Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A09
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: 77927517
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1491452 characters in sequence are not A, C, G, or T
File 133 of 250
Found at i:42918532 original size:36 final size:36
Alignment explanation
Indices: 42918487--42918679 Score: 129
Period size: 36 Copynumber: 5.2 Consensus size: 36
42918477 TTCTTTAAAG
* *
42918487 GTTCACATGATATCTATGGTTCA-CATAGTACCTAGA
1 GTTCACATGATATCTATAGCT-AGCATAGTACCTAGA
* *
42918523 GTTCACATGATATGTATAGCTAGCATAGTACCTTGA
1 GTTCACATGATATCTATAGCTAGCATAGTACCTAGA
* * * * * *
42918559 GTTCGCATGTTATGTATAGGGCGT-GCATAATATCTAGG
1 GTTCACATGATATCTATA--GC-TAGCATAGTACCTAGA
** * *
42918597 GTTTGCATGATATCTATAGCTCGCACAGTACCTAGA
1 GTTCACATGATATCTATAGCTAGCATAGTACCTAGA
** * * * * *
42918633 GTTTGCATGTTATATATAAGGCTCGCATAGTATCTAGG
1 GTTCACATGATATCTAT-A-GCTAGCATAGTACCTAGA
42918671 GTTCACATG
1 GTTCACATG
42918680 TTTTATATAC
Statistics
Matches: 126, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
35 2 0.02
36 73 0.58
37 1 0.01
38 49 0.39
39 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (36 bp):
GTTCACATGATATCTATAGCTAGCATAGTACCTAGA
Found at i:42918605 original size:38 final size:37
Alignment explanation
Indices: 42918510--42918688 Score: 121
Period size: 38 Copynumber: 4.8 Consensus size: 37
42918500 CTATGGTTCA
* * ** * * *
42918510 CATAGTACCTAGAGTTCACATGATATGTATA-GCTAG
1 CATAGTATCTAGGGTTTGCATGTTATATATAGGCTCG
* * * * *
42918546 CATAGTACCTTGAGTTCGCATGTTATGTATAGGGCGT-G
1 CATAGTATCTAGGGTTTGCATGTTATATATA-GGC-TCG
* * *
42918584 CATAATATCTAGGGTTTGCATGATATCTATA-GCTCG
1 CATAGTATCTAGGGTTTGCATGTTATATATAGGCTCG
* * *
42918620 CACAGTACCTAGAGTTTGCATGTTATATATAAGGCTCG
1 CATAGTATCTAGGGTTTGCATGTTATATAT-AGGCTCG
** *
42918658 CATAGTATCTAGGGTTCACATGTTTTATATA
1 CATAGTATCTAGGGTTTGCATGTTATATATA
42918689 CTGAGGGATC
Statistics
Matches: 115, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
35 1 0.01
36 55 0.48
37 2 0.02
38 56 0.49
39 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (37 bp):
CATAGTATCTAGGGTTTGCATGTTATATATAGGCTCG
Found at i:42918661 original size:74 final size:74
Alignment explanation
Indices: 42918528--42918673 Score: 204
Period size: 74 Copynumber: 2.0 Consensus size: 74
42918518 CTAGAGTTCA
* * * * *
42918528 CATGATATGTATAGCTAGCATAGTACCTTGAGTTCGCATGTTATGTATAGGGCGTGCATAATATC
1 CATGATATCTATAGCTAGCACAGTACCTAGAGTTCGCATGTTATATATAAGGCGTGCATAATATC
42918593 TAGGGTTTG
66 TAGGGTTTG
* * *
42918602 CATGATATCTATAGCTCGCACAGTACCTAGAGTTTGCATGTTATATATAAGGC-TCGCATAGTAT
1 CATGATATCTATAGCTAGCACAGTACCTAGAGTTCGCATGTTATATATAAGGCGT-GCATAATAT
42918666 CTAGGGTT
65 CTAGGGTT
42918674 CACATGTTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
73 1 0.02
74 62 0.98
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (74 bp):
CATGATATCTATAGCTAGCACAGTACCTAGAGTTCGCATGTTATATATAAGGCGTGCATAATATC
TAGGGTTTG
Found at i:42921762 original size:11 final size:9
Alignment explanation
Indices: 42921736--42921777 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
42921726 AAAAATTAAT
42921736 ATTTAAAAA
1 ATTTAAAAA
42921745 ATTTAAAGAA
1 ATTTAAA-AA
*
42921755 ATTTTAAAA
1 ATTTAAAAA
42921764 A-TTAATAAA
1 ATTTAA-AAA
42921773 ATTTA
1 ATTTA
42921778 CATTTCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 3 0.11
9 14 0.50
10 11 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (9 bp):
ATTTAAAAA
Found at i:42935645 original size:24 final size:24
Alignment explanation
Indices: 42935600--42935646 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
42935590 TCTTACATAA
*
42935600 TTATATATTTTGAAAATTAATTTT
1 TTATATATTTTGAAAATAAATTTT
42935624 TTATATATTTT-AAATATAAATTT
1 TTATATATTTTGAAA-ATAAATTT
42935647 GAATTTTAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTATATATTTTGAAAATAAATTTT
Found at i:42935903 original size:25 final size:25
Alignment explanation
Indices: 42935858--42935908 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
42935848 CCATTCTAAC
* *
42935858 AAAAAAAATATAGTATCAAGATGAA
1 AAAAAAAATATAATATCAAGAGGAA
*
42935883 AAAAAAGAATATAAT-TTAAGAGGAA
1 AAAAAA-AATATAATATCAAGAGGAA
42935908 A
1 A
42935909 TTTTAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.65, C:0.02, G:0.14, T:0.20
Consensus pattern (25 bp):
AAAAAAAATATAATATCAAGAGGAA
Found at i:42940101 original size:15 final size:15
Alignment explanation
Indices: 42940081--42940111 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42940071 TTGATGATAG
42940081 GCTGATTAGAAATTA
1 GCTGATTAGAAATTA
42940096 GCTGATTAGAAATTA
1 GCTGATTAGAAATTA
42940111 G
1 G
42940112 GGCTAATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (15 bp):
GCTGATTAGAAATTA
Found at i:42946111 original size:18 final size:18
Alignment explanation
Indices: 42946090--42946349 Score: 168
Period size: 18 Copynumber: 14.3 Consensus size: 18
42946080 GAACAATTAT
42946090 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
42946108 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
42946126 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
42946144 TTATTCAGTATCGATCA-TCGG
1 TTATTCAGTA---A-CAGTCAG
* *
42946165 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
42946183 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
42946200 ATATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
42946219 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* * *
42946236 TTCATTCAGTGACAATTAG
1 TT-ATTCAGTAACAGTCAG
* *
42946255 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
42946273 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
*
42946291 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
42946309 TTATCCGGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
* * *
42946327 CTATTCAGTAATAATCAG
1 TTATTCAGTAACAGTCAG
42946345 TTATT
1 TTATT
42946350 TTATACCTTT
Statistics
Matches: 182, Mismatches: 49, Indels: 22
0.72 0.19 0.09
Matches are distributed among these distances:
17 18 0.10
18 135 0.74
19 16 0.09
21 12 0.07
22 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:42946130 original size:36 final size:36
Alignment explanation
Indices: 42946077--42946349 Score: 194
Period size: 36 Copynumber: 7.5 Consensus size: 36
42946067 TCATTAACTC
* *
42946077 TCAG-AACAATTATTTATTCAGTAACAGTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAGTTAT
* * * **
42946112 TCGGTAACAATCAATTATTCAATAATAACCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAGTTAT
* ** * *
42946148 TCAGTATCGATCATCGGTTATCCAGTAACAGTCAATTAT
1 TCAGTAAC-A--ATCAATTATTCAGTAACAGTCAGTTAT
* *
42946187 TCAGTAA-AATCAGA-TATTCAGTAACAATTAAGTTAT
1 TCAGTAACAATCA-ATTATTCAGTAAC-AGTCAGTTAT
* * * * *
42946223 TCAGTAGCAGTC-ATTCATTCAGTGACAATTAGTTAT
1 TCAGTAACAATCAATT-ATTCAGTAACAGTCAGTTAT
** * *
42946259 TCAGTAATGATCAATTATTCAGTAATATTCAGTTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAGTTAT
* * * **
42946295 TCAGTAACAGTCAATTATCCGGTAACAGTCAACTAT
1 TCAGTAACAATCAATTATTCAGTAACAGTCAGTTAT
* *
42946331 TCAGTAATAATCAGTTATT
1 TCAGTAACAATCAATTATT
42946350 TTATACCTTT
Statistics
Matches: 178, Mismatches: 50, Indels: 19
0.72 0.20 0.08
Matches are distributed among these distances:
35 17 0.10
36 119 0.67
37 17 0.10
39 25 0.14
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (36 bp):
TCAGTAACAATCAATTATTCAGTAACAGTCAGTTAT
Found at i:42946221 original size:75 final size:75
Alignment explanation
Indices: 42946090--42946228 Score: 183
Period size: 75 Copynumber: 1.9 Consensus size: 75
42946080 GAACAATTAT
* * * * *
42946090 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAATTATTCAATAATAACCAGTTATTCAGTAT
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATCAATTATTCAATAACAACAAGTTATTCAGTAT
42946155 CGATCATCGG
66 CGATCATCGG
* *
42946165 TTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA-TATTCAGTAACAATTAAGTTATTCAGT
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATCA-ATTATTCAATAACAA-CAAGTTATTCAGT
42946228 A
64 A
42946229 GCAGTCATTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
74 16 0.29
75 39 0.71
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (75 bp):
TTATCCAGTAACAGTCAATTATTCAGTAACAATCAATTATTCAATAACAACAAGTTATTCAGTAT
CGATCATCGG
Found at i:42946518 original size:47 final size:47
Alignment explanation
Indices: 42946466--42946582 Score: 182
Period size: 47 Copynumber: 2.5 Consensus size: 47
42946456 CAATAACAGT
* * *
42946466 AACAGTAGCAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
*
42946513 AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCTGA
1 AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
42946560 AACAGTAACAGTAACGGTA-ACAG
1 AACAGTAACAGT-ACGGTACACAG
42946583 TAACAATATC
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
47 59 0.91
48 6 0.09
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (47 bp):
AACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
Found at i:42947248 original size:20 final size:18
Alignment explanation
Indices: 42947214--42947251 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
42947204 AAACTTTCAA
42947214 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
42947232 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
42947252 ATTCCCTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:42952026 original size:18 final size:18
Alignment explanation
Indices: 42951992--42952176 Score: 133
Period size: 18 Copynumber: 10.2 Consensus size: 18
42951982 TCATTAACTC
* *
42951992 TCAG-AACAATTATTTAT
1 TCAGTAACAATCAGTTAT
*
42952009 TCAGTAACAGTCAGTTAT
1 TCAGTAACAATCAGTTAT
* *
42952027 TCGGTAACAATCAATTAT
1 TCAGTAACAATCAGTTAT
* * *
42952045 TCAATAATAACCAGTTAT
1 TCAGTAACAATCAGTTAT
* *
42952063 TCAGTATCGATCATCGGTTAT
1 TCAGTAAC-A--ATCAGTTAT
* * *
42952084 CCAGTAACAGTCAATTAT
1 TCAGTAACAATCAGTTAT
*
42952102 TCAGTAA-AATCAGATAT
1 TCAGTAACAATCAGTTAT
*
42952119 TCAGTAACAATTAAGTTAT
1 TCAGTAACAA-TCAGTTAT
* *
42952138 TCAGTAGCACTCA-TTCAT
1 TCAGTAACAATCAGTT-AT
* *
42952156 TCAGTGACAATTAGTTAT
1 TCAGTAACAATCAGTTAT
42952174 TCA
1 TCA
42952177 ATAATTGTAA
Statistics
Matches: 126, Mismatches: 34, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
17 20 0.16
18 75 0.60
19 17 0.13
20 1 0.01
21 13 0.10
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (18 bp):
TCAGTAACAATCAGTTAT
Found at i:42952136 original size:75 final size:75
Alignment explanation
Indices: 42952005--42952143 Score: 183
Period size: 75 Copynumber: 1.9 Consensus size: 75
42951995 GAACAATTAT
* * * * *
42952005 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAATTATTCAATAATAACCAGTTATTCAGTAT
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATCAATTATTCAATAACAACAAGTTATTCAGTAT
42952070 CGATCATCGG
66 CGATCATCGG
* *
42952080 TTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA-TATTCAGTAACAATTAAGTTATTCAGT
1 TTATCCAGTAACAGTCAATTATTCAGTAACAATCA-ATTATTCAATAACAA-CAAGTTATTCAGT
42952143 A
64 A
42952144 GCACTCATTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
74 16 0.29
75 39 0.71
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (75 bp):
TTATCCAGTAACAGTCAATTATTCAGTAACAATCAATTATTCAATAACAACAAGTTATTCAGTAT
CGATCATCGG
Found at i:42954194 original size:93 final size:93
Alignment explanation
Indices: 42954081--42954252 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42954071 CGCCCATAAG
* *
42954081 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42954146 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
42954174 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
42954239 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
42954253 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:42954249 original size:46 final size:46
Alignment explanation
Indices: 42954074--42954249 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42954064 TGTAACCCGC
* * *
42954074 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
42954120 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
42954170 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
42954213 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
42954250 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:42955603 original size:16 final size:16
Alignment explanation
Indices: 42955582--42955612 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42955572 GATATTTTAA
42955582 TATATTATATTAATAT
1 TATATTATATTAATAT
*
42955598 TATATTATGTTAATA
1 TATATTATATTAATA
42955613 AAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:42957906 original size:18 final size:18
Alignment explanation
Indices: 42957817--42957906 Score: 81
Period size: 18 Copynumber: 5.0 Consensus size: 18
42957807 GGGGGTGTTA
*
42957817 CAGTAATGATCAATTATT
1 CAGTAATAATCAATTATT
* *
42957835 CAGTAATATTCAGTTATT
1 CAGTAATAATCAATTATT
* * *
42957853 CAGTAACAGTCAATTATC
1 CAGTAATAATCAATTATT
* * * *
42957871 CGGTAACAGTCAACTATT
1 CAGTAATAATCAATTATT
*
42957889 CAGTAATAATCAGTTATT
1 CAGTAATAATCAATTATT
42957907 TTATACCTTT
Statistics
Matches: 57, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.36
Consensus pattern (18 bp):
CAGTAATAATCAATTATT
Found at i:42958100 original size:47 final size:47
Alignment explanation
Indices: 42958026--42958139 Score: 176
Period size: 47 Copynumber: 2.4 Consensus size: 47
42958016 TAACAGTAAT
* * *
42958026 AGTAGCAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGGAAC
1 AGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAAC
*
42958073 AGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCTGAAAC
1 AGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAAC
42958120 AGTAACAGTAACGGTA-ACAG
1 AGTAACAGT-ACGGTACACAG
42958140 TAACAATATC
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
47 56 0.90
48 6 0.10
ACGTcount: A:0.40, C:0.23, G:0.21, T:0.16
Consensus pattern (47 bp):
AGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAAC
Found at i:42958805 original size:20 final size:18
Alignment explanation
Indices: 42958771--42958808 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
42958761 AAACTTTCAA
42958771 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
42958789 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
42958809 ATTCCCTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 6 0.33
20 7 0.39
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:42964360 original size:34 final size:34
Alignment explanation
Indices: 42964322--42964445 Score: 185
Period size: 34 Copynumber: 3.6 Consensus size: 34
42964312 TTCTGATTTG
* *
42964322 ATATGACATTTTGATCTGATATATGTTTATAAAA
1 ATATGACATTTTGATATGATATATGTTTATGAAA
* *
42964356 ATATGACATTATGATATGATATATGTTTTTGAAA
1 ATATGACATTTTGATATGATATATGTTTATGAAA
* * *
42964390 ATATGACATTCTGATCTGATATATGTTTATGATA
1 ATATGACATTTTGATATGATATATGTTTATGAAA
42964424 ATATGACATTTTGATATGATAT
1 ATATGACATTTTGATATGATAT
42964446 TTGTAAAAGT
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 80 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (34 bp):
ATATGACATTTTGATATGATATATGTTTATGAAA
Found at i:42964679 original size:5 final size:5
Alignment explanation
Indices: 42964661--42964697 Score: 56
Period size: 5 Copynumber: 7.2 Consensus size: 5
42964651 CGTTTTGGGC
*
42964661 TTTGT TTTGAT TTTTT TTTGT TTTGT TTTGT TTTGT T
1 TTTGT TTTG-T TTTGT TTTGT TTTGT TTTGT TTTGT T
42964698 CATTGATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.86
6 4 0.14
ACGTcount: A:0.03, C:0.00, G:0.16, T:0.81
Consensus pattern (5 bp):
TTTGT
Found at i:42970760 original size:18 final size:19
Alignment explanation
Indices: 42970727--42970764 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
42970717 AGACTCCAGG
*
42970727 TCTGATTCTTTTCAATCAT
1 TCTGATTCTCTTCAATCAT
42970746 TCTGATT-TCTTCAATCAT
1 TCTGATTCTCTTCAATCAT
42970764 T
1 T
42970765 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTCTCTTCAATCAT
Found at i:42976375 original size:45 final size:44
Alignment explanation
Indices: 42976306--42976738 Score: 287
Period size: 45 Copynumber: 9.7 Consensus size: 44
42976296 CGGTGAATTC
* * *
42976306 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT
*
42976350 AGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTTTAAATT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAG------A-T
* * * * *
42976402 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCAA-A-
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT
* * *
42976443 ACAAACCTTATCTCCTTGAAGTTGCAGTGGAACAGGTTGAA-ATT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGA-T
* * * *
42976487 ACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGAT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT
* ** *
42976531 AGCAAATCTTATTTCTTTGAAGTTGCAGTGGAACAGATTGAAACTATAAATT
1 A-CAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTG-----A-AGA-T
* * * * * *
42976583 ACAGATCTTATCTCTCTGAAGTTGTAGTAGAGCAGA-TCAA-A-
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT
* * * ** *
42976624 ACAAACCTTATCTTCTTGAAGTTGCAGTGGAGTAAATTGAA-ATT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGA-T
* * *
42976668 ACAAGTCTTATCTCCCTGAAGTTGCAGCGG---A-ATTGAAGCT
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT
* *
42976708 ACTAATCCTATCTCCCTGAAGTTGCAGTGGA
1 ACAAATCTTATCTCCCTGAAGTTGCAGTGGA
42976739 GCGGATTAAA
Statistics
Matches: 308, Mismatches: 56, Indels: 53
0.74 0.13 0.13
Matches are distributed among these distances:
40 33 0.11
41 57 0.19
42 8 0.03
43 2 0.01
44 65 0.21
45 72 0.23
50 5 0.02
51 62 0.20
52 4 0.01
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.30
Consensus pattern (44 bp):
ACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGAT
Found at i:42976504 original size:44 final size:44
Alignment explanation
Indices: 42976397--42976699 Score: 212
Period size: 44 Copynumber: 6.8 Consensus size: 44
42976387 TTGAAGCTTT
* * *
42976397 AAATTAC-AGATCTTATCT-CTCTGAAGTTGCAGTAGAGCAGA-TC
1 AAATTACAAG-TCTTATCTCCT-TGAAGTTGCAGTGGAACAGATTG
** *
42976440 AAA--ACAAACCTTATCTCCTTGAAGTTGCAGTGGAACAGGTTG
1 AAATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAACAGATTG
* *
42976482 AAATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTG
1 AAATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAACAGATTG
* * *
42976526 AAGA-TAGCAAATCTTATTTCTTTGAAGTTGCAGTGGAACAGATTG
1 AA-ATTA-CAAGTCTTATCTCCTTGAAGTTGCAGTGGAACAGATTG
* * * * *
42976571 AAACTATAAATTACAGATCTTATCT-CTCTGAAGTTGTAGTAGAGCAGA-TC
1 AAA-T-T--A-CA-AG-TCTTATCTCCT-TGAAGTTGCAGTGGAACAGATTG
** * ** *
42976621 AAA--ACAAACCTTATCTTCTTGAAGTTGCAGTGGAGTAAATTG
1 AAATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAACAGATTG
* *
42976663 AAATTACAAGTCTTATCTCCCTGAAGTTGCAGCGGAA
1 AAATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAA
42976700 TTGAAGCTAC
Statistics
Matches: 202, Mismatches: 39, Indels: 37
0.73 0.14 0.13
Matches are distributed among these distances:
41 49 0.24
42 14 0.07
43 4 0.02
44 66 0.33
45 36 0.18
47 1 0.00
49 2 0.01
50 6 0.03
51 24 0.12
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
AAATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAACAGATTG
Found at i:42976614 original size:181 final size:181
Alignment explanation
Indices: 42976301--42976694 Score: 680
Period size: 181 Copynumber: 2.2 Consensus size: 181
42976291 AAGATCGGTG
42976301 AATTCACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCC
1 AATT-ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCC
* *
42976366 CTGAAGTTGCAGTGGAACAGATTGAAGCTTTAAATTACAGATCTTATCTCTCTGAAGTTGCAGTA
65 CTGAAGTTGCAGTGGAACAGATTGAAACTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTA
**
42976431 GAGCAGATCAAAACAAACCTTATCTCCTTGAAGTTGCAGTGGAACAGGTTGA
130 GAGCAGATCAAAACAAACCTTATCTCCTTGAAGTTGCAGTGGAACAAATTGA
* **
42976483 AATTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCTT
1 AATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCC
*
42976548 TGAAGTTGCAGTGGAACAGATTGAAACTATAAATTACAGATCTTATCTCTCTGAAGTTGTAGTAG
66 TGAAGTTGCAGTGGAACAGATTGAAACTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAG
* **
42976613 AGCAGATCAAAACAAACCTTATCTTCTTGAAGTTGCAGTGGAGTAAATTGA
131 AGCAGATCAAAACAAACCTTATCTCCTTGAAGTTGCAGTGGAACAAATTGA
42976664 AATTACAAGTCTTATCTCCCTGAAGTTGCAG
1 AATTACAAGTCTTATCTCCCTGAAGTTGCAG
42976695 CGGAATTGAA
Statistics
Matches: 200, Mismatches: 12, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
181 196 0.98
182 4 0.02
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.30
Consensus pattern (181 bp):
AATTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCTTATTTCCC
TGAAGTTGCAGTGGAACAGATTGAAACTATAAATTACAGATCTTATCTCTCTGAAGTTGCAGTAG
AGCAGATCAAAACAAACCTTATCTCCTTGAAGTTGCAGTGGAACAAATTGA
Found at i:42976943 original size:16 final size:18
Alignment explanation
Indices: 42976912--42976944 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
42976902 GGACTGAAAC
42976912 GAAGCGACCTGAAGAAGA
1 GAAGCGACCTGAAGAAGA
42976930 GAAGC-ACC-GAAGAAG
1 GAAGCGACCTGAAGAAG
42976945 TCAAGACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.45, C:0.18, G:0.33, T:0.03
Consensus pattern (18 bp):
GAAGCGACCTGAAGAAGA
Found at i:42979258 original size:3 final size:3
Alignment explanation
Indices: 42979250--42979301 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
42979240 GATTTTCTCA
* * * *
42979250 ATT ATT ATT ATT ATT GTTT ATT ATT ACT ATT ATT GTT AGT ATT ATT
1 ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
42979296 ATT ATT
1 ATT ATT
42979302 GCCATTATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 38 0.95
4 2 0.05
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:42979365 original size:3 final size:3
Alignment explanation
Indices: 42979357--42979381 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
42979347 TTTATTTACC
42979357 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
42979382 TTTAAAATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:42981221 original size:36 final size:36
Alignment explanation
Indices: 42981174--42981242 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
42981164 TTTTAATAAC
42981174 AACATCGATCTGCGAAATGTGTTGATTATCAATCCG
1 AACATCGATCTGCGAAATGTGTTGATTATCAATCCG
42981210 AACATCGATCTGCGAAATGTGTTGATTATCAAT
1 AACATCGATCTGCGAAATGTGTTGATTATCAAT
42981243 TCGGAACAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (36 bp):
AACATCGATCTGCGAAATGTGTTGATTATCAATCCG
Found at i:42987168 original size:15 final size:15
Alignment explanation
Indices: 42987150--42987186 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42987140 ATATAGCAAG
42987150 CCATCAATGATTGAA
1 CCATCAATGATTGAA
*
42987165 CCATCAATGATTGGA
1 CCATCAATGATTGAA
42987180 CCATCAA
1 CCATCAA
42987187 ACATTTCATG
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:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (15 bp):
CCATCAATGATTGAA
Found at i:42989691 original size:45 final size:45
Alignment explanation
Indices: 42989587--42989706 Score: 143
Period size: 45 Copynumber: 2.6 Consensus size: 45
42989577 GATCGGAATG
* * * *
42989587 TGCCATGGTGTCTTTCAACCATGGTCTTATTCATTTTCCGTCATGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCA-TTTCAGTCATGA
* *
42989633 TGCCATAGTGTCTTTCAACTATGGTCTTATTTC-TTTGATTCATGA
1 TGCCATAGTGTCTTTCAACTATGGTCTTA-TTCATTTCAGTCATGA
* *
42989678 TGTCATAGTGTCTTTCAAATATGGTCTTA
1 TGCCATAGTGTCTTTCAACTATGGTCTTA
42989707 CTCGAGAGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
45 35 0.54
46 27 0.42
47 3 0.05
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (45 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCAGTCATGA
Found at i:42989769 original size:90 final size:89
Alignment explanation
Indices: 42989675--42989885 Score: 235
Period size: 90 Copynumber: 2.4 Consensus size: 89
42989665 CTTTGATTCA
* *
42989675 TGATGTCATAGTGTCTTTCAAATATGGTCTTACTCGAGAGAATCGTGATGCCATAATGTCTTTCA
1 TGATGCCATAGTGTCTTTCAAATATGGTCTTACTCGAGAGAATCGTGATGCCATAACGTCTTTCA
* * *
42989740 TTCACGGTCTTACTCGTTAGAATTT
66 GTCACGGTCTTACTCGTT-GAAGTG
** * * *** *
42989765 TGATGCCATAACGTCTTTC-AGTCATGATCTTACTCGTTTGAATCGTGATGCCATAACGTCTTTT
1 TGATGCCATAGTGTCTTTCAAAT-ATGGTCTTACTCGAGAGAATCGTGATGCCATAACGTCTTTC
* * *
42989829 AGTCATGGTCTTACTCGTTTACGTG
65 AGTCACGGTCTTACTCGTTGAAGTG
* *
42989854 TGGTGCCATAGTGTCTTTCAACTATGGTCTTA
1 TGATGCCATAGTGTCTTTCAAATATGGTCTTA
42989886 ATCATTTCCT
Statistics
Matches: 98, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
89 28 0.29
90 70 0.71
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (89 bp):
TGATGCCATAGTGTCTTTCAAATATGGTCTTACTCGAGAGAATCGTGATGCCATAACGTCTTTCA
GTCACGGTCTTACTCGTTGAAGTG
Found at i:42989848 original size:45 final size:45
Alignment explanation
Indices: 42989698--42989847 Score: 210
Period size: 45 Copynumber: 3.3 Consensus size: 45
42989688 TCTTTCAAAT
** * *
42989698 ATGGTCTTACTCGAGAGAATCGTGATGCCATAATGTCTTTCATTC
1 ATGGTCTTACTCGTTAGAATCGTGATGCCATAACGTCTTTCAGTC
* **
42989743 ACGGTCTTACTCGTTAGAATTTTGATGCCATAACGTCTTTCAGTC
1 ATGGTCTTACTCGTTAGAATCGTGATGCCATAACGTCTTTCAGTC
* * *
42989788 ATGATCTTACTCGTTTGAATCGTGATGCCATAACGTCTTTTAGTC
1 ATGGTCTTACTCGTTAGAATCGTGATGCCATAACGTCTTTCAGTC
42989833 ATGGTCTTACTCGTT
1 ATGGTCTTACTCGTT
42989848 TACGTGTGGT
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 91 1.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.39
Consensus pattern (45 bp):
ATGGTCTTACTCGTTAGAATCGTGATGCCATAACGTCTTTCAGTC
Found at i:42989940 original size:15 final size:15
Alignment explanation
Indices: 42989912--42989944 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
42989902 CAATAAGCTT
42989912 AATTAATATATAAAC
1 AATTAATATATAAAC
42989927 AATT-ATATATTAAAC
1 AATTAATATA-TAAAC
42989942 AAT
1 AAT
42989945 CAAAAGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AATTAATATATAAAC
Found at i:42994680 original size:30 final size:30
Alignment explanation
Indices: 42994621--42994680 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
42994611 TTTTACGAGC
* *
42994621 CTAAGGGCAAAACTGTAATTTTGTAAAAGT
1 CTAAGGGCAAAACGGTAATTTTGGAAAAGT
* *
42994651 CTAAGGGCAAAACGGTCATTTTGGCAAAGT
1 CTAAGGGCAAAACGGTAATTTTGGAAAAGT
42994681 AGGAATTTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (30 bp):
CTAAGGGCAAAACGGTAATTTTGGAAAAGT
Found at i:42995081 original size:48 final size:48
Alignment explanation
Indices: 42994997--42995286 Score: 303
Period size: 48 Copynumber: 6.0 Consensus size: 48
42994987 ATACTAGGGT
* * * *
42994997 TATGTGAGCCAGTGTAAGACCATGTTTGGAAAATGGCATCGGCATTGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGA
*
42995045 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGA
* * * * * **
42995093 TATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATTGACATTTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGA
* * * *
42995141 TATGAGAGCTAGTGTAAGACCATCTCTGGGACATGGCATCGGCCTCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGA
* * * * ** * *
42995189 CATGTGGGCTAGTGTAAGACTATGTTTGGAACATGAAATCGACACCGATA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCG--A
* * *
42995239 TATGAAAGCTAGTGTAAGACCATGTCT-GAGACATAGCATCGGCATCGA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGA-ACATGGCATCGGCATCGA
42995287 CATCTTACCC
Statistics
Matches: 192, Mismatches: 47, Indels: 6
0.78 0.19 0.02
Matches are distributed among these distances:
48 156 0.81
49 2 0.01
50 34 0.18
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (48 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGGCATCGA
Found at i:42995161 original size:96 final size:96
Alignment explanation
Indices: 42994997--42995286 Score: 375
Period size: 96 Copynumber: 3.0 Consensus size: 96
42994987 ATACTAGGGT
* * *
42994997 TATGTGAGCCAGTGTAAGACCATGTTTGGAAAATGGCATCGGCATTGATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
*
42995062 GACCATGTTTGGAACATGGCATCGGCCTCGA
66 GACCATGTCTGGAACATGGCATCGGCCTCGA
* *
42995093 TATGTGAGCCAATGTAAGACCATGTTTGGAACATGGCATTGACATTTATATGAGAGCTAGTGTAA
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
* *
42995158 GACCATCTCTGGGACATGGCATCGGCCTCGA
66 GACCATGTCTGGAACATGGCATCGGCCTCGA
* * * * ** ** *
42995189 CATGTGGGCTAGTGTAAGACTATGTTTGGAACATGAAATCGACACCGATATATGAAAGCTAGTGT
1 TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACA--TTTATATGAGAGCTAGTGT
* *
42995254 AAGACCATGTCT-GAGACATAGCATCGGCATCGA
64 AAGACCATGTCTGGA-ACATGGCATCGGCCTCGA
42995287 CATCTTACCC
Statistics
Matches: 168, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
96 124 0.74
97 1 0.01
98 43 0.26
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.26
Consensus pattern (96 bp):
TATGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
GACCATGTCTGGAACATGGCATCGGCCTCGA
Found at i:43006965 original size:18 final size:17
Alignment explanation
Indices: 43006919--43006965 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
43006909 GTAGTAATCA
43006919 GTTATTCAGTAACGATC
1 GTTATTCAGTAACGATC
*
43006936 GTTGATTTAGTAAC-AGTC
1 GTT-ATTCAGTAACGA-TC
43006954 GGTTATTCAGTA
1 -GTTATTCAGTA
43006966 GCGGTCAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.16
18 18 0.72
19 3 0.12
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (17 bp):
GTTATTCAGTAACGATC
Found at i:43008331 original size:13 final size:12
Alignment explanation
Indices: 43008299--43008332 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
43008289 ACTATATATA
43008299 TATATAATAACT
1 TATATAATAACT
43008311 TA-ATAATATACT
1 TATATAATA-ACT
43008323 TATATAATAA
1 TATATAATAA
43008333 GTAAACATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.30
12 8 0.40
13 6 0.30
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (12 bp):
TATATAATAACT
Found at i:43015152 original size:21 final size:21
Alignment explanation
Indices: 43015126--43015166 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43015116 AATGCTTCGG
43015126 AGACCACCAATACCTAAAAAT
1 AGACCACCAATACCTAAAAAT
*
43015147 AGACCACTAATACCTAAAAA
1 AGACCACCAATACCTAAAAA
43015167 CAGAATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.27, G:0.05, T:0.15
Consensus pattern (21 bp):
AGACCACCAATACCTAAAAAT
Found at i:43039193 original size:9 final size:9
Alignment explanation
Indices: 43039179--43039204 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
43039169 TAGCCTGAGC
43039179 ACCTCCACA
1 ACCTCCACA
43039188 ACCTCCACA
1 ACCTCCACA
43039197 ACCTCCAC
1 ACCTCCAC
43039205 CGCGGCCTCT
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:0.31, C:0.58, G:0.00, T:0.12
Consensus pattern (9 bp):
ACCTCCACA
Found at i:43042005 original size:12 final size:12
Alignment explanation
Indices: 43041990--43042014 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43041980 CTTGATTTTT
43041990 TCCTAAAATCCC
1 TCCTAAAATCCC
43042002 TCCTAAAATCCC
1 TCCTAAAATCCC
43042014 T
1 T
43042015 TAAACCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.40, G:0.00, T:0.28
Consensus pattern (12 bp):
TCCTAAAATCCC
Found at i:43042515 original size:16 final size:17
Alignment explanation
Indices: 43042489--43042520 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43042479 ACTCATTTTC
43042489 CATCATCAAGCATTCAA
1 CATCATCAAGCATTCAA
43042506 CATC-TCAAGCATTCA
1 CATCATCAAGCATTCA
43042521 TCAATGGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.31, G:0.06, T:0.25
Consensus pattern (17 bp):
CATCATCAAGCATTCAA
Found at i:43050310 original size:28 final size:28
Alignment explanation
Indices: 43050228--43050319 Score: 75
Period size: 28 Copynumber: 3.3 Consensus size: 28
43050218 GCCATGAAGG
*
43050228 CGTTCCTTTCTAGAGATTGACACAAA-A
1 CGTTCCTTTCTAGAGATTGCCACAAAGA
* * *
43050255 GGCTATTC-TTC-AGAG-TGTGCCACGAAGA
1 CG-T-TCCTTTCTAGAGAT-TGCCACAAAGA
43050283 CGTTCCTTTCTAGAGATTGCCACAAAGAA
1 CGTTCCTTTCTAGAGATTGCCACAAAG-A
*
43050312 TGTTCCTT
1 CGTTCCTT
43050320 AGAATGTGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 14
0.69 0.11 0.20
Matches are distributed among these distances:
26 3 0.06
27 16 0.33
28 19 0.39
29 11 0.22
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (28 bp):
CGTTCCTTTCTAGAGATTGCCACAAAGA
Found at i:43050372 original size:54 final size:54
Alignment explanation
Indices: 43050193--43050374 Score: 222
Period size: 54 Copynumber: 3.4 Consensus size: 54
43050183 TCACATTACA
* *
43050193 CCACAAAGGCTATTCCTTAGAGTGCGCCATGAAGGCGTTCCTTTCTAGAGATTG
1 CCACAAAGGCTATTCCTTAGAGTGTGCCACGAAGGCGTTCCTTTCTAGAGATTG
* *
43050247 ACACAAAAGGCTATT-CTTCAGAGTGTGCCACGAAGACGTTCCTTTCTAGAGATTG
1 CCAC-AAAGGCTATTCCTT-AGAGTGTGCCACGAAGGCGTTCCTTTCTAGAGATTG
** * * * * * *
43050302 CCACAAAGAATGTTCCTTAGAATGTGCCACGAAGGCATTCTTTTCCAGAGATTT
1 CCACAAAGGCTATTCCTTAGAGTGTGCCACGAAGGCGTTCCTTTCTAGAGATTG
*
43050356 CCACAACGGCTATTCCTTA
1 CCACAAAGGCTATTCCTTA
43050375 TTTTGGTGTG
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
54 58 0.54
55 49 0.46
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.28
Consensus pattern (54 bp):
CCACAAAGGCTATTCCTTAGAGTGTGCCACGAAGGCGTTCCTTTCTAGAGATTG
Found at i:43052350 original size:10 final size:10
Alignment explanation
Indices: 43052332--43052361 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
43052322 ATCCTATTGT
*
43052332 CACATGCATA
1 CACAAGCATA
43052342 CACAAGCATA
1 CACAAGCATA
43052352 CACAAGCATA
1 CACAAGCATA
43052362 AATGCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.47, C:0.30, G:0.10, T:0.13
Consensus pattern (10 bp):
CACAAGCATA
Found at i:43053238 original size:23 final size:23
Alignment explanation
Indices: 43053212--43053274 Score: 58
Period size: 23 Copynumber: 2.7 Consensus size: 23
43053202 TCTATTGAGT
43053212 TGAAACGATAAGCTCTA-ACGAGC
1 TGAAAC-ATAAGCTCTATACGAGC
* *
43053235 TGAATCAATAAGCTC-ATTCGAGC
1 TGAAAC-ATAAGCTCTATACGAGC
43053258 TGAGAACAGTAAGCTCT
1 TGA-AACA-TAAGCTCT
43053275 TACAAGTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 22 0.69
24 9 0.28
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.22
Consensus pattern (23 bp):
TGAAACATAAGCTCTATACGAGC
Found at i:43057042 original size:36 final size:36
Alignment explanation
Indices: 43057001--43057076 Score: 107
Period size: 36 Copynumber: 2.1 Consensus size: 36
43056991 TACCTCCATA
**
43057001 TCCACCTCCACCCCTTAAACCACTTCCAACACTACC
1 TCCACCTCCACCCCTTAAACCACCGCCAACACTACC
* * *
43057037 TCCACCTCCACCCTTTAAACTACCGCCAGCACTACC
1 TCCACCTCCACCCCTTAAACCACCGCCAACACTACC
43057073 TCCA
1 TCCA
43057077 ACACTACCTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.26, C:0.51, G:0.03, T:0.20
Consensus pattern (36 bp):
TCCACCTCCACCCCTTAAACCACCGCCAACACTACC
Found at i:43057047 original size:24 final size:24
Alignment explanation
Indices: 43057020--43057095 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
43057010 ACCCCTTAAA
43057020 CCACTTCCAACACTACCTCCACCT
1 CCACTTCCAACACTACCTCCACCT
* * * *
43057044 CCACCCTT-TAA-ACTACCGCCAGCA
1 CCA--CTTCCAACACTACCTCCACCT
* *
43057068 CTACCTCCAACACTACCTCCACCT
1 CCACTTCCAACACTACCTCCACCT
43057092 CCAC
1 CCAC
43057096 CAACAGCAGC
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
22 2 0.05
23 2 0.05
24 28 0.76
25 2 0.05
26 3 0.08
ACGTcount: A:0.26, C:0.53, G:0.03, T:0.18
Consensus pattern (24 bp):
CCACTTCCAACACTACCTCCACCT
Found at i:43057085 original size:12 final size:12
Alignment explanation
Indices: 43057055--43057088 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
43057045 CACCCTTTAA
* *
43057055 ACTACCGCCAGC
1 ACTACCTCCAAC
43057067 ACTACCTCCAAC
1 ACTACCTCCAAC
43057079 ACTACCTCCA
1 ACTACCTCCA
43057089 CCTCCACCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.29, C:0.50, G:0.06, T:0.15
Consensus pattern (12 bp):
ACTACCTCCAAC
Found at i:43057134 original size:66 final size:66
Alignment explanation
Indices: 43057064--43057228 Score: 267
Period size: 66 Copynumber: 2.5 Consensus size: 66
43057054 AACTACCGCC
* * * *
43057064 AGCACTACCTCCAACACTACCTCCACCTCCACCAACAGCAGCACCACGTCCACCAAGGGAACCGG
1 AGCACTACCTCCAAAACTGCTTCCACCTCCACCAACAGCAGCACCACGTCCACCAACGGAACCGG
43057129 T
66 T
* * *
43057130 AGCACTACCTCCAATACTGCTTCCACCTCCACCAACGGTAGCACCACGTCCACCAACGGAACCGG
1 AGCACTACCTCCAAAACTGCTTCCACCTCCACCAACAGCAGCACCACGTCCACCAACGGAACCGG
43057195 T
66 T
43057196 AGCACTACCTCCAAAACTGCTTCCACCTCCACC
1 AGCACTACCTCCAAAACTGCTTCCACCTCCACC
43057229 TCCACCTCTA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
66 92 1.00
ACGTcount: A:0.28, C:0.45, G:0.13, T:0.14
Consensus pattern (66 bp):
AGCACTACCTCCAAAACTGCTTCCACCTCCACCAACAGCAGCACCACGTCCACCAACGGAACCGG
T
Found at i:43057242 original size:30 final size:30
Alignment explanation
Indices: 43057202--43057259 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
43057192 CGGTAGCACT
*
43057202 ACCTCCAAAACTGCTTCCACCTCCACCTCC
1 ACCTCCAAAACTACTTCCACCTCCACCTCC
*
43057232 ACCTCTAAAACTACTTCCACCTCCACCT
1 ACCTCCAAAACTACTTCCACCTCCACCT
43057260 ATTAAACTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.26, C:0.50, G:0.02, T:0.22
Consensus pattern (30 bp):
ACCTCCAAAACTACTTCCACCTCCACCTCC
Found at i:43057250 original size:24 final size:24
Alignment explanation
Indices: 43057220--43057300 Score: 117
Period size: 24 Copynumber: 3.4 Consensus size: 24
43057210 AACTGCTTCC
*
43057220 ACCTCCACCTCCACCTCTAAAACT
1 ACCTCCACCTCCACCTCTTAAACT
* *
43057244 ACTTCCACCTCCACCTATTAAACT
1 ACCTCCACCTCCACCTCTTAAACT
* *
43057268 GCCTCCTCCTCCACCTCTTAAACT
1 ACCTCCACCTCCACCTCTTAAACT
43057292 ACCTCCACC
1 ACCTCCACC
43057301 AATGCCACCT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.49, G:0.01, T:0.25
Consensus pattern (24 bp):
ACCTCCACCTCCACCTCTTAAACT
Found at i:43057416 original size:57 final size:57
Alignment explanation
Indices: 43057339--43057470 Score: 174
Period size: 57 Copynumber: 2.3 Consensus size: 57
43057329 CGAGCAGCTA
* * ** * *
43057339 CATCAGAAGCAACTTGTGAAGCTGCTTTACGAAAACCAGATTGGGCAGCAGCTGTTC
1 CATCAGCAGCAGCTTGTGAAGCTGCTTTACGAAAACCAGAACGGACAGCAGCTGCTC
* *
43057396 CATCAGCAGCAGCTTGTGAAGCTGCTTTATGAAAAGCAGAACGGACAGCAGCTGCTC
1 CATCAGCAGCAGCTTGTGAAGCTGCTTTACGAAAACCAGAACGGACAGCAGCTGCTC
* *
43057453 TATCAGCAGCAGCATGTG
1 CATCAGCAGCAGCTTGTG
43057471 CAATTGCTCC
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 65 1.00
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (57 bp):
CATCAGCAGCAGCTTGTGAAGCTGCTTTACGAAAACCAGAACGGACAGCAGCTGCTC
Found at i:43059783 original size:16 final size:16
Alignment explanation
Indices: 43059762--43059793 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43059752 TCAATTAATC
*
43059762 TAATTAACCTAAAAAT
1 TAATTAAACTAAAAAT
43059778 TAATTAAACTAAAAAT
1 TAATTAAACTAAAAAT
43059794 CAACCAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
TAATTAAACTAAAAAT
Found at i:43063899 original size:43 final size:44
Alignment explanation
Indices: 43063780--43063899 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 44
43063770 TCGTACAATG
* ** *
43063780 CCAACGTCCCAGATGTGGTCTTACATGT-AATCAAATATCGATA
1 CCAACATCCCAGACATGGTCTTACACGTAAATCAAATATCGATA
*** * * *
43063823 CCAGTGTCCCAGACAGGGTCTTACACG-ACATCAAATAT-GATG
1 CCAACATCCCAGACATGGTCTTACACGTAAATCAAATATCGATA
43063865 CCAACATCCCA-AGCATGGTCTTACACGTAAATCAA
1 CCAACATCCCAGA-CATGGTCTTACACGTAAATCAA
43063900 CCAACATCCC
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
41 1 0.02
42 24 0.39
43 36 0.59
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (44 bp):
CCAACATCCCAGACATGGTCTTACACGTAAATCAAATATCGATA
Found at i:43071474 original size:43 final size:41
Alignment explanation
Indices: 43071408--43071529 Score: 129
Period size: 43 Copynumber: 2.9 Consensus size: 41
43071398 AGCTCGTACA
*
43071408 ATGCCAACGTCCCAGACGTGGTCTTACAT-ATAATCAAATATCG
1 ATGCC-ACGTCCCAGACGGGGTCTTACATGA-AATCAAATAT-G
*
43071451 ATGCCACTGTCCTAGACGGGGTCTTACATGAAATCAAATATG
1 ATGCCAC-GTCCCAGACGGGGTCTTACATGAAATCAAATATG
* ** *
43071493 ATGCCAACGTCCCAAACATGGTCTTACACGTAAATCA
1 ATGCC-ACGTCCCAGACGGGGTCTTACATG-AAATCA
43071530 TAAGTCGATG
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
42 25 0.37
43 42 0.62
44 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (41 bp):
ATGCCACGTCCCAGACGGGGTCTTACATGAAATCAAATATG
Found at i:43073665 original size:50 final size:51
Alignment explanation
Indices: 43073566--43073700 Score: 150
Period size: 50 Copynumber: 2.6 Consensus size: 51
43073556 TGTGTTTAAA
*
43073566 ATAGCTTTAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACCTGTACCAG
1 ATAGC-TTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACCTGTACCAG
* * * * *
43073618 AT-GGTTAGGTCGCATGTGTAGTACTAAGTGCAGGCTATTATGC-GTACCCG
1 ATAGCTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTA-CCTGTACCAG
* *
43073668 ATAGCTTCA-ATCACATGTGTGGTACTAAGTGCA
1 ATAGCTT-AGGTCACATGTGTAGTACTAAGTGCA
43073701 TGCCAATATG
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
50 41 0.59
51 26 0.37
52 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (51 bp):
ATAGCTTAGGTCACATGTGTAGTACTAAGTGCAGGCTACTACCTGTACCAG
Found at i:43073722 original size:51 final size:51
Alignment explanation
Indices: 43073630--43073756 Score: 137
Period size: 51 Copynumber: 2.5 Consensus size: 51
43073620 GGTTAGGTCG
* * * ***
43073630 CATGTGTAGTACTAAGTGCAGGCTATTATGCGTACCCGATAGCTTCAATCA
1 CATGTGTGGTACTAAGTGCAGGCCAATATGCGTAAAAGATAGCTTCAATCA
* * * *
43073681 CATGTGTGGTACTAAGTGCATGCCAATATGTGTAAAAGATAGCTTTATTCA
1 CATGTGTGGTACTAAGTGCAGGCCAATATGCGTAAAAGATAGCTTCAATCA
* * *
43073732 CAAGTGTGGTACTATGTGAAGGCCA
1 CATGTGTGGTACTAAGTGCAGGCCA
43073757 CTTTGTGAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 62 1.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (51 bp):
CATGTGTGGTACTAAGTGCAGGCCAATATGCGTAAAAGATAGCTTCAATCA
Found at i:43076135 original size:93 final size:93
Alignment explanation
Indices: 43076023--43076194 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
43076013 CGCCCATAAG
*
43076023 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
43076087 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
43076116 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43076181 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
43076195 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:43076189 original size:46 final size:46
Alignment explanation
Indices: 43076016--43076191 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
43076006 TGTAACCCGC
* *
43076016 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
43076062 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
43076112 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
43076155 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
43076192 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43083703 original size:93 final size:93
Alignment explanation
Indices: 43083591--43083762 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
43083581 CGCCCATAAG
*
43083591 CGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 CGAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
43083655 AACGAGTTCGGATGCCTAGTTACATCTCA
65 AACGAGTTCGGATGCCTAGTTACATCTCA
*
43083684 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
43083749 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
43083763 TCAATCATCC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:43083757 original size:46 final size:46
Alignment explanation
Indices: 43083584--43083759 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
43083574 TGTAACCCGC
* *
43083584 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCAT
* *
43083630 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
43083680 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
43083723 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
43083760 TGCTCAATCA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 4 0.04
46 61 0.55
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:43088914 original size:33 final size:33
Alignment explanation
Indices: 43088872--43088934 Score: 126
Period size: 33 Copynumber: 1.9 Consensus size: 33
43088862 TATGAATTTT
43088872 GCTTTTCTTGATCTATGTAATCAAAATTAATTC
1 GCTTTTCTTGATCTATGTAATCAAAATTAATTC
43088905 GCTTTTCTTGATCTATGTAATCAAAATTAA
1 GCTTTTCTTGATCTATGTAATCAAAATTAA
43088935 ATTATTTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (33 bp):
GCTTTTCTTGATCTATGTAATCAAAATTAATTC
Found at i:43095258 original size:28 final size:26
Alignment explanation
Indices: 43095218--43095290 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
43095208 TTTCATTAAT
**
43095218 TTGTGATTTTATGAAATAATAACAAAA
1 TTGTGATAATATGAAATAAT-ACAAAA
*
43095245 TTGTGAATAATATGAAATAATATAAAA
1 TTGTG-ATAATATGAAATAATACAAAA
**
43095272 TTGTGATTTTATGAAATAA
1 TTGTGATAATATGAAATAA
43095291 CAACGATTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
26 12 0.30
27 15 0.38
28 13 0.32
ACGTcount: A:0.48, C:0.01, G:0.12, T:0.38
Consensus pattern (26 bp):
TTGTGATAATATGAAATAATACAAAA
Found at i:43097796 original size:42 final size:42
Alignment explanation
Indices: 43097745--43097864 Score: 107
Period size: 42 Copynumber: 2.9 Consensus size: 42
43097735 GCGTTGATAC
* * *
43097745 GAGATTTCGTGTAAGACCACGTCTGGGACATAGCGTCGAAAT
1 GAGAATTCGTGTAAGACCATGTCTGGGACATAGCATCGAAAT
* * * * * * *
43097787 GAGAATTCGTATGAGACCATATCTTGGATATGGCATCGATAT
1 GAGAATTCGTGTAAGACCATGTCTGGGACATAGCATCGAAAT
* * *
43097829 GAG-ATCCCATGTAAGACCATGTCTGGGACATGGCAT
1 GAGAAT-TCGTGTAAGACCATGTCTGGGACATAGCAT
43097865 TGGCATCTTA
Statistics
Matches: 60, Mismatches: 17, Indels: 2
0.76 0.22 0.03
Matches are distributed among these distances:
41 2 0.03
42 58 0.97
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (42 bp):
GAGAATTCGTGTAAGACCATGTCTGGGACATAGCATCGAAAT
Found at i:43102898 original size:41 final size:38
Alignment explanation
Indices: 43102856--43102931 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 38
43102846 TATTTCTTTA
43102856 TTTATTTC-TTATCT-TTTATTATTATTAGATAG-ATTAT
1 TTTATTTCTTTAT-TGTTTATTATTATTAG-TAGTATTAT
43102893 TTTATTTCTTTATTGTTTATTATTATTAGTAGTATTAT
1 TTTATTTCTTTATTGTTTATTATTATTAGTAGTATTAT
43102931 T
1 T
43102932 ATTAGCCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
37 12 0.33
38 24 0.67
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (38 bp):
TTTATTTCTTTATTGTTTATTATTATTAGTAGTATTAT
Found at i:43109027 original size:30 final size:30
Alignment explanation
Indices: 43108953--43109042 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 30
43108943 ATTCATTTTA
* *
43108953 AACTAATTAGAAGGTTTTTTAACTAAATTT
1 AACTAATTAGAAGGTTTTTTAACTCAATTG
*
43108983 AACAAATCATTAGAAGGTTTTTTAACTCAATTG
1 AAC---TAATTAGAAGGTTTTTTAACTCAATTG
43109016 AACTAATTAGAAGGTTTTTTAAGCTCA
1 AACTAATTAGAAGGTTTTTTAA-CTCA
43109043 TTAATGATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
30 21 0.40
31 4 0.08
33 27 0.52
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (30 bp):
AACTAATTAGAAGGTTTTTTAACTCAATTG
Found at i:43110848 original size:68 final size:68
Alignment explanation
Indices: 43110753--43110910 Score: 289
Period size: 68 Copynumber: 2.3 Consensus size: 68
43110743 TTCACTTGGA
* *
43110753 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
43110818 CGT
66 CGT
43110821 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
43110886 CGT
66 CGT
*
43110889 ATCACATATGTGACCTAGCTAC
1 ATCACACATGTGACCTAGCTAC
43110911 TATATAGTAT
Statistics
Matches: 87, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 87 1.00
ACGTcount: A:0.24, C:0.30, G:0.15, T:0.32
Consensus pattern (68 bp):
ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
CGT
Found at i:43110927 original size:68 final size:67
Alignment explanation
Indices: 43110753--43110928 Score: 246
Period size: 68 Copynumber: 2.6 Consensus size: 67
43110743 TTCACTTGGA
* * * *
43110753 ATCACTCATGCGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATATATATCT-ACGTAGCTCTCTTGTCTACATGGGATACATCC
43110818 CGT
65 CGT
* *
43110821 ATCACACATGTGACCTAGCTACATTTATCTCTCACGTAGCTCTCTTGTCTACATGGGATACATCC
1 ATCACACATGTGACCTAGCTACATATATATCT-ACGTAGCTCTCTTGTCTACATGGGATACATCC
43110886 CGT
65 CGT
*
43110889 ATCACATATGTGACCTAGCTACTATATAGTATCT-CGTAGC
1 ATCACACATGTGACCTAGCTAC-ATATA-TATCTACGTAGC
43110929 CTTATTGTAC
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
68 93 0.92
69 4 0.04
70 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.15, T:0.32
Consensus pattern (67 bp):
ATCACACATGTGACCTAGCTACATATATATCTACGTAGCTCTCTTGTCTACATGGGATACATCCC
GT
Found at i:43117362 original size:19 final size:19
Alignment explanation
Indices: 43117338--43117484 Score: 59
Period size: 19 Copynumber: 7.2 Consensus size: 19
43117328 AATGGTAATA
43117338 AAAAATTAATAAAATTTAT
1 AAAAATTAATAAAATTTAT
* *
43117357 AAAAA-TATTAAATTTTAAT
1 AAAAATTAATAAAATTT-AT
43117376 AAAAATATAAAAATATTTAAATTTTATT
1 AAAAAT-T---AATA---AAA-TTTA-T
* * * *
43117404 TAAAATTAGTACAAAATTAC
1 AAAAATTAATA-AAATTTAT
43117424 AAAAATCATAA-AAAATTTAT
1 AAAAAT--TAATAAAATTTAT
*
43117444 AAAAATT-ATAAAGTTTTAT
1 AAAAATTAATAAA-ATTTAT
*
43117463 AAAAA-TCATAAAATTTTAT
1 AAAAATTAATAAAA-TTTAT
43117482 AAA
1 AAA
43117485 GTCATAAGAA
Statistics
Matches: 96, Mismatches: 15, Indels: 34
0.66 0.10 0.23
Matches are distributed among these distances:
17 1 0.01
18 14 0.15
19 35 0.36
20 17 0.18
21 5 0.05
22 5 0.05
24 6 0.06
27 4 0.04
28 9 0.09
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (19 bp):
AAAAATTAATAAAATTTAT
Found at i:43117368 original size:18 final size:19
Alignment explanation
Indices: 43117333--43117389 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
43117323 TAAAAAATGG
*
43117333 TAATAAAAAATTAATAAAATT
1 TAAT-AAAAA-TATTAAAATT
*
43117354 T-ATAAAAATATTAAATTT
1 TAATAAAAATATTAAAATT
*
43117372 TAATAAAAATATAAAAAT
1 TAATAAAAATATTAAAAT
43117390 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
18 9 0.29
19 19 0.61
20 2 0.06
21 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAATAAAAATATTAAAATT
Found at i:43117379 original size:28 final size:29
Alignment explanation
Indices: 43117343--43117410 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 29
43117333 TAATAAAAAA
43117343 TTAATAAAATTTATAAAAATA-TTAAATT
1 TTAATAAAATTTATAAAAATATTTAAATT
*
43117371 TTAATAAAA-ATATAAAAATATTTAAATT
1 TTAATAAAATTTATAAAAATATTTAAATT
*
43117399 TTATTTAAAATT
1 TTA-ATAAAATT
43117411 AGTACAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.29
28 19 0.56
29 5 0.15
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
TTAATAAAATTTATAAAAATATTTAAATT
Found at i:43117436 original size:9 final size:9
Alignment explanation
Indices: 43117338--43117475 Score: 64
Period size: 10 Copynumber: 14.4 Consensus size: 9
43117328 AATGGTAATA
43117338 AAAAATTAAT
1 AAAAATT-AT
*
43117348 AAAATTTAT
1 AAAAATTAT
43117357 AAAAA-TATT
1 AAAAATTA-T
**
43117366 AAATTTTAAT
1 AAAAATT-AT
43117376 AAAAA-TAT
1 AAAAATTAT
*
43117384 AAAAATATTT
1 AAAAAT-TAT
**
43117394 AAATTTTATT
1 AAAAATTA-T
*
43117404 TAAAATTAGT
1 AAAAATTA-T
*
43117414 ACAAAATTAC
1 A-AAAATTAT
*
43117424 AAAAATCAT
1 AAAAATTAT
43117433 AAAAAATTTAT
1 -AAAAA-TTAT
43117444 AAAAATTAT
1 AAAAATTAT
**
43117453 AAAGTTTTAT
1 AAA-AATTAT
*
43117463 AAAAATCAT
1 AAAAATTAT
43117472 AAAA
1 AAAA
43117476 TTTTATAAAG
Statistics
Matches: 94, Mismatches: 24, Indels: 21
0.68 0.17 0.15
Matches are distributed among these distances:
8 9 0.10
9 32 0.34
10 42 0.45
11 11 0.12
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (9 bp):
AAAAATTAT
Found at i:43117447 original size:10 final size:10
Alignment explanation
Indices: 43117434--43117484 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
43117424 AAAAATCATA
43117434 AAAAATTTAT
1 AAAAATTTAT
43117444 AAAAA-TTAT
1 AAAAATTTAT
**
43117453 AAAGTTTTAT
1 AAAAATTTAT
*
43117463 AAAAA-TCAT
1 AAAAATTTAT
*
43117472 AAAATTTTAT
1 AAAAATTTAT
43117482 AAA
1 AAA
43117485 GTCATAAGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 14 0.44
10 18 0.56
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:43117466 original size:29 final size:27
Alignment explanation
Indices: 43117346--43117484 Score: 93
Period size: 28 Copynumber: 4.9 Consensus size: 27
43117336 TAAAAAATTA
*
43117346 ATAAAATTTATAAAAA-TATTAAATTTT
1 ATAAAAATTATAAAAATTA-TAAATTTT
*
43117373 AATAAAAA-TATAAAAATATTTAAATTTT
1 -ATAAAAATTATAAAAAT-TATAAATTTT
* * ** *
43117401 ATTTAAAATTAGTACAAAATTACAAAAATC
1 A-TAAAAATTA-TA-AAAATTATAAATTTT
43117431 ATAAAAAATTTATAAAAATTATAAAGTTTT
1 AT-AAAAA-TTATAAAAATTATAAA-TTTT
* *
43117461 ATAAAAATCATAAAATTTTATAAA
1 ATAAAAATTATAAAA-ATTATAAA
43117485 GTCATAAGAA
Statistics
Matches: 86, Mismatches: 15, Indels: 19
0.72 0.12 0.16
Matches are distributed among these distances:
27 9 0.10
28 26 0.30
29 26 0.30
30 17 0.20
31 8 0.09
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (27 bp):
ATAAAAATTATAAAAATTATAAATTTT
Found at i:43117491 original size:18 final size:19
Alignment explanation
Indices: 43117424--43117484 Score: 86
Period size: 19 Copynumber: 3.2 Consensus size: 19
43117414 ACAAAATTAC
*
43117424 AAAAATCATAAAAAATTTAT
1 AAAAATCAT-AAAATTTTAT
* *
43117444 AAAAATTATAAAGTTTTAT
1 AAAAATCATAAAATTTTAT
43117463 AAAAATCATAAAATTTTAT
1 AAAAATCATAAAATTTTAT
43117482 AAA
1 AAA
43117485 GTCATAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 28 0.78
20 8 0.22
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATCATAAAATTTTAT
Found at i:43117760 original size:20 final size:19
Alignment explanation
Indices: 43117737--43117807 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 19
43117727 TATATTATGA
43117737 TTTTTATAAAATTTTACAAT
1 TTTTTATAAAATTTTA-AAT
* *
43117757 TTTTTAT-TATTTTTATAACTT
1 TTTTTATAAAATTTTA-AA--T
43117778 ATTTTTAATAAAATTTTAATAT
1 -TTTTT-ATAAAATTTTAA-AT
43117800 TTTTTATA
1 TTTTTATA
43117808 GTTTTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
19 8 0.20
20 10 0.25
21 6 0.15
22 6 0.15
23 3 0.08
24 7 0.17
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTTATAAAATTTTAAAT
Found at i:43117791 original size:43 final size:42
Alignment explanation
Indices: 43117736--43117816 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 42
43117726 GTATATTATG
43117736 ATTTTTATAAAATTTTACA-ATTTTTTATTA-TTTTTATAACTT
1 ATTTTTATAAAATTTTA-ATATTTTTTA-TAGTTTTTATAACTT
43117778 ATTTTTAATAAAATTTTAATATTTTTTATAGTTTTTATA
1 ATTTTT-ATAAAATTTTAATATTTTTTATAGTTTTTATA
43117817 TTTTTATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
42 9 0.25
43 27 0.75
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (42 bp):
ATTTTTATAAAATTTTAATATTTTTTATAGTTTTTATAACTT
Found at i:43117850 original size:37 final size:39
Alignment explanation
Indices: 43117776--43117863 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 39
43117766 TTTTTATAAC
* * * *
43117776 TTATTTTTAATAAAATTTTAATATTTTTTATAGTTTTTA
1 TTATTTTTATTAAAATTTTAATAATTTTAATAATTTTTA
*
43117815 -TATTTTTATTATAA-TTTAATAATTTTAATAATTTTTA
1 TTATTTTTATTAAAATTTTAATAATTTTAATAATTTTTA
43117852 TTGATTTTTATT
1 TT-ATTTTTATT
43117864 TTTTTTATAT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
37 20 0.48
38 13 0.31
39 9 0.21
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (39 bp):
TTATTTTTATTAAAATTTTAATAATTTTAATAATTTTTA
Found at i:43118212 original size:89 final size:88
Alignment explanation
Indices: 43117976--43118219 Score: 283
Period size: 89 Copynumber: 2.7 Consensus size: 88
43117966 TTTTTTTGCA
* * * * * * *
43117976 TTTGATAGTTCAAGTAACCAATTGAGTGCAAAAAAAAAATCAGAGACTTGATTACTTTTTTTGAA
1 TTTGAAAGCTCAAGTACCCAATTGAGTGC-AAAAAAAAGTAAG-GGCTTAATTACTTTTTTTGAA
*
43118041 AAGTTTGAGGGTCTTTTTAATCCAT
64 AAGTTTGAGGGTCTTTTTAATACAT
* * * ***
43118066 TTTGAAAGCTCAAGTACCCAATTGAGTGAAAAAAAAAGCAAGGGGCTTAATT-GTTTTTTTTTTA
1 TTTGAAAGCTCAAGTACCCAATTGAGTGCAAAAAAAAGTAA-GGGCTTAATTACTTTTTTTGAAA
*
43118130 AGTTTGAGGGTCTTTTTTATACAT
65 AGTTTGAGGGTCTTTTTAATACAT
* * *
43118154 TTTGAAAGTTTTAAGTACCCAATTGAGTGCAAAAAAAAGTAAGGGCTTAATTACTTTTTTGGAAA
1 TTTGAAAG-CTCAAGTACCCAATTGAGTGCAAAAAAAAGTAAGGGCTTAATTACTTTTTTTGAAA
43118219 A
65 A
43118220 AGTTACAAGA
Statistics
Matches: 127, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
88 48 0.38
89 53 0.42
90 26 0.20
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (88 bp):
TTTGAAAGCTCAAGTACCCAATTGAGTGCAAAAAAAAGTAAGGGCTTAATTACTTTTTTTGAAAA
GTTTGAGGGTCTTTTTAATACAT
Found at i:43118235 original size:89 final size:87
Alignment explanation
Indices: 43117976--43118219 Score: 272
Period size: 88 Copynumber: 2.7 Consensus size: 87
43117966 TTTTTTTGCA
* * * * * * *
43117976 TTTGATAGTTCAAGTAACCAATTGAGTGCAAAAAAAAAATCAGAGACTTGATTACTTTTTTTGAA
1 TTTGAAAGCTCAAGTACCCAATTGAGTGC-AAAAAAAAGTAAG-GGCTTAATTAC-TTTTTTGAA
*
43118041 AAGTTTGAGGGTCTTTTTAATCCAT
63 AAGTTTGAGGGTCTTTTTAATACAT
* * ** ***
43118066 TTTGAAAGCTCAAGTACCCAATTGAGTGAAAAAAAAAGCAAGGGGCTTAATTGTTTTTTTTTTAA
1 TTTGAAAGCTCAAGTACCCAATTGAGTGCAAAAAAAAGTAA-GGGCTTAATTACTTTTTTGAAAA
*
43118131 GTTTGAGGGTCTTTTTTATACAT
65 GTTTGAGGGTCTTTTTAATACAT
* *
43118154 TTTGAAAGTTTTAAGTACCCAATTGAGTGCAAAAAAAAGTAAGGGCTTAATTACTTTTTTGGAAA
1 TTTGAAAG-CTCAAGTACCCAATTGAGTGCAAAAAAAAGTAAGGGCTTAATTACTTTTTT-GAAA
43118219 A
64 A
43118220 AGTTACAAGA
Statistics
Matches: 126, Mismatches: 25, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
88 53 0.42
89 47 0.37
90 26 0.21
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.36
Consensus pattern (87 bp):
TTTGAAAGCTCAAGTACCCAATTGAGTGCAAAAAAAAGTAAGGGCTTAATTACTTTTTTGAAAAG
TTTGAGGGTCTTTTTAATACAT
Found at i:43119199 original size:13 final size:13
Alignment explanation
Indices: 43119181--43119205 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43119171 CATATATAGA
43119181 ACATATACAGAGC
1 ACATATACAGAGC
43119194 ACATATACAGAG
1 ACATATACAGAG
43119206 TTAACAGATT
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:0.48, C:0.20, G:0.16, T:0.16
Consensus pattern (13 bp):
ACATATACAGAGC
Found at i:43127892 original size:14 final size:14
Alignment explanation
Indices: 43127873--43127901 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43127863 AATAAACATC
43127873 TATGCCTACTCGTG
1 TATGCCTACTCGTG
43127887 TATGCCTACTCGTG
1 TATGCCTACTCGTG
43127901 T
1 T
43127902 TTACATTTAT
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:0.14, C:0.28, G:0.21, T:0.38
Consensus pattern (14 bp):
TATGCCTACTCGTG
Found at i:43129728 original size:19 final size:19
Alignment explanation
Indices: 43129704--43129742 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
43129694 ATTACAAACA
* *
43129704 AATTAAATTTAAAAATATC
1 AATTAAATATAAAAAAATC
43129723 AATTAAATATAAAAAAATC
1 AATTAAATATAAAAAAATC
43129742 A
1 A
43129743 TAACTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (19 bp):
AATTAAATATAAAAAAATC
Found at i:43131038 original size:15 final size:15
Alignment explanation
Indices: 43131018--43131070 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
43131008 TAATACAAAC
43131018 TATTTATTATTAATA
1 TATTTATTATTAATA
*
43131033 TATTTATAATTGTAATAAA
1 TATTTATTA-T-TAAT--A
*
43131052 TATTTATTATTAAAA
1 TATTTATTATTAATA
43131067 TATT
1 TATT
43131071 AATATTGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 13 0.42
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TATTTATTATTAATA
Found at i:43131197 original size:18 final size:18
Alignment explanation
Indices: 43131171--43131205 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43131161 AACTTATTAT
43131171 ATAACTAAATATAAATAA
1 ATAACTAAATATAAATAA
* *
43131189 ATAATTAAATATTAATA
1 ATAACTAAATATAAATA
43131206 TTTATGTTTA
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:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAACTAAATATAAATAA
Found at i:43132265 original size:12 final size:12
Alignment explanation
Indices: 43132248--43132272 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43132238 AAAATAGGGC
43132248 TTTAGCGGCGTT
1 TTTAGCGGCGTT
43132260 TTTAGCGGCGTT
1 TTTAGCGGCGTT
43132272 T
1 T
43132273 CATCAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.32, T:0.44
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:43132396 original size:41 final size:41
Alignment explanation
Indices: 43132297--43132557 Score: 134
Period size: 41 Copynumber: 6.3 Consensus size: 41
43132287 ACAAAAATTG
43132297 TAAAACACAGAGCAATA-GCGGCCGTTTTACACAAAAACGCCGC
1 TAAAA-ACAGAGCAATAGGC-G-CGTTTTACACAAAAACGCCGC
*
43132340 TAAAAATAGAGCAATAGGCGCGTTTTA-ACAAAAAACGCCGC
1 TAAAAACAGAGCAATAGGCGCGTTTTACAC-AAAAACGCCGC
* *** *
43132381 TAAAAACAG-GTCAATAGTG-GCGCTTT-CGGTAAAACGCCAC
1 TAAAAACAGAG-CAATAG-GCGCGTTTTACACAAAAACGCCGC
* * ***
43132421 TAAAAACCAGAGCATTA-GCAGCGCTTT-CGGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGGC-GCGTTTTACACAAAAACGCCGC
* * ***
43132462 TAAAAACCAGAGCATTA-GCGGCGCTTT-CGGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGGC-GCGTTTTACACAAAAACGCCGC
* *
43132503 TAAAAACCAGAG-AATTA-GCGGCGCTTT-CTA-TAAAACGCCGC
1 TAAAAA-CAGAGCAA-TAGGC-GCGTTTTAC-ACAAAAACGCCGC
43132544 TAAAAACCAGAGCA
1 TAAAAA-CAGAGCA
43132558 TTAGCGGCGC
Statistics
Matches: 194, Mismatches: 12, Indels: 25
0.84 0.05 0.11
Matches are distributed among these distances:
39 1 0.01
40 19 0.10
41 153 0.79
42 14 0.07
43 7 0.04
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (41 bp):
TAAAAACAGAGCAATAGGCGCGTTTTACACAAAAACGCCGC
Found at i:43132561 original size:41 final size:41
Alignment explanation
Indices: 43132371--43132589 Score: 336
Period size: 41 Copynumber: 5.4 Consensus size: 41
43132361 GTTTTAACAA
* *
43132371 AAAACGCCGCTAAAAA-CAG-GTCAATAGTGGCGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAG-CATTAGCGGCGCTTTCGGT
* *
43132411 AAAACGCCACTAAAAACCAGAGCATTAGCAGCGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
43132452 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
* **
43132493 AAAACGCCGCTAAAAACCAGAGAATTAGCGGCGCTTTCTAT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
43132534 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTT-GTGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCG-GT
43132575 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
43132590 GTCATATAAC
Statistics
Matches: 164, Mismatches: 12, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
40 15 0.09
41 148 0.90
42 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTCGGT
Found at i:43153799 original size:17 final size:17
Alignment explanation
Indices: 43153779--43153814 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43153769 ATATCCTTAG
43153779 CTTTCCTGTATCTCTTT
1 CTTTCCTGTATCTCTTT
* *
43153796 CTTTCTTGTCTCTCTTT
1 CTTTCCTGTATCTCTTT
43153813 CT
1 CT
43153815 CTATCTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTTCCTGTATCTCTTT
Found at i:43167258 original size:19 final size:19
Alignment explanation
Indices: 43167235--43167281 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
43167225 ATTTAATCTA
*
43167235 ATTTTTATTATTTA-TTTT
1 ATTTTTATTATATATTTTT
* *
43167253 AGTTTTGATTCTATATTTTT
1 A-TTTTTATTATATATTTTT
43167273 ATTTTTATT
1 ATTTTTATT
43167282 TTAATATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 1 0.04
19 17 0.74
20 5 0.22
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.72
Consensus pattern (19 bp):
ATTTTTATTATATATTTTT
Found at i:43167616 original size:43 final size:43
Alignment explanation
Indices: 43167544--43167651 Score: 144
Period size: 43 Copynumber: 2.5 Consensus size: 43
43167534 TTTTAAAATT
* * *
43167544 TCATGACCTTTAGCGGCGTTTGGGGAAAAAGTGCCGCTAAAGG
1 TCATGATCTTTAGCGGCGTTTGGGAAAAAAGCGCCGCTAAAGG
* *
43167587 TTATGATCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGG
1 TCATGATCTTTAGCGGCGTTTGGGAAAAAAGCGCCGCTAAAGG
* * *
43167630 TCGTGGTCTTTAGAGGCGTTTG
1 TCATGATCTTTAGCGGCGTTTG
43167652 CTAAAGGTCG
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (43 bp):
TCATGATCTTTAGCGGCGTTTGGGAAAAAAGCGCCGCTAAAGG
Found at i:43167664 original size:29 final size:29
Alignment explanation
Indices: 43167622--43167681 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
43167612 AAAAAGCGCC
*
43167622 GCTAAAGGTCGTGGTCTTTAGAGGCGTTT
1 GCTAAAGGTCGTGGTCTTTAGAGACGTTT
*
43167651 GCTAAAGGTCGTGGTCTTTAGCGACGTTT
1 GCTAAAGGTCGTGGTCTTTAGAGACGTTT
43167680 GC
1 GC
43167682 GAAAAAAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (29 bp):
GCTAAAGGTCGTGGTCTTTAGAGACGTTT
Found at i:43167697 original size:72 final size:72
Alignment explanation
Indices: 43167579--43167723 Score: 218
Period size: 72 Copynumber: 2.0 Consensus size: 72
43167569 AAAAAGTGCC
* * * *
43167579 GCTAAAGGTTATGATCTTTAGCGGCGTTTGTGAAAAAAGCGCCGCTAAAGGTCGTGGTCTTTAGA
1 GCTAAAGGTCATGATCTTTAGCGACGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGA
43167644 GGCGTTT
66 GGCGTTT
* * * *
43167651 GCTAAAGGTCGTGGTCTTTAGCGACGTTTGCGAAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGC
1 GCTAAAGGTCATGATCTTTAGCGACGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGA
43167716 GGCGTTT
66 GGCGTTT
43167723 G
1 G
43167724 TGAAAAAAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.30
Consensus pattern (72 bp):
GCTAAAGGTCATGATCTTTAGCGACGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGA
GGCGTTT
Found at i:43167712 original size:43 final size:43
Alignment explanation
Indices: 43167651--43167808 Score: 235
Period size: 43 Copynumber: 3.7 Consensus size: 43
43167641 AGAGGCGTTT
* * *
43167651 GCTAAAGGTCGTGGTCTTTAGCGACGTTTGCGAAAAAAGCGTC
1 GCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGAAAAAAGCGCC
*
43167694 GCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAAAGCGCC
1 GCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGAAAAAAGCGCC
* * *
43167737 GCTAAAGGTCCTGATCTTTAGAGGCGTTTGCGAAAAAAGCGCC
1 GCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGAAAAAAGCGCC
* *
43167780 GCTAAAAGTCATGGTCTTTAGCAGCGTTT
1 GCTAAAGGTCATGGTCTTTAGCGGCGTTT
43167809 TTTTCGAAAA
Statistics
Matches: 102, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 102 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.27
Consensus pattern (43 bp):
GCTAAAGGTCATGGTCTTTAGCGGCGTTTGCGAAAAAAGCGCC
Found at i:43167755 original size:115 final size:115
Alignment explanation
Indices: 43167551--43167767 Score: 353
Period size: 115 Copynumber: 1.9 Consensus size: 115
43167541 ATTTCATGAC
* * * * *
43167551 CTTTAGCGGCGTTTGGGGAAAAAGTGCCGCTAAAGGTTATGATCTTTAGCGGCGTTTGTGAAAAA
1 CTTTAGCGACGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGAAAAA
* *
43167616 AGCGCCGCTAAAGGTCGTGGTCTTTAGAGGCGTTTGCTAAAGGTCGTGGT
66 AGCGCCGCTAAAGGTCCTGATCTTTAGAGGCGTTTGCTAAAGGTCGTGGT
* *
43167666 CTTTAGCGACGTTTGCGAAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAAAAA
1 CTTTAGCGACGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGAAAAA
43167731 AGCGCCGCTAAAGGTCCTGATCTTTAGAGGCGTTTGC
66 AGCGCCGCTAAAGGTCCTGATCTTTAGAGGCGTTTGC
43167768 GAAAAAAGCG
Statistics
Matches: 93, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
115 93 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.28
Consensus pattern (115 bp):
CTTTAGCGACGTTTGCGAAAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGAAAAA
AGCGCCGCTAAAGGTCCTGATCTTTAGAGGCGTTTGCTAAAGGTCGTGGT
Found at i:43168809 original size:20 final size:20
Alignment explanation
Indices: 43168760--43168798 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43168750 TGTAGTGAGA
*
43168760 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
43168780 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
43168799 AGTATTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:43177470 original size:13 final size:16
Alignment explanation
Indices: 43177434--43177464 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
43177424 TTATATTACA
43177434 ATAATTAATAATAAAG
1 ATAATTAATAATAAAG
43177450 ATAATTAATAATAAA
1 ATAATTAATAATAAA
43177465 AATTAAGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAATTAATAATAAAG
Found at i:43178316 original size:35 final size:34
Alignment explanation
Indices: 43178267--43178335 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
43178257 ATATTATAAA
43178267 TTTTATAAAATTATATTATAAAAATAAT-TTATTTT
1 TTTTATAAAATTATA--ATAAAAATAATATTATTTT
* * *
43178302 TTTTGTAAATTTATAATAAAAATTATATTATTTT
1 TTTTATAAAATTATAATAAAAATAATATTATTTT
43178336 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
33 10 0.33
34 7 0.23
35 13 0.43
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (34 bp):
TTTTATAAAATTATAATAAAAATAATATTATTTT
Found at i:43185131 original size:33 final size:33
Alignment explanation
Indices: 43185085--43185147 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
43185075 TATTGCCATA
43185085 TGAATAGGCCATCTACAAATACTTCAGATAAGT
1 TGAATAGGCCATCTACAAATACTTCAGATAAGT
*
43185118 TGAATAGGTCATCTACAAATACTTCAGATA
1 TGAATAGGCCATCTACAAATACTTCAGATA
43185148 GGCAAGCCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.29
Consensus pattern (33 bp):
TGAATAGGCCATCTACAAATACTTCAGATAAGT
Found at i:43191637 original size:3 final size:3
Alignment explanation
Indices: 43191631--43191657 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
43191621 CCAATCTTCT
43191631 TCC TCC TCC TCC TCC TCC TCC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC
43191658 CCAATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (3 bp):
TCC
Found at i:43192361 original size:23 final size:24
Alignment explanation
Indices: 43192333--43192399 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
43192323 ATATTTTTTT
*
43192333 AATATTATTTAATAAA-ATTTTAA
1 AATATTATTTAATAAATATTTCAA
* *
43192356 AGTATT-TTTCATAAATATTTCAA
1 AATATTATTTAATAAATATTTCAA
* *
43192379 AAAATTATTTAAATAATTATT
1 AATATTATTT-AATAAATATT
43192400 ATTTTTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
22 8 0.24
23 15 0.44
24 3 0.09
25 8 0.24
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (24 bp):
AATATTATTTAATAAATATTTCAA
Found at i:43193920 original size:23 final size:24
Alignment explanation
Indices: 43193894--43193942 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
43193884 AAACAAAAAG
*
43193894 AATAAAAACATTTTAAA-TTTTAA
1 AATAAAAACATTTAAAATTTTTAA
**
43193917 AATAAAATTATTTAAAATTTTTAA
1 AATAAAAACATTTAAAATTTTTAA
43193941 AA
1 AA
43193943 AATTATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
AATAAAAACATTTAAAATTTTTAA
Found at i:43194446 original size:33 final size:35
Alignment explanation
Indices: 43194398--43194473 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
43194388 GTATTTCACC
* * *
43194398 AAAAAAATTTAATTTT-GAAAGTTTTATATTTTTT
1 AAAAAAAGTTAATTTTCGAAACTTTTAGATTTTTT
** *
43194432 AAAAAAAGTT-ATTTTCTTAACTTTTGGATTTTTT
1 AAAAAAAGTTAATTTTCGAAACTTTTAGATTTTTT
43194466 AAAAAAAG
1 AAAAAAAG
43194474 AATTTACAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 5 0.14
34 30 0.86
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (35 bp):
AAAAAAAGTTAATTTTCGAAACTTTTAGATTTTTT
Found at i:43197009 original size:87 final size:87
Alignment explanation
Indices: 43196891--43197108 Score: 188
Period size: 87 Copynumber: 2.4 Consensus size: 87
43196881 CATCCTTTAA
* * ** * * * * *
43196891 TTAATTTCAACCCCACATTGGCTAAATAACACTCTTATGCTTACATTTACCCTGTAAATAAGTG-
1 TTAATTTTAATCCCACATTGATTAGAGAACACTCTTAT-CTCACATTTACCCTATAAATAAATGA
*
43196955 TCAATTTCTTCACTATTTTC-AAG
65 T-AAATTCTTCACTATTTTCAAAG
* ** * * *
43196978 TTAATTTTAATCGCATGTTGATTAGAGAACACCCCATATCTCACATTTACCTTATAAATAAATGA
1 TTAATTTTAATCCCACATTGATTAGAGAACA-CTCTTATCTCACATTTACCCTATAAATAAATGA
*
43197043 TAAATTCTTTACTATTTTCATTAAAAAG
65 TAAATTCTTCACTATTTTC-----AAAG
*
43197071 TTAATTTTAATCCCACATTTATTAGAGAACACTCTTAT
1 TTAATTTTAATCCCACATTGATTAGAGAACACTCTTAT
43197109 AGTTCACTTC
Statistics
Matches: 100, Mismatches: 23, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
87 59 0.59
88 6 0.06
92 5 0.05
93 30 0.30
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (87 bp):
TTAATTTTAATCCCACATTGATTAGAGAACACTCTTATCTCACATTTACCCTATAAATAAATGAT
AAATTCTTCACTATTTTCAAAG
Found at i:43197135 original size:66 final size:66
Alignment explanation
Indices: 43197057--43197183 Score: 182
Period size: 66 Copynumber: 1.9 Consensus size: 66
43197047 TTCTTTACTA
* * * *
43197057 TTTTCATTAAAAAGTTAATTTTAATCCCACATTTATTAGAGAACACTCTTATAGTTCACTTCTTT
1 TTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAAAACACTCTTATAGCTCACTTCTTT
43197122 G
66 G
* * * *
43197123 TTTTTATTAAAAAGTTAATTTTAATTCCATATTAACTAGAAAATACTCTTATAGCTCACTT
1 TTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAAAACACTCTTATAGCTCACTT
43197184 ATTTCATTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (66 bp):
TTTTCATTAAAAAGTTAATTTTAATCCCACATTAACTAGAAAACACTCTTATAGCTCACTTCTTT
G
Found at i:43198442 original size:26 final size:26
Alignment explanation
Indices: 43198406--43198455 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
43198396 TTATTTAACA
43198406 AACACATTAAACACAT-TAAACACACT
1 AACACATTAAACACATGT-AACACACT
43198432 AACACATTAAACACATGTAACACA
1 AACACATTAAACACATGTAACACA
43198456 TGTAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.54, C:0.26, G:0.02, T:0.18
Consensus pattern (26 bp):
AACACATTAAACACATGTAACACACT
Found at i:43198460 original size:9 final size:9
Alignment explanation
Indices: 43198405--43198456 Score: 72
Period size: 9 Copynumber: 5.9 Consensus size: 9
43198395 TTTATTTAAC
43198405 AAACACATT
1 AAACACATT
43198414 AAACACATT
1 AAACACATT
*
43198423 AAACACACT
1 AAACACATT
43198432 -AACACATT
1 AAACACATT
43198440 AAACACATGT
1 AAACACAT-T
43198450 -AACACAT
1 AAACACAT
43198457 GTAATAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 7 0.18
9 31 0.79
10 1 0.03
ACGTcount: A:0.54, C:0.25, G:0.02, T:0.19
Consensus pattern (9 bp):
AAACACATT
Found at i:43207344 original size:44 final size:45
Alignment explanation
Indices: 43207279--43207406 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 45
43207269 CGTGCTTTCA
* *
43207279 CATGATGCCATAACATCTTTCAGTTATGGTCTTACTTAT-TTTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
* * * * *
43207323 CTTGATGCCATAGCATCTTTCAACTGTGGCCTTACTCATCTTTAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
43207368 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCAT
1 CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCAT
43207407 ATTGACATAT
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
44 32 0.45
45 39 0.55
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (45 bp):
CATGATGCCATAACATCTTTCAGCTATGGTCTTACTCATCTTTAT
Found at i:43217850 original size:55 final size:56
Alignment explanation
Indices: 43217780--43217885 Score: 126
Period size: 55 Copynumber: 1.9 Consensus size: 56
43217770 TTATAATTAT
** * *
43217780 TTTTAAACATGTTAT-ATGATTTTAAAATTTTG-AAACATTATAAAGTTTTAATAAA
1 TTTTAAACAAATTATAATG-TTCTAAAATTTTGAAAACATTATAAAATTTTAATAAA
* *
43217835 TTTTAAACAAATTATAATGTTCTAAATTTTTGATAAAGATTATAAAATTTT
1 TTTTAAACAAATTATAATGTTCTAAAATTTTGA-AAACATTATAAAATTTT
43217886 TTAAATAGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
55 24 0.57
56 3 0.07
57 15 0.36
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.46
Consensus pattern (56 bp):
TTTTAAACAAATTATAATGTTCTAAAATTTTGAAAACATTATAAAATTTTAATAAA
Found at i:43220867 original size:20 final size:20
Alignment explanation
Indices: 43220842--43220890 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
43220832 TTTGTATAGT
*
43220842 TGTTCTGTTATGAAGTTAAA
1 TGTTCTGTTATAAAGTTAAA
*
43220862 TGTTCTGTTGTAAAGTTAAA
1 TGTTCTGTTATAAAGTTAAA
43220882 TGTTCTGTT
1 TGTTCTGTT
43220891 TTGCTCGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.49
Consensus pattern (20 bp):
TGTTCTGTTATAAAGTTAAA
Found at i:43224050 original size:5 final size:5
Alignment explanation
Indices: 43224040--43224064 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
43224030 TTAGTTAATA
43224040 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
43224065 TTTAAGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:43224942 original size:26 final size:26
Alignment explanation
Indices: 43224906--43224969 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
43224896 CTTGAATAGT
*
43224906 AGGCCTTGAGTTGGTGTTTATTTAGC
1 AGGCCTTGAGTCGGTGTTTATTTAGC
43224932 AGGCCTTGAGTCGGTGTTTATTTAGC
1 AGGCCTTGAGTCGGTGTTTATTTAGC
**
43224958 AGGATTTGAGTC
1 AGGCCTTGAGTC
43224970 TGTGAATATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.17, C:0.12, G:0.31, T:0.39
Consensus pattern (26 bp):
AGGCCTTGAGTCGGTGTTTATTTAGC
Found at i:43224979 original size:26 final size:26
Alignment explanation
Indices: 43224910--43224981 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 26
43224900 AATAGTAGGC
* ** *
43224910 CTTGAGTTGGTGTTTATTTAGCAGGC
1 CTTGAGTCGGTGAATATTTAGCAGGA
**
43224936 CTTGAGTCGGTGTTTATTTAGCAGGA
1 CTTGAGTCGGTGAATATTTAGCAGGA
* *
43224962 TTTGAGTCTGTGAATATTTA
1 CTTGAGTCGGTGAATATTTA
43224982 ACAAGTACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (26 bp):
CTTGAGTCGGTGAATATTTAGCAGGA
Found at i:43240028 original size:30 final size:30
Alignment explanation
Indices: 43239994--43240053 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
43239984 ACTTAACAAG
43239994 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
* *
43240024 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
43240054 TAATAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:43240754 original size:33 final size:32
Alignment explanation
Indices: 43240715--43240782 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 32
43240705 TACTCCTACA
*
43240715 AAGTCTAAATTAAAATCATCCAATAATTAATAC
1 AAGTCTAAATTAAAATCATCCAATAA-AAATAC
43240748 AAGTCTAAATTAAAATCATCCAATAAAAATAC
1 AAGTCTAAATTAAAATCATCCAATAAAAATAC
43240780 AAG
1 AAG
43240783 CCTCTTCTCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 8 0.24
33 26 0.76
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (32 bp):
AAGTCTAAATTAAAATCATCCAATAAAAATAC
Found at i:43242225 original size:23 final size:23
Alignment explanation
Indices: 43242198--43242274 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 23
43242188 GATAGTTTTA
43242198 TGATTGAAATTTGAGTAAAATAT
1 TGATTGAAATTTGAGTAAAATAT
* * * ** *
43242221 TGATTTAAATTAGAGGGATAGTTTT
1 TGATTGAAATTTGA-GTA-AAATAT
*
43242246 ATGATTGAAATTTGAGTAAAATAG
1 -TGATTGAAATTTGAGTAAAATAT
43242270 TGATT
1 TGATT
43242275 ATGTCGTTGG
Statistics
Matches: 38, Mismatches: 13, Indels: 6
0.67 0.23 0.11
Matches are distributed among these distances:
23 17 0.45
24 4 0.11
25 5 0.13
26 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.21, T:0.40
Consensus pattern (23 bp):
TGATTGAAATTTGAGTAAAATAT
Found at i:43242233 original size:49 final size:49
Alignment explanation
Indices: 43242176--43242274 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
43242166 TGAAGTTAGA
*
43242176 TTAAATTAGAGCGATAGTTTTATGATTGAAATTTGAGTAAAATATTGAT
1 TTAAATTAGAGCGATAGTTTTATGATTGAAATTTGAGTAAAATAGTGAT
*
43242225 TTAAATTAGAGGGATAGTTTTATGATTGAAATTTGAGTAAAATAGTGAT
1 TTAAATTAGAGCGATAGTTTTATGATTGAAATTTGAGTAAAATAGTGAT
43242274 T
1 T
43242275 ATGTCGTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.38, C:0.01, G:0.20, T:0.40
Consensus pattern (49 bp):
TTAAATTAGAGCGATAGTTTTATGATTGAAATTTGAGTAAAATAGTGAT
Done.