Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 166 of 318
Found at i:52383999 original size:29 final size:30
Alignment explanation
Indices: 52383951--52384025 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 30
52383941 AGATGAAGCT
*
52383951 ATCCTTTTTCATAATTTGATGGTCATGACC
1 ATCCTTTTTCATAATTTGATGGTCATCACC
*
52383981 ATCCTTTTTCATTA-TTGATGGTCATCACC
1 ATCCTTTTTCATAATTTGATGGTCATCACC
52384010 ATTCC-TTTTCATAATT
1 A-TCCTTTTTCATAATT
52384026 CTATAGCCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
29 23 0.57
30 17 0.43
ACGTcount: A:0.23, C:0.21, G:0.09, T:0.47
Consensus pattern (30 bp):
ATCCTTTTTCATAATTTGATGGTCATCACC
Found at i:52389610 original size:15 final size:15
Alignment explanation
Indices: 52389590--52389619 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52389580 TGAAATTATG
52389590 TTTGAATGAGTTTAA
1 TTTGAATGAGTTTAA
*
52389605 TTTGAATGTGTTTAA
1 TTTGAATGAGTTTAA
52389620 ATCAAGAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (15 bp):
TTTGAATGAGTTTAA
Found at i:52389980 original size:43 final size:43
Alignment explanation
Indices: 52389919--52390099 Score: 254
Period size: 43 Copynumber: 4.2 Consensus size: 43
52389909 GGATTTTCAG
* * * *
52389919 TATGTGATTACGTGTAAGACCACGTTTGGGACGTTGACATCAA
1 TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCGA
52389962 TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCGA
1 TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCGA
* *
52390005 TATGTGATTACGTGTAAGACCACGTCTGGGATGTTGGCATCGA
1 TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCGA
** * * **
52390048 TATGTGATTACAAGTAAGACCATGTTTAATACGTTGGCATCGA
1 TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCGA
52390091 TATGTGATT
1 TATGTGATT
52390100 CCGATATGTG
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 124 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.31
Consensus pattern (43 bp):
TATGTGATTACGTGTAAGACCACGTCTAGGACGTTGGCATCGA
Found at i:52390131 original size:56 final size:56
Alignment explanation
Indices: 52390060--52390346 Score: 319
Period size: 56 Copynumber: 5.2 Consensus size: 56
52390050 TGTGATTACA
*
52390060 AGTAAGACCATGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
1 AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
* * * *
52390116 AGTAAGACCATGTTTAATACGTTGGCATCGATATATGATTCTG--ATGTGTATGCG
1 AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
* * * * ** * * *
52390170 AGTAACACCACATTTAATACGTTGGCATCAAGATGTGATTAAGGTATGTGTGCGTG
1 AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
* ** **
52390226 AGTAA-AGCCACATTTAATTTGTTGGCATCGATATGTGATTGTGATATGTGTGTGCG
1 AGTAAGA-CCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
* * * * **
52390282 AGTAAGACCACGTTTAATACATTGGCATCAATAGGTGATTCCGATATGTGTTTATG
1 AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
52390338 AGTAAGACC
1 AGTAAGACC
52390347 CTGTCAGGGA
Statistics
Matches: 193, Mismatches: 34, Indels: 8
0.82 0.14 0.03
Matches are distributed among these distances:
54 45 0.23
55 1 0.01
56 146 0.76
57 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (56 bp):
AGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCG
Found at i:52390242 original size:110 final size:111
Alignment explanation
Indices: 52390072--52390332 Score: 310
Period size: 110 Copynumber: 2.4 Consensus size: 111
52390062 TAAGACCATG
* ** * **
52390072 TTTAATACGTTGGCATCGATATGTGATTCCGATATGTGTGTGCGAGTAAGACCATGTTTAATACG
1 TTTAATACGTTGGCATCAATATGTGATTAAGATATGTGTGCGCGAGTAAGACCACATTTAATACG
52390137 TTGGCATCGATATATGATTCTG-ATGTGTATGCGAGTAACACCACA
66 TTGGCATCGATATATGATTCTGAATGTGTATGCGAGTAACACCACA
* * * **
52390182 TTTAATACGTTGGCATCAAGATGTGATTAAGGTATGTGTGCGTGAGTAA-AGCCACATTTAATTT
1 TTTAATACGTTGGCATCAATATGTGATTAAGATATGTGTGCGCGAGTAAGA-CCACATTTAATAC
* * * * *
52390246 GTTGGCATCGATATGTGATTGTGATATGTGTGTGCGAGTAAGACCACG
65 GTTGGCATCGATATATGATTCTGA-ATGTGTATGCGAGTAACACCACA
* * **
52390294 TTTAATACATTGGCATCAATAGGTGATTCCGATATGTGT
1 TTTAATACGTTGGCATCAATATGTGATTAAGATATGTGT
52390333 TTATGAGTAA
Statistics
Matches: 126, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
109 1 0.01
110 72 0.57
112 53 0.42
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.34
Consensus pattern (111 bp):
TTTAATACGTTGGCATCAATATGTGATTAAGATATGTGTGCGCGAGTAAGACCACATTTAATACG
TTGGCATCGATATATGATTCTGAATGTGTATGCGAGTAACACCACA
Found at i:52393816 original size:27 final size:27
Alignment explanation
Indices: 52393786--52393963 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
52393776 ATATTGAGTC
* * * *
52393786 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
52393813 CGCACACTTAGTGCTACATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52393840 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
52393868 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
52393895 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
52393922 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
52393949 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
52393964 GTACAATTTA
Statistics
Matches: 132, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
27 108 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:52393925 original size:82 final size:81
Alignment explanation
Indices: 52393807--52393962 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
52393797 TGCTATATAA
*
52393807 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
52393872 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
52393889 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
52393953 CACTTAGTGC
65 CACTTAGTGC
52393963 TGTACAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 16 0.24
82 52 0.76
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:52398575 original size:12 final size:12
Alignment explanation
Indices: 52398558--52398584 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
52398548 TTATTATGCA
52398558 ATTATTGTTATT
1 ATTATTGTTATT
52398570 ATTATTGTTATT
1 ATTATTGTTATT
52398582 ATT
1 ATT
52398585 GAGTTATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (12 bp):
ATTATTGTTATT
Found at i:52398864 original size:47 final size:47
Alignment explanation
Indices: 52398746--52398905 Score: 148
Period size: 47 Copynumber: 3.4 Consensus size: 47
52398736 ATTGACGGTT
** ** * *
52398746 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTAG--TAAGAC
1 AAGGATACCATGTAAGACCACATCAAGACATGGCATCGGCATTAGAA
* ** *
52398791 AAGGATCCCATGTAAGACCATGTCAAGACATGGCATCGGCATT-GATT
1 AAGGATACCATGTAAGACCACATCAAGACATGGCATCGGCATTAGA-A
** *
52398838 AAGGACT-CCATGTAAGACCACATCAAGATGTGGCATTGGCATTAGGAA
1 AAGGA-TACCATGTAAGACCACATCAAGACATGGCATCGGCATTA-GAA
52398886 AAGGATACCATGTAAGACCA
1 AAGGATACCATGTAAGACCA
52398906 TGTTTGGAAC
Statistics
Matches: 97, Mismatches: 11, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
45 36 0.37
46 2 0.02
47 38 0.39
48 19 0.20
49 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (47 bp):
AAGGATACCATGTAAGACCACATCAAGACATGGCATCGGCATTAGAA
Found at i:52398945 original size:47 final size:47
Alignment explanation
Indices: 52398883--52399001 Score: 202
Period size: 47 Copynumber: 2.5 Consensus size: 47
52398873 TTGGCATTAG
52398883 GAAAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
1 GAAAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
* * *
52398930 TACAAGGATACCATGTAAGACCATGTTTGGGACATGGCATTTGGTAA
1 GAAAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
*
52398977 GAAAAGGATATCATGTAAGACCATG
1 GAAAAGGATACCATGTAAGACCATG
52399002 CCAAGGCATG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 66 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (47 bp):
GAAAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGGTAA
Found at i:52399109 original size:55 final size:54
Alignment explanation
Indices: 52398974--52399197 Score: 247
Period size: 54 Copynumber: 4.1 Consensus size: 54
52398964 TGGCATTTGG
* * *
52398974 TAAGAAAAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTA
1 TAAGGAAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTA
* * *
52399028 TAAGGCAAGGAAATCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTACTA
1 TAAGGAAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTA
* * * *
52399083 TAAGGAAAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCCA-TGGTGAGTTC-A
1 TAAGG-AAAGGATACCATGTAAGACCATGCCAAGACATGG-CATTGATAAGTTCTA
* * * * * *
52399136 TAAGGTAAGGATACCACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTCAA
1 TAAGGAAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTA
*
52399190 AAAGGAAA
1 TAAGGAAA
52399198 AGGTTCCCGA
Statistics
Matches: 145, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
52 6 0.04
53 39 0.27
54 55 0.38
55 39 0.27
56 6 0.04
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.21
Consensus pattern (54 bp):
TAAGGAAAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTA
Found at i:52399173 original size:108 final size:108
Alignment explanation
Indices: 52398988--52399201 Score: 297
Period size: 108 Copynumber: 2.0 Consensus size: 108
52398978 AAAAGGATAT
* *
52398988 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
* * *
52399053 ATGCCAAGACATGGCATTGATAAGTTACTATAAGGAAAAGGTCC
66 ATGCCAAGACATGGCAATGATAAGTT-CAAAAAGGAAAAGGTCC
* * * *
52399097 CATGTAAGACCATGCCAAGGCATGGCCA-TGGTGAGTTC-ATAAGGTAAGGATACCACGTAAGAC
1 CATGTAAGACCATGCCAAGGCATGG-CATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGAC
* *
52399160 CATGTCAAGACATGGCAATGGTAAGTTCAAAAAGGAAAAGGT
65 CATGCCAAGACATGGCAATGATAAGTTCAAAAAGGAAAAGGT
52399202 TCCCGAGTAA
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 13 0.14
108 45 0.48
109 33 0.35
110 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.21
Consensus pattern (108 bp):
CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAACCACGTAAGACC
ATGCCAAGACATGGCAATGATAAGTTCAAAAAGGAAAAGGTCC
Found at i:52399483 original size:31 final size:31
Alignment explanation
Indices: 52399445--52399508 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
52399435 CCTTTTCATA
52399445 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
**
52399476 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
52399507 TT
1 TT
52399509 ACTGTAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:52399752 original size:24 final size:24
Alignment explanation
Indices: 52399702--52399844 Score: 179
Period size: 23 Copynumber: 6.0 Consensus size: 24
52399692 GTTTTATCAT
*
52399702 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
52399727 ATAATTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52399751 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52399774 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
52399797 ATAACTGGGGCATACG-CCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
52399820 TCATAAC-GGGGCATAAGCCCTTTTA
1 --ATAACTGGGGCATAAGCCCTTTTA
52399845 CACTTCCTCC
Statistics
Matches: 106, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
22 2 0.02
23 46 0.43
24 35 0.33
25 23 0.22
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:52399777 original size:47 final size:46
Alignment explanation
Indices: 52399723--52399844 Score: 165
Period size: 47 Copynumber: 2.6 Consensus size: 46
52399713 CCTAGCCTCT
*
52399723 TTTAATAATTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAA-TGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
* *
52399770 TTTAATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATACGCCT
1 TTTAATAA-TGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
*
52399816 TTTATCATAACGGGGCATAAGCCCTTTTA
1 TTTA--ATAATGGGGCATAAGCCCTTTTA
52399845 CACTTCCTCC
Statistics
Matches: 67, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
46 25 0.37
47 34 0.51
48 8 0.12
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (46 bp):
TTTAATAATGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:52399918 original size:20 final size:20
Alignment explanation
Indices: 52399893--52399959 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
52399883 TTATGATTAC
52399893 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
52399913 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52399933 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
52399953 ACCATGT
1 ATCATGT
52399960 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:52399924 original size:11 final size:11
Alignment explanation
Indices: 52399893--52399948 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
52399883 TTATGATTAC
52399893 ATCATGTGCAT
1 ATCATGTGCAT
*
52399904 ATCA--TACAT
1 ATCATGTGCAT
52399913 ATCATGTGCAT
1 ATCATGTGCAT
*
52399924 ATCA--TACAT
1 ATCATGTGCAT
*
52399933 GTCATGTGCAT
1 ATCATGTGCAT
52399944 ATCAT
1 ATCAT
52399949 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:52404387 original size:21 final size:21
Alignment explanation
Indices: 52404361--52404403 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
52404351 TAAAGGCCAT
52404361 TGCATGTTTATTTTCTCATCA
1 TGCATGTTTATTTTCTCATCA
52404382 TGCATGTTTATTTTCTCATCA
1 TGCATGTTTATTTTCTCATCA
52404403 T
1 T
52404404 CTTCCACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.19, G:0.09, T:0.53
Consensus pattern (21 bp):
TGCATGTTTATTTTCTCATCA
Found at i:52404797 original size:44 final size:43
Alignment explanation
Indices: 52404725--52404888 Score: 136
Period size: 43 Copynumber: 3.8 Consensus size: 43
52404715 AGTTGACATT
* * * * *
52404725 GATTTGAGATATCCTGTAAGATCGTGTCTGGGACACAGGCCTC
1 GATTTGAGATTTCATGTAAGACCATGTCTGGGACACAGGCATC
* * *
52404768 GATTTGAGATTTACGTGTAAGACCATGTCTAGGACATAGGCATC
1 GATTTGAGATTT-CATGTAAGACCATGTCTGGGACACAGGCATC
* * *
52404812 GTATTT--GATTTCATGTAAGACCCTGTCTGGGAAAGAGGCATC
1 G-ATTTGAGATTTCATGTAAGACCATGTCTGGGACACAGGCATC
* * * **
52404854 GATACTGA-ATTACATGTAATACCACATCTGGGACA
1 GAT-TTGAGATTTCATGTAAGACCATGTCTGGGACA
52404889 TTGGCATTGT
Statistics
Matches: 97, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
41 2 0.02
42 28 0.29
43 37 0.38
44 26 0.27
45 4 0.04
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (43 bp):
GATTTGAGATTTCATGTAAGACCATGTCTGGGACACAGGCATC
Found at i:52404839 original size:42 final size:43
Alignment explanation
Indices: 52404739--52404888 Score: 126
Period size: 42 Copynumber: 3.5 Consensus size: 43
52404729 TGAGATATCC
* * * *
52404739 TGTAAGATCGTGTCTGGGACACAGGCCTCGATTTGAGATTTACG
1 TGTAAGACCATGTCTGGGACACAGGCATCGATTT-AGATTTACA
* *
52404783 TGTAAGACCATGTCTAGGACATAGGCATCGTATTT-GATTT-CA
1 TGTAAGACCATGTCTGGGACACAGGCATCG-ATTTAGATTTACA
* * * * *
52404825 TGTAAGACCCTGTCTGGGAAAGAGGCATCGATACT-GAATTACA
1 TGTAAGACCATGTCTGGGACACAGGCATCGAT-TTAGATTTACA
* **
52404868 TGTAATACCACATCTGGGACA
1 TGTAAGACCATGTCTGGGACA
52404889 TTGGCATTGT
Statistics
Matches: 86, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
41 2 0.02
42 32 0.37
43 23 0.27
44 25 0.29
45 4 0.05
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACACAGGCATCGATTTAGATTTACA
Found at i:52407037 original size:10 final size:10
Alignment explanation
Indices: 52407024--52407062 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
52407014 CTGTTTTATA
52407024 CATGATATGC
1 CATGATATGC
*
52407034 CATGATTTGC
1 CATGATATGC
52407044 GCATGATATGC
1 -CATGATATGC
52407055 CATGATAT
1 CATGATAT
52407063 ATTCATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (10 bp):
CATGATATGC
Found at i:52407180 original size:24 final size:25
Alignment explanation
Indices: 52407107--52407178 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
52407097 GGAGGAAGTG
* * *
52407107 CAAAAAGAGCTTTGCCCTAGTTTAC
1 CAAAAAGGGCTTTGCCCCAGTTTAT
*
52407132 CGAAAAGGGCTTTGCCCCAGTTTAT
1 CAAAAAGGGCTTTGCCCCAGTTTAT
*
52407157 CAAAAAGGGATTTGCCCCAGTT
1 CAAAAAGGGCTTTGCCCCAGTT
52407179 ATTAAAAGAG
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (25 bp):
CAAAAAGGGCTTTGCCCCAGTTTAT
Found at i:52408959 original size:46 final size:45
Alignment explanation
Indices: 52408892--52409065 Score: 170
Period size: 46 Copynumber: 3.8 Consensus size: 45
52408882 TTTGGGCATC
52408892 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTT
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTT
*** * * *
52408938 CGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-ACTAAGCATT
1 CGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAAG--TT
* * * **
52408985 CGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCC
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-GTT
* * *
52409031 CGAGCTCGTTGAGTTGAGTCTGAGTTCGCTTATGG
1 CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52409066 GCGGGTTACA
Statistics
Matches: 103, Mismatches: 20, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
45 1 0.01
46 67 0.65
47 34 0.33
48 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.30
Consensus pattern (45 bp):
CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAGTT
Found at i:52411671 original size:12 final size:12
Alignment explanation
Indices: 52411654--52411678 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52411644 CCTTATACAC
52411654 ATTACACATTGA
1 ATTACACATTGA
52411666 ATTACACATTGA
1 ATTACACATTGA
52411678 A
1 A
52411679 ATCAGATTTT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ATTACACATTGA
Found at i:52417704 original size:23 final size:23
Alignment explanation
Indices: 52417678--52417724 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
52417668 TTGTATTATG
*
52417678 AACGTGCATGTTAAGTTGCTTGA
1 AACGTACATGTTAAGTTGCTTGA
52417701 AACGTACATGTTAAGTTGCTTGA
1 AACGTACATGTTAAGTTGCTTGA
52417724 A
1 A
52417725 GCAATTTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (23 bp):
AACGTACATGTTAAGTTGCTTGA
Found at i:52422069 original size:47 final size:47
Alignment explanation
Indices: 52422012--52422133 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
52422002 CATTGGCACT
* *
52422012 AAGACAAGGATACCTTGTAAGACCATGTTTGGAACATGACATTTGGC
1 AAGACAAGGATACCATGTAAGACCATGCTTGGAACATGACATTTGGC
* * *
52422059 AAGACAAGGATACCATGTAAGACCATGCTTGGGACATGGCATTTGGT
1 AAGACAAGGATACCATGTAAGACCATGCTTGGAACATGACATTTGGC
* *
52422106 AAGATAAGGATATCATGTAAGACCATGC
1 AAGACAAGGATACCATGTAAGACCATGC
52422134 CAAGGCATGA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 68 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (47 bp):
AAGACAAGGATACCATGTAAGACCATGCTTGGAACATGACATTTGGC
Found at i:52422240 original size:55 final size:54
Alignment explanation
Indices: 52422111--52422328 Score: 206
Period size: 54 Copynumber: 4.0 Consensus size: 54
52422101 TTGGTAAGAT
* * * * * *
52422111 AAGGATATCATGTAAGACCATGCCAAGGCATGACATTGATAAATTTTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
* * *
52422165 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGG-A
* * * * *
52422221 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
* * * * * * * *
52422273 AAGGATACCACGTAAGACCTTGTCAAGACATGGAAATGGTAAGTTCAAAAAGGA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
52422327 AA
1 AA
52422329 AGGTTCCCGA
Statistics
Matches: 135, Mismatches: 25, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
52 4 0.03
53 39 0.29
54 48 0.36
55 40 0.30
56 4 0.03
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGA
Found at i:52422305 original size:53 final size:53
Alignment explanation
Indices: 52422111--52422319 Score: 204
Period size: 53 Copynumber: 3.9 Consensus size: 53
52422101 TTGGTAAGAT
* * * * * * *
52422111 AAGGATATCATGTAAGACCATGCCAAGGCATGACATTGATAAATTTTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGT-AAGTTCATAAGGC
* * * *
52422165 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGAA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTT-C-ATAAGG-C
* * * *
52422221 AAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTCATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
* * * *
52422273 AAGGATACCACGTAAGACCTTGTCAAGACATGGAAATGGTAAGTTCA
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCA
52422320 AAAAGGAAAA
Statistics
Matches: 128, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
52 4 0.03
53 44 0.34
54 37 0.29
55 39 0.30
56 4 0.03
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCATTGGTAAGTTCATAAGGC
Found at i:52422316 original size:108 final size:108
Alignment explanation
Indices: 52422119--52422332 Score: 286
Period size: 108 Copynumber: 2.0 Consensus size: 108
52422109 ATAAGGATAT
* * * *
52422119 CATGTAAGACCATGCCAAGGCATGACATTGATAAATTTTATAAGGCAAGGAAATCATGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGACATTGATAAAGTTCATAAGGCAAGGAAACCACGTAAGACC
* * * *
52422184 ATGTCAAGACATGGCATTGATAAGTTACTATAAGGAAAAGGTCC
66 ATGTCAAGACATGGAAATGATAAGTT-CAAAAAGGAAAAGGTCC
* * * *
52422228 CATGTAAGACCATGCCAAGGCATGGCATTGGT-GAGTTCATAAGGCAAGGATACCACGTAAGACC
1 CATGTAAGACCATGCCAAGGCATGACATTGATAAAGTTCATAAGGCAAGGAAACCACGTAAGACC
* *
52422292 TTGTCAAGACATGGAAATGGTAAGTTCAAAAAGGAAAAGGT
66 ATGTCAAGACATGGAAATGATAAGTTCAAAAAGGAAAAGGT
52422333 TCCCGAGTAA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 13 0.14
108 48 0.53
109 30 0.33
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (108 bp):
CATGTAAGACCATGCCAAGGCATGACATTGATAAAGTTCATAAGGCAAGGAAACCACGTAAGACC
ATGTCAAGACATGGAAATGATAAGTTCAAAAAGGAAAAGGTCC
Found at i:52429577 original size:11 final size:11
Alignment explanation
Indices: 52429561--52429599 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
52429551 CATGATTGAT
52429561 ATGATATGCAC
1 ATGATATGCAC
*
52429572 ATGATATG--T
1 ATGATATGCAC
52429581 ATGATATGCAC
1 ATGATATGCAC
52429592 ATGATATG
1 ATGATATG
52429600 TATGAAGTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
9 8 0.33
11 16 0.67
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:52429616 original size:20 final size:20
Alignment explanation
Indices: 52429542--52429604 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
52429532 GTACGTGGGA
52429542 TATGATAT--ACATGAT-TG
1 TATGATATGCACATGATATG
52429559 ATATGATATGCACATGATATG
1 -TATGATATGCACATGATATG
52429580 TATGATATGCACATGATATG
1 TATGATATGCACATGATATG
52429600 TATGA
1 TATGA
52429605 AGTGCTCATG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.19
20 32 0.76
21 2 0.05
ACGTcount: A:0.37, C:0.08, G:0.19, T:0.37
Consensus pattern (20 bp):
TATGATATGCACATGATATG
Found at i:52429749 original size:52 final size:51
Alignment explanation
Indices: 52429666--52429800 Score: 197
Period size: 52 Copynumber: 2.7 Consensus size: 51
52429656 GAGGAAGTGC
* *
52429666 AAAAGGGCTTATGCCCCAGTTTATTGAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCTCAGTTTATTGAAAAGGGCTT-TGCCCCAGCTTACCG
*
52429718 AAAATGGCTTATGCCTCAGTTTATTGAAAAGGGCTTTGCCCCAGCTTACCG
1 AAAAGGGCTTATGCCTCAGTTTATTGAAAAGGGCTTTGCCCCAGCTTACCG
52429769 AAAAGGGCTT-TGCCT-AG-TTATT-AAAAGAGGCT
1 AAAAGGGCTTATGCCTCAGTTTATTGAAAAG-GGCT
52429801 AGGCCTCCAG
Statistics
Matches: 78, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
47 5 0.06
48 9 0.12
49 2 0.03
50 5 0.06
51 23 0.29
52 34 0.44
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (51 bp):
AAAAGGGCTTATGCCTCAGTTTATTGAAAAGGGCTTTGCCCCAGCTTACCG
Found at i:52429771 original size:25 final size:26
Alignment explanation
Indices: 52429666--52429782 Score: 157
Period size: 26 Copynumber: 4.6 Consensus size: 26
52429656 GAGGAAGTGC
**
52429666 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
52429692 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
* * **
52429718 AAAATGGCTTATGCCTCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTACCG
*
52429744 AAAAGGGCTT-TGCCCCAGCTTACCG
1 AAAAGGGCTTATGCCCCAGTTTACCG
52429769 AAAAGGGCTT-TGCC
1 AAAAGGGCTTATGCC
52429783 TAGTTATTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
25 25 0.31
26 55 0.69
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTACCG
Found at i:52431267 original size:42 final size:43
Alignment explanation
Indices: 52431171--52431325 Score: 222
Period size: 43 Copynumber: 3.6 Consensus size: 43
52431161 TAGGATTTCT
* * *
52431171 GATATGTGATTACGTGTATGACCACGTCTGGGACATTGGCGTC
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
* *
52431214 GATATGTGATTACGTGTAAGACAACGTC-AGGACGTTGGCATC
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
* * *
52431256 AATATCTGATTACGTGTAAGACCACGTCTGGGATGTTGGCATC
1 GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
*
52431299 GATATGTGATTACGAGTAAGACCACGT
1 GATATGTGATTACGTGTAAGACCACGT
52431326 TTAATACATT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
42 36 0.37
43 62 0.63
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
GATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCATC
Found at i:52431338 original size:43 final size:43
Alignment explanation
Indices: 52431171--52431352 Score: 213
Period size: 43 Copynumber: 4.3 Consensus size: 43
52431161 TAGGATTTCT
* * *
52431171 GATATGTGATTACGTGTATGACCACGTCTGGGACATTGGCGTC
1 GATATGTGATTACGTGTAAGACCACGTCTAGGACATTGGCATC
* *
52431214 GATATGTGATTACGTGTAAGACAACGTC-AGGACGTTGGCATC
1 GATATGTGATTACGTGTAAGACCACGTCTAGGACATTGGCATC
* * * **
52431256 AATATCTGATTACGTGTAAGACCACGTCTGGGATGTTGGCATC
1 GATATGTGATTACGTGTAAGACCACGTCTAGGACATTGGCATC
* * ** *
52431299 GATATGTGATTACGAGTAAGACCACGTTTAATACATTGGCATT
1 GATATGTGATTACGTGTAAGACCACGTCTAGGACATTGGCATC
*
52431342 GGTATGTGATT
1 GATATGTGATT
52431353 CTGATATGTG
Statistics
Matches: 117, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
42 36 0.31
43 81 0.69
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
GATATGTGATTACGTGTAAGACCACGTCTAGGACATTGGCATC
Found at i:52431385 original size:56 final size:56
Alignment explanation
Indices: 52431299--52431517 Score: 300
Period size: 56 Copynumber: 3.9 Consensus size: 56
52431289 TGTTGGCATC
* * *
52431299 GATATGTGAT-TACGAGTAAGACCACGTTTAATACATTGGCATTGGTATGTGATTCT
1 GATATGTG-TGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCT
*
52431355 GATATGTGTGTATGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATT-T
1 GATATGTGTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCT
* *
52431410 CGATATGTGTGTGCCAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTAC-
1 -GATATGTGTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATT-CT
* * * *
52431467 GATATGTTTGTGCGAGTAAGACCACGTCTAATATGTTGGCATCGATATGTG
1 GATATGTGTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTG
52431518 TGTATGAGTA
Statistics
Matches: 148, Mismatches: 11, Indels: 8
0.89 0.07 0.05
Matches are distributed among these distances:
55 2 0.01
56 146 0.99
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (56 bp):
GATATGTGTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTCT
Found at i:52431515 original size:43 final size:43
Alignment explanation
Indices: 52431466--52431551 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
52431456 TATGTGATTA
* * **
52431466 CGATATGTTTGTGCGAGTAAGACCACGTCTAATATGTTGGCAT
1 CGATATGTGTGTACGAGTAAGACCACGTCTAATACATTGGCAT
* *
52431509 CGATATGTGTGTATGAGTAAGACCACGTTTAATACATTGGCAT
1 CGATATGTGTGTACGAGTAAGACCACGTCTAATACATTGGCAT
52431552 TGAAGGTGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (43 bp):
CGATATGTGTGTACGAGTAAGACCACGTCTAATACATTGGCAT
Found at i:52431528 original size:99 final size:98
Alignment explanation
Indices: 52431409--52431587 Score: 252
Period size: 99 Copynumber: 1.8 Consensus size: 98
52431399 ATATGTGATT
* * *
52431409 TCGATATGTGTGTGCCAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTACGATATGT
1 TCGATATGTGTGTACCAGTAAGACCACGTTTAATACATTGGCATCGA-AGGTGATTACGATATGT
*
52431474 -TTGTGCGAGTAAGACCACGTCTAATATGTTGGCA
65 ATT-TACGAGTAAGACCACGTCTAATATGTTGGCA
** * **
52431508 TCGATATGTGTGTATGAGTAAGACCACGTTTAATACATTGGCATTGAAGGTGATTTTGATATGTA
1 TCGATATGTGTGTACCAGTAAGACCACGTTTAATACATTGGCATCGAAGGTGATTACGATATGTA
52431573 TTTACGAGTAAGACC
66 TTTACGAGTAAGACC
52431588 TTATTTGGGA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
98 26 0.37
99 44 0.63
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.34
Consensus pattern (98 bp):
TCGATATGTGTGTACCAGTAAGACCACGTTTAATACATTGGCATCGAAGGTGATTACGATATGTA
TTTACGAGTAAGACCACGTCTAATATGTTGGCA
Found at i:52444373 original size:18 final size:17
Alignment explanation
Indices: 52444350--52444383 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52444340 ACTTAACAGA
*
52444350 TAAATTCTTACTAGACAC
1 TAAATTCGTAC-AGACAC
52444368 TAAATTCGTACAGACA
1 TAAATTCGTACAGACA
52444384 AATGAATGGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.41, C:0.21, G:0.09, T:0.29
Consensus pattern (17 bp):
TAAATTCGTACAGACAC
Found at i:52446623 original size:43 final size:42
Alignment explanation
Indices: 52446561--52446673 Score: 145
Period size: 43 Copynumber: 2.7 Consensus size: 42
52446551 CATCATACAA
* ** *
52446561 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCGTATCG
1 ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
* *
52446603 ATGCCAATACCCCAGCTATGGTCTTACACGAAATCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAATCTCATATCG
**
52446646 ATATCATATCCCAGATATGGTCTTACAC
1 ATGCCATATCCCAGATATGGTCTTACAC
52446674 ATAGCCTCGG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 26 0.43
43 34 0.57
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAATCTCATATCG
Found at i:52454093 original size:15 final size:15
Alignment explanation
Indices: 52454068--52454108 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
52454058 CATGTTATTT
*
52454068 TTCTCTTCTTTTTTG
1 TTCTTTTCTTTTTTG
52454083 TGT-TTTTC-TTTTTG
1 T-TCTTTTCTTTTTTG
52454097 TTCTTTTCTTTT
1 TTCTTTTCTTTT
52454109 CGATAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
13 1 0.05
14 12 0.55
15 8 0.36
16 1 0.05
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (15 bp):
TTCTTTTCTTTTTTG
Found at i:52455793 original size:49 final size:49
Alignment explanation
Indices: 52455721--52455914 Score: 203
Period size: 50 Copynumber: 3.9 Consensus size: 49
52455711 GCCGAAACTA
*
52455721 TCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
* * * *
52455770 TCTGGTACACGTAGTAGTCTGCACTTAGTACTACACATGTGACCTCACCA-
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-C-CAACAG
** * * * *
52455820 TCTAATACACGTAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAG
1 TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
* * *
52455868 TTTTCGGGTACGCATAATAGCCTGCACTTAGTACTACACATGCGACC
1 ---TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACC
52455915 TCACAATAGA
Statistics
Matches: 119, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
49 38 0.32
50 39 0.33
51 39 0.33
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (49 bp):
TCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAACAG
Found at i:52455909 original size:101 final size:99
Alignment explanation
Indices: 52455732--52455918 Score: 259
Period size: 101 Copynumber: 1.9 Consensus size: 99
52455722 CTGGTACGCA
* * * * *
52455732 TAGTAGCCTGCACTTAGTACTACACATGCGACCAACAGTCTGGTACACGTAGTAGTCTGCACTTA
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAATAGCCTGCACTTA
*
52455797 GTACTACACATGTGACCTCACCATCTAATACACG
66 GTACTACACATGCGACCTCACCATCTAATACACG
* * *
52455831 TAGTAGCCTGCACTTAGTACTACACACGTGATC-ACAGTTTTCGGGTACGCATAATAGCCTGCAC
1 TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAG---TCGGGTACACATAATAGCCTGCAC
52455895 TTAGTACTACACATGCGACCTCAC
63 TTAGTACTACACATGCGACCTCAC
52455919 AATAGATCAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
98 4 0.05
99 30 0.39
101 42 0.55
ACGTcount: A:0.28, C:0.28, G:0.18, T:0.26
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACTACACACGCGACCAACAGTCGGGTACACATAATAGCCTGCACTTA
GTACTACACATGCGACCTCACCATCTAATACACG
Found at i:52461910 original size:14 final size:14
Alignment explanation
Indices: 52461893--52461933 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52461883 TTTTGCATTG
*
52461893 GTACATCTGCATAC
1 GTACATATGCATAC
*
52461907 GTACATTTGCATAC
1 GTACATATGCATAC
*
52461921 ATACATATGCATA
1 GTACATATGCATA
52461934 AGCTATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.34, C:0.22, G:0.12, T:0.32
Consensus pattern (14 bp):
GTACATATGCATAC
Found at i:52462246 original size:92 final size:92
Alignment explanation
Indices: 52462071--52462248 Score: 252
Period size: 92 Copynumber: 1.9 Consensus size: 92
52462061 TTACTGATAA
* **
52462071 TGGTATAGCGGATTACCGTATTGCACTGTACCCCATGTACGTTAGCTACGCTACGTACCATTGAC
1 TGGTATAGCGGATTACCGCATTGCACTGTACCCCATGTACGTTAGCTACGCTACGTACCATCCAC
*
52462136 TGAATTGACAATTTTACTGCAACCTAT
66 TGAATCGACAATTTTACTGCAACCTAT
**
52462163 TGGTATAGCGGATTACCGCATTGCACTGTACCGTATGTACGTTAGCTACGCTACGTACCA-CCAT
1 TGGTATAGCGGATTACCGCATTGCACTGTACCCCATGTACGTTAGCTACGCTACGTACCATCCA-
* *
52462227 CTG-ATCGGCAGTTTATACTGCA
65 CTGAATCGACAATTT-TACTGCA
52462249 TGTCTGTACT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
91 9 0.12
92 67 0.88
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (92 bp):
TGGTATAGCGGATTACCGCATTGCACTGTACCCCATGTACGTTAGCTACGCTACGTACCATCCAC
TGAATCGACAATTTTACTGCAACCTAT
Found at i:52465931 original size:12 final size:12
Alignment explanation
Indices: 52465914--52465956 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
52465904 GAACCCTTTT
*
52465914 TCTTTTTCATTC
1 TCTTTTTCAATC
52465926 TCTTTTTCAATC
1 TCTTTTTCAATC
52465938 TCTTTTTCAATC
1 TCTTTTTCAATC
*
52465950 TCATTTT
1 TCTTTTT
52465957 GTTTCCTCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.14, C:0.23, G:0.00, T:0.63
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:52473519 original size:39 final size:40
Alignment explanation
Indices: 52473402--52473586 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
52473392 GCTACTCGTT
*
52473402 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
52473442 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
52473482 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
52473521 CAAATGCCTTC-GGATCTTAGTCCAGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
52473562 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
52473587 CATCATTCGA
Statistics
Matches: 123, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.62
41 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:52473570 original size:79 final size:81
Alignment explanation
Indices: 52473402--52473586 Score: 209
Period size: 79 Copynumber: 2.3 Consensus size: 81
52473392 GCTACTCGTT
* * *
52473402 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAA-GCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCA
* *
52473466 GATTTAGTAACTCGCAC
65 GATATAGTAACTAGCAC
* * **
52473483 CAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCA
1 CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCA
* *
52473545 GATATGGTCACTTAGCA-
65 GATATAGTAAC-TAGCAC
52473562 CAAAGCCTTCGGGACTTAGCCCGGA
1 CAAAGCCTTCGGGACTTAGCCCGGA
52473587 CATCATTCGA
Statistics
Matches: 88, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
78 3 0.03
79 57 0.65
80 25 0.28
81 3 0.03
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (81 bp):
CAAAGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCAG
ATATAGTAACTAGCAC
Found at i:52475598 original size:28 final size:28
Alignment explanation
Indices: 52475516--52475605 Score: 119
Period size: 29 Copynumber: 3.1 Consensus size: 28
52475506 TGAGTATGAC
52475516 TATAAATGTGAATTGGGCCT-GATGGGCCA
1 TATAAATGTG-ATTGGGCCTAG-TGGGCCA
* *
52475545 TATAAATGTGATTTGGGCCAAATGGGCCA
1 TATAAATGTGA-TTGGGCCTAGTGGGCCA
*
52475574 TATAAATGTGATTGGGCCTAGTGGGTCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
52475602 TATA
1 TATA
52475606 CAGGTATGTG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
28 19 0.35
29 35 0.65
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAGTGGGCCA
Found at i:52477982 original size:6 final size:6
Alignment explanation
Indices: 52477964--52478052 Score: 67
Period size: 6 Copynumber: 14.3 Consensus size: 6
52477954 AAGAAACATT
* *
52477964 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA
* *
52478013 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATC-AGA ATCAGA AT
52478053 GTGAATGCAA
Statistics
Matches: 66, Mismatches: 8, Indels: 18
0.72 0.09 0.20
Matches are distributed among these distances:
5 5 0.08
6 47 0.71
7 12 0.18
8 2 0.03
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:52478008 original size:19 final size:19
Alignment explanation
Indices: 52477984--52478041 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
52477974 GAATCAGAAT
52477984 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
*
52478003 CAGAATCA--A--A---AT
1 CAGAATCAGTATCAGGTAA
52478015 CAGAATCAGTATCAGGTAA
1 CAGAATCAGTATCAGGTAA
52478034 CAGAATCA
1 CAGAATCA
52478042 AAAATCAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
12 9 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
19 17 0.57
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.19
Consensus pattern (19 bp):
CAGAATCAGTATCAGGTAA
Found at i:52478016 original size:31 final size:31
Alignment explanation
Indices: 52477973--52478052 Score: 142
Period size: 31 Copynumber: 2.5 Consensus size: 31
52477963 TATCAGAACT
*
52477973 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
52478004 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGTATCAGGTAAC
52478035 AGAATCAAAAATCAGAAT
1 AGAATC-AAAATCAGAAT
52478053 GTGAATGCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
31 36 0.77
32 11 0.23
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGTATCAGGTAAC
Found at i:52478231 original size:27 final size:26
Alignment explanation
Indices: 52478189--52478290 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
52478179 ACTCAGTTAT
* * *
52478189 CAGATATGGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
52478216 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
52478242 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* * *
52478270 TAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
52478291 TTAACAGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 7 0.11
27 52 0.79
28 7 0.11
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:52478483 original size:22 final size:22
Alignment explanation
Indices: 52478449--52478513 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
52478439 GCAAATACGT
* *
52478449 TTGGCACACAGCCATAATCAGG
1 TTGGAACAAAGCCATAATCAGG
* *
52478471 TTGGAACAGAGCCAT-ATGTAGG
1 TTGGAACAAAGCCATAAT-CAGG
52478493 TT-GACACAAAGCCATAATCAG
1 TTGGA-ACAAAGCCATAATCAG
52478514 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.11
22 29 0.83
23 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGAACAAAGCCATAATCAGG
Found at i:52478997 original size:27 final size:27
Alignment explanation
Indices: 52478940--52479323 Score: 538
Period size: 27 Copynumber: 14.3 Consensus size: 27
52478930 GGGGCAAAAT
* * * *
52478940 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52478966 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
52478993 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52479020 GGTAATTCTACCCTACAGTGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52479047 GATAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
52479074 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
52479101 GGTAATTCTACTATACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
52479128 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
52479155 GGTAATTCTACCTTACAAGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52479182 GATAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52479209 GGTAAGTCTGCCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
52479236 GGTAATTCTACCCTACAGGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
52479262 TGGTAATTCTACCCTACAGGGGTATTTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
*
52479290 GGTAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
52479317 GGTAATT
1 GGTAATT
52479324 TTATAAACAA
Statistics
Matches: 316, Mismatches: 39, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
26 17 0.05
27 296 0.94
28 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:52479348 original size:27 final size:27
Alignment explanation
Indices: 52479318--52479378 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
52479308 GGGTATTGCG
* *
52479318 GTAATTTTATAAACAAAGGGTATTTTA
1 GTAATTTTACAAACAAAGGGCATTTTA
* * *
52479345 GTAATTTTACAAACCAGGGGCATTTTG
1 GTAATTTTACAAACAAAGGGCATTTTA
52479372 GTAATTT
1 GTAATTT
52479379 GGTAAACTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACAAAGGGCATTTTA
Found at i:52483735 original size:40 final size:40
Alignment explanation
Indices: 52483660--52483884 Score: 285
Period size: 40 Copynumber: 5.6 Consensus size: 40
52483650 AACACAAGTA
* *
52483660 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* * * *
52483699 CCTTTGGGTCTTAGCCCGAATGTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
52483739 CCTTCGGGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATG
*
52483782 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
** *
52483822 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
52483862 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
52483885 CATCCGAATA
Statistics
Matches: 162, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.07
40 112 0.69
41 1 0.01
43 36 0.22
44 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:52483783 original size:83 final size:80
Alignment explanation
Indices: 52483660--52483884 Score: 335
Period size: 83 Copynumber: 2.8 Consensus size: 80
52483650 AACACAAGTA
* * * *
52483660 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTTGGGTCTTAGCCCGAATGTAG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAG
52483724 TCACTAGCACAAATG
66 TCACTAGCACAAATG
* * *
52483739 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGAATA
52483804 TAGTCACTAGCACAAATG
63 TAGTCACTAGCACAAATG
* *
52483822 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATAT
52483885 CATCCGAATA
Statistics
Matches: 132, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
79 13 0.10
80 45 0.34
81 1 0.01
82 1 0.01
83 72 0.55
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGAATATAG
TCACTAGCACAAATG
Found at i:52491872 original size:39 final size:40
Alignment explanation
Indices: 52491818--52492041 Score: 287
Period size: 40 Copynumber: 5.6 Consensus size: 40
52491808 AACCCAAGTA
*
52491818 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
* *
52491857 CCTTCGGGTCTTAGCCC-GA-AGTAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAG-CAACTCGCACAAATG
*
52491896 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATG
* *
52491939 CCTTCGGGACTTCGCCCGGATATAGTC-ACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CAACTCGCACAAATG
* *
52491979 CCTTCGGGACTTAGCCCGAATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
52492019 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
52492042 CATCCGAATA
Statistics
Matches: 160, Mismatches: 14, Indels: 21
0.82 0.07 0.11
Matches are distributed among these distances:
38 1 0.01
39 46 0.29
40 76 0.47
41 1 0.01
43 35 0.22
44 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATG
Found at i:52491986 original size:83 final size:80
Alignment explanation
Indices: 52491818--52492041 Score: 337
Period size: 83 Copynumber: 2.8 Consensus size: 80
52491808 AACCCAAGTA
* *
52491818 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCC-GA-AGTA
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TA
52491880 GTCACTAGCACAAATG
65 GTCACTAGCACAAATG
* *
52491896 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA
52491961 TAGTCACTAGCACAAATG
63 TAGTCACTAGCACAAATG
* *
52491979 CCTTCGGGACTTAGCCCGAATATAGGAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
52492042 CATCCGAATA
Statistics
Matches: 132, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
78 13 0.10
79 10 0.08
80 36 0.27
82 29 0.22
83 43 0.33
84 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAATG
Found at i:52494224 original size:28 final size:28
Alignment explanation
Indices: 52494142--52494231 Score: 128
Period size: 29 Copynumber: 3.1 Consensus size: 28
52494132 TGAGCATGAC
52494142 TATAAATGTGAATTGGGCCT-GATGGGCCA
1 TATAAATGTG-ATTGGGCCTAG-TGGGCCA
* *
52494171 TATAAATGTGATTTGGGCCTAATGGGCGA
1 TATAAATGTGA-TTGGGCCTAGTGGGCCA
52494200 TATAAATGTGATTGGGCCTAGTGGGCCA
1 TATAAATGTGATTGGGCCTAGTGGGCCA
52494228 TATA
1 TATA
52494232 TAGGTATGTG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
28 20 0.36
29 35 0.64
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (28 bp):
TATAAATGTGATTGGGCCTAGTGGGCCA
Found at i:52501133 original size:28 final size:28
Alignment explanation
Indices: 52501080--52501143 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
52501070 TAGTAAGTTG
* *
52501080 GCACATTTAGTGCTTAATAATCAAACTC
1 GCACACTTAGTGCTTAACAATCAAACTC
*
52501108 GCACACTTAGTG-TTATACAATTAAACTC
1 GCACACTTAGTGCTTA-ACAATCAAACTC
52501136 GCACACTT
1 GCACACTT
52501144 TCTGCCAATC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 3 0.09
28 29 0.91
ACGTcount: A:0.34, C:0.23, G:0.11, T:0.31
Consensus pattern (28 bp):
GCACACTTAGTGCTTAACAATCAAACTC
Found at i:52522764 original size:40 final size:40
Alignment explanation
Indices: 52522709--52522926 Score: 289
Period size: 40 Copynumber: 5.5 Consensus size: 40
52522699 CGGATGATAA
* * *
52522709 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
52522749 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
52522789 CCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
52522829 CCGGGCTAAGTCCCAAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * *
52522869 CCGGTCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* *
52522909 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
52522927 TACTTGGCTT
Statistics
Matches: 160, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
39 15 0.09
40 145 0.91
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:52524495 original size:10 final size:10
Alignment explanation
Indices: 52524468--52524548 Score: 76
Period size: 10 Copynumber: 7.9 Consensus size: 10
52524458 TTAAATTCTA
52524468 AAAGATAAAT
1 AAAGATAAAT
52524478 ACAA-ATAAAT
1 A-AAGATAAAT
*
52524488 AAAGATAATT
1 AAAGATAAAT
52524498 AAAGATAAAT
1 AAAGATAAAT
*
52524508 AACGATAAAT
1 AAAGATAAAT
*
52524518 AAATATAAA-
1 AAAGATAAAT
*
52524527 AGCTAGGATAAAT
1 A---AAGATAAAT
52524540 AAAGATAAA
1 AAAGATAAA
52524549 AGCTAAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
9 3 0.05
10 45 0.79
11 2 0.04
12 6 0.11
13 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.10, T:0.21
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:52524539 original size:22 final size:22
Alignment explanation
Indices: 52524511--52524553 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
52524501 GATAAATAAC
*
52524511 GATAAATAAATATAAAAGCTAG
1 GATAAATAAAGATAAAAGCTAG
52524533 GATAAATAAAGATAAAAGCTA
1 GATAAATAAAGATAAAAGCTA
52524554 AAATTAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (22 bp):
GATAAATAAAGATAAAAGCTAG
Found at i:52532555 original size:20 final size:19
Alignment explanation
Indices: 52532517--52532560 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
52532507 ATCTATATAC
*
52532517 ATTCAAAATTAAATTTTTTT
1 ATTCAAAATTAAA-TATTTT
*
52532537 ATTCAAAATTAACTATTTT
1 ATTCAAAATTAAATATTTT
52532556 ATTCA
1 ATTCA
52532561 TTGAAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTCAAAATTAAATATTTT
Found at i:52532557 original size:19 final size:20
Alignment explanation
Indices: 52532517--52532560 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
52532507 ATCTATATAC
* *
52532517 ATTCAAAATTAAATTTTTTT
1 ATTCAAAATTAAACTATTTT
52532537 ATTCAAAATT-AACTATTTT
1 ATTCAAAATTAAACTATTTT
52532556 ATTCA
1 ATTCA
52532561 TTGAAACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTCAAAATTAAACTATTTT
Found at i:52548754 original size:15 final size:15
Alignment explanation
Indices: 52548715--52548758 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
52548705 GTATTGTAAT
*
52548715 TTGGATTTCCTTATC
1 TTGGATTTCTTTATC
*
52548730 ATGGATTTCTTTATC
1 TTGGATTTCTTTATC
*
52548745 TTGGAATTCTTTAT
1 TTGGATTTCTTTAT
52548759 TCTGGGCTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.18, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
TTGGATTTCTTTATC
Found at i:52549426 original size:14 final size:15
Alignment explanation
Indices: 52549407--52549435 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52549397 AAAGTTAATA
52549407 TGGATT-TTCTTGTC
1 TGGATTATTCTTGTC
52549421 TGGATTATTCTTGTC
1 TGGATTATTCTTGTC
52549436 CTTGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.10, C:0.14, G:0.21, T:0.55
Consensus pattern (15 bp):
TGGATTATTCTTGTC
Found at i:52553060 original size:28 final size:28
Alignment explanation
Indices: 52553016--52553175 Score: 100
Period size: 28 Copynumber: 5.8 Consensus size: 28
52553006 CTGCACAATC
* *
52553016 GATGTCTT-GCACGCTAAGTGCTATACT-G
1 GATGT-TTCGCACACTAAGTGCCAT-CTCG
*
52553044 GATGTTTCGCACACTAAGTGCCATTTCG
1 GATGTTTCGCACACTAAGTGCCATCTCG
*
52553072 GATGTTTCGCACACTAAGTGTCATCATC-
1 GATGTTTCGCACACTAAGTGCCATC-TCG
* ** ** * *
52553100 AATACTTCATACACT--GTGTCATTTCG
1 GATGTTTCGCACACTAAGTGCCATCTCG
52553126 GATGTCTT-GCACACTAAGTGCCATCCTC-
1 GATGT-TTCGCACACTAAGTGCCAT-CTCG
* **
52553154 AATACTTCGCACACTAAGTGCC
1 GATGTTTCGCACACTAAGTGCC
52553176 GTTCGTTTGG
Statistics
Matches: 102, Mismatches: 21, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
25 2 0.02
26 14 0.14
27 7 0.07
28 75 0.74
29 4 0.04
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (28 bp):
GATGTTTCGCACACTAAGTGCCATCTCG
Found at i:52553168 original size:54 final size:55
Alignment explanation
Indices: 52553016--52553175 Score: 171
Period size: 54 Copynumber: 2.9 Consensus size: 55
52553006 CTGCACAATC
* * * ** **
52553016 GATGTCTTGCACGCTAAGTGCTATACTGGATGTTTCGCACACTAAGTGCCATTTCG
1 GATGTCTTGCACACTAAGTGCCATCCTCAATACTTCGCACACT-AGTGCCATTTCG
* * ** *
52553072 GATGT-TTCGCACACTAAGTGTCATCATCAATACTTCATACACT-GTGTCATTTCG
1 GATGTCTT-GCACACTAAGTGCCATCCTCAATACTTCGCACACTAGTGCCATTTCG
52553126 GATGTCTTGCACACTAAGTGCCATCCTCAATACTTCGCACACTAAGTGCC
1 GATGTCTTGCACACTAAGTGCCATCCTCAATACTTCGCACACT-AGTGCC
52553176 GTTCGTTTGG
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
54 46 0.55
55 4 0.05
56 33 0.40
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.31
Consensus pattern (55 bp):
GATGTCTTGCACACTAAGTGCCATCCTCAATACTTCGCACACTAGTGCCATTTCG
Found at i:52558072 original size:43 final size:43
Alignment explanation
Indices: 52557966--52558089 Score: 101
Period size: 43 Copynumber: 2.9 Consensus size: 43
52557956 TATCCCAGAT
* * * * * *
52557966 ATGGTCTTACA-TGTTATCACATATCGATGCCACTGTCCCAGAC
1 ATGGTCTTACACT-TAATCATATAACGATGCCAATGTCCAACAC
* * *
52558009 AGGGTCTTATAC-GAATTCATATAACGATGCCAATGTCCAACAC
1 ATGGTCTTACACTTAA-TCATATAACGATGCCAATGTCCAACAC
* *
52558052 ATGGTCTTACACTTAATCATA-ATACAATGCGAATGTCC
1 ATGGTCTTACACTTAATCATATA-ACGATGCCAATGTCC
52558090 CAGAGATGGT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
42 2 0.03
43 59 0.94
44 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
ATGGTCTTACACTTAATCATATAACGATGCCAATGTCCAACAC
Found at i:52563131 original size:14 final size:14
Alignment explanation
Indices: 52563112--52563140 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52563102 AATCTACGCT
52563112 TCTTTGATAGTAAA
1 TCTTTGATAGTAAA
52563126 TCTTTGATAGTAAA
1 TCTTTGATAGTAAA
52563140 T
1 T
52563141 AGGATGTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.07, G:0.14, T:0.45
Consensus pattern (14 bp):
TCTTTGATAGTAAA
Found at i:52567076 original size:57 final size:57
Alignment explanation
Indices: 52566934--52567121 Score: 207
Period size: 57 Copynumber: 3.3 Consensus size: 57
52566924 ACATAAGTTG
* * * * * * *
52566934 CAGATAGAATTTAGCACGGATGGGTAATTC-TAATTTAAGCCCTCTTGAGCTTAGGCTG
1 CAGATAGGATTTAGCCCGGATGGGTAATTCAT-A-TTAAGCTCTCTAGAGCATATGCTA
* * * * *
52566992 TAAATTGGATTTAGCTCGGACGGGTAATTCATATTAAGCTCTCTAGAGCATATGCTA
1 CAGATAGGATTTAGCCCGGATGGGTAATTCATATTAAGCTCTCTAGAGCATATGCTA
* *
52567049 CAGATAGGATTTAGCCCGGATGAGTAATCCATATTAAGCTCTCTAGAGCATATGCTA
1 CAGATAGGATTTAGCCCGGATGGGTAATTCATATTAAGCTCTCTAGAGCATATGCTA
**
52567106 TGGATAGGATTTAGCC
1 CAGATAGGATTTAGCC
52567122 TGGACTGGTA
Statistics
Matches: 109, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
57 83 0.76
58 25 0.23
59 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (57 bp):
CAGATAGGATTTAGCCCGGATGGGTAATTCATATTAAGCTCTCTAGAGCATATGCTA
Found at i:52567133 original size:57 final size:57
Alignment explanation
Indices: 52566998--52567139 Score: 200
Period size: 57 Copynumber: 2.5 Consensus size: 57
52566988 GCTGTAAATT
* *
52566998 GGATTTAG-CTCGGACGGGTAATTCATATTAAGCTCTCTAGAGCATATGCTACAGATA
1 GGATTTAGCCT-GGACTGGTAATCCATATTAAGCTCTCTAGAGCATATGCTACAGATA
* **
52567055 GGATTTAGCCCGGA-TGAGTAATCCATATTAAGCTCTCTAGAGCATATGCTATGGATA
1 GGATTTAGCCTGGACTG-GTAATCCATATTAAGCTCTCTAGAGCATATGCTACAGATA
52567112 GGATTTAGCCTGGACTGGTAATCC-TATT
1 GGATTTAGCCTGGACTGGTAATCCATATT
52567140 GTAAAATGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
56 5 0.07
57 68 0.89
58 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (57 bp):
GGATTTAGCCTGGACTGGTAATCCATATTAAGCTCTCTAGAGCATATGCTACAGATA
Found at i:52573217 original size:15 final size:15
Alignment explanation
Indices: 52573197--52573244 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52573187 TCAAAGATGG
52573197 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
52573212 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
52573226 GTTTATGGATATAAA
1 GTTTATGGATATGAA
52573241 GTTT
1 GTTT
52573245 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:52573231 original size:14 final size:14
Alignment explanation
Indices: 52573191--52573234 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
52573181 AAGGATTCAA
52573191 AGATGGGTTTATGG
1 AGATGGGTTTATGG
* * *
52573205 ATATGAAGTTTATGT
1 AGATG-GGTTTATGG
52573220 AGATGGGTTTATGG
1 AGATGGGTTTATGG
52573234 A
1 A
52573235 TATAAAGTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.34, T:0.39
Consensus pattern (14 bp):
AGATGGGTTTATGG
Found at i:52573260 original size:29 final size:29
Alignment explanation
Indices: 52573191--52573250 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
52573181 AAGGATTCAA
*
52573191 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
*
52573220 AGATGGGTTTATGGATATAAAGTTTTTGT
1 AGATGGGTTTATGGATATAAAGTTTATGT
52573249 AG
1 AG
52573251 GTTTGGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (29 bp):
AGATGGGTTTATGGATATAAAGTTTATGT
Found at i:52576536 original size:30 final size:28
Alignment explanation
Indices: 52576483--52576538 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
52576473 TTCTTCCACG
* *
52576483 CTTTCTTTTTGCTCACTCTCTTTTTCAA
1 CTTTCTTTTTGCACACACTCTTTTTCAA
52576511 CTTTACTTTCTTGCACACACTCTTTTTC
1 CTTT-CTTT-TTGCACACACTCTTTTTC
52576539 TTTTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.12, C:0.30, G:0.04, T:0.54
Consensus pattern (28 bp):
CTTTCTTTTTGCACACACTCTTTTTCAA
Found at i:52577250 original size:15 final size:15
Alignment explanation
Indices: 52577230--52577277 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
52577220 TCAAAGAAGG
52577230 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
52577245 GTTTATGTAGATG-G
1 GTTTATGGATATGAA
*
52577259 GTTTATGGATATAAA
1 GTTTATGGATATGAA
52577274 GTTT
1 GTTT
52577278 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.29, C:0.00, G:0.27, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:52577293 original size:29 final size:29
Alignment explanation
Indices: 52577228--52577283 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
52577218 ATTCAAAGAA
*
52577228 GGGTTTATGGATATGAAGTTTATGTAGAT
1 GGGTTTATGGATATAAAGTTTATGTAGAT
*
52577257 GGGTTTATGGATATAAAGTTTTTGTAG
1 GGGTTTATGGATATAAAGTTTATGTAG
52577284 GTTTGGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (29 bp):
GGGTTTATGGATATAAAGTTTATGTAGAT
Found at i:52581902 original size:9 final size:9
Alignment explanation
Indices: 52581888--52581918 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
52581878 TTTGGTTAAA
52581888 AATTAACCG
1 AATTAACCG
*
52581897 AATTAACCA
1 AATTAACCG
52581906 AATTAACCG
1 AATTAACCG
52581915 AATT
1 AATT
52581919 GAATCACTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.48, C:0.19, G:0.06, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:52584802 original size:57 final size:57
Alignment explanation
Indices: 52584648--52584912 Score: 244
Period size: 55 Copynumber: 4.8 Consensus size: 57
52584638 ATAGCACAAT
* * * * * * *
52584648 AATGCTTAATTTGAGACA-TGAAGCAAC-ACTTTAATTTAATTTAGGACAGCAT-AA
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGACAGAATGAA
* * **
52584702 TAATACTCAATTTGAAACA-TTAAACAACAAC-TTAATGAAATTTAAGACAGAATGAA
1 -AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGACAGAATGAA
* ** * *
52584758 AATGCTTAATTTGTTACACTAAAACACCAACTTTAATTCAATTTAGGACA-ACATGAA
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGACAGA-ATGAA
* * * *
52584815 AATGCTCAATTTGAAACACTAAAACAACAGC-TTGATTCAATTTAAGATAGTATGAA
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGACAGAATGAA
* *
52584871 TATGCTCAATTTGAAACACT--CA-AACAACTTTAATTCAATTTA
1 AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTA
52584913 TGATAGCATG
Statistics
Matches: 172, Mismatches: 31, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
53 5 0.03
54 13 0.08
55 54 0.31
56 54 0.31
57 46 0.27
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (57 bp):
AATGCTCAATTTGAAACACTAAAACAACAACTTTAATTCAATTTAAGACAGAATGAA
Found at i:52584877 original size:56 final size:56
Alignment explanation
Indices: 52584648--52584912 Score: 238
Period size: 56 Copynumber: 4.8 Consensus size: 56
52584638 ATAGCACAAT
* * * * * * *
52584648 AATGCTTAATTTGAGACA-TGAAGCAAC-ACTTTAATTTAATTTAGGACAGCAT-AA
1 AATGCTCAATTTGAAACACTAAAACAACAAC-TTAATTCAATTTAAGACAGAATGAA
* * **
52584702 TAATACTCAATTTGAAACA-TTAAACAACAACTTAATGAAATTTAAGACAGAATGAA
1 -AATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTAAGACAGAATGAA
* ** * *
52584758 AATGCTTAATTTGTTACACTAAAACACCAACTTTAATTCAATTTAGGACA-ACATGAA
1 AATGCTCAATTTGAAACACTAAAACAACAAC-TTAATTCAATTTAAGACAGA-ATGAA
* * * *
52584815 AATGCTCAATTTGAAACACTAAAACAACAGCTTGATTCAATTTAAGATAGTATGAA
1 AATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTAAGACAGAATGAA
* * *
52584871 TATGCTCAATTTGAAACACTCAAACAAC--TTTAATTCAATTTA
1 AATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTA
52584913 TGATAGCATG
Statistics
Matches: 173, Mismatches: 31, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
54 12 0.07
55 54 0.31
56 61 0.35
57 46 0.27
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (56 bp):
AATGCTCAATTTGAAACACTAAAACAACAACTTAATTCAATTTAAGACAGAATGAA
Found at i:52584890 original size:113 final size:109
Alignment explanation
Indices: 52584675--52584912 Score: 289
Period size: 113 Copynumber: 2.1 Consensus size: 109
52584665 ATGAAGCAAC
* * *
52584675 ACTTTAATTTAATTTAGGACAGCATAATAATACTCAATTTGAAACATTAAACAACAACTTAATGA
1 ACTTTAATTCAATTTAGGACAACATAATAATACTCAATTTGAAACATAAAACAACAACTTAATGA
* **
52584740 AATTTAAGACAGAATGAAAATGCTTAATTTGTTACACTAAAACACCA
66 AATTTAAGACAGAATGAAAATGCTCAATTTGAAACACT-AAA-A-CA
* * *
52584787 ACTTTAATTCAATTTAGGACAACATGAA-AATGCTCAATTTGAAACACTAAAACAACAGCTTGAT
1 ACTTTAATTCAATTTAGGACAACAT-AATAATACTCAATTTGAAACA-TAAAACAACAACTTAAT
** * * * *
52584851 TCAATTTAAGATAGTATGAATATGCTCAATTTGAAACACTCAAACA
64 GAAATTTAAGACAGAATGAAAATGCTCAATTTGAAACACTAAAACA
52584897 ACTTTAATTCAATTTA
1 ACTTTAATTCAATTTA
52584913 TGATAGCATG
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
110 18 0.17
111 1 0.01
112 42 0.39
113 48 0.44
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (109 bp):
ACTTTAATTCAATTTAGGACAACATAATAATACTCAATTTGAAACATAAAACAACAACTTAATGA
AATTTAAGACAGAATGAAAATGCTCAATTTGAAACACTAAAACA
Found at i:52586005 original size:76 final size:76
Alignment explanation
Indices: 52585875--52586020 Score: 238
Period size: 76 Copynumber: 1.9 Consensus size: 76
52585865 TTTCAAACCA
* * *
52585875 AATTAACTGTTAACCGAAAAATCAAAAAATAATTAACCGACCCCGGACCGAAAAAATTCGGTTAA
1 AATTAACCGTTAACCGAAAAATCAAAAAATAATTAACCGACCCCGGACCAAAAAAATTCAGTTAA
52585940 CCGATCGATCG
66 CCGATCGATCG
* * *
52585951 AATTAACCGTTAACTGAAAAATCAAAAAATAATTAACCGACCCCGGACTAAAAAAATTTAGTTAA
1 AATTAACCGTTAACCGAAAAATCAAAAAATAATTAACCGACCCCGGACCAAAAAAATTCAGTTAA
52586016 CCGAT
66 CCGAT
52586021 TGATTAACCG
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
76 64 1.00
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (76 bp):
AATTAACCGTTAACCGAAAAATCAAAAAATAATTAACCGACCCCGGACCAAAAAAATTCAGTTAA
CCGATCGATCG
Found at i:52590708 original size:40 final size:40
Alignment explanation
Indices: 52590625--52590885 Score: 321
Period size: 40 Copynumber: 6.5 Consensus size: 40
52590615 TTGAATGCTG
* * * * *
52590625 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAA
* * * *
52590665 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAA
*
52590705 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
52590745 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* *
52590785 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
52590825 TCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
* * *
52590864 ACCGGGCTATGTCCCGAAGGCA
1 TCCGGGTTAAGTCCCGAAGGCA
52590886 CTTGAACGAG
Statistics
Matches: 196, Mismatches: 22, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
39 34 0.17
40 154 0.79
41 8 0.04
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAA
Found at i:52590907 original size:79 final size:80
Alignment explanation
Indices: 52590664--52590922 Score: 249
Period size: 80 Copynumber: 3.3 Consensus size: 80
52590654 AAGTGAATAT
* * * * *
52590664 ATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCAT
1 ATCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCAT
** * *
52590728 TCGTGCGAGTTA-TTAA
65 TCGAACGAG-GAGCTAA
* * *
52590744 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATT
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
** ** *
52590809 CGTGCGAGTTGTTAA
66 CGAACGAGGAGCTAA
* * *
52590824 ATCCGGGTTATGTCCCGAAGGCA-TTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCACT
1 ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCA-T
*
52590888 T-GAACGAGGAGCTAT
65 TCGAACGAGGAGCTAA
* *
52590903 ATCC-GGTTAAATTCCGAAGG
1 ATCCGGGTTAAGTCCCGAAGG
52590923 TACGTGATTT
Statistics
Matches: 156, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
78 13 0.08
79 48 0.31
80 95 0.61
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (80 bp):
ATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
CGAACGAGGAGCTAA
Found at i:52609607 original size:14 final size:14
Alignment explanation
Indices: 52609590--52609618 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
52609580 TTTTTTTCGA
52609590 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
52609604 TTTTTTTTTGAATT
1 TTTTTTTTTGAATT
52609618 T
1 T
52609619 CTTCTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTGAATT
Found at i:52618683 original size:21 final size:21
Alignment explanation
Indices: 52618657--52618731 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
52618647 CATATAAGAG
52618657 TATAATAAAATATTAAAAATA
1 TATAATAAAATATTAAAAATA
*
52618678 TATAATTGAAA-ATTAAAAAT-
1 TATAA-TAAAATATTAAAAATA
* *
52618698 TAATTATATAAATA--ATAAATA
1 T-ATAATA-AAATATTAAAAATA
52618719 T-TAATAAAATATT
1 TATAATAAAATATT
52618732 TATCTCTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 15
0.68 0.08 0.24
Matches are distributed among these distances:
18 5 0.12
19 4 0.10
20 7 0.17
21 21 0.50
22 5 0.12
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (21 bp):
TATAATAAAATATTAAAAATA
Found at i:52619017 original size:62 final size:62
Alignment explanation
Indices: 52618945--52619070 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
52618935 TGCGGAAGAA
*
52618945 AGAATCAAATAAAATATGAAAAGAAGATTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
1 AGAATCAAATAAAATATGAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
52619007 AGAATCAAATAAAATATGAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
1 AGAATCAAATAAAATATGAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
52619069 AG
1 AG
52619071 TTGGCGAGAG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.25
Consensus pattern (62 bp):
AGAATCAAATAAAATATGAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
Found at i:52619261 original size:3 final size:3
Alignment explanation
Indices: 52619253--52619304 Score: 95
Period size: 3 Copynumber: 17.0 Consensus size: 3
52619243 TCCCAATTGG
52619253 CTT CTT CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
52619299 CTT CTT
1 CTT CTT
52619305 TCACTTTCTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:52624714 original size:24 final size:24
Alignment explanation
Indices: 52624670--52624715 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
52624660 AGCCTTGTCA
* *
52624670 TTTGATGACTATTTACCTTAATAC
1 TTTGATGACCATTTACATTAATAC
52624694 TTTGATGATCCATTTA-ATTAAT
1 TTTGATGA-CCATTTACATTAAT
52624716 CTCAACTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.30, C:0.13, G:0.09, T:0.48
Consensus pattern (24 bp):
TTTGATGACCATTTACATTAATAC
Found at i:52627860 original size:37 final size:37
Alignment explanation
Indices: 52627809--52627882 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
52627799 TTTAATACTT
52627809 ATCTGAATATTATTTTATTAA-T-TTAATATTAACTTTA
1 ATCTGAATATTATTTTATTAACTATT-ATATTAA-TTTA
*
52627846 ATCT-AATATTTATTTTGTTAACTATTATATTAATTTA
1 ATCTGAATA-TTATTTTATTAACTATTATATTAATTTA
52627883 TATTAAAGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 4 0.12
37 19 0.58
38 8 0.24
39 2 0.06
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.55
Consensus pattern (37 bp):
ATCTGAATATTATTTTATTAACTATTATATTAATTTA
Found at i:52629213 original size:18 final size:20
Alignment explanation
Indices: 52629192--52629236 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
52629182 TTATATAAGT
*
52629192 AAATAATAATTAAAT-AA-C
1 AAATAATAAATAAATAAACC
*
52629210 AAATAAAAAATAAATAAACC
1 AAATAATAAATAAATAAACC
52629230 AAATAAT
1 AAATAAT
52629237 TCATGTAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (20 bp):
AAATAATAAATAAATAAACC
Found at i:52630453 original size:31 final size:31
Alignment explanation
Indices: 52630417--52630481 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
52630407 AATTTAGATC
* *
52630417 ATTTCATA-CATAACTTTACTCATATAATTGG
1 ATTTCATATCAGAACTTTACTC-TATAATCGG
52630448 ATTTCATATCAGAACTTTACTCTATAATCGG
1 ATTTCATATCAGAACTTTACTCTATAATCGG
52630479 ATT
1 ATT
52630482 CAGGTTCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.42
Consensus pattern (31 bp):
ATTTCATATCAGAACTTTACTCTATAATCGG
Found at i:52643355 original size:46 final size:47
Alignment explanation
Indices: 52643257--52643431 Score: 238
Period size: 46 Copynumber: 3.8 Consensus size: 47
52643247 GGTTATTGTG
* *
52643257 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
52643304 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
52643351 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGA-TA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGAGTA
*
52643395 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
52643432 ATCCTACCCA
Statistics
Matches: 118, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
44 14 0.12
45 16 0.14
46 60 0.51
47 15 0.13
48 13 0.11
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGTA
Found at i:52657028 original size:12 final size:12
Alignment explanation
Indices: 52657013--52657050 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
52657003 TTCTTTTTTC
*
52657013 TTTTTTTCG-AT
1 TTTTTTTTGAAT
52657024 TTTTTTTTGAATT
1 TTTTTTTTGAA-T
52657037 TTTTTTTTGAAT
1 TTTTTTTTGAAT
52657049 TT
1 TT
52657051 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.13, C:0.03, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:52657045 original size:13 final size:13
Alignment explanation
Indices: 52657023--52657050 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
52657013 TTTTTTTCGA
52657023 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
52657036 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
52657049 TT
1 TT
52657051 CTTCTCTTTT
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:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:52664959 original size:28 final size:28
Alignment explanation
Indices: 52664928--52664986 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
52664918 ATACTTTGTT
52664928 AATAAT-TTTA-ATGATTTTAATTTTTTAA
1 AATAATGTTTATAT-ATTTTAA-TTTTTAA
*
52664956 AATAATGTTTATATTTTTTAATTTTTAA
1 AATAATGTTTATATATTTTAATTTTTAA
52664984 AAT
1 AAT
52664987 TTTTAAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 16 0.57
29 10 0.36
30 2 0.07
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
AATAATGTTTATATATTTTAATTTTTAA
Found at i:52666067 original size:21 final size:21
Alignment explanation
Indices: 52666041--52666081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
52666031 CATATAAGAG
52666041 TATAA-TAAAATATTAAAAATA
1 TATAATTAAAA-ATTAAAAATA
*
52666062 TATAATTGAAAATTAAAAAT
1 TATAATTAAAAATTAAAAAT
52666082 TAATTATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TATAATTAAAAATTAAAAATA
Found at i:52666403 original size:63 final size:63
Alignment explanation
Indices: 52666330--52666457 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
52666320 TGCGGAAGAA
*
52666330 AGAATCAAATAAAATATGAAAAAGAAGATTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
1 AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
52666393 AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
1 AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
52666456 AG
1 AG
52666458 TTGGCGAGAG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (63 bp):
AGAATCAAATAAAATATGAAAAAGAAGACTGAGTTTTAGGGAAATTAAAGGAGTATTCTAGGG
Found at i:52666650 original size:3 final size:3
Alignment explanation
Indices: 52666642--52666689 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
52666632 CCCAATTTGG
52666642 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
52666690 TCACTTTCTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:52675484 original size:48 final size:48
Alignment explanation
Indices: 52675397--52675520 Score: 117
Period size: 48 Copynumber: 2.6 Consensus size: 48
52675387 ATTCCACAAA
* * * * *
52675397 AATATTATTTTAATAGTTTAATATTTTATTTTATTTAATACTTA-TCTG
1 AATATTATTTTATTAATTTAATA-TTAATTTAATCTAATACTTATTCTG
* *
52675445 AATATTATTTTATTAATTTAATATTAACTTTAATCTAATATTTATTTTG
1 AATATTATTTTATTAATTTAATATTAA-TTTAATCTAATACTTATTCTG
* * *
52675494 -TTAACTATTATATTAATTTAATATTAA
1 AAT-ATTATTTTATTAATTTAATATTAA
52675521 AGTGATTATG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.05
48 35 0.56
49 25 0.40
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.56
Consensus pattern (48 bp):
AATATTATTTTATTAATTTAATATTAATTTAATCTAATACTTATTCTG
Found at i:52675514 original size:37 final size:37
Alignment explanation
Indices: 52675440--52675515 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
52675430 TTTAATACTT
52675440 ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
1 ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
*
52675477 ATCT-AATATTTATTTTGTTAACTATT-ATATTAA-TTTA
1 ATCTGAATA-TTATTTTATTAA-T-TTAATATTAACTTTA
52675514 AT
1 AT
52675516 ATTAAAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 21 0.60
38 8 0.23
39 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (37 bp):
ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
Found at i:52678252 original size:33 final size:33
Alignment explanation
Indices: 52678214--52678276 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
52678204 AGTTTAGATC
*
52678214 ATTTCATATCATAACTTTACTCATATTAATTGG
1 ATTTCATATCAGAACTTTACTCATATTAATTGG
52678247 ATTTCATATCAGAACTTTACTCATATTAAT
1 ATTTCATATCAGAACTTTACTCATATTAAT
52678277 CGGAATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (33 bp):
ATTTCATATCAGAACTTTACTCATATTAATTGG
Found at i:52691162 original size:46 final size:47
Alignment explanation
Indices: 52691064--52691238 Score: 238
Period size: 46 Copynumber: 3.8 Consensus size: 47
52691054 GGTTATTGTG
* *
52691064 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
52691111 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
52691158 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGA-TA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGAGTA
*
52691202 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
52691239 ATCCTACCCA
Statistics
Matches: 118, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
44 14 0.12
45 16 0.14
46 60 0.51
47 15 0.13
48 13 0.11
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGTA
Found at i:52710073 original size:48 final size:48
Alignment explanation
Indices: 52709986--52710109 Score: 117
Period size: 48 Copynumber: 2.6 Consensus size: 48
52709976 TATTCCACAA
* * * * *
52709986 AATATTATTTTAATAGTTTAATATTTTATTTTATTTAATACTTA-TCTG
1 AATATTATTTTATTAATTTAATA-TTAATTTAATCTAATACTTATTCTG
* *
52710034 AATATTATTTTATTAATTTAATATTAACTTTAATCTAATATTTATTTTG
1 AATATTATTTTATTAATTTAATATTAA-TTTAATCTAATACTTATTCTG
* * *
52710083 -TTAACTATTATATTAATTTAATATTAA
1 AAT-ATTATTTTATTAATTTAATATTAA
52710110 AGTGATTATG
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
47 3 0.05
48 35 0.56
49 25 0.40
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.56
Consensus pattern (48 bp):
AATATTATTTTATTAATTTAATATTAATTTAATCTAATACTTATTCTG
Found at i:52710103 original size:37 final size:37
Alignment explanation
Indices: 52710029--52710104 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
52710019 TTTAATACTT
52710029 ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
1 ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
*
52710066 ATCT-AATATTTATTTTGTTAACTATT-ATATTAA-TTTA
1 ATCTGAATA-TTATTTTATTAA-T-TTAATATTAACTTTA
52710103 AT
1 AT
52710105 ATTAAAGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 21 0.60
38 8 0.23
39 2 0.06
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (37 bp):
ATCTGAATATTATTTTATTAATTTAATATTAACTTTA
Found at i:52711494 original size:18 final size:18
Alignment explanation
Indices: 52711457--52711495 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52711447 TTATATAAGT
*
52711457 AAATAAATAATTAAATAA
1 AAATAAATAAATAAATAA
52711475 AAATAAATAAAATAAA-AA
1 AAATAAAT-AAATAAATAA
52711493 AAA
1 AAA
52711496 AATAATCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAATAAATAAATAAATAA
Found at i:52712762 original size:33 final size:33
Alignment explanation
Indices: 52712724--52712786 Score: 117
Period size: 33 Copynumber: 1.9 Consensus size: 33
52712714 AGTTTAGATC
*
52712724 ATTTCATATCATAACTTTACTCATATTAATTGG
1 ATTTCATATCAGAACTTTACTCATATTAATTGG
52712757 ATTTCATATCAGAACTTTACTCATATTAAT
1 ATTTCATATCAGAACTTTACTCATATTAAT
52712787 CGGAATATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (33 bp):
ATTTCATATCAGAACTTTACTCATATTAATTGG
Found at i:52725632 original size:46 final size:47
Alignment explanation
Indices: 52725534--52725708 Score: 238
Period size: 46 Copynumber: 3.8 Consensus size: 47
52725524 GGTTATTGTG
* *
52725534 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGACG-A
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
52725581 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATGTA
1 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGA-GTA
52725628 AGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGG-CTACGAGA-TA
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCT-CGAGAGTA
*
52725672 AGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
52725709 ATCCTACCCC
Statistics
Matches: 118, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
44 14 0.12
45 16 0.14
46 60 0.51
47 15 0.13
48 13 0.11
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
AGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAGTA
Found at i:52726847 original size:21 final size:22
Alignment explanation
Indices: 52726808--52726848 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52726798 GTCGAATCGT
52726808 CACACAGGCGTGTTGCCCCTCC
1 CACACAGGCGTGTTGCCCCTCC
*
52726830 CACACGGGCGTG-TGCCCCT
1 CACACAGGCGTGTTGCCCCT
52726849 ATGTCTAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.12, C:0.44, G:0.27, T:0.17
Consensus pattern (22 bp):
CACACAGGCGTGTTGCCCCTCC
Found at i:52728502 original size:20 final size:20
Alignment explanation
Indices: 52728473--52728517 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
52728463 AGCACATGTA
*
52728473 TTCATAAAATTTCATAATTT
1 TTCATAAAATTTCATAACTT
* *
52728493 TTCATCAAATTTTATAACTT
1 TTCATAAAATTTCATAACTT
52728513 TTCAT
1 TTCAT
52728518 TTTAGTCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.00, T:0.51
Consensus pattern (20 bp):
TTCATAAAATTTCATAACTT
Found at i:52736704 original size:25 final size:26
Alignment explanation
Indices: 52736670--52736725 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
52736660 TTCTCTCACC
* * *
52736670 AAAAACGACTTATTTTCCTAA-TTAA
1 AAAAACGACTTATATGCCAAATTTAA
*
52736695 AAAAATGACTTATATGCCAAATTTAA
1 AAAAACGACTTATATGCCAAATTTAA
52736721 AAAAA
1 AAAAA
52736726 AAGGCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.30
Consensus pattern (26 bp):
AAAAACGACTTATATGCCAAATTTAA
Found at i:52738289 original size:9 final size:9
Alignment explanation
Indices: 52738275--52738401 Score: 50
Period size: 10 Copynumber: 13.7 Consensus size: 9
52738265 GTCACATGTG
52738275 ATAAAAATT
1 ATAAAAATT
52738284 ATAAAAA--
1 ATAAAAATT
*
52738291 AT-AAAATCA
1 ATAAAAAT-T
52738300 ATAAAAATT
1 ATAAAAATT
*
52738309 AT-TAAATGT
1 ATAAAAAT-T
*
52738318 -TAATAAAAT
1 ATAA-AAATT
52738327 ATAAAAAATTT
1 AT-AAAAA-TT
52738338 ATAAAAATCGT
1 ATAAAAAT--T
52738349 A-AAAAATAT
1 ATAAAAAT-T
*
52738358 AAAAAAATT
1 ATAAAAATT
* * *
52738367 GTAAGATTT
1 ATAAAAATT
*
52738376 ATAAAAATC
1 ATAAAAATT
52738385 ATAGAAAAGTT
1 ATA-AAAA-TT
52738396 ATAAAA
1 ATAAAA
52738402 TGCATCAAAA
Statistics
Matches: 88, Mismatches: 15, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
6 4 0.05
7 2 0.02
8 5 0.06
9 30 0.34
10 36 0.41
11 11 0.12
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (9 bp):
ATAAAAATT
Found at i:52738351 original size:20 final size:20
Alignment explanation
Indices: 52738328--52738401 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
52738318 TAATAAAATA
52738328 TAAAAAATTTATAAAAATCG
1 TAAAAAATTTATAAAAATCG
* * *
52738348 TAAAAAATATAAAAAAATTG
1 TAAAAAATTTATAAAAATCG
* *
52738368 T--AAGATTTATAAAAATCA
1 TAAAAAATTTATAAAAATCG
* *
52738386 TAGAAAAGTTATAAAA
1 TAAAAAATTTATAAAA
52738402 TGCATCAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
18 13 0.31
20 29 0.69
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAAAAATTTATAAAAATCG
Found at i:52738638 original size:8 final size:9
Alignment explanation
Indices: 52738626--52738711 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
52738616 TTCTTTTCAT
52738626 TTTTTATAA
1 TTTTTATAA
*
52738635 TTTTGTATGA
1 TTTT-TATAA
*
52738645 -CTTTATAAA
1 TTTTTAT-AA
*
52738654 ATTTTATAA
1 TTTTTATAA
52738663 TTTTTAT-A
1 TTTTTATAA
52738671 TTTTTAT-A
1 TTTTTATAA
*
52738679 TATTTTACAA
1 T-TTTTATAA
*
52738689 TTTTTATGA
1 TTTTTATAA
*
52738698 TTTTATAAAA
1 TTTT-TATAA
52738708 TTTT
1 TTTT
52738712 ACATTTTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
8 13 0.21
9 30 0.49
10 18 0.30
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52738690 original size:26 final size:27
Alignment explanation
Indices: 52738627--52738720 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
52738617 TCTTTTCATT
* *
52738627 TTTTATAATTTTGTATGACTTTATAAAA
1 TTTTACAATTTT-TATGATTTTATAAAA
* *
52738655 TTTTATAATTTTTAT-ATTTT-TATATA
1 TTTTACAATTTTTATGATTTTATA-AAA
52738681 TTTTACAATTTTTATGATTTTATAAAA
1 TTTTACAATTTTTATGATTTTATAAAA
*
52738708 TTTTACATTTTTT
1 TTTTACAATTTTT
52738721 TTTCTAATTT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.03
26 20 0.34
27 22 0.38
28 14 0.24
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTACAATTTTTATGATTTTATAAAA
Found at i:52738711 original size:18 final size:18
Alignment explanation
Indices: 52738627--52738712 Score: 72
Period size: 18 Copynumber: 4.8 Consensus size: 18
52738617 TCTTTTCATT
52738627 TTTTAT-AATTTTGTATGA
1 TTTTATAAATTTT-TATGA
* * *
52738645 CTTTATAAAATTTTATAA
1 TTTTATAAATTTTTATGA
*
52738663 TTTT-TATATTTTTAT-A
1 TTTTATAAATTTTTATGA
52738679 TATTT-TACAATTTTTATGA
1 T-TTTATA-AATTTTTATGA
*
52738698 TTTTATAAAATTTTA
1 TTTTATAAATTTTTA
52738713 CATTTTTTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.04
17 14 0.25
18 30 0.55
19 9 0.16
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (18 bp):
TTTTATAAATTTTTATGA
Done.