Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008282.1 Hibiscus syriacus cultivar Beakdansim tig00110944_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: 1335609
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:392699 original size:62 final size:62
Alignment explanation
Indices: 392612--392744 Score: 257
Period size: 62 Copynumber: 2.1 Consensus size: 62
392602 CAGTATCACG
*
392612 TTGCAATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
392674 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
392736 TTGCGATTT
1 TTGCGATTT
392745 ACTTATTCGC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
62 70 1.00
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (62 bp):
TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAATTCGCA
Found at i:392803 original size:21 final size:22
Alignment explanation
Indices: 392751--392803 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
392741 ATTTACTTAT
392751 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
392772 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
392793 TCGCATTGCGA
1 TCGCATTGCGA
392804 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:393367 original size:14 final size:14
Alignment explanation
Indices: 393342--393375 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
393332 TTGGTGATGG
393342 TGTGATGGCAATGA
1 TGTGATGGCAATGA
* *
393356 TTTGATGTCAATGA
1 TGTGATGGCAATGA
393370 TGTGAT
1 TGTGAT
393376 CAACATCATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.38
Consensus pattern (14 bp):
TGTGATGGCAATGA
Found at i:394066 original size:29 final size:29
Alignment explanation
Indices: 394024--394112 Score: 169
Period size: 29 Copynumber: 3.1 Consensus size: 29
394014 ATACAGTGGT
394024 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
394053 CTTGGAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
*
394082 CTTGAAGGTCGCCATGGCATCCGGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGGGCGAC
394111 CT
1 CT
394113 GTGTGTATTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.15, C:0.31, G:0.36, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGGGCGAC
Found at i:394198 original size:15 final size:15
Alignment explanation
Indices: 394158--394336 Score: 144
Period size: 15 Copynumber: 11.1 Consensus size: 15
394148 AACATGGGAC
394158 GTGGGAATGCATGGGG
1 GTGGGAATGCAT-GGG
* *
394174 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
394189 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* *
394204 G-GAGGGATCAACATGGG
1 GTG-GGAAT--GCATGGG
394221 ATGTGGGAATGCATGGGG
1 --GTGGGAATGCAT-GGG
* *
394239 GAGGGGATGCATGGG
1 GTGGGAATGCATGGG
394254 ACGTGGGAATGCATGGG
1 --GTGGGAATGCATGGG
394271 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
* * *
394286 GAGGGGATGGTGCATTGGAC
1 G-TGGGA--ATGCA-TGG-G
394306 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
394321 GTGGGAATGCATGGG
1 GTGGGAATGCATGGG
394336 G
1 G
394337 GAGGGGATGG
Statistics
Matches: 131, Mismatches: 18, Indels: 29
0.74 0.10 0.16
Matches are distributed among these distances:
14 1 0.01
15 56 0.43
16 27 0.21
17 26 0.20
18 7 0.05
19 12 0.09
20 2 0.02
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (15 bp):
GTGGGAATGCATGGG
Found at i:394231 original size:65 final size:66
Alignment explanation
Indices: 394145--394271 Score: 229
Period size: 65 Copynumber: 1.9 Consensus size: 66
394135 TCGCCATGCA
394145 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG-GTGGGAATGCATGGGGGAGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
394209 G
66 G
*
394210 ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGG
1 ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGA-GTGGGAATGCATGGGG
394272 TGGGAATGCA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
65 43 0.73
67 16 0.27
ACGTcount: A:0.24, C:0.09, G:0.50, T:0.17
Consensus pattern (66 bp):
ATCAACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGAGTGGGAATGCATGGGGGAGG
G
Found at i:394269 original size:50 final size:48
Alignment explanation
Indices: 394150--394363 Score: 220
Period size: 50 Copynumber: 4.3 Consensus size: 48
394140 ATGCAATCAA
* * * *
394150 CATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGG-TGGGAATG
1 CATGGGACGTGGGAATGCAT-GGGGTGGGAATGCATGGGGAGGGGAGTG
* * *
394198 CATGGG-GGAGGG-ATCAACATGGGATGTGGGAATGCATGGGGGAGGGGA-TG
1 CATGGGACGTGGGAAT--GCATGGG--GTGGGAATGCAT-GGGGAGGGGAGTG
394248 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGATGGTG
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGA--GTG
*
394298 CATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGGATGGTG
1 CATGGGACGTGGGAATGCATGGGGTGGGAATGCAT-GGGGAGGGGA--GTG
*
394349 CATTGGACGTGGGAA
1 CATGGGACGTGGGAA
394364 CTGTGCATGG
Statistics
Matches: 144, Mismatches: 10, Indels: 21
0.82 0.06 0.12
Matches are distributed among these distances:
46 2 0.01
47 17 0.12
48 21 0.15
49 10 0.07
50 54 0.38
51 38 0.26
52 2 0.01
ACGTcount: A:0.21, C:0.08, G:0.52, T:0.18
Consensus pattern (48 bp):
CATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGAGGGGAGTG
Found at i:394284 original size:65 final size:64
Alignment explanation
Indices: 394148--394340 Score: 214
Period size: 65 Copynumber: 3.0 Consensus size: 64
394138 CCATGCAATC
*
394148 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT
1 AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
*
394212 CAACATGGGATGTGGGAATGCATGGGGGAGGGGATGCATGGGACGTGGGAATGCATGGGGTG-GG
1 -AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGG--GTGGGAATGCATGGGG-GAGG
394276 AAT
62 AAT
* * ** * *
394279 -GCATGGGGA-G-GGGATGGTGCATTGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGG
1 AACAT-GGGACGTGGGA--ATGCA-TGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGG
394341 GGATGGTGCA
Statistics
Matches: 112, Mismatches: 8, Indels: 16
0.82 0.06 0.12
Matches are distributed among these distances:
64 5 0.04
65 62 0.55
66 8 0.07
67 36 0.32
68 1 0.01
ACGTcount: A:0.22, C:0.08, G:0.52, T:0.17
Consensus pattern (64 bp):
AACATGGGACGTGGGAATGCATGGGGGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGAAT
Found at i:394293 original size:82 final size:82
Alignment explanation
Indices: 394160--394335 Score: 223
Period size: 82 Copynumber: 2.2 Consensus size: 82
394150 CATGGGACGT
* * * *
394160 GGGAATGCATGGG-GGAGGGGATGCATGGGGTGGGAATGCATGGGGGAGGGAT-CAACATGGGAT
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGATGCAACATGGGAC
394223 GTGGGAATGCATGGGGGA
66 GTGGGAATGCAT-GGGGA
* *** *
394241 GGGGATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCAT-GGGGAGGGGATGGTGCATTGGA
1 GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGA-GGGATGCAACATGGGA
*
394305 CGTGGGAATGCATGGGGT
65 CGTGGGAATGCATGGGGA
394323 GGGAATGCATGGG
1 GGGAATGCATGGG
394336 GGAGGGGATG
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
81 17 0.21
82 46 0.57
83 18 0.22
ACGTcount: A:0.22, C:0.08, G:0.53, T:0.18
Consensus pattern (82 bp):
GGGAATGCATGGGACGTGGGAATGCATGGGGTGGGAATGCATGGGGGAGGGATGCAACATGGGAC
GTGGGAATGCATGGGGA
Found at i:394359 original size:51 final size:51
Alignment explanation
Indices: 394223--394363 Score: 245
Period size: 50 Copynumber: 2.8 Consensus size: 51
394213 AACATGGGAT
*
394223 GTGGGAATGCATGGGGGAGGGGA---TGCATGGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
394271 GTGGGAATGCAT-GGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
394321 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
1 GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAA
394364 CTGTGCATGG
Statistics
Matches: 88, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
47 10 0.11
48 12 0.14
50 36 0.41
51 30 0.34
ACGTcount: A:0.21, C:0.08, G:0.53, T:0.18
Consensus pattern (51 bp):
GTGGGAATGCATGGGGGAGGGGATGGTGCATTGGACGTGGGAATGCATGGG
Found at i:394845 original size:21 final size:21
Alignment explanation
Indices: 394820--394863 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
394810 AATCTAGTTA
394820 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
394841 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
394862 AT
1 AT
394864 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:394873 original size:28 final size:30
Alignment explanation
Indices: 394840--394902 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
394830 TAGTATAAAT
*
394840 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
394868 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
394898 TATTA
1 TATTA
394903 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:398600 original size:22 final size:19
Alignment explanation
Indices: 398568--398616 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
398558 TATTTCTATG
*
398568 TATTTATTAATCATTATAAAA
1 TATTTAATAATCATT-T-AAA
*
398589 TGATTTAATAATGATTTAAA
1 T-ATTTAATAATCATTTAAA
398609 TATTTAAT
1 TATTTAAT
398617 GATTTGATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 7 0.28
20 4 0.16
21 2 0.08
22 12 0.48
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (19 bp):
TATTTAATAATCATTTAAA
Found at i:398736 original size:19 final size:22
Alignment explanation
Indices: 398643--398739 Score: 83
Period size: 26 Copynumber: 4.2 Consensus size: 22
398633 AATGATTTGA
*
398643 TAATAATCATTATAGTAATGATTT
1 TAATAATCATTATA-AAATGA-TT
398667 GATAATAATCATTATAATAATGATTT
1 --TAATAATCATTATAA-AATGA-TT
398693 AGTAATAATCATTATAAAATGATT
1 --TAATAATCATTATAAAATGATT
*
398717 TAATAATGATT-T-AAAT-ATT
1 TAATAATCATTATAAAATGATT
398736 TAAT
1 TAAT
398740 GATTTGATGA
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 7 0.11
20 4 0.06
21 1 0.02
22 10 0.15
24 2 0.03
25 5 0.08
26 37 0.56
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.43
Consensus pattern (22 bp):
TAATAATCATTATAAAATGATT
Found at i:398889 original size:98 final size:98
Alignment explanation
Indices: 398778--399043 Score: 489
Period size: 98 Copynumber: 2.7 Consensus size: 98
398768 ATAATCATTA
* *
398778 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTT
398842 AATAATGATTTAAATATTTAATGATTTGATGATT
65 AATAATGATTTAAATATTTAATGATTTGATGATT
398876 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
398941 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
398974 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
*
399039 GTAAT
66 ATAAT
399044 AATCATTATA
Statistics
Matches: 164, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
98 163 0.99
99 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.44
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:398928 original size:124 final size:123
Alignment explanation
Indices: 398575--399167 Score: 752
Period size: 124 Copynumber: 4.8 Consensus size: 123
398565 ATGTATTTAT
398575 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
1 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
398640 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
398698 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
1 TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
398763 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
398821 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTAT-AAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
398886 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGA-TT--TAA
65 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
* * * * *
398942 TAATGATT-T-AAAT-ATTTAATGATTTGATGATTTAGTAATGATTTGAT-A-ATAATCATTATA
1 TAATCATTATAAAATGATTTAAT-A----ATGATTTA--AAT-ATTTAATGATTTGATGATT-TA
* * *
399002 GTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAACGA-TT--
57 GTAATGATTTGATAATAATCATTATAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAG
399063 TAA
121 TAA
* * * * *
399066 TAATGATT-T-AAAT-ATTTAATGATTTGATGATTTAGTAATGATTTGAT-A-ATAATCATTATA
1 TAATCATTATAAAATGATTTAAT-A----ATGATTTA--AAT-ATTTAATGATTTGATGATT-TA
* *
399126 GTAATGATTTGATAATAATCATTATAATAATGATTTAATAAT
57 GTAATGATTTGATAATAATCATTATAGTAATGATTTGATAAT
399168 GATTTAAATA
Statistics
Matches: 450, Mismatches: 8, Indels: 23
0.94 0.02 0.05
Matches are distributed among these distances:
117 7 0.02
118 5 0.01
120 1 0.00
121 10 0.02
122 8 0.02
123 142 0.32
124 270 0.60
125 7 0.02
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (123 bp):
TAATCATTATAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATT
TGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
Found at i:398992 original size:222 final size:222
Alignment explanation
Indices: 398655--399366 Score: 1356
Period size: 222 Copynumber: 3.2 Consensus size: 222
398645 ATAATCATTA
398655 TAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAA-AATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAATCATTATAATAATGATTT
398718 AATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTA
65 AATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTA
398783 ATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATAAT
130 ATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATAAT
398848 GATTTAAATATTTAATGATTTGATGATT
195 GATTTAAATATTTAATGATTTGATGATT
*
398876 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTA
398941 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
66 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
*
399006 TGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAACGATTTAATAATG
131 TGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATG
399071 ATTTAAATATTTAATGATTTGATGATT
196 ATTTAAATATTTAATGATTTGATGATT
*
399098 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTA
399163 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
66 ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
*
399228 TGATTTGATAATAATCATTATACTAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATG
131 TGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATG
399293 ATTTAAATATTTAATGATTTGATGATT
196 ATTTAAATATTTAATGATTTGATGATT
*
399320 TAGTAATGATTTGATAATAATCATTATAATAATGATTTTATAATAAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAAT
399367 TATTTAGTTA
Statistics
Matches: 483, Mismatches: 6, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
221 52 0.11
222 431 0.89
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.44
Consensus pattern (222 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTATAGTAA
TGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAATGATTTAATAATG
ATTTAAATATTTAATGATTTGATGATT
Found at i:399226 original size:124 final size:122
Alignment explanation
Indices: 398876--399374 Score: 531
Period size: 124 Copynumber: 4.0 Consensus size: 122
398866 TTTGATGATT
* * * *
398876 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATT--ATA-ATAATGAT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTAAATATTTAATGA-
* * * *
398938 TTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
63 TT--TGATGATTTAAATATTTAATGATATAATCATTTAGTAATGATTTGATAATAATCATTA
* *
399000 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAATAATCATTATAAAAACGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGA-TT--TAATAATGATT-T--AAA-TATTTA
* * *
399065 AT-A----ATGATTTAAATATTTAATGATTTGATGATTTAGTAATGATTTGATAATAATCATTA
59 ATGATTTGATGATTTAAATATTTAATGATATAATCATTTAGTAATGATTTGATAATAATCATTA
399124 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
*
399189 GATGATTTAGTAATGATTTGAT-A-ATAATCATTATAGTAATGATTTGATAATAATCATTA
66 GATGATTTA--AAT-ATTTAATGATATAATCATT-TAGTAATGATTTGATAATAATCATTA
* *
399248 TACTAATGATTT-AGTAATAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATT
1 TAGTAATGATTTGA-TAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATT
* * * *
399312 TGATGATTTAGTAATGATTTGAT-A-ATAATCATTATAATAATGATTTTATAATAATTATT-
65 TGATGATTTA--AAT-ATTTAATGATATAATCATT-TAGTAATGATTTGATAATAATCATTA
399371 TAGT
1 TAGT
399375 TATTATTTAG
Statistics
Matches: 338, Mismatches: 17, Indels: 41
0.85 0.04 0.10
Matches are distributed among these distances:
117 7 0.02
118 4 0.01
120 1 0.00
121 10 0.03
122 8 0.02
123 12 0.04
124 271 0.80
125 9 0.03
126 1 0.00
127 8 0.02
130 1 0.00
131 2 0.01
132 4 0.01
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (122 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGATTTAAATATTTAATGATTT
GATGATTTAAATATTTAATGATATAATCATTTAGTAATGATTTGATAATAATCATTA
Found at i:399255 original size:98 final size:98
Alignment explanation
Indices: 398902--399265 Score: 474
Period size: 98 Copynumber: 3.7 Consensus size: 98
398892 ATAATCATTA
* * *
398902 TAGTAATGATTTGATAATAATCATTATAATAATGATTTAATAATGAT--TTAAATATTTAATGA-
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATT--ATA-ATAATGAT
* * * * *
398964 TT--TGATGATTTAGTAATGATTTGAT-A-ATAATCATT
63 TTAATAATGATTTA--AAT-ATTTAATGATTTGATGATT
* *
398999 ATAGTAATGATTTGATAATAATCATTATAATAATGATTT-AGTAATAATCATTATAAAAACGATT
1 -TAGTAATGATTTGATAATAATCATTATAATAATGATTTGA-TAATAATCATTATAATAATGATT
399063 TAATAATGATTTAAATATTTAATGATTTGATGATT
64 TAATAATGATTTAAATATTTAATGATTTGATGATT
*
399098 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTA
399163 ATAATGATTTAAATATTTAATGATTTGATGATT
66 ATAATGATTTAAATATTTAATGATTTGATGATT
* *
399196 TAGTAATGATTTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATACTAATGATTTA
1 TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTA
*
399261 GTAAT
66 ATAAT
399266 AATCATTATA
Statistics
Matches: 243, Mismatches: 14, Indels: 18
0.88 0.05 0.07
Matches are distributed among these distances:
97 11 0.05
98 214 0.88
99 7 0.03
100 11 0.05
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (98 bp):
TAGTAATGATTTGATAATAATCATTATAATAATGATTTGATAATAATCATTATAATAATGATTTA
ATAATGATTTAAATATTTAATGATTTGATGATT
Found at i:399599 original size:17 final size:17
Alignment explanation
Indices: 399574--399606 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
399564 ACTAAATATT
*
399574 TAATTATTTGATACTAG
1 TAATGATTTGATACTAG
399591 TAATGATTTGATACTA
1 TAATGATTTGATACTA
399607 AAAATCATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.45
Consensus pattern (17 bp):
TAATGATTTGATACTAG
Found at i:399599 original size:25 final size:23
Alignment explanation
Indices: 399520--399599 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
399510 GATTTATTGT
399520 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
399541 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
399568 -AATATTTAATTATTTGATACTA
1 TAATATTTAATTATTTGATACTA
399590 GTAATGATTT
1 -TAAT-ATTT
399600 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 9 0.20
23 8 0.17
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:401911 original size:29 final size:33
Alignment explanation
Indices: 401840--401917 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
401830 CTAAACCCTT
*
401840 AAAC-AACTAATAAAATATTCTTCTATATACTA
1 AAACTAACTAATAAACTATTCTTCTATATACTA
*
401872 AAACTAACTAATAAACTATTTTTC-ATATA-T-
1 AAACTAACTAATAAACTATTCTTCTATATACTA
*
401902 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
401918 TACTAACTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.26
30 4 0.10
31 1 0.02
32 9 0.21
33 17 0.40
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (33 bp):
AAACTAACTAATAAACTATTCTTCTATATACTA
Found at i:402012 original size:42 final size:42
Alignment explanation
Indices: 401958--402045 Score: 113
Period size: 42 Copynumber: 2.0 Consensus size: 42
401948 AACAAAAAAA
401958 TATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 TATAAC-TAACTA-TTAAC-AACAC-AACTAATT-AATAATTTTTTT
* *
402005 TATAACTAACTATTAACAATACAACTAATTAATTATTTTTT
1 TATAACTAACTATTAACAACACAACTAATTAATAATTTTTT
402046 AACTATATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
42 10 0.26
43 8 0.21
44 4 0.10
45 5 0.13
46 6 0.15
47 6 0.15
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.43
Consensus pattern (42 bp):
TATAACTAACTATTAACAACACAACTAATTAATAATTTTTTT
Found at i:402278 original size:4 final size:4
Alignment explanation
Indices: 402242--402307 Score: 55
Period size: 4 Copynumber: 16.5 Consensus size: 4
402232 CCTTATCTCC
* **
402242 CTTT C-TT C-TT CTTA CTTT CCTTT CTCC CTTT CTTT CTTT CTTT CATTT
1 CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT C-TTT
**
402290 CTCC CTTT CTTT CTTT CT
1 CTTT CTTT CTTT CTTT CT
402308 CGGCTGCAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
3 6 0.12
4 35 0.71
5 8 0.16
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (4 bp):
CTTT
Found at i:402284 original size:25 final size:25
Alignment explanation
Indices: 402232--402307 Score: 107
Period size: 25 Copynumber: 2.9 Consensus size: 25
402222 AAAAAATTTA
*
402232 CCTTATCTCCCTTTCTTCTTCTTACTTT
1 CCTT-TCTCCCTTTC-T-TTCTTTCTTT
402260 CCTTTCTCCCTTTCTTTCTTTCTTT
1 CCTTTCTCCCTTTCTTTCTTTCTTT
*
402285 CATTTCTCCCTTTCTTTCTTTCT
1 CCTTTCTCCCTTTCTTTCTTTCT
402308 CGGCTGCAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
25 31 0.67
26 1 0.02
27 10 0.22
28 4 0.09
ACGTcount: A:0.04, C:0.36, G:0.00, T:0.61
Consensus pattern (25 bp):
CCTTTCTCCCTTTCTTTCTTTCTTT
Found at i:402397 original size:25 final size:25
Alignment explanation
Indices: 402369--402420 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
402359 TTTCTTTTAT
*
402369 AACCGGCTGCCTCAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
*
402394 AACCGACTGCCTTAATTATTTCACC
1 AACCGACTGCCTCAATTATTTCACC
402419 AA
1 AA
402421 TAATTGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.29, C:0.33, G:0.10, T:0.29
Consensus pattern (25 bp):
AACCGACTGCCTCAATTATTTCACC
Found at i:402568 original size:23 final size:23
Alignment explanation
Indices: 402541--402587 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
402531 GAATCTATAT
402541 GGCTGCATGTGAATGGATGATGG
1 GGCTGCATGTGAATGGATGATGG
*
402564 GGCTGCATGTGAATGGATGGTGG
1 GGCTGCATGTGAATGGATGATGG
402587 G
1 G
402588 AATGGACGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.19, C:0.09, G:0.47, T:0.26
Consensus pattern (23 bp):
GGCTGCATGTGAATGGATGATGG
Found at i:402644 original size:29 final size:29
Alignment explanation
Indices: 402602--402698 Score: 151
Period size: 29 Copynumber: 3.3 Consensus size: 29
402592 GACGATGGGA
*
402602 ATGGCGACCTACAAGGTCGCCGGGAGTAC
1 ATGGCGACCTACAAGGTCGCCGGGACTAC
402631 ATGGCGACCTACAAGGTCGCCGGGACTAC
1 ATGGCGACCTACAAGGTCGCCGGGACTAC
* *
402660 ATGGCGACCTACAAGGTCGCCTAGG-CTGC
1 ATGGCGACCTACAAGGTCGCC-GGGACTAC
402689 ATGGCGACCT
1 ATGGCGACCT
402699 CTCTATTCCA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
29 62 0.97
30 2 0.03
ACGTcount: A:0.23, C:0.30, G:0.32, T:0.15
Consensus pattern (29 bp):
ATGGCGACCTACAAGGTCGCCGGGACTAC
Found at i:402754 original size:43 final size:43
Alignment explanation
Indices: 402693--402780 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 43
402683 GGCTGCATGG
402693 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATAGGGAGAA
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATAGGGAGAA
*
402736 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGGGAGAA
1 CGACCTCTCTATTCCACTGCATGGCCACCTCGCATAGGGAGAA
402779 CG
1 CG
402781 CTCGTATGGC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.22, C:0.35, G:0.23, T:0.20
Consensus pattern (43 bp):
CGACCTCTCTATTCCACTGCATGGCCACCTCGCATAGGGAGAA
Found at i:402800 original size:26 final size:26
Alignment explanation
Indices: 402764--402819 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
402754 GCATGGCCAC
402764 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
402790 CTCGCATGGGGAGAACGCTCGTATGG
1 CTCGCATGGGGAGAACGCTCGTATGG
402816 CTCG
1 CTCG
402820 TATGCATGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.18, C:0.25, G:0.38, T:0.20
Consensus pattern (26 bp):
CTCGCATGGGGAGAACGCTCGTATGG
Found at i:402845 original size:35 final size:35
Alignment explanation
Indices: 402806--402893 Score: 176
Period size: 35 Copynumber: 2.5 Consensus size: 35
402796 TGGGGAGAAC
402806 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
402841 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
402876 GCTCGTATGGCTCGTATG
1 GCTCGTATGGCTCGTATG
402894 TCACCCCGTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.18, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:402973 original size:35 final size:35
Alignment explanation
Indices: 402927--403005 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
402917 TGGGGAGAAC
402927 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
402962 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
1 GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
402997 GCTCGTATG
1 GCTCGTATG
403006 TTCCCGTATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.19, C:0.20, G:0.34, T:0.27
Consensus pattern (35 bp):
GCTCGTATGGCTCGTATGCATGGGGAGAACCATTG
Found at i:403287 original size:33 final size:33
Alignment explanation
Indices: 403249--403334 Score: 172
Period size: 33 Copynumber: 2.6 Consensus size: 33
403239 ATTACGTAAA
403249 GTGTTGCGGCTGTCGCGGACGCAATTTTTTAAC
1 GTGTTGCGGCTGTCGCGGACGCAATTTTTTAAC
403282 GTGTTGCGGCTGTCGCGGACGCAATTTTTTAAC
1 GTGTTGCGGCTGTCGCGGACGCAATTTTTTAAC
403315 GTGTTGCGGCTGTCGCGGAC
1 GTGTTGCGGCTGTCGCGGAC
403335 AGTTACATTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.13, C:0.22, G:0.34, T:0.31
Consensus pattern (33 bp):
GTGTTGCGGCTGTCGCGGACGCAATTTTTTAAC
Found at i:406044 original size:15 final size:16
Alignment explanation
Indices: 406026--406059 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
406016 AAAATAAAAT
406026 AAATA-AACAAAATAA
1 AAATAGAACAAAATAA
*
406041 AAATAGAACGAAATAA
1 AAATAGAACAAAATAA
406057 AAA
1 AAA
406060 ATAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (16 bp):
AAATAGAACAAAATAA
Found at i:406054 original size:25 final size:25
Alignment explanation
Indices: 406013--406082 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 25
406003 TATATCAACG
* *
406013 ATAAAAATAAAATAAATAAACAA-A
1 ATAAAAATAAAAGAAATAAAAAATA
*
406037 ATAAAAATAGAACGAAATAAAAAATA
1 ATAAAAATA-AAAGAAATAAAAAATA
*
406063 AT-AAGATAAAA-AAAGTAAAA
1 ATAAAAATAAAAGAAA-TAAAA
406083 CAAAGAAGAC
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
23 3 0.08
24 16 0.42
25 16 0.42
26 3 0.08
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.16
Consensus pattern (25 bp):
ATAAAAATAAAAGAAATAAAAAATA
Found at i:406764 original size:36 final size:35
Alignment explanation
Indices: 406702--406858 Score: 158
Period size: 36 Copynumber: 4.3 Consensus size: 35
406692 TTAGTTTGTG
*
406702 CAATAAAAT--AAAATGTTAGTAAGTTAGTAAGAA
1 CAATAAAATAAAAAAAGTTAGTAAGTTAGTAAGAA
* *
406735 CAATAAAAATAAAAAAAGTTAGTATGTTAGTATGAA
1 CAAT-AAAATAAAAAAAGTTAGTAAGTTAGTAAGAA
*
406771 CAATAAAATAAAAGCTAGAATGTTTGTAAGTTAGTAAGAA
1 CAATAAAATAAAA---A-AA-GTTAGTAAGTTAGTAAGAA
* * *
406811 CAATAAAAAAATAAAAAGTTAG-AATGCTAGTATGAA
1 CAATAAAATAA-AAAAAGTTAGTAA-GTTAGTAAGAA
406847 CAATAAAATAAA
1 CAATAAAATAAA
406859 CGTTAGAATG
Statistics
Matches: 103, Mismatches: 11, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
33 4 0.04
34 5 0.05
35 12 0.12
36 48 0.47
37 2 0.02
38 2 0.02
39 2 0.02
40 26 0.25
41 2 0.02
ACGTcount: A:0.56, C:0.04, G:0.14, T:0.25
Consensus pattern (35 bp):
CAATAAAATAAAAAAAGTTAGTAAGTTAGTAAGAA
Found at i:406800 original size:76 final size:76
Alignment explanation
Indices: 406713--406880 Score: 275
Period size: 76 Copynumber: 2.2 Consensus size: 76
406703 AATAAAATAA
* *
406713 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAA-AAAAAGTTAGTATGTTAGTATGAACAATAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAA-AATAAAAAGTTAGAATGCTAGTATGAACAATAA
406777 AATAAAAGCTAG
65 AATAAAAGCTAG
*
406789 AATGTTTGTAAGTTAGTAAGAACAATAAAAAAATAAAAAGTTAGAATGCTAGTATGAACAATAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAAAATAAAAAGTTAGAATGCTAGTATGAACAATAAA
* *
406854 ATAAACGTTAG
66 ATAAAAGCTAG
406865 AATGTTAGTAAGTTAG
1 AATGTTAGTAAGTTAG
406881 AAAAGTTAGC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
75 2 0.02
76 83 0.98
ACGTcount: A:0.52, C:0.04, G:0.17, T:0.27
Consensus pattern (76 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAAAATAAAAAGTTAGAATGCTAGTATGAACAATAAA
ATAAAAGCTAG
Found at i:407007 original size:14 final size:14
Alignment explanation
Indices: 406988--407014 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
406978 AAACATATAA
406988 AAATAAAATAAAAT
1 AAATAAAATAAAAT
407002 AAATAAAATAAAA
1 AAATAAAATAAAA
407015 AAGGTTAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:407167 original size:119 final size:120
Alignment explanation
Indices: 406916--407231 Score: 424
Period size: 119 Copynumber: 2.6 Consensus size: 120
406906 GGGTTCAAAT
* * *
406916 CATAATAATGTGAAT-TATACCCCAGATTTGGTCACCACAAGGTCAAATCAAATAATTCAAACAA
1 CATAATAATGTGAATCT-TACCCCAGATATGGTCACCACAAGGTCAAATCGAAT-ATT---AGAA
*
406980 ACATATAAAAATAAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAAC
61 ACA-ATAAATA-AAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAAC
* * **
407042 CATAATAATGTGGATCTTACCCCGGATATGGTCACCACAAGGTTGAATCGAATATTAGAAACAAT
1 CATAATAATGTGAATCTTACCCCAGATATGGTCACCACAAGGTCAAATCGAATATTAGAAACAAT
*
407107 AAATAAAAATAAAAT-AA-AAAATAAAAAAAGGTTAGTGGTTAGCATAGTCCGAAC
66 AAATAAAAATAAAATAAATAAAAT-AAAAAAGGTTAGTGGTTAGCAAAGTCCGAAC
* *
407161 CATAATAATGTGAATCATACCCCAGATCTGGTCACCACAAGGTCAAATCGAATATTAG-AACAAT
1 CATAATAATGTGAATCTTACCCCAGATATGGTCACCACAAGGTCAAATCGAATATTAGAAACAAT
*
407225 AGATAAA
66 AAATAAA
407232 CAAATAACAA
Statistics
Matches: 172, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
118 17 0.10
119 84 0.49
120 10 0.06
121 6 0.03
122 6 0.03
125 3 0.02
126 45 0.26
127 1 0.01
ACGTcount: A:0.47, C:0.15, G:0.14, T:0.23
Consensus pattern (120 bp):
CATAATAATGTGAATCTTACCCCAGATATGGTCACCACAAGGTCAAATCGAATATTAGAAACAAT
AAATAAAAATAAAATAAATAAAATAAAAAAGGTTAGTGGTTAGCAAAGTCCGAAC
Found at i:407316 original size:29 final size:29
Alignment explanation
Indices: 407254--407316 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
407244 GTTAAAGTGC
* *
407254 AATAAAATAAAAGTTAGTGATTAATGTAC
1 AATAAAATAAAAGTTAGAGATTAATGTAA
* *
407283 GATAAAATAAAAGTTAGCAG-TTAATTTAA
1 AATAAAATAAAAGTTAG-AGATTAATGTAA
407312 AATAA
1 AATAA
407317 TAAAAATGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.30
Consensus pattern (29 bp):
AATAAAATAAAAGTTAGAGATTAATGTAA
Found at i:408600 original size:122 final size:122
Alignment explanation
Indices: 408370--408668 Score: 352
Period size: 122 Copynumber: 2.5 Consensus size: 122
408360 GAGGATTCAG
** * * * *
408370 AGATGACACTGTTCCTTCAT-GTTGAGGACTTCGGGTCAATGTGGATATAACTTGGTGTTGAAGA
1 AGATGACACTGTTCCTTC-TCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGA
* * * *
408434 CGACACTGCTCATTCACGTTAAAGAGATCTGGCTGCTTTCAGATAAATTGTTTGTTGA
65 AGACACTGCTCATCCACGTTAAAGAGATCTGACTGCTTTCAGATAAATTATTTGTTGA
* *
408492 ATATGACACTGTTCCTTCTCGTTGAGAAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAA
1 AGATGACACTGTTCCTTCTCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAA
* * * * *
408557 GATTA-TGCTCATCCATGTTGAAGAGATCT-ACTCGTTTTTAGATAAATTATTTGTTGA
66 GA-CACTGCTCATCCACGTTAAAGAGATCTGACT-GCTTTCAGATAAATTATTTGTTGA
* * * * *
408614 AGATGACAATGTTTCTTTTCGTTGAGGAAGTTGGGTCAATCTGGAGATAATTTGG
1 AGATGACACTGTTCCTTCTCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGG
408669 AGACAACACG
Statistics
Matches: 150, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
121 3 0.02
122 146 0.97
123 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (122 bp):
AGATGACACTGTTCCTTCTCGTTGAGGAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAA
GACACTGCTCATCCACGTTAAAGAGATCTGACTGCTTTCAGATAAATTATTTGTTGA
Found at i:408883 original size:220 final size:220
Alignment explanation
Indices: 408494--409628 Score: 1547
Period size: 220 Copynumber: 5.2 Consensus size: 220
408484 TTTGTTGAAT
* * * * * *
408494 ATGACACTGTTCCTTCTCGTTGAGAAAATAGGGTCAATCTGGAGATAATTTGGTGTTGAAGAAGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * * ** * * * *
408559 TTATGCTCATCCATGTTGAAGAGATCTACTCGTTTTTAGATAAATTATTTGTTGAAGATGACAAT
66 CTCTGCTCATCCGTGTTGAAGAGATCTGGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
* * * *
408624 GTTTCTTTTCGTTGAGGAAGTTGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCAC
131 GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGC
* *
408689 GGTGAGGAAGTCTGATTGTCTAAGG
196 GTTGAGGAAGTCTGATTGTCTGAGG
* * * *
408714 ATGACACTGCTCCTTCGGGTTGAGGAGATCGAGTTAATCTGGAGATAATTTGGTGTTGAAGATGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* *
408779 CTCTGCACATCCGTGTTGAGGAGATCAT-GTAGCTTTTAGATAAATTGTTTGTTGAAGATGACAC
66 CTCTGCTCATCCGTGTTGAAGAGATC-TGGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACAC
* * * *
408843 TATTCCTTCTTGTTGAGGAAGTCGGGTCAATCTAGAGATAATTTGGAGACAACACGGTTTCTTCG
130 TGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCG
**
408908 CGTTGAATAAGTCTGATTGTCTGAGG
195 CGTTGAGGAAGTCTGATTGTCTGAGG
* *
408934 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTATTGAATAGGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * * **
408999 CTCTACTCATTCGTGTTGAAGAGATCTGGTA-TTTTTCAGATAAATTGTTTGTTGAAGATGACGT
66 CTCTGCTCATCCGTGTTGAAGAGATCTGGTAGCTTTT-AGATAAATTGTTTGTTGAAGATGACAC
* * *
409063 TGTTCCTTCTCGTTGAAGAAGTCAGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTGCG
130 TGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCG
* *
409128 CATTGAGGAAGCCTGATTGTCTGAGG
195 CGTTGAGGAAGTCTGATTGTCTGAGG
* *
409154 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTTAATCTAGAGATAATTTGGTGTTGAAGAGGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * * *
409219 CTCTGCTCATCCGTGTTGAAGAGATATGATCA-CTTTCAGATAAATTGTTTTTTGAAGATGACAC
66 CTCTGCTCATCCGTGTTGAAGAGATCTGGT-AGCTTTTAGATAAATTGTTTGTTGAAGATGACAC
* * *
409283 TGTTCCTTCTCATTGAGGAAGTCAGGTCAATCTGGAGATAATTTAGAGACAACACGGTTCCTTCG
130 TGTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCG
409348 CGTTGAGGAAGTCTGATTGTCTGAGG
195 CGTTGAGGAAGTCTGATTGTCTGAGG
* * * *
409374 ATGACAATGCTTCTTCGCGTTGAGAAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGACGA
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
* * * * * * * **
409439 CTCTACTCATCTGTTTTGAAGAGATCTGGTCGCTTTCAGATAAATTATTTGCTGAAGATGATGCT
66 CTCTGCTCATCCGTGTTGAAGAGATCTGGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
* * * * *
409504 GTTCCTTCTCGTTCAGGAAGTCGGGTCAATTTGGAGATAATTTGGAGACAACATGGTTCATTCAC
131 GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGC
*
409569 GTTGAGGAAATCTGATTGTCTGAGG
196 GTTGAGGAAGTCTGATTGTCTGAGG
* *
409594 ATGACACTGCTCCTTCACGTTGAGGAGATCTGGTC
1 ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTC
409629 GGTGGATGAT
Statistics
Matches: 805, Mismatches: 105, Indels: 10
0.88 0.11 0.01
Matches are distributed among these distances:
219 5 0.01
220 795 0.99
221 5 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (220 bp):
ATGACACTGCTCCTTCGCGTTGAGGAGATCGGGTCAATCTGGAGATAATTTGGTGTTGAAGAGGA
CTCTGCTCATCCGTGTTGAAGAGATCTGGTAGCTTTTAGATAAATTGTTTGTTGAAGATGACACT
GTTCCTTCTCGTTGAGGAAGTCGGGTCAATCTGGAGATAATTTGGAGACAACACGGTTCCTTCGC
GTTGAGGAAGTCTGATTGTCTGAGG
Found at i:409648 original size:40 final size:41
Alignment explanation
Indices: 409559--409649 Score: 94
Period size: 43 Copynumber: 2.2 Consensus size: 41
409549 AGACAACATG
* *
409559 GTTCATTCACGTTGAGGAAATCTGATTGTCTGAGGATGACACT
1 GTTCCTTCACGTTGAGGAAATCTG--TGTCGGAGGATGACACT
* * * * *
409602 GCTCCTTCACGTTGAGGAGATCTG-GTCGGTGGATGATATT
1 GTTCCTTCACGTTGAGGAAATCTGTGTCGGAGGATGACACT
409642 GTTCCTTC
1 GTTCCTTC
409650 GTGATGAGGA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
40 19 0.47
43 21 0.52
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (41 bp):
GTTCCTTCACGTTGAGGAAATCTGTGTCGGAGGATGACACT
Found at i:409751 original size:140 final size:139
Alignment explanation
Indices: 409539--409816 Score: 335
Period size: 140 Copynumber: 2.0 Consensus size: 139
409529 TCAATTTGGA
* * *
409539 GATAATTTGGAGACAACATGGTTCATTCACGTTGAGGAAATCTGATTGTCTGAGGATGACACTGC
1 GATAAGTTGGAGACAACATGGTTCATTCACGTTGAGGAAATATGATTGTCTGAGGATGACACTAC
* * * * * * * *
409604 TCCTTCACGTTGAGGAGATCTGGTCGGTGGATGATATTGTTCCTTCGTGATGAGGACGTCTAGCC
66 TCATTCACGTTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTCGTGATGAAGAAGTCTAGCC
409669 ATGTTTAGGG
131 AT-TTTAGGG
* * * * * *
409679 GATAAGTTGGAGACAGCATGGTTCTTTCGCAC-TT-AGGAAGTATGGTTTTCTGAGGATGACTCT
1 GATAAGTTGGAGACAACATGGTTCATT--CACGTTGAGGAAATATGATTGTCTGAGGATGACACT
* *
409742 ACTCATTCACGTTGAGGAGATCTAGTCAGTAGACGACATTGTTTCTTCGTGTTGAAGAAGTCTAG
64 ACTCATTCACGTTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTCGTGATGAAGAAGTCTAG
*
409807 CCGTTTTAGG
129 CCATTTTAGG
409817 AAATAATTTT
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
139 6 0.05
140 105 0.91
141 2 0.02
142 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.32
Consensus pattern (139 bp):
GATAAGTTGGAGACAACATGGTTCATTCACGTTGAGGAAATATGATTGTCTGAGGATGACACTAC
TCATTCACGTTGAGGAGATCTAGTCAGTAGACGACATTGTTCCTTCGTGATGAAGAAGTCTAGCC
ATTTTAGGG
Found at i:413312 original size:16 final size:16
Alignment explanation
Indices: 413293--413330 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
413283 CACTTTCTTC
*
413293 TTCTTTCTTTGCTTTT
1 TTCTTTCTTTACTTTT
413309 TTCTTTCTTTACTTTT
1 TTCTTTCTTTACTTTT
413325 TTCTTT
1 TTCTTT
413331 GTTTTTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (16 bp):
TTCTTTCTTTACTTTT
Found at i:413316 original size:20 final size:20
Alignment explanation
Indices: 413261--413323 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
413251 TCTTTGCATG
*
413261 TGCTTTTTCTCTTTTTTTCTCT
1 TGCTTTTT-TCTTTCTTTCT-T
** *
413283 CACTTTCTTC-TTCTTTCTT
1 TGCTTTTTTCTTTCTTTCTT
413302 TGCTTTTTTCTTTCTTTACTT
1 TGCTTTTTTCTTTCTTT-CTT
413323 T
1 T
413324 TTTCTTTGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
19 8 0.25
20 13 0.41
21 6 0.19
22 5 0.16
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.70
Consensus pattern (20 bp):
TGCTTTTTTCTTTCTTTCTT
Found at i:413330 original size:23 final size:23
Alignment explanation
Indices: 413312--413369 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 23
413302 TGCTTTTTTC
413312 TTTCTTTACTTTTTTCTTTGTTT
1 TTTCTTTACTTTTTTCTTTGTTT
*
413335 TTTCCCTTT--TTTTTGCTTTGTTT
1 TTT--CTTTACTTTTTTCTTTGTTT
413358 TTTCTTTACTTT
1 TTTCTTTACTTT
413370 GATTTGATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
21 4 0.13
23 22 0.73
25 4 0.13
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (23 bp):
TTTCTTTACTTTTTTCTTTGTTT
Found at i:413364 original size:11 final size:11
Alignment explanation
Indices: 413321--413364 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
413311 CTTTCTTTAC
413321 TTTTTTCTTTG
1 TTTTTTCTTTG
413332 TTTTTTCCCTTT-
1 TTTTTT--CTTTG
*
413344 TTTTTGCTTTG
1 TTTTTTCTTTG
413355 TTTTTTCTTT
1 TTTTTTCTTT
413365 ACTTTGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 4 0.14
11 15 0.54
12 5 0.18
13 4 0.14
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTG
Found at i:413369 original size:16 final size:15
Alignment explanation
Indices: 413293--413370 Score: 57
Period size: 16 Copynumber: 4.7 Consensus size: 15
413283 CACTTTCTTC
413293 TTCTTTCTTTGCTTTT
1 TTCTTTCTTTG-TTTT
*
413309 TTCTTTCTTTACTTTT
1 TTCTTTCTTT-GTTTT
* *
413325 TTCTTTGTTTTTTCCCTT
1 TTCTTTCTTTGTT---TT
*
413343 TTTTTTGCTTTGTTTT
1 TTCTTT-CTTTGTTTT
413359 TTCTTTACTTTG
1 TTCTTT-CTTTG
413371 ATTTGATCTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
15 2 0.04
16 35 0.71
18 7 0.14
19 5 0.10
ACGTcount: A:0.03, C:0.17, G:0.06, T:0.74
Consensus pattern (15 bp):
TTCTTTCTTTGTTTT
Found at i:417540 original size:15 final size:16
Alignment explanation
Indices: 417512--417575 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
417502 ATCAACGATA
*
417512 AAAATAAAATAAATAAAC
1 AAAATAAAA-ATAT-AAC
417530 AAAATAAAAATATAAC
1 AAAATAAAAATATAAC
*
417546 AAAATAAAAA-ATAAT
1 AAAATAAAAATATAAC
*
417561 AAGATAAAAAATATA
1 AAAAT-AAAAATATA
417576 TAACAAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.20
16 18 0.44
17 6 0.15
18 9 0.22
ACGTcount: A:0.77, C:0.03, G:0.02, T:0.19
Consensus pattern (16 bp):
AAAATAAAAATATAAC
Found at i:417981 original size:15 final size:15
Alignment explanation
Indices: 417961--417992 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
417951 TATTAGATGT
*
417961 AAATATACCACATGC
1 AAATATACCACAAGC
417976 AAATATACCACAAGC
1 AAATATACCACAAGC
417991 AA
1 AA
417993 GATCAGTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.25, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATATACCACAAGC
Found at i:418288 original size:40 final size:40
Alignment explanation
Indices: 418190--418313 Score: 134
Period size: 40 Copynumber: 3.2 Consensus size: 40
418180 AATAAAATAA
*
418190 AATGTTACTAAGTTAGTAAGAACAATAAAAATAAA---A-
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAGTTAG
* * * *
418226 AAT-TCAGTATGTTTGTATGAACAAT-AAAATAAATGTTAG
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAA-GTTAG
418265 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAGTTAG
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAAT--AAAGTTAG
418307 AATGTTA
1 AATGTTA
418314 ATATGAATAA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
34 8 0.11
35 17 0.24
36 3 0.04
38 1 0.01
39 3 0.04
40 18 0.26
41 5 0.07
42 12 0.17
43 3 0.04
ACGTcount: A:0.52, C:0.04, G:0.15, T:0.30
Consensus pattern (40 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAGTTAG
Found at i:418342 original size:74 final size:75
Alignment explanation
Indices: 418190--418354 Score: 251
Period size: 74 Copynumber: 2.2 Consensus size: 75
418180 AATAAAATAA
* * **
418190 AATGTTACTAAGTTAGTAAGAACAATAAAAATAAAAAATTCAGTATGTTTGTATGAACAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAATTCAGAATGTTAATATGAACAATAAAA
*
418255 TAAATGTTAG
66 TAAAAGTTAG
* *
418265 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAGTT-AGAATGTTAATATGAATAATAAAA
1 AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAATTCAGAATGTTAATATGAACAATAAAA
418329 TAAAAGTTAG
66 TAAAAGTTAG
*
418339 AATGTTAGTAAATTAG
1 AATGTTAGTAAGTTAG
418355 AAAAATTAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
74 44 0.54
75 38 0.46
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (75 bp):
AATGTTAGTAAGTTAGTAAGAACAATAAAAATAAAAAATTCAGAATGTTAATATGAACAATAAAA
TAAAAGTTAG
Found at i:418761 original size:29 final size:29
Alignment explanation
Indices: 418729--418785 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
418719 TAAATAACAA
*
418729 TGGTTAAAGTGTAATAAAATAAAAGTTAG
1 TGGTTAAAGTGCAATAAAATAAAAGTTAG
*
418758 TGGTTAATGTGCAATAAAATAAAAGTTA
1 TGGTTAAAGTGCAATAAAATAAAAGTTA
418786 TCAGTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.47, C:0.02, G:0.19, T:0.32
Consensus pattern (29 bp):
TGGTTAAAGTGCAATAAAATAAAAGTTAG
Found at i:418792 original size:29 final size:29
Alignment explanation
Indices: 418731--418794 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
418721 AATAACAATG
* * *
418731 GTTAAAGTGTAATAAAATAAAAGTTAGTG
1 GTTAATGTGCAATAAAATAAAAGTTAGTA
418760 GTTAATGTGCAATAAAATAAAAGTTA-TCA
1 GTTAATGTGCAATAAAATAAAAGTTAGT-A
418789 GTTAAT
1 GTTAAT
418795 TTAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.03
29 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (29 bp):
GTTAATGTGCAATAAAATAAAAGTTAGTA
Found at i:418802 original size:29 final size:29
Alignment explanation
Indices: 418741--418803 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
418731 GTTAAAGTGT
* **
418741 AATAAAATAAAAGTTAGTGGTTAATGTGC
1 AATAAAATAAAAGTTAGTAGTTAATGTAA
*
418770 AATAAAATAAAAGTTA-TCAGTTAATTTAA
1 AATAAAATAAAAGTTAGT-AGTTAATGTAA
418799 AATAA
1 AATAA
418804 TAAAAATGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.52, C:0.03, G:0.13, T:0.32
Consensus pattern (29 bp):
AATAAAATAAAAGTTAGTAGTTAATGTAA
Found at i:432567 original size:16 final size:16
Alignment explanation
Indices: 432546--432584 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
432536 TTCCTATTCG
432546 TTTATTTACT-TTCAAA
1 TTTATTTA-TATTCAAA
432562 TTTATTTATATTCAAA
1 TTTATTTATATTCAAA
432578 TTATATT
1 TT-TATT
432585 CATTAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATTTATATTCAAA
Found at i:462363 original size:16 final size:16
Alignment explanation
Indices: 462342--462381 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
462332 TTTAGGAGTA
462342 AGGTTTTGTCTAATAC
1 AGGTTTTGTCTAATAC
462358 AGGTTTTGTCTAATAC
1 AGGTTTTGTCTAATAC
462374 AGGTTTTG
1 AGGTTTTG
462382 GAACTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (16 bp):
AGGTTTTGTCTAATAC
Found at i:464763 original size:4 final size:4
Alignment explanation
Indices: 464754--464780 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
464744 TTCAACTATG
464754 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
464781 ACATGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:466208 original size:22 final size:21
Alignment explanation
Indices: 466156--466210 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 21
466146 CTTATAATAT
*
466156 TTTTTATATTTTTAATATGAA
1 TTTTTATTTTTTTAATATGAA
*
466177 TATTTAATTTTTTTAAACTAT-AA
1 T-TTTTATTTTTTT-AA-TATGAA
466200 TTTTTATTTTT
1 TTTTTATTTTT
466211 AGTGTTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 1 0.04
22 19 0.68
23 5 0.18
24 3 0.11
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTATTTTTTTAATATGAA
Found at i:467168 original size:16 final size:16
Alignment explanation
Indices: 467147--467185 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
467137 TTCCTATTCG
467147 TTTATTTACT-TTCAAA
1 TTTATTTA-TATTCAAA
467163 TTTATTTATATTCAAA
1 TTTATTTATATTCAAA
467179 TTATATT
1 TT-TATT
467186 CATTAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTATTTATATTCAAA
Found at i:485037 original size:13 final size:14
Alignment explanation
Indices: 485010--485038 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
485000 AATAAATGAA
485010 CTCACTTTGTATGC
1 CTCACTTTGTATGC
485024 CTCACTTT-TATGC
1 CTCACTTTGTATGC
485037 CT
1 CT
485039 TACTAACGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.14, C:0.31, G:0.10, T:0.45
Consensus pattern (14 bp):
CTCACTTTGTATGC
Found at i:496254 original size:7 final size:8
Alignment explanation
Indices: 496222--496259 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
496212 ATGCACTCAT
496222 GAATCAAA
1 GAATCAAA
*
496230 GAATCAAG
1 GAATCAAA
496238 GAATCAAA
1 GAATCAAA
496246 GAA-CAAA
1 GAATCAAA
496253 GAATCAA
1 GAATCAA
496260 CAAGATAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.61, C:0.13, G:0.16, T:0.11
Consensus pattern (8 bp):
GAATCAAA
Found at i:503695 original size:23 final size:24
Alignment explanation
Indices: 503640--503698 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 24
503630 GATAAATTTT
* *
503640 TAAAATTT-AAAATATATTTTTAA
1 TAAAATTTAAAAATATATATATAA
*
503663 TAAAA-ATAAAAATATATATAT-A
1 TAAAATTTAAAAATATATATATAA
503685 TAAAATTTAAAAAT
1 TAAAATTTAAAAAT
503699 TTTAAGAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 7 0.23
23 23 0.77
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (24 bp):
TAAAATTTAAAAATATATATATAA
Found at i:504771 original size:16 final size:16
Alignment explanation
Indices: 504750--504783 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
504740 AAAGCTAAAA
504750 GACATGGTGGAGAAGG
1 GACATGGTGGAGAAGG
504766 GACATGGTGGAGAAGG
1 GACATGGTGGAGAAGG
504782 GA
1 GA
504784 AGCAGTGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.50, T:0.12
Consensus pattern (16 bp):
GACATGGTGGAGAAGG
Found at i:504798 original size:19 final size:16
Alignment explanation
Indices: 504750--504799 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
504740 AAAGCTAAAA
*
504750 GACATGGTGGAGAAGG
1 GACATGGAGGAGAAGG
*
504766 GACATGGTGGAGAAGG
1 GACATGGAGGAGAAGG
504782 GAAGCAGTGGAGGAGAAG
1 G-A-CA-TGGAGGAGAAG
504800 TGGTGATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 17 0.57
17 1 0.03
18 2 0.07
19 10 0.33
ACGTcount: A:0.34, C:0.06, G:0.50, T:0.10
Consensus pattern (16 bp):
GACATGGAGGAGAAGG
Found at i:514336 original size:27 final size:27
Alignment explanation
Indices: 514286--514337 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
514276 TAATTTAATA
* *
514286 AATACTATACAAATTAAAATATAAACT
1 AATACTATAAAAATTAAAAAATAAACT
514313 AATACTA-AAAAATTAAATAAATAAA
1 AATACTATAAAAATTAAA-AAATAAA
514338 ACATTCACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (27 bp):
AATACTATAAAAATTAAAAAATAAACT
Found at i:515090 original size:3 final size:3
Alignment explanation
Indices: 515082--515119 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
515072 CTTTCTGTTG
* *
515082 AAC AAC AAC AAC AAC AAC AAT AAC AAC AAC AAT AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
515120 TAGTAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.05
Consensus pattern (3 bp):
AAC
Found at i:515099 original size:12 final size:12
Alignment explanation
Indices: 515082--515119 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
515072 CTTTCTGTTG
*
515082 AACAACAACAAC
1 AACAACAATAAC
515094 AACAACAATAAC
1 AACAACAATAAC
515106 AACAACAATAAC
1 AACAACAATAAC
515118 AA
1 AA
515120 TAGTAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.05
Consensus pattern (12 bp):
AACAACAATAAC
Found at i:516531 original size:39 final size:39
Alignment explanation
Indices: 516456--516533 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 39
516446 TTATTATTTG
* *
516456 TCTTTGAATTATTACCCTTGTTTCTTTTATCTTTAATCT
1 TCTTTAAATTATTACCCTTGTTTCTATTATCTTTAATCT
*
516495 TCTTTAAATTTATTACCTTTGCTTTC-ATTATC-TTAATCT
1 TCTTTAAA-TTATTACCCTTG-TTTCTATTATCTTTAATCT
516534 CATCTCATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 14 0.41
40 16 0.47
41 4 0.12
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.58
Consensus pattern (39 bp):
TCTTTAAATTATTACCCTTGTTTCTATTATCTTTAATCT
Found at i:517536 original size:309 final size:313
Alignment explanation
Indices: 516973--517574 Score: 1176
Period size: 309 Copynumber: 1.9 Consensus size: 313
516963 TTTTTAAATT
516973 GTAATGTTTCTGATTTTTAGTATGAAGTTATGTTTTTGCTCTTCTAGTAGCAATGTTTCTTCTCT
1 GTAATGTTTCTGATTTTTAGTATGAAGTTATGTTTTTGCTCTTCTAGTAGCAATGTTTCTTCTCT
517038 TCTTCACATTAAACAAACAATAATTGGCATTAGAGTCATTTTCTTAAGGGATCTGTGAGTGAATT
66 TCTTCACATTAAACAAACAATAATTGGCATTAGAGTCATTTTCTTAAGGGATCTGTGAGTGAATT
517103 TGACACGACATGGAAGTTGAAGCAAGTTTTTCTTCAATTTCTTCACCGGTGTTTGATGGAGAAAA
131 TGACACGACATGGAAGTTGAAGCAAGTTTTTCTTCAATTTCTTCACCGGTGTTTGATGGAGAAAA
517168 CTACCAAATGCGGGCAGTTCGAATGGAAACATATTTGGAGGCTTTGGATCTTTGGGAAGTAGTGG
196 CTACCAAATGCGGGCAGTTCGAATGGAAACATATTTGGAGGCTTTGGATCTTTGGGAAGTAGTGG
517233 AAGAGGACTATATAGTTCCAGCAATTCCAACCAATCCCACTTTGGCTCATATC
261 AAGAGGACTATATAGTTCCAGCAATTCCAACCAATCCCACTTTGGCTCATATC
517286 GTAATGTTTCTGATTTTTAGTATGAAGTTATGTTTTTGCTCTTCTAGTAGCAATGTTTC-TCTCT
1 GTAATGTTTCTGATTTTTAGTATGAAGTTATGTTTTTGCTCTTCTAGTAGCAATGTTTCTTCTCT
517350 TCTTCACATTAAACAAACAATAATTGGCATTA-AGTCATTTTCTTAAGGGATCTGTGAGTGAATT
66 TCTTCACATTAAACAAACAATAATTGGCATTAGAGTCATTTTCTTAAGGGATCTGTGAGTGAATT
517414 TG-CACGACATGGAAGTTGAAGCAAGTTTTTCTTCAA-TTCTTCACCGGTGTTTGATGGAGAAAA
131 TGACACGACATGGAAGTTGAAGCAAGTTTTTCTTCAATTTCTTCACCGGTGTTTGATGGAGAAAA
517477 CTACCAAATGCGGGCAGTTCGAATGGAAACATATTTGGAGGCTTTGGATCTTTGGGAAGTAGTGG
196 CTACCAAATGCGGGCAGTTCGAATGGAAACATATTTGGAGGCTTTGGATCTTTGGGAAGTAGTGG
517542 AAGAGGACTATATAGTTCCAGCAATTCCAACCA
261 AAGAGGACTATATAGTTCCAGCAATTCCAACCA
517575 CTCGAGGATT
Statistics
Matches: 289, Mismatches: 0, Indels: 4
0.99 0.00 0.01
Matches are distributed among these distances:
309 125 0.43
310 34 0.12
311 34 0.12
312 37 0.13
313 59 0.20
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (313 bp):
GTAATGTTTCTGATTTTTAGTATGAAGTTATGTTTTTGCTCTTCTAGTAGCAATGTTTCTTCTCT
TCTTCACATTAAACAAACAATAATTGGCATTAGAGTCATTTTCTTAAGGGATCTGTGAGTGAATT
TGACACGACATGGAAGTTGAAGCAAGTTTTTCTTCAATTTCTTCACCGGTGTTTGATGGAGAAAA
CTACCAAATGCGGGCAGTTCGAATGGAAACATATTTGGAGGCTTTGGATCTTTGGGAAGTAGTGG
AAGAGGACTATATAGTTCCAGCAATTCCAACCAATCCCACTTTGGCTCATATC
Found at i:521714 original size:23 final size:25
Alignment explanation
Indices: 521661--521714 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 25
521651 ATGAATGAAA
521661 TAAAGA-AAGTAATATAAAATAAAG
1 TAAAGATAAGTAATATAAAATAAAG
*
521685 -AAA-ATAAGTGA-ATAAAA-AAAG
1 TAAAGATAAGTAATATAAAATAAAG
521706 TAAAGATAA
1 TAAAGATAA
521715 AAATACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 4 0.15
22 10 0.38
23 12 0.46
ACGTcount: A:0.69, C:0.00, G:0.13, T:0.19
Consensus pattern (25 bp):
TAAAGATAAGTAATATAAAATAAAG
Found at i:521728 original size:14 final size:14
Alignment explanation
Indices: 521711--521743 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
521701 AAAAGTAAAG
521711 ATAAAA-ATACATAA
1 ATAAAATATACA-AA
521725 ATAAAATATACAAA
1 ATAAAATATACAAA
521739 ATAAA
1 ATAAA
521744 CAACAGAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAATATACAAA
Found at i:522145 original size:2 final size:2
Alignment explanation
Indices: 522138--522174 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
522128 TTATTCTTAT
522138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
522175 CATTTGGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:522225 original size:2 final size:2
Alignment explanation
Indices: 522218--522242 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
522208 TATATTTCGT
522218 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
522243 TTTACTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:522333 original size:16 final size:17
Alignment explanation
Indices: 522270--522333 Score: 68
Period size: 16 Copynumber: 4.0 Consensus size: 17
522260 TTCATATATC
522270 ATTATTTATATATATTT
1 ATTATTTATATATATTT
522287 -TTA-TTACTATA-A-TT
1 ATTATTTA-TATATATTT
522301 A-TATGTTATATATATTT
1 ATTAT-TTATATATATTT
522318 ATTATTT-TATATATTT
1 ATTATTTATATATATTT
522334 CATTTTATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 15
0.73 0.00 0.27
Matches are distributed among these distances:
14 4 0.10
15 8 0.20
16 20 0.50
17 5 0.12
18 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTATTTATATATATTT
Found at i:522357 original size:16 final size:16
Alignment explanation
Indices: 522336--522368 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
522326 ATATATTTCA
*
522336 TTTTATCTTTTATTTT
1 TTTTATCTTCTATTTT
522352 TTTTATCTTCTATTTT
1 TTTTATCTTCTATTTT
522368 T
1 T
522369 ATTTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTATCTTCTATTTT
Found at i:522422 original size:15 final size:15
Alignment explanation
Indices: 522257--522438 Score: 52
Period size: 14 Copynumber: 11.6 Consensus size: 15
522247 CTTTTAATTC
*
522257 TTTTTCATATATCATTA
1 TTTTT-ATATAT-TTTA
*
522274 TTTATATATATTTTTA
1 TTTTTATATA-TTTTA
** *
522290 TTACTATA-ATTATA
1 TTTTTATATATTTTA
*
522304 TGTTATATATATTTATTA
1 T-TTTTATATA-TT-TTA
522322 TTTTATATATTTCATTTTA
1 TTTT-TATA--T-ATTTTA
* *
522341 TCTTTTATTTTTTTTA
1 T-TTTTATATATTTTA
* *
522357 -TCTTCTAT-TTTTA
1 TTTTTATATATTTTA
* *
522370 TTTTTGTAT-TGTTA
1 TTTTTATATATTTTA
* *
522384 TTGTTAT-TATCTTCTT
1 TTTTTATATAT-TT-TA
*
522400 TATTTTATGTATTTTA
1 T-TTTTATATATTTTA
*
522416 TTTTTATATATATT-
1 TTTTTATATATTTTA
522430 TTTTTATAT
1 TTTTTATAT
522439 TGTTTTTTTT
Statistics
Matches: 124, Mismatches: 25, Indels: 35
0.67 0.14 0.19
Matches are distributed among these distances:
13 6 0.05
14 35 0.28
15 18 0.15
16 24 0.19
17 17 0.14
18 10 0.08
19 7 0.06
20 6 0.05
21 1 0.01
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTTATATATTTTA
Found at i:533193 original size:11 final size:11
Alignment explanation
Indices: 533177--533201 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
533167 TCAGATAAAG
533177 AAAAAGAAAAA
1 AAAAAGAAAAA
533188 AAAAAGAAAAA
1 AAAAAGAAAAA
533199 AAA
1 AAA
533202 TGAAAAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:534273 original size:105 final size:105
Alignment explanation
Indices: 534086--534455 Score: 564
Period size: 105 Copynumber: 3.5 Consensus size: 105
534076 ATATCGTGCC
* * *
534086 ACTCAAGACAACACAA-TATCAACTTCACAACGAAGGGACGACTGGTTTTCAACAACAATTTTCC
1 ACTCGAGACAACACAAGT-TCAACTTCACAACGAAGGGACGACTGGTTGTCAACAACAATTTCCC
* *
534150 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
534191 ACCCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAATAATTTCCCA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAACAATTTCCCA
534256 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
534296 ACTCGAGATAACACAAG-TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAC-AACAATTTCCC
*
534360 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * *
534401 ACTCAAGACAGCACAAGTTCAACTTCACAACGAAAGGATGGCTGGCTGTCAACAA
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAA
534456 AAAATTCCGA
Statistics
Matches: 244, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
104 34 0.14
105 177 0.73
106 33 0.14
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAACAATTTCCCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:535819 original size:12 final size:12
Alignment explanation
Indices: 535802--535834 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
535792 ACTAAACCCA
535802 GTGGTGACCCGC
1 GTGGTGACCCGC
535814 GTGGTGACCCGC
1 GTGGTGACCCGC
*
535826 GTGTTGACC
1 GTGGTGACC
535835 TGACCCGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.30, G:0.39, T:0.21
Consensus pattern (12 bp):
GTGGTGACCCGC
Found at i:536100 original size:23 final size:26
Alignment explanation
Indices: 536074--536126 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
536064 TTATTATTAC
536074 TATTACATA-TATTTT-T-TATTTTT
1 TATTACATATTATTTTATGTATTTTT
*
536097 TATTATATATTTATTTTATGTATTTTT
1 TATTACATA-TTATTTTATGTATTTTT
536124 TAT
1 TAT
536127 ATATTTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 8 0.32
25 6 0.24
26 1 0.04
27 10 0.40
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (26 bp):
TATTACATATTATTTTATGTATTTTT
Found at i:536126 original size:24 final size:22
Alignment explanation
Indices: 536015--536134 Score: 70
Period size: 23 Copynumber: 5.3 Consensus size: 22
536005 TTTAATTTTA
* * *
536015 ATTTTTTTATTTATAATTTTA-
1 ATTTTTTTATTTTTTATTATAT
536036 ATTTTTGTT-TTTTTTA--ATAT
1 ATTTTT-TTATTTTTTATTATAT
* * *
536056 ATTCCGTTTTATTATTACTATTACAT
1 ATT--TTTTTATT-TT-TTATTATAT
536082 ATATTTTTTATTTTTTATTATAT
1 AT-TTTTTTATTTTTTATTATAT
536105 ATTTATTTTATGTATTTT-TTATAT
1 ATTT-TTTTAT-T-TTTTATTATAT
536129 ATTTTT
1 ATTTTT
536135 CTCCTGTTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 24
0.70 0.08 0.22
Matches are distributed among these distances:
19 2 0.03
20 3 0.04
21 13 0.17
22 8 0.10
23 19 0.25
24 15 0.19
25 11 0.14
26 5 0.06
27 1 0.01
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (22 bp):
ATTTTTTTATTTTTTATTATAT
Found at i:536133 original size:11 final size:11
Alignment explanation
Indices: 536080--536134 Score: 60
Period size: 11 Copynumber: 4.9 Consensus size: 11
536070 TTACTATTAC
536080 ATATATTTTTT
1 ATATATTTTTT
536091 AT-T-TTTTATT
1 ATATATTTT-TT
536101 ATATATTTATTTT
1 ATATA-TT-TTTT
*
536114 ATGTATTTTTT
1 ATATATTTTTT
536125 ATATATTTTT
1 ATATATTTTT
536135 CTCCTGTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 4 0.11
10 5 0.14
11 16 0.43
12 2 0.05
13 8 0.22
14 2 0.05
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (11 bp):
ATATATTTTTT
Found at i:536146 original size:24 final size:24
Alignment explanation
Indices: 536080--536149 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
536070 TTACTATTAC
*
536080 ATATATTT-TTT-AT-TTTTTATT
1 ATATATTTATTTCATGTTTTTTTT
* *
536101 ATATATTTATTTTATGTATTTTTT
1 ATATATTTATTTCATGTTTTTTTT
*
536125 ATATATTT-TTCTCCTGTTTTTTTT
1 ATATATTTATT-TCATGTTTTTTTT
536149 A
1 A
536150 CTTATACTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
21 8 0.20
22 3 0.08
23 4 0.10
24 25 0.62
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.71
Consensus pattern (24 bp):
ATATATTTATTTCATGTTTTTTTT
Found at i:536306 original size:25 final size:24
Alignment explanation
Indices: 536253--536307 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
536243 ATATTTTATA
* *
536253 ATATTGTATATATATTTTTCCATT
1 ATATTTTATATATATTTTACCATT
*
536277 A-ATTTTATATATATATTTACTATT
1 ATATTTTATATATAT-TTTACCATT
536301 ATATTTT
1 ATATTTT
536308 GTTTATTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.46
24 9 0.35
25 5 0.19
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (24 bp):
ATATTTTATATATATTTTACCATT
Found at i:536567 original size:15 final size:15
Alignment explanation
Indices: 536547--536582 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
536537 ATCTTTCTTC
*
536547 ATTTTATTTATTTAT
1 ATTTTATTTATGTAT
536562 ATTTTATTTATGTAT
1 ATTTTATTTATGTAT
536577 -TTTTAT
1 ATTTTAT
536583 CTTTACTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
ATTTTATTTATGTAT
Found at i:538831 original size:41 final size:40
Alignment explanation
Indices: 538786--538927 Score: 119
Period size: 41 Copynumber: 3.5 Consensus size: 40
538776 TTTAGCAGCA
538786 TTTTTATACAAACGCCGCAATAGGTTCATCCATAGTGGCGT
1 TTTTTA-ACAAACGCCGCAATAGGTTCATCCATAGTGGCGT
* **
538827 TTTTTCAACAAACGTCGCAATAGAG-T-AGTACTTTAGTGGCG-
1 TTTTT-AACAAACGCCGCAATAG-GTTCA-T-CCATAGTGGCGT
* ** * * *
538868 TTTTTATACAAATGCTACAATTGTTTCATCCATAGTGGTGT
1 TTTTTA-ACAAACGCCGCAATAGGTTCATCCATAGTGGCGT
*
538909 TTTTTAACAAACACCGCAA
1 TTTTTAACAAACGCCGCAA
538928 CATAGTAGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 17
0.70 0.15 0.15
Matches are distributed among these distances:
40 19 0.25
41 46 0.60
42 12 0.16
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (40 bp):
TTTTTAACAAACGCCGCAATAGGTTCATCCATAGTGGCGT
Found at i:538952 original size:81 final size:82
Alignment explanation
Indices: 538766--538962 Score: 252
Period size: 82 Copynumber: 2.4 Consensus size: 82
538756 ACCTCGTGAT
** * * *
538766 AGAGTAGTACTTTAGCAGCATTTTTATACAAACGCCGCAATAGGTTCATCCATAGTGGCGTTTTT
1 AGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCCACAATAGGTTCATCCATAGTGGCGTTTTT
** *
538831 TCAACAAACGTCGCAAT
66 TCAACAAACACCGCAAC
* * * *
538848 AGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCTACAATTGTTTCATCCATAGTGGTGTTTTT
1 AGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCCACAATAGGTTCATCCATAGTGGCGTTTTT
538913 T-AACAAACACCGCAAC
66 TCAACAAACACCGCAAC
* * *
538929 ATAGTAGTATTTTAGTGGTGTTTTTATACAAATG
1 AGAGTAGTACTTTAGTGGCGTTTTTATACAAATG
538963 GTGTATAAAC
Statistics
Matches: 100, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 43 0.43
82 57 0.57
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (82 bp):
AGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCCACAATAGGTTCATCCATAGTGGCGTTTTT
TCAACAAACACCGCAAC
Found at i:539067 original size:41 final size:42
Alignment explanation
Indices: 539001--539193 Score: 202
Period size: 41 Copynumber: 4.7 Consensus size: 42
538991 TGTGTTTATG
* * *
539001 AACGCCGTTAAAGA-CT-GTACTTTAGTGGCGTTTTTATACA
1 AACGCCGCTATAGATCTAGTACTTTAGTGGCGTTTATATACA
* * * *
539041 AACGCCGCTATAGATTTA-TACTTTAGTGGCATTTTTATATA
1 AACGCCGCTATAGATCTAGTACTTTAGTGGCGTTTATATACA
* * * * *
539082 AACGCTGCTATAGA-CTTA-TACTTTAATGACGTGTATACACA
1 AACGCCGCTATAGATC-TAGTACTTTAGTGGCGTTTATATACA
*
539123 AACGCCGCTAAAGA-CTAGTACTTTAGTGGCGTTTATATACA
1 AACGCCGCTATAGATCTAGTACTTTAGTGGCGTTTATATACA
*
539164 AACGCCCCTATA-ATCTAGTACTTTAGTGGC
1 AACGCCGCTATAGATCTAGTACTTTAGTGGC
539194 ATTTGTGTTT
Statistics
Matches: 126, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
40 15 0.12
41 111 0.88
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (42 bp):
AACGCCGCTATAGATCTAGTACTTTAGTGGCGTTTATATACA
Found at i:542887 original size:42 final size:42
Alignment explanation
Indices: 542818--543251 Score: 319
Period size: 43 Copynumber: 10.2 Consensus size: 42
542808 TATCATGAGC
*
542818 CCTTTTGCAGCGTTTGTATCTAAAAACGCTGCTATAGATCTGA
1 CCTTTTGCAGCGTTTGT-TCCAAAAACGCTGCTATAGATCTGA
* * * * *
542861 CCTTTTGCAGTGTTTATTCTAAAAACG-TCGCTATAGATTTAA
1 CCTTTTGCAGCGTTTGTTCCAAAAACGCT-GCTATAGATCTGA
* * *
542903 CCTTTTGCGGCGTTTGTTCCAAAAACACACTGCTATAGATATGA
1 CCTTTTGCAGCGTTTGTTCC-AAAA-ACGCTGCTATAGATCTGA
* * * *
542947 CCTTTT-TAGTGTTTATTCCGAAAACGCTGCTATAGATCTCGA
1 CCTTTTGCAGCGTTTGTTCCAAAAACGCTGCTATAGATCT-GA
** * * *
542989 CCTTTTGCAGCGTTT-AACACGAAAATGCCGCTATAGATCTGA
1 CCTTTTGCAGCGTTTGTTC-CAAAAACGCTGCTATAGATCTGA
* * *
543031 ACTTTTGCAGCATTTTTTCCAAAACAC-C-GCTATAGATCATGA
1 CCTTTTGCAGCGTTTGTTCCAAAA-ACGCTGCTATAGATC-TGA
* * * * *
543073 CCTTTTACGGCGTTTGTTCCAAAAACGTTGCTATAGATATCAA
1 CCTTTTGCAGCGTTTGTTCCAAAAACGCTGCTATAGATCT-GA
* * * *
543116 TCTTTTGCGGCGTTTGTAT-C-AAAACTCTGCTATAGATATTGA
1 CCTTTTGCAGCGTTTGT-TCCAAAAACGCTGCTATAGAT-CTGA
* ** * *
543158 CCTTTTGC-GACTTTTGTTTTAAAAATG-TCGCTATAGATATCGA
1 CCTTTTGCAG-CGTTTGTTCCAAAAACGCT-GCTATAGATCT-GA
* * *
543201 CCTTTTGCAGCGTTTGTTCCAAAAATGTTGCGATAGATCTTGA
1 CCTTTTGCAGCGTTTGTTCCAAAAACGCTGCTATAGATC-TGA
*
543244 CCTATTGC
1 CCTTTTGC
543252 GACATTTTTT
Statistics
Matches: 312, Mismatches: 56, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
41 29 0.09
42 123 0.39
43 136 0.44
44 23 0.07
45 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (42 bp):
CCTTTTGCAGCGTTTGTTCCAAAAACGCTGCTATAGATCTGA
Found at i:542961 original size:85 final size:86
Alignment explanation
Indices: 542818--543240 Score: 253
Period size: 85 Copynumber: 5.0 Consensus size: 86
542808 TATCATGAGC
* * * *
542818 CCTTTTGCAGCGTTTGTATCTAAAAACGCTGCTATAGATCTGACCTTTTGCAGTGTTTATTCTAA
1 CCTTTTGCAGCGTTTGTATCAAAAAACACTGCTATAGATATGACCTTTTGCAGTGTTTATTCCAA
*
542883 AAACG-TCGCTATAGAT-TTAA
66 AAACGCT-GCTATAGATCTCAA
* *
542903 CCTTTTGCGGCGTTTGT-TCCAAAAACACACTGCTATAGATATGACCTTTT-TAGTGTTTATTCC
1 CCTTTTGCAGCGTTTGTAT-CAAAAA-ACACTGCTATAGATATGACCTTTTGCAGTGTTTATTCC
* *
542966 GAAAACGCTGCTATAGATCTCGA
64 AAAAACGCTGCTATAGATCTCAA
* * ** * * * ** *
542989 CCTTTTGCAGCG-TT-TAACACGAAAATGCCGCTATAGATCTGAACTTTTGCAGCATTTTTTCCA
1 CCTTTTGCAGCGTTTGTATCA-AAAAACACTGCTATAGATATGACCTTTTGCAGTGTTTATTCCA
*
543052 AAACAC-C-GCTATAGATCAT-GA
65 AAA-ACGCTGCTATAGATC-TCAA
* * * ** * * * * *
543073 CCTTTTACGGCGTTTGT-TCCAAAAACGTTGCTATAGATATCAATCTTTTGCGGCGTTTGTAT-C
1 CCTTTTGCAGCGTTTGTATCAAAAAACACTGCTATAGATAT-GACCTTTTGCAGTGTTTAT-TCC
* * **
543136 -AAAACTCTGCTATAGATATTGA
64 AAAAACGCTGCTATAGATCTCAA
* * * *** * *
543158 CCTTTTGC-GACTTTTGTTTTAAAAATGTC-GCTATAGATATCGACCTTTTGCAGCGTTTGTTCC
1 CCTTTTGCAG-CGTTTGTATCAAAAAACACTGCTATAGATAT-GACCTTTTGCAGTGTTTATTCC
* * *
543221 AAAAATGTTGCGATAGATCT
64 AAAAACGCTGCTATAGATCT
543241 TGACCTATTG
Statistics
Matches: 265, Mismatches: 53, Indels: 39
0.74 0.15 0.11
Matches are distributed among these distances:
83 2 0.01
84 67 0.25
85 137 0.52
86 59 0.22
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (86 bp):
CCTTTTGCAGCGTTTGTATCAAAAAACACTGCTATAGATATGACCTTTTGCAGTGTTTATTCCAA
AAACGCTGCTATAGATCTCAA
Found at i:543856 original size:55 final size:55
Alignment explanation
Indices: 543753--544135 Score: 505
Period size: 55 Copynumber: 6.9 Consensus size: 55
543743 TGAATATTAC
* * ** * * *
543753 AACTCATTATAAATTTTCATGGTTTTGTACACATAGTGCCGATACGAAAATTCATA
1 AACTCATTATGAA-TTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* *
543809 AACTCATTATGAATTTCGTGGGGTTGCACACATATTGCCAATACGAAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * *
543864 AACTCATTATGAATTTCGTGAGGTTGCACACATAGTGTCAATACGGGAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* *
543919 AACTCATTATGAATTTCATGGGGTTACACACATAGTGCCAATACGGAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * *
543974 AACTCATTATGAATTTCGTGAGGTTTCACACATAGTGTCAATACGGAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * * * * **
544029 AGCTCATTATGAATTTCATGAGGTTGCAGACATGGTGCCAATACAAAAATTCATA
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
* * * *
544084 AACTCATTATGAATTTTGTGGGGCTGCACATATAGTGCCAATATGGAAATTC
1 AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTC
544136 GCAACATATA
Statistics
Matches: 287, Mismatches: 40, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
55 275 0.96
56 12 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (55 bp):
AACTCATTATGAATTTCGTGGGGTTGCACACATAGTGCCAATACGGAAATTCATA
Found at i:547219 original size:65 final size:64
Alignment explanation
Indices: 547120--547244 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 64
547110 AAGCAAAGAT
547120 AAAATAATAAGTAAAAAAACAAATAATAAAATATATATAAAA-AAGAAAAAGAAAATAAATAAAA
1 AAAATAATAAGTAAAAAAACAAATAATAAAATATATATAAAATAA-AAAAA-AAAATAAATAAAA
547184 C
64 C
* * *
547185 AAAATAATAA-TAACAAAGTACAAATAAT-ATATATATATAAAATAAATAAAAAAATAAATA
1 AAAATAATAAGTAA-AAA-AACAAATAATAAAATATATATAAAATAAAAAAAAAAATAAATA
547245 TATATAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
64 13 0.24
65 30 0.56
66 11 0.20
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (64 bp):
AAAATAATAAGTAAAAAAACAAATAATAAAATATATATAAAATAAAAAAAAAAATAAATAAAAC
Found at i:547240 original size:27 final size:27
Alignment explanation
Indices: 547171--547260 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
547161 AAAGAAAAAG
547171 AAAATAAATAAAACAAA-ATA-ATA-AT
1 AAAATAAATAAAA-AAATATATATATAT
* * *
547196 AACA-AAGTACAAATAATATATATATAT
1 AAAATAAATA-AAAAAATATATATATAT
*
547223 AAAATAAATAAAAAAATAAATATATAT
1 AAAATAAATAAAAAAATATATATATAT
*
547250 -AAATTAATAAA
1 AAAATAAATAAA
547261 TTAAATGACG
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
24 6 0.12
25 9 0.17
26 13 0.25
27 20 0.38
28 4 0.08
ACGTcount: A:0.70, C:0.03, G:0.01, T:0.26
Consensus pattern (27 bp):
AAAATAAATAAAAAAATATATATATAT
Found at i:547716 original size:2 final size:2
Alignment explanation
Indices: 547709--547735 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
547699 GAACATACGC
547709 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
547736 ACAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:547772 original size:12 final size:11
Alignment explanation
Indices: 547744--547790 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
547734 TAACAAAATA
* *
547744 AATAATATAAA
1 AATAATACAAG
547755 AATAATACAAG
1 AATAATACAAG
547766 TAATAATACAAG
1 -AATAATACAAG
*
547778 AATAATAAAAG
1 AATAATACAAG
547789 AA
1 AA
547791 AGAGAAAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.68, C:0.04, G:0.06, T:0.21
Consensus pattern (11 bp):
AATAATACAAG
Found at i:548690 original size:20 final size:21
Alignment explanation
Indices: 548665--548723 Score: 86
Period size: 20 Copynumber: 2.9 Consensus size: 21
548655 GCCTGCTGGA
548665 AACCGGTT-TAACCGGTTTTC
1 AACCGGTTCTAACCGGTTTTC
548685 AACCGGTTCTAACCGG-TTTC
1 AACCGGTTCTAACCGGTTTTC
* *
548705 GACCGGTTCAAACCGGTTT
1 AACCGGTTCTAACCGGTTT
548724 GACCGGTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 26 0.74
21 9 0.26
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (21 bp):
AACCGGTTCTAACCGGTTTTC
Found at i:548700 original size:10 final size:9
Alignment explanation
Indices: 548665--548732 Score: 64
Period size: 10 Copynumber: 7.0 Consensus size: 9
548655 GCCTGCTGGA
548665 AACCGGTTT
1 AACCGGTTT
548674 AACCGGTTTT
1 AACCGG-TTT
548684 CAACCGGTTCT
1 -AACCGGTT-T
548695 AACCGGTTT
1 AACCGGTTT
* *
548704 CGACCGGTTCA
1 -AACCGGTT-T
548715 AACCGGTTT
1 AACCGGTTT
*
548724 GACCGGTTT
1 AACCGGTTT
548733 CGACCGATTC
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
9 15 0.31
10 27 0.55
11 7 0.14
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (9 bp):
AACCGGTTT
Found at i:548728 original size:29 final size:29
Alignment explanation
Indices: 548685--548759 Score: 114
Period size: 29 Copynumber: 2.6 Consensus size: 29
548675 ACCGGTTTTC
* *
548685 AACCGGTTCTAACCGGTTTCGACCGGTTCA
1 AACCGGTT-TGACCGGTTTCGACCGATTCA
*
548715 AACCGGTTTGACCGGTTTCGACCGATTCG
1 AACCGGTTTGACCGGTTTCGACCGATTCA
548744 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
548760 CTGACCCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 34 0.81
30 8 0.19
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTTCGACCGATTCA
Found at i:548729 original size:19 final size:20
Alignment explanation
Indices: 548674--548731 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
548664 AAACCGGTTT
* *
548674 AACCGGTTTTCAACCGGTTCT
1 AACCGG-TTTCGACCGGTTCA
548695 AACCGGTTTCGACCGGTTCA
1 AACCGGTTTCGACCGGTTCA
548715 AACCGGTTT-GACCGGTT
1 AACCGGTTTCGACCGGTT
548732 TCGACCGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.23
20 21 0.60
21 6 0.17
ACGTcount: A:0.19, C:0.28, G:0.24, T:0.29
Consensus pattern (20 bp):
AACCGGTTTCGACCGGTTCA
Found at i:548737 original size:10 final size:10
Alignment explanation
Indices: 548666--548759 Score: 65
Period size: 9 Copynumber: 9.6 Consensus size: 10
548656 CCTGCTGGAA
*
548666 ACCGGTTT-A
1 ACCGGTTTCG
*
548675 ACCGGTTTTCA
1 ACCGG-TTTCG
*
548686 ACCGG-TTCTA
1 ACCGGTTTC-G
548696 ACCGGTTTCG
1 ACCGGTTTCG
*
548706 ACCGG-TTCAA
1 ACCGGTTTC-G
548716 ACCGGTTT-G
1 ACCGGTTTCG
548725 ACCGGTTTCG
1 ACCGGTTTCG
*
548735 ACC-GATTCG
1 ACCGGTTTCG
548744 AACCGGTTT-G
1 -ACCGGTTTCG
548754 ACCGGT
1 ACCGGT
548760 CTGACCCAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
9 30 0.42
10 27 0.38
11 14 0.20
ACGTcount: A:0.18, C:0.28, G:0.26, T:0.29
Consensus pattern (10 bp):
ACCGGTTTCG
Found at i:555256 original size:307 final size:307
Alignment explanation
Indices: 554702--555324 Score: 1228
Period size: 307 Copynumber: 2.0 Consensus size: 307
554692 GAGGACACAG
554702 TCAGATTAATCCGTGACCGTCTGAAGGAGGCATTTAATAGGTAGAAATCTTATGCAGATCAAAGG
1 TCAGATTAATCCGTGACCGTCTGAAGGAGGCATTTAATAGGTAGAAATCTTATGCAGATCAAAGG
*
554767 AGGAAGGATATACAGTTTGAGGTTGGAGATCAGGTCTTTTTGAAAGTTTCACCCTGGAAGAAAGT
66 AGGAAGGATATACAGTTTAAGGTTGGAGATCAGGTCTTTTTGAAAGTTTCACCCTGGAAGAAAGT
554832 ATTGAGATTCGGGCGTAAGGGTAAATTGAGTCCAAGATTTATTGGACCATTTCGTATCTTGAAGA
131 ATTGAGATTCGGGCGTAAGGGTAAATTGAGTCCAAGATTTATTGGACCATTTCGTATCTTGAAGA
554897 GGGTAGGACCTGTTGCATATAAGCTTGAGTTGCCTTCTGAGCTAATTCGTATTCATGATGTCTTT
196 GGGTAGGACCTGTTGCATATAAGCTTGAGTTGCCTTCTGAGCTAATTCGTATTCATGATGTCTTT
554962 CATGTATCAATGTTGAGGAGATACCATCCAGATCCAGGTCACATTAT
261 CATGTATCAATGTTGAGGAGATACCATCCAGATCCAGGTCACATTAT
555009 TCAGATTAATCCGTGACCGTCTGAAGGAGGCATTTAATAGGTAGAAATCTTATGCAGATCAAAGG
1 TCAGATTAATCCGTGACCGTCTGAAGGAGGCATTTAATAGGTAGAAATCTTATGCAGATCAAAGG
555074 AGGAAGGATATACAGTTTAAGGTTGGAGATCAGGTCTTTTTGAAAGTTTCACCCTGGAAGAAAGT
66 AGGAAGGATATACAGTTTAAGGTTGGAGATCAGGTCTTTTTGAAAGTTTCACCCTGGAAGAAAGT
555139 ATTGAGATTCGGGCGTAAGGGTAAATTGAGTCCAAGATTTATTGGACCATTTCGTATCTTGAAGA
131 ATTGAGATTCGGGCGTAAGGGTAAATTGAGTCCAAGATTTATTGGACCATTTCGTATCTTGAAGA
555204 GGGTAGGACCTGTTGCATATAAGCTTGAGTTGCCTTCTGAGCTAATTCGTATTCATGATGTCTTT
196 GGGTAGGACCTGTTGCATATAAGCTTGAGTTGCCTTCTGAGCTAATTCGTATTCATGATGTCTTT
555269 CATGTATCAATGTTGAGGAGATACCATCCAGATCCAGGTCACATTAT
261 CATGTATCAATGTTGAGGAGATACCATCCAGATCCAGGTCACATTAT
*
555316 TCAGGTTAA
1 TCAGATTAA
555325 AGAAGTAGAC
Statistics
Matches: 314, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
307 314 1.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (307 bp):
TCAGATTAATCCGTGACCGTCTGAAGGAGGCATTTAATAGGTAGAAATCTTATGCAGATCAAAGG
AGGAAGGATATACAGTTTAAGGTTGGAGATCAGGTCTTTTTGAAAGTTTCACCCTGGAAGAAAGT
ATTGAGATTCGGGCGTAAGGGTAAATTGAGTCCAAGATTTATTGGACCATTTCGTATCTTGAAGA
GGGTAGGACCTGTTGCATATAAGCTTGAGTTGCCTTCTGAGCTAATTCGTATTCATGATGTCTTT
CATGTATCAATGTTGAGGAGATACCATCCAGATCCAGGTCACATTAT
Found at i:556240 original size:10 final size:10
Alignment explanation
Indices: 556225--556301 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
556215 TACTGGAAAT
556225 CGGTTCTGAC
1 CGGTTCTGAC
556235 CGGTTC-GAAC
1 CGGTTCTG-AC
* *
556245 CAGTT-TGAT
1 CGGTTCTGAC
*
556254 TGG-TCTGAAC
1 CGGTTCTG-AC
556264 CGGTT-TGAC
1 CGGTTCTGAC
556273 CGG-TCTGAAC
1 CGGTTCTG-AC
556283 CGGTT-TGAC
1 CGGTTCTGAC
556292 CGG-TCTGAC
1 CGGTTCTGAC
556301 C
1 C
556302 CGACCCGACC
Statistics
Matches: 52, Mismatches: 6, Indels: 19
0.68 0.08 0.25
Matches are distributed among these distances:
8 3 0.06
9 22 0.42
10 25 0.48
11 2 0.04
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.29
Consensus pattern (10 bp):
CGGTTCTGAC
Found at i:556269 original size:19 final size:19
Alignment explanation
Indices: 556225--556299 Score: 98
Period size: 19 Copynumber: 3.9 Consensus size: 19
556215 TACTGGAAAT
556225 CGGTTCTGACCGGT-TCGAAC
1 CGGTT-TGACCGGTCT-GAAC
* **
556245 CAGTTTGATTGGTCTGAAC
1 CGGTTTGACCGGTCTGAAC
556264 CGGTTTGACCGGTCTGAAC
1 CGGTTTGACCGGTCTGAAC
556283 CGGTTTGACCGGTCTGA
1 CGGTTTGACCGGTCTGA
556300 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 43 0.90
20 5 0.10
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (19 bp):
CGGTTTGACCGGTCTGAAC
Found at i:558497 original size:37 final size:37
Alignment explanation
Indices: 558456--558560 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
558446 GTGCTTGTGG
* *
558456 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * *
558493 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
558530 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
558561 GACGAAAAGG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:559628 original size:106 final size:106
Alignment explanation
Indices: 559290--561287 Score: 2855
Period size: 106 Copynumber: 18.9 Consensus size: 106
559280 AGCATTGTTC
* * * * * ** * *
559290 TGAGTCCAATATCCTCCATCGTGAATTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
559355 ACCAACCGTCTCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
559396 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * * * *
559455 ATCAGCCG-CTCCTTCGTCGTGAAGTTGAGCTTGTGTTGCCT
66 ACCAGCGGTC-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
559496 TGGGTCCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
559561 AACAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
559602 TGAGTCCAATAT-CTTACGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGAC
1 TGAGTCCAATATCCTT-CGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
*
559666 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
559708 GGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
559773 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
559814 TGAATCCAATATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTAGGAAATTGTTTGTTAACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
559879 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTTCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
559920 GGAGTCCAATATCCTTCGTTGTGAAGTTGAAATCGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
559985 ACCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
560026 GGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAGTTATTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
560091 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
560132 TAAGTCCAATATCCTACGTTGTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
560197 ACCAGCTGTCCCTTCGTCGTGAAGTTGAACTTCCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
560238 TGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
560303 ACCAGCGGCCCCTTCGTCGTGAAGTTGAACTTGCATTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
560344 GGAGTCCAATATCCTTCGCTATGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
560409 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
560450 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
560515 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT-T
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
560555 TGGAGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTATTGAC
1 T-GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* *
560620 AACCAGCGGTCCCTTCGTTGTGAAGTTGAACTGGCGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** * * *
560662 GGAGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
560727 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
560768 GGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* * *
560833 ACTAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * ** *
560874 TTAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATATTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
*
560939 ACCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
560980 GGAGTCCAATATCCTTTGTCGTGAAGTTAAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
* *
561045 ACCAGCGGTCCCTTCATTGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
561086 TGGGTCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCTGAAATTGGGAAGTTATTTATTGACA
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
561151 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
561192 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAATTGGGAAACTT-TTTATTGAC
1 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAGTTGTTTGTTGAC
561256 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
561288 CCACTCTCGA
Statistics
Matches: 1707, Mismatches: 172, Indels: 26
0.90 0.09 0.01
Matches are distributed among these distances:
99 1 0.00
100 79 0.05
101 3 0.00
102 4 0.00
104 3 0.00
105 8 0.00
106 1600 0.94
107 9 0.01
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:562023 original size:21 final size:22
Alignment explanation
Indices: 561998--562072 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
561988 TTGTGTTTGG
561998 TCAAAGG-TTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
562019 TCAAAGGTTTGACATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
562041 TCATAGGTTTGGCATTT-ATGC
1 TCAAAGGTTTGGCATTTGATGC
*
562062 TCAACGGTTTG
1 TCAAAGGTTTG
562073 ATGGGGTAGC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
21 20 0.43
22 26 0.57
ACGTcount: A:0.23, C:0.15, G:0.27, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:562684 original size:15 final size:14
Alignment explanation
Indices: 562664--562737 Score: 55
Period size: 15 Copynumber: 4.9 Consensus size: 14
562654 TTTGCATGTG
562664 CTTTTTTGTCTTTTT
1 CTTTTTTGT-TTTTT
562679 C-TTTTTGATTTTTGTT
1 CTTTTTTG--TTTT-TT
562695 CTTTCTTT-TTTTCTT
1 CTTT-TTTGTTTT-TT
562710 C-TTTTTGCTTCTTTT
1 CTTTTTTG-TT-TTTT
562725 CTTTTTTGTTTTT
1 CTTTTTTGTTTTT
562738 GCCCTTTTTG
Statistics
Matches: 49, Mismatches: 1, Indels: 19
0.71 0.01 0.28
Matches are distributed among these distances:
13 3 0.06
14 11 0.22
15 18 0.37
16 12 0.24
17 2 0.04
18 3 0.06
ACGTcount: A:0.01, C:0.14, G:0.07, T:0.78
Consensus pattern (14 bp):
CTTTTTTGTTTTTT
Found at i:562692 original size:21 final size:20
Alignment explanation
Indices: 562666--562704 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
562656 TGCATGTGCT
*
562666 TTTTTGTCTTTTTCTTTTTGA
1 TTTTTGT-TCTTTCTTTTTGA
562687 TTTTTGTTCTTTCTTTTT
1 TTTTTGTTCTTTCTTTTT
562705 TTCTTCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.03, C:0.10, G:0.08, T:0.79
Consensus pattern (20 bp):
TTTTTGTTCTTTCTTTTTGA
Found at i:562697 original size:22 final size:21
Alignment explanation
Indices: 562666--562738 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
562656 TGCATGTGCT
562666 TTTTTG-TCTTTTTCTTTTTG
1 TTTTTGTTCTTTTTCTTTTTG
* *
562686 ATTTTTGTTCTTTCTTTTTTTCTTC
1 -TTTTTGTTC-TT-TTTCTTT-TTG
562711 TTTTTGCTTC-TTTTCTTTTTTG
1 TTTTTG-TTCTTTTTC-TTTTTG
562733 TTTTTG
1 TTTTTG
562739 CCCTTTTTGT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.14
22 13 0.31
23 6 0.14
24 12 0.29
25 5 0.12
ACGTcount: A:0.01, C:0.12, G:0.08, T:0.78
Consensus pattern (21 bp):
TTTTTGTTCTTTTTCTTTTTG
Found at i:562701 original size:26 final size:26
Alignment explanation
Indices: 562672--562731 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
562662 TGCTTTTTTG
*
562672 TCTTTTTCTTTTTGATTTTTG-TTC-TT
1 TCTTTTT-TTCTT-ATTTTTGCTTCTTT
*
562698 TCTTTTTTTCTTCTTTTTGCTTCTTT
1 TCTTTTTTTCTTATTTTTGCTTCTTT
562724 TCTTTTTT
1 TCTTTTTT
562732 GTTTTTGCCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.20
25 7 0.23
26 17 0.57
ACGTcount: A:0.02, C:0.15, G:0.05, T:0.78
Consensus pattern (26 bp):
TCTTTTTTTCTTATTTTTGCTTCTTT
Found at i:562739 original size:22 final size:23
Alignment explanation
Indices: 562675--562739 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
562665 TTTTTTGTCT
562675 TTTTC-TTTTTGATTTTTGTTCTTTC
1 TTTTCTTTTTTG-TTTTTG--CTTTC
* *
562700 TTTT-TTTCTTCTTTTTGC-TTC
1 TTTTCTTTTTTGTTTTTGCTTTC
562721 TTTTCTTTTTTGTTTTTGC
1 TTTTCTTTTTTGTTTTTGC
562740 CCTTTTTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
21 7 0.21
22 13 0.38
24 6 0.18
25 8 0.24
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTTTGTTTTTGCTTTC
Found at i:566137 original size:19 final size:20
Alignment explanation
Indices: 566109--566146 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
566099 TGCAGATGAT
*
566109 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
566128 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
566147 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:567339 original size:28 final size:28
Alignment explanation
Indices: 567246--567339 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 28
567236 AATTAAAATG
567246 AAAAGAAAACAAATTAAGTAAAATGATA-AA
1 AAAAGAAAACAAA-TAA-TAAAAT-ATATAA
* * *
567276 ATGAAGAAAGCAAA-GATAAAATA-ATAA
1 A-AAAGAAAACAAATAATAAAATATATAA
*
567303 GTAAA-AAAACAAATAATAAAATATATAA
1 -AAAAGAAAACAAATAATAAAATATATAA
567331 AAAAGAAAA
1 AAAAGAAAA
567340 AGAAAAAGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
26 8 0.16
27 16 0.32
28 14 0.28
29 1 0.02
30 1 0.02
31 10 0.20
ACGTcount: A:0.71, C:0.03, G:0.10, T:0.16
Consensus pattern (28 bp):
AAAAGAAAACAAATAATAAAATATATAA
Found at i:567417 original size:23 final size:23
Alignment explanation
Indices: 567386--567438 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
567376 AAGTACGAAT
*
567386 AATATATATATATAAAATAAAAA
1 AATAAATATATATAAAATAAAAA
* *
567409 AATAAATATATATAAATTAATAA
1 AATAAATATATATAAAATAAAAA
*
567432 ATTAAAT
1 AATAAAT
567439 GAAGAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (23 bp):
AATAAATATATATAAAATAAAAA
Found at i:567495 original size:2 final size:2
Alignment explanation
Indices: 567490--567522 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
567480 AGATAATACA
567490 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
567523 GTAACAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:567754 original size:11 final size:11
Alignment explanation
Indices: 567726--567791 Score: 55
Period size: 11 Copynumber: 6.1 Consensus size: 11
567716 CAATAATATC
*
567726 AATAAAAAAAG
1 AATAAAAAAAT
567737 AA-AATAAAAAT
1 AATAA-AAAAAT
* **
567748 AATATAATGAT
1 AATAAAAAAAT
567759 AATAAAAAAAT
1 AATAAAAAAAT
*
567770 -ATAGAAAAAT
1 AATAAAAAAAT
*
567780 AATAGAAAAAT
1 AATAAAAAAAT
567791 A
1 A
567792 TATGTATAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
10 11 0.25
11 32 0.73
12 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.20
Consensus pattern (11 bp):
AATAAAAAAAT
Found at i:567934 original size:12 final size:11
Alignment explanation
Indices: 567919--567948 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
567909 TAAATATAAA
567919 AATAATACAAG
1 AATAATACAAG
567930 TAATAATACAAG
1 -AATAATACAAG
567942 AATAATA
1 AATAATA
567949 AAAAGAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.23
Consensus pattern (11 bp):
AATAATACAAG
Found at i:567997 original size:25 final size:26
Alignment explanation
Indices: 567960--568014 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
567950 AAAGAAAGAG
567960 AAAT-TAAAAAATATA-ATAATAATA-
1 AAATATAAAAAATATATAT-ATAATAT
567984 AAATATAAAAAATATATATATAATAT
1 AAATATAAAAAATATATATATAATAT
568010 AAATA
1 AAATA
568015 AGTAGAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.14
25 17 0.61
26 7 0.25
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATATAAAAAATATATATATAATAT
Done.