Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397266.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_20.0, whole genome shotgun sequence
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: 7441454
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 92215 characters in sequence are not A, C, G, or T
File 13 of 18
Found at i:5324638 original size:16 final size:16
Alignment explanation
Indices: 5324618--5324682 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 16
5324608 ATTAATAATA
5324618 AAAAATATAAATATATT
1 AAAAATA-AAATATATT
5324635 AAAAATAAAATATA-T
1 AAAAATAAAATATATT
* *
5324650 AAGATTATAATAATA-AAT
1 AA-A-AATAA-AATATATT
5324668 AAAAATAAAATATAT
1 AAAAATAAAATATAT
5324683 GACATTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
15 7 0.17
16 13 0.32
17 13 0.32
18 7 0.17
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (16 bp):
AAAAATAAAATATATT
Found at i:5324652 original size:114 final size:114
Alignment explanation
Indices: 5324520--5324751 Score: 437
Period size: 114 Copynumber: 2.0 Consensus size: 114
5324510 ATTAAAGAAA
5324520 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
5324585 TTAAGACATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
66 TTAAGACATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
5324634 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
1 TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
* * *
5324699 TTAAGAGATGGTATTATATAAAAATTAATAGTAAAAAATATAAATATAT
66 TTAAGACATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
5324748 TAAA
1 TAAA
5324752 CTTATATTTT
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.32
Consensus pattern (114 bp):
TAAAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATAT
TTAAGACATGATATTATATAAAAATTAATAATAAAAAATATAAATATAT
Found at i:5332176 original size:21 final size:20
Alignment explanation
Indices: 5332142--5332183 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
5332132 TAATTTAAAA
5332142 TAAAATAACATAAAATTTAAC
1 TAAAATAACAT-AAATTTAAC
**
5332163 TAAAATAATTTAAA-TTAAC
1 TAAAATAACATAAATTTAAC
5332182 TA
1 TA
5332184 TTCAATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.37
20 3 0.16
21 9 0.47
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (20 bp):
TAAAATAACATAAATTTAAC
Found at i:5333593 original size:167 final size:166
Alignment explanation
Indices: 5333301--5333787 Score: 571
Period size: 167 Copynumber: 2.9 Consensus size: 166
5333291 GGCTTAGATG
* * * * *
5333301 GCAAATTCACAGATTGTTTGATAAATTTGGCTTTTCACAGTCCAAATCAGGGCTACTCATTATTT
1 GCAAATTCATAGAATGTTT-ATAAATTTGGCTTTTCATAGTCCAAATCA-AGCTACTCACTATTT
** * * *
5333366 ACAAAAAGTGCTAAAGATAGAGATTTTGTTGCTTTACTTGTATATATTGATGATATAGTCATAAC
64 ACAAAAAGAACTAAAGATGGAGATTTTGTTGCTTTACTTGTATATATTGATGACATAGTCATAGC
* *
5333431 TTAGCTTAGATGAGTCATTGCCTCTAAATAGTAGAATT
129 TTAGCTTAGATGAGTCATTGCCTCCAAACAGTAGAATT
* * * * *
5333469 GCAAATTCATAGAATGTTTAAAAAATTTGGCTTTTCGTAGTCTAAATCAAGTTGCTCACTATTTA
1 GCAAATTCATAGAATGTTT-ATAAATTTGGCTTTTCATAGTCCAAATCAAGCTACTCACTATTTA
* * * * *
5333534 CAAAAAGCACTAAAGATGGAGGTTTTGTTGCTTTACTTGTATATGTTAATGACATAGTCATAGCA
65 CAAAAAGAACTAAAGATGGAGATTTTGTTGCTTTACTTGTATATATTGATGACATAGTCATAGCT
* * *
5333599 TAGCTTAGATGAGTCATTTCTTCCAAACAGTGGAATT
130 TAGCTTAGATGAGTCATTGCCTCCAAACAGTAGAATT
* * * * * *
5333636 GTAAATTCATAAAATCCTTTATAGATTAGGCTTTTAATAGTCCAAAGT-AAGCTACTCACTATTT
1 GCAAATTCATAGAAT-GTTTATAAATTTGGCTTTTCATAGTCCAAA-TCAAGCTACTCACTATTT
* * * *
5333700 ACAAAAAGAACTAAGGATGGAAATTTTGTTGCTTTACTTGTATATATTGATGACAGAATCATAGC
64 ACAAAAAGAACTAAAGATGGAGATTTTGTTGCTTTACTTGTATATATTGATGACATAGTCATAGC
5333765 TTAATCAGCTTAGATGAGTCATT
129 -T--T-AGCTTAGATGAGTCATT
5333788 AACTGATAAT
Statistics
Matches: 268, Mismatches: 45, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
167 204 0.76
168 46 0.17
170 1 0.00
171 17 0.06
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (166 bp):
GCAAATTCATAGAATGTTTATAAATTTGGCTTTTCATAGTCCAAATCAAGCTACTCACTATTTAC
AAAAAGAACTAAAGATGGAGATTTTGTTGCTTTACTTGTATATATTGATGACATAGTCATAGCTT
AGCTTAGATGAGTCATTGCCTCCAAACAGTAGAATT
Found at i:5344691 original size:20 final size:20
Alignment explanation
Indices: 5344666--5344717 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
5344656 ATGAACAATG
5344666 ATCAATAGATGAGCCTATCT
1 ATCAATAGATGAGCCTATCT
5344686 ATCAATAGATGAGCCTATCT
1 ATCAATAGATGAGCCTATCT
5344706 ATCAATAGATGA
1 ATCAATAGATGA
5344718 ATATCTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (20 bp):
ATCAATAGATGAGCCTATCT
Found at i:5345510 original size:11 final size:11
Alignment explanation
Indices: 5345480--5345522 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 11
5345470 AAAGAAAAAT
5345480 AAAAAATCACAA
1 AAAAAAT-ACAA
5345492 CCAAAAAATACAA
1 --AAAAAATACAA
5345505 AAAAAATACCAA
1 AAAAAATA-CAA
5345517 AAAAAA
1 AAAAAA
5345523 AAATGGGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.29
12 9 0.32
13 4 0.14
14 7 0.25
ACGTcount: A:0.77, C:0.16, G:0.00, T:0.07
Consensus pattern (11 bp):
AAAAAATACAA
Found at i:5346891 original size:10 final size:10
Alignment explanation
Indices: 5346865--5346901 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
5346855 AGCTCTAAAA
5346865 AATAAATAAT
1 AATAAATAAT
5346875 AAT-AATAAT
1 AATAAATAAT
*
5346884 AATAAATAGT
1 AATAAATAAT
5346894 AATAAATA
1 AATAAATA
5346902 TAAGAACGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (10 bp):
AATAAATAAT
Found at i:5347885 original size:13 final size:14
Alignment explanation
Indices: 5347867--5347901 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
5347857 ATATATTTCT
5347867 AATAATTTTTTA-A
1 AATAATTTTTTATA
5347880 AATAATTTTTTATTA
1 AATAATTTTTTA-TA
5347895 AATAATT
1 AATAATT
5347902 AATATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 12 0.60
15 8 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATAATTTTTTATA
Found at i:5348249 original size:15 final size:16
Alignment explanation
Indices: 5348229--5348258 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5348219 CTGTTATGTG
5348229 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
5348244 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
5348259 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:5356413 original size:74 final size:74
Alignment explanation
Indices: 5356292--5356453 Score: 279
Period size: 74 Copynumber: 2.2 Consensus size: 74
5356282 GTCAACAATG
*
5356292 AAGAACCGACACCTTGAGGCAAAAGAATTAATTATCCAAGATTGCAAAGGTATCACCTTTATGTC
1 AAGAACCGACACCTTGAGGAAAAAGAATTAATTATCCAAGATTGCAAAGGTATCACCTTTATGTC
*
5356357 TAATTGCAA
66 CAATTGCAA
* * *
5356366 AAGAACCGACACCTTGAGGAAAAAGAATTGATTCTCTAAGATTGCAAAGGTATCACCTTTATGTC
1 AAGAACCGACACCTTGAGGAAAAAGAATTAATTATCCAAGATTGCAAAGGTATCACCTTTATGTC
5356431 CAATTGCAA
66 CAATTGCAA
5356440 AAGAACCGACACCT
1 AAGAACCGACACCT
5356454 CATAAAAGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
74 83 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (74 bp):
AAGAACCGACACCTTGAGGAAAAAGAATTAATTATCCAAGATTGCAAAGGTATCACCTTTATGTC
CAATTGCAA
Found at i:5356474 original size:74 final size:74
Alignment explanation
Indices: 5356292--5356474 Score: 251
Period size: 74 Copynumber: 2.5 Consensus size: 74
5356282 GTCAACAATG
* ** *
5356292 AAGAACCGACACCTTGAGGCAAAAGAATTAATTATCCAAGATTGCAAAGGTATCACCTTTATGTC
1 AAGAACCGACACCTTCAGAAAAAAGAATTAATTCTCCAAGATTGCAAAGGTATCACCTTTATGTC
*
5356357 TAATTGCAA
66 CAATTGCAA
* * * *
5356366 AAGAACCGACACCTTGAGGAAAAAGAATTGATTCTCTAAGATTGCAAAGGTATCACCTTTATGTC
1 AAGAACCGACACCTTCAGAAAAAAGAATTAATTCTCCAAGATTGCAAAGGTATCACCTTTATGTC
5356431 CAATTGCAA
66 CAATTGCAA
* *
5356440 AAGAACCGACACC-TCATAAAAGAAGCATTAATTCT
1 AAGAACCGACACCTTCAGAAAA-AAGAATTAATTCT
5356475 TCAAACTTAA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
73 5 0.05
74 93 0.95
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.25
Consensus pattern (74 bp):
AAGAACCGACACCTTCAGAAAAAAGAATTAATTCTCCAAGATTGCAAAGGTATCACCTTTATGTC
CAATTGCAA
Found at i:5358968 original size:29 final size:28
Alignment explanation
Indices: 5358919--5359035 Score: 135
Period size: 28 Copynumber: 4.1 Consensus size: 28
5358909 GCATAACCCC
** **
5358919 TTGCCTTTTCAAGGGCCAGGTAAAACCTT
1 TTGCC-TTTCAAGGATCAGGTGTAACCTT
*
5358948 TTGCCTTTTCAAGGATTAGGTGTAACCTT
1 TTGCC-TTTCAAGGATCAGGTGTAACCTT
* *
5358977 TTACCTTTCAAGGATCAGGGGTAACCTT
1 TTGCCTTTCAAGGATCAGGTGTAACCTT
* *
5359005 TTGCCTTTCAAGGATTAGGCGTAACCTT
1 TTGCCTTTCAAGGATCAGGTGTAACCTT
5359033 TTG
1 TTG
5359036 ACAACATTTC
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
28 49 0.64
29 28 0.36
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (28 bp):
TTGCCTTTCAAGGATCAGGTGTAACCTT
Found at i:5359000 original size:28 final size:28
Alignment explanation
Indices: 5358942--5359035 Score: 143
Period size: 28 Copynumber: 3.3 Consensus size: 28
5358932 GGCCAGGTAA
*
5358942 AACCTTTTGCCTTTTCAAGGATTAGGTGT
1 AACCTTTTGCC-TTTCAAGGATTAGGCGT
* * *
5358971 AACCTTTTACCTTTCAAGGATCAGGGGT
1 AACCTTTTGCCTTTCAAGGATTAGGCGT
5358999 AACCTTTTGCCTTTCAAGGATTAGGCGT
1 AACCTTTTGCCTTTCAAGGATTAGGCGT
5359027 AACCTTTTG
1 AACCTTTTG
5359036 ACAACATTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
28 49 0.83
29 10 0.17
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.37
Consensus pattern (28 bp):
AACCTTTTGCCTTTCAAGGATTAGGCGT
Found at i:5359904 original size:18 final size:18
Alignment explanation
Indices: 5359881--5359916 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5359871 TCAAAAGCAA
5359881 TCAAGAATCACTCAAGCT
1 TCAAGAATCACTCAAGCT
*
5359899 TCAAGAATTACTCAAGCT
1 TCAAGAATCACTCAAGCT
5359917 ATTCTAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.11, T:0.25
Consensus pattern (18 bp):
TCAAGAATCACTCAAGCT
Found at i:5364124 original size:31 final size:31
Alignment explanation
Indices: 5364089--5364150 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
5364079 GAAATAATTG
* * **
5364089 CCAAATCCAAGGACCAAAGTTTAAACAAATA
1 CCAAAACCAAAGACCAAAGTCAAAACAAATA
*
5364120 CCAAAACCAAAGTCCAAAGTCAAAACAAATA
1 CCAAAACCAAAGACCAAAGTCAAAACAAATA
5364151 TTGAATCCCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.55, C:0.24, G:0.08, T:0.13
Consensus pattern (31 bp):
CCAAAACCAAAGACCAAAGTCAAAACAAATA
Found at i:5369381 original size:2 final size:2
Alignment explanation
Indices: 5369374--5369402 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5369364 CTATTTATCG
5369374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5369403 GATTTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5371199 original size:10 final size:10
Alignment explanation
Indices: 5371172--5371288 Score: 62
Period size: 10 Copynumber: 11.9 Consensus size: 10
5371162 ATTCAAGTTT
5371172 TATATA-ATA
1 TATATATATA
5371181 TA-ATATATA
1 TATATATATA
* *
5371190 TGTATGTATA
1 TATATATATA
5371200 TATATATATA
1 TATATATATA
*
5371210 TATATTTATA
1 TATATATATA
*
5371220 TACT-TATCAGA
1 TA-TATAT-ATA
* * *
5371231 CATGTATTTA
1 TATATATATA
*
5371241 TATACATAT-
1 TATATATATA
* *
5371250 TATACATGTA
1 TATATATATA
*
5371260 CATATATATA
1 TATATATATA
* *
5371270 TACATATACA
1 TATATATATA
*
5371280 TACATATAT
1 TATATATAT
5371289 GCATGTATCA
Statistics
Matches: 80, Mismatches: 22, Indels: 11
0.71 0.19 0.10
Matches are distributed among these distances:
8 3 0.04
9 14 0.17
10 56 0.70
11 7 0.09
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (10 bp):
TATATATATA
Found at i:5371203 original size:4 final size:4
Alignment explanation
Indices: 5371172--5371288 Score: 62
Period size: 4 Copynumber: 29.8 Consensus size: 4
5371162 ATTCAAGTTT
* * *
5371172 TATA TA-A TATA -ATA TATA TGTA TGTA TATA TATA TATA TATA TTTA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * * *
5371218 TATA CT-TA TCAGA CATG TATT TATA TACA TAT- TATA CATG TACA TATA
1 TATA -TATA T-ATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * *
5371266 TATA TACA TATA CATA CATA TAT
1 TATA TATA TATA TATA TATA TAT
5371289 GCATGTATCA
Statistics
Matches: 84, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
3 10 0.12
4 72 0.86
5 2 0.02
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (4 bp):
TATA
Found at i:5371207 original size:6 final size:6
Alignment explanation
Indices: 5371172--5371288 Score: 62
Period size: 6 Copynumber: 19.8 Consensus size: 6
5371162 ATTCAAGTTT
* * *
5371172 TATATA -ATATA -ATATA TATGTA TGTATA TATATA TATATA TATTTA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * * * * *
5371218 TATACT- TATCAGA CATGTA TTTATA TACATA T-TATA CATGTA CATATA
1 TATA-TA TAT-ATA TATATA TATATA TATATA TATATA TATATA TATATA
* * *
5371266 TATATA CATATA CATACA TATAT
1 TATATA TATATA TATATA TATAT
5371289 GCATGTATCA
Statistics
Matches: 82, Mismatches: 24, Indels: 10
0.71 0.21 0.09
Matches are distributed among these distances:
5 13 0.16
6 65 0.79
7 4 0.05
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (6 bp):
TATATA
Found at i:5371240 original size:23 final size:23
Alignment explanation
Indices: 5371212--5371259 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
5371202 TATATATATA
*
5371212 TATTTATATACTTATCAGACATG
1 TATTTATATACATATCAGACATG
* *
5371235 TATTTATATACATATTATACATG
1 TATTTATATACATATCAGACATG
5371258 TA
1 TA
5371260 CATATATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (23 bp):
TATTTATATACATATCAGACATG
Found at i:5371265 original size:23 final size:23
Alignment explanation
Indices: 5371216--5371288 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
5371206 TATATATATT
* * * **
5371216 TATATACTTATCAGACATGTATT
1 TATATACATATTATACATGTACA
5371239 TATATACATATTATACATGTACA
1 TATATACATATTATACATGTACA
* *
5371262 TATATATATACATATACA--TACA
1 TATATACATA-TTATACATGTACA
5371284 TATAT
1 TATAT
5371289 GCATGTATCA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 9 0.21
23 27 0.64
24 6 0.14
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.41
Consensus pattern (23 bp):
TATATACATATTATACATGTACA
Found at i:5371273 original size:18 final size:18
Alignment explanation
Indices: 5371246--5371295 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
5371236 ATTTATATAC
5371246 ATAT-TATACATGTACAT
1 ATATATATACATGTACAT
*
5371263 ATATATATACATATACAT
1 ATATATATACATGTACAT
* *
5371281 ACATATATGCATGTA
1 ATATATATACATGTA
5371296 TCAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
ATATATATACATGTACAT
Found at i:5376911 original size:16 final size:16
Alignment explanation
Indices: 5376890--5376922 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5376880 TCAACCATTT
5376890 GAAATGTGGAAAATCC
1 GAAATGTGGAAAATCC
5376906 GAAATGTGGAAAATCC
1 GAAATGTGGAAAATCC
5376922 G
1 G
5376923 TAAAACAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.18
Consensus pattern (16 bp):
GAAATGTGGAAAATCC
Found at i:5378507 original size:21 final size:23
Alignment explanation
Indices: 5378483--5378525 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
5378473 TACCAGTTTC
5378483 ATCGATCAA-TCAA-GTCTAATA
1 ATCGATCAACTCAAGGTCTAATA
*
5378504 ATCGATTAACTCAAGGTCTAAT
1 ATCGATCAACTCAAGGTCTAAT
5378526 CGATTAAGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.30
Consensus pattern (23 bp):
ATCGATCAACTCAAGGTCTAATA
Found at i:5385028 original size:2 final size:2
Alignment explanation
Indices: 5385021--5385046 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5385011 AACATAAGCA
5385021 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5385047 CAAATATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5414519 original size:18 final size:18
Alignment explanation
Indices: 5414496--5414534 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5414486 TTTTTTAAAA
5414496 TTTTAT-TTTATCATATTT
1 TTTTATATTTAT-ATATTT
*
5414514 TTTTATATTTATATCTTT
1 TTTTATATTTATATATTT
5414532 TTT
1 TTT
5414535 AAAATTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTATATTTATATATTT
Found at i:5424801 original size:13 final size:14
Alignment explanation
Indices: 5424767--5424809 Score: 61
Period size: 13 Copynumber: 3.1 Consensus size: 14
5424757 TTTAAACCTA
*
5424767 ATCTATCCATAGAT
1 ATCTATCGATAGAT
5424781 GATCTATCGATAGAT
1 -ATCTATCGATAGAT
5424796 -TCTATCGATAGAT
1 ATCTATCGATAGAT
5424809 A
1 A
5424810 CAATCTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 13 0.50
15 13 0.50
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (14 bp):
ATCTATCGATAGAT
Found at i:5433051 original size:21 final size:21
Alignment explanation
Indices: 5433022--5433069 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
5433012 GACATTTACC
*
5433022 AAAAA-CAAGCCAACAAGTAA
1 AAAAAGCAAGCCAACAAGCAA
*
5433042 AAAAAGCAAGCCAACAAGCAC
1 AAAAAGCAAGCCAACAAGCAA
5433063 AAAAAGC
1 AAAAAGC
5433070 GAGCTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.62, C:0.23, G:0.12, T:0.02
Consensus pattern (21 bp):
AAAAAGCAAGCCAACAAGCAA
Found at i:5448909 original size:47 final size:46
Alignment explanation
Indices: 5448823--5448918 Score: 113
Period size: 47 Copynumber: 2.1 Consensus size: 46
5448813 TTACTTTTAT
* * *
5448823 AAAAAACAAAATTATCCTTATTATAATTTAAAAGTATATTTATCTC
1 AAAAAACAAAATTATCCTAATTATAATTTAAAAGCATATTTATCCC
* **
5448869 AAAAAACAAAATTATCCATAATTGTAATTTGATCA-CATATTTATCCC
1 AAAAAACAAAATTATCC-TAATTATAATTT-AAAAGCATATTTATCCC
5448916 AAA
1 AAA
5448919 TGCTTAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
46 17 0.40
47 23 0.55
48 2 0.05
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (46 bp):
AAAAAACAAAATTATCCTAATTATAATTTAAAAGCATATTTATCCC
Found at i:5449144 original size:24 final size:23
Alignment explanation
Indices: 5449107--5449152 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
5449097 AAATACCGGA
*
5449107 GAAAAAATATTAGAGAA-AAAAAT
1 GAAAAAATAGTAGA-AATAAAAAT
5449130 GAAAAAACTAGTAGAAATAAAAA
1 GAAAAAA-TAGTAGAAATAAAAA
5449153 CTGAGAATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.70, C:0.02, G:0.13, T:0.15
Consensus pattern (23 bp):
GAAAAAATAGTAGAAATAAAAAT
Found at i:5463442 original size:31 final size:31
Alignment explanation
Indices: 5463401--5463572 Score: 111
Period size: 31 Copynumber: 5.5 Consensus size: 31
5463391 CCTTTCTTGA
* *
5463401 AGAGGAATAACCTTATACTACCTTTTGCAAT
1 AGAGGTATAACCTTATACTACCTTTTACAAT
*
5463432 AGAGGTATAA-CTGT-TCATTACCTTTTACAAT
1 AGAGGTATAACCT-TAT-ACTACCTTTTACAAT
* * * *
5463463 GGACGTATAGACAC--ACACTACCTTTTACACT
1 AGAGGTATA-AC-CTTATACTACCTTTTACAAT
* * * *
5463494 AGAAGTCTAACCTTTATGC-ACCTTTTATAAT
1 AGAGGTATAACC-TTATACTACCTTTTACAAT
* * * * * *
5463525 GGAGGTGTAACCTTACATTACCTTTTGCAAC
1 AGAGGTATAACCTTATACTACCTTTTACAAT
5463556 AGAGGTATAACCTTATA
1 AGAGGTATAACCTTATA
5463573 ATAGTGGATT
Statistics
Matches: 104, Mismatches: 27, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
29 1 0.01
30 8 0.08
31 91 0.88
32 3 0.03
34 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (31 bp):
AGAGGTATAACCTTATACTACCTTTTACAAT
Found at i:5463488 original size:62 final size:60
Alignment explanation
Indices: 5463407--5463571 Score: 145
Period size: 62 Copynumber: 2.7 Consensus size: 60
5463397 TTGAAGAGGA
* *
5463407 ATAACCTTATACTACCTTTTGCAATAGAGGTATAACTGTTCAT-TACCTTTTACAATGGACGT
1 ATAACC-TACACTACCTTTTGCAATAGAGGTATAACT-TT-ATGCACCTTTTACAATGGACGT
* * * * * *
5463469 ATAGACAC-ACACTACCTTTTACACTAGAAGTCTAACCTTTATGCACCTTTTATAATGGAGGT
1 ATA-AC-CTACACTACCTTTTGCAATAGAGGTATAA-CTTTATGCACCTTTTACAATGGACGT
* * * *
5463531 GTAACCTTACATTACCTTTTGCAACAGAGGTATAACCTTAT
1 ATAACC-TACACTACCTTTTGCAATAGAGGTATAACTTTAT
5463572 AATAGTGGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 13
0.74 0.15 0.12
Matches are distributed among these distances:
60 1 0.01
61 9 0.11
62 66 0.81
63 4 0.05
64 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.35
Consensus pattern (60 bp):
ATAACCTACACTACCTTTTGCAATAGAGGTATAACTTTATGCACCTTTTACAATGGACGT
Found at i:5464232 original size:143 final size:143
Alignment explanation
Indices: 5463984--5464311 Score: 485
Period size: 143 Copynumber: 2.3 Consensus size: 143
5463974 CTATTTGTTT
* * * * *
5463984 AGAATCAACCTTTCCATTCTTGAGATATCACTTTTTCTTCTCTCACATGAAGTATGGAGCTTCTA
1 AGAATCGATCTTTGCATTCTTGAGATATCA---ATTCTTCTCTCACATGAAGTATGAAGCTTCTA
* * * *
5464049 GTTTTTCGAGAATGGACCATTCCATGCTTGAGATATCGATTCTTTTTATCTCACTTCAAATTTAG
63 GTTTTTAGAGAATCGACCATTCCATCCTTGAGATATCGATTCTTCTTATCTCACTTCAAATTTAG
*
5464114 AGCTTTCTACTGTCTA
128 AGCTTTCTACTATCTA
* *
5464130 AGAATCGATCTTTGCATTCTTGAGATATCAATTCTTCTCTCACTTGAAGTATGAAGCTTTTAGTT
1 AGAATCGATCTTTGCATTCTTGAGATATCAATTCTTCTCTCACATGAAGTATGAAGCTTCTAGTT
* *
5464195 TTTAGAGAATCGACCATTCCATCCTTGAGATATCGATTCTTCTTATCTCATTTCAAATTTGGAGC
66 TTTAGAGAATCGACCATTCCATCCTTGAGATATCGATTCTTCTTATCTCACTTCAAATTTAGAGC
5464260 TTTCTACTATCTA
131 TTTCTACTATCTA
* *
5464273 AGAATCGATCTTTGCATTATTAAGATATCAATTCTTCTC
1 AGAATCGATCTTTGCATTCTTGAGATATCAATTCTTCTC
5464312 ATCCCACTTT
Statistics
Matches: 166, Mismatches: 16, Indels: 3
0.90 0.09 0.02
Matches are distributed among these distances:
143 139 0.84
146 27 0.16
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (143 bp):
AGAATCGATCTTTGCATTCTTGAGATATCAATTCTTCTCTCACATGAAGTATGAAGCTTCTAGTT
TTTAGAGAATCGACCATTCCATCCTTGAGATATCGATTCTTCTTATCTCACTTCAAATTTAGAGC
TTTCTACTATCTA
Found at i:5464299 original size:73 final size:73
Alignment explanation
Indices: 5464075--5464320 Score: 266
Period size: 73 Copynumber: 3.4 Consensus size: 73
5464065 CCATTCCATG
* * * *
5464075 CTTGAGATATCGATTCTTTTTATCTCACTTCAAATTTAGAGCTTTCTACTGTCTAAGAATCGATC
1 CTTGAGATATCAATTCTTCTTATCTCACTTCAAATTTGGAGCTTTCTACTATCTAAGAATCGATC
5464140 TTTGCATT
66 TTTGCATT
* * * * * * * *
5464148 CTTGAGATATCAATTCTTC---TCTCACTTGAAGTATGAAGCTTT-TAGTTTTTAGAGAATCGAC
1 CTTGAGATATCAATTCTTCTTATCTCACTTCAAATTTGGAGCTTTCTACTATCTA-AGAATCGAT
* * *
5464209 CATTCCATC
65 CTTTGCATT
* *
5464218 CTTGAGATATCGATTCTTCTTATCTCATTTCAAATTTGGAGCTTTCTACTATCTAAGAATCGATC
1 CTTGAGATATCAATTCTTCTTATCTCACTTCAAATTTGGAGCTTTCTACTATCTAAGAATCGATC
5464283 TTTGCATT
66 TTTGCATT
* * * *
5464291 ATTAAGATATCAATTCTTCTCATCCCACTT
1 CTTGAGATATCAATTCTTCTTATCTCACTT
5464321 TAAACTTAGT
Statistics
Matches: 135, Mismatches: 33, Indels: 10
0.76 0.19 0.06
Matches are distributed among these distances:
69 6 0.04
70 50 0.37
73 73 0.54
74 6 0.04
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (73 bp):
CTTGAGATATCAATTCTTCTTATCTCACTTCAAATTTGGAGCTTTCTACTATCTAAGAATCGATC
TTTGCATT
Found at i:5477261 original size:33 final size:33
Alignment explanation
Indices: 5477223--5477307 Score: 120
Period size: 33 Copynumber: 2.5 Consensus size: 33
5477213 TTTAATGTCA
*
5477223 TATATTTTATTTTCATTTC-TTATTATAATCTTT
1 TATATTTTATTTTCATTTCTTTAATATAAT-TTT
5477256 TATATTTTATTTTCATTTCTTTAATATAATTTT
1 TATATTTTATTTTCATTTCTTTAATATAATTTT
5477289 TATATTATATATTTT-ATTT
1 TATATT-T-TATTTTCATTT
5477308 TAATTTCTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
33 28 0.58
34 14 0.29
35 6 0.12
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (33 bp):
TATATTTTATTTTCATTTCTTTAATATAATTTT
Found at i:5477304 original size:26 final size:26
Alignment explanation
Indices: 5477275--5477327 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
5477265 TTTTCATTTC
5477275 TTTAATATAATTT-TTATATTATATAT
1 TTTAATATAATTTCTTATA-TATATAT
* * *
5477301 TTTATTTTAATTTCTTTTATATATAT
1 TTTAATATAATTTCTTATATATATAT
5477327 T
1 T
5477328 ACATAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTAATATAATTTCTTATATATATAT
Found at i:5477318 original size:15 final size:15
Alignment explanation
Indices: 5477300--5477369 Score: 52
Period size: 15 Copynumber: 4.7 Consensus size: 15
5477290 ATATTATATA
5477300 TTTTATTTTAATTTC
1 TTTTATTTTAATTTC
* *
5477315 TTTTA-TATATATTAC
1 TTTTATTTTA-ATTTC
* **
5477330 ATAAATTTTAATTTC
1 TTTTATTTTAATTTC
* * *
5477345 TTGTATTTTATTTTA
1 TTTTATTTTAATTTC
5477360 TTTTATTTTA
1 TTTTATTTTA
5477370 TTTATATTTT
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
14 3 0.08
15 34 0.85
16 3 0.08
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (15 bp):
TTTTATTTTAATTTC
Found at i:5477358 original size:5 final size:5
Alignment explanation
Indices: 5477334--5477406 Score: 71
Period size: 5 Copynumber: 15.0 Consensus size: 5
5477324 TATTACATAA
* * * *
5477334 ATTTT AATTT CTTGT ATTTT ATTTT ATTTT ATTTT A-TTT ATATT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
*
5477382 ATTTT ATTTT AATATT -TTTT ATTTT
1 ATTTT ATTTT -ATTTT ATTTT ATTTT
5477407 TATTATAATA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
4 10 0.19
5 40 0.74
6 4 0.07
ACGTcount: A:0.22, C:0.01, G:0.01, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:5477383 original size:23 final size:20
Alignment explanation
Indices: 5477360--5477418 Score: 86
Period size: 21 Copynumber: 3.0 Consensus size: 20
5477350 TTTTATTTTA
5477360 TTTTATTTTA-TTT-ATATT
1 TTTTATTTTATTTTAATATT
5477378 TTTTATTTTATTTTAATATT
1 TTTTATTTTATTTTAATATT
*
5477398 TTTTATTTTTATTATAATATT
1 TTTTA-TTTTATTTTAATATT
5477419 ACAAAATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
18 10 0.27
19 3 0.08
20 10 0.27
21 14 0.38
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTATTTTATTTTAATATT
Found at i:5477386 original size:33 final size:33
Alignment explanation
Indices: 5477348--5477410 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
5477338 TAATTTCTTG
*
5477348 TATTTTATTTT-ATTTTATTTTATTTATATTTTT
1 TATTTTATTTTAATATT-TTTTATTTATATTTTT
*
5477381 TATTTTATTTTAATATTTTTTATTTTTATT
1 TATTTTATTTTAATATTTTTTATTTATATT
5477411 ATAATATTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (33 bp):
TATTTTATTTTAATATTTTTTATTTATATTTTT
Found at i:5483721 original size:11 final size:11
Alignment explanation
Indices: 5483707--5483751 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
5483697 TATTTGCATA
5483707 TTATCTTTATT
1 TTATCTTTATT
*
5483718 TTATTTTTATTT
1 TTATCTTTA-TT
*
5483730 TTATTTTTATT
1 TTATCTTTATT
*
5483741 TTCTCTTTATT
1 TTATCTTTATT
5483752 AGGTTGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
TTATCTTTATT
Found at i:5483725 original size:6 final size:6
Alignment explanation
Indices: 5483707--5483742 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
5483697 TATTTGCATA
*
5483707 TTATCT TTA-TT TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT T
5483743 CTCTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 4 0.14
6 24 0.86
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:5483727 original size:17 final size:17
Alignment explanation
Indices: 5483693--5483751 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
5483683 GTGTAGACAC
** *
5483693 TCTTTATTTGCATATTA
1 TCTTTATTTTTATTTTA
5483710 TCTTTA-TTTTATTTTTA
1 TCTTTATTTTTA-TTTTA
* *
5483727 TTTTTATTTTTATTTTC
1 TCTTTATTTTTATTTTA
5483744 TCTTTATT
1 TCTTTATT
5483752 AGGTTGTTAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
16 3 0.09
17 26 0.76
18 5 0.15
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (17 bp):
TCTTTATTTTTATTTTA
Found at i:5484010 original size:14 final size:15
Alignment explanation
Indices: 5483978--5484015 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
5483968 CACTACATAC
*
5483978 ATACATGTATATCGT
1 ATACATGTACATCGT
5483993 ATACATGTACAT-GT
1 ATACATGTACATCGT
5484007 ATACATGTA
1 ATACATGTA
5484016 TATAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (15 bp):
ATACATGTACATCGT
Found at i:5485891 original size:36 final size:36
Alignment explanation
Indices: 5485841--5485960 Score: 150
Period size: 36 Copynumber: 3.3 Consensus size: 36
5485831 AAAAGGATTC
* *
5485841 TTACTTTTTAATGGGATTAAACAATAACCCTTACAT
1 TTACTTTTTAATGGGATCAAACGATAACCCTTACAT
* *
5485877 TTGCTTTTTAATGGGATCAAGCGATAACCCTTACAT
1 TTACTTTTTAATGGGATCAAACGATAACCCTTACAT
* * * *
5485913 TTACTTTGTCATGGGATCAAACGATGAACCTTTACAC
1 TTACTTTTTAATGGGATCAAACGAT-AACCCTTACAT
*
5485950 TAACTTTTTAA
1 TTACTTTTTAA
5485961 CAATATCAAG
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
36 53 0.76
37 17 0.24
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (36 bp):
TTACTTTTTAATGGGATCAAACGATAACCCTTACAT
Found at i:5487096 original size:74 final size:74
Alignment explanation
Indices: 5487011--5487188 Score: 203
Period size: 74 Copynumber: 2.4 Consensus size: 74
5487001 GAGTTAGTTG
* * * * * * *
5487011 ACTAAAAAGCATGGTTAGTCAACTAAGAGCTTACTACCAGAGACTTTAATTACAAGACAGAGAGA
1 ACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTACCAAAGAATTCAATTACAAGACAAAGAAA
5487076 ACTTAATCA
66 ACTTAATCA
* * * ** * *
5487085 ATTAAGAAGCATGGTTAGTTAACTAAGAGCTCATTGTCAAAGAATTCAATTTCAAGATAAAGAAA
1 ACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTACCAAAGAATTCAATTACAAGACAAAGAAA
*
5487150 ACTTAATCG
66 ACTTAATCA
* *
5487159 ACTAAGAAGTAAGGTTAGTCAACTAAGAGC
1 ACTAAGAAGCATGGTTAGTCAACTAAGAGC
5487189 ACTCTATTTG
Statistics
Matches: 85, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
74 85 1.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.25
Consensus pattern (74 bp):
ACTAAGAAGCATGGTTAGTCAACTAAGAGCTCACTACCAAAGAATTCAATTACAAGACAAAGAAA
ACTTAATCA
Found at i:5496182 original size:2 final size:2
Alignment explanation
Indices: 5496175--5496212 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5496165 AATCAACATT
5496175 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5496213 AAAAGCATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5500315 original size:26 final size:26
Alignment explanation
Indices: 5500276--5500354 Score: 104
Period size: 26 Copynumber: 3.0 Consensus size: 26
5500266 AAATCTAAGA
* *
5500276 ATAATTTTGTCACTTGAAGTGGATAG
1 ATAATTTTGCCACTAGAAGTGGATAG
*
5500302 ATAATTTTGCCACTAGAAGTGGATGG
1 ATAATTTTGCCACTAGAAGTGGATAG
* * *
5500328 ATAATTTTACCACAAGAAGTTGATAG
1 ATAATTTTGCCACTAGAAGTGGATAG
5500354 A
1 A
5500355 CACTTTAACC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.33
Consensus pattern (26 bp):
ATAATTTTGCCACTAGAAGTGGATAG
Found at i:5503830 original size:12 final size:11
Alignment explanation
Indices: 5503791--5503850 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 11
5503781 GACTCCTTCA
5503791 TTTTTTATCCTTT
1 TTTTTTAT--TTT
*
5503804 TTTGTTATTGTT
1 TTTTTTATT-TT
5503816 TTTTTTATTTCT
1 TTTTTTATTT-T
5503828 TTTTTTAATTTT
1 TTTTTT-ATTTT
5503840 TTTTTGTATTT
1 TTTTT-TATTT
5503851 CTTGAGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
11 2 0.05
12 27 0.66
13 12 0.29
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (11 bp):
TTTTTTATTTT
Found at i:5503850 original size:25 final size:26
Alignment explanation
Indices: 5503791--5503853 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 26
5503781 GACTCCTTCA
* *
5503791 TTTTTTA-TCCTTTTTTGTTATTGTT
1 TTTTTTATTTCTTTTTTGTAATTGTT
5503816 TTTTTTATTTCTTTTTT-TAATT-TT
1 TTTTTTATTTCTTTTTTGTAATTGTT
5503840 TTTTTGTATTTCTT
1 TTTTT-TATTTCTT
5503854 GAGTTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 7 0.21
25 19 0.56
26 8 0.24
ACGTcount: A:0.10, C:0.06, G:0.05, T:0.79
Consensus pattern (26 bp):
TTTTTTATTTCTTTTTTGTAATTGTT
Found at i:5509056 original size:87 final size:88
Alignment explanation
Indices: 5508921--5509084 Score: 210
Period size: 87 Copynumber: 1.9 Consensus size: 88
5508911 TTTTATCTAT
* *
5508921 TTTTAAAAATTAATATTTTATCTATAATTCAAATAGTATTATGATTAAAATA-TTTATAATTTAT
1 TTTTAAAAATTAATATTTTATCTATAATTCAAACAGTATTATGATTAAAATACTATATAATTTAT
*
5508985 TTATAATTTAAATCTTAACAATG
66 ATATAATTTAAATCTTAACAATG
* * *
5509008 TTTTAAATATTAATATTTTATTTATAATT-AAACAGTAACATT-TG-TTAAAATACTATATATTT
1 TTTTAAAAATTAATATTTTATCTATAATTCAAACAGT---ATTATGATTAAAATACTATATAATT
*
5509070 TATATATGATTTAAA
63 TATATATAATTTAAA
5509085 CATTATTATG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
86 6 0.09
87 35 0.53
88 22 0.33
89 3 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (88 bp):
TTTTAAAAATTAATATTTTATCTATAATTCAAACAGTATTATGATTAAAATACTATATAATTTAT
ATATAATTTAAATCTTAACAATG
Found at i:5509059 original size:43 final size:42
Alignment explanation
Indices: 5508919--5509086 Score: 135
Period size: 43 Copynumber: 3.9 Consensus size: 42
5508909 TATTTTATCT
* * **
5508919 ATTTTTAAAA-ATTAATATTTTATCTATAATTCAAATAGTATT
1 ATTTTTAAAATATTAATATTTTATTTATAATT-AAACAGTAAC
** * * *
5508961 ATGATTAAAATATTTATAATTTATTTATAATTTAAATC-TTAAC
1 ATTTTTAAAATATTAATATTTTATTTATAA-TTAAA-CAGTAAC
5509004 AATGTTTT-AAATATTAATATTTTATTTATAATTAAACAGTAAC
1 -AT-TTTTAAAATATTAATATTTTATTTATAATTAAACAGTAAC
* * *
5509047 ATTTGTTAAAATACTATATATTTTATATATGATTTAAACA
1 ATTT-TTAAAATATTA-ATATTTTATTTAT-AATTAAACA
5509087 TTATTATGAT
Statistics
Matches: 99, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
41 2 0.02
42 13 0.13
43 37 0.37
44 37 0.37
45 10 0.10
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (42 bp):
ATTTTTAAAATATTAATATTTTATTTATAATTAAACAGTAAC
Found at i:5509068 original size:44 final size:44
Alignment explanation
Indices: 5508965--5509086 Score: 110
Period size: 44 Copynumber: 2.8 Consensus size: 44
5508955 AGTATTATGA
* * *
5508965 TTAAAATATTTATAATTTATTTATAATTTAAATC-TTAACAATGTT
1 TTAAAATATATATATTTTATTTATAA-TTAAA-CAGTAACAATGTT
5509010 TT-AAATAT-TAATATTTTATTTATAATTAAACAGTAAC-AT-TT
1 TTAAAATATAT-ATATTTTATTTATAATTAAACAGTAACAATGTT
* *
5509051 GTTAAAATACTATATATTTTATATATGATTTAAACA
1 -TTAAAATA-TATATATTTTATTTAT-AATTAAACA
5509087 TTATTATGAT
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
41 2 0.03
42 5 0.08
43 15 0.23
44 33 0.50
45 11 0.17
ACGTcount: A:0.43, C:0.05, G:0.03, T:0.48
Consensus pattern (44 bp):
TTAAAATATATATATTTTATTTATAATTAAACAGTAACAATGTT
Found at i:5513166 original size:36 final size:35
Alignment explanation
Indices: 5513079--5513179 Score: 100
Period size: 35 Copynumber: 2.9 Consensus size: 35
5513069 TGCTCTCGTT
* * *
5513079 AAAAGGCATTGTAAGGGTTATCGCTTGATCTAGTG
1 AAAAGGTATTGAAAGGGTTATTGCTTGATCTAGTG
*
5513114 AAAA-GTCGA-T-ATAAGGGTTATTGCTTGATCTCGTG
1 AAAAGGT--ATTGA-AAGGGTTATTGCTTGATCTAGTG
*
5513149 AAAAAGGTATTGAAAGGGTTATTGTTTGATC
1 -AAAAGGTATTGAAAGGGTTATTGCTTGATC
5513180 CAATTACAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
34 1 0.02
35 27 0.50
36 23 0.43
37 3 0.06
ACGTcount: A:0.31, C:0.09, G:0.27, T:0.34
Consensus pattern (35 bp):
AAAAGGTATTGAAAGGGTTATTGCTTGATCTAGTG
Found at i:5513721 original size:21 final size:21
Alignment explanation
Indices: 5513679--5513731 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
5513669 TACATGTTGA
*
5513679 TTAGTTT-AGTTTAAGTTGTT
1 TTAGTTTAAGTTTAAGTTATT
* *
5513699 TTAGTTTAATTTTATGTTATT
1 TTAGTTTAAGTTTAAGTTATT
*
5513720 TTACTTTAAGTT
1 TTAGTTTAAGTT
5513732 ACTTTAAGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.23, C:0.02, G:0.13, T:0.62
Consensus pattern (21 bp):
TTAGTTTAAGTTTAAGTTATT
Found at i:5521154 original size:35 final size:35
Alignment explanation
Indices: 5521105--5521250 Score: 139
Period size: 35 Copynumber: 4.1 Consensus size: 35
5521095 AATTATCACT
*
5521105 TAATTTAATCAATTACGCCCAATAACTTAATTAAA
1 TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
* * * * * *
5521140 TAATATAATTAATTAAGCTCAACAATTTAATTAAC
1 TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
* * * *
5521175 CAATTTTAATCAATTAGGCCCAATTATTTAATTAAA
1 TAA-TTTAATCAATTAAGCCCAATAACTTAATTAAA
* * ** *
5521211 AAATTTAATCAATTATGTTCAATGACTTAATTAAA
1 TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
5521246 TAATT
1 TAATT
5521251 AATTAAACCC
Statistics
Matches: 88, Mismatches: 22, Indels: 2
0.79 0.20 0.02
Matches are distributed among these distances:
35 61 0.69
36 27 0.31
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.38
Consensus pattern (35 bp):
TAATTTAATCAATTAAGCCCAATAACTTAATTAAA
Found at i:5521241 original size:71 final size:71
Alignment explanation
Indices: 5521108--5521244 Score: 175
Period size: 71 Copynumber: 1.9 Consensus size: 71
5521098 TATCACTTAA
* * *
5521108 TTTAATCAATTACGCCCAATAACTTAATTAAATAATATAATTAATTAAGCTCAACAATTTAATTA
1 TTTAATCAATTACGCCCAATAACTTAATTAAAAAATATAATCAATTAAGCTCAACAACTTAATTA
5521173 ACCAAT
66 ACCAAT
* * * * * * **
5521179 TTTAATCAATTAGGCCCAATTATTTAATTAAAAAATTTAATCAATTATGTTCAATGACTTAATTA
1 TTTAATCAATTACGCCCAATAACTTAATTAAAAAATATAATCAATTAAGCTCAACAACTTAATTA
5521244 A
66 A
5521245 ATAATTAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (71 bp):
TTTAATCAATTACGCCCAATAACTTAATTAAAAAATATAATCAATTAAGCTCAACAACTTAATTA
ACCAAT
Found at i:5523877 original size:78 final size:78
Alignment explanation
Indices: 5523743--5523950 Score: 254
Period size: 78 Copynumber: 2.6 Consensus size: 78
5523733 GGTGGACATT
* * * *** * **
5523743 ATGTGCTAAGTGGACATATGGCATTCCTATTATGTGTTAAGGTATAATAATGCCAATATATAAAT
1 ATGTGATAAGTGGGCATGTGGCATTCCTATTATACATTAAGGTATAATGACACCAATATATAAAT
5523808 ACCATCAAAGTCC
66 ACCATCAAAGTCC
*
5523821 ATGTGATAAGTGGGCATGTGGCCTTCCTATTATACATTAAGGTATAATGACACCAATATATAAAT
1 ATGTGATAAGTGGGCATGTGGCATTCCTATTATACATTAAGGTATAATGACACCAATATATAAAT
*
5523886 ACCATCAAGGTCC
66 ACCATCAAAGTCC
** * *
5523899 ACATGATAAGTGGGTGACATGTGGTATTCCTATTATACATAAAGGTATAATG
1 ATGTGATAAGT-GG-G-CATGTGGCATTCCTATTATACATTAAGGTATAATG
5523951 GTGCTAATAT
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
78 76 0.68
79 2 0.02
80 1 0.01
81 32 0.29
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (78 bp):
ATGTGATAAGTGGGCATGTGGCATTCCTATTATACATTAAGGTATAATGACACCAATATATAAAT
ACCATCAAAGTCC
Found at i:5541264 original size:18 final size:18
Alignment explanation
Indices: 5541230--5541268 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5541220 GTGGGAGAAA
*
5541230 TTTATTCTTTTCTTTTCC
1 TTTATCCTTTTCTTTTCC
5541248 TTTATCCTTGTTC-TTTCC
1 TTTATCCTT-TTCTTTTCC
5541266 TTT
1 TTT
5541269 CTTCTACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTATCCTTTTCTTTTCC
Found at i:5544978 original size:24 final size:25
Alignment explanation
Indices: 5544951--5544999 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5544941 ATAATTTTAA
* *
5544951 AAATATTTATTTTTTAA-ATTTTTT
1 AAATATTTATCTTTAAACATTTTTT
*
5544975 AAATTTTTATCTTTAAACATTTTTT
1 AAATATTTATCTTTAAACATTTTTT
5545000 TAGTGGCACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (25 bp):
AAATATTTATCTTTAAACATTTTTT
Found at i:5546016 original size:48 final size:48
Alignment explanation
Indices: 5545950--5546055 Score: 149
Period size: 48 Copynumber: 2.2 Consensus size: 48
5545940 TGGGCAATGC
*
5545950 GGGATCTTAAAGGAAGAGAAAAGATGCGAATCTCAAACCAAAAAGAAT
1 GGGAACTTAAAGGAAGAGAAAAGATGCGAATCTCAAACCAAAAAGAAT
* * * * *
5545998 GGGAACTTAAAGGGAGAGAAAAGGTGGGAGTCTCAAACCAACAAGAAT
1 GGGAACTTAAAGGAAGAGAAAAGATGCGAATCTCAAACCAAAAAGAAT
*
5546046 GGGAAATTAA
1 GGGAACTTAA
5546056 TCTCAATGAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.47, C:0.11, G:0.27, T:0.14
Consensus pattern (48 bp):
GGGAACTTAAAGGAAGAGAAAAGATGCGAATCTCAAACCAAAAAGAAT
Found at i:5555488 original size:20 final size:21
Alignment explanation
Indices: 5555439--5555480 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
5555429 AGAGGAGTAA
5555439 GACTTTACATTTTCTTCCATC
1 GACTTTACATTTTCTTCCATC
5555460 GACTTTACATTTTCTTCCATC
1 GACTTTACATTTTCTTCCATC
5555481 TTTTTACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.29, G:0.05, T:0.48
Consensus pattern (21 bp):
GACTTTACATTTTCTTCCATC
Found at i:5559947 original size:2 final size:2
Alignment explanation
Indices: 5559940--5559974 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5559930 TTCCTACTTG
5559940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5559975 GACGCTTGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5564310 original size:20 final size:19
Alignment explanation
Indices: 5564277--5564316 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
5564267 AGCCAAGTTT
*
5564277 AAAAGTATCGATACATTTC
1 AAAAGTATCAATACATTTC
5564296 AAAATGTATCAATACATTTC
1 AAAA-GTATCAATACATTTC
5564316 A
1 A
5564317 GTAGAATTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAAGTATCAATACATTTC
Found at i:5566567 original size:30 final size:32
Alignment explanation
Indices: 5566533--5566598 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
5566523 CTAAATTTGC
*
5566533 ATTATAAT-AAAA-GAAAATAAAATATATAAG
1 ATTATAATAAAAATAAAAATAAAATATATAAG
* *
5566563 ATTATAATAAAAATAAAAATAAAATATTTGAG
1 ATTATAATAAAAATAAAAATAAAATATATAAG
5566595 ATTA
1 ATTA
5566599 AAAATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 8 0.26
31 4 0.13
32 19 0.61
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (32 bp):
ATTATAATAAAAATAAAAATAAAATATATAAG
Found at i:5572024 original size:24 final size:23
Alignment explanation
Indices: 5571976--5572022 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5571966 AACTTAATTA
*
5571976 ATTAATTAAATAAAATTAAAAAT
1 ATTAATTAAATAAAATAAAAAAT
* *
5571999 ATTAATTTAATAAAA-AACAAAT
1 ATTAATTAAATAAAATAAAAAAT
5572021 AT
1 AT
5572023 ATATACTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTAATTAAATAAAATAAAAAAT
Found at i:5572647 original size:6 final size:6
Alignment explanation
Indices: 5572636--5572660 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5572626 GCTCCAACCA
5572636 AACCCT AACCCT AACCCT AACCCT A
1 AACCCT AACCCT AACCCT AACCCT A
5572661 CCGTGCCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.00, T:0.16
Consensus pattern (6 bp):
AACCCT
Found at i:5576264 original size:16 final size:16
Alignment explanation
Indices: 5576243--5576276 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5576233 ACTTGGGACC
*
5576243 AATTTGGTAAATTAAT
1 AATTTGCTAAATTAAT
*
5576259 AATTTGCTAAATTTAT
1 AATTTGCTAAATTAAT
5576275 AA
1 AA
5576277 GACTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.09, T:0.44
Consensus pattern (16 bp):
AATTTGCTAAATTAAT
Found at i:5576931 original size:24 final size:24
Alignment explanation
Indices: 5576887--5576933 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5576877 AAAGATTAGA
5576887 AAGAGAAACAGAGCGAGAAAGAAT
1 AAGAGAAACAGAGCGAGAAAGAAT
* *
5576911 AAGA-AAAGAGAGGGAGCAAAGAA
1 AAGAGAAACAGAGCGAG-AAAGAA
5576934 GGAAGATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.60, C:0.06, G:0.32, T:0.02
Consensus pattern (24 bp):
AAGAGAAACAGAGCGAGAAAGAAT
Found at i:5577455 original size:6 final size:6
Alignment explanation
Indices: 5577444--5577473 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
5577434 TTTAATTCAA
5577444 TTTTTG TTTTTG TTTTTG TTTTT- TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
5577474 GTGTTGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTTG
Found at i:5577484 original size:19 final size:19
Alignment explanation
Indices: 5577443--5577486 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
5577433 CTTTAATTCA
*
5577443 ATTTTTGTTTTTGTTTTTG
1 ATTTTTGTTTTTGTTGTTG
5577462 -TTTTT-TTTTTGTGTGTTG
1 ATTTTTGTTTTTGT-TGTTG
5577480 ATTTTTG
1 ATTTTTG
5577487 AAATGGACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
17 7 0.33
18 9 0.43
19 5 0.24
ACGTcount: A:0.05, C:0.00, G:0.18, T:0.77
Consensus pattern (19 bp):
ATTTTTGTTTTTGTTGTTG
Found at i:5588130 original size:2 final size:2
Alignment explanation
Indices: 5588123--5588162 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5588113 TGGTCCCTTC
5588123 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5588163 TATTTTCTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5590331 original size:2 final size:2
Alignment explanation
Indices: 5590324--5590351 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5590314 CACAAGCTTC
5590324 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5590352 TCAGGCGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5594730 original size:26 final size:26
Alignment explanation
Indices: 5594677--5594730 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
5594667 AATTTTAAAA
*
5594677 ATAATTTTACCTTCAGAAGTGGACGG
1 ATAATTTTACCTTCAGAAGTGAACGG
*
5594703 ATAATTTTA-CTATCAGAAGTGAATGG
1 ATAATTTTACCT-TCAGAAGTGAACGG
5594729 AT
1 AT
5594731 GTCTTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (26 bp):
ATAATTTTACCTTCAGAAGTGAACGG
Found at i:5595184 original size:23 final size:23
Alignment explanation
Indices: 5595162--5595209 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
5595152 TAATGATATA
5595162 AATAAAGTTTAT-TATAAGTTAT
1 AATAAAGTTTATGTATAAGTTAT
* * *
5595184 AGTAATGTTTATGTATAAATTA-
1 AATAAAGTTTATGTATAAGTTAT
5595206 AATA
1 AATA
5595210 TATGTGTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (23 bp):
AATAAAGTTTATGTATAAGTTAT
Found at i:5599572 original size:17 final size:17
Alignment explanation
Indices: 5599547--5599582 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5599537 TTTGATCCAC
5599547 ACAAAGCTCAATCTCAA
1 ACAAAGCTCAATCTCAA
*
5599564 ACAAGGCTCAATCTCAA
1 ACAAAGCTCAATCTCAA
5599581 AC
1 AC
5599583 TATATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.44, C:0.31, G:0.08, T:0.17
Consensus pattern (17 bp):
ACAAAGCTCAATCTCAA
Found at i:5601090 original size:16 final size:17
Alignment explanation
Indices: 5601061--5601102 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
5601051 ACTAAAATTG
* *
5601061 ATTTTGATTCTTTT-CT
1 ATTTTTATTCTTTTAAT
*
5601077 ATTTTTATTTTTTTAAT
1 ATTTTTATTCTTTTAAT
5601094 ATTTTTATT
1 ATTTTTATT
5601103 GAATCCAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTATTCTTTTAAT
Found at i:5601767 original size:8 final size:8
Alignment explanation
Indices: 5601747--5601783 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
5601737 TTCTTCTTTC
5601747 TATTTATAT
1 TATTTA-AT
5601756 TATTTAAT
1 TATTTAAT
*
5601764 TATTTAAA
1 TATTTAAT
5601772 TATTTAAT
1 TATTTAAT
5601780 TATT
1 TATT
5601784 GTGTAAACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTTAAT
Found at i:5605498 original size:102 final size:103
Alignment explanation
Indices: 5605322--5605532 Score: 334
Period size: 102 Copynumber: 2.1 Consensus size: 103
5605312 AATTTTTTGT
* * * *
5605322 TCAATTTCTTCATCAAGATGAAGCTCATTGATCTTTTTATTAATTTTGCAAAATTTTGAGATGTG
1 TCAATTTCTTCATCAAGATGAAGCTCATTGAGCTTTCTATTAATTTAGCAAAACTTTGAGATGTG
* * *
5605387 ACCAAATTTACCATATTTGTTGCATTTTATT-GTTTTA
66 ACCAAATTTACCACATTTGTAGAATTTTATTAGTTTTA
*
5605424 TCAATTTCTTCATGAAGATGAAGCTCATTGAGCTTTCTATTAATTTAGCAAAACTTTGAGATGTG
1 TCAATTTCTTCATCAAGATGAAGCTCATTGAGCTTTCTATTAATTTAGCAAAACTTTGAGATGTG
*
5605489 ACCAAATTTACCACATTTGTAGAATTTTATTATTTTTA
66 ACCAAATTTACCACATTTGTAGAATTTTATTAGTTTTA
5605527 TCAATT
1 TCAATT
5605533 CTATTTTCTA
Statistics
Matches: 99, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 88 0.89
103 11 0.11
ACGTcount: A:0.30, C:0.13, G:0.12, T:0.45
Consensus pattern (103 bp):
TCAATTTCTTCATCAAGATGAAGCTCATTGAGCTTTCTATTAATTTAGCAAAACTTTGAGATGTG
ACCAAATTTACCACATTTGTAGAATTTTATTAGTTTTA
Found at i:5608804 original size:35 final size:35
Alignment explanation
Indices: 5608765--5608832 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
5608755 GAAGTTACGT
* *
5608765 TTGATCCTACAAAAGGCAAGTTGTGAAAGTTATAC
1 TTGATCCTACAAAAGGCAAGTTATAAAAGTTATAC
*
5608800 TTGATCCTACAAAAGGCATGTTATAAAAGTTAT
1 TTGATCCTACAAAAGGCAAGTTATAAAAGTTAT
5608833 GCCTGATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (35 bp):
TTGATCCTACAAAAGGCAAGTTATAAAAGTTATAC
Found at i:5608840 original size:35 final size:35
Alignment explanation
Indices: 5608766--5608840 Score: 105
Period size: 35 Copynumber: 2.1 Consensus size: 35
5608756 AAGTTACGTT
* * *
5608766 TGATCCTACAAAAGGCAAGTTGTGAAAGTTATACT
1 TGATCCTACAAAAGGCAAGTTATAAAAGTTATACC
* *
5608801 TGATCCTACAAAAGGCATGTTATAAAAGTTATGCC
1 TGATCCTACAAAAGGCAAGTTATAAAAGTTATACC
5608836 TGATC
1 TGATC
5608841 TTGTTAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (35 bp):
TGATCCTACAAAAGGCAAGTTATAAAAGTTATACC
Found at i:5621210 original size:3 final size:3
Alignment explanation
Indices: 5621200--5621236 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5621190 TTCATCGATC
5621200 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
5621237 CCTAAATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:5623031 original size:15 final size:15
Alignment explanation
Indices: 5622981--5623034 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
5622971 ATTACAATGC
* *
5622981 AATGTGATTACAGGT
1 AATGTGATTGCAAGT
*
5622996 AATGTAATTGCAAGT
1 AATGTGATTGCAAGT
*
5623011 AATGTGATTGTAAGT
1 AATGTGATTGCAAGT
5623026 AATGTGATT
1 AATGTGATT
5623035 ACAGGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (15 bp):
AATGTGATTGCAAGT
Found at i:5623245 original size:12 final size:13
Alignment explanation
Indices: 5623222--5623254 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5623212 ATTTTTATAT
5623222 AATATCATTTTTA
1 AATATCATTTTTA
*
5623235 AATAT-ATTTTTT
1 AATATCATTTTTA
5623247 AATATCAT
1 AATATCAT
5623255 ATATTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (13 bp):
AATATCATTTTTA
Found at i:5623266 original size:34 final size:33
Alignment explanation
Indices: 5623228--5623309 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
5623218 ATATAATATC
* * *
5623228 ATTTTTAAATATATTTTTTAATATCA-TATATTTT
1 ATTTTT-AATATATTTTATAAAATAATTATA-TTT
*
5623262 ATTTTT-ATTTATTATTATAAAATAATTATATTT
1 ATTTTTAATATATT-TTATAAAATAATTATATTT
5623295 ATTTTTAATATATTT
1 ATTTTTAATATATTT
5623310 ATATTTATAT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
32 6 0.15
33 18 0.45
34 16 0.40
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (33 bp):
ATTTTTAATATATTTTATAAAATAATTATATTT
Found at i:5623308 original size:15 final size:15
Alignment explanation
Indices: 5623288--5623471 Score: 74
Period size: 15 Copynumber: 11.5 Consensus size: 15
5623278 ATAAAATAAT
5623288 TATATTTATTTTTAA
1 TATATTTATTTTTAA
*
5623303 TATATTTATATTT-A
1 TATATTTATTTTTAA
*
5623317 TATTATTAATTTTT-A
1 TA-TATTTATTTTTAA
*
5623332 TATAATATCATTTCTTAAA
1 TAT-AT-TTATTT-TT-AA
* *
5623351 TATATTT-TTAATGTCA
1 TATATTTATT--TTTAA
5623367 TATATTTTATTTTTATTTA
1 TATA-TTTATTTTTA---A
*
5623386 TTTATTATAATATTTT-A
1 TATATT-T-AT-TTTTAA
5623403 TAT-TTTATTTTTAA
1 TATATTTATTTTTAA
*
5623417 TATATTTATATTT-A
1 TATATTTATTTTTAA
*
5623431 TATTATTAATTTTTATA
1 TA-TATTTATTTTTA-A
* *
5623448 TAATATCATATTTTAAA
1 T-ATAT-TTATTTTTAA
5623465 TATATTT
1 TATATTT
5623472 TTAATGTCAT
Statistics
Matches: 128, Mismatches: 18, Indels: 46
0.67 0.09 0.24
Matches are distributed among these distances:
13 4 0.03
14 13 0.10
15 45 0.35
16 20 0.16
17 17 0.13
18 14 0.11
19 9 0.07
20 2 0.02
21 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.01, T:0.62
Consensus pattern (15 bp):
TATATTTATTTTTAA
Found at i:5623379 original size:50 final size:52
Alignment explanation
Indices: 5623315--5623486 Score: 152
Period size: 52 Copynumber: 3.1 Consensus size: 52
5623305 TATTTATATT
5623315 TATATTATTAATTTTTATATAATATCAT-TTCTTAAATATATTTTTAATGTCA
1 TATATTATTAATTTTTATATAATATCATATT-TTAAATATATTTTTAATGTCA
* * * * * *
5623367 TATATT-TT-ATTTTTATTTATTTATTATAATATTTTATATTTTATTTTTAATATATTTATA
1 TATATTATTAATTTTTA--TA--TAATATCATATTTTA-AATATA-TTTT--TA-ATGT-CA
5623427 TTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCA
1 --TATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCA
5623481 TATATT
1 TATATT
5623487 TTTTTTTTTA
Statistics
Matches: 93, Mismatches: 12, Indels: 30
0.69 0.09 0.22
Matches are distributed among these distances:
50 7 0.08
51 2 0.02
52 14 0.15
54 11 0.12
55 9 0.10
56 6 0.06
58 6 0.06
59 7 0.08
60 14 0.15
62 8 0.09
63 2 0.02
64 7 0.08
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (52 bp):
TATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAATGTCA
Found at i:5623410 original size:114 final size:112
Alignment explanation
Indices: 5623184--5623527 Score: 557
Period size: 114 Copynumber: 3.0 Consensus size: 112
5623174 AAAATATAAA
*
5623184 TTTAATATATTTATATTTTTTATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTTAA
1 TTTAATATATTTATA-TTTATATTATTAATTTTTATATAATATCATTTTTAAATATA-TTTTTAA
* * *
5623249 TATCATATATTTTATTTTTATTTATTATTATAAAATAATTATA-TTTATT
64 TGTCATATATTTTATTTTTATTTATTATTATAATAT-TTTATATTTTATT
5623298 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTT-TTAAATATATTTTTAAT
5623363 GTCATATATTTTATTTTTATTTATTTATTATAATATTTTATATTTTATT
65 GTCATATATTTTATTTTTATTTA-TTATTATAATATTTTATATTTTATT
5623412 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATATTTTAAATATATTTTTAAT
1 TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCAT-TTTTAAATATATTTTTAAT
*
5623477 GTCATATATTTTTTTTTTTATTTATTATTATAAT-TTTATATATTTTATT
65 GTCATATA-TTTTATTTTTATTTATTATTATAATATTT-TATATTTTATT
5623526 TT
1 TT
5623528 CATTTCTTTA
Statistics
Matches: 219, Mismatches: 5, Indels: 12
0.93 0.02 0.05
Matches are distributed among these distances:
113 69 0.32
114 134 0.61
115 16 0.07
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (112 bp):
TTTAATATATTTATATTTATATTATTAATTTTTATATAATATCATTTTTAAATATATTTTTAATG
TCATATATTTTATTTTTATTTATTATTATAATATTTTATATTTTATT
Found at i:5623434 original size:35 final size:35
Alignment explanation
Indices: 5623367--5623443 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
5623357 TTTAATGTCA
*
5623367 TATATTTTATTTTTATTTATTTATTATAATATT-T
1 TATATTTTATTTTTATATATTTATTATAATATTAT
*
5623401 TATATTTTATTTTTAATATATTTA-TATTTATATTAT
1 TATATTTTATTTTT-ATATATTTATTA-TAATATTAT
5623437 TA-ATTTT
1 TATATTTT
5623444 TATATAATAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
34 16 0.42
35 19 0.50
36 3 0.08
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (35 bp):
TATATTTTATTTTTATATATTTATTATAATATTAT
Found at i:5623518 original size:10 final size:9
Alignment explanation
Indices: 5623366--5623524 Score: 54
Period size: 9 Copynumber: 18.2 Consensus size: 9
5623356 TTTTAATGTC
5623366 ATATATTTT
1 ATATATTTT
* *
5623375 ATTTTTATTT
1 ATATAT-TTT
* *
5623385 ATTTATTAT
1 ATATATTTT
5623394 A-ATA-TTT
1 ATATATTTT
5623401 -TATATTTT
1 ATATATTTT
*
5623409 AT-T-TTTA
1 ATATATTTT
5623416 ATATATTTAT
1 ATATATTT-T
* *
5623426 ATTTATATT
1 ATATATTTT
5623435 AT-TAATTTT
1 ATAT-ATTTT
**
5623444 -TATATAAT
1 ATATATTTT
5623452 ATCATATTTT
1 AT-ATATTTT
5623462 AAATATATTTT
1 --ATATATTTT
* *
5623473 -TA-ATGTC
1 ATATATTTT
5623480 ATATATTTT
1 ATATATTTT
*
5623489 -T-TTTTTT
1 ATATATTTT
*
5623496 ATTTATTATT
1 ATATATT-TT
5623506 ATA-ATTTT
1 ATATATTTT
5623514 ATATATTTT
1 ATATATTTT
5623523 AT
1 AT
5623525 TTTCATTTCT
Statistics
Matches: 109, Mismatches: 22, Indels: 38
0.64 0.13 0.22
Matches are distributed among these distances:
7 18 0.17
8 23 0.21
9 36 0.33
10 23 0.21
11 7 0.06
12 2 0.02
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (9 bp):
ATATATTTT
Found at i:5623526 original size:39 final size:41
Alignment explanation
Indices: 5623483--5623623 Score: 125
Period size: 39 Copynumber: 3.5 Consensus size: 41
5623473 TAATGTCATA
*
5623483 TATTTT-TTT-TTTTATTTATTATTATAATTTTATATATTT
1 TATTTTATTTATTTTATTTATTATTATAATATTATATATTT
* * *
5623522 TATTTTCATTTCTTTAATATATT-TT-T-ATATTATATATTT
1 TATTTT-ATTTATTTTATTTATTATTATAATATTATATATTT
* *
5623561 TATTTTAATTTGTTTTATCTATATTA-TATAAATATTA-ATTTTT
1 TATTTT-ATTTATTTTAT-T-TATTATTAT-AATATTATATATTT
5623604 TATATTTATTTATTTTATTT
1 TAT-TTTATTTATTTTATTT
5623624 TAATTTTTAT
Statistics
Matches: 83, Mismatches: 9, Indels: 18
0.75 0.08 0.16
Matches are distributed among these distances:
39 33 0.40
40 1 0.01
41 11 0.13
42 11 0.13
43 18 0.22
44 9 0.11
ACGTcount: A:0.28, C:0.02, G:0.01, T:0.69
Consensus pattern (41 bp):
TATTTTATTTATTTTATTTATTATTATAATATTATATATTT
Found at i:5623668 original size:16 final size:16
Alignment explanation
Indices: 5623606--5623666 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 16
5623596 TAATTTTTTA
5623606 TATTT-ATT-TAT-TT
1 TATTTAATTATATATT
*
5623619 TATTTTAATT-TTTATT
1 TA-TTTAATTATATATT
*
5623635 T-TATAATTATATATT
1 TATTTAATTATATATT
5623650 TATTTAATTATAATATT
1 TATTTAATTAT-ATATT
5623667 ATAAAATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
13 2 0.05
14 9 0.24
15 11 0.29
16 11 0.29
17 5 0.13
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTAATTATATATT
Found at i:5623669 original size:30 final size:32
Alignment explanation
Indices: 5623603--5623670 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
5623593 TATTAATTTT
* * * * *
5623603 TTATATTTATTTATTTTATTTTAATTTTTATT
1 TTATAATTATATATTTTATTTTAATTATAATA
5623635 TTATAATTATATA-TTTA-TTTAATTATAATA
1 TTATAATTATATATTTTATTTTAATTATAATA
5623665 TTATAA
1 TTATAA
5623671 AATATTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 16 0.52
31 4 0.13
32 11 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (32 bp):
TTATAATTATATATTTTATTTTAATTATAATA
Found at i:5633937 original size:17 final size:17
Alignment explanation
Indices: 5633915--5633954 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
5633905 CTTATTCTTC
*
5633915 TTTCTTTTTCTCTTTGT
1 TTTCTTTATCTCTTTGT
*
5633932 TTTCTTTATCTCTTTTT
1 TTTCTTTATCTCTTTGT
5633949 TTTCTT
1 TTTCTT
5633955 CATATTTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTCTTTATCTCTTTGT
Found at i:5640106 original size:109 final size:110
Alignment explanation
Indices: 5639978--5640188 Score: 343
Period size: 109 Copynumber: 1.9 Consensus size: 110
5639968 GTTAGAATGT
* * * *
5639978 CATGTTTTTGTTAACATTTTTTATTGTAAACATGTATGGGAATTAGTCTTGATTCTTCCATTTTG
1 CATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGAGAATTAGTCTTAATTCTTACATTTTG
* **
5640043 ATGATGATTTTGATAGTTTGTTTCAATTTCTTTTAGCTTATATGG
66 ATGACGACCTTGATAGTTTGTTTCAATTTCTTTTAGCTTATATGG
*
5640088 CATG-TTTTGTTAACATTTTTTATTGTAAACATGAATGAGAATTAGTCTTAATTCTTATATTTTG
1 CATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGAGAATTAGTCTTAATTCTTACATTTTG
5640152 ATGACGACCTTGATAGTTTGTTTCAATTTCTTTTAGC
66 ATGACGACCTTGATAGTTTGTTTCAATTTCTTTTAGC
5640189 ATATGTATGA
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
109 89 0.96
110 4 0.04
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (110 bp):
CATGTTTTTGTTAACATTTTTTATTGTAAACATGAATGAGAATTAGTCTTAATTCTTACATTTTG
ATGACGACCTTGATAGTTTGTTTCAATTTCTTTTAGCTTATATGG
Found at i:5641145 original size:12 final size:12
Alignment explanation
Indices: 5641128--5641153 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5641118 TGCAAAAAGA
5641128 AAGAAGCATTAC
1 AAGAAGCATTAC
5641140 AAGAAGCATTAC
1 AAGAAGCATTAC
5641152 AA
1 AA
5641154 AATACATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (12 bp):
AAGAAGCATTAC
Found at i:5650743 original size:31 final size:30
Alignment explanation
Indices: 5650661--5650756 Score: 106
Period size: 29 Copynumber: 3.2 Consensus size: 30
5650651 AAAAAAATTT
**
5650661 AAATAAATTTTTATATTTTTATGATG--TC
1 AAATAAATTTTTATATTTTTATTTTGAATC
* *
5650689 TAATTAAGTTTTTATATTTTTATTTTGAATC
1 -AAATAAATTTTTATATTTTTATTTTGAATC
**
5650720 AAATAAATTTTTATATTTTTTATTTCAAATC
1 AAATAAATTTTTATA-TTTTTATTTTGAATC
5650751 AAATAA
1 AAATAA
5650757 GTTTCTAACT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.39
30 13 0.23
31 21 0.38
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (30 bp):
AAATAAATTTTTATATTTTTATTTTGAATC
Found at i:5658559 original size:21 final size:21
Alignment explanation
Indices: 5658506--5658559 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
5658496 GCAACTAAAG
*
5658506 TAGTTGACTAGAAAGAGTTTC
1 TAGTTGACTATAAAGAGTTTC
*
5658527 TAGTTGATTATAAAGTA-TTTC
1 TAGTTGACTATAAAG-AGTTTC
*
5658548 TAGTCGACTATA
1 TAGTTGACTATA
5658560 CTTGTGAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (21 bp):
TAGTTGACTATAAAGAGTTTC
Found at i:5662189 original size:31 final size:29
Alignment explanation
Indices: 5662154--5662215 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
5662144 AAAATTTGTG
*
5662154 TGGGTTTGTAGTGAGCCCATTAAGAAAACCA
1 TGGGTTTGTAGTGAACCCATT-A-AAAACCA
* *
5662185 TGGGTTTGTGGTGAACCTATTAAAAACCA
1 TGGGTTTGTAGTGAACCCATTAAAAACCA
5662214 TG
1 TG
5662216 TGCTATATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.32
30 1 0.04
31 18 0.64
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.29
Consensus pattern (29 bp):
TGGGTTTGTAGTGAACCCATTAAAAACCA
Found at i:5662957 original size:63 final size:64
Alignment explanation
Indices: 5662858--5662978 Score: 199
Period size: 63 Copynumber: 1.9 Consensus size: 64
5662848 CATATGCATC
* *
5662858 ATAACTCTCTTTGAAACTCTTTTTACATCTTTTG-AAATGACTTTACTAGTTAAGGGTCGAATT
1 ATAACTCTCTTTGAAACTCTTTTTACATCTTTTGAAAATGACTTTACCAGTCAAGGGTCGAATT
* *
5662921 ATAACTCTCTTTGAAACTCTTTTTGCATGTTTTGAAAATGACTTTACCAGTCAAGGGT
1 ATAACTCTCTTTGAAACTCTTTTTACATCTTTTGAAAATGACTTTACCAGTCAAGGGT
5662979 TGACTATAAG
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 32 0.60
64 21 0.40
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (64 bp):
ATAACTCTCTTTGAAACTCTTTTTACATCTTTTGAAAATGACTTTACCAGTCAAGGGTCGAATT
Found at i:5667489 original size:102 final size:101
Alignment explanation
Indices: 5667310--5667514 Score: 290
Period size: 102 Copynumber: 2.0 Consensus size: 101
5667300 AAATCATTCA
* * **
5667310 AAGATGGTTGATTTTCACAACACCAAGGTTGTTTCAAGTCATGAAGTTCACTTTTAACTCAACAT
1 AAGATGGTTGATCTTCACAACACCAAGGTTGTTTCAAGCCATGAAGTTCACTTCCAACTCAACAT
* *
5667375 TTGATCATAAGGAAG-TAATGGGCAAAGCTATGTGCT
66 TTGATCACAAGGAAGAT-ATGGCCAAAGCTATGTGCT
*
5667411 AAGATGGTTGATCTTCACAGCACCAAGGGTCT-TTTCAAGCCATGAAGTTCA-TTCCCAACTCAA
1 AAGATGGTTGATCTTCACAACACCAA-GGT-TGTTTCAAGCCATGAAGTTCACTT-CCAACTCAA
5667474 CATTTGATCACAAGGAAGATATGGCCAAAGCTATGTGCT
63 CATTTGATCACAAGGAAGATATGGCCAAAGCTATGTGCT
5667513 AA
1 AA
5667515 AATTTTGAGG
Statistics
Matches: 93, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
101 26 0.28
102 65 0.70
103 2 0.02
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (101 bp):
AAGATGGTTGATCTTCACAACACCAAGGTTGTTTCAAGCCATGAAGTTCACTTCCAACTCAACAT
TTGATCACAAGGAAGATATGGCCAAAGCTATGTGCT
Found at i:5672411 original size:20 final size:20
Alignment explanation
Indices: 5672363--5672413 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
5672353 AAATGAACCA
*
5672363 ACGATGAGGTTGGGTCAACG
1 ACGACGAGGTTGGGTCAACG
* * *
5672383 ATGACGAGGTTGGGTTAGCG
1 ACGACGAGGTTGGGTCAACG
*
5672403 ACGAGGAGGTT
1 ACGACGAGGTT
5672414 AAGGGGGCTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.43, T:0.22
Consensus pattern (20 bp):
ACGACGAGGTTGGGTCAACG
Found at i:5676440 original size:53 final size:53
Alignment explanation
Indices: 5676383--5676497 Score: 230
Period size: 53 Copynumber: 2.2 Consensus size: 53
5676373 AGACCAAGCA
5676383 ATAACCCTTACAAAGTCCATAAAAAGATTTTTGCTTTTTAACTAGATCAAGTG
1 ATAACCCTTACAAAGTCCATAAAAAGATTTTTGCTTTTTAACTAGATCAAGTG
5676436 ATAACCCTTACAAAGTCCATAAAAAGATTTTTGCTTTTTAACTAGATCAAGTG
1 ATAACCCTTACAAAGTCCATAAAAAGATTTTTGCTTTTTAACTAGATCAAGTG
5676489 ATAACCCTT
1 ATAACCCTT
5676498 CAATAATGGT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 62 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (53 bp):
ATAACCCTTACAAAGTCCATAAAAAGATTTTTGCTTTTTAACTAGATCAAGTG
Found at i:5678239 original size:33 final size:33
Alignment explanation
Indices: 5678202--5678266 Score: 85
Period size: 33 Copynumber: 2.0 Consensus size: 33
5678192 CTGACTTGGT
* * *
5678202 ATGTTGATATGTCATAATTGATGATGACGTAAC
1 ATGTTGACATATCATAATTAATGATGACGTAAC
* *
5678235 ATGTTGACATATCGTAATTAATGATGATGTAA
1 ATGTTGACATATCATAATTAATGATGACGTAA
5678267 TATACTAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (33 bp):
ATGTTGACATATCATAATTAATGATGACGTAAC
Found at i:5678820 original size:15 final size:15
Alignment explanation
Indices: 5678802--5678860 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
5678792 ACTGCATAAG
5678802 GTGTTACAACACAAA
1 GTGTTACAACACAAA
* * *
5678817 GTGTTATAGCACAAG
1 GTGTTACAACACAAA
*
5678832 GTGTTACAACACTAA
1 GTGTTACAACACAAA
*
5678847 GTGTCACAACACAA
1 GTGTTACAACACAA
5678861 TTCGTTACAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 35 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (15 bp):
GTGTTACAACACAAA
Found at i:5678856 original size:45 final size:45
Alignment explanation
Indices: 5678768--5678860 Score: 116
Period size: 45 Copynumber: 2.1 Consensus size: 45
5678758 TGTTACTATC
* * ** *
5678768 CAAAGTATTATAGTACAAGTTGTTACTGCATAAGGTGTTACAACA
1 CAAAGTATTATAGCACAAGGTGTTACAACATAAGGTGTCACAACA
*
5678813 CAAAGTGTTATAGCACAAGGTGTTACAACACTAA-GTGTCACAACA
1 CAAAGTATTATAGCACAAGGTGTTACAACA-TAAGGTGTCACAACA
5678858 CAA
1 CAA
5678861 TTCGTTACAA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 38 0.93
46 3 0.07
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (45 bp):
CAAAGTATTATAGCACAAGGTGTTACAACATAAGGTGTCACAACA
Found at i:5678860 original size:30 final size:30
Alignment explanation
Indices: 5678799--5678860 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
5678789 GTTACTGCAT
* * *
5678799 AAGGTGTTACAACACAAAGTGTTATAGCAC
1 AAGGTGTTACAACACAAAGTGTCACAACAC
*
5678829 AAGGTGTTACAACACTAAGTGTCACAACAC
1 AAGGTGTTACAACACAAAGTGTCACAACAC
5678859 AA
1 AA
5678861 TTCGTTACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (30 bp):
AAGGTGTTACAACACAAAGTGTCACAACAC
Found at i:5678870 original size:15 final size:14
Alignment explanation
Indices: 5678802--5678875 Score: 67
Period size: 15 Copynumber: 5.0 Consensus size: 14
5678792 ACTGCATAAG
5678802 GTGTTACAACACAAA
1 GTGTTACAACAC-AA
* *
5678817 GTGTTATAGCACAA
1 GTGTTACAACACAA
5678831 GGTGTTACAACACTAA
1 -GTGTTACAACAC-AA
*
5678847 GTGTCACAACACAA
1 GTGTTACAACACAA
* *
5678861 TTCGTTACAATACAA
1 GT-GTTACAACACAA
5678876 AACATAACTT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 5 0.10
15 41 0.85
16 2 0.04
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (14 bp):
GTGTTACAACACAA
Found at i:5683747 original size:28 final size:28
Alignment explanation
Indices: 5683715--5683769 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
5683705 TATTAAAATT
* *
5683715 TTATTTATATTTGATATAATTTATTTAC
1 TTATTTATATTAGACATAATTTATTTAC
5683743 TTATTTATATTAGACATAATTTATTTA
1 TTATTTATATTAGACATAATTTATTTA
5683770 TTTGTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (28 bp):
TTATTTATATTAGACATAATTTATTTAC
Found at i:5684018 original size:2 final size:2
Alignment explanation
Indices: 5684011--5684051 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5684001 GAAAGATGAA
5684011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5684052 AAGAAAACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5688346 original size:64 final size:64
Alignment explanation
Indices: 5688245--5688439 Score: 284
Period size: 64 Copynumber: 3.0 Consensus size: 64
5688235 CCAAGGGGCC
* * *
5688245 AAAGGGTGAGGAAATGATGTAGACAGATCACAGATGAATAATGCTGAATCAATCAGCGGCCATT
1 AAAGGGTGAGGAAACGATATAGACAGATCACAGATGAATGATGCTGAATCAATCAGCGGCCATT
* *
5688309 AAAGGGTGAGGAAACGATATAGACAGGTCACAGATGAATGATGTTGAATCAATC-GCCGGCCATT
1 AAAGGGTGAGGAAACGATATAGACAGATCACAGATGAATGATGCTGAATCAATCAG-CGGCCATT
* * * *
5688373 AAGGGGTGAGGAAACGGTATAGACAGATCACAGATGAATGATGCTGAAATCAATCACCAGCCATT
1 AAAGGGTGAGGAAACGATATAGACAGATCACAGATGAATGATGCTG-AATCAATCAGCGGCCATT
5688438 AA
1 AA
5688440 CAATGTCCAG
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
63 1 0.01
64 99 0.85
65 17 0.15
ACGTcount: A:0.38, C:0.15, G:0.27, T:0.19
Consensus pattern (64 bp):
AAAGGGTGAGGAAACGATATAGACAGATCACAGATGAATGATGCTGAATCAATCAGCGGCCATT
Found at i:5688875 original size:6 final size:6
Alignment explanation
Indices: 5688858--5688887 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
5688848 TAAAATAAAA
*
5688858 TTGAAT TGGAAT TTGAAT TTGAAT TTGAAT
1 TTGAAT TTGAAT TTGAAT TTGAAT TTGAAT
5688888 AGAAGATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (6 bp):
TTGAAT
Found at i:5694898 original size:47 final size:47
Alignment explanation
Indices: 5694824--5694949 Score: 173
Period size: 47 Copynumber: 2.7 Consensus size: 47
5694814 AATACGTATT
* * *
5694824 CTAAAAGACCAAA-TACCCTTAAGTATAATTTAATCACATATTTATA
1 CTAAAAGACAAAATTACCCTTGACTATAATTTAATCACATATTTATA
* *
5694870 CTAAAAGATAAAATTACCCTTGATTATAATTTAATCACATATTTATA
1 CTAAAAGACAAAATTACCCTTGACTATAATTTAATCACATATTTATA
* * *
5694917 CCAAAAGACAAAATTATCCTTGACTATATTTTA
1 CTAAAAGACAAAATTACCCTTGACTATAATTTA
5694950 GTAATATTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 11 0.16
47 59 0.84
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (47 bp):
CTAAAAGACAAAATTACCCTTGACTATAATTTAATCACATATTTATA
Found at i:5702696 original size:53 final size:53
Alignment explanation
Indices: 5702629--5702767 Score: 138
Period size: 53 Copynumber: 2.6 Consensus size: 53
5702619 AATTATCAAG
* * * *
5702629 GATTCTTGCTTTTTAAT-GAGATCAAGTAATAACCCTCT-CATAATCTACAAAAA
1 GATTCTTACTTTTTAATAG-GATCAAGCAATAA-CCTCTACACAATCCACAAAAA
* * *
5702682 GATTCTTACGTTTTAATAGGATCAAGCGATAACCTTTACACAATCCACAAAAA
1 GATTCTTACTTTTTAATAGGATCAAGCAATAACCTCTACACAATCCACAAAAA
* * * * *
5702735 GATTTTTACTTTTTGACATGATCAAGCGATAAC
1 GATTCTTACTTTTTAATAGGATCAAGCAATAAC
5702768 TCTTACAATG
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
52 4 0.06
53 67 0.93
54 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.33
Consensus pattern (53 bp):
GATTCTTACTTTTTAATAGGATCAAGCAATAACCTCTACACAATCCACAAAAA
Found at i:5703550 original size:18 final size:18
Alignment explanation
Indices: 5703527--5703563 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5703517 TTCTTAAGCT
5703527 TTCTAGAGCAAGGTCGAC
1 TTCTAGAGCAAGGTCGAC
5703545 TTCTAGAGCAAGGTCGAC
1 TTCTAGAGCAAGGTCGAC
5703563 T
1 T
5703564 ATAAACACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (18 bp):
TTCTAGAGCAAGGTCGAC
Found at i:5718956 original size:2 final size:2
Alignment explanation
Indices: 5718949--5718973 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5718939 TAATTAAGAC
5718949 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5718974 CGCGCGCGCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5732401 original size:27 final size:25
Alignment explanation
Indices: 5732362--5732411 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
5732352 TGAACTTGAT
*
5732362 GCGTATAAATTTTTGTTTGAAAATG
1 GCGTATAAATTTTTGTTTCAAAATG
*
5732387 GCGTATAGAATTTTTTTTTTCAAAA
1 GCGTATA-AA-TTTTTGTTTCAAAA
5732412 CAGCGTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 2 0.10
27 12 0.57
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (25 bp):
GCGTATAAATTTTTGTTTCAAAATG
Found at i:5732417 original size:27 final size:25
Alignment explanation
Indices: 5732362--5732417 Score: 58
Period size: 27 Copynumber: 2.2 Consensus size: 25
5732352 TGAACTTGAT
* **
5732362 GCGTATAAATTTTTGTTTGAAAATG
1 GCGTATAAATTTTTGTTTCAAAACA
*
5732387 GCGTATAGAATTTTTTTTTTCAAAACA
1 GCGTATA-AA-TTTTTGTTTCAAAACA
5732414 GCGT
1 GCGT
5732418 GTAGCAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 7 0.28
26 2 0.08
27 16 0.64
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (25 bp):
GCGTATAAATTTTTGTTTCAAAACA
Found at i:5732446 original size:27 final size:27
Alignment explanation
Indices: 5732415--5732466 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
5732405 TTCAAAACAG
*
5732415 CGTGTAGC-AAGTTGTTTATGAACATGA
1 CGTGTAGCAAAATTGTTT-TGAACATGA
5732442 CGTGTAGCAAAATTGTTTTGAACAT
1 CGTGTAGCAAAATTGTTTTGAACAT
5732467 AACATGTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (27 bp):
CGTGTAGCAAAATTGTTTTGAACATGA
Found at i:5732474 original size:27 final size:27
Alignment explanation
Indices: 5732417--5732474 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
5732407 CAAAACAGCG
* * *
5732417 TGTAGCAAGTTGTTTATGAACATGACG
1 TGTAGCAAATTGTTTATGAACATAACA
5732444 TGTAGCAAAATTGTTT-TGAACATAACA
1 TGTAGC-AAATTGTTTATGAACATAACA
5732471 TGTA
1 TGTA
5732475 AATGTAACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (27 bp):
TGTAGCAAATTGTTTATGAACATAACA
Done.