Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 131 of 207
Found at i:40058889 original size:42 final size:43
Alignment explanation
Indices: 40058751--40058892 Score: 178
Period size: 43 Copynumber: 3.3 Consensus size: 43
40058741 TCCCAGATGT
* * *
40058751 GGTCTTACATGTAATCAAATAACGATGCCACTGTCTCAGACAG
1 GGTCTTACACGTAATTAAATAACGATGCCACTGTCCCAGACAG
* *
40058794 GGTCTTACACGTAATTAAATAACGATGCTACTGTCCTAGACAG
1 GGTCTTACACGTAATTAAATAACGATGCCACTGTCCCAGACAG
* * * * **
40058837 GGTCATACACGTAATTATAT-ACGACGCCAATGTCCCAGACTT
1 GGTCTTACACGTAATTAAATAACGATGCCACTGTCCCAGACAG
40058879 GGTCTTACACGTAA
1 GGTCTTACACGTAA
40058893 ATTTCAAATC
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 29 0.34
43 56 0.66
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (43 bp):
GGTCTTACACGTAATTAAATAACGATGCCACTGTCCCAGACAG
Found at i:40064894 original size:14 final size:14
Alignment explanation
Indices: 40064849--40064901 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
40064839 CCAAAAAAAA
40064849 TAATTTTAAA--TT
1 TAATTTTAAATTTT
40064861 TAATTTTAAATTTT
1 TAATTTTAAATTTT
*
40064875 AAATTTTAAATTTT
1 TAATTTTAAATTTT
* *
40064889 TTATTTTGAATTT
1 TAATTTTAAATTT
40064902 GTTGCCCGCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 10 0.29
14 25 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TAATTTTAAATTTT
Found at i:40064901 original size:7 final size:7
Alignment explanation
Indices: 40064850--40064888 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
40064840 CAAAAAAAAT
40064850 AATTTTA
1 AATTTTA
40064857 AA-TTT-
1 AATTTTA
40064862 AATTTTA
1 AATTTTA
40064869 AATTTTA
1 AATTTTA
40064876 AATTTTA
1 AATTTTA
40064883 AATTTT
1 AATTTT
40064889 TTATTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 22 0.73
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:40068442 original size:29 final size:30
Alignment explanation
Indices: 40068369--40068443 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
40068359 AAACTACACC
* * * *
40068369 ATTGGTCACACAACTATGGATTTTCTTTTA
1 ATTGGTCACTCAACTATGAATTTTCATTAA
* *
40068399 TTTGGCCACTCAACTATGAATTTT-ATTAA
1 ATTGGTCACTCAACTATGAATTTTCATTAA
40068428 ATTGGTCACTCAACTA
1 ATTGGTCACTCAACTA
40068444 ATTGGATTTA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (30 bp):
ATTGGTCACTCAACTATGAATTTTCATTAA
Found at i:40071841 original size:43 final size:43
Alignment explanation
Indices: 40071794--40071874 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
40071784 ATTCTAGAAA
* * *
40071794 AAAAAAGAATTTAAAAA-AGGAGAAGATAATCTTGGGTTGTTG
1 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTTGTTG
40071836 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTT
1 AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTT
40071875 ATTGGATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 17 0.49
43 18 0.51
ACGTcount: A:0.53, C:0.02, G:0.22, T:0.22
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAGAGGAAAAGATAAACATGGGTTGTTG
Found at i:40076700 original size:6 final size:6
Alignment explanation
Indices: 40076685--40076767 Score: 50
Period size: 6 Copynumber: 14.5 Consensus size: 6
40076675 ATATAATTTG
* * ** * *
40076685 AAAAAT -AAAAT -AAAA- ACAAAT AACAAT AAAAAT AAATGT ACAACT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
40076730 AAAAAT AAAAAG AAAAAT --AAAT AAAACAT AAAACT AAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAA-AT AAAAAT AAA
40076768 TAGACTCAGT
Statistics
Matches: 58, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
4 4 0.07
5 12 0.21
6 36 0.62
7 6 0.10
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:40076714 original size:16 final size:15
Alignment explanation
Indices: 40076687--40076721 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
40076677 ATAATTTGAA
40076687 AAATAAAATAAAAAC
1 AAATAAAATAAAAAC
*
40076702 AAATAACAATAAAAAT
1 AAATAA-AATAAAAAC
40076718 AAAT
1 AAAT
40076722 GTACAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAATAAAAAC
Found at i:40076736 original size:24 final size:22
Alignment explanation
Indices: 40076685--40076767 Score: 78
Period size: 24 Copynumber: 3.7 Consensus size: 22
40076675 ATATAATTTG
40076685 AAAAAT-AAAATAAAAACAAAT
1 AAAAATAAAAATAAAAACAAAT
* * *
40076706 AACAATAAAAATAAATGTACAACT
1 AAAAATAAAAATAAA--AACAAAT
* *
40076730 AAAAATAAAAAGAAAAATAAAT
1 AAAAATAAAAATAAAAACAAAT
*
40076752 AAAACATAAAACTAAA
1 AAAA-ATAAAAATAAA
40076768 TAGACTCAGT
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.10
22 16 0.33
23 9 0.19
24 18 0.38
ACGTcount: A:0.75, C:0.07, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACAAAT
Found at i:40076753 original size:16 final size:17
Alignment explanation
Indices: 40076732--40076769 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
40076722 GTACAACTAA
40076732 AAATAAAA-AGAAAAAT
1 AAATAAAACAGAAAAAT
* *
40076748 AAATAAAACATAAAACT
1 AAATAAAACAGAAAAAT
40076765 AAATA
1 AAATA
40076770 GACTCAGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAAACAGAAAAAT
Found at i:40078195 original size:7 final size:8
Alignment explanation
Indices: 40078182--40078210 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
40078172 AAATACTACC
40078182 AAAAAAAT
1 AAAAAAAT
40078190 AAAAAAAT
1 AAAAAAAT
40078198 AAAAAAAT
1 AAAAAAAT
40078206 AAAAA
1 AAAAA
40078211 GTCTAAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:40084695 original size:72 final size:72
Alignment explanation
Indices: 40084613--40084756 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
40084603 AAGGAAATTT
* *
40084613 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGTGGTCTTTCTTCA
1 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
40084678 ACTTTGC
66 ACTTTGC
* *
40084685 AATATGTAATTGTTTAAAAAGTTTAAGAAATTTACCAAATTGTTCGTCCATGCGATCTTTCTTCA
1 AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
40084750 ACTTTGC
66 ACTTTGC
40084757 CGGATATGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (72 bp):
AATATGTAATTGTTTAAAAAGTTCAAGAAATTTACCAAATTGTTCATCCATGCGATCTTTCTTCA
ACTTTGC
Found at i:40084860 original size:27 final size:26
Alignment explanation
Indices: 40084803--40084865 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
40084793 TGTTGTTTGA
40084803 ATTTTCTCATTTTTTGCCACCTCATC
1 ATTTTCTCATTTTTTGCCACCTCATC
40084829 ATTTTCTCATTTTTTGCCACCTCATC
1 ATTTTCTCATTTTTTGCCACCTCATC
40084855 ATTTTTCTCAT
1 A-TTTTCTCAT
40084866 CAGTTTTTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 27 0.75
27 9 0.25
ACGTcount: A:0.16, C:0.29, G:0.03, T:0.52
Consensus pattern (26 bp):
ATTTTCTCATTTTTTGCCACCTCATC
Found at i:40091037 original size:20 final size:20
Alignment explanation
Indices: 40091012--40091060 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
40091002 GGTTTGAAAG
*
40091012 AAGTAAAA-TTTTTGAGGGAA
1 AAGTAAAAGTTTTAGA-GGAA
*
40091032 AAGTAAACGTTTTAGAGGAA
1 AAGTAAAAGTTTTAGAGGAA
40091052 AAGTAAAAG
1 AAGTAAAAG
40091061 AAAAAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.49, C:0.02, G:0.24, T:0.24
Consensus pattern (20 bp):
AAGTAAAAGTTTTAGAGGAA
Found at i:40091829 original size:18 final size:20
Alignment explanation
Indices: 40091782--40091829 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 20
40091772 CTCTAACTTA
40091782 ATTTAAATT-TAATTAAATT
1 ATTTAAATTATAATTAAATT
*
40091801 ACTTAAA--ATAATT-AATT
1 ATTTAAATTATAATTAAATT
40091818 -TTTAAATTATAA
1 ATTTAAATTATAA
40091830 ACAAATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 7
0.73 0.06 0.21
Matches are distributed among these distances:
16 5 0.21
17 4 0.17
18 9 0.38
19 6 0.25
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATTATAATTAAATT
Found at i:40092018 original size:21 final size:20
Alignment explanation
Indices: 40091992--40092031 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
40091982 ATTTTATCAT
40091992 GAACCTCAAACCTAGAACCCC
1 GAACCTCAAA-CTAGAACCCC
* *
40092013 GAACCTTAAACTCGAACCC
1 GAACCTCAAACTAGAACCC
40092032 TGAATCTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (20 bp):
GAACCTCAAACTAGAACCCC
Found at i:40092031 original size:20 final size:21
Alignment explanation
Indices: 40091992--40092042 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
40091982 ATTTTATCAT
*
40091992 GAACCTCAAACCTAGAACCCC
1 GAACCTTAAACCTAGAACCCC
* *
40092013 GAACCTTAAA-CTCGAACCCT
1 GAACCTTAAACCTAGAACCCC
*
40092033 GAATCTTAAA
1 GAACCTTAAA
40092043 TCTTAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.39, C:0.33, G:0.10, T:0.18
Consensus pattern (21 bp):
GAACCTTAAACCTAGAACCCC
Found at i:40092173 original size:35 final size:36
Alignment explanation
Indices: 40092117--40092204 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 36
40092107 TAGGTTTTGG
*
40092117 GTTTAGGGTTCAA-GTTCAAGGGTTCGGGA-TTATGA
1 GTTTAGGGTTTAAGGTTCAAGGGTT-GGGAGTTATGA
* * *
40092152 GTTT-GGGTTTAAGGTTTAAGGGTTTGGAGTTTTGA
1 GTTTAGGGTTTAAGGTTCAAGGGTTGGGAGTTATGA
* *
40092187 GTTTGGGGTTTATGGTTC
1 GTTTAGGGTTTAAGGTTC
40092205 TTGTTTAGGG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
34 10 0.23
35 23 0.52
36 11 0.25
ACGTcount: A:0.17, C:0.05, G:0.36, T:0.42
Consensus pattern (36 bp):
GTTTAGGGTTTAAGGTTCAAGGGTTGGGAGTTATGA
Found at i:40100505 original size:15 final size:15
Alignment explanation
Indices: 40100481--40100513 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
40100471 AACTTAATCT
40100481 ATATAAGTTATAATA
1 ATATAAGTTATAATA
*
40100496 ATATATGTTATAATA
1 ATATAAGTTATAATA
40100511 ATA
1 ATA
40100514 AAATTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (15 bp):
ATATAAGTTATAATA
Found at i:40101343 original size:16 final size:16
Alignment explanation
Indices: 40101280--40101345 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
40101270 GATTGATATT
*
40101280 GAAATGGAAAAGATGA
1 GAAATGGAAAATATGA
40101296 GAAAT-G--AATATGA
1 GAAATGGAAAATATGA
*
40101309 G--ATGAGAAAAATAT-T
1 GAAATG-G-AAAATATGA
40101324 GAAATGGAAAATATGA
1 GAAATGGAAAATATGA
40101340 GAAATG
1 GAAATG
40101346 ATATATGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 16
0.67 0.05 0.28
Matches are distributed among these distances:
11 2 0.05
13 8 0.21
15 9 0.23
16 17 0.44
17 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.20
Consensus pattern (16 bp):
GAAATGGAAAATATGA
Found at i:40102680 original size:49 final size:48
Alignment explanation
Indices: 40102599--40102694 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 48
40102589 TCTAAAAGGG
* *
40102599 ATAAATAGTGATAAGATGTAGACAATGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGATGTAGACAATGGAAGACGAAGTTTAGAAATGT
*
40102647 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACGAAGTTTAGAAATG
1 ATAAATAGTGATAAGA-TGTAGACAATGGAAGACGAAGTTTAGAAATG
40102695 CATAGCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 16 0.36
49 28 0.64
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (48 bp):
ATAAATAGTGATAAGATGTAGACAATGGAAGACGAAGTTTAGAAATGT
Found at i:40108024 original size:15 final size:16
Alignment explanation
Indices: 40107958--40108021 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 16
40107948 ATGATATGTG
40107958 TATATG-TATAATATA
1 TATATGTTATAATATA
40107973 TATTATGTTAGCTTAATATA
1 TA-TATGTTA---TAATATA
*
40107993 TATAAGTTATAATA-A
1 TATATGTTATAATATA
40108008 TATATGTTATAATA
1 TATATGTTATAATA
40108022 ATAAAATTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
15 16 0.38
16 9 0.21
17 2 0.05
19 6 0.14
20 9 0.21
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (16 bp):
TATATGTTATAATATA
Found at i:40108834 original size:43 final size:43
Alignment explanation
Indices: 40108784--40108869 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
40108774 TATGTGATTG
* *
40108784 ATATTGAAATGGCAAAGATGAGAAATGAATATGTGATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
* *
40108827 ATATTGAAATGGAAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTGAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
40108870 TGAGATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.50, C:0.01, G:0.24, T:0.24
Consensus pattern (43 bp):
ATATTGAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:40110974 original size:20 final size:20
Alignment explanation
Indices: 40110949--40110987 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40110939 TGGAGCAGGA
*
40110949 ATATCGATACCTTAGGAAAT
1 ATATCGATACCTTAAGAAAT
40110969 ATATCGATACCTTAAGAAA
1 ATATCGATACCTTAAGAAA
40110988 AATTATTGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.13, T:0.28
Consensus pattern (20 bp):
ATATCGATACCTTAAGAAAT
Found at i:40112982 original size:23 final size:23
Alignment explanation
Indices: 40112956--40113010 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
40112946 GACTAAGCGC
40112956 GCAAGTGATAATGGCACTATAGT
1 GCAAGTGATAATGGCACTATAGT
* * *
40112979 GCAAGTGTTAGTGGCACTTTAGT
1 GCAAGTGATAATGGCACTATAGT
40113002 GCAAAGTGA
1 GC-AAGTGA
40113011 CATCCACATG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 22 0.81
24 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.29, T:0.27
Consensus pattern (23 bp):
GCAAGTGATAATGGCACTATAGT
Found at i:40113047 original size:24 final size:24
Alignment explanation
Indices: 40113000--40113051 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
40112990 TGGCACTTTA
*
40113000 GTGCAAAGTGACATCCACATGTCT
1 GTGCAAAGTGACATCCACAAGTCT
***
40113024 GTGCAAAGTGACATTTGCAAGTCT
1 GTGCAAAGTGACATCCACAAGTCT
40113048 GTGC
1 GTGC
40113052 GAAGAATAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (24 bp):
GTGCAAAGTGACATCCACAAGTCT
Found at i:40116028 original size:16 final size:16
Alignment explanation
Indices: 40115992--40116024 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
40115982 GTCAGATCCC
40115992 TATTTATTCAATTTTA
1 TATTTATTCAATTTTA
40116008 TATTTATT--ATTTTA
1 TATTTATTCAATTTTA
40116022 TAT
1 TAT
40116025 ATTTGAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTATTCAATTTTA
Found at i:40118857 original size:124 final size:126
Alignment explanation
Indices: 40118631--40119037 Score: 613
Period size: 126 Copynumber: 3.2 Consensus size: 126
40118621 AAAAAATCTT
* * * * * *
40118631 CCACGTGGACGCTCTTTTGCTACAGTAGCTCTTGAAAAAATAATTTTGAGAAGACATTTTTGAGC
1 CCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGA
* * *
40118696 AAATAGTGTAAAAAACGCTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTT
66 AAATAGTGTCAAAAACACTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTC
* *
40118757 CCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG-AAAAA-AATTTCAAGTAGACGTTTCTGAGA
1 CCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGA
*
40118820 AAATAGTGTCAAAAACACTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTTAAAGAAGCTC
66 AAATAGTGTCAAAAACACTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTC
* * * * *
40118881 CCACGTGTATGCGCTTTTGCTATAATAGCTCCTGAAAAAATAATTTCGAGCAGACGTTTCTGAGA
1 CCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGA
*
40118946 AAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGAT-AGCAAAAGTACTGAAAGAAGCTC
66 AAATAGTGTCAAAAACACTTTAAGTAGGATGCTTTG-TCAGCAAAAGTACTGAAAGAAGCTC
*
40119007 CCACGAGGACGCGCTTTTGCTACAGTAGCTC
1 CCACGTGGACGCGCTTTTGCTACAGTAGCTC
40119038 ATGTTTGGTC
Statistics
Matches: 253, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
124 105 0.42
125 10 0.04
126 137 0.54
127 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
CCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAGACGTTTCTGAGA
AAATAGTGTCAAAAACACTTTAAGTAGGATGCTTTGTCAGCAAAAGTACTGAAAGAAGCTC
Found at i:40122251 original size:116 final size:116
Alignment explanation
Indices: 40122041--40122251 Score: 287
Period size: 116 Copynumber: 1.8 Consensus size: 116
40122031 GTATTATTTA
* * * *
40122041 TATTTTTTTAAATCAAATAATATGGAAATATTTAGAATATTGACTTATTTAAAAGAAAATCTATT
1 TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATCTATT
* * *
40122106 TTATTAAAAATATTAAAGTGAATTACAATTACTTTATTCAAAACAACGTTT
66 ATATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACAACGTTT
* ** ** *
40122157 TATTTTATTAAATGAAATAATATAGAAATATTCAAAATATTGTGTTATTTAAAAGAATTTTTATT
1 TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATCTATT
* *
40122222 ATATTAAAAATGTAAAAGTAAATTTCAATT
66 ATATTAAAAATATAAAAGTAAATTACAATT
40122252 TTATTACATG
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
116 80 1.00
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (116 bp):
TATTTTATTAAATCAAATAATATAGAAATATTCAAAATATTGACTTATTTAAAAGAAAATCTATT
ATATTAAAAATATAAAAGTAAATTACAATTACTTTATTCAAAACAACGTTT
Found at i:40122455 original size:21 final size:21
Alignment explanation
Indices: 40122431--40122470 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40122421 CAGCTTTCGG
* *
40122431 CGGGGGTTGTGGTTGCTCCAA
1 CGGGGATTGTGGTTCCTCCAA
*
40122452 CGGGGATTTTGGTTCCTCC
1 CGGGGATTGTGGTTCCTCC
40122471 GGTAGGGGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.38, T:0.33
Consensus pattern (21 bp):
CGGGGATTGTGGTTCCTCCAA
Found at i:40122753 original size:18 final size:18
Alignment explanation
Indices: 40122727--40122769 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40122717 GATTAGAAAA
* * *
40122727 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
40122745 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
40122763 AGGATAC
1 AGGATAC
40122770 GTGCCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:40123404 original size:7 final size:7
Alignment explanation
Indices: 40123394--40123419 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40123384 CATAATACAT
40123394 AATACTA
1 AATACTA
40123401 AATACTA
1 AATACTA
40123408 AATACTA
1 AATACTA
40123415 AATAC
1 AATAC
40123420 CAATCGACTA
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:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:40124639 original size:11 final size:11
Alignment explanation
Indices: 40124625--40124661 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
40124615 AGCTTTTTTA
40124625 AGAGGAATTTG
1 AGAGGAATTTG
*
40124636 AGAGGAAATTG
1 AGAGGAATTTG
*
40124647 AAAGGAATTTG
1 AGAGGAATTTG
40124658 AGAG
1 AGAG
40124662 AATATTGGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.35, T:0.22
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:40124652 original size:22 final size:24
Alignment explanation
Indices: 40124627--40124683 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 24
40124617 CTTTTTTAAG
40124627 AGGAATTTGAGAGGAA-ATT-GAA
1 AGGAATTTGAGAGGAATATTGGAA
40124649 AGGAATTTGAGA-GAATATTGGAA
1 AGGAATTTGAGAGGAATATTGGAA
*
40124672 A-GAAATTGAGAG
1 AGGAATTTGAGAG
40124684 AAAGGATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 3 0.10
22 24 0.77
23 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.23
Consensus pattern (24 bp):
AGGAATTTGAGAGGAATATTGGAA
Found at i:40125627 original size:22 final size:22
Alignment explanation
Indices: 40125602--40125650 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
40125592 TTTTCTTATT
*
40125602 ATTTTATCT-TTATTTTGCTACC
1 ATTTTA-CTATTATGTTGCTACC
*
40125624 ATTTTACTATTATGTTGCTACT
1 ATTTTACTATTATGTTGCTACC
40125646 ATTTT
1 ATTTT
40125651 GTTGTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 2 0.08
22 22 0.92
ACGTcount: A:0.20, C:0.14, G:0.06, T:0.59
Consensus pattern (22 bp):
ATTTTACTATTATGTTGCTACC
Found at i:40125895 original size:12 final size:12
Alignment explanation
Indices: 40125874--40125907 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40125864 TATATATTTT
*
40125874 AAAATTATATAA
1 AAAATAATATAA
40125886 AAAATAATATAA
1 AAAATAATATAA
*
40125898 AAATTAATAT
1 AAAATAATAT
40125908 GGGCGAGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:40130063 original size:30 final size:29
Alignment explanation
Indices: 40130028--40130085 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
40130018 CCAAATTCTC
40130028 CCCCAAACGTTTT-TTCCCCCTCTGCTGGTT
1 CCCCAAA--TTTTCTTCCCCCTCTGCTGGTT
*
40130058 CCCCAAATTTTCTTTCCCCTCTGCTGGT
1 CCCCAAATTTTCTTCCCCCTCTGCTGGT
40130086 GAAATTGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 15 0.58
30 7 0.27
ACGTcount: A:0.10, C:0.40, G:0.12, T:0.38
Consensus pattern (29 bp):
CCCCAAATTTTCTTCCCCCTCTGCTGGTT
Found at i:40131510 original size:50 final size:50
Alignment explanation
Indices: 40131430--40131720 Score: 260
Period size: 50 Copynumber: 5.9 Consensus size: 50
40131420 TTTATACACG
* *
40131430 TAGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
* * * * *
40131480 TAGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACC-AAATAGCT
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAT-G-A
* * *
40131531 TCGATCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
* * * *
40131581 TAGGTCACATGTATAGTACTATGTGTAGGCTACTATGCGTA-CTG---GA
1 TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
* * * * * *
40131627 TAGCT-TC--GAT-CACGTACTATGTGCAGGCTACTACGTGTATCAG-ATGAA
1 TAGGTCACATG-TGTA-GTACTATGTGCAGGCTACTATGTGTACCGGAATG-A
* *
40131675 AATGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGAACCGG
1 TA-GGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
40131721 GTATCATTTA
Statistics
Matches: 190, Mismatches: 37, Indels: 27
0.75 0.15 0.11
Matches are distributed among these distances:
43 2 0.01
44 24 0.13
45 3 0.02
46 6 0.03
47 1 0.01
48 2 0.01
49 7 0.04
50 75 0.39
51 65 0.34
52 5 0.03
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (50 bp):
TAGGTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGA
Found at i:40131609 original size:101 final size:101
Alignment explanation
Indices: 40131434--40131712 Score: 394
Period size: 101 Copynumber: 2.8 Consensus size: 101
40131424 TACACGTAGG
*
40131434 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCACATGTGTAGTAC
40131499 TATGTGTAGGCTACTATGCGTACCAAATAGCTTCGA
66 TATGTGTAGGCTACTATGCGTACCAAATAGCTTCGA
* *
40131535 TCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAATGATAGGTCACATGTATAGTAC
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCACATGTGTAGTAC
***
40131600 TATGTGTAGGCTACTATGCGTACTGGATAGCTTCGA
66 TATGTGTAGGCTACTATGCGTACCAAATAGCTTCGA
* * *
40131636 TCAC-------GTACTATGTGCAGGCTACTACGTGTATCAG-ATGAAAATGGTCACATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATG-ATA-GGTCACATGTGTAGT
*
40131693 ACTATGTGCAGGCTACTATG
64 ACTATGTGTAGGCTACTATG
40131713 TGAACCGGGT
Statistics
Matches: 164, Mismatches: 12, Indels: 10
0.88 0.06 0.05
Matches are distributed among these distances:
93 3 0.02
94 29 0.18
95 33 0.20
101 99 0.60
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAATGATAGGTCACATGTGTAGTAC
TATGTGTAGGCTACTATGCGTACCAAATAGCTTCGA
Found at i:40137942 original size:24 final size:24
Alignment explanation
Indices: 40137895--40137942 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40137885 TTACACTAAT
*
40137895 TAGAGTTTAAGTGGAAAACTAAAA
1 TAGAGTTTAAGTGGAAAACGAAAA
*
40137919 TAGAGTTTAATTGGAAGAA-GAAAA
1 TAGAGTTTAAGTGGAA-AACGAAAA
40137943 GTCGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 19 0.90
25 2 0.10
ACGTcount: A:0.50, C:0.02, G:0.23, T:0.25
Consensus pattern (24 bp):
TAGAGTTTAAGTGGAAAACGAAAA
Found at i:40139394 original size:12 final size:12
Alignment explanation
Indices: 40139379--40139404 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40139369 TAAAATATTT
40139379 AATTTTTTTATA
1 AATTTTTTTATA
40139391 AATTTTTTTATA
1 AATTTTTTTATA
40139403 AA
1 AA
40139405 AATGAACCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTTTTATA
Found at i:40140074 original size:20 final size:20
Alignment explanation
Indices: 40140041--40140078 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
40140031 AATGTGAATA
40140041 ATTTTTTTCAAAATATTTATG
1 ATTTTTTTCAAAAT-TTTATG
*
40140062 ATTTTTTT-GAAATTTTA
1 ATTTTTTTCAAAATTTTA
40140079 GTAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 4 0.25
21 8 0.50
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.61
Consensus pattern (20 bp):
ATTTTTTTCAAAATTTTATG
Found at i:40140107 original size:29 final size:30
Alignment explanation
Indices: 40140051--40140105 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
40140041 ATTTTTTTCA
40140051 AAATATTTATGATTTTTTTGAAATTTTAGT
1 AAATATTTATGATTTTTTTGAAATTTTAGT
40140081 AAAT-TTTATG-TATTTTTT-AAATTTT
1 AAATATTTATGAT-TTTTTTGAAATTTT
40140106 TATGAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 8 0.33
29 12 0.50
30 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (30 bp):
AAATATTTATGATTTTTTTGAAATTTTAGT
Found at i:40145105 original size:21 final size:22
Alignment explanation
Indices: 40145079--40145120 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
40145069 CGGGTATTTG
40145079 ACTAAAATAATACA-AAAAAAT
1 ACTAAAATAATACACAAAAAAT
*
40145100 ACTAAAATAATATACAAAAAA
1 ACTAAAATAATACACAAAAAA
40145121 GTTTATTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (22 bp):
ACTAAAATAATACACAAAAAAT
Found at i:40148211 original size:150 final size:151
Alignment explanation
Indices: 40147784--40148305 Score: 735
Period size: 159 Copynumber: 3.4 Consensus size: 151
40147774 GGTTTCGACA
* **
40147784 AATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATCCGGGAAAAAATACGAACAAAGG
1 AATAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAGG
* * * * *
40147849 ACCGAAATAATGGTTTTTTTAAATTTATTTAAAAAACACAGTAAATTAAAACATTTCAAACATAA
66 GCCGAAATAAAGATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAA
*
40147914 TTTACTAAAATAATGTAAAAT
131 TGTACTAAAATAATGTAAAAT
* * * *
40147935 AATAAAA-TACAAAAATAATATATTTTTATTGAAAGTAATAAAATCCGGAAAAAAAAAATATGAA
1 AATAAAATTA-GAAAATAGTATA-TTTT-TTAAAAGTAATAAAATCC-G--AAAAAAAATACGAA
* * ** *
40147999 CAAATGGCCGAAATAAGAGTTTTTTTTTTAAATTTAAATAAAAAACACACTAAATGAATACATTT
60 CAAAGGGCCGAAATAA-AG--ATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTT
40148064 CAAACATAATGTACTAAAATAATGTAAAAT
122 CAAACATAATGTACTAAAATAATGTAAAAT
* * *
40148094 AATAAAATTATAAAATAGCATATTTTTTAAAAGTAATAAAATCCGAGAAAAAATACGAACAAAGG
1 AATAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAGG
*
40148159 GCTGAAATAAAGATTTTTTT-AATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAA
66 GCCGAAATAAAGATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAA
40148223 TGTACTAAAATAATGTAAAAT
131 TGTACTAAAATAATGTAAAAT
*
40148244 AAT-AAATTAGAAAATAGTATTTTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAA
1 AATAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAA
40148306 TGGTTGAAAT
Statistics
Matches: 329, Mismatches: 32, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
149 55 0.17
150 67 0.20
151 24 0.07
152 4 0.01
153 19 0.06
154 27 0.08
156 26 0.08
157 18 0.05
158 4 0.01
159 83 0.25
160 2 0.01
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.30
Consensus pattern (151 bp):
AATAAAATTAGAAAATAGTATATTTTTTAAAAGTAATAAAATCCGAAAAAAAATACGAACAAAGG
GCCGAAATAAAGATTTTTTTAAATTTATTTAAAAAACACACTAAATTAATACATTTCAAACATAA
TGTACTAAAATAATGTAAAAT
Found at i:40148462 original size:19 final size:19
Alignment explanation
Indices: 40148435--40148474 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40148425 CTTTTTTGTA
*
40148435 TATTATTTTGGTATTTTTT
1 TATTATTTTGGTATTATTT
* *
40148454 TATTTTTTTTGTATTATTT
1 TATTATTTTGGTATTATTT
40148473 TA
1 TA
40148475 GTAAAATATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.75
Consensus pattern (19 bp):
TATTATTTTGGTATTATTT
Found at i:40149171 original size:19 final size:20
Alignment explanation
Indices: 40149118--40149171 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
40149108 ATTTTACAAA
*
40149118 TTTTATAAAATTTTATGATT
1 TTTTATAAAATTTAATGATT
* **
40149138 TTTAATTAATTTTTAAT-ATT
1 TTTTA-TAAAATTTAATGATT
40149158 TTTTATAAAATTTA
1 TTTTATAAAATTTA
40149172 TTTTTATTTA
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
19 7 0.27
20 11 0.42
21 8 0.31
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
TTTTATAAAATTTAATGATT
Found at i:40149179 original size:22 final size:21
Alignment explanation
Indices: 40149118--40149210 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 21
40149108 ATTTTACAAA
* *
40149118 TTTTATAA-AATTTTATGA-T
1 TTTTATAATAATTTTTTTATT
* *
40149137 TTTTA-ATTAATTTTTAATATT
1 TTTTATAATAATTTTT-TTATT
40149158 TTTTATAA-AATTTATTTTTATT
1 TTTTATAATAA-TT-TTTTTATT
*
40149180 TAGTTT-TAATGATTTTTTTATT
1 T--TTTATAATAATTTTTTTATT
40149202 TTTTATAAT
1 TTTTATAAT
40149211 TCCATAATGT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
18 1 0.02
19 11 0.19
20 4 0.07
21 12 0.21
22 17 0.30
23 8 0.14
24 4 0.07
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (21 bp):
TTTTATAATAATTTTTTTATT
Found at i:40149321 original size:16 final size:15
Alignment explanation
Indices: 40149300--40149329 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40149290 AATAACTTAC
40149300 ATTTTTTTATTTTTGA
1 ATTTTTTT-TTTTTGA
40149316 ATTTTTTTTTTTTG
1 ATTTTTTTTTTTTG
40149330 CTGATGTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.07, T:0.80
Consensus pattern (15 bp):
ATTTTTTTTTTTTGA
Found at i:40149683 original size:87 final size:88
Alignment explanation
Indices: 40149535--40149731 Score: 263
Period size: 87 Copynumber: 2.2 Consensus size: 88
40149525 ACTTTAAGAA
* ** * *
40149535 AAAAAAACAATTAAGCACCTCTTTTTTCTTTGCACTTAATTGAGCACTTGAACTTTTAAAATGCA
1 AAAAAAACAATTAAGCCCCTAATTTTTCTTT-CACTCAATTGAGCACTTGAACTTTCAAAATGCA
* *** *
40149600 TTAAAAGGGCCCTCAAACTTTTTC
65 TCAAAAACACCCTCAAAATTTTTC
*
40149624 AAAAAAAGCAATTAAGCCCCTAATTTTT-TTT-ACTCAATTGGGCACTTGAACTTTCAAAATGCA
1 AAAAAAA-CAATTAAGCCCCTAATTTTTCTTTCACTCAATTGAGCACTTGAACTTTCAAAATGCA
40149687 TCAAAAACACCCTCAAAATTTTTC
65 TCAAAAACACCCTCAAAATTTTTC
40149711 AAAAAAACAATTAAGCCCCTA
1 AAAAAAACAATTAAGCCCCTA
40149732 TTCTTATTAA
Statistics
Matches: 96, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
86 14 0.15
87 55 0.57
89 10 0.10
90 17 0.18
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (88 bp):
AAAAAAACAATTAAGCCCCTAATTTTTCTTTCACTCAATTGAGCACTTGAACTTTCAAAATGCAT
CAAAAACACCCTCAAAATTTTTC
Found at i:40152783 original size:99 final size:97
Alignment explanation
Indices: 40152581--40152809 Score: 231
Period size: 96 Copynumber: 2.4 Consensus size: 97
40152571 GGAGCCATAA
* * * * *
40152581 AGAATGACTCCACAAAACTAAAATATCATTTTT-AAAATTTTTAAATTAAAAACAACACATTTAA
1 AGAATGGCTCCACCAAA-TAAAATATTATTTTTAAAAAATTTTAAATTAAAAAAAACACATTTAA
* * *
40152645 AAAATATATACAGTACATTGGTGGCGATATTCT
65 AAAATATATACAGTAAAGTGGTGGCGACATTCT
*
40152678 A-TATGGCTCCACCAAATAAAATATTATTTTTAAAAAATTTTAAATTAAAAAAAACCACATTTTA
1 AGAATGGCTCCACCAAATAAAATATTATTTTTAAAAAATTTTAAATTAAAAAAAA-CACA-TTT-
*
40152742 AAAAAATCCTAATA-A-TAAAGTGGTGGC-ACCATT-T
63 AAAAAAT-AT-ATACAGTAAAGTGGTGGCGA-CATTCT
* *
40152776 AGAATGGCTCCACC-AATAAAA-AATAATTTTAAAA
1 AGAATGGCTCCACCAAATAAAATATTATTTTTAAAA
40152810 TTAAAAAAAA
Statistics
Matches: 111, Mismatches: 13, Indels: 16
0.79 0.09 0.11
Matches are distributed among these distances:
95 14 0.13
96 32 0.29
97 16 0.14
98 13 0.12
99 31 0.28
100 2 0.02
101 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.08, T:0.31
Consensus pattern (97 bp):
AGAATGGCTCCACCAAATAAAATATTATTTTTAAAAAATTTTAAATTAAAAAAAACACATTTAAA
AAATATATACAGTAAAGTGGTGGCGACATTCT
Found at i:40153574 original size:10 final size:10
Alignment explanation
Indices: 40153559--40153586 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40153549 TTTTTTTTTA
40153559 AATTAGTATT
1 AATTAGTATT
40153569 AATTAGTATT
1 AATTAGTATT
40153579 AATTAGTA
1 AATTAGTA
40153587 GGGTAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (10 bp):
AATTAGTATT
Found at i:40155615 original size:29 final size:27
Alignment explanation
Indices: 40155576--40155630 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
40155566 AATTTTTAAA
40155576 AATTCTCATTAAACATTTTCAAAATTTTC
1 AATTCTCATTAAAC-TTTT-AAAATTTTC
*
40155605 AATTTTCATTAAACTTTTAAAATTTT
1 AATTCTCATTAAACTTTTAAAATTTT
40155631 TGAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 8 0.32
28 4 0.16
29 13 0.52
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTCTCATTAAACTTTTAAAATTTTC
Found at i:40155951 original size:13 final size:12
Alignment explanation
Indices: 40155933--40155982 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
40155923 TCTTCATTGC
40155933 TTTTGAAAAGTGA
1 TTTTGAAAAGT-A
40155946 TTTTGAAAAGTA
1 TTTTGAAAAGTA
* *
40155958 TTGTAGAAAAATA
1 TT-TTGAAAAGTA
40155971 CTTTTGAAAAGT
1 -TTTTGAAAAGT
40155983 TTGGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 3 0.10
13 26 0.84
14 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.18, T:0.38
Consensus pattern (12 bp):
TTTTGAAAAGTA
Found at i:40164130 original size:21 final size:21
Alignment explanation
Indices: 40164069--40164117 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
40164059 CAGCTTGATG
* *
40164069 TGTTTAGGTAGTCGAATGACT
1 TGTTTAGATAGTTGAATGACT
40164090 TGTTTAGATAGTTGAATGACT
1 TGTTTAGATAGTTGAATGACT
40164111 TGTTTAG
1 TGTTTAG
40164118 TTAGCTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (21 bp):
TGTTTAGATAGTTGAATGACT
Found at i:40168606 original size:13 final size:13
Alignment explanation
Indices: 40168583--40168674 Score: 114
Period size: 13 Copynumber: 7.0 Consensus size: 13
40168573 TGAGTTCGGT
40168583 TATATTGTTTTAA
1 TATATTGTTTTAA
40168596 TATACTT-TTTTAA
1 TATA-TTGTTTTAA
40168609 TATATTGTTTTAA
1 TATATTGTTTTAA
*
40168622 TATATTGTTATAA
1 TATATTGTTTTAA
* *
40168635 TATACTGTTATAA
1 TATATTGTTTTAA
*
40168648 TTATATTATTTTAA
1 -TATATTGTTTTAA
*
40168662 TATAATGTTTTAA
1 TATATTGTTTTAA
40168675 CTTTTGAATT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
12 2 0.03
13 55 0.80
14 12 0.17
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (13 bp):
TATATTGTTTTAA
Found at i:40168715 original size:66 final size:66
Alignment explanation
Indices: 40168582--40168715 Score: 159
Period size: 66 Copynumber: 2.0 Consensus size: 66
40168572 ATGAGTTCGG
* * * *
40168582 TTATATTGTTTTAATATACTTTTTTAATATATTGTTTTAATATATTGTTATAATATACTGTTATA
1 TTATATTATTTTAATATAATGTTTTAATATATTGTTTTAATATATTGTTATAATATACTATTATA
40168647 A
66 A
*
40168648 TTATATTATTTTAATATAATGTTTTAACT-T-TTGAATTTTAGTATATTGTTATAAATATAC-AT
1 TTATATTATTTTAATATAATGTTTTAA-TATATTG--TTTTAATATATTGTTAT-AATATACTAT
40168710 T-TAA
62 TATAA
40168714 TT
1 TT
40168716 TGTAACACAT
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
65 3 0.05
66 30 0.51
67 19 0.32
68 7 0.12
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (66 bp):
TTATATTATTTTAATATAATGTTTTAATATATTGTTTTAATATATTGTTATAATATACTATTATA
A
Found at i:40168730 original size:15 final size:15
Alignment explanation
Indices: 40168710--40168743 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
40168700 AAATATACAT
*
40168710 TTAATTTGTAACACA
1 TTAATTTCTAACACA
40168725 TTAATTTCTAACACA
1 TTAATTTCTAACACA
40168740 TTAA
1 TTAA
40168744 AAAAAAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.41, C:0.15, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAATTTCTAACACA
Found at i:40171345 original size:26 final size:26
Alignment explanation
Indices: 40171316--40171372 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
40171306 AACAGGTATC
*
40171316 AGGATAATGATGATGATGGAAAACAT
1 AGGACAATGATGATGATGGAAAACAT
40171342 AGGACAATGATGATGATGGAAAACAT
1 AGGACAATGATGATGATGGAAAACAT
40171368 AGGAC
1 AGGAC
40171373 TACTTATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.19
Consensus pattern (26 bp):
AGGACAATGATGATGATGGAAAACAT
Found at i:40173060 original size:4 final size:4
Alignment explanation
Indices: 40173046--40173076 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
40173036 AAAAAATGGG
*
40173046 GAAA AAAA GAAA GAAA GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAA
40173077 GGAAGGAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40174716 original size:52 final size:52
Alignment explanation
Indices: 40174656--40174754 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
40174646 ACAAATCCTA
* *
40174656 TCTCAA-TTTCATTCCAAAACCCTCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTTC-TTCCAAAACCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
*
40174708 TCTCAATTTTCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
1 TCTCAATTTTCTTCCAAAACCCTCTCAATTTCATTCCAAAAATCTCT
40174755 CAAATCCATA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 39 0.91
53 4 0.09
ACGTcount: A:0.30, C:0.31, G:0.00, T:0.38
Consensus pattern (52 bp):
TCTCAATTTTCTTCCAAAACCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
Found at i:40174732 original size:22 final size:22
Alignment explanation
Indices: 40174707--40174757 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 22
40174697 TTCTCTTAAA
40174707 CTCTCAATTTTC-TTCC-AAAAT
1 CTCTCAA-TTTCATTCCAAAAAT
40174728 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
40174751 CTCTCAA
1 CTCTCAA
40174758 ATCCATATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.15
22 18 0.67
23 5 0.19
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:40174835 original size:32 final size:32
Alignment explanation
Indices: 40174791--40174859 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
40174781 CCTCAATTTC
40174791 ATTTTTTAAAAATAATTTCAAATTTTTTTTAT
1 ATTTTTTAAAAATAATTTCAAATTTTTTTTAT
* *
40174823 ATTTTTTTAAAATAATTTTAAATTTTTTTTAT
1 ATTTTTTAAAAATAATTTCAAATTTTTTTTAT
40174855 ATTTT
1 ATTTT
40174860 CATCAATGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (32 bp):
ATTTTTTAAAAATAATTTCAAATTTTTTTTAT
Found at i:40175761 original size:21 final size:19
Alignment explanation
Indices: 40175733--40175771 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
40175723 TAACGAGGTA
40175733 AATTTTATATTACATTTTGG
1 AATTTTATA-TACATTTTGG
*
40175753 AATTGTTATATAGATTTTG
1 AATT-TTATATACATTTTG
40175772 TAAGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.13, T:0.54
Consensus pattern (19 bp):
AATTTTATATACATTTTGG
Found at i:40177382 original size:144 final size:144
Alignment explanation
Indices: 40177189--40178016 Score: 1146
Period size: 144 Copynumber: 5.9 Consensus size: 144
40177179 TTTATTTCAT
40177189 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAAACC-TAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCT-AACCTTAACCTAATTTAATTAAAAACCCTA
* * *
40177253 ACCCTAACCTAATTTATTTAAAAACCCTAACCCTACCCTAATTTAATTAAAAACCATAACCCTAA
65 ACCCTAACCTAATTTAATT-AAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAA
40177318 CCTAATTTAATT-AAA
129 CCTAATTTAATTAAAA
* * * *
40177333 ACCTTAACCTTAACCTAATTTAATTAAAAACCCTAACCGTACCCTAATTTAATT--AAA----AA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
* *
40177392 CCCTAACCTAATTTAATTAAAACCTTAACCCTAAACCTAACTTAATTAAAAACCCTAACCCTAAC
66 CCCTAACCTAATTTAATTAAAACCCTAACCCT-AACCTAATTTAATTAAAAACCCTAACCCTAA-
*
40177457 CCTAATTTAATT-GAA
129 CCTAATTTAATTAAAA
* *
40177472 ACCCTAACCCTAAACCTAATTTAATTGAAAACCCTAACCTTAACATAATTTAATTAAAAACCCTA
1 ACCCTAACCCT-AACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTA
* *
40177537 ACCCTAACCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTACC
65 ACCCTAACCTAATTTAATTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAAC
40177602 CTAATTTAATTAAAA
130 CTAATTTAATTAAAA
40177617 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
** **** * *
40177682 CATTAACCTAATTTAACCCTAACCCTAACCCTAACCTAATTTAATT-AAAACCCGAACCTTAACC
66 CCCTAACCTAATTTAATTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACC
40177746 TAATTTAATTAAAA
131 TAATTTAATTAAAA
* *
40177760 ACCCTAA-CCTAAAACCTAATTTATTTAAAAACCCTAACCTTAA-C--A--TAATT--TAACCCT
1 ACCCTAACCCT--AACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCT
*
40177817 AACCCTAACCTAATTTAATTAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA-CCTAA
64 AACCCTAACCTAATTTAATTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT-A
* *
40177881 ACTTAATTTATTTAAAA
128 ACCTAATTTAATTAAAA
40177898 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
* * *
40177963 CCCTACCCTAATTTAATT-AAA----AACCCTAACCTAATTTATTTAAAAATCCTAACC
66 CCCTAACCTAATTTAATTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
40178017 TAATTTTACC
Statistics
Matches: 609, Mismatches: 51, Indels: 52
0.86 0.07 0.07
Matches are distributed among these distances:
137 92 0.15
138 80 0.13
139 59 0.10
140 41 0.07
141 1 0.00
142 14 0.02
143 44 0.07
144 204 0.33
145 42 0.07
146 32 0.05
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.29
Consensus pattern (144 bp):
ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAA
CCCTAACCTAATTTAATTAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACC
TAATTTAATTAAAA
Found at i:40177817 original size:22 final size:22
Alignment explanation
Indices: 40177789--40177834 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
40177779 TTTATTTAAA
*
40177789 AACCCTAACCTTAACATAATTT
1 AACCCTAACCCTAACATAATTT
*
40177811 AACCCTAACCCTAACCTAATTT
1 AACCCTAACCCTAACATAATTT
40177833 AA
1 AA
40177835 TTAAAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.28
Consensus pattern (22 bp):
AACCCTAACCCTAACATAATTT
Found at i:40178016 original size:29 final size:29
Alignment explanation
Indices: 40177189--40177993 Score: 1105
Period size: 29 Copynumber: 28.3 Consensus size: 29
40177179 TTTATTTCAT
40177189 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177218 ACCCTAAACCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177247 ACCCTAACCCTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177276 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177305 ACCATAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
40177333 ACCTTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
40177362 ACCCTAACCGTACCCTAATTTAATT--AA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
40177389 A----AACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
40177413 ACCTTAACCCTAAACCTAACTTAATTAAAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAA
*
40177443 ACCCTAACCCTAACCCTAATTTAATT-GAA
1 ACCCTAACCCTAA-CCTAATTTAATTAAAA
*
40177472 ACCCTAACCCTAAACCTAATTTAATTGAAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAA
* *
40177502 ACCCTAACCTTAACATAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
40177531 ACCCTAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177559 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177588 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
40177617 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177646 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
** ****
40177675 ACCCTAACATTAACCTAATTTAA-CCCTA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
40177703 ACCCTAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
40177731 ACCCGAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177760 ACCCTAA-CCTAAAACCTAATTTATTTAAAA
1 ACCCTAACCCT--AACCTAATTTAATTAAAA
* *
40177790 ACCCTAACCTTAA-C--A--TAATT--TA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
40177812 ACCCTAACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177840 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
40177869 ACCCTAA-CCTAAACTTAATTTATTTAAAA
1 ACCCTAACCCT-AACCTAATTTAATTAAAA
40177898 ACCCTAACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177927 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
40177956 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
40177985 ACCCTAACC
1 ACCCTAACC
40177994 TAATTTATTT
Statistics
Matches: 692, Mismatches: 58, Indels: 52
0.86 0.07 0.06
Matches are distributed among these distances:
22 13 0.02
23 19 0.03
24 7 0.01
25 1 0.00
26 1 0.00
27 8 0.01
28 135 0.20
29 441 0.64
30 65 0.09
31 2 0.00
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (29 bp):
ACCCTAACCCTAACCTAATTTAATTAAAA
Found at i:40178077 original size:56 final size:56
Alignment explanation
Indices: 40178017--40178140 Score: 187
Period size: 56 Copynumber: 2.2 Consensus size: 56
40178007 AATCCTAACC
* * ** *
40178017 TAATTTTACCTAATTTGAT-AATCTTACTAACCATTAACACACTTTTTTGGGCTTAA
1 TAATTTTACATAATTTGATAAAT-TTACTAACCATTAACAAAAGTTATTGGGCTTAA
40178073 TAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTAA
1 TAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTAA
40178129 TAATTTTACATA
1 TAATTTTACATA
40178141 GCTTTACATA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
56 59 0.95
57 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.07, T:0.42
Consensus pattern (56 bp):
TAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTAA
Found at i:40181723 original size:29 final size:28
Alignment explanation
Indices: 40181663--40181725 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
40181653 GCGATTTCCC
*
40181663 AAAAAATGGACCATTCCGGTAAATAATC
1 AAAAAATGGACCATTCCGGTAAATAATA
* * **
40181691 AAAAAATCGGCCCATTTCGGTAAATTTTA
1 AAAAAAT-GGACCATTCCGGTAAATAATA
40181720 AAAAAA
1 AAAAAA
40181726 CAGCTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.48, C:0.16, G:0.13, T:0.24
Consensus pattern (28 bp):
AAAAAATGGACCATTCCGGTAAATAATA
Found at i:40186355 original size:24 final size:24
Alignment explanation
Indices: 40186271--40186368 Score: 76
Period size: 24 Copynumber: 4.0 Consensus size: 24
40186261 TTCGGGAATA
40186271 CTCATACGAG-CACTTAAACGGGAAG
1 CTCATACGAGCCA-TT-AACGGGAAG
* ** *
40186296 CTTATGTGAGCCATGTAACGGAAAG
1 CTCATACGAGCCAT-TAACGGGAAG
40186321 CTC-TGGA-GAGCCATTAACGGGAAG
1 CTCAT--ACGAGCCATTAACGGGAAG
* *
40186345 CTCATACGAGCCAATATCGGGAAG
1 CTCATACGAGCCATTAACGGGAAG
40186369 GTTCAAGTGA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.02
24 28 0.48
25 26 0.45
26 3 0.05
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
CTCATACGAGCCATTAACGGGAAG
Found at i:40186440 original size:25 final size:25
Alignment explanation
Indices: 40186303--40186448 Score: 88
Period size: 25 Copynumber: 5.8 Consensus size: 25
40186293 AAGCTTATGT
* * * *
40186303 GAGCCATGTAACGGAAAGCTCTGGA
1 GAGCCATATATCGGGAAGCTCTGAA
* *
40186328 GAGCCAT-TAACGGGAAGCTCAT-AC
1 GAGCCATATATCGGGAAGCTC-TGAA
* *
40186352 GAGCCA-ATATCGGGAAGGT-TCAA
1 GAGCCATATATCGGGAAGCTCTGAA
40186375 GTGAGCCA-ATATCGGGAAGCTCATGAAA
1 --GAGCCATATATCGGGAAGCTC-TG-AA
* * *
40186403 GAG-CTTTTAATCGAGAAGCTCTGAA
1 GAGCCATAT-ATCGGGAAGCTCTGAA
*
40186428 GAGCCATATATCGGGACGCTC
1 GAGCCATATATCGGGAAGCTC
40186449 ATAAGATTTG
Statistics
Matches: 95, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 28 0.29
25 42 0.44
26 9 0.09
27 12 0.13
28 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.28, T:0.19
Consensus pattern (25 bp):
GAGCCATATATCGGGAAGCTCTGAA
Found at i:40196311 original size:35 final size:34
Alignment explanation
Indices: 40196249--40196318 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 34
40196239 ATTTTATTTG
*
40196249 TTTAATTATATAATTAATGATATTTAAA-TATAA
1 TTTAATTATATAATTAATGATAATTAAATTATAA
*
40196282 TTTACATTATATGAATTTATGATAATTAAATTATAA
1 TTTA-ATTATAT-AATTAATGATAATTAAATTATAA
40196318 T
1 T
40196319 GATATTATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 4 0.12
34 7 0.22
35 15 0.47
36 6 0.19
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (34 bp):
TTTAATTATATAATTAATGATAATTAAATTATAA
Found at i:40196320 original size:25 final size:23
Alignment explanation
Indices: 40196276--40196336 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 23
40196266 TGATATTTAA
*
40196276 ATATAATTTACATTATATGA-ATTT
1 ATATAA-TTAAATTATATGATA-TT
40196300 ATGATAATTAAATTATAATGATATT
1 AT-ATAATTAAATTAT-ATGATATT
*
40196325 ATATTATTAAAT
1 ATATAATTAAAT
40196337 AAATCAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 19 0.59
25 12 0.38
26 1 0.03
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (23 bp):
ATATAATTAAATTATATGATATT
Found at i:40196326 original size:35 final size:34
Alignment explanation
Indices: 40196253--40196334 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 34
40196243 TATTTGTTTA
* *
40196253 ATTATATAATTAATGATATTTAAATATAATTTAC
1 ATTATATAATTAATGATAATTAAATATAATTGAC
* *
40196287 ATTATATGAATTTATGATAATTAAATTATAA-TGAT
1 ATTATAT-AATTAATGATAATTAAA-TATAATTGAC
*
40196322 ATTATATTATTAA
1 ATTATATAATTAA
40196335 ATAAATCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 11 0.28
35 24 0.60
36 5 0.12
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (34 bp):
ATTATATAATTAATGATAATTAAATATAATTGAC
Found at i:40196458 original size:7 final size:7
Alignment explanation
Indices: 40196448--40196474 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40196438 AAGATATTTA
40196448 TTATTAG
1 TTATTAG
40196455 TTATTAG
1 TTATTAG
40196462 TTATTAG
1 TTATTAG
40196469 TTATTA
1 TTATTA
40196475 TTAAGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (7 bp):
TTATTAG
Found at i:40197652 original size:12 final size:12
Alignment explanation
Indices: 40197635--40197671 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40197625 ATGTGAGGTA
*
40197635 AGTATTAATATT
1 AGTATTAATAAT
*
40197647 AGTATTAGTAAT
1 AGTATTAATAAT
40197659 AGTATTAATAAT
1 AGTATTAATAAT
40197671 A
1 A
40197672 ATAATATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (12 bp):
AGTATTAATAAT
Found at i:40197883 original size:24 final size:27
Alignment explanation
Indices: 40197846--40197909 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
40197836 AATTGCGGAT
*
40197846 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
40197870 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
40197896 TTGTGATTGAATTG
1 TAATGATTGAATTG
40197910 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:40217274 original size:14 final size:14
Alignment explanation
Indices: 40217253--40217286 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
40217243 CGGTATGGGT
40217253 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
40217266 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
40217280 TTATAGG
1 TTATAGG
40217287 CAAATGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:40229432 original size:13 final size:13
Alignment explanation
Indices: 40229416--40229440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40229406 AAAAATATTT
40229416 TAAAAATAAAAAA
1 TAAAAATAAAAAA
40229429 TAAAAATAAAAA
1 TAAAAATAAAAA
40229441 TATTTTTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:40232979 original size:9 final size:9
Alignment explanation
Indices: 40232965--40233031 Score: 89
Period size: 9 Copynumber: 7.4 Consensus size: 9
40232955 TTTGGTTAAA
40232965 AATTAACCG
1 AATTAACCG
*
40232974 AATTAACCA
1 AATTAACCG
*
40232983 AATTACCCG
1 AATTAACCG
40232992 AATTAACCG
1 AATTAACCG
* *
40233001 GATTACCCG
1 AATTAACCG
*
40233010 AATTACCCG
1 AATTAACCG
40233019 AATTAACCG
1 AATTAACCG
40233028 AATT
1 AATT
40233032 GAATCACTAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 50 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:40233005 original size:27 final size:27
Alignment explanation
Indices: 40232965--40233031 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
40232955 TTTGGTTAAA
40232965 AATTAACCGAATTAACCAAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
* * *
40232992 AATTAACCGGATTACCCGAATTACCCG
1 AATTAACCGAATTAACCAAATTACCCG
40233019 AATTAACCGAATT
1 AATTAACCGAATT
40233032 GAATCACTAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.24
Consensus pattern (27 bp):
AATTAACCGAATTAACCAAATTACCCG
Found at i:40233068 original size:8 final size:7
Alignment explanation
Indices: 40233055--40233104 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 7
40233045 ATTAAATTAT
40233055 TTTTAGA
1 TTTTAGA
40233062 CTTTTAGA
1 -TTTTAGA
40233070 TTTTAG-
1 TTTTAGA
40233076 TTTTAG-
1 TTTTAGA
40233082 TTTTAG-
1 TTTTAGA
40233088 TTTTAG-
1 TTTTAGA
40233094 TTTTAG-
1 TTTTAGA
40233100 TTTTA
1 TTTTA
40233105 TTTATTAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 29 0.69
7 6 0.14
8 7 0.17
ACGTcount: A:0.20, C:0.02, G:0.14, T:0.64
Consensus pattern (7 bp):
TTTTAGA
Found at i:40233081 original size:6 final size:6
Alignment explanation
Indices: 40233063--40233104 Score: 75
Period size: 6 Copynumber: 6.8 Consensus size: 6
40233053 ATTTTTAGAC
40233063 TTTTAG ATTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTA
1 TTTTAG -TTTTAG TTTTAG TTTTAG TTTTAG TTTTAG TTTTA
40233105 TTTATTAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 29 0.83
7 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (6 bp):
TTTTAG
Found at i:40233172 original size:18 final size:18
Alignment explanation
Indices: 40233132--40233175 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
40233122 AATTTTTATG
**
40233132 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
40233150 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
40233168 CTTGGGTT
1 ATTGGGTT
40233176 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:40234653 original size:6 final size:6
Alignment explanation
Indices: 40234642--40234672 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
40234632 CCCTCCCTAA
40234642 TTTCAC TTTCAC TTTCAC TTTCAC TTTCAC T
1 TTTCAC TTTCAC TTTCAC TTTCAC TTTCAC T
40234673 CACAATCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAC
Found at i:40235761 original size:37 final size:37
Alignment explanation
Indices: 40235652--40235763 Score: 170
Period size: 37 Copynumber: 3.0 Consensus size: 37
40235642 ATTTTAATTC
* *
40235652 AAGACTTATGTAATGTTTTTAGTTATGTAGTGATTCA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
40235689 AAGACTTATGTAATATTTTTAATTATGCAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
* *
40235726 AAGATTTATGTAATGCTTTTAATTATGTAGTGATTTA
1 AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
40235763 A
1 A
40235764 TTTGGATAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 67 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.46
Consensus pattern (37 bp):
AAGACTTATGTAATGTTTTTAATTATGTAGTGATTTA
Found at i:40235782 original size:9 final size:9
Alignment explanation
Indices: 40235770--40235830 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
40235760 TTAATTTGGA
40235770 TAATTCGGG
1 TAATTCGGG
*
40235779 TAATTTGGG
1 TAATTCGGG
*
40235788 TAATTTTCGGT
1 TAA--TTCGGG
40235799 TAATTCGGG
1 TAATTCGGG
*
40235808 TAAATCGGG
1 TAATTCGGG
* *
40235817 TAAATCGGA
1 TAATTCGGG
40235826 TAATT
1 TAATT
40235831 TTTAACCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
9 36 0.84
11 7 0.16
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (9 bp):
TAATTCGGG
Found at i:40235784 original size:18 final size:18
Alignment explanation
Indices: 40235761--40235830 Score: 59
Period size: 18 Copynumber: 3.8 Consensus size: 18
40235751 TGTAGTGATT
*
40235761 TAATTTGGATAATTCGGG
1 TAATTCGGATAATTCGGG
* * *
40235779 TAATTTGGGTAATTTTCGGT
1 TAATTCGGATAA--TTCGGG
* *
40235799 TAATTCGGGTAAATCGGG
1 TAATTCGGATAATTCGGG
*
40235817 TAAATCGGATAATT
1 TAATTCGGATAATT
40235831 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
18 26 0.62
20 16 0.38
ACGTcount: A:0.29, C:0.07, G:0.26, T:0.39
Consensus pattern (18 bp):
TAATTCGGATAATTCGGG
Found at i:40235802 original size:20 final size:18
Alignment explanation
Indices: 40235760--40235815 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 18
40235750 ATGTAGTGAT
*
40235760 TTAATTTGGATAATTCGG
1 TTAATTTGGGTAATTCGG
*
40235778 GTAATTTGGGTAATTTTCGG
1 TTAATTTGGGTAA--TTCGG
* *
40235798 TTAATTCGGGTAAATCGG
1 TTAATTTGGGTAATTCGG
40235816 GTAAATCGGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
18 15 0.48
20 16 0.52
ACGTcount: A:0.25, C:0.07, G:0.27, T:0.41
Consensus pattern (18 bp):
TTAATTTGGGTAATTCGG
Found at i:40235830 original size:38 final size:38
Alignment explanation
Indices: 40235760--40235832 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
40235750 ATGTAGTGAT
* * * * *
40235760 TTAATTTGGATAATTCGGGTAATTTGGGTAATTTTCGG
1 TTAATTCGGATAAATCGGGTAAATCGGATAATTTTCGG
*
40235798 TTAATTCGGGTAAATCGGGTAAATCGGATAATTTT
1 TTAATTCGGATAAATCGGGTAAATCGGATAATTTT
40235833 TAACCAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 29 1.00
ACGTcount: A:0.27, C:0.07, G:0.25, T:0.41
Consensus pattern (38 bp):
TTAATTCGGATAAATCGGGTAAATCGGATAATTTTCGG
Found at i:40237433 original size:30 final size:30
Alignment explanation
Indices: 40237368--40237439 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
40237358 ATGACGACGT
40237368 AGGCCCATCAACGAGGCCCAAAAATTCATC
1 AGGCCCATCAACGAGGCCCAAAAATTCATC
* * * * *
40237398 CGGCCCATCATC-AGCGCCCATAACTTTATC
1 AGGCCCATCAACGAG-GCCCAAAAATTCATC
*
40237428 AGGCCCAGCAAC
1 AGGCCCATCAAC
40237440 AGCACCGACA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
29 2 0.06
30 31 0.94
ACGTcount: A:0.31, C:0.38, G:0.17, T:0.15
Consensus pattern (30 bp):
AGGCCCATCAACGAGGCCCAAAAATTCATC
Found at i:40237846 original size:21 final size:21
Alignment explanation
Indices: 40237822--40237861 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
40237812 CTACCGGATG
*
40237822 AACCAAAATCCACGCCGGAGC
1 AACCAAAACCCACGCCGGAGC
* *
40237843 AACCACAACCCCCGCCGGA
1 AACCAAAACCCACGCCGGA
40237862 AGCTGGACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.45, G:0.17, T:0.03
Consensus pattern (21 bp):
AACCAAAACCCACGCCGGAGC
Found at i:40238037 original size:49 final size:49
Alignment explanation
Indices: 40237983--40238286 Score: 509
Period size: 49 Copynumber: 6.2 Consensus size: 49
40237973 TATATTAATG
* * *
40237983 TAATAAAAGACAAAATAGTTTATTTTGAATATTTTGATATTATTTGATA
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
* *
40238032 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTAATG
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
*
40238081 TAATAAAATACAAAATAGTTTATTTTGAATTTTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
* * *
40238130 TAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTATTTGATG
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
*
40238179 TAATAAAATACAAAATAGTTTATTTTGAATTTTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
*
40238228 TAATAAAATATAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
1 TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
40238277 TAATAAAATA
1 TAATAAAATA
40238287 ATGAATATTT
Statistics
Matches: 239, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 239 1.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (49 bp):
TAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTCATT
Found at i:40241503 original size:125 final size:124
Alignment explanation
Indices: 40241242--40241653 Score: 664
Period size: 125 Copynumber: 3.3 Consensus size: 124
40241232 CCCAAACATG
* * *
40241242 CTACTGTAGTAAAAATGCGTCCATGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
40241307 TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGGTTTTTTATACTATTTGCTCAGAAACGTCAACTAGAAATTATTTTTTCAGGAC
*
40241366 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
40241431 TTGAAGTGTTTTTTATACTATTTGCTCAGAAACGTCAACTAGAAATTATTTTTTCAGGAC
66 TTGAAG-GTTTTTTATACTATTTGCTCAGAAACGTCAACTAGAAATTATTTTTTCAGGAC
* * * *
40241491 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAACATCCTAC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
40241556 TTGAAGCGTTTTTTATACTATTTGCTCAGAAACATCAACTCA-AAATTATTTTTTCAGGAC
66 TTGAAG-GTTTTTTATACTATTTGCTCAGAAACGTCAACT-AGAAATTATTTTTTCAGGAC
* * *
40241616 CTACTTTAGCAAAAACGCGCCCACGTGGGAGTGATTTC
1 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTC
40241654 CTTAATAAAT
Statistics
Matches: 270, Mismatches: 16, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
124 67 0.25
125 202 0.75
126 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (124 bp):
CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGGTTTTTTATACTATTTGCTCAGAAACGTCAACTAGAAATTATTTTTTCAGGAC
Found at i:40241859 original size:6 final size:6
Alignment explanation
Indices: 40241848--40241873 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
40241838 AAAAATCCTA
40241848 AACCCT AACCCT AACCCT AACCCT AA
1 AACCCT AACCCT AACCCT AACCCT AA
40241874 AAACCCAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.38, C:0.46, G:0.00, T:0.15
Consensus pattern (6 bp):
AACCCT
Found at i:40258784 original size:12 final size:13
Alignment explanation
Indices: 40258758--40258785 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40258748 ACTTTTCCAC
40258758 AATACTTTTTAAA
1 AATACTTTTTAAA
40258771 AATACTTTTTAAA
1 AATACTTTTTAAA
40258784 AA
1 AA
40258786 CAATGCTAAA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AATACTTTTTAAA
Found at i:40262196 original size:3 final size:3
Alignment explanation
Indices: 40262184--40262213 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
40262174 CTAACCAAAA
40262184 CTT C-T CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
40262214 CTCAGTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:40265424 original size:27 final size:28
Alignment explanation
Indices: 40265364--40265425 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
40265354 AAGTCAACTA
40265364 CGAACCCCCAGTTCGCCAAACAAACTGG
1 CGAACCCCCAGTTCGCCAAACAAACTGG
* *
40265392 CAAACCCCCAGTTCG-C-AACTTAACTGG
1 CGAACCCCCAGTTCGCCAAAC-AAACTGG
40265419 CGAACCC
1 CGAACCC
40265426 ACCTGTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 3 0.10
27 13 0.43
28 14 0.47
ACGTcount: A:0.31, C:0.40, G:0.16, T:0.13
Consensus pattern (28 bp):
CGAACCCCCAGTTCGCCAAACAAACTGG
Found at i:40269436 original size:42 final size:42
Alignment explanation
Indices: 40269370--40269703 Score: 524
Period size: 42 Copynumber: 7.9 Consensus size: 42
40269360 AGCGTTTACA
*
40269370 AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * *
40269412 AAAAAAGCGCCTCTAAATACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* * *
40269454 AAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
40269496 AAAAAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
*
40269538 AAAAAAAAAGGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 --AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
40269582 AAAAAAAACGCCGCTAAAGACCATATTCTTTAGTGGCGCTTAG
1 -AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
40269625 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
* *
40269667 AAAAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCG
1 AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
40269704 TTTTTATACA
Statistics
Matches: 267, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
42 187 0.70
43 40 0.15
44 40 0.15
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG
Found at i:40269653 original size:171 final size:170
Alignment explanation
Indices: 40269369--40269703 Score: 544
Period size: 171 Copynumber: 2.0 Consensus size: 170
40269359 CAGCGTTTAC
* * *
40269369 AAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAGCGCCTCTAAATACCA
1 AAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCA
*
40269434 TGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAAA
66 TATTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAAA
*
40269499 AAAACGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
131 AAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
* *
40269539 AAAAAAAAGGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCGCTAAAGACC
1 AAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACC
* * * *
40269604 ATATTCTTTAGTGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
65 ATATTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAA
* *
40269669 AAAAACGCCGCTAAAGATCATGTTTTTTAGCGGCG
130 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
40269704 TTTTTATACA
Statistics
Matches: 151, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
170 41 0.27
171 110 0.73
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (170 bp):
AAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCA
TATTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGAACATGTTCTTTAACAGCGCTTAGAAA
AAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA
Found at i:40270072 original size:21 final size:21
Alignment explanation
Indices: 40270023--40270072 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
40270013 TTTTGGCCTG
*
40270023 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
40270044 TTCCGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
40270065 CTCTGCTT
1 CTCTGCTT
40270073 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.46, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:40275603 original size:9 final size:9
Alignment explanation
Indices: 40275585--40275809 Score: 179
Period size: 9 Copynumber: 24.8 Consensus size: 9
40275575 TGATATATTT
40275585 TTATGTAAG
1 TTATGTAAG
*
40275594 TTATGCAAG
1 TTATGTAAG
40275603 TTTATGTAAG
1 -TTATGTAAG
*
40275613 TTACT-TAAT
1 TTA-TGTAAG
40275622 TTATGTAAG
1 TTATGTAAG
40275631 TTATAG-AAG
1 TTAT-GTAAG
* *
40275640 TTATTTAAT
1 TTATGTAAG
*
40275649 TTATGTAGG
1 TTATGTAAG
40275658 TTATGTAAG
1 TTATGTAAG
* *
40275667 TTATTTAAT
1 TTATGTAAG
*
40275676 TTATGCAAG
1 TTATGTAAG
* *
40275685 TTTATGCATG
1 -TTATGTAAG
*
40275695 TTATGTAGG
1 TTATGTAAG
*
40275704 TTACT-TAAT
1 TTA-TGTAAG
40275713 TTATGTAAG
1 TTATGTAAG
40275722 TTATGTAAG
1 TTATGTAAG
* *
40275731 TTATTTAAT
1 TTATGTAAG
*
40275740 TTATGTAGG
1 TTATGTAAG
40275749 TTATGTAAG
1 TTATGTAAG
*
40275758 TTATGTAAC
1 TTATGTAAG
* *
40275767 TTATTTAAT
1 TTATGTAAG
40275776 TTAT-TCAAG
1 TTATGT-AAG
40275785 TTATGTAAG
1 TTATGTAAG
* * *
40275794 TAATTTAAT
1 TTATGTAAG
40275803 TTATGTA
1 TTATGTA
40275810 TAAGCTTGTA
Statistics
Matches: 170, Mismatches: 36, Indels: 20
0.75 0.16 0.09
Matches are distributed among these distances:
8 3 0.02
9 147 0.86
10 20 0.12
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:40279320 original size:114 final size:114
Alignment explanation
Indices: 40279113--40279329 Score: 251
Period size: 114 Copynumber: 1.9 Consensus size: 114
40279103 ATTAAGTTTC
* * *
40279113 TTGCGGCGTTTTAATCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTCCAAATAAGCGCCA
1 TTGCGGCGTCTTAAGCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
* ** * *
40279178 CTAATGAATCTATACGTGTAGTCGAAACGATGCGTTTCCCTAAGAAATT
66 CTAATGAAGCTATACGTCAAGACCAAACGATGCGTTTCCCTAAGAAATT
* ** *
40279227 TTGCGGCG-CTTAAGCATAAGCGCCACTAAAAGCTGATATTCAGCGGCGTTTACGGATAAGCGTC
1 TTGCGGCGTCTTAAGCAAAAGCGCCACTAAAAGCTGATA-TCAGCGGCGTTTACAAATAAGCGCC
* * *
40279291 AGTAAATG-CGCTATA-GCTCAAGACCAAACGTTGCGTTTC
65 ACT-AATGAAGCTATACG-TCAAGACCAAACGATGCGTTTC
40279330 GGTTTCATAT
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
113 28 0.33
114 53 0.62
115 4 0.05
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (114 bp):
TTGCGGCGTCTTAAGCAAAAGCGCCACTAAAAGCTGATATCAGCGGCGTTTACAAATAAGCGCCA
CTAATGAAGCTATACGTCAAGACCAAACGATGCGTTTCCCTAAGAAATT
Found at i:40279598 original size:116 final size:114
Alignment explanation
Indices: 40279475--40279691 Score: 344
Period size: 115 Copynumber: 1.9 Consensus size: 114
40279465 TTTTCCCTAG
*** * * *
40279475 CGCCGCTAATAATGTGCTTTAGCGGCGTTTTTTATAGAAACGCCACCAATTCTACTATACCTCAA
1 CGCCGCTAATAATCCACTTCAGCGGCG-TTTTTATAGAAACGCCACAAATTCAACTATACCTCAA
40279540 TCTTGTACGCTGCGTTTTGTTTAACATTTTTTTGCGGCGCTTACAAACAAA
65 TCTTGTACGCTGCGTTTTGTTTAACA-TTTTTTGCGGCGCTTACAAACAAA
* *
40279591 CGCCGCTAATGATCCACTTCAGCGGCGTTTTTATAGAAACGTCACAAATTCAACTATACCTCAAT
1 CGCCGCTAATAATCCACTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCAACTATACCTCAAT
40279656 CTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
66 CTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGC
40279692 ATTTTTACAG
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
114 11 0.12
115 60 0.65
116 22 0.24
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (114 bp):
CGCCGCTAATAATCCACTTCAGCGGCGTTTTTATAGAAACGCCACAAATTCAACTATACCTCAAT
CTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCGCTTACAAACAAA
Found at i:40279735 original size:75 final size:75
Alignment explanation
Indices: 40279612--40279766 Score: 247
Period size: 75 Copynumber: 2.1 Consensus size: 75
40279602 ATCCACTTCA
* * * *
40279612 GCGGCGTTTTTATAGAAACGTCACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCATTTTTACAGAAACGCCACAAATTCAACCATACCTCAATCTTGTACGCTGCGTTTTGTTT
40279677 AACATTTTTT
66 AACATTTTTT
** *
40279687 GCGGCATTTTTACAGAAACGCCATTAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCATTTTTACAGAAACGCCACAAATTCAACCATACCTCAATCTTGTACGCTGCGTTTTGTTT
40279752 AACATTTTTT
66 AACATTTTTT
40279762 GCGGC
1 GCGGC
40279767 GCTTACAAGC
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (75 bp):
GCGGCATTTTTACAGAAACGCCACAAATTCAACCATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTT
Found at i:40279838 original size:189 final size:190
Alignment explanation
Indices: 40279503--40279880 Score: 614
Period size: 189 Copynumber: 2.0 Consensus size: 190
40279493 TTAGCGGCGT
* * *
40279503 TTTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATT
1 TTTTTACAGAAACGCCACCAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATT
* * *
40279568 TTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTTATAGAAACGT
66 TTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAGAAACGC
* *
40279633 CACAAATTCAACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTGCGGCA
131 CACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCA
**
40279693 TTTTTACAGAAACGCCATTAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTTAACA-T
1 TTTTTACAGAAACGCCACCAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATT
* * *
40279757 TTTTTGCGGCGCTTACAAGCAAATGCTGCTAATGATCCACTTCAGCGGCGTTTTGACAGAAACGC
66 TTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAGAAACGC
* *
40279822 CACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGC
131 CACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGC
40279881 GCTTACAAAC
Statistics
Matches: 173, Mismatches: 15, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
189 115 0.66
190 58 0.34
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (190 bp):
TTTTTACAGAAACGCCACCAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATT
TTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAGAAACGC
CACAAATTCAACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCA
Found at i:40279887 original size:114 final size:114
Alignment explanation
Indices: 40279687--40280242 Score: 862
Period size: 114 Copynumber: 4.9 Consensus size: 114
40279677 AACATTTTTT
* ** * *
40279687 GCGGCATTTTTACAGAAACGCCATTAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
40279752 AACATTTTTTGCGGCGCTTACAAGCAAATGCTGCTAATGATCCACTTCA
66 AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATCCACTTCA
* *
40279801 GCGGCGTTTTGACAGAAACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
40279866 AACATTTTTTACGGCGCTTACAAACAAATGTCGCTAATGATACACTTCA
66 AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATCCACTTCA
* * *
40279915 GTGGCG-TTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGTTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
40279979 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTATTTATCCACTTCA
66 AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATCCACTTCA
*
40280028 GCGGCGTTTTTATAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
40280093 AACATTTTTTACGGCGCTTACAAATAAATGCCGCTAATGATCCACTCCA
66 AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATCCACTTCA
* * *
40280142 GCGGTGTTTTTATAAAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* *
40280207 AACATTGTTTGCGGCGCTTACAAACAAACGCCGCTA
66 AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTA
40280243 CTGCCACTAT
Statistics
Matches: 402, Mismatches: 39, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
113 102 0.25
114 300 0.75
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (114 bp):
GCGGCGTTTTTACAGAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTTGCGGCGCTTACAAACAAATGCCGCTAATGATCCACTTCA
Found at i:40280089 original size:227 final size:228
Alignment explanation
Indices: 40279687--40280242 Score: 889
Period size: 227 Copynumber: 2.4 Consensus size: 228
40279677 AACATTTTTT
* ** * *
40279687 GCGGCATTTTTACAGAAACGCCATTAATTCCACCATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * *
40279752 AACATTTTTTGCGGCGCTTACAAGCAAATGCTGCTAATGATCCACTTCAGCGGCGTTTTGACAGA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAGA
40279817 AACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCG
131 AACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCG
* *
40279882 CTTACAAACAAATGTCGCTAATGATACACTTCA
196 CTTACAAACAAATGCCGCTAATGATACACTCCA
* *
40279915 GTGGCG-TTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGTTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
* * * *
40279979 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTATTTATCCACTTCAGCGGCGTTTTTATAGA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAGA
*
40280044 AACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCG
131 AACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCG
* *
40280109 CTTACAAATAAATGCCGCTAATGATCCACTCCA
196 CTTACAAACAAATGCCGCTAATGATACACTCCA
* * * *
40280142 GCGGTGTTTTTATAAAAACGCCACCAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
1 GCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
*
40280207 AACATTGTTTGCGGCGCTTACAAACAAACGCCGCTA
66 AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTA
40280243 CTGCCACTAT
Statistics
Matches: 301, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
227 208 0.69
228 93 0.31
ACGTcount: A:0.26, C:0.25, G:0.16, T:0.33
Consensus pattern (228 bp):
GCGGCGTTTTTACAGAAACGCCACAAATTCTACTATACCTCAATCTTGTACGCTGCGTTTTGTTT
AACATTTTTTGCGGCGCTTACAAACAAACGCCGCTAATGATCCACTTCAGCGGCGTTTTGACAGA
AACGCCACCAATTCTACTATACCTCAATCCTGTACGCTGCGTTTTGTTTAACATTTTTTACGGCG
CTTACAAACAAATGCCGCTAATGATACACTCCA
Found at i:40283662 original size:43 final size:45
Alignment explanation
Indices: 40283536--40283662 Score: 102
Period size: 42 Copynumber: 2.8 Consensus size: 45
40283526 AAAGATTGCT
40283536 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTGACAACTTAAA
1 TATGTAAGCTATATTTAAATTTTATTAATAAT--ATT-ACAACTTAAA
* * * * **
40283584 TAAGTATTA-CTATATTTTTAATATTA-TACAT-ATATT-C-ATTTACG
1 TATGTA--AGCTATA-TTTAAATTTTATTA-ATAATATTACAACTTAAA
40283628 TATGTAAGCTATATTTAAATTTTATTAATAATATT
1 TATGTAAGCTATATTTAAATTTTATTAATAATATT
40283663 TAAACATATT
Statistics
Matches: 63, Mismatches: 9, Indels: 19
0.69 0.10 0.21
Matches are distributed among these distances:
42 12 0.19
43 12 0.19
44 9 0.14
45 1 0.02
47 3 0.05
48 5 0.08
49 9 0.14
50 12 0.19
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (45 bp):
TATGTAAGCTATATTTAAATTTTATTAATAATATTACAACTTAAA
Found at i:40288021 original size:21 final size:21
Alignment explanation
Indices: 40287995--40288041 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
40287985 CTACAACTTA
* *
40287995 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAACGAGGG
40288016 AAGCAGAGGCCGCAACGAGGG
1 AAGCAGAGGCCGCAACGAGGG
40288037 AAGCA
1 AAGCA
40288042 AAGCAGACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.45, T:0.00
Consensus pattern (21 bp):
AAGCAGAGGCCGCAACGAGGG
Found at i:40288501 original size:43 final size:43
Alignment explanation
Indices: 40288450--40288571 Score: 192
Period size: 42 Copynumber: 2.9 Consensus size: 43
40288440 TAAGAATAAA
40288450 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAG
* *
40288493 CGCCGCTAACGAACATAGTCTTTAGCGGCG-TTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAG
** *
40288535 CGATGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT
40288572 CAAAGGCGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 37 0.52
43 34 0.48
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCTAAG
Found at i:40288605 original size:98 final size:100
Alignment explanation
Indices: 40288476--40288667 Score: 316
Period size: 98 Copynumber: 1.9 Consensus size: 100
40288466 GGTCTTTAGC
* *
40288476 GGCGTTTTTTTTCTAAGCGCCGCTAACGAACATAGTCTTTAGCGGCGTTTTTTTCTAAGCGATGC
1 GGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATAGTCTTTAGCGGCGTTTTTTTCTAAGCGACGC
40288541 TAAAGAACATGGTCTTTAGAGGCGTTTTTTTCAAA
66 TAAAGAACATGGTCTTTAGAGGCGTTTTTTTCAAA
* * *
40288576 GGCG-TTTTTTT-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTGAGCGCCGC
1 GGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATAGTCTTTAGCGGCGTTTTTTTCTAAGCGACGC
*
40288639 TAAAGAACATGGTCTTTAGCGGCGTTTTT
66 TAAAGAACATGGTCTTTAGAGGCGTTTTT
40288668 GTTTGTAAAC
Statistics
Matches: 86, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
98 75 0.87
99 7 0.08
100 4 0.05
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (100 bp):
GGCGTTTTTTTTCTAAGCGCCGCTAAAGAACATAGTCTTTAGCGGCGTTTTTTTCTAAGCGACGC
TAAAGAACATGGTCTTTAGAGGCGTTTTTTTCAAA
Found at i:40288606 original size:56 final size:57
Alignment explanation
Indices: 40288519--40288628 Score: 186
Period size: 56 Copynumber: 1.9 Consensus size: 57
40288509 AGTCTTTAGC
*
40288519 GGCGTTTTTTTCTAAGCGATGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCAAA
1 GGCGTTTTTTTCTAAGCGACGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCAAA
* *
40288576 GGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTC
1 GGCGTTTTTTTCTAAGCGACGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTC
40288629 TGAGCGCCGC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
56 39 0.78
57 11 0.22
ACGTcount: A:0.21, C:0.16, G:0.24, T:0.39
Consensus pattern (57 bp):
GGCGTTTTTTTCTAAGCGACGCTAAAGAACATGGTCTTTAGAGGCGTTTTTTTCAAA
Found at i:40288635 original size:42 final size:41
Alignment explanation
Indices: 40288576--40288667 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 41
40288566 TTTTTTCAAA
40288576 GGCGTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTAGC
1 GGCGTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTAGC
*
40288617 GGCGTTTTTTTCTGAGCGCCGCTAAAGAACATGGTCTTTAGC
1 GGCGTTTTTTT-TAAGCGCCGCTAAAGAACATGGTCTTTAGC
40288659 GGCGTTTTT
1 GGCGTTTTT
40288668 GTTTGTAAAC
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 11 0.22
42 38 0.78
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (41 bp):
GGCGTTTTTTTTAAGCGCCGCTAAAGAACATGGTCTTTAGC
Found at i:40289641 original size:16 final size:16
Alignment explanation
Indices: 40289611--40289647 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
40289601 AAAAAAATAA
40289611 AAAAAATAAAAAATTT
1 AAAAAATAAAAAATTT
* *
40289627 AAAAAATATATAATTT
1 AAAAAATAAAAAATTT
40289643 AAAAA
1 AAAAA
40289648 GATTGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATAAAAAATTT
Found at i:40302613 original size:18 final size:19
Alignment explanation
Indices: 40302574--40302614 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
40302564 GTTTTTTTAA
*
40302574 TTTTGTTAGGTTTAAGGTT
1 TTTTGTTAGGTTTAAGGAT
40302593 TTTTGTTAAGG-TT-AGGAT
1 TTTTGTT-AGGTTTAAGGAT
40302611 TTTT
1 TTTT
40302615 AAGGGTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 8 0.40
19 9 0.45
20 3 0.15
ACGTcount: A:0.17, C:0.00, G:0.24, T:0.59
Consensus pattern (19 bp):
TTTTGTTAGGTTTAAGGAT
Found at i:40306746 original size:11 final size:9
Alignment explanation
Indices: 40306716--40306754 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
40306706 AATTTAAAAC
40306716 AGAACTTGAG
1 AGAA-TTGAG
40306726 AGAATTGAG
1 AGAATTGAG
*
40306735 AGAATTAAG
1 AGAATTGAG
*
40306744 AGAGTTGAG
1 AGAATTGAG
40306753 AG
1 AG
40306755 TTTAGAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 22 0.85
10 4 0.15
ACGTcount: A:0.44, C:0.03, G:0.33, T:0.21
Consensus pattern (9 bp):
AGAATTGAG
Found at i:40308719 original size:46 final size:44
Alignment explanation
Indices: 40308645--40308769 Score: 146
Period size: 44 Copynumber: 2.8 Consensus size: 44
40308635 CCACTAAATA
*
40308645 TTTAATTAAATTACATAGTATCTATTATAAATTATTAAAAACGAAT
1 TTTAATTAAATTACATAGTATTTATTAT-AATTATT-AAAACGAAT
* * * * *
40308691 TTTAACTAAATTACATAGTATTTGTTATAATTATTCATACTAAT
1 TTTAATTAAATTACATAGTATTTATTATAATTATTAAAACGAAT
* *
40308735 TTTAATTAAATTATATAGTATTCATTAT--TTATTAA
1 TTTAATTAAATTACATAGTATTTATTATAATTATTAA
40308770 GACTTAGCTA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 6 0.09
44 30 0.44
45 7 0.10
46 25 0.37
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (44 bp):
TTTAATTAAATTACATAGTATTTATTATAATTATTAAAACGAAT
Found at i:40319211 original size:32 final size:32
Alignment explanation
Indices: 40319175--40319260 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
40319165 ACTTTTTCGA
* *
40319175 AAAATATTTTCAGGAAATC-TGCCAAACAGCAG
1 AAAATATTTTCAGCAAATCAT-CCAAACACCAG
*
40319207 AAAATATTTTACA-CAGATTCATCCAAACACCAG
1 AAAATATTTT-CAGCA-AATCATCCAAACACCAG
*
40319240 AAAATATTTTCAGTAAATCAT
1 AAAATATTTTCAGCAAATCAT
40319261 TTTCTAGAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
32 18 0.40
33 26 0.58
34 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (32 bp):
AAAATATTTTCAGCAAATCATCCAAACACCAG
Found at i:40319276 original size:20 final size:20
Alignment explanation
Indices: 40319251--40319290 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40319241 AAATATTTTC
* *
40319251 AGTAAATCATTTTCTAGAAA
1 AGTAAATCACTTTCCAGAAA
40319271 AGTAAATCACTTTCCAGAAA
1 AGTAAATCACTTTCCAGAAA
40319291 TTATTTTACG
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:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (20 bp):
AGTAAATCACTTTCCAGAAA
Found at i:40322587 original size:69 final size:66
Alignment explanation
Indices: 40322490--40322620 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 66
40322480 TTCAAATAAG
** *
40322490 AAAAGACAAAACTACATCGTTTTGATAAATGTTCACCTTTTCTAAATTAAAAGTCAAAATCATTA
1 AAAAGACAAAACTACATCGTTTTGATAAA-GTTCA-CTCAT-TAAATTAAAAGGCAAAATCATTA
40322555 AGTT
63 AGTT
* *
40322559 AAAAGACAAAACTACGA-CGTTTTGATAAAGTTTACTCATTAAGTTAAAAGGCAAAATCATTA
1 AAAAGACAAAACTAC-ATCGTTTTGATAAAGTTCACTCATTAAATTAAAAGGCAAAATCATTA
40322621 TATTGTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
66 21 0.38
67 3 0.05
68 4 0.07
69 27 0.48
70 1 0.02
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.31
Consensus pattern (66 bp):
AAAAGACAAAACTACATCGTTTTGATAAAGTTCACTCATTAAATTAAAAGGCAAAATCATTAAGT
T
Done.