Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold84
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: 4163231
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 246351 characters in sequence are not A, C, G, or T
File 9 of 11
Found at i:3374155 original size:42 final size:41
Alignment explanation
Indices: 3374081--3374192 Score: 145
Period size: 42 Copynumber: 2.7 Consensus size: 41
3374071 CGAATACGCC
* * *
3374081 AACAGAAGCTCG-AAAGCTGAACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCGTAAAGCTAAACAAAAGCTCATAAGAACTT
*
3374121 AATAGAAGCTCGTAAGAGCTAAACAAAAGCTCATAAGAACTT
1 AACAGAAGCTCGTAA-AGCTAAACAAAAGCTCATAAGAACTT
*
3374163 AACAGAAGCTCGTAAAAAGCTAAAAAAAAG
1 AACAGAAGCTCGT--AAAGCTAAACAAAAG
3374193 TAAAACATGA
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
40 11 0.18
41 2 0.03
42 35 0.56
43 12 0.19
44 2 0.03
ACGTcount: A:0.49, C:0.17, G:0.19, T:0.15
Consensus pattern (41 bp):
AACAGAAGCTCGTAAAGCTAAACAAAAGCTCATAAGAACTT
Found at i:3374276 original size:21 final size:21
Alignment explanation
Indices: 3374252--3374310 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
3374242 AAAATGTTCG
3374252 TAAGAGCTGAACAAAAGCTCA
1 TAAGAGCTGAACAAAAGCTCA
* * *
3374273 TAAGAACTTAACAAAAGCTCG
1 TAAGAGCTGAACAAAAGCTCA
* *
3374294 TAAAAGCTGAAAAAAAG
1 TAAGAGCTGAACAAAAG
3374311 TAAAACACGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.53, C:0.15, G:0.17, T:0.15
Consensus pattern (21 bp):
TAAGAGCTGAACAAAAGCTCA
Found at i:3374359 original size:118 final size:119
Alignment explanation
Indices: 3374130--3374365 Score: 402
Period size: 118 Copynumber: 2.0 Consensus size: 119
3374120 TAATAGAAGC
*
3374130 TCGTAAGAGCTAAACAAAAGCTCATAAGAACTTAACAGAAGCTCGTAAAAAGCTAAAAAAAAGTA
1 TCGTAAGAGCTAAACAAAAGCTCATAAGAACTTAACAAAAGCTCGTAAAAAGCTAAAAAAAAGTA
* * * *
3374195 AAACATGAGAGTTTGCAACAAATTTTGAACCCTGGTTTAGTTGGGAAAAAATGT
66 AAACACGAGAGTTTGCAACAAATTTTGAACCCCGATTTACTTGGGAAAAAATGT
* *
3374249 TCGTAAGAGCTGAACAAAAGCTCATAAGAACTTAACAAAAGCTCGT-AAAAGCTGAAAAAAAGTA
1 TCGTAAGAGCTAAACAAAAGCTCATAAGAACTTAACAAAAGCTCGTAAAAAGCTAAAAAAAAGTA
3374313 AAACACGAGAGTTTGCAACAAATTTTGAACCCCGATTTACTTGGGAAAAAATG
66 AAACACGAGAGTTTGCAACAAATTTTGAACCCCGATTTACTTGGGAAAAAATG
3374366 CTATTGTCTC
Statistics
Matches: 110, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
118 66 0.60
119 44 0.40
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.22
Consensus pattern (119 bp):
TCGTAAGAGCTAAACAAAAGCTCATAAGAACTTAACAAAAGCTCGTAAAAAGCTAAAAAAAAGTA
AAACACGAGAGTTTGCAACAAATTTTGAACCCCGATTTACTTGGGAAAAAATGT
Found at i:3377897 original size:13 final size:12
Alignment explanation
Indices: 3377862--3377900 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3377852 TATTTTCATC
3377862 TTTCTTCTTTAT
1 TTTCTTCTTTAT
3377874 TTTCTTCTTTAT
1 TTTCTTCTTTAT
3377886 TGTTCTAT-TTTAT
1 T-TTCT-TCTTTAT
3377899 TT
1 TT
3377901 ACCTTAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 14 0.56
13 10 0.40
14 1 0.04
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTCTTCTTTAT
Found at i:3377924 original size:13 final size:13
Alignment explanation
Indices: 3377908--3377948 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
3377898 TTTACCTTAG
3377908 TTATTTATTTTAA
1 TTATTTATTTTAA
3377921 TTATTTTATTTT-A
1 TTA-TTTATTTTAA
*
3377934 TTTTTTATTTTAA
1 TTATTTATTTTAA
3377947 TT
1 TT
3377949 GGATTCGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
13 9 0.36
14 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTATTTATTTTAA
Found at i:3377924 original size:26 final size:26
Alignment explanation
Indices: 3377898--3377948 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
3377888 TTCTATTTTA
3377898 TTTACCTTAGTTATTTATTTTAATTAT
1 TTTACCTTA-TTATTTATTTTAATTAT
** *
3377925 TTTATTTTATTTTTTATTTTAATT
1 TTTACCTTATTATTTATTTTAATT
3377949 GGATTCGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTACCTTATTATTTATTTTAATTAT
Found at i:3378779 original size:21 final size:21
Alignment explanation
Indices: 3378754--3378804 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
3378744 GAGTTAATGC
*
3378754 AAGAATTGATATCTCA-ATTGA
1 AAGAATTGA-ATCGCACATTGA
3378775 AAGAATTG-ATCGCACATTGA
1 AAGAATTGAATCGCACATTGA
3378795 AAGAATTGAA
1 AAGAATTGAA
3378805 AGGATTGAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 5 0.19
20 13 0.48
21 9 0.33
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (21 bp):
AAGAATTGAATCGCACATTGA
Found at i:3381505 original size:12 final size:13
Alignment explanation
Indices: 3381481--3381509 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
3381471 GGGCTATAAC
3381481 TATTGCATTTATT
1 TATTGCATTTATT
3381494 TATTGC-TTTATT
1 TATTGCATTTATT
3381506 TATT
1 TATT
3381510 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:3402459 original size:38 final size:37
Alignment explanation
Indices: 3402385--3402459 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
3402375 TGAACTCATG
* *
3402385 GTACATTTATTAGATATCTAATTCGGGTATGTTTGAAT
1 GTACATTTATTAGATATCTAATTC-AGTATGATTGAAT
*
3402423 GTACATTTATTAGATATCTAGTT-AGTCATGAATTGAA
1 GTACATTTATTAGATATCTAATTCAGT-ATG-ATTGAA
3402460 GTATTAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
36 2 0.06
37 3 0.09
38 27 0.84
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (37 bp):
GTACATTTATTAGATATCTAATTCAGTATGATTGAAT
Found at i:3403253 original size:26 final size:27
Alignment explanation
Indices: 3403223--3403288 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 27
3403213 ATGCGGTAAG
3403223 GGGGTTCGCTAGTTAAGTTGCGAACTA
1 GGGGTTCGCTAGTTAAGTTGCGAACTA
** *
3403250 -GGGTTCATTAGGTAAGTTGCGAACTA
1 GGGGTTCGCTAGTTAAGTTGCGAACTA
3403276 GGGGTTCGCTAGT
1 GGGGTTCGCTAGT
3403289 CAAAGTCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 23 0.72
27 9 0.28
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.30
Consensus pattern (27 bp):
GGGGTTCGCTAGTTAAGTTGCGAACTA
Found at i:3404388 original size:38 final size:40
Alignment explanation
Indices: 3404318--3404392 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 40
3404308 TTTATATATA
* *
3404318 TTACTATTTTTATTTCTTCTTTGTTCTCAAATTTCTTCTT
1 TTACTATTTTTATTTCTTCTATGTACTCAAATTTCTTCTT
3404358 TTACTATTTTTTATTTCTT-TAT-TACT-AAATTTCTT
1 TTACTA-TTTTTATTTCTTCTATGTACTCAAATTTCTT
3404393 TATTTCTTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
38 9 0.28
39 3 0.09
40 8 0.25
41 12 0.38
ACGTcount: A:0.19, C:0.15, G:0.01, T:0.65
Consensus pattern (40 bp):
TTACTATTTTTATTTCTTCTATGTACTCAAATTTCTTCTT
Found at i:3406121 original size:28 final size:28
Alignment explanation
Indices: 3406081--3406136 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
3406071 ATTTACCTGA
* **
3406081 ATCATACATGCACGTTGCATCTAATGTT
1 ATCATACATGCACATCACATCTAATGTT
*
3406109 ATCATACTTGCACATCACATCTAATGTT
1 ATCATACATGCACATCACATCTAATGTT
3406137 TCAAGAACCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (28 bp):
ATCATACATGCACATCACATCTAATGTT
Found at i:3406927 original size:27 final size:26
Alignment explanation
Indices: 3406866--3406933 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
3406856 GATTTTCCAT
* *
3406866 AAAGACTTCCATTTCTTAAATCGCCAA
1 AAAG-CTTCCATCTCTTAAATCCCCAA
* *
3406893 AAAGGCTTCCATCTCTTAGATCACCCTA
1 AAA-GCTTCCATCTCTTAAATC-CCCAA
*
3406921 AAAGCTTTCATCT
1 AAAGCTTCCATCT
3406934 ATCAAATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
27 27 0.79
28 7 0.21
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (26 bp):
AAAGCTTCCATCTCTTAAATCCCCAA
Found at i:3412125 original size:14 final size:15
Alignment explanation
Indices: 3412106--3412138 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3412096 CTATCAATTC
3412106 AATAAAA-TTTATAT
1 AATAAAATTTTATAT
3412120 AATAAAATTTTATAT
1 AATAAAATTTTATAT
3412135 AATA
1 AATA
3412139 TTAAAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATAAAATTTTATAT
Found at i:3412617 original size:67 final size:66
Alignment explanation
Indices: 3412531--3412674 Score: 152
Period size: 67 Copynumber: 2.2 Consensus size: 66
3412521 GGTTATTTTC
* * **
3412531 TTTCA-TTTTTAGCCTTAGAATCTT-G-ATTATTACGTTTTATTAAATTTTCATTTAGC-GTTTG
1 TTTCATTTTTTAACCTTAGAAT-TTAGAATT-TTACGTTTTAATAAATTTT-ATTT-GCAGTGGG
3412592 ATTTA
62 ATTTA
* * * *
3412597 TTTCATTTTTTAACTTTAGAATTTAGAATTTTATGTTTTAATAGATTTTATTTGCAGTGGGGTTT
1 TTTCATTTTTTAACCTTAGAATTTAGAATTTTACGTTTTAATAAATTTTATTTGCAGTGGGATTT
3412662 A
66 A
3412663 TTTCATTTTTTA
1 TTTCATTTTTTA
3412675 GCATTAGAGA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
65 2 0.03
66 30 0.45
67 31 0.47
68 3 0.05
ACGTcount: A:0.24, C:0.08, G:0.12, T:0.56
Consensus pattern (66 bp):
TTTCATTTTTTAACCTTAGAATTTAGAATTTTACGTTTTAATAAATTTTATTTGCAGTGGGATTT
A
Found at i:3420630 original size:19 final size:19
Alignment explanation
Indices: 3420608--3420647 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3420598 GACAATAACA
3420608 CAATCACATACATA-AAATT
1 CAATCA-ATACATATAAATT
*
3420627 CAATTAATACATATAAATT
1 CAATCAATACATATAAATT
3420646 CA
1 CA
3420648 CAATTTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.30
Consensus pattern (19 bp):
CAATCAATACATATAAATT
Found at i:3420798 original size:21 final size:21
Alignment explanation
Indices: 3420764--3420813 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3420754 TGTATGAGTA
*
3420764 AATTTA-ACTCAATTCAATAC
1 AATTTACATTCAATTCAATAC
* *
3420784 AATTTACATTCAATTTAATCC
1 AATTTACATTCAATTCAATAC
*
3420805 AATTCACAT
1 AATTTACAT
3420814 CTTAGGCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTACATTCAATTCAATAC
Found at i:3430904 original size:13 final size:13
Alignment explanation
Indices: 3430886--3430929 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
3430876 GTCACACAGT
*
3430886 CGTGTCGCCAGAC
1 CGTGTCGCCAGGC
* *
3430899 CGTGTCACTAGGC
1 CGTGTCGCCAGGC
3430912 CGTGTCGCCAGGC
1 CGTGTCGCCAGGC
3430925 CGTGT
1 CGTGT
3430930 AACTCTTTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.11, C:0.34, G:0.34, T:0.20
Consensus pattern (13 bp):
CGTGTCGCCAGGC
Found at i:3431001 original size:13 final size:13
Alignment explanation
Indices: 3430983--3431010 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3430973 AGAGGCACAG
3430983 GCTCATGTGGGTT
1 GCTCATGTGGGTT
3430996 GCTCATGTGGGTT
1 GCTCATGTGGGTT
3431009 GC
1 GC
3431011 CCGTGTGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.18, G:0.39, T:0.36
Consensus pattern (13 bp):
GCTCATGTGGGTT
Found at i:3434858 original size:19 final size:18
Alignment explanation
Indices: 3434836--3434880 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
3434826 TCTTTATTAT
*
3434836 AATAATATTTTAGAAATAA
1 AATAATATCTTAGAAA-AA
*
3434855 AATAATAATCTTATAAAAA
1 AATAAT-ATCTTAGAAAAA
3434874 AATAATA
1 AATAATA
3434881 CAATGGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.61
20 8 0.35
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (18 bp):
AATAATATCTTAGAAAAA
Found at i:3435721 original size:14 final size:14
Alignment explanation
Indices: 3435704--3435750 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
3435694 TATAGTGTGT
3435704 TCAATATTTAACTA
1 TCAATATTTAACTA
* *
3435718 TCAA-ATTAAATTAA
1 TCAATATTTAACT-A
3435732 TTCAATATTTAACTA
1 -TCAATATTTAACTA
3435747 TCAA
1 TCAA
3435751 CTATAGGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 6 0.23
14 9 0.35
15 5 0.19
16 6 0.23
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TCAATATTTAACTA
Found at i:3439082 original size:20 final size:20
Alignment explanation
Indices: 3439057--3439096 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3439047 CGTAAAATGA
*
3439057 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3439077 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3439097 GGAAAGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3439225 original size:14 final size:14
Alignment explanation
Indices: 3439206--3439233 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3439196 ATTTTACATA
3439206 TATTAATATATATT
1 TATTAATATATATT
3439220 TATTAATATATATT
1 TATTAATATATATT
3439234 AATAAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTAATATATATT
Found at i:3439858 original size:15 final size:16
Alignment explanation
Indices: 3439838--3439870 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3439828 AGTACCACTT
3439838 AAAATGAAAGCA-TGA
1 AAAATGAAAGCATTGA
3439853 AAAATGAAAGCATTGA
1 AAAATGAAAGCATTGA
3439869 AA
1 AA
3439871 GTACCACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.61, C:0.06, G:0.18, T:0.15
Consensus pattern (16 bp):
AAAATGAAAGCATTGA
Found at i:3440466 original size:2 final size:2
Alignment explanation
Indices: 3440459--3440490 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3440449 ACGATTCATT
3440459 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
3440491 TATATATCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:3440866 original size:23 final size:23
Alignment explanation
Indices: 3440840--3440889 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
3440830 TTTTGAAATC
*
3440840 TAAAGTGAA-AGTTGAATTTGTTT
1 TAAAGTGAATAGTTGAA-TTGATT
* *
3440863 TAAATTGAATTGTTGAATTGATT
1 TAAAGTGAATAGTTGAATTGATT
3440886 TAAA
1 TAAA
3440890 CAGGTAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (23 bp):
TAAAGTGAATAGTTGAATTGATT
Found at i:3442800 original size:25 final size:25
Alignment explanation
Indices: 3442744--3442810 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
3442734 AGCTTTGAGG
*
3442744 AATGGAAAATGTCTGCTGCTTAGAAGAG
1 AATGGAAAATG--T-CTGCTTAGAAGAA
3442772 AATGGAAAATGTCTGCTTAG-AGAAA
1 AATGGAAAATGTCTGCTTAGAAG-AA
3442797 AATGGAAAATGTCT
1 AATGGAAAATGTCT
3442811 TACCAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
24 2 0.05
25 23 0.62
26 1 0.03
28 11 0.30
ACGTcount: A:0.40, C:0.09, G:0.25, T:0.25
Consensus pattern (25 bp):
AATGGAAAATGTCTGCTTAGAAGAA
Found at i:3444156 original size:2 final size:2
Alignment explanation
Indices: 3444149--3444177 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3444139 AATATGTATG
3444149 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3444178 CAATTAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3448905 original size:19 final size:19
Alignment explanation
Indices: 3448883--3448982 Score: 51
Period size: 19 Copynumber: 5.2 Consensus size: 19
3448873 AAAACATAAC
3448883 AAAATTTATAAAAATTATA
1 AAAATTTATAAAAATTATA
* * *
3448902 AAAAATCATTAAAATTAT-
1 AAAATTTATAAAAATTATA
* *
3448920 ACAATTT-TTAAAATTATTA
1 AAAATTTATAAAAATTA-TA
* * * **
3448939 GATATTAATAAAATAAAAATA
1 AAAATTTAT-AAA-AATTATA
* *
3448960 AAAATTTATAACATTTATA
1 AAAATTTATAAAAATTATA
3448979 AAAA
1 AAAA
3448983 ATAATTTATT
Statistics
Matches: 56, Mismatches: 20, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
17 9 0.16
18 5 0.09
19 26 0.46
20 3 0.05
21 10 0.18
22 3 0.05
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAATTTATAAAAATTATA
Found at i:3448906 original size:20 final size:20
Alignment explanation
Indices: 3448866--3448920 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
3448856 TTTGGACTAG
*
3448866 AATTATAAAAA-CATAACAA
1 AATTATAAAAATTATAACAA
3448885 AATTTATAAAAATTATAA-AA
1 AA-TTATAAAAATTATAACAA
* *
3448905 AATCATTAAAATTATA
1 AATTATAAAAATTATA
3448921 CAATTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 14 0.45
20 13 0.42
21 4 0.13
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTATAAAAATTATAACAA
Found at i:3449098 original size:43 final size:43
Alignment explanation
Indices: 3449050--3449192 Score: 130
Period size: 43 Copynumber: 3.3 Consensus size: 43
3449040 AAAATCAATA
* *
3449050 TTAATAATTTTTTTTATAAAATTTTATGGTTTTTAACTCATTT
1 TTAATAATTTTTTTTATAAAATTTTATGGTTTTTAAATAATTT
* ** *
3449093 TTAATAATTATTTTTATACATTTTTTATGGTTTTTAGTAAATTATTT
1 TTAATAATTTTTTTTATA-AAATTTTATGG-TTTT--TAAATAATTT
* * *
3449140 TTTATAA---TTTTTATAAAAGTTTATGGTTTTTAATTAATTTT
1 TTAATAATTTTTTTTATAAAATTTTATGGTTTTTAAATAA-TTT
*
3449181 TTTATAATTTTT
1 TTAATAATTTTT
3449193 ATAAACTTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
40 5 0.06
41 10 0.12
42 4 0.05
43 25 0.31
44 19 0.23
45 4 0.05
47 14 0.17
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (43 bp):
TTAATAATTTTTTTTATAAAATTTTATGGTTTTTAAATAATTT
Found at i:3449150 original size:24 final size:23
Alignment explanation
Indices: 3449112--3449156 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3449102 ATTTTTATAC
**
3449112 ATTTTTTATGGTTTTTAGTAAATT
1 ATTTTTTATAATTTTTA-TAAATT
3449136 ATTTTTTATAATTTTTATAAA
1 ATTTTTTATAATTTTTATAAA
3449157 AGTTTATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (23 bp):
ATTTTTTATAATTTTTATAAATT
Found at i:3449211 original size:40 final size:41
Alignment explanation
Indices: 3449137--3449213 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
3449127 TAGTAAATTA
* **
3449137 TTTTTTATAATTTTTATAAAAGTTTATGGTTTTTAATTAAT
1 TTTTTTATAATTTTTATAAAACTTTATGCATTTTAATTAAT
3449178 TTTTTTATAATTTTTAT-AAACTTTAAT-CATTTTAAT
1 TTTTTTATAATTTTTATAAAACTTT-ATGCATTTTAAT
3449214 GATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
40 13 0.41
41 19 0.59
ACGTcount: A:0.32, C:0.03, G:0.04, T:0.61
Consensus pattern (41 bp):
TTTTTTATAATTTTTATAAAACTTTATGCATTTTAATTAAT
Found at i:3450013 original size:11 final size:11
Alignment explanation
Indices: 3449990--3450052 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
3449980 ACAATAACAA
*
3449990 AAAATAGTAGC
1 AAAATAATAGC
*
3450001 AATATAATAGC
1 AAAATAATAGC
*
3450012 AAAATGATAGC
1 AAAATAATAGC
3450023 AAAATAAT-G-
1 AAAATAATAGC
* *
3450032 AAAAAAATAGT
1 AAAATAATAGC
3450043 AATAATAATA
1 AA-AATAATA
3450053 AAAAACAGCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
9 7 0.17
10 2 0.05
11 27 0.64
12 6 0.14
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:3451937 original size:20 final size:21
Alignment explanation
Indices: 3451912--3451953 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3451902 AAATAAAAGA
* *
3451912 TGGAAACGAGCT-CATTGAGC
1 TGGAAACAAGCTGAATTGAGC
3451932 TGGAAACAAGCTGAATTGAGC
1 TGGAAACAAGCTGAATTGAGC
3451953 T
1 T
3451954 CAACAAGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (21 bp):
TGGAAACAAGCTGAATTGAGC
Found at i:3453732 original size:23 final size:23
Alignment explanation
Indices: 3453704--3453812 Score: 127
Period size: 23 Copynumber: 4.9 Consensus size: 23
3453694 TGTGAAACTT
3453704 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
* * * * *
3453727 TTCATA---ATGTGT-GTAACTT
1 TTCATATTCAAGTCTCTTCACTC
*
3453746 TTCATCTTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
3453769 TTCATATTCAAGTCTCTTCACTC
1 TTCATATTCAAGTCTCTTCACTC
*
3453792 TTCATATTCTAGTCTCTTCAC
1 TTCATATTCAAGTCTCTTCAC
3453813 ATTTCTAACT
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.13
20 4 0.06
22 4 0.06
23 52 0.75
ACGTcount: A:0.21, C:0.28, G:0.06, T:0.45
Consensus pattern (23 bp):
TTCATATTCAAGTCTCTTCACTC
Found at i:3453745 original size:42 final size:42
Alignment explanation
Indices: 3453691--3453774 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
3453681 CTATTCATGC
3453691 ATGTGTGAAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
1 ATGTGTGAAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
* *
3453733 ATGTGTGTAACTTTTCATCTTCAAGTCTCTTCACTCTTCATA
1 ATGTGTGAAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
3453775 TTCAAGTCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.44
Consensus pattern (42 bp):
ATGTGTGAAACTTTTCATATTCAAGTCTCTTCACTCTTCATA
Found at i:3453885 original size:81 final size:81
Alignment explanation
Indices: 3453794--3453956 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
3453784 CTTCACTCTT
3453794 CATATTCTAGTCTCTTCACATTTCTAACTTTTCATAATTTATTTGTGCAAGATTAATTTAATTAT
1 CATATTCTAGTCTCTTCACATTTCTAACTTTTCATAATTTATTTGTGCAAGATTAATTTAATTAT
3453859 GTGCCAACAATGCCTC
66 GTGCCAACAATGCCTC
3453875 CATATTCTAGTCTCTTCACATTTCTAACTTTTCATAATTTATTTGTGCAAGATTAATTTAATTAT
1 CATATTCTAGTCTCTTCACATTTCTAACTTTTCATAATTTATTTGTGCAAGATTAATTTAATTAT
3453940 GTGCCAACAATGCCTC
66 GTGCCAACAATGCCTC
3453956 C
1 C
3453957 CTTAAATTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (81 bp):
CATATTCTAGTCTCTTCACATTTCTAACTTTTCATAATTTATTTGTGCAAGATTAATTTAATTAT
GTGCCAACAATGCCTC
Found at i:3467386 original size:26 final size:25
Alignment explanation
Indices: 3467357--3467406 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3467347 CAATTCAATG
3467357 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
3467383 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
3467407 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:3472719 original size:21 final size:18
Alignment explanation
Indices: 3472679--3472732 Score: 54
Period size: 21 Copynumber: 2.8 Consensus size: 18
3472669 TAGGTCTTTT
* *
3472679 TTTTTTTTTTACTTTTTTC
1 TTTTTTTTTT-CATTATTC
3472698 TTGTATTTTTATTCATTATTC
1 TT-T-TTTTT-TTCATTATTC
3472719 TTTTTTTTTTCATT
1 TTTTTTTTTTCATT
3472733 TTATTCATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 2 0.07
21 13 0.43
22 2 0.07
ACGTcount: A:0.11, C:0.09, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTTTTTTCATTATTC
Found at i:3472721 original size:28 final size:27
Alignment explanation
Indices: 3472690--3472742 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 27
3472680 TTTTTTTTTA
3472690 CTTTTTTCTTGT-ATTTTTATTCATTATT
1 CTTTTTT-TTGTCA-TTTTATTCATTATT
*
3472718 CTTTTTTTTTTCATTTTATTCATTA
1 CTTTTTTTTGTCATTTTATTCATTA
3472743 CGCTACTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (27 bp):
CTTTTTTTTGTCATTTTATTCATTATT
Found at i:3474414 original size:22 final size:23
Alignment explanation
Indices: 3474386--3474428 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3474376 ATTAATTTAG
3474386 AGGAAAA-AAAAGAAATAAAAAT
1 AGGAAAAGAAAAGAAATAAAAAT
*
3474408 AGGAAAAGGAAAGAAATAAAA
1 AGGAAAAGAAAAGAAATAAAA
3474429 GAAAGGAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (23 bp):
AGGAAAAGAAAAGAAATAAAAAT
Found at i:3474593 original size:68 final size:69
Alignment explanation
Indices: 3474484--3474633 Score: 212
Period size: 68 Copynumber: 2.2 Consensus size: 69
3474474 AATGGCATTG
* * * * * * *
3474484 TAATCAATTTGATCAATTATTTTAACAGTAGTAATTAAATTAAAA-AATAAATGTGATCAAAATA
1 TAATCAATTTAATCAATTATTTTAACAATAATAACTAAATTAAAAGAAAAAAAGTGATAAAAATA
3474548 AAAA
66 AAAA
3474552 TAATCAATTTAATCAATTATTTTAACAATAATAACTAAATTAAAAGAAAAAAAGTGATAAAAATA
1 TAATCAATTTAATCAATTATTTTAACAATAATAACTAAATTAAAAGAAAAAAAGTGATAAAAATA
3474617 AAAA
66 AAAA
*
3474621 TAATTCACTTTAA
1 TAA-TCAATTTAA
3474634 AGTTACTAAC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
68 41 0.57
69 23 0.32
70 8 0.11
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (69 bp):
TAATCAATTTAATCAATTATTTTAACAATAATAACTAAATTAAAAGAAAAAAAGTGATAAAAATA
AAAA
Found at i:3475132 original size:3 final size:3
Alignment explanation
Indices: 3475124--3475152 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3475114 TGATAAAATT
3475124 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3475153 CTAATGATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3476118 original size:20 final size:20
Alignment explanation
Indices: 3476093--3476132 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3476083 AAATATTTGT
3476093 GTATGCAATATATAAACATA
1 GTATGCAATATATAAACATA
3476113 GTATGCAATATATAAACATA
1 GTATGCAATATATAAACATA
3476133 AAATGTTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (20 bp):
GTATGCAATATATAAACATA
Found at i:3480091 original size:3 final size:3
Alignment explanation
Indices: 3480085--3480112 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3480075 AAAGAAGAAT
3480085 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG A
3480113 AGATTCATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:3481232 original size:5 final size:5
Alignment explanation
Indices: 3481222--3481248 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3481212 GAAATAATGT
3481222 AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AA
3481249 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:3482250 original size:48 final size:46
Alignment explanation
Indices: 3482181--3482271 Score: 155
Period size: 48 Copynumber: 1.9 Consensus size: 46
3482171 ACAAGAAAAT
*
3482181 AAAAAAACAGGCCTATGGCCTTACAAAAGAAAAATCCAGAAAACAAA
1 AAAAAAACAGGCCTATAGCCTTACAAAAG-AAAATCCAGAAAACAAA
3482228 AAAAGAAACAGGCCTATAGCCTTACAAAAGAAAATCCAGAAAAC
1 AAAA-AAACAGGCCTATAGCCTTACAAAAGAAAATCCAGAAAAC
3482272 GGACAGCAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
47 18 0.43
48 24 0.57
ACGTcount: A:0.56, C:0.20, G:0.13, T:0.11
Consensus pattern (46 bp):
AAAAAAACAGGCCTATAGCCTTACAAAAGAAAATCCAGAAAACAAA
Found at i:3488118 original size:15 final size:17
Alignment explanation
Indices: 3488098--3488130 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3488088 TGATAAAACA
3488098 AATAAA-AT-GTTTTTG
1 AATAAAGATGGTTTTTG
3488113 AATAAAGATGGTTTTTG
1 AATAAAGATGGTTTTTG
3488130 A
1 A
3488131 GCAAAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 2 0.12
17 8 0.50
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (17 bp):
AATAAAGATGGTTTTTG
Found at i:3489864 original size:27 final size:27
Alignment explanation
Indices: 3489817--3489884 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 27
3489807 TTAAAAAATA
*
3489817 ATAAATAATACTTTTAAATTAAT-TAAT
1 ATAAATAATA-TTTAAAATTAATATAAT
3489844 GATAAA-AATATTTAAATATTAATATAAT
1 -ATAAATAATATTTAAA-ATTAATATAAT
3489872 ATAATATAATATT
1 ATAA-ATAATATT
3489885 ATTTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
26 5 0.14
27 14 0.40
28 10 0.29
29 6 0.17
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (27 bp):
ATAAATAATATTTAAAATTAATATAAT
Found at i:3496657 original size:8 final size:8
Alignment explanation
Indices: 3496637--3496706 Score: 53
Period size: 8 Copynumber: 9.4 Consensus size: 8
3496627 TTAAAGCTAA
3496637 AATA-TAT
1 AATATTAT
3496644 ATATATTAT
1 A-ATATTAT
3496653 AATATTAT
1 AATATTAT
3496661 AATATTAT
1 AATATTAT
*
3496669 -ATCTTA-
1 AATATTAT
*
3496675 ATTATTA-
1 AATATTAT
*
3496682 AGTA-TAT
1 AATATTAT
3496689 -ATATTAT
1 AATATTAT
*
3496696 TATATTAT
1 AATATTAT
3496704 AAT
1 AAT
3496707 GATAAGATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 4 0.08
7 16 0.31
8 27 0.53
9 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (8 bp):
AATATTAT
Found at i:3496756 original size:25 final size:23
Alignment explanation
Indices: 3496727--3496784 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
3496717 AAAAAAATAG
*
3496727 AAAAAGAAAGAAAGAAACAGAGAA
1 AAAAAGAAA-AAAGAAAAAGAGAA
* *
3496751 GCAAAACGAAAAAGGAAAAAGAGAA
1 --AAAAAGAAAAAAGAAAAAGAGAA
3496776 AAAAAGAAA
1 AAAAAGAAA
3496785 TGAGAAAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
25 12 0.43
26 8 0.29
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAGAAAAAGAGAA
Found at i:3497791 original size:40 final size:40
Alignment explanation
Indices: 3497667--3497806 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
3497657 AACTTCGAGT
* *
3497667 CGATGAGACACTGGGTGTCAAATTATTACTT-TAGATATATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGA-AT-TATC
* * * * ** *
3497708 TGATGAGGCACTAGGTG-CTAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* *
3497745 CAATGAGAAACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* *
3497785 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
3497807 CTGGTGTGTT
Statistics
Matches: 73, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
37 14 0.19
38 10 0.14
39 2 0.03
40 33 0.45
41 14 0.19
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:3499496 original size:29 final size:28
Alignment explanation
Indices: 3499460--3499514 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
3499450 TATGTTTTTG
*
3499460 AAAATTTAAAGT-TTTTTTTACAATTTTCT
1 AAAATTTAAA-TACTTTTTT-CAATTTTCT
3499489 AAAATTTAAATACTTTTTTCAATTTT
1 AAAATTTAAATACTTTTTTCAATTTT
3499515 ATATATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (28 bp):
AAAATTTAAATACTTTTTTCAATTTTCT
Found at i:3499506 original size:28 final size:29
Alignment explanation
Indices: 3499460--3499514 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
3499450 TATGTTTTTG
**
3499460 AAAATTTAAAGTTTTTTTTACAATTTTCT
1 AAAATTTAAAGTACTTTTTACAATTTTCT
*
3499489 AAAATTTAAA-TACTTTTTTCAATTTT
1 AAAATTTAAAGTACTTTTTACAATTTT
3499515 ATATATTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 13 0.57
29 10 0.43
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (29 bp):
AAAATTTAAAGTACTTTTTACAATTTTCT
Found at i:3499548 original size:27 final size:28
Alignment explanation
Indices: 3499503--3499562 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
3499493 TTTAAATACT
* *
3499503 TTTTTCAATTTTATATA-TTATTCTAAA
1 TTTTTAAATTTTATATATTTATTATAAA
*
3499530 TTTTTAAATTTTA-AGTATTTTTTATAAA
1 TTTTTAAATTTTATA-TATTTATTATAAA
3499558 TTTTT
1 TTTTT
3499563 TTGAATTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 14 0.50
28 13 0.46
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTAAATTTTATATATTTATTATAAA
Found at i:3500200 original size:25 final size:26
Alignment explanation
Indices: 3500172--3500220 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3500162 CACTCATAGA
3500172 TTTAAAATTATATTTTG-AAAAGAAT
1 TTTAAAATTATATTTTGTAAAAGAAT
* * *
3500197 TTTAAAGTTCTTTTTTGTAAAAGA
1 TTTAAAATTATATTTTGTAAAAGA
3500221 CTTTAATAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (26 bp):
TTTAAAATTATATTTTGTAAAAGAAT
Found at i:3500773 original size:14 final size:14
Alignment explanation
Indices: 3500756--3500784 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3500746 CCTAGACAAA
3500756 ATTTCATCTAATGT
1 ATTTCATCTAATGT
3500770 ATTTCATCTAATGT
1 ATTTCATCTAATGT
3500784 A
1 A
3500785 ATTTTAGTAA
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:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTTCATCTAATGT
Found at i:3501558 original size:90 final size:90
Alignment explanation
Indices: 3501404--3501650 Score: 275
Period size: 90 Copynumber: 2.7 Consensus size: 90
3501394 TTCAGTTTAA
* * * * *
3501404 AAATTC-AGTGAATTCATCAAGCCCATCTCACTAGGACCACCCAAAAC-CTGGGATATGAATTCA
1 AAATTCGA-TGAATTCATCAAGTCCATCTTAATAGGACCACCC-AAACTCTAGGATATGAACTCA
* *
3501467 TTAAGAGCATTTAGTGGCTCATCCTAT
64 TTAAGAGCATCTAGTAGCTCATCCTAT
* * * * * *
3501494 AAATTTGAT-AGGTTCATCAAGTTCGTCTTAATAGGATCACCCAAACTCTAGGTTATGAACTCAT
1 AAATTCGATGA-ATTCATCAAGTCCATCTTAATAGGACCACCCAAACTCTAGGATATGAACTCAT
*
3501558 TAAGAGCATCTAGTAGTTCATCCTAT
65 TAAGAGCATCTAGTAGCTCATCCTAT
* ** * *
3501584 ATATTCGATGAATTCATCAAGTCCATCTTAGCAGGACCACCCAAACTTTAGGCTATGAACTCATT
1 AAATTCGATGAATTCATCAAGTCCATCTTAATAGGACCACCCAAACTCTAGGATATGAACTCATT
3501649 AA
66 AA
3501651 AACCAAGGAG
Statistics
Matches: 129, Mismatches: 24, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
89 5 0.04
90 122 0.95
91 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (90 bp):
AAATTCGATGAATTCATCAAGTCCATCTTAATAGGACCACCCAAACTCTAGGATATGAACTCATT
AAGAGCATCTAGTAGCTCATCCTAT
Found at i:3516841 original size:8 final size:8
Alignment explanation
Indices: 3516821--3516890 Score: 53
Period size: 8 Copynumber: 9.4 Consensus size: 8
3516811 TTAAAGCTAA
3516821 AATA-TAT
1 AATATTAT
3516828 ATATATTAT
1 A-ATATTAT
3516837 AATATTAT
1 AATATTAT
3516845 AATATTAT
1 AATATTAT
*
3516853 -ATCTTA-
1 AATATTAT
*
3516859 ATTATTA-
1 AATATTAT
*
3516866 AGTA-TAT
1 AATATTAT
3516873 -ATATTAT
1 AATATTAT
*
3516880 TATATTAT
1 AATATTAT
3516888 AAT
1 AAT
3516891 GATAAGATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 4 0.08
7 16 0.31
8 27 0.53
9 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (8 bp):
AATATTAT
Found at i:3516940 original size:25 final size:23
Alignment explanation
Indices: 3516911--3516968 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
3516901 AAAAAAATAG
*
3516911 AAAAAGAAAGAAAGAAACAGAGAA
1 AAAAAGAAA-AAAGAAAAAGAGAA
* *
3516935 GCAAAACGAAAAAGGAAAAAGAGAA
1 --AAAAAGAAAAAAGAAAAAGAGAA
3516960 AAAAAGAAA
1 AAAAAGAAA
3516969 TGAGAAAGCA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 8 0.29
25 12 0.43
26 8 0.29
ACGTcount: A:0.74, C:0.05, G:0.21, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAGAAAAAGAGAA
Found at i:3517975 original size:40 final size:40
Alignment explanation
Indices: 3517851--3517990 Score: 117
Period size: 40 Copynumber: 3.5 Consensus size: 40
3517841 AACTTCGAGT
* *
3517851 CGATGAGACACTGGGTGTCAAATTATTACTT-TAGATATATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGA-AT-TATC
* * * * ** *
3517892 TGATGAGGCACTAGGTG-CTAA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* *
3517929 CAATGAGAAACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
* *
3517969 CGATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGTCAAA
3517991 CTGGTGTGTT
Statistics
Matches: 73, Mismatches: 22, Indels: 9
0.70 0.21 0.09
Matches are distributed among these distances:
37 14 0.19
38 10 0.14
39 2 0.03
40 33 0.45
41 14 0.19
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:3524430 original size:142 final size:142
Alignment explanation
Indices: 3524174--3524457 Score: 505
Period size: 142 Copynumber: 2.0 Consensus size: 142
3524164 TAAGGGGAAA
*
3524174 GGAATGAAGCATTTTCGGCACAAGGCAATTCTTTGTTTGGTTTTGAGAGGGTTGAAAGGAAGGTA
1 GGAATGAAGCATTTTCGGCACAAGGCAATTCTTTGTTCGGTTTTGAGAGGGTTGAAAGGAAGGTA
3524239 CCGAATGTTCTTTGAGATTTTTCTACCATTAAGGGTTCCTTTCGGGTTTGCGTTTTAGCTAGTGA
66 CCGAATGTTCTTTGAGATTTTTCTACCATTAAGGGTTCCTTTCGGGTTTGCGTTTTAGCTAGTGA
3524304 AGTGATCAAAAT
131 AGTGATCAAAAT
* * * *
3524316 GGAATGGAGCATTTTTGGCACAAGGCAATTTTTTGTTCGGTTTTGAGAGGGTTGAAAGGAAGGTG
1 GGAATGAAGCATTTTCGGCACAAGGCAATTCTTTGTTCGGTTTTGAGAGGGTTGAAAGGAAGGTA
**
3524381 CCGAATGTTCTTTGAGATTTTTCTACCATTCGGGGTTCCTTTCGGGTTTGCGTTTTAGCTAGTGA
66 CCGAATGTTCTTTGAGATTTTTCTACCATTAAGGGTTCCTTTCGGGTTTGCGTTTTAGCTAGTGA
3524446 AGTGATCAAAAT
131 AGTGATCAAAAT
3524458 TTCCACTACT
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 135 1.00
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (142 bp):
GGAATGAAGCATTTTCGGCACAAGGCAATTCTTTGTTCGGTTTTGAGAGGGTTGAAAGGAAGGTA
CCGAATGTTCTTTGAGATTTTTCTACCATTAAGGGTTCCTTTCGGGTTTGCGTTTTAGCTAGTGA
AGTGATCAAAAT
Found at i:3525819 original size:27 final size:27
Alignment explanation
Indices: 3525779--3526068 Score: 266
Period size: 27 Copynumber: 10.7 Consensus size: 27
3525769 CCCAATATTT
* *
3525779 GTAAAATTATCGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
*
3525806 GTATAATGACCGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
* * *
3525833 GTAAAATTACCAAAATACACTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
* *
3525860 ATAAAATGACTGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
3525887 GTAAAATGACCGAAATACCCTCGATGG
1 GTAAAATGACCGAAATACCCTCGATGG
* * ** **
3525914 GTAAATTTATTGAAATACCCTTAATGG
1 GTAAAATGACCGAAATACCCTCGATGG
*
3525941 GTAAAATGATCGAAATACCCTCG-TAGG
1 GTAAAATGACCGAAATACCCTCGAT-GG
** *
3525968 GTAAAATGATTGAAATACCCTAG-TAGG
1 GTAAAATGACCGAAATACCCTCGAT-GG
* * * * *
3525995 GTAAAATGATCGTAATGCCCTTG-TAAG
1 GTAAAATGACCGAAATACCCTCGAT-GG
*
3526022 GTAAAATGACC-ATAATACCTTC-ATAGG
1 GTAAAATGACCGA-AATACCCTCGAT-GG
* *
3526049 GTTAAATGACTGAAATACCC
1 GTAAAATGACCGAAATACCC
3526069 CTATAAGGTA
Statistics
Matches: 218, Mismatches: 41, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.00
27 216 0.99
28 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCTCGATGG
Found at i:3526088 original size:81 final size:80
Alignment explanation
Indices: 3525861--3526111 Score: 228
Period size: 81 Copynumber: 3.1 Consensus size: 80
3525851 ACTCGATGGA
* * * * * *
3525861 TAAAATGACTGAAATACCCTCGAT-GGGTAAAATGACCGAAATACCCTCG-ATGGGTAAATTTAT
1 TAAAATGAC-CAAATACCCTC-ATAGGGTAAAATGACTGAAATACCCTAGTA-AGGTAAAATGAT
* * *
3525924 TGAAATACCC-TT-AATGGG
63 CGTAATGCCCATTGAA--GG
* * * *
3525942 TAAAATGATCGAAATACCCTCGTAGGGTAAAATGATTGAAATACCCTAGTAGGGTAAAATGATCG
1 TAAAATGA-CCAAATACCCTCATAGGGTAAAATGACTGAAATACCCTAGTAAGGTAAAATGATCG
3526007 TAATGCCC-TTGTAAGG
65 TAATGCCCATTG-AAGG
* *
3526023 TAAAATGACCATAATACCTTCATAGGGTTAAATGACTGAAATACCCCTA-TAAGGTAAAATGATC
1 TAAAATGACCA-AATACCCTCATAGGGTAAAATGACTGAAATA-CCCTAGTAAGGTAAAATGATC
*
3526087 GTAATGCCCATTGAGGG
64 GTAATGCCCATTGAAGG
3526104 T-AAATGAC
1 TAAAATGAC
3526112 TATTTTGCCC
Statistics
Matches: 146, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
80 10 0.07
81 124 0.85
82 10 0.07
83 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (80 bp):
TAAAATGACCAAATACCCTCATAGGGTAAAATGACTGAAATACCCTAGTAAGGTAAAATGATCGT
AATGCCCATTGAAGG
Found at i:3526105 original size:27 final size:27
Alignment explanation
Indices: 3525779--3526107 Score: 194
Period size: 27 Copynumber: 12.2 Consensus size: 27
3525769 CCCAATATTT
* *
3525779 GTAAAATTATCGAAATACCCTCG-ATGG
1 GTAAAATGATCGAAATACCCTTGTA-GG
* * *
3525806 GTATAATGACCGAAATACCCTCG-ATGG
1 GTAAAATGATCGAAATACCCTTGTA-GG
* * * * *
3525833 GTAAAATTACCAAAATACACTCG-ATGG
1 GTAAAATGATCGAAATACCCTTGTA-GG
* *
3525860 ATAAAATGA-CTGAAATACCCTCG-ATGG
1 GTAAAATGATC-GAAATACCCTTGTA-GG
* *
3525887 GTAAAATGACCGAAATACCCTCG-ATGG
1 GTAAAATGATCGAAATACCCTTGTA-GG
* * * *
3525914 GTAAATTTATTGAAATACCCTT-AATGG
1 GTAAAATGATCGAAATACCCTTGTA-GG
*
3525941 GTAAAATGATCGAAATACCCTCGTAGG
1 GTAAAATGATCGAAATACCCTTGTAGG
* *
3525968 GTAAAATGATTGAAATACCCTAGTAGG
1 GTAAAATGATCGAAATACCCTTGTAGG
* * *
3525995 GTAAAATGATCGTAATGCCCTTGTAAG
1 GTAAAATGATCGAAATACCCTTGTAGG
* *
3526022 GTAAAATGA-CCATAATA-CCTTCATAGG
1 GTAAAATGATCGA-AATACCCTT-GTAGG
* * * *
3526049 GTTAAATGA-CTGAAATACCCCTATAAG
1 GTAAAATGATC-GAAATACCCTTGTAGG
* *
3526076 GTAAAATGATCGTAATGCCCATTG-AGG
1 GTAAAATGATCGAAATACCC-TTGTAGG
3526103 GTAAA
1 GTAAA
3526108 TGACTATTTT
Statistics
Matches: 248, Mismatches: 44, Indels: 20
0.79 0.14 0.06
Matches are distributed among these distances:
26 6 0.02
27 234 0.94
28 8 0.03
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.25
Consensus pattern (27 bp):
GTAAAATGATCGAAATACCCTTGTAGG
Found at i:3526120 original size:26 final size:27
Alignment explanation
Indices: 3526091--3526143 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3526081 ATGATCGTAA
*
3526091 TGCCCATTGAGGGTAAATGACT-ATTT
1 TGCCCATCGAGGGTAAATGACTGATTT
* *
3526117 TGCCCCTCGAGTGTAAATGACTGATTT
1 TGCCCATCGAGGGTAAATGACTGATTT
3526144 GTCTATGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (27 bp):
TGCCCATCGAGGGTAAATGACTGATTT
Found at i:3526165 original size:24 final size:24
Alignment explanation
Indices: 3526130--3526214 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
3526120 CCCTCGAGTG
* *
3526130 TAAATGACTGATTTGTCTATGATT
1 TAAATGATTGATTTGTCTGTGATT
3526154 TAAATGATTGATTTGTCTGTGATT
1 TAAATGATTGATTTGTCTGTGATT
***
3526178 GGTATGATTGATTTGTCTGTGATT
1 TAAATGATTGATTTGTCTGTGATT
**
3526202 TGTATGATTGATT
1 TAAATGATTGATT
3526215 CTGAGCATGA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.24, C:0.05, G:0.22, T:0.49
Consensus pattern (24 bp):
TAAATGATTGATTTGTCTGTGATT
Found at i:3526332 original size:26 final size:26
Alignment explanation
Indices: 3526303--3526360 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
3526293 TTGGCCACAT
3526303 ATACTATTACGGGCAGCTTTGCTGCG
1 ATACTATTACGGGCAGCTTTGCTGCG
* ***
3526329 ATACTGTTGTTGGCAGCTTTGCTGCG
1 ATACTATTACGGGCAGCTTTGCTGCG
3526355 ATACTA
1 ATACTA
3526361 CTGATGGCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.34
Consensus pattern (26 bp):
ATACTATTACGGGCAGCTTTGCTGCG
Found at i:3526368 original size:26 final size:26
Alignment explanation
Indices: 3526314--3526368 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
3526304 TACTATTACG
** *
3526314 GGCAGCTTTGCTGCGATACTGTTGTT
1 GGCAGCTTTGCTGCGATACTACTGAT
3526340 GGCAGCTTTGCTGCGATACTACTGAT
1 GGCAGCTTTGCTGCGATACTACTGAT
3526366 GGC
1 GGC
3526369 TTTGTGCCGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.22, G:0.31, T:0.33
Consensus pattern (26 bp):
GGCAGCTTTGCTGCGATACTACTGAT
Found at i:3526407 original size:32 final size:32
Alignment explanation
Indices: 3526358--3526465 Score: 128
Period size: 32 Copynumber: 3.4 Consensus size: 32
3526348 TGCTGCGATA
3526358 CTACTGATGGCTTTGTGCCGATCATATTACCG
1 CTACTGATGGCTTTGTGCCGATCATATTACCG
* * * * * *
3526390 TTGCTGATGGCTGTGTGCCGGTCATATCACTG
1 CTACTGATGGCTTTGTGCCGATCATATTACCG
* *
3526422 CTACTGATGGCTTTGTGCCAATCATATTACTG
1 CTACTGATGGCTTTGTGCCGATCATATTACCG
*
3526454 -TACTTATGGCTT
1 CTACTGATGGCTT
3526466 GTAGCCATTT
Statistics
Matches: 63, Mismatches: 13, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
31 11 0.17
32 52 0.83
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (32 bp):
CTACTGATGGCTTTGTGCCGATCATATTACCG
Found at i:3530218 original size:27 final size:27
Alignment explanation
Indices: 3530122--3530309 Score: 119
Period size: 27 Copynumber: 7.0 Consensus size: 27
3530112 GATATACCAT
* * *
3530122 CGTAATGCCCCTGTAAGGTAAAATGAC
1 CGTAATACCCCTATAGGGTAAAATGAC
* * * *
3530149 TGTAATACCTCTGTAGGGTAAAATAAC
1 CGTAATACCCCTATAGGGTAAAATGAC
* * * **
3530176 TG-AAAAACTGTCATAGGGTAAAATGAC
1 CGTAATACCCCT-ATAGGGTAAAATGAC
** * *
3530203 CGTAACGCCCCTATAGGGTAAAATAAT
1 CGTAATACCCCTATAGGGTAAAATGAC
* *
3530230 CGTAATACCCCCATAGGGTTAAATGAC
1 CGTAATACCCCTATAGGGTAAAATGAC
*** * *
3530257 TAAAATACTCCTATATGGTAAAATGAC
1 CGTAATACCCCTATAGGGTAAAATGAC
* * *
3530284 CGTAATGCCTCTAGAGGGT-AAATGAC
1 CGTAATACCCCTATAGGGTAAAATGAC
3530310 TATTTTTCCC
Statistics
Matches: 120, Mismatches: 39, Indels: 5
0.73 0.24 0.03
Matches are distributed among these distances:
26 13 0.11
27 103 0.86
28 4 0.03
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (27 bp):
CGTAATACCCCTATAGGGTAAAATGAC
Found at i:3530598 original size:32 final size:32
Alignment explanation
Indices: 3530559--3530683 Score: 160
Period size: 32 Copynumber: 3.9 Consensus size: 32
3530549 TGCTGCGTGC
*
3530559 TACTGATGGCTTTGTGCTGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
3530591 TATTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * * * ***
3530623 TACTGATGGCTGTGTACCGGTCATATCACTAC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
3530655 TACTGATGGCTTTGTGCCAATCATATTAC
1 TACTGATGGCTTTGTGCCGATCATATTAC
3530684 TGTACTTGTG
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 78 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:3539557 original size:27 final size:26
Alignment explanation
Indices: 3539522--3539621 Score: 76
Period size: 27 Copynumber: 3.7 Consensus size: 26
3539512 ATTCCCCGTG
* *
3539522 TTTATTGTCTCAGTGAACTATCTCGTG
1 TTTAATGTCTC-GTGAACTATCTCGTA
* * * * *
3539549 TTTAATGTCCCATTAGACTATCCCGCA
1 TTTAATGTCTCGTGA-ACTATCTCGTA
*
3539576 TTTAACGTCTCGTCAGAAC-ATCTCGTA
1 TTTAATGTCTCGT--GAACTATCTCGTA
3539603 TTTAATGTCTCGTTGAACT
1 TTTAATGTCTCG-TGAACT
3539622 TTCTATGATG
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
26 6 0.11
27 44 0.81
28 3 0.06
29 1 0.02
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (26 bp):
TTTAATGTCTCGTGAACTATCTCGTA
Found at i:3539780 original size:45 final size:44
Alignment explanation
Indices: 3539694--3539862 Score: 178
Period size: 45 Copynumber: 3.8 Consensus size: 44
3539684 AAAGTATACT
* * * *
3539694 ATAGCCTCTTTCAGCTATGGTCTTAGTCCTGTTCA-CTATGATGCC
1 ATAGCATCTTTCAGCTATGGTCTTACTCAT-TTTATC-ATGATGCC
* *
3539739 ATAGCGTCTTTCAGCCATGGTCTTACTCATTTATATCATGATGCC
1 ATAGCATCTTTCAGCTATGGTCTTACTCATTT-TATCATGATGCC
* * * * **
3539784 ACAACATCTTTAAGCTGTGGTCTTACTCATCTTTATCATGATTTC
1 ATAGCATCTTTCAGCTATGGTCTTACTCAT-TTTATCATGATGCC
*
3539829 ATAGCATCTTTCAGTTATGGTCTTACTCATTTTA
1 ATAGCATCTTTCAGCTATGGTCTTACTCATTTTA
3539863 GGTGTATAAC
Statistics
Matches: 103, Mismatches: 18, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
44 6 0.06
45 94 0.91
46 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (44 bp):
ATAGCATCTTTCAGCTATGGTCTTACTCATTTTATCATGATGCC
Found at i:3541359 original size:22 final size:22
Alignment explanation
Indices: 3541323--3541367 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
3541313 TTGATGTTCT
3541323 AGTTGGAATTGTAATGTGTCTAA
1 AGTTGGAATTGTAATGTGT-TAA
*
3541346 AGTTGGTA-TGTAATGTGTTAA
1 AGTTGGAATTGTAATGTGTTAA
3541367 A
1 A
3541368 CTTAATGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 10 0.48
23 7 0.33
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.40
Consensus pattern (22 bp):
AGTTGGAATTGTAATGTGTTAA
Found at i:3553983 original size:32 final size:32
Alignment explanation
Indices: 3553932--3554142 Score: 178
Period size: 32 Copynumber: 6.6 Consensus size: 32
3553922 CGATGCTACC
** *
3553932 GATGGCTTTGTGCTTATCATAGTACCATTACT
1 GATGGCTTTGTGCCGATCATAGTACCGTTACT
* * *
3553964 GATGGCTTTCTGCCGATCATATTACCGTTACC
1 GATGGCTTTGTGCCGATCATAGTACCGTTACT
* * *
3553996 GATGGCTGTGTGCCGATCAT-TTCACTGTTACT
1 GATGGCTTTGTGCCGATCATAGT-ACCGTTACT
* * * * *
3554028 AATGGCTGTGTACCGATCATA-TCACTGCTACT
1 GATGGCTTTGTGCCGATCATAGT-ACCGTTACT
*
3554060 GATGGCTTTGTGCCGATCA-CGTTACCGTTACT
1 GATGGCTTTGTGCCGATCATAG-TACCGTTACT
* * * *
3554092 GACGACTTTGTGCCGATCATA-TCACTGCTACT
1 GATGGCTTTGTGCCGATCATAGT-ACCGTTACT
*
3554124 GATGGCTTTGTGCCAATCA
1 GATGGCTTTGTGCCGATCA
3554143 CATTACTGTA
Statistics
Matches: 146, Mismatches: 27, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
31 3 0.02
32 142 0.97
33 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (32 bp):
GATGGCTTTGTGCCGATCATAGTACCGTTACT
Found at i:3554033 original size:64 final size:64
Alignment explanation
Indices: 3553925--3554148 Score: 236
Period size: 64 Copynumber: 3.5 Consensus size: 64
3553915 TTTGTTGCGA
* ** * * * *
3553925 TGCTACCGATGGCTTTGTGCTTATCATAG-TACCATTACTGATGGCTTTCTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCA-CGTTACCGTTACTGATGGCTTTGTGCCGATCATATCAC
* * * * * * * * *
3553989 CGTTACCGATGGCTGTGTGCCGATCA-TTTCACTGTTACTAATGGCTGTGTACCGATCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCACGTT-ACCGTTACTGATGGCTTTGTGCCGATCATATCAC
* *
3554053 TGCTACTGATGGCTTTGTGCCGATCACGTTACCGTTACTGACGACTTTGTGCCGATCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCACGTTACCGTTACTGATGGCTTTGTGCCGATCATATCAC
* *
3554117 TGCTACTGATGGCTTTGTGCCAATCACATTAC
1 TGCTACTGATGGCTTTGTGCCGATCACGTTAC
3554149 TGTACTTATG
Statistics
Matches: 131, Mismatches: 26, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
63 1 0.01
64 128 0.98
65 2 0.02
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.34
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCACGTTACCGTTACTGATGGCTTTGTGCCGATCATATCAC
Found at i:3564756 original size:56 final size:50
Alignment explanation
Indices: 3564693--3564984 Score: 266
Period size: 50 Copynumber: 5.7 Consensus size: 50
3564683 GGGAATGAGA
* *
3564693 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATAAGAGG
* * *
3564749 TTCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
** *
3564799 TCCCATGTAAGACCATGTCTGGGACATGGCGCTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
** * * * * **
3564849 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
* * * * * *
3564899 TCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTACAAGA-AACA--
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA--CCGAGATAAGAGG
* * *
3564948 TCCCATGTAAGACCATGTCTGAGACATGACTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
3564985 TGTTATTATC
Statistics
Matches: 200, Mismatches: 34, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
49 31 0.16
50 126 0.63
51 2 0.01
52 3 0.01
53 3 0.01
55 1 0.00
56 34 0.17
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATAAGAGG
Found at i:3564813 original size:50 final size:50
Alignment explanation
Indices: 3564693--3564933 Score: 284
Period size: 50 Copynumber: 4.7 Consensus size: 50
3564683 GGGAATGAGA
* * *
3564693 TCCCATGTAAGACCATGTATGGGACATGGCATTGGCATCATTGAGATTATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
3564749 TTCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
**
3564799 TCCCATGTAAGACCATGTCTGGGACATGGCGCTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
3564849 TCCCCCGTAAGACCATGTCTAGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
3564899 TCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
3564934 TAGTACAAGA
Statistics
Matches: 163, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
50 125 0.77
53 3 0.02
55 1 0.01
56 34 0.21
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:3566489 original size:27 final size:27
Alignment explanation
Indices: 3566459--3566625 Score: 124
Period size: 27 Copynumber: 6.2 Consensus size: 27
3566449 CCTAATATTT
* *
3566459 GTAAAATGACCATAATATCCCTGTAGG
1 GTAAAATAACCATAATACCCCTGTAGG
* * *
3566486 GTAAAATAACCA-AAAAACCCTCATAGG
1 GTAAAATAACCATAATACCCCT-GTAGG
* * **
3566513 GTAAAATGAA-CGTAATGCCATTGTAGG
1 GTAAAAT-AACCATAATACCCCTGTAGG
* **
3566540 GTAAAATAACCGTAATACCCCCATAGG
1 GTAAAATAACCATAATACCCCTGTAGG
* * * *
3566567 GTTAAATGACCAAAATACCCCTGTAAG
1 GTAAAATAACCATAATACCCCTGTAGG
* *
3566594 GTAAAATAACCGTAATGCCCCTAG-AGG
1 GTAAAATAACCATAATACCCCT-GTAGG
3566621 GTAAA
1 GTAAA
3566626 TGACTATTTT
Statistics
Matches: 106, Mismatches: 29, Indels: 10
0.73 0.20 0.07
Matches are distributed among these distances:
26 9 0.08
27 90 0.85
28 7 0.07
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (27 bp):
GTAAAATAACCATAATACCCCTGTAGG
Found at i:3566597 original size:81 final size:81
Alignment explanation
Indices: 3566459--3566612 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
3566449 CCTAATATTT
* * ** *
3566459 GTAAAATGACCATAATATCCCTGTAGGGTAAAATAACCAAAAAACCCTCATAGGGTAAAATGAA-
1 GTAAAATAACCATAATACCCCCATAGGGTAAAATAACCAAAAAACCCTCATAAGGTAAAAT-AAC
3566523 CGTAATGCCATTGTAGG
65 CGTAATGCCATTGTAGG
* * * * *
3566540 GTAAAATAACCGTAATACCCCCATAGGGTTAAATGACCAAAATACCC-CTGTAAGGTAAAATAAC
1 GTAAAATAACCATAATACCCCCATAGGGTAAAATAACCAAAAAACCCTC-ATAAGGTAAAATAAC
3566604 CGTAATGCC
65 CGTAATGCC
3566613 CCTAGAGGGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
80 3 0.05
81 58 0.95
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (81 bp):
GTAAAATAACCATAATACCCCCATAGGGTAAAATAACCAAAAAACCCTCATAAGGTAAAATAACC
GTAATGCCATTGTAGG
Found at i:3566605 original size:54 final size:54
Alignment explanation
Indices: 3566462--3566629 Score: 185
Period size: 54 Copynumber: 3.1 Consensus size: 54
3566452 AATATTTGTA
* ** * * *
3566462 AAATGACCATAATATCCCTGTAGGGTAAAATAACCAAAAAACCCTCATAGGGTA
1 AAATGACCATAATACCCCTGTAGGGTAAAATAACCGTAATACCCCCATAGGGTT
* * * **
3566516 AAATGAACGTAATGCCATTGTAGGGTAAAATAACCGTAATACCCCCATAGGGTT
1 AAATGACCATAATACCCCTGTAGGGTAAAATAACCGTAATACCCCCATAGGGTT
* * * * *
3566570 AAATGACCAAAATACCCCTGTAAGGTAAAATAACCGTAATGCCCCTAGAGGG-T
1 AAATGACCATAATACCCCTGTAGGGTAAAATAACCGTAATACCCCCATAGGGTT
3566623 AAATGAC
1 AAATGAC
3566630 TATTTTTCCC
Statistics
Matches: 93, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
53 8 0.09
54 85 0.91
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (54 bp):
AAATGACCATAATACCCCTGTAGGGTAAAATAACCGTAATACCCCCATAGGGTT
Found at i:3566677 original size:24 final size:25
Alignment explanation
Indices: 3566646--3566743 Score: 96
Period size: 24 Copynumber: 4.0 Consensus size: 25
3566636 TCCCTTTGAG
*
3566646 TGTAAATGATTGATTTGTCCGTG-T
1 TGTAAATGACTGATTTGTCCGTGAT
*
3566670 TGTAAATGACTGATTTGTCTGTGAT
1 TGTAAATGACTGATTTGTCCGTGAT
* **
3566695 T-TAAATGACTAATTTGTTTGTGAT
1 TGTAAATGACTGATTTGTCCGTGAT
* *
3566719 TGGT--ATGACTAATTTGTCTGTGAT
1 T-GTAAATGACTGATTTGTCCGTGAT
3566743 T
1 T
3566744 TGTATAACTA
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
24 63 0.95
25 2 0.03
26 1 0.02
ACGTcount: A:0.23, C:0.07, G:0.22, T:0.47
Consensus pattern (25 bp):
TGTAAATGACTGATTTGTCCGTGAT
Found at i:3566710 original size:48 final size:48
Alignment explanation
Indices: 3566648--3566744 Score: 117
Period size: 48 Copynumber: 2.0 Consensus size: 48
3566638 CCTTTGAGTG
* * *
3566648 TAAATGATTGATTTGTCCGTG-TT-GTAAATGACTGATTTGTCTGTGATT
1 TAAATGACTAATTTGTCCGTGATTGGT--ATGACTAATTTGTCTGTGATT
**
3566696 TAAATGACTAATTTGTTTGTGATTGGTATGACTAATTTGTCTGTGATT
1 TAAATGACTAATTTGTCCGTGATTGGTATGACTAATTTGTCTGTGATT
3566744 T
1 T
3566745 GTATAACTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 38 0.90
49 2 0.05
50 2 0.05
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (48 bp):
TAAATGACTAATTTGTCCGTGATTGGTATGACTAATTTGTCTGTGATT
Found at i:3566748 original size:24 final size:24
Alignment explanation
Indices: 3566675--3566757 Score: 112
Period size: 24 Copynumber: 3.5 Consensus size: 24
3566665 CGTGTTGTAA
* **
3566675 ATGACTGATTTGTCTGTGATTTAA
1 ATGACTAATTTGTCTGTGATTTGT
* *
3566699 ATGACTAATTTGTTTGTGATTGGT
1 ATGACTAATTTGTCTGTGATTTGT
3566723 ATGACTAATTTGTCTGTGATTTGT
1 ATGACTAATTTGTCTGTGATTTGT
*
3566747 ATAACTAATTT
1 ATGACTAATTT
3566758 TGAGCATGAC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.25, C:0.07, G:0.19, T:0.48
Consensus pattern (24 bp):
ATGACTAATTTGTCTGTGATTTGT
Found at i:3569784 original size:19 final size:18
Alignment explanation
Indices: 3569760--3569802 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3569750 TGGGCCTCGT
3569760 TGGGCCAAAATGGGCTGTG
1 TGGGCCAAAATGGGCT-TG
* *
3569779 TGGGCC-TAGTGGGCTTG
1 TGGGCCAAAATGGGCTTG
3569796 TGGGCCA
1 TGGGCCA
3569803 CACAGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.14, C:0.19, G:0.44, T:0.23
Consensus pattern (18 bp):
TGGGCCAAAATGGGCTTG
Found at i:3570163 original size:27 final size:27
Alignment explanation
Indices: 3570132--3570282 Score: 160
Period size: 27 Copynumber: 5.6 Consensus size: 27
3570122 CCCAATATTT
*
3570132 GTAAAATGACCGTAATACCCCTGTAGG
1 GTAAAATGACCGTAATACCCCTATAGG
* * * *
3570159 GTAAAATGACC-AAAAAACCCTCAGAGG
1 GTAAAATGACCGTAATACCCCT-ATAGG
* * *
3570186 GTGAAATGATCGTAATGCCCCTATAGG
1 GTAAAATGACCGTAATACCCCTATAGG
*
3570213 GTAAAATGACCGTAATACCCCTATTGG
1 GTAAAATGACCGTAATACCCCTATAGG
* ** * *
3570240 GTTAAATGATTGAAATACCCCTATAAG
1 GTAAAATGACCGTAATACCCCTATAGG
3570267 GTAAAATGACCGTAAT
1 GTAAAATGACCGTAAT
3570283 GCCTTTAGAG
Statistics
Matches: 96, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
26 7 0.07
27 83 0.86
28 6 0.06
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (27 bp):
GTAAAATGACCGTAATACCCCTATAGG
Found at i:3570274 original size:81 final size:81
Alignment explanation
Indices: 3570132--3570285 Score: 193
Period size: 81 Copynumber: 1.9 Consensus size: 81
3570122 CCCAATATTT
* * * *
3570132 GTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACCAAAAAACCCTCAGAGGGTGAAATGATC
1 GTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCAAAAAACCCTCAGAAGGTAAAATGACC
3570197 GTAATGCCCCTATAGG
66 GTAATGCCCCTATAGG
* * *** * *
3570213 GTAAAATGACCGTAATACCCCTATTGGGTTAAATGATTGAAATACCC-CTATAAGGTAAAATGAC
1 GTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCAAAAAACCCTC-AGAAGGTAAAATGAC
3570277 CGTAATGCC
65 CGTAATGCC
3570286 TTTAGAGGGT
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
80 1 0.02
81 60 0.98
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.23
Consensus pattern (81 bp):
GTAAAATGACCGTAATACCCCTATAGGGTAAAATGACCAAAAAACCCTCAGAAGGTAAAATGACC
GTAATGCCCCTATAGG
Found at i:3570372 original size:24 final size:24
Alignment explanation
Indices: 3570345--3570429 Score: 107
Period size: 24 Copynumber: 3.5 Consensus size: 24
3570335 GTCCATATTG
3570345 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*
3570369 TAAATGACTGATTTCTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
****
3570393 GGTTTGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
**
3570417 TGTATGACTGATT
1 TAAATGACTGATT
3570430 CTAAGCATGG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 53 1.00
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.47
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:3579040 original size:6 final size:7
Alignment explanation
Indices: 3579023--3579048 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3579013 TTTTCAGGTC
3579023 TTTTTCA
1 TTTTTCA
3579030 TTTTTCA
1 TTTTTCA
3579037 TTTTTCA
1 TTTTTCA
3579044 TTTTT
1 TTTTT
3579049 GTTTTGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:3584998 original size:43 final size:42
Alignment explanation
Indices: 3584917--3585024 Score: 107
Period size: 43 Copynumber: 2.6 Consensus size: 42
3584907 TAACTCATAT
* *
3584917 TTTAATCC-TATTGGGTTTCCGTTCAGATCTTTTAAGC-TTCA
1 TTTAACCCTTATTGGGTTTCTGTTCAGA-CTTTTAAGCTTTCA
*
3584958 GTTTAACCCTTATTGGGTTTCTGTTCAG-CTTTAATGAGCTTTCA
1 -TTTAACCCTTATTGGGTTTCTGTTCAGACTTT--TAAGCTTTCA
* *
3585002 TTCAACCCTTA-TGGGTTTTTGTT
1 TTTAACCCTTATTGGGTTTCTGTT
3585025 TAGCACTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
41 4 0.07
42 18 0.32
43 31 0.54
44 4 0.07
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.47
Consensus pattern (42 bp):
TTTAACCCTTATTGGGTTTCTGTTCAGACTTTTAAGCTTTCA
Found at i:3588093 original size:43 final size:43
Alignment explanation
Indices: 3588046--3588186 Score: 133
Period size: 43 Copynumber: 3.2 Consensus size: 43
3588036 TATCTTCAGC
*
3588046 CTGCTCCACTACAACCGAGGGAGGCAAGGCTTGTGTCTTCGAT
1 CTGCTCCACTACAAACGAGGGAGGCAAGGCTTGTGTCTTCGAT
* * ** * * * * *
3588089 CTGCTTCACTGTCGATGCG-GGAAGGCAA-GATCTGCTATCTTCAAC
1 CTGCTCCACT-AC-AAACGAGGGAGGCAAGGCT-TG-TGTCTTCGAT
3588134 CTGCTCCACTACAAACGAGGGAGGCAAGGCTTGTGTCTTCGAT
1 CTGCTCCACTACAAACGAGGGAGGCAAGGCTTGTGTCTTCGAT
*
3588177 CTGCTTCACT
1 CTGCTCCACT
3588187 GTCGATGTAG
Statistics
Matches: 73, Mismatches: 19, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
43 30 0.41
44 22 0.30
45 21 0.29
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (43 bp):
CTGCTCCACTACAAACGAGGGAGGCAAGGCTTGTGTCTTCGAT
Found at i:3588115 original size:44 final size:44
Alignment explanation
Indices: 3588067--3588205 Score: 131
Period size: 44 Copynumber: 3.2 Consensus size: 44
3588057 CAACCGAGGG
3588067 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGCGGGA
1 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGCGGGA
* * * * * * ** *
3588111 AGGCAA-GATCTGCTATCTTCAACCTGCTCCACT-AC-AAACGAGGG
1 AGGCAAGGCT-TG-TGTCTTCGATCTGCTTCACTGTCGATGCG-GGA
**
3588155 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGTAGGA
1 AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGCGGGA
3588199 AGGCAAG
1 AGGCAAG
3588206 ATCTACTATC
Statistics
Matches: 69, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
43 21 0.30
44 29 0.42
45 19 0.28
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (44 bp):
AGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGCGGGA
Found at i:3588124 original size:88 final size:88
Alignment explanation
Indices: 3587994--3588244 Score: 412
Period size: 88 Copynumber: 2.9 Consensus size: 88
3587984 GGACCATTGG
* * * * * *
3587994 CTTCGATCTACTTCAGTATCGACGCAGGAAGGCAAGACCTGCTATCTTCAGCCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
3588059 ACCGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
*
3588082 CTTCGATCTGCTTCACTGTCGATGCGGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
*
3588147 AACGAGGGAGGCAAGGCTTGTGT
66 ACCGAGGGAGGCAAGGCTTGTGT
* *
3588170 CTTCGATCTGCTTCACTGTCGATGTAGGAAGGCAAGATCTACTATCTTCAACCTGCTCCACTACA
1 CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
3588235 ACCGAGGGAG
66 ACCGAGGGAG
3588245 ATAAGATCTG
Statistics
Matches: 151, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 151 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (88 bp):
CTTCGATCTGCTTCACTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACA
ACCGAGGGAGGCAAGGCTTGTGT
Found at i:3588138 original size:45 final size:45
Alignment explanation
Indices: 3588020--3588231 Score: 125
Period size: 44 Copynumber: 4.8 Consensus size: 45
3588010 TATCGACGCA
* * * **
3588020 GGAAGGCAAGACCTGCTATCTTCAGCCTGCTCCACT-AC-AACCG
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGTCGATGCG
* * * * * *
3588063 AGGGAGGCAAG-GCTTG-TGTCTTCGATCTGCTTCACTGTCGATGCG
1 -GGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACTGTCGATGCG
* **
3588108 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT-AC-AAACG
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGTCGATGCG
* * * * * * **
3588151 AGGGAGGCAAG-GCTTG-TGTCTTCGATCTGCTTCACTGTCGATGTA
1 -GGAAGGCAAGATC-TGCTATCTTCAACCTGCTCCACTGTCGATGCG
*
3588196 GGAAGGCAAGATCTACTATCTTCAACCTGCTCCACT
1 GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
3588232 ACAACCGAGG
Statistics
Matches: 120, Mismatches: 37, Indels: 21
0.67 0.21 0.12
Matches are distributed among these distances:
43 36 0.30
44 46 0.38
45 38 0.32
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (45 bp):
GGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTGTCGATGCG
Found at i:3588312 original size:44 final size:44
Alignment explanation
Indices: 3588264--3588602 Score: 426
Period size: 44 Copynumber: 7.7 Consensus size: 44
3588254 GTAATTGTCA
* * * *
3588264 ACCTACTCCACAGCTGCTCAGGGAGCTAGGACTTACAATCTTCT
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* *
3588308 ACCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCC
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* * * *
3588352 GCCTATTCCACTGCTGTTCAGGGAGTTAGGACTTTCAGTCTTCC
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* * *
3588396 ACCTATTCCACTACTGGTCAGGGAGCTAGGACTTAGAATCTTCC
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* * * * * *
3588440 GCCTATTCCACTGCTGTTCAAGGAGCTAGCACTTTCAGTTTTCC
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* * * *
3588484 TCCTATTCCACTGCTGGTCAGGGAGCTAGGATTTACAATCTTCT
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* * *
3588528 GCCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCC
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
* *
3588572 ACCTATTCCACTGTTGTTCAGAGAGCTAGGA
1 ACCTATTCCACTGCTGTTCAGGGAGCTAGGA
3588603 TTTATAGTTT
Statistics
Matches: 250, Mismatches: 45, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 250 1.00
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.31
Consensus pattern (44 bp):
ACCTATTCCACTGCTGTTCAGGGAGCTAGGACTTACAATCTTCC
Found at i:3588373 original size:88 final size:88
Alignment explanation
Indices: 3588265--3588606 Score: 522
Period size: 88 Copynumber: 3.9 Consensus size: 88
3588255 TAATTGTCAA
* * * * * *
3588265 CCTACTCCACAGCTGCTCAGGGAGCTAGGACTTACAATCTTCTACCTATTCCACTGCTGGTCAGG
1 CCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGG
3588330 GAGCTAGGATTTACAATCTTCCG
66 GAGCTAGGATTTACAATCTTCCG
* *
3588353 CCTATTCCACTGCTGTTCAGGGAGTTAGGACTTTCAGTCTTCCACCTATTCCACTACTGGTCAGG
1 CCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGG
* *
3588418 GAGCTAGGACTTAGAATCTTCCG
66 GAGCTAGGATTTACAATCTTCCG
* * * *
3588441 CCTATTCCACTGCTGTTCAAGGAGCTAGCACTTTCAGTTTTCCTCCTATTCCACTGCTGGTCAGG
1 CCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGG
*
3588506 GAGCTAGGATTTACAATCTTCTG
66 GAGCTAGGATTTACAATCTTCCG
* * *
3588529 CCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGTTGTTCAGA
1 CCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGG
3588594 GAGCTAGGATTTA
66 GAGCTAGGATTTA
3588607 TAGTTTCACC
Statistics
Matches: 228, Mismatches: 26, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 228 1.00
ACGTcount: A:0.21, C:0.27, G:0.20, T:0.31
Consensus pattern (88 bp):
CCTATTCCACTGCTGTTCAGGGAGCTAGGACTTTCAGTCTTCCACCTATTCCACTGCTGGTCAGG
GAGCTAGGATTTACAATCTTCCG
Found at i:3588755 original size:22 final size:22
Alignment explanation
Indices: 3588730--3588803 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
3588720 AGGTATGTAT
3588730 GAATGATGTTTGCATGAATGCA
1 GAATGATGTTTGCATGAATGCA
* *
3588752 GAATGTCATTTTTTGACAACG-AT--A
1 GAATG--A-TGTTTG-C-ATGAATGCA
3588776 TGAATGATGTTTGCATGAATGCA
1 -GAATGATGTTTGCATGAATGCA
3588799 GAATG
1 GAATG
3588804 TCATTTTTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 18
0.64 0.07 0.30
Matches are distributed among these distances:
20 2 0.05
21 3 0.08
22 15 0.38
23 2 0.05
24 2 0.05
25 10 0.26
26 3 0.08
27 2 0.05
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.34
Consensus pattern (22 bp):
GAATGATGTTTGCATGAATGCA
Found at i:3588778 original size:47 final size:47
Alignment explanation
Indices: 3588727--3588821 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
3588717 ACTAGGTATG
3588727 TATGAATGATGTTTGCATGAATGCAGAATGTCATTTTTTGACAACGA
1 TATGAATGATGTTTGCATGAATGCAGAATGTCATTTTTTGACAACGA
3588774 TATGAATGATGTTTGCATGAATGCAGAATGTCATTTTTTGACAACGA
1 TATGAATGATGTTTGCATGAATGCAGAATGTCATTTTTTGACAACGA
3588821 T
1 T
3588822 TTTTGGTTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.37
Consensus pattern (47 bp):
TATGAATGATGTTTGCATGAATGCAGAATGTCATTTTTTGACAACGA
Found at i:3603681 original size:43 final size:43
Alignment explanation
Indices: 3603599--3603695 Score: 115
Period size: 43 Copynumber: 2.3 Consensus size: 43
3603589 ATGAGTTTCG
* * *
3603599 GTTTAACCC-TATTGGGTTTTCGCTCAACTCTTTTGAGCTTCA
1 GTTTAACCCTTATTGGGTTTTCGCTCAACTATTATAAGCTTCA
* ** *
3603641 GTTTAACCCTTATTGGGTTTTCGTTCAGTTATTATAAGCTTCT
1 GTTTAACCCTTATTGGGTTTTCGCTCAACTATTATAAGCTTCA
*
3603684 GTTCAACCCTTA
1 GTTTAACCCTTA
3603696 CAGGTTTCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
42 9 0.20
43 37 0.80
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (43 bp):
GTTTAACCCTTATTGGGTTTTCGCTCAACTATTATAAGCTTCA
Found at i:3607249 original size:15 final size:15
Alignment explanation
Indices: 3607229--3607264 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
3607219 AACGTTTTGG
*
3607229 TTTGTATAGTAATGC
1 TTTGTACAGTAATGC
3607244 TTTGTACAGTAATGC
1 TTTGTACAGTAATGC
3607259 TTTGTA
1 TTTGTA
3607265 ACCCTAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.08, G:0.19, T:0.47
Consensus pattern (15 bp):
TTTGTACAGTAATGC
Found at i:3609039 original size:17 final size:18
Alignment explanation
Indices: 3609017--3609057 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3609007 CATTTCCGTA
*
3609017 TCATTTCCATATATCA-T
1 TCATTTACATATATCACT
*
3609034 TCATTTACATATTTCACT
1 TCATTTACATATATCACT
3609052 TCATTT
1 TCATTT
3609058 TTACATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.27, C:0.22, G:0.00, T:0.51
Consensus pattern (18 bp):
TCATTTACATATATCACT
Found at i:3612009 original size:18 final size:18
Alignment explanation
Indices: 3611986--3612023 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
3611976 ATAGACGTTA
3611986 AATAAATATTAAAATACT
1 AATAAATATTAAAATACT
3612004 AATAAATATTAAAATACT
1 AATAAATATTAAAATACT
3612022 AA
1 AA
3612024 CTCACTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
AATAAATATTAAAATACT
Found at i:3634670 original size:88 final size:89
Alignment explanation
Indices: 3634557--3634733 Score: 347
Period size: 88 Copynumber: 2.0 Consensus size: 89
3634547 TTTTATAGTT
3634557 AATGGTGCAGATGCATGTGTGTATTCTAAAATGTTTGGTTCTGATTGCATTATCATAAGTTTGTA
1 AATGGTGCAGATGCATGTGTGTATTCTAAAATGTTTGGTTCTGATTGCATTATCATAAGTTTGTA
3634622 TGTAGATGACATGTTAATTTCCAA
66 TGTAGATGACATGTTAATTTCCAA
3634646 AATGGTGCAG-TGCATGTGTGTATTCTAAAATGTTTGGTTCTGATTGCATTATCATAAGTTTGTA
1 AATGGTGCAGATGCATGTGTGTATTCTAAAATGTTTGGTTCTGATTGCATTATCATAAGTTTGTA
3634710 TGTAGATGACATGTTAATTTCCAA
66 TGTAGATGACATGTTAATTTCCAA
3634734 TTCCAATATA
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
88 78 0.89
89 10 0.11
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (89 bp):
AATGGTGCAGATGCATGTGTGTATTCTAAAATGTTTGGTTCTGATTGCATTATCATAAGTTTGTA
TGTAGATGACATGTTAATTTCCAA
Found at i:3635565 original size:26 final size:26
Alignment explanation
Indices: 3635536--3635598 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
3635526 TTACTCTCGA
3635536 TAAAATTTTGAC-ATTTCACCCCTTAG
1 TAAAATTTTGACGATTTCACCCC-TAG
* ** *
3635562 TAAAATTTTTACGATTTTGCCCCTGG
1 TAAAATTTTGACGATTTCACCCCTAG
3635588 TAAAATTTTGA
1 TAAAATTTTGA
3635599 GAAAATATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 23 0.74
27 8 0.26
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.41
Consensus pattern (26 bp):
TAAAATTTTGACGATTTCACCCCTAG
Found at i:3639533 original size:40 final size:40
Alignment explanation
Indices: 3639479--3639638 Score: 320
Period size: 40 Copynumber: 4.0 Consensus size: 40
3639469 ATTGGCGAAC
3639479 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
1 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
3639519 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
1 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
3639559 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
1 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
3639599 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
1 CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
3639639 GCAGACTAGC
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 120 1.00
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (40 bp):
CCCCAGTTCGTAACTCAACTGGTGAACACCATTTCATCGA
Found at i:3642430 original size:43 final size:42
Alignment explanation
Indices: 3642377--3642522 Score: 159
Period size: 43 Copynumber: 3.4 Consensus size: 42
3642367 CCCGAGGTGT
*
3642377 GATTTCGTGTAAGACCATGTCTGGGACATTGGCATCTATATG
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCTATATG
*
3642419 AGATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTATAT-
1 -GATTACGTGTAAGACCATGTCTGGGACATTGGCATC-TATATG
* * * * * * * *
3642462 GATTTCATATAAAACCCTATCTGGGACAGTGGCATCGATATG
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCTATATG
*
3642504 TGATAACGTGTAAGACCAT
1 -GATTACGTGTAAGACCAT
3642523 ATCGGGAATA
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
41 4 0.05
42 28 0.34
43 46 0.55
44 5 0.06
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (42 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCTATATG
Found at i:3657865 original size:18 final size:18
Alignment explanation
Indices: 3657840--3657896 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
3657830 GATGGGGTAA
3657840 CAGGCCTAGTGATTACTC
1 CAGGCCTAGTGATTACTC
*
3657858 CCGGCCTAGTGATTACTC
1 CAGGCCTAGTGATTACTC
*
3657876 CAGGCCAAGTGATTACTC
1 CAGGCCTAGTGATTACTC
3657894 CAG
1 CAG
3657897 ATGGGGTTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.23, C:0.30, G:0.23, T:0.25
Consensus pattern (18 bp):
CAGGCCTAGTGATTACTC
Found at i:3663038 original size:19 final size:19
Alignment explanation
Indices: 3663014--3663051 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3663004 TGATATAAGC
*
3663014 AAAATATATTAAAATAGGT
1 AAAATATAATAAAATAGGT
3663033 AAAATATAATAAAATAGGT
1 AAAATATAATAAAATAGGT
3663052 TTTTCCCCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (19 bp):
AAAATATAATAAAATAGGT
Found at i:3663330 original size:3 final size:3
Alignment explanation
Indices: 3663286--3663384 Score: 87
Period size: 3 Copynumber: 33.7 Consensus size: 3
3663276 TATTCGGGGT
* * * * * * *
3663286 TAA TAA AAA TAA AAA TAA AAA T-A TAA AAA TAG TAC CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
3663333 TAG T-A TAGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AT
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3663377 TAA TAA TA
1 TAA TAA TA
3663385 GTATTAAACT
Statistics
Matches: 75, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
2 4 0.05
3 68 0.91
4 3 0.04
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:3663390 original size:12 final size:12
Alignment explanation
Indices: 3663342--3663391 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
3663332 ATAGTATAGA
*
3663342 TAATAATAATAA
1 TAATAATAATAT
*
3663354 TAATAATAATAA
1 TAATAATAATAT
3663366 TAATAATAA-AT
1 TAATAATAATAT
*
3663377 TAATAATAGTAT
1 TAATAATAATAT
3663389 TAA
1 TAA
3663392 ACTAATTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:3665509 original size:20 final size:21
Alignment explanation
Indices: 3665484--3665525 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
3665474 TTCGTCTATT
3665484 TATTTATTTATTA-TT-TTAAA
1 TATTTATTT-TTAGTTCTTAAA
3665504 TATTTATTTTTAGTTCTTAAA
1 TATTTATTTTTAGTTCTTAAA
3665525 T
1 T
3665526 TTCTTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 3 0.15
20 11 0.55
21 6 0.30
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTTATTTTTAGTTCTTAAA
Found at i:3668933 original size:20 final size:19
Alignment explanation
Indices: 3668907--3669006 Score: 76
Period size: 20 Copynumber: 5.1 Consensus size: 19
3668897 ATAGATGTGT
3668907 AACAGAGGCACCGAAGTGC
1 AACAGAGGCACCGAAGTGC
* *
3668926 AGACAGAGGCA-TGATTGTGC
1 A-ACAGAGGCACCGA-AGTGC
* *
3668946 AATTAGAGGCACCAAAGTGC
1 AA-CAGAGGCACCGAAGTGC
* *
3668966 AAACAGAGACACCGAAGTGT
1 -AACAGAGGCACCGAAGTGC
* **
3668986 AAAAGAGGCATTGAAGTGC
1 AACAGAGGCACCGAAGTGC
3669005 AA
1 AA
3669007 TCCCGTACAA
Statistics
Matches: 61, Mismatches: 15, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
19 20 0.33
20 38 0.62
21 3 0.05
ACGTcount: A:0.40, C:0.18, G:0.29, T:0.13
Consensus pattern (19 bp):
AACAGAGGCACCGAAGTGC
Found at i:3672242 original size:24 final size:23
Alignment explanation
Indices: 3672215--3672274 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
3672205 TAATAATAAT
* *
3672215 ATGCAAAAAATTCTGCTAGTAAAA
1 ATGCAAAAAA-TCTGCAAGGAAAA
* *
3672239 ATGCAGACAATCTGCAAGGAAAA
1 ATGCAAAAAATCTGCAAGGAAAA
* *
3672262 ATGCGACAAATCT
1 ATGCAAAAAATCT
3672275 CGATTCCTCT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.47, C:0.17, G:0.17, T:0.20
Consensus pattern (23 bp):
ATGCAAAAAATCTGCAAGGAAAA
Found at i:3672274 original size:23 final size:23
Alignment explanation
Indices: 3672226--3672270 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
3672216 TGCAAAAAAT
* *
3672226 TCTGCTAGTAAAAATGCAGACAA
1 TCTGCAAGGAAAAATGCAGACAA
3672249 TCTGCAAGGAAAAATGC-GACAA
1 TCTGCAAGGAAAAATGCAGACAA
3672271 ATCTCGATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (23 bp):
TCTGCAAGGAAAAATGCAGACAA
Found at i:3676259 original size:17 final size:17
Alignment explanation
Indices: 3676243--3676274 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3676233 GTTTGATTAT
3676243 TTTTC-TTATTTATTTA
1 TTTTCGTTATTTATTTA
3676259 TTTTCGTTATTTATTT
1 TTTTCGTTATTTATTT
3676275 GTATCTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.16, C:0.06, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTCGTTATTTATTTA
Found at i:3683802 original size:859 final size:858
Alignment explanation
Indices: 3681793--3683827 Score: 3242
Period size: 858 Copynumber: 2.4 Consensus size: 858
3681783 GAAATACATT
* * *
3681793 TGATACGAACTCATTTCGGCATAATTTGAGTTGTTTAGATTGCCCGATCATGAATTGAGTAAGGA
1 TGATACGAACTCATTTCGGTATAATTTGAGTTATTTAGATT-CCCGATCGTGAATTGAGTAAGGA
* *
3681858 TAAGTTCGTTTTGATTAAATGAAAC-AAATAGGATAAATGGCTTCAAATAATGGTAGTAGGTAAA
65 TAAGTTCGTTTCGATTAAATGAAACAAAATAGGATAAATGGCTTCAAAAAATGGTAGTAGGTAAA
* *
3681922 ATGGTTAAGTAAATAATAGATGATTTGGCTAAGACCGAGAATGAACCAAAAATATTGGATTGTTG
130 ATGGTTAAGTAAATAATGGATAATTTGGCTAAGACCGAGAATGAACCAAAAATATTGGATTGTTG
* *
3681987 ACCCGGGTCTCAAAATGGCTCTTAGGTGATTTACTGTTTAAAGAAAACAATAAGGACCTTGAACC
195 ACCCGAGTCTCAAAATGGCTCTTAGGTGATTTACTGTTTAAAGAAAACAACAAGGACCTTGAACC
3682052 ACTATCAAAAGTGATAGGAACCAAAGGTATATGAACGCCACACCAAAAGGTGATAAGTTCCGCCT
260 ACTATCAAAAGTGATAGGAACCAAAGGTATATGAACGCCACACCAAAAGGTGATAAGTTCCGCCT
* * *
3682117 CCACCAACATTCCTTATAGGTTGAAAACCACTTCCTTCGTTTGGGTTTCTTTTCGGACTTCTTGA
325 CCACCAACATTCCTTATAGGTTGAAAACCACTTCCCTCATTTGGGTTTCTTTTCGGACTTCTTAA
* * *
3682182 CATCTTAAGTTCACACAAACAAAAGCCACTATTTCTCTCCAAAGAAAATTCATTCACTTGGCTTT
390 CATCTTAAGTTCACACAAACAAAACCCACTATATCTCTCCAAAGAAAATTCACTCACTTGGCTTT
3682247 TGTTCACTCGAATAGACTCACCACTCTCTTGCCTTTTTCCGCTCAATCCGCCTCTCTATGTTCGC
455 TGTTCACTCGAATAGACTCACCACTCTCTTGCCTTTTTCCGCTCAATCCGCCTCTCTATGTTCGC
* * *
3682312 AATGGACTATATTAACTTAGCGGAAGGCGATATGGGTCGGCTTGCAAAAATGATGTTCAGTTATG
520 AATGGACTATATTAACTTAGCAGAAGGCGATATGGGTCAGCTTGCAAAAATGATGTTCAATTATG
*
3682377 GGTATGTAATATTGTTAGGACGAAGGGTAGGCTAGAAAACAAACAAAGGAAAAAAGATGTAAGTG
585 GGTAGGTAATATTGTTAGGACGAAGGGTAGGCTAGAAAACAAACAAAGGAAAAAAGATGTAAGTG
* *
3682442 TGGCCAAATGGTAGGAGGGTGGATAAGTGACTTCGGACAGCAAGAAGCAATTCTGAACTAGCTTT
650 TGGCCAAATGGTAGGAGGGTGGATAAGTGACTTCGGACAGCAAGAAGAAATTCTAAACTAGCTTT
* *
3682507 TTTTTAATCCATGAATTTTGTACCCCAAATGCTGATTTTCACACTTTTTGAGCTCAATAGAAACT
715 TTTTTAATCCATGAATTTAGTACCCCAAATGCTGATTTTCACACTTTTTGAACTCAATAGAAACT
** *
3682572 GGATTTTTTTTATCTCTTACAATCTCGTAATGCTACGAACGTCAATACTCACTTCAATTTCACTA
780 AAATTTTTCTTATCTCTTACAATCTCGTAATGCTACGAACGTCAATACTCACTTCAATTTCACTA
3682637 GCTCTGACACCAAA
845 GCTCTGACACCAAA
* * *
3682651 TGATACGAACTCGTTTCAGTATAATTTGAGTTATTTAGATTGCCGATCGTGAATTGAGTAAGGAT
1 TGATACGAACTCATTTCGGTATAATTTGAGTTATTTAGATTCCCGATCGTGAATTGAGTAAGGAT
* *
3682716 AAGTTCGTTTCGATTAAATGAAAAAAAATAGGATAAATGGCTTCAAAAAATGGTAGTAGGCAAAA
66 AAGTTCGTTTCGATTAAATGAAACAAAATAGGATAAATGGCTTCAAAAAATGGTAGTAGGTAAAA
* * **
3682781 TGGTTAAGTAAATAATGAATAATTTGGCTAAGACCGAGACTGAAGAAAAAATATTGGATTGTTGA
131 TGGTTAAGTAAATAATGGATAATTTGGCTAAGACCGAGAATGAACCAAAAATATTGGATTGTTGA
*
3682846 CCCGAGTCTCAAAATGGCTCTTAGGTGATTTACTGTTTAAAGAAAACAACAAGGGCCTTGAACCA
196 CCCGAGTCTCAAAATGGCTCTTAGGTGATTTACTGTTTAAAGAAAACAACAAGGACCTTGAACCA
* * *
3682911 CTATCAAAAGTGATAGGAACCAAAGGTATATGAATGCCACACCAAAAGGTAATAAGTTCTGCCTC
261 CTATCAAAAGTGATAGGAACCAAAGGTATATGAACGCCACACCAAAAGGTGATAAGTTCCGCCTC
* * * * *
3682976 TACCAACATTCCTTATATGTTTAAAACTACTTCCCTCATTTGGGTTTCTTTTCGGAGTTCTTAAC
326 CACCAACATTCCTTATAGGTTGAAAACCACTTCCCTCATTTGGGTTTCTTTTCGGACTTCTTAAC
3683041 ATCTTAAGTTCACACAAACAAAAACCTCACTATATCTCTCCAAAGAAAATTCACTCACTTGGCTT
391 ATCTTAAGTTCACACAAAC-AAAACC-CACTATATCTCTCCAAAGAAAATTCACTCACTTGGCTT
* * *
3683106 TTGTTCACTCGAATAGACGT-ACCACTCTCTTATCC-TTTTCTGCTCAATCTGCCTCTCTATGTT
454 TTGTTCACTCGAATAGAC-TCACCACTCTCTT-GCCTTTTTCCGCTCAATCCGCCTCTCTATGTT
* * * *
3683169 CGCAATGGACTATTTTAACTTAGCAGAAGGTGATGTGGGTTAGCTTGCAAAAATGATGTTCAATT
517 CGCAATGGACTATATTAACTTAGCAGAAGGCGATATGGGTCAGCTTGCAAAAATGATGTTCAATT
*
3683234 ATGGGTAGGTAATATTGTTAGGACGAAGGGTAGGCTAGAAAACAAGA-AAAGG-AAAAATATGTA
582 ATGGGTAGGTAATATTGTTAGGACGAAGGGTAGGCTAGAAAACAA-ACAAAGGAAAAAAGATGTA
*
3683297 AGTGTGGCCGAAA-GGTAGGAGGGTGGATAAGTGACTTCGGGCAGCAAGAAGAAATTTCTAAACT
646 AGTGTGGCC-AAATGGTAGGAGGGTGGATAAGTGACTTCGGACAGCAAGAAGAAA-TTCTAAACT
* *
3683361 AG-TTTTTTTTAATCCATGAA-TTAGTACCCCGAATGCTGATTTTCGCACTTTTTGAACTCAATA
709 AGCTTTTTTTTAATCCATGAATTTAGTACCCCAAATGCTGATTTTCACACTTTTTGAACTCAATA
* *
3683424 GAAACTAAATTTTTCTTATCTCTTACAATCTCGTAATGCTATGAACGTCAATACTCACTTTAATT
774 GAAACTAAATTTTTCTTATCTCTTACAATCTCGTAATGCTACGAACGTCAATACTCACTTCAATT
*
3683489 TCACTAGCTCTGATACCAAA
839 TCACTAGCTCTGACACCAAA
* * * * *
3683509 TGATACGAAATCCTTTCGGTATAATTCGAGTCATTTAGATTACCCAATCGTGAATTGAGTAAGGA
1 TGATACGAACTCATTTCGGTATAATTTGAGTTATTTAGATT-CCCGATCGTGAATTGAGTAAGGA
* * *
3683574 TAAATTTGTTTC-AGTTAAATGAAACAAAATAGGATAAATGGCTTCAAACAATGGTAGTAGGTAA
65 TAAGTTCGTTTCGA-TTAAATGAAACAAAATAGGATAAATGGCTTCAAAAAATGGTAGTAGGTAA
* * *
3683638 AATGGTTAAGTAAATAATGGATAATTTAGCTAAGATCGAGAATGAACCAACAATATTGGATTGTT
129 AATGGTTAAGTAAATAATGGATAATTTGGCTAAGACCGAGAATGAACCAAAAATATTGGATTGTT
* * * * *
3683703 GACTCGAGCCTCAAAATGGCTCTTAGGTGATTTACAGTTTAAAGAAAACAGCAAGGACCTTGACC
194 GACCCGAGTCTCAAAATGGCTCTTAGGTGATTTACTGTTTAAAGAAAACAACAAGGACCTTGAAC
*
3683768 CACTATCAAAAGTGATAGGAACCAAAGGTATATGAACGCCACACCAAAGGGTGATAAGTT
259 CACTATCAAAAGTGATAGGAACCAAAGGTATATGAACGCCACACCAAAAGGTGATAAGTT
3683828 TAGTTTAAAC
Statistics
Matches: 1081, Mismatches: 86, Indels: 19
0.91 0.07 0.02
Matches are distributed among these distances:
857 44 0.04
858 489 0.45
859 333 0.31
860 211 0.20
861 4 0.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (858 bp):
TGATACGAACTCATTTCGGTATAATTTGAGTTATTTAGATTCCCGATCGTGAATTGAGTAAGGAT
AAGTTCGTTTCGATTAAATGAAACAAAATAGGATAAATGGCTTCAAAAAATGGTAGTAGGTAAAA
TGGTTAAGTAAATAATGGATAATTTGGCTAAGACCGAGAATGAACCAAAAATATTGGATTGTTGA
CCCGAGTCTCAAAATGGCTCTTAGGTGATTTACTGTTTAAAGAAAACAACAAGGACCTTGAACCA
CTATCAAAAGTGATAGGAACCAAAGGTATATGAACGCCACACCAAAAGGTGATAAGTTCCGCCTC
CACCAACATTCCTTATAGGTTGAAAACCACTTCCCTCATTTGGGTTTCTTTTCGGACTTCTTAAC
ATCTTAAGTTCACACAAACAAAACCCACTATATCTCTCCAAAGAAAATTCACTCACTTGGCTTTT
GTTCACTCGAATAGACTCACCACTCTCTTGCCTTTTTCCGCTCAATCCGCCTCTCTATGTTCGCA
ATGGACTATATTAACTTAGCAGAAGGCGATATGGGTCAGCTTGCAAAAATGATGTTCAATTATGG
GTAGGTAATATTGTTAGGACGAAGGGTAGGCTAGAAAACAAACAAAGGAAAAAAGATGTAAGTGT
GGCCAAATGGTAGGAGGGTGGATAAGTGACTTCGGACAGCAAGAAGAAATTCTAAACTAGCTTTT
TTTTAATCCATGAATTTAGTACCCCAAATGCTGATTTTCACACTTTTTGAACTCAATAGAAACTA
AATTTTTCTTATCTCTTACAATCTCGTAATGCTACGAACGTCAATACTCACTTCAATTTCACTAG
CTCTGACACCAAA
Found at i:3683856 original size:15 final size:15
Alignment explanation
Indices: 3683836--3683867 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
3683826 TTTAGTTTAA
3683836 ACAAAAGCAAGAATG
1 ACAAAAGCAAGAATG
3683851 ACAAAAGCAAGAATG
1 ACAAAAGCAAGAATG
3683866 AC
1 AC
3683868 GCCACAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.16, G:0.19, T:0.06
Consensus pattern (15 bp):
ACAAAAGCAAGAATG
Found at i:3684387 original size:9 final size:9
Alignment explanation
Indices: 3684362--3684408 Score: 76
Period size: 9 Copynumber: 5.0 Consensus size: 9
3684352 ACCTACAAAC
3684362 AAACACATT
1 AAACACATT
3684371 AAAAACACATT
1 --AAACACATT
3684382 AAACACATT
1 AAACACATT
3684391 AAACACATT
1 AAACACATT
3684400 AAACACATT
1 AAACACATT
3684409 TTAACACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
9 27 0.75
11 9 0.25
ACGTcount: A:0.57, C:0.21, G:0.00, T:0.21
Consensus pattern (9 bp):
AAACACATT
Done.