Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, whole genome shotgun sequence
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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 5 of 126
Found at i:1260518 original size:20 final size:20
Alignment explanation
Indices: 1260493--1260530 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1260483 AAGAAAAAAG
1260493 TTTGCATGATTATTTATTTA
1 TTTGCATGATTATTTATTTA
1260513 TTTGCATGATTATTTATT
1 TTTGCATGATTATTTATT
1260531 ATGATTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.61
Consensus pattern (20 bp):
TTTGCATGATTATTTATTTA
Found at i:1260527 original size:16 final size:16
Alignment explanation
Indices: 1260506--1260568 Score: 58
Period size: 16 Copynumber: 3.9 Consensus size: 16
1260496 GCATGATTAT
1260506 TTATTTATTTGCATGA
1 TTATTTATTTGCATGA
*
1260522 TTATTTATTATG-ATTAA
1 TTATTTATT-TGCA-TGA
* *
1260539 TAATATATTTGCATGA
1 TTATTTATTTGCATGA
1260555 TT-TGTTATTTGCAT
1 TTAT-TTATTTGCAT
1260569 AACTTATTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
15 1 0.03
16 24 0.65
17 12 0.32
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.56
Consensus pattern (16 bp):
TTATTTATTTGCATGA
Found at i:1260832 original size:13 final size:13
Alignment explanation
Indices: 1260816--1260870 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1260806 TTTTACTATG
1260816 ATTTTTGCATGAT
1 ATTTTTGCATGAT
*
1260829 ATTTTTGGTATGAT
1 ATTTTT-GCATGAT
*
1260843 -TTATT--AT-AT
1 ATTTTTGCATGAT
1260852 ATTTTTGCATGAT
1 ATTTTTGCATGAT
1260865 ATTTTT
1 ATTTTT
1260871 TATAGAATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
9 2 0.06
10 6 0.18
12 2 0.06
13 18 0.53
14 6 0.18
ACGTcount: A:0.24, C:0.04, G:0.13, T:0.60
Consensus pattern (13 bp):
ATTTTTGCATGAT
Found at i:1263554 original size:28 final size:27
Alignment explanation
Indices: 1263499--1263583 Score: 73
Period size: 28 Copynumber: 3.0 Consensus size: 27
1263489 AGGTTTTCAA
* *
1263499 AATTTTAGGTTTTAAGGTTTAGGATTTT
1 AATTTTAGG-GTTAAGGTTTAAGATTTT
1263527 GAATTTTAGGGTTAAGGTTTCAAG-TTTT
1 -AATTTTAGGGTTAAGGTTT-AAGATTTT
* * **
1263555 AGATTTTGGGGTTTAGGTTTTTGATTTT
1 A-ATTTTAGGGTTAAGGTTTAAGATTTT
1263583 A
1 A
1263584 GGGTTTGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.04
28 34 0.72
29 11 0.23
ACGTcount: A:0.22, C:0.01, G:0.25, T:0.52
Consensus pattern (27 bp):
AATTTTAGGGTTAAGGTTTAAGATTTT
Found at i:1263574 original size:21 final size:21
Alignment explanation
Indices: 1263550--1263589 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1263540 AAGGTTTCAA
*
1263550 GTTTTAGATTTTGGGGTTTAG
1 GTTTTAGATTTTAGGGTTTAG
*
1263571 GTTTTTGATTTTAGGGTTT
1 GTTTTAGATTTTAGGGTTT
1263590 GAGATTTAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.30, T:0.57
Consensus pattern (21 bp):
GTTTTAGATTTTAGGGTTTAG
Found at i:1263584 original size:28 final size:28
Alignment explanation
Indices: 1263551--1263777 Score: 100
Period size: 28 Copynumber: 7.9 Consensus size: 28
1263541 AGGTTTCAAG
* * * *
1263551 TTTTAGATTTTGGGGTTTAGGTTTTTGA
1 TTTTAGAGTTTGAGATTTAGGGTTTTGA
*
1263579 TTTTAGGGTTTGAGATTTAGGGTTTTGA
1 TTTTAGAGTTTGAGATTTAGGGTTTTGA
* * *
1263607 TTTTAGGGTTTGAGATTT-GAAGTTTTGG
1 TTTTAGAGTTTGAGATTTAG-GGTTTTGA
* * * * *
1263635 TTTTAGGGTTTAAAGGATTTA-CGATTTAA
1 TTTTAGAGTTT-GA-GATTTAGGGTTTTGA
* * *
1263664 TTTTAGGGTTTGAAGGTTT-GGAGTTTTTA
1 TTTTAGAGTTTG-AGATTTAGG-GTTTTGA
* * **
1263693 TTTTAGAGCTTGGAGGTTCGGGGTTTTGA
1 TTTTAGAG-TTTGAGATTTAGGGTTTTGA
* * * * * *
1263722 TTGTAGGGTTTGAAATGTGAAGGTTTTAA
1 TTTTAGAGTTTGAGAT-TTAGGGTTTTGA
* *
1263751 TTTTAGGGTTTGAAAGGTTTAGGGTTT
1 TTTTAGAGTTTG--AGATTTAGGGTTT
1263778 CATTTTTAAG
Statistics
Matches: 152, Mismatches: 35, Indels: 22
0.73 0.17 0.11
Matches are distributed among these distances:
27 1 0.01
28 67 0.44
29 65 0.43
30 17 0.11
31 2 0.01
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.48
Consensus pattern (28 bp):
TTTTAGAGTTTGAGATTTAGGGTTTTGA
Found at i:1263588 original size:15 final size:15
Alignment explanation
Indices: 1263566--1263617 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 15
1263556 GATTTTGGGG
1263566 TTTA-GGTTTTTGAT
1 TTTAGGGTTTTTGAT
**
1263580 TTTAGGGTTTGAGA-
1 TTTAGGGTTTTTGAT
1263594 TTTAGGG-TTTTGAT
1 TTTAGGGTTTTTGAT
1263608 TTTAGGGTTT
1 TTTAGGGTTT
1263618 GAGATTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 18 0.58
15 9 0.29
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (15 bp):
TTTAGGGTTTTTGAT
Found at i:1263623 original size:15 final size:15
Alignment explanation
Indices: 1263577--1263645 Score: 74
Period size: 14 Copynumber: 4.9 Consensus size: 15
1263567 TTAGGTTTTT
1263577 GATTTTAGGGTTTGA
1 GATTTTAGGGTTTGA
*
1263592 GA-TTTAGGGTTT-T
1 GATTTTAGGGTTTGA
1263605 GATTTTAGGGTTTGA
1 GATTTTAGGGTTTGA
* * *
1263620 GATTTGAAGTTTTG-
1 GATTTTAGGGTTTGA
1263634 G-TTTTAGGGTTT
1 GATTTTAGGGTTT
1263646 AAAGGATTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 10 0.23
14 21 0.48
15 13 0.30
ACGTcount: A:0.17, C:0.00, G:0.32, T:0.51
Consensus pattern (15 bp):
GATTTTAGGGTTTGA
Found at i:1263645 original size:14 final size:14
Alignment explanation
Indices: 1263566--1263645 Score: 58
Period size: 14 Copynumber: 5.7 Consensus size: 14
1263556 GATTTTGGGG
* *
1263566 TTTAGGTTTTTGAT
1 TTTAGGGTTTTGGT
*
1263580 TTTAGGG-TTTGAGA
1 TTTAGGGTTTTG-GT
*
1263594 TTTAGGGTTTTGAT
1 TTTAGGGTTTTGGT
*
1263608 TTTAGGG-TTTGAGA
1 TTTAGGGTTTTG-GT
*
1263622 TTT-GAAGTTTTGGT
1 TTTAG-GGTTTTGGT
1263636 TTTAGGGTTT
1 TTTAGGGTTT
1263646 AAAGGATTTA
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
13 9 0.18
14 32 0.64
15 9 0.18
ACGTcount: A:0.16, C:0.00, G:0.30, T:0.54
Consensus pattern (14 bp):
TTTAGGGTTTTGGT
Found at i:1263695 original size:29 final size:29
Alignment explanation
Indices: 1263573--1263822 Score: 147
Period size: 29 Copynumber: 8.7 Consensus size: 29
1263563 GGGTTTAGGT
* *
1263573 TTTTGATTTTAGGGTTTG-AGATTTAGG-G
1 TTTTAATTTTAGGGTTTGAAGGTTT-GGAG
* * *
1263601 TTTTGATTTTAGGGTTTG-AGATTTGAAG
1 TTTTAATTTTAGGGTTTGAAGGTTTGGAG
** *
1263629 TTTTGGTTTTAGGGTTTAAAGGATTT--ACG
1 TTTTAATTTTAGGGTTTGAAGG-TTTGGA-G
*
1263658 ATTTAATTTTAGGGTTTGAAGGTTTGGAG
1 TTTTAATTTTAGGGTTTGAAGGTTTGGAG
* * * * * *
1263687 TTTTTATTTTAGAGCTTGGAGGTTCGGGG
1 TTTTAATTTTAGGGTTTGAAGGTTTGGAG
* * * * *
1263716 TTTTGATTGTAGGGTTTGAA-ATGTGAAGG
1 TTTTAATTTTAGGGTTTGAAGGTTTGGA-G
1263745 TTTTAATTTTAGGGTTTGAAAGGTTTAGG-G
1 TTTTAATTTTAGGGTTTG-AAGGTTT-GGAG
* * * * * *
1263775 TTTCATTTTTAAGGTTAGGAGGTTT-AAG
1 TTTTAATTTTAGGGTTTGAAGGTTTGGAG
*
1263803 GTTTAATTTTAGGGTTTGAA
1 TTTTAATTTTAGGGTTTGAA
1263823 AAATTTAGAG
Statistics
Matches: 169, Mismatches: 42, Indels: 22
0.73 0.18 0.09
Matches are distributed among these distances:
27 1 0.01
28 62 0.37
29 82 0.49
30 21 0.12
31 2 0.01
32 1 0.01
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.47
Consensus pattern (29 bp):
TTTTAATTTTAGGGTTTGAAGGTTTGGAG
Found at i:1263785 original size:30 final size:30
Alignment explanation
Indices: 1263635--1263908 Score: 113
Period size: 29 Copynumber: 9.4 Consensus size: 30
1263625 GAAGTTTTGG
* *
1263635 TTTTAGGGTTT-AAAGGATTTACGATTT-AA
1 TTTTAGGGTTTGAAAGG-TTTAAGGTTTCAA
* **
1263664 TTTTAGGGTTTG-AAGGTTT-GGAGTTTTTA
1 TTTTAGGGTTTGAAAGGTTTAAG-GTTTCAA
* * * *** **
1263693 TTTTAGAGCTTG-GAGGTTCGGGGTTTTGA
1 TTTTAGGGTTTGAAAGGTTTAAGGTTTCAA
* * * *
1263722 TTGTAGGGTTTGAAATG-TGAAGGTTTTAA
1 TTTTAGGGTTTGAAAGGTTTAAGGTTTCAA
* *
1263751 TTTTAGGGTTTGAAAGGTTTAGGGTTTCAT
1 TTTTAGGGTTTGAAAGGTTTAAGGTTTCAA
* * *
1263781 TTTTAAGGTTAG-GAGGTTTAAGGTTT-AA
1 TTTTAGGGTTTGAAAGGTTTAAGGTTTCAA
** **
1263809 TTTTAGGGTTTGAAAAATTT-AGAGTTTCGT
1 TTTTAGGGTTTGAAAGGTTTAAG-GTTTCAA
* * * * **
1263839 TTTTAAGGTTTG-GA-TTTTAGGGTTTTGGA
1 TTTTAGGGTTTGAAAGGTTTAAGG-TTTCAA
* * *
1263868 TTTGAGGGTTTGGAAGTTTTAAGGTTT-AA
1 TTTTAGGGTTTGAAAGGTTTAAGGTTTCAA
1263897 TTTTAGGGTTTG
1 TTTTAGGGTTTG
1263909 GGAAATTTAG
Statistics
Matches: 185, Mismatches: 47, Indels: 26
0.72 0.18 0.10
Matches are distributed among these distances:
27 1 0.01
28 23 0.12
29 117 0.63
30 37 0.20
31 7 0.04
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.46
Consensus pattern (30 bp):
TTTTAGGGTTTGAAAGGTTTAAGGTTTCAA
Found at i:1263804 original size:59 final size:58
Alignment explanation
Indices: 1263741--1263900 Score: 178
Period size: 58 Copynumber: 2.7 Consensus size: 58
1263731 TTGAAATGTG
*
1263741 AAGGTTTTAATTTTAGGGTTTGAAAGGTTTAGGGTTTCATTTTTAAGGTTAGGAGGTTT
1 AAGGTTTTAATTTTAGGGTTTGAAAGATTTAGGGTTTCATTTTTAAGGTTAGGA-GTTT
* * * * *
1263800 AAGG-TTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTTTTTAAGGTTTGGATTTT
1 AAGGTTTTAATTTTAGGGTTTGAAAGATTTAGGGTTTCATTTTTAAGGTTAGGAGTTT
* * * * * * *
1263857 AGGGTTTTGGATTTGAGGGTTTGGAAGTTTTAAGGTTTAATTTT
1 AAGGTTTT-AATTTTAGGGTTTGAAAGATTTAGGGTTTCATTTT
1263901 AGGGTTTGGG
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
57 6 0.07
58 47 0.57
59 30 0.36
ACGTcount: A:0.24, C:0.01, G:0.28, T:0.47
Consensus pattern (58 bp):
AAGGTTTTAATTTTAGGGTTTGAAAGATTTAGGGTTTCATTTTTAAGGTTAGGAGTTT
Found at i:1263816 original size:87 final size:87
Alignment explanation
Indices: 1263659--1263823 Score: 203
Period size: 87 Copynumber: 1.9 Consensus size: 87
1263649 GGATTTACGA
* ** *
1263659 TTTAATTTTAGGGTTTGAAGGTTTGGAGTTTTTATTTTAGAGCTTGGAGGTTCGGGGTTTTGATT
1 TTTAATTTTAGGGTTTGAAGGTTTGGAGTTTATATTTTAGAGCTTGGAGGTTCAAGGTTTTAATT
1263724 GTAGGGTTTGAAATGTGAAGGT
66 GTAGGGTTTGAAATGTGAAGGT
* *
1263746 TTTAATTTTAGGGTTTGAAAGGTTTAGG-GTTTCAT-TTTTA-AGGTTAGGAGGTTTAAGG-TTT
1 TTTAATTTTAGGGTTTG-AAGGTTT-GGAGTTT-ATATTTTAGAGCTT-GGAGGTTCAAGGTTTT
*
1263807 AATTTTAGGGTTTGAAA
62 AATTGTAGGGTTTGAAA
1263824 AATTTAGAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
87 39 0.58
88 25 0.37
89 3 0.04
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.45
Consensus pattern (87 bp):
TTTAATTTTAGGGTTTGAAGGTTTGGAGTTTATATTTTAGAGCTTGGAGGTTCAAGGTTTTAATT
GTAGGGTTTGAAATGTGAAGGT
Found at i:1263849 original size:88 final size:89
Alignment explanation
Indices: 1263751--1263940 Score: 226
Period size: 88 Copynumber: 2.1 Consensus size: 89
1263741 AAGGTTTTAA
* *
1263751 TTTTAGGGTTTGAAAGGTTTAGGG-TTT-CATTTTTAAGGTTAGG-AGGTTTAAGGTTTAATTTT
1 TTTTAAGGTTTGAAA-GTTTAGGGTTTTGCA-TTTGAAGGTTAGGAAGGTTTAAGGTTTAATTTT
1263813 AGGGTTTGAAAAATTTAGAGTTTCGT
64 AGGGTTTGAAAAATTTAGAGTTTCGT
* * * * * *
1263839 TTTTAAGGTTTG-GATTTTAGGGTTTTGGATTTGAGGGTTTGGAAGTTTTAAGGTTTAATTTTAG
1 TTTTAAGGTTTGAAAGTTTAGGGTTTTGCATTTGAAGGTTAGGAAGGTTTAAGGTTTAATTTTAG
**
1263903 GGTTTGGGAAATTTAGAGTTTCGT
66 GGTTTGAAAAATTTAGAGTTTCGT
*
1263927 TTTTAGAGTTTTGA
1 TTTTA-AGGTTTGA
1263941 TTTTTAAAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
86 7 0.08
87 14 0.16
88 59 0.69
89 6 0.07
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (89 bp):
TTTTAAGGTTTGAAAGTTTAGGGTTTTGCATTTGAAGGTTAGGAAGGTTTAAGGTTTAATTTTAG
GGTTTGAAAAATTTAGAGTTTCGT
Found at i:1263861 original size:44 final size:41
Alignment explanation
Indices: 1263797--1263931 Score: 137
Period size: 43 Copynumber: 3.1 Consensus size: 41
1263787 GGTTAGGAGG
1263797 TTTAAGGTTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTT
1 TTTAAGGTTTAATTTTAGGGTTTG--AAATTTAGAGTTTCGTT
* * * * *
1263840 TTTAAGGTTTGGATTTTAGGGTTTTG-GATTTGAGGGTTTGGAAGT
1 TTTAAGGTTT-AATTTTAGGG-TTTGAAATTT-AGAGTTTCG--TT
1263885 TTTAAGGTTTAATTTTAGGGTTTGGGAAATTTAGAGTTTCGTT
1 TTTAAGGTTTAATTTTAGGGTTT--GAAATTTAGAGTTTCGTT
1263928 TTTA
1 TTTA
1263932 GAGTTTTGAT
Statistics
Matches: 74, Mismatches: 10, Indels: 16
0.74 0.10 0.16
Matches are distributed among these distances:
42 4 0.05
43 25 0.34
44 18 0.24
45 23 0.31
46 4 0.05
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (41 bp):
TTTAAGGTTTAATTTTAGGGTTTGAAATTTAGAGTTTCGTT
Found at i:1263879 original size:14 final size:14
Alignment explanation
Indices: 1263845--1263881 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
1263835 TCGTTTTTAA
*
1263845 GGTTTGGATTTTAG
1 GGTTTGGATTTGAG
1263859 GGTTTTGGATTTGAG
1 GG-TTTGGATTTGAG
1263874 GGTTTGGA
1 GGTTTGGA
1263882 AGTTTTAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.14, C:0.00, G:0.41, T:0.46
Consensus pattern (14 bp):
GGTTTGGATTTGAG
Found at i:1263929 original size:29 final size:29
Alignment explanation
Indices: 1263577--1263937 Score: 97
Period size: 29 Copynumber: 12.4 Consensus size: 29
1263567 TTAGGTTTTT
* * *
1263577 GATTTTAGGGTTT-GAGATTTAGGGTTTT
1 GATTTTAGGGTTTGGAAATTTAGAGTTTC
* *
1263605 GATTTTAGGGTTT-GAGATTT-GAAGTTTT
1 GATTTTAGGGTTTGGAAATTTAG-AGTTTC
* *
1263633 GGTTTTAGGGTTT-AAAGGATTTACGA-TTT-
1 GATTTTAGGGTTTGGAA--ATTTA-GAGTTTC
* * * *
1263662 AATTTTAGGGTTT-GAAGGTTTGGAGTTTT
1 GATTTTAGGGTTTGGAA-ATTTAGAGTTTC
* * * ** ** * *
1263691 TATTTTAGAGCTTGGAGGTTCGGGGTTTT
1 GATTTTAGGGTTTGGAAATTTAGAGTTTC
* * *
1263720 GATTGTAGGGTTT-GAAATGT-GAAGGTTTT
1 GATTTTAGGGTTTGGAAATTTAG-A-GTTTC
* *
1263749 AATTTTAGGGTTT-GAAAGGTTTAGGGTTTC
1 GATTTTAGGGTTTGGAAA--TTTAGAGTTTC
* * **
1263779 -ATTTTTAAGGTTAGGAGGTTTA-AGGTTT-
1 GA-TTTTAGGGTTTGGAAATTTAGA-GTTTC
* *
1263807 AATTTTAGGGTTTGAAAAATTTAGAGTTTC
1 GATTTTAGGGTTTG-GAAATTTAGAGTTTC
* * * * *
1263837 GTTTTTAAGGTTTGG-ATTTTAGGGTTTTG
1 GATTTTAGGGTTTGGAAATTTAGAG-TTTC
* *
1263866 GATTTGAGGGTTTGGAAGTTTTA-AGGTTT-
1 GATTTTAGGGTTTGGAA-ATTTAGA-GTTTC
*
1263895 AATTTTAGGGTTTGGGAAATTTAGAGTTTC
1 GATTTTAGGGTTT-GGAAATTTAGAGTTTC
* *
1263925 GTTTTTAGAGTTT
1 GATTTTAGGGTTT
1263938 TGATTTTTAA
Statistics
Matches: 250, Mismatches: 56, Indels: 52
0.70 0.16 0.15
Matches are distributed among these distances:
27 4 0.02
28 65 0.26
29 115 0.46
30 53 0.21
31 11 0.04
32 2 0.01
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.47
Consensus pattern (29 bp):
GATTTTAGGGTTTGGAAATTTAGAGTTTC
Found at i:1263944 original size:44 final size:43
Alignment explanation
Indices: 1263797--1263944 Score: 138
Period size: 44 Copynumber: 3.4 Consensus size: 43
1263787 GGTTAGGAGG
* * **
1263797 TTTAAGGTTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTT
1 TTTAAGTTTTGATTTTAGGGTTTGGGAAATTTAGAGTTTCGTT
* * * * *
1263840 TTTAAGGTTTGGATTTTAGGGTTTTGG--ATTTGAGGGTTTGGAAGT
1 TTTAA-GTTTTGATTTTAGGGTTTGGGAAATTT-AGAGTTTCG--TT
* *
1263885 TTTAAGGTTTAATTTTAGGGTTTGGGAAATTTAGAGTTTCGTT
1 TTTAAGTTTTGATTTTAGGGTTTGGGAAATTTAGAGTTTCGTT
1263928 TTTAGAGTTTTGATTTT
1 TTTA-AGTTTTGATTTT
1263945 TAAAATTTAA
Statistics
Matches: 80, Mismatches: 18, Indels: 13
0.72 0.16 0.12
Matches are distributed among these distances:
42 4 0.05
43 17 0.21
44 42 0.52
45 13 0.16
46 4 0.05
ACGTcount: A:0.22, C:0.01, G:0.26, T:0.50
Consensus pattern (43 bp):
TTTAAGTTTTGATTTTAGGGTTTGGGAAATTTAGAGTTTCGTT
Found at i:1263965 original size:88 final size:88
Alignment explanation
Indices: 1263797--1263966 Score: 229
Period size: 88 Copynumber: 1.9 Consensus size: 88
1263787 GGTTAGGAGG
***
1263797 TTTAAGGTTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTTTTTAAGGTTTGGATTTTAGGGT
1 TTTAAGGTTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTTTTTAAGGTTTGGATTTTAAAAT
*
1263862 TTTGGATTTGAGGGTTTGGAAGT
66 TTAGGATTTGAGGGTTTGGAAGT
** *
1263885 TTTAAGGTTTAATTTTAGGGTTTGGGAAATTTAGAGTTTCGTTTTT-AGAGTTTTGATTTTTAAA
1 TTTAAGGTTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTTTTTAAG-GTTTGGA-TTTTAAA
1263949 ATTTAAGG-TTTG-GGGTTT
64 ATTT-AGGATTTGAGGGTTT
1263967 TAATTTAAGG
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 2 0.03
88 56 0.78
89 12 0.17
90 2 0.03
ACGTcount: A:0.23, C:0.01, G:0.26, T:0.49
Consensus pattern (88 bp):
TTTAAGGTTTAATTTTAGGGTTTGAAAAATTTAGAGTTTCGTTTTTAAGGTTTGGATTTTAAAAT
TTAGGATTTGAGGGTTTGGAAGT
Found at i:1263986 original size:14 final size:14
Alignment explanation
Indices: 1263969--1264090 Score: 84
Period size: 14 Copynumber: 8.4 Consensus size: 14
1263959 TGGGGTTTTA
1263969 ATTTAAGGGTTTGG
1 ATTTAAGGGTTTGG
*
1263983 ATTTTAGGAGTTTTGG
1 ATTTAAGG-G-TTTGG
*
1263999 ATTT-TGGGCTTTGG
1 ATTTAAGGG-TTTGG
* * *
1264013 ATTTAAAGGTTAGT
1 ATTTAAGGGTTTGG
*
1264027 ATTTTAGGGGTTTGG
1 A-TTTAAGGGTTTGG
* *
1264042 ATTTAAAGGTTAGG
1 ATTTAAGGGTTTGG
* *
1264056 ATTTTAGGGTTTTGA
1 ATTTAAGGG-TTTGG
*
1264071 ATTTTAGGGGTTTGG
1 A-TTTAAGGGTTTGG
1264086 ATTTA
1 ATTTA
1264091 GGAATTTGTG
Statistics
Matches: 81, Mismatches: 21, Indels: 12
0.71 0.18 0.11
Matches are distributed among these distances:
14 42 0.52
15 24 0.30
16 15 0.19
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (14 bp):
ATTTAAGGGTTTGG
Found at i:1263987 original size:20 final size:20
Alignment explanation
Indices: 1263948--1263988 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1263938 TGATTTTTAA
*
1263948 AATTTAAGGTTTGGGGTTTT
1 AATTTAAGGTTTGGGATTTT
1263968 AATTTAAGGGTTT-GGATTTT
1 AATTTAA-GGTTTGGGATTTT
1263988 A
1 A
1263989 GGAGTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (20 bp):
AATTTAAGGTTTGGGATTTT
Found at i:1264006 original size:44 final size:43
Alignment explanation
Indices: 1263957--1264045 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 43
1263947 AAATTTAAGG
* * * * *
1263957 TTTGGGGTTTTAATTTAAGGGTTTGGATTTTAGGAGTTTTGGAT
1 TTTGGGCTTTGAATTTAAAGGTTAGGATTTTAGG-GGTTTGGAT
* *
1264001 TTTGGGCTTTGGATTTAAAGGTTAGTATTTTAGGGGTTTGGAT
1 TTTGGGCTTTGAATTTAAAGGTTAGGATTTTAGGGGTTTGGAT
1264044 TT
1 TT
1264046 AAAGGTTAGG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 10 0.26
44 28 0.74
ACGTcount: A:0.18, C:0.01, G:0.31, T:0.49
Consensus pattern (43 bp):
TTTGGGCTTTGAATTTAAAGGTTAGGATTTTAGGGGTTTGGAT
Found at i:1264016 original size:73 final size:74
Alignment explanation
Indices: 1263939--1264089 Score: 159
Period size: 73 Copynumber: 2.1 Consensus size: 74
1263929 TTAGAGTTTT
* * * * *
1263939 GATTTTTAAAATTTA-AGGTTT-GGGGTTTTAATTTAAGGGTTTGGATTTTAGGAGTTTTGGATT
1 GATTTTTAAAAGTTAGA-GTTTAGGGGTTTGAATTTAAAGGTTAGGATTTTAGG-GTTTTGAATT
1264002 TT-GGGCTTTG
64 TTAGGGCTTTG
* * *
1264012 GA--TTTAAAGGTTAGTATTTTAGGGGTTTGGATTTAAAGGTTAGGATTTTAGGGTTTTGAATTT
1 GATTTTTAAAAGTTAG-AGTTTAGGGGTTTGAATTTAAAGGTTAGGATTTTAGGGTTTTGAATTT
*
1264075 TAGGGGTTTG
65 TAGGGCTTTG
1264085 GATTT
1 GATTT
1264090 AGGAATTTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
71 9 0.14
72 14 0.22
73 39 0.62
75 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.48
Consensus pattern (74 bp):
GATTTTTAAAAGTTAGAGTTTAGGGGTTTGAATTTAAAGGTTAGGATTTTAGGGTTTTGAATTTT
AGGGCTTTG
Found at i:1264041 original size:29 final size:29
Alignment explanation
Indices: 1263997--1264074 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
1263987 TAGGAGTTTT
1263997 GGATTTT-GGGCTTTGGATTTAAAGGTTA
1 GGATTTTAGGGCTTTGGATTTAAAGGTTA
* *
1264025 GTATTTTAGGGGTTTGGATTTAAAGGTTA
1 GGATTTTAGGGCTTTGGATTTAAAGGTTA
* *
1264054 GGATTTTAGGGTTTTGAATTT
1 GGATTTTAGGGCTTTGGATTT
1264075 TAGGGGTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 6 0.14
29 38 0.86
ACGTcount: A:0.22, C:0.01, G:0.31, T:0.46
Consensus pattern (29 bp):
GGATTTTAGGGCTTTGGATTTAAAGGTTA
Found at i:1264092 original size:14 final size:14
Alignment explanation
Indices: 1263969--1264092 Score: 86
Period size: 15 Copynumber: 8.5 Consensus size: 14
1263959 TGGGGTTTTA
*
1263969 ATTTAAGGGTTTGG
1 ATTTAGGGGTTTGG
*
1263983 ATTTTAGGAGTTTTGG
1 A-TTTAGG-GGTTTGG
* *
1263999 ATTTTGGGCTTTGG
1 ATTTAGGGGTTTGG
** * *
1264013 ATTTAAAGGTTAGT
1 ATTTAGGGGTTTGG
1264027 ATTTTAGGGGTTTGG
1 A-TTTAGGGGTTTGG
** *
1264042 ATTTAAAGGTTAGG
1 ATTTAGGGGTTTGG
* *
1264056 ATTTTAGGGTTTTGA
1 A-TTTAGGGGTTTGG
1264071 ATTTTAGGGGTTTGG
1 A-TTTAGGGGTTTGG
1264086 ATTTAGG
1 ATTTAGG
1264093 AATTTGTGTT
Statistics
Matches: 82, Mismatches: 24, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
14 33 0.40
15 42 0.51
16 7 0.09
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (14 bp):
ATTTAGGGGTTTGG
Found at i:1264492 original size:10 final size:9
Alignment explanation
Indices: 1264479--1264521 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 9
1264469 AAAAATACTC
1264479 AAAATAACAA
1 AAAATAA-AA
1264489 AAAATAATAA
1 AAAATAA-AA
* *
1264499 TATATAAAA
1 AAAATAAAA
1264508 AAAATAAAA
1 AAAATAAAA
1264517 AAAAT
1 AAAAT
1264522 TTTTTTACCT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
9 14 0.50
10 14 0.50
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (9 bp):
AAAATAAAA
Found at i:1264792 original size:28 final size:28
Alignment explanation
Indices: 1264750--1264805 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1264740 TTATGTTTGA
* *
1264750 CTCAAAATGACGTCGTTTTGGTCCTATG
1 CTCAAAACGACGTCGTTTTGCTCCTATG
*
1264778 CTCAAAACGATGTCGTTTTGCTCCTATG
1 CTCAAAACGACGTCGTTTTGCTCCTATG
1264806 TTTTCTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (28 bp):
CTCAAAACGACGTCGTTTTGCTCCTATG
Found at i:1265978 original size:42 final size:43
Alignment explanation
Indices: 1265902--1265998 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 43
1265892 AGTGTATCAA
*
1265902 ATATAAATTCTAAAAAATAGTTTATATTTGATACATTGTCAGT
1 ATATAAATTCTAAAAAATAGTTTATATTTAATACATTGTCAGT
1265945 ATATAAATTCTAAAAAA-AGTTTATATTTAATACATTGTCAGT
1 ATATAAATTCTAAAAAATAGTTTATATTTAATACATTGTCAGT
*
1265987 ATGTAAATTCTA
1 ATATAAATTCTA
1265999 TACACTGCCA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
42 35 0.67
43 17 0.33
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.41
Consensus pattern (43 bp):
ATATAAATTCTAAAAAATAGTTTATATTTAATACATTGTCAGT
Found at i:1266173 original size:25 final size:24
Alignment explanation
Indices: 1266145--1266196 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
1266135 GAGTTGTAAT
*
1266145 AATCTGATTTACTAACAATGTATAA
1 AATCT-ATATACTAACAATGTATAA
* *
1266170 AATCTATATACTAACAGTGTATCA
1 AATCTATATACTAACAATGTATAA
1266194 AAT
1 AAT
1266197 ATAAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.44, C:0.13, G:0.08, T:0.35
Consensus pattern (24 bp):
AATCTATATACTAACAATGTATAA
Found at i:1266397 original size:31 final size:30
Alignment explanation
Indices: 1266342--1266399 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
1266332 TTTAAAAAAC
*
1266342 TTATTCATTAACGAGGTGTTATCATCTTAT
1 TTATTCATTAACGAGGTGTAATCATCTTAT
* *
1266372 TTATCTCATTAATGAGTTGTAATCATCT
1 TTAT-TCATTAACGAGGTGTAATCATCT
1266400 GATTCACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.47
Consensus pattern (30 bp):
TTATTCATTAACGAGGTGTAATCATCTTAT
Found at i:1266812 original size:251 final size:251
Alignment explanation
Indices: 1265945--1267524 Score: 1730
Period size: 250 Copynumber: 6.2 Consensus size: 251
1265935 CATTGTCAGT
* * * * * * *
1265945 ATATAAATTC-TAAAAAAAGTTTATATTTAATACATTGTCAGTATGTAAATTCTATACACTGCCA
1 ATATAAATTCTTAAAAAGAGTTTATATTTGATACACTATCAGTATATAGATTCTATACACTGTCA
* * * *
1266009 GTGAATCAAATGATGGCACTTCATTAATGAGCAAATATCAACTCTTAAAATAAATGTAAACAAAT
66 GTGAATCAGATGATGGCATTTCATTAATGAACAAATATCAACTCTTAAAATAAATGTACACAAAT
* * *
1266074 TAAAATTTTTTAAAAAACTTATTCATTAATGAAGTGTTATCATCTAGTTTATCTCATTAATGAGT
131 TAAAATTTTTTAAAAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAATGAGT
* *
1266139 TGTAATAATCTGATTTACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
196 TATAATAATCTGATTCACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
* * *
1266195 ATATAAATT-TTAAAAAAGAGTTTATATTTGATACATTGTCAATATATAGATT-TCATACACTGT
1 ATATAAATTCTT-AAAAAGAGTTTATATTTGATACACTATCAGTATATAGATTCT-ATACACTGT
* ** **
1266258 CAGTGAATC-GAAGATGGCACTTT-ATTAATGAGTAAATATCAA-TCCTTAAAATAAATGTACGT
64 CAGTGAATCAGATGATGGCA-TTTCATTAATGAACAAATATCAACT-CTTAAAATAAATGTACAC
* * *
1266320 AAATTAAAATTTTTTAAAAAACTTATTCATTAACGAGGTGTTATCATCTTATTTATCTCATTAAT
127 AAATTAAAATTTTTTAAAAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAAT
* * * * *
1266385 GAGTTGTAATCATCTGATTCACTAATAATATATAAAATCTATATA-TAATAGTGTATCAA
192 GAGTTATAATAATCTGATTCACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
* * * * * *
1266444 ATATAAATTC-TAAACAAGAGTTTATATTTGATATACCATCAGTATATAAATTTTATATACTGTT
1 ATATAAATTCTTAAA-AAGAGTTTATATTTGATACACTATCAGTATATAGATTCTATACACTGTC
* * *
1266508 AGTGAATAAGATGATGGTATTTCATTAATGAACAAATATTAAC-CTTTAAAATAAATGTACACAA
65 AGTGAATCAGATGATGGCATTTCATTAATGAACAAATATCAACTC-TTAAAATAAATGTACACAA
* * *
1266572 ACTAAAATTTTTTGAGAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAATGA
129 ATTAAAATTTTTTAAAAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAATGA
* * * * *
1266637 GTTATAATTATTTGATTCACTAACAATATATAAAATCTATATACTGATAGTGTATCAA
194 GTTATAATAATCTGATTCACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
* * * *
1266695 ACATAAATTCTTAACAAGAGTTTATATTTGATACATTGTCAGTATATAGATTCTATACACTGTCA
1 ATATAAATTCTTAAAAAGAGTTTATATTTGATACACTATCAGTATATAGATTCTATACACTGTCA
* * *
1266760 GTGAATCAGATGATGGCATTTCATTAATGAATAAATATTAACTCTTAAAATAAATGTATACAAAT
66 GTGAATCAGATGATGGCATTTCATTAATGAACAAATATCAACTCTTAAAATAAATGTACACAAAT
* * * *
1266825 TAAAATTTTTTAAAACA-TTATTCATTAATAAGGTGTTATCAGCTACTTTATCTCATTAATGAGT
131 TAAAATTTTTTAAAAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAATGAGT
* * * * * *
1266889 TATAATAATCTGATTCACTAACAGTGTATAAAATTTATATATTGATAGTGTATTAA
196 TATAATAATCTGATTCACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
* * * * *
1266945 ATATAAATTCTAAAAAAAAATTTATATTTGATACACTATCAGTGTAT-GAATTTTATACACTG-C
1 ATATAAATTCTTAAAAAGAGTTTATATTTGATACACTATCAGTATATAG-ATTCTATACACTGTC
* * * * * * *
1267008 TAGTAAATTAGATGATGGCACTTCATTAATAAACAAATATTAACCCTTAAAATAAATGTACATAA
65 -AGTGAATCAGATGATGGCATTTCATTAATGAACAAATATCAACTCTTAAAATAAATGTACACAA
* * * * * * **
1267073 ATT-AAATGTTTTAAAAAAATTTATTCATTAGTAAGGTCTTATCATCTTATTTATGTTGTTAATG
129 ATTAAAAT-TTTTTAAAAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAATG
* * * * * *
1267137 AGTTATAATCATCTTATTCATTAATAATGTACAAAATCTATATACTGACAGTGTATCAA
193 AGTTATAATAATCTGATTCACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
* * * *
1267196 ATATAAATTCTTTGTATCAAATATAAATTCTAAAAAAAAATTTATATTTGATACCCTATTAGTAT
1 ATATAAA-------T-TC----------T-T-AAAAAGAGTTTATATTTGATACACTATCAGTAT
* ** * ** * * *
1267261 ATAGATTCTATACACTGTCAGTGAATCAAATGATATCAATTCATTAATGAGTAAATAGCAATTTT
46 ATAGATTCTATACACTGTCAGTGAATCAGATGATGGCATTTCATTAATGAACAAATATCAACTCT
** * * * * *
1267326 TAAAAAATAAACATACACAAAGTAAAATTTTTTAAAAAATTTATTTATTAATGATGTATTATTAT
111 T--AAAATAAATGTACACAAATTAAAATTTTTTAAAAAATTTATTCATTAATGAGGTGTTATCAT
* * * *
1267391 CTAATTTATCTCATTAATGAGTTGTAATAATTTGATTCACTAATAGTGTATAAAATCTATATACT
174 CTAATTTATCTCATTAATGAGTTATAATAATCTGATTCACTAACAATGTATAAAATCTATATACT
1267456 AACAGTGTATCAA
239 AACAGTGTATCAA
1267469 ATATAAATT-TTAAAAAAGAGTTTATATTTGATACACTATCAGTATATAGATTCTAT
1 ATATAAATTCTT-AAAAAGAGTTTATATTTGATACACTATCAGTATATAGATTCTAT
1267525 GTACTGCTAA
Statistics
Matches: 1126, Mismatches: 160, Indels: 85
0.82 0.12 0.06
Matches are distributed among these distances:
248 3 0.00
249 80 0.07
250 506 0.45
251 282 0.25
252 4 0.00
253 42 0.04
254 1 0.00
258 1 0.00
259 2 0.00
265 1 0.00
266 1 0.00
269 1 0.00
271 77 0.07
272 2 0.00
273 119 0.11
274 4 0.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (251 bp):
ATATAAATTCTTAAAAAGAGTTTATATTTGATACACTATCAGTATATAGATTCTATACACTGTCA
GTGAATCAGATGATGGCATTTCATTAATGAACAAATATCAACTCTTAAAATAAATGTACACAAAT
TAAAATTTTTTAAAAAATTTATTCATTAATGAGGTGTTATCATCTAATTTATCTCATTAATGAGT
TATAATAATCTGATTCACTAACAATGTATAAAATCTATATACTAACAGTGTATCAA
Found at i:1267211 original size:20 final size:20
Alignment explanation
Indices: 1267188--1267226 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1267178 ATACTGACAG
1267188 TGTATCAAATATAAATTCTT
1 TGTATCAAATATAAATTCTT
1267208 TGTATCAAATATAAATTCT
1 TGTATCAAATATAAATTCT
1267227 AAAAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
TGTATCAAATATAAATTCTT
Found at i:1267877 original size:22 final size:22
Alignment explanation
Indices: 1267852--1267905 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1267842 ATGAGTAATA
**
1267852 ATTAAATTATTAATTATTTACC
1 ATTAAATTATTAAAGATTTACC
* *
1267874 ATTAAGTTATTAAAGATTTACT
1 ATTAAATTATTAAAGATTTACC
1267896 ATTAAATTAT
1 ATTAAATTAT
1267906 CTTAAGGATG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (22 bp):
ATTAAATTATTAAAGATTTACC
Found at i:1268434 original size:2 final size:2
Alignment explanation
Indices: 1268427--1268456 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1268417 GCATACATAC
1268427 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1268457 TTGGCATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1268523 original size:41 final size:41
Alignment explanation
Indices: 1268457--1268539 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1268447 ATATATATAT
* *
1268457 TTGGCATTGCATTTGTGTGTTGGAAATGATATCATACATAA
1 TTGGCATTGCATTTGTATGTGGGAAATGATATCATACATAA
*
1268498 TTGGCATTGCATTTGTATGTGGGAAATGATATCATATATAA
1 TTGGCATTGCATTTGTATGTGGGAAATGATATCATACATAA
1268539 T
1 T
1268540 GTATACATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (41 bp):
TTGGCATTGCATTTGTATGTGGGAAATGATATCATACATAA
Found at i:1268548 original size:15 final size:15
Alignment explanation
Indices: 1268530--1268559 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1268520 GAAATGATAT
1268530 CATATATAATGTATA
1 CATATATAATGTATA
*
1268545 CATATATCATGTATA
1 CATATATAATGTATA
1268560 TTTACATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.40
Consensus pattern (15 bp):
CATATATAATGTATA
Found at i:1271681 original size:129 final size:129
Alignment explanation
Indices: 1271451--1271706 Score: 494
Period size: 129 Copynumber: 2.0 Consensus size: 129
1271441 GCCAAGAATG
*
1271451 TGTTTTAGATTGGAATTTAGGGATTTTGCAGCAGAATTCAGTTCAAAGTTCCTTTCTTTTTTCTT
1 TGTTTTAGATTGGAATTTAGGGATTTTGCAGCAGAATTCAATTCAAAGTTCCTTTCTTTTTTCTT
*
1271516 TTTTTGGTGGTGGTGAATTTAATTCTGGGTTATGAATTATTGGTGCTTGAATTCTGAAGGTGCT
66 TTTTTGGTGGGGGTGAATTTAATTCTGGGTTATGAATTATTGGTGCTTGAATTCTGAAGGTGCT
1271580 TGTTTTAGATTGGAATTTAGGGATTTTGCAGCAGAATTCAATTCAAAGTTCCTTTCTTTTTTCTT
1 TGTTTTAGATTGGAATTTAGGGATTTTGCAGCAGAATTCAATTCAAAGTTCCTTTCTTTTTTCTT
1271645 TTTTTGGTGGGGGTGAATTTAATTCTGGGTTATGAATTATTGGTGCTTGAATTCTGAAGGTG
66 TTTTTGGTGGGGGTGAATTTAATTCTGGGTTATGAATTATTGGTGCTTGAATTCTGAAGGTG
1271707 ATTTTTTTCT
Statistics
Matches: 125, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 125 1.00
ACGTcount: A:0.21, C:0.09, G:0.24, T:0.46
Consensus pattern (129 bp):
TGTTTTAGATTGGAATTTAGGGATTTTGCAGCAGAATTCAATTCAAAGTTCCTTTCTTTTTTCTT
TTTTTGGTGGGGGTGAATTTAATTCTGGGTTATGAATTATTGGTGCTTGAATTCTGAAGGTGCT
Found at i:1274831 original size:32 final size:33
Alignment explanation
Indices: 1274794--1274858 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1274784 CCTATATATG
1274794 TATATA-TTTAATCTGTGACTTTTATTATATCA
1 TATATATTTTAATCTGTGACTTTTATTATATCA
1274826 TATATATTTTAATCTGTGACTTTTATTATATCA
1 TATATATTTTAATCTGTGACTTTTATTATATCA
1274859 AAAAAATTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (33 bp):
TATATATTTTAATCTGTGACTTTTATTATATCA
Found at i:1278336 original size:15 final size:15
Alignment explanation
Indices: 1278286--1278339 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
1278276 TAGAAAAGAG
1278286 AAAAAT-AAATTAATA
1 AAAAATAAAATTAA-A
1278301 AAAAATAAAAATTTAGAA
1 AAAAAT-AAAA-TTA-AA
*
1278319 AAAAATAAAATTACA
1 AAAAATAAAATTAAA
1278334 AAAAAT
1 AAAAAT
1278340 TTAGAGAAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
15 13 0.38
16 3 0.09
17 7 0.21
18 10 0.29
19 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
AAAAATAAAATTAAA
Found at i:1278337 original size:17 final size:16
Alignment explanation
Indices: 1278286--1278338 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
1278276 TAGAAAAGAG
*
1278286 AAAAAT-AAATTAATA
1 AAAAATAAAATTAAAA
*
1278301 AAAAATAAAAATTTAGAA
1 AAAAAT-AAAA-TTAAAA
1278319 AAAAATAAAATTACAAA
1 AAAAATAAAATTA-AAA
1278336 AAA
1 AAA
1278339 TTTAGAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 6 0.19
16 3 0.10
17 12 0.39
18 10 0.32
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATTAAAA
Found at i:1278505 original size:16 final size:16
Alignment explanation
Indices: 1278471--1278513 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
1278461 ATTAATTCAA
**
1278471 ATATAAAACATGATTTT
1 ATATAAAA-ATGAAGTT
1278488 ATATAAAAATGAAGTT
1 ATATAAAAATGAAGTT
1278504 ATATAAAAAT
1 ATATAAAAAT
1278514 CTATGAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 16 0.67
17 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.35
Consensus pattern (16 bp):
ATATAAAAATGAAGTT
Found at i:1280798 original size:19 final size:18
Alignment explanation
Indices: 1280774--1280818 Score: 74
Period size: 17 Copynumber: 2.5 Consensus size: 18
1280764 TCACCATGCT
1280774 CTCATCATCCTCTCTCAAA
1 CTCATCA-CCTCTCTCAAA
1280793 CTCATC-CCTCTCTCAAA
1 CTCATCACCTCTCTCAAA
1280810 CTCATCACC
1 CTCATCACC
1280819 AATTGCCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.68
18 2 0.08
19 6 0.24
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (18 bp):
CTCATCACCTCTCTCAAA
Found at i:1282964 original size:33 final size:33
Alignment explanation
Indices: 1282927--1282991 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
1282917 CAATTTTTTT
1282927 ATATAATAAAAGTCACAGATTAAAATATATATG
1 ATATAATAAAAGTCACAGATTAAAATATATATG
*
1282960 ATATAATAAAAGTCACAGATTAAATTATATAT
1 ATATAATAAAAGTCACAGATTAAAATATATAT
1282992 AGGTAATGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.32
Consensus pattern (33 bp):
ATATAATAAAAGTCACAGATTAAAATATATATG
Found at i:1285852 original size:105 final size:104
Alignment explanation
Indices: 1285671--1285879 Score: 391
Period size: 105 Copynumber: 2.0 Consensus size: 104
1285661 ATATATCCAG
1285671 CTAGAACTTTAAGTCATTAAATGTAGTTGAATCAACTGACAACTTCAATTTCTTCATACTTTTCA
1 CTAGAACTTTAAGTCATTAAATGTAGTTGAATCAACTGACAACTTCAATTTCTTCATACTTTTCA
1285736 TGTTCAATTTTCCAAAACACCTAAAGACTGGCTCAAAGA
66 TGTTCAATTTTCCAAAACACCTAAAGACTGGCTCAAAGA
**
1285775 CTAGAACTTTAAGTCATTAAATGTAGTTGAATCAATCTGACAACTTCGGTTTCTTCATACTTTTC
1 CTAGAACTTTAAGTCATTAAATGTAGTTGAATCAA-CTGACAACTTCAATTTCTTCATACTTTTC
1285840 ATGTTCAATTTTCCAAAACACCTAAAGACTGGCTCAAAGA
65 ATGTTCAATTTTCCAAAACACCTAAAGACTGGCTCAAAGA
1285880 GTCACCTCTG
Statistics
Matches: 102, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
104 35 0.34
105 67 0.66
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (104 bp):
CTAGAACTTTAAGTCATTAAATGTAGTTGAATCAACTGACAACTTCAATTTCTTCATACTTTTCA
TGTTCAATTTTCCAAAACACCTAAAGACTGGCTCAAAGA
Found at i:1289094 original size:15 final size:15
Alignment explanation
Indices: 1289057--1289086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1289047 TATATGTAAA
*
1289057 TATACATGATATATG
1 TATACATTATATATG
1289072 TATACATTATATATG
1 TATACATTATATATG
1289087 ATATCATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (15 bp):
TATACATTATATATG
Found at i:1289122 original size:41 final size:41
Alignment explanation
Indices: 1289077--1289172 Score: 140
Period size: 41 Copynumber: 2.3 Consensus size: 41
1289067 ATATGTATAC
* *
1289077 ATTATATATGATATCATTTCCCACATACAAATGCAATGCCA
1 ATTATATATGATATCATTTCCAACACACAAATGCAATGCCA
*
1289118 ATTATGTATGATATCATTTCCAACACACAAATGCAATGCCA
1 ATTATATATGATATCATTTCCAACACACAAATGCAATGCCA
*
1289159 AATATTATAT-ATAT
1 ATTA-TATATGATAT
1289173 ATATATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 45 0.92
42 4 0.08
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.33
Consensus pattern (41 bp):
ATTATATATGATATCATTTCCAACACACAAATGCAATGCCA
Found at i:1289732 original size:22 final size:22
Alignment explanation
Indices: 1289707--1289760 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
1289697 CATCCTTAAG
**
1289707 ATAATTTAATAGTAAATCTTTA
1 ATAATTTAATAGTAAATAATTA
* *
1289729 ATAACTTAATGGTAAATAATTA
1 ATAATTTAATAGTAAATAATTA
1289751 ATAATTTAAT
1 ATAATTTAAT
1289761 TATTACTCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (22 bp):
ATAATTTAATAGTAAATAATTA
Found at i:1290411 original size:20 final size:20
Alignment explanation
Indices: 1290386--1290424 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1290376 ATTTTTTTTT
1290386 AGAATTTATATTTGATACAA
1 AGAATTTATATTTGATACAA
1290406 AGAATTTATATTTGATACA
1 AGAATTTATATTTGATACA
1290425 CTGTCAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
AGAATTTATATTTGATACAA
Found at i:1290656 original size:273 final size:272
Alignment explanation
Indices: 1290135--1290675 Score: 642
Period size: 273 Copynumber: 2.0 Consensus size: 272
1290125 TCCTTTTTAA
* * *
1290135 AATTTATATTTGATACACTGTTAGTATATAGATTTTATACACTATTAGTGAATCAAATTATTACA
1 AATTTATATTTGATACACTGTCAGTATATAGATTTTATACACTATTAATGAATCAAATGATTACA
** * * *
1290200 ACTCATTAATGAGATAAATTAGATAATAACACATCATTAATAAATAAATTTTTTTAAAAATTTTA
66 ACTCATTAACAACATAAATAAGATAATAACACATCACTAATAAATAAATTTTTTTAAAAATTTTA
* * ** ** * * * *
1290265 CTTTGTGTATGTTTATTTTTTAAAAATTGCTATTTACTCATTAATGAATTGATATCATTTGATTC
131 ATTTATGTACATTTA-TTTTTAAAAATTAATATTTACTCATTAATGAAGTGACATCATCTAATTC
* *
1290330 ACTGACAGTGTATAGAATCTATATACTAATAGGGTATCAAATATAAATTTTTTTTTAGAATTTAT
195 ACTGACAGTGTATAAAATCTATACACTAATAGGGTATCAAATATAAATTTTTTTTTAGAATTTAT
*
1290395 ATTTGATACAAAG
260 ATTTAATACAAAG
* * *
1290408 AATTTATATTTGATACACTGTCAGTATATAGATTTTGTACATTATTAATGAAT-AAGATGATTAT
1 AATTTATATTTGATACACTGTCAGTATATAGATTTTATACACTATTAATGAATCAA-ATGATTAC
* * * * * *
1290472 AACTCATTAACAACATAAATAAGATGATAAGACCTTACTAATGAATAATTTTTTTTAAAACA-TT
65 AACTCATTAACAACATAAATAAGATAATAACACATCACTAATAAATAAATTTTTTTAAAA-ATTT
*** ** * *
1290536 TAATTTATGTACATTTA-TTTTAAGGGTTAATATTTGTTTATTAATGAAGTGCCATCATCTAATT
129 TAATTTATGTACATTTATTTTTAAAAATTAATATTTACTCATTAATGAAGTGACATCATCTAATT
* * *
1290600 TACT-AGCAGTGTATAAAAT-TCATACACTGATAGTGTATCAAATATAAATTTTTTTTTAGAATT
194 CACTGA-CAGTGTATAAAATCT-ATACACTAATAGGGTATCAAATATAAATTTTTTTTTAGAATT
1290663 TATATTTAATACA
257 TATATTTAATACA
1290676 CTATCAATAT
Statistics
Matches: 224, Mismatches: 40, Indels: 10
0.82 0.15 0.04
Matches are distributed among these distances:
270 2 0.01
271 100 0.45
272 2 0.01
273 119 0.53
274 1 0.00
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.43
Consensus pattern (272 bp):
AATTTATATTTGATACACTGTCAGTATATAGATTTTATACACTATTAATGAATCAAATGATTACA
ACTCATTAACAACATAAATAAGATAATAACACATCACTAATAAATAAATTTTTTTAAAAATTTTA
ATTTATGTACATTTATTTTTAAAAATTAATATTTACTCATTAATGAAGTGACATCATCTAATTCA
CTGACAGTGTATAAAATCTATACACTAATAGGGTATCAAATATAAATTTTTTTTTAGAATTTATA
TTTAATACAAAG
Found at i:1290862 original size:250 final size:251
Alignment explanation
Indices: 1290406--1291667 Score: 1576
Period size: 250 Copynumber: 5.0 Consensus size: 251
1290396 TTTGATACAA
* * * * *
1290406 AGAATTTATATTTGATACACTGTCAGTATATAGATTTTGTACATTATTAATGAATAAGATGATTA
1 AGAATTTATATTTGATACACTATCAGTATATAGATTTTATACATTGTTAGTGAATCAGATGATTA
** * * * * * *
1290471 TAACTCATTAACAACATAAATAAGATGATAAGACCTTACTAATGAATAATTTTTTTTAAAACA-T
66 TAACTCATTAATGAGATAAATTAGATGATAACACCTTATTAATGAATAA-GTTTTTTAAAAAATT
* * * * * *
1290535 TTAATTTATGTACATTTATTTTAAGGGTTAATATTTGTTTATTAATGAAGTGCCATCATCTAATT
130 TTAATTTGTGTACATTTATTTTAAGAGTTGATATTTGTTCATTAATGAAATGCCATCATCTGATT
* * * * *
1290600 TACT-AGCAGTGTATAAAATTCATACACTGATAGTGTATCAAATATAAATTTTTTTTT
195 CACTGA-CAGTGTATAAAATTCATATACTGATAATGTATCAAATATAAACTCTTTTTT
* * * * *
1290657 AGAATTTATATTTAATACACTATCAATATATAAATTTTATACACTGTTAGTGAATCAGATTATTA
1 AGAATTTATATTTGATACACTATCAGTATATAGATTTTATACATTGTTAGTGAATCAGATGATTA
* *
1290722 TAACTCATTAATGAGATAAATTAGCTGATAACACCTTATTAATGAATAA-TGTTTTAAAAAATTT
66 TAACTCATTAATGAGATAAATTAGATGATAACACCTTATTAATGAATAAGTTTTTTAAAAAATTT
* *
1290786 TAATTTGTATACATTTATTTTAAGAGTTGATATTTATTCATTAATGAAATGCCATCATCTGATTC
131 TAATTTGTGTACATTTATTTTAAGAGTTGATATTTGTTCATTAATGAAATGCCATCATCTGATTC
* * * *
1290851 ACTGACAGTGTATAGAA-TCTATATACTGACAATGTATCAAATATAAACTCTTGTTA
196 ACTGACAGTGTATAAAATTC-ATATACTGATAATGTATCAAATATAAACTCTTTTTT
* * * *
1290907 AGAATTTATGTTTGATACACTATCAGTATATAGATTTTATATATTGTTAGTGAATCAAATAATTA
1 AGAATTTATATTTGATACACTATCAGTATATAGATTTTATACATTGTTAGTGAATCAGATGATTA
* * * *
1290972 TAACTCATTAATGAGATAAATTAGATGATAACACCTCATTAATGAATAAATTTCTCAAAAAATTT
66 TAACTCATTAATGAGATAAATTAGATGATAACACCTTATTAATGAATAAGTTTTTTAAAAAATTT
* * * *
1291037 TAGTTTGTGTACATTTATTTTAA-AGGTTAATATTTGTTCATTAATGAAATACCATCATCTTATT
131 TAATTTGTGTACATTTATTTTAAGA-GTTGATATTTGTTCATTAATGAAATGCCATCATCTGATT
* * * * ** * *
1291101 CACTAACAGTATATAGAATTTATATACTGATGGTATATCAAATATAAACTCTTGTTT
195 CACTGACAGTGTATAAAATTCATATACTGATAATGTATCAAATATAAACTCTTTTTT
* * *
1291158 AGAATTTATATTTGATACACTATTA-TATATAGATTTTATATATTATTAGTGAATCAGATGATTA
1 AGAATTTATATTTGATACACTATCAGTATATAGATTTTATACATTGTTAGTGAATCAGATGATTA
* * **
1291222 CAACTCATTAATGAGATAAATAAGATGATAACACCTCGTTAATGAATAAGTTTTTTAAAAAATTT
66 TAACTCATTAATGAGATAAATTAGATGATAACACCTTATTAATGAATAAGTTTTTTAAAAAATTT
** **
1291287 TAATTTACGTACATTTATTTTAAG-GATTGATATTTACTCATTAAT-AAAGTGCCATC-TCTGAT
131 TAATTTGTGTACATTTATTTTAAGAG-TTGATATTTGTTCATTAATGAAA-TGCCATCATCTGAT
* *
1291349 TCACTGACAGTGTATGAAA-TCTATATATTGATAATGTATCAAATATAAACTCTTTTTT
194 TCACTGACAGTGTATAAAATTC-ATATACTGATAATGTATCAAATATAAACTCTTTTTT
* * * * *
1291407 AAAATTTATATTTGATACACTGTTAGTATATAGATTTTATACATTGTTAGTAAATCAGATTATTA
1 AGAATTTATATTTGATACACTATCAGTATATAGATTTTATACATTGTTAGTGAATCAGATGATTA
* *
1291472 CAACTCATTAATGAGATAAACTAGATGATAACA-CTTCATTAATGAATAAGTTTTTTAAAAAATT
66 TAACTCATTAATGAGATAAATTAGATGATAACACCTT-ATTAATGAATAAGTTTTTTAAAAAATT
* * * *
1291536 TTAATTTGTTTACATTTATTTTAAGAGTTGATATTTGCTCATTAATGAAGTGCCATCATTTGATT
130 TTAATTTGTGTACATTTATTTTAAGAGTTGATATTTGTTCATTAATGAAATGCCATCATCTGATT
* * * * * * *
1291601 CACTGGCAGTGTATAGAATTTACATACAGACAATGTATTAAATATAAACT-TTTTTT
195 CACTGACAGTGTATAAAATTCATATACTGATAATGTATCAAATATAAACTCTTTTTT
1291657 AGAATTTATAT
1 AGAATTTATAT
1291668 ACTGACAATG
Statistics
Matches: 877, Mismatches: 118, Indels: 33
0.85 0.11 0.03
Matches are distributed among these distances:
248 1 0.00
249 92 0.10
250 498 0.57
251 284 0.32
252 2 0.00
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (251 bp):
AGAATTTATATTTGATACACTATCAGTATATAGATTTTATACATTGTTAGTGAATCAGATGATTA
TAACTCATTAATGAGATAAATTAGATGATAACACCTTATTAATGAATAAGTTTTTTAAAAAATTT
TAATTTGTGTACATTTATTTTAAGAGTTGATATTTGTTCATTAATGAAATGCCATCATCTGATTC
ACTGACAGTGTATAAAATTCATATACTGATAATGTATCAAATATAAACTCTTTTTT
Found at i:1291248 original size:31 final size:30
Alignment explanation
Indices: 1291213--1291270 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
1291203 TTAGTGAATC
*
1291213 AGATGATTACAACTCATTAATGAGATAAATA
1 AGATGATAACAACTCATTAATGA-ATAAATA
* *
1291244 AGATGATAACACCTCGTTAATGAATAA
1 AGATGATAACAACTCATTAATGAATAA
1291271 GTTTTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 4 0.17
31 20 0.83
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.28
Consensus pattern (30 bp):
AGATGATAACAACTCATTAATGAATAAATA
Found at i:1291443 original size:24 final size:25
Alignment explanation
Indices: 1291416--1291467 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
1291406 TAAAATTTAT
*
1291416 ATTTGATACACTGTTAGTATAT-AG
1 ATTTGATACACTGTTAGTAAATCAG
* *
1291440 ATTTTATACATTGTTAGTAAATCAG
1 ATTTGATACACTGTTAGTAAATCAG
1291465 ATT
1 ATT
1291468 ATTACAACTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (25 bp):
ATTTGATACACTGTTAGTAAATCAG
Found at i:1291473 original size:24 final size:24
Alignment explanation
Indices: 1291421--1291473 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1291411 TTTATATTTG
* *
1291421 ATACACTGTTAGTATATAGATTTT
1 ATACACTGTTAGTAAATAGATTAT
*
1291445 ATACATTGTTAGTAAATCAGATTAT
1 ATACACTGTTAGTAAAT-AGATTAT
1291470 -TACA
1 ATACA
1291474 ACTCATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (24 bp):
ATACACTGTTAGTAAATAGATTAT
Found at i:1291675 original size:42 final size:43
Alignment explanation
Indices: 1291614--1291710 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 43
1291604 TGGCAGTGTA
* *
1291614 TAGAATTTACATACAGACAATGTATTAAATATAAACT-TTTTT
1 TAGAATTTATATACAGACAATGTATCAAATATAAACTATTTTT
*
1291656 TAGAATTTATATACTGACAATGTATCAAATATAAACTATTTTT
1 TAGAATTTATATACAGACAATGTATCAAATATAAACTATTTTT
1291699 TAGAATTTATAT
1 TAGAATTTATAT
1291711 TTGATACACT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
42 34 0.67
43 17 0.33
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.42
Consensus pattern (43 bp):
TAGAATTTATATACAGACAATGTATCAAATATAAACTATTTTT
Found at i:1294454 original size:2 final size:2
Alignment explanation
Indices: 1294447--1294471 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1294437 TGCCAACTTG
1294447 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
1294472 ATCTGTATTA
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:1294990 original size:16 final size:16
Alignment explanation
Indices: 1294971--1295025 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
1294961 TAGATAATTA
*
1294971 AAAACAAAAAAAAGCC
1 AAAACAAAAAAAAACC
1294987 AAAACTTAAAAAAACAACCC
1 AAAAC--AAAAAAA-AA-CC
*
1295007 AAAAAAAAAAAAAACC
1 AAAACAAAAAAAAACC
1295023 AAA
1 AAA
1295026 TTAATAGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
16 10 0.30
17 2 0.06
18 14 0.42
19 1 0.03
20 6 0.18
ACGTcount: A:0.76, C:0.18, G:0.02, T:0.04
Consensus pattern (16 bp):
AAAACAAAAAAAAACC
Found at i:1300830 original size:12 final size:12
Alignment explanation
Indices: 1300813--1300837 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1300803 ACCGAATGTA
1300813 AACATCCCATTC
1 AACATCCCATTC
1300825 AACATCCCATTC
1 AACATCCCATTC
1300837 A
1 A
1300838 GCATGCGGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.40, G:0.00, T:0.24
Consensus pattern (12 bp):
AACATCCCATTC
Found at i:1301423 original size:22 final size:22
Alignment explanation
Indices: 1301398--1301441 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1301388 TCCACGGGAA
*
1301398 GCATTTATGGTCCATTTAAATT
1 GCATATATGGTCCATTTAAATT
1301420 GCATATATGGTCCATTTAAATT
1 GCATATATGGTCCATTTAAATT
1301442 CTACAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.43
Consensus pattern (22 bp):
GCATATATGGTCCATTTAAATT
Found at i:1301676 original size:17 final size:16
Alignment explanation
Indices: 1301656--1301703 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1301646 AGAAAACAGA
*
1301656 AAAAATAAAAAAAAAT
1 AAAATTAAAAAAAAAT
*
1301672 GAAAATTTAGAAAAAAAT
1 -AAAA-TTAAAAAAAAAT
1301690 AAAATTACAAAAAA
1 AAAATTA-AAAAAA
1301704 TTTAGAGAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.12
17 13 0.50
18 10 0.38
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (16 bp):
AAAATTAAAAAAAAAT
Found at i:1304888 original size:3 final size:3
Alignment explanation
Indices: 1304880--1304942 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
1304870 TAATTTTAAG
1304880 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TT- TTCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
* *
1304924 TT- TTA TTT TTA TTT TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1304943 CGATCCGAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
2 6 0.12
3 44 0.85
4 2 0.04
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:1305757 original size:11 final size:10
Alignment explanation
Indices: 1305725--1305759 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1305715 TTTTAATTAT
*
1305725 TAAATTAAAA
1 TAAAGTAAAA
1305735 TAAAGTAAAA
1 TAAAGTAAAA
1305745 TAAAGTAAAAA
1 TAAAGT-AAAA
1305756 TAAA
1 TAAA
1305760 ATTTTAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 15 0.65
11 8 0.35
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (10 bp):
TAAAGTAAAA
Found at i:1307467 original size:51 final size:51
Alignment explanation
Indices: 1307404--1307504 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
1307394 TTACAACATG
* *
1307404 CATCCTCATGTTTTAAGCATTATTATGTTACATCATTCTATGCATCATTTC
1 CATCCTCATGTTTTAAGCATTATTATATCACATCATTCTATGCATCATTTC
* *
1307455 CATCCTCATGTTTTAAGCATTATTATATCATATCATTTTATGCATCATTT
1 CATCCTCATGTTTTAAGCATTATTATATCACATCATTCTATGCATCATTT
1307505 TCATAATCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (51 bp):
CATCCTCATGTTTTAAGCATTATTATATCACATCATTCTATGCATCATTTC
Found at i:1307515 original size:51 final size:51
Alignment explanation
Indices: 1307409--1307516 Score: 153
Period size: 51 Copynumber: 2.1 Consensus size: 51
1307399 ACATGCATCC
* * **
1307409 TCATGTTTTAAGCATTATTATGTTACATCATTCTATGCATCATTTCCATCC
1 TCATGTTTTAAGCATTATTATATCACATCATTCTATGCATCATTTCCATAA
* * *
1307460 TCATGTTTTAAGCATTATTATATCATATCATTTTATGCATCATTTTCATAA
1 TCATGTTTTAAGCATTATTATATCACATCATTCTATGCATCATTTCCATAA
1307511 TCATGT
1 TCATGT
1307517 CTAACACCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 50 1.00
ACGTcount: A:0.28, C:0.18, G:0.07, T:0.47
Consensus pattern (51 bp):
TCATGTTTTAAGCATTATTATATCACATCATTCTATGCATCATTTCCATAA
Found at i:1316889 original size:16 final size:16
Alignment explanation
Indices: 1316868--1316908 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1316858 ACTATGCTTA
*
1316868 AAAAAAGAGAAAAAAT
1 AAAAAAGAAAAAAAAT
*
1316884 AAAAAATAAAAAAAAT
1 AAAAAAGAAAAAAAAT
*
1316900 GAAAAAGAA
1 AAAAAAGAA
1316909 GGACTCAAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.10, T:0.07
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAT
Found at i:1317964 original size:41 final size:41
Alignment explanation
Indices: 1317895--1318195 Score: 408
Period size: 41 Copynumber: 7.4 Consensus size: 41
1317885 ATGATTGTCA
*
1317895 AGGAG-CATTTATTTTC-CTAAGTTCGTTGCCTCTATTCAG
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
* * *
1317934 ATGAGCTATTTATTTTCTCAAAGTTTGTTGCCTCTATTCAG
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
* *
1317975 AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAA
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
* * *
1318016 AGGAGCTATTTATTTTTTCAAAGTTTGTTGCCTCTATTCAG
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
* * *
1318057 ATGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCCATTCAG
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
* * *
1318098 AGGAGCTATTTATTTTCTCAAAGTTCATTGCCTCTATTTAG
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
* * * *
1318139 AGGAGCCATTTATTTCCTGAAAGGTCGTTGTCTCTATTCAG
1 AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
*
1318180 ATGAGCCATTTATTTT
1 AGGAGCCATTTATTTT
1318196 TGNNNNNNNN
Statistics
Matches: 225, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
39 4 0.02
40 10 0.04
41 211 0.94
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (41 bp):
AGGAGCCATTTATTTTCTCAAAGTTCGTTGCCTCTATTCAG
Found at i:1318037 original size:82 final size:82
Alignment explanation
Indices: 1317895--1318195 Score: 453
Period size: 82 Copynumber: 3.7 Consensus size: 82
1317885 ATGATTGTCA
*
1317895 AGGAG-CATTTATTTTC-CTAAGTTCGTTGCCTCTATTCAGATGAGCTATTTATTTTCTCAAAGT
1 AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAGAGGAGCTATTTATTTTCTCAAAGT
1317958 TTGTTGCCTCTATTCAG
66 TTGTTGCCTCTATTCAG
* *
1317975 AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAAAGGAGCTATTTATTTTTTCAAAGT
1 AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAGAGGAGCTATTTATTTTCTCAAAGT
1318040 TTGTTGCCTCTATTCAG
66 TTGTTGCCTCTATTCAG
* *
1318057 ATGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCCATTCAGAGGAGCTATTTATTTTCTCAAAGT
1 AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAGAGGAGCTATTTATTTTCTCAAAGT
** *
1318122 TCATTGCCTCTATTTAG
66 TTGTTGCCTCTATTCAG
* ** * * * *
1318139 AGGAGCCATTTATTTCCTGAAAGGTCGTTGTCTCTATTCAGATGAGCCATTTATTTT
1 AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAGAGGAGCTATTTATTTT
1318196 TGNNNNNNNN
Statistics
Matches: 200, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
80 5 0.03
81 11 0.05
82 184 0.92
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.43
Consensus pattern (82 bp):
AGGAGCCATTTATTTTCTCTAAGTTCGTTGCCTCTATTCAGAGGAGCTATTTATTTTCTCAAAGT
TTGTTGCCTCTATTCAG
Found at i:1320255 original size:14 final size:14
Alignment explanation
Indices: 1320236--1320270 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1320226 ATTTATGCTC
1320236 TTTTTTTATT-TTA
1 TTTTTTTATTATTA
1320249 TTTTTTTATTATTA
1 TTTTTTTATTATTA
1320263 TTTTTTTA
1 TTTTTTTA
1320271 AACAAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTTTATTATTA
Found at i:1320353 original size:41 final size:41
Alignment explanation
Indices: 1320306--1320611 Score: 366
Period size: 41 Copynumber: 7.4 Consensus size: 41
1320296 ACAGACTTCA
* * * *
1320306 AAAATAAATGGCTCATCTGAATAGAGACAACGACCTTTCAG
1 AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
* * *
1320347 GAAATAAATGGCTCCTCTAAATAGAGGCAATGAACTTTGAG
1 AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
* * *
1320388 AAAATAAATAGCTCCTCTGAATGGAGGCAACGAACTTAGAG
1 AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
* * *
1320429 AAAATAAATGGCTCATCTGAATAGAGGCAACAAACTTTGAA
1 AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
* * *
1320470 AAAATAAATAGCTCCTTTGAATAGAGGCAACGAACTTAGAG
1 AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
1320511 AAAATAAATGGCTCCTCT-AATAGAGGCAACAGGGCAAAACTTTGAG
1 AAAATAAATGGCTCCTCTGAATAGAGGCAAC---G---AACTTTGAG
* * *
1320557 AAAATAAATAGCTCATCTGAATAGAGGCAACGAACTTAG-G
1 AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
1320597 AAAATAAAT-GCTCCT
1 AAAATAAATGGCTCCT
1320612 TGACAATCAT
Statistics
Matches: 226, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
39 5 0.02
40 22 0.10
41 161 0.71
43 1 0.00
44 1 0.00
46 24 0.11
47 12 0.05
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.22
Consensus pattern (41 bp):
AAAATAAATGGCTCCTCTGAATAGAGGCAACGAACTTTGAG
Found at i:1332580 original size:9 final size:9
Alignment explanation
Indices: 1332538--1332579 Score: 50
Period size: 9 Copynumber: 4.4 Consensus size: 9
1332528 ATTTTCAAAA
1332538 TTTTATATT
1 TTTTATATT
1332547 TTTTATTATAT
1 TTTTA-TAT-T
1332558 TTATTATATT
1 TT-TTATATT
1332568 TTTTAT-TT
1 TTTTATATT
1332576 TTTT
1 TTTT
1332580 TGATTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 6 0.20
9 9 0.30
10 6 0.20
11 6 0.20
12 3 0.10
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTATATT
Found at i:1332765 original size:10 final size:10
Alignment explanation
Indices: 1332745--1332779 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
1332735 TTCCTAAAAT
1332745 TTTATTTTTAC
1 TTTA-TTTTAC
1332756 TTTATTTTAC
1 TTTATTTTAC
*
1332766 TTTATTTTAA
1 TTTATTTTAC
1332776 TTTA
1 TTTA
1332780 ATAATTAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATTTTAC
Found at i:1333590 original size:20 final size:23
Alignment explanation
Indices: 1333571--1333623 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1333561 AATAAAAATA
1333571 AAAATAA-AATAACGAAAATAAT
1 AAAATAATAATAACGAAAATAAT
*
1333593 AAAATAATAATAA-TAATAATAAT
1 AAAATAATAATAACGAA-AATAAT
1333616 AATAATAA
1 AA-AATAA
1333624 CTTAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 9 0.33
23 13 0.48
24 5 0.19
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.25
Consensus pattern (23 bp):
AAAATAATAATAACGAAAATAAT
Found at i:1333593 original size:17 final size:17
Alignment explanation
Indices: 1333561--1333623 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
1333551 TTTCGGATCG
* *
1333561 AATAAAAATAAAAATAA
1 AATAAGAATAATAATAA
1333578 AATAACGAA-AATAATAA
1 AATAA-GAATAATAATAA
*
1333595 AATAATAATAATAATAA
1 AATAAGAATAATAATAA
*
1333612 TAATAATAATAA
1 -AATAAGAATAA
1333624 CTTAAAATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
16 2 0.05
17 25 0.62
18 13 0.32
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (17 bp):
AATAAGAATAATAATAA
Found at i:1333601 original size:3 final size:3
Alignment explanation
Indices: 1333561--1333623 Score: 69
Period size: 3 Copynumber: 21.7 Consensus size: 3
1333551 TTTCGGATCG
* * *
1333561 AAT AAA AAT AAA AAT AA- AAT AACG AA- AAT AAT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT
1333604 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
1333624 CTTAAAATTA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.12
3 43 0.84
4 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:1336833 original size:17 final size:16
Alignment explanation
Indices: 1336795--1336831 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
1336785 CTTCTCTAAA
1336795 TTTTTTGTAATTTTAT
1 TTTTTTGTAATTTTAT
1336811 TTTTTTGTAATTTT-T
1 TTTTTTGTAATTTTAT
1336826 TTTTTT
1 TTTTTT
1336832 TTTCTGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (16 bp):
TTTTTTGTAATTTTAT
Found at i:1337076 original size:22 final size:22
Alignment explanation
Indices: 1337048--1337091 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1337038 ACAATTGTAG
*
1337048 AATTTAAATGGACCATATATGC
1 AATTTAAATGGACCATAAATGC
1337070 AATTTAAATGGACCATAAATGC
1 AATTTAAATGGACCATAAATGC
1337092 TTCCCGTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.30
Consensus pattern (22 bp):
AATTTAAATGGACCATAAATGC
Found at i:1341107 original size:13 final size:13
Alignment explanation
Indices: 1341091--1341162 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 13
1341081 TTTTTATTTG
1341091 TTATATTAATAAT
1 TTATATTAATAAT
* *
1341104 TTATGTTAAGAA-
1 TTATATTAATAAT
* *
1341116 TTAAAAT-ATAAT
1 TTATATTAATAAT
*
1341128 TTATATTAA-AAA
1 TTATATTAATAAT
*
1341140 TTATAATTATTAAT
1 TTAT-ATTAATAAT
1341154 GTTATATTA
1 -TTATATTA
1341163 TTGAATTGAT
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
11 3 0.07
12 15 0.35
13 15 0.35
14 6 0.14
15 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (13 bp):
TTATATTAATAAT
Found at i:1348288 original size:28 final size:28
Alignment explanation
Indices: 1348231--1348291 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1348221 TTTAATTCAC
* *
1348231 ATATATATAAAAATTAAAATATATATTT
1 ATATATATAAAAATTAAAATATAAAATT
*
1348259 ATATTTATAAAAATTAAAA-ATAAAAATT
1 ATATATATAAAAATTAAAATAT-AAAATT
1348287 ATATA
1 ATATA
1348292 AAAGTAACAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATATATATAAAAATTAAAATATAAAATT
Found at i:1349997 original size:21 final size:23
Alignment explanation
Indices: 1349955--1349997 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1349945 GGCATTTTGC
* *
1349955 TATATTAAAAGAAAATTGTTTTA
1 TATACTAAAAGAAAATTATTTTA
1349978 TATACTAAAA-AAAA-TATTTT
1 TATACTAAAAGAAAATTATTTT
1349998 CAAATAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (23 bp):
TATACTAAAAGAAAATTATTTTA
Found at i:1355783 original size:16 final size:16
Alignment explanation
Indices: 1355762--1355794 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1355752 TTTGAATTTC
1355762 TTGAATCACTTGAACT
1 TTGAATCACTTGAACT
1355778 TTGAATCACTTGAACT
1 TTGAATCACTTGAACT
1355794 T
1 T
1355795 GTCCTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (16 bp):
TTGAATCACTTGAACT
Found at i:1362916 original size:13 final size:14
Alignment explanation
Indices: 1362892--1362920 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1362882 CTTCTCTAAA
1362892 TTTTATGTAATTTT
1 TTTTATGTAATTTT
1362906 TTTTATG-AATTTT
1 TTTTATGTAATTTT
1362919 TT
1 TT
1362921 AGGGATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTATGTAATTTT
Found at i:1363078 original size:30 final size:29
Alignment explanation
Indices: 1363010--1363096 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
1363000 CTCTAAATCT
* *
1363010 TCTA-TTTCAAATCAATTGAACCTTTGAATA
1 TCTATTTTC-AATCAATT-AAACTTTTAATA
* *
1363040 TATTTTTTCAATCAATTAAACTTTTACATA
1 TCTATTTTCAATCAATTAAACTTTTA-ATA
*
1363070 TCTATTTTCATTCAATTAAACTCTTTA
1 TCTATTTTCAATCAATTAAACT-TTTA
1363097 TTGGATGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.15
30 32 0.68
31 8 0.17
ACGTcount: A:0.34, C:0.16, G:0.02, T:0.47
Consensus pattern (29 bp):
TCTATTTTCAATCAATTAAACTTTTAATA
Found at i:1365575 original size:10 final size:11
Alignment explanation
Indices: 1365560--1365588 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1365550 AGTTTCTCTA
1365560 AATTTTTT-GT
1 AATTTTTTCGT
1365570 AATTTTTTCGT
1 AATTTTTTCGT
1365581 AATTTTTT
1 AATTTTTT
1365589 TTCATTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (11 bp):
AATTTTTTCGT
Found at i:1366244 original size:13 final size:14
Alignment explanation
Indices: 1366220--1366248 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1366210 CTTCTCTAAA
1366220 TTTTATGTAATTTT
1 TTTTATGTAATTTT
1366234 TTTTATG-AATTTT
1 TTTTATGTAATTTT
1366247 TT
1 TT
1366249 AGGGATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTATGTAATTTT
Found at i:1366383 original size:30 final size:31
Alignment explanation
Indices: 1366343--1366424 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 31
1366333 AAATCTTCTA
*
1366343 TTTCAAATCAATTAAACCTTTGA-ATATATTT
1 TTTC-AATCAATTAAACCTTTGACATATATAT
* *
1366374 TTTCAATCAATTAAA-CTTTTACATATCTAT
1 TTTCAATCAATTAAACCTTTGACATATATAT
*
1366404 TTTCAGTCAATTAAACTCTTT
1 TTTCAATCAATTAAAC-CTTT
1366425 ATTGGATGAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
29 5 0.11
30 31 0.70
31 4 0.09
32 4 0.09
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.46
Consensus pattern (31 bp):
TTTCAATCAATTAAACCTTTGACATATATAT
Found at i:1371139 original size:30 final size:30
Alignment explanation
Indices: 1371096--1371172 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
1371086 TTTTTGTCCA
* * *
1371096 ATAAAGAGCTTAATTGAATGAAAACAGATGT
1 ATAAA-AGTTTAATTGAATGAAAAAAGATAT
* *
1371127 ATAAAAGTTTAATTGAGTGAAAAAATATAT
1 ATAAAAGTTTAATTGAATGAAAAAAGATAT
* *
1371157 GTAAAGGTTTAATTGA
1 ATAAAAGTTTAATTGA
1371173 TTTGAAATAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 34 0.87
31 5 0.13
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (30 bp):
ATAAAAGTTTAATTGAATGAAAAAAGATAT
Found at i:1371290 original size:13 final size:14
Alignment explanation
Indices: 1371274--1371302 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1371264 CCTTATCCCT
1371274 AAAAAATT-CATAA
1 AAAAAATTACATAA
1371287 AAAAAATTACATAA
1 AAAAAATTACATAA
1371301 AA
1 AA
1371303 TTTAGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAATTACATAA
Found at i:1371949 original size:11 final size:11
Alignment explanation
Indices: 1371934--1371966 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
1371924 TAGAAATGAG
1371934 AAAAAAATTTA
1 AAAAAAATTTA
1371945 CAAAAAAA-TTA
1 -AAAAAAATTTA
1371956 AAAAAAATTTA
1 AAAAAAATTTA
1371967 GAGAAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.35
11 6 0.30
12 7 0.35
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAAAATTTA
Found at i:1375609 original size:58 final size:58
Alignment explanation
Indices: 1375519--1375904 Score: 434
Period size: 58 Copynumber: 6.7 Consensus size: 58
1375509 TCTTGTGCAG
* * * **
1375519 GGAAAATTAATACTTTCAACTTTTCCCCAAAAATATTCTTTTG-AAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATT-TTTTGAAAACTTTATTTTTAA
*
1375577 GGAAAATTGATACTTTCAACTTTTCCTC-AAAA-A---TTT-AAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTATTTTTAA
* * *
1375629 GGAAAATTGATACTTTCAACTTCTCC-CAAAAGTATTTTTTGAAAACTTTGATTTTAAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTT-ATTTTTAA
* * * *
1375687 GGAAAATTTATACTTTCAACTTTTCCTCGAAAATCTTTTTTTTGAAAACTTTGATTTTAAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAA-ATATTTTTTGAAAACTTT-ATTTTTAA
* ** * *
1375748 GGAAAATTGATACTTTCAACTTTTCCTCGAAAA-CCTTTTTGAAAAATTTATCTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTATTTTTAA
* *
1375805 GGAAAATTGATACTTTCAACTTTTTCTCAAAAACCTTTTTTTTGAAAAC-TTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA--TATTTTTTGAAAACTTTATTTTTAA
*
1375864 GAAAAATTGATACTTTCAACTTTTCC-CTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTT
1375905 TTTGGAAATT
Statistics
Matches: 282, Mismatches: 31, Indels: 31
0.82 0.09 0.09
Matches are distributed among these distances:
51 1 0.00
52 42 0.15
53 1 0.00
56 4 0.01
57 55 0.20
58 71 0.25
59 39 0.14
60 17 0.06
61 52 0.18
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAAACTTTATTTTTAA
Found at i:1375855 original size:118 final size:115
Alignment explanation
Indices: 1375519--1375904 Score: 452
Period size: 118 Copynumber: 3.3 Consensus size: 115
1375509 TCTTGTGCAG
* **
1375519 GGAAAATTAATACTTTCAACTTTTCCCCAAAAATATTCTTTTG-AAACTTTAATTTCGAGGAAAA
1 GGAAAATTGATACTTTCAACTTTT-CCC-AAAATATT-TTTTGAAAACTTTAATTTTAAGGAAAA
*
1375583 TTGATACTTTCAACTTTTCCTCAAAAA------TTT-AAAAATTTATTTTTAA
63 TTGATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAAACTTTATTTTTAA
* *
1375629 GGAAAATTGATACTTTCAACTTCTCCCAAAAGTATTTTTTGAAAACTTTGATTTTAAAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCAAAA-TATTTTTTGAAAACTTTAATTTT-AAGGAAAAT
* * *
1375694 TTATACTTTCAACTTTTCCTCGAAAATCTTTTTTTTGAAAACTTTGATTTTAAA
64 TGATACTTTCAACTTTTCCTC-AAAAACTTTTTTTTGAAAACTTT-ATTTTTAA
** *
1375748 GGAAAATTGATACTTTCAACTTTTCCTCGAAAA-CCTTTTTGAAAAATTT-ATCTTTAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCC-C-AAAATATTTTTTGAAAACTTTAAT-TTTAAGGAAAA
*
1375811 TTGATACTTTCAACTTTTTCTCAAAAACCTTTTTTTTGAAAAC-TTATTTTTAA
63 TTGATACTTTCAACTTTTCCTCAAAAA-CTTTTTTTTGAAAACTTTATTTTTAA
*
1375864 GAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCC--AAAATATTTTTT
1375905 TTTGGAAATT
Statistics
Matches: 237, Mismatches: 21, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
108 9 0.04
109 18 0.08
110 50 0.21
111 4 0.02
115 1 0.00
116 36 0.15
117 14 0.06
118 52 0.22
119 48 0.20
120 1 0.00
121 4 0.02
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (115 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAATATTTTTTGAAAACTTTAATTTTAAGGAAAATTG
ATACTTTCAACTTTTCCTCAAAAACTTTTTTTTGAAAACTTTATTTTTAA
Found at i:1375950 original size:16 final size:15
Alignment explanation
Indices: 1375929--1376012 Score: 62
Period size: 18 Copynumber: 5.1 Consensus size: 15
1375919 TTTTTATTTA
*
1375929 AAAAAAATAGAATAAT
1 AAAAAAATA-AAAAAT
1375945 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
1375960 -AAAAAATAAAGGAAAGT
1 AAAAAAATAAA--AAA-T
*
1375977 AAAACAAAAATAAAAAT
1 AAAA-AAATA-AAAAAT
1375994 AAGATAAAGATAAAAAAT
1 AA-A-AAA-ATAAAAAAT
1376012 A
1 A
1376013 TTAAATAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.18
15 5 0.09
16 12 0.21
17 4 0.07
18 16 0.29
19 7 0.12
20 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:1375958 original size:7 final size:7
Alignment explanation
Indices: 1375930--1375969 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
1375920 TTTTATTTAA
1375930 AAAAAAT
1 AAAAAAT
*
1375937 AGAATAAT
1 A-AAAAAT
1375945 AAAAAAAT
1 -AAAAAAT
1375953 AAAAAAT
1 AAAAAAT
1375960 AAAAAAT
1 AAAAAAT
1375967 AAA
1 AAA
1375970 GGAAAGTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 18 0.62
8 10 0.34
9 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (7 bp):
AAAAAAT
Found at i:1376079 original size:22 final size:22
Alignment explanation
Indices: 1376033--1376078 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
1376023 CTAATCTAAT
1376033 AAATAAAAAAAATTAAATTAAA
1 AAATAAAAAAAATTAAATTAAA
1376055 AAAT-AAAAAAATTAAATTAAA
1 AAATAAAAAAAATTAAATTAAA
1376076 AAA
1 AAA
1376079 AAATATGGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (22 bp):
AAATAAAAAAAATTAAATTAAA
Found at i:1376162 original size:5 final size:5
Alignment explanation
Indices: 1376152--1376177 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1376142 AGACTTGGAA
1376152 GCTCG GCTCG GCTCG GCTCG GCTCG G
1 GCTCG GCTCG GCTCG GCTCG GCTCG G
1376178 GGGCTGGCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.42, T:0.19
Consensus pattern (5 bp):
GCTCG
Found at i:1377111 original size:16 final size:16
Alignment explanation
Indices: 1377082--1377132 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
1377072 AATAATTATA
1377082 ATATAA-TA-ATAAAT
1 ATATAACTATATAAAT
1377096 ATATAACTATATAAAT
1 ATATAACTATATAAAT
1377112 ATA-ATAC-ATATAAAT
1 ATATA-ACTATATAAAT
1377127 AT-TAAC
1 ATATAAC
1377133 AGAGAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.24
15 14 0.42
16 11 0.33
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAACTATATAAAT
Found at i:1377311 original size:20 final size:21
Alignment explanation
Indices: 1377286--1377325 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1377276 CTTACCCATT
1377286 TGGGCCAGG-CCCAATTGGGC
1 TGGGCCAGGACCCAATTGGGC
*
1377306 TGGGCCTGGACCCAATTGGG
1 TGGGCCAGGACCCAATTGGG
1377326 TGTCTACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.28, G:0.40, T:0.17
Consensus pattern (21 bp):
TGGGCCAGGACCCAATTGGGC
Found at i:1377439 original size:10 final size:10
Alignment explanation
Indices: 1377418--1377473 Score: 60
Period size: 10 Copynumber: 5.6 Consensus size: 10
1377408 AACATTGTCA
1377418 TTTTTTTGT-
1 TTTTTTTGTG
* * *
1377427 TTTTTGTATT
1 TTTTTTTGTG
1377437 TTTTTTTGTG
1 TTTTTTTGTG
1377447 TTTTTTTGTG
1 TTTTTTTGTG
*
1377457 TTTTTTTTTTG
1 -TTTTTTTGTG
1377468 TTTTTT
1 TTTTTT
1377474 ACCAAAGCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
9 7 0.18
10 23 0.59
11 9 0.23
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (10 bp):
TTTTTTTGTG
Found at i:1377443 original size:12 final size:11
Alignment explanation
Indices: 1377421--1377473 Score: 70
Period size: 12 Copynumber: 4.5 Consensus size: 11
1377411 ATTGTCATTT
1377421 TTTTGTTTTTTG
1 TTTT-TTTTTTG
1377433 TATTTTTTTTTG
1 T-TTTTTTTTTG
*
1377445 TGTTTTTTTGTG
1 T-TTTTTTTTTG
1377457 TTTTTTTTTTG
1 TTTTTTTTTTG
1377468 TTTTTT
1 TTTTTT
1377474 ACCAAAGCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.41
12 19 0.51
13 3 0.08
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:1377448 original size:21 final size:20
Alignment explanation
Indices: 1377418--1377473 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 20
1377408 AACATTGTCA
1377418 TTTTTTTGTTTTTTGTATTT
1 TTTTTTTGTTTTTTGTATTT
*
1377438 TTTTTTGTGTTTTTTTGTGTTT
1 TTTTTT-TG-TTTTTTGTATTT
1377460 TTTTTTTGTTTTTT
1 TTTTTTTGTTTTTT
1377474 ACCAAAGCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 12 0.36
21 4 0.12
22 17 0.52
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (20 bp):
TTTTTTTGTTTTTTGTATTT
Found at i:1377537 original size:41 final size:41
Alignment explanation
Indices: 1377480--1377647 Score: 266
Period size: 41 Copynumber: 4.1 Consensus size: 41
1377470 TTTTACCAAA
1377480 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
* *
1377521 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
* * *
1377562 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
*
1377603 GCTCCTCTAAACAGAGGCAACGA-AACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGC-ACCACAACTTTGAAAAATAAATT
1377644 GCTC
1 GCTC
1377648 ATTGACAATC
Statistics
Matches: 119, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
41 116 0.97
42 3 0.03
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACAACTTTGAAAAATAAATT
Found at i:1378916 original size:19 final size:17
Alignment explanation
Indices: 1378894--1378957 Score: 58
Period size: 19 Copynumber: 3.5 Consensus size: 17
1378884 AATTTGAATC
1378894 TTTTTTTTTCATTTTCTCA
1 TTTTTTTTT--TTTTCTCA
*
1378913 TTTTTCCATTTTTTTCTCA
1 TTTTT--TTTTTTTTCTCA
*
1378932 TTTTTTCTTTTTTTTTC-
1 TTTTTT-TTTTTTTCTCA
1378949 TTTTTTTTT
1 TTTTTTTTT
1378958 CCTCATCTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.08
17 6 0.15
18 9 0.23
19 18 0.46
21 3 0.08
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTTTTTTTCTCA
Found at i:1378955 original size:18 final size:18
Alignment explanation
Indices: 1378905--1378954 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
1378895 TTTTTTTTCA
*
1378905 TTTTCTCATTTTTCCATTT
1 TTTTCTCATTTTTTC-TTT
1378924 TTTTCTCATTTTTTCTTT
1 TTTTCTCATTTTTTCTTT
*
1378942 TTTTTTC-TTTTTT
1 TTTTCTCATTTTTT
1378955 TTTCCTCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 14 0.48
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTCATTTTTTCTTT
Found at i:1378958 original size:20 final size:20
Alignment explanation
Indices: 1378905--1378949 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1378895 TTTTTTTTCA
**
1378905 TTTTCTCA-TTTTTCCATTT
1 TTTTCTCATTTTTTCTTTTT
1378924 TTTTCTCATTTTTTCTTTTT
1 TTTTCTCATTTTTTCTTTTT
1378944 TTTTCT
1 TTTTCT
1378950 TTTTTTTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTCTCATTTTTTCTTTTT
Found at i:1383096 original size:58 final size:59
Alignment explanation
Indices: 1383006--1383452 Score: 510
Period size: 59 Copynumber: 7.7 Consensus size: 59
1382996 GTTCTTGTGC
* * * **
1383006 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTCTTTTG-AAACTTTAATTTCG
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTTATTTTTA
*
1383064 AGGAAAATTGATACTTTCAACTTTTCCTC-AAAA-A----TTT-AAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTTATTTTTA
* * *
1383116 AGGAAAATTGATACTTTCAACTTCTCC-CAAAAATATTTTTTTGAAAATTTTGATTTTAA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTT-ATTTTTA
* * *
1383175 AGGAAAATTGATACTTTCAACTTTTCCTCGAAAATCTTTTTTTTGAAAACTTTGATTTTAA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAAT-ATTTTTTTGAAAACTTT-ATTTTTA
* ** * *
1383236 AGGAAAATTGATACTTTCAACTTTTCCTCGAAAA-CCTTTTTGGAAAA-TTTATCTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTTATTTTTA
* * * *
1383293 AGGAAAATTGATATTTTCAACTTTTCCT-AAAAATA-TTTTTCGAAAATTTTGATTTTCA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTT-ATTTTTA
* * **
1383351 AGAAAAATTGATACTTTCAACTTTTTCTCAAAAACCCTTTTTTTGAAAAC-TTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATTTTTTTGAAAACTTTATTTTTA
1383410 AGGAAAATTGATACTTTCAACTTTT-CTCTAAAAATATTTTTTT
1 AGGAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTT
1383453 TTTTGGAAAT
Statistics
Matches: 337, Mismatches: 34, Indels: 36
0.83 0.08 0.09
Matches are distributed among these distances:
51 1 0.00
52 43 0.13
53 1 0.00
56 15 0.04
57 42 0.12
58 78 0.23
59 82 0.24
60 8 0.02
61 67 0.20
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (59 bp):
AGGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAAACTTTATTTTTA
Found at i:1383499 original size:15 final size:15
Alignment explanation
Indices: 1383477--1383562 Score: 73
Period size: 18 Copynumber: 5.1 Consensus size: 15
1383467 ATTTTTATTT
*
1383477 TAAAAAAATAGAATAA
1 TAAAAAAATA-AAAAA
1383493 TAAAAAAATAAAAAA
1 TAAAAAAATAAAAAA
1383508 TAAAAAAATAAAGAAAA
1 TAAAAAAAT-AA-AAAA
*
1383525 GTAAAACAAAAATAAAAA
1 -TAAAA-AAATA-AAAAA
1383543 TAAGATAAAGATAAAAAA
1 TAA-A-AAA-ATAAAAAA
1383561 TA
1 TA
1383563 TTAAATAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
15 13 0.22
16 12 0.20
17 7 0.12
18 20 0.34
19 7 0.12
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (15 bp):
TAAAAAAATAAAAAA
Found at i:1383567 original size:27 final size:26
Alignment explanation
Indices: 1383479--1383571 Score: 72
Period size: 27 Copynumber: 3.7 Consensus size: 26
1383469 TTTTATTTTA
* *
1383479 AAAAAATAGAATAAT-AA-AAAA-AT
1 AAAAAATATAAAAATAAAGAAAAGAT
*
1383502 AAAAAATAAAAAAATAAAGAAAAG-T
1 AAAAAATATAAAAATAAAGAAAAGAT
*
1383527 AAAACAAAAATAAAAAT-AAGATAAAGAT
1 -AAA-AAATATAAAAATAAAGA-AAAGAT
*
1383555 AAAAAATAT-TAAATAAA
1 AAAAAATATAAAAATAAA
1383572 TCTAATCTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
23 13 0.23
24 2 0.04
25 9 0.16
26 14 0.25
27 17 0.30
28 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.05, T:0.16
Consensus pattern (26 bp):
AAAAAATATAAAAATAAAGAAAAGAT
Found at i:1383600 original size:8 final size:8
Alignment explanation
Indices: 1383587--1383612 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1383577 TCTAATAAAT
1383587 AAAAATTA
1 AAAAATTA
1383595 AAAAATTA
1 AAAAATTA
1383603 AAAAATTA
1 AAAAATTA
1383611 AA
1 AA
1383613 TTAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAATTA
Found at i:1384162 original size:26 final size:26
Alignment explanation
Indices: 1384124--1384181 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
1384114 AAATCTGGAA
*
1384124 ATTTCCCAAAAATTTCCAGAAAAATT
1 ATTTCCCAAAAATTTCCAAAAAAATT
*
1384150 -TTTCGCCAAAAATTTCTAAAAAAATT
1 ATTTC-CCAAAAATTTCCAAAAAAATT
1384176 ATTTCC
1 ATTTCC
1384182 GATCCCTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 4 0.14
26 20 0.71
27 4 0.14
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.34
Consensus pattern (26 bp):
ATTTCCCAAAAATTTCCAAAAAAATT
Found at i:1384660 original size:16 final size:16
Alignment explanation
Indices: 1384631--1384681 Score: 58
Period size: 15 Copynumber: 3.4 Consensus size: 16
1384621 TATAATTATA
1384631 ATATAA-TA-ATAAAT
1 ATATAACTATATAAAT
1384645 ATATAACTATATAAAT
1 ATATAACTATATAAAT
1384661 ATA-ATAC-ATATAAAT
1 ATATA-ACTATATAAAT
1384676 AT-TAAC
1 ATATAAC
1384682 AGAGAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
14 8 0.24
15 14 0.42
16 11 0.33
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATAACTATATAAAT
Found at i:1384841 original size:20 final size:21
Alignment explanation
Indices: 1384816--1384855 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1384806 CTTACCCATT
1384816 TGGGCCAGG-CCCAATTGGGC
1 TGGGCCAGGACCCAATTGGGC
*
1384836 TGGGCCTGGACCCAATTGGG
1 TGGGCCAGGACCCAATTGGG
1384856 TGTCTACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.15, C:0.28, G:0.40, T:0.17
Consensus pattern (21 bp):
TGGGCCAGGACCCAATTGGGC
Found at i:1394929 original size:19 final size:19
Alignment explanation
Indices: 1394901--1394938 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1394891 GGTGCCAGAT
1394901 TCTGGAAATTTCACCGGAA
1 TCTGGAAATTTCACCGGAA
*
1394920 TCTGGGAATTTCACCGGAA
1 TCTGGAAATTTCACCGGAA
1394939 ATTGGCCGGA
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:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (19 bp):
TCTGGAAATTTCACCGGAA
Found at i:1395456 original size:42 final size:45
Alignment explanation
Indices: 1395408--1395515 Score: 118
Period size: 42 Copynumber: 2.5 Consensus size: 45
1395398 AAATCAAAAA
* * *
1395408 TAAAAAAATACTAGATAATAATCA-GATAAATCA-AA-AGATATT
1 TAAAAAAATAATAGATAATAATCAGGAAAAATCAGAACAGATAAT
** *
1395450 TAAAAAAA-AATATCTGATAATCAGGAAAAATCAGAACAGATAAT
1 TAAAAAAATAATAGATAATAATCAGGAAAAATCAGAACAGATAAT
1395494 TAAAAATAATAAT-GATAATAAT
1 TAAAAA-AATAATAGATAATAAT
1395516 AATAATAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
41 11 0.21
42 16 0.31
43 2 0.04
44 12 0.23
45 8 0.15
46 3 0.06
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.25
Consensus pattern (45 bp):
TAAAAAAATAATAGATAATAATCAGGAAAAATCAGAACAGATAAT
Found at i:1395660 original size:40 final size:41
Alignment explanation
Indices: 1395559--1395660 Score: 113
Period size: 40 Copynumber: 2.5 Consensus size: 41
1395549 ATTACAAAAA
* *
1395559 AATAATAATAATAATAAATATATAACTATATACATATAAATCT
1 AATAATAATAA-AATAAATAAATAAATATATACATATAAA-CT
*
1395602 AAT-CTAATAAAA-AAATAAATAAATATATACATA-ATAA-T
1 AATAATAATAAAATAAATAAATAAATATATACATATA-AACT
*
1395640 AATAATAATAAAATACATAAA
1 AATAATAATAAAATAAATAAA
1395661 ATACAAAAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 4 0.08
39 9 0.18
40 27 0.53
41 2 0.04
42 6 0.12
43 3 0.06
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (41 bp):
AATAATAATAAAATAAATAAATAAATATATACATATAAACT
Found at i:1401656 original size:11 final size:11
Alignment explanation
Indices: 1401622--1401649 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1401612 TTTCTCTAAA
1401622 TTTTTTGTAAT
1 TTTTTTGTAAT
1401633 TTTTTTGTAAT
1 TTTTTTGTAAT
1401644 TTTTTT
1 TTTTTT
1401650 TTCATTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (11 bp):
TTTTTTGTAAT
Found at i:1402305 original size:13 final size:14
Alignment explanation
Indices: 1402281--1402309 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1402271 CTTCTCTAAA
1402281 TTTTATGTAATTTT
1 TTTTATGTAATTTT
1402295 TTTTATG-AATTTT
1 TTTTATGTAATTTT
1402308 TT
1 TT
1402310 AGGGATAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.00, G:0.07, T:0.72
Consensus pattern (14 bp):
TTTTATGTAATTTT
Found at i:1402445 original size:30 final size:30
Alignment explanation
Indices: 1402411--1402478 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
1402401 CTATTTCAAA
* *
1402411 TCAATTAAACCTTTACATATATTTTTTCAC
1 TCAATTAAACCTTTACACATATGTTTTCAC
* * * *
1402441 TCAATTAAACTTTTATACATCTGTTTTCAT
1 TCAATTAAACCTTTACACATATGTTTTCAC
1402471 TCAATTAA
1 TCAATTAA
1402479 GCTCTTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.18, G:0.01, T:0.47
Consensus pattern (30 bp):
TCAATTAAACCTTTACACATATGTTTTCAC
Found at i:1409165 original size:20 final size:20
Alignment explanation
Indices: 1409128--1409166 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1409118 TTTTTGTAGT
* *
1409128 TTTTTTTTTCTATATTTTCA
1 TTTTTATTTATATATTTTCA
*
1409148 TTTTTATTTATATTTTTTC
1 TTTTTATTTATATATTTTC
1409167 TCTTTTCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTATTTATATATTTTCA
Found at i:1413344 original size:168 final size:171
Alignment explanation
Indices: 1413019--1413364 Score: 531
Period size: 168 Copynumber: 2.0 Consensus size: 171
1413009 AAGGTTTTTA
* *
1413019 AAATGTTTATAAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATCGTTTATAAATT
1 AAATGTTCATAAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATAGTTTATAAATT
* * *
1413084 TAAAAAATAAAAAATAAAAGTTCACATCATCGCACAAAAAAAGCCAACAACAAAAACGTATTCAT
66 TAAAAAATAAAAAATAAAAGTTCACATCATAGCACAAAAAAAACCAACAACAAAAACGTAATCAT
*
1413149 AATATATTATTATTTTTAGTTTTGATATATTTATAAGATTC
131 AATATATTATTATTTTTAATTTTGATATATTTATAAGATTC
*
1413190 AAATGTTCAT-AATTTAAAATAAATTGAAAAAAGGTCATAGATTTGATCAAATAGTTTA-AAATT
1 AAATGTTCATAAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATAGTTTATAAATT
* *
1413253 T-AAAAATAAAAAATGAAAGTTCACTTCATAG-A-AAAAACAAACCAACAACAAAAACGTAATCA
66 TAAAAAATAAAAAATAAAAGTTCACATCATAGCACAAAAA-AAACCAACAACAAAAACGTAATCA
**
1413315 TCGTATATTAATTATTTTTAATTTTGATATATTTATAAGATTC
130 TAATATATT-ATTATTTTTAATTTTGATATATTTATAAGATTC
1413358 AACATGT
1 AA-ATGT
1413365 GAGTATTTTT
Statistics
Matches: 161, Mismatches: 11, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
166 5 0.03
167 30 0.19
168 61 0.38
169 10 0.06
170 46 0.29
171 9 0.06
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.34
Consensus pattern (171 bp):
AAATGTTCATAAATTTAAAATAAATTGAAAAAACGTCATAGATTTGATCAAATAGTTTATAAATT
TAAAAAATAAAAAATAAAAGTTCACATCATAGCACAAAAAAAACCAACAACAAAAACGTAATCAT
AATATATTATTATTTTTAATTTTGATATATTTATAAGATTC
Found at i:1413421 original size:21 final size:21
Alignment explanation
Indices: 1413381--1413422 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1413371 TTTTTTTTTG
* * *
1413381 TATTAAAAATAATTATAAATA
1 TATTAAAAACAATGAAAAATA
1413402 TATTAAAAACAATGAAAAATA
1 TATTAAAAACAATGAAAAATA
1413423 ACTTATCCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (21 bp):
TATTAAAAACAATGAAAAATA
Found at i:1413928 original size:32 final size:33
Alignment explanation
Indices: 1413876--1413958 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
1413866 TTTTTATAAA
*
1413876 ATAAA-AATAATAATTGTATATG-AA-AATATAT
1 ATAAATAATAA-AATTTTATATGAAATAATATAT
*
1413907 TTAAATATATAAAATTTTATATGAAATAATATAT
1 ATAAATA-ATAAAATTTTATATGAAATAATATAT
*
1413941 ATAAATAATTAAATTTTA
1 ATAAATAATAAAATTTTA
1413959 AAATTGATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
31 4 0.09
32 11 0.25
33 16 0.36
34 13 0.30
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (33 bp):
ATAAATAATAAAATTTTATATGAAATAATATAT
Found at i:1417270 original size:52 final size:52
Alignment explanation
Indices: 1417209--1417313 Score: 149
Period size: 52 Copynumber: 2.0 Consensus size: 52
1417199 TATAAGTATA
**
1417209 CAAACTTGCCTATTAGA-AATCCCTTTCCTCTTAGAATTCTTCTTCTACAAGT
1 CAAACTTGCCTATTA-ATAATCAATTTCCTCTTAGAATTCTTCTTCTACAAGT
* * *
1417261 CAAACTTGCCTATTAATAATCAATTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAATAATCAATTTCCTCTTAGAATTCTTCTTCTACAAGT
1417313 C
1 C
1417314 TTCTTGTCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 1 0.02
52 46 0.98
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAATAATCAATTTCCTCTTAGAATTCTTCTTCTACAAGT
Done.