Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2323
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: 48695
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Found at i:351 original size:175 final size:170
Alignment explanation
Indices: 152--748 Score: 503
Period size: 173 Copynumber: 3.5 Consensus size: 170
142 AATCAATTAT
* * *
152 AAAAA-TAAAACAGAAAACAATTAAAAAAAAAAAAAATAAATAATCGAAAAAAAAAAAAAAAAAA
1 AAAAATTAAAAAAAAAAAAAATTAAAAAAAAAAAAAA-AAATAATC-AAAAAAAAAAAAAAAAAA
** * ** *
216 AAAATAATAAAATTAAAATAAAAGAAAAAAAAAAATATTTAAAAAAA-CACTATAAAAAAAAAAA
64 AAAATAA-AAAATTAAAATAAAA-AAAAAAAAAAA-A-AAAAAAAAATAAAAAAAAAAAAAAAAA
*
280 A-TTAAAAACAAAAACTTAAAAAAA-AAAAACA-AATATAAAAAATAA
125 ATTTAAAAACAAAAAC-TAAAAAAATAAAAA-ATAATAAAAAAAATAA
* * *
325 ACATA-TAAAAAATTAAACAAAATTAAAAAAAAAAAAAAAAAT--TCAAAAAAAAAATAAAAAAA
1 AAAAATTAAAAAA--AAAAAAAATTAAAAAAAAAAAAAAAAATAATCAAAAAAAAAA-AAAAAAA
* **
387 CAATTTAAAAAA--AAAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATT
63 AAAAATAAAAAATTAAAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATT
** *** *
450 TAAAAATTATTGCTAAAAAAATAAAAAATTATAAAAAAAATAA
128 TAAAAACAAAAACTAAAAAAATAAAAAATAATAAAAAAAATAA
*
493 AAAAATTAAAAAAAAAAAAAAATAAAAAAATAAAAAAAAAATAAATACAAAAAAAAAAAAAAATA
1 AAAAATTAAAAAAAAAAAAAATTAAAAAAA-AAAAAAAAAAT-AAT-C-AAAAAAAAAAAAAA-A
* * ** *
558 AAAAAAAAAAAAAATTAAAATAAAAAAAAAAAAAAGAAAAAACTATTAAAAAAAAAAAAATATAA
61 AAAAAAATAAAAAATTAAAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAA-A-AA
** **
623 AA---AAAAA-AAAAAAAAAAAAAATCATTAAA-AATGAAAAAAAA-AA
124 AATTTAAAAACAAAAACTAAAAAAAT-AAAAAATAAT-AAAAAAAATAA
* * * * *
666 ACAAATTATAAAAAAAAATAA-TAATTAAAAAAAATAAAAA-AATCAAAAAAAACAAAAATATAA
1 AAAAATTAAAAAAAAAAAAAATTAA-AAAAAAAAAAAAAAATAATCAAAAAAAA-AAAAA-A-AA
729 AAAAAA-AAAAATATTAAAAT
62 AAAAAATAAAAA-ATTAAAAT
749 CTGAAAAAAT
Statistics
Matches: 351, Mismatches: 48, Indels: 53
0.78 0.11 0.12
Matches are distributed among these distances:
166 7 0.02
167 39 0.11
168 59 0.17
169 27 0.08
170 21 0.06
171 15 0.04
172 31 0.09
173 65 0.19
174 21 0.06
175 61 0.17
176 1 0.00
177 4 0.01
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.14
Consensus pattern (170 bp):
AAAAATTAAAAAAAAAAAAAATTAAAAAAAAAAAAAAAAATAATCAAAAAAAAAAAAAAAAAAAA
AATAAAAAATTAAAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAA
AAACAAAAACTAAAAAAATAAAAAATAATAAAAAAAATAA
Found at i:419 original size:112 final size:107
Alignment explanation
Indices: 128--875 Score: 379
Period size: 112 Copynumber: 6.7 Consensus size: 107
118 AATGACAGAG
* * *
128 AAAAAGAAAAAAAAAATCAATTATAAAAATAAAA-CAGAAAACAAT-TAAAAAAAAAA-AAAATA
1 AAAAA-AAAAAAAAAA--AATTA-AAAAA-AAAATAAAAAAAAAATATAAAAAAAAAATAAAA-A
** *
190 AATAATCGAAAAAAAAAA-A-AAAAAAAAAAATAATAAAATTAAAATAA--
60 AA-AA-AAAAAAAAAAAATATAAAAAAAAAAATAA-AAAATTAAAAAAATT
* * * * * * * ***
237 AAGAAAAAAAAAAATATTTAAAAAAACACTATAAAAAAAAAAAATTAAAAACAAA-AACTTAAAA
1 AAAAAAAAAAAAAAAAATTAAAAAAA-A-AATAAAAAAAAAATATAAAAAAAAAATAAAAAAAAA
*
301 AAAAAAAACAAATATAAAAAATAAACATATAAAAAATTAAACAAAATT
64 AAAAAAAAAAAATATAAAAAA-AAA-A-ATAAAAAATTAAA-AAAATT
* *
349 AAAAAAAAAAAAAAAAATTCAAAAAAAAAATAAAAAAACAATTTAAAAAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAATT-AAAAAAAAAATAAAAAAAAAATATAAAAAAAAAAT--AAAAAAAA
* * *
414 AAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAAAATTATT
63 AAAAAAAAAAAAATATAAAAAAAAAAATAAAAAA-TTAAAAA-AATT
*** * * *
461 GCTAAAAAAATAAAAAATTATAAAAAAAATAAAAAAATTAAA-AAAAAAAAAAAATAAAAAAATA
1 AAAAAAAAAAAAAAAAATTAAAAAAAAAATAAAAAAA--AAATATAAAAAAAAAAT-AAAAAA-A
* * **
525 AAAAAAAAATAAATACAAAAAAAAAAAAAAATAAAAAAAAAAAAAAATT
62 AAAAAAAAA-AAA-A-ATATAAAAAAAAAAATAAAAAATTAAAAAAATT
**
574 AAAATAAAAAAAAAAAAAAGAAAAAACTATTAAA-AAAAAAAAAATATAAAAAAAAAA-AAAAAA
1 AAAA-AAAAAAAAAAAAATTAAAAAA--A--AAATAAAAAAAAAATATAAAAAAAAAATAAAAAA
* ** * *
637 AAAAAAATCATTAAAA-AT-GAAAAAAAAA-AACAAATTATAAAAAA--
61 AAAAAAA-AAAAAAAATATAAAAAAAAAAATAAAAAATTA-AAAAAATT
** * *
681 AAATAATAATTAAAAAAAA-TAAAAAAATCAAA-AAAAACAAAAATATAAAAAAAAAA-AAATAT
1 AAA-AA-AAAAAAAAAAAATTAAAAAAA--AAATAAAAA-AAAAATATAAAAAAAAAATAAAAAA
* **** ** *
743 TAAAATCTGAAAAAATCATAAATAAAAATAAATTTGAAAA--AAAAAACTT
61 AAAAAAAAAAAAAAAT-ATAAA-AAAAA-AAA-TAAAAAATTAAAAAAATT
* * *
792 -AAAAAAAAAAAAAAAATGAAAACAACAAAATAAAATTACAAAAAAAAAAAAAAAAAAATTCAAA
1 AAAAAAAAAAAAAAAAATTAAAA-AA-AAAAT-AAA--A-AAAAAATATAAAAAAAAAA-T-AAA
* *
856 AAAAAAAAATAAATAAAATA
58 AAAAAAAAAAAAAAAAAATA
876 AACAAATTTA
Statistics
Matches: 491, Mismatches: 93, Indels: 104
0.71 0.14 0.15
Matches are distributed among these distances:
104 1 0.00
105 29 0.06
106 34 0.07
107 27 0.05
108 51 0.10
109 48 0.10
110 16 0.03
111 58 0.12
112 66 0.13
113 45 0.09
114 56 0.11
115 24 0.05
116 26 0.05
117 7 0.01
118 3 0.01
ACGTcount: A:0.81, C:0.04, G:0.01, T:0.14
Consensus pattern (107 bp):
AAAAAAAAAAAAAAAAATTAAAAAAAAAATAAAAAAAAAATATAAAAAAAAAATAAAAAAAAAAA
AAAAAAAAAATATAAAAAAAAAAATAAAAAATTAAAAAAATT
Found at i:424 original size:122 final size:110
Alignment explanation
Indices: 173--873 Score: 409
Period size: 122 Copynumber: 6.0 Consensus size: 110
163 AGAAAACAAT
*
173 TAAAAAAAAAAAAAATAAATAATCGAAAAAAAAA-AAAAAAAAAAAAATA-ATAAAATT---AAA
1 TAAAAAAAAAAAAAATAAA-AA--AAAAAAAAAATAAAAAAAAAAAAATATA-AAAATTAAAAAA
* *** * ** *
233 AT-AAAAGAAAAAAAAAAATATTTAAAAAAACACTATAAAAAAAAAAAA
62 ATAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** * *
281 TTAAAAACAAAAACTTAAAAAAAAAAAACAAATATAAAAAATAAACATATAAAAAATTAAACAAA
1 TAAAAAAAAAAAAAATAAAAAAAAAAAA-AAATA-AAAAAAAAAAAATAT-AAAAATTAAA-AAA
346 ATTAAAAAAAAAAAAAAAAATTCAAAAAAAAAATAAAAAAACAATTTAAAAAAAAAA
62 A-TAAAAAAAAAAAAAAAAA-T-AAAAAAAAAA-AAAAAAA-AA---AAAAAAAAAA
* *
403 TAAAAAAAAAAAAAA-AAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAAAATTATTGCTAAA
1 TAAAAAAAAAAAAAATAAAAAAAAAAA-AAAATAAAAAAAAAAAAATAT-AAAA--A-T--TAAA
* *
467 AAAATAAAAAATTATAAAAAAAATAAAAAAATTAAAAAAAAAAAAAAATAAAAAAA
59 AAAATAAAAAA-AAAAAAAAAAATAAAAAAA--AAAAAAAAAAAAAAA-AAAAAAA
* * *
523 TAAAAAAAAAATAAATACAAAAAAAAAAAAAAATAAAAAAAAAAAAAAATTAAAA-TAAAAAAA-
1 TAAAAAAAAAA-AAA-ATAAAAAAAAAAAAAAATAAAAAAAAAAAAATATAAAAATTAAAAAAAT
** *
586 AAAAAAAGAAAAAACTATTAAAAAAAAAAAAATATAAAAAAAAAAAAAAA
64 AAAAAAA-AAAAAAAAAATAAAAAAAAAAAAA-A-AAAAAAAAAAAAAAA
* *
636 -AAAAAAAATCATTAAAAATGAAAAAAAAAAACAAATTATAAAAAAAAATAATAATTAAAAAAAA
1 TAAAAAAAA--A--AAAAAT-AAAAAAAAAAA-AAA--ATAAAAAAAAA-AA-AA-TATAAAAAT
* * * * ****
700 TAAAAAAATCAAAAAAAACAAAAATATAAAAAAAAAAAAATATTAAAATCTGAAAAAA
55 TAAAAAAATAAAAAAAAAAAAAAAAATAAAAAAAAAAAAA-A-AAAAAAAAAAAAAAA
* * *** ** * * * *
758 TCATAAATAAAAATAAATTTGAAAAAAAAAACTTAAAAAAAAAAAAAAAATGAAAA-CAACAAAA
1 T-A-AAAAAAAAAAAAATAAAAAAAAAAAAAAAT-AAAAAAAAAAAAATATAAAAATTAAAAAAA
** * *** *
822 TAAAATTACAAAAAAAAA-AAAAAAAAAATTCAAAAAAAAAAAATAAA
63 TAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
869 TAAAA
1 TAAAA
874 TAAACAAATT
Statistics
Matches: 466, Mismatches: 76, Indels: 101
0.72 0.12 0.16
Matches are distributed among these distances:
105 6 0.01
106 3 0.01
107 3 0.01
108 27 0.06
109 9 0.02
110 2 0.00
111 10 0.02
112 15 0.03
113 22 0.05
114 49 0.11
115 42 0.09
116 7 0.02
117 10 0.02
118 23 0.05
119 10 0.02
120 45 0.10
121 31 0.07
122 91 0.20
123 34 0.07
124 17 0.04
125 10 0.02
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.14
Consensus pattern (110 bp):
TAAAAAAAAAAAAAATAAAAAAAAAAAAAAATAAAAAAAAAAAAATATAAAAATTAAAAAAATAA
AAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:431 original size:195 final size:180
Alignment explanation
Indices: 174--739 Score: 259
Period size: 184 Copynumber: 3.1 Consensus size: 180
164 GAAAACAATT
* * *
174 AAAAAAAAAAAAAATAAATAATCGAAAAAAAAAAAAAAAAAAAAAATAAT-AAAAT-TAAAATAA
1 AAAAAAAAAAAAAAAAAAAAAT--AAAAAAAAAAAAAAAAAAAAAAAAATAAAAATATAAAA-AA
* * * *
237 AAGAAAAAAA-AAAATATT--TAAAAA-AACAC-TATA-AAAAAAAAAAATTAAAA-ACAAAAAC
63 AA-AAAAAAACAAAA-ATTAAAAAAAATAAAACAAATATAAAAAAAAAAA-TAAAATAAAAAAAC
** *
295 TTAAAA-AAAAAAAACAAATATAAAAAATAAACATATAAAAAATTAAACAAAATTAAAAAAAAA
125 --AAAATAAAAAAAA-AAA-A-AAAAAA-AAA-ATA-AAAAAAAAAAAAAAAATTAAAAAAAAA
***
358 AAAAAAAATTCAAAAAAAAAATAAAAAAACAATTTAAAAAAAAAATAAAAAA-AAAAA-A-AAAA
1 AAAAAAAAAAAAAAAAAAAAATAAAAAAA-AA---AAAAAAAAAA-AAAAAATAAAAATATAAAA
* ** * * * * * *
420 AAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAA-AATTATTGCTAAAAAAATAA-AAAATTATA
61 AAAAAAAAA-AACAAAAATTAAAAAAAA-TAAAACAAATA-T--AAAAAAAAAAATAAAATAAAA
483 AAA-AAAATAAAAAAATTAAAAAAAAAAAAAAATAAAAAAATAAAAAAAAAA-TAAATACAAAAA
121 AAACAAAATAAAAAAA--AAAAAAAAAAAAAAATAAAAAAA-AAAAAAAAAATTAAA-A-AAAAA
* *
546 AAAAAAAAAATAAAAAAAAAAA-AAAATTAAAATAAAAAAAAAAAAAAGAA-AAAACTATTAAAA
1 AAAAAAAAAA-AAAAAAAAAAATAAAA--AAAA-AAAAAAAAAAAAAAAAATAAAAATA-TAAAA
* * * **
609 AAAAAAAAATATAAAAA--AAAAAAAA-AAAA-AAA-A-AATCATTAAAAATGAAAA-AAAAAAA
61 AAAAAAAAAAACAAAAATTAAAAAAAATAAAACAAATATAA-AAAAAAAAAT-AAAATAAAAAAA
* ** * * *
667 CAAATTATAAAAAAAAATAATAATTAAAAAAAATAAAAAAATCAAAAAAAA-CAAAAATATA
124 CAAA--ATAAAAAAAAA-AA-AA-AAAAAAAAATAAAAAAAAAAAAAAAAATTAAAAAAAAA
728 AAAAAAAAAAAA
1 AAAAAAAAAAAA
740 TATTAAAATC
Statistics
Matches: 298, Mismatches: 43, Indels: 85
0.70 0.10 0.20
Matches are distributed among these distances:
179 1 0.00
180 5 0.02
181 7 0.02
182 29 0.10
183 6 0.02
184 49 0.16
185 23 0.08
186 45 0.15
187 36 0.12
188 26 0.09
189 38 0.13
190 12 0.04
191 7 0.02
192 5 0.02
193 9 0.03
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.14
Consensus pattern (180 bp):
AAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAAATATAAAAAAAAA
AAAAAACAAAAATTAAAAAAAATAAAACAAATATAAAAAAAAAAATAAAATAAAAAAACAAAATA
AAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAATTAAAAAAAAA
Found at i:442 original size:149 final size:140
Alignment explanation
Indices: 198--873 Score: 407
Period size: 152 Copynumber: 4.6 Consensus size: 140
188 TAAATAATCG
** ***
198 AAAAAAAAAAAAAAAAA-AAAAATAATAAAATTAAAATAA-AAGAAAAAAAAAAATATTTAAAAA
1 AAAAAAAAAAAAAAAAACAAAAA-AA-AAAA--AAAA-AACAATTAAAAAAAAAATAAAAAAAAA
* *
261 AACACTATAAAAAAAAAAAAT-TAAAAACAAAAACTTAAAAAAAAAAAACAAATATAAAAAATAA
61 AA-A--A-AAAAAAAAAAAATAAAAAAAAAAAAAC-TAAAAAAAAAAAA-AAATATAAAAAATAA
325 ACATATAAAAAATTAAACAAAATT
120 A-ATATAAAAAA-TAAA-AAAATT
349 AAAAAAAAAAAAAAAAATTCAAAAAAAAAATAAAAAAACAATTTAAAAAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAA--CAAAAAAAAAA-AAAAAAACAA-TTAAAAAAAAAATAAAAAAAAAA
* ** * *
414 AAAAAAAAAAAAAAATAAAAAAAAAAAAA--AAAAATTTAAAAATTATTGCTAAAAAAATAAAAA
62 AAAAAAAAAAAAAAATAAAAAAAAAAAAACTAAAAA--AAAAAAAAAAT-AT-AAAAAAT--AAA
477 ATTATAAAAAAAATAAAAAAATT
121 A-TAT--AAAAAATAAAAAAATT
* **
500 AAAAAAAAAAAAAAATAAAAAAATAAAAAAAAAATAAATACAAAAAAAAAAAAAAATAAAAAAAA
1 -AAAAAAAAAAAAAA-AAACAAA-AAAAAAAAAA-AAA-AC-AATTAAAAAAAAAATAAAAAAAA
* *
565 AAAAAAATTAAAATAAAAAAAAAAAAAAGAAAAAACTATTAAAAAAAAAAAAATATAAAAAA-AA
60 AAAAAAA--AAAA-AAAAAATAAAAAAA-AAAAAACTA-AAAAAAAAAAAAAATATAAAAAATAA
629 AA-A-AAAAAA-AAAAAATCATT
120 AATATAAAAAATAAAAAA--ATT
* * * * **
649 AAAAATGAAAAAAAAAAACAAATTATAAAAAAAAATAATAATT--AAAAAAAATAAAAAAATCAA
1 AAAAA-AAAAAAAAAAAACAAA--AAAAAAAAAAAAAACAATTAAAAAAAAAATAAAAAAAAAAA
* * **** *
712 AAAAAACAAAAATATAAAAAAAAAAAAA-TATTAAAATCTGAAAAAATCATAAATAAAAATAAAT
63 AAAAAAAAAAAAAATAAAAAAAAAAAAACTA--AAAAAAAAAAAAAAT-ATAAA-AAATA-AAAT
** *
776 -TTGAAAA-AAAAAACTT
123 ATAAAAAATAAAAAAATT
** * * * ***
792 -AAAAAAAAAAAAAAAA-TGAAAACAACAAAATAA-AATTACAAAAAAAAA-AAAAAAAAAATTC
1 AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAACAATTA-AAAAAAAAATAAAAAAAAAAAAA
*
853 AAAAAAAAAAAATAAATAAAA
65 AAAAAAAAAAAATAAAAAAAA
874 TAAACAAATT
Statistics
Matches: 426, Mismatches: 56, Indels: 98
0.73 0.10 0.17
Matches are distributed among these distances:
137 4 0.01
138 11 0.03
139 28 0.07
140 26 0.06
141 28 0.07
142 10 0.02
143 3 0.01
144 25 0.06
145 10 0.02
146 7 0.02
147 9 0.02
148 38 0.09
149 39 0.09
150 3 0.01
151 43 0.10
152 50 0.12
153 44 0.10
154 7 0.02
155 4 0.01
156 19 0.04
157 7 0.02
158 7 0.02
159 1 0.00
160 3 0.01
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.14
Consensus pattern (140 bp):
AAAAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAACAATTAAAAAAAAAATAAAAAAAAAAAAAA
AAAAAAAAAAATAAAAAAAAAAAAACTAAAAAAAAAAAAAAATATAAAAAATAAAATATAAAAAA
TAAAAAAATT
Found at i:611 original size:210 final size:206
Alignment explanation
Indices: 198--889 Score: 510
Period size: 215 Copynumber: 3.3 Consensus size: 206
188 TAAATAATCG
* * * * * *
198 AAAAAAAAAAAAAAAAAAAAAATAATAAA-ATTAAAATAAAAGAAAAAAAAAAATATTTAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACATAAAAAGAAAA-AAAAAAACAAAT-TATAAAAAA
* * *** * * *
262 ACACTATAAAAA--AAAAAAATTAAAAACA--AAAACTTAAAAAAAA-AAAACAAATATAAAAAA
64 A-A--ATAAAAATTAAAAAAAATAAAAAAATTAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAA
* * * * ** *
322 TAAACATATAAAAAATTAAACAAAAT-TAAAAAAAAAAAAA--AAAATTCAAAAAAAAAATA-AA
126 T-AA-ATACAAAAAATAAAAAAAAATAAAAAAAAAAAAAAATTAAAATAAAAAAAAAAAAAAGAA
* *
383 AAAACAATTTAAAAAAA-
189 AAAACTATTAAAAAAAAT
* * * * * **
400 AAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAATTTAAAAATTATTGCTA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACATAAAAAGAAAAAAAAAA---ACAAATTA-T-AAA
465 AAAAAATAAAAAATTATAAAAAAAATAAAAAAATTAAAAAAAAAAAAAAATAAAAAAATAAAAAA
61 AAAAAAT-AAAAA-T-TAAAAAAAATAAAAAAATTAAAAAAAAAAAAAAATAAAAAAA-AAAAAA
530 AAAATAAATACAAAAAA-AAAAAAAAATAAAAAAAAAAAAAAATTAAAATAAAAAAAAAAAAAAG
122 AAAATAAATACAAAAAATAAAAAAAAATAAAAAAAAAAAAAAATTAAAATAAAAAAAAAAAAAAG
594 AAAAAACTATTAAAAAAAA-
187 AAAAAACTATTAAAAAAAAT
613 AAAAATATAAAAAAAAAAAAAAAAAAAAAAATCATTAAAAATGAAAAAAAAAAACAAATTATAAA
1 AAAAA-A-AAAAAAAAAAAAAAAAAAAAAAA-CA-TAAAAA-GAAAAAAAAAAACAAATTATAAA
* * * *
678 AAAAAATAATAATTAAAAAAAATAAAAAAA-TCAAAAAAAACAAAAATATAAAAAAAAAAAAATA
61 AAAAAATAAAAATTAAAAAAAATAAAAAAATTAAAAAAAAAAAAAAATA-AAAAAAAAAAAAAAA
* * *
742 TTAAA-ATCTGAAAAAATCATAAATAAAAATAAATTTGAAAAAAAAAACTT-AAA-AAAAAAAAA
125 ATAAATA-C--AAAAAAT-A-AAA-AAAAATAAA---AAAAAAAAAAAATTAAAATAAAAAAAAA
* *
804 AAAATGAAAACAAC-A--AAATAAAATT
181 AAAAAGAAAA-AACTATTAAA-AAAAAT
*** * *
829 ACAAAAAAAAAAAAAAAAAAATTCAAAAAA-A-AAAAATAAATAAAATAAACAAATTTATAAA
1 A-AAAAAAAAAAAAAAAAAAAAAAAAAAAACATAAAAAGAAA-AAAAAAAACAAA-TTATAAA
890 TCATAATTAT
Statistics
Matches: 402, Mismatches: 47, Indels: 72
0.77 0.09 0.14
Matches are distributed among these distances:
202 32 0.08
203 11 0.03
204 6 0.01
205 8 0.02
206 5 0.01
208 15 0.04
209 37 0.09
210 60 0.15
211 31 0.08
212 36 0.09
213 31 0.08
214 8 0.02
215 63 0.16
216 22 0.05
217 15 0.04
218 22 0.05
ACGTcount: A:0.81, C:0.03, G:0.01, T:0.15
Consensus pattern (206 bp):
AAAAAAAAAAAAAAAAAAAAAAAAAAAAACATAAAAAGAAAAAAAAAAACAAATTATAAAAAAAA
ATAAAAATTAAAAAAAATAAAAAAATTAAAAAAAAAAAAAAATAAAAAAAAAAAAAAAAATAAAT
ACAAAAAATAAAAAAAAATAAAAAAAAAAAAAAATTAAAATAAAAAAAAAAAAAAGAAAAAACTA
TTAAAAAAAAT
Found at i:757 original size:1 final size:1
Alignment explanation
Indices: 174--739 Score: 232
Period size: 1 Copynumber: 566.0 Consensus size: 1
164 GAAAACAATT
* * *** * * ** *
174 AAAAAAAAAAAAAATAAATAATCGAAAAAAAAAAAAAAAAAAAAAATAATAAAATTAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *** * ** * ** * ***
239 GAAAAAAAAAAATATTTAAAAAAACACTATAAAAAAAAAAAATTAAAAACAAAAACTTAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * ** * ** ***
304 AAAAACAAATATAAAAAATAAACATATAAAAAATTAAACAAAATTAAAAAAAAAAAAAAAAATTC
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *** * *
369 AAAAAAAAAATAAAAAAACAATTTAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAATAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*** ** ***** * ** * * *
434 AAAAAAAAAAAAAATTTAAAAATTATTGCTAAAAAAATAAAAAATTATAAAAAAAATAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
499 TAAAAAAAAAAAAAAATAAAAAAATAAAAAAAAAATAAATACAAAAAAAAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * ** ** * *
564 AAAAAAAATTAAAATAAAAAAAAAAAAAAGAAAAAACTATTAAAAAAAAAAAAATATAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** ** ** * ** * * * **
629 AAAAAAAAAAAAAAATCATTAAAAATGAAAAAAAAAAACAAATTATAAAAAAAAATAATAATTAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * *
694 AAAAAATAAAAAAATCAAAAAAAACAAAAATATAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
740 TATTAAAATC
Statistics
Matches: 419, Mismatches: 146, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 419 1.00
ACGTcount: A:0.82, C:0.03, G:0.01, T:0.14
Consensus pattern (1 bp):
A
Found at i:813 original size:13 final size:12
Alignment explanation
Indices: 779--877 Score: 60
Period size: 11 Copynumber: 8.2 Consensus size: 12
769 AATAAATTTG
*
779 AAAAAAAAAACTT
1 AAAAAAAAAA-AT
792 AAAAAAAAAAA-
1 AAAAAAAAAAAT
** *
803 AAAAATGAAAAC
1 AAAAAAAAAAAT
*
815 AACAAAATAAAATT
1 AA-AAAA-AAAAAT
*
829 ACAAAAAAAAA-
1 AAAAAAAAAAAT
*
840 AAAAAAAAAATT
1 AAAAAAAAAAAT
*
852 CAAAAAAAAAA-
1 AAAAAAAAAAAT
* *
863 AATAAATAAAAT
1 AAAAAAAAAAAT
875 AAA
1 AAA
878 CAAATTTATA
Statistics
Matches: 64, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
11 26 0.41
12 17 0.27
13 17 0.27
14 4 0.06
ACGTcount: A:0.83, C:0.05, G:0.01, T:0.11
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:1059 original size:22 final size:21
Alignment explanation
Indices: 1034--1380 Score: 182
Period size: 21 Copynumber: 16.2 Consensus size: 21
1024 CAAAATTTCT
*
1034 AAAAAAAT-CAAAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
*
1054 AAAAAAA-AAAGAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
* ** *
1074 AAAAAACTTGAAAAAAACAAA
1 AAAAAAATAAAAAAAAAAAAA
* *
1095 AAAAAAAT--AAAAAACAAAT
1 AAAAAAATAAAAAAAAAAAAA
*
1114 AAAAAAAGAAAAAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
* * * **
1135 AACACAATCAAAAAAAAAATC
1 AAAAAAATAAAAAAAAAAAAA
* * ** *
1156 TAAAACATACCAAAAATAAAA
1 AAAAAAATAAAAAAAAAAAAA
* * ** *
1177 CAAAAACTTCAATAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
* *
1198 AAACAATTAAAAAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
1219 TATAAAAAATTAATAAAAAAAAAAA
1 -A-AAAAAA-TAA-AAAAAAAAAAA
*** * *
1244 AAAATTTTTAAAATAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
**
1265 AAAAACTTAAAAAAAAAATAAA
1 AAAAAAATAAAAAAAAAA-AAA
1287 TAAAAAAA-AAAAAAATAATTAAAA
1 -AAAAAAATAAAAAAA-AA--AAAA
**
1311 AAAAAATATAAAAAAATTTAAAA
1 AAAAAA-ATAAAAAAA-AAAAAA
*** *
1334 AAAATTTTTAAAAAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
* **
1355 AAAAAAACAAATTAAAAAAAA
1 AAAAAAATAAAAAAAAAAAAA
1376 AAAAA
1 AAAAA
1381 TTGATTTTAA
Statistics
Matches: 241, Mismatches: 71, Indels: 29
0.71 0.21 0.09
Matches are distributed among these distances:
19 15 0.06
20 23 0.10
21 127 0.53
22 20 0.08
23 28 0.12
24 8 0.03
25 20 0.08
ACGTcount: A:0.81, C:0.05, G:0.01, T:0.13
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAAAAAA
Found at i:1088 original size:49 final size:50
Alignment explanation
Indices: 1034--1129 Score: 149
Period size: 49 Copynumber: 1.9 Consensus size: 50
1024 CAAAATTTCT
1034 AAAAAAATCAAAAAAAAAAAAAAAAAAAAAGAAAAAAA-AAAAAAAACTTG
1 AAAAAAA-CAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAAAAACTTG
* * *
1084 AAAAAAACAAAAAAAAAATAAAAAACAAATAAAAAAAGAAAAAAAA
1 AAAAAAACAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAAAAA
1130 AAAAAAACAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 27 0.64
50 15 0.36
ACGTcount: A:0.88, C:0.04, G:0.03, T:0.05
Consensus pattern (50 bp):
AAAAAAACAAAAAAAAAAAAAAAAAAAAAGAAAAAAAGAAAAAAAACTTG
Found at i:1171 original size:52 final size:53
Alignment explanation
Indices: 1043--1154 Score: 133
Period size: 57 Copynumber: 2.1 Consensus size: 53
1033 TAAAAAAATC
1043 AAAAA-AAAAAA-AAA-AAAAAAAGAAAAAAAAAAAAAAACTTGAAAAAAACAAAAA
1 AAAAATAAAAAACAAACAAAAAAAGAAAAAAAAAAAAAAAC----AAAAAACAAAAA
* * *
1097 AAAAATAAAAAACAAATAAAAAAAGAAAAAAAAAAAAAAAC-ACAATCAAAAA
1 AAAAATAAAAAACAAACAAAAAAAGAAAAAAAAAAAAAAACAAAAAACAAAAA
1149 AAAAAT
1 AAAAAT
1155 CTAAAACATA
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
52 15 0.28
54 5 0.09
55 6 0.11
56 3 0.06
57 24 0.45
ACGTcount: A:0.87, C:0.05, G:0.03, T:0.05
Consensus pattern (53 bp):
AAAAATAAAAAACAAACAAAAAAAGAAAAAAAAAAAAAAACAAAAAACAAAAA
Found at i:1217 original size:65 final size:66
Alignment explanation
Indices: 1144--1380 Score: 175
Period size: 67 Copynumber: 3.5 Consensus size: 66
1134 AAACACAATC
* * * * *
1144 AAAAAAAAAATCTAAAACA-TACCAAAAATAAAACAAAAA-CTT-CAATAAAAAAAAAAACAATT
1 AAAAAAAAAATATAAAAAATTAACAAAAA-AAAAAAAAAATCTTAAAATAAAAAAAAAAA-AATT
1206 AAA
64 AAA
* * *
1209 AAAAAAAAAATATAAAAAATTAATAAAAAAAAAAAAAAATTTTTAAAATAAAAAAAAAAAACTTA
1 AAAAAAAAAATATAAAAAATTAACAAAAAAAAAAAAAAA-TCTTAAAATAAAAAAAAAAAAATTA
1274 AA
65 AA
* * *
1276 AAAAAAATAAATA-AAAAAA-AAAAAAATAATTAAAAAAAAAAT-ATAAAA-AAATTTAAAAAAA
1 AAAAAAA-AAATATAAAAAATTAACAAA-AA--AAAAAAAAAATCTTAAAATAAA---AAAAAAA
**
1337 ATTTTTAAA
59 A-AATTAAA
* *
1346 AAAAAAAAAAAAAAAACAAATTAA-AAAAAAAAAAA
1 AAAAAAAAAATATAAA-AAATTAACAAAAAAAAAAA
1381 TTGATTTTAA
Statistics
Matches: 142, Mismatches: 15, Indels: 27
0.77 0.08 0.15
Matches are distributed among these distances:
65 26 0.18
66 15 0.11
67 28 0.20
68 26 0.18
69 22 0.15
70 17 0.12
71 6 0.04
72 2 0.01
ACGTcount: A:0.79, C:0.04, G:0.00, T:0.16
Consensus pattern (66 bp):
AAAAAAAAAATATAAAAAATTAACAAAAAAAAAAAAAAATCTTAAAATAAAAAAAAAAAAATTAA
A
Found at i:1237 original size:66 final size:65
Alignment explanation
Indices: 1033--1379 Score: 174
Period size: 67 Copynumber: 5.4 Consensus size: 65
1023 TCAAAATTTC
* *** * * *
1033 TAAAAAA-ATCAAAAAAAAAAAAAAA-AAAAAAGAAAAAAAAAAAAAAACTT-GAAAAAAACAAA
1 TAAAAAATAACAAAAAAAAAAAAAAATCTTAAA-ATAAAAAAAAAAAAA-TTAAAAAAAAAAAAA
1095 -A
64 TA
* * * * *
1096 -AAAAAATAA-AAAACAAATAAAAAAA---GAAAA-AAAAAAAAAAACA-CAATCAAAAAAAAAA
1 TAAAAAATAACAAAA-AAAAAAAAAAATCTTAAAATAAAAAAAAAAAAATTAA-AAAAAAAAAAA
*
1154 TC
64 TA
* * * *
1156 TAAAACATACCAAAAATAAAACAAAAA-CTT-CAATAAAAAAAAAAACAATTAAAAAAAAAAAAA
1 TAAAAAATAACAAAAA-AAAAAAAAAATCTTAAAATAAAAAAAAAAA-AATTAAAAAAAAAAAAA
1219 TA
64 TA
* * *
1221 TAAAAAATTAATAAAAAAAAAAAAAAATTTTTAAAATAAAAAAAAAAAACTTAAAAAAAAAATAA
1 TAAAAAA-TAACAAAAAAAAAAAAAAA-TCTTAAAATAAAAAAAAAAAAATTAAAAAAAAAA-AA
1286 ATA
63 ATA
* * * ** ***
1289 -AAAAAAAAAAAAATAATTAAAAAAAAAAT-ATAAAA-AAATTTAAAAAAAATTTTTAAAAAAAA
1 TAAAAAATAACAAA-AA--AAAAAAAAAATCTTAAAATAAA-AAAAAAAAAATTAAAAAAAAAAA
1351 AA-A
62 AATA
1354 -AAAAAA-AACAAATTAAAAAAAAAAAA
1 TAAAAAATAACAAA--AAAAAAAAAAAA
1380 ATTGATTTTA
Statistics
Matches: 225, Mismatches: 36, Indels: 46
0.73 0.12 0.15
Matches are distributed among these distances:
59 21 0.09
60 1 0.00
61 11 0.05
62 22 0.10
63 23 0.10
64 16 0.07
65 37 0.16
66 20 0.09
67 44 0.20
68 20 0.09
69 10 0.04
ACGTcount: A:0.81, C:0.05, G:0.01, T:0.13
Consensus pattern (65 bp):
TAAAAAATAACAAAAAAAAAAAAAAATCTTAAAATAAAAAAAAAAAAATTAAAAAAAAAAAAATA
Found at i:1295 original size:57 final size:57
Alignment explanation
Indices: 1233--1430 Score: 165
Period size: 57 Copynumber: 3.4 Consensus size: 57
1223 AAAAATTAAT
** * *
1233 AAAAAAAAAAAAAAATTTTTAAAATAAAA-A-AAAAAAACTTAAAAAAAA-AATAAA
1 AAAAAAAAAAAAAAAAATTAAAAAAAAAATATAAAAAAACTTAAAAAAAATAATAAA
* *
1287 TAAAAAAAAAAAAAATAATTAAAAAAAAAATATAAAAAAATTTAAAAAAAATTTTTAA-AAA
1 -AAAAAAAAAAAAAAAAATTAAAAAAAAAATATAAAAAAACTTAAAAAAAA----TAATAAA
*** ** * *
1348 AAAAAAAAAAAAAACAAATTAAAAAAAAAA-A-AATTGATTTTAATAAAAATTATAAA
1 AAAAAAAAAAAAAA-AAATTAAAAAAAAAATATAAAAAAACTTAAAAAAAATAATAAA
1404 ATATAAAAAAAAAAAAAAATTAAAAAA
1 A-A-AAAAAAAAAAAAAAATTAAAAAA
1431 TATTAACTAA
Statistics
Matches: 119, Mismatches: 13, Indels: 20
0.78 0.09 0.13
Matches are distributed among these distances:
55 26 0.22
56 5 0.04
57 29 0.24
58 12 0.10
59 13 0.11
60 15 0.13
61 17 0.14
62 2 0.02
ACGTcount: A:0.79, C:0.01, G:0.01, T:0.20
Consensus pattern (57 bp):
AAAAAAAAAAAAAAAAATTAAAAAAAAAATATAAAAAAACTTAAAAAAAATAATAAA
Found at i:1311 original size:68 final size:67
Alignment explanation
Indices: 1187--1380 Score: 182
Period size: 68 Copynumber: 2.8 Consensus size: 67
1177 CAAAAACTTC
*
1187 AATAAAAAAAAAAACAATTAAAAAAAAAAAAATATAAAAAATTAATAAAAAAAAAAAAAAATTTT
1 AATAAAAAAAAAAACAATTAAAAAAAAAAAAATATAAAAAA-TAAAAAAAAAAAAAAAAAATTTT
1252 TAA
65 TAA
*
1255 AATAAAAAAAAAAA-ACTTAAAAAAAAAATAAATA-AAAAAA-AAAAAAATAATTAAAAAAAAA-
1 AATAAAAAAAAAAACAATTAAAAAAAAAA-AAATATAAAAAATAAAAAAA-AA--AAAAAAAAAT
* *
1316 ATATAA
62 TTTTAA
*** * * *
1322 AA-AAATTTAAAAAAAATTTTTAAAAAAAAAAAAAAAAAAACAAATTAAAAAAAAAAAAA
1 AATAAA---AAAAAAAACAATTAAAAAAAAAAAAATATAAA-AAATAAAAAAAAAAAAAA
1381 TTGATTTTAA
Statistics
Matches: 107, Mismatches: 8, Indels: 21
0.79 0.06 0.15
Matches are distributed among these distances:
65 6 0.06
66 5 0.05
67 25 0.23
68 28 0.26
69 17 0.16
70 15 0.14
71 5 0.05
72 6 0.06
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (67 bp):
AATAAAAAAAAAAACAATTAAAAAAAAAAAAATATAAAAAATAAAAAAAAAAAAAAAAAATTTTT
AA
Found at i:1396 original size:1 final size:1
Alignment explanation
Indices: 1043--1380 Score: 109
Period size: 1 Copynumber: 338.0 Consensus size: 1
1033 TAAAAAAATC
* **** * *
1043 AAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAACTTGAAAAAAACAAAAAAAAAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * ** *** * * ** *
1108 ACAAATAAAAAAAGAAAAAAAAAAAAAAACACAATCAAAAAAAAAATCTAAAACATACCAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* **** * * ** * * ** *
1173 AAAACAAAAACTTCAATAAAAAAAAAAACAATTAAAAAAAAAAAAATATAAAAAATTAATAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
***** * *** * * *
1238 AAAAAAAAAATTTTTAAAATAAAAAAAAAAAACTTAAAAAAAAAATAAATAAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * *** ***** * **
1303 AATTAAAAAAAAAATATAAAAAAATTTAAAAAAAATTTTTAAAAAAAAAAAAAAAAAAACAAATT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1368 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
1381 TTGATTTTAA
Statistics
Matches: 255, Mismatches: 82, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 255 1.00
ACGTcount: A:0.81, C:0.05, G:0.01, T:0.13
Consensus pattern (1 bp):
A
Found at i:1476 original size:13 final size:12
Alignment explanation
Indices: 1460--1519 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 12
1450 CGAAAAAATG
1460 TAAACAAAATAAA
1 TAAA-AAAATAAA
1473 TAAAAAAAAATAAAA
1 T--AAAAAAAT-AAA
* *
1488 AAAAAAAATAGAG
1 TAAAAAAATA-AA
1501 TAAAAAAA-AAA
1 TAAAAAAATAAA
1512 TAAAAAAA
1 TAAAAAAA
1520 CATCAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
11 9 0.23
12 2 0.05
13 17 0.44
14 5 0.13
15 6 0.15
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (12 bp):
TAAAAAAATAAA
Found at i:1483 original size:10 final size:10
Alignment explanation
Indices: 1465--1530 Score: 55
Period size: 10 Copynumber: 6.6 Consensus size: 10
1455 AAATGTAAAC
*
1465 AAAATAAATA
1 AAAAAAAATA
1475 AAAAAAAAT-
1 AAAAAAAATA
1484 AAAAAAAA-A
1 AAAAAAAATA
* * *
1493 AAATAGAGTAA
1 AAAAAAAAT-A
1504 AAAAAAAATA
1 AAAAAAAATA
*
1514 AAAAAACATCA
1 AAAAAAAAT-A
1525 AAAAAA
1 AAAAAA
1531 CATTCTATAA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
9 13 0.30
10 17 0.39
11 14 0.32
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (10 bp):
AAAAAAAATA
Found at i:1495 original size:27 final size:29
Alignment explanation
Indices: 1465--1519 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1455 AAATGTAAAC
1465 AAAATA-AAT-AAAAAAAAATAAAAAAAA
1 AAAATAGAATAAAAAAAAAATAAAAAAAA
*
1492 AAAATAGAGTAAAAAAAAAATAAAAAAA
1 AAAATAGAATAAAAAAAAAATAAAAAAA
1520 CATCAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.24
28 2 0.08
29 17 0.68
ACGTcount: A:0.85, C:0.00, G:0.04, T:0.11
Consensus pattern (29 bp):
AAAATAGAATAAAAAAAAAATAAAAAAAA
Found at i:1550 original size:23 final size:23
Alignment explanation
Indices: 1501--1573 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
1491 AAAAATAGAG
* *
1501 TAAAAAAAAAAT--AAAAAAACA
1 TAAAAAAACAATCAAAAAAAAAA
* * * *
1522 TCAAAAAAACATTCTATAACAAAA
1 T-AAAAAAACAATCAAAAAAAAAA
*
1546 TAAAAGAACAATCAAAAAAAAAA
1 TAAAAAAACAATCAAAAAAAAAA
1569 TAAAA
1 TAAAA
1574 TCCAAATCAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
21 1 0.03
22 9 0.23
23 22 0.56
24 7 0.18
ACGTcount: A:0.75, C:0.10, G:0.01, T:0.14
Consensus pattern (23 bp):
TAAAAAAACAATCAAAAAAAAAA
Found at i:1579 original size:18 final size:18
Alignment explanation
Indices: 1558--1605 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1548 AAAGAACAAT
1558 CAAAAAAAAAATAAAATC
1 CAAAAAAAAAATAAAATC
* * *
1576 CAAATCAAAAAA-AATATG
1 CAAA-AAAAAAATAAAATC
1594 CAAAAAAAAAAT
1 CAAAAAAAAAAT
1606 TCATTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 6 0.25
18 12 0.50
19 6 0.25
ACGTcount: A:0.75, C:0.10, G:0.02, T:0.12
Consensus pattern (18 bp):
CAAAAAAAAAATAAAATC
Found at i:1644 original size:14 final size:14
Alignment explanation
Indices: 1627--1774 Score: 77
Period size: 14 Copynumber: 10.6 Consensus size: 14
1617 AAAAAAATTT
1627 AAAAA-AAAAAAAA
1 AAAAATAAAAAAAA
1640 AAAAATAAAAAAAA
1 AAAAATAAAAAAAA
*
1654 AAGAATTAAAAAAAA
1 AA-AAATAAAAAAAA
** *
1669 AATTATCAAAAAAA
1 AAAAATAAAAAAAA
* * **
1683 ATAAATAAATATTA
1 AAAAATAAAAAAAA
*
1697 AAAAA-AAAAACAA
1 AAAAATAAAAAAAA
*** * ***
1710 TCCAATATACTTAA
1 AAAAATAAAAAAAA
*
1724 AAAAATAAAAAAAT
1 AAAAATAAAAAAAA
*
1738 AAAAATAAAACTAAA
1 AAAAATAAAA-AAAA
**
1753 AAAAAT-TCAAAAA
1 AAAAATAAAAAAAA
1766 AAAAATAAA
1 AAAAATAAA
1775 TTTAATGAAA
Statistics
Matches: 92, Mismatches: 38, Indels: 9
0.66 0.27 0.06
Matches are distributed among these distances:
13 21 0.23
14 50 0.54
15 21 0.23
ACGTcount: A:0.79, C:0.05, G:0.01, T:0.16
Consensus pattern (14 bp):
AAAAATAAAAAAAA
Found at i:1654 original size:35 final size:34
Alignment explanation
Indices: 1615--1706 Score: 96
Period size: 35 Copynumber: 2.7 Consensus size: 34
1605 TTCATTTTTC
1615 AAAAAAAAATTTAAAAAAAAAAAAAAAAAATAAAA
1 AAAAAAAAATTTAAAAAAAAAAAAAAAAAA-AAAA
* ** **
1650 AAAAAAGAA-TTAAAAAAAAAATTATCAAAAAAA
1 AAAAAAAAATTTAAAAAAAAAAAAAAAAAAAAAA
* *
1683 ATAAATAAATATTAAAAAAAAAAA
1 AAAAAAAAAT-TTAAAAAAAAAAA
1707 CAATCCAATA
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
33 10 0.22
34 16 0.35
35 20 0.43
ACGTcount: A:0.83, C:0.01, G:0.01, T:0.15
Consensus pattern (34 bp):
AAAAAAAAATTTAAAAAAAAAAAAAAAAAAAAAA
Found at i:1683 original size:1 final size:1
Alignment explanation
Indices: 1627--1670 Score: 52
Period size: 1 Copynumber: 44.0 Consensus size: 1
1617 AAAAAAATTT
* * **
1627 AAAAAAAAAAAAAAAAAATAAAAAAAAAAGAATTAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1671 TTATCAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 37 1.00
ACGTcount: A:0.91, C:0.00, G:0.02, T:0.07
Consensus pattern (1 bp):
A
Found at i:1744 original size:28 final size:28
Alignment explanation
Indices: 1638--1795 Score: 80
Period size: 29 Copynumber: 5.5 Consensus size: 28
1628 AAAAAAAAAA
1638 AAAAAAATAAAAAAA-AAAGAATTAAA---
1 AAAAAAATAAAAAAATAAA-AA-TAAACTT
*
1664 AAAAAAATTATCAAAAAA-AATAAATAAATATT
1 AAAAAAA-TA--AAAAAATAA-AAATAAA-CTT
* ** *
1696 AAAAAAA-AAAACAAT-CCAATATACTT
1 AAAAAAATAAAAAAATAAAAATAAACTT
*
1722 AAAAAAATAAAAAAATAAAAATAAAACTA
1 AAAAAAATAAAAAAATAAAAAT-AAACTT
** *
1751 AAAAAAATTCAAAAA-AAAAATAAATTT
1 AAAAAAATAAAAAAATAAAAATAAACTT
1778 AATGAAAAATAATAAAAA
1 AA--AAAAATAA-AAAAA
1796 CAATTAAAAC
Statistics
Matches: 101, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
26 16 0.16
27 20 0.20
28 18 0.18
29 33 0.33
30 7 0.07
32 7 0.07
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.18
Consensus pattern (28 bp):
AAAAAAATAAAAAAATAAAAATAAACTT
Found at i:1870 original size:34 final size:35
Alignment explanation
Indices: 1821--1887 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
1811 ACCAATTAAC
* *
1821 ATAATAAAAAAAAAAAAAA-AAAATTAAAAAAAAG
1 ATAACAAAAAAAAAAAAAACAAAAATAAAAAAAAG
* *
1855 ATAACAAAAACAAAAAAAACAAAAATGAAAAAA
1 ATAACAAAAAAAAAAAAAACAAAAATAAAAAAA
1888 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 17 0.61
35 11 0.39
ACGTcount: A:0.84, C:0.04, G:0.03, T:0.09
Consensus pattern (35 bp):
ATAACAAAAAAAAAAAAAACAAAAATAAAAAAAAG
Found at i:1879 original size:36 final size:34
Alignment explanation
Indices: 1821--1887 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
1811 ACCAATTAAC
* *
1821 ATAATAAAAAAAAAAAAAAAAAATTAAAAAAAAG
1 ATAACAAAAAAAAAAAAAAAAAATGAAAAAAAAG
1855 ATAACAAAAACAAAAAAAACAAAAATGAAAAAA
1 ATAACAAAAA-AAAAAAAA-AAAAATGAAAAAA
1888 TAAAAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 9 0.31
35 8 0.28
36 12 0.41
ACGTcount: A:0.84, C:0.04, G:0.03, T:0.09
Consensus pattern (34 bp):
ATAACAAAAAAAAAAAAAAAAAATGAAAAAAAAG
Found at i:1887 original size:15 final size:15
Alignment explanation
Indices: 1826--1879 Score: 51
Period size: 14 Copynumber: 3.8 Consensus size: 15
1816 TTAACATAAT
1826 AAAAAA-AAAAA-AA
1 AAAAAACAAAAACAA
**
1839 AAAAATTAAAAA-AA
1 AAAAAACAAAAACAA
* *
1853 AGATAACAAAAACAA
1 AAAAAACAAAAACAA
1868 AAAAAACAAAAA
1 AAAAAACAAAAA
1880 TGAAAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
13 5 0.16
14 15 0.47
15 12 0.38
ACGTcount: A:0.87, C:0.06, G:0.02, T:0.06
Consensus pattern (15 bp):
AAAAAACAAAAACAA
Found at i:2105 original size:16 final size:16
Alignment explanation
Indices: 2064--2191 Score: 87
Period size: 16 Copynumber: 7.7 Consensus size: 16
2054 AAAATATATT
*
2064 AAAAAATAAAATCATAAA
1 AAAAAAAAAAAT-A-AAA
2082 AAAAAAAAAAATAAAA
1 AAAAAAAAAAATAAAA
** **
2098 AAAAAAAAATTTCATTCA
1 AAAAAAAAAAAT-A-AAA
* *
2116 AAAAAAACAAATAACA
1 AAAAAAAAAAATAAAA
*
2132 AAAATAAAAAAT-AAA
1 AAAAAAAAAAATAAAA
* **
2147 AATAATTAAAATAAAA
1 AAAAAAAAAAATAAAA
*
2163 AAAAAAATAAATAAATA
1 AAAAAAAAAAATAAA-A
2180 AAAAAAATAAAA
1 AAAAAAA-AAAA
2192 AATCATTAAA
Statistics
Matches: 84, Mismatches: 21, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
15 10 0.12
16 39 0.46
17 11 0.13
18 24 0.29
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAAAAAAATAAAA
Found at i:2135 original size:43 final size:40
Alignment explanation
Indices: 2079--2205 Score: 141
Period size: 43 Copynumber: 3.1 Consensus size: 40
2069 ATAAAATCAT
2079 AAAAAAA-AAAAAAATAAAAAAAAAAAAATTTCATTCAAAA
1 AAAAAAATAAAAAAATAAAAAAAAAAAAATTTCATT-AAAA
** *
2119 AAAACAAATAACAAAAATAAAAAATAAAAATAATTAAAATAAAA
1 AAAA-AAATAA-AAAAATAAAAAA-AAAAA-AATTTCATTAAAA
* *
2163 AAAAAAATAAATAAATAAAAAAAATAAAAA-ATCATTAAAA
1 AAAAAAATAAAAAAATAAAAAAAA-AAAAATTTCATTAAAA
2203 AAA
1 AAA
2206 TTGACTCAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
40 13 0.18
41 7 0.10
42 16 0.22
43 18 0.25
44 13 0.18
45 6 0.08
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (40 bp):
AAAAAAATAAAAAAATAAAAAAAAAAAAATTTCATTAAAA
Found at i:2136 original size:9 final size:8
Alignment explanation
Indices: 2115--2193 Score: 72
Period size: 8 Copynumber: 9.5 Consensus size: 8
2105 AATTTCATTC
2115 AAAAA-AA
1 AAAAATAA
*
2122 ACAAATAA
1 AAAAATAA
2130 CAAAAAT-A
1 -AAAAATAA
2138 AAAAATAA
1 AAAAATAA
2146 AAATAATTAA
1 AAA-AA-TAA
*
2156 AATAAAAAA
1 AA-AAATAA
2165 AAAAATAA
1 AAAAATAA
*
2173 ATAAATAAA
1 AAAAAT-AA
2182 AAAAATAA
1 AAAAATAA
2190 AAAA
1 AAAA
2194 TCATTAAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
7 10 0.17
8 23 0.39
9 18 0.31
10 7 0.12
11 1 0.02
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAAATAA
Found at i:2165 original size:25 final size:27
Alignment explanation
Indices: 2124--2194 Score: 94
Period size: 25 Copynumber: 2.7 Consensus size: 27
2114 CAAAAAAAAC
*
2124 AAATAACAAAAATAAAAAATAA-AAAT
1 AAATAAAAAAAATAAAAAATAATAAAT
* *
2150 AATTAAAATAAA-AAAAAA-AATAAAT
1 AAATAAAAAAAATAAAAAATAATAAAT
2175 AAATAAAAAAAATAAAAAAT
1 AAATAAAAAAAATAAAAAAT
2195 CATTAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
24 2 0.05
25 20 0.54
26 15 0.41
ACGTcount: A:0.82, C:0.01, G:0.00, T:0.17
Consensus pattern (27 bp):
AAATAAAAAAAATAAAAAATAATAAAT
Found at i:2193 original size:29 final size:27
Alignment explanation
Indices: 2132--2193 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 27
2122 ACAAATAACA
* **
2132 AAAATAAAAAATAAAAATAATTAAAAT
1 AAAAAAAAAAATAAAAATAAAAAAAAT
2159 AAAAAAAAAAATAAATAAATAAAAAAAAT
1 AAAAAAAAAAAT-AA-AAATAAAAAAAAT
2188 AAAAAA
1 AAAAAA
2194 TCATTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 11 0.37
28 2 0.07
29 17 0.57
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (27 bp):
AAAAAAAAAAATAAAAATAAAAAAAAT
Found at i:2194 original size:16 final size:16
Alignment explanation
Indices: 2064--2194 Score: 106
Period size: 17 Copynumber: 7.9 Consensus size: 16
2054 AAAATATATT
*
2064 AAAAAATAAAATCATAA
1 AAAAAATAAAA-AATAA
2081 AAAAAA-AAAAAATAA
1 AAAAAATAAAAAATAA
**
2096 AAAAAA-AAAAATTTCATTC
1 AAAAAATAAAAA----ATAA
*
2115 AAAAAA-AACAAATAA
1 AAAAAATAAAAAATAA
*
2130 CAAAAATAAAAAATAA
1 AAAAAATAAAAAATAA
* *
2146 AAATAATTAAAATAAAAA
1 AAA-AAATAAAA-AATAA
2164 AAAAAATAAATAAATAA
1 AAAAAATAAA-AAATAA
2181 AAAAAATAAAAAAT
1 AAAAAATAAAAAAT
2195 CATTAAAAAA
Statistics
Matches: 93, Mismatches: 13, Indels: 17
0.76 0.11 0.14
Matches are distributed among these distances:
15 22 0.24
16 18 0.19
17 33 0.35
18 8 0.09
19 12 0.13
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAAATAAAAAATAA
Found at i:2252 original size:11 final size:11
Alignment explanation
Indices: 2232--2280 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
2222 AATTCTGTTT
2232 ATTAAAAAAAA
1 ATTAAAAAAAA
2243 ATTAACAAAAAAA
1 ATT-A-AAAAAAA
2256 ATTAAAAAAAA
1 ATTAAAAAAAA
**
2267 AAAAAAAAAAA
1 ATTAAAAAAAA
2278 ATT
1 ATT
2281 TATAACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 20 0.62
12 2 0.06
13 10 0.31
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (11 bp):
ATTAAAAAAAA
Found at i:2254 original size:14 final size:13
Alignment explanation
Indices: 2235--2904 Score: 106
Period size: 13 Copynumber: 49.8 Consensus size: 13
2225 TCTGTTTATT
2235 AAAAAAAAATTAA
1 AAAAAAAAATTAA
*
2248 CAAAAAAAATT--
1 AAAAAAAAATTAA
2259 AAAAAAAAA--AA
1 AAAAAAAAATTAA
*
2270 AAAAAAAAATTTA
1 AAAAAAAAATTAA
* * *
2283 TAACAAAAA--CA
1 AAAAAAAAATTAA
* *
2294 AACACAAAA-TAA
1 AAAAAAAAATTAA
* *
2306 CAATAATAAATTAA
1 -AAAAAAAAATTAA
*
2320 AAAAATAAAA-TCA
1 AAAAA-AAAATTAA
*
2333 AAAAAATAATTAA
1 AAAAAAAAATTAA
* ****
2346 ATAAAGTGGTCTAA
1 AAAAAAAAAT-TAA
2360 AGAAAAAAAGATTTAA
1 A-AAAAAAA-A-TTAA
*
2376 AAAAATAAAGA-AAA
1 AAAAA-AAA-ATTAA
2390 AAAAAAAAATTTTAA
1 AAAAAAAAA--TTAA
2405 AAAAAAAAA--AA
1 AAAAAAAAATTAA
2416 AAACAAAAAA--AA
1 AAA-AAAAAATTAA
*
2428 AAATAGAAAAA-AAA
1 AAA-A-AAAAATTAA
*
2442 AAACGCAAAAAATAAA
1 AAA---AAAAAATTAA
2458 AAAAAAATAATCTTTAA
1 AAAAAAA-AA---TTAA
**
2475 TTAACAAAAAAAAAAA
1 --AA-AAAAAAATTAA
*
2491 TATAAAAAAAACTAA
1 -A-AAAAAAAATTAA
2506 ATAAAAAAAATTAA
1 A-AAAAAAAATTAA
*
2520 AAAAAAAAA-AAA
1 AAAAAAAAATTAA
*
2532 AATAATTATAAAATAAA
1 AA-AA--A-AAAATTAA
*
2549 GAAAAAAATAAGTACAA
1 -AAAAAAA-AA-T-TAA
2566 AAAAAAAAATTAA
1 AAAAAAAAATTAA
*
2579 AACAATATGCGAAATTTTAA
1 AA-AA-A----AAA-ATTAA
** *
2599 AAAATTAATTTAA
1 AAAAAAAAATTAA
2612 AAAAAAAAA--AA
1 AAAAAAAAATTAA
* *
2623 AAAAATAAA-GAA
1 AAAAAAAAATTAA
*
2635 ATAAAAAAA--AA
1 AAAAAAAAATTAA
* *
2646 AAAAATAAA-CAA
1 AAAAAAAAATTAA
2658 AAAAAAAAATT-A
1 AAAAAAAAATTAA
2670 AAAAAAAAA--AA
1 AAAAAAAAATTAA
*
2681 AAGAAAAAATT--
1 AAAAAAAAATTAA
* *
2692 AAACAAATA-TAA
1 AAAAAAAAATTAA
2704 AAAAAAAAATTTCAA
1 AAAAAAAAA-TT-AA
*
2719 TCATTCCAATAAAACAACATAA
1 --A----AA-AAAA-AA-TTAA
2741 AAAAAAAAA--AA
1 AAAAAAAAATTAA
*
2752 AAAAAACATAAATAA
1 AAAAAA-A-AATTAA
2767 ATAAAATAAAA--AA
1 A-AAAA-AAAATTAA
2780 AAACAAAAAA-TAA
1 AAA-AAAAAATTAA
*
2793 AAAAAAAAA-CAGA
1 AAAAAAAAATTA-A
2806 AAAAAAAAA-TAA
1 AAAAAAAAATTAA
*
2818 AAAAAAAATATTACTTT
1 AAAAAAAA-ATTA---A
*
2835 AAAAATAAA--AA
1 AAAAAAAAATTAA
2846 AAAAAAAAATTAA
1 AAAAAAAAATTAA
2859 TAAAAAAAAATTAA
1 -AAAAAAAAATTAA
2873 AAAAAAAAA--AA
1 AAAAAAAAATTAA
*
2884 AAAAAATAA--AA
1 AAAAAAAAATTAA
2895 AAAAAAAAAT
1 AAAAAAAAAT
2905 AAATGAAAAT
Statistics
Matches: 503, Mismatches: 70, Indels: 169
0.68 0.09 0.23
Matches are distributed among these distances:
10 1 0.00
11 98 0.19
12 80 0.16
13 115 0.23
14 64 0.13
15 52 0.10
16 39 0.08
17 20 0.04
18 2 0.00
19 9 0.02
20 12 0.02
21 2 0.00
22 6 0.01
23 3 0.01
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTAA
Found at i:2290 original size:23 final size:22
Alignment explanation
Indices: 2232--2907 Score: 212
Period size: 23 Copynumber: 29.3 Consensus size: 22
2222 AATTCTGTTT
*
2232 ATTAAAAAAAAATTAACAAAAAAA
1 ATTAAAAAAAAA--AAAAAAAAAA
2256 ATTAAAAAAAAAAAAAAAAAAA
1 ATTAAAAAAAAAAAAAAAAAAA
2278 ATTTATAACAAAAACAAACACAAAATAACA
1 A-TTA-AA-AAAAA-AAA-A-AAAA-AA-A
* ** *
2308 A-TAATAAATTAAAAAAATAAA
1 ATTAAAAAAAAAAAAAAAAAAA
* * ***
2329 ATCAAAAAAATAATTAAATAAAGTG
1 ATTAAAAAAA-AA--AAAAAAAAAA
* **
2354 GTCTAAAGAAAAAAAGATTTAAAAAA
1 AT-TAAA-AAAAAAA-A-AAAAAAAA
* *
2380 A-T-AAAGAAAAAAAAAAAAAT
1 ATTAAAAAAAAAAAAAAAAAAA
*
2400 TTTAAAAAAAAAAAAAAAACAAA
1 ATTAAAAAAAAAAAAAAAA-AAA
2423 A--AAAAAAATAGAAAAAAAAAAA
1 ATTAAAAAAA-A-AAAAAAAAAAA
*** * *
2445 CGCAAAAAATAAAAAAAAAATA
1 ATTAAAAAAAAAAAAAAAAAAA
** ** *
2467 ATCTTTAATTAACAAAAAAAAAA
1 AT-TAAAAAAAAAAAAAAAAAAA
*
2490 ATATAAAAAAAACTAAATAAAAAAA
1 AT-TAAAAAAAA--AAAAAAAAAAA
*
2515 ATT-AAAAAAAAAAAAAAAATA
1 ATTAAAAAAAAAAAAAAAAAAA
* * *
2536 ATTATAAAATAAAGAAAAAAATA
1 ATTA-AAAAAAAAAAAAAAAAAA
* * *
2559 AGTACAAAAAAAAAAATTAAAACA
1 ATTA-AAAAAAAAAAA-AAAAAAA
*** **** **
2583 ATATGCGAAATTTTAAAAAATTA
1 AT-TAAAAAAAAAAAAAAAAAAA
*
2606 ATTTAAAA-AAAAAAAAAAAAA
1 ATTAAAAAAAAAAAAAAAAAAA
* *
2627 A-T--AAAGAAATAAAAAAAAA
1 ATTAAAAAAAAAAAAAAAAAAA
* *
2646 A--AAAATAAACAAAAAAAAAA
1 ATTAAAAAAAAAAAAAAAAAAA
*
2666 ATTAAAAAAAAAAAAAAGAAAAA
1 ATT-AAAAAAAAAAAAAAAAAAA
*
2689 ATTAAACAAATATAAAAAAAAAAA
1 ATTAAA-AAA-AAAAAAAAAAAAA
* * **** * * *
2713 TTTCAATCATTCCAATAAAACAAC
1 ATT-AA-AAAAAAAAAAAAAAAAA
2737 A-TAAAAAAAAAAAAAAAAAAA
1 ATTAAAAAAAAAAAAAAAAAAA
*
2758 CA-TAAATAAATAAAATAAAAAAAA
1 -ATTAAA-AAA-AAAAAAAAAAAAA
* * *
2782 A-CAAAAAATAAAAAAAAAAAC
1 ATTAAAAAAAAAAAAAAAAAAA
**
2803 AGAAAAAAAAAATAAAAAAAAAA
1 ATTAAAAAAAAA-AAAAAAAAAA
2826 TATTACTTTAAAAATAAAAAAAAAAAAA
1 -ATTA----AAAAA-AAAAAAAAAAAAA
2854 ATTAATAAAAAAAAATTAAAAAAAA
1 ATTAA-AAAAAAAAA--AAAAAAAA
**
2879 AAAAAAAAAAATAAAAAAAAAAA
1 ATTAAAAAAAA-AAAAAAAAAAA
*
2902 AATAAA
1 ATTAAA
2908 TGAAAATAAA
Statistics
Matches: 477, Mismatches: 120, Indels: 111
0.67 0.17 0.16
Matches are distributed among these distances:
18 3 0.01
19 13 0.03
20 20 0.04
21 51 0.11
22 75 0.16
23 138 0.29
24 80 0.17
25 44 0.09
26 15 0.03
27 10 0.02
28 21 0.04
29 5 0.01
30 2 0.00
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (22 bp):
ATTAAAAAAAAAAAAAAAAAAA
Found at i:2378 original size:1 final size:1
Alignment explanation
Indices: 2374--2464 Score: 65
Period size: 1 Copynumber: 91.0 Consensus size: 1
2364 AAAAAGATTT
* * **** * * *
2374 AAAAAAATAAAGAAAAAAAAAAAAATTTTAAAAAAAAAAAAAAAACAAAAAAAAAAATAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*** *
2439 AAAAAACGCAAAAAATAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2465 TAATCTTTAA
Statistics
Matches: 72, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.86, C:0.03, G:0.03, T:0.08
Consensus pattern (1 bp):
A
Found at i:2394 original size:29 final size:30
Alignment explanation
Indices: 2362--2428 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
2352 TGGTCTAAAG
* *
2362 AAAAAAAGA-TTTAAAAAAATAAAGAAAA-A
1 AAAAAAA-ATTTTAAAAAAAAAAAAAAAACA
2391 AAAAAAAATTTTAAAAAAAAAAAAAAAACA
1 AAAAAAAATTTTAAAAAAAAAAAAAAAACA
2421 AAAAAAAA
1 AAAAAAAA
2429 AATAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 24 0.71
30 9 0.26
ACGTcount: A:0.84, C:0.01, G:0.03, T:0.12
Consensus pattern (30 bp):
AAAAAAAATTTTAAAAAAAAAAAAAAAACA
Found at i:2461 original size:69 final size:66
Alignment explanation
Indices: 2386--2712 Score: 219
Period size: 72 Copynumber: 4.9 Consensus size: 66
2376 AAAAATAAAG
2386 AAAAAAAAAAA-AATTTTAAAAAAAAAAAAAAAACAAAAAAAAAAATAGAAAAAAAAAAACGCAA
1 AAAAAAAAAAATAATTTTAAAAAAAAAAAAAAAACAAAAAAAAAAATA-AAAAAAAAAAA-GCAA
2450 AAA
64 AAA
* * * * * **
2453 ATAAAAAAAAAATAATCTTTAATTAACAAAAAAAAAAATATAAAAAAAACTAAATAAAAAAAATT
1 A-AAAAAAAAAATAAT-TTTAA--AAAAAAAAAAAAAACAAAAAAAAAAATAAAAAAAAAAAAGC
2518 AAAAA
62 AAAAA
* * * * *
2523 AAAAAAAAAAATAATTATAAAATAAAGAAAAAAATAAGTACAAAAAAAAAAAT-TAAAACAATAT
1 AAAAAAAAAAATAATT-TTAAA-AAA-AAAAAAA-AA--ACAAAAAAAAAAATAAAAAAAAAAAA
*
2587 GC-GAAA
60 GCAAAAA
**** * * * *
2593 TTTTAAAAAATTAA-TTT-AAAAAAAAAAAAAAA-AAATAAAGAAATAAAAAAAAAAAA--AATA
1 AAAAAAAAAAATAATTTTAAAAAAAAAAAAAAAACAAAAAAAAAAATAAAAAAAAAAAAGCAAAA
2653 A
66 A
* *
2654 ACAAAAAAAAA-AA--TTAAAAAAAAAAAAAAGAA-AAAATTAAACAAATATAAAAAAAAAAA
1 AAAAAAAAAAATAATTTTAAAAAAAAAAAAAA-AACAAAA--AAAAAAATA-AAAAAAAAAAA
2713 TTTCAATCAT
Statistics
Matches: 201, Mismatches: 41, Indels: 39
0.72 0.15 0.14
Matches are distributed among these distances:
59 2 0.01
60 15 0.07
61 23 0.11
62 8 0.04
63 8 0.04
64 13 0.06
65 7 0.03
66 3 0.01
67 4 0.02
68 14 0.07
69 28 0.14
70 25 0.12
71 16 0.08
72 35 0.17
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (66 bp):
AAAAAAAAAAATAATTTTAAAAAAAAAAAAAAAACAAAAAAAAAAATAAAAAAAAAAAAGCAAAA
A
Found at i:2620 original size:91 final size:89
Alignment explanation
Indices: 2507--2672 Score: 228
Period size: 91 Copynumber: 1.8 Consensus size: 89
2497 AAAAACTAAA
* * * *
2507 TAAAAAAAATTAAAAAAAAAAAAAAAATAATTATA-AAATAAAGAAAAAAATAAGT-ACAAAAAA
1 TAAAAAAAATTAAAAAAAAAAAAAAAA-AAATAAAGAAATAAA-AAAAAAAAAAATAACAAAAAA
2570 AAAAATTAAAACAATATGCGAAATTT
64 AAAAATTAAAACAATATGCGAAATTT
*
2596 TAAAAAATTAATTTAAAAAAAAAAAAAAAAAATAAAGAAATAAAAAAAAAAAAAATAAACAAAAA
1 TAAAAAA--AATTAAAAAAAAAAAAAAAAAAATAAAGAAATAAAAAAAAAAAAAAT-AACAAAAA
2661 AAAAAATTAAAA
63 AAAAAATTAAAA
2673 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
89 7 0.10
90 15 0.22
91 26 0.39
92 19 0.28
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (89 bp):
TAAAAAAAATTAAAAAAAAAAAAAAAAAAATAAAGAAATAAAAAAAAAAAAAATAACAAAAAAAA
AAATTAAAACAATATGCGAAATTT
Found at i:2706 original size:132 final size:128
Alignment explanation
Indices: 2480--2919 Score: 307
Period size: 131 Copynumber: 3.4 Consensus size: 128
2470 TTTAATTAAC
* * * * ** *
2480 AAAAAAAAAAATATAAA-AAAAACTAAATAAAAAAAATTAA-AAAAAAAAAAAAAATAATTATAA
1 AAAAAAAAAAAAAAAAATAAAAAATAAA-AAAAAAAA-AAATAAAAAAAAAAAAAATAAAAAAAA
* ** **
2543 AATAAAGAAAAAAATAAGTACAAAAAAAAAAATTAAAACAATATGCGAA-ATTTTAA-AAAATTA
64 AAAAAAGAAAAAAATAAG-ACAAAAAAAAAAA--AAAA-AAT-TGC-AACATTCCAATAAAACAA
**
2606 -ATTTA
123 CATAAA
2611 AAAAAAAAAAAAAAAAATAAAGAAATAAAAAAAAAAAAAATAAACAAAAAAAAAAATTAAAAAAA
1 AAAAAAAAAAAAAAAAATAAA-AAATAAAAAAAAAAAAAATAAA-AAAAAAAAAAA-TAAAAAAA
* * * *
2676 AAAAAAAGAAAAAATTAA-ACAAATATAAAAAAAAAAATTTCAATCATTCCAATAAAACAACATA
63 AAAAAAAGAAAAAAATAAGACAAAAAAAAAAAAAAAAATTGCAA-CATTCCAATAAAACAACATA
2740 AA
127 AA
*
2742 AAAAAAAAAAAAAAAACATAAATAAATAAAATAAAAAAAAACA-AAAAATAAAAAAAAAAACAGA
1 AAAAAAAAAAAAAAAA-ATAAA-AAATAAAA-AAAAAAAAA-ATAAAAA-AAAAAAAAATA-A-A
* ** *
2806 AAAAAAAAATAAAAAAAAAATATTACTTTAAAAATAAAAAAAAAAA----AA-ATT--AATAAAA
59 AAAAAAAAA-AAGAAAAAAATAAGAC---AAAAAAAAAAAAAAAAATTGCAACATTCCAATAAAA
* * *
2864 AAAAATTAA
120 CAACATAAA
2873 AAAAAAAAAAAAAAAAATAAAAAA-AAAAAAATAAATGAAAATAAAAA
1 AAAAAAAAAAAAAAAAATAAAAAATAAAAAAA-AAA--AAAATAAAAA
2920 CAAATTTAAT
Statistics
Matches: 258, Mismatches: 27, Indels: 49
0.77 0.08 0.15
Matches are distributed among these distances:
127 5 0.02
128 9 0.03
129 12 0.05
130 22 0.09
131 65 0.25
132 41 0.16
133 42 0.16
134 32 0.12
135 12 0.05
136 2 0.01
139 16 0.06
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.15
Consensus pattern (128 bp):
AAAAAAAAAAAAAAAAATAAAAAATAAAAAAAAAAAAAATAAAAAAAAAAAAAATAAAAAAAAAA
AAAAGAAAAAAATAAGACAAAAAAAAAAAAAAAAATTGCAACATTCCAATAAAACAACATAAA
Found at i:2879 original size:136 final size:131
Alignment explanation
Indices: 2610--2923 Score: 318
Period size: 135 Copynumber: 2.3 Consensus size: 131
2600 AAATTAATTT
* * **
2610 AAAAAAAAAAAAAAAAAATAAAGAAATAAA-AAAAAAAAA-AATAAACAAAAAAAAAAATTAAAA
1 AAAAAAAAAAAAAAAAAATAAAAAAATAAATAAAAAAAAACAAAAAACAAAAAAAAAAAAGAAAA
* * * * *
2673 AAAAAAAAAAGAAAAAATTAAACAAATATAAAAAAAAAAATTTCAATCATTCCAATAAAACAACA
66 AAAAAAAAAAAAAAAAATTAAACAAATAAAAAAAAAAAAAATTCAATCA-T-AAAAAAAACAACA
2738 TAAA
129 -AAA
* * *
2742 AAAAAAAAAAAAAAAACATAAATAAATAAAATAAAAAAAAACAAAAAATAAAAAAAAAAACAGAA
1 AAAAAAAAAAAAAAAAAATAAAAAAAT-AAATAAAAAAAAACAAAAAACAAAAAAAAAAA-AGAA
2807 AAAAAAAATAAAAAAAAAATATTACTTTAA-AAATAAAAAAAAAAAAAATT-AAT-A-AAAAAAA
64 AAAAAAAA-AAAAAAAAAA-ATTA----AACAAATAAAAAAAAAAAAAATTCAATCATAAAAAAA
*
2868 ATTAA-AAAA
123 A-CAACAAAA
*
2877 AAAAAAAAAAAAATAAAAAAAAAAAAATAAATGAAAATAAAAACAAA
1 AAAAAAAAAAAAA-AAAAATAAAAAAATAAAT-AAAA-AAAAACAAA
2924 TTTAATATAA
Statistics
Matches: 153, Mismatches: 15, Indels: 23
0.80 0.08 0.12
Matches are distributed among these distances:
132 25 0.16
133 3 0.02
134 9 0.06
135 36 0.24
136 32 0.21
137 20 0.13
138 4 0.03
139 1 0.01
140 3 0.02
141 18 0.12
142 2 0.01
ACGTcount: A:0.82, C:0.04, G:0.01, T:0.12
Consensus pattern (131 bp):
AAAAAAAAAAAAAAAAAATAAAAAAATAAATAAAAAAAAACAAAAAACAAAAAAAAAAAAGAAAA
AAAAAAAAAAAAAAAAATTAAACAAATAAAAAAAAAAAAAATTCAATCATAAAAAAAACAACAAA
A
Found at i:2919 original size:1 final size:1
Alignment explanation
Indices: 2610--2903 Score: 129
Period size: 1 Copynumber: 294.0 Consensus size: 1
2600 AAATTAATTT
* * * * * **
2610 AAAAAAAAAAAAAAAAAATAAAGAAATAAAAAAAAAAAAAATAAACAAAAAAAAAAATTAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * * **** ** **** * * * *
2675 AAAAAAAAGAAAAAATTAAACAAATATAAAAAAAAAAATTTCAATCATTCCAATAAAACAACATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * * * *
2740 AAAAAAAAAAAAAAAAAACATAAATAAATAAAATAAAAAAAAACAAAAAATAAAAAAAAAAACAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * ** **** * ** * *
2805 AAAAAAAAAATAAAAAAAAAATATTACTTTAAAAATAAAAAAAAAAAAAATTAATAAAAAAAAAT
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2870 TAAAAAAAAAAAAAAAAAAATAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2904 TAAATGAAAA
Statistics
Matches: 217, Mismatches: 76, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 217 1.00
ACGTcount: A:0.83, C:0.04, G:0.01, T:0.12
Consensus pattern (1 bp):
A
Found at i:3028 original size:1 final size:1
Alignment explanation
Indices: 3024--3117 Score: 98
Period size: 1 Copynumber: 94.0 Consensus size: 1
3014 AAATTAAATT
* * * * * *
3024 AAAAAAAAAAATAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAATATAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** **
3089 AAAGTAAAAAAAAAAACGAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3118 TTATAAATTA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 75 1.00
ACGTcount: A:0.89, C:0.03, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:3040 original size:12 final size:12
Alignment explanation
Indices: 3023--3118 Score: 108
Period size: 12 Copynumber: 8.1 Consensus size: 12
3013 CAAATTAAAT
3023 TAAAAAAAAAAA
1 TAAAAAAAAAAA
3035 TAAAAAACAAAAA
1 TAAAAAA-AAAAA
3048 -AAAAAAAAAAA
1 TAAAAAAAAAAA
3059 -AAAAAAAAAAA
1 TAAAAAAAAAAA
*
3070 -ATAAAAAAAAA
1 TAAAAAAAAAAA
* * *
3081 TATAACAAAAAG
1 TAAAAAAAAAAA
3093 TAAAAAAAAAAA
1 TAAAAAAAAAAA
*
3105 CGAAAAAAAAAAA
1 -TAAAAAAAAAAA
3118 T
1 T
3119 TATAAATTAA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
11 26 0.36
12 31 0.42
13 16 0.22
ACGTcount: A:0.88, C:0.03, G:0.02, T:0.07
Consensus pattern (12 bp):
TAAAAAAAAAAA
Found at i:3042 original size:29 final size:26
Alignment explanation
Indices: 3000--3117 Score: 105
Period size: 25 Copynumber: 4.5 Consensus size: 26
2990 AAGATTCGTC
*
3000 AAAATAAAAAAAACAAATTAAATTAAAAA
1 AAAAAAAAAAAAACAAA-TAAA--AAAAA
*
3029 AAAAAATAAAAAACAAA-AAAAAAAA
1 AAAAAAAAAAAAACAAATAAAAAAAA
*
3054 AAAAAAAAAAAAAAAAATAAAAAAAA
1 AAAAAAAAAAAAACAAATAAAAAAAA
* * * **
3080 ATATAACAAAAAGTAAA-AAAAAAAA
1 AAAAAAAAAAAAACAAATAAAAAAAA
**
3105 CGAAAAAAAAAAA
1 AAAAAAAAAAAAA
3118 TTATAAATTA
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
25 36 0.49
26 20 0.27
27 3 0.04
29 15 0.20
ACGTcount: A:0.86, C:0.03, G:0.02, T:0.08
Consensus pattern (26 bp):
AAAAAAAAAAAAACAAATAAAAAAAA
Found at i:3048 original size:38 final size:36
Alignment explanation
Indices: 3000--3155 Score: 129
Period size: 36 Copynumber: 4.3 Consensus size: 36
2990 AAGATTCGTC
*
3000 AAAATAAAAAAAACAAATTAAATTAAAAAAAAAAATA
1 AAAAAAAAAAAAACAAA-TAAATTAAAAAAAAAAATA
* **
3037 AAAAACAAAAAAAA-AAAAAAAAAAAAAAAAAAAATA
1 AAAAA-AAAAAAAACAAATAAATTAAAAAAAAAAATA
* * * *
3073 AAAAAAAATATAAC-AA-AAAGTAAAAAAAAAAACGA
1 AAAAAAAAAAAAACAAATAAATTAAAAAAAAAAA-TA
** * * * *
3108 AAAAAAAAAATTATAAATTAATTATAAAATAAAATA
1 AAAAAAAAAAAAACAAATAAATTAAAAAAAAAAATA
*
3144 AAATAAAAAAAA
1 AAAAAAAAAAAA
3156 CATATAATCA
Statistics
Matches: 94, Mismatches: 20, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
34 14 0.15
35 20 0.21
36 33 0.35
37 19 0.20
38 8 0.09
ACGTcount: A:0.83, C:0.03, G:0.01, T:0.13
Consensus pattern (36 bp):
AAAAAAAAAAAAACAAATAAATTAAAAAAAAAAATA
Found at i:3162 original size:18 final size:17
Alignment explanation
Indices: 2374--3155 Score: 184
Period size: 17 Copynumber: 44.2 Consensus size: 17
2364 AAAAAGATTT
2374 AAAAAAATAAAGA-AAAA
1 AAAAAAATAAA-ATAAAA
***
2391 AAAAAAA-ATTTTAAAA
1 AAAAAAATAAAATAAAA
* *
2407 AAAAAAAAAAAACAAAA
1 AAAAAAATAAAATAAAA
2424 AAAAAAATAGAAA-AAAA
1 AAAAAAATA-AAATAAAA
*
2441 AAAACGCAA-AAAAT-AAA
1 AAAA--AAATAAAATAAAA
* *
2458 AAAAAAATAATCTTTAATTAAC
1 AAAAAAATAA-----AATAAAA
*
2480 AAAAAAA-AAAATATAA
1 AAAAAAATAAAATAAAA
*
2496 AAAAAACT-AAATAAAA
1 AAAAAAATAAAATAAAA
*
2512 AAAATTAAA-AAAAAAAAA
1 AAAA--AAATAAAATAAAA
*
2530 AAAATAATTATAAAATAAAG
1 AAAA-AA--ATAAAATAAAA
* *
2550 AAAAAAATAAGTACAAAA
1 AAAAAAATAA-AATAAAA
* *
2568 AAAAAAATTAAAACAATA
1 AAAAAAA-TAAAATAAAA
**** **
2586 TGCGAAAT--TTTAAAA
1 AAAAAAATAAAATAAAA
2601 AATTAATTTAAA-AAAA-AAAA
1 AA--AA---AAATAAAATAAAA
2621 AAAAAAATAAAGA-AATAA
1 AAAAAAATAAA-ATAA-AA
* *
2639 AAAAAAAAAAAATAAAC
1 AAAAAAATAAAATAAAA
*
2656 AAAAAAA-AAAATTAAA
1 AAAAAAATAAAATAAAA
*
2672 AAAAAAA-AAAAGAAAA
1 AAAAAAATAAAATAAAA
** *
2688 AATTAAACAAATATAAAA
1 AAAAAAATAAA-ATAAAA
** ***
2706 AAAAAAATTTCAATCATTCC
1 AAAAAAA-TAAAAT-A-AAA
* * *
2726 AATAAAACAACATAAAA
1 AAAAAAATAAAATAAAA
2743 AAAAAAA-AAAA-AAAA
1 AAAAAAATAAAATAAAA
2758 CATAAATAAATAAAATAAAA
1 -A-AAA-AAATAAAATAAAA
2778 AAAAACAA-AAAATAAAA
1 AAAAA-AATAAAATAAAA
* *
2795 AAAAAAACAGAAAAAAAA
1 AAAAAAATA-AAATAAAA
* **
2813 AATAAAAAAAAAATATTACT
1 AA-AAAAATAAAATA--AAA
**
2833 TTAAAAATAAAA-AAAA
1 AAAAAAATAAAATAAAA
*
2849 AAAAAATTAATAA-AAAA
1 AAAAAAATAA-AATAAAA
2866 AAATTAAAA-AAAA-AAAA
1 AAA--AAAATAAAATAAAA
*
2883 AAAAAAATAAAAAAAAA
1 AAAAAAATAAAATAAAA
2900 AAAATAAATGAAAATAAAA
1 AAAA-AAAT-AAAATAAAA
* ** *
2919 ACAAATTTAATATAAGATA
1 AAAAAAATAAAATAA-A-A
* ** **
2938 CTAAAATTTCTAA-AAAA
1 -AAAAAAATAAAATAAAA
* * *
2955 AAAAAATTAACAT-ATA
1 AAAAAAATAAAATAAAA
* * **
2971 TAAAAATTTCAATAACCAA
1 AAAAAAATAAAATAA--AA
****
2990 AAGATTCGTCAAAATAAAA
1 AA-AAAAAT-AAAATAAAA
*
3009 AAAACAAATTAAATTAAAA
1 AAAA-AAA-TAAAATAAAA
3028 AAAAAAATAAAA-AACAA
1 AAAAAAATAAAATAA-AA
3045 AAAAAAA-AAAA-AAAA
1 AAAAAAATAAAATAAAA
3060 AAAAAAA-AAAATAAAA
1 AAAAAAATAAAATAAAA
*
3076 AAAAATATAACAA-AAAGTA
1 AAAAAAATAA-AATAAA--A
**
3095 AAAAAAA-AAACGAAAA
1 AAAAAAATAAAATAAAA
3111 AAAAAAATTATAAATTAATTATA
1 AAAAAAA-TA-AAA-TAA--A-A
3134 AAATAAAATAAAATAAAA
1 AAA-AAAATAAAATAAAA
3152 AAAA
1 AAAA
3156 CATATAATCA
Statistics
Matches: 564, Mismatches: 119, Indels: 164
0.67 0.14 0.19
Matches are distributed among these distances:
15 29 0.05
16 126 0.22
17 140 0.25
18 113 0.20
19 77 0.14
20 43 0.08
21 13 0.02
22 13 0.02
23 6 0.01
24 4 0.01
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAAAAATAAAATAAAA
Found at i:3652 original size:28 final size:29
Alignment explanation
Indices: 3590--3652 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
3580 AAAGATCTAA
*
3590 ACAAAATAAAAAATAAATAAATTAATTAT
1 ACAAAATAAAAAATAAACAAATTAATTAT
* *
3619 -CTAAATAAAAAA-AAACAAATCT-CTTAT
1 ACAAAATAAAAAATAAACAAAT-TAATTAT
3646 ACAAAAT
1 ACAAAAT
3653 TCAAAAACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
27 11 0.39
28 17 0.61
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (29 bp):
ACAAAATAAAAAATAAACAAATTAATTAT
Found at i:13895 original size:39 final size:40
Alignment explanation
Indices: 13818--13964 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
13808 TAGCTCCTCG
* * *
13818 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
13858 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
13897 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
13937 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
13965 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:13975 original size:80 final size:80
Alignment explanation
Indices: 13864--14044 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
13854 CTCATTCAAT
* * *
13864 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
13927 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
13943 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
14007 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
14024 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
14045 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:14004 original size:40 final size:40
Alignment explanation
Indices: 13861--14044 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
13851 TAACTCATTC
* *
13861 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
13901 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
13941 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
13981 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
14022 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
14045 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:21725 original size:39 final size:40
Alignment explanation
Indices: 21648--21794 Score: 120
Period size: 40 Copynumber: 3.7 Consensus size: 40
21638 TAGCTCCTCG
* * *
21648 TTCAAGTGCCTTCGGGACATAGCCCGG-TTATAGTAACTCA
1 TTCAA-TGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
* *
21688 TTCAATGCCTTCGGGACTTAACCCGGATTTTA-AAACTCG
1 TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** * * * *
21727 CACGAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCG
1 TTC-AATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
** *
21767 CACAAAGGCCTTCGGGACTTAACCCGGA
1 TTC-AATGCCTTCGGGACTTAACCCGGA
21795 ATTAATAACT
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
39 27 0.29
40 65 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
TTCAATGCCTTCGGGACTTAACCCGGATTATAGAAACTCA
Found at i:21805 original size:80 final size:80
Alignment explanation
Indices: 21694--21874 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
21684 CTCATTCAAT
* * *
21694 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCGGA-AT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTC-GGATCTTAACCCGGATA-
*
21757 TAGT-A-TCTCGCACAAA
64 TAGTCACT-TAGCACAAA
**
21773 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTCGGATCTTAGTCCGGATA
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGATCTTAACCCGGATA
21837 TAGTCACTTAGCACAAA
64 TAGTCACTTAGCACAAA
*
21854 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
21875 CAGCATTCAA
Statistics
Matches: 89, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
79 7 0.08
80 71 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGATCTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:21834 original size:40 final size:40
Alignment explanation
Indices: 21691--21874 Score: 196
Period size: 40 Copynumber: 4.6 Consensus size: 40
21681 TAACTCATTC
* *
21691 AATGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACA
* *
21731 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
*
21771 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
* ** * * *
21811 AATACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAATAAC-TCGCACA
*
21852 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
21875 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
39 8 0.07
40 103 0.84
41 11 0.09
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
Found at i:35514 original size:25 final size:25
Alignment explanation
Indices: 35485--35568 Score: 80
Period size: 25 Copynumber: 3.4 Consensus size: 25
35475 AGCTATAAAT
*
35485 GATAAGCTCCTCTGAGCTGAATAAC
1 GATAAGCTCCTCCGAGCTGAATAAC
* *
35510 GATAAGCTCTTCCGAGTTGAATAAC
1 GATAAGCTCCTCCGAGCTGAATAAC
* * * *
35535 -AGTAAGCTCCTTCAAACTGAATAAT
1 GA-TAAGCTCCTCCGAGCTGAATAAC
*
35560 GGTAAGCTC
1 GATAAGCTC
35569 ATACGAATGA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
24 1 0.02
25 46 0.98
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (25 bp):
GATAAGCTCCTCCGAGCTGAATAAC
Done.