Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 170 of 240
Found at i:52748042 original size:29 final size:29
Alignment explanation
Indices: 52747991--52748052 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
52747981 TGACATCCCC
* * *
52747991 CACCAGTACATAATACCTGATAAATATAG
1 CACCAGCACATAATACCTAATAAATATAA
* *
52748020 CACCAGCACATAGTTCCTAATAAATATAA
1 CACCAGCACATAATACCTAATAAATATAA
52748049 CACC
1 CACC
52748053 GGTAGAAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.23
Consensus pattern (29 bp):
CACCAGCACATAATACCTAATAAATATAA
Found at i:52752816 original size:29 final size:29
Alignment explanation
Indices: 52752779--52752835 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
52752769 CACCTTGACA
* * *
52752779 CGAATTCTCAATGAACAAGTTCTTCACCG
1 CGAACTCTCAACGAACAAGTTCTCCACCG
52752808 CGAACTCTCAACGAACAAGTTCTCCACC
1 CGAACTCTCAACGAACAAGTTCTCCACC
52752836 TCTTCCATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.33, G:0.12, T:0.23
Consensus pattern (29 bp):
CGAACTCTCAACGAACAAGTTCTCCACCG
Found at i:52757152 original size:16 final size:18
Alignment explanation
Indices: 52757131--52757168 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
52757121 TTCTATAGGG
52757131 ATTTTA-CTTT-TATTTT
1 ATTTTACCTTTATATTTT
52757147 ATTTTACCTTTATATTTT
1 ATTTTACCTTTATATTTT
52757165 ATTT
1 ATTT
52757169 AAATAAAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 4 0.20
18 10 0.50
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTTACCTTTATATTTT
Found at i:52761085 original size:23 final size:23
Alignment explanation
Indices: 52761055--52761104 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
52761045 GAAGATGAGG
52761055 AAAAGG-AAAGGAGAGAGAAAAAA
1 AAAAGGAAAAGGAGA-AGAAAAAA
*
52761078 AAAAGGAAAAAGGAGAAGGAAAAA
1 AAAAGG-AAAAGGAGAAGAAAAAA
52761102 AAA
1 AAA
52761105 TAAAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 6 0.25
24 10 0.42
25 8 0.33
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (23 bp):
AAAAGGAAAAGGAGAAGAAAAAA
Found at i:52769691 original size:20 final size:20
Alignment explanation
Indices: 52769654--52769691 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
52769644 TTGTACGGGA
* *
52769654 TCGCACTTCGGTGTCTCTAT
1 TCGCACTTCAGTGCCTCTAT
52769674 TCGCACTTCAGTGCCTCT
1 TCGCACTTCAGTGCCTCT
52769692 GTATTTGCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.34, G:0.18, T:0.37
Consensus pattern (20 bp):
TCGCACTTCAGTGCCTCTAT
Found at i:52773154 original size:12 final size:11
Alignment explanation
Indices: 52773131--52773162 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
52773121 TACAGTTTGG
52773131 CACATTGTTGA
1 CACATTGTTGA
52773142 CACATTAGTTGA
1 CACATT-GTTGA
52773154 CACATTGTT
1 CACATTGTT
52773163 CTCTATGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (11 bp):
CACATTGTTGA
Found at i:52781584 original size:22 final size:22
Alignment explanation
Indices: 52781551--52781593 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
52781541 ATATTTGTTC
52781551 AATTCTAATTTGAATTCTTGGT
1 AATTCTAATTTGAATTCTTGGT
*
52781573 AATT-TAAGTTTGATTTCTTGG
1 AATTCTAA-TTTGAATTCTTGG
52781594 ACATAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.51
Consensus pattern (22 bp):
AATTCTAATTTGAATTCTTGGT
Found at i:52782386 original size:50 final size:50
Alignment explanation
Indices: 52782327--52782422 Score: 174
Period size: 50 Copynumber: 1.9 Consensus size: 50
52782317 CGTCCTCCTG
52782327 CATTGATTACAATATTTATGCCGATCGAGTTAAGACTCAGTCGGCTCTTA
1 CATTGATTACAATATTTATGCCGATCGAGTTAAGACTCAGTCGGCTCTTA
* *
52782377 CATTGATTACAATATTTATGCTGGTCGAGTTAAGACTCAGTCGGCT
1 CATTGATTACAATATTTATGCCGATCGAGTTAAGACTCAGTCGGCT
52782423 AAAGTGAAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (50 bp):
CATTGATTACAATATTTATGCCGATCGAGTTAAGACTCAGTCGGCTCTTA
Found at i:52783310 original size:16 final size:16
Alignment explanation
Indices: 52783286--52783327 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
52783276 TTTGGTTCGC
* *
52783286 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
52783302 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
52783318 TGTAATGGAA
1 TGTAATGGAA
52783328 AAGCTGTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.31
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:52783593 original size:18 final size:17
Alignment explanation
Indices: 52783572--52783606 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52783562 TTATTATTAA
*
52783572 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52783590 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52783607 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52783743 original size:16 final size:16
Alignment explanation
Indices: 52783706--52783747 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52783696 TTAATCATAT
*
52783706 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52783722 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52783737 TTAAAATATAT
1 TTAAAATATAT
52783748 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52783745 original size:154 final size:156
Alignment explanation
Indices: 52783459--52783772 Score: 569
Period size: 154 Copynumber: 2.0 Consensus size: 156
52783449 TAGAATACCC
52783459 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
52783524 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
52783589 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAAAAA
* *
52783616 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
52783679 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
52783744 ATATAATTTAATAAAATTCTTAAAAA
131 ATATAATTTAATAAAATTCTTAAAAA
52783770 TTA
1 TTA
52783773 ATATTATTAT
Statistics
Matches: 153, Mismatches: 4, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
154 92 0.60
155 1 0.01
157 60 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAAAAA
Found at i:52783754 original size:14 final size:15
Alignment explanation
Indices: 52783715--52783756 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52783705 TTTAAACATA
*
52783715 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52783730 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52783744 A-TATAATTTAATA
1 ATTATAATTAAATA
52783757 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52783833 original size:120 final size:121
Alignment explanation
Indices: 52783704--52784000 Score: 453
Period size: 120 Copynumber: 2.5 Consensus size: 121
52783694 ATTTAATCAT
*
52783704 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-A
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
52783768 AATTAATATTATTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 AA-TAAAATTATTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
52783826 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
52783889 AATAAAATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 AATAAAATTATTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
52783945 ATTTCAA-ATAATTAATATTAAATATGATT-TAATT-AAATATATGATTTAATAAAATT
1 ATTTCAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATT
52784001 TAAAATTATT
Statistics
Matches: 164, Mismatches: 7, Indels: 11
0.90 0.04 0.06
Matches are distributed among these distances:
119 24 0.15
120 129 0.79
121 10 0.06
122 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (121 bp):
ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
AATAAAATTATTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:52783874 original size:14 final size:15
Alignment explanation
Indices: 52783825--52783876 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
52783815 GTAAAATATA
52783825 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
52783840 TATTAAATATATTAT
1 AATTAAATATATTAT
52783855 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
52783868 AATTTAATA
1 AATTAAATA
52783877 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:52783891 original size:44 final size:43
Alignment explanation
Indices: 52783802--52783892 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
52783792 CTCAAATCAT
* * *
52783802 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
52783845 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
52783889 AATA
1 AATA
52783893 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:52783981 original size:15 final size:15
Alignment explanation
Indices: 52783961--52783999 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
52783951 AATAATTAAT
52783961 ATTAAATATGATTTA
1 ATTAAATATGATTTA
52783976 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
52783993 ATAAAAT
1 ATTAAAT
52784000 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:52783986 original size:17 final size:17
Alignment explanation
Indices: 52783966--52783999 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
52783956 TTAATATTAA
*
52783966 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
52783983 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
52784000 TTAAAATTAT
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:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:52784142 original size:93 final size:92
Alignment explanation
Indices: 52784032--52784226 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
52784022 GATTATAGTT
* * *
52784032 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
52784095 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
52784125 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
52784190 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
52784217 TATGAATTTA
1 TATGAATTTA
52784227 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:52786856 original size:24 final size:24
Alignment explanation
Indices: 52786829--52786879 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
52786819 TGGGAAAAAC
52786829 ATTGGCAGATTAATTTAGGTCAGA
1 ATTGGCAGATTAATTTAGGTCAGA
52786853 ATTGGCAGATTAATTTAGGTCAGA
1 ATTGGCAGATTAATTTAGGTCAGA
52786877 ATT
1 ATT
52786880 TAAAACTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (24 bp):
ATTGGCAGATTAATTTAGGTCAGA
Found at i:52791331 original size:17 final size:19
Alignment explanation
Indices: 52791311--52791345 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
52791301 ATTTTAATAT
52791311 ATGTA-TAT-ATTTATAAA
1 ATGTATTATAATTTATAAA
52791328 ATGTATTATAATTTATAA
1 ATGTATTATAATTTATAA
52791346 TTTATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (19 bp):
ATGTATTATAATTTATAAA
Found at i:52805293 original size:20 final size:20
Alignment explanation
Indices: 52805268--52805314 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
52805258 CAATTAAGTG
52805268 CTTTTATTGGATTTTCAAAA
1 CTTTTATTGGATTTTCAAAA
*
52805288 CTTTTATTGGATTTTCAAAT
1 CTTTTATTGGATTTTCAAAA
52805308 CTTTTAT
1 CTTTTAT
52805315 CTAATAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.55
Consensus pattern (20 bp):
CTTTTATTGGATTTTCAAAA
Found at i:52808159 original size:37 final size:34
Alignment explanation
Indices: 52808079--52808159 Score: 83
Period size: 36 Copynumber: 2.3 Consensus size: 34
52808069 TCTTCTATTG
52808079 ATTTTTTTTGAATTTTAAAAAATATATAATTTTT
1 ATTTTTTTTGAATTTTAAAAAATATATAATTTTT
* *
52808113 ATATGTTTTTCTGAATTTT-GAAAATTTATATATATTTT
1 AT-T-TTTTT-TGAATTTTAAAAAATATATA-AT-TTTT
*
52808151 CTTTTTTTT
1 ATTTTTTTT
52808160 AAAAAAATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
34 2 0.05
35 2 0.05
36 19 0.49
37 11 0.28
38 5 0.13
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (34 bp):
ATTTTTTTTGAATTTTAAAAAATATATAATTTTT
Found at i:52808238 original size:69 final size:69
Alignment explanation
Indices: 52808103--52808229 Score: 163
Period size: 67 Copynumber: 1.9 Consensus size: 69
52808093 TTAAAAAATA
* * *
52808103 TATAATTTTTATATGTTTTTCTGAATTTTGAAAATTTATATATATTTTCTTTTTTTTAAAAAAAT
1 TATAAATTTTATATGTTTTTCTGAATTTTAAAAATTTATACATATTTTCTTTTTTTTAAAAAAAT
52808168 TTGT
66 TTGT
* *
52808172 TATAAATTTTATATAGTTTTT-TTAA-TTTAAAAATTT-TACCTATTTT-TTATTTTTTAAA
1 TATAAATTTTATAT-GTTTTTCTGAATTTTAAAAATTTATACATATTTTCTT-TTTTTTAAA
52808230 TTATAATTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
66 2 0.04
67 17 0.33
68 10 0.20
69 16 0.31
70 6 0.12
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.60
Consensus pattern (69 bp):
TATAAATTTTATATGTTTTTCTGAATTTTAAAAATTTATACATATTTTCTTTTTTTTAAAAAAAT
TTGT
Found at i:52809576 original size:29 final size:29
Alignment explanation
Indices: 52809544--52809621 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
52809534 ATGTTTAATA
52809544 TGGTACTTCT-ATTTCGAAAATATCCAATG
1 TGGTACTTCTAATTT-GAAAATATCCAATG
* * *
52809573 TGGTACTTGTAATTTGGAAATGTCCAATG
1 TGGTACTTCTAATTTGAAAATATCCAATG
* *
52809602 TAGTACTTGTAATTTAGAAA
1 TGGTACTTCTAATTT-GAAA
52809622 TGTTCAATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 35 0.83
30 7 0.17
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (29 bp):
TGGTACTTCTAATTTGAAAATATCCAATG
Found at i:52809622 original size:29 final size:29
Alignment explanation
Indices: 52809561--52809631 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
52809551 TCTATTTCGA
* * *
52809561 AAATATCCAATGTGGTACTTGTAATTTGG
1 AAATGTCCAATGTAGTACTTGTAATTTAG
52809590 AAATGTCCAATGTAGTACTTGTAATTTAG
1 AAATGTCCAATGTAGTACTTGTAATTTAG
*
52809619 AAATGTTCAATGT
1 AAATGTCCAATGT
52809632 GATAACTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (29 bp):
AAATGTCCAATGTAGTACTTGTAATTTAG
Found at i:52809934 original size:15 final size:16
Alignment explanation
Indices: 52809914--52809944 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
52809904 AAATTTAAAA
52809914 TTAATTTT-AATATTT
1 TTAATTTTAAATATTT
52809929 TTAATTTTAAATATTT
1 TTAATTTTAAATATTT
52809945 CTTTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTAATTTTAAATATTT
Found at i:52831409 original size:9 final size:9
Alignment explanation
Indices: 52831392--52831428 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52831382 TGAGTTTTCG
52831392 AATTCGAAT
1 AATTCGAAT
*
52831401 AACTCGAAT
1 AATTCGAAT
52831410 AATTCGAAT
1 AATTCGAAT
52831419 AATTCGAAT
1 AATTCGAAT
52831428 A
1 A
52831429 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52831511 original size:30 final size:31
Alignment explanation
Indices: 52831477--52831537 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
52831467 AAACCTTTTT
* * *
52831477 ACTTTTCCCTCAAAATTTTTACTCCT-TCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
52831507 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
1 ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
52831538 CTCCCAACCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 23 0.85
31 4 0.15
ACGTcount: A:0.20, C:0.43, G:0.00, T:0.38
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACTCCTCTCCC
Found at i:52831830 original size:20 final size:18
Alignment explanation
Indices: 52831779--52831839 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
52831769 ACTCCCCCTA
*
52831779 TTTATTTTCTCTC-AAACT
1 TTTATTTTC-CCCAAAACT
52831797 TTTA--TTCCCCAAAACTT
1 TTTATTTTCCCCAAAAC-T
52831814 TTTATTTTCCTCCAAAACT
1 TTTATTTTCC-CCAAAACT
52831833 TTTATTT
1 TTTATTT
52831840 CTCACTAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 2 0.05
16 7 0.19
17 5 0.14
18 4 0.11
19 12 0.32
20 7 0.19
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATTTTCCCCAAAACT
Found at i:52832051 original size:19 final size:19
Alignment explanation
Indices: 52832027--52832095 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
52832017 TAAATATATT
52832027 TATTTTTTAAATTTTAAAA
1 TATTTTTTAAATTTTAAAA
**
52832046 TATTTTTTACATACTTTT-TTA
1 TATTTTTTA-A-A-TTTTAAAA
52832067 -ATTTTTT-AATTTTAAAA
1 TATTTTTTAAATTTTAAAA
*
52832084 TATTTTTAAAAT
1 TATTTTTTAAAT
52832096 ACTTTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 4 0.10
17 2 0.05
18 7 0.18
19 12 0.31
20 8 0.21
21 2 0.05
22 4 0.10
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTTTAAATTTTAAAA
Found at i:52832080 original size:38 final size:38
Alignment explanation
Indices: 52832028--52832168 Score: 186
Period size: 38 Copynumber: 3.8 Consensus size: 38
52832018 AAATATATTT
* *
52832028 ATTTTTTAAATTTTAAAATATTTTTTACATACTTTTTTA
1 ATTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTA
52832067 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTAATTTTAAAATATTTTTAAAATAC-TTTTTTA
52832106 ATTTTTTAATTTTAAAATA-TTTTAAAATAC--TTTT-
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
*
52832140 -TTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 ATTTTTTAA-TTTTAAAATATTTTTAAAATA
52832169 AAAATGGGCC
Statistics
Matches: 96, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
33 9 0.09
34 17 0.18
35 4 0.04
38 33 0.34
39 33 0.34
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (38 bp):
ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
Found at i:52832143 original size:39 final size:39
Alignment explanation
Indices: 52832028--52832142 Score: 189
Period size: 38 Copynumber: 3.0 Consensus size: 39
52832018 AAATATATTT
* *
52832028 ATTTTTTAAATTTTAAAATATTTTTTACATAC-TTTTTTA
1 ATTTTTT-AATTTTAAAATATTTTTAAAATACTTTTTTTA
52832067 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
52832106 ATTTTTTAATTTTAAAATA-TTTTAAAATACTTTTTTT
1 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
52832143 TTTAATTTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
38 40 0.55
39 33 0.45
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:52837827 original size:18 final size:18
Alignment explanation
Indices: 52837792--52837829 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
52837782 GCAATACGTG
*
52837792 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
52837810 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
52837828 AC
1 AC
52837830 TGTTGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:52838772 original size:30 final size:30
Alignment explanation
Indices: 52838715--52838773 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
52838705 AGCTAGACTA
*
52838715 GAATTTTTAAATTTAAAAGGTAGAAGAATT
1 GAATTTTTAAATTAAAAAGGTAGAAGAATT
*
52838745 GAATTTTTAAATATAAAAATGTA-AAGAAT
1 GAATTTTTAAAT-TAAAAAGGTAGAAGAAT
52838774 ATATTCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.36
Consensus pattern (30 bp):
GAATTTTTAAATTAAAAAGGTAGAAGAATT
Found at i:52842791 original size:44 final size:43
Alignment explanation
Indices: 52842728--52842853 Score: 121
Period size: 44 Copynumber: 2.9 Consensus size: 43
52842718 TTATGGTAAA
* * *
52842728 TTTAATCCGAC-CTACTGCAACTTCAGAAGTATAGGATTCATCA-T
1 TTTAATCCG-CTCCACTGCAACTTCAGAAG-ATAGGATTAAT-AGC
* *
52842772 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAGAATTAATAGC
1 TTTAATCCGCTCCACTGCAACTTCA-GAAGATAGGATTAATAGC
** *
52842816 TTTAATCTACTCCGCTGCAACTTCAGAGAGATAGGATT
1 TTTAATCCGCTCCACTGCAACTTCAGA-AGATAGGATT
52842854 TGCTATCCTC
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.04
44 62 0.91
45 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (43 bp):
TTTAATCCGCTCCACTGCAACTTCAGAAGATAGGATTAATAGC
Found at i:52843056 original size:132 final size:132
Alignment explanation
Indices: 52842908--52843166 Score: 421
Period size: 132 Copynumber: 2.0 Consensus size: 132
52842898 TAGTGGCTTC
* *
52842908 AATCTGCTTCCCTACTACTTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCTACTACTGCTT
1 AATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTT
* *
52842973 AGAGAGACAGGATCTACAATCTTCGACCTACTCCACTACTGCTTAGGGAA-ATAGGACTGGTGAT
66 AGAGAGACAAGATCTACAATCTTCGACCTACTCCACTACTGCTCA-GGAAGATAGGACTGGTGAT
52843037 TTA
130 TTA
*
52843040 AATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTT
1 AATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTT
* * * *
52843105 AGGGAGATAAGATCTACAATCTTCGACCTACTCCACTGCTGCTCAGGAAGATAGGGCTGGTG
66 AGAGAGACAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGAAGATAGGACTGGTG
52843167 CTTTCTATCT
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
131 4 0.03
132 113 0.97
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
AATCTGCTTCCCTACTACCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTT
AGAGAGACAAGATCTACAATCTTCGACCTACTCCACTACTGCTCAGGAAGATAGGACTGGTGATT
TA
Found at i:52843128 original size:44 final size:45
Alignment explanation
Indices: 52842933--52843157 Score: 151
Period size: 44 Copynumber: 5.1 Consensus size: 45
52842923 TACTTTGGAA
** * *
52842933 AGATAAGAT-TCACCGTCTTCGATCTGCTCTACTACTGCTTAGAG
1 AGATAAGATCTCACAATCTTCGATCTGCTCCACTACTGCTTAGGG
* * * *
52842977 AGACAGGATCT-ACAATCTTCGACCTACTCCACTACTGCTTAGGG
1 AGATAAGATCTCACAATCTTCGATCTGCTCCACTACTGCTTAGGG
* * **** ** *
52843021 AAATAGGA-CTGGTGAT-TTAAATCTGCTTCC-CTACTACCTT-GGG
1 AGATAAGATCTCACAATCTTCGATCTGC-TCCACTACT-GCTTAGGG
**
52843064 AAGATAAGAT-TCACCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 -AGATAAGATCTCACAATCTTCGATCTGCTCCACTACTGCTTAGGG
* * * * *
52843109 AGATAAGATCT-ACAATCTTCGACCTACTCCACTGCTGCTCAGGA
1 AGATAAGATCTCACAATCTTCGATCTGCTCCACTACTGCTTAGGG
52843153 AGATA
1 AGATA
52843158 GGGCTGGTGC
Statistics
Matches: 136, Mismatches: 35, Indels: 20
0.71 0.18 0.10
Matches are distributed among these distances:
43 16 0.12
44 102 0.75
45 18 0.13
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (45 bp):
AGATAAGATCTCACAATCTTCGATCTGCTCCACTACTGCTTAGGG
Found at i:52847166 original size:51 final size:51
Alignment explanation
Indices: 52847090--52847374 Score: 303
Period size: 51 Copynumber: 5.6 Consensus size: 51
52847080 GATGAACACG
* * * * *
52847090 TGTGTAGCACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGATCACA
* * * * * *
52847141 TGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTTG-TCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATTGATCACA
* * * *
52847192 TGTGTAGTATTGTGTGAAGGCTACTACGTGTACAGATAAATGA-TGAACACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATTGATCACA
* * *
52847243 TGTGTAGTACTAAGTGAAGGCTACTACGTGAACCG-TAAA-ATTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGATCACA
*
52847293 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TTGATCACA
* *
52847343 TGTGTAGTACTATGTGAAGGTTATTACGTGTA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTA
52847375 TCGAATGATA
Statistics
Matches: 196, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
48 1 0.01
50 89 0.45
51 103 0.53
52 3 0.02
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATTGATCACA
Found at i:52847262 original size:102 final size:100
Alignment explanation
Indices: 52847086--52847372 Score: 357
Period size: 102 Copynumber: 2.8 Consensus size: 100
52847076 TATCGATGAA
* *
52847086 CACGTGTGTAGCACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTA-CGATAAATAATGATCACATGTGTAGTAC
* * *
52847151 TAAGTGAAGGCTACTATGTGTACCG-AGAAGTTTTTG-T
65 TAAGTGAAGGCTACTACGTGAACCGTA-AA--ATTTGAT
* * *
52847188 CACGTGTGTAGTATTGTGTGAAGGCTACTACGTGTACAGATAAATGATGAACACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTAC-GATAAATAATGATCACATGTGTAGTAC
52847253 TAAGTGAAGGCTACTACGTGAACCGTAAAATTTGAT
65 TAAGTGAAGGCTACTACGTGAACCGTAAAATTTGAT
* * *
52847289 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACATGTGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTA-CGATAAATA-ATGATCACATGTGTAGTA
* * *
52847352 CTATGTGAAGGTTATTACGTG
64 CTAAGTGAAGGCTACTACGTG
52847373 TATCGAATGA
Statistics
Matches: 163, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
100 42 0.26
101 36 0.22
102 84 0.52
103 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.30
Consensus pattern (100 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTACGATAAATAATGATCACATGTGTAGTACT
AAGTGAAGGCTACTACGTGAACCGTAAAATTTGAT
Found at i:52850737 original size:23 final size:23
Alignment explanation
Indices: 52850701--52850755 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
52850691 ATGAAGGATG
**
52850701 AATGAGAGAAAATTGAAATGTGA
1 AATGAGAGTTAATTGAAATGTGA
*
52850724 AATGGGAGTTAATTGAAATGTGA
1 AATGAGAGTTAATTGAAATGTGA
52850747 AATGAGAGT
1 AATGAGAGT
52850756 GGGTATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.29, T:0.25
Consensus pattern (23 bp):
AATGAGAGTTAATTGAAATGTGA
Found at i:52853574 original size:22 final size:20
Alignment explanation
Indices: 52853526--52853575 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
52853516 TATCTGACAA
*
52853526 ATACTTATATATCTATCAAT
1 ATACTTATATATCAATCAAT
*
52853546 ATCACTTTTATATACAATCAATT
1 AT-ACTTATATAT-CAATCAA-T
52853569 ATACTTA
1 ATACTTA
52853576 CCTCAACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 10 0.42
23 3 0.12
ACGTcount: A:0.40, C:0.16, G:0.00, T:0.44
Consensus pattern (20 bp):
ATACTTATATATCAATCAAT
Found at i:52853785 original size:41 final size:41
Alignment explanation
Indices: 52853740--52853880 Score: 201
Period size: 41 Copynumber: 3.4 Consensus size: 41
52853730 TGATTCAATA
* * * *
52853740 CACCGGCATTAAACCTGCTACAGGTAAGGTCTAAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
* * *
52853781 CACCGGTATTAAGCCTGCTAGACATAAAGTCTGAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
* *
52853822 CACCGGTATTAAGCCTGCTAGACGTAAAGTCCAAAATATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
52853863 CACCGGCATTAAGCCTGC
1 CACCGGCATTAAGCCTGC
52853881 AGGCACAAAG
Statistics
Matches: 89, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 89 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTAAAATATTT
Found at i:52853826 original size:82 final size:81
Alignment explanation
Indices: 52853740--52853897 Score: 217
Period size: 82 Copynumber: 1.9 Consensus size: 81
52853730 TGATTCAATA
* * * *
52853740 CACCGGCATTAAACCTGCTACAGGTAAGGTCTAAAATATTTCACCGGTATTAAGCCTGCTAGACA
1 CACCGGCATTAAACCTGCTACACGTAAAGTCCAAAATATTTCACCGGCATTAAGCCTGC-AGACA
* *
52853805 TAAAGTCTGAAATATTT
65 CAAAGCCTGAAATATTT
* * * *
52853822 CACCGGTATTAAGCCTGCTAGACGTAAAGTCCAAAATATTTCACCGGCATTAAGCCTGCAGGCAC
1 CACCGGCATTAAACCTGCTACACGTAAAGTCCAAAATATTTCACCGGCATTAAGCCTGCAGACAC
52853887 AAAGCCTGAAA
66 AAAGCCTGAAA
52853898 ATCTCATATA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
81 14 0.21
82 52 0.79
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (81 bp):
CACCGGCATTAAACCTGCTACACGTAAAGTCCAAAATATTTCACCGGCATTAAGCCTGCAGACAC
AAAGCCTGAAATATTT
Found at i:52853899 original size:41 final size:42
Alignment explanation
Indices: 52853772--52853899 Score: 174
Period size: 41 Copynumber: 3.1 Consensus size: 42
52853762 GGTAAGGTCT
*
52853772 AAAATATTTCACCGGTATTAAGCCTGCTAGACATAAAGTCTG
1 AAAATATTTCACCGGTATTAAGCCTGCTAGACATAAAGCCTG
*
52853814 -AAATATTTCACCGGTATTAAGCCTGCTAGACGTAAAGTCC--
1 AAAATATTTCACCGGTATTAAGCCTGCTAGACATAAAG-CCTG
* * *
52853854 AAAATATTTCACCGGCATTAAGCCTGC-AGGCACAAAGCCTG
1 AAAATATTTCACCGGTATTAAGCCTGCTAGACATAAAGCCTG
52853895 AAAAT
1 AAAAT
52853900 CTCATATACA
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
39 2 0.03
40 7 0.09
41 66 0.87
42 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (42 bp):
AAAATATTTCACCGGTATTAAGCCTGCTAGACATAAAGCCTG
Found at i:52854222 original size:64 final size:65
Alignment explanation
Indices: 52854061--52854274 Score: 188
Period size: 65 Copynumber: 3.3 Consensus size: 65
52854051 CTCAAAGAAT
52854061 TTGTAAC-TAATATTC-AAGCCACATATGTATATAAAATTCATACATTAAAATTCAACTTAAGAA
1 TTGTAACAT-ATATTCGAA-CCACATATGTATATAAAATTCATACATTAAAATTCAACTTAAGAA
*
52854124 AT
64 AC
* * * * *
52854126 TTGTAACCTATATTTGAACCACACATGTATATAAAATTTATACATT-GAATTCAACTTAAG-AAC
1 TTGTAACATATATTCGAACCACATATGTATATAAAATTCATACATTAAAATTCAACTTAAGAAAC
* * * * * *
52854189 TTG-AATATATATTCGAATCACACATATATATATATGAAATTCATA-ATATTAAGTTCAGCTCAA
1 TTGTAACATATATTCGAA-C-CACATATGTATATA--AAATTCATACAT-TAAAATTCAACTTAA
*
52854252 TAAAC
61 GAAAC
* *
52854257 TTGTATCATAAATTCGAA
1 TTGTAACATATATTCGAA
52854275 ATTTAACCAT
Statistics
Matches: 120, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
62 11 0.09
63 6 0.05
64 25 0.21
65 40 0.33
66 12 0.10
67 9 0.08
68 6 0.05
69 11 0.09
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.35
Consensus pattern (65 bp):
TTGTAACATATATTCGAACCACATATGTATATAAAATTCATACATTAAAATTCAACTTAAGAAAC
Found at i:52858749 original size:15 final size:15
Alignment explanation
Indices: 52858729--52858758 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52858719 TCTCTAGGCA
*
52858729 TTCATTTCATGCATT
1 TTCATTACATGCATT
52858744 TTCATTACATGCATT
1 TTCATTACATGCATT
52858759 AAAGTCCATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (15 bp):
TTCATTACATGCATT
Found at i:52861455 original size:6 final size:6
Alignment explanation
Indices: 52861444--52861500 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
52861434 GGGGGGAAGA
* * *
52861444 AAAATC AAAATC AAAATC AAAAGC ATAAA-G AAAA-A AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC A-AAATC AAAATC AAAATC AAAATC
*
52861491 AAAGTC AAAA
1 AAAATC AAAA
52861501 AATGAAAATG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
5 7 0.16
6 33 0.77
7 3 0.07
ACGTcount: A:0.70, C:0.12, G:0.05, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:52861515 original size:21 final size:20
Alignment explanation
Indices: 52861477--52861529 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 20
52861467 CATAAAGAAA
* * *
52861477 AAAAAATCAAAATCAAAGTC
1 AAAAAATGAAAATAAAAGAC
*
52861497 AAAAAATGAAAATGAAAAGAG
1 AAAAAATGAAAAT-AAAAGAC
*
52861518 AAAAAAAGAAAA
1 AAAAAATGAAAA
52861530 GGAGAGGCAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (20 bp):
AAAAAATGAAAATAAAAGAC
Found at i:52862384 original size:7 final size:7
Alignment explanation
Indices: 52862372--52862421 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
52862362 CAAAAAAATG
52862372 TGAAAAA
1 TGAAAAA
52862379 TGAAAAA
1 TGAAAAA
52862386 TGAAAACA
1 TGAAAA-A
*
52862394 --AAGAA
1 TGAAAAA
52862399 TGAAAAA
1 TGAAAAA
52862406 TGAAAAA
1 TGAAAAA
52862413 -GTAAAAA
1 TG-AAAAA
52862420 TG
1 TG
52862422 GAGAGGCTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
5 1 0.03
6 4 0.11
7 29 0.81
8 2 0.06
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:52863920 original size:50 final size:50
Alignment explanation
Indices: 52863866--52864324 Score: 288
Period size: 50 Copynumber: 9.2 Consensus size: 50
52863856 GCAATGGAAC
* * * * *
52863866 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * ** *
52863916 AGATTAAAGCTACAACAACGAATCTTAC-TCCCCAGTAGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCC-G-ACATTGCAGTTAAAA
* * * *
52863966 AGATTAACGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * ** *
52864016 AGATTAAAGCTACCACAGTGAATCTTACTT-CTC-A-AGTGGTGTAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACA-T--TGCAGTTAAAA
* * * *
52864066 AGATTAATGCCATAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * * ** *
52864116 AGATTAAAGCTACCACAGTGAATCTTACTT-CTCAAGC-TGTGCAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGA-CAT-TGCAGTTAAAA
* * *
52864166 CGATTAACGCCACAAC-GACGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAG-CGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * *** * ** *
52864216 AGATTAAAGCTACAACAGCGAATCTTACTTCCCAGATGGTGTAGTGGAAC
1 AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
* * * * ** *
52864266 AGATTGAAA-CTACAACAACGAATCTTGCTTCCTCGACATCACAGTTAAAC
1 AGATT-AAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
52864316 AGATTAAAG
1 AGATTAAAG
52864325 TTACGAGTTA
Statistics
Matches: 299, Mismatches: 92, Indels: 36
0.70 0.22 0.08
Matches are distributed among these distances:
47 1 0.00
48 2 0.01
49 16 0.05
50 260 0.87
51 17 0.06
52 2 0.01
53 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACAACAGCGAATCTTACTTCCCCGACATTGCAGTTAAAA
Found at i:52864011 original size:100 final size:100
Alignment explanation
Indices: 52863855--52864324 Score: 615
Period size: 100 Copynumber: 4.7 Consensus size: 100
52863845 CCTCTGAGGT
* * * * *
52863855 TGCAATGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCTGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * *
52863920 TAAAGCTACAACAACGAATCTTAC-TCCCCAGTAGA
66 TAAAGCTACAACAGCGAATCTTACTTCCCAAGT-GG
*
52863955 TGCAGTGGAACAGATTAACGCCACAACGGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * *
52864020 TAAAGCTACCACAGTGAATCTTACTTCTCAAGTGG
66 TAAAGCTACAACAGCGAATCTTACTTCCCAAGTGG
* * *
52864055 TGTAGTGGAACAGATTAATGCCATAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * *
52864120 TAAAGCTACCACAGTGAATCTTACTTCTCAAGCT-G
66 TAAAGCTACAACAGCGAATCTTACTTCCCAAG-TGG
* *
52864155 TGCAGTGGAACCGATTAACGCCACAACGACGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
52864220 TAAAGCTACAACAGCGAATCTTACTTCCC-AGATGG
66 TAAAGCTACAACAGCGAATCTTACTTCCCAAG-TGG
* * * ** * ** *
52864255 TGTAGTGGAACAGATTGAA-ACTACAACAACGAATCTTGCTTCCTCGACATCACAGTTAAACAGA
1 TGCAGTGGAACAGATT-AACGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
52864319 TTAAAG
65 TTAAAG
52864325 TTACGAGTTA
Statistics
Matches: 332, Mismatches: 34, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
99 3 0.01
100 320 0.96
101 9 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAACGCCACAACGGCGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
TAAAGCTACAACAGCGAATCTTACTTCCCAAGTGG
Found at i:52865824 original size:3 final size:3
Alignment explanation
Indices: 52865816--52865858 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
52865806 TAATATCTCC
*
52865816 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
52865859 GTTTTTTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:52871767 original size:15 final size:15
Alignment explanation
Indices: 52871749--52871777 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52871739 TTTTTAATTG
52871749 ATGGTTTGTTAAATA
1 ATGGTTTGTTAAATA
52871764 ATGGTTTGTTAAAT
1 ATGGTTTGTTAAAT
52871778 GTTTCGATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (15 bp):
ATGGTTTGTTAAATA
Found at i:52888062 original size:31 final size:31
Alignment explanation
Indices: 52888019--52888081 Score: 101
Period size: 31 Copynumber: 2.0 Consensus size: 31
52888009 TCGTCACACA
52888019 TGTCTCTCGAGAAGCGCAATATTAAAAAGCC
1 TGTCTCTCGAGAAGCGCAATATTAAAAAGCC
*
52888050 TGTCTC-CTGAGAAGTGCAATATTAAAAAGCC
1 TGTCTCTC-GAGAAGCGCAATATTAAAAAGCC
52888081 T
1 T
52888082 CAAGTCCTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (31 bp):
TGTCTCTCGAGAAGCGCAATATTAAAAAGCC
Found at i:52893409 original size:51 final size:52
Alignment explanation
Indices: 52893333--52893437 Score: 160
Period size: 54 Copynumber: 2.0 Consensus size: 52
52893323 ATATAAATAA
52893333 AATTATTAATATATAGATTTAGGGA-TTTTTTGGATGATTTTAATTTTTGAT
1 AATTATTAATATATAGATTTAGGGATTTTTTTGGATGATTTTAATTTTTGAT
*
52893384 AATTATTATTATATA-AGTTTAGGGATTTTTTTTTGGATGATTTTAATTTTTGAT
1 AATTATTAATATATAGA-TTTAGGGA--TTTTTTTGGATGATTTTAATTTTTGAT
52893438 TTGAGAGTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
50 1 0.02
51 22 0.45
54 26 0.53
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (52 bp):
AATTATTAATATATAGATTTAGGGATTTTTTTGGATGATTTTAATTTTTGAT
Found at i:52894210 original size:14 final size:15
Alignment explanation
Indices: 52894183--52894211 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52894173 TTATATTCTA
52894183 TATATGTATCATTAT
1 TATATGTATCATTAT
52894198 TATATGT-TCATTAT
1 TATATGTATCATTAT
52894212 GCTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.55
Consensus pattern (15 bp):
TATATGTATCATTAT
Found at i:52916910 original size:30 final size:31
Alignment explanation
Indices: 52916868--52916928 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
52916858 GGGTTGGGAG
* *
52916868 GGGAAGGGAGTAAAAGTTTTGGGGGGAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
52916899 GGGAA-GGAGTAAAAGTTTTGAGGGAAAAGT
1 GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
52916929 AAAAGGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (31 bp):
GGGAAGGGAGTAAAAGTTTTGAGGGAAAAGT
Found at i:52916990 original size:9 final size:9
Alignment explanation
Indices: 52916976--52917012 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52916966 TATAGTTTGA
52916976 TATTCGAAT
1 TATTCGAAT
52916985 TATTCGAAT
1 TATTCGAAT
*
52916994 TATTCGAGT
1 TATTCGAAT
52917003 TATTCGAAT
1 TATTCGAAT
52917012 T
1 T
52917013 CAAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52921223 original size:19 final size:19
Alignment explanation
Indices: 52921201--52921275 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 19
52921191 TAAAGATCAA
52921201 TAAAAATTATAAAAATAAG
1 TAAAAATTATAAAAATAAG
**
52921220 TAAATTTTAATAAAAAT-A-
1 TAAAAATT-ATAAAAATAAG
52921238 TAAAAATTTATTAAAAATTAGAAG
1 TAAAAA-TTA-TAAAAA-T--AAG
*
52921262 AAAAAATTATAAAA
1 TAAAAATTATAAAA
52921276 TATATAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
18 5 0.12
19 15 0.35
20 9 0.21
22 5 0.12
23 4 0.09
24 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (19 bp):
TAAAAATTATAAAAATAAG
Found at i:52921348 original size:19 final size:20
Alignment explanation
Indices: 52921326--52921365 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
52921316 GTAAGAAAAT
52921326 TATAAAAAATAT-AAAGAAA
1 TATAAAAAATATAAAAGAAA
**
52921345 TATAAAATTTATAAAAGAAA
1 TATAAAAAATATAAAAGAAA
52921365 T
1 T
52921366 TTATAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (20 bp):
TATAAAAAATATAAAAGAAA
Found at i:52921367 original size:13 final size:13
Alignment explanation
Indices: 52921349--52921373 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52921339 AAGAAATATA
52921349 AAATTTATAAAAG
1 AAATTTATAAAAG
52921362 AAATTTATAAAA
1 AAATTTATAAAA
52921374 CTTATCGTAC
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:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTATAAAAG
Found at i:52921582 original size:20 final size:20
Alignment explanation
Indices: 52921559--52921624 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 20
52921549 TTTTGATGCA
52921559 TTTTATAATTTTTTTATGAT
1 TTTTATAATTTTTTTATGAT
***
52921579 TTTTATAAAATTTTACAAT-AT
1 TTTTAT--AATTTTTTTATGAT
*
52921600 TTTTATAA--TTTTTACGAT
1 TTTTATAATTTTTTTATGAT
52921618 TTTTATA
1 TTTTATA
52921625 TTTGTAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
17 3 0.08
18 9 0.25
19 2 0.06
20 6 0.17
21 8 0.22
22 8 0.22
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTATAATTTTTTTATGAT
Found at i:52924833 original size:28 final size:29
Alignment explanation
Indices: 52924792--52924856 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
52924782 CAATAATTTT
*
52924792 TTTTTCTATTTTTTAATAAAATTTAA-ATA
1 TTTTTATATTTTTTAATAAAATTTAATA-A
*
52924821 TTTTTATA-TTTTTATTAAAATTTAATAA
1 TTTTTATATTTTTTAATAAAATTTAATAA
52924849 TTTTTATA
1 TTTTTATA
52924857 ACTTCCATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 25 0.76
29 8 0.24
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTTATATTTTTTAATAAAATTTAATAA
Found at i:52925186 original size:91 final size:89
Alignment explanation
Indices: 52925060--52925310 Score: 262
Period size: 91 Copynumber: 2.8 Consensus size: 89
52925050 TAAATTTTTG
* * * * *
52925060 TTTTTGAAAAAATTTGA-GAGCTTTTTTAATACATTTTAAAAGTTCAAGTACTCAATTGAGTACA
1 TTTTTTAAAAAGTTTGATGA-CATTTTTAATGCATTTTGAAAGTTCAAGTACTCAATTGAGT-CA
**
52925124 AAAGAAAAAAGTAGGGACTTAATTACT
64 AAA-AAAAAAGTAAAGACTTAATTACT
* *
52925151 CTTTTTT-TAAAGTTTGATGACCTTTTTAATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGC-
1 -TTTTTTAAAAAGTTTGATGACATTTTTAATGCATTTTGAAAGTTCAAGTACTCAATTGAGT-CA
*
52925214 --AAAAAAAGTAAAGACTTAATTGCT
64 AAAAAAAAAGTAAAGACTTAATTACT
* * * * * *
52925238 TTTTTTGAAAAAGTTTGATGTCATTTTTGATGCAATTTGAAAGTTTAAATAC-CAATTGAGTGAA
1 TTTTTT-AAAAAGTTTGATGACATTTTTAATGCATTTTGAAAGTTCAAGTACTCAATTGAGTCAA
52925302 AAAAAAAAG
65 AAAAAAAAG
52925311 AGTTTAATTA
Statistics
Matches: 135, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
86 6 0.04
87 29 0.21
88 38 0.28
89 8 0.06
91 47 0.35
92 7 0.05
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (89 bp):
TTTTTTAAAAAGTTTGATGACATTTTTAATGCATTTTGAAAGTTCAAGTACTCAATTGAGTCAAA
AAAAAAAGTAAAGACTTAATTACT
Found at i:52925278 original size:88 final size:87
Alignment explanation
Indices: 52925082--52925339 Score: 249
Period size: 88 Copynumber: 2.9 Consensus size: 87
52925072 TTTGAGAGCT
* * * * **
52925082 TTTTTAATACATTTTAAAAGTTCAAGTACTCAATTGAGTACAAAAGAAAAAAGTAGGGACTTAAT
1 TTTTTAATGCAATTTGAAAGTTCAAGTACTCAATTGAGTGC---A-AAAAAAGTAAAGACTTAAT
* *
52925147 TACTCTTTTTTTAAAGTTTGATGACC
62 TACTCTTTTTTAAAAGTTTGATGACA
* *
52925173 TTTTTAATGCATTTTGAAAGTTCAAGTACTCAATTGAGTGCAAAAAAAGTAAAGACTTAATTGCT
1 TTTTTAATGCAATTTGAAAGTTCAAGTACTCAATTGAGTGCAAAAAAAGTAAAGACTTAATTACT
*
52925238 -TTTTTTGAAAAAGTTTGATGTCA
66 CTTTTTT--AAAAGTTTGATGACA
* * * *
52925261 TTTTTGATGCAATTTGAAAGTTTAAATAC-CAATTGAGTG-AAAAAAA--AAAGAGTTTAATTAA
1 TTTTTAATGCAATTTGAAAGTTCAAGTACTCAATTGAGTGCAAAAAAAGTAAAGA-CTTAATT-A
* *
52925322 AT-TCTTTTAAAAGTTTGA
64 CTCTTTTTTAAAAGTTTGA
52925340 AAACTTTTTA
Statistics
Matches: 146, Mismatches: 17, Indels: 15
0.82 0.10 0.08
Matches are distributed among these distances:
84 15 0.10
85 6 0.04
86 19 0.13
87 30 0.21
88 38 0.26
91 38 0.26
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (87 bp):
TTTTTAATGCAATTTGAAAGTTCAAGTACTCAATTGAGTGCAAAAAAAGTAAAGACTTAATTACT
CTTTTTTAAAAGTTTGATGACA
Found at i:52933327 original size:12 final size:12
Alignment explanation
Indices: 52933310--52933339 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
52933300 CTAAACAATG
52933310 CAATAATCCTAA
1 CAATAATCCTAA
52933322 CAATAATCCTAA
1 CAATAATCCTAA
*
52933334 AAATAA
1 CAATAA
52933340 AATTCAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (12 bp):
CAATAATCCTAA
Found at i:52933623 original size:24 final size:24
Alignment explanation
Indices: 52933591--52933639 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
52933581 CACATAAAAG
52933591 TAAGTCATTTTAGAGTATTGTCAA
1 TAAGTCATTTTAGAGTATTGTCAA
52933615 TAAGTCATTTTAGAGTATTGTCAA
1 TAAGTCATTTTAGAGTATTGTCAA
52933639 T
1 T
52933640 GGCTCTAGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (24 bp):
TAAGTCATTTTAGAGTATTGTCAA
Found at i:52946535 original size:21 final size:21
Alignment explanation
Indices: 52946511--52946557 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
52946501 CTTGCCCGTG
*
52946511 TGGCCCACAAAGCTTGGCTCA
1 TGGCCCACAAAGCCTGGCTCA
**
52946532 TGGCCCACACGGCCTGGCTCA
1 TGGCCCACAAAGCCTGGCTCA
52946553 TGGCC
1 TGGCC
52946558 TACACGCCCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.17
Consensus pattern (21 bp):
TGGCCCACAAAGCCTGGCTCA
Found at i:52958965 original size:3 final size:3
Alignment explanation
Indices: 52958957--52958997 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
52958947 ATGTACAAGC
*
52958957 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TTA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
52958998 GATGTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:52961374 original size:42 final size:42
Alignment explanation
Indices: 52961285--52961529 Score: 348
Period size: 42 Copynumber: 5.8 Consensus size: 42
52961275 TAGAAAAAAA
* * * *
52961285 GCCGCTACAGATCATGTTCTTTAGCGACGTTTTTTTCCTAAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTT-CTAAGC
* *
52961328 GCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGT
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGC
*
52961370 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTGTCTAAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGC
* *
52961412 GCCGCTAAAGAACATTATCTTTAGCGGC-TTTTTTGTCTAATC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TCTAAGC
* *
52961454 GCCGCTAAAGAACATTATCTTTAGCGGTGTTTTTTTCTAAGC
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGC
* *
52961496 GCCGCTAAAGAACATGTTCTTTAGCGGCGCTTTT
1 GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT
52961530 GTACAAAAAG
Statistics
Matches: 183, Mismatches: 17, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
41 5 0.03
42 140 0.77
43 38 0.21
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (42 bp):
GCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCTAAGC
Found at i:52961530 original size:84 final size:83
Alignment explanation
Indices: 52961246--52961531 Score: 337
Period size: 84 Copynumber: 3.4 Consensus size: 83
52961236 ACAAAAACGT
* *** * * *
52961246 CGCTAAAG-ACTATGTTCTTTAGCGGCGC-TTAGAAAAAAAGCCGCTACAGATCATGT-TCTTTA
1 CGCTAAAGAAC-ATGTTCTTTAGCGGCGCTTTTG-TCTAATGCCGCTAAAGAACAT-TATCTTTA
*
52961308 GCGACGTTTTTTTCCTAAGCGC
63 GCGGCGTTTTTTT-CTAAGCGC
* * * *
52961330 CGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGTGCCGCTAAAGAACATGATCTTTAGC
1 CGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGTCTAA-TGCCGCTAAAGAACATTATCTTTAGC
*
52961395 GGCGTTTTTGTCTAAGCGC
65 GGCGTTTTTTTCTAAGCGC
**
52961414 CGCTAAAGAACAT-TATCTTTAGCGGCTTTTTTGTCTAATCGCCGCTAAAGAACATTATCTTTAG
1 CGCTAAAGAACATGT-TCTTTAGCGGCGCTTTTGTCTAAT-GCCGCTAAAGAACATTATCTTTAG
*
52961478 CGGTGTTTTTTTCTAAGCGC
64 CGGCGTTTTTTTCTAAGCGC
52961498 CGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGT
1 CGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGT
52961532 ACAAAAAGGC
Statistics
Matches: 174, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
83 1 0.01
84 138 0.79
85 35 0.20
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (83 bp):
CGCTAAAGAACATGTTCTTTAGCGGCGCTTTTGTCTAATGCCGCTAAAGAACATTATCTTTAGCG
GCGTTTTTTTCTAAGCGC
Found at i:52961939 original size:21 final size:21
Alignment explanation
Indices: 52961911--52961961 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
52961901 TTCTTTTGAA
*
52961911 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
52961932 CCTTTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
52961953 CCTCTGCTT
1 CCTCTGCTT
52961962 TAAGTTGTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.02, C:0.45, G:0.18, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:52969603 original size:29 final size:29
Alignment explanation
Indices: 52969561--52969735 Score: 201
Period size: 29 Copynumber: 6.4 Consensus size: 29
52969551 CCAACTGATG
52969561 AGGTTA-GGTTAGGGTTTTTAATTAGGTT
1 AGGTTAGGGTTAGGGTTTTTAATTAGGTT
52969589 AGGTTAGGGTTAGGGTTTTTAATTAGGTT
1 AGGTTAGGGTTAGGGTTTTTAATTAGGTT
52969618 AGGTTAGGGTTAGGGTTTTTAATTAGG--
1 AGGTTAGGGTTAGGGTTTTTAATTAGGTT
* * **
52969645 -GTTTA-AGTTAGGG-TTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAGGTT
*
52969671 AGGTTAGGGTTAGGATTTTTAATT-GG--
1 AGGTTAGGGTTAGGGTTTTTAATTAGGTT
**
52969697 -GGTTTA-GGTTAGGGTTTTTAATTAAATT
1 AGG-TTAGGGTTAGGGTTTTTAATTAGGTT
52969725 AGGTTAGGGTT
1 AGGTTAGGGTT
52969736 TTTATTACAT
Statistics
Matches: 123, Mismatches: 12, Indels: 23
0.78 0.08 0.15
Matches are distributed among these distances:
24 9 0.07
25 25 0.20
26 7 0.06
27 4 0.03
28 15 0.12
29 63 0.51
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.45
Consensus pattern (29 bp):
AGGTTAGGGTTAGGGTTTTTAATTAGGTT
Found at i:52969649 original size:11 final size:12
Alignment explanation
Indices: 52969627--52969666 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
52969617 TAGGTTAGGG
52969627 TTAGGGTTTTTAA
1 TTAGGG-TTTTAA
52969640 TTAGGG-TTTAA
1 TTAGGGTTTTAA
52969651 GTTAGGGTTTTAA
1 -TTAGGGTTTTAA
52969664 TTA
1 TTA
52969667 AATTAGGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 5 0.20
12 9 0.36
13 11 0.44
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (12 bp):
TTAGGGTTTTAA
Found at i:52969673 original size:53 final size:54
Alignment explanation
Indices: 52969561--52969735 Score: 246
Period size: 53 Copynumber: 3.2 Consensus size: 54
52969551 CCAACTGATG
* **
52969561 AGGTTA-GGTTAGGGTTTTTAATTAGGTTAGGTTAGGGTTAGGGTTTTTAATTAGGTT
1 AGGTTAGGGTTAGGGTTTTTAATTAGG---GTTTA-GGTTAGGGTTTTTAATTAAATT
*
52969618 AGGTTAGGGTTAGGGTTTTTAATTAGGGTTTAAGTTAGGG-TTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAGGGTTTAGGTTAGGGTTTTTAATTAAATT
* *
52969671 AGGTTAGGGTTAGGATTTTTAATTGGGGTTTAGGTTAGGGTTTTTAATTAAATT
1 AGGTTAGGGTTAGGGTTTTTAATTAGGGTTTAGGTTAGGGTTTTTAATTAAATT
52969725 AGGTTAGGGTT
1 AGGTTAGGGTT
52969736 TTTATTACAT
Statistics
Matches: 109, Mismatches: 7, Indels: 7
0.89 0.06 0.06
Matches are distributed among these distances:
53 48 0.44
54 31 0.28
55 4 0.04
57 6 0.06
58 20 0.18
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.45
Consensus pattern (54 bp):
AGGTTAGGGTTAGGGTTTTTAATTAGGGTTTAGGTTAGGGTTTTTAATTAAATT
Found at i:52969763 original size:25 final size:25
Alignment explanation
Indices: 52969735--52969848 Score: 98
Period size: 25 Copynumber: 4.7 Consensus size: 25
52969725 AGGTTAGGGT
52969735 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
52969760 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * *
52969783 --AAATAAC-TCGAA-AAACTTTCTA
1 TTTTATTACATCAAATAAAC-TTCTA
**
52969805 TGCGTATTACATCAAATAAACTTCTA
1 T-TTTATTACATCAAATAAACTTCTA
52969831 TTTTATTACATCAAATAA
1 TTTTATTACATCAAATAA
52969849 TAAATTTAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
20 6 0.09
21 6 0.09
22 2 0.03
23 2 0.03
24 4 0.06
25 35 0.51
26 10 0.14
27 4 0.06
ACGTcount: A:0.43, C:0.16, G:0.03, T:0.39
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:52970896 original size:7 final size:7
Alignment explanation
Indices: 52970886--52970938 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
52970876 TTATATACAT
52970886 AATACTA
1 AATACTA
52970893 AATACTA
1 AATACTA
52970900 AATACTA
1 AATACTA
52970907 AATACTA
1 AATACTA
52970914 AATACTA
1 AATACTA
52970921 AATACTA
1 AATACTA
52970928 AATACTA
1 AATACTA
52970935 AATA
1 AATA
52970939 TCTATTTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:52971117 original size:20 final size:20
Alignment explanation
Indices: 52971079--52971117 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52971069 TTTTATTTTT
*
52971079 TAAAATCTACATAATAATTG
1 TAAAATCTACATAAAAATTG
52971099 TAAAATCTA-ATATAAAATT
1 TAAAATCTACATA-AAAATT
52971118 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
TAAAATCTACATAAAAATTG
Found at i:52972168 original size:11 final size:11
Alignment explanation
Indices: 52972152--52972187 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
52972142 GAATTTTGGA
52972152 AGGAAATTGAG
1 AGGAAATTGAG
52972163 AGGAAATTGAG
1 AGGAAATTGAG
52972174 AGGAAATATGAG
1 AGGAAAT-TGAG
52972186 AG
1 AG
52972188 AGGATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.75
12 6 0.25
ACGTcount: A:0.47, C:0.00, G:0.36, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:52972183 original size:51 final size:52
Alignment explanation
Indices: 52972049--52972172 Score: 182
Period size: 51 Copynumber: 2.4 Consensus size: 52
52972039 TATTTTAAAA
* *
52972049 AAGGAAATTGAGAGCAAATTGAAATTAAATAT-GAGTTTGAGAGATTTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGAGTTTGAGAGAATTTTGG
* *
52972100 AATGAATTTGAGAGGAAATTGAAATTAAATATGGA-TTT-ATGAGAATTTTGG
1 AAGGAAATTGAGAGGAAATTGAAATTAAATATGGAGTTTGA-GAGAATTTTGG
52972151 AAGGAAATTGAGAGGAAATTGA
1 AAGGAAATTGAGAGGAAATTGA
52972173 GAGGAAATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
50 1 0.02
51 62 0.95
52 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.26, T:0.31
Consensus pattern (52 bp):
AAGGAAATTGAGAGGAAATTGAAATTAAATATGGAGTTTGAGAGAATTTTGG
Found at i:52972505 original size:5 final size:5
Alignment explanation
Indices: 52972462--52972501 Score: 62
Period size: 5 Copynumber: 7.8 Consensus size: 5
52972452 ACATATAATA
*
52972462 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT CAAAAC AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAA
52972502 CAAATCCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
5 29 0.88
6 4 0.12
ACGTcount: A:0.80, C:0.05, G:0.00, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:52973767 original size:21 final size:21
Alignment explanation
Indices: 52973728--52973767 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
52973718 ACGTTAATAA
*
52973728 AAAATTAAAAAAATCAAAATT
1 AAAATTAAAAAAATAAAAATT
*
52973749 AAAATTAAAAATATAAAAA
1 AAAATTAAAAAAATAAAAA
52973768 ATTTATAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATTAAAAAAATAAAAATT
Found at i:52974473 original size:22 final size:22
Alignment explanation
Indices: 52974448--52974539 Score: 141
Period size: 22 Copynumber: 4.2 Consensus size: 22
52974438 AAATTCAATA
52974448 TCAATTTCCTTCAAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
52974470 TCAA-TTCCTTTCAAAAATTCTC
1 TCAATTTCC-TTCAAAAATTCTC
* *
52974492 TCAATTCCCTTCAAAATTTCTC
1 TCAATTTCCTTCAAAAATTCTC
*
52974514 TCAATTTCCTTCCAAAATTCTC
1 TCAATTTCCTTCAAAAATTCTC
52974536 TCAA
1 TCAA
52974540 ACTCTCAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
21 4 0.06
22 56 0.89
23 3 0.05
ACGTcount: A:0.30, C:0.29, G:0.00, T:0.40
Consensus pattern (22 bp):
TCAATTTCCTTCAAAAATTCTC
Found at i:52974545 original size:30 final size:30
Alignment explanation
Indices: 52974511--52974569 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
52974501 TTCAAAATTT
* *
52974511 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
52974541 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
52974570 TTTCCTTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:52974555 original size:52 final size:51
Alignment explanation
Indices: 52974489--52974591 Score: 138
Period size: 52 Copynumber: 2.0 Consensus size: 51
52974479 TTCAAAAATT
* * *
52974489 CTCTCAATTCCCTT-CAAAATTTCTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAATTCCCTTCCAAAA-TCCTCTCAATTTCCTTCAAAAAATCTC-CAAA
52974541 CTCTCAAATT-CCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 CTCTC-AATTCCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
52974592 TCCATATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
51 4 0.09
52 33 0.72
53 9 0.20
ACGTcount: A:0.32, C:0.33, G:0.00, T:0.35
Consensus pattern (51 bp):
CTCTCAATTCCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
Found at i:52974580 original size:21 final size:22
Alignment explanation
Indices: 52974541--52974582 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
52974531 TTCTCTCAAA
52974541 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
52974563 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
52974583 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:52974688 original size:29 final size:30
Alignment explanation
Indices: 52974626--52974688 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
52974616 TAAATTTCAT
* *
52974626 TTTTTTAAGAAAATTTTAAAATTTTTTATT
1 TTTTTTAAGAAAATTTTAAAATTTTTAATA
*
52974656 TTTTTTAA-ATAATTTTAAAATTTTTAATA
1 TTTTTTAAGAAAATTTTAAAATTTTTAATA
52974685 TTTT
1 TTTT
52974689 CAACAATGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 22 0.73
30 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
TTTTTTAAGAAAATTTTAAAATTTTTAATA
Found at i:52976670 original size:21 final size:21
Alignment explanation
Indices: 52976621--52976670 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
52976611 CAGATGCCGA
52976621 ACCGGAAGAACAACAATCACC
1 ACCGGAAGAACAACAATCACC
* * *
52976642 ACCCGAAGAAGAACAATCGCC
1 ACCGGAAGAACAACAATCACC
*
52976663 TCCGGAAG
1 ACCGGAAG
52976671 CTAGAGGAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.32, G:0.20, T:0.06
Consensus pattern (21 bp):
ACCGGAAGAACAACAATCACC
Found at i:52977030 original size:149 final size:151
Alignment explanation
Indices: 52976845--52977694 Score: 916
Period size: 149 Copynumber: 5.6 Consensus size: 151
52976835 ACATTATTTG
* *
52976845 ATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAACCTAACCCT-ACTTAATTAAAAACCCT
1 ATTAAAAACCCTAA-CCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTAAAAA--CT
* *
52976909 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTAATTAAAAACCCTAACCTAA-T-TT-
63 AACCCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAACTATTA
*
52976971 AATTAAAAACCCTAACATAACTCA
128 AATTAAAAACCCTAACATAACTTA
* * * *
52976995 ATTAAAAAACCTAACCTAACTTAATTAAATTAAAAACCCTAACCCT-ACTTAATTAAAAACT---
1 ATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTAAAAACTAAC
*
52977056 -CTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAAACCTAACCTAACTTAATTAA
66 CCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAAC-T-ATTAA
52977120 ATTAAAAACCCTAACATAACTTA
129 ATTAAAAACCCTAACATAACTTA
* *
52977143 ATTAAAAACCCTAA-C---CCT-ACTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAA--
1 ATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA-TTAA--AAACT
52977201 AACCCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAACTTAAT
63 AACCCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAAC-T-AT
52977266 TAAATTAAAAACCCTAACATAACTTA
126 TAAATTAAAAACCCTAACATAACTTA
* * *
52977292 ATTAAAACCCCTAA-C---CCT-ACTTAATTAAAAACCATAACCCTAACCTAATTTAATTAAA--
1 ATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAA-TTAA--AAACT
* *
52977350 AACCCTAACCTAATTTAATTAAAAACCCTAAGATAACTTAATTAAAAAACCTAACCTAACTTAAT
63 AACCCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAAC-T-AT
*
52977415 TAAATTAAAAACCCTAACCCT-ACTTA
126 TAAATTAAAAACCCTAA-CATAACTTA
**
52977441 ATTAAAAACCCTAAACCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATT--AAA--AA
1 ATTAAAAACCCT-AACCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTAAAAACTAA
* * * * *
52977501 CCCTAACATAACTTAATTAAAAACCCTAACATAAC-TAATTAAAAACCCTAAGCTAATTTAATTT
65 CCCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAA-CT-ATTA
* *
52977565 AATTAAAAACCCTAACCCTAACCTA
128 AATTAAAAACCCTAA-CATAACTTA
* * *
52977590 ATTTAATTGAAATCTCTAACCTAACCTAATTTAATTAAAAACCCCAACCCTAACCTATTTTACAT
1 A-TTAA---AAA-CCCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTA-ATT--A-
*
52977655 GAAAACCCTAACCCTAACCT-ATTTAATTAAAATCCCTAAC
57 -AAAA--CTAACCCTAACCTAATTTAATTAAAAACCCTAAC
52977695 CCTAACCTAA
Statistics
Matches: 619, Mismatches: 42, Indels: 64
0.85 0.06 0.09
Matches are distributed among these distances:
143 72 0.12
144 7 0.01
145 5 0.01
147 8 0.01
148 79 0.13
149 321 0.52
150 21 0.03
151 1 0.00
153 34 0.05
154 21 0.03
155 19 0.03
161 3 0.00
164 18 0.03
165 10 0.02
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (151 bp):
ATTAAAAACCCTAACCTAACCTAATTTAATTAAAAACCCTAACCCTAACCTAATTAAAAACTAAC
CCTAACCTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAACCCTAACCTAACTATTAAAT
TAAAAACCCTAACATAACTTA
Found at i:52977238 original size:126 final size:127
Alignment explanation
Indices: 52976840--52977717 Score: 737
Period size: 126 Copynumber: 6.9 Consensus size: 127
52976830 TTTTGACATT
* * * *
52976840 ATTTGATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAACCTAACCCT-ACTTAATTAAAA
1 ATTTAATTAAAAACCCTAA-CCTAACTTAATTTAATTAAAAACCCTAA-CATAACTTAATTAAAA
*
52976904 ACCCTAACCCTAACCTAATTTAATTAAA----AACCCTAACCTAATTTAATTAAAAACCCTAACC
64 ACCCTAACCCTAACTTAA-TTAA--AAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACC
52976965 TA
126 TA
* * * *
52976967 ATTTAATTAAAAACCCTAACATAACTCAA-TTAA--AAAACCTAACCTAACTTAA-TTAAATTAA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAA---ACCCTAACATAACTT-AATTAA
*
52977028 AAACCCTAACCCT-ACTTAATTAAAAA--CT----CTAACCTAATTTAATTAAAAACCCTAACAT
62 AAACCCTAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCT
52977086 A
127 A
* * *
52977087 ACTTAATTAAAAAACCTAACCTAACTTAATTAAATTAAAAACCCTAACATAACTTAATTAAAAAC
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAAC
*
52977152 CCTAACCCT-ACTTAATTAAAAACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCTA
66 CCTAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
* *
52977213 ATTTAATTAAAAACCCTAA-C--A--TAACTTAATTAAAAACCCTAACCTAACTTAATTAAATTA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACATAAC----TT-AATTA
* * * *
52977273 AAAACCCTAA-CATAACTTAATTAAAACCCCTAACCCT-ACTTAA-TTAA-AAACCATAACCCTA
61 AAAACCCTAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAA--A-AACCCTA
52977334 ACCTA
123 ACCTA
* *
52977339 ATTTAATTAAAAACCCTAA-C---C-TAATTTAATTAAAAACCCTAAGATAACTTAATTAAAAAA
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAAC
* *
52977399 CCTAA-CCTAACTTAATTAAATTAAAAACCCTAACCCT-ACTTAA-TTAA--AAACCCTAAACCT
66 CCTAACCCTAAC----TT-AATTAAAAACCCTAACCCTAACCTAATTTAATTAAA----AACCCT
52977459 AACCTA
122 AACCTA
52977465 ATTTAATTAAAAACCCTAA-C---C-TAATTTAATTAAAAACCCTAACATAACTTAATTAAAAAC
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAAC
* * **
52977525 CCTAA-CATAAC-TAATTAAAAACCCTAA-GCTAATTTAATTTAATTAAAAACCCTAACCCTAAC
66 CCTAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATT--AAA----AACCCTAAC
52977587 CTA
125 CTA
* * * * * * * *
52977590 ATTTAATTGAAATCTCTAACCTAACCTAATTTAATTAAAAACCCCAACCCTAACCTATTTTACAT
1 ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAA-CATAACTTA-ATT--A-
*
52977655 GAAAACCCTAACCCTAACCTATTTAATTAAAATCCCTAACCCTAACCTAATTTAATTAAAAAC
61 -AAAACCCTAACCCTAA-C---TTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAC
52977718 TCTTACCCTG
Statistics
Matches: 641, Mismatches: 51, Indels: 108
0.80 0.06 0.14
Matches are distributed among these distances:
119 2 0.00
120 117 0.18
121 53 0.08
122 7 0.01
123 12 0.02
124 8 0.01
125 62 0.10
126 281 0.44
127 18 0.03
129 1 0.00
130 20 0.03
131 7 0.01
132 2 0.00
134 1 0.00
136 10 0.02
137 7 0.01
138 1 0.00
141 3 0.00
142 15 0.02
143 14 0.02
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.28
Consensus pattern (127 bp):
ATTTAATTAAAAACCCTAACCTAACTTAATTTAATTAAAAACCCTAACATAACTTAATTAAAAAC
CCTAACCCTAACTTAATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCTA
Found at i:52977579 original size:23 final size:23
Alignment explanation
Indices: 52976857--52977563 Score: 661
Period size: 23 Copynumber: 28.9 Consensus size: 23
52976847 TAAAAACCCT
52976857 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
52976880 AAACCTAACCCT-ACTTAATTAAAAA
1 AACCCTAA-CCTAATTTAATT--AAA
52976905 CCCTAACCCTAACCTAATTTAATTAAA
1 ----AACCCTAACCTAATTTAATTAAA
52976932 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
52976955 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* * *
52976978 AACCCTAACATAACTCAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
52977001 AAACCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAA--T--TT-AATTAAA
*
52977029 AACCCTAACCCT-ACTTAATTAAA
1 AACCCTAA-CCTAATTTAATTAAA
*
52977052 AACTCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
52977075 AACCCTAACATAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
52977098 AAACCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAA--T--TT-AATTAAA
* *
52977126 AACCCTAACATAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
52977149 AACCCTAACCCT-ACTTAATTAAA
1 AACCCTAA-CCTAATTTAATTAAA
52977172 AACCCTAACCTTAACCTAATTTAATTAAA
1 AA--C---CC-TAACCTAATTTAATTAAA
52977201 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
52977224 AACCCTAACATAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
52977247 AACCCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAA--T--TT-AATTAAA
* *
52977275 AACCCTAACATAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
52977298 ACCCCTAACCCT-ACTTAATTAAAAACCA
1 AACCCTAA-CCTAATTTAATT---AA--A
52977326 TAACCCTAACCTAATTTAATTAAA
1 -AACCCTAACCTAATTTAATTAAA
52977350 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
** *
52977373 AACCCTAAGATAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
52977396 AAACCTAACCTAACTTAATTAAATTAAA
1 AACCCTAACCTAA--T--TT-AATTAAA
*
52977424 AACCCTAACCCT-ACTTAATTAAA
1 AACCCTAA-CCTAATTTAATTAAA
52977447 AACCCTAAACCTAACCTAATTTAATTAAA
1 AA--C----CCTAACCTAATTTAATTAAA
52977476 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
52977499 AACCCTAACATAACTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
* *
52977522 AACCCTAACATAA-CTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
52977544 AACCCTAAGCTAATTTAATT
1 AACCCTAACCTAATTTAATT
52977564 TAATTAAAAA
Statistics
Matches: 577, Mismatches: 52, Indels: 110
0.78 0.07 0.15
Matches are distributed among these distances:
22 22 0.04
23 368 0.64
24 18 0.03
25 5 0.01
26 4 0.01
27 12 0.02
28 82 0.14
29 66 0.11
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:52977725 original size:29 final size:29
Alignment explanation
Indices: 52976840--52977774 Score: 552
Period size: 23 Copynumber: 36.3 Consensus size: 29
52976830 TTTTGACATT
*
52976840 ATTTGATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52976869 ATTTAATTAAAAAACCTAACCCT-A-C--
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52976894 --TTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52976921 ATTTAATT--AAA----AACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52976944 ATTTAATTAAAAA-CC---C--TAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52976967 ATTTAATTAAAAACCCTAA-CATAA-CTCA
1 ATTTAATTAAAAACCCTAACCCTAACCT-A
*
52976995 A-TT-A--AAAAA-CCTAA-CCTAACTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977018 ATTAAATTAAAAACCCTAACCCT-A-C--
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977043 --TTAATTAAAAACTCTAA-CC-----TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977064 ATTTAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977087 ACTTAATTAAAAAACCTAA-CCTAACTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977115 ATTAAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977138 ACTTAATTAAAAACCCTAACCCT-A-C--
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977163 --TTAATTAAAAACCCTAACCTTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977190 ATTTAATT--AAA----AACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977213 ATTTAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* *
52977236 ACTTAATTAAAAACCCTAA-CCTAACTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977264 ATTAAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* *
52977287 ACTTAATTAAAACCCCTAACCCT-A-C--
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977312 --TTAATTAAAAACCATAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977339 ATTTAATT--AAA----AACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977362 ATTTAATTAAAAACCCTAA----GA--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977385 ACTTAATTAAAAAACCTAA-CCTAACTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977413 ATTAAATTAAAAACCCTAACCCT-A-C--
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977438 --TTAATTAAAAACCCTAAACCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977465 ATTTAATT--AAA----AACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977488 ATTTAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977511 ACTTAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * **
52977534 A-CTAATTAAAAACCCTAA-GCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
52977561 ATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977590 ATTTAATTGAAATCTCTAA-CCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
*
52977618 ATTTAATTAAAAACCCCAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* *
52977647 TTTTACA-TGAAAACCCTAACCCTAACCT-
1 ATTTA-ATTAAAAACCCTAACCCTAACCTA
*
52977675 ATTTAATTAAAATCCCTAACCCTAACCTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * * **
52977704 ATTTAATTAAAAACTCTTACCCTGATTTA
1 ATTTAATTAAAAACCCTAACCCTAACCTA
* * * *
52977733 TCATTTTATTTGAAATCCCAAACCCTAACCTA
1 --A-TTTAATTAAAAACCCTAACCCTAACCTA
52977765 ATTTAATTAA
1 ATTTAATTAA
52977775 TGTAAAAACC
Statistics
Matches: 729, Mismatches: 74, Indels: 206
0.72 0.07 0.20
Matches are distributed among these distances:
22 19 0.03
23 339 0.47
24 15 0.02
25 26 0.04
26 6 0.01
27 30 0.04
28 131 0.18
29 141 0.19
30 2 0.00
31 1 0.00
32 19 0.03
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.29
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAACCTA
Found at i:52977726 original size:57 final size:57
Alignment explanation
Indices: 52976840--52977726 Score: 304
Period size: 51 Copynumber: 17.4 Consensus size: 57
52976830 TTTTGACATT
* * * *
52976840 ATTTGATTAAAAACCCTAACCCTAACCTAATTTAATTAAAAAACCTAACCCT-A-C--
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* *
52976894 --TTAATTAAAAACCCTAACCCTAACCTAATTTAATT--AAA----AACCCTAACCTA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
*
52976944 ATTTAATT-AAAA-----ACCCTAACCTAATTTAATTAAAAACCCTAA-CATAA-CTCA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCT-A
* * *
52976995 A-TT-A--AAAAAC-C-TAACCTAACTTAATTAAATTAAAAACCCTAACCCT-A-C--
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977043 --TTAATTAAAAACTC-TAACCT-A---ATTTAATTAAAAACCCTAA-CATAACTTA
1 ATTTAATTAAAAACTCTTACCCTAACCTATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977092 A-TT-A--AAAAAC-C-TAACCTAACTTAATTAAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * * *
52977138 ACTTAATTAAAAACCCTAACCCT-A-C---TTAATTAAAAACCCTAACCTTAACCTA
1 ATTTAATTAAAAACTCTTACCCTAACCTATTTAATTAAAAACCCTAACCCTAACCTA
52977190 ATTTAATT-AAAA-----ACCCTAACCTAATTTAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * * * *
52977236 ACTTAATTAAAAAC-CCTAACCTAACTTAATTAAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977287 ACTTAATT-AAAA--C---CCCTAACCCTACTTAATTAAAAACCATAACCCTAACCTA
1 ATTTAATTAAAAACTCTTACCCTAA-CCTATTTAATTAAAAACCCTAACCCTAACCTA
** *
52977339 ATTTAATT-AAAA-----ACCCTAACCTAATTTAATTAAAAACCCTAA-GATAACTTA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977390 A-TT-A--AAAAAC-C-TAACCTAACTTAATTAAATTAAAAACCCTAACCCT-A-C--
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977438 --TTAATTAAAAACCCTAAACCTAACCTAATTTAATT--AAA----AACCCTAACCTA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * *
52977488 ATTTAATTAAAAAC-CCTAACATAA-C---TTAATTAAAAACCCTAA--C--A--TA
1 ATTTAATTAAAAACTCTTACCCTAACCTATTTAATTAAAAACCCTAACCCTAACCTA
* * ** **
52977534 A-CTAATTAAAAAC-CCTAAGCTAATTTAATTTAATTAAAAACCCTAACCCTAACCTA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * * *
52977590 ATTTAATTGAAATCTC-TAACCTAACCTAATTTAATTAAAAACCCCAACCCTAACCTA
1 ATTTAATTAAAAACTCTTACCCTAACCT-ATTTAATTAAAAACCCTAACCCTAACCTA
* * * * *
52977647 TTTTACA-TGAAAACCCTAACCCTAACCTATTTAATTAAAATCCCTAACCCTAACCTA
1 ATTTA-ATTAAAAACTCTTACCCTAACCTATTTAATTAAAAACCCTAACCCTAACCTA
52977704 ATTTAATTAAAAACTCTTACCCT
1 ATTTAATTAAAAACTCTTACCCT
52977727 GATTTATCAT
Statistics
Matches: 664, Mismatches: 67, Indels: 201
0.71 0.07 0.22
Matches are distributed among these distances:
45 21 0.03
46 120 0.18
47 22 0.03
48 24 0.04
49 4 0.01
50 58 0.09
51 155 0.23
52 143 0.22
54 1 0.00
56 4 0.01
57 101 0.15
58 11 0.02
ACGTcount: A:0.47, C:0.24, G:0.01, T:0.29
Consensus pattern (57 bp):
ATTTAATTAAAAACTCTTACCCTAACCTATTTAATTAAAAACCCTAACCCTAACCTA
Found at i:52979491 original size:125 final size:125
Alignment explanation
Indices: 52979269--52979525 Score: 356
Period size: 125 Copynumber: 2.1 Consensus size: 125
52979259 CCACGAGGGC
*
52979269 GCGATTTGATACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCCTACATGAGCAACTGTAGC
1 GCGATTTGATACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCCTACACGAGCAACTGTAGC
* * * **
52979334 GAAATCGCGACCACGAGGGCGCGATTTCACAATTTCTTCTCATATAGCATCCTGGTATCA
66 GAAATCGCGACCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
* * * * *
52979394 GCGATTTTATACTATTTGCTCAGAAAACGTCAAAAAAAATTTTATTTCTTACACGA-CCACTGTA
1 GCGATTTGATACTATTTACTCAG-AAACGTCAAAAAAAA-ATTATTTCCTACACGAGCAACTGTA
* * *
52979458 GCGAAATCGCG-TCACGAGGCCACTATTTCACAATTTCTTCTTAAATAGCATCCTGGTAGAA
64 GCGAAATCGCGACCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
52979519 GCGATTT
1 GCGATTT
52979526 CCCACTATTT
Statistics
Matches: 116, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
125 70 0.60
126 33 0.28
127 13 0.11
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (125 bp):
GCGATTTGATACTATTTACTCAGAAACGTCAAAAAAAAATTATTTCCTACACGAGCAACTGTAGC
GAAATCGCGACCACGAGGCCACGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAA
Found at i:52999116 original size:30 final size:30
Alignment explanation
Indices: 52999077--52999134 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
52999067 TGGAACTAAT
*
52999077 AATGTAAGATGAATTAAGTTAACAGAGAAG
1 AATGCAAGATGAATTAAGTTAACAGAGAAG
52999107 AATGCAAGATGAATTAAGTTAACAGAGA
1 AATGCAAGATGAATTAAGTTAACAGAGA
52999135 CTTGAGCTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.22, T:0.22
Consensus pattern (30 bp):
AATGCAAGATGAATTAAGTTAACAGAGAAG
Found at i:53005909 original size:44 final size:44
Alignment explanation
Indices: 53005850--53005982 Score: 203
Period size: 44 Copynumber: 3.0 Consensus size: 44
53005840 AGGAAAGTAA
* * *
53005850 GATTCGCAATTTTCAACCTATTCCACTGCTAACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
53005894 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
* * * *
53005938 GATTCACAATCTTCATCCTATTCCATTGTTGTCCAGGGAGATAG
1 GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
53005982 G
1 G
53005983 GTTGGGGTTA
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 82 1.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
GATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGATAG
Found at i:53006112 original size:44 final size:45
Alignment explanation
Indices: 53005993--53006302 Score: 159
Period size: 44 Copynumber: 7.0 Consensus size: 45
53005983 GTTGGGGTTA
* * * *
53005993 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
** * * ** * * *
53006038 TTAACCTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCT
1 TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
* *
53006081 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTAT-T
1 TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
* * * * ** * * *
53006125 TTGAACCTACTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCT
1 TCG-ATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
** * * *
53006169 TCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTT
1 TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
** * * ** * *
53006214 TTAACCTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTAG-TGTCT
1 TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCT-GCTATCT
* * * * **
53006257 TCAATCAGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCT
1 TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
53006302 T
1 T
53006303 TAACCTGCTC
Statistics
Matches: 181, Mismatches: 74, Indels: 20
0.66 0.27 0.07
Matches are distributed among these distances:
43 49 0.27
44 81 0.45
45 51 0.28
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.27
Consensus pattern (45 bp):
TCGATCTGCTTCGCTGTCAGTCCAGGAAGGCAAGAGCTGCTATCT
Found at i:53006119 original size:88 final size:88
Alignment explanation
Indices: 53005993--53006646 Score: 801
Period size: 88 Copynumber: 7.4 Consensus size: 88
53005983 GTTGGGGTTA
*
53005993 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
53006058 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* *
53006081 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTGAACCTACTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
53006146 CCAGGGAGGCAAGGCTGGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
**
53006169 TCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
53006234 CCAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * * * * * * *
53006257 TCAATCAGCTTCACTGTCAGTACAGGAAGGCAAGATTTGCTATCTTTAACCTGCTCCGCTGCCAT
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* * * *
53006322 CGAGAGAGGCAAGGCTACTGCCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * * * ** * * * *
53006345 TCAATCTACTTCACTGTTAGTATAGGAAGGCAAGATTTGCTATCTTTAACCTGCTTCGCTGCCAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
* *
53006410 CTAGGGAGGCAAGGTTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* ** * * ** * * * *
53006433 TCGATCTAC-TC-CACT-ACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCTGCTGCA
1 TCGATCTGCTTCGCTGTCAGTGC--AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCA
*
53006495 ACCCAGGGAGGCAAGGCTGGTGTCT
64 ACCCAGGGAGGCAAGGCTAGTGTCT
* * * *
53006520 TTGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAAC
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
*
53006585 CTAGGGAGGCAAGGCTAGTGTCT
66 CCAGGGAGGCAAGGCTAGTGTCT
* * * *
53006608 TCGATCTACTTCACTGTCGGTGTAGGAAGGCAAGATCTG
1 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTG
53006647 TTATCTTCAC
Statistics
Matches: 486, Mismatches: 75, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
85 2 0.00
86 2 0.00
87 60 0.12
88 418 0.86
89 2 0.00
90 2 0.00
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.27
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAAC
CCAGGGAGGCAAGGCTAGTGTCT
Found at i:53006528 original size:351 final size:352
Alignment explanation
Indices: 53006016--53006653 Score: 969
Period size: 351 Copynumber: 1.8 Consensus size: 352
53006006 CTGTCGGTGC
* *
53006016 AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTCT
1 AGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCT
* ** * * * *
53006081 TCGATCTGCTTCGCTGTCAGTGCAGGAAGGCAAGATCTGCTATTTTGAACCTACTCCGCTGCAAC
66 TCGATCTACTTCGCACTCACTGCAGGAAGACAAGATCTGCAATTTTCAACCTACTCCGCTGCAAC
* *
53006146 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTA
131 CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTA
53006211 TTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATC-AGCTTCACTGTC
196 TTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTA-CTTCACTGTC
*
53006275 AGTACAGGAAGGCAAGATTTGCTATCTTTAACCTGCTCCGCTGCCATCGAGAGAGGCAAGGCTAC
260 AGTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCCATCGAGAGAGGCAAGGCTAC
53006340 TGCCTTCAATCTACTTCACTGTTAGTAT
325 TGCCTTCAATCTACTTCACTGTTAGTAT
* * * * *
53006368 AGGAAGGCAAGATTTGCTATCTTTAACCTGCTTCGCTGCCACCTAGGGAGGCAAGGTTAGTGTCT
1 AGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCT
* * *
53006433 TCGATCTAC-TC-CACT-ACTGCTTAGGGAGATAAGATCTGCAATTTTCAACCTACTCTGCTGCA
66 TCGATCTACTTCGCACTCACTGC--AGGAAGACAAGATCTGCAATTTTCAACCTACTCCGCTGCA
*
53006495 ACCCAGGGAGGCAAGGCTGGTGTCTTTGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGC
129 ACCCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGC
* * *
53006560 TATTTTTAACCTGCTCCGCTGTAACCTAGGGAGGCAAGGCTAGTGTCTTCGATCTACTTCACTGT
194 TATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTACTTCACTGT
* ** *
53006625 CGGTGTAGGAAGGCAAGATCTGTTATCTT
259 CAGTACAGGAAGGCAAGATCTGCTATCTT
53006654 CACTGATCTA
Statistics
Matches: 255, Mismatches: 28, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
349 4 0.02
350 2 0.01
351 182 0.71
352 67 0.26
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (352 bp):
AGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCT
TCGATCTACTTCGCACTCACTGCAGGAAGACAAGATCTGCAATTTTCAACCTACTCCGCTGCAAC
CCAGGGAGGCAAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTACAGGAAGGCAAGATCTGCTA
TTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTAGTGTCTTCAATCTACTTCACTGTCA
GTACAGGAAGGCAAGATCTGCTATCTTTAACCTGCTCCGCTGCCATCGAGAGAGGCAAGGCTACT
GCCTTCAATCTACTTCACTGTTAGTAT
Found at i:53026893 original size:19 final size:18
Alignment explanation
Indices: 53026858--53026893 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
53026848 TCTTACTACA
*
53026858 GTTTTCAGTTTCACTATT
1 GTTTTCAGTTACACTATT
53026876 GTTTTCAGTATACACTAT
1 GTTTTCAGT-TACACTAT
53026894 CTACAGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (18 bp):
GTTTTCAGTTACACTATT
Found at i:53033246 original size:18 final size:21
Alignment explanation
Indices: 53033217--53033260 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
53033207 AAAAATAATA
53033217 AAAATAATTTTT-AAAATTC-
1 AAAATAATTTTTAAAAATTCT
53033236 AAAAT-ATTTTTAAAAATTCT
1 AAAATAATTTTTAAAAATTCT
53033256 AAAAT
1 AAAAT
53033261 TTATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
19 12 0.52
20 5 0.22
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATAATTTTTAAAAATTCT
Found at i:53033262 original size:18 final size:17
Alignment explanation
Indices: 53033222--53033262 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
53033212 TAATAAAAAT
53033222 AATTTTTAAAATTCAAA
1 AATTTTTAAAATTCAAA
*
53033239 ATATTTTTAAAAATTCTAA
1 A-ATTTTT-AAAATTCAAA
53033258 AATTT
1 AATTT
53033263 ATATTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 10 0.48
19 10 0.48
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTTTAAAATTCAAA
Found at i:53036572 original size:57 final size:57
Alignment explanation
Indices: 53036484--53036591 Score: 207
Period size: 57 Copynumber: 1.9 Consensus size: 57
53036474 TTCAATCAAG
*
53036484 CCAAACCCTAACTTGTGGATGATGAAGGTGATTGTGGGAATGGTCTCAGACATCGAA
1 CCAAACCCTAACTTGTGGATGATGAAGGTGATGGTGGGAATGGTCTCAGACATCGAA
53036541 CCAAACCCTAACTTGTGGATGATGAAGGTGATGGTGGGAATGGTCTCAGAC
1 CCAAACCCTAACTTGTGGATGATGAAGGTGATGGTGGGAATGGTCTCAGAC
53036592 GAAGTTTTTA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.24
Consensus pattern (57 bp):
CCAAACCCTAACTTGTGGATGATGAAGGTGATGGTGGGAATGGTCTCAGACATCGAA
Found at i:53042145 original size:29 final size:30
Alignment explanation
Indices: 53042113--53042179 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
53042103 GAAAAATGCC
*
53042113 TCAATTGAACCCTCA-A-TAATGAAAATAA
1 TCAATTGAACCCTCATATTAATAAAAATAA
**
53042141 TTCAATTGGCCCCTCATATTAATAAAAATAA
1 -TCAATTGAACCCTCATATTAATAAAAATAA
53042172 TCAATTGA
1 TCAATTGA
53042180 CCAATTTGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 13 0.41
30 8 0.25
31 11 0.34
ACGTcount: A:0.45, C:0.18, G:0.07, T:0.30
Consensus pattern (30 bp):
TCAATTGAACCCTCATATTAATAAAAATAA
Found at i:53042172 original size:31 final size:28
Alignment explanation
Indices: 53042074--53042179 Score: 81
Period size: 29 Copynumber: 3.6 Consensus size: 28
53042064 TGTCTTCGGT
*
53042074 ATAAAAAAAATCAATT-AAGCCCTC-ATA
1 ATAAAAATAATCAATTGAA-CCCTCAATA
* **
53042101 AGGAAAAATGCCTCAATTGAACCCTCAATA
1 A-TAAAAAT-AATCAATTGAACCCTCAATA
* **
53042131 ATGAAAATAATTCAATTGGCCCCTCATATTA
1 ATAAAAATAA-TCAATTGAACCCTCA-A-TA
53042162 ATAAAAATAATCAATTGA
1 ATAAAAATAATCAATTGA
53042180 CCAATTTGAT
Statistics
Matches: 60, Mismatches: 12, Indels: 11
0.72 0.14 0.13
Matches are distributed among these distances:
27 1 0.02
28 5 0.08
29 29 0.48
30 14 0.23
31 11 0.18
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.25
Consensus pattern (28 bp):
ATAAAAATAATCAATTGAACCCTCAATA
Found at i:53044822 original size:21 final size:21
Alignment explanation
Indices: 53044796--53044836 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
53044786 ATCTGCTCAA
* *
53044796 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
53044817 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
53044837 TTGCTCGTCT
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:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:53053451 original size:7 final size:8
Alignment explanation
Indices: 53053432--53053459 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
53053422 ATTATTCTAT
53053432 TTTTTTAA
1 TTTTTTAA
53053440 TTTTTTAA
1 TTTTTTAA
53053448 TTTTTTAA
1 TTTTTTAA
53053456 TTTT
1 TTTT
53053460 ATTTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTAA
Found at i:53053471 original size:21 final size:20
Alignment explanation
Indices: 53053429--53053497 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
53053419 ATTATTATTC
*
53053429 TATTTTTTTAAT-TTTT-TA
1 TATTTTTTAAATCTTTTATA
* *
53053447 -ATTTTTTAATTTTATTTATA
1 TATTTTTTAAATCT-TTTATA
53053467 TATTTTTTAGAATCTTTTATA
1 TATTTTTTA-AATCTTTTATA
53053488 T-TTTTTTAAA
1 TATTTTTTAAA
53053498 ATATAAATTT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
17 9 0.21
18 1 0.02
19 5 0.12
20 9 0.21
21 15 0.36
22 3 0.07
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (20 bp):
TATTTTTTAAATCTTTTATA
Found at i:53053677 original size:16 final size:16
Alignment explanation
Indices: 53053656--53053686 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
53053646 AATTGTAAAA
53053656 TTCAACTCAATTCAAC
1 TTCAACTCAATTCAAC
53053672 TTCAACTCAATTCAA
1 TTCAACTCAATTCAA
53053687 ACTCGAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.29, G:0.00, T:0.32
Consensus pattern (16 bp):
TTCAACTCAATTCAAC
Found at i:53056584 original size:14 final size:14
Alignment explanation
Indices: 53056550--53056586 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
53056540 TTTAATTAAT
*
53056550 TATAATCAATTTAG
1 TATAATTAATTTAG
53056564 TATAATTAATTTAG
1 TATAATTAATTTAG
53056578 TATAATTAA
1 TATAATTAA
53056587 AGTATACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (14 bp):
TATAATTAATTTAG
Found at i:53058648 original size:21 final size:22
Alignment explanation
Indices: 53058613--53058665 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
53058603 ATTTGATCTG
53058613 AAAAGAAGAAA---AAAATAGT
1 AAAAGAAGAAATTGAAAATAGT
*
53058632 AATA-AAGAAATTGAAAATAGT
1 AAAAGAAGAAATTGAAAATAGT
53058653 AAAAGAAGAAATT
1 AAAAGAAGAAATT
53058666 TGAGATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 6 0.21
19 3 0.11
21 11 0.39
22 8 0.29
ACGTcount: A:0.68, C:0.00, G:0.15, T:0.17
Consensus pattern (22 bp):
AAAAGAAGAAATTGAAAATAGT
Found at i:53060157 original size:39 final size:40
Alignment explanation
Indices: 53060055--53060162 Score: 116
Period size: 39 Copynumber: 2.7 Consensus size: 40
53060045 GCGTTTGTAC
* *
53060055 AAAAAGCGCCGCTAAAAATCGAGCATTAGCGGCGCCTTACG
1 AAAAAGCGCCGCT-AAAATCGAGCATTAGCAGCGCCTTACA
* * *
53060096 TAAAA-CG-CACTAAAGATCGAGCATTAGCAGCG-CTTTCA
1 AAAAAGCGCCGCTAAA-ATCGAGCATTAGCAGCGCCTTACA
53060134 AAAAAGCGCCGCTAAAA-CTGAGCATTAGC
1 AAAAAGCGCCGCTAAAATC-GAGCATTAGC
53060163 GGCGTTTTTC
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
38 12 0.21
39 32 0.57
40 8 0.14
41 4 0.07
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (40 bp):
AAAAAGCGCCGCTAAAATCGAGCATTAGCAGCGCCTTACA
Found at i:53060303 original size:41 final size:41
Alignment explanation
Indices: 53060228--53060380 Score: 193
Period size: 41 Copynumber: 3.7 Consensus size: 41
53060218 CCTTTCGGGG
* * *
53060228 CTTTAGCGGCGTTTTTAAAAAAAGCGTCGCTAATGCTCAAAT
1 CTTTAGCGGCGTTTTT-TAAAAAGCGCCGCTAATGCTCAGAT
*
53060270 CTTTAGTGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGAT
* * * *
53060311 CTTTAGCGTCG-TTTCTAGAAAAGCGCCGCTAATGCTCGGGGT
1 CTTTAGCGGCGTTTTTTA-AAAAGCGCCGCTAATGCTC-AGAT
53060353 -TTTAGCGGCGTTTTTTAAAAAGCGCCGC
1 CTTTAGCGGCGTTTTTTAAAAAGCGCCGC
53060381 AAAATCATTT
Statistics
Matches: 97, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
40 5 0.05
41 70 0.72
42 22 0.23
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTCAGAT
Found at i:53060811 original size:14 final size:15
Alignment explanation
Indices: 53060779--53060811 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
53060769 AAGGTTTATA
*
53060779 GATTATGGAATTGGG
1 GATTATGGAATTAGG
53060794 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
53060808 GATT
1 GATT
53060812 CTGATTTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.27, C:0.00, G:0.36, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:53061653 original size:108 final size:109
Alignment explanation
Indices: 53061539--53061734 Score: 315
Period size: 108 Copynumber: 1.8 Consensus size: 109
53061529 TTTTTAACAG
*
53061539 AAAAAATAAAAGAT-TTTTAGCATAGCAAAACAGTGTCGTTTTATTCGAAATGAAATAA-TTTTT
1 AAAAAAT-AAAGATATTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTT
53061602 TGCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTA
65 TGCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTA
**** *
53061647 AAAAAATAGCTCTATTTTAGCATAGCAAAACATTGTCGTTTTATTCCAAATGAAATAATTTTTTT
1 AAAAAATAAAGATATTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTT
53061712 GCGGCGTTTTTATGAAAAACGCC
66 GCGGCGTTTTTATGAAAAACGCC
53061735 GTAAAAGGTA
Statistics
Matches: 80, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
107 2 0.03
108 49 0.61
109 29 0.36
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (109 bp):
AAAAAATAAAGATATTTTAGCATAGCAAAACAGTGTCGTTTTATTCCAAATGAAATAATTTTTTT
GCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTA
Found at i:53061782 original size:149 final size:149
Alignment explanation
Indices: 53061603--53061900 Score: 413
Period size: 149 Copynumber: 2.0 Consensus size: 149
53061593 ATAATTTTTT
* * * * *
53061603 GCGGCGTTTTTATGAAAAACGCCACAAAAAATAATTTTACTTTAAAAAAATAGCTCTATTTTAGC
1 GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTAATTTAAAAAAATAACGCCATTTTAGC
* * * *
53061668 ATAGCAAAACATTGTCGTTTTATTCCAAATGAAATAA-TTTTTTTGCGGCGTTTTTATGAAAAAC
66 ATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTTGCGGCATTTTTAT-AAAAAC
*
53061732 GCCGT-AAAAGGTAAGCAATA
130 GCC-TCAAAAGATAAGCAATA
*
53061752 GCGGTGTTTTTATAAAAAAACGCCAC-AAAAATAATTTTAATTTAAAAAAATAACGCCATTTTAG
1 GCGGCGTTTTTAT-AAAAAACGCCACAAAAAATAATTTTAATTTAAAAAAATAACGCCATTTTAG
* * * *
53061816 CGTAACAAAACAGTGTCGTTTTATTCTAAATAAAATAATTTTTTTTGCGTCATTTTTGTAAAAAC
65 CATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTTGCGGCATTTTTATAAAAAC
53061881 GCCTCAAAAGATAAGCAATA
130 GCCTCAAAAGATAAGCAATA
53061901 TAAAAACGCT
Statistics
Matches: 131, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
148 1 0.01
149 102 0.78
150 28 0.21
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (149 bp):
GCGGCGTTTTTATAAAAAACGCCACAAAAAATAATTTTAATTTAAAAAAATAACGCCATTTTAGC
ATAACAAAACAGTGTCGTTTTATTCCAAATAAAATAATTTTTTTTGCGGCATTTTTATAAAAACG
CCTCAAAAGATAAGCAATA
Found at i:53066535 original size:43 final size:43
Alignment explanation
Indices: 53066483--53066667 Score: 246
Period size: 43 Copynumber: 4.3 Consensus size: 43
53066473 AGATTATGTT
* * *
53066483 TTTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTGATAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
53066526 -TAAGGCGGCGTTTGTGGGAAAAGTGCCGTTAAAGGTCATGGTC
1 TTTA-GCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
53066569 TTTAGCGGCTTTTGTGGGAAAAGCGCCGCTAAAGATCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
* * *
53066612 TTTAGCGGCGTTTGTGGGAAAAGCGCCGTTAAAGGTCTTGGTT
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
53066655 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
53066668 ATTTCTAAAA
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 2 0.02
43 120 0.97
44 2 0.02
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:53066788 original size:22 final size:22
Alignment explanation
Indices: 53066762--53066803 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
53066752 AGCGGCACTG
*
53066762 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
53066784 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
53066804 GTTTTGGTGT
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:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:53067448 original size:17 final size:16
Alignment explanation
Indices: 53067419--53067461 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
53067409 CATAAAAAAT
*
53067419 TTAAAAATAATATTAA
1 TTAAAAATTATATTAA
*
53067435 CTTAATAATTATATTAA
1 -TTAAAAATTATATTAA
53067452 TTAAAAATTA
1 TTAAAAATTA
53067462 AATAATATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAAAATTATATTAA
Done.