Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 267 of 322
Found at i:88468299 original size:44 final size:46
Alignment explanation
Indices: 88468210--88468300 Score: 150
Period size: 44 Copynumber: 2.0 Consensus size: 46
88468200 GAATAGAGGC
*
88468210 GTAATGGAACAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAACAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
*
88468256 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAAT
1 GTAATGGAACAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
88468300 G
1 G
88468301 GAATAGAGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 20 0.47
45 3 0.07
46 20 0.47
ACGTcount: A:0.26, C:0.05, G:0.31, T:0.37
Consensus pattern (46 bp):
GTAATGGAACAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAAT
Found at i:88468301 original size:39 final size:44
Alignment explanation
Indices: 88468210--88468317 Score: 136
Period size: 46 Copynumber: 2.5 Consensus size: 44
88468200 GAATAGAGGC
* *
88468210 GTAATGGAACAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--AT
88468256 GTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
*
88468296 G-AATGGAATAGAGGTGTAATAG
1 GTAATGGAATAGAGGCGTAATAG
88468318 CATAAGGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
39 18 0.31
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 20 0.34
ACGTcount: A:0.29, C:0.05, G:0.31, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:88468479 original size:15 final size:15
Alignment explanation
Indices: 88468459--88468497 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 15
88468449 CATAATTGTT
88468459 ATAAAATATAATTTA
1 ATAAAATATAATTTA
88468474 ATAAAATATATAATTTA
1 AT-AAA-ATATAATTTA
88468491 ATAAAAT
1 ATAAAAT
88468498 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 6 0.27
17 12 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATATAATTTA
Found at i:88468504 original size:17 final size:17
Alignment explanation
Indices: 88468464--88468497 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
88468454 TTGTTATAAA
88468464 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
88468481 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
88468498 TGTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:88468569 original size:20 final size:21
Alignment explanation
Indices: 88468530--88468569 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
88468520 AATTTACTAA
*
88468530 TAAAATCATAATATATAATAC
1 TAAAATCATAATATAAAATAC
*
88468551 TAAAAT-ATAATTTAAAATA
1 TAAAATCATAATATAAAATA
88468570 ATTATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATCATAATATAAAATAC
Found at i:88468611 original size:54 final size:54
Alignment explanation
Indices: 88468421--88468616 Score: 144
Period size: 54 Copynumber: 3.4 Consensus size: 54
88468411 TATTAATATA
* * * * * *
88468421 AATAATAAATAATTTAATCATATTTTAACATAATTGTTATAAAATATAATTTAAT
1 AATAATAAATAATTAAAT-AAAATTTAAAATAATTATTATTAAATATAATTTAAT
* * * **
88468476 AA-AATATATAATTTAATAAAATTGTTAATAA-ATATTCTTATATAAATTTACTAATAAAAT
1 AATAATAAATAATTAAATAAAA-T-TTAA-AATA-ATTATTAT-TAAA--TA-TAATTTAAT
* * *
88468536 CATAATATATAATACTAAAATATAATTTAAAATAATTATTATTAAATATAATTTAAT
1 AATAATAAATAAT--T-AAATAAAATTTAAAATAATTATTATTAAATATAATTTAAT
88468593 AATAATAAATAATTAAATAAAATT
1 AATAATAAATAATTAAATAAAATT
88468617 CTTATTCTTA
Statistics
Matches: 111, Mismatches: 17, Indels: 27
0.72 0.11 0.17
Matches are distributed among these distances:
53 2 0.02
54 24 0.22
55 8 0.07
56 8 0.07
57 21 0.19
58 2 0.02
59 2 0.02
60 12 0.11
61 19 0.17
62 5 0.05
63 2 0.02
64 6 0.05
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (54 bp):
AATAATAAATAATTAAATAAAATTTAAAATAATTATTATTAAATATAATTTAAT
Found at i:88468695 original size:32 final size:32
Alignment explanation
Indices: 88468659--88468722 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
88468649 TATATAATAC
*
88468659 TATAAAATATAATTTAAATAATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
** ** *
88468691 TATAATTTATAATCTACTTTATTATTATTAAA
1 TATAAAATATAATCTAAATAATTATTATTAAA
88468723 CTGCAATACA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAAAATATAATCTAAATAATTATTATTAAA
Found at i:88470134 original size:49 final size:49
Alignment explanation
Indices: 88470062--88470165 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
88470052 GAAAAAAAAC
* * ** * *
88470062 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
*
88470111 AAATTAAAATTGAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
88470160 AAATTA
1 AAATTA
88470166 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
Found at i:88472316 original size:12 final size:12
Alignment explanation
Indices: 88472292--88472325 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
88472282 CCGCATTTTA
88472292 AGCAAAAGAACG
1 AGCAAAAGAACG
* *
88472304 AGCCAAAGCACG
1 AGCAAAAGAACG
88472316 AGCAAAAGAA
1 AGCAAAAGAA
88472326 AATAAATAAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.56, C:0.21, G:0.24, T:0.00
Consensus pattern (12 bp):
AGCAAAAGAACG
Found at i:88473436 original size:23 final size:22
Alignment explanation
Indices: 88473392--88473436 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
88473382 ATAAAAAATC
*
88473392 TATTTAAAAAAAGGTCAAATTT
1 TATTTAAAAAAAGGTAAAATTT
88473414 TATTTAAAATAAAGG-AAATATTT
1 TATTTAAAA-AAAGGTAAA-ATTT
88473437 CCACTTTGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.38
Consensus pattern (22 bp):
TATTTAAAAAAAGGTAAAATTT
Found at i:88474297 original size:13 final size:13
Alignment explanation
Indices: 88474279--88474303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88474269 AACATTCGGC
88474279 CGGTGGGAATAAT
1 CGGTGGGAATAAT
88474292 CGGTGGGAATAA
1 CGGTGGGAATAA
88474304 ACAAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.40, T:0.20
Consensus pattern (13 bp):
CGGTGGGAATAAT
Found at i:88475366 original size:21 final size:22
Alignment explanation
Indices: 88475313--88475366 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
88475303 CTTAATTAAG
88475313 TAAATTAAGATTAATTAAAACTA
1 TAAA-TAAGATTAATTAAAACTA
88475336 -AAA-AATGATTAATTAAAA-TA
1 TAAATAA-GATTAATTAAAACTA
88475356 TAAATAAGATT
1 TAAATAAGATT
88475367 TATGAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 4 0.14
21 19 0.68
22 5 0.18
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (22 bp):
TAAATAAGATTAATTAAAACTA
Found at i:88475559 original size:14 final size:14
Alignment explanation
Indices: 88475540--88475575 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
88475530 TAAAAGTAAG
*
88475540 TCATTTTTCAGAAA
1 TCATTTTCCAGAAA
88475554 TCATTTTCCAGAAA
1 TCATTTTCCAGAAA
*
88475568 TTATTTTC
1 TCATTTTC
88475576 AGCGAAACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (14 bp):
TCATTTTCCAGAAA
Found at i:88481900 original size:50 final size:49
Alignment explanation
Indices: 88481714--88482067 Score: 334
Period size: 50 Copynumber: 7.3 Consensus size: 49
88481704 GTGCTAATGT
* *
88481714 TGTCTGGGACAT-GCATCGGC-C-ATATTATGAGAGCCAGTGTAAGACTA
1 TGTCTGGGACATGGCATCGGCTCGATA-TATGAGAGTCAGTGTAAGACCA
* * *
88481761 TGTCTGGGACATGGCATCGGCCTCGAGACT-TGAAAG-CTAGTATAAGACCA
1 TGTCTGGGACATGGCATCGG-CTCGATA-TATGAGAGTC-AGTGTAAGACCA
* * * * *
88481811 AGTCTAGGACATGGAATCGGCTTG--ATAT--GTGTCAGTGTAAGACCA
1 TGTCTGGGACATGGCATCGGCTCGATATATGAGAGTCAGTGTAAGACCA
* *
88481856 TGTCTGGGACATGGCATCAGTCTCAATATATGAGAGTCAGTGTAAGACCA
1 TGTCTGGGACATGGCATC-GGCTCGATATATGAGAGTCAGTGTAAGACCA
* * * * *
88481906 TGTCTGAGACATGACATCGATCTCGATATATGAAAGTCAGTGTAAGGCCA
1 TGTCTGGGACATGGCATCG-GCTCGATATATGAGAGTCAGTGTAAGACCA
*
88481956 TGTCTGGGACATGGCATCGACTTCGATATATGAGAGTCAGTGTAAGACCA
1 TGTCTGGGACATGGCATCGGC-TCGATATATGAGAGTCAGTGTAAGACCA
* ** * *
88482006 TGTCTGGGACATGGCATCGACTTCGATGCAT--GAGCCAATGTAAGACCA
1 TGTCTGGGACATGGCATCGGC-TCGATATATGAGAGTCAGTGTAAGACCA
* *
88482054 TGTTTGGGATATGG
1 TGTCTGGGACATGG
88482068 TGTCGGCATC
Statistics
Matches: 258, Mismatches: 35, Indels: 27
0.81 0.11 0.08
Matches are distributed among these distances:
45 27 0.10
46 5 0.02
47 14 0.05
48 38 0.15
49 7 0.03
50 164 0.64
51 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (49 bp):
TGTCTGGGACATGGCATCGGCTCGATATATGAGAGTCAGTGTAAGACCA
Found at i:88484503 original size:19 final size:19
Alignment explanation
Indices: 88484492--88484529 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
88484482 TTTCTTTTGC
*
88484492 TATTTTAATTTTGTAGTGA
1 TATTTTAATTTTCTAGTGA
*
88484511 TATTTTAATTTTGTAGTGA
1 TATTTTAATTTTCTAGTGA
88484530 AAAGCTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (19 bp):
TATTTTAATTTTCTAGTGA
Found at i:88485197 original size:23 final size:23
Alignment explanation
Indices: 88485151--88485197 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
88485141 TTTACTTTAG
*
88485151 TTTTCTTAGGTTTTCTCTTCTTC
1 TTTTCTTAGGTTTTCTATTCTTC
*
88485174 TTTTC-TAGGTTTTCATATTTTTC
1 TTTTCTTAGGTTTTC-TATTCTTC
88485197 T
1 T
88485198 ATCTTCTTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.66
Consensus pattern (23 bp):
TTTTCTTAGGTTTTCTATTCTTC
Found at i:88485360 original size:21 final size:21
Alignment explanation
Indices: 88485334--88485374 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
88485324 CTTGTTTTGA
*
88485334 CATTTTC-GTCTTTGTTTAATG
1 CATTTTCAGT-TTTCTTTAATG
88485355 CATTTTCAGTTTTCTTTAAT
1 CATTTTCAGTTTTCTTTAAT
88485375 TTTGGTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.17, C:0.15, G:0.10, T:0.59
Consensus pattern (21 bp):
CATTTTCAGTTTTCTTTAATG
Found at i:88488739 original size:13 final size:13
Alignment explanation
Indices: 88488723--88488748 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
88488713 TCAATGGCAG
88488723 TGTCAAATGTTCT
1 TGTCAAATGTTCT
88488736 TGTCAAATGTTCT
1 TGTCAAATGTTCT
88488749 AAGGCAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
TGTCAAATGTTCT
Found at i:88490674 original size:21 final size:21
Alignment explanation
Indices: 88490607--88490666 Score: 102
Period size: 21 Copynumber: 2.9 Consensus size: 21
88490597 CGCTGTTTCT
*
88490607 AATCTCACTGCTACAGTATCC
1 AATCTTACTGCTACAGTATCC
*
88490628 AATCTTACTGCTATAGTATCC
1 AATCTTACTGCTACAGTATCC
88490649 AATCTTACTGCTACAGTA
1 AATCTTACTGCTACAGTA
88490667 ATTAATCTCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (21 bp):
AATCTTACTGCTACAGTATCC
Found at i:88500100 original size:79 final size:79
Alignment explanation
Indices: 88499967--88500131 Score: 321
Period size: 79 Copynumber: 2.1 Consensus size: 79
88499957 TCTATGTATT
88499967 ATTCTGAATTTACCAGCTTTACAATTTGTATATCTAGCATTATCCAAGTCAAAGTTGTCTTCAGA
1 ATTCTGAATTTACCAGCTTTACAATTTGTATATCTAGCATTATCCAAGTCAAAGTTGTCTTCAGA
88500032 GATACCCGTGCATG
66 GATACCCGTGCATG
*
88500046 ATTCTGAATTTACCAGCTTTACAATTTGTATATCTAGCATTATCCAAGTTAAAGTTGTCTTCAGA
1 ATTCTGAATTTACCAGCTTTACAATTTGTATATCTAGCATTATCCAAGTCAAAGTTGTCTTCAGA
88500111 GATACCCGTGCATG
66 GATACCCGTGCATG
88500125 ATTCTGA
1 ATTCTGA
88500132 TTTTTCTATG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 85 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.36
Consensus pattern (79 bp):
ATTCTGAATTTACCAGCTTTACAATTTGTATATCTAGCATTATCCAAGTCAAAGTTGTCTTCAGA
GATACCCGTGCATG
Found at i:88521143 original size:26 final size:26
Alignment explanation
Indices: 88521122--88521171 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
88521112 AACAGGAAGT
*
88521122 TCACAAAGAACTTTTAATCAGGAAAC
1 TCACAAAGAACCTTTAATCAGGAAAC
* *
88521148 TCACGAAGAGCCTTTAATCAGGAA
1 TCACAAAGAACCTTTAATCAGGAA
88521172 CTCCGGATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (26 bp):
TCACAAAGAACCTTTAATCAGGAAAC
Found at i:88524765 original size:44 final size:44
Alignment explanation
Indices: 88524702--88524789 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
88524692 TGATAGAGAG
88524702 AGTGTAAATTGCATATTTGCAATTCAGAGCTTTAACCAGTTGAA
1 AGTGTAAATTGCATATTTGCAATTCAGAGCTTTAACCAGTTGAA
88524746 AGTGTAAATTGCATATTTGCAATTCAGAGCTTTAACCAGTTGAA
1 AGTGTAAATTGCATATTTGCAATTCAGAGCTTTAACCAGTTGAA
88524790 GTAGAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (44 bp):
AGTGTAAATTGCATATTTGCAATTCAGAGCTTTAACCAGTTGAA
Found at i:88526246 original size:42 final size:42
Alignment explanation
Indices: 88526200--88526287 Score: 158
Period size: 42 Copynumber: 2.1 Consensus size: 42
88526190 CACATGCCCA
*
88526200 TGTGCTAGGCCGTGTGTCACACACGGCTGAGACACACACCCG
1 TGTGCTAGGCCATGTGTCACACACGGCTGAGACACACACCCG
*
88526242 TGTGCTAGGCCATGTGTCACACACGGCTGAGACATACACCCG
1 TGTGCTAGGCCATGTGTCACACACGGCTGAGACACACACCCG
88526284 TGTG
1 TGTG
88526288 TCTGCTCGTG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.22, C:0.31, G:0.28, T:0.19
Consensus pattern (42 bp):
TGTGCTAGGCCATGTGTCACACACGGCTGAGACACACACCCG
Found at i:88527781 original size:26 final size:25
Alignment explanation
Indices: 88527752--88527805 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
88527742 AACAGGAAGT
* *
88527752 TCACAAAGAACTTTTAATCAGGAAAC
1 TCACAAAGAACCTTTAACCAGG-AAC
* *
88527778 TCACCAAGAGCCTTTAACCAGGAAC
1 TCACAAAGAACCTTTAACCAGGAAC
88527803 TCA
1 TCA
88527806 GGATAGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (25 bp):
TCACAAAGAACCTTTAACCAGGAAC
Found at i:88530462 original size:14 final size:14
Alignment explanation
Indices: 88530443--88530471 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
88530433 ATATGTATGA
88530443 GATATGTATATGTG
1 GATATGTATATGTG
88530457 GATATGTATATGTG
1 GATATGTATATGTG
88530471 G
1 G
88530472 TAAAGCCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (14 bp):
GATATGTATATGTG
Found at i:88530518 original size:48 final size:48
Alignment explanation
Indices: 88530457--88530901 Score: 773
Period size: 48 Copynumber: 9.3 Consensus size: 48
88530447 TGTATATGTG
88530457 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
88530505 GATGTGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
* *
88530553 GATGTGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
88530601 GATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
88530649 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
88530697 GATATGTATATGTGGTAAAGCCGAATGGCTAATCTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
* *
88530745 GATATGTATATGTGGTAAAGCGGAATGGCTAATGTGAAATATATATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
*
88530793 GATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
* * *
88530841 GATATGTATATTTGCTAAAGCCGAATGGCTAATGTGAAATATGTAGGA
1 GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
* *
88530889 GATGTGTGTATGT
1 GATATGTATATGT
88530902 TGTGGCCGAA
Statistics
Matches: 377, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 377 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.32
Consensus pattern (48 bp):
GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGA
Found at i:88531082 original size:37 final size:37
Alignment explanation
Indices: 88531032--88531208 Score: 327
Period size: 37 Copynumber: 4.8 Consensus size: 37
88531022 GGAAATATAT
88531032 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
88531069 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
88531106 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
88531143 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
88531180 TCCGGGTAAGACCCGATAACTACATGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
88531209 GGACTATTCG
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 137 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:88533994 original size:22 final size:22
Alignment explanation
Indices: 88533948--88534010 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
88533938 AGTAGGCACC
* * * *
88533948 GAAGTGCAAAACAGTAGGCACT
1 GAAGTGCAGAACAATAAGCATT
* *
88533970 GAAGTGTAGAACGATAAGCATT
1 GAAGTGCAGAACAATAAGCATT
88533992 GAAGTGCAGAACAATAAGC
1 GAAGTGCAGAACAATAAGC
88534011 GCTAAAGCGC
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (22 bp):
GAAGTGCAGAACAATAAGCATT
Found at i:88534432 original size:32 final size:32
Alignment explanation
Indices: 88534391--88534456 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
88534381 TAATATTCCA
88534391 AAATTCACGACAACATCAAATTTTCTCATTCT
1 AAATTCACGACAACATCAAATTTTCTCATTCT
88534423 AAATTCACGACAACATCAAATTTTCTCATTCT
1 AAATTCACGACAACATCAAATTTTCTCATTCT
88534455 AA
1 AA
88534457 GTATTATGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.39, C:0.24, G:0.03, T:0.33
Consensus pattern (32 bp):
AAATTCACGACAACATCAAATTTTCTCATTCT
Found at i:88538846 original size:38 final size:38
Alignment explanation
Indices: 88538801--88538962 Score: 175
Period size: 38 Copynumber: 4.2 Consensus size: 38
88538791 GGCTTAAAGA
88538801 CCCGCAGGCTATATGCTGGTATTATATCTGGGTTAAAT
1 CCCGCAGGCTATATGCTGGTATTATATCTGGGTTAAAT
* ** * *
88538839 CCTGCAGGCT-TCGCGCTAGTAATATATCTGGGTTAAAT
1 CCCGCAGGCTAT-ATGCTGGTATTATATCTGGGTTAAAT
* *
88538877 CCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAAT
1 CCCGCAGGCTATATGCTGGTATTATATCTGGGTTAAAT
* * *
88538915 CCCGCAGGCCTA-GTGTTGGTATTATATCTGAGCTTAAAGT
1 CCCGCAGG-CTATATGCTGGTATTATATCTG-GGTTAAA-T
*
88538955 CTCGCAGG
1 CCCGCAGG
88538963 TTTTGTGCTG
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
37 1 0.01
38 84 0.82
39 9 0.09
40 8 0.08
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (38 bp):
CCCGCAGGCTATATGCTGGTATTATATCTGGGTTAAAT
Found at i:88538941 original size:76 final size:78
Alignment explanation
Indices: 88538792--88538974 Score: 226
Period size: 76 Copynumber: 2.4 Consensus size: 78
88538782 GTGTACCCAG
* * * * * *
88538792 GCTTAAAGACCCGCAGGCTATATGCTGGTATTATATCTGGGTTAAATCCTGCAGGCTTCGCGCTA
1 GCTTAAAGTCCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGCGCTA
88538857 GTAATATATCTG-
66 GTAATATATCTGA
* * * *
88538869 GGTTAAA-TCCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGTGTTG
1 GCTTAAAGTCCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGCGCTA
*
88538933 GTATTATATCTGA
66 GTAATATATCTGA
* * *
88538946 GCTTAAAGTCTCGCAGGTTTTGTGCTGGT
1 GCTTAAAGTCCCGCAGGCTTTATGCTGGT
88538975 GACTGGATTC
Statistics
Matches: 89, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
76 59 0.66
77 12 0.13
78 18 0.20
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (78 bp):
GCTTAAAGTCCCGCAGGCTTTATGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAGCGCTA
GTAATATATCTGA
Found at i:88540823 original size:18 final size:18
Alignment explanation
Indices: 88540802--88540838 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
88540792 AGAATTAGAG
88540802 TAAGTTTCTTTTGCCGCA
1 TAAGTTTCTTTTGCCGCA
88540820 TAAGTTTCTTTTGCCGCA
1 TAAGTTTCTTTTGCCGCA
88540838 T
1 T
88540839 CCCATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.16, T:0.46
Consensus pattern (18 bp):
TAAGTTTCTTTTGCCGCA
Found at i:88542813 original size:34 final size:34
Alignment explanation
Indices: 88542775--88542856 Score: 164
Period size: 34 Copynumber: 2.4 Consensus size: 34
88542765 TTCTCAATGC
88542775 TTTCTCAAACAGCTTCTTCAATGCTTTTAATGTT
1 TTTCTCAAACAGCTTCTTCAATGCTTTTAATGTT
88542809 TTTCTCAAACAGCTTCTTCAATGCTTTTAATGTT
1 TTTCTCAAACAGCTTCTTCAATGCTTTTAATGTT
88542843 TTTCTCAAACAGCT
1 TTTCTCAAACAGCT
88542857 CCTCCTTTCA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (34 bp):
TTTCTCAAACAGCTTCTTCAATGCTTTTAATGTT
Found at i:88545946 original size:47 final size:47
Alignment explanation
Indices: 88545866--88546238 Score: 505
Period size: 47 Copynumber: 7.9 Consensus size: 47
88545856 TTAGGATTTT
* ** * * * *
88545866 ATGTGATGGATGTGAATGTGTATATATGAGCTAAGGCCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
88545913 ATGTGATGAATATGAACATGCATTTGTGTGCTAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
88545960 ATGTGATGAATGTGAACGTGCATTTGTGTGATAAGACCGAATGGTCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
**
88546007 ATGTGATGAATGTGAACATTTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
88546054 ATGTGATGAATGTGAACATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
88546101 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
88546148 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * *
88546195 ATGTGATGAACGTGGAA-GTGTATATATGTGGTAAAGCCGAATGG
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGG
88546239 TTAATGCGAA
Statistics
Matches: 293, Mismatches: 32, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
47 290 0.99
48 3 0.01
ACGTcount: A:0.32, C:0.11, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:88546060 original size:22 final size:22
Alignment explanation
Indices: 88546032--88546154 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 22
88546022 ACATTTATAT
88546032 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCCGAATGGCCA
* *
88546054 ATGTGATGAATG-TGAACAT-G-CA
1 ATGTGAT-AAGGCCG-A-ATGGCCA
88546076 TATGTGTGATAAGGCCGAATGGCCA
1 -A--TGTGATAAGGCCGAATGGCCA
* * *
88546101 ATGTGATGAATG-TGAACAT-GCATA
1 ATGTGAT-AAGGCCG-A-ATGGC-CA
88546125 TATGTGATAAGGCCGAATGGCCA
1 -ATGTGATAAGGCCGAATGGCCA
88546148 ATGTGAT
1 ATGTGAT
88546155 GAATGTGAAC
Statistics
Matches: 75, Mismatches: 10, Indels: 32
0.64 0.09 0.27
Matches are distributed among these distances:
22 24 0.32
23 17 0.23
24 17 0.23
25 17 0.23
ACGTcount: A:0.33, C:0.13, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCCGAATGGCCA
Found at i:88546201 original size:22 final size:22
Alignment explanation
Indices: 88546126--88546201 Score: 59
Period size: 22 Copynumber: 3.3 Consensus size: 22
88546116 ACATGCATAT
*
88546126 ATGTGATAAGGCCGAATGGCCA
1 ATGTGATAAGGCAGAATGGCCA
*
88546148 ATGTGATGAATGTG-A-ACAT-GCATA
1 ATGTGAT-AA-G-GCAGA-ATGGC-CA
88546172 TATGTGATAAGGCAGAATGGCCA
1 -ATGTGATAAGGCAGAATGGCCA
88546195 ATGTGAT
1 ATGTGAT
88546202 GAACGTGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 18
0.67 0.05 0.29
Matches are distributed among these distances:
22 15 0.36
23 10 0.24
24 9 0.21
25 8 0.19
ACGTcount: A:0.34, C:0.12, G:0.29, T:0.25
Consensus pattern (22 bp):
ATGTGATAAGGCAGAATGGCCA
Found at i:88546271 original size:46 final size:46
Alignment explanation
Indices: 88546218--88546308 Score: 128
Period size: 46 Copynumber: 2.0 Consensus size: 46
88546208 GGAAGTGTAT
* * * *
88546218 ATATGTGGTAAAGCCGAATGGTTAATGCGAAATGTGTATGAGATGG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATATGTATAAGATGG
* *
88546264 ATATGTGGTAAAGCCAAATGGCTAATGTGAGATATGTATAAGATG
1 ATATGTGGTAAAGCCAAATGGCTAATGCGAAATATGTATAAGATG
88546309 TGTATATATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.29
Consensus pattern (46 bp):
ATATGTGGTAAAGCCAAATGGCTAATGCGAAATATGTATAAGATGG
Found at i:88546315 original size:141 final size:139
Alignment explanation
Indices: 88545866--88546293 Score: 396
Period size: 141 Copynumber: 3.0 Consensus size: 139
88545856 TTAGGATTTT
* ** * * * * * **
88545866 ATGTGATGGATGTGAATGTGTATATATGAGCTAAGGCCGAATGGCAAATGTGATGAATATGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACA
* * * * * * ** *
88545931 TGCATTTGTGTGCTAAGGCCGAATGGCCAATGTGATGAATGTGAACGTGCATTTGTGTGAT-AAG
66 TGCATATATGTGATAAAGCCGAATGGCCAATGCGA-GAATGTGAACATG-AGATATGTGATAAAG
* *
88545995 ACCGAATGGTCA
129 -CCAAATGGCCA
** * *
88546007 ATGTGATGAATGTGAACATTTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACA
* * * * *
88546072 TGCATATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGTGATAAGG
66 TGCATATATGTGATAAAGCCGAATGGCCAATGCGA-GAATGTGAACATG-AGATATGTGATAAAG
*
88546137 CCGAATGGCCA
129 CCAAATGGCCA
88546148 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGGAA-
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGT-GAAC
* * * ** * *
88546212 GTGTATATATGTGGTAAAGCCGAATGGTTAATGCGA-AATGTGTATGAGATG-GATATGTGGTAA
65 ATGCATATATGTGATAAAGCCGAATGGCCAATGCGAGAATGTG-A--ACATGAGATATGTGATAA
*
88546275 AGCCAAATGGCTA
127 AGCCAAATGGCCA
88546288 ATGTGA
1 ATGTGA
88546294 GATATGTATA
Statistics
Matches: 249, Mismatches: 33, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
139 6 0.02
140 27 0.11
141 207 0.83
142 9 0.04
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.28
Consensus pattern (139 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACA
TGCATATATGTGATAAAGCCGAATGGCCAATGCGAGAATGTGAACATGAGATATGTGATAAAGCC
AAATGGCCA
Found at i:88555425 original size:40 final size:40
Alignment explanation
Indices: 88555355--88555452 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
88555345 AAACCAAGTA
* * *
88555355 CCTTCGGGATTTAG-CCGGATATAACTACTCGCTCAACTG
1 CCTTCGGGACTTAGCCCGGATATAACTACTCGCACAAATG
*
88555394 CCTTCGGGACTTAGCCCGGATAT-AGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAACT-ACTCGCACAAATG
88555434 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
88555453 TCGGCATTAG
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.28
40 38 0.72
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAACTACTCGCACAAATG
Found at i:88556470 original size:32 final size:32
Alignment explanation
Indices: 88556429--88556493 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
88556419 AGTGGTGGTG
88556429 GCGTGAGTTGGCATGTGAGAGGACTTTGGTTC
1 GCGTGAGTTGGCATGTGAGAGGACTTTGGTTC
88556461 GCGTGAGTTGGCATGTGAGAGGACTTTGGTTC
1 GCGTGAGTTGGCATGTGAGAGGACTTTGGTTC
88556493 G
1 G
88556494 AATCCCTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.15, C:0.12, G:0.42, T:0.31
Consensus pattern (32 bp):
GCGTGAGTTGGCATGTGAGAGGACTTTGGTTC
Found at i:88556504 original size:32 final size:32
Alignment explanation
Indices: 88556436--88556505 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
88556426 GTGGCGTGAG
** * *
88556436 TTGGCATGTGAGAGGACTTTGGTTCGCGTGAG
1 TTGGCATGTGAGAGGACTTTGGTTCGAATCAC
*
88556468 TTGGCATGTGAGAGGACTTTGGTTCGAATCCC
1 TTGGCATGTGAGAGGACTTTGGTTCGAATCAC
88556500 TTGGCA
1 TTGGCA
88556506 CGCAAAGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.17, C:0.16, G:0.36, T:0.31
Consensus pattern (32 bp):
TTGGCATGTGAGAGGACTTTGGTTCGAATCAC
Found at i:88558302 original size:15 final size:16
Alignment explanation
Indices: 88558282--88558311 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88558272 TTTTAAAGAT
88558282 TAAAATT-GGTTTTTC
1 TAAAATTAGGTTTTTC
88558297 TAAAATTAGGTTTTT
1 TAAAATTAGGTTTTT
88558312 TTTAGAAGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (16 bp):
TAAAATTAGGTTTTTC
Found at i:88561279 original size:39 final size:40
Alignment explanation
Indices: 88561180--88561317 Score: 208
Period size: 40 Copynumber: 3.5 Consensus size: 40
88561170 ATATTCTCAN
*
88561180 GGGACTTAGCCCGG-ATATAGTAACTCGCACAAATTCCTTC
1 GGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC
*
88561220 GGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC
* * *
88561260 GGG-CTTAGCCCAGAATTAGTCACTGGCACAAATGCCTTC
1 GGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC
88561299 GGGACTTAGCCCGGAATTA
1 GGGACTTAGCCCGGAATTA
88561318 TCATCCGAAT
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
39 35 0.39
40 53 0.60
41 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
GGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTC
Found at i:88565566 original size:98 final size:98
Alignment explanation
Indices: 88565397--88565586 Score: 353
Period size: 98 Copynumber: 1.9 Consensus size: 98
88565387 GTTGGCAGAG
* *
88565397 TTTGCATACAACAACAGTTATCAGGCAAGTATTCGAATGGCTCCTTATGAGGCACTGTATGGGCG
1 TTTGCATACAACAACAGTTATAAGGCAAGTATTCGAATGGCTCCTTATGAGGCACTGTATGGACG
88565462 AAGATGTCGTACACCTAGTTGTTGGACGCAAAA
66 AAGATGTCGTACACCTAGTTGTTGGACGCAAAA
*
88565495 TTTGCATACAACAATAGTTATAAGGCAAGTATTCGAATGGCTCCTTATGAGGCACTGTATGGACG
1 TTTGCATACAACAACAGTTATAAGGCAAGTATTCGAATGGCTCCTTATGAGGCACTGTATGGACG
88565560 AAGATGTCGTACACCTAGTTGTTGGAC
66 AAGATGTCGTACACCTAGTTGTTGGAC
88565587 CGAGTTGGGT
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 89 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (98 bp):
TTTGCATACAACAACAGTTATAAGGCAAGTATTCGAATGGCTCCTTATGAGGCACTGTATGGACG
AAGATGTCGTACACCTAGTTGTTGGACGCAAAA
Found at i:88566029 original size:17 final size:17
Alignment explanation
Indices: 88566007--88566042 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
88565997 AGGTTAGTGG
88566007 ACCATTGGAAGGCCCAA
1 ACCATTGGAAGGCCCAA
88566024 ACCATTGGAAGGCCCAA
1 ACCATTGGAAGGCCCAA
88566041 AC
1 AC
88566043 TTAAGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.11
Consensus pattern (17 bp):
ACCATTGGAAGGCCCAA
Found at i:88566895 original size:8 final size:8
Alignment explanation
Indices: 88566882--88566909 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
88566872 GCCGAAAACA
88566882 GGCCAATG
1 GGCCAATG
88566890 GGCCAATG
1 GGCCAATG
88566898 GGCCAATG
1 GGCCAATG
88566906 GGCC
1 GGCC
88566910 CACTTTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.39, T:0.11
Consensus pattern (8 bp):
GGCCAATG
Found at i:88567253 original size:67 final size:67
Alignment explanation
Indices: 88567145--88567298 Score: 290
Period size: 67 Copynumber: 2.3 Consensus size: 67
88567135 GAAGAAACGT
* *
88567145 TCTGGTAGCCTCGCTACAATCTGGTGGCCTCGCCACATATTTCTGTTCTGGTGGCTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATTTCTGTTCTGGTGGCTTCGTCACAA
88567210 TA
66 TA
88567212 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATTTCTGTTCTGGTGGCTTCGTCACAA
1 TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATTTCTGTTCTGGTGGCTTCGTCACAA
88567277 TA
66 TA
88567279 TCTGGCAGCCTCGCTGCAAT
1 TCTGGCAGCCTCGCTGCAAT
88567299 TTCTGTGGTA
Statistics
Matches: 85, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 85 1.00
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.31
Consensus pattern (67 bp):
TCTGGCAGCCTCGCTGCAATCTGGTGGCCTCGCCACATATTTCTGTTCTGGTGGCTTCGTCACAA
TA
Found at i:88569640 original size:14 final size:14
Alignment explanation
Indices: 88569621--88569650 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88569611 ACCCCTTCAT
*
88569621 TCCCTCATTCATCA
1 TCCCTCATCCATCA
88569635 TCCCTCATCCATCA
1 TCCCTCATCCATCA
88569649 TC
1 TC
88569651 ATCCTATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.47, G:0.00, T:0.33
Consensus pattern (14 bp):
TCCCTCATCCATCA
Found at i:88577017 original size:16 final size:16
Alignment explanation
Indices: 88576996--88577029 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
88576986 CGTGTGGTTC
88576996 TTAGAAGCATACTGCT
1 TTAGAAGCATACTGCT
88577012 TTAGAAGCATACTGCT
1 TTAGAAGCATACTGCT
88577028 TT
1 TT
88577030 TCTTACATGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (16 bp):
TTAGAAGCATACTGCT
Found at i:88581844 original size:24 final size:24
Alignment explanation
Indices: 88581796--88581841 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
88581786 TTCTTTCCTC
*
88581796 CTTTTCCCTCTTTATTCCTTTCCT
1 CTTTTCCCTCTTTATTCCTTCCCT
88581820 CTTTTCCC-CTTT-TCTCCTTCCC
1 CTTTTCCCTCTTTAT-TCCTTCCC
88581842 CTCCGACTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 11 0.55
24 8 0.40
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.54
Consensus pattern (24 bp):
CTTTTCCCTCTTTATTCCTTCCCT
Found at i:88583543 original size:17 final size:17
Alignment explanation
Indices: 88583513--88583559 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
88583503 TTATTTCTAC
88583513 TTTA-TTTTACTTTTCCT
1 TTTATTTTTA-TTTTCCT
* *
88583530 TTTGTTTTTATTTTTCT
1 TTTATTTTTATTTTCCT
*
88583547 TTTATATTTATTT
1 TTTATTTTTATTT
88583560 CTATTTCCAG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTATTTTTATTTTCCT
Found at i:88593710 original size:14 final size:14
Alignment explanation
Indices: 88593691--88593720 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88593681 ATTCAACTAA
*
88593691 ACTAAAATGATTAT
1 ACTAAAATGATCAT
88593705 ACTAAAATGATCAT
1 ACTAAAATGATCAT
88593719 AC
1 AC
88593721 ATATTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.13, G:0.07, T:0.30
Consensus pattern (14 bp):
ACTAAAATGATCAT
Found at i:88599977 original size:33 final size:33
Alignment explanation
Indices: 88599904--88600010 Score: 142
Period size: 33 Copynumber: 3.2 Consensus size: 33
88599894 AATAACACAT
* * * *
88599904 TATCAATACAATCTGGGCCAAAGCCCTATTCAG
1 TATCAGTACAGTCTGGGCCTAAGCCCTATACAG
* * *
88599937 TAACAGTACAGTCTGGGCCTAAGCTCTATACAA
1 TATCAGTACAGTCTGGGCCTAAGCCCTATACAG
88599970 TATCAGTACAGTCTGGGCCTAAGCCCTATACAG
1 TATCAGTACAGTCTGGGCCTAAGCCCTATACAG
*
88600003 TAGCAGTA
1 TATCAGTA
88600011 TGGGCCTAAG
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (33 bp):
TATCAGTACAGTCTGGGCCTAAGCCCTATACAG
Found at i:88600184 original size:26 final size:26
Alignment explanation
Indices: 88600155--88600206 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
88600145 CACCAATATC
* *
88600155 GCAGCAAAGCTGCCAGAAATAATAAT
1 GCAGCAAAGCTACCAGAAACAATAAT
*
88600181 GCAGCATAGCTACCAGAAACAATAAT
1 GCAGCAAAGCTACCAGAAACAATAAT
88600207 TGTTGCAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.15
Consensus pattern (26 bp):
GCAGCAAAGCTACCAGAAACAATAAT
Found at i:88600245 original size:27 final size:26
Alignment explanation
Indices: 88600184--88600284 Score: 87
Period size: 27 Copynumber: 3.8 Consensus size: 26
88600174 TAATAATGCA
* * * *
88600184 GCATAGCTACCAGAAACAATAATTGTT
1 GCATAGCCACCAG-TACAGTAATTGTG
* *
88600211 GCAAAGCCACTAGTATCAGTAATTGTG
1 GCATAGCCACCAGTA-CAGTAATTGTG
88600238 GCATAGCCACCAGTAACAGTGAA-TGTG
1 GCATAGCCACCAGT-ACAGT-AATTGTG
* *
88600265 ACATAGTCACCAGTACAGTA
1 GCATAGCCACCAGTACAGTA
88600285 CTTCCTCCAT
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
25 1 0.02
26 6 0.10
27 51 0.84
28 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (26 bp):
GCATAGCCACCAGTACAGTAATTGTG
Found at i:88612448 original size:48 final size:48
Alignment explanation
Indices: 88612176--88612447 Score: 402
Period size: 48 Copynumber: 5.5 Consensus size: 48
88612166 GCTGAAATTG
88612176 ATGTAT-AGGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAGTAT
1 ATGTATGA-GATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA--AT
*
88612226 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAAATATAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG----A-A-AT
*
88612280 ATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
88612328 ATGTATGAGATATGTATATGTGGTGAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
* *
88612376 ATGTATGAGATATGTATATGTGGTGAAGCCGAATGGCTAGTGTGAAAT
1 ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
88612424 ATGTATGAGATATGTATATGTGGT
1 ATGTATGAGATATGTATATGTGGT
88612448 GTGTATATAT
Statistics
Matches: 212, Mismatches: 4, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
48 119 0.56
49 1 0.00
50 42 0.20
51 1 0.00
54 48 0.23
55 1 0.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.32
Consensus pattern (48 bp):
ATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAAT
Found at i:88612687 original size:37 final size:37
Alignment explanation
Indices: 88612631--88612709 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
88612621 CCGAGCTCTA
* * *
88612631 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
88612668 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
88612705 AAGAC
1 AAGAC
88612710 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:88621671 original size:33 final size:33
Alignment explanation
Indices: 88621629--88621766 Score: 168
Period size: 33 Copynumber: 4.2 Consensus size: 33
88621619 ACAGTATAAA
* * *
88621629 TACAATCTGGGCCAAAGCCCTATTCAGTAACAG
1 TACAGTCTGGGCCTAAGCCCTATACAGTAACAG
*
88621662 TACAGTCTGGGCCTAAGCCCTATACAGTATCAG
1 TACAGTCTGGGCCTAAGCCCTATACAGTAACAG
* * * *
88621695 TACGGTCTGCGCCTAAGCCCTATACAATATCAG
1 TACAGTCTGGGCCTAAGCCCTATACAGTAACAG
* * * *
88621728 TACAGTCTAGGCCTAAGCCCTGTGCAGTAACAA
1 TACAGTCTGGGCCTAAGCCCTATACAGTAACAG
88621761 TACAGT
1 TACAGT
88621767 ACGATGTAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.23
Consensus pattern (33 bp):
TACAGTCTGGGCCTAAGCCCTATACAGTAACAG
Found at i:88621954 original size:27 final size:27
Alignment explanation
Indices: 88621924--88622002 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
88621914 TGCCAGAAAT
* *
88621924 AGTAATTGTGGCAAAGCCACCAGTATC
1 AGTAATTGTGGCATAGCCACCAGTAAC
*
88621951 AGTAATTGTGGCATGGCCACCAGTAAC
1 AGTAATTGTGGCATAGCCACCAGTAAC
* *
88621978 AGTGAA-TGTGACATAGTCACCAGTA
1 AGT-AATTGTGGCATAGCCACCAGTA
88622003 CAATACTTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 43 0.96
28 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (27 bp):
AGTAATTGTGGCATAGCCACCAGTAAC
Found at i:88625690 original size:67 final size:66
Alignment explanation
Indices: 88625563--88625691 Score: 147
Period size: 67 Copynumber: 1.9 Consensus size: 66
88625553 TACTATGTGT
* * * * *
88625563 ACACCATGTAGACAAGAGAGCTACAGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAA
1 ACACCATGTAGACAAGAGAGCTACAGGATAAATG-AGCTAGGTCACATGCATGATACCAAGTGAA
88625628 GG
65 GG
88625630 ACACCATGTAGACAAGAGAGCTAC-GAGATAAACTG-GCTAGGTCACATGCCAT-ATAACCAAGT
1 ACACCATGTAGACAAGAGAGCTACAG-GATAAA-TGAGCTAGGTCACATG-CATGAT-ACCAAGT
88625692 TACAAGTGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
66 14 0.26
67 37 0.70
68 2 0.04
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (66 bp):
ACACCATGTAGACAAGAGAGCTACAGGATAAATGAGCTAGGTCACATGCATGATACCAAGTGAAG
G
Found at i:88626572 original size:41 final size:42
Alignment explanation
Indices: 88626456--88626585 Score: 185
Period size: 42 Copynumber: 3.1 Consensus size: 42
88626446 ATGTTATAGT
88626456 ATATCGATGCCAATAG-CCCAG-CTATGGTCTTACACGAATCTC
1 ATATCGATGCCAAT-GTCCCAGAC-ATGGTCTTACACGAATCTC
* * *
88626498 ATATCGATGCCAATGTCTCAGATATGGTGTTACACGAATCTC
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCTC
*
88626540 ATATCGATGCC-ATGTCCCAGACATGGTCTTACACAAATCTC
1 ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCTC
88626581 ATATC
1 ATATC
88626586 CCGGTAATCC
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
41 32 0.41
42 47 0.59
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.28
Consensus pattern (42 bp):
ATATCGATGCCAATGTCCCAGACATGGTCTTACACGAATCTC
Found at i:88628965 original size:29 final size:29
Alignment explanation
Indices: 88628908--88629009 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 29
88628898 TACCTATATC
* * **
88628908 TGGCCCATTAAGCCC-AATCATATCCATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
* *
88628936 TGGCCCATTAGGCCTAAATCACCTGTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
*
88628965 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATGTATA
*
88628994 TGGCCCGTTAGGCCCA
1 TGGCCCATTAGGCCCA
88629010 GTCACATTCA
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
28 13 0.21
29 50 0.79
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATGTATA
Found at i:88629005 original size:58 final size:57
Alignment explanation
Indices: 88628899--88629007 Score: 146
Period size: 58 Copynumber: 1.9 Consensus size: 57
88628889 AATTTCACAT
* *
88628899 ACCTATATCTGGCCCATTAAGCCCAATCATATCCATATGGCCCATTAGGCCTAAATC
1 ACCTATATATGGCCCATTAAGCCCAATCACATCCATATGGCCCATTAGGCCTAAATC
* * ** *
88628956 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCC
1 ACCTATATATGGCCCATTAAGCCC-AATCACATCCATATGGCCCATTAGGCC
88629008 CAGTCACATT
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 21 0.48
58 23 0.52
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.27
Consensus pattern (57 bp):
ACCTATATATGGCCCATTAAGCCCAATCACATCCATATGGCCCATTAGGCCTAAATC
Found at i:88631131 original size:40 final size:40
Alignment explanation
Indices: 88631031--88631295 Score: 286
Period size: 40 Copynumber: 6.7 Consensus size: 40
88631021 GCTCCTCGTT
* * * *
88631031 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* **
88631071 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
88631110 CGAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
88631150 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
88631190 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
88631230 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
88631271 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
88631296 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 22, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
39 39 0.20
40 143 0.73
41 15 0.08
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:88631255 original size:80 final size:80
Alignment explanation
Indices: 88630998--88631295 Score: 263
Period size: 80 Copynumber: 3.7 Consensus size: 80
88630988 AAATCACGTA
* ** * * *
88630998 CCTTCGGGATTTAA-CCGGATATAGCTC-CTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTTT
1 CCTTCGGGACTTAACCCGGATATAG-TCACTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
88631060 AGTAACTCACAC-AATG
64 AATAACTCGCACAAATG
* * * *
88631076 CCTTCGGGACATAACCCGGATTTA-ACAACTCGCACGAATGCCTTCGGGACTTAACCCGG-ATTT
1 CCTTCGGGACTTAACCCGGATATAGTC-ACTCGCAC-AAAGCCTTCGGGACTTAACCCGGAATTT
*
88631139 AATAACTCGCACGAATG
64 AATAACTCGCACAAATG
* *
88631156 CCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGAATTT
1 CCTTCGGGACTTAACCCGGATATAGTCA-CTCGCACAAA-GCCTTCGGGACTTAACCCGGAATTT
* *
88631220 -GTATCTCGCACAAATG
64 AATAACTCGCACAAATG
** * * *
88631236 CCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTAACCCGGATATAGTCAC-TCGCACAAAGCCTTCGGGACTTAACCCGGA
88631296 CAGCATTCAA
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
77 1 0.01
78 12 0.07
79 50 0.27
80 106 0.58
81 13 0.07
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (80 bp):
CCTTCGGGACTTAACCCGGATATAGTCACTCGCACAAAGCCTTCGGGACTTAACCCGGAATTTAA
TAACTCGCACAAATG
Found at i:88631304 original size:41 final size:41
Alignment explanation
Indices: 88631227--88631304 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
88631217 TTTGTATCTC
* * *
88631227 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
88631268 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
88631305 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:88639320 original size:49 final size:49
Alignment explanation
Indices: 88639146--88639461 Score: 509
Period size: 49 Copynumber: 6.6 Consensus size: 49
88639136 CCCTTCGGGA
* * * * **
88639146 CTTATCACAT-T-TATGCACTTTCACATCCATCACATTGGCCACTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
* * *
88639193 CCTGTCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
88639240 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
88639287 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
88639336 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
88639385 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
88639434 CTTATCACATATATATACACTTTCACAT
1 CTTATCACATATATATACACTTTCACAT
88639462 ATGGGTTTAA
Statistics
Matches: 255, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 89 0.35
49 165 0.65
ACGTcount: A:0.31, C:0.30, G:0.07, T:0.33
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAAGC
Found at i:88645624 original size:29 final size:29
Alignment explanation
Indices: 88645569--88645668 Score: 123
Period size: 29 Copynumber: 3.5 Consensus size: 29
88645559 CCTGTATCTA
* *
88645569 GCCCATTAAGCCC-AATCATAT-TCATATG
1 GCCCATTAGGCCCAAATCACATGT-ATATG
* *
88645597 GCCCATTAGGCCTAAATCACCTGTATATG
1 GCCCATTAGGCCCAAATCACATGTATATG
*
88645626 GCCCATTAGGCCCAAATCACATTTATATG
1 GCCCATTAGGCCCAAATCACATGTATATG
*
88645655 GCCCGTTAGGCCCA
1 GCCCATTAGGCCCA
88645669 GTCACATTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.18
29 50 0.81
30 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.16, T:0.26
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATGTATATG
Found at i:88645916 original size:16 final size:16
Alignment explanation
Indices: 88645895--88645933 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
88645885 CCAAACTTTT
88645895 GGCTTTTCGGCATTTC
1 GGCTTTTCGGCATTTC
*
88645911 GGCTTTTTGGCATTTC
1 GGCTTTTCGGCATTTC
*
88645927 GACTTTT
1 GGCTTTT
88645934 GCCGATACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.08, C:0.21, G:0.23, T:0.49
Consensus pattern (16 bp):
GGCTTTTCGGCATTTC
Found at i:88650154 original size:37 final size:37
Alignment explanation
Indices: 88650104--88650256 Score: 225
Period size: 37 Copynumber: 4.1 Consensus size: 37
88650094 TTATTACGAA
* * *
88650104 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
88650141 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* * *
88650178 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
* *
88650215 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGA
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
88650252 GTCTT
1 GTCTT
88650257 TAGAGCTCGG
Statistics
Matches: 103, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 103 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:88650225 original size:74 final size:74
Alignment explanation
Indices: 88650103--88650256 Score: 299
Period size: 74 Copynumber: 2.1 Consensus size: 74
88650093 CTTATTACGA
88650103 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCCCCACACG
1 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCCCCACACG
88650168 TAGTCATCG
66 TAGTCATCG
*
88650177 GGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCCCCACACG
1 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCCCCACACG
88650242 TAGTCATCG
66 TAGTCATCG
88650251 AGTCTT
1 AGTCTT
88650257 TAGAGCTCGG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
74 78 1.00
ACGTcount: A:0.27, C:0.32, G:0.18, T:0.23
Consensus pattern (74 bp):
AGTCTTACCCGGACATAATCTCCACACGAAGTTATCGGGTCTTACCCGGACAAAATCCCCACACG
TAGTCATCG
Found at i:88650453 original size:47 final size:47
Alignment explanation
Indices: 88650375--88650721 Score: 613
Period size: 47 Copynumber: 7.4 Consensus size: 47
88650365 CCCTTCGGGA
* * * * * *
88650375 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
88650422 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
88650469 ATTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88650516 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88650563 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88650610 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88650657 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
88650704 CTTATCACATATATACAC
1 CTTATCACATATATACAC
88650722 ATATATACAC
Statistics
Matches: 288, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 288 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:88650749 original size:25 final size:25
Alignment explanation
Indices: 88650426--88650503 Score: 72
Period size: 25 Copynumber: 3.2 Consensus size: 25
88650416 CTCGGCCCTG
88650426 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
**** ***
88650451 TCACAT-CGGCCA-TTAGGCATT-A
1 TCACATATATACACTTTCACATTCA
88650473 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
88650498 TCACAT
1 TCACAT
88650504 CGGCCATTAG
Statistics
Matches: 36, Mismatches: 14, Indels: 6
0.64 0.25 0.11
Matches are distributed among these distances:
22 7 0.19
23 8 0.22
24 8 0.22
25 13 0.36
ACGTcount: A:0.33, C:0.28, G:0.05, T:0.33
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:88654097 original size:39 final size:40
Alignment explanation
Indices: 88653908--88654117 Score: 296
Period size: 40 Copynumber: 5.3 Consensus size: 40
88653898 CGAGGTTTAA
* * * *
88653908 CCCGGATATATCACTAGCACGATTTCTCTTTGGGACTTAG
1 CCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAG
*
88653948 CCCGGTTATATCACTAGCACGAATGCTCTTCGGAACTTAG
1 CCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAG
** *
88653988 CCCAAATATATCACTAGCACGAATGCTCTTTGGAACTTAG
1 CCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAG
*
88654028 CCCGGATATATCATTAGCACGAATGCTCTTCGGAACTTAG
1 CCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAG
* * * *
88654068 CCCGGACAT-TTACCAGCACGAATGCTCTTCGGGACTTAG
1 CCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAG
88654107 CCCGGATATAT
1 CCCGGATATAT
88654118 AACTCTCAAT
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
39 34 0.23
40 116 0.77
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (40 bp):
CCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAG
Found at i:88655664 original size:46 final size:46
Alignment explanation
Indices: 88655611--88655702 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 46
88655601 TATATATACA
* *
88655611 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
* * * *
88655657 CATCTCATACACGTTTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
88655703 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.25, C:0.32, G:0.09, T:0.35
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCGGCTTTACCACATATC
Found at i:88661371 original size:6 final size:6
Alignment explanation
Indices: 88661360--88661391 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
88661350 CTTATCTTTT
88661360 TATTTC TATTTC TATTTC TATTTC TATTTC TA
1 TATTTC TATTTC TATTTC TATTTC TATTTC TA
88661392 CTTTTATGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTC
Found at i:88661406 original size:18 final size:17
Alignment explanation
Indices: 88661357--88661398 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
88661347 CCTCTTATCT
88661357 TTTTATTTCTATTTCTA
1 TTTTATTTCTATTTCTA
88661374 TTTCTATTTCTATTTCTA
1 TTT-TATTTCTATTTCTA
88661392 CTTTTAT
1 -TTTTAT
88661399 GTTTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.13
18 17 0.74
19 3 0.13
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATTTCTATTTCTA
Found at i:88662473 original size:118 final size:117
Alignment explanation
Indices: 88662225--88662458 Score: 441
Period size: 118 Copynumber: 2.0 Consensus size: 117
88662215 ATGTCGAGAT
88662225 CACATGTATGATTTGATGTACTGAAATGATAAAGGCACTTAGGATTTAACCCACTTACTCCATAA
1 CACATGTATGATTTGATGTACTGAAATGATAAAGGCACTTAGGATTTAACCCACTTACTCCATAA
*
88662290 AAAGCCTTCCCACATAATTAAACCCTTAGTGAAACCCCTTGAGCCTACTAAC
66 AAAGCCTTCCCACATAATTAAACCATTAGTGAAACCCCTTGAGCCTACTAAC
88662342 CNACATGTATGATTTGATGTACTGAAATGATAAAGGCACTTAGGATTTAACCCACTTACTCCATA
1 C-ACATGTATGATTTGATGTACTGAAATGATAAAGGCACTTAGGATTTAACCCACTTACTCCATA
*
88662407 AAAAGCCTTCCCACATAATTAAACCATTAGTGAACCCCCTTGAGCCTACTAA
65 AAAAGCCTTCCCACATAATTAAACCATTAGTGAAACCCCTTGAGCCTACTAA
88662459 TCCTTTTTAT
Statistics
Matches: 114, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
117 1 0.01
118 113 0.99
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.27
Consensus pattern (117 bp):
CACATGTATGATTTGATGTACTGAAATGATAAAGGCACTTAGGATTTAACCCACTTACTCCATAA
AAAGCCTTCCCACATAATTAAACCATTAGTGAAACCCCTTGAGCCTACTAAC
Found at i:88662982 original size:38 final size:38
Alignment explanation
Indices: 88662931--88663008 Score: 129
Period size: 38 Copynumber: 2.1 Consensus size: 38
88662921 TTAGACAATG
* *
88662931 TATCTCGAATCTAACCCTTGTTCTTTAGCTTGTATCCA
1 TATCTCGAATCTAACCCCTGTTCTTCAGCTTGTATCCA
*
88662969 TATCTCGATTCTAACCCCTGTTCTTCAGCTTGTATCCA
1 TATCTCGAATCTAACCCCTGTTCTTCAGCTTGTATCCA
88663007 TA
1 TA
88663009 CCTGTAACCT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (38 bp):
TATCTCGAATCTAACCCCTGTTCTTCAGCTTGTATCCA
Found at i:88663115 original size:203 final size:203
Alignment explanation
Indices: 88662766--88663132 Score: 725
Period size: 203 Copynumber: 1.8 Consensus size: 203
88662756 ATATTGAAAT
88662766 TATCTCGATTCTAACCCCTGTTCTTCAGCTTGTATCCATACCTGTAACCTAAACCCCATTACAAC
1 TATCTCGATTCTAACCCCTGTTCTTCAGCTTGTATCCATACCTGTAACCTAAACCCCATTACAAC
*
88662831 AATGCAAAGACCTTTTGATTAGTGTGTCATATCATTTACAAGTGGTGGAGATTTGATTTTCATGC
66 AATGCAAAGACCTTTTGATTAGTGTGTCATATCATGTACAAGTGGTGGAGATTTGATTTTCATGC
88662896 AAGCCTATGGTAATAACTTTTCATGTTAGACAATGTATCTCGAATCTAACCCTTGTTCTTTAGCT
131 AAGCCTATGGTAATAACTTTTCATGTTAGACAATGTATCTCGAATCTAACCCTTGTTCTTTAGCT
88662961 TGTATCCA
196 TGTATCCA
88662969 TATCTCGATTCTAACCCCTGTTCTTCAGCTTGTATCCATACCTGTAACCTAAACCCCATTACAAC
1 TATCTCGATTCTAACCCCTGTTCTTCAGCTTGTATCCATACCTGTAACCTAAACCCCATTACAAC
88663034 AATGCAAAGACCTTTTGATTAGTGTGTCATATCATGTACAAGTGGTGGAGATTTGATTTTCATGC
66 AATGCAAAGACCTTTTGATTAGTGTGTCATATCATGTACAAGTGGTGGAGATTTGATTTTCATGC
88663099 AAGCCTATGGTAATAACTTTTCATGTTAGACAAT
131 AAGCCTATGGTAATAACTTTTCATGTTAGACAAT
88663133 CGAGTGCTTA
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
203 163 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (203 bp):
TATCTCGATTCTAACCCCTGTTCTTCAGCTTGTATCCATACCTGTAACCTAAACCCCATTACAAC
AATGCAAAGACCTTTTGATTAGTGTGTCATATCATGTACAAGTGGTGGAGATTTGATTTTCATGC
AAGCCTATGGTAATAACTTTTCATGTTAGACAATGTATCTCGAATCTAACCCTTGTTCTTTAGCT
TGTATCCA
Found at i:88664667 original size:13 final size:13
Alignment explanation
Indices: 88664651--88664675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
88664641 TTAAATTAGT
88664651 TAATTAGTTTAAA
1 TAATTAGTTTAAA
88664664 TAATTAGTTTAA
1 TAATTAGTTTAA
88664676 TAAACAAACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:88667094 original size:24 final size:24
Alignment explanation
Indices: 88667062--88667110 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
88667052 GAGATTTGTG
88667062 AGAAAGGGGTGTAAAGCTTATCTT
1 AGAAAGGGGTGTAAAGCTTATCTT
88667086 AGAAAGGGGTGTAAAGCTTATCTT
1 AGAAAGGGGTGTAAAGCTTATCTT
88667110 A
1 A
88667111 CTTATGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (24 bp):
AGAAAGGGGTGTAAAGCTTATCTT
Found at i:88670271 original size:47 final size:47
Alignment explanation
Indices: 88670218--88670338 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
88670208 GACAAGAACA
*
88670218 TATACCATGGCCCTTAGCCAAATCAAGGTAACTTATCCC-AATGTACC
1 TATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGAA-GTACC
88670265 TATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGAAGTACC
1 TATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGAAGTACC
88670312 TATACCATGGCCCGTAGCCAAATCAAG
1 TATACCATGGCCCGTAGCCAAATCAAG
88670339 ATATTATTCG
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
47 70 0.97
48 2 0.03
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (47 bp):
TATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCCGAAGTACC
Found at i:88672700 original size:55 final size:53
Alignment explanation
Indices: 88672637--88672770 Score: 151
Period size: 53 Copynumber: 2.5 Consensus size: 53
88672627 GGAAATCATC
* * * *
88672637 TAAGACCATGTCAAGACATGGCATTGATAAACTACTATGAGGCAAAGATCCCATG
1 TAAGACCATGTCAAGACATGGCAATG-TAAACTAC-ATAAGGCAAAGATACCACG
* * ** * * *
88672692 TAAGACCATGCCAAGGCATGGCAATGTTGAGTTCATAAGGCAAGGATACCACG
1 TAAGACCATGTCAAGACATGGCAATGTAAACTACATAAGGCAAAGATACCACG
88672745 TAAGACCATGTCAAGACATGGCAATG
1 TAAGACCATGTCAAGACATGGCAATG
88672771 GTAAGTTTAA
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
53 39 0.59
54 4 0.06
55 23 0.35
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (53 bp):
TAAGACCATGTCAAGACATGGCAATGTAAACTACATAAGGCAAAGATACCACG
Found at i:88675016 original size:27 final size:27
Alignment explanation
Indices: 88674986--88675163 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
88674976 ATATTGAGTC
* * * *
88674986 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
88675013 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
88675040 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
88675068 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
88675095 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
88675122 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
88675149 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
88675164 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:88675125 original size:82 final size:81
Alignment explanation
Indices: 88675007--88675162 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
88674997 TGCTATATAA
* *
88675007 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
88675072 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
88675089 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
88675153 CACTTAGTGC
65 CACTTAGTGC
88675163 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:88683082 original size:27 final size:27
Alignment explanation
Indices: 88683052--88683229 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
88683042 ATATTGAGTC
* * * *
88683052 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
88683079 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
88683106 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
88683134 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
88683161 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
88683188 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
88683215 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
88683230 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:88683191 original size:82 final size:81
Alignment explanation
Indices: 88683073--88683228 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
88683063 TGCTATATAA
* *
88683073 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
88683138 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
88683155 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
88683219 CACTTAGTGC
65 CACTTAGTGC
88683229 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:88694063 original size:47 final size:48
Alignment explanation
Indices: 88693993--88694124 Score: 178
Period size: 47 Copynumber: 2.8 Consensus size: 48
88693983 CACAATCGAT
* * *
88693993 AAGTACATATACCACGGCCCGTAGCCAAATCAAGGTAACTGATCTC-G
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTGATCCCAG
* * *
88694040 GAGTACCTAT-CACATGGCTCGTAGCCAAATCAAGGTAACTTATCCCAG
1 AAGTACCTATAC-CATGGCCCGTAGCCAAATCAAGGTAACTGATCCCAG
*
88694088 AAGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
88694125 TTATTCGCAC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
46 1 0.01
47 38 0.52
48 33 0.45
49 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTGATCCCAG
Found at i:88695121 original size:32 final size:32
Alignment explanation
Indices: 88695080--88695147 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
88695070 GAATCGATCT
88695080 AGAGTCTGCAAATCATTCCCATTGTCGGGTTG
1 AGAGTCTGCAAATCATTCCCATTGTCGGGTTG
*
88695112 AGAGTCTGCAAATCATTCCTATTGTCGGGTTG
1 AGAGTCTGCAAATCATTCCCATTGTCGGGTTG
88695144 AGAG
1 AGAG
88695148 CGTCAACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (32 bp):
AGAGTCTGCAAATCATTCCCATTGTCGGGTTG
Found at i:88696323 original size:46 final size:46
Alignment explanation
Indices: 88696247--88696459 Score: 302
Period size: 46 Copynumber: 4.6 Consensus size: 46
88696237 TGATGTCATA
* * *
88696247 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCATGTTGCCATG
* **
88696293 GTATCTTTCAACCATGGTCTTATTCATTTTCCCGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATGTCATGTTGCCATG
*
88696340 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
* * *
88696386 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
*
88696432 GTATCTTTCAACCATGGTCTTACACATT
1 GTATCTTTCAACCATGGTCTTACTCATT
88696460 CCATATCAGA
Statistics
Matches: 151, Mismatches: 14, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
46 112 0.74
47 39 0.26
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.42
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCATGTTGCCATG
Found at i:88696406 original size:93 final size:92
Alignment explanation
Indices: 88696247--88696468 Score: 320
Period size: 93 Copynumber: 2.4 Consensus size: 92
88696237 TGATGTCATA
* * * *
88696247 GTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAACCATGGT
1 GTATCTTTCAACCATGGTCTTACTC-ATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGT
* * *
88696311 CTTATTCATTTTCCCGTCATGTTGCCATG
65 CTTATTCA-TTTCACATCACGTTGCCATG
88696340 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
*
88696405 TTATTCATTTCATATCACGTTGCCATG
66 TTATTCATTTCACATCACGTTGCCATG
* * *
88696432 GTATCTTTCAACCATGGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAG
88696469 AGAGCACACT
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
92 54 0.46
93 63 0.54
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (92 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATGGTATCTTTCAACCATGGTC
TTATTCATTTCACATCACGTTGCCATG
Found at i:88703284 original size:32 final size:33
Alignment explanation
Indices: 88703243--88703307 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
88703233 TTAATGTGTA
88703243 AAAATGCCCAAATGTATATTTTTGGACTAAATT
1 AAAATGCCCAAATGTATATTTTTGGACTAAATT
88703276 AAAA-GCCCAAATGTATATTTTTGGACTAAATT
1 AAAATGCCCAAATGTATATTTTTGGACTAAATT
88703308 GAATAAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 28 0.88
33 4 0.12
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (33 bp):
AAAATGCCCAAATGTATATTTTTGGACTAAATT
Found at i:88709503 original size:24 final size:25
Alignment explanation
Indices: 88709467--88709513 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
88709457 TAGCCTGAAA
88709467 TTAGATAATTTAGGTT-GTTTATAT
1 TTAGATAATTTAGGTTAGTTTATAT
*
88709491 TTAGACTAA-TTAGTTTAGTTTAT
1 TTAGA-TAATTTAGGTTAGTTTAT
88709514 TAGACTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (25 bp):
TTAGATAATTTAGGTTAGTTTATAT
Found at i:88711374 original size:18 final size:17
Alignment explanation
Indices: 88711341--88711375 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
88711331 AATCCTTTTG
88711341 TTTAATTTTCTTATTTA
1 TTTAATTTTCTTATTTA
*
88711358 TTTATTTTTCGTTATTTA
1 TTTAATTTTC-TTATTTA
88711376 ATTTTATCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTAATTTTCTTATTTA
Found at i:88711746 original size:24 final size:25
Alignment explanation
Indices: 88711700--88711749 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
88711690 TTAGTTGCGG
88711700 AAACGTAGTATATAAAAAAAAACTA
1 AAACGTAGTATATAAAAAAAAACTA
88711725 AAACGTAGTATAT-AAAAAAAACTA
1 AAACGTAGTATATAAAAAAAAACTA
88711749 A
1 A
88711750 GATTTAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.20
Consensus pattern (25 bp):
AAACGTAGTATATAAAAAAAAACTA
Found at i:88712721 original size:28 final size:28
Alignment explanation
Indices: 88712690--88712792 Score: 102
Period size: 28 Copynumber: 3.7 Consensus size: 28
88712680 CATACATGCG
* *
88712690 TATGGCCCACTAGGCTCAATCTCTTTCA
1 TATGGCCCACTAGGCCCAATCACTTTCA
* * *
88712718 TATGGCCCATTAAGCCCATTCACATTT-A
1 TATGGCCCACTAGGCCCAATCAC-TTTCA
* * *
88712746 TGTGGCCCATTAGGCCCAAATCACATTCA
1 TATGGCCCACTAGGCCC-AATCACTTTCA
88712775 TATGG-CCACTAGGCCCAA
1 TATGGCCCACTAGGCCCAA
88712793 ACCACATTTA
Statistics
Matches: 61, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
27 2 0.03
28 46 0.75
29 13 0.21
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (28 bp):
TATGGCCCACTAGGCCCAATCACTTTCA
Found at i:88713059 original size:16 final size:16
Alignment explanation
Indices: 88713017--88713059 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
88713007 GTAGCCAAAC
*
88713017 TTTCGGCTTTTTTGCA
1 TTTCGGCTTTTTAGCA
**
88713033 TTTCAACTTTTTAGCA
1 TTTCGGCTTTTTAGCA
*
88713049 TTTCGGGTTTT
1 TTTCGGCTTTT
88713060 CAGGATTTGC
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.12, C:0.16, G:0.16, T:0.56
Consensus pattern (16 bp):
TTTCGGCTTTTTAGCA
Found at i:88717286 original size:28 final size:28
Alignment explanation
Indices: 88717255--88717367 Score: 113
Period size: 28 Copynumber: 4.0 Consensus size: 28
88717245 CATACATGCG
*
88717255 TATGGCCCATTAGGCCCAATCTC-TTTCA
1 TATGGCCCATTAGGCCCAATCACATTT-A
* *
88717283 TATGGGCCATTAGGCCCATTCACATTTA
1 TATGGCCCATTAGGCCCAATCACATTTA
* *
88717311 TGTGGCCCATTAGGCCCAAATCACATTCA
1 TATGGCCCATTAGGCCC-AATCACATTTA
* * *
88717340 TATAG-CCACTGGGCCCAAATCACATTTA
1 TATGGCCCATTAGGCCC-AATCACATTTA
88717368 CAGTCATGCT
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
28 56 0.79
29 15 0.21
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (28 bp):
TATGGCCCATTAGGCCCAATCACATTTA
Found at i:88717355 original size:56 final size:57
Alignment explanation
Indices: 88717257--88717367 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 57
88717247 TACATGCGTA
* * * * *
88717257 TGGCCCATTAGGCCCAATCTCTTTCATATGGGCCATTAGGCCC-ATTCACATTTATG
1 TGGCCCATTAGGCCCAATCACATTCATATGAGCCACTAGGCCCAAATCACATTTATG
*
88717313 TGGCCCATTAGGCCCAAATCACATTCATAT-AGCCACTGGGCCCAAATCACATTTA
1 TGGCCCATTAGGCCC-AATCACATTCATATGAGCCACTAGGCCCAAATCACATTTA
88717368 CAGTCATGCT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
56 25 0.53
57 22 0.47
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (57 bp):
TGGCCCATTAGGCCCAATCACATTCATATGAGCCACTAGGCCCAAATCACATTTATG
Found at i:88717631 original size:16 final size:16
Alignment explanation
Indices: 88717587--88717624 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
88717577 AAACTTTCGG
*
88717587 CTTTTCGACATTTTGA
1 CTTTTCGGCATTTTGA
88717603 CTTTTCGGCATTTTGA
1 CTTTTCGGCATTTTGA
88717619 CTTTTC
1 CTTTTC
88717625 AGGATTTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.13, C:0.21, G:0.13, T:0.53
Consensus pattern (16 bp):
CTTTTCGGCATTTTGA
Found at i:88721028 original size:18 final size:18
Alignment explanation
Indices: 88721007--88721085 Score: 61
Period size: 18 Copynumber: 4.4 Consensus size: 18
88720997 TAACTGCCAT
88721007 TGAATAATCGACTGTTAC
1 TGAATAATCGACTGTTAC
* **
88721025 TGAATAA-CTAACTACTAC
1 TGAATAATC-GACTGTTAC
* * *
88721043 TGAATAATTGACTGATAT
1 TGAATAATCGACTGTTAC
* * *
88721061 TGAATAAACGACCGTTAT
1 TGAATAATCGACTGTTAC
88721079 TGAATAA
1 TGAATAA
88721086 CTGATTATTA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
17 1 0.02
18 46 0.98
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (18 bp):
TGAATAATCGACTGTTAC
Found at i:88724077 original size:49 final size:49
Alignment explanation
Indices: 88724015--88724146 Score: 149
Period size: 48 Copynumber: 2.7 Consensus size: 49
88724005 ATGAGATCTC
88724015 ATGTAAGACCATGTCTGGGAAATGGCATCGGCATCCAAGATGAGAGCCA
1 ATGTAAGACCATGTCTGGGAAATGGCATCGGCATCCAAGATGAGAGCCA
* * * * * *
88724064 ATGTAAGACCATGTCTGGGACATGGCATCAGCA-CCAATATGTGATCCC
1 ATGTAAGACCATGTCTGGGAAATGGCATCGGCATCCAAGATGAGAGCCA
* * * * * *
88724112 GTATAAGACCATATCAGGGATATGGCTTCGGCATC
1 ATGTAAGACCATGTCTGGGAAATGGCATCGGCATC
88724147 ATTAAGTGAT
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
48 37 0.54
49 32 0.46
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (49 bp):
ATGTAAGACCATGTCTGGGAAATGGCATCGGCATCCAAGATGAGAGCCA
Found at i:88724137 original size:48 final size:48
Alignment explanation
Indices: 88724067--88724187 Score: 127
Period size: 48 Copynumber: 2.5 Consensus size: 48
88724057 AGAGCCAATG
* * *
88724067 TAAGACCATGTCTGGGACATGGCATCAGCACCAATATGTGATCCCGTA
1 TAAGACCATATCAGGGACATGGCATCAGCACCAATAAGTGATCCCGTA
* * * * * **
88724115 TAAGACCATATCAGGGATATGGCTTCGGCATCATTAAGTGATTTCGTA
1 TAAGACCATATCAGGGACATGGCATCAGCACCAATAAGTGATCCCGTA
*
88724163 TAAGACCATTTCTA-GGACATGGCAT
1 TAAGACCATATC-AGGGACATGGCAT
88724188 TGATATGAGG
Statistics
Matches: 59, Mismatches: 13, Indels: 2
0.80 0.18 0.03
Matches are distributed among these distances:
48 58 0.98
49 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (48 bp):
TAAGACCATATCAGGGACATGGCATCAGCACCAATAAGTGATCCCGTA
Found at i:88727379 original size:18 final size:19
Alignment explanation
Indices: 88727356--88727396 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
88727346 GTATTTTTCT
88727356 AAAAAT-TATAAAAAATAA
1 AAAAATATATAAAAAATAA
*
88727374 AAAAATCATTTAAAAAATAA
1 AAAAAT-ATATAAAAAATAA
88727394 AAA
1 AAA
88727397 TATTCAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
20 14 0.70
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAATATATAAAAAATAA
Found at i:88727745 original size:10 final size:10
Alignment explanation
Indices: 88727732--88727782 Score: 59
Period size: 10 Copynumber: 5.1 Consensus size: 10
88727722 CTTTTTTTGA
88727732 AATTTTTAAT
1 AATTTTTAAT
88727742 AATTTTT-AT
1 AATTTTTAAT
88727751 AATTTTTATAT
1 AATTTTTA-AT
* *
88727762 TATATTTAAT
1 AATTTTTAAT
*
88727772 AAATTTTAAT
1 AATTTTTAAT
88727782 A
1 A
88727783 TTTGTTTTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.26
10 17 0.50
11 8 0.24
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
AATTTTTAAT
Found at i:88727871 original size:18 final size:19
Alignment explanation
Indices: 88727850--88727890 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
88727840 AAGTATATTT
*
88727850 TTTTCTATT-TTTAAATTA
1 TTTTCTATTAATTAAATTA
*
88727868 TTTTCTATTAATTATATTA
1 TTTTCTATTAATTAAATTA
88727887 TTTT
1 TTTT
88727891 TAATCATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTCTATTAATTAAATTA
Found at i:88727917 original size:16 final size:16
Alignment explanation
Indices: 88727898--88727962 Score: 62
Period size: 15 Copynumber: 4.0 Consensus size: 16
88727888 TTTTAATCAT
88727898 TTTTAATTTTTTTAAA
1 TTTTAATTTTTTTAAA
*
88727914 TTTTTAA-ATTTTTAAA
1 -TTTTAATTTTTTTAAA
*
88727930 TTTT-ATTTTTTTGAA
1 TTTTAATTTTTTTAAA
*
88727945 TTTTTATGATTTTTTAAA
1 TTTTAAT--TTTTTTAAA
88727963 CAAATATACC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 1 0.03
15 15 0.38
16 10 0.25
17 6 0.15
18 8 0.20
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTAATTTTTTTAAA
Found at i:88727949 original size:8 final size:8
Alignment explanation
Indices: 88727886--88727933 Score: 60
Period size: 8 Copynumber: 5.6 Consensus size: 8
88727876 TAATTATATT
88727886 ATTTTTAA
1 ATTTTTAA
88727894 TCATTTTTAA
1 --ATTTTTAA
*
88727904 TTTTTTTAA
1 -ATTTTTAA
88727913 ATTTTTAA
1 ATTTTTAA
88727921 ATTTTTAA
1 ATTTTTAA
88727929 ATTTT
1 ATTTT
88727934 ATTTTTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
8 20 0.57
9 7 0.20
10 8 0.23
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTTTTAA
Found at i:88729139 original size:42 final size:40
Alignment explanation
Indices: 88729059--88729139 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 40
88729049 AACACTATTT
* *
88729059 TTATATTTTTTAATCAATTTAAAATTTTTAAAAATAATTC
1 TTATATTTTTTAATAAATTTAAAATTTTAAAAAATAATTC
88729099 TTATATATTTTTAA-AAATTTAAAAATTTTAAAAAATTAATT
1 TTATAT-TTTTTAATAAATTT-AAAATTTTAAAAAA-TAATT
88729140 AAATACTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
40 11 0.31
41 20 0.56
42 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (40 bp):
TTATATTTTTTAATAAATTTAAAATTTTAAAAAATAATTC
Found at i:88729496 original size:31 final size:31
Alignment explanation
Indices: 88729460--88729522 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
88729450 AATGCAATAC
88729460 AATAAATGAAGCTTATTTAAGTGATTCATTA
1 AATAAATGAAGCTTATTTAAGTGATTCATTA
*
88729491 AATAAATGAAGCTTATTTATGTGATTCATTA
1 AATAAATGAAGCTTATTTAAGTGATTCATTA
88729522 A
1 A
88729523 CACATTAAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.06, G:0.13, T:0.40
Consensus pattern (31 bp):
AATAAATGAAGCTTATTTAAGTGATTCATTA
Found at i:88747326 original size:40 final size:40
Alignment explanation
Indices: 88747276--88747358 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
88747266 AAGGGTATTA
** *
88747276 ATAAAATAGGGAAGGTATCTATACTTTGTTAAAAGTATCG
1 ATAAAATAGGGAAAATATCGATACTTTGTTAAAAGTATCG
* *
88747316 ATAAACTAGGGAAAATATCGATACTTTGTTAAATGTATCG
1 ATAAAATAGGGAAAATATCGATACTTTGTTAAAAGTATCG
88747356 ATA
1 ATA
88747359 CTTTTGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (40 bp):
ATAAAATAGGGAAAATATCGATACTTTGTTAAAAGTATCG
Found at i:88751334 original size:47 final size:47
Alignment explanation
Indices: 88751225--88751335 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
88751215 CCGGGATAAG
* *
88751225 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
88751272 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
88751319 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
88751336 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:88759493 original size:41 final size:39
Alignment explanation
Indices: 88759342--88759522 Score: 159
Period size: 40 Copynumber: 4.5 Consensus size: 39
88759332 AATCAAGCAT
** ** * * *
88759342 CTTCGGGGTTTAGCCGGATATAACCACTCGCAC-AAGGC
1 CTTCGGGACTTAGCCGGATATAGTCGCTAGCACAAATGC
* * * * * *
88759380 CTTCGGGTCTTAACCCGGATATGGTCACTAGTATAAATGC
1 CTTCGGGACTT-AGCCGGATATAGTCGCTAGCACAAATGC
88759420 CTTCGGGACTTAGCCGGAATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCGG-ATATAGTCGCTAGCACAAATGC
* *
88759460 CTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGA-CTTAG-CCGGATATAGTCGC-TAGCACAAATGC
88759501 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAG-CCGGATAT
88759523 CATTCGAGTA
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
38 9 0.08
39 23 0.20
40 50 0.43
41 31 0.27
42 3 0.03
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (39 bp):
CTTCGGGACTTAGCCGGATATAGTCGCTAGCACAAATGC
Found at i:88770084 original size:68 final size:63
Alignment explanation
Indices: 88770003--88770159 Score: 174
Period size: 63 Copynumber: 2.4 Consensus size: 63
88769993 TATAGTGCTG
* * *
88770003 AGTGCACATCATGTGTACAAGAGAGCTACAAGACATTATGA-TGTAGCTAGGTCACATGGGTGAT
1 AGTGTACACCATGTGTACAAGAGAGCTAC--GACA-TA-AACTG--GCTAGGTCACATGGGTGAT
88770067 ACTA
60 ACTA
* * *
88770071 TGTGTACACCATGTAG-ACAAGAGAGCTACGAGATAAACTGGCTAGGTCACATGGGTGGTACTA
1 AGTGTACACCATGT-GTACAAGAGAGCTACGACATAAACTGGCTAGGTCACATGGGTGATACTA
*
88770134 AGTGTTCACCATGTGTACAAGAGAGC
1 AGTGTACACCATGTGTACAAGAGAGC
88770160 CGAACTATAT
Statistics
Matches: 78, Mismatches: 8, Indels: 11
0.80 0.08 0.11
Matches are distributed among these distances:
62 1 0.01
63 44 0.56
64 1 0.01
65 4 0.05
66 3 0.04
68 24 0.31
69 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (63 bp):
AGTGTACACCATGTGTACAAGAGAGCTACGACATAAACTGGCTAGGTCACATGGGTGATACTA
Found at i:88775326 original size:18 final size:19
Alignment explanation
Indices: 88775305--88775341 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
88775295 TTAACCTACC
88775305 GATAATAT-TTTTCATACT
1 GATAATATATTTTCATACT
88775323 GATAATATATTTTCATACT
1 GATAATATATTTTCATACT
88775342 AACTTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (19 bp):
GATAATATATTTTCATACT
Found at i:88777795 original size:13 final size:13
Alignment explanation
Indices: 88777763--88777795 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
88777753 CAATTTAGGG
*
88777763 TCACACAGCCGTA
1 TCACACGGCCGTA
88777776 TCACACGGCCGTA
1 TCACACGGCCGTA
88777789 TCACACG
1 TCACACG
88777796 ACTGTGTGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (13 bp):
TCACACGGCCGTA
Found at i:88781554 original size:20 final size:21
Alignment explanation
Indices: 88781529--88781568 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
88781519 ATCTTGAAAC
88781529 AGGGCA-CACACCCGTGTGGA
1 AGGGCAGCACACCCGTGTGGA
**
88781549 AGGGCAGCATGCCCGTGTGG
1 AGGGCAGCACACCCGTGTGG
88781569 TCATTATAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.20, C:0.28, G:0.40, T:0.12
Consensus pattern (21 bp):
AGGGCAGCACACCCGTGTGGA
Found at i:88783272 original size:46 final size:44
Alignment explanation
Indices: 88783173--88783343 Score: 150
Period size: 46 Copynumber: 3.7 Consensus size: 44
88783163 TCATCTCGTA
* * *
88783173 GCTGATGCATGTCCCAGACATGTCTTACA-TAGGCTTACGTCTCACG
1 GCTGATGCATGTCCCAGACATGTCTTACACTA-GCCT-CGTCTGA-T
* *
88783219 GCCGATGCATGCCCCAGACATGTCTTACACTAGCACTCGTCTTGAT
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGC-CTCGTC-TGAT
* *
88783265 GCTGATGCCATGTCCCATACATGGTCTTACACT-GGCTC-TCATGATGT
1 GCTGATG-CATGTCCCAGACAT-GTCTTACACTAGCCTCGTC-TGA--T
*
88783312 GGCTGATGCATGTCCCAGTCATGTCTTACACT
1 -GCTGATGCATGTCCCAGACATGTCTTACACT
88783344 GGCTCACAAT
Statistics
Matches: 105, Mismatches: 12, Indels: 16
0.79 0.09 0.12
Matches are distributed among these distances:
45 5 0.05
46 52 0.50
47 31 0.30
48 17 0.16
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.29
Consensus pattern (44 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCCTCGTCTGAT
Found at i:88783345 original size:46 final size:46
Alignment explanation
Indices: 88783148--88783348 Score: 148
Period size: 46 Copynumber: 4.3 Consensus size: 46
88783138 CCCATACATG
* * *
88783148 GTCTTACACTGACTATCATC-TCG-TAGCTGATGCATGTCCCAGACAT
1 GTCTTACACTGGCTCTCATCAT-GAT-GCTGATGCATGTCCCAGTCAT
* * * *
88783194 GTCTTACA-TAGGCTTACGTC-TCACG--GCCGATGCATGCCCCAGACAT
1 GTCTTACACT-GGC-T-C-TCATCATGATGCTGATGCATGTCCCAGTCAT
* * * *
88783240 GTCTTACACTAGCACTCGTCTTGATGCTGATGCCATGTCCCA-TACAT
1 GTCTTACACTGGCTCTCATCATGATGCTGATG-CATGTCCCAGT-CAT
*
88783287 GGTCTTACACTGGCTCTCATGATG-TGGCTGATGCATGTCCCAGTCAT
1 -GTCTTACACTGGCTCTCATCATGAT-GCTGATGCATGTCCCAGTCAT
88783334 GTCTTACACTGGCTC
1 GTCTTACACTGGCTC
88783349 ACAATAATCC
Statistics
Matches: 124, Mismatches: 17, Indels: 28
0.73 0.10 0.17
Matches are distributed among these distances:
43 2 0.02
44 4 0.03
45 1 0.01
46 60 0.48
47 26 0.21
48 29 0.23
49 2 0.02
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.30
Consensus pattern (46 bp):
GTCTTACACTGGCTCTCATCATGATGCTGATGCATGTCCCAGTCAT
Done.