGAGATA-TGTCAGTTTGTGAGTTACTAT
1 GGTCAGTGAGATAGT-TCAGATAGTGAGTTACTAT
* *
461662 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAA
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461695 GGTCAGTGAGATA-TGTCAGATTGTGAGTTACTAT
1 GGTCAGTGAGATAGT-TCAGATAGTGAGTTACTAT
*
461729 AGTCAGTGAGATAGTT-AGATAGTGAGTTACTAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
* ** * * *
461762 GGTTAGTGAGATAGGACAGATAGTTAGTTCCCAT
1 GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
*
461796 AGTCAGTGAGATAGT
1 GGTCAGTGAGATAGT
461811 GAGTTACTAT
Statistics
Matches: 749, Mismatches: 112, Indels: 50
0.82 0.12 0.05
Matches are distributed among these distances:
29 22 0.03
30 3 0.00
31 1 0.00
32 6 0.01
33 229 0.31
34 481 0.64
35 6 0.01
36 1 0.00
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (34 bp):
GGTCAGTGAGATAGTTCAGATAGTGAGTTACTAT
Found at i:461267 original size:17 final size:17
Alignment explanation
Indices: 461247--461301 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
461237 AGGTCAGATT
461247 GTGAGTTACAATAGTCA
1 GTGAGTTACAATAGTCA
* **
461264 GTGAGATA-GTTAGAT-A
1 GTGAGTTACAATAG-TCA
*
461280 GTGAGTTACTATAGTCA
1 GTGAGTTACAATAGTCA
461297 GTGAG
1 GTGAG
461302 ATAGGACAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.33, C:0.07, G:0.29, T:0.31
Consensus pattern (17 bp):
GTGAGTTACAATAGTCA
Found at i:461287 original size:67 final size:67
Alignment explanation
Indices: 460891--461810 Score: 1168
Period size: 67 Copynumber: 13.7 Consensus size: 67
460881 GAGTCAATAC
* * * * * * **
460891 GGTCATTGAGATAGGTCAGGTAGTGAGTTACAATGGTCAGTAAGATAGAACAGATAGTGAGTTAC
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAG-TTAGATAGTGAGTTAC
*
460956 TAC
65 TAT
* ** * * *
460959 GGTCAGTGAGAAAGGTCA-AAGGATGAGTTAATATGGTCAGTGAGATAGGTCAGATAGTGAGTTA
1 GGTCAGTGAGATAGGTCAGATTG-TGAGTTACTATAGTCAGTGAGATA-GTTAGATAGTGAGTTA
461023 CTAT
64 CTAT
* * * * * * * * *
461027 TGTCAGTGAGATAGTTCAGATAGTGAGTTACTATGGTTAGTGAAATAGGTCAAATTGTGAGTTAC
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATA-GTTAGATAGTGAGTTAC
461092 TAT
65 TAT
* ** * * *
461095 GGTTAGTGAGATAGGTCAGATTGTGAGTTGTTATGGTTAGTGAGATAGTCAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461160 AT
66 AT
* * * *
461162 GGTCAGTGAGTTA-GTTAGA---T-AGTTACTATTGTCAGTGAGATAGGTCAGATAGTGAGTTAC
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATA-GTTAGATAGTGAGTTAC
*
461222 TAC
65 TAT
* *
461225 GGTCAGTGAGGTAGGTCAGATTGTGAGTTACAATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461290 AT
66 AT
* * * * * * **
461292 AGTCAGTGAGATAGGACAGATGGTTAGTTCCTATAGTCAGTGAGAAAGCACAGATAGTGAGTTAC
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAG-TTAGATAGTGAGTTAC
461357 TAT
65 TAT
* *
461360 GATCAGTGAGATAGGTCAGATTGTGAATTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461425 AT
66 AT
*
461427 GGTCAGTGAGATATGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461492 AT
66 AT
*
461494 GGTCAGTGAGATATGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461559 AT
66 AT
* * * * *
461561 GGTCAGTGAGATGGGACAGATGGTTAGTTCCTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461626 AT
66 AT
* *
461628 GGTCAGTGAGATATGTCAGTTTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
*
461693 AA
66 AT
*
461695 GGTCAGTGAGATATGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
461760 AT
66 AT
* * * * * *
461762 GGTTAGTGAGATAGGACAGATAGTTAGTTCCCATAGTCAGTGAGATAGT
1 GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGT
461811 GAGTTACTAT
Statistics
Matches: 753, Mismatches: 89, Indels: 21
0.87 0.10 0.02
Matches are distributed among these distances:
62 18 0.02
63 32 0.04
64 5 0.01
66 5 0.01
67 464 0.62
68 226 0.30
69 3 0.00
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (67 bp):
GGTCAGTGAGATAGGTCAGATTGTGAGTTACTATAGTCAGTGAGATAGTTAGATAGTGAGTTACT
AT
Found at i:461807 original size:25 final size:25
Alignment explanation
Indices: 461779--461833 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
461769 GAGATAGGAC
* *
461779 AGATAGTTAGTTCCCATAGTCAGTG
1 AGATAGTGAGTTACCATAGTCAGTG
* *
461804 AGATAGTGAGTTACTATGGTCAGTG
1 AGATAGTGAGTTACCATAGTCAGTG
461829 AGATA
1 AGATA
461834 ATACAGATAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (25 bp):
AGATAGTGAGTTACCATAGTCAGTG
Found at i:461860 original size:59 final size:59
Alignment explanation
Indices: 461745--461867 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 59
461735 TGAGATAGTT
* * ** *
461745 AGATAGTGAGTTACTATGGTTAGTGAGATAGGACAGATAGTTAGTTCCCATAGTCAGTG
1 AGATAGTGAGTTACTATGGTCAGTGAGATAAGACAGATAGTTAACTCCAATAGTCAGTG
* *
461804 AGATAGTGAGTTACTATGGTCAGTGAGATAATACAGATAG-TAACTCACAATGGTCAGTG
1 AGATAGTGAGTTACTATGGTCAGTGAGATAAGACAGATAGTTAACTC-CAATAGTCAGTG
461863 AGATA
1 AGATA
461868 TGTTATAGGA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 4 0.07
59 52 0.93
ACGTcount: A:0.34, C:0.11, G:0.27, T:0.28
Consensus pattern (59 bp):
AGATAGTGAGTTACTATGGTCAGTGAGATAAGACAGATAGTTAACTCCAATAGTCAGTG
Found at i:462228 original size:1 final size:1
Alignment explanation
Indices: 462222--462252 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
462212 GGCAGGCAGG
462222 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
462253 GGAGACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:465699 original size:11 final size:11
Alignment explanation
Indices: 465683--465714 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
465673 CCGCATTTGC
465683 CGTGGGACTTA
1 CGTGGGACTTA
465694 CGTGGGACTTA
1 CGTGGGACTTA
465705 CGTGGGACTT
1 CGTGGGACTT
465715 GTTTTCTCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.28
Consensus pattern (11 bp):
CGTGGGACTTA
Found at i:470400 original size:34 final size:34
Alignment explanation
Indices: 470356--470598 Score: 179
Period size: 34 Copynumber: 7.1 Consensus size: 34
470346 TTAGATGTGT
* *
470356 GTGAGATAGGTCA-AAAGGTGAGTCAGTATGGTTA
1 GTGAGATAGGTCAGAAA-GTGAGTCACTATGGTCA
* *** * *
470390 TTGAGATAGGTCAGTTTGTGAGTCAATACGGTCA
1 GTGAGATAGGTCAGAAAGTGAGTCACTATGGTCA
* * * *
470424 TTGAGATAGGTCAGATAGTGAGTAACAATGGTCA
1 GTGAGATAGGTCAGAAAGTGAGTCACTATGGTCA
* ** * *
470458 GTAAGATAGAACAGATAA-TGAGTTACTACGGTCA
1 GTGAGATAGGTCAGA-AAGTGAGTCACTATGGTCA
* * *
470492 GTGAGA-ACGGTCA-AAGGGTGAGTCAATATGGTTA
1 GTGAGATA-GGTCAGAA-AGTGAGTCACTATGGTCA
* * *
470526 GTGAGATAGGTCAGATAGTGAGTTACTATGGTTA
1 GTGAGATAGGTCAGAAAGTGAGTCACTATGGTCA
** * *
470560 GTGAGATAGGTCAGATTGTGAGTTACTATGTTCA
1 GTGAGATAGGTCAGAAAGTGAGTCACTATGGTCA
470594 GTGAG
1 GTGAG
470599 TAAGTTACTA
Statistics
Matches: 166, Mismatches: 36, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
32 1 0.01
33 2 0.01
34 160 0.96
35 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (34 bp):
GTGAGATAGGTCAGAAAGTGAGTCACTATGGTCA
Found at i:470535 original size:102 final size:102
Alignment explanation
Indices: 470407--470598 Score: 267
Period size: 102 Copynumber: 1.9 Consensus size: 102
470397 AGGTCAGTTT
*
470407 GTGAGTCAATACGGTCATTGAGATAGGTCAGATAGTGAGTAACAATGGTCAGTAAGATAGAACAG
1 GTGAGTCAATACGGTCAGTGAGATAGGTCAGATAGTGAGTAACAATGGTCAGTAAGATAGAACAG
470472 ATAATGAGTTACTACGGTCAGTGAGAACGGTCAAAGG
66 ATAATGAGTTACTACGGTCAGTGAGAACGGTCAAAGG
* * * * * * **
470509 GTGAGTCAATATGGTTAGTGAGATAGGTCAGATAGTGAGTTACTATGGTTAGTGAGATAGGTCAG
1 GTGAGTCAATACGGTCAGTGAGATAGGTCAGATAGTGAGTAACAATGGTCAGTAAGATAGAACAG
** * *
470574 ATTGTGAGTTACTATGTTCAGTGAG
66 ATAATGAGTTACTACGGTCAGTGAG
470599 TAAGTTACTA
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
102 77 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (102 bp):
GTGAGTCAATACGGTCAGTGAGATAGGTCAGATAGTGAGTAACAATGGTCAGTAAGATAGAACAG
ATAATGAGTTACTACGGTCAGTGAGAACGGTCAAAGG
Found at i:470597 original size:68 final size:68
Alignment explanation
Indices: 470356--470598 Score: 208
Period size: 68 Copynumber: 3.6 Consensus size: 68
470346 TTAGATGTGT
* * * * * * * *
470356 GTGAGATAGGTCA-AAAGGTGAGTCAGTATGGTT-ATTGAGATAGGTCAGTTTGTGAGTCAATAC
1 GTGAGATAGGTCAGATA-GTGAGTAACTAT-GTTCAGTGAGATAGGTCAGATAGTGAGTTACTAC
470419 GGTCA
64 GGTCA
* * * * ** *
470424 TTGAGATAGGTCAGATAGTGAGTAACAATGGTCAGTAAGATAGAACAGATAATGAGTTACTACGG
1 GTGAGATAGGTCAGATAGTGAGTAACTATGTTCAGTGAGATAGGTCAGATAGTGAGTTACTACGG
470489 TCA
66 TCA
* **
470492 GTGAGA-ACGGTCAAAGGGTGAGTCAA-TATGGTT-AGTGAGATAGGTCAGATAGTGAGTTACTA
1 GTGAGATA-GGTCAGATAGTGAGT-AACTAT-GTTCAGTGAGATAGGTCAGATAGTGAGTTACTA
* *
470554 TGGTTA
63 CGGTCA
* *
470560 GTGAGATAGGTCAGATTGTGAGTTACTATGTTCAGTGAG
1 GTGAGATAGGTCAGATAGTGAGTAACTATGTTCAGTGAG
470599 TAAGTTACTA
Statistics
Matches: 136, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
67 7 0.05
68 122 0.90
69 7 0.05
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (68 bp):
GTGAGATAGGTCAGATAGTGAGTAACTATGTTCAGTGAGATAGGTCAGATAGTGAGTTACTACGG
TCA
Found at i:470604 original size:21 final size:21
Alignment explanation
Indices: 470580--470619 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
470570 TCAGATTGTG
470580 AGTTACTA-TGTTCAGTGAGTA
1 AGTTACTATTG-TCAGTGAGTA
470601 AGTTACTATTGTCAGTGAG
1 AGTTACTATTGTCAGTGAG
470620 ATAGGTCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (21 bp):
AGTTACTATTGTCAGTGAGTA
Found at i:470618 original size:55 final size:55
Alignment explanation
Indices: 470546--470653 Score: 180
Period size: 55 Copynumber: 2.0 Consensus size: 55
470536 TCAGATAGTG
* * *
470546 AGTTACTATGGTTAGTGAGATAGGTCAGATTGTGAGTTACTATGTTCAGTGAGTA
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGTA
*
470601 AGTTACTATTGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAG
470654 ATATGTCAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.28, C:0.08, G:0.30, T:0.34
Consensus pattern (55 bp):
AGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGTA
Found at i:470639 original size:34 final size:34
Alignment explanation
Indices: 470601--471343 Score: 728
Period size: 34 Copynumber: 22.0 Consensus size: 34
470591 TCAGTGAGTA
*
470601 AGTTACTATTGTCAGTGAGATAGGTCAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
*
470635 AGTTACTATGGTCAGTGAGATATGTCAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * * *
470669 AGTTACTATGGTTAGTGAGAAAGGACAGATGGTT
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * ** * *
470703 A-TTACCTATAGTTAGTGAGATAGCACAGATGGTT
1 AGTTA-CTATGGTCAGTGAGATAGGTCAGATAGTG
* * **
470737 AGTTCCTATAGTCAGTGAGATAGCACAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
*
470771 AGTTACTATGGTCAGTGAGATAGGTCAGGTAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * * *
470805 AGTTTCCAAGGTCAGTGAGATATGTCAGATTGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * *
470839 AGTTTCTATGGTTAGTGAGATATGTCAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * *
470873 AGTTACTATGGTTAGTGAGATAGGACAGATGGTT
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * ** * *
470907 A-TTACCTATAGTTAGTGAGATAGCACAGATGGTT
1 AGTTA-CTATGGTCAGTGAGATAGGTCAGATAGTG
* *
470941 AGTTCCTA----CAGTGAGATAGGTCAGGTAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * *
470971 AGTTTCTAAGGTCAGTGAGATATGTCAGATTGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* *
471005 AGTTACTATGGTTAGTGAGATATGTCAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * * *
471039 AGTTACTATGGTTAGTGAGATAAGACAGATGGTT
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * ** * *
471073 A-TTACCTATAGTTAGTGAGATAGCACAGATGGTT
1 AGTTA-CTATGGTCAGTGAGATAGGTCAGATAGTG
* * **
471107 AGTTCCTATAGTCAGTGAGATAGCACAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
471141 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* *
471175 AGTTTCTATGGTCAGTGAGATAGGTCAGGTAGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * *
471209 AGTTTCTAAGGTCAGTGAGATATGTCAGATTGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * *
471243 AGTTACTATAGTCAGTGAGATATGTCAGATTGTG
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* * * *
471277 AGTTACTATGGTCAGTGAGATGGGACAGATGGTT
1 AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
* *
471311 AGTTCCTATAGTCAGTGAGATA-GTACAGATAGT
1 AGTTACTATGGTCAGTGAGATAGGT-CAGATAGT
471344 AATCTCACAA
Statistics
Matches: 611, Mismatches: 87, Indels: 22
0.85 0.12 0.03
Matches are distributed among these distances:
30 23 0.04
33 10 0.02
34 572 0.94
35 6 0.01
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (34 bp):
AGTTACTATGGTCAGTGAGATAGGTCAGATAGTG
Found at i:470639 original size:89 final size:89
Alignment explanation
Indices: 470525--470687 Score: 283
Period size: 89 Copynumber: 1.8 Consensus size: 89
470515 CAATATGGTT
* *
470525 AGTGAGATAGGTCAGATAGTGAGTTACTATGGTTAGTGAGATAGGTCAGATTGTGAGTTACTAT-
1 AGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTACTATG
470589 GTTCAGTGAGTAAGTTACTATTGTC
66 GTT-AGTGAGTAAGTTACTATTGTC
*
470614 AGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATATGTCAGATAGTGAGTTACTATG
1 AGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTACTATG
470679 GTTAGTGAG
66 GTTAGTGAG
470688 AAAGGACAGA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
89 67 0.96
90 3 0.04
ACGTcount: A:0.29, C:0.07, G:0.31, T:0.33
Consensus pattern (89 bp):
AGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTACTATG
GTTAGTGAGTAAGTTACTATTGTC
Found at i:470684 original size:17 final size:17
Alignment explanation
Indices: 470630--470687 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
470620 ATAGGTCAGA
470630 TAGTGAGTTACTATGGT
1 TAGTGAGTTACTATGGT
* * * * *
470647 CAGTGAGATA-TGTCAGA
1 TAGTGAGTTACTAT-GGT
470664 TAGTGAGTTACTATGGT
1 TAGTGAGTTACTATGGT
470681 TAGTGAG
1 TAGTGAG
470688 AAAGGACAGA
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.34
Consensus pattern (17 bp):
TAGTGAGTTACTATGGT
Found at i:470720 original size:123 final size:126
Alignment explanation
Indices: 470470--471264 Score: 423
Period size: 136 Copynumber: 6.0 Consensus size: 126
470460 AAGATAGAAC
** * ** * * *
470470 AGATAATGAGTTACTACGGTCAGTGAGA-ACGGTCAAAGGGTGAGTCAATATGGTTAGTGAGATA
1 AGATAA-GAGTTACTATAGTCAGTGAGATA-GGTCAGATAGTGAGTTACTATGGTCAGTGAGATA
* * *
470534 GGTCAGATAGTGAGTTACTATGGTTAGTGAGATAGGTCAGATTGTGAGTTACTATGTTCAGTG
64 GGTCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTGAGTTACTATGTTCAGTG
* *
470597 AG-T-A-AGTTACTATTGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATATG
1 AGATAAGAGTTACTATAGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATAGG
*
470659 TCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTTA-TTACCTATAGTT-AGTG
66 TCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTGAGTTA-CTAT-GTTCAGTG
**
470720 AGATAGCACAGATGGTTAGTTCCTATAGTCAGTGAGATAGCACAGATAGTGAGTTACTATGGTCA
1 AGAT---A-AGA--GTTA----CTATAGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCA
* * * * * * * * * *
470785 GTGAGATAGGTCAGGTAGTGAGTTTCCAAGGTCAGTGAGATATGTCAGATTGTGAGTTTCTATGG
56 GTGAGATAGGTCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTGAGTTACTAT-G
470850 TT-AGTG
120 TTCAGTG
* * * * * * *
470856 AGATATGTCAGATAGTGAGTTACTATGGTTAGTGAGATAGGACAGATGGTTA-TTACCTATAGTT
1 AG--A--T---A-A--GAGTTACTATAGTCAGTGAGATAGGTCAGATAGTGAGTTA-CTATGGTC
** * * * * * * * * * *
470920 AGTGAGATAGCACAGATGGTTAGTTCCTA----CAGTGAGATAGGTCAGGTAGTGAGTTTCTAAG
55 AGTGAGATAGGTCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTGAGTTACTATG
*
470981 GTCAGTG
120 TTCAGTG
* * * *
470988 AGATATGTCAGATTGTGAGTTACTATGGTTAGTGAGATATGTCAGATAGTGAGTTACTATGGTTA
1 AG--A--T-A-A----GAGTTACTATAGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCA
* * * * * * * * *
471053 GTGAGATAAGACAGATGGTTA-TTACCTATAGTTAGTGAGATAGCACAGATGGTTAGTTCCTATA
56 GTGAGATAGGTCAGATAGTGAGTTA-CTATGGTTAGTGAGAAAGGACAGATGGTGAGTTACTAT-
471117 G-TCAGTG
119 GTTCAGTG
* *
471124 AGATAGCACAGATAGTGAGTTACTATGGTCAGTGAGATAGGTCAGATAGTGAGTTTCTATGGTCA
1 AGAT-------A-A--GAGTTACTATAGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCA
* * * * * * * *
471189 GTGAGATAGGTCAGGTAGTGAGTTTCTAAGGTCAGTGAGATATGTCAGATTGTGAGTTACTATAG
56 GTGAGATAGGTCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTGAGTTACTAT-G
471254 -TCAGTG
120 TTCAGTG
471260 AGATA
1 AGATA
471265 TGTCAGATTG
Statistics
Matches: 536, Mismatches: 91, Indels: 80
0.76 0.13 0.11
Matches are distributed among these distances:
122 3 0.01
123 98 0.18
124 5 0.01
125 1 0.00
126 1 0.00
127 2 0.00
129 2 0.00
130 3 0.01
131 4 0.01
132 108 0.20
133 3 0.01
134 1 0.00
135 3 0.01
136 285 0.53
137 5 0.01
138 3 0.01
140 7 0.01
142 2 0.00
ACGTcount: A:0.30, C:0.09, G:0.30, T:0.31
Consensus pattern (126 bp):
AGATAAGAGTTACTATAGTCAGTGAGATAGGTCAGATAGTGAGTTACTATGGTCAGTGAGATAGG
TCAGATAGTGAGTTACTATGGTTAGTGAGAAAGGACAGATGGTGAGTTACTATGTTCAGTG
Found at i:470888 original size:17 final size:17
Alignment explanation
Indices: 470836--470891 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
470826 ATGTCAGATT
*
470836 GTGAGTTTCTATGGTTA
1 GTGAGTTACTATGGTTA
* * * *
470853 GTGAGATA-TGTCAGATA
1 GTGAGTTACTAT-GGTTA
470870 GTGAGTTACTATGGTTA
1 GTGAGTTACTATGGTTA
470887 GTGAG
1 GTGAG
470892 ATAGGACAGA
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
16 2 0.07
17 24 0.86
18 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.38
Consensus pattern (17 bp):
GTGAGTTACTATGGTTA
Found at i:471022 original size:17 final size:17
Alignment explanation
Indices: 471002--471057 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
470992 ATGTCAGATT
471002 GTGAGTTACTATGGTTA
1 GTGAGTTACTATGGTTA
* * * *
471019 GTGAGATA-TGTCAGATA
1 GTGAGTTACTAT-GGTTA
471036 GTGAGTTACTATGGTTA
1 GTGAGTTACTATGGTTA
471053 GTGAG
1 GTGAG
471058 ATAAGACAGA
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.27, C:0.05, G:0.32, T:0.36
Consensus pattern (17 bp):
GTGAGTTACTATGGTTA
Found at i:471243 original size:17 final size:17
Alignment explanation
Indices: 471223--471278 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
471213 TCTAAGGTCA
471223 GTGAGATATGTCAGATT
1 GTGAGATATGTCAGATT
* * *
471240 GTGAGTTACTAT-AG-TCA
1 GTGAGATA-TGTCAGAT-T
471257 GTGAGATATGTCAGATT
1 GTGAGATATGTCAGATT
471274 GTGAG
1 GTGAG
471279 TTACTATGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
16 3 0.10
17 23 0.79
18 3 0.10
ACGTcount: A:0.29, C:0.07, G:0.30, T:0.34
Consensus pattern (17 bp):
GTGAGATATGTCAGATT
Found at i:476048 original size:11 final size:11
Alignment explanation
Indices: 476017--476076 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
476007 GGAGCAGAGA
476017 GCACAAGTGAAC
1 GCAC-AGTGAAC
* *
476029 ACACGGTGAAC
1 GCACAGTGAAC
*
476040 GCACTGTGAGA-
1 GCACAGTGA-AC
*
476051 GCACAGTGAAT
1 GCACAGTGAAC
*
476062 GCACAGTGAAT
1 GCACAGTGAAC
476073 GCAC
1 GCAC
476077 GAAAAAAGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
10 1 0.02
11 36 0.88
12 4 0.10
ACGTcount: A:0.35, C:0.23, G:0.28, T:0.13
Consensus pattern (11 bp):
GCACAGTGAAC
Found at i:476071 original size:33 final size:34
Alignment explanation
Indices: 476013--476076 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 34
476003 GAGCGGAGCA
*
476013 GAGAGCACAAGTGAACACACGGTGAACGCACTGT
1 GAGAGCACAAGTGAACACACAGTGAACGCACTGT
** *
476047 GAGAGCAC-AGTGAATGCACAGTGAATGCAC
1 GAGAGCACAAGTGAACACACAGTGAACGCAC
476077 GAAAAAAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 18 0.69
34 8 0.31
ACGTcount: A:0.36, C:0.22, G:0.30, T:0.12
Consensus pattern (34 bp):
GAGAGCACAAGTGAACACACAGTGAACGCACTGT
Found at i:525392 original size:2 final size:2
Alignment explanation
Indices: 525385--525424 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
525375 CAAAGATATT
525385 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
525425 ATTGACGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:528547 original size:2 final size:2
Alignment explanation
Indices: 528540--528578 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
528530 GTGGGTACAT
*
528540 TC TC TC TC TC TC TC TC TT TC TC TC -C TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
528579 CTAGAGAGGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:533429 original size:17 final size:17
Alignment explanation
Indices: 533407--533442 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
533397 ACCTTAAATA
533407 TATCAACATTATATATG
1 TATCAACATTATATATG
533424 TATCAACATTATATATG
1 TATCAACATTATATATG
533441 TA
1 TA
533443 AAAAATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.06, T:0.42
Consensus pattern (17 bp):
TATCAACATTATATATG
Found at i:538990 original size:22 final size:22
Alignment explanation
Indices: 538964--539007 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
538954 GGAAGACTGA
*
538964 ATTCTTCCTTGACAACAGACTT
1 ATTCTTCCATGACAACAGACTT
538986 ATTCTTCCATGACAACAGACTT
1 ATTCTTCCATGACAACAGACTT
539008 TATAATGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (22 bp):
ATTCTTCCATGACAACAGACTT
Found at i:541699 original size:145 final size:146
Alignment explanation
Indices: 541433--541851 Score: 540
Period size: 146 Copynumber: 2.9 Consensus size: 146
541423 TTTTAAACAA
* * * * * * *
541433 TGACCTTGAACTT-CCTCAATTGGCCTTGGGTCAAGGTCATGACACACTCTCAGGTTATAAGTAA
1 TGACCTTGACCTTGCC-CAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAA
* * * * * * *
541497 TC-TTGATGTGAATTAAGATCTTCCAATATTTGTTCATT-AGAAAGATATAGACTGGACATGAAT
65 TCTTTG-TGTGAACTAAGAACTTCCAATGTTT-CTCCTTAAGAAAGATATGGACCGGACATGAAT
* *
541560 TTTGCACT-TTTGTGCCAG
128 TTTGAACTGTTTCTGCCAG
* *
541578 TGACCTTGGCCTTGCCCAAATGACCTTGGGTCAAGGTCATGACATACCCTTAGGTCATAAGCAAT
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
*
541643 CTTTGTGTGAACTGAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACATGAATTTT
66 CTTTGTGTGAACTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACATGAATTTT
541708 GAACTGTTTCTGCCAG
131 GAACTGTTTCTGCCAG
* * * *
541724 TGACCTTGACCTTGTCCGAATGACCTTGGGTCAAAGTCATGACACACCCTTAGGTCATAAGCAAA
1 TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
* * * *
541789 CTTTGTGTGAAGTAAGAACTTCCAATGTTTCCCCATAAGAAAGATATGGACCGGACACGAATT
66 CTTTGTGTGAACTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACATGAATT
541852 GAACAGACAG
Statistics
Matches: 240, Mismatches: 30, Indels: 7
0.87 0.11 0.03
Matches are distributed among these distances:
144 4 0.02
145 105 0.44
146 131 0.55
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (146 bp):
TGACCTTGACCTTGCCCAAATGACCTTGGGTCAAGGTCATGACACACCCTTAGGTCATAAGCAAT
CTTTGTGTGAACTAAGAACTTCCAATGTTTCTCCTTAAGAAAGATATGGACCGGACATGAATTTT
GAACTGTTTCTGCCAG
Found at i:547232 original size:2 final size:2
Alignment explanation
Indices: 547225--547260 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
547215 AGCGATTATT
*
547225 TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
547261 AAATGTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:549138 original size:2 final size:2
Alignment explanation
Indices: 549127--549177 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
549117 TCAGTGCAAT
549127 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
549168 AG AG AG AG AG
1 AG AG AG AG AG
549178 GAAATCCATA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:552289 original size:33 final size:32
Alignment explanation
Indices: 552211--552289 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
552201 TTTTGATGCA
* * *
552211 GCGAAATATTGAACCCGGGTTCAATATATTAT
1 GCGATATATTGAACCCGGGTTCAAAATATGAT
*
552243 GCGATAT-TATGAACCCGGGTTCAAAATATCGCT
1 GCGATATAT-TGAACCCGGGTTCAAAATAT-GAT
552276 GCGATATATTGAAC
1 GCGATATATTGAAC
552290 TCCCCCATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
31 1 0.03
32 25 0.62
33 13 0.32
34 1 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (32 bp):
GCGATATATTGAACCCGGGTTCAAAATATGAT
Found at i:552410 original size:65 final size:65
Alignment explanation
Indices: 552313--553804 Score: 1115
Period size: 65 Copynumber: 22.6 Consensus size: 65
552303 ATTGAACCCC
* *
552313 GGGTTCAAAATATTATGGCAGCGATATTTTGAAACCCCCTCTAATTTTCATTGCTATTGGAGAGG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
* * * * * * *
552378 GGGTTCAAAATATTATGGCTGCGATATATTGAA-CTCCCTACT-GTTTCCAATTCCCT-TTAGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTAATTTTC-ATT-GCTATTGGAG
552440 AGG
63 AGG
* * * * * * ** *
552443 GGGGTAAAAATATCAGGGTCGCGATATATTGAACCCCTATCCT-A-TTTCAAATTCCCT-TTGGA
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTAATTTTC--ATT-GCTATTGGA
552505 GAGG
62 GAGG
* * * *
552509 GGGTTCAAAATATTCTAGCCACGATATTTTGAACCCCCCTCTAATTTTCAGTGCTATGGCTACTG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCA----T-T-GCTATTG
552574 GAGAGG
60 GAGAGG
* * * * * *
552580 GAGTTCAAAATATTATGGCCCCAAAATTTTGACACCCCCCCCCCTATTTTTCATTGCTATTGGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGA-A--CCCCCCTCTAATTTTCATTGCTATTGGAG
552645 AGG
63 AGG
* * * * * ** * * * *
552648 GGGTTCATAATATTATGGCTGCGATATATTG-ATCCCCTTACCCATTTTAAATTCCCATTGGAGT
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTAATTTT-CATTGCTATTGGAGA
552712 GG
64 GG
* * *
552714 GGGTTCAAAATATTATGGCCGCGGT-TTTTGAACCCCCCTCTATTTTTCATTGCTTTTGGAGAGG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
* * *
552778 GGGTTCAAAATATTATGGGCGTGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
* * * * * * * *
552843 GGGTTCCAAATATAATGACTGCGAT-TTTTGAACCCCCTTCCT-ACTTCCAATTCCCT-TTGGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTAATTTTC-ATT-GCTATTGGAG
552905 AGG
63 AGG
* *
552908 GGGTTCAAAATATTATGGCTGCGATATTTTGAA-CCCCCTCTATTTTTCATTGCCT-TTGGAGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTG-CTATTGGAGA-
552971 GGGGTTCACAATG
64 ---G--------G
* *
552984 GGGTTCAAAATATTATGGCCGCGATATTTTGAA-CCCCCTTTATTTTTCATTGCCT-TTGGAGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTG-CTATTGGAGAG
553047 G
65 G
* * * * *
553048 GGGTTCACAATGTTATGGCCACAATATTTTGAACCCCCCTCTTATTTTCATTGCTATTGGAGA-G
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
** * * ** * * *
553112 GGG------ATATTATGGTTGTGATATATTGAACCCCTATC-ATATTTCCAATTCCCT-TCGGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTA-ATTTTC-ATT-GCTATTGGAG
553169 AGG
63 AGG
* * * * *
553172 GAGTTTAAAATATTATGGCCCCAATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
* * *
553237 GGGTTCAAAATATTATGTCCGCGATATTTTGAACCCCCCTCTATTTTTTCATTGCTACTGGAGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTA-ATTTTCATTGCTATTGGAGAG
*
553302 A
65 G
* * * * * * *
553303 GGGTTCAAAATATTATGGCTGCGATATATTGAA-CTCCCTACT-GTTTCCAATTCCCT-TTAGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTAATTTTC-ATT-GCTATTGGAG
553365 AGG
63 AGG
* * * * * * *
553368 GGGCTCAAAATATTATGGCTGCAATATATTG-AGCCCCCTACCT-ATTTCCAATTCCCT-TTGGA
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT--CTAATTTTC-ATT-GCTATTGGA
553430 GAGG
62 GAGG
* * * *
553434 GGGTTCAAAATATTCTAGCCACGATATTTTGAACCCCCCTCTAATTTTCAGTGCTATGGCTAATG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCA----T-T-GCTATTG
553499 GAGAGG
60 GAGAGG
* * * * * *
553505 GAGTTCAAAATATTATGGCCCCAAAATTTTGACACCCCCCCCCCTATTTTTCATTGCTATTGGAG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGA-A--CCCCCCTCTAATTTTCATTGCTATTGGAG
553570 AGG
63 AGG
* * * * * ** * * * *
553573 GGGTTCATAATATTATGGCTGCGATATATTG-ATCCCCTTACCCATTTTAAATTCCCATTGGAGT
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTAATTTT-CATTGCTATTGGAGA
553637 GG
64 GG
* * *
553639 GGGTTCAAAATATTATGGCCGCGGT-TTTTGAACCCCCCTCTATTTTTCATTGCTTTTGGAGAGG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
* * *
553703 GGGTTCAAAATATTATGGGCGTGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAGG
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
* * * *
553768 GGGTTCCAAATATAATGACTGCGAT-TTTTGAACCCCC
1 GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCC
553805 TTCCTACTTC
Statistics
Matches: 1137, Mismatches: 217, Indels: 147
0.76 0.14 0.10
Matches are distributed among these distances:
58 28 0.02
59 9 0.01
60 5 0.00
64 170 0.15
65 386 0.34
66 280 0.25
67 12 0.01
68 73 0.06
69 4 0.00
70 8 0.01
71 68 0.06
72 3 0.00
74 30 0.03
76 61 0.05
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (65 bp):
GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAATTTTCATTGCTATTGGAGAGG
Found at i:553033 original size:76 final size:76
Alignment explanation
Indices: 552907--553059 Score: 288
Period size: 76 Copynumber: 2.0 Consensus size: 76
552897 CTTTGGAGAG
*
552907 GGGGTTCAAAATATTATGGCTGCGATATTTTGAACCCCCTCTATTTTTCATTGCCTTTGGAGAGG
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCTCTATTTTTCATTGCCTTTGGAGAGG
552972 GGGTTCACAAT
66 GGGTTCACAAT
*
552983 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCTTTATTTTTCATTGCCTTTGGAGAGG
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCTCTATTTTTCATTGCCTTTGGAGAGG
553048 GGGTTCACAAT
66 GGGTTCACAAT
553059 G
1 G
553060 TTATGGCCAC
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 75 1.00
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.35
Consensus pattern (76 bp):
GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCTCTATTTTTCATTGCCTTTGGAGAGG
GGGTTCACAAT
Found at i:553045 original size:270 final size:265
Alignment explanation
Indices: 552313--553769 Score: 1095
Period size: 270 Copynumber: 5.5 Consensus size: 265
552303 ATTGAACCCC
* * * *
552313 GGGTTCAAAATATTATGGCAGCGATATTTTGAAACCCCC-T-CTAATTTTC-ATT-GCTATTGGA
1 GGGTTCAAAATATTATGGCTGCGATATATTG-AACCCCCTTCCT-ATTTCCAATTCCCT-TTGGA
* * * * * *
552374 GAGGGGGTTCAAAATATTATGGCTGCGATATATTGAA-CTCCCTACT-GTTTCCAATTCCCT-TT
63 GAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTATTTTTC-ATT-GCTATT
* * * * * * ** ***
552436 --AGAGAGG--GGGG-TAAAAATATCAGGGTCGCGATATATTGAACCCCTATCCTATTTCAAATT
125 GGAGAGGGGAAGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTATTTTTCATT
* * * ** *
552496 CCCT-TTGGAGAGGGGGTTCAAAATATTCTAGCCACGATATTTTGAACCCCCCTCTAATTTTCAG
189 -GCTATTGGAGAGGGGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCCTCT--TTTT---
** *
552560 TGCTATGGCTACTGGAGAGG
248 T-C-ATTCCTATTGGAGAGG
* ** * * * ** * *
552580 GAGTTCAAAATATTATGGCCCCAAAATTTTGACACCCCCCCCCCTATTTTTC-ATT-GCTATTGG
1 GGGTTCAAAATATTATGGCTGCGATATATTGA-A-CCCCCTTCCTA-TTTCCAATTCCCT-TTGG
* * * * ** * *
552643 AGAGGGGGTTCATAATATTATGGCTGCGATATATTGATCCCCTTACC-C-ATTTTAAATTCCCAT
62 AGAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCC---CCTCTATTTTTCATTGCTAT
* *
552706 T-G-GA-GTG--GGGGTTCAAAATATTATGGCCGCGGT-TTTTGAACCCCCCTCTATTTTTCATT
124 TGGAGAGGGGAAGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATT
* * *
552765 GCTTTTGGAGAGGGGGTTCAAAATATTATGGGC-GTGATATTTTGAACCCCCCTCTATTTTTCAT
189 GCTATTGGAGAGGGGGTTCAAAATATTAT-GGCTGCGATATATTGAACCCCCCTCT-TTTTTCAT
*
552829 TGCTATTGGAGAGG
252 TCCTATTGGAGAGG
* * * * *
552843 GGGTTCCAAATATAATGACTGCGAT-TTTTGAACCCCCTTCCTACTTCCAATTCCCTTTGGAGAG
1 GGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCTTCCTATTTCCAATTCCCTTTGGAGAG
*
552907 GGGGTTCAAAATATTATGGCTGCGATATTTTGAA-CCCCCTCTATTTTTCATTGCCT-TTGGAGA
66 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTG-CTATTGGAGA
*
552970 GGGGGTTCACAATGGGGTTCAAAATATTATGGCCGCGATATTTTGAA-CCCCCTTTATTTTTCAT
130 -GGGG-----AA-GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCAT
* * ** * *
553034 TGCCT-TTGGAGAGGGGGTTCACAATGTTATGGCCACAATATTTTGAACCCCCCTCTTATTTTCA
188 TG-CTATTGGAGAGGGGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCCTCTT-TTTTCA
*
553098 TTGCTATTGGAGA-G
251 TTCCTATTGGAGAGG
* * * *
553112 GGG------ATATTATGGTTGTGATATATTGAA-CCCCTATCATATTTCCAATTCCCTTCGGAGA
1 GGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCT-TCCTATTTCCAATTCCCTTTGGAGA
* * * *
553170 GGGAGTTTAAAATATTATGGCCCCAATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGA
65 GGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGA
* *
553235 ---G--GGGGTTCAAAATATTATGTCCGCGATATTTTGAACCCCCCTCTATTTTTTCATTGCTAC
130 GGGGAAGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTA-TTTTTCATTGCTAT
* * * *
553295 TGGAGAGAGGGTTCAAAATATTATGGCTGCGATATATTGAA-CTCCCTACTGTTTCCAATTCCCT
194 TGGAGAGGGGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCCT-CTTTTTTC-ATT-CCT
*
553359 -TTAGAGAGG
256 ATTGGAGAGG
* * * *
553368 GGGCTCAAAATATTATGGCTGCAATATATTGAGCCCCCTACCTATTTCCAATTCCCTTTGGAGAG
1 GGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCTTCCTATTTCCAATTCCCTTTGGAGAG
* * * * * ** *
553433 GGGGTTCAAAATATTCTAGCCACGATATTTTGAACCCCCCTCTAATTTTCAGTGCTA-TGGCTAA
66 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAG
* * * * *
553497 TGGAGAGGGAGTTCAAAATATTATGGCCCCAAAATTTTGACACCCCCCCCCCTATTTTTCATTGC
131 GGGA-AGGG-GTTCAAAATATTATGGCCGCGATATTTTGA-A--CCCCCCTCTATTTTTCATTGC
* * * **
553562 TATTGGAGAGGGGGTTCATAATATTATGGCTGCGATATATTGATCCCCTTACC-CATTTTAAATT
191 TATTGGAGAGGGGGTTCAAAATATTATGGCTGCGATATATTGAACCCC---CCTCTTTTTTCATT
* *
553626 CCCATTGGAGTGG
253 CCTATTGGAGAGG
* * * * * * *
553639 GGGTTCAAAATATTATGGCCGCGGT-TTTTGAACCCCCCT-CTATTTTTC-ATTGCTTTTGGAGA
1 GGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCTTCCTA-TTTCCAATTCCCTTTGGAGA
* *
553701 GGGGGTTCAAAATATTATGGGCGTGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGA
65 GGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGA
553766 GGGG
130 GGGG
553770 GTTCCAAATA
Statistics
Matches: 974, Mismatches: 145, Indels: 139
0.77 0.12 0.11
Matches are distributed among these distances:
253 33 0.03
254 19 0.02
255 55 0.06
256 8 0.01
257 1 0.00
258 10 0.01
259 8 0.01
260 53 0.05
261 8 0.01
262 100 0.10
263 53 0.05
264 62 0.06
265 27 0.03
266 1 0.00
267 30 0.03
268 38 0.04
269 129 0.13
270 251 0.26
271 76 0.08
272 8 0.01
274 4 0.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (265 bp):
GGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCTTCCTATTTCCAATTCCCTTTGGAGAG
GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAG
GGGAAGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTG
GAGAGGGGGTTCAAAATATTATGGCTGCGATATATTGAACCCCCCTCTTTTTTCATTCCTATTGG
AGAGG
Found at i:553335 original size:131 final size:129
Alignment explanation
Indices: 552983--553804 Score: 710
Period size: 131 Copynumber: 6.3 Consensus size: 129
552973 GGTTCACAAT
*
552983 GGGGTTCAAAATATTATGGCCGCGATATTTTGAA-CCCCCTTTATTTTTCATTGCCTTTGGAGAG
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTG-CTTTGGAGAG
* * * *
553047 GGGGTTCACAATGTTATGGCCACAATATTTTGAACCCCCCTCT-TATTTTCATTGCTATTGGAGA
65 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAT-TTTTCATTGCTATTGGAGA
553111 -
129 G
** * * ** * * *
553111 GGGG------ATATTATGGTTGTGATATATTGAACCCCTATC-ATATTTCCAATTCCCTTCGGAG
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTAT-TTTTC-ATT-GCTTTGGAG
* * * *
553169 AGGGAGTTTAAAATATTATGGCCCCAATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAG
63 AGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAG
553234 AG
128 AG
* *
553236 GGGGTTCAAAATATTATGTCCGCGATATTTTGAACCCCCCTCTATTTTTTCATTGCTACTGGAGA
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTA-TTTTTCATTGCT-TTGGAGA
* * * * * * * *
553301 GAGGGTTCAAAATATTATGGCTGCGATATATTGAA-CTCCCTACT-GTTTCCAATTCCCT-TTAG
64 GGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT-CTATTTTTC-ATT-GCTATTGG
553363 AGAG
126 AGAG
* * * * * * *
553367 GGGGCTCAAAATATTATGGCTGCAATATATTG-AGCCCCCTACCTA-TTTCCAATTCCCTTTGGA
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCT--CTATTTTTC-ATT-GCTTTGGA
* * * *
553430 GAGGGGGTTCAAAATATTCTAGCCACGATATTTTGAACCCCCCTCTAATTTTCAGTGCTATGGCT
62 GAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCT-ATTTT---T-C-ATTGCT
*
553495 AATGGAGAG
121 ATTGGAGAG
* * * * *
553504 GGAGTTCAAAATATTATGGCCCCAAAATTTTGACACCCCCCCCCCTATTTTTCATTGCTATTGGA
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGA-A--CCCCCCTCTATTTTTCATTGCT-TTGGA
* * * * ** * *
553569 GAGGGGGTTCATAATATTATGGCTGCGATATATTGATCCCCTTACC-C-ATTTTAAATTCCCATT
62 GAGGGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCC---CCTCTATTTTTCATTGCTATT
*
553632 GGAGTG
124 GGAGAG
*
553638 GGGGTTCAAAATATTATGGCCGCGGT-TTTTGAACCCCCCTCTATTTTTCATTGCTTTTGGAGAG
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGC-TTTGGAGAG
* *
553702 GGGGTTCAAAATATTATGGGCGTGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAG
65 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAG
* * * *
553767 GGGGTTCCAAATATAATGACTGCGAT-TTTTGAACCCCC
1 GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCC
553805 TTCCTACTTC
Statistics
Matches: 545, Mismatches: 107, Indels: 83
0.74 0.15 0.11
Matches are distributed among these distances:
122 22 0.04
123 8 0.01
124 69 0.13
125 5 0.01
127 2 0.00
128 5 0.01
129 50 0.09
130 82 0.15
131 141 0.26
132 18 0.03
133 10 0.02
134 31 0.06
136 2 0.00
137 35 0.06
138 2 0.00
139 51 0.09
140 4 0.01
141 6 0.01
142 2 0.00
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (129 bp):
GGGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTTTGGAGAGG
GGGTTCAAAATATTATGGCCGCGATATTTTGAACCCCCCTCTATTTTTCATTGCTATTGGAGAG
Found at i:553643 original size:205 final size:194
Alignment explanation
Indices: 553227--553805 Score: 565
Period size: 205 Copynumber: 2.9 Consensus size: 194
553217 TTTCATTGCT
* * *
553227 ATTGGAGAGGGGGTTCAAAATATTAT-GTCCGCGATATTTTGAACCCCCCTCTATTTTTTCATTG
1 ATTGGAGAGGGGGTTCAAAATATTATAG-CCACGAT-TTTTGAACCCCCCTCTA-ATTTTCAGTG
** ** * * * * ** * *
553291 CTACTGGAGAGAGG-GTTCAAAATATTATGGCTGCGATATATTGAACTCCCTACT-GTTTCCAAT
63 CTTTTGGAGAG-GGAGTTCAAAATATTATGGCCCCAAAATTTTGAACCCCCCCCTATTTTTC-AT
* * * * * *
553354 TCCCT-TTAGAGAGGGGGCTCAAAATATTATGGCTGCAATATATTGAGCCCCCTACCTATTTCCA
126 T-GCTATTGGAGAGGGGGTTC-AAATATTATGGCTGCGATATATTGAGCCCCCTACCCATTTCAA
553418 ATTCCC
189 ATTCCC
* *
553424 TTTGGAGAGGGGGTTCAAAATATTCTAGCCACGATATTTTGAACCCCCCTCTAATTTTCAGTGCT
1 ATTGGAGAGGGGGTTCAAAATATTATAGCCACGAT-TTTTGAACCCCCCTCTAATTTTCAGTGCT
553489 ATGGCTAATGGAGAGGGAGTTCAAAATATTATGGCCCCAAAATTTTGACACCCCCCCCCCTATTT
65 -T---T--TGGAGAGGGAGTTCAAAATATTATGGCCCCAAAATTTTGA-A--CCCCCCCCTATTT
* *
553554 TTCATTGCTATTGGAGAGGGGGTTCATAATATTATGGCTGCGATATATTGATCCCCTTACCCATT
121 TTCATTGCTATTGGAGAGGGGGTTCA-AATATTATGGCTGCGATATATTGAGCCCCCTACCCATT
*
553619 TTAAATTCCC
185 TCAAATTCCC
* * * * * *
553629 ATTGGAGTGGGGGTTCAAAATATTATGGCCGCGGTTTTTGAACCCCCCTCTATTTTTCATTGCTT
1 ATTGGAGAGGGGGTTCAAAATATTATAGCCACGATTTTTGAACCCCCCTCTAATTTTCAGTGCTT
* * *** * *
553694 TTGGAGAGGGGGTTCAAAATATTATGGGCGTGATATTTTGAACCCCCCTCTATTTTTCATTGCTA
66 TTGGAGAGGGAGTTCAAAATATTATGGCCCCAAAATTTTGAACCCCCCCCTATTTTTCATTGCTA
* * * *
553759 TTGGAGAGGGGGTTCCAAATATAATGACTGCGAT-TTTTGAACCCCCT
131 TTGGAGAGGGGGTT-CAAATATTATGGCTGCGATATATTGAGCCCCCT
553806 TCCTACTTCC
Statistics
Matches: 321, Mismatches: 46, Indels: 33
0.80 0.12 0.08
Matches are distributed among these distances:
194 10 0.03
195 51 0.16
196 12 0.04
197 49 0.15
198 35 0.11
200 1 0.00
201 2 0.01
202 32 0.10
203 2 0.01
204 30 0.09
205 93 0.29
206 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (194 bp):
ATTGGAGAGGGGGTTCAAAATATTATAGCCACGATTTTTGAACCCCCCTCTAATTTTCAGTGCTT
TTGGAGAGGGAGTTCAAAATATTATGGCCCCAAAATTTTGAACCCCCCCCTATTTTTCATTGCTA
TTGGAGAGGGGGTTCAAATATTATGGCTGCGATATATTGAGCCCCCTACCCATTTCAAATTCCC
Found at i:553949 original size:66 final size:65
Alignment explanation
Indices: 553841--553995 Score: 172
Period size: 65 Copynumber: 2.4 Consensus size: 65
553831 AAAAAACGCG
* * * * * *
553841 GCCATAATATTTTGAACCCCCTCTCCTATGGGAATTGGAAATA-AGTAGGGGTTTCAATATAT-A
1 GCCATAATATTTTGAACCCCCTCTCCAATAGCAATTGAAAATAGAG--GGGGGTTCAAAATATCA
553904 GCA
64 -CA
* *
553907 GCCATAATATTTTGAATCCCCTCTCCAATAGCAA-TGAAAAATAGAGGGGGGTTCAAAATTTCAC
1 GCCATAATATTTTGAACCCCCTCTCCAATAGCAATTG-AAAATAGAGGGGGGTTCAAAATATCAC
553971 A
65 A
*
553972 GCCATAATACTTTGAACCCCCTCT
1 GCCATAATATTTTGAACCCCCTCT
553996 AAACCTGGGG
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
65 38 0.50
66 36 0.47
67 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (65 bp):
GCCATAATATTTTGAACCCCCTCTCCAATAGCAATTGAAAATAGAGGGGGGTTCAAAATATCACA
Found at i:559946 original size:31 final size:31
Alignment explanation
Indices: 559908--559971 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
559898 ACCAGTGTGC
559908 AATTACAACTTGTGTTGCTGTACATGTTCAG
1 AATTACAACTTGTGTTGCTGTACATGTTCAG
559939 AATTACAACTTGTGTTGCTGTACATGTTCAG
1 AATTACAACTTGTGTTGCTGTACATGTTCAG
559970 AA
1 AA
559972 AACTATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (31 bp):
AATTACAACTTGTGTTGCTGTACATGTTCAG
Found at i:560958 original size:33 final size:31
Alignment explanation
Indices: 560880--560946 Score: 127
Period size: 31 Copynumber: 2.2 Consensus size: 31
560870 ACAATGGTAA
560880 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
560911 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
1 CATTCTCAGCAGTTATCTCTCTTTGCCCATT
560942 C-TTCT
1 CATTCT
560947 TATGCATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.11
31 32 0.89
ACGTcount: A:0.15, C:0.33, G:0.09, T:0.43
Consensus pattern (31 bp):
CATTCTCAGCAGTTATCTCTCTTTGCCCATT
Found at i:561147 original size:16 final size:16
Alignment explanation
Indices: 561126--561163 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
561116 ACGGAAGAGT
*
561126 GACAGACGGACGGACG
1 GACAGAAGGACGGACG
561142 GACAGAAGGACGGACG
1 GACAGAAGGACGGACG
561158 GACAGA
1 GACAGA
561164 GTGATTACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.37, C:0.21, G:0.42, T:0.00
Consensus pattern (16 bp):
GACAGAAGGACGGACG
Found at i:564507 original size:2 final size:2
Alignment explanation
Indices: 564500--564536 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
564490 CAATCAATCA
564500 AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
564537 TGATTGTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:564525 original size:17 final size:17
Alignment explanation
Indices: 564503--564536 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
564493 TCAATCAAGA
564503 GAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAG
564520 GAGAGAGAGAGAGAGAG
1 GAGAGAGAGAGAGAGAG
564537 TGATTGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (17 bp):
GAGAGAGAGAGAGAGAG
Found at i:570815 original size:161 final size:161
Alignment explanation
Indices: 570550--571374 Score: 1094
Period size: 161 Copynumber: 5.1 Consensus size: 161
570540 GGTCCACCAA
* *
570550 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGCTTA
* *
570615 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
* *
570680 CCCTTGGACGTAGAAAAATTCTAGTTTTTTG
131 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
* *
570711 CAGTTTCCGTTCATTTTCTTCGCAGAGGATAAACATATTGAAAGGAAATTTGGTATACAGGCTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGCTTA
* *
570776 TCATGATTATATCTAAGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
* * * * *
570841 CCGTTGGACTTAACAAAAATTCTAGTTTTTTG
131 CCCTTGGACGT-AGAAAAATTCCAGTTATTTG
*
570873 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGCTTA
* *
570938 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
**
571003 CGTTTGGACGTAGAAAAATTCCAGTTATTTG
131 CCCTTGGACGTAGAAAAATTCCAGTTATTTG
* * *
571034 CAGTTTCCGCTCATGTTCTTAGCAGAGGATGAACATATTGAAATGAAATTTGGTATACA-GCTTT
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGC-TT
* *
571098 ATCATGATAATATCTAGGTCAAGTTCGATATTGGGTACGATTGAGCAATTTTCGACAGAGTTAT-
65 ATCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATG
* *
571162 GCCTCTTGGACATAGAAAAACTCCAGTTATTTG
130 GCC-CTTGGACGTAGAAAAATTCCAGTTATTTG
* * ** * *
571195 CAGTTTCTGCTCATTTTCTTCGCAGAGGGTGCACATATGGATAATTTATGAAATTAT-TTAT-CA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTG--AA---ATGAAATT-TGGTATACA
* ** *
571258 GTC-TA--A--ATAATATCTAGGTCAAGTTCGAT-TTCGGGTATGATAGAGCAATTTTCGACAGA
60 GGCTTATCATGATAATATCTAGGTCAAGTTCGATATT-GGGTACAATCGAGCAATTTTCGACAGA
** * *
571317 GTTATGGCCCTTTAACTTAGAAAAATACCAGTTATTTG
124 GTTATGGCCCTTGGACGTAGAAAAATTCCAGTTATTTG
* * *
571355 CAGTATACGTTCATTTTCTT
1 CAGTTTCCGCTCATTTTCTT
571375 TGTGGATGTT
Statistics
Matches: 599, Mismatches: 53, Indels: 25
0.88 0.08 0.04
Matches are distributed among these distances:
159 2 0.00
160 96 0.16
161 331 0.55
162 151 0.25
163 2 0.00
164 2 0.00
165 2 0.00
166 12 0.02
167 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (161 bp):
CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGCTTA
TCATGATAATATCTAGGTCAAGTTCGATATTGGGTACAATCGAGCAATTTTCGACAGAGTTATGG
CCCTTGGACGTAGAAAAATTCCAGTTATTTG
Found at i:571146 original size:323 final size:322
Alignment explanation
Indices: 570550--571358 Score: 1136
Period size: 323 Copynumber: 2.5 Consensus size: 322
570540 GGTCCACCAA
570550 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* *
570615 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACAATCGAGCAATTTTCAACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
* * * * * *
570680 CCCTTGGACGTAGAAAAATTCTAGTTTTTTGCAGTTTCCGTTCATTTTCTTCGCAGAGGATAAAC
131 CCTTTGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATGTTCTTAGCAGAGGATAAAC
*
570745 ATATTGAAAGGAAATTTGGTATACAGGCTTATCATGATTATATCTAAGTCAAGTTCGATATTGGG
196 ATATTGAAAGGAAATTTGGTATACAGGCTTATCATGATAATATCTAAGTCAAGTTCGATATTGGG
* * * * *
570810 TACAATCGAGCAATTTTCGACAGAGTTATGGCC-GTTGGACTTAACAAAAATTCTAGTTTTTTG
261 TACAATCGAGCAATTTTCGACAGAGTTAT-GCCTCTTGGACAT-ACAAAAACTCCAGTTATTTG
*
570873 CAGTTTCCGCTCATTTTCTTCGCAGAGGATAAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
570938 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
66 TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
* *
571003 CGTTTGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATGTTCTTAGCAGAGGATGAAC
131 CCTTTGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATGTTCTTAGCAGAGGATAAAC
* *
571068 ATATTGAAATGAAATTTGGTATACA-GCTTTATCATGATAATATCTAGGTCAAGTTCGATATTGG
196 ATATTGAAAGGAAATTTGGTATACAGGC-TTATCATGATAATATCTAAGTCAAGTTCGATATTGG
* * *
571132 GTACGATTGAGCAATTTTCGACAGAGTTATGCCTCTTGGACATAGAAAAACTCCAGTTATTTG
260 GTACAATCGAGCAATTTTCGACAGAGTTATGCCTCTTGGACATACAAAAACTCCAGTTATTTG
* * * * *
571195 CAGTTTCTGCTCATTTTCTTCGCAGAGGGTGCACATATGGATAATTTATGAAATTAT-TTAT-CA
1 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTG--AA---ATGAAATT-TGGTATACA
* * * *
571258 -GTCTA--A--ATAATATCTAGGTCAAGTTCGAT-TTCGGGTATGATAGAGCAATTTTCGACAGA
60 GGTTTATCATGATAATATCTAGGTCAAGTTTGATATT-GGGTACGATCGAGCAATTTTCGACAGA
* * *
571317 GTTATGGCCCTTT-AACTTAGAAAAATACCAGTTATTTGCAGT
124 GTTATGG-CCTTTGGACGTAGAAAAATTCCAGTTATTTGCAGT
571359 ATACGTTCAT
Statistics
Matches: 440, Mismatches: 36, Indels: 22
0.88 0.07 0.04
Matches are distributed among these distances:
320 2 0.00
321 80 0.18
322 60 0.14
323 278 0.63
324 2 0.00
325 4 0.01
326 2 0.00
327 11 0.03
328 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (322 bp):
CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
TCATGATAATATCTAGGTCAAGTTTGATATTGGGTACGATCGAGCAATTTTCGACAGAGTTATGG
CCTTTGGACGTAGAAAAATTCCAGTTATTTGCAGTTTCCGCTCATGTTCTTAGCAGAGGATAAAC
ATATTGAAAGGAAATTTGGTATACAGGCTTATCATGATAATATCTAAGTCAAGTTCGATATTGGG
TACAATCGAGCAATTTTCGACAGAGTTATGCCTCTTGGACATACAAAAACTCCAGTTATTTG
Found at i:573231 original size:166 final size:166
Alignment explanation
Indices: 572456--573232 Score: 1187
Period size: 166 Copynumber: 4.7 Consensus size: 166
572446 GGTATTTTTC
* * * * * *
572456 AAAAATCTTCTTCTCAAAAACTA-AATGGCCTGAAAAGCTTAAACTTGTGTGGAGGCATCCTCAG
1 AAAAATCTTCTTCTCAAAAACTATTA-GGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAG
* *
572520 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGAGGAGCCACAAGAGGGGG
65 GTAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGAGGGGG
* *
572585 ATCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
130 ATCAAGTTTAACATAGGAATATACAGAGAAAATCTTT
** *
572622 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
* *
572687 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGAGGGGCCACAAGAGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGAGGGGGA
*
572752 TCAAGTTTAACATATGAATATACAGAGAAAATCTTT
131 TCAAGTTTAACATAGGAATATACAGAGAAAATCTTT
* * ** *
572788 AAAAATCTTCTTCTCCAAAACTATTAAGCCAGAAAAGCTCAAATTAAAATGGAAGCATCCTCAGG
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
* * **
572853 TAGTGTAGATTCAAGTTTGTTCAAATCATGATCCCCGGGGGTAGGGTGGGGTCACAATTGGGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGAGGGGGA
*
572918 TCAAGTTTAACATATGAATATACAGAGAAAATCTTT
131 TCAAGTTTAACATAGGAATATACAGAGAAAATCTTT
* *
572954 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
* * ** *
573019 TAGTGTTGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGTCACAATTGAGGGA
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGAGGGGGA
* *
573084 TCAAGTTTTACATAGGAATATATAGAGAAAATCTTT
131 TCAAGTTTAACATAGGAATATACAGAGAAAATCTTT
* * *
573120 AAAAATCTTCTTCTCAAAAACTATTAGACCAGGAAAGCTCAAATTTGAGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
*
573185 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAGGGTG
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTG
573233 TATAAATTGT
Statistics
Matches: 572, Mismatches: 38, Indels: 2
0.93 0.06 0.00
Matches are distributed among these distances:
166 571 1.00
167 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACTATTAGGCCAGAAAAGCTCAAATTTGAGTGGAAGCATCCTCAGG
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCCGGGGGTAGGGTGGGGCCACAAGAGGGGGA
TCAAGTTTAACATAGGAATATACAGAGAAAATCTTT
Found at i:579628 original size:25 final size:25
Alignment explanation
Indices: 579591--579648 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
579581 TGTGACAGTG
579591 CATTCTTGAGTATAATTGATTCTAAA
1 CATT-TTGAGTATAATTGATTCTAAA
*
579617 CATTTTGAGTATAATTGATTCTTAA
1 CATTTTGAGTATAATTGATTCTAAA
579642 CATTTTG
1 CATTTTG
579649 TATACTAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 27 0.87
26 4 0.13
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.47
Consensus pattern (25 bp):
CATTTTGAGTATAATTGATTCTAAA
Found at i:591544 original size:94 final size:91
Alignment explanation
Indices: 591372--591559 Score: 259
Period size: 94 Copynumber: 2.0 Consensus size: 91
591362 CCTCCAAAAG
* *
591372 AAAATCTGGATATGACTTAGAGCTTTGTAACAAGTCAGTTAATTGTATCTTGTTTATTTACATTC
1 AAAATCTGGATATGACTTAGAGCCTTGTAACAAGTCAGTGAATTGTATCTTGTTTATTTACATTC
** * * *
591437 ATTTTTCAGTAAACTATAAGATATAA
66 ATTTGGCACTAAACCATAAAATATAA
* *
591463 AAAATCTGGATATGACTTAATAGTGCCTTGTTACAAGTCAGTGAATTGTATCTTGTTTATTTACA
1 AAAATCTGGATATGAC-T--TAGAGCCTTGTAACAAGTCAGTGAATTGTATCTTGTTTATTTACA
*
591528 TTCATTTGGCACTAAACCATAAAATATGA
63 TTCATTTGGCACTAAACCATAAAATATAA
591557 AAA
1 AAA
591560 TTTCGATAAT
Statistics
Matches: 84, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
91 16 0.19
92 1 0.01
94 67 0.80
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (91 bp):
AAAATCTGGATATGACTTAGAGCCTTGTAACAAGTCAGTGAATTGTATCTTGTTTATTTACATTC
ATTTGGCACTAAACCATAAAATATAA
Found at i:603507 original size:55 final size:55
Alignment explanation
Indices: 603435--603548 Score: 219
Period size: 55 Copynumber: 2.1 Consensus size: 55
603425 AATGAAGAGC
*
603435 CAGAACTTTTCATCCATAGCATTAAGGTGACTCACTACACCTTGAAATATTTTCT
1 CAGAACTTTTCATCCATAGCATTAAGGTGACGCACTACACCTTGAAATATTTTCT
603490 CAGAACTTTTCATCCATAGCATTAAGGTGACGCACTACACCTTGAAATATTTTCT
1 CAGAACTTTTCATCCATAGCATTAAGGTGACGCACTACACCTTGAAATATTTTCT
603545 CAGA
1 CAGA
603549 TCAGTAGAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (55 bp):
CAGAACTTTTCATCCATAGCATTAAGGTGACGCACTACACCTTGAAATATTTTCT
Found at i:606486 original size:27 final size:26
Alignment explanation
Indices: 606434--606504 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
606424 TGAATAGATG
* **
606434 TTCCTAAATGTTAACAGTTTGTAGACC
1 TTCCTAAATGTTAACAATTTACAGA-C
606461 TTCCTAAATGTTAACAATTTACAGAC
1 TTCCTAAATGTTAACAATTTACAGAC
* *
606487 TTTCTAAATGTTCACAAT
1 TTCCTAAATGTTAACAAT
606505 CTGTGGACAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 17 0.44
27 22 0.56
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (26 bp):
TTCCTAAATGTTAACAATTTACAGAC
Found at i:615004 original size:21 final size:19
Alignment explanation
Indices: 614953--615006 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 19
614943 ATTCAGTGCA
614953 CTGTTGTTTTGCATCGGTT
1 CTGTTGTTTTGCATCGGTT
*
614972 ATCGTTTGTTTTGCATCGGTGT
1 CT-G-TTGTTTTGCATCGGT-T
614994 CTGTTGATTTTGC
1 CTGTTG-TTTTGC
615007 GAAAGAGGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 4 0.14
21 22 0.76
22 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (19 bp):
CTGTTGTTTTGCATCGGTT
Found at i:622504 original size:3 final size:3
Alignment explanation
Indices: 622496--622531 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
622486 TTTTAGCTTA
622496 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
622532 AAATGCATAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:622638 original size:1 final size:1
Alignment explanation
Indices: 622623--622667 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
622613 TGATAGAAGA
* *
622623 GGGGAGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
622668 TAGTAAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.04, C:0.00, G:0.96, T:0.00
Consensus pattern (1 bp):
G
Found at i:623145 original size:2 final size:2
Alignment explanation
Indices: 623138--623180 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
623128 TCTTTCGTTG
623138 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
623180 C
1 C
623181 AGCGCCGAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:624096 original size:18 final size:18
Alignment explanation
Indices: 624073--624107 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
624063 AATACATGTA
624073 GGCGACATTGCTGACATG
1 GGCGACATTGCTGACATG
624091 GGCGACATTGCTGACAT
1 GGCGACATTGCTGACAT
624108 AGCGATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (18 bp):
GGCGACATTGCTGACATG
Found at i:638443 original size:11 final size:11
Alignment explanation
Indices: 638436--638477 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
638426 ACTAGAGTGG
638436 ACCCAGAGTAA
1 ACCCAGAGTAA
638447 ACCCAGAGTAA
1 ACCCAGAGTAA
638458 ACCCCA-AGTAA
1 A-CCCAGAGTAA
*
638469 ATCCAGAGT
1 ACCCAGAGT
638478 GGACACAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 3 0.11
11 21 0.75
12 4 0.14
ACGTcount: A:0.43, C:0.29, G:0.17, T:0.12
Consensus pattern (11 bp):
ACCCAGAGTAA
Found at i:644973 original size:11 final size:11
Alignment explanation
Indices: 644954--644987 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
644944 ACTTGGAAAG
644954 AAAGTAATTGA
1 AAAGTAATTGA
* *
644965 GATGTAATTGA
1 AAAGTAATTGA
644976 AAAGTAATTGA
1 AAAGTAATTGA
644987 A
1 A
644988 CATACACCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (11 bp):
AAAGTAATTGA
Found at i:647168 original size:2 final size:2
Alignment explanation
Indices: 647161--647203 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
647151 AATATGCATT
647161 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
647203 G
1 G
647204 CATTCTTACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:648245 original size:2 final size:2
Alignment explanation
Indices: 648238--648301 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
648228 TTGACCCCAT
648238 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
648280 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
648302 ACTAGTCTTC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:651732 original size:2 final size:2
Alignment explanation
Indices: 651725--651765 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
651715 AAAAATGCAC
*
651725 CT CT CT CT CT CT CT CT CT CT CT AT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
651766 ACACACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.02, C:0.49, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:658780 original size:2 final size:2
Alignment explanation
Indices: 658773--658838 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
658763 TTATGCATGT
* *
658773 TC TC TC TC TC TC TC TT TC TT TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
658815 TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC
658839 ATGGTTAATC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:660467 original size:192 final size:191
Alignment explanation
Indices: 660269--661007 Score: 897
Period size: 192 Copynumber: 3.9 Consensus size: 191
660259 TGCAACTATA
** ** * *
660269 AGTGGTGTTTTAATTCCATTGCTTTTATTGACATCT-GCCCCACCCTTTATCAAATGGC-CGATT
1 AGTGGTGTTTTGTTTCCATCACTTTGATTGACAT-TAGCCCCACCCTTTATTAAAT-GCTCGA-T
* * * * *
660332 GCACATCTAT-T-CCCTCTCTCACATGCAATCGTCAGTGGTGTTTCT-TTTCCATCACTTTGATT
63 GCACATC-ATGTGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTT-TGTTTCCATCACTTTGATT
*
660394 GACATCAGCTCCCGCTTTTATAAGCTCCTTGACCACATAAGTGTATCCTCTTTCACATGCAGTTG
126 GACATCAGCTCCCGCTTTTATTAGCTCCTTGACCACATAA-TGTATCCTCTTTCACATGCAGTTG
660459 TT
190 TT
* * ** *
660461 AGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGCCCCAGCTTTTATTAGCTTCTCGAT-CA
1 AGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGCCCCACCCTTTATTAAATGCTCGATGCA
* * *
660525 TATAATTATGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACA
66 CATCA-TGTGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACA
*
660590 TCAGCTCCCGCATTTATTAGCTCCTTGACCACATAATTGTATCCTCTTTCACATGCAGTTGTT
130 TCAGCTCCCGCTTTTATTAGCTCCTTGACCACATAA-TGTATCCTCTTTCACATGCAGTTGTT
* * * *
660653 AGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGCCCCAGCTTTTATTAGCAT-C-CAGA-C
1 AGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGCCCCACCCTTTATTA-AATGCTC-GATG
*
660715 CACATCATCGTGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCGCTTTGATTGA
64 CACATCAT-GTGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGA
* * * *
660780 CATCAGCTCCCGCTTTTATTAGCTCCTTGACCACATCATCGTGTCTTTTTTCACATGCAGTTGTT
128 CATCAGCTCCCGCTTTTATTAGCTCCTTGACCACATAAT-GTATCCTCTTTCACATGCAGTTGTT
* * * * ** * * *
660845 AGTGGTGTTTTGTTTCCATCGCTTTGATTGACATCAGCTCCC-GCTTTTATTAGCTCCTTGA-CC
1 AGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGC-CCCACCCTTTATTAAATGCTCGATGC
* * *
660908 ACATCATCGTGTCTTTTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCGCTTTGATTGAC
65 ACATCAT-GTGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGAC
660973 ATCAGCTCCCGCTTTTATTAGCTCCTTGACCACAT
129 ATCAGCTCCCGCTTTTATTAGCTCCTTGACCACAT
661008 CANNNNNNNN
Statistics
Matches: 494, Mismatches: 39, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
189 1 0.00
190 5 0.01
191 9 0.02
192 475 0.96
193 4 0.01
ACGTcount: A:0.19, C:0.25, G:0.16, T:0.41
Consensus pattern (191 bp):
AGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGCCCCACCCTTTATTAAATGCTCGATGCA
CATCATGTGTCCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACAT
CAGCTCCCGCTTTTATTAGCTCCTTGACCACATAATGTATCCTCTTTCACATGCAGTTGTT
Found at i:660993 original size:96 final size:96
Alignment explanation
Indices: 660344--661009 Score: 1000
Period size: 96 Copynumber: 6.9 Consensus size: 96
660334 ACATCTATTC
* * * *
660344 CCTCTCTCACATGCAATCGTCAGTGGTGTTTCT-TTTCCATCACTTTGATTGACATCAGCTCCCG
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTT-TGTTTCCATCACTTTGATTGACATCAGCTCCCG
* * *
660408 CTTTTATAAGCTCCTTGACCACATAAGT-GTAT
65 CTTTTATTAGCTCCTTGACCACATCA-TCGTGT
*
660440 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGC-CCCAG
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCC-G
* * * * * **
660504 CTTTTATTAGCTTCTCGATCATATAATTATGT
65 CTTTTATTAGCTCCTTGACCACATCATCGTGT
660536 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCCGC
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCCGC
* * * *
660601 ATTTATTAGCTCCTTGACCACATAATTGTAT
66 TTTTATTAGCTCCTTGACCACATCATCGTGT
*
660632 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATTAGC-CCCAG
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCC-G
*
660696 CTTTTATTAGCATCC-AGACCACATCATCGTGT
65 CTTTTATTAGC-TCCTTGACCACATCATCGTGT
*
660728 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCGCTTTGATTGACATCAGCTCCCGC
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCCGC
660793 TTTTATTAGCTCCTTGACCACATCATCGTGT
66 TTTTATTAGCTCCTTGACCACATCATCGTGT
* * *
660824 CTTTTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCGCTTTGATTGACATCAGCTCCCGC
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCCGC
660889 TTTTATTAGCTCCTTGACCACATCATCGTGT
66 TTTTATTAGCTCCTTGACCACATCATCGTGT
* * *
660920 CTTTTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCGCTTTGATTGACATCAGCTCCCGC
1 CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCCGC
660985 TTTTATTAGCTCCTTGACCACATCA
66 TTTTATTAGCTCCTTGACCACATCA
661010 NNNNNNNNNN
Statistics
Matches: 531, Mismatches: 31, Indels: 16
0.92 0.05 0.03
Matches are distributed among these distances:
95 11 0.02
96 511 0.96
97 9 0.02
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.41
Consensus pattern (96 bp):
CCTCTTTCACATGCAGTTGTTAGTGGTGTTTTGTTTCCATCACTTTGATTGACATCAGCTCCCGC
TTTTATTAGCTCCTTGACCACATCATCGTGT
Found at i:670779 original size:34 final size:34
Alignment explanation
Indices: 670730--671125 Score: 510
Period size: 34 Copynumber: 11.6 Consensus size: 34
670720 AAAGCAANAT
* * *
670730 GTGTGATACACAGGCCTCCAGAAGAAAGGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* * * *
670764 GTGTGACACATAGGCCTACAGAACTAGAGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* *
670798 GTTTGATTCACAGGCCTACAGAACAAAAGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
*
670832 GTGTGATACACAGGCCTAAAGAACAAAAGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* *
670866 GTGTGTTACACAGGCCTACAGAACAAAAGGATAT
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* * *
670900 GTGTGATACACAGGCCTCCAGAAGAAAGGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* * *
670934 GTGTGACACATAGGCCTACAGAACTAAAGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
*
670968 GAT-TGATACACAGGCCTCCAGAACAAAAGGATAG
1 G-TGTGATACACAGGCCTACAGAACAAAAGGATAG
* *
671002 GTGTGATACACAGACATACAGAACAAAAGGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* *
671036 GTGTGTTACACAGGCCTACAGAACAAAATGATAG
1 GTGTGATACACAGGCCTACAGAACAAAAGGATAG
* *
671070 GTGTGAAACACAGGCC-ACCAGAACAAAAGTATA-
1 GTGTGATACACAGGCCTA-CAGAACAAAAGGATAG
*
671103 GTTTAGATACACAGGCCTACAGA
1 GTGT-GATACACAGGCCTACAGA
671126 GGAAAGATGA
Statistics
Matches: 310, Mismatches: 47, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
33 5 0.02
34 303 0.98
35 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.26, T:0.17
Consensus pattern (34 bp):
GTGTGATACACAGGCCTACAGAACAAAAGGATAG
Found at i:685248 original size:21 final size:21
Alignment explanation
Indices: 685199--685255 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
685189 TTAAGTCAAA
*
685199 ATACAAGATAAAT-TGTCTAC
1 ATACAAGATAATTATGTCTAC
* *
685219 TTACGAGATAATTATGTCTAC
1 ATACAAGATAATTATGTCTAC
* *
685240 ATGCAAGATGATTATG
1 ATACAAGATAATTATG
685256 ATGAAAGTTA
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (21 bp):
ATACAAGATAATTATGTCTAC
Found at i:685561 original size:17 final size:18
Alignment explanation
Indices: 685534--685570 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
685524 GTCAACATGC
685534 GAAATTATCTTGCATGTT
1 GAAATTATCTTGCATGTT
685552 GAAATT-TCTTGCATGTT
1 GAAATTATCTTGCATGTT
685569 GA
1 GA
685571 CATAAATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (18 bp):
GAAATTATCTTGCATGTT
Found at i:685615 original size:21 final size:21
Alignment explanation
Indices: 685553--685641 Score: 65
Period size: 21 Copynumber: 4.2 Consensus size: 21
685543 TTGCATGTTG
* *
685553 AAATTTCTTGCATGTTGACAT
1 AAATATCTTGCATGTCGACAT
** * *
685574 AAATATCTCACATATTGACAT
1 AAATATCTTGCATGTCGACAT
*
685595 AAATATCTTGCATGTCAACAT
1 AAATATCTTGCATGTCGACAT
* *
685616 TATTAAT-TTGCATGTTC-ACAT
1 AAAT-ATCTTGCATG-TCGACAT
685637 AAATA
1 AAATA
685642 AATTGAATAC
Statistics
Matches: 53, Mismatches: 13, Indels: 5
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 48 0.91
22 4 0.08
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (21 bp):
AAATATCTTGCATGTCGACAT
Found at i:685776 original size:21 final size:21
Alignment explanation
Indices: 685748--685843 Score: 129
Period size: 21 Copynumber: 4.6 Consensus size: 21
685738 CAAAGATTTG
*
685748 TAACTTGCATGTCAACATATT
1 TAACTTGCATGTCAACATAAT
*
685769 TAATTTGCATGTCAACATAAT
1 TAACTTGCATGTCAACATAAT
**
685790 TAACAGGCATGTCAACATAAT
1 TAACTTGCATGTCAACATAAT
*
685811 TAACTTGCATGTCAACATAGT
1 TAACTTGCATGTCAACATAAT
* *
685832 TATCTGGCATGT
1 TAACTTGCATGT
685844 AGATATAATT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (21 bp):
TAACTTGCATGTCAACATAAT
Found at i:685863 original size:42 final size:42
Alignment explanation
Indices: 685754--685863 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
685744 TTTGTAACTT
* * *
685754 GCATGTCAACATATTTAATTTGCATGTCAACATAATTAACAG
1 GCATGTCAACATAATTAACTGGCATGTCAACATAATTAACAG
* * * *
685796 GCATGTCAACATAATTAACTTGCATGTCAACATAGTTATCTG
1 GCATGTCAACATAATTAACTGGCATGTCAACATAATTAACAG
* *
685838 GCATGT-AGATATAATTATCTGGCATG
1 GCATGTCA-ACATAATTAACTGGCATG
685864 CTGACATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 58 0.98
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (42 bp):
GCATGTCAACATAATTAACTGGCATGTCAACATAATTAACAG
Found at i:685872 original size:21 final size:21
Alignment explanation
Indices: 685783--685874 Score: 82
Period size: 21 Copynumber: 4.4 Consensus size: 21
685773 TTGCATGTCA
* *
685783 ACATAATTAACAGGCATGTCA-
1 ACATAATTATCTGGCATGT-AG
* *
685804 ACATAATTAACTTGCATGTCA-
1 ACATAATTATCTGGCATGT-AG
*
685825 ACATAGTTATCTGGCATGTAG
1 ACATAATTATCTGGCATGTAG
*
685846 ATATAATTATCTGGCATGCT-G
1 ACATAATTATCTGGCATG-TAG
685867 ACATAATT
1 ACATAATT
685875 TATTTTGCAT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (21 bp):
ACATAATTATCTGGCATGTAG
Found at i:694466 original size:40 final size:40
Alignment explanation
Indices: 694411--694675 Score: 408
Period size: 40 Copynumber: 6.7 Consensus size: 40
694401 TGTTCCTAAA
694411 AACAACAC-TGGTAGATTCAGTCTTATTACAGGGTGCTAT
1 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
694450 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
1 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
* * * *
694490 AACATCACATGGTAGATTCAGTCCTATCACAGGGTGTTAT
1 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
*
694530 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGTTAT
1 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
* *
694570 AACAACACATGGTAAATTCAGTCTGATTACAGGGTGCT-T
1 AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
** * *
694609 CGCCAACACATGGTAGATTCAGTCTAATGACAGGGTGCTAT
1 -AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
694650 AACAACACATGGTAGATTCAGTCTTA
1 AACAACACATGGTAGATTCAGTCTTA
694676 CTTTTTTTTT
Statistics
Matches: 205, Mismatches: 18, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
39 9 0.04
40 195 0.95
41 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (40 bp):
AACAACACATGGTAGATTCAGTCTTATTACAGGGTGCTAT
Found at i:699712 original size:14 final size:14
Alignment explanation
Indices: 699693--699719 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
699683 GTTTACGGAC
699693 AGACAGACAGACAG
1 AGACAGACAGACAG
699707 AGACAGACAGACA
1 AGACAGACAGACA
699720 AACAAACGCC
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:0.52, C:0.22, G:0.26, T:0.00
Consensus pattern (14 bp):
AGACAGACAGACAG
Found at i:705635 original size:15 final size:15
Alignment explanation
Indices: 705617--705675 Score: 68
Period size: 15 Copynumber: 3.9 Consensus size: 15
705607 TCTTTTCAGA
705617 TGTTTGAATTTCTGG
1 TGTTTGAATTTCTGG
705632 TG-TTGAACTTTCTGG
1 TGTTTGAA-TTTCTGG
* *
705647 TGTTGGAATTTCGGG
1 TGTTTGAATTTCTGG
705662 T-TTTGGAATTTCTG
1 TGTTT-GAATTTCTG
705676 AAGTTGGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 7 0.19
15 26 0.70
16 4 0.11
ACGTcount: A:0.14, C:0.08, G:0.29, T:0.49
Consensus pattern (15 bp):
TGTTTGAATTTCTGG
Found at i:705657 original size:30 final size:30
Alignment explanation
Indices: 705610--705685 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
705600 GAATTTTTCT
* * *
705610 TTTCAGATGTTTGAATTTCTGGTGTT-GAA
1 TTTCTGATGTTGGAATTTCGGGTGTTGGAA
* *
705639 CTTTCTGGTGTTGGAATTTCGGGTTTTGGAA
1 -TTTCTGATGTTGGAATTTCGGGTGTTGGAA
*
705670 TTTCTGAAGTTGGAAT
1 TTTCTGATGTTGGAAT
705686 GTTGGATGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
30 35 0.92
31 3 0.08
ACGTcount: A:0.18, C:0.08, G:0.28, T:0.46
Consensus pattern (30 bp):
TTTCTGATGTTGGAATTTCGGGTGTTGGAA
Found at i:743883 original size:16 final size:17
Alignment explanation
Indices: 743847--743884 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
743837 ATGTTGGGGG
743847 AAAATGAACTCCCTTCA
1 AAAATGAACTCCCTTCA
743864 AAAATGAACTCCCTTCA
1 AAAATGAACTCCCTTCA
743881 AAAA
1 AAAA
743885 CCATTCACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.21
Consensus pattern (17 bp):
AAAATGAACTCCCTTCA
Found at i:745715 original size:160 final size:155
Alignment explanation
Indices: 745392--745715 Score: 350
Period size: 163 Copynumber: 2.1 Consensus size: 155
745382 ACATTTTTTA
* * *
745392 AAGATTTTTCGCTATGTATTCCTATGTAAAATTCGACCCTCCCACTGTGGCCGCACCCTATCCCG
1 AAGATTTTTCGCTATGTATTCCTATGTAAAATTCGACCCCCCCACTGTGGCCCCACCCTACCCCG
* * * *
745457 GGGATTATGGTTTAAACAAATTTAAATCTACACTACCTGACGATGCTTCTAAACAAGTTACAGCA
66 GGGATCATGATTTAAACAAATTTAAATCTACACTACATGAAGATGCTTC-AAACAAGTTACAGCA
***
745522 TTTCTGGCCTACTGGTTTTTGTTGAG
130 TTTCTGGCCTACTGGTTTTTGCAAAG
* * * *
745548 AAGATTTTTCTCTATGTATTCCTGTGTAAAAATTTCGACCCCCCCCCCCATTGTGGCCCCACCTT
1 AAGATTTTTCGCTATGTATTCCTATGT-AAAA-TTCGA----CCCCCCCACTGTGGCCCCACCCT
* * * *
745613 ACCCCCGGGGATCGTGATTTGAAA-AAATTTGAATCTACACTACATGAAGATGCTTC-CAC-TGT
60 A-CCCCGGGGATCATGATTT-AAACAAATTTAAATCTACACTACATGAAGATGCTTCAAACAAGT
* *
745675 TCCAGCTTTTCTGG-CTAACTGGTTTTTGCAAAG
123 TACAGCATTTCTGGCCT-ACTGGTTTTTGCAAAG
745708 AAGATTTT
1 AAGATTTT
745716 AATGATTTTT
Statistics
Matches: 139, Mismatches: 20, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
156 25 0.18
157 4 0.03
158 5 0.04
159 2 0.01
160 35 0.25
161 2 0.01
162 20 0.14
163 43 0.31
164 3 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (155 bp):
AAGATTTTTCGCTATGTATTCCTATGTAAAATTCGACCCCCCCACTGTGGCCCCACCCTACCCCG
GGGATCATGATTTAAACAAATTTAAATCTACACTACATGAAGATGCTTCAAACAAGTTACAGCAT
TTCTGGCCTACTGGTTTTTGCAAAG
Found at i:746734 original size:14 final size:15
Alignment explanation
Indices: 746715--746750 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
746705 TCCCTAAGTT
*
746715 AAATAAAT-AAAATA
1 AAATAAATAAAAAAA
746729 AAATAAATAAAAAAA
1 AAATAAATAAAAAAA
746744 AAATAAA
1 AAATAAA
746751 AATAAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAATAAAAAAA
Found at i:751222 original size:13 final size:13
Alignment explanation
Indices: 751201--751238 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
751191 AAAGAGTGAA
751201 GAAATTGTGAAAC
1 GAAATTGTGAAAC
*
751214 GATATTGTGAAAC
1 GAAATTGTGAAAC
751227 GAAATTGTGAAA
1 GAAATTGTGAAA
751239 TGTACTTGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.45, C:0.05, G:0.24, T:0.26
Consensus pattern (13 bp):
GAAATTGTGAAAC
Found at i:768416 original size:2 final size:2
Alignment explanation
Indices: 768409--768433 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
768399 TTACATGTAA
768409 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
768434 ATCGTAAATT
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:778459 original size:18 final size:18
Alignment explanation
Indices: 778438--778474 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
778428 AAAACATATG
778438 CAATATTAAATATGCACA
1 CAATATTAAATATGCACA
778456 CAATATTAAATATGCACA
1 CAATATTAAATATGCACA
778474 C
1 C
778475 CTTCGAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.19, G:0.05, T:0.27
Consensus pattern (18 bp):
CAATATTAAATATGCACA
Found at i:786115 original size:16 final size:16
Alignment explanation
Indices: 786071--786116 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
786061 ATAGTGATCA
786071 GTCTGTCCGTCCATCT
1 GTCTGTCCGTCCATCT
* ** *
786087 TTCCATCCTTCCATCT
1 GTCTGTCCGTCCATCT
786103 GTCTGTCCGTCCAT
1 GTCTGTCCGTCCAT
786117 GATCACTTGT
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.09, C:0.39, G:0.13, T:0.39
Consensus pattern (16 bp):
GTCTGTCCGTCCATCT
Found at i:786244 original size:24 final size:23
Alignment explanation
Indices: 786192--786237 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
786182 TTGTTATATC
786192 TGTATAACGAATTCACAATAATA
1 TGTATAACGAATTCACAATAATA
* *
786215 TCTATAGCGAATTCACTAATAAT
1 TGTATAACGAATTCAC-AATAAT
786238 GAGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (23 bp):
TGTATAACGAATTCACAATAATA
Found at i:787697 original size:19 final size:20
Alignment explanation
Indices: 787663--787707 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
787653 CCGTGTCGCA
*
787663 CCGTGGCCGCCTGTGTAACT
1 CCGTGGCCGACTGTGTAACT
*
787683 CCGTGGCC-ACTGTGTTACT
1 CCGTGGCCGACTGTGTAACT
787702 CCGTGG
1 CCGTGG
787708 ATATTGTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.09, C:0.33, G:0.31, T:0.27
Consensus pattern (20 bp):
CCGTGGCCGACTGTGTAACT
Found at i:789195 original size:2 final size:2
Alignment explanation
Indices: 789188--789234 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
789178 ACAAAAGTAC
789188 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
789230 AG AG A
1 AG AG A
789235 TTTTACAGCG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:789578 original size:2 final size:2
Alignment explanation
Indices: 789571--789619 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
789561 ATGCCAGTAT
789571 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
789613 TC TC TC T
1 TC TC TC T
789620 GACGATCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:792555 original size:2 final size:2
Alignment explanation
Indices: 792548--792604 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
792538 ACAAAAGTAC
792548 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
792590 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
792605 TTTTACAGCG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:792948 original size:2 final size:2
Alignment explanation
Indices: 792941--792989 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
792931 ATGCCAGTAT
792941 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
792983 TC TC TC T
1 TC TC TC T
792990 GACGATCATT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:794085 original size:21 final size:21
Alignment explanation
Indices: 794042--794086 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
794032 TACAAGATAA
*
794042 ACGATAGGATAAGATTCACGC
1 ACGATAGGATAAGATTAACGC
* *
794063 ACGATAGGATAGGATTAATGC
1 ACGATAGGATAAGATTAACGC
794084 ACG
1 ACG
794087 CACGCACGGA
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:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (21 bp):
ACGATAGGATAAGATTAACGC
Found at i:799591 original size:22 final size:22
Alignment explanation
Indices: 799559--799637 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
799549 AATGAAAACA
* *
799559 AAACCTTGGGGACAGATTGACC
1 AAACATTGGGGGCAGATTGACC
*
799581 AAAC-TTGGGGGCAGATAACGAACC
1 AAACATTGGGGGCAGAT--TG-ACC
* *
799605 AAACTTTGGGGGCGGATTGACC
1 AAACATTGGGGGCAGATTGACC
799627 AAACATTGGGG
1 AAACATTGGGG
799638 ACGGATAAGC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
21 11 0.23
22 17 0.35
23 2 0.04
24 7 0.15
25 11 0.23
ACGTcount: A:0.32, C:0.19, G:0.32, T:0.18
Consensus pattern (22 bp):
AAACATTGGGGGCAGATTGACC
Found at i:799935 original size:21 final size:21
Alignment explanation
Indices: 799911--799982 Score: 92
Period size: 21 Copynumber: 3.4 Consensus size: 21
799901 CGATAAACCT
799911 GATAGGATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
*
799932 GATAGCATTAACGCACGATAG
1 GATAGGATTAACGCACGATAG
* * *
799953 AACAGTA-TACACGCACGATAG
1 GATAGGATTA-ACGCACGATAG
799974 GATAGGATT
1 GATAGGATT
799983 GATACACAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.05
21 39 0.93
22 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (21 bp):
GATAGGATTAACGCACGATAG
Found at i:806042 original size:22 final size:22
Alignment explanation
Indices: 806017--806058 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
806007 TCCAATTTAA
806017 TGAGTACATGTGT-GAAATTGTG
1 TGAGTACATGT-TCGAAATTGTG
*
806039 TGAGTATATGTTCGAAATTG
1 TGAGTACATGTTCGAAATTG
806059 ATCTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.29, C:0.05, G:0.29, T:0.38
Consensus pattern (22 bp):
TGAGTACATGTTCGAAATTGTG
Found at i:806324 original size:17 final size:16
Alignment explanation
Indices: 806302--806336 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 16
806292 GTTACTGGGG
806302 TTTTTTTAAAACTAGAC
1 TTTTTTT-AAACTAGAC
806319 TTTTTTTAAACTAGAC
1 TTTTTTTAAACTAGAC
806335 TT
1 TT
806337 GTGAGCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (16 bp):
TTTTTTTAAACTAGAC
Found at i:807667 original size:16 final size:16
Alignment explanation
Indices: 807644--807705 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
807634 GAAATGCCGG
*
807644 GCGTCCGTCCGTCCGT
1 GCGTCCGTCCGTCAGT
* ** *
807660 GTGTCCGTGGGTCTGT
1 GCGTCCGTCCGTCAGT
* **
807676 GGGTCCGTGTGTCAGT
1 GCGTCCGTCCGTCAGT
807692 GCGTCCGTCCGTCA
1 GCGTCCGTCCGTCA
807706 TACTTTTTTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.03, C:0.31, G:0.37, T:0.29
Consensus pattern (16 bp):
GCGTCCGTCCGTCAGT
Found at i:818761 original size:15 final size:15
Alignment explanation
Indices: 818741--818795 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
818731 ATCAAATATT
818741 ATACAATATCATACA
1 ATACAATATCATACA
818756 ATACAATAT-AT-C-
1 ATACAATATCATACA
* *
818768 ATACTATATTATACA
1 ATACAATATCATACA
**
818783 ATATTATATCATA
1 ATACAATATCATA
818796 TGTTTCAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 3 0.09
15 20 0.59
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (15 bp):
ATACAATATCATACA
Found at i:825032 original size:15 final size:15
Alignment explanation
Indices: 825012--825041 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
825002 GGTAAGTGAA
825012 GCGTCCGGATATCTG
1 GCGTCCGGATATCTG
825027 GCGTCCGGATATCTG
1 GCGTCCGGATATCTG
825042 AGGCTCCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GCGTCCGGATATCTG
Found at i:838106 original size:17 final size:18
Alignment explanation
Indices: 838084--838118 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
838074 GTATAACTGG
838084 TATTTTCTGCGGT-TTTT
1 TATTTTCTGCGGTATTTT
838101 TATTTTCTGCGGTATTTT
1 TATTTTCTGCGGTATTTT
838119 GCGGATAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.09, C:0.11, G:0.17, T:0.63
Consensus pattern (18 bp):
TATTTTCTGCGGTATTTT
Found at i:838765 original size:2 final size:2
Alignment explanation
Indices: 838758--838787 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
838748 AAAGACTGAA
*
838758 TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
838788 ATGCTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:861617 original size:2 final size:2
Alignment explanation
Indices: 861610--861654 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
861600 ACCAATGCAA
861610 TC TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
861651 TC TC
1 TC TC
861655 AACTCCCACA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:866146 original size:16 final size:16
Alignment explanation
Indices: 866125--866163 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
866115 GTCAAGTCGT
*
866125 ACCCAACCCAACTCGC
1 ACCCAAACCAACTCGC
*
866141 ACCCAAACCAACTCGT
1 ACCCAAACCAACTCGC
866157 ACCCAAA
1 ACCCAAA
866164 TATTTGAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.49, G:0.05, T:0.08
Consensus pattern (16 bp):
ACCCAAACCAACTCGC
Found at i:891768 original size:36 final size:36
Alignment explanation
Indices: 891721--891795 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
891711 ATATAAAAGA
891721 TTGTTCTCAATGTCTGAATATAGAAGACTGGAAGCT
1 TTGTTCTCAATGTCTGAATATAGAAGACTGGAAGCT
891757 TTGTTCTCAATGTCTGAATATAGAAGACTGGAAGCT
1 TTGTTCTCAATGTCTGAATATAGAAGACTGGAAGCT
891793 TTG
1 TTG
891796 CTGATATAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (36 bp):
TTGTTCTCAATGTCTGAATATAGAAGACTGGAAGCT
Found at i:892677 original size:44 final size:44
Alignment explanation
Indices: 892585--892681 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 44
892575 AATGTCAGCT
* * * * *
892585 TTCCATTTGGTCCTATTCCAGAGCACTTTCAGGTAACCAACGAT
1 TTCCATATGGTCCTATTCCAGACCACTTTCAGATAACCAACAAC
* * **
892629 TTCCATATGGTCCTGTTTCAGACCACTTTCAGATAACTGACAAC
1 TTCCATATGGTCCTATTCCAGACCACTTTCAGATAACCAACAAC
892673 TTCCATATG
1 TTCCATATG
892682 ATTATTGAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (44 bp):
TTCCATATGGTCCTATTCCAGACCACTTTCAGATAACCAACAAC
Done.