Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 132 of 203
Found at i:41969103 original size:266 final size:268
Alignment explanation
Indices: 41968793--41969279 Score: 845
Period size: 266 Copynumber: 1.8 Consensus size: 268
41968783 TTTTTTAAAT
*
41968793 TTTATGCTATTTTAATTACTAAAAACATTTTTGTTTTGTTTTCTTTTAGTTTTAATTTACCTAAT
1 TTTATGCTATTTTAATCACTAAAAACATTTTTGTTTTGTTTTCTTTTAGTTTTAATTTACCTAAT
* *
41968858 TAAATAAATTGTATTCAAAGTTATATTTTAAATAGTTTATTTAATTTGAATGATGGAAAAAATTT
66 TAAATAAAATGTATTCAAAGTTATATTTTAAATAGTTTATTTAATTTGAATGAGGGAAAAAATTT
41968923 TCAAACTTTTAATTTATTTTAAAGTTCAA-ATTTACATAACTTACATAAATTAAAGTTCAAATTT
131 TCAAACTTTTAATTTATTTTAAAGTT-AATATTTACATAACTTACATAAATTAAAGTTCAAATTT
*
41968987 CATAACTTACATAATTTACATAACTTATATAATTTCAGAATGTTTTCATTCTTCTTTTATCTTTT
195 CATAACTTACATAAATTACATAACTTATATAATTTCAGAATGTTTTCATTCTTCTTTTATCTTTT
41969052 TTTACTTAA
260 TTTACTTAA
* * * *
41969061 TTTATGCTATTTTAATCA-TGAAAATA-TTTTGTTTTGTTTTCTTTTATTTTTAATTTACCTAGT
1 TTTATGCTATTTTAATCACTAAAAACATTTTTGTTTTGTTTTCTTTTAGTTTTAATTTACCTAAT
* *
41969124 TAAATAAAATGTATTCAAAGTTATATTTTAAATATTTTATTTAATTTGAATGAGGGAAAAATTTT
66 TAAATAAAATGTATTCAAAGTTATATTTTAAATAGTTTATTTAATTTGAATGAGGGAAAAAATTT
41969189 TCAAACTTTTAATTTATTTTAAAGTTAATATTTACATAACTTACATAAATTAAAGTTCAAATTTC
131 TCAAACTTTTAATTTATTTTAAAGTTAATATTTACATAACTTACATAAATTAAAGTTCAAATTTC
*
41969254 ATAACTTGCATAAATTACATAACTTA
196 ATAACTTACATAAATTACATAACTTA
41969280 CTTAATACAA
Statistics
Matches: 207, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
265 2 0.01
266 182 0.88
267 6 0.03
268 17 0.08
ACGTcount: A:0.36, C:0.09, G:0.06, T:0.49
Consensus pattern (268 bp):
TTTATGCTATTTTAATCACTAAAAACATTTTTGTTTTGTTTTCTTTTAGTTTTAATTTACCTAAT
TAAATAAAATGTATTCAAAGTTATATTTTAAATAGTTTATTTAATTTGAATGAGGGAAAAAATTT
TCAAACTTTTAATTTATTTTAAAGTTAATATTTACATAACTTACATAAATTAAAGTTCAAATTTC
ATAACTTACATAAATTACATAACTTATATAATTTCAGAATGTTTTCATTCTTCTTTTATCTTTTT
TTACTTAA
Found at i:41969259 original size:30 final size:30
Alignment explanation
Indices: 41969207--41969356 Score: 99
Period size: 30 Copynumber: 4.8 Consensus size: 30
41969197 TTAATTTATT
41969207 TTAAAGTT-AATATTTACATAACTTACATAAA
1 TTAAAGTTCAA-ATTT-CATAACTTACATAAA
*
41969238 TTAAAGTTCAAATTTCATAACTTGCATAAA
1 TTAAAGTTCAAATTTCATAACTTACATAAA
* * * * *
41969268 TTACATAACTTACTTAA-TACAAAACTTAGATAATA
1 TT--A-AAGTT-C-AAATTTCATAACTTACATAA-A
* * *
41969303 TT-AAGATCAAATTTCATAACTTGCATAAT
1 TTAAAGTTCAAATTTCATAACTTACATAAA
* * *
41969332 TTTAAGATCAGATTTCATAACTTAC
1 TTAAAGTTCAAATTTCATAACTTAC
41969357 GTAATTTATA
Statistics
Matches: 93, Mismatches: 17, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
29 4 0.04
30 49 0.53
31 15 0.16
32 3 0.03
33 4 0.04
34 13 0.14
35 5 0.05
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.37
Consensus pattern (30 bp):
TTAAAGTTCAAATTTCATAACTTACATAAA
Found at i:41970192 original size:43 final size:43
Alignment explanation
Indices: 41970039--41970192 Score: 191
Period size: 43 Copynumber: 3.6 Consensus size: 43
41970029 CAAAATTATT
* * * *
41970039 AAAGTCGTGTTCTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTA
1 AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCTGCTA
* * * *
41970082 AAAGTCATAATCTATAGCAGCGTTTGTAGGAAAAGCGCTGCTA
1 AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCTGCTA
*
41970125 AAAGTCATGATCTATAGCGACGTTTGTGGGAGAAGCGCTGCTA
1 AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCTGCTA
* * * *
41970168 AAGGTCATGACCTTTAGTGGCGTTT
1 AAAGTCATGATCTATAGCGGCGTTT
41970193 CTTTCTAAAA
Statistics
Matches: 93, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 93 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (43 bp):
AAAGTCATGATCTATAGCGGCGTTTGTGGGAGAAGCGCTGCTA
Found at i:41972129 original size:43 final size:42
Alignment explanation
Indices: 41972047--41972131 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
41972037 TAGCAGCTTT
*
41972047 CTTTTTCACAAACGCCGCTAAAGAACATGATCTTTAGCGGCG
1 CTTTTTCACAAACGCCGCTAAAGAACATGATCTTCAGCGGCG
** * *
41972089 CTTTTATCACAAACGTTGCTAAAAGTAC-TGTTCTTCAGCGGCG
1 CTTTT-TCACAAACGCCGCT-AAAGAACATGATCTTCAGCGGCG
41972132 TTTATAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 5 0.14
43 25 0.69
44 6 0.17
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (42 bp):
CTTTTTCACAAACGCCGCTAAAGAACATGATCTTCAGCGGCG
Found at i:41976304 original size:16 final size:16
Alignment explanation
Indices: 41976283--41976315 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
41976273 TTCGCTGTAT
*
41976283 TGGAATAGAGGCGTAA
1 TGGAATAGAGCCGTAA
41976299 TGGAATAGAGCCGTAA
1 TGGAATAGAGCCGTAA
41976315 T
1 T
41976316 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.33, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGCCGTAA
Found at i:41976564 original size:18 final size:17
Alignment explanation
Indices: 41976543--41976577 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41976533 TTATTATTAA
*
41976543 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41976561 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41976578 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41976662 original size:120 final size:120
Alignment explanation
Indices: 41976523--41977136 Score: 967
Period size: 120 Copynumber: 5.1 Consensus size: 120
41976513 ATAATCATAT
* *
41976523 TTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* * *
41976588 CAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * *
41976643 TTTAACATAATTATTATTAAATACATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAAT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* * * *
41976708 CAATATTCTTATATGAATTTACTAAAATTATAATATATGATATTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* *
41976763 TTTGAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
* *
41976828 AAATATTCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * *
41976883 TTTAAAATAATAATTATTAAATATAATTTAATAAAAAAACTATAATTTAATAAAATTCTTAATAT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATA-TATAATTTAATAAAATTCTTAATAT
41976948 TAAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 T-AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * * *
41977005 TCTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATT
1 TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
*
41977070 AAATATTCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
*
41977125 TCTAAAATAATT
1 TTTAAAATAATT
41977137 GATTTTGTGG
Statistics
Matches: 467, Mismatches: 25, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
120 328 0.70
121 50 0.11
122 89 0.19
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATT
AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:41976761 original size:22 final size:24
Alignment explanation
Indices: 41976717--41976763 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
41976707 TCAATATTCT
41976717 TATATGAATTTACTAAAATTATAA
1 TATATGAATTTACTAAAATTATAA
41976741 TATATG-ATATTA-TAAAA-TATAA
1 TATATGAAT-TTACTAAAATTATAA
41976763 T
1 T
41976764 TTGAAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 6 0.27
23 7 0.32
24 9 0.41
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (24 bp):
TATATGAATTTACTAAAATTATAA
Found at i:41976804 original size:18 final size:17
Alignment explanation
Indices: 41976781--41976817 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
41976771 AATTATTATT
41976781 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
41976797 AAATATATGATTTAATA
1 AAATATATGATTTAATA
41976814 AAAT
1 AAAT
41976818 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:41976897 original size:13 final size:12
Alignment explanation
Indices: 41976873--41976913 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
41976863 TATAATAGTA
41976873 TAAAATATAATT
1 TAAAATATAATT
41976885 TAAAATAATAATT
1 TAAAAT-ATAATT
*
41976898 ATTAAATATAATT
1 -TAAAATATAATT
41976911 TAA
1 TAA
41976914 TAAAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAAAATATAATT
Found at i:41977046 original size:242 final size:240
Alignment explanation
Indices: 41976529--41977135 Score: 962
Period size: 242 Copynumber: 2.5 Consensus size: 240
41976519 ATATTTTAAC
* *
41976529 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
* * * *
41976594 TCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAACATAATTATTA
66 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATTA
* * * * *
41976659 TTAAATACATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATATTCTTATATGA
131 TTAAATACAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGA
* * * * *
41976724 ATTTACTAAAATTATAATATATGATATTATAAAATATAATTTGAA
196 ATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
*
41976769 ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
* *
41976834 TCTTATATGAATTTACTAAAATTATAATATATAATAGTATAAAATATAATTTAAAATAATAATTA
66 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATTA
* *
41976899 TTAAATATAATTTAATAAAAAAACTATAATTTAATAAAATTCTTAATATTAAAATATTCTTATAT
131 TTAAATACAATTTAATAAAAAAA-TATAATTTAATAAAATTCTTAATAAT-AAATATTCTTATAT
41976964 GAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
194 GAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
* * *
41977011 ATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAGTATTAAATAT
1 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
* *
41977076 TCTTATACGAATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAAATAAT
66 TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAAT
41977136 TGATTTTGTG
Statistics
Matches: 336, Mismatches: 29, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
240 140 0.42
241 24 0.07
242 172 0.51
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.43
Consensus pattern (240 bp):
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
TCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAATAATAATTA
TTAAATACAATTTAATAAAAAAATATAATTTAATAAAATTCTTAATAATAAATATTCTTATATGA
ATTTACTAAAATCATAATATATAATACTATAAAATATAATCTAAA
Found at i:41978874 original size:13 final size:13
Alignment explanation
Indices: 41978858--41978887 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41978848 TAGATCAAGC
41978858 TTTTCAAAAGCAT
1 TTTTCAAAAGCAT
*
41978871 TTTTCATAAGCAT
1 TTTTCAAAAGCAT
41978884 TTTT
1 TTTT
41978888 TTGCAGCACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (13 bp):
TTTTCAAAAGCAT
Found at i:41979062 original size:19 final size:19
Alignment explanation
Indices: 41979038--41979076 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
41979028 CATATGCCCT
41979038 ACACATATTCAAAGGATTG
1 ACACATATTCAAAGGATTG
*
41979057 ACACATATTCAGAGGATTG
1 ACACATATTCAAAGGATTG
41979076 A
1 A
41979077 GATAAAATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (19 bp):
ACACATATTCAAAGGATTG
Found at i:41980134 original size:19 final size:19
Alignment explanation
Indices: 41980107--41980143 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41980097 AACAGAAGAC
41980107 GCAAATCGGCAGAAACTGA
1 GCAAATCGGCAGAAACTGA
*
41980126 GCAAGTCGGCAGAAACTG
1 GCAAATCGGCAGAAACTG
41980144 TGAGAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.30, T:0.11
Consensus pattern (19 bp):
GCAAATCGGCAGAAACTGA
Found at i:41980179 original size:5 final size:5
Alignment explanation
Indices: 41980169--41980193 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
41980159 GCAAATCGAC
41980169 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
41980194 CAGAGGGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:41984064 original size:15 final size:15
Alignment explanation
Indices: 41984035--41984072 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
41984025 AACCCTTAAA
*
41984035 CCATAAATC-ATAAT
1 CCATAAACCAATAAT
*
41984049 CCCTAAACCAATAAT
1 CCATAAACCAATAAT
41984064 CCATAAACC
1 CCATAAACC
41984073 TTAAAATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (15 bp):
CCATAAACCAATAAT
Found at i:41984077 original size:22 final size:21
Alignment explanation
Indices: 41984028--41984077 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
41984018 AAACCCCAAC
*
41984028 CCTTAAACCATAAATCATAAT
1 CCTTAAACCATAAATCATAAA
*
41984049 CCCTAAACCA-ATAATCCATAAA
1 CCTTAAACCATA-AAT-CATAAA
41984071 CCTTAAA
1 CCTTAAA
41984078 ATAGTAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 12 0.50
22 11 0.46
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTTAAACCATAAATCATAAA
Found at i:41984456 original size:40 final size:40
Alignment explanation
Indices: 41984412--41984892 Score: 462
Period size: 40 Copynumber: 12.2 Consensus size: 40
41984402 TTTTTACGGT
* * *
41984412 GTTTTTGATAAAGCGCCGCTAATGCTCGATCTATAGCGTC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * * *
41984452 GTTTTTCTAAAAGCGACGCTAATGCTCCATTTATAGCGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * *
41984492 GTTTTTCAAAAAGTGCCGCTAATGGTCGA-CATATAGCGAC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATC-TATAGCGGC
* *
41984532 GTTTTTCAAAAAACGCCGCTAATGCTCGATCTATAGAGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * * *
41984572 GATTTTCAAAAAGCGCCACTAATGCTCTATCTATAGCGGT
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* *
41984612 GTTTTTCAAAAAGCGCCGCTAATGGTCGA-CATATAGCGAC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATC-TATAGCGGC
* *
41984652 GTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGAGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
* * *
41984692 GATTTTCAAAAACCGCCGCTAATGCTCGATCTATAGCAGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
*
41984732 GTTTTTCAAAAAGCGCCTG-TAATGC-C-A-CTA-A--AGC
1 GTTTTTCAAAAAGCGCC-GCTAATGCTCGATCTATAGCGGC
*** * * ** ** * * * *
41984766 --TCAACAAAAAACGACGACGTTGTGCTTAATTTTTTGCGGT
1 GTTTTTCAAAAAGCGCCG-C-TAATGCTCGATCTATAGCGGC
* * *
41984806 GTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATAGTGGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
*
41984846 GTTTTTCAAAAAAGCGCCGCTAATGCTCGATCTATAGCGGT
1 GTTTTTC-AAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
41984887 GTTTTT
1 GTTTTT
41984893 TTATTCAAAC
Statistics
Matches: 349, Mismatches: 75, Indels: 33
0.76 0.16 0.07
Matches are distributed among these distances:
31 1 0.00
32 10 0.03
34 7 0.02
36 2 0.01
37 4 0.01
38 1 0.00
39 2 0.01
40 272 0.78
41 39 0.11
42 11 0.03
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGC
Found at i:41984755 original size:120 final size:120
Alignment explanation
Indices: 41984412--41984748 Score: 521
Period size: 120 Copynumber: 2.8 Consensus size: 120
41984402 TTTTTACGGT
* * * * * * *
41984412 GTTTTTGATAAAGCGCCGCTAATGCTCGATCTATAGCGTCGTTTTTCTAAAAGCGACGCTAATGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGGCGATTTTCAAAAAGCGCCGCTAATGC
* *
41984477 TCCATTTATAGCGGCGTTTTTCAAAAAGTGCCGCTAATGGTCGACATATAGCGAC
66 TCCATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACATATAGCGAC
* *
41984532 GTTTTTCAAAAAACGCCGCTAATGCTCGATCTATAGAGGCGATTTTCAAAAAGCGCCACTAATGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGGCGATTTTCAAAAAGCGCCGCTAATGC
* *
41984597 TCTATCTATAGCGGTGTTTTTCAAAAAGCGCCGCTAATGGTCGACATATAGCGAC
66 TCCATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACATATAGCGAC
* *
41984652 GTTTTTCAAAAAGCGCCGCTAATACTCGATCTATAGAGGCGATTTTCAAAAACCGCCGCTAATGC
1 GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGGCGATTTTCAAAAAGCGCCGCTAATGC
* *
41984717 TCGATCTATAGCAGCGTTTTTCAAAAAGCGCC
66 TCCATCTATAGCGGCGTTTTTCAAAAAGCGCC
41984749 TGTAATGCCA
Statistics
Matches: 197, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 197 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.28
Consensus pattern (120 bp):
GTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGAGGCGATTTTCAAAAAGCGCCGCTAATGC
TCCATCTATAGCGGCGTTTTTCAAAAAGCGCCGCTAATGGTCGACATATAGCGAC
Found at i:41984870 original size:41 final size:40
Alignment explanation
Indices: 41984801--41984892 Score: 130
Period size: 41 Copynumber: 2.3 Consensus size: 40
41984791 TTAATTTTTT
* *
41984801 GCGGTGTTTTTCAAAAAGCGCCGCTAATGGTCGACCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
* *
41984841 GTGGCGTTTTTCAAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTC-AAAAAGCGCCGCTAATGCTCGACCTATA
*
41984882 GCGGTGTTTTT
1 GCGGCGTTTTT
41984893 TTATTCAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
40 10 0.22
41 35 0.78
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
Found at i:41990024 original size:20 final size:20
Alignment explanation
Indices: 41989935--41990024 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
41989925 TTTAGATTTT
41989935 TTTTGAATTTTTAAAAATATAAA
1 TTTTGAATTTTTAAAAAT-T--A
* *
41989958 TTTTGAAATTTATATAAA-TA
1 TTTTG-AATTTTTAAAAATTA
41989978 TTTTGAA--TTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
*
41989996 TTTTAAATTTTTAAAAATTA
1 TTTTGAATTTTTAAAAATTA
41990016 TTTTGAATT
1 TTTTGAATT
41990025 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
17 6 0.11
18 8 0.14
19 2 0.04
20 25 0.44
22 1 0.02
23 5 0.09
24 10 0.18
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTGAATTTTTAAAAATTA
Found at i:41995821 original size:13 final size:13
Alignment explanation
Indices: 41995803--41995827 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41995793 TCAAGGCAAA
41995803 TAATGCTATCAAC
1 TAATGCTATCAAC
41995816 TAATGCTATCAA
1 TAATGCTATCAA
41995828 TACTTGATGT
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:0.20, G:0.08, T:0.32
Consensus pattern (13 bp):
TAATGCTATCAAC
Found at i:41998171 original size:6 final size:6
Alignment explanation
Indices: 41998157--41998210 Score: 99
Period size: 6 Copynumber: 9.0 Consensus size: 6
41998147 AACGGAAGAG
*
41998157 AGTGGA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA
1 AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA AGTGAA
41998205 AGTGAA
1 AGTGAA
41998211 GAGGCAGCTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.17
Consensus pattern (6 bp):
AGTGAA
Found at i:42007135 original size:15 final size:15
Alignment explanation
Indices: 42007110--42007144 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42007100 AACTCTATTT
*
42007110 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
42007124 TAATTAATATTAAGA
1 TAATTAATATTAAGA
42007139 TAATTA
1 TAATTA
42007145 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:42027335 original size:22 final size:21
Alignment explanation
Indices: 42027309--42027367 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
42027299 TAAATAATTT
42027309 AAAATTTATAAAAATATTAAA
1 AAAATTTATAAAAATATTAAA
* * * *
42027330 CAAAATTAATTCAAAATTTTTAA
1 -AAAATTTA-TAAAAATATTAAA
42027353 AAAATTATATAAAAA
1 AAAATT-TATAAAAA
42027368 GTTTAGGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATTTATAAAAATATTAAA
Found at i:42029825 original size:30 final size:31
Alignment explanation
Indices: 42029781--42029840 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
42029771 TTCTTATGCC
42029781 AATATTTCGATACCCATATCTTTGACTTTTT
1 AATATTTCGATACCCATATCTTTGACTTTTT
42029812 AATATTT-GATACCCATATCTTTGACTTTT
1 AATATTTCGATACCCATATCTTTGACTTTT
42029841 CATAATATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (31 bp):
AATATTTCGATACCCATATCTTTGACTTTTT
Found at i:42031205 original size:30 final size:30
Alignment explanation
Indices: 42031171--42031235 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
42031161 AGTTAGGAGT
42031171 ATTTGTATGTAGTTTAAAGGTGGAGAAGAG
1 ATTTGTATGTAGTTTAAAGGTGGAGAAGAG
*
42031201 ATTTGTATGTAGTTTAAAGGTGGATAAGAG
1 ATTTGTATGTAGTTTAAAGGTGGAGAAGAG
42031231 ATTTG
1 ATTTG
42031236 GATTACCCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.31, T:0.37
Consensus pattern (30 bp):
ATTTGTATGTAGTTTAAAGGTGGAGAAGAG
Found at i:42044879 original size:15 final size:15
Alignment explanation
Indices: 42044824--42044880 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
42044814 TTTATATTAC
42044824 AAAATATTTATTATT
1 AAAATATTTATTATT
** *
42044839 AATGTATTTATAATTGT
1 AAAATATTTATTA-T-T
42044856 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
42044873 AAAATATT
1 AAAATATT
42044881 AATATTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 17 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:42044945 original size:14 final size:14
Alignment explanation
Indices: 42044914--42044952 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
42044904 ATATGAAGAA
42044914 TATTATTTAAAA-T
1 TATTATTTAAAATT
42044927 TATTATTTAAAATT
1 TATTATTTAAAATT
42044941 TATTA-TTAAAAT
1 TATTATTTAAAAT
42044953 AAAATTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 19 0.76
14 6 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTTAAAATT
Found at i:42057555 original size:27 final size:27
Alignment explanation
Indices: 42057525--42057702 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42057515 ATATTGAGTC
* * * *
42057525 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42057552 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42057579 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42057607 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42057634 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42057661 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42057688 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42057703 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42057664 original size:82 final size:81
Alignment explanation
Indices: 42057546--42057701 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42057536 TGCTATATAA
* *
42057546 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42057611 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42057628 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42057692 CACTTAGTGC
65 CACTTAGTGC
42057702 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42059935 original size:13 final size:14
Alignment explanation
Indices: 42059911--42059946 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
42059901 TTTATATATT
42059911 TTTCCTTATAACCA
1 TTTCCTTATAACCA
42059925 TTTCC-TATAACCA
1 TTTCCTTATAACCA
42059938 TTTCACTTA
1 TTTC-CTTA
42059947 AACGTTTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 12 0.60
14 6 0.30
15 2 0.10
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTCCTTATAACCA
Found at i:42060477 original size:21 final size:21
Alignment explanation
Indices: 42060441--42060536 Score: 87
Period size: 20 Copynumber: 4.8 Consensus size: 21
42060431 TGCAGGCAAG
42060441 GGCA-CAAATGTG-AAACCAG-
1 GGCACCAAA-GTGCAAACCAGA
*
42060460 GGACACCGAAGTGCAAA-CAGA
1 GG-CACCAAAGTGCAAACCAGA
42060481 GGCACCAAAGTGCAAA-CAGA
1 GGCACCAAAGTGCAAACCAGA
* *
42060501 GGCACCAGAGTGCAAA-TAGA
1 GGCACCAAAGTGCAAACCAGA
**
42060521 GGCACTGAAGTGCAAA
1 GGCACCAAAGTGCAAA
42060537 TCCCGTACAA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.03
20 56 0.85
21 8 0.12
ACGTcount: A:0.42, C:0.22, G:0.28, T:0.08
Consensus pattern (21 bp):
GGCACCAAAGTGCAAACCAGA
Found at i:42060491 original size:20 final size:20
Alignment explanation
Indices: 42060463--42060536 Score: 103
Period size: 20 Copynumber: 3.7 Consensus size: 20
42060453 AAACCAGGGA
*
42060463 CACCGAAGTGCAAACAGAGG
1 CACCAAAGTGCAAACAGAGG
42060483 CACCAAAGTGCAAACAGAGG
1 CACCAAAGTGCAAACAGAGG
* *
42060503 CACCAGAGTGCAAATAGAGG
1 CACCAAAGTGCAAACAGAGG
**
42060523 CACTGAAGTGCAAA
1 CACCAAAGTGCAAA
42060537 TCCCGTACAA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.42, C:0.23, G:0.27, T:0.08
Consensus pattern (20 bp):
CACCAAAGTGCAAACAGAGG
Found at i:42065859 original size:19 final size:19
Alignment explanation
Indices: 42065835--42065881 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
42065825 TTATTCCACA
42065835 ATTTTCACAATATCATTTC
1 ATTTTCACAATATCATTTC
42065854 ATTTTCACAATATCATTTC
1 ATTTTCACAATATCATTTC
42065873 ATTTTCACA
1 ATTTTCACA
42065882 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTCACAATATCATTTC
Found at i:42069126 original size:29 final size:29
Alignment explanation
Indices: 42069089--42069215 Score: 121
Period size: 29 Copynumber: 4.4 Consensus size: 29
42069079 TGAGCTTTTT
* * *
42069089 TGGCTATCTCTGGTATAAGAAAGTCTTTG
1 TGGCGATCTCTGTTATAAGAAAGCCTTTG
* * *
42069118 TGGTGATCTCTGTTATAAGGAAGTCTTTG
1 TGGCGATCTCTGTTATAAGAAAGCCTTTG
* ***
42069147 TGGCAATCTCCAATA-AATGAAAGCCTTTG
1 TGGCGATCTCTGTTATAA-GAAAGCCTTTG
*
42069176 TGGCGATCTCTGTTATAAGGAAGCCTTTG
1 TGGCGATCTCTGTTATAAGAAAGCCTTTG
* *
42069205 TGACTATCTCT
1 TGGCGATCTCT
42069216 TAATGAATGC
Statistics
Matches: 78, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
28 2 0.03
29 74 0.95
30 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (29 bp):
TGGCGATCTCTGTTATAAGAAAGCCTTTG
Found at i:42069469 original size:16 final size:16
Alignment explanation
Indices: 42069400--42069467 Score: 118
Period size: 16 Copynumber: 4.2 Consensus size: 16
42069390 TTTGGTTCGC
42069400 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
42069416 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
42069432 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
42069448 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
42069464 TGTA
1 TGTA
42069468 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:42069502 original size:45 final size:44
Alignment explanation
Indices: 42069448--42069542 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42069438 GGATTAGAGG
* *
42069448 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
42069493 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
42069537 TGTAAT
1 TGTAAT
42069543 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:42069725 original size:18 final size:17
Alignment explanation
Indices: 42069704--42069738 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42069694 TTATTATTTA
*
42069704 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42069722 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42069739 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42069732 original size:28 final size:27
Alignment explanation
Indices: 42069662--42069734 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
42069652 TTTATTATCA
*
42069662 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
42069690 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
42069717 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
42069735 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:42069872 original size:18 final size:17
Alignment explanation
Indices: 42069851--42069885 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42069841 TTATTATTAA
*
42069851 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42069869 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42069886 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42069897 original size:147 final size:149
Alignment explanation
Indices: 42069623--42069897 Score: 509
Period size: 147 Copynumber: 1.9 Consensus size: 149
42069613 ATGATTATTG
*
42069623 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
*
42069688 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
42069753 AGAAATTTGTTTTGGTAAA
131 AGAAATTTGTTTTGGTAAA
*
42069772 TTATT-TTATTTAAATTTTAATAAGATTA-TTAATATCAATAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
42069835 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
42069898 ATATTCTTAT
Statistics
Matches: 123, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
147 95 0.77
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (149 bp):
TTATTGTTATTTAAATTTTAATAAGATTATTTAATATCAAAAATAAATAATTTAATCATATTTAA
ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
AGAAATTTGTTTTGGTAAA
Found at i:42070000 original size:18 final size:17
Alignment explanation
Indices: 42069961--42069992 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
42069951 TTTTAAATAA
42069961 TTAATATTAAATATATT
1 TTAATATTAAATATATT
42069978 TTAAT-TTAAATATAT
1 TTAATATTAAATATAT
42069993 GATTTAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAATATTAAATATATT
Found at i:42070117 original size:91 final size:91
Alignment explanation
Indices: 42070022--42070229 Score: 258
Period size: 91 Copynumber: 2.3 Consensus size: 91
42070012 TAATTATAAC
* * * *
42070022 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAA
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAA
*
42070086 TAATATAAAATTTCATAAAATTCTTGA
65 TAATATAAAATTTCATAAAATTCTTAA
* * *
42070113 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAGT
1 TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
* * * *
42070178 GATATATAATTTCATGAAATTGTTAA
66 AATATAAAATTTCATAAAATTCTTAA
*
42070204 TAATAAAATGT-TCTTATATGAATTTA
1 TAAT-AAAT-TATATTATATGAATTTA
42070230 CTAAAATCAA
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
91 79 0.77
92 22 0.22
93 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (91 bp):
TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
AATATAAAATTTCATAAAATTCTTAA
Found at i:42070758 original size:12 final size:12
Alignment explanation
Indices: 42070743--42070772 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42070733 AATACAAACA
42070743 ACAGAAGCTGCT
1 ACAGAAGCTGCT
42070755 ACAGAAGCTGCT
1 ACAGAAGCTGCT
*
42070767 AAAGAA
1 ACAGAA
42070773 ATTAACCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.13
Consensus pattern (12 bp):
ACAGAAGCTGCT
Found at i:42071051 original size:14 final size:14
Alignment explanation
Indices: 42071032--42071062 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
42071022 AAAATATTAA
42071032 CAACAAATAGTTCC
1 CAACAAATAGTTCC
42071046 CAACAAATAGTTCC
1 CAACAAATAGTTCC
42071060 CAA
1 CAA
42071063 TTGCCAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.29, G:0.06, T:0.19
Consensus pattern (14 bp):
CAACAAATAGTTCC
Found at i:42075300 original size:16 final size:17
Alignment explanation
Indices: 42075279--42075323 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
42075269 ATAAAACAAT
*
42075279 TTAAAATAAT-TTAATA
1 TTAAAATAATAATAATA
42075295 TTAAAATAATAAAATAATA
1 TTAAAATAAT--AATAATA
42075314 TTAAAATAAT
1 TTAAAATAAT
42075324 CAAAACAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 10 0.40
19 15 0.60
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAATAATAATAATA
Found at i:42075312 original size:19 final size:20
Alignment explanation
Indices: 42075290--42075333 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
42075280 TAAAATAATT
42075290 TAATATTAAAATAAT-AAAA
1 TAATATTAAAATAATCAAAA
42075309 TAATATTAAAATAATCAAAA
1 TAATATTAAAATAATCAAAA
*
42075329 CAATA
1 TAATA
42075334 ATCTTTCAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATATTAAAATAATCAAAA
Found at i:42076302 original size:19 final size:18
Alignment explanation
Indices: 42076278--42076312 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42076268 AACAAATAAT
*
42076278 TTAAAATTTATAAAAAAA
1 TTAAAAATTATAAAAAAA
42076296 TTAAAAATTATAAAAAA
1 TTAAAAATTATAAAAAA
42076313 GTACAAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAATTATAAAAAAA
Found at i:42080322 original size:9 final size:9
Alignment explanation
Indices: 42080308--42080337 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42080298 GTTAAACGAA
42080308 TCGAGTTAT
1 TCGAGTTAT
*
42080317 TCGAGTTAA
1 TCGAGTTAT
42080326 TCGAGTTAT
1 TCGAGTTAT
42080335 TCG
1 TCG
42080338 GATCAACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:42080408 original size:9 final size:9
Alignment explanation
Indices: 42080391--42080427 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42080381 TGAGTTTTCG
42080391 AATTCGAAT
1 AATTCGAAT
*
42080400 AACTCGAAT
1 AATTCGAAT
42080409 AATTCGAAT
1 AATTCGAAT
42080418 AATTCGAAT
1 AATTCGAAT
42080427 A
1 A
42080428 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:42080675 original size:30 final size:31
Alignment explanation
Indices: 42080641--42080700 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
42080631 AAACCTTTTA
*
42080641 TTTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
* *
42080671 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCCAAAACTTTTACTCCCTTCCCA
42080701 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:42082546 original size:29 final size:29
Alignment explanation
Indices: 42082483--42082554 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 29
42082473 TATAAAGGCT
* * **
42082483 TATTCTTGTAAATTTTTAAAAAATTGGTC
1 TATTTTTGTAAATTTTTAAAAAAATGACC
42082512 TATTTTTGT-AATATTTTAAAAAAATGACC
1 TATTTTTGTAAAT-TTTTAAAAAAATGACC
* *
42082541 T-CTTTTGAAAATTT
1 TATTTTTGTAAATTT
42082555 AGTCTGAGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
28 10 0.29
29 25 0.71
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (29 bp):
TATTTTTGTAAATTTTTAAAAAAATGACC
Found at i:42083149 original size:31 final size:30
Alignment explanation
Indices: 42083108--42083166 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
42083098 ACAAGGTCAG
*
42083108 TTTTTACAAAACATTATCAGATTAGGCCATT
1 TTTTTACAAAA-ATTATCAGATTAAGCCATT
* *
42083139 TTTTTTCAAAATTTATCAGATTAAGCCA
1 TTTTTACAAAAATTATCAGATTAAGCCA
42083167 ATTTGGGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (30 bp):
TTTTTACAAAAATTATCAGATTAAGCCATT
Found at i:42087930 original size:13 final size:13
Alignment explanation
Indices: 42087912--42087936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42087902 TAATGGTATA
42087912 TTGAATCCATGAT
1 TTGAATCCATGAT
42087925 TTGAATCCATGA
1 TTGAATCCATGA
42087937 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGAATCCATGAT
Found at i:42099843 original size:40 final size:40
Alignment explanation
Indices: 42099788--42099869 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
42099778 CTTAAACTCA
42099788 CTTTTCTAGTCAACAACACGATGAAGCAAACAAATTGGTG
1 CTTTTCTAGTCAACAACACGATGAAGCAAACAAATTGGTG
*
42099828 CTTTTCTAGTCAACAACACGATGGAGCAAACAAATTGGTG
1 CTTTTCTAGTCAACAACACGATGAAGCAAACAAATTGGTG
42099868 CT
1 CT
42099870 AACTTACTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (40 bp):
CTTTTCTAGTCAACAACACGATGAAGCAAACAAATTGGTG
Found at i:42106503 original size:36 final size:35
Alignment explanation
Indices: 42106456--42106525 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
42106446 GGAGCACATC
*
42106456 AGTCAAAATAGATCCGAAAGACTGCTGAACTGAATT
1 AGTCAAAATAGATCC-AAAGACTACTGAACTGAATT
* *
42106492 AGTCAGAATAGATCCAAAGGCTACTGAACTGAAT
1 AGTCAAAATAGATCCAAAGACTACTGAACTGAAT
42106526 AGAGTTTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 17 0.55
36 14 0.45
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.21
Consensus pattern (35 bp):
AGTCAAAATAGATCCAAAGACTACTGAACTGAATT
Found at i:42109118 original size:23 final size:22
Alignment explanation
Indices: 42109078--42109137 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
42109068 AATTATTGTA
* * * *
42109078 ATTATAATTTAAGATCAAATATT
1 ATTATAA-TTATGGTCAAACATC
42109101 ATTATAATTACTGGTCAAACATC
1 ATTATAATTA-TGGTCAAACATC
42109124 ATTATAATTATGGT
1 ATTATAATTATGGT
42109138 AATTATAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 7 0.22
23 25 0.78
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (22 bp):
ATTATAATTATGGTCAAACATC
Found at i:42111060 original size:21 final size:20
Alignment explanation
Indices: 42111022--42111064 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
42111012 ATCTTGTGAT
*
42111022 TTTTTTATGTTAAATGATGAA
1 TTTTTAATGTTAAATGAT-AA
* *
42111043 TTTTTAATGTTGATTGATAA
1 TTTTTAATGTTAAATGATAA
42111063 TT
1 TT
42111065 AAAATTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (20 bp):
TTTTTAATGTTAAATGATAA
Found at i:42123053 original size:20 final size:20
Alignment explanation
Indices: 42123025--42123150 Score: 110
Period size: 20 Copynumber: 6.3 Consensus size: 20
42123015 TACCGAAGTA
42123025 CAAACAGGGGCACGTATGTG
1 CAAACAGGGGCACGTATGTG
* *
42123045 CAAATAGGGGCACGTACGTG
1 CAAACAGGGGCACGTATGTG
* * * *
42123065 CAAACAGGGGTATC-AAAGTA
1 CAAACAGGGGCA-CGTATGTG
* * *
42123085 CAAATAGGGGCGCGTATATG
1 CAAACAGGGGCACGTATGTG
* ** * *
42123105 CAAACAGGGGTACCAAAGTA
1 CAAACAGGGGCACGTATGTG
42123125 CAAACAGGGGCACGTATGTG
1 CAAACAGGGGCACGTATGTG
42123145 CAAACA
1 CAAACA
42123151 TTCAACAATT
Statistics
Matches: 77, Mismatches: 27, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
19 1 0.01
20 75 0.97
21 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.14
Consensus pattern (20 bp):
CAAACAGGGGCACGTATGTG
Found at i:42123070 original size:40 final size:39
Alignment explanation
Indices: 42123045--42123150 Score: 158
Period size: 40 Copynumber: 2.7 Consensus size: 39
42123035 CACGTATGTG
*
42123045 CAAATAGGGGCACGTACGTGCAAACAGGGGTATCAAAGTA
1 CAAATAGGGGCACGTATGTGCAAACAGGGGTA-CAAAGTA
* *
42123085 CAAATAGGGGCGCGTATATGCAAACAGGGGTACCAAAGTA
1 CAAATAGGGGCACGTATGTGCAAACAGGGGTA-CAAAGTA
*
42123125 CAAACAGGGGCACGTATGTGCAAACA
1 CAAATAGGGGCACGTATGTGCAAACA
42123151 TTCAACAATT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.38, C:0.19, G:0.29, T:0.14
Consensus pattern (39 bp):
CAAATAGGGGCACGTATGTGCAAACAGGGGTACAAAGTA
Found at i:42123129 original size:60 final size:60
Alignment explanation
Indices: 42123020--42123134 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
42123010 CAGGGTACCG
* * ** * *
42123020 AAGTACAAACAGGGGCACGTATGTGCAAATAGGGGCACGTACGTGCAAACAGGGGTATCA
1 AAGTACAAACAGGGGCACGTATATGCAAACAGGGGCACCAAAGTACAAACAGGGGTATCA
* * *
42123080 AAGTACAAATAGGGGCGCGTATATGCAAACAGGGGTACCAAAGTACAAACAGGGG
1 AAGTACAAACAGGGGCACGTATATGCAAACAGGGGCACCAAAGTACAAACAGGGG
42123135 CACGTATGTG
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 46 1.00
ACGTcount: A:0.37, C:0.17, G:0.31, T:0.14
Consensus pattern (60 bp):
AAGTACAAACAGGGGCACGTATATGCAAACAGGGGCACCAAAGTACAAACAGGGGTATCA
Found at i:42129517 original size:46 final size:46
Alignment explanation
Indices: 42129465--42129558 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
42129455 TTCAATTGGG
* *
42129465 TTTATCATCCATCTCAACATAACATATTTTCCATATAGCTCACCAT
1 TTTATCACCCATCTCAACATAACATATTTTACATATAGCTCACCAT
*
42129511 TTTATCACCCATCTCAACATAACATATTTTACATGTAGCTCACCAT
1 TTTATCACCCATCTCAACATAACATATTTTACATATAGCTCACCAT
42129557 TT
1 TT
42129559 CAAAGTCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (46 bp):
TTTATCACCCATCTCAACATAACATATTTTACATATAGCTCACCAT
Found at i:42131478 original size:46 final size:46
Alignment explanation
Indices: 42131426--42131519 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
42131416 TTCAATTGGG
* *
42131426 TTTATCATCCATCTCAACATAACATATTTTCCATATAGCTCACCAT
1 TTTATCACCCATCTCAACATAACATATTTTACATATAGCTCACCAT
*
42131472 TTTATCACCCATCTCAACATAACATATTTTACATGTAGCTCACCAT
1 TTTATCACCCATCTCAACATAACATATTTTACATATAGCTCACCAT
42131518 TT
1 TT
42131520 CAAAGTCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (46 bp):
TTTATCACCCATCTCAACATAACATATTTTACATATAGCTCACCAT
Found at i:42132568 original size:18 final size:18
Alignment explanation
Indices: 42132545--42132582 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
42132535 AAAAATCACT
42132545 TAACAA-AATACTTTTAAA
1 TAACAACAATA-TTTTAAA
42132563 TAACAACTAATATTTTAAA
1 TAACAAC-AATATTTTAAA
42132582 T
1 T
42132583 TCATCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 8 0.44
20 4 0.22
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (18 bp):
TAACAACAATATTTTAAA
Found at i:42134700 original size:24 final size:24
Alignment explanation
Indices: 42134673--42134721 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
42134663 ATTATGAACT
*
42134673 TTTATGCATACCTTCATAAGTTTC
1 TTTATGCATACCCTCATAAGTTTC
* *
42134697 TTTATTCATACCCTCATGAGTTTC
1 TTTATGCATACCCTCATAAGTTTC
42134721 T
1 T
42134722 ACTTATCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (24 bp):
TTTATGCATACCCTCATAAGTTTC
Found at i:42142940 original size:20 final size:20
Alignment explanation
Indices: 42142915--42142958 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
42142905 TACGTATGTG
*
42142915 CAAACAGGAGTACCAAAGTA
1 CAAACAGAAGTACCAAAGTA
**
42142935 CAAACAGAAGTACTGAAGTA
1 CAAACAGAAGTACCAAAGTA
42142955 CAAA
1 CAAA
42142959 TAGGGGCATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.18, G:0.18, T:0.11
Consensus pattern (20 bp):
CAAACAGAAGTACCAAAGTA
Found at i:42143004 original size:40 final size:40
Alignment explanation
Indices: 42142935--42143038 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
42142925 TACCAAAGTA
** *
42142935 CAAACAGAAGTACTGAAGTACAAATAGGGGCA-TATATGTG
1 CAAACAGGGGTACCGAAGTACAAATAGGGGCACT-TATGTG
* *
42142975 CAAATAGGGGTACCGAAGTATAAATAGGGGCACTTATGTG
1 CAAACAGGGGTACCGAAGTACAAATAGGGGCACTTATGTG
* *
42143015 CTAACAGGGGTACCGAAGTGCAAA
1 CAAACAGGGGTACCGAAGTACAAA
42143039 CTAAGAAACC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 53 0.98
41 1 0.02
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.19
Consensus pattern (40 bp):
CAAACAGGGGTACCGAAGTACAAATAGGGGCACTTATGTG
Found at i:42145307 original size:21 final size:21
Alignment explanation
Indices: 42145281--42145326 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
42145271 AGTGTAAATC
42145281 GGGGCACGTATGCGCAATTCA
1 GGGGCACGTATGCGCAATTCA
* *
42145302 GGGGCACGTATGTGTAATTCA
1 GGGGCACGTATGCGCAATTCA
42145323 GGGG
1 GGGG
42145327 ATAATTAACT
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:0.22, C:0.17, G:0.39, T:0.22
Consensus pattern (21 bp):
GGGGCACGTATGCGCAATTCA
Found at i:42147165 original size:30 final size:30
Alignment explanation
Indices: 42147129--42147189 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
42147119 ATCCTAACGG
*
42147129 ATCGAAAGAACAAAGTGATAGTACTATCTC
1 ATCGAAAGAACAAAATGATAGTACTATCTC
42147159 ATCGAAAGAACAAAATGATAGTACTATCTC
1 ATCGAAAGAACAAAATGATAGTACTATCTC
42147189 A
1 A
42147190 AGCTTCATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.23
Consensus pattern (30 bp):
ATCGAAAGAACAAAATGATAGTACTATCTC
Found at i:42156800 original size:19 final size:19
Alignment explanation
Indices: 42156776--42156831 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
42156766 ACATATTAAA
42156776 CCGAGTTATAAAATTTCAT
1 CCGAGTTATAAAATTTCAT
42156795 CCGAGTTATAAAATTTCAT
1 CCGAGTTATAAAATTTCAT
* * *
42156814 CCAAATTAAAAAATTTCA
1 CCGAGTTATAAAATTTCA
42156832 AATTATTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (19 bp):
CCGAGTTATAAAATTTCAT
Found at i:42158403 original size:16 final size:16
Alignment explanation
Indices: 42158382--42158413 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42158372 ATTTTGTTAC
*
42158382 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
42158398 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
42158414 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:42160536 original size:42 final size:42
Alignment explanation
Indices: 42160456--42160537 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
42160446 CGTTTTCTCT
**
42160456 ATGCCATAGTCCAACTATGGTCTTACACATATTTACATATTG
1 ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
*
42160498 ATGCCATAG-CCTAGCTATGGTCTTACACAGTA-GCACATAT
1 ATGCCATAGTCC-AACTATGGTCTTACACA-TATGCACATAT
42160538 CACACCGATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 2 0.06
42 31 0.89
43 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (42 bp):
ATGCCATAGTCCAACTATGGTCTTACACATATGCACATATTG
Found at i:42163350 original size:16 final size:16
Alignment explanation
Indices: 42163329--42163360 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42163319 GTTTTGTTGC
*
42163329 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
42163345 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
42163361 CTTTCAATCA
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:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:42163646 original size:51 final size:51
Alignment explanation
Indices: 42163588--42163778 Score: 185
Period size: 51 Copynumber: 3.8 Consensus size: 51
42163578 CCGGTTCACA
* *
42163588 TAGTAGCCTGCACATAGTACTACACATGTGGCCATCACTATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATTCGATACACG
* * * ** *
42163639 TAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTATGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATTCGATACACG
* * * * *
42163690 TAGTAGCTTGCACATAGTACTATACATGCGACC-T-A-TCATTCTAGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT-ATTCGA-TACACG
*
42163740 TAGTAGCCTGCACAAAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
42163779 TTCACTTTCA
Statistics
Matches: 108, Mismatches: 24, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
48 1 0.01
49 3 0.03
50 34 0.31
51 66 0.61
52 3 0.03
53 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATTCGATACACG
Found at i:42163767 original size:101 final size:102
Alignment explanation
Indices: 42163586--42163770 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 102
42163576 TACCGGTTCA
* * *
42163586 CATAGTAGCCTGCACATAGTACTACACATGTGGCCATCACTATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATTAGATACACGTAGTAGCCTGCA
*
42163651 CATAGTACTACACACGTGATCGAAGCTATCCGGTATG
66 CAAAGTACTACACACGTGATCGAAGCTATCCGGTATG
* *
42163688 CATAGTAGCTTGCACATAGTACTATACATGCGACCTATCA-T-TCTAG-TACACGTAGTAGCCTG
1 CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTAT-TAGATACACGTAGTAGCCTG
42163750 CACAAAGTACTACACACGTGA
64 CACAAAGTACTACACACGTGA
42163771 CCATCACTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 37 0.49
102 34 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (102 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATTAGATACACGTAGTAGCCTGCA
CAAAGTACTACACACGTGATCGAAGCTATCCGGTATG
Found at i:42168091 original size:22 final size:21
Alignment explanation
Indices: 42168056--42168114 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
42168046 AAAGGATATC
* *
42168056 TACAAATTAAATCTATAAGAT
1 TACAAATCATATCTATAAGAT
*
42168077 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TATAAGAT
* *
42168100 TGCATATCATATCTA
1 TACAAATCATATCTA
42168115 AGATTGCATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTATAAGAT
Found at i:42168924 original size:44 final size:44
Alignment explanation
Indices: 42168841--42168958 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
42168831 TTTCGATTTG
* * * * *
42168841 CTCCACTGCTGCTTAGGGAGATAAGA-TCTGTAATTTTCAACCTA
1 CTCCACTGCTGCTCAGAGAGATAGGATTC-ATAATCTTCAACCTA
42168885 CTCCACTGCTGCTCAGAGAGATAGGATTCATAATCTTCAACCTA
1 CTCCACTGCTGCTCAGAGAGATAGGATTCATAATCTTCAACCTA
* *
42168929 TTCCACTGCTGAC-CAGTGAGATAGGATTCA
1 CTCCACTGCTG-CTCAGAGAGATAGGATTCA
42168959 CCTATTCCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 62 0.95
45 3 0.05
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
CTCCACTGCTGCTCAGAGAGATAGGATTCATAATCTTCAACCTA
Found at i:42168967 original size:34 final size:34
Alignment explanation
Indices: 42168924--42169100 Score: 230
Period size: 34 Copynumber: 4.9 Consensus size: 34
42168914 ATAATCTTCA
*
42168924 ACCTATTCCACTGCTGACCAGTGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
42168958 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGG-------A--TTC
42169001 AACCTATTCCACTGCTGACCAGGGAGATCA-GATTC
1 -ACCTATTCCACTGCTGACCAGGGAGAT-AGGATTC
42169036 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
*
42169070 ACCTATTCCACTGCTGACTAGGGAGATAGGA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA
42169101 CTTACAATCT
Statistics
Matches: 129, Mismatches: 2, Indels: 24
0.83 0.01 0.15
Matches are distributed among these distances:
33 1 0.01
34 91 0.71
35 3 0.02
37 1 0.01
41 1 0.01
43 3 0.02
44 28 0.22
45 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (34 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTC
Found at i:42169009 original size:78 final size:78
Alignment explanation
Indices: 42168880--42169181 Score: 333
Period size: 78 Copynumber: 3.9 Consensus size: 78
42168870 GTAATTTTCA
* * *
42168880 ACCTACTCCACTGCTG-CTCAGAGAGATAGGATTCATAATCTTCAACCTATTCCACTGCTGACCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCA
*
42168944 GTGAGATAGGATTC
65 GGGAGATAGGATTC
42168958 ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGACCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTGACCA
42169022 GGGAGATCA-GATTC
65 GGGAGAT-AGGATTC
*
42169036 ACCTATTCCACTGCTGACCAGGGAGATAGG-------A--TTC-ACCTATTCCACTGCTGACTAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAG
42169091 GGAGATAGGACTTAC
66 GGAGATAGGA-TT-C
* *
42169106 AATCTTCAATCTCTTCCACTGCTGACCAGGAAGATAGGATTCACAATCTTCAACCTATTCCACTG
1 -A----C---CTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTG
42169171 CTGACCAGGGA
58 CTGACCAGGGA
42169182 AGTAGGACTT
Statistics
Matches: 192, Mismatches: 8, Indels: 38
0.81 0.03 0.16
Matches are distributed among these distances:
67 1 0.01
68 28 0.15
69 5 0.03
70 1 0.01
71 2 0.01
75 1 0.01
78 123 0.64
79 4 0.02
85 1 0.01
87 3 0.02
88 23 0.12
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.25
Consensus pattern (78 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACCAG
GGAGATAGGATTC
Found at i:42169021 original size:44 final size:44
Alignment explanation
Indices: 42168958--42169229 Score: 327
Period size: 44 Copynumber: 6.6 Consensus size: 44
42168948 GATAGGATTC
42168958 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
*
42169002 ACCTATTCCACTGCTGACCAGGGAGAT----C--A-GA--TTC-
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
42169036 ACCTATTCCACTGCTGACCAGGGAGATAGG-------A--TTC-
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
*
42169070 ACCTATTCCACTGCTGACTAGGGAGATAGGACTTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
* * *
42169114 ATCTCTTCCACTGCTGACCAGGAAGATAGGA-TTCACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCA
42169158 ACCTATTCCACTGCTGACCAGGGA-AGTAGGACTTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGA-TAGGACTTACAATCTTCA
42169202 ACCTATTCCACTGCTGACCAGGGAGATA
1 ACCTATTCCACTGCTGACCAGGGAGATA
42169230 AAGTTTTGTG
Statistics
Matches: 202, Mismatches: 9, Indels: 34
0.82 0.04 0.14
Matches are distributed among these distances:
34 60 0.30
35 3 0.01
37 1 0.00
38 1 0.00
40 1 0.00
41 1 0.00
43 6 0.03
44 126 0.62
45 3 0.01
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCA
Found at i:42169123 original size:112 final size:112
Alignment explanation
Indices: 42168924--42169149 Score: 391
Period size: 112 Copynumber: 2.0 Consensus size: 112
42168914 ATAATCTTCA
*
42168924 ACCTATTCCACTGCTGACCAGTGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGA
*
42168989 CTTACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATCA-GATTC
66 CTTACAATCTTCAACCTATTCCACTGCTGACCAGGAAGAT-AGGATTC
*
42169036 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTATTCCACTGCTGACTAGGGAGATAGGA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGA
* *
42169101 CTTACAATCTTCAATCTCTTCCACTGCTGACCAGGAAGATAGGATTC
66 CTTACAATCTTCAACCTATTCCACTGCTGACCAGGAAGATAGGATTC
42169148 AC
1 AC
42169150 AATCTTCAAC
Statistics
Matches: 108, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 1 0.01
112 107 0.99
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (112 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACCTATTCCACTGCTGACCAGGGAGATAGGA
CTTACAATCTTCAACCTATTCCACTGCTGACCAGGAAGATAGGATTC
Found at i:42170510 original size:6 final size:6
Alignment explanation
Indices: 42170501--42170529 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42170491 CTTTGTCTTT
42170501 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
42170530 TTATCACTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:42171401 original size:25 final size:25
Alignment explanation
Indices: 42171348--42171413 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
42171338 AAGAAAATCC
* *
42171348 AAAAGAATGAAAGAATAATTATTCG
1 AAAAGAATGAAAGAATAATTACTCA
*
42171373 AAAAGAATGAAAGAAT-ATTGGCTCA
1 AAAAGAATGAAAGAATAATT-ACTCA
42171398 AAAATGAATGCAAAGA
1 AAAA-GAATG-AAAGA
42171414 TGTATTTCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
24 3 0.09
25 22 0.63
26 5 0.14
27 5 0.14
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.20
Consensus pattern (25 bp):
AAAAGAATGAAAGAATAATTACTCA
Found at i:42175456 original size:23 final size:22
Alignment explanation
Indices: 42175416--42175458 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
42175406 AAATTATAAA
*
42175416 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
42175438 ATATAAGAAAAATATATATGT
1 ATATAA-AAAAATATATATGT
42175459 GTGTGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:42175587 original size:36 final size:36
Alignment explanation
Indices: 42175547--42175622 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
42175537 TGAAACATAG
*
42175547 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
42175583 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
42175620 AAA
1 AAA
42175623 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:42176158 original size:23 final size:22
Alignment explanation
Indices: 42176115--42176181 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
42176105 AAAGGATATC
* *
42176115 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
42176136 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* * *
42176159 TGCATATCGTATCTTCTAAGAT
1 TACAAATCATATCTTCTAAGAT
42176181 T
1 T
42176182 GCATATCCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 3 0.08
22 26 0.67
23 10 0.26
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:42176182 original size:22 final size:22
Alignment explanation
Indices: 42176128--42176188 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
42176118 AAATTAAATC
* *
42176128 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
*
42176151 TCTAAGATTGCATATCGTATCT
1 TCTAAGATTGCATATCATATCT
42176173 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
42176189 CTTGAAGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 25 0.71
23 10 0.29
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:42191381 original size:20 final size:20
Alignment explanation
Indices: 42191356--42191421 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
42191346 CACATTAATG
42191356 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
42191376 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * *
42191396 CTCTTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTCGGTA
42191416 CCCCTG
1 CCCCTG
42191422 AATGCACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.09, C:0.29, G:0.20, T:0.42
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:42191559 original size:40 final size:40
Alignment explanation
Indices: 42191360--42191550 Score: 249
Period size: 40 Copynumber: 4.8 Consensus size: 40
42191350 TTAATGCCCC
** * * *
42191360 TGTTTGTACTTCGGTACCCCTGTTTGTAC-TTCGGTACTCT
1 TGTTTGTACTTCGGTACCCCTGAATGCACATAC-GTGCTCT
* *
42191400 TGTTTGTACTTTGGTACCCCTGAATGCACATACGTGCTAT
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCT
*
42191440 TGTTTGTACTTCGGTACCTCTGAATGCACATACGTGCTCT
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCT
* * * *
42191480 TGCTTGTACTTCGATACCCCTGAATGCACATGCATGCTCT
1 TGTTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCT
*
42191520 TGTTTGTACTTCGGTACCCCTAAATGCACAT
1 TGTTTGTACTTCGGTACCCCTGAATGCACAT
42191551 TTTTGCTCTG
Statistics
Matches: 132, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 130 0.98
41 2 0.02
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.38
Consensus pattern (40 bp):
TGTTTGTACTTCGGTACCCCTGAATGCACATACGTGCTCT
Found at i:42192597 original size:19 final size:19
Alignment explanation
Indices: 42192573--42192618 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
42192563 GTGACCCATG
42192573 TTTCTCAAATTTTC-ATGTT
1 TTTCTCAAATTTTCTAT-TT
42192592 TTTCTCAAATTTTCTATTT
1 TTTCTCAAATTTTCTATTT
*
42192611 TATCTCAA
1 TTTCTCAA
42192619 TTAGATCCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 23 0.92
20 2 0.08
ACGTcount: A:0.24, C:0.17, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTCTCAAATTTTCTATTT
Found at i:42199043 original size:40 final size:40
Alignment explanation
Indices: 42198927--42199043 Score: 126
Period size: 40 Copynumber: 2.9 Consensus size: 40
42198917 AGTACCTCGA
* * * *
42198927 TTTGTACTTTGGTAGCCCTGAATGCATAAACATGCTCCTG
1 TTTGTACTTCGGTACCCCTGAATGCACATACATGCTCCTG
* * * * *
42198967 TTTATTCTTCGGTACCCCTGAATACACATGCGTGCTCCTG
1 TTTGTACTTCGGTACCCCTGAATGCACATACATGCTCCTG
* * *
42199007 TTTGTACTTCGGTATCCTTGAATGCACATTCATGCTC
1 TTTGTACTTCGGTACCCCTGAATGCACATACATGCTC
42199044 TAAATGCACT
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.37
Consensus pattern (40 bp):
TTTGTACTTCGGTACCCCTGAATGCACATACATGCTCCTG
Found at i:42215713 original size:79 final size:82
Alignment explanation
Indices: 42215602--42215786 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 82
42215592 GCTACTCGTT
* *
42215602 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
42215665 GGATTTAGTAAC-TCGCA
65 GGATATAGTAACTTAGCA
* **
42215682 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
* *
42215745 GATATGGTCACTTAGCA
66 GATATAGTAACTTAGCA
42215762 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42215787 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:42215786 original size:40 final size:40
Alignment explanation
Indices: 42215583--42215786 Score: 238
Period size: 40 Copynumber: 5.1 Consensus size: 40
42215573 CGGAATTTAA
** *
42215583 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42215623 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42215663 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42215702 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42215742 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42215782 CCGGA
1 CCGGA
42215787 CATCATTCAA
Statistics
Matches: 141, Mismatches: 16, Indels: 14
0.82 0.09 0.08
Matches are distributed among these distances:
38 2 0.01
39 33 0.23
40 94 0.67
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42225589 original size:12 final size:12
Alignment explanation
Indices: 42225569--42225604 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
42225559 CAAAAAGATC
42225569 ATTTCCATTTTT
1 ATTTCCATTTTT
* *
42225581 ATTTTCATTTTC
1 ATTTCCATTTTT
42225593 ATTTCCATTTTT
1 ATTTCCATTTTT
42225605 GGAAACCTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTCCATTTTT
Found at i:42234557 original size:18 final size:16
Alignment explanation
Indices: 42234536--42234579 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
42234526 ACATTTGCTC
*
42234536 TTTCTTTTTTCCTTTTTT
1 TTTCTTTTTT-C-TATTT
*
42234554 TTTCTTTTCTCTATTT
1 TTTCTTTTTTCTATTT
42234570 TTTCTTTTTT
1 TTTCTTTTTT
42234580 ATTCGAGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 13 0.57
17 1 0.04
18 9 0.39
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTCTATTT
Found at i:42237506 original size:15 final size:16
Alignment explanation
Indices: 42237479--42237508 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42237469 GATAATAATT
42237479 AATATATATTATATAA
1 AATATATATTATATAA
42237495 AATATA-ATTATATA
1 AATATATATTATATA
42237509 TTAGTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:42240094 original size:20 final size:20
Alignment explanation
Indices: 42240069--42240109 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
42240059 TTGTAAGGGA
*
42240069 TTGCACTTCGGTACCTTTGT
1 TTGCACTTCAGTACCTTTGT
*
42240089 TTGCACTTCAGTGCCTTTGT
1 TTGCACTTCAGTACCTTTGT
42240109 T
1 T
42240110 AGCATTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.24, G:0.20, T:0.46
Consensus pattern (20 bp):
TTGCACTTCAGTACCTTTGT
Found at i:42240824 original size:21 final size:21
Alignment explanation
Indices: 42240798--42240844 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
42240788 GTAATAATGA
42240798 TCATGTTTGATTTGCCTTCGG
1 TCATGTTTGATTTGCCTTCGG
*
42240819 TCATGTTTGATTTGCCTTTGG
1 TCATGTTTGATTTGCCTTCGG
42240840 T-ATGT
1 TCATGT
42240845 GGTGGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.11, C:0.15, G:0.23, T:0.51
Consensus pattern (21 bp):
TCATGTTTGATTTGCCTTCGG
Found at i:42243275 original size:41 final size:42
Alignment explanation
Indices: 42243206--42243284 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 42
42243196 CTGATAATTG
* * *
42243206 GCCCGTGTGACTCCACACAGTCGAGCACATGCCTGTGTGCTT
1 GCCCGTGTGACCCCACACAGCCGAGCACATGCCCGTGTGCTT
*
42243248 GCCCGTGTG-CCCCACACAGCCTAGCACATGCCCGTGT
1 GCCCGTGTGACCCCACACAGCCGAGCACATGCCCGTGT
42243285 CACTTCTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 24 0.73
42 9 0.27
ACGTcount: A:0.16, C:0.38, G:0.25, T:0.20
Consensus pattern (42 bp):
GCCCGTGTGACCCCACACAGCCGAGCACATGCCCGTGTGCTT
Found at i:42243389 original size:42 final size:42
Alignment explanation
Indices: 42243323--42243445 Score: 129
Period size: 42 Copynumber: 2.9 Consensus size: 42
42243313 ACAGTGAGTT
*
42243323 ACATAGCCTGAACACACGCCTATGTCCTTGTCTGTGTGGCTC
1 ACATAGCCTGAACACACGCCTATGTCCTTGCCTGTGTGGCTC
* * * * * ** *
42243365 ACATAGCCTGACCACATGCATATGTGCTTACCAATATGGCTC
1 ACATAGCCTGAACACACGCCTATGTCCTTGCCTGTGTGGCTC
** * *
42243407 ACATAGCCTGGGCACACGCCTATGTCCCTGGCTGTGTGG
1 ACATAGCCTGAACACACGCCTATGTCCTTGCCTGTGTGG
42243446 TTCTAAAGTG
Statistics
Matches: 61, Mismatches: 20, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (42 bp):
ACATAGCCTGAACACACGCCTATGTCCTTGCCTGTGTGGCTC
Found at i:42243518 original size:42 final size:42
Alignment explanation
Indices: 42243471--42243551 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
42243461 ATTGAGTTAT
42243471 ACGGCCTGGGCACACGACCATATCCTTGCCCGTATGGCTCAC
1 ACGGCCTGGGCACACGACCATATCCTTGCCCGTATGGCTCAC
* * * *
42243513 ACGGCCTGGGCACACGCCCATGTCCTTGGCCGTGTGGCT
1 ACGGCCTGGGCACACGACCATATCCTTGCCCGTATGGCT
42243552 TTGACAGTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.15, C:0.37, G:0.28, T:0.20
Consensus pattern (42 bp):
ACGGCCTGGGCACACGACCATATCCTTGCCCGTATGGCTCAC
Found at i:42251173 original size:49 final size:49
Alignment explanation
Indices: 42251117--42251480 Score: 546
Period size: 49 Copynumber: 7.6 Consensus size: 49
42251107 TATTTGAATA
42251117 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
42251166 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
42251215 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
42251264 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATATGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
42251313 AATGTGAAAGTG--TATATATGAGATAAGGCCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* * * * *
42251360 AATGTGAAAGTG--TATATATGAGATAAGGCCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
*
42251407 AATGTGAAAGTG--TGTATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
* *
42251454 GATGTGGAAGTGTATA-A-ATGTGATAAG
1 AATGTGAAAGTGTATATATATGTGATAAG
42251481 TCCCGAAGGG
Statistics
Matches: 297, Mismatches: 16, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
47 137 0.46
48 1 0.00
49 159 0.54
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.29
Consensus pattern (49 bp):
AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:42268060 original size:171 final size:169
Alignment explanation
Indices: 42267734--42268065 Score: 583
Period size: 171 Copynumber: 2.0 Consensus size: 169
42267724 GCTCTTTTTC
42267734 AAGAGGGGAAATCGACAAGGGAAGAATGGAGTTGAAAGGCAACTAGAAGGGAGAAAGAGAGAAAA
1 AAGAGGGGAAATCGACAAGGGAAGAATGGAGTTGAAAGGCAACTAGAAGGGAGAAAGAGAGAAAA
* * **
42267799 TGTGAGAGAGATGTGTAAAGTGAGGGATGAGAAATAAGGGAGTGAAGGGGGATTTTTATGGGTGG
66 TGTGAGAGAGATGTGTAAAGTGAAGGATAAGAAATAAGGGAGTGAAGGGGGATTTTTACAGGTGG
42267864 AGATGGCTGCTAAAAGTAGCAGCCAATCCCCTCTTGAAA
131 AGATGGCTGCTAAAAGTAGCAGCCAATCCCCTCTTGAAA
*
42267903 AAGAGGGGAAATCGACAAGGGAAGAATGGAGTTGAAAGGCAATTAGAAGGGAGAAAGAGAGAAAA
1 AAGAGGGGAAATCGACAAGGGAAGAATGGAGTTGAAAGGCAACTAGAAGGGAGAAAGAGAGAAAA
*
42267968 TGTGAGTGAGAGATGTGTAAAGTGAAGGATAAGAAATAAGGGAGTGAAGGGGGCTTTTTACAGGT
66 TGTGA--GAGAGATGTGTAAAGTGAAGGATAAGAAATAAGGGAGTGAAGGGGGATTTTTACAGGT
*
42268033 GGAGATGGCTTCTAAAAGTAGCAGCCAATCCCC
129 GGAGATGGCTGCTAAAAGTAGCAGCCAATCCCC
42268066 CTTCCTTTGG
Statistics
Matches: 154, Mismatches: 7, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
169 69 0.45
171 85 0.55
ACGTcount: A:0.39, C:0.08, G:0.36, T:0.17
Consensus pattern (169 bp):
AAGAGGGGAAATCGACAAGGGAAGAATGGAGTTGAAAGGCAACTAGAAGGGAGAAAGAGAGAAAA
TGTGAGAGAGATGTGTAAAGTGAAGGATAAGAAATAAGGGAGTGAAGGGGGATTTTTACAGGTGG
AGATGGCTGCTAAAAGTAGCAGCCAATCCCCTCTTGAAA
Found at i:42269223 original size:26 final size:27
Alignment explanation
Indices: 42269161--42269225 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
42269151 CCAAACCCCA
*
42269161 ATAAAATTTTGACAATTTTACCCTTTG
1 ATAAAATTTTGACAATTTTACCCTTCG
**
42269188 ATAAAATTTTGATGATTTTACCC-TCG
1 ATAAAATTTTGACAATTTTACCCTTCG
*
42269214 ATAAGATTTTGA
1 ATAAAATTTTGA
42269226 GAAAATTCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 13 0.38
27 21 0.62
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (27 bp):
ATAAAATTTTGACAATTTTACCCTTCG
Found at i:42272856 original size:6 final size:6
Alignment explanation
Indices: 42272845--42272876 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
42272835 ACAATAGAAT
42272845 TTTTTA TTTTTA -TTTTA TTTTTA -TTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
42272877 CGGATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:42272862 original size:11 final size:11
Alignment explanation
Indices: 42272846--42272876 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
42272836 CAATAGAATT
42272846 TTTTATTTTTA
1 TTTTATTTTTA
42272857 TTTTATTTTTA
1 TTTTATTTTTA
42272868 TTTTATTTT
1 TTTTATTTT
42272877 CGGATATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:42274023 original size:3 final size:3
Alignment explanation
Indices: 42274017--42274068 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
42274007 TAGCGTTGTT
* * * *
42274017 TTA TTA TTA ATA TTA TTA GTA TTA TTG TTA TTA TTT TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42274064 TTA TT
1 TTA TT
42274069 GTTTTTGCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42280515 original size:51 final size:51
Alignment explanation
Indices: 42280433--42280533 Score: 148
Period size: 51 Copynumber: 2.0 Consensus size: 51
42280423 GAGTAGACTG
* *
42280433 AAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTA
1 AAGGCAGCGAATCTTATTTCACTAGCATTGCAGTGGAATAGATTAAAGCTA
* * **
42280484 AAGGTAGCGAATCTTGTTTCACTAGTGTTGCAGTGGAATAGATTAAAGCT
1 AAGGCAGCGAATCTTATTTCACTAGCATTGCAGTGGAATAGATTAAAGCT
42280534 GAAGTGGAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.30
Consensus pattern (51 bp):
AAGGCAGCGAATCTTATTTCACTAGCATTGCAGTGGAATAGATTAAAGCTA
Found at i:42280541 original size:21 final size:21
Alignment explanation
Indices: 42280515--42280554 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
42280505 CTAGTGTTGC
42280515 AGTGGA-ATAGATTAAAGCTGA
1 AGTGGAGA-AGATTAAAGCTGA
*
42280536 AGTGGAGAGGATTAAAGCT
1 AGTGGAGAAGATTAAAGCT
42280555 AAAGACAGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.40, C:0.05, G:0.33, T:0.23
Consensus pattern (21 bp):
AGTGGAGAAGATTAAAGCTGA
Found at i:42280616 original size:51 final size:50
Alignment explanation
Indices: 42280545--42280683 Score: 161
Period size: 51 Copynumber: 2.7 Consensus size: 50
42280535 AAGTGGAGAG
* * * *
42280545 GATTAAAGCTAAAGACAGCGAATCCTATCTCCTTGGCATTACAGTGGAACA
1 GATTAAAGCTAAAG-CAGCGAATCTTATCTCCCTAGCATTACAGCGGAACA
* * * * *
42280596 GATTAAAGCTAAATGTAGCGAATCTTGTTTCCCTAGCATTGCAGCGGAGCA
1 GATTAAAGCTAAA-GCAGCGAATCTTATCTCCCTAGCATTACAGCGGAACA
*
42280647 GATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAGC
1 GATTAAAGCT-AAAGCAGCGAATCTTATCTCCCTAGC
42280684 GTTAAAGCTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
51 70 0.96
52 3 0.04
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.25
Consensus pattern (50 bp):
GATTAAAGCTAAAGCAGCGAATCTTATCTCCCTAGCATTACAGCGGAACA
Found at i:42280638 original size:123 final size:123
Alignment explanation
Indices: 42280430--42280865 Score: 415
Period size: 123 Copynumber: 3.4 Consensus size: 123
42280420 GTGGAGTAGA
* * * * *
42280430 CTGAAGGCAGCGAATCTTATTTCCCTGGCATTGCAGTGGAATAGATTAAAGCTAAAGGTAGCGAA
1 CTGAAGACAGCGAATCCTATCTCCCTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAA
* **
42280495 TCTTGTTTCACTAGTGTTGCAGTGGAATAGATTAAAGCTGAAGTGGAGAGGATTAAAG
66 TCTTGTTTCCCTAGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGAGGATTAAAG
* * *
42280553 CTAAAGACAGCGAATCCTATCTCCTTGGCATTACAGTGGAACAGATTAAAGCTAAATGTAGCGAA
1 CTGAAGACAGCGAATCCTATCTCCCTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAA
* ** * *
42280618 TCTTGTTTCCCTAGCATTGCAGCGGAGCAGATTAAAGCTGAAGGCAGCGAATCTTATCTCCCTAG
66 TCTTGTTTCCCTAGCATTGCAGTGGAATAGATTAAAGCTGAA-G-TG-G------A------GAG
42280683 CG-TTAAAG
116 -GATTAAAG
* * * * * * *
42280691 CTGAAGACAACAAATCTTATTTCCCTGGCTTTATAGTGGAACAGATTAAAGCTAAAGGTAACGAA
1 CTGAAGACAGCGAATCCTATCTCCCTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAA
* * * * * *
42280756 TCTTGTTTCCTTGGCATTGTAGTGGAATAGATTAAAGCTAAAGTTGAGCGGATTAAAG
66 TCTTGTTTCCCTAGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGAGGATTAAAG
* ** * *
42280814 CTGAAGGCAGCGAATCCTATCTCATTGGCGTTACAGTGGAACAGATTGAAGC
1 CTGAAGACAGCGAATCCTATCTCCCTGGCATTACAGTGGAACAGATTAAAGC
42280866 CACTAGCCTT
Statistics
Matches: 249, Mismatches: 47, Indels: 34
0.75 0.14 0.10
Matches are distributed among these distances:
122 1 0.00
123 142 0.57
124 1 0.00
125 1 0.00
126 1 0.00
129 1 0.00
132 1 0.00
135 1 0.00
137 1 0.00
138 98 0.39
139 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (123 bp):
CTGAAGACAGCGAATCCTATCTCCCTGGCATTACAGTGGAACAGATTAAAGCTAAAGGTAGCGAA
TCTTGTTTCCCTAGCATTGCAGTGGAATAGATTAAAGCTGAAGTGGAGAGGATTAAAG
Found at i:42280765 original size:51 final size:51
Alignment explanation
Indices: 42280685--42280798 Score: 147
Period size: 51 Copynumber: 2.2 Consensus size: 51
42280675 CTCCCTAGCG
* *
42280685 TTAAAGCTGAAGACAACAAATCTTATTTCCCTGGCTTTATAGTGGAACAGA
1 TTAAAGCTAAAGACAACAAATCTTATTTCCCTGGCATTATAGTGGAACAGA
** * * * * *
42280736 TTAAAGCTAAAGGTAACGAATCTTGTTTCCTTGGCATTGTAGTGGAATAGA
1 TTAAAGCTAAAGACAACAAATCTTATTTCCCTGGCATTATAGTGGAACAGA
42280787 TTAAAGCTAAAG
1 TTAAAGCTAAAG
42280799 TTGAGCGGAT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (51 bp):
TTAAAGCTAAAGACAACAAATCTTATTTCCCTGGCATTATAGTGGAACAGA
Found at i:42280971 original size:89 final size:88
Alignment explanation
Indices: 42280872--42281481 Score: 361
Period size: 89 Copynumber: 6.8 Consensus size: 88
42280862 AAGCCACTAG
* *
42280872 CCTTATCTCCCTGTAGTTGCAATGGAGCAGGCTGAAGATAGCAAATCTTATCTCTCTGAAGTTGC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATA-CAAATCTTATCTCTCTGAAGTTGC
* *
42280937 AGTAGAGTAGATTAAAGCTATAAG
65 AGTAGAGTAGAATAAAGCTATAAA
* * * *
42280961 TCTTATCTCCCTGAAGTTGCAGTAGAACAGGCTGAAGATCATAAATCTTATCTCTCTGAAGTTGC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGAT-ACAAATCTTATCTCTCTGAAGTTGC
*
42281026 ACTAGAGTAGAATAAAGCTATAAA
65 AGTAGAGTAGAATAAAGCTATAAA
* * * * * * *
42281050 CCTTATCTCCCTAAAGTTGCAGTGGGGCAGGTTGAAGACACAAGTCTTATCTCTATGAAGTTACA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATACAAATCTTATCTCTCTGAAGTTGCA
* * * * ** *
42281115 GTGGAGCAGACTGAAGAAACAAA
66 GTAGAGTAGAATAAAGCTATAAA
* * * * * * * * * *
42281138 TCTTATCTCCCTGAAATTGCAGTGGAG-TGGATTGAAGTTGCAAGTCTTATCTCCCTAAAGTTAC
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGG-CTGAAGATACAAATCTTATCTCTCTGAAGTTGC
* * * * *
42281202 AGTGGATTAGACTGAAGATATCAAA
65 AGTAGAGTAGAATAAAGCTAT-AAA
* * * * * **
42281227 TCTTATTTCCCTGAAGTTGCAGTGGAACAAATTGAAGCT-ATAAATTACAGATCACATCTCTCTG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGC--A--G--GCTGA-AGA-TACAAATCTTATCTCTCTG
* * * * *
42281291 AAGTTGCAGTGGAGCAGACTGAAGATATCAAA
58 AAGTTGCAGTAGAGTAGAATAAAGCTAT-AAA
* * * * * *
42281323 TCTTATTTCCCTGAAGTTGCAGTGGAACAAATTGAAGCT-ATAAATTACAGATCTCATCTCTCTG
1 CCTTATCTCCCTGAAGTTGCAGTGGAGC--A--G--GCTGA-AGA-TACAAATCTTATCTCTCTG
* *
42281387 AAGTTGCAGTAGAGCAG-AT-CA--TATCAAA
58 AAGTTGCAGTAGAGTAGAATAAAGCTAT-AAA
* * ** * * * * * *
42281415 CCCTATTTCCCTGAAGTTGCAGTGGAATAGGTTAAAGTTACAAGTCTTATCTCCCTGAAATTGCA
1 CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATACAAATCTTATCTCTCTGAAGTTGCA
42281480 GT
66 GT
42281482 CGAGCAGACT
Statistics
Matches: 433, Mismatches: 75, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
85 24 0.06
86 3 0.01
87 3 0.01
88 105 0.24
89 137 0.32
90 2 0.00
92 32 0.07
94 3 0.01
95 3 0.01
96 121 0.28
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (88 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAGCAGGCTGAAGATACAAATCTTATCTCTCTGAAGTTGCA
GTAGAGTAGAATAAAGCTATAAA
Found at i:42280975 original size:44 final size:44
Alignment explanation
Indices: 42280873--42281348 Score: 349
Period size: 44 Copynumber: 10.6 Consensus size: 44
42280863 AGCCACTAGC
* * * * *
42280873 CTTATCTCCCTGTAGTTGCAATGGAGCAGGCTGAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATA-TAAAT
* * * * * *
42280918 CTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAGCTATAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATATAAAT
* ** *
42280962 CTTATCTCCCTGAAGTTGCAGTAGAACAGGCTGAAGATCATAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGAT-ATAAAT
* * * * * * *
42281007 CTTATCTCTCTGAAGTTGCACTAGAGTAGAATAAAGCTATAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATATAAAT
* * * ** * * *
42281051 CTTATCTCCCTAAAGTTGCAGTGGGGCAGGTTGAAGACACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATATAAAT
** * * * *
42281095 CTTATCTCTATGAAGTTACAGTGGAGCAGACTGAAGAAACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATATAAAT
* * * * ** *
42281139 CTTATCTCCCTGAAATTGCAGTGGAGTGGATTGAAGTTGCAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATATAAAT
* * *
42281183 CTTATCTCCCTAAAGTTACAGTGGATTAGACTGAAGATATCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAT-AAAT
* ** * *
42281228 CTTATTTCCCTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAG--AT--A-TA-A-AT
** * *
42281279 CACATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATAT-AAAT
*
42281324 CTTATTTCCCTGAAGTTGCAGTGGA
1 CTTATCTCCCTGAAGTTGCAGTGGA
42281349 ACAAATTGAA
Statistics
Matches: 331, Mismatches: 90, Indels: 20
0.75 0.20 0.05
Matches are distributed among these distances:
44 168 0.51
45 120 0.36
46 2 0.01
47 4 0.01
49 4 0.01
50 2 0.01
51 31 0.09
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGATATAAAT
Found at i:42281057 original size:133 final size:132
Alignment explanation
Indices: 42280918--42281158 Score: 295
Period size: 133 Copynumber: 1.8 Consensus size: 132
42280908 GATAGCAAAT
* * * * * *
42280918 CTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAG-CTATAAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGAC-ACAAGTCTTATCTCCATGAAGTTACA
* * * * *
42280982 GTAGAACAGGCTGAAGATCATAAATCTTATCTCTCTGAAGTTGCACTAGAGTAGAATAAAGCTAT
65 GTAGAACAGACTGAAGA-AACAAATCTTATCTCCCTGAAATTGCACTAGAGTAGAATAAAGCTAT
42281047 AAAC
129 AAAC
* * * * *
42281051 CTTATCTCCCTAAAGTTGCAGTGGGGCAGGTTGAAGACACAAGTCTTATCTCTATGAAGTTACAG
1 CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGACACAAGTCTTATCTCCATGAAGTTACAG
* *
42281116 TGGAGCAGACTGAAGAAACAAATCTTATCTCCCTGAAATTGCA
66 TAGAACAGACTGAAGAAACAAATCTTATCTCCCTGAAATTGCA
42281159 GTGGAGTGGA
Statistics
Matches: 89, Mismatches: 18, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
132 23 0.26
133 65 0.73
134 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.29
Consensus pattern (132 bp):
CTTATCTCCCTAAAGTTGCAGTAGAGCAGATTAAAGACACAAGTCTTATCTCCATGAAGTTACAG
TAGAACAGACTGAAGAAACAAATCTTATCTCCCTGAAATTGCACTAGAGTAGAATAAAGCTATAA
AC
Found at i:42281314 original size:51 final size:51
Alignment explanation
Indices: 42281237--42281396 Score: 206
Period size: 51 Copynumber: 3.3 Consensus size: 51
42281227 TCTTATTTCC
*
42281237 CTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGATCACATCTCT
1 CTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGATCTCATCTCT
* * * * * * *
42281288 CTGAAGTTGCAGTGGAGCAGACTGAAG--AT--A-T-CAAATCTTATTTCC
1 CTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGATCTCATCTCT
42281333 CTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGATCTCATCTCT
1 CTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGATCTCATCTCT
42281384 CTGAAGTTGCAGT
1 CTGAAGTTGCAGT
42281397 AGAGCAGATC
Statistics
Matches: 88, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
45 33 0.38
46 1 0.01
47 3 0.03
49 3 0.03
50 1 0.01
51 47 0.53
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (51 bp):
CTGAAGTTGCAGTGGAACAAATTGAAGCTATAAATTACAGATCTCATCTCT
Found at i:42281321 original size:96 final size:96
Alignment explanation
Indices: 42281098--42281441 Score: 406
Period size: 96 Copynumber: 3.7 Consensus size: 96
42281088 CACAAGTCTT
* * * *
42281098 ATCTCTATGAAGTTACAGTGGAGCAGACTGAAGA-AACAAATCTTATCTCCCTGAAATTGCAGTG
1 ATCTCTCTGAAGTTACAGTGGAGCAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
**** ** *
42281162 GAGTGGATTGAAG-T-T---GCA-AG-TCTT
66 GAACAAATTGAAGCTATAAATTACAGATCTC
* * **
42281186 ATCTCCCTAAAGTTACAGTGGATTAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
1 ATCTCTCTGAAGTTACAGTGGAGCAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
*
42281251 GAACAAATTGAAGCTATAAATTACAGATCAC
66 GAACAAATTGAAGCTATAAATTACAGATCTC
*
42281282 ATCTCTCTGAAGTTGCAGTGGAGCAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
1 ATCTCTCTGAAGTTACAGTGGAGCAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
42281347 GAACAAATTGAAGCTATAAATTACAGATCTC
66 GAACAAATTGAAGCTATAAATTACAGATCTC
* * * * *
42281378 ATCTCTCTGAAGTTGCAGTAGAGCAGA-T---CATATCAAACCCTATTTCCCTGAAGTTGCAGTG
1 ATCTCTCTGAAGTTACAGTGGAGCAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
42281439 GAA
66 GAA
42281442 TAGGTTAAAG
Statistics
Matches: 222, Mismatches: 26, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
88 29 0.13
89 36 0.16
90 1 0.00
91 1 0.00
92 33 0.15
94 1 0.00
95 3 0.01
96 118 0.53
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (96 bp):
ATCTCTCTGAAGTTACAGTGGAGCAGACTGAAGATATCAAATCTTATTTCCCTGAAGTTGCAGTG
GAACAAATTGAAGCTATAAATTACAGATCTC
Found at i:42282999 original size:3 final size:3
Alignment explanation
Indices: 42282993--42283044 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
42282983 TAGCGTTGTT
* * * *
42282993 TTA TTA TTA ATA TTA TTA GTA TTA TTG TTA TTA TTT TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
42283040 TTA TT
1 TTA TT
42283045 GTTTTTGCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:42285299 original size:9 final size:9
Alignment explanation
Indices: 42285282--42285318 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
42285272 TGAGTTTTCG
42285282 AATTCGAAT
1 AATTCGAAT
*
42285291 AACTCGAAT
1 AATTCGAAT
42285300 AATTCGAAT
1 AATTCGAAT
42285309 AATTCGAAT
1 AATTCGAAT
42285318 A
1 A
42285319 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Done.