Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 171 of 253
Found at i:55553097 original size:5 final size:5
Alignment explanation
Indices: 55553084--55553116 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
55553074 TTCAATTTTC
*
55553084 TGCCA TGCCG TGCCA TGCCA TGCCA TGCCA TGC
1 TGCCA TGCCA TGCCA TGCCA TGCCA TGCCA TGC
55553117 TACATTCCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.15, C:0.39, G:0.24, T:0.21
Consensus pattern (5 bp):
TGCCA
Found at i:55564103 original size:68 final size:67
Alignment explanation
Indices: 55564031--55564216 Score: 177
Period size: 67 Copynumber: 2.8 Consensus size: 67
55564021 CATCATGTGT
* * *
55564031 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACC
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACC
55564093 ATGTAG
62 ATGTAG
** * * *
55564099 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGTGTGGTTCCAAGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACCATGT
55564164 AG
66 AG
* * *
55564166 ACAAGAGAGCTACGAGATAAACTG--GCTAGGTCACATGGGTGG-TACTAAGTG
1 ACAAGAGAGCTACGACATATA-TGTAGCTAGGTCGCATGGGTGGATAC-AAGTG
55564217 TTCACCATGT
Statistics
Matches: 100, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
64 20 0.20
65 9 0.09
66 25 0.25
67 31 0.31
68 15 0.15
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.23
Consensus pattern (67 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGGGTGGATACAAGTGAAGGACACCATGT
AG
Found at i:55564136 original size:64 final size:64
Alignment explanation
Indices: 55564055--55564238 Score: 194
Period size: 67 Copynumber: 2.8 Consensus size: 64
55564045 AGACATTATG
* *
55564055 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
55564119 ATGTAGCTAGGTCGCATGTGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
55564184 AA
63 AA
* * * *
55564186 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
55564239 CGAACTATAT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 21 0.21
65 8 0.08
66 16 0.16
67 31 0.32
68 2 0.02
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:55574725 original size:46 final size:47
Alignment explanation
Indices: 55574662--55574828 Score: 137
Period size: 49 Copynumber: 3.5 Consensus size: 47
55574652 AATGTAAGAT
55574662 ATGTCTAGGACAT-GCATCGGCTAC-GAGATGT-GTCAGTATAAGACC
1 ATGTCTAGGACATGGCATCGGC-ACGGAGATGTAGTCAGTATAAGACC
* * *
55574707 ATGTCTAGGACATGGCATCGGCACGGATATGTGAGAGTTAGTGTAAGACC
1 ATGTCTAGGACATGGCATCGGCACGGAGATGT---AGTCAGTATAAGACC
* * ** * *
55574757 ATGTCTGGGACATGGCATCAGC-CTCA-ATTTCGATAGTCAATGTAAGACC
1 ATGTCTAGGACATGGCATCGGCACGGAGA--T-G-TAGTCAGTATAAGACC
*
55574806 ATGTCTGGGACATGGCATCGGCA
1 ATGTCTAGGACATGGCATCGGCA
55574829 TTATACCCTA
Statistics
Matches: 101, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
45 15 0.15
46 14 0.14
48 1 0.01
49 36 0.36
50 33 0.33
51 1 0.01
52 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (47 bp):
ATGTCTAGGACATGGCATCGGCACGGAGATGTAGTCAGTATAAGACC
Found at i:55574768 original size:50 final size:50
Alignment explanation
Indices: 55574700--55574828 Score: 163
Period size: 49 Copynumber: 2.6 Consensus size: 50
55574690 TGTGTCAGTA
* * * *
55574700 TAAGACCATGTCTAGGACATGGCATCGGCACGGATATGT-GAGAGTTAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCACGCA-ATGTCGAGAGTCAATG
* * * *
55574750 TAAGACCATGTCTGGGACATGGCATCAGC-CTCAATTTCGATAGTCAATG
1 TAAGACCATGTCTGGGACATGGCATCGGCACGCAATGTCGAGAGTCAATG
55574799 TAAGACCATGTCTGGGACATGGCATCGGCA
1 TAAGACCATGTCTGGGACATGGCATCGGCA
55574829 TTATACCCTA
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
48 3 0.04
49 38 0.56
50 27 0.40
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATCGGCACGCAATGTCGAGAGTCAATG
Found at i:55578248 original size:15 final size:15
Alignment explanation
Indices: 55578230--55578266 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
55578220 AACCGTGTGT
55578230 CACACACGGCTGAGA
1 CACACACGGCTGAGA
*
55578245 CACACACGGTTGAGA
1 CACACACGGCTGAGA
55578260 CACACAC
1 CACACAC
55578267 CCGTGTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.35, G:0.22, T:0.08
Consensus pattern (15 bp):
CACACACGGCTGAGA
Found at i:55579195 original size:22 final size:23
Alignment explanation
Indices: 55579170--55579267 Score: 76
Period size: 23 Copynumber: 4.3 Consensus size: 23
55579160 TAATAAACAA
*
55579170 TAAGCTCTATTGAGCTGAAT-AG
1 TAAGCTCTATTGAGCTAAATCAG
* *
55579192 TAAGCTCTATCGAGCTAAATCGG
1 TAAGCTCTATTGAGCTAAATCAG
* * *
55579215 TAAGCCCCAATGAGCTAAAAT-AG
1 TAAGCTCTATTGAGCT-AAATCAG
* * *
55579238 TAACCTCT-TATGAGCTGAATCGG
1 TAAGCTCTAT-TGAGCTAAATCAG
55579261 TAAGCTC
1 TAAGCTC
55579268 ATACGAGCTA
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
22 21 0.37
23 32 0.56
24 4 0.07
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
TAAGCTCTATTGAGCTAAATCAG
Found at i:55579275 original size:23 final size:22
Alignment explanation
Indices: 55579181--55579277 Score: 54
Period size: 23 Copynumber: 4.3 Consensus size: 22
55579171 AAGCTCTATT
*
55579181 GAGCTGAATAGTAAGCTC-TATC
1 GAGCTAAATAGTAAGCTCATA-C
* * *
55579203 GAGCTAAATCGGTAAGCCCCA-AT
1 GAGCTAAAT-AGTAAG-CTCATAC
* * *
55579226 GAGCTAAAATAGTAACCTCTTAT
1 GAGCT-AAATAGTAAGCTCATAC
* *
55579249 GAGCTGAATCGGTAAGCTCATAC
1 GAGCTAAAT-AGTAAGCTCATAC
55579272 GAGCTA
1 GAGCTA
55579278 CGGTGAGTTC
Statistics
Matches: 55, Mismatches: 14, Indels: 11
0.69 0.17 0.14
Matches are distributed among these distances:
22 13 0.24
23 35 0.64
24 7 0.13
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.24
Consensus pattern (22 bp):
GAGCTAAATAGTAAGCTCATAC
Found at i:55585963 original size:40 final size:40
Alignment explanation
Indices: 55585908--55586112 Score: 265
Period size: 40 Copynumber: 5.2 Consensus size: 40
55585898 CGGATGATAA
*
55585908 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATA-TCCGGGCTAAGTCC
*
55585948 CGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
* * *
55585988 CGAAGGCATTTGTGCGAGTTACTCTATCCGGGCTAAGTCT
1 CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
* *
55586028 CGAAGGCATTGGTGCGAGCT-ACTATATCCGGGCTAAGCCC
1 CGAAGGCATTTGTGCGAG-TGACTATATCCGGGCTAAGTCC
* * *
55586068 CGAAGGCATTTGAGCGAGT-AGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTGA-CTATATCCGGGCTAAGTCC
55586107 CGAAGG
1 CGAAGG
55586113 TACTTGGTTT
Statistics
Matches: 149, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
39 15 0.10
40 132 0.89
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTGACTATATCCGGGCTAAGTCC
Found at i:55589044 original size:47 final size:47
Alignment explanation
Indices: 55588993--55589421 Score: 732
Period size: 47 Copynumber: 9.1 Consensus size: 47
55588983 GATTCTATAA
55588993 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* * *
55589040 GATGAATGTGAACGTGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
*
55589087 GATGAATGTGAACTTGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
*
55589134 GATGAATGTGAACATGCATATGTGTGATAAGGTCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
55589181 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
55589228 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* * * *
55589275 GATGAATGTGGACATGCAAATATGTGATAAGGTCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* *
55589322 GATGAATGTGAACATGCAAATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
* **
55589369 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
55589416 GATGAA
1 GATGAA
55589422 CGTGGAAGCG
Statistics
Matches: 364, Mismatches: 18, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 364 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCAATGT
Found at i:55589418 original size:22 final size:22
Alignment explanation
Indices: 55589015--55589418 Score: 122
Period size: 22 Copynumber: 17.3 Consensus size: 22
55589005 CATGCATATG
*
55589015 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
* * *
55589037 TGTGATGAATGT-GAACGTGCAAATA
1 TGTGAT-AAGGTCGAATG-GC-CA-A
*
55589062 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
* *
55589084 TGTGATGAATGT-GAACTTG-CATA
1 TGTGAT-AAGGTCGAA-TGGCCA-A
*
55589107 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGTCGAATGGCCAA
*
55589131 TGTGATGAATGT-GAACAT-G-CATA
1 TGTGAT-AAGGTCG-A-ATGGCCA-A
55589154 TGTGTGATAAGGTCGAATGGCCAA
1 --TGTGATAAGGTCGAATGGCCAA
*
55589178 TGTGATGAATGT-GAACAT-G-CATA
1 TGTGAT-AAGGTCG-A-ATGGCCA-A
*
55589201 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGTCGAATGGCCAA
*
55589225 TGTGATGAATGT-GAACAT-G-CATA
1 TGTGAT-AAGGTCG-A-ATGGCCA-A
*
55589248 TGTGTGATAAGGCCGAATGGCCAA
1 --TGTGATAAGGTCGAATGGCCAA
* * *
55589272 TGTGATGAATGTGGACAT-GCAAATA
1 TGTGAT-AAGGTCGA-ATGGC-CA-A
55589297 TGTGATAAGGTCGAATGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
* *
55589319 TGTGATGAATGT-GAACAT-GCAAATA
1 TGTGAT-AAGGTCG-A-ATGGC-CA-A
*
55589344 TGTGATAAGGCCGAATGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
* *
55589366 TGTGATGAATGT-GAACAT-GCATATA
1 TGTGAT-AAGGTCG-A-ATGGC-CA-A
*
55589391 TGTGATAAGGTAGAATGGCCAA
1 TGTGATAAGGTCGAATGGCCAA
55589413 TGTGAT
1 TGTGAT
55589419 GAACGTGGAA
Statistics
Matches: 283, Mismatches: 41, Indels: 116
0.64 0.09 0.26
Matches are distributed among these distances:
22 78 0.28
23 66 0.23
24 67 0.24
25 72 0.25
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (22 bp):
TGTGATAAGGTCGAATGGCCAA
Found at i:55598199 original size:40 final size:40
Alignment explanation
Indices: 55598144--55598428 Score: 414
Period size: 40 Copynumber: 7.2 Consensus size: 40
55598134 CGGATGATAA
* *
55598144 CGAAGGCATTTGTGCTAGTGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATA-TCCGGGCTAAGTCC
* * *
55598184 CGAAGGCATTTGTGCTAGTGACTATATCTGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
55598224 CGAAGGCATTTGTGCGAGTTACTATATCTGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
*
55598264 CAAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
55598304 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
55598344 CGAAGGCATTGGTGCGAGCTACTATATCCGGGCTAAGCCC
1 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
* * *
55598384 CGAAGGCATTTGAGCGAG-TAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGTTA-CTATATCCGGGCTAAGTCC
55598423 CGAAGG
1 CGAAGG
55598429 TACTTGGTTT
Statistics
Matches: 229, Mismatches: 14, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
39 15 0.07
40 213 0.93
41 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
Found at i:55602459 original size:24 final size:23
Alignment explanation
Indices: 55602432--55602507 Score: 84
Period size: 24 Copynumber: 3.3 Consensus size: 23
55602422 TGATAAACAA
55602432 TAAGCTCTATTGAGCAGAAAACGG
1 TAAGCTCTATTGAGC-GAAAACGG
*
55602456 TAAGCTCTATTGAGCTGAATA--G
1 TAAGCTCTATTGAGC-GAAAACGG
* * *
55602478 TAAGCTCTATCGAGCTAAATCGG
1 TAAGCTCTATTGAGCGAAAACGG
55602501 TAAGCTC
1 TAAGCTC
55602508 CAATGAGCTG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.05
22 15 0.34
23 8 0.18
24 19 0.43
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.26
Consensus pattern (23 bp):
TAAGCTCTATTGAGCGAAAACGG
Found at i:55602487 original size:46 final size:46
Alignment explanation
Indices: 55602432--55602528 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
55602422 TGATAAACAA
* * *
55602432 TAAGCTCTATTGAGCAGAAAACGGTAAGCTCTATTGAGCTG-AATAG
1 TAAGCTCTATCGAGC-GAAAACGGTAAGCTCCAATGAGCTGAAATAG
* *
55602478 TAAGCTCTATCGAGCTAAATCGGTAAGCTCCAATGAGCTGAAATAG
1 TAAGCTCTATCGAGCGAAAACGGTAAGCTCCAATGAGCTGAAATAG
55602524 TAAGC
1 TAAGC
55602529 ACTCATGAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
45 21 0.47
46 24 0.53
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (46 bp):
TAAGCTCTATCGAGCGAAAACGGTAAGCTCCAATGAGCTGAAATAG
Found at i:55602515 original size:23 final size:23
Alignment explanation
Indices: 55602453--55602552 Score: 64
Period size: 23 Copynumber: 4.4 Consensus size: 23
55602443 GAGCAGAAAA
* * *
55602453 CGGTAAGCTCTATTGAGCTGAAT
1 CGGTAAGCTCCAATGAGCTAAAT
* *
55602476 -AGTAAGCT-CTATCGAGCTAAAT
1 CGGTAAGCTCCAAT-GAGCTAAAT
55602498 CGGTAAGCTCCAATGAGCTGAAAT
1 CGGTAAGCTCCAATGAGCT-AAAT
* * * *
55602522 -AGTAAGCACTC-ATGAGTTGAAT
1 CGGTAAGCTC-CAATGAGCTAAAT
55602544 CGGTAAGCT
1 CGGTAAGCT
55602553 AATACGAGCT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
21 1 0.02
22 18 0.31
23 31 0.53
24 8 0.14
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (23 bp):
CGGTAAGCTCCAATGAGCTAAAT
Found at i:55602545 original size:46 final size:45
Alignment explanation
Indices: 55602453--55602552 Score: 130
Period size: 46 Copynumber: 2.2 Consensus size: 45
55602443 GAGCAGAAAA
* * *
55602453 CGGTAAGCTCTATTGAGCTGAATAGTAAGCTCTATCGAGCTAAAT
1 CGGTAAGCTCCAATGAGCTGAATAGTAAGCACTATCGAGCTAAAT
* *
55602498 CGGTAAGCTCCAATGAGCTGAAATAGTAAGCACTCAT-GAGTTGAAT
1 CGGTAAGCTCCAATGAGCTG-AATAGTAAGCACT-ATCGAGCTAAAT
55602544 CGGTAAGCT
1 CGGTAAGCT
55602553 AATACGAGCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
45 18 0.38
46 28 0.58
47 2 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (45 bp):
CGGTAAGCTCCAATGAGCTGAATAGTAAGCACTATCGAGCTAAAT
Found at i:55613189 original size:30 final size:30
Alignment explanation
Indices: 55613155--55613211 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
55613145 TTTTCGGGCA
* *
55613155 TAGGGGTAAAATGGTCATTTTGCCAAAGTC
1 TAGGGGCAAAATGGTCATTTTACCAAAGTC
*
55613185 TAGGGGCAAAATGGTTATTTTACCAAA
1 TAGGGGCAAAATGGTCATTTTACCAAA
55613212 AATGTGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (30 bp):
TAGGGGCAAAATGGTCATTTTACCAAAGTC
Found at i:55614294 original size:13 final size:13
Alignment explanation
Indices: 55614276--55614306 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
55614266 TCTTGGAGAT
55614276 TTGGCCAAATGTG
1 TTGGCCAAATGTG
55614289 TTGGCCAAATGTG
1 TTGGCCAAATGTG
55614302 TTGGC
1 TTGGC
55614307 TTAGGATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.32, T:0.32
Consensus pattern (13 bp):
TTGGCCAAATGTG
Found at i:55615845 original size:41 final size:41
Alignment explanation
Indices: 55615784--55615974 Score: 235
Period size: 41 Copynumber: 4.7 Consensus size: 41
55615774 CTATCTTAAA
*
55615784 TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTTGATC
1 TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGATC
* * *
55615825 TCGTAAACTAAGTGCCATATATAGCCT-AAACTATCTCGATC
1 TCGCACACTAAGTGCCATATATAG-CTGAAGCTATCTCGATC
* * * *
55615866 TTGCACACTAAGTGCTATATATAGCCGAAGCTATGTCGATC
1 TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGATC
* *
55615907 TCGCACACTAAGTGCCATATATAG-TCGAAGCTATGTCGA-A
1 TCGCACACTAAGTGCCATATATAGCT-GAAGCTATCTCGATC
* *
55615947 TCGCACACTAAGTGCCACATGTAGCTGA
1 TCGCACACTAAGTGCCATATATAGCTGA
55615975 TTTGTCATCG
Statistics
Matches: 129, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
40 25 0.19
41 102 0.79
42 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (41 bp):
TCGCACACTAAGTGCCATATATAGCTGAAGCTATCTCGATC
Found at i:55615889 original size:82 final size:81
Alignment explanation
Indices: 55615750--55615963 Score: 252
Period size: 82 Copynumber: 2.6 Consensus size: 81
55615740 CATCTTACAC
** * ** *
55615750 ACTAAGTGCTGTACATAGCC-AAAGCTATCTTAAATCGCACACTAAGTGCCATATATAGCTGAAG
1 ACTAAGTGCCATATATAGCCGAAA-CTATCTCGAATCGCACACTAAGTGCCATATATAGCCGAAG
* *
55615814 CTATCTTGATCTCGTAA
65 CTATCTCGATCTCGCAA
* *
55615831 ACTAAGTGCCATATATAGCCTAAACTATCTCG-ATCTTGCACACTAAGTGCTATATATAGCCGAA
1 ACTAAGTGCCATATATAGCCGAAACTATCTCGAATC--GCACACTAAGTGCCATATATAGCCGAA
* *
55615895 GCTATGTCGATCTCGCAC
64 GCTATCTCGATCTCGCAA
* * *
55615913 ACTAAGTGCCATATATAGTCGAAGCTATGTCGAATCGCACACTAAGTGCCA
1 ACTAAGTGCCATATATAGCCGAAACTATCTCGAATCGCACACTAAGTGCCA
55615964 CATGTAGCTG
Statistics
Matches: 113, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
80 3 0.03
81 37 0.33
82 70 0.62
83 3 0.03
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (81 bp):
ACTAAGTGCCATATATAGCCGAAACTATCTCGAATCGCACACTAAGTGCCATATATAGCCGAAGC
TATCTCGATCTCGCAA
Found at i:55616309 original size:8 final size:9
Alignment explanation
Indices: 55616289--55616314 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55616279 TTATTAACTA
55616289 TTTTACCAT
1 TTTTACCAT
55616298 TTTTACCAT
1 TTTTACCAT
55616307 TTTTACCA
1 TTTTACCA
55616315 CTTGCCAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (9 bp):
TTTTACCAT
Found at i:55617897 original size:19 final size:19
Alignment explanation
Indices: 55617875--55617913 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55617865 TATAAATCAC
55617875 ATCAATGATCATAAT-TTAA
1 ATCAATGATCA-AATATTAA
*
55617894 ATCAATTATCAAATATTAA
1 ATCAATGATCAAATATTAA
55617913 A
1 A
55617914 ATCATATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.51, C:0.10, G:0.03, T:0.36
Consensus pattern (19 bp):
ATCAATGATCAAATATTAA
Found at i:55617961 original size:21 final size:21
Alignment explanation
Indices: 55617932--55617973 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
55617922 ATTTACAACA
*
55617932 TAGCGTAATTAAAAACATAAC
1 TAGCATAATTAAAAACATAAC
55617953 TAGCATAATTAAAAACATAAC
1 TAGCATAATTAAAAACATAAC
55617974 CCAACATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.07, T:0.24
Consensus pattern (21 bp):
TAGCATAATTAAAAACATAAC
Found at i:55622739 original size:43 final size:43
Alignment explanation
Indices: 55622654--55622735 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
55622644 ATATAGTACA
* * *
55622654 ATGCCAATGTCCCAGGCGTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCG
* *
55622697 ATGCCACTGTCCCAGACATGGTCTTACTTGC-A-CACATAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATAT
55622736 ATCGGAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 7 0.21
42 1 0.03
43 26 0.76
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGCAATCACATATCG
Found at i:55622773 original size:56 final size:56
Alignment explanation
Indices: 55622687--55622793 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
55622677 TTACATGTAA
* * * * *
55622687 TCACATATCGATGCCACTGTCCCAGACATGGTCTTACTTGCACACATATATCGGAG
1 TCACATATCGATGCCAATGTACAAAACATGGTCTTACTCGCACACATATATCGGAG
*
55622743 TCACATATCGATGCCAATGTATAAAACATGGTCTTACTCGCACACATATAT
1 TCACATATCGATGCCAATGTACAAAACATGGTCTTACTCGCACACATATAT
55622794 TGATGCCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (56 bp):
TCACATATCGATGCCAATGTACAAAACATGGTCTTACTCGCACACATATATCGGAG
Found at i:55624602 original size:25 final size:26
Alignment explanation
Indices: 55624569--55624623 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 26
55624559 CGTGGATTTA
* * *
55624569 ATTTGCCTTTTCAATCGAAACGAAGT
1 ATTTGCCTTTTCAACCAAAACAAAGT
55624595 ATTT-CCTTTTCAACCAAAACAAAGT
1 ATTTGCCTTTTCAACCAAAACAAAGT
55624620 ATTT
1 ATTT
55624624 TCTTCCATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (26 bp):
ATTTGCCTTTTCAACCAAAACAAAGT
Found at i:55626325 original size:43 final size:43
Alignment explanation
Indices: 55626278--55626429 Score: 154
Period size: 43 Copynumber: 3.6 Consensus size: 43
55626268 GTTCTCATGA
*
55626278 AAGACCACGTCTAGGA-AGTTGGCATCGATATGTGATTATGTGT
1 AAGACCACGTCTAGGACAGTTGGCATCGATATGTGATT-CGTGT
* * * * *
55626321 AAGACCATGTCTGGGACA-TTGGCATCG-TATTTAATTCGTAT
1 AAGACCACGTCTAGGACAGTTGGCATCGATATGTGATTCGTGT
* *
55626362 AAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTGCATGT
1 AAGACCAC-GTCTAGGACAGTTGGCATCGATATGTGATT-CGTGT
*
55626405 AAGACCATGTCTAGGAC-GTTGGCAT
1 AAGACCACGTCTAGGACAGTTGGCAT
55626430 TGTATGATAT
Statistics
Matches: 89, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
41 27 0.30
42 15 0.17
43 46 0.52
44 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
AAGACCACGTCTAGGACAGTTGGCATCGATATGTGATTCGTGT
Found at i:55626373 original size:41 final size:42
Alignment explanation
Indices: 55626320--55626435 Score: 135
Period size: 41 Copynumber: 2.8 Consensus size: 42
55626310 TGATTATGTG
* *
55626320 TAAGACCATGTCTGGGACATTGGCATCGTATTTAATT-CGTA
1 TAAGACCATGTCTGGGACATTGGCATCGTATGTAATTGCATA
* * * *
55626361 TAAGACCCTGTCTGGGACAGTGGCATCGATATGTGATTGCATG
1 TAAGACCATGTCTGGGACATTGGCATCG-TATGTAATTGCATA
* * *
55626404 TAAGACCATGTCTAGGACGTTGGCATTGTATG
1 TAAGACCATGTCTGGGACATTGGCATCGTATG
55626436 ATATGCATGA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
41 26 0.42
42 11 0.18
43 25 0.40
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATTGGCATCGTATGTAATTGCATA
Found at i:55626966 original size:58 final size:58
Alignment explanation
Indices: 55626899--55627019 Score: 242
Period size: 58 Copynumber: 2.1 Consensus size: 58
55626889 TTGAGTTATT
55626899 TATTTGCTTATGACCTACTAAGCTATGATAGCTTACTGTGCATGTCTATGTTTGTCTC
1 TATTTGCTTATGACCTACTAAGCTATGATAGCTTACTGTGCATGTCTATGTTTGTCTC
55626957 TATTTGCTTATGACCTACTAAGCTATGATAGCTTACTGTGCATGTCTATGTTTGTCTC
1 TATTTGCTTATGACCTACTAAGCTATGATAGCTTACTGTGCATGTCTATGTTTGTCTC
55627015 TATTT
1 TATTT
55627020 TATAGATTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 63 1.00
ACGTcount: A:0.21, C:0.18, G:0.17, T:0.45
Consensus pattern (58 bp):
TATTTGCTTATGACCTACTAAGCTATGATAGCTTACTGTGCATGTCTATGTTTGTCTC
Found at i:55634051 original size:41 final size:41
Alignment explanation
Indices: 55633848--55634070 Score: 276
Period size: 41 Copynumber: 5.5 Consensus size: 41
55633838 AAAACTCGAT
* * * *
55633848 ATCTCACACACTAAGTGTCGTACATAGCCGAAGCTATCTC-
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
* *
55633888 A-CATCGCACACTAAGTGCCATATATAGCTGAAGCTATCTTG
1 ATC-TCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
* * *
55633929 ATCTCACACACTAAGTGCCATATATAGCTGAAGCTATCTTG
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
* *
55633970 ATCTCG-AGCACTAAGTGCCATATATAGCCGAAGCTCTGTCG
1 ATCTCGCA-CACTAAGTGCCATATATAGCCGAAGCTATCTCG
*
55634011 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATGTCGG
1 ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTC-G
55634053 A--TCGCACACTAAGTGCCA
1 ATCTCGCACACTAAGTGCCA
55634071 CATGTAGCTG
Statistics
Matches: 164, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 50 0.30
41 109 0.66
42 4 0.02
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (41 bp):
ATCTCGCACACTAAGTGCCATATATAGCCGAAGCTATCTCG
Found at i:55635959 original size:21 final size:21
Alignment explanation
Indices: 55635919--55635959 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
55635909 ATTGTTGAGA
* *
55635919 AGGAAGTTGCTATTGCAGAAG
1 AGGAAGTTGCTACTGAAGAAG
*
55635940 AGGAAGTTGTTACTGAAGAA
1 AGGAAGTTGCTACTGAAGAA
55635960 AAATTTGTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.32, T:0.24
Consensus pattern (21 bp):
AGGAAGTTGCTACTGAAGAAG
Found at i:55651413 original size:31 final size:31
Alignment explanation
Indices: 55651370--55651448 Score: 124
Period size: 31 Copynumber: 2.5 Consensus size: 31
55651360 TTTAACGGTT
*
55651370 ACTAAGCCGAAGCCTTTTCATAAATCAAATC
1 ACTAGGCCGAAGCCTTTTCATAAATCAAATC
*
55651401 ACTAGGCCGAAGCCTTTTCATAAATCATATC
1 ACTAGGCCGAAGCCTTTTCATAAATCAAATC
55651432 ACT-GTGCCGAAGCCTTT
1 ACTAG-GCCGAAGCCTTT
55651449 ATTATAAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 1 0.02
31 44 0.98
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.28
Consensus pattern (31 bp):
ACTAGGCCGAAGCCTTTTCATAAATCAAATC
Found at i:55651532 original size:42 final size:42
Alignment explanation
Indices: 55651472--55651562 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
55651462 TGGCCCATAG
*
55651472 GCCCATTTCAATAACACATGAAATATCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
*
55651514 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
55651556 GCCCATT
1 GCCCATT
55651563 CGGGGAGACT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (42 bp):
GCCCATTTCAATAACACATGAAATACCAATGAATGTATGCAA
Found at i:55651779 original size:26 final size:26
Alignment explanation
Indices: 55651708--55651830 Score: 196
Period size: 26 Copynumber: 4.8 Consensus size: 26
55651698 CCTCTTTAAT
**
55651708 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
55651733 AACTGGGGCA-AAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
55651758 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
55651784 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
55651810 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
55651831 GCACTTCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
25 33 0.36
26 58 0.64
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:55651819 original size:52 final size:51
Alignment explanation
Indices: 55651708--55651830 Score: 230
Period size: 52 Copynumber: 2.4 Consensus size: 51
55651698 CCTCTTTAAT
55651708 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
55651758 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCA-AAGCCCTTTTCAATA
55651810 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
55651831 GCACTTCCTC
Statistics
Matches: 71, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
50 10 0.14
51 25 0.35
52 36 0.51
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.26
Consensus pattern (51 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCAAAGCCCTTTTCAATA
Found at i:55651905 original size:20 final size:19
Alignment explanation
Indices: 55651880--55651954 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
55651870 TTATGAATTC
* *
55651880 ATCATGTGGATCTCATACA
1 ATCATGTGCATATCATACA
55651899 TATCATGTGCATATCATACA
1 -ATCATGTGCATATCATACA
55651919 CATCATGTGCATATCATATCA
1 -ATCATGTGCATATCATA-CA
55651940 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
55651955 TCCCACGTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
18 8 0.16
20 41 0.80
21 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.35
Consensus pattern (19 bp):
ATCATGTGCATATCATACA
Found at i:55652753 original size:27 final size:27
Alignment explanation
Indices: 55652658--55652736 Score: 117
Period size: 27 Copynumber: 2.9 Consensus size: 27
55652648 TATTCGAGAT
55652658 TTTA-CCATACAGGGG-TATTACGGTCAC
1 TTTACCCA-ACAGGGGCT-TTACGGTCAC
*
55652685 TTTACCCTACAGGGGCTTTACGGTCAC
1 TTTACCCAACAGGGGCTTTACGGTCAC
55652712 TTTACCCAACAGGGGCTTTACGGTC
1 TTTACCCAACAGGGGCTTTACGGTC
55652737 TTTTTACCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
27 45 0.94
28 3 0.06
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.29
Consensus pattern (27 bp):
TTTACCCAACAGGGGCTTTACGGTCAC
Found at i:55652901 original size:27 final size:27
Alignment explanation
Indices: 55652847--55653027 Score: 177
Period size: 27 Copynumber: 6.7 Consensus size: 27
55652837 TTTCTATAAT
*
55652847 TTTTATAAAGTCAAGGGTACTTCT-GTAA
1 TTTTATAAA-TCAAGGGTA-TTTTGGTAA
* *
55652875 CTTTGTAAATCAAGGGTATTTTGGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* * *
55652902 TTTTACAAATCGAGGGTATTTCGGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* * *
55652929 TTTCACAAACCAAGGGTATTTTGGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* *
55652956 TTTTACAAA-CTAGGGGTATTTTGGTAA
1 TTTTATAAATC-AAGGGTATTTTGGTAA
* * *
55652983 TTTTACAAACCAAGGGTATTTTAGTAA
1 TTTTATAAATCAAGGGTATTTTGGTAA
* *
55653010 TTTTGTAAATCGAGGGTA
1 TTTTATAAATCAAGGGTA
55653028 AAACAGTAAT
Statistics
Matches: 130, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.03
27 118 0.91
28 8 0.06
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.38
Consensus pattern (27 bp):
TTTTATAAATCAAGGGTATTTTGGTAA
Found at i:55652944 original size:54 final size:54
Alignment explanation
Indices: 55652885--55653027 Score: 216
Period size: 54 Copynumber: 2.6 Consensus size: 54
55652875 CTTTGTAAAT
55652885 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
* * *
55652939 CAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAATCGA-GGGTATTTCGGTAATTTCACAAAC
* **
55652993 CAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTA
1 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTA
55653028 AAACAGTAAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 2 0.03
54 76 0.95
55 2 0.03
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
Found at i:55653035 original size:27 final size:27
Alignment explanation
Indices: 55653005--55653216 Score: 250
Period size: 27 Copynumber: 7.9 Consensus size: 27
55652995 AGGGTATTTT
*
55653005 AGTAATTTTGTAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
* *
55653032 AGTAATTCTGTAAATCAAGGGTAAAAT
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55653059 AGTAATTCTATAAATCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55653086 -GATAATTCTGTAAATCAAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
55653113 GGTAATTCTATAAGTCGAGGGTAAAAC
1 AGTAATTCTGTAAATCGAGGGTAAAAC
*
55653140 -GATAATTATGTAAATCGAGGGTAAAAC
1 AG-TAATTCTGTAAATCGAGGGTAAAAC
* * *
55653167 GGTAATTATGTAAATC-AGGGGTAAACC
1 AGTAATTCTGTAAATCGA-GGGTAAAAC
* *
55653194 GGTAATTCTGTAAATCGGGGGTA
1 AGTAATTCTGTAAATCGAGGGTA
55653217 CTTTGGTAAT
Statistics
Matches: 162, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
26 3 0.02
27 157 0.97
28 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
AGTAATTCTGTAAATCGAGGGTAAAAC
Found at i:55653037 original size:54 final size:54
Alignment explanation
Indices: 55652885--55653092 Score: 184
Period size: 54 Copynumber: 3.9 Consensus size: 54
55652875 CTTTGTAAAT
* *** *
55652885 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAAC
* * ****
55652939 CAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAATCGA-GGGTAAAACGGTAATTTTACAAAC
** * * ** *
55652993 CAAGGGTATTTTAGTAATTTTGTAAATCGAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAAC
*** * * *
55653047 CAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATT
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATT
55653093 CTGTAAATCA
Statistics
Matches: 129, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
53 2 0.02
54 125 0.97
55 2 0.02
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (54 bp):
CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAAC
Found at i:55653216 original size:54 final size:54
Alignment explanation
Indices: 55653006--55653209 Score: 277
Period size: 54 Copynumber: 3.8 Consensus size: 54
55652996 GGGTATTTTA
* * **
55653006 GTAATTTTGTAAATCGAGGGTAAAAC-AGTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTATAAATCGAGGGTAAAACGA-TAATTCTGTAAATCAAGGGTAAAACG
55653060 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAACG
* * *
55653114 GTAATTCTATAAGTCGAGGGTAAAACGATAATTATGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAACG
* * * *
55653168 GTAATTATGTAAATC-AGGGGTAAACCGGTAATTCTGTAAATC
1 GTAATTCTATAAATCGA-GGGTAAAACGATAATTCTGTAAATC
55653210 GGGGGTACTT
Statistics
Matches: 135, Mismatches: 13, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 133 0.99
55 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.28
Consensus pattern (54 bp):
GTAATTCTATAAATCGAGGGTAAAACGATAATTCTGTAAATCAAGGGTAAAACG
Found at i:55653243 original size:27 final size:27
Alignment explanation
Indices: 55653213--55653311 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
55653203 GTAAATCGGG
*
55653213 GGTACTTT-GGTAATTTTACAAGTCGAA
1 GGTA-TTTCGGTAATTTTACAAATCGAA
*
55653240 GGTATTTCGGTAATTTTACAAATCGAG
1 GGTATTTCGGTAATTTTACAAATCGAA
* * * *
55653267 GGTAATTCAGTATTTTTACAAA-CTAA
1 GGTATTTCGGTAATTTTACAAATCGAA
**
55653293 GGGTATTTTAGTAATTTTA
1 -GGTATTTCGGTAATTTTA
55653312 GTAAACTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 5 0.08
27 55 0.92
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (27 bp):
GGTATTTCGGTAATTTTACAAATCGAA
Found at i:55653270 original size:81 final size:80
Alignment explanation
Indices: 55652878--55653271 Score: 265
Period size: 81 Copynumber: 4.9 Consensus size: 80
55652868 TCTGTAACTT
* *** *
55652878 TGTAAATCAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAACCAAG
1 TGTAAATCAAGGGTAATTTGGTAATTTTAC-AATCGAGGGTATTTCGGTAATTTTGTAAATCAAG
****
55652943 GGTATTTTGGTAATT-
65 GGTAAAACGGTAATTC
* * * * * ** *
55652958 T-TACAAACTAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCG
1 TGTA-AATC-AAGGGTAATTTGGTAATTTTAC-AATCGAGGGTATTTCGGTAATTTTGTAAATCA
*
55653022 AGGGTAAAACAGTAATTC
63 AGGGTAAAACGGTAATTC
** * *** * *
55653040 TGTAAATCAAGGGTAAAATAGTAATTCTATA-AATCGAGGGTAAAACGATAATTCTGTAAATCAA
1 TGTAAATCAAGGGTAATTTGGTAATT-T-TACAATCGAGGGTATTTCGGTAATTTTGTAAATCAA
55653104 GGGTAAAACGGTAATTC
64 GGGTAAAACGGTAATTC
* * * *** * *** * *
55653121 TATAAGTCGAGGGTAAAACGATAATTATGTA-AATCGAGGGTAAAACGGTAATTATGTAAATCAG
1 TGTAAATCAAGGGTAATTTGGTAATT-T-TACAATCGAGGGTATTTCGGTAATTTTGTAAATCAA
*
55653185 GGGTAAACCGGTAATTC
64 GGGTAAAACGGTAATTC
** * * ** *
55653202 TGTAAATCGGGGGTACTTTGGTAATTTTACAAGTCGAAGGTATTTCGGTAATTTTACAAATCGAG
1 TGTAAATCAAGGGTAATTTGGTAATTTTACAA-TCGAGGGTATTTCGGTAATTTTGTAAATCAAG
55653267 GGTAA
65 GGTAA
55653272 TTCAGTATTT
Statistics
Matches: 244, Mismatches: 62, Indels: 15
0.76 0.19 0.05
Matches are distributed among these distances:
79 4 0.02
80 7 0.03
81 224 0.92
82 5 0.02
83 4 0.02
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.32
Consensus pattern (80 bp):
TGTAAATCAAGGGTAATTTGGTAATTTTACAATCGAGGGTATTTCGGTAATTTTGTAAATCAAGG
GTAAAACGGTAATTC
Found at i:55654453 original size:17 final size:17
Alignment explanation
Indices: 55654431--55654464 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55654421 ATCCATCGGA
55654431 GCAAATAGATTTC-ACAT
1 GCAAATA-ATTTCTACAT
55654448 GCAAATAATTTCTACAT
1 GCAAATAATTTCTACAT
55654465 TTCCAGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (17 bp):
GCAAATAATTTCTACAT
Found at i:55655571 original size:31 final size:31
Alignment explanation
Indices: 55655533--55655611 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
55655523 TTTAACGGTT
55655533 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
* *
55655564 ACTGGGCCGAAGCATTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCAAATC
*
55655595 ACTGGGTCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
55655612 ATTATAAACG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCAAATC
Found at i:55655893 original size:26 final size:26
Alignment explanation
Indices: 55655840--55656041 Score: 300
Period size: 26 Copynumber: 7.8 Consensus size: 26
55655830 CCTCTTTAAT
**
55655840 AACTGGGGCA-AAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
*
55655865 AACTGGGGCA-AAGCCTTCTTTCAATA
1 AACTGGGGCATAAGCCCT-TTTCAATA
**
55655891 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
55655917 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
55655943 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
**
55655969 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAATA
55655995 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAATA
55656021 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
55656042 GCACTTCCTT
Statistics
Matches: 163, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
25 16 0.10
26 141 0.87
27 6 0.04
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAATA
Found at i:55655968 original size:78 final size:78
Alignment explanation
Indices: 55655840--55656041 Score: 354
Period size: 78 Copynumber: 2.6 Consensus size: 78
55655830 CCTCTTTAAT
*
55655840 AACTGGGGCA-AAGCCCTTTTCGGTAAACTGGGGCA-AAGCCTTCTTTCAATAAACTGGGGCATA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCT-TTTCAATAAACTGGGGCATA
55655903 AGCCCTTTTCGGTA
65 AGCCCTTTTCGGTA
55655917 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAA
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAA
55655982 GCCCTTTTCGGTA
66 GCCCTTTTCGGTA
**
55655995 AACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTT
55656042 GCACTTCCTT
Statistics
Matches: 120, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
77 10 0.08
78 104 0.87
79 6 0.05
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (78 bp):
AACTGGGGCATAAGCCCTTTTCGGTAAACTGGGGCATAAGCCCTTTTCAATAAACTGGGGCATAA
GCCCTTTTCGGTA
Found at i:55656116 original size:20 final size:20
Alignment explanation
Indices: 55656091--55656165 Score: 111
Period size: 20 Copynumber: 3.9 Consensus size: 20
55656081 TTATGAATTC
*
55656091 ATCATGTGCATCTCATACAT
1 ATCATGTGCATATCATACAT
55656111 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
55656131 ATCATGTGCATATCATATCA-
1 ATCATGTGCATATCATA-CAT
55656151 ATCATGT--ATATCATA
1 ATCATGTGCATATCATA
55656166 TCCCGCGTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
18 8 0.15
20 43 0.81
21 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:55656122 original size:11 final size:11
Alignment explanation
Indices: 55656091--55656146 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
55656081 TTATGAATTC
55656091 ATCATGTGCAT
1 ATCATGTGCAT
* *
55656102 CTCA--TACAT
1 ATCATGTGCAT
55656111 ATCATGTGCAT
1 ATCATGTGCAT
*
55656122 ATCA--TACAT
1 ATCATGTGCAT
55656131 ATCATGTGCAT
1 ATCATGTGCAT
55656142 ATCAT
1 ATCAT
55656147 ATCAATCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:55656163 original size:9 final size:10
Alignment explanation
Indices: 55656108--55656164 Score: 57
Period size: 9 Copynumber: 5.8 Consensus size: 10
55656098 GCATCTCATA
55656108 CATATCATGT
1 CATATCATGT
*
55656118 GCATATCAT-A
1 -CATATCATGT
55656128 CATATCATGT
1 CATATCATGT
*
55656138 GCATATCATAT
1 -CATATCATGT
55656149 CA-ATCATGT
1 CATATCATGT
55656158 -ATATCAT
1 CATATCAT
55656165 ATCCCGCGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
8 1 0.03
9 19 0.49
10 2 0.05
11 17 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (10 bp):
CATATCATGT
Found at i:55656916 original size:27 final size:27
Alignment explanation
Indices: 55656869--55656947 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
55656859 TATTCATCAT
* *
55656869 TTTACCATACATGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCAC
*
55656896 TTTACCCT-CTAGGGGCTTTACGGTCAG
1 TTTACCCTAC-AGGGGCTTTACGGTCAC
55656923 TTTACCCTACAGGGGCTTTACGGTC
1 TTTACCCTACAGGGGCTTTACGGTC
55656948 TTTTGGCCTA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 1 0.02
27 43 0.93
28 2 0.04
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCAC
Found at i:55657039 original size:27 final size:27
Alignment explanation
Indices: 55657009--55657060 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
55656999 GTAAATCTAC
55657009 AAACAAAAGGTATTTC-AGTAATTTTGT
1 AAACAAAAGGTATTTCTA-TAATTTTGT
* *
55657036 AAACCAATGGTATTTCTATAATTTT
1 AAACAAAAGGTATTTCTATAATTTT
55657061 TATAAAGTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (27 bp):
AAACAAAAGGTATTTCTATAATTTTGT
Found at i:55657103 original size:27 final size:27
Alignment explanation
Indices: 55657017--55657265 Score: 177
Period size: 27 Copynumber: 9.1 Consensus size: 27
55657007 ACAAACAAAA
* * * *
55657017 GGTATTTCAGTAATTTTGTAAACCAAT
1 GGTATTTCTGTAATTTTATAAATCAAG
*
55657044 GGTATTTCTATAATTTTTATAAAGTCAAG
1 GGTATTTCTGTAA-TTTTATAAA-TCAAG
* *
55657073 GGTATTTCTGTAACTTTGTAAATCAAG
1 GGTATTTCTGTAATTTTATAAATCAAG
* *
55657100 GGTATTT-TGGTAATTTTACAAATCGAG
1 GGTATTTCT-GTAATTTTATAAATCAAG
* * * *
55657127 GGTATTTCGGTAATTTCACAAACCAAG
1 GGTATTTCTGTAATTTTATAAATCAAG
* *
55657154 GGTATTT-TGGTAATTTTACAAA-CTAGG
1 GGTATTTCT-GTAATTTTATAAATC-AAG
* *
55657181 GGTATTT-TGGTAATTTTACAAACCAAG
1 GGTATTTCT-GTAATTTTATAAATCAAG
*
55657208 GGTATTT-TAGTAATTTTGTAAATCGAA-
1 GGTATTTCT-GTAATTTTATAAATC-AAG
*** * *
55657235 GGTAAAACAGTAATTTTGTAAATCAAG
1 GGTATTTCTGTAATTTTATAAATCAAG
55657262 GGTA
1 GGTA
55657266 AAATAGTAAT
Statistics
Matches: 184, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
26 4 0.02
27 147 0.80
28 18 0.10
29 15 0.08
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
GGTATTTCTGTAATTTTATAAATCAAG
Found at i:55657154 original size:54 final size:54
Alignment explanation
Indices: 55657017--55657238 Score: 223
Period size: 54 Copynumber: 4.1 Consensus size: 54
55657007 ACAAACAAAA
* ** * * * *
55657017 GGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAATTTTTATAAAGTCAAG
1 GGTATTTCGGTAATTTTACAAACCAAGGGTATTT-TGGTAA-TTTTACAAA-TCGAG
* * ** *
55657073 GGTATTTCTGTAACTTTGTAAATCAAGGGTATTTTGGTAATTTTACAAATCGAG
1 GGTATTTCGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAATCGAG
* *
55657127 GGTATTTCGGTAATTTCACAAACCAAGGGTATTTTGGTAATTTTACAAA-CTAGG
1 GGTATTTCGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAATCGA-G
* * ** *
55657181 GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAA
1 GGTATTTCGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAATCGAG
55657235 GGTA
1 GGTA
55657239 AAACAGTAAT
Statistics
Matches: 142, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
53 2 0.01
54 96 0.68
55 11 0.08
56 33 0.23
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (54 bp):
GGTATTTCGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTACAAATCGAG
Found at i:55657248 original size:54 final size:54
Alignment explanation
Indices: 55657096--55657303 Score: 193
Period size: 54 Copynumber: 3.9 Consensus size: 54
55657086 CTTTGTAAAT
* *** *
55657096 CAAGGGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAAC
* * ****
55657150 CAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTACAAATCGA-GGGTAAAACGGTAATTTTACAAAC
** * * ** *
55657204 CAAGGGTATTTTAGTAATTTTGTAAATCGAAGGTAAAACAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAAC
*** * *
55657258 CAAGGGTAAAATAGTAATTCTATAAATCGAGGGTAAAACGGTAATT
1 CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATT
55657304 CTGTAAGTCG
Statistics
Matches: 129, Mismatches: 23, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
53 2 0.02
54 125 0.97
55 2 0.02
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (54 bp):
CAAGGGTATTTTAGTAATTTTACAAATCGAGGGTAAAACGGTAATTTTACAAAC
Found at i:55657275 original size:81 final size:81
Alignment explanation
Indices: 55657190--55657394 Score: 198
Period size: 81 Copynumber: 2.5 Consensus size: 81
55657180 GGGTATTTTG
* **** * *
55657190 GTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAATCGAAGGTAAAAC-AGTAATTTTGT
1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTGTAAATCGAAGGTAAAACGA-TAATTATGT
55657254 AAATCAAGGGTAAAATA
65 AAATCAAGGGTAAAATA
* * * * * *
55657271 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGATAATTATGTA
1 GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTGTAAATCGAAGGTAAAACGATAATTATGTA
* **
55657336 AATCGAGGGTAAAACG
66 AATCAAGGGTAAAATA
* ** *
55657352 GTAATTATGTAAATCAAGGGTAAAAC-GATAATTCTGTAAATCG
1 GTAATTCTACAAACCAAGGGTAAAACAG-TAATTCTGTAAATCG
55657395 GGGGTACTTT
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
80 1 0.01
81 100 0.98
82 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (81 bp):
GTAATTCTACAAACCAAGGGTAAAACAGTAATTCTGTAAATCGAAGGTAAAACGATAATTATGTA
AATCAAGGGTAAAATA
Found at i:55657399 original size:27 final size:27
Alignment explanation
Indices: 55657218--55657400 Score: 217
Period size: 27 Copynumber: 6.8 Consensus size: 27
55657208 GGTATTTTAG
* *
55657218 TAATTTTGTAAATCGAAGGTAAAAC-A
1 TAATTCTGTAAATCGAGGGTAAAACGA
* * *
55657244 GTAATTTTGTAAATCAAGGGTAAAA-TA
1 -TAATTCTGTAAATCGAGGGTAAAACGA
* *
55657271 GTAATTCTATAAATCGAGGGTAAAACGG
1 -TAATTCTGTAAATCGAGGGTAAAACGA
*
55657299 TAATTCTGTAAGTCGAGGGTAAAACGA
1 TAATTCTGTAAATCGAGGGTAAAACGA
* *
55657326 TAATTATGTAAATCGAGGGTAAAACGG
1 TAATTCTGTAAATCGAGGGTAAAACGA
* *
55657353 TAATTATGTAAATCAAGGGTAAAACGA
1 TAATTCTGTAAATCGAGGGTAAAACGA
*
55657380 TAATTCTGTAAATCGGGGGTA
1 TAATTCTGTAAATCGAGGGTA
55657401 CTTTGGTAAT
Statistics
Matches: 136, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
27 136 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.28
Consensus pattern (27 bp):
TAATTCTGTAAATCGAGGGTAAAACGA
Found at i:55657400 original size:81 final size:81
Alignment explanation
Indices: 55657218--55657400 Score: 242
Period size: 81 Copynumber: 2.3 Consensus size: 81
55657208 GGTATTTTAG
* * * * *
55657218 TAATTTTGTAAATCGAAGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAATAGTAATTCTATAA
1 TAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATAA
* *
55657283 ATCGAGGGTAAAACGG
66 ATCAAGGGTAAAACGA
* * * *
55657299 TAATTCTGTAAGTCGAGGGTAAAAC-GATAATTATGTAAATCGAGGGTAAAACGGTAATTATGTA
1 TAATTCTGTAAATCGAGGGTAAAACAG-TAATTATGTAAATCAAGGGTAAAACAGTAATTATATA
55657363 AATCAAGGGTAAAACGA
65 AATCAAGGGTAAAACGA
*
55657380 TAATTCTGTAAATCGGGGGTA
1 TAATTCTGTAAATCGAGGGTA
55657401 CTTTGGTAAT
Statistics
Matches: 88, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
80 1 0.01
81 87 0.99
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.28
Consensus pattern (81 bp):
TAATTCTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAAGGGTAAAACAGTAATTATATAA
ATCAAGGGTAAAACGA
Found at i:55657411 original size:54 final size:54
Alignment explanation
Indices: 55657218--55657400 Score: 251
Period size: 54 Copynumber: 3.4 Consensus size: 54
55657208 GGTATTTTAG
* * * * *
55657218 TAATTTTGTAAATCGAAGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAA-TA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
* * * *
55657271 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAGTCGAGGGTAAAACGA
1 -TAATTCTGTAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
*
55657326 TAATTATGTAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
1 TAATTCTGTAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
*
55657380 TAATTCTGTAAATCGGGGGTA
1 TAATTCTGTAAATCGAGGGTA
55657401 CTTTGGTAAT
Statistics
Matches: 113, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
54 112 0.99
55 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.28
Consensus pattern (54 bp):
TAATTCTGTAAATCGAGGGTAAAACGGTAATTATGTAAATCAAGGGTAAAACGA
Found at i:55657427 original size:27 final size:27
Alignment explanation
Indices: 55657406--55657495 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
55657396 GGGTACTTTG
*
55657406 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
55657433 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
55657460 GTATTTTTACAAA-CTAAGGGTATTTCG
1 GTAATTTTACAAATCGAA-GGTATTTCA
55657487 GTAATTTTA
1 GTAATTTTA
55657496 GTAAACAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:55657447 original size:54 final size:54
Alignment explanation
Indices: 55657389--55657495 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
55657379 ATAATTCTGT
* * *
55657389 AAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAA-GGTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTTCAGTAATTTTAC
* * *
55657443 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTTCGGTAATTTTA
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTA
55657496 GTAAACAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.13
54 39 0.87
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTAC
Found at i:55665701 original size:40 final size:40
Alignment explanation
Indices: 55665656--55665920 Score: 383
Period size: 40 Copynumber: 6.6 Consensus size: 40
55665646 ACTACTTGCT
* * *
55665656 CAAATGCCCTCGGGACTTAGCCCGGTTATAGTAAATCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
55665696 CAAATGCCTTCGGGTCTGAGCCCAGATATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
55665736 CAAATGCCTTCGAGACTTAGCCCAGG-TATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCC-GGATATAGTAACTCGCA
55665776 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
55665816 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
55665856 CAAATGCCTTC-GGAGCTTAGCCCGGA-ATTAGTCACTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATA-TAGTAACTCGCA
*
55665896 CAAATGCCTTCGGGACTTGGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
55665921 TTATCATCCA
Statistics
Matches: 204, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
39 6 0.03
40 194 0.95
41 4 0.02
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:55675407 original size:40 final size:40
Alignment explanation
Indices: 55675221--55675505 Score: 388
Period size: 39 Copynumber: 7.2 Consensus size: 40
55675211 GGATTGATAC
* *
55675221 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
55675261 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
55675300 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
55675339 CCGGGCTAAG-CCTGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
55675378 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
55675418 CTGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
55675458 CCGGGCTAAGTCCCGAAGGCATTTGAGCTAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
55675498 CC-GGCTAA
1 CCGGGCTAA
55675506 ACTCCGAAGG
Statistics
Matches: 232, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
39 120 0.52
40 112 0.48
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:55679632 original size:15 final size:16
Alignment explanation
Indices: 55679612--55679642 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55679602 TGCATATGTA
55679612 TGAATG-AATTTTATG
1 TGAATGAAATTTTATG
55679627 TGAATGAAATTTTATG
1 TGAATGAAATTTTATG
55679643 GCCTGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.45
Consensus pattern (16 bp):
TGAATGAAATTTTATG
Found at i:55682570 original size:38 final size:38
Alignment explanation
Indices: 55682527--55682599 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
55682517 TTTCAAATTA
55682527 ACATGTATAACCGTGACATATCCACTTAGCACCACATT
1 ACATGTATAACCGTGACATATCCACTTAGCACCACATT
* **
55682565 ACATGTTTAACCGTGGTATATCCACTTAGCACCAC
1 ACATGTATAACCGTGACATATCCACTTAGCACCAC
55682600 GTTAATGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (38 bp):
ACATGTATAACCGTGACATATCCACTTAGCACCACATT
Found at i:55682681 original size:48 final size:48
Alignment explanation
Indices: 55682576--55682701 Score: 209
Period size: 48 Copynumber: 2.6 Consensus size: 48
55682566 CATGTTTAAC
55682576 CGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATGTAAT
1 CGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAAT
* * *
55682623 CGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTGTAAT
1 CGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAAT
*
55682671 CTTGGTATATCCACTTAGCACCACGTTACAT
1 CGTGGTATATCCACTTAGCACCACGTTACAT
55682702 TTATAACCGT
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
47 27 0.37
48 46 0.63
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (48 bp):
CGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATGTAAT
Found at i:55684945 original size:17 final size:18
Alignment explanation
Indices: 55684912--55684946 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55684902 TATTTTCTTT
*
55684912 GAGGTCCATGATAATTGG
1 GAGGTCCAAGATAATTGG
55684930 GAGGTCCAAG-TAATTGG
1 GAGGTCCAAGATAATTGG
55684947 AAATTCCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (18 bp):
GAGGTCCAAGATAATTGG
Found at i:55692645 original size:46 final size:46
Alignment explanation
Indices: 55692595--55692770 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
55692585 TGGTTGAGCA
55692595 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
55692641 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* *
55692686 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * *
55692734 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55692771 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 6 0.05
45 4 0.04
46 63 0.56
47 30 0.27
48 4 0.04
50 5 0.04
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:55692751 original size:93 final size:93
Alignment explanation
Indices: 55692592--55692762 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
55692582 GGATGGTTGA
* *
55692592 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
55692657 TGAGTCCGAGTTCATGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAGATGTAACTAG
* *
55692685 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
55692750 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55692763 GCTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:55699897 original size:46 final size:46
Alignment explanation
Indices: 55699847--55700022 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
55699837 TGGTTGAGCA
*
55699847 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
55699893 TCCGAACTCGTTGAGTTGAGTCCGAGTTCA-TGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* *
55699940 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
55699986 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55700023 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
45 3 0.03
46 64 0.58
47 30 0.27
48 3 0.03
50 5 0.05
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:55700003 original size:93 final size:93
Alignment explanation
Indices: 55699844--55700014 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
55699834 GGATGGTTGA
* * *
55699844 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
55699909 TGAGTCCGAGTTCATGAGATGTAACTAG
66 TGAGTCCGAGTTCATGAGATGTAACTAG
* *
55699937 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
55700002 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
55700015 GCTTATGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCATGAGATGTAACTAG
Found at i:55702674 original size:137 final size:135
Alignment explanation
Indices: 55702376--55702797 Score: 625
Period size: 137 Copynumber: 3.1 Consensus size: 135
55702366 TAGAAAAATG
*
55702376 AATTATATTCTTTCCAAAAAATTATTAATTTACATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATA-TCTTTCCAAAAAA-TATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
* *
55702441 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
64 TATAA-TTTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
55702506 CATATATT
128 CATATATT
* * * * *
55702514 AACTATATTTTTTCAAAGGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAAT
1 AATTATATCTTTCCAAA-AAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAAT
55702579 ATAATTGTTTATATTAATAAATTTC-GTAAAATA-ATACAATTAATATTTTGTATGAATCAAATT
65 ATAATT-TTTATATTAATAAA-TTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
55702642 CATATATT
128 CATATATT
*
55702650 AATTATGATCTTTCCAAAACAATATTAATTTCCA-GATCTTTTATATTTTGACTAAAATTAATTA
1 AATTAT-ATCTTTCCAAAA-AATATTAATTTCCATG-TCTTTTATATTTTGACTGAAATTAATTA
* *
55702714 ATATAACTTTTTATTTTAATAAATCCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
63 ATATAA-TTTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
*
55702779 TTATATATT
127 TCATATATT
55702788 AATTATATCT
1 AATTATATCT
55702798 ATGTTCTCTA
Statistics
Matches: 259, Mismatches: 16, Indels: 19
0.88 0.05 0.06
Matches are distributed among these distances:
136 47 0.18
137 156 0.60
138 56 0.22
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (135 bp):
AATTATATCTTTCCAAAAAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAATA
TAATTTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATTCAT
ATATT
Found at i:55704375 original size:20 final size:20
Alignment explanation
Indices: 55704339--55704377 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55704329 ATTTGTGTTG
*
55704339 TAATTCATAATTCTATTTTC
1 TAATTCATAATTATATTTTC
55704359 TAATTC-TAATATATATTTT
1 TAATTCATAAT-TATATTTT
55704378 ATTATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATTCATAATTATATTTTC
Found at i:55721321 original size:39 final size:39
Alignment explanation
Indices: 55721262--55721541 Score: 454
Period size: 39 Copynumber: 7.2 Consensus size: 39
55721252 AAGACACTAA
*
55721262 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
55721301 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
55721340 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
55721379 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGTTGG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
55721418 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
55721457 AAATGTATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
55721496 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCT-G
1 AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
55721534 ATAATATA
1 A-AATATA
55721542 ATTTCGGGTT
Statistics
Matches: 227, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
38 2 0.01
39 225 0.99
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.24
Consensus pattern (39 bp):
AAATATATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:55723392 original size:40 final size:40
Alignment explanation
Indices: 55723259--55723403 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
55723249 CGAATGATGT
* * *
55723259 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CATA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAATA
* *
55723298 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 -CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAATA
*
55723339 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-A
* * *
55723379 CTGGGCTATGTCCCAAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
55723404 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
39 3 0.03
40 75 0.85
41 10 0.11
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATA
Found at i:55730864 original size:14 final size:14
Alignment explanation
Indices: 55730833--55730884 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
55730823 TGCAAACAGA
*
55730833 TTTTACATTATAAG
1 TTTTACATTATAAC
* * *
55730847 TTTTTCTTTGTAAC
1 TTTTACATTATAAC
55730861 TTTTACATTATAAC
1 TTTTACATTATAAC
55730875 TTTTACATTA
1 TTTTACATTA
55730885 CAACCTGACC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.56
Consensus pattern (14 bp):
TTTTACATTATAAC
Found at i:55731670 original size:26 final size:27
Alignment explanation
Indices: 55731641--55731693 Score: 99
Period size: 26 Copynumber: 2.0 Consensus size: 27
55731631 ATACATATTG
55731641 CAAAATTATTTCAAAAATAAG-AAATA
1 CAAAATTATTTCAAAAATAAGTAAATA
55731667 CAAAATTATTTCAAAAATAAGTAAATA
1 CAAAATTATTTCAAAAATAAGTAAATA
55731694 ACCTAGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (27 bp):
CAAAATTATTTCAAAAATAAGTAAATA
Found at i:55734301 original size:38 final size:38
Alignment explanation
Indices: 55734257--55734332 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
55734247 GATAAGGTAA
55734257 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTACCCT
1 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTACCCT
*
55734295 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTTCCCT
1 CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTACCCT
55734333 GCATTAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (38 bp):
CTAAGTTTCCAAAATGACTTAAAAAATAGTTTTACCCT
Found at i:55736409 original size:27 final size:27
Alignment explanation
Indices: 55736358--55736447 Score: 110
Period size: 27 Copynumber: 3.2 Consensus size: 27
55736348 GTGACAGAGT
55736358 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* * *
55736387 CACCAGAAGAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
55736414 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
55736442 CACCAG
1 CACCAG
55736448 GACGCTTCCT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
27 23 0.43
28 23 0.43
29 7 0.13
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:55736600 original size:28 final size:28
Alignment explanation
Indices: 55736553--55736643 Score: 155
Period size: 28 Copynumber: 3.2 Consensus size: 28
55736543 AAATTAACCC
* * *
55736553 TAGGGGTATAAAGGTCATTTTTCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
55736581 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
55736609 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAATGGTAATTTTGCATACA
55736637 TAGGGGT
1 TAGGGGT
55736644 GTTCTAGTAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
TAGGGGTATAATGGTAATTTTGCATACA
Found at i:55744015 original size:26 final size:26
Alignment explanation
Indices: 55743986--55744052 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
55743976 CACCAGTATA
* * *
55743986 AGATTTTTGTGGCAGTGACACAGAAG
1 AGATATTTGTGGCAGGGACACAGAAC
* *
55744012 AGATATATGTGGCAGGGCCACAGAAC
1 AGATATTTGTGGCAGGGACACAGAAC
55744038 AGATAATTTGTGGCA
1 AGAT-ATTTGTGGCA
55744053 TAGCCACCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
26 25 0.74
27 9 0.26
ACGTcount: A:0.33, C:0.13, G:0.30, T:0.24
Consensus pattern (26 bp):
AGATATTTGTGGCAGGGACACAGAAC
Found at i:55744215 original size:28 final size:28
Alignment explanation
Indices: 55744170--55744257 Score: 140
Period size: 28 Copynumber: 3.1 Consensus size: 28
55744160 TTAACCCTAT
* **
55744170 GGGTATAAAGGTCTTTTTGCATACATAG
1 GGGTATAATGGTAATTTTGCATACATAG
*
55744198 GGGTATAATGGTAATTTTGCATACATAA
1 GGGTATAATGGTAATTTTGCATACATAG
55744226 GGGTATAATGGTAATTTTGCATACATAG
1 GGGTATAATGGTAATTTTGCATACATAG
55744254 GGGT
1 GGGT
55744258 TTCTAGTACA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 55 1.00
ACGTcount: A:0.31, C:0.08, G:0.26, T:0.35
Consensus pattern (28 bp):
GGGTATAATGGTAATTTTGCATACATAG
Found at i:55747960 original size:50 final size:50
Alignment explanation
Indices: 55747906--55748286 Score: 246
Period size: 50 Copynumber: 7.5 Consensus size: 50
55747896 CTGGTATGCA
55747906 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACG
* * * ** *
55747956 TAGTAGCCTGCACTTAGTACTACACACGT-GATCGAAGCT-ATC-GAGTATGCA
1 TAGTAGCCTGCACTTAGTACTACACA-TTCGACCTAA--TAATCTG-GTACACG
* * * * * *
55748007 TAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTATATG
1 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACG
** * *
55748057 TAGTAGCCTGCACTTAGTACTACACATGT-GACCTAACCATCTGATACATG
1 TAGTAGCCTGCACTTAGTACTACACAT-TCGACCTAATAATCTGGTACACG
* * * * ***
55748107 TAGTAGCTTGCAC-TATGTACTACACA--CGTAATCGAAGCT-ATCGGGTACGTA
1 TAGTAGCCTGCACTTA-GTACTACACATTCG--ACCTAA--TAATCTGGTACACG
* *
55748158 TAGTAGCCTGAACTTAGTA-TAC-CATGCGA-CTAATTACAATCTGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATTCGACCTAA-T--AATCTGGTACACG
* * *** *
55748208 TAGTAGCCTGCACTTAGTACTACACACGT-GACCTAAAACCATCTTAAACACA
1 TAGTAGCCTGCACTTAGTACTACACA-TTCGACCTAATA--ATCTGGTACACG
*
55748260 TAGTAGCCTGCACATAGTACTACACAT
1 TAGTAGCCTGCACTTAGTACTACACAT
55748287 GTGTTCTCAC
Statistics
Matches: 257, Mismatches: 48, Indels: 51
0.72 0.13 0.14
Matches are distributed among these distances:
47 1 0.00
48 4 0.02
49 5 0.02
50 137 0.53
51 66 0.26
52 40 0.16
53 4 0.02
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACG
Found at i:55748018 original size:101 final size:101
Alignment explanation
Indices: 55747899--55748087 Score: 315
Period size: 101 Copynumber: 1.9 Consensus size: 101
55747889 AAGCTCTCTG
* * * *
55747899 GTATGCATAGTAGCCTGCACTTAGTACTACACATTCGACCTAATAATCTGGTACACGTAGTAGCC
1 GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTACACGTAGTAGCC
55747964 TGCACTTAGTACTACACACGTGATCGAAGCTATCGA
66 TGCACTTAGTACTACACACGTGATCGAAGCTATCGA
* *
55748000 GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTATATGTAGTAGCC
1 GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTACACGTAGTAGCC
*
55748065 TGCACTTAGTACTACACATGTGA
66 TGCACTTAGTACTACACACGTGA
55748088 CCTAACCATC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 81 1.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (101 bp):
GTATGCATAGTAGACTGCACTTAGTACTACACATGCGACCTAACAACCTGGTACACGTAGTAGCC
TGCACTTAGTACTACACACGTGATCGAAGCTATCGA
Found at i:55748173 original size:151 final size:151
Alignment explanation
Indices: 55747906--55748285 Score: 493
Period size: 151 Copynumber: 2.5 Consensus size: 151
55747896 CTGGTATGCA
** *
55747906 TAGTAGCCTGCACTTAGTACTACACAT-TCGACCTAATAATCTGGTACACGTAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACATGT-GACCTAACCATCTGATACACGTAGTAGCCTGCACT
* * *
55747970 -TAGTACTACACACGTGATCGAAGCTATCGAGTATGCATAGTAGACTGCACTTAGTACTACACAT
65 ATAGTACTACACACGTAATCGAAGCTATCGAGTACGCATAGTAGACTGAACTTAGTA-TAC-CAT
* *
55748034 GCGACCT-A-ACAACCTGGTATATG
128 GCGA-CTAATACAACCTGGTACACG
* *
55748057 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACATGTAGTAGCTTGCACTA
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTA
* * *
55748122 T-GTACTACACACGTAATCGAAGCTATCGGGTACGTATAGTAGCCTGAACTTAGTATACCATGCG
66 TAGTACTACACACGTAATCGAAGCTATCGAGTACGCATAGTAGACTGAACTTAGTATACCATGCG
*
55748186 ACTAATTACAATCTGGTACACG
131 ACTAA-TACAACCTGGTACACG
* * * *
55748208 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAAAACCATCTTAAACACATAGTAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACATGTGACCT--AACCATCTGATACACGTAGTAGCCTGCAC
55748273 -ATAGTACTACACA
64 TATAGTACTACACA
55748286 TGTGTTCTCA
Statistics
Matches: 201, Mismatches: 20, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
148 2 0.01
149 8 0.04
150 3 0.01
151 150 0.75
152 4 0.02
153 34 0.17
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (151 bp):
TAGTAGCCTGCACTTAGTACTACACATGTGACCTAACCATCTGATACACGTAGTAGCCTGCACTA
TAGTACTACACACGTAATCGAAGCTATCGAGTACGCATAGTAGACTGAACTTAGTATACCATGCG
ACTAATACAACCTGGTACACG
Found at i:55751392 original size:25 final size:25
Alignment explanation
Indices: 55751364--55751442 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
55751354 CTAATGGCCG
55751364 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
55751389 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
55751411 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
55751436 ATGTGAT
1 ATGTGAT
55751443 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:55751414 original size:47 final size:47
Alignment explanation
Indices: 55751351--55751731 Score: 627
Period size: 47 Copynumber: 8.0 Consensus size: 47
55751341 ATGATAGTAT
55751351 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55751398 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
55751445 GGCCTAATGGCCGATGTGATGAATGTGGAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
*
55751492 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
55751541 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAA
*
55751590 GGCCTAATGGCTGATGTGATGAATGTGAAAGTGTATATATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* *
55751637 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
* * * * * *
55751684 GGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAA
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55751731 G
1 G
55751732 TCCCGAAGGG
Statistics
Matches: 316, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 223 0.71
49 93 0.29
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (47 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
Found at i:55751676 original size:192 final size:188
Alignment explanation
Indices: 55751351--55751729 Score: 641
Period size: 192 Copynumber: 2.0 Consensus size: 188
55751341 ATGATAGTAT
55751351 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
*
55751416 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGGAAGTGTAT
66 ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * *
55751481 ATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAG
131 ATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATA-A-ATGTGATAG
*
55751541 GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCTGATG
1 GGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATG
55751606 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
64 TGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGT
* * *
55751671 ATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATA
129 ATATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATA
55751730 AGTCCCGAAG
Statistics
Matches: 178, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
190 41 0.23
191 1 0.01
192 136 0.76
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (188 bp):
GGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTG
ATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
ATATGTGACAAGGCCGAATGGCCAACGTGATGAATGTGAAAGTGTATAAATGTGATAG
Found at i:55751906 original size:37 final size:37
Alignment explanation
Indices: 55751850--55751928 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
55751840 CCGAGCTCTA
* * * * *
55751850 AAGACCCGATGACTACGTGTGGGGATTTTTTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
55751887 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55751924 AAGAC
1 AAGAC
55751929 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55757874 original size:21 final size:21
Alignment explanation
Indices: 55757850--55757971 Score: 72
Period size: 21 Copynumber: 5.8 Consensus size: 21
55757840 GTCCCTAATC
*
55757850 CACACGGGCGTATGCCTCAGT
1 CACACGGGCGTGTGCCTCAGT
* **
55757871 CACAC-GGTGTGTGCCTCTCTT
1 CACACGGGCGTGTGCCTC-AGT
** *
55757892 CACACGGGTATGTGCCTCAGC
1 CACACGGGCGTGTGCCTCAGT
* * *
55757913 CACAC-GACGATATGCTTCTC-TT
1 CACACGGGCG-TGTGC--CTCAGT
*
55757935 CACACGGGCGTGTGCCTCAGC
1 CACACGGGCGTGTGCCTCAGT
55757956 CACAC-GGCTGTGTGCC
1 CACACGGGC-GTGTGCC
55757972 CCTCTTCACA
Statistics
Matches: 75, Mismatches: 18, Indels: 16
0.69 0.17 0.15
Matches are distributed among these distances:
20 17 0.23
21 32 0.43
22 20 0.27
23 6 0.08
ACGTcount: A:0.16, C:0.34, G:0.26, T:0.23
Consensus pattern (21 bp):
CACACGGGCGTGTGCCTCAGT
Found at i:55757977 original size:43 final size:43
Alignment explanation
Indices: 55757850--55757982 Score: 171
Period size: 43 Copynumber: 3.1 Consensus size: 43
55757840 GTCCCTAATC
* *
55757850 CACACGGGCGTATGCCTCAGTCACACGG-TGTGTGCCTCTCTT
1 CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCTCTCTT
** * * *
55757892 CACACGGGTATGTGCCTCAGCCACACGAC-GATATGCTTCTCTT
1 CACACGGGCGTGTGCCTCAGCCACACGGCTG-TGTGCCTCTCTT
*
55757935 CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCCCTCTT
1 CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCTCTCTT
55757978 CACAC
1 CACAC
55757983 AAGCTTTTGA
Statistics
Matches: 75, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
42 24 0.32
43 50 0.67
44 1 0.01
ACGTcount: A:0.17, C:0.36, G:0.24, T:0.23
Consensus pattern (43 bp):
CACACGGGCGTGTGCCTCAGCCACACGGCTGTGTGCCTCTCTT
Found at i:55759903 original size:37 final size:37
Alignment explanation
Indices: 55759848--55759934 Score: 113
Period size: 37 Copynumber: 2.4 Consensus size: 37
55759838 CACAAGTAGG
* ** *
55759848 CCAACCGA-AACACGCCAAACGCTCATAAGTGGTAAT
1 CCAACCGATAACACGCCAAACACTCATAAAAGCTAAT
* *
55759884 CCAACCAATAACATGCCAAACACTCATAAAAGCTAAT
1 CCAACCGATAACACGCCAAACACTCATAAAAGCTAAT
55759921 CCAACCGATAACAC
1 CCAACCGATAACAC
55759935 ACCTATTTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 7 0.17
37 35 0.83
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (37 bp):
CCAACCGATAACACGCCAAACACTCATAAAAGCTAAT
Found at i:55764878 original size:8 final size:8
Alignment explanation
Indices: 55764865--55764898 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
55764855 AGTCCCTAAT
55764865 TCACAAAA
1 TCACAAAA
55764873 TCACAAAA
1 TCACAAAA
*
55764881 TCAAAAAA
1 TCACAAAA
55764889 TACACAAAA
1 T-CACAAAA
55764898 T
1 T
55764899 TTCCTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.65, C:0.21, G:0.00, T:0.15
Consensus pattern (8 bp):
TCACAAAA
Found at i:55781938 original size:44 final size:44
Alignment explanation
Indices: 55781890--55781978 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
55781880 TATATACACA
55781890 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
1 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
55781934 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
1 ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
55781978 A
1 A
55781979 AACCTATCAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (44 bp):
ATTTAAGCAATTAACATATCATAACATAACTCATATTGATCCGC
Found at i:55785281 original size:28 final size:25
Alignment explanation
Indices: 55785250--55785309 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 25
55785240 TTCCATATTA
*
55785250 TCACATCATTTCATATACTATTATCAAT
1 TCACATCATTT--TATACCATT-TCAAT
55785278 TCACA--ATTTTATACCATTTCAAT
1 TCACATCATTTTATACCATTTCAAT
*
55785301 TCAAATCAT
1 TCACATCAT
55785310 ACATTATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
23 9 0.32
24 8 0.29
25 2 0.07
26 4 0.14
28 5 0.18
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
TCACATCATTTTATACCATTTCAAT
Found at i:55797657 original size:7 final size:7
Alignment explanation
Indices: 55797647--55797671 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55797637 AGAAAAAGAG
55797647 AAAAAAT
1 AAAAAAT
55797654 AAAAAAT
1 AAAAAAT
55797661 AAAAAAT
1 AAAAAAT
55797668 AAAA
1 AAAA
55797672 TAAAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:55800910 original size:25 final size:25
Alignment explanation
Indices: 55800876--55800945 Score: 113
Period size: 25 Copynumber: 2.8 Consensus size: 25
55800866 CTCTTTTAAT
*
55800876 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55800901 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
55800926 AATTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
55800946 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:55801217 original size:27 final size:27
Alignment explanation
Indices: 55801152--55801290 Score: 172
Period size: 27 Copynumber: 5.2 Consensus size: 27
55801142 GGCAAAATGG
* * * * **
55801152 TAATTTTACCCCACAAGAGTATCTCGG
1 TAATTCTACCCTACAAGGGTATTTCAA
* *
55801179 TAATTCTACCCTAAAAGGGTATTTCGA
1 TAATTCTACCCTACAAGGGTATTTCAA
* *
55801206 TAATTTTACCCTACAGGGGTATTTCAA
1 TAATTCTACCCTACAAGGGTATTTCAA
*
55801233 TAATTCTACCCTAC-AGGGTATTTCCA
1 TAATTCTACCCTACAAGGGTATTTCAA
55801259 TAATTCTACCCTACAAGGGTATTTCAA
1 TAATTCTACCCTACAAGGGTATTTCAA
55801286 TAATT
1 TAATT
55801291 TTGTAAATCG
Statistics
Matches: 97, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 24 0.25
27 73 0.75
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (27 bp):
TAATTCTACCCTACAAGGGTATTTCAA
Found at i:55801270 original size:53 final size:54
Alignment explanation
Indices: 55801152--55801290 Score: 181
Period size: 53 Copynumber: 2.6 Consensus size: 54
55801142 GGCAAAATGG
* * * * ** *
55801152 TAATTTTACCCCACAAGAGTATCTCGGTAATTCTACCCTAAAAGGGTATTTCGA
1 TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTAAAAGGGTATTTCCA
* * *
55801206 TAATTTTACCCTACAGGGGTATTTCAATAATTCTACCCT-ACAGGGTATTTCCA
1 TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTAAAAGGGTATTTCCA
55801259 TAATTCTACCCTACAAGGGTATTTCAATAATT
1 TAATTCTACCCTACAAGGGTATTTCAATAATT
55801291 TTGTAAATCG
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 42 0.56
54 33 0.44
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.35
Consensus pattern (54 bp):
TAATTCTACCCTACAAGGGTATTTCAATAATTCTACCCTAAAAGGGTATTTCCA
Found at i:55801304 original size:27 final size:27
Alignment explanation
Indices: 55801274--55801643 Score: 194
Period size: 27 Copynumber: 13.7 Consensus size: 27
55801264 CTACCCTACA
* *
55801274 AGGGTATTTCAATAATTTTGTAAATCG
1 AGGGTATTTCAGTAATTTTATAAATCG
*** * * **
55801301 AGGGTAAAACGGTAATTTTGTAAATTT
1 AGGGTATTTCAGTAATTTTATAAATCG
*
55801328 AGGGTACTTT-GGTAATTTT-TACAAGTCG
1 AGGGTA-TTTCAGTAATTTTATA-AA-TCG
* *
55801356 AGAGTATTTCAGTAATTTTAAAAATCG
1 AGGGTATTTCAGTAATTTTATAAATCG
*
55801383 AGGGTATTTCAGTAATTTTACAAA-CTG
1 AGGGTATTTCAGTAATTTTATAAATC-G
* * *
55801410 AGGGTATTTCGGTAATTTTACAAAT-T
1 AGGGTATTTCAGTAATTTTATAAATCG
** * *
55801436 AGGGGTATTTTGGTAATTTTACAAACCG
1 A-GGGTATTTCAGTAATTTTATAAATCG
* ** * * *
55801464 GGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTCAGTAATTTTATAAATCG
** * * *
55801491 AGGGTATTTTGGTAATTTTACAAGTCA
1 AGGGTATTTCAGTAATTTTATAAATCG
* *
55801518 AGGGTATTTCAGTAATTTCACAAATC-
1 AGGGTATTTCAGTAATTTTATAAATCG
** * * *
55801544 AGGGGTATTTTGGTAATTTCACAAA-CT
1 A-GGGTATTTCAGTAATTTTATAAATCG
** * * *
55801571 AGGGGTATTTTGGTAATTTTACAAACCA
1 A-GGGTATTTCAGTAATTTTATAAATCG
* * * *
55801599 ACGGTATTTTAGTAATTTTACAAATTG
1 AGGGTATTTCAGTAATTTTATAAATCG
* *
55801626 AGGGCATTTTAGTAATTT
1 AGGGTATTTCAGTAATTT
55801644 GGTAAACTAA
Statistics
Matches: 285, Mismatches: 46, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
26 6 0.02
27 260 0.91
28 18 0.06
29 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCAGTAATTTTATAAATCG
Found at i:55801426 original size:54 final size:54
Alignment explanation
Indices: 55801328--55801643 Score: 305
Period size: 54 Copynumber: 5.8 Consensus size: 54
55801318 TTGTAAATTT
* * * * *
55801328 AGGGTACTTTGGTAATTTTTAC-AAGTCGAGAGTATTTCAGTAATTTTAAAAATCG
1 AGGGTATTTTGGTAA-TTTTACAAACT-GAGGGTATTTCAGTAATTTTACAAATCA
** * *
55801383 AGGGTATTTCAGTAATTTTACAAACTGAGGGTATTTCGGTAATTTTACAAATTA
1 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATCA
* * * ** ** *
55801437 GGGGTATTTTGGTAATTTTACAAACCGGGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATCA
* * *
55801491 AGGGTATTTTGGTAATTTTAC-AAGTCAAGGGTATTTCAGTAATTTCACAAATCA
1 AGGGTATTTTGGTAATTTTACAAACT-GAGGGTATTTCAGTAATTTTACAAATCA
* * ** *
55801545 GGGGTATTTTGGTAATTTCACAAACT-AGGGGTATTTTGGTAATTTTACAAACCA
1 AGGGTATTTTGGTAATTTTACAAACTGA-GGGTATTTCAGTAATTTTACAAATCA
* * * * *
55801599 ACGGTATTTTAGTAATTTTACAAATTGAGGGCATTTTAGTAATTT
1 AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCAGTAATTT
55801644 GGTAAACTAA
Statistics
Matches: 212, Mismatches: 44, Indels: 11
0.79 0.16 0.04
Matches are distributed among these distances:
53 3 0.01
54 190 0.90
55 19 0.09
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCAGTAATTTTACAAATCA
Found at i:55801652 original size:81 final size:81
Alignment explanation
Indices: 55801329--55801643 Score: 346
Period size: 81 Copynumber: 3.9 Consensus size: 81
55801319 TGTAAATTTA
* * * * * *
55801329 GGGTACTTTGGTAATTTTTACAAGTCGAGAGTATTTCAGTAATTTTAAAAATCGAGGGTATTTCA
1 GGGTATTTTGGTAA-TTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTA
55801394 GTAATTTTACAAACT-G
65 GTAATTTTACAAACTAG
* * * ** * * *
55801410 AGGGTATTTCGGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAACCGGGGGTATTTTG
1 -GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTA
** * *
55801475 GTAATTTTGTAAACCAA
65 GTAATTTTACAAACTAG
* * *
55801492 GGGTATTTTGGTAATTTTACAAGTCAAGGGTATTTCAGTAATTTCACAAATC-AGGGGTATTTTG
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGA-GGGTATTTTA
*
55801556 GTAATTTCACAAACTAG
65 GTAATTTTACAAACTAG
* * * * *
55801573 GGGTATTTTGGTAATTTTACAAACCAACGGTATTTTAGTAATTTTACAAATTGAGGGCATTTTAG
1 GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAG
55801638 TAATTT
66 TAATTT
55801644 GGTAAACTAA
Statistics
Matches: 190, Mismatches: 40, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
81 177 0.93
82 13 0.07
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAATCAAGGGTATTTCAGTAATTTTACAAATCGAGGGTATTTTAG
TAATTTTACAAACTAG
Found at i:55804293 original size:19 final size:18
Alignment explanation
Indices: 55804252--55804296 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
55804242 GGTTCTTTTG
55804252 ATTTTTTTTATTTTAATT
1 ATTTTTTTTATTTTAATT
* *
55804270 ATTTTTTTTCTTTT--GT
1 ATTTTTTTTATTTTAATT
55804286 ATTTTTTTTAT
1 ATTTTTTTTAT
55804297 CTTCTCGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.16, C:0.02, G:0.02, T:0.80
Consensus pattern (18 bp):
ATTTTTTTTATTTTAATT
Found at i:55804299 original size:18 final size:18
Alignment explanation
Indices: 55804245--55804299 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
55804235 TGTTCTTGGT
55804245 TCTTTTG-ATTTTTTTTA
1 TCTTTTGTATTTTTTTTA
55804262 T-TTTAAT-TA-TTTTTTT-
1 TCTTT--TGTATTTTTTTTA
55804278 TCTTTTGTATTTTTTTTA
1 TCTTTTGTATTTTTTTTA
55804296 TCTT
1 TCTT
55804300 CTCGAATCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 13
0.70 0.00 0.30
Matches are distributed among these distances:
15 1 0.03
16 6 0.19
17 18 0.58
18 6 0.19
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (18 bp):
TCTTTTGTATTTTTTTTA
Found at i:55805330 original size:60 final size:60
Alignment explanation
Indices: 55805261--55805384 Score: 221
Period size: 60 Copynumber: 2.1 Consensus size: 60
55805251 GTCATTATCA
*
55805261 ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTTTCTATTTTATTATTATT
1 ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
* *
55805321 ATATGCTATCATTATTCTCATTAATGTATTGTCATTATTAGTCTCTATTTTATTATTATT
1 ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
55805381 ATAT
1 ATAT
55805385 TATTACTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.27, C:0.12, G:0.06, T:0.54
Consensus pattern (60 bp):
ATATGCTATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
Found at i:55805598 original size:27 final size:26
Alignment explanation
Indices: 55805487--55805639 Score: 120
Period size: 24 Copynumber: 6.0 Consensus size: 26
55805477 TACCATTATT
* *
55805487 ATTATCATATATTTTATATTATTTT--
1 ATTATTATATATATTAT-TTATTTTAA
* * *
55805512 ATT-TTACATATGTTATTTCTTTTAA
1 ATTATTATATATATTATTTATTTTAA
* * *
55805537 ACTATTATACATATTGTTTATTTTGAA
1 ATTATTATATATATTATTTATTTT-AA
* *
55805564 ACTT-TTATATACATTTTTGTATTTTAA
1 A-TTATTATATATATTATT-TATTTTAA
* *
55805591 ATTATTATGTATATTATTTACTTT-A
1 ATTATTATATATATTATTTATTTTAA
55805616 A-TATTATATATATTATTTATTTTA
1 ATTATTATATATATTATTTATTTTA
55805640 GACCTTTTTA
Statistics
Matches: 100, Mismatches: 20, Indels: 16
0.74 0.15 0.12
Matches are distributed among these distances:
23 6 0.06
24 30 0.30
25 7 0.07
26 22 0.22
27 28 0.28
28 7 0.07
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTATTATATATATTATTTATTTTAA
Found at i:55805848 original size:20 final size:22
Alignment explanation
Indices: 55805808--55805850 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55805798 TACTTAGTCA
55805808 AAATTGTTTAATCATTTATTTC
1 AAATTGTTTAATCATTTATTTC
*
55805830 AAATTGTTTTAT-A-TTATTTC
1 AAATTGTTTAATCATTTATTTC
55805850 A
1 A
55805851 TTCTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
AAATTGTTTAATCATTTATTTC
Found at i:55807052 original size:47 final size:47
Alignment explanation
Indices: 55806981--55807430 Score: 756
Period size: 47 Copynumber: 9.6 Consensus size: 47
55806971 CCCTTCGAGA
* * * * * *
55806981 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
55807028 CCTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55807075 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
55807122 CTTATCATATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55807169 CTTATCACATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55807216 CTTATCACATATATACACTTTCACATTCGTCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55807263 CTTATCACATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55807310 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
55807357 CTTATCACATATATACACTTTCACATTCATCACATCAGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
55807404 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
55807431 TATTCAACTA
Statistics
Matches: 386, Mismatches: 17, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 386 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:55807059 original size:25 final size:25
Alignment explanation
Indices: 55807031--55807109 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 25
55807021 ACTCGGCCCT
55807031 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
** * * *
55807056 ATCACAT-T-GGC-CATTCGGCCTT-
1 ATCACATATATACACTTTC-ACATTC
55807078 ATCACATATATACACTTTCACATTC
1 ATCACATATATACACTTTCACATTC
55807103 ATCACAT
1 ATCACAT
55807110 CGGCCATTAG
Statistics
Matches: 39, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 11 0.28
23 5 0.13
24 5 0.13
25 18 0.46
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (25 bp):
ATCACATATATACACTTTCACATTC
Found at i:55819532 original size:205 final size:205
Alignment explanation
Indices: 55819159--55819871 Score: 1054
Period size: 205 Copynumber: 3.5 Consensus size: 205
55819149 AGCATAACAA
* * *
55819159 ATCTGGCCTTCAGATG-TTATACTGAAGCTGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
1 ATCTCGCCTTCGGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
*
55819223 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
66 GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
55819288 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
131 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
55819353 CACATAGCAG
196 CACATAGCAG
* * * *
55819363 ATCTCGCCTTTGGATGTTTATGCTGAAGCGGATCCAAGATGGTTTGGCATCCTTATGTTTATAAG
1 ATCTCGCCTTCGGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
* *
55819428 GAGCAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTATGATGAAGCAAATCTAAGATGAT
66 GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
* * * * *
55819493 TTATCATCTCTATATTGTCAAAGAATGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
131 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
*
55819558 CACATAGCAA
196 CACATAGCAG
* * *
55819568 ATCTCGCCTTCGGCTGTTTATGCTGAAGCGGATCCAAGATGGTTTGGAATCCTTGTGTTTACAAG
1 ATCTCGCCTTCGGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
* * * *
55819633 GAACAAATCGAAGACATAGCTGATTTGGTTTTCACGTGTTTACGTTGAAACAAATCTAAGATGAT
66 GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
* * * * *
55819698 TTGTCGTCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCA-TTTCAATGGAAAGCAG
131 TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTT-GATGGAGAGCAG
*
55819762 ATACATAGCAG
195 ACACATAGCAG
* * * * *
55819773 ATCT-GATCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACA
1 ATCTCG-CCTTCGGATGTTTATACTGAAGC-GGATCCAAGATGGTTTGGCATCCTTGTGTTTACA
* *
55819837 AGGAACAAATCGAAGACATAGCAGATTTGACTTTC
64 AGGAACAAATCGAAGACATAGCTGATTTGGCTTTC
55819872 GGATGTTCCC
Statistics
Matches: 457, Mismatches: 48, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
204 17 0.04
205 378 0.83
206 62 0.14
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (205 bp):
ATCTCGCCTTCGGATGTTTATACTGAAGCGGATCCAAGATGGTTTGGCATCCTTGTGTTTACAAG
GAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGATTACGATGAAGCAAATCTAAGATGAT
TTGTCGTCTCTGTATTGTCAGAGAACGAATCGAAGTTTGGCATCTTCACTTTGATGGAGAGCAGA
CACATAGCAG
Found at i:55820036 original size:44 final size:44
Alignment explanation
Indices: 55819954--55820038 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
55819944 GAGATCAGCA
* * *
55819954 TGGCATCCCTGTGCTTATAGGGAACAAGTTGGAAATAGCAGATT
1 TGGCATCCCTGTGCTTATAAGGAACAAGATCGAAATAGCAGATT
*
55819998 TGGCATCCCTGTGTTTATAAGGAACAA-ATCGAAGATAGCAG
1 TGGCATCCCTGTGCTTATAAGGAACAAGATCGAA-ATAGCAG
55820039 GTCTGACATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
43 4 0.11
44 32 0.89
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (44 bp):
TGGCATCCCTGTGCTTATAAGGAACAAGATCGAAATAGCAGATT
Found at i:55820784 original size:18 final size:18
Alignment explanation
Indices: 55820758--55820792 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55820748 TCTTGGTTCT
55820758 TTTGATTTTTTTATTTTA
1 TTTGATTTTTTTATTTTA
* *
55820776 TTTGTTTTTTTTCTTTT
1 TTTGATTTTTTTATTTT
55820793 GTATTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.83
Consensus pattern (18 bp):
TTTGATTTTTTTATTTTA
Found at i:55821857 original size:60 final size:60
Alignment explanation
Indices: 55821771--55821889 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
55821761 GTCATTATCA
*
55821771 ATATGCCATCATTATTCTCATCAATGTATTGTCATCATTAGTTTCTATTTTATTATTATT
1 ATATGCCATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
* *
55821831 ATATGCTATCATTATTCTCATTAATGTATTGTCATCATTAGTCTCTATTTTATTATTAT
1 ATATGCCATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTAT
55821890 ATTATTACTA
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.27, C:0.14, G:0.07, T:0.52
Consensus pattern (60 bp):
ATATGCCATCATTATTCTCATCAATGTATTGTCATCATTAGTCTCTATTTTATTATTATT
Found at i:55822105 original size:27 final size:26
Alignment explanation
Indices: 55821994--55822146 Score: 120
Period size: 24 Copynumber: 6.0 Consensus size: 26
55821984 TACCATTATT
* *
55821994 ATTATCATATATTTTATATTATTTT--
1 ATTATTATATATATTAT-TTATTTTAA
* * *
55822019 ATT-TTACATATGTTATTTCTTTTAA
1 ATTATTATATATATTATTTATTTTAA
* * *
55822044 ACTATTATACATATTGTTTATTTTGAA
1 ATTATTATATATATTATTTATTTT-AA
* *
55822071 ACTT-TTATATACATTTTTGTATTTTAA
1 A-TTATTATATATATTATT-TATTTTAA
* *
55822098 ATTATTATGTATATTATTTACTTT-A
1 ATTATTATATATATTATTTATTTTAA
55822123 A-TATTATATATATTATTTATTTTA
1 ATTATTATATATATTATTTATTTTA
55822147 GACCTTTTTA
Statistics
Matches: 100, Mismatches: 20, Indels: 16
0.74 0.15 0.12
Matches are distributed among these distances:
23 6 0.06
24 30 0.30
25 7 0.07
26 22 0.22
27 28 0.28
28 7 0.07
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (26 bp):
ATTATTATATATATTATTTATTTTAA
Found at i:55822355 original size:20 final size:22
Alignment explanation
Indices: 55822315--55822357 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55822305 TACTTAGTCA
55822315 AAATTGTTTAATCATTTATTTC
1 AAATTGTTTAATCATTTATTTC
*
55822337 AAATTGTTTTAT-A-TTATTTC
1 AAATTGTTTAATCATTTATTTC
55822357 A
1 A
55822358 TTCTTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (22 bp):
AAATTGTTTAATCATTTATTTC
Found at i:55831768 original size:6 final size:6
Alignment explanation
Indices: 55831748--55831946 Score: 124
Period size: 6 Copynumber: 32.3 Consensus size: 6
55831738 AAGAAACATT
* *
55831748 ATCAGA A-CTAGA ATCAAA ATCAGA ATCAAA ATCAGA ATCAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* *
55831796 ATCAGA TGAT-AGA ATCAAA ATCCA-A ATCAGA ATCAGA ATTAGGTA A-CAGA
1 ATCAGA --ATCAGA ATCAGA AT-CAGA ATCAGA ATCAGA ATCA-G-A ATCAGA
* * * * *
55831846 ATCAAA ATCAGT ATCAGGTA A-CAAA ATCAGA ATCAGA ACCAGA ATCAAA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
* * * *
55831895 ATTAGGTA A-CAGA ATCAGA ATCAGT ATCAGGTA A-CAAA ATCATA ATCAGA
1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA
55831945 AT
1 AT
55831947 GTGAATGTGA
Statistics
Matches: 150, Mismatches: 24, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
5 13 0.09
6 114 0.76
7 15 0.10
8 8 0.05
ACGTcount: A:0.51, C:0.16, G:0.14, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:55831847 original size:19 final size:19
Alignment explanation
Indices: 55831823--55831915 Score: 73
Period size: 19 Copynumber: 4.6 Consensus size: 19
55831813 AAATCCAAAT
55831823 CAGAATCAGAATTAGGTAA
1 CAGAATCAGAATTAGGTAA
*
55831842 CAGAATCAAAATCAGTATCAGGTAA
1 CAGAATC-AGA--A-T-T-AGGTAA
* *
55831867 CAAAATCAGAATCA-G-AA
1 CAGAATCAGAATTAGGTAA
*
55831884 CCAGAATCAAAATTAGGTAA
1 -CAGAATCAGAATTAGGTAA
55831904 CAGAATCAGAAT
1 CAGAATCAGAAT
55831916 CAGTATCAGG
Statistics
Matches: 57, Mismatches: 8, Indels: 18
0.69 0.10 0.22
Matches are distributed among these distances:
17 2 0.04
18 12 0.21
19 20 0.35
20 4 0.07
21 1 0.02
22 2 0.04
23 1 0.02
24 3 0.05
25 12 0.21
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18
Consensus pattern (19 bp):
CAGAATCAGAATTAGGTAA
Found at i:55831848 original size:25 final size:25
Alignment explanation
Indices: 55831819--55831883 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 25
55831809 ATCAAAATCC
*
55831819 AAATCAGAATCAGAATTAGGTAACA
1 AAATCAGAATCAGAATCAGGTAACA
* * *
55831844 GAATCAAAATCAGTATCAGGTAACA
1 AAATCAGAATCAGAATCAGGTAACA
55831869 AAATCAGAATCAGAA
1 AAATCAGAATCAGAA
55831884 CCAGAATCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.52, C:0.14, G:0.15, T:0.18
Consensus pattern (25 bp):
AAATCAGAATCAGAATCAGGTAACA
Found at i:55831856 original size:62 final size:62
Alignment explanation
Indices: 55831780--55831945 Score: 217
Period size: 62 Copynumber: 2.7 Consensus size: 62
55831770 GAATCAAAAT
* * * * * *
55831780 CAGAATCAGAATCAGAATCAGATGATAGAATCAAAATCCA-AATCAGAATCAGAATTAGGTAA
1 CAGAATCAGAATCAGTATCAGATAACAAAATCAAAAT-CAGAACCAGAATCAAAATTAGGTAA
* * *
55831842 CAGAATCAAAATCAGTATCAGGTAACAAAATCAGAATCAGAACCAGAATCAAAATTAGGTAA
1 CAGAATCAGAATCAGTATCAGATAACAAAATCAAAATCAGAACCAGAATCAAAATTAGGTAA
* *
55831904 CAGAATCAGAATCAGTATCAGGTAACAAAATCATAATCAGAA
1 CAGAATCAGAATCAGTATCAGATAACAAAATCAAAATCAGAA
55831946 TGTGAATGTG
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
61 2 0.02
62 90 0.98
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.19
Consensus pattern (62 bp):
CAGAATCAGAATCAGTATCAGATAACAAAATCAAAATCAGAACCAGAATCAAAATTAGGTAA
Done.