Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 129 of 295
Found at i:44269992 original size:21 final size:21
Alignment explanation
Indices: 44269926--44270002 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
44269916 TTAGGGTGTT
**
44269926 GGGTTTAT-GGTTTAGTTTATA
1 GGGTTT-TGGGTTTAGGATATA
* **
44269947 GGGTTTAGGGTTTAGTCTATA
1 GGGTTTTGGGTTTAGGATATA
*
44269968 GGGTTTTGGGTTTAGGATATT
1 GGGTTTTGGGTTTAGGATATA
*
44269989 GGGTATTGGGTTTA
1 GGGTTTTGGGTTTA
44270003 CAAATTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.17, C:0.01, G:0.35, T:0.47
Consensus pattern (21 bp):
GGGTTTTGGGTTTAGGATATA
Found at i:44273689 original size:34 final size:34
Alignment explanation
Indices: 44273648--44273764 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 34
44273638 AATAACTTAT
*
44273648 ATAAATATATATCATATCATAACTTACATAATAC
1 ATAAATATATATCATATAATAACTTACATAATAC
44273682 ATAAATATATATCATATAATAACTTACATAACTTACGTAATAC
1 ATAAATATATATCATATAATAAC-T---T-AC--A--TAATAC
44273725 ATAAATATATATCATATAATAACTTACATAACTTAC
1 ATAAATATATATCATATAATAACTTACATAA--TAC
44273761 ATAA
1 ATAA
44273765 TACATAAATA
Statistics
Matches: 71, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
34 25 0.35
35 1 0.01
36 8 0.11
38 3 0.04
39 3 0.04
41 1 0.01
42 1 0.01
43 29 0.41
ACGTcount: A:0.50, C:0.14, G:0.01, T:0.35
Consensus pattern (34 bp):
ATAAATATATATCATATAATAACTTACATAATAC
Found at i:44273709 original size:27 final size:27
Alignment explanation
Indices: 44273622--44273712 Score: 92
Period size: 27 Copynumber: 3.1 Consensus size: 27
44273612 ACCTTAATGT
* *
44273622 TAAATATATATCATACAATAACTTATA
1 TAAATATATATCATATAATAACTTACA
*
44273649 TAAATATATATCATATCATAACTTACATAATACA
1 TAAATATATATC--AT-ATAA-TAAC-T--TACA
44273683 TAAATATATATCATATAATAACTTACA
1 TAAATATATATCATATAATAACTTACA
44273710 TAA
1 TAA
44273713 CTTACGTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
27 19 0.36
29 3 0.06
30 6 0.11
31 7 0.13
32 3 0.06
34 15 0.28
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAATATATATCATATAATAACTTACA
Found at i:44273712 original size:9 final size:9
Alignment explanation
Indices: 44273700--44273866 Score: 89
Period size: 9 Copynumber: 19.0 Consensus size: 9
44273690 ATATCATATA
44273700 ATAACTTAC
1 ATAACTTAC
44273709 ATAACTTAC
1 ATAACTTAC
*
44273718 GTAA--TAC
1 ATAACTTAC
* *
44273725 ATAA-ATAT
1 ATAACTTAC
*
44273733 ATATCATATA-
1 ATAAC-T-TAC
44273743 ATAACTTAC
1 ATAACTTAC
44273752 ATAACTTAC
1 ATAACTTAC
44273761 ATAA--TAC
1 ATAACTTAC
* *
44273768 ATAA-ATAT
1 ATAACTTAC
** *
44273776 ATTTCATATC
1 ATAACTTA-C
*
44273786 ATAATTTAC
1 ATAACTTAC
44273795 ATAACTTAC
1 ATAACTTAC
*
44273804 ATACCTTAC
1 ATAACTTAC
* *
44273813 ATAAATT-T
1 ATAACTTAC
* *
44273821 ATATCATAGC
1 ATAACTTA-C
44273831 ATAACTTAC
1 ATAACTTAC
44273840 ATAACTTAC
1 ATAACTTAC
*
44273849 AAAACTTAC
1 ATAACTTAC
*
44273858 TTAACTTAC
1 ATAACTTAC
44273867 GTAATACATA
Statistics
Matches: 120, Mismatches: 28, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
7 13 0.11
8 15 0.12
9 76 0.63
10 14 0.12
11 2 0.02
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:44273712 original size:43 final size:43
Alignment explanation
Indices: 44273665--44273849 Score: 280
Period size: 43 Copynumber: 4.3 Consensus size: 43
44273655 TATATCATAT
44273665 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
1 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
*
44273708 CATAACTTACGTAATACATAAATATATATCATATAATAACTTA
1 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
* * *
44273751 CATAACTTACATAATACATAAATATATTTCATATCATAATTTA
1 CATAACTTACATAATACATAAATATATATCATATAATAACTTA
* * **
44273794 CATAACTTACATACCTTACATAAATTTATATCATAGCATAACTTA
1 CATAACTTACATA--ATACATAAATATATATCATATAATAACTTA
44273839 CATAACTTACA
1 CATAACTTACA
44273850 AAACTTACTT
Statistics
Matches: 130, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
43 94 0.72
45 36 0.28
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (43 bp):
CATAACTTACATAATACATAAATATATATCATATAATAACTTA
Found at i:44273877 original size:88 final size:86
Alignment explanation
Indices: 44273665--44273877 Score: 223
Period size: 86 Copynumber: 2.5 Consensus size: 86
44273655 TATATCATAT
* ** * * *
44273665 CATAACTTACATAATACATAAATATATATCATATAATAACTTACATAACTTACGTAATACATAAA
1 CATAACTTACAAAATACATAAATATACGTAATATCATAACTTACATAACTTACATAATACATAAA
*
44273730 TATATATCATATAATAACTTA
66 TATATATCATAGAATAACTTA
* ** * * *
44273751 CATAACTTACATAATACATAAATATATTTCATATCATAATTTACATAACTTACATACCTTACATA
1 CATAACTTACAAAATACATAAATATACGTAATATCATAACTTACATAACTTACATA--ATACATA
* *
44273816 AATTTATATCATAGCATAACTTA
64 AATATATATCATAGAATAACTTA
* *
44273839 CATAACTTACAAAACTTACTTAACT-TACGTAATA-CATAA
1 CATAACTTACAAAA--TACATAAATATACGTAATATCATAA
44273878 ATATACACTT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
86 52 0.48
88 44 0.40
89 6 0.06
90 7 0.06
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.35
Consensus pattern (86 bp):
CATAACTTACAAAATACATAAATATACGTAATATCATAACTTACATAACTTACATAATACATAAA
TATATATCATAGAATAACTTA
Found at i:44278955 original size:13 final size:14
Alignment explanation
Indices: 44278939--44278967 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
44278929 TTATAAATAT
44278939 TTATAAT-GTTTAA
1 TTATAATGGTTTAA
44278952 TTATAATGGTTTAA
1 TTATAATGGTTTAA
44278966 TT
1 TT
44278968 CGCCATTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (14 bp):
TTATAATGGTTTAA
Found at i:44279696 original size:33 final size:33
Alignment explanation
Indices: 44279659--44279745 Score: 106
Period size: 31 Copynumber: 2.7 Consensus size: 33
44279649 ATCATTTTAG
* * *
44279659 ATTTAATATTTTTGGTTGTATTTTTTATGCTAC
1 ATTTACTATTTTTGGTTGGATTTTTCATGCTAC
* *
44279692 ATTTACTGTTTTTGGTTGGA--TTTCATGCTAT
1 ATTTACTATTTTTGGTTGGATTTTTCATGCTAC
*
44279723 ATTTGCTATTTTTGGTTGGATTT
1 ATTTACTATTTTTGGTTGGATTT
44279746 AATGCAGGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
31 27 0.60
33 18 0.40
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (33 bp):
ATTTACTATTTTTGGTTGGATTTTTCATGCTAC
Found at i:44279884 original size:43 final size:43
Alignment explanation
Indices: 44279837--44279973 Score: 143
Period size: 43 Copynumber: 3.2 Consensus size: 43
44279827 AAAAAAGTCG
*
44279837 TGACTTTTAGAGGCACTTTTCCCACAAACGTCGCTAAAAGCCA
1 TGACTTTTAGCGGCACTTTTCCCACAAACGTCGCTAAAAGCCA
* * * * * *
44279880 TGACTTTTTGCGGCGCTTCT-CCAGAAACCTCCGCTAAAAGCCG
1 TGACTTTTAGCGGCACTTTTCCCACAAACGT-CGCTAAAAGCCA
* * *
44279923 TGACTTTTAGCGGCACTTTCCCCACAAATG-CTGCTAAAAGTCA
1 TGACTTTTAGCGGCACTTTTCCCACAAACGTC-GCTAAAAGCCA
*
44279966 TGATTTTT
1 TGACTTTT
44279974 TTTGGCATCT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
42 9 0.12
43 59 0.80
44 6 0.08
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (43 bp):
TGACTTTTAGCGGCACTTTTCCCACAAACGTCGCTAAAAGCCA
Found at i:44288692 original size:43 final size:42
Alignment explanation
Indices: 44288577--44288693 Score: 112
Period size: 41 Copynumber: 2.8 Consensus size: 42
44288567 TATTACGTGT
* * * * *
44288577 TTACGTGTAAGACCATGTCTAGAACATCGGCATCGTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACGTTGGCATCGTATGTGA
* * * *
44288619 TT-CGTGCAAGACCTTGTTTGAGACAG-TGGCATCGATATGTGA
1 TTACGTGTAAGACCATGTCTGGGAC-GTTGGCATCG-TATGTGA
*
44288661 TTACATGTAAGACCATGTCTGGGACGTTGGCAT
1 TTACGTGTAAGACCATGTCTGGGACGTTGGCAT
44288694 TGTACGATAT
Statistics
Matches: 57, Mismatches: 14, Indels: 7
0.73 0.18 0.09
Matches are distributed among these distances:
41 23 0.40
42 11 0.19
43 23 0.40
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.31
Consensus pattern (42 bp):
TTACGTGTAAGACCATGTCTGGGACGTTGGCATCGTATGTGA
Found at i:44288897 original size:18 final size:19
Alignment explanation
Indices: 44288863--44288900 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
44288853 GATGCAAATT
44288863 ATATATGATGTAAATGAAA
1 ATATATGATGTAAATGAAA
*
44288882 ATATATG-TGTATATGAAA
1 ATATATGATGTAAATGAAA
44288900 A
1 A
44288901 GTACGTTCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (19 bp):
ATATATGATGTAAATGAAA
Found at i:44298691 original size:17 final size:17
Alignment explanation
Indices: 44298665--44298697 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44298655 CCATTTGAGC
44298665 CGTGTAGGTCACACGGA
1 CGTGTAGGTCACACGGA
*
44298682 CGTGTGGGTCACACGG
1 CGTGTAGGTCACACGG
44298698 GTGAACCACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.24, G:0.39, T:0.18
Consensus pattern (17 bp):
CGTGTAGGTCACACGGA
Found at i:44299202 original size:40 final size:40
Alignment explanation
Indices: 44299158--44299234 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
44299148 ACAGTACCAC
44299158 TTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCCATAT
1 TTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCCATAT
* * *
44299198 TTGGTGTGTAGTGCTGGCTGGGTTGATTTTATCCCCA
1 TTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCCA
44299235 CATGGTATGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.13, C:0.16, G:0.32, T:0.39
Consensus pattern (40 bp):
TTGGTGTGTAGGGCTGGATGGGTCGATTTTATCCCCATAT
Found at i:44302416 original size:24 final size:24
Alignment explanation
Indices: 44302389--44302434 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
44302379 GGAAAGAAAA
*
44302389 TATGTTACTATGAACATATATACT
1 TATGTTACTACGAACATATATACT
*
44302413 TATGTTGCTACGAACATATATA
1 TATGTTACTACGAACATATATA
44302435 TGTTTCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (24 bp):
TATGTTACTACGAACATATATACT
Found at i:44307755 original size:19 final size:20
Alignment explanation
Indices: 44307731--44307781 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
44307721 CATTCAAACA
44307731 CCAGAAAATATTAT-ATTTT
1 CCAGAAAATATTATCATTTT
*
44307750 CCAGAAAAGTA-AATCATTTT
1 CCAGAAAA-TATTATCATTTT
*
44307770 CTAGAAAATATT
1 CCAGAAAATATT
44307782 TTACTAGCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (20 bp):
CCAGAAAATATTATCATTTT
Found at i:44318070 original size:18 final size:17
Alignment explanation
Indices: 44318037--44318070 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
44318027 GTTTGAGCCG
*
44318037 TATGGGCCACATAGGCA
1 TATGGGCCACACAGGCA
44318054 TATGGGCCCACACAGGC
1 TATGGG-CCACACAGGC
44318071 TGGCTACGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.15
Consensus pattern (17 bp):
TATGGGCCACACAGGCA
Found at i:44319640 original size:6 final size:6
Alignment explanation
Indices: 44319609--44319647 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
44319599 GGTTTCTAAG
* **
44319609 AATGGA AATGAA AATGGA AACAGA AATGGA AATGGA AAT
1 AATGGA AATGGA AATGGA AATGGA AATGGA AATGGA AAT
44319648 TTGCAATCCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.56, C:0.03, G:0.26, T:0.15
Consensus pattern (6 bp):
AATGGA
Found at i:44319827 original size:25 final size:25
Alignment explanation
Indices: 44319793--44319883 Score: 94
Period size: 25 Copynumber: 3.7 Consensus size: 25
44319783 TTCTTGAAAT
*
44319793 TTTTATTAGGGTAAAATCGTCAAAA
1 TTTTACTAGGGTAAAATCGTCAAAA
* *
44319818 ATTTACTAGGAT-AAATCGTCAAAA
1 TTTTACTAGGGTAAAATCGTCAAAA
* * ** *
44319842 TTTTATTGGGGTAAAAGAGTCAACA
1 TTTTACTAGGGTAAAATCGTCAAAA
*
44319867 TTTTACTAGGTTAAAAT
1 TTTTACTAGGGTAAAAT
44319884 TGGGGTAAGA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
24 20 0.39
25 31 0.61
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (25 bp):
TTTTACTAGGGTAAAATCGTCAAAA
Found at i:44319856 original size:24 final size:24
Alignment explanation
Indices: 44319793--44319856 Score: 83
Period size: 24 Copynumber: 2.6 Consensus size: 24
44319783 TTCTTGAAAT
44319793 TTTTATTAGGGTAAAATCGTCAAAA
1 TTTTATTAGGGT-AAATCGTCAAAA
* * *
44319818 ATTTACTAGGATAAATCGTCAAAA
1 TTTTATTAGGGTAAATCGTCAAAA
*
44319842 TTTTATTGGGGTAAA
1 TTTTATTAGGGTAAA
44319857 AGAGTCAACA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.39, C:0.08, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTTATTAGGGTAAATCGTCAAAA
Found at i:44330379 original size:12 final size:12
Alignment explanation
Indices: 44330362--44330392 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
44330352 CACCACACGA
44330362 CCGTGTGGTAGG
1 CCGTGTGGTAGG
44330374 CCGTGTGGTAGG
1 CCGTGTGGTAGG
44330386 CCGTGTG
1 CCGTGTG
44330393 CTAGAACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.19, G:0.48, T:0.26
Consensus pattern (12 bp):
CCGTGTGGTAGG
Found at i:44348447 original size:34 final size:33
Alignment explanation
Indices: 44348409--44348525 Score: 110
Period size: 34 Copynumber: 3.5 Consensus size: 33
44348399 TTATGCTTAT
*
44348409 TGTCCTAGTAGACTTATCTTTGATCTATATTTAC
1 TGTCCTAGCAGAC-TATCTTTGATCTATATTTAC
* *
44348443 TGTCCTAGCAGACTATCTTTGTTCTGTATTTAC
1 TGTCCTAGCAGACTATCTTTGATCTATATTTAC
* * * * **
44348476 T-ACCTTAGCTGACTTATCTCTGTTCTGCATTTAC
1 TGTCC-TAGCAGAC-TATCTTTGATCTATATTTAC
*
44348510 TGTCCCAGCAGACTAT
1 TGTCCTAGCAGACTAT
44348526 GTCTATTCTG
Statistics
Matches: 70, Mismatches: 10, Indels: 7
0.80 0.11 0.08
Matches are distributed among these distances:
32 2 0.03
33 29 0.41
34 37 0.53
35 2 0.03
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.43
Consensus pattern (33 bp):
TGTCCTAGCAGACTATCTTTGATCTATATTTAC
Found at i:44348473 original size:33 final size:34
Alignment explanation
Indices: 44348409--44348559 Score: 137
Period size: 33 Copynumber: 4.5 Consensus size: 34
44348399 TTATGCTTAT
* * * *
44348409 TGTCCTAGTAGACTTATCTTTGATCTATATTTAC
1 TGTCCTAGCAGACTTATCTCTGTTCTGTATTTAC
*
44348443 TGTCCTAGCAGAC-TATCTTTGTTCTGTATTTAC
1 TGTCCTAGCAGACTTATCTCTGTTCTGTATTTAC
* * *
44348476 T-ACCTTAGCTGACTTATCTCTGTTCTGCATTTAC
1 TGTCC-TAGCAGACTTATCTCTGTTCTGTATTTAC
* * * *
44348510 TGTCCCAGCAGAC-TATGTCTATTCTGTGTTTAC
1 TGTCCTAGCAGACTTATCTCTGTTCTGTATTTAC
* * *
44348543 TATCCCAACAGACTTAT
1 TGTCCTAGCAGACTTAT
44348560 TATGTCTGTG
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.02
33 53 0.55
34 40 0.41
35 2 0.02
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.42
Consensus pattern (34 bp):
TGTCCTAGCAGACTTATCTCTGTTCTGTATTTAC
Found at i:44348508 original size:67 final size:67
Alignment explanation
Indices: 44348419--44348544 Score: 171
Period size: 67 Copynumber: 1.9 Consensus size: 67
44348409 TGTCCTAGTA
* * * * *
44348419 GACTTATCTTTGATCTATATTTACTGTCCTAGCAGACTATCTTTGTTCTGTATTTACTACCTTAG
1 GACTTATCTCTGATCTACATTTACTGTCCCAGCAGACTATCTCTATTCTGTATTTACTACCTTAG
44348484 CT
66 CT
* * * *
44348486 GACTTATCTCTGTTCTGCATTTACTGTCCCAGCAGACTATGTCTATTCTGTGTTTACTA
1 GACTTATCTCTGATCTACATTTACTGTCCCAGCAGACTATCTCTATTCTGTATTTACTA
44348545 TCCCAACAGA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
67 50 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (67 bp):
GACTTATCTCTGATCTACATTTACTGTCCCAGCAGACTATCTCTATTCTGTATTTACTACCTTAG
CT
Found at i:44348557 original size:67 final size:67
Alignment explanation
Indices: 44348418--44348559 Score: 160
Period size: 67 Copynumber: 2.1 Consensus size: 67
44348408 TTGTCCTAGT
* * * * * *
44348418 AGACTTATCTTTGATCTATATTTACTGTCCTAGCAGACTATCTTTGTTCTGTATTTACTACCTTA
1 AGACTTATCTCTGATCTACATTTACTGTCCCAGCAGACTATCTCTATTCTGTATTTACTACCTCA
*
44348483 GC
66 AC
* * * * *
44348485 TGACTTATCTCTGTTCTGCATTTACTGTCCCAGCAGACTATGTCTATTCTGTGTTTACTATCC-C
1 AGACTTATCTCTGATCTACATTTACTGTCCCAGCAGACTATCTCTATTCTGTATTTACTA-CCTC
44348549 AAC
65 AAC
44348552 AGACTTAT
1 AGACTTAT
44348560 TATGTCTGTG
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
67 59 0.97
68 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (67 bp):
AGACTTATCTCTGATCTACATTTACTGTCCCAGCAGACTATCTCTATTCTGTATTTACTACCTCA
AC
Found at i:44350246 original size:26 final size:26
Alignment explanation
Indices: 44350217--44350277 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
44350207 AATTTTCTCG
*
44350217 AAATTTTATCAAGGGTAAAATCGTCA
1 AAATTTTACCAAGGGTAAAATCGTCA
* * * *
44350243 AAATTTTACCAGGGGTAAATTTGTTA
1 AAATTTTACCAAGGGTAAAATCGTCA
44350269 AAATTTTAC
1 AAATTTTAC
44350278 TAAAGTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (26 bp):
AAATTTTACCAAGGGTAAAATCGTCA
Found at i:44361053 original size:13 final size:13
Alignment explanation
Indices: 44361033--44361071 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
44361023 CCATTTCAAA
44361033 TACAGATAA-CAG
1 TACAGATAAGCAG
44361045 TATCAGATAAGCAG
1 TA-CAGATAAGCAG
*
44361059 TACAGATATGCAG
1 TACAGATAAGCAG
44361072 AATCCTACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 2 0.08
13 17 0.71
14 5 0.21
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (13 bp):
TACAGATAAGCAG
Found at i:44362955 original size:53 final size:53
Alignment explanation
Indices: 44362893--44362997 Score: 201
Period size: 53 Copynumber: 2.0 Consensus size: 53
44362883 GATTAAATCG
44362893 GTACTGCCTCAAGATTGAGACATGAAACACATCGTAGATACGGTCTAACTCTA
1 GTACTGCCTCAAGATTGAGACATGAAACACATCGTAGATACGGTCTAACTCTA
*
44362946 GTACTGCCTCAAGATTGAGACGTGAAACACATCGTAGATACGGTCTAACTCT
1 GTACTGCCTCAAGATTGAGACATGAAACACATCGTAGATACGGTCTAACTCT
44362998 GGAGGTAGCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (53 bp):
GTACTGCCTCAAGATTGAGACATGAAACACATCGTAGATACGGTCTAACTCTA
Found at i:44370787 original size:13 final size:13
Alignment explanation
Indices: 44370771--44370795 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44370761 TTAAATGAGT
44370771 TAATTAGTTTAAA
1 TAATTAGTTTAAA
44370784 TAATTAGTTTAA
1 TAATTAGTTTAA
44370796 TAAACAAACC
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TAATTAGTTTAAA
Found at i:44376194 original size:6 final size:6
Alignment explanation
Indices: 44376170--44376250 Score: 64
Period size: 6 Copynumber: 13.7 Consensus size: 6
44376160 TCCTCCTATT
*
44376170 TTTTTA TTTATTTA GTTTTA TTTTTA -TTTTA -TTTTA -TTTTA -TTTTA
1 TTTTTA -TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
44376216 TTTTTA TTTTCA -TTTTA ATTTTA TTATTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA -T-TTTTA TTTT
44376251 GAAAGACATA
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
5 24 0.38
6 27 0.42
7 4 0.06
8 9 0.14
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:44376199 original size:5 final size:5
Alignment explanation
Indices: 44376171--44376250 Score: 87
Period size: 5 Copynumber: 15.8 Consensus size: 5
44376161 CCTCCTATTT
44376171 TTTTA -TTTA -TTTA GTTTTA TTTTTA TTTTA TTTTA TTTTA TTTTA TTTTTA
1 TTTTA TTTTA TTTTA -TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
44376222 TTTTCA TTTTAA TTTTA --TTA TTTTA TTTT
1 TTTT-A TTTT-A TTTTA TTTTA TTTTA TTTT
44376251 GAAAGACATA
Statistics
Matches: 67, Mismatches: 2, Indels: 12
0.83 0.02 0.15
Matches are distributed among these distances:
3 3 0.04
4 8 0.12
5 32 0.48
6 24 0.36
ACGTcount: A:0.20, C:0.01, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:44376242 original size:26 final size:25
Alignment explanation
Indices: 44376186--44376250 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 25
44376176 TTTATTTAGT
44376186 TTTATTTTTATTTTATTTTATTTTA
1 TTTATTTTTATTTTATTTTATTTTA
44376211 TTTTATTTTTATTTTCATTTTAATTTTA
1 -TTTATTTTTATTTT-ATTTT-ATTTTA
44376239 -TTA-TTTTATTTT
1 TTTATTTTTATTTT
44376251 GAAAGACATA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.24
26 17 0.46
27 5 0.14
28 6 0.16
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTATTTTTATTTTATTTTATTTTA
Found at i:44383596 original size:3 final size:3
Alignment explanation
Indices: 44383588--44383619 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44383578 TGCTCTTTGC
44383588 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44383620 ATAACAACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44383665 original size:16 final size:15
Alignment explanation
Indices: 44383624--44383667 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
44383614 TATTATATAA
44383624 CAACACTTA-TTTTT
1 CAACACTTATTTTTT
44383638 CAACACTTATTTTTT
1 CAACACTTATTTTTT
*
44383653 CAACATTTAATTTTT
1 CAACACTT-ATTTTT
44383668 AATTTATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 9 0.33
15 12 0.44
16 6 0.22
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (15 bp):
CAACACTTATTTTTT
Found at i:44384413 original size:20 final size:22
Alignment explanation
Indices: 44384373--44384414 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
44384363 TTTAATCATA
*
44384373 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
44384395 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
44384415 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:44384438 original size:13 final size:14
Alignment explanation
Indices: 44384422--44384463 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
44384412 TTTCAATTTT
44384422 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
44384435 ATTTTAAAAATAATA
1 ATTTTAATAAT-ATA
44384450 ATTTTAAATAATAT
1 ATTTT-AATAATAT
44384464 TATTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:44384448 original size:16 final size:16
Alignment explanation
Indices: 44384426--44384462 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
44384416 AATTTTATTT
44384426 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
44384443 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
44384458 TAATA
1 TAATA
44384463 TTATTCACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:44387960 original size:6 final size:6
Alignment explanation
Indices: 44387949--44387983 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
44387939 AACTTGATAG
*
44387949 TAGTGA TAGTGA TAGTGA TAGTGA TAGTAA TAGTG
1 TAGTGA TAGTGA TAGTGA TAGTGA TAGTGA TAGTG
44387984 GAAAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (6 bp):
TAGTGA
Found at i:44390806 original size:33 final size:33
Alignment explanation
Indices: 44390729--44390807 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 33
44390719 TAAGTCCGCT
*
44390729 GAGACAGTAAACACAAAACAGGATAAGTTCATC
1 GAGACAGTAAACACAAAACAGGATAAGTTCACC
* * **
44390762 GGGACAATAAACACGGAACATGG-TAAG-TCTACC
1 GAGACAGTAAACACAAAACA-GGATAAGTTC-ACC
44390795 GAGACAGTAAACA
1 GAGACAGTAAACA
44390808 TAGGTAAGTC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (33 bp):
GAGACAGTAAACACAAAACAGGATAAGTTCACC
Found at i:44395291 original size:21 final size:20
Alignment explanation
Indices: 44395263--44395303 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
44395253 GTATTTTCAG
*
44395263 TTTTTATTGAGAGAAATTAC
1 TTTTTATTGAAAGAAATTAC
*
44395283 TTTTCTATTGAAAGTAATTAC
1 TTTT-TATTGAAAGAAATTAC
44395304 ATTGTTTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTTTATTGAAAGAAATTAC
Found at i:44398035 original size:27 final size:27
Alignment explanation
Indices: 44398005--44398064 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
44397995 ATAAGGGCAT
* * * *
44398005 TTCCTTCATAGTTCACCATGTATACCG
1 TTCCTTCAAAGTTCACCACGAATACCA
*
44398032 TTCCTTCAAAGTTCGCCACGAATACCA
1 TTCCTTCAAAGTTCACCACGAATACCA
44398059 TTCCTT
1 TTCCTT
44398065 TAGAATTCAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.23, C:0.32, G:0.10, T:0.35
Consensus pattern (27 bp):
TTCCTTCAAAGTTCACCACGAATACCA
Found at i:44398202 original size:27 final size:27
Alignment explanation
Indices: 44398155--44398227 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
44398145 TTCTATTTTT
* ** *
44398155 GCCAGAAAGGCTTTCAATTCATTGTTC
1 GCCACAAAGGCTTTCTTTTCATGGTTC
* *
44398182 GTCACAAAGGCTTTCTTTTCATGGTTT
1 GCCACAAAGGCTTTCTTTTCATGGTTC
* *
44398209 GCCATAAATGCTTTCTTTT
1 GCCACAAAGGCTTTCTTTT
44398228 TTTACATGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (27 bp):
GCCACAAAGGCTTTCTTTTCATGGTTC
Found at i:44400409 original size:98 final size:98
Alignment explanation
Indices: 44400240--44400421 Score: 303
Period size: 98 Copynumber: 1.9 Consensus size: 98
44400230 TAAAATTGTG
44400240 ATTAAGTCCTTCATATTTCTCCACTCATTCAATTTGGTCCCTACACACCAATCCCACGTTACAAG
1 ATTAAGTCCTTCATATTTCTCCACTCATTCAATTTGGTCCCTACACACCAATCCCACGTTACAAG
44400305 AAATTGGGTTATTTTCACTCTTAGTAATATTAT
66 AAATTGGGTTATTTTCACTCTTAGTAATATTAT
* * * * *
44400338 ATTAAGTCCCTT-ATATTTCTCCATTTATTCAATTTGGTCCTTACATACCAATCCCATGTTACAA
1 ATTAAGT-CCTTCATATTTCTCCACTCATTCAATTTGGTCCCTACACACCAATCCCACGTTACAA
44400402 GAAATTGGGTTATTTTCACT
65 GAAATTGGGTTATTTTCACT
44400422 TTTGGTCCTT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 74 0.95
99 4 0.05
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (98 bp):
ATTAAGTCCTTCATATTTCTCCACTCATTCAATTTGGTCCCTACACACCAATCCCACGTTACAAG
AAATTGGGTTATTTTCACTCTTAGTAATATTAT
Found at i:44402405 original size:11 final size:11
Alignment explanation
Indices: 44402389--44402427 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
44402379 TATTTATTTT
44402389 TAAAAAAATTC
1 TAAAAAAATTC
*
44402400 T-AAAAATTTC
1 TAAAAAAATTC
*
44402410 AAAAAAAATTC
1 TAAAAAAATTC
44402421 TAAAAAA
1 TAAAAAA
44402428 TATAAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.67, C:0.08, G:0.00, T:0.26
Consensus pattern (11 bp):
TAAAAAAATTC
Found at i:44413919 original size:16 final size:15
Alignment explanation
Indices: 44413898--44413930 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
44413888 ATTTTAATTC
44413898 TTTATTTATTCATCTA
1 TTTATTTATTCAT-TA
44413914 TTTATTTATTCATTA
1 TTTATTTATTCATTA
44413929 TT
1 TT
44413931 CCTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATTTATTCATTA
Found at i:44417423 original size:16 final size:15
Alignment explanation
Indices: 44417402--44417443 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
44417392 TAATTGTTTA
44417402 TAATATTTATATTATG
1 TAATATTTATATT-TG
*
44417418 TAATA-TTATAATTG
1 TAATATTTATATTTG
*
44417432 TGATATTTATAT
1 TAATATTTATAT
44417444 GAGATGATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 6 0.27
15 11 0.50
16 5 0.23
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TAATATTTATATTTG
Found at i:44426030 original size:30 final size:30
Alignment explanation
Indices: 44425994--44426053 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
44425984 TTCTCGAGCC
* *
44425994 TAGGGGAAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGAAAAAATATAATTATGCAAAAGTT
* *
44426024 TAGGGGAAAAAATATAATTTTGCCAAAGTT
1 TAGGGGAAAAAATATAATTATGCAAAAGTT
44426054 CATATTAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.23, T:0.28
Consensus pattern (30 bp):
TAGGGGAAAAAATATAATTATGCAAAAGTT
Found at i:44428263 original size:3 final size:3
Alignment explanation
Indices: 44428230--44428304 Score: 60
Period size: 3 Copynumber: 24.7 Consensus size: 3
44428220 TTGAAAGGGG
* * * * *
44428230 TTC TTC TTTC TTT TTC TTT TTC TTA TTC TTC TTC TTC TTC CTC GTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * *
44428276 CTC TTC ATC TTC CTC TTC TTC TTC CTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
44428305 TCTTAAGTGG
Statistics
Matches: 55, Mismatches: 16, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
3 52 0.95
4 3 0.05
ACGTcount: A:0.03, C:0.33, G:0.01, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:44430370 original size:48 final size:48
Alignment explanation
Indices: 44430312--44430677 Score: 296
Period size: 48 Copynumber: 7.6 Consensus size: 48
44430302 TATGTGTGCT
* * *
44430312 AGTGTAAGACCATGTCTAGGACATGGCGTCGGCCATGATATGAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
* * * * *
44430360 AGTGTAAGACCATGTCTAGGACATGGCAACGG-CATTGATATGTGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAGAGCC
* * *
44430408 AGTGTAAGACCATGTCTGGGATATGGCATCGACCA-CATCATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGAT-ATGAGAGCC
* * * * * * * * *
44430456 AGTGTAAGGCGATGCCTAGGACATGGTATCAG-CATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAGAGCC
* * * * * *
44430504 AATGTAAGACGATGTCTGGGACATGGCATCGACCA-CATCATAAAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGAT-ATGAGAGCC
* ** * *
44430552 AGTGTAAGACCATGTCTGGGACATGGCAT-TGATATTGAGATGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-TGATATGAGAGCC
* * *
44430600 AGTGTGAGACCATGTCTGGGACATGGCATCGACC-TCGACATGTA-AGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-GATATG-AGAGCC
* *
44430648 AGTGTAAGACCATGTTTGGAACATGGCATC
1 AGTGTAAGACCATGTCTGGGACATGGCATC
44430678 AGCAATTCAC
Statistics
Matches: 246, Mismatches: 60, Indels: 24
0.75 0.18 0.07
Matches are distributed among these distances:
47 10 0.04
48 228 0.93
49 8 0.03
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.23
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCATGATATGAGAGCC
Found at i:44430463 original size:96 final size:96
Alignment explanation
Indices: 44430299--44430677 Score: 467
Period size: 96 Copynumber: 3.9 Consensus size: 96
44430289 AACATTTGGG
* * * *
44430299 TGATATGTGTGCTAGTGTAAGACCATGTCTAGGACATGGCGTCGGCCATGAT-ATGAAAGCCAGT
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCA-CATCATGAAAGCCAGT
*
44430363 GTAAGACCATGTCTAGGACATGGCAACGGCAT
65 GTAAGACCATGTCTAGGACATGGCATCGGCAT
* *
44430395 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGATATGGCATCGACCACATCATGAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATCATGAAAGCCAGTG
* * * * *
44430460 TAAGGCGATGCCTAGGACATGGTATCAGCAT
66 TAAGACCATGTCTAGGACATGGCATCGGCAT
* * * *
44430491 TGATATGTGCGCTAATGTAAGACGATGTCTGGGACATGGCATCGACCACATCATAAAAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATCATGAAAGCCAGTG
* * **
44430556 TAAGACCATGTCTGGGACATGGCATTGATAT
66 TAAGACCATGTCTAGGACATGGCATCGGCAT
* * * * * *
44430587 TGAGATGAGAGCTAGTGTGAGACCATGTCTGGGACATGGCATCGACCTCGA-CATGTAAGCCAGT
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCAC-ATCATGAAAGCCAGT
*
44430651 GTAAGACCATGT-TTGGAACATGGCATC
65 GTAAGACCATGTCTAGG-ACATGGCATC
44430678 AGCAATTCAC
Statistics
Matches: 242, Mismatches: 38, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
95 5 0.02
96 236 0.98
97 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (96 bp):
TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGACCACATCATGAAAGCCAGTG
TAAGACCATGTCTAGGACATGGCATCGGCAT
Found at i:44437299 original size:24 final size:24
Alignment explanation
Indices: 44437272--44437321 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
44437262 TTTAGTAGGG
44437272 TTGGTATTTGATGACATTAGCTAA
1 TTGGTATTTGATGACATTAGCTAA
*
44437296 TTGGTATTTTATGACATTAGCTAA
1 TTGGTATTTGATGACATTAGCTAA
44437320 TT
1 TT
44437322 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.18, T:0.46
Consensus pattern (24 bp):
TTGGTATTTGATGACATTAGCTAA
Found at i:44438223 original size:48 final size:49
Alignment explanation
Indices: 44438165--44438483 Score: 321
Period size: 48 Copynumber: 6.6 Consensus size: 49
44438155 TGTGTGCTAA
* *
44438165 TGTAAGACCATGTCTAGGACATGGCGTCGGCCA-TGATATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATTGATATGAGAGCCAG
* * * * *
44438213 TGTAAAACCATGTCTGGGACATGGCAACGG-CATTGATATGTGTGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATTGATATGAGAGCCAG
* *
44438261 GGTAAGACCATGTCTGGGACATGGCATCGGCCA-T-ATCATAAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATTGAT-ATGAGAGCCAG
* * * * * *
44438309 TGTAAGATCATGTCTAGGACATGGTATCGG-CATTGATATGTGCGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATTGATATGAGAGCCAG
* * * * *
44438357 TGTAAGACAATGTCTGGGACATGGCATC-GACATTGAGACGAGAGCTAG
1 TGTAAGACCATGTCTGGGACATGGCATCGGCCATTGATATGAGAGCCAG
* * * *
44438405 TGTGAA-ACCATGTCTGGGACATGGCATCGACC-TTGACATGTGAGGCAG
1 TGT-AAGACCATGTCTGGGACATGGCATCGGCCATTGATATGAGAGCCAG
* * *
44438453 TGTAAGACCATGTTTTGAACATGGCATCGGC
1 TGTAAGACCATGTCTGGGACATGGCATCGGC
44438484 AATTCACCCT
Statistics
Matches: 220, Mismatches: 42, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
47 9 0.04
48 204 0.93
49 7 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (49 bp):
TGTAAGACCATGTCTGGGACATGGCATCGGCCATTGATATGAGAGCCAG
Found at i:44438321 original size:96 final size:94
Alignment explanation
Indices: 44438150--44438483 Score: 377
Period size: 96 Copynumber: 3.5 Consensus size: 94
44438140 GATATTTGGG
* * * *
44438150 TGATATGTGTGCTAATGTAAGACCATGTCTAGGACATGGCGTCGGCCATGATATGAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCAT-ATATAAGAGCCAGTG
*
44438215 TAAAACCATGTCTGGGACATGGCAACGGCAT
65 T-AAACCATGTCTGGGACATGGCATCGGCAT
*
44438246 TGATATGTGTGCTAGGGTAAGACCATGTCTGGGACATGGCATCGGCCATATCATAAGAGCCAGTG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATAT-ATAAGAGCCAGTG
* * *
44438311 TAAGATCATGTCTAGGACATGGTATCGGCAT
65 TAA-ACCATGTCTGGGACATGGCATCGGCAT
* * * * *
44438342 TGATATGTGCGCTAGTGTAAGACAATGTCTGGGACATGGCATC-GACAT-TGAGACGAGAGCTAG
1 TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATAT-ATA--AGAGCCAG
* *
44438405 TGTGAAACCATGTCTGGGACATGGCATCGACCT
63 TGT-AAACCATGTCTGGGACATGGCATCGGCAT
* * * * *
44438438 TGACATGTGAGGC-AGTGTAAGACCATGTTTTGAACATGGCATCGGC
1 TGATATGTG-TGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC
44438484 AATTCACCCT
Statistics
Matches: 203, Mismatches: 28, Indels: 13
0.83 0.11 0.05
Matches are distributed among these distances:
94 3 0.01
95 8 0.04
96 187 0.92
97 5 0.02
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (94 bp):
TGATATGTGTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCATATATAAGAGCCAGTGT
AAACCATGTCTGGGACATGGCATCGGCAT
Found at i:44438484 original size:144 final size:143
Alignment explanation
Indices: 44438165--44438484 Score: 383
Period size: 144 Copynumber: 2.2 Consensus size: 143
44438155 TGTGTGCTAA
* *
44438165 TGTAAGACCATGTCTAGGACATGGCGTCGGCCATGATATGAGAGCCAGTGTAAAACCATGTCTGG
1 TGTAAGACCATGTCTAGGACATGGCATCGG-CATGATATGAGAGCCAGTGTAAAACAATGTCTGG
* * * * * *
44438230 GACATGGCAACGGCATTGATATGTGTGCTAGGGTAAGACCATGTCTGGGACATGGCATCGGCCAT
65 GACATGGCAACGACATTGAGACGAGAGCTAGGGTAAGACCATGTCTGGGACATGGCATCGACCAT
44438295 ATCATAAGAGCCAG
130 ATCATAAGAGCCAG
* * * * * *
44438309 TGTAAGATCATGTCTAGGACATGGTATCGGCATTGATATGTGCGCTAGTGTAAGACAATGTCTGG
1 TGTAAGACCATGTCTAGGACATGGCATCGGCA-TGATATGAGAGCCAGTGTAAAACAATGTCTGG
* * *
44438374 GACATGGCATCGACATTGAGACGAGAGCTAGTGTGAA-ACCATGTCTGGGACATGGCATCGACCT
65 GACATGGCAACGACATTGAGACGAGAGCTAGGGT-AAGACCATGTCTGGGACATGGCATCGACCA
** *
44438438 TGA-CATGTGAGGCAG
129 T-ATCATAAGAGCCAG
* * *
44438453 TGTAAGACCATGTTTTGAACATGGCATCGGCA
1 TGTAAGACCATGTCTAGGACATGGCATCGGCA
44438485 ATTCACCCTC
Statistics
Matches: 148, Mismatches: 25, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
143 2 0.01
144 143 0.97
145 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.24
Consensus pattern (143 bp):
TGTAAGACCATGTCTAGGACATGGCATCGGCATGATATGAGAGCCAGTGTAAAACAATGTCTGGG
ACATGGCAACGACATTGAGACGAGAGCTAGGGTAAGACCATGTCTGGGACATGGCATCGACCATA
TCATAAGAGCCAG
Found at i:44441508 original size:28 final size:29
Alignment explanation
Indices: 44441463--44441517 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
44441453 GCGAACTCTG
44441463 AAAGAATAGCCTGTGTGGCAAACTCTAAA
1 AAAGAATAGCCTGTGTGGCAAACTCTAAA
*
44441492 AAAGAAT-GCCT-TGGTGGCATACTCTA
1 AAAGAATAGCCTGT-GTGGCAAACTCTA
44441518 TGTGGTTGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 16 0.67
29 7 0.29
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (29 bp):
AAAGAATAGCCTGTGTGGCAAACTCTAAA
Found at i:44445694 original size:45 final size:45
Alignment explanation
Indices: 44445639--44445742 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
44445629 GCAGTAGCAG
* * *
44445639 TAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCTGTAATAA
1 TAACGGTAACAGTATTCAACACACAAAGTGTC-GAATCGGTAACAA
* *
44445684 TAACGGTAACAGTATTCAACATACAAAGTGTCGAATCGGTAACAG
1 TAACGGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAACAA
*
44445729 TAATGGTAACAGTA
1 TAACGGTAACAGTA
44445743 ATAGTAGCCA
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 51 0.98
46 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (45 bp):
TAACGGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAACAA
Found at i:44446031 original size:40 final size:40
Alignment explanation
Indices: 44445955--44446035 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
44445945 CTTCATTAGA
** *
44445955 AATTTTACAGTTCAATGCAATATACGTAACATTATTCAAT
1 AATTTTACAGTTCAATGCAATATACAAAACAATATTCAAT
* ** *
44445995 AATTTTACAGTTCAATTCGGTATTCAAAACAATATTCAAT
1 AATTTTACAGTTCAATGCAATATACAAAACAATATTCAAT
44446035 A
1 A
44446036 TCCCATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (40 bp):
AATTTTACAGTTCAATGCAATATACAAAACAATATTCAAT
Found at i:44446373 original size:13 final size:12
Alignment explanation
Indices: 44446342--44446400 Score: 59
Period size: 13 Copynumber: 4.7 Consensus size: 12
44446332 ATGTTCTCTG
44446342 TTTCTTTTTTT-
1 TTTCTTTTTTTA
44446353 TTTACTTTGTTTTA
1 TTT-CTTT-TTTTA
44446367 TTTCTTTATTTTA
1 TTTCTTT-TTTTA
44446380 TTTCATTTCTTTTA
1 TTTC-TTT-TTTTA
44446394 -TTCTTTT
1 TTTCTTTT
44446401 ATTTTATTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 4 0.10
12 7 0.17
13 20 0.48
14 11 0.26
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTTTA
Found at i:44446378 original size:27 final size:27
Alignment explanation
Indices: 44446348--44446414 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
44446338 TCTGTTTCTT
* *
44446348 TTTTTTTTACTTTGTTTTATT-TCTTTA
1 TTTTATTTACTTTCTTTTATTCT-TTTA
44446375 TTTTATTT-CATTTCTTTTATTCTTTTA
1 TTTTATTTAC-TTTCTTTTATTCTTTTA
*
44446402 TTTTATTAACTTT
1 TTTTATTTACTTT
44446415 ATAATAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 1 0.03
27 31 0.91
28 2 0.06
ACGTcount: A:0.15, C:0.09, G:0.01, T:0.75
Consensus pattern (27 bp):
TTTTATTTACTTTCTTTTATTCTTTTA
Found at i:44446407 original size:13 final size:13
Alignment explanation
Indices: 44446362--44446408 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
44446352 TTTTACTTTG
44446362 TTTTATT-TCTTTA
1 TTTTATTCT-TTTA
* *
44446375 TTTTATTTCATTTC
1 TTTTA-TTCTTTTA
44446389 TTTTATTCTTTTA
1 TTTTATTCTTTTA
44446402 TTTTATT
1 TTTTATT
44446409 AACTTTATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 18 0.64
14 10 0.36
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTATTCTTTTA
Found at i:44446704 original size:20 final size:20
Alignment explanation
Indices: 44446681--44446746 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
44446671 GTCTTTATTT
44446681 TAATTTATTTTTAATAATAA
1 TAATTTATTTTTAATAATAA
* *
44446701 TAA-TCATAATTTAATAAT-A
1 TAATTTAT-TTTTAATAATAA
*
44446720 TAAATTATTATTTAATAGAATAA
1 TAATTTATT-TTTAAT--AATAA
44446743 TAAT
1 TAAT
44446747 AAATAGTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
19 7 0.20
20 21 0.60
22 3 0.09
23 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATTTTTAATAATAA
Found at i:44452914 original size:45 final size:45
Alignment explanation
Indices: 44452857--44452963 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
44452847 GTAGCAATAG
* *
44452857 CAGTAACAGTAACAGTATTCAACACACAAAATG-CTGAATCTGTAA
1 CAGTAACGGTAACAGTATTCAACACACAAAATGTC-GAATCGGTAA
* *
44452902 TAGTAACGGTAACAGTATTCAACACACAAAGTGTCGAATCGGTAA
1 CAGTAACGGTAACAGTATTCAACACACAAAATGTCGAATCGGTAA
*
44452947 CAATAACGGTAACAGTA
1 CAGTAACGGTAACAGTA
44452964 ACAGTAGTCT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 54 0.98
46 1 0.02
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
CAGTAACGGTAACAGTATTCAACACACAAAATGTCGAATCGGTAA
Found at i:44453604 original size:27 final size:27
Alignment explanation
Indices: 44453574--44453640 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
44453564 TATGTTTCTT
* * *
44453574 TTTTTTTTACTTTGTTTTATTTTTTTA
1 TTTTATTTACTTTCTTTTATTCTTTTA
*
44453601 TTTTATTT-CATTTCTTTTGTTCTTTTA
1 TTTTATTTAC-TTTCTTTTATTCTTTTA
*
44453628 TTTTATTAACTTT
1 TTTTATTTACTTT
44453641 ATAATAATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
26 1 0.03
27 31 0.94
28 1 0.03
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.76
Consensus pattern (27 bp):
TTTTATTTACTTTCTTTTATTCTTTTA
Found at i:44453613 original size:18 final size:18
Alignment explanation
Indices: 44453575--44453618 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44453565 ATGTTTCTTT
* *
44453575 TTTTTTTACTTTGTTTTA
1 TTTTTTTACTTTATTTCA
*
44453593 TTTTTTTATTTTATTTCA
1 TTTTTTTACTTTATTTCA
44453611 TTTCTTTT
1 TTT-TTTT
44453619 GTTCTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (18 bp):
TTTTTTTACTTTATTTCA
Found at i:44453618 original size:22 final size:21
Alignment explanation
Indices: 44453568--44453630 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
44453558 ATATCTTATG
**
44453568 TTTC-TTTTTTTTTTACTTTGT
1 TTTCTTTTTTTTTTTA-TTTCA
*
44453589 TTTATTTTTTTATTTTATTTCA
1 TTTCTTTTTTT-TTTTATTTCA
*
44453611 TTTCTTTTGTTCTTTTATTT
1 TTTCTTTT-TTTTTTTATTT
44453631 TATTAACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 3 0.09
22 24 0.71
23 7 0.21
ACGTcount: A:0.10, C:0.08, G:0.03, T:0.79
Consensus pattern (21 bp):
TTTCTTTTTTTTTTTATTTCA
Found at i:44453931 original size:20 final size:20
Alignment explanation
Indices: 44453908--44453973 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
44453898 GTCTTTATTT
44453908 TAATTTATTTTTAATAATAA
1 TAATTTATTTTTAATAATAA
* *
44453928 TAA-TCATAATTTAATAAT-A
1 TAATTTAT-TTTTAATAATAA
*
44453947 TAAATTATTATTTAATAGAATAA
1 TAATTTATT-TTTAAT--AATAA
44453970 TAAT
1 TAAT
44453974 AATAAATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
19 7 0.20
20 21 0.60
22 3 0.09
23 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
TAATTTATTTTTAATAATAA
Found at i:44455408 original size:19 final size:19
Alignment explanation
Indices: 44455379--44455422 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
44455369 TTAAAGGCTG
44455379 AAATT-GTTGAATTTTTTA
1 AAATTAGTTGAATTTTTTA
*
44455397 GAATTAGTTGAATTTTTTA
1 AAATTAGTTGAATTTTTTA
44455416 AAATTAG
1 AAATTAG
44455423 GACTAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (19 bp):
AAATTAGTTGAATTTTTTA
Found at i:44456808 original size:32 final size:30
Alignment explanation
Indices: 44456762--44456833 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 30
44456752 AAGAAAAAAT
*
44456762 AAATATAAATTTTTA-AAT-TTTTAGAAATTTA
1 AAATAAAAATTTTTATAATATTTT-G-AA-TTA
*
44456793 ACATAAAAATGTTTTATAATATTTTGAATTA
1 AAATAAAAAT-TTTTATAATATTTTGAATTA
44456824 AAATAAAAAT
1 AAATAAAAAT
44456834 AAAAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
31 20 0.57
32 7 0.20
33 4 0.11
34 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.43
Consensus pattern (30 bp):
AAATAAAAATTTTTATAATATTTTGAATTA
Found at i:44459720 original size:28 final size:28
Alignment explanation
Indices: 44459680--44459737 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
44459670 GTTAAGCCTC
44459680 GTATGGACTTAGTCGAGGGAAAGATAAA
1 GTATGGACTTAGTCGAGGGAAAGATAAA
44459708 GTATGGACTTAGTCGAGGGAAAGATAAA
1 GTATGGACTTAGTCGAGGGAAAGATAAA
44459736 GT
1 GT
44459738 GTCAGACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (28 bp):
GTATGGACTTAGTCGAGGGAAAGATAAA
Found at i:44470059 original size:26 final size:26
Alignment explanation
Indices: 44470006--44470065 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
44469996 CTCATGGTTT
* *
44470006 TCCGACCAACTCAAACTCAAGGGTCC
1 TCCGACCAACTCAAACTCAAGAGACC
* * *
44470032 TCTGACCAATTTAAACTCAAGAGACC
1 TCCGACCAACTCAAACTCAAGAGACC
44470058 TCCGACCA
1 TCCGACCA
44470066 GCTAAAATAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.35, G:0.13, T:0.18
Consensus pattern (26 bp):
TCCGACCAACTCAAACTCAAGAGACC
Found at i:44476908 original size:17 final size:17
Alignment explanation
Indices: 44476888--44476921 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
44476878 AAAAAAATTA
*
44476888 TTCATCCTTTAAAACTC
1 TTCATCCTTAAAAACTC
44476905 TTCATCCTTAAAAACTC
1 TTCATCCTTAAAAACTC
44476922 ATCAATCTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.38
Consensus pattern (17 bp):
TTCATCCTTAAAAACTC
Found at i:44481297 original size:20 final size:20
Alignment explanation
Indices: 44481272--44481312 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
44481262 TCAGTTAGTG
*
44481272 TCTCAAAATCGTAAGAAAGT
1 TCTCAAAACCGTAAGAAAGT
44481292 TCTCAAAACCGTAAGAAAGT
1 TCTCAAAACCGTAAGAAAGT
44481312 T
1 T
44481313 AATTCAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (20 bp):
TCTCAAAACCGTAAGAAAGT
Found at i:44486809 original size:3 final size:3
Alignment explanation
Indices: 44486801--44486826 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
44486791 GGCTTCGGTG
44486801 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
44486827 CTCTTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:44487558 original size:7 final size:7
Alignment explanation
Indices: 44487546--44487574 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
44487536 AATCATGTTC
44487546 TTAAATA
1 TTAAATA
44487553 TTAAATA
1 TTAAATA
44487560 TTAAATA
1 TTAAATA
44487567 TT-AATA
1 TTAAATA
44487573 TT
1 TT
44487575 TATCGAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTAAATA
Found at i:44488827 original size:26 final size:26
Alignment explanation
Indices: 44488798--44488847 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44488788 TCTCATCCTT
*
44488798 ATTTTACCACCAGTAAATTTTTGATA
1 ATTTTACCACCAGTAAAATTTTGATA
* *
44488824 ATTTTACCCCCGGTAAAATTTTGA
1 ATTTTACCACCAGTAAAATTTTGA
44488848 GAAAATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (26 bp):
ATTTTACCACCAGTAAAATTTTGATA
Found at i:44491557 original size:28 final size:28
Alignment explanation
Indices: 44491494--44491591 Score: 128
Period size: 27 Copynumber: 3.5 Consensus size: 28
44491484 ATATTAAGTC
*
44491494 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
44491521 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * *
44491549 CGCACACTTAGTGCTGA-ACAATTTAAACC
1 CGCACACTTAGTGCT-ATATAA-TCAAACT
44491578 CGCACACTTAGTGC
1 CGCACACTTAGTGC
44491592 CAATCTCATG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
27 22 0.34
28 22 0.34
29 20 0.31
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:44496003 original size:19 final size:19
Alignment explanation
Indices: 44495979--44496020 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
44495969 AAGTCCGCAC
44495979 ACTCAGTGCTATATAATCA
1 ACTCAGTGCTATATAATCA
44495998 ACTCAGTGCTATATAATCA
1 ACTCAGTGCTATATAATCA
44496017 ACTC
1 ACTC
44496021 GCACACTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.24, G:0.10, T:0.31
Consensus pattern (19 bp):
ACTCAGTGCTATATAATCA
Found at i:44496056 original size:28 final size:28
Alignment explanation
Indices: 44496002--44496089 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 28
44495992 TAATCAACTC
44496002 AGTGCTATATAATC-AACTCGCACACTT
1 AGTGCTATATAATCAAACTCGCACACTT
44496029 AGTGCTATATAATCAAACTCGCACACTT
1 AGTGCTATATAATCAAACTCGCACACTT
* *
44496057 AGTGCTGA-A-AATTTAAACCCGCACACTT
1 AGTGCT-ATATAA-TCAAACTCGCACACTT
44496085 AGTGC
1 AGTGC
44496090 CAATCTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
27 16 0.29
28 39 0.70
29 1 0.02
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (28 bp):
AGTGCTATATAATCAAACTCGCACACTT
Found at i:44501662 original size:15 final size:16
Alignment explanation
Indices: 44501642--44501671 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44501632 CAACCATCCA
44501642 CTAAAT-TAGAATTTT
1 CTAAATATAGAATTTT
44501657 CTAAATATAGAATTT
1 CTAAATATAGAATTT
44501672 GTCAAAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (16 bp):
CTAAATATAGAATTTT
Found at i:44503118 original size:15 final size:15
Alignment explanation
Indices: 44503081--44503121 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
44503071 ATTAACACTA
* *
44503081 TTAAAAGAATTAACT
1 TTAAAAGGATAAACT
44503096 TTAAAAGGATAAACT
1 TTAAAAGGATAAACT
44503111 TTAAAAGGATA
1 TTAAAAGGATA
44503122 GTGCTAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.54, C:0.05, G:0.12, T:0.29
Consensus pattern (15 bp):
TTAAAAGGATAAACT
Found at i:44515172 original size:40 final size:40
Alignment explanation
Indices: 44515068--44515208 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
44515058 AGTGTAAATA
* *
44515068 GGGCACGTATGTGCAATTCAAGGGTACCGAAGTACAAACAT
1 GGGCACGTAAGTGCAATTCAAGGGTACCGAAGTAC-AACAG
** *
44515109 GGATACGTAAGTGCAATTTAAGGGTACCGAAGTACAACAG
1 GGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAACAG
** * *
44515149 GGGCACGTAAGTGTGATTCAAGGGTATCGAAGTACTACAG
1 GGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAACAG
*
44515189 GGGCATGTAAGTGCAATTCA
1 GGGCACGTAAGTGCAATTCA
44515209 TGGCATAATT
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 54 0.64
41 31 0.36
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.21
Consensus pattern (40 bp):
GGGCACGTAAGTGCAATTCAAGGGTACCGAAGTACAACAG
Found at i:44517543 original size:31 final size:31
Alignment explanation
Indices: 44517505--44517569 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
44517495 CATCTCAGAG
44517505 TCATTCGAAACCAGACCGCAAGCATACCTGC
1 TCATTCGAAACCAGACCGCAAGCATACCTGC
* *
44517536 TCATTCGAAACTAGACCGCAAGTATACCTGC
1 TCATTCGAAACCAGACCGCAAGCATACCTGC
44517567 TCA
1 TCA
44517570 ATCTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.20
Consensus pattern (31 bp):
TCATTCGAAACCAGACCGCAAGCATACCTGC
Found at i:44521563 original size:41 final size:41
Alignment explanation
Indices: 44521467--44521563 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 41
44521457 TTTTTAGCAA
*
44521467 CGTTTGTATAAAAAAATGCCGCTATAGATCGAGCATTAGCGG
1 CGTTT-TATAAAAAAATGCCGCTATAGATCAAGCATTAGCGG
* * *
44521509 TGCTTTTTTAAAAAAA-GCCGCTATAGATTAAGCATTAGCGG
1 CG-TTTTATAAAAAAATGCCGCTATAGATCAAGCATTAGCGG
*
44521550 CGTTTTATGAAAAA
1 CGTTTTATAAAAAA
44521564 CACCGCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
40 10 0.21
41 24 0.51
42 10 0.21
43 3 0.06
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (41 bp):
CGTTTTATAAAAAAATGCCGCTATAGATCAAGCATTAGCGG
Found at i:44521701 original size:41 final size:41
Alignment explanation
Indices: 44521633--44521759 Score: 128
Period size: 41 Copynumber: 3.1 Consensus size: 41
44521623 ATGCTTTTTG
* *
44521633 AAAAACGCCGCTATAGATCGAGTATTAGCAGCGTTTTTTAA
1 AAAAACGCCGCTATAGATCAAGCATTAGCAGCGTTTTTTAA
** * * * **
44521674 AAAGGCGCTGCTATAGATTAAGCATTAGCGGCACTTTTTAA
1 AAAAACGCCGCTATAGATCAAGCATTAGCAGCGTTTTTTAA
* ** * *
44521715 AAAAACGCCGCTATAGGTCATCCATTAGCAGCGCTTTTTGA
1 AAAAACGCCGCTATAGATCAAGCATTAGCAGCGTTTTTTAA
44521756 AAAA
1 AAAA
44521760 CTCCACAAAA
Statistics
Matches: 67, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
41 67 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (41 bp):
AAAAACGCCGCTATAGATCAAGCATTAGCAGCGTTTTTTAA
Found at i:44522121 original size:21 final size:21
Alignment explanation
Indices: 44522029--44522126 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 21
44522019 CTCTAAACCT
* *
44522029 TAAACCCTAAACCC-GAATCAC
1 TAAACCTTAAACCCTAAAT-AC
*
44522050 TAAACCCTTAAGCCCTTAAATAC
1 TAAA-CCTTAAACCC-TAAATAC
* *
44522073 AAAATCC-TAAATCCTAAA-AC
1 TAAA-CCTTAAACCCTAAATAC
44522093 TGTAAACCTTAAACCCTAAATAC
1 --TAAACCTTAAACCCTAAATAC
44522116 TAAACCTTAAA
1 TAAACCTTAAA
44522127 TCTTAAACGT
Statistics
Matches: 61, Mismatches: 9, Indels: 14
0.73 0.11 0.17
Matches are distributed among these distances:
20 2 0.03
21 21 0.34
22 26 0.43
23 9 0.15
24 3 0.05
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.22
Consensus pattern (21 bp):
TAAACCTTAAACCCTAAATAC
Found at i:44522133 original size:21 final size:21
Alignment explanation
Indices: 44522048--44522133 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
44522038 AACCCGAATC
**
44522048 ACTAAACCCTTAAGCCCTTAAAT
1 ACTAAA-CCTTAAATCC-TAAAT
*
44522071 ACAAAATCC-TAAATCCTAAA-
1 ACTAAA-CCTTAAATCCTAAAT
*
44522091 ACTGTAAACCTTAAACCCTAAAT
1 AC--TAAACCTTAAATCCTAAAT
*
44522114 ACTAAACCTTAAATCTTAAA
1 ACTAAACCTTAAATCCTAAA
44522134 CGTTAAATAG
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
20 2 0.04
21 22 0.43
22 18 0.35
23 9 0.18
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.26
Consensus pattern (21 bp):
ACTAAACCTTAAATCCTAAAT
Found at i:44524571 original size:29 final size:29
Alignment explanation
Indices: 44524539--44524596 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
44524529 CCTCTCCAAA
44524539 CTCCATTCTTTTCAACTGAGTTCTCAATT
1 CTCCATTCTTTTCAACTGAGTTCTCAATT
*
44524568 CTCCATTCTTTTCAACTTAGTTCTCAATT
1 CTCCATTCTTTTCAACTGAGTTCTCAATT
44524597 TTTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.28, G:0.05, T:0.47
Consensus pattern (29 bp):
CTCCATTCTTTTCAACTGAGTTCTCAATT
Found at i:44528874 original size:28 final size:28
Alignment explanation
Indices: 44528809--44528959 Score: 223
Period size: 28 Copynumber: 5.4 Consensus size: 28
44528799 GATCTCGGCG
* * * *
44528809 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
44528838 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
44528866 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
44528894 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
44528922 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
44528949 CTGAGTGTGCG
1 CTAAGTGTGCG
44528960 GACTTAATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
27 24 0.21
28 76 0.66
29 15 0.13
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.34
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:44534988 original size:17 final size:16
Alignment explanation
Indices: 44534956--44535000 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
44534946 GAAAATAACT
44534956 AAATAAAATTAAAAATA
1 AAATAAAA-TAAAAATA
**
44534973 TTATAAAATAATAAATA
1 AAATAAAATAA-AAATA
44534990 AAATAAAATAA
1 AAATAAAATAA
44535001 CCAAAAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 3 0.13
17 20 0.87
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:44536972 original size:21 final size:21
Alignment explanation
Indices: 44536943--44536988 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
44536933 ATTTGGCCAT
* * *
44536943 TTTATGGTTTAGGGTGTATAA
1 TTTAGGGTTTAAGGTGTAAAA
*
44536964 TTTAGGGTTTAAGGTTTAAAA
1 TTTAGGGTTTAAGGTGTAAAA
44536985 TTTA
1 TTTA
44536989 CTATTTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (21 bp):
TTTAGGGTTTAAGGTGTAAAA
Found at i:44537011 original size:7 final size:7
Alignment explanation
Indices: 44536998--44537096 Score: 58
Period size: 7 Copynumber: 13.9 Consensus size: 7
44536988 ACTATTTAAA
44536998 GGTTTAT
1 GGTTTAT
*
44537005 GGATTAT
1 GGTTTAT
*
44537012 GGGTTTAG
1 -GGTTTAT
*
44537020 GGATTAT
1 GGTTTAT
44537027 -GTTTAT
1 GGTTTAT
*
44537033 GGCTTAT
1 GGTTTAT
44537040 GGTTTAAT
1 GGTTT-AT
44537048 GG-TTAT
1 GGTTTAT
*
44537054 GGGTTAGT
1 GGTTTA-T
* *
44537062 GGTTAAG
1 GGTTTAT
*
44537069 GGTTTAG
1 GGTTTAT
*
44537076 GGGTTAT
1 GGTTTAT
*
44537083 GGGTTAAT
1 -GGTTTAT
44537091 GGTTTA
1 GGTTTA
44537097 AGGGTTAAGG
Statistics
Matches: 69, Mismatches: 17, Indels: 12
0.70 0.17 0.12
Matches are distributed among these distances:
6 9 0.13
7 41 0.59
8 19 0.28
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.44
Consensus pattern (7 bp):
GGTTTAT
Found at i:44537016 original size:15 final size:14
Alignment explanation
Indices: 44536998--44537094 Score: 76
Period size: 15 Copynumber: 6.8 Consensus size: 14
44536988 ACTATTTAAA
44536998 GGTTTATGGATTATG
1 GGTTTATGG-TTATG
*
44537013 GGTTTAGGGATTAT-
1 GGTTTATGG-TTATG
44537027 -GTTTATGGCTTAT-
1 GGTTTATGG-TTATG
44537040 GGTTTAATGGTTATG
1 GGTTT-ATGGTTATG
*
44537055 GG-TTAGTGGTTAAG
1 GGTTTA-TGGTTATG
*
44537069 GGTTTAGGGGTTATG
1 GGTTTA-TGGTTATG
*
44537084 GGTTAATGGTT
1 GGTTTATGGTT
44537095 TAAGGGTTAA
Statistics
Matches: 69, Mismatches: 8, Indels: 11
0.78 0.09 0.12
Matches are distributed among these distances:
13 12 0.17
14 23 0.33
15 34 0.49
ACGTcount: A:0.19, C:0.01, G:0.36, T:0.44
Consensus pattern (14 bp):
GGTTTATGGTTATG
Found at i:44537073 original size:29 final size:30
Alignment explanation
Indices: 44537040--44537117 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 30
44537030 TATGGCTTAT
* *
44537040 GGTTTAATGGTTATGGGTTAGTGG-TTAAG
1 GGTTTAAGGGTTATGGGTTAATGGTTTAAG
*
44537069 GGTTTAGGGGTTATGGGTTAATGGTTTAAG
1 GGTTTAAGGGTTATGGGTTAATGGTTTAAG
* *
44537099 GG-TTAAGGCTTAGGGGTTA
1 GGTTTAAGGGTTATGGGTTA
44537118 TTGTTTTGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.21, C:0.01, G:0.40, T:0.38
Consensus pattern (30 bp):
GGTTTAAGGGTTATGGGTTAATGGTTTAAG
Found at i:44537104 original size:7 final size:7
Alignment explanation
Indices: 44537043--44537117 Score: 53
Period size: 7 Copynumber: 10.4 Consensus size: 7
44537033 GGCTTATGGT
*
44537043 TTAATGG
1 TTAAGGG
*
44537050 TTATGGG
1 TTAAGGG
44537057 TT-AGTGG
1 TTAAG-GG
44537064 TTAAGGG
1 TTAAGGG
*
44537071 TTTAGGGG
1 -TTAAGGG
*
44537079 TTATGGG
1 TTAAGGG
*
44537086 TTAATGGT
1 TTAA-GGG
44537094 TTAAGGG
1 TTAAGGG
*
44537101 TTAAGGC
1 TTAAGGG
*
44537108 TTAGGGG
1 TTAAGGG
44537115 TTA
1 TTA
44537118 TTGTTTTGTG
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
6 1 0.02
7 38 0.72
8 14 0.26
ACGTcount: A:0.21, C:0.01, G:0.39, T:0.39
Consensus pattern (7 bp):
TTAAGGG
Found at i:44537116 original size:22 final size:22
Alignment explanation
Indices: 44537064--44537116 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
44537054 GGGTTAGTGG
* * *
44537064 TTAAGGGTTTAGGGGTTATGGG
1 TTAAGGGTTTAAGGGTTAAGGC
*
44537086 TTAATGGTTTAAGGGTTAAGGC
1 TTAAGGGTTTAAGGGTTAAGGC
*
44537108 TTAGGGGTT
1 TTAAGGGTT
44537117 ATTGTTTTGT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.38
Consensus pattern (22 bp):
TTAAGGGTTTAAGGGTTAAGGC
Found at i:44537117 original size:14 final size:15
Alignment explanation
Indices: 44537031--44537117 Score: 63
Period size: 14 Copynumber: 6.0 Consensus size: 15
44537021 GATTATGTTT
* *
44537031 ATGGCTTATGGTTTA
1 ATGGCTTAAGGGTTA
*
44537046 ATGG-TTATGGGTTA
1 ATGGCTTAAGGGTTA
* *
44537060 GTGG-TTAAGGGTTT
1 ATGGCTTAAGGGTTA
* * *
44537074 AGGGGTTATGGGTTA
1 ATGGCTTAAGGGTTA
*
44537089 ATGGTTTAAGGGTTA
1 ATGGCTTAAGGGTTA
*
44537104 A-GGCTTAGGGGTTA
1 ATGGCTTAAGGGTTA
44537118 TTGTTTTGTG
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
14 33 0.57
15 25 0.43
ACGTcount: A:0.21, C:0.02, G:0.38, T:0.39
Consensus pattern (15 bp):
ATGGCTTAAGGGTTA
Found at i:44537154 original size:14 final size:14
Alignment explanation
Indices: 44537135--44537180 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
44537125 GTGGTTTAGG
44537135 GTTTAGGGGATATA
1 GTTTAGGGGATATA
* *
44537149 GTTTAGGGTACTTTA
1 GTTTAGGGGA-TATA
44537164 G--TAGGGGATATA
1 GTTTAGGGGATATA
44537176 GTTTA
1 GTTTA
44537181 ATGGTTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 6
0.71 0.11 0.17
Matches are distributed among these distances:
12 4 0.16
13 6 0.24
14 11 0.44
15 4 0.16
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.39
Consensus pattern (14 bp):
GTTTAGGGGATATA
Found at i:44537334 original size:29 final size:28
Alignment explanation
Indices: 44537275--44537334 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
44537265 AATTCATACA
* *
44537275 TTTTGTGGTTAAGGCTTAGGGGTTATTG
1 TTTTGTGGTTAAGGCTTAGGGGATATAG
* *
44537303 TTTTGTGGTTTATGGTTTAGGGGATATAG
1 TTTTGTGG-TTAAGGCTTAGGGGATATAG
44537332 TTT
1 TTT
44537335 AAGGTTTAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.15, C:0.02, G:0.33, T:0.50
Consensus pattern (28 bp):
TTTTGTGGTTAAGGCTTAGGGGATATAG
Found at i:44537361 original size:28 final size:27
Alignment explanation
Indices: 44537330--44537400 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 27
44537320 TAGGGGATAT
44537330 AGTTTAAGGTTTAGGGGATATAGTTTA
1 AGTTTAAGGTTTAGGGGATATAGTTTA
*
44537357 GAGTTTAAGG-CTATGGGGATATAGTTTA
1 -AGTTTAAGGTTTA-GGGGATATAGTTTA
44537385 ATGGTTTAAGGTTTAG
1 A--GTTTAAGGTTTAG
44537401 AGTTTTGATT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
27 3 0.08
28 23 0.62
29 9 0.24
30 2 0.05
ACGTcount: A:0.28, C:0.01, G:0.31, T:0.39
Consensus pattern (27 bp):
AGTTTAAGGTTTAGGGGATATAGTTTA
Found at i:44537363 original size:21 final size:21
Alignment explanation
Indices: 44537310--44537356 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
44537300 TTGTTTTGTG
*
44537310 GTTTATGGTTTAGGGGATATA
1 GTTTAAGGTTTAGGGGATATA
44537331 GTTTAAGGTTTAGGGGATATA
1 GTTTAAGGTTTAGGGGATATA
44537352 GTTTA
1 GTTTA
44537357 GAGTTTAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.43
Consensus pattern (21 bp):
GTTTAAGGTTTAGGGGATATA
Found at i:44537902 original size:11 final size:11
Alignment explanation
Indices: 44537886--44537910 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
44537876 TAGTGGATTT
44537886 CCCCGATTTCC
1 CCCCGATTTCC
44537897 CCCCGATTTCC
1 CCCCGATTTCC
44537908 CCC
1 CCC
44537911 AACTTCTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.60, G:0.08, T:0.24
Consensus pattern (11 bp):
CCCCGATTTCC
Found at i:44539912 original size:98 final size:99
Alignment explanation
Indices: 44539810--44540129 Score: 310
Period size: 100 Copynumber: 3.2 Consensus size: 99
44539800 TAAGTTGTAT
44539810 TTAAAGTTTT-TTTTAAATATTTTAATTTATTTTACTTTAATTTAATCACGAAAAATATTTTATT
1 TTAAAGTTTTATTTTAAATATTTTAATTTATTTTACTTTAATTTAATCACGAAAAATATTTTATT
44539874 TTCTTTAATTTTATTTTCAATTTACCTAATTAAA
66 TTCTTTAATTTTATTTTCAATTTACCTAATTAAA
* * * *
44539908 TTAAA-TTATA-TTTAAAGTTTCATTTTAA-ATATTTTA-TTTTATTTGAATCACGAAAATTAAT
1 TTAAAGTTTTATTTTAAA---T-ATTTTAATTTATTTTACTTTAATTT-AATCACGAAAAAT-AT
* * * * * * ** * *
44539969 TTCAATATTTATTTTATTTTAACATTACATAATTAAATTAAGTTGTAT
60 TT-TAT-TTTCTTTAATTTT-A-TTTTC--AATTTACCTAA-TT-AAA
* * * *
44540017 TTAAAGTTTTATTTTAAATATTTTATTTTATTTCACTTTAATTTAATCATGAAAAATATTTTGTT
1 TTAAAGTTTTATTTTAAATATTTTAATTTATTTTACTTTAATTTAATCACGAAAAATATTTTATT
44540082 TTCTTTAATTTTATTTTCAATTTACCTAATTAAA
66 TTCTTTAATTTTATTTTCAATTTACCTAATTAAA
44540116 TT-AAGTTTTATTTT
1 TTAAAGTTTTATTTT
44540130 CAAGTTCACC
Statistics
Matches: 171, Mismatches: 32, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
97 9 0.05
98 17 0.10
99 10 0.06
100 22 0.13
101 19 0.11
102 2 0.01
103 14 0.08
104 2 0.01
105 14 0.08
106 1 0.01
107 18 0.11
108 20 0.12
109 13 0.08
110 4 0.02
111 6 0.04
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (99 bp):
TTAAAGTTTTATTTTAAATATTTTAATTTATTTTACTTTAATTTAATCACGAAAAATATTTTATT
TTCTTTAATTTTATTTTCAATTTACCTAATTAAA
Found at i:44540034 original size:208 final size:208
Alignment explanation
Indices: 44539664--44540128 Score: 833
Period size: 208 Copynumber: 2.2 Consensus size: 208
44539654 CATACATTTG
*
44539664 TTTTCTTTAATTTTATTTTCAATTTACCTAATAAAATTAAATTATATTTAAAGTTTCATTTCAAA
1 TTTTCTTTAATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTCAAA
*
44539729 TATTTTGTTTTATTTGAATCACGAAAATTAATTTCAATATTTTATTTTATTTTAACATTACATAA
66 TATTTTATTTTATTTGAATCACGAAAATTAATTTCAATATTTTATTTTATTTTAACATTACATAA
*
44539794 TTAAATTAAGTTGTATTTAAAGTTTTTTTTAAATATTTTAATTTATTTTACTTTAATTTAATCAC
131 TTAAATTAAGTTGTATTTAAAGTTTTTTTTAAATATTTTAATTTATTTCACTTTAATTTAATCAC
44539859 GAAAAATATTTTA
196 GAAAAATATTTTA
*
44539872 TTTTCTTTAATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTTAAA
1 TTTTCTTTAATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTCAAA
44539937 TATTTTATTTTATTTGAATCACGAAAATTAATTTCAATA-TTTATTTTATTTTAACATTACATAA
66 TATTTTATTTTATTTGAATCACGAAAATTAATTTCAATATTTTATTTTATTTTAACATTACATAA
*
44540001 TTAAATTAAGTTGTATTTAAAGTTTTATTTTAAATATTTTATTTTATTTCACTTTAATTTAATCA
131 TTAAATTAAGTTGTATTTAAAGTTTT-TTTTAAATATTTTAATTTATTTCACTTTAATTTAATCA
* *
44540066 TGAAAAATATTTTG
195 CGAAAAATATTTTA
* *
44540080 TTTTCTTTAATTTTATTTTCAATTTACCTAATTAAATTAAGTTTTATTT
1 TTTTCTTTAATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTT
44540129 TCAAGTTCAC
Statistics
Matches: 247, Mismatches: 9, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
207 51 0.21
208 196 0.79
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (208 bp):
TTTTCTTTAATTTTATTTTCAATTTACCTAATTAAATTAAATTATATTTAAAGTTTCATTTCAAA
TATTTTATTTTATTTGAATCACGAAAATTAATTTCAATATTTTATTTTATTTTAACATTACATAA
TTAAATTAAGTTGTATTTAAAGTTTTTTTTAAATATTTTAATTTATTTCACTTTAATTTAATCAC
GAAAAATATTTTA
Found at i:44540162 original size:9 final size:9
Alignment explanation
Indices: 44540148--44540412 Score: 147
Period size: 9 Copynumber: 30.8 Consensus size: 9
44540138 CCAGCAACTC
44540148 ACATAATTT
1 ACATAATTT
44540157 ACATAATTT
1 ACATAATTT
44540166 ACATAA--T
1 ACATAATTT
* *
44540173 GCATAACTT
1 ACATAATTT
44540182 ACATAATTT
1 ACATAATTT
*
44540191 --A-AAGTT
1 ACATAATTT
44540197 -CA-AATTT
1 ACATAATTT
*
44540204 -CATAACTT
1 ACATAATTT
44540212 ACATAATTT
1 ACATAATTT
*
44540221 ACATAACTT
1 ACATAATTT
44540230 ACATAA--T
1 ACATAATTT
* *
44540237 ACATAACTA
1 ACATAATTT
*
44540246 ATATAATTT
1 ACATAATTT
*
44540255 --A-AAGTT
1 ACATAATTT
44540261 -CA-AATTT
1 ACATAATTT
*
44540268 -CATAACTT
1 ACATAATTT
44540276 ACATAATTT
1 ACATAATTT
* *
44540285 ACATAACTA
1 ACATAATTT
44540294 ACATAATTT
1 ACATAATTT
*
44540303 AAAGATCAAATTT
1 --ACAT--AATTT
*
44540316 -CATAACTT
1 ACATAATTT
44540324 ACATAATTT
1 ACATAATTT
*
44540333 ACATAACTT
1 ACATAATTT
44540342 ACATAA--T
1 ACATAATTT
*
44540349 ACATAACTT
1 ACATAATTT
44540358 ACATAATTT
1 ACATAATTT
*
44540367 AAAGATCAAATTT
1 --ACAT--AATTT
*
44540380 -CATAACTT
1 ACATAATTT
44540388 ACATAATTT
1 ACATAATTT
*
44540397 ACATAACTT
1 ACATAATTT
44540406 ACATAAT
1 ACATAAT
44540413 ACATAAATAT
Statistics
Matches: 202, Mismatches: 32, Indels: 44
0.73 0.12 0.16
Matches are distributed among these distances:
6 8 0.04
7 36 0.18
8 16 0.08
9 122 0.60
10 4 0.02
11 6 0.03
13 10 0.05
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (9 bp):
ACATAATTT
Found at i:44540210 original size:30 final size:30
Alignment explanation
Indices: 44540174--44540285 Score: 136
Period size: 30 Copynumber: 3.6 Consensus size: 30
44540164 TTACATAATG
44540174 CATAACTTACATAATTTAAAGTTCAAATTT
1 CATAACTTACATAATTTAAAGTTCAAATTT
* *
44540204 CATAACTTACATAATTTACATAACTTACATAA-TA
1 CATAACTTACATAATTT--A-AAGTT-CA-AATTT
* *
44540238 CATAACTAATATAATTTAAAGTTCAAATTT
1 CATAACTTACATAATTTAAAGTTCAAATTT
44540268 CATAACTTACATAATTTA
1 CATAACTTACATAATTTA
44540286 CATAACTAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
29 2 0.03
30 36 0.53
31 4 0.06
32 2 0.03
33 4 0.06
34 18 0.26
35 2 0.03
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (30 bp):
CATAACTTACATAATTTAAAGTTCAAATTT
Found at i:44540219 original size:64 final size:64
Alignment explanation
Indices: 44540143--44540364 Score: 265
Period size: 64 Copynumber: 3.5 Consensus size: 64
44540133 GTTCACCAGC
* * * *
44540143 AACTCACATAATTTACATAATTTACATAATGCATAACTTACATAATTTAAAGTTCAAATTTCAT
1 AACTTACATAATTTACATAACTTACATAATACATAACTAACATAATTTAAAGTTCAAATTTCAT
*
44540207 AACTTACATAATTTACATAACTTACATAATACATAACTAATATAATTTAAAGTTCAAATTTCAT
1 AACTTACATAATTTACATAACTTACATAATACATAACTAACATAATTTAAAGTTCAAATTTCAT
* * ** * *
44540271 AACTTACATAATTTACATAACTAACATAAT--TTAAAGATCA-AATTTCATAACTTACATAATTT
1 AACTTACATAATTTACATAACTTACATAATACATAACTAACATAATTT-A-AAGTT-CA-AATTT
44540333 ACAT
62 -CAT
44540337 AACTTACATAA--TACATAACTTACATAAT
1 AACTTACATAATTTACATAACTTACATAAT
44540365 TTAAAGATCA
Statistics
Matches: 140, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
61 5 0.04
62 6 0.04
63 4 0.03
64 106 0.76
65 5 0.04
66 14 0.10
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.36
Consensus pattern (64 bp):
AACTTACATAATTTACATAACTTACATAATACATAACTAACATAATTTAAAGTTCAAATTTCAT
Found at i:44540300 original size:48 final size:48
Alignment explanation
Indices: 44540216--44540348 Score: 216
Period size: 48 Copynumber: 2.8 Consensus size: 48
44540206 TAACTTACAT
* *
44540216 AATTTACATAACTTACATAA--TACATAACTAATATAATTTAAAGTTCA
1 AATTT-CATAACTTACATAATTTACATAACTAACATAATTTAAAGATCA
44540263 AATTTCATAACTTACATAATTTACATAACTAACATAATTTAAAGATCA
1 AATTTCATAACTTACATAATTTACATAACTAACATAATTTAAAGATCA
*
44540311 AATTTCATAACTTACATAATTTACATAACTTACATAAT
1 AATTTCATAACTTACATAATTTACATAACTAACATAAT
44540349 ACATAACTTA
Statistics
Matches: 81, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
46 14 0.17
47 5 0.06
48 62 0.77
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (48 bp):
AATTTCATAACTTACATAATTTACATAACTAACATAATTTAAAGATCA
Found at i:44540312 original size:112 final size:112
Alignment explanation
Indices: 44540152--44540412 Score: 436
Period size: 112 Copynumber: 2.3 Consensus size: 112
44540142 CAACTCACAT
* * *
44540152 AATTTACATAATTTACATAA--TGCATAACTTACATAATTTAAAGTTCAAATTTCATAACTTACA
1 AATTT-CATAACTTACATAATTTACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACA
* *
44540215 TAATTTACATAACTTACATAATACATAACTAATATAATTTAAAGTTCA
65 TAATTTACATAACTTACATAATACATAACTAACATAATTTAAAGATCA
*
44540263 AATTTCATAACTTACATAATTTACATAACTAACATAATTTAAAGATCAAATTTCATAACTTACAT
1 AATTTCATAACTTACATAATTTACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACAT
*
44540328 AATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCA
66 AATTTACATAACTTACATAATACATAACTAACATAATTTAAAGATCA
44540375 AATTTCATAACTTACATAATTTACATAACTTACATAAT
1 AATTTCATAACTTACATAATTTACATAACTTACATAAT
44540413 ACATAAATAT
Statistics
Matches: 140, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
110 13 0.09
111 5 0.04
112 122 0.87
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (112 bp):
AATTTCATAACTTACATAATTTACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACAT
AATTTACATAACTTACATAATACATAACTAACATAATTTAAAGATCA
Found at i:44540320 original size:30 final size:30
Alignment explanation
Indices: 44540280--44540397 Score: 141
Period size: 30 Copynumber: 3.8 Consensus size: 30
44540270 TAACTTACAT
*
44540280 AATTTACATAACTAACATAATTTAAAGATCA
1 AATTT-CATAACTTACATAATTTAAAGATCA
44540311 AATTTCATAACTTACATAATTTACATA-ACTTACA
1 AATTTCATAACTTACATAATTTA-A-AGA--T-CA
*
44540345 TAA-TACATAACTTACATAATTTAAAGATCA
1 -AATTTCATAACTTACATAATTTAAAGATCA
44540375 AATTTCATAACTTACATAATTTA
1 AATTTCATAACTTACATAATTTA
44540398 CATAACTTAC
Statistics
Matches: 76, Mismatches: 3, Indels: 17
0.79 0.03 0.18
Matches are distributed among these distances:
29 2 0.03
30 38 0.50
31 8 0.11
32 2 0.03
33 3 0.04
34 21 0.28
35 2 0.03
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.36
Consensus pattern (30 bp):
AATTTCATAACTTACATAATTTAAAGATCA
Found at i:44540365 original size:64 final size:64
Alignment explanation
Indices: 44540263--44540418 Score: 278
Period size: 64 Copynumber: 2.4 Consensus size: 64
44540253 TTAAAGTTCA
44540263 AATTT-CATAACTTACATAATTTACATAACTAACATAATTTAAAGATCAAATTTCATAACTTACA
1 AATTTACATAACTTACATAA--TACATAACTAACATAATTTAAAGATCAAATTTCATAACTTACA
44540327 T
64 T
*
44540328 AATTTACATAACTTACATAATACATAACTTACATAATTTAAAGATCAAATTTCATAACTTACAT
1 AATTTACATAACTTACATAATACATAACTAACATAATTTAAAGATCAAATTTCATAACTTACAT
44540392 AATTTACATAACTTACATAATACATAA
1 AATTTACATAACTTACATAATACATAA
44540419 ATATATATCA
Statistics
Matches: 89, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
64 70 0.79
65 5 0.06
66 14 0.16
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.36
Consensus pattern (64 bp):
AATTTACATAACTTACATAATACATAACTAACATAATTTAAAGATCAAATTTCATAACTTACAT
Found at i:44545475 original size:13 final size:14
Alignment explanation
Indices: 44545459--44545487 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
44545449 TTATAAATAT
44545459 TTATAATG-TTTAA
1 TTATAATGATTTAA
44545472 TTATAATGATTTAA
1 TTATAATGATTTAA
44545486 TT
1 TT
44545488 CGTCGTTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATAATGATTTAA
Found at i:44545917 original size:21 final size:21
Alignment explanation
Indices: 44545893--44545950 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
44545883 ACAACTTAGA
* * *
44545893 GCAGATGCAGCAGCGAGGGAG
1 GCAGACGCAGTAGCGAGAGAG
44545914 GCAG-CGACAGTAGCGAGAGAG
1 GCAGACG-CAGTAGCGAGAGAG
*
44545935 GCAGAGGCAGTAGCGA
1 GCAGACGCAGTAGCGA
44545951 TGGCAGCAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.31, C:0.19, G:0.45, T:0.05
Consensus pattern (21 bp):
GCAGACGCAGTAGCGAGAGAG
Found at i:44546251 original size:31 final size:31
Alignment explanation
Indices: 44546203--44546299 Score: 158
Period size: 31 Copynumber: 3.1 Consensus size: 31
44546193 TGTATTTTTT
* *
44546203 ATGCTACATTTACTGTTTTTGGTTGGATTCA
1 ATGCTATATTTGCTGTTTTTGGTTGGATTCA
*
44546234 ATGTTATATTTGCTGTTTTTGGTTGGATTCA
1 ATGCTATATTTGCTGTTTTTGGTTGGATTCA
*
44546265 ATGCTATATTTGCTGTTTTTGGTTGGATTTA
1 ATGCTATATTTGCTGTTTTTGGTTGGATTCA
44546296 ATGC
1 ATGC
44546300 AGGAAGGGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.18, C:0.09, G:0.22, T:0.52
Consensus pattern (31 bp):
ATGCTATATTTGCTGTTTTTGGTTGGATTCA
Found at i:44548712 original size:2 final size:2
Alignment explanation
Indices: 44548705--44548733 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
44548695 TAATTTAGCA
44548705 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44548734 AAAGTTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44554818 original size:26 final size:26
Alignment explanation
Indices: 44554782--44554833 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
44554772 TGTGAGAGTC
44554782 AAGTCATTCGTCAAATCAGCAAACCT
1 AAGTCATTCGTCAAATCAGCAAACCT
*
44554808 AAGTCTTTCGTCAAATCAGCAAACCT
1 AAGTCATTCGTCAAATCAGCAAACCT
44554834 TTCTTTGTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25
Consensus pattern (26 bp):
AAGTCATTCGTCAAATCAGCAAACCT
Found at i:44556365 original size:32 final size:29
Alignment explanation
Indices: 44556288--44556370 Score: 87
Period size: 32 Copynumber: 2.7 Consensus size: 29
44556278 ATTTATGGGT
*
44556288 TTAATTAAAATTTTTAAAATATTTGTAAGA
1 TTAATTAAAATTTTCAAAA-ATTTGTAAGA
* *
44556318 TTAATGAAAAATTTCAAAAATTT-TAAAGGA
1 TTAATTAAAATTTTCAAAAATTTGT-AA-GA
44556348 GCTTAATTAAAATTTTCAAAAAT
1 --TTAATTAAAATTTTCAAAAAT
44556371 AATAATAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.02
29 6 0.14
30 18 0.41
32 19 0.43
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (29 bp):
TTAATTAAAATTTTCAAAAATTTGTAAGA
Found at i:44559717 original size:48 final size:48
Alignment explanation
Indices: 44559663--44560043 Score: 410
Period size: 48 Copynumber: 8.0 Consensus size: 48
44559653 AGGGTAGATT
* * * * *
44559663 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGTTCGCATGTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAG
* * * *
44559711 GCCGATGCCACGTCCCAGACATGGTCTTA-ACTAGCTCTCGTCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAG
** * * *
44559758 GCCGATGCCATGTCATAGACATGATCTTACACTGGCTCTCATAAT-ATG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCAAG
* * *
44559806 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAG
* * * * **
44559854 GTCGATGCCATGTCTCAGACGTGGTCTTACACTGGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCAAG
** * * *
44559902 GCCGATGCCATGTCTTAGACATGGTCTTACACTAGCACACATATCAAC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAG
**
44559950 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAAT-GTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCAT-ATCAAG
* * *
44559998 GCTGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA
44560044 CCCAATTATC
Statistics
Matches: 272, Mismatches: 54, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
47 43 0.16
48 224 0.82
49 5 0.02
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (48 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCAAG
Found at i:44559888 original size:96 final size:96
Alignment explanation
Indices: 44559663--44560043 Score: 527
Period size: 96 Copynumber: 4.0 Consensus size: 96
44559653 AGGGTAGATT
* * * *
44559663 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGTTCGCAT-GTCGA-GGCCGATGCCACGTCC
1 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAAT--ATGGCCGATGCCATGTCC
* * * * *
44559726 CAGACATGGTCTTA-ACTAGCTCTCGTCTCAAT
64 CAGACATGGTCTTACACTAGCACACATATCAAC
* *
44559758 GCCGATGCCATGTCAT-AGACATGATCTTACACTGGCTCTCATAATATGGCCGATGCCATGTCCC
1 GCCGATGCCATGTC-TCAGACATGGTCTTACACTAGCTCTCATAATATGGCCGATGCCATGTCCC
44559822 AGACATGGTCTTACACTAGCACACATATCAAC
65 AGACATGGTCTTACACTAGCACACATATCAAC
* * * * **
44559854 GTCGATGCCATGTCTCAGACGTGGTCTTACACTGGCTCTCATAATGTGGCCGATGCCATGTCTTA
1 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAATATGGCCGATGCCATGTCCCA
44559919 GACATGGTCTTACACTAGCACACATATCAAC
66 GACATGGTCTTACACTAGCACACATATCAAC
* * *
44559950 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAATGTGGCTGATGCCATGTCCCA
1 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAATATGGCCGATGCCATGTCCCA
44560015 GACATGGTCTTACACTAGCACACATATCA
66 GACATGGTCTTACACTAGCACACATATCA
44560044 CCCAATTATC
Statistics
Matches: 257, Mismatches: 24, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
94 1 0.00
95 66 0.26
96 190 0.74
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (96 bp):
GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCATAATATGGCCGATGCCATGTCCCA
GACATGGTCTTACACTAGCACACATATCAAC
Found at i:44562585 original size:19 final size:20
Alignment explanation
Indices: 44562546--44562586 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
44562536 AAATCAAGCA
*
44562546 ATGAAAATCCCAAATAATCC
1 ATGAAAATCCCAAAGAATCC
*
44562566 ATGAAAAT-CCAAAGATTCC
1 ATGAAAATCCCAAAGAATCC
44562585 AT
1 AT
44562587 TATTACAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (20 bp):
ATGAAAATCCCAAAGAATCC
Found at i:44568353 original size:77 final size:81
Alignment explanation
Indices: 44568211--44568393 Score: 234
Period size: 77 Copynumber: 2.3 Consensus size: 81
44568201 GCTACTCGTT
* *
44568211 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
44568276 ATTTAGTAAC-TCGCA
66 ATATAGTAACTTAGCA
* **
44568291 CAAATGCCTTCGGG-CTTA-CCCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
* *
44568352 GATATGGTCACTTAGCA
65 GATATAGTAACTTAGCA
44568369 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
44568394 CATCATTCAA
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
76 3 0.03
77 46 0.51
78 18 0.20
79 9 0.10
80 14 0.16
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATATAGTAACTTAGCA
Found at i:44568393 original size:40 final size:40
Alignment explanation
Indices: 44568192--44568393 Score: 236
Period size: 40 Copynumber: 5.1 Consensus size: 40
44568182 CGGAATTTAA
** *
44568192 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
44568232 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
44568272 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTA-C
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
44568310 CCGGAT-TAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
44568349 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
44568389 CCGGA
1 CCGGA
44568394 CATCATTCAA
Statistics
Matches: 141, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
36 2 0.01
37 22 0.16
38 11 0.08
39 11 0.08
40 84 0.60
41 11 0.08
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Done.