Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 13 of 34
Found at i:1921196 original size:257 final size:258
Alignment explanation
Indices: 1920732--1921247 Score: 953
Period size: 257 Copynumber: 2.0 Consensus size: 258
1920722 TCTATATCAG
* **
1920732 GCACTGAAGAGATACTGACATGGAACATTGCTTTTGTGATTTTTGAAACAAATTTTTGAAAAACA
1 GCACTGAAGAGATACTGACACGGAACATTGCTTTTGCCATTTTTGAAACAAATTTTTGAAAAACA
*
1920797 TGAATGCACATAATGGTCAGCAAAAATGTTAGTAGAACAACAAGTGAAATTATGTTGTATAAAAT
66 TGAATGCACATAATGGTCAGCAAAAATGTTAGTAGAACAACAAGTGAAATGATGTTGTATAAAAT
* *
1920862 AATCTACATAAAATAACAATAAAGAAAATGAGGAACGATAAAAATATATCTCATAATTGTCCTTG
131 AATCTACACAAAATAACAATAAAGAAAATGAGGAACGATAAAAATATATCTCATAATTGTCCTCG
1920927 ATATCCAAAAAATAATCGAATTGATAATATTAGATGCGTGTTTGGATTCATTACTTAATTGAA
196 ATATCCAAAAAATAATCGAATTGATAATATTAGATGCGTGTTTGGATTCATTACTTAATTGAA
1920990 GCACTGAAGAGATACTGACACGGAACATTGCTTTTGCCATTTTTGAAACAAATTTTTGAAAAACA
1 GCACTGAAGAGATACTGACACGGAACATTGCTTTTGCCATTTTTGAAACAAATTTTTGAAAAACA
1921055 TGAATGCACATAATGGTCAG-AAAAATGTTAGTAGAACAACAAGTGAAATGATGTTGTATAAAAT
66 TGAATGCACATAATGGTCAGCAAAAATGTTAGTAGAACAACAAGTGAAATGATGTTGTATAAAAT
*
1921119 AATCTACACAAAATAACAATAAAGAAAATGAGGAACGATCAAAATATATCTCATAATTGTCCTCG
131 AATCTACACAAAATAACAATAAAGAAAATGAGGAACGATAAAAATATATCTCATAATTGTCCTCG
*
1921184 ATATCTAAAAAATAATCGAATTGATAATATTAGATGCGTGTTTGGATTCATTACTTAATTGAA
196 ATATCCAAAAAATAATCGAATTGATAATATTAGATGCGTGTTTGGATTCATTACTTAATTGAA
1921247 G
1 G
1921248 TCCGAAAATG
Statistics
Matches: 250, Mismatches: 8, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
257 168 0.67
258 82 0.33
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.30
Consensus pattern (258 bp):
GCACTGAAGAGATACTGACACGGAACATTGCTTTTGCCATTTTTGAAACAAATTTTTGAAAAACA
TGAATGCACATAATGGTCAGCAAAAATGTTAGTAGAACAACAAGTGAAATGATGTTGTATAAAAT
AATCTACACAAAATAACAATAAAGAAAATGAGGAACGATAAAAATATATCTCATAATTGTCCTCG
ATATCCAAAAAATAATCGAATTGATAATATTAGATGCGTGTTTGGATTCATTACTTAATTGAA
Found at i:1924088 original size:20 final size:20
Alignment explanation
Indices: 1924060--1924214 Score: 104
Period size: 20 Copynumber: 7.7 Consensus size: 20
1924050 AGGCCCCAAC
* *
1924060 GTATTGATACATTGTTCACT
1 GTATCGATACATTGTTCAAT
*
1924080 GTATCGATACATTGTTCATT
1 GTATCGATACATTGTTCAAT
* *
1924100 GTATCGATATAATGTATCAAT
1 GTATCGATACATTGT-TCAAT
* ** *
1924121 ATATTC--TAGGTT-TACCTAGAT
1 GTA-TCGATACATTGT-TC-A-AT
*
1924142 GTATCGATACATT-TTGCATT
1 GTATCGATACATTGTT-CAAT
* *
1924162 GTATCGATACATTGCTCATT
1 GTATCGATACATTGTTCAAT
1924182 GTATCGATACATT-TTACAAT
1 GTATCGATACATTGTT-CAAT
1924202 GTATCGATACATT
1 GTATCGATACATT
1924215 CGGGCATTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
19 4 0.04
20 84 0.78
21 12 0.11
22 8 0.07
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (20 bp):
GTATCGATACATTGTTCAAT
Found at i:1926591 original size:50 final size:52
Alignment explanation
Indices: 1926515--1926628 Score: 117
Period size: 50 Copynumber: 2.2 Consensus size: 52
1926505 TTTCATCTAA
* * **
1926515 GGGATACTCCAA-TCCTGGTTCCATTTCCAAAACATCAATTTTT-TTAATCG
1 GGGATACTCCAACTCCTGATTCCATTTCCAAAACACCAATTTTTCACAATCG
** * ** *
1926565 GGGATACTCCAACTCC-GATTTTATTTCTAAAGTACCAATTTTTCACAATTG
1 GGGATACTCCAACTCCTGATTCCATTTCCAAAACACCAATTTTTCACAATCG
1926616 GGGATACTCCAAC
1 GGGATACTCCAAC
1926629 CCCGTTATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
50 32 0.62
51 20 0.38
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (52 bp):
GGGATACTCCAACTCCTGATTCCATTTCCAAAACACCAATTTTTCACAATCG
Found at i:1926647 original size:28 final size:28
Alignment explanation
Indices: 1926615--1926688 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
1926605 TTTCACAATT
*
1926615 GGGGATACTCCAACCCCGTTATTTCAT-C
1 GGGGATACTCCAACCCCGTTATTT-ATAA
* *
1926643 GGGGATACGT-CAACCTCGTTATTTTTAA
1 GGGGATAC-TCCAACCCCGTTATTTATAA
1926671 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1926689 GCTTTATATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.05
28 36 0.92
29 1 0.03
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTATAA
Found at i:1926695 original size:107 final size:108
Alignment explanation
Indices: 1926555--1926757 Score: 259
Period size: 107 Copynumber: 1.9 Consensus size: 108
1926545 AACATCAATT
* * * *
1926555 TTTTTAATCGGGGATACTCCAACTCCGATTTTAT-TTCTAAAGTA-CCAATTTTTCACAATTGGG
1 TTTTTAA-CGGGGATACTCCAACCCCGACTTTATATT-TAAAATATCCAATTTTTCACAATCGGG
*
1926618 GATACTCCAACCCCGTTATTTCATCGGGGATACGTCAACCTCGTTA
64 G-TACTCCAACCCCGTTATGTCATCGGGGATACGTCAACCTCGTTA
* * * **
1926664 TTTTTAA-GGGGATACTCCAACCCCGGCTTTATATTTAAAATATCGATTTTTTCATTATCGGGGT
1 TTTTTAACGGGGATACTCCAACCCCGACTTTATATTTAAAATATCCAATTTTTCACAATCGGGGT
*
1926728 ACTTCAACCCCGTTATGTCATCGGGGATAC
66 ACTCCAACCCCGTTATGTCATCGGGGATAC
1926758 TCCAATCCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
107 57 0.70
108 17 0.21
109 7 0.09
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (108 bp):
TTTTTAACGGGGATACTCCAACCCCGACTTTATATTTAAAATATCCAATTTTTCACAATCGGGGT
ACTCCAACCCCGTTATGTCATCGGGGATACGTCAACCTCGTTA
Found at i:1926828 original size:51 final size:50
Alignment explanation
Indices: 1926747--1926969 Score: 162
Period size: 51 Copynumber: 4.4 Consensus size: 50
1926737 CCGTTATGTC
* ** *
1926747 ATCGGGGATACTCCAATCCC-AGTTCCATTTCCAAAACATCAAATTTTCTTA
1 ATCGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACA-CAAATTTTCTCA
* * * *
1926798 ATCGGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACA
1 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACA-CAAATTTTCTCA
** * * *
1926849 ATCGTAGATACTCCAACTCTGATTTTATTTCCAAAACACCAA-TTTCTCA
1 ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACAAATTTTCTCA
* * *** ** * *
1926898 CCATCAGGGATACTTCAACCTTTATTTTATTTTTAAAACACCAATTTTCTATA
1 --ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACAAATTTTCT-CA
**
1926951 ATCAAGGATACTCCAACCC
1 ATCGGGGATACTCCAACCC
1926970 TGTTATTTTT
Statistics
Matches: 136, Mismatches: 31, Indels: 10
0.77 0.18 0.06
Matches are distributed among these distances:
49 6 0.04
50 2 0.01
51 121 0.89
52 6 0.04
53 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (50 bp):
ATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACAAATTTTCTCA
Found at i:1928869 original size:79 final size:78
Alignment explanation
Indices: 1928776--1929327 Score: 530
Period size: 79 Copynumber: 7.0 Consensus size: 78
1928766 GAGATAAAAA
* *
1928776 GGGGCTTGGAGTATCCCCTACAAAATTACGAGGTTGGAGTATCCTCGATGGTGAAAAATCT-GTG
1 GGGG-TTGGAGTATCCCCTTCAAAATAACG-GGTTGGAGTATCCTCGATGGTGAAAAAT-TGGTG
1928840 TTTTAGGAATAAAACT
63 TTTTAGGAATAAAACT
* * ***
1928856 GGGGTTGGAGTAT-CCCTTCAGAAATAATGGGGTTGGAGTATCC-CGATGGTGGAAAATCAATGT
1 GGGGTTGGAGTATCCCCTTCA-AAATAA-CGGGTTGGAGTATCCTCGATGGTGAAAAATTGGTGT
1928919 TTTAGGAATAAAACT
64 TTTAGGAATAAAACT
* * * * * * * *
1928934 AGGGTTGGAGTATCCCCTTGAAAATAACGGGCATGAAGTATCCTCGATAGTGGAAAATCGATGTT
1 GGGGTTGGAGTATCCCCTTCAAAATAACGGG-TTGGAGTATCCTCGATGGTGAAAAATTGGTGTT
*
1928999 TTAGGAATAAAACC
65 TTAGGAATAAAACT
* *
1929013 AGGGTTGGAGTATCCCC-TCGAAAATAACGAGGTTGTAGTATCC-CTGATGGTGAAAAATTGGTG
1 GGGGTTGGAGTATCCCCTTC-AAAATAACG-GGTTGGAGTATCCTC-GATGGTGAAAAATTGGTG
* *
1929076 TTTTAGGAATACAACG
63 TTTTAGGAATAAAACT
* * *
1929092 GGGGTTGGAGTAT-ACCTTCAGAAATAACGCGGTTGGAGTATCCCCGATGGTGAAAAATTGGTAT
1 GGGGTTGGAGTATCCCCTTCA-AAATAACG-GGTTGGAGTATCCTCGATGGTGAAAAATTGGTGT
* *
1929156 TTTAGAAATAAAACC
64 TTTAGGAATAAAACT
* * * * * **
1929171 GAGGTTGGAGAATCTCC-TCAAAAATAACTGGCTTAGAGTATCCTCGATGGTGAAAAATTAATGT
1 GGGGTTGGAGTATCCCCTTC-AAAATAAC-GGGTTGGAGTATCCTCGATGGTGAAAAATTGGTGT
*
1929235 TTTAGAAATAAAA-T
64 TTTAGGAATAAAACT
* * * *
1929249 CAGGGTTAGAGTAT-CCCTTCGGAAAATAACGGGGTTGGAGTATCCCCGATAGT-AGAAAATTGG
1 -GGGGTTGGAGTATCCCCTTC--AAAATAAC-GGGTTGGAGTATCCTCGATGGTGA-AAAATTGG
*
1929312 TGTTTTAGAAATAAAA
61 TGTTTTAGGAATAAAA
1929328 ACATCAATGA
Statistics
Matches: 399, Mismatches: 54, Indels: 38
0.81 0.11 0.08
Matches are distributed among these distances:
77 3 0.01
78 71 0.18
79 265 0.66
80 60 0.15
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (78 bp):
GGGGTTGGAGTATCCCCTTCAAAATAACGGGTTGGAGTATCCTCGATGGTGAAAAATTGGTGTTT
TAGGAATAAAACT
Found at i:1930038 original size:20 final size:20
Alignment explanation
Indices: 1929943--1930039 Score: 106
Period size: 20 Copynumber: 4.8 Consensus size: 20
1929933 TTTTACCGAG
* *
1929943 ATGTATCCATACATTTTTCA
1 ATGTATCAATACATTCTTCA
* * *
1929963 ATGTATCGATACATGT-ATGA
1 ATGTATCAATACAT-TCTTCA
* *
1929983 ATGTATCGATACATTCTTTA
1 ATGTATCAATACATTCTTCA
*
1930003 ATGTATTAATACATTCTTCA
1 ATGTATCAATACATTCTTCA
1930023 ATGTATCAATACATTCT
1 ATGTATCAATACATTCT
1930040 GTCTTTTCAC
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
19 1 0.02
20 64 0.97
21 1 0.02
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (20 bp):
ATGTATCAATACATTCTTCA
Found at i:1930132 original size:51 final size:51
Alignment explanation
Indices: 1930003--1930135 Score: 212
Period size: 51 Copynumber: 2.6 Consensus size: 51
1929993 ACATTCTTTA
* * *
1930003 ATGTATTAATACATTCTTCAATGTATCAATACATTCTGTCTTTTCACCCAG
1 ATGTATTGATACATTTTTCAATGTATCGATACATTCTGTCTTTTCACCCAG
* **
1930054 ATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTTCCCAG
1 ATGTATTGATACATTTTTCAATGTATCGATACATTCTGTCTTTTCACCCAG
1930105 ATGTATTGATACATTTTTCAATGTATCGATA
1 ATGTATTGATACATTTTTCAATGTATCGATA
1930136 TATCTAGTTA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.44
Consensus pattern (51 bp):
ATGTATTGATACATTTTTCAATGTATCGATACATTCTGTCTTTTCACCCAG
Found at i:1934005 original size:9 final size:9
Alignment explanation
Indices: 1933991--1934015 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1933981 CTAAACTTTT
1933991 TAGCCATCA
1 TAGCCATCA
1934000 TAGCCATCA
1 TAGCCATCA
1934009 TAGCCAT
1 TAGCCAT
1934016 TTCTTCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.24
Consensus pattern (9 bp):
TAGCCATCA
Found at i:1938881 original size:20 final size:19
Alignment explanation
Indices: 1938856--1938926 Score: 97
Period size: 20 Copynumber: 3.6 Consensus size: 19
1938846 GATACATTGC
1938856 ATCGATACATTATTCAATGT
1 ATCGATACATTATT-AATGT
*
1938876 ATCGATACATTGTATAATGT
1 ATCGATACATTAT-TAATGT
*
1938896 ATCGATACATTGAATAATGT
1 ATCGATACATT-ATTAATGT
1938916 ATCGATACATT
1 ATCGATACATT
1938927 TCCTTGGCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
20 45 0.98
21 1 0.02
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (19 bp):
ATCGATACATTATTAATGT
Found at i:1939925 original size:49 final size:49
Alignment explanation
Indices: 1939763--1940770 Score: 775
Period size: 49 Copynumber: 21.0 Consensus size: 49
1939753 CGAAGAATGG
* * * *
1939763 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTAAAGAAGAA--TGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* ** * * * *
1939810 CAATGTGCTGAGACAAGGCCAACGACTTTGGGCTT-AAGAATGTTAAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG-ATG---AAGGTGC
* ** * *
1939862 CAATATGTTGATTCAAGGCCAATGATATCGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
1939911 CAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGATAAAAGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGA-CTTAAAGATGAAGGTGC
* * * * * *
1939960 CAATATGCTGATTCAAGGTCAGTGATATTAGACTTAAAGATTAAGATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * * **
1940009 CACTGTGTTGATTCAAGGCCAGCTACATCAGACTTAAAGATGGTTAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G--AAGGTGC
* * * * * *
1940061 CAATGTGCTGATTCTACGCCAACGACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
1940110 CAATATGTTGATTTAAGGCCAGCGATATTAGG-C-T-----T----GTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGACTTAAAGATGAAGGTGC
* * * * *
1940149 CAATGTGCTGATTCAAGGCCAACAACATTGGTCTTAAAGA-CAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
1940197 CAATATGCTGATTCAAGGCTAGCGATATTGGAC-TCAAGATGGTAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAT-G--AAGGTGC
* * *
1940248 CAATATGCTGATTCAAAGCCAACGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* *
1940291 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1940340 CAATATGATAATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1940383 CAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGCTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * * *
1940432 TAATTTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGGACAAATGAGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGC
* *
1940484 CAATATGCTGATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * *
1940527 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1940576 TAATATGCTGATTCAAGGCAAGCGATATTGGA-TT-TA-A--AA-GTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * * *
1940619 CAATGTGCTGATTCAAGGCCTGCAACATTGGATTTAAAGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
* * * *
1940668 TAATGTGTTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAAGGCGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGC
* * * *
1940720 CAATATGCTGATTCAAGGCCAGCAATATTAGACTTAAATATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
1940769 CA
1 CA
1940771 CCAACTTGTG
Statistics
Matches: 761, Mismatches: 141, Indels: 116
0.75 0.14 0.11
Matches are distributed among these distances:
38 2 0.00
39 28 0.04
40 1 0.00
43 141 0.19
44 4 0.01
45 2 0.00
46 4 0.01
47 38 0.05
48 40 0.05
49 308 0.40
50 6 0.01
51 37 0.05
52 147 0.19
53 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGC
Found at i:1939947 original size:101 final size:99
Alignment explanation
Indices: 1939763--1940770 Score: 556
Period size: 92 Copynumber: 10.5 Consensus size: 99
1939753 CGAAGAATGG
* * ** * * * **
1939763 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTAAAGAAGAA--TGCCAATGTGCTGAGACAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * *
1939826 GGCCAACGACTTTGGGCTTAAGAATGTTAAAGATGC
66 GGCCAGCGACATT-GACTTAA-AATGTTAAAGATGC
* *
1939862 CAATATGTTGATTCAAGGCCAATGATATCGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
*
1939927 GGCCAGCGACATTGATCTT-AAA-GATAAA-AGTGC
66 GGCCAGCGACATTGA-CTTAAAATGTTAAAGA-TGC
* * * * * * *
1939960 CAATATGCTGATTCAAGGTCAGTGATATTAGACTTAAAGATTAAGATGCCACTGTGTTGATTCAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * *
1940025 GGCCAGCTACATCAGACTTAAAGATGGTT-AAGGTGC
66 GGCCAGCGACAT-TGACTTAAA-AT-GTTAAAGATGC
* * * * * * * * * *
1940061 CAATGTGCTGATTCTACGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGTTGATTTAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
*
1940126 GGCCAGCG--A-T-A-TT---AGGCTT---G-TGC
66 GGCCAGCGACATTGACTTAAAATG-TTAAAGATGC
* ** * * * *
1940149 CAATGTGCTGATTCAAGGCCAACAACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * * * * *
1940213 GGCTAGCGATATTGGACTCAAGATGGTAAAGGTGC
66 GGCCAGCGACATT-GACTTAAAATGTTAAAGATGC
* * *
1940248 CAATATGCTGATTCAAAGCCAACGATATTGGACTT----A--AAGGTGCCAATATGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * *
1940307 GGCCAGCGACATTGGTCTT-AAA-GATAAAGGTGC
66 GGCCAGCGACATT-GACTTAAAATGTTAAAGATGC
* * * **
1940340 CAATATGATAATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* * * *
1940399 GGCCAGCAACATTGGACTT-AAA-GGTGAAGCTGC
66 GGCCAGCGACATT-GACTTAAAATGTTAAAGATGC
* * ** * * * * *
1940432 TAATTTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGGACAAATGAGCCAATATGCTGATT
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATG---AAGGTGCCAATGTGCTGATT
* *
1940497 CAAGGCTAGCGATATTGGACTT-AAA-G-----G-TGC
63 CAAGGCCAGCGACATT-GACTTAAAATGTTAAAGATGC
* ** * * * * *
1940527 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCTAATATGCTGATTCAA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
* **
1940592 GGCAAGCG--A-T-A-TT-GGAT-TTAAA-AGTGC
66 GGCCAGCGACATTGACTTAAAATGTTAAAGA-TGC
* * * * * *
1940619 CAATGTGCTGATTCAAGGCC--TGCAACATTGGATTTAAAGGTGAAGGTGCTAATGTGTTGATTC
1 CAATATGCTGATTCAAGGCCAATG--ATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
** **
1940682 AAGGCCAGCGACATTGGACTTAAAGATGAAAAAGGCGC
64 AAGGCCAGCGACATT-GACTTAAA-ATGTTAAAGATGC
*** * *
1940720 CAATATGCTGATTCAAGGCCAGCAATATTAGACTTAAATATGAAGGTGCCA
1 CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCA
1940771 CCAACTTGTG
Statistics
Matches: 731, Mismatches: 123, Indels: 108
0.76 0.13 0.11
Matches are distributed among these distances:
86 3 0.00
87 29 0.04
88 40 0.05
89 3 0.00
90 4 0.01
91 3 0.00
92 213 0.29
93 3 0.00
94 39 0.05
95 45 0.06
96 5 0.01
97 2 0.00
98 81 0.11
99 75 0.10
100 5 0.01
101 179 0.24
102 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (99 bp):
CAATATGCTGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAA
GGCCAGCGACATTGACTTAAAATGTTAAAGATGC
Found at i:1940067 original size:150 final size:149
Alignment explanation
Indices: 1939763--1940770 Score: 490
Period size: 144 Copynumber: 7.0 Consensus size: 149
1939753 CGAAGAATGG
* * * **
1939763 CAATGTGCTGATTCATGGCCAGCGACATTAGA-CTTAAAGA-AGAA-TGCCAATGTGCTGAGACA
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGATAAAAGTGCCAATATGCTGATTCA
* * * *
1939825 AGGCCAACGACT-TTGGGCTTAAGAATGTTAAAGATGCCAATATGTTGATTCAAGGCCAATGATA
65 AGGCCAGCGA-TATTAGACTTAAGAA-GTTAAAGATGCCAATATGTTGATTCAAGGCCAATGACA
*
1939889 TCGGACTTAAAGATGAAGGTGC
128 TCAGACTTAAAGATGAAGGTGC
1939911 CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATAAAAGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATAAAAGTGCCAATATGCTGATTCAA
* * * * *
1939976 GGTCAGTGATATTAGACTT-A-AAGATT-AAGATGCCACTGTGTTGATTCAAGGCCAGCT-ACAT
66 GGCCAGCGATATTAGACTTAAGAAG-TTAAAGATGCCAATATGTTGATTCAAGGCCA-ATGACAT
1940037 CAGACTTAAAGATGGTTAAGGTGC
129 CAGACTTAAAGAT-G--AAGGTGC
* * * * * * *
1940061 CAATGTGCTGATTCTACGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGTTGATTTAA
1 CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATAAAAGTGCCAATATGCTGATTCAA
* * * ** **
1940126 GGCCAGCGATATTAG------G--CTT---G-TGCCAATGTGCTGATTCAAGGCCAACAACATTG
66 GGCCAGCGATATTAGACTTAAGAAGTTAAAGATGCCAATATGTTGATTCAAGGCCAATGACATCA
* *
1940179 GTCTTAAAGA-CAAGGTGC
131 GACTTAAAGATGAAGGTGC
* * * * * *
1940197 CAATATGCTGATTCAAGGCTAGCGATATTGGA-CTCAAGATGGTAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAA-A-GATAAAAGTGCCAATATGCTGATT
* * * * **
1940261 CAAAGCCAACGATATTGGACTT-A-AAG-----G-TGCCAATATGCTGATTCAAGGCCAGCGACA
63 CAAGGCCAGCGATATTAGACTTAAGAAGTTAAAGATGCCAATATGTTGATTCAAGGCCAATGACA
** * *
1940318 TTGGTCTTAAAGATAAAGGTGC
128 TCAGACTTAAAGATGAAGGTGC
* * * * * *
1940340 CAATATGATAATTCAAGGCTAGCGATATTGGA-CTTAAAG------GTGCCAATGTGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGATAAAAGTGCCAATATGCTGATTCA
* * * * * * * * * ** *
1940398 AGGCCAGCAACATTGGACTT-A-AAGGTGAAGCTGCTAATTTGCTGATTCAAGGCCAGCGACATT
65 AGGCCAGCGATATTAGACTTAAGAAGTTAAAGATGCCAATATGTTGATTCAAGGCCAATGACATC
* * * *
1940461 GGACTTAAAGAGGACAAATGAGC
130 AGACTTAAAGATG---AAGGTGC
* * * *
1940484 CAATATGCTGATTCAAGGCTAGCGATATTGGA-CTTAAAG------GTGCCAATGTGCTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGATAAAAGTGCCAATATGCTGATTCA
* * * * * * * * *
1940542 AGGCCAGCGACATTGGTCTT-A-AAGATAAAGGTGCTAATATGCTGATTCAAGG-CAAGCGATAT
65 AGGCCAGCGATATTAGACTTAAGAAGTTAAAGATGCCAATATGTTGATTCAAGGCCAA-TGACAT
** *
1940604 TGGA-TT-TA-A--AA-GTGC
129 CAGACTTAAAGATGAAGGTGC
* * * * * * * *
1940619 CAATGTGCTGATTCAAGGCCTGCAACATTGGAT-TTAAAGGTGAAGGTGCTAATGTGTTGATTCA
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGATAAAAGTGCCAATATGCTGATTCA
* * * ** ** * *** *
1940683 AGGCCAGCGACATTGGACTTAAAGATGAAAAAGGCGCCAATATGCTGATTCAAGGCCAGCAATAT
65 AGGCCAGCGATATTAGACTT-AAGAAGTTAAAGATGCCAATATGTTGATTCAAGGCCAATGACAT
* *
1940748 TAGACTTAAATATGAAGGTGC
129 CAGACTTAAAGATGAAGGTGC
1940769 CA
1 CA
1940771 CCAACTTGTG
Statistics
Matches: 716, Mismatches: 95, Indels: 96
0.79 0.10 0.11
Matches are distributed among these distances:
135 74 0.10
136 36 0.05
137 2 0.00
138 36 0.05
140 36 0.05
141 79 0.11
142 43 0.06
143 48 0.07
144 151 0.21
145 4 0.01
146 1 0.00
147 45 0.06
148 42 0.06
149 7 0.01
150 112 0.16
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (149 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGATCTTAAAGATAAAAGTGCCAATATGCTGATTCAA
GGCCAGCGATATTAGACTTAAGAAGTTAAAGATGCCAATATGTTGATTCAAGGCCAATGACATCA
GACTTAAAGATGAAGGTGC
Found at i:1940300 original size:43 final size:43
Alignment explanation
Indices: 1940239--1940706 Score: 396
Period size: 43 Copynumber: 10.1 Consensus size: 43
1940229 CTCAAGATGG
* * *
1940239 TAAAGGTGCCAATATGCTGATTCAAAGCCAACGATATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
*
1940282 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T
* * * *
1940326 AAAGATAAAGGTGCCAATATGATAATTCAAGGCTAGCGATATTGGACT
1 -----TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
* *
1940374 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
*
1940417 TAAAGGTGAAGCTGCTAATTTGCTGATTCAAGGCCAGCGACATTGGACT
1 TAAAGGT---GC--C-AATATGCTGATTCAAGGCCAGCGACATTGGACT
* *
1940466 TAAAGAGGACAAATGAGCCAATATGCTGATTCAAGGCTAGCGATATTGGACT
1 T-AA-AGG-----T--GCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
* *
1940518 TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGAC-T
* * * *
1940562 AAAGATAAAGGTGCTAATATGCTGATTCAAGGCAAGCGATATTGGATT
1 -----TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
* * * * *
1940610 TAAAAGTGCCAATGTGCTGATTCAAGGCCTGCAACATTGGATT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
* * *
1940653 TAAAGGTGAAGGTGCTAATGTGTTGATTCAAGGCCAGCGACATTGGACT
1 T--A----AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
1940702 TAAAG
1 TAAAG
1940707 ATGAAAAAGG
Statistics
Matches: 350, Mismatches: 44, Indels: 62
0.77 0.10 0.14
Matches are distributed among these distances:
43 153 0.44
44 2 0.01
45 2 0.01
46 2 0.01
47 1 0.00
48 3 0.01
49 141 0.40
50 5 0.01
51 5 0.01
52 31 0.09
53 1 0.00
55 3 0.01
56 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (43 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACT
Found at i:1940308 original size:21 final size:21
Alignment explanation
Indices: 1940241--1940308 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
1940231 CAAGATGGTA
1940241 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
* * ** *
1940262 AA--AGCCAACGATATTGGACTTA
1 AAGGTGCCAA-TATGCT-GA-TTC
1940284 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGCTGATTC
1940305 AAGG
1 AAGG
1940309 CCAGCGACAT
Statistics
Matches: 32, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 5 0.16
20 3 0.09
21 10 0.31
22 6 0.19
23 3 0.09
24 5 0.16
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (21 bp):
AAGGTGCCAATATGCTGATTC
Found at i:1940538 original size:236 final size:235
Alignment explanation
Indices: 1939763--1940757 Score: 1008
Period size: 236 Copynumber: 4.2 Consensus size: 235
1939753 CGAAGAATGG
* * * * **
1939763 CAATGTGCTGATTCATGGCCAGCGACATTAGACTTAAAGAAGAATGCCAATGTGCTGAGACAAGG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG--G--TGCCAATGTGCTGATTCAAGG
* * * * * * * *
1939828 CCAACGACTTTGGGCTTAAGAATGTTAAAGATGCCAATATGTTGATTCAAGGCCAA-TGATATCG
62 CCAGCGACATTGGTCTT-A-AA-GATAAAGGTGCCAATATGATGATTCAAGG-CAAGCGATATTG
* * * *
1939892 GACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT-GATCTTAAAGATAAAA
123 GACTT----A--AA-GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGA-CTTAAAGGTGAAG
* * * * * **
1939956 GTGCCAATATGCTGATTCAAGGTCAGTGATATTAGACTT-AA-A-GATTAA-GATGC
180 GTGCTAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGAGGAAAAAGGA-GC
* * * * * **
1940009 CACTGTGTTGATTCAAGGCCAGCTACATCAGACTTAAAGATGGTTAAGGTGCCAATGTGCTGATT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-----AAGGTGCCAATGTGCTGATT
* * * * * *
1940074 CTACGCCAACGACATTGGTCTTAAAGATAAAGGTGCCAATATGTTGATTTAAGGCCAGCGATATT
57 CAAGGCCAGCGACATTGGTCTTAAAGATAAAGGTGCCAATATGATGATTCAAGGCAAGCGATATT
* * ** *
1940139 AGG-CTT---GTGCCAATGTGCTGATTCAAGGCCAACAACATTGGTCTTAAA-GACAAGGTGCCA
122 -GGACTTAAAGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTA
* * * * *
1940199 ATATGCTGATTCAAGGCTAGCGATATTGGAC-TCAAGATGG-TAAAGGTGC
186 ATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGA-GGAAAAAGGAGC
* * *
1940248 CAATATGCTGATTCAAAGCCAACGATATTGGACTTAAAGGTGCCAATATGCTGATTCAAGGCCAG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAG
* *
1940313 CGACATTGGTCTTAAAGATAAAGGTGCCAATATGATAATTCAAGGCTAGCGATATTGGACTTAAA
66 CGACATTGGTCTTAAAGATAAAGGTGCCAATATGATGATTCAAGGCAAGCGATATTGGACTTAAA
* *
1940378 GGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGCTGCTAATTTGCTGA
131 -GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATATGCTGA
* *
1940443 TTCAAGGCCAGCGACATTGGACTTAAAGAGGACAAATGAGC
195 TTCAAGGCCAGCGACATTGGACTTAAAGAGGAAAAAGGAGC
*
1940484 CAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAG
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAG
* * *
1940549 CGACATTGGTCTTAAAGATAAAGGTGCTAATATGCTGATTCAAGGCAAGCGATATTGGATTTAAA
66 CGACATTGGTCTTAAAGATAAAGGTGCCAATATGATGATTCAAGGCAAGCGATATTGGACTT-AA
* * * *
1940614 AGTGCCAATGTGCTGATTCAAGGCCTGCAACATTGGATTTAAAGGTGAAGGTGCTAATGTGTTGA
130 AGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATATGCTGA
* *
1940679 TTCAAGGCCAGCGACATTGGACTTAAAGATGAAAAAGGCGC
195 TTCAAGGCCAGCGACATTGGACTTAAAGAGGAAAAAGGAGC
* *
1940720 CAATATGCTGATTCAAGGCCAGCAATATTAGACTTAAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1940758 TATGAAGGTG
Statistics
Matches: 642, Mismatches: 81, Indels: 62
0.82 0.10 0.08
Matches are distributed among these distances:
229 2 0.00
230 80 0.12
234 40 0.06
235 39 0.06
236 261 0.41
237 40 0.06
238 38 0.06
239 32 0.05
240 2 0.00
246 30 0.05
247 2 0.00
248 34 0.05
249 4 0.01
250 2 0.00
251 32 0.05
253 1 0.00
255 3 0.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (235 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAG
CGACATTGGTCTTAAAGATAAAGGTGCCAATATGATGATTCAAGGCAAGCGATATTGGACTTAAA
GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGGTGAAGGTGCTAATATGCTGAT
TCAAGGCCAGCGACATTGGACTTAAAGAGGAAAAAGGAGC
Found at i:1940879 original size:29 final size:29
Alignment explanation
Indices: 1940762--1941164 Score: 357
Period size: 29 Copynumber: 14.0 Consensus size: 29
1940752 CTTAAATATG
**
1940762 AAGGTGCCACCAACTTGTGTGGACTTTTGAA
1 AAGGTGCCACTGACTTGTG-GG-CTTTTGAA
* ** *
1940793 AGGGTTG-CACCAACTTGTGTGCTTTTG--
1 AAGG-TGCCACTGACTTGTGGGCTTTTGAA
*
1940820 AAGGTTGCCACT-ACCTTGTGGGC-TTCGAA
1 AAGG-TGCCACTGA-CTTGTGGGCTTTTGAA
* *
1940849 AAGGCGCCACTAACTTGTGGGCTTTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
* *
1940878 AAGATGCCACT-AGCTTATGGGCTTTTG--
1 AAGGTGCCACTGA-CTTGTGGGCTTTTGAA
* *
1940905 AAGGTTGCCACTAACTTGTGAGCTTTTGAA
1 AAGG-TGCCACTGACTTGTGGGCTTTTGAA
* *
1940935 AAGATGCCAATGACTTGTGGGC-TTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
** * * *
1940963 AAAATGCCATTGACATGTGGGCTTTTAAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
* *
1940992 AAGATACCACTGACTTGTGGGC-TTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
*
1941020 AATGGTGCCACTGACTTGTGAGCTTTTGAA
1 AA-GGTGCCACTGACTTGTGGGCTTTTGAA
* *
1941050 AAGATGCCACTGACTTGTGGGC-TTTGAG
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
* *
1941078 AAGATGCCACTGACTTGTTGGG-TTTTAAA
1 AAGGTGCCACTGACTTG-TGGGCTTTTGAA
*
1941107 AAGATGCCACTGACTTGTGGGC-TTTGAA
1 AAGGTGCCACTGACTTGTGGGCTTTTGAA
*
1941135 AAGGGTGCCACTGACTTATGGGC-TTTGAA
1 AA-GGTGCCACTGACTTGTGGGCTTTTGAA
1941164 A
1 A
1941165 GGCGAGGAAT
Statistics
Matches: 315, Mismatches: 38, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
27 13 0.04
28 111 0.35
29 162 0.51
30 12 0.04
31 15 0.05
32 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (29 bp):
AAGGTGCCACTGACTTGTGGGCTTTTGAA
Found at i:1940888 original size:57 final size:57
Alignment explanation
Indices: 1940805--1941164 Score: 419
Period size: 57 Copynumber: 6.3 Consensus size: 57
1940795 GGTTGCACCA
* * * * * *
1940805 ACTTGTGTGCTTTTG-AAGGTTGCCACT-ACCTTGTGGGCTTCGAAAAGGCGCCACTA
1 ACTTGTGGGCTTTTGAAAAGATGCCACTGA-CTTGTGGGCTTTGAAAAGGTGCCACTG
* *
1940861 ACTTGTGGGCTTTTGAAAAGATGCCACT-AGCTTATGGGCTTTTG--AAGGTTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGATGCCACTGA-CTTGTGGGC-TTTGAAAAGG-TGCCACTG
* * ** *
1940918 ACTTGTGAGCTTTTGAAAAGATGCCAATGACTTGTGGGCTTTGAAAAAATGCCATTG
1 ACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
* * *
1940975 ACATGTGGGCTTTTAAAAAGATACCACTGACTTGTGGGCTTTGAAAATGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTG
* * *
1941033 ACTTGTGAGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAGAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
*
1941090 ACTTGTTGGG-TTTTAAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTG
1 ACTTG-TGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTG
*
1941148 ACTTATGGGC-TTTGAAA
1 ACTTGTGGGCTTTTGAAA
1941165 GGCGAGGAAT
Statistics
Matches: 260, Mismatches: 34, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
56 22 0.08
57 167 0.64
58 71 0.27
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (57 bp):
ACTTGTGGGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
Found at i:1941072 original size:115 final size:114
Alignment explanation
Indices: 1940805--1941164 Score: 446
Period size: 115 Copynumber: 3.2 Consensus size: 114
1940795 GGTTGCACCA
* * * * ** *
1940805 ACTTGTGTGCTTTTG-AAGGTTGCCACT-ACCTTGTGGGCTTCGAAAAGGCGCCACTAACTTGTG
1 ACTTGTGAGCTTTTGAAAAGATGCCACTGA-CTTGTGGGCTTTGAAAAGATGCCACTGACTTGTG
* * *
1940868 GGCTTTTGAAAAGATGCCACT-AGCTTATGGGCTTTTG--AAGGTTGCCACTA
65 GGCTTTTAAAAAGATGCCACTGA-CTTGTGGGC-TTTGAAAAGG-TGCCACTG
* * * *
1940918 ACTTGTGAGCTTTTGAAAAGATGCCAATGACTTGTGGGCTTTGAAAAAATGCCATTGACATGTGG
1 ACTTGTGAGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGG
*
1940983 GCTTTTAAAAAGATACCACTGACTTGTGGGCTTTGAAAATGGTGCCACTG
66 GCTTTTAAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTG
*
1941033 ACTTGTGAGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAGAAGATGCCACTGACTTGTTG
1 ACTTGTGAGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTG-TG
1941098 GG-TTTTAAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTG
65 GGCTTTTAAAAAGATGCCACTGACTTGTGGGCTTTGAAAA-GGTGCCACTG
* *
1941148 ACTTATGGGC-TTTGAAA
1 ACTTGTGAGCTTTTGAAA
1941165 GGCGAGGAAT
Statistics
Matches: 216, Mismatches: 24, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
113 18 0.08
114 70 0.32
115 122 0.56
116 6 0.03
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (114 bp):
ACTTGTGAGCTTTTGAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGATGCCACTGACTTGTGG
GCTTTTAAAAAGATGCCACTGACTTGTGGGCTTTGAAAAGGTGCCACTG
Found at i:1942615 original size:16 final size:15
Alignment explanation
Indices: 1942596--1942652 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
1942586 CATTCGGACC
1942596 CTTTTTGTTGTTTTCT
1 CTTTTTGTT-TTTTCT
*
1942612 CTTTTTGTTTTTTGT
1 CTTTTTGTTTTTTCT
*
1942627 TTTTTTGTCTCTTTTCT
1 CTTTTTGT-T-TTTTCT
1942644 -TTTTT-TTTT
1 CTTTTTGTTTT
1942653 GGCGGATGAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 13 0.36
16 15 0.42
17 5 0.14
ACGTcount: A:0.00, C:0.11, G:0.09, T:0.81
Consensus pattern (15 bp):
CTTTTTGTTTTTTCT
Found at i:1942627 original size:23 final size:24
Alignment explanation
Indices: 1942597--1942648 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
1942587 ATTCGGACCC
*
1942597 TTTTTGTTGTTTTCTCT-TTTTGT
1 TTTTTGTTGTTTTCTCTCTTTTCT
* *
1942620 TTTTTGTTTTTTTGTCTCTTTTCT
1 TTTTTGTTGTTTTCTCTCTTTTCT
1942644 TTTTT
1 TTTTT
1942649 TTTTGGCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (24 bp):
TTTTTGTTGTTTTCTCTCTTTTCT
Found at i:1949102 original size:15 final size:15
Alignment explanation
Indices: 1949082--1949111 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1949072 GATAAAGTGT
1949082 TTGAAAAAAAAAAAA
1 TTGAAAAAAAAAAAA
1949097 TTGAAAAAAAAAAAA
1 TTGAAAAAAAAAAAA
1949112 AAAAAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
TTGAAAAAAAAAAAA
Found at i:1949146 original size:21 final size:21
Alignment explanation
Indices: 1949122--1949178 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
1949112 AAAAAATTTA
1949122 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
1949143 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
1949164 AATGTATCGATACAT
1 AATGTATCGATACAT
1949179 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:1949258 original size:19 final size:19
Alignment explanation
Indices: 1949234--1949301 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
1949224 AATTCAACAA
1949234 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
1949253 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
1949268 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
1949285 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
1949302 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:1949273 original size:13 final size:13
Alignment explanation
Indices: 1949255--1949279 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1949245 ACATAAGTTT
1949255 TGTATCGATACAA
1 TGTATCGATACAA
1949268 TGTATCGATACA
1 TGTATCGATACA
1949280 TAAGTATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1949277 original size:32 final size:32
Alignment explanation
Indices: 1949236--1949298 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1949226 TTCAACAATT
*
1949236 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
1949268 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
1949299 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:1949359 original size:13 final size:13
Alignment explanation
Indices: 1949341--1949366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1949331 CATTTTTCTG
1949341 TGTATCGATACAT
1 TGTATCGATACAT
1949354 TGTATCGATACAT
1 TGTATCGATACAT
1949367 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1949363 original size:33 final size:33
Alignment explanation
Indices: 1949321--1949387 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1949311 GCCAAGGAAA
***
1949321 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
1949354 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
1949387 T
1 T
1949388 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:1951917 original size:52 final size:52
Alignment explanation
Indices: 1951844--1952016 Score: 167
Period size: 52 Copynumber: 3.3 Consensus size: 52
1951834 TTATTTTCGA
*
1951844 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCC-ACAATC
1 GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAA-TTTTCCTACAATC
* * **
1951896 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTCCTACAATC
* *
1951948 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAAAACACCAA-TTTCTTCACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C---AAAACACCAATTTTCCT-ACAATC
*
1952003 GGGGACACTCCAAC
1 GGGGATACTCCAAC
1952017 CCCGTTAATC
Statistics
Matches: 101, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
51 13 0.13
52 54 0.53
53 3 0.03
54 5 0.05
55 26 0.26
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATGTTCAAAACACCAATTTTCCTACAATC
Found at i:1952013 original size:55 final size:53
Alignment explanation
Indices: 1951844--1952227 Score: 156
Period size: 52 Copynumber: 7.3 Consensus size: 53
1951834 TTATTTTCGA
* *
1951844 GGGGATACTCCAACTCC-GGTTTTATCGTT--AAAACACTAATTT-TTCCACAATC
1 GGGGATACTCCAACTCCTGATTTTAT--TTCCAAAACACCAATTTCTT-CACAATC
* * * *
1951896 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTT--TAATC
1 GGGGATACTCCAACTCCTGATTTTATTTCCAAAACACCAA-TTT-CTTCACAATC
1951948 GGGGATACTCCAACTCC-GATTTTATTTCCAAAAAAACACCAATTTCTTCACAATC
1 GGGGATACTCCAACTCCTGATTTTATTTCC---AAAACACCAATTTCTTCACAATC
* * * * ** * * *** **
1952003 GGGGACACTCCAAC-CCCG--TTAATCATCGGGGATACTCCAACCCCGTT-A-TTTC
1 GGGGATACTCCAACTCCTGATTTTAT-TTC--CAAAACACCAATTTC-TTCACAATC
* * * * * * *
1952055 TGAGGGGATACTCCAAC-CCCGACTTTATTTTCAAAATATCGATTT-TTCATAATC
1 ---GGGGATACTCCAACTCCTGATTTTATTTCCAAAACACCAATTTCTTCACAATC
* * * * * * **
1952109 GGGGATACTCCAAC-CCCGGTTTTATTTTCACAACACCCATTTCTCCTTTAATC
1 GGGGATACTCCAACTCCTGATTTTATTTCCAAAACACCAATTTCTTC-ACAATC
* *
1952162 GGGGATACTCCAATTCC-GATTTTATTTCCAAAAATACCAATTT-TTCACAATC
1 GGGGATACTCCAACTCCTGATTTTATTTCC-AAAACACCAATTTCTTCACAATC
*
1952214 GAGGATACTCCAAC
1 GGGGATACTCCAAC
1952228 CTCGTTATTT
Statistics
Matches: 250, Mismatches: 54, Indels: 56
0.69 0.15 0.16
Matches are distributed among these distances:
50 2 0.01
51 39 0.16
52 78 0.31
53 53 0.21
54 27 0.11
55 46 0.18
56 1 0.00
57 4 0.02
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (53 bp):
GGGGATACTCCAACTCCTGATTTTATTTCCAAAACACCAATTTCTTCACAATC
Found at i:1952070 original size:28 final size:27
Alignment explanation
Indices: 1952003--1952075 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
1951993 CTTCACAATC
* *
1952003 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
1952030 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
1952058 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
1952076 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:1952120 original size:51 final size:51
Alignment explanation
Indices: 1952058--1952228 Score: 189
Period size: 51 Copynumber: 3.3 Consensus size: 51
1952048 TTATTTCTGA
* * *
1952058 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * * *
1952109 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCCATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
1952162 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
1952214 GAGGATACTCCAACC
1 GGGGATACTCCAACC
1952229 TCGTTATTTC
Statistics
Matches: 96, Mismatches: 21, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
51 36 0.38
52 18 0.19
53 32 0.33
54 10 0.10
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:1952158 original size:214 final size:214
Alignment explanation
Indices: 1951729--1952272 Score: 787
Period size: 214 Copynumber: 2.5 Consensus size: 214
1951719 AATTCTCCAC
* *
1951729 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTTCACAATCGGGGA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAAAAACACCAATTTCTTCACAATCGGGGA
1951794 TACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTT-TCGAGGGGATACTCCAAC
65 TACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCT-GAGGGGATACTCCAAC
* ** * *
1951858 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
129 CCCGACTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT
*
1951923 TCAAAACGCCAATTTTCCTTT
194 TCAAAACACCAATTTTCCTTT
*
1951944 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGAT
1952009 ACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCC
66 ACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCC
* * * *
1952074 CGACTTTAT-TTTCAAAATA-TCGATTTTT-CATAATCGGGGATACTCCAACCCCGGTTTTATTT
131 CGACTTTATCGTT-AAAACACT-AATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTT
* *
1952136 TCACAACACCCATTTCTCCTTT
194 TCAAAACACCAATTT-TCCTTT
* * *
1952158 AATCGGGGATACTCCAATTCCGATTTTATTTCC--AAAAATACCAATTT-TTCACAATCGAGGAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGAT
* * * *
1952220 ACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGG
66 ACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGG
1952273 AACATTCCAA
Statistics
Matches: 301, Mismatches: 23, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
211 27 0.09
212 47 0.16
213 46 0.15
214 149 0.50
215 32 0.11
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (214 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCACAATCGGGGAT
ACTCCAACCCCGTTAATCATCGGGGATACTCCAACCCCGTTATTTCTGAGGGGATACTCCAACCC
CGACTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAACCCCGGTTTTATTTTC
AAAACACCAATTTTCCTTT
Found at i:1952247 original size:28 final size:28
Alignment explanation
Indices: 1952211--1952292 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
1952201 ATTTTTCACA
*
1952211 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
1952239 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
1952267 --CGAGGGA-ACATTCCAACCTCGTTATT
1 ATCG-GGGATAC--TCCAACCTCGTTATT
1952293 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
26 4 0.09
27 4 0.09
28 38 0.83
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.28
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:1960512 original size:775 final size:775
Alignment explanation
Indices: 1958993--1960540 Score: 2738
Period size: 775 Copynumber: 2.0 Consensus size: 775
1958983 TTAAAACATG
1958993 AATGCCATCAAGATTAATAAGGAGGAAGCATACTGATAATGCGATAAAAGCATATGATATTTCAA
1 AATGCCATCAAGATTAATAAGGAGGAAGCATACTGATAATGCGATAAAAGCATATGATATTTCAA
1959058 ACAAATGAATTAATTACGCCAAATAAGGAAGAAGAAAGAAAATGTAATAGTTGTAATGTATCTCG
66 ACAAATGAATTAATTACGCCAAATAAGGAAGAAGAAAGAAAATGTAATAGTTGTAATGTATCTCG
1959123 TAATTACCACCGATTATCTTGAAATAATCGAATTGACAACTTAGATTTGTCCGGATTCTTTGATT
131 TAATTACCACCGATTATCTTGAAATAATCGAATTGACAACTTAGATTTGTCCGGATTCTTTGATT
*
1959188 AATTGAAGTCCAAAAATGGATTTGACTCAAAATTTGGGAGAGAAAATGGAATTTAATTTTTGGTT
196 AATTGAAGTCCAAAAACGGATTTGACTCAAAATTTGGGAGAGAAAATGGAATTTAATTTTTGGTT
* * *
1959253 GAGAACGGGGTTGGAGTGTCCCCTCGGAGGAATGGGGTTGAAGTGTCCCCGACAATGATAACTTA
261 GAGAACAGGGTTGGAGTGTCCCCTCAGAGGAATGGGGTTGAAGTGTCCCCGACAATAATAACTTA
* *
1959318 GATAAAAATACAAATGATCTTGACAAGTTTAAAAATAGGGTTGGAGTATCCCCAATGAATAAAAT
326 GATAAAAATACAAATAATCTTGACAAGTTTAAAAACAGGGTTGGAGTATCCCCAATGAATAAAAT
* *
1959383 TTTGATATTTTTAATGATGGAAATGATATGAATGGAGACGCTAAAGATGTAAAAGCATTTGTGCC
391 TTTGATATTTTTAATGAAGGAAATGATATGAATGAAGACGCTAAAGATGTAAAAGCATTTGTGCC
*
1959448 TTGACATGCTCTAAATGAGGTTCAAAAAAGGTTTTGAGACTGATCGGGATGGCACGGAGACATCT
456 TTGACATGCTCTAAATGAGGTTCAAAAAAGGTTTTGAGACTGATCGGGATGGCACGGAGACATCC
*
1959513 GAGTACCTTGAGGTGAAACCTGAGAAGAATAAACCAATTTTGACCAAAACCAAAACAGGGGACAA
521 GAGTACCTTGAGGTGAAACCCGAGAAGAATAAACCAATTTTGACCAAAACCAAAACAGGGGACAA
* *
1959578 CATCGCGCTATCCCGCTTTTCGAATTTATTTCAGATTGATTTGAAGGTTCTAGAGGGTGGACAAG
586 CATCGCGCTATCCCGATTTTCGAATTTATTTCAGATTGATTTGAAGGTTCTAGAAGGTGGACAAG
*
1959643 GTACAGTTGGAAAGGTAACTTGATGGGGGTTGATATAAAAATATTTCAAAAATCTAGAAAAATCA
651 GTACAGTTGGAAAGGTAACTTGATGGGGGTTGATATAAAAATATTTCAAAAATCCAGAAAAATCA
1959708 TTTTCTAGGTGGAATAAATTCTCAAATAGGGTGAATTGCATTGCTAGCAGAGCACATGAT
716 TTTTCTAGGTGGAATAAATTCTCAAATAGGGTGAATTGCATTGCTAGCAGAGCACATGAT
* *
1959768 AATGCGATCAAGATTAATAAGGAGGAAGCATACTGATAATGCGATAAAAGCATATGATATTTCAT
1 AATGCCATCAAGATTAATAAGGAGGAAGCATACTGATAATGCGATAAAAGCATATGATATTTCAA
* *
1959833 ACAAATGAATTAATTACGTCGAATAAGGAAGAAGAAAGAAAATGTAATAGTTGTAATGTATCTCG
66 ACAAATGAATTAATTACGCCAAATAAGGAAGAAGAAAGAAAATGTAATAGTTGTAATGTATCTCG
* *
1959898 TAATTGCCACCGATTATCTTGAAATAATCGAATTGACAACTTAGATTTGTCCTGATTCTTTGATT
131 TAATTACCACCGATTATCTTGAAATAATCGAATTGACAACTTAGATTTGTCCGGATTCTTTGATT
* * *
1959963 AATTGAAGTCCGAAAACGGGTTTGACTCGAAATTTGGGAGAGAAAATGGAATTTAATTTTTGGTT
196 AATTGAAGTCCAAAAACGGATTTGACTCAAAATTTGGGAGAGAAAATGGAATTTAATTTTTGGTT
*
1960028 GAGAATAGGGTTGGAGTGTCCCCTCAGAGGAATGGGGTTGAAGTGTCCCCGACAATAATAACTTA
261 GAGAACAGGGTTGGAGTGTCCCCTCAGAGGAATGGGGTTGAAGTGTCCCCGACAATAATAACTTA
* ** *
1960093 GGTAAAAATATGAATAATCTTGACAAGTTTAAAAACAGGGTTGGAGTATCCCCGATGAATAAAAT
326 GATAAAAATACAAATAATCTTGACAAGTTTAAAAACAGGGTTGGAGTATCCCCAATGAATAAAAT
* * *
1960158 TTTGATATTTTTGATGAAGGAAATGATGTGAATGAAGACGCTAAAGATGTAAAAGTATTTGTGCC
391 TTTGATATTTTTAATGAAGGAAATGATATGAATGAAGACGCTAAAGATGTAAAAGCATTTGTGCC
1960223 TTGACATGCTCTAAATGAGGTTCAAAAAAGGTTTTGAGACTGATCGGGATGGCACGGAGACATCC
456 TTGACATGCTCTAAATGAGGTTCAAAAAAGGTTTTGAGACTGATCGGGATGGCACGGAGACATCC
1960288 GAGTACCTTGAGGTGAAACCCGAGAAGAATAAACCAATTTTGACCAAAACCAAAACAGGGGACAA
521 GAGTACCTTGAGGTGAAACCCGAGAAGAATAAACCAATTTTGACCAAAACCAAAACAGGGGACAA
* **
1960353 CATCGCGCTATCTC-ATTTTCGAATTTATTTTGGATTGATTTGAAGGTTCTAGAAGGTGGACAAG
586 CATCGCGCTATCCCGATTTTCGAATTTATTTCAGATTGATTTGAAGGTTCTAGAAGGTGGACAAG
* * *
1960417 GTACCGTTGGAAAGGTAACTTGATGGGGGTTGATCTAAAAATATTTCAAAAATCCAGAAAAATCG
651 GTACAGTTGGAAAGGTAACTTGATGGGGGTTGATATAAAAATATTTCAAAAATCCAGAAAAATCA
**
1960482 TTTTCTAGGTGGAATAAATTCTCAAAATAGGGTGAATTGTTTTGCTAGCAGAGCACATG
716 TTTTCTAGGTGGAATAAATTCTC-AAATAGGGTGAATTGCATTGCTAGCAGAGCACATG
1960541 TAGAAAAAGG
Statistics
Matches: 734, Mismatches: 38, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
774 130 0.18
775 604 0.82
ACGTcount: A:0.36, C:0.13, G:0.23, T:0.28
Consensus pattern (775 bp):
AATGCCATCAAGATTAATAAGGAGGAAGCATACTGATAATGCGATAAAAGCATATGATATTTCAA
ACAAATGAATTAATTACGCCAAATAAGGAAGAAGAAAGAAAATGTAATAGTTGTAATGTATCTCG
TAATTACCACCGATTATCTTGAAATAATCGAATTGACAACTTAGATTTGTCCGGATTCTTTGATT
AATTGAAGTCCAAAAACGGATTTGACTCAAAATTTGGGAGAGAAAATGGAATTTAATTTTTGGTT
GAGAACAGGGTTGGAGTGTCCCCTCAGAGGAATGGGGTTGAAGTGTCCCCGACAATAATAACTTA
GATAAAAATACAAATAATCTTGACAAGTTTAAAAACAGGGTTGGAGTATCCCCAATGAATAAAAT
TTTGATATTTTTAATGAAGGAAATGATATGAATGAAGACGCTAAAGATGTAAAAGCATTTGTGCC
TTGACATGCTCTAAATGAGGTTCAAAAAAGGTTTTGAGACTGATCGGGATGGCACGGAGACATCC
GAGTACCTTGAGGTGAAACCCGAGAAGAATAAACCAATTTTGACCAAAACCAAAACAGGGGACAA
CATCGCGCTATCCCGATTTTCGAATTTATTTCAGATTGATTTGAAGGTTCTAGAAGGTGGACAAG
GTACAGTTGGAAAGGTAACTTGATGGGGGTTGATATAAAAATATTTCAAAAATCCAGAAAAATCA
TTTTCTAGGTGGAATAAATTCTCAAATAGGGTGAATTGCATTGCTAGCAGAGCACATGAT
Found at i:1962321 original size:13 final size:13
Alignment explanation
Indices: 1962303--1962363 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 13
1962293 ATACAAAGAT
1962303 CAATGTATCGATA
1 CAATGTATCGATA
1962316 CAATGTATCGAT-
1 CAATGTATCGATA
*
1962328 --A--TATTGA-A
1 CAATGTATCGATA
* *
1962336 TAATGTATCCATA
1 CAATGTATCGATA
1962349 CAATGTATCGATA
1 CAATGTATCGATA
1962362 CA
1 CA
1962364 TTGAATAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 12
0.69 0.09 0.22
Matches are distributed among these distances:
8 5 0.14
10 2 0.05
12 4 0.11
13 26 0.70
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1962323 original size:33 final size:33
Alignment explanation
Indices: 1962304--1962385 Score: 146
Period size: 33 Copynumber: 2.5 Consensus size: 33
1962294 TACAAAGATC
*
1962304 AATGTATCGATACAATGTATCGATATATTGAAT
1 AATGTATCGATACAATGTATCGATACATTGAAT
*
1962337 AATGTATCCATACAATGTATCGATACATTGAAT
1 AATGTATCGATACAATGTATCGATACATTGAAT
1962370 AATGTATCGATACAAT
1 AATGTATCGATACAAT
1962386 TCCTTGGCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACAATGTATCGATACATTGAAT
Found at i:1962450 original size:32 final size:32
Alignment explanation
Indices: 1962414--1962520 Score: 205
Period size: 32 Copynumber: 3.3 Consensus size: 32
1962404 GTAGCTTTTT
1962414 ATCGATACATTGTATCGATACAACACTTATGC
1 ATCGATACATTGTATCGATACAACACTTATGC
1962446 ATCGATACATTGTATCGATACAACACTTATGC
1 ATCGATACATTGTATCGATACAACACTTATGC
*
1962478 ATCGATACATTGTATCGATACAACACTTATGT
1 ATCGATACATTGTATCGATACAACACTTATGC
1962510 ATCGATACATT
1 ATCGATACATT
1962521 TAATGTTTAT
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 74 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (32 bp):
ATCGATACATTGTATCGATACAACACTTATGC
Found at i:1962451 original size:19 final size:19
Alignment explanation
Indices: 1962424--1962518 Score: 88
Period size: 19 Copynumber: 5.6 Consensus size: 19
1962414 ATCGATACAT
1962424 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
1962443 TGCATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1962456 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
1962475 TGCATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1962488 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1962507 TGTATCGATACA
1 TGTATCGATACA
1962519 TTTAATGTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 24
0.68 0.05 0.27
Matches are distributed among these distances:
13 16 0.27
14 2 0.03
16 12 0.20
18 2 0.03
19 28 0.47
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1962862 original size:20 final size:20
Alignment explanation
Indices: 1962837--1962886 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1962827 GTTGGGCACA
* *
1962837 ATGTATCGATACAATTTACT
1 ATGTATCGATACAATGTACC
* *
1962857 ATGTATCGATATAATGTCCC
1 ATGTATCGATACAATGTACC
1962877 ATGTATCGAT
1 ATGTATCGAT
1962887 GCAAACAGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1962942 original size:20 final size:20
Alignment explanation
Indices: 1962917--1962954 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1962907 TACTACTAGT
1962917 TTCATGTATCAATACAATTC
1 TTCATGTATCAATACAATTC
*
1962937 TTCATGTATCGATACAAT
1 TTCATGTATCAATACAAT
1962955 GTATCGATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (20 bp):
TTCATGTATCAATACAATTC
Found at i:1962958 original size:13 final size:13
Alignment explanation
Indices: 1962940--1962968 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1962930 ACAATTCTTC
1962940 ATGTATCGATACA
1 ATGTATCGATACA
1962953 ATGTATCGATACA
1 ATGTATCGATACA
1962966 ATG
1 ATG
1962969 AACATGTATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1962980 original size:32 final size:33
Alignment explanation
Indices: 1962939--1963018 Score: 108
Period size: 32 Copynumber: 2.5 Consensus size: 33
1962929 TACAATTCTT
* *
1962939 CATGTATCGATACAATGTATCGATACAATG-AA
1 CATGTATCGATACAATATATCGATACAAAGCAA
*
1962971 CATGTATCGATACATTATATCGATACAAAGCAA
1 CATGTATCGATACAATATATCGATACAAAGCAA
* *
1963004 TACGTATCGATACAA
1 CATGTATCGATACAA
1963019 AGTAATATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
32 27 0.66
33 14 0.34
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
CATGTATCGATACAATATATCGATACAAAGCAA
Found at i:1963013 original size:20 final size:20
Alignment explanation
Indices: 1962988--1963025 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1962978 CGATACATTA
1962988 TATCGATACAAAGCAATACG
1 TATCGATACAAAGCAATACG
*
1963008 TATCGATACAAAGTAATA
1 TATCGATACAAAGCAATA
1963026 TGCATCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.16, G:0.13, T:0.24
Consensus pattern (20 bp):
TATCGATACAAAGCAATACG
Found at i:1963036 original size:20 final size:20
Alignment explanation
Indices: 1962993--1963036 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1962983 CATTATATCG
* *
1962993 ATACAAAGCAATACGTATCG
1 ATACAAAGCAATACGCATCA
* *
1963013 ATACAAAGTAATATGCATCA
1 ATACAAAGCAATACGCATCA
1963033 ATAC
1 ATAC
1963037 TTCTAGACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.48, C:0.18, G:0.11, T:0.23
Consensus pattern (20 bp):
ATACAAAGCAATACGCATCA
Found at i:1963526 original size:28 final size:28
Alignment explanation
Indices: 1963478--1963570 Score: 114
Period size: 28 Copynumber: 3.3 Consensus size: 28
1963468 CCTCCCTAGG
*
1963478 AGGTGCCAACTAGTATAGGCTTTGACTT
1 AGGTGCCAACTAGTATGGGCTTTGACTT
* * *
1963506 AGATGCCAACTACTATGGGCTTTAACTT
1 AGGTGCCAACTAGTATGGGCTTTGACTT
* * * *
1963534 AGGTGCTAGCTAGTGTGGGCTTTGACTC
1 AGGTGCCAACTAGTATGGGCTTTGACTT
1963562 AGGTGCCAA
1 AGGTGCCAA
1963571 ACAATGTGGG
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (28 bp):
AGGTGCCAACTAGTATGGGCTTTGACTT
Found at i:1963717 original size:28 final size:26
Alignment explanation
Indices: 1963645--1963888 Score: 150
Period size: 26 Copynumber: 9.1 Consensus size: 26
1963635 ACTTACTTGC
* **
1963645 GTGCCAACAAATGTGGTTTTTGACTT
1 GTGCCAACGAATGTGGGCTTTGACTT
* * *
1963671 GTGCCAA-TAAGTATAGGCTTTGACATAT
1 GTGCCAACGAA-TGTGGGCTTTGAC-T-T
**
1963699 GTGCCAACGAATGTGGGCTTAAACTTT
1 GTGCCAACGAATGTGGGCTTTGAC-TT
* * * *
1963726 ATACCAATGAATGTGGGCTTTGATTT
1 GTGCCAACGAATGTGGGCTTTGACTT
* * *
1963752 ATGACAACAAATGTGGGCTTTGACTT
1 GTGCCAACGAATGTGGGCTTTGACTT
* *
1963778 GTGCCAGC-AAGTGTGGGCTTTAACTTAT
1 GTGCCAACGAA-TGTGGGCTTTGAC-T-T
* * **
1963806 GTGCCAGCAAATGTGGGCTTAAACTT
1 GTGCCAACGAATGTGGGCTTTGACTT
* *
1963832 GTGCGCCAATGAATGTTGGCTTTGACTT
1 GT--GCCAACGAATGTGGGCTTTGACTT
* * * *
1963860 ATGCTAACGAATGTTGGCTTTAACTT
1 GTGCCAACGAATGTGGGCTTTGACTT
1963886 GTG
1 GTG
1963889 TTCTAGTAAA
Statistics
Matches: 170, Mismatches: 38, Indels: 20
0.75 0.17 0.09
Matches are distributed among these distances:
25 4 0.02
26 82 0.48
27 22 0.13
28 58 0.34
29 4 0.02
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (26 bp):
GTGCCAACGAATGTGGGCTTTGACTT
Found at i:1963879 original size:82 final size:82
Alignment explanation
Indices: 1963761--1963913 Score: 191
Period size: 82 Copynumber: 1.9 Consensus size: 82
1963751 TATGACAACA
* * *
1963761 AATGTGGGCTTTGACTTGTGCCAGCAAGTGTGGGCTTTAACTTATGTGCCAGCAAATGTGGGCTT
1 AATGTGGGCTTTGACTTATGCCAACAAGTGTGGGCTTTAACTTATGTGCCAGCAAATGTAGGCTT
1963826 AAACTTGTGCGCCAATG
66 AAACTTGTGCGCCAATG
* * * * * * *
1963843 AATGTTGGCTTTGACTTATGCTAACGAA-TGTTGGCTTTAACTTGTGTTCTAGTAAATGTAGGCT
1 AATGTGGGCTTTGACTTATGCCAAC-AAGTGTGGGCTTTAACTTATGTGCCAGCAAATGTAGGCT
*
1963907 TCAACTT
65 TAAACTT
1963914 ACATGCCAAC
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
82 57 0.97
83 2 0.03
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.35
Consensus pattern (82 bp):
AATGTGGGCTTTGACTTATGCCAACAAGTGTGGGCTTTAACTTATGTGCCAGCAAATGTAGGCTT
AAACTTGTGCGCCAATG
Found at i:1971238 original size:19 final size:19
Alignment explanation
Indices: 1971214--1971268 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1971204 TGTATCGATG
1971214 CATTGTATCGATACAT-TC
1 CATTGTATCGATACATATC
*
1971232 TCATTGTATCGATAAATATC
1 -CATTGTATCGATACATATC
*
1971252 CAATTGTATCTATACAT
1 C-ATTGTATCGATACAT
1971269 GAAACTAGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.40
Consensus pattern (19 bp):
CATTGTATCGATACATATC
Found at i:1976275 original size:13 final size:13
Alignment explanation
Indices: 1976257--1976283 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1976247 ATACATTAAA
1976257 AGTGTATCGATAT
1 AGTGTATCGATAT
1976270 AGTGTATCGATAT
1 AGTGTATCGATAT
1976283 A
1 A
1976284 ATTTTCTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.37
Consensus pattern (13 bp):
AGTGTATCGATAT
Found at i:1978431 original size:13 final size:13
Alignment explanation
Indices: 1978413--1978437 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1978403 CATTTTGGGA
1978413 TGTATCGATACAG
1 TGTATCGATACAG
1978426 TGTATCGATACA
1 TGTATCGATACA
1978438 TATTGTGTGT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1978435 original size:33 final size:32
Alignment explanation
Indices: 1978393--1978456 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1978383 TACAAGCCAA
*
1978393 TGTATCGATACATTTTGGGATGTATCGATACAG
1 TGTATCGATACATATTGGG-TGTATCGATACAG
*
1978426 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
1978457 AATTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAG
Found at i:1978536 original size:20 final size:21
Alignment explanation
Indices: 1978489--1978543 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1978479 GCCAATGACC
**
1978489 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1978510 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1978530 TGTATCGATACATT
1 TGTATCGATACATT
1978544 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1979135 original size:22 final size:22
Alignment explanation
Indices: 1979108--1979152 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1979098 TTTTCTTTTC
*
1979108 TCTCCCCCCTAATCAAAA-AATT
1 TCTCCCACCTAAT-AAAATAATT
*
1979130 TCTCCCACTTAATAAAATAATT
1 TCTCCCACCTAATAAAATAATT
1979152 T
1 T
1979153 AACAATTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.38, C:0.29, G:0.00, T:0.33
Consensus pattern (22 bp):
TCTCCCACCTAATAAAATAATT
Found at i:1980900 original size:20 final size:21
Alignment explanation
Indices: 1980871--1980911 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1980861 TGTTTTTGTT
1980871 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1980890 GATGCATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1980912 AAGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1983891 original size:33 final size:32
Alignment explanation
Indices: 1983854--1983917 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 32
1983844 TACAAGCCAA
* *
1983854 TGTATCGATATATTTTGGGATGTATCGATACAG
1 TGTATCGATACATATTGGG-TGTATCGATACAG
*
1983887 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
1983918 AATTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.43
33 16 0.57
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAG
Found at i:1983892 original size:13 final size:13
Alignment explanation
Indices: 1983874--1983898 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1983864 TATTTTGGGA
1983874 TGTATCGATACAG
1 TGTATCGATACAG
1983887 TGTATCGATACA
1 TGTATCGATACA
1983899 TATTGTGTGT
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1983997 original size:20 final size:21
Alignment explanation
Indices: 1983950--1984004 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1983940 GCCAATGACC
**
1983950 TGTATCGATACATTCTTTTCA
1 TGTATCGATACATTCTGGTCA
*
1983971 AGTATCGATACATT-TGGTCA
1 TGTATCGATACATTCTGGTCA
1983991 TGTATCGATACATT
1 TGTATCGATACATT
1984005 GTATCGATAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (21 bp):
TGTATCGATACATTCTGGTCA
Found at i:1984047 original size:20 final size:20
Alignment explanation
Indices: 1984024--1984064 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1984014 CTGTGCAATT
1984024 TGTATCGATACATTTAAAGG
1 TGTATCGATACATTTAAAGG
* *
1984044 TGTATCGATACTTTTCAAGG
1 TGTATCGATACATTTAAAGG
1984064 T
1 T
1984065 TTTGTCCTTT
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:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTAAAGG
Found at i:1984467 original size:21 final size:21
Alignment explanation
Indices: 1984443--1984497 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1984433 CACTTGCAAC
*
1984443 TCATTTCTTTTCTCATCTAAT
1 TCATTTATTTTCTCATCTAAT
**
1984464 TCATTTATTTTCTTTTCTAAT
1 TCATTTATTTTCTCATCTAAT
* *
1984485 TCACTTAATTTCT
1 TCATTTATTTTCT
1984498 TTTCAAAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (21 bp):
TCATTTATTTTCTCATCTAAT
Found at i:1984498 original size:21 final size:21
Alignment explanation
Indices: 1984458--1984501 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1984448 TCTTTTCTCA
* *
1984458 TCTAATTCATTTATTTTCTTT
1 TCTAATTCACTTAATTTCTTT
1984479 TCTAATTCACTTAATTTCTTT
1 TCTAATTCACTTAATTTCTTT
1984500 TC
1 TC
1984502 AAAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.18, G:0.00, T:0.61
Consensus pattern (21 bp):
TCTAATTCACTTAATTTCTTT
Found at i:1986538 original size:13 final size:13
Alignment explanation
Indices: 1986520--1986544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1986510 TTTGGGACAA
1986520 TGTATCGATACAT
1 TGTATCGATACAT
1986533 TGTATCGATACA
1 TGTATCGATACA
1986545 AATAGTGGTA
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):
TGTATCGATACAT
Found at i:1995745 original size:10 final size:10
Alignment explanation
Indices: 1995730--1995765 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1995720 ATCCTTCGTA
1995730 AAAAAAACAC
1 AAAAAAACAC
*
1995740 AAAAAAAAAC
1 AAAAAAACAC
*
1995750 AAAAACACAC
1 AAAAAAACAC
1995760 AAAAAA
1 AAAAAA
1995766 TAAAAAATGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAC
Found at i:1995771 original size:18 final size:17
Alignment explanation
Indices: 1995729--1995772 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1995719 CATCCTTCGT
1995729 AAAAAAAACACAAAAAA
1 AAAAAAAACACAAAAAA
1995746 AAACAAAAACACACAAAAA
1 AAA-AAAAACACA-AAAAA
*
1995765 ATAAAAAA
1 AAAAAAAA
1995773 TGGGGGGAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 3 0.12
18 14 0.58
19 7 0.29
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (17 bp):
AAAAAAAACACAAAAAA
Found at i:1995965 original size:39 final size:39
Alignment explanation
Indices: 1995906--1995984 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
1995896 CCTACGAAAG
*
1995906 AATGTGAAGTAATCCTAGGGAACTTTCGAAGATCAGCTT
1 AATGCGAAGTAATCCTAGGGAACTTTCGAAGATCAGCTT
*
1995945 AATGCGAAGTAATCCTAGGGAACTTTCGAAGATCGGCTT
1 AATGCGAAGTAATCCTAGGGAACTTTCGAAGATCAGCTT
1995984 A
1 A
1995985 CACTAGTCAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (39 bp):
AATGCGAAGTAATCCTAGGGAACTTTCGAAGATCAGCTT
Found at i:1997198 original size:28 final size:28
Alignment explanation
Indices: 1997151--1997229 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 28
1997141 GAATCCCTTC
* *
1997151 TCAAAGGCCACTAGTCAGTGGCACCTCT
1 TCAAAGTCCACAAGTCAGTGGCACCTCT
* * *
1997179 TCGAAGTCCACAAGTCAGTGGCATCTTT
1 TCAAAGTCCACAAGTCAGTGGCACCTCT
1997207 TCAAAGTCCACAA-TCAGTGGCAC
1 TCAAAGTCCACAAGTCAGTGGCAC
1997230 TTACTATATC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 9 0.20
28 35 0.80
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (28 bp):
TCAAAGTCCACAAGTCAGTGGCACCTCT
Found at i:1997446 original size:32 final size:32
Alignment explanation
Indices: 1997401--1997583 Score: 196
Period size: 32 Copynumber: 5.8 Consensus size: 32
1997391 TCAGTGGAGA
* *
1997401 AACCTTCTCCAAAGCCCACATAAGCTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
*
1997433 AACCTTCTTCAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
* * *
1997465 AACC-TCTTTAAAAGCCCACACAAGTTAGTGGC
1 AACCTTC-TTCAAAGCCCACACAAGCTGGTGGC
* ** *
1997497 AACC-CCTTCAAAGCCCACACAAGCTACTGGT
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
1997528 AACCCTTCTT-AAAGCCCACACAAG-TCGGTGGC
1 AA-CCTTCTTCAAAGCCCACACAAGCT-GGTGGC
*
1997560 AACCCT-TTCAAAAGCCCACACAAG
1 AACCTTCTTC-AAAGCCCACACAAG
1997584 TTAGTCACAT
Statistics
Matches: 130, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
30 2 0.02
31 29 0.22
32 96 0.74
33 3 0.02
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.19
Consensus pattern (32 bp):
AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
Found at i:1997515 original size:95 final size:95
Alignment explanation
Indices: 1997410--1997588 Score: 281
Period size: 95 Copynumber: 1.9 Consensus size: 95
1997400 AAACCTTCTC
* ** *
1997410 CAAAGCCCACATAAGCTGGTGGCAA-CCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCTCTTT
1 CAAAGCCCACACAAGCTACTGGCAACCCTTCTT-AAAGCCCACACAAGTCGGTGGCAACC-CTTT
1997474 -AAAAGCCCACACAAGTTAGTGGCAACCCCTT
64 CAAAAGCCCACACAAGTTAGTGGCAACCCCTT
*
1997505 CAAAGCCCACACAAGCTACTGGTAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCA
1 CAAAGCCCACACAAGCTACTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCA
1997570 AAAGCCCACACAAGTTAGT
66 AAAGCCCACACAAGTTAGT
1997589 CACATCTCCT
Statistics
Matches: 77, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
94 4 0.05
95 66 0.86
96 7 0.09
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (95 bp):
CAAAGCCCACACAAGCTACTGGCAACCCTTCTTAAAGCCCACACAAGTCGGTGGCAACCCTTTCA
AAAGCCCACACAAGTTAGTGGCAACCCCTT
Found at i:1997542 original size:63 final size:63
Alignment explanation
Indices: 1997411--1997583 Score: 213
Period size: 63 Copynumber: 2.7 Consensus size: 63
1997401 AACCTTCTCC
* * * * **
1997411 AAAGCCCACATAAGCTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCTCTTTA
1 AAAGCCCACACAAGTTGGTGGCAACC-CCTTCAAAGCCCACACAAGCTACTGGCAACCTCTTTA
* * *
1997475 AAAGCCCACACAAGTTAGTGGCAACCCCTTCAAAGCCCACACAAGCTACTGGTAACC-CTTCTT
1 AAAGCCCACACAAGTTGGTGGCAACCCCTTCAAAGCCCACACAAGCTACTGGCAACCTCTT-TA
* *
1997538 AAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAAGCCCACACAAG
1 AAAGCCCACACAAGTTGGTGGCAACCCCTTC-AAAGCCCACACAAG
1997584 TTAGTCACAT
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
62 3 0.03
63 55 0.58
64 37 0.39
ACGTcount: A:0.32, C:0.33, G:0.17, T:0.18
Consensus pattern (63 bp):
AAAGCCCACACAAGTTGGTGGCAACCCCTTCAAAGCCCACACAAGCTACTGGCAACCTCTTTA
Found at i:1997606 original size:63 final size:61
Alignment explanation
Indices: 1997412--1997606 Score: 160
Period size: 63 Copynumber: 3.1 Consensus size: 61
1997402 ACCTTCTCCA
* * * * * **
1997412 AAGCCCACATAAG-CTGGTGGCAACCTTCTTCAAAGCCCACACAAGTTGGTGGCAACCTCTTTAA
1 AAGCCCACACAAGTC-GGTGGCAACCCT-TTCAAAGCCCACACAAGTTAGT--CAAACTCCTTCT
** * * * **
1997476 AAGCCCACACAAGTTAGTGGCAACCCCTTCAAAGCCCACACAAGCTACTGGTAAC-CCTTCTT
1 AAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTTAGT-CAAACTCCTTC-T
*
1997538 AAAGCCCACACAAGTCGGTGGCAACCCTTTCAAAAGCCCACACAAGTTAGTCACATCTCCTTCT
1 -AAGCCCACACAAGTCGGTGGCAACCCTTTC-AAAGCCCACACAAGTTAGTCA-AACTCCTTCT
1997602 AAGCC
1 AAGCC
1997607 TAATGTCCTT
Statistics
Matches: 103, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
61 3 0.03
62 3 0.03
63 51 0.50
64 41 0.40
65 5 0.05
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (61 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTTCAAAGCCCACACAAGTTAGTCAAACTCCTTCT
Found at i:1997719 original size:52 final size:51
Alignment explanation
Indices: 1997644--1997950 Score: 239
Period size: 52 Copynumber: 6.0 Consensus size: 51
1997634 TTAGCACCTT
* * *
1997644 TAAGTCCAATATCGATGGCCTTGAATTAGCACATTGGCACCTTTACCATCTT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTA-CATCTC
* * *
1997696 TAAGTACAATGTCGCTGGCCTTGAATCAGCACATTGGCACC-TT-CATCCC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTACATCTC
* * * * *
1997745 TAAGTCCGATATCACTGGCCTTGAATCAGCATATTGACATCTTTAACAT-TGC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTT-ACATCT-C
* * * *
1997797 TAAGCCCATTGTCGCTGGCCTTGAATCAGCACATTGGCATTCTTCT-CATCT-
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-CCTT-TACATCTC
* * * ** * ** *
1997848 TCAAGTCTAATGTCGCTGG-CTATGAATCAGCATATTAACATTCTTCGCATCTT
1 T-AAGTCCAATATCGCTGGCCT-TGAATCAGCACATTGGCA-CCTTTACATCTC
* * * *
1997901 TAAGTCCAATATCGTTGGTCTTGAATCAGCATATTGGCACTTTTATCATC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTA-CATC
1997951 CTTTTCATCT
Statistics
Matches: 205, Mismatches: 37, Indels: 26
0.76 0.14 0.10
Matches are distributed among these distances:
49 38 0.19
50 2 0.01
51 7 0.03
52 149 0.73
53 8 0.04
54 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.33
Consensus pattern (51 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTACATCTC
Found at i:1997789 original size:101 final size:101
Alignment explanation
Indices: 1997644--1997940 Score: 291
Period size: 101 Copynumber: 2.9 Consensus size: 101
1997634 TTAGCACCTT
* * * * *
1997644 TAAGTCCAATATCGA-TGGCCTTGAATTAGCACATTGGCACCTTTACCATCTTTAAGTACAATGT
1 TAAGTCCAATATC-ACTGGCCTTGAATCAGCATATTGACATCTTTACCATCTTTAAGTCCAATGT
1997708 CGCTGGCCTTGAATCAGCACATTGGCACCTTCATC-CC
65 CGCTGGCCTTGAATCAGCACATTGGCACCTTC-TCACC
* * * * *
1997745 TAAGTCCGATATCACTGGCCTTGAATCAGCATATTGACATCTTTAACAT-TGCTAAGCCCATTGT
1 TAAGTCCAATATCACTGGCCTTGAATCAGCATATTGACATCTTTACCATCT-TTAAGTCCAATGT
* *
1997809 CGCTGGCCTTGAATCAGCACATTGGCATTCTTCTCATCT
65 CGCTGGCCTTGAATCAGCACATTGGCA-CCTTCTCA-CC
* * * *
1997848 TCAAGTCTAATGTCGCTGG-CTATGAATCAGCATATTAACAT-TCTT-CGCATCTTTAAGTCCAA
1 T-AAGTCCAATATCACTGGCCT-TGAATCAGCATATTGACATCT-TTAC-CATCTTTAAGTCCAA
* * * *
1997910 TATCGTTGGTCTTGAATCAGCATATTGGCAC
62 TGTCGCTGGCCTTGAATCAGCACATTGGCAC
1997941 TTTTATCATC
Statistics
Matches: 160, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
100 2 0.01
101 79 0.49
102 4 0.03
103 5 0.03
104 69 0.43
105 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (101 bp):
TAAGTCCAATATCACTGGCCTTGAATCAGCATATTGACATCTTTACCATCTTTAAGTCCAATGTC
GCTGGCCTTGAATCAGCACATTGGCACCTTCTCACC
Found at i:1998009 original size:61 final size:61
Alignment explanation
Indices: 1997889--1998024 Score: 168
Period size: 61 Copynumber: 2.2 Consensus size: 61
1997879 ATATTAACAT
* * * * * * *
1997889 TCTTCGCATCTTTAAGTCCAATATCGTTGGTCTTGAATCAGCATATTGGCACTTTTATCA-
1 TCTTCTCATCTTTAAGCCCAATATCGCTGGCCCTGAATCAGCATATTAGCACTTATATCAC
*
1997949 TCCTTTTCATCTTTAAGCCCAATATCGCTGGCCCTGAATCAGCATATTAGCA-TCTATATCAC
1 T-CTTCTCATCTTTAAGCCCAATATCGCTGGCCCTGAATCAGCATATTAGCACT-TATATCAC
1998011 TCTTCTCATCTTTA
1 TCTTCTCATCTTTA
1998025 TCATCTTTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 2 0.03
61 61 0.95
62 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.39
Consensus pattern (61 bp):
TCTTCTCATCTTTAAGCCCAATATCGCTGGCCCTGAATCAGCATATTAGCACTTATATCAC
Found at i:2003562 original size:19 final size:19
Alignment explanation
Indices: 2003538--2003630 Score: 102
Period size: 19 Copynumber: 5.5 Consensus size: 19
2003528 TATCGATACA
2003538 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTG
2003557 TATCGATAC--AA----TG
1 TATCGATACATAAGTGTTG
2003570 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTG
2003589 TATCGATAC--AA----TG
1 TATCGATACATAAGTGTTG
2003602 TATCGATACATAAGTGTTG
1 TATCGATACATAAGTGTTG
2003621 TATCGATACA
1 TATCGATACA
2003631 ATGTATCGCT
Statistics
Matches: 62, Mismatches: 0, Indels: 24
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.35
15 4 0.06
17 4 0.06
19 32 0.52
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (19 bp):
TATCGATACATAAGTGTTG
Found at i:2003573 original size:13 final size:13
Alignment explanation
Indices: 2003555--2003644 Score: 63
Period size: 13 Copynumber: 6.0 Consensus size: 13
2003545 ACATAAGTGT
2003555 TGTATCGATACAA
1 TGTATCGATACAA
2003568 TGTATCGATACATAA
1 TGTATCGATAC--AA
2003583 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2003600 TGTATCGATACATAA
1 TGTATCGATAC--AA
2003615 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
*
2003632 TGTATCGCTACAA
1 TGTATCGATACAA
2003645 AGCTACTGCC
Statistics
Matches: 64, Mismatches: 1, Indels: 24
0.72 0.01 0.27
Matches are distributed among these distances:
13 34 0.53
15 4 0.06
17 4 0.06
19 22 0.34
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2003685 original size:20 final size:20
Alignment explanation
Indices: 2003660--2003758 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
2003650 CTGCCAAGGA
2003660 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
2003680 AATGTATCGATACATTGTA-TC
1 AATGTATCGATACA-T-TACTC
* ** * ** *
2003701 GATACATCTAGAAATTTTACCC
1 AATGTATC--GATACATTACTC
*
2003723 AGATGTATCGATACATTATTC
1 A-ATGTATCGATACATTACTC
2003744 AATGTATCGATACAT
1 AATGTATCGATACAT
2003759 GCAGGCAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
20 28 0.48
21 18 0.31
22 4 0.07
23 8 0.14
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTACTC
Found at i:2003700 original size:13 final size:13
Alignment explanation
Indices: 2003682--2003707 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2003672 CATTACTCAA
2003682 TGTATCGATACAT
1 TGTATCGATACAT
2003695 TGTATCGATACAT
1 TGTATCGATACAT
2003708 CTAGAAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2007113 original size:78 final size:77
Alignment explanation
Indices: 2007006--2007251 Score: 257
Period size: 79 Copynumber: 3.1 Consensus size: 77
2006996 ACCACGGGGC
** *
2007006 TGGAGTATCTCT-TCGAAAATAACACGGTTGGAGTATCCCTGATTATAGAAAATTGGTGTTTTGA
1 TGGAGTATC-CTGTCGAAAATAACGGGGTTGGAGTATCCCCGATTAT-GAAAATTGGTGTTTTGA
2007070 AAATAAAATCAGGGT
64 AAATAAAATC-GGGT
* * * *
2007085 TGGAGTATCCTGTC-AAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTT-AG
1 TGGAGTATCCTGTCGAAAATAACGGGGTTGGAGTATCCCCGATTATG-AAAATTGGTGTTTTGA-
***
2007148 AAATAAGGCCGGGAT
64 AAATAAAATCGGG-T
* * *
2007163 TAGAGTATCCTCG-CGAAAATAACGGGATTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGG
1 TGGAGTATCCT-GTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGA-AAATTGGTGTTTTGA
*
2007227 AAATAAAATCGAAGT
64 AAATAAAATCG-GGT
2007242 TGGAGTATCC
1 TGGAGTATCC
2007252 CCGATTGTGA
Statistics
Matches: 136, Mismatches: 22, Indels: 18
0.77 0.12 0.10
Matches are distributed among these distances:
77 5 0.04
78 60 0.44
79 70 0.51
80 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (77 bp):
TGGAGTATCCTGTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAATTGGTGTTTTGAAA
ATAAAATCGGGT
Found at i:2007230 original size:79 final size:77
Alignment explanation
Indices: 2007008--2007233 Score: 235
Period size: 78 Copynumber: 2.9 Consensus size: 77
2006998 CACGGGGCTG
* * *
2007008 GAGTATCTCT-TCGAAAATAACACGGTTGGAGTATCCCTGATTAT-AGAAAATTGGTGTTTTGAA
1 GAGTATC-CTGTCGAAAATAAC-GGGTTGGAGTATCCCCGATTATGAG-AAATTGGTGTTTTGGA
* *
2007071 AATAAAATCAGGGTTG
63 AAT-AAAGCAGGGTTA
* * * * * *
2007087 GAGTATCCTGTC-AAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAA
1 GAGTATCCTGTCGAAAATAAC-GGGTTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAAA
* *
2007151 TAAGGCCGGGATTA
65 TAAAGCAGGG-TTA
2007165 GAGTATCCTCG-CGAAAATAACGGGATTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAA
1 GAGTATCCT-GTCGAAAATAACGGG-TTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAA
2007229 ATAAA
64 ATAAA
2007234 ATCGAAGTTG
Statistics
Matches: 120, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
77 6 0.05
78 58 0.48
79 56 0.47
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.28
Consensus pattern (77 bp):
GAGTATCCTGTCGAAAATAACGGGTTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAAAT
AAAGCAGGGTTA
Found at i:2007284 original size:49 final size:51
Alignment explanation
Indices: 2007188--2007302 Score: 155
Period size: 49 Copynumber: 2.3 Consensus size: 51
2007178 AAAATAACGG
* * *
2007188 GATTGGAGTATCCCCGATTATGAGAAATTGGTGTTTTGGAAATAAAATCGA
1 GATTGGAGTATCCCCGATTATGAGAAATTGGTATTTTAGAAAAAAAATCGA
* *
2007239 -AGTTGGAGTATCCCCGA-T-TGTGAAATTGGTATTTTAGAAAAAAAATCGG
1 GA-TTGGAGTATCCCCGATTATGAGAAATTGGTATTTTAGAAAAAAAATCGA
2007288 GATTGGAGTATCCCC
1 GATTGGAGTATCCCC
2007303 TCGGAAATAA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
49 39 0.68
50 3 0.05
51 15 0.26
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.30
Consensus pattern (51 bp):
GATTGGAGTATCCCCGATTATGAGAAATTGGTATTTTAGAAAAAAAATCGA
Found at i:2007361 original size:28 final size:28
Alignment explanation
Indices: 2007285--2007361 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2007275 GAAAAAAAAT
***
2007285 CGGGATTGGAGTATCCCCTCGGAAATAA
1 CGGGATTGGAGTATCCCCGATGAAATAA
*
2007313 CGGGATTGGAGTATCCCCGATGACATAA
1 CGGGATTGGAGTATCCCCGATGAAATAA
* *
2007341 TGGGGTTGGAGTATCCCCGAT
1 CGGGATTGGAGTATCCCCGAT
2007362 TATGAAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (28 bp):
CGGGATTGGAGTATCCCCGATGAAATAA
Found at i:2007430 original size:108 final size:106
Alignment explanation
Indices: 2007285--2007478 Score: 291
Period size: 108 Copynumber: 1.8 Consensus size: 106
2007275 GAAAAAAAAT
* * * *
2007285 CGGGATTGGAGTATCCCCTCGGAAATAACGGGATTGGAGTATCCCCGATGACATAATGGGGTTGG
1 CGGGATTGGAGTATCCCCTCGAAAATAAAGGGATTGGAGTATCCCCGATGAAATAACGGGGTTGG
2007350 AGTATCCCCGATTATGAAAAAATCAATATTTTAGATATAAAGC
66 AGTATCCCC-ATT-TGAAAAAATCAATATTTTAGATATAAAGC
* *
2007393 CGGGGTTGGAGTATCCCCTCGAAAATAATAGGG-TTGGAGTATCCCTGATGAAATAACGGGGTTG
1 CGGGATTGGAGTATCCCCTCGAAAATAA-AGGGATTGGAGTATCCCCGATGAAATAACGGGGTTG
*
2007457 GAGTATCCCCATTTGTAAAAAT
65 GAGTATCCCCATTTGAAAAAAT
2007479 TTGGTGTTTT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 8 0.10
107 3 0.04
108 64 0.82
109 3 0.04
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (106 bp):
CGGGATTGGAGTATCCCCTCGAAAATAAAGGGATTGGAGTATCCCCGATGAAATAACGGGGTTGG
AGTATCCCCATTTGAAAAAATCAATATTTTAGATATAAAGC
Found at i:2007435 original size:28 final size:28
Alignment explanation
Indices: 2007395--2007466 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
2007385 TATAAAGCCG
*
2007395 GGGTTGGAGTATCCCCTCGA-AAATAATA
1 GGGTTGGAGTATCCCCT-GAGAAATAACA
*
2007423 GGGTTGGAGTAT-CCCTGATGAAATAACG
1 GGGTTGGAGTATCCCCTGA-GAAATAACA
2007451 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
2007467 ATTTGTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
26 2 0.05
27 4 0.10
28 30 0.77
29 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTGAGAAATAACA
Found at i:2007596 original size:51 final size:51
Alignment explanation
Indices: 2007473--2007596 Score: 140
Period size: 51 Copynumber: 2.4 Consensus size: 51
2007463 CCCCATTTGT
* * *
2007473 AAAAATTTGGTGTTTTGGAAATAAAATCAGAGTTGGAGTATCCCCGATTACG
1 AAAAA-TTGATGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAAG
* ** * * * **
2007525 ATAAATCAATGCTTTAGAAATAAAATCGGAGTTGGAATATCTTCGATTAAG
1 AAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAAG
2007576 AAAAATTGATGTTTTGGAAAT
1 AAAAATTGATGTTTTGGAAAT
2007597 GGAACCAGGA
Statistics
Matches: 56, Mismatches: 16, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
51 52 0.93
52 4 0.07
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.32
Consensus pattern (51 bp):
AAAAATTGATGTTTTGGAAATAAAATCAGAGTTGGAATATCCCCGATTAAG
Found at i:2008966 original size:12 final size:12
Alignment explanation
Indices: 2008949--2008973 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2008939 AGATGTGAAT
2008949 ATGTGAATATGG
1 ATGTGAATATGG
2008961 ATGTGAATATGG
1 ATGTGAATATGG
2008973 A
1 A
2008974 AGGAATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
ATGTGAATATGG
Found at i:2009985 original size:20 final size:20
Alignment explanation
Indices: 2009956--2010010 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
2009946 GGAAACCCAA
2009956 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
* *
2009976 AATGTCTCGATATAATGAAC
1 AATGTATCGATACAATGAAC
2009996 AATGTATCGATACAA
1 AATGTATCGATACAA
2010011 ATTGTGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:2010621 original size:40 final size:41
Alignment explanation
Indices: 2010577--2010661 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
2010567 TCACTTTTAG
* *
2010577 AGGACAAAGG-A-AAAGAGAATGAAATGGGTCTTGCTCCTTA
1 AGGACAAAGGAAGAAAGAAAAGGAAA-GGGTCTTGCTCCTTA
* *
2010617 AGGACAAAGGAAGAAAGAAAAGGAAAGTGTCTTGCTTCTTA
1 AGGACAAAGGAAGAAAGAAAAGGAAAGGGTCTTGCTCCTTA
2010658 AGGA
1 AGGA
2010662 AAAAATGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
40 10 0.26
41 18 0.46
42 11 0.28
ACGTcount: A:0.42, C:0.11, G:0.28, T:0.19
Consensus pattern (41 bp):
AGGACAAAGGAAGAAAGAAAAGGAAAGGGTCTTGCTCCTTA
Found at i:2010822 original size:45 final size:42
Alignment explanation
Indices: 2010662--2010827 Score: 142
Period size: 42 Copynumber: 3.9 Consensus size: 42
2010652 TTCTTAAGGA
* * * * *
2010662 AAAAATGAAAA-AGAGTACGTCCTGCT-TTTCAAGGACAAAGG
1 AAAAAGGAAAATAAAGTGCGTCCTGCTCTTT-GAGGACAAAAG
* * *
2010703 AAAAAAGGAAAACGAAA-TGCGTCATGCTCTTTGAGGATAAAAG
1 -AAAAAGGAAAA-TAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
2010746 AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAGGG
1 AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAA--G
* * *
2010790 AAATGAAGG-AAATGAAGTGCGTCCTGCCCTTTGGGGAC
1 AAA--AAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGAC
2010828 TAGGAGGTGC
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
41 3 0.03
42 44 0.43
43 17 0.17
44 9 0.09
45 26 0.25
46 4 0.04
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.19
Consensus pattern (42 bp):
AAAAAGGAAAATAAAGTGCGTCCTGCTCTTTGAGGACAAAAG
Found at i:2010909 original size:59 final size:59
Alignment explanation
Indices: 2010803--2011007 Score: 239
Period size: 59 Copynumber: 3.4 Consensus size: 59
2010793 TGAAGGAAAT
* * * * * *
2010803 GAAGTGCGTCCTGCCCTTTGGGGACTAGGAGGTGCTACCAACTTGTGTGGGGTTCGAAGGA
1 GAAG-GCGTCCTGCTCTTTGAGGACTA-AAGGTGCCACCAACTTGTGTGGGCTTCGAAAGA
*
2010864 GAAGGCGTCCTACTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTCGAAAGA
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTCGAAAGA
* * * * *
2010923 GAAGGTGTCCTGCTCTTTGAGGACTAAAAGTGCCCCCAACTCGTGTGGGCTTTGAAAAGAA
1 GAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTCG-AAAG-A
* * *
2010984 AAAGGCATCATGCTCTTTGAGGAC
1 GAAGGCGTCCTGCTCTTTGAGGAC
2011008 AAAAAAAAAA
Statistics
Matches: 125, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
59 77 0.62
60 23 0.18
61 25 0.20
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (59 bp):
GAAGGCGTCCTGCTCTTTGAGGACTAAAGGTGCCACCAACTTGTGTGGGCTTCGAAAGA
Found at i:2011158 original size:107 final size:105
Alignment explanation
Indices: 2010927--2011158 Score: 304
Period size: 105 Copynumber: 2.2 Consensus size: 105
2010917 GAAAGAGAAG
*
2010927 GTGTCCTGCTCTTTGAGGACTAAAAGTGCCCCCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCAT
1 GTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCAT
*
2010992 CATGCTCTTTGAGGACAAAAAAAAAAGAAGGAAATGAAGT
66 CATGCTCTTTGAGGACAAAAAAAAAAGAAGGAAATGAAAT
** * * * * *
2011032 ACGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTGAAAATAGAAA-GCA
1 GTGTCCTGCTCTTTGAGGACTA-AAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCA
* ***
2011096 TCTTGCTCTTTGAGGACTAGAAGGGAAAAGAAGGAAATGAAAT
65 TCATGCTCTTTGAGGAC-A-AAAAAAAAAGAAGGAAATGAAAT
*
2011139 GTGTCCTGCTCCTTGAGGAC
1 GTGTCCTGCTCTTTGAGGAC
2011159 AAAGGAGAAA
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
105 38 0.36
106 34 0.32
107 35 0.33
ACGTcount: A:0.33, C:0.18, G:0.26, T:0.24
Consensus pattern (105 bp):
GTGTCCTGCTCTTTGAGGACTAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAGGCAT
CATGCTCTTTGAGGACAAAAAAAAAAGAAGGAAATGAAAT
Found at i:2011268 original size:61 final size:61
Alignment explanation
Indices: 2011180--2011893 Score: 691
Period size: 61 Copynumber: 11.9 Consensus size: 61
2011170 CGAAAAGGTG
* * * *
2011180 TCCTACTCTTTGAGGGCTAAAAAGTGCCACCAACTCGTGTGGGCTTT-GAA-GAGAAAAGGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAG-AAA-GCA
* ** * *
2011241 TCTTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGGAAA-GAGAAAGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAGAAAGCA
* *
2011302 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGAGTGGTCTTTAAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAAGCA
** * *
2011363 TCCTGCTCTTTGAGGACTGGAAGGTGCCACCAACTTGTGTGGGCTTTGGAAA-GAGAAAGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTT-AAAAGGAGAAAGCA
* *
2011424 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGAGTGGTCTTTAAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAAGCA
* * **
2011485 TCCTGCTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGGCTTTAAAAGGA-AAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAA-GCA
* * **
2011546 TCCTACTCTTTGAGGACT-AAAGGTGCCACCAACTCGTGTGGGCTTTTAAAA-GAAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGC-TTTAAAAGGAGAAA-GCA
* * * * * *
2011607 TCTTGCTCTTTCAAGACTAAAAGGGTGCCACCAACTCGAGTAGTCTTTAAAAGGAGAAAGCA
1 TCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAAGCA
* * *
2011669 TCCTGCTCTTTGAGGACTGGAAAA--TGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
1 TCCTGCTCTTTGAGGACT--AAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAAGCA
* ** ** * *
2011724 TCCTGTTCTTTGAGGACTAAAAAATGCCACCAACTTTTGTGCGCTTTAAAAGGA-AAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAA-GCA
* * * * * *
2011785 TCCTACTCTTTGAGGGCTAGAAAAGTGCTACCAACTTC-TGTGGGCTTT-----GA-AAGGCG
1 TCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAAC-TCGTGTGGGCTTTAAAAGGAGAAAGCA
* * **
2011841 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTTTGTGGGCTTTAAAAGG
1 TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGG
2011894 TGTCCTGCTC
Statistics
Matches: 552, Mismatches: 72, Indels: 59
0.81 0.11 0.09
Matches are distributed among these distances:
53 4 0.01
54 1 0.00
55 65 0.12
56 22 0.04
57 4 0.01
60 39 0.07
61 329 0.60
62 54 0.10
63 30 0.05
64 4 0.01
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (61 bp):
TCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTCGTGTGGGCTTTAAAAGGAGAAAGCA
Found at i:2011748 original size:55 final size:55
Alignment explanation
Indices: 2011669--2011916 Score: 289
Period size: 55 Copynumber: 4.4 Consensus size: 55
2011659 GGAGAAAGCA
** *
2011669 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTTTGTGGGCTTTGAAAGGCG
* *
2011724 TCCTGTTCTTTGAGGACTAAAAAATGCCACCAACTTTTGTGCGCTTTAAAAGGAAAAGGCG
1 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTTTGTGGGCTTT-----G-AAAGGCG
* * * * *
2011785 TCCTACTCTTTGAGGGCTAGAAAAGTGCTACCAACTTCTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTA-AAAAATGCCACCAACTTTTGTGGGCTTTGAAAGGCG
* * ** * *
2011841 TCCTACTCTTTGAGGACTGAAAGGTGCCACCAACTTTTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTTTGTGGGCTTTGAAAGGCG
2011896 TCCTGCTCTTTGAGGACTAAA
1 TCCTGCTCTTTGAGGACTAAA
2011917 GGGTAAAAGG
Statistics
Matches: 165, Mismatches: 21, Indels: 14
0.82 0.10 0.07
Matches are distributed among these distances:
55 92 0.56
56 24 0.15
57 1 0.01
60 1 0.01
61 23 0.14
62 24 0.15
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTAAAAAATGCCACCAACTTTTGTGGGCTTTGAAAGGCG
Found at i:2011808 original size:28 final size:29
Alignment explanation
Indices: 2011776--2011855 Score: 78
Period size: 28 Copynumber: 2.8 Consensus size: 29
2011766 GCTTTAAAAG
2011776 GAAAAGGCGTCCTACTCTTTGAGGGC-TA
1 GAAAAGGCGTCCTACTCTTTGAGGGCTTA
* * * *
2011804 GAAAAGTGC-TACCAACT-TCTGTGGGCTTT
1 GAAAAG-GCGT-CCTACTCTTTGAGGGCTTA
2011833 G-AAAGGCGTCCTACTCTTTGAGG
1 GAAAAGGCGTCCTACTCTTTGAGG
2011856 ACTGAAAGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
27 7 0.17
28 24 0.60
29 9 0.22
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.28
Consensus pattern (29 bp):
GAAAAGGCGTCCTACTCTTTGAGGGCTTA
Found at i:2013018 original size:11 final size:11
Alignment explanation
Indices: 2013015--2013058 Score: 63
Period size: 11 Copynumber: 4.0 Consensus size: 11
2013005 TTTTTCTTTG
2013015 TTTTGTTTTTT
1 TTTTGTTTTTT
*
2013026 TTTT-TATTATT
1 TTTTGT-TTTTT
2013037 TTTTGTTTTTT
1 TTTTGTTTTTT
2013048 TTTTGTTTTTT
1 TTTTGTTTTTT
2013059 AAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 1 0.03
11 27 0.93
12 1 0.03
ACGTcount: A:0.05, C:0.00, G:0.07, T:0.89
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:2013028 original size:21 final size:22
Alignment explanation
Indices: 2013004--2013051 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2012994 CTTTTCTCTC
*
2013004 TTTTTTCTT-TGTTTTGTTTTT
1 TTTTTTATTATGTTTTGTTTTT
*
2013025 TTTTTTATTATTTTTTGTTTTT
1 TTTTTTATTATGTTTTGTTTTT
2013047 TTTTT
1 TTTTT
2013052 GTTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.04, C:0.02, G:0.06, T:0.88
Consensus pattern (22 bp):
TTTTTTATTATGTTTTGTTTTT
Found at i:2025587 original size:79 final size:78
Alignment explanation
Indices: 2025454--2025677 Score: 288
Period size: 79 Copynumber: 2.8 Consensus size: 78
2025444 GATAACCATG
** * *
2025454 GGGTTGGAGTATCCCCGATTATGGAAAATTGGTGTTTTGAAAATAAAATTGGGGTTGGAGTATCC
1 GGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCC
*
2025519 CTTC-AGAAATAATA
66 C-TCGA-AAATAACA
* ** * * *
2025533 GGGTTTGAGTATCCCTAATTATAGAAAATCAGTATTTTGAAAATAAAATCGGGGTTAGAGTATTT
1 GGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTA-TC
2025598 CCTCGAAAATAACA
65 CCTCGAAAATAACA
* * *
2025612 AGGTTGGAGTATCCCTAATTAGAGAAAATTGGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCC
1 GGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCC
2025677 C
66 C
2025678 CGATTGTGAA
Statistics
Matches: 123, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
78 3 0.02
79 116 0.94
80 4 0.03
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (78 bp):
GGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCC
CTCGAAAATAACA
Found at i:2025691 original size:51 final size:51
Alignment explanation
Indices: 2025612--2025730 Score: 125
Period size: 51 Copynumber: 2.3 Consensus size: 51
2025602 GAAAATAACA
* * * *
2025612 AGGTTGGAGTATCCCTAATTAGAGAAAATTGGTG-TTTTGAAAATAAAATCG
1 AGGTTGGAGTATCCCCAATTAGAGAAAATCGATGCTTTAG-AAATAAAATCG
* * **
2025663 AGGTTGGAGTATCCCCGATT-GTGAAAAATCGATGCTTTAGAAATAAGGTCG
1 AGGTTGGAGTATCCCCAATTAGAG-AAAATCGATGCTTTAGAAATAAAATCG
*
2025714 GGGTTGGAGTATCCCCA
1 AGGTTGGAGTATCCCCA
2025731 TGAAAATAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
50 2 0.04
51 50 0.89
52 4 0.07
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.29
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCAATTAGAGAAAATCGATGCTTTAGAAATAAAATCG
Found at i:2025744 original size:79 final size:79
Alignment explanation
Indices: 2025661--2025808 Score: 215
Period size: 79 Copynumber: 1.9 Consensus size: 79
2025651 AAAATAAAAT
** **
2025661 CGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAGGTCGGGGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAAATCGAAGTTGGAGTAT
2025726 CCCCATGAAAATAA
66 CCCCATGAAAATAA
* * * * *
2025740 CGAGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGAAGTTGGAGTAT
1 CGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAAATCGAAGTTGGAGTAT
2025805 CCCC
66 CCCC
2025809 GATTGTGAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 60 1.00
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.27
Consensus pattern (79 bp):
CGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTAGAAATAAAATCGAAGTTGGAGTAT
CCCCATGAAAATAA
Found at i:2025807 original size:51 final size:51
Alignment explanation
Indices: 2025742--2025858 Score: 191
Period size: 51 Copynumber: 2.3 Consensus size: 51
2025732 GAAAATAACG
* * *
2025742 AGGTTGGAGTATCCCCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGA
1 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATC-A
2025794 A-GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCA
1 AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCA
2025844 AGGTTGGAGTATCCC
1 AGGTTGGAGTATCCC
2025859 TTCGGAAATA
Statistics
Matches: 61, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
50 2 0.03
51 58 0.95
52 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
AGGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCA
Found at i:2025832 original size:130 final size:130
Alignment explanation
Indices: 2025573--2025889 Score: 390
Period size: 130 Copynumber: 2.4 Consensus size: 130
2025563 AGTATTTTGA
** * * * **
2025573 AAATAAAATCGGGGTTAGAGTATTTCC-TCGAAAATAACAAGGTTGGAGTATCCCTAATTAGAGA
1 AAATAAAATCAAGGTTGGAGTA-TCCCATCGAAAATAACGAGGTTGGAGTATCCCCGATTAGAGA
* *
2025637 AAATTGGTGTTTTGAAAATAAAATCGAGGTTGGAGTATCCCCGATTGTGAAAAATCGATGCTTTA
65 AAATTGGTGTTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTGTGAAAAATCGATACTTTA
2025702 G
130 G
** ** *
2025703 AAATAAGGTCGGGGTTGGAGTATCCCCAT-GAAAATAACGAGGTTGGAGTATCCCCGATT-GTGA
1 AAATAAAATCAAGGTTGGAGTAT-CCCATCGAAAATAACGAGGTTGGAGTATCCCCGATTAGAGA
* * * *
2025766 GAAATTGGTGTTTTGGAAATAAAATCGAAGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTT
65 -AAATTGGTGTTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTGTGAAAAATCGATACTTT
2025831 AG
129 AG
* *
2025833 AAATAAAATCAAGGTTGGAGTATCCCTTCGGAAATAACG-GGATTGGAGTATCCCCGA
1 AAATAAAATCAAGGTTGGAGTATCCCATCGAAAATAACGAGG-TTGGAGTATCCCCGA
2025890 GGACATAACG
Statistics
Matches: 162, Mismatches: 20, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
129 10 0.06
130 151 0.93
131 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (130 bp):
AAATAAAATCAAGGTTGGAGTATCCCATCGAAAATAACGAGGTTGGAGTATCCCCGATTAGAGAA
AATTGGTGTTTTGAAAATAAAATCGAAGTTGGAGTATCCCCGATTGTGAAAAATCGATACTTTAG
Found at i:2025878 original size:28 final size:28
Alignment explanation
Indices: 2025847--2025917 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2025837 AAAATCAAGG
***
2025847 TTGGAGTATCCCTTCGGAAATAACGGGA
1 TTGGAGTATCCCCGAGGAAATAACGGGA
* *
2025875 TTGGAGTATCCCCGAGGACATAACGGGG
1 TTGGAGTATCCCCGAGGAAATAACGGGA
*
2025903 TTGGAGTACCCCCGA
1 TTGGAGTATCCCCGA
2025918 TTATGAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (28 bp):
TTGGAGTATCCCCGAGGAAATAACGGGA
Found at i:2025957 original size:108 final size:107
Alignment explanation
Indices: 2025795--2026036 Score: 270
Period size: 108 Copynumber: 2.3 Consensus size: 107
2025785 TAAAATCGAA
* * *** *
2025795 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTAGAAATAAAATCAAGGTTGGAGTAT-CCC
1 GTTGGAGTACCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCCC
** * *
2025859 TTCGGAAATAACGGGATTGGAGTATCCCCGAGGACATAACGGG
66 TT-AAAAATAACGGGATTGGAGTATCCCCAAGGAAATAACGGG
* * **
2025902 GTTGGAGTACCCCCGATTATGAAAAAATCAATATTTTAGATATAAAGCCGGGGTTGGAGTATCCC
1 GTTGGAGTACCCCCGATTATG-AAAAATCAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCC
* * *
2025967 CTTAAAAATAACGGGGTTGGAGTATCTCCAATGAAATAACGGG
65 CTTAAAAATAACGGGATTGGAGTATCCCCAAGGAAATAACGGG
* * * *
2026010 GTTGGAGTATCTCCAATTGTGAAAAAT
1 GTTGGAGTACCCCCGATTATGAAAAAT
2026037 TGGTGTTTTG
Statistics
Matches: 112, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
107 25 0.22
108 82 0.73
109 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (107 bp):
GTTGGAGTACCCCCGATTATGAAAAATCAATATTTTAGAAATAAAACCAAGGTTGGAGTATCCCC
TTAAAAATAACGGGATTGGAGTATCCCCAAGGAAATAACGGG
Found at i:2026026 original size:28 final size:27
Alignment explanation
Indices: 2025950--2026026 Score: 111
Period size: 28 Copynumber: 2.8 Consensus size: 27
2025940 GATATAAAGC
*
2025950 CGGGGTTGGAGTATCCCCTTAA-AAATAA
1 CGGGGTTGGAGTATCTCC--AATAAATAA
2025978 CGGGGTTGGAGTATCTCCAATGAAATAA
1 CGGGGTTGGAGTATCTCCAAT-AAATAA
2026006 CGGGGTTGGAGTATCTCCAAT
1 CGGGGTTGGAGTATCTCCAAT
2026027 TGTGAAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.04
28 44 0.96
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.26
Consensus pattern (27 bp):
CGGGGTTGGAGTATCTCCAATAAATAA
Found at i:2026153 original size:51 final size:51
Alignment explanation
Indices: 2026010--2026178 Score: 169
Period size: 51 Copynumber: 3.3 Consensus size: 51
2026000 AAATAACGGG
* * * * *
2026010 GTTGGAGTATCTCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCAGA
* * * ** * * *
2026061 GTTGGAGTGTCCTCGATTGCGGTAAATCGATGCTTTAGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCAGA
* ** *
2026112 GTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGGAA-CCGA
1 GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCAGA
2026162 GATTGGAGTATCCCCGA
1 G-TTGGAGTATCCCCGA
2026179 GATGAAAAAT
Statistics
Matches: 93, Mismatches: 24, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
50 4 0.04
51 89 0.96
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGAGAAAAATTGATGTTTTGGAAATAAAATCAGA
Found at i:2034278 original size:21 final size:20
Alignment explanation
Indices: 2034231--2034286 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
2034221 TATTTGAGAC
**
2034231 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACCA
2034251 ATGTATCGATACATTCACCA
1 ATGTATCGATACATTCACCA
2034271 ATTGTATCGATACATT
1 A-TGTATCGATACATT
2034287 TTATCGAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
20 19 0.58
21 14 0.42
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATTCACCA
Found at i:2037655 original size:13 final size:13
Alignment explanation
Indices: 2037637--2037664 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2037627 ATACAAAGAT
2037637 CAATGTATCGATA
1 CAATGTATCGATA
2037650 CAATGTATCGATA
1 CAATGTATCGATA
2037663 CA
1 CA
2037665 TTGAATAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2037750 original size:32 final size:32
Alignment explanation
Indices: 2037709--2037780 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
2037699 GCTTTGTAGG
* *
2037709 GATACATTGTATCGATACAATATTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
2037741 GATACATTGTATCGATACAACACTTATGTATC
1 GATACATTGTATCGATACAACACTTATGTATC
*
2037773 GATTCATT
1 GATACATT
2037781 TACTGTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (32 bp):
GATACATTGTATCGATACAACACTTATGTATC
Found at i:2037753 original size:13 final size:13
Alignment explanation
Indices: 2037735--2037759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2037725 ACAATATTTA
2037735 TGTATCGATACAT
1 TGTATCGATACAT
2037748 TGTATCGATACA
1 TGTATCGATACA
2037760 ACACTTATGT
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):
TGTATCGATACAT
Found at i:2037772 original size:19 final size:18
Alignment explanation
Indices: 2037716--2037775 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 18
2037706 AGGGATACAT
*
2037716 TGTATCGATACAATATTTA
1 TGTATCGATACAACA-TTA
2037735 TGTATCGAT---ACA-T-
1 TGTATCGATACAACATTA
2037748 TGTATCGATACAACACTTA
1 TGTATCGATACAACA-TTA
2037767 TGTATCGAT
1 TGTATCGAT
2037776 TCATTTACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.26
14 1 0.03
16 5 0.15
18 1 0.03
19 18 0.53
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (18 bp):
TGTATCGATACAACATTA
Found at i:2038349 original size:21 final size:20
Alignment explanation
Indices: 2038302--2038353 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 20
2038292 CATTTCAAGC
2038302 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
2038322 ATGTATCGATACATT-ACCTT
1 ATGTATCGATACATTCA-CTT
2038342 ATTGTATCGATA
1 A-TGTATCGATA
2038354 TAAATTGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.03
20 19 0.63
21 10 0.33
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:2046695 original size:23 final size:25
Alignment explanation
Indices: 2046639--2046686 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
2046629 TTGCATGGAT
2046639 TAAAAAATTAATTTAGATATAAAAA
1 TAAAAAATTAATTTAGATATAAAAA
* *
2046664 TAAAAAATTTATTTAAATATAAA
1 TAAAAAATTAATTTAGATATAAA
2046687 TTAAAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
TAAAAAATTAATTTAGATATAAAAA
Found at i:2049609 original size:78 final size:78
Alignment explanation
Indices: 2049513--2049724 Score: 271
Period size: 78 Copynumber: 2.7 Consensus size: 78
2049503 TCACCTAATT
* * * * * * * * *
2049513 AGCCAACCGTCACCTGTCACGTGTCTTCGCTGCCACATCATCACCCAGTTAGCATAGTTGTTCGG
1 AGCCAACCATCACTTGTCACGTATCCTCACTGCCACGTCATCACCCAGTTAGCATAGTTCTCCGA
2049578 CCATCACCACATC
66 CCATCACCACATC
* * *
2049591 AGCCAACCATCACTTGTCATGTATCCTCATTGCCACGTCATCACACAGTTAGCATAGTTCTCCGA
1 AGCCAACCATCACTTGTCACGTATCCTCACTGCCACGTCATCACCCAGTTAGCATAGTTCTCCGA
** *
2049656 CCATCGTCACGTC
66 CCATCACCACATC
* *
2049669 AGCCAACCATCACTTGTCGCGTATCCTCACTGCCACGTCATCACCCAGTCAGCATA
1 AGCCAACCATCACTTGTCACGTATCCTCACTGCCACGTCATCACCCAGTTAGCATA
2049725 CTTTTCCTTA
Statistics
Matches: 114, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 114 1.00
ACGTcount: A:0.24, C:0.37, G:0.15, T:0.25
Consensus pattern (78 bp):
AGCCAACCATCACTTGTCACGTATCCTCACTGCCACGTCATCACCCAGTTAGCATAGTTCTCCGA
CCATCACCACATC
Found at i:2049844 original size:29 final size:30
Alignment explanation
Indices: 2049748--2049841 Score: 120
Period size: 29 Copynumber: 3.2 Consensus size: 30
2049738 ACACTCTAAT
* * *
2049748 CCTTAAACTTTTTAAAATTGCAGAACAACC
1 CCTTAAACTTTTTAAAATTGCATATCAGCC
* *
2049778 CCTT-AACTTTTCAAAATTGCTTATCAG-C
1 CCTTAAACTTTTTAAAATTGCATATCAGCC
*
2049806 CCTTAAACTTTTTAAAATTGCATATTAGCC
1 CCTTAAACTTTTTAAAATTGCATATCAGCC
2049836 CCTTAA
1 CCTTAA
2049842 CTTCTAGAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.09
29 38 0.70
30 11 0.20
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.36
Consensus pattern (30 bp):
CCTTAAACTTTTTAAAATTGCATATCAGCC
Found at i:2049852 original size:29 final size:28
Alignment explanation
Indices: 2049748--2049853 Score: 97
Period size: 29 Copynumber: 3.6 Consensus size: 28
2049738 ACACTCTAAT
* * *
2049748 CCTTAAACTTTTTAAAATTGCAGAACAACC
1 CCTT-AAC-TTTTAAAATTGCATATCAGCC
*
2049778 CCTTAACTTTTCAAAATTGCTTATCAG-C
1 CCTTAACTTTT-AAAATTGCATATCAGCC
*
2049806 CCTTAAACTTTTTAAAATTGCATATTAGCC
1 CCTT-AAC-TTTTAAAATTGCATATCAGCC
*
2049836 CCTTAACTTCTAGAAATT
1 CCTTAACTTTTA-AAATT
2049854 TCATTCTAGC
Statistics
Matches: 64, Mismatches: 7, Indels: 11
0.78 0.09 0.13
Matches are distributed among these distances:
28 13 0.20
29 38 0.59
30 13 0.20
ACGTcount: A:0.34, C:0.23, G:0.07, T:0.37
Consensus pattern (28 bp):
CCTTAACTTTTAAAATTGCATATCAGCC
Found at i:2057665 original size:25 final size:25
Alignment explanation
Indices: 2057637--2057698 Score: 97
Period size: 25 Copynumber: 2.5 Consensus size: 25
2057627 TTAGTAATAT
*
2057637 TAAACATAATTATATTATTATAAAA
1 TAAACAAAATTATATTATTATAAAA
*
2057662 TAAATAAAATTATATTATTATAAAA
1 TAAACAAAATTATATTATTATAAAA
*
2057687 TAAATAAAATTA
1 TAAACAAAATTA
2057699 GATAAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAACAAAATTATATTATTATAAAA
Found at i:2057748 original size:27 final size:27
Alignment explanation
Indices: 2057718--2057866 Score: 97
Period size: 27 Copynumber: 5.7 Consensus size: 27
2057708 ATATATATTT
*
2057718 TAAAAT-TTTTATAATATTATGTA-AATA
1 TAAAATATTTTA-AATATAAT-TATAATA
2057745 TAAAATATTTTAAATATAATTATAATA
1 TAAAATATTTTAAATATAATTATAATA
*
2057772 TAATAA-A---TACATA-AA-TATAATA
1 TAA-AATATTTTAAATATAATTATAATA
* * *
2057794 -AAAATATTTAAAATA-AATATATATTT
1 TAAAATATTTTAAATATAAT-TATAATA
* *
2057820 TAAAA-ATTATATAATATTA-TATAAATA
1 TAAAATATTTTA-AATATAATTAT-AATA
2057847 TAAAATATTTTAAATATAAT
1 TAAAATATTTTAAATATAAT
2057867 AAATATTATC
Statistics
Matches: 94, Mismatches: 13, Indels: 29
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.02
21 3 0.03
22 7 0.07
23 2 0.02
24 11 0.12
26 14 0.15
27 42 0.45
28 13 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (27 bp):
TAAAATATTTTAAATATAATTATAATA
Found at i:2057753 original size:18 final size:16
Alignment explanation
Indices: 2057739--2057865 Score: 59
Period size: 16 Copynumber: 7.6 Consensus size: 16
2057729 TAATATTATG
2057739 TAAATATAAAATATTT
1 TAAATATAAAATATTT
**
2057755 TAAATATAATTATAATATAA
1 TAAATAT-A--A-AATATTT
*
2057775 TAAATACATAAATA---
1 TAAATATA-AAATATTT
2057789 T-AATA-AAAATATTT
1 TAAATATAAAATATTT
*
2057803 AAAATA-AATATATATTT
1 TAAATATAA-A-ATATTT
*
2057820 TAAAAATTATATAATATTAT
1 T--AAA-TATAAAATATT-T
2057840 ATAAATATAAAATATTT
1 -TAAATATAAAATATTT
2057857 TAAATATAA
1 TAAATATAA
2057866 TAAATATTAT
Statistics
Matches: 88, Mismatches: 7, Indels: 32
0.69 0.06 0.25
Matches are distributed among these distances:
11 5 0.06
12 1 0.01
13 4 0.05
14 1 0.01
15 6 0.07
16 17 0.19
17 12 0.14
18 12 0.14
19 13 0.15
20 15 0.17
21 2 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATATAAAATATTT
Found at i:2057754 original size:37 final size:35
Alignment explanation
Indices: 2057712--2057860 Score: 116
Period size: 37 Copynumber: 4.3 Consensus size: 35
2057702 AAAGTAATAT
* * *
2057712 ATATTTTAAAATTTTTATAATATTATGTAAATATAAA
1 ATATTTTAAAAATATTATAATA-TA-ATAAATATAAA
* *
2057749 ATATTTTAAATATAATTATAATATAATAAATACATAA
1 ATATTTTAAAAAT-ATTATAATATAATAAATATA-AA
**
2057786 ATATAATAAAAATATT-T-A-A-AATAAATAT---
1 ATATTTTAAAAATATTATAATATAATAAATATAAA
2057814 ATATTTTAAAAAT-TATATAATATTATATAAATATAAA
1 ATATTTTAAAAATAT-TATAATA-TA-ATAAATATAAA
2057851 ATATTTTAAA
1 ATATTTTAAA
2057861 TATAATAAAT
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
27 1 0.01
28 12 0.13
29 1 0.01
30 1 0.01
31 1 0.01
32 8 0.09
33 2 0.02
34 9 0.10
35 1 0.01
36 10 0.11
37 35 0.39
38 8 0.09
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
ATATTTTAAAAATATTATAATATAATAAATATAAA
Found at i:2057836 original size:47 final size:48
Alignment explanation
Indices: 2057741--2057871 Score: 123
Period size: 48 Copynumber: 2.8 Consensus size: 48
2057731 ATATTATGTA
*
2057741 AATATAAAATATTTTAAATATAATTATAATATAATAAATACATAAATAT
1 AATA-AAAATATTTAAAATATAATTATAATATAATAAATACATAAATAT
* * *
2057790 AATAAAAATATTTAAAATA-AATATATATTTTAA-AAAT-TATATAATAT
1 AATAAAAATATTTAAAATATAAT-TATAATATAATAAATACATA-AATAT
* * *
2057837 TATATAAATA--TAAAATAT-TTTA-AATATAATAAATA
1 AATAAAAATATTTAAAATATAATTATAATATAATAAATA
2057872 TTATCAGTAA
Statistics
Matches: 68, Mismatches: 9, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
43 5 0.07
44 6 0.09
45 8 0.12
46 3 0.04
47 20 0.29
48 22 0.32
49 4 0.06
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.40
Consensus pattern (48 bp):
AATAAAAATATTTAAAATATAATTATAATATAATAAATACATAAATAT
Done.