Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold39
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: 4724573
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 178835 characters in sequence are not A, C, G, or T
File 20 of 27
Found at i:3374815 original size:83 final size:84
Alignment explanation
Indices: 3374700--3374981 Score: 277
Period size: 83 Copynumber: 3.4 Consensus size: 84
3374690 TGGGAAATAG
* * ** *
3374700 CCTTTATCCATTATTTACCTGTCGGCTTAGTCCCTAATAAACCTTATCTTTCCTTGGTGGCCTGT
1 CCTTCATCCATTATTTACCTATCGGCTTAGTCCCTAATAAACCCCATCTCTCCTTGGTGGCCTGT
* * *
3374765 CAGCTCTGTCTCTGATC-A
66 CAGCTCAGTCTCCGACCAA
* * * * *
3374783 CCTTCATCCTTTATTTACCTATCGACTTAGTCCTTAGTAAACCCCATCTCTCCTTGGTGGCTTGT
1 CCTTCATCCATTATTTACCTATCGGCTTAGTCCCTAATAAACCCCATCTCTCCTTGGTGGCCTGT
*
3374848 CAGCTCAGTCTCCGGCCAA
66 CAGCTCAGTCTCCGACCAA
* * * *
3374867 TCTTCATCCATTATTTACCTATTGGCTTAGTCCCAAAT-AACCCC--CTC-CCTTATGGTGACCT
1 CCTTCATCCATTATTTACCTATCGGCTTAGTCCCTAATAAACCCCATCTCTCC-T-TGGTGGCCT
* * **
3374928 GTCAGCTTAGTCTTCGGTCAA
64 GTCAGCTCAGTCTCCGACCAA
* * * *
3374949 CCTTCATCTATTGTTTACCTGTCAGCTTAGTCC
1 CCTTCATCCATTATTTACCTATCGGCTTAGTCC
3374982 TTGGTAAACT
Statistics
Matches: 164, Mismatches: 32, Indels: 7
0.81 0.16 0.03
Matches are distributed among these distances:
80 2 0.01
81 4 0.02
82 52 0.32
83 74 0.45
84 32 0.20
ACGTcount: A:0.18, C:0.31, G:0.14, T:0.37
Consensus pattern (84 bp):
CCTTCATCCATTATTTACCTATCGGCTTAGTCCCTAATAAACCCCATCTCTCCTTGGTGGCCTGT
CAGCTCAGTCTCCGACCAA
Found at i:3375073 original size:84 final size:84
Alignment explanation
Indices: 3374912--3375088 Score: 214
Period size: 84 Copynumber: 2.1 Consensus size: 84
3374902 AATAACCCCC
* * * *
3374912 TCCCTTATGGTGACCTGTCAGCTTAGTCTTCGGTCAACCTTCATCTATTGTTTACCTGTCAGCTT
1 TCCCTTATGGTGACCTGTCAGCTCAGTCTTCAGTCAACCTTCATCCATTGTTTACCTGTCAGCTC
***
3374977 AGTCCTTGGTAAA-CTTAT
66 AGTCCCCCGTAAACCTTAT
* * * *
3374995 TACCCTTATGGTGACCTGTTAGCTCAGTC-TCTAGTCAGCCTTCATCCATTGTTTACTTGTCGGC
1 T-CCCTTATGGTGACCTGTCAGCTCAGTCTTC-AGTCAACCTTCATCCATTGTTTACCTGTCAGC
3375059 TCAGTCCCCCGTAAACCCTTAT
64 TCAGTCCCCCGTAAA-CCTTAT
3375081 TCCCTTAT
1 TCCCTTAT
3375089 TGACTTGTCG
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
83 3 0.04
84 63 0.80
85 7 0.09
86 6 0.08
ACGTcount: A:0.18, C:0.29, G:0.16, T:0.38
Consensus pattern (84 bp):
TCCCTTATGGTGACCTGTCAGCTCAGTCTTCAGTCAACCTTCATCCATTGTTTACCTGTCAGCTC
AGTCCCCCGTAAACCTTAT
Found at i:3376728 original size:32 final size:30
Alignment explanation
Indices: 3376692--3376750 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
3376682 GAAATCAAAT
3376692 ACAAAGAGCT-TAGAAAAATAATAACAATATGA
1 ACAAA-AGCTCTAGAAAAAT-ATAA-AATATGA
*
3376724 ACAAAAGCTCTTGAAAAATATAAAATA
1 ACAAAAGCTCTAGAAAAATATAAAATA
3376751 CTTTGATCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 4 0.16
31 8 0.32
32 13 0.52
ACGTcount: A:0.59, C:0.10, G:0.10, T:0.20
Consensus pattern (30 bp):
ACAAAAGCTCTAGAAAAATATAAAATATGA
Found at i:3377047 original size:13 final size:13
Alignment explanation
Indices: 3377029--3377054 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3377019 CAATTTTTTG
3377029 TGTATCGATACAT
1 TGTATCGATACAT
3377042 TGTATCGATACAT
1 TGTATCGATACAT
3377055 ACTTTGGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3377051 original size:33 final size:33
Alignment explanation
Indices: 3377009--3377073 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3376999 TACAAGCCAA
* *
3377009 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
3377042 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
3377074 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:3377529 original size:42 final size:43
Alignment explanation
Indices: 3377482--3377564 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 43
3377472 AAAGGGGGAG
3377482 AAATTTTTGAAAATAAATTTTTATCAAG-GGGAGAAAATTTCA
1 AAATTTTTGAAAATAAATTTTTATCAAGAGGGAGAAAATTTCA
3377524 AAATTTTTGAAAATAAATTTTTATCAAGAGGGAGAAAATTT
1 AAATTTTTGAAAATAAATTTTTATCAAGAGGGAGAAAATTT
3377565 TTTAACGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 28 0.70
43 12 0.30
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.36
Consensus pattern (43 bp):
AAATTTTTGAAAATAAATTTTTATCAAGAGGGAGAAAATTTCA
Found at i:3379089 original size:10 final size:9
Alignment explanation
Indices: 3379058--3379099 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
3379048 CATCATTCTT
3379058 CAAAAAAAA
1 CAAAAAAAA
*
3379067 -AACAAAAA
1 CAAAAAAAA
*
3379075 CAAAAAAAC
1 CAAAAAAAA
3379084 CAAAAAAAA
1 CAAAAAAAA
3379093 CAAAAAA
1 CAAAAAA
3379100 TGAGGGGTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 7 0.25
9 21 0.75
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:3380454 original size:28 final size:29
Alignment explanation
Indices: 3380419--3380739 Score: 376
Period size: 28 Copynumber: 11.4 Consensus size: 29
3380409 AAAGCCTAGT
3380419 AGTCAGTGGCATCCTTTCAAAAG-CCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
**
3380447 AGGT-AGTGGCA-CCTTTTTAAAGCCCACA
1 A-GTCAGTGGCATCCTTTCAAAAGCCCACA
* * *
3380475 AGTTAATGGAATCCTTTCAAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
3380504 AGTCAGTGGCATCCTTTC-AAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
*
3380532 AGTAAGTGGCATCCTTTC-AAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
* *
3380560 AGTCAATGGCATTCTTTCAAAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
3380589 AGTCAGTGGCATCCTTTC-AAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
3380617 AGTCAGTGGCA-CCTTTC-AAAGCCCACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
* * *
3380644 AGTTAGTGGCA-CATTTCAAAAGCCAACA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
* ** *
3380672 AGTCAATGGCAT-CTTTCAAAAGCTAATA
1 AGTCAGTGGCATCCTTTCAAAAGCCCACA
* * *
3380700 AGTTAATGGCA-CCTTTTCAAAAGCCAACA
1 AGTCAGTGGCATCC-TTTCAAAAGCCCACA
*
3380729 AGTCAATGGCA
1 AGTCAGTGGCA
3380740 CCCCTTTTCA
Statistics
Matches: 257, Mismatches: 27, Indels: 17
0.85 0.09 0.06
Matches are distributed among these distances:
27 42 0.16
28 134 0.52
29 81 0.32
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (29 bp):
AGTCAGTGGCATCCTTTCAAAAGCCCACA
Found at i:3380513 original size:57 final size:57
Alignment explanation
Indices: 3380425--3380741 Score: 346
Period size: 57 Copynumber: 5.6 Consensus size: 57
3380415 TAGTAGTCAG
* *
3380425 TGGCATCCTTTCAAAAG-CCACAAGGT-AGTGGCACCTTTTTAAAGCCCACAAGTTAA
1 TGGCATCCTTTCAAAAGCCCACAA-GTCAATGGCACCTTTTAAAAGCCCACAAGTTAA
* * *
3380481 TGGAATCCTTTCAAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAG-TAA
1 TGGCATCCTTTCAAAAGCCCACAAGTCAATGGCA-CCTTTTAAAAGCCCACAAGTTAA
* * * *
3380537 GTGGCATCCTTTC-AAAGCCCACAAGTCAATGGCATTCTTTCAAAAGCCCACAAGTCAG
1 -TGGCATCCTTTCAAAAGCCCACAAGTCAATGGCA-CCTTTTAAAAGCCCACAAGTTAA
* * *
3380595 TGGCATCCTTTC-AAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTTAG
1 TGGCATCCTTTCAAAAGCCCACAAGTCAATGGCACCTTTTAAAAGCCCACAAGTTAA
* * * * ** *
3380650 TGGCA-CATTTCAAAAGCCAACAAGTCAATGGCATCTTTCAAAAGCTAATAAGTTAA
1 TGGCATCCTTTCAAAAGCCCACAAGTCAATGGCACCTTTTAAAAGCCCACAAGTTAA
*
3380706 TGGCA-CCTTTTCAAAAGCCAACAAGTCAATGGCACC
1 TGGCATCC-TTTCAAAAGCCCACAAGTCAATGGCACC
3380742 CCTTTTCAAA
Statistics
Matches: 226, Mismatches: 26, Indels: 17
0.84 0.10 0.06
Matches are distributed among these distances:
54 5 0.02
55 42 0.19
56 64 0.28
57 112 0.50
58 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (57 bp):
TGGCATCCTTTCAAAAGCCCACAAGTCAATGGCACCTTTTAAAAGCCCACAAGTTAA
Found at i:3380554 original size:85 final size:83
Alignment explanation
Indices: 3380419--3380739 Score: 405
Period size: 85 Copynumber: 3.8 Consensus size: 83
3380409 AAAGCCTAGT
*
3380419 AGTCAGTGGCATCCTTTCAAAAG-CCACAAGGTAGTGGCACCTTTTTAAAGCCCACAAGTTAATG
1 AGTCAGTGGCATCCTTTC-AAAGCCCACAA-GTAGTGGCACC-TTTCAAAGCCCACAAGTTAATG
*
3380483 GAATCCTTTCAAAAGCCCACA
63 GCATCCTTTCAAAAGCCCACA
*
3380504 AGTCAGTGGCATCCTTTCAAAGCCCACAAGTAAGTGGCATCCTTTCAAAGCCCACAAGTCAATGG
1 AGTCAGTGGCATCCTTTCAAAGCCCACAAGT-AGTGGCA-CCTTTCAAAGCCCACAAGTTAATGG
*
3380569 CATTCTTTCAAAAGCCCACA
64 CATCCTTTCAAAAGCCCACA
*
3380589 AGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTTAGTGGC
1 AGTCAGTGGCATCCTTTCAAAGCCCACAAGT-AGTGGCACCTTTCAAAGCCCACAAGTTAATGGC
* *
3380654 A-CATTTCAAAAGCCAACA
65 ATCCTTTCAAAAGCCCACA
* ** * * * *
3380672 AGTCAATGGCAT-CTTTCAAAAGCTAATAAGTTAATGGCACCTTTTCAAAAGCCAACAAGTCAAT
1 AGTCAGTGGCATCCTTTC-AAAGCCCACAAG-TAGTGGCACC-TTTC-AAAGCCCACAAGTTAAT
3380736 GGCA
62 GGCA
3380740 CCCCTTTTCA
Statistics
Matches: 211, Mismatches: 18, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
82 5 0.02
83 42 0.20
84 36 0.17
85 126 0.60
86 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (83 bp):
AGTCAGTGGCATCCTTTCAAAGCCCACAAGTAGTGGCACCTTTCAAAGCCCACAAGTTAATGGCA
TCCTTTCAAAAGCCCACA
Found at i:3380792 original size:31 final size:31
Alignment explanation
Indices: 3380742--3380810 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 31
3380732 CAATGGCACC
*
3380742 CCTTT-TCAAAGTCTACACAAATTAGTGGCA
1 CCTTTGTCAAAGCCTACACAAATTAGTGGCA
* * *
3380772 CCTTTGTCAAAGCCTGCACAAGTTGGTGGCA
1 CCTTTGTCAAAGCCTACACAAATTAGTGGCA
*
3380803 CCTATGTC
1 CCTTTGTC
3380811 CGAGTCAAGT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
CCTTTGTCAAAGCCTACACAAATTAGTGGCA
Found at i:3382104 original size:12 final size:12
Alignment explanation
Indices: 3382087--3382140 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
3382077 AGGTTCAACT
3382087 AAAAAAAGAGAA
1 AAAAAAAGAGAA
*
3382099 AAAAAAAGAGTGA
1 AAAAAAAGAG-AA
**
3382112 AAAAAGGGAGAA
1 AAAAAAAGAGAA
*
3382124 AAAAAGGAGAGAA
1 AAAAA-AAGAGAA
3382137 AAAA
1 AAAA
3382141 TAGAAACAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
12 16 0.46
13 19 0.54
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (12 bp):
AAAAAAAGAGAA
Found at i:3382162 original size:24 final size:22
Alignment explanation
Indices: 3382088--3382166 Score: 61
Period size: 24 Copynumber: 3.4 Consensus size: 22
3382078 GGTTCAACTA
* * *
3382088 AAAAAAGAGAAAAAAAAAGAGTG
1 AAAAAATAG-AAAAAAAGGAGAG
*
3382111 AAAAAAGGGAGAAAAAAAGGAGAG
1 AAAAAA--TAGAAAAAAAGGAGAG
3382135 AAAAAATAGAAACAAAGAGGTAGA-
1 AAAAAATAGAAA-AAA-AGG-AGAG
3382159 AAAAAATA
1 AAAAAATA
3382167 AGGCTAGCTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
22 5 0.10
23 9 0.19
24 28 0.58
25 6 0.12
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.05
Consensus pattern (22 bp):
AAAAAATAGAAAAAAAGGAGAG
Found at i:3383946 original size:97 final size:97
Alignment explanation
Indices: 3383791--3384003 Score: 363
Period size: 97 Copynumber: 2.2 Consensus size: 97
3383781 AATTTTATTT
* * *
3383791 ATCAAGGATACTCCAACCCTATTCCTCCGAGGGGATACTCCAACCTCGCTTTTAAACACATCAAA
1 ATCAAGGACACTCCAACCCCATTCCTCCGAGGGAATACTCCAACCTCGCTTTTAAACACATCAAA
3383856 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* *
3383888 ATCAGGGACACTCCAACCCCATTCCTCTGAGGGAATACTCCAACCTCGCTTTTAAACACATCAAA
1 ATCAAGGACACTCCAACCCCATTCCTCCGAGGGAATACTCCAACCTCGCTTTTAAACACATCAAA
3383953 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* *
3383985 ATCACGGACACTCTAACCC
1 ATCAAGGACACTCCAACCC
3384004 TGTTTTTCAA
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 109 1.00
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.29
Consensus pattern (97 bp):
ATCAAGGACACTCCAACCCCATTCCTCCGAGGGAATACTCCAACCTCGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:3386927 original size:20 final size:20
Alignment explanation
Indices: 3386902--3386955 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3386892 GTTACAAGCA
*
3386902 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
3386922 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
3386942 ATGTATCGATACAA
1 ATGTATCGATACAA
3386956 ACAGTGCTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:3387028 original size:19 final size:18
Alignment explanation
Indices: 3386983--3387040 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
3386973 ACTGTTAGTT
*
3386983 TCATCTATCGATACAATTG
1 TCATGTATCGATACAA-TG
3387002 TCCATGTATCGATACAATG
1 T-CATGTATCGATACAATG
3387021 ATCATGTATCGATACAATG
1 -TCATGTATCGATACAATG
3387040 T
1 T
3387041 ATAGATGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
18 1 0.03
19 20 0.56
20 15 0.42
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (18 bp):
TCATGTATCGATACAATG
Found at i:3392881 original size:33 final size:33
Alignment explanation
Indices: 3392844--3392910 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3392834 TTCAACGATT
3392844 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3392877 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3392910 T
1 T
3392911 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3392882 original size:13 final size:13
Alignment explanation
Indices: 3392864--3392888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3392854 CATAAAATGT
3392864 TGTATCGATACAA
1 TGTATCGATACAA
3392877 TGTATCGATACA
1 TGTATCGATACA
3392889 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3392969 original size:13 final size:13
Alignment explanation
Indices: 3392951--3392975 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3392941 ATTACTCAAA
3392951 TGTATCGATACAT
1 TGTATCGATACAT
3392964 TGTATCGATACA
1 TGTATCGATACA
3392976 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3399928 original size:1 final size:1
Alignment explanation
Indices: 3399924--3399984 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
3399914 AAAAGTGATG
* * * * * * * *
3399924 AAAAAAAAAACAAACAAAAAAAACACACAAAAAAAAACAAAAAAAAAAACACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3399985 TGCAAAGGCA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:3399942 original size:13 final size:13
Alignment explanation
Indices: 3399926--3399983 Score: 77
Period size: 13 Copynumber: 4.6 Consensus size: 13
3399916 AAGTGATGAA
3399926 AAAAAAAACAAAC
1 AAAAAAAACAAAC
*
3399939 AAAAAAAACACAC
1 AAAAAAAACAAAC
3399952 AAAAAAAAACAAA-
1 -AAAAAAAACAAAC
3399965 AAAAAAAAC--AC
1 AAAAAAAACAAAC
3399976 AAAAAAAA
1 AAAAAAAA
3399984 ATGCAAAGGC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
10 1 0.02
11 8 0.20
12 9 0.22
13 12 0.29
14 11 0.27
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAC
Found at i:3399942 original size:14 final size:13
Alignment explanation
Indices: 3399924--3399984 Score: 86
Period size: 14 Copynumber: 4.5 Consensus size: 13
3399914 AAAAGTGATG
3399924 AAAAAAAAAACAA
1 AAAAAAAAAACAA
*
3399937 ACAAAAAAAACACA
1 AAAAAAAAAACA-A
*
3399951 CAAAAAAAAACAA
1 AAAAAAAAAACAA
3399964 AAAAAAAAACACAA
1 AAAAAAAAA-ACAA
3399978 AAAAAAA
1 AAAAAAA
3399985 TGCAAAGGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
13 20 0.48
14 22 0.52
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:3399984 original size:13 final size:12
Alignment explanation
Indices: 3399924--3399984 Score: 86
Period size: 12 Copynumber: 4.8 Consensus size: 12
3399914 AAAAGTGATG
3399924 AAAAAAAAAACA
1 AAAAAAAAAACA
3399936 AACAAAAAAAACA
1 AA-AAAAAAAACA
3399949 CACAAAAAAAAACA
1 -A-AAAAAAAAACA
3399963 AAAAAAAAAACA
1 AAAAAAAAAACA
*
3399975 CAAAAAAAAA
1 AAAAAAAAAA
3399985 TGCAAAGGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 6
0.87 0.02 0.12
Matches are distributed among these distances:
12 22 0.49
13 11 0.24
14 11 0.24
15 1 0.02
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:3399990 original size:26 final size:26
Alignment explanation
Indices: 3399924--3399984 Score: 106
Period size: 26 Copynumber: 2.3 Consensus size: 26
3399914 AAAAGTGATG
3399924 AAAAAAAAAACAAACAAAAAAAACAC
1 AAAAAAAAAACAAACAAAAAAAACAC
3399950 ACAAAAAAAAACAAA-AAAAAAAACAC
1 A-AAAAAAAAACAAACAAAAAAAACAC
3399976 AAAAAAAAA
1 AAAAAAAAA
3399985 TGCAAAGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
25 8 0.24
26 13 0.38
27 13 0.38
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAACAAACAAAAAAAACAC
Found at i:3399997 original size:26 final size:26
Alignment explanation
Indices: 3399925--3399984 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 26
3399915 AAAGTGATGA
3399925 AAAAAAAAACAAACAAAAAAAACACAC
1 AAAAAAAAACAAA-AAAAAAAACACAC
3399952 AAAAAAAAACAAAAAAAAAAACACA-
1 AAAAAAAAACAAAAAAAAAAACACAC
3399977 AAAAAAAA
1 AAAAAAAA
3399985 TGCAAAGGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 8 0.24
26 12 0.36
27 13 0.39
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (26 bp):
AAAAAAAAACAAAAAAAAAAACACAC
Found at i:3400243 original size:19 final size:18
Alignment explanation
Indices: 3400221--3400275 Score: 78
Period size: 17 Copynumber: 3.1 Consensus size: 18
3400211 ATTCTTTTCC
3400221 AAAAAAAGAAACAAAACAA
1 AAAAAAAGAAA-AAAACAA
3400240 AAAAAAAG-AAAAAA-AA
1 AAAAAAAGAAAAAAACAA
*
3400256 AAGAAAAGAAAAAAACAA
1 AAAAAAAGAAAAAAACAA
3400274 AA
1 AA
3400276 CAGAAAAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 9 0.27
17 10 0.30
18 6 0.18
19 8 0.24
ACGTcount: A:0.87, C:0.05, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAAAACAA
Found at i:3400251 original size:15 final size:14
Alignment explanation
Indices: 3400221--3400282 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 14
3400211 ATTCTTTTCC
* *
3400221 AAAAAAAGAAACAA
1 AAAAAAAAAAAGAA
3400235 AACAAAAAAAAAGAAA
1 AA-AAAAAAAAAG-AA
3400251 AAAAAAAGAAAAGAA
1 AAAAAAA-AAAAGAA
*
3400266 AAAAACAAAACAGAA
1 AAAAA-AAAAAAGAA
3400281 AA
1 AA
3400283 GCTCGATAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
14 2 0.05
15 28 0.68
16 11 0.27
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:3400252 original size:11 final size:11
Alignment explanation
Indices: 3400238--3400269 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
3400228 GAAACAAAAC
3400238 AAAAAAAAAGA
1 AAAAAAAAAGA
3400249 AAAAAAAAAGA
1 AAAAAAAAAGA
3400260 AAAGAAAAAA
1 AAA-AAAAAA
3400270 ACAAAACAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:3400257 original size:30 final size:31
Alignment explanation
Indices: 3400221--3400282 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
3400211 ATTCTTTTCC
3400221 AAAAAAAGAAACA-AAACAAAA-AAAA-AGAAA
1 AAAAAAAGAAA-AGAAA-AAAACAAAACAGAAA
3400251 AAAAAAAGAAAAGAAAAAAACAAAACAGAAA
1 AAAAAAAGAAAAGAAAAAAACAAAACAGAAA
3400282 A
1 A
3400283 GCTCGATAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
29 5 0.17
30 18 0.62
31 6 0.21
ACGTcount: A:0.85, C:0.06, G:0.08, T:0.00
Consensus pattern (31 bp):
AAAAAAAGAAAAGAAAAAAACAAAACAGAAA
Found at i:3400262 original size:16 final size:16
Alignment explanation
Indices: 3400221--3400270 Score: 68
Period size: 15 Copynumber: 3.2 Consensus size: 16
3400211 ATTCTTTTCC
*
3400221 AAAAAAAG-AAACAAA
1 AAAAAAAGAAAAGAAA
*
3400236 ACAAAAA-AAAAGAAA
1 AAAAAAAGAAAAGAAA
3400251 AAAAAAAGAAAAGAAA
1 AAAAAAAGAAAAGAAA
3400267 AAAA
1 AAAA
3400271 CAAAACAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.88, C:0.04, G:0.08, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAA
Found at i:3401333 original size:30 final size:31
Alignment explanation
Indices: 3401296--3401380 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 31
3401286 CAAATACCTT
3401296 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
* *
3401327 -TCAAAGTCCACGACTTAGTGGCATTTTTTC
1 TTCAAAGTCCACGACTCAGTGGCATTTTGTC
* * * *
3401357 TTTAAAGCCCACAACTCTGTGGCA
1 TTCAAAGTCCACGACTCAGTGGCA
3401381 CACTTTTTCT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
30 28 0.61
31 18 0.39
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (31 bp):
TTCAAAGTCCACGACTCAGTGGCATTTTGTC
Found at i:3401426 original size:70 final size:69
Alignment explanation
Indices: 3401350--3401869 Score: 641
Period size: 71 Copynumber: 7.7 Consensus size: 69
3401340 CTTAGTGGCA
* * * * **
3401350 TTTTTTCTTTAAAGCCCACAACTCTGTGGCACACTTTTT-CTTTTTAAAGCCCACAACTTTGTGG
1 TTTTTTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTCAAAGCCCACAACTCCGTGG
3401414 CACTC
66 CAC-C
* *
3401419 TTTTTTTCTTCT-AAGCCCACAACTCCGTGGCACT-TTTTTCATCTTT--AAGTCCACAACTCCG
1 TTTTTTT-TT-TAAAGCCCACAACTCCGTGGCACTCTTTTTCCT-TTTCAAAGCCCACAACTCCG
3401480 TGGCA-C
63 TGGCACC
*
3401486 ---TCTTTTT-AA---CACAACTCCGTGGCACTC----T--TTTT-AAAGCCCACAACTCCGTGG
1 TTTTTTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTCAAAGCCCACAACTCCGTGG
3401537 CACC
66 CACC
3401541 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGT
1 TTTTT-TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTTCAAAGCCCACAACTCCGT
3401606 GGCACC
64 GGCACC
3401612 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGT
1 TTTTT-TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTTCAAAGCCCACAACTCCGT
3401677 GGCACC
64 GGCACC
3401683 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGT
1 TTTTT-TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTTCAAAGCCCACAACTCCGT
3401748 GGCA-C
64 GGCACC
* * *
3401753 TTTTTTCTTTTAAAGCCCATAACTCCGTGGCACTCTTTTTCCCTCTTCAAAGCTCACAACTCCGT
1 TTTTTT-TTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTTCAAAGCCCACAACTCCGT
*
3401818 GGCACA
64 GGCACC
* *
3401824 TTTTTCTTTTAAAGCCCACAATTCCGTGGCACTCTTTTTCCCTTTT
1 TTTTTTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTTT
3401870 AAGTCCACAA
Statistics
Matches: 408, Mismatches: 18, Indels: 49
0.86 0.04 0.10
Matches are distributed among these distances:
53 3 0.01
54 20 0.05
55 1 0.00
56 1 0.00
58 1 0.00
59 22 0.05
60 2 0.00
62 3 0.01
63 20 0.05
64 3 0.01
67 2 0.00
69 29 0.07
70 129 0.32
71 172 0.42
ACGTcount: A:0.20, C:0.33, G:0.11, T:0.36
Consensus pattern (69 bp):
TTTTTTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTCAAAGCCCACAACTCCGTGG
CACC
Found at i:3401473 original size:34 final size:34
Alignment explanation
Indices: 3401350--3401889 Score: 542
Period size: 34 Copynumber: 15.9 Consensus size: 34
3401340 CTTAGTGGCA
* *
3401350 TTTTT-TCTTTAAAGCCCACAACTCTGTGGCACAC
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCAC-T
* **
3401384 TTTTTCTTTTTAAAGCCCACAACTTTGTGGCACT
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
*
3401418 CTTTTTTTCTTCT-AAGCCCACAACTCCGTGGCACT
1 -TTTTTCTCTT-TAAAGCCCACAACTCCGTGGCACT
*
3401453 TTTTTCATCTTT-AAGTCCACAACTCCGTGGCAC-
1 TTTTTC-TCTTTAAAGCCCACAACTCCGTGGCACT
*
3401486 ----TCT-TTTTAA---CACAACTCCGTGGCAC-
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
* *
3401511 ----TCTTTTTAAAGCCCACAACTCCGTGGCACC
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
*
3401541 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
* *
3401575 CTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1 -TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGCACT
*
3401612 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
* *
3401646 CTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACC
1 -TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGCACT
*
3401683 TTTTTCTTTTTAAAGCCCACAACTCCGTGGCACT
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
*
3401717 CTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACT
1 -TTTTTCTC-TTT-AAAGCCCACAACTCCGTGGCACT
*
3401754 TTTTTCT-TTTAAAGCCCATAACTCCGTGGCACT
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
* * *
3401787 CTTTTTCCCTCTTCAAAGCTCACAACTCCGTGGCACA
1 -TTTTT--CTCTTTAAAGCCCACAACTCCGTGGCACT
*
3401824 TTTTTCT-TTTAAAGCCCACAATTCCGTGGCACT
1 TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
* * * * *
3401857 CTTTTTCCCTTTTAAGTCCACAAGTCGGTGGCA
1 -TTTTTCTCTTTAAAGCCCACAACTCCGTGGCA
3401890 ACCACTCTCT
Statistics
Matches: 437, Mismatches: 40, Indels: 57
0.82 0.07 0.11
Matches are distributed among these distances:
25 19 0.04
26 5 0.01
27 3 0.01
28 3 0.01
29 18 0.04
33 44 0.10
34 120 0.27
35 101 0.23
36 35 0.08
37 89 0.20
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (34 bp):
TTTTTCTCTTTAAAGCCCACAACTCCGTGGCACT
Found at i:3401937 original size:30 final size:33
Alignment explanation
Indices: 3401875--3401937 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3401865 CTTTTAAGTC
3401875 CACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
1 CACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
3401908 CACAAGTCGGTGGCAACC-CT-TCT-AAGCCCA
1 CACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
3401938 ATATAGCCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 7 0.23
31 3 0.10
32 2 0.07
33 18 0.60
ACGTcount: A:0.29, C:0.37, G:0.19, T:0.16
Consensus pattern (33 bp):
CACAAGTCGGTGGCAACCACTCTCTAAAGCCCA
Found at i:3401988 original size:49 final size:49
Alignment explanation
Indices: 3401930--3402731 Score: 1048
Period size: 49 Copynumber: 16.7 Consensus size: 49
3401920 GCAACCCTTC
* * * * *
3401930 TAAGCCCAATATAGCCGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3401979 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3402028 TAAGTCCAATATAGCTGGTCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
3402077 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3402126 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3402175 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
3402224 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3402273 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * *
3402322 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
3402371 TAAGACCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3402420 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * *
3402463 TAAG-CCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
3402512 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-T-TT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * *
3402555 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
3402604 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * * * * *
3402647 TAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
*
3402696 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
3402732 ACATCCTTTT
Statistics
Matches: 655, Mismatches: 78, Indels: 40
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.00
43 109 0.17
44 1 0.00
45 3 0.00
47 3 0.00
48 1 0.00
49 534 0.82
50 2 0.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:3402480 original size:43 final size:43
Alignment explanation
Indices: 3402417--3402740 Score: 299
Period size: 43 Copynumber: 7.1 Consensus size: 43
3402407 GCACCTTCAT
* * *
3402417 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
3402460 CTTTAAG-CCTGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCC-AATATCGCTGGCCTTGAATCAGCACATTGGCA----C
* *
3402507 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
3402552 TTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C
* *
3402599 ATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
3402644 CTTTAAGCCCGATATCGCTGGCCTTGAATCAGCATATTGGCATCTTC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA----C
* * * *
3402691 ATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATC
1 --CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA-C
3402737 CTTT
1 CTTT
3402741 TTCTCATCTT
Statistics
Matches: 232, Mismatches: 29, Indels: 39
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.01
43 109 0.47
44 4 0.02
45 2 0.01
46 2 0.01
47 3 0.01
49 108 0.47
50 2 0.01
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:3402525 original size:92 final size:91
Alignment explanation
Indices: 3402384--3402740 Score: 606
Period size: 92 Copynumber: 3.9 Consensus size: 91
3402374 GACCAATGTA
* * * *
3402384 GCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAG
1 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
3402449 CACATTGGCACCTTTAAGCCTGATATC
66 CACATTGGCACCTTTAAGCC-GATATC
3402476 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
* *
3402541 CACATTGGCACTTTTAAGTCCAATATC
66 CACATTGGCACCTTTAAG-CCGATATC
3402568 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
3402633 CACATTGGCACCTTTAAGCCCGATATC
66 CACATTGGCACCTTTAAG-CCGATATC
*
3402660 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAATGTAGCTGGCCTTGAATCAG
1 GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
*
3402725 CACATTGACATCCTTT
66 CACATTGGCA-CCTTT
3402741 TTCTCATCTT
Statistics
Matches: 252, Mismatches: 11, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
92 245 0.97
93 7 0.03
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (91 bp):
GCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAG
CACATTGGCACCTTTAAGCCGATATC
Found at i:3403694 original size:33 final size:33
Alignment explanation
Indices: 3403657--3403723 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3403647 TTCAACGATT
3403657 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3403690 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3403723 T
1 T
3403724 TTAAGTTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3403695 original size:13 final size:13
Alignment explanation
Indices: 3403677--3403701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3403667 CATAAAATGT
3403677 TGTATCGATACAA
1 TGTATCGATACAA
3403690 TGTATCGATACA
1 TGTATCGATACA
3403702 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3403782 original size:13 final size:13
Alignment explanation
Indices: 3403764--3403788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3403754 ATTACTCAAA
3403764 TGTATCGATACAT
1 TGTATCGATACAT
3403777 TGTATCGATACA
1 TGTATCGATACA
3403789 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3410219 original size:20 final size:21
Alignment explanation
Indices: 3410189--3410246 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 21
3410179 GCTACTACTA
*
3410189 GTTTCATGTATTGATACAATT
1 GTTTCATGTATCGATACAATT
3410210 GTTT-ATGTATCGATACAA-T
1 GTTTCATGTATCGATACAATT
**
3410229 -AATCATGTATCGATACAA
1 GTTTCATGTATCGATACAA
3410247 AGCAAAATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 1 0.03
19 15 0.45
20 13 0.39
21 4 0.12
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (21 bp):
GTTTCATGTATCGATACAATT
Found at i:3410921 original size:19 final size:19
Alignment explanation
Indices: 3410896--3410944 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3410886 GTATGTAAAG
3410896 TAATATTTTATGTAATTTAA
1 TAATATTTTATGTAA-TTAA
*
3410916 -AATATTTACATGTAATTAA
1 TAATATTT-TATGTAATTAA
3410935 TAAT-TTTTAT
1 TAATATTTTAT
3410945 AAATTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 2 0.08
19 14 0.56
20 9 0.36
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (19 bp):
TAATATTTTATGTAATTAA
Found at i:3412841 original size:18 final size:19
Alignment explanation
Indices: 3412809--3412844 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3412799 TAACATAGTA
3412809 AGCGTTGCTTGCATGGGTT
1 AGCGTTGCTTGCATGGGTT
3412828 AGCGTTGC-TGCATGGGT
1 AGCGTTGCTTGCATGGGT
3412845 ATGACGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.17, G:0.39, T:0.33
Consensus pattern (19 bp):
AGCGTTGCTTGCATGGGTT
Found at i:3417375 original size:21 final size:21
Alignment explanation
Indices: 3417351--3417391 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3417341 TGCTCTTCTT
3417351 TCTGGGAGGACTACTGTTTCC
1 TCTGGGAGGACTACTGTTTCC
*
3417372 TCTGGGAGGACTGCTGTTTC
1 TCTGGGAGGACTACTGTTTC
3417392 AAGCAAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.22, G:0.32, T:0.34
Consensus pattern (21 bp):
TCTGGGAGGACTACTGTTTCC
Found at i:3418719 original size:128 final size:128
Alignment explanation
Indices: 3418491--3418750 Score: 484
Period size: 128 Copynumber: 2.0 Consensus size: 128
3418481 TGCATGTGGA
3418491 TCCACATGTAAAACAAAGTGCAAGCTAAAGAAGGATTAGAGAAGCAATGAAACAAAATAGGCAAT
1 TCCACATGTAAAACAAAGTGCAAGCTAAAGAAGGATTAGAGAAGCAATGAAACAAAATAGGCAAT
*
3418556 AAGACACTAGGTTCAAGATACAAACTTGAGGGTTATACCATGTTATTTTGGATGATCAATTCC
66 AAGACACTAGGTTCAAGATACAAACTTGAGAGTTATACCATGTTATTTTGGATGATCAATTCC
* *
3418619 TCCACGTGTAGAACAAAGTGCAAGCTAAAGAAGGATTAGAGAAGCAATGAAACAAAATAGGCAAT
1 TCCACATGTAAAACAAAGTGCAAGCTAAAGAAGGATTAGAGAAGCAATGAAACAAAATAGGCAAT
*
3418684 AAGACGCTAGGTTCAAGATACAAACTTGAGAGTTATACCATGTTATTTTGGATGATCAATTCC
66 AAGACACTAGGTTCAAGATACAAACTTGAGAGTTATACCATGTTATTTTGGATGATCAATTCC
3418747 TCCA
1 TCCA
3418751 AAAGCTTAAC
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.23
Consensus pattern (128 bp):
TCCACATGTAAAACAAAGTGCAAGCTAAAGAAGGATTAGAGAAGCAATGAAACAAAATAGGCAAT
AAGACACTAGGTTCAAGATACAAACTTGAGAGTTATACCATGTTATTTTGGATGATCAATTCC
Found at i:3420634 original size:10 final size:10
Alignment explanation
Indices: 3420607--3420657 Score: 54
Period size: 10 Copynumber: 5.2 Consensus size: 10
3420597 ATTAATACAT
*
3420607 AAATGTATTA
1 AAATTTATTA
3420617 AAATTTATATA
1 AAATTTAT-TA
3420628 AAA-TTATTA
1 AAATTTATTA
3420637 AAA--TATTA
1 AAATTTATTA
3420645 AAATTTATATA
1 AAATTTAT-TA
3420656 AA
1 AA
3420658 TATATAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
8 8 0.22
9 5 0.14
10 14 0.39
11 9 0.25
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (10 bp):
AAATTTATTA
Found at i:3421410 original size:6 final size:6
Alignment explanation
Indices: 3421401--3421443 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
3421391 AATATTATCT
*
3421401 TATGTA TATGAA TATGAA TATGAA TATGAA TATGAA TATGAA T
1 TATGAA TATGAA TATGAA TATGAA TATGAA TATGAA TATGAA T
3421444 TTAAATCTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (6 bp):
TATGAA
Found at i:3422858 original size:13 final size:13
Alignment explanation
Indices: 3422840--3422870 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3422830 ATAATTCATT
3422840 ATGTATCGATACA
1 ATGTATCGATACA
3422853 ATGTATCGATACA
1 ATGTATCGATACA
3422866 ATGTA
1 ATGTA
3422871 CCATGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3422860 original size:33 final size:33
Alignment explanation
Indices: 3422818--3422886 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
3422808 TCGTTAGAAG
* **
3422818 CAATGTATCGATATAAT-TCATTATGTATCGATA
1 CAATGTATCGATACAATGT-ACCATGTATCGATA
3422851 CAATGTATCGATACAATGTACCATGTATCGATA
1 CAATGTATCGATACAATGTACCATGTATCGATA
3422884 CAA
1 CAA
3422887 ATAATGGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (33 bp):
CAATGTATCGATACAATGTACCATGTATCGATA
Found at i:3424445 original size:13 final size:13
Alignment explanation
Indices: 3424427--3424451 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3424417 ACACATAGTA
3424427 TGTATCGATACAT
1 TGTATCGATACAT
3424440 TGTATCGATACA
1 TGTATCGATACA
3424452 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3424448 original size:32 final size:33
Alignment explanation
Indices: 3424407--3424474 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
3424397 GTAGCTAAAC
**
3424407 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
3424439 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
3424472 TTG
1 TTG
3424475 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:3430638 original size:13 final size:13
Alignment explanation
Indices: 3430620--3430658 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
3430610 ACAGCATTCT
3430620 TTGTATCGATACA
1 TTGTATCGATACA
*
3430633 TTGTATCGACACA
1 TTGTATCGATACA
*
3430646 CTGTATCGATACA
1 TTGTATCGATACA
3430659 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3432674 original size:13 final size:13
Alignment explanation
Indices: 3432656--3432680 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3432646 ACACATAGTA
3432656 TGTATCGATACAT
1 TGTATCGATACAT
3432669 TGTATCGATACA
1 TGTATCGATACA
3432681 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3432677 original size:32 final size:33
Alignment explanation
Indices: 3432636--3432703 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
3432626 GTAGCTAAAC
**
3432636 TTGTATCGATACA-CATAGTATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
3432668 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
3432701 TTG
1 TTG
3432704 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:3436281 original size:33 final size:32
Alignment explanation
Indices: 3436239--3436300 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
3436229 CACACCCAGA
*
3436239 TGTATCGATACAT-TATGCTTTGTATCGATATAT
1 TGTATCGATACATGT-T-CATTGTATCGATATAT
3436272 TGTATCGATACATGTTCATTGTATCGATA
1 TGTATCGATACATGTTCATTGTATCGATA
3436301 CTTGAAACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (32 bp):
TGTATCGATACATGTTCATTGTATCGATATAT
Found at i:3436358 original size:20 final size:20
Alignment explanation
Indices: 3436333--3436386 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
3436323 CTACCACTGT
*
3436333 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
3436353 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
3436373 TTGTATCGATACAT
1 TTGTATCGATACAT
3436387 TACTTCTAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:3437979 original size:9 final size:9
Alignment explanation
Indices: 3437962--3437995 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
3437952 GTCAACCATC
3437962 AATGATGAT
1 AATGATGAT
3437971 GAA-GATGAT
1 -AATGATGAT
3437980 AATGATGAT
1 AATGATGAT
3437989 AATGATG
1 AATGATG
3437996 GTGACTCGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 2 0.09
9 19 0.83
10 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.26, T:0.29
Consensus pattern (9 bp):
AATGATGAT
Found at i:3439570 original size:21 final size:20
Alignment explanation
Indices: 3439533--3439571 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3439523 AAACCTTGTT
*
3439533 ATTTGATTGCCTAAAGTTAA
1 ATTTGATTGCATAAAGTTAA
3439553 ATTTGATTGCGATAAAGTT
1 ATTTGATTGC-ATAAAGTT
3439572 TGTGATGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTTGATTGCATAAAGTTAA
Found at i:3445214 original size:20 final size:20
Alignment explanation
Indices: 3445172--3445217 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
3445162 CTACCACTGT
*
3445172 TTGTATCGATACATGGTACA
1 TTGTATCGATACATGATACA
3445192 TTGTATCGATACATGATGA-A
1 TTGTATCGATACATGAT-ACA
3445212 TTGTAT
1 TTGTAT
3445218 TATACATTGC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:3447400 original size:17 final size:16
Alignment explanation
Indices: 3447352--3447403 Score: 50
Period size: 20 Copynumber: 2.9 Consensus size: 16
3447342 TTTTGATCCA
3447352 AATGTATCGATACATT
1 AATGTATCGATACATT
*
3447368 ATTTATTGTATTGATACATT
1 A---A-TGTATCGATACATT
3447388 GAATGTATCGATACAT
1 -AATGTATCGATACAT
3447404 GCAGACCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 1 0.03
17 12 0.41
18 1 0.03
19 1 0.03
20 13 0.45
21 1 0.03
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.42
Consensus pattern (16 bp):
AATGTATCGATACATT
Found at i:3449867 original size:80 final size:78
Alignment explanation
Indices: 3449756--3449974 Score: 219
Period size: 78 Copynumber: 2.8 Consensus size: 78
3449746 TATATTTCTT
* *
3449756 CATCTCTAGGGATACTCCAACCCCA-TCATTTCCGAGAGGATACTTCAACCCCTTTTTTCCTTCT
1 CATCTCTGGGGATACTCCAACCCCACT-ATTTCCGA-AGGATACTTCAACCCCTTTTTT-ATTCT
* **
3449820 TA-AACTTTGAATTTTT
63 TAGAACATT-AATTTAA
* * * * * * *
3449836 TATTTCTGGGGATACTCCAACCCCACTATTTCTGAAGGAATAC-TCTAGCCCTATTTTATTTTTA
1 CATCTCTGGGGATACTCCAACCCCACTATTTCCGAAGG-ATACTTCAACCCCTTTTTTATTCTTA
3449900 GAACATTAATTTAA
65 GAACATTAATTTAA
* * * *
3449914 CATCTCTGGGGATACTTCAACCCCACTATCTCCGAAAGGATACTCCAACCCCATTTTTATT
1 CATCTCTGGGGATACTCCAACCCCACTATTTCCG-AAGGATACTTCAACCCCTTTTTTATT
3449975 TCCTAAACAC
Statistics
Matches: 112, Mismatches: 22, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
78 43 0.38
79 35 0.31
80 33 0.29
81 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.11, T:0.36
Consensus pattern (78 bp):
CATCTCTGGGGATACTCCAACCCCACTATTTCCGAAGGATACTTCAACCCCTTTTTTATTCTTAG
AACATTAATTTAA
Found at i:3449970 original size:78 final size:79
Alignment explanation
Indices: 3449756--3450257 Score: 256
Period size: 80 Copynumber: 6.3 Consensus size: 79
3449746 TATATTTCTT
* * * *
3449756 CATCTCTAGGGATACTCCAACCCCA-TCATTTCCGAGAGGATACTTCAACCCC-TTTTTTCCTTC
1 CATCTCTGGGGATACTCCAACCCCACT-ATTTCCGAAAGGATACTCCAACCCCATTTTAT--TTC
* **
3449819 TTAAACTTTGAATTTTT
63 TTAAACATTGAATTTAA
* * * * * *
3449836 TATTTCTGGGGATACTCCAACCCCACTATTTCTG-AAGGAATACTCTAGCCCTATTTTATTT-TT
1 CATCTCTGGGGATACTCCAACCCCACTATTTCCGAAAGG-ATACTCCAACCCCATTTTATTTCTT
3449899 AGAACATT-AATTTAA
65 A-AACATTGAATTTAA
* * *
3449914 CATCTCTGGGGATACTTCAACCCCACTATCTCCGAAAGGATACTCCAACCCCATTTTTATTTCCT
1 CATCTCTGGGGATACTCCAACCCCACTATTTCCGAAAGGATACTCCAACCCCA-TTTTATTTCTT
** *
3449979 AAACACAGAATTCT-T
65 AAACATTGAATT-TAA
* ** * ** * * *
3449994 CATC-CTGAGGATACTTTAACCCCA-TCACTTCCGATGGGATACTTCAACCCCGTTTTTATTTCC
1 CATCTCTGGGGATACTCCAACCCCACT-ATTTCCGAAAGGATACTCCAACCCC-ATTTTATTTCT
* **
3450057 CAAACATTGAATTTTTT
64 TAAACATTGAA-TTTAA
* ** * * ** * * **
3450074 GAT-TCTCACGGATACTACAACTCCA-TCATTTTTGAGAGGATACTCCAACTTCGTTTTTATTTC
1 CATCTCT-GGGGATACTCCAACCCCACT-ATTTCCGAAAGGATACTCCAAC-CCCATTTTATTTC
** * **
3450137 CCAAACGTTGAATTTTT
63 TTAAACATTGAATTTAA
* * ** * *
3450154 CATCTC-GGGGAATACTCTAACTCCA-TCAGCTCCCAAGGGATACTCCAACCCCATATTTATTT-
1 CATCTCTGGGG-ATACTCCAACCCCACT-ATTTCCGAAAGGATACTCCAACCCCAT-TTTATTTC
**
3450216 TTAAAACATTGAATTTCTT
63 TT-AAACATTGAATTT-AA
3450235 CATCTCTGGGGATACTCCAACCC
1 CATCTCTGGGGATACTCCAACCC
3450258 TATTTTTACT
Statistics
Matches: 329, Mismatches: 71, Indels: 43
0.74 0.16 0.10
Matches are distributed among these distances:
78 49 0.15
79 87 0.26
80 109 0.33
81 79 0.24
82 5 0.02
ACGTcount: A:0.27, C:0.27, G:0.11, T:0.35
Consensus pattern (79 bp):
CATCTCTGGGGATACTCCAACCCCACTATTTCCGAAAGGATACTCCAACCCCATTTTATTTCTTA
AACATTGAATTTAA
Found at i:3450015 original size:79 final size:80
Alignment explanation
Indices: 3449914--3450257 Score: 234
Period size: 81 Copynumber: 4.3 Consensus size: 80
3449904 ATTAATTTAA
*
3449914 CATCTCTGGGGATACTTCAACCCCA-CTA-TCTCCGAAAGGATACTCCAACCCCATTTTTATTTC
1 CATCTCTGAGGATACTTCAACCCCATC-ACT-TCCGAAAGGATACTCCAACCCCATTTTTATTTC
*
3449977 CTAAACACAGAATTCTT
64 CCAAACACAGAATTCTT
* ** * *
3449994 CATC-CTGAGGATACTTTAACCCCATCACTTCCGATGGGATACTTCAACCCCGTTTTTATTTCCC
1 CATCTCTGAGGATACTTCAACCCCATCACTTCCGAAAGGATACTCCAACCCCATTTTTATTTCCC
** *
3450058 AAACATTGAATTTTTT
66 AAACACAGAA-TTCTT
* * * * * ** * ** *
3450074 GAT-TCTCACGGATACTACAACTCCATCATTTTTGAGAGGATACTCCAACTTCGTTTTTATTTCC
1 CATCTCTGA-GGATACTTCAACCCCATCACTTCCGAAAGGATACTCCAACCCCATTTTTATTTCC
*** *
3450138 CAAACGTTGAATTTTT
65 CAAACACAGAATTCTT
* * * * *
3450154 CATCTC-GGGGAATAC-TCTAACTCCATCAGC-TCCCAAGGGATACTCCAACCCCATATTTATTT
1 CATCTCTGAGG-ATACTTC-AACCCCATCA-CTTCCGAAAGGATACTCCAACCCCATTTTTATTT
*** **
3450216 TTAAAACATTGAATTTCTT
63 CCCAAACACAGAA-TTCTT
* *
3450235 CATCTCTGGGGATACTCCAACCC
1 CATCTCTGAGGATACTTCAACCC
3450258 TATTTTTACT
Statistics
Matches: 207, Mismatches: 45, Indels: 23
0.75 0.16 0.08
Matches are distributed among these distances:
79 60 0.29
80 68 0.33
81 74 0.36
82 5 0.02
ACGTcount: A:0.27, C:0.28, G:0.12, T:0.33
Consensus pattern (80 bp):
CATCTCTGAGGATACTTCAACCCCATCACTTCCGAAAGGATACTCCAACCCCATTTTTATTTCCC
AAACACAGAATTCTT
Found at i:3450276 original size:53 final size:50
Alignment explanation
Indices: 3450190--3450306 Score: 126
Period size: 53 Copynumber: 2.3 Consensus size: 50
3450180 CAGCTCCCAA
* * ** *
3450190 GGGATACTCCAACCCCATATTTATTTTTAAAACATTGAATTTCTTCATCTCT
1 GGGATACTCCAACCCCATATTTACTTCTAAAACATCAAAATT-TTCATCT-T
* * *
3450242 GGGGATACTCCAACCCTATTTTTACTTCTCAAACATCAAAATTTTCATCTT
1 -GGGATACTCCAACCCCATATTTACTTCTAAAACATCAAAATTTTCATCTT
*
3450293 GGGATACTCTAACC
1 GGGATACTCCAACC
3450307 TATCACTTCT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
50 13 0.24
51 1 0.02
52 7 0.13
53 34 0.62
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.37
Consensus pattern (50 bp):
GGGATACTCCAACCCCATATTTACTTCTAAAACATCAAAATTTTCATCTT
Found at i:3450421 original size:80 final size:76
Alignment explanation
Indices: 3450246--3450434 Score: 193
Period size: 80 Copynumber: 2.4 Consensus size: 76
3450236 ATCTCTGGGG
* * *
3450246 ATACTCCAACCCTATTTTTACTTCTCAAACATCAAAATTTTCATCTTGGGATACTCTAACCTATC
1 ATACTCCAACCC-ATTTTTATTTCCCAAACATCAAAATTTTCATCTTGGGATACTCGAACCTATC
*
3450311 ACTTCTGAAGGG
65 ACTTCTGAAGGA
* *
3450323 ATACTCAAACCCCATTTTTATTTCCCAAACATCAAATTTTTTCAT-TTCGTGGATACTCGAATCC
1 ATACTCCAA-CCCATTTTTATTTCCCAAACATCAAA-ATTTTCATCTT-G-GGATACTCGAA-CC
* **
3450387 TATCA-TTTTTTAGAGA
61 TATCACTTCTGAAG-GA
* *
3450403 ATACTCCAACCTCGTTTTTATTTCCTAAACAT
1 ATACTCCAACC-CATTTTTATTTCCCAAACAT
3450435 TGAATTCTTC
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
77 31 0.33
78 11 0.12
79 17 0.18
80 34 0.37
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (76 bp):
ATACTCCAACCCATTTTTATTTCCCAAACATCAAAATTTTCATCTTGGGATACTCGAACCTATCA
CTTCTGAAGGA
Found at i:3450470 original size:51 final size:52
Alignment explanation
Indices: 3450403--3450516 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 52
3450393 TTTTTAGAGA
* * *
3450403 ATACTCCAACCTCGTTTTTATTTCCT-AAACATTGAA-TTCTTCATCTCGGGG
1 ATACTCCAACCCCGTTTTCATTT-CTAAAACATTAAATTTCTTCATCTCGGGG
* * **
3450454 ATACTCTAACCCCGTTTTCATTTCTAAAACCTTAAATTTCTTCATCTCCAAGG
1 ATACTCCAACCCCGTTTTCATTTCTAAAACATTAAATTTCTTCATCT-CGGGG
3450507 ATACTCCAAC
1 ATACTCCAAC
3450517 TCCACCATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
50 2 0.04
51 28 0.54
52 10 0.19
53 12 0.23
ACGTcount: A:0.27, C:0.28, G:0.08, T:0.37
Consensus pattern (52 bp):
ATACTCCAACCCCGTTTTCATTTCTAAAACATTAAATTTCTTCATCTCGGGG
Found at i:3450619 original size:56 final size:58
Alignment explanation
Indices: 3450549--3450660 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
3450539 TCCAACCTCA
**
3450549 TTTTTACTTCCCAAACA-CCAAA-TTTTTCATC-CTGGGGATACTCCAACCCCATCACT
1 TTTTTACTTCCCAAACATCCAAATTTTTTCATCTC-GAAGATACTCCAACCCCATCACT
* *
3450605 TTTTTATTTCCCAAACATCGAAATTTTTTCATCTCGAAGATACTCCAACCCCATCA
1 TTTTTACTTCCCAAACATCCAAATTTTTTCATCTCGAAGATACTCCAACCCCATCA
3450661 TTTCTGAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 16 0.33
57 4 0.08
58 28 0.57
59 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.34
Consensus pattern (58 bp):
TTTTTACTTCCCAAACATCCAAATTTTTTCATCTCGAAGATACTCCAACCCCATCACT
Found at i:3450690 original size:137 final size:130
Alignment explanation
Indices: 3450320--3450735 Score: 395
Period size: 137 Copynumber: 3.1 Consensus size: 130
3450310 CACTTCTGAA
* * * ** * *
3450320 GGGATACTCAAACCCCATTTTTATTTCCCAAACATCAAATTTTTTCATTTCGTGGATACTCGAAT
1 GGGATACTCCAACCCCGTTTTTATTTCCCAAACATCAAATTTTTTCATCTCGAAGATACTCCAAC
* ** * * *
3450385 CCTATCATTTTTTAGAGAATACTCCAACCTCGTTTTTATTTCCTAAACATTGAATTCTTCATCTC
66 CCCATCATTTTGAAG-GGATACTCCAACCTCGTTTTTATTTCCTAAACACTGAATTTTTCATCTC
3450450 G
130 G
* * ** * * * *
3450451 GGGATACTCTAACCCCGTTTTCATTTCTAAAACCTTAAATTTCTTCATCTCCAAGGATACTCCAA
1 GGGATACTCCAACCCCGTTTTTATTTCCCAAACATCAAATTTTTTCATCTCGAA-GATACTCCAA
* * * * * * **
3450516 CTCCACCATTTTTGACGGGATACTCCAACCTCATTTTTACTTCCCAAACACCAAATTTTTCATC-
65 CCCCATCA-TTTTGAAGGGATACTCCAACCTCGTTTTTATTTCCTAAACACTGAATTTTTCATCT
3450580 CTG
129 C-G
*
3450583 GGGATACTCCAACCCCATCACTTTTTTATTTCCCAAACATCGAAATTTTTTCATCTCGAAGATAC
1 GGGATACTCCAA--CC--C-CGTTTTTATTTCCCAAACATC-AAATTTTTTCATCTCGAAGATAC
*
3450648 TCCAACCCCATCATTTCTGAAGGGATACTCCAA-CTCTGTTTTTATTTCCTAAATACTGAATTTT
60 TCCAACCCCATCATTT-TGAAGGGATACTCCAACCTC-GTTTTTATTTCCTAAACACTGAATTTT
* *
3450712 TCATTTCA
123 TCATCTCG
* *
3450720 GGCATACTCTAACCCC
1 GGGATACTCCAACCCC
3450736 ATTAGTTCCT
Statistics
Matches: 223, Mismatches: 50, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
131 43 0.19
132 65 0.29
133 6 0.03
134 2 0.01
135 2 0.01
136 7 0.03
137 81 0.36
138 17 0.08
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (130 bp):
GGGATACTCCAACCCCGTTTTTATTTCCCAAACATCAAATTTTTTCATCTCGAAGATACTCCAAC
CCCATCATTTTGAAGGGATACTCCAACCTCGTTTTTATTTCCTAAACACTGAATTTTTCATCTCG
Found at i:3450875 original size:80 final size:81
Alignment explanation
Indices: 3450749--3450903 Score: 179
Period size: 80 Copynumber: 1.9 Consensus size: 81
3450739 AGTTCCTAGG
* * * * * * *
3450749 GGATACTCCAACCCCATTTTTACTTCTAAAATATTGAATTTTTTCATCTTTGGGGATATTTC-AA
1 GGATACTCCAACCCCATTTTTACTTCTAAAACATTAAATATCTTCATCTCTAGGGATA-CTCAAA
3450813 CCCTACCATTTTCGAAA
65 CCCTACCATTTTCGAAA
** * *
3450830 GGATA-TCCAACTTCATTTTTACTTTTAAAACCTTAAATATCTTCATCTCTAGGGATACTCAAAC
1 GGATACTCCAACCCCATTTTTACTTCTAAAACATTAAATATCTTCATCTCTAGGGATACTCAAAC
*
3450894 TCTACCATTT
66 CCTACCATTT
3450904 CTTAAGAAAT
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
79 2 0.03
80 54 0.89
81 5 0.08
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (81 bp):
GGATACTCCAACCCCATTTTTACTTCTAAAACATTAAATATCTTCATCTCTAGGGATACTCAAAC
CCTACCATTTTCGAAA
Found at i:3455217 original size:52 final size:52
Alignment explanation
Indices: 3455146--3455521 Score: 169
Period size: 52 Copynumber: 7.4 Consensus size: 52
3455136 GTGATAAAGG
* * * * *
3455146 TGCCAATATGCTGATTCAAGACT-AGTGATATTAGGCTTAAATATGTA-AAGAA
1 TGCCAATGTGCTGATTCAAG-CTCAGCGACATTAGACTTAAAGATG-AGAAGAA
* * * *
3455198 TGTCAATGTGCTGTTTCAAGGTCAGCGACATTAGACTTGAAGATGAGAAGAA
1 TGCCAATGTGCTGATTCAAGCTCAGCGACATTAGACTTAAAGATGAGAAGAA
* * **
3455250 TGCCAATGTGCTGATTCAAGGC-CAACGACATTGGGTTTAAAGAT--GAAG-A
1 TGCCAATGTGCTGATTCAA-GCTCAGCGACATTAGACTTAAAGATGAGAAGAA
** * * * *
3455299 TGCCAATGTATTGATTCAAGGCT-AGCGACATTGGTCTTGAAGATGCCG--G--
1 TGCCAATGTGCTGATTCAA-GCTCAGCGACATTAGACTTAAAGATG-AGAAGAA
* * * * * * *
3455348 TGCCAATATGCTGATTCAAGGC-CAGCGATATTGGGCTTGAAGATGACAA-AGG
1 TGCCAATGTGCTGATTCAA-GCTCAGCGACATTAGACTTAAAGATGAGAAGA-A
* * * * * *
3455400 TGCCAATATGCTGATTCAAGGCT-AGCGATATTGGACTTAAAGGTGACAA-AGG
1 TGCCAATGTGCTGATTCAA-GCTCAGCGACATTAGACTTAAAGATGAGAAGA-A
* * * * * * *
3455452 CGCCAATATGCTGATTTAAGGC-CAGCGATATTGGATTTAAAGAT--GAAG-G
1 TGCCAATGTGCTGATTCAA-GCTCAGCGACATTAGACTTAAAGATGAGAAGAA
*
3455501 TGCTAATGTGCTGATTCAAGC
1 TGCCAATGTGCTGATTCAAGC
3455522 CCGACAACAT
Statistics
Matches: 266, Mismatches: 42, Indels: 36
0.77 0.12 0.10
Matches are distributed among these distances:
48 2 0.01
49 93 0.35
50 7 0.03
51 2 0.01
52 161 0.61
53 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (52 bp):
TGCCAATGTGCTGATTCAAGCTCAGCGACATTAGACTTAAAGATGAGAAGAA
Found at i:3455320 original size:49 final size:49
Alignment explanation
Indices: 3455201--3455520 Score: 246
Period size: 52 Copynumber: 6.3 Consensus size: 49
3455191 TAAAGAATGT
* * * **
3455201 CAATGTGCTGTTTCAAGGTCAGCGACATTAGACTTGAAGATGAGAAGAATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTGAAGAT--GAAG-ATGC
* *
3455253 CAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTGAAGATGAAGATGC
** * ** *
3455302 CAATGTATTGATTCAAGGCTAGCGACATT-GGTCTTGAAGATGCCGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGT-TTGAAGATGAAGATGC
* * * *
3455351 CAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGACAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTGAAGATG---AAGATGC
* * * ** * * **
3455403 CAATATGCTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGACAAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTGAAGATG---AAGATGC
* * * * * *
3455455 CAATATGCTGATTTAAGGCCAGCGATATTGGATTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTGAAGATGAAGATGC
*
3455504 TAATGTGCTGATTCAAG
1 CAATGTGCTGATTCAAG
3455521 CCCGACAACA
Statistics
Matches: 227, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
48 3 0.01
49 94 0.41
50 6 0.03
52 124 0.55
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGGTTTGAAGATGAAGATGC
Found at i:3455338 original size:101 final size:100
Alignment explanation
Indices: 3455146--3455520 Score: 362
Period size: 101 Copynumber: 3.7 Consensus size: 100
3455136 GTGATAAAGG
* * * * * * * *
3455146 TGCCAATATGCTGATTCAAGACTAGTGATATTAGGCTTAAATATGTAAAGAATGTCAATGTGCTG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTAAAGATG--AAG-GTGCCAATGTGCTG
* *
3455211 TTTCAAGG-TCAGCGACATTAGACTTGAAGATGAGAAGAA
63 ATTCAAGGCT-AGCGACATTGGACTTGAAGATGAGAAG-A
* * * * **
3455250 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTAAAGATGAAGATGCCAATGTATTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTAAAGATGAAGGTGCCAATGTGCTGATT
* *
3455315 CAAGGCTAGCGACATTGGTCTTGAAGATGCCG--G-
66 CAAGGCTAGCGACATTGGACTTGAAGATG-AGAAGA
* * *
3455348 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGACAAAGGTGCCAATATGCTG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTAAAGATG---AAGGTGCCAATGTGCTG
* * * * *
3455413 ATTCAAGGCTAGCGATATTGGACTTAAAGGTGACAAAGG
63 ATTCAAGGCTAGCGACATTGGACTTGAAGATGA-GAAGA
* * * *
3455452 CGCCAATATGCTGATTTAAGGCCAGCGATATTGGATTTAAAGATGAAGGTGCTAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTAAAGATGAAGGTGCCAATGTGCTGATT
3455517 CAAG
66 CAAG
3455521 CCCGACAACA
Statistics
Matches: 224, Mismatches: 38, Indels: 21
0.79 0.13 0.07
Matches are distributed among these distances:
98 40 0.18
100 1 0.00
101 101 0.45
102 5 0.02
103 1 0.00
104 76 0.34
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (100 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTAAAGATGAAGGTGCCAATGTGCTGATT
CAAGGCTAGCGACATTGGACTTGAAGATGAGAAGA
Found at i:3455518 original size:202 final size:202
Alignment explanation
Indices: 3455144--3455520 Score: 463
Period size: 202 Copynumber: 1.9 Consensus size: 202
3455134 GAGTGATAAA
* * * * * *
3455144 GGTGCCAATATGCTGATTCAAGACTAGTGATATTAGGCTTAAATATGTAAAGAATGTCAATGTGC
1 GGTGCCAATATGCTGATTCAAGACCAGCGATATTAGGCTTAAAGATGCAAAGAATGCCAATATGC
* * * * *
3455209 TGTTTCAAGGTCAGCGACATTAGACTTGAAGATGAGAAGAATGCCAATGTGCTGATTCAAGGCCA
66 TGATTCAAGGTCAGCGACATTAGACTTAAAGATGAAAAGAACGCCAATATGCTGATTCAAGGCCA
* *
3455274 ACGACATTGGGTTTAAAGATGAAGATGCCAATGTATTGATTCAAGGCTAGCGACATTGGTCTTGA
131 ACGACATTGGATTTAAAGATGAAGATGCCAATGTACTGATTCAAGGCTAGCGACATTGGTCTTGA
3455339 AGATGCC
196 AGATGCC
* * * *
3455346 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGACAAAG-GTGCCAATATG
1 GGTGCCAATATGCTGATTCAAGACCAGCGATATTAGGCTTAAAGATG-CAAAGAATGCCAATATG
* * * * *
3455410 CTGATTCAAGG-CTAGCGATATTGGACTTAAAGGTGACAAAG-GCGCCAATATGCTGATTTAAGG
65 CTGATTCAAGGTC-AGCGACATTAGACTTAAAGATGA-AAAGAACGCCAATATGCTGATTCAAGG
* * * * *
3455473 CCAGCGATATTGGATTTAAAGATGAAGGTGCTAATGTGCTGATTCAAG
128 CCAACGACATTGGATTTAAAGATGAAGATGCCAATGTACTGATTCAAG
3455521 CCCGACAACA
Statistics
Matches: 145, Mismatches: 27, Indels: 6
0.81 0.15 0.03
Matches are distributed among these distances:
201 1 0.01
202 137 0.94
203 7 0.05
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.27
Consensus pattern (202 bp):
GGTGCCAATATGCTGATTCAAGACCAGCGATATTAGGCTTAAAGATGCAAAGAATGCCAATATGC
TGATTCAAGGTCAGCGACATTAGACTTAAAGATGAAAAGAACGCCAATATGCTGATTCAAGGCCA
ACGACATTGGATTTAAAGATGAAGATGCCAATGTACTGATTCAAGGCTAGCGACATTGGTCTTGA
AGATGCC
Found at i:3455534 original size:153 final size:144
Alignment explanation
Indices: 3455310--3455582 Score: 307
Period size: 153 Copynumber: 1.8 Consensus size: 144
3455300 GCCAATGTAT
* * ** * *
3455310 TGATTCAAGGCTAGCGACATTGGTCTTGAAGATGCCGGTGCCAATATGCTGATTCAAGGCCAGCG
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGCCCAGCA
* * *
3455375 ATATTGGGCTTGAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTGGACTTAA
66 ACATTGGAC-T-----T-A-AAA-GTGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTAA
3455440 AGGTGACAAAGGCGCCAATATGC
122 AGGTGACAAAGGCGCCAATATGC
* * * *
3455463 TGATTTAAGGCCAGCGATATTGGAT-TTAAAGATGAAGGTGCTAATGTGCTGATTCAAGCCC-GA
1 TGATTCAAGGCCAGCGACATTGG-TCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGCCCAG-
*
3455526 CAACATTGGACTTAAAAGTGCCAATATGCTGATTCAATGCTAGCGATATTAGACTTA
64 CAACATTGGACTTAAAAGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTA
3455583 GAAAAAGATG
Statistics
Matches: 104, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
144 38 0.37
145 3 0.03
146 1 0.01
147 1 0.01
152 2 0.02
153 58 0.56
154 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (144 bp):
TGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAAGCCCAGCA
ACATTGGACTTAAAAGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGACTTAAAGGTGACAA
AGGCGCCAATATGC
Found at i:3455534 original size:202 final size:196
Alignment explanation
Indices: 3455140--3455582 Score: 462
Period size: 202 Copynumber: 2.2 Consensus size: 196
3455130 AGAAGAGTGA
* * * * *
3455140 TAAAGGTGCCAATATGCTGATTCAAGACTAGTGATATTAGGCTTAAATATGTAAAGAATGTCAAT
1 TAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGGCTTAAAGATGCAAAGAATGCCAAT
* * * * * *
3455205 GTGCTGTTTCAAGGTCAGCGACATTAGACTTGAAGATGAGAAGAATGCCAATGTGCTGATTCAAG
66 ATGCTGATTCAAGGTCAGCGACATTAGACTTAAAGATGAAAAGAACGCCAATATGCTGATTCAAG
* * * * * *
3455270 GCCAACGACATTGGGTTTAAAGATGAAGATGCCAATGTATTGATTCAAGGCTAGCGACATTGGTC
131 GCCAACGACATTGGATTTAAAGATGAAGATGCCAATGTACTGATTCAAGCCGAGCAACATTGGAC
3455335 T
196 T
* * * *
3455336 TGAAGATGCCGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTGAAGATGACAAAG-G
1 T-AA-A----GGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGGCTTAAAGATG-CAAAGAA
* * * *
3455400 TGCCAATATGCTGATTCAAGG-CTAGCGATATTGGACTTAAAGGTGACAAAG-GCGCCAATATGC
59 TGCCAATATGCTGATTCAAGGTC-AGCGACATTAGACTTAAAGATGA-AAAGAACGCCAATATGC
* * * * * *
3455463 TGATTTAAGGCCAGCGATATTGGATTTAAAGATGAAGGTGCTAATGTGCTGATTCAAGCCCGA-C
122 TGATTCAAGGCCAACGACATTGGATTTAAAGATGAAGATGCCAATGTACTGATTCAAG-CCGAGC
3455527 AACATTGGACT
186 AACATTGGACT
* * *
3455538 TAAAAGTGCCAATATGCTGATTCAATGCTAGCGATATTAGACTTA
1 TAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGGCTTA
3455583 GAAAAAGATG
Statistics
Matches: 200, Mismatches: 37, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
196 36 0.18
197 2 0.01
198 1 0.00
200 1 0.00
201 3 0.01
202 148 0.74
203 9 0.05
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (196 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCTAGCGATATTAGGCTTAAAGATGCAAAGAATGCCAAT
ATGCTGATTCAAGGTCAGCGACATTAGACTTAAAGATGAAAAGAACGCCAATATGCTGATTCAAG
GCCAACGACATTGGATTTAAAGATGAAGATGCCAATGTACTGATTCAAGCCGAGCAACATTGGAC
T
Found at i:3455650 original size:29 final size:29
Alignment explanation
Indices: 3455604--3455935 Score: 365
Period size: 29 Copynumber: 11.6 Consensus size: 29
3455594 CACCAACTTA
*
3455604 TGTGGGCTTTTG-AAAGGTTGCCACT-ACCT
1 TGTGGGC-TTTGAAAAGGGTGCCACTGA-CT
* * *
3455633 TATGGGCTTTCAAGA-GGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
* *
3455661 TATGGGCTTCT--AAAGGTTGCCACTGACT
1 TGTGGGCTT-TGAAAAGGGTGCCACTGACT
* * *
3455689 TTTGGGCTTTGAAAA-GATGCCACTAACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
* *
3455717 TGTGGGCTTTG-AGAGGGTATGCTACTGACT
1 TGTGGGCTTTGAAAAGGG--TGCCACTGACT
*
3455747 TTTGGGCTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
* * *
3455776 TGTGGGCTTTTAAAAAGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
* * *
3455805 TGTGGGCTTTG-GAAGGTTGCCACTGAAT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
3455833 TGTGGGCTTTGAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
*
3455862 TGTGGGCTTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
* *
3455891 TGTGGGCTTTTAAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAAGGGTGCCACTGACT
*
3455920 TGTGGGCTTTGGAAAG
1 TGTGGGCTTTGAAAAG
3455936 TGAGGAGTGT
Statistics
Matches: 258, Mismatches: 34, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
27 5 0.02
28 87 0.34
29 142 0.55
30 19 0.07
31 5 0.02
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.31
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGGTGCCACTGACT
Found at i:3455870 original size:115 final size:114
Alignment explanation
Indices: 3455586--3455935 Score: 431
Period size: 115 Copynumber: 3.0 Consensus size: 114
3455576 AGACTTAGAA
* * *
3455586 AAAGATGCCACCAACTTATGTGGGCTTTTGAAAGGTTGCCACT-ACCTTATGGGCTTTCAAGA-G
1 AAAGATGCCACTAAC-T-TGTGGGC-TTTGAAAGGGTGCCACTGA-CTTATGGGCTTTCAAAAGG
* * * * *
3455649 GTGCCACTGACTTATGGGCTTCT--AAAGGTTGCCACTGACTTTTGGGCTTTGA
62 GTGCCACTGACTTGTGGGCTTTTAAAAAGG-TGCCACTAACTTGTGGGCTTTGG
* * * *
3455701 AAAGATGCCACTAACTTGTGGGCTTTGAGAGGGTATGCTACTGACTTTTGGGCTTTGAAAAGGGT
1 AAAGATGCCACTAACTTGTGGGCTTTGAAAGGG--TGCCACTGACTTATGGGCTTTCAAAAGGGT
3455766 GCCACTGACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGG
64 GCCACTGACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGG
* * * *
3455817 AAGGTTGCCACTGAA-TTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAGGGT
1 AAAGATGCCACT-AACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTATGGGCTTTCAAAAGGGT
*
3455881 GCCACTGACTTGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTTGG
64 GCCACTGACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGG
3455932 AAAG
1 AAAG
3455936 TGAGGAGTGT
Statistics
Matches: 207, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
112 8 0.04
113 7 0.03
114 21 0.10
115 117 0.57
116 42 0.20
117 12 0.06
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.31
Consensus pattern (114 bp):
AAAGATGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCTTTCAAAAGGGTGC
CACTGACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTGTGGGCTTTGG
Found at i:3455888 original size:144 final size:142
Alignment explanation
Indices: 3455604--3455929 Score: 408
Period size: 144 Copynumber: 2.3 Consensus size: 142
3455594 CACCAACTTA
* * * * *
3455604 TGTGGGCTTTTG-AAAGGTTGCCACTACCTTATGGGC-TTTCAAGAGGTGCCACTGACTTATGGG
1 TGTGGGC-TTTGAAAAGGGTGCCACTA-CTTGTGGGCTTTTAAAAAGGTGCCACTAACTTATGGG
* * * *
3455667 CTTCTAAAGGTTGCCACTGACTTTTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTGAGAG
64 CTTCTAAAGGTTGCCACTGAATTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTAAAAG
*
3455732 GGTATGCTACTGACT
129 GG-ATGCCACTGACT
* *
3455747 TTTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTGTGGGC
1 TGTGGGCTTTGAAAAGGGTGCCACT-ACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTATGGGC
* * *
3455812 TT-TGGAAGGTTGCCACTGAATTGTGGGCTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTAAA
65 TTCT-AAAGGTTGCCACTGAATTGTGGGCTTTGAAAA-GATGCCACTAACTTGTGGGC-TTTAAA
3455876 AGGG-TGCCACTGACT
127 AGGGATGCCACTGACT
*
3455891 TGTGGGCTTTTAAAAGGGTGCCACTAACTTGTGGGCTTT
1 TGTGGGCTTTGAAAAGGGTGCCACT-ACTTGTGGGCTTT
3455930 GGAAAGTGAG
Statistics
Matches: 159, Mismatches: 18, Indels: 11
0.85 0.10 0.06
Matches are distributed among these distances:
142 4 0.03
143 27 0.17
144 102 0.64
145 18 0.11
146 8 0.05
ACGTcount: A:0.21, C:0.17, G:0.30, T:0.32
Consensus pattern (142 bp):
TGTGGGCTTTGAAAAGGGTGCCACTACTTGTGGGCTTTTAAAAAGGTGCCACTAACTTATGGGCT
TCTAAAGGTTGCCACTGAATTGTGGGCTTTGAAAAGATGCCACTAACTTGTGGGCTTTAAAAGGG
ATGCCACTGACT
Found at i:3456322 original size:37 final size:37
Alignment explanation
Indices: 3456280--3456364 Score: 152
Period size: 37 Copynumber: 2.3 Consensus size: 37
3456270 AAAGATGAAG
*
3456280 CACAAATGCATCATGCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATCCAAAATGAAATGTTATGAATGT
*
3456317 CACAAATGCATTATCCAAAATGAAATGTTATGAATGT
1 CACAAATGCATCATCCAAAATGAAATGTTATGAATGT
3456354 CACAAATGCAT
1 CACAAATGCAT
3456365 GATTGTGGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.44, C:0.15, G:0.14, T:0.27
Consensus pattern (37 bp):
CACAAATGCATCATCCAAAATGAAATGTTATGAATGT
Found at i:3457408 original size:6 final size:6
Alignment explanation
Indices: 3457397--3457459 Score: 69
Period size: 6 Copynumber: 11.0 Consensus size: 6
3457387 TTTTTATTGT
* * *
3457397 TTTTTG TTTTTG TTTTTG TTTTT- CTTTTG TTTTTC TTTTT- TTTTCG
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
*
3457443 -TTTTG TTTTTT TTTTTG
1 TTTTTG TTTTTG TTTTTG
3457460 AAGGATGCCT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 12 0.26
6 35 0.74
ACGTcount: A:0.00, C:0.05, G:0.11, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:3457412 original size:11 final size:11
Alignment explanation
Indices: 3457398--3457456 Score: 77
Period size: 11 Copynumber: 5.4 Consensus size: 11
3457388 TTTTATTGTT
*
3457398 TTTTGTTTTTGT
1 TTTTGTTTTT-C
3457410 TTTTGTTTTTC
1 TTTTGTTTTTC
3457421 TTTTGTTTTTC
1 TTTTGTTTTTC
3457432 TTTT-TTTTTC
1 TTTTGTTTTTC
3457442 GTTTTGTTTTT-
1 -TTTTGTTTTTC
3457453 TTTT
1 TTTT
3457457 TTGAAGGATG
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
10 10 0.23
11 19 0.43
12 15 0.34
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTTC
Found at i:3457451 original size:16 final size:16
Alignment explanation
Indices: 3457398--3457456 Score: 75
Period size: 17 Copynumber: 3.6 Consensus size: 16
3457388 TTTTATTGTT
3457398 TTTTGTTTTTGTTTTTG
1 TTTT-TTTTTGTTTTTG
*
3457415 TTTTTCTTTTGTTTTTC
1 TTTTT-TTTTGTTTTTG
3457432 TTTTTTTTTCG-TTTTG
1 TTTTTTTTT-GTTTTTG
3457448 TTTTTTTTT
1 TTTTTTTTT
3457457 TTGAAGGATG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
16 18 0.47
17 20 0.53
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTGTTTTTG
Found at i:3459635 original size:20 final size:20
Alignment explanation
Indices: 3459590--3459641 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
3459580 GTAGCCAAAC
* **
3459590 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
3459610 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
3459629 TTGTATCGATACA
1 TTGTATCGATACA
3459642 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:3464265 original size:15 final size:15
Alignment explanation
Indices: 3464245--3464275 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3464235 TAAAAATGTC
*
3464245 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
3464260 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
3464275 C
1 C
3464276 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:3466377 original size:13 final size:13
Alignment explanation
Indices: 3466359--3466396 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
3466349 CATTTTTCTT
3466359 TGTATCGATACAA
1 TGTATCGATACAA
*
3466372 TGTATCGATACAC
1 TGTATCGATACAA
3466385 TGTATCGATACA
1 TGTATCGATACA
3466397 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3466551 original size:20 final size:20
Alignment explanation
Indices: 3466508--3466553 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
3466498 AAATCTTTTG
3466508 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
3466529 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
3466549 CAAAA
1 CAAAA
3466554 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:3468980 original size:13 final size:13
Alignment explanation
Indices: 3468962--3468987 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3468952 TACACCAAGT
3468962 ATGTATCGATACA
1 ATGTATCGATACA
3468975 ATGTATCGATACA
1 ATGTATCGATACA
3468988 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:3482050 original size:13 final size:13
Alignment explanation
Indices: 3482032--3482057 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3482022 AGGGTAGCTT
3482032 TTGTATCGATACA
1 TTGTATCGATACA
3482045 TTGTATCGATACA
1 TTGTATCGATACA
3482058 ACACTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:3484361 original size:207 final size:207
Alignment explanation
Indices: 3484006--3484420 Score: 830
Period size: 207 Copynumber: 2.0 Consensus size: 207
3483996 GTTAAAGGAA
3484006 AAAAAGGTCAATTGGAAATGGATCTCTACCTTTGAGATAAGGAGATAGACCATATGACCAAGAAA
1 AAAAAGGTCAATTGGAAATGGATCTCTACCTTTGAGATAAGGAGATAGACCATATGACCAAGAAA
3484071 CAAGATAGCTTTAGGGAGGATCTTTAGAGTCTGACTAACGATTACGTAGCATTCTAGAAAGCAAA
66 CAAGATAGCTTTAGGGAGGATCTTTAGAGTCTGACTAACGATTACGTAGCATTCTAGAAAGCAAA
3484136 CAAGTCTTGATATGTCAGCAAGTCACTTGTCGAGTGGCAAGCAAAGATCGTTACTCTCAAATGCG
131 CAAGTCTTGATATGTCAGCAAGTCACTTGTCGAGTGGCAAGCAAAGATCGTTACTCTCAAATGCG
3484201 AGATAAAATTAT
196 AGATAAAATTAT
3484213 AAAAAGGTCAATTGGAAATGGATCTCTACCTTTGAGATAAGGAGATAGACCATATGACCAAGAAA
1 AAAAAGGTCAATTGGAAATGGATCTCTACCTTTGAGATAAGGAGATAGACCATATGACCAAGAAA
3484278 CAAGATAGCTTTAGGGAGGATCTTTAGAGTCTGACTAACGATTACGTAGCATTCTAGAAAGCAAA
66 CAAGATAGCTTTAGGGAGGATCTTTAGAGTCTGACTAACGATTACGTAGCATTCTAGAAAGCAAA
3484343 CAAGTCTTGATATGTCAGCAAGTCACTTGTCGAGTGGCAAGCAAAGATCGTTACTCTCAAATGCG
131 CAAGTCTTGATATGTCAGCAAGTCACTTGTCGAGTGGCAAGCAAAGATCGTTACTCTCAAATGCG
3484408 AGATAAAATTAT
196 AGATAAAATTAT
3484420 A
1 A
3484421 GTGAGAAAAA
Statistics
Matches: 208, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
207 208 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (207 bp):
AAAAAGGTCAATTGGAAATGGATCTCTACCTTTGAGATAAGGAGATAGACCATATGACCAAGAAA
CAAGATAGCTTTAGGGAGGATCTTTAGAGTCTGACTAACGATTACGTAGCATTCTAGAAAGCAAA
CAAGTCTTGATATGTCAGCAAGTCACTTGTCGAGTGGCAAGCAAAGATCGTTACTCTCAAATGCG
AGATAAAATTAT
Found at i:3486881 original size:4 final size:4
Alignment explanation
Indices: 3486866--3486921 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
3486856 TTTAACATTT
* * * *
3486866 ATAA AAAA ATAA ATAA ATAA ATAA GTAT ATATA A-AA AT-A ATAT ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA ATAA ATAA
3486913 ATAA ATAA A
1 ATAA ATAA A
3486922 GAAAAAAACC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
3 5 0.12
4 35 0.85
5 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:3486996 original size:14 final size:14
Alignment explanation
Indices: 3486975--3487136 Score: 105
Period size: 14 Copynumber: 11.4 Consensus size: 14
3486965 CATATTTTCA
3486975 TGCATTTCATGCAT
1 TGCATTTCATGCAT
*
3486989 TACATTTCATGCA-
1 TGCATTTCATGCAT
* *
3487002 TGCATTTCACGTAATT
1 TGCATTTCATG-CA-T
** * *
3487018 TTTAGTTCATGTAT
1 TGCATTTCATGCAT
*
3487032 TACATTTCATGCA-
1 TGCATTTCATGCAT
* *
3487045 TGGATTTCATGTAATT
1 TGCATTTCATG-CA-T
3487061 TGCATTTCATGCAT
1 TGCATTTCATGCAT
* *
3487075 TACATTGCATGCA-
1 TGCATTTCATGCAT
* *
3487088 TGCATTTCACGTAATT
1 TGCATTTCATG-CA-T
*
3487104 TTCATTTCATGCAT
1 TGCATTTCATGCAT
*
3487118 TTCATTTCATGCAT
1 TGCATTTCATGCAT
3487132 TGCAT
1 TGCAT
3487137 GCATTAAATT
Statistics
Matches: 111, Mismatches: 28, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
13 26 0.23
14 56 0.50
15 3 0.03
16 26 0.23
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (14 bp):
TGCATTTCATGCAT
Found at i:3487137 original size:23 final size:23
Alignment explanation
Indices: 3487106--3487154 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
3487096 ACGTAATTTT
* **
3487106 CATTTCATGCATTTCATTTCATG
1 CATTGCATGCATTAAATTTCATG
3487129 CATTGCATGCATTAAATTTCATG
1 CATTGCATGCATTAAATTTCATG
3487152 CAT
1 CAT
3487155 GTTTCACGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (23 bp):
CATTGCATGCATTAAATTTCATG
Found at i:3487147 original size:43 final size:43
Alignment explanation
Indices: 3486977--3487136 Score: 239
Period size: 43 Copynumber: 3.7 Consensus size: 43
3486967 TATTTTCATG
3486977 CATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTTT
1 CATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTTT
* * * * * *
3487020 TAGTTCATGTATTACATTTCATGCATGGATTTCATGTAATTTG
1 CATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTTT
*
3487063 CATTTCATGCATTACATTGCATGCATGCATTTCACGTAATTTT
1 CATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTTT
*
3487106 CATTTCATGCATTTCATTTCATGCATTGCAT
1 CATTTCATGCATTACATTTCATGCA-TGCAT
3487137 GCATTAAATT
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
43 96 0.95
44 5 0.05
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (43 bp):
CATTTCATGCATTACATTTCATGCATGCATTTCACGTAATTTT
Found at i:3487886 original size:15 final size:15
Alignment explanation
Indices: 3487868--3487927 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 15
3487858 GCAGCAATAG
3487868 CACAAGCAAACAAGC
1 CACAAGCAAACAAGC
3487883 CACAAGCAATGGTAGCAATAG-
1 CACAAGCAA----A-C-A-AGC
3487904 CACAAGCAAACAAGC
1 CACAAGCAAACAAGC
3487919 CACAAGCAA
1 CACAAGCAA
3487928 TGGCAACAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
14 2 0.05
15 19 0.51
16 1 0.03
17 1 0.03
19 1 0.03
20 1 0.03
21 10 0.27
22 2 0.05
ACGTcount: A:0.50, C:0.28, G:0.17, T:0.05
Consensus pattern (15 bp):
CACAAGCAAACAAGC
Found at i:3487900 original size:36 final size:36
Alignment explanation
Indices: 3487833--3487932 Score: 152
Period size: 36 Copynumber: 2.9 Consensus size: 36
3487823 GCAACAAAAC
* *
3487833 AGCACAAGAAAACAAG---CAAGCAACGGCAGCAAT
1 AGCACAAGCAAACAAGCCACAAGCAATGGCAGCAAT
*
3487866 AGCACAAGCAAACAAGCCACAAGCAATGGTAGCAAT
1 AGCACAAGCAAACAAGCCACAAGCAATGGCAGCAAT
3487902 AGCACAAGCAAACAAGCCACAAGCAATGGCA
1 AGCACAAGCAAACAAGCCACAAGCAATGGCA
3487933 ACAAAACCAG
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
33 15 0.25
36 45 0.75
ACGTcount: A:0.49, C:0.26, G:0.20, T:0.05
Consensus pattern (36 bp):
AGCACAAGCAAACAAGCCACAAGCAATGGCAGCAAT
Found at i:3487964 original size:23 final size:21
Alignment explanation
Indices: 3487930--3487971 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
3487920 ACAAGCAATG
*
3487930 GCAACAAAACCAGTAAAAACA
1 GCAACAAAACCAATAAAAACA
3487951 GCAAGCAAATACCAATAAAAA
1 GCAA-CAAA-ACCAATAAAAA
3487972 ATACCAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 4 0.22
23 10 0.56
ACGTcount: A:0.62, C:0.21, G:0.10, T:0.07
Consensus pattern (21 bp):
GCAACAAAACCAATAAAAACA
Found at i:3487982 original size:23 final size:21
Alignment explanation
Indices: 3487931--3487987 Score: 51
Period size: 23 Copynumber: 2.5 Consensus size: 21
3487921 CAAGCAATGG
* *
3487931 CAACAAAACCAGTAAAAACAG
1 CAACAAAACCAATAAAAACAC
*
3487952 CAAGCAAATACCAATAAAAAATAC
1 CAA-CAAA-ACCAAT-AAAAACAC
3487976 CAACAAACACCA
1 CAACAAA-ACCA
3487988 GCAAAATAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.10
22 4 0.14
23 13 0.45
24 9 0.31
ACGTcount: A:0.61, C:0.26, G:0.05, T:0.07
Consensus pattern (21 bp):
CAACAAAACCAATAAAAACAC
Found at i:3491718 original size:20 final size:20
Alignment explanation
Indices: 3491690--3491764 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
3491680 TCATACCCTG
3491690 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
3491710 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
3491730 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
3491750 ATGTATCGATACATT
1 ATGTATCGATACATT
3491765 ATGTCTTTTT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:3491757 original size:40 final size:39
Alignment explanation
Indices: 3491690--3491767 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
3491680 TCATACCCTG
* *
3491690 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* *
3491730 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
3491768 TCTTTTTACC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:3492683 original size:22 final size:22
Alignment explanation
Indices: 3492657--3492711 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
3492647 AGCCTTTGAC
3492657 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
3492679 CATGCATTTTTTTATTATGTTT
1 CATGCATTTTTTTATTATGTTT
3492701 CATGCATTTTT
1 CATGCATTTTT
3492712 AACATGTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.18, C:0.11, G:0.09, T:0.62
Consensus pattern (22 bp):
CATGCATTTTTTTATTATGTTT
Found at i:3492718 original size:20 final size:21
Alignment explanation
Indices: 3492657--3492718 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
3492647 AGCCTTTGAC
**
3492657 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
**
3492679 CATGCATTTTTTTATTATGTTT
1 CATGCA-TTTTTTAACATGTTT
3492701 CATGCA-TTTTTAACATGT
1 CATGCATTTTTTAACATGT
3492719 CCAGCATCTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.26
22 28 0.74
ACGTcount: A:0.21, C:0.11, G:0.10, T:0.58
Consensus pattern (21 bp):
CATGCATTTTTTAACATGTTT
Found at i:3499561 original size:18 final size:18
Alignment explanation
Indices: 3499540--3499593 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 18
3499530 AAAAAAAAGT
3499540 TAAAAATTTTTAAAAAAA
1 TAAAAATTTTTAAAAAAA
* ** *
3499558 TAAAAAATAATAAAAAAG
1 TAAAAATTTTTAAAAAAA
* *
3499576 TCAAAATTTTCAAAAAAA
1 TAAAAATTTTTAAAAAAA
3499594 ATCAATTAAA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (18 bp):
TAAAAATTTTTAAAAAAA
Found at i:3501519 original size:19 final size:18
Alignment explanation
Indices: 3501494--3501559 Score: 79
Period size: 19 Copynumber: 3.8 Consensus size: 18
3501484 AATTCAACAA
3501494 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3501512 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
3501528 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
3501544 TATTGTATCGATACAT
1 T-TTGTATCGATACAT
3501560 TTTCTGTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 13
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.27
15 2 0.05
17 2 0.05
18 1 0.02
19 25 0.61
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:3501533 original size:13 final size:13
Alignment explanation
Indices: 3501515--3501539 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3501505 ACATAAGTGT
3501515 TGTATCGATACAA
1 TGTATCGATACAA
3501528 TGTATCGATACA
1 TGTATCGATACA
3501540 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3501533 original size:32 final size:32
Alignment explanation
Indices: 3501496--3501558 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
3501486 TTCAACAATT
*
3501496 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
3501528 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
3501559 TTTTCTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:3503844 original size:51 final size:52
Alignment explanation
Indices: 3503787--3504172 Score: 182
Period size: 52 Copynumber: 7.4 Consensus size: 52
3503777 CAATTCTCCG
* * * *
3503787 CAATCGGGGATATTCCATCTCTGATTTTATTTTC-AAAACACTAA-TTTTCTA
1 CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTC-A
* *
3503838 TAATCGGGGATACCCCAACTCTGATTTTATTTCCAAAAAACACCAATTTTTCA
1 CAATCGGGGATACTCCAACTCTGATTTTATTTCC-AAAAACACCAATTTTTCA
* * * * *** * *
3503891 CAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCGTTATTTC-
1 CAATCGGGGATACTCCAACTCTGATTTTAT-TTC-CAAAAACACCAA-----TT-TTTCA
* * * ** * *** *
3503948 CGA--GGGGATACTCCAACCCCTG-CTTTA-TTCTTAAAATATTGATTTCTCA
1 CAATCGGGGATACTCCAA-CTCTGATTTTATTTCCAAAAACACCAATTTTTCA
* * * * * *
3503997 TAATCGGGGATACTCCAACCCCGATTTTA-TTGCTAAAACACTAATTTTTCCA
1 CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTT-CA
* * * * * *
3504049 CAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACAAATTTTCCA
1 CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCA
* * * **
3504100 TTAATCAGGGATACTCCAGCTCCAATTTTATTTCCAAAAACACCAATTTTTTCA
1 -CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAA-TTTTTCA
*
3504154 CAATCGAGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
3504173 CTCGTTATTT
Statistics
Matches: 254, Mismatches: 59, Indels: 42
0.72 0.17 0.12
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 4 0.02
51 66 0.26
52 78 0.31
53 56 0.22
54 14 0.06
55 15 0.06
56 4 0.02
57 7 0.03
58 4 0.02
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAAACACCAATTTTTCA
Found at i:3503900 original size:53 final size:51
Alignment explanation
Indices: 3503787--3503909 Score: 158
Period size: 53 Copynumber: 2.4 Consensus size: 51
3503777 CAATTCTCCG
* * * *
3503787 CAATCGGGGATATTCCATCTCTGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTCTA
* *
3503838 TAATCGGGGATACCCCAACTCTGATTTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCTGATTTTATTTCC--AAAACACCAATTTTCT-A
3503891 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
3503910 CCCGTTAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 29 0.48
52 1 0.02
53 31 0.51
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCTGATTTTATTTCCAAAACACCAATTTTCTA
Found at i:3503923 original size:27 final size:28
Alignment explanation
Indices: 3503893--3503967 Score: 107
Period size: 27 Copynumber: 2.7 Consensus size: 28
3503883 ATTTTTCACA
3503893 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
3503920 ATCGGGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
***
3503948 CGAGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
3503968 TGCTTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.56
28 19 0.44
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.21
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:3504077 original size:52 final size:51
Alignment explanation
Indices: 3503951--3504173 Score: 200
Period size: 52 Copynumber: 4.3 Consensus size: 51
3503941 TTATTTCCGA
* * * * * *
3503951 GGGGATACTCCAACCCCTG-CTTTATTCTTAAAATATTGATTTCT-CATAATC
1 GGGGATACTCCAACCCC-GATTTTATTC-TAAAACACTAATTTTTCCACAATC
3504002 GGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATT-CTAAAACACTAATTTTTCCACAATC
* * * *
3504054 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACAC-AAATTTTCCATTAATC
1 GGGGATACTCCAACCCCGATTTTATTCT-AAAACACTAATTTTTCCA-CAATC
* * * * * * *
3504106 AGGGATACTCCAGCTCCAATTTTATTTCCAAAAACACCAATTTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTA-TT-CTAAAACACTAATTTTTCCACAATC
*
3504159 GAGGATACTCCAACC
1 GGGGATACTCCAACC
3504174 TCGTTATTTC
Statistics
Matches: 140, Mismatches: 24, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
50 1 0.01
51 45 0.32
52 62 0.44
53 24 0.17
54 8 0.06
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTCTAAAACACTAATTTTTCCACAATC
Found at i:3504184 original size:31 final size:28
Alignment explanation
Indices: 3504156--3504232 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
3504146 TTTTTTCACA
*
3504156 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
**
3504184 ATCGAGGATACTCCAACCCCGTTACCTC
1 ATCGAGGATACTCCAACCCCGTTATTTC
3504212 --CGAGGAGATACTCCAACCCCG
1 ATCGA-G-GATACTCCAACCCCG
3504233 GCTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 3 0.07
27 1 0.02
28 40 0.91
ACGTcount: A:0.26, C:0.35, G:0.17, T:0.22
Consensus pattern (28 bp):
ATCGAGGATACTCCAACCCCGTTATTTC
Found at i:3504255 original size:264 final size:262
Alignment explanation
Indices: 3503787--3504283 Score: 753
Period size: 264 Copynumber: 1.9 Consensus size: 262
3503777 CAATTCTCCG
* * * * * * *
3503787 CAATCGGGGATATTCCATCTCTGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGATACC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCCATAATCAGGGATACC
** *
3503852 CCAACTCTGATTTTATTTCCAAAAAACACCAATTTTTCACAATCGGGGATACTCCAACCCCGTTA
66 CCAACTCCAATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
* ** * * **
3503917 ATCATCGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCTGCTTTATTCTTAA
131 ATCATCGAGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGGCTTTATTCCCAA
3503982 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTC
3504047 CA
261 CA
*
3504049 CAATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACAAATTTTCCATTAATCAGGGATAC
1 CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCCA-TAATCAGGGATAC
* * *
3504114 TCCAGCTCCAATTTTATTTCC-AAAAACACCAATTTTTTCACAATCGAGGATACTCCAACCTCGT
65 CCCAACTCCAATTTTATTTCCAAAAAACACCAA-TTTTTCACAATCGAGGATACTCCAACCCCGT
*
3504178 TATTTCATCGAGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGGCTTTATTCC
129 TA-ATCATCGAGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGGCTTTATTCC
*
3504243 CAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCCG
193 CAAAATATTGATTTCTCATAATCGGGGATACTCCAACCCCG
3504284 TTATTTTCGA
Statistics
Matches: 209, Mismatches: 23, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
262 55 0.26
263 60 0.29
264 94 0.45
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
CAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCCATAATCAGGGATACC
CCAACTCCAATTTTATTTCCAAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCCCGTTA
ATCATCGAGGATACTCCAACCCCGTTACCTCCGAGGAGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCCCGATTTTATTGCTAAAACACTAATTTTTC
CA
Found at i:3505561 original size:30 final size:28
Alignment explanation
Indices: 3505475--3505633 Score: 124
Period size: 30 Copynumber: 5.5 Consensus size: 28
3505465 TAACTTTCTT
*
3505475 AAAGCCCACAAGT-AATGGCACCCTTTC
1 AAAGCCCACAAGTCAATGGCACCTTTTC
* * * * *
3505502 AAAGCCTACAAGTTAGTGGAATCTTTTTTC
1 AAAGCCCACAAGTCAATGGCA-C-CTTTTC
* *
3505532 AAAGCCCATAAGTCAATAGCACACATTTTC
1 AAAGCCCACAAGTCAATGGCAC-C-TTTTC
* * *
3505562 AATGCCCACAAGTCAGTGGCACCCTTTC
1 AAAGCCCACAAGTCAATGGCACCTTTTC
* *
3505590 AAAGCTCACAAAT-AAGTGGCACCTTTTTC
1 AAAGCCCACAAGTCAA-TGGCACC-TTTTC
*
3505619 AAAGCCCATAAGTCA
1 AAAGCCCACAAGTCA
3505634 GTGGTAATTT
Statistics
Matches: 99, Mismatches: 26, Indels: 11
0.73 0.19 0.08
Matches are distributed among these distances:
27 13 0.13
28 26 0.26
29 17 0.17
30 43 0.43
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (28 bp):
AAAGCCCACAAGTCAATGGCACCTTTTC
Found at i:3505698 original size:28 final size:29
Alignment explanation
Indices: 3505658--3505728 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
3505648 GCAATCTTTC
* * *
3505658 AAAGTCCATAAGTTAATAGC-ACCTTTTT
1 AAAGCCCACAAGTCAATAGCAACCTTTTT
* *
3505686 AAAGCCCACAAGTCAGTGGCAACCTTTTT
1 AAAGCCCACAAGTCAATAGCAACCTTTTT
3505715 AAAGCCCACAAGTC
1 AAAGCCCACAAGTC
3505729 GGTGGCAACT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 15 0.41
29 22 0.59
ACGTcount: A:0.35, C:0.25, G:0.14, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAATAGCAACCTTTTT
Found at i:3505717 original size:29 final size:29
Alignment explanation
Indices: 3505678--3505817 Score: 131
Period size: 29 Copynumber: 4.6 Consensus size: 29
3505668 AGTTAATAGC
3505678 ACCTTTTTAAAGCCCACAAGTCAGTGGCA
1 ACCTTTTTAAAGCCCACAAGTCAGTGGCA
*
3505707 ACCTTTTTAAAGCCCACAAGTCGGTGGCA
1 ACCTTTTTAAAGCCCACAAGTCAGTGGCA
* ** *
3505736 A-CTCTTTCAAAGCCCACACAAGTTGGTGG-T
1 ACCT-TTTTAAAG-CC-CACAAGTCAGTGGCA
*
3505766 ACCTTTTTCAAAAGCCCACACAAGTTAGTGGCA
1 ACCTTTTT--AAAG-CC-CACAAGTCAGTGGCA
*
3505799 ACCTTCTTAAAAGCCCACA
1 ACCTT-TTTAAAGCCCACA
3505818 CAAGTTGGTG
Statistics
Matches: 95, Mismatches: 8, Indels: 15
0.81 0.07 0.13
Matches are distributed among these distances:
28 2 0.02
29 36 0.38
30 10 0.11
31 16 0.17
32 24 0.25
33 5 0.05
34 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (29 bp):
ACCTTTTTAAAGCCCACAAGTCAGTGGCA
Found at i:3505829 original size:32 final size:32
Alignment explanation
Indices: 3505692--3505830 Score: 146
Period size: 32 Copynumber: 4.5 Consensus size: 32
3505682 TTTTAAAGCC
** *
3505692 CACAAGTCAGTGGCAACCTT-TTTAAAG-CC-
1 CACAAGTTGGTGGCAACCTTCTTAAAAGCCCA
* *
3505721 CACAAGTCGGTGGCAA-C-TCTTTCAAAGCCCA
1 CACAAGTTGGTGGCAACCTTC-TTAAAAGCCCA
* *
3505752 CACAAGTTGGTGG-TACCTTTTTCAAAAGCCCA
1 CACAAGTTGGTGGCAACCTTCTT-AAAAGCCCA
*
3505784 CACAAGTTAGTGGCAACCTTCTTAAAAGCCCA
1 CACAAGTTGGTGGCAACCTTCTTAAAAGCCCA
3505816 CACAAGTTGGTGGCA
1 CACAAGTTGGTGGCA
3505831 TCTCCTCCTA
Statistics
Matches: 92, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.01
28 1 0.01
29 21 0.23
30 3 0.03
31 15 0.16
32 44 0.48
33 7 0.08
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (32 bp):
CACAAGTTGGTGGCAACCTTCTTAAAAGCCCA
Found at i:3506136 original size:163 final size:161
Alignment explanation
Indices: 3505857--3506164 Score: 379
Period size: 163 Copynumber: 1.9 Consensus size: 161
3505847 ATATCATTGA
* * *
3505857 CCTTGAATTAAAACATTGGCATTTGTCAAATCATCTATTTCTAAGTCTAATGCCATTGACTGTGA
1 CCTTGAATTAAAACATTGGCATTTGTCAAATAATCTACTTCTAAGTCTAATGCCATGGACTGTGA
* * * * * * * *
3505922 ATCAGCACATTGGCGCTCTTGTCATCTTTAAGTCCAATATCGTTGGCCTTGAATCAGCATATTGG
66 ATCAGCACATTAGCACTCCTCTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGA
3505987 CACCTTCATCATCTTTAAAACTATGTCATAGG
131 CACCTTCATC-TCTTTAAAACTATGTCATAGG
* * * *
3506019 CCTTGAATTTATACATTGGCACATTTGTCAAA-AATCTCCTTCTAAGTCTAATGTCGC-TGGCCT
1 CCTTGAATTAAAACATTGG--CATTTGTCAAATAATCTACTTCTAAGTCTAATG-C-CATGGACT
* * *
3506082 -TGAATTAGCACATTAGCATTCCTCTCATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACA
62 GTGAATCAGCACATTAGCACTCCTCTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACA
*
3506146 TTGACACCTTTATCTCTTT
127 TTGACACCTTCATCTCTTT
3506165 TTAATTCAAA
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
162 22 0.18
163 84 0.68
164 16 0.13
165 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (161 bp):
CCTTGAATTAAAACATTGGCATTTGTCAAATAATCTACTTCTAAGTCTAATGCCATGGACTGTGA
ATCAGCACATTAGCACTCCTCTCATCTTTAAGTCCAATATCGCTAGCCTTGAATCAGCACATTGA
CACCTTCATCTCTTTAAAACTATGTCATAGG
Found at i:3507056 original size:51 final size:52
Alignment explanation
Indices: 3506980--3507118 Score: 178
Period size: 52 Copynumber: 2.7 Consensus size: 52
3506970 TCTAGAATGA
* *
3506980 AAATGTATTGATATAATT-TTCATTGTACCGATACATTCT-GGGTTTTAACAC-
1 AAATGTATTGATAT-ATTCTTAATTGTATCGATACATTCTAGGGTTTTAAC-CT
* *
3507031 AAATGTATTGATATATTCTTAATTGTATCGATACATTTTAGGGTTTTGACCT
1 AAATGTATTGATATATTCTTAATTGTATCGATACATTCTAGGGTTTTAACCT
*
3507083 AAATGTATTGATACATTCTTCAA-TGTATCGATACAT
1 AAATGTATTGATATATTCTT-AATTGTATCGATACAT
3507119 GCAGCAAAAT
Statistics
Matches: 79, Mismatches: 5, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
50 3 0.04
51 33 0.42
52 41 0.52
53 2 0.03
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (52 bp):
AAATGTATTGATATATTCTTAATTGTATCGATACATTCTAGGGTTTTAACCT
Found at i:3512579 original size:13 final size:13
Alignment explanation
Indices: 3512561--3512586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3512551 ACAATTCTTC
3512561 ATGTATTGATACA
1 ATGTATTGATACA
3512574 ATGTATTGATACA
1 ATGTATTGATACA
3512587 TTGTCCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
ATGTATTGATACA
Found at i:3512606 original size:33 final size:33
Alignment explanation
Indices: 3512540--3512606 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
3512530 CGTTGGACAT
* **
3512540 AATGTATTGATACAATTCTTCATGTATTGATAC
1 AATGTATTGATACAATTCCTCATGTATCAATAC
*
3512573 AATGTATTGATACATTGTCCT-ATGTATCAATAC
1 AATGTATTGATACAAT-TCCTCATGTATCAATAC
3512606 A
1 A
3512607 TTTGACTTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 26 0.90
34 3 0.10
ACGTcount: A:0.34, C:0.13, G:0.12, T:0.40
Consensus pattern (33 bp):
AATGTATTGATACAATTCCTCATGTATCAATAC
Found at i:3512680 original size:19 final size:19
Alignment explanation
Indices: 3512635--3512690 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
3512625 CTGCCACTTT
*
3512635 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAA
* *
3512655 TATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
3512674 CATGTATCGATACAATG
1 CATGTATCGATACAATG
3512691 TTTCGATTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 18 0.58
20 13 0.42
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Done.