Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009582.1 Hibiscus syriacus cultivar Beakdansim tig00116959_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: 4978262
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 24
Found at i:4147951 original size:15 final size:15
Alignment explanation
Indices: 4147917--4147964 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
4147907 AATGTCCTAC
* *
4147917 TTATATAAATTATAT
1 TTATTTAAATTATTT
* *
4147932 ATATTTAATTTATTT
1 TTATTTAAATTATTT
4147947 TTATTTAAATTATTT
1 TTATTTAAATTATTT
4147962 TTA
1 TTA
4147965 GAATATTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTATTTAAATTATTT
Found at i:4148104 original size:27 final size:27
Alignment explanation
Indices: 4148061--4148112 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4148051 CGTTTTTTGA
*
4148061 TATTTTTAAATAAATAAATAAATATCC
1 TATTTATAAATAAATAAATAAATATCC
*
4148088 TATTTATAAA-AACATAAATATATAT
1 TATTTATAAATAA-ATAAATAAATAT
4148113 ATATATACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (27 bp):
TATTTATAAATAAATAAATAAATATCC
Found at i:4148144 original size:170 final size:170
Alignment explanation
Indices: 4147832--4148144 Score: 377
Period size: 170 Copynumber: 1.8 Consensus size: 170
4147822 TGAGGATGAT
* *
4147832 ATTTATTTTTTAATATTAAGAAAGGGGCTGTCTTAAATTAACTAGATGTCCTTTTCTGATATTTT
1 ATTTATTTTTTAATATTAAGAAAAGGGCTGTCTTAAAGTAACTAGATGTCCTTTTCTGATATTTT
* * * * * * * * *
4147897 TAAATAAATAAATGTCCTACTTATATAAATTATATATATTTAATTTATTTTTATTTAAATTATTT
66 TAAATAAATAAATATCCTACTTATATAAATAACATAAATATAATATATATATATTTAAATTATTA
* *
4147962 TTAGAATATTTTATTAAAAAATTATCATATTTTTATTAAA
131 TAAAAATATTTTATTAAAAAATTATCATATTTTTATTAAA
* * * *
4148002 ATTTATTTTTTAATATTAAGAAAATGGTTGTCTTAAAGTAACTAGATGTCGTTTTTTGATATTTT
1 ATTTATTTTTTAATATTAAGAAAAGGGCTGTCTTAAAGTAACTAGATGTCCTTTTCTGATA-TTT
4148067 TAAATAAATAAATAAATATCCTA-TT-TATAAA-AACATAAATAT-ATATATATATACTTT-AAT
65 T---TAAATAAATAAATATCCTACTTATATAAATAACATAAATATAATATATATATA-TTTAAAT
4148127 T-TTATAAAAATTATTTTA
126 TATTATAAAAA-TATTTTA
4148145 ATATATTTTC
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
169 6 0.05
170 74 0.62
171 14 0.12
172 6 0.05
173 2 0.02
174 18 0.15
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.48
Consensus pattern (170 bp):
ATTTATTTTTTAATATTAAGAAAAGGGCTGTCTTAAAGTAACTAGATGTCCTTTTCTGATATTTT
TAAATAAATAAATATCCTACTTATATAAATAACATAAATATAATATATATATATTTAAATTATTA
TAAAAATATTTTATTAAAAAATTATCATATTTTTATTAAA
Found at i:4151031 original size:31 final size:31
Alignment explanation
Indices: 4150987--4151117 Score: 102
Period size: 31 Copynumber: 4.1 Consensus size: 31
4150977 GAGCCAACAT
*
4150987 AAGGTAATGCCTTGGGGCCTTAGAGCCTACCC
1 AAGG-AATACCTTGGGGCCTTAGAGCCTACCC
* * *
4151019 AAGGAATACCTTGAGGTCTTAGAGCCTACTC
1 AAGGAATACCTTGGGGCCTTAGAGCCTACCC
* * * * *
4151050 AAGGAAGCACCTT-GGGTCTTGAGAGCTTATCG
1 AAGGAA-TACCTTGGGGCCTT-AGAGCCTACCC
* * * *
4151082 AATGGAATATCTCGGGGCCTAAGAGCTTACCC
1 AA-GGAATACCTTGGGGCCTTAGAGCCTACCC
4151114 AAGG
1 AAGG
4151118 TTCACCTTAG
Statistics
Matches: 78, Mismatches: 17, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
31 37 0.47
32 32 0.41
33 9 0.12
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (31 bp):
AAGGAATACCTTGGGGCCTTAGAGCCTACCC
Found at i:4153168 original size:13 final size:13
Alignment explanation
Indices: 4153150--4153176 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4153140 ATAGTTAAAA
4153150 CAGTCTTCATATG
1 CAGTCTTCATATG
4153163 CAGTCTTCATATG
1 CAGTCTTCATATG
4153176 C
1 C
4153177 TCGTTTGTAA
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:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:4153213 original size:14 final size:14
Alignment explanation
Indices: 4153194--4153225 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4153184 TAATGGGGGT
4153194 AATCCCTGCGAAAA
1 AATCCCTGCGAAAA
*
4153208 AATCCCTGCGTAAA
1 AATCCCTGCGAAAA
4153222 AATC
1 AATC
4153226 TCTGTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.28, G:0.12, T:0.19
Consensus pattern (14 bp):
AATCCCTGCGAAAA
Found at i:4158334 original size:209 final size:209
Alignment explanation
Indices: 4157889--4158571 Score: 1008
Period size: 209 Copynumber: 3.3 Consensus size: 209
4157879 ATTTAATAAT
*
4157889 TAAATTGAACAAATATGAAATTGCAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-A-ACACATTGATGAG
* *
4157954 GGATCAAATCGAAATAATTTTAAACTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
64 GGATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * *
4158019 CCATTTAAAAAGTTATGGGCCAATTAAAAA-AGAATTAAGTAAAAGTATAGATCAATTTCATATG
129 CCATTTAAAAAGTTATGGGCCAATTAAAAATAGAAATAA-T--AAGTATGGGTCAATTTCAGATG
4158083 CAAATAAAATTTGGAGGAC
191 CAAATAAAATTTGGAGGAC
*
4158102 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATTAATTAAACGAACACATTGATGAGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAAC-AACACATTGATGAGG
*
4158167 GATCAAATCAAAATAATTTTAAATTATGATGTTGAAATT-ATACAAAAAAGTACTAAATTATACC
65 GATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATACC
4158231 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAATAA-TATGGGTCAATTTCAGATGCAA
130 CATTTAAAAAGTTATGGGCCAA-TTAAAAATAGAAATAATAAGTATGGGTCAATTTCAGATGCAA
*
4158295 ATAAAATTTAGAGGAC
194 ATAAAATTTGGAGGAC
* *
4158311 TAAATTGAACAAATATAAAATTACAAATAAAAATTTAAATAAACTAAACAACACA---A--AGGG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATTGATGAGGG
* * * * **
4158371 ATCAAATTGAAATAA-TTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATACTA
66 ATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
* *
4158435 ATTTAAAAAGTTATAGGCCAATTAATAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGC
131 ATTTAAAAAGTTATGGGCCAATTAAAAATAG--A-AA-TAATAAGTATGGGTCAATTTCAGATGC
*
4158500 AAATAAAATGTGGAGGAC
192 AAATAAAATTTGGAGGAC
4158518 TAAATTGAACAAATATGAAATTAC-AATAAAAATTTAAATAAATTAAACAACACA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA
4158572 AAAGGGATCA
Statistics
Matches: 435, Mismatches: 27, Indels: 23
0.90 0.06 0.05
Matches are distributed among these distances:
202 29 0.07
203 60 0.14
204 1 0.00
205 3 0.01
206 35 0.08
207 59 0.14
208 6 0.01
209 80 0.18
210 2 0.00
211 47 0.11
212 58 0.13
213 55 0.13
ACGTcount: A:0.51, C:0.09, G:0.12, T:0.29
Consensus pattern (209 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACATTGATGAGGG
ATCAAATCGAAATAATTTTAAATTATGATGTTGAAATTAATACAAAAAAGTACTAAATTATACCC
ATTTAAAAAGTTATGGGCCAATTAAAAATAGAAATAATAAGTATGGGTCAATTTCAGATGCAAAT
AAAATTTGGAGGAC
Found at i:4158828 original size:53 final size:52
Alignment explanation
Indices: 4158659--4158834 Score: 165
Period size: 53 Copynumber: 3.5 Consensus size: 52
4158649 ATAATATATA
* * *
4158659 TATAATATA-ATATATAT-ATATAT-AATATAAACTATATA-ATA--TAAAC
1 TATACTATATATATATATAATATATGTATATATACTATATATATATGTAAAC
**
4158705 TATA-TAGTATATATATATAATATATGTATATATA-TATAACTATATATGTTTA-
1 TATACTA-TATATATATATAATATATGTATATATACTAT-A-TATATATGTAAAC
4158757 TATAACTATATATATATATAA-ACTATGTATATATACTATATATATATGTAAAC
1 TAT-ACTATATATATATATAATA-TATGTATATATACTATATATATATGTAAAC
* *
4158810 TATACTATATAATTTATATTATATA
1 TATACTATAT-ATATATATAATATA
4158835 AACTATTGAA
Statistics
Matches: 106, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
45 2 0.02
46 6 0.06
47 8 0.08
48 9 0.08
49 7 0.07
50 2 0.02
51 3 0.03
52 21 0.20
53 42 0.40
54 6 0.06
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (52 bp):
TATACTATATATATATATAATATATGTATATATACTATATATATATGTAAAC
Found at i:4158851 original size:2 final size:2
Alignment explanation
Indices: 4158652--4158834 Score: 132
Period size: 2 Copynumber: 91.5 Consensus size: 2
4158642 TTAAACAATA
*
4158652 AT AT AT AT AT A- AT AT A- AT AT AT AT AT AT AT A- AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
4158692 AT AT A- AT AT AA ACT AT AT AGT AT AT AT AT AT A- AT AT AT GT AT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
4158734 AT AT AT AT A- ACT AT AT AT GT TT AT AT A- ACT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * * *
4158776 AA ACT AT GT AT AT AT ACT AT AT AT AT AT GT AA ACT AT ACT AT AT
1 AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT A-T AT AT
*
4158820 A- AT TT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT A
4158835 AACTATTGAA
Statistics
Matches: 144, Mismatches: 19, Indels: 36
0.72 0.10 0.18
Matches are distributed among these distances:
1 9 0.06
2 123 0.85
3 12 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:4158889 original size:19 final size:18
Alignment explanation
Indices: 4158865--4158908 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
4158855 CCTACATAGT
*
4158865 TTATATATAAATTATACAA
1 TTATATAT-AACTATACAA
4158884 TTATATATAACTATACAA
1 TTATATATAACTATACAA
4158902 TT-TATAT
1 TTATATAT
4158909 TATATATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 5 0.21
18 11 0.46
19 8 0.33
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
TTATATATAACTATACAA
Found at i:4158911 original size:32 final size:32
Alignment explanation
Indices: 4158869--4158953 Score: 91
Period size: 32 Copynumber: 2.7 Consensus size: 32
4158859 CATAGTTTAT
*
4158869 ATATAAATTATACAATTATATATAACTAT-ACA
1 ATATATATTATA-AATTATATATAACTATAACA
* * * * *
4158901 ATTTATATTATATATTATGTATAATTATAATA
1 ATATATATTATAAATTATATATAACTATAACA
*
4158933 ATATATTTTATAAATTATATA
1 ATATATATTATAAATTATATA
4158954 GTTTATTAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
31 13 0.31
32 29 0.69
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (32 bp):
ATATATATTATAAATTATATATAACTATAACA
Found at i:4158966 original size:22 final size:19
Alignment explanation
Indices: 4158941--4158996 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 19
4158931 TAATATATTT
4158941 TATAAATTATATAGTTTATTAA
1 TATAAA-TATATAGTTT-TT-A
4158963 TATAAACTATATAGTTTTTA
1 TATAAA-TATATAGTTTTTA
*
4158983 TATATATATATAGT
1 TATAAATATATAGT
4158997 ATATATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 8 0.25
20 6 0.19
21 2 0.06
22 16 0.50
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (19 bp):
TATAAATATATAGTTTTTA
Found at i:4158982 original size:24 final size:24
Alignment explanation
Indices: 4158941--4158990 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
4158931 TAATATATTT
*
4158941 TATAAATTATATAGTTTAT-TA-A
1 TATAAACTATATAGTTTATATATA
*
4158963 TATAAACTATATAGTTTTTATATA
1 TATAAACTATATAGTTTATATATA
4158987 TATA
1 TATA
4158991 TATAGTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 17 0.71
23 2 0.08
24 5 0.21
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (24 bp):
TATAAACTATATAGTTTATATATA
Found at i:4159071 original size:6 final size:6
Alignment explanation
Indices: 4159060--4159096 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
4159050 GGGTTTAGGG
4159060 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA T
4159097 AAACTACATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTATA
Found at i:4159118 original size:29 final size:29
Alignment explanation
Indices: 4159083--4159156 Score: 86
Period size: 24 Copynumber: 2.7 Consensus size: 29
4159073 TTATATTTAT
4159083 ATTTATATTTATATAAACTACATACTATA
1 ATTTATATTTATATAAACTACATACTATA
*
4159112 ATTTATATTTAT-T----TATATACTATA
1 ATTTATATTTATATAAACTACATACTATA
*
4159136 TTTTACTATTTATATAAACTA
1 ATTTA-TATTTATATAAACTA
4159157 TAGTTTATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
24 14 0.38
25 7 0.19
26 1 0.03
28 1 0.03
29 12 0.32
30 2 0.05
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTTATATTTATATAAACTACATACTATA
Found at i:4159210 original size:20 final size:20
Alignment explanation
Indices: 4159187--4159306 Score: 64
Period size: 20 Copynumber: 6.2 Consensus size: 20
4159177 TATATATGAA
4159187 ATATAGTTTACATATGAACT
1 ATATAGTTTACATATGAACT
*
4159207 ATATA---TAC-TA--AAGT
1 ATATAGTTTACATATGAACT
*
4159221 -TGATA-TTTATATATGAAC-
1 AT-ATAGTTTACATATGAACT
*
4159239 -TATAGTTTACATATAAACT
1 ATATAGTTTACATATGAACT
*
4159258 ATATAGTTTATATACT-AACT
1 ATATAGTTTACATA-TGAACT
*
4159278 ATAGTTGATATTTACATATGAACT
1 ATA--T-A-GTTTACATATGAACT
4159302 ATATA
1 ATATA
4159307 TATAAATTAT
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
13 1 0.01
14 6 0.08
16 4 0.05
17 8 0.10
18 12 0.16
19 2 0.03
20 24 0.31
21 2 0.03
22 2 0.03
23 2 0.03
24 14 0.18
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (20 bp):
ATATAGTTTACATATGAACT
Found at i:4159213 original size:62 final size:61
Alignment explanation
Indices: 4159146--4159371 Score: 194
Period size: 60 Copynumber: 3.6 Consensus size: 61
4159136 TTTTACTATT
* *
4159146 TATATA-AACTATAGTTTATATTTATATACTATATATATGAAATATAGTTTACATATGAAC
1 TATATATAACTATAGTTGATATTTATATACTATATATATAAAATATAGTTTACATATGAAC
* * * *** * **
4159206 TATATAT-ACTAAAGTTGATATTTATATA-TGA-ACTATAGTTTACATATAAACTATATA-G-TT
1 TATATATAACTATAGTTGATATTTATATACT-ATA-TATA--TAAAATATAGTTTACATATGAAC
4159266 TATATACTAACTATAGTTGATATTTACATATGAACTATATATATAAATTATATAGTTTACATATG
1 TATATA-TAACTATAGTTGATATTT--ATAT--ACTATATATATAAA--ATATAGTTTACATATG
*
4159331 ACC
59 AAC
4159334 TATATATATACTATAGTTGATATTTATATACTATATAT
1 TATATATA-ACTATAGTTGATATTTATATACTATATAT
4159372 TTACATATGA
Statistics
Matches: 129, Mismatches: 19, Indels: 32
0.72 0.11 0.18
Matches are distributed among these distances:
59 2 0.02
60 36 0.28
61 2 0.02
62 27 0.21
64 15 0.12
66 20 0.16
67 5 0.04
68 22 0.17
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.44
Consensus pattern (61 bp):
TATATATAACTATAGTTGATATTTATATACTATATATATAAAATATAGTTTACATATGAAC
Found at i:4159235 original size:33 final size:33
Alignment explanation
Indices: 4159193--4159359 Score: 109
Period size: 33 Copynumber: 5.1 Consensus size: 33
4159183 TGAAATATAG
*
4159193 TTTACATATGAACTATATATACTAAAGTTGATA
1 TTTACATATGAACTATATATACTATAGTTGATA
* *
4159226 TTTATATATGAACTATAGTTTAC-ATA--T-A-A
1 TTTACATATGAACTATA-TATACTATAGTTGATA
** * **
4159255 ACTATATA-G-TTTATATACTAACTATAGTTGATA
1 TTTACATATGAACTATATA-T-ACTATAGTTGATA
* *
4159288 TTTACATATGAACTATATATA-TA-AATTATATA
1 TTTACATATGAACTATATATACTATAGTT-GATA
*
4159320 GTTTACATATGACCTATATATATACTATAGTTGATA
1 -TTTACATATGAAC--TATATATACTATAGTTGATA
4159356 TTTA
1 TTTA
4159360 TATACTATAT
Statistics
Matches: 100, Mismatches: 18, Indels: 30
0.68 0.12 0.20
Matches are distributed among these distances:
26 1 0.01
27 5 0.05
28 3 0.03
29 10 0.10
30 1 0.01
31 5 0.05
32 6 0.06
33 37 0.37
34 6 0.06
35 18 0.18
36 5 0.05
37 3 0.03
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (33 bp):
TTTACATATGAACTATATATACTATAGTTGATA
Found at i:4159247 original size:18 final size:17
Alignment explanation
Indices: 4159226--4159288 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 17
4159216 AAAGTTGATA
4159226 TTTATATATGAACTATAG
1 TTTATATAT-AACTATAG
*
4159244 TTTACATATAAACTATATAG
1 TTTATATAT-AAC--TATAG
4159264 TTTATATACTAACTATAG
1 TTTATATA-TAACTATAG
*
4159282 TTGATAT
1 TTTATAT
4159289 TTACATATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
18 22 0.58
20 15 0.39
21 1 0.03
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (17 bp):
TTTATATATAACTATAG
Found at i:4159348 original size:9 final size:9
Alignment explanation
Indices: 4159336--4159454 Score: 73
Period size: 9 Copynumber: 12.7 Consensus size: 9
4159326 ATATGACCTA
4159336 TATATATAC
1 TATATATAC
4159345 TATAGTTGATA-
1 TATA--T-ATAC
*
4159356 TTTATATAC
1 TATATATAC
*
4159365 TATATAT-T
1 TATATATAC
*
4159373 TACATATGACC
1 TATATAT-A-C
4159384 TATATATAC
1 TATATATAC
*
4159393 TATAGTTTAC
1 TATA-TATAC
* *
4159403 TATATAAAA
1 TATATATAC
*
4159412 TATATATAGT
1 TATATATA-C
4159422 TATATTATA-
1 TATA-TATAC
*
4159431 TATATAAAC
1 TATATATAC
4159440 TATATATAC
1 TATATATAC
4159449 TATATA
1 TATATA
4159455 GTATAATTTA
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
8 12 0.14
9 43 0.51
10 13 0.15
11 14 0.16
12 3 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (9 bp):
TATATATAC
Found at i:4159393 original size:28 final size:28
Alignment explanation
Indices: 4159358--4159454 Score: 108
Period size: 28 Copynumber: 3.5 Consensus size: 28
4159348 AGTTGATATT
* *
4159358 TATATACTATATATTTACATATGACCTA
1 TATATACTATATATTTACATATAAACTA
* *
4159386 TATATACTATA-GTTTACTATATAAAATA
1 TATATACTATATATTTAC-ATATAAACTA
* *
4159414 TATATAGT-TATATTATATATATAAACTA
1 TATATACTATATATT-TACATATAAACTA
4159442 TATATACTATATA
1 TATATACTATATA
4159455 GTATAATTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
27 7 0.12
28 43 0.77
29 6 0.11
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (28 bp):
TATATACTATATATTTACATATAAACTA
Found at i:4159452 original size:18 final size:18
Alignment explanation
Indices: 4159383--4159666 Score: 60
Period size: 18 Copynumber: 15.3 Consensus size: 18
4159373 TACATATGAC
**
4159383 CTATATATACTATAGTTTA
1 CTATATATACTATA-TAAA
* * *
4159402 CTATATAAAATATATATAG
1 CTATATATACTATATA-AA
*
4159421 TTATATTATA-TATATAAA
1 CTATA-TATACTATATAAA
4159439 CTATATATACTATAT--A
1 CTATATATACTATATAAA
* * *
4159455 GTATAATTTAC-ATATGAA
1 CTAT-ATATACTATATAAA
*
4159473 CTATATATAAAAACCATATAAA
1 CTATATAT----ACTATATAAA
4159495 C--TATATACTATAGTTGATAA
1 CTATATATACTATA--T-A-AA
4159515 -T-TATATACTATATAAA
1 CTATATATACTATATAAA
* *
4159531 ATAATTTATACTATAGT--A
1 CT-ATATATACTATA-TAAA
* *
4159549 -TATATAAACAATATAATA
1 CTATATATACTATATAA-A
* *
4159567 -TATATAAACTATATATTA
1 CTATATATACTATATA-AA
*
4159585 -TATAGTTCATTAGTATATATAAA
1 CTATA--T-A-TACTATAT--AAA
4159608 CTATATAATA-TATATAAA
1 CTATAT-ATACTATATAAA
*
4159626 CTATATGGTA-TATATAAA
1 CTATAT-ATACTATATAAA
*
4159644 CTATATGGTA-TATATAAA
1 CTATAT-ATACTATATAAA
4159662 CTATA
1 CTATA
4159667 CATTATATAT
Statistics
Matches: 207, Mismatches: 27, Indels: 63
0.70 0.09 0.21
Matches are distributed among these distances:
15 1 0.00
16 24 0.12
17 15 0.07
18 80 0.39
19 33 0.16
20 28 0.14
21 5 0.02
22 15 0.07
23 1 0.00
24 5 0.02
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (18 bp):
CTATATATACTATATAAA
Found at i:4159519 original size:20 final size:21
Alignment explanation
Indices: 4159496--4159548 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
4159486 CCATATAAAC
**
4159496 TATATACTATAGT-TGATAAT
1 TATATACTATAGTAAAATAAT
4159516 TATATACTATA-TAAAATAAT
1 TATATACTATAGTAAAATAAT
4159536 T-TATACTATAGTA
1 TATATACTATAGTA
4159549 TATATAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.34
20 19 0.66
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
Consensus pattern (21 bp):
TATATACTATAGTAAAATAAT
Found at i:4159571 original size:9 final size:9
Alignment explanation
Indices: 4159537--4159660 Score: 50
Period size: 9 Copynumber: 14.0 Consensus size: 9
4159527 TAAAATAATT
*
4159537 TATACTATAG
1 TATA-TATAA
4159547 TATATATAA
1 TATATATAA
*
4159556 -ACAATATAA
1 TA-TATATAA
4159565 TATATATAA
1 TATATATAA
4159574 -ACTATAT-A
1 TA-TATATAA
*
4159582 T-TATATAG
1 TATATATAA
*
4159590 T-TCAT-TAG
1 TAT-ATATAA
4159598 TATATATAA
1 TATATATAA
4159607 -ACTATATAA
1 TA-TATATAA
4159616 TATATATAA
1 TATATATAA
**
4159625 -ACTATATGG
1 TA-TATATAA
4159634 TATATATAA
1 TATATATAA
**
4159643 -ACTATATGG
1 TA-TATATAA
4159652 TATATATAA
1 TATATATAA
4159661 ACTATACATT
Statistics
Matches: 87, Mismatches: 13, Indels: 29
0.67 0.10 0.22
Matches are distributed among these distances:
7 5 0.06
8 14 0.16
9 60 0.69
10 8 0.09
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (9 bp):
TATATATAA
Found at i:4159673 original size:18 final size:18
Alignment explanation
Indices: 4159542--4159676 Score: 152
Period size: 18 Copynumber: 7.7 Consensus size: 18
4159532 TAATTTATAC
*
4159542 TATAGTATATATAAACAA
1 TATAGTATATATAAACTA
*
4159560 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
**
4159578 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
4159594 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
*
4159611 TATAATATATATAAACTA
1 TATAGTATATATAAACTA
*
4159629 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
*
4159647 TATGGTATATATAAACTA
1 TATAGTATATATAAACTA
* *
4159665 TACATTATATAT
1 TATAGTATATAT
4159677 TTCATTAGTA
Statistics
Matches: 100, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
15 4 0.04
16 8 0.08
17 8 0.08
18 80 0.80
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:4159681 original size:87 final size:85
Alignment explanation
Indices: 4159516--4159706 Score: 249
Period size: 87 Copynumber: 2.2 Consensus size: 85
4159506 AGTTGATAAT
* * * * *
4159516 TATATACTATATAAAATAATTTATACTATAGTATATATAAACAATATAATATATATAAACTATAT
1 TATAAACTATATAATAT-ATATAAACTATAGTATATATAAACAATATAATATATATAAACTATAC
4159581 ATTATATAGTTCATTAGTATA
65 ATTATATAGTTCATTAGTATA
* **
4159602 TATAAACTATATAATATATATAAACTATATGGTATATATAAACTATATGGTATATATAAACTATA
1 TATAAACTATATAATATATATAAACTATA--GTATATATAAACAATATAATATATATAAACTATA
*
4159667 CATTATATATTTCATTAGTATA
64 CATTATATAGTTCATTAGTATA
*
4159689 TACT-AACTATATTATATA
1 TA-TAAACTATATAATATA
4159707 GTTCATTAGT
Statistics
Matches: 92, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
85 10 0.11
86 15 0.16
87 66 0.72
88 1 0.01
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (85 bp):
TATAAACTATATAATATATATAAACTATAGTATATATAAACAATATAATATATATAAACTATACA
TTATATAGTTCATTAGTATA
Found at i:4159703 original size:31 final size:32
Alignment explanation
Indices: 4159651--4159721 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 32
4159641 AAACTATATG
*
4159651 GTATATATAAACTATACATTATATATTTCATTA
1 GTATATATAAACTATA-ATTATATAGTTCATTA
4159684 GTATATACT-AACTAT-ATTATATAGTTCATTA
1 GTATATA-TAAACTATAATTATATAGTTCATTA
4159715 GTATATA
1 GTATATA
4159722 AAGTATAAAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 22 0.61
33 13 0.36
34 1 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (32 bp):
GTATATATAAACTATAATTATATAGTTCATTA
Found at i:4159729 original size:87 final size:86
Alignment explanation
Indices: 4159550--4159741 Score: 228
Period size: 87 Copynumber: 2.2 Consensus size: 86
4159540 ACTATAGTAT
* * *
4159550 ATATAAACAATATAATATATATAAACTATATATTATATAGTTCATTAGTATATATAAACTATATA
1 ATATAAACTATATAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATAT-
* *
4159615 ATATATATAAACTATATGGTAT
65 ATATATATAAACTATATGATAA
* *
4159637 ATATAAACTATATGGTATATATAAACTATACATTATATATTTCATTAGTATATACT-AACTATAT
1 ATATAAACTATATAGTATATATAAACTATACATTATATAGTTCATTAGTATATA-TAAACTATAT
** *
4159701 -TATATAGTTCATTAGTAT-ATAA
65 ATATATA-TAAACTA-TATGATAA
4159723 AGTATAAACTATATAGTAT
1 A-TATAAACTATATAGTAT
4159742 GTAAACTATT
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
85 6 0.07
86 7 0.08
87 76 0.84
88 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (86 bp):
ATATAAACTATATAGTATATATAAACTATACATTATATAGTTCATTAGTATATATAAACTATATA
TATATATAAACTATATGATAA
Found at i:4159786 original size:21 final size:21
Alignment explanation
Indices: 4159761--4159813 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
4159751 TAGTGTACTA
* *
4159761 TATAGTTTATACTTTATAACC
1 TATAGTTTATAATTTATAAAC
*
4159782 TATAGTATATAATTTATAAAC
1 TATAGTTTATAATTTATAAAC
4159803 TATAGTTTATA
1 TATAGTTTATA
4159814 TTAATGTACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.47
Consensus pattern (21 bp):
TATAGTTTATAATTTATAAAC
Found at i:4159937 original size:13 final size:14
Alignment explanation
Indices: 4159903--4159941 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4159893 ATTATATTAA
*
4159903 TATAAATTATAAAC
1 TATAATTTATAAAC
*
4159917 TATAATTTATAGAC
1 TATAATTTATAAAC
*
4159931 TATATTTTATA
1 TATAATTTATA
4159942 TTAATATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (14 bp):
TATAATTTATAAAC
Found at i:4159960 original size:50 final size:48
Alignment explanation
Indices: 4159896--4160050 Score: 150
Period size: 50 Copynumber: 3.3 Consensus size: 48
4159886 AAACTAGATT
4159896 ATATTAA-TATAAATTATAAACTATAATTTATAGACTATATTTTATATTA
1 ATATTAATTATAAATTATAAACTATAATTTATA-A-TATATTTTATATTA
* * *
4159945 ATATTAATTATAAATTATAAACTA-GATTATATTAATATAAGTTAATATTA
1 ATATTAATTATAAATTATAAACTATAATT-TA-TAATAT-ATTTTATATTA
*
4159995 ATATTAATTAT--ATTA-ATA-T-TAA-TTATAATATATATTT-T-TTA
1 ATATTAATTATAAATTATAAACTATAATTTATAATATAT-TTTATATTA
4160036 ATATTAATTATAAAT
1 ATATTAATTATAAAT
4160051 AGTTTATTAA
Statistics
Matches: 91, Mismatches: 7, Indels: 22
0.76 0.06 0.18
Matches are distributed among these distances:
41 14 0.15
42 2 0.02
43 10 0.11
44 2 0.02
45 1 0.01
46 2 0.02
47 2 0.02
48 4 0.04
49 13 0.14
50 39 0.43
51 2 0.02
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (48 bp):
ATATTAATTATAAATTATAAACTATAATTTATAATATATTTTATATTA
Found at i:4159994 original size:16 final size:14
Alignment explanation
Indices: 4159831--4160047 Score: 99
Period size: 15 Copynumber: 14.4 Consensus size: 14
4159821 ACTATATAGT
*
4159831 TTATATTAATGTTAA
1 TTATATTAAT-ATAA
*
4159846 TTATCTTAACTATAA
1 TTATATTAA-TATAA
*
4159861 TTTATATTAATATAG
1 -TTATATTAATATAA
4159876 TATATAGTTTAA-ACTAGA
1 T-TATA--TTAATA-TA-A
4159894 TTATATTAATATAAA
1 TTATATTAATAT-AA
4159909 TTATA--AACTATAA
1 TTATATTAA-TATAA
*
4159922 TT-TA-TAGACTATATT
1 TTATATTA-A-TATA-A
4159937 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
4159952 TTATAAATTATAAACTAGA
1 TTAT--ATTA-ATA-TA-A
4159971 TTATATTAATATAA
1 TTATATTAATATAA
4159985 GTTAATATTAATATTAA
1 -TT-ATATTAATA-TAA
4160002 TTATATTAATATTAA
1 TTATATTAATA-TAA
*
4160017 TTATAAT-ATAT-A
1 TTATATTAATATAA
*
4160029 TT-TTTTAATATTAA
1 TTATATTAATA-TAA
4160043 TTATA
1 TTATA
4160048 AATAGTTTAT
Statistics
Matches: 161, Mismatches: 14, Indels: 54
0.70 0.06 0.24
Matches are distributed among these distances:
11 2 0.01
12 8 0.05
13 9 0.06
14 17 0.11
15 62 0.39
16 30 0.19
17 23 0.14
18 5 0.03
19 5 0.03
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (14 bp):
TTATATTAATATAA
Found at i:4160030 original size:31 final size:30
Alignment explanation
Indices: 4159937--4160048 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 30
4159927 AGACTATATT
*
4159937 TTATATTAATATTAATTATAAATTATAAACTAGA
1 TTATATTAATATTAATTAT-AA-TATATA-TA-A
*
4159971 TTATATTAATA-TAAGT-TAATATTAATATTAA
1 TTATATTAATATTAATTATAATA-T-ATA-TAA
4160002 TTATATTAATATTAATTATAATATATAT--
1 TTATATTAATATTAATTATAATATATATAA
4160030 TT-T-TTAATATTAATTATAA
1 TTATATTAATATTAATTATAA
4160049 ATAGTTTATT
Statistics
Matches: 70, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
26 16 0.23
27 1 0.01
28 2 0.03
30 3 0.04
31 18 0.26
32 10 0.14
33 9 0.13
34 11 0.16
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.50
Consensus pattern (30 bp):
TTATATTAATATTAATTATAATATATATAA
Found at i:4160072 original size:26 final size:25
Alignment explanation
Indices: 4160005--4160073 Score: 70
Period size: 26 Copynumber: 2.8 Consensus size: 25
4159995 ATATTAATTA
* *
4160005 TATTAATATTAATTATAATATATATT
1 TATTAATATTAATT-TTATAAATATT
*
4160031 TTTTAATATTAA--TTATAAATAGTT
1 TATTAATATTAATTTTATAAATA-TT
*
4160055 TATTAATATAAATTTTATA
1 TATTAATATTAATTTTATA
4160074 GGAATGAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 7 0.20
24 12 0.34
26 16 0.46
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (25 bp):
TATTAATATTAATTTTATAAATATT
Found at i:4162489 original size:23 final size:23
Alignment explanation
Indices: 4162459--4162512 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
4162449 CTTAATGCAG
*
4162459 GATGCTTGCTGAATCGATGCAAT
1 GATGCTTGCTGAATCGATACAAT
* *
4162482 GATGCTTGCTGAATTGATACATT
1 GATGCTTGCTGAATCGATACAAT
4162505 GATGCTTG
1 GATGCTTG
4162513 TTGTTGCTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (23 bp):
GATGCTTGCTGAATCGATACAAT
Found at i:4163196 original size:18 final size:18
Alignment explanation
Indices: 4163145--4163196 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
4163135 AATTAACATA
4163145 AAAATTAAATTTATAATAT
1 AAAATTAAATTT-TAATAT
4163164 AAACATTATAA--TTAATAT
1 AAA-ATTA-AATTTTAATAT
*
4163182 AAAACTAAATTTTAA
1 AAAATTAAATTTTAA
4163197 AAAGTAATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
16 2 0.07
17 3 0.11
18 13 0.46
19 4 0.14
20 4 0.14
21 2 0.07
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTAAATTTTAATAT
Found at i:4163243 original size:51 final size:51
Alignment explanation
Indices: 4163188--4163284 Score: 167
Period size: 51 Copynumber: 1.9 Consensus size: 51
4163178 ATATAAAACT
* * *
4163188 AAATTTTAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
1 AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTATGATA
4163239 AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTA
4163285 ATTATAATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.40
Consensus pattern (51 bp):
AAATTTCAAAAAGTAACCACATTAATTTAATTATCATAATAATTTATGATA
Found at i:4164063 original size:21 final size:20
Alignment explanation
Indices: 4163977--4164134 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
4163967 AAATGACCAA
**
4163977 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
4163996 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
4164016 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
4164036 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
4164057 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
4164078 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
4164098 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
4164119 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
4164135 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:4164163 original size:20 final size:20
Alignment explanation
Indices: 4164101--4164370 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
4164091 CGATTTTCCA
* ** *
4164101 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
4164121 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
4164141 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4164161 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4164181 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4164201 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4164221 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
4164241 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
4164261 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
4164281 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
4164301 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
4164321 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
4164341 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
4164361 AAATCACAAC
1 AAATCGCAAC
4164371 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:4165086 original size:22 final size:23
Alignment explanation
Indices: 4165044--4165088 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4165034 AAATTTGGTC
4165044 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATA-CCGGACTTTGATA
*
4165068 TTGGTCAATA-CGGATTTTGAT
1 TTGGTCAATACCGGACTTTGAT
4165089 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
24 10 0.50
ACGTcount: A:0.24, C:0.13, G:0.22, T:0.40
Consensus pattern (23 bp):
TTGGTCAATACCGGACTTTGATA
Found at i:4168287 original size:14 final size:14
Alignment explanation
Indices: 4168268--4168324 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4168258 GCGAAATGAA
*
4168268 AATCGCAACGACAG
1 AATCGCAACGAAAG
4168282 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
4168299 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
4168315 AATCGCAACG
1 AATCGCAACG
4168325 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:4168295 original size:33 final size:33
Alignment explanation
Indices: 4168249--4168341 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
4168239 GCGAAACCAA
*
4168249 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
4168282 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
4168315 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
4168342 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:4168306 original size:19 final size:19
Alignment explanation
Indices: 4168212--4168346 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
4168202 TAGTTTACTT
* *
4168212 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
4168232 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
4168251 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4168270 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
4168284 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
4168303 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
4168317 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
4168336 TCGCAATGCGA
1 TCGCAACGCGA
4168347 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:4168429 original size:20 final size:19
Alignment explanation
Indices: 4168342--4168437 Score: 112
Period size: 19 Copynumber: 5.3 Consensus size: 19
4168332 AAAATCGCAA
4168342 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
4168361 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
4168375 TGCAATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
4168394 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
4168413 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
4168433 TGCGA
1 TGCGA
4168438 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 6, Indels: 11
0.79 0.07 0.13
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 38 0.58
20 13 0.20
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:4168732 original size:93 final size:93
Alignment explanation
Indices: 4168485--4168951 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
4168475 ATGGATTGCA
4168485 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4168549 TAGCAGAATTGGCAGCAACCGAAC-AAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4168576 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4168641 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4168669 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4168734 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4168762 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4168827 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4168855 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4168919 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
4168947 TTACT
1 TTACT
4168952 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
91 4 0.01
92 161 0.43
93 208 0.56
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4168880 original size:185 final size:186
Alignment explanation
Indices: 4168485--4168951 Score: 904
Period size: 185 Copynumber: 2.5 Consensus size: 186
4168475 ATGGATTGCA
4168485 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4168549 TAGCAGAATTGGCAGCAACCGAAC-AATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4168613 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
4168669 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
4168734 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
4168799 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
4168855 TTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
4168919 TAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACT
4168952 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
184 4 0.01
185 161 0.57
186 115 0.41
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:4170673 original size:14 final size:14
Alignment explanation
Indices: 4170654--4170743 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
4170644 TTGAAATGAT
4170654 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4170668 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4170687 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4170701 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4170720 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4170734 AATCGCAACG
1 AATCGCAACG
4170744 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4170684 original size:33 final size:33
Alignment explanation
Indices: 4170646--4170760 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
4170636 TATTTTGGTT
*
4170646 GAAATGATAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4170679 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4170712 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4170745 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
4170761 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4170692 original size:19 final size:19
Alignment explanation
Indices: 4170668--4170765 Score: 99
Period size: 19 Copynumber: 5.7 Consensus size: 19
4170658 GCAACGAGAG
4170668 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4170687 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
4170701 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4170720 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
4170734 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4170753 AATCGCAATGCGA
1 AATCGCAACGCGA
4170766 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 32 0.50
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:4170796 original size:14 final size:14
Alignment explanation
Indices: 4170777--4170833 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4170767 TTTGGTTTCG
4170777 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4170791 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
4170810 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4170824 CGTTGCGATT
1 CGTTGCGATT
4170834 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4170809 original size:33 final size:33
Alignment explanation
Indices: 4170761--4170841 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
4170751 AAAATCGCAA
**
4170761 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
4170794 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
4170827 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
4170842 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:4170844 original size:21 final size:21
Alignment explanation
Indices: 4170818--4170893 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4170808 CGCGTTGCGA
4170818 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
4170839 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
4170859 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
4170880 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
4170894 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:4170874 original size:41 final size:41
Alignment explanation
Indices: 4170817--4170894 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
4170807 TCGCGTTGCG
*
4170817 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
4170858 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
4170895 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:4171014 original size:33 final size:33
Alignment explanation
Indices: 4170972--4171042 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
4170962 AATACTAACT
*
4170972 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
4171005 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
4171038 TGAAA
1 TGAAA
4171043 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:4171256 original size:25 final size:25
Alignment explanation
Indices: 4171228--4171280 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 25
4171218 TGTGAGGGAT
4171228 TTCGCCGGAGATGGGGACGGAAATC
1 TTCGCCGGAGATGGGGACGGAAATC
**
4171253 TT---C-GAGATGGGGACGGATTTC
1 TTCGCCGGAGATGGGGACGGAAATC
4171274 TTCGCCG
1 TTCGCCG
4171281 TAGAGAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 8
0.69 0.06 0.25
Matches are distributed among these distances:
21 18 0.82
22 1 0.05
24 1 0.05
25 2 0.09
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.23
Consensus pattern (25 bp):
TTCGCCGGAGATGGGGACGGAAATC
Found at i:4171449 original size:20 final size:20
Alignment explanation
Indices: 4171424--4171577 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
4171414 CTTTAAATAT
4171424 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4171444 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
4171466 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
4171485 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
4171505 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
4171525 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
4171545 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
4171565 CGCGTTGCGATTT
1 CGCGTTGCGATTT
4171578 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:4171551 original size:40 final size:40
Alignment explanation
Indices: 4171423--4171577 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
4171413 GCTTTAAATA
*
4171423 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
4171464 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
4171504 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
4171544 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
4171578 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:4171594 original size:21 final size:21
Alignment explanation
Indices: 4171564--4171646 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
4171554 ATTTTCATAT
*
4171564 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
4171585 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
4171606 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
4171627 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
4171647 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:4171637 original size:42 final size:43
Alignment explanation
Indices: 4171544--4171642 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
4171534 ATTTATGTGT
* *
4171544 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
4171585 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
4171627 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
4171643 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:4175775 original size:35 final size:34
Alignment explanation
Indices: 4175690--4175776 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
4175680 ATTTGATATT
*
4175690 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
4175724 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
4175762 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
4175777 ACTAAAATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:4176407 original size:18 final size:18
Alignment explanation
Indices: 4176384--4176441 Score: 107
Period size: 18 Copynumber: 3.2 Consensus size: 18
4176374 AAAGGCGATG
4176384 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
4176402 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
*
4176420 GCGACATCATATATGGCT
1 GCGGCATCATATATGGCT
4176438 GCGG
1 GCGG
4176442 TGGCTGCTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.26
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:4178086 original size:111 final size:111
Alignment explanation
Indices: 4177947--4178168 Score: 381
Period size: 111 Copynumber: 2.0 Consensus size: 111
4177937 ATTACAAAAA
* * * *
4177947 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* *
4178012 AATTAAAATGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
4178058 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
4178123 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
4178169 ATGATTTCCA
Statistics
Matches: 104, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCATAATCTAATAATCATACATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:4178508 original size:50 final size:49
Alignment explanation
Indices: 4178454--4178579 Score: 171
Period size: 50 Copynumber: 2.5 Consensus size: 49
4178444 AGATATCCAA
*
4178454 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGG-TCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* * * *
4178504 GTATATCGCGGGGCAGGGGGCGCGCTATACTCACGTGGCGCCAAATCAGC
1 GTATAGCGC-GGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
*
4178554 ATATAGCGCGGTGCAGGGGGCGCGCT
1 GTATAGCGCGGT-CAGGGGGCGCGCT
4178580 TTCCTACTAA
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 2 0.03
50 62 0.94
51 2 0.03
ACGTcount: A:0.19, C:0.29, G:0.37, T:0.15
Consensus pattern (49 bp):
GTATAGCGCGGTCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:4189082 original size:20 final size:21
Alignment explanation
Indices: 4189047--4189092 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
4189037 CTCTCATAAG
* *
4189047 AGTATCGATATTGAGG-GTCT
1 AGTATCGAGATCGAGGAGTCT
*
4189067 AGTATCGAGATCGAGGAGTTT
1 AGTATCGAGATCGAGGAGTCT
4189088 AGTAT
1 AGTAT
4189093 TGAGTTCGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (21 bp):
AGTATCGAGATCGAGGAGTCT
Found at i:4198988 original size:27 final size:27
Alignment explanation
Indices: 4198958--4199017 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
4198948 GTTATTCTGG
*
4198958 TCATTTTAGGGCTC-AAGGGTATTTCCA
1 TCATTTT-GGGCTCTAAAGGTATTTCCA
* *
4198985 TCATTTTGGGGTCTAAAGGTATTTTCA
1 TCATTTTGGGCTCTAAAGGTATTTCCA
*
4199012 TAATTT
1 TCATTT
4199018 CAAAAATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.18
27 23 0.82
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.43
Consensus pattern (27 bp):
TCATTTTGGGCTCTAAAGGTATTTCCA
Found at i:4203550 original size:32 final size:32
Alignment explanation
Indices: 4203475--4203550 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
4203465 CTATATTGAA
* * *
4203475 CATTATCTGAATGCTAGACTAATTCTTTTGTG
1 CATTATCTGAATGCAAGACTAATTATGTTGTG
* **
4203507 CATTAGT-TGAATGCAATACTGGTTATGTTGTG
1 CATTA-TCTGAATGCAAGACTAATTATGTTGTG
4203539 CATTATCTGAAT
1 CATTATCTGAAT
4203551 TCTAGTATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
31 1 0.03
32 34 0.94
33 1 0.03
ACGTcount: A:0.26, C:0.13, G:0.18, T:0.42
Consensus pattern (32 bp):
CATTATCTGAATGCAAGACTAATTATGTTGTG
Found at i:4209698 original size:27 final size:27
Alignment explanation
Indices: 4209658--4209747 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
4209648 TATTTTTTTC
* * *
4209658 TTTTTTTTTCTATTCTAAACAGTTAATA
1 TTTTTTTGT-TATTCGAAACAGTGAATA
* *
4209686 TTTTTTTGTTATTCGAAACGGTGAGTA
1 TTTTTTTGTTATTCGAAACAGTGAATA
* *
4209713 TTTTTTTGTTATTCGAAACAATGAACAA
1 TTTTTTTGTTATTCGAAACAGTGAA-TA
4209741 TTTTTTT
1 TTTTTTT
4209748 CAATTTTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
27 36 0.69
28 16 0.31
ACGTcount: A:0.27, C:0.09, G:0.11, T:0.53
Consensus pattern (27 bp):
TTTTTTTGTTATTCGAAACAGTGAATA
Found at i:4213454 original size:21 final size:21
Alignment explanation
Indices: 4213410--4213467 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
4213400 GATTTAGAAT
* * * *
4213410 TTTTTCTGGGAAGCAATTAGC
1 TTTTCCTGGGAAGTAATCAAC
4213431 TTTTCCTGGGAAGTAATCAAC
1 TTTTCCTGGGAAGTAATCAAC
* *
4213452 TTTTCTTGGGATGTAA
1 TTTTCCTGGGAAGTAA
4213468 CCAGTTTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (21 bp):
TTTTCCTGGGAAGTAATCAAC
Found at i:4222583 original size:31 final size:31
Alignment explanation
Indices: 4222547--4222606 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4222537 AACTTAAAAG
* *
4222547 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
4222578 AGTTTTACAATTCTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
4222607 CATACAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:4223226 original size:12 final size:12
Alignment explanation
Indices: 4223181--4223231 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
4223171 ATTTATTTAA
4223181 AAAATT-AATATT
1 AAAATTAAATA-T
4223193 AAAATTAAA-AT
1 AAAATTAAATAT
4223204 AAAA-TATAATAT
1 AAAATTA-AATAT
4223216 AAAATTAAATAT
1 AAAATTAAATAT
4223228 AAAA
1 AAAA
4223232 CCTCTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
10 2 0.06
11 7 0.20
12 22 0.63
13 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:4228152 original size:16 final size:16
Alignment explanation
Indices: 4228141--4228172 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4228131 ATTATTCATT
4228141 AAGTTGTATATTATGA
1 AAGTTGTATATTATGA
4228157 AAGTTGTATATTATGA
1 AAGTTGTATATTATGA
4228173 GAATTGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
AAGTTGTATATTATGA
Found at i:4233007 original size:31 final size:31
Alignment explanation
Indices: 4232972--4233031 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
4232962 AACTTAAAAG
* *
4232972 AGTTTTGCAATAT-TGAGATTTAAATAATTTT
1 AGTTTTACAAT-TCTGAAATTTAAATAATTTT
4233003 AGTTTTACAATTCTGAAATTTAAATAATT
1 AGTTTTACAATTCTGAAATTTAAATAATT
4233032 CATACAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (31 bp):
AGTTTTACAATTCTGAAATTTAAATAATTTT
Found at i:4233540 original size:34 final size:34
Alignment explanation
Indices: 4233483--4233558 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
4233473 AACTTAAATC
* *
4233483 AAAATAATTAAATAAATATAAATTTAGTATATAT
1 AAAATAATTAAATAAATATAAATTAAATATATAT
* * *
4233517 AAAATAATTATAT-GATATAAAATTAAATATCTAT
1 AAAATAATTAAATAAATAT-AAATTAAATATATAT
*
4233551 AATATAAT
1 AAAATAAT
4233559 ATTAAAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAATAATTAAATAAATATAAATTAAATATATAT
Found at i:4233566 original size:28 final size:26
Alignment explanation
Indices: 4233535--4233595 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 26
4233525 TATATGATAT
4233535 AAAATTAAATATCTATAATATAATATTAA
1 AAAATTAAATAT-T-TAAT-TAATATTAA
* *
4233564 AAAATT-AATATTTAATTTAT-TTTA
1 AAAATTAAATATTTAATTAATATTAA
4233588 AAAATTAA
1 AAAATTAA
4233596 GATTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 9 0.31
25 4 0.14
26 4 0.14
27 1 0.03
28 5 0.17
29 6 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
AAAATTAAATATTTAATTAATATTAA
Found at i:4233620 original size:64 final size:65
Alignment explanation
Indices: 4233489--4233693 Score: 218
Period size: 64 Copynumber: 3.1 Consensus size: 65
4233479 AATCAAAATA
* * * *
4233489 ATTAAATAAATATAA-ATTTAGTATATATAAAATAATTATATGATATAAAATTAAATATCTATAA
1 ATTAAA-AAATATAATATTTAATTTATTTAAAA-AATTA-A-GAT-TAAAATT-AATATATATAA
4233553 TATAAT
60 TATAAT
* * *
4233559 ATTAAAAAAT-TAATATTTAATTTATTTTAAAAATTAAGATTAAAATTAATATTTATAATATAGT
1 ATTAAAAAATATAATATTTAATTTATTTAAAAAATTAAGATTAAAATTAATATATATAATATAAT
* * * *
4233623 ATT-ACAAATATAATATTTAATTTATTTAAAAAATTAATATTAAAATAAAAATAATATAATATAA
1 ATTAAAAAATATAATATTTAATTTATTTAAAAAATTAAGATTAAAATTAATAT-ATATAATATAA
*
4233687 A
65 T
4233688 ATTAAA
1 ATTAAA
4233694 TATAAAACCT
Statistics
Matches: 116, Mismatches: 15, Indels: 12
0.81 0.10 0.08
Matches are distributed among these distances:
63 5 0.04
64 56 0.48
65 19 0.16
66 4 0.03
67 1 0.01
68 8 0.07
69 17 0.15
70 6 0.05
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (65 bp):
ATTAAAAAATATAATATTTAATTTATTTAAAAAATTAAGATTAAAATTAATATATATAATATAAT
Found at i:4233693 original size:22 final size:21
Alignment explanation
Indices: 4233650--4233698 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
4233640 TAATTTATTT
4233650 AAAA-AATTAATATTAAAATA
1 AAAATAATTAATATTAAAATA
4233670 AAAATAATATAATA-TAAAATTA
1 AAAATAAT-TAATATTAAAA-TA
*
4233692 AATATAA
1 AAAATAA
4233699 AACCTCTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 4 0.16
21 8 0.32
22 13 0.52
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAATAATTAATATTAAAATA
Found at i:4233695 original size:17 final size:16
Alignment explanation
Indices: 4233652--4233700 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
4233642 ATTTATTTAA
4233652 AAAATTAATATTAAAAT
1 AAAATTAATA-TAAAAT
* *
4233669 AAAAATAATATAATAT
1 AAAATTAATATAAAAT
4233685 AAAATTAAATATAAAA
1 AAAATT-AATATAAAA
4233701 CCTCTTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 10 0.37
17 17 0.63
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTAATATAAAAT
Found at i:4235762 original size:4 final size:4
Alignment explanation
Indices: 4235753--4235777 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4235743 ATTCTAACCA
4235753 TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT T
4235778 GTTTCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:4236473 original size:4 final size:4
Alignment explanation
Indices: 4236464--4236492 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
4236454 ATTCTAACCA
4236464 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT T
4236493 GTTTCTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:4245380 original size:51 final size:51
Alignment explanation
Indices: 4245325--4245539 Score: 324
Period size: 51 Copynumber: 4.2 Consensus size: 51
4245315 TGTTTATTGT
* * * *
4245325 TACACTTTTTAAATTTATTTACTTACACCGTTGTAAGTATGTGTTAAGTGC
1 TACACTTTTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
* * * *
4245376 TACACTTTTTTTATTTTATTCACGTACACTGGTGT-ATTATGTGTTAAGTGT
1 TACAC-TTTTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
*
4245427 TACACTTTTTTGTTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
1 TACACTTTTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
4245478 TACACTTTTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
1 TACACTTTTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
*
4245529 TACATTTTTTT
1 TACACTTTTTT
4245540 GTAATATGAA
Statistics
Matches: 147, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
50 26 0.18
51 98 0.67
52 23 0.16
ACGTcount: A:0.23, C:0.14, G:0.15, T:0.48
Consensus pattern (51 bp):
TACACTTTTTTATTTTATTCACTTACACCGGTGTAAGTATGTGTTAAGTGC
Found at i:4252931 original size:34 final size:33
Alignment explanation
Indices: 4252893--4252963 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
4252883 TAATAATAAT
4252893 ATTTTCAAAATATTAAAACAATTTATTTAATATG
1 ATTTTCAAAATATT-AAACAATTTATTTAATATG
* * * * *
4252927 ATTTTTAAATTATTAGATAATTTATTTAATATT
1 ATTTTCAAAATATTAAACAATTTATTTAATATG
4252960 ATTT
1 ATTT
4252964 ATGTCAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
33 20 0.62
34 12 0.38
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (33 bp):
ATTTTCAAAATATTAAACAATTTATTTAATATG
Found at i:4253102 original size:42 final size:42
Alignment explanation
Indices: 4253048--4253127 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 42
4253038 AAATAAAATT
4253048 ATTATAAATTATATTAATTATTTATTAAAATAAGAATAATAC
1 ATTATAAATTATATTAATTATTTATTAAAATAAGAATAATAC
* *
4253090 ATTATTAATTATATTAATTATTTATTAAAATAATAATA
1 ATTATAAATTATATTAATTATTTATTAAAATAAGAATA
4253128 TTTTAAATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (42 bp):
ATTATAAATTATATTAATTATTTATTAAAATAAGAATAATAC
Found at i:4259049 original size:45 final size:45
Alignment explanation
Indices: 4258993--4259097 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
4258983 TGCATCAATC
* *
4258993 CATGCATCGATGTACCATT-GAATAAATT-GAACATCGAATGCATTT
1 CATGCATCGATGCA-C-TTGGAATAAATTAAAACATCGAATGCATTT
** **
4259038 CATGCATCGATGCACTTGGGTTTTATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTT
4259083 CATGCATCGATGCAC
1 CATGCATCGATGCAC
4259098 AAGCAATGCA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
43 2 0.04
44 6 0.12
45 44 0.85
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (45 bp):
CATGCATCGATGCACTTGGAATAAATTAAAACATCGAATGCATTT
Found at i:4261142 original size:21 final size:21
Alignment explanation
Indices: 4261103--4261142 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4261093 AAGACTCTAT
*
4261103 TTTCAAAATACAAATATGATA
1 TTTCAAAATACAAAAATGATA
**
4261124 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
4261143 AAATAGTCTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:4266247 original size:21 final size:21
Alignment explanation
Indices: 4266205--4266248 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
4266195 ACTCTGGGAG
* *
4266205 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
4266226 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
4266247 CT
1 CT
4266249 CTGGCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:4267361 original size:45 final size:46
Alignment explanation
Indices: 4267305--4267409 Score: 135
Period size: 45 Copynumber: 2.3 Consensus size: 46
4267295 TGCATCAATC
*
4267305 CATGCATCGATGCACCATT-GAATAAATT-GAACATCGAATGCATTT
1 CATGCATCGATGCACC-TTGGAATAAATTAAAACATCGAATGCATTT
** **
4267350 CATGCATCGATGCA-CTTGGGTTTTATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACCTTGGAATAAATTAAAACATCGAATGCATTT
4267395 CATGCATCGATGCAC
1 CATGCATCGATGCAC
4267410 AAGCAATGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 2 0.04
44 6 0.12
45 44 0.85
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.30
Consensus pattern (46 bp):
CATGCATCGATGCACCTTGGAATAAATTAAAACATCGAATGCATTT
Found at i:4272787 original size:116 final size:111
Alignment explanation
Indices: 4272583--4272825 Score: 278
Period size: 116 Copynumber: 2.1 Consensus size: 111
4272573 TTTTTTAACA
* * * * * *
4272583 ATTTATTTCATTTTATAAAATAGAATCTTTCAGATCATGAAATAAATTTGATGATTTATTTGCTT
1 ATTTATTTCCTTTTACAAAATAGAATCTATAAGATCATGAAATAAATTTAATGATTTATTTCCTT
4272648 TCATAAATTAGAATCATATAAGATTCTC-ATGAATATAAATTCAAAC
66 TCATAAATTAGAATCATATAAGATTCTCAATGAA-ATAAATTCAAAC
4272694 ATTTATTTCCTTTTACAAAATAGAATCATATAAGATTCCATAGAAAATAAATTTAATGATTTATT
1 ATTTATTTCCTTTTACAAAATAGAATC-TATAAGA-T-CAT-G-AAATAAATTTAATGATTTATT
* * **
4272759 TCCTTTTACA-AAATT-GAATCAT-TCAAGATTCTCAATTAAATAAATTCGATG
61 TCC-TTT-CATAAATTAGAATCATAT-AAGATTCTCAATGAAATAAATTCAAAC
*
4272810 ATTGATTTCCTTTTAC
1 ATTTATTTCCTTTTAC
4272826 TGTAACCCCA
Statistics
Matches: 112, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
111 25 0.22
112 5 0.04
113 1 0.01
114 3 0.03
115 2 0.02
116 62 0.55
117 12 0.11
118 2 0.02
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.42
Consensus pattern (111 bp):
ATTTATTTCCTTTTACAAAATAGAATCTATAAGATCATGAAATAAATTTAATGATTTATTTCCTT
TCATAAATTAGAATCATATAAGATTCTCAATGAAATAAATTCAAAC
Found at i:4272811 original size:58 final size:58
Alignment explanation
Indices: 4272449--4272825 Score: 222
Period size: 58 Copynumber: 6.5 Consensus size: 58
4272439 AGATTTTACG
* * * * * * *
4272449 AAAATAAATTGAAT-AGTTTATTTCATTTCATAAAATTAAATCAT-TCAAGATTTTCAAG
1 AAAATAAATTCAATGA-TTTATTTCCTTTTACAAAATTGAATCATAT-AAGATTCTCAAT
* * * * * * * **
4272507 AAAATGAATTCAAAGATATATTTCTTTTTACAAAATAGAGTCATGTAAGATTGC-CAGG
1 AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATT-CTCAAT
* * ** * * * * *
4272565 AAAATAATTTTTTTAACAATTTATTTCATTTTATAAAATAGAATC-TTTCAGA---TC-AT
1 AAAATAA---ATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATTCTCAAT
* ** *
4272621 GAAATAAATTTGATGATTTATTTGC-TTT-CATAAATTAGAATCATATAAGATTCTC-AT
1 AAAATAAATTCAATGATTTATTTCCTTTTACA-AAATT-GAATCATATAAGATTCTCAAT
* ** * *
4272678 GAATATAAATTCAAACATTTATTTCCTTTTACAAAATAGAATCATATAAGATTC-CATAG
1 -AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATTCTCA-AT
*
4272737 AAAATAAATTTAATGATTTATTTCCTTTTACAAAATTGAATCAT-TCAAGATTCTCAAT
1 AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATAT-AAGATTCTCAAT
* * *
4272795 TAAATAAATTCGATGATTGATTTCCTTTTAC
1 AAAATAAATTCAATGATTTATTTCCTTTTAC
4272826 TGTAACCCCA
Statistics
Matches: 244, Mismatches: 55, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
51 1 0.00
52 7 0.03
53 17 0.07
54 5 0.02
56 6 0.02
57 7 0.03
58 155 0.64
59 12 0.05
60 7 0.03
61 27 0.11
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.40
Consensus pattern (58 bp):
AAAATAAATTCAATGATTTATTTCCTTTTACAAAATTGAATCATATAAGATTCTCAAT
Found at i:4273852 original size:13 final size:13
Alignment explanation
Indices: 4273821--4273854 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4273811 TTGACTTTTT
*
4273821 GGTCAAAGTCAAC
1 GGTCAAAGTCAAA
*
4273834 GATCAAAGTCAAA
1 GGTCAAAGTCAAA
4273847 GGTCAAAG
1 GGTCAAAG
4273855 GTCGGACAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (13 bp):
GGTCAAAGTCAAA
Found at i:4273869 original size:13 final size:13
Alignment explanation
Indices: 4273853--4273896 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
4273843 CAAAGGTCAA
4273853 AGGTCGGACAGTC
1 AGGTCGGACAGTC
* *
4273866 AGGTCGGATAGTT
1 AGGTCGGACAGTC
*
4273879 AGGTCGGGCAGTC
1 AGGTCGGACAGTC
*
4273892 GGGTC
1 AGGTC
4273897 AGACCAGGTC
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.18, G:0.43, T:0.20
Consensus pattern (13 bp):
AGGTCGGACAGTC
Found at i:4275117 original size:44 final size:45
Alignment explanation
Indices: 4275036--4275141 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
4275026 TAATCATTTC
* *
4275036 ATTTTAAATTTGACAACCCAACAATCAAAAAGAACTAATTCTTTA
1 ATTTTAATTTTGACAACCCAACAATCAAAAAGAACTAATACTTTA
* * * * *
4275081 ATTTTAATTTTGGCAA-CCAATAATTAAAATGAACTAATACTTTG
1 ATTTTAATTTTGACAACCCAACAATCAAAAAGAACTAATACTTTA
* *
4275125 ATTTTAGTTTTAACAAC
1 ATTTTAATTTTGACAAC
4275142 TCAATTATCA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
44 36 0.72
45 14 0.28
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.37
Consensus pattern (45 bp):
ATTTTAATTTTGACAACCCAACAATCAAAAAGAACTAATACTTTA
Found at i:4279229 original size:32 final size:32
Alignment explanation
Indices: 4279158--4279232 Score: 105
Period size: 32 Copynumber: 2.3 Consensus size: 32
4279148 ATGTACATAC
** * *
4279158 TCTAAATATAACACTGACACTGTTGTGCATTA
1 TCTAAATGCAACACTAACACTGTTATGCATTA
*
4279190 TCTAAATGCAACACTAACTCTGTTATGCATTA
1 TCTAAATGCAACACTAACACTGTTATGCATTA
4279222 TCTAAATGCAA
1 TCTAAATGCAA
4279233 TACACTGCTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (32 bp):
TCTAAATGCAACACTAACACTGTTATGCATTA
Found at i:4283647 original size:24 final size:25
Alignment explanation
Indices: 4283601--4283652 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
4283591 CTTGGAAAGG
*
4283601 AAAGGAAATGAAGAAATAAAAATGA
1 AAAGGAAATGAAGAAATAAAAATAA
*
4283626 AAAGG-AATGAAGGGAAT-AAAATAA
1 AAAGGAAATGAA-GAAATAAAAATAA
4283650 AAA
1 AAA
4283653 TAGAGATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 15 0.62
25 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (25 bp):
AAAGGAAATGAAGAAATAAAAATAA
Found at i:4295266 original size:29 final size:28
Alignment explanation
Indices: 4295225--4295293 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 28
4295215 CCGGCAACTC
4295225 CGAG-CAACTCGGTCGGAGTCAA-CAGGTT
1 CGAGTCAACTCGGTCGGAGTCAACCA-G-T
*
4295253 CGAGTCAACTCGGTCTGAGTCAACCAGT
1 CGAGTCAACTCGGTCGGAGTCAACCAGT
4295281 CTGAGTCAACTCG
1 C-GAGTCAACTCG
4295294 TTGACTTTGA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 6 0.16
29 29 0.78
30 2 0.05
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.20
Consensus pattern (28 bp):
CGAGTCAACTCGGTCGGAGTCAACCAGT
Found at i:4295274 original size:15 final size:15
Alignment explanation
Indices: 4295229--4295293 Score: 73
Period size: 14 Copynumber: 4.5 Consensus size: 15
4295219 CAACTCCGAG
*
4295229 CAACTCGGTCGGAGT
1 CAACTCGGTCTGAGT
*
4295244 CAAC-AGGT-TCGAGT
1 CAACTCGGTCT-GAGT
4295258 CAACTCGGTCTGAGT
1 CAACTCGGTCTGAGT
*
4295273 CAAC-CAGTCTGAGT
1 CAACTCGGTCTGAGT
4295287 CAACTCG
1 CAACTCG
4295294 TTGACTTTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
14 24 0.59
15 16 0.39
16 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.22
Consensus pattern (15 bp):
CAACTCGGTCTGAGT
Found at i:4295309 original size:14 final size:14
Alignment explanation
Indices: 4295292--4295346 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
4295282 TGAGTCAACT
4295292 CGTTGACTTTGACC
1 CGTTGACTTTGACC
* *
4295306 CGTTGATTTTGTCC
1 CGTTGACTTTGACC
*
4295320 CGTTTACTTTGA-C
1 CGTTGACTTTGACC
* *
4295333 TGTTGATTTTGACC
1 CGTTGACTTTGACC
4295347 AAAAAGTCAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (14 bp):
CGTTGACTTTGACC
Found at i:4312969 original size:3 final size:3
Alignment explanation
Indices: 4312961--4313005 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
4312951 TTGCATCTTA
* *
4312961 ATT ATT ATT ATT ATT ATT AAT GTT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4313006 GTATTTTTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:4314681 original size:179 final size:179
Alignment explanation
Indices: 4314376--4314700 Score: 387
Period size: 179 Copynumber: 1.8 Consensus size: 179
4314366 TGACAAATTT
*
4314376 TGTTTGTAATTATATATTTTAATTATAGTGACAAAATGTATAGTCACAAATGATTATCTCCAATT
1 TGTTTGTAATTATATATTGTAATTATAGTGACAAAA-GTATAGTCACAAATGATTATCTCCAATT
* * * *
4314441 TTCGATACAAAAAAAATTATATAGTGTCAGTTTTTAAAATATAACCTATAATTATTATTACAAAT
65 TTCGATACAAAAAAAATTATATAGTGACAATTTTTAAAATATAACCTATAATAATTATTACAAAA
*
4314506 CAAAGTTGTTACAAAAAATAATGAGAATCAAGTTTCTAGTGAAAAAAATAA
130 CAAA-TTGTCACAAAAAATAATGAGAATCAAGTTTCTAGTGAAAAAAATAA
* *
4314557 TGTTTGTAGTTATATATTGTAATTATAGTGAC-AAA-TAT-GTCATAAA-GATT-TCCCTCCATA
1 TGTTTGTAATTATATATTGTAATTATAGTGACAAAAGTATAGTCACAAATGATTAT--CTCCA-A
* * * * *
4314617 TTTTTTGA-ACAAAAAGAATTCATATAGTGACAAATTTTT-AACTATAA-GTGTTAATAATTATT
63 -TTTTCGATACAAAAAAAATT-ATATAGTGAC-AATTTTTAAAATATAACCT-ATAATAATTATT
*
4314679 ACAAAACATATTGTCACAAAAA
124 ACAAAACAAATTGTCACAAAAA
4314701 TATGATATTC
Statistics
Matches: 123, Mismatches: 14, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
175 1 0.01
176 4 0.03
177 12 0.10
178 27 0.22
179 40 0.33
180 9 0.07
181 30 0.24
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (179 bp):
TGTTTGTAATTATATATTGTAATTATAGTGACAAAAGTATAGTCACAAATGATTATCTCCAATTT
TCGATACAAAAAAAATTATATAGTGACAATTTTTAAAATATAACCTATAATAATTATTACAAAAC
AAATTGTCACAAAAAATAATGAGAATCAAGTTTCTAGTGAAAAAAATAA
Found at i:4315019 original size:39 final size:39
Alignment explanation
Indices: 4314975--4315049 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
4314965 TTTTATTTTA
4314975 AAAATATTTAAA-AATTTATTATTTAAAATTTAAATTATG
1 AAAATA-TTAAATAATTTATTATTTAAAATTTAAATTATG
* * * *
4315014 AAAATATTAAATTATTTGTTTTTTAAATTTTAAATT
1 AAAATATTAAATAATTTATTATTTAAAATTTAAATT
4315050 TAAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 5 0.16
39 26 0.84
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (39 bp):
AAAATATTAAATAATTTATTATTTAAAATTTAAATTATG
Found at i:4315023 original size:16 final size:15
Alignment explanation
Indices: 4314999--4315028 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4314989 TTTATTATTT
4314999 AAAATTTAAATTATG
1 AAAATTTAAATTATG
4315014 AAAATATTAAATTAT
1 AAAAT-TTAAATTAT
4315029 TTGTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AAAATTTAAATTATG
Found at i:4315299 original size:21 final size:22
Alignment explanation
Indices: 4315252--4315329 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 22
4315242 TTTGAAAATG
*
4315252 ATAAAAATATTAAATTATTATT
1 ATAAAAATATTAAAATATTATT
*
4315274 CTAAAAA-ATTAAAAT-TTATT
1 ATAAAAATATTAAAATATTATT
*
4315294 A-ATAAAAT-CTAAAATA-TA-T
1 ATA-AAAATATTAAAATATTATT
*
4315313 ATAAAAAT-CTAAAATAT
1 ATAAAAATATTAAAATAT
4315330 AAAAAATACA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
19 16 0.34
20 18 0.38
21 7 0.15
22 6 0.13
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (22 bp):
ATAAAAATATTAAAATATTATT
Found at i:4320932 original size:18 final size:18
Alignment explanation
Indices: 4320909--4320951 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
4320899 TTATTCCTCA
4320909 TGTTTCTGTTCCTAGTAC
1 TGTTTCTGTTCCTAGTAC
4320927 TGTTTCTGTTCCTAGTAC
1 TGTTTCTGTTCCTAGTAC
4320945 TGTTTCT
1 TGTTTCT
4320952 ACTAGGGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.09, C:0.21, G:0.16, T:0.53
Consensus pattern (18 bp):
TGTTTCTGTTCCTAGTAC
Found at i:4327646 original size:21 final size:21
Alignment explanation
Indices: 4327620--4327661 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
4327610 CAGAATGGGG
*
4327620 GGGAATCGGTACCCCTGCATA
1 GGGAATCGATACCCCTGCATA
*
4327641 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTGCATA
4327662 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.21
Consensus pattern (21 bp):
GGGAATCGATACCCCTGCATA
Found at i:4327807 original size:19 final size:19
Alignment explanation
Indices: 4327766--4327813 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4327756 TGAGCCTCGG
* *
4327766 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAACAGTAAA
*
4327785 TTACTGTTCAAATAGTAAA
1 TTACTGTTCAAACAGTAAA
*
4327804 TTACTATTCA
1 TTACTGTTCA
4327814 TAAAAACATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (19 bp):
TTACTGTTCAAACAGTAAA
Found at i:4327925 original size:30 final size:31
Alignment explanation
Indices: 4327878--4327968 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
4327868 AAATTTTGAA
4327878 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4327907 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4327938 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
4327969 CCTTAAATTG
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 11 0.18
31 38 0.63
ACGTcount: A:0.43, C:0.18, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:4328220 original size:20 final size:20
Alignment explanation
Indices: 4328178--4328221 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4328168 CTTAGGTAGG
* *
4328178 GTATTGATACTGAAAAGCGA
1 GTATTGATACTCAAAAGCCA
* *
4328198 GTATTGATACTCTAAGGCCA
1 GTATTGATACTCAAAAGCCA
4328218 GTAT
1 GTAT
4328222 CAATACCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (20 bp):
GTATTGATACTCAAAAGCCA
Found at i:4331037 original size:29 final size:29
Alignment explanation
Indices: 4330995--4331081 Score: 156
Period size: 29 Copynumber: 3.0 Consensus size: 29
4330985 GATCTAGGTG
*
4330995 TGTATGTCAGACATGGTCATACATCCAAT
1 TGTATGCCAGACATGGTCATACATCCAAT
4331024 TGTATGCCAGACATGGTCATACATCCAAT
1 TGTATGCCAGACATGGTCATACATCCAAT
*
4331053 TGTATGCCAGACATAGTCATACATCCAAT
1 TGTATGCCAGACATGGTCATACATCCAAT
4331082 ACAGTTACGT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.29
Consensus pattern (29 bp):
TGTATGCCAGACATGGTCATACATCCAAT
Found at i:4332444 original size:19 final size:18
Alignment explanation
Indices: 4332419--4332646 Score: 69
Period size: 19 Copynumber: 11.9 Consensus size: 18
4332409 ACTATTCTTC
*
4332419 TTATTATTTATTATTGTTTA
1 TTATTATTT-TT-TTATTTA
4332439 TT-TTATTTCTTATTATTT-
1 TTATTATTT-TT-TTATTTA
* *
4332457 TT-TTATTTTGTTTATATG
1 TTATTATTTT-TTTATTTA
* * *
4332475 TTATTATATATATATTTA
1 TTATTATTTTTTTATTTA
*
4332493 TT-TTATTTTAATCCT-TTTA
1 TTATTATTTT--T-TTATTTA
*
4332512 TTATTATTTTATTA-TTA
1 TTATTATTTTTTTATTTA
* *
4332529 TTTTTATTTGTTTCTTTTTA
1 TTATTATTT-TTT-TATTTA
4332549 TT-TTATTTCTTATTATATATACA
1 TTATTATTT-TT-TTAT-T-T--A
*
4332572 TT-TTATTTATTTCTTTTTA
1 TTATTATTT-TTT-TATTTA
*
4332591 TTATTATTCTTATTA-TTA
1 TTATTATT-TTTTTATTTA
*
4332609 TTATTATTATTATTATTCTTA
1 TTATTATT-TTTTTA-T-TTA
4332630 TTATTATTTTCTTTATT
1 TTATTATTTT-TTTATT
4332647 CTACTTATAT
Statistics
Matches: 161, Mismatches: 24, Indels: 47
0.69 0.10 0.20
Matches are distributed among these distances:
17 23 0.14
18 37 0.23
19 42 0.26
20 27 0.17
21 17 0.11
22 2 0.01
23 13 0.08
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (18 bp):
TTATTATTTTTTTATTTA
Found at i:4332497 original size:27 final size:27
Alignment explanation
Indices: 4332417--4332498 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 27
4332407 TTACTATTCT
* * *
4332417 TCTTATTATTTATTATTGTTTATTTTATT
1 TCTTATTATATA-TA-TATTTATTTTATA
* * *
4332446 TCTTATTATTTTTTTATTT-TGTTTATA
1 TCTTATTATATATATATTTAT-TTTATA
*
4332473 TGTTATTATATATATATTTATTTTAT
1 TCTTATTATATATATATTTATTTTAT
4332499 TTTAATCCTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 1 0.02
27 29 0.67
28 2 0.05
29 11 0.26
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (27 bp):
TCTTATTATATATATATTTATTTTATA
Found at i:4332514 original size:83 final size:83
Alignment explanation
Indices: 4332425--4332616 Score: 195
Period size: 83 Copynumber: 2.3 Consensus size: 83
4332415 CTTCTTATTA
* *
4332425 TTTATTATT-GTTTATT-TTATTTCTTATTAT-TTT-TTTATTTTGTTTATATGTTATTATATAT
1 TTTATTATTAGTTTATTATTATTT-TTATT-TGTTTCTTT-TTAT-TTTATATCTTATTATATAT
*
4332486 ATA-TTTATTTTATTTTAATCCT
62 ACATTTTA-TTTATTTTAATCCT
* *
4332508 TTTATTATTATTTTATTATTATTTTTATTTGTTTCTTTTTATTTTATTTCTTATTATATATACAT
1 TTTATTATTAGTTTATTATTATTTTTATTTGTTTCTTTTTATTTTATATCTTATTATATATACAT
*
4332573 TTTATTTA--TT--TCTT
66 TTTATTTATTTTAATCCT
* *
4332587 TTTATTATTATTCTTATTATTATTATTATT
1 TTTATTATTAGT-TTATTATTATTTTTATT
4332617 ATTATTATTC
Statistics
Matches: 96, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
79 15 0.16
80 16 0.17
81 2 0.02
83 33 0.34
84 21 0.22
85 9 0.09
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (83 bp):
TTTATTATTAGTTTATTATTATTTTTATTTGTTTCTTTTTATTTTATATCTTATTATATATACAT
TTTATTTATTTTAATCCT
Found at i:4332517 original size:3 final size:3
Alignment explanation
Indices: 4332509--4332637 Score: 88
Period size: 3 Copynumber: 42.7 Consensus size: 3
4332499 TTTAATCCTT
* * *
4332509 TTA TTA TTA TT- TTA TTA TTA TTT TTA TT- TGT- TTC TTT TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
* * * *
4332551 TTA TTTC TTA TTA TATA TACA TT- TTA TTTA TTTC TTT TTA TTA TTA
1 TTA -TTA TTA TTA T-TA T-TA TTA TTA -TTA -TTA TTA TTA TTA TTA
* *
4332597 TTC TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
4332638 TTCTTTATTC
Statistics
Matches: 103, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
2 8 0.08
3 81 0.79
4 14 0.14
ACGTcount: A:0.24, C:0.05, G:0.01, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:4332553 original size:42 final size:42
Alignment explanation
Indices: 4332507--4332642 Score: 138
Period size: 42 Copynumber: 3.2 Consensus size: 42
4332497 ATTTTAATCC
* *
4332507 TTTTATTATTATTTTATTATTATTTTTATTTGTTTCTTTTTA
1 TTTTATTCTTATTTTATTATTATTTTTATTTATTTCTTTTTA
* *
4332549 TTTTATTTCTTATTATA-TA-TACATTTTATTTATTTCTTTTTA
1 TTTTA-TTCTTATTTTATTATTA-TTTTTATTTATTTCTTTTTA
* *
4332591 TTATTATTCTTATTATTATTATTATTATTA-TTA-TTCTTATTA
1 TT-TTATTCTTATT-TTATTATTATTTTTATTTATTTCTTTTTA
4332633 TTATT-TTCTT
1 TT-TTATTCTT
4332643 TATTCTACTT
Statistics
Matches: 80, Mismatches: 8, Indels: 13
0.79 0.08 0.13
Matches are distributed among these distances:
41 7 0.09
42 48 0.60
43 17 0.21
44 6 0.08
45 2 0.03
ACGTcount: A:0.23, C:0.05, G:0.01, T:0.71
Consensus pattern (42 bp):
TTTTATTCTTATTTTATTATTATTTTTATTTATTTCTTTTTA
Found at i:4332619 original size:83 final size:83
Alignment explanation
Indices: 4332425--4332619 Score: 201
Period size: 79 Copynumber: 2.4 Consensus size: 83
4332415 CTTCTTATTA
* *
4332425 TTTATTATT-GTTTATT-TTATTTCTTATTATTTTTTTATTTTGTTTATATGTTATTATATATAT
1 TTTATTATTATTTTATTATTA-TT-TTATTATTTTTTTATTTTATTTATATGTTATTATATATAT
** * *
4332488 ATTTATTTTATTTTAATCCT
64 ATACATTTTATTTTATTCTT
*
4332508 TTTATTATTATTTTATTATTA-TTT-TTATTTGTTTCT-TTTTATTT-TAT-TTCTTAT-TATAT
1 TTTATTATTATTTTATTATTATTTTATTATTT-TTT-TATTTTATTTATATGTTATTATATATAT
4332567 ATACATTTTA-TTTATTTCTT
64 ATACATTTTATTTTA-TTCTT
4332587 TTTATTATTATTCTTATTATTATTATTATTATT
1 TTTATTATTATT-TTATTATTATT-TTATTATT
4332620 ATTATTCTTA
Statistics
Matches: 96, Mismatches: 7, Indels: 18
0.79 0.06 0.15
Matches are distributed among these distances:
78 4 0.04
79 28 0.29
80 15 0.16
81 10 0.10
82 14 0.15
83 16 0.17
84 6 0.06
85 3 0.03
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (83 bp):
TTTATTATTATTTTATTATTATTTTATTATTTTTTTATTTTATTTATATGTTATTATATATATAT
ACATTTTATTTTATTCTT
Found at i:4339166 original size:18 final size:18
Alignment explanation
Indices: 4339143--4339189 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
4339133 TCCACTCATC
*
4339143 CATGATTGTGTATCCCAT
1 CATGATTGAGTATCCCAT
* *
4339161 CATGATTAAGTATCTCAT
1 CATGATTGAGTATCCCAT
4339179 CATGATTGAGT
1 CATGATTGAGT
4339190 TCCAAGTACC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (18 bp):
CATGATTGAGTATCCCAT
Found at i:4347592 original size:19 final size:18
Alignment explanation
Indices: 4347553--4347587 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
4347543 AAAAAAATAA
4347553 AATTTTTAATTTGATTTAT
1 AATTTTTAATTT-ATTTAT
4347572 AATTTTTAATTT-TTTA
1 AATTTTTAATTTATTTA
4347588 AATAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
AATTTTTAATTTATTTAT
Found at i:4354252 original size:18 final size:19
Alignment explanation
Indices: 4354208--4354252 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
4354198 CTATGTCATC
*
4354208 ATTATCA-TCATCAATATT
1 ATTATCATTCATCAATAGT
*
4354226 CTTATCATTC-TCAATAGT
1 ATTATCATTCATCAATAGT
4354244 ATTATCATT
1 ATTATCATT
4354253 AATCCTAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTATCATTCATCAATAGT
Found at i:4354495 original size:23 final size:23
Alignment explanation
Indices: 4354469--4354536 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
4354459 TGCCATATAA
** *
4354469 AATTGTCCCGAAGGACTTCGTAG
1 AATTGTCCCGAAGGACCACATAG
*
4354492 AATTGTCTCGAAGGACCACATAG
1 AATTGTCCCGAAGGACCACATAG
*
4354515 AATTGTCCCTAAGGACCACATA
1 AATTGTCCCGAAGGACCACATA
4354537 TATGTTCCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (23 bp):
AATTGTCCCGAAGGACCACATAG
Found at i:4354558 original size:21 final size:21
Alignment explanation
Indices: 4354502--4354620 Score: 114
Period size: 21 Copynumber: 5.6 Consensus size: 21
4354492 AATTGTCTCG
* * *
4354502 AAGGACCACATAGAATTGTCCCT
1 AAGGACCACATA-TA-TGTTCCA
4354525 AAGGACCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* * *
4354546 AAAGACCAAATATATG-TCTCG
1 AAGGACCACATATATGTTC-CA
*
4354567 AAGGACCGCATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* *
4354588 AAGGATCACATATATGTCCCA
1 AAGGACCACATATATGTTCCA
*
4354609 AAGGACCGCATA
1 AAGGACCACATA
4354621 GAACCCTCGA
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
20 2 0.03
21 62 0.78
22 3 0.04
23 12 0.15
ACGTcount: A:0.38, C:0.24, G:0.17, T:0.22
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:4354572 original size:42 final size:42
Alignment explanation
Indices: 4354518--4354620 Score: 143
Period size: 42 Copynumber: 2.5 Consensus size: 42
4354508 CACATAGAAT
* *
4354518 TGTCCCTAAGGACCACATATATGTTCCAAAAGACCAAATATA
1 TGTCCCAAAGGACCGCATATATGTTCCAAAAGACCAAATATA
* * * * *
4354560 TGTCTCGAAGGACCGCATATATGTTCCAAAGGATCACATATA
1 TGTCCCAAAGGACCGCATATATGTTCCAAAAGACCAAATATA
4354602 TGTCCCAAAGGACCGCATA
1 TGTCCCAAAGGACCGCATA
4354621 GAACCCTCGA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (42 bp):
TGTCCCAAAGGACCGCATATATGTTCCAAAAGACCAAATATA
Found at i:4354602 original size:63 final size:65
Alignment explanation
Indices: 4354495--4354615 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 65
4354485 TTCGTAGAAT
* *
4354495 TGTCTCGAAGGACCACATAGAATTGTCCCTAAGGACCACATATATGTTCCAAAAGACCAAATATA
1 TGTCTCGAAGGACCACATAGAATTGTCCCAAAGGACCACATATATGTCCCAAAAGACCAAATATA
* * * * *
4354560 TGTCTCGAAGGACCGCATA-TA-TGTTCCAAAGGATCACATATATGTCCCAAAGGACC
1 TGTCTCGAAGGACCACATAGAATTGTCCCAAAGGACCACATATATGTCCCAAAAGACC
4354616 GCATAGAACC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
63 30 0.61
64 1 0.02
65 18 0.37
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (65 bp):
TGTCTCGAAGGACCACATAGAATTGTCCCAAAGGACCACATATATGTCCCAAAAGACCAAATATA
Done.