Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 60 of 311
Found at i:17702004 original size:25 final size:25
Alignment explanation
Indices: 17701976--17702024 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
17701966 TTAAAATATG
* * *
17701976 AAAAATGACTGTTTTGCCCCTAGGT
1 AAAAATGACTATTATACCCCTAGGT
17702001 AAAAATGACTATTATACCCCTAGG
1 AAAAATGACTATTATACCCCTAGG
17702025 GTTAAATTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (25 bp):
AAAAATGACTATTATACCCCTAGGT
Found at i:17702205 original size:24 final size:24
Alignment explanation
Indices: 17702173--17702219 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
17702163 TAGCTTACCA
**
17702173 AAAAGGGCTTTGCC-CCAGTTATT
1 AAAAGGGCTAGGCCTCCAGTTATT
17702196 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAG-GGCTAGGCCTCCAGTTAT
17702220 ATGGTAAAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTAGGCCTCCAGTTATT
Found at i:17708199 original size:20 final size:20
Alignment explanation
Indices: 17708174--17708212 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17708164 AGATTTTCAT
* *
17708174 AATTTTTGAGAATTTGGTAA
1 AATTTTTAAAAATTTGGTAA
17708194 AATTTTTAAAAATTTGGTA
1 AATTTTTAAAAATTTGGTA
17708213 TTTGGTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (20 bp):
AATTTTTAAAAATTTGGTAA
Found at i:17708839 original size:22 final size:22
Alignment explanation
Indices: 17708813--17708855 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17708803 AAACCAAACC
17708813 ACTACTCCCTTTCTTTTCATCT
1 ACTACTCCCTTTCTTTTCATCT
*
17708835 ACTACTTCCTTTCTTTTCATC
1 ACTACTCCCTTTCTTTTCATC
17708856 ACCCTTACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.35, G:0.00, T:0.51
Consensus pattern (22 bp):
ACTACTCCCTTTCTTTTCATCT
Found at i:17709882 original size:352 final size:352
Alignment explanation
Indices: 17709238--17710645 Score: 2559
Period size: 352 Copynumber: 4.0 Consensus size: 352
17709228 ACTATGGTAG
* *
17709238 GTGGACTTTGGGTTTGATTAGCATGAACTATAAACTAAGAATGGTGGTGATTAATTGTAGGTTTT
1 GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGGTGATTAATTGTAGGTTGT
* *
17709303 CGTGGGAGACTTTGTTGGCAAACATCACAAAAAAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
66 CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
* *
17709368 TAATATTCGCTGAAAAGCCGAAATACTAAAATTCTGGCATTTTGGGAATGTGAGATTTTGCATGT
131 TAATATTCGCTGAAAAGCCGAAATACTAAAATTCCGGCATTTTGGGAACGTGAGATTTTGCATGT
17709433 GGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAAT
196 GGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAAT
17709498 TTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTAGAATTGGGCCCAATGGGCTTCCGGGCCCA
261 TTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTAGAATTGGGCCCAATGGGCTTCCGGGCCCA
17709563 TTTGGGTAAAATGGATAGAAAATGGAA
326 TTTGGGTAAAATGGATAGAAAATGGAA
*
17709590 GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACAAAGAATGGTGGTGATTAATTGTAGGTT-T
1 GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGGTGATTAATTGTAGGTTGT
*
17709654 CCGTGGGAGACTTTGTTGGCGAACATCACAAAACAGATGTGTAACAACCCTCGTAGTAGCTTAGG
66 -CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGG
* **
17709719 CTAATATTCGCTGAAAAGCCGGAATACTAAAATTCCGGCATTTCAGGAACGTGAGATTTTGCATG
130 CTAATATTCGCTGAAAAGCCGAAATACTAAAATTCCGGCATTTTGGGAACGTGAGATTTTGCATG
17709784 TGGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAA
195 TGGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAA
* * *
17709849 TTTTGAGCACGATGGTAAGTTGGGTCTCAATGGGCTAAAATTGGGCCCAATGGGCTTCCGGGCCC
260 TTTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTAGAATTGGGCCCAATGGGCTTCCGGGCCC
*
17709914 ATTTGGATAAAATGGATAGAAAATGGAA
325 ATTTGGGTAAAATGGATAGAAAATGGAA
17709942 GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGGTGATTAATTGTAGGTTGT
1 GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGGTGATTAATTGTAGGTTGT
17710007 CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
66 CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
* * * *
17710072 TAATATTCGTTGAAAAGCCAAAATACTAAAATTCTGGCATTTTGGGAAAGTGAGATTTTGCATGT
131 TAATATTCGCTGAAAAGCCGAAATACTAAAATTCCGGCATTTTGGGAACGTGAGATTTTGCATGT
*
17710137 GGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAAAGCACAAT
196 GGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAAT
*
17710202 TTTGTGCACGATGGTAAGTTGGGCCTCAACGGGCT-GAAATTGGGCCCAATGGGCTTCCGGGCCC
261 TTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTAG-AATTGGGCCCAATGGGCTTCCGGGCCC
17710266 ATTTGGGTAAAATGGATAGAAAATGGAA
325 ATTTGGGTAAAATGGATAGAAAATGGAA
* *
17710294 GTGGGCTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGATGATTAATTGTAGGTTGT
1 GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGGTGATTAATTGTAGGTTGT
17710359 CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
66 CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
17710424 TAATATTCGCTGAAAAGCCGAAATACTAAAATTCCGGCATTTTGGGAACGTGAGATTTTGCATGT
131 TAATATTCGCTGAAAAGCCGAAATACTAAAATTCCGGCATTTTGGGAACGTGAGATTTTGCATGT
*
17710489 GGTTTTAGATGTGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAAT
196 GGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAAT
*
17710554 TTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTGGAATTGGGCCCAATGGGCTTCCGGGCCCA
261 TTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTAGAATTGGGCCCAATGGGCTTCCGGGCCCA
17710619 TTTGGGTAAAATGGATAGAAAATGGAA
326 TTTGGGTAAAATGGATAGAAAATGGAA
17710646 CTTGGAAAAG
Statistics
Matches: 1014, Mismatches: 38, Indels: 8
0.96 0.04 0.01
Matches are distributed among these distances:
351 1 0.00
352 1011 1.00
353 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (352 bp):
GTGGACTTTGGGTTTGATTAGCATGAACTGTAAACTAAGAATGGTGGTGATTAATTGTAGGTTGT
CGTGGGAGACTTTGTTGGCGAACATCACAAAACAGGTGTGTAACAACCCTCGTAGTAGCTTAGGC
TAATATTCGCTGAAAAGCCGAAATACTAAAATTCCGGCATTTTGGGAACGTGAGATTTTGCATGT
GGTTTTAGATGCGATAAGTACGATATGATCGGTGTTTGGATCGATGAAACAGGTAAGAGCACAAT
TTTGTGCACGATGGTAAGTTGGGCCTCAATGGGCTAGAATTGGGCCCAATGGGCTTCCGGGCCCA
TTTGGGTAAAATGGATAGAAAATGGAA
Found at i:17710979 original size:10 final size:10
Alignment explanation
Indices: 17710958--17710991 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
17710948 CATGAGATTT
17710958 TGATAT-ACA
1 TGATATGACA
17710967 TGATATGACA
1 TGATATGACA
17710977 TGATATGCACA
1 TGATATG-ACA
17710988 TGAT
1 TGAT
17710992 TTGTTATGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 6 0.26
10 10 0.43
11 7 0.30
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (10 bp):
TGATATGACA
Found at i:17710990 original size:21 final size:21
Alignment explanation
Indices: 17710964--17711014 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
17710954 ATTTTGATAT
*
17710964 ACATGATATGACATGATATGC
1 ACATGATATGACATGAGATGC
* **
17710985 ACATGATTTGTTATGAGATGC
1 ACATGATATGACATGAGATGC
*
17711006 ACACGATAT
1 ACATGATAT
17711015 ACTCATTATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (21 bp):
ACATGATATGACATGAGATGC
Found at i:17711119 original size:24 final size:24
Alignment explanation
Indices: 17711063--17711133 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
17711053 GGAAGTGGGG
*
17711063 AAAG-GGCTTTGCCCCAGTTTACCA
1 AAAGAGGCTTTGCCCCAG-TTATCA
*
17711087 AAA-AGGGCTTTGCCCCAGTTATTA
1 AAAGA-GGCTTTGCCCCAGTTATCA
**
17711111 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAGAGGCTTTGCC-CCAGTTAT
17711134 ATGATAAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
24 17 0.44
25 22 0.56
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (24 bp):
AAAGAGGCTTTGCCCCAGTTATCA
Found at i:17712030 original size:51 final size:51
Alignment explanation
Indices: 17711975--17712077 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 51
17711965 AAACTTCAAT
* *
17711975 GTGACACGTCGGA-TCCAGCCATAACGTCTGGGCC-AGGTTTGGGGTGTTACA
1 GTGACACGTCAGATTCCAGCC-TAACGTCTAGGCCGA-GTTTGGGGTGTTACA
* *
17712026 GTGACACGTCAGATTCGAGCCTAACTTCTAGGCCGAGTTTGGGGTGTTACA
1 GTGACACGTCAGATTCCAGCCTAACGTCTAGGCCGAGTTTGGGGTGTTACA
17712077 G
1 G
17712078 CTTGTACAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
51 39 0.85
52 7 0.15
ACGTcount: A:0.20, C:0.22, G:0.32, T:0.25
Consensus pattern (51 bp):
GTGACACGTCAGATTCCAGCCTAACGTCTAGGCCGAGTTTGGGGTGTTACA
Found at i:17712151 original size:43 final size:42
Alignment explanation
Indices: 17712086--17712203 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
17712076 AGCTTGTACA
* *
17712086 ATGCCAAC-GTCCCAGACGGGGTCTTACATGTAATCAAATATCG
1 ATGCC-ACTGTCCCAGACAGGGTCTTACACGTAATCAAATAT-G
* * *
17712129 ATGCCACTGTCCCAAACAGGGTCTTACACGAAATCATATATG
1 ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAATATG
* * *
17712171 ATGCCAATGTCCCAGACATGGTTTTACACGTAA
1 ATGCCACTGTCCCAGACAGGGTCTTACACGTAA
17712204 ATCTCAAATC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
42 31 0.48
43 33 0.52
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACGTAATCAAATATG
Found at i:17717759 original size:18 final size:17
Alignment explanation
Indices: 17717738--17717779 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
17717728 AACATTAGGT
17717738 AACTATATAACATAACC
1 AACTATATAACATAACC
*
17717755 AAACTATATAATATAACC
1 -AACTATATAACATAACC
17717773 AACTATA
1 AACTATA
17717780 CTTTTAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (17 bp):
AACTATATAACATAACC
Found at i:17719198 original size:43 final size:44
Alignment explanation
Indices: 17719137--17719309 Score: 151
Period size: 43 Copynumber: 4.0 Consensus size: 44
17719127 AAAGCTCATA
* * * *
17719137 CAATGCCAA-TGTCTCAGACGTGGTCTTACATGTAATCAAATAT
1 CAATGCCAACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
* * *
17719180 CAATGCC-ACTATCCCAGACACGGTCTTACACGAAATCATATA-
1 CAATGCCAACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
* * * * *
17719222 CGATGCCGA-TGTTCCAGACATGGTCTTACATGTAAATCTCAA-AT
1 CAATGCCAACTGTCCCAGACATGGTCTTACACG-AAATC-AAATAT
* * *
17719266 CAATGCCAAC-GTCTCAGACGTGGTCTTACACGAAATCACATAT
1 CAATGCCAACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
17719309 C
1 C
17719310 GGAATCCTAT
Statistics
Matches: 101, Mismatches: 22, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
42 27 0.27
43 48 0.48
44 26 0.26
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (44 bp):
CAATGCCAACTGTCCCAGACATGGTCTTACACGAAATCAAATAT
Found at i:17719296 original size:86 final size:85
Alignment explanation
Indices: 17719134--17719303 Score: 211
Period size: 86 Copynumber: 2.0 Consensus size: 85
17719124 CAGAAAGCTC
*
17719134 ATACAATGCCAATGTCTCAGACGTGGTCTTACATGTAATCAAATATCAATGCCACTATCCCAGAC
1 ATACAATGCCAATGTCTCAGACATGGTCTTACATGTAATCAAATATCAATGCCACTATCCCAGAC
17719199 ACGGTCTTACACGAAATCAT
66 ACGGTCTTACACGAAATCAT
* * * * *
17719219 ATACGATGCCGATGT-TCCAGACATGGTCTTACATGTAAATCTCAA-ATCAATGCCAAC-GTCTC
1 ATACAATGCCAATGTCT-CAGACATGGTCTTACATGT-AATC-AAATATCAATGCC-ACTATCCC
**
17719281 AGACGTGGTCTTACACGAAATCA
62 AGACACGGTCTTACACGAAATCA
17719304 CATATCGGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
84 1 0.01
85 31 0.42
86 37 0.51
87 4 0.05
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (85 bp):
ATACAATGCCAATGTCTCAGACATGGTCTTACATGTAATCAAATATCAATGCCACTATCCCAGAC
ACGGTCTTACACGAAATCAT
Found at i:17721925 original size:23 final size:23
Alignment explanation
Indices: 17721889--17722114 Score: 156
Period size: 23 Copynumber: 9.9 Consensus size: 23
17721879 GGACTCACCA
*
17721889 TAGCTCGTATGAGCTTACTGATT
1 TAGCTCGTAAGAGCTTACTGATT
*
17721912 TAGCTCGCAAGAGCTTACT-ATT
1 TAGCTCGTAAGAGCTTACTGATT
* * *
17721934 TCAGATCATTAGAGCTTACTGATT
1 T-AGCTCGTAAGAGCTTACTGATT
* *
17721958 CAGCTCGTAAGAGCTTACTGTTT
1 TAGCTCGTAAGAGCTTACTGATT
* * *
17721981 TAGTTCATTAGAGCTTACTGATT
1 TAGCTCGTAAGAGCTTACTGATT
*
17722004 TAGCTCGCAAGAGCTTACTG-TT
1 TAGCTCGTAAGAGCTTACTGATT
* ** **
17722026 TCAACTTATTGGAGCTTACTGATT
1 T-AGCTCGTAAGAGCTTACTGATT
* *
17722050 CATCTCG-ATAGAGCTTACTG-TT
1 TAGCTCGTA-AGAGCTTACTGATT
* * * * *
17722072 CAACTC-AATAGAGCTTACCGTTT
1 TAGCTCGTA-AGAGCTTACTGATT
* *
17722095 TAGCTCATTAGAGCTTACTG
1 TAGCTCGTAAGAGCTTACTG
17722115 TCCATCAATT
Statistics
Matches: 156, Mismatches: 39, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
22 26 0.17
23 125 0.80
24 5 0.03
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (23 bp):
TAGCTCGTAAGAGCTTACTGATT
Found at i:17721970 original size:46 final size:46
Alignment explanation
Indices: 17721899--17722115 Score: 251
Period size: 46 Copynumber: 4.7 Consensus size: 46
17721889 TAGCTCGTAT
*
17721899 GAGCTTACTGATTTAGCTCGCAAGAGCTTACTATTTCAGA-TCATTA
1 GAGCTTACTGATTTAGCTCGCAAGAGCTTACTGTTTCA-ACTCATTA
* * * **
17721945 GAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTTTAGTTCATTA
1 GAGCTTACTGATTTAGCTCGCAAGAGCTTACTGTTTCAACTCATTA
* *
17721991 GAGCTTACTGATTTAGCTCGCAAGAGCTTACTGTTTCAACTTATTG
1 GAGCTTACTGATTTAGCTCGCAAGAGCTTACTGTTTCAACTCATTA
* * *
17722037 GAGCTTACTGATTCATCTCG-ATAGAGCTTACTG-TTCAACTCAATA
1 GAGCTTACTGATTTAGCTCGCA-AGAGCTTACTGTTTCAACTCATTA
* * ***
17722082 GAGCTTACCGTTTTAGCTCATTAGAGCTTACTGT
1 GAGCTTACTGATTTAGCTCGCAAGAGCTTACTGT
17722116 CCATCAATTC
Statistics
Matches: 144, Mismatches: 23, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
45 36 0.25
46 108 0.75
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (46 bp):
GAGCTTACTGATTTAGCTCGCAAGAGCTTACTGTTTCAACTCATTA
Found at i:17723126 original size:40 final size:40
Alignment explanation
Indices: 17723082--17723161 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
17723072 ATAATTAACA
*
17723082 TAATACTATAACCTAACATAATAATTCACAATAAATGGGT
1 TAATACTATAACCTAACATAATAATTCACAAGAAATGGGT
*
17723122 TAATACTATACCCTAACATAATAATTCACAAGAAATGGGT
1 TAATACTATAACCTAACATAATAATTCACAAGAAATGGGT
17723162 GAGTTTGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.46, C:0.16, G:0.09, T:0.29
Consensus pattern (40 bp):
TAATACTATAACCTAACATAATAATTCACAAGAAATGGGT
Found at i:17723362 original size:21 final size:20
Alignment explanation
Indices: 17723338--17723405 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
17723328 ACATCAGGGA
*
17723338 GCACCATAGTGCAGAACAAGG
1 GCACCAAAGTGCA-AACAAGG
* *
17723359 GCA-CAGAAGTGCATACAGGG
1 GCACCA-AAGTGCAAACAAGG
* *
17723379 GCACCACAGTGCAAGCAAGG
1 GCACCAAAGTGCAAACAAGG
17723399 GCACCAA
1 GCACCAA
17723406 TGTGTAAGTC
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
20 26 0.70
21 11 0.30
ACGTcount: A:0.37, C:0.26, G:0.29, T:0.07
Consensus pattern (20 bp):
GCACCAAAGTGCAAACAAGG
Found at i:17726283 original size:54 final size:53
Alignment explanation
Indices: 17726186--17726300 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 53
17726176 CAAGTCAGGT
*
17726186 AGTTACACGGCCTAGCACACGACCTGCCACACAGGGGTGTGAGGCCATTTCGAG
1 AGTTACACGGCCTAGCACACGACCTG-CACACAGGGGTCTGAGGCCATTTCGAG
* *
17726240 AGTTACACGGCCTAGTACACGGCCTG-ACACATGGGTGTCTGAGGCCATTTCGAG
1 AGTTACACGGCCTAGCACACGACCTGCACACA-GGG-GTCTGAGGCCATTTCGAG
17726294 AGTTACA
1 AGTTACA
17726301 TAGCCTGACA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
52 5 0.09
53 3 0.05
54 48 0.86
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (53 bp):
AGTTACACGGCCTAGCACACGACCTGCACACAGGGGTCTGAGGCCATTTCGAG
Found at i:17729164 original size:39 final size:39
Alignment explanation
Indices: 17729121--17729198 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
17729111 CCAAACTTAG
17729121 TTTGCTATATATACCGAAGAGTCCGAGGGATAGTGTGAT
1 TTTGCTATATATACCGAAGAGTCCGAGGGATAGTGTGAT
17729160 TTTGCTATATATACCGAAGAGTCCGAGGGATAGTGTGAT
1 TTTGCTATATATACCGAAGAGTCCGAGGGATAGTGTGAT
17729199 GTAGCTCTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (39 bp):
TTTGCTATATATACCGAAGAGTCCGAGGGATAGTGTGAT
Found at i:17729775 original size:24 final size:25
Alignment explanation
Indices: 17729710--17729775 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
17729700 GCTATATAAC
*
17729710 GGGAAGCTCATGTGAGCCATGTAAT
1 GGGAAGCTCATATGAGCCATGTAAT
* *
17729735 GGGAAGCAC-TAGAGAGCCAT-TAAT
1 GGGAAGCTCATA-TGAGCCATGTAAT
*
17729759 TGGAAGCTCATATGAGC
1 GGGAAGCTCATATGAGC
17729776 TAATATAGGA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 16 0.48
25 17 0.52
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (25 bp):
GGGAAGCTCATATGAGCCATGTAAT
Found at i:17741900 original size:43 final size:42
Alignment explanation
Indices: 17741852--17741989 Score: 115
Period size: 43 Copynumber: 3.2 Consensus size: 42
17741842 GTTCCGGACG
*
17741852 TGGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAGACA
1 TGGTCTTACA-GTAATTCAATATCGATGCCTATGTCCCAGACA
** *
17741895 TGGTCTTACACAAAATCAGATA-CGATG-CTGATGTCCCAGACA
1 TGGTCTTACAGTAATTCA-ATATCGATGCCT-ATGTCCCAGACA
* * *
17741937 TGG-CTTTATACGTAAATCTCAAT-T-GAGGCCTGTGTCCCAGACA
1 TGGTC-TTACA-GT-AAT-TCAATATCGATGCCTATGTCCCAGACA
17741980 TGGTCTTACA
1 TGGTCTTACA
17741990 CAATGTCTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
41 3 0.04
42 28 0.37
43 34 0.45
44 7 0.09
45 3 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
TGGTCTTACAGTAATTCAATATCGATGCCTATGTCCCAGACA
Found at i:17752320 original size:13 final size:13
Alignment explanation
Indices: 17752302--17752327 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17752292 GCTCGACAGG
17752302 GACACGCCCGTGT
1 GACACGCCCGTGT
17752315 GACACGCCCGTGT
1 GACACGCCCGTGT
17752328 TTGATTACTT
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:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:17752746 original size:20 final size:20
Alignment explanation
Indices: 17752721--17752760 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
17752711 ATGACATTTT
17752721 TCACCAAACAGATAGTGACG
1 TCACCAAACAGATAGTGACG
17752741 TCACCAAACAGATAGTGACG
1 TCACCAAACAGATAGTGACG
17752761 CCAAATCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.20, T:0.15
Consensus pattern (20 bp):
TCACCAAACAGATAGTGACG
Found at i:17765711 original size:42 final size:42
Alignment explanation
Indices: 17765598--17765770 Score: 197
Period size: 43 Copynumber: 4.0 Consensus size: 42
17765588 AGAAAGGTTG
* * *
17765598 TACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
* *
17765640 TATCAATACC-ACTGTCCCAGACAGGGTCTTACACGAAATCAAA
1 TA-CAATGCCAAC-GTCCCAGACATGGTCTTACACGAAATCAAA
*
17765683 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACG-AAA--TCAAA
* ** *
17765728 TA-GATGCCAACGTCCCAGATGTGGTCTTACACAAAATCAAA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
17765769 TA
1 TA
17765771 TCGAAAATCC
Statistics
Matches: 112, Mismatches: 13, Indels: 13
0.81 0.09 0.09
Matches are distributed among these distances:
41 7 0.06
42 31 0.28
43 41 0.37
44 26 0.23
45 7 0.06
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (42 bp):
TACAATGCCAACGTCCCAGACATGGTCTTACACGAAATCAAA
Found at i:17770707 original size:43 final size:43
Alignment explanation
Indices: 17770659--17770781 Score: 138
Period size: 43 Copynumber: 2.9 Consensus size: 43
17770649 ATTGAGATGT
* * * *
17770659 GATTACATGTAAAACCATGTCTGGGACGTTGGCATTGTCTTGA
1 GATTACGTGTAAAACCATGTCTGGGACATTGGCATCGTATTGA
* * *
17770702 GATTACGTGTAAGACCATGTCTAGGACATTGGCATCGTATTGT
1 GATTACGTGTAAAACCATGTCTGGGACATTGGCATCGTATTGA
* * * * *
17770745 GATTTCGTGTAAAACCCTGTTTGGGATAGTGGCATCG
1 GATTACGTGTAAAACCATGTCTGGGACATTGGCATCG
17770782 ATATGTATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
43 66 1.00
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
GATTACGTGTAAAACCATGTCTGGGACATTGGCATCGTATTGA
Found at i:17773903 original size:13 final size:13
Alignment explanation
Indices: 17773885--17773909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17773875 ACAAACGATA
17773885 AAATTTTCACACG
1 AAATTTTCACACG
17773898 AAATTTTCACAC
1 AAATTTTCACAC
17773910 ATATCACATA
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:17779926 original size:43 final size:44
Alignment explanation
Indices: 17779795--17779932 Score: 158
Period size: 43 Copynumber: 3.2 Consensus size: 44
17779785 TGATTACATT
* * * * *
17779795 TAAGACTATGTTTGGGACATTGGCATTGTATTGAGA-TTACGTG
1 TAAGACCATGTCTGGGACAATGGCATCGTATTGTGATTTACGTG
*
17779838 TAAGACCATGTCTGGGACATTGGCATCGTATTGTGATTT-CGTG
1 TAAGACCATGTCTGGGACAATGGCATCGTATTGTGATTTACGTG
* *
17779881 TAAGACCCTGTCTGGGACAATGGCATCG-ATATGT-ATTTACATG
1 TAAGACCATGTCTGGGACAATGGCATCGTAT-TGTGATTTACGTG
*
17779924 TAAAACCAT
1 TAAGACCAT
17779933 ACCTATGATA
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
42 6 0.07
43 75 0.90
44 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (44 bp):
TAAGACCATGTCTGGGACAATGGCATCGTATTGTGATTTACGTG
Found at i:17783268 original size:25 final size:25
Alignment explanation
Indices: 17783216--17783276 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
17783206 AGATGCTCCG
* *
17783216 AAGAGCTAT-TAATGGGAAGGTCGC
1 AAGAGCTATATAATGGGAAGCTCAC
* *
17783240 AAGAACTATATAATGGGAAGCTCAT
1 AAGAGCTATATAATGGGAAGCTCAC
17783265 AAGAGCTA-ATAA
1 AAGAGCTATATAA
17783277 CGAGATGCTC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 12 0.39
25 19 0.61
ACGTcount: A:0.43, C:0.11, G:0.25, T:0.21
Consensus pattern (25 bp):
AAGAGCTATATAATGGGAAGCTCAC
Found at i:17788606 original size:22 final size:22
Alignment explanation
Indices: 17788578--17788651 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
17788568 CACCAAGTCA
*
17788578 ACAGGACGGCTCAATTCCGTAG
1 ACAGGACGGCTCAATGCCGTAG
*
17788600 ACAGGACGGCTCAACGCCGTAG
1 ACAGGACGGCTCAATGCCGTAG
**
17788622 ACAGGACAACTCAATGCCGTAG
1 ACAGGACGGCTCAATGCCGTAG
*
17788644 ACATGACG
1 ACAGGACG
17788652 ACTAAAGGCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.31, C:0.28, G:0.27, T:0.14
Consensus pattern (22 bp):
ACAGGACGGCTCAATGCCGTAG
Found at i:17788662 original size:22 final size:22
Alignment explanation
Indices: 17788578--17788664 Score: 93
Period size: 22 Copynumber: 4.0 Consensus size: 22
17788568 CACCAAGTCA
* **
17788578 ACAGGACGGCTCAATTCCGTAG
1 ACAGGACGACTCAACGCCGTAG
*
17788600 ACAGGACGGCTCAACGCCGTAG
1 ACAGGACGACTCAACGCCGTAG
* *
17788622 ACAGGACAACTCAATGCCGTAG
1 ACAGGACGACTCAACGCCGTAG
* * *
17788644 ACATGACGACTAAAGGCCGTA
1 ACAGGACGACTCAACGCCGTA
17788665 AATATCGCAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 56 1.00
ACGTcount: A:0.32, C:0.28, G:0.26, T:0.14
Consensus pattern (22 bp):
ACAGGACGACTCAACGCCGTAG
Found at i:17788663 original size:44 final size:44
Alignment explanation
Indices: 17788578--17788664 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
17788568 CACCAAGTCA
** * * *
17788578 ACAGGACGGCTCAATTCCGTAGACAGGACGGCTCAACGCCGTAG
1 ACAGGACAACTCAATGCCGTAGACAGGACGACTAAACGCCGTAG
* *
17788622 ACAGGACAACTCAATGCCGTAGACATGACGACTAAAGGCCGTA
1 ACAGGACAACTCAATGCCGTAGACAGGACGACTAAACGCCGTA
17788665 AATATCGCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.32, C:0.28, G:0.26, T:0.14
Consensus pattern (44 bp):
ACAGGACAACTCAATGCCGTAGACAGGACGACTAAACGCCGTAG
Found at i:17800882 original size:79 final size:77
Alignment explanation
Indices: 17800799--17801098 Score: 244
Period size: 79 Copynumber: 3.8 Consensus size: 77
17800789 AAGAAATGAA
*
17800799 AAAAATTGAAATGAAATGAAATAAAAAAA-GAAGTGAAACTAAAAATTGAAATGAAATAAATTCA
1 AAAAATTGAAATGAAATGAAATAAAAAAATGAAATGAAACTAAAAATTGAAATGAAATAAA-T-A
17800863 AAAGGAAATTAAATG
64 AAAGGAAA-TAAATG
* *
17800878 AAAAATTGAAATTAAATGAAATAAATTAAAAAATGAAATGAAACTAAAAATTGAAATTAAATTAA
1 AAAAATTGAAATGAAATGAAAT--A--AAAAAATGAAATGAAACTAAAAATTGAAATGAAA-TAA
* * *
17800943 ATGAAATGAAATAAATT
61 ATAAAAGGAAATAAATG
* * *
17800960 AAAAA-TGAAATGAAATGAACAAAAAATTGAAATGAAAT-AAA-TAAAAATTGAAATGAAATGAG
1 AAAAATTGAAATGAAATGAA-ATAAAA---AAATGAAATGAAACTAAAAATTGAAATGAAATAAA
*
17801022 T----TGATAATGAAATG
62 TAAAAGGA-AAT-AAATG
* * * * *
17801036 AAAATTTCAAATGAAATGAAATGAAATAAAT-TAA--AAATTAAAAATTGAAATGAAATGAAATA
1 AAAAATTGAAATGAAATGAAAT-AAAAAAATGAAATGAAACTAAAAATTGAAATGAAAT-AAATA
17801098 A
64 A
17801099 TTTAAAAGTT
Statistics
Matches: 184, Mismatches: 19, Indels: 39
0.76 0.08 0.16
Matches are distributed among these distances:
72 3 0.02
73 20 0.11
74 9 0.05
75 3 0.02
76 9 0.05
77 16 0.09
78 6 0.03
79 37 0.20
80 4 0.02
81 23 0.12
82 11 0.06
83 13 0.07
84 26 0.14
85 4 0.02
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.24
Consensus pattern (77 bp):
AAAAATTGAAATGAAATGAAATAAAAAAATGAAATGAAACTAAAAATTGAAATGAAATAAATAAA
AGGAAATAAATG
Found at i:17800890 original size:45 final size:45
Alignment explanation
Indices: 17800801--17800949 Score: 152
Period size: 45 Copynumber: 3.4 Consensus size: 45
17800791 GAAATGAAAA
* *
17800801 AAATTGAAATGAAATGAAA-TAAAAAAAGAAGTGAAACTAAAAATTG
1 AAATT-AAATGAAAT-AAATTAAAAAAGGAAATGAAACTAAAAATTG
* *
17800847 -----AAATGAAATAAATT-CAAAAGGAAATTAAA-TGAAAAATTG
1 AAATTAAATGAAATAAATTAAAAAAGGAAATGAAACT-AAAAATTG
*
17800886 AAATTAAATGAAATAAATTAAAAAATGAAATGAAACTAAAAATTG
1 AAATTAAATGAAATAAATTAAAAAAGGAAATGAAACTAAAAATTG
*
17800931 AAATTAAATTAAATGAAAT
1 AAATTAAATGAAAT-AAAT
17800950 GAAATAAATT
Statistics
Matches: 85, Mismatches: 8, Indels: 20
0.75 0.07 0.18
Matches are distributed among these distances:
38 1 0.01
39 22 0.26
40 10 0.12
44 14 0.16
45 33 0.39
46 5 0.06
ACGTcount: A:0.63, C:0.02, G:0.11, T:0.23
Consensus pattern (45 bp):
AAATTAAATGAAATAAATTAAAAAAGGAAATGAAACTAAAAATTG
Found at i:17800908 original size:27 final size:27
Alignment explanation
Indices: 17800867--17801128 Score: 143
Period size: 27 Copynumber: 9.4 Consensus size: 27
17800857 AATTCAAAAG
* *
17800867 GAAATTAAATGAAAAATTGAAATTAAAT
1 GAAA-TAAATTAAAAATTGAAATGAAAT
*
17800895 GAAATAAATTAAAAAATGAAATGAAACT
1 GAAATAAATTAAAAATTGAAATGAAA-T
*
17800923 AAAAATTGAAATT--AAATT-AAATGAAAT
1 -GAAA-T-AAATTAAAAATTGAAATGAAAT
17800950 GAAATAAATTAAAAA-TGAAATGAAAT
1 GAAATAAATTAAAAATTGAAATGAAAT
*
17800976 G--A-ACA--AAAAATTGAAATGAAAT
1 GAAATAAATTAAAAATTGAAATGAAAT
* **
17800998 -AAATAAAAATT-GAAA-TGAAATGAGTT
1 GAAAT--AAATTAAAAATTGAAATGAAAT
* *
17801024 GATAATGAAATGAAAATTTCAAATGAAATGAAAT
1 GA-AAT-AAAT-TAAA----AATTGAAATGAAAT
17801058 GAAATAAATTAAAAATTAAAAATTGAAATGAAAT
1 GAAATAAATT----A---AAAATTGAAATGAAAT
* *
17801092 GAAATAATTTAAAAGTTGAAATGAAAT
1 GAAATAAATTAAAAATTGAAATGAAAT
17801119 GAAATAAATT
1 GAAATAAATT
17801129 TATTATTTAA
Statistics
Matches: 182, Mismatches: 21, Indels: 63
0.68 0.08 0.24
Matches are distributed among these distances:
21 5 0.03
22 11 0.06
23 3 0.02
24 6 0.03
25 2 0.01
26 27 0.15
27 52 0.29
28 16 0.09
29 8 0.04
30 2 0.01
31 5 0.03
32 4 0.02
33 5 0.03
34 33 0.18
35 1 0.01
38 2 0.01
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (27 bp):
GAAATAAATTAAAAATTGAAATGAAAT
Found at i:17800938 original size:31 final size:32
Alignment explanation
Indices: 17800900--17801001 Score: 105
Period size: 26 Copynumber: 3.4 Consensus size: 32
17800890 TAAATGAAAT
17800900 AAATTAAA-AAATGAAATGAAACTAAAAATTG
1 AAATTAAATAAATGAAATGAAACTAAAAATTG
17800931 AAATTAAATTAAATGAAATGAAA-T--AAATT-
1 AAATTAAA-TAAATGAAATGAAACTAAAAATTG
*
17800960 -AA--AAATGAAATGAAATG-AACAAAAAATTG
1 AAATTAAAT-AAATGAAATGAAACTAAAAATTG
*
17800989 AAATGAAATAAAT
1 AAATTAAATAAAT
17801002 AAAAATTGAA
Statistics
Matches: 60, Mismatches: 1, Indels: 20
0.74 0.01 0.25
Matches are distributed among these distances:
25 3 0.05
26 13 0.22
28 7 0.12
30 7 0.12
31 12 0.20
32 5 0.08
33 13 0.22
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.24
Consensus pattern (32 bp):
AAATTAAATAAATGAAATGAAACTAAAAATTG
Found at i:17800965 original size:21 final size:22
Alignment explanation
Indices: 17800838--17800926 Score: 67
Period size: 22 Copynumber: 4.0 Consensus size: 22
17800828 GAAGTGAAAC
17800838 TAAAAATTGAAATGAAAT-AAAT
1 TAAAAA-TGAAATGAAATAAAAT
* * *
17800860 TCAAAAGGAAATTAAATGAAAAAT
1 TAAAAATGAAATGAAAT--AAAAT
* *
17800884 T-GAAATTAAATGAAAT-AAAT
1 TAAAAATGAAATGAAATAAAAT
17800904 TAAAAAATGAAATGAAACTAAAA
1 T-AAAAATGAAATGAAA-TAAAA
17800927 ATTGAAATTA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
20 5 0.10
21 9 0.18
22 17 0.33
23 12 0.24
24 8 0.16
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (22 bp):
TAAAAATGAAATGAAATAAAAT
Found at i:17800966 original size:21 final size:22
Alignment explanation
Indices: 17800929--17801073 Score: 87
Period size: 21 Copynumber: 6.8 Consensus size: 22
17800919 AACTAAAAAT
*
17800929 TGAAATTAAATT--AAATGAAA
1 TGAAATAAAATTAAAAATGAAA
17800949 TGAAAT-AAATTAAAAATGAAA
1 TGAAATAAAATTAAAAATGAAA
*
17800970 TGAAATGAACAA--AAAATTGAAA
1 TGAAAT-AA-AATTAAAAATGAAA
17800992 TGAAAT-AAA-TAAAAATTGAAA
1 TGAAATAAAATTAAAAA-TGAAA
* * * *
17801013 TGAAAT-GAGTTGATAATGAAA
1 TGAAATAAAATTAAAAATGAAA
* *
17801034 TGAAAATTTCAAA-T-GAAATGAAA
1 TG-AAA--TAAAATTAAAAATGAAA
17801057 TGAAAT-AAATTAAAAAT
1 TGAAATAAAATTAAAAAT
17801074 TAAAAATTGA
Statistics
Matches: 100, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
19 10 0.10
20 13 0.13
21 37 0.37
22 25 0.25
23 10 0.10
24 4 0.04
25 1 0.01
ACGTcount: A:0.61, C:0.01, G:0.12, T:0.26
Consensus pattern (22 bp):
TGAAATAAAATTAAAAATGAAA
Found at i:17801085 original size:34 final size:31
Alignment explanation
Indices: 17801053--17801127 Score: 80
Period size: 34 Copynumber: 2.3 Consensus size: 31
17801043 CAAATGAAAT
*
17801053 GAAATGAAATAAATTAAAAATTAAAAATTGAAAT
1 GAAATGAAATAAA-TAAAAATT-GAAA-TGAAAT
* *
17801087 GAAATGAAATAATTTAAAAGTTGAAATGAAAT
1 GAAATGAAATAA-ATAAAAATTGAAATGAAAT
17801119 GAAAT-AAAT
1 GAAATGAAAT
17801128 TTATTATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 4 0.11
32 11 0.30
33 3 0.08
34 19 0.51
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (31 bp):
GAAATGAAATAAATAAAAATTGAAATGAAAT
Found at i:17801086 original size:6 final size:5
Alignment explanation
Indices: 17800791--17801127 Score: 114
Period size: 5 Copynumber: 66.0 Consensus size: 5
17800781 TAATAATTAA
* * *
17800791 GAAAT GAAA- AAAATT GAAAT GAAAT GAAAT -AAA- -AAAA GAAGT GAAACT
1 GAAAT GAAAT GAAA-T GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAA-T
* * * * *
17800839 AAAAATT GAAAT GAAAT -AAATT CAAAAG GAAAT TAAAT GAAA- -AATT
1 -GAAA-T GAAAT GAAAT GAAA-T -GAAAT GAAAT GAAAT GAAAT GAAAT
* * *
17800885 GAAAT TAAAT GAAAT -AAAT TAAA- -AAAT GAAAT GAAACT AAAAATT
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAAT GAAA-T -GAAA-T
* * * *
17800930 GAAAT TAAAT TAAAT GAAAT GAAAT -AAATT AAAAAT GAAAT GAAAT GAACAA
1 GAAAT GAAAT GAAAT GAAAT GAAAT GAAA-T -GAAAT GAAAT GAAAT GAA-AT
* * **
17800982 AAAATT GAAAT GAAAT -AAAT AAAAATT GAAAT GAAAT GAGTT GATAAT
1 GAAA-T GAAAT GAAAT GAAAT -GAAA-T GAAAT GAAAT GAAAT GA-AAT
* * *
17801030 GAAAT GAAAATTT CAAAT GAAAT GAAAT GAAAT -AAATT AAAAAT TAAA-
1 GAAAT G-AAA--T GAAAT GAAAT GAAAT GAAAT GAAA-T -GAAAT GAAAT
* * *
17801078 -AATT GAAAT GAAAT GAAAT -AATTT AAAAGTT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAA-AT GAAA--T GAAAT GAAAT GAAAT
17801124 -AAAT
1 GAAAT
17801128 TTATTATTTA
Statistics
Matches: 255, Mismatches: 40, Indels: 75
0.69 0.11 0.20
Matches are distributed among these distances:
3 10 0.04
4 29 0.11
5 157 0.62
6 33 0.13
7 25 0.10
8 1 0.00
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.24
Consensus pattern (5 bp):
GAAAT
Found at i:17801145 original size:66 final size:58
Alignment explanation
Indices: 17800909--17801128 Score: 170
Period size: 59 Copynumber: 3.7 Consensus size: 58
17800899 TAAATTAAAA
* * * * *
17800909 AATGAAATG-AAACTAAAAATTGAAATTAAATTAAATGAAATGAAATAAATTAAAAA-TGA-
1 AATGAAATGAAAATTTAAAA-TGAAATGAAATGAAAT-AAAT-TAA-AAATTAAAAATTGAT
* * *
17800968 AATGAAATGAACAA---AAAATTGAAATGAAAT-AAATAAAAATT-GAAATGAAATGAGTTGAT
1 AATGAAATGAA-AATTTAAAA-TGAAATGAAATGAAAT--AAATTAAAAATTAAA--AATTGAT
*
17801027 AATGAAATGAAAATTTCAAATGAAATGAAATGAAATAAATTAAAAATTAAAAATTGA-
1 AATGAAATGAAAATTTAAAATGAAATGAAATGAAATAAATTAAAAATTAAAAATTGAT
17801084 AATGAAATGAAATAATTTAAAAGTTGAAATGAAATGAAATAAATT
1 AATGAAATG-AA-AATTTAAAA--TGAAATGAAATGAAATAAATT
17801129 TATTATTTAA
Statistics
Matches: 134, Mismatches: 11, Indels: 30
0.77 0.06 0.17
Matches are distributed among these distances:
55 7 0.05
57 14 0.10
58 31 0.23
59 33 0.25
60 19 0.14
61 30 0.22
ACGTcount: A:0.60, C:0.01, G:0.12, T:0.26
Consensus pattern (58 bp):
AATGAAATGAAAATTTAAAATGAAATGAAATGAAATAAATTAAAAATTAAAAATTGAT
Found at i:17801745 original size:20 final size:20
Alignment explanation
Indices: 17801720--17801759 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17801710 CAATATGGTC
*
17801720 AAATATTCACTAATTTATAA
1 AAATATTCACTAATTGATAA
17801740 AAATATTCACTAATTGATAA
1 AAATATTCACTAATTGATAA
17801760 TATATTGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (20 bp):
AAATATTCACTAATTGATAA
Found at i:17806079 original size:6 final size:6
Alignment explanation
Indices: 17806061--17806109 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
17806051 GAAATCTAAG
* *
17806061 AAAATA ACAATA AACATA AAAATA AAAATA TAAAATA TAAAATA TAAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA -AAAATA -AAAATA -AAAA
17806110 CAAATGGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
6 20 0.53
7 18 0.47
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (6 bp):
AAAATA
Found at i:17806095 original size:14 final size:15
Alignment explanation
Indices: 17806076--17806109 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
17806066 AACAATAAAC
17806076 ATAAAA-ATAAAAAT
1 ATAAAATATAAAAAT
17806090 ATAAAATAT-AAAAT
1 ATAAAATATAAAAAT
17806104 ATAAAA
1 ATAAAA
17806110 CAAATGGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAATATAAAAAT
Found at i:17807720 original size:3 final size:3
Alignment explanation
Indices: 17807712--17807764 Score: 72
Period size: 3 Copynumber: 17.0 Consensus size: 3
17807702 CAGTAAAACC
17807712 AAT AAT AAT AA- AAT AAT AAT AAT AAAT AAAT AAT AATT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AA-T AAT AAT AAT
17807759 AAT AAT
1 AAT AAT
17807765 GCTAGAGCTA
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.04
3 35 0.74
4 10 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17807731 original size:14 final size:13
Alignment explanation
Indices: 17807712--17807763 Score: 77
Period size: 14 Copynumber: 3.8 Consensus size: 13
17807702 CAGTAAAACC
17807712 AATAATAATAAAAT
1 AATAATAAT-AAAT
17807726 AATAATAATAAAT
1 AATAATAATAAAT
*
17807739 AAATAATAATTAAT
1 -AATAATAATAAAT
17807753 AATAATAATAA
1 AATAATAATAA
17807764 TGCTAGAGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
13 14 0.40
14 21 0.60
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:17807734 original size:17 final size:17
Alignment explanation
Indices: 17807712--17807764 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 17
17807702 CAGTAAAACC
17807712 AATAATAATAAAATAAT
1 AATAATAATAAAATAAT
17807729 AATAATAA-ATAAATAAT
1 AATAATAATA-AAATAAT
17807746 AATTAATAATAATAATAAT
1 AA-TAATAATAA-AATAAT
17807765 GCTAGAGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.03
17 17 0.53
18 7 0.22
19 7 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AATAATAATAAAATAAT
Found at i:17811456 original size:25 final size:22
Alignment explanation
Indices: 17811427--17811476 Score: 55
Period size: 25 Copynumber: 2.1 Consensus size: 22
17811417 CCGCATATGT
*
17811427 CGACGGAGATATAGCAGCGGGCTAC
1 CGACGAAGATATAG-A--GGGCTAC
*
17811452 CGACGAAGATGTAGAGGGCTAC
1 CGACGAAGATATAGAGGGCTAC
17811474 CGA
1 CGA
17811477 TTTGGGGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
24 1 0.04
25 12 0.52
ACGTcount: A:0.30, C:0.22, G:0.36, T:0.12
Consensus pattern (22 bp):
CGACGAAGATATAGAGGGCTAC
Found at i:17811651 original size:82 final size:80
Alignment explanation
Indices: 17811552--17811704 Score: 186
Period size: 79 Copynumber: 1.9 Consensus size: 80
17811542 AAATGGGAAA
* *
17811552 AAAAAGAGAAGAAATTTCA-GGCAAAATTTTAGGATTTATTTGGGGAG-GGGGAGGGAACCGATT
1 AAAAAGAGAAGAAATTTCATGGC-AAATTTTAGGA--T-TTCGGGGAGAAGGGA-GGAACCGATT
17811615 TTGGGAAAAAGAAAGGAGGG
61 TTGGGAAAAAGAAAGGAGGG
* * * *
17811635 AAAAA-AGAAGATATTTCATGTCAAATTTTGGGATTTCGGGGCGAAGGGAGGAACCGATTTTGGG
1 AAAAAGAGAAGAAATTTCATGGCAAATTTTAGGATTTCGGGGAGAAGGGAGGAACCGATTTTGGG
17811699 AAAAAG
66 AAAAAG
17811705 TCTTAAGGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
79 28 0.45
80 5 0.08
82 22 0.35
83 7 0.11
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.22
Consensus pattern (80 bp):
AAAAAGAGAAGAAATTTCATGGCAAATTTTAGGATTTCGGGGAGAAGGGAGGAACCGATTTTGGG
AAAAAGAAAGGAGGG
Found at i:17813042 original size:13 final size:13
Alignment explanation
Indices: 17813024--17813083 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
17813014 TATTTACCCC
17813024 TAAACCC-AACCT
1 TAAACCCAAACCT
17813036 ATAAACCCCAAACCT
1 -TAAA-CCCAAACCT
*
17813051 TAAACCCTAAACCC
1 TAAACCC-AAACCT
*
17813065 TAAACCCCAAACCA
1 TAAA-CCCAAACCT
17813079 TAAAC
1 TAAAC
17813084 TCTAAATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 8 0.20
14 25 0.61
15 8 0.20
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (13 bp):
TAAACCCAAACCT
Found at i:17813054 original size:14 final size:14
Alignment explanation
Indices: 17813031--17813083 Score: 70
Period size: 14 Copynumber: 3.7 Consensus size: 14
17813021 CCCTAAACCC
17813031 AACCTATAAACCCCA
1 AACCT-TAAACCCCA
*
17813046 AACCTTAAACCCTA
1 AACCTTAAACCCCA
*
17813060 AACCCTAAACCCCA
1 AACCTTAAACCCCA
*
17813074 AACCATAAAC
1 AACCTTAAAC
17813084 TCTAAATCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.13
Consensus pattern (14 bp):
AACCTTAAACCCCA
Found at i:17813055 original size:7 final size:7
Alignment explanation
Indices: 17813037--17813118 Score: 76
Period size: 7 Copynumber: 11.7 Consensus size: 7
17813027 ACCCAACCTA
17813037 TAAACCC
1 TAAACCC
* *
17813044 CAAACCT
1 TAAACCC
17813051 TAAACCC
1 TAAACCC
17813058 TAAACCC
1 TAAACCC
17813065 TAAACCC
1 TAAACCC
* *
17813072 CAAACCA
1 TAAACCC
*
17813079 TAAACTC
1 TAAACCC
*
17813086 TAAATCC
1 TAAACCC
*
17813093 TAAACCT
1 TAAACCC
*
17813100 TAAACCA
1 TAAACCC
17813107 T-AACCC
1 TAAACCC
17813113 ATAAAC
1 -TAAAC
17813119 TAAATTTAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
6 4 0.07
7 51 0.88
8 3 0.05
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
TAAACCC
Found at i:17813071 original size:28 final size:28
Alignment explanation
Indices: 17813037--17813118 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
17813027 ACCCAACCTA
*
17813037 TAAACCCCAAACCTTAAACCCTAAACCC
1 TAAACCCCAAACCATAAACCCTAAACCC
* *
17813065 TAAACCCCAAACCATAAACTCTAAATCC
1 TAAACCCCAAACCATAAACCCTAAACCC
**
17813093 TAAACCTTAAACCAT-AACCCATAAAC
1 TAAACCCCAAACCATAAACCC-TAAAC
17813119 TAAATTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
27 4 0.09
28 42 0.91
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (28 bp):
TAAACCCCAAACCATAAACCCTAAACCC
Found at i:17819670 original size:40 final size:40
Alignment explanation
Indices: 17819596--17819671 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 40
17819586 TTTTTACGGT
* * * *
17819596 ATTTTTTAAAAAGTGCCTCTAATGGTCAACCTATAGTAGC
1 ATTTTTCAAAAAGCGCCACTAATGCTCAACCTATAGTAGC
* *
17819636 ATTTTTCAAAAAGCGCCACTAATGCTCGATCTATAG
1 ATTTTTCAAAAAGCGCCACTAATGCTCAACCTATAG
17819672 CGGCGTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 30 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (40 bp):
ATTTTTCAAAAAGCGCCACTAATGCTCAACCTATAGTAGC
Found at i:17821100 original size:19 final size:19
Alignment explanation
Indices: 17821069--17821118 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
17821059 TCTAAAGAAA
17821069 TTGAATGGAGATATTCAATC
1 TTGAAT-GAGATATTCAATC
17821089 TTGAATGAGATATTCAATC
1 TTGAATGAGATATTCAATC
*
17821108 TTGAAGGAGAT
1 TTGAATGAGAT
17821119 CCGCTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.34
Consensus pattern (19 bp):
TTGAATGAGATATTCAATC
Found at i:17822242 original size:21 final size:21
Alignment explanation
Indices: 17822216--17822261 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
17822206 AATTATTTAT
17822216 AATTTATATATGAAAACATAA
1 AATTTATATATGAAAACATAA
*
17822237 AATTTATATATGAAAATATAA
1 AATTTATATATGAAAACATAA
17822258 AATT
1 AATT
17822262 CGACCAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
AATTTATATATGAAAACATAA
Found at i:17823400 original size:376 final size:376
Alignment explanation
Indices: 17822707--17823458 Score: 1504
Period size: 376 Copynumber: 2.0 Consensus size: 376
17822697 CTTGAGAAAG
17822707 CTAAAGTTAGCCATCTAGTTCCCCCAAACCCCAAAATATTTTTTTAAAAAAAAAATAAGTACCGA
1 CTAAAGTTAGCCATCTAGTTCCCCCAAACCCCAAAATATTTTTTTAAAAAAAAAATAAGTACCGA
17822772 CTGTTAGTTGGCCAGCACCCAAAATAAATTTGGTTCCGGCCATCAGGGTCCCCCTGCCCAAATTT
66 CTGTTAGTTGGCCAGCACCCAAAATAAATTTGGTTCCGGCCATCAGGGTCCCCCTGCCCAAATTT
17822837 TTTTTCAAATACTCGTGTAAAATATACCAATATGATACGGGTAGAAAAAAATACTAGGGAGCTAG
131 TTTTTCAAATACTCGTGTAAAATATACCAATATGATACGGGTAGAAAAAAATACTAGGGAGCTAG
17822902 CCACTTATGTCCCCCAACCCCAAAAAATAATTTTTTAACACCTGAGAAAATTTTTAAGTGATGAT
196 CCACTTATGTCCCCCAACCCCAAAAAATAATTTTTTAACACCTGAGAAAATTTTTAAGTGATGAT
17822967 TGGCACAAATATCTAGGTGATACCGCCTTTTAAGTCCCCACCTTAATTTACTGTTCATTTCAGGT
261 TGGCACAAATATCTAGGTGATACCGCCTTTTAAGTCCCCACCTTAATTTACTGTTCATTTCAGGT
17823032 TATTTGACTGTTCATTTTTTAATTTGGGTCAATTATGTAATTAATTACTTT
326 TATTTGACTGTTCATTTTTTAATTTGGGTCAATTATGTAATTAATTACTTT
17823083 CTAAAGTTAGCCATCTAGTTCCCCCAAACCCCAAAATATTTTTTTAAAAAAAAAATAAGTACCGA
1 CTAAAGTTAGCCATCTAGTTCCCCCAAACCCCAAAATATTTTTTTAAAAAAAAAATAAGTACCGA
17823148 CTGTTAGTTGGCCAGCACCCAAAATAAATTTGGTTCCGGCCATCAGGGTCCCCCTGCCCAAATTT
66 CTGTTAGTTGGCCAGCACCCAAAATAAATTTGGTTCCGGCCATCAGGGTCCCCCTGCCCAAATTT
17823213 TTTTTCAAATACTCGTGTAAAATATACCAATATGATACGGGTAGAAAAAAATACTAGGGAGCTAG
131 TTTTTCAAATACTCGTGTAAAATATACCAATATGATACGGGTAGAAAAAAATACTAGGGAGCTAG
17823278 CCACTTATGTCCCCCAACCCCAAAAAATAATTTTTTAACACCTGAGAAAATTTTTAAGTGATGAT
196 CCACTTATGTCCCCCAACCCCAAAAAATAATTTTTTAACACCTGAGAAAATTTTTAAGTGATGAT
17823343 TGGCACAAATATCTAGGTGATACCGCCTTTTAAGTCCCCACCTTAATTTACTGTTCATTTCAGGT
261 TGGCACAAATATCTAGGTGATACCGCCTTTTAAGTCCCCACCTTAATTTACTGTTCATTTCAGGT
17823408 TATTTGACTGTTCATTTTTTAATTTGGGTCAATTATGTAATTAATTACTTT
326 TATTTGACTGTTCATTTTTTAATTTGGGTCAATTATGTAATTAATTACTTT
17823459 TTTGAGCTAT
Statistics
Matches: 376, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
376 376 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (376 bp):
CTAAAGTTAGCCATCTAGTTCCCCCAAACCCCAAAATATTTTTTTAAAAAAAAAATAAGTACCGA
CTGTTAGTTGGCCAGCACCCAAAATAAATTTGGTTCCGGCCATCAGGGTCCCCCTGCCCAAATTT
TTTTTCAAATACTCGTGTAAAATATACCAATATGATACGGGTAGAAAAAAATACTAGGGAGCTAG
CCACTTATGTCCCCCAACCCCAAAAAATAATTTTTTAACACCTGAGAAAATTTTTAAGTGATGAT
TGGCACAAATATCTAGGTGATACCGCCTTTTAAGTCCCCACCTTAATTTACTGTTCATTTCAGGT
TATTTGACTGTTCATTTTTTAATTTGGGTCAATTATGTAATTAATTACTTT
Found at i:17829136 original size:40 final size:34
Alignment explanation
Indices: 17829061--17829130 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
17829051 AGTAACAGTC
17829061 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
*
17829095 CAGTATCAGTGTGGGCCTTAGCCCATTACAGTAA
1 CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
17829129 CA
1 CA
17829131 ATAACAGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (34 bp):
CAGTATCAGTGTGGGCCTTAGCCCATTACAATAA
Found at i:17836796 original size:34 final size:34
Alignment explanation
Indices: 17836758--17836827 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
17836748 AGTAACAATC
* * *
17836758 CAGTATCAGTGTGGGCCTTAGTCCATTACAATAA
1 CAGTATCAATATGGGCCTTAGCCCATTACAATAA
*
17836792 CAGTATCAATATGGGCCTTAGCCCATTACAGTAA
1 CAGTATCAATATGGGCCTTAGCCCATTACAATAA
17836826 CA
1 CA
17836828 ATAACAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (34 bp):
CAGTATCAATATGGGCCTTAGCCCATTACAATAA
Found at i:17836985 original size:21 final size:21
Alignment explanation
Indices: 17836961--17837007 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
17836951 CGGCATTATT
17836961 CAGTAATTGCAGCAAAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
* *
17836982 CAGTAATTGTAGCAGAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
17837003 CAGTA
1 CAGTA
17837008 CAGTACACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.21
Consensus pattern (21 bp):
CAGTAATTGCAGCAAAGCTGC
Found at i:17840554 original size:43 final size:43
Alignment explanation
Indices: 17840491--17840601 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 43
17840481 GCAAAATACG
* *
17840491 CCGCTATAGAACATGACCTTTAGCGGCACTTTTACAACAAACA
1 CCGCTAAAGAACATGGCCTTTAGCGGCACTTTTACAACAAACA
* * * * *
17840534 CCGCTAAAAAACATGGCCTTTGGCGGCACTTTTCCCACAAACG
1 CCGCTAAAGAACATGGCCTTTAGCGGCACTTTTACAACAAACA
* * *
17840577 TCGTTAAAGAATATGGCCTTTAGCG
1 CCGCTAAAGAACATGGCCTTTAGCG
17840602 ACGCTTTTCT
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (43 bp):
CCGCTAAAGAACATGGCCTTTAGCGGCACTTTTACAACAAACA
Found at i:17840814 original size:34 final size:35
Alignment explanation
Indices: 17840776--17840841 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
17840766 CTATTAAAAT
*
17840776 TTTAACTTTA-AAACTAAATATAA-AAATTAATGAG
1 TTTAAATTTAGAAACTAAA-ATAATAAATTAATGAG
*
17840810 TTTAAATTTAGAATCTAAAATAATAAATTAAT
1 TTTAAATTTAGAAACTAAAATAATAAATTAAT
17840842 AACACAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (35 bp):
TTTAAATTTAGAAACTAAAATAATAAATTAATGAG
Found at i:17840936 original size:19 final size:19
Alignment explanation
Indices: 17840891--17840939 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
17840881 TAAATATTAA
* **
17840891 AATAAAAATAAAAATTTAG
1 AATAAAAATTAAAATAAAG
* *
17840910 AATCAAAATTAAAATAAAT
1 AATAAAAATTAAAATAAAG
17840929 AATAAAAATTA
1 AATAAAAATTA
17840940 TCTAATACTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
AATAAAAATTAAAATAAAG
Found at i:17844048 original size:17 final size:18
Alignment explanation
Indices: 17844015--17844048 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17844005 TATTTTTTAA
17844015 ATAATTTAAACTATATTG
1 ATAATTTAAACTATATTG
*
17844033 ATAATTTTAA-TATATT
1 ATAATTTAAACTATATT
17844049 AAAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATAATTTAAACTATATTG
Found at i:17844267 original size:14 final size:14
Alignment explanation
Indices: 17844248--17844300 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
17844238 TTTTCAACAG
*
17844248 TAAACCCTAAATCT
1 TAAACCCTAAATCA
*
17844262 TAAACCCCAAATCA
1 TAAACCCTAAATCA
* * *
17844276 TAAA-CCTACACCC
1 TAAACCCTAAATCA
17844289 TAAACCCTAAAT
1 TAAACCCTAAAT
17844301 ATATATTACA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 9 0.30
14 21 0.70
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:17844475 original size:15 final size:15
Alignment explanation
Indices: 17844455--17844490 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
17844445 GACCCTAACT
17844455 ATAAAACAAAAAACC
1 ATAAAACAAAAAACC
*
17844470 ATAAAACCAAAAACC
1 ATAAAACAAAAAACC
17844485 A-AAAAC
1 ATAAAAC
17844491 TCTAAACCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.72, C:0.22, G:0.00, T:0.06
Consensus pattern (15 bp):
ATAAAACAAAAAACC
Found at i:17844482 original size:7 final size:7
Alignment explanation
Indices: 17844457--17844490 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
17844447 CCCTAACTAT
*
17844457 AAAACAA
1 AAAACCA
17844464 AAAACCA
1 AAAACCA
17844471 TAAAACCA
1 -AAAACCA
17844479 AAAACCA
1 AAAACCA
17844486 AAAAC
1 AAAAC
17844491 TCTAAACCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.74, C:0.24, G:0.00, T:0.03
Consensus pattern (7 bp):
AAAACCA
Found at i:17844488 original size:22 final size:22
Alignment explanation
Indices: 17844457--17844503 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
17844447 CCCTAACTAT
17844457 AAAACAAAAAAC-CATAAAACCA
1 AAAACAAAAAACTC-TAAAACCA
* *
17844479 AAAACCAAAAACTCTAAACCCA
1 AAAACAAAAAACTCTAAAACCA
17844501 AAA
1 AAA
17844504 TAATAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 21 0.95
23 1 0.05
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (22 bp):
AAAACAAAAAACTCTAAAACCA
Found at i:17844540 original size:43 final size:42
Alignment explanation
Indices: 17844480--17844615 Score: 112
Period size: 43 Copynumber: 3.2 Consensus size: 42
17844470 ATAAAACCAA
* *
17844480 AAACCAAAAACTCTAAACCCAAAATAATAAACATTATATCAT
1 AAACCATAAACCCTAAACCCAAAATAATAAACATTATATCAT
* * ** * * * *
17844522 AAACCCTAAACCCCTAAA-CCATGAGCATTAAACCTTAAATCTT
1 AAACCATAAA-CCCTAAACCCA-AAATAATAAACATTATATCAT
* * *
17844565 AAATCATAAACTCTAAACCCCAAAATAATAAACACTATATCAT
1 AAACCATAAACCCTAAA-CCCAAAATAATAAACATTATATCAT
*
17844608 AACCCATA
1 AAACCATA
17844616 TCCCTTAAAT
Statistics
Matches: 67, Mismatches: 23, Indels: 7
0.69 0.24 0.07
Matches are distributed among these distances:
42 17 0.25
43 47 0.70
44 3 0.04
ACGTcount: A:0.51, C:0.26, G:0.01, T:0.22
Consensus pattern (42 bp):
AAACCATAAACCCTAAACCCAAAATAATAAACATTATATCAT
Found at i:17845134 original size:14 final size:15
Alignment explanation
Indices: 17845103--17845192 Score: 59
Period size: 14 Copynumber: 6.5 Consensus size: 15
17845093 ATATTTACCC
17845103 CTAAA-CCC-AACCT
1 CTAAACCCCAAACCT
17845116 CTAAACCCCAAACCT
1 CTAAACCCCAAACCT
*
17845131 -TAAACCCTAAACC-
1 CTAAACCCCAAACCT
* **
17845144 CCAAACCATAAA-CT
1 CTAAACCCCAAACCT
* *
17845158 CTAAGCCCTAAA-CT
1 CTAAACCCCAAACCT
* *
17845172 CTAAATCCTAAACCT
1 CTAAACCCCAAACCT
17845187 -TAAACC
1 CTAAACC
17845193 ATAACCCATA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
13 6 0.10
14 50 0.79
15 7 0.11
ACGTcount: A:0.42, C:0.39, G:0.01, T:0.18
Consensus pattern (15 bp):
CTAAACCCCAAACCT
Found at i:17845140 original size:21 final size:21
Alignment explanation
Indices: 17845111--17845185 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 21
17845101 CCCTAAACCC
17845111 AACCTCTAAACCCCAAACCTTA
1 AACC-CTAAACCCCAAACCTTA
*
17845133 AACCCTAAACCCCAAACCATA
1 AACCCTAAACCCCAAACCTTA
* * *
17845154 AACTCTAAGCCCTAAA-CTCTA
1 AACCCTAAACCCCAAACCT-TA
*
17845175 AATCCTAAACC
1 AACCCTAAACC
17845186 TTAAACCATA
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 1 0.02
21 39 0.89
22 4 0.09
ACGTcount: A:0.43, C:0.39, G:0.01, T:0.17
Consensus pattern (21 bp):
AACCCTAAACCCCAAACCTTA
Found at i:17845306 original size:40 final size:40
Alignment explanation
Indices: 17845210--17845309 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
17845200 ATAAACTAAA
* * * *
17845210 TTTAAAAA-TGCCGGTAATGCTCGATCTATAGCGGCGTTG
1 TTTAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCATTG
*** *
17845249 TTTAAAAAGCATTGCTAATGGTCGACCTATAGCGGCATT-
1 TTTAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCATTG
17845288 TTTCAAAAAGCGCCGCTAATGC
1 TTT-AAAAAGCGCCGCTAATGC
17845310 CACTAAAGTT
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
39 11 0.23
40 36 0.77
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (40 bp):
TTTAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCATTG
Found at i:17845538 original size:114 final size:115
Alignment explanation
Indices: 17845249--17845539 Score: 413
Period size: 116 Copynumber: 2.5 Consensus size: 115
17845239 AGCGGCGTTG
* * *
17845249 TTTAAAAAGCATTGCTAATGGTCGACCTATAGCGGCATTTTTCAAAAAGCGCCGCTAATGCCACT
1 TTTAAAAAGCACTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCCACT
* * *
17845314 AAAGTTCACATAAAACAACAGCATTGTGCTTAATTTTTTTGTGGCGTTTT
66 AAAGCTCACATAAAACAACAGCATTGTGCTTAATTTTTTTATGGCGATTT
** * *
17845364 TTTAAAAAAGCACCACTAATAGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGTTAATGCCAC
1 TTT-AAAAAGCACTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCCAC
* *
17845429 TAAAGCTCACATAAAACGACGGCATTGTGCTTAATTTTTTTATGGC-ATTT
65 TAAAGCTCACATAAAACAACAGCATTGTGCTTAATTTTTTTATGGCGATTT
* * ** *
17845479 TTTAAAAAGCGCTGCTAATGGTCAACCTATAGTAGCGTTTTTCAAAAAGCACCACTAATGC
1 TTTAAAAAGCACTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGC
17845540 TCGATCTATA
Statistics
Matches: 154, Mismatches: 21, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
114 49 0.32
115 9 0.06
116 96 0.62
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.31
Consensus pattern (115 bp):
TTTAAAAAGCACTGCTAATGGTCGACCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCCACT
AAAGCTCACATAAAACAACAGCATTGTGCTTAATTTTTTTATGGCGATTT
Found at i:17847008 original size:23 final size:19
Alignment explanation
Indices: 17846949--17846999 Score: 84
Period size: 19 Copynumber: 2.6 Consensus size: 19
17846939 TCTAAAGAAA
17846949 TTGAATGGAGATCTTCAAAC
1 TTGAA-GGAGATCTTCAAAC
*
17846969 TTGAAGGAGATCTTCAATC
1 TTGAAGGAGATCTTCAAAC
17846988 TTGAAGGAGATC
1 TTGAAGGAGATC
17847000 CGCTTTCAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 25 0.83
20 5 0.17
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (19 bp):
TTGAAGGAGATCTTCAAAC
Found at i:17848131 original size:21 final size:21
Alignment explanation
Indices: 17848105--17848150 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
17848095 AATTATTTAT
**
17848105 AATTTATATATGAAAATATAA
1 AATTTATATACAAAAATATAA
17848126 AATTTATATACAAAAATATAA
1 AATTTATATACAAAAATATAA
17848147 AATT
1 AATT
17848151 CGACCAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AATTTATATACAAAAATATAA
Found at i:17856503 original size:34 final size:34
Alignment explanation
Indices: 17856465--17856534 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
17856455 AGTAACAATC
* *
17856465 CAGTATCAATGTGGGCCTTAGTCCATTACAATAA
1 CAGTATCAATATGGGCCTTAGCCCATTACAATAA
*
17856499 CAGTATCAATATGGGCCTTAGCCCATTACAGTAA
1 CAGTATCAATATGGGCCTTAGCCCATTACAATAA
17856533 CA
1 CA
17856535 ATAACAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (34 bp):
CAGTATCAATATGGGCCTTAGCCCATTACAATAA
Found at i:17856536 original size:40 final size:38
Alignment explanation
Indices: 17856453--17856541 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 38
17856443 TAGGCTCGAT
* * *
17856453 TCAGTAACAAT-CCAGTATCAATGTGGGCCTTAGTCCA
1 TCAGTAACAATAACAGTATCAATATGGGCCTTAGCCCA
17856490 T---T-ACAATAACAGTATCAATATGGGCCTTAGCCCA
1 TCAGTAACAATAACAGTATCAATATGGGCCTTAGCCCA
17856524 TTACAGTAACAATAACAG
1 -T-CAGTAACAATAACAG
17856542 AAATGCAGCA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
33 5 0.12
34 24 0.57
35 1 0.02
37 1 0.02
39 1 0.02
40 10 0.24
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (38 bp):
TCAGTAACAATAACAGTATCAATATGGGCCTTAGCCCA
Found at i:17856710 original size:21 final size:21
Alignment explanation
Indices: 17856668--17856714 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
17856658 CGACATTATT
* * * *
17856668 CAGTAATTGTAGTATAGTTGC
1 CAGTAATTGCAGCAAAGCTGC
17856689 CAGTAATTGCAGCAAAGCTGC
1 CAGTAATTGCAGCAAAGCTGC
17856710 CAGTA
1 CAGTA
17856715 CAGTACACTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (21 bp):
CAGTAATTGCAGCAAAGCTGC
Found at i:17857015 original size:17 final size:19
Alignment explanation
Indices: 17856980--17857016 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
17856970 AAAGTTCACA
17856980 ACACAGCCCATGTGTGCCC
1 ACACAGCCCATGTGTGCCC
*
17856999 ACAC-GCCCGTGTG-GCCC
1 ACACAGCCCATGTGTGCCC
17857016 A
1 A
17857017 TTAAGCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (19 bp):
ACACAGCCCATGTGTGCCC
Found at i:17863380 original size:91 final size:91
Alignment explanation
Indices: 17863220--17863412 Score: 350
Period size: 91 Copynumber: 2.1 Consensus size: 91
17863210 AATATGGGGT
* *
17863220 ATTAGCCAAGCCCTTAATAGTCCTATTAAAGGAGTAGGTTTGGAATTAGTCTAATAATGTACTAG
1 ATTACCCAAGCCCTTAATAATCCTATTAAAGGAGTAGGTTTGGAATTAGTCTAATAATGTACTAG
17863285 AAGCTTTTGAACAGCTCAAAACAACA
66 AAGCTTTTGAACAGCTCAAAACAACA
* *
17863311 ATTACCCAAGCCCTTAATAATCCTATTAAAGGAGTTGGTTTGGAATTAGTCTAATAGTGTACTAG
1 ATTACCCAAGCCCTTAATAATCCTATTAAAGGAGTAGGTTTGGAATTAGTCTAATAATGTACTAG
17863376 AAGCTTTTGAACAGCTCAAAACAACA
66 AAGCTTTTGAACAGCTCAAAACAACA
17863402 ATTACCCAAGC
1 ATTACCCAAGC
17863413 ACCATAACTA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
91 98 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (91 bp):
ATTACCCAAGCCCTTAATAATCCTATTAAAGGAGTAGGTTTGGAATTAGTCTAATAATGTACTAG
AAGCTTTTGAACAGCTCAAAACAACA
Found at i:17872105 original size:44 final size:42
Alignment explanation
Indices: 17872039--17872126 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 42
17872029 CTAAACTCAG
*
17872039 AAAAAATATCTTATTTATTTCAAAATAAAAATAAAATAATTA
1 AAAAAATATCTTATTTACTTCAAAATAAAAATAAAATAATTA
*
17872081 AAAAATATAATCTTATTTACTTCAAAATAAAAATATAATAATTA
1 AAAAA-AT-ATCTTATTTACTTCAAAATAAAAATAAAATAATTA
17872125 AA
1 AA
17872127 TTAAGTTTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 5 0.12
43 2 0.05
44 35 0.83
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (42 bp):
AAAAAATATCTTATTTACTTCAAAATAAAAATAAAATAATTA
Found at i:17873572 original size:36 final size:36
Alignment explanation
Indices: 17873532--17873615 Score: 100
Period size: 36 Copynumber: 2.3 Consensus size: 36
17873522 ATAATATTAC
17873532 TTAAATCTATTTTAACTT-A-AAAAATATTTATTAAAA
1 TTAAAT-TATTTT-ACTTCAGAAAAATATTTATTAAAA
** **
17873568 TTAAATTATTTTTTTTCAGTCAAATATTTATTAAAA
1 TTAAATTATTTTACTTCAGAAAAATATTTATTAAAA
17873604 TTAAATTATTTT
1 TTAAATTATTTT
17873616 TTTCACTCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 2 0.05
35 7 0.17
36 33 0.79
ACGTcount: A:0.43, C:0.05, G:0.01, T:0.51
Consensus pattern (36 bp):
TTAAATTATTTTACTTCAGAAAAATATTTATTAAAA
Found at i:17873613 original size:18 final size:18
Alignment explanation
Indices: 17873556--17873614 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
17873546 ACTTAAAAAA
17873556 TATTTATTAAAATTAAAT
1 TATTTATTAAAATTAAAT
* ** * *
17873574 TATTTTTTTTCAGTCAAA-
1 TA-TTTATTAAAATTAAAT
17873592 TATTTATTAAAATTAAAT
1 TATTTATTAAAATTAAAT
17873610 TATTT
1 TATTT
17873615 TTTTCACTCT
Statistics
Matches: 29, Mismatches: 10, Indels: 4
0.67 0.23 0.09
Matches are distributed among these distances:
17 10 0.34
18 9 0.31
19 10 0.34
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (18 bp):
TATTTATTAAAATTAAAT
Found at i:17888149 original size:22 final size:22
Alignment explanation
Indices: 17888124--17888171 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
17888114 TGGTAGCAGT
17888124 TTTGACAAATACCATTCTGTTA
1 TTTGACAAATACCATTCTGTTA
***
17888146 TTTGGTTAATACCATTCTGTTA
1 TTTGACAAATACCATTCTGTTA
17888168 TTTG
1 TTTG
17888172 GTTTATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (22 bp):
TTTGACAAATACCATTCTGTTA
Found at i:17888172 original size:22 final size:22
Alignment explanation
Indices: 17888131--17888174 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
17888121 AGTTTTGACA
17888131 AATACCATTCTGTTATTTGGTT
1 AATACCATTCTGTTATTTGGTT
17888153 AATACCATTCTGTTATTTGGTT
1 AATACCATTCTGTTATTTGGTT
17888175 TATTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (22 bp):
AATACCATTCTGTTATTTGGTT
Found at i:17888625 original size:18 final size:19
Alignment explanation
Indices: 17888602--17888639 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
17888592 CATGACATGA
17888602 TTTAAT-TGGTCAAGTTTT
1 TTTAATATGGTCAAGTTTT
*
17888620 TTTAATAGTGGTTAAGTTTT
1 TTTAATA-TGGTCAAGTTTT
17888640 GGATCAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (19 bp):
TTTAATATGGTCAAGTTTT
Found at i:17890310 original size:23 final size:23
Alignment explanation
Indices: 17890283--17890326 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
17890273 TAGACTCCAT
17890283 CCAGCTTCCTAAAGTCAAAATCC
1 CCAGCTTCCTAAAGTCAAAATCC
*
17890306 CCAGCTTTCTAAAGTCAAAAT
1 CCAGCTTCCTAAAGTCAAAAT
17890327 TCTACTCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.30, G:0.09, T:0.25
Consensus pattern (23 bp):
CCAGCTTCCTAAAGTCAAAATCC
Found at i:17891553 original size:16 final size:17
Alignment explanation
Indices: 17891534--17891566 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17891524 GCAAAAAGAT
*
17891534 TACAAGTTAAC-CATAA
1 TACAAGTGAACACATAA
17891550 TACAAGTGAACACATAA
1 TACAAGTGAACACATAA
17891567 CATTACCATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (17 bp):
TACAAGTGAACACATAA
Found at i:17894785 original size:16 final size:16
Alignment explanation
Indices: 17894764--17894795 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17894754 TCAATTAATC
*
17894764 TAATTAACCTAAAAAT
1 TAATTAAACTAAAAAT
17894780 TAATTAAACTAAAAAT
1 TAATTAAACTAAAAAT
17894796 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:17904575 original size:193 final size:191
Alignment explanation
Indices: 17904201--17904579 Score: 548
Period size: 193 Copynumber: 2.0 Consensus size: 191
17904191 CAGTATCCCT
* * *
17904201 TACTAGAATACTAAAAAAAGCTTATTTCCATATAGATAACCAGATCCCAATGGCCGAAAAATCCC
1 TACTAGAATACTAAAAAAAGCTTATTTACATACAGATAACCAGATCCCAATGGCCAAAAAATCCC
*
17904266 AAAATTTCCTCCCTCTTTATAATTTGATCCACTCTTATAAGCAAAGTCCGAATCCACCAACCTAA
66 AAAATTTCCTCCCTCTTTATAATTTCATCCACTCTTATAAGCAAAGTCCGAATCCACCAACCTAA
** * *
17904331 GTTGGTTAATCTTATTAACATCTGCATCCTAATCCATTAATCTTCCCATATTAGCATCCTC
131 AATGGTTAATCTTATTAACATCTACATCATAATCCATTAATCTTCCCATATTAGCATCCTC
* * *
17904392 TACTAGAATACTAATAAAATGCTTATTTACATCACAGATAATCAG-TGCCCAATGG-TAAACAAA
1 TACTAGAATACTAA-AAAAAGCTTATTTACAT-ACAGATAACCAGAT-CCCAATGGCCAAA-AAA
* * * * *
17904455 TCCCAAAATTTCCTCTCTGTTTATAATTTCATCCACTCTTATATGCACAGTCGGAATCCACCAAC
62 TCCCAAAATTTCCTCCCTCTTTATAATTTCATCCACTCTTATAAGCAAAGTCCGAATCCACCAAC
17904520 CTAAAATGGTTAATCTTATTAACATAC-ACATCATAATCCATTAATCTTCCCATATTAGCA
127 CTAAAATGGTTAATCTTATTAACAT-CTACATCATAATCCATTAATCTTCCCATATTAGCA
17904580 CAGTCTTCCC
Statistics
Matches: 167, Mismatches: 16, Indels: 8
0.87 0.08 0.04
Matches are distributed among these distances:
191 14 0.08
192 18 0.11
193 134 0.80
194 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.31
Consensus pattern (191 bp):
TACTAGAATACTAAAAAAAGCTTATTTACATACAGATAACCAGATCCCAATGGCCAAAAAATCCC
AAAATTTCCTCCCTCTTTATAATTTCATCCACTCTTATAAGCAAAGTCCGAATCCACCAACCTAA
AATGGTTAATCTTATTAACATCTACATCATAATCCATTAATCTTCCCATATTAGCATCCTC
Found at i:17920503 original size:17 final size:17
Alignment explanation
Indices: 17920478--17920516 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17920468 AAGAGTTTGT
*
17920478 CAAACCCTAGAGTTCAC
1 CAAATCCTAGAGTTCAC
*
17920495 TAAATCCTAGAGTTCAC
1 CAAATCCTAGAGTTCAC
17920512 CAAAT
1 CAAAT
17920517 GGTGAATCCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (17 bp):
CAAATCCTAGAGTTCAC
Found at i:17926843 original size:49 final size:49
Alignment explanation
Indices: 17926774--17927018 Score: 292
Period size: 49 Copynumber: 4.9 Consensus size: 49
17926764 TAGCCAAAGC
*
17926774 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
* * * * *
17926823 TATTTGGCACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC-AAT
* * * *
17926873 CATCTGATACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGA-CCAA-T
* * *
17926924 TATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
** * * * *
17926973 TATCCAGTACACGTAGTAGCTTGCACTTAGTGCTACACACGTGACC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACC
17927019 TCACAATAGA
Statistics
Matches: 165, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
49 80 0.48
50 46 0.28
51 39 0.24
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACACGCGACCAAT
Found at i:17927010 original size:100 final size:101
Alignment explanation
Indices: 17926781--17927016 Score: 291
Period size: 101 Copynumber: 2.4 Consensus size: 101
17926771 AGCTATCTGG
* * * ** * * *
17926781 TACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-TTATTTGGCACACGTAGTAGCC
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCC
* *
17926844 TGCACTTAGTACTACACACGTGACCTAACCATCTGA
66 TGCACTTAGTACTACACACGCGACCTAACCATCAGA
17926880 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCC
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCC
* **
17926945 TGCACTTAGTACTACACATGCGACC-AATTATCCAG-
66 TGCACTTAGTACTACACACGCGACCTAACCAT-CAGA
* * *
17926980 TACACGTAGTAGCTTGCACTTAGTGCTACACACGTGA
1 TACACATAGTAGCCTGCACTTAGTACTACACACGTGA
17927017 CCTCACAATA
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
99 35 0.30
100 41 0.35
101 42 0.36
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (101 bp):
TACACATAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCC
TGCACTTAGTACTACACACGCGACCTAACCATCAGA
Found at i:17927655 original size:13 final size:13
Alignment explanation
Indices: 17927637--17927663 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17927627 ACGTCGAAAT
17927637 TTTCATGAAATCA
1 TTTCATGAAATCA
17927650 TTTCATGAAATCA
1 TTTCATGAAATCA
17927663 T
1 T
17927664 AGACCATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTCATGAAATCA
Found at i:17929009 original size:20 final size:20
Alignment explanation
Indices: 17928936--17929030 Score: 86
Period size: 20 Copynumber: 4.8 Consensus size: 20
17928926 GCAATTAAGC
*
17928936 TAGAAATTTTGGTATCACAT
1 TAGAAATATTGGTATCACAT
** * *
17928956 TAGCTATATTGGTGTCA-GT
1 TAGAAATATTGGTATCACAT
* * **
17928975 TAGAAATTTTAGTATCATGTT
1 TAGAAATATTGGTATCA-CAT
17928996 TA-AAATATTGGTATCACAT
1 TAGAAATATTGGTATCACAT
17929015 TAGAAATATTGGTATC
1 TAGAAATATTGGTATC
17929031 TCGTTAAAAA
Statistics
Matches: 57, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
19 16 0.28
20 38 0.67
21 3 0.05
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (20 bp):
TAGAAATATTGGTATCACAT
Found at i:17929060 original size:59 final size:58
Alignment explanation
Indices: 17928943--17929064 Score: 138
Period size: 59 Copynumber: 2.1 Consensus size: 58
17928933 AGCTAGAAAT
** * * * * *
17928943 TTTGGTATCACATTAGCTATATTGGTGTCAGTTAGAAATTTTAGTATCATGTTTAAAA
1 TTTGGTATCACATTAGAAATATTGGTATCAGTTAAAAAATTTAGCATCATGTTAAAAA
* *
17929001 TATTGGTATCACATTAGAAATATTGGTATCTCGTTAAAAAATTTGGCATCA-GTTAAAAA
1 T-TTGGTATCACATTAGAAATATTGGTATC-AGTTAAAAAATTTAGCATCATGTTAAAAA
17929060 TTTGG
1 TTTGG
17929065 CATTGATTAG
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
58 5 0.09
59 33 0.62
60 15 0.28
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (58 bp):
TTTGGTATCACATTAGAAATATTGGTATCAGTTAAAAAATTTAGCATCATGTTAAAAA
Found at i:17929789 original size:29 final size:30
Alignment explanation
Indices: 17929715--17929796 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 30
17929705 TTTTAAATTT
* *
17929715 TGAAAAGTACAAAGACTAAAATTTACCAATT
1 TGAAAAGTAC-AAGACTAAAATTAACCAATA
* *
17929746 TGAAAATTA-AAGACTAAAATTAATCAA-A
1 TGAAAAGTACAAGACTAAAATTAACCAATA
17929774 T-AAAAGTACAAGGACTACAAATT
1 TGAAAAGTACAA-GACTA-AAATT
17929797 TTGCTAAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 6 0.14
28 3 0.07
29 21 0.49
30 5 0.12
31 8 0.19
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (30 bp):
TGAAAAGTACAAGACTAAAATTAACCAATA
Found at i:17932860 original size:23 final size:23
Alignment explanation
Indices: 17932832--17932880 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
17932822 TCCTGAAGTG
17932832 AATGTTGCATATAATTGTTTGCA
1 AATGTTGCATATAATTGTTTGCA
*
17932855 AATGTTGTATATAATTGTTTGCA
1 AATGTTGCATATAATTGTTTGCA
17932878 AAT
1 AAT
17932881 TTTATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (23 bp):
AATGTTGCATATAATTGTTTGCA
Found at i:17942708 original size:20 final size:20
Alignment explanation
Indices: 17942685--17942735 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
17942675 GAACCCAATA
17942685 TTTTATTTATTAAATTTTAT
1 TTTTATTTATTAAATTTTAT
17942705 TTTTATTTATTAAATTTTAT
1 TTTTATTTATTAAATTTTAT
17942725 TTTTATTTATT
1 TTTTATTTATT
17942736 TATTCTAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTATTTATTAAATTTTAT
Found at i:17946380 original size:23 final size:23
Alignment explanation
Indices: 17946352--17946407 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
17946342 CTATAATATC
17946352 CAAATAATATTAAAAATGACAGT
1 CAAATAATATTAAAAATGACAGT
17946375 CAAATAATATTAAAAATGACAGT
1 CAAATAATATTAAAAATGACAGT
* *
17946398 GAAAAAATAT
1 CAAATAATAT
17946408 AATAAACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.59, C:0.07, G:0.09, T:0.25
Consensus pattern (23 bp):
CAAATAATATTAAAAATGACAGT
Found at i:17946481 original size:23 final size:23
Alignment explanation
Indices: 17946455--17946498 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
17946445 AAACAAAAAT
17946455 AAAA-AACATAAAAAAACAACACC
1 AAAATAACA-AAAAAAACAACACC
* *
17946478 AAAATAGCACAAAAAACAACA
1 AAAATAACAAAAAAAACAACA
17946499 TGCAAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (23 bp):
AAAATAACAAAAAAAACAACACC
Found at i:17946915 original size:21 final size:20
Alignment explanation
Indices: 17946868--17946915 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
17946858 TGGCACGTTA
17946868 TTTTTTGTTTTGTTTCTTCT
1 TTTTTTGTTTTGTTTCTTCT
17946888 TGGTTTTTGTTCTTGTGTTCTTCT
1 T--TTTTTGTT-TTGT-TTCTTCT
17946912 TTTT
1 TTTT
17946916 GCTTTTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 1 0.04
22 11 0.46
23 4 0.17
24 8 0.33
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (20 bp):
TTTTTTGTTTTGTTTCTTCT
Found at i:17952790 original size:40 final size:40
Alignment explanation
Indices: 17952720--17953004 Score: 416
Period size: 40 Copynumber: 7.2 Consensus size: 40
17952710 CGGATGATAA
*
17952720 CGAAGGCATTTGTGCTAG-TGACTA-ATTCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGCT-ACTATA-TCCGGGCTAAGTCC
*
17952760 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
*
17952800 CGAAGGCATTTGTGCGAGTTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
* *
17952840 TGAAGGCATTTGTGCGAGCTACTATATCTGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
* *
17952880 CAAAGGCATTTGTGCAAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
17952920 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
1 CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
* * * *
17952960 CGAAGGCATTTGAGCGA-ATAGCTATATCC-GGTTAAATCC
1 CGAAGGCATTTGTGCGAGCTA-CTATATCCGGGCTAAGTCC
17952999 CGAAGG
1 CGAAGG
17953005 TACTTGGTTT
Statistics
Matches: 228, Mismatches: 14, Indels: 7
0.92 0.06 0.03
Matches are distributed among these distances:
39 16 0.07
40 210 0.92
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CGAAGGCATTTGTGCGAGCTACTATATCCGGGCTAAGTCC
Found at i:17954787 original size:29 final size:29
Alignment explanation
Indices: 17954745--17954807 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
17954735 GGAGTTAAAA
*
17954745 AAGAATGAGGACTTTTAATTATATCAAGT
1 AAGACTGAGGACTTTTAATTATATCAAGT
17954774 AAGACTGAGGACTTTTAATTATATCAAGT
1 AAGACTGAGGACTTTTAATTATATCAAGT
17954803 AAGAC
1 AAGAC
17954808 CTTATGAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (29 bp):
AAGACTGAGGACTTTTAATTATATCAAGT
Found at i:17964678 original size:19 final size:18
Alignment explanation
Indices: 17964645--17964680 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17964635 ATTTTTTTTC
17964645 TTAAATTAAACATTAAAA
1 TTAAATTAAACATTAAAA
*
17964663 TTAAATTTAAATATTAAA
1 TTAAA-TTAAACATTAAA
17964681 TGTGTTTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAATTAAACATTAAAA
Found at i:17971616 original size:12 final size:12
Alignment explanation
Indices: 17971569--17971618 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
17971559 ACTTAATCAC
17971569 TTTAATATTAAA
1 TTTAATATTAAA
17971581 -TTAATA-TAACA
1 TTTAATATTAA-A
*
17971592 TTTATCTTATTAAA
1 TTTA--ATATTAAA
17971606 TTTAATATTAAA
1 TTTAATATTAAA
17971618 T
1 T
17971619 CTTATCAACT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
12 11 0.35
14 7 0.23
15 3 0.10
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTAATATTAAA
Found at i:17973851 original size:20 final size:20
Alignment explanation
Indices: 17973826--17973870 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
17973816 AGGGACTAAA
* *
17973826 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
17973846 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
17973866 ATGAA
1 ATGAA
17973871 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:17976006 original size:92 final size:92
Alignment explanation
Indices: 17975883--17976110 Score: 330
Period size: 92 Copynumber: 2.5 Consensus size: 92
17975873 GCGTAGGTAG
* * * *
17975883 CGTACATATGGTACAGTGCAATGCGGTAATCTGCTATATCGATAGATTGCAGTAAAATTGCCAGT
1 CGTACATGTGGTACAGTGCAATGCGGTAATCTGCTATACCGATAGATTGCAATAAAACTGCCAGT
*
17975948 TCAGTCAATGGTATATAACATAACTAA
66 TCAGTCAATGGTACATAACATAACTAA
* *
17975975 GGTACATGTGGTACAGTGCAATGCGGTAATCTGCTATACCGATAGATTGCAATAAAACTGTCAGT
1 CGTACATGTGGTACAGTGCAATGCGGTAATCTGCTATACCGATAGATTGCAATAAAACTGCCAGT
* * * *
17976040 TCAGTCAATGGTACGTAGCGTAGCTAA
66 TCAGTCAATGGTACATAACATAACTAA
* * *
17976067 CGTATATGCGGTACAGTGCAATGCGGTAATCTGCTATACTGATA
1 CGTACATGTGGTACAGTGCAATGCGGTAATCTGCTATACCGATA
17976111 TGATGTCATC
Statistics
Matches: 121, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 121 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.29
Consensus pattern (92 bp):
CGTACATGTGGTACAGTGCAATGCGGTAATCTGCTATACCGATAGATTGCAATAAAACTGCCAGT
TCAGTCAATGGTACATAACATAACTAA
Found at i:17978780 original size:75 final size:75
Alignment explanation
Indices: 17978675--17978855 Score: 267
Period size: 75 Copynumber: 2.4 Consensus size: 75
17978665 CTATATATAT
* * * *
17978675 TAGCACTTAGTGTGCAAGTT-CATTGATTTGGTTTCGGGCCATGATATTAATGATTTGGGTTTGG
1 TAGCACTTAGTGTGCGAGTTACATTGATTTGGGTTCGGGCCATGATATCAATGATTTGGGTTCGG
17978739 GCCATGATAA
66 GCCATGATAA
*
17978749 TAGTACTTAGTGTGCGAGTTACATTGATTTGGGTTCGGGCCATGATATCAATGATTTGGGTTCGG
1 TAGCACTTAGTGTGCGAGTTACATTGATTTGGGTTCGGGCCATGATATCAATGATTTGGGTTCGG
*
17978814 GCCATGATAG
66 GCCATGATAA
* *
17978824 TAGCACTTTG-GTTACGAGTTACATTGATTTGG
1 TAGCACTTAGTG-TGCGAGTTACATTGATTTGG
17978856 CTTCAGGTAA
Statistics
Matches: 96, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
74 19 0.20
75 77 0.80
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (75 bp):
TAGCACTTAGTGTGCGAGTTACATTGATTTGGGTTCGGGCCATGATATCAATGATTTGGGTTCGG
GCCATGATAA
Found at i:17978834 original size:27 final size:26
Alignment explanation
Indices: 17978698--17978822 Score: 98
Period size: 27 Copynumber: 4.9 Consensus size: 26
17978688 GCAAGTTCAT
*
17978698 TGATTTGGTTTCGGGCCATGATATTAA
1 TGATTTGGGTTCGGGCCATGATA-TAA
* *
17978725 TGATTTGGGTTTGGGCCATGATAATAG
1 TGATTTGGGTTCGGGCCATGAT-ATAA
* * * * * * *
17978752 T-ACTT-AG-T-GTGCGA-GTTACAT
1 TGATTTGGGTTCGGGCCATGATATAA
17978773 TGATTTGGGTTCGGGCCATGATATCAA
1 TGATTTGGGTTCGGGCCATGATAT-AA
17978800 TGATTTGGGTTCGGGCCATGATA
1 TGATTTGGGTTCGGGCCATGATA
17978823 GTAGCACTTT
Statistics
Matches: 74, Mismatches: 17, Indels: 14
0.70 0.16 0.13
Matches are distributed among these distances:
21 3 0.04
22 5 0.07
23 5 0.07
24 2 0.03
25 5 0.07
26 6 0.08
27 47 0.64
28 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.30, T:0.37
Consensus pattern (26 bp):
TGATTTGGGTTCGGGCCATGATATAA
Found at i:17980574 original size:30 final size:30
Alignment explanation
Indices: 17980540--17980597 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
17980530 CTAACCACGA
*
17980540 TGAACAACATTTGATTTTTGTGTTTTACGG
1 TGAACAACATTTGATTTGTGTGTTTTACGG
17980570 TGAACAACATTTGATTTGTGTGTTTTAC
1 TGAACAACATTTGATTTGTGTGTTTTAC
17980598 TCATCCATGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (30 bp):
TGAACAACATTTGATTTGTGTGTTTTACGG
Found at i:17981304 original size:46 final size:46
Alignment explanation
Indices: 17981201--17981375 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
17981191 TTTACTCGTA
* * *
17981201 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TGCATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CGTCTCAAT
**
17981247 GTTGATGCATGTCCCAGACATGTCTTACACT-GCTCTCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTCTCAAT
* *
17981292 GCCGATGCCATGTCCCA-AAATTGGTCTTACACTGGCTCTCG--TAATAT
1 GCCGATG-CATGTCCCAGACA-T-GTCTTACACTGGCTCTCGTCTCA-AT
* *
17981339 GACCGATGCATGTCCCAGACATATCTTACACTAGCTC
1 G-CCGATGCATGTCCCAGACATGTCTTACACTGGCTC
17981376 ACAATAATCC
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
45 16 0.15
46 55 0.50
47 23 0.21
48 15 0.14
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCGTCTCAAT
Found at i:17984368 original size:40 final size:40
Alignment explanation
Indices: 17984313--17984394 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
17984303 TGGCTAAATT
* *
17984313 ACGTAATGATATCTCTTCTTTTGTGCAGATGGATTTAGAA
1 ACGTAACGATATCTCTTATTTTGTGCAGATGGATTTAGAA
17984353 ACGTAACGATATCTCTTATTTTGTGCAGATGGATTTAGAA
1 ACGTAACGATATCTCTTATTTTGTGCAGATGGATTTAGAA
17984393 AC
1 AC
17984395 ACTCTACGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.20, T:0.38
Consensus pattern (40 bp):
ACGTAACGATATCTCTTATTTTGTGCAGATGGATTTAGAA
Found at i:17985609 original size:31 final size:31
Alignment explanation
Indices: 17985571--17985632 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
17985561 AAGATCTAGG
17985571 AAGTTTTACGATTCCTTGTTTTATTGGTAGC
1 AAGTTTTACGATTCCTTGTTTTATTGGTAGC
17985602 AAGTTTTACGATTCCTTGTTTTATTGGTAGC
1 AAGTTTTACGATTCCTTGTTTTATTGGTAGC
17985633 TTAGATGTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (31 bp):
AAGTTTTACGATTCCTTGTTTTATTGGTAGC
Found at i:17996192 original size:46 final size:44
Alignment explanation
Indices: 17996095--17996307 Score: 157
Period size: 46 Copynumber: 4.6 Consensus size: 44
17996085 ATGCCTACGT
* * *
17996095 CATGTCCCGGACATGGTCTTACACTAGCTTTACTTGTAGCTGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTTCACTCGTAGCTGATG
*
17996140 CATGTCCCAGACATGTCTTACACTGGCTTGCATCTCG-AGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-CA-CTCGTA-GCTGATG
* * *
17996186 CATGTCCCAAACATGTCTTACACTAGCTCTCGTCTC-AATG-TCGATG
1 CATGTCCCAGACATGTCTTACACTAGCT-TC-ACTCGTA-GCT-GATG
* * * *
17996232 CCATGTCCC-GAACATGGTCTTACAGTAGCTCTCGTAAT-GTGGCCGATG
1 -CATGTCCCAG-ACAT-GTCTTACACTAGCT-TC--ACTCGTAGCTGATG
*
17996280 CATGTCCTAGACATGTCTTACACTAGCT
1 CATGTCCCAGACATGTCTTACACTAGCT
17996308 CAAATAATCC
Statistics
Matches: 136, Mismatches: 18, Indels: 27
0.75 0.10 0.15
Matches are distributed among these distances:
44 14 0.10
45 16 0.12
46 59 0.43
47 24 0.18
48 22 0.16
49 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (44 bp):
CATGTCCCAGACATGTCTTACACTAGCTTCACTCGTAGCTGATG
Found at i:17999869 original size:40 final size:40
Alignment explanation
Indices: 17999832--18000015 Score: 189
Period size: 40 Copynumber: 4.6 Consensus size: 40
17999822 GCTACTCGTT
*
17999832 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
17999872 CAATTGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* * *
17999912 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
** * * * *
17999951 CAAATGCCTTC-GGATCTTAGTTCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
17999992 CAAA-GCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
18000016 ACATCATTCA
Statistics
Matches: 118, Mismatches: 18, Indels: 16
0.78 0.12 0.11
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 72 0.61
41 14 0.12
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:17999977 original size:79 final size:81
Alignment explanation
Indices: 17999834--18000016 Score: 205
Period size: 79 Copynumber: 2.3 Consensus size: 81
17999824 TACTCGTTCA
* * *
17999834 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGACTTAACCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
* *
17999898 TTTAGTAAC-TCGCACC
66 TATAGTAACTTAGCA-C
* ***
17999914 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTTCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
* *
17999976 ATATGGTCACTTAGCAC
65 ATATAGTAACTTAGCAC
*
17999993 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
18000017 CATCATTCAA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
78 3 0.03
79 56 0.64
80 28 0.32
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:18013029 original size:29 final size:27
Alignment explanation
Indices: 18012971--18013029 Score: 73
Period size: 29 Copynumber: 2.1 Consensus size: 27
18012961 AATCTCACCT
*
18012971 AAAAAAAAAAAAGAAAACCTAATCTAA
1 AAAAAAAAAAAAGAAAACCTAACCTAA
*
18012998 AAAAGAAAAGAAAAGAAAACCTGACCCTAA
1 AAAA-AAAA-AAAAGAAAACCT-AACCTAA
18013028 AA
1 AA
18013030 CTATGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 4 0.15
28 4 0.15
29 12 0.44
30 7 0.26
ACGTcount: A:0.69, C:0.14, G:0.08, T:0.08
Consensus pattern (27 bp):
AAAAAAAAAAAAGAAAACCTAACCTAA
Found at i:18013809 original size:40 final size:40
Alignment explanation
Indices: 18013754--18013833 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
18013744 AAAAAATATC
18013754 GAATTATTTAGATTACTAATCAAGTTGATGAGAGATTTAA
1 GAATTATTTAGATTACTAATCAAGTTGATGAGAGATTTAA
18013794 GAATTATTTAGATTACTAATCAAGTTGATGAGAGATTTAA
1 GAATTATTTAGATTACTAATCAAGTTGATGAGAGATTTAA
18013834 CATGTCATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (40 bp):
GAATTATTTAGATTACTAATCAAGTTGATGAGAGATTTAA
Found at i:18017232 original size:49 final size:49
Alignment explanation
Indices: 18017155--18017278 Score: 162
Period size: 49 Copynumber: 2.5 Consensus size: 49
18017145 ATACTAACGC
*
18017155 CATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGTGAG-GTCGATG-
1 CATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGTG-GTGTCGATGT
* * * *
18017204 CTATGTCCTAGACAGGTCTTACATTGGCTCTCATCTATTGGTGTCGATGT
1 C-ATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGTGGTGTCGATGT
18017254 CATGTCCCAGACAGGTCTTACACTG
1 CATGTCCCAGACAGGTCTTACACTG
18017279 ACACACAACA
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
48 1 0.02
49 52 0.80
50 12 0.18
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (49 bp):
CATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGTGGTGTCGATGT
Found at i:18017369 original size:48 final size:47
Alignment explanation
Indices: 18017298--18017511 Score: 193
Period size: 46 Copynumber: 4.6 Consensus size: 47
18017288 AAGCTAACAC
* * *
18017298 CATGTCCCAGACAGGTCTTACACTAGCTTGCCTATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-CATATCTCGAGGCTGATG
* * * * * *
18017346 CATGTCCCAGGCATGTCTTACACTAGC-TC-TCGTCTCAACGCTTATT
1 CATGTCCCAGACATGTCTTACACTAGCTTCAT-ATCTCGAGGCTGATG
* * * *
18017392 CATGTCCCAAACATGTCTTACTCTGGCTTAAATATCTCGAGGCTGATG
1 CATGTCCCAGACATGTCTTACACTAGCTT-CATATCTCGAGGCTGATG
* * * * *
18017440 CATGTCCTAGACATGTCTTTCACTGGCTTTCATAT-T-GTGGCTGATT
1 CATGTCCCAGACATGTCTTACACTAGC-TTCATATCTCGAGGCTGATG
*
18017486 CATGTCCCAGACATGTTTTACACTAG
1 CATGTCCCAGACATGTCTTACACTAG
18017512 TACACATATC
Statistics
Matches: 132, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
45 1 0.01
46 63 0.48
47 3 0.02
48 62 0.47
49 3 0.02
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTTCATATCTCGAGGCTGATG
Done.