Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 73 of 202
Found at i:21634084 original size:102 final size:102
Alignment explanation
Indices: 21633866--21634156 Score: 413
Period size: 102 Copynumber: 2.8 Consensus size: 102
21633856 ATCGGTGGAT
* * *
21633866 TCAACACTTAGCAACCACCAATGATTCGGGGAATCAACACTTAGCAACCACCAATGAATCGGGGA
1 TCAACACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACC-CC--T---TGGGGGA
* * * *
21633931 ATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGTGGGA
60 ATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGTAGAA
* *
21633974 TCAACACTTAGCAACCACCAATAATTCAGGGAATCAGGACTTAGCAACCCCTTGGGGGAATCAGC
1 TCAACACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGC
21634039 ACTTAGCAACCCCCTTCACATTTAAAATACGGTAGAA
66 ACTTAGCAACCCCCTTCACATTTAAAATACGGTAGAA
*
21634076 TCAGCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAG
1 TCAACACTTAGCAACCACCAAT-AATTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAG
*
21634140 CACTTAACAACCCCCTT
65 CACTTAGCAACCCCCTT
21634157 ATATTCAATG
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
102 119 0.70
103 2 0.01
105 1 0.01
107 2 0.01
108 45 0.27
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.20
Consensus pattern (102 bp):
TCAACACTTAGCAACCACCAATAATTCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGC
ACTTAGCAACCCCCTTCACATTTAAAATACGGTAGAA
Found at i:21635364 original size:25 final size:25
Alignment explanation
Indices: 21635330--21635385 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
21635320 CCTAAAACAA
21635330 CAAATATGTTTAAAATCAAAGAGAT
1 CAAATATGTTTAAAATCAAAGAGAT
21635355 CAAATATGTTTAAAATCAAAGAGAT
1 CAAATATGTTTAAAATCAAAGAGAT
*
21635380 TAAATA
1 CAAATA
21635386 GAAAATCAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.29
Consensus pattern (25 bp):
CAAATATGTTTAAAATCAAAGAGAT
Found at i:21643051 original size:45 final size:41
Alignment explanation
Indices: 21642941--21643044 Score: 111
Period size: 41 Copynumber: 2.4 Consensus size: 41
21642931 TATCTCATAT
* * * *
21642941 CGATGCCACTGTCCCGGGCAAGGTCTTACACGAATCAAATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAATCAAATA
*
21642982 CGATGCCAATGTCCTAGACATGGTCTTACACGTAATCATATATA
1 CGATGCCAATGTCCCAGACATGGTCTTACACG-AATCA-A-ATA
21643026 TCGATGCC-ATCGTCCCAGA
1 -CGATGCCAAT-GTCCCAGA
21643045 AGTGGTCACA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
41 27 0.52
42 5 0.10
43 1 0.02
44 5 0.10
45 14 0.27
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (41 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGAATCAAATA
Found at i:21653349 original size:25 final size:26
Alignment explanation
Indices: 21653307--21653358 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
21653297 AAGTTGTAAA
21653307 TAAAAAAATATCTCCAGA-AATTTTC
1 TAAAAAAATATCTCCAGATAATTTTC
* * *
21653332 TAAAATAATTTCTTCAGATAATTTTC
1 TAAAAAAATATCTCCAGATAATTTTC
21653358 T
1 T
21653359 CTATAGAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.42, C:0.13, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAAAAAATATCTCCAGATAATTTTC
Found at i:21653575 original size:62 final size:59
Alignment explanation
Indices: 21653467--21653667 Score: 172
Period size: 62 Copynumber: 3.2 Consensus size: 59
21653457 ATCACTTTAA
* * *
21653467 TATTAAATTAATATAATACTTATCAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
* *
21653526 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAAATTAAATTTAATGTTAAGATAATC
1 TATTAAATTAATAGAATACTTA--T-CAAGATAAACATTAAATTAAATTTAATATT---A-AAT-
21653591 ACTT
58 -C-T
* * ** *
21653595 TAACATTAAATTAATAAAATA-TTATTAAGATAAGTATTAAATTTAATTTAATATTAAAT-T
1 T---ATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
*
21653655 TATTAAAATAATA
1 TATTAAATTAATA
21653668 TTATTTTTAG
Statistics
Matches: 117, Mismatches: 12, Indels: 28
0.75 0.08 0.18
Matches are distributed among these distances:
57 11 0.09
59 20 0.17
60 2 0.02
61 1 0.01
62 27 0.23
64 3 0.03
65 2 0.02
66 3 0.03
68 26 0.22
69 3 0.03
71 3 0.03
72 16 0.14
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (59 bp):
TATTAAATTAATAGAATACTTATCAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:21653664 original size:17 final size:17
Alignment explanation
Indices: 21653629--21653661 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21653619 TTAAGATAAG
*
21653629 TATTAAATTTAATTTAA
1 TATTAAATTTAATTAAA
21653646 TATTAAATTT-ATTAAA
1 TATTAAATTTAATTAAA
21653662 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAAATTTAATTAAA
Found at i:21654931 original size:15 final size:15
Alignment explanation
Indices: 21654892--21654923 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21654882 TATTCATGCA
21654892 AAATATGAAAGACAT
1 AAATATGAAAGACAT
*
21654907 AAATACGAAAGACAT
1 AAATATGAAAGACAT
21654922 AA
1 AA
21654924 TAGTGAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.16
Consensus pattern (15 bp):
AAATATGAAAGACAT
Found at i:21664948 original size:47 final size:47
Alignment explanation
Indices: 21664897--21665039 Score: 136
Period size: 47 Copynumber: 3.1 Consensus size: 47
21664887 ATATAAGAAA
* *
21664897 ATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTTT
1 ATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
* * ** *
21664944 ATTTAATATTAATTA-TTT-T-AAATTATATA-AATTCATATAAGA--AA
1 ATTTATTATCAAGAATTTTATGAAATTATATATAATT-AT-TAA-ATTAT
* *
21664988 ATTTATTATCAAGAATTTTATGCAATTATATATTATTATTAAATTAT
1 ATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
21665035 ATTTA
1 ATTTA
21665040 ATAATAATTA
Statistics
Matches: 73, Mismatches: 14, Indels: 18
0.70 0.13 0.17
Matches are distributed among these distances:
43 3 0.04
44 23 0.32
45 8 0.11
46 8 0.11
47 28 0.38
48 3 0.04
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (47 bp):
ATTTATTATCAAGAATTTTATGAAATTATATATAATTATTAAATTAT
Found at i:21665015 original size:91 final size:91
Alignment explanation
Indices: 21664861--21665086 Score: 400
Period size: 91 Copynumber: 2.5 Consensus size: 91
21664851 NNNNNNNNNN
21664861 ATTAATTA-TTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTA
1 ATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTA
*
21664925 TATATCATTATTAAATTTTATTTAAT
66 TATATCATTATTAAATTATATTTAAT
*
21664951 ATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGCAATTA
1 ATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTA
*
21665016 TATATTATTATTAAATTATATTTAAT
66 TATATCATTATTAAATTATATTTAAT
* *
21665042 AATAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTA
1 ATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTA
21665087 GTTATAATTA
Statistics
Matches: 130, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
90 8 0.06
91 122 0.94
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (91 bp):
ATTAATTATTTTAAATTATATAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTA
TATATCATTATTAAATTATATTTAAT
Found at i:21665053 original size:47 final size:46
Alignment explanation
Indices: 21664911--21665061 Score: 120
Period size: 44 Copynumber: 3.3 Consensus size: 46
21664901 ATTATCAAGA
* * *
21664911 ATTTTATGAAATTATATATCATTATTAAATTTTATTTAATATTAATT
1 ATTTTATG-AATTATATATAATTATTAAATTATATTTAATAATAATT
* * **
21664958 ATTTTA--AATTATATA-AATTCATATAAGA--AAATTT-ATTATCAAGA
1 ATTTTATGAATTATATATAATT-AT-TAA-ATTATATTTAATAAT-AATT
*
21665002 ATTTTATGCAATTATATATTATTATTAAATTATATTTAATAATAATT
1 ATTTTATG-AATTATATATAATTATTAAATTATATTTAATAATAATT
21665049 ATTTTA--AATTATA
1 ATTTTATGAATTATA
21665062 CAAATTCATA
Statistics
Matches: 81, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
43 6 0.07
44 30 0.37
45 4 0.05
46 4 0.05
47 30 0.37
48 7 0.09
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (46 bp):
ATTTTATGAATTATATATAATTATTAAATTATATTTAATAATAATT
Found at i:21665231 original size:120 final size:120
Alignment explanation
Indices: 21665105--21665399 Score: 477
Period size: 120 Copynumber: 2.5 Consensus size: 120
21665095 TATTTTAAAT
* * * *
21665105 TTTATTAAGTCATATAATTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTATATTTTAT
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTATATTTTAT
*
21665169 AGTATCATATATTATGATTT-TAGTAAATTCATATAAGAATATTGATTATTAAGAAA
65 AGTATCATATATTATGATTTGT-GTAAATTCATATAAGAATATTAATTATTAAGAAA
*
21665225 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATCTTTTATA
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
*
21665290 GTATCATATATTATGATTTGTGTAAATTCATATAAGAATATTAATTATTAAGAAT
66 GTATCATATATTATGATTTGTGTAAATTCATATAAGAATATTAATTATTAAGAAA
*
21665345 TTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAAT
1 TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
21665400 ATGATTAAAT
Statistics
Matches: 164, Mismatches: 8, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
120 155 0.95
121 9 0.05
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTATA
GTATCATATATTATGATTTGTGTAAATTCATATAAGAATATTAATTATTAAGAAA
Found at i:21665242 original size:61 final size:60
Alignment explanation
Indices: 21665175--21665362 Score: 151
Period size: 61 Copynumber: 3.1 Consensus size: 60
21665165 TTATAGTATC
21665175 ATATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAAATTTATTAAATT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATT-ATTATTAAGAAATTTATTAAATT
* * * * * *
21665236 ATATATT-TTA-ATTA--AAATAT-ATTTAATAATAATTA-TGTTAA-ATTATCTT-TTATAGTA
1 ATATATTATGATTTTAGTAAAT-TCATATAAGAAT-ATTATTATTAAGA-AAT-TTATTA-A--A
*
21665293 TC
59 TT
*
21665295 ATATATTATGATTTGT-GTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTT-TAGTAAATTCATATAAGAATATT-ATTATTAAGAAATTTATTAAATT
21665356 ATATATT
1 ATATATT
21665363 TTAATTATAA
Statistics
Matches: 95, Mismatches: 15, Indels: 34
0.66 0.10 0.24
Matches are distributed among these distances:
55 1 0.01
56 10 0.11
57 16 0.17
58 4 0.04
59 12 0.13
60 4 0.04
61 17 0.18
62 5 0.05
63 16 0.17
64 9 0.09
65 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTATTATTAAGAAATTTATTAAATT
Found at i:21665300 original size:59 final size:57
Alignment explanation
Indices: 21665090--21665301 Score: 138
Period size: 59 Copynumber: 3.6 Consensus size: 57
21665080 TTTATTAGTT
* *
21665090 ATAATTATTTTAAATT-TTATTA-AG--TCATATAATTTAATTAAAATATATTTAATA
1 ATAATTA-TTTAAATTATTTTTATAGTATCATATATTTTAATTAAAATATATTTAATA
* * * * *
21665144 TTAATTATTTCAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAAT-TCATATAAGA
1 ATAATTATTT-AAATTAT-TTTTATAGTATCATATATT-TTA-ATTA--AAATAT-ATTTAATA
* *
21665207 AT-ATTGATTATTAAGA-AATTTATTA-A--ATTATATATTTTAATTAAAATATATTTAATA
1 ATAATT-A-T-TTAA-ATTATTT-TTATAGTATCATATATTTTAATTAAAATATATTTAATA
21665264 ATAATTATGTTAAATTATCTTTTATAGTATCATATATT
1 ATAATTAT-TTAAATTAT-TTTTATAGTATCATATATT
21665302 ATGATTTGTG
Statistics
Matches: 118, Mismatches: 17, Indels: 41
0.67 0.10 0.23
Matches are distributed among these distances:
53 3 0.03
54 11 0.09
55 2 0.02
56 14 0.12
57 18 0.15
58 4 0.03
59 20 0.17
60 4 0.03
61 12 0.10
62 4 0.03
63 15 0.13
64 8 0.07
65 3 0.03
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (57 bp):
ATAATTATTTAAATTATTTTTATAGTATCATATATTTTAATTAAAATATATTTAATA
Found at i:21665359 original size:59 final size:58
Alignment explanation
Indices: 21665176--21665359 Score: 139
Period size: 66 Copynumber: 3.1 Consensus size: 58
21665166 TATAGTATCA
* *
21665176 TATATTATGATTTTAGTAAATTCATATAAGAATATTGATTATTAAGAAATTTATTAAAT
1 TATATTATGATTTT-GTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
* ** * * *
21665235 TATA-TAT--TTTAAT-TAAAAT-ATAT-TTAATAATAATTATGTTA-AATTATCTTTTATAGTA
1 TATATTATGATTT--TGTAAATTCATATAAGAATATTAATTAT-TAAGAATT-T-TATTA-A--A
21665293 T
58 T
21665294 CATATATTATGATTTGTGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
1 --TATATTATGATTT-TGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
21665355 TATAT
1 TATAT
21665360 ATTTTAATTA
Statistics
Matches: 93, Mismatches: 15, Indels: 34
0.65 0.11 0.24
Matches are distributed among these distances:
54 13 0.14
55 7 0.08
56 12 0.13
57 1 0.01
58 4 0.04
59 11 0.12
61 6 0.06
62 3 0.03
63 2 0.02
64 12 0.13
65 7 0.08
66 15 0.16
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (58 bp):
TATATTATGATTTTGTAAATTCATATAAGAATATTAATTATTAAGAATTTTATTAAAT
Found at i:21665377 original size:16 final size:16
Alignment explanation
Indices: 21665356--21665397 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21665346 TTATTAAATT
*
21665356 ATATATTTTAATTATA
1 ATATATTTTAATAATA
21665372 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
21665387 AT-TATGTTTAA
1 ATATAT-TTTAA
21665398 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:21665382 original size:15 final size:15
Alignment explanation
Indices: 21665347--21665388 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21665337 TTAAGAATTT
*
21665347 TATTAAATTAT-ATA
1 TATTTAATTATAATA
21665361 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
21665375 TATTTAATAATAAT
1 TATTTAATTATAAT
21665389 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:21665635 original size:16 final size:16
Alignment explanation
Indices: 21665611--21665643 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21665601 TTGATTTGCT
21665611 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
21665627 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
21665643 A
1 A
21665644 ATACAGTGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:21667186 original size:19 final size:18
Alignment explanation
Indices: 21667158--21667198 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
21667148 ATTTCGGGTA
*
21667158 AATTCGGGTAATTTGGTT
1 AATTCGGGTAATTCGGTT
21667176 AATTCCGGGTAATTCGGTT
1 AATT-CGGGTAATTCGGTT
21667195 AATT
1 AATT
21667199 TTTAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (18 bp):
AATTCGGGTAATTCGGTT
Found at i:21667190 original size:10 final size:9
Alignment explanation
Indices: 21667150--21667198 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
21667140 NNNNNNNAAT
21667150 TTCGGGTAAA
1 TTCGGGT-AA
21667160 TTCGGGTAA
1 TTCGGGTAA
* *
21667169 TTTGGTTAA
1 TTCGGGTAA
21667178 TTCCGGGTAA
1 TT-CGGGTAA
*
21667188 TTCGGTTAA
1 TTCGGGTAA
21667197 TT
1 TT
21667199 TTTAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 19 0.58
10 14 0.42
ACGTcount: A:0.22, C:0.10, G:0.27, T:0.41
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:21668882 original size:24 final size:24
Alignment explanation
Indices: 21668837--21668883 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
21668827 CTGAGTGCTG
* *
21668837 AAGCTCCAACTTCTTTGTCACAAC
1 AAGCACCAACTTCTTTGACACAAC
21668861 AAGCACCAACTTCTGTT-ACACAA
1 AAGCACCAACTTCT-TTGACACAA
21668884 GGTATATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.34, C:0.32, G:0.09, T:0.26
Consensus pattern (24 bp):
AAGCACCAACTTCTTTGACACAAC
Found at i:21680082 original size:2 final size:2
Alignment explanation
Indices: 21680075--21680102 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
21680065 AGGTAGATTC
21680075 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21680103 GAGAGAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21680662 original size:2 final size:2
Alignment explanation
Indices: 21680655--21680688 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21680645 TTAAACGTAC
21680655 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21680689 TCACAAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21683424 original size:6 final size:6
Alignment explanation
Indices: 21683394--21683435 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
21683384 AATTTCATCG
* *
21683394 AATTG- AATTGTA CATTGA AAGTGA AATTGA AATTGA AATTGA
1 AATTGA AATTG-A AATTGA AATTGA AATTGA AATTGA AATTGA
21683436 GAAAGTGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
5 5 0.16
6 22 0.71
7 4 0.13
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.33
Consensus pattern (6 bp):
AATTGA
Found at i:21683860 original size:23 final size:23
Alignment explanation
Indices: 21683834--21684011 Score: 138
Period size: 23 Copynumber: 8.1 Consensus size: 23
21683824 GGATTTGCTG
* *
21683834 ATCAGGCACTTTATGTGTCATAT
1 ATCAGGCACCTTATGTGTCGTAT
* * *
21683857 ATCAGGAACTTTATATGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* **
21683880 TTCAGGCACCTCGTGTGTCGT-T
1 ATCAGGCACCTTATGTGTCGTAT
*
21683902 -TCAGGCA-CTTATGTGTTGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* *
21683923 ATCAAGCACTTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
* * **
21683946 TTCAGACACCTCGTGTGTCG--T
1 ATCAGGCACCTTATGTGTCGTAT
**
21683967 ATCAGGCACCTCGTGTGTC--AT
1 ATCAGGCACCTTATGTGTCGTAT
*
21683988 TTCAGGCA-CTTATGTGTCGTAT
1 ATCAGGCACCTTATGTGTCGTAT
21684010 AT
1 AT
21684012 TGATCAGGTA
Statistics
Matches: 122, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
20 17 0.14
21 34 0.28
22 10 0.08
23 61 0.50
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (23 bp):
ATCAGGCACCTTATGTGTCGTAT
Found at i:21683905 original size:21 final size:21
Alignment explanation
Indices: 21683879--21683996 Score: 103
Period size: 21 Copynumber: 5.5 Consensus size: 21
21683869 ATATGTCGTA
21683879 TTTCAGGCACCTCGTGTGTCG
1 TTTCAGGCACCTCGTGTGTCG
** *
21683900 TTTCAGGCA-CTTATGTGTTG
1 TTTCAGGCACCTCGTGTGTCG
* * **
21683920 TATATCAAGCACTTTATGTGTCG
1 T-T-TCAGGCACCTCGTGTGTCG
*
21683943 TATTTCAGACACCTCGTGTGTCG
1 --TTTCAGGCACCTCGTGTGTCG
* *
21683966 TATCAGGCACCTCGTGTGTCA
1 TTTCAGGCACCTCGTGTGTCG
21683987 TTTCAGGCAC
1 TTTCAGGCAC
21683997 TTATGTGTCG
Statistics
Matches: 77, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
20 9 0.12
21 37 0.48
22 6 0.08
23 23 0.30
24 1 0.01
25 1 0.01
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.36
Consensus pattern (21 bp):
TTTCAGGCACCTCGTGTGTCG
Found at i:21683942 original size:66 final size:66
Alignment explanation
Indices: 21683834--21684009 Score: 223
Period size: 66 Copynumber: 2.7 Consensus size: 66
21683824 GGATTTGCTG
** * * *
21683834 ATCAGGCACTTTATGTGTCATATATCAGGAACTTTATATGTCGTATTTCAGGCACCTCGTGTGTC
1 ATCAGGCAC-TTATGTGTTGTATATCAGGCACTTTATGTGTCGTATTTCAGACACCTCGTGTGTC
21683899 GT
65 GT
* *
21683901 TTCAGGCACTTATGTGTTGTATATCAAGCACTTTATGTGTCGTATTTCAGACACCTCGTGTGTCG
1 ATCAGGCACTTATGTGTTGTATATCAGGCACTTTATGTGTCGTATTTCAGACACCTCGTGTGTCG
21683966 T
66 T
* * *
21683967 ATCAGGCACCT-CGTG-TGTCATTTCAGGCAC-TTATGTGTCGTAT
1 ATCAGGCACTTATGTGTTGT-ATATCAGGCACTTTATGTGTCGTAT
21684010 ATTGATCAGG
Statistics
Matches: 96, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
64 16 0.17
65 12 0.12
66 60 0.62
67 8 0.08
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (66 bp):
ATCAGGCACTTATGTGTTGTATATCAGGCACTTTATGTGTCGTATTTCAGACACCTCGTGTGTCG
T
Found at i:21688984 original size:45 final size:45
Alignment explanation
Indices: 21688920--21689090 Score: 193
Period size: 45 Copynumber: 3.8 Consensus size: 45
21688910 TACTGAGTAT
* ***
21688920 CATTGATTATAAAGGTGGTTGCTATATGTTGATTCCACCGGGTAC
1 CATTGATTATAAAGGTGGTTGCTATATGCTGATTCCACCGAAAAC
* * *
21688965 CATTGATTATAAAGGTGGTTGCTATGTGCTGACTCCACCGAAAAT
1 CATTGATTATAAAGGTGGTTGCTATATGCTGATTCCACCGAAAAC
** * *
21689010 CATTGAAAATAAAGGTGGTTGCTATATGCTGATTCCACCGAATAT
1 CATTGATTATAAAGGTGGTTGCTATATGCTGATTCCACCGAAAAC
* * * *
21689055 AATTAATTATAAGGGTGG-TGCTATGTGCTGA-TCCAC
1 CATTGATTATAAAGGTGGTTGCTATATGCTGATTCCAC
21689091 AGTGTAACGG
Statistics
Matches: 108, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
43 5 0.05
44 12 0.11
45 91 0.84
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (45 bp):
CATTGATTATAAAGGTGGTTGCTATATGCTGATTCCACCGAAAAC
Found at i:21689072 original size:90 final size:88
Alignment explanation
Indices: 21688918--21689090 Score: 247
Period size: 90 Copynumber: 1.9 Consensus size: 88
21688908 TGTACTGAGT
** * ** * *
21688918 ATCATTGATTATAAAGGTGGTTGCTATATGTTGATTCCACCGGGTACCATTGATTATAAAGGTGG
1 ATCATTGAAAATAAAGGTGGTTGCTATATGCTGATTCCACCGAATACAATTAATTATAAAGGTGG
21688983 TTGCTATGTGCTGACTCCACCGAAA
66 -TGCTATGTGCTGA-TCCACCGAAA
* *
21689008 ATCATTGAAAATAAAGGTGGTTGCTATATGCTGATTCCACCGAATATAATTAATTATAAGGGTGG
1 ATCATTGAAAATAAAGGTGGTTGCTATATGCTGATTCCACCGAATACAATTAATTATAAAGGTGG
21689073 TGCTATGTGCTGATCCAC
66 TGCTATGTGCTGATCCAC
21689091 AGTGTAACGG
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
88 5 0.07
89 13 0.18
90 56 0.76
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.33
Consensus pattern (88 bp):
ATCATTGAAAATAAAGGTGGTTGCTATATGCTGATTCCACCGAATACAATTAATTATAAAGGTGG
TGCTATGTGCTGATCCACCGAAA
Found at i:21693339 original size:18 final size:16
Alignment explanation
Indices: 21693302--21693360 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 16
21693292 ATTATCCAAC
*
21693302 ATGTAT-TAGAAT-AG
1 ATGTATCTAGTATAAG
*
21693316 ATGTATCTAGTTTAATG
1 ATGTATCTAGTATAA-G
*
21693333 AATGTATTTAG-ATAAG
1 -ATGTATCTAGTATAAG
21693349 ATGTATCTAGTA
1 ATGTATCTAGTA
21693361 GTCATGCATG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.17
15 13 0.37
16 3 0.09
17 4 0.11
18 9 0.26
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.41
Consensus pattern (16 bp):
ATGTATCTAGTATAAG
Found at i:21694258 original size:13 final size:13
Alignment explanation
Indices: 21694240--21694267 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
21694230 ACAAAATTGG
21694240 AAAGATGAAAAAT
1 AAAGATGAAAAAT
21694253 AAAGATGAAAAAT
1 AAAGATGAAAAAT
21694266 AA
1 AA
21694268 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAAGATGAAAAAT
Found at i:21695349 original size:23 final size:25
Alignment explanation
Indices: 21695298--21695350 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
21695288 TCTTTGTAAG
* *
21695298 CTTCCTGATTAGTGGCTCTCCTGAG
1 CTTCCTGATTAGTGGCTCGCCTGAA
*
21695323 CTTCCTGA-TA-TGGCTCGCTTGAA
1 CTTCCTGATTAGTGGCTCGCCTGAA
21695346 CTTCC
1 CTTCC
21695351 CAATATATGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.60
24 2 0.08
25 8 0.32
ACGTcount: A:0.13, C:0.30, G:0.21, T:0.36
Consensus pattern (25 bp):
CTTCCTGATTAGTGGCTCGCCTGAA
Found at i:21695506 original size:25 final size:25
Alignment explanation
Indices: 21695428--21695510 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
21695418 GCTTCCCGAT
* *
21695428 TATGGCTCTTATGAGCTTCCCGTTA
1 TATGGCTCATATGAGCTTCCTGTTA
* * *
21695453 TATAGCCCGA-ATAAGCTTCCTGTTA
1 TATGGCTC-ATATGAGCTTCCTGTTA
21695478 TATGGCTCATATGAGCTTCCTGTTA
1 TATGGCTCATATGAGCTTCCTGTTA
21695503 TATGGCTC
1 TATGGCTC
21695511 GAGAGAGAGC
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
24 1 0.02
25 47 0.98
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.37
Consensus pattern (25 bp):
TATGGCTCATATGAGCTTCCTGTTA
Found at i:21701746 original size:11 final size:13
Alignment explanation
Indices: 21701722--21701753 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
21701712 TAGTTTATTA
21701722 ATATTTTAATATG
1 ATATTTTAATATG
21701735 AT-TTTTAA-ATG
1 ATATTTTAATATG
21701746 ATATTTTA
1 ATATTTTA
21701754 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:21705364 original size:32 final size:33
Alignment explanation
Indices: 21705323--21705388 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
21705313 TGTACTTATA
*
21705323 TTTAATGAATGTA-TTAGAGTAGATGCATCTAG
1 TTTAATGAATGTATTTAGAGAAGATGCATCTAG
*
21705355 TTTAATGAATGTATTTGGAGAAGATGCATCTAG
1 TTTAATGAATGTATTTAGAGAAGATGCATCTAG
21705388 T
1 T
21705389 AGTCATGCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.42
33 18 0.58
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.38
Consensus pattern (33 bp):
TTTAATGAATGTATTTAGAGAAGATGCATCTAG
Found at i:21706994 original size:238 final size:236
Alignment explanation
Indices: 21706527--21706995 Score: 663
Period size: 238 Copynumber: 2.0 Consensus size: 236
21706517 TTTTAGGATA
* *
21706527 TGTTTTCTAAGAATTGACCTTTGAGGGCTATAGGCTCAATTGCCACTACTTAATATTCATATGAT
1 TGTTTTCTAAGAATTGACCTTTGAGGGCTATAGACTAAATTGCCACTACTTAATATTCATATGAT
* * * *
21706592 AAGGTCATCTTACTTAGATCCTTGGCCTCACTTTTGGTTTCAATATGTAAAGGTTGTTTCTTTGT
66 AAGATAATCTTAATTAGATCCTTGGCCTCACTTTTGGTTTCAATATGTAAAGGTTGTTCCTTTGT
* * * *
21706657 GTGTGTTTCATTTTAGTGAAATACCAAAAAAATTATACTAAAATGGATGTTCTCTCTTTTGTTAA
131 GTGTGTTTCATTGTAATGAAATACCAAAAAAATGATACTAAAATGGATGTTCTCTCTTTTGTGAA
**
21706722 AAATGCTGGAAAGATAGGTTTTGCTGCAAAAGAGATAATTT
196 AAATGCTGGAAAGATAGCATTTGCTGCAAAAGAGATAATTT
* * * * *
21706763 TGTTTTCTAAAGAATTGATCTTTGAGGGCTATA-ACTAAACTTTGTCAGTATTTAATATTTATAT
1 TGTTTTCT-AAGAATTGACCTTTGAGGGCTATAGACTAAA--TTGCCACTACTTAATATTCATAT
* *
21706827 GGTAAGATAATCTTAATTAGATCCTTGGCTTCA-TTCTTGGTTTCAATATGTAAAGGTTGTTCCT
63 GATAAGATAATCTTAATTAGATCCTTGGCCTCACTT-TTGGTTTCAATATGTAAAGGTTGTTCCT
* * * * *
21706891 TTGTGTGTGTTTCATTGTAATGAAATTCCAAGACAATGATACTAAAATGGTTGTTGTCTCTTTTG
127 TTGTGTGTGTTTCATTGTAATGAAATACCAAAAAAATGATACTAAAATGGATGTTCTCTCTTTTG
*
21706956 TGAAAAATGCTGGAAAGATCGCATTTGCTGCAAAAGAGAT
192 TGAAAAATGCTGGAAAGATAGCATTTGCTGCAAAAGAGAT
21706996 CGATGTGGGA
Statistics
Matches: 204, Mismatches: 25, Indels: 6
0.87 0.11 0.03
Matches are distributed among these distances:
236 12 0.06
237 25 0.12
238 167 0.82
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (236 bp):
TGTTTTCTAAGAATTGACCTTTGAGGGCTATAGACTAAATTGCCACTACTTAATATTCATATGAT
AAGATAATCTTAATTAGATCCTTGGCCTCACTTTTGGTTTCAATATGTAAAGGTTGTTCCTTTGT
GTGTGTTTCATTGTAATGAAATACCAAAAAAATGATACTAAAATGGATGTTCTCTCTTTTGTGAA
AAATGCTGGAAAGATAGCATTTGCTGCAAAAGAGATAATTT
Found at i:21713802 original size:20 final size:20
Alignment explanation
Indices: 21713767--21713806 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
21713757 ACCATCCTAT
*
21713767 TTTATTTATATATATTTAAAA
1 TTTAATTATATATA-TTAAAA
21713788 TTTAATTAT-TATATTAAAA
1 TTTAATTATATATATTAAAA
21713807 CATTGCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 4 0.22
21 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTAATTATATATATTAAAA
Found at i:21714061 original size:5 final size:5
Alignment explanation
Indices: 21714034--21714081 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
21714024 TAATAAACAC
* * * *
21714034 CAAACG CAAAG CAAAA CATAG CAAAG CATAG CATAG CAAAG CAAAG CA
1 CAAA-G CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CA
21714082 GGCTGGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
5 32 0.89
6 4 0.11
ACGTcount: A:0.54, C:0.23, G:0.17, T:0.06
Consensus pattern (5 bp):
CAAAG
Found at i:21714081 original size:15 final size:15
Alignment explanation
Indices: 21714039--21714081 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
21714029 AACACCAAAC
*
21714039 GCAAAGCAAAACATA
1 GCAAAGCAAAGCATA
*
21714054 GCAAAGCATAGCATA
1 GCAAAGCAAAGCATA
21714069 GCAAAGCAAAGCA
1 GCAAAGCAAAGCA
21714082 GGCTGGTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.53, C:0.21, G:0.19, T:0.07
Consensus pattern (15 bp):
GCAAAGCAAAGCATA
Found at i:21715295 original size:24 final size:24
Alignment explanation
Indices: 21715265--21715326 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
21715255 TTTTTTCAAA
*
21715265 TTTCGAGTTCGAATTGAGTTGAGT
1 TTTCGAGTTCGAATCGAGTTGAGT
*
21715289 TTTCGAGTTCGAATCGATTTGAGT
1 TTTCGAGTTCGAATCGAGTTGAGT
*
21715313 TTTCGAATTCGAAT
1 TTTCGAGTTCGAAT
21715327 AACTTGAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.42
Consensus pattern (24 bp):
TTTCGAGTTCGAATCGAGTTGAGT
Found at i:21716269 original size:5 final size:5
Alignment explanation
Indices: 21716259--21716289 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
21716249 GAACAAATAT
21716259 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG A
21716290 ATTCCATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (5 bp):
ATTCG
Found at i:21720392 original size:17 final size:18
Alignment explanation
Indices: 21720360--21720393 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21720350 AGAACTCGAA
*
21720360 TGATTTAAACTCAAAATC
1 TGATTCAAACTCAAAATC
21720378 TGATTCAAA-TCAAAAT
1 TGATTCAAACTCAAAAT
21720394 GGCCGAAATG
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:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (18 bp):
TGATTCAAACTCAAAATC
Found at i:21721655 original size:32 final size:33
Alignment explanation
Indices: 21721604--21721673 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
21721594 GTTAACAACA
*
21721604 AGTGATAAAATAAAG-AAAAATTCAAATAGTTG
1 AGTGATAAAATAAAGAAAAAAGTCAAATAGTTG
* *
21721636 GGTGATCAAA-AAAGAAAAAAAGTCAAATAGTTG
1 AGTGATAAAATAAAG-AAAAAAGTCAAATAGTTG
21721669 AGTGA
1 AGTGA
21721674 CCATTTTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 4 0.12
32 8 0.25
33 20 0.62
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.21
Consensus pattern (33 bp):
AGTGATAAAATAAAGAAAAAAGTCAAATAGTTG
Found at i:21725407 original size:16 final size:16
Alignment explanation
Indices: 21725378--21725419 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
21725368 TTACTTTAAA
*
21725378 AACTC-AAATGATTTG
1 AACTCAAAATTATTTG
21725393 AACTCAAAATTATTTG
1 AACTCAAAATTATTTG
*
21725409 AATTCAAAATT
1 AACTCAAAATT
21725420 GATCCAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (16 bp):
AACTCAAAATTATTTG
Found at i:21732200 original size:17 final size:19
Alignment explanation
Indices: 21732178--21732217 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
21732168 AAAATTAACC
21732178 TTTTTTAT-ATTTTCAAT-
1 TTTTTTATAATTTTCAATA
21732195 TTTTTTATAATTTTCAATA
1 TTTTTTATAATTTTCAATA
21732214 TTTT
1 TTTT
21732218 AAATAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.38
18 9 0.43
19 4 0.19
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTTTATAATTTTCAATA
Found at i:21732218 original size:17 final size:17
Alignment explanation
Indices: 21732180--21732218 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
21732170 AATTAACCTT
*
21732180 TTTTATATTTTCAATTT
1 TTTTATATTTTCAATTA
21732197 TTTTATAATTTTCAA-TA
1 TTTTAT-ATTTTCAATTA
21732214 TTTTA
1 TTTTA
21732219 AATAAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATATTTTCAATTA
Found at i:21754294 original size:17 final size:17
Alignment explanation
Indices: 21754231--21754294 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
21754221 AAATATTTAT
**
21754231 TTTTTA-ATTTATGATA
1 TTTTTATATTTAAAATA
*
21754247 TGTTTATATTTAAAAT-
1 TTTTTATATTTAAAATA
*
21754263 TTTAATT-TATATAAAATA
1 TTT--TTATATTTAAAATA
21754281 TTTTTATATTTAAA
1 TTTTTATATTTAAA
21754295 TTCAAATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
16 9 0.24
17 23 0.62
18 5 0.14
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TTTTTATATTTAAAATA
Found at i:21755798 original size:16 final size:16
Alignment explanation
Indices: 21755777--21755809 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
21755767 TTCGCTGTAT
21755777 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
*
21755793 TGGAATAGATGCGTAA
1 TGGAATAGAGGCGTAA
21755809 T
1 T
21755810 AACAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:21759433 original size:33 final size:33
Alignment explanation
Indices: 21759396--21759461 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
21759386 ATCATAAAGC
*
21759396 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTACAATTGACCTAAAATTAATTGTTGGTAT
21759429 ATGTACAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTACAATTGACCTAAAATTAATTGTTGGTAT
21759462 TTGTTAGATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (33 bp):
ATGTACAATTGACCTAAAATTAATTGTTGGTAT
Found at i:21759761 original size:37 final size:37
Alignment explanation
Indices: 21759676--21759762 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
21759666 GTATAAATAT
* * *
21759676 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
21759713 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
21759750 ATTGATTAGTTTA
1 ATTGATTAGTTTA
21759763 TTTATTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
Found at i:21760996 original size:23 final size:24
Alignment explanation
Indices: 21760935--21760997 Score: 87
Period size: 23 Copynumber: 2.7 Consensus size: 24
21760925 TCTACTGGTT
21760935 AACAAATCAAGAACAATTTCCAGC
1 AACAAATCAAGAACAATTTCCAGC
*
21760959 AGAC-AATCAA-TACAATTTCCAG-
1 A-ACAAATCAAGAACAATTTCCAGC
21760981 AACAAATCAAGAACAAT
1 AACAAATCAAGAACAAT
21760998 ATCAAAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 2 0.06
22 7 0.21
23 16 0.47
24 7 0.21
25 2 0.06
ACGTcount: A:0.52, C:0.22, G:0.08, T:0.17
Consensus pattern (24 bp):
AACAAATCAAGAACAATTTCCAGC
Found at i:21761098 original size:107 final size:106
Alignment explanation
Indices: 21760911--21761194 Score: 398
Period size: 107 Copynumber: 2.7 Consensus size: 106
21760901 ACAAATCAAG
** * *
21760911 TTCCAGTTTCATATTCTACTGGTTAACAAATCAAGAACAATTTCCAGCAGACAATCAATACAATT
1 TTCCAGTTTCAT-TTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
*
21760976 TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAT
65 TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAC
* *
21761018 TTCCAGTTTCATCTTCTACTGACTAACAAATCAAGAATAATTTCCAGCAGACTATCAAAACAACT
1 TTCCAGTTTCAT-TTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
* *
21761083 GCCAGAACAATTCAAGAACAATATCAAAACAAATGCAACAAC
65 TCCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAC
* * * *
21761125 TTCCA---TC-TTT-TACTCACTAACAAATCAATAACATTTTCCAGTAGACTATCAAAACAATTT
1 TTCCAGTTTCATTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATTT
21761185 CCAGAACAAA
66 CCAGAACAAA
21761195 CCAACAAAAT
Statistics
Matches: 159, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
101 52 0.33
102 2 0.01
103 1 0.01
104 2 0.01
107 102 0.64
ACGTcount: A:0.44, C:0.23, G:0.07, T:0.25
Consensus pattern (106 bp):
TTCCAGTTTCATTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATTT
CCAGAACAAATCAAGAACAATATCAAAACAAATGCAACAAC
Found at i:21765074 original size:16 final size:16
Alignment explanation
Indices: 21765053--21765083 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
21765043 TTCACTATTA
*
21765053 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
21765069 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
21765084 GTATGCATAG
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:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:21769703 original size:14 final size:14
Alignment explanation
Indices: 21769674--21769715 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
21769664 TCAAAATGAC
21769674 TAATTAATTTAA-TT
1 TAATT-ATTTAATTT
21769688 TAATT-TTTGAATTT
1 TAATTATTT-AATTT
21769702 TAATTATTTAATTT
1 TAATTATTTAATTT
21769716 AATAATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 2 0.08
14 17 0.68
15 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TAATTATTTAATTT
Found at i:21774643 original size:25 final size:26
Alignment explanation
Indices: 21774584--21774703 Score: 85
Period size: 25 Copynumber: 4.8 Consensus size: 26
21774574 AATTCATATT
21774584 CAGGAATGCTC-ATGTGAG-CATATAAA
1 CAGGAA-GCTCTATGTGAGCCATAT-AA
* * *
21774610 CGGGTAGCTCTTTG-GAGCCATATAA
1 CAGGAAGCTCTATGTGAGCCATATAA
* *
21774635 TAGGAAGCTC-ATGTGAGCCATGTAA
1 CAGGAAGCTCTATGTGAGCCATATAA
* *
21774660 CGGGAAGCTCTA-GAGAGCCAT-TAA
1 CAGGAAGCTCTATGTGAGCCATATAA
*
21774684 C-GAGAAGCTC-ATATGAGCCA
1 CAG-GAAGCTCTATGTGAGCCA
21774704 ATATCGGGAA
Statistics
Matches: 75, Mismatches: 13, Indels: 14
0.74 0.13 0.14
Matches are distributed among these distances:
23 2 0.03
24 19 0.25
25 42 0.56
26 12 0.16
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.22
Consensus pattern (26 bp):
CAGGAAGCTCTATGTGAGCCATATAA
Found at i:21774662 original size:50 final size:49
Alignment explanation
Indices: 21774585--21774703 Score: 127
Period size: 50 Copynumber: 2.4 Consensus size: 49
21774575 ATTCATATTC
* *
21774585 AGGAATGCTCATGTGAG-CATATAAACGGGTAGCTCTTTG-GAGCCATATAA
1 AGGAA-GCTCATGTGAGCCATATAAACGGGAAGCTC-TAGAGAGCCAT-TAA
*
21774635 TAGGAAGCTCATGTGAGCCATGT-AACGGGAAGCTCTAGAGAGCCATTAA
1 -AGGAAGCTCATGTGAGCCATATAAACGGGAAGCTCTAGAGAGCCATTAA
* *
21774684 CGAGAAGCTCATATGAGCCA
1 AG-GAAGCTCATGTGAGCCA
21774704 ATATCGGGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
48 1 0.02
49 21 0.35
50 29 0.48
51 9 0.15
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (49 bp):
AGGAAGCTCATGTGAGCCATATAAACGGGAAGCTCTAGAGAGCCATTAA
Found at i:21774701 original size:24 final size:25
Alignment explanation
Indices: 21774638--21774703 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
21774628 CATATAATAG
* *
21774638 GAAGCTCATGTGAGCCATGTAACGG
1 GAAGCTCATATGAGCCATGTAACGA
*
21774663 GAAGCTC-TAGAGAGCCAT-TAACGA
1 GAAGCTCATA-TGAGCCATGTAACGA
21774687 GAAGCTCATATGAGCCA
1 GAAGCTCATATGAGCCA
21774704 ATATCGGGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
24 19 0.54
25 16 0.46
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.18
Consensus pattern (25 bp):
GAAGCTCATATGAGCCATGTAACGA
Found at i:21774714 original size:24 final size:24
Alignment explanation
Indices: 21774637--21774714 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
21774627 CCATATAATA
* *
21774637 GGAAGCTCATGTGAGCCATGTAACG
1 GGAAGCTCATATGAGCCA-ATAACG
* *
21774662 GGAAGCTC-TAGAGAGCCATTAACG
1 GGAAGCTCATA-TGAGCCAATAACG
* *
21774686 AGAAGCTCATATGAGCCAATATCG
1 GGAAGCTCATATGAGCCAATAACG
21774710 GGAAG
1 GGAAG
21774715 GTTCAAACGA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
24 27 0.63
25 16 0.37
ACGTcount: A:0.33, C:0.19, G:0.29, T:0.18
Consensus pattern (24 bp):
GGAAGCTCATATGAGCCAATAACG
Found at i:21774729 original size:25 final size:25
Alignment explanation
Indices: 21774701--21774764 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
21774691 CTCATATGAG
*
21774701 CCAATATCGGGAAGGTTCAAACGAA
1 CCAATATCGGGAAGATTCAAACGAA
* * *
21774726 CCAATATCGGGAATATTCAAGCGAG
1 CCAATATCGGGAAGATTCAAACGAA
*
21774751 CCAATATCAGGAAG
1 CCAATATCGGGAAG
21774765 CTCCGGAGAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.17
Consensus pattern (25 bp):
CCAATATCGGGAAGATTCAAACGAA
Found at i:21782582 original size:26 final size:26
Alignment explanation
Indices: 21782553--21782619 Score: 93
Period size: 25 Copynumber: 2.7 Consensus size: 26
21782543 TCATATGAGT
* *
21782553 ATATAAACGGGTAGCTCTTTCGAGCC
1 ATATAAACAGGAAGCTCTTTCGAGCC
*
21782579 ATAT-AACAGGAAGCTTTTTCGAGCC
1 ATATAAACAGGAAGCTCTTTCGAGCC
21782604 ATAT-AACAGGAAGCTC
1 ATATAAACAGGAAGCTC
21782620 ATGGGAGCCA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
25 33 0.89
26 4 0.11
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
ATATAAACAGGAAGCTCTTTCGAGCC
Found at i:21782593 original size:25 final size:25
Alignment explanation
Indices: 21782565--21782644 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
21782555 ATAAACGGGT
21782565 AGCTCTTTCGAGCCATATAACAGGA
1 AGCTCTTTCGAGCCATATAACAGGA
*
21782590 AGCTTTTTCGAGCCATATAACAGGA
1 AGCTCTTTCGAGCCATATAACAGGA
* ** * *
21782615 AGCTCATGGGAGCCATGTAACGGGA
1 AGCTCTTTCGAGCCATATAACAGGA
21782640 AGCTC
1 AGCTC
21782645 ATACGAGATA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.23
Consensus pattern (25 bp):
AGCTCTTTCGAGCCATATAACAGGA
Found at i:21782682 original size:25 final size:24
Alignment explanation
Indices: 21782654--21782715 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
21782644 CATACGAGAT
*
21782654 AATATCTAGAAGATTCAAACGAACC
1 AATATCGAGAAG-TTCAAACGAACC
* * *
21782679 AATATCGAGAATGTTTAAGCGAGCC
1 AATATCGAGAA-GTTCAAACGAACC
21782704 AATATCGAGAAG
1 AATATCGAGAAG
21782716 CTCCAAAGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 1 0.03
25 30 0.94
26 1 0.03
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (24 bp):
AATATCGAGAAGTTCAAACGAACC
Found at i:21785652 original size:40 final size:41
Alignment explanation
Indices: 21785581--21785657 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
21785571 TTTATTACTT
* *
21785581 ATTTTATTACTATAATATAATATATATACTTAAACATTAAG
1 ATTTTATTACTATAATATAATAAATACACTTAAACATTAAG
* *
21785622 ATTTTA-TATTATAATAT-ATAGAATACACTTACACAT
1 ATTTTATTACTATAATATAATA-AATACACTTAAACAT
21785658 ATTTTAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
39 3 0.10
40 22 0.71
41 6 0.19
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (41 bp):
ATTTTATTACTATAATATAATAAATACACTTAAACATTAAG
Found at i:21798096 original size:14 final size:14
Alignment explanation
Indices: 21798077--21798106 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
21798067 AGTTAGAGAG
*
21798077 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
21798091 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
21798105 GA
1 GA
21798107 ACGAGGGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:21800171 original size:15 final size:13
Alignment explanation
Indices: 21800131--21800163 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
21800121 TGAGTAGGGT
21800131 CACGCCCGTGTCA
1 CACGCCCGTGTCA
*
21800144 CACGGCCGTGTCA
1 CACGCCCGTGTCA
21800157 CACGCCC
1 CACGCCC
21800164 ATGTGTCAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
CACGCCCGTGTCA
Found at i:21801100 original size:41 final size:41
Alignment explanation
Indices: 21801055--21801263 Score: 208
Period size: 41 Copynumber: 5.1 Consensus size: 41
21801045 TACAAAAGTT
*
21801055 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATATGCA
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCA
* * * *
21801096 ATTCAGAGGTATCGAAGTACAAATAGGGGCACGTATGTGCA
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCA
* * *
21801137 ATTTAGGGGTACCGAAGTAC-AAC-AGGGTCACATATGTTCA
1 ATTCAGGGGTACCGAAGTACAAACAAGGG-CACGTATGTGCA
* * * ** *
21801177 ATTCAAGGGTACCAAAGTACAAACAGGGGCATATATGTGTA
1 ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCA
* ** * *
21801218 ATTCAGGGTTATTGAGGTACAAAC-AGAGGTACGTATGTGCA
1 ATTCAGGGGTACCGAAGTACAAACAAG-GGCACGTATGTGCA
21801259 ATTCA
1 ATTCA
21801264 ACAATAATAT
Statistics
Matches: 134, Mismatches: 30, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
39 3 0.02
40 30 0.22
41 98 0.73
42 3 0.02
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (41 bp):
ATTCAGGGGTACCGAAGTACAAACAAGGGCACGTATGTGCA
Found at i:21801238 original size:81 final size:82
Alignment explanation
Indices: 21801055--21801264 Score: 221
Period size: 81 Copynumber: 2.6 Consensus size: 82
21801045 TACAAAAGTT
* * * * *
21801055 ATTCAGGGGTACCGAAGTACAAACA-AGGGCACGTATATGCAATTC-AGAGGTATCGAAGTACAA
1 ATTCAGGGGTACCGAAGTACAAACAGA-GGTACATATGTGCAATTCAAG-GGTACCAAAGTACAA
* *
21801118 ATAGGGGCACGTATGTGCA
64 ACAGGGGCACATATGTGCA
* *
21801137 ATTTAGGGGTACCGAAGTAC-AACAG-GGTCACATATGTTCAATTCAAGGGTACCAAAGTACAAA
1 ATTCAGGGGTACCGAAGTACAAACAGAGGT-ACATATGTGCAATTCAAGGGTACCAAAGTACAAA
* *
21801200 CAGGGGCATATATGTGTA
65 CAGGGGCACATATGTGCA
* ** * *
21801218 ATTCAGGGTTATTGAGGTACAAACAGAGGTACGTATGTGCAATTCAA
1 ATTCAGGGGTACCGAAGTACAAACAGAGGTACATATGTGCAATTCAA
21801265 CAATAATATT
Statistics
Matches: 105, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
80 2 0.02
81 59 0.56
82 41 0.39
83 3 0.03
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (82 bp):
ATTCAGGGGTACCGAAGTACAAACAGAGGTACATATGTGCAATTCAAGGGTACCAAAGTACAAAC
AGGGGCACATATGTGCA
Found at i:21805778 original size:198 final size:198
Alignment explanation
Indices: 21805440--21805835 Score: 765
Period size: 198 Copynumber: 2.0 Consensus size: 198
21805430 CGATACCACT
21805440 GTAGGTGGTCTTCATCTTTGGGGCCTGTTTGAGGTATCACGATTCCAAGGGTAGGATAGTGCAAT
1 GTAGGTGGTCTTCATCTTTGGGGCCTGTTTGAGGTATCACGATTCCAAGGGTAGGATAGTGCAAT
21805505 ACCCTCTCCCTTGGTGATGTTCTCACTCGATTCCGACCTCCAATGTGTCCCTACAACACAATCAC
66 ACCCTCTCCCTTGGTGATGTTCTCACTCGATTCCGACCTCCAATGTGTCCCTACAACACAATCAC
21805570 ATATTAGGGCCTCCAATGGCACAATTGGCCAATTTGGGTATCAAAATAAGTAAAAAGAGACATTT
131 ATATTAGGGCCTCCAATGGCACAATTGGCCAATTTGGGTATCAAAATAAGTAAAAAGAGACATTT
21805635 ACA
196 ACA
*
21805638 GTAGGTGGTCTTCATCTTTGGGGCCTGTTTGAGGTATCATGATTCCAAGGGTAGGATAGTGCAAT
1 GTAGGTGGTCTTCATCTTTGGGGCCTGTTTGAGGTATCACGATTCCAAGGGTAGGATAGTGCAAT
21805703 ACCCTCTCCCTTGGTGATGTTCTCACTCGATTCCGACCTCCAATGTGTCCCTACAACACAATCAC
66 ACCCTCTCCCTTGGTGATGTTCTCACTCGATTCCGACCTCCAATGTGTCCCTACAACACAATCAC
* *
21805768 ATATTAGGGCCTCCACTGGCACAATTGGCCAATTTGGGTATCAAAATAAGTAAAACGAGACATTT
131 ATATTAGGGCCTCCAATGGCACAATTGGCCAATTTGGGTATCAAAATAAGTAAAAAGAGACATTT
21805833 ACA
196 ACA
21805836 CTTAGTAAAT
Statistics
Matches: 195, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
198 195 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (198 bp):
GTAGGTGGTCTTCATCTTTGGGGCCTGTTTGAGGTATCACGATTCCAAGGGTAGGATAGTGCAAT
ACCCTCTCCCTTGGTGATGTTCTCACTCGATTCCGACCTCCAATGTGTCCCTACAACACAATCAC
ATATTAGGGCCTCCAATGGCACAATTGGCCAATTTGGGTATCAAAATAAGTAAAAAGAGACATTT
ACA
Found at i:21810768 original size:100 final size:100
Alignment explanation
Indices: 21810590--21810790 Score: 276
Period size: 100 Copynumber: 2.0 Consensus size: 100
21810580 CAATTCGGCA
* * * * *
21810590 TGAACTTTTGGATGGGATCTAAGTAGTTACAGGTTGAGATGTTTGTATAGCATTTGAAGAATTAT
1 TGAACTTTTGGATGGGATCCAAGTAGTTACAGGCTGAAATGCTTGCATAGCATTTGAAGAATTAT
* * *
21810655 TTTTTAGTTTCGAAATGCACATTGAATCACTTGAT
66 ATATTAGTTTCGAAATGCACATTGAATCACTCGAT
* ** *
21810690 TGAATTTTTGGATGGGATCCAAGTAGTTATGGGCTGAAATGCTTGCATAGCGTTTGAAGAATTAT
1 TGAACTTTTGGATGGGATCCAAGTAGTTACAGGCTGAAATGCTTGCATAGCATTTGAAGAATTAT
* *
21810755 ATATTAGTTTCGAAATGTACTTTGAATCACTCGAT
66 ATATTAGTTTCGAAATGCACATTGAATCACTCGAT
21810790 T
1 T
21810791 TTGAGTTCGG
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
100 87 1.00
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (100 bp):
TGAACTTTTGGATGGGATCCAAGTAGTTACAGGCTGAAATGCTTGCATAGCATTTGAAGAATTAT
ATATTAGTTTCGAAATGCACATTGAATCACTCGAT
Found at i:21817691 original size:13 final size:13
Alignment explanation
Indices: 21817673--21817697 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21817663 CGTGTGCCAT
21817673 ACACAGCCTCTCC
1 ACACAGCCTCTCC
21817686 ACACAGCCTCTC
1 ACACAGCCTCTC
21817698 AACAAGTCCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.52, G:0.08, T:0.16
Consensus pattern (13 bp):
ACACAGCCTCTCC
Found at i:21821064 original size:26 final size:26
Alignment explanation
Indices: 21821030--21821084 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
21821020 CTCGAGTAAG
21821030 AAGAAGCTCCTAGGCAATGAAAAGGT
1 AAGAAGCTCCTAGGCAATGAAAAGGT
* *
21821056 AAGATGCTCCTGGGCAATGAAAAGGT
1 AAGAAGCTCCTAGGCAATGAAAAGGT
21821082 AAG
1 AAG
21821085 TGCCGGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.16
Consensus pattern (26 bp):
AAGAAGCTCCTAGGCAATGAAAAGGT
Found at i:21825102 original size:26 final size:27
Alignment explanation
Indices: 21825064--21825118 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
21825054 CCTAACACTC
21825064 AAACAAACACCAATTACACAAAACCCA
1 AAACAAACACCAATTACACAAAACCCA
* *
21825091 AAACAAAC-CCAATTCCCCAAAACCCA
1 AAACAAACACCAATTACACAAAACCCA
21825117 AA
1 AA
21825119 CAAGCCAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.56, C:0.36, G:0.00, T:0.07
Consensus pattern (27 bp):
AAACAAACACCAATTACACAAAACCCA
Found at i:21829680 original size:26 final size:26
Alignment explanation
Indices: 21829649--21829710 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
21829639 TAACCCTAAC
*
21829649 AAAATTTTGATGATTTTACCTCTGGT
1 AAAATTTTGATGATTTTACCCCTGGT
*
21829675 AAAATTTTGATGATTTTGCCCCTGGT
1 AAAATTTTGATGATTTTACCCCTGGT
21829701 AAAATTTTGA
1 AAAATTTTGA
21829711 GAAATATGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (26 bp):
AAAATTTTGATGATTTTACCCCTGGT
Found at i:21829871 original size:6 final size:6
Alignment explanation
Indices: 21829855--21829895 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
21829845 GCAAATAGAT
* * *
21829855 CATTTC TATTTC CATTTT CATTTT CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
21829896 TTGGAAACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.24, G:0.00, T:0.59
Consensus pattern (6 bp):
CATTTC
Found at i:21829877 original size:18 final size:18
Alignment explanation
Indices: 21829857--21829896 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
21829847 AAATAGATCA
21829857 TTTCTATTTCCATTTTCAT
1 TTTC-ATTTCCATTTTCAT
*
21829876 TTTCATTTCCATTTCCAT
1 TTTCATTTCCATTTTCAT
21829894 TTT
1 TTT
21829897 TGGAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTCATTTCCATTTTCAT
Found at i:21836541 original size:32 final size:32
Alignment explanation
Indices: 21836486--21836624 Score: 154
Period size: 32 Copynumber: 4.4 Consensus size: 32
21836476 GAATGGCTAC
* *
21836486 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
21836517 AAGCCATCAGTAGCAGTGATATGATCGGCATA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * * * *
21836549 CAGCCATTAGTAACGGTAATATAATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
** *
21836581 AAGCCATCAGTAATGGTAATATGACCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
21836613 AAGCCATCAGTA
1 AAGCCATCAGTA
21836625 GCATCGTAGC
Statistics
Matches: 88, Mismatches: 19, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
31 10 0.11
32 78 0.89
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:21836841 original size:48 final size:48
Alignment explanation
Indices: 21836782--21836878 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
21836772 TCAGTCATAC
*
21836782 AAATCACAAACAAATCAGTCATACCAATCACAGG-CAAATCAATCATTT
1 AAATCACAAACAAATCAGTCATACAAATCAC-GGACAAATCAATCATTT
** *
21836830 AAATCACAAACAAATCAGTCATTTAAATCACGGACAAATTAATCATTT
1 AAATCACAAACAAATCAGTCATACAAATCACGGACAAATCAATCATTT
21836878 A
1 A
21836879 CACTCGAAGG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
47 2 0.05
48 42 0.95
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (48 bp):
AAATCACAAACAAATCAGTCATACAAATCACGGACAAATCAATCATTT
Found at i:21836866 original size:24 final size:24
Alignment explanation
Indices: 21836770--21836878 Score: 110
Period size: 24 Copynumber: 4.5 Consensus size: 24
21836760 CCATGCTCAG
**
21836770 AATCAGTCATACAAATCACAAACA
1 AATCAGTCATTTAAATCACAAACA
*** **
21836794 AATCAGTCATACCAATCACAGGCA
1 AATCAGTCATTTAAATCACAAACA
*
21836818 AATCAATCATTTAAATCACAAACA
1 AATCAGTCATTTAAATCACAAACA
**
21836842 AATCAGTCATTTAAATCACGGACA
1 AATCAGTCATTTAAATCACAAACA
* *
21836866 AATTAATCATTTA
1 AATCAGTCATTTA
21836879 CACTCGAAGG
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 71 1.00
ACGTcount: A:0.48, C:0.22, G:0.06, T:0.24
Consensus pattern (24 bp):
AATCAGTCATTTAAATCACAAACA
Found at i:21836955 original size:27 final size:26
Alignment explanation
Indices: 21836923--21837163 Score: 166
Period size: 27 Copynumber: 8.9 Consensus size: 26
21836913 GGAATTACGA
21836923 TCATTTTACCTTACAGGGGTATTTCGG
1 TCATTTTACC-TACAGGGGTATTTCGG
* * * *
21836950 TTATTTAACCCTA-TGAGGGTATTACGG
1 TCATTTTA-CCTACAG-GGGTATTTCGG
* *
21836977 TCATTTTATCCTACAGGGGCATTACGG
1 TCATTTTA-CCTACAGGGGTATTTCGG
* *
21837004 TCATTTTACCTTATCA-GGGTTTTTTGG
1 TCATTTTACC-TA-CAGGGGTATTTCGG
*
21837031 TCATTTTATCCTACAGGGGTATTACGG
1 TCATTTTA-CCTACAGGGGTATTTCGG
21837058 TCATTTTATCCTACAGGGGTATTAT-GG
1 TCATTTTA-CCTACAGGGGTATT-TCGG
**
21837085 TCATTTTACCCTAC-GAGGGTATTTTTG
1 TCATTTTA-CCTACAG-GGGTATTTCGG
* * ** *
21837112 CCATTTTACCCATCAATGGTATTTTGG
1 TCATTTTACCTA-CAGGGGTATTTCGG
* * *
21837139 TAATTTTACCCATCAAGGGTATTTC
1 TCATTTTACCTA-CAGGGGTATTTC
21837164 AATCAATTTA
Statistics
Matches: 174, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
26 10 0.06
27 157 0.90
28 7 0.04
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.41
Consensus pattern (26 bp):
TCATTTTACCTACAGGGGTATTTCGG
Found at i:21836974 original size:54 final size:54
Alignment explanation
Indices: 21836896--21837107 Score: 227
Period size: 54 Copynumber: 3.9 Consensus size: 54
21836886 AGGGCAAATA
* * *
21836896 GTCA-TTTACCCT-TCAGAGGAATTACGATCATTTTA-CCTTACAGGGGTATTTCG
1 GTCATTTTACCCTATCAG-GGTATTACGGTCATTTTATCC-TACAGGGGTATTACG
* * * *
21836949 GTTATTTAACCCTATGAGGGTATTACGGTCATTTTATCCTACAGGGGCATTACG
1 GTCATTTTACCCTATCAGGGTATTACGGTCATTTTATCCTACAGGGGTATTACG
* * **
21837003 GTCATTTTACCTTATCAGGGTTTTTTGGTCATTTTATCCTACAGGGGTATTACG
1 GTCATTTTACCCTATCAGGGTATTACGGTCATTTTATCCTACAGGGGTATTACG
* * *
21837057 GTCATTTTATCCTA-CAGGGGTATTATGGTCATTTTACCCTAC-GAGGGTATT
1 GTCATTTTACCCTATCA-GGGTATTACGGTCATTTTATCCTACAG-GGGTATT
21837108 TTTGCCATTT
Statistics
Matches: 134, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
53 6 0.04
54 123 0.92
55 5 0.04
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (54 bp):
GTCATTTTACCCTATCAGGGTATTACGGTCATTTTATCCTACAGGGGTATTACG
Found at i:21837014 original size:81 final size:81
Alignment explanation
Indices: 21836916--21837108 Score: 248
Period size: 81 Copynumber: 2.4 Consensus size: 81
21836906 CTTCAGAGGA
* * *
21836916 ATTACGATCATTTTACCTTACAGGGGTATTTCGGTTATTTAACCCTA-TGAGGGTATTACGGTCA
1 ATTACGGTCATTTTACCTTACAGGGGTATTTCGGTCATTTAACCCTACAG-GGGTATTACGGTCA
21836980 TTTTATCCTACAGGGGC
65 TTTTATCCTACAGGGGC
* * * *
21836997 ATTACGGTCATTTTACCTTATCA-GGGTTTTTTGGTCATTTTATCCTACAGGGGTATTACGGTCA
1 ATTACGGTCATTTTACCTTA-CAGGGGTATTTCGGTCATTTAACCCTACAGGGGTATTACGGTCA
*
21837061 TTTTATCCTACAGGGGT
65 TTTTATCCTACAGGGGC
* *
21837078 ATTATGGTCATTTTACCCTAC-GAGGGTATTT
1 ATTACGGTCATTTTACCTTACAG-GGGTATTT
21837109 TTGCCATTTT
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
80 1 0.01
81 93 0.96
82 3 0.03
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (81 bp):
ATTACGGTCATTTTACCTTACAGGGGTATTTCGGTCATTTAACCCTACAGGGGTATTACGGTCAT
TTTATCCTACAGGGGC
Found at i:21837145 original size:81 final size:81
Alignment explanation
Indices: 21836916--21837146 Score: 218
Period size: 81 Copynumber: 2.9 Consensus size: 81
21836906 CTTCAGAGGA
* * * * ** * ** *
21836916 ATTACGATCATTTTACCTTA-CAGGGGTATTTCGGTTATTTAACCCTATGAGGGTATTACGGTCA
1 ATTACGGTCATTTTACCCTATCA-GGGTTTTTTGGCCATTTTACCCTACAAGGGTATTACGGTAA
21836980 TTTTATCCTACAGGGGC
65 TTTTATCCTACAGGGGC
* * * * *
21836997 ATTACGGTCATTTTACCTTATCAGGGTTTTTTGGTCATTTTATCCTACAGGGGTATTACGGTCAT
1 ATTACGGTCATTTTACCCTATCAGGGTTTTTTGGCCATTTTACCCTACAAGGGTATTACGGTAAT
*
21837062 TTTATCCTACAGGGGT
66 TTTATCCTACAGGGGC
* * **
21837078 ATTATGGTCATTTTACCCTA-CGAGGGTATTTTT-GCCATTTTACCC-ATCAATGGTATTTTGGT
1 ATTACGGTCATTTTACCCTATC-AGGGT-TTTTTGGCCATTTTACCCTA-CAAGGGTATTACGGT
21837140 AATTTTA
63 AATTTTA
21837147 CCCATCAAGG
Statistics
Matches: 127, Mismatches: 19, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
80 2 0.02
81 118 0.93
82 7 0.06
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.41
Consensus pattern (81 bp):
ATTACGGTCATTTTACCCTATCAGGGTTTTTTGGCCATTTTACCCTACAAGGGTATTACGGTAAT
TTTATCCTACAGGGGC
Found at i:21837173 original size:27 final size:27
Alignment explanation
Indices: 21837114--21837324 Score: 239
Period size: 27 Copynumber: 7.8 Consensus size: 27
21837104 TATTTTTGCC
* * * *
21837114 ATTTTACCCATCAATGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
21837141 ATTTTACCCATCAAGGGTATTTCAATCA
1 ATTTTACCCATCGAGGGTATTTCGAT-A
* * *
21837169 A-TTTACCCATTGAGGATATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCGATA
*
21837195 ATTTTACCCATCGAGGGTATTTC-AGTC
1 ATTTTACCCATCGAGGGTATTTCGA-TA
*
21837222 ATTTTACCCATCGGGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCGATA
* *
21837249 ATTTTACCCATCGAGGGTATTTTGATC
1 ATTTTACCCATCGAGGGTATTTCGATA
*
21837276 GTTTTACCCATCG-GGAGTATTTCGATA
1 ATTTTACCCATCGAGG-GTATTTCGATA
*
21837303 ATTTTACCCATCGAGTGTATTT
1 ATTTTACCCATCGAGGGTATTT
21837325 AGGTCATTTA
Statistics
Matches: 158, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
26 5 0.03
27 149 0.94
28 4 0.03
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTCGATA
Found at i:21837174 original size:54 final size:54
Alignment explanation
Indices: 21837087--21837324 Score: 273
Period size: 54 Copynumber: 4.4 Consensus size: 54
21837077 TATTATGGTC
**** * * * *
21837087 ATTTTACCC-TACGAGGGTATTTTTGCCATTTTACCCATCAATGGTATTTTGGTA
1 ATTTTACCCAT-CGAGGGTATTTCAATCATTTTACCCATCGAGGGTATTTCGATA
* * * * *
21837141 ATTTTACCCATCAAGGGTATTTCAATCAATTTACCCATTGAGGATATTTCAATA
1 ATTTTACCCATCGAGGGTATTTCAATCATTTTACCCATCGAGGGTATTTCGATA
* *
21837195 ATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCATCGGGGGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCAATCATTTTACCCATCGAGGGTATTTCGATA
** *
21837249 ATTTTACCCATCGAGGGTATTTTGATCGTTTTACCCATCG-GGAGTATTTCGATA
1 ATTTTACCCATCGAGGGTATTTCAATCATTTTACCCATCGAGG-GTATTTCGATA
*
21837303 ATTTTACCCATCGAGTGTATTT
1 ATTTTACCCATCGAGGGTATTT
21837325 AGGTCATTTA
Statistics
Matches: 157, Mismatches: 25, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
53 2 0.01
54 154 0.98
55 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTATTTCAATCATTTTACCCATCGAGGGTATTTCGATA
Found at i:21837174 original size:81 final size:80
Alignment explanation
Indices: 21837087--21837324 Score: 239
Period size: 81 Copynumber: 2.9 Consensus size: 80
21837077 TATTATGGTC
* * *
21837087 ATTTTACCC-TACGAGGGTATTTTTGCCATTTTACCCATCAATGGTATTTTGGTAATTTTACCCA
1 ATTTTACCCAT-CGAGGGTATTTTTGTCATTTTACCCATC-AGGGTATTTCGGTAATTTTACCCA
*
21837151 TCAAGGGTATTTCAATCA
64 TCGAGGGTATTTCAAT-A
* * *** * * *
21837169 A-TTTACCCATTGAGGATATTTCAATAATTTTACCCATCGAGGGTATTTCAGTCATTTTACCCAT
1 ATTTTACCCATCGAGGGTATTTTTGTCATTTTACCCATC-AGGGTATTTCGGTAATTTTACCCAT
* *
21837233 CGGGGGTATTTCGATA
65 CGAGGGTATTTCAATA
* * *
21837249 ATTTTACCCATCGAGGGTA-TTTTGATCGTTTTACCCATCGGGAGTATTTCGATAATTTTACCCA
1 ATTTTACCCATCGAGGGTATTTTTG-TCATTTTACCCATCAGG-GTATTTCGGTAATTTTACCCA
*
21837313 TCGAGTGTATTT
64 TCGAGGGTATTT
21837325 AGGTCATTTA
Statistics
Matches: 124, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
80 6 0.05
81 116 0.94
82 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (80 bp):
ATTTTACCCATCGAGGGTATTTTTGTCATTTTACCCATCAGGGTATTTCGGTAATTTTACCCATC
GAGGGTATTTCAATA
Found at i:21837333 original size:27 final size:27
Alignment explanation
Indices: 21837085--21837333 Score: 213
Period size: 27 Copynumber: 9.2 Consensus size: 27
21837075 GGTATTATGG
*
21837085 TCATTTTACCC-TACGAGGGTATTTTTG-
1 TCATTTTACCCAT-CGAGGGTA-TTTAGA
* * * * *
21837112 CCATTTTACCCATCAATGGTATTTTGG
1 TCATTTTACCCATCGAGGGTATTTAGA
* *
21837139 TAATTTTACCCATCAAGGGTATTTCA-A
1 TCATTTTACCCATCGAGGGTATTT-AGA
* * *
21837166 TCAATTTACCCATTGAGGATATTTCA-A
1 TCATTTTACCCATCGAGGGTATTT-AGA
*
21837193 TAATTTTACCCATCGAGGGTATTTCAG-
1 TCATTTTACCCATCGAGGGTATTT-AGA
* *
21837220 TCATTTTACCCATCGGGGGTATTTCGA
1 TCATTTTACCCATCGAGGGTATTTAGA
* *
21837247 TAATTTTACCCATCGAGGGTATTTTGA
1 TCATTTTACCCATCGAGGGTATTTAGA
* *
21837274 TCGTTTTACCCATCG-GGAGTATTTCGA
1 TCATTTTACCCATCGAGG-GTATTTAGA
* * *
21837301 TAATTTTACCCATCGAGTGTATTTAGG
1 TCATTTTACCCATCGAGGGTATTTAGA
21837328 TCATTT
1 TCATTT
21837334 AACAAATATT
Statistics
Matches: 183, Mismatches: 32, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
26 8 0.04
27 173 0.95
28 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCATCGAGGGTATTTAGA
Found at i:21840165 original size:18 final size:19
Alignment explanation
Indices: 21840137--21840172 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21840127 ATAAAATTTT
21840137 TAAATACAATAAAGAAAAA
1 TAAATACAATAAAGAAAAA
*
21840156 TAAATA-AATAAATAAAA
1 TAAATACAATAAAGAAAA
21840173 TGGGAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (19 bp):
TAAATACAATAAAGAAAAA
Found at i:21852503 original size:41 final size:41
Alignment explanation
Indices: 21852444--21852526 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
21852434 ATTTTTTTTT
* *
21852444 TCCAAAGTTCTGATTTTACCCAAAATTATTCAAAGCAAAAA
1 TCCAAAGTTCTGACTTTACCCAAAATCATTCAAAGCAAAAA
* *
21852485 TCCAAAGTTTTGGCTTTACCCAAAATCATTCAAAGCAAAAA
1 TCCAAAGTTCTGACTTTACCCAAAATCATTCAAAGCAAAAA
21852526 T
1 T
21852527 TTAACCCAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (41 bp):
TCCAAAGTTCTGACTTTACCCAAAATCATTCAAAGCAAAAA
Found at i:21853781 original size:15 final size:15
Alignment explanation
Indices: 21853761--21853792 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
21853751 TATGAATTAC
*
21853761 ATGTTATATGTAAAA
1 ATGTTATAAGTAAAA
21853776 ATGTTATAAGTAAAA
1 ATGTTATAAGTAAAA
21853791 AT
1 AT
21853793 CGACTAGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (15 bp):
ATGTTATAAGTAAAA
Found at i:21854482 original size:24 final size:23
Alignment explanation
Indices: 21854442--21854558 Score: 74
Period size: 24 Copynumber: 4.8 Consensus size: 23
21854432 GGCTCTTTGT
*
21854442 GAGCTTCTAGTTAATGGCTCTCCG
1 GAGCTTCTCGTT-ATGGCTCTCCG
* **
21854466 GAGCTTCTCGATTATGGCTCGCTT
1 GAGCTTCTCG-TTATGGCTCTCCG
* * *
21854490 GAACTTCTCGATATATGGCTATCTG
1 GAGCTTCTCG-T-TATGGCTCTCCG
* *
21854515 GAGCTTCAT-GTTAATGGCTTTTCG
1 GAGCTTC-TCGTT-ATGGCTCTCCG
*
21854539 GAGCTACTCGTTATTGGCTC
1 GAGCTTCTCGTTA-TGGCTC
21854559 GCATGAGCTT
Statistics
Matches: 73, Mismatches: 14, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
23 3 0.04
24 51 0.70
25 18 0.25
26 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (23 bp):
GAGCTTCTCGTTATGGCTCTCCG
Found at i:21854521 original size:25 final size:25
Alignment explanation
Indices: 21854432--21854521 Score: 85
Period size: 24 Copynumber: 3.6 Consensus size: 25
21854422 CCCGATTAAA
* * *
21854432 GGCTCTTTGTGAGCTTCTAGTTA-AT
1 GGCTCTCTG-GAGCTTCTCGATATAT
*
21854457 GGCTCTCCGGAGCTTCTCGAT-TAT
1 GGCTCTCTGGAGCTTCTCGATATAT
* * *
21854481 GGCTCGCTTGAACTTCTCGATATAT
1 GGCTCTCTGGAGCTTCTCGATATAT
*
21854506 GGCTATCTGGAGCTTC
1 GGCTCTCTGGAGCTTC
21854522 ATGTTAATGG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
24 29 0.57
25 22 0.43
ACGTcount: A:0.16, C:0.23, G:0.24, T:0.37
Consensus pattern (25 bp):
GGCTCTCTGGAGCTTCTCGATATAT
Found at i:21854531 original size:73 final size:72
Alignment explanation
Indices: 21854442--21854581 Score: 178
Period size: 73 Copynumber: 1.9 Consensus size: 72
21854432 GGCTCTTTGT
* *
21854442 GAGCTTCTAGTTAATGGCTCTCCGGAGCTTCTCGATTA-TGGCTCGCTTGAACTT-CTCGATATA
1 GAGCTTCTAGTTAATGGCTCTCCGGAGCTACTCG-TTATTGGCTCGCATGAACTTCCT-GAT-TA
21854505 TGGCTATCTG
63 TGGCTATCTG
* * *
21854515 GAGCTTC-ATGTTAATGGCTTTTCGGAGCTACTCGTTATTGGCTCGCATGAGCTTCCTGATTATG
1 GAGCTTCTA-GTTAATGGCTCTCCGGAGCTACTCGTTATTGGCTCGCATGAACTTCCTGATTATG
21854579 GCT
65 GCT
21854582 CTTATGAGCT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
72 11 0.19
73 46 0.78
74 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.36
Consensus pattern (72 bp):
GAGCTTCTAGTTAATGGCTCTCCGGAGCTACTCGTTATTGGCTCGCATGAACTTCCTGATTATGG
CTATCTG
Found at i:21866370 original size:13 final size:13
Alignment explanation
Indices: 21866352--21866380 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
21866342 ACAGACTGTC
21866352 ATATCTTTCATAT
1 ATATCTTTCATAT
21866365 ATATCTTTCATAT
1 ATATCTTTCATAT
21866378 ATA
1 ATA
21866381 AAAAGATAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATCTTTCATAT
Found at i:21871361 original size:50 final size:50
Alignment explanation
Indices: 21871237--21871483 Score: 219
Period size: 50 Copynumber: 4.8 Consensus size: 50
21871227 GATAATAACA
* * ** * * *
21871237 TGCCAAAGCCATGTCGCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * **
21871286 TGTCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
21871336 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
** * *
21871386 TGCCAACACCATGTCCCAGACATGGTCTAACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* *
21871442 TGCCAATGCCATGTCACAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21871484 TTACCCAAAT
Statistics
Matches: 158, Mismatches: 32, Indels: 9
0.79 0.16 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.23
50 80 0.51
53 2 0.01
56 38 0.24
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:21873140 original size:19 final size:19
Alignment explanation
Indices: 21873116--21873153 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
21873106 TTCCACAGGG
21873116 ATACTTTCAAAAACACTTT
1 ATACTTTCAAAAACACTTT
21873135 ATACTTTCAAAAACACTTT
1 ATACTTTCAAAAACACTTT
21873154 GTCACCAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (19 bp):
ATACTTTCAAAAACACTTT
Found at i:21878946 original size:56 final size:51
Alignment explanation
Indices: 21878826--21878974 Score: 167
Period size: 50 Copynumber: 2.8 Consensus size: 51
21878816 TGATAATAAC
*
21878826 ATGCCAAAGCCATGTCCCAGACATGGTCTTAC-GGAGGACCTCTCATCTCAG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATG-GGACCTCTCATCTCAG
*
21878877 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTC-A-G
* * * * *
21878932 ATGCCAATGACATGTCCCAAACACGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
21878975 TTACCCAAAT
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
50 41 0.49
51 1 0.01
53 3 0.04
54 1 0.01
55 1 0.01
56 37 0.44
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (51 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAG
Found at i:21888389 original size:36 final size:36
Alignment explanation
Indices: 21888342--21888413 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
21888332 TTTAAGGAAG
*
21888342 ATCGAGAAATCCCCATTCTATTGGGTAGGTCATTTC
1 ATCGAGAAATCCCCATTCTATTCGGTAGGTCATTTC
* *
21888378 ATCGAGAAATCCCCATTTTGTTCGGTAGGTCATTTC
1 ATCGAGAAATCCCCATTCTATTCGGTAGGTCATTTC
21888414 TGGTCACTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (36 bp):
ATCGAGAAATCCCCATTCTATTCGGTAGGTCATTTC
Found at i:21889760 original size:29 final size:29
Alignment explanation
Indices: 21889718--21889775 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
21889708 TTTCCCGCAC
21889718 TTAATGATAACTTTATGTCGACAAGCAAA
1 TTAATGATAACTTTATGTCGACAAGCAAA
21889747 TTAATGATAACTTTATGTCGACAAGCAAA
1 TTAATGATAACTTTATGTCGACAAGCAAA
21889776 GGTGCCGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (29 bp):
TTAATGATAACTTTATGTCGACAAGCAAA
Found at i:21894462 original size:13 final size:12
Alignment explanation
Indices: 21894445--21894480 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
21894435 ATTTAAGTCG
21894445 TTTATTTATTTT
1 TTTATTTATTTT
21894457 TCTTATTTATTTT
1 T-TTATTTATTTT
*
21894470 TTTAGTTATTT
1 TTTATTTATTT
21894481 AATTTCTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:21895493 original size:20 final size:20
Alignment explanation
Indices: 21895468--21895506 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
21895458 ATTCAACAAC
21895468 TTCTCTTTTAAGTTAATAAA
1 TTCTCTTTTAAGTTAATAAA
*
21895488 TTCTCTTTTGAGTTAATAA
1 TTCTCTTTTAAGTTAATAA
21895507 GTTCCCTTTG
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:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (20 bp):
TTCTCTTTTAAGTTAATAAA
Found at i:21895515 original size:20 final size:20
Alignment explanation
Indices: 21895472--21895520 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
21895462 AACAACTTCT
* *
21895472 CTTTTAAGTTAATAAATTCT
1 CTTTTGAGTTAATAAATTCC
*
21895492 CTTTTGAGTTAATAAGTTCC
1 CTTTTGAGTTAATAAATTCC
21895512 C-TTTGAGTT
1 CTTTTGAGTT
21895521 TTATTTTCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.49
Consensus pattern (20 bp):
CTTTTGAGTTAATAAATTCC
Found at i:21900930 original size:12 final size:12
Alignment explanation
Indices: 21900892--21900923 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
21900882 GGAAGATATA
21900892 AAATATATTTCT
1 AAATATATTTCT
*
21900904 AAATATATTTTT
1 AAATATATTTCT
21900916 AAATATAT
1 AAATATAT
21900924 GCCTAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
AAATATATTTCT
Found at i:21903449 original size:25 final size:26
Alignment explanation
Indices: 21903412--21903479 Score: 95
Period size: 25 Copynumber: 2.7 Consensus size: 26
21903402 ATTTGACCCT
*
21903412 ATTAATTTAAATTTAAA-TTCGATGCA
1 ATTAATTTAAATTTAAATTTC-ATCCA
*
21903438 ATT-ATTTAAATTTAAATTTCATCCC
1 ATTAATTTAAATTTAAATTTCATCCA
21903463 ATTAATTTAAATTTAAA
1 ATTAATTTAAATTTAAA
21903480 CTAAATTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 19 0.50
26 19 0.50
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.46
Consensus pattern (26 bp):
ATTAATTTAAATTTAAATTTCATCCA
Found at i:21904118 original size:14 final size:16
Alignment explanation
Indices: 21904098--21904137 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
21904088 ACCCAAAACT
21904098 CAAATTTTATATG-AA
1 CAAATTTTATATGTAA
*
21904113 -AAATTTTCTATGTAA
1 CAAATTTTATATGTAA
21904128 CAAATTTTAT
1 CAAATTTTAT
21904138 TTCATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 11 0.52
15 2 0.10
16 8 0.38
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (16 bp):
CAAATTTTATATGTAA
Found at i:21904583 original size:19 final size:19
Alignment explanation
Indices: 21904559--21904610 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
21904549 AAATTTTATT
* *
21904559 TTTATTACTTTTACACAAA
1 TTTATTAATTTAACACAAA
21904578 TTTATTAATTTAACACAAA
1 TTTATTAATTTAACACAAA
**
21904597 AGTATTAATATTAA
1 TTTATTAAT-TTAA
21904611 TTAATTCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (19 bp):
TTTATTAATTTAACACAAA
Found at i:21904861 original size:29 final size:28
Alignment explanation
Indices: 21904829--21904889 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
21904819 AAAAAGCCCT
21904829 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** * *
21904858 TTTTTTGATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
21904886 TTTT
1 TTTT
21904890 CTGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:21905107 original size:22 final size:22
Alignment explanation
Indices: 21905081--21905131 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
21905071 CTAATTTTTC
*
21905081 CTCTCAATTTCCTTCTAAAATT
1 CTCTCAATTTCCTTCCAAAATT
21905103 CTCTCAATTTCCTTCCAAAATT
1 CTCTCAATTTCCTTCCAAAATT
21905125 CTCTCAA
1 CTCTCAA
21905132 ACTCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.00, T:0.41
Consensus pattern (22 bp):
CTCTCAATTTCCTTCCAAAATT
Found at i:21905217 original size:29 final size:30
Alignment explanation
Indices: 21905176--21905239 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 30
21905166 TCTCAAATCC
21905176 ATTTTTTAAAATAATTAT-AA-TTTTTTAT
1 ATTTTTTAAAATAATTATAAATTTTTTTAT
*
21905204 ATTTTTTAAAAATAATTTTAAATTTTTTTAT
1 ATTTTTT-AAAATAATTATAAATTTTTTTAT
21905235 ATTTT
1 ATTTT
21905240 CATCAATCGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 7 0.22
29 10 0.31
30 2 0.06
31 13 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATTTTTTAAAATAATTATAAATTTTTTTAT
Found at i:21906330 original size:7 final size:7
Alignment explanation
Indices: 21906318--21906342 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21906308 AGTTGATTGA
21906318 TATTTAG
1 TATTTAG
21906325 TATTTAG
1 TATTTAG
21906332 TATTTAG
1 TATTTAG
21906339 TATT
1 TATT
21906343 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:21907015 original size:18 final size:18
Alignment explanation
Indices: 21906994--21907028 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21906984 AGGTATGTTT
* *
21906994 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
21907012 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
21907029 TCCTTTTCTG
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:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:21907585 original size:34 final size:32
Alignment explanation
Indices: 21907547--21907922 Score: 115
Period size: 29 Copynumber: 12.3 Consensus size: 32
21907537 AAATAAAAAC
*
21907547 CCTAATTTACTTGAAAACCTTAACCTAACACTAA
1 CCTAATTTAC-TAAAAACCTTAACCTAAC-CTAA
* * * *
21907581 CCTAAATTAATTAAAA----AACCTAATCTAA
1 CCTAATTTACTAAAAACCTTAACCTAACCTAA
* *
21907609 CCTAAATTAACTAAAAACCCTAACCTAACCCTAA
1 CCT-AATTTACTAAAAACCTTAACCTAA-CCTAA
* *
21907643 CCTAAATTAACTAAAAACCTTAATCTAACCTAA
1 CCT-AATTTACTAAAAACCTTAACCTAACCTAA
** * *
21907676 ATTAA-TT--T-AAAACCCTAACCCAAACCTAA
1 CCTAATTTACTAAAAACCTTAA-CCTAACCTAA
* * * * *
21907705 CCTAAATTAATTTAAAACCCTAA-C---CCAAA
1 CCT-AATTTACTAAAAACCTTAACCTAACCTAA
* * * *
21907734 CCTAAATTAATTAAAAACCCTAAACTAACCT-A
1 CCT-AATTTACTAAAAACCTTAACCTAACCTAA
* * *
21907766 ---AATTAACTAAAAACCCTAATCTAACCTAA
1 CCTAATTTACTAAAAACCTTAACCTAACCTAA
** *
21907795 ATTAA-TT--T-AAAACCCTAACCCTAACCTAA
1 CCTAATTTACTAAAAACCTTAA-CCTAACCTAA
** *
21907824 ATTAA-TTA--AAAAACC-TAATCTAACCT-A
1 CCTAATTTACTAAAAACCTTAACCTAACCTAA
* *
21907851 ---AATTAACTAAAAACCCTAACCTAACCCTAA
1 CCTAATTTACTAAAAACCTTAACCTAA-CCTAA
* * *
21907881 CCTAAATTAACTAAAAACCCTAATCTAACCTAA
1 CCT-AATTTACTAAAAACCTTAACCTAACCTAA
**
21907914 ATTAATTTA
1 CCTAATTTA
21907923 AAACCCTAAC
Statistics
Matches: 275, Mismatches: 34, Indels: 68
0.73 0.09 0.18
Matches are distributed among these distances:
24 2 0.01
25 2 0.01
27 8 0.03
28 65 0.24
29 76 0.28
30 10 0.04
31 3 0.01
32 11 0.04
33 27 0.10
34 71 0.26
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.26
Consensus pattern (32 bp):
CCTAATTTACTAAAAACCTTAACCTAACCTAA
Found at i:21907611 original size:28 final size:28
Alignment explanation
Indices: 21907570--21908115 Score: 606
Period size: 28 Copynumber: 18.6 Consensus size: 28
21907560 AAAACCTTAA
*
21907570 CCTAACACTAACCTAAATTAATTAAAAAA
1 CCTAAC-CTAACCTAAATTAATTAAAAAC
* *
21907599 CCTAATCTAACCTAAATTAACTAAAAACCC
1 CCTAACCTAACCTAAATTAATTAAAAA--C
*
21907629 TAACCTAACCCTAACCTAAATTAACTAAAAAC
1 ---CCTAA-CCTAACCTAAATTAATTAAAAAC
* *
21907661 CTTAATCTAACCTAAATTAATTTAAAACCCTAAC
1 CCTAACCTAACCTAAATTAA-TT-AAA----AAC
* *
21907695 CCAAACCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
21907723 CCTAACCCAAACCTAAATTAATTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAAC
* *
21907752 CCTAAACTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* *
21907780 CCTAATCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
21907808 CCTAACCCTAACCTAAATTAATTAAAAAA
1 CCTAA-CCTAACCTAAATTAATTAAAAAC
* *
21907837 CCTAATCTAACCTAAATTAACTAAAAACCC
1 CCTAACCTAACCTAAATTAATTAAAAA--C
*
21907867 TAACCTAACCCTAACCTAAATTAACTAAAAAC
1 ---CCTAA-CCTAACCTAAATTAATTAAAAAC
* *
21907899 CCTAATCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
21907927 CCTAACCCAAACCTAAATTAATTAAAAAC
1 CCTAA-CCTAACCTAAATTAATTAAAAAC
* *
21907956 CCTAAACTAACCTAAATTAACTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
* *
21907984 CCTAATCTAACCTAAATTAATTTAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
21908012 CCTAATCTAACCTAAATTAATTAAAAAC
1 CCTAACCTAACCTAAATTAATTAAAAAC
*
21908040 CCTAAACCAAACCTAAATTAATTAAAAAC
1 CCT-AACCTAACCTAAATTAATTAAAAAC
*
21908069 CCAAAACCTAACCTAAATTAATTAAAAAC
1 CC-TAACCTAACCTAAATTAATTAAAAAC
* * *
21908098 CCAAAACTAAGCTAAATT
1 CCTAACCTAACCTAAATT
21908116 TTTTTGGTAG
Statistics
Matches: 448, Mismatches: 46, Indels: 47
0.83 0.09 0.09
Matches are distributed among these distances:
28 225 0.50
29 142 0.32
30 3 0.01
32 4 0.01
33 12 0.03
34 62 0.14
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (28 bp):
CCTAACCTAACCTAAATTAATTAAAAAC
Found at i:21907775 original size:119 final size:116
Alignment explanation
Indices: 21907560--21908115 Score: 707
Period size: 119 Copynumber: 4.7 Consensus size: 116
21907550 AATTTACTTG
* * *
21907560 AAAACCTTAACCTAACACTAACCTAAATTAATTAAAAAACCTAATCTAACCTAAATTAACTAAAA
1 AAAACCCTAACC-AAC-CTAACCTAAATTAATTAAAAACCCTAACCTAACCTAAATTAACTAAAA
*
21907625 ACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCTTAATCTAACCTAAATTAATTT
64 ACCCT-A---AA--CTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
* * *
21907684 AAAACCCTAACCCAAACCTAACCTAAATTAATTTAAAACCCTAACCCAAACCTAAATTAATTAAA
1 AAAACCCTAA-CC-AACCTAACCTAAATTAATTAAAAACCCTAA-CCTAACCTAAATTAACTAAA
21907749 AACCCTAAACTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
63 AACCCTAAACTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
* *
21907803 AAAACCCTAA-C--CCTAACCTAAATTAATTAAAAAACCTAATCTAACCTAAATTAACTAAAAAC
1 AAAACCCTAACCAACCTAACCTAAATTAATTAAAAACCCTAACCTAACCTAAATTAACTAAAAAC
21907865 CCTAACCTAACCCTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
66 CCT-A---AA--CTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
* *
21907922 AAAACCCTAA-C--CCAAACCTAAATTAATTAAAAACCCTAAACTAACCTAAATTAACTAAAAAC
1 AAAACCCTAACCAACCTAACCTAAATTAATTAAAAACCCTAACCTAACCTAAATTAACTAAAAAC
* * * *
21907984 CCTAATCTAACCTAAATTAATTTAAAACCCTAATCTAACCTAAATTAATTA
66 CCTAAACTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
* * *
21908035 AAAACCCT-A--AACCAAACCTAAATTAATTAAAAACCCAAAACCTAACCTAAATTAATTAAAAA
1 AAAACCCTAACCAACCTAACCTAAATTAATTAAAAACCC-TAACCTAACCTAAATTAACTAAAAA
* *
21908097 CCCAAAACTAAGCTAAATT
65 CCCTAAACTAACCTAAATT
21908116 TTTTTGGTAG
Statistics
Matches: 395, Mismatches: 26, Indels: 32
0.87 0.06 0.07
Matches are distributed among these distances:
112 1 0.00
113 98 0.25
114 65 0.16
115 1 0.00
117 3 0.01
118 1 0.00
119 161 0.41
121 2 0.01
124 35 0.09
125 28 0.07
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (116 bp):
AAAACCCTAACCAACCTAACCTAAATTAATTAAAAACCCTAACCTAACCTAAATTAACTAAAAAC
CCTAAACTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTT
Found at i:21907801 original size:85 final size:85
Alignment explanation
Indices: 21907570--21908115 Score: 628
Period size: 85 Copynumber: 6.2 Consensus size: 85
21907560 AAAACCTTAA
*
21907570 CCTAACACTAACCTAAATTAATTAAAAAACCTAATCTAACCTAAATTAACTAAAAACCCTAACCT
1 CCTAA-ACTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAA--C---CCT
*
21907635 AACCCTAACCTAAATTAACTAAAAAC
60 AACCCTAACCTAAATTAATTAAAAAC
* * * * * *
21907661 CTTAATCTAACCTAAATTAATTTAAAACCCTAACCCAAACCTAACCTAAATTAATTTAAAACCCT
1 CCTAAACTAACCTAAATTAA-TT-AAA----AACCCTAATCTAACCTAAATTAACTAAAAACCCT
*
21907726 AACCCAAACCTAAATTAATTAAAAAC
60 AACCCTAACCTAAATTAATTAAAAAC
* * *
21907752 CCTAAACTAACCTAAATTAACTAAAAACCCTAATCTAACCTAAATTAATTTAAAACCCTAACCCT
1 CCTAAACTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCCT
*
21907817 AACCTAAATTAATTAAAAAA
66 AACCTAAATTAATTAAAAAC
* *
21907837 CCTAATCTAACCTAAATTAACTAAAAACCCTAACCTAACCCTAACCTAAATTAACTAAAAACCCT
1 CCTAAACTAACCTAAATTAATTAAAAACCCTAA--T----CTAACCTAAATTAACTAAAAACCCT
* *
21907902 AA-TCTAACCTAAATTAATTTAAAAC
60 AACCCTAACCTAAATTAATTAAAAAC
* * * *
21907927 CCTAACCCAAACCTAAATTAATTAAAAACCCTAAACTAACCTAAATTAACTAAAAACCCTAA-TC
1 CCTAA-ACTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCC
*
21907991 TAACCTAAATTAATTTAAAAC
65 TAACCTAAATTAATTAAAAAC
* * * * * *
21908012 CCTAATCTAACCTAAATTAATTAAAAACCCTAAACCAAACCTAAATTAATTAAAAACCCAAAACC
1 CCTAAACTAACCTAAATTAATTAAAAACCCT-AATCTAACCTAAATTAACTAAAAACCCTAACCC
21908077 TAACCTAAATTAATTAAAAAC
65 TAACCTAAATTAATTAAAAAC
* *
21908098 CCAAAACTAAGCTAAATT
1 CCTAAACTAACCTAAATT
21908116 TTTTTGGTAG
Statistics
Matches: 403, Mismatches: 37, Indels: 35
0.85 0.08 0.07
Matches are distributed among these distances:
84 24 0.06
85 169 0.42
86 36 0.09
87 1 0.00
89 3 0.01
90 40 0.10
91 101 0.25
92 3 0.01
94 1 0.00
96 25 0.06
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (85 bp):
CCTAAACTAACCTAAATTAATTAAAAACCCTAATCTAACCTAAATTAACTAAAAACCCTAACCCT
AACCTAAATTAATTAAAAAC
Found at i:21910227 original size:123 final size:124
Alignment explanation
Indices: 21910003--21910338 Score: 575
Period size: 125 Copynumber: 2.7 Consensus size: 124
21909993 CCCAAACTTG
*
21910003 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCATAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCAAATAGCATCCTCG
*
21910068 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAG-AAAAATTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAATTATTTCTTACATGAC
21910126 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCAAATAGCATCCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCAAATAGCATCCTCG
*
21910191 TACAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAAATTATTTCTTACATGAC
66 TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAG-AAAAAATTATTTCTTACATGAC
* * * * *
21910251 CTACTGTAGCAAAATCGTGTCCATGAGGGTGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCAAATAGCATCCTCG
*
21910316 TAGAAGCGATTTTATACTATTTG
66 TAGAAACGATTTTATACTATTTG
21910339 ACCATAGACG
Statistics
Matches: 201, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
123 99 0.49
125 102 0.51
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCAAATAGCATCCTCG
TAGAAACGATTTTATACTATTTGCTCAGAAAAATCAGAAAAAATTATTTCTTACATGAC
Found at i:21911737 original size:22 final size:22
Alignment explanation
Indices: 21911707--21911748 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
21911697 ACACCAAAAC
*
21911707 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
21911729 AGGCCTTTAGCGGCGCTTTT
1 AGGCCTTTAGCGGCGCTTTT
21911749 AGCACCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.10, C:0.21, G:0.29, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:21912051 original size:43 final size:43
Alignment explanation
Indices: 21911832--21912039 Score: 283
Period size: 43 Copynumber: 4.8 Consensus size: 43
21911822 TTATAGAAAA
* *
21911832 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCCCAC
* *
21911875 AAACGCCGCTATAGACCATGACCTTTAGCGTCGCTTTTCCCAC
1 AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCCCAC
* * * *
21911918 AAACGTCGCTATAGACCATGACCTTTAGCGACGCTTTTCGCAC
1 AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCCCAC
* * **
21911961 AAATGCCGCTAT-GAACCACGATCTTTAGCGGCGCTTTTCTTAC
1 AAACGCCGCTATAG-ACCACGACCTTTAGCGGCGCTTTTCCCAC
*
21912004 AAACGCCGCTATAGACCGCGACCTTTAGCGGCGCTT
1 AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTT
21912040 CTCGCAAAAA
Statistics
Matches: 147, Mismatches: 16, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
42 1 0.01
43 145 0.99
44 1 0.01
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTATAGACCACGACCTTTAGCGGCGCTTTTCCCAC
Found at i:21912125 original size:23 final size:21
Alignment explanation
Indices: 21912078--21912125 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 21
21912068 CTTTAAAAAA
21912078 ATTATTTTAATAAAATAGTAT
1 ATTATTTTAATAAAATAGTAT
*
21912099 -TTATTTTAATGATAAATATTAT
1 ATTATTTTAAT-A-AAATAGTAT
21912121 ATTAT
1 ATTAT
21912126 GTTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 10 0.43
21 1 0.04
22 8 0.35
23 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (21 bp):
ATTATTTTAATAAAATAGTAT
Found at i:21915604 original size:22 final size:21
Alignment explanation
Indices: 21915577--21915625 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
21915567 GGGGTTTCAA
21915577 GGGGGAAAATTAGGGATTTTAG
1 GGGGGAAAATTAGGGATTTT-G
* *
21915599 GGGGGAAAGTTGGGGATTTTG
1 GGGGGAAAATTAGGGATTTTG
21915620 GGGGGA
1 GGGGGA
21915626 GGGGATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.24, C:0.00, G:0.51, T:0.24
Consensus pattern (21 bp):
GGGGGAAAATTAGGGATTTTG
Found at i:21915892 original size:41 final size:40
Alignment explanation
Indices: 21915804--21915892 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
21915794 TTTTTAAAGT
* * *
21915804 AAAA-TTATATTTTGTGGCGTTTTTTATAAAAACGCCGCT
1 AAAACTTATATTTTGCGGCGTTTTTTAAAAAAACGCCGCA
*** * *
21915843 ATTGCTTATCTTTTGCGGTGTTTTTATAAAAAAACGCCGCA
1 AAAACTTATATTTTGCGGCGTTTTT-TAAAAAAACGCCGCA
21915884 AAAACTTAT
1 AAAACTTAT
21915893 TTCATTTGGA
Statistics
Matches: 37, Mismatches: 11, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
39 1 0.03
40 17 0.46
41 19 0.51
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.39
Consensus pattern (40 bp):
AAAACTTATATTTTGCGGCGTTTTTTAAAAAAACGCCGCA
Found at i:21915922 original size:148 final size:143
Alignment explanation
Indices: 21915634--21915925 Score: 417
Period size: 148 Copynumber: 2.0 Consensus size: 143
21915624 GAGGGGATTT
* *
21915634 TATAAAATGGCGCTATTTTTTTTAAGTAAATTTTTTGTGGCGTTTTTAACAAAAACGCCTCTATT
1 TATAAAATGGCGCTATTTTTTTAAAGTAAATTTTTTGTGGCGTTTTTAACAAAAACGCCGCTATT
*
21915699 GCTTACTTTTTGCGGCGTTTTTCATAAAAACGCCGCAAAAAAATATTTTATTTGGAATAAAACGA
66 GCTTACTTTTTGCGGCGTTTTTCATAAAAACGCCGCAAAAAAATATTTCATTTGGAATAAAACGA
21915764 CACTGTTTTGCTA
131 CACTGTTTTGCTA
* * *
21915777 TATAAAATGGTGCTATTTTTTTAAAGTAAAATTATATTTTGTGGCGTTTTTTATAAAAACGCCGC
1 TATAAAATGGCGCTATTTTTTTAAAGT-AAA-T-T-TTTTGTGGCGTTTTTAACAAAAACGCCGC
* **
21915842 TATTGCTTA-TCTTTTGCGGTGTTTTT-ATAAAAAAACGCCGCAAAAACTTATTTCATTTGGAAT
62 TATTGCTTACT-TTTTGCGGCGTTTTTCAT--AAAAACGCCGCAAAAAAATATTTCATTTGGAAT
*
21915905 AAAATGACACTGTTTTGCTA
124 AAAACGACACTGTTTTGCTA
21915925 T
1 T
21915926 GCTAAATCTT
Statistics
Matches: 132, Mismatches: 10, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
143 25 0.19
144 3 0.02
145 1 0.01
146 4 0.03
147 49 0.37
148 50 0.38
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (143 bp):
TATAAAATGGCGCTATTTTTTTAAAGTAAATTTTTTGTGGCGTTTTTAACAAAAACGCCGCTATT
GCTTACTTTTTGCGGCGTTTTTCATAAAAACGCCGCAAAAAAATATTTCATTTGGAATAAAACGA
CACTGTTTTGCTA
Done.