Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007707.1 Hibiscus syriacus cultivar Beakdansim tig00109922_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 300401
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4176 original size:73 final size:77
Alignment explanation
Indices: 3971--4177 Score: 273
Period size: 73 Copynumber: 2.8 Consensus size: 77
3961 CAAAGCAAAA
* * * **
3971 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
4036 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
4049 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGA-T-CCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
4112 TTT-GCTCCGA-
66 TTTGGCCCCGAG
* * *
4122 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
4178 TATACAACGG
Statistics
Matches: 116, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
71 10 0.09
72 9 0.08
73 31 0.27
74 6 0.05
75 14 0.12
76 1 0.01
77 20 0.17
78 25 0.22
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:9934 original size:21 final size:21
Alignment explanation
Indices: 9908--9970 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
9898 TTTTGGTGCA
*
9908 GAGGGAATCGATCCCCCCCCT
1 GAGGGAACCGATCCCCCCCCT
* **
9929 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCCT
*
9950 GAATGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATCCCCCCC
9971 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.38, G:0.24, T:0.17
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCCT
Found at i:12717 original size:76 final size:77
Alignment explanation
Indices: 12550--12760 Score: 300
Period size: 76 Copynumber: 2.8 Consensus size: 77
12540 CAAAGCCAAA
* * * **
12550 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
12615 TTTTGGCCCCGAG
65 TTTTGGCCCCGAG
*
12628 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
*
12693 TTT-GCTCCGAG
66 TTTGGCCCCGAG
* * * *
12704 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
12761 TGTACAACAG
Statistics
Matches: 121, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
75 19 0.16
76 40 0.33
77 37 0.31
78 25 0.21
ACGTcount: A:0.24, C:0.33, G:0.23, T:0.20
Consensus pattern (77 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTTGGCCCCGAG
Found at i:14058 original size:92 final size:93
Alignment explanation
Indices: 13872--14059 Score: 238
Period size: 92 Copynumber: 2.0 Consensus size: 93
13862 ACAAAAATGT
* *
13872 GCTTAATGAGGTTTACTTAATAAATACTTTTATTCAAAACATCCATTACTGACACGAAATCGGCA
1 GCTTAATGAGCTTTACTTAATAAATAC-TTTATTCAAAACATCCATTACTGACACGAAATCAGCA
* *
13937 TTTACTTGCACAGGAAGGTTCACCCATCG
65 TTTACTTGAACAGGAAGGTTCACCAATCG
* * * *
13966 GCTTAATGAGCTTTTCTTGATAAATAC-TTCTTCAAAACATCCATTACTGACCCGAAATCAGC-T
1 GCTTAATGAGCTTTACTTAATAAATACTTTATTCAAAACATCCATTACTGACACGAAATCAGCAT
* *
14029 CTTACTTGAACCGG-AGGATTCGCCAATCG
66 -TTACTTGAACAGGAAGG-TTCACCAATCG
14058 GC
1 GC
14060 AGGCCATGTC
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
91 4 0.05
92 54 0.66
94 24 0.29
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (93 bp):
GCTTAATGAGCTTTACTTAATAAATACTTTATTCAAAACATCCATTACTGACACGAAATCAGCAT
TTACTTGAACAGGAAGGTTCACCAATCG
Found at i:22890 original size:85 final size:85
Alignment explanation
Indices: 22801--22963 Score: 267
Period size: 85 Copynumber: 1.9 Consensus size: 85
22791 TTAATATTTT
* *
22801 ATTAATATTTTTTTATACATTTTTATTAA-CCCCGTCTTCTTCCTCATC-AGACTTCGTTAACTT
1 ATTAAT-TATTTTTATACATTATTATTAATCCCCGTCTTCTTCCTCATCGA-ACTTCGTTAACTT
22864 CATTTGTCTTTTTCATTCGTTA
64 CATTTGTCTTTTTCATTCGTTA
*
22886 ATTAATTATTTTTATACATTATTATTAATCCCCGTCTTCTTCTTCATCGAACTTCGTTAACTTCA
1 ATTAATTATTTTTATACATTATTATTAATCCCCGTCTTCTTCCTCATCGAACTTCGTTAACTTCA
22951 TTTGTCTTTTTCA
66 TTTGTCTTTTTCA
22964 CCGCATCATC
Statistics
Matches: 73, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
84 20 0.27
85 52 0.71
86 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.06, T:0.52
Consensus pattern (85 bp):
ATTAATTATTTTTATACATTATTATTAATCCCCGTCTTCTTCCTCATCGAACTTCGTTAACTTCA
TTTGTCTTTTTCATTCGTTA
Found at i:23987 original size:16 final size:16
Alignment explanation
Indices: 23963--24004 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
23953 TGTTTGGCAG
23963 AAAGGAAAAGAAAAGA
1 AAAGGAAAAGAAAAGA
* *
23979 AAAGAAAAAAAAAAGA
1 AAAGGAAAAGAAAAGA
*
23995 GAAGGAAAAG
1 AAAGGAAAAG
24005 GACACAGACC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (16 bp):
AAAGGAAAAGAAAAGA
Found at i:36676 original size:14 final size:14
Alignment explanation
Indices: 36657--36686 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
36647 CTAATTAGCA
36657 TATTTATTTAGAAT
1 TATTTATTTAGAAT
36671 TATTTATTTAGAAT
1 TATTTATTTAGAAT
36685 TA
1 TA
36687 GAAGAAATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (14 bp):
TATTTATTTAGAAT
Found at i:44462 original size:23 final size:23
Alignment explanation
Indices: 44436--44504 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
44426 CACCATAACT
*
44436 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
44459 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
44482 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
44505 TATAATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:44789 original size:30 final size:30
Alignment explanation
Indices: 44714--44781 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
44704 ACATAATTTG
* * *
44714 TATCACGTAGACATATTATTTTCATACCTT
1 TATCACATAGACATATCAATTTCATACCTT
44744 TATCACATAGACATATCAATTTCATA-CTT
1 TATCACATAGACATATCAATTTCATACCTT
44773 TATCACATA
1 TATCACATA
44782 ACTCATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 12 0.34
30 23 0.66
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (30 bp):
TATCACATAGACATATCAATTTCATACCTT
Found at i:45122 original size:20 final size:20
Alignment explanation
Indices: 45099--45191 Score: 168
Period size: 20 Copynumber: 4.7 Consensus size: 20
45089 TAATGGAGAT
*
45099 ATGCATCGATGCATTACACC
1 ATGCATCGATGCACTACACC
*
45119 ATGCATCGGTGCACTACACC
1 ATGCATCGATGCACTACACC
45139 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
45159 ATGCATCGATGCACTACACC
1 ATGCATCGATGCACTACACC
45179 ATGCATCGATGCA
1 ATGCATCGATGCA
45192 TAAATCTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (20 bp):
ATGCATCGATGCACTACACC
Found at i:45302 original size:56 final size:54
Alignment explanation
Indices: 45200--45304 Score: 129
Period size: 56 Copynumber: 1.9 Consensus size: 54
45190 CATAAATCTT
** * * *
45200 ATTCGATTTTGTATTTAATGGGGTGCATCGATGCACTCCTTATGCATCGATGGC
1 ATTCGATTTTGTATTTAAAAGAGTGCATCAATGCACTCCATATGCATCGATGGC
* *
45254 ATTCGATGTTTGTATTTTAAAAGAGTGCATCAATGCACTTCATGTGCATCG
1 ATTCGAT-TTTGTA-TTTAAAAGAGTGCATCAATGCACTCCATATGCATCG
45305 GTACACCTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 7 0.17
55 6 0.14
56 29 0.69
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (54 bp):
ATTCGATTTTGTATTTAAAAGAGTGCATCAATGCACTCCATATGCATCGATGGC
Found at i:52809 original size:21 final size:21
Alignment explanation
Indices: 52765--52810 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
52755 GATTTCTGGG
* * *
52765 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCACT
*
52786 CAAGGGGAACCGATACCCCCT
1 CAAGGGGAACCGATACCCACT
52807 CAAG
1 CAAG
52811 CGAACCAGAA
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:0.30, C:0.30, G:0.26, T:0.13
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCACT
Found at i:53251 original size:19 final size:21
Alignment explanation
Indices: 53227--53269 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
53217 ATATGTTATA
53227 ATGAT-ATAAACCATATG-AT
1 ATGATAATAAACCATATGAAT
*
53246 ATGATAATAAACTATATGAAT
1 ATGATAATAAACCATATGAAT
53267 ATG
1 ATG
53270 TGATTATGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 11 0.52
21 5 0.24
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
ATGATAATAAACCATATGAAT
Found at i:53838 original size:31 final size:31
Alignment explanation
Indices: 53800--53893 Score: 188
Period size: 31 Copynumber: 3.0 Consensus size: 31
53790 AGGGTCGAGG
53800 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
53831 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
53862 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
53893 G
1 G
53894 GTCCTTCGGG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:59943 original size:7 final size:8
Alignment explanation
Indices: 59912--59941 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
59902 TAGTTTATGT
59912 ATTTTTAAA
1 ATTTTT-AA
59921 ATTTTTAA
1 ATTTTTAA
59929 ATTTTTAA
1 ATTTTTAA
59937 ATTTT
1 ATTTT
59942 AACCTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
ATTTTTAA
Found at i:64212 original size:17 final size:17
Alignment explanation
Indices: 64190--64222 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
64180 AATAAATATA
64190 TTAAAT-TGATAGAATTT
1 TTAAATATGA-AGAATTT
64207 TTAAATATGAAGAATT
1 TTAAATATGAAGAATT
64223 AAATTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (17 bp):
TTAAATATGAAGAATTT
Found at i:70039 original size:40 final size:40
Alignment explanation
Indices: 69995--70094 Score: 164
Period size: 40 Copynumber: 2.5 Consensus size: 40
69985 GGGGTTTGCA
* *
69995 TTGAACAAAAGATTATGATTATCATAAATGTTTGATTCTT
1 TTGAATAAAAGATAATGATTATCATAAATGTTTGATTCTT
*
70035 TTGAATAAAAGATAATAATTATCATAAATGTTTGATTCTT
1 TTGAATAAAAGATAATGATTATCATAAATGTTTGATTCTT
*
70075 TTGAATAAAAGATGATGATT
1 TTGAATAAAAGATAATGATT
70095 TGCAACAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (40 bp):
TTGAATAAAAGATAATGATTATCATAAATGTTTGATTCTT
Found at i:71449 original size:28 final size:28
Alignment explanation
Indices: 71375--71447 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
71365 TCAAGTAGAG
71375 TAAA-GAAACAAAAGAAAATCAAAAGGC
1 TAAAGGAAACAAAAGAAAATCAAAAGGC
71402 TAAAGGAAACAAAAGAAAATCAAAAGGC
1 TAAAGGAAACAAAAGAAAATCAAAAGGC
71430 TAAAGGAAAC-AAAGAAAA
1 TAAAGGAAACAAAAGAAAA
71448 ATACCATGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 12 0.27
28 33 0.73
ACGTcount: A:0.67, C:0.10, G:0.16, T:0.07
Consensus pattern (28 bp):
TAAAGGAAACAAAAGAAAATCAAAAGGC
Found at i:74972 original size:21 final size:22
Alignment explanation
Indices: 74941--74984 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
74931 TTATATAATA
*
74941 TATTTATTTAAATTTTAAAATC
1 TATTTATTTAAATCTTAAAATC
74963 TATTT-TTTAAATCTTAAAATC
1 TATTTATTTAAATCTTAAAATC
74984 T
1 T
74985 TAAACGGGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTATTTAAATCTTAAAATC
Found at i:77991 original size:12 final size:12
Alignment explanation
Indices: 77970--78008 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
77960 CAACCTAATT
*
77970 AAAATGACAATA
1 AAAATAACAATA
77982 AAAATAACAATA
1 AAAATAACAATA
*
77994 ACAATAACAATA
1 AAAATAACAATA
78006 AAA
1 AAA
78009 TATTTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAATAACAATA
Found at i:77993 original size:6 final size:6
Alignment explanation
Indices: 77976--78010 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
77966 AATTAAAATG
*
77976 ACAATA AAAATA ACAATA ACAATA ACAATA A-AATA
1 ACAATA ACAATA ACAATA ACAATA ACAATA ACAATA
78011 TTTTATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 4 0.15
6 23 0.85
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.17
Consensus pattern (6 bp):
ACAATA
Found at i:77999 original size:18 final size:17
Alignment explanation
Indices: 77969--78010 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
77959 TCAACCTAAT
*
77969 TAAAATGACAATAAAAA
1 TAAAATAACAATAAAAA
*
77986 TAACAATAACAATAACAA
1 TAA-AATAACAATAAAAA
78004 TAAAATA
1 TAAAATA
78011 TTTTATTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.19
Consensus pattern (17 bp):
TAAAATAACAATAAAAA
Found at i:81969 original size:26 final size:26
Alignment explanation
Indices: 81940--81990 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
81930 TCCTAACTTA
*
81940 ACATGTTGATATGTAAGTAAATAAGG
1 ACATGTTGATACGTAAGTAAATAAGG
81966 ACATGTTGATACGTAAGTAAATAAG
1 ACATGTTGATACGTAAGTAAATAAG
81991 TAAGGAATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.43, C:0.06, G:0.22, T:0.29
Consensus pattern (26 bp):
ACATGTTGATACGTAAGTAAATAAGG
Found at i:89978 original size:29 final size:29
Alignment explanation
Indices: 89936--89994 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
89926 CGACATAACC
89936 CTCCTTGTTCCATCAACAAAGTTCATATT
1 CTCCTTGTTCCATCAACAAAGTTCATATT
89965 CTCCTTGTTCCATCAACAAAGTTCATATT
1 CTCCTTGTTCCATCAACAAAGTTCATATT
89994 C
1 C
89995 AGCTAGAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.37
Consensus pattern (29 bp):
CTCCTTGTTCCATCAACAAAGTTCATATT
Found at i:91176 original size:6 final size:6
Alignment explanation
Indices: 91160--91614 Score: 855
Period size: 6 Copynumber: 76.3 Consensus size: 6
91150 ATCAAAAACC
* *
91160 ATGTGAT ATGCAT ATGCAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGT-AT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91209 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91257 ATGTAT ATGTAT ATGTAT ATGTAT ATG--T ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91303 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91351 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91399 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91447 A--TAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91493 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91541 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
1 ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT ATGTAT
91589 ATGTAT ATGTAT ATGTAT ATGTAT AT
1 ATGTAT ATGTAT ATGTAT ATGTAT AT
91615 TGAAGATATT
Statistics
Matches: 442, Mismatches: 2, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
4 8 0.02
6 431 0.98
7 3 0.01
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.49
Consensus pattern (6 bp):
ATGTAT
Found at i:91646 original size:3 final size:3
Alignment explanation
Indices: 91638--91744 Score: 169
Period size: 3 Copynumber: 35.7 Consensus size: 3
91628 TTTTTATCCA
* * *
91638 TAT TAT TAT TAT TAG TAT TTT TAT TAT TAT TAT TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
91686 TAT TAT TAT TAT TAT TAT TAT TAT AAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
91734 TAT TAT TAT TA
1 TAT TAT TAT TA
91745 AATATATATT
Statistics
Matches: 95, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:92267 original size:26 final size:26
Alignment explanation
Indices: 92216--92268 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
92206 ATCTGCAAGA
* * *
92216 AACCAGAGAGACAAAAACAGAGACAG
1 AACCAGAGAGACAAAAAAAAAAACAG
92242 AACCAGAGAGA-AAGAAAAAAAAACAG
1 AACCAGAGAGACAA-AAAAAAAAACAG
92268 A
1 A
92269 GAAAGAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 2 0.09
26 21 0.91
ACGTcount: A:0.64, C:0.15, G:0.21, T:0.00
Consensus pattern (26 bp):
AACCAGAGAGACAAAAAAAAAAACAG
Found at i:92271 original size:18 final size:18
Alignment explanation
Indices: 92248--92284 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
92238 ACAGAACCAG
92248 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
92266 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
92284 A
1 A
92285 ACAACAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:93083 original size:22 final size:21
Alignment explanation
Indices: 93044--93086 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
93034 AGAATTTTTC
**
93044 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
93065 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
93087 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:104386 original size:1 final size:1
Alignment explanation
Indices: 104382--104433 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
104372 ATTATGCTTG
* * * ** *
104382 AAAAAAAAAAAAAAAAAAAGAAGAAAAAAAGAAAATGAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
104434 GGGGGTCAAG
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.88, C:0.00, G:0.10, T:0.02
Consensus pattern (1 bp):
A
Found at i:104407 original size:23 final size:23
Alignment explanation
Indices: 104381--104433 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
104371 TATTATGCTT
104381 GAAAAAAAAAAAAAAAAAAAGAA
1 GAAAAAAAAAAAAAAAAAAAGAA
* **
104404 GAAAAAAAGAAAATGAAAAAGAA
1 GAAAAAAAAAAAAAAAAAAAGAA
104427 -AAAAAAA
1 GAAAAAAA
104434 GGGGGTCAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (23 bp):
GAAAAAAAAAAAAAAAAAAAGAA
Found at i:104410 original size:17 final size:16
Alignment explanation
Indices: 104382--104434 Score: 63
Period size: 17 Copynumber: 3.3 Consensus size: 16
104372 ATTATGCTTG
104382 AAAA-AAAAAAAAAAA
1 AAAAGAAAAAAAAAAA
*
104397 AAAAGAAGAAAAAAAGA
1 AAAAGAA-AAAAAAAAA
* *
104414 AAATGAAAAAGAAAAA
1 AAAAGAAAAAAAAAAA
104430 AAAAG
1 AAAAG
104435 GGGGTCAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 4 0.13
16 13 0.42
17 14 0.45
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.02
Consensus pattern (16 bp):
AAAAGAAAAAAAAAAA
Found at i:106768 original size:113 final size:112
Alignment explanation
Indices: 106392--107140 Score: 855
Period size: 113 Copynumber: 6.6 Consensus size: 112
106382 ATTCAAATCT
* *
106392 ATCATTTGATGGATTATCTTTGCCAGGTAAAGTTCATAATGAG-AGAACTCATCTGAAGAAGGAA
1 ATCATTTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
106456 GAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTGAATTC
66 GAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTGAATTC
* * * * * * *
106503 ATCAAATTGATGGATTATCTTTTCCAGAGAAG-GTTCATAATGAGAAAAAATCATTTGAAGAAGG
1 ATC-ATTTGATGGATTATCTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGG
*
106567 AAGAAGAAGTTCATAAT--GAAGAATTTGTTCAACCTTTTACCCGAA-TC
64 AAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTGAATTC
* * *
106614 ATCATTTGATGGATCAGTCTTTTCCAGAG-AAAG-TCATAATGAGAAGAACTTATCTGAAGAAGG
1 ATCATTTGATGGATTA-TCTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGG
**
106677 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTC
64 AAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTGAATTC
*
106727 ATCAAGTTGATGGATTATCTTTGCCAGGTAGAG-TCATAATGAGAAGAACTCGTCATCTGAAGAA
1 ATC-ATTTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACT--T-ATCTGAAGAA
* *
106791 GGAAGAAGAAGTTCATAATGAGAACG---TGTTCAATCTTTTGCCTGAATTC
62 GGAAGAAGAAGTTCATAATGAGAA-GAATTGTTCAACCTTTTACCTGAATTC
* *
106840 ATCAAGTTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATTTGAAGAA
1 ATC-ATTTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACT--T-ATCTGAAGAA
* * *
106905 GGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATC-TTTGCTTGAATT-
62 GGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTGAATTC
* * *
106955 ATCATTTGATGGATCAACATTG-CAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 ATCATTTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACT--T-ATCTGAAGAAG
* * * *
107019 GAAGAAGAAGTTCATAATGAGAAAAACTTGTTCAATCTTTTGCTTGAATTC
63 GAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTACCTGAATTC
* * ** * * *
107070 ATCATTTGATGGATCATCATCCCCAGCAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG
1 ATCATTTGATGGATTATCTTTGCCAG--GTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGG
107134 -AGAAGAA
64 AAGAAGAA
107141 TTATTCAATA
Statistics
Matches: 574, Mismatches: 39, Indels: 48
0.87 0.06 0.07
Matches are distributed among these distances:
110 55 0.10
111 27 0.05
112 79 0.14
113 207 0.36
114 103 0.18
115 23 0.04
116 48 0.08
117 31 0.05
118 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (112 bp):
ATCATTTGATGGATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTGAATTC
Found at i:106940 original size:230 final size:228
Alignment explanation
Indices: 106392--107140 Score: 955
Period size: 227 Copynumber: 3.3 Consensus size: 228
106382 ATTCAAATCT
*
106392 ATCATTTGATGGATTATCTTTGCCAG-GTAAAGTTCATAATGAG-AGAA--CTCATCTGAAGAAG
1 ATCATTTGATGGATCATCTTTGCCAGAG-AAAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
*
106453 GAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTACCTGAATTCATCAAATTGATGGAT
65 GAAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGAT
* * ** *
106518 TATCTTTTCCAGAGAAG-GTTCATAATGAGAA-AA--AATCATTTGAAGAAGGAAGAAGAAGTTC
130 TATCTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
* * * *
106579 ATAATGAAGAATTTGTTCAACCTTTTACCCGAA-TC
194 ATAATG-AGAACTTGTTCAATCTTTTGCCTGAATTC
*
106614 ATCATTTGATGGATCAGTCTTTTCCAGAGAAAG-TCATAATGAGAAGAACT-T-ATCTGAAGAAG
1 ATCATTTGATGGATCA-TCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
* *
106676 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAGTTGATGGA
65 GAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGA
106741 TTATCTTTGCCAGGTAGAG-TCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
129 TTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
*
106805 ATAATGAGAACGTGTTCAATCTTTTGCCTGAATTC
194 ATAATGAGAACTTGTTCAATCTTTTGCCTGAATTC
* * * *
106840 ATCAAGTTGATGGATTATCTTTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATTTGAAGA
1 ATC-ATTTGATGGATCATCTTTGCCAGAG-AAAGTTCATAATGAGAAGAACTC-TCATCTGAAGA
* ** *
106904 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTGCT-TGAATT-ATC-ATTTGATG
63 AGGAAGAAGAAGTTCATAATGAGAAGAA-TTGTTCAACCTTTTATCTGAATTCATCAAATTGATG
* * *
106966 GATCAACATTG-CAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGT
127 GATTATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGT
*
107030 TCATAATGAGAAAAACTTGTTCAATCTTTTGCTTGAATTC
192 TCATAATGAG---AACTTGTTCAATCTTTTGCCTGAATTC
* ** *
107070 ATCATTTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAA--CTCATCTGAAGAAA
1 ATCATTTGATGGATCATCTTTGCCAG-AGAAAGTTCATAATGAGAAGAACTCTCATCTGAAGAAG
107133 G-AGAAGAA
65 GAAGAAGAA
107141 TTATTCAATA
Statistics
Matches: 466, Mismatches: 38, Indels: 42
0.85 0.07 0.08
Matches are distributed among these distances:
222 25 0.05
223 69 0.15
224 52 0.11
225 22 0.05
226 64 0.14
227 108 0.23
228 4 0.01
229 25 0.05
230 96 0.21
231 1 0.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.30
Consensus pattern (228 bp):
ATCATTTGATGGATCATCTTTGCCAGAGAAAGTTCATAATGAGAAGAACTCTCATCTGAAGAAGG
AAGAAGAAGTTCATAATGAGAAGAATTGTTCAACCTTTTATCTGAATTCATCAAATTGATGGATT
ATCTTTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAACTTGTTCAATCTTTTGCCTGAATTC
Found at i:107284 original size:3 final size:3
Alignment explanation
Indices: 107269--107353 Score: 120
Period size: 3 Copynumber: 28.7 Consensus size: 3
107259 AATTATCCCA
*
107269 TAT TAT TAG TAT TAT T-T TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
107315 TAT TAT ATAT TAT TAT AAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
107354 AATATATATT
Statistics
Matches: 74, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
2 4 0.05
3 67 0.91
4 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:107304 original size:31 final size:32
Alignment explanation
Indices: 107269--107353 Score: 120
Period size: 31 Copynumber: 2.7 Consensus size: 32
107259 AATTATCCCA
* *
107269 TATTATTAGTATTATT-TTATTATTTTATTAT
1 TATTATTATTATTATTATTATTATATTATTAT
107300 TATTATTATTATTATTATTA-TATATTATTAT
1 TATTATTATTATTATTATTATTATATTATTAT
* *
107331 AATCATTATTATTATTATTATTA
1 TATTATTATTATTATTATTATTA
107354 AATATATATT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
31 43 0.90
32 5 0.10
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
TATTATTATTATTATTATTATTATATTATTAT
Found at i:107316 original size:34 final size:37
Alignment explanation
Indices: 107269--107364 Score: 126
Period size: 37 Copynumber: 2.6 Consensus size: 37
107259 AATTATCCCA
* * *
107269 TATTATTAGTATTATT-T-TATTATT-TTATTATTAT
1 TATTATTATTATTATTATATATTATTATAATCATTAT
107303 TATTATTATTATTATTATATATTATTATAATCATTAT
1 TATTATTATTATTATTATATATTATTATAATCATTAT
*
107340 TATTATTATTATTAAATATATATTA
1 TATTATTATTATT-ATTATATATTA
107365 AAATATATAT
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
34 15 0.28
35 1 0.02
36 7 0.13
37 21 0.39
38 10 0.19
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (37 bp):
TATTATTATTATTATTATATATTATTATAATCATTAT
Found at i:107368 original size:12 final size:11
Alignment explanation
Indices: 107349--107391 Score: 52
Period size: 12 Copynumber: 3.8 Consensus size: 11
107339 TTATTATTAT
107349 TATTAAATATA
1 TATTAAATATA
107360 TATTAAA-ATA
1 TATTAAATATA
*
107370 TATATATATATA
1 TAT-TAAATATA
107382 TATATAAATA
1 TAT-TAAATA
107392 ATAATTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 6 0.21
11 10 0.36
12 12 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TATTAAATATA
Found at i:107893 original size:21 final size:20
Alignment explanation
Indices: 107852--107890 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
107842 ACAGAACCAG
107852 AGAGAAAGAAAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAAAC
107872 AGAGAAAGAAAAAAAAAAA
1 AGAGAAAGAAAAAAAAAAA
107891 ACAACAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (20 bp):
AGAGAAAGAAAAAAAAAAAC
Found at i:108618 original size:12 final size:13
Alignment explanation
Indices: 108601--108630 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
108591 TATATATATA
108601 TAATATATT-TTT
1 TAATATATTGTTT
108613 TAATATATTGTTT
1 TAATATATTGTTT
108626 TAATA
1 TAATA
108631 GAATTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (13 bp):
TAATATATTGTTT
Found at i:108677 original size:20 final size:21
Alignment explanation
Indices: 108640--108680 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
108630 AGAATTTTTC
**
108640 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
108661 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
108681 ATATAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:108882 original size:16 final size:16
Alignment explanation
Indices: 108861--108910 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
108851 TATTTTTAAT
108861 AAATAAATATATTTTG
1 AAATAAATATATTTTG
* *
108877 AAAT-AATA-AGATTAG
1 AAATAAATATA-TTTTG
108892 AAATTAAATATATTTTG
1 AAA-TAAATATATTTTG
108909 AA
1 AA
108911 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.38
16 5 0.19
17 9 0.35
18 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (16 bp):
AAATAAATATATTTTG
Found at i:120358 original size:33 final size:35
Alignment explanation
Indices: 120299--120366 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 35
120289 GGCAAGAATA
*
120299 AAATTATAAGATTTTAAAGAGTTTAAA-TATAATTT
1 AAATTATAAGATTTTAAAGAGATTAAACTA-AATTT
120334 AAATTAT-A-ATTTTAAA-AGGATTAAACTAAATTT
1 AAATTATAAGATTTTAAAGA-GATTAAACTAAATTT
120367 TTATCATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
32 1 0.03
33 19 0.63
34 3 0.10
35 7 0.23
ACGTcount: A:0.50, C:0.01, G:0.07, T:0.41
Consensus pattern (35 bp):
AAATTATAAGATTTTAAAGAGATTAAACTAAATTT
Found at i:120551 original size:17 final size:18
Alignment explanation
Indices: 120529--120566 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
120519 TACTTCCTTT
120529 ATTTTAAG-TATATTTTG
1 ATTTTAAGTTATATTTTG
*
120546 ATTTTAAGTTTTATTTTG
1 ATTTTAAGTTATATTTTG
120564 ATT
1 ATT
120567 AAATTTGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
ATTTTAAGTTATATTTTG
Found at i:136554 original size:21 final size:19
Alignment explanation
Indices: 136530--136575 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
136520 AAAAATAAGG
136530 ATAAAGAAA-AATAAAAATGAA
1 ATAAA-AAATAATAAAAA-G-A
136551 ATAAAAAATAATAAAAAGA
1 ATAAAAAATAATAAAAAGA
136570 ATAAAA
1 ATAAAA
136576 GGGAAGATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.29
20 4 0.17
21 13 0.54
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (19 bp):
ATAAAAAATAATAAAAAGA
Found at i:136709 original size:18 final size:17
Alignment explanation
Indices: 136664--136720 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
136654 ACATATATAC
*
136664 AAATGTTAAAATAAAAG
1 AAATATTAAAATAAAAG
*
136681 AAATATGTAAAATAATAG
1 AAATAT-TAAAATAAAAG
* *
136699 CATATATT-AAATAAAAC
1 -AAATATTAAAATAAAAG
136716 AAATA
1 AAATA
136721 AATAACAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.12
17 12 0.38
18 11 0.34
19 5 0.16
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (17 bp):
AAATATTAAAATAAAAG
Found at i:137968 original size:2 final size:2
Alignment explanation
Indices: 137958--138003 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
137948 CAAAAAATGC
137958 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
137999 AT AT A
1 AT AT A
138004 CAATATACGC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:138856 original size:36 final size:36
Alignment explanation
Indices: 138804--139244 Score: 166
Period size: 36 Copynumber: 13.0 Consensus size: 36
138794 ATTCAAAGAT
* * *
138804 TTTGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
138840 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * * * *
138876 TTCATTTCAA-GGAAAATGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* *
138904 TTATGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAA
1 TT-TGTTTCAAG-GGAAACTGTCTCAAGAGAGACAAAA
*
138942 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
** * * * *
138978 TTCATTTCAAGGTAAA-TGTTTTC-A-A-TG-----T
1 TTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAA
* * *
139006 TTATGTTTCAAGAGAAAACTATCTCAAGGGAGACAAAA
1 TT-TGTTTCAAG-GGAAACTGTCTCAAGAGAGACAAAA
* **
139044 TTTGTTTTAAGGG-AA--G--T--A-A-ATTCAAAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA-A
** *
139072 TTTTGTGTTTCAAAAGAAAC-GTCTCAAGGGAGACAAAA
1 --TT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
139110 -TT-TTTCAAGAGAAACTGTCTCGAGAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
139144 TTTGTTTAAAGGAAAACATAT-T-AA-A-AG----AT
1 TTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACAAAA
139173 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * *
139209 TTTATTTTAAGAGAAAATGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
139245 CTTTATTTTG
Statistics
Matches: 290, Mismatches: 67, Indels: 96
0.64 0.15 0.21
Matches are distributed among these distances:
27 5 0.02
28 7 0.02
29 31 0.11
30 14 0.05
31 19 0.07
32 4 0.01
33 19 0.07
34 19 0.07
35 16 0.06
36 126 0.43
37 20 0.07
38 5 0.02
39 5 0.02
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:138958 original size:102 final size:102
Alignment explanation
Indices: 138806--139058 Score: 463
Period size: 102 Copynumber: 2.5 Consensus size: 102
138796 TCAAAGATTT
*
138806 TGTTTCAAGAG-AAACTGTCTCAAGGGAGATAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
138870 ACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTTA
138907 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
138972 ACAAAATTCATTTCAAGGTAAATGTTTTCAATGTTTA
66 ACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTTA
* *
139009 TGTTTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAA
1 TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAA
139059 GTAAATTCAA
Statistics
Matches: 147, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
101 11 0.07
102 136 0.93
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTCATTTCAAGGAAAATGTTTTCAATGTTTA
Found at i:139068 original size:66 final size:66
Alignment explanation
Indices: 138944--139112 Score: 180
Period size: 66 Copynumber: 2.6 Consensus size: 66
138934 AGACAAAATT
* * * * *** *
138944 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGTAAATGTTTTCAATG-TTT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTATTTCAAGGGAAATAAATTCAAAGATTT
139008 A
66 A
* * *
139009 TGTTTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAGTAAATTCAAAGATT
1 TGTTTCAAGAG-AAACTATCTCAAGGGAGACAAAATTTATTTCAAGGGAAATAAATTCAAAGA-T
*
139074 TTG
64 TTA
* *
139077 TGTTTCAAAAGAAAC-GTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
139113 TTCAAGAGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
65 10 0.11
66 60 0.69
67 4 0.05
68 13 0.15
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (66 bp):
TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTATTTCAAGGGAAATAAATTCAAAGATTT
A
Found at i:139104 original size:168 final size:165
Alignment explanation
Indices: 138840--139226 Score: 447
Period size: 166 Copynumber: 2.3 Consensus size: 165
138830 GGAGATAAAA
* * *** *
138840 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTT
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTTAAGGAAAATAAATTCAAAGTT
* *
138905 TATGTTTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGAG
66 TATGTTTCAAAAGAAAACTGTCTCAAGGGAGACAAAA-TT-TTTCAAGAGAAACTATCTCAAGAG
* * ** * * *
138970 AGACAAAATTCATTTCAAGGTAAATGTTTTCAATG-T
129 AGACAAAATTCATTTAAAGGAAAACATATTAAAAGAT
* * * * *
139006 TTATGTTTCAAGAGAAAACTATCTCAAGGGAGACAAAATTTGTTTTAAGGGAAGTAAATTCAAAG
1 TT-TGTTTCAAG-GGAAACTATCTCAAGAGAGACAAAATTTATTTTAAGGAAAATAAATTCAAAG
* * *
139071 ATTTTGTGTTTCAAAAG-AAAC-GTCTCAAGGGAGACAAAATTTTTCAAGAGAAACTGTCTCGAG
64 --TTTATGTTTCAAAAGAAAACTGTCTCAAGGGAGACAAAATTTTTCAAGAGAAACTATCTCAAG
* **
139134 AGAGACGAAATTTGTTTAAAGGAAAACATATTAAAAGAT
127 AGAGACAAAATTCATTTAAAGGAAAACATATTAAAAGAT
*
139173 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTTAAGAGAAAAT
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTTAAG-GAAAAT
139227 GTCTCAAGAG
Statistics
Matches: 183, Mismatches: 32, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
165 32 0.17
166 61 0.33
167 14 0.08
168 59 0.32
169 4 0.02
170 13 0.07
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (165 bp):
TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTTATTTTAAGGAAAATAAATTCAAAGTT
TATGTTTCAAAAGAAAACTGTCTCAAGGGAGACAAAATTTTTCAAGAGAAACTATCTCAAGAGAG
ACAAAATTCATTTAAAGGAAAACATATTAAAAGAT
Found at i:139139 original size:34 final size:33
Alignment explanation
Indices: 139079--139146 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
139069 AGATTTTGTG
*
139079 TTTCAAAAGAAACGTCTCAAGGGAGACAAAATT
1 TTTCAAAAGAAACGTCTCAAGAGAGACAAAATT
* * *
139112 TTTCAAGAGAAACTGTCTCGAGAGAGACGAAATT
1 TTTCAAAAGAAAC-GTCTCAAGAGAGACAAAATT
139146 T
1 T
139147 GTTTAAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 12 0.40
34 18 0.60
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.24
Consensus pattern (33 bp):
TTTCAAAAGAAACGTCTCAAGAGAGACAAAATT
Found at i:139935 original size:2 final size:2
Alignment explanation
Indices: 139928--139969 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
139918 AAATAATTAT
139928 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
139969 T
1 T
139970 TAATAAATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:139973 original size:6 final size:7
Alignment explanation
Indices: 139920--140009 Score: 57
Period size: 8 Copynumber: 13.0 Consensus size: 7
139910 AATATTAAAA
139920 ATAAT-T
1 ATAATAT
*
139926 ATTATAT
1 ATAATAT
139933 AT-ATAT
1 ATAATAT
139939 ATATATAT
1 ATA-ATAT
139947 ATATATAT
1 ATA-ATAT
139955 ATATATAT
1 ATA-ATAT
139963 ATAATAT
1 ATAATAT
*
139970 -TAATAA
1 ATAATAT
139976 ATTAA-AT
1 A-TAATAT
*
139983 TTAA-AT
1 ATAATAT
*
139989 -TAAAAT
1 ATAATAT
139995 ATATATAT
1 ATA-ATAT
140003 ATAATAT
1 ATAATAT
140010 TTATTTATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
5 3 0.04
6 22 0.31
7 14 0.20
8 32 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATAATAT
Found at i:139997 original size:40 final size:40
Alignment explanation
Indices: 139953--140028 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
139943 ATATATATAT
139953 ATATATATATATAATATTAATAAATTAAATTTAAATTAAA
1 ATATATATATATAATATTAATAAATTAAATTTAAATTAAA
* ** *
139993 ATATATATATATAATATTTATTTATTTAATTTAAAT
1 ATATATATATATAATATTAATAAATTAAATTTAAAT
140029 ATATGTATAC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
ATATATATATATAATATTAATAAATTAAATTTAAATTAAA
Found at i:141280 original size:95 final size:95
Alignment explanation
Indices: 141114--141289 Score: 266
Period size: 95 Copynumber: 1.9 Consensus size: 95
141104 ATGTAAACAG
* * * *
141114 CTTTATCAGGTTAGCTAAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTAACTTAGAGGGAC
1 CTTTATCAGGCTAGCTAAATATTATCCATAAAGCCGAGGCGTTTAACCAATTAACTTAGAGGGAC
*
141179 AGCTCAAGCTTTATTGTATAGTATAATCAC
66 AACTCAAGCTTTATTGTATAGTATAATCAC
*
141209 CTTTATCAGGCTAGCCT-AATATTATCCATAAAGCCGAGGCGTTTAACCAATT-GCTCTAGAGGG
1 CTTTATCAGGCTAG-CTAAATATTATCCATAAAGCCGAGGCGTTTAACCAATTAACT-TAGAGGG
141272 ACAACTCAAGCTTTATTG
64 ACAACTCAAGCTTTATTG
141290 AATATAAAAT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 2 0.03
95 69 0.95
96 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (95 bp):
CTTTATCAGGCTAGCTAAATATTATCCATAAAGCCGAGGCGTTTAACCAATTAACTTAGAGGGAC
AACTCAAGCTTTATTGTATAGTATAATCAC
Found at i:143007 original size:21 final size:21
Alignment explanation
Indices: 142952--143008 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
142942 CTTTGACTAC
142952 CTTT-ATTTGCTCCTCCAACTG
1 CTTTGATTTG-TCCTCCAACTG
* * *
142973 C-TTGATTTTCTCCTCCATCTT
1 CTTTGA-TTTGTCCTCCAACTG
142994 CTTTGATTTGTCCTC
1 CTTTGATTTGTCCTC
143009 TTCGTCCGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 2 0.07
21 20 0.69
22 7 0.24
ACGTcount: A:0.11, C:0.32, G:0.09, T:0.49
Consensus pattern (21 bp):
CTTTGATTTGTCCTCCAACTG
Found at i:145493 original size:18 final size:17
Alignment explanation
Indices: 145448--145504 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
145438 ACATATATAC
*
145448 AAATGTTAAAATAAAAG
1 AAATATTAAAATAAAAG
*
145465 AAATATGTAAAATAATAG
1 AAATAT-TAAAATAAAAG
* *
145483 CATATATT-AAATAAAAC
1 -AAATATTAAAATAAAAG
145500 AAATA
1 AAATA
145505 AATAACAAAG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.12
17 12 0.38
18 11 0.34
19 5 0.16
ACGTcount: A:0.63, C:0.04, G:0.07, T:0.26
Consensus pattern (17 bp):
AAATATTAAAATAAAAG
Found at i:145672 original size:2 final size:2
Alignment explanation
Indices: 145667--145706 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
145657 ATAAAAAGAA
* *
145667 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
145707 GTATGATAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146775 original size:2 final size:2
Alignment explanation
Indices: 146760--146794 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
146750 TAAAAAATGC
146760 AT AT A- AT AT A- 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 AT AT AT AT A
146795 CACATTAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 29 0.94
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:155836 original size:36 final size:36
Alignment explanation
Indices: 155796--155868 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
155786 TGATTATAGT
155796 AGAACTTCAAAATGTCCAAATGTTTAGGTAATGATA
1 AGAACTTCAAAATGTCCAAATGTTTAGGTAATGATA
155832 AGAACTTCAAAATGTCCAAATGTTTAGGTAATGATA
1 AGAACTTCAAAATGTCCAAATGTTTAGGTAATGATA
155868 A
1 A
155869 AACAAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.30
Consensus pattern (36 bp):
AGAACTTCAAAATGTCCAAATGTTTAGGTAATGATA
Found at i:161841 original size:38 final size:38
Alignment explanation
Indices: 161790--161864 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
161780 TTGTTAATAT
*
161790 ATATATATATATATGTATAATTTTTTTAGATTTTATTA
1 ATATATATATATATATATAATTTTTTTAGATTTTATTA
161828 ATATATATATATATATATAATTTTTTTAGATTTTATT
1 ATATATATATATATATATAATTTTTTTAGATTTTATT
161865 GTGTGTAATT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (38 bp):
ATATATATATATATATATAATTTTTTTAGATTTTATTA
Found at i:164530 original size:18 final size:19
Alignment explanation
Indices: 164495--164531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
164485 CACGGAATGT
164495 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
164515 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
164532 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:165399 original size:32 final size:33
Alignment explanation
Indices: 165340--165401 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
165330 TTTTTAGAAT
* * *
165340 CAACTTAAAATTTTAATTTTTTTAACATTTGTG
1 CAACCTAAAATGTTAATTTTTTAAACATTTGTG
165373 CAACCTAAAATGTTAA-TTTTTAAACATTT
1 CAACCTAAAATGTTAATTTTTTAAACATTT
165402 CTGGTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 12 0.46
33 14 0.54
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (33 bp):
CAACCTAAAATGTTAATTTTTTAAACATTTGTG
Found at i:166046 original size:29 final size:28
Alignment explanation
Indices: 166014--166075 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
166004 ATTTACTCCT
* * *
166014 ATATATCATTTTTAATATTATTTATAAAA
1 ATATAT-ATTCTTAAAATTATTTAAAAAA
166043 ATATTATATTCTTAAAATTATTTAAAAAA
1 ATA-TATATTCTTAAAATTATTTAAAAAA
166072 ATAT
1 ATAT
166076 GTTCTGTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 25 0.86
30 3 0.10
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (28 bp):
ATATATATTCTTAAAATTATTTAAAAAA
Found at i:170056 original size:2 final size:2
Alignment explanation
Indices: 170049--170091 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
170039 TTTCTGTCTG
* * *
170049 TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC CC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
170091 T
1 T
170092 TTCTTTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:179616 original size:2 final size:2
Alignment explanation
Indices: 179609--179652 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
179599 CAGAGAATTT
*
179609 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
179651 TA
1 TA
179653 CTTTTGAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:179884 original size:4 final size:4
Alignment explanation
Indices: 179877--180192 Score: 564
Period size: 4 Copynumber: 79.5 Consensus size: 4
179867 AGTATCTGCA
*
179877 ATAC ATAC GTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
179925 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
179973 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * *
180021 ATAC ATAC ATAC ATAC ACAC ACAC ACAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
180069 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
180117 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
180163 ACAC ACAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
180193 GTCTAATGAT
Statistics
Matches: 305, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
2 2 0.01
4 303 0.99
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:184081 original size:28 final size:29
Alignment explanation
Indices: 184041--184112 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 29
184031 AAATTTTGTA
184041 TTTAATCTTTATATTT-T-AATTTGATT-AAT
1 TTTAATC-TTATATTTCTAAATTT--TTAAAT
184070 TTTAATCTTATATTTCTAAATTTTTAAAT
1 TTTAATCTTATATTTCTAAATTTTTAAAT
184099 TTTAATCTTA-ATTT
1 TTTAATCTTATATTT
184113 AATAATATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
28 14 0.35
29 21 0.52
30 5 0.12
ACGTcount: A:0.32, C:0.06, G:0.01, T:0.61
Consensus pattern (29 bp):
TTTAATCTTATATTTCTAAATTTTTAAAT
Found at i:184489 original size:32 final size:32
Alignment explanation
Indices: 184441--184537 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
184431 CGATGATTGT
* *
184441 ACGGGAGTTGGGTGCCATGTCAGCAAAAACTA
1 ACGGGAGTTAGTTGCCATGTCAGCAAAAACTA
*
184473 ACGGGAGTTAGTTGCCATGTTAGCAAAAACTA
1 ACGGGAGTTAGTTGCCATGTCAGCAAAAACTA
184505 ACGGGAGTTAGTTGCCATGTCAGCAAAAACTA
1 ACGGGAGTTAGTTGCCATGTCAGCAAAAACTA
184537 A
1 A
184538 AGGAGGTAAC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.22
Consensus pattern (32 bp):
ACGGGAGTTAGTTGCCATGTCAGCAAAAACTA
Found at i:190601 original size:22 final size:21
Alignment explanation
Indices: 190576--190629 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 21
190566 TATTATGCCC
190576 TAGCTGGTAATCTATATAATTT
1 TAGCTGGTAATC-ATATAATTT
190598 TAGCTGGTTATAATCATATAATTT
1 TAGCTGG---TAATCATATAATTT
190622 TAGCTGGT
1 TAGCTGGT
190630 TAAAAACAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 1 0.03
22 7 0.24
24 16 0.55
25 5 0.17
ACGTcount: A:0.30, C:0.09, G:0.17, T:0.44
Consensus pattern (21 bp):
TAGCTGGTAATCATATAATTT
Found at i:190620 original size:24 final size:25
Alignment explanation
Indices: 190583--190631 Score: 91
Period size: 24 Copynumber: 2.0 Consensus size: 25
190573 CCCTAGCTGG
190583 TAATCTATATAATTTTAGCTGGTTA
1 TAATCTATATAATTTTAGCTGGTTA
190608 TAATC-ATATAATTTTAGCTGGTTA
1 TAATCTATATAATTTTAGCTGGTTA
190632 AAAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (25 bp):
TAATCTATATAATTTTAGCTGGTTA
Found at i:192196 original size:17 final size:17
Alignment explanation
Indices: 192143--192198 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 17
192133 CACATAACAT
* * *
192143 AATAAGATTATTTTGAA
1 AATAAAATTCTTTTTAA
192160 AAT-AAATTCTTTTT--
1 AATAAAATTCTTTTTAA
192174 -ATAAAATTCTTTTTAA
1 AATAAAATTCTTTTTAA
192190 AATAAAATT
1 AATAAAATT
192199 ATTAAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 2 0.06
14 11 0.34
16 8 0.25
17 11 0.34
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (17 bp):
AATAAAATTCTTTTTAA
Found at i:192203 original size:14 final size:16
Alignment explanation
Indices: 192186--192217 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
192176 AAAATTCTTT
192186 TTAAAATA-AA-ATTA
1 TTAAAATATAATATTA
192200 TTAAAATATAATATTA
1 TTAAAATATAATATTA
192216 TT
1 TT
192218 CTAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 2 0.12
16 6 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATAATATTA
Found at i:192614 original size:17 final size:17
Alignment explanation
Indices: 192592--192624 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
192582 ATATTTATTT
*
192592 ATATAAAAATTAATATA
1 ATATAAAAAATAATATA
192609 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
192625 TATAGTATGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:193898 original size:14 final size:13
Alignment explanation
Indices: 193879--193914 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
193869 TTACTTTATT
193879 TTTAAAAAAATATA
1 TTTAAAAAAA-ATA
193893 TTTAAAATAAAATA
1 TTTAAAA-AAAATA
193907 TTTAAAAA
1 TTTAAAAA
193915 CATTTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 17 0.81
15 3 0.14
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTTAAAAAAAATA
Found at i:194702 original size:19 final size:20
Alignment explanation
Indices: 194663--194702 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
194653 AAAAAAACTC
*
194663 AATAATATTTTTGATATAAAT
1 AATAATATTTCTGA-ATAAAT
194684 AATAATATTTCTG-ATAAAT
1 AATAATATTTCTGAATAAAT
194703 TTTATCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
AATAATATTTCTGAATAAAT
Found at i:195024 original size:15 final size:15
Alignment explanation
Indices: 194996--195037 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
194986 ACGTATTCTT
*
194996 TTAATAATAGTTAAGA
1 TTAATAATATTTAA-A
195012 TTAA-AATATTTAAA
1 TTAATAATATTTAAA
*
195026 ATAATAATATTT
1 TTAATAATATTT
195038 GTAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 4 0.17
15 15 0.65
16 4 0.17
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (15 bp):
TTAATAATATTTAAA
Found at i:195163 original size:21 final size:20
Alignment explanation
Indices: 195130--195168 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
195120 AACAGATAAG
*
195130 ATAAAATAATTAATAAGAATA
1 ATAAAAGAATTAA-AAGAATA
*
195151 ATAAAAGATTTAAAAGAA
1 ATAAAAGAATTAAAAGAA
195169 AAATGAGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.26
Consensus pattern (20 bp):
ATAAAAGAATTAAAAGAATA
Found at i:197310 original size:5 final size:5
Alignment explanation
Indices: 197300--197367 Score: 56
Period size: 5 Copynumber: 14.4 Consensus size: 5
197290 GTTAATTTGA
* * **
197300 AAAAT AAAAT --AAT AAAAT AAAA- ATAAGT GAAAT AAAAT AACCT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
197347 -AAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AA
197368 GAACGAAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
3 3 0.06
4 7 0.14
5 40 0.80
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:197316 original size:14 final size:13
Alignment explanation
Indices: 197300--197367 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 13
197290 GTTAATTTGA
197300 AAAATAAAATAAT
1 AAAATAAAATAAT
197313 AAAATAAAAATAAGT
1 AAAAT-AAAATAA-T
*
197328 GAAATAAAATAACCT
1 AAAATAAAATAA--T
*
197343 -AAATAAATAAAAT
1 AAAATAAA-ATAAT
197356 AAAATAAAATAA
1 AAAATAAAATAA
197368 GAACGAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
13 9 0.20
14 28 0.61
15 9 0.20
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:208370 original size:2 final size:2
Alignment explanation
Indices: 208363--208396 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
208353 TGCTAGACAA
208363 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
208397 CTAGTTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:209270 original size:20 final size:21
Alignment explanation
Indices: 209245--209287 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
209235 TCTGAGAGAT
*
209245 GGAGATA-GACGGATTTCGCC
1 GGAGATAGGACGGATGTCGCC
209265 GGAGATAGGGACGGATGTCGCC
1 GGAGATA-GGACGGATGTCGCC
209287 G
1 G
209288 TAGAGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 7 0.35
22 13 0.65
ACGTcount: A:0.23, C:0.19, G:0.42, T:0.16
Consensus pattern (21 bp):
GGAGATAGGACGGATGTCGCC
Found at i:209413 original size:19 final size:20
Alignment explanation
Indices: 209391--209428 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
209381 AATATTGTGT
209391 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
209410 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
209429 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:209460 original size:20 final size:20
Alignment explanation
Indices: 209435--209483 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
209425 TAAACGCGCT
209435 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
* *
209455 TTGCGAAATTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
209475 TTGCGAATT
1 TTGCGAATT
209484 ACAAATTCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.10, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:209497 original size:20 final size:20
Alignment explanation
Indices: 209474--209523 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
209464 TGACTTTTGT
209474 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACAAATTCGC
* *
209494 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAAATTCGC
209514 GTTGCGAATT
1 GTTGCGAATT
209524 TGGAAACTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAAATTCGC
Found at i:209654 original size:2 final size:2
Alignment explanation
Indices: 209647--209699 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
209637 TTATTTTCTC
209647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
209689 AT AT AT AT AT A
1 AT AT AT AT AT A
209700 GTTAGATTGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:212279 original size:2 final size:2
Alignment explanation
Indices: 212272--212312 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
212262 GCCATTATTA
* *
212272 AT AT AT AT AT AT AT AT AT AT AT AT AT GCT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
212313 GCTTTAGCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
2 34 0.97
3 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:220642 original size:24 final size:24
Alignment explanation
Indices: 220613--220658 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
220603 TAATTTTCAA
* *
220613 TTTTAAAATTAAATGGATCAAATT
1 TTTTAAAACTAAATCGATCAAATT
*
220637 TTTTAAAACTAGATCGATCAAA
1 TTTTAAAACTAAATCGATCAAA
220659 AATTTATCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (24 bp):
TTTTAAAACTAAATCGATCAAATT
Found at i:229292 original size:21 final size:21
Alignment explanation
Indices: 229267--229311 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
229257 TTGTTGGACA
229267 AGAGTAAGATATTATGTTAAG
1 AGAGTAAGATATTATGTTAAG
229288 AGAGTAAGATATTATGTTAAG
1 AGAGTAAGATATTATGTTAAG
229309 AGA
1 AGA
229312 ATAACTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.31
Consensus pattern (21 bp):
AGAGTAAGATATTATGTTAAG
Found at i:232119 original size:29 final size:28
Alignment explanation
Indices: 232064--232138 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
232054 AAGAGGCATG
* *
232064 ATTTTTTTTATTACTAA-AATAACAATTT
1 ATTTTTTTTATTA-AAATAATAACAATTA
* *
232092 GTTTTTTTTATTAAAATAATTAATAATTA
1 ATTTTTTTTATTAAAATAA-TAACAATTA
232121 ATTTTTTTTATTGAAAAT
1 ATTTTTTTTATT-AAAAT
232139 CCTTTCCCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
27 2 0.05
28 14 0.36
29 18 0.46
30 5 0.13
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
ATTTTTTTTATTAAAATAATAACAATTA
Found at i:235194 original size:24 final size:24
Alignment explanation
Indices: 235184--235295 Score: 145
Period size: 24 Copynumber: 4.7 Consensus size: 24
235174 CATAATTCAC
* * *
235184 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
235208 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
**
235232 GTCAAGTAAAAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
235256 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
235280 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
235296 TAATTCAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.03
24 74 0.95
25 2 0.03
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:239815 original size:35 final size:35
Alignment explanation
Indices: 239772--239838 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
239762 CGTCACGTCC
* *
239772 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTGTA
1 AGTAAGGCCATAAGCACACAGCCGAGGAACCTGTA
239807 AGTAAGGCCATAAGCACACAGCCGAGGAACCT
1 AGTAAGGCCATAAGCACACAGCCGAGGAACCT
239839 CCATGCATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.34, C:0.28, G:0.27, T:0.10
Consensus pattern (35 bp):
AGTAAGGCCATAAGCACACAGCCGAGGAACCTGTA
Found at i:239936 original size:24 final size:24
Alignment explanation
Indices: 239926--240037 Score: 154
Period size: 24 Copynumber: 4.7 Consensus size: 24
239916 CATAATTCAC
* * *
239926 GTCAAGTATCATATCAAAATCCAG
1 GTCAAGTATCAGATCAGAATCCAT
* *
239950 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
239974 GTCAAGTATTAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
239998 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
240022 GTCAAGTATCAGATCA
1 GTCAAGTATCAGATCA
240038 TAATTCAAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
23 2 0.03
24 74 0.95
25 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:244841 original size:34 final size:34
Alignment explanation
Indices: 244793--244865 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
244783 GTAGATATGC
* *
244793 TAATGATTTGAAGTTGCTGCAGTGAGATTGTTGA
1 TAATGATTTAAAGTTGCTGCAGTGAGATAGTTGA
244827 TAATGATTTAAAGTTGCTGCAGTGAGATAGTTGA
1 TAATGATTTAAAGTTGCTGCAGTGAGATAGTTGA
*
244861 AAATG
1 TAATG
244866 GAATGGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (34 bp):
TAATGATTTAAAGTTGCTGCAGTGAGATAGTTGA
Found at i:272090 original size:183 final size:185
Alignment explanation
Indices: 271765--272107 Score: 557
Period size: 183 Copynumber: 1.9 Consensus size: 185
271755 TTTTCTAATT
*
271765 TATATAAAAATTAAATATTTTTTAATTCAAAAAAAAAAGTTTATAATTAATTTAAATAATATATA
1 TATATAAAAATTAAATATTTTTTAATT-AAAAAAAAAAGTTTACAATTAATTTAAATAATATATA
* *
271830 ATTATAAAATAAAAATTTCAGATAAATTTTTGAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAATTTCAGATAAATTTGTGAATTAATTAATATTGATTTAAGTTTAAAAGTTA
271895 TTAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTATACCATATGTTA
130 TTAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTATACCATATGTTA
* * *
271951 TATATAATATATTTAATATTTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAA-AAATTAAATATTTTTTAATTAAAAAAAAAAGTTTACAATTAATTTAAATAATATATA
* * *
272015 ATTATAAAATAAAAATTTTATAT-AATTTGT-AATTAATTAATATTGATTTAATTTTAAAAGTTA
65 ATTATAAAATAAAAATTTCAGATAAATTTGTGAATTAATTAATATTGATTTAAGTTTAAAAGTTA
*
272078 TTTGATCTTAAATTATTAATTGGGTTTTAA
130 TTAGATCTTAAATTATTAATTGGGTTTTAA
272108 GCCCATATGT
Statistics
Matches: 146, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
183 60 0.41
184 6 0.04
185 55 0.38
186 7 0.05
187 18 0.12
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (185 bp):
TATATAAAAATTAAATATTTTTTAATTAAAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTCAGATAAATTTGTGAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
TAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTATACCATATGTTA
Found at i:272150 original size:183 final size:184
Alignment explanation
Indices: 271766--272150 Score: 492
Period size: 183 Copynumber: 2.1 Consensus size: 184
271756 TTTCTAATTT
* *
271766 ATATAAAAATTAAATATTTTTTAATTCAAAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 ATAT-AAAATTTAATATTTTTTAATT-AAAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
* *
271831 TTATAAAATAAAAATTTCAGATAAATTTTTGAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
64 TTATAAAATAAAAATTTCAGATAAATTTGTGAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
*** * * *
271896 TAGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTTATACCATATGTTAT
129 TAGATCTTAAATTATTAATTGGGTTTTAAATGCCATAGGTTTATACAATATGTTAA
*
271952 ATATAATATATTTAATATTTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 ATATAA-A-ATTTAATATTTTTTAATTAAAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
* * *
272016 TTATAAAATAAAAATTTTATAT-AATTTGT-AATTAATTAATATTGATTTAATTTTAAAAGTTAT
64 TTATAAAATAAAAATTTCAGATAAATTTGTGAATTAATTAATATTGATTTAAGTTTAAAAGTTAT
* * * *
272079 TTGATCTTAAATTATTAATTGGGTTTT-AA-GCCCATATGTTATATATAATATATTTAAA
129 TAGATCTTAAATTATTAATTGGGTTTTAAATG-CCATAGGTT-TATACAATAT-GTT-AA
*
272137 ATTTAAAATTTAAT
1 ATATAAAATTTAAT
272151 TTCGGTTAAT
Statistics
Matches: 174, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
181 1 0.01
182 6 0.03
183 73 0.42
184 9 0.05
185 63 0.36
186 5 0.03
187 17 0.10
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (184 bp):
ATATAAAATTTAATATTTTTTAATTAAAAAAAAAAGTTTACAATTAATTTAAATAATATATAATT
ATAAAATAAAAATTTCAGATAAATTTGTGAATTAATTAATATTGATTTAAGTTTAAAAGTTATTA
GATCTTAAATTATTAATTGGGTTTTAAATGCCATAGGTTTATACAATATGTTAA
Found at i:284921 original size:28 final size:28
Alignment explanation
Indices: 284868--284923 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
284858 GTTTAATAAT
* * *
284868 ATGTTTAGAGATTCATATTTGAGGTTTA
1 ATGTTTAAAGATTCAAAGTTGAGGTTTA
284896 ATGTTTAAAGATT-AAAGTTGAGGGTTTA
1 ATGTTTAAAGATTCAAAGTTGA-GGTTTA
284924 GAAAATTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.32, C:0.02, G:0.23, T:0.43
Consensus pattern (28 bp):
ATGTTTAAAGATTCAAAGTTGAGGTTTA
Found at i:286239 original size:2 final size:2
Alignment explanation
Indices: 286228--286277 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
286218 CCTTTAACAT
* *
286228 TA TA TA -A TA TA TT TA CA T- TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
286267 TA TA TA TA TA T
1 TA TA TA TA TA T
286278 TTTACATATG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:286247 original size:18 final size:19
Alignment explanation
Indices: 286224--286284 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
286214 TTATCCTTTA
286224 ACATTATATA-ATATATTT
1 ACATTATATATATATATTT
*
286242 ACATTATA-ATATATATAT
1 ACATTATATATATATATTT
*
286260 ATATATATATATATATATTTT
1 ACAT-TATATATATATA-TTT
286281 ACAT
1 ACAT
286285 ATGGTGCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 1 0.03
18 18 0.51
19 4 0.11
20 7 0.20
21 5 0.14
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
ACATTATATATATATATTT
Found at i:287324 original size:63 final size:63
Alignment explanation
Indices: 287225--287344 Score: 204
Period size: 63 Copynumber: 1.9 Consensus size: 63
287215 TTGTTAAAAG
*
287225 GGGTAAACTTCATTTTGGCTCCCTCTATTTTGAAAAACATTCAATTTGGTCCCCAAACCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTATTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
* * *
287288 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACGTTTAATTTGGTCCCCAAA
1 GGGTAAACTTCATTTTGGCTCCCTCTATTTTAAAAAACATTCAATTTGGTCCCCAAA
287345 TTGGTTTAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.36
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTATTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
Found at i:287860 original size:12 final size:12
Alignment explanation
Indices: 287845--287879 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
287835 TTATATTTTA
*
287845 ATATATATATAT
1 ATATGTATATAT
287857 ATATGTATATAT
1 ATATGTATATAT
*
287869 CTATGTATATA
1 ATATGTATATA
287880 CTTGTAATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (12 bp):
ATATGTATATAT
Found at i:287885 original size:10 final size:12
Alignment explanation
Indices: 287850--287917 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 12
287840 TTTTAATATA
*
287850 TATATATATATG
1 TATATATCTATG
287862 TATATATCTATG
1 TATATATCTATG
287874 TATATA-CT-TG
1 TATATATCTATG
* *
287884 TA-ATAGTTTATT
1 TATATA-TCTATG
287896 TATATATCTAT-
1 TATATATCTATG
287907 TAT-TAT-TATG
1 TATATATCTATG
287917 T
1 T
287918 GTACATTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 6 0.13
10 8 0.17
11 6 0.13
12 24 0.51
13 3 0.06
ACGTcount: A:0.34, C:0.04, G:0.07, T:0.54
Consensus pattern (12 bp):
TATATATCTATG
Found at i:299491 original size:103 final size:105
Alignment explanation
Indices: 299255--300102 Score: 1329
Period size: 103 Copynumber: 8.2 Consensus size: 105
299245 GGTTTTACCC
299255 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299320 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
299360 AGCCAA-TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299424 AA-GGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
299463 AGCCAATTTC-ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299527 AAGGGACCGCTGGTTGTCAAC--A-ATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
299564 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGAC-ACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299628 AAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
299668 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
299733 AAGGGACCGCTGGTTGTCAACAAACA-TTCT-CAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
*
299771 AGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCC-GACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299835 AAGGGACCGCTGGTTGTCAATAAACA--TCT-CAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAA-TTCAG
**
299873 AGCCAATTTCAACTTTGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299938 AAGGGACCGCTGGTTGTCAACAAACATCTCT-CAATGTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAAT-TCAG
* * * * * * *
299978 AGCCAATTTCAACTTCACAGCAAAGGATATTGGACT-CAGACAGCACAAGCTCGACTTCACAACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
** *
300042 AAGGGA-CGACTGACTGTCAACGAATA-ATTTCT-CAATTCCAT
66 AAGGGACCG-CTGGTTGTCAAC-AA-ACATTTCTCCAATT-CAG
300083 AGCC-ATTTCCAACTTCACAA
1 AGCCAATTT-CAACTTCACAA
300103 ACAGGTTGAC
Statistics
Matches: 699, Mismatches: 27, Indels: 34
0.92 0.04 0.04
Matches are distributed among these distances:
101 72 0.10
102 123 0.18
103 196 0.28
104 185 0.26
105 122 0.17
106 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAG
Found at i:299845 original size:207 final size:209
Alignment explanation
Indices: 299255--300048 Score: 1344
Period size: 207 Copynumber: 3.8 Consensus size: 209
299245 GGTTTTACCC
299255 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
299320 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAA-TTCAACTTCACAACGAAG
66 AAGGGACCGCTGGTTGTCAACAAACA-TTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAG
299384 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAA-GGACCGCTGGTTGTCACCAAAC
130 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAAC
299448 ATTTCTCCAATTCAG
195 ATTTCTCCAATTCAG
299463 AGCCAATTTC-ACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299527 AAGGGACCGCTGGTTGTCAAC-AA-TTTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGG
66 AAGGGACCGCTGGTTGTCAACAAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGG
299590 ATATTGGACTCCAGAC-ACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACA
299654 TTTCTCCAATTCAG
196 TTTCTCCAATTCAG
299668 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
299733 AAGGGACCGCTGGTTGTCAACAAACATTCTC-AATTCAGAGCCAATTTCAACTTCACAGCGAAGG
66 AAGGGACCGCTGGTTGTCAACAAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGG
**
299797 ATATTGGACTCC-GACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
131 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACA
299861 --TCT-CAATTTCAG
196 TTTCTCCAA-TTCAG
**
299873 AGCCAATTTCAACTTTGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
299938 AAGGGACCGCTGGTTGTCAACAAACATCTCTC-AATGTCAGAGCCAATTTCAACTTCACAGCAAA
66 AAGGGACCGCTGGTTGTCAACAAACAT-TCTCAAAT-TCAGAGCCAATTTCAACTTCACAACGAA
* * * * *
300002 GGATATTGGACT-CAGACAGCACAAGCTCGACTTCACAACGAAGGGAC
129 GGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
300049 GACTGACTGT
Statistics
Matches: 563, Mismatches: 13, Indels: 21
0.94 0.02 0.04
Matches are distributed among these distances:
204 46 0.08
205 180 0.32
206 88 0.16
207 234 0.42
208 15 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (209 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTCTCAAATTCAGAGCCAATTTCAACTTCACAACGAAGG
ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCACCAAACA
TTTCTCCAATTCAG
Done.