Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 14 of 34
Found at i:2057854 original size:7 final size:8
Alignment explanation
Indices: 2057739--2057872 Score: 53
Period size: 9 Copynumber: 15.9 Consensus size: 8
2057729 TAATATTATG
2057739 TAAATATA
1 TAAATATA
*
2057747 -AAATATTT
1 TAAATA-TA
2057755 TAAATATAA
1 TAAATAT-A
2057764 TTATAATATAA
1 -TA-AATAT-A
*
2057775 TAAATACA
1 TAAATATA
2057783 TAAATATAA
1 TAAATAT-A
*
2057792 TAAAAATA
1 TAAATATA
*
2057800 TTTAA-A-A
1 -TAAATATA
2057807 TAAATATA
1 TAAATATA
* *
2057815 T-ATTTTA
1 TAAATATA
*
2057822 AAAATTATA
1 TAAA-TATA
2057831 TAATATTATA
1 TAA-A-TATA
2057841 TAAATATA
1 TAAATATA
*
2057849 -AAATATTT
1 TAAATA-TA
2057857 TAAATATAA
1 TAAATAT-A
2057866 TAAATAT
1 TAAATAT
2057873 TATCAGTAAT
Statistics
Matches: 96, Mismatches: 15, Indels: 29
0.69 0.11 0.21
Matches are distributed among these distances:
6 3 0.03
7 16 0.17
8 20 0.21
9 37 0.39
10 13 0.14
11 7 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAATATA
Found at i:2057870 original size:18 final size:18
Alignment explanation
Indices: 2057768--2057873 Score: 85
Period size: 18 Copynumber: 5.8 Consensus size: 18
2057758 ATATAATTAT
**
2057768 AATATAATAAATA-CATA
1 AATATAATAAATATTTTA
*
2057785 AATATAATAAAAATATTTA
1 AATATAATAAATAT-TTTA
*
2057804 AA-ATAAATATATATTTTA
1 AATAT-AATAAATATTTTA
* *
2057822 AAAATTATATAATATTATATA
1 AATATAATA-AATATT-T-TA
2057843 AATAT-A-AAATATTTTA
1 AATATAATAAATATTTTA
2057859 AATATAATAAATATT
1 AATATAATAAATATT
2057874 ATCAGTAATC
Statistics
Matches: 72, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
16 7 0.10
17 14 0.19
18 24 0.33
19 19 0.26
20 2 0.03
21 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATAAATATTTTA
Found at i:2061323 original size:17 final size:17
Alignment explanation
Indices: 2061303--2061343 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2061293 ATGCATCACA
* *
2061303 ATTTATTTTATTCGTTT
1 ATTTATTTTAATCATTT
*
2061320 ATTTACTTTAATCATTT
1 ATTTATTTTAATCATTT
2061337 ATTTATT
1 ATTTATT
2061344 AATTTACTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (17 bp):
ATTTATTTTAATCATTT
Found at i:2066685 original size:37 final size:37
Alignment explanation
Indices: 2066637--2066709 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
2066627 TTTCTTTTGA
*
2066637 TTTTATGTCTTAATAGTCGTTAAGAAAAGTACAAAAT
1 TTTTATGTCTTAATAGTCATTAAGAAAAGTACAAAAT
2066674 TTTTATGTCTTAATAGTCATTAAGAAAAGTACAAAA
1 TTTTATGTCTTAATAGTCATTAAGAAAAGTACAAAA
2066710 AACTAACACT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.37
Consensus pattern (37 bp):
TTTTATGTCTTAATAGTCATTAAGAAAAGTACAAAAT
Found at i:2069792 original size:13 final size:13
Alignment explanation
Indices: 2069774--2069800 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2069764 TCTGCTTTTA
2069774 TGAAAAATCATTT
1 TGAAAAATCATTT
2069787 TGAAAAATCATTT
1 TGAAAAATCATTT
2069800 T
1 T
2069801 TTGTGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TGAAAAATCATTT
Found at i:2069801 original size:14 final size:14
Alignment explanation
Indices: 2069769--2069801 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2069759 AAATATCTGC
2069769 TTTTATGAAAAATCA
1 TTTT-TGAAAAATCA
2069784 -TTTTGAAAAATCA
1 TTTTTGAAAAATCA
2069797 TTTTT
1 TTTTT
2069802 TGTGAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTTTGAAAAATCA
Found at i:2075903 original size:13 final size:13
Alignment explanation
Indices: 2075885--2075910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2075875 TACAGCAAGT
2075885 ATGTATCGATACA
1 ATGTATCGATACA
2075898 ATGTATCGATACA
1 ATGTATCGATACA
2075911 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2077165 original size:58 final size:58
Alignment explanation
Indices: 2077075--2077342 Score: 238
Period size: 58 Copynumber: 4.8 Consensus size: 58
2077065 GATGTTTTCG
* *
2077075 TGATTTATGAGCC-TTTATGCAATTTCATGCACTTTAAGATCATTCTAGTCATTTTGCA
1 TGATTTATGA-CCATTTATGTAATTTCATGCACTTTAAGATCATTCTAGTCATTTTCCA
* *
2077133 TGATTTATGACCACTTATGTAATTTCATGCACTTT-AGAGTCATTTTAGTCATTTTCCA
1 TGATTTATGACCATTTATGTAATTTCATGCACTTTAAGA-TCATTCTAGTCATTTTCCA
* * * * * * *
2077191 TGATTTATGACGATTTAGGCATTTTTCAAGCACTTTAAG---------GGCATTTTTCA
1 TGATTTATGACCATTTATGTA-ATTTCATGCACTTTAAGATCATTCTAGTCATTTTCCA
* * * * *
2077241 TAATTTATGACCATTTATATAATCTCAAGCA-TTTTAGAGTCATTCTAGTCATTTTCCA
1 TGATTTATGACCATTTATGTAATTTCATGCACTTTAAGA-TCATTCTAGTCATTTTCCA
* *
2077299 TGATTTATGACCATTTAT-TCAATTTCATGCATTTTAGGATCATT
1 TGATTTATGACCATTTATGT-AATTTCATGCACTTTAAGATCATT
2077343 TTCCATGATT
Statistics
Matches: 167, Mismatches: 27, Indels: 32
0.74 0.12 0.14
Matches are distributed among these distances:
48 5 0.03
49 8 0.05
50 25 0.15
57 6 0.04
58 104 0.62
59 17 0.10
60 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (58 bp):
TGATTTATGACCATTTATGTAATTTCATGCACTTTAAGATCATTCTAGTCATTTTCCA
Found at i:2077186 original size:29 final size:29
Alignment explanation
Indices: 2077096--2077186 Score: 66
Period size: 29 Copynumber: 3.1 Consensus size: 29
2077086 CCTTTATGCA
*
2077096 ATTTCATGCACTTTA-AGATCATTCTAGTC
1 ATTTCATGCACTTTAGAG-TCATTTTAGTC
* * *
2077125 ATTTTGCATG-A-TTTATGA-CCA-CTTATGTA
1 A-TTT-CATGCACTTTA-GAGTCATTTTA-GTC
2077154 ATTTCATGCACTTTAGAGTCATTTTAGTC
1 ATTTCATGCACTTTAGAGTCATTTTAGTC
2077183 ATTT
1 ATTT
2077187 TCCATGATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 18
0.65 0.10 0.25
Matches are distributed among these distances:
27 4 0.09
28 8 0.17
29 22 0.48
30 7 0.15
31 5 0.11
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (29 bp):
ATTTCATGCACTTTAGAGTCATTTTAGTC
Found at i:2077315 original size:108 final size:107
Alignment explanation
Indices: 2077124--2077365 Score: 315
Period size: 108 Copynumber: 2.3 Consensus size: 107
2077114 TCATTCTAGT
* * * * * *
2077124 CATTTTGCATGATTTATGACCACTTATGTAATTTCATGCACTTTAGAGTCATTTTAGTCATTTTC
1 CATTTTCCATGATTTATGACCATTTATATAATCTCAAGCACTTTAGAGTCATTCTAGTCATTTTC
* *
2077189 CATGATTTATGACGATTTAGGCATTTTTCAAGCACTTTAAGG-G
66 CATGATTTATGACCATTTAGGCA-ATTTCAAGCA-TTTAAGGAG
* * *
2077232 CATTTTTCATAATTTATGACCATTTATATAATCTCAAGCATTTTAGAGTCATTCTAGTCATTTTC
1 CATTTTCCATGATTTATGACCATTTATATAATCTCAAGCACTTTAGAGTCATTCTAGTCATTTTC
** * * *
2077297 CATGATTTATGACCATTTATTCAATTTCATGCATTTTAGGAT
66 CATGATTTATGACCATTTAGGCAATTTCAAGCATTTAAGGAG
2077339 CATTTTCCATGATTTATGACCATTTAT
1 CATTTTCCATGATTTATGACCATTTAT
2077366 GCAATTTTAT
Statistics
Matches: 116, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
106 6 0.05
107 33 0.28
108 77 0.66
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (107 bp):
CATTTTCCATGATTTATGACCATTTATATAATCTCAAGCACTTTAGAGTCATTCTAGTCATTTTC
CATGATTTATGACCATTTAGGCAATTTCAAGCATTTAAGGAG
Found at i:2077334 original size:29 final size:29
Alignment explanation
Indices: 2077244--2077343 Score: 73
Period size: 29 Copynumber: 3.4 Consensus size: 29
2077234 TTTTTCATAA
* *
2077244 TTTATGACCATTTATAT-AATCTCAAGCAT
1 TTTATGACCATTTAT-TCAATTTCATGCAT
* * *
2077273 TTTA-GAGTCATTCTAGTCATTTTCCATG-A-
1 TTTATGA-CCATT-TATTCAATTT-CATGCAT
2077302 TTTATGACCATTTATTCAATTTCATGCAT
1 TTTATGACCATTTATTCAATTTCATGCAT
* *
2077331 TTTAGGATCATTT
1 TTTATGACCATTT
2077344 TCCATGATTT
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
27 4 0.07
28 11 0.20
29 28 0.52
30 8 0.15
31 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (29 bp):
TTTATGACCATTTATTCAATTTCATGCAT
Found at i:2077425 original size:58 final size:58
Alignment explanation
Indices: 2077361--2077873 Score: 356
Period size: 58 Copynumber: 8.9 Consensus size: 58
2077351 TTTATGACCA
* * * * *
2077361 TTTATGCAATTTTATGTATGATGGGGTTATTTAAGTCATTTTTCATAATCTAAAGACC
1 TTTATGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTCATAATCTAAGGACT
* * * * * *
2077419 TTTATGCAATTTTATTTATGTTAGGGT-ATTTTGTTCA-TTTTCTATGATCTAAGGACT
1 TTTATGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTC-ATAATCTAAGGACT
* * * * *
2077476 TTTATGCCATTTCATATATGCTAGGGGTCATTTAAGTCATTTTTCATGATCTAAGGACT
1 TTTATGCAATTTTATATATGAT-GGGGTCATTTAGGTCATTTTTCATAATCTAAGGACT
* * * * * *
2077535 TTTATTTC-ATTTCATATATGTTAGGTTCATTTAGGTCATTTTTCATGAA-CTAGGGACT
1 TTTA-TGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTCAT-AATCTAAGGACT
* ** * * * *
2077593 ATTATATAATTTTATGTATGTTAGAGTCATTTAGGTCA-TTTTCTATAATCTAAGGACT
1 TTTATGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTC-ATAATCTAAGGACT
* * * * * * * *
2077651 TTTATTCCATTTCATATATGCTGGAGTCATTTAGGTCATTTTTTATTATCTAAAGACT
1 TTTATGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTCATAATCTAAGGACT
* * * * *
2077709 TTTATGCAACTTTATGA-AT-ATTGGGGTCATTTAAGT-AATTTTCATGAT-TTAGGAACT
1 TTTATGCAATTTTAT-ATATGA-TGGGGTCATTTAGGTCATTTTTCATAATCTAAGG-ACT
* * * * *
2077766 TTTATGTAATTTTATATAT-ATTGGGGTTATTTAGGTTA-TATTC-TAAGATCTAAAGACT
1 TTTATGCAATTTTATATATGA-TGGGGTCATTTAGGTCATTTTTCAT-A-ATCTAAGGACT
* ** *
2077824 TTTATGCAATTTCATATAT-ATTAGG--A-TTAGGTCATTTTTCATGATCTAAG
1 TTTATGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTCATAATCTAAG
2077874 AATTTTCATG
Statistics
Matches: 364, Mismatches: 71, Indels: 44
0.76 0.15 0.09
Matches are distributed among these distances:
54 13 0.04
55 5 0.01
56 11 0.03
57 93 0.26
58 188 0.52
59 47 0.13
60 7 0.02
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (58 bp):
TTTATGCAATTTTATATATGATGGGGTCATTTAGGTCATTTTTCATAATCTAAGGACT
Found at i:2077487 original size:29 final size:29
Alignment explanation
Indices: 2077454--2077539 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 29
2077444 GTATTTTGTT
2077454 CATTTTCTATGATCTAAGGACTTTTATGC
1 CATTTTCTATGATCTAAGGACTTTTATGC
* * * * *
2077483 CA-TTTCATAT-ATGCTAGGGGTCATTTAAGT
1 CATTTTC-TATGAT-CTA-AGGACTTTTATGC
2077513 CATTTT-TCATGATCTAAGGACTTTTAT
1 CATTTTCT-ATGATCTAAGGACTTTTAT
2077540 TTCATTTCAT
Statistics
Matches: 42, Mismatches: 9, Indels: 12
0.67 0.14 0.19
Matches are distributed among these distances:
28 6 0.14
29 16 0.38
30 15 0.36
31 5 0.12
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (29 bp):
CATTTTCTATGATCTAAGGACTTTTATGC
Found at i:2077512 original size:116 final size:115
Alignment explanation
Indices: 2077361--2077842 Score: 424
Period size: 116 Copynumber: 4.2 Consensus size: 115
2077351 TTTATGACCA
* * * * *
2077361 TTTATGCAATTTTATGTATGATGGGGTTATTTAAGTCATTTTTCATAATCTAAAGACCTTTATGC
1 TTTATGCAATTTCATATATG-TGGGGTCATTTAAGTCATTTTTCATAATCTAAGGACTTTTATGC
* * * * *
2077426 AATTTTATTTATGTTAGGGT-ATTTTGTTCATTTTCTATGATCTAAGGACT
65 AATTTCATATATGTTAGGGTCATTTAGGTCATTTTCTATGATCTAAAGACT
* *
2077476 TTTATGCCATTTCATATATGCTAGGGGTCATTTAAGTCATTTTTCATGATCTAAGGACTTTTATT
1 TTTATGCAATTTCATATATG-T-GGGGTCATTTAAGTCATTTTTCATAATCTAAGGACTTTTA-T
* * * **
2077541 TC-ATTTCATATATGTTAGGTTCATTTAGGTCATTTT-TCATGAACTAGGGACT
63 GCAATTTCATATATGTTAGGGTCATTTAGGTCATTTTCT-ATGATCTAAAGACT
* ** * * * * * *
2077593 ATTATATAATTTTATGTATGTTAGAGTCATTTAGGTCA-TTTTCTATAATCTAAGGACTTTTATT
1 TTTATGCAATTTCATATATG-TGGGGTCATTTAAGTCATTTTTC-ATAATCTAAGGACTTTTATG
* * * *
2077657 CCATTTCATATATGCT-GGAGTCATTTAGGTCATTTTTTATTATCTAAAGACT
64 CAATTTCATATATGTTAGG-GTCATTTAGGTCATTTTCTATGATCTAAAGACT
* * *
2077709 TTTATGCAACTTT-ATGAATAT-TGGGGTCATTTAAGT-AATTTTCATGAT-TTAGGAACTTTTA
1 TTTATGCAA-TTTCAT--ATATGTGGGGTCATTTAAGTCATTTTTCATAATCTAAGG-ACTTTTA
* * * * * * * *
2077770 TGTAATTTTATATATATTGGGGTTATTTAGGTTATATTCTAAGATCTAAAGACT
62 TGCAATTTCATATATGTTAGGGTCATTTAGGTCATTTTCTATGATCTAAAGACT
2077824 TTTATGCAATTTCATATAT
1 TTTATGCAATTTCATATAT
2077843 ATTAGGATTA
Statistics
Matches: 298, Mismatches: 54, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
113 4 0.01
114 7 0.02
115 90 0.30
116 149 0.50
117 45 0.15
118 3 0.01
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (115 bp):
TTTATGCAATTTCATATATGTGGGGTCATTTAAGTCATTTTTCATAATCTAAGGACTTTTATGCA
ATTTCATATATGTTAGGGTCATTTAGGTCATTTTCTATGATCTAAAGACT
Found at i:2080156 original size:13 final size:13
Alignment explanation
Indices: 2080138--2080163 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2080128 TGGTTGATTC
2080138 TTGTATCGATACA
1 TTGTATCGATACA
2080151 TTGTATCGATACA
1 TTGTATCGATACA
2080164 ATCTTCCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2080232 original size:13 final size:13
Alignment explanation
Indices: 2080214--2080240 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2080204 CGCCAGTTTT
2080214 ATGTATCGATACA
1 ATGTATCGATACA
2080227 ATGTATCGATACA
1 ATGTATCGATACA
2080240 A
1 A
2080241 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2082645 original size:22 final size:21
Alignment explanation
Indices: 2082610--2082659 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2082600 TTTATTGATG
*
2082610 ATTTTG-A-TGAAAAATGAAGT
1 ATTTTGAAGTGAAAAAT-AAGA
2082630 ATTTTGAAGTGAAAAATAAGA
1 ATTTTGAAGTGAAAAATAAGA
*
2082651 AATTTGAAG
1 ATTTTGAAG
2082660 AAGATTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.23
21 12 0.46
22 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAATAAGA
Found at i:2082656 original size:21 final size:22
Alignment explanation
Indices: 2082617--2082659 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2082607 ATGATTTTGA
* *
2082617 TGAAAAATGAAGTATTTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
2082639 TGAAAAAT-AAGAAATTTGAAG
1 TGAAAAATGAAGAAATTTGAAG
2082660 AAGATTTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (22 bp):
TGAAAAATGAAGAAATTTGAAG
Found at i:2088354 original size:19 final size:20
Alignment explanation
Indices: 2088310--2088362 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 20
2088300 CTTCCAGTTT
* **
2088310 CATGTATCGATACAGTTGTC
1 CATGTATCGATACAGATGAA
2088330 CATGTATCGATACA-ATGAA
1 CATGTATCGATACAGATGAA
*
2088349 CATGTATTGATACA
1 CATGTATCGATACA
2088363 TTGTATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAGATGAA
Found at i:2091305 original size:19 final size:19
Alignment explanation
Indices: 2091281--2091334 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
2091271 TTTGTATCGA
2091281 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
2091300 TACATTGTATCGATACATG
1 TACATTGTATCGATACATG
*
2091319 CACAATTGTATCGATA
1 TAC-ATTGTATCGATA
2091335 TATGAAACTG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
TACATTGTATCGATACATG
Found at i:2091317 original size:13 final size:13
Alignment explanation
Indices: 2091272--2091298 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2091262 ACATTATTCT
2091272 TTGTATCGATACA
1 TTGTATCGATACA
2091285 TTGTATCGATACA
1 TTGTATCGATACA
2091298 T
1 T
2091299 GTACATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2092645 original size:13 final size:13
Alignment explanation
Indices: 2092627--2092652 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2092617 TACAGCAAGT
2092627 ATGTATCGATACA
1 ATGTATCGATACA
2092640 ATGTATCGATACA
1 ATGTATCGATACA
2092653 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2094194 original size:15 final size:15
Alignment explanation
Indices: 2094174--2094208 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
2094164 AACCATCAAA
2094174 GATGATGAAGATAAT
1 GATGATGAAGATAAT
*
2094189 GATGATGATGATAAT
1 GATGATGAAGATAAT
2094204 GATGA
1 GATGA
2094209 AGTTGACTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (15 bp):
GATGATGAAGATAAT
Found at i:2095213 original size:19 final size:19
Alignment explanation
Indices: 2095166--2095251 Score: 85
Period size: 19 Copynumber: 4.7 Consensus size: 19
2095156 ATTCCAATAA
*
2095166 TTTGTATCGATACATTCAGT
1 TTTGTATCGATACA-TAAGT
**
2095186 AAATGTATCGATACATAAGT
1 -TTTGTATCGATACATAAGT
2095206 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2095221 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2095238 TTTGTATCGATACA
1 TTTGTATCGATACA
2095252 ATGTATCGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 23 0.43
20 4 0.07
21 12 0.22
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:2095226 original size:13 final size:13
Alignment explanation
Indices: 2095208--2095232 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2095198 ACATAAGTTT
2095208 TGTATCGATACAA
1 TGTATCGATACAA
2095221 TGTATCGATACA
1 TGTATCGATACA
2095233 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2095228 original size:32 final size:32
Alignment explanation
Indices: 2095187--2095259 Score: 146
Period size: 32 Copynumber: 2.3 Consensus size: 32
2095177 ACATTCAGTA
2095187 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTTTGTATCGATAC
2095219 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTTTTGTATCGATAC
2095251 AATGTATCG
1 AATGTATCG
2095260 CTACGAAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTTTTGTATCGATAC
Found at i:2095302 original size:21 final size:21
Alignment explanation
Indices: 2095276--2095317 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
2095266 AGCTACTGCC
*
2095276 AAGGAAATGTATTGATACATT
1 AAGGAAATGTATCGATACATT
2095297 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
2095318 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:2095322 original size:13 final size:13
Alignment explanation
Indices: 2095304--2095329 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2095294 ATTAAGGAAA
2095304 TGTATCGATACAT
1 TGTATCGATACAT
2095317 TGTATCGATACAT
1 TGTATCGATACAT
2095330 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2096679 original size:52 final size:51
Alignment explanation
Indices: 2096549--2096722 Score: 217
Period size: 52 Copynumber: 3.4 Consensus size: 51
2096539 AATTGTTCAT
* * *
2096549 AATCGGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCAC
1 AATCGAGGATACTCCAACCCCGATTTTATTTCAAAAACACCAATTTTCCAC
* **
2096600 AATC-AGGGATACTCCAACCCCGGTTTTATCTTC-AAAACACCAATTTTCCTTT
1 AATCGA-GGATACTCCAACCCCGATTTTAT-TTCAAAAACACCAATTTTCC-AC
* *
2096652 AATCGAGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCAC
1 AATCGAGGATACTCCAACCCCGATTTTATTT-CAAAAACACCAATTTTCCAC
*
2096704 AATCGAGGATACTCTAACC
1 AATCGAGGATACTCCAACC
2096723 TCGTTATTTC
Statistics
Matches: 105, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
51 43 0.41
52 46 0.44
53 16 0.15
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.30
Consensus pattern (51 bp):
AATCGAGGATACTCCAACCCCGATTTTATTTCAAAAACACCAATTTTCCAC
Found at i:2096884 original size:79 final size:77
Alignment explanation
Indices: 2096735--2096916 Score: 195
Period size: 79 Copynumber: 2.3 Consensus size: 77
2096725 GTTATTTCAT
* ** * **
2096735 CAGGGATACTCCAACCCTGTTACCTCCGAGGGGATACTCCAGCCCCGGCTTTATTCCTAAAATAT
1 CAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGAATTTATTCCT-AAATAT
* *
2096800 TGATTTCTCATAA
65 CGATTTCTCACAA
* * *
2096813 TTAGGGATACTCCGACCCCGTTATTTCCGAGGGGATACTCTAACCCCGAATTTATTTCCT-AATC
1 -CAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGAATTTA-TTCCTAAAT-
*
2096877 ATCGATTTTTCACAA
63 ATCGATTTCTCACAA
*
2096892 CCGGCGATACTCCAACCCCGTTATT
1 CAGG-GATACTCCAACCCCGTTATT
2096917 ATCTCCAAAA
Statistics
Matches: 85, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
78 5 0.06
79 75 0.88
80 5 0.06
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.30
Consensus pattern (77 bp):
CAGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGAATTTATTCCTAAATATC
GATTTCTCACAA
Found at i:2103248 original size:20 final size:20
Alignment explanation
Indices: 2103225--2103297 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2103215 ACAATTCAAA
2103225 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2103245 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2103266 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2103286 GTATCGATACAT
1 GTATCGATACAT
2103298 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2103269 original size:21 final size:21
Alignment explanation
Indices: 2103243--2103318 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2103233 ACATGTTGCA
2103243 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2103264 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2103284 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
2103305 TTGTATCGATACAT
1 ATGTATCGATACAT
2103319 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2103276 original size:41 final size:41
Alignment explanation
Indices: 2103225--2103318 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2103215 ACAATTCAAA
*
2103225 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
2103266 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2103307 GTATCGATACAT
1 GTATCGATACAT
2103319 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2103375 original size:13 final size:13
Alignment explanation
Indices: 2103357--2103382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2103347 TACATCAAGT
2103357 ATGTATCGATACA
1 ATGTATCGATACA
2103370 ATGTATCGATACA
1 ATGTATCGATACA
2103383 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2108385 original size:52 final size:52
Alignment explanation
Indices: 2108252--2108392 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
2108242 TGAAAAGTTA
2108252 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
2108304 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
2108356 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
2108393 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:2108399 original size:13 final size:13
Alignment explanation
Indices: 2108381--2108405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2108371 CAAAAATCAG
2108381 TGTATCGATACAA
1 TGTATCGATACAA
2108394 TGTATCGATACA
1 TGTATCGATACA
2108406 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2108488 original size:13 final size:13
Alignment explanation
Indices: 2108470--2108494 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2108460 CAAAAAAATA
2108470 TGTATCGATACAT
1 TGTATCGATACAT
2108483 TGTATCGATACA
1 TGTATCGATACA
2108495 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2108490 original size:33 final size:33
Alignment explanation
Indices: 2108448--2108514 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2108438 AGTAGCTTAA
2108448 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2108481 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2108514 A
1 A
2108515 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:2108593 original size:21 final size:21
Alignment explanation
Indices: 2108552--2108593 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2108542 GTTGGGACCT
*
2108552 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
2108573 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
2108594 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:2109508 original size:171 final size:168
Alignment explanation
Indices: 2109313--2109697 Score: 611
Period size: 171 Copynumber: 2.3 Consensus size: 168
2109303 TTTTAGAGAT
2109313 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAA-GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
2109378 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
* *
2109443 TGTCAACGTGCTGATTCAAGGCCAGC-TACATTGAACT-TAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTA-A-AG-A-TGGAAA
* * *
2109484 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAG-TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
2109549 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
2109614 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
*
2109653 -AT---GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
2109698 GTGCCAATGT
Statistics
Matches: 203, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
164 40 0.20
165 1 0.00
168 3 0.01
169 4 0.02
170 2 0.01
171 151 0.74
172 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (168 bp):
GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAG
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGAT
GTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
Found at i:2109530 original size:49 final size:49
Alignment explanation
Indices: 2109384--2109542 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
2109374 AAAAGTGATA
* * * * *
2109384 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
2109435 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
2109488 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
2109537 ATGATG
1 AAGATG
2109543 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:2109645 original size:45 final size:42
Alignment explanation
Indices: 2109593--2109722 Score: 120
Period size: 43 Copynumber: 3.0 Consensus size: 42
2109583 ACGATATTGG
* *
2109593 GCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 GCTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCA
* *
2109638 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
* * **
2109680 GC-TATA-TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTTAAAGATGGA---AAAGGTGCCAACATGCTGATTCAAGGCCA
2109723 TCTACATTGG
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
40 4 0.05
41 3 0.04
42 23 0.31
43 32 0.43
44 1 0.01
45 11 0.15
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (42 bp):
GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
Found at i:2109674 original size:42 final size:41
Alignment explanation
Indices: 2109622--2109773 Score: 126
Period size: 43 Copynumber: 3.4 Consensus size: 41
2109612 GATGTCAACG
*
2109622 TGCTGATTCAAGGCCAGCTTAAAGATGGA-AAATGTGCCAATA
1 TGCTGATTCAAGGCCAGC-TAAA-ATGGATAAAGGTGCCAATA
* * *
2109664 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTAAAATGGA--TAAAGGTGCCAATA
* * *
2109707 TGCTGATTCAAGGCCATCTACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTAAAATGGA--T-AA-A-G--G-TGCCAATA
2109756 TGCTGATTCAAGGCCAGC
1 TGCTGATTCAAGGCCAGC
2109774 GATATTGGAC
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
40 4 0.04
41 3 0.03
42 18 0.19
43 39 0.42
44 2 0.02
45 1 0.01
46 1 0.01
48 1 0.01
49 24 0.26
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.26
Consensus pattern (41 bp):
TGCTGATTCAAGGCCAGCTAAAATGGATAAAGGTGCCAATA
Found at i:2109754 original size:49 final size:49
Alignment explanation
Indices: 2109656--2110135 Score: 704
Period size: 49 Copynumber: 9.9 Consensus size: 49
2109646 ATGGAAAATG
*
2109656 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-G--G-
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
2109699 TGCCAATGTGCTGATTCAAGGCCATCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
2109748 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
2109797 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
2109846 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
2109895 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
2109944 TGCCAATATGCTGATTCAAGGCCAG-TGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCT-ACATTGGACTTAAAGATGAAGA
* *
2109993 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* * *
2110042 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
* *
2110091 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG
1 TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
2110136 GAAAAGGCCA
Statistics
Matches: 389, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
43 35 0.09
44 2 0.01
45 1 0.00
46 1 0.00
48 2 0.01
49 347 0.89
50 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:2109835 original size:98 final size:98
Alignment explanation
Indices: 2109656--2110135 Score: 882
Period size: 98 Copynumber: 5.0 Consensus size: 98
2109646 ATGGAAAATG
* *
2109656 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGATT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
*
2109715 CAAGGCCATCTACATTGGACTTAAAGATGAAGA
66 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
2109748 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
2109813 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
66 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
2109846 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
2109911 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
66 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
*
2109944 TGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
2110009 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
66 CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
2110042 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
2110107 CAAGGCCAGCTACATTGGACTTAAAGATG
66 CAAGGCCAGCTACATTGGACTTAAAGATG
2110136 GAAAAGGCCA
Statistics
Matches: 377, Mismatches: 5, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
92 37 0.10
96 1 0.00
98 339 0.90
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (98 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGT
CAAGGCCAGCTACATTGGACTTAAAGATGAAGA
Found at i:2110204 original size:33 final size:34
Alignment explanation
Indices: 2110165--2110229 Score: 123
Period size: 33 Copynumber: 1.9 Consensus size: 34
2110155 GGCTTAGAGG
2110165 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
2110198 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
2110230 GGAGAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.84
34 5 0.16
ACGTcount: A:0.17, C:0.18, G:0.37, T:0.28
Consensus pattern (34 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
Found at i:2110272 original size:34 final size:33
Alignment explanation
Indices: 2110234--2110647 Score: 412
Period size: 34 Copynumber: 12.8 Consensus size: 33
2110224 AGGAAGGGAG
* *
2110234 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
2110268 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
2110303 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
2110333 --A-GTGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
2110364 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
2110398 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA--AA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGAA
**
2110430 AAA-GTGCCACGGAGTTGTGGGCTTTGAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
2110462 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
2110497 GAAGGTGCCACGGAGTTGTGGCCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
2110529 AAAGGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AGGAA
* *
2110563 AAAAGTGCCACGGAATTGTGGGCTTTAAAA-G--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
2110594 ---GGTGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
2110623 AAAGGTGCCACGGAGTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
2110648 TGAAGAAAAA
Statistics
Matches: 321, Mismatches: 35, Indels: 50
0.79 0.09 0.12
Matches are distributed among these distances:
27 23 0.07
28 25 0.08
29 1 0.00
30 23 0.07
32 59 0.18
33 16 0.05
34 113 0.35
35 55 0.17
36 6 0.02
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:2110449 original size:160 final size:154
Alignment explanation
Indices: 2110266--2110653 Score: 494
Period size: 160 Copynumber: 2.4 Consensus size: 154
2110256 CTTAAAAGGG
*
2110266 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAGGAA-AAGGTGCCACGGAGTTGTGGGCTTTAA
* *
2110331 AGA-GTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAG
64 AGAGGTGCCACGGAGTCGTGGCCTTT-AAAGG-AAAA-GGTGCCACGGAGTTATGGACTTA-AAG
*
2110395 -GAAAAAGAGTGCCACAGAGTTGTGGGCTTTT
125 AGAAAAA-AGTGCCACAGAATTGTGGGC-TTT
* * *
2110426 AAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGG-AAAAG-GTGCCACGGAGTTGTGGGCTTT--
* *
2110491 AAAGAAGAAGGTGCCACGGAGTTGTGGCCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAA
62 --A-AAG-AGGTGCCACGGAGTCGTGGCCTTTAAAGGAAAAGGTGCCACGGAGTTATGGACTTAA
*
2110556 AGATGAAAAAAGTGCCACGGAATTGTGGGCTTT
123 AGA-GAAAAAAGTGCCACAGAATTGTGGGCTTT
* *
2110589 -AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAG
2110653 A
66 A
2110654 AAAAATGCCA
Statistics
Matches: 202, Mismatches: 15, Indels: 28
0.82 0.06 0.11
Matches are distributed among these distances:
154 1 0.00
155 3 0.01
159 6 0.03
160 72 0.36
161 5 0.02
162 30 0.15
163 6 0.03
164 40 0.20
165 13 0.06
166 6 0.03
167 20 0.10
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (154 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTAAAG
AGGTGCCACGGAGTCGTGGCCTTTAAAGGAAAAGGTGCCACGGAGTTATGGACTTAAAGAGAAAA
AAGTGCCACAGAATTGTGGGCTTT
Found at i:2110451 original size:64 final size:65
Alignment explanation
Indices: 2110329--2110658 Score: 313
Period size: 64 Copynumber: 5.0 Consensus size: 65
2110319 TGTGGGCTTT
* * *
2110329 AAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-TAA--AAAAA-GGTGCCACGGAGTTGTGGGCTTAGAA
2110394 GGAA
62 GGAA
* *
2110398 AAAGAGTGCCACAGAGTTGTGGGCTTTTAAAAAAA-GTGCCACGGAGTTGTGGGCTTTGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTTAAAAAAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAA
* * *
2110462 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGCCTTTA-AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-TAAA-AA-AAGGTGCCACGGAGTTGTGGGC-TTAGAA
2110526 GG-A
62 GGAA
* ** * *
2110529 AAAG-GTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTT-----
1 AAAGAGTGCCACGGAGTTGTGGGCTTTTA-A--AAAAAGGTGCCACGGAGTTGTGGGCTTAGAAG
*
2110588 -TA
63 GAA
* * *
2110590 AAAGGGTGCCACGGAGTTGTGGGC-TTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTTAAA--AAAAGGTGCCACGGAGTTGTGGGCTTAGAAGG
2110654 AA
64 AA
2110656 AAA
1 AAA
2110659 TGCCATTGAG
Statistics
Matches: 223, Mismatches: 20, Indels: 39
0.79 0.07 0.14
Matches are distributed among these distances:
58 1 0.00
60 25 0.11
61 7 0.03
62 18 0.08
64 54 0.24
65 7 0.03
66 50 0.22
67 9 0.04
68 25 0.11
69 27 0.12
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (65 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTTAAAAAAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAA
Found at i:2110464 original size:32 final size:32
Alignment explanation
Indices: 2110214--2110741 Score: 410
Period size: 34 Copynumber: 16.3 Consensus size: 32
2110204 CACCGACTTG
*
2110214 TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGT
1 TGTGGGCTTTA--AA-GGAAAAAG-TGCCACGGAGT
* *
2110250 TGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAA-GG-AAAA-AGTGCCACGGAGT
* *
2110285 TGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAGGAA-AAAGTGCCACGGAGT
2110319 TGTGGGCTTTAAA-G----AGTGCCACGGAGT
1 TGTGGGCTTTAAAGGAAAAAGTGCCACGGAGT
*
2110346 CGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGT
1 TGTGGGCTTT-AAAGGAAAAA--GTGCCACGGAGT
* *
2110381 TATGGGC-TTAGAAGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTA-AAGG-AAAA-AGTGCCACGGAGT
*
2110415 TGTGGGCTTTTAA--AAAAAGTGCCACGGAGT
1 TGTGGGCTTTAAAGGAAAAAGTGCCACGGAGT
* *
2110445 TGTGGGCTTTGAAGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTTAAAGG-AAAA-AGTGCCACGGAGT
* *
2110479 TGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTT-AAAGGAA-AAAGTGCCACGGAGT
* *
2110513 TGTGGCCTTTAAAGGAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAGGAAAAAGTGCCACGGAGT
* *
2110545 TGTGGAC-TTAAAGATGAAAAAAGTGCCACGGAAT
1 TGTGGGCTTTAAAG--G-AAAAAGTGCCACGGAGT
2110579 TGTGGGCTTTAAAAGG-----GTGCCACGGAGT
1 TGTGGGCTTT-AAAGGAAAAAGTGCCACGGAGT
*
2110607 TGTGGGCTTTAAAGGAAAAGGTGCCACGGAGT
1 TGTGGGCTTTAAAGGAAAAAGTGCCACGGAGT
* * **
2110639 TGTGGGCTTTGAA-GAAAAAATGCCATTGAGT
1 TGTGGGCTTTAAAGGAAAAAGTGCCACGGAGT
* * * * *
2110670 CGTGGACCTT-GA-GACAAAA-TGCCACTGAGT
1 TGTGGGCTTTAAAGGA-AAAAGTGCCACGGAGT
* * *
2110700 CGTGGACTTTAAA-GAAAAAGATGCCACTGAGT
1 TGTGGGCTTTAAAGGAAAAAG-TGCCACGGAGT
* *
2110732 CGTGGACTTT
1 TGTGGGCTTT
2110742 GAGCAGAGAT
Statistics
Matches: 416, Mismatches: 40, Indels: 76
0.78 0.08 0.14
Matches are distributed among these distances:
27 26 0.06
28 24 0.06
29 1 0.00
30 50 0.12
31 38 0.09
32 67 0.16
33 16 0.04
34 120 0.29
35 55 0.13
36 19 0.05
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.22
Consensus pattern (32 bp):
TGTGGGCTTTAAAGGAAAAAGTGCCACGGAGT
Found at i:2110481 original size:194 final size:190
Alignment explanation
Indices: 2110234--2110658 Score: 545
Period size: 194 Copynumber: 2.2 Consensus size: 190
2110224 AGGAAGGGAG
* ** *
2110234 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAG-TGCCACGGAGTTGTGGGCTTTGAA-GGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAA
* *
2110299 AGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA-G-A-GTGCCACGGAGTCGTGGGCTTTAAA-A
64 AGAAGAAGGTGCCACGGAGTTGTGGCCTTTAAAGGAAGGTGCCACGGAGTCGTGGAC-TTAAAGA
* *
2110360 GGAAAAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
128 GGAAAAA-AGTGCCACGGAATTATGGGCTT------AAAAAGAGTGCCACAGAGTTGTGGGC-TT
2110425 TAAA-A
185 TAAAGA
2110430 AAAGTGCCACGGAGTTGTGGGCTTTGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAG
1 AAAGTGCCACGGAGTTGTGGGCTTTGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAG
* *
2110495 AAGAAGGTGCCACGGAGTTGTGGCCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGACTTAAAGAT
66 AAGAAGGTGCCACGGAGTTGTGGCCTTTAAAGG--AAGGTGCCACGGAGTCGTGGACTTAAAGAG
* * * *
2110560 GAAAAAAGTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGA
129 GAAAAAAGTGCCACGGAATTATGGGCTTAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAA-GA
*
2110623 AAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 AAA-GTGCCACGGAGTTGTGGGCTTTGAAGGAAAAA
2110659 TGCCATTGAG
Statistics
Matches: 205, Mismatches: 15, Indels: 20
0.85 0.06 0.08
Matches are distributed among these distances:
191 6 0.03
192 23 0.11
193 4 0.02
194 97 0.47
195 22 0.11
196 4 0.02
198 25 0.12
199 24 0.12
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (190 bp):
AAAGTGCCACGGAGTTGTGGGCTTTGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAG
AAGAAGGTGCCACGGAGTTGTGGCCTTTAAAGGAAGGTGCCACGGAGTCGTGGACTTAAAGAGGA
AAAAAGTGCCACGGAATTATGGGCTTAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAGA
Found at i:2110689 original size:30 final size:30
Alignment explanation
Indices: 2110628--2110772 Score: 157
Period size: 31 Copynumber: 4.7 Consensus size: 30
2110618 AAGGAAAAGG
* * * *
2110628 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAA
1 TGCCACTGAGTCGTGGACTTTG-AGACAAAA
* *
2110659 TGCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTGAGACAAAA
* *
2110689 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGA
1 TGCCACTGAGTCGTGGACTTT-GAGACAAA-A
*
2110721 TGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAGACA-A-AA
2110752 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
2110773 TTTTTTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 27 0.28
31 47 0.48
32 23 0.24
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.25
Consensus pattern (30 bp):
TGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:2110742 original size:93 final size:93
Alignment explanation
Indices: 2110596--2110769 Score: 224
Period size: 93 Copynumber: 1.9 Consensus size: 93
2110586 TTTAAAAGGG
* * * * * *
2110596 TGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAG-AAAAAAT
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTG-AGCAAAAAAT
*
2110660 GCCATTGAGTCGTGGACCTTGAGACAAAA
65 GCCACTGAGTCGTGGACCTTGAGACAAAA
* * * * *
2110689 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGCAGAGATTG
1 TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
2110754 CCACTGAGTCGTGGAC
66 CCACTGAGTCGTGGAC
2110770 TTTTTTTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 2 0.03
93 66 0.97
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (93 bp):
TGCCACGGAGTCGTGGACTTTAAAGAAAAAGATGCCACGGAGTCGTGGACTTTGAGCAAAAAATG
CCACTGAGTCGTGGACCTTGAGACAAAA
Found at i:2111825 original size:15 final size:15
Alignment explanation
Indices: 2111805--2111844 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
2111795 CTCACCGAGA
2111805 TTTTCTGTTTTGTTT
1 TTTTCTGTTTTGTTT
* *
2111820 TTTTCTTTTTTTTTT
1 TTTTCTGTTTTGTTT
*
2111835 TTTTGTGTTT
1 TTTTCTGTTT
2111845 GGAAAAGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (15 bp):
TTTTCTGTTTTGTTT
Found at i:2118082 original size:20 final size:21
Alignment explanation
Indices: 2118003--2118081 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 21
2117993 AATGTCCAAA
*
2118003 ATGTATCGATACATGTTTT-T
1 ATGTATCGATACATCTTTTCT
* *
2118023 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACATCT----TTTCT
2118048 ATGTATCGATACAT-TTTTCT
1 ATGTATCGATACATCTTTTCT
*
2118068 TTGTATCGATACAT
1 ATGTATCGATACAT
2118082 TGTATCGATA
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
20 31 0.65
24 3 0.06
25 14 0.29
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.44
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTCT
Found at i:2118086 original size:13 final size:13
Alignment explanation
Indices: 2118068--2118106 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2118058 ACATTTTTCT
2118068 TTGTATCGATACA
1 TTGTATCGATACA
2118081 TTGTATCGATACA
1 TTGTATCGATACA
*
2118094 CTGTATCGATACA
1 TTGTATCGATACA
2118107 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2119952 original size:53 final size:53
Alignment explanation
Indices: 2119890--2119996 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
2119880 AGTGCAAATA
2119890 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGGGGG
1 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGGGGG
2119943 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGGGGG
1 AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGGGGG
2119996 A
1 A
2119997 GATAAAGGAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.34
Consensus pattern (53 bp):
AATTTTGATATGAATCACTTGATTAAGGGGGAGATTTTTTAAATAAACGGGGG
Found at i:2120627 original size:20 final size:20
Alignment explanation
Indices: 2120604--2120676 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
2120594 ACAATTCAAA
2120604 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
2120624 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
2120645 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
2120665 GTATCGATACAT
1 GTATCGATACAT
2120677 AAAAAAGTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:2120648 original size:21 final size:21
Alignment explanation
Indices: 2120622--2120697 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
2120612 ACATGTTGCA
2120622 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
2120643 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
2120663 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
*
2120684 TTGTATCGATACAT
1 ATGTATCGATACAT
2120698 TTCTTGGCAG
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:2120655 original size:41 final size:41
Alignment explanation
Indices: 2120604--2120697 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
2120594 ACAATTCAAA
*
2120604 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
*
2120645 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
2120686 GTATCGATACAT
1 GTATCGATACAT
2120698 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Found at i:2120754 original size:13 final size:13
Alignment explanation
Indices: 2120736--2120761 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2120726 TACATCAAGT
2120736 ATGTATCGATACA
1 ATGTATCGATACA
2120749 ATGTATCGATACA
1 ATGTATCGATACA
2120762 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2123049 original size:21 final size:21
Alignment explanation
Indices: 2123023--2123078 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
2123013 TTTTTATCCA
2123023 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2123044 AATGTATCAATACATTTGTAG
1 AATGTATCGATACATTTGTAG
2123065 AATGTATCGATACA
1 AATGTATCGATACA
2123079 AGGTCCCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:2123217 original size:13 final size:13
Alignment explanation
Indices: 2123199--2123224 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2123189 GCCAAGGAAA
2123199 TGTATCGATACAT
1 TGTATCGATACAT
2123212 TGTATCGATACAT
1 TGTATCGATACAT
2123225 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2124550 original size:51 final size:50
Alignment explanation
Indices: 2124488--2124661 Score: 190
Period size: 52 Copynumber: 3.4 Consensus size: 50
2124478 AATTGTTCAT
*
2124488 AATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACACTAATTTTCCAC
1 AATCGAGGATACTCCAACCCCGGTTTTATTTC-AAAACACTAATTTTCCAC
* **
2124539 AATCG-GAGATACTCTAACCCCGGTTTTATCTTCAAAACACTAATTTTCCTTT
1 AATCGAG-GATACTCCAACCCCGGTTTTAT-TTCAAAACACTAATTTTCC-AC
* * * *
2124591 AATCAAGGATACTCCAACTCCGATTTTATTTCCAAAA-ACATCAATTTTTCAC
1 AATCGAGGATACTCCAACCCCGGTTTTATTT-CAAAACAC-T-AATTTTCCAC
*
2124643 AATCGATGATACTCCAACC
1 AATCGAGGATACTCCAACC
2124662 TCGTTATTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
50 1 0.01
51 46 0.45
52 48 0.47
53 8 0.08
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (50 bp):
AATCGAGGATACTCCAACCCCGGTTTTATTTCAAAACACTAATTTTCCAC
Found at i:2129674 original size:20 final size:20
Alignment explanation
Indices: 2129645--2129694 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2129635 AACCCAGATG
2129645 TATCGATACAATGTTCTTTA
1 TATCGATACAATGTTCTTTA
* *
2129665 TATTGATACAATGTTCTTTG
1 TATCGATACAATGTTCTTTA
2129685 TATCGATACA
1 TATCGATACA
2129695 TTGTATCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (20 bp):
TATCGATACAATGTTCTTTA
Found at i:2129700 original size:13 final size:13
Alignment explanation
Indices: 2129682--2129721 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
2129672 ACAATGTTCT
2129682 TTGTATCGATACA
1 TTGTATCGATACA
2129695 TTGTATCGATACA
1 TTGTATCGATACA
*
2129708 ATGTATCGATACA
1 TTGTATCGATACA
2129721 T
1 T
2129722 GGGTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2132239 original size:19 final size:20
Alignment explanation
Indices: 2132215--2132268 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
2132205 ATATTATGCT
*
2132215 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGTACAA
*
2132234 TTGTATCGATACACGTACAA
1 TTGTATCGATACATGTACAA
2132254 TTGTATCGATACATG
1 TTGTATCGATACATG
2132269 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGTACAA
Found at i:2132336 original size:13 final size:13
Alignment explanation
Indices: 2132314--2132343 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2132304 GATACATGGC
*
2132314 ACATTGTATCGAT
1 ACATTATATCGAT
2132327 ACATTATATCGAT
1 ACATTATATCGAT
2132340 ACAT
1 ACAT
2132344 AAGGAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (13 bp):
ACATTATATCGAT
Found at i:2132337 original size:33 final size:32
Alignment explanation
Indices: 2132300--2132366 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 32
2132290 CCACTGTTTG
2132300 TATCGATACAT-GGCACATTGTATCGATACATTA
1 TATCGATACATAGG-A-ATTGTATCGATACATTA
*
2132333 TATCGATACATAAGGAATTGTATTGATACATTA
1 TATCGATACAT-AGGAATTGTATCGATACATTA
2132366 T
1 T
2132367 CCCAAATGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 28 0.90
34 1 0.03
35 2 0.06
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (32 bp):
TATCGATACATAGGAATTGTATCGATACATTA
Found at i:2133189 original size:354 final size:354
Alignment explanation
Indices: 2132574--2133271 Score: 1360
Period size: 354 Copynumber: 2.0 Consensus size: 354
2132564 AGAAATGCTC
2132574 GACACAAGAGTTTACAGAAGTTCAGTCCAATTCGGAACCTATGTCTTCTCTCCTCGACACTTCCT
1 GACACAAGAGTTTACAGAAGTTCAGTCCAATTCGGAACCTATGTCTTCTCTCCTCGACACTTCCT
2132639 CATCGAGTGGTTATCTAATTCACTACAAGAATTGATTACCTTTAAGGCAAAGGTACAACCTTACA
66 CATCGAGTGGTTATCTAATTCACTACAAGAATTGATTACCTTTAAGGCAAAGGTACAACCTTACA
*
2132704 AACCTTATCTTTTAAAGGCTAAGATAACAACCGCTCAATCTCTCTAAGAACTATGTCCCAAGTTC
131 AACCTTATCTTTTAAAGGCTAAGATAACAACCGCTCAATCTCTCCAAGAACTATGTCCCAAGTTC
2132769 CTAAGAGATTATGACATAAGGTTGAACACAACCTTATGTAAACAAAGAAATTATACAAATAAGAA
196 CTAAGAGATTATGACATAAGGTTGAACACAACCTTATGTAAACAAAGAAATTATACAAATAAGAA
2132834 TTGCCTCTAAATAGGCTGGTGTTTGTGAAGGAATAAGCTCAAAACAAATACAAAAGAGCTTTCGA
261 TTGCCTCTAAATAGGCTGGTGTTTGTGAAGGAATAAGCTCAAAACAAATACAAAAGAGCTTTCGA
2132899 AAAATAACAACAATGAATGTTGTCTTCTT
326 AAAATAACAACAATGAATGTTGTCTTCTT
2132928 GACACAAGAGTTTACAGAAGTTCAGTCCAATTCGGAACCTATGTCTTCTCTCCTCGACACTTCCT
1 GACACAAGAGTTTACAGAAGTTCAGTCCAATTCGGAACCTATGTCTTCTCTCCTCGACACTTCCT
*
2132993 CATCGAGTGGTTATCTAATTTACTACAAGAATTGATTACCTTTAAGGCAAAGGTACAACCTTACA
66 CATCGAGTGGTTATCTAATTCACTACAAGAATTGATTACCTTTAAGGCAAAGGTACAACCTTACA
2133058 AACCTTATCTTTTAAAGGCTAAGATAACAACCGCTCAATCTCTCCAAGAACTATGTCCCAAGTTC
131 AACCTTATCTTTTAAAGGCTAAGATAACAACCGCTCAATCTCTCCAAGAACTATGTCCCAAGTTC
* *
2133123 CTCAGAGATTGTGACATAAGGTTGAACACAACCTTATGTAAACAAAGAAATTATACAAATAAGAA
196 CTAAGAGATTATGACATAAGGTTGAACACAACCTTATGTAAACAAAGAAATTATACAAATAAGAA
2133188 TTGCCTCTAAATAGGCTGGTGTTTGTGAAGGAATAAGCTCAAAACAAATACAAAAGAGCTTTCGA
261 TTGCCTCTAAATAGGCTGGTGTTTGTGAAGGAATAAGCTCAAAACAAATACAAAAGAGCTTTCGA
2133253 AAAATAACAACAATGAATG
326 AAAATAACAACAATGAATG
2133272 CAAAAGCTCT
Statistics
Matches: 340, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
354 340 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.27
Consensus pattern (354 bp):
GACACAAGAGTTTACAGAAGTTCAGTCCAATTCGGAACCTATGTCTTCTCTCCTCGACACTTCCT
CATCGAGTGGTTATCTAATTCACTACAAGAATTGATTACCTTTAAGGCAAAGGTACAACCTTACA
AACCTTATCTTTTAAAGGCTAAGATAACAACCGCTCAATCTCTCCAAGAACTATGTCCCAAGTTC
CTAAGAGATTATGACATAAGGTTGAACACAACCTTATGTAAACAAAGAAATTATACAAATAAGAA
TTGCCTCTAAATAGGCTGGTGTTTGTGAAGGAATAAGCTCAAAACAAATACAAAAGAGCTTTCGA
AAAATAACAACAATGAATGTTGTCTTCTT
Found at i:2133587 original size:13 final size:13
Alignment explanation
Indices: 2133569--2133593 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2133559 CACTTCATCA
2133569 TGTATCGATACAT
1 TGTATCGATACAT
2133582 TGTATCGATACA
1 TGTATCGATACA
2133594 ATATGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2136908 original size:26 final size:25
Alignment explanation
Indices: 2136872--2136923 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 25
2136862 TACATTGCAC
*
2136872 AATGTATCGATACATCTGGGTTAAAA
1 AATGTATCGATACATCTAGG-TAAAA
2136898 AATGTATCGATACATCTAGGTAAAA
1 AATGTATCGATACATCTAGGTAAAA
2136923 A
1 A
2136924 GACAGAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (25 bp):
AATGTATCGATACATCTAGGTAAAA
Found at i:2151866 original size:21 final size:20
Alignment explanation
Indices: 2151842--2151913 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 20
2151832 GTCCTCCGCA
2151842 AAAAAAAATAAAAAATAAAAT
1 AAAAAAAA-AAAAAATAAAAT
2151863 AAAAATAAAAAAAAAT-AAAT
1 AAAAA-AAAAAAAAATAAAAT
*
2151883 AGAAAAAAAAACAAAA-AAAAC
1 A-AAAAAAAAA-AAAATAAAAT
2151904 AAAAAAAAAA
1 AAAAAAAAAA
2151914 CAACAACAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
20 19 0.41
21 24 0.52
22 3 0.07
ACGTcount: A:0.88, C:0.03, G:0.01, T:0.08
Consensus pattern (20 bp):
AAAAAAAAAAAAAATAAAAT
Found at i:2151872 original size:25 final size:26
Alignment explanation
Indices: 2151843--2151902 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
2151833 TCCTCCGCAA
* * *
2151843 AAAAAAATAAAAAATA-AAATAAAAAT
1 AAAAAAA-AATAAATAGAAAAAAAAAC
2151869 AAAAAAAAATAAATAGAAAAAAAAAC
1 AAAAAAAAATAAATAGAAAAAAAAAC
2151895 AAAAAAAA
1 AAAAAAAA
2151903 CAAAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 7 0.23
26 23 0.77
ACGTcount: A:0.87, C:0.02, G:0.02, T:0.10
Consensus pattern (26 bp):
AAAAAAAAATAAATAGAAAAAAAAAC
Found at i:2151883 original size:32 final size:32
Alignment explanation
Indices: 2151841--2151913 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
2151831 CGTCCTCCGC
*
2151841 AAAAAAAAATA-AAAAATAAAATAAAAATAAA-A
1 AAAAAAAAATAGAAAAA-AAAACAAAAA-AAACA
*
2151873 AAAAATAAATAGAAAAAAAAACAAAAAAAACA
1 AAAAAAAAATAGAAAAAAAAACAAAAAAAACA
2151905 AAAAAAAAA
1 AAAAAAAAA
2151914 CAACAACAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 3 0.08
32 28 0.78
33 5 0.14
ACGTcount: A:0.88, C:0.03, G:0.01, T:0.08
Consensus pattern (32 bp):
AAAAAAAAATAGAAAAAAAAACAAAAAAAACA
Found at i:2151911 original size:20 final size:20
Alignment explanation
Indices: 2151840--2151916 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 20
2151830 GCGTCCTCCG
*
2151840 CAAAAAAAAATAAAAAATAAAA
1 CAAAAAAAAA-ACAAAA-AAAA
* *
2151862 TAAAAATAAAAA-AAAATAAA
1 CAAAAA-AAAAACAAAAAAAA
*
2151882 TAGAAAAAAAAACAAAAAAAA
1 CA-AAAAAAAAACAAAAAAAA
2151903 CAAAAAAAAAACAA
1 CAAAAAAAAAACAA
2151917 CAACAAAAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
20 22 0.46
21 16 0.33
22 6 0.12
23 4 0.08
ACGTcount: A:0.86, C:0.05, G:0.01, T:0.08
Consensus pattern (20 bp):
CAAAAAAAAAACAAAAAAAA
Found at i:2151924 original size:11 final size:9
Alignment explanation
Indices: 2151842--2151925 Score: 59
Period size: 9 Copynumber: 9.6 Consensus size: 9
2151832 GTCCTCCGCA
*
2151842 AAAAAAAAT
1 AAAAAAAAC
2151851 AAAAAATAA-
1 AAAAAA-AAC
* *
2151860 AATAAAAAT
1 AAAAAAAAC
2151869 AAAAAAAA-
1 AAAAAAAAC
* *
2151877 ATAAATAGA-
1 A-AAAAAAAC
2151886 AAAAAAAAC
1 AAAAAAAAC
2151895 AAAAAAAAC
1 AAAAAAAAC
2151904 AAAAAAAA-
1 AAAAAAAAC
* *
2151912 AACAACAAC
1 AAAAAAAAC
2151921 AAAAA
1 AAAAA
2151926 GGGTCCGGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
8 14 0.23
9 45 0.74
10 2 0.03
ACGTcount: A:0.86, C:0.06, G:0.01, T:0.07
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:2151925 original size:1 final size:1
Alignment explanation
Indices: 2151841--2151913 Score: 65
Period size: 1 Copynumber: 73.0 Consensus size: 1
2151831 CGTCCTCCGC
* * * * * * * * *
2151841 AAAAAAAAATAAAAAATAAAATAAAAATAAAAAAAAATAAATAGAAAAAAAAACAAAAAAAACAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2151906 AAAAAAAA
1 AAAAAAAA
2151914 CAACAACAAA
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 54 1.00
ACGTcount: A:0.88, C:0.03, G:0.01, T:0.08
Consensus pattern (1 bp):
A
Found at i:2151925 original size:36 final size:37
Alignment explanation
Indices: 2151851--2151925 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 37
2151841 AAAAAAAAAT
* * *
2151851 AAAAAATAAAATAAAAATAAAAAAAAATAAATAGAAA
1 AAAAAACAAAATAAAAATAAAAAAAAACAAATACAAA
2151888 AAAAAACAAAA-AAAACA-AAAAAAAAACAACA-ACAAA
1 AAAAAACAAAATAAAA-ATAAAAAAAAACAA-ATACAAA
2151924 AA
1 AA
2151926 GGGTCCGGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
36 21 0.64
37 12 0.36
ACGTcount: A:0.85, C:0.07, G:0.01, T:0.07
Consensus pattern (37 bp):
AAAAAACAAAATAAAAATAAAAAAAAACAAATACAAA
Found at i:2153401 original size:29 final size:29
Alignment explanation
Indices: 2153362--2153887 Score: 230
Period size: 29 Copynumber: 17.7 Consensus size: 29
2153352 TCACCCTTCA
2153362 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
*
2153391 AAAGCCCACAAGTCAGTGGCATCTTTTTT
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2153420 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2153447 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
2153477 GAAGCCCACAAGTCGGTGACATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
2153506 AAAGTCCACAACTCCGTGGCACTATTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
2153536 TTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTC
1 -----AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
**** * * *
2153571 ----CTTTTAAGCTTAGTGGCACCCTTTTC
1 AAAGCCCACAAG-TCAGTGGCATCTTTTTC
* * *
2153597 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
2153626 AAAGCCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2153653 AAAGCCCACAAATCAGTGGCACCCTTTTCC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * *
2153683 GAAGCCCACAAGTCGGTGACATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * * *
2153712 AAAGTCCACAACTCCGTGGCACTATTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * * * *
2153742 TTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTCC
1 -----AAAGCCCACAAGTCAGTGGCA-TCTTTTT-C
* * * *
2153778 TTTTAAGCCCACAAGTTAGTGGCACCCTTTTC
1 ---AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
2153810 AAAAGCCCACAAGTCAGTGGCAAC-CTTTA
1 -AAAGCCCACAAGTCAGTGGCATCTTTTTC
** *
2153839 AAAGCAGACAAGTCAGTGGCAATC--TTTA
1 AAAGCCCACAAGTCAGTGGC-ATCTTTTTC
2153867 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
2153888 ACCTTCAAAA
Statistics
Matches: 385, Mismatches: 86, Indels: 54
0.73 0.16 0.10
Matches are distributed among these distances:
26 10 0.03
27 50 0.13
28 65 0.17
29 103 0.27
30 79 0.21
31 4 0.01
32 1 0.00
33 5 0.01
34 18 0.05
35 49 0.13
36 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:2153484 original size:86 final size:86
Alignment explanation
Indices: 2153356--2153526 Score: 236
Period size: 86 Copynumber: 2.0 Consensus size: 86
2153346 CATTCCTCAC
* * * * **
2153356 CCTTCAAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTTTA
1 CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGACATCTTTTCCA
*
2153421 AAGTCCACAAGTCAGTGGCAA
66 AAGTCCACAACTCAGTGGCAA
* *
2153442 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGACATCTTTTCC
1 CCTTCAAAAGCCCACAAATCAGTGGCA-CCTTTTCCAAAGCCCACAAGTCAGTGACATCTTTTCC
*
2153506 AAAGTCCACAACTCCGTGGCA
65 AAAGTCCACAACTCAGTGGCA
2153527 CTATTTTTCT
Statistics
Matches: 74, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 20 0.27
86 54 0.73
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (86 bp):
CCTTCAAAAGCCCACAAATCAGTGGCACCTTTTCCAAAGCCCACAAGTCAGTGACATCTTTTCCA
AAGTCCACAACTCAGTGGCAA
Found at i:2153552 original size:35 final size:34
Alignment explanation
Indices: 2153512--2153580 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
2153502 TTCCAAAGTC
* *
2153512 CACAACTCCGTGGCACTATTTTTCTTTTGTAAGCT
1 CACAACTCCGTAGCACTATTTTTCCTTT-TAAGCT
*
2153547 CACAACTCCGTAGCACTCTTTTTCCTTTTAAGCT
1 CACAACTCCGTAGCACTATTTTTCCTTTTAAGCT
2153581 TAGTGGCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.20, C:0.29, G:0.12, T:0.39
Consensus pattern (34 bp):
CACAACTCCGTAGCACTATTTTTCCTTTTAAGCT
Found at i:2153636 original size:28 final size:28
Alignment explanation
Indices: 2153582--2153933 Score: 181
Period size: 28 Copynumber: 11.9 Consensus size: 28
2153572 TTTTAAGCTT
*
2153582 AGTGGCACCCTTTTCAAAAGCCCACAAGTC
1 AGTGGCAACC-TTT-AAAAGCCCACAAGTC
2153612 AGTGGCAACCTTTAAAAGCCCACAAGTC
1 AGTGGCAACCTTTAAAAGCCCACAAGTC
* *
2153640 AGTGGCAACC-TTCAAAGCCCACAAATC
1 AGTGGCAACCTTTAAAAGCCCACAAGTC
* **
2153667 AGTGGCACCCTTTTCCGAAGCCCACAAGTC
1 AGTGGCAACC-TTT-AAAAGCCCACAAGTC
* * * * * * *
2153697 GGTGACATCTTTTCCAAAGTCCACAACTC
1 AGTGGCAACCTTT-AAAAGCCCACAAGTC
* * ** * *
2153726 CGTGGCACTATTTTTCTTTTGTAAGCTCACAACTC
1 AGTGGCA--A-----CCTTTAAAAGCCCACAAGTC
* * ** *
2153761 CGTAGC-ACTCTTTTTCCTTTTAAGCCCACAAGTT
1 AGTGGCAAC-C----T--TTAAAAGCCCACAAGTC
*
2153795 AGTGGCACCCTTTTCAAAAGCCCACAAGTC
1 AGTGGCAACC-TTT-AAAAGCCCACAAGTC
**
2153825 AGTGGCAACCTTTAAAAGCAGACAAGTC
1 AGTGGCAACCTTTAAAAGCCCACAAGTC
*
2153853 AGTGGCAATCTTTAAAAGCCCACAAGTC
1 AGTGGCAACCTTTAAAAGCCCACAAGTC
* *
2153881 AGTGGCAACCTTCAAAAGCACACAAGT-
1 AGTGGCAACCTTTAAAAGCCCACAAGTC
*
2153908 TGAT-GCAAACCTTTCAAAAGCCCACA
1 AG-TGGC-AACCTTT-AAAAGCCCACA
2153934 CAAGTTGGTG
Statistics
Matches: 256, Mismatches: 44, Indels: 45
0.74 0.13 0.13
Matches are distributed among these distances:
27 28 0.11
28 94 0.37
29 41 0.16
30 49 0.19
31 2 0.01
32 2 0.01
34 18 0.07
35 17 0.07
36 5 0.02
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
AGTGGCAACCTTTAAAAGCCCACAAGTC
Found at i:2153668 original size:27 final size:27
Alignment explanation
Indices: 2153597--2153678 Score: 128
Period size: 27 Copynumber: 3.0 Consensus size: 27
2153587 CACCCTTTTC
2153597 AAAAGCCCACAAGTCAGTGGCAACCTTT
1 AAAAGCCCACAAGTCAGTGGCAACC-TT
2153625 AAAAGCCCACAAGTCAGTGGCAACCTT
1 AAAAGCCCACAAGTCAGTGGCAACCTT
* * *
2153652 CAAAGCCCACAAATCAGTGGCACCCTT
1 AAAAGCCCACAAGTCAGTGGCAACCTT
2153679 TTCCGAAGCC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 26 0.51
28 25 0.49
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.16
Consensus pattern (27 bp):
AAAAGCCCACAAGTCAGTGGCAACCTT
Found at i:2153730 original size:206 final size:208
Alignment explanation
Indices: 2153376--2153892 Score: 842
Period size: 206 Copynumber: 2.5 Consensus size: 208
2153366 CCCACAAGTC
* * * * * *
2153376 AGTGGCATCTTTTTC-AAAGCCCACAAGTCAGTGGCATCTTTTTTAAAGTCCACAAGTCAGTGGC
1 AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAAC-CTTTAAAAGCCCACAAGTCAGTGGC
2153440 AACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGACATCTTTTC
65 AACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGACATCTTTTC
2153505 CAAAGTCCACAACTCCGTGGCACTATTTTTCTTTTGTAAGCTCACAACTCCGTAGCACTCTTTTT
130 CAAAGTCCACAACTCCGTGGCACTATTTTTCTTTTGTAAGCTCACAACTCCGTAGCACTCTTTTT
2153570 CCTTTTAAG-C-TT
195 CCTTTTAAGCCATT
2153582 AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCA
1 AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCA
2153647 ACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGACATCTTTTCC
66 ACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGACATCTTTTCC
2153712 AAAGTCCACAACTCCGTGGCACTATTTTTCTTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTC
131 AAAGTCCACAACTCCGTGGCACTATTTTTCTTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTC
2153777 CTTTTAAGCCCACAAGTT
196 CTTTTAAG--C-C-A-TT
**
2153795 AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCAGACAAGTCAGTGGCA
1 AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCA
* * * *
2153860 ATCTTTAAAAGCCCACAAGTCAGTGGCAACCTT
66 A-CCTTCAAAGCCCACAAATCAGTGGCACCCTT
2153893 CAAAAGCACA
Statistics
Matches: 290, Mismatches: 12, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
206 174 0.60
207 22 0.08
210 1 0.00
213 66 0.23
214 27 0.09
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.27
Consensus pattern (208 bp):
AGTGGCACCCTTTTCAAAAGCCCACAAGTCAGTGGCAACCTTTAAAAGCCCACAAGTCAGTGGCA
ACCTTCAAAGCCCACAAATCAGTGGCACCCTTTTCCGAAGCCCACAAGTCGGTGACATCTTTTCC
AAAGTCCACAACTCCGTGGCACTATTTTTCTTTTGTAAGCTCACAACTCCGTAGCACTCTTTTTC
CTTTTAAGCCATT
Found at i:2153791 original size:34 final size:35
Alignment explanation
Indices: 2153717--2153791 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
2153707 TTTCCAAAGT
* *
2153717 CCACAACTCCGTGGCACTATTTTTCTTTTGTAAGC
1 CCACAACTCCGTAGCACTATTTTTCCTTTGTAAGC
* *
2153752 TCACAACTCCGTAGCACTCTTTTTCCTTT-TAAGC
1 CCACAACTCCGTAGCACTATTTTTCCTTTGTAAGC
2153786 CCACAA
1 CCACAA
2153792 GTTAGTGGCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
34 10 0.29
35 25 0.71
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.35
Consensus pattern (35 bp):
CCACAACTCCGTAGCACTATTTTTCCTTTGTAAGC
Found at i:2154171 original size:52 final size:52
Alignment explanation
Indices: 2154093--2154224 Score: 246
Period size: 52 Copynumber: 2.5 Consensus size: 52
2154083 ACATTGGCAC
2154093 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
*
2154145 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGTCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
*
2154197 CTTTAAGTCCAATGTCGCTGGCCTTGAA
1 CTTTAAGTCCAATATCGCTGGCCTTGAA
2154225 GTCATCTTTA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
52 78 1.00
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
Found at i:2164399 original size:13 final size:13
Alignment explanation
Indices: 2164381--2164405 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2164371 CAATTCATCA
2164381 TGTATCGATACAT
1 TGTATCGATACAT
2164394 TGTATCGATACA
1 TGTATCGATACA
2164406 ATGTGCCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2164403 original size:33 final size:33
Alignment explanation
Indices: 2164361--2164425 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2164351 TTAGAAGCAA
2164361 TGTATCGATACAAT-T-CATCATGTATCGATACAT
1 TGTATCGATACAATGTGC--CATGTATCGATACAT
2164394 TGTATCGATACAATGTGCCATGTATCGATACA
1 TGTATCGATACAATGTGCCATGTATCGATACA
2164426 AACAGTGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAATGTGCCATGTATCGATACAT
Found at i:2164499 original size:19 final size:20
Alignment explanation
Indices: 2164455--2164505 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
2164445 CTGCCAGTTT
* **
2164455 CATGTATTGATACAATTGTC
1 CATGTATCGATACAATTGAA
2164475 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
2164494 CATGTATCGATA
1 CATGTATCGATA
2164506 TATTGTATCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:2164518 original size:32 final size:33
Alignment explanation
Indices: 2164477--2164541 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2164467 CAATTGTCCA
*
2164477 TGTATCGATACAATG-A-ACATGTATCGATATAT
1 TGTATCGATACAAAGCATA-ATGTATCGATATAT
2164509 TGTATCGATACAAAGCATAATGTATCGATATAT
1 TGTATCGATACAAAGCATAATGTATCGATATAT
2164542 CTGGGTGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 14 0.47
33 15 0.50
34 1 0.03
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (33 bp):
TGTATCGATACAAAGCATAATGTATCGATATAT
Found at i:2173258 original size:13 final size:13
Alignment explanation
Indices: 2173218--2173269 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
2173208 TCGTTAGAAG
2173218 CAATGTATCGATA
1 CAATGTATCGATA
2173231 CAA--T-TC-AT-
1 CAATGTATCGATA
2173239 C-ATGTATCGATA
1 CAATGTATCGATA
2173251 CAATGTATCGATA
1 CAATGTATCGATA
*
2173264 TAATGT
1 CAATGT
2173270 GCCATGTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2173260 original size:33 final size:33
Alignment explanation
Indices: 2173218--2173286 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
2173208 TCGTTAGAAG
2173218 CAATGTATCGATACAAT-T-CATCATGTATCGATA
1 CAATGTATCGATACAATGTGC--CATGTATCGATA
*
2173251 CAATGTATCGATATAATGTGCCATGTATCGATA
1 CAATGTATCGATACAATGTGCCATGTATCGATA
2173284 CAA
1 CAA
2173287 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 31 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:2173340 original size:20 final size:20
Alignment explanation
Indices: 2173315--2173373 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
2173305 CTGCCAGTTT
*
2173315 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTA
* * *
2173335 CATGTATTGATACAAATGAA
1 CATGTATCGATACAATTGTA
2173355 CATGTATCGATAC-ATTGTA
1 CATGTATCGATACAATTGTA
2173374 TCGATACAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 4 0.12
20 28 0.88
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (20 bp):
CATGTATCGATACAATTGTA
Found at i:2173375 original size:13 final size:13
Alignment explanation
Indices: 2173357--2173381 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2173347 CAAATGAACA
2173357 TGTATCGATACAT
1 TGTATCGATACAT
2173370 TGTATCGATACA
1 TGTATCGATACA
2173382 AAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2175560 original size:13 final size:13
Alignment explanation
Indices: 2175520--2175571 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
2175510 CCGTTTGAAG
2175520 CAATGTATCGATA
1 CAATGTATCGATA
2175533 CAA--T-TC-AT-
1 CAATGTATCGATA
2175541 C-ATGTATCGATA
1 CAATGTATCGATA
2175553 CAATGTATCGATA
1 CAATGTATCGATA
*
2175566 TAATGT
1 CAATGT
2175572 GCCATGTATC
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.09
10 4 0.12
11 3 0.09
12 1 0.03
13 19 0.59
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:2175562 original size:33 final size:33
Alignment explanation
Indices: 2175520--2175587 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
2175510 CCGTTTGAAG
2175520 CAATGTATCGATACAAT-T-CATCATGTATCGATA
1 CAATGTATCGATACAATGTGC--CATGTATCGATA
*
2175553 CAATGTATCGATATAATGTGCCATGTATCGATA
1 CAATGTATCGATACAATGTGCCATGTATCGATA
2175586 CA
1 CA
2175588 GTTGTGCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTGCCATGTATCGATA
Found at i:2175618 original size:19 final size:19
Alignment explanation
Indices: 2175555--2175648 Score: 116
Period size: 19 Copynumber: 4.8 Consensus size: 19
2175545 TATCGATACA
**
2175555 ATGTATCGATATAATGTGCC
1 ATGTATCGATATAATG-AAC
* * **
2175575 ATGTATCGATACAGTTGTGC
1 ATGTATCGATATA-ATGAAC
2175595 ATGTATCGATATAATGAAC
1 ATGTATCGATATAATGAAC
2175614 ATGTATCGATATAATGAAC
1 ATGTATCGATATAATGAAC
2175633 ATGTATCGATATAATG
1 ATGTATCGATATAATG
2175649 CATCGATACA
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
19 38 0.58
20 25 0.38
21 2 0.03
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (19 bp):
ATGTATCGATATAATGAAC
Found at i:2178618 original size:3 final size:3
Alignment explanation
Indices: 2178610--2178641 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2178600 GCTAGGGTCT
2178610 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2178642 CTAAAATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2186120 original size:23 final size:23
Alignment explanation
Indices: 2186069--2186130 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
2186059 TTATTAATAA
*
2186069 CTTTTAATTCATTTAATTGTTTG
1 CTTTTAATTTATTTAATTGTTTG
*
2186092 CCTTTAATTTATTTAATTGATTT-
1 CTTTTAATTTATTTAATTG-TTTG
* *
2186115 CTTTTAGTTTTTTTAA
1 CTTTTAATTTATTTAA
2186131 AATTTATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.23, C:0.08, G:0.06, T:0.63
Consensus pattern (23 bp):
CTTTTAATTTATTTAATTGTTTG
Found at i:2186249 original size:25 final size:25
Alignment explanation
Indices: 2186197--2186251 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2186187 AAATGCTTTA
*
2186197 TTTATTTTATTTTAATTTATAGTTT
1 TTTATTTTATTTTAATTTATAGTCT
* *
2186222 TTTATTTTATTTTTGATTT-TTGTCT
1 TTTATTTTA-TTTTAATTTATAGTCT
2186247 TTTAT
1 TTTAT
2186252 CCTTTAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.18, C:0.02, G:0.05, T:0.75
Consensus pattern (25 bp):
TTTATTTTATTTTAATTTATAGTCT
Found at i:2186615 original size:3 final size:3
Alignment explanation
Indices: 2186602--2186647 Score: 65
Period size: 3 Copynumber: 15.0 Consensus size: 3
2186592 GGAAATTACA
* *
2186602 AAT ATAT AAT AAT AAT CAT AAC AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2186648 TTGAATGTAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2188488 original size:40 final size:40
Alignment explanation
Indices: 2188443--2188523 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
2188433 GTAGGAAAGT
2188443 TGCATTGGCATCATATAGTAGTTGGGCTGGTAATGCTACC
1 TGCATTGGCATCATATAGTAGTTGGGCTGGTAATGCTACC
2188483 TGCATTGGCATCATATAGTAGTTGGGCTGGTAATGCTACC
1 TGCATTGGCATCATATAGTAGTTGGGCTGGTAATGCTACC
2188523 T
1 T
2188524 AAATTTGAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.22, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TGCATTGGCATCATATAGTAGTTGGGCTGGTAATGCTACC
Found at i:2188956 original size:2 final size:2
Alignment explanation
Indices: 2188949--2188984 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2188939 TAATTGCCTT
2188949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2188985 TGATTTGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2191316 original size:26 final size:26
Alignment explanation
Indices: 2191269--2191324 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
2191259 CTTATCTCAC
* * *
2191269 TAAAGTTCTTTCATGTATATTTTAAT
1 TAAAATTCTTGCATGTAAATTTTAAT
* *
2191295 TAAAATTCTTGCATTTAAATTTTTAT
1 TAAAATTCTTGCATGTAAATTTTAAT
2191321 TAAA
1 TAAA
2191325 TCTCTTCTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (26 bp):
TAAAATTCTTGCATGTAAATTTTAAT
Found at i:2193750 original size:155 final size:156
Alignment explanation
Indices: 2193582--2193863 Score: 347
Period size: 155 Copynumber: 1.8 Consensus size: 156
2193572 CGATTTTAAT
* *
2193582 AAAATTATAAAAATGCCCCTATGAGATA-TCTT-AGACTTAGAAA-TACTCGAAACCCCTAAAGG
1 AAAATTATAAAAATGCCCCTATGAGATACT-TTCA-ACGTA-AAAGTACCCGAAACCCCTAAAGG
* * *
2193644 ACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATA-CCACTTTCGGCATAAAAATGAAC
63 ACCTAAAAAGGATTATAGATAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAATGAAC
2193708 CTAATGACAACCTAGGACTCAGTTCTGGA
128 CTAATGACAACCTAGGACTCAGTTCTGGA
* * * * * * ** ** *
2193737 AAAATTATGAAAATGTCTCTGTGGGGTACTTTCAACGTAAAAGTACCCGGTACCTTTAAAGGGCC
1 AAAATTATAAAAATGCCCCTATGAGATACTTTCAACGTAAAAGTACCCGAAACCCCTAAAGGACC
* *
2193802 TAAAAATGATTATAGATAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGTGAAC
66 TAAAAAGGATTATAGATAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAATGAAC
2193864 TTGGTGACAA
Statistics
Matches: 105, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
154 3 0.03
155 79 0.75
156 23 0.22
ACGTcount: A:0.39, C:0.19, G:0.17, T:0.25
Consensus pattern (156 bp):
AAAATTATAAAAATGCCCCTATGAGATACTTTCAACGTAAAAGTACCCGAAACCCCTAAAGGACC
TAAAAAGGATTATAGATAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAATGAACCTA
ATGACAACCTAGGACTCAGTTCTGGA
Found at i:2193937 original size:156 final size:155
Alignment explanation
Indices: 2193638--2193992 Score: 394
Period size: 156 Copynumber: 2.3 Consensus size: 155
2193628 TCGAAACCCC
* * *
2193638 TAAAGGACTTAAAAAGGATTATAGATGGGATGAACCTATCCTAAATACCACTTTCGGCATAAAAA
1 TAAAGGACTTAAAAACGATTATAGATAGGATGAACCTATCCTAAATACCACCTTCGGCATAAAAA
* ** * ** * * *
2193703 TGAACCTAATGACAACCTAGGACTCAGTTCTGGAAAAATTATGAAAATGTCTCTGTGGGGTACTT
66 TGAACCTAATGACAAACTAGGACTCAGTTCTAAAAAAATGACAAAAATGCCTCTGTGGGATACCT
* *
2193768 TCAACGTAAAAGTACCCGGTAC-CTT
131 TCAACATAAAAGTACCCAGTACTC-T
* * *
2193793 TAAAGGGCCTAAAAATGATTATAGATAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAA
1 TAAAGGACTTAAAAACGATTATAGATAGGATGAACCTATCCTAAATA-CCACCTTCGGCATAAAA
* * ** * *
2193858 GTGAACTTGGTGACAAACTAAGG-CTTAGTTCTAAAAAAATGACAAAAATGCCTCTAG-GGGATT
65 ATGAACCTAATGACAAACT-AGGACTCAGTTCTAAAAAAATGACAAAAATGCCTCT-GTGGGATA
* **
2193921 CCTTCAACATAGAAGTACGTAGTACTCT
128 CCTTCAACATAAAAGTACCCAGTACTCT
* *
2193949 TAAAGGACTTAAAAACGATCATAGA-AAGATGAACCTATCCTAAA
1 TAAAGGACTTAAAAACGATTATAGATAGGATGAACCTATCCTAAA
2193993 GGTGCACCTT
Statistics
Matches: 166, Mismatches: 30, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
155 61 0.37
156 100 0.60
157 5 0.03
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (155 bp):
TAAAGGACTTAAAAACGATTATAGATAGGATGAACCTATCCTAAATACCACCTTCGGCATAAAAA
TGAACCTAATGACAAACTAGGACTCAGTTCTAAAAAAATGACAAAAATGCCTCTGTGGGATACCT
TCAACATAAAAGTACCCAGTACTCT
Found at i:2194274 original size:154 final size:154
Alignment explanation
Indices: 2193887--2194274 Score: 383
Period size: 155 Copynumber: 2.5 Consensus size: 154
2193877 AAGGCTTAGT
* * * * * * * * *
2193887 TCTAAAAAAATGACAAAAATGCCTC-TAGGGGATTCCTTCAACATAGAAGTACGT-AGTACTCTT
1 TCTAAGAAAATTACAAAAATGCC-CATAGAGGATACCTTCGACATAAAAGTAC-TCGGTACCCCT
* * * *
2193950 AAAG-GACTTAAAAACGATCATAGAAAGATGAACCTATCCTAAAGGTGCACCTTTGGCGTAAAAG
64 AAAGAG-CTTAAAAACGATCATAAAAAGATGAACCTATCCTAAAGGCGCACCTCTAGCGTAAAAG
* * *
2194014 CGGACCTAGTAGTATCTAGGATTCAAC
128 CAGACCTAGTAGTACCTAAGATTCAAC
** *
2194041 TCTAAAGAAAATTATGAAAATGCCCATAGAGGATACCTTCGACATAGAAGTACTCGGTACCCCTA
1 TCT-AAGAAAATTACAAAAATGCCCATAGAGGATACCTTCGACATAAAAGTACTCGGTACCCCTA
* *
2194106 AAGGGCTTAAAAACGATCATAAAAAGATGAATCTATCCTAAAGGCGCACCTCTAGCGTAAAAGCA
65 AAGAGCTTAAAAACGATCATAAAAAGATGAACCTATCCTAAAGGCGCACCTCTAGCGTAAAAGCA
* * *
2194171 GA-CTCGGTGGTAACCTAAGACTT-AAT
130 GACCT-AGTAGT-ACCTAAGA-TTCAAC
* * ** * * *
2194197 TCT-AGAGAATTACAAAAATGTCTTTAGAGGATACCTTTGACGTAAAAGTACTCGGTACCCTTAA
1 TCTAAGAAAATTACAAAAATGCCCATAGAGGATACCTTCGACATAAAAGTACTCGGTACCCCTAA
*
2194261 AGAGTTTAAAAACG
66 AGAGCTTAAAAACG
2194275 TGAGGGAATG
Statistics
Matches: 194, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
154 70 0.36
155 110 0.57
156 12 0.06
157 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (154 bp):
TCTAAGAAAATTACAAAAATGCCCATAGAGGATACCTTCGACATAAAAGTACTCGGTACCCCTAA
AGAGCTTAAAAACGATCATAAAAAGATGAACCTATCCTAAAGGCGCACCTCTAGCGTAAAAGCAG
ACCTAGTAGTACCTAAGATTCAAC
Found at i:2196764 original size:166 final size:166
Alignment explanation
Indices: 2196591--2196899 Score: 386
Period size: 166 Copynumber: 1.9 Consensus size: 166
2196581 CTTGAAAATC
** * *
2196591 TTTATGGAATAGAAAACTCTATATTTTAAAAACAAGG-GAATTTCAAAGAAAAAATGAAAAACTT
1 TTTATGGAATAGAAAACTCTATATTCCAAAAA-AAGGTGAATTTCAAAGAAAAAATAAAAAAATT
* * * * * * * *
2196655 ATGAAAATAACTGAATTTTTCAAAACTAATTTATTGTGAATTAGATGATGATATTTGATAAATTT
65 ATGAAAATAAATAAAATTTTCAAAACTAATTTAATATGAATTAAAAGATAATATTTGATAAATTT
2196720 TAAAAATTATAAACCAAGAGAAATCCCCCCGAAAACA
130 TAAAAATTATAAACCAAGAGAAATCCCCCCGAAAACA
* * ** * * ** *
2196757 TTTATGGAGTAGAAAACTCTGTATTCCGGAAATAGGTGAATTTTAGGGAACAAATAAAAAAATTA
1 TTTATGGAATAGAAAACTCTATATTCCAAAAAAAGGTGAATTTCAAAGAAAAAATAAAAAAATTA
* *
2196822 TGAAAATAAATAAAATTTTCAAAACTAATTTAATATGAGTTAAAAGATAATATTTGATTAATTTT
66 TGAAAATAAATAAAATTTTCAAAACTAATTTAATATGAATTAAAAGATAATATTTGATAAATTTT
*
2196887 AAAAATTTTAAAC
131 AAAAATTATAAAC
2196900 TAATGAAAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
165 3 0.03
166 115 0.97
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (166 bp):
TTTATGGAATAGAAAACTCTATATTCCAAAAAAAGGTGAATTTCAAAGAAAAAATAAAAAAATTA
TGAAAATAAATAAAATTTTCAAAACTAATTTAATATGAATTAAAAGATAATATTTGATAAATTTT
AAAAATTATAAACCAAGAGAAATCCCCCCGAAAACA
Found at i:2200057 original size:20 final size:20
Alignment explanation
Indices: 2200020--2200073 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
2200010 TTCTATAATT
*
2200020 TGTATTGATACGATAAGTGAG
1 TGTATTGATAC-ATAAGTGAA
2200041 TGTATTGATACATAAGTGAA
1 TGTATTGATACATAAGTGAA
*
2200061 TGTATCGATACAT
1 TGTATTGATACAT
2200074 GTCTGAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.35, C:0.07, G:0.22, T:0.35
Consensus pattern (20 bp):
TGTATTGATACATAAGTGAA
Found at i:2200207 original size:20 final size:20
Alignment explanation
Indices: 2200182--2200229 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
2200172 ATTTGACCCA
2200182 AATGTATCAATATATTCTTC
1 AATGTATCAATATATTCTTC
2200202 AATGTATCAATATATTCTTC
1 AATGTATCAATATATTCTTC
2200222 AATGTATC
1 AATGTATC
2200230 GACACATGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (20 bp):
AATGTATCAATATATTCTTC
Found at i:2200846 original size:29 final size:29
Alignment explanation
Indices: 2200805--2200884 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 29
2200795 CCAAGTTGTT
*
2200805 GACTTT-AAGAAGGGTGCCATTAAGTCGTG
1 GACTTTGAA-AAGGGTGCCAGTAAGTCGTG
* *
2200834 GACTTTGAAAAGGTGGGTACCAGTAAGTTGTG
1 GACTTTGAAAA---GGGTGCCAGTAAGTCGTG
*
2200866 GACTTTGAAAAAGGTGCCA
1 GACTTTGAAAAGGGTGCCA
2200885 CGGAGTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
29 14 0.33
30 2 0.05
32 26 0.62
ACGTcount: A:0.30, C:0.12, G:0.31, T:0.26
Consensus pattern (29 bp):
GACTTTGAAAAGGGTGCCAGTAAGTCGTG
Found at i:2200867 original size:32 final size:33
Alignment explanation
Indices: 2200816--2200881 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
2200806 ACTTTAAGAA
* *
2200816 GGGTGCCATTAAGTCGTGGACTTTG-AAAAGGT
1 GGGTACCAGTAAGTCGTGGACTTTGAAAAAGGT
*
2200848 GGGTACCAGTAAGTTGTGGACTTTGAAAAAGGT
1 GGGTACCAGTAAGTCGTGGACTTTGAAAAAGGT
2200881 G
1 G
2200882 CCACGGAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 22 0.73
33 8 0.27
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (33 bp):
GGGTACCAGTAAGTCGTGGACTTTGAAAAAGGT
Found at i:2200929 original size:30 final size:29
Alignment explanation
Indices: 2200859--2200930 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
2200849 GGTACCAGTA
* *
2200859 AGTTGTGGACTTTGAAAAAGGTGCCACGG
1 AGTTGTAGACTTTGAAAAAGGTGCCACAG
* * * * *
2200888 AGTTATTGACTTCTGAGAAGGGTGTCACAG
1 AGTTGTAGACTT-TGAAAAAGGTGCCACAG
2200918 AGTTGTAGACTTT
1 AGTTGTAGACTTT
2200931 AGGAAGGGTG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
29 11 0.32
30 23 0.68
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.31
Consensus pattern (29 bp):
AGTTGTAGACTTTGAAAAAGGTGCCACAG
Found at i:2200941 original size:59 final size:59
Alignment explanation
Indices: 2200858--2201107 Score: 247
Period size: 59 Copynumber: 4.2 Consensus size: 59
2200848 GGGTACCAGT
* * *
2200858 AAGTTGTGGACTTTGAAAAA-GGTGCCACGGAGTTATTGACTTCTGAGAAGGGTGTCACA
1 AAGTTGTGGACTTT-AAAAAGGGTGCCACGGAGTTATGGACTTTTGAGAAGGGTGCCACA
* * ** * * * *
2200917 GAGTTGTAGACTTTAGGAAGGGTGCCACTGAATTATGGA-TTTTGAAAAGGTTGCCACA
1 AAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATGGACTTTTGAGAAGGGTGCCACA
** * * * *
2200975 AAGTCATGGACTTTTTAAAAAAGTTGCCATGGAGTTATGGACTTTTGAGAGGGGTGCCACA
1 AAGTTGTGGAC--TTTAAAAAGGGTGCCACGGAGTTATGGACTTTTGAGAAGGGTGCCACA
* * *
2201036 AAGGTGTGGACTTTAAAAAGGGTGCCATGGAGTTATGGAC-TTTGA-AAGGGATGCCACG
1 AAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATGGACTTTTGAGAAGGG-TGCCACA
*
2201094 GAGTTGTGGACTTT
1 AAGTTGTGGACTTT
2201108 GAGAAGGTTA
Statistics
Matches: 152, Mismatches: 34, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
57 4 0.03
58 48 0.32
59 55 0.36
60 21 0.14
61 24 0.16
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (59 bp):
AAGTTGTGGACTTTAAAAAGGGTGCCACGGAGTTATGGACTTTTGAGAAGGGTGCCACA
Found at i:2201104 original size:119 final size:119
Alignment explanation
Indices: 2200858--2201107 Score: 290
Period size: 119 Copynumber: 2.1 Consensus size: 119
2200848 GGGTACCAGT
* * * * *
2200858 AAGTTGTGGAC--TTTGAAAAAGGTGCCACGGAGTTATTGACTTCTGAGAAGGGTGTCACAGAGT
1 AAGTTGTGGACTTTTTAAAAAAGGTGCCACGGAGTTATGGACTTCTGAGAAGGGTGCCACAAAGG
** * *
2200921 TGTAGACTTTAGGAAGGGTGCCACTGAATTATGGATTTTGAAAAGGTTGCCACA
66 TGTAGACTTTAAAAAGGGTGCCACTGAATTATGGACTTTGAAAAGGATGCCACA
** * * * *
2200975 AAGTCATGGACTTTTTAAAAAAGTTGCCATGGAGTTATGGACTTTTGAGAGGGGTGCCACAAAGG
1 AAGTTGTGGACTTTTTAAAAAAGGTGCCACGGAGTTATGGACTTCTGAGAAGGGTGCCACAAAGG
* * * *
2201040 TGTGGACTTTAAAAAGGGTGCCA-TGGAGTTATGGACTTTGAAAGGGATGCCACG
66 TGTAGACTTTAAAAAGGGTGCCACT-GAATTATGGACTTTGAAAAGGATGCCACA
*
2201094 GAGTTGTGGACTTT
1 AAGTTGTGGACTTT
2201108 GAGAAGGTTA
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
117 9 0.08
118 1 0.01
119 98 0.91
ACGTcount: A:0.28, C:0.12, G:0.31, T:0.28
Consensus pattern (119 bp):
AAGTTGTGGACTTTTTAAAAAAGGTGCCACGGAGTTATGGACTTCTGAGAAGGGTGCCACAAAGG
TGTAGACTTTAAAAAGGGTGCCACTGAATTATGGACTTTGAAAAGGATGCCACA
Found at i:2201108 original size:29 final size:28
Alignment explanation
Indices: 2200859--2201114 Score: 152
Period size: 29 Copynumber: 8.7 Consensus size: 28
2200849 GGTACCAGTA
* *
2200859 AGTTGTGGACTTTGAAAAAGGTGCCACGG
1 AGTTATGGACTTTG-AAAGGGTGCCACGG
* * *
2200888 AGTTATTGACTTCTGAGAAGGGTGTCACAG
1 AGTTATGGACTT-TGA-AAGGGTGCCACGG
* * * *
2200918 AGTTGTAGACTTTAGGAAGGGTGCCACTG
1 AGTTATGGACTTT-GAAAGGGTGCCACGG
* * * **
2200947 AATTATGGATTTTGAAAAGGTTGCCACAA
1 AGTTATGGACTTTG-AAAGGGTGCCACGG
* * * * *
2200976 AGTCATGGACTTTTTAAAAAAGTTGCCATGG
1 AGTTATGGAC--TTT-GAAAGGGTGCCACGG
* **
2201007 AGTTATGGACTTTTGAGAGGGGTGCCACAA
1 AGTTATGGAC-TTTGA-AAGGGTGCCACGG
* * * *
2201037 AGGTGTGGACTTTAAAAAGGGTGCCATGG
1 AGTTATGGACTTT-GAAAGGGTGCCACGG
2201066 AGTTATGGACTTTGAAAGGGATGCCACGG
1 AGTTATGGACTTTGAAAGGG-TGCCACGG
*
2201095 AGTTGTGGACTTTGAGAAGG
1 AGTTATGGACTTTGA-AAGG
2201115 TTACTCTATT
Statistics
Matches: 170, Mismatches: 46, Indels: 21
0.72 0.19 0.09
Matches are distributed among these distances:
28 7 0.04
29 94 0.55
30 47 0.28
31 22 0.13
ACGTcount: A:0.29, C:0.12, G:0.32, T:0.28
Consensus pattern (28 bp):
AGTTATGGACTTTGAAAGGGTGCCACGG
Found at i:2203593 original size:13 final size:13
Alignment explanation
Indices: 2203577--2203614 Score: 58
Period size: 15 Copynumber: 2.8 Consensus size: 13
2203567 CTCAATGTCA
2203577 CAAGAAAATGAAC
1 CAAGAAAATGAAC
2203590 CAAGGAATAATGAAC
1 CAA-GAA-AATGAAC
2203605 CAAGAAAATG
1 CAAGAAAATG
2203615 GGCGAATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 7 0.30
14 6 0.26
15 10 0.43
ACGTcount: A:0.58, C:0.13, G:0.18, T:0.11
Consensus pattern (13 bp):
CAAGAAAATGAAC
Found at i:2204428 original size:20 final size:19
Alignment explanation
Indices: 2204399--2204457 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2204389 TAACTACTGC
2204399 CAGT-TTCATGTATCGATA
1 CAGTGTTCATGTATCGATA
* *
2204417 CATTTGTTCATGTATCAATA
1 CA-GTGTTCATGTATCGATA
**
2204437 CAGTGAACATGTATCGATA
1 CAGTGTTCATGTATCGATA
2204456 CA
1 CA
2204458 ATGTATAGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.06
19 16 0.48
20 15 0.45
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (19 bp):
CAGTGTTCATGTATCGATA
Found at i:2204470 original size:32 final size:32
Alignment explanation
Indices: 2204426--2204522 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
2204416 ACATTTGTTC
*
2204426 ATGTATCAATACAGTGAACATGTATCGATACA
1 ATGTATCAATACAATGAACATGTATCGATACA
*
2204458 ATGTAT-AGATACAATGAACATGTATCGATATA
1 ATGTATCA-ATACAATGAACATGTATCGATACA
*
2204490 ATGTATCAATACAAAGCATA-ATGTATCGATACA
1 ATGTATCAATACAATG-A-ACATGTATCGATACA
2204523 TCTGAAACTG
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
31 1 0.02
32 41 0.72
33 14 0.25
34 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.29
Consensus pattern (32 bp):
ATGTATCAATACAATGAACATGTATCGATACA
Done.