Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 43 of 438
Found at i:10810529 original size:17 final size:17
Alignment explanation
Indices: 10810485--10810542 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 17
10810475 GAAGAAAAAA
*
10810485 GAAAAAGAAAAAGAGAAG
1 GAAAAAG-AAGAGAGAAG
*
10810503 GAGAAGAAGAAGAGGGAAG
1 GA-AA-AAGAAGAGAGAAG
10810522 GAAAAAGAAG-GA-AA-
1 GAAAAAGAAGAGAGAAG
10810536 GAAAAAG
1 GAAAAAG
10810543 GTAATTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 7 0.20
15 2 0.06
16 1 0.03
17 6 0.17
18 4 0.11
19 12 0.34
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGAGAGAAG
Found at i:10811021 original size:30 final size:31
Alignment explanation
Indices: 10810981--10811039 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
10810971 TTTTGTTAAA
10810981 ATAATATAAAAAAATAAAATATGAAAATAGT
1 ATAATATAAAAAAATAAAATATGAAAATAGT
*
10811012 ATAAT-TAAAAAAATAAAATTTGAAAATA
1 ATAATATAAAAAAATAAAATATGAAAATA
10811040 AAAAAATACG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (31 bp):
ATAATATAAAAAAATAAAATATGAAAATAGT
Found at i:10811144 original size:136 final size:133
Alignment explanation
Indices: 10810991--10811247 Score: 320
Period size: 136 Copynumber: 1.9 Consensus size: 133
10810981 ATAATATAAA
** * * *
10810991 AAAATAAAATATGAAAATAGTATAATTAAAAAAATAAAATTTGAAAATAAAAAAATACGAACAAG
1 AAAATAAAATACCAAAATAATATAATTAAAAAAAT--AA--T-AAAAGAAAAAAATACGAACAAA
* **
10811056 GTGCCAAAGTCA-GGTTACTTATTAAATTAATATAAAAAA-ACTTAAATAATACATTTGAATGAT
61 GTGCCAAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAATGAT
10811119 TTTATGCT
126 TTTATGCT
* * * * * *
10811127 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATACCAAAATAATATAATTAAAAAAATAATAAAAGAAAAAAATACGAACAAAGTGCC
*
10811192 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
66 AAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAA
10811248 GCATTATGTA
Statistics
Matches: 104, Mismatches: 15, Indels: 7
0.83 0.12 0.06
Matches are distributed among these distances:
131 27 0.26
132 25 0.24
133 20 0.19
134 2 0.02
136 30 0.29
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (133 bp):
AAAATAAAATACCAAAATAATATAATTAAAAAAATAATAAAAGAAAAAAATACGAACAAAGTGCC
AAAATCAGGGTTACTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAATGATTTTAT
GCT
Found at i:10811303 original size:146 final size:146
Alignment explanation
Indices: 10811127--10812042 Score: 946
Period size: 146 Copynumber: 6.1 Consensus size: 146
10811117 ATTTTATGCT
* *
10811127 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAAAACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
10811192 -AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATG
66 CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
10811256 TACTAAAATAATATAA
131 TACTAAAATAATATAA
* *
10811272 AGAAATAAAAAACGAAAATAATATATATTAAAAAATAATATACGAAAATAAAAAAATTACGAAGA
1 A-AAATAAAAAACGAAAATAATATATTTTAAAAAATAATATACG-----AAAAAAA-TACGAATA
* * * * *
10811337 AAGT-ATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAACAGTTAATTAATACA
59 AAGTGCTCAAAATCAGGGTTATTTA-TTAAAAA-----AATATAAA-AAATACTTAAATAATACA
*** * * *
10811401 TTTGAATTTTTTTTTGCTAAAATAATATAA
117 TTTGAAACATTATGTACTAAAATAATATAA
10811431 AAAATAAAATAA-GAAAA-AATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
1 AAAATAAAA-AACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
* *
10811494 T-AAAATCAGGGATATTTATTGAAAAAATATAAAAAATA-TTGAAATAATACATTTGAAACATTA
65 TCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTT-AAATAATACATTTGAAACATTA
10811557 TGTACTAAAATAATATGAA
129 TGTACTAAAATAATAT-AA
* * * *
10811576 GAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAAAATACGAAAAAAGTG-T
1 AAAATAAAAAACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
** *
10811639 CAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAATATACATAATACATTTG
66 CAAAATCAGGGTTATTTATTAAA--AAAATATAAAAA-A--TAC-T--TA-A-ATAATACATTTG
* * *
10811704 AAACATTTTTTGCTAAAATAATATAAA
121 AAACATTATGTACTAAAATAATAT-AA
* *
10811731 AAAATAAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGC
1 AAAATAAAAA-ACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
** * * * *
10811795 T-AAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAATATTAT
65 TCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTAT
* *
10811859 GTACTAAAATAAGGGTTTTA
130 GTACTAAAATAA---TATAA
* * *
10811879 AAATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACGAAAAAAATACGAA-AAA-TG
1 AAAATAAA-AA-ACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTG
* ** *
10811940 -TCAAAATCAGTGTTATTTATTAAATTAATATAAAAAATACTTACATAATAATACATTTAAAACA
64 CTCAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTT--A-AATAATACATTTGAAACA
* *
10812004 TT-TTTGCTAAAATAATATAA
126 TTATGTACTAAAATAATATAA
* *
10812024 AAAATAATATACGAAAATA
1 AAAATAAAAAACGAAAATA
10812043 TTTTACTTAT
Statistics
Matches: 643, Mismatches: 83, Indels: 92
0.79 0.10 0.11
Matches are distributed among these distances:
143 10 0.02
144 38 0.06
145 73 0.11
146 125 0.19
147 20 0.03
148 43 0.07
149 35 0.05
150 8 0.01
151 37 0.06
152 37 0.06
153 8 0.01
154 9 0.01
155 43 0.07
156 69 0.11
157 25 0.04
158 21 0.03
159 42 0.07
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (146 bp):
AAAATAAAAAACGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
CAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
TACTAAAATAATATAA
Found at i:10811308 original size:30 final size:29
Alignment explanation
Indices: 10811262--10811322 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 29
10811252 TATGTACTAA
10811262 AATAATATAAAGAAATAAAAAACGAAAAT
1 AATAATATAAAGAAATAAAAAACGAAAAT
* *
10811291 AATATATATTAAA-AAATAATATACGAAAAT
1 AATA-ATA-TAAAGAAATAAAAAACGAAAAT
10811321 AA
1 AA
10811323 AAAAATTACG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 4 0.14
30 20 0.71
31 4 0.14
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (29 bp):
AATAATATAAAGAAATAAAAAACGAAAAT
Found at i:10811860 original size:301 final size:298
Alignment explanation
Indices: 10811127--10812042 Score: 1161
Period size: 303 Copynumber: 3.1 Consensus size: 298
10811117 ATTTTATGCT
**
10811127 AAAATAAAATACCAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
*
10811192 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAGCATTATGT
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
* * *
10811257 ACTAAAATAATATAAAGAAATAAAAAACGAAAATAATATATATTAAAAAATAATATACGAAAATA
131 ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC----A-A
* * * *
10811322 AAAAAATTACGAAGAAAGTATCAAAATCAGGGTTATTTAGTAAAAAACCCTTAATATAAAGAAAC
191 AAAAAA-TACGAAAAAAGTGTCAAAATCAGGGTTATTTA-T--TAAA---TTAATATAAAAAAAC
* ***
10811387 A-GT--TAAT--TAATACATTTGAATTTTTTTTTGCTAAAATAATAT-AA
249 ACTTACTAATAATAATACATTTGAAACATTTTTTGCTAAAATAATATAAA
10811431 AAAATAAAATAAGAAAA-AATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
1 AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
* *
10811495 AAAATCAGGGATATTTATTGAAAAAATATAAAAAATA-TTGAAATAATACATTTGAAACATTATG
66 AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTT-AAATAATACATTTGAAACATTATG
*
10811559 TACTAAAATAATATGAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATAC-AAAAA
130 TACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAA
*
10811623 AATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAGTATAAAAAAACACTTACATAAT
195 AATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTAC-T-A-
10811688 ATACATAATACATTTGAAACATTTTTTGCTAAAATAATATAAA
257 ATA-ATAATACATTTGAAACATTTTTTGCTAAAATAATATAAA
* *
10811731 AAAATAAAAATAGGAAAATAATATATTTTAAAAAATAATATACG-AAAAAATATGAATAAAGTGC
1 AAAAT-AAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGC
** * * * *
10811795 TAAAATCAGGGTTATTTATTAAAAAAATATTTAAAACACTTAAATAATATATTTAAAATATTATG
65 TAAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATG
* * * * *
10811860 TACTAAAATAAGGGTTTTAA-AATTAAATAATACGAAAGTAATATA-TTTAAAAAA-AAGATACG
130 TACTAAAATAA---TATAAAGAAAT-AA-AATACGAAAATAATATATTTTAAAAAATAAGATACA
* *
10811922 AAAAAAATACG-AAAAA-TGTCAAAATCAGTGTTATTTATTAAATTAATAT-AAAAAATACTTAC
190 AAAAAAATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTAC
*
10811984 --ATAATAATACATTTAAAACA-TTTTTGCTAAAATAATAT-AA
255 TAATAATAATACATTTGAAACATTTTTTGCTAAAATAATATAAA
* *
10812024 AAAATAATATACGAAAATA
1 AAAATAAAATAAGAAAATA
10812043 TTTTACTTAT
Statistics
Matches: 554, Mismatches: 38, Indels: 52
0.86 0.06 0.08
Matches are distributed among these distances:
290 14 0.03
291 1 0.00
292 12 0.02
293 10 0.02
294 19 0.03
295 18 0.03
296 35 0.06
297 7 0.01
299 32 0.06
300 7 0.01
301 107 0.19
302 60 0.11
303 175 0.32
304 41 0.07
305 16 0.03
ACGTcount: A:0.56, C:0.06, G:0.08, T:0.30
Consensus pattern (298 bp):
AAAATAAAATAAGAAAATAATATATTTTAAAAAATAATATACGAAAAAAATACGAATAAAGTGCT
AAAATCAGGGTTATTTATTAAAAAAATATAAAAAATACTTAAATAATACATTTGAAACATTATGT
ACTAAAATAATATAAAGAAATAAAATACGAAAATAATATATTTTAAAAAATAAGATACAAAAAAA
ATACGAAAAAAGTGTCAAAATCAGGGTTATTTATTAAATTAATATAAAAAAACACTTACTAATAA
TAATACATTTGAAACATTTTTTGCTAAAATAATATAAA
Found at i:10813998 original size:72 final size:72
Alignment explanation
Indices: 10813905--10814045 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
10813895 AGTCCGAGAG
*
10813905 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTAACAGGCAATGACTATTTCCCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTAACAGGCAATGACAATTTCCCGG
10813970 GCTCGTC
66 GCTCGTC
* * ** * *
10813977 ATCGCATTCACTTTCGGCTGATACTTCTTATCATCCGGATTTTGCGGGCAATGACAATTTCTCGG
1 ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTAACAGGCAATGACAATTTCCCGG
10814042 GCTC
66 GCTC
10814046 ATCGGGGGCG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.33
Consensus pattern (72 bp):
ATCGCATTCACATTCGACTGATACTTCTTATCATCCGGATTTAACAGGCAATGACAATTTCCCGG
GCTCGTC
Found at i:10814138 original size:33 final size:33
Alignment explanation
Indices: 10814092--10814165 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
10814082 GGGTCGTACA
*
10814092 CACCGCAGCATAGCACCT-CTCCCGGCCCATATC
1 CACCGCAGCATAGCA-CTGCCCCCGGCCCATATC
** *
10814125 CACCGCATTATAGCACTGCCCCCGGCCCGTATC
1 CACCGCAGCATAGCACTGCCCCCGGCCCATATC
*
10814158 CACTGCAG
1 CACCGCAG
10814166 TACTCCACTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 2 0.06
33 32 0.94
ACGTcount: A:0.20, C:0.46, G:0.18, T:0.16
Consensus pattern (33 bp):
CACCGCAGCATAGCACTGCCCCCGGCCCATATC
Found at i:10818204 original size:15 final size:16
Alignment explanation
Indices: 10818185--10818246 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
10818175 TACCTTCTTT
10818185 TTTTCTTCTCCTTCT-
1 TTTTCTTCTCCTTCTA
*
10818200 TTTTCTTCCTTCTCTTCTC
1 TTTTCTT-C-TC-CTTCTA
* *
10818219 CTTTCTT-TCCTTTTA
1 TTTTCTTCTCCTTCTA
10818234 TTTTCTTCTCCTT
1 TTTTCTTCTCCTT
10818247 ACTGCTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 17 0.45
16 8 0.21
17 2 0.05
18 5 0.13
19 6 0.16
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTCTTCTCCTTCTA
Found at i:10819475 original size:21 final size:22
Alignment explanation
Indices: 10819439--10819495 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
10819429 ATATCAAATA
* **
10819439 ATATATAATATATTAAT-ATTTT
1 ATATAT-ATGTATTAATGATTAG
10819461 ATATATATGTATTAATGATTAG
1 ATATATATGTATTAATGATTAG
10819483 ATAT-TATGTATTA
1 ATATATATGTATTA
10819496 TGTGATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (22 bp):
ATATATATGTATTAATGATTAG
Found at i:10820565 original size:2 final size:2
Alignment explanation
Indices: 10820558--10820583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10820548 TTGTCCATGC
10820558 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
10820584 GCATTAATGA
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):
AT
Found at i:10820623 original size:18 final size:20
Alignment explanation
Indices: 10820600--10820639 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
10820590 ATGATTAGAC
10820600 ATTATAT-TATTATT-TAAT
1 ATTATATCTATTATTATAAT
*
10820618 ATTATATCTTTTATTATAAT
1 ATTATATCTATTATTATAAT
10820638 AT
1 AT
10820640 ATAATATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 6 0.32
20 6 0.32
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
ATTATATCTATTATTATAAT
Found at i:10820670 original size:32 final size:31
Alignment explanation
Indices: 10820634--10820704 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
10820624 TCTTTTATTA
*
10820634 TAATATATAATA-TAATAGTTATATATATGTAT
1 TAATATAT-ATAGTAATAGTTATATAT-TATAT
*
10820666 TAATAGT-TTTAGTAATAGTTATATATTATAT
1 TAATA-TATATAGTAATAGTTATATATTATAT
*
10820697 TATTATAT
1 TAATATAT
10820705 TATTATATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
30 1 0.03
31 11 0.33
32 20 0.61
33 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (31 bp):
TAATATATATAGTAATAGTTATATATTATAT
Found at i:10820702 original size:8 final size:8
Alignment explanation
Indices: 10820600--10820712 Score: 58
Period size: 8 Copynumber: 13.9 Consensus size: 8
10820590 ATGATTAGAC
10820600 ATTATATT
1 ATTATATT
10820608 ATTAT-TT
1 ATTATATT
10820615 A--ATATT
1 ATTATATT
* *
10820621 ATATCTTTT
1 AT-TATATT
*
10820630 ATTATAAT
1 ATTATATT
*
10820638 A-TATAAT
1 ATTATATT
*
10820645 ATAATAGTT
1 ATTATA-TT
10820654 ATATATATGT
1 AT-TATAT-T
10820664 ATTAATAGTT
1 ATT-ATA-TT
*
10820674 -TTAGTAAT
1 ATTA-TATT
10820682 AGTTATA-T
1 A-TTATATT
10820690 ATTATATT
1 ATTATATT
10820698 ATTATATT
1 ATTATATT
10820706 ATTATAT
1 ATTATAT
10820713 GATGTAATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 28
0.69 0.08 0.24
Matches are distributed among these distances:
5 2 0.02
6 3 0.04
7 15 0.18
8 32 0.39
9 16 0.20
10 13 0.16
11 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (8 bp):
ATTATATT
Found at i:10832853 original size:31 final size:31
Alignment explanation
Indices: 10832818--10832879 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
10832808 AAAATTATAA
10832818 TTCATGGTCTAAATGCATGATGTCGTATCTG
1 TTCATGGTCTAAATGCATGATGTCGTATCTG
10832849 TTCATGGTCTAAATGCATGATGTCGTATCTG
1 TTCATGGTCTAAATGCATGATGTCGTATCTG
10832880 CAAGGCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.23, T:0.39
Consensus pattern (31 bp):
TTCATGGTCTAAATGCATGATGTCGTATCTG
Found at i:10839665 original size:125 final size:125
Alignment explanation
Indices: 10839474--10839712 Score: 460
Period size: 125 Copynumber: 1.9 Consensus size: 125
10839464 AGGTCTAAGG
10839474 GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTGTGG
1 GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTGTGG
10839539 AGTACCTAGATCAATAAAATGATTAAATTTGTGAATTTATATCATTATAAAAATTGTAGA
66 AGTACCTAGATCAATAAAATGATTAAATTTGTGAATTTATATCATTATAAAAATTGTAGA
*
10839599 GTAAAATGGTCATTTTGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTGTGG
1 GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTGTGG
*
10839664 AGTACCTAGATCAATAAAATGATTAAATTTGTGAATTTTTATCATTATA
66 AGTACCTAGATCAATAAAATGATTAAATTTGTGAATTTATATCATTATA
10839713 GATCAAGAAT
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
125 112 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (125 bp):
GTAAAATGGTCATTTCGTGAAAGTCTAAGGGCAAAATGGTTATTTTGCCCAATTATGAATTGTGG
AGTACCTAGATCAATAAAATGATTAAATTTGTGAATTTATATCATTATAAAAATTGTAGA
Found at i:10839773 original size:18 final size:18
Alignment explanation
Indices: 10839750--10839789 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
10839740 GACCGGGGAA
10839750 AAGCAAAACAAGTGGACT
1 AAGCAAAACAAGTGGACT
10839768 AAGCAAAACAAGTGGACT
1 AAGCAAAACAAGTGGACT
10839786 AAGC
1 AAGC
10839790 CGAACTAGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.23, T:0.10
Consensus pattern (18 bp):
AAGCAAAACAAGTGGACT
Found at i:10840135 original size:46 final size:48
Alignment explanation
Indices: 10840002--10840262 Score: 222
Period size: 46 Copynumber: 5.5 Consensus size: 48
10839992 TTTGTATGCC
* * * *
10840002 AGTGTAAGACCATGTCTGGGACATGGCATCAG-TATTGAGACGAAAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTA-CGAGATGTAAGCT
* * * *
10840050 AGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCTTC-AGATGTAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GGCTACGAGATGTAAGCT
*
10840096 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGATGT--GTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGAGATGTAAGCT
* * * *
10840140 AGTGTAAGGCCATGTCTAGGACATGGCATCGGC-ACGTATAGAGGT--GTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACG---AGATGTAAGCT
* * *
10840188 AGTGTAAGACCATGTCTTGGACATGGCATCGAC-ACGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCTAC-GAGATGT-A-AGCT
10840238 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTGGGACATG
10840263 ACGTCGGCCT
Statistics
Matches: 177, Mismatches: 23, Indels: 24
0.79 0.10 0.11
Matches are distributed among these distances:
44 9 0.05
45 20 0.11
46 58 0.33
47 13 0.07
48 50 0.28
49 1 0.01
50 26 0.15
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCTACGAGATGTAAGCT
Found at i:10840201 original size:48 final size:47
Alignment explanation
Indices: 10840096--10840316 Score: 189
Period size: 48 Copynumber: 4.6 Consensus size: 47
10840086 GATGTAAGCC
*
10840096 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACG--AGATGTGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACGATAGAGGTGTT
* *
10840140 AGTGTAAGGCCATGTCTAGGACATGGCATCGGCACGTATAGAGGTGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACG-ATAGAGGTGTT
* * * * *
10840188 AGTGTAAGACCATGTCTTGGACATGGCATCGACACGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GATA-GAG-GTGTT
* * * *** * *
10840238 AGTGTAAGACCATGTCTGGGACATGACGTCGGCCTCGATTTTGATAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACGATAGAGGT-GTT
* *
10840287 AGTGTAAGATCATGCCTGGGACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
10840317 TACAACATAC
Statistics
Matches: 143, Mismatches: 24, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
44 8 0.06
45 16 0.11
46 8 0.06
48 43 0.30
49 32 0.22
50 34 0.24
51 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (47 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACGATAGAGGTGTT
Found at i:10840252 original size:50 final size:48
Alignment explanation
Indices: 10840002--10840262 Score: 159
Period size: 48 Copynumber: 5.5 Consensus size: 48
10839992 TTTGTATGCC
* * ** * *
10840002 AGTGTAAGACCATGTCTGGGACATGGCATC-AGTATTGAGACGA-AAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGA-CACGGATA-GAGGAGCT
* * * *
10840050 AGTGTAAGA-CATGTCTAGGACAT-GCATCAGCCTTCAGAT-GTA--AGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATC-GAC-ACGGATAG-AGGAGCT
* * * * *
10840096 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTAC-G--AGATGTGTT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGAC-ACGGATAGAGGAGCT
* * * * *
10840140 AGTGTAAGGCCATGTCTAGGACATGGCATCGGCACGTATAGAGGTGTT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGACACGGATAGAGGAGCT
* *
10840188 AGTGTAAGACCATGTCTTGGACATGGCATCGACACGGATATGTGAGAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGACACGGATA-GAG-GAGCT
*
10840238 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGACCATGTCTAGGACATG
10840263 ACGTCGGCCT
Statistics
Matches: 173, Mismatches: 26, Indels: 26
0.77 0.12 0.12
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 10 0.06
45 19 0.11
46 44 0.25
47 14 0.08
48 55 0.32
49 2 0.01
50 27 0.16
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.25
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGACACGGATAGAGGAGCT
Found at i:10846877 original size:2 final size:2
Alignment explanation
Indices: 10846872--10846902 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
10846862 GAAAAAAATA
*
10846872 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10846903 ATAAATTAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:10847650 original size:10 final size:10
Alignment explanation
Indices: 10847631--10847667 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
10847621 AATTTTAGCT
*
10847631 TTTATTTCTA
1 TTTATCTCTA
10847641 TTTATCTCTA
1 TTTATCTCTA
*
10847651 TTTATCTTTA
1 TTTATCTCTA
10847661 TTTATCT
1 TTTATCT
10847668 TTTAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.68
Consensus pattern (10 bp):
TTTATCTCTA
Found at i:10851951 original size:11 final size:11
Alignment explanation
Indices: 10851935--10851960 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
10851925 CCAACAGATT
10851935 TAACTAACAGC
1 TAACTAACAGC
10851946 TAACTAACAGC
1 TAACTAACAGC
10851957 TAAC
1 TAAC
10851961 AGATTAACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.27, G:0.08, T:0.19
Consensus pattern (11 bp):
TAACTAACAGC
Found at i:10859810 original size:25 final size:26
Alignment explanation
Indices: 10859782--10859832 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
10859772 ATTTGTAATT
* *
10859782 TAATACATTT-AAAATATTAAATATA
1 TAATAAATTTAAAAAAATTAAATATA
10859807 TAATAAATTTAAAAAAATTAAATATA
1 TAATAAATTTAAAAAAATTAAATATA
10859833 ATTATCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TAATAAATTTAAAAAAATTAAATATA
Found at i:10866318 original size:16 final size:17
Alignment explanation
Indices: 10866287--10866320 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
10866277 ATTGTGCATA
10866287 AAAAGAAAGAAAAATAT
1 AAAAGAAAGAAAAATAT
*
10866304 AAAAG-AAGGAAAATAT
1 AAAAGAAAGAAAAATAT
10866320 A
1 A
10866321 GTGAGGATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (17 bp):
AAAAGAAAGAAAAATAT
Found at i:10871619 original size:20 final size:21
Alignment explanation
Indices: 10871591--10871630 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10871581 CTTTTATACC
10871591 AATAAATAC-ATAAAATAAAA
1 AATAAATACTATAAAATAAAA
*
10871611 AATATATACTATAAAATAAA
1 AATAAATACTATAAAATAAA
10871631 TTAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (21 bp):
AATAAATACTATAAAATAAAA
Found at i:10872508 original size:36 final size:37
Alignment explanation
Indices: 10872468--10872542 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 37
10872458 TATAGAATGC
*
10872468 TTTTTA-GTTCTTATATATATTTGTA-ATTTTATAAAT
1 TTTTTATG-TCTTATATATATTTATATATTTTATAAAT
*
10872504 TTTTTATGTCTTTTATATATTTATATATTTTATAAAT
1 TTTTTATGTCTTATATATATTTATATATTTTATAAAT
10872541 TT
1 TT
10872543 ATATTTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 21 0.60
37 14 0.40
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (37 bp):
TTTTTATGTCTTATATATATTTATATATTTTATAAAT
Found at i:10872528 original size:8 final size:8
Alignment explanation
Indices: 10872515--10872571 Score: 66
Period size: 7 Copynumber: 7.4 Consensus size: 8
10872505 TTTTATGTCT
10872515 TTTATATA
1 TTTATATA
10872523 TTTATATA
1 TTTATATA
*
10872531 TTTTATAAA
1 -TTTATATA
10872540 TTTATAT-
1 TTTATATA
*
10872547 TTTTTA-A
1 TTTATATA
10872554 TTTATATA
1 TTTATATA
10872562 -TTATATA
1 TTTATATA
10872569 TTT
1 TTT
10872572 TTCAAAATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 17 0.41
8 17 0.41
9 7 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTATATA
Found at i:10872545 original size:15 final size:15
Alignment explanation
Indices: 10872527--10872571 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
10872517 TATATATTTA
10872527 TATATTTTATAAATT
1 TATATTTTATAAATT
*
10872542 TATATTTT-TTAATT
1 TATATTTTATAAATT
* *
10872556 TATATATTATATATT
1 TATATTTTATAAATT
10872571 T
1 T
10872572 TTCAAAATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATATTTTATAAATT
Found at i:10873966 original size:16 final size:16
Alignment explanation
Indices: 10873939--10873979 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
10873929 GTGGCCGGAG
*
10873939 CTCTCCCCTTTCCCCT
1 CTCTCCCTTTTCCCCT
*
10873955 CTCTTCCTTTTCCCCT
1 CTCTCCCTTTTCCCCT
10873971 CTCTCCCTT
1 CTCTCCCTT
10873980 CTTTCTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (16 bp):
CTCTCCCTTTTCCCCT
Found at i:10873982 original size:23 final size:23
Alignment explanation
Indices: 10873942--10873988 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
10873932 GCCGGAGCTC
*
10873942 TCCCCTTTCCCCTCTCTTCCTTT
1 TCCCCTCTCCCCTCTCTTCCTTT
*
10873965 TCCCCTCTCTCCCT-TCTTTCTTT
1 TCCCCTCTC-CCCTCTCTTCCTTT
10873988 T
1 T
10873989 TTTTTCTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (23 bp):
TCCCCTCTCCCCTCTCTTCCTTT
Found at i:10873984 original size:18 final size:17
Alignment explanation
Indices: 10873939--10873984 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
10873929 GTGGCCGGAG
10873939 CTCTCCC-CTTTCCCCT
1 CTCTCCCTCTTTCCCCT
*
10873955 CTCTTCCT-TTTCCCCT
1 CTCTCCCTCTTTCCCCT
10873971 CTCTCCCTTCTTTC
1 CTCTCCC-TCTTTC
10873985 TTTTTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 20 0.80
17 1 0.04
18 4 0.16
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (17 bp):
CTCTCCCTCTTTCCCCT
Found at i:10874879 original size:27 final size:27
Alignment explanation
Indices: 10874839--10874900 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
10874829 GTTGTATGTA
* *
10874839 TATTTTTTAT-TATTAGTT-ATGTAT-
1 TATTTTTTATATACTATTTCATGTATG
10874863 T-TTTTTTATATACTATTTCATGTATG
1 TATTTTTTATATACTATTTCATGTATG
10874889 TATTTTTTATAT
1 TATTTTTTATAT
10874901 GTTATCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 6 0.19
26 1 0.03
27 10 0.31
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.66
Consensus pattern (27 bp):
TATTTTTTATATACTATTTCATGTATG
Found at i:10874885 original size:25 final size:24
Alignment explanation
Indices: 10874833--10874900 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
10874823 TATGTCGTTG
* *
10874833 TATGTATATTTTTTAT-TATTAGT
1 TATGTATTTTTTTTATATACTAGT
*
10874856 TATGTATTTTTTTTATATACTATT
1 TATGTATTTTTTTTATATACTAGT
10874880 TCATGTATGTATTTTTTATAT
1 T-ATGTAT-T-TTTTTTATAT
10874901 GTTATCCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 15 0.39
24 6 0.16
25 6 0.16
26 1 0.03
27 10 0.26
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (24 bp):
TATGTATTTTTTTTATATACTAGT
Found at i:10874993 original size:2 final size:2
Alignment explanation
Indices: 10874938--10874984 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
10874928 AGTATATGTT
* *
10874938 TA TA TA TA TA TA TA TA TA TA TA TA TC TT TA -A TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10874979 TA TA TA
1 TA TA TA
10874985 GGCATATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10887537 original size:71 final size:70
Alignment explanation
Indices: 10887438--10887613 Score: 230
Period size: 71 Copynumber: 2.5 Consensus size: 70
10887428 CTTTTCAAGG
* *
10887438 AAAATCAACTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAATTTT
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTA
10887502 TGTTTT
65 TGTTTT
** * *
10887508 CAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTTAGTTTA
1 -AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTA
10887573 TGTTTT
65 TGTTTT
** * *
10887579 -AAATTGACTCATATTGCGAGAGGTGAGTTAAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
10887614 TTTAATTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
69 31 0.33
71 61 0.65
72 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (70 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTTAATTTAT
GTTTT
Found at i:10887728 original size:71 final size:72
Alignment explanation
Indices: 10887613--10887806 Score: 230
Period size: 71 Copynumber: 2.7 Consensus size: 72
10887603 GAGTTAAGCC
* * * *
10887613 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGGCACGCT
1 TTTTAATTTTTGTTTTTCAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGAT
10887678 GAGGT-A
66 GAGGTAA
** * * *
10887684 TTTTAATTTTTGTGTTTT-AATTTTAACTCATATTACGAGAGGTGAGTTGTGCCTCAGGATACGA
1 TTTTAATTTTTGT-TTTTCAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGA
10887748 TGAGGTAA
65 TGAGGTAA
* * * * *
10887756 TTTCAATTTCTGTTTGTCAGGAATCAACTCATATTACGAGAGGTGGGTTGA
1 TTTTAATTTTTGTTTTTCA-AAATCAACTCATATTACGAGAGGTGAGTTGA
10887807 ACCTTTTAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
71 59 0.58
72 17 0.17
73 25 0.25
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (72 bp):
TTTTAATTTTTGTTTTTCAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGAT
GAGGTAA
Found at i:10887909 original size:126 final size:127
Alignment explanation
Indices: 10887710--10888150 Score: 742
Period size: 127 Copynumber: 3.5 Consensus size: 127
10887700 TTAATTTTAA
* *
10887710 CTCATATTACGAGAGGTGAGTTGTGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCA
* *
10887775 GGAATCAACTCATATTACGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATTAG
66 GGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAG
*
10887837 CTCATATTGCGAG-GGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTTAATTTCTGTTTGTCA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCA
10887901 GGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAG
66 GGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAG
* * * *
10887963 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACTATGAGATAATTTCAATTTCTGCTTGTCA
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCA
* *
10888028 AGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTAAAAATCAG
66 GGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAG
* *
10888090 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-TCACGCTGAGGTATTTTCAATTTCTGTTT
1 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAT-ACGATGAGGTAATTTCAATTTCTGTTT
10888151 TCAATTTATG
Statistics
Matches: 294, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
126 122 0.41
127 172 0.59
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (127 bp):
CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGATGAGGTAATTTCAATTTCTGTTTGTCA
GGAATCAACTCATATTGCGAGAGGTGGGTTGAACCTTTTAATTTCTACTTTTTCAAAATCAG
Found at i:10888153 original size:13 final size:13
Alignment explanation
Indices: 10888135--10888168 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10888125 CGCTGAGGTA
*
10888135 TTTTCAATTTCTG
1 TTTTCAATTTATG
10888148 TTTTCAATTTATG
1 TTTTCAATTTATG
10888161 TTGTTCAA
1 TT-TTCAA
10888169 GAATCAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.59
Consensus pattern (13 bp):
TTTTCAATTTATG
Found at i:10888219 original size:86 final size:88
Alignment explanation
Indices: 10888084--10888293 Score: 343
Period size: 86 Copynumber: 2.4 Consensus size: 88
10888074 ACTTTTTAAA
* *
10888084 AATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATTTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
*
10888149 TTTCAAT-TTATGTTGTT-CAAG
66 TTTCAATATTATGTTGTTGAAAG
*
10888170 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTTACGCCGAGGTATTTTCAATTTCTGT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
* *
10888235 TTTCATTATTATGTTTTTGAAAG
66 TTTCAATATTATGTTGTTGAAAG
*
10888258 AATCAACTCATATTGCGAGAGGTGAGTCGAGCCTCA
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCA
10888294 AGCCACGCAC
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
86 68 0.59
87 9 0.08
88 38 0.33
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (88 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGTCACGCCGAGGTATTTTCAATTTCTGT
TTTCAATATTATGTTGTTGAAAG
Found at i:10888512 original size:55 final size:56
Alignment explanation
Indices: 10888383--10888537 Score: 260
Period size: 56 Copynumber: 2.8 Consensus size: 56
10888373 GCTGAGGTAT
*
10888383 TTTTAATTTCTGTTGTTTC-AAAAATCAACTCATGTTGCGAGAGGTGAGTTAAGCC
1 TTTTAATTTCTGTTGTTTCAAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAACC
10888438 TTTTAATTTCTGTTGTTTCAAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAACC
1 TTTTAATTTCTGTTGTTTCAAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAACC
* *
10888494 TTTTAATTTCTGTT-TTTCAAAAAAATCAACTCATATTACGAGAG
1 TTTTAATTTCTGTTGTTTC-AAAAAATCAACTCATGTTGCGAGAG
10888538 AGTCAATTCA
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
55 23 0.24
56 72 0.76
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (56 bp):
TTTTAATTTCTGTTGTTTCAAAAAATCAACTCATGTTGCGAGAGGTGAGTTAAACC
Found at i:10889874 original size:16 final size:16
Alignment explanation
Indices: 10889845--10889887 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
10889835 GTAGCCGGAG
10889845 CTCTC-CCCTT-TCCC
1 CTCTCTCCCTTCTCCC
*
10889859 CTCTCTTCCTTCTCCC
1 CTCTCTCCCTTCTCCC
10889875 CTCTCTCCCTTCT
1 CTCTCTCCCTTCT
10889888 TTCTTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 16 0.64
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (16 bp):
CTCTCTCCCTTCTCCC
Found at i:10890793 original size:27 final size:27
Alignment explanation
Indices: 10890753--10890814 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
10890743 GTTGTATGTA
* *
10890753 TATTTTTTAT-TATTAGTT-ATGTAT-
1 TATTTTTTATATACTATTTCATGTATG
10890777 T-TTTTTTATATACTATTTCATGTATG
1 TATTTTTTATATACTATTTCATGTATG
10890803 TATTTTTTATAT
1 TATTTTTTATAT
10890815 GTTATCCTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 6 0.19
26 1 0.03
27 10 0.31
ACGTcount: A:0.24, C:0.03, G:0.06, T:0.66
Consensus pattern (27 bp):
TATTTTTTATATACTATTTCATGTATG
Found at i:10890799 original size:25 final size:24
Alignment explanation
Indices: 10890747--10890814 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 24
10890737 TATGTCGTTG
* *
10890747 TATGTATATTTTTTAT-TATTAGT
1 TATGTATTTTTTTTATATACTAGT
*
10890770 TATGTATTTTTTTTATATACTATT
1 TATGTATTTTTTTTATATACTAGT
10890794 TCATGTATGTATTTTTTATAT
1 T-ATGTAT-T-TTTTTTATAT
10890815 GTTATCCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
23 15 0.39
24 6 0.16
25 6 0.16
26 1 0.03
27 10 0.26
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (24 bp):
TATGTATTTTTTTTATATACTAGT
Found at i:10890931 original size:2 final size:2
Alignment explanation
Indices: 10890852--10890922 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
10890842 AGTATATGTT
10890852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
10890894 TA TA TA TA TC TT TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10890923 GGCATATATT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10894384 original size:21 final size:19
Alignment explanation
Indices: 10894353--10894403 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
10894343 GTACAAAAAA
*
10894353 AAAAATTAATTGAATCAATT
1 AAAAATTAATTAAATCAA-T
*
10894373 AAAAATTAAATTAAATCGAT
1 AAAAATT-AATTAAATCAAT
*
10894393 AAAAAGTAATT
1 AAAAATTAATT
10894404 TTATGAGGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 4 0.15
20 14 0.52
21 9 0.33
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAAATTAATTAAATCAAT
Found at i:10895200 original size:2 final size:2
Alignment explanation
Indices: 10895193--10895223 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10895183 TGTATTGTGT
10895193 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 T
10895224 TGGTACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10896307 original size:20 final size:22
Alignment explanation
Indices: 10896253--10896295 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
10896243 AAAGACATGC
10896253 ATAATA-TCAAATAATAATAATA
1 ATAATATTCAAA-AATAATAATA
10896275 ATAATATTCAAAAATAA-AATA
1 ATAATATTCAAAAATAATAATA
10896296 TATTATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 11 0.55
23 5 0.25
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAATATTCAAAAATAATAATA
Found at i:10897769 original size:30 final size:30
Alignment explanation
Indices: 10897711--10897777 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
10897701 AATTTTTACT
*
10897711 TAAATAATTAATTAAGTCCTTAGTAAAATAA
1 TAAA-AATTAATTAAGTCCCTAGTAAAATAA
* *
10897742 TAAAAATTCAATTAAG-CCCTCGTAAAATGA
1 TAAAAATT-AATTAAGTCCCTAGTAAAATAA
10897772 TAAAAA
1 TAAAAA
10897778 AAATTTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 21 0.66
31 11 0.34
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.30
Consensus pattern (30 bp):
TAAAAATTAATTAAGTCCCTAGTAAAATAA
Found at i:10897788 original size:33 final size:32
Alignment explanation
Indices: 10897738--10897799 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
10897728 CCTTAGTAAA
*
10897738 ATAATAAAAATTCAATTAAGCCCTCGTAAAATG
1 ATAAAAAAAATTCAATTAAGCCCTC-TAAAATG
* *
10897771 ATAAAAAAAATTTAATTAAGCTCTCTAAA
1 ATAAAAAAAATTCAATTAAGCCCTCTAAA
10897800 TCATCATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (32 bp):
ATAAAAAAAATTCAATTAAGCCCTCTAAAATG
Found at i:10916778 original size:13 final size:13
Alignment explanation
Indices: 10916748--10916791 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
10916738 ATTGGTTGAG
*
10916748 AAATTAATTTAGTT
1 AAATTAA-TTAATT
10916762 AAATTAATTAATT
1 AAATTAATTAATT
*
10916775 AAATTAATTGATT
1 AAATTAATTAATT
10916788 AAAT
1 AAAT
10916792 AAATAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
13 21 0.75
14 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:10916956 original size:93 final size:93
Alignment explanation
Indices: 10916797--10916983 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
10916787 TAAATAAATA
10916797 ATATTTTGGGAAATAGAAATAGTTACTAAGTTGCATAAATTATAAGTGTTGGATAAAAGTTTATA
1 ATATTTTGGGAAATAGAAATAGTTACTAAGTTGCATAAATTATAAGTGTTGGATAAAAGTTTATA
10916862 TAACACATATAATGATACTCAATACATG
66 TAACACATATAATGATACTCAATACATG
*
10916890 ATATTTTGGGAAATAGAAATAGTTACTGAGTTGCATAAATTATAAGTGTTGGATAAAAGTTTATA
1 ATATTTTGGGAAATAGAAATAGTTACTAAGTTGCATAAATTATAAGTGTTGGATAAAAGTTTATA
10916955 TAACACATATAATGATACTCAATACATG
66 TAACACATATAATGATACTCAATACATG
10916983 A
1 A
10916984 AAGGCCTAAA
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (93 bp):
ATATTTTGGGAAATAGAAATAGTTACTAAGTTGCATAAATTATAAGTGTTGGATAAAAGTTTATA
TAACACATATAATGATACTCAATACATG
Found at i:10918632 original size:3 final size:3
Alignment explanation
Indices: 10918624--10918649 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10918614 CCAGTATGGA
10918624 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10918650 AAAATAAAGT
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:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10919185 original size:3 final size:3
Alignment explanation
Indices: 10919177--10919212 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
10919167 TTTAATTGTA
10919177 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
10919213 TGATAGTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:10921096 original size:31 final size:33
Alignment explanation
Indices: 10921047--10921150 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 33
10921037 TTTTGCATTA
* *
10921047 ATTTATATTTTATGTATTATTATA-TT-AAATT
1 ATTTAAATATTATGTATTATTATATTTAAAATT
*
10921078 ATTTAAATATTATTTATTATTATATTTAAAATT
1 ATTTAAATATTATGTATTATTATATTTAAAATT
* * * *
10921111 -TTAAAATATTTCATGTATAATTAAATTTACAAATA
1 ATTTAAATA-TT-ATGTATTATTATATTTA-AAATT
10921146 ATTTA
1 ATTTA
10921151 CTAATTATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 7
0.78 0.12 0.09
Matches are distributed among these distances:
31 21 0.36
32 9 0.16
33 7 0.12
34 14 0.24
35 4 0.07
36 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (33 bp):
ATTTAAATATTATGTATTATTATATTTAAAATT
Found at i:10922459 original size:80 final size:80
Alignment explanation
Indices: 10922321--10922480 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
10922311 TACTGACTAA
*
10922321 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAGTGCATATCATGTTAGT
1 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAGTGCACATCATGTTAGT
10922386 ATAACACCATTTGTT
66 ATAACACCATTTGTT
10922401 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAGTGCACATCATGTTAGT
1 AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAGTGCACATCATGTTAGT
10922466 ATAACACCATTTGTT
66 ATAACACCATTTGTT
10922481 TTATATGTCA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.39
Consensus pattern (80 bp):
AACATTAATTTTTAATATTGTTGGCATGACAACTTGTATGGTAATCCAGTGCACATCATGTTAGT
ATAACACCATTTGTT
Found at i:10922556 original size:16 final size:16
Alignment explanation
Indices: 10922507--10922557 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
10922497 TAAATAATTA
10922507 AAAATTTTAAAAA-AT
1 AAAATTTTAAAAATAT
** *
10922522 AAAATACATCAAAAT-T
1 AAAAT-TTTAAAAATAT
10922538 AAAATTTTAAAAATAT
1 AAAATTTTAAAAATAT
10922554 AAAA
1 AAAA
10922558 AGTTCATAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATTTTAAAAATAT
Found at i:10928576 original size:43 final size:42
Alignment explanation
Indices: 10928509--10928598 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 42
10928499 CAAGGCACAA
*
10928509 TTTTCCTAACATGTCAACAAAAAATGCTTCCAACTTGGTGTG
1 TTTTCCTAACATGTCAACAAAAAATGCTTCCAACTAGGTGTG
* * * *
10928551 TTTTCCTCGACATGTCAGCAGAAAATGCTTCTAACTAGGTGTG
1 TTTTCCT-AACATGTCAACAAAAAATGCTTCCAACTAGGTGTG
*
10928594 CTTTC
1 TTTTC
10928599 TTTCCTCCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
42 7 0.17
43 34 0.83
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (42 bp):
TTTTCCTAACATGTCAACAAAAAATGCTTCCAACTAGGTGTG
Found at i:10934220 original size:13 final size:13
Alignment explanation
Indices: 10934202--10934244 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
10934192 AAAAGTTTGT
10934202 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
*
10934215 AAAAAGAAAACAA
1 AAAAAGAAAAGAA
*
10934228 ACAAAAAAAAACGAA
1 A-AAAAGAAAA-GAA
10934243 AA
1 AA
10934245 GAAAAGTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 13 0.52
14 9 0.36
15 3 0.12
ACGTcount: A:0.84, C:0.07, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:10936291 original size:21 final size:22
Alignment explanation
Indices: 10936250--10936308 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
10936240 AATTTTTTAA
*
10936250 ATTTTAAAAAATTATAGAATTT
1 ATTTTAAAAAATTATAAAATTT
*
10936272 ATTTTGAAAAATTA-AAAA-TT
1 ATTTTAAAAAATTATAAAATTT
*
10936292 A--TTATAAAATTATAAAA
1 ATTTTAAAAAATTATAAAA
10936309 AATATTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 9 0.28
19 4 0.12
20 3 0.09
21 3 0.09
22 13 0.41
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (22 bp):
ATTTTAAAAAATTATAAAATTT
Found at i:10936307 original size:20 final size:20
Alignment explanation
Indices: 10936248--10936314 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
10936238 TTAATTTTTT
* *
10936248 AAATT-TTAAAAAATTATAG
1 AAATTATTATAAAATTATAA
* * *
10936267 AATTTATTTTGAAAAAT-TAA
1 AAATTATTAT-AAAATTATAA
10936287 AAATTATTATAAAATTATAA
1 AAATTATTATAAAATTATAA
*
10936307 AAAATATT
1 AAATTATT
10936315 TTTTTAAATT
Statistics
Matches: 36, Mismatches: 9, Indels: 5
0.72 0.18 0.10
Matches are distributed among these distances:
19 9 0.25
20 22 0.61
21 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATTATTATAAAATTATAA
Found at i:10940675 original size:38 final size:38
Alignment explanation
Indices: 10940618--10940754 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
10940608 TGTAATAGAA
* ** *
10940618 CAATTCAACACTAGTAGTAGACATGTATAACAAGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
* *
10940656 CAATTCAGCACTAACAGTAGAAATGTTTAAC-AGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
* * *
10940693 CAATTTATCATTAACAGTAGACATGTTTAACATGTACT
1 CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
*
10940731 CAATTCATCATTAACAGTAGACAT
1 CAATTCATCACTAACAGTAGACAT
10940755 ACTTATCATG
Statistics
Matches: 87, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
37 33 0.38
38 54 0.62
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (38 bp):
CAATTCATCACTAACAGTAGACATGTTTAACAAGTACT
Found at i:10940765 original size:38 final size:38
Alignment explanation
Indices: 10940633--10940754 Score: 183
Period size: 38 Copynumber: 3.2 Consensus size: 38
10940623 CAACACTAGT
* * * *
10940633 AGTAGACATGTATAACAAGTACTCAATTCAGCACTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
* *
10940671 AGTAGAAATGTTTAACA-GTACTCAATTTATCATTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
10940708 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
1 AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
10940746 AGTAGACAT
1 AGTAGACAT
10940755 ACTTATCATG
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
37 33 0.43
38 43 0.57
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.30
Consensus pattern (38 bp):
AGTAGACATGTTTAACATGTACTCAATTCATCATTAAC
Found at i:10942183 original size:20 final size:21
Alignment explanation
Indices: 10942129--10942183 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
10942119 TTTGCCTAAG
* * *
10942129 ATGTGAATTGGATTGAATTGA
1 ATGTAAATTGTATTAAATTGA
10942150 ATGTAAATTGTATTAAATTG-
1 ATGTAAATTGTATTAAATTGA
10942170 ATGTTAAATT-TATT
1 ATG-TAAATTGTATT
10942184 CGTATAGATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (21 bp):
ATGTAAATTGTATTAAATTGA
Found at i:10942524 original size:24 final size:25
Alignment explanation
Indices: 10942486--10942544 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
10942476 CAACTCGAAA
* * *
10942486 GAGCATTCCGTTA-TTAGCTTTCAT
1 GAGCATCCCGATATTTAGCTCTCAT
*
10942510 GAGCATCCCGATATTTGGCTCTCAT
1 GAGCATCCCGATATTTAGCTCTCAT
*
10942535 GAGCTTCCCG
1 GAGCATCCCG
10942545 TTATATGGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
GAGCATCCCGATATTTAGCTCTCAT
Found at i:10942817 original size:25 final size:25
Alignment explanation
Indices: 10942788--10942850 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
10942778 ATGGCTTTCT
*
10942788 AGAGCTTCCCGTTGCATGGCTC-ACA
1 AGAGCTTCCCGTTACATGGCTCGA-A
* *
10942813 TGAGCTTCCCGTTATATGGCTCGAA
1 AGAGCTTCCCGTTACATGGCTCGAA
10942838 AGAGCTTCCCGTT
1 AGAGCTTCCCGTT
10942851 TATGTACTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
25 32 0.97
26 1 0.03
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGCTTCCCGTTACATGGCTCGAA
Found at i:10942860 original size:25 final size:25
Alignment explanation
Indices: 10942788--10942867 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
10942778 ATGGCTTTCT
** *
10942788 AGAGCTTCCCGTTGCATGGCTC-ACA
1 AGAGCTTCCCGTTATATGACTCGA-A
* *
10942813 TGAGCTTCCCGTTATATGGCTCGAA
1 AGAGCTTCCCGTTATATGACTCGAA
*
10942838 AGAGCTTCCCGTT-TATGTACTCGTA
1 AGAGCTTCCCGTTATATG-ACTCGAA
10942863 AGAGC
1 AGAGC
10942868 ATTATTGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
24 4 0.09
25 42 0.89
26 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.24, T:0.29
Consensus pattern (25 bp):
AGAGCTTCCCGTTATATGACTCGAA
Found at i:10950598 original size:24 final size:24
Alignment explanation
Indices: 10950552--10950599 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
10950542 TGTTTACCTC
* *
10950552 CGGTGAGGTTAAAAACAGCGGTGG
1 CGGTGAGATTAAAAACAACGGTGG
* *
10950576 CGGTGAGATTAGAAACAATGGTGG
1 CGGTGAGATTAAAAACAACGGTGG
10950600 AGTGTGTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.40, T:0.19
Consensus pattern (24 bp):
CGGTGAGATTAAAAACAACGGTGG
Found at i:10952625 original size:32 final size:32
Alignment explanation
Indices: 10952573--10952743 Score: 285
Period size: 32 Copynumber: 5.4 Consensus size: 32
10952563 AAAATACCAA
10952573 ATATAAAAAA-T--ATCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
10952602 ATATAAAAAAGTAGATCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
*
10952634 ATATAAAAAAGTAGATCATACATTAGGTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
* *
10952666 ATATAAAAAAGTTGATCATACATTAGTTTTGC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
*
10952698 ATATAAAAAAGTAGAGCATACATTAGTTTTAC
1 ATATAAAAAAGTAGATCATACATTAGTTTTAC
10952730 ATATAAAAAAGTAG
1 ATATAAAAAAGTAG
10952744 TATAGTTATA
Statistics
Matches: 132, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
29 10 0.08
30 1 0.01
32 121 0.92
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (32 bp):
ATATAAAAAAGTAGATCATACATTAGTTTTAC
Found at i:10955503 original size:5 final size:5
Alignment explanation
Indices: 10955493--10955549 Score: 96
Period size: 5 Copynumber: 11.4 Consensus size: 5
10955483 AGCTACAATC
* *
10955493 ATTAG ATTAG ATTAG ATTAG ACTAG ATTAG ATTAG ATTAG AATAG ATTAG
1 ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG ATTAG
10955543 ATTAG AT
1 ATTAG AT
10955550 GTTTATCTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.42, C:0.02, G:0.19, T:0.37
Consensus pattern (5 bp):
ATTAG
Found at i:10957356 original size:35 final size:34
Alignment explanation
Indices: 10957307--10957405 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 34
10957297 TTTGGTACCT
*
10957307 ATACAAGTAAAAATCTCAATGTTAAGTACAGACCC
1 ATACAAGTAGAAATCTCAATGTT-AGTACAGACCC
10957342 ATACAAGTAGAAATCTC-A-GCTT-G--CA-ACCC
1 ATACAAGTAGAAATCTCAATG-TTAGTACAGACCC
*
10957371 ATACAAGTAGAAATCTCAATGTTAGGTATAGACCC
1 ATACAAGTAGAAATCTCAATGTTA-GTACAGACCC
10957406 CCAACATTCC
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
29 21 0.39
30 5 0.09
31 1 0.02
32 2 0.04
33 1 0.02
34 4 0.07
35 20 0.37
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.23
Consensus pattern (34 bp):
ATACAAGTAGAAATCTCAATGTTAGTACAGACCC
Found at i:10958374 original size:30 final size:30
Alignment explanation
Indices: 10958338--10958397 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
10958328 TATTTTATTA
*
10958338 TTAATTTTGTTATTATTTTAAAGGAATTTG
1 TTAATTTTATTATTATTTTAAAGGAATTTG
* *
10958368 TTAATTTTATTATTATTTTAGAGGCATTTG
1 TTAATTTTATTATTATTTTAAAGGAATTTG
10958398 CTTGTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTTATTATTATTTTAAAGGAATTTG
Found at i:10960259 original size:21 final size:21
Alignment explanation
Indices: 10960234--10960274 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
10960224 AATATATTTG
* *
10960234 ACATATAATTTTTATTTTTAA
1 ACATATAATGTTTAATTTTAA
10960255 ACATATAATGTTTAATTTTA
1 ACATATAATGTTTAATTTTA
10960275 GATGAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (21 bp):
ACATATAATGTTTAATTTTAA
Found at i:10964867 original size:10 final size:9
Alignment explanation
Indices: 10964844--10964869 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10964834 ATGTTGACGG
10964844 TAAAAATTT
1 TAAAAATTT
10964853 TAAAAATTT
1 TAAAAATTT
10964862 TAAAAATT
1 TAAAAATT
10964870 AATTGACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAAAATTT
Found at i:10965149 original size:15 final size:14
Alignment explanation
Indices: 10965086--10965135 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
10965076 TAACATTGAA
*
10965086 TTTTAGAATTATTTTT
1 TTTTA-AATT-TTATT
10965102 TTTTAAATTTTATT
1 TTTTAAATTTTATT
10965116 TTTTAAAATTTTATT
1 TTTT-AAATTTTATT
10965131 TTTTA
1 TTTTA
10965136 TTTTTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 9 0.28
15 18 0.56
16 5 0.16
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTAAATTTTATT
Found at i:10965754 original size:18 final size:18
Alignment explanation
Indices: 10965733--10965767 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10965723 TCAAAAATGG
* *
10965733 TAAAAATTATTAAAAATA
1 TAAAAATAATAAAAAATA
10965751 TAAAAATAATAAAAAAT
1 TAAAAATAATAAAAAAT
10965768 GAACCCCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAATAATAAAAAATA
Found at i:10968767 original size:14 final size:14
Alignment explanation
Indices: 10968748--10968777 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
10968738 AAGATATTCT
10968748 TTTTCTAAATAAAG
1 TTTTCTAAATAAAG
*
10968762 TTTTCTAAATGAAG
1 TTTTCTAAATAAAG
10968776 TT
1 TT
10968778 GAACCAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.47
Consensus pattern (14 bp):
TTTTCTAAATAAAG
Found at i:10974111 original size:26 final size:26
Alignment explanation
Indices: 10974082--10974186 Score: 165
Period size: 26 Copynumber: 4.0 Consensus size: 26
10974072 TGGTACAAAT
10974082 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
10974108 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
10974134 CGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
**
10974160 TGATAATGATTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
10974186 T
1 T
10974187 TATGGGCATT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:10980387 original size:204 final size:205
Alignment explanation
Indices: 10980021--10980673 Score: 1049
Period size: 204 Copynumber: 3.2 Consensus size: 205
10980011 TGATTTGGCT
* * * *
10980021 TGATTTGGTATCTCTGTATTGTCATAGAACAAATCGAAGTCTGGCATCTCCACTTCGACGGGGAG
1 TGATTTGGTAT-TCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGATGGAGAG
* *
10980086 TAGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGTAAGATCCAAGATGATTTGGCAT
65 CAGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAAGATCCAAGATGATTTGGCAT
10980151 CCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAG
130 CCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAG
10980216 CAAATCTAAGA
195 CAAATCTAAGA
10980227 TGATTTGGT-TTCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGATGGAGAGC
1 TGATTTGGTATTCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGATGGAGAGC
10980291 AGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAAGATCCAAGATGATTTGGCATC
66 AGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAAGATCCAAGATGATTTGGCATC
*
10980356 CTTGTGCTTACAAGGAACAAATCGAAGACATAACTGATTTGGCTTTCACGTGTTTACGCTGAAGC
131 CTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGC
10980421 AAATCTAAGA
196 AAATCTAAGA
10980431 TGATTTGGTA-TCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGATGGAGAGC
1 TGATTTGGTATTCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGATGGAGAGC
* * * * * *
10980495 AGATAAATAGTAGATCTCACCTTCAGATAATTTCACTGAAGCAAGATCTAAGATGGTTTGGTATC
66 AGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAAGATCCAAGATGATTTGGCATC
* * * ** * * *
10980560 CTTGTGCTTACAAGGAACAAATCAAAGACATAGTTGATTTGGTTTTTGCGTGCTTACGCTAAAAC
131 CTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGC
10980625 AAATCTAAGA
196 AAATCTAAGA
* * * *
10980635 TGATTTGGCATCTTTGTATTGTTAGAGAACAAATCGAAG
1 TGATTTGGTAT-TCTCTATTGTCAGAGAACAAATCGAAG
10980674 AAGCAGATTT
Statistics
Matches: 418, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
204 384 0.92
205 1 0.00
206 33 0.08
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (205 bp):
TGATTTGGTATTCTCTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCACTTCGATGGAGAGC
AGATACATAGCAGATCTCACCTTCAGATGATTTCACTGAAGCAAGATCCAAGATGATTTGGCATC
CTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGCTGAAGC
AAATCTAAGA
Found at i:10982356 original size:20 final size:19
Alignment explanation
Indices: 10982311--10982361 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
10982301 TTTAATATGA
*
10982311 ATATATGTAC-TATATTTT
1 ATATATTTACTTATATTTT
10982329 ATATTATTTACTTATATTTT
1 ATA-TATTTACTTATATTTT
10982349 AT-TATATTACTTA
1 ATATAT-TTACTTA
10982362 ATATCTTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.21
19 13 0.45
20 10 0.34
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (19 bp):
ATATATTTACTTATATTTT
Found at i:10982498 original size:16 final size:15
Alignment explanation
Indices: 10982479--10982547 Score: 67
Period size: 13 Copynumber: 4.8 Consensus size: 15
10982469 ATTAACCATA
10982479 TATTATTTCATATTAT
1 TATTATTT-ATATTAT
10982495 TATTA-TT-TATTAT
1 TATTATTTATATTAT
*
10982508 ATATT-TTTAAATTAT
1 -TATTATTTATATTAT
*
10982523 TATTATTT-TA-CAT
1 TATTATTTATATTAT
10982536 TATTATTTATAT
1 TATTATTTATAT
10982548 ATTTTTACTT
Statistics
Matches: 44, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
13 16 0.36
14 13 0.30
15 10 0.23
16 5 0.11
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATTTATATTAT
Found at i:10982522 original size:38 final size:38
Alignment explanation
Indices: 10982480--10982554 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
10982470 TTAACCATAT
*
10982480 ATTATT-TCATATTATTATTATT-TATTATATATTTTTAA
1 ATTATTATCATATTA-CATTATTAT-TTATATATTTTTAA
* *
10982518 ATTATTATTATTTTACATTATTATTTATATATTTTTA
1 ATTATTATCATATTACATTATTATTTATATATTTTTA
10982555 CTTGTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 25 0.78
39 7 0.22
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (38 bp):
ATTATTATCATATTACATTATTATTTATATATTTTTAA
Found at i:10982540 original size:57 final size:58
Alignment explanation
Indices: 10982478--10982632 Score: 158
Period size: 57 Copynumber: 2.6 Consensus size: 58
10982468 TATTAACCAT
*
10982478 ATATTATTTCATATTATTATTATTTATTATATATTT-TTAAATTA-TTAT-TATTTTAC
1 ATATTATTTCATATTATTATTATTTATTATATATTTATT-AATTATTTATGTATTATAC
* *
10982534 ATTATTATTT-ATA-TATTTTTACTTGTATTATATCTTTATTAATTATTTATGTATTATAC
1 A-TATTATTTCATATTATTATTA-TT-TATTATATATTTATTAATTATTTATGTATTATAC
*
10982593 ATATATACTTTCATATTATATATTATAATTATTTTATATT
1 ATAT-TA-TTTCATATTAT-TATTAT--TTATTATATATT
10982633 ATGTCATTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 19
0.76 0.06 0.18
Matches are distributed among these distances:
55 7 0.09
56 6 0.08
57 24 0.30
58 9 0.11
59 10 0.12
60 3 0.04
61 3 0.04
62 4 0.05
63 13 0.16
64 1 0.01
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.61
Consensus pattern (58 bp):
ATATTATTTCATATTATTATTATTTATTATATATTTATTAATTATTTATGTATTATAC
Found at i:10982566 original size:19 final size:18
Alignment explanation
Indices: 10982500--10982566 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 18
10982490 ATTATTATTA
*
10982500 TTTATTATATATTTTTAA
1 TTTATTATATATTTTTAC
*
10982518 ATTATTAT-TA-TTTTAC
1 TTTATTATATATTTTTAC
10982534 ATTATTATTTATATATTTTTAC
1 --T-TTA-TTATATATTTTTAC
10982556 TTGTATTATAT
1 TT-TATTATAT
10982567 CTTTATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
16 5 0.13
17 2 0.05
18 7 0.18
19 10 0.26
20 7 0.18
21 2 0.05
22 6 0.15
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATTATATATTTTTAC
Found at i:10982579 original size:38 final size:37
Alignment explanation
Indices: 10982489--10982588 Score: 98
Period size: 38 Copynumber: 2.6 Consensus size: 37
10982479 TATTATTTCA
*
10982489 TATTATTATTATTTA-TTATATATTTTTAAATTATTAT
1 TATT-TTATTAATTATTTATATATTTTTAAATTATTAT
**
10982526 TATTTTACATT-ATTATTTATATATTTTTACTTGTATTA-
1 TATTTT--ATTAATTATTTATATATTTTTAAAT-TATTAT
*
10982564 TATCTTTATTAATTATTTATGTATT
1 TAT-TTTATTAATTATTTATATATT
10982589 ATACATATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
36 2 0.04
37 10 0.19
38 33 0.62
39 8 0.15
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.64
Consensus pattern (37 bp):
TATTTTATTAATTATTTATATATTTTTAAATTATTAT
Found at i:10982658 original size:23 final size:22
Alignment explanation
Indices: 10982632--10982677 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
10982622 TATTTTATAT
10982632 TATGTCATTTT-TTTATACTATTA
1 TATGT-ATTTTATTTATAC-ATTA
*
10982655 TATGTTTTTTATTTATACATTA
1 TATGTATTTTATTTATACATTA
10982677 T
1 T
10982678 TATCATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.63
Consensus pattern (22 bp):
TATGTATTTTATTTATACATTA
Found at i:10984529 original size:30 final size:30
Alignment explanation
Indices: 10984421--10984530 Score: 82
Period size: 30 Copynumber: 3.5 Consensus size: 30
10984411 AAAATTTTAA
* *
10984421 AAAATATTAAAATTTTTAATATAT-TTTTTA
1 AAAAT-TTTAAATTTTTAATATATATTTTTT
* *
10984451 AAAATTTT-AGTAGTTT-ATATATATTGCAATTTT
1 AAAATTTTAAAT-TTTTAATATATATT----TTTT
**
10984484 ATAAATTTTCTATTTTTAATATATATTTTTT
1 A-AAATTTTAAATTTTTAATATATATTTTTT
10984515 AAAATTTTAAATTTTT
1 AAAATTTTAAATTTTT
10984531 TTGTAAATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
28 8 0.13
29 7 0.11
30 18 0.29
31 5 0.08
33 4 0.06
34 10 0.16
35 10 0.16
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (30 bp):
AAAATTTTAAATTTTTAATATATATTTTTT
Found at i:10984532 original size:18 final size:20
Alignment explanation
Indices: 10984497--10984550 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
10984487 AATTTTCTAT
*
10984497 TTTTAATATATATTTTTTAAAA
1 TTTTAATAT-T-TTTTTGAAAA
*
10984519 TTTTAA-ATTTTTTTGTAAA
1 TTTTAATATTTTTTTGAAAA
10984538 TTTTAATATTTTT
1 TTTTAATATTTTT
10984551 ATTTTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 14 0.48
20 7 0.24
21 2 0.07
22 6 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTAATATTTTTTTGAAAA
Found at i:10987005 original size:26 final size:26
Alignment explanation
Indices: 10986952--10987084 Score: 209
Period size: 26 Copynumber: 5.2 Consensus size: 26
10986942 TGATACAAAT
10986952 TGATAATAGGTTAGGT--A-GTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10986975 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
10987001 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10987027 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
10987053 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10987079 TGATAA
1 TGATAA
10987085 GAATTTCATG
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
23 16 0.16
25 1 0.01
26 84 0.83
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:10991230 original size:25 final size:26
Alignment explanation
Indices: 10991191--10991323 Score: 218
Period size: 25 Copynumber: 5.2 Consensus size: 26
10991181 TGATACAAAT
10991191 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10991217 TGATAAT-GGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
10991241 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
10991267 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
10991292 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
10991318 TGATAA
1 TGATAA
10991324 GAATTTCATG
Statistics
Matches: 103, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
24 9 0.09
25 54 0.52
26 40 0.39
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:10991245 original size:50 final size:51
Alignment explanation
Indices: 10991191--10991323 Score: 241
Period size: 50 Copynumber: 2.6 Consensus size: 51
10991181 TGATACAAAT
10991191 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTTCA
10991241 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTTCA
* *
10991292 TGATAATGGGTTAGGTAAATGTTTCATGATAA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAA
10991324 GAATTTCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
50 46 0.57
51 34 0.43
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (51 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGTTAGGTAAATGTTTCA
Found at i:10993003 original size:26 final size:27
Alignment explanation
Indices: 10992936--10993074 Score: 174
Period size: 27 Copynumber: 5.2 Consensus size: 27
10992926 GAGGAAGCGT
*
10992936 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
10992963 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
10992990 TCT-GTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
10993016 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
10993044 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
10993070 TCTGG
1 TCTGG
10993075 CAGCCATGCT
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
26 29 0.29
27 56 0.56
28 15 0.15
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.35
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:10993020 original size:53 final size:55
Alignment explanation
Indices: 10992936--10993074 Score: 194
Period size: 53 Copynumber: 2.6 Consensus size: 55
10992926 GAGGAAGCGT
* * *
10992936 TCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
10992990 TCT-GTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
* *
10993044 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
10993075 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
53 44 0.58
54 19 0.25
55 13 0.17
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCTCTGCCACAAATATCTGTA
Found at i:10999018 original size:98 final size:98
Alignment explanation
Indices: 10998842--10999034 Score: 280
Period size: 98 Copynumber: 2.0 Consensus size: 98
10998832 AATTGACGGA
* *
10998842 TAAGACCATGGTTGGACCATGGCAATGTTTAAATGAAAGACCATAGCTGAGCTATGGCATTTTAA
1 TAAGACCATGGTTGGACCATAGCAATGTTTAAATGAAAGACCATAGCTGAGCTATGGCATTCTAA
10998907 TAAAAAGACCATAACT-GGATTATGGCACTATCG
66 TAAAAAGACCATAACTAGG-TTATGGCACTATCG
* * * * *
10998940 TAAGACTATGGTTGGACCATAGCAGTGTTTATATGCAAGACCATAGCTGAGCTATGGCATTCTAG
1 TAAGACCATGGTTGGACCATAGCAATGTTTAAATGAAAGACCATAGCTGAGCTATGGCATTCTAA
* * *
10999005 TGATAAGAGCATAACTAGGTTATGGCACTA
66 TAAAAAGACCATAACTAGGTTATGGCACTA
10999035 CGAATGTAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
98 82 0.98
99 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (98 bp):
TAAGACCATGGTTGGACCATAGCAATGTTTAAATGAAAGACCATAGCTGAGCTATGGCATTCTAA
TAAAAAGACCATAACTAGGTTATGGCACTATCG
Found at i:11005608 original size:26 final size:26
Alignment explanation
Indices: 11005579--11005686 Score: 182
Period size: 26 Copynumber: 4.2 Consensus size: 26
11005569 TGGTACAAAT
11005579 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
11005605 TGATAATGGATTAGGTAAATAG-TCTA
1 TGATAATGGGTTAGGTAAAT-GTTCCA
11005631 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11005657 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
11005683 TGAT
1 TGAT
11005687 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
25 1 0.01
26 74 0.97
27 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:11008068 original size:64 final size:64
Alignment explanation
Indices: 11007995--11008205 Score: 151
Period size: 64 Copynumber: 3.2 Consensus size: 64
11007985 CTGGGCCAGA
*
11007995 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
* * * *** * ** *
11008059 GCCCATTTCAAAATAC-ATGCAACATCAGTAAACATATGCAAGCCC--ATTTGGGTAACAGTGGT
1 GCCCATTTCAGATTACAAT--AA-A-CTG-GGCCTTA-GC---CCCTTATTCAGATAACA---GT
* *
11008121 ACTGGGCCAGA-
54 A-TGGCCCATAG
*
11008132 GCCCTTTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
1 GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
11008196 GCCCATTTCA
1 GCCCATTTCA
11008206 AAATACATGC
Statistics
Matches: 103, Mismatches: 27, Indels: 34
0.63 0.16 0.21
Matches are distributed among these distances:
63 9 0.09
64 25 0.24
65 5 0.05
66 1 0.01
67 11 0.11
68 5 0.05
69 5 0.05
70 11 0.11
71 1 0.01
72 5 0.05
73 16 0.16
74 9 0.09
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (64 bp):
GCCCATTTCAGATTACAATAAACTGGGCCTTAGCCCCTTATTCAGATAACAGTATGGCCCATAG
Found at i:11008207 original size:137 final size:136
Alignment explanation
Indices: 11007961--11008246 Score: 536
Period size: 137 Copynumber: 2.1 Consensus size: 136
11007951 TATTGGGCCT
**
11007961 AAGCCCATTCAGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
*
11008026 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAAT-AA
11008091 CATATGC
130 CATATGC
11008098 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
11008163 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
66 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
11008228 ATATGC
131 ATATGC
11008234 AAGCCCATTTGGG
1 AAGCCCATTTGGG
11008247 GAGACTACTC
Statistics
Matches: 146, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
136 22 0.15
137 124 0.85
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.24
Consensus pattern (136 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAATAAC
ATATGC
Found at i:11010051 original size:26 final size:26
Alignment explanation
Indices: 11010015--11010150 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
11010005 ACATGAATTC
11010015 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
11010041 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
11010067 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
11010093 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
11010119 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
11010145 TTATCA
1 TTATCA
11010151 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:11012997 original size:71 final size:72
Alignment explanation
Indices: 11012820--11013074 Score: 234
Period size: 71 Copynumber: 3.6 Consensus size: 72
11012810 GTAAATAATG
* *
11012820 AAATGCGCCTTGCACTGGCCAGTAAAACCGACAAATG-GTGTG-CCAGCACTGGTCAGTATAACC
1 AAATGCGCCTTGCGCTGGTCAGTAAAACCGACAAATGAGTGTGCCCAGCACTGGTCAGTATAACC
*
11012883 GAAAAAT
66 AAAAAAT
* * * * * *
11012890 AAATGCGCCTTGCGCTGGTTAGCAAAATCAATAAATGAGTGTGCCCAGCACTGGTCGGTAT-A-C
1 AAATGCGCCTTGCGCTGGTCAGTAAAACCGACAAATGAGTGTGCCCAGCACTGGTCAGTATAACC
11012953 AAAAAAGT
66 AAAAAA-T
* * * * ** * *
11012961 AAATGCATCC-TGCGTTGGTCGGTAAAACCGACAAATGAGTGTGCCCAGCAGTGCCCAATACAAC
1 AAATGC-GCCTTGCGCTGGTCAGTAAAACCGACAAATGAGTGTGCCCAGCACTGGTCAGTATAAC
* *
11013025 TAACAAAT
65 CAAAAAAT
* * * *
11013033 AAATGCGCCCTGCACTGGTC-GATGAAACCAACAAATGAGTGT
1 AAATGCGCCTTGCGCTGGTCAG-TAAAACCGACAAATGAGTGT
11013075 TCATTTATTC
Statistics
Matches: 147, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
70 36 0.24
71 54 0.37
72 52 0.35
73 5 0.03
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (72 bp):
AAATGCGCCTTGCGCTGGTCAGTAAAACCGACAAATGAGTGTGCCCAGCACTGGTCAGTATAACC
AAAAAAT
Found at i:11013604 original size:23 final size:23
Alignment explanation
Indices: 11013577--11013669 Score: 98
Period size: 23 Copynumber: 4.1 Consensus size: 23
11013567 AATGTCTAGC
* *
11013577 TTGGACAACACTTAAAACATGCT
1 TTGGACAACATTTAAAACATACT
** *
11013600 TTGGATGACATTTAAAACATATT
1 TTGGACAACATTTAAAACATACT
* *
11013623 TTGTACAACATTTAAAACTTACT
1 TTGGACAACATTTAAAACATACT
* *
11013646 TT-GACAGCATTTGAAACATACT
1 TTGGACAACATTTAAAACATACT
11013668 TT
1 TT
11013670 TGCCAGCATC
Statistics
Matches: 56, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
22 18 0.32
23 38 0.68
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (23 bp):
TTGGACAACATTTAAAACATACT
Found at i:11013676 original size:23 final size:23
Alignment explanation
Indices: 11013608--11013688 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
11013598 CTTTGGATGA
*
11013608 CATTTAAAACATA-TTTTGTACAA
1 CATTTAAAACATACTTTTG-ACAG
*
11013631 CATTTAAAACTTAC-TTTGACAG
1 CATTTAAAACATACTTTTGACAG
* *
11013653 CATTTGAAACATACTTTTGCCAG
1 CATTTAAAACATACTTTTGACAG
* *
11013676 CATCTAAAGCATA
1 CATTTAAAACATA
11013689 TCAAATGTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 15 0.31
23 33 0.69
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (23 bp):
CATTTAAAACATACTTTTGACAG
Found at i:11021872 original size:30 final size:32
Alignment explanation
Indices: 11021836--11021903 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 32
11021826 GGTTTCATTT
* *
11021836 CAGTCACCTAAC-TTTTGAAAAA-TAACAAAA
1 CAGTCACCTAACGTTATAAAAAAGTAACAAAA
*
11021866 CAGTCA-CTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACCTAACGTTATAAAAAAGTAACAAAA
11021897 CAGTCAC
1 CAGTCAC
11021904 TGACTAACAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.16
30 14 0.44
31 13 0.41
ACGTcount: A:0.49, C:0.21, G:0.10, T:0.21
Consensus pattern (32 bp):
CAGTCACCTAACGTTATAAAAAAGTAACAAAA
Found at i:11021885 original size:29 final size:30
Alignment explanation
Indices: 11021836--11021904 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
11021826 GGTTTCATTT
* *
11021836 CAGTCACCTAACTTTTGAAAAA-TAACAAAA
1 CAGTCA-CTAACTTATAAAAAAGTAACAAAA
*
11021866 CAGTCACTAACGTTATAAAAAAGTGACAAAA
1 CAGTCACTAAC-TTATAAAAAAGTAACAAAA
11021897 CAGTCACT
1 CAGTCACT
11021905 GACTAACAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 5 0.15
30 14 0.41
31 15 0.44
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (30 bp):
CAGTCACTAACTTATAAAAAAGTAACAAAA
Found at i:11023007 original size:3 final size:3
Alignment explanation
Indices: 11022994--11023034 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
11022984 GCTGCTACTG
*
11022994 CTT CTT TTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
11023035 CTATTAAAGG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:11023114 original size:21 final size:21
Alignment explanation
Indices: 11023090--11023130 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
11023080 CAACGTGGCA
*
11023090 AGTTAACTGGCCACGTCAGCC
1 AGTTAACTGGCCACATCAGCC
*
11023111 AGTTAACTTGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
11023131 GGTTCTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.22
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCC
Found at i:11023225 original size:29 final size:31
Alignment explanation
Indices: 11023165--11023233 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
11023155 ATTGTTAGTC
* *
11023165 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
* *
11023196 AGTGATTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
11023225 AGGTGACTG
1 A-GTGACTG
11023234 AAATGAAACC
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
29 6 0.19
30 12 0.38
31 14 0.44
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:11023324 original size:2 final size:2
Alignment explanation
Indices: 11023319--11023353 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
11023309 TACATTATTA
*
11023319 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11023354 ATACTTTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11024375 original size:18 final size:17
Alignment explanation
Indices: 11024339--11024370 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
11024329 ATTAAAATTT
11024339 TAAAAAAATATTTAAAC
1 TAAAAAAATATTTAAAC
11024356 TAAAAAAA-ATTTAAA
1 TAAAAAAATATTTAAA
11024371 AACTAGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAAAATATTTAAAC
Found at i:11026229 original size:4 final size:5
Alignment explanation
Indices: 11026210--11026249 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
11026200 AAAAAAATTC
11026210 TTATT TTATT TT-TAT TTATT TTATT TTATT TTGATT TTAT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TT-ATT TTAT
11026250 GTTAAATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 1 0.03
5 25 0.78
6 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:11026230 original size:15 final size:14
Alignment explanation
Indices: 11026210--11026240 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 14
11026200 AAAAAAATTC
11026210 TTATTTTATTTTTAT
1 TTATTTTA-TTTTAT
11026225 TTATTTTATTTTAT
1 TTATTTTATTTTAT
11026239 TT
1 TT
11026241 TGATTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTATTTTATTTTAT
Found at i:11028430 original size:13 final size:13
Alignment explanation
Indices: 11028412--11028437 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11028402 TGAATCACGA
11028412 CTCACACGGGCGT
1 CTCACACGGGCGT
11028425 CTCACACGGGCGT
1 CTCACACGGGCGT
11028438 GTCCCTACCG
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:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
CTCACACGGGCGT
Found at i:11034970 original size:13 final size:13
Alignment explanation
Indices: 11034952--11034995 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
11034942 TCCATGCCAT
11034952 CACCATCCACCGC
1 CACCATCCACCGC
11034965 CACCATCCACCGC
1 CACCATCCACCGC
**
11034978 CGTC-TCCACCGC
1 CACCATCCACCGC
11034990 CACCAT
1 CACCAT
11034996 AACAAACAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.20, C:0.59, G:0.09, T:0.11
Consensus pattern (13 bp):
CACCATCCACCGC
Found at i:11036983 original size:19 final size:19
Alignment explanation
Indices: 11036955--11036997 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
11036945 TTGTTTGAAA
11036955 AAAT-ATTTGCTTGTACAT
1 AAATAATTTGCTTGTACAT
*
11036973 ACATAATTTGCTTGTACAT
1 AAATAATTTGCTTGTACAT
11036992 AAATAA
1 AAATAA
11036998 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.40
Consensus pattern (19 bp):
AAATAATTTGCTTGTACAT
Found at i:11036999 original size:4 final size:4
Alignment explanation
Indices: 11036990--11037023 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
11036980 TTGCTTGTAC
*
11036990 ATAA ATAA ATAA ATAAA ATGA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA A
11037024 GGCTCAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:11037418 original size:25 final size:25
Alignment explanation
Indices: 11037384--11037459 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
11037374 ATCCTTAGCA
11037384 TTTATTTATTTTTGCCTATGTTGTT
1 TTTATTTATTTTTGCCTATGTTGTT
11037409 TTTATTTATTTTTGCCTATGTTGTT
1 TTTATTTATTTTTGCCTATGTTGTT
11037434 TTTATTTATTTTTGCCTATGTTGTT
1 TTTATTTATTTTTGCCTATGTTGTT
11037459 T
1 T
11037460 ACATTGATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.12, C:0.08, G:0.12, T:0.68
Consensus pattern (25 bp):
TTTATTTATTTTTGCCTATGTTGTT
Found at i:11038057 original size:3 final size:3
Alignment explanation
Indices: 11038051--11038103 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
11038041 AAATAGATAT
* * *
11038051 TTA TTA TTA TAA TTA TTAA TTA TTA TTA TTG TT- TATA TTA TTA TTT
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA T-TA TTA TTA TTA
11038097 TTA TTA T
1 TTA TTA T
11038104 GGAATAAATT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
2 1 0.02
3 37 0.88
4 4 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:11038728 original size:17 final size:18
Alignment explanation
Indices: 11038706--11038741 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11038696 TAAATGAGTT
11038706 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
11038723 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
11038741 A
1 A
11038742 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:11039223 original size:21 final size:21
Alignment explanation
Indices: 11039199--11039244 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
11039189 AGGCACTATA
*
11039199 TGTGTCGTATCAAGTACCTCC
1 TGTGTCGTATCAAGCACCTCC
*
11039220 TGTGTCGTATCAAGCACCTCG
1 TGTGTCGTATCAAGCACCTCC
11039241 TGTG
1 TGTG
11039245 CCGTTTTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (21 bp):
TGTGTCGTATCAAGCACCTCC
Found at i:11040126 original size:22 final size:22
Alignment explanation
Indices: 11040076--11040126 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
11040066 TATTTAAAGG
11040076 TGAA-TTGGATTGGTTGTGATT
1 TGAATTTGGATTGGTTGTGATT
***
11040097 TTTTTTTGGATTGGTT-TCGATT
1 TGAATTTGGATTGGTTGT-GATT
11040119 TGAATTTG
1 TGAATTTG
11040127 CAGGGAATGT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.55
Consensus pattern (22 bp):
TGAATTTGGATTGGTTGTGATT
Found at i:11041001 original size:4 final size:5
Alignment explanation
Indices: 11040982--11041021 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
11040972 AAAAAAAATC
11040982 TTATT TTATT TT-TAT TTATT TTATT TTATT TTGATT TTAT
1 TTATT TTATT TTAT-T TTATT TTATT TTATT TT-ATT TTAT
11041022 GTTAAATTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 1 0.03
5 25 0.78
6 6 0.19
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (5 bp):
TTATT
Done.