Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 133 of 193
Found at i:41953146 original size:246 final size:247
Alignment explanation
Indices: 41952691--41953214 Score: 1005
Period size: 246 Copynumber: 2.1 Consensus size: 247
41952681 AATAATTATA
*
41952691 TAATTAAATATTTCGGGTTATTTTTAATAATTAAATATAATTAAGTAATTAAATATTTTGAATTA
1 TAATTAAATATTTC-GGTTGTTTTTAATAATTAAATATAATTAAGTAATTAAATATTTTGAATTA
*
41952756 AGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAACTAAATAATTAAATATTTGAATTGTT
65 AGTATTTGGGTTGTTTTTAATAAATAACCAATTATTAAACTAAATAATTAAATATTTGAATTGTT
41952821 TTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGA
130 TTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGA
41952886 TTGTTTTAATAATTAAATATTTAATTAAATGTATTCAAATAATAACATATTTT
195 TTGTTTTAATAATTAAATATTTAATTAAATGTATTCAAATAATAACATATTTT
41952939 TAATTAAATATTTCGGTTGTTTTTAATAATTAAATATAATTAAGTAATTAAATATTTTGAATTAA
1 TAATTAAATATTTCGGTTGTTTTTAATAATTAAATATAATTAAGTAATTAAATATTTTGAATTAA
41953004 GTATTTGGGTTG-TTTTAATAAATAACCAATTATTAAACTAAATAATTAAATATTTGAATTGTTT
66 GTATTTGGGTTGTTTTTAATAAATAACCAATTATTAAACTAAATAATTAAATATTTGAATTGTTT
41953068 TTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGAT
131 TTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGAT
*
41953133 TGTTTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATTTT
196 TGTTTTAATAATTAAATATTTAATTAAATGTATTCAAATAATAACATATTTT
41953185 TAATTAAATATTTCGGTTGTTTTTAATAAT
1 TAATTAAATATTTCGGTTGTTTTTAATAAT
41953215 GGTTCAATTA
Statistics
Matches: 273, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
246 197 0.72
247 62 0.23
248 14 0.05
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (247 bp):
TAATTAAATATTTCGGTTGTTTTTAATAATTAAATATAATTAAGTAATTAAATATTTTGAATTAA
GTATTTGGGTTGTTTTTAATAAATAACCAATTATTAAACTAAATAATTAAATATTTGAATTGTTT
TTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGAT
TGTTTTAATAATTAAATATTTAATTAAATGTATTCAAATAATAACATATTTT
Found at i:41953271 original size:112 final size:115
Alignment explanation
Indices: 41953118--41953444 Score: 418
Period size: 112 Copynumber: 2.8 Consensus size: 115
41953108 AATATTTTGA
* *
41953118 ATTAAATATTTGGATTG-TTTTAATAATTAAATATTTAATTAAATGTATTTAAATAA-TAACATA
1 ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAA-ATA
* *** *
41953181 TTTTTAATTAAATATTTCGGTTGTTTTTAATAATGGTTCA-ATTAAA-T-AT
65 TTTTGAATTAAATATTT-GGTTGTTTTTAATAATAACTAATATTAAACTAAT
* *
41953230 -TTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAGTAATTAAATAT
1 ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAATAT
*
41953294 TTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAACTAAAT
66 TTTGAATTAAATATTT-GGTTGTTTTTAAT-AATAACTAA-TATTAAACT-AAT
* *
41953348 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
1 -ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAATA
41953413 -TTTGAATTAAATATTTGGATTG-TTTTAATAAT
65 TTTTGAATTAAATATTTGG-TTGTTTTTAATAAT
41953445 TAAATATTTA
Statistics
Matches: 188, Mismatches: 16, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
111 16 0.09
112 66 0.35
113 8 0.04
115 6 0.03
116 1 0.01
117 3 0.02
118 11 0.06
119 18 0.10
120 59 0.31
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (115 bp):
ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAATAT
TTTGAATTAAATATTTGGTTGTTTTTAATAATAACTAATATTAAACTAAT
Found at i:41953295 original size:300 final size:300
Alignment explanation
Indices: 41952965--41953711 Score: 1243
Period size: 300 Copynumber: 2.5 Consensus size: 300
41952955 TTGTTTTTAA
41952965 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTAATAAATAAC
1 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTAATAAATAAC
*
41953030 CAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATAT
66 TAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATAT
41953095 AATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAA
131 AATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAA
**
41953160 ATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAAT-AATGGTTCAATT
196 ATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATAATT-AATT
41953224 AAATATTTAAATATTTGGATTGTTTTTAATTATTAAATATT
260 AAATATTTAAATATTTGGATTGTTTTTAATTATTAAATATT
41953265 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAA
1 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTG-TTTTAATAAATAA
41953330 CTAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATA
65 CTAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATA
41953395 TAATTAAATAATTAAATA-TTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTA
130 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTA
41953459 AATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATAATTAATT
195 AATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATAATTAATT
*
41953524 AAATATTTAAATATTTGGATTGTTTTTAATTATTAAATTTT
260 AAATATTTAAATATTTGGATTGTTTTTAATTATTAAATATT
* * * * * *
41953565 TAATTAAATATAATTAACTAATAAAATATTTTTAATTAAATATTTGGGTTATTTT--T-AATAAT
1 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTAATAAATAAC
* * ** ** * * * *
41953627 TATTTATTTATTTATTTATTTAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTATATAT
66 TAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATAT
* *
41953692 AACTAAATAATAAAATATTT
131 AATTAAATAATTAAATATTT
41953712 AATTATATAT
Statistics
Matches: 422, Mismatches: 22, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
296 75 0.18
297 3 0.01
299 4 0.01
300 240 0.57
301 100 0.24
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (300 bp):
TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTAATAAATAAC
TAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATAT
AATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAA
ATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATAATTAATTA
AATATTTAAATATTTGGATTGTTTTTAATTATTAAATATT
Found at i:41953354 original size:120 final size:118
Alignment explanation
Indices: 41953117--41953443 Score: 395
Period size: 120 Copynumber: 2.8 Consensus size: 118
41953107 AAATATTTTG
* * * *
41953117 AATTAAATATTTGGATTG-TTTTAATAATTAAATATTTAATTAAATGTATTTAAATAA-TAACAT
1 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAA-AT
* ** * *
41953180 ATTTTTAATTAAATATTTCGG-TTG-TTT--T---TAA-TAATGGTTCAATTAAAT
65 A-TTTGAATTAAATATTT-GGATTGTTTTAATAAATAACTAATTATTAAACTAAAT
* * * * *
41953228 ATTTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAGTAATTAAATA
1 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
* *
41953293 TTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAACTAAAT
66 -TTTGAATTAAATATTTGGATTG-TTTTAATAAATAACTAATTATTAAACTAAAT
41953348 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
1 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
41953413 TTTGAATTAAATATTTGGATTGTTTTAATAA
66 TTTGAATTAAATATTTGGATTGTTTTAATAA
41953444 TTAAATATTT
Statistics
Matches: 187, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
111 19 0.10
112 56 0.30
113 3 0.02
114 3 0.02
116 1 0.01
118 9 0.05
119 23 0.12
120 73 0.39
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.48
Consensus pattern (118 bp):
AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAAATA
TTTGAATTAAATATTTGGATTGTTTTAATAAATAACTAATTATTAAACTAAAT
Found at i:41953391 original size:38 final size:37
Alignment explanation
Indices: 41953348--41953461 Score: 125
Period size: 38 Copynumber: 3.2 Consensus size: 37
41953338 TAAACTAAAT
41953348 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTA
1 AATTAAATATTTGAATTG-TTTTAATAATTAAATATTA
* *
41953386 AATTAAATA--T-AA----TTAAATAATTAAATATTTG
1 AATTAAATATTTGAATTGTTTTAATAATTAAATA-TTA
* *
41953417 AATTAAATATTTGGATTGTTTTAATAATTAAATATTT
1 AATTAAATATTTGAATTGTTTTAATAATTAAATATTA
41953454 AATTAAAT
1 AATTAAAT
41953462 GTATTTAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
30 14 0.22
31 11 0.17
33 1 0.02
34 1 0.02
35 2 0.03
36 1 0.02
37 10 0.16
38 23 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (37 bp):
AATTAAATATTTGAATTGTTTTAATAATTAAATATTA
Found at i:41953422 original size:13 final size:13
Alignment explanation
Indices: 41953404--41953429 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41953394 ATAATTAAAT
41953404 AATTAAATATTTG
1 AATTAAATATTTG
41953417 AATTAAATATTTG
1 AATTAAATATTTG
41953430 GATTGTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AATTAAATATTTG
Found at i:41953681 original size:46 final size:46
Alignment explanation
Indices: 41953595--41953687 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
41953585 ATAAAATATT
** ** *
41953595 TTTAATTAAATATTTGGGTTATTTTTAATAATTATTTATTTATTTA
1 TTTAATTAAATATTTGAATTATTTTTAATAATTAAATATTTAATTA
* * *
41953641 TTTATTTAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTA
1 TTTAATTAAATATTTGAATTATTTTTAATAATTAAATATTTAATTA
41953687 T
1 T
41953688 ATATAACTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.60
Consensus pattern (46 bp):
TTTAATTAAATATTTGAATTATTTTTAATAATTAAATATTTAATTA
Found at i:41953686 original size:116 final size:114
Alignment explanation
Indices: 41953419--41953796 Score: 453
Period size: 112 Copynumber: 3.3 Consensus size: 114
41953409 AATATTTGAA
* * * *
41953419 TTAAATATTTGGATTG-TTTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATT
1 TTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAATAATAAAATATT
* *
41953483 TTTAATTAAATATTTCGGTTGTTTTTAATAA--ATAATTAATTAAATAT
66 TTTAATTAAATATTTGGGTTATTTTTAATAATTATAATTAATTAAATAT
* *
41953530 TTAAATATTTGGATTGTTTTTAATTATTAAATTTTTAATTAAATATAATTAACTAATAAAATATT
1 TTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAATAATAAAATATT
* * **
41953595 TTTAATTAAATATTTGGGTTATTTTTAATAATTATTTATTTATTTATTTAT
66 TTTAATTAAATATTTGGGTTATTTTTAATAATTA--TAATTAATTAAATAT
* * *
41953646 TTAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTATATATAACTAAATAATAAAATATT
1 TTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAATAATAAAATA-T
* *
41953711 TAATTATATATAACTAAATATTTGGGTTATTTTTAATAATTA-AA-TAATTAACTAA
65 T--TT-TA-AT---TAAATATTTGGGTTATTTTTAATAATTATAATTAATTAAATAT
* *
41953766 TTAAATATTTGAATT-TTTTTAATAATTAAAT
1 TTAAATATTTGGATTGTTTTTAATTATTAAAT
41953797 TATTAAATAT
Statistics
Matches: 231, Mismatches: 23, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
111 16 0.07
112 71 0.31
114 1 0.00
116 69 0.30
117 2 0.01
119 17 0.07
120 24 0.10
121 3 0.01
124 28 0.12
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.51
Consensus pattern (114 bp):
TTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAATAATAAAATATT
TTTAATTAAATATTTGGGTTATTTTTAATAATTATAATTAATTAAATAT
Found at i:41953708 original size:30 final size:30
Alignment explanation
Indices: 41953674--41953730 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
41953664 TTTAATTATT
41953674 AAATATTTAATTATATATAACTAAATAATA
1 AAATATTTAATTATATATAACTAAATAATA
41953704 AAATATTTAATTATATATAACTAAATA
1 AAATATTTAATTATATATAACTAAATA
41953731 TTTGGGTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (30 bp):
AAATATTTAATTATATATAACTAAATAATA
Found at i:41953710 original size:180 final size:179
Alignment explanation
Indices: 41952796--41953713 Score: 505
Period size: 180 Copynumber: 5.1 Consensus size: 179
41952786 ATTATTAAAC
* *
41952796 TAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATT
1 TAAATATTTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATA
*
41952861 AAATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTCAAAT
66 AAATA-TTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTTAAAT
** * * * *
41952926 AATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAATTAAATATAA
130 AATAACATATTTTTAATTAAATATTTCAATTATATATAATAAAT-AAT-TAA
* * ** *** *
41952978 TTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTAA-TAAATAACCAATT-ATTA-A
1 -TAAATATTTAAATA-TTTGAATT--G---TT---TT-TAATAATTAAATATTAAATTAAATATA
* * *
41953040 ACTAAATAATTAAATATTTG------A-A-TT-G--T-TTTTAATAATTAAATATTAAATTAAAT
55 ATTAAATAATAAAATATTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAAT
* * * ** * * *
41953093 ATAATTAAATAATTAA-ATATTTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAA
120 GTATTTAAATAA-TAACATATTTTTAATTAAATATTTCAATT-ATAT-ATAA-TAAATAATTAA
* * * *** *** *
41953156 TTAAATGTATTTAAATA-AT-AACAT-ATTTT--TAATTAAATATTTCGGTTGTTTTTAA-T-AA
1 -TAAA--TATTTAAATATTTGAA-TTGTTTTTAATAATTAAATA-TTAAATTAAATATAATTAAA
** * * ** * * * *
41953214 TGGTTCAATTAAAT-ATTTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAA
61 T-AATAAAATATTTGAATTAAATATTTGGATTG-TTTTAATAATTAAATATTTAATTAAATGTAT
* * * *** * * *
41953278 TTAAGTAATTAA-ATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAA
124 TTAAATAA-TAACATATTTTTAATTAAATATTT-CAAT-TATAT-AT-AAT-A--AATAATT-AA
*
41953342 CTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAAT
1 -TAAATATTTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAAT
*
41953407 TAAATATTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTTAAAT
65 AAAATATTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTTAAAT
** * * *
41953472 AATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATAATTAA
130 AATAACATATTTTTAATTAAATATTTCAATTATATATAATAAATAATTAA
* * * * *
41953522 TTAAATATTTAAATATTTGGATTGTTTTTAATTATTAAATTTTTAATTAAATATAATTAACTAAT
1 -TAAATATTTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAAT
* * * ** * *
41953587 AAAATATTTTTAATTAAATATTTGGGTTATTTTTAATAATTATTTATTT-ATT-TATTTATTTAA
65 AAAATA-TTTGAATTAAATATTTGGATT-GTTTTAATAATTAAATATTTAATTAAATGTATTTAA
* * *
41953650 ATATTTGAA-TTGTTTTTAATTATTAAATATTT-AATTATATATAACTAAATAA-T-A
128 ATA-AT-AACATATTTTT-A--ATTAAATATTTCAATTATATATAA-TAAATAATTAA
41953704 -AAATATTTAA
1 TAAATATTTAA
41953714 TTATATATAA
Statistics
Matches: 580, Mismatches: 96, Indels: 121
0.73 0.12 0.15
Matches are distributed among these distances:
166 3 0.01
167 6 0.01
168 7 0.01
169 11 0.02
170 2 0.00
172 1 0.00
174 1 0.00
175 1 0.00
176 2 0.00
177 60 0.10
178 16 0.03
179 6 0.01
180 101 0.17
181 96 0.17
182 33 0.06
183 27 0.05
184 38 0.07
185 8 0.01
186 17 0.03
187 13 0.02
188 70 0.12
189 26 0.04
190 16 0.03
191 3 0.01
192 12 0.02
193 4 0.01
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.49
Consensus pattern (179 bp):
TAAATATTTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATA
AAATATTTGAATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTTAAATA
ATAACATATTTTTAATTAAATATTTCAATTATATATAATAAATAATTAA
Found at i:41953758 original size:8 final size:8
Alignment explanation
Indices: 41953745--41953818 Score: 58
Period size: 8 Copynumber: 9.1 Consensus size: 8
41953735 GGTTATTTTT
41953745 AATAATTA
1 AATAATTA
41953753 AATAATTA
1 AATAATTA
*
41953761 ACTAATTA
1 AATAATTA
*
41953769 AATATTTGA
1 AATAATT-A
* ** *
41953778 ATTTTTTT
1 AATAATTA
41953786 AATAATTA
1 AATAATTA
*
41953794 AATTATTA
1 AATAATTA
*
41953802 AATATTTA
1 AATAATTA
*
41953810 AATATTTA
1 AATAATTA
41953818 A
1 A
41953819 TTAGTAATAA
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
8 46 0.88
9 6 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (8 bp):
AATAATTA
Found at i:41953790 original size:33 final size:36
Alignment explanation
Indices: 41953749--41953842 Score: 106
Period size: 33 Copynumber: 2.7 Consensus size: 36
41953739 ATTTTTAATA
*
41953749 ATTA-AATAATTAACTAATTAAATATTTGAAT-TTT
1 ATTATAATAATTAACTAATTAAATATTTAAATATTT
* *
41953783 -TT-TAATAATTAAATTATTAAATATTTAAATATTT
1 ATTATAATAATTAACTAATTAAATATTTAAATATTT
*
41953817 AATTAGTAATAATTAACTAATGAAAT
1 -ATTA-TAATAATTAACTAATTAAAT
41953843 TTGTTAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
33 26 0.54
34 3 0.06
36 2 0.04
38 17 0.35
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (36 bp):
ATTATAATAATTAACTAATTAAATATTTAAATATTT
Found at i:41953790 original size:41 final size:42
Alignment explanation
Indices: 41953711--41953821 Score: 136
Period size: 41 Copynumber: 2.6 Consensus size: 42
41953701 ATAAAATATT
* **
41953711 TAATTATATATAACTAAATATTTGGGTTATTTTTAATAATTAAA
1 TAATTA-A-ATAATTAAATATTTGAATTATTTTTAATAATTAAA
*
41953755 TAATTAACTAATTAAATATTTGAATT-TTTTTAATAATTAAA
1 TAATTAAATAATTAAATATTTGAATTATTTTTAATAATTAAA
* *
41953796 TTATTAAATATTTAAATATTT-AATTA
1 TAATTAAATAATTAAATATTTGAATTA
41953822 GTAATAATTA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
40 4 0.07
41 33 0.56
42 15 0.25
43 1 0.02
44 6 0.10
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.50
Consensus pattern (42 bp):
TAATTAAATAATTAAATATTTGAATTATTTTTAATAATTAAA
Found at i:41957403 original size:24 final size:23
Alignment explanation
Indices: 41957371--41957442 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
41957361 TTTATTTGTG
41957371 ATATATATTAACTAAATATGGTAA
1 ATATATATTAA-TAAATATGGTAA
41957395 ATATATATTATGATAAATAT-GTAA
1 ATATATATTA--ATAAATATGGTAA
*
41957419 AT-TA-ATT--TATATATGGTAA
1 ATATATATTAATAAATATGGTAA
41957438 ATATA
1 ATATA
41957443 CATGATTTCT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
18 6 0.14
19 6 0.14
20 2 0.05
22 3 0.07
23 2 0.05
24 16 0.37
25 7 0.16
26 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (23 bp):
ATATATATTAATAAATATGGTAA
Found at i:41958193 original size:41 final size:40
Alignment explanation
Indices: 41958158--41958352 Score: 230
Period size: 41 Copynumber: 4.8 Consensus size: 40
41958148 CGCTTATGGG
* * *
41958158 TAAGCGTCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCTA
1 TAAGCGCCGCTATTGCTCCGACCTTTAGCGACGC-TTCCGA
*
41958199 TAAGCGCCGCTATTGCTCCGACCTTTAGCGACACTTCCCGA
1 TAAGCGCCGCTATTGCTCCGACCTTTAGCGACGCTT-CCGA
*
41958240 TAAGCGCCGCTGTTGCTCCGACCTTTAGCGACGCTTGCAC-A
1 TAAGCGCCGCTATTGCTCCGACCTTTAGCGACGCTT-C-CGA
* * * *
41958281 TAAGCGCCGCTGTTGCTCCGACCTTTTAGCGGCGCCTGCCCA
1 TAAGCGCCGCTATTGCTCCGACC-TTTAGCGACG-CTTCCGA
* *
41958323 TAAGCGCCGCTGTTGCTCCGACATTTAGCG
1 TAAGCGCCGCTATTGCTCCGACCTTTAGCG
41958353 GTTGCGGCGT
Statistics
Matches: 139, Mismatches: 10, Indels: 10
0.87 0.06 0.06
Matches are distributed among these distances:
40 2 0.01
41 101 0.73
42 34 0.24
43 2 0.01
ACGTcount: A:0.16, C:0.34, G:0.24, T:0.26
Consensus pattern (40 bp):
TAAGCGCCGCTATTGCTCCGACCTTTAGCGACGCTTCCGA
Found at i:41958284 original size:82 final size:83
Alignment explanation
Indices: 41958158--41958352 Score: 270
Period size: 82 Copynumber: 2.4 Consensus size: 83
41958148 CGCTTATGGG
* * * *
41958158 TAAGCGTCGCTATTGCTCCGACCTTTAGCGGCGCTTTCCTATAAGCGCCGCTATTGCTCCGACC-
1 TAAGCGCCGCTGTTGCTCCGACCTTTAGCGACGCTTGCCTATAAGCGCCGCTATTGCTCCGACCT
*
41958222 TTTAGCGAC-ACTTCCCGA
66 TTTAGCGACGACTGCCC-A
*
41958240 TAAGCGCCGCTGTTGCTCCGACCTTTAGCGACGCTTGCAC-ATAAGCGCCGCTGTTGCTCCGACC
1 TAAGCGCCGCTGTTGCTCCGACCTTTAGCGACGCTTGC-CTATAAGCGCCGCTATTGCTCCGACC
* *
41958304 TTTTAGCGGCGCCTGCCCA
65 TTTTAGCGACGACTGCCCA
*
41958323 TAAGCGCCGCTGTTGCTCCGACATTTAGCG
1 TAAGCGCCGCTGTTGCTCCGACCTTTAGCG
41958353 GTTGCGGCGT
Statistics
Matches: 101, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
82 57 0.56
83 39 0.39
84 5 0.05
ACGTcount: A:0.16, C:0.34, G:0.24, T:0.26
Consensus pattern (83 bp):
TAAGCGCCGCTGTTGCTCCGACCTTTAGCGACGCTTGCCTATAAGCGCCGCTATTGCTCCGACCT
TTTAGCGACGACTGCCCA
Found at i:41962096 original size:2 final size:2
Alignment explanation
Indices: 41962089--41962123 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
41962079 CTTTTAATTT
41962089 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41962124 TAATGACAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41963658 original size:19 final size:18
Alignment explanation
Indices: 41963636--41963674 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
41963626 ATTTTATTTA
41963636 TTCTTCTCCTTTTTCTATT
1 TTCTTCTCCTTTTTC-ATT
* *
41963655 TTCTTTTTCTTTTTCATT
1 TTCTTCTCCTTTTTCATT
41963673 TT
1 TT
41963675 TGCCAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (18 bp):
TTCTTCTCCTTTTTCATT
Found at i:41968132 original size:25 final size:24
Alignment explanation
Indices: 41968079--41968133 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 24
41968069 GAAAATACTC
41968079 TAGCGATTGAATAAAAATTTATCT
1 TAGCGATTGAATAAAAATTTATCT
41968103 TAGCGATTGAATAAAAATTTATCT
1 TAGCGATTGAATAAAAATTTATCT
41968127 TAAGCGA
1 T-AGCGA
41968134 GGTTCCACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 25 0.83
25 5 0.17
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.35
Consensus pattern (24 bp):
TAGCGATTGAATAAAAATTTATCT
Found at i:41968352 original size:15 final size:15
Alignment explanation
Indices: 41968332--41968379 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
41968322 CAATGTTGAC
41968332 AATAAAAATATTATT
1 AATAAAAATATTATT
*
41968347 AAT--AAA-ATTATC
1 AATAAAAATATTATT
*
41968359 AAAAAAAATATTATT
1 AATAAAAATATTATT
41968374 AATAAA
1 AATAAA
41968380 TAATTATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
12 7 0.27
13 3 0.12
14 3 0.12
15 13 0.50
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAAAATATTATT
Found at i:41974788 original size:57 final size:57
Alignment explanation
Indices: 41974700--41974807 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
41974690 ATATCAAAAA
* * *
41974700 TTAACTTGAATAAAAAAATTTAGAGTTCAATGTGTG-AACAATTACTAAATTTGAAAG
1 TTAACTTGAAAAAAAAAATTCAAAGTTCAATGTG-GAAACAATTACTAAATTTGAAAG
* *
41974757 TTAACTTGAAAAAAAAAATTCAAATTTCAATGTGGAAACAATTTCTAAATT
1 TTAACTTGAAAAAAAAAATTCAAAGTTCAATGTGGAAACAATTACTAAATT
41974808 CAAGGCATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
56 1 0.02
57 44 0.98
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.33
Consensus pattern (57 bp):
TTAACTTGAAAAAAAAAATTCAAAGTTCAATGTGGAAACAATTACTAAATTTGAAAG
Found at i:41977964 original size:17 final size:17
Alignment explanation
Indices: 41977944--41978029 Score: 127
Period size: 17 Copynumber: 5.1 Consensus size: 17
41977934 CCAATTTTAA
*
41977944 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
41977961 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
41977978 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* *
41977995 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
41978012 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
41978029 A
1 A
41978030 ATTAAAAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 60 1.00
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:41977972 original size:6 final size:6
Alignment explanation
Indices: 41977939--41978030 Score: 66
Period size: 6 Copynumber: 15.8 Consensus size: 6
41977929 TGAACCCAAT
* * * *
41977939 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
41977986 TTTAAA CTT-AT TTTGAG TTTAAA TTT-AT TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
41978031 TTAAAAAAAG
Statistics
Matches: 67, Mismatches: 14, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
5 15 0.22
6 46 0.69
7 6 0.09
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:41977986 original size:34 final size:34
Alignment explanation
Indices: 41977944--41978029 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
41977934 CCAATTTTAA
*
41977944 ATTTTAAATTTTAATTTATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTTAAGTTTAAATTT
* *
41977978 ATTTTAAATTTAAACTTATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTTATTTTAAGTTTAAATTT
41978012 ATTTTAAATTTAAATTTA
1 ATTTTAAATTTAAATTTA
41978030 ATTAAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (34 bp):
ATTTTAAATTTAAATTTATTTTAAGTTTAAATTT
Found at i:41978603 original size:4 final size:4
Alignment explanation
Indices: 41978594--41978637 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
41978584 ATAACTACAT
* * *
41978594 ATAA ATAA ATAT ATTA TTAA ATAA AT-A ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
41978638 AGAAGTTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAA
Found at i:41978869 original size:20 final size:21
Alignment explanation
Indices: 41978844--41978890 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
41978834 ATCATTTCTT
*
41978844 TTAAAAAAAATAAAA-AAGGG
1 TTAAAAAAAATAAAAGAAGCG
* *
41978864 TTAAAAATAGTAAAAGAAGCG
1 TTAAAAAAAATAAAAGAAGCG
41978885 TTAAAA
1 TTAAAA
41978891 CAGATCTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.64, C:0.02, G:0.15, T:0.19
Consensus pattern (21 bp):
TTAAAAAAAATAAAAGAAGCG
Found at i:41980350 original size:30 final size:28
Alignment explanation
Indices: 41980316--41980609 Score: 176
Period size: 30 Copynumber: 9.9 Consensus size: 28
41980306 CGAACTTCTC
41980316 AAAAATCACATTTTGACCCATAAACTTTGT
1 AAAAATCACATTTTGACCC-TAAACTTT-T
*
41980346 AAAAATTACATTTTGACCCTCAAACTTTTTT
1 AAAAATCACATTTTGACCCT-AAAC--TTTT
* * * * *
41980377 CAAAATTACATTTTAACCTTAAACTTCTC
1 AAAAATCACATTTTGACCCTAAACTT-TT
41980406 AAAAAGT-ACATTTTTGACCCCTAAACTTTT
1 AAAAA-TCACA-TTTTGA-CCCTAAACTTTT
* * * * *
41980436 CTAATATTATATTTTGACCCCTACACTTTT
1 -AAAAATCACATTTTGA-CCCTAAACTTTT
* * *
41980466 CTAAAATTACATTTTCACTCCTAAACTTTT
1 -AAAAATCACATTTTGAC-CCTAAACTTTT
* * **
41980496 CAAAAATCACATTTTTACCCCCAAACTTCC
1 -AAAAATCACATTTTGA-CCCTAAACTTTT
* * **
41980526 AAAAATCACATTTTTACCGTCAAACTTCC
1 AAAAATCACATTTTGACCCT-AAACTTTT
* *
41980555 CAAAATCACATTTTTACCCTCAAACTTTT
1 AAAAATCACATTTTGACCCT-AAACTTTT
* * *
41980584 CAAAAATAACATTTTAACCCCAAACT
1 -AAAAATCACATTTTGACCCTAAACT
41980610 CTTCGAAACT
Statistics
Matches: 218, Mismatches: 33, Indels: 27
0.78 0.12 0.10
Matches are distributed among these distances:
28 4 0.02
29 64 0.29
30 114 0.52
31 33 0.15
32 3 0.01
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (28 bp):
AAAAATCACATTTTGACCCTAAACTTTT
Found at i:41980402 original size:60 final size:59
Alignment explanation
Indices: 41980303--41980626 Score: 212
Period size: 60 Copynumber: 5.5 Consensus size: 59
41980293 CTCAAAAGGT
* * * *
41980303 CCTCGAACTTCTCAAAAATCACATTTTGACCCATAAACTTTGTAAAAATTACATTTTGAC
1 CCTCAAACTTTTCTAAAATTACATTTTGACCCATAAACTTT-TAAAAATTACATTTTGAC
* * * * *
41980363 CCTCAAACTTTTTTCAAAATTACATTTT-AACCTTAAACTTCTCAAAAAGTACATTTTTGAC
1 CCTCAAACTTTTCT-AAAATTACATTTTGACCCATAAACTT-TTAAAAATTACA-TTTTGAC
* * * * * *
41980424 CC-CTAAACTTTTCTAATATTATATTTTGACCCCTACACTTTTCTAAAATTACATTTTCAC
1 CCTC-AAACTTTTCTAAAATTACATTTTGACCCATAAACTTTT-AAAAATTACATTTTGAC
* * * ** ** * *
41980484 TCCT-AAACTTTTCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCACATTTTTAC
1 -CCTCAAACTTTTCTAAAATTACATTTTGACCCATAAACTTTTAAAAATTACATTTTGAC
* * * * * * *
41980543 CGTCAAAC-TTCCCAAAATCACATTTTTACCC-TCAAACTTTTCAAAAATAACATTTTAAC
1 CCTCAAACTTTTCTAAAATTACATTTTGACCCAT-AAACTTTT-AAAAATTACATTTTGAC
* * *
41980602 CC-CAAACTCTTCGAAACTT-CATTTT
1 CCTCAAACTTTTCTAAAATTACATTTT
41980627 TGACTCCGTT
Statistics
Matches: 207, Mismatches: 45, Indels: 26
0.74 0.16 0.09
Matches are distributed among these distances:
58 40 0.19
59 40 0.19
60 77 0.37
61 50 0.24
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
CCTCAAACTTTTCTAAAATTACATTTTGACCCATAAACTTTTAAAAATTACATTTTGAC
Found at i:41980450 original size:91 final size:91
Alignment explanation
Indices: 41980308--41980598 Score: 269
Period size: 91 Copynumber: 3.2 Consensus size: 91
41980298 AAGGTCCTCG
*
41980308 AACTTCTCAAAAATCACA-TTTTGACCCATAAACTTTGTAAAAATTACATTTTGA-CCCTCAAAC
1 AACTTCTCAAAAATCACATTTTTGACCCCTAAACTTTGTAAAAATTACATTTTGACCCCT-AAAC
* *
41980371 TTTTTTCAAAATTACATTTTAAC-CTTA
65 TTTTCT-AAAATTACATTTTAACTCCTA
* * * *
41980398 AACTTCTCAAAAAGT-ACATTTTTGACCCCTAAACTTT-TCTAATATTATATTTTGACCCCTACA
1 AACTTCTCAAAAA-TCACATTTTTGACCCCTAAACTTTGT-AAAAATTACATTTTGACCCCTAAA
*
41980461 CTTTTCTAAAATTACATTTTCACTCCTA
64 CTTTTCTAAAATTACATTTTAACTCCTA
* * ** * * *
41980489 AACTTTTCAAAAATCACATTTTT-ACCCCCAAAC-TTCCAAAAATCACATTTTTA-CCGTCAAAC
1 AACTTCTCAAAAATCACATTTTTGACCCCTAAACTTTGTAAAAATTACATTTTGACCCCT-AAAC
* * * *
41980551 -TTCCCAAAATCACATTTTTAC-CCTCA
65 TTTTCTAAAATTACATTTTAACTCCT-A
* *
41980577 AACTTTTCAAAAATAACATTTT
1 AACTTCTCAAAAATCACATTTT
41980599 AACCCCAAAC
Statistics
Matches: 169, Mismatches: 23, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
87 3 0.02
88 42 0.25
89 16 0.09
90 42 0.25
91 62 0.37
92 4 0.02
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.37
Consensus pattern (91 bp):
AACTTCTCAAAAATCACATTTTTGACCCCTAAACTTTGTAAAAATTACATTTTGACCCCTAAACT
TTTCTAAAATTACATTTTAACTCCTA
Found at i:41980537 original size:29 final size:29
Alignment explanation
Indices: 41980468--41980609 Score: 151
Period size: 29 Copynumber: 4.9 Consensus size: 29
41980458 ACACTTTTCT
* * * * *
41980468 AAAATTACATTTTCACTCCTAAACTTTTCA
1 AAAATCACATTTTTACCCCCAAAC-TTCCA
41980498 AAAATCACATTTTTACCCCCAAACTTCCA
1 AAAATCACATTTTTACCCCCAAACTTCCA
** *
41980527 AAAATCACATTTTTACCGTCAAACTTCCC
1 AAAATCACATTTTTACCCCCAAACTTCCA
* *
41980556 AAAATCACATTTTTACCCTCAAACTTTTCA
1 AAAATCACATTTTTACCCCCAAAC-TTCCA
* *
41980586 AAAATAACA-TTTTAACCCCAAACT
1 AAAATCACATTTTTACCCCCAAACT
41980610 CTTCGAAACT
Statistics
Matches: 97, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
28 1 0.01
29 65 0.67
30 31 0.32
ACGTcount: A:0.39, C:0.28, G:0.01, T:0.32
Consensus pattern (29 bp):
AAAATCACATTTTTACCCCCAAACTTCCA
Found at i:41986184 original size:9 final size:9
Alignment explanation
Indices: 41986172--41986212 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
41986162 AAATAAATAA
41986172 AAAAGAAAG
1 AAAAGAAAG
41986181 AAAAGAAAG
1 AAAAGAAAG
41986190 AAAAG--AG
1 AAAAGAAAG
41986197 AAAAGAAA-
1 AAAAGAAAG
41986205 AAAAGAAA
1 AAAAGAAA
41986213 AAAGAAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.23
8 8 0.27
9 15 0.50
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:41986200 original size:7 final size:7
Alignment explanation
Indices: 41986155--41986244 Score: 85
Period size: 7 Copynumber: 12.6 Consensus size: 7
41986145 CAGATTCAAT
41986155 AAAGAAA
1 AAAGAAA
*
41986162 AAATAAA
1 AAAGAAA
41986169 TAAA-AAA
1 -AAAGAAA
41986176 GAAAGAAA
1 -AAAGAAA
*
41986184 AGAA-AGA
1 A-AAGAAA
*
41986191 AAAGAGA
1 AAAGAAA
41986198 AAAGAAAA
1 AAAG-AAA
41986206 AAAGAAA
1 AAAGAAA
41986213 AAAGAAA
1 AAAGAAA
*
41986220 AAAGGAA
1 AAAGAAA
41986227 AAAGAAA
1 AAAGAAA
*
41986234 ATAGAAA
1 AAAGAAA
41986241 AAAG
1 AAAG
41986245 GGGAAAAAGA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
6 2 0.03
7 54 0.77
8 14 0.20
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (7 bp):
AAAGAAA
Found at i:41986210 original size:15 final size:15
Alignment explanation
Indices: 41986179--41986234 Score: 78
Period size: 15 Copynumber: 3.7 Consensus size: 15
41986169 TAAAAAAGAA
41986179 AGAAAAGAAAGAAAAG
1 AGAAAAGAAA-AAAAG
41986195 AGAAAAGAAAAAAAG
1 AGAAAAGAAAAAAAG
* *
41986210 AAAAAAGAAAAAAGG
1 AGAAAAGAAAAAAAG
41986225 A-AAAAGAAAA
1 AGAAAAGAAAA
41986235 TAGAAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.24
15 19 0.50
16 10 0.26
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAAAG
Found at i:41986217 original size:36 final size:36
Alignment explanation
Indices: 41986155--41986258 Score: 97
Period size: 36 Copynumber: 2.9 Consensus size: 36
41986145 CAGATTCAAT
* * *
41986155 AAAGAAAAAATAAATAAAA-AAGAAAGAAAAGAAAGA
1 AAAGAGAAAAGAAA-AAAAGAAAAAAGAAAAGAAAGA
*
41986191 AAAGAGAAAAGAAAAAAAGAAAAAAGAAAA-AAGGA
1 AAAGAGAAAAGAAAAAAAGAAAAAAGAAAAGAAAGA
* *
41986226 AAA-AGAAAATAGAAAAAAGGGGAAAAAGAAAAG
1 AAAGAG-AAA-AGAAAAAA-AGAAAAAAGAAAAG
41986259 GGGAGGTCGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
34 2 0.04
35 14 0.25
36 30 0.53
37 11 0.19
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (36 bp):
AAAGAGAAAAGAAAAAAAGAAAAAAGAAAAGAAAGA
Found at i:41986242 original size:21 final size:21
Alignment explanation
Indices: 41986206--41986257 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
41986196 GAAAAGAAAA
41986206 AAAGAAAAAAGAAAAAAGGAA
1 AAAGAAAAAAGAAAAAAGGAA
*
41986227 AAAGAAAATAGAAAAAAGGGGAA
1 AAAGAAAAAAGAAAAAA--GGAA
41986250 AAAGAAAA
1 AAAGAAAA
41986258 GGGGAGGTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
21 16 0.57
23 12 0.43
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAGAAAAAAGGAA
Found at i:41987242 original size:50 final size:50
Alignment explanation
Indices: 41987188--41987777 Score: 438
Period size: 49 Copynumber: 11.9 Consensus size: 50
41987178 GTGAATTCGA
** * *
41987188 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGTAGCAACGACGAACCCAG
1 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * * * *
41987238 TACC-TAAGAAGATGTGATGGGAAAGGTTGAGACCGTAATGGCAAACCCGA
1 TACCTTAA-AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
*
41987288 TACC-TAAGAAGA--TGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
1 TACCTTAA-AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * * * **
41987336 TACCAT-GAAGATGTAAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAA
1 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * * * * * * *
41987385 TACCGT-GAAGATATAAAAGAAAAGGTTGAGGCCGCAATGGTGAACCCGA
1 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * *
41987434 TA-CTTAAGAAGATGTGATGGGAAAGGTTGAGGTCGCAACAGTGAACCCGG
1 TACCTTAA-AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * ** **
41987484 TACCATGAAAAGA--TGAAGGG-AAGGATTGAGGCCGCGATGGTAAATTCGG
1 TACC-TTAAAAGATGTGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGG
* * * * *
41987533 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGACGAACCTGG
1 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * *
41987583 TACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
1 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * *
41987632 TACC-TAAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGTGAACCCGG
1 TACCTTAA-AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
* * * ** * *
41987682 TACC--ACGAAGA-GATGAAGGG-AAGGATTGAGGCCGCGACAGTAAATCCAG
1 TACCTTA-AAAGATG-TGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACCCGG
* * * *
41987731 TACCTTAGACGATGTGATGGAAAAGGTTGAGGCCGCAACGGCGAACC
1 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
41987778 TAGCACCTTA
Statistics
Matches: 431, Mismatches: 88, Indels: 42
0.77 0.16 0.07
Matches are distributed among these distances:
47 4 0.01
48 53 0.12
49 179 0.42
50 177 0.41
51 15 0.03
52 3 0.01
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (50 bp):
TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
Found at i:41987471 original size:99 final size:99
Alignment explanation
Indices: 41987202--41987777 Score: 527
Period size: 99 Copynumber: 5.8 Consensus size: 99
41987192 TTAAAAGATG
* ** ** * *
41987202 TGAAGGGAAAGGTTGAGGTAGCAACGACGAACCCAGTACCTAAGAAGATGTGATGGGAAAGGTTG
1 TGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTTAAGAAGATGTGATGGGAAAGGTTG
* * *
41987267 AGACCGTAATGGCAAACCCGATACC-T-AAGAAGA
66 AGGCCGCAACGGCAAACCCGATACCATGAAG-AGA
** * * * * *
41987300 TGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGGTAC-CATGAAGATGTAAAGGGAAAGGTTG
1 TGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTTAAGAAGATGTGATGGGAAAGGTTG
* * * *
41987364 AGGCCGCAATGGCAAACCCAATACCGTGAAGATA
66 AGGCCGCAACGGCAAACCCGATACCATGAAGAGA
* * * *
41987398 TAAAAGAAAAGGTTGAGGCCGCAATGGTGAACCCGATACTTAAGAAGATGTGATGGGAAAGGTTG
1 TGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTTAAGAAGATGTGATGGGAAAGGTTG
* * ** * *
41987463 AGGTCGCAACAGTGAACCCGGTACCATGAAAAGA
66 AGGCCGCAACGGCAAACCCGATACCATGAAGAGA
* * * * **
41987497 TG-AAGGGAAGGATTGAGGCCGCGATGGTAAATTCGGTACCTT-AGAAGATGTGATGGGAAAGGT
1 TGAAAGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTA-CTTAAGAAGATGTGATGGGAAAGGT
* * * * * *
41987560 TGAGGCCGTAACGACGAACCTGGTACCATGAAGATA
64 TGAGGCCGCAACGGCAAACCCGATACCATGAAGAGA
* *
41987596 TGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATGTGATGGGAAAGGTTG
1 TGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTTAAGAAGATGTGATGGGAAAGGTTG
* ** * *
41987661 AGGCTGCAACGGTGAACCCGGTACCACGAAGAGA
66 AGGCCGCAACGGCAAACCCGATACCATGAAGAGA
* * * * * * * *
41987695 TG-AAGGGAAGGATTGAGGCCGCGACAGTAAATCCAGTACCTT-AGACGATGTGATGGAAAAGGT
1 TGAAAGGAAAGG-TTGAGGCCGCAACGGTGAACCCGGTA-CTTAAGAAGATGTGATGGGAAAGGT
*
41987758 TGAGGCCGCAACGGCGAACC
64 TGAGGCCGCAACGGCAAACC
41987778 TAGCACCTTA
Statistics
Matches: 392, Mismatches: 77, Indels: 17
0.81 0.16 0.03
Matches are distributed among these distances:
97 43 0.11
98 85 0.22
99 252 0.64
100 12 0.03
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (99 bp):
TGAAAGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACTTAAGAAGATGTGATGGGAAAGGTTG
AGGCCGCAACGGCAAACCCGATACCATGAAGAGA
Found at i:41987492 original size:148 final size:146
Alignment explanation
Indices: 41987196--41987669 Score: 445
Period size: 148 Copynumber: 3.2 Consensus size: 146
41987186 GATACCTTAA
** * * * * * * ** *
41987196 AAGATGTGAAGGGAAAGGTTGAGGTAGCAACGACGAACCCAGTACC-TAAGAAGATGTGATGGGA
1 AAGATGT-AAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAATACCGT-AGAAGATATAAAAGAA
* *
41987260 AAGGTTGAGACCGTAATGGCAAACCCGATACCTAAGAAGA-TGATGGGAAAGGTTGAGGCCGCAA
64 AAGGTTGAGGCCGTAATGGCGAACCCGATA-CTAAGAAGATTGATGGGAAAGGTTGAGGCCGCAA
*
41987324 CGGCGAACCCGGTACCATG
128 CGGTGAACCCGGTACCATG
41987343 AAGATGTAAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAATACCGT-GAAGATATAAAAGAAA
1 AAGATGT-AAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAATACCGTAGAAGATATAAAAGAAA
* * *
41987407 AGGTTGAGGCCGCAATGGTGAACCCGATACTTAAGAAGATGTGATGGGAAAGGTTGAGGTCGCAA
65 AGGTTGAGGCCGTAATGGCGAACCCGATAC-TAAGAAGAT-TGATGGGAAAGGTTGAGGCCGCAA
*
41987472 CAGTGAACCCGGTACCATG
128 CGGTGAACCCGGTACCATG
* * ** ** * * * ** *
41987491 AAAAGATG-AAGGG-AAGGATTGAGGCCGCGATGGTAAATTCGGTACCTTAGAAGATGTGATGGG
1 --AAGATGTAAGGGAAAGG-TTGAGGCCGCAATGGCAAACCCAATACCGTAGAAGATATAAAAGA
* * * * * * *
41987554 AAAGGTTGAGGCCGTAACGACGAACCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGCCGCA
63 AAAGGTTGAGGCCGTAATGGCGAACCCGATACTAAGAAGAT-TGATGGGAAAGGTTGAGGCCGCA
*
41987619 ACGGTGAACCCGGTACCTAAG
127 ACGGTGAACCCGGTACC-ATG
* *
41987640 AAGATGTGATGGGAAAGGTTGAGGCTGCAA
1 AAGATGT-AAGGGAAAGGTTGAGGCCGCAA
41987670 CGGTGAACCC
Statistics
Matches: 268, Mismatches: 47, Indels: 22
0.80 0.14 0.07
Matches are distributed among these distances:
145 1 0.00
146 44 0.16
147 49 0.18
148 113 0.42
149 51 0.19
150 10 0.04
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.17
Consensus pattern (146 bp):
AAGATGTAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAATACCGTAGAAGATATAAAAGAAAA
GGTTGAGGCCGTAATGGCGAACCCGATACTAAGAAGATTGATGGGAAAGGTTGAGGCCGCAACGG
TGAACCCGGTACCATG
Found at i:41987609 original size:198 final size:197
Alignment explanation
Indices: 41987196--41987779 Score: 701
Period size: 198 Copynumber: 3.0 Consensus size: 197
41987186 GATACCTTAA
* ** **
41987196 AAGATGTGAAGGGAAAGGTTGAGGTAGCAACGACGAACCC-AGTACCTAAGAAGATGTGATGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGA-TACCTAAGAAGATGTGATGGGA
* * * ** * *
41987260 AAGGTTGAGACCGTAATGGCAAACCCGATACC-T-AAGAAGATGATGGGAAAGG-TTGAGGCCGC
65 AAGGTTGAG-GCGCAACGGTGAACCCGGTACCATGAA-AAGATGAAGGG-AAGGATTGAGGCCGC
* ** * * * * * * *
41987322 AACGGCGAACCCGGTACCAT-GAAGATGTAAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAAT
127 GACGGTAAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTAAT
*
41987386 ACCGTG
192 ACCATG
* * * * *
41987392 AAGATATAAAAGAAAAGGTTGAGGCCGCAATGGTGAACCCGATACTTAAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTAAGAAGATGTGATGGGAA
* *
41987457 AGGTTGAGGTCGCAACAGTGAACCCGGTACCATGAAAAGATGAAGGGAAGGATTGAGGCCGCGAT
66 AGGTTGAGG-CGCAACGGTGAACCCGGTACCATGAAAAGATGAAGGGAAGGATTGAGGCCGCGAC
* * * **
41987522 GGTAAATTCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGACGAACCTGGTACC
130 GGTAAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTAATACC
41987587 ATG
195 ATG
*
41987590 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTAAGAAGATGTGATGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTAAGAAGATGTGATGGGAA
* *
41987655 AGGTTGAGGCTGCAACGGTGAACCCGGTACCACGAAGAGATGAAGGGAAGGATTGAGGCCGCGAC
66 AGGTTGAGGC-GCAACGGTGAACCCGGTACCATGAAAAGATGAAGGGAAGGATTGAGGCCGCGAC
* * * *
41987720 AGTAAATCCAGTACCTTAGACGATGTGATGGAAAAGGTTGAGGCCGCAACGGCGAACCTA
130 GGTAAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTA
41987780 GCACCTTAGA
Statistics
Matches: 328, Mismatches: 53, Indels: 12
0.83 0.13 0.03
Matches are distributed among these distances:
196 80 0.24
197 36 0.11
198 212 0.65
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (197 bp):
AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTAAGAAGATGTGATGGGAA
AGGTTGAGGCGCAACGGTGAACCCGGTACCATGAAAAGATGAAGGGAAGGATTGAGGCCGCGACG
GTAAATCCGGTACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGCGAACCTAATACCA
TG
Found at i:41987789 original size:50 final size:50
Alignment explanation
Indices: 41987188--41987777 Score: 495
Period size: 50 Copynumber: 11.9 Consensus size: 50
41987178 GTGAATTCGA
* * ** ** *
41987188 TACCTTAAAAGATGTGAAGGGAAAGGTTGAGGTAGCAACGACGAACCCAG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* * * * ** *
41987238 TACCTAAGAAGATGTGATGGGAAAGGTTGAGACCGTAATGGCAAACCCGA
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* *
41987288 TACCTAAGAAGA--TGATGGGAAAGGTTGAGGCCGCAACGGCGAACCCGG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* * * * ** **
41987336 TACCAT-GAAGATGTAAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCAA
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* * * ** * * *
41987385 TACCGT-GAAGATATAAAAGAAAAGGTTGAGGCCGCAATGGTGAACCCGA
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* *
41987434 TA-CTTAAGAAGATGTGATGGGAAAGGTTGAGGTCGCAACAGTGAACCCGG
1 TACCTT-AGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* * * * * * **
41987484 TACCAT-GAA-AAGATGAAGGG-AAGGATTGAGGCCGCGATGGTAAATTCGG
1 TACCTTAGAAGATG-TGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGG
* ** *
41987533 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGTAACGACGAACCTGG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* * *
41987583 TACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* *
41987632 TACCTAAGAAGATGTGATGGGAAAGGTTGAGGCTGCAACGGTGAACCCGG
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
* * * * * *
41987682 TACC--ACGAAGA-GATGAAGGG-AAGGATTGAGGCCGCGACAGTAAATCCAG
1 TACCTTA-GAAGATG-TGATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCGG
* * *
41987731 TACCTTAGACGATGTGATGGAAAAGGTTGAGGCCGCAACGGCGAACC
1 TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACC
41987778 TAGCACCTTA
Statistics
Matches: 431, Mismatches: 91, Indels: 36
0.77 0.16 0.06
Matches are distributed among these distances:
47 5 0.01
48 49 0.11
49 179 0.42
50 184 0.43
51 14 0.03
ACGTcount: A:0.34, C:0.17, G:0.33, T:0.16
Consensus pattern (50 bp):
TACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCGCAACGGTGAACCCGG
Found at i:41988225 original size:39 final size:39
Alignment explanation
Indices: 41988182--41988281 Score: 128
Period size: 39 Copynumber: 2.6 Consensus size: 39
41988172 CCATTAGCAA
* *
41988182 TTACCCCGAGCTTGGGGCAGATTACAACCATCCGATCTT
1 TTACCCCGAGCTTGGGGCAGATAACAACCATCCGATCTC
* * * * * *
41988221 TTACCCCGAGCCTGGGGTAAATAACTATCATTCGATCTC
1 TTACCCCGAGCTTGGGGCAGATAACAACCATCCGATCTC
41988260 TTACCCCGAGCTTGGGGCAGAT
1 TTACCCCGAGCTTGGGGCAGAT
41988282 CACCATCAGC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (39 bp):
TTACCCCGAGCTTGGGGCAGATAACAACCATCCGATCTC
Found at i:41988313 original size:43 final size:43
Alignment explanation
Indices: 41988249--41988448 Score: 125
Period size: 43 Copynumber: 4.8 Consensus size: 43
41988239 AAATAACTAT
* *
41988249 CATTCGATCTCTTACCCCGAGCTTGGGGCAGATCACCATCAGC
1 CATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGC
* * * * *
41988292 CATTTGATCTTTTACCTCGAGCCTAGGGTAGATCACCATCAAC
1 CATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGC
* ** * * * *
41988335 CA----ATCTCTTACCCCGAGCCCAAAGCTTGGGGT-A-GATTGAAGC
1 CATTCGATCTCTTACCCCGAGCCTAGGGC---AGATCACCA-T-CAGC
* *
41988377 CATCCGATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGC
1 CATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGC
41988420 CA----ATCTCTTACCCCGAGCCT-GGAGCAGAT
1 CATTCGATCTCTTACCCCGAGCCTAGG-GCAGAT
41988449 TGCAATCATC
Statistics
Matches: 120, Mismatches: 25, Indels: 28
0.69 0.14 0.16
Matches are distributed among these distances:
38 1 0.01
39 41 0.34
40 1 0.01
41 2 0.02
42 6 0.05
43 45 0.38
44 2 0.02
45 1 0.01
46 21 0.17
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (43 bp):
CATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACCATCAGC
Found at i:41988321 original size:82 final size:78
Alignment explanation
Indices: 41988064--41988448 Score: 253
Period size: 78 Copynumber: 4.9 Consensus size: 78
41988054 TGAAGATTCT
* * * * * * *
41988064 GATCTTTTACCCCGAGCCTGGGGTAAATCA-TAGTCAGCCAATCTCTTACCCCGAGCCTAGGACA
1 GATCTTTTACCCCGAGCCTAGGGTAAATAACCA-TCAACCAATCTCTTACCCCGAGCTTGGGGCA
** *
41988128 GATTGCAGCCATCC
65 GATCACAACCATCC
* * * * * * *
41988142 AATCTCTTATCCCGAGCCTAGGGCAAATCACCAT-TAGCAA----TTACCCCGAGCTTGGGGCAG
1 GATCTTTTACCCCGAGCCTAGGGTAAATAACCATCAACCAATCTCTTACCCCGAGCTTGGGGCAG
*
41988202 ATTACAACCATCC
66 ATCACAACCATCC
* * ** *
41988215 GATCTTTTACCCCGAGCCTGGGGTAAATAACTATCATTCGATCTCTTACCCCGAGCTTGGGGCAG
1 GATCTTTTACCCCGAGCCTAGGGTAAATAACCATCAACCAATCTCTTACCCCGAGCTTGGGGCAG
**
41988280 ATCACCATCAGCCATTT
66 ATCA-CA--A-CCATCC
* * *
41988297 GATCTTTTACCTCGAGCCTAGGGTAGATCACCATCAACCAATCTCTTACCCCGAGCCCAAAGCTT
1 GATCTTTTACCCCGAGCCTAGGGTAAATAACCATCAACCAATCTCTTACCCC--G-----AGCTT
* * *
41988362 GGGGTAGATTGA-AGCCATCC
59 GGGGCAGA-TCACAACCATCC
* * * * * * * *
41988382 GATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGAGCAG
1 GATCTTTTACCCCGAGCCTAGGGTAAATAACCATCAACCAATCTCTTACCCCGAGCTTGGGGCAG
41988447 AT
66 AT
41988449 TGCAATCATC
Statistics
Matches: 240, Mismatches: 49, Indels: 37
0.74 0.15 0.11
Matches are distributed among these distances:
73 55 0.23
74 2 0.01
77 4 0.02
78 59 0.25
79 3 0.01
81 1 0.00
82 48 0.20
83 1 0.00
84 1 0.00
85 51 0.21
88 1 0.00
89 12 0.05
90 2 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.23
Consensus pattern (78 bp):
GATCTTTTACCCCGAGCCTAGGGTAAATAACCATCAACCAATCTCTTACCCCGAGCTTGGGGCAG
ATCACAACCATCC
Found at i:41988447 original size:39 final size:39
Alignment explanation
Indices: 41988383--41988466 Score: 107
Period size: 39 Copynumber: 2.2 Consensus size: 39
41988373 AAGCCATCCG
*
41988383 ATCTCTTACCCCGAGCCTAAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTAAGGCAGATCACAATCAGCCA
* ** *
41988422 ATCTCTTACCCCGAGCCT-GGAGCAGATTGCAATCATCCA
1 ATCTCTTACCCCGAGCCTAAG-GCAGATCACAATCAGCCA
41988461 ATCTCT
1 ATCTCT
41988467 GAAAAAAAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 1 0.03
39 38 0.97
ACGTcount: A:0.26, C:0.36, G:0.15, T:0.23
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTAAGGCAGATCACAATCAGCCA
Found at i:41988974 original size:17 final size:17
Alignment explanation
Indices: 41988954--41989005 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
41988944 CCAATTTTAA
*
41988954 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
41988971 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
41988988 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
41989005 A
1 A
41989006 ATTAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:41988982 original size:6 final size:6
Alignment explanation
Indices: 41988949--41989006 Score: 57
Period size: 6 Copynumber: 9.8 Consensus size: 6
41988939 TGAGCCCAAT
* * * *
41988949 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41988996 TTTAAA TTTAA
1 TTTAAA TTTAA
41989007 TTAAAAAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
5 8 0.19
6 29 0.67
7 6 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (6 bp):
TTTAAA
Found at i:41988999 original size:23 final size:23
Alignment explanation
Indices: 41988950--41989006 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
41988940 GAGCCCAATT
*
41988950 TTAAATTTTAAATTTTAATTTATT
1 TTAAA-TTTAAATTTTAATTTAAT
* *
41988974 TTAAGTTTAAA-TTTATTTTAAAT
1 TTAAATTTAAATTTTAATTT-AAT
41988997 TTAAATTTAA
1 TTAAATTTAA
41989007 TTAAAAAAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 7 0.25
23 17 0.61
24 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTAAATTTAAATTTTAATTTAAT
Found at i:41989537 original size:4 final size:4
Alignment explanation
Indices: 41989528--41989571 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
41989518 GTTTTTACAT
* * *
41989528 ATAA ATAA ATAT ATTA TTAA ATAA AT-A ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
41989572 AGAAGTTGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (4 bp):
ATAA
Found at i:41990631 original size:30 final size:29
Alignment explanation
Indices: 41990584--41990855 Score: 200
Period size: 30 Copynumber: 9.3 Consensus size: 29
41990574 CTCAGGAGGT
* *
41990584 CCTCGAACTTCTCAAAAATCATATTTTGAC
1 CCTCAAACTTCT-AAAAATCACATTTTGAC
*
41990614 CCTCAAACTTCGTAAAAATTACATTTTGAC
1 CCTCAAACTTC-TAAAAATCACATTTTGAC
* * * * *
41990644 CCTTGAATATTTCT-AATATTACATTTTAAC
1 CC-TCAA-ACTTCTAAAAATCACATTTTGAC
*
41990674 CCT-AAACTTTTTCT-AAAATCACATTTTTA-
1 CCTCAAAC---TTCTAAAAATCACATTTTGAC
* * *
41990703 CCTCGAACTTCCAAAAATCACATTTTTAC
1 CCTCAAACTTCTAAAAATCACATTTTGAC
* * *
41990732 CCCCAAACTTCCAAAAATCATATTTT-AC
1 CCTCAAACTTCTAAAAATCACATTTTGAC
** *
41990760 CCTTGAACTTCTAAAAATCACATTTTTACC
1 CCTCAAACTTCTAAAAATCACATTTTGA-C
*
41990790 CCCCAAACTT-TCAAAAATCACATTTTGAC
1 CCTCAAACTTCT-AAAAATCACATTTTGAC
* * *
41990819 CATCGAACTT-TCCAAAATCACATTTTGAC
1 CCTCAAACTTCT-AAAAATCACATTTTGAC
41990848 CC-CAAACT
1 CCTCAAACT
41990856 CTTCGAAAAT
Statistics
Matches: 199, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
27 4 0.02
28 45 0.23
29 56 0.28
30 85 0.43
31 5 0.03
32 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (29 bp):
CCTCAAACTTCTAAAAATCACATTTTGAC
Found at i:41990741 original size:29 final size:29
Alignment explanation
Indices: 41990688--41990855 Score: 173
Period size: 29 Copynumber: 5.9 Consensus size: 29
41990678 AACTTTTTCT
* *
41990688 AAAATCACATTTTTA-CCTCGAACTTCCA
1 AAAATCACATTTTTACCCCCAAACTTCCA
41990716 AAAATCACATTTTTACCCCCAAACTTCCA
1 AAAATCACATTTTTACCCCCAAACTTCCA
* *** *
41990745 AAAATCATA-TTTTACCCTTGAACTTCTA
1 AAAATCACATTTTTACCCCCAAACTTCCA
*
41990773 AAAATCACATTTTTACCCCCCAAACTTTCA
1 AAAATCACATTTTTA-CCCCCAAACTTCCA
* ** *
41990803 AAAATCACATTTTGACCATCGAACTTTCC-
1 AAAATCACATTTTTACCCCCAAAC-TTCCA
*
41990832 AAAATCACATTTTGA-CCCCAAACT
1 AAAATCACATTTTTACCCCCAAACT
41990856 CTTCGAAAAT
Statistics
Matches: 115, Mismatches: 21, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
27 1 0.01
28 43 0.37
29 45 0.39
30 26 0.23
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (29 bp):
AAAATCACATTTTTACCCCCAAACTTCCA
Found at i:41990757 original size:57 final size:57
Alignment explanation
Indices: 41990584--41990855 Score: 228
Period size: 59 Copynumber: 4.7 Consensus size: 57
41990574 CTCAGGAGGT
* * * * * *
41990584 CCTCGAACTTCTCAAAAATCATATTTTGACCCTCAAACTTCGTAAAAATTACATTTTGA
1 CCTCGAACTTC-CAAAAATCACATTTTTACCCCCAAACTTC-CAAAAATCACATTTTTA
* * * * * * * * * *
41990643 CCCTTGAATATTTCTAATATTACA-TTTTAACCCTAAACTTTTTCTAAAATCACATTTTTA
1 -CCTCGAA-CTTCCAAAAATCACATTTTTACCCCCAAAC--TTCCAAAAATCACATTTTTA
*
41990703 CCTCGAACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCATA-TTTTA
1 CCTCGAACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCACATTTTTA
* * * *
41990759 CCCTTGAACTTCTAAAAATCACATTTTTACCCCCCAAACTTTCAAAAATCACATTTTGA
1 -CCTCGAACTTCCAAAAATCACATTTTTA-CCCCCAAACTTCCAAAAATCACATTTTTA
*
41990818 CCATCGAACTTTCC-AAAATCACATTTTGA-CCCCAAACT
1 CC-TCGAAC-TTCCAAAAATCACATTTTTACCCCCAAACT
41990856 CTTCGAAAAT
Statistics
Matches: 168, Mismatches: 35, Indels: 21
0.75 0.16 0.09
Matches are distributed among these distances:
56 5 0.03
57 46 0.27
58 33 0.20
59 51 0.30
60 29 0.17
61 4 0.02
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (57 bp):
CCTCGAACTTCCAAAAATCACATTTTTACCCCCAAACTTCCAAAAATCACATTTTTA
Found at i:41999685 original size:16 final size:16
Alignment explanation
Indices: 41999644--41999761 Score: 93
Period size: 16 Copynumber: 7.6 Consensus size: 16
41999634 TTTACTTAAA
* **
41999644 AAAGTCAACCCTGGTC
1 AAAGTCAACTCTTATC
41999660 AAAGTCAACTCTTATC
1 AAAGTCAACTCTTATC
*
41999676 AAAGTCAACTTTTATC
1 AAAGTCAACTCTTATC
** *
41999692 AAAGTTGA--CTTA-A
1 AAAGTCAACTCTTATC
41999705 AAGAGTCAA-TCTTATC
1 AA-AGTCAACTCTTATC
* *
41999721 AAAGTCAACCCTAATC
1 AAAGTCAACTCTTATC
*
41999737 AATGTCAACT-TTAGTC
1 AAAGTCAACTCTTA-TC
41999753 AAAGTCAAC
1 AAAGTCAAC
41999762 ACAACTAACC
Statistics
Matches: 80, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
13 2 0.03
14 7 0.09
15 12 0.15
16 59 0.74
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (16 bp):
AAAGTCAACTCTTATC
Found at i:42001939 original size:28 final size:25
Alignment explanation
Indices: 42001873--42001929 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
42001863 ACTTGTTCGA
42001873 CAAATTAAAAGAAAACTAATACCAC
1 CAAATTAAAAGAAAACTAATACCAC
42001898 CAAATTAAAAGAAAACTAATACCAC
1 CAAATTAAAAGAAAACTAATACCAC
42001923 CAAATTA
1 CAAATTA
42001930 TTGGAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.60, C:0.19, G:0.04, T:0.18
Consensus pattern (25 bp):
CAAATTAAAAGAAAACTAATACCAC
Found at i:42005687 original size:8 final size:8
Alignment explanation
Indices: 42005674--42005699 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
42005664 GACACTAATT
42005674 AATTTTAA
1 AATTTTAA
42005682 AATTTTAA
1 AATTTTAA
42005690 AATTTTAA
1 AATTTTAA
42005698 AA
1 AA
42005700 AAATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AATTTTAA
Found at i:42005706 original size:16 final size:16
Alignment explanation
Indices: 42005687--42005756 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 16
42005677 TTTAAAATTT
42005687 TAAAATTTTAAAAAAA
1 TAAAATTTTAAAAAAA
42005703 TAAAA-TTTAAAAAACA
1 TAAAATTTTAAAAAA-A
*
42005719 TTAAAATTATTTAAAAATA
1 -TAAAA-T-TTTAAAAAAA
* *
42005738 TACGAATTATAAAAAAA
1 TA-AAATTTTAAAAAAA
42005755 TA
1 TA
42005757 TTTTTAATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
15 9 0.20
16 6 0.14
17 15 0.34
18 3 0.07
19 3 0.07
20 8 0.18
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (16 bp):
TAAAATTTTAAAAAAA
Found at i:42005716 original size:17 final size:16
Alignment explanation
Indices: 42005687--42005726 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
42005677 TTTAAAATTT
*
42005687 TAAAATTTTAAAAAAA
1 TAAAATTTAAAAAAAA
*
42005703 TAAAATTTAAAAAACAT
1 TAAAATTTAAAAAA-AA
42005720 TAAAATT
1 TAAAATT
42005727 ATTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (16 bp):
TAAAATTTAAAAAAAA
Found at i:42009193 original size:15 final size:16
Alignment explanation
Indices: 42009165--42009197 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
42009155 TCGTTTTATT
*
42009165 ATTTATAAATAATAAA
1 ATTTATAAAAAATAAA
42009181 ATTT-TAAAAAATAAA
1 ATTTATAAAAAATAAA
42009196 AT
1 AT
42009198 AAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTATAAAAAATAAA
Found at i:42013503 original size:20 final size:22
Alignment explanation
Indices: 42013458--42013509 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 22
42013448 CCTGAATCAT
**
42013458 AAACTCTAAATCCTTAAACTTT
1 AAACTCTAAATCCTTAAACTAC
42013480 AAACT-TAAAT-CTTAAACTAC
1 AAACTCTAAATCCTTAAACTAC
*
42013500 AAACCCTAAA
1 AAACTCTAAA
42013510 CTTCGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 12 0.46
21 9 0.35
22 5 0.19
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (22 bp):
AAACTCTAAATCCTTAAACTAC
Found at i:42014202 original size:37 final size:37
Alignment explanation
Indices: 42014160--42014244 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
42014150 ACGTCAACAG
* * * *
42014160 AATGTTGAATTTAGGCATCAGATAAAATAGTATTAAT
1 AATGTTGAATTTAGACATCACATAAAAGAGAATTAAT
* *
42014197 AATGTTGAGTTTAGACATCACATATAAGAGAATTAAT
1 AATGTTGAATTTAGACATCACATAAAAGAGAATTAAT
42014234 AATGTTGAATT
1 AATGTTGAATT
42014245 GATTGCTCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.35
Consensus pattern (37 bp):
AATGTTGAATTTAGACATCACATAAAAGAGAATTAAT
Found at i:42016373 original size:6 final size:6
Alignment explanation
Indices: 42016362--42016422 Score: 63
Period size: 6 Copynumber: 10.2 Consensus size: 6
42016352 TGAAATTTGA
* *
42016362 TTAAAT TTAAAT TTAAA- GTAAAT TTAAAT AGGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
42016410 ATAAAT TTAAAT T
1 TTAAAT TTAAAT T
42016423 CAATTAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
5 8 0.18
6 32 0.71
8 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:42016383 original size:17 final size:17
Alignment explanation
Indices: 42016363--42016422 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
42016353 GAAATTTGAT
42016363 TAAATTTAAATTTAAAG
1 TAAATTTAAATTTAAAG
*
42016380 TAAATTTAAA--T-AGG
1 TAAATTTAAATTTAAAG
*
42016394 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAG
42016411 TAAATTTAAATT
1 TAAATTTAAATT
42016423 CAATTAAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 12 0.32
15 1 0.03
16 1 0.03
17 23 0.62
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAG
Found at i:42016399 original size:31 final size:31
Alignment explanation
Indices: 42016363--42016421 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
42016353 GAAATTTGAT
*
42016363 TAAATTTAAATTTAAAGTAAATTTAAATAGG
1 TAAATTTAAATTTAAAATAAATTTAAATAGG
42016394 TAAATTTAAATTTAAAATAAATTTAAAT
1 TAAATTTAAATTTAAAATAAATTTAAAT
42016422 TCAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (31 bp):
TAAATTTAAATTTAAAATAAATTTAAATAGG
Found at i:42016722 original size:76 final size:76
Alignment explanation
Indices: 42016626--42017451 Score: 1393
Period size: 76 Copynumber: 10.9 Consensus size: 76
42016616 CTATTCCGAT
* *
42016626 CTTCAATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42016691 TCTTGCTCTTA
66 TCTTGCTCTTA
* * *
42016702 CTT-ATATTTCAGAGATAAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGACAGGAAATG
1 CTTCA-ATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATG
42016766 ATCTTGCTCTTA
65 ATCTTGCTCTTA
* * *
42016778 CTTCAATTTTAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAAGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42016843 TCTTGCTCTTA
66 TCTTGCTCTTA
* *
42016854 CTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42016919 TCTTGCTCTTA
66 TCTTGCTCTTA
* * *
42016930 CTTTAATTTCAGAGATAAAGACTTGTTATCCAGCGTTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
*
42016995 TCTTACTCTTA
66 TCTTGCTCTTA
* * * *
42017006 CTTTAATTTCAGAGATAAAGACTTGTTATCCAGCGTTACTTCAATTTCAAGAGGATAAGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42017071 TCTTGCTCTTA
66 TCTTGCTCTTA
* *
42017082 CTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
*
42017147 TATTGCTCTTA
66 TCTTGCTCTTA
* * *
42017158 CTTCAATTTCAGAGATAAAGACTTGTTATCTAGCTTTACTTCAATTTCAAGAGGACAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42017223 TCTTGCTCTTA
66 TCTTGCTCTTA
42017234 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42017299 TCTTGCTCTTA
66 TCTTGCTCTTA
*
42017310 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
*
42017375 TCTTACTCTTA
66 TCTTGCTCTTA
*
42017386 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAATGA
1 CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
42017451 T
66 T
42017452 GTTTGATTGA
Statistics
Matches: 714, Mismatches: 34, Indels: 4
0.95 0.05 0.01
Matches are distributed among these distances:
75 1 0.00
76 712 1.00
77 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (76 bp):
CTTCAATTTCAGAGATAAAGACTTGTTATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGA
TCTTGCTCTTA
Found at i:42029435 original size:28 final size:28
Alignment explanation
Indices: 42029404--42029466 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
42029394 AAAACGGGAC
42029404 TTTTGGATACCCG-GGGGCAAAATGGTAA
1 TTTTGGA-ACCCGCGGGGCAAAATGGTAA
* *
42029432 TTTTGG-ACTCGCGGGGTAAAATGGTAA
1 TTTTGGAACCCGCGGGGCAAAATGGTAA
42029459 TTTTGGAA
1 TTTTGGAA
42029467 AGTTCGAGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 4 0.13
27 20 0.65
28 7 0.23
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.30
Consensus pattern (28 bp):
TTTTGGAACCCGCGGGGCAAAATGGTAA
Found at i:42029487 original size:29 final size:28
Alignment explanation
Indices: 42029417--42029609 Score: 150
Period size: 29 Copynumber: 6.7 Consensus size: 28
42029407 TGGATACCCG
* * *
42029417 GGGGCAAAATGGTAATTTTGG--ACTCGC
1 GGGGTAAAATGGTAATTTTGGAAAGT-TC
42029444 GGGGTAAAATGGTAATTTTGGAAAGTTC
1 GGGGTAAAATGGTAATTTTGGAAAGTTC
*
42029472 GAGGGTAAATTGGTAATTTTTTGGTGAAA--TC
1 G-GGGTAAAATGGTAA--TTTT-G-GAAAGTTC
*
42029503 GGGGTTAAAATGG-AATTTTAGAAAGTTC
1 GGGG-TAAAATGGTAATTTTGGAAAGTTC
*
42029531 GGCGGTAAATTGGTAATTTTTGGTGAAA--TC
1 GG-GGTAAAATGGTAA-TTTT-G-GAAAGTTC
42029561 GGGGTCAAAAATGG-AATTTTGGAAAGTTC
1 GGGGT--AAAATGGTAATTTTGGAAAGTTC
42029590 GGGGGTAAAATGGTAATTTT
1 -GGGGTAAAATGGTAATTTT
42029610 TGGACAGTCC
Statistics
Matches: 136, Mismatches: 9, Indels: 40
0.74 0.05 0.22
Matches are distributed among these distances:
26 4 0.03
27 24 0.18
28 25 0.18
29 34 0.25
30 20 0.15
31 20 0.15
32 5 0.04
33 4 0.03
ACGTcount: A:0.31, C:0.06, G:0.31, T:0.33
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGAAAGTTC
Found at i:42029611 original size:59 final size:58
Alignment explanation
Indices: 42029443--42029612 Score: 261
Period size: 59 Copynumber: 2.9 Consensus size: 58
42029433 TTTGGACTCG
*
42029443 CGGGGT-AAAATGGTAATTTTGGAAAGTTCGAGGGTAAATTGGTAATTTTTTGGTGAAAT
1 CGGGGTAAAAATGG-AATTTTGGAAAGTTCGGGGGTAAATTGGTAA-TTTTTGGTGAAAT
* * *
42029502 CGGGGTTAAAATGGAATTTTAGAAAGTTCGGCGGTAAATTGGTAATTTTTGGTGAAAT
1 CGGGGTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAATTGGTAATTTTTGGTGAAAT
*
42029560 CGGGGTCAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 CGGGGT-AAAAATGGAATTTTGGAAAGTTCGGGGGTAAATTGGTAATTTTTGG
42029613 ACAGTCCAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
58 19 0.19
59 76 0.75
60 7 0.07
ACGTcount: A:0.31, C:0.05, G:0.31, T:0.34
Consensus pattern (58 bp):
CGGGGTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAATTGGTAATTTTTGGTGAAAT
Found at i:42039658 original size:31 final size:31
Alignment explanation
Indices: 42039634--42039740 Score: 142
Period size: 31 Copynumber: 3.4 Consensus size: 31
42039624 TAAAATTTTA
*
42039634 AATATAATAATAAATGATATTTAAATAATTT
1 AATATAATGATAAATGATATTTAAATAATTT
* *
42039665 AATACAATGATAAATTATATTTAAATAATTT
1 AATATAATGATAAATGATATTTAAATAATTT
* *
42039696 AATATAATGATAACCTAAATATTTAAATAATTT
1 AATATAATGATAA-AT-GATATTTAAATAATTT
*
42039729 AGTATAATGATA
1 AATATAATGATA
42039741 CTAAATATAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
31 40 0.60
32 1 0.01
33 26 0.39
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (31 bp):
AATATAATGATAAATGATATTTAAATAATTT
Found at i:42039708 original size:16 final size:16
Alignment explanation
Indices: 42039658--42039708 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
42039648 TGATATTTAA
*
42039658 ATAATTTAATACAATG
1 ATAATTTAATATAATG
* *
42039674 ATAAATTATATTTAA--
1 ATAATTTA-ATATAATG
42039689 ATAATTTAATATAATG
1 ATAATTTAATATAATG
42039705 ATAA
1 ATAA
42039709 CCTAAATATT
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
14 5 0.19
15 7 0.26
16 11 0.41
17 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (16 bp):
ATAATTTAATATAATG
Found at i:42039723 original size:33 final size:32
Alignment explanation
Indices: 42039616--42039748 Score: 139
Period size: 31 Copynumber: 4.2 Consensus size: 32
42039606 ATGATATATA
* * *
42039616 AAATATTTTAAA-ATTTTAAATATAATAATAAAT
1 AAATA-TTTAAATAATTT-AATATAATGATAACT
* * *
42039649 -GATATTTAAATAATTTAATACAATGATAAAT
1 AAATATTTAAATAATTTAATATAATGATAACT
*
42039680 -TATATTTAAATAATTTAATATAATGATAACCT
1 AAATATTTAAATAATTTAATATAATGATAA-CT
*
42039712 AAATATTTAAATAATTTAGTATAATGAT-ACT
1 AAATATTTAAATAATTTAATATAATGATAACT
42039743 AAATAT
1 AAATAT
42039749 AAATTAATCT
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
31 54 0.61
32 9 0.10
33 25 0.28
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (32 bp):
AAATATTTAAATAATTTAATATAATGATAACT
Found at i:42042073 original size:15 final size:15
Alignment explanation
Indices: 42042033--42042075 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
42042023 CTTACTTTTC
*
42042033 AGATGCTGATGAAGA
1 AGATGATGATGAAGA
* * *
42042048 GGAGGAGGATGAAGA
1 AGATGATGATGAAGA
42042063 AGATGATGATGAA
1 AGATGATGATGAA
42042076 TTCGACAGTG
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.40, T:0.16
Consensus pattern (15 bp):
AGATGATGATGAAGA
Found at i:42061400 original size:3 final size:3
Alignment explanation
Indices: 42061392--42061418 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42061382 ATAAATCAAT
42061392 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
42061419 CTTTTTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:42086480 original size:18 final size:18
Alignment explanation
Indices: 42086457--42086493 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42086447 ACAATTCATA
42086457 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
42086475 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
42086493 T
1 T
42086494 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:42090471 original size:18 final size:18
Alignment explanation
Indices: 42090448--42090499 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
42090438 TTTTCAGTTA
42090448 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
42090466 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
42090484 TAATTAA--AAAATTATT
1 TAATTAATTAAAATTATT
42090500 CTTATTCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 8 0.26
17 7 0.23
18 16 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:42091578 original size:2 final size:2
Alignment explanation
Indices: 42091571--42091606 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42091561 GTCTCGTTAA
42091571 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42091607 ATATATATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:42091611 original size:2 final size:2
Alignment explanation
Indices: 42091606--42091640 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
42091596 TCTCTCTCTC
42091606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
42091641 GTGTATGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:42092584 original size:20 final size:21
Alignment explanation
Indices: 42092554--42092603 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
42092544 TAAGTTCCCT
42092554 TTTTTTGTTTTGATTAT-TGGG
1 TTTTTTGTTTT-ATTATCTGGG
*
42092575 TTTTTT-TTTTATTTTCTGGG
1 TTTTTTGTTTTATTATCTGGG
42092595 TTTTTTGTT
1 TTTTTTGTT
42092604 GTTGATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
19 4 0.15
20 14 0.54
21 8 0.31
ACGTcount: A:0.06, C:0.02, G:0.18, T:0.74
Consensus pattern (21 bp):
TTTTTTGTTTTATTATCTGGG
Found at i:42093233 original size:16 final size:16
Alignment explanation
Indices: 42093212--42093243 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
42093202 TGCATGTTAC
42093212 ATCAAAGAGCAAATTG
1 ATCAAAGAGCAAATTG
42093228 ATCAAAGAGCAAATTG
1 ATCAAAGAGCAAATTG
42093244 GTCCATTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (16 bp):
ATCAAAGAGCAAATTG
Found at i:42103077 original size:12 final size:12
Alignment explanation
Indices: 42103060--42103085 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42103050 AAGTAAATGC
42103060 TATAACTGTACT
1 TATAACTGTACT
42103072 TATAACTGTACT
1 TATAACTGTACT
42103084 TA
1 TA
42103086 AGAGAGCATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (12 bp):
TATAACTGTACT
Found at i:42105364 original size:3 final size:3
Alignment explanation
Indices: 42105356--42105381 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42105346 TACATCCCAA
42105356 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
42105382 TAATAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:42105386 original size:3 final size:3
Alignment explanation
Indices: 42105380--42105415 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
42105370 CAACAACAAC
42105380 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
42105416 GAATAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42106516 original size:21 final size:20
Alignment explanation
Indices: 42106478--42106546 Score: 84
Period size: 21 Copynumber: 3.4 Consensus size: 20
42106468 CAACGATCAA
** *
42106478 CGGTCAACGGTCAATCAACAC
1 CGGTCAAC-GTCGGTCAACAT
*
42106499 CGGTCAACGATCGGTCAACGT
1 CGGTCAACG-TCGGTCAACAT
42106520 CGGTCAACGTCGGTCAACAT
1 CGGTCAACGTCGGTCAACAT
42106540 CGGTCAA
1 CGGTCAA
42106547 TGGTTTGACT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
20 18 0.43
21 24 0.57
ACGTcount: A:0.28, C:0.30, G:0.25, T:0.17
Consensus pattern (20 bp):
CGGTCAACGTCGGTCAACAT
Found at i:42106522 original size:10 final size:10
Alignment explanation
Indices: 42106499--42106546 Score: 78
Period size: 10 Copynumber: 4.7 Consensus size: 10
42106489 CAATCAACAC
42106499 CGGTCAACGAT
1 CGGTCAACG-T
42106510 CGGTCAACGT
1 CGGTCAACGT
42106520 CGGTCAACGT
1 CGGTCAACGT
*
42106530 CGGTCAACAT
1 CGGTCAACGT
42106540 CGGTCAA
1 CGGTCAA
42106547 TGGTTTGACT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
10 27 0.75
11 9 0.25
ACGTcount: A:0.25, C:0.29, G:0.27, T:0.19
Consensus pattern (10 bp):
CGGTCAACGT
Found at i:42106601 original size:15 final size:15
Alignment explanation
Indices: 42106583--42106612 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42106573 TGGTTCATTT
42106583 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
42106598 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
42106613 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:42113357 original size:15 final size:15
Alignment explanation
Indices: 42113337--42113367 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42113327 GATTATATGT
42113337 ACTTTTTGATATGAA
1 ACTTTTTGATATGAA
42113352 ACTTTTTGATATGAA
1 ACTTTTTGATATGAA
42113367 A
1 A
42113368 AATTGAAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.06, G:0.13, T:0.45
Consensus pattern (15 bp):
ACTTTTTGATATGAA
Found at i:42114456 original size:6 final size:7
Alignment explanation
Indices: 42114440--42114464 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42114430 TCAAATAATA
42114440 TTTTTCT
1 TTTTTCT
42114447 TTTTTCT
1 TTTTTCT
42114454 TTTTTCT
1 TTTTTCT
42114461 TTTT
1 TTTT
42114465 AAAATATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTCT
Found at i:42114967 original size:14 final size:14
Alignment explanation
Indices: 42114935--42114988 Score: 74
Period size: 14 Copynumber: 3.9 Consensus size: 14
42114925 AACAAAACGA
42114935 TAAAATA-AATAAT
1 TAAAATATAATAAT
*
42114948 TAAAATATAATATT
1 TAAAATATAATAAT
*
42114962 TTAAATATAAATAAT
1 TAAAATAT-AATAAT
42114977 TAAAATATAATA
1 TAAAATATAATA
42114989 TAAATAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 7 0.20
14 16 0.46
15 12 0.34
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAAAATATAATAAT
Found at i:42114976 original size:29 final size:28
Alignment explanation
Indices: 42114935--42114989 Score: 101
Period size: 29 Copynumber: 1.9 Consensus size: 28
42114925 AACAAAACGA
42114935 TAAAATAAATAATTAAAATATAATATTT
1 TAAAATAAATAATTAAAATATAATATTT
42114963 TAAATATAAATAATTAAAATATAATAT
1 TAAA-ATAAATAATTAAAATATAATAT
42114990 AAATAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
TAAAATAAATAATTAAAATATAATATTT
Found at i:42115000 original size:29 final size:28
Alignment explanation
Indices: 42114934--42115001 Score: 100
Period size: 29 Copynumber: 2.4 Consensus size: 28
42114924 TAACAAAACG
*
42114934 ATAAAATAAATAATTAAAATATAATATT
1 ATAAAATAAATAATTAAAATATAATATA
*
42114962 TTAAATATAAATAATTAAAATATAATATAA
1 ATAAA-ATAAATAATTAAAATATAATAT-A
42114992 ATAAAATAAA
1 ATAAAATAAA
42115002 AGTAATTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 27 0.77
30 4 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (28 bp):
ATAAAATAAATAATTAAAATATAATATA
Found at i:42115639 original size:2 final size:2
Alignment explanation
Indices: 42115632--42115657 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42115622 TACTTTGCGC
42115632 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
42115658 AATGCAGCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42129477 original size:23 final size:22
Alignment explanation
Indices: 42129436--42129478 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
42129426 CCATATACAT
42129436 TTAATTTTTTATTTATTTAAAA
1 TTAATTTTTTATTTATTTAAAA
42129458 TTAACTTTTTCTATTT-TTTAA
1 TTAA-TTTTT-TATTTATTTAA
42129479 GTGTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 10 0.53
24 5 0.26
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TTAATTTTTTATTTATTTAAAA
Found at i:42144041 original size:3 final size:3
Alignment explanation
Indices: 42144033--42144062 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42144023 AGCTATGACC
42144033 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
42144063 GGCTGCTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:42149130 original size:28 final size:27
Alignment explanation
Indices: 42149098--42149160 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
42149088 TTTTCCTCTC
42149098 ATTTTCTCTCACTTTATCTATTTTTTAA
1 ATTTTCTCT-ACTTTATCTATTTTTTAA
* * *
42149126 ATTTTCATCTATTTTATTTATTTTTTGA
1 ATTTTC-TCTACTTTATCTATTTTTTAA
42149154 ATTTTCT
1 ATTTTCT
42149161 ATGTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.87
29 3 0.10
ACGTcount: A:0.21, C:0.13, G:0.02, T:0.65
Consensus pattern (27 bp):
ATTTTCTCTACTTTATCTATTTTTTAA
Found at i:42152465 original size:29 final size:30
Alignment explanation
Indices: 42152416--42152477 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
42152406 AATAGTTAAT
*
42152416 AAATAATAAAATTGTATTTTAA-CCTTTTA
1 AAATAATAAAATTGTAATTTAATCCTTTTA
* *
42152445 AAATTATAAAACTT-TAATTTAATCTTTTTA
1 AAATAATAAAA-TTGTAATTTAATCCTTTTA
42152475 AAA
1 AAA
42152478 ATTCTGAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (30 bp):
AAATAATAAAATTGTAATTTAATCCTTTTA
Found at i:42155097 original size:22 final size:21
Alignment explanation
Indices: 42155057--42155103 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
42155047 TGATCTAAGG
* *
42155057 AAAAATAAAAGAAACAGAATT
1 AAAAATAAAAAAAACAGAACT
*
42155078 AAAAATAAAATAAAATAGAACT
1 AAAAATAAAA-AAAACAGAACT
42155100 AAAA
1 AAAA
42155104 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAAAAACAGAACT
Found at i:42155941 original size:19 final size:19
Alignment explanation
Indices: 42155917--42155959 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42155907 AAACATAAAT
42155917 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
42155936 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
42155955 TAAAT
1 TAAAT
42155960 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:42157547 original size:18 final size:18
Alignment explanation
Indices: 42157508--42157551 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
42157498 TTTCCTGGAC
42157508 AAAAATAAATAAATAAAT
1 AAAAATAAATAAATAAAT
*
42157526 -AAAATAAGATAGA-AAAT
1 AAAAATAA-ATAAATAAAT
42157543 AAAAATAAA
1 AAAAATAAA
42157552 AATAATTAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAAATAAATAAATAAAT
Found at i:42161082 original size:21 final size:21
Alignment explanation
Indices: 42161056--42161095 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42161046 ATAGATGCCT
42161056 CAGTTT-TCTTTTGAAAATCCA
1 CAGTTTGT-TTTTGAAAATCCA
*
42161077 CAGTTTGTTTTTGGAAATC
1 CAGTTTGTTTTTGAAAATC
42161096 TATAAATTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.25, C:0.15, G:0.15, T:0.45
Consensus pattern (21 bp):
CAGTTTGTTTTTGAAAATCCA
Found at i:42162665 original size:21 final size:22
Alignment explanation
Indices: 42162619--42162680 Score: 74
Period size: 22 Copynumber: 2.9 Consensus size: 22
42162609 TGATCTAAGG
* *
42162619 AAAAATAAAAG-AAACAGAATT
1 AAAAATAAAAGAAAATAGAACT
42162640 AAAAATAAAAGAAAATAGAACT
1 AAAAATAAAAGAAAATAGAACT
*
42162662 AAAAGA-AATAGAAAATAGA
1 AAAA-ATAAAAGAAAATAGA
42162681 GAAGTCGAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
21 11 0.31
22 24 0.67
23 1 0.03
ACGTcount: A:0.73, C:0.03, G:0.11, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAACT
Found at i:42162670 original size:15 final size:16
Alignment explanation
Indices: 42162645--42162674 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42162635 GAATTAAAAA
42162645 TAAAAGAAAATAGAAC
1 TAAAAGAAAATAGAAC
42162661 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
42162675 AATAGAGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.03, G:0.13, T:0.13
Consensus pattern (16 bp):
TAAAAGAAAATAGAAC
Found at i:42163502 original size:19 final size:19
Alignment explanation
Indices: 42163478--42163520 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
42163468 AAACATAAAT
42163478 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
42163497 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
42163516 TAAAT
1 TAAAT
42163521 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:42164587 original size:19 final size:20
Alignment explanation
Indices: 42164550--42164589 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42164540 AAAACAATAA
*
42164550 AGACGTTTATTATTTTTATT
1 AGACATTTATTATTTTTATT
42164570 AGACATTTATTA-TTTTATT
1 AGACATTTATTATTTTTATT
42164589 A
1 A
42164590 TTCTACATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (20 bp):
AGACATTTATTATTTTTATT
Found at i:42167135 original size:3 final size:3
Alignment explanation
Indices: 42167123--42167166 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
42167113 GATAAACAAG
*
42167123 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42167167 GAAAAGTAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:42168172 original size:30 final size:31
Alignment explanation
Indices: 42168102--42168174 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
42168092 AATTTAGTGT
* * ** *
42168102 AATTATACACATGGAACTTTGATTGTGGTTT
1 AATTATATACATGAAACTTTGATTGTAATTC
*
42168133 AAATATATACATGAAACTTTGATT-TAATTC
1 AATTATATACATGAAACTTTGATTGTAATTC
42168163 AATTATATACAT
1 AATTATATACAT
42168175 CTAAAGAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 14 0.40
31 21 0.60
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (31 bp):
AATTATATACATGAAACTTTGATTGTAATTC
Found at i:42190376 original size:15 final size:16
Alignment explanation
Indices: 42190348--42190377 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42190338 TAACCCCACC
42190348 GCCTCCGCCGCTTTGG
1 GCCTCCGCCGCTTTGG
42190364 GCCTCCG-CGCTTTG
1 GCCTCCGCCGCTTTG
42190378 ACCTAACGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.43, G:0.30, T:0.27
Consensus pattern (16 bp):
GCCTCCGCCGCTTTGG
Found at i:42194317 original size:37 final size:37
Alignment explanation
Indices: 42194267--42194343 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
42194257 CTCAGGTCTT
*
42194267 TAACGGATCATATTAAGAAGTTCTTTTAAGTATAATA
1 TAACGGATCATATTAAGAAGTACTTTTAAGTATAATA
* *
42194304 TAACGGGTCATATTAGGAAGTACTTTTAAGTATAATA
1 TAACGGATCATATTAAGAAGTACTTTTAAGTATAATA
42194341 TAA
1 TAA
42194344 GTTATTAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (37 bp):
TAACGGATCATATTAAGAAGTACTTTTAAGTATAATA
Found at i:42194702 original size:12 final size:12
Alignment explanation
Indices: 42194685--42194713 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42194675 CATTACAGTG
42194685 CATTCGAATCCA
1 CATTCGAATCCA
42194697 CATTCGAATCCA
1 CATTCGAATCCA
42194709 CATTC
1 CATTC
42194714 TCTTACATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.31, C:0.34, G:0.07, T:0.28
Consensus pattern (12 bp):
CATTCGAATCCA
Found at i:42195342 original size:6 final size:6
Alignment explanation
Indices: 42195331--42195358 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42195321 TGTGCTCTTT
42195331 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTT
42195359 CTAAAGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:42195632 original size:20 final size:20
Alignment explanation
Indices: 42195588--42195625 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42195578 AATATATTTA
*
42195588 AAATTTATATTATATAAAAT
1 AAATATATATTATATAAAAT
*
42195608 AAATATATATTATTTAAA
1 AAATATATATTATATAAA
42195626 TTCAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATATATATTATATAAAAT
Found at i:42195916 original size:43 final size:43
Alignment explanation
Indices: 42195868--42195955 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
42195858 GTAAGCATTT
*
42195868 TTAATCCGATAAAATTATCAATATATAAATACCAAATTTTTTC
1 TTAATCCGACAAAATTATCAATATATAAATACCAAATTTTTTC
* * * *
42195911 TTAATCCGACAAGATTGTCGATATATAAATACCAAGTTTTTTC
1 TTAATCCGACAAAATTATCAATATATAAATACCAAATTTTTTC
42195954 TT
1 TT
42195956 TATAGTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (43 bp):
TTAATCCGACAAAATTATCAATATATAAATACCAAATTTTTTC
Found at i:42197392 original size:17 final size:17
Alignment explanation
Indices: 42197372--42197415 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
42197362 TTCAAACTCC
42197372 TTTTATATTTTTAATTT
1 TTTTATATTTTTAATTT
**
42197389 TTTTATAAATTTAATTT
1 TTTTATATTTTTAATTT
*
42197406 CTTTAT-TTTT
1 TTTTATATTTT
42197416 GGATACAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTATATTTTTAATTT
Found at i:42201284 original size:21 final size:21
Alignment explanation
Indices: 42201260--42201320 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
42201250 GTTTGACTTG
42201260 GATTACGTTTTAATCATTGAC
1 GATTACGTTTTAATCATTGAC
** *
42201281 GATTTTG-TTTGA-C-TTG--
1 GATTACGTTTTAATCATTGAC
42201297 GATTACGTTTTAATCATTGAC
1 GATTACGTTTTAATCATTGAC
42201318 GAT
1 GAT
42201321 ATTGTTTTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 10
0.64 0.13 0.22
Matches are distributed among these distances:
16 5 0.17
17 4 0.14
18 4 0.14
19 4 0.14
20 4 0.14
21 8 0.28
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.46
Consensus pattern (21 bp):
GATTACGTTTTAATCATTGAC
Found at i:42201296 original size:37 final size:37
Alignment explanation
Indices: 42201246--42201327 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
42201236 AACTAGTCAC
42201246 TTTTGTTTGACTTGGATTACGTTTTAATCATTGACGA
1 TTTTGTTTGACTTGGATTACGTTTTAATCATTGACGA
42201283 TTTTGTTTGACTTGGATTACGTTTTAATCATTGACGA
1 TTTTGTTTGACTTGGATTACGTTTTAATCATTGACGA
*
42201320 TATTGTTT
1 TTTTGTTT
42201328 TGTTATGAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.21, C:0.10, G:0.18, T:0.51
Consensus pattern (37 bp):
TTTTGTTTGACTTGGATTACGTTTTAATCATTGACGA
Found at i:42202919 original size:23 final size:26
Alignment explanation
Indices: 42202873--42202919 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
42202863 TAATGACGTT
*
42202873 AAAAAAATATCAAGTTAATTAATAAA
1 AAAAAAATATCAAGTTAATCAATAAA
42202899 AAAAAAAT-TCAAG-T-ATCAATA
1 AAAAAAATATCAAGTTAATCAATA
42202920 TGGAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 6 0.30
24 1 0.05
25 5 0.25
26 8 0.40
ACGTcount: A:0.64, C:0.06, G:0.04, T:0.26
Consensus pattern (26 bp):
AAAAAAATATCAAGTTAATCAATAAA
Found at i:42203616 original size:33 final size:33
Alignment explanation
Indices: 42203560--42203638 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
42203550 CATCACATCA
* *
42203560 TTCA-TAATTTTTTTCAATTATTTA-ATA-ATAT
1 TTCAGTAATTTTTTCCAATCATTTACATATA-AT
42203591 TTCAGTAATTTTTTCCATATCATTTACATATAAT
1 TTCAGTAATTTTTTCCA-ATCATTTACATATAAT
*
42203625 TTTAGTAATTTTTT
1 TTCAGTAATTTTTT
42203639 TTATCCCGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
31 4 0.10
32 11 0.27
33 7 0.17
34 18 0.44
35 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.03, T:0.57
Consensus pattern (33 bp):
TTCAGTAATTTTTTCCAATCATTTACATATAAT
Found at i:42203990 original size:25 final size:22
Alignment explanation
Indices: 42203953--42204007 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
42203943 ATTTATTGAA
42203953 ATTTTTTGTATACTA-ATCTTAAT
1 ATTTTTT-TATA-TACATCTTAAT
42203976 ATTTTTTTATGATACATCTTAAT
1 ATTTTTTTAT-ATACATCTTAAT
*
42203999 ATTATTTTA
1 ATTTTTTTA
42204008 ATGTTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.31, C:0.07, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTTTTTATATACATCTTAAT
Found at i:42207221 original size:5 final size:6
Alignment explanation
Indices: 42207195--42207219 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
42207185 TAAAACATGC
42207195 AAGAAA AAGAAA AAGAAA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA A
42207220 GATAGATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:42210901 original size:29 final size:30
Alignment explanation
Indices: 42210860--42210928 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
42210850 AAAATACAAT
42210860 AATC-AAATTTATGTACAAAATT-ACATAA
1 AATCAAAATTTATGTACAAAATTAACATAA
* *
42210888 AATCAAAATTTATGTATATAATTACACATAA
1 AATCAAAATTTATGTACAAAATTA-ACATAA
*
42210919 AATCATAATT
1 AATCAAAATT
42210929 AACGTATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 16 0.46
31 15 0.43
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (30 bp):
AATCAAAATTTATGTACAAAATTAACATAA
Found at i:42211991 original size:32 final size:32
Alignment explanation
Indices: 42211927--42211988 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
42211917 AAATAATATA
*
42211927 AAAAATTATTAACTAATTACATATTATTTATT
1 AAAAATTATTAACTAATAACATATTATTTATT
*
42211959 AAAAATTATTTA-TAATAACA-A-TATTTATT
1 AAAAATTATTAACTAATAACATATTATTTATT
42211988 A
1 A
42211989 TTAGTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 9 0.32
30 1 0.04
31 7 0.25
32 11 0.39
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (32 bp):
AAAAATTATTAACTAATAACATATTATTTATT
Found at i:42212784 original size:20 final size:21
Alignment explanation
Indices: 42212737--42212785 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
42212727 CTATCAAACG
42212737 TAATAC-AAAAAATCATAATA
1 TAATACTAAAAAATCATAATA
*
42212757 TAATTACTAAAAAATCCTAAT-
1 TAA-TACTAAAAAATCATAATA
*
42212778 TTATACTA
1 TAATACTA
42212786 CCAATCCTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 8 0.32
21 5 0.20
22 12 0.48
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATACTAAAAAATCATAATA
Found at i:42212902 original size:2 final size:2
Alignment explanation
Indices: 42212895--42212932 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
42212885 AAACAAACAA
42212895 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42212933 TGAAGTTTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.