Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 166 of 190
Found at i:48511239 original size:6 final size:6
Alignment explanation
Indices: 48511207--48511250 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
48511197 ATAGTACCTA
* * *
48511207 AACAGT AATCAGT AACGGT AGCAGT AACAGT AACAGT AATAGT A
1 AACAGT AA-CAGT AACAGT AACAGT AACAGT AACAGT AACAGT A
48511251 TTCAACACAC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 26 0.81
7 6 0.19
ACGTcount: A:0.45, C:0.14, G:0.20, T:0.20
Consensus pattern (6 bp):
AACAGT
Found at i:48511329 original size:39 final size:39
Alignment explanation
Indices: 48511236--48511416 Score: 191
Period size: 39 Copynumber: 4.4 Consensus size: 39
48511226 AGCAGTAACA
* *
48511236 GTAACAGTAATAGTATTCAACACACAAAGTGCCGAATCTG
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-TG
* *
48511276 TAATAGTACGGTAACAGTATTCGACACACAAAGTGCCGAATTG
1 --GTA--ACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
* *
48511319 GTAACAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAATCG
1 GTAACAGTAAC----A--GTATTCGACACACAAAGTGCCGAATTG
* *
48511364 ATAACAGTAACAGTATTCGACACACAAAGTGCCGAATTA
1 GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
48511403 GTAACAGTAACAGT
1 GTAACAGTAACAGT
48511417 GGTCGGCATA
Statistics
Matches: 118, Mismatches: 13, Indels: 19
0.79 0.09 0.13
Matches are distributed among these distances:
39 44 0.37
41 3 0.03
42 2 0.02
43 3 0.03
44 31 0.26
45 35 0.30
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (39 bp):
GTAACAGTAACAGTATTCGACACACAAAGTGCCGAATTG
Found at i:48511407 original size:84 final size:87
Alignment explanation
Indices: 48511229--48511416 Score: 276
Period size: 84 Copynumber: 2.2 Consensus size: 87
48511219 TAACGGTAGC
* *
48511229 AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGCCGAATCTGTAATAGTACGGTAACAGT
1 AGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTG-AATAG-ACAGTAACAGT
48511294 ATTCGACACACAAAGTGCCGAATT
64 ATTCGACACACAAAGTGCCGAATT
* * *
48511318 GGTAACAGTAACGGTAACCGTATTCGAA-ACACAAAGTGCCGAATC-G-ATA-ACAGTAACAGTA
1 AGTAACAGTAACAGTAACAGTATTC-AACACACAAAGTGCCGAATCTGAATAGACAGTAACAGTA
48511379 TTCGACACACAAAGTGCCGAATT
65 TTCGACACACAAAGTGCCGAATT
48511402 AGTAACAGTAACAGT
1 AGTAACAGTAACAGT
48511417 GGTCGGCATA
Statistics
Matches: 91, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
84 47 0.52
86 3 0.03
88 1 0.01
89 38 0.42
90 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (87 bp):
AGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGCCGAATCTGAATAGACAGTAACAGTAT
TCGACACACAAAGTGCCGAATT
Found at i:48511414 original size:45 final size:45
Alignment explanation
Indices: 48511229--48511416 Score: 230
Period size: 45 Copynumber: 4.3 Consensus size: 45
48511219 TAACGGTAGC
* *
48511229 AGTAACAGTAACAGTAATAGTATTCAACACACAAAGTGCCGAATCT
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT-T
* *
48511275 -GTAATAGT-ACGGTAACAGTATTCGACACACAAAGTGCCGAATT
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
* * * *
48511318 GGTAACAGTAACGGTAACCGTATTCGAAACACAAAGTGCCGAA-T
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
*
48511362 CG----A-TAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
1 AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
48511402 AGTAACAGTAACAGT
1 AGTAACAGTAACAGT
48511417 GGTCGGCATA
Statistics
Matches: 122, Mismatches: 12, Indels: 17
0.81 0.08 0.11
Matches are distributed among these distances:
39 32 0.26
40 3 0.02
43 1 0.01
44 41 0.34
45 45 0.37
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (45 bp):
AGTAACAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATT
Found at i:48515091 original size:5 final size:5
Alignment explanation
Indices: 48515081--48515112 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
48515071 ACTACACGAT
48515081 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GA
48515113 TTATATATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:48520174 original size:22 final size:22
Alignment explanation
Indices: 48520149--48520212 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
48520139 TCTCCGATTA
48520149 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
* *
48520171 TTAGCACATTTGTGCTCTATGT
1 TTAGCACATTAGTGCTCTCTGT
* *
48520193 ATAGCACTTTAGTGCTCTCT
1 TTAGCACATTAGTGCTCTCT
48520213 ATTCAATAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.19, C:0.22, G:0.17, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:48528339 original size:15 final size:14
Alignment explanation
Indices: 48528316--48528347 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
48528306 TTAAGTGATG
48528316 AAAATTTAAATATT
1 AAAATTTAAATATT
48528330 AAAATATTAAATATT
1 AAAAT-TTAAATATT
48528345 AAA
1 AAA
48528348 TTGAAGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATTTAAATATT
Found at i:48529220 original size:11 final size:11
Alignment explanation
Indices: 48529156--48529229 Score: 60
Period size: 11 Copynumber: 6.5 Consensus size: 11
48529146 TAAATAATAA
*
48529156 AAAATATTTTT
1 AAAATATATTT
*
48529167 AAAATTTAATTAT
1 AAAATAT-ATT-T
*
48529180 AAAA-ATATAT
1 AAAATATATTT
**
48529190 AAAATATCAACT
1 AAAATAT-ATTT
48529202 AAATATATATTT
1 AAA-ATATATTT
48529214 AAAATATATTT
1 AAAATATATTT
48529225 AAAAT
1 AAAAT
48529230 TTTTAATTGT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
10 5 0.10
11 23 0.46
12 13 0.26
13 9 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAATATATTT
Found at i:48529579 original size:36 final size:36
Alignment explanation
Indices: 48529532--48529601 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
48529522 TTTTTATGGA
48529532 TAAACTATAAAAACAGTCATCCAGCTATGCCTTTTG
1 TAAACTATAAAAACAGTCATCCAGCTATGCCTTTTG
*
48529568 TAAACTATAAAAACGGTCATCCAGCTATGCCTTT
1 TAAACTATAAAAACAGTCATCCAGCTATGCCTTT
48529602 CGTTCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.30
Consensus pattern (36 bp):
TAAACTATAAAAACAGTCATCCAGCTATGCCTTTTG
Found at i:48531059 original size:61 final size:61
Alignment explanation
Indices: 48530932--48531058 Score: 175
Period size: 61 Copynumber: 2.1 Consensus size: 61
48530922 TATATTTAAA
*** *
48530932 ATTTTTAGAATTAGAACTAAATTGACAAATTTTGTAAATATTGAGGGCAAAATTTATTGAT
1 ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
* ** *
48530993 ATTTTTAGAATTAGAACTAAAACAATAAATTTTGTAAACATTGAGGGTTAAATTTGTTGA-
1 ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
48531053 ATTTTT
1 ATTTTT
48531059 TTTATATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 6 0.10
61 52 0.90
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.41
Consensus pattern (61 bp):
ATTTTTAGAATTAGAACTAAAACAACAAATTTTGTAAACATTGAGGGCAAAATTTATTGAT
Found at i:48534300 original size:7 final size:6
Alignment explanation
Indices: 48534281--48534316 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
48534271 TGCAGTGAAT
*
48534281 ATAAATA ATAAAA ATAAAA ATAAAA ATAAAA GTAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
48534317 GGTATAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:48542997 original size:7 final size:6
Alignment explanation
Indices: 48542978--48543013 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
48542968 TGCAGTGAAT
*
48542978 ATAAATA ATAAAA ATAAAA ATAAAA ATAAAA GTAAA
1 ATAAA-A ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
48543014 GGTATAGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (6 bp):
ATAAAA
Found at i:48545346 original size:17 final size:17
Alignment explanation
Indices: 48545319--48545352 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
48545309 CGATTCAAAG
48545319 TAAATAAATTATTAAAAA
1 TAAATAAATTA-TAAAAA
48545337 TAAA-AAATTATAAAAA
1 TAAATAAATTATAAAAA
48545353 CCAATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 6 0.38
18 4 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
TAAATAAATTATAAAAA
Found at i:48547192 original size:9 final size:9
Alignment explanation
Indices: 48547178--48547209 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
48547168 AACTTGGTGC
48547178 ATTTTGTTT
1 ATTTTGTTT
48547187 ATTTTGTTT
1 ATTTTGTTT
48547196 ATTTTGTTT
1 ATTTTGTTT
48547205 ATTTT
1 ATTTT
48547210 TAATATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (9 bp):
ATTTTGTTT
Found at i:48547290 original size:23 final size:23
Alignment explanation
Indices: 48547260--48547311 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
48547250 TGCAACTTGG
48547260 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAGCTATA-ATGC
*
48547283 TTTCATAATGATAGCTATAATGC
1 TTTCATAATAATAGCTATAATGC
48547306 TTTCAT
1 TTTCAT
48547312 CTTTTGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAGCTATAATGC
Found at i:48547323 original size:59 final size:59
Alignment explanation
Indices: 48547260--48547375 Score: 196
Period size: 59 Copynumber: 2.0 Consensus size: 59
48547250 TGCAACTTGG
*
48547260 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTATAATGCTTTCATCTTTTGC
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
* * *
48547319 TTTCATAATGATAGCTAATATGCTTTCATAATGGTAGTTACAATGCTTTCATCTTTT
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTT
48547376 TAATTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (59 bp):
TTTCATAATAATAGCTAATATGCTTTCATAATGATAGCTACAATGCTTTCATCTTTTGC
Found at i:48547344 original size:23 final size:23
Alignment explanation
Indices: 48547316--48547370 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
48547306 TTTCATCTTT
48547316 TGCTTTCATAATGATAGCTA-ATA
1 TGCTTTCATAATGATAGCTACA-A
* *
48547339 TGCTTTCATAATGGTAGTTACAA
1 TGCTTTCATAATGATAGCTACAA
48547362 TGCTTTCAT
1 TGCTTTCAT
48547371 CTTTTTAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (23 bp):
TGCTTTCATAATGATAGCTACAA
Found at i:48551795 original size:23 final size:23
Alignment explanation
Indices: 48551765--48551816 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
48551755 TGCAACTTGG
*
48551765 TTTCATAATAATAGCTA-ATATGC
1 TTTCATAATAATAACTATA-ATGC
*
48551788 TTTCATAATGATAACTATAATGC
1 TTTCATAATAATAACTATAATGC
48551811 TTTCAT
1 TTTCAT
48551817 CTTTTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 25 0.96
24 1 0.04
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
TTTCATAATAATAACTATAATGC
Found at i:48551851 original size:23 final size:23
Alignment explanation
Indices: 48551823--48551875 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
48551813 TCATCTTTTA
48551823 CTTTCATAATGATAGCTA-ATATG
1 CTTTCATAATGATAGCTACA-ATG
* *
48551846 CTTTCATAATGGTAGTTACAATG
1 CTTTCATAATGATAGCTACAATG
48551869 CTTTCAT
1 CTTTCAT
48551876 CTTTTTAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (23 bp):
CTTTCATAATGATAGCTACAATG
Found at i:48551869 original size:59 final size:59
Alignment explanation
Indices: 48551765--48551880 Score: 187
Period size: 59 Copynumber: 2.0 Consensus size: 59
48551755 TGCAACTTGG
*
48551765 TTTCATAATAATAGCTAATATGCTTTCATAATGATAACTATAATGCTTTCATCTTTTAC
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAACTACAATGCTTTCATCTTTTAC
* * **
48551824 TTTCATAATGATAGCTAATATGCTTTCATAATGGTAGTTACAATGCTTTCATCTTTT
1 TTTCATAATAATAGCTAATATGCTTTCATAATGATAACTACAATGCTTTCATCTTTT
48551881 TAATTATTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (59 bp):
TTTCATAATAATAGCTAATATGCTTTCATAATGATAACTACAATGCTTTCATCTTTTAC
Found at i:48555476 original size:16 final size:16
Alignment explanation
Indices: 48555428--48555476 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
48555418 TCAAGAATAC
48555428 TTATATTTAGAACAA-
1 TTATATTTAGAACAAT
* * *
48555443 CTATTATTTGGAAAAAT
1 TTA-TATTTAGAACAAT
48555460 TTATATTTAGAACAAT
1 TTATATTTAGAACAAT
48555476 T
1 T
48555477 ATGTTTTTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 2 0.08
16 22 0.85
17 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (16 bp):
TTATATTTAGAACAAT
Found at i:48557567 original size:4 final size:4
Alignment explanation
Indices: 48557558--48557584 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
48557548 NNNNNNNNNN
48557558 GCGT GCGT GCGT GCGT GCGT GCGT GCG
1 GCGT GCGT GCGT GCGT GCGT GCGT GCG
48557585 CATGCGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.52, T:0.22
Consensus pattern (4 bp):
GCGT
Found at i:48557597 original size:2 final size:2
Alignment explanation
Indices: 48557590--48557631 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
48557580 GTGCGCATGC
* * *
48557590 GT GT GT GT GT GT GT GT GT GT GT GT GT GT CT AT GT AT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
48557632 ATGTATGTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.05, C:0.02, G:0.43, T:0.50
Consensus pattern (2 bp):
GT
Found at i:48557634 original size:12 final size:12
Alignment explanation
Indices: 48557590--48557689 Score: 119
Period size: 12 Copynumber: 8.3 Consensus size: 12
48557580 GTGCGCATGC
* *
48557590 GTGTGTGTGTGT
1 GTGTGTATGTAT
* *
48557602 GTGTGTGTGTGT
1 GTGTGTATGTAT
*
48557614 GTGTCTATGTAT
1 GTGTGTATGTAT
48557626 GTGTGTATGTAT
1 GTGTGTATGTAT
*
48557638 GTATGTATGTAT
1 GTGTGTATGTAT
*
48557650 GTATGTATGTAT
1 GTGTGTATGTAT
*
48557662 GTATGTATGTAT
1 GTGTGTATGTAT
*
48557674 GTATGTATGTAT
1 GTGTGTATGTAT
48557686 GTGT
1 GTGT
48557690 ATGTATACGA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 82 1.00
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (12 bp):
GTGTGTATGTAT
Found at i:48557636 original size:4 final size:4
Alignment explanation
Indices: 48557619--48557695 Score: 131
Period size: 4 Copynumber: 19.8 Consensus size: 4
48557609 TGTGTGTGTC
*
48557619 TATG TATG TGTG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
48557667 TATG TATG TATG TATG TATG --TG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
48557696 ACGATCCATC
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
2 2 0.03
4 67 0.97
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:48557797 original size:17 final size:17
Alignment explanation
Indices: 48557775--48557807 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
48557765 GCCCATCTCC
48557775 GAAGCTTGGCAAATATG
1 GAAGCTTGGCAAATATG
48557792 GAAGCTTGGCAAATAT
1 GAAGCTTGGCAAATAT
48557808 AATCTTTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.24
Consensus pattern (17 bp):
GAAGCTTGGCAAATATG
Found at i:48573803 original size:2 final size:2
Alignment explanation
Indices: 48573796--48573825 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
48573786 ACCTTTATAA
*
48573796 GT GT GT GT GT GT GT GT GT GT GT TT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
48573826 ATAATTTTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (2 bp):
GT
Found at i:48575000 original size:29 final size:32
Alignment explanation
Indices: 48574958--48575019 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
48574948 TAGTAATTAT
48574958 AAAATTACACTTTAATC-CTAAAAAATTATAA
1 AAAATTACACTTTAATCACTAAAAAATTATAA
* *
48574989 AAAATTA-A-TTTAATCATTTAAAAATTATAA
1 AAAATTACACTTTAATCACTAAAAAATTATAA
48575019 A
1 A
48575020 GATATAAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 7 0.25
30 14 0.50
31 7 0.25
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAATTACACTTTAATCACTAAAAAATTATAA
Found at i:48581885 original size:16 final size:17
Alignment explanation
Indices: 48581859--48581895 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
48581849 GTTTTTTCCG
*
48581859 GGAGAAGTGGGAAAGGA
1 GGAGAAGTGGGAAAGCA
48581876 GGAG-AGTGGGAAAGCA
1 GGAGAAGTGGGAAAGCA
48581892 GGAG
1 GGAG
48581896 TTGAAGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.38, C:0.03, G:0.54, T:0.05
Consensus pattern (17 bp):
GGAGAAGTGGGAAAGCA
Found at i:48587007 original size:24 final size:24
Alignment explanation
Indices: 48586980--48587031 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
48586970 TTTCTAGAAG
* **
48586980 ATTTAGTATTTATGAGTATAATAT
1 ATTTAGCATTTATGAACATAATAT
*
48587004 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATGAACATAATAT
48587028 ATTT
1 ATTT
48587032 GACTTTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATGAACATAATAT
Found at i:48599028 original size:33 final size:33
Alignment explanation
Indices: 48598985--48599052 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
48598975 CAAAGTTACC
* *
48598985 TTCACGAGCAACGACATCATCTTAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
48599018 TTCACAAGCAACGACATCATCTCAGTGGAAACA
1 TTCACAAGCAACGACATCATCTCAGTGGAAACA
48599051 TT
1 TT
48599053 GCTAAAGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.22
Consensus pattern (33 bp):
TTCACAAGCAACGACATCATCTCAGTGGAAACA
Found at i:48604484 original size:12 final size:11
Alignment explanation
Indices: 48604465--48604528 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 11
48604455 GCAACCCAAT
48604465 TTTTATTTTTA
1 TTTTATTTTTA
48604476 TTATTATTTATT-
1 TT-TTATTT-TTA
*
48604488 TTTT-TCTTTA
1 TTTTATTTTTA
*
48604498 CTTTATTTATTA
1 TTTTATTT-TTA
48604510 TTTTA-TTTTA
1 TTTTATTTTTA
48604520 TTTTATTTT
1 TTTTATTTT
48604529 ACTTATTTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
9 2 0.05
10 13 0.30
11 11 0.26
12 15 0.35
13 2 0.05
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:48604497 original size:22 final size:20
Alignment explanation
Indices: 48604463--48604527 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 20
48604453 AGGCAACCCA
48604463 ATTTTTATTTTTATTATTATTT
1 ATTTTT-TTTTTATT-TTATTT
*
48604485 ATTTTTTTCTTTACTTTATTT
1 ATTTTTTT-TTTATTTTATTT
48604506 ATTATTTTATTTTATTTTATTT
1 ATT-TTTT-TTTTATTTTATTT
48604528 TACTTATTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 11 0.29
22 26 0.68
23 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (20 bp):
ATTTTTTTTTTATTTTATTT
Found at i:48604502 original size:17 final size:16
Alignment explanation
Indices: 48604466--48604536 Score: 76
Period size: 17 Copynumber: 4.4 Consensus size: 16
48604456 CAACCCAATT
48604466 TTTATTTTTATTATTA-
1 TTTATTTTTATT-TTAC
*
48604482 TTTATTTTTTTCTTTAC
1 TTTATTTTTAT-TTTAC
*
48604499 TTTATTTATTATTTTAT
1 TTTATTT-TTATTTTAC
48604516 TTTA-TTTTATTTTAC
1 TTTATTTTTATTTTAC
48604531 -TTATTT
1 TTTATTT
48604537 GGATATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
14 3 0.06
15 10 0.21
16 15 0.32
17 16 0.34
18 3 0.06
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTTATTTTAC
Found at i:48604515 original size:5 final size:5
Alignment explanation
Indices: 48604465--48604529 Score: 51
Period size: 5 Copynumber: 12.0 Consensus size: 5
48604455 GCAACCCAAT
* *
48604465 TTTTA TTTTTA TTATTA -TTTA TTTTTT TCTTTA CTTTA TTTATTA TTTTA
1 TTTTA -TTTTA TT-TTA TTTTA -TTTTA T-TTTA TTTTA -TT-TTA TTTTA
48604515 TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA
48604530 CTTATTTGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
4 3 0.06
5 26 0.53
6 17 0.35
7 3 0.06
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:48604518 original size:27 final size:27
Alignment explanation
Indices: 48604472--48604535 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
48604462 AATTTTTATT
*
48604472 TTTATTATTATTTAT-TTTTTTCTTTAC
1 TTTATTATTATTTATATTTTAT-TTTAC
*
48604499 TTTATTTATTATTT-TATTTTATTTTAT
1 TTTA-TTATTATTTATATTTTATTTTAC
48604526 TTTACTTATT
1 TTTA-TTATT
48604536 TGGATATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTATTATTATTTATATTTTATTTTAC
Found at i:48604534 original size:24 final size:23
Alignment explanation
Indices: 48604465--48604536 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 23
48604455 GCAACCCAAT
48604465 TTTTATTTTTATTATTA-TTTATT-
1 TTTTA-TTTTATT-TTATTTTATTA
*
48604488 TTTT-TCTTTACTTTA-TTTATTA
1 TTTTAT-TTTATTTTATTTTATTA
48604510 TTTTATTTTATTTTATTTTACTTA
1 TTTTATTTTATTTTATTTTA-TTA
48604534 TTT
1 TTT
48604537 GGATATTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
21 10 0.24
22 17 0.40
23 9 0.21
24 6 0.14
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTTATTTTATTTTATTTTATTA
Found at i:48604535 original size:31 final size:33
Alignment explanation
Indices: 48604466--48604536 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
48604456 CAACCCAATT
*
48604466 TTTATTTTTATTATTATTTATTTTTTTCTTTAC
1 TTTATTTTTATTATTATTTATTTTTATCTTTAC
48604499 TTTATTTATTATT-TTATTT-TATTTTAT-TTTAC
1 TTTATTT-TTATTATTATTTAT-TTTTATCTTTAC
48604531 -TTATTT
1 TTTATTT
48604537 GGATATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
31 6 0.17
32 6 0.17
33 18 0.51
34 5 0.14
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (33 bp):
TTTATTTTTATTATTATTTATTTTTATCTTTAC
Found at i:48606306 original size:20 final size:20
Alignment explanation
Indices: 48606281--48606325 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
48606271 CACTATAAAT
48606281 AGGGGGTGAAGTGACTCAAA
1 AGGGGGTGAAGTGACTCAAA
48606301 AGGGGGTGAAGTGACTCAAA
1 AGGGGGTGAAGTGACTCAAA
48606321 AGGGG
1 AGGGG
48606326 ATCCCATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.44, T:0.13
Consensus pattern (20 bp):
AGGGGGTGAAGTGACTCAAA
Found at i:48610017 original size:20 final size:20
Alignment explanation
Indices: 48609983--48610032 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
48609973 CTTTGATTTA
* *
48609983 TATATACATA-CTTATATTT
1 TATATACATATTTTATAATT
* *
48610002 TTTATATATATTTTATAATT
1 TATATACATATTTTATAATT
48610022 TATATACATAT
1 TATATACATAT
48610033 ACATATATAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (20 bp):
TATATACATATTTTATAATT
Found at i:48611598 original size:23 final size:23
Alignment explanation
Indices: 48611564--48611613 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
48611554 AACAACCATA
*
48611564 AAAATATATTTAAAAAAATAATT
1 AAAATATATTTAAAAAAATAAAT
* *
48611587 AAAATA-AGTTTAAGAAACTAAAT
1 AAAATATA-TTTAAAAAAATAAAT
48611610 AAAA
1 AAAA
48611614 AATAAAGCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAATATATTTAAAAAAATAAAT
Found at i:48618405 original size:29 final size:30
Alignment explanation
Indices: 48618351--48618415 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
48618341 AGGAACCTGT
* *
48618351 AAAT-AAAATAAAAATTAGAAAAACAATTA
1 AAATAAAAACAAAAATTAGAAAAACAATAA
*
48618380 AACTAAAAACAAAAA-TA-AAAATACAATAA
1 AAATAAAAACAAAAATTAGAAAA-ACAATAA
48618409 AAATAAA
1 AAATAAA
48618416 TTGCTAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 4 0.13
29 17 0.57
30 9 0.30
ACGTcount: A:0.75, C:0.06, G:0.02, T:0.17
Consensus pattern (30 bp):
AAATAAAAACAAAAATTAGAAAAACAATAA
Found at i:48622311 original size:24 final size:24
Alignment explanation
Indices: 48622274--48622430 Score: 105
Period size: 23 Copynumber: 6.8 Consensus size: 24
48622264 TAATCATACG
**
48622274 TGATAAATCCAAAATAATAGTATA
1 TGATAAATTTAAAATAATAGTATA
* *
48622298 TAATAAATTT-AAA-AATATTA-A
1 TGATAAATTTAAAATAATAGTATA
* * *
48622319 GGATAAATTTGAAATAGATA-TACA
1 TGATAAATTTAAAATA-ATAGTATA
48622343 TGATAAATTTAAAATAAT-GT-TAA
1 TGATAAATTTAAAATAATAGTAT-A
* * *
48622366 CGATGAATTTAAAATAATAATAT-
1 TGATAAATTTAAAATAATAGTATA
** *
48622389 TGATAAA-TTACAAATAATAAAACA
1 TGATAAATTTA-AAATAATAGTATA
*
48622413 TGATAAATCTAAAATAAT
1 TGATAAATTTAAAATAAT
48622431 GATATAAAAT
Statistics
Matches: 105, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
21 9 0.09
22 12 0.11
23 41 0.39
24 40 0.38
25 3 0.03
ACGTcount: A:0.55, C:0.04, G:0.08, T:0.32
Consensus pattern (24 bp):
TGATAAATTTAAAATAATAGTATA
Found at i:48622334 original size:45 final size:46
Alignment explanation
Indices: 48622275--48622436 Score: 136
Period size: 47 Copynumber: 3.5 Consensus size: 46
48622265 AATCATACGT
** * *
48622275 GATAAATCCAAAATAATAGTATATAATAAATTT-AAA-AATATTAAG
1 GATAAATTTAAAATAATA-TATATGATAAATTTAAAATAATATTAAC
* * *
48622320 GATAAATTTGAAATAGATATACATGATAAATTTAAAATAATGTTAAC
1 GATAAATTTAAAATA-ATATATATGATAAATTTAAAATAATATTAAC
* *
48622367 GATGAATTTAAAATAATA-ATATTGATAAA-TTACAAATAATA-AAAC
1 GATAAATTTAAAATAATATATA-TGATAAATTTA-AAATAATATTAAC
*
48622412 ATGATAAATCTAAAATAATGATATA
1 --GATAAATTTAAAATAAT-ATATA
48622437 AAATACACTT
Statistics
Matches: 94, Mismatches: 14, Indels: 14
0.77 0.11 0.11
Matches are distributed among these distances:
45 32 0.34
46 23 0.24
47 35 0.37
48 1 0.01
49 3 0.03
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (46 bp):
GATAAATTTAAAATAATATATATGATAAATTTAAAATAATATTAAC
Found at i:48623261 original size:19 final size:19
Alignment explanation
Indices: 48623237--48623297 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
48623227 TTTTCCCTCC
48623237 CTTTACACTGATTTTTTCT
1 CTTTACACTGATTTTTTCT
** *
48623256 CTTTACACTGATTTTCCCC
1 CTTTACACTGATTTTTTCT
*
48623275 CTTTACACTGATTTCTTCT
1 CTTTACACTGATTTTTTCT
48623294 CTTT
1 CTTT
48623298 TTTATGAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.15, C:0.28, G:0.05, T:0.52
Consensus pattern (19 bp):
CTTTACACTGATTTTTTCT
Found at i:48624137 original size:15 final size:15
Alignment explanation
Indices: 48624117--48624154 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
48624107 ACCGTTGAAA
48624117 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
48624132 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
48624147 CCCTAAAT
1 CCCTAAAT
48624155 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:48624685 original size:41 final size:41
Alignment explanation
Indices: 48624640--48625081 Score: 328
Period size: 41 Copynumber: 10.8 Consensus size: 41
48624630 AGGCAGGAGA
* *
48624640 ATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATCCAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
** * * *
48624681 ATTAGCAACGCTTAAATAAAATCGCCGCTAAAGA-CCTAA-T
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAGT
* * * * *
48624721 CTTTTGCGGCGTTCATATAAGAACGCCACTAAAGATCCAAGT
1 -ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* * * *
48624763 ATTAGCGGCGCTGAAATAAAATCGCCGCTAAAGA-CCTGAGCT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAG-T
* * * *
48624805 -TTTGCGGCGTTCATATAAAAACACCACTAAAGATCCAAGT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* * * * *
48624845 ATTAGCGTCGCTGAAATAAAATCGCCGCTAAAGA-CCTGAGCT
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCC-AAG-T
* * *
48624887 -TTTGCGGCGTTCATATAAAAACGCCACTAAAGAT-CAGAG-
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCA-AGT
* * *
48624926 ATTTAGCGGCGCTCAGATAAAAATGCCACTAAAGAT-CAGAGA
1 A-TTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCA-AGT
* * * ** *
48624968 ATTAGCCGCGCCCAGATAAAAACGCCACTAAAGATCGGAGA
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
* ** *
48625009 ATTAGCGGCGCT-AAGATAAAAACGCCACTATAGATCCGTGC
1 ATTAGCGGCGCTCAA-ATAAAAACGCCACTAAAGATCCAAGT
* * *
48625050 ATTAGTGGCGCACAAATAAAAACGCCGCTAAA
1 ATTAGCGGCGCTCAAATAAAAACGCCACTAAA
48625082 TGTTTAAAAA
Statistics
Matches: 312, Mismatches: 71, Indels: 36
0.74 0.17 0.09
Matches are distributed among these distances:
40 9 0.03
41 293 0.94
42 10 0.03
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTCAAATAAAAACGCCACTAAAGATCCAAGT
Found at i:48624746 original size:82 final size:82
Alignment explanation
Indices: 48624646--48625034 Score: 462
Period size: 82 Copynumber: 4.7 Consensus size: 82
48624636 GAGAATTAGT
* * * *
48624646 GGCGCTCAGATAAAAACGCCACTAAAGATCCAAGTATTAGCAACGCTTAAATAAAATCGCCGCTA
1 GGCGTTCATATAAAAACGCCACTAAAGATCCAAGTATTAGCGACGCTGAAATAAAATCGCCGCTA
* *
48624711 AAGACCTAATCTTTTGC
66 AAGACCTGAGCTTTTGC
* *
48624728 GGCGTTCATATAAGAACGCCACTAAAGATCCAAGTATTAGCGGCGCTGAAATAAAATCGCCGCTA
1 GGCGTTCATATAAAAACGCCACTAAAGATCCAAGTATTAGCGACGCTGAAATAAAATCGCCGCTA
48624793 AAGACCTGAGCTTTTGC
66 AAGACCTGAGCTTTTGC
* *
48624810 GGCGTTCATATAAAAACACCACTAAAGATCCAAGTATTAGCGTCGCTGAAATAAAATCGCCGCTA
1 GGCGTTCATATAAAAACGCCACTAAAGATCCAAGTATTAGCGACGCTGAAATAAAATCGCCGCTA
48624875 AAGACCTGAGCTTTTGC
66 AAGACCTGAGCTTTTGC
* * * *
48624892 GGCGTTCATATAAAAACGCCACTAAAGAT-CAGAG-ATTTAGCGGCGCTCAGATAAAAAT-GCCA
1 GGCGTTCATATAAAAACGCCACTAAAGATCCA-AGTA-TTAGCGACGCTGAAAT-AAAATCGCCG
* * ** *
48624954 CTAAAGATCAGAGAATTAGC
63 CTAAAGACCTGAGCTTTTGC
* ** * ** * * *
48624974 CGCGCCCAGATAAAAACGCCACTAAAGATCGGAGAATTAGCGGCGCT-AAGATAAAAACGCC
1 GGCGTTCATATAAAAACGCCACTAAAGATCCAAGTATTAGCGACGCTGAA-ATAAAATCGCC
48625035 ACTATAGATC
Statistics
Matches: 271, Mismatches: 29, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
81 8 0.03
82 257 0.95
83 6 0.02
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (82 bp):
GGCGTTCATATAAAAACGCCACTAAAGATCCAAGTATTAGCGACGCTGAAATAAAATCGCCGCTA
AAGACCTGAGCTTTTGC
Found at i:48625036 original size:82 final size:81
Alignment explanation
Indices: 48624616--48625081 Score: 429
Period size: 82 Copynumber: 5.7 Consensus size: 81
48624606 GCGCTTGGGA
* * * *
48624616 AAAAACGCCGCTAAAG-GCAGGAGAATTAGTGGCGCTCAGATAAAAACGCCACTAAAGATCCAAG
1 AAAAACGCCGCTAAAGACCA-GAGCATTAGCGGCGCTCATATAAAAACGCCACTAAAGATCCAAG
**
48624680 TATTAGCAACGCTTAAAT
65 TATTAGCGGCGC-TAAAT
* * * * * *
48624698 AAAATCGCCGCTAAAGACCTA-ATCTTTTGCGGCGTTCATATAAGAACGCCACTAAAGATCCAAG
1 AAAAACGCCGCTAAAGACC-AGAGCATTAGCGGCGCTCATATAAAAACGCCACTAAAGATCCAAG
48624762 TATTAGCGGCGCTGAAAT
65 TATTAGCGGCGCT-AAAT
* * * * * *
48624780 AAAATCGCCGCTAAAGACCTGAGCTTTTGCGGCGTTCATATAAAAACACCACTAAAGATCCAAGT
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCATATAAAAACGCCACTAAAGATCCAAGT
*
48624845 ATTAGCGTCGCTGAAAT
66 ATTAGCGGCGCT-AAAT
* * * * *
48624862 AAAATCGCCGCTAAAGACCTGAGCTTTTGCGGCGTTCATATAAAAACGCCACTAAAGAT-CAGAG
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCATATAAAAACGCCACTAAAGATCCA-AG
*
48624926 -ATTTAGCGGCGCTCAGAT
65 TA-TTAGCGGCGCT-AAAT
* * * * * * * ** *
48624944 AAAAATGCCACTAAAGATCAGAGAATTAGCCGCGCCCAGATAAAAACGCCACTAAAGATCGGAGA
1 AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCATATAAAAACGCCACTAAAGATCCAAGT
48625009 ATTAGCGGCGCTAAGAT
66 ATTAGCGGCGCTAA-AT
* * * * * * *
48625026 AAAAACGCCACTATAGATCC-GTGCATTAGTGGCGCACAAATAAAAACGCCGCTAAA
1 AAAAACGCCGCTAAAGA-CCAGAGCATTAGCGGCGCTCATATAAAAACGCCACTAAA
48625082 TGTTTAAAAA
Statistics
Matches: 328, Mismatches: 46, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
81 5 0.02
82 319 0.97
83 3 0.01
84 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.20
Consensus pattern (81 bp):
AAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTCATATAAAAACGCCACTAAAGATCCAAGT
ATTAGCGGCGCTAAAT
Found at i:48631791 original size:6 final size:6
Alignment explanation
Indices: 48631780--48631830 Score: 59
Period size: 6 Copynumber: 8.5 Consensus size: 6
48631770 GTTTCCCTGC
* * *
48631780 AAAATA AAAATA AAAATA AAAATA AATAATA AGAA-A AAATTA AAATTA
1 AAAATA AAAATA AAAATA AAAATA AA-AATA AAAATA AAAATA AAAATA
48631828 AAA
1 AAA
48631831 TGTGTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
5 3 0.08
6 32 0.80
7 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:48652205 original size:18 final size:19
Alignment explanation
Indices: 48652160--48652205 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
48652150 TGTAATTAGA
*
48652160 AAAATGAATAAAAACTATT
1 AAAATAAATAAAAACTATT
*
48652179 ATAAA-AAATAAAACCT-TT
1 A-AAATAAATAAAAACTATT
48652197 AAAATAAAT
1 AAAATAAAT
48652206 TCAAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 10 0.43
20 3 0.13
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATAAATAAAAACTATT
Found at i:48666726 original size:18 final size:19
Alignment explanation
Indices: 48666703--48666739 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
48666693 CACACTTCCA
48666703 ATTGTATGTACTT-ATCTT
1 ATTGTATGTACTTAATCTT
*
48666721 ATTGTATGTGCTTAATCTT
1 ATTGTATGTACTTAATCTT
48666740 GTTTATCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.54
Consensus pattern (19 bp):
ATTGTATGTACTTAATCTT
Found at i:48671647 original size:3 final size:3
Alignment explanation
Indices: 48671639--48671664 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48671629 TTCATCCTCA
48671639 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
48671665 ATCATGCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:48672724 original size:21 final size:21
Alignment explanation
Indices: 48672700--48672745 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
48672690 ATAAAAATTT
*
48672700 AAAATAT-ATAAATAATTATTA
1 AAAATATCATAAA-AATTATAA
*
48672721 AAAATATCTTAAAAATTATAA
1 AAAATATCATAAAAATTATAA
48672742 AAAA
1 AAAA
48672746 AACCCAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATATCATAAAAATTATAA
Found at i:48673456 original size:30 final size:29
Alignment explanation
Indices: 48673433--48673488 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
48673423 ATTAATGATA
*
48673433 ATTAACATTCA-TAAAAATTAATTAAAAT
1 ATTAAAATTCATTAAAAATTAATTAAAAT
*
48673461 TTTAAAATTCATTAAAAATTCAATTAAA
1 ATTAAAATTCATTAAAAATT-AATTAAA
48673489 TGTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 8 0.33
30 7 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (29 bp):
ATTAAAATTCATTAAAAATTAATTAAAAT
Found at i:48673870 original size:29 final size:30
Alignment explanation
Indices: 48673806--48673872 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
48673796 ATTTATTTGT
48673806 GGGTTAAAATTAAATTATAAATTTTTAAAA
1 GGGTTAAAATTAAATTATAAATTTTTAAAA
* *
48673836 GAGTTAAAATTAAATTATAAA-TTTTAAAG
1 GGGTTAAAATTAAATTATAAATTTTTAAAA
48673865 GGGTTAAA
1 GGGTTAAA
48673873 GTATATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 14 0.41
30 20 0.59
ACGTcount: A:0.49, C:0.00, G:0.13, T:0.37
Consensus pattern (30 bp):
GGGTTAAAATTAAATTATAAATTTTTAAAA
Found at i:48682632 original size:21 final size:21
Alignment explanation
Indices: 48682567--48682633 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
48682557 TTACTTTCCA
* *
48682567 TTTAGCTCTCTCGAGCTTTTG
1 TTTAGCTCTTTTGAGCTTTTG
* * * * *
48682588 TTTAACACATATGAG-TTTCCG
1 TTTAGCTCTTTTGAGCTTT-TG
48682609 TTTAGCTCTTTTGAGCTTTTG
1 TTTAGCTCTTTTGAGCTTTTG
48682630 TTTA
1 TTTA
48682634 ACCCTTATGG
Statistics
Matches: 32, Mismatches: 12, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
20 3 0.09
21 26 0.81
22 3 0.09
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.49
Consensus pattern (21 bp):
TTTAGCTCTTTTGAGCTTTTG
Found at i:48682716 original size:42 final size:42
Alignment explanation
Indices: 48682567--48682717 Score: 144
Period size: 42 Copynumber: 3.6 Consensus size: 42
48682557 TTACTTTCCA
* * * *
48682567 TTTAGCTCTC-TCGAGCTTTTGTTTAACACA-TATGAGTTTCCG
1 TTTAGCTCTCAT-GAGCTTCTGTTCAAC-CATTATGGGTTTCTG
** * * * *
48682609 TTTAGCTCTTTTGAGCTTTTGTTTAACCCTTATGGGTTTCTA
1 TTTAGCTCTCATGAGCTTCTGTTCAACCATTATGGGTTTCTG
* * **
48682651 TTCAGCTCTTACAAGCTTCTGTTCAACCATTATGGGTTTCTG
1 TTTAGCTCTCATGAGCTTCTGTTCAACCATTATGGGTTTCTG
48682693 TTTAGCTCTCATGAGCTTCTGTTCA
1 TTTAGCTCTCATGAGCTTCTGTTCA
48682718 GCCTTCGAGC
Statistics
Matches: 90, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 88 0.98
43 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (42 bp):
TTTAGCTCTCATGAGCTTCTGTTCAACCATTATGGGTTTCTG
Found at i:48687824 original size:25 final size:25
Alignment explanation
Indices: 48687787--48687853 Score: 80
Period size: 25 Copynumber: 2.7 Consensus size: 25
48687777 TGTAAACAAT
* * *
48687787 AAGCTCTTTCGAGCTGAATAGCGAG
1 AAGCTCATGCGAGCTGAATAACGAG
* * *
48687812 AAGCTTATGCGAGCTAAATAACGGG
1 AAGCTCATGCGAGCTGAATAACGAG
48687837 AAGCTCATGCGAGCTGA
1 AAGCTCATGCGAGCTGA
48687854 GTATTGGGAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.21
Consensus pattern (25 bp):
AAGCTCATGCGAGCTGAATAACGAG
Found at i:48687862 original size:25 final size:25
Alignment explanation
Indices: 48687787--48687869 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
48687777 TGTAAACAAT
* * * * *
48687787 AAGCTCTTTCGAGCTGAATAGCGAG
1 AAGCTCATGCGAGCTAAATAACGGG
*
48687812 AAGCTTATGCGAGCTAAATAACGGG
1 AAGCTCATGCGAGCTAAATAACGGG
* * **
48687837 AAGCTCATGCGAGCTGAGTATTGGG
1 AAGCTCATGCGAGCTAAATAACGGG
48687862 AAGCTCAT
1 AAGCTCAT
48687870 AAGAGTTGTG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 47 1.00
ACGTcount: A:0.30, C:0.18, G:0.29, T:0.23
Consensus pattern (25 bp):
AAGCTCATGCGAGCTAAATAACGGG
Found at i:48691768 original size:27 final size:27
Alignment explanation
Indices: 48691717--48691788 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
48691707 TAGTGGAGGG
* *
48691717 ACTGCCACAGGTGGCACCAATGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
* * *
48691744 AGTGGCAGAGGCGGCACCAAAGGTGCC
1 ACTGCCACAGGCGGCACCAAAGGTGCC
48691771 ACTGCCACAGGCGGCACC
1 ACTGCCACAGGCGGCACC
48691789 CCCTTTATTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.10
Consensus pattern (27 bp):
ACTGCCACAGGCGGCACCAAAGGTGCC
Found at i:48692180 original size:157 final size:156
Alignment explanation
Indices: 48691894--48692216 Score: 486
Period size: 157 Copynumber: 2.1 Consensus size: 156
48691884 TACGAAAAGA
* * * *
48691894 AATAAAAAATGAAAATAGTATATTTACTGAAAGTAATAAAATCCGAAAAAGGAAAAATACGAACA
1 AATAAAATACGAAAATAATATATTTACTGAAAGTAATAAAATCCGAAAAAAGAAAAATACGAACA
*
48691959 AAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACATACTAAAATAATAGATTTCAA
66 AAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACA-ACTAAAATAATACATTTCAA
*
48692024 ACATTATGTACTAAAATAATATAAAAT
130 ACATTATGTAATAAAATAATATAAAAT
** *
48692051 AATAAAATACGAAAATAATATATTTTTTGAAAGTAATAAAATCTGAAAATAAGAAAAATACGAAC
1 AATAAAATACGAAAATAATATATTTACTGAAAGTAATAAAATCCGAAAA-AAGAAAAATACGAAC
* * * *
48692116 AAATGGCCAAAATGAGGGTTTTTTACTAAATTTATATAAAAATAC-ACTAAATTAATACATTTCA
65 AAAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAA-ACAACTAAAATAATACATTTCA
*
48692180 AACTTTATGTAATAAAATAATATAAAAT
129 AACATTATGTAATAAAATAATATAAAAT
48692208 AATAAAATA
1 AATAAAATA
48692217 GTATTAATTC
Statistics
Matches: 150, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
157 95 0.63
158 53 0.35
159 2 0.01
ACGTcount: A:0.54, C:0.08, G:0.09, T:0.28
Consensus pattern (156 bp):
AATAAAATACGAAAATAATATATTTACTGAAAGTAATAAAATCCGAAAAAAGAAAAATACGAACA
AAGGGCCAAAATAAGGGTTTTTCACTAAATTTATATAAAAAACAACTAAAATAATACATTTCAAA
CATTATGTAATAAAATAATATAAAAT
Found at i:48692471 original size:160 final size:159
Alignment explanation
Indices: 48692226--48692525 Score: 460
Period size: 160 Copynumber: 1.9 Consensus size: 159
48692216 AGTATTAATT
*
48692226 CATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAATCTTCATTT
1 CATAATATTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAATCTTCATTT
**
48692291 TGGCCATTTGTTCGTATTTTTCTTATTTT-CGGATTTTATTACTTTCAAAAAATATACTATTTTC
66 TGGCCATTTGTTCGTATTTTTCTTATTTTCCAAATTTTATTACTTTCAAAAAATATACTATTTTC
48692355 GTATTTTATTATTTTATATTATTTTAGTA
131 GTATTTTATTATTTTATATTATTTTAGTA
*
48692384 CATAATATTTGAAATGTATTATTTTAGTGTGTTTTTTTTATATAAATTTAGTGAAAAACTCTT-A
1 CATAATATTTGAAATGTATTATTTTAGTGTG--TTTTTTATATAAATTTAGT-AAAAAATCTTCA
* * * **
48692448 TTTTGGCCCTTTGTTCGTATTTTTGTTTTTTTCCAAATTTTATTACTTTCAGTAAATATACTATT
63 TTTTGGCCATTTGTTCGTATTTTTCTTATTTTCCAAATTTTATTACTTTCAAAAAATATACTATT
* *
48692513 TTTGTTTTTTATT
128 TTCGTATTTTATT
48692526 TCTTTCCGTA
Statistics
Matches: 127, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
158 30 0.24
160 49 0.39
161 48 0.38
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (159 bp):
CATAATATTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGTAAAAAATCTTCATTT
TGGCCATTTGTTCGTATTTTTCTTATTTTCCAAATTTTATTACTTTCAAAAAATATACTATTTTC
GTATTTTATTATTTTATATTATTTTAGTA
Found at i:48719561 original size:15 final size:15
Alignment explanation
Indices: 48719543--48719572 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
48719533 ATAAATGCAG
48719543 AAAAATTAAAGTATT
1 AAAAATTAAAGTATT
*
48719558 AAAAATTTAAGTATT
1 AAAAATTAAAGTATT
48719573 CAATTTAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (15 bp):
AAAAATTAAAGTATT
Found at i:48722012 original size:3 final size:3
Alignment explanation
Indices: 48722004--48722056 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
48721994 AGGTATTCAT
48722004 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48722052 TTA TT
1 TTA TT
48722057 GTGTTGTGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:48742322 original size:20 final size:19
Alignment explanation
Indices: 48742297--48742335 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
48742287 GTGCGTCTGC
48742297 TTCTTTCCTTCTTTCTCTTT
1 TTCTTTCCTTCTTT-TCTTT
*
48742317 TTCTTTCTTTCTTTTCTTT
1 TTCTTTCCTTCTTTTCTTT
48742336 CTAATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (19 bp):
TTCTTTCCTTCTTTTCTTT
Found at i:48744909 original size:2 final size:2
Alignment explanation
Indices: 48744902--48744934 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
48744892 TCATTTTTAT
48744902 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48744935 CAAATGCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48745023 original size:41 final size:41
Alignment explanation
Indices: 48744966--48745078 Score: 192
Period size: 41 Copynumber: 2.8 Consensus size: 41
48744956 TTTAACGTAT
* *
48744966 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCCA-A
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-CAGA
48745007 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
48745048 TCACCGGCACTTAGCCTGCTAGGTTTATAAC
1 TCACCGGCACTTAGCCTGCTAGGTTTATAAC
48745079 TGCAATGACT
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
40 2 0.03
41 67 0.97
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:48746724 original size:25 final size:25
Alignment explanation
Indices: 48746696--48746777 Score: 103
Period size: 25 Copynumber: 3.3 Consensus size: 25
48746686 ACTTTAGCGC
*
48746696 GCTCTTTGATTATTAGCACGTTAGT
1 GCTCTCTGATTATTAGCACGTTAGT
* * * *
48746721 GCTCTCTGACTACTAGAACGTTGGT
1 GCTCTCTGATTATTAGCACGTTAGT
*
48746746 GCTCTCTGATT-TTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTTAGT
48746770 GCTCTCTG
1 GCTCTCTG
48746778 TTTAGCACAT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 17 0.36
25 30 0.64
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.38
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTAGT
Found at i:48746792 original size:13 final size:13
Alignment explanation
Indices: 48746774--48746803 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
48746764 GTCAGTGCTC
48746774 TCTGTTTAGCACA
1 TCTGTTTAGCACA
48746787 TCTG-TTAGCACA
1 TCTGTTTAGCACA
48746799 TCTGT
1 TCTGT
48746804 GCTCTCTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (13 bp):
TCTGTTTAGCACA
Found at i:48746818 original size:22 final size:21
Alignment explanation
Indices: 48746787--48746835 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
48746777 GTTTAGCACA
48746787 TCTGTTAGCACATCT-GTGCTC
1 TCTGTTAGCAC-TCTAGTGCTC
*
48746808 TCTGTATAGCACTTTAGTGCTC
1 TCTGT-TAGCACTCTAGTGCTC
48746830 TCTGTT
1 TCTGTT
48746836 CATTAGTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (21 bp):
TCTGTTAGCACTCTAGTGCTC
Found at i:48747765 original size:2 final size:2
Alignment explanation
Indices: 48747758--48747795 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
48747748 AGAATTTTAC
48747758 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48747796 TCACCTATTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48752842 original size:3 final size:3
Alignment explanation
Indices: 48752834--48752884 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
48752824 CAAGCCTGTT
* * * *
48752834 TCA TCA TCA ACA TCA TCA TCG TCCA -CA CCA TTA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA T-CA TCA TCA TCA TCA TCA TCA TCA
48752879 TCA TCA
1 TCA TCA
48752885 CTGTCATCTC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.92
4 1 0.03
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.29
Consensus pattern (3 bp):
TCA
Found at i:48760963 original size:17 final size:18
Alignment explanation
Indices: 48760933--48760974 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
48760923 TCGAAATTCA
*
48760933 TCAAATTAACTAATTT-TC
1 TCAAA-TAAATAATTTATC
48760951 TCAAATAAATAATTTATC
1 TCAAATAAATAATTTATC
48760969 -CAAATA
1 TCAAATA
48760975 TTCTAAGCCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
TCAAATAAATAATTTATC
Found at i:48762422 original size:43 final size:42
Alignment explanation
Indices: 48762375--48762476 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 42
48762365 CTAATGTCCT
*
48762375 AGACATAGTCTTACATGTTTCCTCACTTCGATTCCAATATCCC
1 AGACAT-GTCTTACATGTTTCCTCACTTCGATGCCAATATCCC
* * * *
48762418 AGACATGATCTTACACGTTTTCTCACTTCGATGCTAATGTCCC
1 AGACATG-TCTTACATGTTTCCTCACTTCGATGCCAATATCCC
*
48762461 AAACATGGTCTTACAT
1 AGACAT-GTCTTACAT
48762477 CAGAAGTCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 1 0.02
43 48 0.96
44 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.34
Consensus pattern (42 bp):
AGACATGTCTTACATGTTTCCTCACTTCGATGCCAATATCCC
Found at i:48764246 original size:19 final size:19
Alignment explanation
Indices: 48764222--48764313 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
48764212 AATCATATCT
48764222 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
48764241 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
48764260 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
48764279 TCCAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
48764298 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
48764314 CTTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:48764271 original size:38 final size:38
Alignment explanation
Indices: 48764199--48764313 Score: 176
Period size: 38 Copynumber: 2.9 Consensus size: 38
48764189 AAATTAAATC
*
48764199 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
48764241 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
48764279 TCCAAGATTACATATCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
48764314 CTTGAAGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
38 53 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:48765139 original size:88 final size:88
Alignment explanation
Indices: 48764975--48765819 Score: 890
Period size: 88 Copynumber: 9.6 Consensus size: 88
48764965 ATAAGACTGA
* * * * * *
48764975 TGTCTTCGATCTGCTTCACTGCTAGTAAAGGAAGGCAAGATCTACTATTTTCAACCTACTCCACT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
** * *
48765040 GC-TGCTCAGGGAGACAAGGCCGG
66 GCAACCT-AGGGAGGCAAGGCTGG
* * * **
48765063 AGT-TTTCAATCTGCTTCACTGCCGGTACAGGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCAC
1 TGTCTTT-GATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
* * *
48765127 TGCAACCTAGGGAGGTAAGACCGG
65 TGCAACCTAGGGAGGCAAGGCTGG
* * * * * * * *
48765151 TGTCTTCGATCAGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATTTTCAACCTACTCCGCT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
48765216 GCAACCCAGGGAGGCAAGGCTGG
66 GCAACCTAGGGAGGCAAGGCTGG
** * * **
48765239 TGTCTTTGATCTGCTTCGTTGCCGGTACAAGAAGGCAAGATCTGCTATCTTCAGTCTGCTCCACT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
* * *
48765304 GTAACCTAAGGAGGCAAGACTGG
66 GCAACCTAGGGAGGCAAGGCTGG
* * * *
48765327 TGTCTTTGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATGTGCTATTTTCAACCTGCTCCGCT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
** *
48765392 GCAATCC-AGGGAAACAAGGCTAG
66 GCAA-CCTAGGGAGGCAAGGCTGG
** * * * * * ** *
48765415 TGTCTTTGATCTGCTTCGTTGTCGGTACAAGAAGGTAGGATCTGCTATCTTCAGTCTACTCCACT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
*
48765480 GCAACCTAGGGAGGCAAGACTGG
66 GCAACCTAGGGAGGCAAGGCTGG
* * * **
48765503 TGTCTTTGATCTACTTCACTGTCAGTACAGGAAGGTAAGATCTGCTA-CTTTCAACCTGCTCCGT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATC-TTCAACCTGCTCCAC
* * *
48765567 TACAACCCAGGGAGGCAAGGCTAG
65 TGCAACCTAGGGAGGCAAGGCTGG
** * * **
48765591 TGTCTTTGATCTGCTTCGTTGCCAGTACAAGAAGGCAAGATCTACTATCTTCAGTCTGCTCCACT
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
* *
48765656 ACAACCTAGGGAGGCAAGACTGG
66 GCAACCTAGGGAGGCAAGGCTGG
* * * ***
48765679 TGTCTTTGATCTACTTCACTGTCAGTACAGGAAGGTAAGATCTGCTA-CTTTCAACCTGCTTTGC
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATC-TTCAACCTGCTCCAC
* * *
48765743 TACAACCCAGGAAGGCAAGGCTGG
65 TGCAACCTAGGGAGGCAAGGCTGG
*
48765767 TGTCTTTGATCTGCTTCACTGCCGGTACAGGAAGGCAAGATCTGCTATCTTCA
1 TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCA
48765820 CTGATCTGTT
Statistics
Matches: 619, Mismatches: 129, Indels: 18
0.81 0.17 0.02
Matches are distributed among these distances:
87 6 0.01
88 605 0.98
89 8 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (88 bp):
TGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
GCAACCTAGGGAGGCAAGGCTGG
Found at i:48765275 original size:176 final size:176
Alignment explanation
Indices: 48764967--48765819 Score: 1174
Period size: 176 Copynumber: 4.8 Consensus size: 176
48764957 TCAAGGCAAT
* * * * *
48764967 AAGACTGATGTCTTCGATCTGCTTCACTG-CTAGTAAAGGAAGGCAAGATCTACTATTTTCAACC
1 AAGACTGGTGTCTTTGATCAGCTTCACTGTC-AGTACAGGAAGGCAAGATCTGCTATTTTCAACC
* * ** * * * * * ** *
48765031 TACTCCACTGCTGCTCAGGGAGACAAGGCCGGAGT-TTTCAATCTGCTTCACTGCCGGTACAGGA
65 TGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTT-GATCTGCTTCGTTGCCGGTACAAGA
*
48765095 AGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGT
129 AGGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* * * *
48765143 AAGACCGGTGTCTTCGATCAGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGTTATTTTCAACCT
1 AAGACTGGTGTCTTTGATCAGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCT
*
48765208 ACTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGCCGGTACAAGAAG
66 GCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGCCGGTACAAGAAG
* *
48765273 GCAAGATCTGCTATCTTCAGTCTGCTCCACTGTAACCTAAGGAGGC
131 GCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* *
48765319 AAGACTGGTGTCTTTGATCTGCTTCACTGTCAGTACAGGAAGGCAAGATGTGCTATTTTCAACCT
1 AAGACTGGTGTCTTTGATCAGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCT
* ** * *
48765384 GCTCCGCTGCAATCCAGGGAAACAAGGCTAGTGTCTTTGATCTGCTTCGTTGTCGGTACAAGAAG
66 GCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGCCGGTACAAGAAG
* * *
48765449 GTAGGATCTGCTATCTTCAGTCTACTCCACTGCAACCTAGGGAGGC
131 GCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* *
48765495 AAGACTGGTGTCTTTGATCTA-CTTCACTGTCAGTACAGGAAGGTAAGATCTGCTACTTTCAACC
1 AAGACTGGTGTCTTTGATC-AGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACC
* * * *
48765559 TGCTCCGTTACAACCCAGGGAGGCAAGGCTAGTGTCTTTGATCTGCTTCGTTGCCAGTACAAGAA
65 TGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGCCGGTACAAGAA
* *
48765624 GGCAAGATCTACTATCTTCAGTCTGCTCCACTACAACCTAGGGAGGC
130 GGCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
* *
48765671 AAGACTGGTGTCTTTGATCTA-CTTCACTGTCAGTACAGGAAGGTAAGATCTGCTACTTTCAACC
1 AAGACTGGTGTCTTTGATC-AGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACC
** * * ** *
48765735 TGCTTTGCTACAACCCAGGAAGGCAAGGCTGGTGTCTTTGATCTGCTTCACTGCCGGTACAGGAA
65 TGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGCCGGTACAAGAA
48765800 GGCAAGATCTGCTATCTTCA
130 GGCAAGATCTGCTATCTTCA
48765820 CTGATCTGTT
Statistics
Matches: 610, Mismatches: 64, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
176 606 0.99
177 4 0.01
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (176 bp):
AAGACTGGTGTCTTTGATCAGCTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATTTTCAACCT
GCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGTTGCCGGTACAAGAAG
GCAAGATCTGCTATCTTCAGTCTGCTCCACTGCAACCTAGGGAGGC
Found at i:48767041 original size:21 final size:23
Alignment explanation
Indices: 48766999--48767042 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
48766989 TCACATTGGC
*
48766999 CTCTCCATTTTCTTTCTTCTTTT
1 CTCTCCATTTTCTTTCTACTTTT
*
48767022 CTCTCTATTTT-TTT-TACTTTT
1 CTCTCCATTTTCTTTCTACTTTT
48767043 TTTTATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (23 bp):
CTCTCCATTTTCTTTCTACTTTT
Found at i:48768037 original size:25 final size:26
Alignment explanation
Indices: 48767986--48768040 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
48767976 AAGAAAATCC
* **
48767986 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
48768012 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
48768037 AAAA
1 AAAA
48768041 TAAATGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:48770619 original size:18 final size:18
Alignment explanation
Indices: 48770596--48770630 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48770586 CCTGCAAGTT
48770596 TTCAAACACAA-TTCAATA
1 TTCAAAC-CAAGTTCAATA
48770614 TTCAAACCAAGTTCAAT
1 TTCAAACCAAGTTCAAT
48770631 TGTATAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.46, C:0.23, G:0.03, T:0.29
Consensus pattern (18 bp):
TTCAAACCAAGTTCAATA
Found at i:48771836 original size:27 final size:27
Alignment explanation
Indices: 48771801--48771878 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
48771791 CCAATGATTC
* *
48771801 GGGGAATCAACACTTAGCAACTCCTCG
1 GGGGAATCAGCACTTAGCAACCCCTCG
*
48771828 GGGGAATCAGCACTTAGCAACCCCTTG
1 GGGGAATCAGCACTTAGCAACCCCTCG
*
48771855 GGGGAATCAGCATTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
48771879 CTTCACATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.18
Consensus pattern (27 bp):
GGGGAATCAGCACTTAGCAACCCCTCG
Found at i:48771907 original size:129 final size:129
Alignment explanation
Indices: 48771729--48771980 Score: 389
Period size: 129 Copynumber: 2.0 Consensus size: 129
48771719 ATGAGTCGGA
* ** * ** *
48771729 GAATCAGCACTTAGGAACCCTTTTCACATTTAAGATACGGTGGGTTCAGCACTTAGCAACCACCA
1 GAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGAAACCACCA
* *
48771794 ATGATTCGGGGAATCAACACTTAGCAACTCC-TCGGGGGAATCAGCACTTAGCAACCCCTTGGGG
66 ATGATTCGGGGAATCAACACTTAACAAC-CCATCAGGGGAATCAGCACTTAGCAACCCCTTGGGG
*
48771858 GAATCAGCATTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGAAACCACCA
1 GAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGAAACCACCA
*
48771923 ATGATTCGGGGAATCAGCACTTAACAACCCATCAGGGGAATCAGCACTTAGCAACCCC
66 ATGATTCGGGGAATCAACACTTAACAACCCATCAGGGGAATCAGCACTTAGCAACCCC
48771981 CTTTTTATTC
Statistics
Matches: 111, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
128 2 0.02
129 109 0.98
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.21
Consensus pattern (129 bp):
GAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGAAACCACCA
ATGATTCGGGGAATCAACACTTAACAACCCATCAGGGGAATCAGCACTTAGCAACCCCTTGGGG
Found at i:48772353 original size:30 final size:30
Alignment explanation
Indices: 48772319--48772376 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
48772309 CCACCCAACT
*
48772319 TTTTGAAAAATTATAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
48772349 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
48772377 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:48779258 original size:33 final size:33
Alignment explanation
Indices: 48779211--48779436 Score: 158
Period size: 33 Copynumber: 6.5 Consensus size: 33
48779201 TACGATGGGT
*
48779211 TCAGTACTTAGCAACCACCAATGATTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
*
48779244 TCAGCACTTAGCAACC-CC-----TTGGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* * *
48779271 TCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGGTGAAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGAA
*
48779313 TCAGCACTTAGCAACCACCAATGAGTCGGGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
* * *
48779346 TCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAA
1 TCAGCACTTAGCAA-CCAC--CA-A--T--GATTCGG-GGAA
*
48779388 TCAGCACTTAGCAACCACCAATGATTCGAGGAA
1 TCAGCACTTAGCAACCACCAATGATTCGGGGAA
48779421 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
48779437 CCTCGAGGGA
Statistics
Matches: 152, Mismatches: 17, Indels: 48
0.70 0.08 0.22
Matches are distributed among these distances:
27 22 0.14
28 2 0.01
29 1 0.01
31 1 0.01
32 2 0.01
33 52 0.34
34 12 0.08
36 4 0.03
37 1 0.01
38 2 0.01
39 5 0.03
41 13 0.09
42 35 0.23
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.20
Consensus pattern (33 bp):
TCAGCACTTAGCAACCACCAATGATTCGGGGAA
Found at i:48779328 original size:42 final size:41
Alignment explanation
Indices: 48779267--48779403 Score: 164
Period size: 42 Copynumber: 3.5 Consensus size: 41
48779257 ACCCCTTGGG
48779267 GGAATCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACA-TTAAGATACGGT
* * *
48779309 GAAATCAGCACTTAGCAA-CCAC--CA-A-TGAG-T-CGG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGGT
*
48779342 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACA-TTAAGATACGGT
48779384 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
48779404 ACCAATGATT
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
33 17 0.22
34 6 0.08
35 1 0.01
36 5 0.06
37 1 0.01
38 1 0.01
39 4 0.05
40 1 0.01
41 6 0.08
42 37 0.47
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTAAGATACGGT
Found at i:48779345 original size:102 final size:102
Alignment explanation
Indices: 48779169--48779363 Score: 309
Period size: 102 Copynumber: 1.9 Consensus size: 102
48779159 ATCGGTGGAT
** * *** *
48779169 TCAGCACTTAGCAACCCTTTTCACATTTAAGATACGATGGGTTCAGTACTTAGCAACCACCAATG
1 TCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGATGAAATCAGCACTTAGCAACCACCAATG
*
48779234 ATTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAA
66 AGTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAA
*
48779271 TCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGGTGAAATCAGCACTTAGCAACCACCAATG
1 TCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGATGAAATCAGCACTTAGCAACCACCAATG
48779336 AGTCGGGGAATCAGCACTTAGCAACCCC
66 AGTCGGGGAATCAGCACTTAGCAACCCC
48779364 CTTCACATTT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 84 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (102 bp):
TCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGATGAAATCAGCACTTAGCAACCACCAATG
AGTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAA
Found at i:48779359 original size:75 final size:75
Alignment explanation
Indices: 48779265--48779438 Score: 303
Period size: 75 Copynumber: 2.3 Consensus size: 75
48779255 CAACCCCTTG
*
48779265 GGGGAATCAGCACTTAGCAACCCCCTTCACAGTTAAGATACGGTGAAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAGTTAAAATACGGTGAAATCAGCACTTAGCAACCA
48779330 CCAATGAGTC
66 CCAATGAGTC
* *
48779340 GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCA
1 GGGGAATCAGCACTTAGCAACCCCCTTCACAGTTAAAATACGGTGAAATCAGCACTTAGCAACCA
*
48779405 CCAATGATTC
66 CCAATGAGTC
*
48779415 GAGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
48779439 TCGAGGGAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 94 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (75 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCACAGTTAAAATACGGTGAAATCAGCACTTAGCAACCA
CCAATGAGTC
Found at i:48779442 original size:26 final size:27
Alignment explanation
Indices: 48779413--48779465 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
48779403 CACCAATGAT
*
48779413 TCGA-GGAATCAGCACTTAGCAACCCC
1 TCGAGGGAATCAACACTTAGCAACCCC
48779439 TCGAGGGAATCAACACTTAGCAACCCC
1 TCGAGGGAATCAACACTTAGCAACCCC
48779466 CTTTTTATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.32, C:0.34, G:0.19, T:0.15
Consensus pattern (27 bp):
TCGAGGGAATCAACACTTAGCAACCCC
Found at i:48779835 original size:31 final size:30
Alignment explanation
Indices: 48779804--48779861 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
48779794 CCACTCAACT
48779804 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
48779834 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
48779862 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:48782311 original size:42 final size:42
Alignment explanation
Indices: 48782255--48782401 Score: 143
Period size: 43 Copynumber: 3.5 Consensus size: 42
48782245 TTACGGCGCT
* * *
48782255 TTTTCCACAAACGCCGTTATAGATCATGACCTTTAGCGACGC
1 TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGACGC
* * * * *
48782297 TTTTACACAAACGCCGCTATAGCTCAGGATCTTTAACGACAC
1 TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGACGC
* * *
48782339 TTTTTTCAAAAACGCCACTATA-ACTCAAGACCTTTAGCGACGC
1 -TTTTACACAAACGCCGCTATAGA-TCAAGACCTTTAGCGACGC
* *
48782382 TTTGATTACAAACGCCGCTA
1 TTTTA-CACAAACGCCGCTA
48782402 AAAGTACCGT
Statistics
Matches: 82, Mismatches: 20, Indels: 5
0.77 0.19 0.05
Matches are distributed among these distances:
42 38 0.46
43 44 0.54
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.28
Consensus pattern (42 bp):
TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGACGC
Found at i:48787257 original size:15 final size:14
Alignment explanation
Indices: 48787215--48787265 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
48787205 AGTTAAGTAA
**
48787215 TTTTATAAAACATT
1 TTTTATAAATTATT
*
48787229 TTTTAT-TATTATT
1 TTTTATAAATTATT
48787242 TTTTATAAATTGATT
1 TTTTATAAATT-ATT
48787257 TTTTATAAA
1 TTTTATAAA
48787266 ATAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 10 0.32
14 9 0.29
15 12 0.39
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
TTTTATAAATTATT
Found at i:48788121 original size:16 final size:17
Alignment explanation
Indices: 48788085--48788126 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
48788075 CACTATAATC
48788085 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
48788103 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
48788119 ATTATTTA
1 ATTATTTA
48788127 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:48788267 original size:14 final size:14
Alignment explanation
Indices: 48788233--48788293 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
48788223 ACTAATTAAT
* *
48788233 CTAATCCCTAAATC
1 CTAACCCCTAACTC
48788247 CTAAACCCCTAACTC
1 CT-AACCCCTAACTC
* *
48788262 TTAA-CCCTCAACCC
1 CTAACCCCT-AACTC
48788276 CTAACCCCTAACTC
1 CTAACCCCTAACTC
48788290 CTAA
1 CTAA
48788294 ACCTTAAACC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.11
14 19 0.50
15 15 0.39
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAACCCCTAACTC
Found at i:48788269 original size:28 final size:27
Alignment explanation
Indices: 48788238--48788365 Score: 82
Period size: 28 Copynumber: 4.6 Consensus size: 27
48788228 TTAATCTAAT
48788238 CCCTAAATCCTAAACCCCTAACTCTTAA
1 CCCTAAA-CCTAAACCCCTAACTCTTAA
* *
48788266 CCCTCAACCCCT-AACCCCTAACTCCTAAA
1 CCCT-AA-ACCTAAACCCCTAACT-CTTAA
* ** *
48788295 CCTTAAACCCCAACCCTTAA-TCTATAA
1 CCCTAAACCTAAACCCCTAACTCT-TAA
* * *
48788322 CCTTAAACCATAAA-CCGTAACCCTTAAA
1 CCCTAAACC-TAAACCCCTAACTCTT-AA
48788350 CCCTAAACCCTAAACC
1 CCCTAAA-CCTAAACC
48788366 TTAAACCATA
Statistics
Matches: 78, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
26 2 0.03
27 20 0.26
28 41 0.53
29 15 0.19
ACGTcount: A:0.37, C:0.41, G:0.01, T:0.21
Consensus pattern (27 bp):
CCCTAAACCTAAACCCCTAACTCTTAA
Found at i:48788301 original size:7 final size:7
Alignment explanation
Indices: 48788291--48788400 Score: 64
Period size: 7 Copynumber: 15.9 Consensus size: 7
48788281 CCCTAACTCC
48788291 TAAACCT
1 TAAACCT
*
48788298 TAAACCC
1 TAAACCT
* *
48788305 CAACCCT
1 TAAACCT
*
48788312 T-AATCT
1 TAAACCT
48788318 ATA-ACCT
1 -TAAACCT
*
48788325 TAAACCA
1 TAAACCT
*
48788332 TAAACCG
1 TAAACCT
*
48788339 TAACCCT
1 TAAACCT
*
48788346 TAAACCC
1 TAAACCT
*
48788353 TAAACCC
1 TAAACCT
48788360 TAAACCT
1 TAAACCT
*
48788367 TAAACCA
1 TAAACCT
48788374 TAAA-CT
1 TAAACCT
*
48788380 GTAAACCA
1 -TAAACCT
* *
48788388 TAACCCC
1 TAAACCT
48788395 TAAACC
1 TAAACC
48788401 CATAATTCAT
Statistics
Matches: 77, Mismatches: 21, Indels: 10
0.71 0.19 0.09
Matches are distributed among these distances:
6 6 0.08
7 70 0.91
8 1 0.01
ACGTcount: A:0.43, C:0.35, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAACCT
Found at i:48788323 original size:27 final size:29
Alignment explanation
Indices: 48788250--48788330 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
48788240 CTAAATCCTA
* * *
48788250 AACCCCTAACT-CTTAACCCTCAACCCCT
1 AACCCCTAACTCCTAAACCTTAAACCCCT
48788278 AACCCCTAACTCCTAAACCTTAAACCCC-
1 AACCCCTAACTCCTAAACCTTAAACCCCT
*
48788306 AACCCTTAA-T-CTATAACCTTAAACC
1 AACCCCTAACTCCTA-AACCTTAAACC
48788331 ATAAACCGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 3 0.06
27 12 0.26
28 19 0.40
29 13 0.28
ACGTcount: A:0.35, C:0.43, G:0.00, T:0.22
Consensus pattern (29 bp):
AACCCCTAACTCCTAAACCTTAAACCCCT
Found at i:48788337 original size:14 final size:14
Alignment explanation
Indices: 48788291--48788456 Score: 95
Period size: 14 Copynumber: 11.9 Consensus size: 14
48788281 CCCTAACTCC
*
48788291 TAAACCTTAAACCC
1 TAAACCTTAAACCA
* * * *
48788305 CAACCCTTAATCTA
1 TAAACCTTAAACCA
48788319 T-AACCTTAAACCA
1 TAAACCTTAAACCA
* * *
48788332 TAAACCGTAACCCT
1 TAAACCTTAAACCA
* *
48788346 TAAACCCTAAACCC
1 TAAACCTTAAACCA
48788360 TAAACCTTAAACCA
1 TAAACCTTAAACCA
48788374 TAAA-CTGTAAACCA
1 TAAACCT-TAAACCA
* *
48788388 TAACCCCTAAACCCA
1 TAAACCTTAAA-CCA
** * * *
48788403 TAATTCATAAAACT
1 TAAACCTTAAACCA
*
48788417 TAAA-CTCTATACCA
1 TAAACCT-TAAACCA
* *
48788431 TATACCCTAAACCA
1 TAAACCTTAAACCA
*
48788445 AAAACCTTAAAC
1 TAAACCTTAAAC
48788457 TATAGAGATA
Statistics
Matches: 111, Mismatches: 35, Indels: 12
0.70 0.22 0.08
Matches are distributed among these distances:
13 13 0.12
14 85 0.77
15 13 0.12
ACGTcount: A:0.45, C:0.32, G:0.01, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:48788346 original size:21 final size:21
Alignment explanation
Indices: 48788320--48788400 Score: 99
Period size: 21 Copynumber: 3.9 Consensus size: 21
48788310 CTTAATCTAT
48788320 AACCTTAAACCATAAACCGTA
1 AACCTTAAACCATAAACCGTA
* * *
48788341 ACCCTTAAACCCTAAACCCTA
1 AACCTTAAACCATAAACCGTA
*
48788362 AACCTTAAACCATAAACTGTA
1 AACCTTAAACCATAAACCGTA
* * *
48788383 AACCATAACCCCTAAACC
1 AACCTTAAACCATAAACC
48788401 CATAATTCAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (21 bp):
AACCTTAAACCATAAACCGTA
Found at i:48788850 original size:41 final size:41
Alignment explanation
Indices: 48788764--48788972 Score: 233
Period size: 41 Copynumber: 4.9 Consensus size: 41
48788754 AAATGTTTTT
*
48788764 GCGGCGCTTTTACAAAAACGCCGCTAAAG-CCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * *
48788804 GCGGCGCTTTTCCAAAAACGCTGTTAAAGCCCTGAGTATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
*
48788845 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAG-CCCTGAGCATTA
48788887 GCGGCG-TTTCTCCAAAAACGCCGCAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTT-TCC----A------AAAACGCCGCTAAAGCCCTGAGCATTA
* *
48788938 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
1 GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGA
48788973 AAGGTAAGAA
Statistics
Matches: 144, Mismatches: 11, Indels: 27
0.79 0.06 0.15
Matches are distributed among these distances:
40 26 0.18
41 59 0.41
42 20 0.14
46 1 0.01
47 1 0.01
51 20 0.14
52 17 0.12
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:48788892 original size:42 final size:42
Alignment explanation
Indices: 48788764--48788969 Score: 229
Period size: 42 Copynumber: 4.8 Consensus size: 42
48788754 AAATGTTTTT
* *
48788764 GCGGCGCTTTTACAAAAACGCCGCTAAAG--CCTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
* * * *
48788804 GCGGCGCTTTTCCAAAAACGCTGTTAAAG-CCCTGAGTATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
48788845 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
* *
48788887 GCGGCGTTTCTCCAAAAACGCCGCAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTCCAAAAACGCCGCTAAA----GC-----CCCTGAGCATTA
*
48788938 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCC
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCC
48788970 TGAAAGGTAA
Statistics
Matches: 142, Mismatches: 13, Indels: 20
0.81 0.07 0.11
Matches are distributed among these distances:
40 26 0.18
41 36 0.25
42 39 0.27
46 2 0.01
47 2 0.01
51 37 0.26
ACGTcount: A:0.28, C:0.32, G:0.22, T:0.18
Consensus pattern (42 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCCTGAGCATTA
Found at i:48788943 original size:51 final size:52
Alignment explanation
Indices: 48788859--48788961 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 52
48788849 CGCTTCTCCA
* *
48788859 AAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGTTTCTCCAAAAACGCCGC
1 AAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTCTACAAAAACGCCGC
48788911 AAAACGCCGCTAAAG-CCCTGAGCATTAGCGGCGCTTCTACAAAAACGCCGC
1 AAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTCTACAAAAACGCCGC
48788962 TAAAGCCCTG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 34 0.69
52 15 0.31
ACGTcount: A:0.30, C:0.34, G:0.21, T:0.15
Consensus pattern (52 bp):
AAAACGCCGCTAAAGCCCCTGAGCATTAGCGGCGCTTCTACAAAAACGCCGC
Found at i:48789861 original size:19 final size:19
Alignment explanation
Indices: 48789837--48789928 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
48789827 AATCATATCT
48789837 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
48789856 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
48789875 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
48789894 TCTAAGATTACATACCATA
1 TCTAAGATTGCATATCATA
48789913 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
48789929 CTTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:48789886 original size:38 final size:38
Alignment explanation
Indices: 48789814--48789928 Score: 176
Period size: 38 Copynumber: 2.9 Consensus size: 38
48789804 AAATTAAATC
*
48789814 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
48789856 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
48789894 TCTAAGATTACATACCATATCTAAGATTGCATATC
1 TCTAAGATTACATATCATATCTAAGATTGCATATC
48789929 CTTGAAGATT
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
38 53 0.75
41 7 0.10
42 11 0.15
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:48790191 original size:64 final size:63
Alignment explanation
Indices: 48790094--48790427 Score: 551
Period size: 64 Copynumber: 5.2 Consensus size: 63
48790084 TATTACAAGA
* * * *
48790094 TCAATTCGGCAATAGGTATATACCCATACAATTCAATTCAGCAATATATGTATACATATACAAT
1 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTC-GCAATATAAGTATATATATACAAT
48790158 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATATATACAAT
1 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCG-CAATATAAGTATATATATACAAT
*
48790222 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCATCAATATAAGTATATATATACAAT
1 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTC-GCAATATAAGTATATATATACAAT
**
48790286 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGTCAATATAAGTATATGCATACAAT
1 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCG-CAATATAAGTATATATATACAAT
*
48790350 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAAT
1 TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTC-GCAATATAAGTATATATATACAAT
48790414 TCAATTCGGCAATA
1 TCAATTCGGCAATA
48790428 TATAGCCATG
Statistics
Matches: 255, Mismatches: 11, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
63 1 0.00
64 253 0.99
65 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (63 bp):
TCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGCAATATAAGTATATATATACAAT
Found at i:48790428 original size:32 final size:32
Alignment explanation
Indices: 48790094--48790429 Score: 390
Period size: 32 Copynumber: 10.5 Consensus size: 32
48790084 TATTACAAGA
*
48790094 TCAATTCGGCAATAGGT-A-TATACCCATACAAT
1 TCAATTCGGCAATA--TAAGTATACCTATACAAT
* * *
48790126 TCAATTCAGCAATATATGTATACATATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
***
48790158 TCAATTCGGCAATAGGTGTATACCTATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
* **
48790190 TCAATTCGTCAATATAAGTATATATATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
***
48790222 TCAATTCGGCAATAGGTGTATACCTATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
** **
48790254 TCAATTCATCAATATAAGTATATATATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
***
48790286 TCAATTCGGCAATAGGTGTATACCTATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
* *
48790318 TCAATTCGTCAATATAAGTATATGC-ATACAAT
1 TCAATTCGGCAATATAAGTATA-CCTATACAAT
***
48790350 TCAATTCGGCAATAGGTGTATACCTATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
*
48790382 TCAATTCGGCAATATAAGTATACATATACAAT
1 TCAATTCGGCAATATAAGTATACCTATACAAT
48790414 TCAATTCGGCAATATA
1 TCAATTCGGCAATATA
48790430 TAGCCATGTA
Statistics
Matches: 252, Mismatches: 48, Indels: 8
0.82 0.16 0.03
Matches are distributed among these distances:
30 1 0.00
31 1 0.00
32 249 0.99
33 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (32 bp):
TCAATTCGGCAATATAAGTATACCTATACAAT
Found at i:48792637 original size:54 final size:55
Alignment explanation
Indices: 48792554--48792657 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 55
48792544 TCTTCCACGG
*
48792554 AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATTTTTTCCTTGA
1 AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATCTTTTCCTTGA
* * *
48792609 AGAAACTTTCAG-GATACTCGATCGCCAACTGTAAATTCAATATCTTTTC
1 AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATCTTTTC
48792658 TTTTCAGATC
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 33 0.73
55 12 0.27
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.33
Consensus pattern (55 bp):
AGAAACTTTCAGAAATACTCGATCACCAACTGCAAATTCAATATCTTTTCCTTGA
Found at i:48795544 original size:15 final size:15
Alignment explanation
Indices: 48795524--48795556 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
48795514 AACTCCAATT
48795524 TTTTAGGGTTTAAGG
1 TTTTAGGGTTTAAGG
*
48795539 TTTTAGGGTTTATGG
1 TTTTAGGGTTTAAGG
48795554 TTT
1 TTT
48795557 AAGGTTTAGG
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:0.15, C:0.00, G:0.30, T:0.55
Consensus pattern (15 bp):
TTTTAGGGTTTAAGG
Found at i:48795555 original size:22 final size:21
Alignment explanation
Indices: 48795525--48795567 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
48795515 ACTCCAATTT
48795525 TTTAGGGTTTAAGGTTTTAGGG
1 TTTAGGGTTTAAGG-TTTAGGG
*
48795547 TTTATGGTTTAAGGTTTAGGG
1 TTTAGGGTTTAAGGTTTAGGG
48795568 ATCCCCCACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTTTAGGG
Found at i:48797870 original size:39 final size:39
Alignment explanation
Indices: 48797813--48797932 Score: 186
Period size: 39 Copynumber: 3.1 Consensus size: 39
48797803 TCCAATACAC
* *
48797813 CGGCACATAGCCTACTAGGCACTTAGCCCGAATAATCAT
1 CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
* *
48797852 CGGCACAAAGCCTGCTAGGCAATTAGCCCGAATAATCAC
1 CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
* *
48797891 CGGCACAAAGCCTGCTAGGCACTTATCCCAAATAATCAT
1 CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
48797930 CGG
1 CGG
48797933 ATTTCTATTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.32, C:0.31, G:0.19, T:0.18
Consensus pattern (39 bp):
CGGCACAAAGCCTGCTAGGCACTTAGCCCGAATAATCAT
Found at i:48799421 original size:44 final size:44
Alignment explanation
Indices: 48799372--48799457 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
48799362 TATCAACATA
*
48799372 AATTTTCTTTCCATA-AGTATGTTTGGTAGGAAAGATGAAAAAAT
1 AATTTTCTTTCAATAGA-TATGTTTGGTAGGAAAGATGAAAAAAT
48799416 AATTTTCTTTCAATAGATATGTTTGGTAGGAAAGATGAAAAA
1 AATTTTCTTTCAATAGATATGTTTGGTAGGAAAGATGAAAAA
48799458 TAGAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.36
Consensus pattern (44 bp):
AATTTTCTTTCAATAGATATGTTTGGTAGGAAAGATGAAAAAAT
Found at i:48800648 original size:20 final size:20
Alignment explanation
Indices: 48800615--48800653 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
48800605 AAGACTTCCA
48800615 AACATCTTACAAAATATTTTT
1 AACATCTTACAAAA-ATTTTT
*
48800636 AACA-CTTAGAAAAATTTT
1 AACATCTTACAAAAATTTT
48800654 GGACAAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 8 0.47
21 4 0.24
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (20 bp):
AACATCTTACAAAAATTTTT
Found at i:48800788 original size:27 final size:27
Alignment explanation
Indices: 48800758--48800813 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
48800748 TTTCAAAAAG
48800758 TATGGATACCTATTGTATTTTTATCGA
1 TATGGATACCTATTGTATTTTTATCGA
*
48800785 TATGGATATCTATTGTATTTTTATCGA
1 TATGGATACCTATTGTATTTTTATCGA
48800812 TA
1 TA
48800814 CCATCTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (27 bp):
TATGGATACCTATTGTATTTTTATCGA
Found at i:48801332 original size:41 final size:40
Alignment explanation
Indices: 48801287--48801415 Score: 111
Period size: 40 Copynumber: 3.2 Consensus size: 40
48801277 AAACAGGCTT
48801287 TTAGCGGC-ATTTGGATAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGATTT-GAT-AAAAACGCCACTAAAAATCAAGCA
* * * ** *
48801328 TTAGCGGCGCTTTTATAAAAACGCCGCTAAAGGTCGAGCA
1 TTAGCGGCGATTTGATAAAAACGCCACTAAAAATCAAGCA
* * * *
48801368 TTAGCGGCGCTTT-TTGGAAAACGCCGCTAAAAAT-AAGCA
1 TTAGCGGCGATTTGAT-AAAAACGCCACTAAAAATCAAGCA
*
48801407 TTACCGGCG
1 TTAGCGGCG
48801416 TTTTCAAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
39 13 0.18
40 48 0.65
41 10 0.14
42 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGATTTGATAAAAACGCCACTAAAAATCAAGCA
Found at i:48801368 original size:40 final size:40
Alignment explanation
Indices: 48801304--48801419 Score: 148
Period size: 40 Copynumber: 3.0 Consensus size: 40
48801294 CATTTGGATA
*
48801304 AAAAACGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-TG
** *
48801344 AAAAACGCCGCTAAAGGTCGAGCATTAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
* *
48801384 GAAAACGCCGCTAAAAAT-AAGCATTACCGGCG-TTTT
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT
48801420 CAAAAAAGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
38 4 0.06
39 13 0.20
40 49 0.74
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
Found at i:48801532 original size:41 final size:41
Alignment explanation
Indices: 48801475--48801718 Score: 398
Period size: 41 Copynumber: 6.0 Consensus size: 41
48801465 TGAGTTTTTG
*
48801475 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATTCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
48801516 GGGCCTTTAGCGGCGTTTGTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
48801557 GGGCCTTTAGTGGCGTTTTGGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
*
48801598 GGGCCTTTAGCGGCGTTTTTGAATAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
48801639 GGGCCTTTAGCGGCGTTTTTTAAAAAGCGCAGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
48801680 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC
48801719 CCGCTTTTGA
Statistics
Matches: 188, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 188 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:48802101 original size:14 final size:14
Alignment explanation
Indices: 48802084--48802120 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
48802074 AGGTTTAATA
*
48802084 TATACGGTTTAGGG
1 TATATGGTTTAGGG
*
48802098 TATATGATTTAGGG
1 TATATGGTTTAGGG
48802112 TATATGGTT
1 TATATGGTT
48802121 AATTTAGGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.24, C:0.03, G:0.30, T:0.43
Consensus pattern (14 bp):
TATATGGTTTAGGG
Found at i:48802197 original size:14 final size:15
Alignment explanation
Indices: 48802169--48802201 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
48802159 AAGATTTATA
48802169 GATTATGGAATTAGG
1 GATTATGGAATTAGG
48802184 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
48802198 GATT
1 GATT
48802202 CTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:48802443 original size:7 final size:7
Alignment explanation
Indices: 48802420--48802471 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
48802410 TAAATAAGAT
48802420 TTAGGGG
1 TTAGGGG
**
48802427 TTAGTAG
1 TTAGGGG
48802434 TTAGGGG
1 TTAGGGG
48802441 TTAGGGG
1 TTAGGGG
*
48802448 TTATGGG
1 TTAGGGG
**
48802455 TTAAAGG
1 TTAGGGG
*
48802462 TTAGAGG
1 TTAGGGG
48802469 TTA
1 TTA
48802472 AGAGTTAGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (7 bp):
TTAGGGG
Done.