Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 67 of 93
Found at i:9412010 original size:120 final size:119
Alignment explanation
Indices: 9411886--9412379 Score: 490
Period size: 121 Copynumber: 4.1 Consensus size: 119
9411876 TCCTGGTTGG
* * *
9411886 TTTATCTTTTTGACTCATGATTTCATCCTGATCATTCAATTTTGACTCTGTCTAGATCATTTTTT
1 TTTATCTTTTTGACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTGTCTAGATCATTTTTT
* * *
9411951 GACTCGCGATTCCATCCCACTCAACCATCTTCAACCTCGACTCGGTCCTAGTCAT
66 GACTCGCGATTCCATCCCA-TCAACCATCTTTAACCTCGACTCGGTCCTGGTCAC
** * *
9412006 TTTATCTTTTCAACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTATCTAGATCATTTTCC
1 TTTATCTTTTTGACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTGTCTAGATCATTTT-T
* * * * * *
9412071 TGATTCGCGGTTCCATCTCGATCAGCTATCTTTAACCTCGACTCGGTTCTGGTCAC
65 TGACTCGCGATTCCATC-CCATCAACCATCTTTAACCTCGACTCGGTCCTGGTCAC
* * * * * *
9412127 TTTATCTTTTTAACTCATGGTTTTATCCT-AGTCATTCGATCTCGGTTCTGTCTAGATTATTTTT
1 TTTATCTTTTTGACTCATGGTTTCATCCTGA-TCATTCAATCTTGGCTCTGTCTAGATCATTTTT
* * * * * * *
9412191 TGACTAG-TAGTTTCAT-CCAGGTCAGCCATCTTTAATCTCGACTTGATCCTGGTCAC
65 TGACTCGCGA-TTCCATCCCA--TCAACCATCTTTAACCTCGACTCGGTCCTGGTCAC
* * * * * *
9412247 TTTATCTTTTTGACTCGTGGTTTCATCTTGGTCATTCGATCTTGGTTCTAGTCTAGATCATTTGT
1 TTTATCTTTTTGACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCT-GTCTAGATCATTTTT
* * * * * * ** *
9412312 TGACTTGCGATTCTATCTCAATCAATCACCTTTGACCTCGACTTAGTCATGGTCAC
65 TGACTCGCGATTCCATC-CCATCAACCATCTTTAACCTCGACTCGGTCCTGGTCAC
9412368 TTTATCTTTTTG
1 TTTATCTTTTTG
9412380 TAGTTTCATC
Statistics
Matches: 307, Mismatches: 56, Indels: 21
0.80 0.15 0.05
Matches are distributed among these distances:
118 2 0.01
120 140 0.46
121 160 0.52
122 3 0.01
123 2 0.01
ACGTcount: A:0.19, C:0.24, G:0.14, T:0.43
Consensus pattern (119 bp):
TTTATCTTTTTGACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTGTCTAGATCATTTTTT
GACTCGCGATTCCATCCCATCAACCATCTTTAACCTCGACTCGGTCCTGGTCAC
Found at i:9412352 original size:241 final size:240
Alignment explanation
Indices: 9411886--9412378 Score: 541
Period size: 241 Copynumber: 2.0 Consensus size: 240
9411876 TCCTGGTTGG
* * *
9411886 TTTATCTTTTTGACTCATGATTTCATCCTGATCATTCAATTTTGACTCTGTCTAGATCATTTTTT
1 TTTATCTTTTTAACTCATGATTTCATCCTGATCATTCAATCTCGACTCTGTCTAGATCATTTTTT
* * * *
9411951 GACTCGCGATTCCATCCCACTCAACCATCTTCAACCTCGACTCGGTCCTAGTCATTTTATCTTTT
66 GACTAGAGATTCCATCCCACTCAACCATCTTCAACCTCGACTCGATCCTAGTCACTTTATCTTTT
*
9412016 CAACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTATCTAGATCATTTTCCTGATTCGCGG
131 CAACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTATCTAGATCATTTT-CTGATTCGCGA
* * *
9412081 TTCCATCTCGATCAGCTATCTTTAACCTCGACTCGGTTC-TGGTCAC
195 TTCCATCTCAATCAGCTACCTTTAACCTCGACTCAG-TCATGGTCAC
* * * ** *
9412127 TTTATCTTTTTAACTCATGGTTTTATCCT-AGTCATTCGATCTCGGTTCTGTCTAGATTATTTTT
1 TTTATCTTTTTAACTCATGATTTCATCCTGA-TCATTCAATCTCGACTCTGTCTAGATCATTTTT
* * * * * * *
9412191 TGACTAGTAG-TTTCAT-CCAGGTCAGCCATCTTTAATCTCGACTTGATCCTGGTCACTTTATCT
65 TGACTAG-AGATTCCATCCCA-CTCAACCATCTTCAACCTCGACTCGATCCTAGTCACTTTATCT
** * * * * *
9412254 TTTTGACTCGTGGTTTCATCTTGGTCATTCGATCTTGGTTCTAGTCTAGATCATTTGT-TGACTT
128 TTTCAACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTA-TCTAGATCATTT-TCTGA-TT
* * * *
9412318 -GCGATTCTATCTCAATCA-ATCACCTTTGACCTCGACTTAGTCATGGTCAC
190 CGCGATTCCATCTCAATCAGCT-ACCTTTAACCTCGACTCAGTCATGGTCAC
9412368 TTTATCTTTTT
1 TTTATCTTTTT
9412379 GTAGTTTCAT
Statistics
Matches: 209, Mismatches: 35, Indels: 16
0.80 0.13 0.06
Matches are distributed among these distances:
240 7 0.03
241 186 0.89
242 15 0.07
243 1 0.00
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.43
Consensus pattern (240 bp):
TTTATCTTTTTAACTCATGATTTCATCCTGATCATTCAATCTCGACTCTGTCTAGATCATTTTTT
GACTAGAGATTCCATCCCACTCAACCATCTTCAACCTCGACTCGATCCTAGTCACTTTATCTTTT
CAACTCATGGTTTCATCCTGATCATTCAATCTTGGCTCTATCTAGATCATTTTCTGATTCGCGAT
TCCATCTCAATCAGCTACCTTTAACCTCGACTCAGTCATGGTCAC
Found at i:9412725 original size:3 final size:3
Alignment explanation
Indices: 9412704--9412858 Score: 153
Period size: 3 Copynumber: 53.3 Consensus size: 3
9412694 ATTTTTGTCA
* * * *
9412704 TAT TA- TAT TA- TAG TAT TAT TAT TAC TA- TAT TA- TAG TAT CAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
9412747 TAT TAT TAT TAT TAT TAG TAG TAG TA- TAT TA- TAT GGTGT TAC TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT --TAT TAT TAT
*
9412792 TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9412840 TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT T
9412859 TTTTTTTTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 18
0.81 0.07 0.11
Matches are distributed among these distances:
2 14 0.11
3 115 0.88
5 2 0.02
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:9413245 original size:20 final size:21
Alignment explanation
Indices: 9413203--9413245 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
9413193 TTTGATTTTG
* *
9413203 GGTTAGATTTAGGTTTTTGGA
1 GGTTAGATTAAGGTTTTTAGA
*
9413224 GGTTGGATTAAGG-TTTTAGA
1 GGTTAGATTAAGGTTTTTAGA
9413244 GG
1 GG
9413246 ATTCAGGGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (21 bp):
GGTTAGATTAAGGTTTTTAGA
Found at i:9413645 original size:5 final size:5
Alignment explanation
Indices: 9413635--9413733 Score: 64
Period size: 5 Copynumber: 19.6 Consensus size: 5
9413625 CTATTTTCAT
*
9413635 TTTTA TTTTA -TTT- TTTGA TTTTCA -TTTA TTTTCA TATTTAAA TTTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTT-A T-TTT--A -TTTTA
* * * *
9413683 TTTTA TTTTA TTTTA TCTTA TTGTA TTTTA CTAT- TTTTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
9413731 TTT
1 TTT
9413734 AGTAATTCAA
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
4 12 0.16
5 49 0.67
6 4 0.05
7 3 0.04
8 4 0.05
9 1 0.01
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:9413655 original size:19 final size:18
Alignment explanation
Indices: 9413628--9413666 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
9413618 AAGGCTTCTA
*
9413628 TTTTCATTTTTATTTTATT
1 TTTTCATTTTCA-TTTATT
*
9413647 TTTTGATTTTCATTTATT
1 TTTTCATTTTCATTTATT
9413665 TT
1 TT
9413667 CATATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTCATTTTCATTTATT
Found at i:9413673 original size:18 final size:18
Alignment explanation
Indices: 9413626--9413698 Score: 50
Period size: 18 Copynumber: 4.2 Consensus size: 18
9413616 GCAAGGCTTC
9413626 TATTTTCAT-TTTTATTT
1 TATTTTCATATTTTATTT
*
9413643 TATTTT-TTGATTTTCA-TT
1 TATTTTCAT-ATTTT-ATTT
*
9413661 TATTTTCATATTTAAATTT
1 TATTTTCATATTT-TATTT
9413680 T-TATTT--TATTTTATTT
1 TAT-TTTCATATTTTATTT
9413696 TAT
1 TAT
9413699 CTTATTGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
16 6 0.14
17 12 0.27
18 18 0.41
19 8 0.18
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.73
Consensus pattern (18 bp):
TATTTTCATATTTTATTT
Found at i:9413691 original size:35 final size:34
Alignment explanation
Indices: 9413626--9413733 Score: 82
Period size: 35 Copynumber: 3.1 Consensus size: 34
9413616 GCAAGGCTTC
* *
9413626 TATTTTCATTTTTATTTTATTTTTTGATTTTCATT
1 TATTTTCATTTTAATTTTATATTTTGATTTT-ATT
9413661 TATTTTCATATTTAAATTTT-TATTTT-ATTTTATTT
1 TATTTTCAT-TTT-AATTTTATATTTTGATTTTA-TT
* * *
9413696 TATCTT-ATTGT-ATTTTACTATTTTTA-TTTATTT
1 TATTTTCATTTTAATTTTA-TATTTTGATTTTA-TT
9413729 TATTT
1 TATTT
9413734 AGTAATTCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
31 5 0.08
33 19 0.31
34 4 0.06
35 21 0.34
36 8 0.13
37 5 0.08
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (34 bp):
TATTTTCATTTTAATTTTATATTTTGATTTTATT
Found at i:9414763 original size:3 final size:3
Alignment explanation
Indices: 9414757--9414804 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
9414747 TAATTTTTTT
* * * * *
9414757 TAA TAA TAG TAA TAA TAA TAA TAA TAA CAA CAA CAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9414805 AAGGAAAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:9426223 original size:153 final size:153
Alignment explanation
Indices: 9426019--9426320 Score: 365
Period size: 153 Copynumber: 2.0 Consensus size: 153
9426009 AAAAAAAAAA
** * * **
9426019 AAAGTTTCAAAGCCTCTTTTTAGGGGGAGCCATTTTCATACAAAATTTTTAAAGTTTCAAAGCCT
1 AAAGTTTCAAAGCCTCTAATTAGGGGAAGCCATTTTCAGACAAAATTTTTAAAGTCCCAAAGCCT
* *
9426084 CTGAATAGAGGATCTTTCATATATGTTAAGATTTGTAAGACAT-CTGAGCATAATCT-TTAAGAC
66 CTGAATAGAGGAGCTTTCATACATGTTAAGATTTGTAAGACATAC-GAGCATAATCTCTT-AGAC
*
9426147 CTCTAGGTAAAATATTTTAAAATTT
129 CTCTAGGCAAAATATTTTAAAATTT
* * ** * *
9426172 AAAGTTTCAAAGCCTCTAATTAGGGGAAGTCATTTTTAGATGAGATTTTTAAAGTCCCAAGGCCT
1 AAAGTTTCAAAGCCTCTAATTAGGGGAAGCCATTTTCAGACAAAATTTTTAAAGTCCCAAAGCCT
* * * * * *
9426237 TTGATTAGAGGAGCTTTCATACGTGTTGAGATTTGTAAGATATACGGGCATAATCTCTTAGACCT
66 CTGAATAGAGGAGCTTTCATACATGTTAAGATTTGTAAGACATACGAGCATAATCTCTTAGACCT
* *
9426302 TTGGGCAAAATATTTTAAA
131 CTAGGCAAAATATTTTAAA
9426321 TTTTTAGGCA
Statistics
Matches: 124, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
153 121 0.98
154 3 0.02
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (153 bp):
AAAGTTTCAAAGCCTCTAATTAGGGGAAGCCATTTTCAGACAAAATTTTTAAAGTCCCAAAGCCT
CTGAATAGAGGAGCTTTCATACATGTTAAGATTTGTAAGACATACGAGCATAATCTCTTAGACCT
CTAGGCAAAATATTTTAAAATTT
Found at i:9430764 original size:2 final size:2
Alignment explanation
Indices: 9430757--9430782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9430747 TTCATAATTC
9430757 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
9430783 TTGTTAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9433808 original size:27 final size:25
Alignment explanation
Indices: 9433777--9433847 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 25
9433767 CGATGAGATG
*
9433777 AAAAAAAAAGATAGCAAAAGGAAAAA
1 AAAAAAAAAGAAAGCAAAA-GAAAAA
* * *
9433803 AGAAAAAGAAGAAAGGC-TAATAAAAA
1 A-AAAAAAAAGAAA-GCAAAAGAAAAA
*
9433829 AAAAAAAAAGAGAGCAAAA
1 AAAAAAAAAGAAAGCAAAA
9433848 ACACACAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 7
0.71 0.14 0.14
Matches are distributed among these distances:
24 2 0.06
25 12 0.34
26 7 0.20
27 12 0.34
28 2 0.06
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (25 bp):
AAAAAAAAAGAAAGCAAAAGAAAAA
Found at i:9437938 original size:7 final size:7
Alignment explanation
Indices: 9437926--9437961 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
9437916 TTCAGATGGC
9437926 TTCTTTT
1 TTCTTTT
9437933 TTCTTTT
1 TTCTTTT
*
9437940 TTATTTT
1 TTCTTTT
9437947 TTCTTTT
1 TTCTTTT
9437954 TCTCTTTT
1 T-TCTTTT
9437962 CCCTTCCTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (7 bp):
TTCTTTT
Found at i:9437971 original size:13 final size:13
Alignment explanation
Indices: 9437955--9437979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9437945 TTTTCTTTTT
9437955 CTCTTTTCCCTTC
1 CTCTTTTCCCTTC
9437968 CTCTTTTCCCTT
1 CTCTTTTCCCTT
9437980 TAGTTTTCTG
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:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (13 bp):
CTCTTTTCCCTTC
Found at i:9439644 original size:35 final size:34
Alignment explanation
Indices: 9439552--9439646 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 34
9439542 AGTGATTGGG
** * * *
9439552 ATTGAACTACAAGTCAAAAATAAATATGACTAGG
1 ATTGAACTATGAGTCAAAAATAAAAATGACAAGA
* * * *
9439586 ATTAAACCATGAGTTGAAGAATAAAAATGACAAGA
1 ATTGAACTATGAG-TCAAAAATAAAAATGACAAGA
9439621 ATTGAACTATGAGTCAAAAAATAAAA
1 ATTGAACTATGAGTC-AAAAATAAAA
9439647 TATTATTGAT
Statistics
Matches: 46, Mismatches: 13, Indels: 3
0.74 0.21 0.05
Matches are distributed among these distances:
34 10 0.22
35 36 0.78
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (34 bp):
ATTGAACTATGAGTCAAAAATAAAAATGACAAGA
Found at i:9439747 original size:19 final size:19
Alignment explanation
Indices: 9439723--9439759 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
9439713 GAAAATGATT
9439723 GGGATTGAACCACGAGTTA
1 GGGATTGAACCACGAGTTA
*
9439742 GGGATTGAACCATGAGTT
1 GGGATTGAACCACGAGTT
9439760 GAAGAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.14, G:0.32, T:0.24
Consensus pattern (19 bp):
GGGATTGAACCACGAGTTA
Found at i:9439781 original size:35 final size:35
Alignment explanation
Indices: 9439742--9439826 Score: 134
Period size: 35 Copynumber: 2.4 Consensus size: 35
9439732 CCACGAGTTA
* *
9439742 GGGATTGAACCATGAGTTGAAGAATAAATATGATC
1 GGGATTGAACCATGAGTCGAAAAATAAATATGATC
*
9439777 GGGATTGAAACATGAGTCGAAAAATAAATATGATC
1 GGGATTGAACCATGAGTCGAAAAATAAATATGATC
*
9439812 AGGATTGAACCATGA
1 GGGATTGAACCATGA
9439827 ATCAAAGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.24
Consensus pattern (35 bp):
GGGATTGAACCATGAGTCGAAAAATAAATATGATC
Found at i:9439856 original size:18 final size:18
Alignment explanation
Indices: 9439833--9439892 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
9439823 ATGAATCAAA
9439833 GAATGAAAATATGACTAG
1 GAATGAAAATATGACTAG
* *
9439851 GAATGAACCATATG-TTAG
1 GAATGAA-AATATGACTAG
9439869 GAAATGAAAAT-T-ACTAG
1 G-AATGAAAATATGACTAG
*
9439886 GATTGAA
1 GAATGAA
9439893 CAAAGAGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 5 0.15
17 5 0.15
18 13 0.38
19 11 0.32
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.25
Consensus pattern (18 bp):
GAATGAAAATATGACTAG
Found at i:9439920 original size:35 final size:35
Alignment explanation
Indices: 9439881--9439995 Score: 85
Period size: 35 Copynumber: 3.3 Consensus size: 35
9439871 AATGAAAATT
9439881 ACTAGGATTGAACAAAGAGTCAAAGAATAAATAGA
1 ACTAGGATTGAACAAAGAGTCAAAGAATAAATAGA
* * * * *
9439916 ACTAGGACTAAACTACAAG-TTGAAA-AATAAA-AAA
1 ACTAGGATTGAAC-A-AAGAGTCAAAGAATAAATAGA
* ** *
9439950 GACCAGGATTGAATTATGAGTCAAAGAATAAATATG-
1 -ACTAGGATTGAACAAAGAGTCAAAGAATAAATA-GA
9439986 ACTAGGATTG
1 ACTAGGATTG
9439996 GACTGCAAGT
Statistics
Matches: 58, Mismatches: 15, Indels: 14
0.67 0.17 0.16
Matches are distributed among these distances:
33 2 0.03
34 6 0.10
35 41 0.71
36 6 0.10
37 3 0.05
ACGTcount: A:0.50, C:0.10, G:0.19, T:0.21
Consensus pattern (35 bp):
ACTAGGATTGAACAAAGAGTCAAAGAATAAATAGA
Found at i:9441162 original size:9 final size:9
Alignment explanation
Indices: 9441141--9441212 Score: 58
Period size: 9 Copynumber: 8.0 Consensus size: 9
9441131 AAATCGTCTC
9441141 CTTTTT-TT
1 CTTTTTCTT
*
9441149 GTTTTTCTT
1 CTTTTTCTT
9441158 CTTTTTTCTAT
1 C-TTTTTCT-T
*
9441169 CTTTTTTTT
1 CTTTTTCTT
9441178 CTTTTT-TT
1 CTTTTTCTT
***
9441186 CTTTTTAAG
1 CTTTTTCTT
*
9441195 CTTTTTTTT
1 CTTTTTCTT
9441204 CTTTTTCTT
1 CTTTTTCTT
9441213 TTATTTTTTT
Statistics
Matches: 51, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
8 13 0.25
9 23 0.45
10 13 0.25
11 2 0.04
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (9 bp):
CTTTTTCTT
Found at i:9441190 original size:26 final size:28
Alignment explanation
Indices: 9441142--9441212 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 28
9441132 AATCGTCTCC
* * *
9441142 TTTTTTTGTTTTTCTTCTTTTTTCTATCT
1 TTTTTTTCTTTTTCTTCTTTTTT-AAGCT
9441171 TTTTTTTCTTTTT-TTC-TTTTTAAGCT
1 TTTTTTTCTTTTTCTTCTTTTTTAAGCT
9441197 TTTTTTTCTTTTTCTT
1 TTTTTTTCTTTTTCTT
9441213 TTATTTTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 16 0.42
27 7 0.18
28 3 0.08
29 12 0.32
ACGTcount: A:0.04, C:0.13, G:0.03, T:0.80
Consensus pattern (28 bp):
TTTTTTTCTTTTTCTTCTTTTTTAAGCT
Found at i:9444694 original size:11 final size:11
Alignment explanation
Indices: 9444678--9444703 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9444668 ATGAATAACA
9444678 AGAAAAAATAG
1 AGAAAAAATAG
9444689 AGAAAAAATAG
1 AGAAAAAATAG
9444700 AGAA
1 AGAA
9444704 GATGGTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (11 bp):
AGAAAAAATAG
Found at i:9448258 original size:10 final size:10
Alignment explanation
Indices: 9448243--9448275 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
9448233 CTTTGGTGGA
9448243 TCTCCATTAC
1 TCTCCATTAC
9448253 TCTCCATTAC
1 TCTCCATTAC
9448263 TCTCCATTAC
1 TCTCCATTAC
9448273 TCT
1 TCT
9448276 TTCTCTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.18, C:0.39, G:0.00, T:0.42
Consensus pattern (10 bp):
TCTCCATTAC
Found at i:9448415 original size:36 final size:36
Alignment explanation
Indices: 9448361--9448431 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
9448351 AGAACAAACA
* * *
9448361 TTATATCTGTGTATGATTGATTGACTTGTCTTTGGG
1 TTATATCTATGTAGGATTGATTAACTTGTCTTTGGG
*
9448397 TTATATCTATGTGGGATTGATTAACTTGTCTTTGG
1 TTATATCTATGTAGGATTGATTAACTTGTCTTTGG
9448432 CTTCGCTATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.49
Consensus pattern (36 bp):
TTATATCTATGTAGGATTGATTAACTTGTCTTTGGG
Found at i:9451857 original size:15 final size:16
Alignment explanation
Indices: 9451839--9451888 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 16
9451829 AAATTCTAAG
9451839 CCCTAAAACCAT-AAA
1 CCCTAAAACCATGAAA
* *
9451854 CCCTTAAACCTTGAAA
1 CCCTAAAACCATGAAA
9451870 CCCT-AAA--ATGAAA
1 CCCTAAAACCATGAAA
9451883 CCCTAA
1 CCCTAA
9451889 CTCAAAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 9 0.30
14 1 0.03
15 13 0.43
16 7 0.23
ACGTcount: A:0.46, C:0.32, G:0.04, T:0.18
Consensus pattern (16 bp):
CCCTAAAACCATGAAA
Found at i:9454163 original size:3 final size:3
Alignment explanation
Indices: 9454155--9454218 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
9454145 GCAAAAGGAG
*
9454155 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* **
9454201 TAA CAA TGT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
9454219 CACAAATGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9455290 original size:3 final size:3
Alignment explanation
Indices: 9455284--9455330 Score: 71
Period size: 3 Copynumber: 16.3 Consensus size: 3
9455274 TAGATAATAA
*
9455284 TAT TAT TA- CAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9455330 T
1 T
9455331 TTTTAAAGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 3 0.08
3 37 0.93
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9460795 original size:11 final size:12
Alignment explanation
Indices: 9460778--9460819 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
9460768 GAGGGCATGT
9460778 AAAAAAAAGA-A
1 AAAAAAAAGATA
9460789 GAAAAAAAAGATA
1 -AAAAAAAAGATA
*
9460802 AAAAAAAGACATA
1 AAAAAAA-AGATA
9460815 AAAAA
1 AAAAA
9460820 TGGTTATGAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (12 bp):
AAAAAAAAGATA
Found at i:9460795 original size:12 final size:12
Alignment explanation
Indices: 9460778--9460810 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
9460768 GAGGGCATGT
9460778 AAAAAAAAGAAG
1 AAAAAAAAGAAG
*
9460790 AAAAAAAAG-AT
1 AAAAAAAAGAAG
9460801 AAAAAAAAGA
1 AAAAAAAAGA
9460811 CATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAG
Found at i:9460806 original size:13 final size:13
Alignment explanation
Indices: 9460778--9460819 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
9460768 GAGGGCATGT
*
9460778 AAAAAAAAGA-AG
1 AAAAAAAAGATAA
9460790 AAAAAAAAGATAA
1 AAAAAAAAGATAA
* *
9460803 AAAAAAGACATAA
1 AAAAAAAAGATAA
9460816 AAAA
1 AAAA
9460820 TGGTTATGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.83, C:0.02, G:0.10, T:0.05
Consensus pattern (13 bp):
AAAAAAAAGATAA
Found at i:9462295 original size:22 final size:22
Alignment explanation
Indices: 9462242--9462302 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
9462232 AACCAGCATA
* * *
9462242 TAAGCCCAGTTTAGTTGACATG
1 TAAGCCCAGATTAGCTGACACG
*
9462264 TAA-CCCAGATTAGCTGGCACG
1 TAAGCCCAGATTAGCTGACACG
9462285 TAAGCCCAGATTAGCTGA
1 TAAGCCCAGATTAGCTGA
9462303 AAAATATACA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (22 bp):
TAAGCCCAGATTAGCTGACACG
Found at i:9462503 original size:32 final size:33
Alignment explanation
Indices: 9462467--9462536 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
9462457 TACCTTAATT
* *
9462467 TTTAAGTCTAGTTT-ATATGGCA-ACAATGAAAA
1 TTTAAGCCTAATTTAAT-TGGCATACAATGAAAA
*
9462499 TTTAAGCCTAATTTAATTGGCATCCAATGAAAA
1 TTTAAGCCTAATTTAATTGGCATACAATGAAAA
9462532 TTTAA
1 TTTAA
9462537 ACCCAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (33 bp):
TTTAAGCCTAATTTAATTGGCATACAATGAAAA
Found at i:9462532 original size:33 final size:32
Alignment explanation
Indices: 9462484--9463119 Score: 314
Period size: 33 Copynumber: 19.6 Consensus size: 32
9462474 CTAGTTTATA
* **
9462484 TGGCAACAATGAAAATTTAAGCCTAATTTAAT
1 TGGCACCAATGAAAATTTAAGCCTAATTTAGC
* * * *
9462516 TGGCATCCAATGAAAATTTAAACCCAAATTAGT
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
*** * * * *
9462549 TGATGCCAATGAAATTTTAAG-GTTATATTATC
1 TGGCACCAATGAAAATTTAAGCCTAAT-TTAGC
* ** *
9462581 TAGCACCAATGAAGTTTTAAGCC-AGTTTAGC
1 TGGCACCAATGAAAATTTAAGCCTAATTTAGC
*
9462612 TAGCACTCAATGAAAATTTAAGTCC--ATATTAGC
1 TGGCAC-CAATGAAAATTTAAG-CCTAAT-TTAGC
** * ** *
9462645 TAACATCTAATGAAAATTTAAATCTAGTTTAGC
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
9462678 TGGCACCTATATG--AA-TTAAG-CTAAGTTTAGC
1 TGGCACC-A-ATGAAAATTTAAGCCTAA-TTTAGC
* * * *
9462709 TCGCACCCAATGAAAATTTAAACCTAATCTAGT
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
** * *
9462742 TAACACCCAATGAAAATTTAAGCCCAATTTATC
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
* * *
9462775 TGACACTAATGAAAATTTAAG-CTAAGATTAGC
1 TGGCACCAATGAAAATTTAAGCCTAA-TTTAGC
* * * *
9462807 AGGCACCCAATGCAAATTTAAG-CTAGTTTAGT
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
*
9462839 TGGCACCAATGCAAATTTAAGCCTAGA-TTAGC
1 TGGCACCAATGAAAATTTAAGCCTA-ATTTAGC
* * * **
9462871 TAGTACCTAATGAAAAATTTAAG-CTCAAATTATT
1 TGGCACC-AATG-AAAATTTAAGCCT-AATTTAGC
** * *
9462905 TGGCACCAATGAAGGTTTAAGCTTAGTTTAGC
1 TGGCACCAATGAAAATTTAAGCCTAATTTAGC
* *
9462937 TAGCACCCAATGAAATTTTAAGCCTAGA-TTAGC
1 TGGCA-CCAATGAAAATTTAAGCCTA-ATTTAGC
* * * *
9462970 TGGCACCCAATGCAAATCTAAGCCCAGTTTAGC
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
* ** * *
9463003 TAGCATAAATGCAAATTTAATCCTAGA-TTAGC
1 TGGCACCAATGAAAATTTAAGCCTA-ATTTAGC
* * * *
9463035 TGGCACCTGATAAAAATTTAA--ATACATTTAAC
1 TGGCACC-AATGAAAATTTAAGCCTA-ATTTAGC
* * *
9463067 TAGCACCCAATGAAATTTTATGCCTAATTTAGC
1 TGGCA-CCAATGAAAATTTAAGCCTAATTTAGC
* *
9463100 TGACACCAATAAAAATTTAA
1 TGGCACCAATGAAAATTTAA
9463120 ACCCAGTTTA
Statistics
Matches: 452, Mismatches: 117, Indels: 70
0.71 0.18 0.11
Matches are distributed among these distances:
30 6 0.01
31 48 0.11
32 172 0.38
33 197 0.44
34 29 0.06
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (32 bp):
TGGCACCAATGAAAATTTAAGCCTAATTTAGC
Found at i:9462719 original size:129 final size:126
Alignment explanation
Indices: 9462583--9463022 Score: 352
Period size: 130 Copynumber: 3.4 Consensus size: 126
9462573 ATATTATCTA
* *
9462583 GCACCAATGAAGTTTTAAGCC-AGTTTAGCTAGCACTCAATGAAAATTTAAGTCC-ATATTAGCT
1 GCACCAATGAA-ATTTAAGCCTAGTTTAGCTAGCAC-CAATGAAAATTTAAGCCCAAT-TTAGCT
* * * *
9462646 AACATCTAATGAAAATTTAAATCT-AGTTTAGCTGGCACCTATATG-AA-TTAAGCTAAGTTTAG
63 AACA-CTAATGAAAATTT-AAGCTAAGATTAGCAGGCACCCA-ATGAAATTTAAGCT-AGTTTAG
9462708 CTC
124 CTC
* * * * * *
9462711 GCACCCAATGAAAATTTAAACCTAATCTAGTTAACACCCAATGAAAATTTAAGCCCAATTTATCT
1 GCA-CCAATG-AAATTTAAGCCTAGTTTAGCTAGCA-CCAATGAAAATTTAAGCCCAATTTAGCT
* * *
9462776 GACACTAATGAAAATTTAAGCTAAGATTAGCAGGCACCCAATGCAAATTTAAGCTAGTTTAGTTG
63 AACACTAATGAAAATTTAAGCTAAGATTAGCAGGCACCCAATG-AAATTTAAGCTAGTTTAGCTC
* * * * **
9462841 GCACCAATGCAAATTTAAGCCTAGATTAGCTAGTACCTAATGAAAAATTTAAGCTCAAATTATTT
1 GCACCAATG-AAATTTAAGCCTAGTTTAGCTAGCACC-AATG-AAAATTTAAGCCCAATTTAGCT
** * ** * * *
9462906 GGCACCAATGAAGGTTTAAGCTTAGTTTAGCTA-GCACCCAATGAAATTTTAAGCCTAGATTAGC
63 AACACTAATGAAAATTTAAGCTAAGATTAGC-AGGCACCCAATGAAA-TTTAAG-CTAGTTTAGC
*
9462970 TG
125 TC
* * ** *
9462972 GCACCCAATGCAAATCTAAGCCCAGTTTAGCTAGCATAAATGCAAATTTAA
1 GCA-CCAATG-AAATTTAAGCCTAGTTTAGCTAGCACCAATGAAAATTTAA
9463023 TCCTAGATTA
Statistics
Matches: 256, Mismatches: 41, Indels: 28
0.79 0.13 0.09
Matches are distributed among these distances:
128 12 0.05
129 71 0.28
130 117 0.46
131 28 0.11
132 28 0.11
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.29
Consensus pattern (126 bp):
GCACCAATGAAATTTAAGCCTAGTTTAGCTAGCACCAATGAAAATTTAAGCCCAATTTAGCTAAC
ACTAATGAAAATTTAAGCTAAGATTAGCAGGCACCCAATGAAATTTAAGCTAGTTTAGCTC
Found at i:9462814 original size:65 final size:63
Alignment explanation
Indices: 9462490--9463119 Score: 246
Period size: 65 Copynumber: 9.7 Consensus size: 63
9462480 TATATGGCAA
* * * * *
9462490 CAATGAAAATTTAAGCCTAATTTAATTGGCATCCAATGAAAATTTAAACCCAAATTAG-TTG-AT
1 CAATGAAAATTTAAGCCCAATTT-ATTGGCA-CCAATGAAAATTT-AAGCTAGATTAGCTAGCA-
*
9462553 GC
62 CC
* *** * ** * * *
9462555 CAATGAAATTTTAAG-GTTATATTATCTAGCACCAATGAAGTTTTAAGCCAGTTTAGCTAGCACT
1 CAATGAAAATTTAAGCCCAAT-TTAT-TGGCACCAATGAAAATTTAAGCTAGATTAGCTAGCACC
* * ** * * * *
9462619 CAATGAAAATTTAAGTCC-ATATTAGCTAACATCTAATGAAAATTTAAATCTAGTTTAGCTGGCA
1 CAATGAAAATTTAAGCCCAAT-TTA-TTGGCA-CCAATGAAAATTT-AAGCTAGATTAGCTAGCA
9462683 CC
62 CC
* * * * * * *
9462685 TATATG--AA-TTAAG-CTAAGTTTAGCTCGCACCCAATGAAAATTTAAACCTA-ATCTAGTTAA
1 CA-ATGAAAATTTAAGCCCAA-TTTA-TTGGCA-CCAATGAAAATTT-AAGCTAGAT-TAGCTAG
9462745 CACC
60 CACC
* *
9462749 CAATGAAAATTTAAGCCCAATTTATCTGACACTAATGAAAATTTAAGCTAAGATTAGC-AGGCAC
1 CAATGAAAATTTAAGCCCAATTTAT-TGGCACCAATGAAAATTTAAGCT-AGATTAGCTA-GCAC
9462813 C
63 C
* * * * *
9462814 CAATGCAAATTTAAG-CTAGTTTAGTTGGCACCAATGCAAATTTAAGCCTAGATTAGCTAGTACC
1 CAATGAAAATTTAAGCCCAATTTA-TTGGCACCAATGAAAATTTAAG-CTAGATTAGCTAGCACC
* * * ** *
9462878 TAATGAAAAATTTAAGCTCAAATTATTTGGCACCAATGAAGGTTTAAGCTTAGTTTAGCTAGCAC
1 CAATG-AAAATTTAAGCCCAATTTA-TTGGCACCAATGAAAATTTAAGC-TAGATTAGCTAGCAC
9462943 C
63 C
* * * * * * *
9462944 CAATGAAATTTTAAGCCTAGA-TTAGCTGGCACCCAATGCAAATCTAAGCCCAGTTTAGCTAGCA
1 CAATGAAAATTTAAGCCCA-ATTTA-TTGGCA-CCAATGAAAATTTAAG-CTAGATTAGCTAGCA
*
9463008 -T
62 CC
* * * * * * * * * *
9463009 AAATGCAAATTTAATCCTAGA-TTAGCTGGCACCTGATAAAAATTTAA-ATACATTTAACTAGCA
1 CAATGAAAATTTAAGCCCA-ATTTA-TTGGCACC-AATGAAAATTTAAGCTAGA-TTAGCTAGCA
9463072 CC
62 CC
* * * * * *
9463074 CAATGAAATTTTATGCCTAATTTAGCTGACACCAATAAAAATTTAA
1 CAATGAAAATTTAAGCCCAATTTA-TTGGCACCAATGAAAATTTAA
9463120 ACCCAGTTTA
Statistics
Matches: 436, Mismatches: 96, Indels: 67
0.73 0.16 0.11
Matches are distributed among these distances:
63 15 0.03
64 152 0.35
65 164 0.38
66 98 0.22
67 7 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (63 bp):
CAATGAAAATTTAAGCCCAATTTATTGGCACCAATGAAAATTTAAGCTAGATTAGCTAGCACC
Found at i:9462925 original size:66 final size:64
Alignment explanation
Indices: 9462490--9463007 Score: 258
Period size: 64 Copynumber: 8.0 Consensus size: 64
9462480 TATATGGCAA
* * * * *
9462490 CAATGAAAATTTAAGC-CTAATTTAATTGGCATCCAATGAAAATTTAAACCCAAATTAG-TTG-A
1 CAATGAAAATTTAAGCTC-AATTTATTTGGCA-CCAATG-AAATTTAAGCCTAGATTAGCTAGCA
*
9462552 TGC
63 -CC
* * * * * * *
9462555 CAATGAAATTTTAAGGT-TATATTATCTAGCACCAATGAAGTTTTAAGCC-AGTTTAGCTAGCAC
1 CAATGAAAATTTAAGCTCAAT-TTATTTGGCACCAATGAA-ATTTAAGCCTAGATTAGCTAGCAC
*
9462618 T
64 C
* ** ** * ** * *
9462619 CAATGAAAATTTAAG-TCCATATTAGCTAACATCTAATGAAAATTTAAATCTAGTTTAGCTGGCA
1 CAATGAAAATTTAAGCTCAAT-TTATTTGGCA-CCAATG-AAATTTAAGCCTAGATTAGCTAGCA
9462683 CC
63 CC
* ** * * * *
9462685 TATATG--AA-TTAAGCT-AAGTTTAGCTCGCACCCAATGAAAATTTAAACCTA-ATCTAGTTAA
1 CA-ATGAAAATTTAAGCTCAA-TTTATTTGGCA-CCAATG-AAATTTAAGCCTAGAT-TAGCTAG
9462745 CACC
61 CACC
* * * *
9462749 CAATGAAAATTTAAGCCCAATTTATCTGACACTAATGAAAATTTAAG-CTAAGATTAGC-AGGCA
1 CAATGAAAATTTAAGCTCAATTTATTTGGCACCAATG-AAATTTAAGCCT-AGATTAGCTA-GCA
9462812 CC
63 CC
* * * *
9462814 CAATGCAAATTTAAGCT-AGTTTAGTTGGCACCAATGCAAATTTAAGCCTAGATTAGCTAGTACC
1 CAATGAAAATTTAAGCTCAATTTATTTGGCACCAATG-AAATTTAAGCCTAGATTAGCTAGCACC
* * * * *
9462878 TAATGAAAAATTTAAGCTCAAATTATTTGGCACCAATGAAGGTTTAAGCTTAGTTTAGCTAGCAC
1 CAATG-AAAATTTAAGCTCAATTTATTTGGCACCAATGAA-ATTTAAGCCTAGATTAGCTAGCAC
9462943 C
64 C
* ** * * *
9462944 CAATGAAATTTTAAGC-CTAGA-TTAGCTGGCACCCAATGCAAATCTAAGCCCAGTTTAGCTAGC
1 CAATGAAAATTTAAGCTC-A-ATTTATTTGGCA-CCAATG-AAATTTAAGCCTAGATTAGCTAGC
9463007 A
62 A
9463008 TAAATGCAAA
Statistics
Matches: 355, Mismatches: 69, Indels: 57
0.74 0.14 0.12
Matches are distributed among these distances:
63 12 0.03
64 126 0.35
65 111 0.31
66 99 0.28
67 7 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (64 bp):
CAATGAAAATTTAAGCTCAATTTATTTGGCACCAATGAAATTTAAGCCTAGATTAGCTAGCACC
Found at i:9463039 original size:130 final size:131
Alignment explanation
Indices: 9462554--9463137 Score: 345
Period size: 130 Copynumber: 4.5 Consensus size: 131
9462544 TTAGTTGATG
** * * * *
9462554 CCAATGAAATTTTAAGGTTATATTATCTAGCACCAATG-AAGTTTTAAG-CCAGTTTAGCTAG-C
1 CCAATGAAATTTTAAGCCTAGATTAGCTGGCACCAATGCAA-ATTTAAGCCCAGTTTAGCTAGAC
* * ** * * *
9462616 ACTCAATG-AAAATTTAA-GTCCATATTAGCTAACATCTAATGAAAATTTAA-ATCTAGTTTAGC
65 A-T-AATGAAAAATTTAACCT-CAAATTAGCTGGCACCTAATAAAAATTTAAGCT-TAGTTTAGC
*
9462678 TGGCAC
126 TAGCAC
* * * * * * * * *
9462684 CTATATG-AA--TTAAG-CTAAGTTTAGCTCGCACCCAATGAAAATTTAAACCTAATCTAGTTA-
1 CCA-ATGAAATTTTAAGCCT-AGATTAGCTGGCA-CCAATGCAAATTTAAGCCCAGTTTAGCTAG
* * * * * * *
9462744 ACACCCAATG-AAAATTTAAGCC-CAATTTATCTGACA-CTAATGAAAATTTAAGCTAAGATTAG
63 ACA--TAATGAAAAATTTAA-CCTCAAATTAGCTGGCACCTAATAAAAATTTAAGCTTAGTTTAG
9462806 C-AGGCAC
125 CTA-GCAC
* * * *
9462813 CCAATGCAAA-TTTAAG-CTAGTTTAGTTGGCACCAATGCAAATTTAAGCCTAGATTAGCTAGTA
1 CCAATG-AAATTTTAAGCCTAGATTAGCTGGCACCAATGCAAATTTAAGCCCAGTTTAGCTAG-A
* * ** * **
9462876 CCTAATGAAAAATTTAAGCTCAAATTATTTGGCACC-AATGAAGGTTTAAGCTTAGTTTAGCTAG
64 CATAATGAAAAATTTAACCTCAAATTAGCTGGCACCTAATAAAAATTTAAGCTTAGTTTAGCTAG
9462940 CAC
129 CAC
*
9462943 CCAATGAAATTTTAAGCCTAGATTAGCTGGCACCCAATGCAAATCTAAGCCCAGTTTAGCTAG-C
1 CCAATGAAATTTTAAGCCTAGATTAGCTGGCA-CCAATGCAAATTTAAGCCCAGTTTAGCTAGAC
* * * * * *
9463007 ATAAATG-CAAATTTAATCCT-AGATTAGCTGGCACCTGATAAAAATTTAA--ATACATTTAACT
65 AT-AATGAAAAATTTAA-CCTCAAATTAGCTGGCACCTAATAAAAATTTAAGCTTA-GTTTAGCT
9463068 AGCAC
127 AGCAC
* * ** *
9463073 CCAATGAAATTTTATGCCTA-ATTTAGCTGACACCAATAAAAATTTAAACCCAGTTTAGCTA-AC
1 CCAATGAAATTTTAAGCCTAGA-TTAGCTGGCACCAATGCAAATTTAAGCCCAGTTTAGCTAGAC
9463136 AT
65 AT
9463138 CTACAAAAAT
Statistics
Matches: 360, Mismatches: 65, Indels: 59
0.74 0.13 0.12
Matches are distributed among these distances:
127 1 0.00
128 17 0.05
129 101 0.28
130 171 0.47
131 43 0.12
132 27 0.08
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (131 bp):
CCAATGAAATTTTAAGCCTAGATTAGCTGGCACCAATGCAAATTTAAGCCCAGTTTAGCTAGACA
TAATGAAAAATTTAACCTCAAATTAGCTGGCACCTAATAAAAATTTAAGCTTAGTTTAGCTAGCA
C
Found at i:9463130 original size:32 final size:31
Alignment explanation
Indices: 9463094--9463169 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
9463084 TTATGCCTAA
*
9463094 TTTAGCTGACACCAATAAAAATTTAAACCCAG
1 TTTAGCTGACACCAACAAAAA-TTAAACCCAG
* * * * *
9463126 TTTAGCTAACATCTACAAAAATTAAGCTCAG
1 TTTAGCTGACACCAACAAAAATTAAACCCAG
*
9463157 TTTAGCTGGCACC
1 TTTAGCTGACACC
9463170 CAAATTTTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 18 0.51
32 17 0.49
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (31 bp):
TTTAGCTGACACCAACAAAAATTAAACCCAG
Found at i:9463556 original size:7 final size:7
Alignment explanation
Indices: 9463522--9463564 Score: 52
Period size: 7 Copynumber: 5.9 Consensus size: 7
9463512 GGAAAAAAGT
9463522 AAAAATA
1 AAAAATA
9463529 ATAAAATA
1 A-AAAATA
9463537 ATAAACA-A
1 A-AAA-ATA
9463545 AAAAATA
1 AAAAATA
9463552 AAAAATA
1 AAAAATA
9463559 AAAAAT
1 AAAAAT
9463565 TTTCCTTCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 1 0.03
7 18 0.55
8 13 0.39
9 1 0.03
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (7 bp):
AAAAATA
Found at i:9464649 original size:3 final size:3
Alignment explanation
Indices: 9464641--9464670 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
9464631 AGGCGTGAAA
9464641 AAG AAG AAG AAG AAG AAG AAG AAG AA- AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
9464671 GCCATTAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:9465712 original size:3 final size:3
Alignment explanation
Indices: 9465704--9465733 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
9465694 AAATTAAATT
9465704 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9465734 AGAAGAGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:9466289 original size:25 final size:26
Alignment explanation
Indices: 9466245--9466294 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
9466235 AAGATTTATC
9466245 ATAATATTCCTTCTAAAAATAATAAA
1 ATAATATTCCTTCTAAAAATAATAAA
* *
9466271 ATAATATT-CTTCTATAAATGATAA
1 ATAATATTCCTTCTAAAAATAATAA
9466295 TTATTGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.50, C:0.10, G:0.02, T:0.38
Consensus pattern (26 bp):
ATAATATTCCTTCTAAAAATAATAAA
Found at i:9468843 original size:13 final size:13
Alignment explanation
Indices: 9468817--9468869 Score: 70
Period size: 13 Copynumber: 4.1 Consensus size: 13
9468807 CTATGATTTC
**
9468817 AAATGAAATTCTA
1 AAATGAAACCCTA
9468830 AAATGAAACCCTA
1 AAATGAAACCCTA
* *
9468843 AAGTAAAACCCTA
1 AAATGAAACCCTA
9468856 AAATGAAACCCTA
1 AAATGAAACCCTA
9468869 A
1 A
9468870 GTCCTATGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.55, C:0.19, G:0.08, T:0.19
Consensus pattern (13 bp):
AAATGAAACCCTA
Found at i:9485300 original size:23 final size:22
Alignment explanation
Indices: 9485281--9485338 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
9485271 AAATTTTCAA
9485281 CCTTCATTGCTGACTTTTTTAGG
1 CCTTCATTGCTGAC-TTTTTAGG
*
9485304 CCTTCATTGCCGACTTTTTAGG
1 CCTTCATTGCTGACTTTTTAGG
9485326 CCTTCATTGCTGA
1 CCTTCATTGCTGA
9485339 ACCCTTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
22 20 0.61
23 13 0.39
ACGTcount: A:0.14, C:0.26, G:0.17, T:0.43
Consensus pattern (22 bp):
CCTTCATTGCTGACTTTTTAGG
Found at i:9487407 original size:23 final size:23
Alignment explanation
Indices: 9487377--9487421 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
9487367 ACTATTTCTG
9487377 TATCCAGTGAGAAATGGAGGCAT
1 TATCCAGTGAGAAATGGAGGCAT
9487400 TATCCAGTGAGAAATGGAGGCA
1 TATCCAGTGAGAAATGGAGGCA
9487422 AGCCATGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (23 bp):
TATCCAGTGAGAAATGGAGGCAT
Found at i:9489003 original size:22 final size:22
Alignment explanation
Indices: 9488977--9489020 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9488967 TGTATATTTA
*
9488977 TATTTGTATCTCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
9488999 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
9489021 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:9491182 original size:11 final size:11
Alignment explanation
Indices: 9491166--9491198 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
9491156 ATAGATAAAT
9491166 CCGCACTCAAA
1 CCGCACTCAAA
9491177 CCGCACTCAAA
1 CCGCACTCAAA
*
9491188 CCACACTCAAA
1 CCGCACTCAAA
9491199 ATCTAGACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.39, C:0.45, G:0.06, T:0.09
Consensus pattern (11 bp):
CCGCACTCAAA
Found at i:9501070 original size:11 final size:12
Alignment explanation
Indices: 9501032--9501082 Score: 50
Period size: 13 Copynumber: 4.2 Consensus size: 12
9501022 TGATAATTTT
*
9501032 AAATATTATAAA
1 AAATATAATAAA
* *
9501044 ATAATAAAATATA
1 A-AATATAATAAA
9501057 AAA-ATAATAAA
1 AAATATAATAAA
9501068 AAATATATATAAA
1 AAATATA-ATAAA
9501081 AA
1 AA
9501083 TTCTGAATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 9 0.29
12 6 0.19
13 16 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATATAATAAA
Found at i:9501079 original size:16 final size:16
Alignment explanation
Indices: 9501041--9501072 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9501031 TAAATATTAT
*
9501041 AAAATAATAAAATATA
1 AAAATAATAAAAAATA
9501057 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
9501073 TATATAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAATAATAAAAAATA
Found at i:9501177 original size:78 final size:76
Alignment explanation
Indices: 9501095--9501338 Score: 180
Period size: 78 Copynumber: 3.2 Consensus size: 76
9501085 CTGAATTTTA
*
9501095 TTTAATTAAATTATACATGATGTAATATTTTAAAAATTAATATTTAAATTTTAATATTTACAATC
1 TTTAATTAAATTATAC-T-ATCTAATATTTTAAAAATTAATATTTAAATTTTAATATTTACAATC
9501160 TTCTTTCATATTT
64 TTCTTTCATATTT
* * * ** * * ***
9501173 TTTAATTAGATTATGACTTTTTAA-A-AATAATACATGTAA-ATCATAAAAAATACATA--TA-A
1 TTTAATTAAATTAT-ACTATCTAATATTTTAA-AAAT-TAATAT-TTAAATTTTA-ATATTTACA
** **
9501232 AAATTC-TGAAT-TTT
61 ATCTTCTTTCATATTT
*
9501246 ATTTAATTAAATTATATGTAATCTAATATTTTAAAAATTAATATTTAAATTTTAATATTTACAAT
1 -TTTAATTAAATTATA-CT-ATCTAATATTTTAAAAATTAATATTTAAATTTTAATATTTACAAT
*
9501311 CTACTTTCATATTT
63 CTTCTTTCATATTT
*
9501325 TTTAATTAGATTAT
1 TTTAATTAAATTAT
9501339 GACTTTTTAA
Statistics
Matches: 119, Mismatches: 31, Indels: 32
0.65 0.17 0.18
Matches are distributed among these distances:
73 4 0.03
74 20 0.17
75 21 0.18
76 16 0.13
77 20 0.17
78 33 0.28
79 5 0.04
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (76 bp):
TTTAATTAAATTATACTATCTAATATTTTAAAAATTAATATTTAAATTTTAATATTTACAATCTT
CTTTCATATTT
Found at i:9501322 original size:152 final size:152
Alignment explanation
Indices: 9501058--9501371 Score: 538
Period size: 152 Copynumber: 2.1 Consensus size: 152
9501048 TAAAATATAA
* * * *
9501058 AAATAATAAAAAATATATATAAAAATTCTGAATTTTATTTAATTAAATTATACATGATGTAATAT
1 AAATCATAAAAAATACATATAAAAATTCTGAATTTTATTTAATTAAATTATACATAATCTAATAT
*
9501123 TTTAAAAATTAATATTTAAATTTTAATATTTACAATCTTCTTTCATATTTTTTAATTAGATTATG
66 TTTAAAAATTAATATTTAAATTTTAATATTTACAATCTACTTTCATATTTTTTAATTAGATTATG
* *
9501188 ACTTTTTAAAAATAATACATGT
131 ACTTTTTAAAAACAATACATGC
**
9501210 AAATCATAAAAAATACATATAAAAATTCTGAATTTTATTTAATTAAATTATATGTAATCTAATAT
1 AAATCATAAAAAATACATATAAAAATTCTGAATTTTATTTAATTAAATTATACATAATCTAATAT
9501275 TTTAAAAATTAATATTTAAATTTTAATATTTACAATCTACTTTCATATTTTTTAATTAGATTATG
66 TTTAAAAATTAATATTTAAATTTTAATATTTACAATCTACTTTCATATTTTTTAATTAGATTATG
9501340 ACTTTTTAAAAACAATACATGC
131 ACTTTTTAAAAACAATACATGC
*
9501362 GAATCATAAA
1 AAATCATAAA
9501372 TGCATAAAAT
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
152 152 1.00
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (152 bp):
AAATCATAAAAAATACATATAAAAATTCTGAATTTTATTTAATTAAATTATACATAATCTAATAT
TTTAAAAATTAATATTTAAATTTTAATATTTACAATCTACTTTCATATTTTTTAATTAGATTATG
ACTTTTTAAAAACAATACATGC
Found at i:9502371 original size:20 final size:21
Alignment explanation
Indices: 9502337--9502390 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
9502327 CATAATGACA
* *
9502337 TTATTATT-TATGTATATAT-
1 TTATTATTACATGTATACATC
9502356 TTATTATTACATGTATACATC
1 TTATTATTACATGTATACATC
9502377 TTA-TATTGACATGT
1 TTATTATT-ACATGT
9502391 CATGTTATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 8 0.27
20 13 0.43
21 9 0.30
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.54
Consensus pattern (21 bp):
TTATTATTACATGTATACATC
Found at i:9508107 original size:9 final size:9
Alignment explanation
Indices: 9508093--9508144 Score: 56
Period size: 8 Copynumber: 5.9 Consensus size: 9
9508083 AAAATATAGG
9508093 TATAAAAAA
1 TATAAAAAA
9508102 TAT-AAAAA
1 TATAAAAAA
*
9508110 TAT-AATAA
1 TATAAAAAA
9508118 TAATAAAAAA
1 T-ATAAAAAA
9508128 TATAATAAAA
1 TATAA-AAAA
9508138 -ATAAAAA
1 TATAAAAA
9508145 TAATGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
8 16 0.42
9 13 0.34
10 9 0.24
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
TATAAAAAA
Found at i:9508128 original size:18 final size:18
Alignment explanation
Indices: 9508073--9508144 Score: 81
Period size: 18 Copynumber: 3.7 Consensus size: 18
9508063 TGAACAAGTT
*
9508073 ATAAAATTAAAAAATATA
1 ATAAAAATAAAAAATATA
9508091 GGTATAAAAAATATAAAAATATA
1 ---AT-AAAAATA-AAAAATATA
*
9508114 ATAATAATAAAAAATATA
1 ATAAAAATAAAAAATATA
9508132 ATAAAAATAAAAA
1 ATAAAAATAAAAA
9508145 TAATGAAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
18 21 0.46
19 6 0.13
20 2 0.04
21 2 0.04
22 6 0.13
23 9 0.20
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
ATAAAAATAAAAAATATA
Found at i:9508141 original size:27 final size:26
Alignment explanation
Indices: 9508094--9508153 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
9508084 AAATATAGGT
* *
9508094 ATAAAAAATATAAAAATATAATAATA
1 ATAAAAAATATAAAAAAATAAAAATA
9508120 ATAAAAAATATAATAAAAATAAAAATA
1 ATAAAAAATATAA-AAAAATAAAAATA
*
9508147 ATGAAAA
1 ATAAAAA
9508154 TTTCCAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 13 0.43
27 17 0.57
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (26 bp):
ATAAAAAATATAAAAAAATAAAAATA
Found at i:9508153 original size:15 final size:16
Alignment explanation
Indices: 9508093--9508154 Score: 56
Period size: 18 Copynumber: 3.8 Consensus size: 16
9508083 AAAATATAGG
9508093 TATAA-AAAATATAAAAA
1 TATAATAAAA-AT-AAAA
*
9508110 TATAATAATAATAAAAAA
1 TATAATAA-AA-ATAAAA
9508128 TATAATAAAAATAAAA
1 TATAATAAAAATAAAA
*
9508144 -ATAATGAAAAT
1 TATAATAAAAAT
9508155 TTCCAAATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 10 0.25
16 5 0.12
17 7 0.17
18 14 0.35
19 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.26
Consensus pattern (16 bp):
TATAATAAAAATAAAA
Found at i:9508403 original size:20 final size:21
Alignment explanation
Indices: 9508375--9508427 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
9508365 GAAGAAAATA
* *
9508375 ATGAATCTTGGTAAATC-TAG
1 ATGATTCTTGATAAATCTTAG
*
9508395 ATGATTCTTGATCAATCTTAG
1 ATGATTCTTGATAAATCTTAG
*
9508416 ACGATTCTTGAT
1 ATGATTCTTGAT
9508428 GCATAATATG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (21 bp):
ATGATTCTTGATAAATCTTAG
Found at i:9508421 original size:21 final size:20
Alignment explanation
Indices: 9508388--9508427 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
9508378 AATCTTGGTA
*
9508388 AATCTAGATGATTCTTGATC
1 AATCTAGACGATTCTTGATC
9508408 AATCTTAGACGATTCTTGAT
1 AATC-TAGACGATTCTTGAT
9508428 GCATAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (20 bp):
AATCTAGACGATTCTTGATC
Found at i:9513316 original size:7 final size:7
Alignment explanation
Indices: 9513296--9513336 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
9513286 GAAAATTGAG
9513296 AGAAAAA
1 AGAAAAA
9513303 ATGAAAAA
1 A-GAAAAA
9513311 A-AAAAA
1 AGAAAAA
9513317 GAGAAAAA
1 -AGAAAAA
9513325 AGAAAAA
1 AGAAAAA
9513332 AGAAA
1 AGAAA
9513337 TTGAAGAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 5 0.16
7 14 0.45
8 12 0.39
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AGAAAAA
Found at i:9514263 original size:18 final size:18
Alignment explanation
Indices: 9514232--9514271 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9514222 TCACATGCAT
* *
9514232 AATTCCCATGAAATTCCA
1 AATTCCCATAAAATCCCA
*
9514250 AATTCTCATAAAATCCCA
1 AATTCCCATAAAATCCCA
9514268 AATT
1 AATT
9514272 TGAAACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (18 bp):
AATTCCCATAAAATCCCA
Found at i:9515438 original size:16 final size:18
Alignment explanation
Indices: 9515401--9515439 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
9515391 ATTTCATGCA
*
9515401 TATTTTAATTATGTTAGT
1 TATTTTAAATATGTTAGT
9515419 TATTTTAAAT-TGTT-GT
1 TATTTTAAATATGTTAGT
9515435 TATTT
1 TATTT
9515440 ATCCTACTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (18 bp):
TATTTTAAATATGTTAGT
Found at i:9516082 original size:17 final size:16
Alignment explanation
Indices: 9516055--9516086 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
9516045 AGAAAAATTA
9516055 AACAAAAAAACAAAAC
1 AACAAAAAAACAAAAC
9516071 AACAACAAAAACAAAA
1 AACAA-AAAAACAAAA
9516087 TTTGTCAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (16 bp):
AACAAAAAAACAAAAC
Found at i:9516385 original size:37 final size:37
Alignment explanation
Indices: 9516330--9516529 Score: 112
Period size: 37 Copynumber: 5.5 Consensus size: 37
9516320 AATTAATGAG
*
9516330 ATAGCACATGCATTCCATTTCATCTACATTCTAATAA
1 ATAGTACATGCATTCCATTTCATCTACATTCTAATAA
* * *
9516367 ATAGTACATGCATTCCATTT--TATGCA---T-ATAG
1 ATAGTACATGCATTCCATTTCATCTACATTCTAATAA
* * * *
9516398 GTAGAACATGCATTCCATTTTATCCACA-TCTTAATAA
1 ATAGTACATGCATTCCATTTCATCTACATTC-TAATAA
** * * *
9516435 GATAAGTGTATGCATTCCATCTCATGTACATTTTAATAA
1 -AT-AGTACATGCATTCCATTTCATCTACATTCTAATAA
* * * * *
9516474 AGCAATACATGCATTCCATCTCA--TGCATATCGTAATAG
1 A-TAGTACATGCATTCCATTTCATCTACAT-TC-TAATAA
*
9516512 ATAATACATGCATTCCAT
1 ATAGTACATGCATTCCAT
9516530 CTCAGGCATA
Statistics
Matches: 124, Mismatches: 27, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
31 21 0.17
32 1 0.01
33 3 0.02
35 4 0.03
36 5 0.04
37 39 0.31
38 25 0.20
39 25 0.20
40 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.35
Consensus pattern (37 bp):
ATAGTACATGCATTCCATTTCATCTACATTCTAATAA
Found at i:9516471 original size:39 final size:38
Alignment explanation
Indices: 9516403--9516542 Score: 140
Period size: 37 Copynumber: 3.7 Consensus size: 38
9516393 TATAGGTAGA
* * *
9516403 ACATGCATTCCATTTTATCCACATCTTAATAAGATAAGT
1 ACATGCATTCCATCTCATGCACATCTTAATAAGATAA-T
** * * *
9516442 GTATGCATTCCATCTCATGTACATTTTAATAA-AGCAAT
1 ACATGCATTCCATCTCATGCACATCTTAATAAGA-TAAT
* *
9516480 ACATGCATTCCATCTCATGCATATCGTAAT-AGATAAT
1 ACATGCATTCCATCTCATGCACATCTTAATAAGATAAT
* *
9516517 ACATGCATTCCATCTCAGGCATATCT
1 ACATGCATTCCATCTCATGCACATCT
9516543 CAAATAATAG
Statistics
Matches: 82, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
37 28 0.34
38 27 0.33
39 27 0.33
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (38 bp):
ACATGCATTCCATCTCATGCACATCTTAATAAGATAAT
Found at i:9516530 original size:37 final size:37
Alignment explanation
Indices: 9516403--9516542 Score: 136
Period size: 38 Copynumber: 3.7 Consensus size: 37
9516393 TATAGGTAGA
* * *
9516403 ACATGCATTCCATTTTATCCACATCTTAATAAGATAAGT
1 ACATGCATTCCATCTCATGCACATCTTAAT-AGATAA-T
** * * * *
9516442 GTATGCATTCCATCTCATGTACATTTTAATAAAGCAAT
1 ACATGCATTCCATCTCATGCACATCTTAATAGA-TAAT
* *
9516480 ACATGCATTCCATCTCATGCATATCGTAATAGATAAT
1 ACATGCATTCCATCTCATGCACATCTTAATAGATAAT
* *
9516517 ACATGCATTCCATCTCAGGCATATCT
1 ACATGCATTCCATCTCATGCACATCT
9516543 CAAATAATAG
Statistics
Matches: 81, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
37 27 0.33
38 29 0.36
39 25 0.31
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (37 bp):
ACATGCATTCCATCTCATGCACATCTTAATAGATAAT
Found at i:9518506 original size:28 final size:26
Alignment explanation
Indices: 9518475--9518561 Score: 86
Period size: 27 Copynumber: 3.1 Consensus size: 26
9518465 AAAACATATG
9518475 AAAAAAAAAATAAAAGAGAAGAAAAAGA
1 AAAAAAAAAATAAAAGA-AA-AAAAAGA
9518503 AAAAGAAAAAATAGAAAGAACAAAAAAG-
1 AAAA-AAAAAATA-AAAGAA-AAAAAAGA
* *
9518531 AACAAAAAAATGAGAAGAAATAAAAAGA
1 AAAAAAAAAAT-AAAAGAAA-AAAAAGA
9518559 AAA
1 AAA
9518562 GAAGAAGAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
26 1 0.02
27 18 0.36
28 10 0.20
29 15 0.30
30 6 0.12
ACGTcount: A:0.79, C:0.02, G:0.14, T:0.05
Consensus pattern (26 bp):
AAAAAAAAAATAAAAGAAAAAAAAGA
Found at i:9518518 original size:21 final size:20
Alignment explanation
Indices: 9518457--9518519 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 20
9518447 AAAAAAGGTG
* *
9518457 AAAAAAGGAAAACATATGAAA
1 AAAAAAAGAAAAAATA-GAAA
*
9518478 AAAAAAATAAAAGAGA-AGAAA
1 AAAAAAAGAAAA-A-ATAGAAA
9518499 AAGAAAAAGAAAAAATAGAAA
1 AA-AAAAAGAAAAAATAGAAA
9518520 GAACAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.03
21 22 0.65
22 10 0.29
23 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.06
Consensus pattern (20 bp):
AAAAAAAGAAAAAATAGAAA
Found at i:9518527 original size:14 final size:13
Alignment explanation
Indices: 9518481--9518560 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 13
9518471 TATGAAAAAA
9518481 AAAATAAAAGAGAAG
1 AAAA-AAAAGA-AAG
*
9518496 AAAAAGAA-AAAG
1 AAAAAAAAGAAAG
*
9518508 AAAAAATAGAAAG
1 AAAAAAAAGAAAG
*
9518521 AACAAAAAAG-AAC
1 AA-AAAAAAGAAAG
*
9518534 AAAAAAATGAGAAG
1 AAAAAAAAGA-AAG
9518548 AAATAAAAAGAAA
1 AAA-AAAAAGAAA
9518561 AGAAGAAGAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
12 15 0.29
13 11 0.21
14 16 0.31
15 10 0.19
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.05
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:9518570 original size:24 final size:22
Alignment explanation
Indices: 9518474--9518571 Score: 74
Period size: 24 Copynumber: 4.2 Consensus size: 22
9518464 GAAAACATAT
* *
9518474 GAAAAAAAAAA-TAAAAGAGAA
1 GAAAAAAAAAAGAAAAAAAGAA
9518495 GAAAAAGAAAAAGAAAAAATAGAAA
1 GAAAAA-AAAAAGAAAAAA-AG-AA
*
9518520 GAACAAAAAAGAACAAAAAAATG-A
1 GAA-AAAAAA-AAGAAAAAAA-GAA
*
9518544 GAAGAAATAAAAAGAAAAGAAGAA
1 GAA-AAA-AAAAAGAAAAAAAGAA
9518568 GAAA
1 GAAA
9518572 TGAATAAGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.10
22 5 0.08
23 6 0.10
24 21 0.34
25 12 0.19
26 12 0.19
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
GAAAAAAAAAAGAAAAAAAGAA
Found at i:9519826 original size:18 final size:18
Alignment explanation
Indices: 9519787--9519829 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
9519777 AGAAATCTTC
*
9519787 TTTTTGGAAAAAAATGCA
1 TTTTTGGTAAAAAATGCA
9519805 -TTTTGGTAAAAAATGCA
1 TTTTTGGTAAAAAATGCA
9519822 TTTTTGGT
1 TTTTTGGT
9519830 GTTTAGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.42
Consensus pattern (18 bp):
TTTTTGGTAAAAAATGCA
Found at i:9520133 original size:37 final size:37
Alignment explanation
Indices: 9520081--9520174 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 37
9520071 ATCATTTATG
* * *
9520081 TTTGCGAATCCTTGAAATTTGA-GAATCTTTAA-CCTT
1 TTTGCAAATCTTTGAAATTT-ATGAATCTTTAACCCCT
9520117 ATTTGCAAATCTTTGAAATTTATGAATCTTTAACCCCT
1 -TTTGCAAATCTTTGAAATTTATGAATCTTTAACCCCT
*
9520155 CTTGCAAATCTTTGAAATTT
1 TTTGCAAATCTTTGAAATTT
9520175 CCAAATCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 1 0.02
37 47 0.92
38 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (37 bp):
TTTGCAAATCTTTGAAATTTATGAATCTTTAACCCCT
Found at i:9520502 original size:42 final size:42
Alignment explanation
Indices: 9520405--9520930 Score: 356
Period size: 42 Copynumber: 12.7 Consensus size: 42
9520395 GAATCAAAGT
* * *
9520405 ATTTACTCTATTGTGAATCCAAAGT-TTGTCAAA-TGTGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTT-CCAAACTATGAATC
* * *
9520446 GTTTACTCTATTGTGAATCCATAGTCTTCCAAACTATGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * * * *
9520488 ATTTACTTTGTTGTGAAACCAAAGT-TCTCCTAACTGTGAATT
1 ATTTACTCTGTTGTGAATCCAAAGTCT-TCCAAACTATGAATC
* * *
9520530 ATTTACTCTATTGTGAATCTAAAGTATTCCAAACTATGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * *
9520572 -TTTACTCTGATGTGAATCTAGAG--TTCTCACAACTATGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTC-CA-AACTATGAATC
* * * *
9520613 ATTTACTCTATTATGAATCCAAAGTCTTCCAAATTGTGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * * *
9520655 ATTTACTCTGTTATGAAT-TAAGAGTCTTTC-AACTGTGAATC
1 ATTTACTCTGTTGTGAATCCAA-AGTCTTCCAAACTATGAATC
* * **** * * * *
9520696 ATTTATTCTGCTGTGAATTTGGAGT-TCCCCCAACTATGATTT
1 ATTTACTCTGTTGTGAATCCAAAGTCT-TCCAAACTATGAATC
* * * ** * * * *
9520738 GTTTACTCTATTATGAAT-TTAGGTCTTTCAAATTGTGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * *
9520779 ATTTACTCTGTTGTAAATCCAAAGTCTTCCAAACTATAAATT
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * *
9520821 GTTTACTCTGTTATAAATCCAAAGTCTTCC-AACTATGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * ** * * *
9520862 ATTTGCTTTGTAATGAATCCATAGTCTT-CTAACCATGAATC
1 ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
* * * **
9520903 ATTTTCTCTGATATGAATATAAAGTCTT
1 ATTTACTCTGTTGTGAATCCAAAGTCTT
9520931 TTGGTTTTGA
Statistics
Matches: 381, Mismatches: 88, Indels: 32
0.76 0.18 0.06
Matches are distributed among these distances:
39 3 0.01
40 4 0.01
41 177 0.46
42 191 0.50
43 3 0.01
44 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (42 bp):
ATTTACTCTGTTGTGAATCCAAAGTCTTCCAAACTATGAATC
Found at i:9520510 original size:83 final size:82
Alignment explanation
Indices: 9520405--9520912 Score: 369
Period size: 83 Copynumber: 6.1 Consensus size: 82
9520395 GAATCAAAGT
* * *
9520405 ATTTACTCTATTGTGAATCCAAAGTTTGTCAAATGTGAATCGTTTACTCTATTGTGAATCCATAG
1 ATTTACTCTGTTGTGAATCCAAAGTTT-TCAAATGTGAATCATTTACTCTATTGTGAATCCAAAG
9520470 TCTTCCAAACTATGAATC
65 TCTTCCAAACTATGAATC
* * * * * *
9520488 ATTTACTTTGTTGTGAAACCAAAGTTCTCCTAACTGTGAATTATTTACTCTATTGTGAATCTAAA
1 ATTTACTCTGTTGTGAATCCAAAGTT-TTC-AAATGTGAATCATTTACTCTATTGTGAATCCAAA
*
9520553 GTATTCCAAACTATGAATC
64 GTCTTCCAAACTATGAATC
* * * * * *
9520572 -TTTACTCTGATGTGAATCTAGAGTTCTCACAACTATGAATCATTTACTCTATTATGAATCCAAA
1 ATTTACTCTGTTGTGAATCCAAAGTTTTCA-AA-TGTGAATCATTTACTCTATTGTGAATCCAAA
* *
9520636 GTCTTCCAAATTGTGAATC
64 GTCTTCCAAACTATGAATC
* * * * ** ****
9520655 ATTTACTCTGTTATGAAT-TAAGAGTCTTTCAACTGTGAATCATTTATTCTGCTGTGAATTTGGA
1 ATTTACTCTGTTGTGAATCCAA-AGT-TTTCAAATGTGAATCATTTACTCTATTGTGAATCCAAA
* * * *
9520719 GT-TCCCCCAACTATGATTT
64 GTCT-TCCAAACTATGAATC
* * * ** * * *
9520738 GTTTACTCTATTATGAAT-TTAGGTCTTTCAAATTGTGAATCATTTACTCTGTTGTAAATCCAAA
1 ATTTACTCTGTTGTGAATCCAAAGT-TTTCAAA-TGTGAATCATTTACTCTATTGTGAATCCAAA
* *
9520802 GTCTTCCAAACTATAAATT
64 GTCTTCCAAACTATGAATC
* * * * * * * * * ** *
9520821 GTTTACTCTGTTATAAATCCAAAGTCTTCCAACTATGAATCATTTGCTTTGTAATGAATCCATAG
1 ATTTACTCTGTTGTGAATCCAAAGT-TTTCAAATGTGAATCATTTACTCTATTGTGAATCCAAAG
* *
9520886 TCTT-CTAACCATGAATC
65 TCTTCCAAACTATGAATC
*
9520903 ATTTTCTCTG
1 ATTTACTCTG
9520913 ATATGAATAT
Statistics
Matches: 333, Mismatches: 81, Indels: 23
0.76 0.19 0.05
Matches are distributed among these distances:
81 1 0.00
82 29 0.09
83 222 0.67
84 77 0.23
85 4 0.01
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (82 bp):
ATTTACTCTGTTGTGAATCCAAAGTTTTCAAATGTGAATCATTTACTCTATTGTGAATCCAAAGT
CTTCCAAACTATGAATC
Found at i:9520579 original size:125 final size:125
Alignment explanation
Indices: 9520404--9520830 Score: 334
Period size: 125 Copynumber: 3.4 Consensus size: 125
9520394 TGAATCAAAG
* *
9520404 TATTTACTCTATTGTGAATCCAAAGTTTGTCAAATGTGAATCGTTTACTCT-ATTGTGAATCCAT
1 TATTTACTCTATTGTGAATCCAAAGTTTGCCAAATATGAATCGTTTACTCTGA-TGTGAAT-C-T
* * * * *
9520468 AGTCTTC-CA-AACTATGAATCATTTACTTTGTTGTGAAACCAAAGT-TCTCCTAACTGTGAAT
63 AGACTTCTCACAACTATGAATCATTTACTCTATTATGAAACCAAAGTCT-TCCAAACTGTGAAT
*
9520529 TATTTACTCTATTGTGAATCTAAAGTATT-CCAAACTATGAATC-TTTACTCTGATGTGAATCTA
1 TATTTACTCTATTGTGAATCCAAAGT-TTGCCAAA-TATGAATCGTTTACTCTGATGTGAATCTA
* * *
9520592 GAGTTCTCACAACTATGAATCATTTACTCTATTATGAATCCAAAGTCTTCCAAATTGTGAAT
64 GACTTCTCACAACTATGAATCATTTACTCTATTATGAAACCAAAGTCTTCCAAACTGTGAAT
* * * * * * * * * * * *
9520654 CATTTACTCTGTTATGAAT-TAAGAGTCTT-TCAACTGTGAATCATTTATTCTGCTGTGAATTTG
1 TATTTACTCTATTGTGAATCCAA-AGT-TTGCCAAATATGAATCGTTTACTCTGATGTGAATCTA
* * * * ** *** * * *
9520717 GAGTTCCCCCAACTATGATTTGTTTACTCTATTATG-AATTTAGGTCTTTCAAATTGTGAAT
64 GACTTCTCACAACTATGAATCATTTACTCTATTATGAAACCAAAGTCTTCCAAACTGTGAAT
* * * * *
9520778 CATTTACTCTGTTGTAAATCCAAAGTCTT-CCAAACTATAAATTGTTTACTCTG
1 TATTTACTCTATTGTGAATCCAAAGT-TTGCCAAA-TATGAATCGTTTACTCTG
9520831 TTATAAATCC
Statistics
Matches: 249, Mismatches: 43, Indels: 20
0.80 0.14 0.06
Matches are distributed among these distances:
123 6 0.02
124 58 0.23
125 174 0.70
126 11 0.04
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (125 bp):
TATTTACTCTATTGTGAATCCAAAGTTTGCCAAATATGAATCGTTTACTCTGATGTGAATCTAGA
CTTCTCACAACTATGAATCATTTACTCTATTATGAAACCAAAGTCTTCCAAACTGTGAAT
Found at i:9520993 original size:18 final size:17
Alignment explanation
Indices: 9520968--9521052 Score: 75
Period size: 18 Copynumber: 4.9 Consensus size: 17
9520958 GAATCTACAA
*
9520968 AAAACAAAAAACAAAAAT
1 AAAACAAAAAA-AAAAAC
*
9520986 AGAACAAAAAAAACAAAC
1 AAAACAAAAAAAA-AAAC
9521004 AAAACAAAAAAAAAAAC
1 AAAACAAAAAAAAAAAC
* *
9521021 -CAA-AAAGAAAAAAAC
1 AAAACAAAAAAAAAAAC
**
9521036 AAAGTAAAGAAAAAAAA
1 AAAACAAA-AAAAAAAA
9521053 GCCAAAGAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
15 11 0.20
16 3 0.05
17 9 0.16
18 32 0.58
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (17 bp):
AAAACAAAAAAAAAAAC
Found at i:9521051 original size:20 final size:19
Alignment explanation
Indices: 9520964--9521052 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 19
9520954 TTATGAATCT
*
9520964 ACAAA-AAACAAAAAACAA
1 ACAAAGAAAAAAAAAACAA
9520982 A-AATAGAACAAAAAAAACAA
1 ACAA-AGAA-AAAAAAAACAA
9521002 ACAAA-ACAAAAAAAAA-AA
1 ACAAAGA-AAAAAAAAACAA
* *
9521020 CCAAA-AAGAAAAAAACAA
1 ACAAAGAAAAAAAAAACAA
*
9521038 AGTAAAGAAAAAAAA
1 A-CAAAGAAAAAAAA
9521053 GCCAAAGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
17 10 0.18
18 11 0.19
19 14 0.25
20 20 0.35
21 2 0.04
ACGTcount: A:0.82, C:0.11, G:0.04, T:0.02
Consensus pattern (19 bp):
ACAAAGAAAAAAAAAACAA
Found at i:9521058 original size:20 final size:18
Alignment explanation
Indices: 9520991--9521067 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 18
9520981 AAAATAGAAC
* *
9520991 AAAAAAAACAAACAAAAC
1 AAAAAAAACAAAGAAAAG
*
9521009 AAAAAAAA-AAACCAAAA-
1 AAAAAAAACAAA-GAAAAG
*
9521026 AGAAAAAAACAAAGTAAAG
1 A-AAAAAAACAAAGAAAAG
9521045 AAAAAAAAGCCAAAGAAAAG
1 AAAAAAAA--CAAAGAAAAG
9521065 AAA
1 AAA
9521068 GAATCTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
17 4 0.08
18 30 0.60
19 4 0.08
20 12 0.24
ACGTcount: A:0.81, C:0.10, G:0.08, T:0.01
Consensus pattern (18 bp):
AAAAAAAACAAAGAAAAG
Found at i:9521060 original size:32 final size:31
Alignment explanation
Indices: 9520969--9521063 Score: 79
Period size: 32 Copynumber: 3.0 Consensus size: 31
9520959 AATCTACAAA
* *
9520969 AAACAAAA-AACAAAAATAGAA-CAAAAAAAAC
1 AAACAAAACAA-AAAAA-AAAACCAAAGAAAAC
9521000 AAACAAAACAAAAAAAAAAACCAAAAAGAAAA-
1 AAACAAAACAAAAAAAAAAACC--AAAGAAAAC
**
9521032 AAACAAAGTAAAGAAAAAAAAGCCAAAGAAAA
1 AAACAAAACAAA-AAAAAAAA-CCAAAGAAAA
9521064 GAAAGAATCT
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
30 3 0.06
31 14 0.26
32 20 0.37
33 15 0.28
34 2 0.04
ACGTcount: A:0.80, C:0.12, G:0.06, T:0.02
Consensus pattern (31 bp):
AAACAAAACAAAAAAAAAAACCAAAGAAAAC
Found at i:9523038 original size:23 final size:22
Alignment explanation
Indices: 9523003--9523053 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
9522993 TTTCATCTTG
9523003 CATTTT-CATGCATTCTCATCA-
1 CATTTTGCATGCATTCTCAT-AT
*
9523024 CATTTTGCATAGCATTTTCATAT
1 CATTTTGCAT-GCATTCTCATAT
9523047 CATTTTG
1 CATTTTG
9523054 TTTACATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 16 0.62
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.47
Consensus pattern (22 bp):
CATTTTGCATGCATTCTCATAT
Found at i:9523045 original size:11 final size:11
Alignment explanation
Indices: 9523002--9523052 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
9522992 CTTTCATCTT
9523002 GCATTTTCAT-
1 GCATTTTCATA
*
9523012 GCATTCTCATCA
1 GCATTTTCAT-A
9523024 -CATTTTGCATA
1 GCATTTT-CATA
9523035 GCATTTTCATA
1 GCATTTTCATA
*
9523046 TCATTTT
1 GCATTTT
9523053 GTTTACATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
10 9 0.26
11 16 0.47
12 9 0.26
ACGTcount: A:0.24, C:0.22, G:0.08, T:0.47
Consensus pattern (11 bp):
GCATTTTCATA
Found at i:9523983 original size:14 final size:14
Alignment explanation
Indices: 9523931--9523983 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
9523921 TTTGAAACTC
9523931 TAAACCCTAAACCT
1 TAAACCCTAAACCT
** *
9523945 TAGGCCCTAAACCA
1 TAAACCCTAAACCT
***
9523959 TAAATTATAAACCT
1 TAAACCCTAAACCT
9523973 TAAACCCTAAA
1 TAAACCCTAAA
9523984 ATCACTTCCT
Statistics
Matches: 27, Mismatches: 12, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.45, C:0.28, G:0.04, T:0.23
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:9523998 original size:20 final size:21
Alignment explanation
Indices: 9523973--9524022 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 21
9523963 TTATAAACCT
*
9523973 TAAACCCTAAAATCACT-TCC
1 TAAACCCTAAAACCACTCTCC
*
9523993 TAAACCC-AAAGCCACTCTCC
1 TAAACCCTAAAACCACTCTCC
9524013 -AAACCCTAAA
1 TAAACCCTAAA
9524023 CAATCTTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.42, C:0.38, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAAACCACTCTCC
Found at i:9525439 original size:3 final size:3
Alignment explanation
Indices: 9525431--9525490 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
9525421 GCTTCGTATA
9525431 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9525479 TAT TAT TAT TAT
1 TAT TAT TAT TAT
9525491 AAGGCACTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9532930 original size:34 final size:34
Alignment explanation
Indices: 9532892--9532978 Score: 102
Period size: 34 Copynumber: 2.6 Consensus size: 34
9532882 TAGTCCCAGC
9532892 CATTTCGTTTTTTGACTTATAGTTCAATCCCAAT
1 CATTTCGTTTTTTGACTTATAGTTCAATCCCAAT
** * * * **
9532926 CATTTCGTTTTTCAAGTTGTGGTTCAATCCTGAT
1 CATTTCGTTTTTTGACTTATAGTTCAATCCCAAT
*
9532960 CATTTCATTTTTTGACTTA
1 CATTTCGTTTTTTGACTTA
9532979 GGCTCAGTCC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.49
Consensus pattern (34 bp):
CATTTCGTTTTTTGACTTATAGTTCAATCCCAAT
Found at i:9533023 original size:33 final size:33
Alignment explanation
Indices: 9532986--9533074 Score: 90
Period size: 34 Copynumber: 2.7 Consensus size: 33
9532976 TTAGGCTCAG
* * *
9532986 TCCAAGTTATTTAATTTTCAAAATTTTGTTCAA
1 TCCAAGTTAATCAATTTTCAAAATTTAGTTCAA
* * * *
9533019 TCCAAGTCAAATCATTTTTCAAACTTTAGTTTAA
1 TCCAAGT-TAATCAATTTTCAAAATTTAGTTCAA
9533053 TCCAAGTTAAATC-ATTTTCAAA
1 TCCAAGTT-AATCAATTTTCAAA
9533075 CTTCGGCTCA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
33 15 0.33
34 30 0.67
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.43
Consensus pattern (33 bp):
TCCAAGTTAATCAATTTTCAAAATTTAGTTCAA
Found at i:9533076 original size:33 final size:33
Alignment explanation
Indices: 9532999--9533077 Score: 113
Period size: 34 Copynumber: 2.4 Consensus size: 33
9532989 AAGTTATTTA
* *
9532999 ATTTTCAAAATTTTGTTCAATCCAAGTCAAATC
1 ATTTTCAAACTTTAGTTCAATCCAAGTCAAATC
* *
9533032 ATTTTTCAAACTTTAGTTTAATCCAAGTTAAATC
1 A-TTTTCAAACTTTAGTTCAATCCAAGTCAAATC
9533066 ATTTTCAAACTT
1 ATTTTCAAACTT
9533078 CGGCTCAGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
33 12 0.29
34 29 0.71
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.43
Consensus pattern (33 bp):
ATTTTCAAACTTTAGTTCAATCCAAGTCAAATC
Found at i:9533297 original size:34 final size:34
Alignment explanation
Indices: 9533135--9533320 Score: 134
Period size: 34 Copynumber: 5.6 Consensus size: 34
9533125 CCAAGTCAAA
* * **
9533135 TCATTTTTAGACTT-TGGTTCAATCTAAGTCATT
1 TCATTTTTTGACTTGTGGTTTAATCTTGGTCATT
** * *
9533168 TCA--TTTTGACTT-CAGTTCAATCAAT-GTCATT
1 TCATTTTTTGACTTGTGGTTTAATC-TTGGTCATT
* * *
9533199 TTA-TTTTTGACCT-TGGATTAATCTTGGTCATT
1 TCATTTTTTGACTTGTGGTTTAATCTTGGTCATT
*** *
9533231 TCATTTTTTGACTTGTGGCCCAATCTCGGTCATT
1 TCATTTTTTGACTTGTGGTTTAATCTTGGTCATT
* * *
9533265 TCATTTTTTGACTTATGGTTTAGTCTTAGTCATT
1 TCATTTTTTGACTTGTGGTTTAATCTTGGTCATT
* *
9533299 TCACTTTTTAACTTGTGGTTTA
1 TCATTTTTTGACTTGTGGTTTA
9533321 GTCTCTGTCA
Statistics
Matches: 120, Mismatches: 28, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
31 25 0.21
32 22 0.18
33 12 0.10
34 61 0.51
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (34 bp):
TCATTTTTTGACTTGTGGTTTAATCTTGGTCATT
Found at i:9533503 original size:39 final size:35
Alignment explanation
Indices: 9533470--9533549 Score: 110
Period size: 35 Copynumber: 2.3 Consensus size: 35
9533460 TCATTTAATC
*
9533470 TTTAGACTTTAGTTCAATCTAAGTCAAAATCATTT
1 TTTAGACTTTAGTTCAATCAAAGTCAAAATCATTT
* **
9533505 TTTAGACTTTTGTTCAATCAAAGTC-ATTTCA-TT
1 TTTAGACTTTAGTTCAATCAAAGTCAAAATCATTT
9533538 TTTAGACTTTAG
1 TTTAGACTTTAG
9533550 CTCACTTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 13 0.32
34 4 0.10
35 23 0.57
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTAGACTTTAGTTCAATCAAAGTCAAAATCATTT
Found at i:9533545 original size:33 final size:33
Alignment explanation
Indices: 9533135--9533606 Score: 178
Period size: 33 Copynumber: 14.2 Consensus size: 33
9533125 CCAAGTCAAA
*
9533135 TCATTTTTAGACTTTGGTTCAATCTAAGTCATT
1 TCATTTTTAGACTTTAGTTCAATCTAAGTCATT
*
9533168 TCA-TTTT-GACTTCAGTTCAATC-AATGTCATT
1 TCATTTTTAGACTTTAGTTCAATCTAA-GTCATT
* * * **
9533199 TTATTTTT-GACCTTGGATT-AATCTTGGTCATT
1 TCATTTTTAGACTTTAG-TTCAATCTAAGTCATT
* * ** **
9533231 TCATTTTTTGACTTGTGGCCCAATCTCGGTCATT
1 TCATTTTTAGACTT-TAGTTCAATCTAAGTCATT
* * * * *
9533265 TCATTTTTTGACTTATGGTTTAGTCTTAGTCATT
1 TCATTTTTAGACTT-TAGTTCAATCTAAGTCATT
* * * **
9533299 TCACTTTTTA-ACTTGTGGTTTAGTCTCTGTCACTT
1 TCA-TTTTTAGACTT-TAGTTCAATCTAAGTCA-TT
* * *
9533334 T-GTTTTTCA-AC-TTAGGCTCAGT-TCAAGTCATT
1 TCATTTTT-AGACTTTA-GTTCAATCT-AAGTCATT
* * * * * **
9533366 TAATTTTCAAATTTTAGTTCAATCTGAGTCAAA
1 TCATTTTTAGACTTTAGTTCAATCTAAGTCATT
* * * * * **
9533399 TCATTTTTAGACTTTGGCTGAGT-TCAAGTTAAA
1 TCATTTTTAGACTTTAGTTCAATCT-AAGTCATT
** * * *
9533432 T-ATTTTTTAGACTTCGGCTT-AGTCCAGGTCATT
1 TCA-TTTTTAGACTTTAG-TTCAATCTAAGTCATT
* * **
9533465 TAATCTTTAGACTTTAGTTCAATCTAAGTCAAAA
1 TCATTTTTAGACTTTAGTTCAATCTAAGTC-ATT
* *
9533499 TCATTTTTTAGACTTTTGTTCAATCAAAGTCATT
1 TCA-TTTTTAGACTTTAGTTCAATCTAAGTCATT
* * * **
9533533 TCATTTTTAGACTTTAGCTCACTTTGGGTCATT
1 TCATTTTTAGACTTTAGTTCAATCTAAGTCATT
* * * *
9533566 TAATTTTTAAACTTTGGTTCAATCTAAGTTATT
1 TCATTTTTAGACTTTAGTTCAATCTAAGTCATT
9533599 TCATTTTT
1 TCATTTTT
9533607 GACCTTGGCT
Statistics
Matches: 329, Mismatches: 86, Indels: 48
0.71 0.19 0.10
Matches are distributed among these distances:
30 2 0.01
31 21 0.06
32 40 0.12
33 154 0.47
34 80 0.24
35 32 0.10
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.48
Consensus pattern (33 bp):
TCATTTTTAGACTTTAGTTCAATCTAAGTCATT
Found at i:9533650 original size:66 final size:66
Alignment explanation
Indices: 9533503--9533652 Score: 169
Period size: 66 Copynumber: 2.3 Consensus size: 66
9533493 TCAAAATCAT
* * *
9533503 TTTTTAGACTTTTGTTCAATCAAAGTCATTTCATTTTTAGACTTTAGCTCACTTTGGGTCATTTA
1 TTTTTAAACTTTGGTTCAATCAAAGTCATTTCATTTTTAGACCTTAGCTCACTTTGGGTCATTTA
9533568 A
66 A
* * * * *
9533569 TTTTTAAACTTTGGTTCAATCTAAGTTATTTCATTTTT-GACCTTGGCTTAGTCTT-GGTCATTT
1 TTTTTAAACTTTGGTTCAATCAAAGTCATTTCATTTTTAGACCTTAGCTCACT-TTGGGTCATTT
*
9533632 CA
65 AA
* *
9533634 TTTTTCAAGTTGTGGTTCA
1 TTTTTAAACTT-TGGTTCA
9533653 GTCCCGATCA
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
65 28 0.39
66 43 0.61
ACGTcount: A:0.21, C:0.15, G:0.14, T:0.50
Consensus pattern (66 bp):
TTTTTAAACTTTGGTTCAATCAAAGTCATTTCATTTTTAGACCTTAGCTCACTTTGGGTCATTTA
A
Found at i:9533744 original size:33 final size:33
Alignment explanation
Indices: 9533707--9533772 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
9533697 TTTGTTTGTT
9533707 GACTTAGACTCAGTCCAAGTCAAATCATTTTCA
1 GACTTAGACTCAGTCCAAGTCAAATCATTTTCA
* * *
9533740 GACTTTGATTTAGTCCAAGTCAAATCATTTTCA
1 GACTTAGACTCAGTCCAAGTCAAATCATTTTCA
9533773 AATTTTGGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (33 bp):
GACTTAGACTCAGTCCAAGTCAAATCATTTTCA
Found at i:9533938 original size:34 final size:34
Alignment explanation
Indices: 9533900--9533978 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
9533890 TCATTTCTTT
* *
9533900 TTTTTTCACTTGT-AGTTCAGTCCTAGTCATTTCA
1 TTTTTTGACTTGTGA-TTCAGTCCTAGTCACTTCA
* * *
9533934 TTTTTTGACTTGTGATTTATTTCTAGTCACTTCA
1 TTTTTTGACTTGTGATTCAGTCCTAGTCACTTCA
9533968 TTTTTTGACTT
1 TTTTTTGACTT
9533979 AGGCTTAGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 38 0.97
35 1 0.03
ACGTcount: A:0.16, C:0.16, G:0.11, T:0.56
Consensus pattern (34 bp):
TTTTTTGACTTGTGATTCAGTCCTAGTCACTTCA
Found at i:9536524 original size:15 final size:16
Alignment explanation
Indices: 9536501--9536531 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
9536491 ATAGGTATAC
9536501 AAAATATAATAAAAAT
1 AAAATATAATAAAAAT
9536517 AAAA-ATAATAAAAAT
1 AAAATATAATAAAAAT
9536532 CTCTAAGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATATAATAAAAAT
Found at i:9542847 original size:67 final size:67
Alignment explanation
Indices: 9542770--9542901 Score: 228
Period size: 67 Copynumber: 2.0 Consensus size: 67
9542760 ATTACTAAAG
*
9542770 GAACATCCATCAGACTTTAAATAGCTATTGCATCAATTTATAATCTCATAATTCACCAAATGGAT
1 GAACATCCATCAGACTTTAAATAGCTACTGCATCAATTTATAATCTCATAATTCACCAAATGGAT
9542835 AA
66 AA
* * *
9542837 GAACATCCATCAGATTTTAAATAGCTACTGCATTAATTTCTAATCTCATAATTCACCAAATGGAT
1 GAACATCCATCAGACTTTAAATAGCTACTGCATCAATTTATAATCTCATAATTCACCAAATGGAT
9542902 GTCAAAACAA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 61 1.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.33
Consensus pattern (67 bp):
GAACATCCATCAGACTTTAAATAGCTACTGCATCAATTTATAATCTCATAATTCACCAAATGGAT
AA
Found at i:9543889 original size:47 final size:47
Alignment explanation
Indices: 9543820--9543915 Score: 138
Period size: 47 Copynumber: 2.0 Consensus size: 47
9543810 AAAGTGCATA
* * *
9543820 ATTGTTATTATAATGGTAAATCCATATCTATTAGAAAGAAGCACACT
1 ATTGTTATTACAACGATAAATCCATATCTATTAGAAAGAAGCACACT
* * *
9543867 ATTGTTATTACAACGATAAATCCATATCTATTATAAGGAAGCATACT
1 ATTGTTATTACAACGATAAATCCATATCTATTAGAAAGAAGCACACT
9543914 AT
1 AT
9543916 AGTGAGGTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (47 bp):
ATTGTTATTACAACGATAAATCCATATCTATTAGAAAGAAGCACACT
Found at i:9545334 original size:25 final size:24
Alignment explanation
Indices: 9545298--9545368 Score: 97
Period size: 25 Copynumber: 2.9 Consensus size: 24
9545288 ATTATGCAAA
*
9545298 AAAAAAAAATCATGCAAAGATCAT
1 AAAAAAAAATCATGCAAAAATCAT
*
9545322 AATAAAAATATCATGCAATAAATCAT
1 AA-AAAAAAATCATGCAA-AAATCAT
*
9545348 AAAAAAACATCATGCAAAAAT
1 AAAAAAAAATCATGCAAAAAT
9545369 ATATTATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
24 6 0.14
25 28 0.67
26 8 0.19
ACGTcount: A:0.62, C:0.13, G:0.06, T:0.20
Consensus pattern (24 bp):
AAAAAAAAATCATGCAAAAATCAT
Found at i:9545462 original size:24 final size:24
Alignment explanation
Indices: 9545418--9545503 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
9545408 TAAATTAGAT
* * * *
9545418 TCATGCAAATATATATTATAATCAT
1 TCATGCAAA-AAATATCATAATAAA
9545443 TCATGCAAAAAATATCATAATAAAAA
1 TCATGCAAAAAATATCATAAT--AAA
* *
9545469 TCATGCAACTAAATATCAT-ATGAA
1 TCATGCAA-AAAATATCATAATAAA
9545493 TCATGCAAAAA
1 TCATGCAAAAA
9545504 TAAACTATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
23 2 0.04
24 20 0.39
25 9 0.18
26 11 0.22
27 9 0.18
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (24 bp):
TCATGCAAAAAATATCATAATAAA
Found at i:9546914 original size:26 final size:26
Alignment explanation
Indices: 9546884--9546934 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
9546874 ACGAAAATTT
*
9546884 AAATAAATAAAAGTATA-AAAAATATC
1 AAATAAA-AAAAGTAAATAAAAATATC
*
9546910 AAATAAAAAAATTAAATAAAAATAT
1 AAATAAAAAAAGTAAATAAAAATAT
9546935 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (26 bp):
AAATAAAAAAAGTAAATAAAAATATC
Found at i:9546980 original size:40 final size:36
Alignment explanation
Indices: 9546884--9547008 Score: 107
Period size: 40 Copynumber: 3.4 Consensus size: 36
9546874 ACGAAAATTT
* *
9546884 AAATA-AATAA-AAGTATA-AAAAATATCAAATAAA
1 AAATATAATAATAAATATATAAAAATATAAAATAAA
9546917 AAA-ATTAAATAA-AAATATATAAAAATATAACAATACAA
1 AAATA-T-AATAATAAATATATAAAAATATAA-AATA-AA
*
9546955 AAATATAATAATAAATATAATTAAAATAATAAAGAATAAA
1 AAATATAATAATAAATAT-ATAAAAAT-AT-AA-AATAAA
*
9546995 AAATATAAAAATAA
1 AAATATAATAATAA
9547009 TAAAAAGAAG
Statistics
Matches: 76, Mismatches: 5, Indels: 15
0.79 0.05 0.16
Matches are distributed among these distances:
32 1 0.01
33 3 0.04
35 11 0.14
36 9 0.12
37 9 0.12
38 12 0.16
39 8 0.11
40 17 0.22
41 6 0.08
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (36 bp):
AAATATAATAATAAATATATAAAAATATAAAATAAA
Found at i:9546994 original size:7 final size:7
Alignment explanation
Indices: 9546883--9547013 Score: 66
Period size: 8 Copynumber: 17.0 Consensus size: 7
9546873 AACGAAAATT
9546883 TAAATAAA
1 TAAA-AAA
*
9546891 TAAAAGTA
1 TAAAA-AA
9546899 TAAAAAA
1 TAAAAAA
**
9546906 TATCAAA
1 TAAAAAA
9546913 TAAAAAA
1 TAAAAAA
**
9546920 -ATTAAA
1 TAAAAAA
9546926 TAAAAATA
1 TAAAAA-A
9546934 TATAAAAA
1 TA-AAAAA
*
9546942 TATAACAA
1 TA-AAAAA
9546950 TACAAAAA
1 TA-AAAAA
*
9546958 TATAATAA
1 TA-AAAAA
9546966 TAAATATAA
1 TAAA-A-AA
9546975 TTAAAATAA
1 -TAAAA-AA
*
9546984 TAAAGAA
1 TAAAAAA
9546991 TAAAAAA
1 TAAAAAA
9546998 TATAAAAA
1 TA-AAAAA
9547006 TAATAAAA
1 TAA-AAAA
9547014 AGAAGTGGGC
Statistics
Matches: 96, Mismatches: 18, Indels: 18
0.73 0.14 0.14
Matches are distributed among these distances:
6 4 0.04
7 28 0.29
8 50 0.52
9 10 0.10
10 4 0.04
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (7 bp):
TAAAAAA
Found at i:9547002 original size:16 final size:15
Alignment explanation
Indices: 9546898--9547013 Score: 78
Period size: 16 Copynumber: 7.5 Consensus size: 15
9546888 AAATAAAAGT
*
9546898 ATAAAAAATAT-CAA
1 ATAAAAAATATAAAA
*
9546912 ATAAAAAA-AT-TAA
1 ATAAAAAATATAAAA
9546925 ATAAAAATATATAAAA
1 ATAAAAA-ATATAAAA
* *
9546941 ATATAACAATACAAAA
1 ATA-AAAAATATAAAA
* * *
9546957 ATATAATA-ATAAAT
1 ATAAAAAATATAAAA
9546971 ATAATTAAAATAATAAAGA
1 ATAA--AAAAT-ATAAA-A
9546990 ATAAAAAATATAAAA
1 ATAAAAAATATAAAA
9547005 ATAATAAAA
1 ATAA-AAAA
9547014 AGAAGTGGGC
Statistics
Matches: 80, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
13 11 0.14
14 16 0.20
15 9 0.11
16 27 0.34
17 8 0.10
18 5 0.06
19 4 0.05
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (15 bp):
ATAAAAAATATAAAA
Found at i:9547010 original size:28 final size:27
Alignment explanation
Indices: 9546961--9547017 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
9546951 ACAAAAATAT
* *
9546961 AATAATAAATATAATTAAAATAATAAAG
1 AATAAAAAATATAATAAAAATAA-AAAG
9546989 AATAAAAAATATAA-AAATAATAAAAAG
1 AATAAAAAATATAATAAA-AATAAAAAG
9547016 AA
1 AA
9547018 GTGGGCTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (27 bp):
AATAAAAAATATAATAAAAATAAAAAG
Found at i:9549112 original size:45 final size:45
Alignment explanation
Indices: 9549056--9549162 Score: 126
Period size: 45 Copynumber: 2.4 Consensus size: 45
9549046 AAAATTAGAT
* **
9549056 AAAACCCTAAAATGAAACCCTAAAAGGAACTTTAATTAAAA-CCC
1 AAAACCTTAAAATGAAACCCTAAAAGGAACCCTAATTAAAATCCC
* * * *
9549100 TAAAATCTTAAAATGAAACCTTAAAGGGAACCCTAGTTAAAATCCC
1 -AAAACCTTAAAATGAAACCCTAAAAGGAACCCTAATTAAAATCCC
*
9549146 AGAACCTTAAAATGAAA
1 AAAACCTTAAAATGAAA
9549163 TCTTATGTGT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 49 0.94
46 3 0.06
ACGTcount: A:0.50, C:0.20, G:0.09, T:0.21
Consensus pattern (45 bp):
AAAACCTTAAAATGAAACCCTAAAAGGAACCCTAATTAAAATCCC
Found at i:9549235 original size:17 final size:17
Alignment explanation
Indices: 9549201--9549235 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9549191 GATAAATGGA
* *
9549201 GAAAGTGTGATTCTTAG
1 GAAAGTGTGATACCTAG
9549218 GAAAGTGTGATACCTAG
1 GAAAGTGTGATACCTAG
9549235 G
1 G
9549236 TTTTTCTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.09, G:0.31, T:0.29
Consensus pattern (17 bp):
GAAAGTGTGATACCTAG
Found at i:9549619 original size:64 final size:64
Alignment explanation
Indices: 9549522--9549665 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
9549512 ATTTATTTAA
* * *
9549522 AAAAGGATCATTTAAGGCATTTTCTATACAGAAAATGCCTT-ACATGATCATTTTT-TAAATAAA
1 AAAAGGATTATTTAAGGCATTTTCTATACAGAAAATGCCTTAAC-TAATC-TTTTTATAAAAAAA
9549585 T
64 T
* * * * * *
9549586 TAAAGGATTATTTGAGGTATTTTTTGTATAGAAAATGCCTTAACTAATCTTTTTATAAAAAAAT
1 AAAAGGATTATTTAAGGCATTTTCTATACAGAAAATGCCTTAACTAATCTTTTTATAAAAAAAT
*
9549650 AAAAGGATTAATTAAG
1 AAAAGGATTATTTAAG
9549666 AGGTTTCTGT
Statistics
Matches: 66, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
63 5 0.08
64 59 0.89
65 2 0.03
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (64 bp):
AAAAGGATTATTTAAGGCATTTTCTATACAGAAAATGCCTTAACTAATCTTTTTATAAAAAAAT
Found at i:9549896 original size:88 final size:88
Alignment explanation
Indices: 9549745--9549993 Score: 383
Period size: 90 Copynumber: 2.8 Consensus size: 88
9549735 TCTTTTCATT
* * *
9549745 TATAAAAAGATTATTTAAGGCGTTTCTGTACAGAAAATGCCTTAAATAATCCATTTATTAAAATA
1 TATAAAAAGATTATTTAAGGTGTTTCTGTACAAAAAATGCCTTAAATAATCC-TTTATAAAAATA
*
9549810 TAAAAATACT-TTTATTATAAAAA
65 TAAAAATACTCTATATTATAAAAA
9549833 TATAAAAAGATTATTTAAGGTGTTTCTGTACAAAAAATGCCTTAAATAATCACTTTATAAAAATA
1 TATAAAAAGATTATTTAAGGTGTTTCTGTACAAAAAATGCCTTAAATAATC-CTTTATAAAAATA
*
9549898 TAAAAATACTCCTATGTTATAAAAA
65 TAAAAATACT-CTATATTATAAAAA
* * *
9549923 TATAAAAAGATTATTTAAGGTATTTTTGTACAAAAAATGCATTAAATAATCTCTTTATAAAAATA
1 TATAAAAAGATTATTTAAGGTGTTTCTGTACAAAAAATGCCTTAAATAATC-CTTTATAAAAATA
9549988 TAAAAA
65 TAAAAA
9549994 GATTATTTAA
Statistics
Matches: 149, Mismatches: 9, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
88 70 0.47
89 1 0.01
90 78 0.52
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (88 bp):
TATAAAAAGATTATTTAAGGTGTTTCTGTACAAAAAATGCCTTAAATAATCCTTTATAAAAATAT
AAAAATACTCTATATTATAAAAA
Found at i:9549958 original size:63 final size:63
Alignment explanation
Indices: 9549891--9550067 Score: 166
Period size: 63 Copynumber: 2.8 Consensus size: 63
9549881 ATCACTTTAT
* * *
9549891 AAAAATAT-A-AAAATACTCCTATGTTATAAAAATATAAAAAGATTATTTAAGGTATTTTTGTAC
1 AAAAATATCATAAAATAAT-CTAT-TTATAAAAATATAAAAAGATTATTTAAGATATTTCTGTAC
* * *
9549954 AAAAA-ATGCATTAAATAATCTCTTTATAAAAATATAAAAAGATTATTTAAGATGTTTCTGTAC
1 AAAAATAT-CATAAAATAATCTATTTATAAAAATATAAAAAGATTATTTAAGATATTTCTGTAC
* * * * * *
9550017 ATAAAAT-GCCTTAAATAATC-ACCTTATAAACATATAAAAGGATTATTTAAG
1 A-AAAATATCATAAAATAATCTA-TTTATAAAAATATAAAAAGATTATTTAAG
9550068 GTGTTTTTCA
Statistics
Matches: 96, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
62 2 0.02
63 80 0.83
64 8 0.08
65 6 0.06
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (63 bp):
AAAAATATCATAAAATAATCTATTTATAAAAATATAAAAAGATTATTTAAGATATTTCTGTAC
Found at i:9550073 original size:63 final size:63
Alignment explanation
Indices: 9549914--9550170 Score: 272
Period size: 63 Copynumber: 4.1 Consensus size: 63
9549904 TACTCCTATG
* * * * *
9549914 TTATAAAAATATAAAAAGATTATTTAAGGTATTTTTGTACAAAAAATGCATTAAATAATCTCT
1 TTATAAAAATATAAAAAGATTATTTAAGGTGTTTCTGTACATAAAATGCCTTAAATAATCACT
* *
9549977 TTATAAAAATATAAAAAGATTATTTAAGATGTTTCTGTACATAAAATGCCTTAAATAATCACC
1 TTATAAAAATATAAAAAGATTATTTAAGGTGTTTCTGTACATAAAATGCCTTAAATAATCACT
* * * *
9550040 TTATAAACATATAAAAGGATTATTTAAGGTGTTT-T-TCATATAGAAATGCCTTAAATAATCATT
1 TTATAAAAATATAAAAAGATTATTTAAGGTGTTTCTGT-ACATA-AAATGCCTTAAATAATCACT
* ** * * * * * * *
9550103 TTATTAAAATATAAATGGATCATTTAAGGCGTTTCAGCAAAT-AAATGACTTAAATGATCA-T
1 TTATAAAAATATAAAAAGATTATTTAAGGTGTTTCTGTACATAAAATGCCTTAAATAATCACT
9550164 TT-TAAAA
1 TTATAAAA
9550171 GGTTCATTCC
Statistics
Matches: 166, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
60 4 0.02
61 4 0.02
62 21 0.13
63 134 0.81
64 3 0.02
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (63 bp):
TTATAAAAATATAAAAAGATTATTTAAGGTGTTTCTGTACATAAAATGCCTTAAATAATCACT
Found at i:9558216 original size:9 final size:8
Alignment explanation
Indices: 9558170--9558225 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
9558160 ATTCGTAACT
9558170 TAAAATAA
1 TAAAATAA
9558178 TAAAATTAAA
1 TAAAA-T-AA
9558188 TAAAA-AA
1 TAAAATAA
9558195 TAAAA-AA
1 TAAAATAA
*
9558202 TTAAAGTAA
1 -TAAAATAA
9558211 TAAAAGTAA
1 TAAAA-TAA
9558220 TAAAAT
1 TAAAAT
9558226 GGGATTTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
7 9 0.22
8 14 0.34
9 11 0.27
10 7 0.17
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (8 bp):
TAAAATAA
Found at i:9560794 original size:17 final size:18
Alignment explanation
Indices: 9560765--9560802 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
9560755 TTTACATAGA
9560765 AGGGGGCTAAAAAAGAAG
1 AGGGGGCTAAAAAAGAAG
9560783 AGGGGGCT-AAAAAGAAG
1 AGGGGGCTAAAAAAGAAG
9560800 AGG
1 AGG
9560803 AGACTTGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.47, C:0.05, G:0.42, T:0.05
Consensus pattern (18 bp):
AGGGGGCTAAAAAAGAAG
Found at i:9561840 original size:19 final size:19
Alignment explanation
Indices: 9561808--9561879 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
9561798 ATGCATTTTT
*
9561808 CATGAAACCTTAAACCACC
1 CATGAAACCCTAAACCACC
* * * *
9561827 CTTTAAACCCTAAATCATC
1 CATGAAACCCTAAACCACC
*
9561846 CATGAAACCCCAAACCACC
1 CATGAAACCCTAAACCACC
*
9561865 CATGAAGCCCTAAAC
1 CATGAAACCCTAAAC
9561880 TAACCCAAAC
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.40, C:0.38, G:0.06, T:0.17
Consensus pattern (19 bp):
CATGAAACCCTAAACCACC
Found at i:9561936 original size:7 final size:7
Alignment explanation
Indices: 9561924--9562120 Score: 105
Period size: 7 Copynumber: 29.9 Consensus size: 7
9561914 CTACCTATCT
9561924 CTAAACC
1 CTAAACC
9561931 CTAAACC
1 CTAAACC
9561938 C-AAACC
1 CTAAACC
*
9561944 TTAAACC
1 CTAAACC
*
9561951 TTAAA-C
1 CTAAACC
*
9561957 CTAAACT
1 CTAAACC
* *
9561964 TTAAA-T
1 CTAAACC
9561970 CTAAACC
1 CTAAACC
9561977 CTAAACC
1 CTAAACC
* *
9561984 TTACACC
1 CTAAACC
* *
9561991 ATAAATC
1 CTAAACC
9561998 CTAAACC
1 CTAAACC
9562005 CTAAACC
1 CTAAACC
*
9562012 CCAAACC
1 CTAAACC
9562019 CTAAA--
1 CTAAACC
* * **
9562024 GTTAATT
1 CTAAACC
*
9562031 GTAAACC
1 CTAAACC
9562038 C-AAA-C
1 CTAAACC
*
9562043 AT-AA-C
1 CTAAACC
9562048 CTAAACC
1 CTAAACC
*
9562055 CTGAACC
1 CTAAACC
*
9562062 CAAAACC
1 CTAAACC
9562069 C-AAACC
1 CTAAACC
*
9562075 C-AAAAC
1 CTAAACC
*
9562081 TTAAACC
1 CTAAACC
9562088 CTAAACC
1 CTAAACC
*
9562095 TTAAA--
1 CTAAACC
9562100 CTAAACC
1 CTAAACC
9562107 CTTAAACC
1 C-TAAACC
9562115 CTAAAC
1 CTAAAC
9562121 TTAAACTAAA
Statistics
Matches: 146, Mismatches: 32, Indels: 24
0.72 0.16 0.12
Matches are distributed among these distances:
5 12 0.08
6 30 0.21
7 97 0.66
8 7 0.05
ACGTcount: A:0.46, C:0.34, G:0.02, T:0.19
Consensus pattern (7 bp):
CTAAACC
Found at i:9561950 original size:20 final size:20
Alignment explanation
Indices: 9561925--9562126 Score: 100
Period size: 20 Copynumber: 10.2 Consensus size: 20
9561915 TACCTATCTC
9561925 TAAACCCTAAACCCAAACCT
1 TAAACCCTAAACCCAAACCT
* * *
9561945 TAAACCTTAAACCTAAACTT
1 TAAACCCTAAACCCAAACCT
*
9561965 TAAA-TCTAAACCCTAAACCT
1 TAAACCCTAAACCC-AAACCT
* * * *
9561985 TACACCATAAATCCTAAACCC
1 TAAACCCTAAA-CCCAAACCT
* *
9562006 TAAACCCCAAACCCTAAA-GT
1 TAAACCCTAAACCC-AAACCT
*** *
9562026 T-AATTGTAAACCCAAA-CA
1 TAAACCCTAAACCCAAACCT
* *
9562044 T-AA-CCTAAACCCTGAACCC
1 TAAACCCTAAACCC-AAACCT
* *
9562063 AAAACCC-AAACCCAAAACT
1 TAAACCCTAAACCCAAACCT
*
9562082 TAAACCCTAAACCTTAAA-C-
1 TAAACCCTAAACC-CAAACCT
9562101 TAAACCCTTAAACCCTAAA-CT
1 TAAACCC-TAAACCC-AAACCT
9562122 TAAAC
1 TAAAC
9562127 TAAATCCCAA
Statistics
Matches: 134, Mismatches: 35, Indels: 25
0.69 0.18 0.13
Matches are distributed among these distances:
17 7 0.05
18 8 0.06
19 31 0.23
20 56 0.42
21 30 0.22
22 2 0.01
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.19
Consensus pattern (20 bp):
TAAACCCTAAACCCAAACCT
Found at i:9562123 original size:13 final size:14
Alignment explanation
Indices: 9561924--9562126 Score: 99
Period size: 13 Copynumber: 14.9 Consensus size: 14
9561914 CTACCTATCT
*
9561924 CTAAACCCTAAACC
1 CTAAACCTTAAACC
9561938 C-AAACCTTAAACC
1 CTAAACCTTAAACC
* *
9561951 TTAAACC-TAAACT
1 CTAAACCTTAAACC
* *
9561964 TTAAATC-TAAACC
1 CTAAACCTTAAACC
*
9561977 CTAAACCTTACACC
1 CTAAACCTTAAACC
*
9561991 ATAAATCC-TAAACC
1 CTAAA-CCTTAAACC
**
9562005 CTAAACCCCAAACC
1 CTAAACCTTAAACC
**
9562019 CTAAAGTTAATTGTAAACC
1 CT-AA---ACCT-TAAACC
*
9562038 C-AAA-CAT-AA-C
1 CTAAACCTTAAACC
* *
9562048 CTAAACCCTGAACC
1 CTAAACCTTAAACC
* *
9562062 CAAAACC-CAAACC
1 CTAAACCTTAAACC
*
9562075 C-AAAACTTAAACC
1 CTAAACCTTAAACC
9562088 CTAAACCTTAAA--
1 CTAAACCTTAAACC
9562100 CTAAACCCTTAAACC
1 CTAAA-CCTTAAACC
9562115 CTAAA-CTTAAAC
1 CTAAACCTTAAAC
9562127 TAAATCCCAA
Statistics
Matches: 146, Mismatches: 25, Indels: 37
0.70 0.12 0.18
Matches are distributed among these distances:
10 2 0.01
11 5 0.03
12 12 0.08
13 61 0.42
14 48 0.33
15 9 0.06
17 2 0.01
18 1 0.01
19 6 0.04
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.19
Consensus pattern (14 bp):
CTAAACCTTAAACC
Found at i:9563219 original size:21 final size:23
Alignment explanation
Indices: 9563195--9563246 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
9563185 TAAAAGGATG
*
9563195 AAAATTTTGAA-AAAAAAT-AAA
1 AAAATTATGAAGAAAAAATCAAA
* *
9563216 AAAATCATGAAGAAAAATTCAAA
1 AAAATTATGAAGAAAAAATCAAA
9563239 AAAATTAT
1 AAAATTAT
9563247 TTTGATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 9 0.36
22 6 0.24
23 10 0.40
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAATTATGAAGAAAAAATCAAA
Found at i:9563893 original size:17 final size:16
Alignment explanation
Indices: 9563871--9563914 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
9563861 AATTCTTTAT
9563871 AAAAAAAATAAAACACA
1 AAAAAAAATAAAA-ACA
*
9563888 AAAAAAGAAGAAAAACA
1 AAAAAA-AATAAAAACA
9563905 AAGAAAAAAT
1 AA-AAAAAAT
9563915 GAAATGAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.82, C:0.07, G:0.07, T:0.05
Consensus pattern (16 bp):
AAAAAAAATAAAAACA
Found at i:9575489 original size:16 final size:15
Alignment explanation
Indices: 9575456--9575523 Score: 70
Period size: 15 Copynumber: 4.6 Consensus size: 15
9575446 AGAAAAAAAT
9575456 AAAAAAAAAAGAGAG
1 AAAAAAAAAAGAGAG
*
9575471 AAAAAAGAAAGAGATG
1 AAAAAAAAAAGAGA-G
*
9575487 -AAAAGAAAAG-G-G
1 AAAAAAAAAAGAGAG
*
9575499 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAGAG
9575514 AAGAAAAAAA
1 AA-AAAAAAA
9575524 TATTTTATTG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
12 1 0.02
13 9 0.21
14 1 0.02
15 24 0.56
16 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAGAGAG
Found at i:9575513 original size:17 final size:19
Alignment explanation
Indices: 9575487--9575523 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
9575477 GAAAGAGATG
*
9575487 AAAAGAAAAG-GGAAAAAA
1 AAAAGAAAAGAAGAAAAAA
9575505 AAAAG-AAAGAAGAAAAAA
1 AAAAGAAAAGAAGAAAAAA
9575523 A
1 A
9575524 TATTTTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAGAAGAAAAAA
Found at i:9576020 original size:18 final size:18
Alignment explanation
Indices: 9575999--9576050 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
9575989 AGAAAGTGAA
9575999 AAAAAATAAGAAAATAAG-
1 AAAAAATAAGAAAA-AAGC
9576017 -AAAAATGAAAGAAAAAAGC
1 AAAAAAT--AAGAAAAAAGC
*
9576036 AAAAAAAAAGAAAAA
1 AAAAAATAAGAAAAA
9576051 GAAAAATGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 6 0.21
18 11 0.38
19 7 0.24
20 5 0.17
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.06
Consensus pattern (18 bp):
AAAAAATAAGAAAAAAGC
Found at i:9577578 original size:411 final size:415
Alignment explanation
Indices: 9576808--9577580 Score: 1063
Period size: 411 Copynumber: 1.9 Consensus size: 415
9576798 GAGCAAACAT
9576808 ATATATATATATGCATTATAAATGAAAACATTAATTTAAAAACAAAACATATGCAAATGATGATC
1 ATATATATATATGCATTATAAATGAAAACATTAATTTAAAAACAAAACATATGCAAATGATGAT-
* * *** * ** *
9576873 AAATGCAAATTTAAGAATTGAGTTTTCAAATATAAAGAGATGACTTGGACTCTCCAACATCTAGA
65 AAATACAAATATAAGAAACAAATTTTCAAATATAAAGAGACCACTTGGACACTCCAACATCTAGA
* *
9576938 CAGAATTTGGATGCGAATTTTTATACTTAAAATCTCGTCCTATTATTTTTTATTATTTTGTATTT
130 CAGAATTTGGATACGAATTTTTATACTTAAAATCCCGTCCTATTATTTTTTATTATTTTGTATTT
* * * *
9577003 TTCTAATCATGGTTTTTACAAAATAAATATATTTTGAGCTGTGGAAATGTATGAAAATTCTTAAT
195 TTATAATCATGG---TTACAAAACAAATATATTTTGAGCTGTGGAAATATATAAAAATTCTTAAT
* * *
9577068 GAAATAAAATTTCTTAAATGCCCCAACAACTAGGCAACATTCGGGAACAAATTACTTTATAAAAG
257 GAAATAAAATTTCCTAAATACCCCAACAACTAGGCAACATTCGGAAACAAATTACTTTATAAAAG
*
9577133 GTTTTCATGCAACTCCTTAGAAATTTAAAATGAGTTTGAGATTTTGGGTAGGTTTGGGTTCAAAT
322 GTTTTCATGCAAATCCTTAGAAATTTAAAATGAGTTTGAGATTTTGGGTAGGTTTGGGTTCAAAT
9577198 TTTAAGAATTTATGAACCTCTCTAAAAAC
387 TTTAAGAATTTATGAACCTCTCTAAAAAC
** * ** *
9577227 ATATATATATATGCATTATAAATGAGGACATTAATTTGAAAATGAAACATATGCCAATGATGAT-
1 ATATATATATATGCATTATAAATGAAAACATTAATTTAAAAACAAAACATATGCAAATGATGATA
* ** * **
9577291 AATACATATATAAGAAACAAATTTTCGTATATAAATAGACCACTTGGACACTCCAACATCTAGGT
66 AATACAAATATAAGAAACAAATTTTCAAATATAAAGAGACCACTTGGACACTCCAACATCTAGAC
* * * *
9577356 AGAGTTTGGGTACGAATTTTTATATTTGAAATCCCGTCCTATTA-TTTTTATTATTTTGTATTTT
131 AGAATTTGGATACGAATTTTTATACTTAAAATCCCGTCCTATTATTTTTTATTATTTTGTATTTT
* *
9577420 TATAATCATGG-T-CAAAACAAATTTATTTTGA-CTTGTGGAAGTATATAAAAATTCTTAATGAA
196 TATAATCATGGTTACAAAACAAATATATTTTGAGC-TGTGGAAATATATAAAAATTCTTAATGAA
* * ***
9577482 ATAAAATTTCCTAAATACCCTAACATCTAGGTGCCATTC-GAAAGCAAATTACTTTATAAAAGGT
260 ATAAAATTTCCTAAATACCCCAACAACTAGGCAACATTCGGAAA-CAAATTACTTTATAAAAGGT
*
9577546 TTTCATGCAAATGCTTAGAAATTTAAAATGAGTTT
324 TTTCATGCAAATCCTTAGAAATTTAAAATGAGTTT
9577581 AGGGTTTGAA
Statistics
Matches: 309, Mismatches: 43, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
410 4 0.01
411 128 0.41
412 1 0.00
416 30 0.10
417 88 0.28
419 58 0.19
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (415 bp):
ATATATATATATGCATTATAAATGAAAACATTAATTTAAAAACAAAACATATGCAAATGATGATA
AATACAAATATAAGAAACAAATTTTCAAATATAAAGAGACCACTTGGACACTCCAACATCTAGAC
AGAATTTGGATACGAATTTTTATACTTAAAATCCCGTCCTATTATTTTTTATTATTTTGTATTTT
TATAATCATGGTTACAAAACAAATATATTTTGAGCTGTGGAAATATATAAAAATTCTTAATGAAA
TAAAATTTCCTAAATACCCCAACAACTAGGCAACATTCGGAAACAAATTACTTTATAAAAGGTTT
TCATGCAAATCCTTAGAAATTTAAAATGAGTTTGAGATTTTGGGTAGGTTTGGGTTCAAATTTTA
AGAATTTATGAACCTCTCTAAAAAC
Done.