Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold46
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: 2524624
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 119418 characters in sequence are not A, C, G, or T
File 10 of 15
Found at i:1534050 original size:31 final size:31
Alignment explanation
Indices: 1533994--1534152 Score: 150
Period size: 31 Copynumber: 5.2 Consensus size: 31
1533984 GATGCCACCG
* *
1533994 ACTTGTGTGGGCTTTAGAAAGGGTTGCCTCTA
1 ACTTGTGTGGACTTTAG-AAGGGTTGCCACTA
**
1534026 ACTTGTGTGGACTTTAGAAGGGTTGCCACCG
1 ACTTGTGTGGACTTTAGAAGGGTTGCCACTA
* *
1534057 ACTTGTGTGGACTTTAGAAGGGTTACCACTG
1 ACTTGTGTGGACTTTAGAAGGGTTGCCACTA
* * *
1534088 ACTTATGTGGGCTTTAAGAA-AG-TGCCACTA
1 ACTTGTGTGGACTTT-AGAAGGGTTGCCACTA
* *
1534118 AC-T-TGTGGCCTTTGAGAA-GG-TGCCCCTA
1 ACTTGTGTGGACTTT-AGAAGGGTTGCCACTA
1534146 ACTTGTG
1 ACTTGTG
1534153 GGCATTGAGA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
28 23 0.21
29 2 0.02
30 10 0.09
31 54 0.50
32 20 0.18
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.31
Consensus pattern (31 bp):
ACTTGTGTGGACTTTAGAAGGGTTGCCACTA
Found at i:1534072 original size:63 final size:62
Alignment explanation
Indices: 1533986--1534103 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 62
1533976 TAGAAAAAGA
* * * *
1533986 TGCCACCGACTTGTGTGGGCTTTAGAAAGGGTTGCCTCTAACTTGTGTGGACTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGACTTTAG-AAGGGTTACCACTAACTTATGTGGACTTTAGAAGGGT
* *
1534049 TGCCACCGACTTGTGTGGACTTTAGAAGGGTTACCACTGACTTATGTGGGCTTTA
1 TGCCACCGACTTGTGTGGACTTTAGAAGGGTTACCACTAACTTATGTGGACTTTA
1534104 AGAAAGTGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
62 25 0.51
63 24 0.49
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (62 bp):
TGCCACCGACTTGTGTGGACTTTAGAAGGGTTACCACTAACTTATGTGGACTTTAGAAGGGT
Found at i:1534130 original size:28 final size:28
Alignment explanation
Indices: 1533999--1534181 Score: 120
Period size: 28 Copynumber: 6.2 Consensus size: 28
1533989 CACCGACTTG
*
1533999 TGTGGGCTTT-AGAAAGGGTTGCCTCTAACT
1 TGTGGGCTTTGAG-AA-GG-TGCCACTAACT
**
1534029 TGTGTGGACTTT-AGAAGGGTTGCCACCGACT
1 TGTG-GG-CTTTGAGAA-GG-TGCCACTAACT
* *
1534060 TGTGTGGACTTT-AGAAGGGTTACCACTGACTT
1 TGTG-GG-CTTTGAGAA-GG-TGCCACTAAC-T
* *
1534092 ATGTGGGCTTTAAGAAAGTGCCACTAACT
1 -TGTGGGCTTTGAGAAGGTGCCACTAACT
* *
1534121 TGTGGCCTTTGAGAAGGTGCCCCTAACT
1 TGTGGGCTTTGAGAAGGTGCCACTAACT
* * *
1534149 TGTGGGCATTGAGAAGGTGCCACTGATT
1 TGTGGGCTTTGAGAAGGTGCCACTAACT
1534177 TGTGG
1 TGTGG
1534182 ACTTAAAAGG
Statistics
Matches: 131, Mismatches: 17, Indels: 12
0.82 0.11 0.08
Matches are distributed among these distances:
28 52 0.40
29 1 0.01
30 12 0.09
31 49 0.37
32 13 0.10
33 4 0.03
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (28 bp):
TGTGGGCTTTGAGAAGGTGCCACTAACT
Found at i:1534296 original size:31 final size:28
Alignment explanation
Indices: 1534245--1534305 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
1534235 GTTGTGGACC
*
1534245 TAGAAGGGTGCCACCGACTTGTGTGGGCTT
1 TAGAAGGGTGCCACCAAC-T-TGTGGGCTT
*
1534275 TAGAAGGGTTGCCACTAACTTGTGGGCTT
1 TAGAAGGG-TGCCACCAACTTGTGGGCTT
1534304 TA
1 TA
1534306 AAAAGATGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 11 0.39
30 9 0.32
31 8 0.29
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.30
Consensus pattern (28 bp):
TAGAAGGGTGCCACCAACTTGTGGGCTT
Found at i:1537931 original size:52 final size:52
Alignment explanation
Indices: 1537783--1537911 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
1537773 CAAAATATGA
1537783 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1537835 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1537887 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1537912 AAGATCAGTA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1538009 original size:19 final size:18
Alignment explanation
Indices: 1537985--1538082 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1537975 TAGCTTGTAT
1537985 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
*
1538004 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
1538017 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1538036 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1538049 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
1538069 TGTATCGATACAAA
1 TGTATCGATACAAA
1538083 TCATTGGAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1538024 original size:32 final size:32
Alignment explanation
Indices: 1537983--1538080 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
1537973 AGTAGCTTGT
* *
1537983 ATTGTATCGATACAAAACTTATGTATCAATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1538015 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
1538047 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
1538080 A
1 A
1538081 AATCATTGGA
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 48 0.76
33 15 0.24
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:1538054 original size:13 final size:13
Alignment explanation
Indices: 1538004--1538060 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
1537994 ACAAAACTTA
*
1538004 TGTATCAATACAT
1 TGTATCGATACAT
1538017 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1538035 ATGTATCGATACAT
1 -TGTATCGATACAT
1538049 TGTATCGATACA
1 TGTATCGATACA
1538061 ACACTTTATG
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 20 0.54
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1538516 original size:28 final size:28
Alignment explanation
Indices: 1538485--1538539 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
1538475 CTTGACTTTA
*
1538485 TTAGGAAT-TGCATTTTGTCATGATTCCT
1 TTAGGAATCAGCATTTT-TCATGATTCCT
* *
1538513 TTAGGGATCAGCATTTTTCTTGATTCC
1 TTAGGAATCAGCATTTTTCATGATTCC
1538540 ATTGAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.45
Consensus pattern (28 bp):
TTAGGAATCAGCATTTTTCATGATTCCT
Found at i:1539448 original size:22 final size:22
Alignment explanation
Indices: 1539420--1539474 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
1539410 AATATTTAAT
1539420 TTATTATGTTTATTTATGTAAC
1 TTATTATGTTTATTTATGTAAC
1539442 TTATTATGTTTATTTATGTAAC
1 TTATTATGTTTATTTATGTAAC
*
1539464 TTGTTCATGTT
1 TTATT-ATGTT
1539475 GATACGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 26 0.84
23 5 0.16
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.60
Consensus pattern (22 bp):
TTATTATGTTTATTTATGTAAC
Found at i:1547540 original size:49 final size:49
Alignment explanation
Indices: 1547441--1547920 Score: 240
Period size: 49 Copynumber: 10.4 Consensus size: 49
1547431 TGTGTTGAGA
* * * * **
1547441 CAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGCCAATACACTGATT
1 CAAGGCCAACGACATTGGACTTA--AA-GATGAAGATGCCAATATGCTGATT
* * *
1547493 CAAGGCCAACGATATTGGACTTAAAGCTGAAGATGCCAACATGCTGATT
1 CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* * **
1547542 CAAGGCCAGCGACATTGGTCTTAAAGATGAGGAAGGCGCCAATATGCTGATT
1 CAAGGCCAACGACATTGGACTTAAAGAT---GAAGATGCCAATATGCTGATT
* * * * *
1547594 CGAGGCCAACGACA-TCGATCTTAAAGATGATGGTGACAATATGCTGATT
1 CAAGGCCAACGACATTGGA-CTTAAAGATGAAGATGCCAATATGCTGATT
* * *
1547643 CAAGGCCAACGATATTGGGC-T-----T---G-TGCCAATGTGCTGATT
1 CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* *
1547682 CAAGGCCAGCGATATTAGG-C-T-----T---G-TGCCAATATGCTGATT
1 CAAGGCCAACGACATT-GGACTTAAAGATGAAGATGCCAATATGCTGATT
* ** ** *
1547721 CAAGGCCAGCGACATTGGTTTTAAAGATGGTGGTGCCAATATGCTGATT
1 CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* * *
1547770 CAAGGCCAGCGACATTGGTCTTAAAGATG--G-TGCCAACATGCTGATT
1 CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* * * * *
1547816 CAAGGCCAGCGATATTGGGC-T-----T----ATGCCAATGTGCCGATT
1 CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* * * * *
1547855 CAAGGCCAGCGACATTGGTCTTAGAGA-CAAGGTGCCAATATGCTGATT
1 CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* *
1547903 CAAGGCCAGCGATATTGG
1 CAAGGCCAACGACATTGG
1547921 TCTTGTGCCA
Statistics
Matches: 355, Mismatches: 45, Indels: 60
0.77 0.10 0.13
Matches are distributed among these distances:
38 2 0.01
39 94 0.26
40 6 0.02
43 1 0.00
45 2 0.01
46 33 0.09
47 1 0.00
48 33 0.09
49 118 0.33
50 4 0.01
51 2 0.01
52 59 0.17
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (49 bp):
CAAGGCCAACGACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
Found at i:1547557 original size:101 final size:101
Alignment explanation
Indices: 1547441--1547664 Score: 245
Period size: 101 Copynumber: 2.2 Consensus size: 101
1547431 TGTGTTGAGA
* ** *
1547441 CAAGGCCAGCGACATTGGGCTT-AGGAATGTTAAAGATGCCAATACACTGATTCAAGGCCAACGA
1 CAAGGCCAGCGACATTGGGCTTAAAG-ATGAGAAAGACGCCAATACACTGATTCAAGGCCAACGA
* * * *
1547505 TATTGGA-CTTAAAGCTGAAGATGCCAACATGCTGATT
65 CA-TCGATCTTAAAGATGAAGATGACAACATGCTGATT
* * * ** *
1547542 CAAGGCCAGCGACATTGGTCTTAAAGATGAGGAAGGCGCCAATATGCTGATTCGAGGCCAACGAC
1 CAAGGCCAGCGACATTGGGCTTAAAGATGAGAAAGACGCCAATACACTGATTCAAGGCCAACGAC
* * *
1547607 ATCGATCTTAAAGATGATGGTGACAATATGCTGATT
66 ATCGATCTTAAAGATGAAGATGACAACATGCTGATT
* *
1547643 CAAGGCCAACGATATTGGGCTT
1 CAAGGCCAGCGACATTGGGCTT
1547665 GTGCCAATGT
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
100 3 0.03
101 96 0.95
102 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (101 bp):
CAAGGCCAGCGACATTGGGCTTAAAGATGAGAAAGACGCCAATACACTGATTCAAGGCCAACGAC
ATCGATCTTAAAGATGAAGATGACAACATGCTGATT
Found at i:1547689 original size:39 final size:39
Alignment explanation
Indices: 1547630--1548050 Score: 349
Period size: 39 Copynumber: 9.9 Consensus size: 39
1547620 ATGATGGTGA
* * *
1547630 CAATATGCTGATTCAAGGCCAACGATATTGGGCTTGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTGTGC
* *
1547669 CAATGTGCTGATTCAAGGCCAGCGATATTAGG-CTTGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTGTGC
*
1547708 CAATATGCTGATTCAAGGCCAGCGACATTGGTTTTAAAGATGGTGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGG---T----CT--T-GTGC
1547757 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTC-T-----T-GTGC
* * * *
1547803 CAACATGCTGATTCAAGGCCAGCGATATTGGGCTTATGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTGTGC
* *
1547842 CAATGTGCCGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTT---------GTGC
*
1547890 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTGTGC
* *
1547929 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTGAAGACAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTT---------GTGC
* *
1547977 CAATATGCTGATTCAAAGCCAGCGATATTGGTCTTGTGC
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTGTGC
*
1548016 TAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
1 CAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
1548051 AAAGACAAAG
Statistics
Matches: 318, Mismatches: 30, Indels: 68
0.76 0.07 0.16
Matches are distributed among these distances:
38 2 0.01
39 166 0.52
40 3 0.01
43 1 0.00
45 1 0.00
46 39 0.12
48 71 0.22
49 35 0.11
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (39 bp):
CAATATGCTGATTCAAGGCCAGCGACATTGGTCTTGTGC
Found at i:1547910 original size:48 final size:46
Alignment explanation
Indices: 1547839--1548089 Score: 242
Period size: 39 Copynumber: 5.6 Consensus size: 46
1547829 ATTGGGCTTA
* *
1547839 TGCCAATGTGCCGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT--AGACAAGG
*
1547887 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGTCTT-------G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGACAAGG
* *
1547926 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTGAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT--AGACAAGG
* *
1547974 TGCCAATATGCTGATTCAAAGCCAGCGATATTGGTCTT-------G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGACAAGG
*
1548013 TGCTAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT--AGAC-AAGG
** *
1548062 TGCTGATACGCTGATTCAAGGCCAGCGA
1 TGCCAATATGCTGATTCAAGGCCAGCGA
1548090 TATTAGACTT
Statistics
Matches: 169, Mismatches: 15, Indels: 37
0.76 0.07 0.17
Matches are distributed among these distances:
39 72 0.43
48 70 0.41
49 27 0.16
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (46 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGACAAGG
Found at i:1547919 original size:87 final size:87
Alignment explanation
Indices: 1547753--1548093 Score: 508
Period size: 87 Copynumber: 3.9 Consensus size: 87
1547743 AAAGATGGTG
* * *
1547753 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA-A-AGATGGTGCCAACATGCTGATT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATT
*
1547816 CAAGGCCAGCGATATTGGGCTT
66 CAAGGCCAGCGATATTGGTCTT
* * *
1547838 ATGCCAATGTGCCGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATT
1547903 CAAGGCCAGCGATATTGGTCTT
66 CAAGGCCAGCGATATTGGTCTT
* *
1547925 GTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT-GAAGACAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAG-AGACAAGGTGCCAATATGCTGAT
*
1547989 TCAAAGCCAGCGATATTGGTCTT
65 TCAAGGCCAGCGATATTGGTCTT
* * ** *
1548012 GTGCTAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAAGGTGCTGATACGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGAC-AAGGTGCCAATATGCTGAT
1548077 TCAAGGCCAGCGATATT
65 TCAAGGCCAGCGATATT
1548094 AGACTTAGAA
Statistics
Matches: 232, Mismatches: 19, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
85 37 0.16
86 2 0.01
87 161 0.69
88 32 0.14
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (87 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAGAGACAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGTCTT
Found at i:1548211 original size:29 final size:28
Alignment explanation
Indices: 1548122--1548216 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 28
1548112 CACCAACTTG
1548122 TGTGGGCTTTTGAAAGGGTTGTACCA--ACT
1 TGTGGGCTTTTGAAAGGG-TG--CCATGACT
* *
1548151 TGTGTGCTTTTG-AAGGTTGCCATTGACT
1 TGTGGGCTTTTGAAAGGGTGCCA-TGACT
1548179 TGTGGGCTTTTGAAAAGGGTGCCATGACT
1 TGTGGGCTTTTG-AAAGGGTGCCATGACT
1548208 TGTGGGCTT
1 TGTGGGCTT
1548217 AAAGGAAGAA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.05
27 2 0.04
28 18 0.32
29 25 0.44
30 9 0.16
ACGTcount: A:0.17, C:0.14, G:0.33, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAAGGGTGCCATGACT
Found at i:1548251 original size:33 final size:34
Alignment explanation
Indices: 1548196--1548472 Score: 219
Period size: 34 Copynumber: 8.5 Consensus size: 34
1548186 TTTTGAAAAG
* *
1548196 GGTGCCAT-GACTTGTGGGCTT-AAAGGAAGAAA
1 GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
* *
1548228 GATGCCATGGAGTTGTGGACTTAAAAGGGAA-AAG
1 GGTGCCATGGAGTTGTGGACTTAAAA-GGAAGAAA
* * *
1548262 GGTGCCACGGAGTCGTGGACTTAAAAAG-A-AAA
1 GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
* **
1548294 GGTGCCACGGAGTTGTGGACTTAAAAGG-ATCAA
1 GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
*
1548327 GGTGCCATGGAGTTGTGGACTT--CA--AAG---
1 GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
*
1548354 GGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAA
1 GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
*
1548387 GATGCCATGGAGTTGTGGACTTAAAAGG--GAATA
1 GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAA-A
** * *
1548420 GAGTGAGACGGAGTTGTGGGCTTAAAAGGAA-AAA
1 G-GTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
* * *
1548454 TGGTGTCACGGAGTCGTGG
1 -GGTGCCATGGAGTTGTGG
1548473 GGGGCTTTGA
Statistics
Matches: 200, Mismatches: 27, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
27 21 0.10
29 1 0.00
30 1 0.00
31 3 0.01
32 39 0.19
33 63 0.31
34 65 0.32
35 7 0.04
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (34 bp):
GGTGCCATGGAGTTGTGGACTTAAAAGGAAGAAA
Found at i:1548373 original size:60 final size:59
Alignment explanation
Indices: 1548230--1548415 Score: 237
Period size: 60 Copynumber: 3.0 Consensus size: 59
1548220 GGAAGAAAGA
* * *
1548230 TGCCATGGAGTTGTGGACTTAAAAGGGAAAAGGGTGCCACGGAGTCGTGGACTTAAAAAGAAAAG
1 TGCCACGGAGTTGTGGACTTAAAA-GGAAAA-GGTGCCATGGAGTTGTGGACTT-AAAAG----G
1548295 G
59 G
* *
1548296 TGCCACGGAGTTGTGGACTTAAAAGGATCAAGGTGCCATGGAGTTGTGGACTTCAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA-AAAGGTGCCATGGAGTTGTGGACTTAAAAGGG
*
1548356 TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGG-AAAAGGTGCCATGGAGTTGTGGACTTAAAAGGG
1548416 AATAGAGTGA
Statistics
Matches: 110, Mismatches: 8, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
60 57 0.52
61 1 0.01
64 4 0.04
65 23 0.21
66 25 0.23
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (59 bp):
TGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCATGGAGTTGTGGACTTAAAAGGG
Found at i:1548473 original size:34 final size:33
Alignment explanation
Indices: 1548354--1548508 Score: 150
Period size: 34 Copynumber: 4.5 Consensus size: 33
1548344 GACTTCAAAG
1548354 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * * *
1548387 GATGCCATGGAGTTGTGGACTTAAAAGGGAATA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
** *
1548420 GAGTGAGACGGAGTTGTGGGCTTAAAAGGAAAAA
1 G-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
* * *
1548454 TGGTGTCACGGAGTCGTGGGGGGCTTTGAAAA-GAAAAA
1 -GGTGCCACGGAGT--T-GTGGAC-TT-AAAAGGAAAAA
1548492 GGTGCCACGGAGTTGTG
1 GGTGCCACGGAGTTGTG
1548509 AGCTTTGAAG
Statistics
Matches: 99, Mismatches: 16, Indels: 13
0.77 0.12 0.10
Matches are distributed among these distances:
33 30 0.30
34 37 0.37
35 2 0.02
36 1 0.01
37 17 0.17
38 8 0.08
39 4 0.04
ACGTcount: A:0.32, C:0.10, G:0.37, T:0.21
Consensus pattern (33 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
Found at i:1548517 original size:34 final size:32
Alignment explanation
Indices: 1548190--1548513 Score: 227
Period size: 33 Copynumber: 9.8 Consensus size: 32
1548180 GTGGGCTTTT
* * *
1548190 GAAAAGGGTGCCA-TGACTTGTGGGCTT-AAAG
1 GAAAAAGGTGCCACGGAGTTGT-GGCTTAAAAG
* *
1548221 GAAGAAAGATGCCATGGAGTTGTGGACTTAAAAGG
1 GAA-AAAGGTGCCACGGAGTTGTGG-CTTAAAA-G
* * *
1548256 GAAAAGGGTGCCACGGAGTCGTGGACTTAAAAA
1 GAAAAAGGTGCCACGGAGTTGTGG-CTTAAAAG
1548289 G-AAAAGGTGCCACGGAGTTGTGGACTTAAAAG
1 GAAAAAGGTGCCACGGAGTTGTGG-CTTAAAAG
** * *
1548321 GATCAAGGTGCCATGGAGTTGTGGACTTCAAA-
1 GAAAAAGGTGCCACGGAGTTGTGG-CTTAAAAG
1548353 G-----GGTGCCACGGAGTTGTGGACTTAAAAG
1 GAAAAAGGTGCCACGGAGTTGTGG-CTTAAAAG
* *
1548381 GAAAAAGATGCCATGGAGTTGTGGACTTAAAAG
1 GAAAAAGGTGCCACGGAGTTGTGG-CTTAAAAG
* * **
1548414 GGAATAGAGTGAGACGGAGTTGTGGGCTTAAAAG
1 GAAAAAG-GTGCCACGGAGTTGT-GGCTTAAAAG
* *
1548448 GAAAAATGGTGTCACGGAGTCGTGGGGGGCTTTGAAAA-
1 GAAAAA-GGTGCCACGGAGT--T--GTGGC-TT-AAAAG
1548486 GAAAAAGGTGCCACGGAGTTGTGAGCTT
1 GAAAAAGGTGCCACGGAGTTGTG-GCTT
1548514 TGAAGAAAAG
Statistics
Matches: 238, Mismatches: 33, Indels: 42
0.76 0.11 0.13
Matches are distributed among these distances:
27 24 0.10
28 1 0.00
31 3 0.01
32 40 0.17
33 70 0.29
34 63 0.26
35 8 0.03
36 1 0.00
37 15 0.06
38 9 0.04
39 4 0.02
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (32 bp):
GAAAAAGGTGCCACGGAGTTGTGGCTTAAAAG
Found at i:1548529 original size:31 final size:31
Alignment explanation
Indices: 1548488--1548709 Score: 281
Period size: 31 Copynumber: 7.2 Consensus size: 31
1548478 TTTGAAAAGA
* * *
1548488 AAAAGGTGCCACGGAGTTGT-GAGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGA-CTTTGAAG
1548519 AAAAGATGCCACTGAGTCGTGGACTTTG--G
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1548548 AAAGAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAA-AGATGCCACTGAGTCGTGGACTTTGAAG
1548580 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * **
1548611 AAGAGATGCCACTGAGTCGTAGACTTTGGGG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
* * *
1548642 AAAAAATGCCACTAAGTCGTGGACTTGGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
**
1548673 AAAAGATGCCACTGAGTCACGGACTTTG-AG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
*
1548703 AAGAGAT
1 AAAAGAT
1548710 ATTTGAAGAA
Statistics
Matches: 167, Mismatches: 20, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
29 4 0.02
30 33 0.20
31 124 0.74
32 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.22
Consensus pattern (31 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAG
Found at i:1548627 original size:92 final size:92
Alignment explanation
Indices: 1548488--1548709 Score: 306
Period size: 92 Copynumber: 2.4 Consensus size: 92
1548478 TTTGAAAAGA
* * * * *
1548488 AAAAGGTGCCACGGAGTTGT-GAGCTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTT-GGAAA
1 AAAAGATGCCACTGAGTCGTGGA-CTTTGAAGAAGAGATGCCACTGAGTCGTAGACTTTGGGAAA
* * *
1548551 GAGATGCCACTGAGTCGTGGACTTTGAAG
65 -AAATGCCACTAAGTCGTGGACTTGGAAG
1548580 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAGAGATGCCACTGAGTCGTAGACTTTGGGGAAA
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAGAGATGCCACTGAGTCGTAGACTTT-GGGAAA
1548645 AAATGCCACTAAGTCGTGGACTTGGAAG
65 AAATGCCACTAAGTCGTGGACTTGGAAG
**
1548673 AAAAGATGCCACTGAGTCACGGACTTTG-AGAAGAGAT
1 AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAGAGAT
1548710 ATTTGAAGAA
Statistics
Matches: 117, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
92 59 0.50
93 53 0.45
94 5 0.04
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.22
Consensus pattern (92 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAAGAAGAGATGCCACTGAGTCGTAGACTTTGGGAAAA
AATGCCACTAAGTCGTGGACTTGGAAG
Found at i:1549396 original size:31 final size:29
Alignment explanation
Indices: 1549355--1549413 Score: 73
Period size: 31 Copynumber: 2.0 Consensus size: 29
1549345 TGACAAAAGG
*
1549355 TTTGCTTGACAATAAAGATGATATGGTTTGA
1 TTTGCTTGACAAGAAAGAT-A-ATGGTTTGA
* *
1549386 TTTGTTTGACAAGAACGATAATGGTTTG
1 TTTGCTTGACAAGAAAGATAATGGTTTG
1549414 TTTCCAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.32
30 1 0.04
31 16 0.64
ACGTcount: A:0.31, C:0.07, G:0.24, T:0.39
Consensus pattern (29 bp):
TTTGCTTGACAAGAAAGATAATGGTTTGA
Found at i:1558392 original size:13 final size:13
Alignment explanation
Indices: 1558351--1558404 Score: 57
Period size: 13 Copynumber: 4.6 Consensus size: 13
1558341 AGCCGTTACA
1558351 ACAATGTATCGAT
1 ACAATGTATCGAT
1558364 ACAA--T-TC-AT
1 ACAATGTATCGAT
1558373 -C-ATGTATCGAT
1 ACAATGTATCGAT
1558384 ACAATGTATCGAT
1 ACAATGTATCGAT
*
1558397 ACATTGTA
1 ACAATGTA
1558405 CCATGTATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 21 0.62
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
ACAATGTATCGAT
Found at i:1558392 original size:33 final size:33
Alignment explanation
Indices: 1558351--1558420 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
1558341 AGCCGTTACA
*
1558351 ACAATGTATCGATACAATT-CATCATGTATCGAT
1 ACAATGTATCGATAC-ATTGCACCATGTATCGAT
*
1558384 ACAATGTATCGATACATTGTACCATGTATCGAT
1 ACAATGTATCGATACATTGCACCATGTATCGAT
1558417 ACAA
1 ACAA
1558421 ATAGTGATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 3 0.09
33 31 0.91
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (33 bp):
ACAATGTATCGATACATTGCACCATGTATCGAT
Found at i:1558478 original size:19 final size:20
Alignment explanation
Indices: 1558450--1558502 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
1558440 TGCCAATCTT
* *
1558450 ATGTAGCGATACAATTG-TC
1 ATGTATCGATACAATTGAAC
*
1558469 ATGTGTCGATACAA-TGAAC
1 ATGTATCGATACAATTGAAC
1558488 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1558503 GTATCGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 2 0.07
19 26 0.93
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATTGAAC
Found at i:1558506 original size:13 final size:13
Alignment explanation
Indices: 1558488--1558514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1558478 TACAATGAAC
1558488 ATGTATCGATACA
1 ATGTATCGATACA
1558501 ATGTATCGATACA
1 ATGTATCGATACA
1558514 A
1 A
1558515 AGCATAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1560003 original size:22 final size:22
Alignment explanation
Indices: 1559971--1560018 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1559961 AATTTTAATT
* *
1559971 AAAAAATTGAGAAGAAATAAAG
1 AAAAAAATGAGAAGAAAGAAAG
**
1559993 AAAAAAATGAGTTGAAAGAAAG
1 AAAAAAATGAGAAGAAAGAAAG
1560015 AAAA
1 AAAA
1560019 TCAAACACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAAAATGAGAAGAAAGAAAG
Found at i:1561597 original size:25 final size:25
Alignment explanation
Indices: 1561546--1561598 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1561536 ATTATATAAG
* * *
1561546 TATTGTAATATATAATATGTTATTA
1 TATTATAATATATAACATGTTAGTA
1561571 TATTATAATATATAAACAT-TTAGTA
1 TATTATAATATAT-AACATGTTAGTA
1561596 TAT
1 TAT
1561599 AATTATCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 20 0.83
26 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (25 bp):
TATTATAATATATAACATGTTAGTA
Found at i:1561640 original size:26 final size:26
Alignment explanation
Indices: 1561594--1561643 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1561584 AAACATTTAG
*
1561594 TATATAATTATCCATATATTATATCA
1 TATATAATCATCCATATATTATATCA
*
1561620 TATATAATACATCTATA-ATTATAT
1 TATATAAT-CATCCATATATTATAT
1561644 TCCAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (26 bp):
TATATAATCATCCATATATTATATCA
Found at i:1565820 original size:20 final size:20
Alignment explanation
Indices: 1565767--1565920 Score: 77
Period size: 20 Copynumber: 7.7 Consensus size: 20
1565757 AAAACCCAAA
* * * *
1565767 ATGTATCGATACAATGAATA
1 ATGTATCGATACATTTACTT
1565787 ATGTATCGATACATTTACTT
1 ATGTATCGATACATTTACTT
*
1565807 ATGTATCGATACATTTCCTT
1 ATGTATCGATACATTTACTT
** *
1565827 -TCCAAAAT-G-TAGAATGTT--TT
1 AT---GTATCGATA-CAT-TTACTT
**
1565847 -TGTATCGATACATTTCAAGT
1 ATGTATCGATACATTT-ACTT
* * *
1565867 ATGTATTGATACATATATTT
1 ATGTATCGATACATTTACTT
1565887 ATGTATCGATACATTTACTGT
1 ATGTATCGATACATTTACT-T
*
1565908 TTGTATCGATACA
1 ATGTATCGATACA
1565921 AATTGTAAAA
Statistics
Matches: 102, Mismatches: 20, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
17 4 0.04
18 3 0.03
19 3 0.03
20 59 0.58
21 29 0.28
22 4 0.04
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTACTT
Found at i:1565912 original size:21 final size:21
Alignment explanation
Indices: 1565845--1565920 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
1565835 GTAGAATGTT
*
1565845 TTTGTATCGATACATTT-CAAG
1 TTTGTATCGATACATTTAC-TG
* * *
1565866 TATGTATTGATACATATA-T-
1 TTTGTATCGATACATTTACTG
1565885 TTATGTATCGATACATTTACTG
1 TT-TGTATCGATACATTTACTG
1565907 TTTGTATCGATACA
1 TTTGTATCGATACA
1565921 AATTGTAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 1 0.02
20 14 0.32
21 27 0.61
22 2 0.05
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (21 bp):
TTTGTATCGATACATTTACTG
Found at i:1566132 original size:62 final size:61
Alignment explanation
Indices: 1566029--1566343 Score: 375
Period size: 62 Copynumber: 5.1 Consensus size: 61
1566019 AAAGGTATGG
* ** *
1566029 GGACGCC--TTTCTTTTTAAAGCTCACATGAGTTGATGGCACCTTTTAGTCCTCAAAGAGTA
1 GGACGCCTTTTTCCTTTTAAAGC-CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTA
* * *
1566089 GGACGCCTTTTTCATTTTAAATCACACACAAGTTGGTGACACCTTTTAGTCCTCAAAGAGTA
1 GGACGCCTTTTTCCTTTTAAAGC-CACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTA
* *
1566151 GGACGCCTTTTTTCTTTTTAAAGCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTA
1 GGACGCC-TTTTTCCTTTTAAAGCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTA
* * * * *
1566213 GGATGCC-TTTTCCTTTTAAAGCCTACACAAGTTGATAGCACCTTCTAGTCCTCAAAGAGCA
1 GGACGCCTTTTTCCTTTTAAAGCC-ACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTA
* * *
1566274 GGACACTTTCCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTTAGTCATCAAAGAGT
1 GG--AC--GCCTTTTTCCTTTTAAAG-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGT
1566339 A
61 A
1566340 GGAC
1 GGAC
1566344 TCATTCCCCT
Statistics
Matches: 219, Mismatches: 26, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
60 22 0.10
61 34 0.16
62 95 0.43
63 15 0.07
64 2 0.01
65 2 0.01
66 47 0.21
67 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (61 bp):
GGACGCCTTTTTCCTTTTAAAGCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTA
Found at i:1566338 original size:127 final size:125
Alignment explanation
Indices: 1566036--1566343 Score: 408
Period size: 123 Copynumber: 2.5 Consensus size: 125
1566026 TGGGGACGCC
* * *
1566036 TTTCTTTTTAAAGCTCACATGAGTTGATGGCACCTTTTAGTCCTCAAAGAGTAGGACGCCTTTTT
1 TTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCCTTTTT
* * * * * *
1566101 CATTTTAAATCACACACAAGTTGGTGACACCTTTTAGTCCTCAAAGAGTAGGACGCCTTT
66 CATTTTAAAGCACACACAAGTTGATGACACCTTCTAGTCCTCAAAGAGCAGGACACCCTT
*
1566161 TTTCTTTTTAAAG-CCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGATGCC-TTTT
1 TTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCCTTTTT
*
1566224 CCTTTTAAAGC-CTACACAAGTTGAT-AGCACCTTCTAGTCCTCAAAGAGCAGGACACTTTCCTT
66 CATTTTAAAGCAC-ACACAAGTTGATGA-CACCTTCTAGTCCTCAAAGAGCAGGACAC---CCTT
* * * *
1566287 TTTCCTTTTAAAGCCCACACAAGTTGGTGGCATCTTTTAGTCATCAAAGAGTAGGAC
1 TTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGAC
1566344 TCATTCCCCT
Statistics
Matches: 161, Mismatches: 16, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
122 2 0.01
123 50 0.31
124 42 0.26
125 13 0.08
126 15 0.09
127 39 0.24
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (125 bp):
TTTCTTTTTAAAGCCCACACGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGTAGGACGCCTTTTT
CATTTTAAAGCACACACAAGTTGATGACACCTTCTAGTCCTCAAAGAGCAGGACACCCTT
Found at i:1569496 original size:80 final size:79
Alignment explanation
Indices: 1569364--1569627 Score: 250
Period size: 80 Copynumber: 3.3 Consensus size: 79
1569354 TCATTGATGT
* * * * * * *
1569364 TTTTATTTCTAAAACACCAATTTTCCACCATTGGGGATACTCCAA-CTCCGTTATTTTCAAGAAG
1 TTTTATTCCTAAAACACGATTTTTTCACCATCGAGGATACTTCAACCT-CGTTATTTTCAAGAAG
*
1569428 ACACTCTAACCACGG
65 ACACTCTAACCTCGG
**
1569443 TTTTATTCCTAAAACATCGATTTTTTCACCATCGAGGATACTTCAACCTCGTTATTTTTTAGAAG
1 TTTTATTCCTAAAACA-CGATTTTTTCACCATCGAGGATACTTCAACCTCGTTATTTTCAAGAAG
*
1569508 ACACTAC-AACCTCGA
65 ACACT-CTAACCTCGG
* * * * * **
1569523 TTTTATT-TTAAAACACTGATTTTTT-ACAATC-AGAGATACTTCAACCCCATTATTTTCGAGGG
1 TTTTATTCCTAAAACAC-GATTTTTTCACCATCGAG-GATACTTCAACCTCGTTATTTTCAAGAA
* *
1569585 GACACTCTAATCTCAG
64 GACACTCTAACCTCGG
*
1569601 TTTTATTCCTAAAACACCAATTTTTTC
1 TTTTATTCCTAAAACA-CGATTTTTTC
1569628 GTTGTTGGGG
Statistics
Matches: 152, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
77 3 0.02
78 46 0.30
79 44 0.29
80 56 0.37
81 3 0.02
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.36
Consensus pattern (79 bp):
TTTTATTCCTAAAACACGATTTTTTCACCATCGAGGATACTTCAACCTCGTTATTTTCAAGAAGA
CACTCTAACCTCGG
Found at i:1569683 original size:28 final size:28
Alignment explanation
Indices: 1569634--1569703 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
1569624 TTTCGTTGTT
* * *
1569634 GGGGATACTTCAATTCCGTTA-TTTCTAA
1 GGGGATACTCCAACTCCATTATTTTC-AA
* *
1569662 GGGGATACTCCAACTCTATTATTTTCGA
1 GGGGATACTCCAACTCCATTATTTTCAA
*
1569690 GGGTATACTCCAAC
1 GGGGATACTCCAAC
1569704 CTCGGTGTTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 31 0.89
29 4 0.11
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (28 bp):
GGGGATACTCCAACTCCATTATTTTCAA
Found at i:1569788 original size:107 final size:108
Alignment explanation
Indices: 1569555--1569788 Score: 247
Period size: 108 Copynumber: 2.2 Consensus size: 108
1569545 TTTACAATCA
* * * * *
1569555 GAGATACTTCAACCCCATTATTTTCGAGGGGACACTCTAATCTCAGTTTTATTCCTAAAACACCA
1 GAGATACTTCAACACTATTATTTTCGAGGGGACACTCCAACCTCAGTGTTATTCCTAAAACACCA
* ** * * *
1569620 ATTTTTTCGTTGTTGGGGATACTTCAATTCCGTTATTTCTAAG
66 ATTTTTTCATCATCGAGGATACTTCAATCCCGTTATTTCTAAG
* * * * * * * * *
1569663 GGGATACTCCAACTCTATTATTTTCGAGGGTATACTCCAACCTCGGTGTTATTTCTAAAACATCG
1 GAGATACTTCAACACTATTATTTTCGAGGGGACACTCCAACCTCAGTGTTATTCCTAAAACACCA
*
1569728 A-TTTTTCATCATCGAGGATA-TTCCAATCCCGTTATTTCTGAG
66 ATTTTTTCATCATCGAGGATACTT-CAATCCCGTTATTTCTAAG
*
1569770 GAGATACTTTAACACTATT
1 GAGATACTTCAACACTATT
1569789 TTTATCTCCA
Statistics
Matches: 101, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
106 2 0.02
107 46 0.46
108 53 0.52
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.37
Consensus pattern (108 bp):
GAGATACTTCAACACTATTATTTTCGAGGGGACACTCCAACCTCAGTGTTATTCCTAAAACACCA
ATTTTTTCATCATCGAGGATACTTCAATCCCGTTATTTCTAAG
Found at i:1574676 original size:2 final size:2
Alignment explanation
Indices: 1574669--1574693 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1574659 TAATTGATAC
1574669 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1574694 AGGTGATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1575125 original size:24 final size:24
Alignment explanation
Indices: 1575052--1575126 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 24
1575042 TAGACGTTAT
*
1575052 AATAA-TATTTTATTTTAAGTAAA
1 AATAATTAATTTATTTTAAGTAAA
* * * * *
1575075 AAT-ACTAA-CT-TTTTAAATGAT
1 AATAATTAATTTATTTTAAGTAAA
*
1575096 AGTAATTAATTTATTTTAAGTAAA
1 AATAATTAATTTATTTTAAGTAAA
1575120 AATAATT
1 AATAATT
1575127 TAATAAATTT
Statistics
Matches: 36, Mismatches: 12, Indels: 7
0.65 0.22 0.13
Matches are distributed among these distances:
21 10 0.28
22 6 0.17
23 6 0.17
24 14 0.39
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (24 bp):
AATAATTAATTTATTTTAAGTAAA
Found at i:1581498 original size:23 final size:22
Alignment explanation
Indices: 1581462--1581510 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
1581452 AACAAAAAAG
**
1581462 AAAATAACAAACAAATTTATAT
1 AAAATAACAAACAAAAATATAT
*
1581484 AAAATAAACACACAAAAATATAT
1 AAAAT-AACAAACAAAAATATAT
1581507 AAAA
1 AAAA
1581511 AGGAGGGACA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATAACAAACAAAAATATAT
Found at i:1582113 original size:20 final size:20
Alignment explanation
Indices: 1582088--1582141 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1582078 TTTTACCTAG
*
1582088 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
1582108 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1582128 ATGTATCGATACAT
1 ATGTATCGATACAT
1582142 CTAGTTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1582131 original size:71 final size:71
Alignment explanation
Indices: 1582006--1582138 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
1581996 AAAAATCACA
* * * *
1582006 TTTTTACCCAGATGTATTGATACGTTTTTTAATGTATCGATACATGTATGAATGTATCGATATAT
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATATAT
1582071 TCTATC
66 TCTATC
* * * *
1582077 TTTTTACCTAGATGTATCGATATATTTTTCAATGTATCGATACATTTTTCAATGTATCGATA
1 TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATA
1582139 CATCTAGTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
71 54 1.00
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (71 bp):
TTTTTACCCAGATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATATAT
TCTATC
Found at i:1585671 original size:28 final size:28
Alignment explanation
Indices: 1585614--1585671 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1585604 GTGAAAATTA
* * * * *
1585614 GGGTTGGAGTATCCCTTCGGAGATGGTG
1 GGGTTAGAGTACCCCTTCGAAAATGATG
1585642 GGGTTAGAGTACCCCTTCGAAAATGATG
1 GGGTTAGAGTACCCCTTCGAAAATGATG
1585670 GG
1 GG
1585672 TTTGAAGTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.16, G:0.38, T:0.26
Consensus pattern (28 bp):
GGGTTAGAGTACCCCTTCGAAAATGATG
Found at i:1585744 original size:51 final size:51
Alignment explanation
Indices: 1585677--1585787 Score: 136
Period size: 52 Copynumber: 2.2 Consensus size: 51
1585667 ATGGGTTTGA
*
1585677 AGTATCCCTAAGGTGAAAAA-TCGATATTTTAGAAATAAAAATAGGGTTAG
1 AGTATCCCTAAGGTGAAAAATTCGATATTTTAGAAATAAAAACAGGGTTAG
* * * * *
1585727 AGTATCCCTGATA-GTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGG
1 AGTATCCCT-A-AGGTGAAAAATTCGATATTTTAGAAATAAAAACAGGGTTAG
1585779 AGTATCCCT
1 AGTATCCCT
1585788 TTGAAAATGA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 9 0.17
51 9 0.17
52 34 0.65
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (51 bp):
AGTATCCCTAAGGTGAAAAATTCGATATTTTAGAAATAAAAACAGGGTTAG
Found at i:1585813 original size:80 final size:80
Alignment explanation
Indices: 1585720--1586412 Score: 524
Period size: 80 Copynumber: 8.7 Consensus size: 80
1585710 AATAAAAATA
* * *
1585720 GGGTTAGAGTATCCCTGATAGTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTATC
1 GGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTATC
*
1585785 CCTTTGAAAATGATG
66 CCTTCGAAAATGATG
* * **
1585800 GGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATTTTGGAAGTAAAAACGAGGCTAAAGTATC
1 GGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTATC
1585865 CCTTCGAAAATGATG
66 CCTTCGAAAATGATG
* * ** * * * ** *
1585880 AGGTTGGATTATCCCCGATGGTGAAAAATTTGATGCTTTTGGAAGGAGAAATAGGTTTGGAGTAT
1 GGGTTGGAGTATCCCTAATGGTGAAAAATTTGAT-ATTTTGGAAGTAAAAACGGGGTTGGAGTA-
1585945 TCCC-TCGAAAATGATG
64 TCCCTTCGAAAATGATG
* * *** ** * * * ***
1585961 GGATTAGAGTATCCCTAAAAATCG--AGGTTGGAGTATCCCCTCGG-AG-ATGGTA--GGGTTGG
1 GGGTTGGAGTATCCCTAATGGT-GAAAAATTTGA-TAT---TTTGGAAGTA-AAAACGGGGTTGG
1586020 AGTATCCTCTT-GAAAATGATG
60 AGTATCC-CTTCGAAAATGATG
* **
1586041 GGGTTGGAGTA-CCCTCAATGGTGAAAAA-TTGATATTTTGGAAATAAAAACAAGGTTGGAGTAT
1 GGGTTGGAGTATCCCT-AATGGTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTAT
* * *
1586104 CCTTTCAAAAATAATG
65 CCCTTCGAAAATGATG
* * * * *
1586120 GGGTTAGAGTAT-CGTCGATGGTG-AAAATATTGATATTTTGGAAAG-AGAAACGAGGTTGGAGT
1 GGGTTGGAGTATCCCT-AATGGTGAAAAAT-TTGATATTTTGG-AAGTAAAAACGGGGTTGGAGT
*
1586182 AT-CCTCTCGAAAATGATT
63 ATCCCT-TCGAAAATGATG
* ** *
1586200 GGGTTGGAGTATCCCCAATGGTGAAAAATACGATATTTTGGAAGTAAAAATGGGG-TGGAGTATC
1 GGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTATC
*
1586264 TCC-TCGGAAATGAT-
66 -CCTTCGAAAATGATG
* * * * * * *
1586278 GGGTTGGAGTATCCCCACTGGTGAAAGATTTGATGCTTTTGGAAGGAGAAACAGGGTTGGAGTAT
1 GGGTTGGAGTATCCCTAATGGTGAAAAATTTGAT-ATTTTGGAAGTAAAAACGGGGTTGGAGTAT
* *
1586343 CCCCTCGAAAATGATA
65 CCCTTCGAAAATGATG
* ** * * * *
1586359 GGGTTAGAGTATCCCCGACGGTG-AAAATTTCAATATTTT-GAAATAAAAATGGGG
1 GGGTTGGAGTATCCCTAATGGTGAAAAATTT-GATATTTTGGAAGTAAAAACGGGG
1586413 GTTGATGTAC
Statistics
Matches: 480, Mismatches: 100, Indels: 67
0.74 0.15 0.10
Matches are distributed among these distances:
76 3 0.01
77 2 0.00
78 37 0.08
79 102 0.21
80 245 0.51
81 79 0.16
82 9 0.02
83 3 0.01
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.29
Consensus pattern (80 bp):
GGGTTGGAGTATCCCTAATGGTGAAAAATTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTATC
CCTTCGAAAATGATG
Found at i:1586044 original size:28 final size:27
Alignment explanation
Indices: 1585936--1586056 Score: 99
Period size: 28 Copynumber: 4.5 Consensus size: 27
1585926 AGAAATAGGT
*
1585936 TTGGAGTATTCCCTCGAAAATGATGGGA
1 TTGGAGTA-TCCCTCGAAAATGATGGGG
* *
1585964 TTAGAGTATCCCT--AAAA--ATCGAGG
1 TTGGAGTATCCCTCGAAAATGAT-GGGG
* * * *
1585988 TTGGAGTATCCCCTCGGAGATGGTAGGG
1 TTGGAGTAT-CCCTCGAAAATGATGGGG
*
1586016 TTGGAGTATCCTCTTGAAAATGATGGGG
1 TTGGAGTATCC-CTCGAAAATGATGGGG
1586044 TTGGAGTA-CCCTC
1 TTGGAGTATCCCTC
1586057 AATGGTGAAA
Statistics
Matches: 71, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
23 2 0.03
24 10 0.14
25 8 0.11
26 2 0.03
27 11 0.15
28 37 0.52
29 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (27 bp):
TTGGAGTATCCCTCGAAAATGATGGGG
Found at i:1586414 original size:159 final size:159
Alignment explanation
Indices: 1586012--1586412 Score: 476
Period size: 159 Copynumber: 2.5 Consensus size: 159
1586002 CGGAGATGGT
* *
1586012 AGGGTTGGAGTATCCTCTTGAAAATGATGGGGTTGGAGTA-CCCTCAATGGTGAAAAATT-GATA
1 AGGGTTGGAGTATCCTCTCGAAAATGATAGGGTTGGAGTATCCC-CAATGGTGAAAAATTCGATA
** * * * *
1586075 TTTTGGAAATAAAAACAAGGTTGGAGTATCCTTTCAAAAATAATGGGGTTAGAGTATCGTCGATG
65 TTTTGGAAATAAAAA-TGGGGTGGAGTATCCTCTCAAAAATAATGGGGTTAGAGTATCGCCCATG
1586140 GTGAAAATATTGATATTTTGGAAAGAGAAAC
129 GTGAAAATATTGATATTTTGGAAAGAGAAAC
* *
1586171 -GAGGTTGGAGTATCCTCTCGAAAATGATTGGGTTGGAGTATCCCCAATGGTGAAAAATACGATA
1 AG-GGTTGGAGTATCCTCTCGAAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATTCGATA
* ** * *
1586235 TTTTGGAAGTAAAAATGGGGTGGAGTAT-CTCCTCGGAAATGAT-GGGTTGGAGTATC-CCCACT
65 TTTTGGAAATAAAAATGGGGTGGAGTATCCT-CTCAAAAATAATGGGGTTAGAGTATCGCCCA-T
* *
1586297 GGTGAAAGAT-TTGATGCTTTTGGAAGGAGAAAC
128 GGTGAAA-ATATTGAT-ATTTTGGAAAGAGAAAC
* * * * * *
1586330 AGGGTTGGAGTATCCCCTCGAAAATGATAGGGTTAGAGTATCCCCGACGGTGAAAATTTCAATAT
1 AGGGTTGGAGTATCCTCTCGAAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATTCGATAT
1586395 TTT-GAAATAAAAATGGGG
66 TTTGGAAATAAAAATGGGG
1586413 GTTGATGTAC
Statistics
Matches: 209, Mismatches: 25, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
157 2 0.01
158 42 0.20
159 143 0.68
160 22 0.11
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (159 bp):
AGGGTTGGAGTATCCTCTCGAAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATTCGATAT
TTTGGAAATAAAAATGGGGTGGAGTATCCTCTCAAAAATAATGGGGTTAGAGTATCGCCCATGGT
GAAAATATTGATATTTTGGAAAGAGAAAC
Found at i:1588858 original size:21 final size:20
Alignment explanation
Indices: 1588833--1588889 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
1588823 TACAATGAGA
*
1588833 AATGTATCGATACATTGTAAT
1 AATGTATCGATACATTG-AAG
* * *
1588854 CATGTATTGATACTTTGAAG
1 AATGTATCGATACATTGAAG
*
1588874 AATGTATCAATACATT
1 AATGTATCGATACATT
1588890 TAGCTAAAAC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTGAAG
Found at i:1588928 original size:50 final size:49
Alignment explanation
Indices: 1588874--1589041 Score: 144
Period size: 50 Copynumber: 3.3 Consensus size: 49
1588864 TACTTTGAAG
* *
1588874 AATGTATCAATACATTTAGCTAAAACTTAGAATGTATCGATATAATAAGA
1 AATGTATCGATACATTTAGCTAAAACTAAGAAT-TATCGATATAATAAGA
* * * * * * * *
1588924 AATGTATTGATACATTACAAGC-ATATCTCGATACATAATCGATACT-TTGAAG-
1 AATGTATCGATACATT--TAGCTAAAACT-AAGA-ATTATCGATA-TAAT-AAGA
*
1588976 AATGTATCGATACATTTAGCTAAAACTAAGAATATATCGATATAATGAGA
1 AATGTATCGATACATTTAGCTAAAACTAAGAAT-TATCGATATAATAAGA
1589026 AATGTATCGATACATT
1 AATGTATCGATACATT
1589042 ACAAGCATGT
Statistics
Matches: 90, Mismatches: 18, Indels: 20
0.70 0.14 0.16
Matches are distributed among these distances:
49 5 0.06
50 43 0.48
51 8 0.09
52 28 0.31
53 6 0.07
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (49 bp):
AATGTATCGATACATTTAGCTAAAACTAAGAATTATCGATATAATAAGA
Found at i:1589038 original size:102 final size:102
Alignment explanation
Indices: 1588862--1589049 Score: 331
Period size: 102 Copynumber: 1.8 Consensus size: 102
1588852 ATCATGTATT
* *
1588862 GATACTTTGAAGAATGTATCAATACATTTAGCTAAAACTTAGAATGTATCGATATAATAAGAAAT
1 GATACTTTGAAGAATGTATCAATACATTTAGCTAAAACTAAGAATATATCGATATAATAAGAAAT
*
1588927 GTATTGATACATTACAAGCATATCTCGATACATAATC
66 GTATCGATACATTACAAGCATATCTCGATACATAATC
* *
1588964 GATACTTTGAAGAATGTATCGATACATTTAGCTAAAACTAAGAATATATCGATATAATGAGAAAT
1 GATACTTTGAAGAATGTATCAATACATTTAGCTAAAACTAAGAATATATCGATATAATAAGAAAT
1589029 GTATCGATACATTACAAGCAT
66 GTATCGATACATTACAAGCAT
1589050 GTAGCGATAC
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (102 bp):
GATACTTTGAAGAATGTATCAATACATTTAGCTAAAACTAAGAATATATCGATATAATAAGAAAT
GTATCGATACATTACAAGCATATCTCGATACATAATC
Found at i:1589148 original size:20 final size:20
Alignment explanation
Indices: 1589123--1589172 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
1589113 ATGGTCTAGT
**
1589123 ATCGATACATTTACTTATGA
1 ATCGATACATACACTTATGA
* *
1589143 ATCGATATATACACTTATGT
1 ATCGATACATACACTTATGA
*
1589163 ATCAATACAT
1 ATCGATACAT
1589173 CACCTTATTG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (20 bp):
ATCGATACATACACTTATGA
Found at i:1590810 original size:20 final size:19
Alignment explanation
Indices: 1590764--1590812 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
1590754 AAATTTTCTG
*
1590764 TATATCGATACCAAGATCA
1 TATATCGATACAAAGATCA
*
1590783 TGTATCGATACAAAGCAAT-A
1 TATATCGATACAAAG--ATCA
1590803 TATATCGATA
1 TATATCGATA
1590813 TTTCTAGGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.52
20 10 0.40
21 2 0.08
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (19 bp):
TATATCGATACAAAGATCA
Found at i:1593743 original size:21 final size:21
Alignment explanation
Indices: 1593718--1593757 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1593708 ATGCAAGTTC
1593718 TTGTTCTTC-TTAGCCAATTTG
1 TTGTT-TTCATTAGCCAATTTG
*
1593739 TTGTTTTCATTAGCTAATT
1 TTGTTTTCATTAGCCAATT
1593758 CTTTATTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (21 bp):
TTGTTTTCATTAGCCAATTTG
Found at i:1593800 original size:20 final size:21
Alignment explanation
Indices: 1593775--1593820 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1593765 ACCAACTTAC
*
1593775 AATTCAATTATCTTCTTTT-T
1 AATTCAATTATCTTATTTTCT
* *
1593795 AATTCACTTATTTTATTTTCT
1 AATTCAATTATCTTATTTTCT
1593816 AATTC
1 AATTC
1593821 TTTTTCTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTCAATTATCTTATTTTCT
Found at i:1614366 original size:12 final size:12
Alignment explanation
Indices: 1614345--1614399 Score: 67
Period size: 12 Copynumber: 4.6 Consensus size: 12
1614335 GTCCTTTGCA
*
1614345 AAAAAAAAAAAC
1 AAAAAAACAAAC
*
1614357 AACCAAAA-AAAC
1 AA-AAAAACAAAC
1614369 AAAAAAACAAAC
1 AAAAAAACAAAC
*
1614381 AAACAAACAAAC
1 AAAAAAACAAAC
1614393 AAAAAAA
1 AAAAAAA
1614400 AGAGCCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
11 4 0.11
12 29 0.78
13 4 0.11
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:1614371 original size:8 final size:8
Alignment explanation
Indices: 1614343--1614399 Score: 71
Period size: 8 Copynumber: 7.0 Consensus size: 8
1614333 GTGTCCTTTG
1614343 CAAAAAAA
1 CAAAAAAA
1614351 -AAAAACAA
1 CAAAAA-AA
1614359 CCAAAAAAA
1 -CAAAAAAA
1614368 CAAAAAAA
1 CAAAAAAA
*
1614376 CAAACAAA
1 CAAAAAAA
*
1614384 CAAACAAA
1 CAAAAAAA
1614392 CAAAAAAA
1 CAAAAAAA
1614400 AGAGCCAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
7 5 0.11
8 32 0.73
9 2 0.05
10 5 0.11
ACGTcount: A:0.82, C:0.18, G:0.00, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:1614400 original size:4 final size:4
Alignment explanation
Indices: 1614353--1614395 Score: 59
Period size: 4 Copynumber: 10.8 Consensus size: 4
1614343 CAAAAAAAAA
* * *
1614353 AAAC AACC AAAA AAAC AAAA AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1614396 AAAAAGAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.79, C:0.21, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1615826 original size:20 final size:20
Alignment explanation
Indices: 1615801--1615857 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
1615791 TTTTCACAAT
1615801 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTGTTCA
*
1615821 TTGTATCGATACACTGTTCA
1 TTGTATCGATACATTGTTCA
* *
1615841 TTGTACCAATACATTGT
1 TTGTATCGATACATTGT
1615858 ATCGATACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (20 bp):
TTGTATCGATACATTGTTCA
Found at i:1615919 original size:13 final size:13
Alignment explanation
Indices: 1615901--1615930 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1615891 ATACATTTTG
1615901 CATTGTATCAATA
1 CATTGTATCAATA
*
1615914 CATTGTATCGATA
1 CATTGTATCAATA
1615927 CATT
1 CATT
1615931 ACCTAAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTGTATCAATA
Found at i:1615926 original size:33 final size:32
Alignment explanation
Indices: 1615819--1615930 Score: 106
Period size: 33 Copynumber: 3.5 Consensus size: 32
1615809 ATACATTGTT
*
1615819 CATTGTATCGATACACTGTT-CATTGTACCAATA
1 CATTGTATCGATACA-TTTTGCATTGTA-CAATA
* ** **
1615852 CATTGTATCGATACATTCTGGGTT-TAC-CCA
1 CATTGTATCGATACATTTTGCATTGTACAATA
*
1615882 GA-TGTATCGATACATTTTGCATTGTATCAATA
1 CATTGTATCGATACATTTTGCATTGTA-CAATA
1615914 CATTGTATCGATACATT
1 CATTGTATCGATACATT
1615931 ACCTAAACGT
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
29 18 0.30
30 4 0.07
31 2 0.03
32 6 0.10
33 31 0.51
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (32 bp):
CATTGTATCGATACATTTTGCATTGTACAATA
Found at i:1616357 original size:33 final size:33
Alignment explanation
Indices: 1616320--1616386 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1616310 TTCAACGATT
1616320 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1616353 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1616386 T
1 T
1616387 TTAAGTAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1616358 original size:13 final size:13
Alignment explanation
Indices: 1616340--1616364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1616330 CATAAAGTGT
1616340 TGTATCGATACAA
1 TGTATCGATACAA
1616353 TGTATCGATACA
1 TGTATCGATACA
1616365 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1616445 original size:13 final size:13
Alignment explanation
Indices: 1616427--1616451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1616417 ATCACTTAAG
1616427 TGTATCGATACAT
1 TGTATCGATACAT
1616440 TGTATCGATACA
1 TGTATCGATACA
1616452 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1616516 original size:52 final size:52
Alignment explanation
Indices: 1616460--1616588 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
1616450 CACTGATCTT
*
1616460 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* **
1616512 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1616564 TGTATCAATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1616589 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1623787 original size:11 final size:11
Alignment explanation
Indices: 1623746--1623780 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
1623736 GTTCTTTTCC
*
1623746 AAAAAAAAAAC
1 AAAAAAAAAAG
1623757 AAAACAAAAAAG
1 AAAA-AAAAAAG
1623769 AAAAAAAAAAG
1 AAAAAAAAAAG
1623780 A
1 A
1623781 GGAAAAACCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.89, C:0.06, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1624758 original size:33 final size:32
Alignment explanation
Indices: 1624714--1624858 Score: 213
Period size: 33 Copynumber: 4.5 Consensus size: 32
1624704 TTCTTCAAAT
1624714 CTCTTCCTAAAGCCCACACAAGTCGGTGGCAAC
1 CTCTT-CTAAAGCCCACACAAGTCGGTGGCAAC
1624747 CTTCTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 C-TCTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
1624780 CTTCTTCCAAAGCCCACACAAGTCGGTGGCAAC
1 C-TCTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
1624813 CACTCTCTAAAGCCCACACAAGTCGATGGCAAC
1 CTCT-TCTAAAGCCCACACAAGTCGGTGGCAAC
1624846 C-CTTCT-AAGCCCA
1 CTCTTCTAAAGCCCA
1624859 ATATAGCTGG
Statistics
Matches: 106, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
30 7 0.07
31 3 0.03
32 4 0.04
33 88 0.83
34 4 0.04
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.19
Consensus pattern (32 bp):
CTCTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:1624915 original size:49 final size:49
Alignment explanation
Indices: 1624851--1625794 Score: 1165
Period size: 49 Copynumber: 19.9 Consensus size: 49
1624841 GCAACCCTTC
* * *
1624851 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * * *
1624900 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1624949 TAAGTCCAATGTAGCTGGCCTT-AACTCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAA-TCAGCACATTGGCACCTTTATCTT
*
1624997 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---A---T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * *
1625040 TATGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
*
1625089 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---A---T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625132 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
*
1625181 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC---A---T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625224 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC---A---T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625267 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * *
1625316 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625365 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTT
1625417 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * * * *
1625460 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625509 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625558 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* * *
1625607 TAAGTCCAATGTAGCTGTCCTTGAATCAGCACATTGGCACC-TCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
1625655 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
1625698 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TTT--ATCTT
* *
1625750 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
1625795 TTCTCATCTT
Statistics
Matches: 797, Mismatches: 59, Indels: 75
0.86 0.06 0.08
Matches are distributed among these distances:
43 239 0.30
44 2 0.00
46 6 0.01
47 1 0.00
48 89 0.11
49 372 0.47
50 2 0.00
51 1 0.00
52 83 0.10
53 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
Found at i:1625129 original size:92 final size:92
Alignment explanation
Indices: 1624943--1625785 Score: 1041
Period size: 92 Copynumber: 9.0 Consensus size: 92
1624933 TTGGCACCTT
* * * *
1624943 CACCATTAAGTCCAATGTAGCTGGCCTT-AACTCAGCACATTGGCACC-TCACCTTTAAGTCCAA
1 CACCATTAAGTCCAATATAGCTGGCCTTGAA-TCAGCATATTGGCACCTTTATCTTTAAGTCCAA
*
1625006 TGTAGCTGGCCTTGACTCAGCACATTGG
65 TGTAGCTGGCCTTGAATCAGCACATTGG
*
1625034 CACCATTATGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
1 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
*
1625099 GTAGCTGGCCTTGACTCAGCACATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
1625126 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
1 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
*
1625191 GTAGCTGGCCTTGACTCAGCACATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
1625218 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC---A---TTAAGTCCAAT
1 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
* *
1625277 ATAGCTGGCCTTGAATCAGCATATTGG
66 GTAGCTGGCCTTGAATCAGCACATTGG
* * * * *
1625304 CACCTTTATCTTTAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAG
1 CACC---A---TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
* *
1625369 TCCAATATAGCTGGCCTTGAATCAGCATATTGG
60 TCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* *
1625402 CACCTTTTCCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-----CTTT
1 CA------CCA---TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTT
* *
1625461 AAGTCCAATATAGCTGGCCTTGAATCAGCATATTGG
57 AAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG
1625497 CACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
1 ------CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
*
1625562 TCCAATGTAGCTGGCCTTGACTCAGCACATTGG
60 TCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* * * * *
1625595 CACCTTCATCTTTAAGTCCAATGTAGCTGTCCTTGAATCAGCACATTGGCACC-TCACCTTTAAG
1 CA-C--CA---TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAG
1625659 TCCAATGTAGCTGGCCTTGAATCAGCACATTGG
60 TCCAATGTAGCTGGCCTTGAATCAGCACATTGG
* *
1625692 CACCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTC
1 CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCC
1625757 AATGTAGCTGGCCTTGAATCAGCACATTG
63 AATGTAGCTGGCCTTGAATCAGCACATTG
1625786 ACATCCTTTT
Statistics
Matches: 677, Mismatches: 33, Indels: 80
0.86 0.04 0.10
Matches are distributed among these distances:
86 39 0.06
89 2 0.00
91 80 0.12
92 260 0.38
93 3 0.00
94 1 0.00
95 85 0.13
96 1 0.00
97 43 0.06
98 116 0.17
100 1 0.00
101 44 0.06
104 2 0.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (92 bp):
CACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGG
Found at i:1625285 original size:24 final size:24
Alignment explanation
Indices: 1625215--1625285 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 24
1625205 CTCAGCACAT
1625215 TGGCACCATTAAGTCCAATATAGC
1 TGGCACCATTAAGTCCAATATAGC
** *
1625239 TGG--CC-TTGAA-T-CAGCATA-T
1 TGGCACCATT-AAGTCCAATATAGC
1625258 TGGCACCATTAAGTCCAATATAGC
1 TGGCACCATTAAGTCCAATATAGC
1625282 TGGC
1 TGGC
1625286 CTTGAATCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 7 0.21
22 7 0.21
23 5 0.15
24 7 0.21
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (24 bp):
TGGCACCATTAAGTCCAATATAGC
Found at i:1625309 original size:21 final size:21
Alignment explanation
Indices: 1625242--1625309 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1625232 ATATAGCTGG
1625242 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
** *
1625263 CCATT-AAGTCCAATATAGCTGG--
1 CC-TTGAA-T-CAGCATA-TTGGCA
1625285 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
1625306 CCTT
1 CCTT
1625310 TATCTTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 14
0.63 0.11 0.26
Matches are distributed among these distances:
19 3 0.09
20 5 0.15
21 11 0.32
22 7 0.21
23 5 0.15
24 3 0.09
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:1625824 original size:55 final size:52
Alignment explanation
Indices: 1625695--1625832 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
1625685 ACATTGGCAC
* *
1625695 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* *
1625747 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* * * *
1625802 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
1625833 ACATATTGGC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
52 38 0.52
53 2 0.03
54 5 0.07
55 28 0.38
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:1626682 original size:33 final size:33
Alignment explanation
Indices: 1626645--1626711 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1626635 TTCAACGATT
1626645 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1626678 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1626711 T
1 T
1626712 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1626683 original size:13 final size:13
Alignment explanation
Indices: 1626665--1626689 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1626655 CATAAAGTGT
1626665 TGTATCGATACAA
1 TGTATCGATACAA
1626678 TGTATCGATACA
1 TGTATCGATACA
1626690 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1626770 original size:13 final size:13
Alignment explanation
Indices: 1626752--1626776 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1626742 ATCACTTAAG
1626752 TGTATCGATACAT
1 TGTATCGATACAT
1626765 TGTATCGATACA
1 TGTATCGATACA
1626777 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1626841 original size:52 final size:52
Alignment explanation
Indices: 1626785--1626913 Score: 206
Period size: 52 Copynumber: 2.5 Consensus size: 52
1626775 CACTGATCTT
*
1626785 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
**
1626837 TGTATCGATACATGCA-AGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGA-CAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1626889 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGACAAATTT
1626914 TCATATTTCG
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
51 1 0.01
52 70 0.99
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGACAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1627725 original size:14 final size:14
Alignment explanation
Indices: 1627706--1627734 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1627696 TTTGATGATT
1627706 TAAAGTCATTTGTG
1 TAAAGTCATTTGTG
1627720 TAAAGTCATTTGTG
1 TAAAGTCATTTGTG
1627734 T
1 T
1627735 GCCTAAAATG
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:0.28, C:0.07, G:0.21, T:0.45
Consensus pattern (14 bp):
TAAAGTCATTTGTG
Found at i:1632393 original size:28 final size:26
Alignment explanation
Indices: 1632361--1632437 Score: 109
Period size: 28 Copynumber: 2.8 Consensus size: 26
1632351 AATTTTCACA
1632361 ATCGGGGATACTCCAACCCCGTTATT
1 ATCGGGGATACTCCAACCCCGTTATT
1632387 CCATCGGGGATACTCCAACCCCGTTATT
1 --ATCGGGGATACTCCAACCCCGTTATT
*
1632415 TTCGAGGGGATACTCCAACCCCG
1 ATC--GGGGATACTCCAACCCCG
1632438 ACTTTGTATC
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
26 2 0.04
28 44 0.96
ACGTcount: A:0.22, C:0.34, G:0.21, T:0.23
Consensus pattern (26 bp):
ATCGGGGATACTCCAACCCCGTTATT
Found at i:1632558 original size:108 final size:108
Alignment explanation
Indices: 1632315--1632592 Score: 312
Period size: 108 Copynumber: 2.6 Consensus size: 108
1632305 TCTTAATCGA
* * * * * * * *
1632315 GGATACTCCAACTCCGATTTTATTTCCAAAATACCAA-ATTTTCACAATCGGGGATACTCCAACC
1 GGATACTCCAACCCCGACTTTATATCTAAAATACTAATTTTTTTATAATCGGGGATACTCCAACC
*
1632379 CCGTTATTCCATCGGGGATACTCCAACCCCGTTATTTTCGAGG
66 CCGTTATTCCATCGGGGATACTCCAACCCCGTTATTTTCAAGG
* * * * *
1632422 GGATACTCCAACCCCGACTTTGTATCTAAAATATTGATTTTTTTATAATCGGGGGTACTCTAACC
1 GGATACTCCAACCCCGACTTTATATCTAAAATACTAATTTTTTTATAATCGGGGATACTCCAACC
*
1632487 CCGTTATGT-CATCGGGGATACTCCAATCCCGTT-TTTTCCAAGG
66 CCGTTAT-TCCATCGGGGATACTCCAACCCCGTTATTTT-CAAGG
** * * * * *
1632530 GGATACTCCAACCTTGATTTTATTTCTAAAATACTAA-TTTTTCACAATCAGGGATACTCCAAC
1 GGATACTCCAACCCCGACTTTATATCTAAAATACTAATTTTTTTATAATCGGGGATACTCCAAC
1632593 TTCGATTTTA
Statistics
Matches: 141, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
107 54 0.38
108 86 0.61
109 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (108 bp):
GGATACTCCAACCCCGACTTTATATCTAAAATACTAATTTTTTTATAATCGGGGATACTCCAACC
CCGTTATTCCATCGGGGATACTCCAACCCCGTTATTTTCAAGG
Found at i:1632589 original size:51 final size:52
Alignment explanation
Indices: 1632529--1632643 Score: 171
Period size: 51 Copynumber: 2.2 Consensus size: 52
1632519 TTTTTCCAAG
* * * *
1632529 GGGATACTCCAACCTT-GATTTTATTTCTAAAATACTAATTTTTCACAATCA
1 GGGATACTCCAACCTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCA
*
1632580 GGGATACTCCAA-CTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCG
1 GGGATACTCCAACCTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCA
1632631 GGGATACTCCAAC
1 GGGATACTCCAAC
1632644 ACCCGTTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
50 3 0.05
51 54 0.95
ACGTcount: A:0.32, C:0.24, G:0.10, T:0.33
Consensus pattern (52 bp):
GGGATACTCCAACCTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCA
Found at i:1632763 original size:79 final size:79
Alignment explanation
Indices: 1632578--1632796 Score: 253
Period size: 79 Copynumber: 2.7 Consensus size: 79
1632568 TTTTCACAAT
** *
1632578 CAGGGATACTCCAACTTCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAA
1 CAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCATTTTC-CACAATCGGGGATACTCCAA
1632643 CACCCGTTATTTTCA
65 CACCCGTTATTTTCA
* *** * * * * *
1632658 CAGGGATACTCCAACCCTGGCCTTATTTCTAAAGCATCGATTTTCCACAATTGGGGATACTCTAA
1 CAGGGATACTCCAACCCCGATTTTATTTCCAAAACA-CCATTTTCCACAATCGGGGATACTCCAA
1632723 C-CCCGTTATTTTCGA
65 CACCCGTTATTTTC-A
* * *
1632738 -GGGGATACTCCAACCCCGATTTTATTTCCAAAACACCTATTTTCCATAATCAGGGATAC
1 CAGGGATACTCCAACCCCGATTTTATTTCCAAAACACC-ATTTTCCACAATCGGGGATAC
1632797 CCCACCTCTG
Statistics
Matches: 113, Mismatches: 23, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
78 1 0.01
79 58 0.51
80 48 0.42
81 6 0.05
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (79 bp):
CAGGGATACTCCAACCCCGATTTTATTTCCAAAACACCATTTTCCACAATCGGGGATACTCCAAC
ACCCGTTATTTTCA
Found at i:1637987 original size:8 final size:8
Alignment explanation
Indices: 1637970--1638000 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
1637960 TTTCTTCTTA
1637970 AAAAAAAC
1 AAAAAAAC
*
1637978 AAACAAAC
1 AAAAAAAC
1637986 AAAAAAAC
1 AAAAAAAC
1637994 AAAAAAA
1 AAAAAAA
1638001 AACCTTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:1639089 original size:61 final size:61
Alignment explanation
Indices: 1638989--1639197 Score: 303
Period size: 61 Copynumber: 3.4 Consensus size: 61
1638979 CTCTTTTAGC
* * * * *
1638989 CCTTCTAGTCCTCAAAGAGGAGGATGCCTTTTCCTTTTAAAGCCCATACAAGTTGATGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1639050 CTTTTTAGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1639111 CCTTTTAGTCCTCAAAGAGCGGGATGCCTTCTAC-TTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
*
1639171 CCTCTTAGTCCTCAAAGAGCAGGATGC
1 CCTTTTAGTCCTCAAAGAGCAGGATGC
1639198 ACTTTACTTT
Statistics
Matches: 132, Mismatches: 16, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
60 50 0.38
61 82 0.62
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (61 bp):
CCTTTTAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1639325 original size:43 final size:43
Alignment explanation
Indices: 1639178--1639474 Score: 361
Period size: 43 Copynumber: 6.8 Consensus size: 43
1639168 GCACCTCTTA
* * * *
1639178 GTCCTCAAAGAGCAGGATGCACTTTACTTTCCTCTTCCCGCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTC-CTTT
* *
1639222 GTCCTCAAAGAGCAGGACGCACTTCA-TTTCCTTCTTTTCCCTTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTT-TTCT-CC-TTT
*
1639267 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCATTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTTT
* *
1639310 GTCCTCAAAGAGCAGGACGCATTTTATTTTCCTTTGCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTTT
1639353 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTTT
1639396 GTCCTCAAAGAGCAGGA--CACGTTCTATTCCCTT-CTTTTCTCCTTTT
1 GTCCTCAAAGAGCAGGACGCAC-TT-TATT---TTCCTTTTCTCC-TTT
* * *
1639442 GTCCTCAAAGAGTAGGACACACTTCA-TTTCCTT
1 GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTT
1639475 CTTTTCCCTT
Statistics
Matches: 225, Mismatches: 15, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
41 3 0.01
42 4 0.02
43 114 0.51
44 29 0.13
45 42 0.19
46 28 0.12
47 2 0.01
48 3 0.01
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.37
Consensus pattern (43 bp):
GTCCTCAAAGAGCAGGACGCACTTTATTTTCCTTTTCTCCTTT
Found at i:1639573 original size:62 final size:62
Alignment explanation
Indices: 1639475--1639595 Score: 199
Period size: 62 Copynumber: 2.0 Consensus size: 62
1639465 TCATTTCCTT
* *
1639475 CTTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGC
1 CTTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCT-TAGTCCTCAAAGAGCAGGACGC
*
1639538 CTTTT-CCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGTAGGA
1 CTTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGA
1639596 TGCTCTCTCC
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
61 17 0.31
62 33 0.60
63 5 0.09
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (62 bp):
CTTTTCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGCAGGACGC
Found at i:1639739 original size:61 final size:61
Alignment explanation
Indices: 1639674--1639813 Score: 167
Period size: 61 Copynumber: 2.3 Consensus size: 61
1639664 CATATTTCAA
*
1639674 TCCTCAAAGAGTAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGAAACCTTC-CAC
1 TCCTCAAAGAGTAGGACGCCTTTC-CTTTGCAAAGCCCACACAAGTTGGTGAAA-CTTCACAC
* ** * ** * *
1639735 TCCTCAAAGAGCAGGACGCCTTTCCTTTTTAAAGGCCACACAAGTTGGTGGCACTTCATAG
1 TCCTCAAAGAGTAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGAAACTTCACAC
1639796 TCCTCAAAGAGTAGGACG
1 TCCTCAAAGAGTAGGACG
1639814 ATCTCTCCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
60 4 0.06
61 58 0.87
62 5 0.07
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (61 bp):
TCCTCAAAGAGTAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGAAACTTCACAC
Found at i:1639767 original size:216 final size:216
Alignment explanation
Indices: 1639481--1640022 Score: 761
Period size: 216 Copynumber: 2.5 Consensus size: 216
1639471 CCTTCTTTTC
* *
1639481 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTTAAAGAGCAGGACGCCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
* *
1639546 TTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGTAGGATGCTCTCTCCTTTCG
66 TTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGTAGGACGATCTCTCCTTTCG
* * * *
1639611 CCCTTTAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACATAA-CTTGGTGGCATATTTCAAT
131 CCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGC-TGGTGGCA-ACTTCAAT
* * *
1639675 CCTCAAAGAGTAGGATGCTTTCT
194 CCTCAAAGAGCAGGACGCCTTCT
** * * *
1639698 -CTTTGCAAAGCCCACACAAGTTGGTGAAAC-CTTCCACTCCTCAAAGAGCAGGACGCC-TTTCC
1 CCTTT-CAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCC
* *
1639760 TTTTTAAAGGCCACACAAGTTGGTGGCACTTCATAGTCCTCAAAGAGTAGGACGATCTCTCCTTT
65 -TTTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGTAGGACGATCTCTCCTTT
* * * * * *
1639825 TGCCTTTTTGTCCTCAAAGAGCAGGACGCCTTTTAAAACCCACACAAGCTGGTGGCACCTTCAGT
129 CGCCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGCTGGTGGCAACTTCAAT
1639890 CCTCAAAGAGCAGGACGCCTTCT
194 CCTCAAAGAGCAGGACGCCTTCT
* *
1639913 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTTCCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
*
1639978 TTTAAAGCCCACACAAGTTGGTGGTACCTT-TTAGTCCTCAAAGAG
66 TTTAAAGCCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAG
1640023 CAAGACACCT
Statistics
Matches: 284, Mismatches: 34, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
215 52 0.18
216 201 0.71
217 31 0.11
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.28
Consensus pattern (216 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTTTCCT
TTTAAAGCCCACACAAGTTGGTGGCACTTCTTAGTCCTCAAAGAGTAGGACGATCTCTCCTTTCG
CCCTTTAGTCCTCAAAGAGCAGGACGCCTTTCAAAACCCACACAAGCTGGTGGCAACTTCAATCC
TCAAAGAGCAGGACGCCTTCT
Found at i:1639978 original size:62 final size:61
Alignment explanation
Indices: 1639853--1640090 Score: 345
Period size: 62 Copynumber: 3.9 Consensus size: 61
1639843 GAGCAGGACG
* * * *
1639853 CCTTTTAAAACCCACACAAGCTGGTGGCACCTTC-AGTCCTCAAAGAGCAGGACGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
*
1639913 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * *
1639975 CCTTTTAAAGCCCACACAAGTTGGTGGTACCTTT-TAGTCCTCAAAGAGCAAGACACCTTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCAGGACGCC-TTTT
* *
1640037 CTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGAC
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGAC
1640091 ACTCTCTCCT
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
60 28 0.17
61 26 0.16
62 105 0.66
63 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1640079 original size:123 final size:122
Alignment explanation
Indices: 1639853--1640090 Score: 361
Period size: 123 Copynumber: 1.9 Consensus size: 122
1639843 GAGCAGGACG
* *
1639853 CCTTTTAAAACCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTT
1 CCTTTTAAAACCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAAGACACCTTCTCCTTT
* *
1639918 TAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGTAGGACGCCTTTT
66 TAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGACGCCTTTT
* * * * * *
1639975 CCTTTTAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCCTCAAAGAGCAAGACACCTTTTTCTT
1 CCTTTTAAAACCCACACAAGCTGGTGGCACC-TTCAGTCCTCAAAGAGCAAGACACC-TTCTCCT
1640040 TTTAAAGCCCACACAAGTTGGTGGCAC-TTCCTAGTCCTCAAAGAGCAGGAC
64 TTTAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGAC
1640091 ACTCTCTCCT
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
122 28 0.27
123 44 0.42
124 32 0.31
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.27
Consensus pattern (122 bp):
CCTTTTAAAACCCACACAAGCTGGTGGCACCTTCAGTCCTCAAAGAGCAAGACACCTTCTCCTTT
TAAAGCCCACACAAGTTGGTGGCACTTTCCTAGTCCTCAAAGAGCAGGACGCCTTTT
Found at i:1640192 original size:218 final size:226
Alignment explanation
Indices: 1639888--1640775 Score: 756
Period size: 218 Copynumber: 3.9 Consensus size: 226
1639878 GGCACCTTCA
1639888 GTCCTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTC
1 GTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCACTTTTCTAGTC
* *
1639953 CTCAAAGAGTAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCCTCA
60 CTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCA
* * *
1640018 AAGAGCAAGACACCTTTTTCTTTTTAAAGCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAG
125 AAGAGCAAGACACCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAG
* *
1640083 AGCAGGACACTCTC-TCCT-T-T-CG-CCCT-T-TT-
190 AGCAGGACACTCTCAACCTATATAAGTCCCTGTATTC
* *
1640112 GTCCTCAAAGAGCAGGGCGCCTTTCAAAGCTCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
1 GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
* * *
1640177 GAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTTAAAGAG
66 GAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAG
** * * * *
1640241 CAAGA-TGCTTTCTCCTTTTAAAGACCACTCGAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGTA
130 CAAGACACCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCTAGTCCTCAAAGAGCA
* * ***
1640304 GGACGCCTTTCAAAACCTATATAAGTTGGTGGTACTTCCC
194 GGAC-ACTCTC--AACCTATATAAGTCCCT-GTA-TT--C
* * *
1640344 AGTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTTAA
1 -GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAA
* *
1640408 AGAGCAGGACGCC---T-C---TAAACGCGCACACAAGTTGGTGGCACC-TCTAGTCCTCAAAGA
65 AGAGCAGGACGCCTTTTCCTTTTAAA-GCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA
* * * * *
1640465 GCAGGACACC-TTCACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTTGTCCTCAAAAAGC
129 GCAAGACACCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGC
* * * *** *
1640529 AGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTC
193 AGGACA-C----TC---TC-AA-CCTATATAAGTCCCT-G---TATTC
* * * *
1640577 TGTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTC-AG
1 -GTCCTCAAAGAGCAGGAC-GC-----C-TTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAG
1640641 TCCTCAAAGAGCAGGACG------CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTTCAGTCC
58 TCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT-AGTCC
* * * * *
1640699 TCAAGGAGCAGGAC-GCATTCGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCA
122 TCAAAGAGCAAGACACCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCA
1640763 AAGAGCAGGACAC
187 AAGAGCAGGACAC
1640776 ATCTTCCTTT
Statistics
Matches: 551, Mismatches: 63, Indels: 85
0.79 0.09 0.12
Matches are distributed among these distances:
217 51 0.09
218 107 0.19
221 3 0.01
222 2 0.00
223 2 0.00
224 24 0.04
225 54 0.10
226 38 0.07
227 1 0.00
228 1 0.00
229 3 0.01
230 1 0.00
232 28 0.05
233 80 0.15
234 1 0.00
235 2 0.00
236 1 0.00
238 1 0.00
239 3 0.01
240 90 0.16
241 58 0.11
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (226 bp):
GTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAA
GAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGC
AAGACACCTTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTAGTCCTCAAAGAGCAGG
ACACTCTCAACCTATATAAGTCCCTGTATTC
Found at i:1640347 original size:55 final size:55
Alignment explanation
Indices: 1640112--1640773 Score: 328
Period size: 55 Copynumber: 11.3 Consensus size: 55
1640102 TCGCCCTTTT
* * * * * *
1640112 GTCCTCAAAGAGCAGGGCGCCTTTCAAAGCTCACACAAGTTGGTGGCACTTTTCTA
1 GTCCTCAAAGAGTAGGACGCCTTTCAAAACCCACACAAGTTGGTGGCAC-TTCCCA
* * * * * *
1640168 GTCCTCAAAGAGCAGGATGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCATTTTCTA
1 GTCCTCAAAGAGTAGGACGCC-TTT-C----AAAACCCACACAAGTTGGTGGCACTTCCCA
* * * * * * * *
1640229 GTCCTTAAAGAGCAAGATGCTTTCTCCTTTTAAAGA-CCACTCGAGTTGGTGGCACCTT-TCA
1 GTCCTCAAAGAG-TAG--G---ACGCCTTTCAAA-ACCCACACAAGTTGGTGGCA-CTTCCCA
* * * *
1640290 GTCCTCAAAGAGTAGGACGCCTTTCAAAACCTATATAAGTTGGTGGTACTTCCCA
1 GTCCTCAAAGAGTAGGACGCCTTTCAAAACCCACACAAGTTGGTGGCACTTCCCA
* * *
1640345 GTCCTCAAAGAGTAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCATTTTCCA
1 GTCCTCAAAGAGTAGGACGCCTTTCAAAACCCACACAAGTTGGTGGCACTTCCCA
* * * * *
1640400 GTCCTTAAAGAGCAGGACGCC--TCTAAACGCGCACACAAGTTGGTGGCACCT-CTA
1 GTCCTCAAAGAGTAGGACGCCTTTCAAAAC-C-CACACAAGTTGGTGGCACTTCCCA
* * * * **
1640454 GTCCTCAAAGAGCAGGACACCTTCACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTT
1 GTCCTCAAAGAGTAGG--A----CGCCTTTCAAAACCCACACAAGTTGGTGGCAC-TTCCCA
* * * * ** *
1640516 GTCCTCAAAAAGCAGGACACCTTTTTCTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCT
1 GTCCTCAAAGAGTAGGAC-GC-----C-TTTCAAAACCCACACAAGTTGGTGGCACTTCCCA
* * * *
1640578 GTCCTCAAAGAGTAGGACACCTTTTTCTTTTCAAAGCCCACATAAGTTGGTGGCACCTT-TCA
1 GTCCTCAAAGAGTAGGAC-GC-----C-TTTCAAAACCCACACAAGTTGGTGGCA-CTTCCCA
* * * **
1640640 GTCCTCAAAGAGCAGGACGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCA
1 GTCCTCAAAGAGTAGGACGCCTTTCAAAACCCACACAAGTTGGTGGCACTTCCCA
* * * * * *
1640695 GTCCTCAAGGAGCAGGACGCATTCGCCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCTA
1 GTCCTCAA--AG-AGTA-GGA--CGCCTTTCAAAACCCACACAAGTTGGTGGCACTTCCCA
*
1640756 GTCCTCAAAGAGCAGGAC
1 GTCCTCAAAGAGTAGGAC
1640774 ACATCTTCCT
Statistics
Matches: 497, Mismatches: 66, Indels: 87
0.76 0.10 0.13
Matches are distributed among these distances:
53 5 0.01
54 25 0.05
55 145 0.29
56 22 0.04
57 8 0.02
58 8 0.02
59 4 0.01
60 24 0.05
61 95 0.19
62 124 0.25
63 31 0.06
64 1 0.00
66 3 0.01
67 2 0.00
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (55 bp):
GTCCTCAAAGAGTAGGACGCCTTTCAAAACCCACACAAGTTGGTGGCACTTCCCA
Found at i:1640534 original size:62 final size:62
Alignment explanation
Indices: 1640131--1640900 Score: 734
Period size: 61 Copynumber: 13.0 Consensus size: 62
1640121 GAGCAGGGCG
* * *
1640131 CCTTTCAAAGCTCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * *
1640193 CCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTTAAAGAGCAAGATGCTTTCT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * * *
1640254 CCTTTTAAAGACCACTCGAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGTAGGACG------
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * * * * * *
1640309 CCTTTCAAAACCTATATAAGTTGGTGGTAC-TTCCCAGTCCTCAAAGAGTAGGACG------
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* *
1640364 CCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGACG-C--CT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * *
1640422 -C--T-AAACGCGCACACAAGTTGGTGGCAC--CTCTAGTCCTCAAAGAGCAGGACACCTTCA
1 CCTTTCAAA-GCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * * *
1640479 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTTGTCCTCAAAAAGCAGGACACCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCC-TTCT
* * * *
1640542 CTTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCT-GTCCTCAAAGAGTAGGACACCTTTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCC-TTCT
* * *
1640604 CTTTTCAAAGCCCACATAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACG-C--CT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * *
1640662 --TTT-AAAGCCCACACAAGTTGGTGGCACTTTTC-AGTCCTCAAGGAGCAGGACGCATTCG
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
* * *
1640720 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-TTTCTAGTCCTCAAAGAGCAGGAC-ACATCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTC-T
* * * * * * * * * *
1640781 CCTTTTAAAGTCCACACAAGTTAGTGGCATTTTTC-AATCCACAAGGAGCATGACGCATTTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
*
1640842 CCTTTCAAAGCCCACACGAGTTGGTGGCACTTTT-TAGTCCTCAAAGAGCAGGACGCCTT
1 CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTT
1640901 TTTCTTTTCT
Statistics
Matches: 595, Mismatches: 83, Indels: 61
0.81 0.11 0.08
Matches are distributed among these distances:
54 26 0.04
55 154 0.26
56 3 0.01
57 2 0.00
58 3 0.01
60 30 0.05
61 207 0.35
62 133 0.22
63 37 0.06
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.27
Consensus pattern (62 bp):
CCTTTCAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAGGACGCCTTCT
Found at i:1640997 original size:45 final size:43
Alignment explanation
Indices: 1640903--1641095 Score: 159
Period size: 45 Copynumber: 4.5 Consensus size: 43
1640893 GACGCCTTTT
* * * *
1640903 TCTTTTCTCCTTTGTCCTCAAAGAGCAGGACAAACTTCATTCCC
1 TCTTTTC-CCTTTGTCCTCAAAGAGCAGGACACATTTCTTTTCC
* *
1640947 TTCTTTTCCCTTTTGTCCTCAAAGAGTAGGACGCATTTCGTTTTCC
1 -TCTTTTCCC-TTTGTCCTCAAAGAGCAGGACACATTTC-TTTTCC
*
1640993 TCTTTTTCACTTTGTCCTC-AAGAAGCAGGACAC-TTTCCTTTT-C
1 TC-TTTTCCCTTTGTCCTCAAAG-AGCAGGACACATTT-CTTTTCC
* * * *
1641036 T-TTTTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTC-ATT-C
1 TCTTTTCCCTTTGTCCTCAAAGAGCAGGACAC-ATTTCTTTTCC
1641076 TCTTTT-CCTTTGTCCTCAAA
1 TCTTTTCCCTTTGTCCTCAAA
1641096 AAATGGGACA
Statistics
Matches: 124, Mismatches: 15, Indels: 23
0.77 0.09 0.14
Matches are distributed among these distances:
40 18 0.15
41 26 0.21
42 5 0.04
43 2 0.02
44 12 0.10
45 51 0.41
46 10 0.08
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (43 bp):
TCTTTTCCCTTTGTCCTCAAAGAGCAGGACACATTTCTTTTCC
Found at i:1641090 original size:40 final size:41
Alignment explanation
Indices: 1640996--1641094 Score: 121
Period size: 40 Copynumber: 2.4 Consensus size: 41
1640986 GTTTTCCTCT
* * *
1640996 TTTTCACTTTGTCCTCAAGAAGCAGGACACTTTCCTTTTCTT
1 TTTTC-CTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTC
* *
1641038 TTTTCCTTTGTCCTCAAGGAGCAAGAC-CTATTTC-ATTCTC
1 TTTTCCTTTGTCCTCAAGAAGCAAGACACT-TTCCTATTCTC
1641078 TTTTCCTTTGTCCTCAA
1 TTTTCCTTTGTCCTCAA
1641095 AAAATGGGAC
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 23 0.45
41 23 0.45
42 5 0.10
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.43
Consensus pattern (41 bp):
TTTTCCTTTGTCCTCAAGAAGCAAGACACTTTCCTATTCTC
Found at i:1641713 original size:20 final size:19
Alignment explanation
Indices: 1641688--1641816 Score: 90
Period size: 20 Copynumber: 6.8 Consensus size: 19
1641678 TTTTCACAAT
1641688 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATT-TTCA
*
1641708 TTGTATCGATACACTATTCA
1 TTGTATCGATACA-TTTTCA
*
1641728 TTGTACCGAT--A----CA
1 TTGTATCGATACATTTTCA
*
1641741 TTGTATCGATACATTGCTCA
1 TTGTATCGATACATT-TTCA
**
1641761 TTGTATCGATACATTACCCA
1 TTGTATCGATACATT-TTCA
*
1641781 GATGTATCGATACATTTTACA
1 -TTGTATCGATACATTTT-CA
* *
1641802 ATGTATCCATACATT
1 TTGTATCGATACATT
1641817 CAGGCATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
13 11 0.12
15 1 0.01
18 1 0.01
20 60 0.67
21 17 0.19
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.39
Consensus pattern (19 bp):
TTGTATCGATACATTTTCA
Found at i:1641748 original size:33 final size:33
Alignment explanation
Indices: 1641706--1641775 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1641696 ATACATTGTT
*
1641706 CATTGTATCGATACACTATTCATTGTACCGATA
1 CATTGTATCGATACACTACTCATTGTACCGATA
* * *
1641739 CATTGTATCGATACATTGCTCATTGTATCGATA
1 CATTGTATCGATACACTACTCATTGTACCGATA
1641772 CATT
1 CATT
1641776 ACCCAGATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.39
Consensus pattern (33 bp):
CATTGTATCGATACACTACTCATTGTACCGATA
Found at i:1641775 original size:13 final size:13
Alignment explanation
Indices: 1641726--1641756 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1641716 ATACACTATT
1641726 CATTGTACCGATA
1 CATTGTACCGATA
*
1641739 CATTGTATCGATA
1 CATTGTACCGATA
1641752 CATTG
1 CATTG
1641757 CTCATTGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.35
Consensus pattern (13 bp):
CATTGTACCGATA
Found at i:1645326 original size:29 final size:29
Alignment explanation
Indices: 1645285--1645600 Score: 360
Period size: 29 Copynumber: 11.1 Consensus size: 29
1645275 ATTCCTCATA
*
1645285 TTTTC-AAAGCCCACAAGTCAGTGGCATC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
* *
1645313 TTTTCAAAAGCCCACAAGTTAATGGCATA
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
*
1645342 TTTTC-AAAGCCCACAAGTTAGTGGCAAC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
* * *
1645370 -GTTC-AAAGCCCACAAGGTAGTGGCAAC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
*
1645397 -CTTCAAAAGCCCACAAGTTAGTGGCATC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
*
1645425 TTTTCAAAAGCCCACAAGTCAGTGGCATC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
* * *
1645454 TTTTCAAAAACCCACAAGTCAATGGCATC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
* *
1645483 TTTTCAAAAACCCACAAGTTAGTGGCACC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
* *
1645512 TTTT-TAAAGCCCACAAGTTAGTGGCAAC
1 TTTTCAAAAGCCCACAAGTTAGTGGCATC
* * *
1645540 -CTTC-AAAGCCCACAAGGTAGTGGCAACC
1 TTTTCAAAAGCCCACAAGTTAGTGGC-ATC
* *
1645568 CTTTCAAAAGCCCATACAAGTTGGTGGCATC
1 TTTTCAAAAGCCC--ACAAGTTAGTGGCATC
1645599 TT
1 TT
1645601 CTTCTAAGCC
Statistics
Matches: 250, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
27 49 0.20
28 69 0.28
29 111 0.44
30 7 0.03
31 3 0.01
32 11 0.04
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (29 bp):
TTTTCAAAAGCCCACAAGTTAGTGGCATC
Found at i:1645675 original size:48 final size:48
Alignment explanation
Indices: 1645600--1645871 Score: 204
Period size: 48 Copynumber: 6.0 Consensus size: 48
1645590 GGTGGCATCT
* * * * *
1645600 TCTTCTAAGCCCAATATCGTTGTCCTTGAATCAGCATATTGGCACCTTA
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTA
* *
1645649 TCTTTAAGACCAACGTTGCTGGCCTTGAATCAGCACATTGG---C--A
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTA
* * *
1645692 -C---AAG-CCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTG
1 TCTTTAAGACC-AATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTA
* *
1645736 TCTTTAAGACCAACGTCGCTGGCTTTGAATCAGCACATTGG---C--A
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTA
* * * *
1645779 -C---AAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTT-A
* * * *
1645824 TCTTTAAGACCGATGTCGTTGGCCTTGAATTAGCACATTGACACCTTA
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTA
1645872 ACTGACACCT
Statistics
Matches: 171, Mismatches: 31, Indels: 43
0.70 0.13 0.18
Matches are distributed among these distances:
38 2 0.01
39 59 0.35
42 4 0.02
43 1 0.01
45 4 0.02
46 1 0.01
48 60 0.35
49 40 0.23
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (48 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTA
Found at i:1645720 original size:39 final size:38
Alignment explanation
Indices: 1645666--1645818 Score: 144
Period size: 39 Copynumber: 3.7 Consensus size: 38
1645656 GACCAACGTT
1645666 GCTGGCCTTGAATCAGCACATTGGCACAAGCCTAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACAAGCC-AATATC
* **
1645705 GCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAACGTC
1 GCTGGCCTTGAATCAGCACATTGGCA------C---AAG-CCAATATC
*
1645753 GCTGGCTTTGAATCAGCACATTGGCACAAGCCCAATATC
1 GCTGGCCTTGAATCAGCACATTGGCACAAG-CCAATATC
* *
1645792 GCTAGCCTTGAATCAGCATATTGGCAC
1 GCTGGCCTTGAATCAGCACATTGGCAC
1645819 CTTCATCTTT
Statistics
Matches: 93, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
39 58 0.62
42 1 0.01
45 1 0.01
48 31 0.33
49 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (38 bp):
GCTGGCCTTGAATCAGCACATTGGCACAAGCCAATATC
Found at i:1645757 original size:87 final size:87
Alignment explanation
Indices: 1645606--1645863 Score: 408
Period size: 87 Copynumber: 3.0 Consensus size: 87
1645596 ATCTTCTTCT
* * *
1645606 AAGCCCAATATCGTTGTCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAACGTTGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAACGTCGCTGG
1645671 CCTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
* *
1645693 AAGCCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAACGTCGCTGG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAACGTCGCTGG
*
1645758 CTTTGAATCAGCACATTGGCAC
66 CCTTGAATCAGCACATTGGCAC
* * * *
1645780 AAGCCCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGACCGATGTCGTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATCTTTAAGACCAACGTCGCTG
*
1645845 GCCTTGAATTAGCACATTG
65 GCCTTGAATCAGCACATTG
1645864 ACACCTTAAC
Statistics
Matches: 156, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
87 121 0.78
88 35 0.22
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (87 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATCTTTAAGACCAACGTCGCTGG
CCTTGAATCAGCACATTGGCAC
Found at i:1646005 original size:52 final size:51
Alignment explanation
Indices: 1645899--1646034 Score: 143
Period size: 52 Copynumber: 2.6 Consensus size: 51
1645889 CTCAAAACCC
* *
1645899 AATGTCACT-AGCCTTGAATCAGCACATTGGCATTCTTCTTATTTTCAAGTCT
1 AATGTCACTGA-CC-TGAATCAGCACATTGGCATTCTTCTCATTTTCAAGCCT
1645951 AATGTCACTGACCGTGAATCAGCACATTGGCATTCTT-TACATCTTT-AAGCCT
1 AATGTCACTGACC-TGAATCAGCACATTGGCATTCTTCT-CAT-TTTCAAGCCT
* * * *
1646003 AATATCACTAGTCCTGACTCAGCATATTGGCA
1 AATGTCACT-GACCTGAATCAGCACATTGGCA
1646035 CCTTTATCAC
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
51 1 0.01
52 65 0.89
53 7 0.10
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (51 bp):
AATGTCACTGACCTGAATCAGCACATTGGCATTCTTCTCATTTTCAAGCCT
Found at i:1653042 original size:3 final size:3
Alignment explanation
Indices: 1653034--1653067 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1653024 TTTTTTACTA
*
1653034 TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1653068 TTGGATTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (3 bp):
TAT
Found at i:1658999 original size:20 final size:19
Alignment explanation
Indices: 1658970--1659044 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
1658960 TACTGCCAGA
* *
1658970 TTCATTTATCGATACATTTG
1 TTCATGTATCGATACA-ATG
1658990 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
** *
1659009 AACATGTATCGATACAAAG
1 TTCATGTATCGATACAATG
* *
1659028 CATAATGTATCGATACA
1 -TTCATGTATCGATACA
1659045 TCTGAAAGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 18 0.38
20 29 0.62
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:1659016 original size:19 final size:18
Alignment explanation
Indices: 1658993--1659064 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 18
1658983 ACATTTGTTC
1658993 ATGTATCGATACAATGAA
1 ATGTATCGATACAATGAA
*
1659011 CATGTATCGATACAAAGCATA
1 -ATGTATCGATACAATG-A-A
*
1659032 ATGTATCGATACATCTGAA
1 ATGTATCGATACA-ATGAA
1659051 AGTGTATCGATACA
1 A-TGTATCGATACA
1659065 TACAAGGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
19 17 0.37
20 27 0.59
21 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (18 bp):
ATGTATCGATACAATGAA
Found at i:1659246 original size:89 final size:89
Alignment explanation
Indices: 1659132--1659311 Score: 333
Period size: 89 Copynumber: 2.0 Consensus size: 89
1659122 TATGTATCGA
1659132 TACTTTGAAGTATTTTTACTTAAAATCAATTTAAAGCTCGAAAACATTTGTTCATAACTTAAAAA
1 TACTTTGAAGTATTTTTACTTAAAATCAATTTAAAGCTCGAAAACATTTGTTCATAACTTAAAAA
1659197 CACTTTTTGAAAATAAAGATTACT
66 CACTTTTTGAAAATAAAGATTACT
* *
1659221 TACTTTGAAGTATTTTTACTTAAAATCGATTTAAAGCTTGAAAACATTTGTTCATAACTTAAAAA
1 TACTTTGAAGTATTTTTACTTAAAATCAATTTAAAGCTCGAAAACATTTGTTCATAACTTAAAAA
*
1659286 CACTTTTTGAAAATGAAGATTACT
66 CACTTTTTGAAAATAAAGATTACT
1659310 TA
1 TA
1659312 GAATACTGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.39
Consensus pattern (89 bp):
TACTTTGAAGTATTTTTACTTAAAATCAATTTAAAGCTCGAAAACATTTGTTCATAACTTAAAAA
CACTTTTTGAAAATAAAGATTACT
Found at i:1660079 original size:28 final size:28
Alignment explanation
Indices: 1660037--1660097 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
1660027 AAGAGAACTA
* *
1660037 AAGTGCTTATCCATGCACTGCGATAGTG
1 AAGTGCTCATCCATGCACTGCGAAAGTG
* **
1660065 AAGTGCTCATTCATGTGCTGCGAAAGTG
1 AAGTGCTCATCCATGCACTGCGAAAGTG
1660093 AAGTG
1 AAGTG
1660098 ATCAACTCTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (28 bp):
AAGTGCTCATCCATGCACTGCGAAAGTG
Found at i:1661595 original size:13 final size:13
Alignment explanation
Indices: 1661576--1661615 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
1661566 ATAGTCACCC
1661576 ATGTATCGATACA
1 ATGTATCGATACA
* *
1661589 TTGTATCGATATA
1 ATGTATCGATACA
1661602 ATGTATCGATACA
1 ATGTATCGATACA
1661615 A
1 A
1661616 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1667895 original size:19 final size:20
Alignment explanation
Indices: 1667851--1667923 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 20
1667841 ACTGTCAATT
* * **
1667851 CATGTATCGATACATTGGTT
1 CATGTATCGATACAATCGAA
1667871 CATGTATCGATACAAT-GAA
1 CATGTATCGATACAATCGAA
* *
1667890 CATGTAGCGATAC-ATCTAA
1 CATGTATCGATACAATCGAA
*
1667909 AATGTATCGATACAA
1 CATGTATCGATACAA
1667924 CAAGGGTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 2 0.05
19 26 0.59
20 16 0.36
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (20 bp):
CATGTATCGATACAATCGAA
Found at i:1668308 original size:48 final size:48
Alignment explanation
Indices: 1668188--1668413 Score: 210
Period size: 47 Copynumber: 4.6 Consensus size: 48
1668178 GATCCTAACA
* * *
1668188 AAGGCCAACGATATTGGGCTTAAAGATTGCAAAGGTGCCATGT-CTGATTC
1 AAGGCCAGCGATATTGGACTT-AAGA-TG-AAAGGTGCCATATGCTGATTC
* * *
1668238 AAGGCCAACGACA-TGAGACTTAAGATGAAA-GTGCCAATATACTGATTC
1 AAGGCCAGCGATATTG-GACTTAAGATGAAAGGTGCC-ATATGCTGATTC
* * *
1668286 AAGGCCAGCGATATTGGGCTTAAGA-AAAAGGTGCCATGTGCTGATTC
1 AAGGCCAGCGATATTGGACTTAAGATGAAAGGTGCCATATGCTGATTC
* *
1668333 AAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGCCAGTATGCTGATTC
1 AAGGCCAGCGATATTGGACTT-AAGATG--AAAGGTGCCA-TATGCTGATTC
*
1668385 AAAGGCAATG-GATATTGGACTTAAGATGA
1 -AAGGCCA-GCGATATTGGACTTAAGATGA
1668414 TGGTGTTAAT
Statistics
Matches: 147, Mismatches: 17, Indels: 24
0.78 0.09 0.13
Matches are distributed among these distances:
46 5 0.03
47 37 0.25
48 37 0.25
49 8 0.05
50 17 0.12
51 10 0.07
52 16 0.11
53 16 0.11
54 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (48 bp):
AAGGCCAGCGATATTGGACTTAAGATGAAAGGTGCCATATGCTGATTC
Found at i:1668446 original size:100 final size:95
Alignment explanation
Indices: 1668218--1668447 Score: 241
Period size: 100 Copynumber: 2.4 Consensus size: 95
1668208 TAAAGATTGC
* * *
1668218 AAAGGTGCCATGT-CTGATTCAAGGCCAACGACATGAGACTTAAGATGAAAGTGCCAATATACTG
1 AAAGGTGCAATGTGCTAATTCAAGGCCAACGACATTAGACTTAAGATGAAAGTGCCAATATACTG
* *
1668282 ATTCAAGGCCAGCGATATTGGGCTTAAGAA
66 ATTCAAGGCAAGCGATATTGGACTTAAGAA
* * * *
1668312 AAAGGTGCCATGTGCTGATTCAAGGCCAGCGACATTAGACTTAAAGATGACAAAGGTGCCAGTAT
1 AAAGGTGCAATGTGCTAATTCAAGGCCAACGACATTAGACTT-AAGATG--AAA-GTGCCAATAT
* *
1668377 GCTGATTCAAAGGCAATG-GATATTGGACTTAAGAT
62 ACTGATTC-AAGGCAA-GCGATATTGGACTTAAGAA
* * * *
1668412 GATGGTGTTAATGTGCTAATTC-AGGCCAATGACATT
1 AAAGGTG-CAATGTGCTAATTCAAGGCCAACGACATT
1668448 GGATTAGAAA
Statistics
Matches: 114, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
94 13 0.11
95 26 0.23
96 6 0.05
98 3 0.03
99 16 0.14
100 38 0.33
101 12 0.11
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (95 bp):
AAAGGTGCAATGTGCTAATTCAAGGCCAACGACATTAGACTTAAGATGAAAGTGCCAATATACTG
ATTCAAGGCAAGCGATATTGGACTTAAGAA
Found at i:1668536 original size:31 final size:31
Alignment explanation
Indices: 1668462--1668549 Score: 115
Period size: 31 Copynumber: 2.8 Consensus size: 31
1668452 TAGAAAAAGA
*
1668462 TGCCACCGACTTGTGTGGGC-TTAGAAAGGGT
1 TGCCACCGACTTGTGTGGACTTTAG-AAGGGT
* * **
1668493 TACCTCTAACTTGTGTGGACTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGACTTTAGAAGGGT
1668524 TGCCACCGACTTGTGTGGACTTTAGA
1 TGCCACCGACTTGTGTGGACTTTAGA
1668550 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 43 0.91
32 4 0.09
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.31
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGACTTTAGAAGGGT
Found at i:1725165 original size:28 final size:28
Alignment explanation
Indices: 1725125--1725196 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
1725115 AAAAAAAAAT
* ** *
1725125 CGGGATTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1725153 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1725181 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1725197 TCGATTGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1725316 original size:52 final size:53
Alignment explanation
Indices: 1725185--1725574 Score: 190
Period size: 52 Copynumber: 7.4 Consensus size: 53
1725175 AAATAACGAG
* * * * *
1725185 GTTGGAGTATCCTCGATTG-TGAAAAATTGGTATTTTTGGAAATAGAATCGGA
1 GTTGGAGTATCCCCGATTGAGGAAAAATTGGTAGTTTTGAAAATAAAATCGGA
* * *
1725237 GTTGGAATATCCCCGATTAAAGG-AAAATTGG-CGTTTTGAAAATAAAATCGG-
1 GTTGGAGTATCCCCGATT-GAGGAAAAATTGGTAGTTTTGAAAATAAAATCGGA
* ** * * *
1725288 GATTGGAGTATCCCCGATTGAGGAAAAATTAGT-GTTTT-AGCGACAAAACCGGG
1 G-TTGGAGTATCCCCGATTGAGGAAAAATTGGTAGTTTTGA-AAATAAAATCGGA
* ** ** * *
1725341 GTTGGAGTATCCCC---T-CGGAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGAGGAAA-AA-----TTGGTAGT-T--TTGAAAATAAAATCGGA
*
1725396 GTTGGAGTATCCCCGATTG-TGAAGAAATTGGT-GTTTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGGAA-AAATTGGTAG--TTTTGAAAATAAAATCGGA
* * * *
1725450 GTTAGATTATCCCCGATTG-TGAAGAAATTGGT-GTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGGAA-AAATTGGTAG---TTTTGAAAATAAAATCGGA
* * *
1725505 GTTAGAGTATCCCCGATT-A-TAGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGAGGA-AAAATTGGTAGTTTTGAAAATAAAATCGGA
*
1725556 GTTGGAATATCCCCGATTG
1 GTTGGAGTATCCCCGATTG
1725575 TGGAGAATTG
Statistics
Matches: 268, Mismatches: 38, Indels: 64
0.72 0.10 0.17
Matches are distributed among these distances:
48 5 0.02
49 3 0.01
51 39 0.15
52 85 0.32
53 16 0.06
54 50 0.19
55 58 0.22
56 2 0.01
57 2 0.01
58 7 0.03
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTGAGGAAAAATTGGTAGTTTTGAAAATAAAATCGGA
Found at i:1725400 original size:27 final size:28
Alignment explanation
Indices: 1725337--1725412 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 28
1725327 GCGACAAAAC
***
1725337 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1725365 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1725392 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1725413 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1725426 original size:212 final size:213
Alignment explanation
Indices: 1725120--1725540 Score: 577
Period size: 212 Copynumber: 2.0 Consensus size: 213
1725110 AGAAGAAAAA
* *
1725120 AAAATCGGGATTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* * * *
1725185 GTTGGAGTATCCTCGATTGTGAAAAATTGGT-ATTTTTGGAAATAGAATCGGAGTTGGAATATCC
66 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGAAAATAAAATCGGAGTTAGAATATCC
*
1725249 CCGA-T-TAAAGGAAAATTGGCG-TTTTGAAAATAAAATCGG-GATTGGAGTATCCCCGATT-GA
131 CCGATTGTAAA-G-AAATTGGCGTTTTTGAAAATAAAATCGGAG-TTAGAGTATCCCCGATTAGA
1725309 GGAAAAATTAGTGTTTTAGCGAC
193 -G-AAAATTAGTGTTTTAGCGAC
* * *
1725332 AAAACCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGG
1 AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
* *
1725396 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGGAGTTAGATTATC
66 GTTGGAGTATCCCCGATTGTGAA-AAATTGGTGATTTTTGAAAATAAAATCGGAGTTAGAATATC
* * * *
1725461 CCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTAGAGTATCCCCGATTATA
130 CCCGATTGTAAAGAAATTGGCG--TTTTTGAAAATAAAATCGGAGTTAGAGTATCCCCGATTAGA
1725526 GAAAATTAGTGTTTT
193 GAAAATTAGTGTTTT
1725541 GAAAATAAAA
Statistics
Matches: 184, Mismatches: 16, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
211 29 0.16
212 60 0.33
213 40 0.22
214 2 0.01
215 17 0.09
216 34 0.18
217 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (213 bp):
AAAACCGGGATTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAG
GTTGGAGTATCCCCGATTGTGAAAAATTGGTGATTTTTGAAAATAAAATCGGAGTTAGAATATCC
CCGATTGTAAAGAAATTGGCGTTTTTGAAAATAAAATCGGAGTTAGAGTATCCCCGATTAGAGAA
AATTAGTGTTTTAGCGAC
Found at i:1725516 original size:55 final size:54
Alignment explanation
Indices: 1725400--1725581 Score: 255
Period size: 55 Copynumber: 3.4 Consensus size: 54
1725390 AACGGGGTTG
1725400 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGGAGTTA
* *
1725454 GATTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTGAAGAAATTGGTG-TTTTTTGAAAATAAAATCGGAGTTA
* * *
1725509 GAGTATCCCCGATTAT--AGAAAATTAGTG--TTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAAG-AAATTGGTGTTTTTTGAAAATAAAATCGGAGTTA
* *
1725560 GAATATCCCCGATTGTGGAGAA
1 GAGTATCCCCGATTGTGAAGAA
1725582 TTGATAAACT
Statistics
Matches: 115, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
51 35 0.30
52 2 0.02
53 4 0.03
54 36 0.31
55 38 0.33
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (54 bp):
GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGAAAATAAAATCGGAGTTA
Found at i:1727961 original size:13 final size:13
Alignment explanation
Indices: 1727943--1727968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1727933 ACAAAGATCC
1727943 ATGTATCGATACA
1 ATGTATCGATACA
1727956 ATGTATCGATACA
1 ATGTATCGATACA
1727969 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1727964 original size:33 final size:33
Alignment explanation
Indices: 1727922--1727988 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1727912 AAAATTTCCA
***
1727922 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1727955 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1727988 A
1 A
1727989 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1728032 original size:19 final size:18
Alignment explanation
Indices: 1728008--1728075 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1727998 CAGTAGCTAA
1728008 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1728027 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1728042 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1728059 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1728076 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1728048 original size:13 final size:13
Alignment explanation
Indices: 1728030--1728054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1728020 ACAATACTTA
1728030 TGTATCGATACAT
1 TGTATCGATACAT
1728043 TGTATCGATACA
1 TGTATCGATACA
1728055 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.