Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 142 of 335
Found at i:41725590 original size:23 final size:22
Alignment explanation
Indices: 41725563--41725614 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
41725553 ATATCCATTA
41725563 GTTTATTCGATCTATCTTCTATTT
1 GTTTATTCGATC-AT-TTCTATTT
* *
41725587 -TTTATTCTATCATTTTTATTT
1 GTTTATTCGATCATTTCTATTT
41725608 GTTTATT
1 GTTTATT
41725615 ATGTTGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 7 0.28
22 8 0.32
23 10 0.40
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.65
Consensus pattern (22 bp):
GTTTATTCGATCATTTCTATTT
Found at i:41725850 original size:17 final size:19
Alignment explanation
Indices: 41725822--41725858 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
41725812 GAAAACAAGA
41725822 AAAATAAAGAAA-TTAAGT
1 AAAATAAAGAAATTTAAGT
41725840 AAAAT-AAGAAATTTAAGT
1 AAAATAAAGAAATTTAAGT
41725858 A
1 A
41725859 TAAAGAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (19 bp):
AAAATAAAGAAATTTAAGT
Found at i:41733679 original size:27 final size:27
Alignment explanation
Indices: 41733651--41733933 Score: 311
Period size: 27 Copynumber: 10.6 Consensus size: 27
41733641 ACATAGCGGT
* * *
41733651 AAAACAGTCATCTTACCATAAAAGGGT
1 AAAACAGTCATTTTACCATATAAGGGC
* *
41733678 AAAACAATCATTTTACCACATAAGGG-
1 AAAACAGTCATTTTACCATATAAGGGC
* * *
41733704 ATAAACAATCATTTTATC--ATAAGGGA
1 A-AAACAGTCATTTTACCATATAAGGGC
* * *
41733730 AAAATAGTTATTTTACCTTATAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGC
* * *
41733757 AAAATAGTCATTTTACCATGTAAGAGC
1 AAAACAGTCATTTTACCATATAAGGGC
* * **
41733784 AAAATAATCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGC
* *
41733811 AAAACAGTAATTTTACCATGTAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGC
* *
41733838 AAAATAGTCATTTTACCATATAAGCGC
1 AAAACAGTCATTTTACCATATAAGGGC
*
41733865 AAAACAGTCATTTTACCATAAAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGC
* *
41733892 AAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCATATAAGGGC
41733919 AAAACAGTCATTTTA
1 AAAACAGTCATTTTA
41733934 TCAATTAGGG
Statistics
Matches: 220, Mismatches: 32, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
25 19 0.09
26 2 0.01
27 199 0.90
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (27 bp):
AAAACAGTCATTTTACCATATAAGGGC
Found at i:41733699 original size:54 final size:54
Alignment explanation
Indices: 41733651--41733933 Score: 347
Period size: 54 Copynumber: 5.3 Consensus size: 54
41733641 ACATAGCGGT
* * * *
41733651 AAAACAGTCATCTTACCATAAAAGGGTAAAACAATCATTTTACCACATAAGGG-
1 AAAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
* * * * **
41733704 ATAAACAATCATTTTATCAT--AAGGGAAAAATAGTTATTTTACCTTATAAGGGC
1 A-AAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
* ** * * *
41733757 AAAATAGTCATTTTACCATGTAAGAGCAAAATAATCATTTTACCACGTAAGGGC
1 AAAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
* ** * *
41733811 AAAACAGTAATTTTACCATGTAAGGGCAAAATAGTCATTTTACCATATAAGCGC
1 AAAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
41733865 AAAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
1 AAAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
41733919 AAAACAGTCATTTTA
1 AAAACAGTCATTTTA
41733934 TCAATTAGGG
Statistics
Matches: 195, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
52 41 0.21
53 2 0.01
54 152 0.78
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (54 bp):
AAAACAGTCATTTTACCATAAAAGGGCAAAATAGTCATTTTACCACATAAGGGC
Found at i:41736903 original size:17 final size:17
Alignment explanation
Indices: 41736881--41736930 Score: 55
Period size: 20 Copynumber: 2.8 Consensus size: 17
41736871 TATCAAGATA
41736881 AATATTAGATTAAATTT
1 AATATTAGATTAAATTT
*
41736898 AATATTAAGATAATAACTTT
1 AATATT-AGAT--TAAATTT
*
41736918 AATATTAAATTAA
1 AATATTAGATTAA
41736931 TAAAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 9 0.32
18 4 0.14
19 3 0.11
20 12 0.43
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (17 bp):
AATATTAGATTAAATTT
Found at i:41736990 original size:36 final size:35
Alignment explanation
Indices: 41736921--41736991 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
41736911 TAACTTTAAT
*
41736921 ATTAAATTAATAAAATACTATTAAGAAAGTATTAC
1 ATTAAATTAATAAAATACTATTAAGAAAATATTAC
*
41736956 ATTAAATTTAATATTAA-ACTATTAA-AATAATATTAC
1 ATTAAA-TTAATA-AAATACTATTAAGAA-AATATTAC
41736992 TTTTGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
35 8 0.26
36 21 0.68
37 2 0.06
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAGAAAATATTAC
Found at i:41741892 original size:40 final size:39
Alignment explanation
Indices: 41741847--41742054 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 39
41741837 CGGAATACAA
*
41741847 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41741887 CCGGATAGAACGACTTGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* * *
41741927 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACAAATGCCTTCGGGTCTTAGC
* ** * *
41741967 CCGGATGTAGTCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
** * * *
41742007 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGC
1 CCGGATATAACCACT-GCACAAATGCCTTCGGGTCTTAGC
41742047 CCGGATAT
1 CCGGATAT
41742055 CATTCAATTG
Statistics
Matches: 142, Mismatches: 25, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
39 1 0.01
40 141 0.99
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (39 bp):
CCGGATATAACCACTGCACAAATGCCTTCGGGTCTTAGC
Found at i:41741987 original size:80 final size:81
Alignment explanation
Indices: 41741847--41742052 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 81
41741837 CGGAATACAA
* * *
41741847 CCGGATATAACCACATGCACGAATGCCTTCGGGTCTTAGCCCGGA-TAGAACGACTTGCACAAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
*
41741911 GCCTTCGGGTATTAGC
66 GCCTTCGGGTATTAAC
* * *
41741927 CCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAG-TC-ACTAGCACAAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT-TAGAACGACTAGCACAAA
*
41741990 TGCCTTCGGGTCTTAAC
65 TGCCTTCGGGTATTAAC
** * ** * *
41742007 CCGGATATAATTACTAGCATAAATGTCTTCGGGACTTAGCCCGGAT
1 CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGAT
41742053 ATCATTCAAT
Statistics
Matches: 108, Mismatches: 16, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
80 104 0.96
81 1 0.01
82 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (81 bp):
CCGGATATAACAACTTGCACGAATGCCTTCGGGTCTTAGCCCGGATTAGAACGACTAGCACAAAT
GCCTTCGGGTATTAAC
Found at i:41746788 original size:33 final size:36
Alignment explanation
Indices: 41746751--41746829 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 36
41746741 TAAGGTAATA
41746751 TAATATTAT-ACCTGTTTTTTATTTT-TTTC-AATT
1 TAATATTATAACCTGTTTTTTATTTTATTTCAAATT
* *
41746784 TAATATTATAACTTTTTTTTTATTTTAGTTTCAAATT
1 TAATATTATAACCTGTTTTTTATTTTA-TTTCAAATT
41746821 TATATATTA
1 TA-ATATTA
41746830 AATGTAATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 9 0.23
34 14 0.36
36 4 0.10
37 6 0.15
38 6 0.15
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (36 bp):
TAATATTATAACCTGTTTTTTATTTTATTTCAAATT
Found at i:41746995 original size:20 final size:20
Alignment explanation
Indices: 41746972--41747021 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
41746962 AAATCCAAAT
41746972 TAAAATACTAAAATTCAGGA
1 TAAAATACTAAAATTCAGGA
*
41746992 TAAAAT-CTTGAAATTCAGGA
1 TAAAATAC-TAAAATTCAGGA
41747012 TAAGAATACT
1 TAA-AATACT
41747022 GATGTAGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 4 0.15
22 1 0.04
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (20 bp):
TAAAATACTAAAATTCAGGA
Found at i:41748522 original size:20 final size:21
Alignment explanation
Indices: 41748478--41748531 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
41748468 TAGATATTAA
*
41748478 TAAAAAAAATAAA--AATCTT
1 TAAAAAATATAAATTAATCTT
*
41748497 TTAAAAATATAAATTAAT-TT
1 TAAAAAATATAAATTAATCTT
*
41748517 TAAAAAGTATAAATT
1 TAAAAAATATAAATT
41748532 TTTGGAAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.38
20 15 0.52
21 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAAAATATAAATTAATCTT
Found at i:41750190 original size:17 final size:17
Alignment explanation
Indices: 41750170--41750204 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
41750160 AAGATGTATT
41750170 AAAAATAAATTTTATAA
1 AAAAATAAATTTTATAA
*
41750187 AAAAATGAATTTTATAA
1 AAAAATAAATTTTATAA
41750204 A
1 A
41750205 TTGTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (17 bp):
AAAAATAAATTTTATAA
Found at i:41752012 original size:5 final size:5
Alignment explanation
Indices: 41752002--41752047 Score: 85
Period size: 5 Copynumber: 9.4 Consensus size: 5
41751992 TTATGTTTTA
41752002 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A-TAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
41752048 AAACTAAAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.10
5 36 0.90
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:41753251 original size:47 final size:48
Alignment explanation
Indices: 41753197--41753300 Score: 131
Period size: 47 Copynumber: 2.2 Consensus size: 48
41753187 TTACCGTTAT
* * * *
41753197 TGTTACTGTTTCAGG-TTCGTTCCGATGAGGTACTGTGTGTATCGTAC
1 TGTTACTGTTTCAGGATTCGTTCCGATGAAGTACTCTGTGTACCATAC
* *
41753244 TGTTACTG-TTCTGGATTTGTTCCGATGAAGTACTCTGTGTACCATAC
1 TGTTACTGTTTCAGGATTCGTTCCGATGAAGTACTCTGTGTACCATAC
*
41753291 TGCTACTGTT
1 TGTTACTGTT
41753301 ACTGTTACTG
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
46 5 0.10
47 42 0.88
48 1 0.02
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.41
Consensus pattern (48 bp):
TGTTACTGTTTCAGGATTCGTTCCGATGAAGTACTCTGTGTACCATAC
Found at i:41753572 original size:36 final size:36
Alignment explanation
Indices: 41753501--41753608 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
41753491 ATAACCAATC
* * * *
41753501 AATTGATTGATACTGAATAACTTATTATTATTGAAT
1 AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
* *
41753537 AATTGATTGTTACTGAATAACTGACTGTTACTGAAT
1 AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
* * * *
41753573 AAATAATTGTT-CTGATTGACTGATTGTTAATGAAT
1 AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
41753608 A
1 A
41753609 TTACTGATTG
Statistics
Matches: 61, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 21 0.34
36 40 0.66
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (36 bp):
AATTGATTGTTACTGAATAACTGATTGTTAATGAAT
Found at i:41753583 original size:18 final size:18
Alignment explanation
Indices: 41753504--41753618 Score: 106
Period size: 18 Copynumber: 6.3 Consensus size: 18
41753494 ACCAATCAAT
*
41753504 TGATTGATACTGAATAAC
1 TGATTGTTACTGAATAAC
* * * *
41753522 TTATTATTATTGAATAAT
1 TGATTGTTACTGAATAAC
41753540 TGATTGTTACTGAATAAC
1 TGATTGTTACTGAATAAC
* *
41753558 TGACTGTTACTGAATAAA
1 TGATTGTTACTGAATAAC
* * *
41753576 TAATTGTT-CTGATTGAC
1 TGATTGTTACTGAATAAC
*
41753593 TGATTGTTAATGAATATTAC
1 TGATTGTTACTGAATA--AC
41753613 TGATTG
1 TGATTG
41753619 ATTATTTGCT
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
17 13 0.18
18 53 0.72
20 8 0.11
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.43
Consensus pattern (18 bp):
TGATTGTTACTGAATAAC
Found at i:41759195 original size:47 final size:47
Alignment explanation
Indices: 41759118--41759224 Score: 133
Period size: 47 Copynumber: 2.3 Consensus size: 47
41759108 CTGTTACCGT
* * * * * *
41759118 TACTGTTACTGTTTCAGATTCGTTCTGATGAGTTACTGTGTGTATCG
1 TACTGTTACTGTTCCAGATTCGTTCCGATGAGGTACTCTGTGTACCA
* *
41759165 TACTGTTACTGTTCCGGATTTGTTCCGATGAGGTACTCTGTGTACCA
1 TACTGTTACTGTTCCAGATTCGTTCCGATGAGGTACTCTGTGTACCA
*
41759212 TACTGCTACTGTT
1 TACTGTTACTGTT
41759225 ACTGTTACTG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (47 bp):
TACTGTTACTGTTCCAGATTCGTTCCGATGAGGTACTCTGTGTACCA
Found at i:41759227 original size:6 final size:6
Alignment explanation
Indices: 41759212--41759242 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
41759202 CTGTGTACCA
*
41759212 TACTGC TACTGT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT T
41759243 CCGGCTTCAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:41759486 original size:18 final size:18
Alignment explanation
Indices: 41759434--41759539 Score: 81
Period size: 18 Copynumber: 5.9 Consensus size: 18
41759424 AACTGATCAG
* *
41759434 TTGATTGATACTGAGTAA
1 TTGATTGTTACTGAATAA
* *
41759452 CTT-ATTATTATTGAATAA
1 -TTGATTGTTACTGAATAA
41759470 TTGATTGTTACTGAATAA
1 TTGATTGTTACTGAATAA
* *
41759488 CTGACTGTTACTGAATAA
1 TTGATTGTTACTGAATAA
* * * *
41759506 ATAATTGTT-CTGATTGA
1 TTGATTGTTACTGAATAA
* *
41759523 CTGATTGTTAATGAATA
1 TTGATTGTTACTGAATA
41759540 TTACTGATTG
Statistics
Matches: 67, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
17 15 0.22
18 50 0.75
19 2 0.03
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (18 bp):
TTGATTGTTACTGAATAA
Found at i:41759503 original size:36 final size:36
Alignment explanation
Indices: 41759434--41759539 Score: 106
Period size: 36 Copynumber: 3.0 Consensus size: 36
41759424 AACTGATCAG
* * * * *
41759434 TTGATTGATACTGAGTAACTTATTATTATTGAATAA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
* *
41759470 TTGATTGTTACTGAATAACTGACTGTTACTGAATAA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
* * * *
41759506 ATAATTGTT-CTGATTGACTGATTGTTAATGAATA
1 TTGATTGTTACTGAATAACTGATTGTTAATGAATA
41759540 TTACTGATTG
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
35 21 0.36
36 37 0.64
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (36 bp):
TTGATTGTTACTGAATAACTGATTGTTAATGAATAA
Found at i:41759538 original size:35 final size:36
Alignment explanation
Indices: 41759463--41759539 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 36
41759453 TTATTATTAT
* * *
41759463 TGAATAATTGATTGTTACTGAATAACTGACTGTTAC
1 TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
* * *
41759499 TGAATAAATAATTGTT-CTGATTGACTGATTGTTAA
1 TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
41759534 TGAATA
1 TGAATA
41759540 TTACTGATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
35 21 0.60
36 14 0.40
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (36 bp):
TGAATAAATAATTGTTACTGAATAACTGACTGTTAA
Found at i:41772138 original size:32 final size:32
Alignment explanation
Indices: 41772093--41772157 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
41772083 CTTGGGTCAC
* *
41772093 AACCCATAATAGAATCAATTGAGCCT-AGCCCA
1 AACCAATAATAGAA-CAAATGAGCCTAAGCCCA
*
41772125 AACCAATAATAGAACAAATGGGCCTAAGCCCA
1 AACCAATAATAGAACAAATGAGCCTAAGCCCA
41772157 A
1 A
41772158 TACAGTGACA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 9 0.31
32 20 0.69
ACGTcount: A:0.45, C:0.26, G:0.14, T:0.15
Consensus pattern (32 bp):
AACCAATAATAGAACAAATGAGCCTAAGCCCA
Found at i:41772916 original size:27 final size:27
Alignment explanation
Indices: 41772886--41772973 Score: 81
Period size: 27 Copynumber: 3.3 Consensus size: 27
41772876 CAAAATAGTC
41772886 ATTTTACCCTATAAGGGTATTTCAGTA
1 ATTTTACCCTATAAGGGTATTTCAGTA
* * *
41772913 ATTTTACACTACAATGGTATTTC-GATA
1 ATTTTACCCTATAAGGGTATTTCAG-TA
** **
41772940 ATTTTA-CAAATTGGGGGTATTTCAGTA
1 ATTTTACCCTA-TAAGGGTATTTCAGTA
41772967 ATTTTAC
1 ATTTTAC
41772974 AAGTCGGGGT
Statistics
Matches: 47, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
26 2 0.04
27 44 0.94
28 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTATAAGGGTATTTCAGTA
Found at i:41772974 original size:27 final size:27
Alignment explanation
Indices: 41772928--41773082 Score: 143
Period size: 27 Copynumber: 5.8 Consensus size: 27
41772918 ACACTACAAT
41772928 GGTATTTC-GATAATTTTACAAATTGGG
1 GGTATTTCAG-TAATTTTACAAATTGGG
* *
41772955 GGTATTTCAGTAATTTTAC-AAGTCGG
1 GGTATTTCAGTAATTTTACAAATTGGG
** * * *
41772981 GGTATTTTGGTAGTTTCACAAATTGAG
1 GGTATTTCAGTAATTTTACAAATTGGG
* * *
41773008 GATATTTCAATAATTTTACAAATTAGG
1 GGTATTTCAGTAATTTTACAAATTGGG
*** *
41773035 GGTATTTCAGTAATTTTACAACCCGAG
1 GGTATTTCAGTAATTTTACAAATTGGG
* *
41773062 GGTATTTTAATAATTTTACAA
1 GGTATTTCAGTAATTTTACAA
41773083 GTCAGGGGTC
Statistics
Matches: 100, Mismatches: 26, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
26 20 0.20
27 79 0.79
28 1 0.01
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
GGTATTTCAGTAATTTTACAAATTGGG
Found at i:41773091 original size:27 final size:27
Alignment explanation
Indices: 41772900--41773091 Score: 131
Period size: 27 Copynumber: 7.1 Consensus size: 27
41772890 TACCCTATAA
* * *
41772900 GGGTATTTCAGTAATTTTAC-ACTACAA
1 GGGTATTTCAATAATTTTACAAAT-CAG
* * **
41772927 TGGTATTTCGATAATTTTACAAATTGG
1 GGGTATTTCAATAATTTTACAAATCAG
* *
41772954 GGGTATTTCAGTAATTTTACAAGTC-G
1 GGGTATTTCAATAATTTTACAAATCAG
*** * * *
41772980 GGGTATTTTGGTAGTTTCACAAAT-TG
1 GGGTATTTCAATAATTTTACAAATCAG
* *
41773006 AGGATATTTCAATAATTTTACAAATTAG
1 -GGGTATTTCAATAATTTTACAAATCAG
* * *
41773034 GGGTATTTCAGTAATTTTAC-AACCCG
1 GGGTATTTCAATAATTTTACAAATCAG
* *
41773060 AGGGTATTTTAATAATTTTACAAGTCAG
1 -GGGTATTTCAATAATTTTACAAATCAG
41773088 GGGT
1 GGGT
41773092 CTTAACGACC
Statistics
Matches: 125, Mismatches: 34, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
26 24 0.19
27 95 0.76
28 6 0.05
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (27 bp):
GGGTATTTCAATAATTTTACAAATCAG
Found at i:41782794 original size:26 final size:26
Alignment explanation
Indices: 41782758--41782822 Score: 121
Period size: 26 Copynumber: 2.5 Consensus size: 26
41782748 ATTTTTGAAT
*
41782758 CATGGGCCCACATGCCTATGTAGGCC
1 CATGCGCCCACATGCCTATGTAGGCC
41782784 CATGCGCCCACATGCCTATGTAGGCC
1 CATGCGCCCACATGCCTATGTAGGCC
41782810 CATGCGCCCACAT
1 CATGCGCCCACAT
41782823 TGGCCTTGGC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.20, C:0.38, G:0.23, T:0.18
Consensus pattern (26 bp):
CATGCGCCCACATGCCTATGTAGGCC
Found at i:41783998 original size:21 final size:21
Alignment explanation
Indices: 41783956--41783999 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41783946 GGTCTACACA
*
41783956 CCTATGTGAAGGCCACACACG
1 CCTATGTGAAGGCCACAAACG
* **
41783977 CCTATGTGGAGGGGACAAACG
1 CCTATGTGAAGGCCACAAACG
41783998 CC
1 CC
41784000 CGTGTGAGTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.14
Consensus pattern (21 bp):
CCTATGTGAAGGCCACAAACG
Found at i:41788954 original size:15 final size:16
Alignment explanation
Indices: 41788920--41788959 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
41788910 TATATATTCT
41788920 TTTTATTTTAAATTAG
1 TTTTATTTTAAATTAG
*
41788936 TTTTATTTTAATTTA-
1 TTTTATTTTAAATTAG
*
41788951 TTTTCTTTT
1 TTTTATTTT
41788960 CCCAAATCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTATTTTAAATTAG
Found at i:41795008 original size:40 final size:40
Alignment explanation
Indices: 41794942--41795092 Score: 173
Period size: 40 Copynumber: 3.8 Consensus size: 40
41794932 AAATTGAATG
* * *
41794942 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41794981 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41795021 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
41795061 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
41795093 ACTTGATTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 16 0.17
40 77 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41795106 original size:40 final size:40
Alignment explanation
Indices: 41794978--41795108 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
41794968 TATGCTGGAA
* * * *
41794978 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
* *
41795018 GTTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
41795058 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
41795098 ATTATATCCGG
1 ATTATATCCGG
41795109 TTATATTCCG
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.95
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:41802189 original size:40 final size:40
Alignment explanation
Indices: 41802123--41802273 Score: 173
Period size: 40 Copynumber: 3.8 Consensus size: 40
41802113 AAATTGAATG
* * *
41802123 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41802162 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41802202 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
41802242 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
41802274 ACTTGATTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 16 0.17
40 77 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41802287 original size:40 final size:40
Alignment explanation
Indices: 41802159--41802289 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
41802149 TATGCTGGAA
* * * *
41802159 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
* *
41802199 GTTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
41802239 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
41802279 ATTATATCCGG
1 ATTATATCCGG
41802290 TTATATTCGA
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.95
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:41804683 original size:40 final size:40
Alignment explanation
Indices: 41804623--41804840 Score: 291
Period size: 40 Copynumber: 5.5 Consensus size: 40
41804613 CGGATGATAA
* * *
41804623 CCGGGCTAAGTTCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-T
*
41804663 CCGGGCTAAG-CCCAATAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGA-AGGCATTTGTGCGAGTTACTATAT
41804703 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
41804743 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
41804783 CCGGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
** *
41804823 -CTAGCTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
41804841 TACTTGGTTT
Statistics
Matches: 161, Mismatches: 13, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
39 20 0.12
40 136 0.84
41 5 0.03
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:41806300 original size:28 final size:27
Alignment explanation
Indices: 41806247--41806310 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 27
41806237 AAATTAACCC
*
41806247 TAGGGGTATAAGGTCATTTTGCATACA
1 TAGGGGTATAAGGTAATTTTGCATACA
41806274 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAA-GGTAATTTTGCATACA
41806302 TAGGGGTAT
1 TAGGGGTAT
41806311 TCTAGTACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 11 0.31
28 24 0.69
ACGTcount: A:0.30, C:0.08, G:0.28, T:0.34
Consensus pattern (27 bp):
TAGGGGTATAAGGTAATTTTGCATACA
Found at i:41816186 original size:28 final size:28
Alignment explanation
Indices: 41816146--41816210 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
41816136 ATGTACTAGA
*
41816146 ATACCCCTATGTATGCAAAATTACCAT-T
1 ATACCCCTATGTATGCAAAATGACC-TCT
41816174 ATACCCCTATGTATGCAAAATGACCTCT
1 ATACCCCTATGTATGCAAAATGACCTCT
41816202 ATACCCCTA
1 ATACCCCTA
41816211 GGGTTAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 1 0.03
28 34 0.97
ACGTcount: A:0.34, C:0.29, G:0.08, T:0.29
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCTCT
Found at i:41816357 original size:28 final size:28
Alignment explanation
Indices: 41816316--41816406 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
41816306 AGGAAGCGTC
**
41816316 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCCCTGCCACAAATTATCTGTT
41816344 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCCCTGCCACAAATTATCTGTT
* * *
41816372 CTGGTGGCGCTGCTACAAAATATCTGTAT
1 CTGGTGGCCCTGCCACAAATTATCTGT-T
41816401 CTGGTG
1 CTGGTG
41816407 ACTCTGTCAC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 50 0.88
29 7 0.12
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (28 bp):
CTGGTGGCCCTGCCACAAATTATCTGTT
Found at i:41816431 original size:56 final size:55
Alignment explanation
Indices: 41816316--41816431 Score: 126
Period size: 56 Copynumber: 2.1 Consensus size: 55
41816306 AGGAAGCGTC
* * *
41816316 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCGATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTT
* * * * *
41816372 CTGGTGGCGCTGCTACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCGATGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-T
41816428 CTGG
1 CTGG
41816432 CAGCCATGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 8 0.16
56 28 0.56
57 14 0.28
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (55 bp):
CTGGTGGCGATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTT
Found at i:41821048 original size:3 final size:3
Alignment explanation
Indices: 41821040--41821074 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
41821030 GAGCTTTTAG
41821040 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
41821075 GATCACTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41822731 original size:3 final size:3
Alignment explanation
Indices: 41822719--41822757 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
41822709 AGCAGAGGAG
*
41822719 AGA A-A AGA AGA AGA AGA AAA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
41822758 TAAAACGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41827980 original size:28 final size:28
Alignment explanation
Indices: 41827946--41828010 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
41827936 TCAGTGTACG
* *
41827946 AAATATTGAGAATGGCACTTAATGTGCG
1 AAATATTGAGAATGACACTTAATGTGCA
* *
41827974 AGATATTGAGAATGACACTTAGTGTGCA
1 AAATATTGAGAATGACACTTAATGTGCA
41828002 AAATATTGA
1 AAATATTGA
41828011 ATGATTAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.29
Consensus pattern (28 bp):
AAATATTGAGAATGACACTTAATGTGCA
Found at i:41828127 original size:39 final size:39
Alignment explanation
Indices: 41828083--41828304 Score: 322
Period size: 39 Copynumber: 5.7 Consensus size: 39
41828073 GACTTTATAA
*
41828083 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGT
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
41828122 TGGTGTTATATCCGGGCTAAGTCCTGAAGGCATTCATGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
*
41828161 TGGTGTTATATCCGGGCTAAGT-CCAAAGGCATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
41828199 TGGTGTTATATCCGGGCTAAGCCCCGAAGGTATTCGTGC
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
* *
41828238 TGGTGTTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGC
1 TGGTGTTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGC
*
41828277 TGGTATTATATCCGGGCTTAAAGTCCCG
1 TGGTGTTATATCCGGGC-T-AAGTCCCG
41828305 TATGCTTTGT
Statistics
Matches: 166, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
38 34 0.20
39 112 0.67
40 20 0.12
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.30
Consensus pattern (39 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGC
Found at i:41828211 original size:77 final size:78
Alignment explanation
Indices: 41828083--41828294 Score: 320
Period size: 77 Copynumber: 2.7 Consensus size: 78
41828073 GACTTTATAA
* * *
41828083 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCTG
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGCCCCG
41828148 AAGGCATTCATGC
66 AAGGCATTCATGC
*
41828161 TGGTGTTATATCCGGGCTAAGT-CCAAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGCCCCG
1 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGCCCCG
* *
41828225 AAGGTATTCGTGC
66 AAGGCATTCATGC
* * *
41828238 TGGTGTTATATCCGGGCTAAAGTCCCGCAGGC-TTTGTGCTGGTATTATATCCGGGCT
1 TGGTGTTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCT
41828295 TAAAGTCCCG
Statistics
Matches: 122, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
77 67 0.55
78 49 0.40
79 6 0.05
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (78 bp):
TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGCCCCG
AAGGCATTCATGC
Found at i:41828287 original size:116 final size:116
Alignment explanation
Indices: 41828083--41828294 Score: 336
Period size: 116 Copynumber: 1.8 Consensus size: 116
41828073 GACTTTATAA
* * *
41828083 TGGTGTTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTGTTATATCCGGGCTAAGTCCTG
1 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCG
*
41828148 AAGGCATTCATGCTGGTGTTATATCCGGGCTAAGTCCAAAGGCATTCGTGC
66 AAGGCATTCATGCTGGTATTATATCCGGGCTAAGTCCAAAGGCATTCGTGC
*
41828199 TGGTGTTATATCCGGGCTAAGCCCCGAAGGTATTCGTGCTGGTGTTATATCCGGGCTAAAGTCCC
1 TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCT-AAGTCCC
* **
41828264 GCAGGC-TTTGTGCTGGTATTATATCCGGGCT
65 GAAGGCATTCATGCTGGTATTATATCCGGGCT
41828295 TAAAGTCCCG
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
116 76 0.87
117 11 0.13
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.31
Consensus pattern (116 bp):
TGGTGTTATATCCGGGCTAAGCCCCGAAGGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCG
AAGGCATTCATGCTGGTATTATATCCGGGCTAAGTCCAAAGGCATTCGTGC
Found at i:41837331 original size:9 final size:9
Alignment explanation
Indices: 41837319--41837375 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
41837309 TTAATCATTT
41837319 TATTATTAC
1 TATTATTAC
**
41837328 TATTATTTT
1 TATTATTAC
41837337 TATTATTAC
1 TATTATTAC
41837346 TATTATTAC
1 TATTATTAC
** *
41837355 TCCTATTTC
1 TATTATTAC
41837364 T-TTATTAC
1 TATTATTAC
41837372 TATT
1 TATT
41837376 CTATCTTATT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
8 6 0.16
9 32 0.84
ACGTcount: A:0.26, C:0.12, G:0.00, T:0.61
Consensus pattern (9 bp):
TATTATTAC
Found at i:41837339 original size:18 final size:18
Alignment explanation
Indices: 41837316--41837352 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41837306 ATTTTAATCA
41837316 TTTTATTATTACTATTAT
1 TTTTATTATTACTATTAT
41837334 TTTTATTATTACTATTAT
1 TTTTATTATTACTATTAT
41837352 T
1 T
41837353 ACTCCTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTATTATTACTATTAT
Found at i:41838953 original size:6 final size:6
Alignment explanation
Indices: 41838944--41838993 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
41838934 TTGCTTTCCC
* *
41838944 TTTTGT TTTTAT TTTTAT TTTTAC TTTTAT TTTTAT TTTTAT TTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
41838992 TT
1 TT
41838994 ACACATTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:41842478 original size:31 final size:31
Alignment explanation
Indices: 41842440--41842502 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
41842430 GTTTATTGAC
41842440 AATATACTAATCTATTCAAAGACAGAATTCG
1 AATATACTAATCTATTCAAAGACAGAATTCG
41842471 AATATACTAATCTATTCAAAGACAGAATTCG
1 AATATACTAATCTATTCAAAGACAGAATTCG
41842502 A
1 A
41842503 GCATGCACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.29
Consensus pattern (31 bp):
AATATACTAATCTATTCAAAGACAGAATTCG
Found at i:41846245 original size:21 final size:21
Alignment explanation
Indices: 41846219--41846385 Score: 133
Period size: 21 Copynumber: 8.0 Consensus size: 21
41846209 AGCTCTTGTG
*
41846219 TGTTCAGCTCTTACGAGCTTT
1 TGTTCAACTCTTACGAGCTTT
*
41846240 TGTTCAACTCTT-CTAAG-TTT
1 TGTTCAACTCTTAC-GAGCTTT
* * * *
41846260 CTGTTTAGCTCTTACGAACTTC
1 -TGTTCAACTCTTACGAGCTTT
* *
41846282 TGTTCAACTCTTATGAGTTTT
1 TGTTCAACTCTTACGAGCTTT
* *
41846303 TGTTTAGCTCTTACGAG-TTT
1 TGTTCAACTCTTACGAGCTTT
* *
41846323 CTGTTCAACTCTTACCAGCTTC
1 -TGTTCAACTCTTACGAGCTTT
* *
41846345 TGTTCAACTCTTATGAGTTTT
1 TGTTCAACTCTTACGAGCTTT
* * *
41846366 TGTTTAGCTCTTACCAGCTT
1 TGTTCAACTCTTACGAGCTT
41846386 CTATTCAAGT
Statistics
Matches: 111, Mismatches: 29, Indels: 12
0.73 0.19 0.08
Matches are distributed among these distances:
20 7 0.06
21 99 0.89
22 5 0.05
ACGTcount: A:0.17, C:0.22, G:0.14, T:0.46
Consensus pattern (21 bp):
TGTTCAACTCTTACGAGCTTT
Found at i:41846271 original size:42 final size:42
Alignment explanation
Indices: 41846219--41846378 Score: 169
Period size: 42 Copynumber: 3.8 Consensus size: 42
41846209 AGCTCTTGTG
* *
41846219 TGTTCAGCTCTTACGAGCTTTTGTTCAACTCTTCTAAGTTTC
1 TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTATAAGTTTC
* * * *
41846261 TGTTTAGCTCTTACGAACTTCTGTTCAACTCTTATGAGTTTT
1 TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTATAAGTTTC
** *
41846303 TGTTTAGCTCTTACGAG-TTTCTGTTCAACTCTTACCAGCTTC
1 TGTTTAGCTCTTACGAGCTTT-TGTTCAACTCTTATAAGTTTC
* * * * * *
41846345 TGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTA
1 TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTA
41846379 CCAGCTTCTA
Statistics
Matches: 99, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
41 2 0.02
42 94 0.95
43 3 0.03
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.47
Consensus pattern (42 bp):
TGTTTAGCTCTTACGAGCTTTTGTTCAACTCTTATAAGTTTC
Found at i:41846304 original size:63 final size:63
Alignment explanation
Indices: 41846219--41846393 Score: 199
Period size: 63 Copynumber: 2.8 Consensus size: 63
41846209 AGCTCTTGTG
* * * * * *
41846219 TGTTCAGCTCTTACGAGCTTTTGTTCAACTCTT-CTAAGTTTCTGTTTAGCTCTTACGAACTTC
1 TGTTCAACTCTTATGAGTTTTTGTTCAACTCTTAC-AAGTTTCTGTTCAACTCTTACCAACTTC
* * * *
41846282 TGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACGAGTTTCTGTTCAACTCTTACCAGCTTC
1 TGTTCAACTCTTATGAGTTTTTGTTCAACTCTTACAAGTTTCTGTTCAACTCTTACCAACTTC
* * * * *
41846345 TGTTCAACTCTTATGAGTTTTTGTTTAGCTCTTACCAGCTTCTATTCAA
1 TGTTCAACTCTTATGAGTTTTTGTTCAACTCTTACAAGTTTCTGTTCAA
41846394 GTTTGAAGCT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
63 97 0.99
64 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.14, T:0.46
Consensus pattern (63 bp):
TGTTCAACTCTTATGAGTTTTTGTTCAACTCTTACAAGTTTCTGTTCAACTCTTACCAACTTC
Found at i:41856820 original size:24 final size:24
Alignment explanation
Indices: 41856788--41856836 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
41856778 GTTTATTAAG
*
41856788 GAAAATTGGAAGATTTACTAAGGT
1 GAAAATTGGAAGATTCACTAAGGT
41856812 GAAAATTGGAAGATTCACTAAGGT
1 GAAAATTGGAAGATTCACTAAGGT
41856836 G
1 G
41856837 TTGCGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (24 bp):
GAAAATTGGAAGATTCACTAAGGT
Found at i:41861231 original size:17 final size:18
Alignment explanation
Indices: 41861209--41861243 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41861199 GATATGATAC
*
41861209 TAAAAT-TATTAAAAAAT
1 TAAAATATATAAAAAAAT
41861226 TAAAATATATAAAAAAAT
1 TAAAATATATAAAAAAAT
41861244 CAGGGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAATATATAAAAAAAT
Found at i:41861531 original size:22 final size:21
Alignment explanation
Indices: 41861496--41861553 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
41861486 TAAAGGTATC
* *
41861496 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
*
41861517 TACAAAATCATATCTTTTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
41861540 TGCATATCATATCT
1 TACAAATCATATCT
41861554 AAGATTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:41861611 original size:36 final size:36
Alignment explanation
Indices: 41861525--41861612 Score: 126
Period size: 36 Copynumber: 2.4 Consensus size: 36
41861515 ATTACAAAAT
*
41861525 CATATCTTTTAAGATTGCATATCATATCTAAGATTG
1 CATATCATTTAAGATTGCATATCATATCTAAGATTG
41861561 --TATCATATCTAAGATTGCATATCATATCTAAGATTG
1 CATATCAT-T-TAAGATTGCATATCATATCTAAGATTG
*
41861597 CATATCATTGAAGATT
1 CATATCATTTAAGATT
41861613 ATATTTCATA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
34 5 0.11
35 1 0.02
36 33 0.72
37 1 0.02
38 6 0.13
ACGTcount: A:0.35, C:0.14, G:0.11, T:0.40
Consensus pattern (36 bp):
CATATCATTTAAGATTGCATATCATATCTAAGATTG
Found at i:41861612 original size:17 final size:19
Alignment explanation
Indices: 41861534--41861604 Score: 128
Period size: 19 Copynumber: 3.8 Consensus size: 19
41861524 TCATATCTTT
41861534 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
41861553 TAAGATTG--TATCATATC
1 TAAGATTGCATATCATATC
41861570 TAAGATTGCATATCATATC
1 TAAGATTGCATATCATATC
41861589 TAAGATTGCATATCAT
1 TAAGATTGCATATCAT
41861605 TGAAGATTAT
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.34
19 33 0.66
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.38
Consensus pattern (19 bp):
TAAGATTGCATATCATATC
Found at i:41861622 original size:36 final size:36
Alignment explanation
Indices: 41861535--41861623 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
41861525 CATATCTTTT
* *
41861535 AAGATTGCATATCATATCTAAGATTGTATCATATCT
1 AAGATTACATATCATATCTAAGATTGTATCATATCG
*
41861571 AAGATTGCATATCATATCTAAGATTGCATATCAT-T-G
1 AAGATTACATATCATATCTAAGATTG--TATCATATCG
* *
41861607 AAGATTATATTTCATAT
1 AAGATTACATATCATAT
41861624 GAGTCAAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 40 0.85
37 1 0.02
38 6 0.13
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (36 bp):
AAGATTACATATCATATCTAAGATTGTATCATATCG
Found at i:41862005 original size:45 final size:45
Alignment explanation
Indices: 41861937--41862087 Score: 166
Period size: 44 Copynumber: 3.4 Consensus size: 45
41861927 GGAAGGCGAT
* *
41861937 ATCTGCTATCTTTGATC-AGCTCCCCATCTAATACAAAGACGCAAA
1 ATCTGCTATCTTTGATCTA-CTCCCCGTCTAATACAAAGACGCCAA
* * *
41861982 ATCTGTTATCTTCGATCTTCT-CCCGTCTAATACAAAGACGCCAA
1 ATCTGCTATCTTTGATCTACTCCCCGTCTAATACAAAGACGCCAA
* * * *
41862026 ATCTGCT-TCTTTAATCTACTCCCTGTCTAATACAGAGATGCCAA
1 ATCTGCTATCTTTGATCTACTCCCCGTCTAATACAAAGACGCCAA
*
41862070 ATCTG-TCATCTTGGATCT
1 ATCTGCT-ATCTTTGATCT
41862088 GCTTCAATGT
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
43 11 0.12
44 52 0.59
45 25 0.28
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (45 bp):
ATCTGCTATCTTTGATCTACTCCCCGTCTAATACAAAGACGCCAA
Found at i:41862236 original size:78 final size:78
Alignment explanation
Indices: 41862107--41862320 Score: 329
Period size: 78 Copynumber: 2.7 Consensus size: 78
41862097 TAAACACATG
41862107 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
41862172 ATCTGCTTCAATA
66 ATCTGCTTCAATA
* * *
41862185 AAGGTCAGATCTACTGTGTCTTCAATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
*
41862250 ATCTGCTTCAATG
66 ATCTGCTTCAATA
* * * * ** *
41862263 AAGGTTAGATCTGCTATGTCTTCGATCTACTCTCCGTCGAATATGGAGATGTCAAATC
1 AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATC
41862321 TGTTTCTTCG
Statistics
Matches: 122, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 122 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (78 bp):
AAGGTCAGATCTGCTATGTCTTCGATCTGCTCCCCGTCTAATACAGAGATGCCAAATCATCTTGG
ATCTGCTTCAATA
Found at i:41867959 original size:40 final size:40
Alignment explanation
Indices: 41867915--41868099 Score: 289
Period size: 40 Copynumber: 4.6 Consensus size: 40
41867905 CTCGCTTAAC
*
41867915 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAT
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
*
41867955 TGCCTTCGGGACTTAGCCCGGTTATGGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
** *
41867995 TGCCTTCGGGACTTAGCCCGGACATAGTTACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
*** *
41868035 TGCCTTCGGGACTTAGCCCGAACATACTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
41868075 TGCCTTCGGGACTTAGCCCGGTTAT
1 TGCCTTCGGGACTTAGCCCGGTTAT
41868100 CATCCGAATA
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 133 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
Found at i:41877005 original size:28 final size:28
Alignment explanation
Indices: 41876973--41877071 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
41876963 GCAATAAGCC
*
41876973 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
41877001 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
41877029 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
41877058 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41877072 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:41884684 original size:28 final size:28
Alignment explanation
Indices: 41884652--41884750 Score: 112
Period size: 28 Copynumber: 3.5 Consensus size: 28
41884642 GCAATAAGCC
*
41884652 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
41884680 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* * *
41884708 TGCACACTTAGTGCTGT-ATAATTTGAACC
1 CGCACACTTAGTGCT-TAATAA-TCGAACT
41884737 CGCACACTTAGTGC
1 CGCACACTTAGTGC
41884751 CAATTTGTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
27 2 0.03
28 40 0.67
29 17 0.28
30 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:41891672 original size:28 final size:28
Alignment explanation
Indices: 41891633--41891723 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
41891623 TGTGACAGAT
* *
41891633 CACCAGATACAGATATTTTGTGGCAGCGC
1 CACCAGA-ACAGATAATTTGTGGCAGAGC
* *
41891662 CACCAGAACAGATAATTTATGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGAGC
*
41891690 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAGAGC
41891718 CACCAG
1 CACCAG
41891724 GACGCTTCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
28 49 0.88
29 7 0.12
ACGTcount: A:0.33, C:0.24, G:0.23, T:0.20
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGAGC
Found at i:41891876 original size:28 final size:28
Alignment explanation
Indices: 41891832--41891893 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
41891822 TTAACCCTAA
*
41891832 GGGTATAGAGGTCATTTTGCATACATAG
1 GGGTATAGAGGTAATTTTGCATACATAG
41891860 GGGTATA-ATGGTAATTTTGCATACATAG
1 GGGTATAGA-GGTAATTTTGCATACATAG
41891888 GGGTAT
1 GGGTAT
41891894 TCTAGTACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.03
28 31 0.97
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (28 bp):
GGGTATAGAGGTAATTTTGCATACATAG
Found at i:41893190 original size:24 final size:24
Alignment explanation
Indices: 41893163--41893209 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
41893153 CTAGATTTCC
**
41893163 TCCCTTATTTGCTCCTAAATCCTA
1 TCCCTTATCAGCTCCTAAATCCTA
41893187 TCCCTTATCAGCTCCTAAATCCT
1 TCCCTTATCAGCTCCTAAATCCT
41893210 TTACTTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.21, C:0.36, G:0.04, T:0.38
Consensus pattern (24 bp):
TCCCTTATCAGCTCCTAAATCCTA
Found at i:41902479 original size:9 final size:9
Alignment explanation
Indices: 41902465--41902491 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
41902455 TTTGATTTTA
41902465 GTTAAATTG
1 GTTAAATTG
41902474 GTTAAATTG
1 GTTAAATTG
41902483 GTTAAATTG
1 GTTAAATTG
41902492 CAAGTTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (9 bp):
GTTAAATTG
Found at i:41902792 original size:29 final size:29
Alignment explanation
Indices: 41902750--41902809 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41902740 TATAGAATTA
41902750 TTCATATATATACATAATGTTATTGCTGC
1 TTCATATATATACATAATGTTATTGCTGC
41902779 TTCATATATATACATAATGTTATTGCTGC
1 TTCATATATATACATAATGTTATTGCTGC
41902808 TT
1 TT
41902810 TATGAATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.10, T:0.47
Consensus pattern (29 bp):
TTCATATATATACATAATGTTATTGCTGC
Found at i:41903211 original size:20 final size:20
Alignment explanation
Indices: 41903097--41903211 Score: 88
Period size: 20 Copynumber: 5.8 Consensus size: 20
41903087 TTGTACAGGA
* **
41903097 TTTGCACTTTGGTGCCTTTG
1 TTTGCACTTCGGTGCCCCTG
41903117 TTTGCACTTCGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
* * * * * *
41903137 TATACACTTTGGTGTCCTTA
1 TTTGCACTTCGGTGCCCCTG
** *
41903157 TTCACACTACGGTGCCCCTG
1 TTTGCACTTCGGTGCCCCTG
*
41903177 TTTGCACATT-TGTGCCCCTG
1 TTTGCAC-TTCGGTGCCCCTG
*
41903197 TCTGCACTTCGGTGC
1 TTTGCACTTCGGTGC
41903212 TCTTGTTATA
Statistics
Matches: 71, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
19 2 0.03
20 68 0.96
21 1 0.01
ACGTcount: A:0.10, C:0.30, G:0.22, T:0.38
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCCCTG
Found at i:41917434 original size:42 final size:42
Alignment explanation
Indices: 41917387--41917535 Score: 271
Period size: 42 Copynumber: 3.5 Consensus size: 42
41917377 TATTGGTCTC
41917387 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
41917429 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
* *
41917471 GGCACTAAGTGTGCAGGTATAAATGGACACGGTGACAAGATC
1 GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
*
41917513 GGCACTAAGTGTGCGGGTTTAAA
1 GGCACTAAGTGTGCGGGTATAAA
41917536 ATTTGTACAG
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 103 1.00
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (42 bp):
GGCACTAAGTGTGCGGGTATAAATGGACACGGTGACAAGATT
Found at i:41917601 original size:27 final size:28
Alignment explanation
Indices: 41917544--41917613 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
41917534 AAATTTGTAC
**
41917544 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
*
41917572 AGCACTATGTGTGCG-AGCTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
41917599 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
41917614 GACTCACTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 24 0.63
28 14 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:41922806 original size:22 final size:22
Alignment explanation
Indices: 41922749--41922792 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41922739 GACTAAATTG
41922749 CAATAGGTGCAAAACTTGAGTT
1 CAATAGGTGCAAAACTTGAGTT
41922771 CAATAGGTGCAAAACTTGAGTT
1 CAATAGGTGCAAAACTTGAGTT
41922793 TTATAGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (22 bp):
CAATAGGTGCAAAACTTGAGTT
Found at i:41923793 original size:29 final size:31
Alignment explanation
Indices: 41923744--41923818 Score: 106
Period size: 29 Copynumber: 2.6 Consensus size: 31
41923734 AGCTTCAGCT
41923744 ATCG-ATTATGG-AAAGGAATGGTGACGACC
1 ATCGAATTATGGAAAAGGAATGGTGACGACC
41923773 ATC-AATTATGGAAAAGG-ATGGTGACGACC
1 ATCGAATTATGGAAAAGGAATGGTGACGACC
*
41923802 GTCGAATTAT-GAAAAGG
1 ATCGAATTATGGAAAAGG
41923819 GATAGCCTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
29 31 0.74
30 11 0.26
ACGTcount: A:0.37, C:0.12, G:0.29, T:0.21
Consensus pattern (31 bp):
ATCGAATTATGGAAAAGGAATGGTGACGACC
Found at i:41927912 original size:13 final size:13
Alignment explanation
Indices: 41927894--41927933 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
41927884 GGAGCAATCG
41927894 CACACGGGCGTGT
1 CACACGGGCGTGT
*
41927907 CACACGGGCATGT
1 CACACGGGCGTGT
*
41927920 CACATGGGCGTGT
1 CACACGGGCGTGT
41927933 C
1 C
41927934 CCTGTCAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.17
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:41929733 original size:18 final size:17
Alignment explanation
Indices: 41929710--41929743 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
41929700 TTTTGAATTT
41929710 TATTATTTATTTAATATA
1 TATTA-TTATTTAATATA
*
41929728 TATTATTATTTTATAT
1 TATTATTATTTAATAT
41929744 TAAAATTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATTATTTAATATA
Found at i:41934772 original size:46 final size:46
Alignment explanation
Indices: 41934722--41934896 Score: 230
Period size: 46 Copynumber: 3.8 Consensus size: 46
41934712 TATTTGGGCA
41934722 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
41934768 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG--CGA-GCG
*
41934814 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
41934860 CCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
41934897 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
43 4 0.04
45 4 0.04
46 95 0.86
47 4 0.04
49 4 0.04
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:41934875 original size:92 final size:92
Alignment explanation
Indices: 41934718--41934888 Score: 306
Period size: 92 Copynumber: 1.9 Consensus size: 92
41934708 TGGATATTTG
* *
41934718 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
41934783 TTGAGTCCGAGTTCGTGAGATGTACTA
66 TTGAGTCCGAGTTCGTGAGATGTACTA
*
41934810 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
41934875 TTGAGTCTGAGTTC
66 TTGAGTCCGAGTTC
41934889 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (92 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTACTA
Found at i:41940888 original size:40 final size:40
Alignment explanation
Indices: 41940822--41940988 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
41940812 AAATTGAATG
* * *
41940822 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41940861 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41940901 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
41940941 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
41940981 ATATCCGG
1 ATATCCGG
41940989 TTATATTCCG
Statistics
Matches: 107, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
39 16 0.15
40 89 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41948082 original size:40 final size:40
Alignment explanation
Indices: 41948016--41948166 Score: 173
Period size: 40 Copynumber: 3.8 Consensus size: 40
41948006 AAATTGAATG
* * *
41948016 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
41948055 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
41948095 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* *
41948135 CTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGC
41948167 ACTTGATTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
39 16 0.17
40 77 0.81
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:41948180 original size:40 final size:40
Alignment explanation
Indices: 41948052--41948182 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
41948042 TATGCTGGAA
* * * *
41948052 ATTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
* *
41948092 GTTATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTT-
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
*
41948132 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACTTG
1 ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-TTG
41948172 ATTATATCCGG
1 ATTATATCCGG
41948183 TTATATTCCG
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.95
41 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGATTG
Found at i:41957735 original size:19 final size:17
Alignment explanation
Indices: 41957711--41957745 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
41957701 AATACTCAAA
41957711 TATTTATTATGGTATGAGG
1 TATTTATT-TGGT-TGAGG
41957730 TATTTATTTGGTTGAG
1 TATTTATTTGGTTGAG
41957746 ATATGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (17 bp):
TATTTATTTGGTTGAGG
Found at i:41959436 original size:30 final size:29
Alignment explanation
Indices: 41959385--41959475 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 29
41959375 AGTTTATTTA
*
41959385 AATGTGTACAATTGAATCAAAATCAAAGTTT
1 AATGTATAC-ATTGAA-CAAAATCAAAGTTT
* *
41959416 TATGTATACATTTGAACAAAAACCAAAGTTT
1 AATGTATACA-TTGAAC-AAAATCAAAGTTT
*
41959447 AATGTGCATA-ATTGCACAAAATCAAAGTT
1 AATGT--ATACATTGAACAAAATCAAAGTT
41959476 CATGTATCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
30 13 0.26
31 33 0.66
32 1 0.02
33 3 0.06
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (29 bp):
AATGTATACATTGAACAAAATCAAAGTTT
Found at i:41959817 original size:23 final size:22
Alignment explanation
Indices: 41959785--41959839 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
41959775 ACCAATCCAA
*
41959785 TTCAACATATTT-TCAAGATAGA-
1 TTCATCATATTTAT-AAGATA-AC
41959807 TTCATGCATATTTATAAGATAAC
1 TTCAT-CATATTTATAAGATAAC
41959830 TTCATCATAT
1 TTCATCATAT
41959840 ACCAAAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 10 0.34
23 18 0.62
24 1 0.03
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.40
Consensus pattern (22 bp):
TTCATCATATTTATAAGATAAC
Found at i:41963514 original size:28 final size:28
Alignment explanation
Indices: 41963457--41963512 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
41963447 CAAACGAACT
41963457 ATTTTTTAAAATTATAAAAAATAATTTTA
1 ATTTTTTAAAATTATAAAAAATAA-TTTA
* *
41963486 ATTTTTATAAATTTATAAAATATAATT
1 ATTTTT-TAAAATTATAAAAAATAATT
41963513 AAAAATTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (28 bp):
ATTTTTTAAAATTATAAAAAATAATTTA
Found at i:41967920 original size:17 final size:19
Alignment explanation
Indices: 41967898--41967935 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
41967888 AAGGGAGAAT
41967898 AAAG-AAATG-GAAAAAAA
1 AAAGAAAATGAGAAAAAAA
41967915 AAAGAAAATGATGAAAAAAA
1 AAAGAAAATGA-GAAAAAAA
41967935 A
1 A
41967936 TGTGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
20 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAGAAAATGAGAAAAAAA
Found at i:41969274 original size:29 final size:29
Alignment explanation
Indices: 41969242--41969344 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
41969232 GTGACGAGAT
* *
41969242 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
41969271 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
41969300 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
41969329 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41969345 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:41975990 original size:17 final size:19
Alignment explanation
Indices: 41975968--41976005 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
41975958 AAGGGAGAAT
41975968 AAAG-AAATG-GAAAAAAA
1 AAAGAAAATGAGAAAAAAA
41975985 AAAGAAAATGATGAAAAAAA
1 AAAGAAAATGA-GAAAAAAA
41976005 A
1 A
41976006 TGTGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
20 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (19 bp):
AAAGAAAATGAGAAAAAAA
Found at i:41977345 original size:29 final size:29
Alignment explanation
Indices: 41977313--41977415 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
41977303 GTGACGAGAT
* *
41977313 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
41977342 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
41977371 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
41977400 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41977416 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:41984058 original size:18 final size:20
Alignment explanation
Indices: 41984035--41984073 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
41984025 AAGGGAGAAT
41984035 AAAG-AAATG-GAAAAAAAA
1 AAAGAAAATGAGAAAAAAAA
41984053 AAAGAAAATGATGAAAAAAAA
1 AAAGAAAATGA-GAAAAAAAA
41984074 TGTGTGTGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 5 0.28
21 9 0.50
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (20 bp):
AAAGAAAATGAGAAAAAAAA
Found at i:41985409 original size:29 final size:29
Alignment explanation
Indices: 41985377--41985479 Score: 118
Period size: 29 Copynumber: 3.6 Consensus size: 29
41985367 GTGACGAGAT
* *
41985377 TGGCACTGAGTGTGCGAGCTTGAAATGTA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
41985406 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTTGAAATATA
* * *
41985435 TGGCACTATGTGTGCGGGCTT-AAATCACA
1 TGGCACTAAGTGTGCGAGCTTGAAAT-ATA
41985464 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41985480 TGATCGAGTA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.23, C:0.17, G:0.32, T:0.28
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGCTTGAAATATA
Found at i:41997487 original size:25 final size:25
Alignment explanation
Indices: 41997457--41997509 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 25
41997447 TTAAAAAAAG
41997457 TATGAATTTATCATAAGT-ATTTTCT
1 TATGAATTTATCATAA-TCATTTTCT
41997482 TATGAATTTATCATAATCATTTTCT
1 TATGAATTTATCATAATCATTTTCT
41997507 TAT
1 TAT
41997510 AGCACTAGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 1 0.04
25 26 0.96
ACGTcount: A:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (25 bp):
TATGAATTTATCATAATCATTTTCT
Found at i:42017470 original size:3 final size:3
Alignment explanation
Indices: 42017464--42017533 Score: 53
Period size: 3 Copynumber: 24.7 Consensus size: 3
42017454 TTATTAATCG
* *
42017464 TAT TAT TAC TAT TAT T-T CT-T TAT TTT TAT T-T TA- TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
42017505 TA- CAT TAT TAGT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA
42017534 GTTTTAGCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
2 9 0.17
3 42 0.78
4 3 0.06
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:42024452 original size:30 final size:30
Alignment explanation
Indices: 42024416--42024476 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
42024406 TTTAACCTCT
42024416 ATACATAGATTGTATTCTACACAATCTACC
1 ATACATAGATTGTATTCTACACAATCTACC
42024446 ATACATAGATTGTATTCTACACAATCTACC
1 ATACATAGATTGTATTCTACACAATCTACC
42024476 A
1 A
42024477 CAAAATCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (30 bp):
ATACATAGATTGTATTCTACACAATCTACC
Found at i:42031656 original size:36 final size:36
Alignment explanation
Indices: 42031540--42031655 Score: 144
Period size: 36 Copynumber: 3.2 Consensus size: 36
42031530 TCCAAAAAAC
* *
42031540 ACACACCAGATGCTCATAAGAGCTAATACATCCAAA
1 ACACACCAGATGCTCATAAGAGCTAATCCATCCGAA
* * *
42031576 ACACACTAGATGCTTATAAGAGCTAATCCATCTGAA
1 ACACACCAGATGCTCATAAGAGCTAATCCATCCGAA
* * *
42031612 ACACACCA-ATAGCTCAAAAGAGCTAGTCCAACCGAA
1 ACACACCAGAT-GCTCATAAGAGCTAATCCATCCGAA
42031648 ACACACCA
1 ACACACCA
42031656 AAACAGAGAG
Statistics
Matches: 68, Mismatches: 11, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
35 2 0.03
36 66 0.97
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.16
Consensus pattern (36 bp):
ACACACCAGATGCTCATAAGAGCTAATCCATCCGAA
Found at i:42037616 original size:40 final size:40
Alignment explanation
Indices: 42037571--42037737 Score: 158
Period size: 40 Copynumber: 4.2 Consensus size: 40
42037561 CGGAATATAA
*
42037571 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42037611 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42037651 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * ** *
42037691 CCGGATATAATTTCCAGCATAGTTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42037730 CCGGATAT
1 CCGGATAT
42037738 CATTCAATTT
Statistics
Matches: 103, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
39 14 0.14
40 89 0.86
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42045633 original size:40 final size:40
Alignment explanation
Indices: 42045588--42045754 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
42045578 CGGAATATAA
*
42045588 CCGGATTTAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42045628 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42045668 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42045708 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42045747 CCGGATAT
1 CCGGATAT
42045755 CATTCAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
39 14 0.13
40 90 0.87
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42045738 original size:80 final size:79
Alignment explanation
Indices: 42045604--42045754 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
42045594 TTAATCACGT
*
42045604 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
42045669 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
42045684 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
42045747 CCGGATAT
64 CCGGATAT
42045755 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:42049779 original size:43 final size:42
Alignment explanation
Indices: 42049688--42049782 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 42
42049678 TGTCAAACTA
* * * *
42049688 TGTCTGGGACATTAGCATCATATTTGATTTCGTGTAAGACCC
1 TGTCTGGGACAGTAGAATCATATTTGATTACATGTAAGACCC
* *
42049730 TATCTGGGACAGTGGAATCGATATTTGATTACATGTAAGACCAC
1 TGTCTGGGACAGTAGAATC-ATATTTGATTACATGTAAGACC-C
42049774 -GTCTGGGAC
1 TGTCTGGGAC
42049783 GTTGGCATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
42 15 0.34
43 28 0.64
44 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
TGTCTGGGACAGTAGAATCATATTTGATTACATGTAAGACCC
Found at i:42051687 original size:12 final size:12
Alignment explanation
Indices: 42051653--42051688 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
42051643 TATACATCAT
42051653 ATTGACTGTTCG
1 ATTGACTGTTCG
*
42051665 ATTGAAATGTTCG
1 ATTG-ACTGTTCG
42051678 ATTGACTGTTC
1 ATTGACTGTTC
42051689 AATTTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (12 bp):
ATTGACTGTTCG
Found at i:42062468 original size:43 final size:41
Alignment explanation
Indices: 42062372--42062473 Score: 123
Period size: 43 Copynumber: 2.4 Consensus size: 41
42062362 TATGGATATG
* * *
42062372 TGATTTCATGTAAAACCATGTCTGGGAAATTGGCATTGTAT
1 TGATTTCATGTAAGACCATGTCGGGGAAATTGGCATCGTAT
* *
42062413 TGAGATTACATGTAAGACCATGTCGGGGACATTGGCATCGTTAAT
1 T--GATTTCATGTAAGACCATGTCGGGGAAATTGGCATCG-T-AT
42062458 TGATTTCATGTAAGAC
1 TGATTTCATGTAAGAC
42062474 TCTATATGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
41 1 0.02
43 46 0.90
44 1 0.02
45 3 0.06
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (41 bp):
TGATTTCATGTAAGACCATGTCGGGGAAATTGGCATCGTAT
Found at i:42064075 original size:40 final size:40
Alignment explanation
Indices: 42064031--42064215 Score: 262
Period size: 40 Copynumber: 4.6 Consensus size: 40
42064021 CTCGCTTAAC
* *
42064031 TGCCTTCGGGACTTAGCCCAGTTATAGTAACTCGCACAAT
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* *
42064071 TGCCTTCGGGACTTAGCCCGGTTATGGTAACTAGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
* ** * *
42064111 TGCCTTCGGGACTTAGCCTGGACATAGTTACTTGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
**
42064151 TGCCTTCGGGACTTAGCCCGGACATAGTAACTCGCACAAA
1 TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
*
42064191 TGCCTTCGGGACTTAGCCCAGTTAT
1 TGCCTTCGGGACTTAGCCCGGTTAT
42064216 CATCCGAATA
Statistics
Matches: 129, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 129 1.00
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAA
Found at i:42069385 original size:35 final size:35
Alignment explanation
Indices: 42069345--42069414 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
42069335 AAATTTTCAC
42069345 ACAATCATGCAATCATATCATAGACCTCAAAATAA
1 ACAATCATGCAATCATATCATAGACCTCAAAATAA
42069380 ACAATCATGCAATCATATCATAGACCTCAAAATAA
1 ACAATCATGCAATCATATCATAGACCTCAAAATAA
42069415 TCATAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.23
Consensus pattern (35 bp):
ACAATCATGCAATCATATCATAGACCTCAAAATAA
Found at i:42073202 original size:27 final size:27
Alignment explanation
Indices: 42073172--42073321 Score: 117
Period size: 27 Copynumber: 5.5 Consensus size: 27
42073162 CATAGGGGTC
*
42073172 AAACAGTCATCTTACCATAAAAGGGCA
1 AAACAGTCATTTTACCATAAAAGGGCA
** * * *
42073199 AAACAAACATTTTACCACATAAGGGAA
1 AAACAGTCATTTTACCATAAAAGGGCA
42073226 AAACAGTCATTTTACCCCAT-AAAGGGCA
1 AAACAGTCATTTTA--CCATAAAAGGGCA
* *
42073254 AAATAATCATTTTACC-TCATAAA-GGCA
1 AAACAGTCATTTTACCAT-A-AAAGGGCA
* * ** *
42073281 GAATAGTCATTTTACCCCATAAGGGCA
1 AAACAGTCATTTTACCATAAAAGGGCA
*
42073308 AAATAGTCATTTTA
1 AAACAGTCATTTTA
42073322 TCGATTATGG
Statistics
Matches: 98, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
25 1 0.01
26 4 0.04
27 69 0.70
28 21 0.21
29 3 0.03
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.25
Consensus pattern (27 bp):
AAACAGTCATTTTACCATAAAAGGGCA
Found at i:42073275 original size:55 final size:55
Alignment explanation
Indices: 42073172--42073321 Score: 189
Period size: 55 Copynumber: 2.8 Consensus size: 55
42073162 CATAGGGGTC
* * * *
42073172 AAACAGTCATCTTA--CCATAAAAGGGCAAAACAAACATTTTACCACATAAGGGAA
1 AAACAGTCATTTTACCCCAT-AAAGGGCAAAATAATCATTTTACCACATAAAGGAA
* *
42073226 AAACAGTCATTTTACCCCATAAAGGGCAAAATAATCATTTTACCTCATAAAGGCA
1 AAACAGTCATTTTACCCCATAAAGGGCAAAATAATCATTTTACCACATAAAGGAA
* * *
42073281 GAATAGTCATTTTACCCCAT-AAGGGCAAAATAGTCATTTTA
1 AAACAGTCATTTTACCCCATAAAGGGCAAAATAATCATTTTA
42073322 TCGATTATGG
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
54 33 0.39
55 48 0.56
56 4 0.05
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.25
Consensus pattern (55 bp):
AAACAGTCATTTTACCCCATAAAGGGCAAAATAATCATTTTACCACATAAAGGAA
Found at i:42080057 original size:39 final size:39
Alignment explanation
Indices: 42080014--42080183 Score: 259
Period size: 39 Copynumber: 4.3 Consensus size: 39
42080004 GGACTTTAAC
* * *
42080014 CCGGATATTTTTCCAGCACATAGCCTACGGACCTCAAGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
* * *
42080053 CCGGATATATTTCTAGCATATAGCCTGCGGATCTCATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
42080092 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTTATGT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
*
42080131 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATTT
1 CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
42080170 CCGGATATATTTTC
1 CCGGATAT-TTTTC
42080184 AATCTCATAC
Statistics
Matches: 118, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 113 0.96
40 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (39 bp):
CCGGATATTTTTCCAGCATATAGCCTGCGGACCTCATGT
Found at i:42087139 original size:40 final size:40
Alignment explanation
Indices: 42087021--42087241 Score: 269
Period size: 38 Copynumber: 5.7 Consensus size: 40
42087011 GCTACTCGTT
* *
42087021 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
* *
42087060 -AAATACCTTCGGGACTTAA-CCGGATTTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
42087098 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
42087138 CAAATGCCTTC-GGACTT-ACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * *
42087176 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
42087217 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
42087242 CATCATTCGA
Statistics
Matches: 162, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
37 2 0.01
38 63 0.39
39 29 0.18
40 57 0.35
41 11 0.07
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42087161 original size:78 final size:79
Alignment explanation
Indices: 42087021--42087241 Score: 283
Period size: 78 Copynumber: 2.8 Consensus size: 79
42087011 GCTACTCGTT
* * *
42087021 CAAATGCCTTCGGGACATAGCCC-G-TTATAGTAACTCGCA-AAATACCTTCGGGACTTAACCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTCGGGACTTACCCGG
*
42087083 ATTTAGTAACTTGCA
65 ATTTAGTAACTCGCA
*
42087098 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTC-GGACTTACCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTACCCGGA
42087162 TTTAGTAACTCGCA
66 TTTAGTAACTCGCA
* * * *
42087176 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAAATGCCTTCGGGACTTA-CCC
42087239 GGA
63 GGA
42087242 CATCATTCGA
Statistics
Matches: 127, Mismatches: 10, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
77 24 0.19
78 71 0.56
79 26 0.20
80 6 0.05
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGGACTTACCCGGA
TTTAGTAACTCGCA
Found at i:42095192 original size:39 final size:40
Alignment explanation
Indices: 42095110--42095292 Score: 218
Period size: 39 Copynumber: 4.7 Consensus size: 40
42095100 GCTACTCGTT
* *
42095110 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGACCGGATT-TAGTAACTCGCA
42095150 CAAATGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGACCGGATTTAGTAACTCGCA
42095189 CAAATGCCTT-GGGACTTA-ACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGA-CCGGATTTAGTAACTCGCA
* * * *
42095228 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGACCGGATTTAGTAAC-TCGCA
*
42095269 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGACCGGA
42095293 CATCATTCGA
Statistics
Matches: 130, Mismatches: 7, Indels: 13
0.87 0.05 0.09
Matches are distributed among these distances:
38 9 0.07
39 68 0.52
40 45 0.35
41 8 0.06
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGACCGGATTTAGTAACTCGCA
Found at i:42095212 original size:78 final size:80
Alignment explanation
Indices: 42095110--42095292 Score: 241
Period size: 79 Copynumber: 2.3 Consensus size: 80
42095100 GCTACTCGTT
*
42095110 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTA-ACC
1 CAAATGCCTT-GGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGACC
* *
42095172 GGATTTAGTAAC-TCGCA
63 GGATATAGTAACTTAGCA
* *
42095189 CAAATGCCTTGGGACTTAACCCGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 CAAATGCCTTGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGACCGGA
*
42095254 TATAGTCACTTAGCA
66 TATAGTAACTTAGCA
*
42095269 CAAA-GCCTTCGGACTTAGCCCGGA
1 CAAATGCCTTGGGACTTAGCCCGGA
42095293 CATCATTCGA
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
77 3 0.03
78 39 0.42
79 42 0.46
80 8 0.09
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTGGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTCGGATCTTAGACCGGA
TATAGTAACTTAGCA
Found at i:42099407 original size:39 final size:39
Alignment explanation
Indices: 42099364--42099531 Score: 264
Period size: 39 Copynumber: 4.3 Consensus size: 39
42099354 ACTTTAACCT
** *
42099364 GGATATTTTTCCAGCACGTAGCCTGCGGACCTCAAGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
* * * *
42099403 GGATATATTTCTAGCATATAGCATGCGGATCTCATGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
42099442 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
42099481 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
1 GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
42099520 GGATATATTTTC
1 GGATAT-TTTTC
42099532 AATCTCATAC
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
39 112 0.96
40 5 0.04
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.32
Consensus pattern (39 bp):
GGATATTTTTCCAGCATATAGCCTGCGGACCTCATGTCC
Found at i:42128160 original size:38 final size:35
Alignment explanation
Indices: 42128101--42128218 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
42128091 TCAATCATGC
*
42128101 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
42128140 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
42128171 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
42128202 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
42128219 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Found at i:42128162 original size:31 final size:31
Alignment explanation
Indices: 42128124--42128218 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
42128114 CCTTTTCATA
*
42128124 TTTCATATTTCATAATACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42128155 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42128186 TTTCATATTTCATATTACTGGGCCGAAGCCT
1 TTTCATATTTCATATTACTGGGCCGAAGCCT
42128217 TT
1 TT
42128219 ACTGTAAACG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATATTACTGGGCCGAAGCCT
Found at i:42128461 original size:24 final size:24
Alignment explanation
Indices: 42128410--42128552 Score: 209
Period size: 24 Copynumber: 6.0 Consensus size: 24
42128400 GCTTTATCAT
*
42128410 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
42128435 ATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGGGGCATAAGCCCTTTTA
42128459 ATAACTGGGGCATAAGCCCTTTT-
1 ATAACTGGGGCATAAGCCCTTTTA
*
42128482 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
*
42128506 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
42128530 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
42128553 TCACTTCCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
23 23 0.21
24 76 0.68
25 12 0.11
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:42128489 original size:47 final size:48
Alignment explanation
Indices: 42128410--42128551 Score: 207
Period size: 47 Copynumber: 3.0 Consensus size: 48
42128400 GCTTTATCAT
* *
42128410 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTCA
**
42128459 ATAACTGGGGCATAAGCCCTTTT-ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
*
42128506 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTT
42128552 TTCACTTCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
47 44 0.51
48 31 0.36
49 12 0.14
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTCA
Found at i:42128510 original size:71 final size:72
Alignment explanation
Indices: 42128409--42128552 Score: 220
Period size: 71 Copynumber: 2.0 Consensus size: 72
42128399 TGCTTTATCA
*
42128409 TATAACTGGAGGCCTAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
1 TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
42128474 GCCCTTT
66 GCCCTTT
* * **
42128481 TATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 TATAACTGGAGGCAT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATA
42128544 AGCCCTTT
65 AGCCCTTT
42128552 T
1 T
42128553 TCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
71 53 0.80
72 13 0.20
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (72 bp):
TATAACTGGAGGCATAGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTCAATAACTGGGGCATAA
GCCCTTT
Found at i:42128628 original size:20 final size:20
Alignment explanation
Indices: 42128603--42128662 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
42128593 TATGATTACC
42128603 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
* *
42128623 TCATGTGCATAGCATACATT
1 TCATGTGCATATCATACATA
42128643 TCATGTGCATATCATACATA
1 TCATGTGCATATCATACATA
42128663 CCATATTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (20 bp):
TCATGTGCATATCATACATA
Found at i:42128737 original size:25 final size:25
Alignment explanation
Indices: 42128705--42128752 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
42128695 ATACATAAAC
* * *
42128705 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
42128730 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
42128753 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:42129972 original size:27 final size:27
Alignment explanation
Indices: 42129910--42129974 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
42129900 GGGCATATTC
42129910 GTCATTTTACCATACAGGGGTATTACG
1 GTCATTTTACCATACAGGGGTATTACG
* *
42129937 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTACCATACAGGGG-TATTACG
*
42129964 GTCTTTTTACC
1 GTCATTTTACC
42129975 TTTTAGGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAGGGGTATTACG
Found at i:42130131 original size:27 final size:27
Alignment explanation
Indices: 42130090--42130176 Score: 79
Period size: 27 Copynumber: 3.2 Consensus size: 27
42130080 TAAAAAGTCA
*
42130090 AGGGTATTTCT-GTAACTTTGTAAATCAG
1 AGGGTATTT-TGGTAATTTTGTAAAT-AG
** *
42130118 -GGGTATTTTGGTAATTTTACAAATTG
1 AGGGTATTTTGGTAATTTTGTAAATAG
* **
42130144 AGGGTATTTCGGTAATTTTGTAAACCG
1 AGGGTATTTTGGTAATTTTGTAAATAG
42130171 AGGGTA
1 AGGGTA
42130177 AAATAGTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
26 2 0.04
27 46 0.96
ACGTcount: A:0.28, C:0.08, G:0.25, T:0.39
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTGTAAATAG
Found at i:42130185 original size:27 final size:27
Alignment explanation
Indices: 42130153--42130473 Score: 405
Period size: 27 Copynumber: 11.9 Consensus size: 27
42130143 GAGGGTATTT
* *
42130153 CGGTAATTTTGTAAACCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
** *
42130180 TAGTAATTCTGTAAATCAAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
** *
42130207 TAGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
42130234 CGGTAATTCTGTAAATCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
*
42130261 CGGTAATTCTGTAAGTCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
* *
42130288 CGATAATTATGTAAATC-AGGGGTAAAA
1 CGGTAATTCTGTAAATCGA-GGGTAAAA
* *
42130315 CGGTAATTATGTAAAT-TAGGGGTAAAA
1 CGGTAATTCTGTAAATCGA-GGGTAAAA
*
42130342 CGGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
**
42130369 TAGTAATTCTGTAAA-CTGAGGGTAAAA
1 CGGTAATTCTGTAAATC-GAGGGTAAAA
*
42130396 CGGTAATTCTATAAATCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
* **
42130423 CGGTAATTTTACAAATCGAGGGTAAAA
1 CGGTAATTCTGTAAATCGAGGGTAAAA
*
42130450 CGGTAATTCTATAAATCGAGGGTA
1 CGGTAATTCTGTAAATCGAGGGTA
42130474 CTTTGGTAAT
Statistics
Matches: 261, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
26 2 0.01
27 257 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (27 bp):
CGGTAATTCTGTAAATCGAGGGTAAAA
Found at i:42130495 original size:27 final size:27
Alignment explanation
Indices: 42130397--42130675 Score: 226
Period size: 27 Copynumber: 10.4 Consensus size: 27
42130387 AGGGTAAAAC
* * ****
42130397 GGTAATTCTATAAATCGAGGGTAAAAC
1 GGTAATTTTACAAATCGAGGGTATTTT
****
42130424 GGTAATTTTACAAATCGAGGGTAAAAC
1 GGTAATTTTACAAATCGAGGGTATTTT
* * *
42130451 GGTAATTCTATAAATCGAGGGTACTTT
1 GGTAATTTTACAAATCGAGGGTATTTT
* *
42130478 GGTAATTTTACAAGTCGAGGGTATTTC
1 GGTAATTTTACAAATCGAGGGTATTTT
** ** *
42130505 AATAATTTTACAGGTCGAGGGTATTTC
1 GGTAATTTTACAAATCGAGGGTATTTT
* * *
42130532 AGTAATTTCACAAAT-TAGGGGTATTTT
1 GGTAATTTTACAAATCGA-GGGTATTTT
*
42130559 GGTAATTTTACAAA-CTAGGGGTATTTT
1 GGTAATTTTACAAATCGA-GGGTATTTT
* *
42130586 GATAATTTTACAAA-CTAGGGGTATTTT
1 GGTAATTTTACAAATCGA-GGGTATTTT
*
42130613 GGTAATTTTACAAAATAG-GGGTATTTT
1 GGTAATTTTAC-AAATCGAGGGTATTTT
* *
42130640 AGTAATTTTACAAAGC-AGGGTATTTT
1 GGTAATTTTACAAATCGAGGGTATTTT
42130666 GGTAATTTTA
1 GGTAATTTTA
42130676 TAAACCAAAG
Statistics
Matches: 215, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
26 22 0.10
27 190 0.88
28 3 0.01
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (27 bp):
GGTAATTTTACAAATCGAGGGTATTTT
Found at i:42133432 original size:38 final size:35
Alignment explanation
Indices: 42133373--42133490 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 35
42133363 TCAATCATGC
*
42133373 ACTGGGCCGTAGCCCTTTTCATATTTCATATTTCATAAT
1 ACTGGGCCGAAG-CCTTTTCATATTTCATATTT-AT--T
42133412 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
42133443 ACTGGGCCGAAGCCTTTTCATATTTC--A--TATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
42133474 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
42133491 ACTGTAAACG
Statistics
Matches: 78, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
31 49 0.63
33 2 0.03
34 1 0.01
36 1 0.01
38 14 0.18
39 11 0.14
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (35 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATATTTATT
Done.