Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D05
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: 64368997
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1610000 characters in sequence are not A, C, G, or T
File 8 of 208
Found at i:3120627 original size:4 final size:4
Alignment explanation
Indices: 3120618--3120658 Score: 57
Period size: 4 Copynumber: 10.0 Consensus size: 4
3120608 GTACTATCAG
3120618 CAAA CAAA CAAA CAAA CAAA CAAA CAAA -AAA GCAAA TCAAA
1 CAAA CAAA CAAA CAAA CAAA CAAA CAAA CAAA -CAAA -CAAA
3120659 TGATGATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
3 3 0.09
4 24 0.71
5 7 0.21
ACGTcount: A:0.73, C:0.22, G:0.02, T:0.02
Consensus pattern (4 bp):
CAAA
Found at i:3132687 original size:18 final size:19
Alignment explanation
Indices: 3132639--3132687 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
3132629 AATGAAAATG
*
3132639 AATAAATTATA-TATTTTT
1 AATAATTTATATTATTTTT
*
3132657 ACTATATTT-TATTA-TTTT
1 AATA-ATTTATATTATTTTT
3132675 AATAATTTATATT
1 AATAATTTATATT
3132688 TTTATAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
17 4 0.16
18 16 0.64
19 5 0.20
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
AATAATTTATATTATTTTT
Found at i:3132952 original size:7 final size:7
Alignment explanation
Indices: 3132936--3132966 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3132926 ACATTTTCTT
3132936 AAAATTA
1 AAAATTA
*
3132943 AAAGTTA
1 AAAATTA
3132950 AAAATTA
1 AAAATTA
3132957 AAAATTA
1 AAAATTA
3132964 AAA
1 AAA
3132967 TTTACTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (7 bp):
AAAATTA
Found at i:3153598 original size:18 final size:19
Alignment explanation
Indices: 3153546--3153598 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
3153536 AAGCATAATT
3153546 ATATTTGAAATAATTAATTAAA
1 ATATTTGAAAT-A-TAA-TAAA
* *
3153568 ATATTTCACATATAA-AAA
1 ATATTTGAAATATAATAAA
3153586 ATATTTGAAATAT
1 ATATTTGAAATAT
3153599 TATACTCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 14 0.52
20 3 0.11
21 1 0.04
22 9 0.33
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (19 bp):
ATATTTGAAATATAATAAA
Found at i:3155246 original size:21 final size:21
Alignment explanation
Indices: 3155220--3155262 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
3155210 ATTGGGTGGA
3155220 TCAGCTCTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
*
3155241 TCAGCTTTTACGAGCTTCTGT
1 TCAGCTCTTACGAGCTTCTGT
3155262 T
1 T
3155263 GGTATTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.26, G:0.19, T:0.42
Consensus pattern (21 bp):
TCAGCTCTTACGAGCTTCTGT
Found at i:3155866 original size:58 final size:58
Alignment explanation
Indices: 3155742--3155859 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
3155732 TGTGCAAATA
3155742 ACCAATTTGCAAAGGGTTTGAGAATGAGGTATAGTTGTTATGCTAGTATGTGTGGCTT
1 ACCAATTTGCAAAGGGTTTGAGAATGAGGTATAGTTGTTATGCTAGTATGTGTGGCTT
3155800 ACCAATTTGCAAAGGGTTTGAGAATGAGGTATAGTTGTTATGCTAGTATGTGTGGCTT
1 ACCAATTTGCAAAGGGTTTGAGAATGAGGTATAGTTGTTATGCTAGTATGTGTGGCTT
3155858 AC
1 AC
3155860 ATATTTGATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (58 bp):
ACCAATTTGCAAAGGGTTTGAGAATGAGGTATAGTTGTTATGCTAGTATGTGTGGCTT
Found at i:3157036 original size:16 final size:16
Alignment explanation
Indices: 3157012--3157042 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3157002 AATTCGAGTT
*
3157012 GAATTTGAAAATATCC
1 GAATATGAAAATATCC
3157028 GAATATGAAAATATC
1 GAATATGAAAATATC
3157043 ATGTTGGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.13, T:0.29
Consensus pattern (16 bp):
GAATATGAAAATATCC
Found at i:3158007 original size:17 final size:17
Alignment explanation
Indices: 3157987--3158040 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
3157977 TTAGCTAAGA
3157987 TTTTTTAGATTCAAAAT
1 TTTTTTAGATTCAAAAT
3158004 TTTTTTAG-TTC-AAAT
1 TTTTTTAGATTCAAAAT
* *
3158019 TTTTTAAGATT-AGAAT
1 TTTTTTAGATTCAAAAT
3158035 TTTTTT
1 TTTTTT
3158041 TTTCAAGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
15 11 0.34
16 13 0.41
17 8 0.25
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (17 bp):
TTTTTTAGATTCAAAAT
Found at i:3158009 original size:31 final size:31
Alignment explanation
Indices: 3157971--3158040 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3157961 TTGGATTTGG
3157971 ATTTTTTTAGCT-AAGATTTTTT-AGATTCAAA
1 ATTTTTTTAGCTCAA-ATTTTTTAAGATT-AAA
* *
3158002 ATTTTTTTAGTTCAAATTTTTTAAGATTAGA
1 ATTTTTTTAGCTCAAATTTTTTAAGATTAAA
3158033 ATTTTTTT
1 ATTTTTTT
3158041 TTTCAAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 28 0.80
32 7 0.20
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (31 bp):
ATTTTTTTAGCTCAAATTTTTTAAGATTAAA
Found at i:3158086 original size:16 final size:16
Alignment explanation
Indices: 3158040--3158087 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
3158030 AGAATTTTTT
*
3158040 TTTTCAAGTTTAAACC
1 TTTTCAAGTTTAAATC
* *
3158056 TTTTCAGGTTCAAATC
1 TTTTCAAGTTTAAATC
3158072 TTTTCAAGTTTAAATC
1 TTTTCAAGTTTAAATC
3158088 AAATTAAGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (16 bp):
TTTTCAAGTTTAAATC
Found at i:3158641 original size:19 final size:21
Alignment explanation
Indices: 3158598--3158641 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
3158588 TTTAATACTA
*
3158598 AAAATATTACTTGATAAATAG
1 AAAATATTACATGATAAATAG
*
3158619 AAAATA-TACATGTTAAA-AG
1 AAAATATTACATGATAAATAG
3158638 AAAA
1 AAAA
3158642 AAAAATACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.27
Consensus pattern (21 bp):
AAAATATTACATGATAAATAG
Found at i:3162754 original size:91 final size:91
Alignment explanation
Indices: 3162616--3162823 Score: 335
Period size: 91 Copynumber: 2.3 Consensus size: 91
3162606 TTGATTTTAG
* *
3162616 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTAT
* * *
3162681 ATTTAATATTAATTATTTTAAATTGTA
65 ATGTAATAATAATTATTTTAAATTATA
*
3162708 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
3162773 TGTAATAATAATTATTTTAAATTATA
66 TGTAATAATAATTATTTTAAATTATA
* *
3162799 CAAATTCATATAAGATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
3162824 GTTATAATTA
Statistics
Matches: 108, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 92 0.85
92 16 0.15
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TGTAATAATAATTATTTTAAATTATA
Found at i:3162792 original size:26 final size:28
Alignment explanation
Indices: 3162738--3162798 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3162728 TATTATCAAG
* *
3162738 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
3162766 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
3162792 AATTATA
1 AATTATA
3162799 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:3162798 original size:44 final size:43
Alignment explanation
Indices: 3162656--3162798 Score: 121
Period size: 44 Copynumber: 3.2 Consensus size: 43
3162646 GAATTTTATG
* *
3162656 AAATTATATATCATTATTAAATTATATTTAATATTAATTATTTT
1 AAATTATATATTATTATTAAATTATA-TTAATAATAATTATTTT
* ** * *
3162700 AAATTGTATAAATTCATATAAGAAAATT-TATT-ATCAAGAATT-TTATG
1 AAA-T-TATATATT-AT-T-ATTAAATTATATTAAT-AATAATTATT-TT
3162747 AAATTATATATTATTATTAAATTATATGTAATAATAATTATTTT
1 AAATTATATATTATTATTAAATTATAT-TAATAATAATTATTTT
3162791 AAATTATA
1 AAATTATA
3162799 CAAATTCATA
Statistics
Matches: 76, Mismatches: 12, Indels: 22
0.69 0.11 0.20
Matches are distributed among these distances:
42 6 0.08
43 4 0.05
44 21 0.28
45 12 0.16
46 11 0.14
47 13 0.17
48 3 0.04
49 6 0.08
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
AAATTATATATTATTATTAAATTATATTAATAATAATTATTTT
Found at i:3162916 original size:59 final size:57
Alignment explanation
Indices: 3162850--3163038 Score: 152
Period size: 59 Copynumber: 3.2 Consensus size: 57
3162840 ATTTTATTAA
3162850 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATCTTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTATTT-AAATTAT-TTTTATAGT
* * ** * *
3162909 ATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATT-TTATTA-A--
1 ATCATATATT-TTAATT-A--AAA-T-ATAT-TTAATATTAATTATTTA-AATTATTTTTATAGT
* * * *
3162970 ATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGT
1 ATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTAAATTAT-TTTTATAGT
3163029 ATCATATATT
1 ATCATATATT
3163039 ATGATTTGAG
Statistics
Matches: 99, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
59 20 0.20
60 8 0.08
61 10 0.10
63 4 0.04
64 5 0.05
65 6 0.06
66 17 0.17
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (57 bp):
ATCATATATTTTAATTAAAATATATTTAATATTAATTATTTAAATTATTTTTATAGT
Found at i:3162947 original size:66 final size:64
Alignment explanation
Indices: 3162877--3163075 Score: 186
Period size: 66 Copynumber: 3.2 Consensus size: 64
3162867 AAATATATTT
3162877 AATATTAATTATTTCAAATTATCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT-AAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
3162942 G
64 G
* * * * * **
3162943 AATATTAATTATTAAGAATT-TTATTA-A--ATTATATATT-TTAATT-A-T-AA-T-ATAT-TT
1 AATATTAATTATTTA-AATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
* *
3162997 AATAATAATTATGTTAATTTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTAT-TTAAATTAT-TTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
3163062 G
64 G
*
3163063 AATATTGATTATT
1 AATATTAATTATT
3163076 AAGAATTTTA
Statistics
Matches: 101, Mismatches: 18, Indels: 29
0.68 0.12 0.20
Matches are distributed among these distances:
54 14 0.14
55 7 0.07
56 5 0.05
57 3 0.03
58 1 0.01
59 10 0.10
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 5 0.05
65 7 0.07
66 27 0.27
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (64 bp):
AATATTAATTATTTAAATTATTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAAG
Found at i:3162963 original size:120 final size:120
Alignment explanation
Indices: 3162839--3163137 Score: 510
Period size: 120 Copynumber: 2.5 Consensus size: 120
3162829 AATTATTTTA
* * *
3162839 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTT
3162903 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
* *
3162959 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
*
3163024 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
3163079 AATTTTATTAAATTATATATTTTAATTAAAAATATATTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATT-AAAATATATTTAATAATAATTATG-TTAAAT
3163138 ATGATTAAAT
Statistics
Matches: 168, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
120 138 0.82
121 25 0.15
122 5 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:3162979 original size:61 final size:61
Alignment explanation
Indices: 3162912--3163099 Score: 192
Period size: 61 Copynumber: 3.1 Consensus size: 61
3162902 TTATAGTATC
3162912 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
* * * * * * * *
3162973 ATATATT-TTAATT-A-T-AATAT-ATTTAATAATAATTATGTTAATTTA-TATTTTA-TAGTAT
1 ATATATTATGATTTGAGTAAAT-TCATATAAGAAT-ATTA-ATT-ATTAAGAATTTTATTA-AAT
*
3163031 C
61 T
*
3163032 ATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
3163093 ATATATT
1 ATATATT
3163100 TTAATTAAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 24
0.69 0.14 0.17
Matches are distributed among these distances:
57 11 0.11
58 8 0.08
59 18 0.19
60 16 0.17
61 25 0.26
62 7 0.07
63 11 0.11
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (61 bp):
ATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
Found at i:3162999 original size:15 final size:15
Alignment explanation
Indices: 3162964--3163015 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3162954 TTAAGAATTT
*
3162964 TATTAAATTAT-ATA
1 TATTTAATTATAATA
3162978 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
3162992 TATTTAATAATAAT-
1 TATTTAATTATAATA
3163006 TATGTTAATT
1 TAT-TTAATT
3163016 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:3163100 original size:17 final size:17
Alignment explanation
Indices: 3163080--3163117 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3163070 ATTATTAAGA
*
3163080 ATTTT-ATTAAATTATAT
1 ATTTTAATTAAA-AATAT
3163097 ATTTTAATTAAAAATAT
1 ATTTTAATTAAAAATAT
3163114 ATTT
1 ATTT
3163118 AATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATTAAAAATAT
Found at i:3163369 original size:16 final size:16
Alignment explanation
Indices: 3163348--3163416 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
3163338 GATTAGTTAT
*
3163348 TACACCTCTAATCAAA
1 TACACCTCTAATCCAA
3163364 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
3163381 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3163397 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
3163413 TACA
1 TACA
3163417 GCGAACCAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 36 0.71
17 15 0.29
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:3163390 original size:33 final size:32
Alignment explanation
Indices: 3163348--3163416 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
3163338 GATTAGTTAT
3163348 TACACCTCTAATCAAATACACCTCTAATCCCAA
1 TACACCTCTAATCAAATACACCTCTAAT-CCAA
*
3163381 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCAAATACACCTCTAATCCAA
3163413 TACA
1 TACA
3163417 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCAAATACACCTCTAATCCAA
Found at i:3183599 original size:14 final size:14
Alignment explanation
Indices: 3183580--3183614 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
3183570 ATTTTTTAAG
3183580 AAATTTCAAACGTA
1 AAATTTCAAACGTA
3183594 AAATTTCAAACGTA
1 AAATTTCAAACGTA
3183608 AAATTTC
1 AAATTTC
3183615 TTTAAGTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (14 bp):
AAATTTCAAACGTA
Found at i:3195760 original size:95 final size:94
Alignment explanation
Indices: 3195627--3195811 Score: 282
Period size: 95 Copynumber: 1.9 Consensus size: 94
3195617 GTTACATATC
* * *
3195627 AAATCTGATTACATAGAGTCATCTCTCCTAATTTCTATTCTCGACAACAAAACTGTTGGTTGG-T
1 AAATCTGATTACAGAGAGTCATCTCTCCTAATCTCTATTCTCGACAACAAAACTGTTAGTTGGTT
3195691 TGTGGTTTCGAGAATTTACAACTAGTAAA
66 TGTGGTTTCGAGAATTTACAACTAGTAAA
* *
3195720 AAATCTGATTACAGAGAGAGTCGTCTCTCCTAATCTCTATTCTCGACAACAAAATTGTTAGTTGG
1 AAATCTGATTAC--AGAGAGTCATCTCTCCTAATCTCTATTCTCGACAACAAAACTGTTAGTTGG
*
3195785 TTTTGTGGTTTTGAGAATTTACAACTA
64 -TTTGTGGTTTCGAGAATTTACAACTA
3195812 TTTTACTATC
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
93 12 0.15
95 46 0.56
97 24 0.29
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (94 bp):
AAATCTGATTACAGAGAGTCATCTCTCCTAATCTCTATTCTCGACAACAAAACTGTTAGTTGGTT
TGTGGTTTCGAGAATTTACAACTAGTAAA
Found at i:3202499 original size:16 final size:17
Alignment explanation
Indices: 3202467--3202499 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3202457 AAACCCTAAT
*
3202467 AAATAAATAAATTCAAA
1 AAATAAATAAATACAAA
3202484 AAATAAA-AAATACAAA
1 AAATAAATAAATACAAA
3202500 TTCAATACCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
AAATAAATAAATACAAA
Found at i:3202729 original size:22 final size:20
Alignment explanation
Indices: 3202681--3202745 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 20
3202671 GTCTAGTCAC
*
3202681 TTTTTAAATTTTAAAATT-T
1 TTTTTAAAATTTAAAATTAT
* *
3202700 ATTATTAACACTGTTAAAATTAT
1 -TTTTTAA-AAT-TTAAAATTAT
*
3202723 TTTTTAAAATTTAAAACTAT
1 TTTTTAAAATTTAAAATTAT
3202743 TTT
1 TTT
3202746 AATCACATTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 18 0.49
21 4 0.11
22 14 0.38
23 1 0.03
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
TTTTTAAAATTTAAAATTAT
Found at i:3204753 original size:31 final size:31
Alignment explanation
Indices: 3204718--3204783 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3204708 AAAAACACTT
* *
3204718 AATAGTCTAGTCATTTAAATAAAAATTTTAG
1 AATAGTCTAGTCACTTAAATAAAAATTTTAA
* * *
3204749 AATAGTTTAGTGACTTAAATGAAAATTTTAA
1 AATAGTCTAGTCACTTAAATAAAAATTTTAA
3204780 AATA
1 AATA
3204784 ATTCAATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.38
Consensus pattern (31 bp):
AATAGTCTAGTCACTTAAATAAAAATTTTAA
Found at i:3205969 original size:18 final size:18
Alignment explanation
Indices: 3205942--3206034 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
3205932 TACGACCGTT
3205942 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3205960 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
**
3205978 TATAGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3205996 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
3206014 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
3206032 TAC
1 TAC
3206035 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:3210666 original size:18 final size:18
Alignment explanation
Indices: 3210637--3210705 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
3210627 TACGACCGTT
* *
3210637 TACGGTACTATTTACGTA
1 TACGGCACTATTCACGTA
*
3210655 TATGGCACTATTCACGTA
1 TACGGCACTATTCACGTA
* *
3210673 TACAGTACTATTCACGTA
1 TACGGCACTATTCACGTA
3210691 TACGGCACTATTCAC
1 TACGGCACTATTCAC
3210706 CATCAATGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.33
Consensus pattern (18 bp):
TACGGCACTATTCACGTA
Found at i:3211806 original size:18 final size:18
Alignment explanation
Indices: 3211785--3211822 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3211775 CTTCTACCCT
3211785 TTCCCCTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
*
3211803 TTCCCTTTTCCCTTCCCC
1 TTCCCCTTTCCCTTCCCC
3211821 TT
1 TT
3211823 GGATTGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (18 bp):
TTCCCCTTTCCCTTCCCC
Found at i:3215301 original size:15 final size:15
Alignment explanation
Indices: 3215262--3215314 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 15
3215252 GAACATTTGG
3215262 AATTTAATTAGATAAAA
1 AATTT-ATTA-ATAAAA
3215279 AACTTTTATTAATAAAA
1 AA--TTTATTAATAAAA
*
3215296 AATTTATTTATAAATA
1 AATTTATTAATAAA-A
3215312 AAT
1 AAT
3215315 CATTGCAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 10 0.31
18 4 0.12
19 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (15 bp):
AATTTATTAATAAAA
Found at i:3215388 original size:22 final size:20
Alignment explanation
Indices: 3215345--3215383 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3215335 TAATTTAAAA
3215345 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
3215365 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
3215384 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:3215528 original size:34 final size:35
Alignment explanation
Indices: 3215470--3215536 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
3215460 CAAACACTAG
3215470 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
3215505 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
3215537 CATTTTACTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:3217845 original size:18 final size:17
Alignment explanation
Indices: 3217809--3217848 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3217799 TATTAAAAAT
3217809 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
3217826 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
3217841 ATAATTTT
1 ATAATTTT
3217849 TGAATGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:3217890 original size:26 final size:26
Alignment explanation
Indices: 3217838--3217890 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
3217828 AATTTATATC
* * *
3217838 TTTATAATTTTTGAATGATTAATTTT
1 TTTATAATTTTTGAAGGATCAAATTT
*
3217864 TTTATCATTTTTGAAGGATCAAATTT
1 TTTATAATTTTTGAAGGATCAAATTT
3217890 T
1 T
3217891 AATTTTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (26 bp):
TTTATAATTTTTGAAGGATCAAATTT
Found at i:3230082 original size:16 final size:18
Alignment explanation
Indices: 3230061--3230101 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
3230051 GTAAAAATCG
3230061 ATCTAAAACT-AAAA-TA
1 ATCTAAAACTCAAAATTA
3230077 ATCT-AAACTCAAAATTA
1 ATCTAAAACTCAAAATTA
*
3230094 ATTTAAAA
1 ATCTAAAA
3230102 AAAGTAATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 8 0.38
17 5 0.24
18 3 0.14
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (18 bp):
ATCTAAAACTCAAAATTA
Found at i:3235495 original size:17 final size:18
Alignment explanation
Indices: 3235475--3235514 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3235465 TTTTATGTAA
*
3235475 AAAATTAT-TTTTTATAT
1 AAAATTATGTTATTATAT
*
3235492 AAAATTATGTTATTATTT
1 AAAATTATGTTATTATAT
3235510 AAAAT
1 AAAAT
3235515 AATATTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
AAAATTATGTTATTATAT
Found at i:3235495 original size:18 final size:19
Alignment explanation
Indices: 3235474--3235537 Score: 51
Period size: 22 Copynumber: 3.3 Consensus size: 19
3235464 ATTTTATGTA
*
3235474 AAAAATTAT-TTTTTATAT
1 AAAAATTATGTTATTATAT
*
3235492 -AAAATTATGTTATTATTT
1 AAAAATTATGTTATTATAT
* *
3235510 AAAATAATATTTGTTATTTTAT
1 -AAA-AAT-TATGTTATTATAT
3235532 AAAAAT
1 AAAAAT
3235538 AAATTGAGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
17 8 0.22
18 7 0.19
20 5 0.14
21 6 0.17
22 10 0.28
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (19 bp):
AAAAATTATGTTATTATAT
Found at i:3235510 original size:22 final size:22
Alignment explanation
Indices: 3235490--3235540 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
3235480 TATTTTTTAT
3235490 ATAAAATTATGTTATTATTTAAA
1 ATAAAATT-TGTTATTATTTAAA
*
3235513 ATAATATTTGTTATT-TTATAAAA
1 ATAAAATTTGTTATTATT-T-AAA
3235536 ATAAA
1 ATAAA
3235541 TTGAGTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 2 0.08
22 8 0.33
23 14 0.58
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (22 bp):
ATAAAATTTGTTATTATTTAAA
Found at i:3247122 original size:11 final size:12
Alignment explanation
Indices: 3247094--3247123 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
3247084 AAGGGATTGG
3247094 TTTTCTTTTTCCA
1 TTTT-TTTTTCCA
3247107 TTTTTTTTTCCA
1 TTTTTTTTTCCA
3247119 TTTTT
1 TTTTT
3247124 CGGGTTTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTTTTTTTCCA
Found at i:3265866 original size:90 final size:92
Alignment explanation
Indices: 3265755--3265929 Score: 205
Period size: 90 Copynumber: 1.9 Consensus size: 92
3265745 ATATGAGAAT
* * *
3265755 AATTGTCAAGTTTAGGCCTCAATATGAGAACAATTGTCAAT-TTT-TGAGCTTAACTTGGATAAA
1 AATTGTCAAGTTTAGGCCTCAATATGAGAAAAATTGTCAATGTTTAGGA-CCTAACTTGGATAAA
*
3265818 A-AAAAATTCAAATCTCAATGCGGGAAA
65 AGAAAAATTCAAACCTCAATGCGGGAAA
* * * * **
3265845 AATTTTCAAGTCTTA-GTCTCAATGTGGGAAAAATTGTCAATGTTTAGGACCTAGTTTGGATAAA
1 AATTGTCAAGT-TTAGGCCTCAATATGAGAAAAATTGTCAATGTTTAGGACCTAACTTGGATAAA
*
3265909 AGAAAAGTTCAAACCTCAATG
65 AGAAAAATTCAAACCTCAATG
3265930 TGAAGAAAGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
90 32 0.46
91 19 0.27
92 19 0.27
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (92 bp):
AATTGTCAAGTTTAGGCCTCAATATGAGAAAAATTGTCAATGTTTAGGACCTAACTTGGATAAAA
GAAAAATTCAAACCTCAATGCGGGAAA
Found at i:3271399 original size:60 final size:60
Alignment explanation
Indices: 3271335--3271474 Score: 226
Period size: 60 Copynumber: 2.3 Consensus size: 60
3271325 ATAATGGAGC
*
3271335 TGGAGCTGGTGGAAATGATGCTTTGGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTT
1 TGGAGCTGGTGGAAATGATGCTTTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTT
* * *
3271395 TGGAGCTGGTGGAAATAATGCTTTCGGAGCTGGAGCTGGAGCCGCTGGAGCTGGTGGTTT
1 TGGAGCTGGTGGAAATGATGCTTTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTT
* *
3271455 TGGAGATGGTGGAGATGATG
1 TGGAGCTGGTGGAAATGATG
3271475 GTTTTGGCGG
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.18, C:0.13, G:0.43, T:0.26
Consensus pattern (60 bp):
TGGAGCTGGTGGAAATGATGCTTTCGGAGCTGGAGCTGGAGCCGCTGCAGCTAGTGGTTT
Found at i:3271514 original size:21 final size:21
Alignment explanation
Indices: 3271489--3271529 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3271479 TGGCGGAGAC
*
3271489 GGTGGGGTCGACGGAGTTGAG
1 GGTGGGGTCGAAGGAGTTGAG
*
3271510 GGTGGGGTTGAAGGAGTTGA
1 GGTGGGGTCGAAGGAGTTGA
3271530 CGGAGGAGGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.05, G:0.56, T:0.22
Consensus pattern (21 bp):
GGTGGGGTCGAAGGAGTTGAG
Found at i:3275462 original size:18 final size:18
Alignment explanation
Indices: 3275441--3275489 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
3275431 ATCATTTATT
3275441 TATAAAATTTAATTTAAA
1 TATAAAATTTAATTTAAA
3275459 TAT--AATTTAAATATTAAA
1 TATAAAATTT-AAT-TTAAA
*
3275477 -ATAAATTTTAATT
1 TATAAAATTTAATT
3275490 AAAAAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 9
0.72 0.03 0.25
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 11 0.42
19 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TATAAAATTTAATTTAAA
Found at i:3276162 original size:21 final size:21
Alignment explanation
Indices: 3276136--3276180 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3276126 TTCATGTTAC
3276136 TTTTTTAAAATTTTTATGAAT
1 TTTTTTAAAATTTTTATGAAT
* * *
3276157 TTTTTTAATATTTTTTTGAGT
1 TTTTTTAAAATTTTTATGAAT
3276178 TTT
1 TTT
3276181 GAATATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
TTTTTTAAAATTTTTATGAAT
Found at i:3276597 original size:27 final size:25
Alignment explanation
Indices: 3276567--3276630 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
3276557 AAATATTTTA
* *
3276567 AAATAATAATAATTTTATATTTATATT
1 AAATAAAAATAA--TTATATTGATATT
*
3276594 AAATAAAAATCATTATATTGATATT
1 AAATAAAAATAATTATATTGATATT
3276619 AAATATAAAATA
1 AAATA-AAAATA
3276631 CTCTCCCACC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 17 0.53
26 5 0.16
27 10 0.31
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
AAATAAAAATAATTATATTGATATT
Found at i:3276612 original size:25 final size:26
Alignment explanation
Indices: 3276581--3276629 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
3276571 AATAATAATT
*
3276581 TTATATTTATATTAAATA-AAAATCA
1 TTATATTGATATTAAATATAAAATCA
3276606 TTATATTGATATTAAATATAAAAT
1 TTATATTGATATTAAATATAAAAT
3276630 ACTCTCCCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TTATATTGATATTAAATATAAAATCA
Found at i:3276798 original size:20 final size:21
Alignment explanation
Indices: 3276775--3276823 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
3276765 AATATAAATA
3276775 TAAATTTATTGTTAT-ATTTT
1 TAAATTTATTGTTATAATTTT
** *
3276795 TAAAAATATTTTTATAATTTT
1 TAAATTTATTGTTATAATTTT
3276816 TATAATTT
1 TA-AATTT
3276824 TTTTTATTTC
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 12 0.55
21 7 0.32
22 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TAAATTTATTGTTATAATTTT
Found at i:3276827 original size:21 final size:20
Alignment explanation
Indices: 3276776--3276830 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
3276766 ATATAAATAT
*
3276776 AAATTTATTGTTATATTTTTA
1 AAATTT-TTTTTATATTTTTA
* *
3276797 AAAATATTTTTATAATTTTTA
1 AAATTTTTTTTAT-ATTTTTA
*
3276818 TAATTTTTTTTAT
1 AAATTTTTTTTAT
3276831 TTCCTTATAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
AAATTTTTTTTATATTTTTA
Found at i:3310293 original size:11 final size:11
Alignment explanation
Indices: 3310278--3310307 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
3310268 AAAAAAATAA
3310278 AAAAAGTATTTT
1 AAAAA-TATTTT
3310290 AAAAATATTTT
1 AAAAATATTTT
3310301 AAAAATA
1 AAAAATA
3310308 AAAAAGTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3311451 original size:12 final size:12
Alignment explanation
Indices: 3311391--3311467 Score: 51
Period size: 12 Copynumber: 6.6 Consensus size: 12
3311381 TTAATATAGT
3311391 TTTAATATTTAA
1 TTTAATATTTAA
*
3311403 TTTGATATTTAAA
1 TTTAATATTT-AA
3311416 TTT--T-TTT-A
1 TTTAATATTTAA
3311424 TCTT-A-ATTTAGTA
1 T-TTAATATTTA--A
3311437 TTTAA-ATTTAAA
1 TTTAATATTT-AA
3311449 TTTAATATTTAA
1 TTTAATATTTAA
3311461 TTTAATA
1 TTTAATA
3311468 CTCAAATTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 20
0.72 0.01 0.27
Matches are distributed among these distances:
8 2 0.04
9 2 0.04
10 6 0.11
11 1 0.02
12 26 0.48
13 16 0.30
14 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (12 bp):
TTTAATATTTAA
Found at i:3311452 original size:19 final size:18
Alignment explanation
Indices: 3311391--3311465 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 18
3311381 TTAATATAGT
*
3311391 TTTAATATTTAATTTGATA
1 TTTAATATTTAATTT-AAA
* *
3311410 TTTAAATTTTTTTATCTT-AA
1 TTT-AA-TATTTAAT-TTAAA
*
3311430 TTTAGTATTTAAATTTAAA
1 TTTAATATTT-AATTTAAA
3311449 TTTAATATTTAATTTAA
1 TTTAATATTTAATTTAA
3311466 TACTCAAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 11
0.71 0.11 0.18
Matches are distributed among these distances:
18 13 0.30
19 17 0.39
20 6 0.14
21 6 0.14
22 2 0.05
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTAATATTTAATTTAAA
Found at i:3313306 original size:215 final size:210
Alignment explanation
Indices: 3312932--3313358 Score: 728
Period size: 215 Copynumber: 2.0 Consensus size: 210
3312922 AATTGTTAGG
3312932 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
*
3312997 GGTATATAGCTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
* * *
3313062 GCGGGACAAACTTAAAAGGAAACGAGGAAAAAAAAAAGAGCAATCAATTTATGGTTGTTGTTACC
131 GCGGGACAAACTTAAAAAGAAAAGAGG--AAAAAAAAGAGCAATCAATCTAT-G--GTTGTTACC
3313127 GCATGACGATGTATCTAACC
191 GCATGACGATGTATCTAACC
* *
3313147 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTTATGTTTTCCTTT
1 ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
3313212 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
66 GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
* * *
3313277 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAGAGAGCAATCAATCTATGGTTGTTACGGCATT
131 GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAGAGCAATCAATCTATGGTTGTTACCGCATG
3313342 ACGATGTATCTAACC
196 ACGATGTATCTAACC
3313357 AT
1 AT
3313359 ATAACTAACA
Statistics
Matches: 203, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
210 29 0.14
212 1 0.00
213 21 0.10
215 152 0.75
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (210 bp):
ATTTTGTTGAATTCTAAATCTCATAGTTCTTTTGAGGGCTTCTAGTTCTAGTCATGTTTTCCCTT
GGTATATAACTTTTTCCATAGCACTTGAAGATGTTCTATTCTTCTTGTATTCTACAATATTTATA
GCGGGACAAACTTAAAAAGAAAAGAGGAAAAAAAAGAGCAATCAATCTATGGTTGTTACCGCATG
ACGATGTATCTAACC
Found at i:3316710 original size:2 final size:2
Alignment explanation
Indices: 3316705--3316730 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3316695 ATGCACACAC
3316705 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
3316731 GTGTCTCTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3321798 original size:42 final size:42
Alignment explanation
Indices: 3321719--3321799 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
3321709 TATATTTTAT
* *
3321719 ATTTATTTTAATTTAATATTTAATGATTTAATATTTTTATTG
1 ATTTATTTTAATTTAATATATAATCATTTAATATTTTTATTG
* * * *
3321761 ATTTATTTTAGTTTTATATATAGTCATCTTAATTTTTTT
1 ATTTATTTTAATTTAATATATAATCAT-TTAATATTTTT
3321800 TAATGTTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
42 22 0.69
43 10 0.31
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (42 bp):
ATTTATTTTAATTTAATATATAATCATTTAATATTTTTATTG
Found at i:3329620 original size:29 final size:30
Alignment explanation
Indices: 3329550--3329620 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
3329540 ACTTTTTAAA
*
3329550 AAAAATTAATGACCAAATTTAACTTAAAAAAG
1 AAAAA-TAAAGACCAAATTTAAC-TAAAAAAG
*
3329582 AAAGAATAAAGACC-AATTTAA-TAAAAAAT
1 AAA-AATAAAGACCAAATTTAACTAAAAAAG
3329611 AAAAACTAAA
1 AAAAA-TAAA
3329621 TCTATCTGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
28 2 0.06
29 14 0.40
31 7 0.20
32 10 0.29
33 2 0.06
ACGTcount: A:0.65, C:0.08, G:0.06, T:0.21
Consensus pattern (30 bp):
AAAAATAAAGACCAAATTTAACTAAAAAAG
Found at i:3333437 original size:74 final size:71
Alignment explanation
Indices: 3333348--3333495 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 71
3333338 CCAAGCAGGA
3333348 TTTCCATCTATAACCTCCAAAATCTCAACCCCTTTCTTTAGATTTTACCACCCTAAAATGCTCAT
1 TTTCCATCTATAACCTCCAAAATCTCAACCCCTTTCTTTAGATTTTACCACCCTAAAATG--C-T
3333413 GAGGATATG
63 GAGGATATG
3333422 TTTCCATCTATAACCTCCAAAATCTCAACCCCTTTCTTTAGATTTTACCACCCTAAAATGCTGAG
1 TTTCCATCTATAACCTCCAAAATCTCAACCCCTTTCTTTAGATTTTACCACCCTAAAATGCTGAG
3333487 GATATG
66 GATATG
3333493 TTT
1 TTT
3333496 ACACTGAATC
Statistics
Matches: 74, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
71 13 0.18
72 1 0.01
74 60 0.81
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.35
Consensus pattern (71 bp):
TTTCCATCTATAACCTCCAAAATCTCAACCCCTTTCTTTAGATTTTACCACCCTAAAATGCTGAG
GATATG
Found at i:3340372 original size:31 final size:31
Alignment explanation
Indices: 3340334--3340394 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
3340324 CAAGCCAATA
* *
3340334 ACTTAAATAAAATATTT-TAAATAATTTAATT
1 ACTTAAATAAAA-ATTTATAAACAAATTAATT
3340365 ACTTAAATAAAAATTTATAAACAAATTAAT
1 ACTTAAATAAAAATTTATAAACAAATTAAT
3340395 AATTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 4 0.15
31 23 0.85
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (31 bp):
ACTTAAATAAAAATTTATAAACAAATTAATT
Found at i:3351306 original size:30 final size:31
Alignment explanation
Indices: 3351253--3351337 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 31
3351243 TATAAAAAAT
* *
3351253 AAATTTATT-AAATTTAAATAAAAATATT-TG
1 AAATTTATTAAAAATTAAA-AAAAATATTATA
*
3351283 AAATTTATTAAAAATTAGAAAAAA-ATTATA
1 AAATTTATTAAAAATTAAAAAAAATATTATA
* *
3351313 AAATATA-TAGAAAATTATAAAAAAT
1 AAATTTATTA-AAAATTAAAAAAAAT
3351338 GTAAAGAAAC
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 5 0.11
30 34 0.74
31 7 0.15
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (31 bp):
AAATTTATTAAAAATTAAAAAAAATATTATA
Found at i:3351315 original size:10 final size:10
Alignment explanation
Indices: 3351287--3351337 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
3351277 TATTTGAAAT
*
3351287 TTATTAAAAA
1 TTATAAAAAA
*
3351297 TTAGAAAAAAA
1 TTA-TAAAAAA
*
3351308 TTATAAAATA
1 TTATAAAAAA
*
3351318 -TATAGAAAA
1 TTATAAAAAA
3351327 TTATAAAAAA
1 TTATAAAAAA
3351337 T
1 T
3351338 GTAAAGAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
9 7 0.22
10 17 0.53
11 8 0.25
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:3351570 original size:18 final size:19
Alignment explanation
Indices: 3351546--3351592 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
3351536 TATATTTTGT
3351546 AATTTTTATAAAAATTTAC
1 AATTTTTATAAAAATTTAC
3351565 AATTTTTATAAAAATTTAC
1 AATTTTTATAAAAATTTAC
3351584 AATTTTTAT
1 AATTTTTAT
3351593 GTTTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTTTTATAAAAATTTAC
Found at i:3351591 original size:28 final size:28
Alignment explanation
Indices: 3351560--3351618 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
3351550 TTTATAAAAA
*
3351560 TTTACAATTTTTATAAAAATTTACAATT
1 TTTACAATTTTTATAAAAATTTAAAATT
*** *
3351588 TTTATGTTTTTTATTAAAATTTAAAATT
1 TTTACAATTTTTATAAAAATTTAAAATT
3351616 TTT
1 TTT
3351619 TATTTTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTACAATTTTTATAAAAATTTAAAATT
Found at i:3351625 original size:28 final size:28
Alignment explanation
Indices: 3351567--3351628 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
3351557 AAATTTACAA
* *
3351567 TTTTTATAAAAATTTACAATTTTTATGT
1 TTTTTATTAAAATTTAAAATTTTTATGT
*
3351595 TTTTTATTAAAATTTAAAATTTTT-TAT
1 TTTTTATTAAAATTTAAAATTTTTATGT
3351622 TTTTTAT
1 TTTTTAT
3351629 ATTTTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
27 9 0.29
28 22 0.71
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.63
Consensus pattern (28 bp):
TTTTTATTAAAATTTAAAATTTTTATGT
Found at i:3355963 original size:30 final size:31
Alignment explanation
Indices: 3355927--3355996 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
3355917 ATTTATTCGT
*
3355927 AGTTAAATTTAATT-TTAATATTTTGAAAAG
1 AGTTAAATTTAATTATTAATATTTTAAAAAG
* * *
3355957 AGTTAAACTTAATTATTAATTTTTTAAAAAT
1 AGTTAAATTTAATTATTAATATTTTAAAAAG
*
3355988 AGTCAAATT
1 AGTTAAATT
3355997 GTTATTTTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 13 0.39
31 20 0.61
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (31 bp):
AGTTAAATTTAATTATTAATATTTTAAAAAG
Found at i:3361019 original size:18 final size:18
Alignment explanation
Indices: 3360998--3361032 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3360988 AATTTAATTT
3360998 TTAAAAAATTATAAAAAC
1 TTAAAAAATTATAAAAAC
**
3361016 TTAAACTATTATAAAAA
1 TTAAAAAATTATAAAAA
3361033 TATACAATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
TTAAAAAATTATAAAAAC
Found at i:3370229 original size:831 final size:831
Alignment explanation
Indices: 3368628--3370287 Score: 3320
Period size: 831 Copynumber: 2.0 Consensus size: 831
3368618 ATCCACGGCG
3368628 GTGAACCAAAGGAAAGAGGTGGAGGAAGATGATTGGAGGAGTTCATCGTCTACCACCACGACGTC
1 GTGAACCAAAGGAAAGAGGTGGAGGAAGATGATTGGAGGAGTTCATCGTCTACCACCACGACGTC
3368693 GTCGTCTTGGATCGGGATGAATAGTGATGGATCTGCCGATGGTGGAGATTGCGACGGAGATGATG
66 GTCGTCTTGGATCGGGATGAATAGTGATGGATCTGCCGATGGTGGAGATTGCGACGGAGATGATG
3368758 ATGAGGTGGAAAGCTCTTATAAAGGTGGCTTAGACATTATGGATTCGCTTCAACAGGTTTTGCCT
131 ATGAGGTGGAAAGCTCTTATAAAGGTGGCTTAGACATTATGGATTCGCTTCAACAGGTTTTGCCT
3368823 ATGAGGTTCGTATCTACTCTCCGCCGCTTACATTAAAATTTCTTCTTATGATTTCATAATGTAAA
196 ATGAGGTTCGTATCTACTCTCCGCCGCTTACATTAAAATTTCTTCTTATGATTTCATAATGTAAA
3368888 CAAAAAATTGGGTTTATGAACAGGAGAGGGATCTCAAGTTTTTACAATGGGAAATCCAAGTGTTT
261 CAAAAAATTGGGTTTATGAACAGGAGAGGGATCTCAAGTTTTTACAATGGGAAATCCAAGTGTTT
3368953 CACAAATTTAGCTGAAGGCTCATCCACTTCATCGATTAAAGAGATAGCAAAACCTGAAAACGCCT
326 CACAAATTTAGCTGAAGGCTCATCCACTTCATCGATTAAAGAGATAGCAAAACCTGAAAACGCCT
3369018 ATACACGGAGGAGGAGAAACCTGTTAGCAATCAACTATGCATGGGACAAGAACAAGTTCAAAAGA
391 ATACACGGAGGAGGAGAAACCTGTTAGCAATCAACTATGCATGGGACAAGAACAAGTTCAAAAGA
3369083 CCCATCAAATCCATAATGAATTCAAGAAAAAGCAGATTGACTTTTCTAGCTGTTGCAATGGGTAG
456 CCCATCAAATCCATAATGAATTCAAGAAAAAGCAGATTGACTTTTCTAGCTGTTGCAATGGGTAG
3369148 CTCTGAAAGTATCTCTGCTACCACAAGTGACCACTCTACTTCTAACTTCATGCCCTCTGCACCCG
521 CTCTGAAAGTATCTCTGCTACCACAAGTGACCACTCTACTTCTAACTTCATGCCCTCTGCACCCG
3369213 CCCTCAAACCCCCACTTCTTTCAATAATATAAGACCCCCTTACTCGTCGTAGCCGGAATTTCTCT
586 CCCTCAAACCCCCACTTCTTTCAATAATATAAGACCCCCTTACTCGTCGTAGCCGGAATTTCTCT
3369278 AATTGGTTGTCCTTTTCGTTGTCTGGTGTACGGCACTGTCATGGGAAGCGTTCATCCCGATTGCT
651 AATTGGTTGTCCTTTTCGTTGTCTGGTGTACGGCACTGTCATGGGAAGCGTTCATCCCGATTGCT
3369343 CATTACTTGAGGATAAAACTAACTCTTAAGAAACAAAATTGATACTAATTTGCTTTGCTTCTTAC
716 CATTACTTGAGGATAAAACTAACTCTTAAGAAACAAAATTGATACTAATTTGCTTTGCTTCTTAC
3369408 AGAGCTTGATATATATTTTATTGACCCTAATGCATGTGGATGATCATGCAT
781 AGAGCTTGATATATATTTTATTGACCCTAATGCATGTGGATGATCATGCAT
3369459 GTGAACCAAAGGAAAGAGGTGGAGGAAGATGATTGGAGGAGTTCATCGTCTACCACCACGACGTC
1 GTGAACCAAAGGAAAGAGGTGGAGGAAGATGATTGGAGGAGTTCATCGTCTACCACCACGACGTC
3369524 GTCGTCTTGGATCGGGATGAATAGTGATGGATCTGCCGATGGTGGAGATTGCGACGGAGATGATG
66 GTCGTCTTGGATCGGGATGAATAGTGATGGATCTGCCGATGGTGGAGATTGCGACGGAGATGATG
3369589 ATGAGGTGGAAAGCTCTTATAAAGGTGGCTTAGACATTATGGATTCGCTTCAACAGGTTTTGCCT
131 ATGAGGTGGAAAGCTCTTATAAAGGTGGCTTAGACATTATGGATTCGCTTCAACAGGTTTTGCCT
3369654 ATGAGGTTCGTATCTACTCTCCGCCGCTTACATTAAAATTTCTTCTTATGATTTCATAATGTAAA
196 ATGAGGTTCGTATCTACTCTCCGCCGCTTACATTAAAATTTCTTCTTATGATTTCATAATGTAAA
3369719 CAAAAAATTGGGTTTATGAACAGGAGAGGGATCTCAAGTTTTTACAATGGGAAATCCAAGTGTTT
261 CAAAAAATTGGGTTTATGAACAGGAGAGGGATCTCAAGTTTTTACAATGGGAAATCCAAGTGTTT
3369784 CACAAATTTAGCTGAAGGCTCATCCACTTCATCGATTAAAGAGATAGCAAAACCTGAAAACGCCT
326 CACAAATTTAGCTGAAGGCTCATCCACTTCATCGATTAAAGAGATAGCAAAACCTGAAAACGCCT
3369849 ATACACGGAGGAGGAGAAACCTGTTAGCAATCAACTATGCATGGGACAAGAACAAGTTCAAAAGA
391 ATACACGGAGGAGGAGAAACCTGTTAGCAATCAACTATGCATGGGACAAGAACAAGTTCAAAAGA
3369914 CCCATCAAATCCATAATGAATTCAAGAAAAAGCAGATTGACTTTTCTAGCTGTTGCAATGGGTAG
456 CCCATCAAATCCATAATGAATTCAAGAAAAAGCAGATTGACTTTTCTAGCTGTTGCAATGGGTAG
3369979 CTCTGAAAGTATCTCTGCTACCACAAGTGACCACTCTACTTCTAACTTCATGCCCTCTGCACCCG
521 CTCTGAAAGTATCTCTGCTACCACAAGTGACCACTCTACTTCTAACTTCATGCCCTCTGCACCCG
3370044 CCCTCAAACCCCCACTTCTTTCAATAATATAAGACCCCCTTACTCGTCGTAGCCGGAATTTCTCT
586 CCCTCAAACCCCCACTTCTTTCAATAATATAAGACCCCCTTACTCGTCGTAGCCGGAATTTCTCT
3370109 AATTGGTTGTCCTTTTCGTTGTCTGGTGTACGGCACTGTCATGGGAAGCGTTCATCCCGATTGCT
651 AATTGGTTGTCCTTTTCGTTGTCTGGTGTACGGCACTGTCATGGGAAGCGTTCATCCCGATTGCT
3370174 CATTACTTGAGGATAAAACTAACTCTTAAGAAACAAAATTGATACTAATTTGCTTTGCTTCTTAC
716 CATTACTTGAGGATAAAACTAACTCTTAAGAAACAAAATTGATACTAATTTGCTTTGCTTCTTAC
3370239 AGAGCTTGATATATATTTTATTGACCCTAATGCATGTGGATGATCATGC
781 AGAGCTTGATATATATTTTATTGACCCTAATGCATGTGGATGATCATGC
3370288 TGAGCGGCAC
Statistics
Matches: 829, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
831 829 1.00
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (831 bp):
GTGAACCAAAGGAAAGAGGTGGAGGAAGATGATTGGAGGAGTTCATCGTCTACCACCACGACGTC
GTCGTCTTGGATCGGGATGAATAGTGATGGATCTGCCGATGGTGGAGATTGCGACGGAGATGATG
ATGAGGTGGAAAGCTCTTATAAAGGTGGCTTAGACATTATGGATTCGCTTCAACAGGTTTTGCCT
ATGAGGTTCGTATCTACTCTCCGCCGCTTACATTAAAATTTCTTCTTATGATTTCATAATGTAAA
CAAAAAATTGGGTTTATGAACAGGAGAGGGATCTCAAGTTTTTACAATGGGAAATCCAAGTGTTT
CACAAATTTAGCTGAAGGCTCATCCACTTCATCGATTAAAGAGATAGCAAAACCTGAAAACGCCT
ATACACGGAGGAGGAGAAACCTGTTAGCAATCAACTATGCATGGGACAAGAACAAGTTCAAAAGA
CCCATCAAATCCATAATGAATTCAAGAAAAAGCAGATTGACTTTTCTAGCTGTTGCAATGGGTAG
CTCTGAAAGTATCTCTGCTACCACAAGTGACCACTCTACTTCTAACTTCATGCCCTCTGCACCCG
CCCTCAAACCCCCACTTCTTTCAATAATATAAGACCCCCTTACTCGTCGTAGCCGGAATTTCTCT
AATTGGTTGTCCTTTTCGTTGTCTGGTGTACGGCACTGTCATGGGAAGCGTTCATCCCGATTGCT
CATTACTTGAGGATAAAACTAACTCTTAAGAAACAAAATTGATACTAATTTGCTTTGCTTCTTAC
AGAGCTTGATATATATTTTATTGACCCTAATGCATGTGGATGATCATGCAT
Found at i:3385381 original size:33 final size:34
Alignment explanation
Indices: 3385337--3385405 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 34
3385327 AATAAGAAAA
3385337 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
1 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
*
3385371 ATAAA-GTTTGATCCATTCTATAAGTAATCTGCT
1 ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
3385404 AT
1 AT
3385406 CAACCTAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 29 0.85
34 5 0.15
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (34 bp):
ATAAAGGTTTGATCCATTCTAAAAGTAATCTGCT
Found at i:3385393 original size:19 final size:19
Alignment explanation
Indices: 3385337--3385393 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
3385327 AATAAGAAAA
3385337 ATAAAGGTTTGATCCATTCT
1 ATAAA-GTTTGATCCATTCT
* *
3385357 A-AAAG--TAAT-C-TGCT
1 ATAAAGTTTGATCCATTCT
3385371 ATAAAGTTTGATCCATTCT
1 ATAAAGTTTGATCCATTCT
3385390 ATAA
1 ATAA
3385394 GTAATCTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 11
0.65 0.09 0.26
Matches are distributed among these distances:
14 4 0.14
15 5 0.18
16 3 0.11
17 3 0.11
18 2 0.07
19 10 0.36
20 1 0.04
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
ATAAAGTTTGATCCATTCT
Found at i:3386925 original size:28 final size:28
Alignment explanation
Indices: 3386893--3386949 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
3386883 ATTTTGAACA
3386893 TCACTTGAGTAGCTAACGGAATCAAACT
1 TCACTTGAGTAGCTAACGGAATCAAACT
3386921 TCACTTGAGTAGCTAACGGAATCAAACT
1 TCACTTGAGTAGCTAACGGAATCAAACT
3386949 T
1 T
3386950 ACATAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (28 bp):
TCACTTGAGTAGCTAACGGAATCAAACT
Found at i:3397094 original size:17 final size:17
Alignment explanation
Indices: 3397072--3397105 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3397062 ATCCACTAAT
*
3397072 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3397089 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3397106 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3401733 original size:17 final size:17
Alignment explanation
Indices: 3401711--3401744 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3401701 ATCCACTAAT
*
3401711 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3401728 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3401745 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3411030 original size:67 final size:67
Alignment explanation
Indices: 3410922--3411052 Score: 217
Period size: 67 Copynumber: 2.0 Consensus size: 67
3410912 TTTCCAATTC
* *
3410922 AGAGAGCACACTCCCACGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTA
1 AGAGAGCACACTCCCACAAACCTCATTTCTTACAGCCGGATTACCAGTCCAGGCTAAATCCCCTA
3410987 CA
66 CA
* * *
3410989 AGAGAGCACACTCTCGCAAACCTCATTTCTTATAGCCGGATTACCAGTCCAGGCTAAATCCCCT
1 AGAGAGCACACTCCCACAAACCTCATTTCTTACAGCCGGATTACCAGTCCAGGCTAAATCCCCT
3411053 GTAATATAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (67 bp):
AGAGAGCACACTCCCACAAACCTCATTTCTTACAGCCGGATTACCAGTCCAGGCTAAATCCCCTA
CA
Found at i:3414396 original size:21 final size:20
Alignment explanation
Indices: 3414368--3414441 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 20
3414358 TTTGTATTAT
3414368 TTAAGTATAAAACTTTTTTC
1 TTAAGTATAAAACTTTTTTC
** *
3414388 TTAATGTATTTTCAA-TTTGTATTAT
1 TTAA-GTA--TAAAACTTT-T-TT-C
3414413 TTAAGTATAAAACTTTTTTC
1 TTAAGTATAAAACTTTTTTC
3414433 TTAATGTAT
1 TTAA-GTAT
3414442 TTTCAATTTG
Statistics
Matches: 40, Mismatches: 6, Indels: 15
0.66 0.10 0.25
Matches are distributed among these distances:
20 8 0.20
21 9 0.22
22 7 0.17
23 7 0.17
24 5 0.12
25 4 0.10
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (20 bp):
TTAAGTATAAAACTTTTTTC
Found at i:3414408 original size:45 final size:45
Alignment explanation
Indices: 3414357--3414452 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
3414347 TTGCAACTAT
3414357 ATTTGTATTATTTAAGTATAAAACTTTTTTCTTAATGTATTTTCA
1 ATTTGTATTATTTAAGTATAAAACTTTTTTCTTAATGTATTTTCA
3414402 ATTTGTATTATTTAAGTATAAAACTTTTTTCTTAATGTATTTTCA
1 ATTTGTATTATTTAAGTATAAAACTTTTTTCTTAATGTATTTTCA
3414447 ATTTGT
1 ATTTGT
3414453 TGAGAAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.30, C:0.06, G:0.07, T:0.56
Consensus pattern (45 bp):
ATTTGTATTATTTAAGTATAAAACTTTTTTCTTAATGTATTTTCA
Found at i:3415104 original size:17 final size:17
Alignment explanation
Indices: 3415082--3415114 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3415072 ATACAAAATA
3415082 AAAACTAAATGCTACAG
1 AAAACTAAATGCTACAG
*
3415099 AAAACTTAATGCTACA
1 AAAACTAAATGCTACA
3415115 AAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (17 bp):
AAAACTAAATGCTACAG
Found at i:3417314 original size:55 final size:55
Alignment explanation
Indices: 3417230--3417338 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
3417220 ATCTAAAGCA
*
3417230 CCAAGCAAAGGCTTAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
*
3417285 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAATGAAACACAAAGAAAT
1 CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAAT
3417339 ACATCACAGA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.17
Consensus pattern (55 bp):
CCAAGCAAAGGCATAATCTAAAGTACTAGTAATCCAAACGAAACACAAAGAAATT
Found at i:3419034 original size:14 final size:14
Alignment explanation
Indices: 3419017--3419064 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
3419007 CCCTAAATCA
3419017 CTAACCACAAACCC
1 CTAACCACAAACCC
* *
3419031 CTAACCTCTAACCC
1 CTAACCACAAACCC
*
3419045 CTAACCACAAACCT
1 CTAACCACAAACCC
3419059 CTAACC
1 CTAACC
3419065 CCTGACTACT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.38, C:0.48, G:0.00, T:0.15
Consensus pattern (14 bp):
CTAACCACAAACCC
Found at i:3419078 original size:21 final size:21
Alignment explanation
Indices: 3419017--3419083 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
3419007 CCCTAAATCA
* * *
3419017 CTAACCACAAACCCCTAACCT
1 CTAACCCCTAACCACTAACCT
*
3419038 CTAACCCCTAACCACAAACCT
1 CTAACCCCTAACCACTAACCT
* * *
3419059 CTAACCCCTGACTACTAACCC
1 CTAACCCCTAACCACTAACCT
3419080 CTAA
1 CTAA
3419084 ACCTTATTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.36, C:0.46, G:0.01, T:0.16
Consensus pattern (21 bp):
CTAACCCCTAACCACTAACCT
Found at i:3419407 original size:14 final size:14
Alignment explanation
Indices: 3419362--3419399 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
3419352 ATCCTAAATT
3419362 AACCATATATCCTA
1 AACCATATATCCTA
*
3419376 AACCATATACCCTA
1 AACCATATATCCTA
3419390 AACCATATAT
1 AACCATATAT
3419400 ATTAAACCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
AACCATATATCCTA
Found at i:3419862 original size:38 final size:39
Alignment explanation
Indices: 3419820--3419924 Score: 113
Period size: 40 Copynumber: 2.7 Consensus size: 39
3419810 TCTCAAAGAA
* *
3419820 CGCCGCTAATTCTC-ATTTTAGCGGCACTTTCCCTAAAG
1 CGCCGCTAATGCTCGATTTTAGCGGCACTTTACCTAAAG
* * ** **
3419858 CGCCGCTAATGCTCTATCTTTAGTGGCGTTTTATGTAAAG
1 CGCCGCTAATGCTCGAT-TTTAGCGGCACTTTACCTAAAG
3419898 CGCCGCTAATGCTCGATTTTTAGCGGC
1 CGCCGCTAATGCTCGA-TTTTAGCGGC
3419925 GTTTTTTCTC
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
38 13 0.24
39 2 0.04
40 39 0.71
41 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.21, T:0.33
Consensus pattern (39 bp):
CGCCGCTAATGCTCGATTTTAGCGGCACTTTACCTAAAG
Found at i:3419897 original size:40 final size:40
Alignment explanation
Indices: 3419853--3419929 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
3419843 GCACTTTCCC
* *
3419853 TAAAGCGCCGCTAATGCTCTATCTTTAGTGGCGTTTTATG
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATG
*
3419893 TAAAGCGCCGCTAATGCTCGATTTTTAGCGGCGTTTT
1 TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTT
3419930 TTCTCCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.36
Consensus pattern (40 bp):
TAAAGCGCCGCTAATGCTCGATCTTTAGCGGCGTTTTATG
Found at i:3442239 original size:13 final size:15
Alignment explanation
Indices: 3442209--3442241 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
3442199 TTTATTGTTT
3442209 TAATAAATTTTAAAA
1 TAATAAATTTTAAAA
3442224 TAATAAA-TTT-AAA
1 TAATAAATTTTAAAA
3442237 TAATA
1 TAATA
3442242 TTATTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 3 0.17
15 7 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATAAATTTTAAAA
Found at i:3442742 original size:32 final size:34
Alignment explanation
Indices: 3442706--3442777 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
3442696 GACTTTTATG
*
3442706 AAATATTTTTA-AGAAATCTA-CCAAACAACAGA
1 AAATATTTTTACACAAATCTATCCAAACAACAGA
* * *
3442738 AAATA-TTTTACACAGATTTATCCAAACACCAGA
1 AAATATTTTTACACAAATCTATCCAAACAACAGA
3442771 AAATATT
1 AAATATT
3442778 AACTTTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
31 5 0.15
32 11 0.33
33 16 0.48
34 1 0.03
ACGTcount: A:0.50, C:0.17, G:0.06, T:0.28
Consensus pattern (34 bp):
AAATATTTTTACACAAATCTATCCAAACAACAGA
Found at i:3448378 original size:18 final size:18
Alignment explanation
Indices: 3448355--3448423 Score: 111
Period size: 18 Copynumber: 3.8 Consensus size: 18
3448345 CGTTTATGGC
3448355 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGT
**
3448373 ACTATTCACGTATACGAC
1 ACTATTCACGTATACGGT
3448391 ACTATTCACGTATACGGT
1 ACTATTCACGTATACGGT
*
3448409 ACTGTTCACGTATAC
1 ACTATTCACGTATAC
3448424 AGTAGTTGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (18 bp):
ACTATTCACGTATACGGT
Found at i:3448401 original size:36 final size:36
Alignment explanation
Indices: 3448354--3448423 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
3448344 CCGTTTATGG
3448354 CACTATTCACGTATACGGTACTATTCACGTATACGA
1 CACTATTCACGTATACGGTACTATTCACGTATACGA
*
3448390 CACTATTCACGTATACGGTACTGTTCACGTATAC
1 CACTATTCACGTATACGGTACTATTCACGTATAC
3448424 AGTAGTTGGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (36 bp):
CACTATTCACGTATACGGTACTATTCACGTATACGA
Found at i:3468315 original size:17 final size:17
Alignment explanation
Indices: 3468280--3468318 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3468270 ATAAATGTTC
*
3468280 TATTGTTGGAATTTAAT
1 TATTGTTGGAATATAAT
3468297 TATTGTTGGAA-ATATAT
1 TATTGTTGGAATATA-AT
3468314 TATTG
1 TATTG
3468319 AATTTAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (17 bp):
TATTGTTGGAATATAAT
Found at i:3468528 original size:21 final size:21
Alignment explanation
Indices: 3468502--3468584 Score: 103
Period size: 21 Copynumber: 4.0 Consensus size: 21
3468492 CGAGTGGATA
3468502 AGCTCTTACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTC
*
3468523 AACTCTTACGAGCTTCTGTTC
1 AGCTCTTACGAGCTTCTGTTC
** * *
3468544 AGCTCTTTTGAGCTTTTTTTC
1 AGCTCTTACGAGCTTCTGTTC
**
3468565 AGCTCTTATAAGCTTCTGTT
1 AGCTCTTACGAGCTTCTGTT
3468585 AGCGTGTTCG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.45
Consensus pattern (21 bp):
AGCTCTTACGAGCTTCTGTTC
Found at i:3470504 original size:61 final size:61
Alignment explanation
Indices: 3470427--3470557 Score: 156
Period size: 61 Copynumber: 2.1 Consensus size: 61
3470417 ATACATTTTA
* * * * *
3470427 TATATATATGTGGTTCGAATATAGGT-TACAAATTCATTGAGCTGAATTTAATGTTTTGAAC
1 TATATATATGAGGTTCGAATATA-ATATACAAATTCATTGAGCTAAAGTTAATGTTATGAAC
* * * * *
3470488 TATACATATGAGGTTCGAATGTAATATACAAGTTCTTTGAGCTAAAGTTAATGTTATGAAT
1 TATATATATGAGGTTCGAATATAATATACAAATTCATTGAGCTAAAGTTAATGTTATGAAC
3470549 TATATATAT
1 TATATATAT
3470558 TCATGTGGAT
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 1 0.02
61 57 0.98
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (61 bp):
TATATATATGAGGTTCGAATATAATATACAAATTCATTGAGCTAAAGTTAATGTTATGAAC
Found at i:3470765 original size:41 final size:41
Alignment explanation
Indices: 3470664--3470765 Score: 159
Period size: 41 Copynumber: 2.5 Consensus size: 41
3470654 GCTCTGTGCT
* *
3470664 TAGCAGGCTTAATGCCAGTGAAATAATTCAAACTTTATGTC
1 TAGCAGGCTTAATGCCGGTGAAATAATTCAAACTTTACGTC
* *
3470705 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATAATTCAAACTTTACGTC
*
3470746 TAGCAGGCTTAATGTCGGTG
1 TAGCAGGCTTAATGCCGGTG
3470766 TTCTGAATCA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAATAATTCAAACTTTACGTC
Found at i:3470782 original size:41 final size:41
Alignment explanation
Indices: 3470664--3470808 Score: 143
Period size: 41 Copynumber: 3.5 Consensus size: 41
3470654 GCTCTGTGCT
* * *
3470664 TAGCAGGCTTAATGCCAGTGAAATA-ATTCAAACTTTATGTC
1 TAGCAGGCTTAATGCCGGTGAAATATA-TCAGACTTTAAGTC
* *
3470705 TAGCAGGCTTAATGCCGGTGAAATATTTCAGACTTTACGTC
1 TAGCAGGCTTAATGCCGGTGAAATATATCAGACTTTAAGTC
* *** * *
3470746 TAGCAGGCTTAATGTCGGTGTTCTGA-ATCAGGCTTTAAGCC
1 TAGCAGGCTTAATGCCGGTGAAAT-ATATCAGACTTTAAGTC
3470787 TAGCAGGC-TACATGCCGGTGAA
1 TAGCAGGCTTA-ATGCCGGTGAA
3470809 TCATTTTAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 2 0.02
41 83 0.97
42 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (41 bp):
TAGCAGGCTTAATGCCGGTGAAATATATCAGACTTTAAGTC
Found at i:3474162 original size:45 final size:45
Alignment explanation
Indices: 3474096--3474182 Score: 129
Period size: 45 Copynumber: 1.9 Consensus size: 45
3474086 CAGATACTCG
* * * *
3474096 GTGGATTCAGCACATAACAACCACCTTATTAATTAATGATGTCCA
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATCATGTCCA
*
3474141 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATCATGT
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATCATGT
3474183 TCGGTTCACA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAACAACCACCTTACTAATCAATCATGTCCA
Found at i:3474249 original size:51 final size:50
Alignment explanation
Indices: 3474184--3474327 Score: 191
Period size: 50 Copynumber: 2.9 Consensus size: 50
3474174 CAATCATGTT
* *
3474184 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGATCGAAAC-TATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGA-CCAAACAT-TC
* * * *
3474235 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTC
* *
3474285 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCA
3474328 TCACTTTCAC
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
50 43 0.53
51 38 0.47
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (50 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGTGACCAAACATTC
Found at i:3474308 original size:50 final size:51
Alignment explanation
Indices: 3474184--3474319 Score: 186
Period size: 51 Copynumber: 2.7 Consensus size: 51
3474174 CAATCATGTT
* * *
3474184 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGATCGAAACTATC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCGAAACTATC
* * *
3474235 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-TATC-ATTC
1 CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCGAAACTA-TC
*
3474285 CGGTACACGTAGTAGCCTGCACATAGTACTACACA
1 CGGTACACATAGTAGCCTGCACATAGTACTACACA
3474320 CGTGACCATC
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
49 1 0.01
50 37 0.49
51 38 0.50
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (51 bp):
CGGTACACATAGTAGCCTGCACATAGTACTACACATGCGACCGAAACTATC
Found at i:3477520 original size:22 final size:23
Alignment explanation
Indices: 3477490--3477544 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
3477480 ACCTACTTTC
* *
3477490 TTACTGTAGTAATTTT-GGGGTA
1 TTACAGTAGTAATTTTCGGGATA
3477512 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
*
3477535 TTACATTAGT
1 TTACAGTAGT
3477545 CTTATTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 15 0.52
23 14 0.48
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:3481171 original size:20 final size:20
Alignment explanation
Indices: 3481148--3481187 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3481138 ACTGTTTCTG
3481148 CTTAAATTGTACTTTTCCCT
1 CTTAAATTGTACTTTTCCCT
3481168 CTTAAATTGTACTTTTCCCT
1 CTTAAATTGTACTTTTCCCT
3481188 TTGAAAATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.25, G:0.05, T:0.50
Consensus pattern (20 bp):
CTTAAATTGTACTTTTCCCT
Found at i:3496597 original size:25 final size:25
Alignment explanation
Indices: 3496555--3496604 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3496545 TAAGATTACT
*
3496555 TTAAAATAATATTATAAATTAATAA
1 TTAAAATAATATTATAAAATAATAA
*
3496580 TTAAAATTAA-ATTTTAAAATAATAA
1 TTAAAA-TAATATTATAAAATAATAA
3496605 AATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAAATAATATTATAAAATAATAA
Found at i:3499245 original size:27 final size:27
Alignment explanation
Indices: 3499193--3499247 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
3499183 ACAAACTTAA
*
3499193 TATTTTTTAAAATTCTAATTTATTTTT
1 TATTTTTTAAAATTCAAATTTATTTTT
*
3499220 TATTTTTATGAAATTCAAATTT-TTTTT
1 TATTTTT-TAAAATTCAAATTTATTTTT
3499247 T
1 T
3499248 GCTAATTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 13 0.52
28 12 0.48
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (27 bp):
TATTTTTTAAAATTCAAATTTATTTTT
Found at i:3501615 original size:5 final size:5
Alignment explanation
Indices: 3501605--3501631 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
3501595 TTTTTCCTTG
3501605 GATTT GATTT GATTT GATTT GATTT GA
1 GATTT GATTT GATTT GATTT GATTT GA
3501632 CTGTGTCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (5 bp):
GATTT
Found at i:3511468 original size:76 final size:76
Alignment explanation
Indices: 3511342--3511570 Score: 458
Period size: 76 Copynumber: 3.0 Consensus size: 76
3511332 AATAGTGAAG
3511342 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
1 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
3511407 TACATTACCAT
66 TACATTACCAT
3511418 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
1 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
3511483 TACATTACCAT
66 TACATTACCAT
3511494 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
1 AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
3511559 TACATTACCAT
66 TACATTACCAT
3511570 A
1 A
3511571 TATAGAACCA
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 153 1.00
ACGTcount: A:0.48, C:0.10, G:0.22, T:0.20
Consensus pattern (76 bp):
AAAGGCAAATTATAACATCTATTACTCTAATGGTAGGAGGAGAAAGAAGAAGAAGAAAGAGAAGG
TACATTACCAT
Found at i:3523922 original size:2 final size:2
Alignment explanation
Indices: 3523917--3523959 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3523907 ATATCTTATG
*
3523917 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3523959 G
1 G
3523960 TGAGGAGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3531791 original size:47 final size:47
Alignment explanation
Indices: 3531722--3531815 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
3531712 TCGTGTAGCC
3531722 TTGCTGAACAACTGGAAATCCGTATCACCATTAGCCATGCACACATA
1 TTGCTGAACAACTGGAAATCCGTATCACCATTAGCCATGCACACATA
3531769 TTGCTGAACAACTGGAAATCCGTATCACCATTAGCCATGCACACATA
1 TTGCTGAACAACTGGAAATCCGTATCACCATTAGCCATGCACACATA
3531816 CTTGGCTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (47 bp):
TTGCTGAACAACTGGAAATCCGTATCACCATTAGCCATGCACACATA
Found at i:3547262 original size:23 final size:24
Alignment explanation
Indices: 3547214--3547262 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
3547204 TAAACAACAA
*
3547214 AGAGAAAGAGTGAGTGAGAGAGAG
1 AGAGAAAGAGTGAGTGACAGAGAG
*
3547238 AGAGAAA-AGTG-GATGACAGATAG
1 AGAGAAAGAGTGAG-TGACAGAGAG
3547261 AG
1 AG
3547263 GGTGAGCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.47, C:0.02, G:0.41, T:0.10
Consensus pattern (24 bp):
AGAGAAAGAGTGAGTGACAGAGAG
Found at i:3551815 original size:22 final size:21
Alignment explanation
Indices: 3551790--3551837 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
3551780 AAATTCATAA
3551790 TTATTCAAATTAAAATTTATTT
1 TTATTCAAATTAAAA-TTATTT
* * *
3551812 TTATTTAATTTATAATTATTT
1 TTATTCAAATTAAAATTATTT
3551833 TTATT
1 TTATT
3551838 TTTATAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTCAAATTAAAATTATTT
Found at i:3558521 original size:12 final size:13
Alignment explanation
Indices: 3558504--3558540 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3558494 GAACCGGACA
3558504 CGAACCGAA-CTC
1 CGAACCGAAGCTC
3558516 CGAACC-AAGCTC
1 CGAACCGAAGCTC
*
3558528 CGAACCGTAGCTC
1 CGAACCGAAGCTC
3558541 TGATGCCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 2 0.09
12 15 0.68
13 5 0.23
ACGTcount: A:0.30, C:0.41, G:0.19, T:0.11
Consensus pattern (13 bp):
CGAACCGAAGCTC
Found at i:3559784 original size:40 final size:41
Alignment explanation
Indices: 3559688--3559784 Score: 117
Period size: 40 Copynumber: 2.4 Consensus size: 41
3559678 CGTTTGGACA
3559688 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTCCAGG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTCCAGG
* * * **
3559729 -AAAGCGCTGCTAAAAAT-GAGCATTAGCGGCGTTTCTTGG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTCCAGG
* *
3559768 AAAAACACCGCAAAAAA
1 AAAAACGCCGCTAAAAA
3559785 CCTAAGCCCA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
39 19 0.41
40 27 0.59
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTCCAGG
Found at i:3559881 original size:41 final size:42
Alignment explanation
Indices: 3559824--3559973 Score: 175
Period size: 41 Copynumber: 3.7 Consensus size: 42
3559814 TTTCGGGGCA
* *
3559824 TTAGCGGT-GTTTTTGAAAAAGCGTCGCTAATGCTCAGGCTT
1 TTAGCAGTCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTT
* *
3559865 TTAGC-GTCGTTTTTGAAAAAGCGCCGCTATTGCTCATGCTT
1 TTAGCAGTCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTT
* * * *
3559906 TTAGC-GGCGTTTTT-AAAGAAGCGCCACTAATGCTCTGACTT
1 TTAGCAGTCGTTTTTGAAA-AAGCGCCGCTAATGCTCAGGCTT
*
3559947 TTAGCAG-CGTTTTTTAAAAAGCGCCGC
1 TTAGCAGTCGTTTTTGAAAAAGCGCCGC
3559974 AAAAACATTG
Statistics
Matches: 95, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
40 5 0.05
41 86 0.91
42 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (42 bp):
TTAGCAGTCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTT
Found at i:3560386 original size:7 final size:7
Alignment explanation
Indices: 3560363--3560421 Score: 82
Period size: 7 Copynumber: 8.4 Consensus size: 7
3560353 TAAATAAGGT
3560363 TTAGGGG
1 TTAGGGG
**
3560370 TTAGTAG
1 TTAGGGG
3560377 TTAGGGG
1 TTAGGGG
3560384 TTAGGGG
1 TTAGGGG
3560391 TTAGGGG
1 TTAGGGG
3560398 TTAGGGG
1 TTAGGGG
*
3560405 TTAGAGG
1 TTAGGGG
*
3560412 TTAGAGG
1 TTAGGGG
3560419 TTA
1 TTA
3560422 AGAGTTAGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:3560428 original size:14 final size:14
Alignment explanation
Indices: 3560383--3560429 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
3560373 GTAGTTAGGG
* *
3560383 GTTAGGGGTTAGGG
1 GTTAGGGGTTAAGA
3560397 GTTAGGGGTT-AGA
1 GTTAGGGGTTAAGA
*
3560410 GGTTAGAGGTTAAGA
1 -GTTAGGGGTTAAGA
3560425 GTTAG
1 GTTAG
3560430 TGATTTAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 24 0.86
15 3 0.11
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (14 bp):
GTTAGGGGTTAAGA
Found at i:3560428 original size:21 final size:21
Alignment explanation
Indices: 3560383--3560429 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3560373 GTAGTTAGGG
* * * *
3560383 GTTAGGGGTTAGGGGTTAGGG
1 GTTAGAGGTTAGAGGTTAAGA
3560404 GTTAGAGGTTAGAGGTTAAGA
1 GTTAGAGGTTAGAGGTTAAGA
3560425 GTTAG
1 GTTAG
3560430 TGATTTAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.47, T:0.30
Consensus pattern (21 bp):
GTTAGAGGTTAGAGGTTAAGA
Found at i:3561020 original size:39 final size:39
Alignment explanation
Indices: 3560965--3561039 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
3560955 ATTTCCTTAA
*
3560965 CCGCTAAAAATAAGCATTAGCGGCGTTTTTCGAAAAATG
1 CCGCTAAAAATAAGCATTAGCGGCGTTTTTAGAAAAATG
* *
3561004 CCGCTAAAAATGAGCATTAGTGGCGTTTTTAGAAAA
1 CCGCTAAAAATAAGCATTAGCGGCGTTTTTAGAAAA
3561040 GCGCCGCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (39 bp):
CCGCTAAAAATAAGCATTAGCGGCGTTTTTAGAAAAATG
Found at i:3561046 original size:39 final size:39
Alignment explanation
Indices: 3560965--3561052 Score: 122
Period size: 39 Copynumber: 2.3 Consensus size: 39
3560955 ATTTCCTTAA
* *
3560965 CCGCTAAAAATAAGCATTAGCGGCGTTTTTCGAAAAATG
1 CCGCTAAAAATAAGCATTAGCGGCGTTTTTAGAAAAACG
* * *
3561004 CCGCTAAAAATGAGCATTAGTGGCGTTTTTAGAAAAGCG
1 CCGCTAAAAATAAGCATTAGCGGCGTTTTTAGAAAAACG
*
3561043 CCGCAAAAAA
1 CCGCTAAAAA
3561053 CCTAAGCCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (39 bp):
CCGCTAAAAATAAGCATTAGCGGCGTTTTTAGAAAAACG
Found at i:3561981 original size:38 final size:38
Alignment explanation
Indices: 3561905--3561982 Score: 120
Period size: 38 Copynumber: 2.1 Consensus size: 38
3561895 ACAAACTTTG
* * *
3561905 TCTGTTTTTTATATGTTTATCTCACAAATTTTCTTTTA
1 TCTGTTTTTTACATGTTTATCTCACAAAGTTTCGTTTA
*
3561943 TCTGTTTTTTACATGTTTATCTCACAAAGTTTGGTTTA
1 TCTGTTTTTTACATGTTTATCTCACAAAGTTTCGTTTA
3561981 TC
1 TC
3561983 AATTGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.21, C:0.14, G:0.09, T:0.56
Consensus pattern (38 bp):
TCTGTTTTTTACATGTTTATCTCACAAAGTTTCGTTTA
Found at i:3568181 original size:43 final size:43
Alignment explanation
Indices: 3568105--3568331 Score: 330
Period size: 43 Copynumber: 5.3 Consensus size: 43
3568095 TTTTTGCAAG
* * *
3568105 AAGCGTCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTATGATAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAA
* *
3568147 AAGCGCCGCTAAAGGCCATGTTCTTTAGCGGCGTTTGTGACAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAA
*
3568190 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTATGATAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAA
* * * *
3568233 AAGCGTCGTTAAAGGTCATGTTCTTTAGCGGCATTTGTGACAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAA
* * *
3568276 AAGCGCCGCGAAAGGTCATATTCTTTAGTGGCGTTTGTGATAA
1 AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAA
3568319 AAGCGCCGCTAAA
1 AAGCGCCGCTAAA
3568332 TGCCTAAAAA
Statistics
Matches: 163, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 14 0.09
43 149 0.91
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGATAA
Found at i:3569639 original size:22 final size:23
Alignment explanation
Indices: 3569586--3569641 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
3569576 TTTAATTAAA
* * *
3569586 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
3569609 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
3569631 ATTAAAATTAA
1 ATTAAAATTAA
3569642 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:3569654 original size:16 final size:16
Alignment explanation
Indices: 3569617--3569656 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3569607 TTAATAAAAT
* *
3569617 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
3569633 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
3569649 TAAAATTA
1 TAAAATTA
3569657 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:3569735 original size:59 final size:59
Alignment explanation
Indices: 3569667--3569836 Score: 322
Period size: 59 Copynumber: 2.9 Consensus size: 59
3569657 TCAAATTATT
*
3569667 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
3569726 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
3569785 AATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAGTAAA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAA
3569837 ACAAACTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 109 1.00
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:3569943 original size:22 final size:24
Alignment explanation
Indices: 3569903--3569946 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
3569893 AAATAAACTT
*
3569903 AAAATGAAAAACTATTATATTTTA
1 AAAATGAAAAAATATTATATTTTA
3569927 AAAAT-AAAAAATA-TATATTT
1 AAAATGAAAAAATATTATATTT
3569947 AATATTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 7 0.37
24 5 0.26
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATGAAAAAATATTATATTTTA
Found at i:3576110 original size:22 final size:24
Alignment explanation
Indices: 3576060--3576110 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
3576050 TTGCGATACT
3576060 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
3576085 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
3576106 TTTAT
1 TTTAT
3576111 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:3577350 original size:5 final size:6
Alignment explanation
Indices: 3577335--3577359 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3577325 AAATGAAGTT
3577335 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
3577360 GTTTCTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:3584480 original size:17 final size:17
Alignment explanation
Indices: 3584458--3584490 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3584448 GTGAGCAATC
3584458 ATCGCATTTTTTTTACT
1 ATCGCATTTTTTTTACT
3584475 ATCGCATTTTTTTTAC
1 ATCGCATTTTTTTTAC
3584491 CAACTGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.58
Consensus pattern (17 bp):
ATCGCATTTTTTTTACT
Done.