Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A01
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: 115637255
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5450143 characters in sequence are not A, C, G, or T
File 20 of 349
Found at i:5527898 original size:34 final size:34
Alignment explanation
Indices: 5527854--5527975 Score: 113
Period size: 34 Copynumber: 3.4 Consensus size: 34
5527844 TCATAACTTA
5527854 CATAACTTACATAATACTTAAATATATTTGATAT
1 CATAACTTACATAATACTTAAATATATTTGATAT
* ** *
5527888 CATAATTTACATAACTAGCTTACGAA-ACTTACCTAACT-T
1 CATAACTTACATAA-TA-CTTA--AATA--TATTTGA-TAT
5527927 ACATAACTTACATAATACTTAAATATATTTGATAT
1 -CATAACTTACATAATACTTAAATATATTTGATAT
*
5527962 CATAATTTACATAA
1 CATAACTTACATAA
5527976 CTAGCTTACG
Statistics
Matches: 69, Mismatches: 9, Indels: 20
0.70 0.09 0.20
Matches are distributed among these distances:
34 27 0.39
35 7 0.10
36 6 0.09
37 2 0.03
38 6 0.09
39 7 0.10
40 14 0.20
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.38
Consensus pattern (34 bp):
CATAACTTACATAATACTTAAATATATTTGATAT
Found at i:5527933 original size:74 final size:74
Alignment explanation
Indices: 5527847--5528006 Score: 311
Period size: 74 Copynumber: 2.2 Consensus size: 74
5527837 TATCATATCA
5527847 TAACTTACATAACTTACATAATACTTAAATATATTTGATATCATAATTTACATAACTAGCTTACG
1 TAACTTACATAACTTACATAATACTTAAATATATTTGATATCATAATTTACATAACTAGCTTACG
5527912 AAACTTACC
66 AAACTTACC
5527921 TAACTTACATAACTTACATAATACTTAAATATATTTGATATCATAATTTACATAACTAGCTTACG
1 TAACTTACATAACTTACATAATACTTAAATATATTTGATATCATAATTTACATAACTAGCTTACG
*
5527986 AAACTTACT
66 AAACTTACC
5527995 TAACTTACATAA
1 TAACTTACATAA
5528007 TACACAAATC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 85 1.00
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (74 bp):
TAACTTACATAACTTACATAATACTTAAATATATTTGATATCATAATTTACATAACTAGCTTACG
AAACTTACC
Found at i:5536011 original size:22 final size:22
Alignment explanation
Indices: 5535986--5536029 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5535976 TTCAAAGATG
5535986 GCTGGATAAAGATTGAAGGGTT
1 GCTGGATAAAGATTGAAGGGTT
*
5536008 GCTGGATAAATATTGAAGGGTT
1 GCTGGATAAAGATTGAAGGGTT
5536030 TTTTATATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.30
Consensus pattern (22 bp):
GCTGGATAAAGATTGAAGGGTT
Found at i:5536152 original size:13 final size:13
Alignment explanation
Indices: 5536098--5536153 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
5536088 AATTTAGAAT
*
5536098 TATTTTGTGATAA
1 TATTTAGTGATAA
* *
5536111 TATTTTGTAATAA
1 TATTTAGTGATAA
*
5536124 TATTTA--GA-AT
1 TATTTAGTGATAA
5536134 TATTTAGTGATAA
1 TATTTAGTGATAA
5536147 TATTTAG
1 TATTTAG
5536154 GAAAAATCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 7 0.20
11 1 0.03
12 2 0.06
13 25 0.71
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:5540932 original size:50 final size:50
Alignment explanation
Indices: 5540857--5541033 Score: 257
Period size: 50 Copynumber: 3.5 Consensus size: 50
5540847 CCATGGAAAC
5540857 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * * *
5540907 AAGTGATAAGTAATAACTTCGGCTACACTTATCTGATTAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
5540957 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGG-CAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAA-GGACAAATGA
* * * *
5541007 CAACTGAAAAGTGGTAGCTTCAGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
5541034 CTGATTAGTG
Statistics
Matches: 113, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
50 89 0.79
51 24 0.21
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:5541219 original size:31 final size:31
Alignment explanation
Indices: 5541011--5541212 Score: 305
Period size: 31 Copynumber: 6.5 Consensus size: 31
5541001 AAATGACAAC
*
5541011 TGAAAAGTGGTAGCTTCAGCTACCTGATTAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
5541042 TGAAAAGTGGTAGTTTCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
5541073 TGAAAAGTGGTAGCTTCTGCTACCTAATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
5541104 TGAAAAGTGGTAGCTTCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* *
5541135 TGAAAAGTGGTAGCTCCGGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
* **
5541166 TGAAAAATGGTAGCACCAGCTACCTGATCAG
1 TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
*
5541197 TGAATAGTGGTAGCTT
1 TGAAAAGTGGTAGCTT
5541213 TGGCTACAAG
Statistics
Matches: 156, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 156 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (31 bp):
TGAAAAGTGGTAGCTTCAGCTACCTGATCAG
Found at i:5541230 original size:7 final size:7
Alignment explanation
Indices: 5541218--5541253 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
5541208 AGCTTTGGCT
5541218 ACAAGTG
1 ACAAGTG
5541225 ACAAGTG
1 ACAAGTG
5541232 ACAAGTG
1 ACAAGTG
5541239 ACAAGTG
1 ACAAGTG
5541246 ACAAGTG
1 ACAAGTG
5541253 A
1 A
5541254 TTTCTGTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.14, G:0.28, T:0.14
Consensus pattern (7 bp):
ACAAGTG
Found at i:5541326 original size:47 final size:48
Alignment explanation
Indices: 5541257--5541382 Score: 157
Period size: 47 Copynumber: 2.7 Consensus size: 48
5541247 CAAGTGATTT
* *
5541257 CTGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATG-CTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * *
5541304 CTGTATAAGACCATATCTGGGATATGACATCAGTGAGATATGTGATTA
1 CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
* * * *
5541352 C-GTGTAAGACCATAGCTAGGCTATGGCATCA
1 CTGTATAAGACCATATCTGGGATATGGCATCA
5541383 TTATGTAAAG
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
47 65 0.96
48 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (48 bp):
CTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGACTA
Found at i:5543886 original size:22 final size:22
Alignment explanation
Indices: 5543812--5543890 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
5543802 TTATTTATCA
*
5543812 ATTTATTTTATTTTCTTAAATTT
1 ATTTATTTTATTTT-TTGAATTT
* *
5543835 ATTT-TTATA-TTTTCGAATATGT
1 ATTTATTTTATTTTTTGAAT-T-T
*
5543857 TTTTATTTTATTTTTTGAATTT
1 ATTTATTTTATTTTTTGAATTT
*
5543879 CTTTATTTTATT
1 ATTTATTTTATT
5543891 ATCTTAATCA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
20 4 0.09
21 4 0.09
22 20 0.44
23 9 0.20
24 8 0.18
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.70
Consensus pattern (22 bp):
ATTTATTTTATTTTTTGAATTT
Found at i:5550535 original size:33 final size:32
Alignment explanation
Indices: 5550496--5550587 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
5550486 AAGTTGTACA
*
5550496 TTCCTTTCCAATTGGTACACACAAATTATACCT
1 TTCCTTTCC-ATTGGTACACACAAAGTATACCT
* *
5550529 TTCCTTTTCATATGGTATACACAAAGTATACCT
1 TTCCTTTCCAT-TGGTACACACAAAGTATACCT
** *
5550562 AACCTTTCCGAGT-GTACACACAAAGT
1 TTCCTTTCC-ATTGGTACACACAAAGT
5550588 GTACATAACC
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
32 14 0.29
33 34 0.69
34 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.10, T:0.34
Consensus pattern (32 bp):
TTCCTTTCCATTGGTACACACAAAGTATACCT
Found at i:5552655 original size:23 final size:23
Alignment explanation
Indices: 5552629--5552703 Score: 123
Period size: 23 Copynumber: 3.3 Consensus size: 23
5552619 TAATTTTTGA
* *
5552629 ATTTTGAATTATTTAATGATAAT
1 ATTTAGAATTATTTAGTGATAAT
5552652 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATTATTTAGTGATAAT
*
5552675 ATTTAGAATTATTTAGCGATAAT
1 ATTTAGAATTATTTAGTGATAAT
5552698 ATTTAG
1 ATTTAG
5552704 GAAAAATCTA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.39, C:0.01, G:0.12, T:0.48
Consensus pattern (23 bp):
ATTTAGAATTATTTAGTGATAAT
Found at i:5552680 original size:13 final size:12
Alignment explanation
Indices: 5552646--5552705 Score: 56
Period size: 13 Copynumber: 5.2 Consensus size: 12
5552636 ATTATTTAAT
5552646 GATAATATTTA-
1 GATAATATTTAG
*
5552657 GA-ATTATTTAG
1 GATAATATTTAG
5552668 TGATAATATTTA-
1 -GATAATATTTAG
*
5552680 GA-ATTATTTAG
1 GATAATATTTAG
5552691 CGATAATATTTAG
1 -GATAATATTTAG
5552704 GA
1 GA
5552706 AAAATCTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
10 14 0.36
11 4 0.10
12 6 0.15
13 15 0.38
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (12 bp):
GATAATATTTAG
Found at i:5554140 original size:17 final size:17
Alignment explanation
Indices: 5554118--5554172 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
5554108 GGTTTTTTTT
5554118 AAATATTTTATTTATAA
1 AAATATTTTATTTATAA
*
5554135 AAATATTGTT-TTAATAA
1 AAATATT-TTATTTATAA
*
5554152 ATAA-ATTTTATGTTAGAA
1 A-AATATTTTAT-TTATAA
5554170 AAA
1 AAA
5554173 AGAGAAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.06
17 20 0.65
18 9 0.29
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.45
Consensus pattern (17 bp):
AAATATTTTATTTATAA
Found at i:5554232 original size:20 final size:20
Alignment explanation
Indices: 5554207--5554244 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5554197 TATAATTGTG
5554207 TTATGTATTTTTATAAAACT
1 TTATGTATTTTTATAAAACT
*
5554227 TTATGTGTTTTTATAAAA
1 TTATGTATTTTTATAAAA
5554245 AAAATGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TTATGTATTTTTATAAAACT
Found at i:5557078 original size:15 final size:14
Alignment explanation
Indices: 5557048--5557093 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
5557038 TTATTATTAC
*
5557048 TATTACTTTTATTAT
1 TATTACTTTT-CTAT
5557063 TATTACTGTTTCTAT
1 TATTACT-TTTCTAT
*
5557078 TATTGCTTTTCTAT
1 TATTACTTTTCTAT
5557092 TA
1 TA
5557094 CTATTTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.32
15 16 0.57
16 3 0.11
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.63
Consensus pattern (14 bp):
TATTACTTTTCTAT
Found at i:5557080 original size:21 final size:21
Alignment explanation
Indices: 5557038--5557254 Score: 71
Period size: 21 Copynumber: 10.2 Consensus size: 21
5557028 TTTTAATCAT
*
5557038 TTATTATTACTATTACTTTTA
1 TTATTATTACTATTACTATTA
* *
5557059 TTATTATTACTGTTTCTATTA
1 TTATTATTACTATTACTATTA
*
5557080 TTGCTT-TT-CTATTACTATTTA
1 TT-ATTATTACTATTACTA-TTA
*
5557101 TGTTATTGTTAGCACTATT-CT-TTA
1 --TTATTATT---ACTATTACTATTA
*
5557125 TT-TTATTATTATTA-T-TTA
1 TTATTATTACTATTACTATTA
* *
5557143 TTATT-TTA-TCATTCCTTTCTA
1 TTATTATTACT-ATTACTAT-TA
* * *
5557164 TTATTGTTATTATTAGTATACTA
1 TTATTATTACTATTACTAT--TA
*
5557187 ATATTATT-CTTATTAACGTATTA
1 TTATTATTAC-TATT-AC-TATTA
* *
5557210 TTATTATTATTTTCTACT-TTA
1 TTATTATTACTAT-TACTATTA
* *
5557231 TTATTA-TATTATTACTATTG
1 TTATTATTACTATTACTATTA
5557251 TTAT
1 TTAT
5557255 CATCATCTTA
Statistics
Matches: 150, Mismatches: 22, Indels: 49
0.68 0.10 0.22
Matches are distributed among these distances:
17 1 0.01
18 17 0.11
19 7 0.05
20 19 0.13
21 45 0.30
22 15 0.10
23 31 0.21
24 5 0.03
25 3 0.02
26 2 0.01
27 5 0.03
ACGTcount: A:0.26, C:0.09, G:0.04, T:0.61
Consensus pattern (21 bp):
TTATTATTACTATTACTATTA
Found at i:5557090 original size:14 final size:15
Alignment explanation
Indices: 5557060--5557093 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5557050 TTACTTTTAT
5557060 TATTATTACTGTTTC
1 TATTATTACTGTTTC
*
5557075 TATTATTGCT-TTTC
1 TATTATTACTGTTTC
5557089 TATTA
1 TATTA
5557094 CTATTTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.21, C:0.12, G:0.06, T:0.62
Consensus pattern (15 bp):
TATTATTACTGTTTC
Found at i:5557135 original size:3 final size:3
Alignment explanation
Indices: 5557122--5557254 Score: 62
Period size: 3 Copynumber: 44.3 Consensus size: 3
5557112 GCACTATTCT
* *
5557122 TTA TT- TTA TTA TTA TTA TTTA TTA TT- TTA TCA TTCC TT- TCTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA T-TA TTA
* * * * * *
5557167 TTG TTA TTA TTA GTA -TA CTA ATA TTA TTC TTA TTAA CGTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A -TTA TTA TTA
* * * *
5557213 TTA TTA TTT TCTA CT- TTA TTA TTA -TA TTA TTA CTA TTG TTA T
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5557255 CATCATCTTA
Statistics
Matches: 98, Mismatches: 20, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
2 10 0.10
3 78 0.80
4 9 0.09
5 1 0.01
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5567977 original size:76 final size:76
Alignment explanation
Indices: 5567851--5568378 Score: 867
Period size: 76 Copynumber: 6.9 Consensus size: 76
5567841 TAAAGCATAG
*
5567851 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGTAG
1 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
5567916 ATCGAAGACAA
66 ATCGAAGACAA
*
5567927 CAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
1 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
*
5567992 ATCGAAGACAC
66 ATCGAAGACAA
*
5568003 CAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
1 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
*
5568068 ATCGAAGACAG
66 ATCGAAGACAA
*
5568079 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGTGAGCAG
1 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
* *
5568144 ATCAAATACATA
66 ATCGAAGACA-A
* * *
5568156 GCAGATCTGACCTTTATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGCA
1 -CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCA
*
5568221 AATCGAAGACAA
65 GATCGAAGACAA
*
5568233 CAGATCTGACCTTCATTGAAGCAGATCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
1 CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
5568298 ATCGAAGACATA
66 ATCGAAGACA-A
* * **
5568310 GCAGATCTAACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGACAGCA
1 -CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCA
5568375 GATC
65 GATC
5568379 AGACCTTCAT
Statistics
Matches: 422, Mismatches: 26, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
76 289 0.68
77 2 0.00
78 131 0.31
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (76 bp):
CAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
ATCGAAGACAA
Found at i:5568229 original size:154 final size:152
Alignment explanation
Indices: 5567849--5568806 Score: 1485
Period size: 154 Copynumber: 6.4 Consensus size: 152
5567839 GCTAAAGCAT
*
5567849 AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGT
1 AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
*
5567914 AGATCGAAGACAACAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATT
66 AGATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
5567979 AGACGGGGAGCAGATCGAAGAC
131 AGACGGGGAGCAGATCGAAGAC
* *
5568001 ACCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
*
5568066 AGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
66 AGATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
* * *
5568131 AGACGGTGAGCAGATCAAATAC
131 AGACGGGGAGCAGATCGAAGAC
* * *
5568153 ATAGCAGATCTGACCTTTATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGA
1 --AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGA
* *
5568218 GCAAATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCTAAGATGATTTGGCATCTCTGTA
64 GCAGATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTA
5568283 TTAGACGGGGAGCAGATCGAAGAC
129 TTAGACGGGGAGCAGATCGAAGAC
* *
5568307 ATAGCAGATCTAACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGAC-----
1 --AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGA
* *
5568367 G--GA-C--AG----CAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTA
64 GCAGATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTA
*
5568423 TTAGACGGGGAGCAGATCAAAGAC
129 TTAGACGGGGAGCAGATCGAAGAC
* *
5568447 AGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
*
5568512 AGATCGAAGACATAACATATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTA
66 AGATCGAAGAC--AACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTA
*
5568577 TTAGACGGGAAGCAGATCGAAGAC
129 TTAGACGGGGAGCAGATCGAAGAC
* * *
5568601 AGCAGATCTGACCTTCATTGAAACAAATCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
** * * *
5568666 AGATCGAAGACAGTAGACCTGAACTTCATTGAAGCAGATCCAAGATAATTTGGCATCTCTGTATT
66 AGATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
5568731 AGACGGGGAGCAGATCGAAGAC
131 AGACGGGGAGCAGATCGAAGAC
*
5568753 AGCAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATT
1 AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
5568807 GTCAGAGAGC
Statistics
Matches: 736, Mismatches: 52, Indels: 36
0.89 0.06 0.04
Matches are distributed among these distances:
138 54 0.07
140 70 0.10
143 1 0.00
144 2 0.00
145 2 0.00
146 2 0.00
147 1 0.00
148 2 0.00
149 1 0.00
152 263 0.36
154 338 0.46
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (152 bp):
AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
AGATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
AGACGGGGAGCAGATCGAAGAC
Found at i:5568406 original size:62 final size:61
Alignment explanation
Indices: 5568309--5568442 Score: 214
Period size: 62 Copynumber: 2.2 Consensus size: 61
5568299 TCGAAGACAT
5568309 AGCAGATCTAACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGAC
1 AGCAGATC-AACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGAC
* * **
5568371 AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 AGCAGATCA-ACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGAC
5568433 AGCAGATCAA
1 AGCAGATCAA
5568443 AGACAGCAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
61 2 0.03
62 65 0.97
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (61 bp):
AGCAGATCAACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGAC
Found at i:5568455 original size:216 final size:214
Alignment explanation
Indices: 5568155--5569019 Score: 1129
Period size: 216 Copynumber: 4.0 Consensus size: 214
5568145 TCAAATACAT
* * *
5568155 AGCAGATCTGACCTTTATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGC
1 AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
* * * *
5568220 AAATCGAAGACAACAGATCTGACCTTCATTGAAGCAGATCTAAGATGATTTGGCATCTCTGTATT
66 AGATCAAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
*
5568285 AGACGGGGAGCAGATCGAAGACATAGCAGATCTAACCTTCATTGAAGCAGATCCAAGATGATTTG
131 AGACGGGGAGCAGATCGAAGAC--AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTG
*
5568350 GCATCTCTATATTAGACGGAC
194 GCATCTCTGTATTAGACGGAC
5568371 AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
* *
5568436 AGATCAAAGACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATT
66 AGATCAAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
* *
5568501 AGACGGGGAGCAGATCGAAGACATAACATATCTGACCTTCATTGAAGCAGATCCAAGATGATTTG
131 AGACGGGGAGCAGATCGAAGAC--AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTG
5568566 GCATCTCTGTATTAGACGGGAAGCAGATCGAAGAC
194 GCATCTCTGTATT-----------AGA-CG--GAC
* ** * *
5568601 AGCAGATCTGACCTTCATTGAAACAAATCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
1 AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
* * * * *
5568666 AGATCGAAGACAGTAGACCTGAACTTCATTGAAGCAGATCCAAGATAATTTGGCATCTCTGTATT
66 AGATCAAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
*
5568731 AGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGC
131 AGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
*
5568796 ATCTCTGTATT-----GTC
196 ATCTCTGTATTAGACGGAC
*
5568810 AG-AGAGCAG------ATTG-A--AGAT---AGCA-GATTTGGCATCTCTGTATTAGACGGGGAG
1 AGCAGATCAGACCTTCATTGAAGTAGATCCAAG-ATGATTTGGCATCTCTGTATTAGACGGGGAG
* * *
5568861 CAGATTAAAGACGCAGCAGATCTTACCTTCATTGAAGCAGATCCAAGATGATTTGGCATTTCTGT
65 CAGATCAAAGA--CAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGT
*
5568926 ATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTT
128 ATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTT
*
5568991 GGCATCTCTGTATTAGACGGAG
193 GGCATCTCTGTATTAGACGGAC
5569013 AGCAGAT
1 AGCAGAT
5569020 TGAAGACAGC
Statistics
Matches: 581, Mismatches: 45, Indels: 58
0.85 0.07 0.08
Matches are distributed among these distances:
196 40 0.07
197 1 0.00
198 123 0.21
199 3 0.01
201 1 0.00
202 4 0.01
203 3 0.01
204 3 0.01
208 5 0.01
209 4 0.01
216 195 0.34
227 3 0.01
228 53 0.09
230 143 0.25
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (214 bp):
AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
AGATCAAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATT
AGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGC
ATCTCTGTATTAGACGGAC
Found at i:5568494 original size:76 final size:76
Alignment explanation
Indices: 5568368--5568834 Score: 720
Period size: 76 Copynumber: 6.1 Consensus size: 76
5568358 ATATTAGACG
* *
5568368 GACAGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 GACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
*
5568433 AGCAGATCAAA
66 AGCAGATCGAA
* *
5568444 GACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 GACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
5568509 AGCAGATCGAA
66 AGCAGATCGAA
* *
5568520 GACATAACATATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG
1 GAC--AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGG
*
5568585 GAAGCAGATCGAA
64 GGAGCAGATCGAA
* * *
5568598 GACAGCAGATCTGACCTTCATTGAAACAAATCTAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 GACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
5568663 AGCAGATCGAA
66 AGCAGATCGAA
* * * *
5568674 GACAGTAGACCTGAACTTCATTGAAGCAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGG
1 GACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
5568739 AGCAGATCGAA
66 AGCAGATCGAA
* * * *
5568750 GACAGCAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATT-GTCAGAG
1 GACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
*
5568814 AGCAGATTGAA
66 AGCAGATCGAA
*
5568825 GATAGCAGAT
1 GACAGCAGAT
5568835 TTGGCATCTC
Statistics
Matches: 356, Mismatches: 33, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
75 23 0.06
76 262 0.74
78 71 0.20
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (76 bp):
GACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
AGCAGATCGAA
Found at i:5568547 original size:370 final size:368
Alignment explanation
Indices: 5567998--5568746 Score: 1230
Period size: 370 Copynumber: 2.0 Consensus size: 368
5567988 GCAGATCGAA
* *
5567998 GACACCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 GACAGCAGATCAGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
* * *
5568063 AGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGT
66 AGCAGATCAAAGACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGT
* * * * *
5568128 ATTAGACGGTGAGCAGATCAAATACATAGCAGATCTGACCTTTATTGAAGTAGATCCAAGATGAT
131 ATTAGACGGGGAGCAGATCAAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGAT
* * *
5568193 TTGGCATCTCTGTATTAAACGGGGAGCAAATCGAAGACAACAGATCTGACCTTCATTGAAGCAGA
196 TTGGCATCTCTGTATTAAACGGGAAGCAAATCGAAGACAACAGATCTGACCTTCATTGAAACAAA
*
5568258 TCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-AACC
261 TCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGAC--AGCAGACCTGAA-C
*
5568322 TTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACG
323 TTCATTGAAGCAGATCCAAGATAATTTGGCATCTCTATATTAGACG
**
5568368 GACAGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 GACAGCAGATCAGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
5568433 AGCAGATCAAAGACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGT
66 AGCAGATCAAAGACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGT
* *
5568498 ATTAGACGGGGAGCAGATCGAAGACATAACATATCTGACCTTCATTGAAGCAGATCCAAGATGAT
131 ATTAGACGGGGAGCAGATCAAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGAT
* * *
5568563 TTGGCATCTCTGTATTAGACGGGAAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAACAAA
196 TTGGCATCTCTGTATTAAACGGGAAGCAAATCGAAGACAACAGATCTGACCTTCATTGAAACAAA
*
5568628 TCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGTAGACCTGAACTTC
261 TCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGACCTGAACTTC
*
5568693 ATTGAAGCAGATCCAAGATAATTTGGCATCTCTGTATTAGACG
326 ATTGAAGCAGATCCAAGATAATTTGGCATCTCTATATTAGACG
**
5568736 GGGAGCAGATC
1 GACAGCAGATC
5568747 GAAGACAGCA
Statistics
Matches: 352, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
368 61 0.17
369 2 0.01
370 289 0.82
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (368 bp):
GACAGCAGATCAGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
AGCAGATCAAAGACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGT
ATTAGACGGGGAGCAGATCAAAGACATAACAGATCTGACCTTCATTGAAGCAGATCCAAGATGAT
TTGGCATCTCTGTATTAAACGGGAAGCAAATCGAAGACAACAGATCTGACCTTCATTGAAACAAA
TCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGACCTGAACTTC
ATTGAAGCAGATCCAAGATAATTTGGCATCTCTATATTAGACG
Found at i:5568695 original size:446 final size:442
Alignment explanation
Indices: 5567846--5569048 Score: 1728
Period size: 446 Copynumber: 2.7 Consensus size: 442
5567836 TAGGCTAAAG
5567846 CATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGG
1 CATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGAC----
*
5567911 AGTAGATCGAAGACAACAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGT
62 -G--GA-C--AG----CAGATCAGACCTTCATTG-AA-AGATCCAAGATGATTTGGCATCTCTGT
* *
5567976 ATTAGACGGGGAGCAGATCGAAGACACCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTT
115 ATTAGACGGGGAGCAGATCAAAGACAGCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTT
5568041 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATC
180 GGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATC
* *
5568106 CAAGATGATTTGGCATCTCTGTATTAGACGGTG-AGCAGATCAAATACATAGCAGATCTGACCTT
245 CAAGATGATTTGGCATCTCTGTATTAGACGG-GAAGCAGATCGAAGAC--AGCAGATCTGACCTT
* ** *
5568170 TATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGCAAATCGAAGACAACA
307 CATTGAAACAAATCCAAGATGATTTGGCATCTCTGTATTAAACGGGGAGCAAATCGAAGACAACA
* * * *
5568235 GATCTGACCTTCATTGAAGCAGATCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
372 GACCTGAACTTCATTGAAGCAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
5568300 CGAAGA
437 CGAAGA
* *
5568306 CATAGCAGATCTAACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTATATTAGACGGAC
1 CATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAC
5568371 AGCAGATCAGACCTTCATTGAAGTAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
66 AGCAGATCAGACCTTCATTGAA--AGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGC
*
5568436 AGATCAAAGACAGCAGATCTGACATTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATT
129 AGATCAAAGACAGCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATT
* *
5568501 AGACGGGGAGCAGATCGAAGACATAACATATCTGACCTTCATTGAAGCAGATCCAAGATGATTTG
194 AGACGGGGAGCAGATCGAAGAC--AGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTG
*
5568566 GCATCTCTGTATTAGACGGGAAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAACAAATCT
257 GCATCTCTGTATTAGACGGGAAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAACAAATCC
* * **
5568631 AAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGTAGACCTGAACTTCATT
322 AAGATGATTTGGCATCTCTGTATTAAACGGGGAGCAAATCGAAGACAACAGACCTGAACTTCATT
5568696 GAAGCAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA
387 GAAGCAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA
* *
5568752 C--AGCAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATT-----GTC
1 CATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAC
*
5568810 AG-AGAGCAG------ATTG-AAGAT---AGCA-GATTTGGCATCTCTGTATTAGACGGGGAGCA
66 AGCAGATCAGACCTTCATTGAAAGATCCAAG-ATGATTTGGCATCTCTGTATTAGACGGGGAGCA
* * * *
5568863 GATTAAAGACGCAGCAGATCTTACCTTCATTGAAGCAGATCCAAGATGATTTGGCATTTCTGTAT
130 GATCAAAGA--CAGCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTAT
*
5568928 TAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGG
193 TAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGG
*
5568993 CATCTCTGTATTAGAC-GGAGAGCAGATTGAAGACAGCAGATCTGACCTTCATTGAA
258 CATCTCTGTATTAGACGGGA-AGCAGATCGAAGACAGCAGATCTGACCTTCATTGAA
5569049 GCAGATCAAA
Statistics
Matches: 697, Mismatches: 38, Indels: 50
0.89 0.05 0.06
Matches are distributed among these distances:
425 3 0.00
426 131 0.19
427 1 0.00
428 73 0.10
429 4 0.01
431 1 0.00
432 4 0.01
438 6 0.01
439 4 0.01
444 51 0.07
445 2 0.00
446 281 0.40
447 1 0.00
448 70 0.10
450 2 0.00
452 1 0.00
453 2 0.00
455 1 0.00
460 59 0.08
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (442 bp):
CATAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAC
AGCAGATCAGACCTTCATTGAAAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAG
ATCAAAGACAGCAGATCTGACCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAG
ACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCAGATCCAAGATGATTTGGCAT
CTCTGTATTAGACGGGAAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAACAAATCCAAGA
TGATTTGGCATCTCTGTATTAAACGGGGAGCAAATCGAAGACAACAGACCTGAACTTCATTGAAG
CAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGA
Found at i:5568913 original size:122 final size:121
Alignment explanation
Indices: 5568713--5568957 Score: 375
Period size: 122 Copynumber: 2.0 Consensus size: 121
5568703 ATCCAAGATA
*
5568713 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAGCA
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACAGCAGATCTGACCTTCATTGAAGCA
* * * *
5568778 GCTCCAAGATGATTTGGCATCTCTGTATT-GTCAGAGAGCAGATTGAAGATAGCAG
66 GATCCAAGATGATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGACAGCAG
* *
5568833 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATTAAAGACGCAGCAGATCTTACCTTCATTGAAG
1 ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGA--CAGCAGATCTGACCTTCATTGAAG
* * *
5568898 CAGATCCAAGATGATTTGGCATTTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAG
64 CAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGACAGCAG
5568956 AT
1 AT
5568958 CTGACCTTCA
Statistics
Matches: 112, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
120 37 0.33
122 52 0.46
123 23 0.21
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (121 bp):
ATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACAGCAGATCTGACCTTCATTGAAGCA
GATCCAAGATGATTTGGCATCTCTGTATTAGACAGAGAGCAGATCGAAGACAGCAG
Found at i:5568972 original size:198 final size:197
Alignment explanation
Indices: 5568636--5569033 Score: 654
Period size: 198 Copynumber: 2.0 Consensus size: 197
5568626 AATCTAAGAT
* *
5568636 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGTAGACCTGAACTTCATTGAAGC
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACAGCAGACCTGAACTTCATTGAAGC
5568701 AGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACC
66 AGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACC
* * * *
5568766 TTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATT-GTCAGAGAGCAGATTGAAGATAG
131 TTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGAGAGCAGATTGAAGACAG
5568830 CA
196 CA
* * * *
5568832 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTAAAGACGCAGCAGATCTTACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGA--CAGCAGACCTGAACTTCATTGAA
* *
5568897 GCAGATCCAAGATGATTTGGCATTTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGA
64 GCAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGA
*
5568962 CCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATTGAAGAC
129 CCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGAGAGCAGATTGAAGAC
5569027 AGCA
194 AGCA
5569031 GAT
1 GAT
5569034 CTGACCTTCA
Statistics
Matches: 186, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
196 38 0.20
198 123 0.66
199 25 0.13
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (197 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCAAAGACAGCAGACCTGAACTTCATTGAAGC
AGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACC
TTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACAGAGAGCAGATTGAAGACAG
CA
Found at i:5568989 original size:76 final size:76
Alignment explanation
Indices: 5568832--5569060 Score: 377
Period size: 76 Copynumber: 3.0 Consensus size: 76
5568822 GAAGATAGCA
* *
5568832 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTAAAGACGCAGCAGATCTTACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGA--CAGCAGATCTGACCTTCATTGAA
5568897 GCAGATCCAAGAT
64 GCAGATCCAAGAT
* * *
5568910 GATTTGGCATTTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAAC
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGACAGCAGATCTGACCTTCATTGAAGC
5568975 AGATCCAAGAT
66 AGATCCAAGAT
*
5568986 GATTTGGCATCTCTGTATTAGACGGAGAGCAGATTGAAGACAGCAGATCTGACCTTCATTGAAGC
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGACAGCAGATCTGACCTTCATTGAAGC
*
5569051 AGATCAAAGA
66 AGATCCAAGA
5569061 CATAACAGAT
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
76 104 0.74
78 37 0.26
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (76 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGACAGCAGATCTGACCTTCATTGAAGC
AGATCCAAGAT
Found at i:5569049 original size:274 final size:272
Alignment explanation
Indices: 5568560--5569052 Score: 833
Period size: 274 Copynumber: 1.8 Consensus size: 272
5568550 GATCCAAGAT
*
5568560 GATTTGGCATCTCTGTATTAGACGGGAAGCAGATCGAAGACAGCAGATCTGACCTTCATTGAAAC
1 GATTTGGCATCTCTGTATTAGACGGGAAGCAGATCAAAGACAGCAGATCTGACCTTCATTGAAAC
* *
5568625 AAATCTAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGTAGACCTGAAC
66 AAATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGACCTGAAC
* *
5568690 TTCATTGAAGCAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAG
131 TTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACAG
5568755 CAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAGA
196 CAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAGA
5568820 TTGAAGATAGCA
261 TTGAAGATAGCA
* * *
5568832 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTAAAGACGCAGCAGATCTTACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGAAGCAGATCAAAGA--CAGCAGATCTGACCTTCATTGAA
* * * *
5568897 GCAGATCCAAGATGATTTGGCATTTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGATCTGA
64 ACAAATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGACCTGA
* * *
5568962 CCTTCATTGAAACAGATCCAAGATGATTTGGCATCTCTGTATTAGACGGAGAGCAGATTGAAGAC
129 ACTTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGAC
5569027 AGCAGATCTGACCTTCATTGAAGCAG
194 AGCAGATCTGACCTTCATTGAAGCAG
5569053 ATCAAAGACA
Statistics
Matches: 204, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
272 37 0.18
274 167 0.82
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (272 bp):
GATTTGGCATCTCTGTATTAGACGGGAAGCAGATCAAAGACAGCAGATCTGACCTTCATTGAAAC
AAATCCAAGATGATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACAGCAGACCTGAAC
TTCATTGAAACAGATCCAAGATAATTTGGCATCTCTGTATTAGACGGAGAGCAGATCGAAGACAG
CAGATCTGACCTTCATTGAAGCAGCTCCAAGATGATTTGGCATCTCTGTATTGTCAGAGAGCAGA
TTGAAGATAGCA
Found at i:5569084 original size:37 final size:35
Alignment explanation
Indices: 5569036--5569105 Score: 104
Period size: 37 Copynumber: 1.9 Consensus size: 35
5569026 CAGCAGATCT
5569036 GACCTTCATTGAAGCAGATCAAAGACATAACAGATTG
1 GACCTTCATTGAAGCAGATCAAA-A-ATAACAGATTG
* *
5569073 GACCTTTATTGAAGCAGATCCAAAATAACAGAT
1 GACCTTCATTGAAGCAGATCAAAAATAACAGAT
5569106 CTTATCCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 9 0.29
36 1 0.03
37 21 0.68
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GACCTTCATTGAAGCAGATCAAAAATAACAGATTG
Found at i:5578210 original size:7 final size:7
Alignment explanation
Indices: 5578198--5578235 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
5578188 CAAACTCTAA
5578198 TTTTTCT
1 TTTTTCT
5578205 TTTTTCT
1 TTTTTCT
5578212 TTTTT-T
1 TTTTTCT
5578218 TTTCTTCT
1 TTT-TTCT
5578226 TTCTTTCT
1 TT-TTTCT
5578234 TT
1 TT
5578236 CTATTTCGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 4 0.14
7 14 0.50
8 9 0.32
9 1 0.04
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:5578450 original size:3 final size:3
Alignment explanation
Indices: 5578429--5578472 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
5578419 TTTTCTGAAT
5578429 TAA TAGA TAA -AA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5578473 GTAAATATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:5585699 original size:33 final size:33
Alignment explanation
Indices: 5585656--5585779 Score: 203
Period size: 33 Copynumber: 3.8 Consensus size: 33
5585646 TTTCTTCTTG
*
5585656 ACATTCCAGCTACTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
5585689 ACATTTCAGCTCCTGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
*
5585722 ACATTCCAGCTCCCGTCCAGCAACCAAACACTC
1 ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
* *
5585755 ACATTCTAGCTCCTATCCAGCAACC
1 ACATTCCAGCTCCTGTCCAGCAACC
5585780 TGAAACAGAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 84 1.00
ACGTcount: A:0.31, C:0.41, G:0.09, T:0.19
Consensus pattern (33 bp):
ACATTCCAGCTCCTGTCCAGCAACCAAACACTC
Found at i:5588290 original size:89 final size:89
Alignment explanation
Indices: 5588125--5588302 Score: 259
Period size: 88 Copynumber: 2.0 Consensus size: 89
5588115 GCATATGTCT
*
5588125 GGTTACATGTAAAATATTACAGTTAATTATTATCGGATGTAACCTTATTAGCAGATTGAATATAC
1 GGTTACATGTAAAATATTAAAGTTAATTATTATCGGATGTAACCTTATTAGCAGATTGAATATAC
5588190 TATGACATTGTA-TTTCATTTCTC
66 TATGACATTGTATTTTCATTTCTC
* * * * *
5588213 GGTTACATGTAAACTATTAAAGTTAATTCTTATTGGATGTTGACCTTATTAGCGGATTGAATATA
1 GGTTACATGTAAAATATTAAAGTTAATTATTATCGGATG-TAACCTTATTAGCAGATTGAATATA
* * *
5588278 GTGTGACATTGTATTTTCCTTTCTC
65 CTATGACATTGTATTTTCATTTCTC
5588303 AAGGAAAATA
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 35 0.44
89 34 0.43
90 10 0.13
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (89 bp):
GGTTACATGTAAAATATTAAAGTTAATTATTATCGGATGTAACCTTATTAGCAGATTGAATATAC
TATGACATTGTATTTTCATTTCTC
Found at i:5598274 original size:18 final size:18
Alignment explanation
Indices: 5598251--5598285 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5598241 TTTAAATTAC
5598251 ATAATATAATACAATACA
1 ATAATATAATACAATACA
*
5598269 ATAATATATTACAATAC
1 ATAATATAATACAATAC
5598286 TTAAAAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAATATAATACAATACA
Found at i:5599976 original size:28 final size:28
Alignment explanation
Indices: 5599920--5599992 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
5599910 CAAATACATT
*
5599920 TAAAACAA-ATATTAAAACAAGAAATAAA
1 TAAAA-AATATATTAAAACAAGAAACAAA
* *
5599948 TAAAAAATATATTAAAACAATACACAAA
1 TAAAAAATATATTAAAACAAGAAACAAA
* *
5599976 TTAAAAATATAATAAAA
1 TAAAAAATATATTAAAA
5599993 ATTGATTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 2 0.05
28 37 0.95
ACGTcount: A:0.70, C:0.07, G:0.01, T:0.22
Consensus pattern (28 bp):
TAAAAAATATATTAAAACAAGAAACAAA
Found at i:5600034 original size:23 final size:23
Alignment explanation
Indices: 5600008--5600052 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
5599998 TTATATTAAA
*
5600008 ATTAAAAATAGAATATAAATATG
1 ATTAAAAATAAAATATAAATATG
*
5600031 ATTAAAAATAAAATATATATAT
1 ATTAAAAATAAAATATAAATAT
5600053 ATTTAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (23 bp):
ATTAAAAATAAAATATAAATATG
Found at i:5600781 original size:65 final size:65
Alignment explanation
Indices: 5600677--5600807 Score: 253
Period size: 65 Copynumber: 2.0 Consensus size: 65
5600667 CAAAAATTGT
*
5600677 GGAAATTGAATTAGAGGTTGAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAA
1 GGAAATTGAATTAAAGGTTGAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAA
5600742 GGAAATTGAATTAAAGGTTGAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAA
1 GGAAATTGAATTAAAGGTTGAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAA
5600807 G
1 G
5600808 AAAACTTTGT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (65 bp):
GGAAATTGAATTAAAGGTTGAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAA
Found at i:5600830 original size:65 final size:63
Alignment explanation
Indices: 5600696--5600830 Score: 182
Period size: 65 Copynumber: 2.1 Consensus size: 63
5600686 ATTAGAGGTT
* ** *
5600696 GAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAAGGAAATTGAATTAAAGGTT
1 GAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAAGAAAATTGAAGCAAA-G-A
5600761 GAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAAGAAAACTTTGTAAGCAAA-
1 GAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAAGAAAA--TTG-AAGCAAAG
5600825 A
63 A
5600826 GAATT
1 GAATT
5600831 TCATATTAAG
Statistics
Matches: 63, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
65 55 0.87
67 3 0.05
68 5 0.08
ACGTcount: A:0.47, C:0.07, G:0.13, T:0.33
Consensus pattern (63 bp):
GAATTAAATATGAAATTAAAACCTATTGAATCTAGTTTCATATAAAGAAAATTGAAGCAAAGA
Found at i:5602657 original size:13 final size:13
Alignment explanation
Indices: 5602641--5602665 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5602631 TTCATAACTA
5602641 CTTTTTAAAAGTC
1 CTTTTTAAAAGTC
5602654 CTTTTTAAAAGT
1 CTTTTTAAAAGT
5602666 ATTGCCAAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.48
Consensus pattern (13 bp):
CTTTTTAAAAGTC
Found at i:5605386 original size:21 final size:23
Alignment explanation
Indices: 5605352--5605400 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
5605342 AAAAAAAATT
5605352 AGAATTTTGAAAAAATTA-AAAA
1 AGAATTTTGAAAAAATTATAAAA
*
5605374 AGAATTTT-TAAAAATTATAAAA
1 AGAATTTTGAAAAAATTATAAAA
5605396 A-AATT
1 AGAATT
5605401 ACTAAAAACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (23 bp):
AGAATTTTGAAAAAATTATAAAA
Found at i:5605396 original size:9 final size:9
Alignment explanation
Indices: 5605382--5605433 Score: 54
Period size: 8 Copynumber: 5.7 Consensus size: 9
5605372 AAAGAATTTT
5605382 TAAAAATTA
1 TAAAAATTA
5605391 TAAAAAAATTA
1 T--AAAAATTA
*
5605402 CTAAAAA-CA
1 -TAAAAATTA
5605411 TAAAAATTA
1 TAAAAATTA
5605420 T-AAAATTA
1 TAAAAATTA
5605428 TAAAAA
1 TAAAAA
5605434 AATGCACGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
8 14 0.39
9 8 0.22
10 5 0.14
11 8 0.22
12 1 0.03
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5605406 original size:21 final size:20
Alignment explanation
Indices: 5605362--5605436 Score: 70
Period size: 21 Copynumber: 3.9 Consensus size: 20
5605352 AGAATTTTGA
*
5605362 AAAAATTA-AAAAAGAATTTTT
1 AAAAATTATAAAAA-AA-TTAT
5605383 AAAAATTATAAAAAAATTACT
1 AAAAATTATAAAAAAATTA-T
*
5605404 AAAAA-CAT--AAAAATTAT
1 AAAAATTATAAAAAAATTAT
5605421 -AAAATTATAAAAAAAT
1 AAAAATTATAAAAAAAT
5605437 GCACGTGTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
16 4 0.09
17 3 0.07
18 8 0.17
19 6 0.13
20 4 0.09
21 16 0.35
22 5 0.11
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAAAAAATTAT
Found at i:5605480 original size:19 final size:19
Alignment explanation
Indices: 5605458--5605497 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
5605448 TATTATAATT
*
5605458 TTTTAAAAAAAGTATAAAA
1 TTTTAAAAAAAGTAAAAAA
*
5605477 TTTTAAAAAATGTAAAAAA
1 TTTTAAAAAAAGTAAAAAA
5605496 TT
1 TT
5605498 ATAATATACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TTTTAAAAAAAGTAAAAAA
Found at i:5606331 original size:29 final size:29
Alignment explanation
Indices: 5606299--5606355 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
5606289 AGGTTAAAAT
*
5606299 ATTTATAATTT-TTTTTGTAGTTTTTATAA
1 ATTTAAAATTTATTTTTGTA-TTTTTATAA
5606328 ATTTAAAATTTAATTTTTGTATTTTTAT
1 ATTTAAAATTT-ATTTTTGTATTTTTAT
5606356 TTTTAAGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 10 0.40
30 7 0.28
31 8 0.32
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (29 bp):
ATTTAAAATTTATTTTTGTATTTTTATAA
Found at i:5607135 original size:14 final size:15
Alignment explanation
Indices: 5607111--5607139 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5607101 GTTACTGTTA
5607111 TGGTAGTTTGCCTTG
1 TGGTAGTTTGCCTTG
5607126 TGGT-GTTTGCCTTG
1 TGGTAGTTTGCCTTG
5607140 AAGCTTAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.03, C:0.14, G:0.34, T:0.48
Consensus pattern (15 bp):
TGGTAGTTTGCCTTG
Found at i:5607522 original size:16 final size:16
Alignment explanation
Indices: 5607489--5607522 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5607479 TGTTATTGTT
* *
5607489 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5607505 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5607521 AA
1 AA
5607523 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:5610348 original size:21 final size:21
Alignment explanation
Indices: 5610322--5610362 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5610312 AGACGAGCAA
* *
5610322 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5610343 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5610363 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5612284 original size:16 final size:16
Alignment explanation
Indices: 5612251--5612284 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5612241 GGAGATTGTT
* *
5612251 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
5612267 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
5612283 AA
1 AA
5612285 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:5615840 original size:31 final size:32
Alignment explanation
Indices: 5615805--5615864 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
5615795 AATTTTCTTT
*
5615805 AAAATATAATAATT-TTTAAAAAATTAATTCC
1 AAAATATAATAATTATTCAAAAAATTAATTCC
* *
5615836 AAAATTTAATAATTATTCAACAAATTAAT
1 AAAATATAATAATTATTCAAAAAATTAAT
5615865 ATCTATGGAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (32 bp):
AAAATATAATAATTATTCAAAAAATTAATTCC
Found at i:5619920 original size:3 final size:3
Alignment explanation
Indices: 5619914--5619943 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5619904 TTCTTTTCCT
*
5619914 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5619944 ATTCTTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5625954 original size:24 final size:24
Alignment explanation
Indices: 5625925--5625976 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
5625915 GGTGGGCTGT
5625925 TTATGTCACAAACTTAGGCTGTAC
1 TTATGTCACAAACTTAGGCTGTAC
*
5625949 TTATGTCACAAACTTAGGCTGTAT
1 TTATGTCACAAACTTAGGCTGTAC
5625973 TTAT
1 TTAT
5625977 TATTTTGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (24 bp):
TTATGTCACAAACTTAGGCTGTAC
Found at i:5627328 original size:24 final size:24
Alignment explanation
Indices: 5627251--5627331 Score: 62
Period size: 24 Copynumber: 3.4 Consensus size: 24
5627241 ACCCTAATTT
* *
5627251 TAATTTAGATTACTTTATGGTTGT
1 TAATTTAGATTAATTTATGGTTGA
*
5627275 TAA-TTA-ATTAGACTTTA--GTTAAA
1 TAATTTAGATTA-A-TTTATGGTT-GA
*
5627298 CATATTTAGATTAATTTATGGTTGA
1 TA-ATTTAGATTAATTTATGGTTGA
5627323 TAATTTAGA
1 TAATTTAGA
5627332 CTTTATTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
22 7 0.16
23 4 0.09
24 19 0.44
25 6 0.14
26 7 0.16
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.48
Consensus pattern (24 bp):
TAATTTAGATTAATTTATGGTTGA
Found at i:5630025 original size:21 final size:21
Alignment explanation
Indices: 5629999--5630041 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5629989 GCAACATTAA
5629999 CTTAATCTAATAACATTAGCC
1 CTTAATCTAATAACATTAGCC
*
5630020 CTTAATTTAATAACATTAGCC
1 CTTAATCTAATAACATTAGCC
5630041 C
1 C
5630042 CAACTTTTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.35
Consensus pattern (21 bp):
CTTAATCTAATAACATTAGCC
Found at i:5634619 original size:18 final size:17
Alignment explanation
Indices: 5634578--5634619 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
5634568 TAAATTTCGG
5634578 TTATTA-ATTTTAATAT
1 TTATTAGATTTTAATAT
5634594 TTGA-TAGATTTTAAATAT
1 TT-ATTAGATTTT-AATAT
5634612 TTATTAGA
1 TTATTAGA
5634620 ATAACTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.18
17 7 0.32
18 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TTATTAGATTTTAATAT
Found at i:5634935 original size:152 final size:151
Alignment explanation
Indices: 5634765--5635171 Score: 628
Period size: 147 Copynumber: 2.7 Consensus size: 151
5634755 TTTTCCTATA
* * * *
5634765 TTATTT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTATTTTTTTATATT
1 TTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTATTTTTTTATATT
** * *
5634829 AATTTAATAAATAACCCTGATTTTGGCACTTTCTTCGTATTTTTTTATTTTCGTATCTTCTTTTT
66 TTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTT-TTTTCGTATCTTCTTTTT
5634894 TAAAATATATTATTTTTGTATT
130 TAAAATATATTATTTTTGTATT
*
5634916 TTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAATATTTTTTTATATT
1 TTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTATTTTTTTATATT
*
5634981 TTTTTAATAAATAACCCTGATTTCAGCACTTTATTCGTA----TTTTTTTCGTATCTTCTTTTTT
66 TTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTTTTTCGTATCTTCTTTTTT
5635042 AAAATATATTATTTTTGTATT
131 AAAATATATTATTTTTGTATT
* *
5635063 TTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTGAGT-CTTTTTTATATT
1 TTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTATTTTTTTATATT
* * *
5635127 TTTTTAATAAATAATCCTTATTTTAGCACTTTATTCTTATTTTTT
66 TTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTT
5635172 AAAATATATT
Statistics
Matches: 234, Mismatches: 17, Indels: 11
0.89 0.06 0.04
Matches are distributed among these distances:
146 46 0.20
147 90 0.38
148 3 0.01
150 2 0.01
151 6 0.03
152 87 0.37
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (151 bp):
TTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTATTTTTTTATATT
TTTTTAATAAATAACCCTGATTTTAGCACTTTATTCGTATTTTTTTTTTTCGTATCTTCTTTTTT
AAAATATATTATTTTTGTATT
Found at i:5635170 original size:129 final size:130
Alignment explanation
Indices: 5635036--5635301 Score: 365
Period size: 130 Copynumber: 2.0 Consensus size: 130
5635026 TCGTATCTTC
** * * *
5635036 TTTTTTAAAATATATTATTTTTGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAA
1 TTTTTTAAAATATATTATTTTCATATTTTATTT-TTTATATTATTTTAGCAAAAAATGTTTCAAA
* * ** * * * *
5635101 TGTATTATTTGAGT-CTTTTTTATATTTTTTTAATAAATAATCCTTATTTT-AGCACTTTATTCT
65 TGTATTATGTAAGTGCTTTTTTATATTAATTGAATAAATAACCCTGATTTTGA-CACTTTATTCG
5635164 TA
129 TA
5635166 TTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAAT
1 TTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAAT
* *
5635231 GTATTATGTAAGTGTTTTTTTATATTAATTGAATAAATAACCCTGATTTTGACACTTTCTTCGTA
66 GTATTATGTAAGTGCTTTTTTATATTAATTGAATAAATAACCCTGATTTTGACACTTTATTCGTA
5635296 TTTTTT
1 TTTTTT
5635302 TATTTTCGTA
Statistics
Matches: 119, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
129 40 0.34
130 78 0.66
131 1 0.01
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (130 bp):
TTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAAT
GTATTATGTAAGTGCTTTTTTATATTAATTGAATAAATAACCCTGATTTTGACACTTTATTCGTA
Found at i:5635321 original size:151 final size:150
Alignment explanation
Indices: 5635161--5635956 Score: 1017
Period size: 152 Copynumber: 5.4 Consensus size: 150
5635151 AGCACTTTAT
5635161 TCTTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTT
1 TCTTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTT
* * *
5635226 CAAATGTATTATGTAAGTGTTTTTTTATATTAATTGAATAAATAACCCTGATTTTGACACTTTCT
66 CAAATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTAT
5635291 TCGTATTTTTTTATTTTCGTA
131 TCGTA-TTTTTTATTTTCGTA
* * * * *
5635312 TCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGTT
1 TCTTATTTTTTAAAATATATTATTTTCATATTTTATTT-TTTATATTATTTTAGCAAAAAATGTT
* *
5635377 TCAAATGTATTATTTAAGTG-TTTTTTATATT-TTTTCAATAAATAACCCTAATTTT-AGCACTT
65 TCAAATGTATTATTTAAGTGTTTTTTTATATTAATTT-AATAAATAACCCTGATTTTGA-CACTT
5635439 TATTCGTA---TTT-TTTTCGTA
128 TATTCGTATTTTTTATTTTCGTA
*
5635458 TATTATTTTTTAAAATATATTATTTTCATATTTTACTTTTTTATATTATTTTAGCAAAAAATGTT
1 TCTTATTTTTTAAAATATATTATTTTCATATTTTA-TTTTTTATATTATTTTAGCAAAAAATGTT
* * *
5635523 TCAAATGTATTACTTAAGTGTTTATTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTC
65 TCAAATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTA
*
5635588 TTCGTAATTTTTTATTTTTGTA
130 TTCGT-ATTTTTTATTTTCGTA
* * * * *
5635610 TCTTATTTTTTAAAATATCTTATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTT
1 TCTTATTTTTTAAAATATATTATTTTCATATTTTATTT-TTTATATTATTTTAGCAAAAAATGTT
* *
5635675 TCAAATGTATTATTTAAGTGTTTTTTTATATT-TTTTAATAAATATCCCTGATTTT-AGCACTTT
65 TCAAATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGA-CACTTT
* *
5635738 ATTCATATTTTTTATTTTTGTA
129 ATTCGTATTTTTTATTTTCGTA
* * * **
5635760 TATTATTTTTTAAAATATATTATTTTC-----GTA-----T-T-TTATTTTAGCATAAAACCTTT
1 TCTTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTT
* * * *
5635813 CAAATGTATTATTTAA--GTTTTTTTATATTAATTTAATAAATAACCCTGAATTTGGCACCTTGT
66 CAAATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTAT
*
5635876 TCGTATTTTTTTATTTTCGGA
131 TCGTA-TTTTTTATTTTCGTA
* * *
5635897 TTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTTTATATTATTTTAACAAAAAA
1 TCTTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAA
5635957 CTCGTCAGCA
Statistics
Matches: 560, Mismatches: 56, Indels: 60
0.83 0.08 0.09
Matches are distributed among these distances:
135 13 0.02
136 30 0.05
137 70 0.12
138 1 0.00
139 1 0.00
142 2 0.00
145 2 0.00
146 82 0.15
147 46 0.08
148 6 0.01
149 14 0.03
150 45 0.08
151 115 0.21
152 133 0.24
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (150 bp):
TCTTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTT
CAAATGTATTATTTAAGTGTTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTAT
TCGTATTTTTTATTTTCGTA
Found at i:5635348 original size:16 final size:16
Alignment explanation
Indices: 5635290--5635348 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
5635280 TGACACTTTC
*
5635290 TTCGTATTTTTTTATT
1 TTCGTATTTTATTATT
*
5635306 TTCGTATCTTATT-TT
1 TTCGTATTTTATTATT
** * *
5635321 TT-AAAATATATTATT
1 TTCGTATTTTATTATT
5635336 TTCGTATTTTATT
1 TTCGTATTTTATT
5635349 TCTTCATATT
Statistics
Matches: 30, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
14 5 0.17
15 8 0.27
16 17 0.57
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (16 bp):
TTCGTATTTTATTATT
Found at i:5635553 original size:298 final size:297
Alignment explanation
Indices: 5635163--5635948 Score: 1183
Period size: 298 Copynumber: 2.7 Consensus size: 297
5635153 CACTTTATTC
5635163 TTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCA
1 TTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCA
*
5635228 AATGTATTATGTAAGTGTTTTTTTATATTAATTGAATAAATAACCCTGATTTTGACACTTTCTTC
66 AATGTATTAT-TAAGTG-TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTC
*
5635293 GTATTTTTTTATTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTCATAT
129 GTATTTTTTTATTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTTATAT
5635358 TATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG-TTTTTTATATTTTTTCAATAAATAA
194 TATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTGTTTTTTTATATTTTTT-AATAAATAA
*
5635422 CCCTAATTTTAGCACTTTATTCGTA-TTT-TTTTCGTATA
258 CCCTAATTTTAGCACTTTATTCATATTTTATTTTCGTATA
5635460 TTATTTTTTAAAATATATTATTTTCATATTTTACTTTTTTATATTATTTTAGCAAAAAATGTTTC
1 TTATTTTTTAAAATATATTATTTTCATATTTTA-TTTTTTATATTATTTTAGCAAAAAATGTTTC
5635525 AAATGTATTACTTAAGTGTTTATTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTT
65 AAATGTATTA-TTAAGTGTTT-TTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTT
* * *
5635590 CGTAATTTTTTATTTTTGTATCTTATTTTTTAAAATATCTTATTTTCGTATTTTATTTCTTTATA
128 CGTATTTTTTTATTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTTATA
*
5635655 TTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTGTTTTTTTATATTTTTTAATAAATAT
193 TTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTGTTTTTTTATATTTTTTAATAAATAA
* *
5635720 CCCTGATTTTAGCACTTTATTCATATTTTTTATTTTTGTATA
258 CCCTAATTTTAGCACTTTATTCATA--TTTTATTTTCGTATA
* * **
5635762 TTATTTTTTAAAATATATTATTTTC-----GTA-----T-T-TTATTTTAGCATAAAACCTTTCA
1 TTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCA
* * * *
5635815 AATGTATTATTTAAGT-TTTTTTATATTAATTTAATAAATAACCCTGAATTTGGCACCTTGTTCG
66 AATGTATTA-TTAAGTGTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCG
* * * *
5635879 TATTTTTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATATTTTATTT-TTTATATT
130 TATTTTTTTATTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTTATATT
5635943 ATTTTA
195 ATTTTA
5635949 ACAAAAAACT
Statistics
Matches: 456, Mismatches: 25, Indels: 27
0.90 0.05 0.05
Matches are distributed among these distances:
286 14 0.03
287 90 0.20
288 3 0.01
289 35 0.08
290 1 0.00
291 1 0.00
297 38 0.08
298 221 0.48
299 16 0.04
301 3 0.01
302 34 0.07
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (297 bp):
TTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCA
AATGTATTATTAAGTGTTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCGT
ATTTTTTTATTTTCGTATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTTATATTA
TTTTAGTACATAATGTTTCAAATGTATTATTTAAGTGTTTTTTTATATTTTTTAATAAATAACCC
TAATTTTAGCACTTTATTCATATTTTATTTTCGTATA
Found at i:5635553 original size:428 final size:428
Alignment explanation
Indices: 5634753--5635956 Score: 1500
Period size: 428 Copynumber: 2.8 Consensus size: 428
5634743 ATAAGTAAAA
* * *
5634753 TATTTTCCTATATTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTAT
1 TATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTGT
*
5634818 TTTTTTATATTAATTTAATAAATAACCCTGATTTTGGCACTTTCTTCGTATTTTTTTATTTTCGT
66 TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGT
* * *
5634883 ATCTTCTTTTTTAAAATATATTATTTTTGTATTTTATTTCTTTATATTATTTTAGTACATAATGT
131 ATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGT
* * *
5634948 TTCAAATGTATTATTTAAATATTTTTTTATATTTTTTTAATAAATAACCCTGATTTCAGCACTTT
196 TTCAAATGTATTATTT-AA-GTTTTTTTATA-TTTTTTAATAAATAACCCTAATTTTAGCACTTT
* * **
5635013 ATTCGTATTTTTTTCGTATCTTCTTTTTTAAAATATATTATTTTTGTATTTTATTTCTTTATATT
258 ATTCGTATTTTTTTCGTATATTATTTTTTAAAATATATTATTTTCATATTTTATTT-TTTATATT
* * * * * ** *
5635078 ATTTTAGTACATAATGTTTCAAATGTATTATTTGAGTCTTTTTTATATTTTTTTAATAAATAATC
322 ATTTTAGCAAAAAATGTTTCAAATGTATTACTTAAGTCTTTTTTATATTAATTTAATAAATAACC
*
5635143 CTTATTTT-AGCA-C-TTTA-T-TCTTATTTTTTAAAATATAT
387 CTGATTTTGA-CATCTTTTATTATCTTATTTTTTAAAATATAT
5635181 TATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTGT
1 TATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTGT
*
5635246 TTTTTTATATTAATTGAATAAATAACCCTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGT
66 TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGT
5635311 ATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGT
131 ATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGT
5635376 TTCAAATGTATTATTTAAGTGTTTTTTATATTTTTTCAATAAATAACCCTAATTTTAGCACTTTA
196 TTCAAATGTATTATTTAAGT-TTTTTTATATTTTTT-AATAAATAACCCTAATTTTAGCACTTTA
5635441 TTCGTATTTTTTTCGTATATTATTTTTTAAAATATATTATTTTCATATTTTACTTTTTTATATTA
259 TTCGTATTTTTTTCGTATATTATTTTTTAAAATATATTATTTTCATATTTTA-TTTTTTATATTA
*
5635506 TTTTAGCAAAAAATGTTTCAAATGTATTACTTAAGTGTTTATTTATATTAATTTAATAAATAACC
323 TTTTAGCAAAAAATGTTTCAAATGTATTACTTAAGTCTTT-TTTATATTAATTTAATAAATAACC
*
5635571 CTGATTTTGACACTTTCTTCGTAATTTTTTATTTTTGTATCTTATTTTTTAAAATATCT
387 CTGATTTTGACA------TC------TTTTA----T-TATCTTATTTTTTAAAATATAT
* * * * *
5635630 TATTTTCGTATTTTATTTCTTTATATTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTG
1 TATTTTCATATTTTATTT-TTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTG
* * * * *
5635695 TTTTTTTATATT-TTTTAATAAATATCCCTGATTTT-AGCACTTTATTCATA-TTTTTTATTTTT
65 TTTTTTTATATTAATTTAATAAATAACCCTGATTTTGA-CACTTTCTTCGTATTTTTTTATTTTC
* *
5635757 GTATATTATTTTTTAAAATATATTATTTTCGTATTTTATTT-TAGCATA--A----A--AC----
129 GTATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCT-TCATATTATTTTAGTACATAA
* * * *
5635809 -CTTTCAAATGTATTATTTAAGTTTTTTTATATTAATTTAATAAATAACCCTGAA-TTTGGCACC
193 TGTTTCAAATGTATTATTTAAGTTTTTTTATATT-TTTTAATAAATAACCCT-AATTTTAGCACT
* * * *
5635872 TTGTTCGTATTTTTTTATTTTCGGATTTTATTTTTTAAAATATACTATTTTCATATTTTATTTTT
256 TTATTCGTA----TTT-TTTTCGTATATTATTTTTTAAAATATATTATTTTCATATTTTATTTTT
*
5635937 TATATTATTTTAACAAAAAA
316 TATATTATTTTAGCAAAAAA
5635957 CTCGTCAGCA
Statistics
Matches: 692, Mismatches: 48, Indels: 62
0.86 0.06 0.08
Matches are distributed among these distances:
426 7 0.01
427 128 0.18
428 236 0.34
429 1 0.00
434 39 0.06
435 27 0.04
438 27 0.04
439 40 0.06
440 2 0.00
442 5 0.01
446 1 0.00
447 1 0.00
448 57 0.08
449 67 0.10
450 54 0.08
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (428 bp):
TATTTTCATATTTTATTTTTTATATTATTTTAGCAAAAAATGTTTCAAATGTATTATGTAAGTGT
TTTTTTATATTAATTTAATAAATAACCCTGATTTTGACACTTTCTTCGTATTTTTTTATTTTCGT
ATCTTATTTTTTAAAATATATTATTTTCGTATTTTATTTCTTCATATTATTTTAGTACATAATGT
TTCAAATGTATTATTTAAGTTTTTTTATATTTTTTAATAAATAACCCTAATTTTAGCACTTTATT
CGTATTTTTTTCGTATATTATTTTTTAAAATATATTATTTTCATATTTTATTTTTTATATTATTT
TAGCAAAAAATGTTTCAAATGTATTACTTAAGTCTTTTTTATATTAATTTAATAAATAACCCTGA
TTTTGACATCTTTTATTATCTTATTTTTTAAAATATAT
Found at i:5635796 original size:137 final size:137
Alignment explanation
Indices: 5635655--5635935 Score: 377
Period size: 137 Copynumber: 2.1 Consensus size: 137
5635645 TTTCTTTATA
* * ** *
5635655 TTATTTTAGTACATAATGTTTCAAATGTATTATTTAAGTGTTTTTTTATATT-TTTTAATAAATA
1 TTATTTTAGCACAAAACCTTTCAAATGTATTATTTAA--GTTTTTTTATATTAATTTAATAAATA
* * * * * *
5635719 TCCCTGATTTTAGCACTTTATTCATA-TTTTTTATTTTTGTATATTATTTTTTAAAATATATTAT
64 ACCCTGAATTTAGCACCTTATTCATATTTTTTTATTTTCGGATATTATTTTTTAAAATATACTAT
*
5635783 TTTCGTATT
129 TTTCATATT
*
5635792 TTATTTTAGCATAAAACCTTTCAAATGTATTATTTAAGTTTTTTTATATTAATTTAATAAATAAC
1 TTATTTTAGCACAAAACCTTTCAAATGTATTATTTAAGTTTTTTTATATTAATTTAATAAATAAC
* * * *
5635857 CCTGAATTTGGCACCTTGTTCGTATTTTTTTATTTTCGGATTTTATTTTTTAAAATATACTATTT
66 CCTGAATTTAGCACCTTATTCATATTTTTTTATTTTCGGATATTATTTTTTAAAATATACTATTT
5635922 TCATATT
131 TCATATT
5635929 TTATTTT
1 TTATTTT
5635936 TTATATTATT
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
135 13 0.10
136 31 0.25
137 81 0.65
ACGTcount: A:0.29, C:0.08, G:0.07, T:0.56
Consensus pattern (137 bp):
TTATTTTAGCACAAAACCTTTCAAATGTATTATTTAAGTTTTTTTATATTAATTTAATAAATAAC
CCTGAATTTAGCACCTTATTCATATTTTTTTATTTTCGGATATTATTTTTTAAAATATACTATTT
TCATATT
Found at i:5636453 original size:17 final size:18
Alignment explanation
Indices: 5636431--5636477 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
5636421 TTTTTTTTTC
5636431 CTTCTTTTTCCTTC-CCT
1 CTTCTTTTTCCTTCTCCT
*
5636448 CTTCTTCTTCTCCTTCTCTT
1 CTTCTT-TT-TCCTTCTCCT
*
5636468 TTTCTTTTTC
1 CTTCTTTTTC
5636478 TTTTTTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 8 0.32
20 7 0.28
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
CTTCTTTTTCCTTCTCCT
Found at i:5636536 original size:3 final size:3
Alignment explanation
Indices: 5636519--5636585 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
5636509 TCCTCCTCCC
* * *
5636519 CTT CTT TTT CTTT CTT CTT CTT C-T CTT CTT -TC CTT CTT CTC CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
*
5636563 CTT -TT CTT TTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT
5636586 TGTTCCCGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 5 0.10
3 44 0.85
4 3 0.06
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:5636777 original size:18 final size:18
Alignment explanation
Indices: 5636756--5636800 Score: 65
Period size: 17 Copynumber: 2.5 Consensus size: 18
5636746 ATTTTTTTTA
5636756 TTTTTTTTATTTTCAGT-
1 TTTTTTTTATTTTCAGTG
*
5636773 TTTTTTTTCTTTTTCAGTG
1 TTTTTTTT-ATTTTCAGTG
5636792 TTTTTTTTA
1 TTTTTTTTA
5636801 CTGTTGCGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 8 0.33
18 8 0.33
19 8 0.33
ACGTcount: A:0.09, C:0.07, G:0.07, T:0.78
Consensus pattern (18 bp):
TTTTTTTTATTTTCAGTG
Found at i:5637860 original size:20 final size:20
Alignment explanation
Indices: 5637824--5637862 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5637814 GAGAATTACA
*
5637824 AAAATATAAAAATTTTAAAG
1 AAAATATAAAAAATTTAAAG
5637844 AAAAT-TAAAATAATTTAAA
1 AAAATATAAAA-AATTTAAA
5637863 TGTTCTTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (20 bp):
AAAATATAAAAAATTTAAAG
Found at i:5640150 original size:21 final size:21
Alignment explanation
Indices: 5640126--5640173 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
5640116 ATGATAGCTT
*
5640126 TTAAAATAA-TTATCTTTTAAA
1 TTAAAATAATTTATCTATT-AA
5640147 TT-AAATAATTTATCTATTAA
1 TTAAAATAATTTATCTATTAA
5640167 TTAAAAT
1 TTAAAAT
5640174 TTAATATTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAATAATTTATCTATTAA
Found at i:5640154 original size:20 final size:20
Alignment explanation
Indices: 5640129--5640171 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
5640119 ATAGCTTTTA
*
5640129 AAATAA-TTATCTTTTAAATT
1 AAATAATTTATCTATT-AATT
5640149 AAATAATTTATCTATTAATT
1 AAATAATTTATCTATTAATT
5640169 AAA
1 AAA
5640172 ATTTAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATAATTTATCTATTAATT
Found at i:5642935 original size:21 final size:21
Alignment explanation
Indices: 5642909--5642949 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5642899 ATCTGCTCAA
* *
5642909 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
5642930 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
5642950 TGCTCGTCTG
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:5646967 original size:43 final size:43
Alignment explanation
Indices: 5646918--5647485 Score: 804
Period size: 43 Copynumber: 13.1 Consensus size: 43
5646908 CCGGCATTAC
* *
5646918 GCCTGCTAGGCACGAAGGCCTGAATACACAACACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5646961 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGTACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
5647004 GCCTGCTAGGCACGAAGGCTCGAATATACATCACCGGAACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5647047 GCCTGCTAGGCACAAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
5647090 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCAAGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
5647133 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
5647176 GCCTGCTAGGCACGAAGGCCCGAAT--ACA-CACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
5647216 GCCTGCTAGGCACGAAGGCCCGAATATACATCATCGGAACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * * *
5647259 ACCTGCTAGGCATGAAGGCCCGAATACACATCATCGGCACAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
5647302 GCCTGCTAGGCACGAAGGCCCGAAGGCCCGAATACACATCACCAGCACAAA
1 GCCTGCTAGG--C--A----CGAAGGCCCGAATACACATCACCGGCACGAA
* *
5647353 GCCTGCTAGGCACGAAGGCCCGAATATACATCACCGGCATGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
5647396 GCTTGCTAGGCACGAAGGCCCGAATACACATCACCGGTAAGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * *
5647439 GCCTGCTAGGCACGAAGGCCTGAATATA-AT-ACCTGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
5647480 GCCTGC
1 GCCTGC
5647486 GGGATTTATC
Statistics
Matches: 476, Mismatches: 38, Indels: 24
0.88 0.07 0.04
Matches are distributed among these distances:
40 37 0.08
41 17 0.04
42 5 0.01
43 375 0.79
45 1 0.00
47 2 0.00
49 1 0.00
51 38 0.08
ACGTcount: A:0.32, C:0.32, G:0.25, T:0.12
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:5647350 original size:51 final size:51
Alignment explanation
Indices: 5647272--5647376 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
5647262 TGCTAGGCAT
* *
5647272 GAAGGCCCGAATACACATCATCGGCACAAAGCCTGCTAGGCACGAAGGCCC
1 GAAGGCCCGAATACACATCACCAGCACAAAGCCTGCTAGGCACGAAGGCCC
5647323 GAAGGCCCGAATACACATCACCAGCACAAAGCCTGCTAGGCACGAAGGCCC
1 GAAGGCCCGAATACACATCACCAGCACAAAGCCTGCTAGGCACGAAGGCCC
5647374 GAA
1 GAA
5647377 TATACATCAC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.33, C:0.33, G:0.25, T:0.09
Consensus pattern (51 bp):
GAAGGCCCGAATACACATCACCAGCACAAAGCCTGCTAGGCACGAAGGCCC
Found at i:5650481 original size:52 final size:53
Alignment explanation
Indices: 5650424--5650547 Score: 180
Period size: 53 Copynumber: 2.4 Consensus size: 53
5650414 AAATTAGTGT
*
5650424 TGGCCTGTCAATGGCCGGCATC-AGTACGAAAAAAAATCAA-TTTTTTTTGTGC
1 TGGCCTGTCAATGGCCGGCACCAAGTACG-AAAAAAATCAATTTTTTTTTGTGC
** *
5650476 TGGCCTGTCAATGGTTGGCACCAAGTACGAAAAAAATTAATTTTTTTTTGTGC
1 TGGCCTGTCAATGGCCGGCACCAAGTACGAAAAAAATCAATTTTTTTTTGTGC
*
5650529 TGGCCTGTCAATAGCCGGC
1 TGGCCTGTCAATGGCCGGC
5650548 TATTGACAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (53 bp):
TGGCCTGTCAATGGCCGGCACCAAGTACGAAAAAAATCAATTTTTTTTTGTGC
Found at i:5651008 original size:15 final size:15
Alignment explanation
Indices: 5650988--5651022 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
5650978 ATTTAGCTCA
5650988 TTTATATTAAAAT-TT
1 TTTATATT-AAATGTT
5651003 TTTATATTAAATGTT
1 TTTATATTAAATGTT
5651018 TTTAT
1 TTTAT
5651023 GTTATAGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (15 bp):
TTTATATTAAATGTT
Found at i:5664859 original size:35 final size:35
Alignment explanation
Indices: 5664805--5665082 Score: 197
Period size: 35 Copynumber: 8.0 Consensus size: 35
5664795 TCCTCATTGA
* * *
5664805 AATACCATACCTACGTTTCACAACTCGGTATGGAA
1 AATACCATACCTACTTTTCACAACTCAGTATGGAT
* ** * *
5664840 AACACCATACCTACTTTTCA-TGCTCGGTATGGAC
1 AATACCATACCTACTTTTCACAACTCAGTATGGAT
* *
5664874 AATACCATTCCTA-TATTTCATAACTCAGTATGGAT
1 AATACCATACCTACT-TTTCACAACTCAGTATGGAT
* * * * * * *
5664909 GATGCCATACCTACGTATCATAGCTCAGTATGGAC
1 AATACCATACCTACTTTTCACAACTCAGTATGGAT
* ** * * * *
5664944 GACGCCATACCTA-TGTTTCATAGCTCGGTAT-GAA
1 AATACCATACCTACT-TTTCACAACTCAGTATGGAT
* * *
5664978 AATACCATACCTACGTTTCACAGCTCAGTATGGTT
1 AATACCATACCTACTTTTCACAACTCAGTATGGAT
* * *
5665013 AATGCCATAACTA-TGTTTCACAACTCAGTATGGCT
1 AATACCATACCTACT-TTTCACAACTCAGTATGGAT
* * *
5665048 AATACTATACCTACATTTCACAACTCGGTATGGAT
1 AATACCATACCTACTTTTCACAACTCAGTATGGAT
5665083 CAACCACGGT
Statistics
Matches: 193, Mismatches: 42, Indels: 16
0.77 0.17 0.06
Matches are distributed among these distances:
33 1 0.01
34 53 0.27
35 139 0.72
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (35 bp):
AATACCATACCTACTTTTCACAACTCAGTATGGAT
Found at i:5664917 original size:69 final size:70
Alignment explanation
Indices: 5664809--5665081 Score: 271
Period size: 69 Copynumber: 3.9 Consensus size: 70
5664799 CATTGAAATA
* * * * * * * *
5664809 CCATACCTACGTTTCACAACTCGGTATGGAAAACACCATACCTACTTTTCA-TGCTCGGTATGGA
1 CCATACCTATGTTTCATAACTCAGTATGGATAATACCATACCTACGTTTCACAGCTCAGTATGGA
*
5664873 CAATA
66 CAATG
* * * * * *
5664878 CCATTCCTATATTTCATAACTCAGTATGGATGATGCCATACCTACGTATCATAGCTCAGTATGGA
1 CCATACCTATGTTTCATAACTCAGTATGGATAATACCATACCTACGTTTCACAGCTCAGTATGGA
* *
5664943 CGACG
66 CAATG
* * * *
5664948 CCATACCTATGTTTCATAGCTCGGTAT-GAAAATACCATACCTACGTTTCACAGCTCAGTATGGT
1 CCATACCTATGTTTCATAACTCAGTATGGATAATACCATACCTACGTTTCACAGCTCAGTATGGA
*
5665012 TAATG
66 CAATG
* * * * * * *
5665017 CCATAACTATGTTTCACAACTCAGTATGGCTAATACTATACCTACATTTCACAACTCGGTATGGA
1 CCATACCTATGTTTCATAACTCAGTATGGATAATACCATACCTACGTTTCACAGCTCAGTATGGA
5665082 TCAACCACGG
Statistics
Matches: 162, Mismatches: 40, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
69 96 0.59
70 66 0.41
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (70 bp):
CCATACCTATGTTTCATAACTCAGTATGGATAATACCATACCTACGTTTCACAGCTCAGTATGGA
CAATG
Found at i:5664997 original size:104 final size:104
Alignment explanation
Indices: 5664809--5665081 Score: 289
Period size: 104 Copynumber: 2.6 Consensus size: 104
5664799 CATTGAAATA
* *
5664809 CCATACCTACGTTTCACAACTCGGTATGGAAAACACCATACCTACTTTTCATGCTCGGTATGGAC
1 CCATACCTACGTTTCACAACTCAGTATGGAAAACACCATACCTACTTTTCATGCTCGGTATGGAA
* * * *
5664874 AATACCATTCCTATATTTCATAACTCAGTATGGATGATG
66 AATACCATACCTACATTTCACAACTCAGTATGGATAATG
* * * ** *
5664913 CCATACCTACGTATCATAGCTCAGTATGGACGACGCCATACCTA-TGTTTCATAGCTCGGTAT-G
1 CCATACCTACGTTTCACAACTCAGTATGGAAAACACCATACCTACT-TTTCAT-GCTCGGTATGG
* * *
5664976 AAAATACCATACCTACGTTTCACAGCTCAGTATGGTTAATG
64 AAAATACCATACCTACATTTCACAACTCAGTATGGATAATG
* * ** * * * **
5665017 CCATAACTATGTTTCACAACTCAGTATGGCTAATACTATACCTACATTTCACAACTCGGTATGGA
1 CCATACCTACGTTTCACAACTCAGTATGGAAAACACCATACCTACTTTTCA-TGCTCGGTATGGA
5665082 TCAACCACGG
Statistics
Matches: 135, Mismatches: 29, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
103 1 0.01
104 123 0.91
105 11 0.08
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (104 bp):
CCATACCTACGTTTCACAACTCAGTATGGAAAACACCATACCTACTTTTCATGCTCGGTATGGAA
AATACCATACCTACATTTCACAACTCAGTATGGATAATG
Found at i:5669741 original size:2 final size:2
Alignment explanation
Indices: 5669734--5669758 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5669724 AGCTTTGGTC
5669734 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5669759 ATGCCCTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5672730 original size:17 final size:17
Alignment explanation
Indices: 5672708--5672745 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
5672698 TAAAAATTAT
*
5672708 AAAATTTATATTTTTTA
1 AAAATTTATAATTTTTA
*
5672725 AAAATTTTTAATTTTTA
1 AAAATTTATAATTTTTA
5672742 AAAA
1 AAAA
5672746 AAATTAAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATTTATAATTTTTA
Found at i:5672746 original size:18 final size:17
Alignment explanation
Indices: 5672708--5672746 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5672698 TAAAAATTAT
*
5672708 AAAATTTATATTTTTTA
1 AAAATTTATATTTTTAA
*
5672725 AAAATTTTTAATTTTTAA
1 AAAATTTAT-ATTTTTAA
5672743 AAAA
1 AAAA
5672747 AATTAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATTTATATTTTTAA
Found at i:5682390 original size:10 final size:10
Alignment explanation
Indices: 5682375--5682399 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5682365 AATTTTATAT
5682375 TTTTAAAAAA
1 TTTTAAAAAA
5682385 TTTTAAAAAA
1 TTTTAAAAAA
5682395 TTTTA
1 TTTTA
5682400 TATAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
TTTTAAAAAA
Found at i:5686364 original size:18 final size:18
Alignment explanation
Indices: 5686334--5686388 Score: 87
Period size: 17 Copynumber: 3.2 Consensus size: 18
5686324 CGTGATCCGA
5686334 TTGAAAA-ACGAAAATTT
1 TTGAAAACACGAAAATTT
*
5686351 TTTAAAACACGAAAA-TT
1 TTGAAAACACGAAAATTT
5686368 TTGAAAACACGAAAATTT
1 TTGAAAACACGAAAATTT
5686386 TTG
1 TTG
5686389 GGATCCGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
17 22 0.65
18 12 0.35
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (18 bp):
TTGAAAACACGAAAATTT
Found at i:5686960 original size:26 final size:27
Alignment explanation
Indices: 5686917--5686970 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
5686907 TATGTATACC
*
5686917 AAATAATACATAATAATACT-AAAATA
1 AAATAATACATAACAATACTGAAAATA
*
5686943 AAATAATA-AGTAACAATAGTGAAAATA
1 AAATAATACA-TAACAATACTGAAAATA
5686970 A
1 A
5686971 TAAGCATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 1 0.04
26 16 0.67
27 7 0.29
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (27 bp):
AAATAATACATAACAATACTGAAAATA
Found at i:5687005 original size:18 final size:17
Alignment explanation
Indices: 5686979--5687031 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 17
5686969 AATAAGCATA
5686979 ATAATAAATATAATGATAT
1 ATAA-AAATATAAT-ATAT
*
5686998 ATAAAAATAATACTATAT
1 ATAAAAAT-ATAATATAT
*
5687016 ATAAAAGTAT-ATATAT
1 ATAAAAATATAATATAT
5687032 GTACAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.17
17 2 0.07
18 15 0.50
19 8 0.27
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (17 bp):
ATAAAAATATAATATAT
Found at i:5688957 original size:20 final size:19
Alignment explanation
Indices: 5688932--5688969 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5688922 AATTTTAACT
*
5688932 ATTAAAATATTTTTTAAATA
1 ATTAAAAT-TTTTTAAAATA
5688952 ATTAAAATTTTTTAAAAT
1 ATTAAAATTTTTTAAAAT
5688970 TAAGAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTAAAATTTTTTAAAATA
Found at i:5692672 original size:22 final size:22
Alignment explanation
Indices: 5692647--5692704 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 22
5692637 ATATAGGCAA
*
5692647 AAATTAAAATATATGTATATAT
1 AAATTAAAATATATGTATATAC
* *
5692669 AAA-TATATATATATGTATTTAC
1 AAATTA-AAATATATGTATATAC
5692691 AAAGGTTAAAATAT
1 AAA--TTAAAATAT
5692705 GTACATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 2 0.07
22 19 0.68
24 5 0.18
25 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
AAATTAAAATATATGTATATAC
Found at i:5692873 original size:26 final size:28
Alignment explanation
Indices: 5692844--5692908 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
5692834 TAAATAAAAA
5692844 AATAGATATGAAATAA-TA-ATATATAT
1 AATAGATATGAAATAATTATATATATAT
* ***
5692870 AATATATATGTTTTAATTATATATATAT
1 AATAGATATGAAATAATTATATATATAT
5692898 AGATAGATATG
1 A-ATAGATATG
5692909 TATATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 12 0.39
27 2 0.06
28 9 0.29
29 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
AATAGATATGAAATAATTATATATATAT
Found at i:5692984 original size:3 final size:3
Alignment explanation
Indices: 5692976--5693018 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
5692966 AAACAATTAT
*
5692976 ATA ATA ATA ATA ACA ATA ATA AT- ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
5693019 TGCTAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5692985 original size:20 final size:22
Alignment explanation
Indices: 5692962--5693008 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
5692952 ACGTATATGC
5692962 ATAAAAACAAT-T-ATATAATA
1 ATAAAAACAATATAATATAATA
*
5692982 ATAATAACAATAATAATATAATA
1 ATAAAAACAAT-ATAATATAATA
5693005 ATAA
1 ATAA
5693009 TAATAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 10 0.43
22 1 0.04
23 12 0.52
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAAACAATATAATATAATA
Found at i:5693000 original size:23 final size:23
Alignment explanation
Indices: 5692974--5693018 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5692964 AAAAACAATT
5692974 ATATAATAATAATAACAATAATA
1 ATATAATAATAATAACAATAATA
*
5692997 ATATAATAATAATAATAATAAT
1 ATATAATAATAATAACAATAAT
5693019 TGCTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
ATATAATAATAATAACAATAATA
Found at i:5693013 original size:20 final size:20
Alignment explanation
Indices: 5692979--5693018 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
5692969 CAATTATATA
5692979 ATAATAATAACAATAATAAT
1 ATAATAATAACAATAATAAT
*
5692999 ATAATAATAATAATAATAAT
1 ATAATAATAACAATAATAAT
5693019 TGCTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATAACAATAATAAT
Found at i:5694699 original size:44 final size:43
Alignment explanation
Indices: 5694638--5695672 Score: 439
Period size: 44 Copynumber: 24.5 Consensus size: 43
5694628 ATCTACTCTG
* * * *
5694638 CTGTAACCTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTT-CTTCAATCTGCTCCA
* * ** * * *
5694682 CTGTAACTTCAGGGAGATAGGATAGTGTCTTCGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* * **
5694725 CTATAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
* ** *
5694769 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
* * * * * * *
5694815 CTATAACCTCAGGGAAATAAGA-CCTGAT-GT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCCT-TTCTTCAATCTGCTCCA
* * *
5694856 CTGTAACTTCAGAGAGATAAGATCC--T-TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* * * * * * ** *
5694895 TTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGA-TCCTTTCTTCAATCTGCTCCA
* **
5694939 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
* ** *
5694983 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTCCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
* * * * *
5695029 CTGTAACCTCAGGGAAATAAGA-CCTGAT-GT-GATCT--T-CT
1 CTGTAACCTCAGGGAGATAAGATCCT-TTCTTCAATCTGCTCCA
* * *
5695067 CTGTAACTTCA-AGAGATAAGATCC--T-TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* * * * * *
5695105 -TGTAATCTCA-GGAGATAGGATTACTATCTT-GATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGA-TCCTTTCTTCAATCTGCTCCA
*
5695146 CTGTAATCTCAGGGAGATAAGATCCTTTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTT--CTTCAATCTGCTCCA
** *
5695191 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTCTTCGGTCTGTTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
* * * * * *
5695237 CTGTAATCTCAGGGAGATAAGA-CCTGAT-GT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCCT-TTCTTCAATCTGCTCCA
* * *
5695278 CTGTAACTTCAGAGAGATAAGATCC--T-TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* * *
5695317 -TGTAA-CTCA-GGAGATAGGA---TTAC-T--ATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* **
5695351 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCA
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
** *
5695395 CTGTAACCTCAGGGAGATAAGAT-CTGAAATTC-TCGGTCTACTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
* * * * *
5695440 CTGTAACCTCAGGGA-ATAAGA-CCTGAT-GT-GATCTTCTCTA
1 CTGTAACCTCAGGGAGATAAGATCCT-TTCTTCAATCTGCTCCA
* * *
5695480 CTGTAACTTCAGAGAGATAAGATCC--T-TT-AATCCGCTCCA
1 CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
* * * * * * ** *
5695519 TTGTAATCTCAAGGAGATAGGATTACTATCTTTGATCTGCTCCG
1 CTGTAACCTCAGGGAGATAAGA-TCCTTTCTTCAATCTGCTCCA
* **
5695563 CTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCC-
1 CTGTAACCTCAGGGAGATAAGATC-CTTTCTTCAATCTGCTCCA
*** *
5695606 CTGTAA-CTCAGGGAGATAAGAT-CTGAAATTCTTTGGTCTGTTCCA
1 CTGTAACCTCAGGGAGATAAGATCCT----TTCTTCAATCTGCTCCA
*
5695651 CTGTAATCTCAGGGAGATAAGA
1 CTGTAACCTCAGGGAGATAAGA
5695673 CCTGTATAAT
Statistics
Matches: 750, Mismatches: 171, Indels: 138
0.71 0.16 0.13
Matches are distributed among these distances:
34 8 0.01
35 11 0.01
36 12 0.02
37 37 0.05
38 21 0.03
39 60 0.08
40 28 0.04
41 76 0.10
42 46 0.06
43 53 0.07
44 216 0.29
45 62 0.08
46 118 0.16
48 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
CTGTAACCTCAGGGAGATAAGATCCTTTCTTCAATCTGCTCCA
Found at i:5694748 original size:87 final size:87
Alignment explanation
Indices: 5694626--5694787 Score: 209
Period size: 87 Copynumber: 1.9 Consensus size: 87
5694616 AGACCTGATG
* * * * * *
5694626 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-CTTTATTTTAATCCGCTCCACTGTAACT
1 CGATCTACTCCGCTATAACCTCAGAGAGATAAGATCTC-TGACTTCAATCCGCTCCACTGTAACC
5694690 TCAGGGAGATAGGATAGTGTCTT
65 TCAGGGAGATAGGATAGTGTCTT
* * * * *
5694713 CGATCTGCTCCGCTATAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTACTCCGCTATAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
5694778 CAGGGAGATA
66 CAGGGAGATA
5694788 AGATCTGAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
87 62 0.98
88 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (87 bp):
CGATCTACTCCGCTATAACCTCAGAGAGATAAGATCTCTGACTTCAATCCGCTCCACTGTAACCT
CAGGGAGATAGGATAGTGTCTT
Found at i:5707917 original size:15 final size:15
Alignment explanation
Indices: 5707897--5707926 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5707887 CAAAAATTAA
*
5707897 AATATATGTATATAT
1 AATATATATATATAT
5707912 AATATATATATATAT
1 AATATATATATATAT
5707927 GTATTTACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
AATATATATATATAT
Found at i:5708117 original size:26 final size:28
Alignment explanation
Indices: 5708088--5708152 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 28
5708078 TAAATAAAAA
5708088 AATAGATATGAAATAA-TA-ATATATAT
1 AATAGATATGAAATAATTATATATATAT
* ***
5708114 AATATATATGTTTTAATTATATATATAT
1 AATAGATATGAAATAATTATATATATAT
5708142 AGATAGATATG
1 A-ATAGATATG
5708153 TATATAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 12 0.39
27 2 0.06
28 9 0.29
29 8 0.26
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (28 bp):
AATAGATATGAAATAATTATATATATAT
Found at i:5708226 original size:3 final size:3
Alignment explanation
Indices: 5708218--5708251 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
5708208 AAAAACAATT
*
5708218 ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5708252 AATTGCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5708246 original size:18 final size:18
Alignment explanation
Indices: 5708206--5708248 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
5708196 ACGTATATGC
* *
5708206 ATAAAAACAATTATAATA
1 ATAATAACAATAATAATA
5708224 ATAATAACAATAATAATA
1 ATAATAACAATAATAATA
5708242 ATAATAA
1 ATAATAA
5708249 TAAAATTGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAATAACAATAATAATA
Found at i:5711852 original size:65 final size:65
Alignment explanation
Indices: 5711770--5711892 Score: 237
Period size: 65 Copynumber: 1.9 Consensus size: 65
5711760 GGCAACTAAG
*
5711770 TCTCAAGTTTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTGCTTCCAACAGCTAGC
1 TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTGCTTCCAACAGCTAGC
5711835 TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTGCTTCCAAC
1 TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTGCTTCCAAC
5711893 CTTGTTGAGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.21, C:0.27, G:0.16, T:0.36
Consensus pattern (65 bp):
TCTCAAGTCTGATTCTTGTCAATCATGCTCATTTCATCGAGCATGGCTTGCTTCCAACAGCTAGC
Found at i:5715873 original size:10 final size:10
Alignment explanation
Indices: 5715858--5715913 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
5715848 ATTTTAAAAT
5715858 ATAAATACAA-
1 ATAAATA-AAG
5715868 ATAAATAAAG
1 ATAAATAAAG
* *
5715878 ATAATTAAAT
1 ATAAATAAAG
5715888 ATAAATAAAG
1 ATAAATAAAG
5715898 ATAAATGAAA-
1 ATAAAT-AAAG
5715908 ATAAAT
1 ATAAAT
5715914 CCTAAAATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
9 2 0.05
10 35 0.88
11 3 0.08
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (10 bp):
ATAAATAAAG
Found at i:5715881 original size:20 final size:19
Alignment explanation
Indices: 5715858--5715913 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
5715848 ATTTTAAAAT
5715858 ATAAATACAAATAAATAAAG
1 ATAAATA-AAATAAATAAAG
*
5715878 ATAATTAAATATAAATAAAG
1 ATAAATAAA-ATAAATAAAG
5715898 ATAAATGAAAATAAAT
1 ATAAAT-AAAATAAAT
5715914 CCTAAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 27 0.84
21 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
ATAAATAAAATAAATAAAG
Found at i:5715888 original size:30 final size:30
Alignment explanation
Indices: 5715854--5715911 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
5715844 TTAAATTTTA
5715854 AAATATAAATACAA-ATAAAT-AAAGATAATT
1 AAATATAAATA-AAGATAAATGAAA-ATAATT
5715884 AAATATAAATAAAGATAAATGAAAATAA
1 AAATATAAATAAAGATAAATGAAAATAA
5715912 ATCCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.08
30 21 0.81
31 3 0.12
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (30 bp):
AAATATAAATAAAGATAAATGAAAATAATT
Found at i:5716725 original size:95 final size:96
Alignment explanation
Indices: 5716557--5716734 Score: 277
Period size: 95 Copynumber: 1.9 Consensus size: 96
5716547 TTTTTATTTA
* * *
5716557 TTTATTTTTGCTTAAGAATATATTGAATATTTTGACGTGAAGAGAGATAACAACCAAGCACCCCA
1 TTTATTTTTGCTTAAGAACATATCGAACATTTTGACGTGAAGAGAGATAACAACCAAGCACCCCA
*
5716622 CCCTGGTTACTCAGCCCATTATACTCCTAAT
66 CCCCGGTTACTCAGCCCATTATACTCCTAAT
* * * *
5716653 TTTATTTTT-CTTAAGAACATATCGAACCTTTTGACGTGAAGAGAGATTACAGCCAAGCACCTCA
1 TTTATTTTTGCTTAAGAACATATCGAACATTTTGACGTGAAGAGAGATAACAACCAAGCACCCCA
5716717 CCCCGGTTACTCAGCCCA
66 CCCCGGTTACTCAGCCCA
5716735 ACACATTCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
95 65 0.88
96 9 0.12
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (96 bp):
TTTATTTTTGCTTAAGAACATATCGAACATTTTGACGTGAAGAGAGATAACAACCAAGCACCCCA
CCCCGGTTACTCAGCCCATTATACTCCTAAT
Found at i:5717870 original size:5 final size:5
Alignment explanation
Indices: 5717860--5717942 Score: 53
Period size: 5 Copynumber: 15.6 Consensus size: 5
5717850 ATTAATATCC
* * *
5717860 AAATA AAATA AAGTA ATAA-A ATAATA AATTAA AAATAA ATAATA AATTAA
1 AAATA AAATA AAATA A-AATA A-AATA AAAT-A AAAT-A A-AATA AAAT-A
*
5717910 AAATA AAGATA AAA-A GAATA AAATA AAATA AAA
1 AAATA AA-ATA AAATA AAATA AAATA AAATA AAA
5717943 ATTGGGTTAC
Statistics
Matches: 63, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
4 3 0.05
5 36 0.57
6 21 0.33
7 3 0.05
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (5 bp):
AAATA
Found at i:5717883 original size:18 final size:16
Alignment explanation
Indices: 5717860--5717943 Score: 59
Period size: 18 Copynumber: 5.1 Consensus size: 16
5717850 ATTAATATCC
5717860 AAATAAAATAAAGTAATA
1 AAATAAAATAAA-TAA-A
*
5717878 AAAT--AATAAATTAA
1 AAATAAAATAAATAAA
*
5717892 AAATAAATAATAAATTAA
1 AAAT-AA-AATAAATAAA
5717910 AAATAAAGAT-AA-AAA
1 AAATAAA-ATAAATAAA
*
5717925 GAATAAAATAAAATAAA
1 AAATAAAAT-AAATAAA
5717942 AA
1 AA
5717944 TTGGGTTACC
Statistics
Matches: 54, Mismatches: 4, Indels: 17
0.72 0.05 0.23
Matches are distributed among these distances:
14 7 0.13
15 10 0.19
16 11 0.20
17 8 0.15
18 18 0.33
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (16 bp):
AAATAAAATAAATAAA
Found at i:5717892 original size:26 final size:24
Alignment explanation
Indices: 5717860--5717942 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 24
5717850 ATTAATATCC
5717860 AAATAAAATAAAGTAATAAAATAA
1 AAATAAAATAAAGTAATAAAATAA
*
5717884 TAAATTAAAAATAAA-TAATAAATTAA
1 -AAA-T-AAAATAAAGTAATAAAATAA
5717910 AAATAAAGATAAAAAG-AATAAAAT-A
1 AAATAAA-AT--AAAGTAATAAAATAA
5717935 AAATAAAA
1 AAATAAAA
5717943 ATTGGGTTAC
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
23 3 0.06
24 4 0.08
25 14 0.28
26 21 0.42
27 8 0.16
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.22
Consensus pattern (24 bp):
AAATAAAATAAAGTAATAAAATAA
Found at i:5720944 original size:50 final size:50
Alignment explanation
Indices: 5720869--5721095 Score: 355
Period size: 50 Copynumber: 4.5 Consensus size: 50
5720859 CCATGGCAAC
* *
5720869 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAATGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
5720919 AAGTGATAAGTGATAGCTTCGGCTACATTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5720969 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGATAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
5721019 AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGGACAAATGGC
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAAT-GA
* * *
5721070 AAGTAAAAAGTGGTAGCTTCGGCTAC
1 AAGTGATAAGTGATAGCTTCGGCTAC
5721096 CTGATCAATG
Statistics
Matches: 162, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
50 139 0.86
51 23 0.14
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:5721115 original size:32 final size:32
Alignment explanation
Indices: 5721074--5721134 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
5721064 AATGGCAAGT
* *
5721074 AAAAAGTGGTAGCTTCGGCTACCTGATCAATG
1 AAAAAGTGGTAGCTTCAGCTACCTAATCAATG
5721106 AAAAAGTGGTAGCTTCAGCTACCTAATCA
1 AAAAAGTGGTAGCTTCAGCTACCTAATCA
5721135 TCGGCTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (32 bp):
AAAAAGTGGTAGCTTCAGCTACCTAATCAATG
Found at i:5721175 original size:46 final size:47
Alignment explanation
Indices: 5721088--5721180 Score: 125
Period size: 46 Copynumber: 2.0 Consensus size: 47
5721078 AGTGGTAGCT
*
5721088 TCGGCTACCTGATCAATGAAAAAGTGGTAGCTTCAGCTACCTAATCA
1 TCGGCTACCTGATCAATGAAAAAGTGGTAGCTCCAGCTACCTAATCA
* * * * *
5721135 TCGGCTACTTGATTAGTGAAAAA-TGGTAGCTCCGGCTACCTGATCA
1 TCGGCTACCTGATCAATGAAAAAGTGGTAGCTCCAGCTACCTAATCA
5721181 GTGAATAGTG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 20 0.50
47 20 0.50
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (47 bp):
TCGGCTACCTGATCAATGAAAAAGTGGTAGCTCCAGCTACCTAATCA
Found at i:5721184 original size:31 final size:31
Alignment explanation
Indices: 5721136--5721204 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
5721126 ACCTAATCAT
* * *
5721136 CGGCTACTTGATTAGTGAAAAATGGTAGCTC
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
* * *
5721167 CGGCTACCTGATCAGTGAATAGTGATAGCTT
1 CGGCTACCTGATCAGTGAAAAATGATAGCTC
5721198 CGGCTAC
1 CGGCTAC
5721205 AAGTGACAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (31 bp):
CGGCTACCTGATCAGTGAAAAATGATAGCTC
Found at i:5722682 original size:33 final size:33
Alignment explanation
Indices: 5722636--5722709 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
5722626 TTTCCTTTTG
* * *
5722636 GAAATCAAGAGTTTGCCGTAGAATTTACTGTTA
1 GAAATCAACAGTTTGCCATAGAATCTACTGTTA
* * *
5722669 GAAATCAACAGTTTGCCATTGTATCTGCTGTTA
1 GAAATCAACAGTTTGCCATAGAATCTACTGTTA
5722702 GAAATCAA
1 GAAATCAA
5722710 ACATATTAGC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (33 bp):
GAAATCAACAGTTTGCCATAGAATCTACTGTTA
Found at i:5725081 original size:10 final size:10
Alignment explanation
Indices: 5725054--5725091 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
5725044 TTAAATTCTA
*
5725054 AAAGATAAAT
1 AAAGATAATT
5725064 ACAA-ATAATT
1 A-AAGATAATT
5725074 AAAGATAATT
1 AAAGATAATT
5725084 AAAGATAA
1 AAAGATAA
5725092 ATGAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.66, C:0.03, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAATT
Found at i:5725101 original size:10 final size:10
Alignment explanation
Indices: 5725088--5725113 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
5725078 ATAATTAAAG
5725088 ATAAATGAAA
1 ATAAATGAAA
5725098 ATAAATGAAA
1 ATAAATGAAA
5725108 ATAAAT
1 ATAAAT
5725114 CCTAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (10 bp):
ATAAATGAAA
Found at i:5735611 original size:17 final size:18
Alignment explanation
Indices: 5735575--5735614 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
5735565 CTTCTAAGAC
*
5735575 GCACTTTTGGGACAAAAA
1 GCACTTTTGAGACAAAAA
*
5735593 GCACTTTTGAGA-TAAAA
1 GCACTTTTGAGACAAAAA
5735610 GCACT
1 GCACT
5735615 CCTAAACAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (18 bp):
GCACTTTTGAGACAAAAA
Found at i:5739014 original size:21 final size:22
Alignment explanation
Indices: 5738988--5739037 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
5738978 ATTTGTGACT
*
5738988 ATTTTTGTCATCTAATTA-TTA
1 ATTTTTGTAATCTAATTATTTA
* *
5739009 ATTTTTTTAATTTAATTATTTA
1 ATTTTTGTAATCTAATTATTTA
5739031 ACTTTTT
1 A-TTTTT
5739038 TGAAATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 15 0.62
22 4 0.17
23 5 0.21
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (22 bp):
ATTTTTGTAATCTAATTATTTA
Found at i:5739036 original size:23 final size:21
Alignment explanation
Indices: 5739000--5739048 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
5738990 TTTTGTCATC
* *
5739000 TAATTATTAATTTTTTTAATT
1 TAATTATTAATTTTTTGAAAT
5739021 TAATTATTTAACTTTTTTGAAAT
1 TAATTA-TTAA-TTTTTTGAAAT
5739044 TAATT
1 TAATT
5739049 TTTTTAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 6 0.25
22 4 0.17
23 14 0.58
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TAATTATTAATTTTTTGAAAT
Found at i:5740339 original size:31 final size:31
Alignment explanation
Indices: 5740271--5740339 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
5740261 GATTAGCCCT
* * *** *
5740271 TAAATTTAGCAATTGTTCCTATATTGGGGGC
1 TAAACTTAGCAATTGTTCCCATATCAAGGCC
*
5740302 TGAACTTAGCAATTGTTCCCATATCAAGGCC
1 TAAACTTAGCAATTGTTCCCATATCAAGGCC
5740333 TAAACTT
1 TAAACTT
5740340 TGGGGTTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (31 bp):
TAAACTTAGCAATTGTTCCCATATCAAGGCC
Found at i:5745026 original size:14 final size:14
Alignment explanation
Indices: 5745009--5745036 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5744999 AAAATAATTT
5745009 AATAAATTTAATAA
1 AATAAATTTAATAA
5745023 AATAAATTTAATAA
1 AATAAATTTAATAA
5745037 TTATTGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
AATAAATTTAATAA
Found at i:5766029 original size:16 final size:18
Alignment explanation
Indices: 5765987--5766024 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
5765977 TTTTTTAAAT
5765987 TTAAAA-AATATTAAAAA
1 TTAAAATAATATTAAAAA
5766004 TTAAAATAATA-TAAAAA
1 TTAAAATAATATTAAAAA
5766021 TTAA
1 TTAA
5766025 TTAATTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAATAATATTAAAAA
Found at i:5768882 original size:4 final size:4
Alignment explanation
Indices: 5768866--5768906 Score: 64
Period size: 4 Copynumber: 10.0 Consensus size: 4
5768856 GTAAGGGCAG
*
5768866 CATA CATTA CATA CATA CATA CATA CATA CATA CATT CATA
1 CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA
5768907 TATATGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 30 0.88
5 4 0.12
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:5771066 original size:24 final size:24
Alignment explanation
Indices: 5771043--5771087 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5771033 ATATTTAATA
*
5771043 ATAAATGTTGT-ATAATATAAAAT
1 ATAAATATTGTAATAATATAAAAT
*
5771066 ATAAATATTTTAATAATATAAA
1 ATAAATATTGTAATAATATAAA
5771088 TAAGAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
ATAAATATTGTAATAATATAAAAT
Found at i:5771470 original size:13 final size:13
Alignment explanation
Indices: 5771452--5771476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5771442 CACAATCATC
5771452 TTGACACAAAAAA
1 TTGACACAAAAAA
5771465 TTGACACAAAAA
1 TTGACACAAAAA
5771477 GAAAAACAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.16, G:0.08, T:0.16
Consensus pattern (13 bp):
TTGACACAAAAAA
Done.