Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 4 of 172
Found at i:1015021 original size:27 final size:27
Alignment explanation
Indices: 1014967--1015021 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
1014957 AATATAATGT
*
1014967 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAAAATAATTAAATTGTAATTA
* *
1014994 AATTATTAAAAT-ATTGAATTTTAATTA
1 AATTA-TAAAATAATTAAATTGTAATTA
1015021 A
1 A
1015022 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.75
28 6 0.25
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
AATTATAAAATAATTAAATTGTAATTA
Found at i:1026234 original size:10 final size:11
Alignment explanation
Indices: 1026218--1026247 Score: 53
Period size: 10 Copynumber: 2.8 Consensus size: 11
1026208 CTTTCAATCC
1026218 TTTTAATTTTA
1 TTTTAATTTTA
1026229 -TTTAATTTTA
1 TTTTAATTTTA
1026239 TTTTAATTT
1 TTTTAATTT
1026248 GGGCCCTGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTAATTTTA
Found at i:1026499 original size:23 final size:24
Alignment explanation
Indices: 1026473--1026518 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1026463 TATTTTCTTT
1026473 ATATAATCTAT-TTATTA-TAAAAA
1 ATATAAT-TATATTATTACTAAAAA
*
1026496 ATATACTTATATTATTACTAAAA
1 ATATAATTATATTATTACTAAAA
1026519 TACCATTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 12 0.60
24 5 0.25
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATAATTATATTATTACTAAAAA
Found at i:1038321 original size:22 final size:22
Alignment explanation
Indices: 1038293--1038337 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1038283 CTCTAGTGTG
1038293 TTTAAATAGGCTTTAGAATGCC
1 TTTAAATAGGCTTTAGAATGCC
1038315 TTTAAATAGGCTTTAGAATGCC
1 TTTAAATAGGCTTTAGAATGCC
1038337 T
1 T
1038338 AAAAGCCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (22 bp):
TTTAAATAGGCTTTAGAATGCC
Found at i:1048260 original size:39 final size:40
Alignment explanation
Indices: 1048159--1048382 Score: 282
Period size: 40 Copynumber: 5.7 Consensus size: 40
1048149 TTGAATGATG
*
1048159 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
1048198 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
1048239 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1048278 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1048317 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
* *
1048356 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
1048383 AACGAGTAGC
Statistics
Matches: 167, Mismatches: 10, Indels: 14
0.87 0.05 0.07
Matches are distributed among these distances:
39 75 0.45
40 78 0.47
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:1048346 original size:79 final size:81
Alignment explanation
Indices: 1048159--1048382 Score: 291
Period size: 79 Copynumber: 2.8 Consensus size: 81
1048149 TTGAATGATG
* * *
1048159 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAATATCCGGGCTAAGACCCGAAGGCA
*
1048221 TTTGTGCGAGATACTAAT
64 TTTGTGCGAGATACTAAA
1048239 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGATACTAAT-TCCGGGCTAAG-CCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
*
1048301 TGTGCGAGTTACTAAA
66 TGTGCGAGATACTAAA
* * * * *
1048317 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
1048381 TG
66 TG
1048383 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
78 37 0.29
79 54 0.42
80 37 0.29
81 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAATATCCGGGCTAAGACCCGAAGGCATT
TGTGCGAGATACTAAA
Found at i:1048413 original size:79 final size:79
Alignment explanation
Indices: 1048159--1048415 Score: 231
Period size: 79 Copynumber: 3.3 Consensus size: 79
1048149 TTGAATGATG
* * * * *
1048159 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-AATATCCGGACTAAGATCCGAAGGCA
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGA-T-ACTAATA-CCGGGCTAAG-CCCGAAGGCA
** * *
1048221 TTTGTGCGAGATACTAAT
62 TTTGAACGAGTTACTAAA
* * *
1048239 TCCGGGCT-AAGCCCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTG
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
**
1048303 TGCGAGTTACTAAA
66 AACGAGTTACTAAA
* * *
1048317 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATT
*
1048381 TGAACGAG-TAGCTATA
64 TGAACGAGTTA-CTAAA
*
1048397 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAATCCCGAAGG
1048416 TACGTGATTT
Statistics
Matches: 151, Mismatches: 19, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
78 34 0.23
79 71 0.47
80 45 0.30
81 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTG
AACGAGTTACTAAA
Found at i:1056207 original size:79 final size:81
Alignment explanation
Indices: 1056071--1056255 Score: 229
Period size: 79 Copynumber: 2.3 Consensus size: 81
1056061 TTGAATGATG
*
1056071 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
1056135 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * **
1056150 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
1056212 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
* *
1056230 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
1056256 AACGAGTAGC
Statistics
Matches: 92, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.02
79 57 0.62
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:1056269 original size:40 final size:39
Alignment explanation
Indices: 1056072--1056274 Score: 191
Period size: 40 Copynumber: 5.1 Consensus size: 39
1056062 TGAATGATGT
* * *
1056072 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGT-ACTATAA
* *
1056112 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAG-TACTATA-A
1056152 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAG-TACTATAA
* *
1056190 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAATTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTACTATAA
* ** *
1056231 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTA-CTATAA
1056271 CCGG
1 CCGG
1056275 TTAAATTCCG
Statistics
Matches: 139, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
39 38 0.27
40 89 0.64
41 12 0.09
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTACTATAA
Found at i:1056277 original size:79 final size:79
Alignment explanation
Indices: 1056124--1056288 Score: 203
Period size: 79 Copynumber: 2.1 Consensus size: 79
1056114 GGACTAAGAT
* **
1056124 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
1056189 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
*
1056203 CCGAAGGCATTTGTGCGA-ATTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 CCGAAGGCATTTGTGCGAGA-TACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
* *
1056265 CTATATCC-GGTTAAATT
62 CTAAATCCGGGTTAAATC
1056282 CCGAAGG
1 CCGAAGG
1056289 TACGTGATTT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
78 3 0.04
79 47 0.63
80 25 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:1060753 original size:53 final size:53
Alignment explanation
Indices: 1060678--1060782 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
1060668 ATAAACTACG
* * * * * *
1060678 ATAAGGCAAAGATCCCATGTAAGACCATGCCAAGGCATGGTAATGGTGAGTTC
1 ATAAGGCAAAGATACCACGTAAGACCATACCAAGACATGGAAATGGTAAGTTC
* *
1060731 ATAAGGCAAGGATACCACGTAAGACCATATCAAGACATGGAAATGGTAAGTT
1 ATAAGGCAAAGATACCACGTAAGACCATACCAAGACATGGAAATGGTAAGTT
1060783 TACAAAGGAA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
53 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (53 bp):
ATAAGGCAAAGATACCACGTAAGACCATACCAAGACATGGAAATGGTAAGTTC
Found at i:1063718 original size:99 final size:92
Alignment explanation
Indices: 1063513--1063734 Score: 248
Period size: 99 Copynumber: 2.3 Consensus size: 92
1063503 TTATTAGAGC
* **
1063513 CAGTGTAAGACCTTGTCTGGGACAT-GCATCGGCCTCGTAAGGTAAGCTAGTATAAGACATGTCA
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTAAGCCAAGCTAGTATAAGACATGTCA
* ***
1063577 GGGACAGGCATCGGCTGTGAGATGTGT
66 GGGACAGGCATCGGCTGTGACAACAGT
* * * *
1063604 CAATGTAAGACCATGTCTGGGACATGGCATCGGCGTGGATAAGCCAGAGCTAGTGTAAGACCATG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCG-TAAGCCA-AGCTAGTATAAGA-CATG
* *
1063669 TCTGGGACATGGCGTCGGCCTCGATGACAACAGT
63 TCAGGGACA-GGCATCGG-CT-G-TGACAACAGT
*
1063703 CAGTGTAAGACCATGTCTCGGACATGGCATCG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCG
1063735 ACTTGAGACA
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
91 23 0.21
92 10 0.09
93 5 0.05
94 12 0.11
95 12 0.11
96 7 0.06
97 2 0.02
98 1 0.01
99 36 0.33
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (92 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGTAAGCCAAGCTAGTATAAGACATGTCA
GGGACAGGCATCGGCTGTGACAACAGT
Found at i:1063773 original size:47 final size:49
Alignment explanation
Indices: 1063508--1063780 Score: 185
Period size: 47 Copynumber: 5.7 Consensus size: 49
1063498 CCACATTATT
* * *
1063508 AGAGCCAGTGTAAGACCTTGTCTGGGACAT-GCATCGGCCTCG-T-A-A
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGACTCGATGACA
* * * *
1063553 GGTAAGCTAGTATAAGA-CATGTC-AGGGACA-GGCATCGG-CT-G-TGAGA
1 AG--AGCCAGTGTAAGACCATGTCTA-GGACATGGCATCGGACTCGATGACA
* * * * * * * *
1063599 TGTGTCAATGTAAGACCATGTCTGGGACATGGCATCGG-CGTGGATAAGCC
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGAC-TCGATGA-CA
* * * *
1063649 AGAGCTAGTGTAAGACCATGTCTGGGACATGGCGTCGGCCTCGATGACA
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGACTCGATGACA
* * * *
1063698 ACAGTCAGTGTAAGACCATGTCTCGGACATGGCATC-GACTTGA-GACA
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGACTCGATGACA
* *
1063745 TGAGCCAGTGTAAGACGATGTCTAGGACATGGCATC
1 AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATC
1063781 AGCATCATAG
Statistics
Matches: 178, Mismatches: 36, Indels: 26
0.74 0.15 0.11
Matches are distributed among these distances:
44 10 0.06
45 15 0.08
46 28 0.16
47 47 0.26
48 6 0.03
49 34 0.19
50 37 0.21
51 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.22
Consensus pattern (49 bp):
AGAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGACTCGATGACA
Found at i:1067872 original size:37 final size:37
Alignment explanation
Indices: 1067822--1067900 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
1067812 TTATTACGAA
* * *
1067822 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
1067859 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
1067896 GTCTT
1 GTCTT
1067901 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:1068097 original size:47 final size:47
Alignment explanation
Indices: 1068019--1068268 Score: 419
Period size: 47 Copynumber: 5.3 Consensus size: 47
1068009 CCCTTCGGGA
* * * * * *
1068019 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
1068066 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1068113 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1068160 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
1068207 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1068254 CTTATCACATATATA
1 CTTATCACATATATA
1068269 TACNAGACTC
Statistics
Matches: 192, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 192 1.00
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:1072153 original size:40 final size:40
Alignment explanation
Indices: 1072090--1072396 Score: 138
Period size: 40 Copynumber: 7.7 Consensus size: 40
1072080 CCAGCATGAT
*
1072090 TGCTCTTCGGGACCTAGCCCGGATATAACACCAGCACAAA
1 TGCTCTTCGGGACCTAGCACGGATATAACACCAGCACAAA
*** * * *
1072130 TGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACCTAGCACGGATATAACACCAGCACAAA
* * * * * * *
1072170 TGCTCTTCAGAACTTAGTC-TGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACCTAG-CACGGATATAACACCAGCACAAA
* * * * * * *
1072210 TGCTCTTCAGAACTTAGTC-TGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACCTAG-CACGGATATAACACCAGCACAAA
* * * * * * *
1072250 TGCTCTTCAGAACTTAGTC-TGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACCTAG-CACGGATATAACACCAGCACAAA
* * * * * * *
1072290 TGCTCTTCAGAACTTAGTC-TGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACCTAG-CACGGATATAACACCAGCACAAA
* * * * * * *
1072330 TGCTCTTCAGAACTTAGTC-TGGATATATCACTAGCACGAA
1 TGCTCTTCGGGACCTAG-CACGGATATAACACCAGCACAAA
* *
1072370 TGCTCTTCGGGACTTAGCCCGGATATA
1 TGCTCTTCGGGACCTAGCACGGATATA
1072397 TCACTCTCAA
Statistics
Matches: 250, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.00
40 248 0.99
41 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (40 bp):
TGCTCTTCGGGACCTAGCACGGATATAACACCAGCACAAA
Found at i:1072303 original size:120 final size:120
Alignment explanation
Indices: 1072110--1072401 Score: 476
Period size: 120 Copynumber: 2.4 Consensus size: 120
1072100 GACCTAGCCC
* * * * *** *
1072110 GGATATAACACCAGCACAAATGCTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATGCTC
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGCCCGGATATATCACTAGCACGAATGCTC
1072175 TTCAGAACTTAGTCTGGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
66 TTCAGAACTTAGTCTGGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
* *
1072230 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCTGGATATATCACTAGCACGAATGCTC
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGCCCGGATATATCACTAGCACGAATGCTC
1072295 TTCAGAACTTAGTCTGGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
66 TTCAGAACTTAGTCTGGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
* *
1072350 GGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGATATATCACT
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGCCCGGATATATCACT
1072402 CTCAATTCTC
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 158 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (120 bp):
GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGCCCGGATATATCACTAGCACGAATGCTC
TTCAGAACTTAGTCTGGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
Found at i:1072397 original size:40 final size:40
Alignment explanation
Indices: 1072150--1072401 Score: 468
Period size: 40 Copynumber: 6.3 Consensus size: 40
1072140 GGTTTAGCAC
1072150 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1072190 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1072230 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1072270 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1072310 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
* * * *
1072350 GGATATATCACTAGCACGAATGCTCTTCGGGACTTAGCCC
1 GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
1072390 GGATATATCACT
1 GGATATATCACT
1072402 CTCAATTCTC
Statistics
Matches: 208, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 208 1.00
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (40 bp):
GGATATATCACTAGCACGAATGCTCTTCAGAACTTAGTCT
Found at i:1077005 original size:50 final size:50
Alignment explanation
Indices: 1076944--1077047 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
1076934 TCCCTAGAGC
1076944 ATTCAGCCTTTGCAAACAGAATTAGTGCAAACCAGCCCCTAAATTTGGGT
1 ATTCAGCCTTTGCAAACAGAATTAGTGCAAACCAGCCCCTAAATTTGGGT
1076994 ATTCAGCCTTTGCAAACAGAATTAGTGCAAACCAGCCCCTAAATTTGGGT
1 ATTCAGCCTTTGCAAACAGAATTAGTGCAAACCAGCCCCTAAATTTGGGT
1077044 ATTC
1 ATTC
1077048 GAATACTTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (50 bp):
ATTCAGCCTTTGCAAACAGAATTAGTGCAAACCAGCCCCTAAATTTGGGT
Found at i:1085548 original size:30 final size:30
Alignment explanation
Indices: 1085514--1085574 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1085504 TCCTTAACTC
1085514 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
1085544 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
1085574 A
1 A
1085575 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:1093186 original size:27 final size:27
Alignment explanation
Indices: 1093131--1093191 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
1093121 ACGGAATAGA
* *
1093131 GTAAGTCCGCCAGGATAATAAACATGG
1 GTAAGTCCGCCAGGACAATAAACACGG
* * *
1093158 GTTAGTCCGCCAGGACAGTATACACGG
1 GTAAGTCCGCCAGGACAATAAACACGG
1093185 GTAAGTC
1 GTAAGTC
1093192 TGAAGGGATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.31, C:0.21, G:0.28, T:0.20
Consensus pattern (27 bp):
GTAAGTCCGCCAGGACAATAAACACGG
Found at i:1094892 original size:20 final size:20
Alignment explanation
Indices: 1094867--1094908 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1094857 GTCGTTCTAA
1094867 GCACCAGCAGCTCCTTTATT
1 GCACCAGCAGCTCCTTTATT
1094887 GCACCAGCAGCTCCTTTATT
1 GCACCAGCAGCTCCTTTATT
1094907 GC
1 GC
1094909 TGCTCTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.19, C:0.36, G:0.17, T:0.29
Consensus pattern (20 bp):
GCACCAGCAGCTCCTTTATT
Found at i:1106267 original size:16 final size:17
Alignment explanation
Indices: 1106241--1106276 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1106231 AAGTAGTCAA
1106241 TTGTGGTATGATAAATG
1 TTGTGGTATGATAAATG
*
1106258 TTGT-GTATGATAGATG
1 TTGTGGTATGATAAATG
1106274 TTG
1 TTG
1106277 ATATTGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.25, C:0.00, G:0.31, T:0.44
Consensus pattern (17 bp):
TTGTGGTATGATAAATG
Found at i:1109137 original size:45 final size:44
Alignment explanation
Indices: 1109051--1109214 Score: 199
Period size: 45 Copynumber: 3.7 Consensus size: 44
1109041 CCAGCATATT
* * *
1109051 GCCTGCTAGGCTCAAAGCCTG-ATA-TCATTTCACCGGCATTATA
1 GCCTGCTAGGCTCAAGGCCCGAATAGT-ATCTCACCGGCATTATA
1109094 GCCTGCTAGGCTCGAAGGCCCGAATAGTATCTCACCGGCATTATA
1 GCCTGCTAGGCTC-AAGGCCCGAATAGTATCTCACCGGCATTATA
* *
1109139 GCCTGCTAAGCTCAAGGGCCC-AATTAGTATCTCATCGGCATTATA
1 GCCTGCTAGGCTCAA-GGCCCGAA-TAGTATCTCACCGGCATTATA
* *
1109184 GCCTGCTAGCCTCAAAGGCCCGATTAGTATC
1 GCCTGCTAGGCTC-AAGGCCCGAATAGTATC
1109215 GTACGATATT
Statistics
Matches: 106, Mismatches: 8, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
43 13 0.12
44 10 0.09
45 79 0.75
46 4 0.04
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (44 bp):
GCCTGCTAGGCTCAAGGCCCGAATAGTATCTCACCGGCATTATA
Found at i:1113547 original size:50 final size:48
Alignment explanation
Indices: 1113420--1113553 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 48
1113410 TAGGGTATAA
* **
1113420 TGCCGATTCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTTAAG
1 TGCCGATTCCATGT-CCAAACATGGTCTTACACTAACTCTCACGTTAAG
**
1113469 T--CGATTCCATGTCCTAAACATGGTCTTACACTAACTCTCACGTATCTG
1 TGCCGATTCCATGTCC-AAACATGGTCTTACACTAACTCTCACGT-TAAG
* *
1113517 TGCCGATGCCATATCTCAAACATGGTCTTACACTAAC
1 TGCCGATTCCATGTC-CAAACATGGTCTTACACTAAC
1113554 ACATCATATA
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
46 2 0.03
47 36 0.49
48 3 0.04
49 1 0.01
50 30 0.41
51 1 0.01
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (48 bp):
TGCCGATTCCATGTCCAAACATGGTCTTACACTAACTCTCACGTTAAG
Found at i:1113604 original size:46 final size:46
Alignment explanation
Indices: 1113429--1113737 Score: 168
Period size: 46 Copynumber: 6.6 Consensus size: 46
1113419 ATGCCGATTC
* * * * *
1113429 CATGTCCCAGACATGGTCTTACACTGGCTCTCA-CGT-TAAGTCGATTC
1 CATGTCCCAAACAT-GTCTTACACTAGCTCTCATC-TATAGGCCGA-TG
* * *
1113476 CATGTCCTAAACATGGTCTTACACTAACTCTCA-CGTATCTGTGCCGATG
1 CATGTCCCAAACAT-GTCTTACACTAGCTCTCATC-TAT-AG-GCCGATG
* * * *
1113525 CCATATCTCAAACATGGTCTTACACTA--ACACATCATATA-GCCGATG
1 -CATGTCCCAAACAT-GTCTTACACTAGCTCTCATC-TATAGGCCGATG
* **
1113571 CATGTCCCAAACATGTCTTACACTGGCT-TACATCTCGAGGCCGATG
1 CATGTCCCAAACATGTCTTACACTAGCTCT-CATCTATAGGCCGATG
* * * * *
1113617 CATGTCCCAAAAATGTCTTACACTAGCTCTCGTCTCA-ATGTCAATG
1 CATGTCCCAAACATGTCTTACACTAGCTCTCATCT-ATAGGCCGATG
* * * * * *
1113663 CCATGTCCCAGATATGGTCTTATACTGGATCTCATAATATA-GCCGATG
1 -CATGTCCCAAACAT-GTCTTACACTAGCTCTCAT-CTATAGGCCGATG
* *
1113711 CATGTCCCAGACATGCCTTACACTAGC
1 CATGTCCCAAACATGTCTTACACTAGC
1113738 ACACAATTAT
Statistics
Matches: 204, Mismatches: 43, Indels: 31
0.73 0.15 0.11
Matches are distributed among these distances:
44 10 0.05
45 14 0.07
46 63 0.31
47 58 0.28
48 25 0.12
49 7 0.03
50 27 0.13
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (46 bp):
CATGTCCCAAACATGTCTTACACTAGCTCTCATCTATAGGCCGATG
Found at i:1120624 original size:83 final size:83
Alignment explanation
Indices: 1120507--1120752 Score: 474
Period size: 83 Copynumber: 3.0 Consensus size: 83
1120497 AAATAGATAG
**
1120507 TTAAGCTATTCTGATCTTAAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1 TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1120572 AAGCTTGTTTGATTTAGA
66 AAGCTTGTTTGATTTAGA
1120590 TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1 TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1120655 AAGCTTGTTTGATTTAGA
66 AAGCTTGTTTGATTTAGA
1120673 TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1 TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
1120738 AAGCTTGTTTGATTT
66 AAGCTTGTTTGATTT
1120753 CATTTTTCTT
Statistics
Matches: 161, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 161 1.00
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (83 bp):
TTAAGCTATTCTGATCTCGAAAATATAAAAATTACTAAAAACGAGGCAAGATTACTTACCCAATT
AAGCTTGTTTGATTTAGA
Found at i:1123322 original size:23 final size:23
Alignment explanation
Indices: 1123278--1123322 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1123268 TTATATTAAA
**
1123278 ATTAAAAATAAAATGTAAATATG
1 ATTAAAAATAAAAAATAAATATG
*
1123301 ATTAAAAATAAAAAATATATAT
1 ATTAAAAATAAAAAATAAATAT
1123323 TTAGTATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
ATTAAAAATAAAAAATAAATATG
Found at i:1126784 original size:27 final size:27
Alignment explanation
Indices: 1126754--1126931 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1126744 ATATTGAGTC
* * * *
1126754 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
1126781 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1126808 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
1126836 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
1126863 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
1126890 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1126917 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1126932 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:1126893 original size:82 final size:81
Alignment explanation
Indices: 1126775--1126930 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1126765 TGCTATATAA
* *
1126775 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
1126840 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
1126857 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
1126921 CACTTAGTGC
65 CACTTAGTGC
1126931 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:1139304 original size:14 final size:14
Alignment explanation
Indices: 1139285--1139315 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1139275 TGCTACCATT
1139285 TTACTATTATGTTG
1 TTACTATTATGTTG
*
1139299 TTACTATTTTGTTG
1 TTACTATTATGTTG
1139313 TTA
1 TTA
1139316 TTGTTTGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:1139380 original size:30 final size:30
Alignment explanation
Indices: 1139346--1139407 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
1139336 ACTTATTTTA
1139346 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
* *
1139376 TTGTTAATTTTTTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1139406 TT
1 TT
1139408 TCTTGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.24, C:0.03, G:0.13, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:1139512 original size:18 final size:18
Alignment explanation
Indices: 1139491--1139535 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1139481 GAAATATTTA
1139491 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTTTAGTAT
1139509 TTTTGATGTTTTTAGTAT
1 TTTTGATGTTTTTAGTAT
1139527 TTTTGATGT
1 TTTTGATGT
1139536 ATTATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.16, C:0.00, G:0.18, T:0.67
Consensus pattern (18 bp):
TTTTGATGTTTTTAGTAT
Found at i:1139969 original size:8 final size:8
Alignment explanation
Indices: 1139956--1139982 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1139946 AATGTTTTTA
1139956 TATGATTT
1 TATGATTT
1139964 TATGATTT
1 TATGATTT
1139972 TATGATTT
1 TATGATTT
1139980 TAT
1 TAT
1139983 TTACAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (8 bp):
TATGATTT
Found at i:1141934 original size:52 final size:52
Alignment explanation
Indices: 1141856--1141960 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 52
1141846 GAAAAGGAAA
* *
1141856 GGGCGCCCAGCTGGACGTGCTTTCCCTCAACATTCAAATGACTGTTGGCCAT
1 GGGCGCCAAGCTGGACGTGCTTTCCCTCAACATTCAAATGACCGTTGGCCAT
*
1141908 GGGCGCCAAGCTGGACGTGCTTTCCCTCAACGTTCAAATGACCGTTGGCCAT
1 GGGCGCCAAGCTGGACGTGCTTTCCCTCAACATTCAAATGACCGTTGGCCAT
1141960 G
1 G
1141961 CAACGATAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.24
Consensus pattern (52 bp):
GGGCGCCAAGCTGGACGTGCTTTCCCTCAACATTCAAATGACCGTTGGCCAT
Found at i:1150986 original size:16 final size:15
Alignment explanation
Indices: 1150960--1150998 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
1150950 CCAAATTCGA
*
1150960 TATTTTT-ATATTATT
1 TATTTTTAATA-TAAT
1150975 TATTTTTAATATAAT
1 TATTTTTAATATAAT
1150990 TATTTTTAA
1 TATTTTTAA
1150999 ATTTGTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.86
16 3 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTAATATAAT
Found at i:1159407 original size:29 final size:28
Alignment explanation
Indices: 1159336--1159409 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 28
1159326 TAAAAAGTTT
*
1159336 TGGGGAGTAAAAGTTTGAGGTAAAGTAAA
1 TGGGGAGT-AAATTTTGAGGTAAAGTAAA
1159365 TAGATGGGAG--AATTTTGAGGTAAAGTAAA
1 T-G--GGGAGTAAATTTTGAGGTAAAGTAAA
1159394 TGGGAGAGTAAATTTT
1 TGGG-GAGTAAATTTT
1159410 TGGTGGGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
26 2 0.05
27 3 0.08
28 1 0.03
29 26 0.68
30 1 0.03
32 5 0.13
ACGTcount: A:0.39, C:0.00, G:0.32, T:0.28
Consensus pattern (28 bp):
TGGGGAGTAAATTTTGAGGTAAAGTAAA
Found at i:1159514 original size:29 final size:29
Alignment explanation
Indices: 1159456--1159514 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
1159446 GATAGGAGGG
* * *
1159456 GAGTAAAAGTTTTGGGGGAAAGTGAGAAA
1 GAGTAAAAGTTTTGGGGAAAAATGAAAAA
1159485 GAGTAAAAGTTTTGAGGGAAAAAT-AAAAA
1 GAGTAAAAGTTTTG-GGGAAAAATGAAAAA
1159514 G
1 G
1159515 GTTTGAGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.20
Consensus pattern (29 bp):
GAGTAAAAGTTTTGGGGAAAAATGAAAAA
Found at i:1163872 original size:86 final size:86
Alignment explanation
Indices: 1163727--1163892 Score: 262
Period size: 86 Copynumber: 1.9 Consensus size: 86
1163717 ACAAAAAACG
*
1163727 TAAGGTTGTATATGGTATGTTACATTACTTTGATTGGCTCATTTGATTGGAATGTATTATCCAAC
1 TAAGGTTGTAGATGGTATGTTACATTACTTTGATTGGCTCATTTGATTGGAATGTATTATCCAAC
1163792 ACTACGTTTGGTTCGCTGACA
66 ACTACGTTTGGTTCGCTGACA
* * * * *
1163813 TAAGGTTGTCGATGGTATGTTACATTA-TCTTGTTTGGTTCATTTGGTTGGAATGTATTATCCAG
1 TAAGGTTGTAGATGGTATGTTACATTACT-TTGATTGGCTCATTTGATTGGAATGTATTATCCAA
1163877 CACTACGTTTGGTTCG
65 CACTACGTTTGGTTCG
1163893 TTGTAATAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
85 1 0.01
86 72 0.99
ACGTcount: A:0.22, C:0.13, G:0.23, T:0.42
Consensus pattern (86 bp):
TAAGGTTGTAGATGGTATGTTACATTACTTTGATTGGCTCATTTGATTGGAATGTATTATCCAAC
ACTACGTTTGGTTCGCTGACA
Found at i:1163913 original size:16 final size:16
Alignment explanation
Indices: 1163892--1163936 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
1163882 CGTTTGGTTC
* *
1163892 GTTGTAATAGAATTGA
1 GTTGTAATACAATAGA
1163908 GTTGTAATACAATAGA
1 GTTGTAATACAATAGA
*
1163924 GCTGTAAT-CAATA
1 GTTGTAATACAATA
1163937 ATTCAATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (16 bp):
GTTGTAATACAATAGA
Found at i:1164139 original size:37 final size:37
Alignment explanation
Indices: 1164097--1164167 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
1164087 TTGTTATTAA
*
1164097 ATTTTAATAGGATTATTATTAAAAATAATTTAATCAT
1 ATTTTAATAGAATTATTATTAAAAATAATTTAATCAT
* *
1164134 ATTTTAATATAATTATTATTAAATATAATTTAAT
1 ATTTTAATAGAATTATTATTAAAAATAATTTAAT
1164168 AAAAATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (37 bp):
ATTTTAATAGAATTATTATTAAAAATAATTTAATCAT
Found at i:1164155 original size:26 final size:25
Alignment explanation
Indices: 1164126--1164197 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 25
1164116 TAAAAATAAT
1164126 TTAATCATATTTTAATATAATTATTA
1 TTAAT-ATATTTTAATATAATTATTA
* *
1164152 TTAAATATAATTTAATA-AA--AATA
1 TT-AATATATTTTAATATAATTATTA
*
1164175 ATAATAT-TTTTAATATAATTATT
1 TTAATATATTTTAATATAATTATT
1164198 TTTATATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 4 0.11
24 2 0.05
25 2 0.05
26 12 0.32
27 3 0.08
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATATATTTTAATATAATTATTA
Found at i:1164192 original size:17 final size:17
Alignment explanation
Indices: 1164172--1164217 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
1164162 TTTAATAAAA
1164172 ATAATAATATTTTTAAT
1 ATAATAATATTTTTAAT
1164189 ATAAT--TATTTTT-AT
1 ATAATAATATTTTTAAT
1164203 ATTAA-AATATTTTTA
1 A-TAATAATATTTTTA
1164218 TTTTAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 7 0.28
17 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAATAATATTTTTAAT
Found at i:1164213 original size:16 final size:16
Alignment explanation
Indices: 1164177--1164256 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
1164167 TAAAAATAAT
1164177 AATATTTTTA-A-TATA
1 AATATTTTTATATTA-A
*
1164192 ATTATTTTTATATTAA
1 AATATTTTTATATTAA
*
1164208 AATATTTTTATTTTAA
1 AATATTTTTATATTAA
* *
1164224 ATTATATTTTGACATT-A
1 A--ATATTTTTATATTAA
1164241 AATA-TTTTATATTAA
1 AATATTTTTATATTAA
1164256 A
1 A
1164257 TTATATTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
14 7 0.13
15 14 0.27
16 17 0.33
17 4 0.08
18 10 0.19
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
AATATTTTTATATTAA
Found at i:1164249 original size:32 final size:33
Alignment explanation
Indices: 1164177--1164263 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 33
1164167 TAAAAATAAT
*
1164177 AATATTTTTA-A-TATAATTAT-TTTTATATTAA
1 AATATTTTTATATTA-AATTATATTTTACATTAA
*
1164208 AATATTTTTATTTTAAATTATATTTTGACATT-A
1 AATATTTTTATATTAAATTATATTTT-ACATTAA
1164241 AATA-TTTTATATTAAATTATATT
1 AATATTTTTATATTAAATTATATT
1164264 AAATTATTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 10 0.20
32 24 0.49
33 11 0.22
34 4 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (33 bp):
AATATTTTTATATTAAATTATATTTTACATTAA
Found at i:1166733 original size:15 final size:15
Alignment explanation
Indices: 1166713--1166745 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1166703 AAGTAAAGTG
1166713 ATTTTGGATATACGA
1 ATTTTGGATATACGA
*
1166728 ATTTTGGATATATGA
1 ATTTTGGATATACGA
1166743 ATT
1 ATT
1166746 AATGAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.18, T:0.45
Consensus pattern (15 bp):
ATTTTGGATATACGA
Found at i:1166817 original size:26 final size:26
Alignment explanation
Indices: 1166788--1166837 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
1166778 GAAAGGACCA
1166788 AATCACAAATTTCGAGAAGTTTAACT
1 AATCACAAATTTCGAGAAGTTTAACT
* *
1166814 AATCCCAAATTTTGAGAAGTTTAA
1 AATCACAAATTTCGAGAAGTTTAA
1166838 GGACTAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (26 bp):
AATCACAAATTTCGAGAAGTTTAACT
Found at i:1173602 original size:22 final size:21
Alignment explanation
Indices: 1173577--1173617 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1173567 TCCACAAGAA
1173577 TAATATAAAATCAAAGAAATAT
1 TAATATAAAAT-AAAGAAATAT
* *
1173599 TAATTTAAAATAAATAAAT
1 TAATATAAAATAAAGAAAT
1173618 TCAAATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.32
Consensus pattern (21 bp):
TAATATAAAATAAAGAAATAT
Found at i:1182916 original size:113 final size:113
Alignment explanation
Indices: 1182718--1182946 Score: 404
Period size: 113 Copynumber: 2.0 Consensus size: 113
1182708 AAGTGCAGGG
* *
1182718 TTGGATGGGGTTATCGTGCATTAATCATATGAGATTGTTTTGTTATGGGCCCAACTGTGTTAATA
1 TTGGATGGGGTTATCATGCATTAATCATATGAGATTCTTTTGTTATGGGCCCAACTGTGTTAATA
* *
1182783 TGGGCAAGGCCCAATATATCTCTACTTGTAATAGGGCAACGACCCTGA
66 TGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCAACGACCCAGA
1182831 TTGGATGGGGTTATCATGCATTAATCATATGAGATTCTTTTGTTATGGGCCCAACTGTGTTAATA
1 TTGGATGGGGTTATCATGCATTAATCATATGAGATTCTTTTGTTATGGGCCCAACTGTGTTAATA
* *
1182896 TGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGA
66 TGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCAACGACCCAGA
1182944 TTG
1 TTG
1182947 ATATTGATAT
Statistics
Matches: 110, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
113 110 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (113 bp):
TTGGATGGGGTTATCATGCATTAATCATATGAGATTCTTTTGTTATGGGCCCAACTGTGTTAATA
TGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCAACGACCCAGA
Found at i:1183000 original size:60 final size:60
Alignment explanation
Indices: 1182893--1183031 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 60
1182883 AACTGTGTTA
* * * * * *
1182893 ATATGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGGCCCAGATTGATATTG
1 ATATGGGCTAGGCCCAGTATATCTCGAATTGTAATAGGGCAACGGCCCAGATTAATATGG
* * *
1182953 ATATGGGCTAGGCCCAGTATA-CTCCGATATTGTAA-GGGGCAATGGCCCATATTAATATGG
1 ATATGGGCTAGGCCCAGTATATCT-CGA-ATTGTAATAGGGCAACGGCCCAGATTAATATGG
1183013 ATATGGGCTAAGGCCCAGT
1 ATATGGGCT-AGGCCCAGT
1183032 TAACTCTAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
59 2 0.03
60 50 0.75
61 15 0.22
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.26
Consensus pattern (60 bp):
ATATGGGCTAGGCCCAGTATATCTCGAATTGTAATAGGGCAACGGCCCAGATTAATATGG
Found at i:1184171 original size:26 final size:28
Alignment explanation
Indices: 1184141--1184195 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
1184131 AAACTCTTCT
1184141 AAAAGAAAACTC-AAGAGAA-ATTATTA
1 AAAAGAAAACTCAAAGAGAATATTATTA
*
1184167 AAAAGAAAACTCAAAGAGAATTTTATTA
1 AAAAGAAAACTCAAAGAGAATATTATTA
1184195 A
1 A
1184196 CTCAAAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 12 0.46
27 7 0.27
28 7 0.27
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.22
Consensus pattern (28 bp):
AAAAGAAAACTCAAAGAGAATATTATTA
Found at i:1194241 original size:31 final size:30
Alignment explanation
Indices: 1194203--1194319 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 30
1194193 TTAATCACAT
*
1194203 TAATATTAAATTAATAAAACATTATCTAAA
1 TAATATTAAATTAATAAAATATTATCTAAA
** * *
1194233 TAAGTATTAAATTAAATTTAATATCA-C-ATAT
1 TAA-TATTAAATT-AATAAAATATTATCTA-AA
* *
1194264 TAATATTAAATTAATAAAATACTATCTAGA
1 TAATATTAAATTAATAAAATATTATCTAAA
*
1194294 TAAATATTAAATTAAATTAAATATTA
1 T-AATATTAAATT-AATAAAATATTA
1194320 AATTTATTAA
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
29 8 0.12
30 15 0.22
31 26 0.39
32 18 0.27
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (30 bp):
TAATATTAAATTAATAAAATATTATCTAAA
Found at i:1194290 original size:61 final size:61
Alignment explanation
Indices: 1194201--1194317 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
1194191 AATTAATCAC
* * *
1194201 ATTAATATTAAATTAATAAAACATTATCTAAATAAGTATTAAATTAAATTTAATATCACAT
1 ATTAATATTAAATTAATAAAACACTATCTAAATAAATATTAAATTAAATTAAATATCACAT
* *
1194262 ATTAATATTAAATTAATAAAATACTATCTAGATAAATATTAAATTAAATTAAATAT
1 ATTAATATTAAATTAATAAAACACTATCTAAATAAATATTAAATTAAATTAAATAT
1194318 TAAATTTATT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (61 bp):
ATTAATATTAAATTAATAAAACACTATCTAAATAAATATTAAATTAAATTAAATATCACAT
Found at i:1197457 original size:17 final size:17
Alignment explanation
Indices: 1197411--1197457 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1197401 TCGTTAAAGG
*
1197411 CCGATAAATGA-AATGC
1 CCGACAAATGATAATGC
*
1197427 CCGATC-AATTATAATGC
1 CCGA-CAAATGATAATGC
1197444 CCGACAAATGATAA
1 CCGACAAATGATAA
1197458 ATGATAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 9 0.36
17 16 0.64
ACGTcount: A:0.43, C:0.21, G:0.15, T:0.21
Consensus pattern (17 bp):
CCGACAAATGATAATGC
Found at i:1204774 original size:312 final size:312
Alignment explanation
Indices: 1204176--1204817 Score: 1070
Period size: 312 Copynumber: 2.1 Consensus size: 312
1204166 ATTTTAACTA
*
1204176 ATTAAATAAATCTCAAATGCACGATTTCAAAATATGAGTTTAATCAAGATGACATAATTGTGTTA
1 ATTAATTAAATCT--AATGCACGATTTCAAAATATGAGTTTAATCAAGATGACATAATTGTGTTA
*
1204241 GATCAATTACATTTCTTAACTTAGAATTATCAAACTCATGTTTATATTGTTACGAACAAATTTAC
64 GATCAATTACATTTCTTAACTTAGAATTATCAAACTCATGTTTATATTGTTACGAACAAATTCAC
* *
1204306 GGCAACTCGGTAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACT
129 GACAACTCGGAAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACT
*
1204371 AGATCCCTATGTCAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGTACATAC
194 AGATCCCTATGTCAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATAC
* * *
1204436 AAATTTATTATATCGAAATGATCTCTTGTACATATCCCTATGTCAATTCAAACG
259 AAACTTATTAGATCGAAATAATCTCTTGTACATATCCCTATGTCAATTCAAACG
*
1204490 ATTAATTAAATCTAATGCATGATTTCAAAATATGA-TTTAAATCAAGATGACATAATTGTGTTAG
1 ATTAATTAAATCTAATGCACGATTTCAAAATATGAGTTT-AATCAAGATGACATAATTGTGTTAG
* * *
1204554 ATTAATTACATTTCTTAACTTAGAATTATTAAACTCATGTTTATATTGTTACGAATAAATTCACG
65 ATCAATTACATTTCTTAACTTAGAATTATCAAACTCATGTTTATATTGTTACGAACAAATTCACG
*
1204619 ACAACTCGGAAATTTGCTAACTTATGAACATACTTACCTACCAAAATCCATTCATCTCTTGACTA
130 ACAACTCGGAAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACTA
* * *
1204684 TATCCCTATGTCAATTCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATTCA
195 GATCCCTATGTCAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATACA
* * * *
1204749 TACTTATTAGATTGAAATAATCTCTTGTACATATCCCTATGTCAATTCCAATG
260 AACTTATTAGATCGAAATAATCTCTTGTACATATCCCTATGTCAATTCAAACG
1204802 ATTAATTAAATCTAAT
1 ATTAATTAAATCTAAT
1204818 AAGCACATAA
Statistics
Matches: 307, Mismatches: 20, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
311 3 0.01
312 292 0.95
314 12 0.04
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.36
Consensus pattern (312 bp):
ATTAATTAAATCTAATGCACGATTTCAAAATATGAGTTTAATCAAGATGACATAATTGTGTTAGA
TCAATTACATTTCTTAACTTAGAATTATCAAACTCATGTTTATATTGTTACGAACAAATTCACGA
CAACTCGGAAATTTGCTAACTTATGAACATACTCACCTACCAAAATCCATTCATCTCTTGACTAG
ATCCCTATGTCAATCCAACCGATTAAACAAATCTTTAATAGGAAAATATGTTATTGCACATACAA
ACTTATTAGATCGAAATAATCTCTTGTACATATCCCTATGTCAATTCAAACG
Found at i:1206050 original size:12 final size:12
Alignment explanation
Indices: 1206033--1206058 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1206023 AAAATTCATC
1206033 AAAATTAATTAA
1 AAAATTAATTAA
1206045 AAAATTAATTAA
1 AAAATTAATTAA
1206057 AA
1 AA
1206059 TTCAACATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAATTAA
Found at i:1218120 original size:21 final size:22
Alignment explanation
Indices: 1218096--1218136 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
1218086 AATCTGTAGA
1218096 ATGTGAAATGGAT-ATATATTT
1 ATGTGAAATGGATGATATATTT
**
1218117 ATGTGTGATGGATGATATAT
1 ATGTGAAATGGATGATATAT
1218137 AAAACCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.34, C:0.00, G:0.24, T:0.41
Consensus pattern (22 bp):
ATGTGAAATGGATGATATATTT
Found at i:1218254 original size:14 final size:14
Alignment explanation
Indices: 1218235--1218262 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1218225 AATGAAAGTA
1218235 CATAGTATATGATG
1 CATAGTATATGATG
1218249 CATAGTATATGATG
1 CATAGTATATGATG
1218263 AAAGTGATAG
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:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
CATAGTATATGATG
Found at i:1220780 original size:49 final size:49
Alignment explanation
Indices: 1220703--1220799 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
1220693 GTCAAAAGCT
* *
1220703 TTAGTTTCATGAGTAAATTACATTTAAATTGTGGTGTGATGTAATACCC
1 TTAGCTTCATGAGTAAATTACATTTAAATTGTGGCGTGATGTAATACCC
*
1220752 TTAGCTTCATGAGTGAATTACATTTAAATTGTGGCGTGATGTAATACC
1 TTAGCTTCATGAGTAAATTACATTTAAATTGTGGCGTGATGTAATACC
1220800 TGACAATCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (49 bp):
TTAGCTTCATGAGTAAATTACATTTAAATTGTGGCGTGATGTAATACCC
Found at i:1223060 original size:24 final size:24
Alignment explanation
Indices: 1223025--1223075 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1223015 ATGAATCGGT
* *
1223025 AAAAGCCGAAATGCCGAAATGCCG
1 AAAAGCCAAAATGCCGAAAGGCCG
1223049 AAAAGCCAAAATGCCGAAAGGCCG
1 AAAAGCCAAAATGCCGAAAGGCCG
1223073 AAA
1 AAA
1223076 GTTTGGCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.24, G:0.24, T:0.06
Consensus pattern (24 bp):
AAAAGCCAAAATGCCGAAAGGCCG
Found at i:1223076 original size:8 final size:8
Alignment explanation
Indices: 1223029--1223075 Score: 67
Period size: 8 Copynumber: 5.9 Consensus size: 8
1223019 ATCGGTAAAA
1223029 GCCGAAAT
1 GCCGAAAT
1223037 GCCGAAAT
1 GCCGAAAT
*
1223045 GCCGAAAA
1 GCCGAAAT
*
1223053 GCCAAAAT
1 GCCGAAAT
*
1223061 GCCGAAAG
1 GCCGAAAT
1223069 GCCGAAA
1 GCCGAAA
1223076 GTTTGGCTAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 34 1.00
ACGTcount: A:0.43, C:0.26, G:0.26, T:0.06
Consensus pattern (8 bp):
GCCGAAAT
Found at i:1223255 original size:29 final size:29
Alignment explanation
Indices: 1223220--1223283 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
1223210 GCCTAACGGG
* *
1223220 CCATATAAATGTGATTTGGTCCCAATGGA
1 CCATATAAAGGTGATTTGGGCCCAATGGA
* * *
1223249 CCATATACAGGTGATTTGGGCCTAATGGG
1 CCATATAAAGGTGATTTGGGCCCAATGGA
1223278 CCATAT
1 CCATAT
1223284 GAATATTATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (29 bp):
CCATATAAAGGTGATTTGGGCCCAATGGA
Found at i:1227629 original size:16 final size:16
Alignment explanation
Indices: 1227608--1227650 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
1227598 AACATTATTT
*
1227608 AGGCTCTGTGTCTAGC
1 AGGCTCTGTGCCTAGC
1227624 AGGCTCTGTGCCTAGC
1 AGGCTCTGTGCCTAGC
*
1227640 AGGCTTTGTGC
1 AGGCTCTGTGC
1227651 TGGTGATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.12, C:0.26, G:0.33, T:0.30
Consensus pattern (16 bp):
AGGCTCTGTGCCTAGC
Found at i:1227684 original size:38 final size:39
Alignment explanation
Indices: 1227623--1227723 Score: 141
Period size: 38 Copynumber: 2.6 Consensus size: 39
1227613 CTGTGTCTAG
* * *
1227623 CAGGCTCTGTGCCTAGCAGGCTTTGTGCTGGTGATAT-T
1 CAGGCTTTGTGCCTAGCAGGCTTTGTGCCGATGATATAT
* *
1227661 CGGGCTTTGTGCCTAGCAAGCTTTGTGCCGATGATATAT
1 CAGGCTTTGTGCCTAGCAGGCTTTGTGCCGATGATATAT
*
1227700 CAGGCTTAGTGCCTAGCAGGCTTT
1 CAGGCTTTGTGCCTAGCAGGCTTT
1227724 ATGTCGGTGT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
38 32 0.59
39 22 0.41
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.33
Consensus pattern (39 bp):
CAGGCTTTGTGCCTAGCAGGCTTTGTGCCGATGATATAT
Found at i:1228778 original size:18 final size:18
Alignment explanation
Indices: 1228755--1228792 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1228745 ATGAAAGGTG
*
1228755 TTAAGTACATGTA-TATGT
1 TTAAGTAAAT-TAGTATGT
1228773 TTAAGTAAATTAGTATGT
1 TTAAGTAAATTAGTATGT
1228791 TT
1 TT
1228793 GCTTTTGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.47
Consensus pattern (18 bp):
TTAAGTAAATTAGTATGT
Found at i:1235593 original size:25 final size:25
Alignment explanation
Indices: 1235551--1235599 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1235541 CTTTATTATT
* *
1235551 ATCATTATGAAGAATTATGTGATTA
1 ATCATTATCAAGAATTATATGATTA
* *
1235576 ATCATTATCATGAGTTATATGATT
1 ATCATTATCAAGAATTATATGATT
1235600 GGTCCTCTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.37, C:0.06, G:0.14, T:0.43
Consensus pattern (25 bp):
ATCATTATCAAGAATTATATGATTA
Found at i:1235726 original size:20 final size:20
Alignment explanation
Indices: 1235698--1235735 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1235688 CTAGGAACTA
1235698 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
1235718 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
1235736 TATATGTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:1241340 original size:46 final size:46
Alignment explanation
Indices: 1241243--1241377 Score: 152
Period size: 46 Copynumber: 2.9 Consensus size: 46
1241233 GGTGGTATGT
**
1241243 GAGCCAGTGTAAGACATGTCTGGGACATGCATCAACCACATT-ATG--AA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCAT---CGGCATTGA-GACAA
* *
1241290 -AGCCAGTGTACGACATGTCTGGGACATTCATCGGCATTGAGACAA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACAA
* *
1241335 GAGCCAGTGTAAGACATGTCTTGGACATGCATCGGCGTTGAGA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGA
1241378 TATGCAAGCT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
43 6 0.08
44 1 0.01
45 2 0.03
46 67 0.88
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACAA
Found at i:1242515 original size:43 final size:44
Alignment explanation
Indices: 1242423--1242516 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 44
1242413 ATATGCCTCC
* *
1242423 TCTGGCCATGGGCGTGTGCCTCAGCCGTGTGGAGGACACGGCCT
1 TCTGGCCATGGGCGTGTGCCTCAGCCGTATGGAGGACACGGACT
* * *
1242467 T-TGGCCATGGGTGTGTGCCTCCA-CCGTATGGAGGATAC-GATT
1 TCTGGCCATGGGCGTGTGCCT-CAGCCGTATGGAGGACACGGACT
1242509 TCTGGCCA
1 TCTGGCCA
1242517 CGAGCATATG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
42 3 0.07
43 37 0.86
44 3 0.07
ACGTcount: A:0.14, C:0.27, G:0.35, T:0.24
Consensus pattern (44 bp):
TCTGGCCATGGGCGTGTGCCTCAGCCGTATGGAGGACACGGACT
Found at i:1242515 original size:109 final size:109
Alignment explanation
Indices: 1242320--1242530 Score: 325
Period size: 109 Copynumber: 1.9 Consensus size: 109
1242310 CGGGCAGAGA
*
1242320 CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTGGCCATGGGCGTGTGCCTCGACCGT
1 CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTGGCCATGGGCGTGTGCCTCCACCGT
* *
1242385 GTGGAGGACATGACTTTTGGCCACGAGCATATGCCTCCTCTGGC
66 ATGGAGGACACGACTTTTGGCCACGAGCATATGCCTCCTCTGGC
* * * * *
1242429 CATGGGCGTGTGCCTCAGCCGTGTGGAGGACACGGCCTTTGGCCATGGGTGTGTGCCTCCACCGT
1 CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTGGCCATGGGCGTGTGCCTCCACCGT
*
1242494 ATGGAGGATACGA-TTTCTGGCCACGAGCATATGCCTC
66 ATGGAGGACACGACTTT-TGGCCACGAGCATATGCCTC
1242531 GACCATGTAC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
108 3 0.03
109 89 0.97
ACGTcount: A:0.16, C:0.29, G:0.33, T:0.23
Consensus pattern (109 bp):
CATGGCCGTGTGCCTCAGCCGTGTAGAGGACACAGCCTCTGGCCATGGGCGTGTGCCTCCACCGT
ATGGAGGACACGACTTTTGGCCACGAGCATATGCCTCCTCTGGC
Found at i:1255145 original size:27 final size:27
Alignment explanation
Indices: 1255111--1255180 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
1255101 CTTCATTCAT
* *
1255111 GAAATAATTACATGAATTGGTTATATG
1 GAAATAATTATATGAATTGGTTAAATG
*
1255138 GATATAATTATATGAATTGGTTAAATG
1 GAAATAATTATATGAATTGGTTAAATG
1255165 GAAATAATTATATGAA
1 GAAATAATTATATGAA
1255181 ATGGAACATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.44, C:0.01, G:0.17, T:0.37
Consensus pattern (27 bp):
GAAATAATTATATGAATTGGTTAAATG
Found at i:1263773 original size:21 final size:22
Alignment explanation
Indices: 1263736--1263776 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1263726 TTATTTGATA
*
1263736 TTTAAATTTATTTTTGAATTGT
1 TTTAAATTTATTATTGAATTGT
1263758 TTTAAA-TTATTATTGAATT
1 TTTAAATTTATTATTGAATT
1263777 CGTTAACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
TTTAAATTTATTATTGAATTGT
Found at i:1270872 original size:13 final size:13
Alignment explanation
Indices: 1270839--1270876 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
1270829 ACTATGATTA
1270839 AATTTTAATATTT
1 AATTTTAATATTT
1270852 AATCTTT-ATATTTT
1 AAT-TTTAATA-TTT
1270866 AATTTTAATAT
1 AATTTTAATAT
1270877 AATTTGGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (13 bp):
AATTTTAATATTT
Found at i:1270875 original size:27 final size:27
Alignment explanation
Indices: 1270778--1270876 Score: 90
Period size: 27 Copynumber: 3.5 Consensus size: 27
1270768 CATTTCAGTC
* * * *
1270778 TTAAATTTGATATTTAATCATTATACT
1 TTAATTTTAATATTTAATCTTTATATT
* *
1270805 TTAATTTTAATTTTTAGACTCTCTACTATGAT
1 TTAATTTTAATATTTA-A-TCTTTA-TAT--T
*
1270837 TAAATTTTAATATTTAATCTTTATATT
1 TTAATTTTAATATTTAATCTTTATATT
1270864 TTAATTTTAATAT
1 TTAATTTTAATAT
1270877 AATTTGGTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
27 26 0.46
28 1 0.02
29 7 0.12
30 7 0.12
31 1 0.02
32 15 0.26
ACGTcount: A:0.34, C:0.07, G:0.03, T:0.56
Consensus pattern (27 bp):
TTAATTTTAATATTTAATCTTTATATT
Found at i:1271601 original size:23 final size:23
Alignment explanation
Indices: 1271531--1271602 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
1271521 TACCTCGTTA
*
1271531 ACAAATTTATTCATTTTTTATAC
1 ACAAATTTATTCATTTTTTATAT
* *
1271554 ACAAATTTATTCGGTTTTTTTTAT
1 ACAAATTTATTC-ATTTTTTATAT
*
1271578 A-AAATTTATTCATTCTTTTGTAT
1 ACAAATTTATTCATT-TTTTATAT
1271601 AC
1 AC
1271603 CTCACAGTCA
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
22 2 0.05
23 30 0.73
24 9 0.22
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.54
Consensus pattern (23 bp):
ACAAATTTATTCATTTTTTATAT
Found at i:1278712 original size:18 final size:18
Alignment explanation
Indices: 1278670--1278714 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
1278660 GAAAAATGAG
1278670 AATTTTT-AAAACACGAA
1 AATTTTTGAAAACACGAA
*
1278687 AA-TTTTGAAAATACGAA
1 AATTTTTGAAAACACGAA
1278704 AATTTTTGAAA
1 AATTTTTGAAA
1278715 CCTGAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 8 0.32
ACGTcount: A:0.51, C:0.07, G:0.09, T:0.33
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:1279005 original size:98 final size:100
Alignment explanation
Indices: 1278884--1279077 Score: 356
Period size: 98 Copynumber: 2.0 Consensus size: 100
1278874 AGAATTTTTT
1278884 AAATTTTCGATTTTTTTTAAAAGGACGTCCCATTTTTAACACGAGCCAATGATATTCACCCAACA
1 AAATTTTCGATTTTTTTTAAAAGGACGTCCCATTTTTAACACGAGCCAATGATATTCACCCAACA
*
1278949 TAGCGATGAAATCAATGACCTTATGTTAAATTGAA
66 TAGCGATGAAATCAACGACCTTATGTTAAATTGAA
1278984 AAATTTT-GA-TTTTTTTAAAAGGACGTCCCATTTTTAACACGAGCCAATGATATTCACCCAACA
1 AAATTTTCGATTTTTTTTAAAAGGACGTCCCATTTTTAACACGAGCCAATGATATTCACCCAACA
*
1279047 TAGCGATGAAATCCACGACCTTATGTTAAAT
66 TAGCGATGAAATCAACGACCTTATGTTAAAT
1279078 CGATACGTTG
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
98 83 0.90
99 2 0.02
100 7 0.08
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (100 bp):
AAATTTTCGATTTTTTTTAAAAGGACGTCCCATTTTTAACACGAGCCAATGATATTCACCCAACA
TAGCGATGAAATCAACGACCTTATGTTAAATTGAA
Found at i:1279435 original size:15 final size:17
Alignment explanation
Indices: 1279415--1279446 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1279405 TTAGGAAACG
1279415 TACATAA-A-AAATATA
1 TACATAATATAAATATA
1279430 TACATAATATAAATATA
1 TACATAATATAAATATA
1279447 ATATATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TACATAATATAAATATA
Found at i:1279988 original size:11 final size:11
Alignment explanation
Indices: 1279954--1279995 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1279944 AAATCATTTT
1279954 GAAGAGAGAAA
1 GAAGAGAGAAA
* *
1279965 GAA-AAAAAAA
1 GAAGAGAGAAA
*
1279975 GAAGGGAGAAA
1 GAAGAGAGAAA
1279986 GAAGAGAGAA
1 GAAGAGAGAA
1279996 GGGAGAGGGG
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (11 bp):
GAAGAGAGAAA
Found at i:1280484 original size:20 final size:19
Alignment explanation
Indices: 1280457--1280511 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 19
1280447 AGGGTTTCTT
1280457 GGTTTTTTTGGGGGGGTTA
1 GGTTTTTTTGGGGGGGTTA
1280476 GGTTTTTTTTGGGGGGGTTA
1 GG-TTTTTTTGGGGGGGTTA
1280496 GGTTTTTTTGGGGGGG
1 GGTTTTTTTGGGGGGG
1280512 CTTAATGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.46
20 19 0.54
ACGTcount: A:0.04, C:0.00, G:0.49, T:0.47
Consensus pattern (19 bp):
GGTTTTTTTGGGGGGGTTA
Found at i:1281560 original size:72 final size:72
Alignment explanation
Indices: 1281343--1282241 Score: 1367
Period size: 72 Copynumber: 12.4 Consensus size: 72
1281333 GTGATCTGAA
* *
1281343 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAGAAATTGAAACTACCTCAGC
**
1281408 ATGTGAACCGAG
63 --GTGTCCCGAG
* * * *
1281420 GCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAAAATACCTCAACG
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAAACAGAAATTGAAACTACCTCAGCG
**
1281485 TGTCTTGAG
64 TGTCCCGAG
** * * *
1281494 GCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGCAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAGCGTG
1281559 TCCCGAG
66 TCCCGAG
*
1281566 GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAGAAATTGAAACTACCTCAGCGT
1281630 GTCCCGAG
65 GTCCCGAG
*
1281638 GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAGAAATTGAAACTACCTCAGCGT
1281702 GTCCCGAG
65 GTCCCGAG
*
1281710 GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAGAAATTGAAACTACCTCAGCGT
1281774 GTCCCGAG
65 GTCCCGAG
*
1281782 GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAGAAATTGAAACTACCTCAGCGT
1281846 GTCCCGAG
65 GTCCCGAG
*
1281854 GCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGT
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAGAAATTGAAACTACCTCAGCGT
1281918 GTCCCGAG
65 GTCCCGAG
* *
1281926 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAGCGTG
1281991 TCCCGAG
66 TCCCGAG
* * *
1281998 GCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAGCGTG
1282063 TCCCGAG
66 TCCCGAG
* * *
1282070 GCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAGCGTG
1282135 TCCCGAG
66 TCCCGAG
* * *
1282142 GCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAGCGTG
1282207 TCCCGAG
66 TCCCGAG
*
1282214 GCTCAACTCACCTCCCGCAATATGAGTT
1 GCTCAACTCACCTCTCGCAATATGAGTT
1282242 TGAAATTACC
Statistics
Matches: 794, Mismatches: 26, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
71 5 0.01
72 689 0.87
73 5 0.01
74 33 0.04
76 22 0.03
77 40 0.05
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (72 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAAACTACCTCAGCGTG
TCCCGAG
Found at i:1281643 original size:144 final size:144
Alignment explanation
Indices: 1281338--1283675 Score: 2105
Period size: 144 Copynumber: 15.9 Consensus size: 144
1281328 AGTGTGTGAT
* * * *
1281338 CTGAAGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--ATTTTGAAA-ACAAAAATTGAAATTACC
** *
1281403 TCAGCATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAA
63 TCAGC--GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAA
* *
1281468 TTGAAAATACCTCAACGTGTC
124 TTGAAATTACCTCAGCGTGTC
* ** *
1281489 TTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGCAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
* * *
1281554 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAAC
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
1281619 TACCTCAGCGTGTC
131 TACCTCAGCGTGTC
* * * *
1281633 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAAAAATTGAAATTACCTC
* *
1281697 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAA
65 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAA
*
1281762 CTACCTCAGCGTGTC
130 TTACCTCAGCGTGTC
* * * *
1281777 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGAAACTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAAAAATTGAAATTACCTC
* *
1281841 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAA
65 AGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAA
*
1281906 CTACCTCAGCGTGTC
130 TTACCTCAGCGTGTC
*
1281921 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
* * *
1281986 GCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAAT
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
1282051 TACCTCAGCGTGTC
131 TACCTCAGCGTGTC
* *
1282065 CCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
* * *
1282130 GCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAAT
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
1282195 TACCTCAGCGTGTC
131 TACCTCAGCGTGTC
* * * * ** ***
1282209 CCGAGGCTCAACTCACCTCCCGCAATATGAGTTTGAA-ATT---ACCTCAGCGTG----T-CCT-
1 CTGAGGCTCAACTCACCTCTCGCAATATGAG-TTGAATTTTGAAAACAAAAATTGAAATTACCTC
* * * * * * * ** *** *
1282264 -GAG-G-CTC-A-ACTCATTTCTCACAATAT-G-AGT-TGA-TTTTTTTAACAACAGAAATTGAA
65 AGCGTGTCCCGAGGCTCA--ACTCAC-CTCTCGCAATATGAGTTGATTTTTGAA-A-ACA--G-A
** * * * **
1282320 AATT-ACCTCAGCGT--GTCCTGAGG
122 AATTGAAATTA-CCTCAG-CGTG-TC
* * * * * * * ** * *
1282343 CTCA-ACTCACCTCTCGCAATAT-G-AGT-TGA----ATTTTGAAA-ACAGAATTTGAAATTACC
1 CTGAGGCTCAACTCAC-C--TCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACC
* * *
1282399 TCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTTGA
63 TCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGA
1282464 AATTACCTCAGCGTGTC
128 AATTACCTCAGCGTGTC
* *
1282481 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTTGAAATTACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
* * *
1282546 GCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTTGAAAT
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
1282611 TACCTCAGCGTGTC
131 TACCTCAGCGTGTC
1282625 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGA---G-------TTG---AAT-T---TTGAAAA-CA
* * * **
1282690 GAAATTGAAATTACCTCAACCTG-CATTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
48 AAAATTGAAATTACCTCAGCGTGTC-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1282754 TGACAAACAGAAATTGAAATTACCTCAGCGTGTC
112 TGA-AAACAGAAATTGAAATTACCTCAGCGTGTC
* ** * *
1282788 CTGAGGCTCAACTTATTTCTCGTAATATGAGTTGATTTTTTGAAAAATAGATTGAAACACAAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGA---G-----TTG---AAT--TTTGAAA-ACAAAAA
* * *
1282853 TTGACAA-TACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAA
52 TTGA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* *
1282917 AACAGAAATTGAAATTACCTTAGCATGTC
116 AACAGAAATTGAAATTACCTCAGCGTGTC
* * *
1282946 CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAAACAAAAATTGAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA------ATTTTG-AAAACAAAAATTGAAAT
* ** ** * *
1283011 TACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAACAGAAA
59 TACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAA
1283076 TTGAAATTACCTCAGCGTGTC
124 TTGAAATTACCTCAGCGTGTC
** * *
1283097 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAAAAATTGAAAATTA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---ATTTTGAA-AACAAAAATTG-AAATTA
* ** * *
1283162 CCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAAA
61 CCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAA-AACAGA
1283227 AATTGAAAATTACCTCAGCGTGTC
122 AATTG-AAATTACCTCAGCGTGTC
* *
1283251 CTGAGGCTCAACTCACCTCTCGC-A-AT--G-TG-A----G----CAGAAATTGAAAATACCTCA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
* * ** * * * * *
1283302 ACTTGTCTTGAGGCTTAACTCACCTCTCGCAATATGACTTAATTTTTGAAAA-ATAAATTGAAAA
66 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
*
1283366 TACCTCAGCGTGCC
131 TACCTCAGCGTGTC
* *
1283380 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACATAAATTGAAATTACCTC
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA-AAACAAAAATTGAAATTACCTC
*
1283445 AGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAA
65 AGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----TTTTTGAAA-ACAGAA
* *
1283510 ATTGAAAATACCTCAACGTGTC
123 ATTGAAATTACCTCAGCGTGTC
* * *
1283532 TTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAACATAAATTAAAACACAAAAA
1 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-ATTTTG------------AAA-ACAAAAA
** * *
1283597 TTGATAA-TACCTCAGCGTACCCCGAGGCTCAACTCACCTCTCGTAATATGAATTGATTTTTGAA
52 TTGA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-A
*
1283661 AAACATAAATTGAAA
115 AAACAGAAATTGAAA
1283676 AATGGAAATC
Statistics
Matches: 1863, Mismatches: 198, Indels: 244
0.81 0.09 0.11
Matches are distributed among these distances:
128 1 0.00
129 46 0.02
130 16 0.01
131 13 0.01
132 16 0.01
133 20 0.01
134 16 0.01
135 46 0.02
136 17 0.01
137 2 0.00
138 14 0.01
139 22 0.01
140 8 0.00
141 10 0.01
142 8 0.00
143 17 0.01
144 764 0.41
145 10 0.01
146 69 0.04
147 4 0.00
148 39 0.02
149 59 0.03
150 15 0.01
151 156 0.08
152 67 0.04
153 18 0.01
154 42 0.02
155 1 0.00
157 3 0.00
158 54 0.03
159 82 0.04
160 7 0.00
161 21 0.01
162 62 0.03
163 92 0.05
164 2 0.00
165 22 0.01
166 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (144 bp):
CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCA
GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAAT
TACCTCAGCGTGTC
Found at i:1281728 original size:216 final size:216
Alignment explanation
Indices: 1281343--1283675 Score: 2638
Period size: 216 Copynumber: 10.6 Consensus size: 216
1281333 GTGATCTGAA
*
1281343 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGACAGAAATTGAAAATACCTCAGC
1 GCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAA-ACAGAAATTGAAATTACCTCAGC
** *
1281408 ATGTGAACCGAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTTGAAAACAGAAATTGAA
63 --GTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAAACAGAAATTGAA
* * * ** *
1281473 AATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAACAAA
124 ATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGA
*
1281538 AATTGCAATTACCTCAGCGTGTCCCGAG
189 AATTGAAATTACCTCAGCGTGTCCCGAG
* * *
1281566 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
* * *
1281631 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAACTACCT
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCT
* *
1281696 CAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTAGAAAACAGAAAGTGA
131 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT-GAAAACAGAAATTGA
*
1281760 AACTACCTCAGCGTGTCCCGAG
195 AATTACCTCAGCGTGTCCCGAG
* * *
1281782 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAACTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
* * *
1281847 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTAGAAAACAGAAAGTGAAACTACCT
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCT
* *
1281912 CAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAA
131 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAA
1281977 ATTACCTCAGCGTGTCCCGAG
196 ATTACCTCAGCGTGTCCCGAG
* * *
1281998 GCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
* * *
1282063 TCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAAATTACCT
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCT
* * *
1282128 CAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAAACAAAAATTGAA
131 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAA
1282193 ATTACCTCAGCGTGTCCCGAG
196 ATTACCTCAGCGTGTCCCGAG
*
1282214 GCTCAACTCACCTCCCGCAATATGA---G-----T-----------TTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
* ** * *
1282260 TCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTAACAACAGAAATTGAAAATTA
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAA-AACAGAAATTG-AAATTA
*
1282325 CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTT
128 CCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATT
*
1282390 GAAATTACCTCAGCGTGTCCTGAG
193 GAAATTACCTCAGCGTGTCCCGAG
* *
1282414 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTTGAAATTACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
* * *
1282479 TCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTTGAAATTACCT
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCT
*
1282544 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAATTTGAA
131 CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAA
*
1282609 ATTACCTCAGCGTGTCCTGAG
196 ATTACCTCAGCGTGTCCCGAG
1282630 GCTCAACTCACCTCTCGCAATATGAGTTGAATTTTTTTGAAAAATATAAATTGAAAAGCAGAAAT
1 GCTCAACTCACCTCTCGCAATATGAGTTG-A------T------T-T---TTGAAAA-CAGAAAT
* * **
1282695 TGAAATTACCTCAACCTG-CATTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACA
48 TGAAATTACCTCAGCGTGTC-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-A
* ** *
1282759 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTTATTTCTCGTAATATGAGTTGAT
111 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA---G--
* * * *
1282824 TTTTTGAAAAATAGATTGAAACACAAAAATTGACAA-TACCTCAGCATGCCCCGAG
171 ---TTG---AAT--TTTGAAA-ACAGAAATTGA-AATTACCTCAGCGTGTCCCGAG
* * *
1282879 GCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTTAGCATG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
1282944 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTTTGAAAAACAAAAATTGAA
66 TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA------TTTTTG-AAAACAGAAATTGAA
* * * ** *
1283009 AATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAATTTTGAAAACAGA
124 ATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGA
*
1283074 AATTGAAATTACCTCAGCGTGTCCTGAG
189 AATTGAAATTACCTCAGCGTGTCCCGAG
** * *
1283102 GCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAAAAATTGAAAATTACCTCA
1 GCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAA-AACAGAAATTG-AAATTACCTCA
* ** * *
1283167 GCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTTAACAACAAAAATTG
61 GCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGAA-AACAGAAATTG
1283232 AAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC-A-AT--G-TG-A----G----C
122 -AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAAC
* * * **
1283283 AGAAATTGAAAATACCTCAACTTGTCTTGAG
186 AGAAATTGAAATTACCTCAGCGTGTCCCGAG
* * * * *
1283314 GCTTAACTCACCTCTCGCAATATGACTTAATTTTTGAAAA-ATAAATTGAAAATACCTCAGCGTG
1 GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
*
1283378 -CCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGACAAACATAAATTGAAATTAC
66 TCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA-AAACAGAAATTGAAATTAC
*
1283442 CTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACA
129 CTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA----ATTTTGAAA-ACA
* * **
1283507 GAAATTGAAAATACCTCAACGTGTCTTGAG
187 GAAATTGAAATTACCTCAGCGTGTCCCGAG
* *
1283537 GCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAACATAAATTAAAACACAAAAATTGAT
1 GCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG------------AAA-ACAGAAATTGA-
** * *
1283602 AA-TACCTCAGCGTACCCCGAGGCTCAACTCACCTCTCGTAATATGAATTGATTTTTGAAAAACA
51 AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAACA
*
1283666 TAAATTGAAA
115 GAAATTGAAA
1283676 AATGGAAATC
Statistics
Matches: 1861, Mismatches: 133, Indels: 217
0.84 0.06 0.10
Matches are distributed among these distances:
197 51 0.03
198 6 0.00
199 10 0.01
200 114 0.06
202 17 0.01
203 17 0.01
204 25 0.01
205 3 0.00
206 48 0.03
207 7 0.00
208 5 0.00
209 9 0.00
212 53 0.03
213 1 0.00
215 5 0.00
216 656 0.35
217 16 0.01
218 44 0.02
219 53 0.03
220 22 0.01
221 10 0.01
222 3 0.00
223 140 0.08
224 16 0.01
225 20 0.01
226 45 0.02
227 10 0.01
228 48 0.03
229 4 0.00
230 1 0.00
231 55 0.03
232 8 0.00
233 8 0.00
234 63 0.03
235 56 0.03
236 4 0.00
237 60 0.03
238 73 0.04
239 6 0.00
242 1 0.00
243 3 0.00
246 3 0.00
248 7 0.00
249 53 0.03
250 2 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.29
Consensus pattern (216 bp):
GCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCTCAGCGTG
TCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAGAAATTGAAATTACCT
CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAAAACAGAAATTGAA
ATTACCTCAGCGTGTCCCGAG
Found at i:1282251 original size:53 final size:53
Alignment explanation
Indices: 1282188--1282294 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
1282178 AAAACAAAAA
*
1282188 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGT
1 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCACAATATGAGT
* ** *
1282241 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGT
1 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCACAATATGAGT
1282294 T
1 T
1282295 GATTTTTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (53 bp):
TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCACAATATGAGT
Found at i:1282368 original size:128 final size:125
Alignment explanation
Indices: 1282116--1282369 Score: 391
Period size: 125 Copynumber: 2.0 Consensus size: 125
1282106 AAAACAAAAA
*
1282116 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGTTGAATTTTGAAA
1 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCACAATATGAGTTGAATTTTGAAA
1282181 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGT
66 ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGT
* ** * * *
1282241 TTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTAA
1 TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCACAATATGAGTTGA-ATTTTGAA
* * *
1282306 CAACAGAAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGT
65 -AACAAAAATTG-AAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGT
1282369 T
1 T
1282370 GAATTTTGAA
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
125 51 0.44
126 6 0.05
127 10 0.09
128 49 0.42
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (125 bp):
TTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCACAATATGAGTTGAATTTTGAAA
ACAAAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCCCGCAATATGAGT
Found at i:1282426 original size:72 final size:72
Alignment explanation
Indices: 1282240--1282664 Score: 769
Period size: 72 Copynumber: 5.9 Consensus size: 72
1282230 GCAATATGAG
** * * *
1282240 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCACAATATGAGTTGATTTTTTTA
1 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-ATTTTGA
1282305 ACAACAGAA
65 A-AACAGAA
*
1282314 ATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
1 TTTG-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGA
1282379 AAACAGAA
65 AAACAGAA
1282387 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
1 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
1282452 AACAGAA
66 AACAGAA
1282459 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
1 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
1282524 AACAGAA
66 AACAGAA
1282531 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
1 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
1282596 AACAGAA
66 AACAGAA
1282603 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
1 TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTT
1282665 TTTGAAAAAT
Statistics
Matches: 343, Mismatches: 7, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
72 274 0.80
73 10 0.03
74 9 0.03
75 50 0.15
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (72 bp):
TTTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTGAA
AACAGAA
Found at i:1282773 original size:73 final size:73
Alignment explanation
Indices: 1282680--1282833 Score: 204
Period size: 73 Copynumber: 2.1 Consensus size: 73
1282670 AAAATATAAA
*
1282680 TTGAAAAGCAGAAATTGAAATTACCTCAACCTG-CATTGAGGCTCAACTCACCTCTCGCAATATG
1 TTGAAAAGCAGAAATTGAAATTACCTCAACCTGTC-CTGAGGCTCAACTCACCTCTCGCAATATG
1282744 AGTTGATTT
65 AGTTGATTT
* * * ** *
1282753 TTGACAAA-CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTTATTTCTCGTAATATG
1 TTGA-AAAGCAGAAATTGAAATTACCTCAACCTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1282817 AGTTGATTTT
65 AGTTGA-TTT
1282827 TTGAAAA
1 TTGAAAA
1282834 ATAGATTGAA
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
73 60 0.85
74 11 0.15
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (73 bp):
TTGAAAAGCAGAAATTGAAATTACCTCAACCTGTCCTGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:1282928 original size:86 final size:86
Alignment explanation
Indices: 1282764--1282930 Score: 212
Period size: 86 Copynumber: 1.9 Consensus size: 86
1282754 TGACAAACAG
* * * * ** **
1282764 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTTATTTCTCGTAATATGAGTTGATTTTTT
1 AAATTGAAATTACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTT
* *
1282829 GAAAAATAGATTGAAACACAA
66 GAAAAAGAAATTGAAACACAA
1282850 AAATTGACAA-TACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA-TTTT
1 AAATTGA-AATTACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTT
1282913 TGAAAACAGAAATTGAAA
65 TGAAAA-AGAAATTGAAA
1282931 TTACCTTAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
85 10 0.14
86 57 0.83
87 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (86 bp):
AAATTGAAATTACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTT
GAAAAAGAAATTGAAACACAA
Found at i:1283199 original size:77 final size:76
Alignment explanation
Indices: 1282846--1283281 Score: 541
Period size: 77 Copynumber: 5.8 Consensus size: 76
1282836 AGATTGAAAC
* * * *
1282846 ACAAAAATTGACAA-TACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGA-
1 ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
*
1282909 --TTTTTGAAA
66 TTTTTTTTAAA
* * *
1282918 ACAGAAATTG-AAATTACCTTAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
1282982 TTTTTTTTTTGAAAA
65 -TTTTTTTTT--AAA
* ** *
1282997 ACAAAAATTGAAAA-TACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGA-
1 ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
* *
1283060 --ATTTTGAAA
66 TTTTTTTTAAA
* * **
1283069 ACAGAAATTG-AAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1 ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1283133 TTTTTTTTAACA
66 TTTTTTTTAA-A
* **
1283145 ACAAAAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAT
1 ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1283210 TTTTTTTTAACA
66 TTTTTTTTAA-A
* *
1283222 ACAAAAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATGTGAG
1 ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1283282 CAGAAATTGA
Statistics
Matches: 324, Mismatches: 25, Indels: 25
0.87 0.07 0.07
Matches are distributed among these distances:
71 5 0.02
72 113 0.35
74 4 0.01
75 6 0.02
76 10 0.03
77 128 0.40
79 55 0.17
80 3 0.01
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (76 bp):
ACAAAAATTGAAAATTACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTTTAAA
Found at i:1283400 original size:129 final size:135
Alignment explanation
Indices: 1283149--1283562 Score: 387
Period size: 152 Copynumber: 3.0 Consensus size: 135
1283139 TTAACAACAA
* ** * *
1283149 AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGACTTGA-TATT
* * *
1283214 TTTTAACAACAAAAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATGT
65 TTTGAACAACAAAAATTGAAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
1283279 GAGCAG
130 GAGCAG
* * *
1283285 AAATTGAAAA-TACCTCAACTTGTCTTGAGGCTTAACTCACCTCTCGCAATATGACTT-A-ATTT
1 AAATTGAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGACTTGATATTT
*
1283347 TTGAA-AA-ATAAATTGAAAA-TACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATG
66 TTGAACAACAAAAATTGAAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGC-A-AT-
*
1283409 AGTTGATTTTTGACAAACAT
128 A--TGA-----G-----CAG
* *
1283429 AAATTG-AAATTACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
1 AAATTGAAAATTACCTCAACGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGACTTGA--T
* * * * * *
1283493 TTTTTTGAA-AGACAGAAATTGAAAA-TACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGTA
62 ATTTTTGAACA-ACAAAAATTGAAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCA
1283556 ATATGAG
126 ATATGAG
1283563 TTGATTTTTT
Statistics
Matches: 230, Mismatches: 24, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
129 36 0.16
130 12 0.05
131 4 0.02
132 7 0.03
134 4 0.02
135 40 0.17
136 10 0.04
139 1 0.00
142 1 0.00
143 3 0.01
144 19 0.08
146 31 0.13
147 4 0.02
149 1 0.00
150 11 0.05
151 2 0.01
152 44 0.19
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.30
Consensus pattern (135 bp):
AAATTGAAAATTACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGACTTGATATTT
TTGAACAACAAAAATTGAAAATTACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATG
AGCAG
Found at i:1283401 original size:71 final size:73
Alignment explanation
Indices: 1283285--1283588 Score: 393
Period size: 71 Copynumber: 4.1 Consensus size: 73
1283275 ATGTGAGCAG
* * * *
1283285 AAATTGAAAATACCTCAACTTGTCTTGAGGCTTAACTCACCTCTCGCAATATGACTT-AATTTTT
1 AAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
1283349 GAAAA-AT
66 GAAAACAT
* *
1283356 AAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTTTT
1 AAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
1283420 GACAAACAT
66 GA-AAACAT
* * *
1283429 AAATTGAAATTACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAACGTGT--CCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---A
*
1283494 TTTTTGAAAGACAG
61 TTTTTGAAA-ACAT
* * *
1283508 AAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
1283573 G-AAACAT
66 GAAAACAT
1283580 AAATT-AAAA
1 AAATTGAAAA
1283589 CACAAAAATT
Statistics
Matches: 208, Mismatches: 15, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
71 63 0.30
72 11 0.05
73 25 0.12
74 7 0.03
75 35 0.17
77 34 0.16
78 2 0.01
79 31 0.15
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (73 bp):
AAATTGAAAATACCTCAACGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAATTTTT
GAAAACAT
Found at i:1283559 original size:152 final size:143
Alignment explanation
Indices: 1282850--1283588 Score: 596
Period size: 151 Copynumber: 5.1 Consensus size: 143
1282840 TGAAACACAA
* * * * * * * *
1282850 AAATTGACAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTG
1 AAATTGAAAATACCTCAACTTGACCTGAGGCTCAACTCACCTCTCGCAATATGACTTAATTTTTG
* * * *
1282915 AAAACAGAAATTGAAATTACCTTAGCATGTCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTT
66 AAAA-AGAAATTGAAAATACCTCAACGTG-CCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
*
1282979 GATTTTTTTTTTTGAAAAACAA
129 GA-----TTTTTTG--AAACAT
* * * * ** * *
1283001 AAATTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCATTTCTCACAATATGAGTTGAA-TTTT
1 AAATTGAAAATACCTCAACTTGACCTGAGGCTCAACTCACCTCTCGCAATATGACTT-AATTTTT
* * * **
1283065 GAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
65 GAAAA-AGAAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
* *
1283130 GATTTTTTTTTAACAACAA
129 GA---TTTTTTGA-AACAT
* * * ** * *
1283149 AAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTT
1 AAATTGAAAA-TACCTCAACTTGACCTGAGGCTCAACTCACCTCTCGCAATATGACTT-A--ATT
* * * *
1283214 TTTTAACAACAAAAATTGAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGC-A-AT
62 TTTGAA-AA-AGAAATTGAAAA-TACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATAT
*
1283277 --G-TGA------G---CAG
124 GAGTTGATTTTTTGAAACAT
* * *
1283285 AAATTGAAAATACCTCAACTTGTCTTGAGGCTTAACTCACCTCTCGCAATATGACTTAATTTTTG
1 AAATTGAAAATACCTCAACTTGACCTGAGGCTCAACTCACCTCTCGCAATATGACTTAATTTTTG
* *
1283350 AAAAATAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
66 AAAAAGAAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1283415 -TTTTTGACAAACAT
131 TTTTTTG--AAACAT
* * * *
1283429 AAATTGAAATTACCTCAGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AAATTGAAAATACCTCAAC-T-TGACCTGAGGCTCAACTCACCTCTCGCAATATGACTT-A---A
* * *
1283494 TTTTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCACCTCTCGTAATA
60 TTTTTGAAA-A-AGAAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATA
1283559 TGAGTTGATTTTTTGAAACAT
123 TGAGTTGATTTTTTGAAACAT
1283580 AAATT-AAAA
1 AAATTGAAAA
1283589 CACAAAAATT
Statistics
Matches: 506, Mismatches: 49, Indels: 67
0.81 0.08 0.11
Matches are distributed among these distances:
129 36 0.07
130 12 0.02
131 4 0.01
132 7 0.01
133 1 0.00
134 4 0.01
135 40 0.08
136 12 0.02
139 1 0.00
144 19 0.04
145 1 0.00
146 33 0.07
147 2 0.00
148 15 0.03
149 58 0.11
150 15 0.03
151 126 0.25
152 65 0.13
153 20 0.04
154 35 0.07
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (143 bp):
AAATTGAAAATACCTCAACTTGACCTGAGGCTCAACTCACCTCTCGCAATATGACTTAATTTTTG
AAAAAGAAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTTGAAACAT
Found at i:1295466 original size:18 final size:18
Alignment explanation
Indices: 1295424--1295468 Score: 76
Period size: 17 Copynumber: 2.6 Consensus size: 18
1295414 GAAAAATGAG
1295424 AATTTTT-AAAACACGAA
1 AATTTTTGAAAACACGAA
1295441 AA-TTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
1295458 AATTTTTGAAA
1 AATTTTTGAAA
1295469 CCTGAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.15
17 14 0.54
18 8 0.31
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:1296090 original size:15 final size:17
Alignment explanation
Indices: 1296070--1296101 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
1296060 ATTAGGAACG
1296070 TACATAA-A-AAATATA
1 TACATAATATAAATATA
1296085 TACATAATATAAATATA
1 TACATAATATAAATATA
1296102 ATATATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 1 0.07
17 7 0.47
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (17 bp):
TACATAATATAAATATA
Found at i:1297134 original size:21 final size:21
Alignment explanation
Indices: 1297109--1297159 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1297099 AGGGTTTCTT
1297109 GGTTTTTTTTTTGGGGGGTTA
1 GGTTTTTTTTTTGGGGGGTTA
***
1297130 GGTTTTTTTTTTTTTGGGTTA
1 GGTTTTTTTTTTGGGGGGTTA
1297151 GGTTTTTTT
1 GGTTTTTTT
1297160 GGGGGGGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.00, G:0.29, T:0.67
Consensus pattern (21 bp):
GGTTTTTTTTTTGGGGGGTTA
Found at i:1298649 original size:27 final size:27
Alignment explanation
Indices: 1298619--1298796 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
1298609 ATATTGAGTC
* * * *
1298619 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
1298646 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1298673 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
1298701 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
1298728 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
1298755 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
1298782 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
1298797 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:1298758 original size:82 final size:81
Alignment explanation
Indices: 1298640--1298795 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
1298630 TGCTATATAA
* *
1298640 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
1298705 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
1298722 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
1298786 CACTTAGTGC
65 CACTTAGTGC
1298796 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:1312437 original size:39 final size:40
Alignment explanation
Indices: 1312271--1312452 Score: 294
Period size: 40 Copynumber: 4.6 Consensus size: 40
1312261 CAAGCTCAAT
* * * * *
1312271 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
1312311 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1312351 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
1312391 TGCCTTCGGGTCTTAGCCCGTATATATCAAC-TGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1312430 TGCCTTCGGGTCTTAGCCCGGAT
1 TGCCTTCGGGTCTTAGCCCGGAT
1312453 GTATTCAAAT
Statistics
Matches: 133, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 30 0.23
40 103 0.77
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:1320939 original size:20 final size:21
Alignment explanation
Indices: 1320914--1320956 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1320904 GGATAAAATT
1320914 GAGCT-CAATGAGCTAGAATC
1 GAGCTCCAATGAGCTAGAATC
*
1320934 GAGCTCCATTGAGCTAGAATC
1 GAGCTCCAATGAGCTAGAATC
1320955 GA
1 GA
1320957 ACTACGTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
GAGCTCCAATGAGCTAGAATC
Found at i:1323088 original size:48 final size:48
Alignment explanation
Indices: 1323004--1323335 Score: 287
Period size: 48 Copynumber: 6.9 Consensus size: 48
1322994 ACATTTGGGT
* * * *
1323004 GATATGTGTGCTAGTGTATGACCATGTCTGGGACATGGCGTCAGCCAC
1 GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* * * * ** *
1323052 GATATGAGAGCTAGTGTAAGACGATGTTTGGAACATGGCATCGGTGAT
1 GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* * * * * *
1323100 GTTGTGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCA-CCGGCATT
1 GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCA-C
* *
1323148 GATATGTGTA-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC
1 GATATGAG-AGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* * * *
1323196 -ATCATGAGAGCTAGTGTAAGAGCATGTCTGGGA-ATGGCAAC-GGCATT
1 GAT-ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCA-C
* * * * *
1323243 GAGACGAGAGCTAGTGTAAGACCATGTCTAGGACATGGCATCAACCTC
1 GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
* * * * * *
1323291 AAAATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAGC
1 GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGC
1323336 AATTCACCCT
Statistics
Matches: 225, Mismatches: 50, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
46 3 0.01
47 40 0.18
48 176 0.78
49 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
GATATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCAC
Found at i:1323184 original size:96 final size:96
Alignment explanation
Indices: 1323016--1323330 Score: 330
Period size: 96 Copynumber: 3.3 Consensus size: 96
1323006 TATGTGTGCT
* * * * * * *
1323016 AGTGTATGACCATGTCTGGGACATGGCGTCAGCCA-CGATATGAGAGCTAGTGTAAGACGATGTT
1 AGTGTAAGACCATGTCTGGGACATGGC-ACCGGCATTGATATGAGAGCTAGTGTAAGACCATGTC
* ** ** **
1323080 TGGAACATGGCATCGGTGATGTTGTGAGAGCC
65 TGGGACATGGCATCGGCCACATCATGAGAGCC
*
1323112 AGTGTAAGACCATGTCTGGGACATGGCACCGGCATTGATATGTGTA-CTAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTGGGACATGGCACCGGCATTGATATGAG-AGCTAGTGTAAGACCATGTC
*
1323176 TGGGACATGGCATCGGCCACATCATGAGAGCT
65 TGGGACATGGCATCGGCCACATCATGAGAGCC
* * * *
1323208 AGTGTAAGAGCATGTCTGGGA-ATGGCAACGGCATTGAGACGAGAGCTAGTGTAAGACCATGTCT
1 AGTGTAAGACCATGTCTGGGACATGGCACCGGCATTGATATGAGAGCTAGTGTAAGACCATGTCT
* ** * ** *
1323272 AGGACATGGCATCAACCTCAAAATGTGAGCC
66 GGGACATGGCATCGGCCACATCATGAGAGCC
* *
1323303 AGTGTAAGACCATGTTTGGAACATGGCA
1 AGTGTAAGACCATGTCTGGGACATGGCA
1323331 TCAGCAATTC
Statistics
Matches: 183, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
94 1 0.01
95 82 0.45
96 99 0.54
97 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.23
Consensus pattern (96 bp):
AGTGTAAGACCATGTCTGGGACATGGCACCGGCATTGATATGAGAGCTAGTGTAAGACCATGTCT
GGGACATGGCATCGGCCACATCATGAGAGCC
Found at i:1323309 original size:143 final size:144
Alignment explanation
Indices: 1323007--1323335 Score: 373
Period size: 143 Copynumber: 2.3 Consensus size: 144
1322997 TTTGGGTGAT
* * *
1323007 ATGTGTGCTAGTGTATGACCATGTCTGGGACATGGCGTCAGCCACGATATGAGAGCTAGTGTAAG
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATGAGAGCTAGTGTAAG
* * * * * *
1323072 ACGATGTTTGGAACATGGCATCGGTGATGTTGTGAGAGCCAGTGTAAGACCATGTCTGGGACATG
66 ACGATGTCTGGAACATGGCAACGGTCATGTAGCGAGAGCCAGTGTAAGACCATGTCTAGGACATG
** ** *
1323137 GCACCGGCATTGAT
131 GCACCAACATCAAA
*
1323151 ATGTGTA-CTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAC-ATCATGAGAGCTAGTGTA
1 ATGTG-AGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGAT-ATGAGAGCTAGTGTA
* *
1323214 AGA-GCATGTCTGGGA-ATGGCAACGG-CAT-TGAGACGAGAGCTAGTGTAAGACCATGTCTAGG
64 AGACG-ATGTCTGGAACATGGCAACGGTCATGT-AG-CGAGAGCCAGTGTAAGACCATGTCTAGG
* *
1323275 ACATGGCATCAACCTCAAA
126 ACATGGCACCAACATCAAA
* * *
1323294 ATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCAGC
1 ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGC
1323336 AATTCACCCT
Statistics
Matches: 156, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
141 1 0.01
142 4 0.03
143 85 0.54
144 66 0.42
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (144 bp):
ATGTGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACGATATGAGAGCTAGTGTAAG
ACGATGTCTGGAACATGGCAACGGTCATGTAGCGAGAGCCAGTGTAAGACCATGTCTAGGACATG
GCACCAACATCAAA
Found at i:1324858 original size:22 final size:23
Alignment explanation
Indices: 1324833--1324883 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
1324823 TTCCATTCCC
1324833 CCCCCA-TGTTTTTGAATATTTT
1 CCCCCATTGTTTTTGAATATTTT
*
1324855 CCCCCATTTTTTTTTGAATATTTT
1 CCCCCA-TTGTTTTTGAATATTTT
1324879 CCCCC
1 CCCCC
1324884 CATTTACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.23
24 20 0.77
ACGTcount: A:0.16, C:0.29, G:0.06, T:0.49
Consensus pattern (23 bp):
CCCCCATTGTTTTTGAATATTTT
Found at i:1324868 original size:24 final size:25
Alignment explanation
Indices: 1324841--1324888 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
1324831 CCCCCCCATG
1324841 TTTTTGAATATTTT-CCCCCATTTT
1 TTTTTGAATATTTTCCCCCCATTTT
1324865 TTTTTGAATATTTTCCCCCCATTT
1 TTTTTGAATATTTTCCCCCCATTT
1324889 ACTTTCCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.17, C:0.23, G:0.04, T:0.56
Consensus pattern (25 bp):
TTTTTGAATATTTTCCCCCCATTTT
Found at i:1325335 original size:10 final size:10
Alignment explanation
Indices: 1325320--1325347 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1325310 GAACAAATAT
1325320 ATTCGATTTA
1 ATTCGATTTA
1325330 ATTCGATTTA
1 ATTCGATTTA
1325340 ATTCGATT
1 ATTCGATT
1325348 CAAATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.50
Consensus pattern (10 bp):
ATTCGATTTA
Found at i:1330494 original size:27 final size:26
Alignment explanation
Indices: 1330449--1330501 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
1330439 CCTCGCTGCA
*
1330449 TTCTGGTGGCCTCGCCACATATATCTG
1 TTCTGGTGACCTCGCCACA-ATATCTG
* *
1330476 TTCTGGTGACTTCGTCACAATATCTG
1 TTCTGGTGACCTCGCCACAATATCTG
1330502 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (26 bp):
TTCTGGTGACCTCGCCACAATATCTG
Found at i:1334317 original size:39 final size:40
Alignment explanation
Indices: 1334263--1334347 Score: 127
Period size: 39 Copynumber: 2.1 Consensus size: 40
1334253 TGGATGATAA
*
1334263 CCGGGCTAAGTCCCGAAGGCATCTGCGCTAGTGACT-AAT
1 CCGGGCTAAGTCCCGAAGGCATCTGCGCGAGTGACTAAAT
* * *
1334302 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAT
1 CCGGGCTAAGTCCCGAAGGCATCTGCGCGAGTGACTAAAT
1334342 CCGGGC
1 CCGGGC
1334348 CTCCAGAAGG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 32 0.78
40 9 0.22
ACGTcount: A:0.22, C:0.27, G:0.29, T:0.21
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATCTGCGCGAGTGACTAAAT
Found at i:1341838 original size:48 final size:46
Alignment explanation
Indices: 1341769--1341888 Score: 125
Period size: 48 Copynumber: 2.6 Consensus size: 46
1341759 TGTCTTCGAC
** * *
1341769 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATAAATATA-TAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCAT--ATA-ACTAAT
* * * *
1341817 ATGGGCTTACATGGCTCATTCCTATCTCTAAAGCCATATAACTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAACTAAT
*
1341863 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
1341889 CTGTCATGTC
Statistics
Matches: 60, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
45 1 0.02
46 29 0.48
48 30 0.50
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATAACTAAT
Found at i:1345212 original size:29 final size:28
Alignment explanation
Indices: 1345159--1345219 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
1345149 TGGTACATAA
1345159 ATATGTGTGGTTCTAATATACATAATAT
1 ATATGTGTGGTTCTAATATACATAATAT
* * *
1345187 ATATGTGTGGGTTTTATTATATATAATAT
1 ATATGTGT-GGTTCTAATATACATAATAT
1345216 ATAT
1 ATAT
1345220 ACAGTTATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 8 0.28
29 21 0.72
ACGTcount: A:0.34, C:0.03, G:0.15, T:0.48
Consensus pattern (28 bp):
ATATGTGTGGTTCTAATATACATAATAT
Found at i:1346745 original size:16 final size:17
Alignment explanation
Indices: 1346726--1346758 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1346716 CGAAAACACT
*
1346726 GAAAAT-AAGAAACGAA
1 GAAAATCAAAAAACGAA
1346742 GAAAATCAAAAAACGAA
1 GAAAATCAAAAAACGAA
1346759 TTTGTTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.70, C:0.09, G:0.15, T:0.06
Consensus pattern (17 bp):
GAAAATCAAAAAACGAA
Found at i:1348194 original size:13 final size:13
Alignment explanation
Indices: 1348176--1348200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1348166 TGGCTGTGTA
1348176 TTGGGTTTTAAAC
1 TTGGGTTTTAAAC
1348189 TTGGGTTTTAAA
1 TTGGGTTTTAAA
1348201 TTTGTAATAC
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:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
TTGGGTTTTAAAC
Found at i:1353488 original size:21 final size:20
Alignment explanation
Indices: 1353464--1353504 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
1353454 CTCTTCGTTC
1353464 AAACACA-AGCATACTACAATT
1 AAACACACA-CATA-TACAATT
1353485 AAACACACACATATACAATT
1 AAACACACACATATACAATT
1353505 CAACCTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.37
21 11 0.58
22 1 0.05
ACGTcount: A:0.54, C:0.24, G:0.02, T:0.20
Consensus pattern (20 bp):
AAACACACACATATACAATT
Found at i:1358217 original size:118 final size:118
Alignment explanation
Indices: 1358009--1358257 Score: 320
Period size: 118 Copynumber: 2.1 Consensus size: 118
1357999 TTAGCTAAGA
* * ** * * * *
1358009 ATACCATCTTGGTCTCATATTCACTAAGGATTACCAAGTAAGCCACCCTCTCGGTCTCTTCTTAG
1 ATACCCTCTCGGTCTCATATTCACTAAAAAATACCAACTAAGCCACCATCTCGGTCTCTTCCTAG
* * * * **
1358074 GCATATGAATACCCTTTTTGTCTCATCGCTTGGCATAAGTTGTGTTCGACAGG
66 GCATAAGAATACCCTCTCTGTCTCATCGCTTGGCACAAGTTACGTTCGACAGG
* * *
1358127 ATACCCTCTCGGTCTCATCTTCACTAAAAAATACCACCTAAGCCACCATTTCGGTCTCTTCCTAG
1 ATACCCTCTCGGTCTCATATTCACTAAAAAATACCAACTAAGCCACCATCTCGGTCTCTTCCTAG
1358192 GCATACAG-ATACCCTCTCTGTCTCATCGCTTGGCACAAGTTACGTTCGACAGG
66 GCATA-AGAATACCCTCTCTGTCTCATCGCTTGGCACAAGTTACGTTCGACAGG
*
1358245 ATATCCTCTCGGT
1 ATACCCTCTCGGT
1358258 TTCACCTGTC
Statistics
Matches: 112, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
118 111 0.99
119 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.31
Consensus pattern (118 bp):
ATACCCTCTCGGTCTCATATTCACTAAAAAATACCAACTAAGCCACCATCTCGGTCTCTTCCTAG
GCATAAGAATACCCTCTCTGTCTCATCGCTTGGCACAAGTTACGTTCGACAGG
Found at i:1360942 original size:21 final size:21
Alignment explanation
Indices: 1360912--1360956 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
1360902 AGTGTGTATC
1360912 TTTCCATACAAATTATTTGGT
1 TTTCCATACAAATTATTTGGT
*
1360933 TTTCCCTACAAATTATTTGGT
1 TTTCCATACAAATTATTTGGT
1360954 TTT
1 TTT
1360957 ACAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (21 bp):
TTTCCATACAAATTATTTGGT
Found at i:1369851 original size:22 final size:22
Alignment explanation
Indices: 1369789--1369853 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
1369779 CTCTGAATAT
* ** *
1369789 TAGCACCTTAGTGCTTTCCATT
1 TAGCACCTTAGTGCTCTCTGTA
* *
1369811 TAGCACATTTGTGCTCTCTGTA
1 TAGCACCTTAGTGCTCTCTGTA
1369833 TAGCACCTTAGTGCTCTCTGT
1 TAGCACCTTAGTGCTCTCTGT
1369854 TCATTAGTGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (22 bp):
TAGCACCTTAGTGCTCTCTGTA
Found at i:1371802 original size:78 final size:80
Alignment explanation
Indices: 1371709--1371905 Score: 294
Period size: 79 Copynumber: 2.5 Consensus size: 80
1371699 AAGAATTCTT
* *
1371709 AAACAGAATTATTCAATTGA-TTTCTATTTGAAACAAAAAATCGAACAAATCCTGTTAAA-TGAC
1 AAACAGAATTGTTCAATTGATTTTCTATTTGAAACAAAAAATCCAACAAATCCTGTTAAATTGAC
*
1371772 AGGAATAAAATCCTG
66 AGGAATAAAATCCTA
* *
1371787 AAACA-AATTTGTTCAATTGATTTTCTATTTAAAAC-AAAAATCCAATAAATCCTGTTAAATTGA
1 AAACAGAA-TTGTTCAATTGATTTTCTATTTGAAACAAAAAATCCAACAAATCCTGTTAAATTGA
1371850 CAGGAATAAAATCCTA
65 CAGGAATAAAATCCTA
* *
1371866 AAACAGAATTGTTCAATTGATTTTTTGTTTGAAACAAAAA
1 AAACAGAATTGTTCAATTGATTTTCTATTTGAAACAAAAA
1371906 TTAAACAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
77 2 0.02
78 38 0.36
79 60 0.57
80 6 0.06
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (80 bp):
AAACAGAATTGTTCAATTGATTTTCTATTTGAAACAAAAAATCCAACAAATCCTGTTAAATTGAC
AGGAATAAAATCCTA
Found at i:1371913 original size:11 final size:11
Alignment explanation
Indices: 1371897--1371925 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1371887 TTTTTGTTTG
1371897 AAACAAAAATT
1 AAACAAAAATT
1371908 AAACAAAAATT
1 AAACAAAAATT
1371919 AAACAAA
1 AAACAAA
1371926 TCCTATTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.10, G:0.00, T:0.14
Consensus pattern (11 bp):
AAACAAAAATT
Found at i:1376300 original size:41 final size:40
Alignment explanation
Indices: 1376203--1376368 Score: 217
Period size: 41 Copynumber: 4.1 Consensus size: 40
1376193 GGACTAAGAT
* *
1376203 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACTAAA-TCCGGGTTAAGTC
* *
1376243 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGATTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGG-TTAAGTC
* *
1376284 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGATTAAGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGG-TTAAGTC
* * *
1376325 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
1376365 CCGA
1 CCGA
1376369 GCATTTGAAC
Statistics
Matches: 117, Mismatches: 7, Indels: 4
0.91 0.05 0.03
Matches are distributed among these distances:
40 38 0.32
41 79 0.68
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGATACTAAATCCGGGTTAAGTC
Found at i:1395421 original size:24 final size:24
Alignment explanation
Indices: 1395349--1395430 Score: 96
Period size: 24 Copynumber: 3.4 Consensus size: 24
1395339 TCATTAGGGA
*
1395349 TTACCCATTGCAGCTCGTGAGAGC
1 TTACCGATTGCAGCTCGTGAGAGC
* *
1395373 TTACCAATT-CTTAACTCGT-AGGAGC
1 TTACCGATTGC--AGCTCGTGA-GAGC
1395398 TTACCGATTGCAGCTCGTGAGAGC
1 TTACCGATTGCAGCTCGTGAGAGC
1395422 TTACCGATT
1 TTACCGATT
1395431 TTCAATTCGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.02
24 28 0.57
25 19 0.39
26 1 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (24 bp):
TTACCGATTGCAGCTCGTGAGAGC
Found at i:1395421 original size:49 final size:49
Alignment explanation
Indices: 1395349--1395450 Score: 152
Period size: 49 Copynumber: 2.1 Consensus size: 49
1395339 TCATTAGGGA
1395349 TTACCCATTGCAGCTCGTGAGAGCTTACCAATTCTT-AACTCGTAGGAGC
1 TTACCCATTGCAGCTCGTGAGAGCTTACCAATT-TTCAACTCGTAGGAGC
* * * *
1395398 TTACCGATTGCAGCTCGTGAGAGCTTACCGATTTTCAATTCGTATGAGC
1 TTACCCATTGCAGCTCGTGAGAGCTTACCAATTTTCAACTCGTAGGAGC
1395447 TTAC
1 TTAC
1395451 TAATTTACAG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
48 2 0.04
49 46 0.96
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (49 bp):
TTACCCATTGCAGCTCGTGAGAGCTTACCAATTTTCAACTCGTAGGAGC
Done.