Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008103.1 Hibiscus syriacus cultivar Beakdansim tig00110633_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1996589
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:135624 original size:23 final size:23
Alignment explanation
Indices: 135594--135671 Score: 120
Period size: 23 Copynumber: 3.4 Consensus size: 23
135584 CTTAATGCAG
*
135594 GATGCTTGCTGAATGGATGCAAT
1 GATGCTTGCTGAATTGATGCAAT
*
135617 GATGCTTGTTGAATTGATGCAAT
1 GATGCTTGCTGAATTGATGCAAT
* *
135640 GATGCTTGCTGAATTGATACAGT
1 GATGCTTGCTGAATTGATGCAAT
135663 GATGCTTGC
1 GATGCTTGC
135672 CAGTTGATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.24, C:0.13, G:0.28, T:0.35
Consensus pattern (23 bp):
GATGCTTGCTGAATTGATGCAAT
Found at i:136294 original size:16 final size:14
Alignment explanation
Indices: 136250--136295 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
136240 TAATTTAATG
136250 ATTATAA-ATAA-A
1 ATTATAATATAAGA
136262 ATTTATAATATAAGA
1 A-TTATAATATAAGA
136277 ATTATAAATATAAAGA
1 ATTAT-AATAT-AAGA
136293 ATT
1 ATT
136296 GGAATTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 1 0.03
13 6 0.21
14 8 0.28
15 7 0.24
16 7 0.24
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
ATTATAATATAAGA
Found at i:136541 original size:16 final size:16
Alignment explanation
Indices: 136507--136542 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
136497 TGAGTCCATT
*
136507 ACAGGTCAGGTTCATA
1 ACAGGTCAGGTTCAAA
*
136523 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTCAAA
136539 ACAG
1 ACAG
136543 ATCGGGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.17, G:0.28, T:0.19
Consensus pattern (16 bp):
ACAGGTCAGGTTCAAA
Found at i:136857 original size:12 final size:12
Alignment explanation
Indices: 136840--136868 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
136830 GTCTCAAATG
136840 TTTTATTGATTT
1 TTTTATTGATTT
136852 TTTTA-TGATTT
1 TTTTATTGATTT
136863 TTTTAT
1 TTTTAT
136869 CGTTTTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTATTGATTT
Found at i:146208 original size:20 final size:20
Alignment explanation
Indices: 146168--146206 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
146158 CATTACAGGA
*
146168 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
146188 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
146207 GACCTTGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:157262 original size:26 final size:27
Alignment explanation
Indices: 157231--157281 Score: 95
Period size: 26 Copynumber: 1.9 Consensus size: 27
157221 AAAAAAATAG
157231 AAAATTATAAAAATAAGT-AACAAAAT
1 AAAATTATAAAAATAAGTAAACAAAAT
157257 AAAATTATAAAAATAAGTAAACAAA
1 AAAATTATAAAAATAAGTAAACAAA
157282 TATTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.22
Consensus pattern (27 bp):
AAAATTATAAAAATAAGTAAACAAAAT
Found at i:157341 original size:10 final size:10
Alignment explanation
Indices: 157326--157368 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
157316 TTATTTTAAA
157326 TTTTACTTAT
1 TTTTACTTAT
157336 TTTTACTTAT
1 TTTTACTTAT
*
157346 TTTTA--TAA
1 TTTTACTTAT
*
157354 TTTTATTTAT
1 TTTTACTTAT
157364 TTTTA
1 TTTTA
157369 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 7 0.24
10 22 0.76
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTACTTAT
Found at i:157433 original size:26 final size:25
Alignment explanation
Indices: 157335--157433 Score: 87
Period size: 26 Copynumber: 3.9 Consensus size: 25
157325 ATTTTACTTA
157335 TTTTTACTTATTTTTATAATTTTAT
1 TTTTTACTTATTTTTATAATTTTAT
*** **
157360 TTATTT--TTAAAAATTA-AATTCAAT
1 TT-TTTACTT-ATTTTTATAATTTTAT
157384 ATTTTTACTTATTTTTATAATTTTAT
1 -TTTTTACTTATTTTTATAATTTTAT
*
157410 TTTTTGACTTATTTTTATACTTTT
1 TTTTT-ACTTATTTTTATAATTTT
157434 CTATTTATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
24 11 0.20
25 17 0.30
26 28 0.50
ACGTcount: A:0.28, C:0.05, G:0.01, T:0.66
Consensus pattern (25 bp):
TTTTTACTTATTTTTATAATTTTAT
Found at i:158992 original size:17 final size:17
Alignment explanation
Indices: 158970--159011 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
158960 ACCCACAGTA
* *
158970 AAAATCCCGAAAATTTT
1 AAAATCCCAAAAAATTT
*
158987 AAAATCCAAAAAAATTT
1 AAAATCCCAAAAAATTT
159004 AAAATCCC
1 AAAATCCC
159012 TGTTAAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.19, G:0.02, T:0.24
Consensus pattern (17 bp):
AAAATCCCAAAAAATTT
Found at i:162156 original size:28 final size:28
Alignment explanation
Indices: 162123--162187 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
162113 CAAAGTCAAC
162123 GAGTTGACTCAAACGAGTTAAATCAGAT
1 GAGTTGACTCAAACGAGTTAAATCAGAT
* * * * *
162151 GAGTTGACTCGAATGAGTTGACTCAGTT
1 GAGTTGACTCAAACGAGTTAAATCAGAT
162179 GAGTTGACT
1 GAGTTGACT
162188 AGGTCAGGTC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (28 bp):
GAGTTGACTCAAACGAGTTAAATCAGAT
Found at i:162181 original size:14 final size:14
Alignment explanation
Indices: 162123--162187 Score: 69
Period size: 14 Copynumber: 4.6 Consensus size: 14
162113 CAAAGTCAAC
* *
162123 GAGTTGACTCAAAC
1 GAGTTGACTCAGAT
* *
162137 GAGTTAAATCAGAT
1 GAGTTGACTCAGAT
162151 GAGTTGACTC-GAAT
1 GAGTTGACTCAG-AT
*
162165 GAGTTGACTCAGTT
1 GAGTTGACTCAGAT
162179 GAGTTGACT
1 GAGTTGACT
162188 AGGTCAGGTC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
13 1 0.02
14 40 0.95
15 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (14 bp):
GAGTTGACTCAGAT
Found at i:164997 original size:15 final size:16
Alignment explanation
Indices: 164967--164997 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
164957 GTTCATAAGC
164967 TAGTAAATCAATAAAT
1 TAGTAAATCAATAAAT
164983 TAGTAAATC-ATAAAT
1 TAGTAAATCAATAAAT
164998 CTCTGTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (16 bp):
TAGTAAATCAATAAAT
Found at i:167765 original size:13 final size:13
Alignment explanation
Indices: 167747--167773 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
167737 CCTTGTTACG
167747 ACTTTAAATTAAT
1 ACTTTAAATTAAT
167760 ACTTTAAATTAAT
1 ACTTTAAATTAAT
167773 A
1 A
167774 AAATTTAGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.44
Consensus pattern (13 bp):
ACTTTAAATTAAT
Found at i:168758 original size:22 final size:22
Alignment explanation
Indices: 168726--168782 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 22
168716 AATAATACAT
168726 TTAT-AAT-TATTTATTTAATA
1 TTATAAATATATTTATTTAATA
168746 TTATAAATATATTT-TTT-ATA
1 TTATAAATATATTTATTTAATA
168766 -TA-AAATA-ATTTTATTTA
1 TTATAAATATA-TTTATTTA
168783 CTCATATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
17 1 0.03
18 8 0.25
19 5 0.16
20 7 0.22
21 6 0.19
22 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATAAATATATTTATTTAATA
Found at i:169075 original size:17 final size:18
Alignment explanation
Indices: 169053--169091 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
169043 GCTATGTTAT
* *
169053 CGGTTC-ATTGGTTTAAC
1 CGGTTCAATCGGTCTAAC
169070 CGGTTCAATCGGTCTAAC
1 CGGTTCAATCGGTCTAAC
169088 CGGT
1 CGGT
169092 CGAACCGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.18, C:0.23, G:0.26, T:0.33
Consensus pattern (18 bp):
CGGTTCAATCGGTCTAAC
Found at i:171084 original size:59 final size:59
Alignment explanation
Indices: 170981--171097 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 59
170971 CATAGTTTAG
** * * ** * *
170981 GATGAAATTAGAATGTTTAAAAGTTTAAGGGCTAATTTAGAATGAGAGTCACAATTTGA
1 GATGAAATTAGAACATTCAAAAGTTTAAAGAATAATTTAAAATGAGAGTAACAATTTGA
* *
171040 GATGAAATTAGAACATTCAAAAGTTTAAAGAATAGTTTAAAATGAGAGTAATAATTTG
1 GATGAAATTAGAACATTCAAAAGTTTAAAGAATAATTTAAAATGAGAGTAACAATTTG
171098 GGGACATATG
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.44, C:0.04, G:0.20, T:0.32
Consensus pattern (59 bp):
GATGAAATTAGAACATTCAAAAGTTTAAAGAATAATTTAAAATGAGAGTAACAATTTGA
Found at i:175541 original size:5 final size:5
Alignment explanation
Indices: 175531--175563 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
175521 CTTCTTAAGG
175531 AAATA AAATA AAAT- AAATA GAAATA AAATA AAA
1 AAATA AAATA AAATA AAATA -AAATA AAATA AAA
175564 ATATTCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 17 0.65
6 5 0.19
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:176210 original size:175 final size:170
Alignment explanation
Indices: 175915--176249 Score: 478
Period size: 175 Copynumber: 1.9 Consensus size: 170
175905 TATTGCCAAC
175915 AACTATAATCCAGGTAAAGAAAAATAAAGAAGAAGATGCAAAACCTGTTTAGAAATAAAGCAACA
1 AACTATAATCCAGGTAAAGAAAAATAAAGAAGAAGATGCAAAACCTGTTTAGAAATAAAGCAACA
* * *
175980 AGCTAGCAACCACAACCGAAAATGATCCTCTTCAGCAATTTGTTCATGCAGAAGATGCAATAAGA
66 AGCCAGCAACCACAACCGAAAATGATCCTCTTCAGCAATTTGTTCAAGCAGAAGATGCAAGAAGA
176045 AAAAGGGGGAAA-A-ACGTTAGTGATAATTTTTTGTATCAGCA
131 AAAA---GGAAACACACGTTAGTGATAATTTTTTGTATCAGCA
* * *
176086 AACTATAATCCA-GTGAAAGAAAAATAAATAAGAATATGCAATTAAAACCTGTTTAGAAATACAG
1 AACTATAATCCAGGT-AAAGAAAAATAAAGAAGAAGATGC----AAAACCTGTTTAGAAATAAAG
* * * *
176150 CAGCAAGCCAGCAACCACAACTGAAGATGATCCTCTTCAGCAATTTGTTCAAGGAGAAGATGCAA
61 CAACAAGCCAGCAACCACAACCGAAAATGATCCTCTTCAGCAATTTGTTCAAGCAGAAGATGCAA
*
176215 GAAGAAAAAGGAAACACACGTTATTGATAATTTTT
126 GAAGAAAAAGGAAACACACGTTAGTGATAATTTTT
176250 CAAGATTGAA
Statistics
Matches: 146, Mismatches: 11, Indels: 11
0.87 0.07 0.07
Matches are distributed among these distances:
170 2 0.01
171 34 0.23
172 5 0.03
173 1 0.01
174 17 0.12
175 87 0.60
ACGTcount: A:0.45, C:0.16, G:0.17, T:0.22
Consensus pattern (170 bp):
AACTATAATCCAGGTAAAGAAAAATAAAGAAGAAGATGCAAAACCTGTTTAGAAATAAAGCAACA
AGCCAGCAACCACAACCGAAAATGATCCTCTTCAGCAATTTGTTCAAGCAGAAGATGCAAGAAGA
AAAAGGAAACACACGTTAGTGATAATTTTTTGTATCAGCA
Found at i:177100 original size:5 final size:5
Alignment explanation
Indices: 177078--177134 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
177068 TTGATTGGAG
* *
177078 AATTA AATT- TATTG AATTA AATTAA AATTA GAATTA AATTAA AATTA
1 AATTA AATTA AATTA AATTA AATT-A AATTA -AATTA AATT-A AATTA
177125 GAATTA AATT
1 -AATTA AATT
177135 GATTGAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
4 3 0.07
5 21 0.48
6 20 0.45
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:177107 original size:6 final size:6
Alignment explanation
Indices: 177092--177132 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
177082 AAATTTATTG
* *
177092 AATT-A AATTAA AATTAG AATT-A AATTAA AATTAG AATTAA A
1 AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA AATTAA A
177133 TTGATTGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (6 bp):
AATTAA
Found at i:177113 original size:17 final size:17
Alignment explanation
Indices: 177091--177134 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
177081 TAAATTTATT
177091 GAATTAAATTAAAATTA
1 GAATTAAATTAAAATTA
177108 GAATTAAATTAAAATTA
1 GAATTAAATTAAAATTA
177125 GAATTAAATT
1 GAATTAAATT
177135 GATTGAATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (17 bp):
GAATTAAATTAAAATTA
Found at i:177624 original size:22 final size:24
Alignment explanation
Indices: 177599--177651 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
177589 GATTATAAAC
177599 ATAATAATATATGA-CTAA-TAAT-
1 ATAATAATATAT-ATCTAACTAATG
177621 ATAATAATATATATCTAACTAATG
1 ATAATAATATATATCTAACTAATG
177645 ATAATAA
1 ATAATAA
177652 CTAATGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 1 0.04
22 16 0.57
23 4 0.14
24 7 0.25
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (24 bp):
ATAATAATATATATCTAACTAATG
Found at i:177654 original size:13 final size:13
Alignment explanation
Indices: 177636--177662 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
177626 AATATATATC
177636 TAACTAATGATAA
1 TAACTAATGATAA
177649 TAACTAATGATAA
1 TAACTAATGATAA
177662 T
1 T
177663 TATTTATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
TAACTAATGATAA
Found at i:177740 original size:18 final size:18
Alignment explanation
Indices: 177692--177741 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
177682 TGCGTGTGTT
177692 TATGA-CTAA-TAATATA
1 TATGATCTAACTAATATA
*
177708 TATGATCATAGCTAATAATA
1 TATGATC-TAACTAAT-ATA
177728 TAT-ATCTAACTAAT
1 TATGATCTAACTAAT
177742 GATAATAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 5 0.18
17 1 0.04
18 9 0.32
19 7 0.25
20 6 0.21
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (18 bp):
TATGATCTAACTAATATA
Found at i:177752 original size:13 final size:13
Alignment explanation
Indices: 177734--177760 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
177724 AATATATATC
177734 TAACTAATGATAA
1 TAACTAATGATAA
177747 TAACTAATGATAA
1 TAACTAATGATAA
177760 T
1 T
177761 GTGTATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (13 bp):
TAACTAATGATAA
Found at i:178745 original size:3 final size:3
Alignment explanation
Indices: 178739--178764 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
178729 AAATCACGTG
178739 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
178765 AGTCCCTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:179929 original size:17 final size:17
Alignment explanation
Indices: 179894--180034 Score: 99
Period size: 18 Copynumber: 8.1 Consensus size: 17
179884 TTAATCTACG
*
179894 TCTGATAACTGTAAAACA
1 TCTGATAACTAT-AAACA
*
179912 TTTGATAACTATAAACA
1 TCTGATAACTATAAACA
*
179929 TTTGATAACTGA-AAATCA
1 TCTGATAACT-ATAAA-CA
* *
179947 TCTGATAACTGTAAATA
1 TCTGATAACTATAAACA
179964 TCTGATAACTGA-AAATCA
1 TCTGATAACT-ATAAA-CA
* * *
179982 TCTGATAATTGTAAATA
1 TCTGATAACTATAAACA
* *
179999 TCTAATAACTTTGAAA-A
1 TCTGATAACTAT-AAACA
*
180016 GTCTAATAACTATAAACA
1 -TCTGATAACTATAAACA
180034 T
1 T
180035 TTAGAATTCA
Statistics
Matches: 100, Mismatches: 14, Indels: 19
0.75 0.11 0.14
Matches are distributed among these distances:
17 47 0.47
18 53 0.53
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (17 bp):
TCTGATAACTATAAACA
Found at i:179935 original size:35 final size:35
Alignment explanation
Indices: 179894--180034 Score: 144
Period size: 35 Copynumber: 4.0 Consensus size: 35
179884 TTAATCTACG
*
179894 TCTGATAACTGTAAAA-CATTTGATAACTATAAACA
1 TCTGATAACTG-AAAATCATCTGATAACTATAAACA
* * *
179929 TTTGATAACTGAAAATCATCTGATAACTGTAAATA
1 TCTGATAACTGAAAATCATCTGATAACTATAAACA
* * *
179964 TCTGATAACTGAAAATCATCTGATAATTGTAAATA
1 TCTGATAACTGAAAATCATCTGATAACTATAAACA
* * *
179999 TCTAATAACTTTGAAAA--GTCTAATAACTATAAACA
1 TCTGATAAC--TGAAAATCATCTGATAACTATAAACA
180034 T
1 T
180035 TTAGAATTCA
Statistics
Matches: 91, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.04
35 81 0.89
37 6 0.07
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
TCTGATAACTGAAAATCATCTGATAACTATAAACA
Found at i:179997 original size:18 final size:18
Alignment explanation
Indices: 179894--180008 Score: 137
Period size: 18 Copynumber: 6.6 Consensus size: 18
179884 TTAATCTACG
*
179894 TCTGATAACTGTAAAACA
1 TCTGATAACTGTAAATCA
* *
179912 TTTGATAACTATAAA-CA
1 TCTGATAACTGTAAATCA
* *
179929 TTTGATAACTGAAAATCA
1 TCTGATAACTGTAAATCA
179947 TCTGATAACTGTAAAT-A
1 TCTGATAACTGTAAATCA
*
179964 TCTGATAACTGAAAATCA
1 TCTGATAACTGTAAATCA
*
179982 TCTGATAATTGTAAAT-A
1 TCTGATAACTGTAAATCA
*
179999 TCTAATAACT
1 TCTGATAACT
180009 TTGAAAAGTC
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
17 40 0.48
18 44 0.52
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (18 bp):
TCTGATAACTGTAAATCA
Found at i:187006 original size:21 final size:21
Alignment explanation
Indices: 186932--187014 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
186922 TATTTGGCAG
*
186932 AGGGAATCGATACCCCC-ATA
1 AGGGAATCGATACCCCCTGTA
* * *
186952 AGGGAATCGATTCCCCATTTGA
1 AGGGAATCGATACCCCCTGT-A
* *
186974 ATGGGAACCGATTCCCCCTGTA
1 A-GGGAATCGATACCCCCTGTA
*
186996 GGGGAATCGATACCCCCTG
1 AGGGAATCGATACCCCCTG
187015 GGGTTCTGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.29
21 17 0.33
22 3 0.06
23 16 0.31
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (21 bp):
AGGGAATCGATACCCCCTGTA
Found at i:192334 original size:14 final size:14
Alignment explanation
Indices: 192315--192343 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
192305 TACGTTTTAG
192315 CACAAATCCCATAC
1 CACAAATCCCATAC
192329 CACAAATCCCATAC
1 CACAAATCCCATAC
192343 C
1 C
192344 GAAATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.45, G:0.00, T:0.14
Consensus pattern (14 bp):
CACAAATCCCATAC
Found at i:192594 original size:3 final size:3
Alignment explanation
Indices: 192586--192662 Score: 154
Period size: 3 Copynumber: 25.7 Consensus size: 3
192576 AATAACTCGC
192586 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
192634 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
192663 ATTAGTCATT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:193986 original size:17 final size:17
Alignment explanation
Indices: 193966--194047 Score: 58
Period size: 15 Copynumber: 5.3 Consensus size: 17
193956 GTATAACCCA
193966 TGATTATGATTGACACT
1 TGATTATGATTGACACT
193983 TGA-T-TG-TTGAACAC-
1 TGATTATGATTG-ACACT
*
193997 -GATTATGACTGACACT
1 TGATTATGATTGACACT
194013 TGA-T-TG-TTGAACAC-
1 TGATTATGATTG-ACACT
*
194027 -GATTATGACTGACACT
1 TGATTATGATTGACACT
194043 TGATT
1 TGATT
194048 GTTGAACACG
Statistics
Matches: 50, Mismatches: 3, Indels: 24
0.65 0.04 0.31
Matches are distributed among these distances:
13 4 0.08
14 7 0.14
15 24 0.48
16 6 0.12
17 9 0.18
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (17 bp):
TGATTATGATTGACACT
Found at i:194003 original size:30 final size:30
Alignment explanation
Indices: 193967--194057 Score: 173
Period size: 30 Copynumber: 3.0 Consensus size: 30
193957 TATAACCCAT
*
193967 GATTATGATTGACACTTGATTGTTGAACAC
1 GATTATGACTGACACTTGATTGTTGAACAC
193997 GATTATGACTGACACTTGATTGTTGAACAC
1 GATTATGACTGACACTTGATTGTTGAACAC
194027 GATTATGACTGACACTTGATTGTTGAACAC
1 GATTATGACTGACACTTGATTGTTGAACAC
194057 G
1 G
194058 TCAGAAAAAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (30 bp):
GATTATGACTGACACTTGATTGTTGAACAC
Found at i:194900 original size:6 final size:6
Alignment explanation
Indices: 194891--194918 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
194881 TTCCCTTCTT
194891 AAGGTA AAGGTA AAGGTA AAGGTA AAGG
1 AAGGTA AAGGTA AAGGTA AAGGTA AAGG
194919 CTGGGCATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (6 bp):
AAGGTA
Found at i:204232 original size:20 final size:20
Alignment explanation
Indices: 204185--204596 Score: 405
Period size: 20 Copynumber: 20.2 Consensus size: 20
204175 AATGACCAAC
204185 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
204204 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
204224 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
204244 AAGATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
204264 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
204286 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
204306 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
204326 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
204346 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
* *
204366 AGAATCGCAACGCGATCCAG
1 AAAATCGCAACGCGATTCAG
204386 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
204406 AGAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
204428 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
204448 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
*
204470 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
204490 AAAATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* *
204512 AGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
*
204532 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
204552 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
204572 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
204592 AAAAT
1 AAAAT
204597 GAGTAAATTC
Statistics
Matches: 333, Mismatches: 34, Indels: 51
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.00
19 28 0.08
20 223 0.67
21 7 0.02
22 68 0.20
23 6 0.02
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:204336 original size:40 final size:40
Alignment explanation
Indices: 204185--204596 Score: 460
Period size: 40 Copynumber: 10.1 Consensus size: 40
204175 AATGACCAAC
*
204185 AAAATCGCAACGCGATAT-CAA-AACCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TCCAAGAATCGCAACGCGATTTAG
* * **** *
204224 AAAAGCGCAACGTTGAAAAGAAG-ATCGCAACGCGATTCAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACGCGATTTAG
*
204264 AAAATCGCAACGCGATCTTCCAAGAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGA--TTCCAAGAATCGCAACGCGATTTAG
204306 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
**
204346 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
**
204386 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATCTTCC
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGAT-TTAG
* **
204427 AAGAATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCC
1 AA-AATCGCAACGCGATTCCA-AGAATCGCAACGCGAT-TTAG
* **
204469 AAGAATCGCAACGCGATT-CAGAAAATCGCAACGCGATCTTCC
1 AA-AATCGCAACGCGATTCCA-AGAATCGCAACGCGAT-TTAG
*
204511 AAGAATCGCAACGCGATT--AAGAAAATCGCAACGCGATTAAG
1 AA-AATCGCAACGCGATTCCAAG--AATCGCAACGCGATTTAG
*
204552 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
204592 AAAAT
1 AAAAT
204597 GAGTAAATTC
Statistics
Matches: 333, Mismatches: 27, Indels: 25
0.86 0.07 0.06
Matches are distributed among these distances:
39 13 0.04
40 166 0.50
41 11 0.03
42 143 0.43
ACGTcount: A:0.39, C:0.26, G:0.20, T:0.16
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTTAG
Found at i:204703 original size:6 final size:6
Alignment explanation
Indices: 204692--204765 Score: 141
Period size: 6 Copynumber: 12.5 Consensus size: 6
204682 GACACGTATT
204692 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
204740 ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
204766 CGAGACGAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.07
6 63 0.93
ACGTcount: A:0.32, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:205275 original size:6 final size:6
Alignment explanation
Indices: 205259--205302 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
205249 TCTCGTCTCG
205259 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
205303 AATACGTGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:205430 original size:20 final size:20
Alignment explanation
Indices: 205405--205849 Score: 511
Period size: 20 Copynumber: 21.8 Consensus size: 20
205395 CTCATTTTCT
205405 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
205425 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
205446 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
205465 GAAGATCGCGTTGCGATTTTCTT-
1 G-A-ATCGCGTTGCGA--TTCTTG
205488 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
205507 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
205529 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
205549 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
205571 GAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
205591 GAAGATCGCGTTGCGATTCTTG
1 G-A-ATCGCGTTGCGATTCTTG
*
205613 GAATCGCGTTGCGATTTTCTG
1 GAATCGCGTTGCGATTCT-TG
205634 G-ATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
205653 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
205673 AAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
205693 GAATCGCGTTGCGATTTTCTG
1 GAATCGCGTTGCGATTCT-TG
205714 G-ATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
205733 GAATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATTCTT-G
*
205753 AAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
205773 GAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGA--TTCTTG
205794 -AATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTCTTG
*
205813 GAAGATCGCGTTGCGATT-TTCT
1 G-A-ATCGCGTTGCGATTCTT-G
205835 GAATCGCGTTGCGAT
1 GAATCGCGTTGCGAT
205850 CTTCTTTTCA
Statistics
Matches: 373, Mismatches: 17, Indels: 70
0.81 0.04 0.15
Matches are distributed among these distances:
18 15 0.04
19 10 0.03
20 227 0.61
21 30 0.08
22 86 0.23
24 5 0.01
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.37
Consensus pattern (20 bp):
GAATCGCGTTGCGATTCTTG
Found at i:205453 original size:40 final size:40
Alignment explanation
Indices: 205398--205855 Score: 428
Period size: 42 Copynumber: 11.2 Consensus size: 40
205388 GAATTTACTC
*
205398 ATTTTCTGAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
205438 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
205480 ATTTTCTTAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
205522 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
205564 ATTTTCTGAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCG
1 ATTTTCTTAATCGCGTTGCGATTCTTGG-A-ATCGCGTTGCG
*
205606 A--TTCTTGGAATCGCGTTGCGATTTTCTGG-ATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCT-TGGAATCGCGTTGCG
**
205646 A--TTCTTGGAATCGCGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
205686 A--TTCTTGGAATCGCGTTGCGATTTTCTGG-ATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCT-TGGAATCGCGTTGCG
**
205726 A--TTCTTGGAATCGCGTTGCGATT-TTCTAAATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
205766 A--TTCTTGGAATCGCGTTGCGATTTTCTT--AATCGCGTTGCG
1 ATTTTCTT--AATCGCGTTGCGA--TTCTTGGAATCGCGTTGCG
*** *
205806 ATTCTTGGAAGATCGCGTTGCGATT-TTCTGAATCGCGTTGCG
1 ATT-TTCTTA-ATCGCGTTGCGATTCTT-GGAATCGCGTTGCG
*
205848 ATCTTCTT
1 ATTTTCTT
205856 TTCAACGTTG
Statistics
Matches: 380, Mismatches: 17, Indels: 41
0.87 0.04 0.09
Matches are distributed among these distances:
38 2 0.01
39 4 0.01
40 180 0.47
41 5 0.01
42 182 0.48
43 7 0.02
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (40 bp):
ATTTTCTTAATCGCGTTGCGATTCTTGGAATCGCGTTGCG
Found at i:205854 original size:20 final size:20
Alignment explanation
Indices: 205401--205908 Score: 396
Period size: 20 Copynumber: 24.9 Consensus size: 20
205391 TTTACTCATT
205401 TTCTGAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205422 TT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATC
*
205441 TTCTTAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205462 TT-GGAAGATCGCGTTGCGATT
1 TTCTG-A-ATCGCGTTGCGATC
*
205483 TTCTTAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205504 TT-GGAAGATCGCGTTGCGATT
1 TTCTG-A-ATCGCGTTGCGATC
205525 TTCTGAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205546 TT-GGAAGATCGCGTTGCGATT
1 TTCTG-A-ATCGCGTTGCGATC
205567 TTCTGAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
*
205588 TT-GGAAGATCGCGTTGCGATTC
1 TTCTG-A-ATCGCGTTGCGA-TC
* *
205610 TT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATC
*
205629 TTCTGGATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205650 TT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATC
*
205669 TTCTAAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205690 TT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATC
*
205709 TTCTGGATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205730 TT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATC
*
205749 TTCTAAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205770 TT-GGAATCGCGTTGCGATT
1 TTCTGAATCGCGTTGCGATC
*
205789 TTCTTAATCGCGTTGCGATTC
1 TTCTGAATCGCGTTGCGA-TC
* *
205810 TT-GGAAGATCGCGTTGCGATT
1 TTCTG-A-ATCGCGTTGCGATC
205831 TTCTGAATCGCGTTGCGATC
1 TTCTGAATCGCGTTGCGATC
** * * *
205851 TTCT-TTTCAACGTTGCGCTT
1 TTCTGAATC-GCGTTGCGATC
* *
205871 TTCTAAATCGCGTTGCGGT-
1 TTCTGAATCGCGTTGCGATC
205890 TT-TGATATCGCGTTGCGAT
1 TTCTGA-ATCGCGTTGCGAT
205909 TTTGTTGGTC
Statistics
Matches: 390, Mismatches: 65, Indels: 66
0.75 0.12 0.13
Matches are distributed among these distances:
18 2 0.01
19 34 0.09
20 231 0.59
21 53 0.14
22 70 0.18
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (20 bp):
TTCTGAATCGCGTTGCGATC
Found at i:205880 original size:40 final size:40
Alignment explanation
Indices: 205405--205911 Score: 548
Period size: 40 Copynumber: 12.4 Consensus size: 40
205395 CTCATTTTCT
**
205405 GAATCGCGTTGCGATTCTT-GGAATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGATT-TTCTAAATCGCGTTGCGA--TTCTTG
**
205446 -AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTTTCTT-
1 GAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGA--TTCTTG
** *
205488 -AATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTT-G
** *
205529 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATT-TTCT
1 GAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTT-G
**
205571 GAATCGCGTTGCGATTCTTGGAAGATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATT-TTCTAA-ATCGCGTTGCGATTCTTG
**
205613 GAATCGCGTTGCGATTTTCTGGATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
205653 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
**
205693 GAATCGCGTTGCGATTTTCTGGATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
205733 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
*
205773 GAATCGCGTTGCGATTTTCTTAATCGCGTTGCGATTCTTG
1 GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
* *
205813 GAAGATCGCGTTGCGATTTTCTGAATCGCGTTGCGA-TCTTC
1 G-A-ATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
*** * * *
205854 TTTTCAACGTTGCGCTTTTCTAAATCGCGTTGCGGTT-TT-
1 GAATC-GCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
205893 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
205912 GTTGGTCATT
Statistics
Matches: 428, Mismatches: 27, Indels: 24
0.89 0.06 0.05
Matches are distributed among these distances:
39 15 0.04
40 221 0.52
41 10 0.02
42 180 0.42
43 2 0.00
ACGTcount: A:0.16, C:0.20, G:0.27, T:0.38
Consensus pattern (40 bp):
GAATCGCGTTGCGATTTTCTAAATCGCGTTGCGATTCTTG
Found at i:207192 original size:56 final size:56
Alignment explanation
Indices: 207101--207208 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
207091 AATTTACTGT
207101 AGTAAATAAGTGTTTGGTCATCTTTTAATCATTCAA-TCTCTTGGTAATTAGACGGC
1 AGTAAATAAGTGTTTGGTCATCTTTTAATCATTCAACT-TCTTGGTAATTAGACGGC
*
207157 AGTAGATAAGTGTTTGGTCATCTTTTAATCATTCAACTTCTTGGTAATTAGA
1 AGTAAATAAGTGTTTGGTCATCTTTTAATCATTCAACTTCTTGGTAATTAGA
207209 GATGAAGTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
56 49 0.98
57 1 0.02
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.41
Consensus pattern (56 bp):
AGTAAATAAGTGTTTGGTCATCTTTTAATCATTCAACTTCTTGGTAATTAGACGGC
Found at i:220057 original size:2 final size:2
Alignment explanation
Indices: 220050--220108 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
220040 AATAAATGAA
220050 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
220092 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
220109 AAAAATGTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:220437 original size:12 final size:13
Alignment explanation
Indices: 220422--220477 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 13
220412 AAAATAGAAA
*
220422 ATATAATCA-AAT
1 ATATAATAATAAT
220434 ATAT-AT-ATAAT
1 ATATAATAATAAT
220445 A-ATAATAATAAT
1 ATATAATAATAAT
220457 A-ATAATAA-AAT
1 ATATAATAATAAT
220468 ATATAATAAT
1 ATATAATAAT
220478 GAAACGTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
10 3 0.08
11 12 0.31
12 24 0.62
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATAATAATAAT
Found at i:220448 original size:3 final size:3
Alignment explanation
Indices: 220440--220477 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
220430 AAATATATAT
220440 ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA TATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA AT
220478 GAAACGTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:223357 original size:7 final size:7
Alignment explanation
Indices: 223305--223575 Score: 176
Period size: 7 Copynumber: 38.9 Consensus size: 7
223295 TGCGACTGGA
223305 ATTATTAT
1 ATTA-TAT
*
223313 ATTATGT
1 ATTATAT
223320 ATTATAT
1 ATTATAT
223327 AGTT-TAT
1 A-TTATAT
223334 ATTATATT
1 ATTATA-T
223342 ATT-TAT
1 ATTATAT
223348 ATTATAT
1 ATTATAT
*
223355 ATTATGT
1 ATTATAT
223362 AGTT-TAT
1 A-TTATAT
*
223369 A-TAGTGT
1 ATTA-TAT
*
223376 ATTATAA
1 ATTATAT
* *
223383 AGTATACA
1 ATTATA-T
*
223391 AATATAT
1 ATTATAT
* *
223398 AGTATGTT
1 ATTAT-AT
223406 ATATAGTAT
1 AT-TA-TAT
223415 ATTATAT
1 ATTATAT
* *
223422 AGTATGT
1 ATTATAT
223429 ATTATAT
1 ATTATAT
223436 ATGT-TAT
1 AT-TATAT
*
223443 AATATAT
1 ATTATAT
223450 ATTAT-T
1 ATTATAT
223456 ATTATAGT
1 ATTATA-T
223464 ATT-TAT
1 ATTATAT
223470 A-TATAT
1 ATTATAT
223476 A-TATTAT
1 ATTA-TAT
223483 ATTATAT
1 ATTATAT
*
223490 -GTATAT
1 ATTATAT
223496 ATTATAT
1 ATTATAT
223503 ATTAT-T
1 ATTATAT
223509 A-TATAT
1 ATTATAT
223515 ATT-TAT
1 ATTATAT
*
223521 GTTATAT
1 ATTATAT
223528 ATTATAGT
1 ATTATA-T
223536 ATATATAT
1 AT-TATAT
*
223544 ATAATAT
1 ATTATAT
223551 A-TA-AT
1 ATTATAT
223556 ATTATAT
1 ATTATAT
223563 ATTATAT
1 ATTATAT
223570 ATTATA
1 ATTATA
223576 GTACATATAT
Statistics
Matches: 210, Mismatches: 26, Indels: 55
0.72 0.09 0.19
Matches are distributed among these distances:
5 8 0.04
6 38 0.18
7 117 0.56
8 37 0.18
9 9 0.04
10 1 0.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (7 bp):
ATTATAT
Found at i:223410 original size:2 final size:2
Alignment explanation
Indices: 223392--223598 Score: 123
Period size: 2 Copynumber: 111.0 Consensus size: 2
223382 AAGTATACAA
* *
223392 AT AT AT AGT AT GT -T AT AT AGT AT AT -T AT AT AGT AT GT AT -T
1 AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT
* *
223432 AT AT AT GT -T AT A- AT AT AT AT -T AT -T AT -T AT AGT AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
*
223470 AT AT AT AT AT -T AT AT -T AT AT GT AT AT AT -T AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
223508 -T AT AT AT AT TT AT GT -T AT AT AT -T AT AGT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
*
223547 AT AT AT A- AT AT -T AT AT AT -T AT AT AT -T AT AGT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* *
223586 TT AT -T AT TT AT AT
1 AT AT AT AT AT AT AT
223599 TTTGGATTTA
Statistics
Matches: 161, Mismatches: 17, Indels: 54
0.69 0.07 0.23
Matches are distributed among these distances:
1 21 0.13
2 128 0.80
3 12 0.07
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (2 bp):
AT
Found at i:223575 original size:12 final size:12
Alignment explanation
Indices: 223307--223569 Score: 158
Period size: 12 Copynumber: 20.7 Consensus size: 12
223297 CGACTGGAAT
*
223307 TATTATATTATG
1 TATTATATTATA
*
223319 TATTATA-TA-G
1 TATTATATTATA
223329 T-TTATATTATA
1 TATTATATTATA
223340 TTATTTATATTATA
1 -TA-TTATATTATA
223354 TATTATGTAGTTTATA
1 TATTA--TA--TTATA
* *
223370 TAGTGTATTATA
1 TATTATATTATA
* * *
223382 AAGTATACAAATATA
1 TA-T-TA-TATTATA
* *
223397 TAGTATGTTATA
1 TATTATATTATA
*
223409 TAGTATATTATA
1 TATTATATTATA
*
223421 TAGTATGTATTATA
1 TA-T-TATATTATA
*
223435 TATGTTATAATATA
1 TA--TTATATTATA
223449 TATTATTATTATA
1 TATTA-TATTATA
223462 GTATTTATATATATA
1 -TA-TTATAT-TATA
223477 TATTATATTATA
1 TATTATATTATA
*
223489 TGTATATATTATA
1 TAT-TATATTATA
223502 TATTAT-TATATA
1 TATTATAT-TATA
*
223514 TATTTATGTTATA
1 TA-TTATATTATA
*
223527 TATTATAGTATA
1 TATTATATTATA
*
223539 TA-TATATAATA
1 TATTATATTATA
*
223550 TATAATATTATA
1 TATTATATTATA
223562 TATTATAT
1 TATTATAT
223570 ATTATAGTAC
Statistics
Matches: 199, Mismatches: 28, Indels: 48
0.72 0.10 0.17
Matches are distributed among these distances:
9 5 0.03
10 4 0.02
11 12 0.06
12 76 0.38
13 37 0.19
14 42 0.21
15 15 0.08
16 8 0.04
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (12 bp):
TATTATATTATA
Found at i:223593 original size:7 final size:6
Alignment explanation
Indices: 223463--223600 Score: 62
Period size: 7 Copynumber: 20.8 Consensus size: 6
223453 ATTATTATAG
* * *
223463 TATTTA TATATA TATATTA TA-TTA TATGTA TATATTA TATATTA TTATATA
1 TATTTA TATTTA TAT-TTA TATTTA TATTTA TAT-TTA TAT-TTA -TATTTA
* * * *
223514 TATTTA TGTTATA TATTATA GTATATA TATATAA TATATAA TATTATA
1 TATTTA TATT-TA TATT-TA -TATTTA TAT-TTA TAT-TTA TATT-TA
**
223562 TATTATA TATTATA GTACATA TATTTA TTATTTA TATTT
1 TATT-TA TATT-TA -TATTTA TATTTA -TATTTA TATTT
223601 TGGATTTATT
Statistics
Matches: 106, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
5 5 0.05
6 34 0.32
7 59 0.56
8 8 0.08
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.56
Consensus pattern (6 bp):
TATTTA
Found at i:225153 original size:15 final size:15
Alignment explanation
Indices: 225133--225165 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
225123 CCCCTAATCT
225133 TTTAATCCT-TTTCAA
1 TTTAATCCTCTTT-AA
225148 TTTAATCCTCTTTAA
1 TTTAATCCTCTTTAA
225163 TTT
1 TTT
225166 TTGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATCCTCTTTAA
Found at i:225190 original size:29 final size:27
Alignment explanation
Indices: 225147--225206 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 27
225137 ATCCTTTTCA
* * *
225147 ATTTAATCCTCTTTAATTTTTGTTTTTTT
1 ATTTAATACTCTTT-ATTATT-TTATTTT
*
225176 ATTTAATACTTTTTATTATTTTATTTT
1 ATTTAATACTCTTTATTATTTTATTTT
225203 ATTT
1 ATTT
225207 TATTGTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 10 0.37
28 5 0.19
29 12 0.44
ACGTcount: A:0.22, C:0.07, G:0.02, T:0.70
Consensus pattern (27 bp):
ATTTAATACTCTTTATTATTTTATTTT
Found at i:228489 original size:30 final size:30
Alignment explanation
Indices: 228454--228621 Score: 131
Period size: 30 Copynumber: 5.5 Consensus size: 30
228444 TTATTTGTGG
*
228454 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTACTAT
* * * * * *
228484 TTTAGTCATTTAAATGTATGTTTTCACTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTACTAT
* *
228514 TTTAGTCCATTAAGTTTCTATTTTTTCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTACTAT
* * * * * *
228544 TTTGGACTTTTAAATTCCTATTTGTACTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTACTAT
* * *
228574 TTTGGTCCTTTAAGTTTATGTTTTT-CTCCAT
1 TTTAGTCCTTTAAGTTTCTATTTTTACT--AT
*
228605 TTTGGTCCTTGTAAGTT
1 TTTAGTCCTT-TAAGTT
228622 CATATACTTA
Statistics
Matches: 105, Mismatches: 30, Indels: 4
0.76 0.22 0.03
Matches are distributed among these distances:
29 2 0.02
30 85 0.81
31 12 0.11
32 6 0.06
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTCTATTTTTACTAT
Found at i:228521 original size:60 final size:60
Alignment explanation
Indices: 228454--228590 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
228444 TTATTTGTGG
* * *
228454 TTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGTCATTTAAA-T-GTATGTTTTCACTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGACATTTAAATTCCTAT-TTGT-ACTAT
* * * *
228514 TTTAGTCCATTAAGTTTCTATTTTTTCTATTTTGGACTTTTAAATTCCTATTTGTACTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGACATTTAAATTCCTATTTGTACTAT
*
228574 TTTGGTCCTTTAAGTTT
1 TTTAGTCCTTTAAGTTT
228591 ATGTTTTTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 59 0.89
61 4 0.06
62 3 0.05
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (60 bp):
TTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGACATTTAAATTCCTATTTGTACTAT
Found at i:229389 original size:16 final size:15
Alignment explanation
Indices: 229368--229400 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 15
229358 CGCATACCAG
229368 TTTTTTTGTCTTAAAA
1 TTTTTTT-TCTTAAAA
229384 TTTTTTTTCTTAAAA
1 TTTTTTTTCTTAAAA
229399 TT
1 TT
229401 GTCTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.24, C:0.06, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTTTTCTTAAAA
Found at i:229542 original size:24 final size:26
Alignment explanation
Indices: 229496--229555 Score: 88
Period size: 24 Copynumber: 2.4 Consensus size: 26
229486 AAATCACCAA
229496 TTTTTTAAAATAAAAGTCATACTTGT
1 TTTTTTAAAATAAAAGTCATACTTGT
* *
229522 TTTTTTAAAATAATA-T-TTACTTGT
1 TTTTTTAAAATAAAAGTCATACTTGT
229546 TTTTTTAAAA
1 TTTTTTAAAA
229556 AATGGTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
24 17 0.53
25 1 0.03
26 14 0.44
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (26 bp):
TTTTTTAAAATAAAAGTCATACTTGT
Found at i:233131 original size:2 final size:2
Alignment explanation
Indices: 233124--233159 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
233114 TATACCCATA
233124 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
233160 CAATAAAGCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:235047 original size:131 final size:130
Alignment explanation
Indices: 234792--235056 Score: 336
Period size: 131 Copynumber: 2.0 Consensus size: 130
234782 AAACCAAAAT
* * *
234792 CCCTAAAGATGGCCTGTCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAAAACTCTTCA
1 CCCTAAAAATGGCCTATCGTCCTCATCACGTAGGAACCGTGTCATCCACCAACCAAAACTCTTCA
* * * * *
234857 TCACGTAGTAGCCGTGTCACCCCTAGATAACCAGCAGTCCTGATTACTTATGAACCGTGTTATCA
66 TCACATAGGAGCCGTGTCACCCCTAGATAACCACCAGTCCTGATTACGTAGGAACCGTGTTATC-
234922 A
130 A
* * * * *
234923 CCCTAAAAATGTCCTATCGTCCTCATCGCGTAGGAACTGTGTCATCC-CCTAACCAGACCTCTTC
1 CCCTAAAAATGGCCTATCGTCCTCATCACGTAGGAACCGTGTCATCCACC-AACCAAAACTCTTC
* * * *
234987 ATCACATAGGAGCCGTGTCACCCTTAGATAACCAACCA-TCCTTATTGCGTAGGAATCGTGTTAT
65 ATCACATAGGAGCCGTGTCACCCCTAGATAACC-ACCAGTCCTGATTACGTAGGAACCGTGTTAT
235051 CA
129 CA
235053 CCCT
1 CCCT
235057 TCCCAAAAAT
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
130 7 0.06
131 105 0.91
132 3 0.03
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (130 bp):
CCCTAAAAATGGCCTATCGTCCTCATCACGTAGGAACCGTGTCATCCACCAACCAAAACTCTTCA
TCACATAGGAGCCGTGTCACCCCTAGATAACCACCAGTCCTGATTACGTAGGAACCGTGTTATCA
Found at i:235345 original size:3 final size:3
Alignment explanation
Indices: 235337--235375 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
235327 GTCTACCAAA
235337 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
235376 CTAACAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:245753 original size:38 final size:37
Alignment explanation
Indices: 245711--245913 Score: 154
Period size: 38 Copynumber: 5.5 Consensus size: 37
245701 TTTAAAAATA
**
245711 TATAATATATAGTTTTTGGAAACTTATTTTTGAAAAAG
1 TATAATATATAGTTTTTAAAAAC-TATTTTTGAAAAAG
* * * *
245749 TATAATATATACTTTTTAAAAAAATAGTTTTGAAAACG
1 TATAATATATAGTTTTT-AAAAACTATTTTTGAAAAAG
* *
245787 TATAATATAT-GATTTTAAAAAAC-ATTTTTGAAAACG
1 TATAATATATAG-TTTTTAAAAACTATTTTTGAAAAAG
* * *
245823 TATAATATAT-G-GTTTAAGAAC-ATTTTTGAAAAACA
1 TATAATATATAGTTTTTAAAAACTATTTTTGAAAAA-G
* *
245858 TATATATAATATAG-TTTTGAAAACATACTTTTG-AAAA-
1 TATA-AT-ATATAGTTTTTAAAAAC-TATTTTTGAAAAAG
*
245895 TGT-ATATATAGTTTTTAAA
1 TATAATATATAGTTTTTAAA
245914 TATTCTTGGA
Statistics
Matches: 135, Mismatches: 21, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
34 24 0.18
35 12 0.09
36 25 0.19
37 11 0.08
38 50 0.37
39 7 0.05
40 6 0.04
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.41
Consensus pattern (37 bp):
TATAATATATAGTTTTTAAAAACTATTTTTGAAAAAG
Found at i:245850 original size:34 final size:36
Alignment explanation
Indices: 245736--245904 Score: 143
Period size: 36 Copynumber: 4.6 Consensus size: 36
245726 TTGGAAACTT
* *
245736 ATTTTTGAAAAAGTATAATATAT-ACTTTTTAAAAAA-
1 ATTTTTGAAAACGTATAATATATGA--GTTTAAAAAAC
*
245772 ATAGTTTTGAAAACGTATAATATATGATTTTAAAAAAC
1 AT--TTTTGAAAACGTATAATATATGAGTTTAAAAAAC
*
245810 ATTTTTGAAAACGTATAATATATG-GTTT-AAGAAC
1 ATTTTTGAAAACGTATAATATATGAGTTTAAAAAAC
* **
245844 ATTTTTGAAAAACATATATATAATAT-AGTTTTGAAAAC
1 ATTTTTG-AAAACGTATA-AT-ATATGAGTTTAAAAAAC
*
245882 ATACTTTTGAAAATGTAT-ATATA
1 AT--TTTTGAAAACGTATAATATA
245905 GTTTTTAAAT
Statistics
Matches: 114, Mismatches: 8, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
34 12 0.11
35 12 0.11
36 29 0.25
37 20 0.18
38 28 0.25
39 8 0.07
40 5 0.04
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (36 bp):
ATTTTTGAAAACGTATAATATATGAGTTTAAAAAAC
Found at i:246044 original size:17 final size:16
Alignment explanation
Indices: 246022--246072 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
246012 GTAAGCTTAT
246022 TATTATTTTATATATTA
1 TATTATTTTATAT-TTA
* *
246039 TATTATATTATATTTT
1 TATTATTTTATATTTA
*
246055 TATTAATTTTATTTTTA
1 TATT-ATTTTATATTTA
246072 T
1 T
246073 TTTTTAGGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTATTTTATATTTA
Found at i:246067 original size:15 final size:15
Alignment explanation
Indices: 246021--246073 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
246011 AGTAAGCTTA
246021 TTATT-ATTTTATATAT
1 TTATTAATTTTAT-T-T
*
246037 TATATTATATTATATTT
1 T-TATTA-ATTTTATTT
246054 TTATTAATTTTATTT
1 TTATTAATTTTATTT
246069 TTATT
1 TTATT
246074 TTTTAGGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 13 0.41
16 6 0.19
17 6 0.19
18 1 0.03
19 6 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTATTAATTTTATTT
Found at i:248383 original size:77 final size:76
Alignment explanation
Indices: 248292--248446 Score: 267
Period size: 76 Copynumber: 2.0 Consensus size: 76
248282 ATTTTTGTGC
248292 GTGTTCTTTTTAAAATTATATAATTTAAATTTTTAAATTTTAAATA-ATTTTTTTAAAATTACTA
1 GTGTTCTTTTTAAAATTATATAATTTAAATTTTT-AATTTTAAATATA-TTTTTTAAAATTACTA
*
248356 GAATGTGACACGT
64 GAATATGACACGT
248369 GTGTTCTTTTTAAAATTATATAATTTAAATTTTTAATTTTAAATATATTTTTTAAAATTACTAGA
1 GTGTTCTTTTTAAAATTATATAATTTAAATTTTTAATTTTAAATATATTTTTTAAAATTACTAGA
*
248434 ATATGGCACGT
66 ATATGACACGT
248445 GT
1 GT
248447 CAATTAATTA
Statistics
Matches: 75, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
76 40 0.53
77 35 0.47
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (76 bp):
GTGTTCTTTTTAAAATTATATAATTTAAATTTTTAATTTTAAATATATTTTTTAAAATTACTAGA
ATATGACACGT
Found at i:258344 original size:65 final size:64
Alignment explanation
Indices: 258208--258352 Score: 161
Period size: 65 Copynumber: 2.2 Consensus size: 64
258198 TGAATTCATT
* * * *
258208 TTATGTACTGATGCACATCCATGCATTGATGCACTCCTGATTTTATTGAAACATCAAATGCATT
1 TTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATTTTATTGAAACATCAAATGCATA
* * * *
258272 TTATGTACCGATGCACAAACCATGCATCGATGCAGTCCTGGCTCTTT-TT-AAACATCGAATGTA
1 TTATGTACCGATGCAC-AACCATGCATCGATGCACTCCT-GAT-TTTATTGAAACATCAAATGCA
258335 -A
63 TA
258336 TTAGTGTACCGATGCAC
1 TTA-TGTACCGATGCAC
258353 CCCAAGTGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
64 18 0.26
65 44 0.64
66 4 0.06
67 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (64 bp):
TTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATTTTATTGAAACATCAAATGCATA
Found at i:259872 original size:116 final size:116
Alignment explanation
Indices: 259694--260005 Score: 518
Period size: 116 Copynumber: 2.7 Consensus size: 116
259684 AACAGACTTG
* *
259694 GAAAATCAAAATGAAATATTGAAAAAGGAGTTAGAGCTTTCAAAAATGAAATCTGAAAACTTTGA
1 GAAAATC-AAATGAAATATTGAAGAAGGATTTAGAGCTTTCAAAAATGAAATCTGAAAACTTTGA
259759 AAAATAAATTTTCAAATTAAACAAACTTCTTCTAGAAACTAAAATGCATTTT
65 AAAATAAATTTTCAAATTAAACAAACTTCTTCTAGAAACTAAAATGCATTTT
259811 GAAAATCAAATGAAATATTGAAGAAGGATTTAGAGCTTTCAAAAATGAAATCTGAAAACTTTGAA
1 GAAAATCAAATGAAATATTGAAGAAGGATTTAGAGCTTTCAAAAATGAAATCTGAAAACTTTGAA
* *
259876 AAAGAAATTTTCAAATTAAACAAACTTCTTCTAGAAACTAAAATGGATTTT
66 AAATAAATTTTCAAATTAAACAAACTTCTTCTAGAAACTAAAATGCATTTT
* * * *
259927 GAAAATCAAATGAAATATTGAAGAAGTATTTAGAGCTTTCAAAAATGAAATTTG-AAAGTATGGA
1 GAAAATCAAATGAAATATTGAAGAAGGATTTAGAGCTTTCAAAAATGAAATCTGAAAACT-TTGA
*
259991 AAAATAAAATTTCAA
65 AAAATAAATTTTCAA
260006 TTTGAAAATT
Statistics
Matches: 184, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
115 4 0.02
116 173 0.94
117 7 0.04
ACGTcount: A:0.50, C:0.09, G:0.13, T:0.29
Consensus pattern (116 bp):
GAAAATCAAATGAAATATTGAAGAAGGATTTAGAGCTTTCAAAAATGAAATCTGAAAACTTTGAA
AAATAAATTTTCAAATTAAACAAACTTCTTCTAGAAACTAAAATGCATTTT
Found at i:263944 original size:44 final size:44
Alignment explanation
Indices: 263859--263970 Score: 122
Period size: 44 Copynumber: 2.6 Consensus size: 44
263849 TTATGTGCAC
* *
263859 TGCATCGATACACTATGACAGTGTACCCATGCAATTTTTGAATA
1 TGCATCGATACACTATGACAGTGCACCCATGCAATTCTTGAATA
* * *
263903 TGTATCGATACACTATGA-AGGTGCACCGATGC-ATTCCTTGAATG
1 TGCATCGATACACTATGACA-GTGCACCCATGCAATT-CTTGAATA
* *
263947 TGCATCGATAGATTATG-CAGTGCA
1 TGCATCGATACACTATGACAGTGCA
263971 TCGATAGATT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
43 9 0.16
44 48 0.84
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (44 bp):
TGCATCGATACACTATGACAGTGCACCCATGCAATTCTTGAATA
Found at i:263971 original size:20 final size:20
Alignment explanation
Indices: 263946--263996 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
263936 TTCCTTGAAT
263946 GTGCATCGATAGATTATGCA
1 GTGCATCGATAGATTATGCA
263966 GTGCATCGATAGATTATGCA
1 GTGCATCGATAGATTATGCA
263986 GTGCATCGATA
1 GTGCATCGATA
263997 AACTCATCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (20 bp):
GTGCATCGATAGATTATGCA
Found at i:266693 original size:64 final size:65
Alignment explanation
Indices: 266619--266774 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
266609 ACACCCTAAT
* *
266619 TCGAATGCATTTTGTGTACCGATGCACA-GCCATGCATCGATACACTCCTGA-TTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATACACTCCTGACTCTT-TTGAAAC
266682 A
65 A
* * *
266683 TCGAATGCATTTTATGTACCGATGCACATATCATGCATCGATGCACTCCTGACTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATACACTCCTGACTCTTTTGAAACA
* * *
266748 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
266775 CCCAAGTGTA
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 27 0.33
65 51 0.63
66 3 0.04
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACATACCATGCATCGATACACTCCTGACTCTTTTGAAACA
Found at i:266784 original size:19 final size:19
Alignment explanation
Indices: 266760--266831 Score: 126
Period size: 19 Copynumber: 3.8 Consensus size: 19
266750 GAATGTAATT
266760 AGTGTACCGATGCACCCCA
1 AGTGTACCGATGCACCCCA
*
266779 AGTGTACCGATGCACTCCA
1 AGTGTACCGATGCACCCCA
*
266798 AGTGTACCGATGCACCCGA
1 AGTGTACCGATGCACCCCA
266817 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
266832 TAGGTCTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.26, C:0.32, G:0.24, T:0.18
Consensus pattern (19 bp):
AGTGTACCGATGCACCCCA
Found at i:267843 original size:10 final size:10
Alignment explanation
Indices: 267830--267854 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
267820 TTTTTCAAGA
267830 TTTTATAATT
1 TTTTATAATT
267840 TTTTATAATT
1 TTTTATAATT
267850 TTTTA
1 TTTTA
267855 AAAAAAATAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATAATT
Found at i:269050 original size:32 final size:32
Alignment explanation
Indices: 269014--269090 Score: 118
Period size: 33 Copynumber: 2.4 Consensus size: 32
269004 ACAAAGTTTA
* *
269014 CGATAATTGAAATACTTAAATACTTCCAAGTT
1 CGATAATTGAAATACTTAAAAACGTCCAAGTT
*
269046 CGATAAATTCAAATACTTAAAAACGTCCAAGTT
1 CGAT-AATTGAAATACTTAAAAACGTCCAAGTT
269079 CGATAATTGAAA
1 CGATAATTGAAA
269091 CAAAGTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
32 11 0.28
33 29 0.73
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (32 bp):
CGATAATTGAAATACTTAAAAACGTCCAAGTT
Found at i:273528 original size:18 final size:19
Alignment explanation
Indices: 273505--273547 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
273495 CAGCAGCACA
*
273505 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
273523 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
273543 TAACT
1 TAACT
273548 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:275556 original size:63 final size:63
Alignment explanation
Indices: 275452--275575 Score: 180
Period size: 63 Copynumber: 2.0 Consensus size: 63
275442 TATTAATCAT
*
275452 CTCGTCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
1 CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
* * *
275515 CTCGGCTTCATTATGTACTT-CTGCATTAC-CATCTTCTTCATGCACGGTGGTGGTATTTGGT
1 CTCGGCTTCATTATG-AATTGCTGCATTACTCA-CTTCTTCATGCACGGTGATGATATTTGGT
275576 AACTGACTTG
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.91
64 3 0.05
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (63 bp):
CTCGGCTTCATTATGAATTGCTGCATTACTCACTTCTTCATGCACGGTGATGATATTTGGTGA
Found at i:278157 original size:18 final size:19
Alignment explanation
Indices: 278134--278176 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
278124 CAACAACACA
*
278134 TAACTGCTC-TTAACAAGC
1 TAACTGCTCGTTAACAAAC
278152 TAACTGCTCGTTTAACAAAC
1 TAACTGCTCG-TTAACAAAC
278172 TAACT
1 TAACT
278177 ACCATTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
20 13 0.59
ACGTcount: A:0.35, C:0.26, G:0.09, T:0.30
Consensus pattern (19 bp):
TAACTGCTCGTTAACAAAC
Found at i:279582 original size:81 final size:81
Alignment explanation
Indices: 279381--279912 Score: 773
Period size: 81 Copynumber: 6.6 Consensus size: 81
279371 CCAAAGTGTC
* * * *
279381 AATTTACACCTTTATACCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCATTAACCG
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
279446 TTCATCTAACT-GCAT
66 TTCATCTAACTGGCAT
*
279461 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCGTTTACTCAACGGTCTTTAACCG
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
*
279526 TTCATCTAATTGGCAT
66 TTCATCTAACTGGCAT
* * * * *
279542 AATTGACATCTTTCTACCAAATACACAGCTAGGCCATTTATCTTTTACGCAACTGTCTTTAACCG
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
279607 TTCATCTAACTGGCAT
66 TTCATCTAACTGGCAT
** *
279623 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACATTCTTTAACCA
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
* *
279688 TTCATTTAACTGACAT
66 TTCATCTAACTGGCAT
* * * * * *
279704 AATTGATACCTTTCTGTCAAATGCACAACTAAGCCATTTATCTTTTACTCAACGATCTTTAATCG
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
279769 TTCATCTAACTGGCAT
66 TTCATCTAACTGGCAT
*
279785 AATTGACACCTTTCTGCCAAATGCATAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
*
279850 TTCATCTAA--AGCAT
66 TTCATCTAACTGGCAT
* ** * **
279864 AATTGATATATTTCTGTCAAATGCACAGCTAGGTTATTTATCTTTTACT
1 AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
279913 TTAGAATAGT
Statistics
Matches: 404, Mismatches: 47, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
79 46 0.11
80 70 0.17
81 288 0.71
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (81 bp):
AATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACTCAACGGTCTTTAACCG
TTCATCTAACTGGCAT
Found at i:280660 original size:19 final size:21
Alignment explanation
Indices: 280616--280667 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 21
280606 ACCCCACCAT
*
280616 GGTATCGATACTACTATACTAT
1 GGTATCGATACTACTATA-TAC
280638 GGTATCGATACT-CTAT-TAC
1 GGTATCGATACTACTATATAC
*
280657 GGTACCGATAC
1 GGTATCGATAC
280668 CATTTTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 12 0.43
21 4 0.14
22 12 0.43
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (21 bp):
GGTATCGATACTACTATATAC
Found at i:285659 original size:10 final size:10
Alignment explanation
Indices: 285626--285671 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
285616 TTTTAATGAA
*
285626 TTTTATTCAT
1 TTTTATTTAT
* *
285636 TTTAATTCAT
1 TTTTATTTAT
285646 TTTTATTGTAT
1 TTTTATT-TAT
285657 TTTTATTTAT
1 TTTTATTTAT
285667 TTTTA
1 TTTTA
285672 AAAAATGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
10 23 0.72
11 9 0.28
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:285668 original size:21 final size:20
Alignment explanation
Indices: 285626--285671 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
285616 TTTTAATGAA
285626 TTTTATTCATTTTAATTCAT
1 TTTTATTCATTTTAATTCAT
* * *
285646 TTTTATTGTATTTTTATTTAT
1 TTTTATT-CATTTTAATTCAT
285667 TTTTA
1 TTTTA
285672 AAAAATGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTATTCATTTTAATTCAT
Found at i:287180 original size:74 final size:74
Alignment explanation
Indices: 287091--287238 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
287081 GATAAAGTCA
287091 CAACTCAAATATTACCATCAATTAATGATCTACTCTCATTTTCTTAAAATATACAGTAAATAACA
1 CAACTCAAATATTACCATCAATTAATGATCTACTCTCATTTTCTTAAAATATACAGTAAATAACA
287156 TACATACAT
66 TACATACAT
*
287165 CAACTCAAATATTACCATCAATTAATGATCTACTCTCATTTTCTTAAAATATTCAGTAAATAACA
1 CAACTCAAATATTACCATCAATTAATGATCTACTCTCATTTTCTTAAAATATACAGTAAATAACA
287230 TACATACAT
66 TACATACAT
287239 GCATACACAC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (74 bp):
CAACTCAAATATTACCATCAATTAATGATCTACTCTCATTTTCTTAAAATATACAGTAAATAACA
TACATACAT
Found at i:291859 original size:419 final size:424
Alignment explanation
Indices: 291068--291868 Score: 1369
Period size: 419 Copynumber: 1.9 Consensus size: 424
291058 GACGACATAG
* **
291068 TGTAAACAGAGAGTTGATCCACAAAATTCAACTCAAACGGTTATGAGCTCAGATTTCATCATATC
1 TGTAAACAGAGAGTTAATCCACAAAATTCAACTCAAACACTTATGAGCTCAGATTTCATCATATC
*
291133 ACAATCAACAGGTTAACATCCATCTCAGACAAACATTAATTTTTTAATGAAAAAGAACGAGTTTA
66 ACAATCAACAGGTTAACATCCATCTCAGACAAACATTAAGTTTTTAATGAAAAAGAACGAG-TT-
* *
291198 AAACATATGAATAGGCCGACAACTATTTTGTAACATTTAATAGTTAGGGGATTCAACAAAGTAGT
129 ----ATATGAATA-G-CAACAACTATTTTGTAACATTTAAAAGTTAGGGGATTCAACAAAGTAGT
*
291263 ACCCTATAGTTGTATGACCGTTGTAACATTTAATAGTTAAAGGACTCAACAAAACAATTCTCTAT
188 ACCCTATAGTCGTATGACCGTTGTAACATTTAATAGTTAAAGGACTCAACAAAACAATTCTCTAT
* *
291328 ATTCGAGAGATCATTTGCGTACTTTACCCAGAATAATAATATCATATAAGAATGTGTATCGAAAC
253 AATCGAGAGATCATTTACGTACTTTACCCAGAATAATAATATCATATAAGAATGTGTATCGAAAC
* *
291393 AGAGTGAAGGTAAATGACTTACTAGAGTAGAGGATGAACAAAATATTGTAAAAACGTGACATAAT
318 AGAGTGAAGGTAAACGACTTACCAGAGTAGAGGATGAACAAAATATTGTAAAAACGTGACATAAT
291458 GTTTCGAGCACTGGCACGACGACATAATGTTTCGAGCACTGA
383 GTTTCGAGCACTGGCACGACGACATAATGTTTCGAGCACTGA
291500 TGTAAACAGAGAGTTAATCCACAAAATTCAACTCAAACACTTATGAGCTCAGATTTCATCATATC
1 TGTAAACAGAGAGTTAATCCACAAAATTCAACTCAAACACTTATGAGCTCAGATTTCATCATATC
*
291565 ACAATCAACGGGTTAACATCCATCTCAGACAAACATTAAGTTTTTAATGAAAAAGAACGAG-T-T
66 ACAATCAACAGGTTAACATCCATCTCAGACAAACATTAAGTTTTTAATGAAAAAGAACGAGTTAT
291628 -TGAA-A-CAACAACTATTTTGTAACATTTAAAAGTTAGGGGATTCAACAAAGTAGTACCCTATA
131 ATGAATAGCAACAACTATTTTGTAACATTTAAAAGTTAGGGGATTCAACAAAGTAGTACCCTATA
* *
291690 GTCGTATGACCGTTGTAACATTTAATAGTTAAAGGACTCAACAAAATAATTCTCTTTAATCGAGA
196 GTCGTATGACCGTTGTAACATTTAATAGTTAAAGGACTCAACAAAACAATTCTCTATAATCGAGA
291755 GATCATTTACGTACTTTACCCAGAATAATAATATCATATAAGAATGTGTATCGAAACAGAGTGAA
261 GATCATTTACGTACTTTACCCAGAATAATAATATCATATAAGAATGTGTATCGAAACAGAGTGAA
291820 GGTAAACGACTTACCAGAGTAGAGGATGAACAAAATATTGTAAAAACGT
326 GGTAAACGACTTACCAGAGTAGAGGATGAACAAAATATTGTAAAAACGT
291869 CAACAGCAAG
Statistics
Matches: 355, Mismatches: 14, Indels: 13
0.93 0.04 0.03
Matches are distributed among these distances:
419 227 0.64
422 1 0.00
423 4 0.01
424 1 0.00
430 1 0.00
432 121 0.34
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (424 bp):
TGTAAACAGAGAGTTAATCCACAAAATTCAACTCAAACACTTATGAGCTCAGATTTCATCATATC
ACAATCAACAGGTTAACATCCATCTCAGACAAACATTAAGTTTTTAATGAAAAAGAACGAGTTAT
ATGAATAGCAACAACTATTTTGTAACATTTAAAAGTTAGGGGATTCAACAAAGTAGTACCCTATA
GTCGTATGACCGTTGTAACATTTAATAGTTAAAGGACTCAACAAAACAATTCTCTATAATCGAGA
GATCATTTACGTACTTTACCCAGAATAATAATATCATATAAGAATGTGTATCGAAACAGAGTGAA
GGTAAACGACTTACCAGAGTAGAGGATGAACAAAATATTGTAAAAACGTGACATAATGTTTCGAG
CACTGGCACGACGACATAATGTTTCGAGCACTGA
Found at i:295977 original size:17 final size:17
Alignment explanation
Indices: 295951--295985 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
295941 TTATGGTGTC
295951 TCGATCACACATTAAAA
1 TCGATCACACATTAAAA
*
295968 TCGATGACACATTAAAA
1 TCGATCACACATTAAAA
295985 T
1 T
295986 GAAACGGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.09, T:0.26
Consensus pattern (17 bp):
TCGATCACACATTAAAA
Found at i:298644 original size:24 final size:23
Alignment explanation
Indices: 298610--298673 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
298600 AAAAAAACAT
* *
298610 AAAAATAGAGAAAATAAATAAATA
1 AAAAAAAGAGAAAA-AAATAAAAA
*
298634 AGAAAAAGAGAAAAAAATAAAAA
1 AAAAAAAGAGAAAAAAATAAAAA
* *
298657 AAAAAAACAAAAAAAAA
1 AAAAAAAGAGAAAAAAA
298674 AGAAGAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 22 0.65
24 12 0.35
ACGTcount: A:0.83, C:0.02, G:0.08, T:0.08
Consensus pattern (23 bp):
AAAAAAAGAGAAAAAAATAAAAA
Found at i:298662 original size:13 final size:13
Alignment explanation
Indices: 298644--298674 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
298634 AGAAAAAGAG
*
298644 AAAAAAATAAAAA
1 AAAAAAACAAAAA
298657 AAAAAAACAAAAA
1 AAAAAAACAAAAA
298670 AAAAA
1 AAAAA
298675 GAAGAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.94, C:0.03, G:0.00, T:0.03
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:298686 original size:13 final size:11
Alignment explanation
Indices: 298591--298687 Score: 61
Period size: 11 Copynumber: 8.5 Consensus size: 11
298581 AATATATAGT
*
298591 AAAAAGAAGAA
1 AAAAAGAAAAA
*
298602 AAAAACATAAAA
1 AAAAAGA-AAAA
* *
298614 ATAGAGAAAATA
1 AAAAAGAAAA-A
* *
298626 AATAAATAAGAA
1 AA-AAAGAAAAA
*
298638 AAAGAGAAAAA
1 AAAAAGAAAAA
*
298649 AATAA-AAAAA
1 AAAAAGAAAAA
*
298659 AAAAACAAAAA
1 AAAAAGAAAAA
298670 AAAAAGAAGAAA
1 AAAAAGAA-AAA
298682 GAAAAA
1 -AAAAA
298688 TACTTCAAGA
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
10 9 0.14
11 30 0.47
12 15 0.23
13 10 0.16
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.06
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:299503 original size:29 final size:28
Alignment explanation
Indices: 299433--299506 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
299423 GCCAACATGT
* *
299433 AACATATTACCTCCCAAAATTAACCTGA
1 AACACATTACTTCCCAAAATTAACCTGA
* *
299461 AACACATTACTTCCCCAAATTAATCTGA
1 AACACATTACTTCCCAAAATTAACCTGA
299489 AACAC-TCTACTTTCCCAA
1 AACACAT-TAC-TTCCCAA
299507 GTCAGCCTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.03
28 32 0.82
29 6 0.15
ACGTcount: A:0.39, C:0.31, G:0.03, T:0.27
Consensus pattern (28 bp):
AACACATTACTTCCCAAAATTAACCTGA
Found at i:301947 original size:54 final size:54
Alignment explanation
Indices: 301872--302268 Score: 476
Period size: 54 Copynumber: 7.4 Consensus size: 54
301862 AGTTTCCTGA
* * **
301872 TGATTTCTTCAAATGATTTTTGAAAGAATTTAAGCATAATTTTTAGGGGTTTCT
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
*
301926 TGATGTCTTCAAATGAATTTTGAAAAAAGCTAAGCATAATTTTTAGGGGTTTCT
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
* * * * * * *
301980 TGATGTATTCAAATGATTTTTGAAAGAAGCTAAGCTTGATTTTCAAGGGTTTTT
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
* * * *
302034 TGATGTTTTC-AATGATTTTTGAAAGAAGCTAAGCATGATTTTTAGGGGGTTTGT
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTA-GGGGTTTCT
* *
302088 TGATGTCTTCAAATGAATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCT
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
* * * * *
302142 TGATCTCTTCAAATGAATTTTGAAAGAAGATGAGCCTGATTTTTAGGGGTTT-T
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
* * * * * * *
302195 TGATGTTTTCAAATGAATTTT-AATGGAGCTAAGCCTTATTTTCAAGGGTTTCT
1 TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
* *
302248 TTATGTCTTCCAATGAATTTT
1 TGATGTCTTCAAATGAATTTT
302269 TTAAGAAACT
Statistics
Matches: 299, Mismatches: 41, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
52 23 0.08
53 71 0.24
54 175 0.59
55 30 0.10
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.43
Consensus pattern (54 bp):
TGATGTCTTCAAATGAATTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCT
Found at i:302120 original size:162 final size:161
Alignment explanation
Indices: 301879--302268 Score: 541
Period size: 162 Copynumber: 2.4 Consensus size: 161
301869 TGATGATTTC
**
301879 TTCAAATGATTTTTGAAAGAATTTAAGCATAATTTTTAGGGGTTTCTTGATGTCTTCAAATGAAT
1 TTCAAATGATTTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCTTGATGTCTTCAAATGAAT
* *
301944 TTTGAAAAAAGCTAAGCATAATTTTTAGGGGTTTCTTGATGTATTCAAATGATTTTTGAAAGAAG
66 TTTGAAAAAAGCTAAGCATAATTTTTAGGGGTTTCTTGATCTATTCAAATGAATTTTGAAAGAAG
* * *
302009 CTAAGCTTGATTTTCAAGGGTTTTTTGATGTT
131 ATAAGCCTGATTTT-AAGGGGTTTTTGATGTT
* *
302041 TTC-AATGATTTTTGAAAGAAGCTAAGCATGATTTTTAGGGGGTTTGTTGATGTCTTCAAATGAA
1 TTCAAATGATTTTTGAAAGAAGCTAAGCATAATTTTTA-GGGGTTTCTTGATGTCTTCAAATGAA
* * *
302105 TTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATCTCTTCAAATGAATTTTGAAAGAA
65 TTTTGAAAAAAGCTAAGCATAATTTTTAGGGGTTTCTTGATCTATTCAAATGAATTTTGAAAGAA
* *
302170 GATGAGCCTGATTTTTAGGGGTTTTTGATGTT
130 GATAAGCCTGATTTTAAGGGGTTTTTGATGTT
* * * * * * * * *
302202 TTCAAATGAATTTT-AATGGAGCTAAGCCTTATTTTCAAGGGTTTCTTTATGTCTTCCAATGAAT
1 TTCAAATGATTTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCTTGATGTCTTCAAATGAAT
302266 TTT
66 TTT
302269 TTAAGAAACT
Statistics
Matches: 202, Mismatches: 24, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
160 26 0.13
161 67 0.33
162 109 0.54
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (161 bp):
TTCAAATGATTTTTGAAAGAAGCTAAGCATAATTTTTAGGGGTTTCTTGATGTCTTCAAATGAAT
TTTGAAAAAAGCTAAGCATAATTTTTAGGGGTTTCTTGATCTATTCAAATGAATTTTGAAAGAAG
ATAAGCCTGATTTTAAGGGGTTTTTGATGTT
Found at i:302290 original size:54 final size:54
Alignment explanation
Indices: 301779--302305 Score: 457
Period size: 54 Copynumber: 9.8 Consensus size: 54
301769 TCGATATCAT
* * *
301779 ATTTTTAAAGAAACTAAGTTTGA-TTTTAGGGGTTTCTTGATGTTTTCAAAT-A
1 ATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* * * * * * * *
301831 ATTTTAAAAAAATCTGAG-TCCGA-TTTTCGGAAGTTTCCTGATGATTTCTTCAAATG-
1 ATTTTTAAAGAAGCTAAGCT-TGATTTTTAGG-GGTTT-CT--TGATGTCTTCAAATGA
** * *
301887 ATTTTTGAAAGAATTTAAGCATAATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
1 ATTTTT-AAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* * * * *
301942 ATTTTGAAAAAAGCTAAGCATAATTTTTAGGGGTTTCTTGATGTATTCAAATG-
1 ATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* * * *
301995 ATTTTTGAAAGAAGCTAAGCTTGATTTTCAAGGGTTTTTTGATGTTTTC-AATG-
1 ATTTTT-AAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* *
302048 ATTTTTGAAAGAAGCTAAGCATGATTTTTAGGGGGTTTGTTGATGTCTTCAAATGA
1 ATTTTT-AAAGAAGCTAAGCTTGATTTTTA-GGGGTTTCTTGATGTCTTCAAATGA
* * * * *
302104 ATTTTGAAATAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATCTCTTCAAATGA
1 ATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* * * * *
302158 ATTTTGAAAGAAGATGAGCCTGATTTTTAGGGGTTT-TTGATGTTTTCAAATGA
1 ATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* * * * * *
302211 A-TTTTAATGGAGCTAAGCCTT-ATTTTCAAGGGTTTCTTTATGTCTTCCAATGA
1 ATTTTTAAAGAAGCTAAG-CTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
* * * * *
302264 ATTTTTTAAGAAACTAAGTTTGATTTTCA-AGGTTTCTTGATG
1 ATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATG
302306 AGTAAGTCCC
Statistics
Matches: 390, Mismatches: 67, Indels: 35
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.00
52 45 0.12
53 87 0.22
54 184 0.47
55 29 0.07
56 24 0.06
57 14 0.04
58 6 0.02
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (54 bp):
ATTTTTAAAGAAGCTAAGCTTGATTTTTAGGGGTTTCTTGATGTCTTCAAATGA
Found at i:302683 original size:239 final size:236
Alignment explanation
Indices: 302352--303114 Score: 951
Period size: 239 Copynumber: 3.2 Consensus size: 236
302342 ATGATGCTTG
* * * *
302352 AATCCTTCGGGTCATCTATAAGCCTTTCCAGCAAGATGATAAGT-TATCCGGGACATCCATAAGA
1 AATCCTTCAGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCT-TTC-GGCCATCCATAAGA
* * *
302416 CCTTCGGGCATGATATTTTCACATGATTTTCAAAAAAAATGAGAAAACGATTCCAAAGTTTCTCA
64 CCTTAGGGTAGGAT-TTTTCACATGATTTTCAAAAAAAATGAGAAAACGATTCCAAAGTTTCTCA
* *
302481 TTTAAATCTGTTCTGAAAATTGATTTTTTTTAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
128 TTTAAATAT-TTATGAAAATTGATTTTTTTTAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
* * * *
302546 GTAAGTCTTTTGGGCCATCAATAAGTATTTCTAGCATGTTGCCTA
192 GTAAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGTTGCCTA
* * *
302591 AATCTTTCAGGTTATCTATAAGCCTTTTGAGCAAGATGATAAGTCTTTCAGGCCATCCATAAGAC
1 AATCCTTCAGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCTTTC-GGCCATCCATAAGAC
** ** *
302656 CTTAGGGTAGGATGTTTTCACATGATTTTCGGAAAAAATGAGGAAATGGTTTCCAAAGTTTCTCA
65 CTTAGGGTAGGAT-TTTTCACATGATTTTCAAAAAAAATGA-GAAAACGATTCCAAAGTTTCTCA
*
302721 TTTAAATATTTTATGAAATTTGATTTTTTTTAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
128 TTTAAATA-TTTATGAAAATTGATTTTTTTTAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTA
*
302786 GTAAGTCCTTTGGGCCATCAGTAAGCCTTTCAAGCAT-TATGCCTA
192 GTAAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGT-TGCCTA
* *
302831 AATCCTTC-GGTCATCTAAAAGCCTTTTGAGCAAGATGATAAGTTCTTT-GGACCATCCATAAGA
1 AATCCTTCAGGTCATCTATAAGCCTTTCGAGCAAGATGATAAG-TCTTTCGG-CCATCCATAAGA
* * * *
302894 CCGTTAGGCT-GGATTTTTCACATGATTTTCAAAACAAATGAGAAAGCGATTTCTAAAGTTTCTC
64 CC-TTAGGGTAGGATTTTTCACATGATTTTCAAAAAAAATGAGAAAACGA-TTCCAAAGTTTCTC
* * * ***
302958 ATTTAAATAATTTTTTAAAATTAATTTTTCAAAAAAAAGTAAGAAAACGATTTCCAAAGTTTCTT
127 ATTTAAAT-ATTTATGAAAATTGATTTTT----TTTAAGTAAGAAAACGATTTCCAAAGTTTCTT
* * * * * *
303023 ACTTAGTAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGTATGATGCTTA
187 ACTTAGTAAGTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGTTGCCTA
*
303073 AATCCTTCAAGTCATCTATAAGCCTTTCGAGCAAGATGATAA
1 AATCCTTCAGGTCATCTATAAGCCTTTCGAGCAAGATGATAA
303115 TTTCTTCGAG
Statistics
Matches: 456, Mismatches: 53, Indels: 26
0.85 0.10 0.05
Matches are distributed among these distances:
237 5 0.01
238 62 0.14
239 142 0.31
240 137 0.30
241 1 0.00
242 79 0.17
243 30 0.07
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Consensus pattern (236 bp):
AATCCTTCAGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGTCTTTCGGCCATCCATAAGACC
TTAGGGTAGGATTTTTCACATGATTTTCAAAAAAAATGAGAAAACGATTCCAAAGTTTCTCATTT
AAATATTTATGAAAATTGATTTTTTTTAAGTAAGAAAACGATTTCCAAAGTTTCTTACTTAGTAA
GTCCTTTGGGCCATCAGTAAGTCTTTCAAGCATGTTGCCTA
Found at i:303195 original size:25 final size:25
Alignment explanation
Indices: 303167--303215 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
303157 ATATGGTGTT
303167 TAAAAAA-AGAAAAATAATAAAATAA
1 TAAAAAAGAGAAAAA-AATAAAATAA
303192 TAAAAAAGAGAAAAAAATAAAATA
1 TAAAAAAGAGAAAAAAATAAAATA
303216 TGCTAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (25 bp):
TAAAAAAGAGAAAAAAATAAAATAA
Found at i:303724 original size:116 final size:115
Alignment explanation
Indices: 303520--304107 Score: 681
Period size: 116 Copynumber: 5.1 Consensus size: 115
303510 GAAGACTTGA
* *
303520 CGATTCCATCACAGAAGGAGGTGGATCAACATTTCAGGGGAGAGTTAATAATGAAAAGAACTC-T
1 CGATTCCATCACAGAAGGAGGTGGATCAACATTTCAGGGGAGAGTTCATAATGAGAAGAACTCAT
* * *
303584 TTCGATGAAGGATAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
66 CT-GATG-AGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
* ** * *
303636 CGATTACATCATGGAAGTAGGTGGATCAACATTTCAGGGGAGAGTTCATAATGAGAACAACTCAT
1 CGATTCCATCACAGAAGGAGGTGGATCAACATTTCAGGGGAGAGTTCATAATGAGAAGAACTCAT
* *
303701 CTGATGAGTGAGAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTT-G-G
66 CTGATGAG-GAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
* * *
303750 AGATTCAATCACAGAAGGAGGTGGATCAACATTTCAAGGGAGAGTTCATAATGAGAAGAACTCAT
1 CGATTCCATCACAGAAGGAGGTGGATCAACATTTCAGGGGAGAGTTCATAATGAGAAGAACTCAT
* *
303815 CTGATGAAGGAGAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTAGCT
66 CTGATG-AGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
* ** * **
303866 CGATTCCATCACAAAATAAGGTGGGTCAACATTTCCAGTAG-GAGTTCATAATGAGAAGAACTCA
1 CGATTCCATCACAGAAGGAGGTGGATCAACATTT-CAGGGGAGAGTTCATAATGAGAAGAACTCA
* * * * * * *
303930 TCCGACGAGGGAGAAGATGTTCATAATTATAAGAACTTGTTTAACCTT-GTT
65 TCTGATGA-GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
* * * ** * *
303981 TGATTCCATCACAGAAGGAGATGGATCAATATTTCCAGTAGAGGGTTCATAATGAGAATAACTCA
1 CGATTCCATCACAGAAGGAGGTGGATCAACATTT-CAGGGGAGAGTTCATAATGAGAAGAACTCA
* *
304046 TCCT-ATGAGG-G-AGAAATTCATAATGAGAATAACTTGTTCAACCTTAGCT
65 T-CTGATGAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
304095 C-ATTTCCATCACA
1 CGA-TTCCATCACA
304108 TAAAGAATTG
Statistics
Matches: 402, Mismatches: 59, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
113 29 0.07
114 111 0.28
115 45 0.11
116 211 0.52
117 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (115 bp):
CGATTCCATCACAGAAGGAGGTGGATCAACATTTCAGGGGAGAGTTCATAATGAGAAGAACTCAT
CTGATGAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
Found at i:303930 original size:230 final size:230
Alignment explanation
Indices: 303521--304107 Score: 749
Period size: 230 Copynumber: 2.6 Consensus size: 230
303511 AAGACTTGAC
* * * *
303521 GATTCCATCACAGAAGGAGGTGGATCAACATTTCAGGGGAGAGTTAATAATGAAAAGAACTC-TT
1 GATTCCATCACAGAAGGAGGTGGATCAACATTTCAAGGGAGAGTTCATAATGAGAAGAACTCATC
* * * * **
303585 TCGATGAAGGATAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTACATCATGG
66 T-GATGAAGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTAGCTCGATTCCATCA-CA
* * * * *
303650 AAGTAGGTGGATCAACATTTCAGGGGAGAGTTCATAATGAGAACAACTCATCTGATGAGTGAGAA
129 AAATAGGTGGATCAACATTTCAGGAGAGAGTTCATAATGAGAACAACTCATCCGACGAGGGAGAA
303715 GAAGTTCATAATGAGAAGAAATTGTTCAACCTTG-GA
194 GAAGTTCATAATGAGAAGAAATTGTTCAACCTTGTGA
*
303751 GATTCAATCACAGAAGGAGGTGGATCAACATTTCAAGGGAGAGTTCATAATGAGAAGAACTCATC
1 GATTCCATCACAGAAGGAGGTGGATCAACATTTCAAGGGAGAGTTCATAATGAGAAGAACTCATC
*
303816 TGATGAAGGAGAAGAAGTTCATAATGAGAATAACTTGTTTAACCTTAGCTCGATTCCATCACAAA
66 TGATGAAGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTAGCTCGATTCCATCACAAA
* * *
303881 ATAAGGTGGGTCAACATTTCCAGTAG-GAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAA
131 AT-AGGTGGATCAACATTT-CAGGAGAGAGTTCATAATGAGAACAACTCATCCGACGAGGGAGAA
* * * * * **
303945 GATGTTCATAATTATAAGAACTTGTTTAACCTTGTTT
194 GAAGTTCATAATGAGAAGAAATTGTTCAACCTTGTGA
* * * * * *
303982 GATTCCATCACAGAAGGAGATGGATCAATATTTCCAGTAGAGGGTTCATAATGAGAATAACTCAT
1 GATTCCATCACAGAAGGAGGTGGATCAACATTTCAAG-GGAGAGTTCATAATGAGAAGAACTCAT
*
304047 CCT-ATG-AGG-G-AGAAATTCATAATGAGAATAACTTGTTCAACCTTAGCTC-ATTTCCATCAC
65 -CTGATGAAGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTAGCTCGA-TTCCATCAC
304107 A
128 A
304108 TAAAGAATTG
Statistics
Matches: 314, Mismatches: 36, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
228 1 0.00
229 50 0.16
230 192 0.61
231 42 0.13
232 27 0.09
233 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (230 bp):
GATTCCATCACAGAAGGAGGTGGATCAACATTTCAAGGGAGAGTTCATAATGAGAAGAACTCATC
TGATGAAGGAGAAGAAGTTCATAATGAGAATAACTTGTTCAACCTTAGCTCGATTCCATCACAAA
ATAGGTGGATCAACATTTCAGGAGAGAGTTCATAATGAGAACAACTCATCCGACGAGGGAGAAGA
AGTTCATAATGAGAAGAAATTGTTCAACCTTGTGA
Found at i:304448 original size:202 final size:200
Alignment explanation
Indices: 303976--304448 Score: 569
Period size: 202 Copynumber: 2.4 Consensus size: 200
303966 TTGTTTAACC
* * * * *
303976 TTGTTTGATTCCATCACAGAAGGAGATGGATCAATATTTCCAGT-AGAGGGTTCATAATGAGAAT
1 TTGTTTGATTCCTTCACAGAAGGAGGTGGATCAACATTTCCAGTGA-AGAGTTCATAATGAGAAA
* * *
304040 AACTCATCCTATGAGGGAGAAATTCATAATGAGAATAACTTGTTCAACCTTAGCTCATTTCCATC
65 AACTCATCCGATCAGGGAGAAATTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATC
* * * *
304105 ACATAAAGAATTGGAACAGCATCAATACTTGGCTCATCCATCGAATATGGAGTTAGATCAGCATC
130 ACATAAAGAATTAGAACAACACCAATACTTGGCTCATCCATCGAATAAGGAGTTAGATCAGCATC
304170 ATCACT
195 ATCACT
** * * * * *
304176 TTGTTCAATT-CTATCACGGAAGAAGGTGGATCAACATTTCCAGTGAAAAGTTCAAAATGAGAAG
1 TTGTTTGATTCCT-TCACAGAAGGAGGTGGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAA
304240 AACTCATCCGATCAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTT-
65 AACTCATCCGATCAGGGAG-A-AA-TTCATAATGAGAAGAACTTGTTCAACCTTAGCTC-ATTTC
* * * * * ** *
304304 CATCACATAAGGAATTAGAATAACACCGA-CCTTGGCTTATCCATCTCATAAGGAGTTGGATCAG
126 CATCACATAAAGAATTAGAACAACACCAATACTTGGCTCATCCATCGAATAAGGAGTTAGATCAG
304368 CATCATCACT
191 CATCATCACT
* * * *
304378 TTGTTTGATTCCTTCCCAGAAGGAGGTGGATCAACATTTCTC-GTGAAGAGTTCGTACTGAAAAA
1 TTGTTTGATTCCTTCACAGAAGGAGGTGGATCAACATTTC-CAGTGAAGAGTTCATAATGAGAAA
304442 AACTCAT
65 AACTCAT
304449 ATGAGGAAAG
Statistics
Matches: 228, Mismatches: 37, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
199 1 0.00
200 66 0.29
201 2 0.01
202 96 0.42
203 59 0.26
204 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (200 bp):
TTGTTTGATTCCTTCACAGAAGGAGGTGGATCAACATTTCCAGTGAAGAGTTCATAATGAGAAAA
ACTCATCCGATCAGGGAGAAATTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATTTCCATCA
CATAAAGAATTAGAACAACACCAATACTTGGCTCATCCATCGAATAAGGAGTTAGATCAGCATCA
TCACT
Found at i:304608 original size:3 final size:3
Alignment explanation
Indices: 304600--304633 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
304590 TTTTACCCAT
304600 ATA ATA ATAA ATA ATA ATA ATA AT- ATA ATA ATA A
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
304634 ATGAATGAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:308875 original size:18 final size:17
Alignment explanation
Indices: 308848--308883 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
308838 GACATATATA
308848 ATATGTGGTCCTTAGGG
1 ATATGTGGTCCTTAGGG
*
308865 ATATAGTGGTCCTTCGGG
1 ATAT-GTGGTCCTTAGGG
308883 A
1 A
308884 CATTTCTACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.33
Consensus pattern (17 bp):
ATATGTGGTCCTTAGGG
Found at i:311254 original size:2 final size:2
Alignment explanation
Indices: 311247--311284 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
311237 ATCGTGATAC
311247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
311285 TTAAATACTT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:311437 original size:2 final size:2
Alignment explanation
Indices: 311430--311487 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
311420 CTTGAAAAAT
311430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
311472 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
311488 ACTTAAATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:316449 original size:14 final size:14
Alignment explanation
Indices: 316430--316460 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
316420 AGATTGGACT
316430 GAATATAAATGAAC
1 GAATATAAATGAAC
316444 GAATATAAATGAAC
1 GAATATAAATGAAC
316458 GAA
1 GAA
316461 CGTAAACGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (14 bp):
GAATATAAATGAAC
Found at i:321289 original size:60 final size:59
Alignment explanation
Indices: 321201--321350 Score: 176
Period size: 60 Copynumber: 2.5 Consensus size: 59
321191 CATCATTTTA
* * * * *
321201 AATTGGTCCTTAGACTTTGGAATATTCTAATCTT-ATCCCTAAACTATGACTCTCATTCT
1 AATTAGTCCTTAAACTTTTGAATATTCTAAT-TTCATCCATAAACTATGAATCTCATTCT
* *
321260 AATTAGTCCTTAAACTTTTGAACATTTCTAATTTCATCCATAAACTATGAATTTCATTCT
1 AATTAGTCCTTAAACTTTTGAATA-TTCTAATTTCATCCATAAACTATGAATCTCATTCT
* **
321320 ATATTAATCCCCAAACTTTTGAATATTCTAA
1 A-ATTAGTCCTTAAACTTTTGAATATTCTAA
321351 ACCATAGTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 22 0.29
60 36 0.47
61 19 0.25
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (59 bp):
AATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCATAAACTATGAATCTCATTCT
Found at i:321541 original size:60 final size:59
Alignment explanation
Indices: 321444--321620 Score: 232
Period size: 60 Copynumber: 3.0 Consensus size: 59
321434 ACTATATGCA
321444 TATAGTTT-GGGATGAAATTAAAATATTCAAAAAGTTTAGGGATTAATTTAGAATGAAATT
1 TATAGTTTAGGGATGAAATTAAAATATT-AAAAAGTTTAGGGATTAATTTAGAATGAAA-T
* * *
321504 TATAGTTTAGGGATGAAAATAAAATATTAAAAAGTTTAAGGATTAATCTAGAATGATAAT
1 TATAGTTTAGGGATGAAATTAAAATATTAAAAAGTTTAGGGATTAATTTAGAATGA-AAT
* * ** *
321564 CATAGTTTAAGGATGAAATTAAAATATTTAAAAA-TTTAGGGACCAATTTAAAATGAA
1 TATAGTTTAGGGATGAAATTAAAATA-TTAAAAAGTTTAGGGATTAATTTAGAATGAA
321621 TGCTATACTT
Statistics
Matches: 103, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
59 1 0.01
60 75 0.73
61 27 0.26
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (59 bp):
TATAGTTTAGGGATGAAATTAAAATATTAAAAAGTTTAGGGATTAATTTAGAATGAAAT
Found at i:322537 original size:2 final size:2
Alignment explanation
Indices: 322530--322577 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
322520 TGTTATGTGA
322530 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
322572 AT AT AT
1 AT AT AT
322578 TTCTTCTTGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:340756 original size:26 final size:26
Alignment explanation
Indices: 340727--340793 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
340717 TAACCTGGAA
*
340727 ACAATTAATAGTTTAACATG-ATTAAT
1 ACAATTAATAGTTT-ACACGCATTAAT
*
340753 ACAATTAATAGTTTCCACGCTATTAAT
1 ACAATTAATAGTTTACACGC-ATTAAT
*
340780 ACAGTTAATAGTTT
1 ACAATTAATAGTTT
340794 CCCACATATG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.08
26 14 0.39
27 19 0.53
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (26 bp):
ACAATTAATAGTTTACACGCATTAAT
Found at i:342205 original size:22 final size:22
Alignment explanation
Indices: 342177--342218 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
342167 GTGGCTGAGG
*
342177 ACTCGGT-TTTTTACTTTTGTCC
1 ACTCGGTCCTTTT-CTTTTGTCC
342199 ACTCGGTCCTTTTCTTTTGT
1 ACTCGGTCCTTTTCTTTTGT
342219 ATTTATAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.07, C:0.24, G:0.14, T:0.55
Consensus pattern (22 bp):
ACTCGGTCCTTTTCTTTTGTCC
Found at i:344458 original size:2 final size:2
Alignment explanation
Indices: 344451--344530 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
344441 TCATTTACAA
344451 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
344493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
344531 TATTCAAATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:345672 original size:35 final size:35
Alignment explanation
Indices: 345631--345710 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
345621 AACACAATCA
* *
345631 TCAATTACATTTTAAACCTCAAAAT-CTAAATAACT
1 TCAATTACATTCTAAACCTCAAAATCCAAAAT-ACT
*
345666 TCAATTACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCTCAAAATCCAAAATACT
345701 TCAATTACAT
1 TCAATTACAT
345711 GCCCAACCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 36 0.88
36 5 0.12
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.34
Consensus pattern (35 bp):
TCAATTACATTCTAAACCTCAAAATCCAAAATACT
Found at i:345724 original size:35 final size:36
Alignment explanation
Indices: 345658--345726 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
345648 CTCAAAATCT
* * *
345658 AAATAACTTCAATTACATTCTAAACCTCAAATTCCA
1 AAATAACTTCAATTACATGCCAAACCCCAAATTCCA
*
345694 AAAT-ACTTCAATTACATGCCCAACCCCAAATTC
1 AAATAACTTCAATTACATGCCAAACCCCAAATTC
345727 ACAATCTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 25 0.86
36 4 0.14
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (36 bp):
AAATAACTTCAATTACATGCCAAACCCCAAATTCCA
Found at i:346182 original size:148 final size:150
Alignment explanation
Indices: 345893--346186 Score: 414
Period size: 153 Copynumber: 2.0 Consensus size: 150
345883 ACTAACTTCT
*
345893 GTTTATAAAATAGTTGACTCGAAATTTTTTCTATTTCATTTTATAAAATTTAAATCAAGTCGAAT
1 GTTTATAAAATAGTTGACTCGAAATTTTTTCTATTTCAGTTTATAAAATTTAAATCAAGTCGAAT
* *
345958 TGAATTGGATTGGATTTTCAAGTTTCTATTTAAATATAATTATAAATATTTATCATATTATAATA
66 TGAATTGGA---GATTTTCAAGTTTCTATTTAAATATAATTATAAATATTTATAATACTATAATA
*
346023 TTGTTTAATTCTAATTCAGTTCA
128 TTATTTAATTCTAATTCAGTTCA
* * * *
346046 GTTTATAAAGTAGTTGACTTG-AATTGTTTTTTATTTGAGTTTATAAAATTTAAATCAAGTCGAA
1 GTTTATAAAATAGTTGACTCGAAATT-TTTTCTATTTCAGTTTATAAAATTTAAATCAAGTCGAA
** * *
346110 TTGAATT-GA-ATTTTTGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATT
65 TTGAATTGGAGATTTTCAAGTTTCTATTTAAATATAATTATAAATATTTATAATACTATAATATT
*
346173 ATTTGATTCTAATT
130 ATTTAATTCTAATT
346187 TAAATAGTTT
Statistics
Matches: 127, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
148 60 0.47
152 6 0.05
153 61 0.48
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (150 bp):
GTTTATAAAATAGTTGACTCGAAATTTTTTCTATTTCAGTTTATAAAATTTAAATCAAGTCGAAT
TGAATTGGAGATTTTCAAGTTTCTATTTAAATATAATTATAAATATTTATAATACTATAATATTA
TTTAATTCTAATTCAGTTCA
Found at i:348804 original size:45 final size:45
Alignment explanation
Indices: 348740--348829 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
348730 GTAACCATGC
* * *
348740 AAATAAGCTTACGAGCTTATGGGATAAATTGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATAGGATAAATGGTAAGCATATTGGTA
348785 AAATAAGCTTACGAGCTTATAGGATAAATGGTAAGCATATTGGTA
1 AAATAAGCTTACGAGCTTATAGGATAAATGGTAAGCATATTGGTA
348830 GATCATGGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATAGGATAAATGGTAAGCATATTGGTA
Found at i:351804 original size:16 final size:18
Alignment explanation
Indices: 351783--351822 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
351773 TGTTTTTGTC
*
351783 ATTTTAA-TAAAA-ATTA
1 ATTTTAATTAAAACAATA
351799 ATTTTAATTAAAACAATA
1 ATTTTAATTAAAACAATA
351817 ATTTTA
1 ATTTTA
351823 CAGTATGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 5 0.24
18 9 0.43
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
ATTTTAATTAAAACAATA
Found at i:353661 original size:13 final size:15
Alignment explanation
Indices: 353631--353668 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
353621 TTTATCTTCT
*
353631 TCTCAATCGTTACTC
1 TCTCAAACGTTACTC
*
353646 TCTCAAACGTTCCTC
1 TCTCAAACGTTACTC
353661 TCTCAAAC
1 TCTCAAAC
353669 TCTTTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.37, G:0.05, T:0.34
Consensus pattern (15 bp):
TCTCAAACGTTACTC
Found at i:354462 original size:9 final size:8
Alignment explanation
Indices: 354449--354505 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 8
354439 AAAGCCTGTA
354449 AAAATAAT
1 AAAATAAT
354457 ATAAATAAAT
1 A-AAAT-AAT
354467 AATAATAAT
1 AA-AATAAT
354476 AATAATAAT
1 AA-AATAAT
354485 AATAATAAT
1 AA-AATAAT
*
354494 AATATAA-
1 AAAATAAT
354501 AAAAT
1 AAAAT
354506 GCAGACAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
7 4 0.09
8 5 0.11
9 28 0.64
10 7 0.16
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AAAATAAT
Found at i:354470 original size:3 final size:3
Alignment explanation
Indices: 354451--354497 Score: 69
Period size: 3 Copynumber: 15.3 Consensus size: 3
354441 AGCCTGTAAA
354451 AAT AAT -AT AAAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
354497 A
1 A
354498 TAAAAAATGC
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:355163 original size:258 final size:259
Alignment explanation
Indices: 354637--355146 Score: 776
Period size: 259 Copynumber: 2.0 Consensus size: 259
354627 AGACTGAAAA
* * *** *
354637 ATGACCCAAAGGATTTAATCATCATGCTCGAAAGACTTGCCGATGGCTTGAAGGACTTACTAATT
1 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACCGATGGCCCAAAGGACTTACAAATT
* *
354702 TGGAAATAGTTTACTAGGTAAGAAACTTTGGAAATTACTTTCTTACTTTTAAAAAATTTCACTTT
66 TGGAAATAGTTTACTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTAAAAAATTTCACTTT
*
354767 TTTGAAAATACTAAATGAGAAACCTTGAAAATTGCTTTCTCATTTTTCAAATTATCTTATGAAAG
131 TTTGAAAATACTAAATGAGAAACCTTGAAAATTGCTTTCTCATTTTTCAAATTATCATATGAAAG
* * *
354832 CATCTTGCCTAAATGTCTTATAGATGGCCCGAAATACTTGCCATCTTGCTCGAAAGATTGATAG
196 CATCTTGCCCAAATGTCTTATAGATGACCCGAAATACTTGCCATCTTGCTCGAAAAATTGATAG
*
354896 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACCAAAT
1 ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACCGATGGCCCAAAGGACTTA-CAAAT
* **
354961 TTGGAAATAGTTTACTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTT-TGTT
65 TTGGAAATAGTTTACTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTAAAAAATTTCACTT
* * *
355025 TTTTGAAAATACTAAATGAGGAACTTTG-AAATCT-CTTTGTCATTTTTCAAATTATCATATGAA
130 TTTTGAAAATACTAAATGAGAAACCTTGAAAAT-TGCTTTCTCATTTTTCAAATTATCATATGAA
* *
355088 AGCATCTTGCCCAAATGTCTTATAGATGACCTG-AATGACTTGTCATCTTGCTCGAAAAA
194 AGCATCTTGCCCAAATGTCTTATAGATGACCCGAAAT-ACTTGCCATCTTGCTCGAAAAA
355147 CTTACTGTTG
Statistics
Matches: 227, Mismatches: 21, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
257 3 0.01
258 81 0.36
259 82 0.36
260 61 0.27
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (259 bp):
ATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACCGATGGCCCAAAGGACTTACAAATT
TGGAAATAGTTTACTAAGTAAGAAACTTTGGAAATCACTTTCTTACTTTTAAAAAATTTCACTTT
TTTGAAAATACTAAATGAGAAACCTTGAAAATTGCTTTCTCATTTTTCAAATTATCATATGAAAG
CATCTTGCCCAAATGTCTTATAGATGACCCGAAATACTTGCCATCTTGCTCGAAAAATTGATAG
Found at i:357769 original size:18 final size:19
Alignment explanation
Indices: 357749--357814 Score: 91
Period size: 18 Copynumber: 3.5 Consensus size: 19
357739 TTTCTTTATT
357749 TTTTTTCTTTTTTCCTAT-
1 TTTTTTCTTTTTTCCTATC
*
357767 TTTCTTCTTTTTTCCTATC
1 TTTTTTCTTTTTTCCTATC
357786 TTTTTTCTATTTTT-CTATC
1 TTTTTTCT-TTTTTCCTATC
*
357805 TTTTCTCTTT
1 TTTTTTCTTT
357815 CTTATTCTTC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
18 19 0.44
19 19 0.44
20 5 0.12
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTTCTTTTTTCCTATC
Found at i:357864 original size:9 final size:9
Alignment explanation
Indices: 357747--357864 Score: 55
Period size: 9 Copynumber: 12.7 Consensus size: 9
357737 ATTTTCTTTA
*
357747 TTTTTTTTC
1 TTTTTTCTC
357756 TTTTTTC-C
1 TTTTTTCTC
*
357764 TATTTTCTTC
1 TTTTTTC-TC
357774 TTTTTTCCTATC
1 TTTTTT-C--TC
357786 TTTTTTCT-
1 TTTTTTCTC
* *
357794 ATTTTTCTA
1 TTTTTTCTC
*
357803 TCTTTTCTC
1 TTTTTTCTC
357812 TTTCTTAT-TC
1 TTT-TT-TCTC
357822 TTCTTCTTCTC
1 TT-TT-TTCTC
* *
357833 CTTCTTCTC
1 TTTTTTCTC
*
357842 -TTTTTCTA
1 TTTTTTCTC
*
357850 TATTTTCTC
1 TTTTTTCTC
357859 TTTTTT
1 TTTTTT
357865 TTTTGTCTTG
Statistics
Matches: 82, Mismatches: 16, Indels: 22
0.68 0.13 0.18
Matches are distributed among these distances:
8 20 0.24
9 31 0.38
10 15 0.18
11 8 0.10
12 8 0.10
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:359201 original size:36 final size:36
Alignment explanation
Indices: 359154--359274 Score: 163
Period size: 36 Copynumber: 3.3 Consensus size: 36
359144 TTTCAAAAAA
* *
359154 ATATATTATATAGTTTTGAAAGTATTTTGAAAATAT
1 ATATAATATATAGTTTTGAAAATATTTTGAAAATAT
* *
359190 ATATAATATATAGTTTTGAAAACATTTTTG-GAATAT
1 ATATAATATATAGTTTTGAAAATA-TTTTGAAAATAT
* *
359226 ATATATTATATAGTTTTGAAAATATTTTGAAAACAT
1 ATATAATATATAGTTTTGAAAATATTTTGAAAATAT
359262 ATATATATATATA
1 ATATA-ATATATA
359275 TAATATAGTT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
35 5 0.07
36 57 0.78
37 11 0.15
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (36 bp):
ATATAATATATAGTTTTGAAAATATTTTGAAAATAT
Found at i:359309 original size:37 final size:38
Alignment explanation
Indices: 359266--359601 Score: 349
Period size: 39 Copynumber: 8.8 Consensus size: 38
359256 AAACATATAT
359266 ATATATATATAATATAGTTTTTAAAAATATTTTGAAAAC
1 ATATATATAT-ATATAGTTTTTAAAAATATTTTGAAAAC
359305 ATATATATAATATATAGTTTTTAAAAATATTTTGAAAAC
1 ATATATAT-ATATATAGTTTTTAAAAATATTTTGAAAAC
* *
359344 ATATATATAATATATAGTTTTTGAAAATATTTT-AAATAT
1 ATATATAT-ATATATAGTTTTTAAAAATATTTTGAAA-AC
359383 ATATATATATAATTTATAGTTTTTTAAAAATATTTTGAAAAC
1 ATATATATAT-A--TATAG-TTTTTAAAAATATTTTGAAAAC
* *
359425 ATATATA-ATATATAG-TTTTGAAAATATTTTTGAAAAT
1 ATATATATATATATAGTTTTTAAAAATA-TTTTGAAAAC
* *
359462 GTATATA-ATATATAG-TTTTGAAAATATTTTG-AAA-
1 ATATATATATATATAGTTTTTAAAAATATTTTGAAAAC
* *
359496 ATATATAT-TATATAG-TTGTAAAAATAATTTTTGAAAAT
1 ATATATATATATATAGTTTTTAAAAAT-A-TTTTGAAAAC
* * *
359534 ACATATAT-TATAT-GTTTTGAAAACA-ATTTTTAAAAAC
1 ATATATATATATATAGTTTTTAAAA-ATA-TTTTGAAAAC
359571 ATATATA-ATATATAG-TTTTAAAAATGATTTT
1 ATATATATATATATAGTTTTTAAAAAT-ATTTT
359602 TTATTTAATA
Statistics
Matches: 261, Mismatches: 17, Indels: 40
0.82 0.05 0.13
Matches are distributed among these distances:
34 21 0.08
35 4 0.02
36 21 0.08
37 70 0.27
38 30 0.11
39 79 0.30
40 3 0.01
41 7 0.03
42 23 0.09
43 3 0.01
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (38 bp):
ATATATATATATATAGTTTTTAAAAATATTTTGAAAAC
Found at i:360764 original size:14 final size:14
Alignment explanation
Indices: 360742--360778 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
360732 GTGTTTTTTA
*
360742 TTTTATTAACATTT
1 TTTTCTTAACATTT
360756 TTTTCTTAACATTT
1 TTTTCTTAACATTT
360770 TTTTACTTA
1 TTTT-CTTA
360779 CAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTCTTAACATTT
Done.