Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D02
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: 67659327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 461372 characters in sequence are not A, C, G, or T
File 167 of 216
Found at i:52683573 original size:16 final size:17
Alignment explanation
Indices: 52683542--52683576 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
52683532 TTCAAAATTT
*
52683542 TAATTATAATTCTTATA
1 TAATTATAATTATTATA
52683559 TAATTA-AATTATTATA
1 TAATTATAATTATTATA
52683575 TA
1 TA
52683577 CTAGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (17 bp):
TAATTATAATTATTATA
Found at i:52698099 original size:16 final size:16
Alignment explanation
Indices: 52698069--52698116 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
52698059 TTCTGAACAT
52698069 AGTTATTCTAGAACAAC
1 AGTTATTCTA-AACAAC
*
52698086 AGTTGTTCTAAACAAC
1 AGTTATTCTAAACAAC
**
52698102 AACTATTCTAAACAA
1 AGTTATTCTAAACAA
52698117 TATTTGTTGC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 18 0.67
17 9 0.33
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (16 bp):
AGTTATTCTAAACAAC
Found at i:52699316 original size:18 final size:19
Alignment explanation
Indices: 52699273--52699317 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
52699263 TTTTATTTAT
52699273 TTAATATTGTTAATAGTAG
1 TTAATATTGTTAATAGTAG
52699292 TTAATATTGTTAA-AGTATG
1 TTAATATTGTTAATAGTA-G
52699311 TT-ATATT
1 TTAATATT
52699318 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (19 bp):
TTAATATTGTTAATAGTAG
Found at i:52702761 original size:5 final size:5
Alignment explanation
Indices: 52702751--52702775 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
52702741 GGTATGTATT
52702751 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
52702776 TTTTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:52712849 original size:15 final size:15
Alignment explanation
Indices: 52712829--52712857 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52712819 TCTTCTTACT
52712829 GATTTATTAATTATC
1 GATTTATTAATTATC
52712844 GATTTATTAATTAT
1 GATTTATTAATTAT
52712858 TGTCATTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.03, G:0.07, T:0.55
Consensus pattern (15 bp):
GATTTATTAATTATC
Found at i:52715063 original size:35 final size:35
Alignment explanation
Indices: 52715017--52715137 Score: 170
Period size: 35 Copynumber: 3.5 Consensus size: 35
52715007 TACACAGTTA
* * *
52715017 ACCATCCAACACACTAGATGCTCATAAGAGCCAAT
1 ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
*
52715052 ACCATCCAACACACCAGATGCTCATAAGAACTAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
* *
52715087 ACCATCCAACACACCAGATGCTTAGAAGAGCTAGT
1 ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
* *
52715122 ACCATCTAGCACACCA
1 ACCATCCAACACACCA
52715138 AATAACATTG
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 77 1.00
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (35 bp):
ACCATCCAACACACCAGATGCTCATAAGAGCTAGT
Found at i:52723625 original size:40 final size:41
Alignment explanation
Indices: 52723543--52723684 Score: 155
Period size: 41 Copynumber: 3.5 Consensus size: 41
52723533 TTTTAATTCT
* * *
52723543 ATGAAAAGGTTGAAAAGGAAGCTATCC-AGAAAGGATAACAA
1 ATGAAAAGGTTGAAAAGGATGCTATCCGA-AAAAGATATCAA
*
52723584 AT-AAACAGGTTGAAAAGGATG-TATCCGAAAATGATATCAA
1 ATGAAA-AGGTTGAAAAGGATGCTATCCGAAAAAGATATCAA
* * *
52723624 ATGAAAAGGTTGAAAATGATGTTATTCGAAAAAGATATCAA
1 ATGAAAAGGTTGAAAAGGATGCTATCCGAAAAAGATATCAA
** *
52723665 GGGAAAATGTTGAAAAGGAT
1 ATGAAAAGGTTGAAAAGGAT
52723685 AGCAATGAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
40 34 0.39
41 53 0.61
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (41 bp):
ATGAAAAGGTTGAAAAGGATGCTATCCGAAAAAGATATCAA
Found at i:52731062 original size:29 final size:30
Alignment explanation
Indices: 52731001--52731059 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
52730991 TTTTCAAACA
52731001 GAGTCATTTTTATAAATATTTATTTTTTTT
1 GAGTCATTTTTATAAATATTTATTTTTTTT
52731031 GAGTCATTTTTATAAATATTTATTTTTTT
1 GAGTCATTTTTATAAATATTTATTTTTTT
52731060 GAGATTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (30 bp):
GAGTCATTTTTATAAATATTTATTTTTTTT
Found at i:52735304 original size:14 final size:14
Alignment explanation
Indices: 52735285--52735312 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52735275 CTAAAAACTT
52735285 TGACAAAACAGTTA
1 TGACAAAACAGTTA
52735299 TGACAAAACAGTTA
1 TGACAAAACAGTTA
52735313 CGCGAAGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.14, T:0.21
Consensus pattern (14 bp):
TGACAAAACAGTTA
Found at i:52738207 original size:25 final size:25
Alignment explanation
Indices: 52738179--52738260 Score: 93
Period size: 25 Copynumber: 3.5 Consensus size: 25
52738169 ATGTTATAAA
*
52738179 ATAATATATAAAAATAATGCATATG
1 ATAATATACAAAAATAATGCATATG
*
52738204 ATAATATACAAAAGTAATGCA-A-G
1 ATAATATACAAAAATAATGCATATG
*
52738227 --AATGTACAAAAAT-ATGCATATG
1 ATAATATACAAAAATAATGCATATG
*
52738249 ATAATACACAAA
1 ATAATATACAAA
52738261 CAAGGTTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
20 5 0.11
21 12 0.26
22 1 0.02
23 1 0.02
24 9 0.19
25 19 0.40
ACGTcount: A:0.56, C:0.09, G:0.10, T:0.26
Consensus pattern (25 bp):
ATAATATACAAAAATAATGCATATG
Found at i:52738554 original size:16 final size:16
Alignment explanation
Indices: 52738522--52738557 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
52738512 GGAATAGAAA
52738522 TGTACTAGAATAAAGT
1 TGTACTAGAATAAAGT
* *
52738538 TGTAGTAGAATAGAGT
1 TGTACTAGAATAAAGT
52738554 TGTA
1 TGTA
52738558 ATCAGTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (16 bp):
TGTACTAGAATAAAGT
Found at i:52738795 original size:62 final size:59
Alignment explanation
Indices: 52738727--52738982 Score: 262
Period size: 62 Copynumber: 4.3 Consensus size: 59
52738717 TTGTTATTAA
* *
52738727 ATTTTAATA-AGATTATTAGTAAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCAT
1 ATTTTAATATA-ATTATTATTAAATATAATTTAATAAA-AT-AAAA-TAAATAATTTAATCAT
* *
52738789 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAT--AATATATAATTTAATAAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAATAAAATAAATAATTTAATCAT
* *
52738846 ATTCTTAATATATTTATTATTAAAATATGAA-TTAATAAATATCATAATAAATAATTTAATCAT
1 ATT-TTAATATAATTATTATT-AAATAT-AATTTAATAAA-AT-AAAATAAATAATTTAATCAT
* * * *
52738909 ATTTTAACAT-A--ATTATT-AATATAATTTAATAAAAT--AATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAATAAAATAAATAATTTAATCAT
52738962 ATTCTTAATATAATTATTATT
1 ATT-TTAATATAATTATTATT
52738983 TTAGATACAT
Statistics
Matches: 168, Mismatches: 13, Indels: 31
0.79 0.06 0.15
Matches are distributed among these distances:
53 18 0.11
54 6 0.04
55 1 0.01
56 4 0.02
57 35 0.21
58 18 0.11
59 20 0.12
60 4 0.02
61 2 0.01
62 40 0.24
63 20 0.12
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.45
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAATAAAATAAATAATTTAATCAT
Found at i:52738940 original size:20 final size:20
Alignment explanation
Indices: 52738793--52738976 Score: 61
Period size: 20 Copynumber: 9.2 Consensus size: 20
52738783 AATCATATTT
* *
52738793 TAATATAATTATTATTAAATA
1 TAATTTAATAATTATT-AATA
* *
52738814 TAATTTAATAA-AATAATATA
1 TAATTTAATAATTATTA-ATA
*
52738834 TAATTTAATAATATTCTTAATA
1 TAATTTAAT-A-ATTATTAATA
* *
52738856 T-ATTT-ATTATTA-AAATA
1 TAATTTAATAATTATTAATA
52738873 TGAA-TTAATAA--A-T-ATCA
1 T-AATTTAATAATTATTAAT-A
*
52738890 TAA-TAAATAA-T-TTAATCA
1 TAATTTAATAATTATTAAT-A
*
52738908 TATTTTAACATAATTATTAATA
1 TAATTT-A-ATAATTATTAATA
* *
52738930 TAATTTAATAA-AATAATATA
1 TAATTTAATAATTATTA-ATA
*
52738950 TAATTTAATAACATTCTTAATA
1 TAATTTAAT-A-ATTATTAATA
52738972 TAATT
1 TAATT
52738977 ATTATTTTAG
Statistics
Matches: 122, Mismatches: 21, Indels: 39
0.67 0.12 0.21
Matches are distributed among these distances:
16 10 0.08
17 9 0.07
18 11 0.09
19 9 0.07
20 33 0.27
21 20 0.16
22 21 0.17
23 9 0.07
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (20 bp):
TAATTTAATAATTATTAATA
Found at i:52738966 original size:116 final size:121
Alignment explanation
Indices: 52738738--52738982 Score: 367
Period size: 116 Copynumber: 2.0 Consensus size: 121
52738728 TTTTAATAAG
*
52738738 ATTATTAGTAAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAATATAATT
1 ATTATTAG-AAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAACATAA-T
* *
52738803 ATTATTAAATATAATTTAATAAAATAATATATAATTTAATAATATTCTTAATATATTT
64 ATTATTAAATATAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
* * *
52738861 ATTATTA-AAATATGAA-TTAATAAATATCATAA-TAAATAATTTAATCATATTTTAACAT-A-A
1 ATTATTAGAAATAT-AATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAACATAATA
52738921 TTATT-AATATAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
65 TTATTAAATATAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
52738977 ATTATT
1 ATTATT
52738983 TTAGATACAT
Statistics
Matches: 115, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
116 55 0.48
117 6 0.05
119 1 0.01
120 24 0.21
121 20 0.17
122 2 0.02
123 7 0.06
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (121 bp):
ATTATTAGAAATATAATTTAATAAATATAAAAAGTAAATAATTAAATCATATTTTAACATAATAT
TATTAAATATAATTTAATAAAATAATATATAATTTAATAACATTCTTAATATAATT
Found at i:52739835 original size:14 final size:14
Alignment explanation
Indices: 52739816--52739843 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52739806 TACAATATAT
52739816 ATAAGAATTATACG
1 ATAAGAATTATACG
52739830 ATAAGAATTATACG
1 ATAAGAATTATACG
52739844 GATCCATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (14 bp):
ATAAGAATTATACG
Found at i:52762771 original size:24 final size:24
Alignment explanation
Indices: 52762739--52762822 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
52762729 GGCTATATAA
52762739 CAGGAAGCTCATAAGAGCCATATT
1 CAGGAAGCTCATAAGAGCCATATT
** * *
52762763 CAGGAAGCTCATGTGAGTCA-ATAA
1 CAGGAAGCTCATAAGAGCCATAT-T
* *
52762787 CGGGTAGCTC-TGAAGAGCCATATT
1 CAGGAAGCTCAT-AAGAGCCATATT
52762811 CAGGAAGCTCAT
1 CAGGAAGCTCAT
52762823 GTGAGTCAAT
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
23 3 0.07
24 38 0.86
25 3 0.07
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.21
Consensus pattern (24 bp):
CAGGAAGCTCATAAGAGCCATATT
Found at i:52762803 original size:48 final size:48
Alignment explanation
Indices: 52762751--52762865 Score: 212
Period size: 48 Copynumber: 2.4 Consensus size: 48
52762741 GGAAGCTCAT
52762751 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
1 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
52762799 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
1 AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
*
52762847 AAGAGCCATTAATCAGGAA
1 AAGAGCCA-TATTCAGGAA
52762866 ACTTCAGATA
Statistics
Matches: 65, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
48 56 0.86
49 9 0.14
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.22
Consensus pattern (48 bp):
AAGAGCCATATTCAGGAAGCTCATGTGAGTCAATAACGGGTAGCTCTG
Found at i:52762843 original size:24 final size:24
Alignment explanation
Indices: 52762768--52762844 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
52762758 ATATTCAGGA
52762768 AGCTCATGTGAGTCAATAACGGGT
1 AGCTCATGTGAGTCAATAACGGGT
* * * * *
52762792 AGCTC-TGAAGAG-CCATATTCAGGA
1 AGCTCATG-TGAGTCAATA-ACGGGT
52762816 AGCTCATGTGAGTCAATAACGGGT
1 AGCTCATGTGAGTCAATAACGGGT
52762840 AGCTC
1 AGCTC
52762845 TGAAGAGCCA
Statistics
Matches: 39, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
23 6 0.15
24 27 0.69
25 6 0.15
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.23
Consensus pattern (24 bp):
AGCTCATGTGAGTCAATAACGGGT
Found at i:52767069 original size:27 final size:28
Alignment explanation
Indices: 52766985--52767082 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
52766975 CATGAGATTG
* * * *
52766985 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
52767014 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
52767042 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52767069 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
52767083 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52767093 original size:27 final size:27
Alignment explanation
Indices: 52767013--52767095 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
52767003 TAAATTGTAC
* *
52767013 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
52767041 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
52767068 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
52767095 A
1 A
52767096 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:52767096 original size:29 final size:27
Alignment explanation
Indices: 52766985--52767096 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
52766975 CATGAGATTG
** * *
52766985 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
52767014 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
52767042 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
52767069 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
52767097 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:52774946 original size:27 final size:28
Alignment explanation
Indices: 52774862--52774959 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
52774852 CATGAGATTG
* * * *
52774862 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
52774891 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
52774919 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
52774946 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
52774960 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:52774970 original size:27 final size:27
Alignment explanation
Indices: 52774890--52774972 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
52774880 TAAATTGTAC
* *
52774890 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
52774918 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
52774945 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
52774972 A
1 A
52774973 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:52774973 original size:29 final size:27
Alignment explanation
Indices: 52774862--52774973 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
52774852 CATGAGATTG
** * *
52774862 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
52774891 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
52774919 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
52774946 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
52774974 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:52780436 original size:41 final size:41
Alignment explanation
Indices: 52780379--52780502 Score: 239
Period size: 41 Copynumber: 3.0 Consensus size: 41
52780369 GAATATTAAG
52780379 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
1 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
52780420 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
1 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
*
52780461 AAACATATATGAGCTAATAAATAATCAATTTTCATATACTT
1 AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
52780502 A
1 A
52780503 TACCTTTCAT
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (41 bp):
AAACATATATGAGCTAATCAATAATCAATTTTCATATACTT
Found at i:52780768 original size:25 final size:25
Alignment explanation
Indices: 52780736--52780839 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
52780726 AGCCCTCTCT
*
52780736 TGAGCCATATAACAGGAAGCTCGTG
1 TGAGCCATATAACAGGAAGCTCATG
* * *
52780761 TGAGCCATGTAACGGGAAGCTTAT-
1 TGAGCCATATAACAGGAAGCTCATG
* * * *
52780785 TCGGGCTATATAACAAGAAGCTCATA
1 T-GAGCCATATAACAGGAAGCTCATG
* *
52780811 AGAGCCATAT-TCAGGAAGCTCATG
1 TGAGCCATATAACAGGAAGCTCATG
52780835 TGAGC
1 TGAGC
52780840 TAATAACGGG
Statistics
Matches: 60, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
24 16 0.27
25 44 0.73
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.22
Consensus pattern (25 bp):
TGAGCCATATAACAGGAAGCTCATG
Found at i:52784062 original size:18 final size:18
Alignment explanation
Indices: 52784035--52784077 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52784025 CGCATAAAAA
* *
52784035 GAAAGTAAATAAATAAAC
1 GAAAGAAAATAAACAAAC
*
52784053 GAAAGAAAATAAACAAAT
1 GAAAGAAAATAAACAAAC
52784071 GAAAGAA
1 GAAAGAA
52784078 GGGGGAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.05, G:0.14, T:0.12
Consensus pattern (18 bp):
GAAAGAAAATAAACAAAC
Found at i:52790030 original size:6 final size:6
Alignment explanation
Indices: 52790019--52790127 Score: 51
Period size: 6 Copynumber: 17.0 Consensus size: 6
52790009 GAAATAATCC
* * * * *
52790019 ATAAAA ATAAAA ATAAAT TTTAAA AGAAAA ATAAACTA A-AAAA GTCTAAGAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA--A ATAAAA --ATAA-AA
* **
52790071 ATAAAA TTAAAAAA ACTAAAA ATAAAAA ATAAAA ATAAAA A-AAGG ATAAAA
1 ATAAAA AT-A-AAA A-TAAAA AT-AAAA ATAAAA ATAAAA ATAAAA ATAAAA
52790122 ATAAAA
1 ATAAAA
52790128 GTGAAAAGAA
Statistics
Matches: 76, Mismatches: 16, Indels: 22
0.67 0.14 0.19
Matches are distributed among these distances:
5 4 0.05
6 44 0.58
7 17 0.22
8 8 0.11
9 3 0.04
ACGTcount: A:0.74, C:0.03, G:0.05, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:52790075 original size:22 final size:20
Alignment explanation
Indices: 52790045--52790096 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 20
52790035 ATTTTAAAAG
*
52790045 AAAAATAAACTAAAAAAGTCT
1 AAAAATAAACTAAAAAA-ACT
*
52790066 AAGAAATAAAATTAAAAAAACT
1 AA-AAAT-AAACTAAAAAAACT
52790088 AAAAATAAA
1 AAAAATAAA
52790097 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 3 0.11
21 6 0.22
22 8 0.30
23 10 0.37
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.17
Consensus pattern (20 bp):
AAAAATAAACTAAAAAAACT
Found at i:52790098 original size:22 final size:23
Alignment explanation
Indices: 52790042--52790105 Score: 62
Period size: 22 Copynumber: 2.8 Consensus size: 23
52790032 TAAATTTTAA
*
52790042 AAGAAA-AATAAACTAAAAAAGTCT
1 AAGAAATAA-AAA-TAAAAAAGACT
*
52790066 AAGAAATAAAATTAAAAAA-ACT
1 AAGAAATAAAAATAAAAAAGACT
52790088 AA-AAATAAAAAATAAAAA
1 AAGAAAT-AAAAATAAAAA
52790106 TAAAAAAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
21 4 0.11
22 14 0.40
23 7 0.20
24 8 0.23
25 2 0.06
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.16
Consensus pattern (23 bp):
AAGAAATAAAAATAAAAAAGACT
Found at i:52790100 original size:28 final size:29
Alignment explanation
Indices: 52790069--52790127 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
52790059 AAAGTCTAAG
* *
52790069 AAATAAAATTAAAAAAA-CTAAAAATAAA
1 AAATAAAAATAAAAAAAGATAAAAATAAA
52790097 AAATAAAAATAAAAAAAGGATAAAAATAAA
1 AAATAAAAATAAAAAAA-GATAAAAATAAA
52790127 A
1 A
52790128 GTGAAAAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 16 0.59
30 11 0.41
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.15
Consensus pattern (29 bp):
AAATAAAAATAAAAAAAGATAAAAATAAA
Found at i:52790103 original size:13 final size:13
Alignment explanation
Indices: 52790069--52790112 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
52790059 AAAGTCTAAG
*
52790069 AAATAAAATTAAAA
1 AAATAAAAAT-AAA
52790083 AAACTAAAAATAAA
1 AAA-TAAAAATAAA
52790097 AAATAAAAATAAA
1 AAATAAAAATAAA
52790110 AAA
1 AAA
52790113 AGGATAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 13 0.46
14 9 0.32
15 6 0.21
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAATAAA
Found at i:52791688 original size:12 final size:12
Alignment explanation
Indices: 52791660--52791696 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
52791650 AGGTAGTAGG
52791660 AATAATAATATAA
1 AATAATAATA-AA
*
52791673 AATAATACTAAA
1 AATAATAATAAA
52791685 AATAATAATAAA
1 AATAATAATAAA
52791697 TGCTAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:52791774 original size:27 final size:30
Alignment explanation
Indices: 52791710--52791777 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
52791700 TAAATAGCAT
52791710 AAATAAAATTAAATTAAATTAAATTAAGCATA
1 AAATAAAATTAAATTAAATTAAATTAAG-A-A
*
52791742 AGAATAAAA-TAAATT-AATTAATTTAAG-A
1 A-AATAAAATTAAATTAAATTAAATTAAGAA
52791770 AAATAAAA
1 AAATAAAA
52791778 ATATAGGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 7 0.21
28 2 0.06
31 11 0.32
32 7 0.21
33 7 0.21
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.29
Consensus pattern (30 bp):
AAATAAAATTAAATTAAATTAAATTAAGAA
Found at i:52796230 original size:30 final size:30
Alignment explanation
Indices: 52796196--52796253 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
52796186 CACGGTCTGG
*
52796196 CACATGGTCGTGTGTCTAGCCCGTGTGGCT
1 CACATGGTCGTGTGTCTAACCCGTGTGGCT
*
52796226 CACATGGTCGTGTGTCTAACTCGTGTGG
1 CACATGGTCGTGTGTCTAACCCGTGTGG
52796254 GAAGGCCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.12, C:0.24, G:0.33, T:0.31
Consensus pattern (30 bp):
CACATGGTCGTGTGTCTAACCCGTGTGGCT
Found at i:52797007 original size:20 final size:20
Alignment explanation
Indices: 52796967--52797018 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
52796957 TTGGAGCCAG
*
52796967 AGATATCGATACCAAAGAAA
1 AGATATTGATACCAAAGAAA
* **
52796987 ATATATTGATACCAATTAAA
1 AGATATTGATACCAAAGAAA
*
52797007 AGGTATTGATAC
1 AGATATTGATAC
52797019 TGGATTGATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (20 bp):
AGATATTGATACCAAAGAAA
Found at i:52797177 original size:21 final size:20
Alignment explanation
Indices: 52797153--52797203 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
52797143 GGAGCAATAC
* *
52797153 TAACTTGTTTTAAAGCAATTT
1 TAACTTGATTGAAA-CAATTT
* *
52797174 TAACTCGATTGAAACCATTT
1 TAACTTGATTGAAACAATTT
52797194 TAACTTGATT
1 TAACTTGATT
52797204 AAAAGTTTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (20 bp):
TAACTTGATTGAAACAATTT
Found at i:52801261 original size:84 final size:83
Alignment explanation
Indices: 52801089--52801246 Score: 223
Period size: 84 Copynumber: 1.9 Consensus size: 83
52801079 AGTGGTGTTG
** * *
52801089 ATACACACCTTGAAGTCTTCATTAATTTCTCATAAGTTCATTTTTATCCCCACACACCAACATAC
1 ATACACACCTTGAAACCTTCATTAATTTCTCATAAGCTCATTTGTAT-CCCACACACCAACATAC
52801154 TGTACATATTAATTATAAA
65 TGTACATATTAATTATAAA
* * *
52801173 ATACACACCTTGAAACCTTCGTTAATTTCTCATAAGCTCA-TTGT-T-CTACACACCAGCATACT
1 ATACACACCTTGAAACCTTCATTAATTTCTCATAAGCTCATTTGTATCCCACACACCAACATACT
52801235 GTACATATTAAT
66 GTACATATTAAT
52801247 CATAGTAATC
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
80 27 0.40
82 1 0.01
83 3 0.04
84 36 0.54
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (83 bp):
ATACACACCTTGAAACCTTCATTAATTTCTCATAAGCTCATTTGTATCCCACACACCAACATACT
GTACATATTAATTATAAA
Found at i:52803472 original size:25 final size:25
Alignment explanation
Indices: 52803422--52803474 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
52803412 TAAAGGAAGA
* *
52803422 AAATAATGTCAATAATAGTATTAAT
1 AAATAATGTCAATAATAGAATAAAT
*
52803447 AAATAATGTTATATAATA-AATAAAT
1 AAATAATGTCA-ATAATAGAATAAAT
52803472 AAA
1 AAA
52803475 AAGAAATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.58, C:0.02, G:0.06, T:0.34
Consensus pattern (25 bp):
AAATAATGTCAATAATAGAATAAAT
Found at i:52805964 original size:27 final size:28
Alignment explanation
Indices: 52805914--52805976 Score: 92
Period size: 27 Copynumber: 2.3 Consensus size: 28
52805904 TACATAGTAC
*
52805914 ATATATATGTGTGGTTGTGCTATATATA
1 ATATATATGTGTGGTTGTACTATATATA
* *
52805942 ATATATATGTG-GGTTTTATTATATATA
1 ATATATATGTGTGGTTGTACTATATATA
52805969 ATATATAT
1 ATATATAT
52805977 ATGCATTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 21 0.66
28 11 0.34
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (28 bp):
ATATATATGTGTGGTTGTACTATATATA
Found at i:52806308 original size:17 final size:18
Alignment explanation
Indices: 52806273--52806310 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
52806263 TGTGAGCCAA
**
52806273 TTATATTTGTAAATTATG
1 TTATATTTGTAAACCATG
52806291 TTATATTT-TAAACCATG
1 TTATATTTGTAAACCATG
52806308 TTA
1 TTA
52806311 ACTTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.08, T:0.53
Consensus pattern (18 bp):
TTATATTTGTAAACCATG
Found at i:52806371 original size:18 final size:18
Alignment explanation
Indices: 52806344--52806384 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
52806334 GGCAACTATG
* **
52806344 TTAATTTGGTGATTTGTA
1 TTAATATGGTGAACTGTA
52806362 TTAATATGGTGAACTGTA
1 TTAATATGGTGAACTGTA
52806380 TTAAT
1 TTAAT
52806385 TTGCCAGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (18 bp):
TTAATATGGTGAACTGTA
Found at i:52806384 original size:36 final size:36
Alignment explanation
Indices: 52806308--52806387 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
52806298 TTAAACCATG
* * *
52806308 TTAACTTGGTGAATTATATTATTATGGGCAACTATG
1 TTAATTTGGTGAATTATATTAATATGGGCAACTATA
* * *
52806344 TTAATTTGGTGATTTGTATTAATATGGTG-AACTGTA
1 TTAATTTGGTGAATTATATTAATATGG-GCAACTATA
52806380 TTAATTTG
1 TTAATTTG
52806388 CCAGACTATG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
36 36 0.97
37 1 0.03
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.46
Consensus pattern (36 bp):
TTAATTTGGTGAATTATATTAATATGGGCAACTATA
Found at i:52807020 original size:51 final size:51
Alignment explanation
Indices: 52806965--52807073 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 51
52806955 TATAATGGAG
* *
52806965 TATGAACTATTATTTTGCATG-GATTGTTATTCGGTATGAATTGTTATT-TCA
1 TATGAACTATTATTTTGCATGAG-TTGTCATTCGGTATGAACTGTTATTAT-A
*
52807016 TATGAACTATTATTTTGCATGAGTTGTCATTTGGTATGAACTGTTATTATA
1 TATGAACTATTATTTTGCATGAGTTGTCATTCGGTATGAACTGTTATTATA
52807067 TATGAAC
1 TATGAAC
52807074 ATATGTTTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
51 51 0.96
52 2 0.04
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (51 bp):
TATGAACTATTATTTTGCATGAGTTGTCATTCGGTATGAACTGTTATTATA
Found at i:52809875 original size:52 final size:51
Alignment explanation
Indices: 52809804--52810110 Score: 391
Period size: 52 Copynumber: 6.1 Consensus size: 51
52809794 ATCAAGTGAC
* *
52809804 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGT-G
* * *
52809856 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC-----
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
52809902 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
*
52809953 AAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
52810005 AAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 -AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
* * *
52810052 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTG-ACAAGTG
52810104 ATAAGTG
1 A-AAGTG
52810111 CTATACTTAT
Statistics
Matches: 225, Mismatches: 17, Indels: 25
0.84 0.06 0.09
Matches are distributed among these distances:
46 82 0.36
47 1 0.00
52 137 0.61
53 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
Found at i:52809906 original size:46 final size:46
Alignment explanation
Indices: 52809856--52810237 Score: 414
Period size: 46 Copynumber: 8.3 Consensus size: 46
52809846 TGACAAGTGG
* * *
52809856 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
52809902 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
*
52809948 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* * *
52810000 AAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* * *
52810052 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
52810098 AAAGTGATAA--G-T-GC-T-A--T--ACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
* *
52810134 AAAGTGATAAGTGTTAGCCTT-AGCTACACTTATCTGATCAAGTGAG
1 AAAGTGATAAGTGATAG-CTTCAGCTACACTTATCTGATCAAGTGAC
* * *
52810180 AAAGTGATAAGTGGTAGCCT-AGCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
52810224 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
52810238 CATATGTAAG
Statistics
Matches: 301, Mismatches: 19, Indels: 35
0.85 0.05 0.10
Matches are distributed among these distances:
36 28 0.09
38 2 0.01
39 1 0.00
40 2 0.01
41 2 0.01
42 4 0.01
43 14 0.05
44 6 0.02
45 20 0.07
46 127 0.42
52 95 0.32
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAC
Found at i:52809910 original size:98 final size:96
Alignment explanation
Indices: 52809790--52810237 Score: 470
Period size: 98 Copynumber: 4.8 Consensus size: 96
52809780 TTTGAGTACT
52809790 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT-
* * *
52809855 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 -AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
52809888 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT-
*
52809953 AAAAGTGATAAGTGATAGCTTCGGCTACACTTA
65 -AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* ** * *
52809986 TCTGATCAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
* *
52810051 C----AAAGTGATAAGTGGTAGCTTTAGCTACACTTA
60 CAAGTAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
52810084 TCTGATCAAGTGAAAAAGTGATAA---GT-GC--TA--T--ACTTATCTGATCAAGTGAC----A
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTA
*
52810135 AAGTGATAAGTGTTAGCCTT-AGCTACACTTA
66 AAGTGATAAGTGATAG-CTTCAGCTACACTTA
* * *
52810166 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AGGGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT-
52810229 ATAAGTGAT
65 A-AAGTGAT
52810238 CATATGTAAG
Statistics
Matches: 309, Mismatches: 19, Indels: 46
0.83 0.05 0.12
Matches are distributed among these distances:
82 68 0.22
83 3 0.01
84 1 0.00
85 2 0.01
86 2 0.01
87 2 0.01
88 2 0.01
89 2 0.01
90 5 0.02
91 12 0.04
92 10 0.03
95 1 0.00
96 7 0.02
98 149 0.48
104 43 0.14
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (96 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTA
AAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:52810010 original size:150 final size:151
Alignment explanation
Indices: 52809796--52810110 Score: 524
Period size: 150 Copynumber: 2.1 Consensus size: 151
52809786 TACTTCTGAT
* * *
52809796 CAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTGGAAAGT
1 CAAGTGA-AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGT
*
52809861 GATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGC
65 GATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGC
52809926 TACACTTATCTGATCAAGTG-A
130 TACACTTATCTGATCAAGTGAA
*
52809947 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTG
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTG
* * *
52810012 ATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCT
66 ATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCT
52810077 ACACTTATCTGATCAAGTGAA
131 ACACTTATCTGATCAAGTGAA
* *
52810098 AAAGTGATAAGTG
1 CAAGTGAAAAGTG
52810111 CTATACTTAT
Statistics
Matches: 153, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
150 134 0.88
151 19 0.12
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (151 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTGAAAAGTG
ATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCAGCT
ACACTTATCTGATCAAGTGAA
Found at i:52810120 original size:36 final size:36
Alignment explanation
Indices: 52810074--52810146 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
52810064 GGTAGCTTTA
52810074 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
52810110 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
52810146 G
1 G
52810147 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:52810165 original size:82 final size:82
Alignment explanation
Indices: 52810028--52810192 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
52810018 GATAGCTTCG
*
52810028 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
52810093 GTGAAAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
* *
52810110 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAA
1 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
*
52810175 GTGAGAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
52810192 G
1 G
52810193 GTAGCCTAGC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (82 bp):
GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
GTGAAAAAGTGATAAGT
Found at i:52818562 original size:13 final size:13
Alignment explanation
Indices: 52818544--52818591 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
52818534 TTCAAATTTT
*
52818544 TCAAAAACACTTC
1 TCAAAAGCACTTC
52818557 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
52818570 TTAAAAGTACTTC
1 TCAAAAGCACTTC
52818583 TCAAAAGCA
1 TCAAAAGCA
52818592 ATGAAGAACT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:52818696 original size:18 final size:17
Alignment explanation
Indices: 52818673--52818706 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
52818663 TTTATTTATA
52818673 TTGTTTCAAGTTTTTTTT
1 TTGTTTCAA-TTTTTTTT
*
52818691 TTGTTTTAATTTTTTT
1 TTGTTTCAATTTTTTT
52818707 AATTTTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.12, C:0.03, G:0.09, T:0.76
Consensus pattern (17 bp):
TTGTTTCAATTTTTTTT
Found at i:52818729 original size:12 final size:12
Alignment explanation
Indices: 52818696--52818737 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
52818686 TTTTTTTGTT
52818696 TTAATTTTTTTAA
1 TTAA-TTTTTTAA
*
52818709 TT-TTATTTTTAA
1 TTAAT-TTTTTAA
52818721 TTAATTTTTTAA
1 TTAATTTTTTAA
52818733 TTAAT
1 TTAAT
52818738 AAACAAGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.04
12 21 0.84
13 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTAATTTTTTAA
Found at i:52819445 original size:2 final size:2
Alignment explanation
Indices: 52819438--52819464 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52819428 TAGATTAATG
52819438 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52819465 TGGTACACGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52824835 original size:29 final size:29
Alignment explanation
Indices: 52824793--52824851 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52824783 TAATAATGTT
52824793 AATGATTATTAAGAATTAAATCAAATCAA
1 AATGATTATTAAGAATTAAATCAAATCAA
52824822 AATGATTATTAAGAATTAAATCAAATCAA
1 AATGATTATTAAGAATTAAATCAAATCAA
52824851 A
1 A
52824852 TTTTCATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AATGATTATTAAGAATTAAATCAAATCAA
Found at i:52830219 original size:34 final size:35
Alignment explanation
Indices: 52830181--52830247 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
52830171 CAGTAAAATA
* *
52830181 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
*
52830215 TTTTCTGTAAAATAATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
52830248 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:52830233 original size:20 final size:20
Alignment explanation
Indices: 52830196--52830235 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
52830186 CGTAAAATAA
**
52830196 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATAATTTACT
*
52830216 TTTCTGTAAAATAATTTACT
1 TTTCTGGAAAATAATTTACT
52830236 GAAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATAATTTACT
Found at i:52831563 original size:3 final size:3
Alignment explanation
Indices: 52831555--52831580 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52831545 GATAGAAATG
52831555 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
52831581 GAAAAGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52838453 original size:30 final size:31
Alignment explanation
Indices: 52838409--52838467 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
52838399 CAATTCATAT
* *
52838409 ATATCTCATGTCACATAACATGTTTCATTCC
1 ATATCTCATATCACATAACATGTATCATTCC
*
52838440 ATAT-TCATATCACATATCATGTATCATT
1 ATATCTCATATCACATAACATGTATCATT
52838468 TATATCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (31 bp):
ATATCTCATATCACATAACATGTATCATTCC
Found at i:52847519 original size:18 final size:19
Alignment explanation
Indices: 52847496--52847531 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52847486 TCAATGTTGT
52847496 AAAATAAA-CAAGAAAAAA
1 AAAATAAAGCAAGAAAAAA
*
52847514 AAAATAAAGGAAGAAAAA
1 AAAATAAAGCAAGAAAAA
52847532 GAAGAGGAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.06
Consensus pattern (19 bp):
AAAATAAAGCAAGAAAAAA
Found at i:52849868 original size:61 final size:59
Alignment explanation
Indices: 52849746--52849883 Score: 168
Period size: 61 Copynumber: 2.3 Consensus size: 59
52849736 TTAATATAAC
* * * ** * * *
52849746 ATTTGGTATTTGAATTTAACACTTTTTCCTAATTTGGTACTTAAACTTTTTTTGGCTCA
1 ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
52849805 ATTTGGTACTTGAACTTGACATTTTTTTCCCTAATTTAATACCTAAACTTTTTTGGGCCCA
1 ATTTGGTACTTGAACTTGACA-CTTTTT-CCTAATTTAATACCTAAACTTTTTTGGGCCCA
*
52849866 ATTTGGTACCTGAACTTG
1 ATTTGGTACTTGAACTTG
52849884 GCACCTAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
59 18 0.27
60 5 0.07
61 44 0.66
ACGTcount: A:0.24, C:0.17, G:0.13, T:0.46
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACACTTTTTCCTAATTTAATACCTAAACTTTTTTGGGCCCA
Found at i:52868078 original size:44 final size:44
Alignment explanation
Indices: 52868018--52868124 Score: 139
Period size: 44 Copynumber: 2.4 Consensus size: 44
52868008 AAGATGGCAA
*
52868018 ATCTTATCTC-CTTGAAGTTACAGTGGAGCAGG-TTAAAGCCGAT-G
1 ATCTTATCTCTC-TGAAGTTACAGTGGAG-AGGATTAAAACC-ATGG
* *
52868062 ATCTTATCTCTCTGAAGTTACAGTGGAGTGGATTAAAACCTTGG
1 ATCTTATCTCTCTGAAGTTACAGTGGAGAGGATTAAAACCATGG
52868106 ATCTTATCTCTCTGAAGTT
1 ATCTTATCTCTCTGAAGTT
52868125 GCAGAGAGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
43 3 0.05
44 53 0.93
45 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (44 bp):
ATCTTATCTCTCTGAAGTTACAGTGGAGAGGATTAAAACCATGG
Found at i:52868162 original size:40 final size:41
Alignment explanation
Indices: 52868107--52868230 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 41
52868097 AAACCTTGGA
*
52868107 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCTAG
1 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCAAG
* ** * * * *
52868147 TCTTATCTCTCTGAAGTTGTAGTGGAGAAGACTAAGTAAGCAAG
1 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGA-T-CG-CATCAAG
*
52868191 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCACATCAA
1 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCAA
52868231 ATTCATCTTT
Statistics
Matches: 65, Mismatches: 15, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
40 21 0.32
41 10 0.15
42 1 0.02
43 2 0.03
44 31 0.48
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (41 bp):
TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCAAG
Found at i:52868163 original size:84 final size:84
Alignment explanation
Indices: 52868063--52868228 Score: 210
Period size: 84 Copynumber: 2.0 Consensus size: 84
52868053 AAGCCGATGA
** * **
52868063 TCTTATCTCTCTGAAGTTACAGTGGAGTGGATTAA-AACCTTGGATCTTATCTCTCTGAAGTTGC
1 TCTTATCTCTCTGAAGTTACAGTGGAGAAGACTAAGAACC-AAG-TCTTATCTCTCTGAAGTTGC
*
52868127 AG-AGAGCAGATCGCATCTAG
64 AGCAGAGCAGATCACATCTAG
** *
52868147 TCTTATCTCTCTGAAGTTGTAGTGGAGAAGACTAAGTAAGCAAGTCTTATCTCTCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTACAGTGGAGAAGACTAAG-AACCAAGTCTTATCTCTCTGAAGTTGCA
52868212 GCAGAGCAGATCACATC
65 GCAGAGCAGATCACATC
52868229 AAATTCATCT
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
84 52 0.74
85 15 0.21
86 3 0.04
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (84 bp):
TCTTATCTCTCTGAAGTTACAGTGGAGAAGACTAAGAACCAAGTCTTATCTCTCTGAAGTTGCAG
CAGAGCAGATCACATCTAG
Found at i:52877384 original size:23 final size:24
Alignment explanation
Indices: 52877352--52877396 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
52877342 TGCATGTTTA
52877352 TTTCTTATTTTCAATTTGTTTTGT
1 TTTCTTATTTTCAATTTGTTTTGT
* *
52877376 TTTC-TATTTTTATTTTGTTTT
1 TTTCTTATTTTCAATTTGTTTT
52877397 TAGTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.11, C:0.07, G:0.07, T:0.76
Consensus pattern (24 bp):
TTTCTTATTTTCAATTTGTTTTGT
Found at i:52877397 original size:24 final size:25
Alignment explanation
Indices: 52877352--52877402 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
52877342 TGCATGTTTA
52877352 TTTCTTATTTTCAATTTGTTTT-GT
1 TTTCTTATTTTCAATTTGTTTTAGT
* *
52877376 TTTC-TATTTTTATTTTGTTTTTAGT
1 TTTCTTATTTTCAATTTG-TTTTAGT
52877401 TT
1 TT
52877403 GTTTAGTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 11 0.48
24 8 0.35
25 4 0.17
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.75
Consensus pattern (25 bp):
TTTCTTATTTTCAATTTGTTTTAGT
Found at i:52879057 original size:31 final size:34
Alignment explanation
Indices: 52878995--52879057 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
52878985 TAAATCTTAT
*
52878995 TAAATTAATAGAATATTTATTTACAAGATAAAAAA
1 TAAATTAATAAAATATTTATTTA-AAGATAAAAAA
52879030 TAAATTAATAAAATA-TTA-TT-AAGATAAA
1 TAAATTAATAAAATATTTATTTAAAGATAAA
52879058 CATTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 8 0.30
33 2 0.07
34 3 0.11
35 14 0.52
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.35
Consensus pattern (34 bp):
TAAATTAATAAAATATTTATTTAAAGATAAAAAA
Found at i:52883543 original size:43 final size:43
Alignment explanation
Indices: 52883496--52883636 Score: 128
Period size: 43 Copynumber: 3.3 Consensus size: 43
52883486 CGGGTAAGTC
*
52883496 GAAGCAATTATACTGACACACGAGGTGCATTATCGAACGAACT
1 GAAGCAATTATACTGACACACGAGGTGCATCATCGAACGAACT
* * * ** *
52883539 GAAGCAATTATACTG--GCACGTATAGTGCATCATAGAATAAATT
1 GAAGCAATTATACTGACACACG-A-GGTGCATCATCGAACGAACT
* * *
52883582 GAAGCAATTATACTAACACATGAGATGCATCATC-AGACGAACT
1 GAAGCAATTATACTGACACACGAGGTGCATCATCGA-ACGAACT
52883625 GCAA-CAATTATA
1 G-AAGCAATTATA
52883637 TTGGCACGCT
Statistics
Matches: 76, Mismatches: 16, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
41 4 0.05
42 2 0.03
43 64 0.84
44 3 0.04
45 3 0.04
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (43 bp):
GAAGCAATTATACTGACACACGAGGTGCATCATCGAACGAACT
Found at i:52886040 original size:41 final size:41
Alignment explanation
Indices: 52885940--52886041 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 41
52885930 GCAATTATCC
* *
52885940 TGGCACGTAACTGCATCAACGATGTACTAAAGCAAATATAT
1 TGGCACGTAACTGCATCATCGATATACTAAAGCAAATATAT
* * * *
52885981 TAGCACGTAAGTGCATCATCGGATATAC-ATAAGTAATTA-AT
1 TGGCACGTAACTGCATCATC-GATATACTA-AAGCAAATATAT
52886022 TGGCACGTAACTGCATCATC
1 TGGCACGTAACTGCATCATC
52886042 ACTAAATCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 38 0.75
42 13 0.25
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (41 bp):
TGGCACGTAACTGCATCATCGATATACTAAAGCAAATATAT
Found at i:52890160 original size:41 final size:41
Alignment explanation
Indices: 52890098--52890217 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 41
52890088 TGATCGAATG
* *
52890098 TAATACAGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
*
52890139 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGATA
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
* * * * * * *
52890180 CATTTCGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTG
52890218 TATTGAATCA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 69 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
TAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAA
Found at i:52897661 original size:41 final size:40
Alignment explanation
Indices: 52897566--52897679 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 40
52897556 AATGTAATAC
* *
52897566 AGACTTTACGTCTAGCAGGCTTGATGCCGGTGAAATAATTT
1 AGACTATACGTCTAGCAGGCTTAATGCCGGTG-AATAATTT
*
52897607 AGACTTTACGTCTAGCAGGCTTAATGCCGGTG-ATACATTT
1 AGACTATACGTCTAGCAGGCTTAATGCCGGTGAATA-ATTT
* * * *
52897647 CGGACTATAGGTCTAGCAGGCTAAAAGCCGGTG
1 -AGACTATACGTCTAGCAGGCTTAATGCCGGTG
52897680 TACTGAATCA
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
39 3 0.05
40 4 0.06
41 58 0.89
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (40 bp):
AGACTATACGTCTAGCAGGCTTAATGCCGGTGAATAATTT
Found at i:52899126 original size:31 final size:31
Alignment explanation
Indices: 52899085--52899168 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
52899075 ATCCAATGCT
*
52899085 CAAATC-AATTCAGTAATATATATCCATATA
1 CAAATCAAATTCAGCAATATATATCCATATA
* * *
52899115 CAAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCAGCAATATATATCCATATA
* *
52899146 CAAATCAAATTCGGCAATGTATA
1 CAAATCAAATTCAGCAATATATA
52899169 AAACATATAC
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 6 0.12
31 43 0.88
ACGTcount: A:0.44, C:0.17, G:0.08, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCAGCAATATATATCCATATA
Found at i:52899187 original size:31 final size:31
Alignment explanation
Indices: 52899110--52899169 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
52899100 ATATATATCC
*
52899110 ATATACAAATCAAATTCGGCAATGTATATCT
1 ATATACAAATCAAATTCGGCAATGTATAACT
52899141 ATATACAAATCAAATTCGGCAATGTATAA
1 ATATACAAATCAAATTCGGCAATGTATAA
52899170 AACATATACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (31 bp):
ATATACAAATCAAATTCGGCAATGTATAACT
Found at i:52901644 original size:37 final size:37
Alignment explanation
Indices: 52901600--52901685 Score: 95
Period size: 37 Copynumber: 2.3 Consensus size: 37
52901590 ACTCTCTATG
* *
52901600 GCATCAAGATGGTGGTACA-TTTGATC-AACCCTTAGTA
1 GCATCAAGATGGTGGGA-AGTCTGATCGAA-CCTTAGTA
* *
52901637 GCATCAAGATAGTGGGAAGTCTGGTCGAACCTTAGTA
1 GCATCAAGATGGTGGGAAGTCTGATCGAACCTTAGTA
*
52901674 ACATCAAGATGG
1 GCATCAAGATGG
52901686 CAGAGAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 1 0.02
37 38 0.93
38 2 0.05
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (37 bp):
GCATCAAGATGGTGGGAAGTCTGATCGAACCTTAGTA
Found at i:52902776 original size:57 final size:57
Alignment explanation
Indices: 52902642--52902777 Score: 148
Period size: 57 Copynumber: 2.4 Consensus size: 57
52902632 TAATGAAAAA
* * **
52902642 TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTATGTCATCTAACTAAAGAT
1 TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
* * * * ** *
52902699 TTTCAACTTAAC-AGGGTTTTTTTCTCTAACTTTTGCTTAAGTTTTCCAAAGAAGGAT
1 TTTCAGCTTAACGA-GCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
*
52902756 TTTTAGCTTAACGAGCTTTTTT
1 TTTCAGCTTAACGAGCTTTTTT
52902778 GTGCAGTTTA
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
56 1 0.02
57 61 0.97
58 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (57 bp):
TTTCAGCTTAACGAGCTTTTTTACCCTAACTTTTGCTTAAGTCATCCAAAGAAAGAT
Found at i:52904560 original size:18 final size:18
Alignment explanation
Indices: 52904537--52904573 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
52904527 AGCAAAGCCA
52904537 TCTCTAACAAAGTTTTCT
1 TCTCTAACAAAGTTTTCT
52904555 TCTCTAACAAAGTTTTCT
1 TCTCTAACAAAGTTTTCT
52904573 T
1 T
52904574 TATCTCTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (18 bp):
TCTCTAACAAAGTTTTCT
Found at i:52908240 original size:27 final size:28
Alignment explanation
Indices: 52908198--52908294 Score: 85
Period size: 27 Copynumber: 3.5 Consensus size: 28
52908188 ATTATTAAAT
*
52908198 AATATATTTAAATTAAATAATAAATT-A
1 AATATATTTATATTAAATAATAAATTAA
* * * **
52908225 TATTTATTTATGTTAAATTGT-AATTAA
1 AATATATTTATATTAAATAATAAATTAA
52908252 AATATATTTATATTAAA-AATAAATTTATA
1 AATATATTTATATTAAATAATAAA-TTA-A
*
52908281 AA-ATAATTATATTA
1 AATATATTTATATTA
52908295 TATTTATGTT
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
26 5 0.09
27 32 0.59
28 14 0.26
29 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
AATATATTTATATTAAATAATAAATTAA
Found at i:52908268 original size:16 final size:17
Alignment explanation
Indices: 52908238--52908280 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
52908228 TTATTTATGT
52908238 TAAATTGTA-ATT-AAAA
1 TAAATT-TATATTAAAAA
*
52908254 TATATTTATATTAAAAA
1 TAAATTTATATTAAAAA
52908271 TAAATTTATA
1 TAAATTTATA
52908281 AAATAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 2 0.09
16 8 0.35
17 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTATATTAAAAA
Found at i:52908308 original size:33 final size:36
Alignment explanation
Indices: 52908220--52908308 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 36
52908210 TTAAATAATA
52908220 AATTATATT-TATTTATGTTAAATTGTAATTAAAAT
1 AATTATATTATATTTATGTTAAATTGTAATTAAAAT
* ***
52908255 -A-TAT-TTATATTAAAAATAAATT-T-A-TAAAAT
1 AATTATATTATATTTATGTTAAATTGTAATTAAAAT
52908285 AATTATATTATATTTATGTTAAAT
1 AATTATATTATATTTATGTTAAAT
52908309 AATAGTATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
30 6 0.14
31 2 0.05
32 6 0.14
33 27 0.64
34 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.49
Consensus pattern (36 bp):
AATTATATTATATTTATGTTAAATTGTAATTAAAAT
Found at i:52908327 original size:26 final size:24
Alignment explanation
Indices: 52908281--52908329 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
52908271 TAAATTTATA
* *
52908281 AAATAATTATATTATATTTATGTT
1 AAATAATTATATTAAAATTATGTT
52908305 AAATAATAGTATATTAAAATTATGT
1 AAATAAT--TATATTAAAATTATGT
52908330 CATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
26 14 0.67
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (24 bp):
AAATAATTATATTAAAATTATGTT
Found at i:52911092 original size:20 final size:21
Alignment explanation
Indices: 52911017--52911093 Score: 78
Period size: 20 Copynumber: 4.0 Consensus size: 21
52911007 CGAGATGCTA
*
52911017 AACAGGGCA-CAAATGTGCAT
1 AACAGGGCACCAGATGTGCAT
*
52911037 -ACAGGAGCACCA-AAGTGCA-
1 AACAGG-GCACCAGATGTGCAT
52911056 AA-AGGGCACCAGA-GTGCAT
1 AACAGGGCACCAGATGTGCAT
52911075 AACAGGGCA-CAGATGTGCA
1 AACAGGGCACCAGATGTGCA
52911094 ATTAGGGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
18 11 0.22
19 15 0.31
20 21 0.43
21 2 0.04
ACGTcount: A:0.39, C:0.22, G:0.29, T:0.10
Consensus pattern (21 bp):
AACAGGGCACCAGATGTGCAT
Found at i:52914918 original size:20 final size:20
Alignment explanation
Indices: 52914893--52914955 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 20
52914883 TTTTACATAG
52914893 AGATAGTTACTCAATTATAC
1 AGATAGTTACTCAATTATAC
*
52914913 AGATAGTTATCTGGTAAATTATAC
1 AGATAGTTA-C---TCAATTATAC
52914937 AGATAGTTACTCAATTATA
1 AGATAGTTACTCAATTATA
52914956 AAAAAATTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
20 17 0.46
21 1 0.03
23 1 0.03
24 18 0.49
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.37
Consensus pattern (20 bp):
AGATAGTTACTCAATTATAC
Found at i:52915781 original size:14 final size:14
Alignment explanation
Indices: 52915758--52915797 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
52915748 AATAAAATAA
*
52915758 AATCCCCAATCCTC
1 AATCCTCAATCCTC
52915772 AATCCTCAATCCTC
1 AATCCTCAATCCTC
52915786 AATTCCT-AATCC
1 AA-TCCTCAATCC
52915798 CTAATCCCTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.30, C:0.42, G:0.00, T:0.28
Consensus pattern (14 bp):
AATCCTCAATCCTC
Found at i:52915788 original size:21 final size:21
Alignment explanation
Indices: 52915758--52915805 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
52915748 AATAAAATAA
52915758 AATCCCCAA-TCCTCAATCCTC
1 AATCCCCAATTCCT-AATCCTC
*
52915779 AATCCTCAATTCCTAATCC-C
1 AATCCCCAATTCCTAATCCTC
52915799 TAATCCC
1 -AATCCC
52915806 TCCCTCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.29, C:0.44, G:0.00, T:0.27
Consensus pattern (21 bp):
AATCCCCAATTCCTAATCCTC
Found at i:52916202 original size:20 final size:20
Alignment explanation
Indices: 52916177--52916239 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
52916167 GCAATATTTT
52916177 TTTATTTTTATATTTTTAAA
1 TTTATTTTTATATTTTTAAA
*
52916197 TTTATTATTATATTTTTTAAA
1 TTTATTTTTATA-TTTTTAAA
* *
52916218 -TTATTTATATATTTTTATA
1 TTTATTTTTATATTTTTAAA
52916237 TTT
1 TTT
52916240 CTTTGAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.19
20 22 0.59
21 8 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTATTTTTATATTTTTAAA
Found at i:52916215 original size:21 final size:20
Alignment explanation
Indices: 52916177--52916255 Score: 76
Period size: 19 Copynumber: 4.0 Consensus size: 20
52916167 GCAATATTTT
52916177 TTTATTTT-TATATTTTTAAA
1 TTTATTTTATAT-TTTTTAAA
52916197 TTTATTATTATATTTTTTAAA
1 TTTATT-TTATATTTTTTAAA
*
52916218 -TTA-TTTATATATTTTTATA
1 TTTATTTTATAT-TTTTTAAA
* *
52916237 TTTCTTTGA-ATTTTTTAAA
1 TTTATTTTATATTTTTTAAA
52916256 ATTAAGATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
18 6 0.12
19 15 0.30
20 13 0.26
21 13 0.26
22 3 0.06
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (20 bp):
TTTATTTTATATTTTTTAAA
Found at i:52916222 original size:40 final size:38
Alignment explanation
Indices: 52916178--52916255 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 38
52916168 CAATATTTTT
* *
52916178 TTATTTTTATATTTTTAAATTTATTATTATATTTTTTAAA
1 TTATTTATATATTTTTAAATTTATT-TGA-ATTTTTTAAA
* *
52916218 TTATTTATATATTTTTATATTTCTTTGAATTTTTTAAA
1 TTATTTATATATTTTTAAATTTATTTGAATTTTTTAAA
52916256 ATTAAGATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 10 0.29
39 2 0.06
40 22 0.65
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (38 bp):
TTATTTATATATTTTTAAATTTATTTGAATTTTTTAAA
Found at i:52916230 original size:28 final size:29
Alignment explanation
Indices: 52916199--52916253 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
52916189 TTTTTAAATT
52916199 TATTATTATATTT-TTTAAATTATTTATA
1 TATTATTATATTTCTTTAAATTATTTATA
* * *
52916227 TATTTTTATATTTCTTTGAATTTTTTA
1 TATTATTATATTTCTTTAAATTATTTA
52916254 AAATTAAGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (29 bp):
TATTATTATATTTCTTTAAATTATTTATA
Found at i:52922757 original size:24 final size:21
Alignment explanation
Indices: 52922713--52922759 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
52922703 TTAAATTTTA
*
52922713 TTTTATTTTATTTGATCTATT
1 TTTTATTTTATTTGATATATT
52922734 TTTTATTTTAATATTGTATATATT
1 TTTTATTTT-AT-TTG-ATATATT
52922758 TT
1 TT
52922760 ATGTACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 3 0.14
24 8 0.36
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.70
Consensus pattern (21 bp):
TTTTATTTTATTTGATATATT
Found at i:52927210 original size:29 final size:31
Alignment explanation
Indices: 52927177--52927237 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
52927167 TATATTTGAA
**
52927177 ATTTACTTTT-ATTTTCAAAAATTTT-GTCC
1 ATTTACTTTTCAAATTCAAAAATTTTGGTCC
*
52927206 ATTTATTTTTCAAATTCAAAAATTTTGGTCC
1 ATTTACTTTTCAAATTCAAAAATTTTGGTCC
52927237 A
1 A
52927238 ATCATTAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 9 0.33
30 13 0.48
31 5 0.19
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (31 bp):
ATTTACTTTTCAAATTCAAAAATTTTGGTCC
Found at i:52934433 original size:17 final size:17
Alignment explanation
Indices: 52934406--52934438 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
52934396 TCACTACATT
52934406 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
52934424 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
52934439 TAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:52935934 original size:17 final size:17
Alignment explanation
Indices: 52935914--52935949 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
52935904 TAAGCTTAGT
52935914 AAGTTCGTATAACTAGA
1 AAGTTCGTATAACTAGA
52935931 AAGTTCGTATAACTAGA
1 AAGTTCGTATAACTAGA
52935948 AA
1 AA
52935950 TACAACTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (17 bp):
AAGTTCGTATAACTAGA
Found at i:52937837 original size:16 final size:17
Alignment explanation
Indices: 52937793--52937843 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
52937783 TTTTTTAAAA
*
52937793 TAAATTATTTTAATATTT
1 TAAA-TATTATAATATTT
*
52937811 TATAATTTTATAAT-TTT
1 TA-AATATTATAATATTT
52937828 TAAATATTATTAATAT
1 TAAATATTA-TAATAT
52937844 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 10 0.37
19 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAAATATTATAATATTT
Found at i:52939330 original size:20 final size:18
Alignment explanation
Indices: 52939296--52939332 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
52939286 CCTTAGCCCA
52939296 TAACAGTATCAGTAGCAG
1 TAACAGTATCAGTAGCAG
52939314 TAACAGTTATGCAGTAGCA
1 TAACAG-TAT-CAGTAGCA
52939333 AAATCCTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 8 0.47
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (18 bp):
TAACAGTATCAGTAGCAG
Found at i:52948191 original size:23 final size:23
Alignment explanation
Indices: 52948164--52948245 Score: 92
Period size: 23 Copynumber: 3.6 Consensus size: 23
52948154 TGGTAGGAGC
* *
52948164 TTATTGGCACTTTGGTGCGATTG
1 TTATTGGCACTTCGGTGTGATTG
** *
52948187 TTATTAACACTTCAGTGTGATTG
1 TTATTGGCACTTCGGTGTGATTG
* * *
52948210 TTATTGGCACATCGGTTTAATTG
1 TTATTGGCACTTCGGTGTGATTG
52948233 TTATTGGCACTTC
1 TTATTGGCACTTC
52948246 AATGCAATTG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.44
Consensus pattern (23 bp):
TTATTGGCACTTCGGTGTGATTG
Found at i:52948254 original size:23 final size:23
Alignment explanation
Indices: 52948164--52948255 Score: 76
Period size: 23 Copynumber: 4.0 Consensus size: 23
52948154 TGGTAGGAGC
** *
52948164 TTATTGGCACTTTGGTGCGATTG
1 TTATTGGCACTTCAGTGCAATTG
** **
52948187 TTATTAACACTTCAGTGTGATTG
1 TTATTGGCACTTCAGTGCAATTG
* * **
52948210 TTATTGGCACATCGGTTTAATTG
1 TTATTGGCACTTCAGTGCAATTG
*
52948233 TTATTGGCACTTCAATGCAATTG
1 TTATTGGCACTTCAGTGCAATTG
52948256 ATACTAGCAC
Statistics
Matches: 53, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.42
Consensus pattern (23 bp):
TTATTGGCACTTCAGTGCAATTG
Found at i:52956410 original size:22 final size:20
Alignment explanation
Indices: 52956370--52956410 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
52956360 TATATGTTTG
*
52956370 AATGTGTTTAAATATGCTTA
1 AATGTGTTTAAACATGCTTA
52956390 AATGATGTTTAGAACATGCTT
1 AATG-TGTTTA-AACATGCTT
52956411 TTAGCGTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (20 bp):
AATGTGTTTAAACATGCTTA
Found at i:52957051 original size:81 final size:81
Alignment explanation
Indices: 52956934--52957174 Score: 286
Period size: 81 Copynumber: 3.0 Consensus size: 81
52956924 GCCTTCGGCA
* * * * * * * *
52956934 CTCCTTCTTCCACCCCTGCCTTTGGCACTCCTTCTTCCACCCCGGCCTTTGGAACTACTCCTTCC
1 CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCCTTCG
*
52956999 ACTCCGGCTTTTGGGG
66 ACACCGGCTTTTGGGG
* ** *
52957015 CTCCTTCTTCCACACCGGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGTCACTCCTTCTTCG
1 CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCCTTCG
* *
52957080 ACACCTGCGTTTGGGG
66 ACACCGGCTTTTGGGG
* * * **
52957096 CTCCGTCTTCGACACCTGCGTTTGGGGCTCCGTCTTCGACACCGGCGTTTGGAACTCCGTCC-TC
1 CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCC-TCCTTC
52957160 GACACCGGCTTTTGG
65 GACACCGGCTTTTGG
52957175 AACTCCATCA
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
81 131 0.98
82 2 0.02
ACGTcount: A:0.10, C:0.39, G:0.21, T:0.30
Consensus pattern (81 bp):
CTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCCTTCG
ACACCGGCTTTTGGGG
Found at i:52957060 original size:54 final size:54
Alignment explanation
Indices: 52956961--52957174 Score: 232
Period size: 54 Copynumber: 4.0 Consensus size: 54
52956951 GCCTTTGGCA
* * * * * *
52956961 CTCCTTCTTCCACCCCGGCCTTTGGAACTAC-TCCTTCCACTCCGGCTTTTGGGG
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGT-CTTCGACACCGGCGTTTGGGG
* * ***
52957015 CTCCTTCTTCCACACCGGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGTCA
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGGGG
* * ** *
52957069 CTCCTTCTTCGACACCTGCGTTTGGGGCTCCGTCTTCGACACCTGCGTTTGGGG
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGGGG
* * * *
52957123 CTCCGTCTTCGACACCGGCGTTTGGAACTCCGTCCTCGACACCGGCTTTTGG
1 CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGG
52957175 AACTCCATCA
Statistics
Matches: 133, Mismatches: 26, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
54 132 0.99
55 1 0.01
ACGTcount: A:0.10, C:0.37, G:0.22, T:0.30
Consensus pattern (54 bp):
CTCCTTCTTCCACACCGGCGTTTGGAACTCCGTCTTCGACACCGGCGTTTGGGG
Found at i:52957089 original size:27 final size:27
Alignment explanation
Indices: 52956930--52957180 Score: 207
Period size: 27 Copynumber: 9.3 Consensus size: 27
52956920 TTCTGCCTTC
* * * * *
52956930 GGCACTCCTTCTTCCACCCCTGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * *
52956957 GGCACTCCTTCTTCCACCCCGGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * * *
52956984 GGAACTAC-TCCTTCCACTCCGGCTTTT
1 GGCACTCCGT-CTTCGACACCGGCGTTT
** * * *
52957011 GGGGCTCCTTCTTCCACACCGGCATTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
52957038 GGCACTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * *
52957065 GTCACTCCTTCTTCGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
** *
52957092 GGGGCTCCGTCTTCGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
**
52957119 GGGGCTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * *
52957146 GGAACTCCGTCCTCGACACCGGCTTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
52957173 GGAACTCC
1 GGCACTCC
52957181 ATCAACGCCG
Statistics
Matches: 195, Mismatches: 27, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 193 0.99
28 1 0.01
ACGTcount: A:0.11, C:0.39, G:0.21, T:0.29
Consensus pattern (27 bp):
GGCACTCCGTCTTCGACACCGGCGTTT
Found at i:52964016 original size:14 final size:14
Alignment explanation
Indices: 52963978--52964020 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
52963968 CAAAATGTAC
52963978 AATATAATTAAA-T
1 AATATAATTAAATT
52963991 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
52964006 AA-ATAATTTAATT
1 AATATAATTAAATT
52964019 AA
1 AA
52964021 CTATTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:52966957 original size:8 final size:8
Alignment explanation
Indices: 52966941--52966972 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
52966931 TCTTTAGATT
*
52966941 TTTTTAAA
1 TTTTAAAA
52966949 TTTTAAAA
1 TTTTAAAA
52966957 TTTTAAAA
1 TTTTAAAA
52966965 TTTTAAAA
1 TTTTAAAA
52966973 AATATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TTTTAAAA
Found at i:52967007 original size:9 final size:9
Alignment explanation
Indices: 52966948--52967016 Score: 54
Period size: 9 Copynumber: 7.9 Consensus size: 9
52966938 ATTTTTTTAA
52966948 ATTTTAAA-
1 ATTTTAAAT
52966956 ATTTTAAA-
1 ATTTTAAAT
*
52966964 ATTTTAAAA
1 ATTTTAAAT
* *
52966973 AATATAAAT
1 ATTTTAAAT
**
52966982 -TTTGGAAT
1 ATTTTAAAT
*
52966990 TTTTATAAAT
1 ATTT-TAAAT
52967000 ATTTTAAAT
1 ATTTTAAAT
52967009 ATTTTAAA
1 ATTTTAAA
52967017 ATTATTTTGA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
8 20 0.42
9 22 0.46
10 6 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:52967013 original size:20 final size:19
Alignment explanation
Indices: 52966987--52967042 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
52966977 TAAATTTTGG
52966987 AATTTTTATAAATATTTTA
1 AATTTTTATAAATATTTTA
*
52967006 AATATTTTA-AAATTATTTTG
1 AAT-TTTTATAAA-TATTTTA
*
52967026 AATTTTTTTAAA-ATTTT
1 AATTTTTATAAATATTTT
52967043 TGTTGAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 5 0.16
19 10 0.31
20 17 0.53
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
AATTTTTATAAATATTTTA
Found at i:52967932 original size:31 final size:27
Alignment explanation
Indices: 52967897--52967960 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 27
52967887 TTTAGAAATC
*
52967897 ATTTTTATTTAATTCTAATATATATTTGATA
1 ATTTTTATTTAA-T-TAAAAT-TATTT-ATA
*
52967928 ATTTTTATTTTATTAAAATTATTTATA
1 ATTTTTATTTAATTAAAATTATTTATA
52967955 ATTTTT
1 ATTTTT
52967961 TACTAAAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 9 0.29
28 5 0.16
29 5 0.16
30 1 0.03
31 11 0.35
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (27 bp):
ATTTTTATTTAATTAAAATTATTTATA
Found at i:52969642 original size:11 final size:11
Alignment explanation
Indices: 52969628--52969688 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
52969618 AAAAAACTCC
52969628 AAAAATTATAT
1 AAAAATTATAT
52969639 AAAAA-TATAAT
1 AAAAATTAT-AT
**
52969650 ATTAATTAT-T
1 AAAAATTATAT
* *
52969660 AAAAATTTTCT
1 AAAAATTATAT
*
52969671 AAAAAGTATAT
1 AAAAATTATAT
52969682 AAAAATT
1 AAAAATT
52969689 TCAAATATGC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
10 10 0.26
11 25 0.66
12 3 0.08
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (11 bp):
AAAAATTATAT
Found at i:52969845 original size:22 final size:23
Alignment explanation
Indices: 52969808--52969852 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
52969798 GTTTATATAT
*
52969808 TATATTTTTTTCATAATTATTAA
1 TATATATTTTTCATAATTATTAA
52969831 TATATATTTTT-ATAATTATTAA
1 TATATATTTTTCATAATTATTAA
52969853 CTTTTTTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATATTTTTCATAATTATTAA
Found at i:52971577 original size:19 final size:19
Alignment explanation
Indices: 52971553--52971606 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
52971543 AATCTTCAAG
*
52971553 GATATGCAATTTTAGATAT
1 GATATGCAATCTTAGATAT
*
52971572 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52971591 GAAATGCAATCTTAGA
1 GATATGCAATCTTAGA
52971607 AGATATGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52971857 original size:23 final size:23
Alignment explanation
Indices: 52971813--52971857 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
52971803 TCTTATTTTG
* *
52971813 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
52971836 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
52971858 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:52978564 original size:44 final size:42
Alignment explanation
Indices: 52978514--52978657 Score: 101
Period size: 44 Copynumber: 3.3 Consensus size: 42
52978504 AGACACTAGC
52978514 CTTGCCTCCTTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCC-TGGGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
**** * ** ** * *
52978558 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAG-T
1 CTTGCC-TCCTGGGTTG-CAGCG-AGCAGGTTAAAAATAGCAGAT
*
52978602 CTTGCCTCCCTGGGTTGCAGCGGAGCAAGTTAAAAATAGCAGAT
1 CTTGCCT-CCTGGGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
52978646 CTTGCCTTCCTG
1 CTTGCC-TCCTG
52978658 CACTGGCAGC
Statistics
Matches: 70, Mismatches: 23, Indels: 14
0.65 0.21 0.13
Matches are distributed among these distances:
43 16 0.23
44 34 0.49
45 20 0.29
ACGTcount: A:0.24, C:0.27, G:0.26, T:0.23
Consensus pattern (42 bp):
CTTGCCTCCTGGGTTGCAGCGAGCAGGTTAAAAATAGCAGAT
Found at i:52979248 original size:88 final size:88
Alignment explanation
Indices: 52978465--52979230 Score: 1073
Period size: 88 Copynumber: 8.7 Consensus size: 88
52978455 GTGAAGATAA
* * * *
52978465 CAGATCTGGCATTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
52978530 GCAGCAGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
52978553 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAGGACACCAGTCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
52978618 GCAGCGGAGCAAGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * * *
52978641 CAGATCTTGCCTTCCTGCACTGGCAGCGAAGCAGATCGAGGACACTAGCCCTGCCTCCCTGAGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
52978706 GCAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
52978729 TAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAGCCCTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
52978794 GTAGCGGAGCAGGTTAAAAATTG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
52978817 CAGATATTGCCTTCCTGCACCGACAGCGAAGCATATCGAAGACACCAGCCTTGCCTCACTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * *
52978882 GTAGCGGAGCAAGTTAAAAATAA
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * *
52978905 CAGATATTGCCTTCCTACACCGACAGCGAAGCAAATCGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
52978970 GTAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
** * *
52978993 CAGATCTTGTTTTCCTGCACCGATAGTGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
52979058 GCAGCGGAGTAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
52979081 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCTCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*** *
52979146 GCAGTAAAGCAGGTTAAAAATAA
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * **
52979169 CAGATCTTGTCTTCCTGCACCGACAGCGAGGCAGATCGATGACCCCAGCCTTATCTCCCTGG
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGG
52979231 ACAACAGTGG
Statistics
Matches: 602, Mismatches: 76, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 602 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:52979309 original size:44 final size:44
Alignment explanation
Indices: 52979218--52979317 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
52979208 TGACCCCAGC
* *
52979218 CTTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATTGTAAGT
1 CTTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGGGAAGT
* *
52979262 CTTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATGGCGAA-T
1 CTTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGG-GAAGT
*
52979306 CTTATCTTCCTG
1 CTTATCTCCCTG
52979318 AAGTTACAGT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
44 48 0.96
45 2 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (44 bp):
CTTATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGGGAAGT
Found at i:52979414 original size:44 final size:44
Alignment explanation
Indices: 52979304--52979936 Score: 273
Period size: 44 Copynumber: 14.6 Consensus size: 44
52979294 AAGATGGCGA
* * * * **
52979304 ATCTTATCTTCCTGAAGTTACAGTGGAACAAATTAAAGCCA-AT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * * **
52979347 AATCATATCTCCCTAAAGCTGCAGTGGAGTGGATTAAAATCACAT
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * * * **
52979392 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCACAT--CGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * ** *
52979432 GTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAA-AACGA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCAC-AT
* **
52979477 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * *
52979520 AATCCTATCTCCCTGAAGTCGCAGTGGAGC-GAATTAAAATCACAA
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAG-ATTAAAATCACAT
* * ***
52979565 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT--C-T
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* *
52979604 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA-A-
1 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAA--AATCACAT
** * * * * ***
52979649 GCCTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGTGA-
1 ATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAAAAT-CACAT
* **
52979694 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCA-AT
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* ** *
52979737 AATCTTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACAG
1 -ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * *** **
52979782 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT--CGG
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
* * **
52979822 GTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAA--AGCGA-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATCA-C-AT
* *
52979867 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCA-A-
1 ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-T-TA-AAATCACAT
* *
52979912 GTCTTATC-CCCTGAAATTGCAGTGG
1 ATCTTATCTCCCTGAAGTTGCAGTGG
52979937 GGCAACTAAA
Statistics
Matches: 441, Mismatches: 105, Indels: 86
0.70 0.17 0.14
Matches are distributed among these distances:
39 1 0.00
40 66 0.15
41 20 0.05
42 13 0.03
43 22 0.05
44 208 0.47
45 103 0.23
46 6 0.01
47 1 0.00
48 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATCACAT
Found at i:52979594 original size:173 final size:172
Alignment explanation
Indices: 52979305--52979760 Score: 533
Period size: 173 Copynumber: 2.6 Consensus size: 172
52979295 AGATGGCGAA
* * * * *
52979305 TCTTATCTTCCTGAAGTTACAGTGGAACAAATTAAAGCCAATAATCATATCTCCCTAAAG-CTGC
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAGTC-GC
* * * *
52979369 AGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGGGT
65 AGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAGT
* *
52979434 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAACGAG
130 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CCAAGAAAACAAG
*
52979478 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAGTCGCA
* *
52979543 GTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTC
66 GTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAGTC
* * *
52979608 TTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAG
131 TTATCTCCCTGAAGTTGCAGTGGAGCAGACCAAGAAAACAAG
* * * * * **** * *
52979650 CCTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAAGTT
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGATTAAAGCCAAT-AATCATATCTCCCTGAAGTC
* ** * *
52979713 GCAGTGGAGCAAATTAAAGCCA-ATAATCTTATCTCCCTAAAGTTGCAG
63 GCAGTGGAGCGAATTAAAATCACA-AATCTTATCTCTCTGAAGTTGCAG
52979761 TGGAGTGGAT
Statistics
Matches: 245, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
171 3 0.01
172 38 0.16
173 203 0.83
174 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (172 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAGTCGCA
GTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATCGAGTC
TTATCTCCCTGAAGTTGCAGTGGAGCAGACCAAGAAAACAAG
Found at i:52979630 original size:84 final size:84
Alignment explanation
Indices: 52979352--52979633 Score: 289
Period size: 84 Copynumber: 3.3 Consensus size: 84
52979342 CCAATAATCA
* * * * *
52979352 TATCTCCCTAAAGCTGCAGTGGAGTGGATTAAAATCACATATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAG
* **
52979417 AGCAGATCACATCGGGTCT
66 AGCAGATCGCATCTAGTCT
* *** * * * *
52979436 TATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAA-AACGAGTCTTATCTCCCTGAAGTTGCAG
1 TATCTCCCTGAAGTTGCAGTGGAGC-GAATTAA-AATCACAAATCTTATCTCTCTGAAGTTGCAG
* * * * *
52979500 TGGAGCAGATTAAAGCCA-ATAATCC
64 -AGAGCAGA-T--CG-CATCTAGTCT
*
52979525 TATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAG
52979590 AGCAGATCGCATCTAGTCT
66 AGCAGATCGCATCTAGTCT
52979609 TATCTCCCTGAAGTTGCAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
52979634 AGACTAAGTA
Statistics
Matches: 153, Mismatches: 36, Indels: 18
0.74 0.17 0.09
Matches are distributed among these distances:
83 2 0.01
84 50 0.33
85 26 0.17
86 10 0.07
87 10 0.07
88 28 0.18
89 25 0.16
90 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAATCACAAATCTTATCTCTCTGAAGTTGCAGAG
AGCAGATCGCATCTAGTCT
Found at i:52979669 original size:217 final size:218
Alignment explanation
Indices: 52979434--52979941 Score: 718
Period size: 217 Copynumber: 2.3 Consensus size: 218
52979424 CACATCGGGT
* *
52979434 CTTATCTCCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAACGAGTCTTATCTCCCTGAAGTTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAAGAAAACGAGTCTTATCTCCCTGAAGTTGCA
* *
52979499 GTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGAATTAAAATCACA
66 GTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTAAAGTCGCAGTGGAGCGAATTAAAATCACA
*
52979564 AATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGT
131 AATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGT
* *
52979629 GGAGCAGA-CTAAGTAAGCAAGC
196 GGAGCAGACCCAAGAAAGCAAGC
* **** *
52979651 CTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGTGAATCTTATCTCCCTGAAGTTG
1 CTTATCTC-CCTAAAGTTGTAGTGGA-GCAGACTCAAGAAAACGAGTCTTATCTCCCTGAAGTTG
* * * *
52979714 CAGTGGAGCAAATTAAAGCCAATAATCTTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCA
64 CAGTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTAAAGTCGCAGTGGAGCGAATTAAAATCA
* *
52979779 CAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGGGTCTTATCTCCCTGAAGTTGCA
129 CAAATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCA
* * *
52979844 GTGGAGTAGACCCAAGAAAGCGAGT
194 GTGGAGCAGACCCAAGAAAGCAAGC
* * * * *
52979869 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAAGTCTTATC-CCCTGAAATTGCA
1 CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAAGAAAACGAGTCTTATCTCCCTGAAGTTGCA
*
52979933 GTGGGGCAA
66 GTGGAGCAA
52979942 CTAAATAAAC
Statistics
Matches: 253, Mismatches: 33, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
216 3 0.01
217 200 0.79
218 47 0.19
219 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (218 bp):
CTTATCTCCCTAAAGTTGTAGTGGAGCAGACTCAAGAAAACGAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAAATTAAAGCCAATAATCCTATCTCCCTAAAGTCGCAGTGGAGCGAATTAAAATCACA
AATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTTGCAGT
GGAGCAGACCCAAGAAAGCAAGC
Found at i:52980553 original size:22 final size:22
Alignment explanation
Indices: 52980493--52980550 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
52980483 AATCTTCAAG
52980493 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
52980512 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
52980534 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
52980551 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:52980778 original size:23 final size:23
Alignment explanation
Indices: 52980734--52980778 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
52980724 TCTTATTTTG
* *
52980734 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
52980757 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
52980779 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:52985071 original size:15 final size:15
Alignment explanation
Indices: 52985053--52985081 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52985043 TTTATAGTTA
52985053 AAAATTTAATTTAAT
1 AAAATTTAATTTAAT
52985068 AAAATTTAATTTAA
1 AAAATTTAATTTAA
52985082 AATTAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AAAATTTAATTTAAT
Found at i:52985762 original size:24 final size:23
Alignment explanation
Indices: 52985718--52985762 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
52985708 GTTTTATGGC
*
52985718 TTTTAGGGTTTAGGGTGCAGGCT
1 TTTTAGGGTTTAGGGTCCAGGCT
52985741 TTTTAGGAG-TTAGGGGTCCAGG
1 TTTTAGG-GTTTA-GGGTCCAGG
52985763 AAAATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.16, C:0.09, G:0.40, T:0.36
Consensus pattern (23 bp):
TTTTAGGGTTTAGGGTCCAGGCT
Done.