Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold18
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: 4432388
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 63034 characters in sequence are not A, C, G, or T
File 7 of 27
Found at i:893268 original size:92 final size:88
Alignment explanation
Indices: 893110--893478 Score: 427
Period size: 92 Copynumber: 4.0 Consensus size: 88
893100 AAAAGATGAC
* *
893110 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGC
* *
893175 TGATTCAAGGCCAGCGATATTGGAC-T-T
60 TGATTCAAGGCCAGCTACATTGGACTTAT
* * *
893202 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGC
893267 TGATTCAAGGCCAGCTACATTGGACTTAAAGAT
60 TGATTCAAGGCCAGCTACATTGGACTT----AT
*
893300 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
893365 AAGGCCAGCTACATTGGACTTTAAGAT
66 AAGGCCAGCTACATTGGAC-TT---AT
* * *
893392 AAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTTAAAGGTGCCAATGTGCTTATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
* *
893457 AAGGCTAGCAACATTGGACTTA
66 AAGGCCAGCTACATTGGACTTA
893479 AAGGTTGCCA
Statistics
Matches: 255, Mismatches: 15, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
88 1 0.00
91 2 0.01
92 208 0.82
93 3 0.01
94 1 0.00
98 40 0.16
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (88 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
AAGGCCAGCTACATTGGACTTAT
Found at i:893320 original size:141 final size:142
Alignment explanation
Indices: 892947--893488 Score: 695
Period size: 141 Copynumber: 3.8 Consensus size: 142
892937 CTTAGGAATG
* * *
892947 TTAAAGATGAAGGTGCTAATGTGCTGATTCAAGCCCAGCGACATTGGACTTAAAAGATGACAAAG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGAT---AAAG
* *
893012 GCGCCAATATGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGATGCCAATGTGCTGAT
62 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-G--GATGCCAATGTGCTGAT
893077 TCAAGGCCAGCGACATTGGAC
122 TCAAGGCCAGCGACATTGGAC
* * *
893098 TTAAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAG
1 TT-AAAGATG---AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAG
893163 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG-TGCCAATGTGCTGATTCAAG
62 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGATGCCAATGTGCTGATTCAAG
*
893227 GCCAGCGACATTGGTC
127 GCCAGCGACATTGGAC
* *
893243 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGC
*
893308 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGG-TGCCAATGTGCTGATTCAAGGCCA
66 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGATGCCAATGTGCTGATTCAAGGCCA
*
893372 GCTACATTGGAC
131 GCGACATTGGAC
* * * * *
893384 TTTAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGAC-T-----TAAAGGTGC
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGC
* * * * * *
893443 CAATGTGCTTATTCAAGGCTAGCAACATTGGACTTAAAGGTTGCCA
66 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGATGCCA
893489 CCGACTTGTG
Statistics
Matches: 359, Mismatches: 27, Indels: 25
0.87 0.07 0.06
Matches are distributed among these distances:
135 44 0.12
136 5 0.01
140 1 0.00
141 168 0.47
144 7 0.02
145 37 0.10
146 1 0.00
148 1 0.00
149 1 0.00
150 2 0.01
151 42 0.12
152 7 0.02
154 6 0.02
155 37 0.10
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (142 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATAAAGGTGC
CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGATGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGAC
Found at i:893529 original size:33 final size:33
Alignment explanation
Indices: 893481--893638 Score: 212
Period size: 33 Copynumber: 4.8 Consensus size: 33
893471 TGGACTTAAA
*
893481 GGTTGCCACCGACTTGTGTGGGCTTCAGAGAAT
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
* *
893514 GGTTACCACCAACTTGTGTGGGCTTTAGAGAAT
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
*
893547 GGTTGCCACCGACTTGTGTGGGCTTTAGAG--G
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
* * *
893578 GGATTGCCACCAACTTGTGTGGGCTTTAGAAAAAA
1 GG-TTGCCACCGACTTGTGTGGGCTTTAG-AGAAT
*
893613 GGTTGCCACCGATTTGTGTGGGCTTT
1 GGTTGCCACCGACTTGTGTGGGCTTT
893639 GAAAAGGGTG
Statistics
Matches: 110, Mismatches: 11, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
31 2 0.02
32 25 0.23
33 59 0.54
34 22 0.20
35 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.32, T:0.30
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
Found at i:893617 original size:66 final size:65
Alignment explanation
Indices: 893478--893638 Score: 234
Period size: 66 Copynumber: 2.4 Consensus size: 65
893468 CATTGGACTT
* *
893478 AAAGGTTGCCACCGACTTGTGTGGGCTTCAGAGAATGGTTACCACCAACTTGTGTGGGCTTTAGA
1 AAAGGTTGCCACCGACTTGTGTGGGCTTTAGAG-AGGGTTACCACCAACTTGTGTGGGCTTTAGA
*
893543 G
65 A
* *
893544 AATGGTTGCCACCGACTTGTGTGGGCTTTAGAG-GGGATTGCCACCAACTTGTGTGGGCTTTAGA
1 AAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGG-TTACCACCAACTTGTGTGGGCTTTAG-
893608 AA
64 AA
*
893610 AAAGGTTGCCACCGATTTGTGTGGGCTTT
1 AAAGGTTGCCACCGACTTGTGTGGGCTTT
893639 GAAAAGGGTG
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 2 0.02
65 25 0.29
66 59 0.69
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (65 bp):
AAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGGGTTACCACCAACTTGTGTGGGCTTTAGAA
Found at i:893683 original size:34 final size:34
Alignment explanation
Indices: 893640--893856 Score: 261
Period size: 34 Copynumber: 6.6 Consensus size: 34
893630 GTGGGCTTTG
* * *
893640 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGA
*
893675 AAAAG-GTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
893708 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
893742 AAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
** *
893776 AAAAGAGTGCCATAGAGTTGTGGGCTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
893808 ----G-GCGCCACAGAGTTGTGGACTAAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
*
893837 AAAAAAGTGCCACGGAGTTG
1 AAAAGAGTGCCACGGAGTTG
893857 CGGGCTTTAC
Statistics
Matches: 158, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
27 21 0.13
28 2 0.01
33 14 0.09
34 116 0.73
35 5 0.03
ACGTcount: A:0.37, C:0.12, G:0.33, T:0.18
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:893724 original size:68 final size:67
Alignment explanation
Indices: 893640--893863 Score: 289
Period size: 68 Copynumber: 3.4 Consensus size: 67
893630 GTGGGCTTTG
*
893640 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAA
893705 GGA
65 GGA
* * * *
893708 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAG-GTGCCACAGAGTTGTGGACTTAAAA
893773 GGA
65 GGA
** * *
893776 AAAAGAGTGCCATAGAGTTGTGGGCTT-AAAAG-----GGCGCCACAGAGTTGTGGACTAAAAAG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
893835 GA
66 GA
* *
893837 AAAAAAGTGCCACGGAGTTGCGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
893864 TACAGAAAAG
Statistics
Matches: 138, Mismatches: 17, Indels: 9
0.84 0.10 0.05
Matches are distributed among these distances:
61 47 0.34
62 1 0.01
67 17 0.12
68 73 0.53
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (67 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAAG
GA
Found at i:893786 original size:102 final size:95
Alignment explanation
Indices: 893640--893865 Score: 265
Period size: 95 Copynumber: 2.3 Consensus size: 95
893630 GTGGGCTTTG
* *
893640 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAA
* * *
893705 GGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
66 -G-----G-GCGCCACAGAGTTGTGGACTAAAAAGGA
* * * *
893742 AAAAGAGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCATAGAGTTGTGGGCTTAAA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAG-GTGCCACAGAGTTGTGGACTTAAA
893806 AGGGCGCCACAGAGTTGTGGACTAAAAAGGA
65 AGGGCGCCACAGAGTTGTGGACTAAAAAGGA
* * *
893837 AAAAAAGTGCCACGGAGTTGCGGGCTTTA
1 AAAAGAGTGCCACGGAGTTGTGGACTTTA
893866 CAGAAAAGGA
Statistics
Matches: 110, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
95 47 0.43
96 4 0.04
101 13 0.12
102 46 0.42
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.19
Consensus pattern (95 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACAGAGTTGTGGACTTAAAA
GGGCGCCACAGAGTTGTGGACTAAAAAGGA
Found at i:893835 original size:27 final size:27
Alignment explanation
Indices: 893775--893835 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
893765 ACTTAGAAGG
* * * *
893775 AAAAAGAGTGCCATAGAGTTGTGGGCT
1 AAAAAGGGCGCCACAGAGTTGTGGACT
*
893802 TAAAAGGGCGCCACAGAGTTGTGGACT
1 AAAAAGGGCGCCACAGAGTTGTGGACT
893829 AAAAAGG
1 AAAAAGG
893836 AAAAAAAGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (27 bp):
AAAAAGGGCGCCACAGAGTTGTGGACT
Found at i:893914 original size:32 final size:31
Alignment explanation
Indices: 893867--894026 Score: 198
Period size: 32 Copynumber: 5.1 Consensus size: 31
893857 CGGGCTTTAC
* * *
893867 AGAAAAGGATACCACTAAGTCGTGGACTTTG
1 AGAAAAAGATGCCACTGAGTCGTGGACTTTG
893898 AGACAAAAGATGCCACTGAGTCGTGGACTTTG
1 AGA-AAAAGATGCCACTGAGTCGTGGACTTTG
* *
893930 AAGAAAAGGATGCCACTAAGTCGTGGACTTTG
1 -AGAAAAAGATGCCACTGAGTCGTGGACTTTG
* *
893962 AGACAAA-ATGCCACTGAGTCGTGGGCTTTG
1 AGAAAAAGATGCCACTGAGTCGTGGACTTTG
* *
893992 AG-AAGAGATTGCCACTGAGTCGTGGACTTTA
1 AGAAAAAGA-TGCCACTGAGTCGTGGACTTTG
894023 AGAA
1 AGAA
894027 GGTATTTGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
29 2 0.02
30 24 0.22
31 30 0.27
32 52 0.47
33 3 0.03
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (31 bp):
AGAAAAAGATGCCACTGAGTCGTGGACTTTG
Found at i:893937 original size:64 final size:61
Alignment explanation
Indices: 893867--894021 Score: 231
Period size: 64 Copynumber: 2.5 Consensus size: 61
893857 CGGGCTTTAC
*
893867 AGAAAAGGATACCACTAAGTCGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGACTTTG
1 AGAAAAGGATGCCACTAAGTCGTGGACTTTGAGAC-AAA-ATGCCACTGAGTCGTGGACTTTG
*
893930 AAGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGGCTTTG
1 -AGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTG
* *
893992 AGAAGA-GATTGCCACTGAGTCGTGGACTTT
1 AGAAAAGGA-TGCCACTAAGTCGTGGACTTT
894022 AAGAAGGTAT
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
60 2 0.02
61 25 0.29
62 22 0.26
63 3 0.03
64 34 0.40
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.23
Consensus pattern (61 bp):
AGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAAATGCCACTGAGTCGTGGACTTTG
Found at i:894027 original size:31 final size:30
Alignment explanation
Indices: 893839--894026 Score: 182
Period size: 32 Copynumber: 6.1 Consensus size: 30
893829 AAAAAGGAAA
* * * *
893839 AAAAG-TGCCACGGAGTTGCGGGCTTTACAG
1 AAAAGATGCCACTGAGTCGTGGACTTTA-AG
* * *
893869 AAAAGGATACCACTAAGTCGTGGACTTTGAGAC
1 AAAA-GATGCCACTGAGTCGTGGACTTT-A-AG
893902 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTT-AAG
* *
893933 AAAAGGATGCCACTAAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTAAG
* *
893964 ACAAA-ATGCCACTGAGTCGTGGGCTTTGAG
1 A-AAAGATGCCACTGAGTCGTGGACTTTAAG
*
893994 AAGAGATTGCCACTGAGTCGTGGACTTTAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTAAG
894025 AA
1 AA
894027 GGTATTTGAA
Statistics
Matches: 133, Mismatches: 18, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.02
30 29 0.22
31 33 0.25
32 63 0.47
33 6 0.05
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.22
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTAAG
Found at i:895354 original size:25 final size:26
Alignment explanation
Indices: 895326--895380 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
895316 TTTTGTGTGT
* **
895326 TTTTTGTTT-TGTTTTTTTTTTTGAC
1 TTTTTGTTTGTGTGTTTACTTTTGAC
895351 -TTTTGTTTGTGTGTTTACTTTTGAC
1 TTTTTGTTTGTGTGTTTACTTTTGAC
895376 TTTTT
1 TTTTT
895381 CATCATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 8 0.32
25 13 0.52
26 4 0.16
ACGTcount: A:0.05, C:0.05, G:0.15, T:0.75
Consensus pattern (26 bp):
TTTTTGTTTGTGTGTTTACTTTTGAC
Found at i:895845 original size:14 final size:14
Alignment explanation
Indices: 895826--895853 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
895816 TTATCAGTGC
895826 ATCTAAATGAACAA
1 ATCTAAATGAACAA
895840 ATCTAAATGAACAA
1 ATCTAAATGAACAA
895854 CTAGGTGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ATCTAAATGAACAA
Found at i:896831 original size:52 final size:52
Alignment explanation
Indices: 896753--896904 Score: 209
Period size: 52 Copynumber: 2.9 Consensus size: 52
896743 CCCGAAATAT
* *
896753 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACAGTTCAAAGTGTATCGATACATCTGG
* * *
896805 GAAAATTTGCCTGTATGTATCAATACAGTTCAAAGTGTATCGATACATCTTG
1 GAAAATTTGCCTGCATGTATCGATACAGTTCAAAGTGTATCGATACATCTGG
* *
896857 GCAAATTTGCCTGCATGTATCGATACAAAGATC--AGTGTATCGATACAT
1 GAAAATTTGCCTGCATGTATCGATAC--AGTTCAAAGTGTATCGATACAT
896905 TTGAGTAATG
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 85 0.96
54 4 0.04
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACAGTTCAAAGTGTATCGATACATCTGG
Found at i:896966 original size:13 final size:13
Alignment explanation
Indices: 896948--896999 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
896938 AGCTTCGTAG
896948 CGATACATTGTAT
1 CGATACATTGTAT
896961 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
896980 CGATACATTGTAT
1 CGATACATTGTAT
896993 CGATACA
1 CGATACA
897000 AAACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:896980 original size:19 final size:19
Alignment explanation
Indices: 896956--897020 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
896946 AGCGATACAT
896956 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
896975 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
896988 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
897007 TGTATCGATACAAA
1 TGTATCGATACAAA
897021 TCATTGAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 25 0.62
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:896989 original size:32 final size:32
Alignment explanation
Indices: 896948--897018 Score: 142
Period size: 32 Copynumber: 2.2 Consensus size: 32
896938 AGCTTCGTAG
896948 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
896980 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
897012 CGATACA
1 CGATACA
897019 AATCATTGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:904405 original size:39 final size:39
Alignment explanation
Indices: 904362--904487 Score: 166
Period size: 39 Copynumber: 3.3 Consensus size: 39
904352 TTGTTTGCTG
*
904362 CATCATTTCATTCTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
* * * * *
904401 CATCACTTCATGCTTTCA-CAACCTT-CATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
*
904438 CATCATTTCATACTTGCATCCATGTTACATGCTTTGCAT
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
*
904477 CGTCATTTCAT
1 CATCATTTCAT
904488 GCTTTCACAA
Statistics
Matches: 73, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
37 27 0.37
38 9 0.12
39 37 0.51
ACGTcount: A:0.21, C:0.29, G:0.10, T:0.40
Consensus pattern (39 bp):
CATCATTTCATACTTGCATCCACGTTACATGCTTTGCAT
Found at i:904437 original size:37 final size:37
Alignment explanation
Indices: 904362--904504 Score: 142
Period size: 39 Copynumber: 3.8 Consensus size: 37
904352 TTGTTTGCTG
* * * *
904362 CATCATTTCATTCTTGCATCCACGTTACATGCTTTGCAT
1 CATCATTTCATGCTTTCA-CAACCTT-CATGCTTTGCAT
*
904401 CATCACTTCATGCTTTCACAACCTTCATGCTTTGCAT
1 CATCATTTCATGCTTTCACAACCTTCATGCTTTGCAT
* * * **
904438 CATCATTTCATACTTGCATCCATGTTACATGCTTTGCAT
1 CATCATTTCATGCTTTCA-CAACCTT-CATGCTTTGCAT
* *
904477 CGTCATTTCATGCTTTCACAACTTTCAT
1 CATCATTTCATGCTTTCACAACCTTCAT
904505 TCATTCATCA
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
37 30 0.35
38 13 0.15
39 42 0.49
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.41
Consensus pattern (37 bp):
CATCATTTCATGCTTTCACAACCTTCATGCTTTGCAT
Found at i:904487 original size:76 final size:76
Alignment explanation
Indices: 904362--904504 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 76
904352 TTGTTTGCTG
*
904362 CATCATTTCATTCTTGCATCCACGTTACATGCTTTGCATCATCACTTCATGCTTTCACAACCTTC
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCACTTCATGCTTTCACAACCTTC
904427 ATGCTTTGCAT
66 ATGCTTTGCAT
* * * *
904438 CATCATTTCATACTTGCATCCATGTTACATGCTTTGCATCGTCATTTCATGCTTTCACAACTTTC
1 CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCACTTCATGCTTTCACAACCTTC
904503 AT
66 AT
904505 TCATTCATCA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.22, C:0.29, G:0.09, T:0.41
Consensus pattern (76 bp):
CATCATTTCATACTTGCATCCACGTTACATGCTTTGCATCATCACTTCATGCTTTCACAACCTTC
ATGCTTTGCAT
Found at i:904488 original size:20 final size:20
Alignment explanation
Indices: 904362--904492 Score: 107
Period size: 20 Copynumber: 6.8 Consensus size: 20
904352 TTGTTTGCTG
*
904362 CATCATTTCATTC-TTGCAT
1 CATCATTTCATGCTTTGCAT
* *
904381 CCA-CGTTACATGCTTTGCAT
1 -CATCATTTCATGCTTTGCAT
*
904401 CATCACTTCATGCTTT-CA-
1 CATCATTTCATGCTTTGCAT
* *
904419 CAAC-CTTCATGCTTTGCAT
1 CATCATTTCATGCTTTGCAT
*
904438 CATCATTTCATAC-TTGCAT
1 CATCATTTCATGCTTTGCAT
904457 C--CATGTTACATGCTTTGCAT
1 CATCAT-TT-CATGCTTTGCAT
*
904477 CGTCATTTCATGCTTT
1 CATCATTTCATGCTTT
904493 CACAACTTTC
Statistics
Matches: 90, Mismatches: 11, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
17 14 0.16
18 7 0.08
19 25 0.28
20 39 0.43
21 2 0.02
22 3 0.03
ACGTcount: A:0.21, C:0.28, G:0.10, T:0.41
Consensus pattern (20 bp):
CATCATTTCATGCTTTGCAT
Found at i:904536 original size:17 final size:18
Alignment explanation
Indices: 904514--904572 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 18
904504 TTCATTCATC
*
904514 ATTTTTTTATAATTTTT-
1 ATTTTTTTATATTTTTTG
*
904531 ATTTTTTATTTATTTTTTG
1 ATTTTTT-TATATTTTTTG
904550 ATTTTTTTA-ATTTTTTG
1 ATTTTTTTATATTTTTTG
904567 ATTTTT
1 ATTTTT
904573 AATTTTTGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 21 0.57
18 9 0.24
19 7 0.19
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.78
Consensus pattern (18 bp):
ATTTTTTTATATTTTTTG
Found at i:904587 original size:17 final size:17
Alignment explanation
Indices: 904518--904590 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 17
904508 TTCATCATTT
* *
904518 TTTTATAATTTTTATTTT
1 TTTT-TAATTTTTGTTTA
* *
904536 TTATTTATTTTTTGATT-
1 TT-TTTAATTTTTGTTTA
*
904553 TTTTTAA-TTTT-TTGA
1 TTTTTAATTTTTGTTTA
904568 TTTTTAATTTTTGTTTA
1 TTTTTAATTTTTGTTTA
904585 TTTTTA
1 TTTTTA
904591 TCATTATGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
14 1 0.02
15 11 0.25
16 8 0.18
17 11 0.25
18 11 0.25
19 2 0.05
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (17 bp):
TTTTTAATTTTTGTTTA
Found at i:911686 original size:52 final size:52
Alignment explanation
Indices: 911608--911756 Score: 230
Period size: 52 Copynumber: 2.9 Consensus size: 52
911598 CGAAATATGA
911608 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGGC
** * *
911660 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATTTGGGC
1 AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGGC
911712 AAATTTGCCTGCATGTATCGATACA--AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTAA-AT-AGTGTATCGATACA
911757 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTAAATAGTGTATCGATACATCTGGGC
Found at i:911763 original size:13 final size:13
Alignment explanation
Indices: 911745--911769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
911735 CAAAGATCAG
911745 TGTATCGATACAA
1 TGTATCGATACAA
911758 TGTATCGATACA
1 TGTATCGATACA
911770 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:911847 original size:33 final size:33
Alignment explanation
Indices: 911810--911876 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
911800 AGTAGCTTAA
911810 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
911843 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
911876 A
1 A
911877 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:911850 original size:13 final size:13
Alignment explanation
Indices: 911832--911856 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
911822 CAAAAAAATA
911832 TGTATCGATACAT
1 TGTATCGATACAT
911845 TGTATCGATACA
1 TGTATCGATACA
911857 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:916009 original size:349 final size:349
Alignment explanation
Indices: 915370--916061 Score: 1287
Period size: 349 Copynumber: 2.0 Consensus size: 349
915360 CAACCTATCC
915370 CATTATTAGCTGAACAACATCATAATGTCAGCACTTTGTCTTGCAAATTGGTGGAGGGAAATGTC
1 CATTATTAGCTGAACAACATCATAATGTCAGCACTTTGTCTTGCAAATTGGTGGAGGGAAATGTC
* * *
915435 CTAAAATACCTCACTTTTCACTCCAAAATTTTGGCAATAAATAGGCCAATTCAATCTAAGCAAAG
66 CCAAAACACCTCACTTTTCACTCCAAAATTTTGGCAATAAATAGGCCAATTCAATCCAAGCAAAG
915500 GATCCTCTCTCTCTAAATCCCCCTTGGAACCACATTTTTTAGTCTCATTAGCATCCATATCTTAG
131 GATCCTCTCTCTCTAAATCCCCCTTGGAACCACATTTTTTAGTCTCATTAGCATCCATATCTTAG
915565 CAAAACATCAACATAAAAACACATTAAAAAGTCCATTCCCGTAGCTCCCTACAGCTCCCAAAAGA
196 CAAAACATCAACATAAAAACACATTAAAAAGTCCATTCCCGTAGCTCCCTACAGCTCCCAAAAGA
*
915630 AACACCTCCAAACACTTCCTTCTTGGTCACTATACAACTCCAATCCATCCCTACTCATACCATAA
261 AACACCTCCAAACACTTCCTTCTTGGTCACTACACAACTCCAATCCATCCCTACTCATACCATAA
915695 CCCAAACATTCACTTTTTTAATGT
326 CCCAAACATTCACTTTTTTAATGT
915719 CATTATTAGCTGAACAACATCATAATGTCAGCACTTTGTCTTGCAAATTGGTGGAGGGAAATGTC
1 CATTATTAGCTGAACAACATCATAATGTCAGCACTTTGTCTTGCAAATTGGTGGAGGGAAATGTC
* *
915784 CCAAAACACCTCACTTTTCACTCCAATATTTTGGCTATAAATAGGCCAATTCAATCCAAGCAAAG
66 CCAAAACACCTCACTTTTCACTCCAAAATTTTGGCAATAAATAGGCCAATTCAATCCAAGCAAAG
915849 GATCCTCTCTCTCTAAATCCCCCTTGGAACCACATTTTTTAGTCTCATTAGCATCCATATCTTAG
131 GATCCTCTCTCTCTAAATCCCCCTTGGAACCACATTTTTTAGTCTCATTAGCATCCATATCTTAG
*
915914 CAAAACATCAACATAAAAGCACATTAAAAAGTCCATTCCCGTAGCTCCCTACAGCTCCCAAAAGA
196 CAAAACATCAACATAAAAACACATTAAAAAGTCCATTCCCGTAGCTCCCTACAGCTCCCAAAAGA
* *
915979 AACACCTCCAAACACCTT-CTTCTTGGTCACTACACAACTCCCATCCATCCCTACTCATACGATA
261 AACACCTCCAAACA-CTTCCTTCTTGGTCACTACACAACTCCAATCCATCCCTACTCATACCATA
916043 ACCCAAACATTCACTTTTT
325 ACCCAAACATTCACTTTTT
916062 CATCATTTTC
Statistics
Matches: 333, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
349 330 0.99
350 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.10, T:0.28
Consensus pattern (349 bp):
CATTATTAGCTGAACAACATCATAATGTCAGCACTTTGTCTTGCAAATTGGTGGAGGGAAATGTC
CCAAAACACCTCACTTTTCACTCCAAAATTTTGGCAATAAATAGGCCAATTCAATCCAAGCAAAG
GATCCTCTCTCTCTAAATCCCCCTTGGAACCACATTTTTTAGTCTCATTAGCATCCATATCTTAG
CAAAACATCAACATAAAAACACATTAAAAAGTCCATTCCCGTAGCTCCCTACAGCTCCCAAAAGA
AACACCTCCAAACACTTCCTTCTTGGTCACTACACAACTCCAATCCATCCCTACTCATACCATAA
CCCAAACATTCACTTTTTTAATGT
Found at i:917227 original size:148 final size:148
Alignment explanation
Indices: 916983--917373 Score: 516
Period size: 148 Copynumber: 2.6 Consensus size: 148
916973 AACTAATAAC
** * *
916983 AAGCTAAAAGAA-ATGATCATGATGGGAAATATGTGGTTCTACAATCTCTTATTAACAACCGAAA
1 AAGCTAAAA-AAGATGATCATGAT-GGAAATATGTGGTTCTACAATCTCCCATCAACAACTGAAA
* * *
917047 CAAACTGACAACAAGCTAAAAAAGAGCCGATGAGGAACATGTGATTTCTACAATTTCCCATCAAC
64 CAAACTGACAACAAGCTAGAAAATAGCTGATGAGGAACATGTGATTTCTACAATTTCCCATCAAC
*
917112 AGCCAAAACAAACTGATAAG
129 AGCCAAAACAAACTGACAAG
917132 -AGCTAAAAAAGATGATCATGATAGGAAATATGTGGTTCTACAATCTCCCATCAACAACTGAAAC
1 AAGCTAAAAAAGATGATCATGAT-GGAAATATGTGGTTCTACAATCTCCCATCAACAACTGAAAC
* * * * * *
917196 AAACTAACAACAAGCTGGAAAATAGCTGATGAGGAATATGTGATTTCTATAATTTCCCATTAATA
65 AAACTGACAACAAGCTAGAAAATAGCTGATGAGGAACATGTGATTTCTACAATTTCCCATCAACA
* * *
917261 GTCGAAACAAATTGACAAG
130 GCCAAAACAAACTGACAAG
* * ** **
917280 AAACTAAAAAAGATGATAATGATGGAAAATATGTGGTTCTACAATCTCCCATCAGTAGTTGAAAC
1 AAGCTAAAAAAGATGATCATGATGG-AAATATGTGGTTCTACAATCTCCCATCAACAACTGAAAC
*
917345 AGACTGACAACAAGCTAGAAAATAGCTGA
65 AAACTGACAACAAGCTAGAAAATAGCTGA
917374 CATGATTTCT
Statistics
Matches: 212, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
147 2 0.01
148 129 0.61
149 81 0.38
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (148 bp):
AAGCTAAAAAAGATGATCATGATGGAAATATGTGGTTCTACAATCTCCCATCAACAACTGAAACA
AACTGACAACAAGCTAGAAAATAGCTGATGAGGAACATGTGATTTCTACAATTTCCCATCAACAG
CCAAAACAAACTGACAAG
Found at i:917344 original size:76 final size:75
Alignment explanation
Indices: 916983--917366 Score: 280
Period size: 73 Copynumber: 5.1 Consensus size: 75
916973 AACTAATAAC
* ** * * ***
916983 AAGCTAAAAGAA-ATGATCATGATGGGAAATATGTGGTTCTACAATCTCTTATTAACAACCGAAA
1 AAGCTAAAA-AAGATGATAATGAT-GGAAATATGTGGTTCTACAATCTCCCATCAATAGTTGAAA
*
917047 CAAACTGACAAC
64 CAAACTGACAAG
*** * * * * ***
917059 AAGCTAAAAAAGA-GCCGATGA-GG-AACATGTGATTTCTACAATTTCCCATCAACAGCCAAAAC
1 AAGCTAAAAAAGATGATAATGATGGAAATATGTG-GTTCTACAATCTCCCATCAATAGTTGAAAC
*
917121 AAACTGATAAG
65 AAACTGACAAG
* * **
917132 -AGCTAAAAAAGATGATCATGATAGGAAATATGTGGTTCTACAATCTCCCATCAACAACTGAAAC
1 AAGCTAAAAAAGATGATAATGAT-GGAAATATGTGGTTCTACAATCTCCCATCAATAGTTGAAAC
* *
917196 AAACTAACAAC
65 AAACTGACAAG
** * * * * * * * *
917207 AAGCTGGAAAATA-GCTGATGA-GG-AATATGTGATTTCTATAATTTCCCATTAATAGTCGAAAC
1 AAGCTAAAAAAGATGATAATGATGGAAATATGTG-GTTCTACAATCTCCCATCAATAGTTGAAAC
*
917269 AAATTGACAAG
65 AAACTGACAAG
* *
917280 AAACTAAAAAAGATGATAATGATGGAAAATATGTGGTTCTACAATCTCCCATCAGTAGTTGAAAC
1 AAGCTAAAAAAGATGATAATGATGG-AAATATGTGGTTCTACAATCTCCCATCAATAGTTGAAAC
* *
917345 AGACTGACAAC
65 AAACTGACAAG
*
917356 AAGCTAGAAAA
1 AAGCTAAAAAA
917367 TAGCTGACAT
Statistics
Matches: 238, Mismatches: 58, Indels: 24
0.74 0.18 0.08
Matches are distributed among these distances:
72 27 0.11
73 80 0.34
74 6 0.03
75 50 0.21
76 67 0.28
77 8 0.03
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (75 bp):
AAGCTAAAAAAGATGATAATGATGGAAATATGTGGTTCTACAATCTCCCATCAATAGTTGAAACA
AACTGACAAG
Found at i:918197 original size:24 final size:24
Alignment explanation
Indices: 918170--918232 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
918160 ATATGCATGA
* *
918170 AAAGATGCAAATGCAAGCATCAAT
1 AAAGAGGCAAATGCAAACATCAAT
918194 AAAGAGGCAAATGCAAACATCAAT
1 AAAGAGGCAAATGCAAACATCAAT
*
918218 AAAGCGGCAAATGCA
1 AAAGAGGCAAATGCA
918233 TATGTAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.51, C:0.17, G:0.19, T:0.13
Consensus pattern (24 bp):
AAAGAGGCAAATGCAAACATCAAT
Found at i:918582 original size:19 final size:20
Alignment explanation
Indices: 918539--918591 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
918529 ATTTCAACGA
918539 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATAAAAT
*
918559 ATTGTATCGATACAT-AAAT
1 TTTGTATCGATACATAAAAT
918578 TTTGTATCGATACA
1 TTTGTATCGATACA
918592 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (20 bp):
TTTGTATCGATACATAAAAT
Found at i:918652 original size:13 final size:13
Alignment explanation
Indices: 918634--918658 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
918624 ATTACTCAAA
918634 TGTATCGATACAT
1 TGTATCGATACAT
918647 TGTATCGATACA
1 TGTATCGATACA
918659 CTAATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:920097 original size:21 final size:20
Alignment explanation
Indices: 920069--920107 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
920059 GCTGCATGTT
920069 TAAAAATTATTT-TAAAATAA
1 TAAAAATT-TTTATAAAATAA
920089 TAAACAATTTTTATAAAAT
1 TAAA-AATTTTTATAAAAT
920108 TTTTTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTTTTATAAAATAA
Found at i:934049 original size:29 final size:29
Alignment explanation
Indices: 933984--934128 Score: 141
Period size: 29 Copynumber: 5.0 Consensus size: 29
933974 TCACCCTTCA
* * *
933984 AAAGCCCACAAGCCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
934011 AAAGCCCACAAGTCAATGGCATCTTTTTG
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
934040 AAAGCCCACAAATCAGTGGCACCCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
934069 AGAAGCCCACAAGTCGGTGGCATCTTTTCC
1 A-AAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
934099 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
934129 TTTTTAAAGC
Statistics
Matches: 95, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
27 20 0.21
29 44 0.46
30 31 0.33
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:934091 original size:59 final size:58
Alignment explanation
Indices: 933984--934126 Score: 164
Period size: 59 Copynumber: 2.5 Consensus size: 58
933974 TCACCCTTCA
** * **
933984 AAAGCCCACAAGCCAGTGGCAACC--TTCAAAGCCCACAAGTCAATGGCATCTTTTTG
1 AAAGCCCACAAATCAGTGGCACCCTTTTCAAAGCCCACAAGTCAATGGCATCTTTTCC
**
934040 AAAGCCCACAAATCAGTGGCACCCTTTTCAGAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAATCAGTGGCACCCTTTTCA-AAGCCCACAAGTCAATGGCATCTTTTCC
* * * *
934099 AAAGTCCACAACTCCGTGGCACTCTTTT
1 AAAGCCCACAAATCAGTGGCACCCTTTT
934127 TCTTTTTAAA
Statistics
Matches: 73, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
56 21 0.29
58 4 0.05
59 48 0.66
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (58 bp):
AAAGCCCACAAATCAGTGGCACCCTTTTCAAAGCCCACAAGTCAATGGCATCTTTTCC
Found at i:934186 original size:34 final size:35
Alignment explanation
Indices: 934099--934261 Score: 210
Period size: 35 Copynumber: 4.8 Consensus size: 35
934089 CATCTTTTCC
*
934099 AAAGTCCACAACTCCGTGGCACTCTTTTTCTTTTT
1 AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
934134 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
*
934169 -AAGTCCACAACTTCGTGGCACTCTTTTTCCCTTTT
1 AAAGTCCACAACTCCGTGGCACTCTTTTT-CCTTTT
* *
934204 AAAGCCCACAACTCCGTGGCAC-CTTGTT-CTTTT
1 AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
* *
934237 -AAGTCCACAACTTCATGGCA-TCTTT
1 AAAGTCCACAACTCCGTGGCACTCTTT
934262 CACCCTTTCT
Statistics
Matches: 112, Mismatches: 13, Indels: 9
0.84 0.10 0.07
Matches are distributed among these distances:
32 20 0.18
33 5 0.04
34 26 0.23
35 42 0.38
36 19 0.17
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (35 bp):
AAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTT
Found at i:934186 original size:69 final size:68
Alignment explanation
Indices: 934061--934281 Score: 263
Period size: 68 Copynumber: 3.2 Consensus size: 68
934051 ATCAGTGGCA
* * * * *
934061 CCCTTTTCAGAAGCCCACAAGTCGGTGGCATCTT-TTC--CAAAGTCCACAACTCCGTGGCACTC
1 CCCTTTT-A-AAGCCCACAACTCCGTGGCACCTTGTTCTTCTAAGTCCACAACTTCGTGGCACTC
934123 TTTTT
64 TTTTT
* *
934128 -CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTTCGTGGCACTC
1 CCCTTTTAAAGCCCACAACTCCGTGGCAC-CTTGTT-CTTCTAAGTCCACAACTTCGTGGCACTC
934192 TTTTT
64 TTTTT
* *
934197 CCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCTTTTAAGTCCACAACTTCATGGCA-TCTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCTTCTAAGTCCACAACTTCGTGGCACTCTT
**
934261 TCA
66 TTT
934264 CCCTTTCTAAAGCCCACA
1 CCCTTT-TAAAGCCCACA
934282 CAAGTCGGTG
Statistics
Matches: 135, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
64 18 0.13
65 4 0.03
66 7 0.05
67 12 0.09
68 34 0.25
69 33 0.24
70 27 0.20
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.33
Consensus pattern (68 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACCTTGTTCTTCTAAGTCCACAACTTCGTGGCACTCTT
TTT
Found at i:934306 original size:33 final size:33
Alignment explanation
Indices: 934265--934557 Score: 385
Period size: 33 Copynumber: 8.9 Consensus size: 33
934255 CATCTTTCAC
934265 CCTT-TCTAAAGCCCACACAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
*
934297 CCTTCTCTAAAGCCCACACAAGTCAGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* * *
934330 CGTTTTCTAAAGCCCACACAAGTCGATGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
934363 CGTTCTCTAAAGCCCACATAAGTCGGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
934396 CCTTCTCTAAAGCCCAAACAAGTCAGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
934429 CCTTTTCTAAAGCCCACACAAGTCAGTGGCAAA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* * *
934462 CCATCTCTAAAGCCCACAAAAGTTGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
** * *
934494 CCCCCTCTAAAGGCCACACAATTCGGTGGC-AA
1 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
* *
934526 CCTTCTTCAAAAGCCCACACAAGTTGGTGGCA
1 CCTTC-TCTAAAGCCCACACAAGTCGGTGGCA
934558 TCTACCTTTA
Statistics
Matches: 227, Mismatches: 31, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
32 35 0.15
33 192 0.85
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (33 bp):
CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAA
Found at i:934623 original size:49 final size:48
Alignment explanation
Indices: 934563--934837 Score: 336
Period size: 43 Copynumber: 5.8 Consensus size: 48
934553 TGGCATCTAC
* *
934563 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC-T
*
934612 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCT
* *
934655 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTC-T
*
934704 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCT
* *
934747 CTTTAAGTCAAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC--TT-C-T
* *
934799 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTG
934838 ACATCATTTT
Statistics
Matches: 195, Mismatches: 16, Indels: 27
0.82 0.07 0.11
Matches are distributed among these distances:
43 78 0.40
45 2 0.01
47 1 0.01
49 78 0.40
50 1 0.01
52 35 0.18
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (48 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACCTTCT
Found at i:934718 original size:92 final size:92
Alignment explanation
Indices: 934561--934837 Score: 491
Period size: 92 Copynumber: 3.0 Consensus size: 92
934551 GGTGGCATCT
934561 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
934626 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
*
934653 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGTCCAATG
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
934718 TAGCTGGCCTTGAATCAGCACATTGGC
66 TAGCTGGCCTTGAATCAGCACATTGGC
* * *
934745 ACCTTTAAGTCAAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCA
1 ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTTTAAGTCCA
934810 ATGTAGCTGGCCTTGAATCAGCACATTG
63 ATGTAGCTGGCCTTGAATCAGCACATTG
934838 ACATCATTTT
Statistics
Matches: 177, Mismatches: 5, Indels: 3
0.96 0.03 0.02
Matches are distributed among these distances:
92 135 0.76
94 2 0.01
95 40 0.23
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
ACCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGC
Found at i:934882 original size:55 final size:52
Alignment explanation
Indices: 934747--934884 Score: 159
Period size: 52 Copynumber: 2.6 Consensus size: 52
934737 ACATTGGCAC
* * *
934747 CTTTAAGTCAAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* * *
934799 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCATTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-C-CTTTTC-CAT
* * * *
934854 CTTTAAGCCCAATATCGTTGGCCGTGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
934885 ACATTTTGGC
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
52 37 0.52
53 1 0.01
54 5 0.07
55 28 0.39
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:934961 original size:67 final size:68
Alignment explanation
Indices: 934850--934976 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
934840 ATCATTTTTC
* * * *
934850 TCATCTTTAAGCCCAATATCGTTGGCCGTGAATCAACATTTTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
934914 TCT
66 TCT
* * * * *
934917 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATTAGCATATTGGCACCTTCATCATCTTT
1 TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTT
934977 AAAAATGACG
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.23, C:0.24, G:0.13, T:0.40
Consensus pattern (68 bp):
TCATCTTTAAGCCCAATATCGCTGGCCGTGAATCAACATATTGGCACCTTCATCATCTTTTCTCA
TCT
Found at i:935705 original size:19 final size:20
Alignment explanation
Indices: 935662--935714 Score: 90
Period size: 19 Copynumber: 2.7 Consensus size: 20
935652 ATTTCAATAA
935662 TTTGTATCGATACATAAAAT
1 TTTGTATCGATACATAAAAT
*
935682 ATTGTATCGATACAT-AAAT
1 TTTGTATCGATACATAAAAT
935701 TTTGTATCGATACA
1 TTTGTATCGATACA
935715 ATTTAAGCTA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (20 bp):
TTTGTATCGATACATAAAAT
Found at i:942152 original size:20 final size:20
Alignment explanation
Indices: 942129--942203 Score: 105
Period size: 20 Copynumber: 3.8 Consensus size: 20
942119 AAGTACCCAG
*
942129 ATGTATCGATAAATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
942149 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
942169 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
942189 ATGTATCGATACATT
1 ATGTATCGATACATT
942204 ATGTCCTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:942189 original size:40 final size:39
Alignment explanation
Indices: 942129--942206 Score: 129
Period size: 40 Copynumber: 2.0 Consensus size: 39
942119 AAGTACCCAG
*
942129 ATGTATCGATAAATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATAAATTCTTCAATGTATCGATACAT-TATGA
*
942169 ATGTATCGATACATTCTTCAATGTATCGATACATTATG
1 ATGTATCGATAAATTCTTCAATGTATCGATACATTATG
942207 TCCTTTTACC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.40
Consensus pattern (39 bp):
ATGTATCGATAAATTCTTCAATGTATCGATACATTATGA
Found at i:954846 original size:13 final size:13
Alignment explanation
Indices: 954828--954853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
954818 CAATTTTTTG
954828 TGTATCGATACAT
1 TGTATCGATACAT
954841 TGTATCGATACAT
1 TGTATCGATACAT
954854 ATTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:954864 original size:32 final size:33
Alignment explanation
Indices: 954808--954871 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
954798 TACAAGCCAA
*
954808 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATATTTTGTGTATCGATACAT
954841 TGTATCGATAC-ATATTTTGTGTATCGATACA
1 TGTATCGATACAATATTTTGTGTATCGATACA
954872 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.63
33 11 0.37
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (33 bp):
TGTATCGATACAATATTTTGTGTATCGATACAT
Found at i:954865 original size:19 final size:19
Alignment explanation
Indices: 954808--954871 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
954798 TACAAGCCAA
*
954808 TGTATCGATACAATTTTTTG
1 TGTATCGATAC-ATATTTTG
954828 TGTATCGATAC--A---T-
1 TGTATCGATACATATTTTG
954841 TGTATCGATACATATTTTG
1 TGTATCGATACATATTTTG
954860 TGTATCGATACA
1 TGTATCGATACA
954872 AGTTTGGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
18 1 0.03
19 12 0.32
20 11 0.30
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.44
Consensus pattern (19 bp):
TGTATCGATACATATTTTG
Found at i:954976 original size:20 final size:20
Alignment explanation
Indices: 954923--954978 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
954913 ACATCTTTTT
*
954923 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
*
954943 CATGTATAGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
954962 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
954979 TAAGGGTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:957362 original size:13 final size:13
Alignment explanation
Indices: 957344--957381 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
957334 ATAATCCCCC
957344 TGTATCGATACAG
1 TGTATCGATACAG
* *
957357 TGTATCGGTACAT
1 TGTATCGATACAG
957370 TGTATCGATACA
1 TGTATCGATACA
957382 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:959484 original size:15 final size:15
Alignment explanation
Indices: 959464--959494 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
959454 ATTTTGTTTG
*
959464 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
959479 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
959494 G
1 G
959495 GATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:963563 original size:20 final size:20
Alignment explanation
Indices: 963538--963589 Score: 88
Period size: 19 Copynumber: 2.6 Consensus size: 20
963528 TACAAGCCAA
*
963538 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATATTTTG
963558 TGTATCGATAC-ATATTTTG
1 TGTATCGATACAATATTTTG
963577 TGTATCGATACAA
1 TGTATCGATACAA
963590 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
20 12 0.40
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACAATATTTTG
Found at i:963693 original size:20 final size:20
Alignment explanation
Indices: 963640--963695 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
963630 ACATCTTTTT
*
963640 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
963660 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
*
963679 CTGTGTATCGATACTTT
1 C-ATGTATCGATACTTT
963696 TAAGGGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.38
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:966128 original size:11 final size:11
Alignment explanation
Indices: 966114--966153 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
966104 AAAAAACAAA
966114 AAACAAAAAAT
1 AAACAAAAAAT
966125 AAACAAAAAAT
1 AAACAAAAAAT
966136 -AA-AAAAAA-
1 AAACAAAAAAT
966144 AAACAAAAAA
1 AAACAAAAAA
966154 ACCAAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.30
10 8 0.30
11 11 0.41
ACGTcount: A:0.88, C:0.07, G:0.00, T:0.05
Consensus pattern (11 bp):
AAACAAAAAAT
Found at i:966154 original size:11 final size:11
Alignment explanation
Indices: 966102--966183 Score: 58
Period size: 11 Copynumber: 7.3 Consensus size: 11
966092 CCTTTATACC
966102 AAAAAAAACAA
1 AAAAAAAACAA
*
966113 AAAACAAAAAATA
1 AAAA-AAAACA-A
*
966126 AACAAAAAATAA
1 AA-AAAAAACAA
*
966138 AAAAAAAA-AC
1 AAAAAAAACAA
*
966148 AAAAAAACCAA
1 AAAAAAAACAA
* * *
966159 GAAAAAAATAG
1 AAAAAAAACAA
*
966170 CAAAAAAACAA
1 AAAAAAAACAA
966181 AAA
1 AAA
966184 GGGGACCAGA
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
10 8 0.15
11 28 0.52
12 8 0.15
13 8 0.15
14 2 0.04
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:966163 original size:19 final size:18
Alignment explanation
Indices: 966102--966183 Score: 85
Period size: 19 Copynumber: 4.2 Consensus size: 18
966092 CCTTTATACC
966102 AAAAAAAAC-AAAAAACA
1 AAAAAAAACAAAAAAACA
*
966119 AAAAATAAACAAAAAATAAA
1 AAAAA-AAACAAAAAA-ACA
966139 AAAAAAAACAAAAAAACCAA
1 AAAAAAAACAAAAAAA-C-A
966159 GAAAAAAATAGCAAAAAAACA
1 -AAAAAAA-A-CAAAAAAACA
966180 AAAA
1 AAAA
966184 GGGGACCAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
17 5 0.09
18 5 0.09
19 15 0.27
20 12 0.22
21 8 0.15
22 2 0.04
23 8 0.15
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (18 bp):
AAAAAAAACAAAAAAACA
Found at i:966164 original size:31 final size:29
Alignment explanation
Indices: 966102--966183 Score: 87
Period size: 29 Copynumber: 2.7 Consensus size: 29
966092 CCTTTATACC
*
966102 AAAAAAAACAAAAAACAAAAAATAAACAA
1 AAAAAAAAAAAAAAACAAAAAATAAACAA
*
966131 AAAATAAAAAAAAAAAC-AAAAA-AACCAA
1 AAAA-AAAAAAAAAAACAAAAAATAAACAA
966159 GAAAAAAATAGCAAAAAAACAAAAA
1 -AAAAAAA-A--AAAAAAACAAAAA
966184 GGGGACCAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
28 8 0.18
29 14 0.31
30 11 0.24
31 8 0.18
32 4 0.09
ACGTcount: A:0.84, C:0.10, G:0.02, T:0.04
Consensus pattern (29 bp):
AAAAAAAAAAAAAAACAAAAAATAAACAA
Found at i:966166 original size:1 final size:1
Alignment explanation
Indices: 966102--966154 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
966092 CCTTTATACC
* * * * * *
966102 AAAAAAAACAAAAAACAAAAAATAAACAAAAAATAAAAAAAAAAACAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
966155 CCAAGAAAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.08, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:967439 original size:28 final size:28
Alignment explanation
Indices: 967396--968252 Score: 996
Period size: 28 Copynumber: 29.9 Consensus size: 28
967386 CATTCATCTC
967396 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
967424 TTTAAAGCCCATAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
967453 TTCAAAGCCCACAAGCCAGTGGCACACT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967481 TTCAAAGCCCACAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
967510 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967538 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967566 TTCAAAGCCCACAAGTCAGTGACACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
967594 TTCAAAACACACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967622 TTCAAAGCCCGCGTAAGTTAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCACCCT
* *
967652 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
967680 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
967709 TTCAATGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
967737 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967765 TTCAAAGCCCATGCAAGTTAGTGGCACCTT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCT
* **
967795 TTCAAAGCCCACAAGTTAGTGGCACTTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967823 TCTCAAAGCCCGCAAGTTAGTGGCACCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACCCT
** *
967852 TTCAAAGCCCACAAGTTGGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
*
967881 TTCAGAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967909 TTCAAAGCCCACAAGTCAGTGACACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
967937 TTCAAAGCCCACAAGTCAGTAGCAGTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCCT
* *
967966 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
967994 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
968022 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
968050 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
968078 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
968106 TTTAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* ** *
968135 TTTAAAGCCCACAAGTCAGTGGCTTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
968163 TTCAAAGCCCACAAGGT-AGTGGTAACTCAT
1 TTCAAAGCCCACAA-GTCAGTGG-CAC-CCT
* * *
968193 TTCAAAGCCCACACGAGTCGGTGACAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
*
968225 TTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAAAG-CC-CACAAGTCAGTGGCACC
968253 TTTTTTTTTT
Statistics
Matches: 724, Mismatches: 85, Indels: 38
0.85 0.10 0.04
Matches are distributed among these distances:
28 453 0.63
29 171 0.24
30 67 0.09
31 4 0.01
32 23 0.03
33 2 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:967488 original size:57 final size:55
Alignment explanation
Indices: 967396--968252 Score: 960
Period size: 57 Copynumber: 15.0 Consensus size: 55
967386 CATTCATCTC
* * * *
967396 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCATAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
967453 TTCAAAGCCCACAAGCCAGTGGCACACTTTCAAAGCCCACAAGTCAATGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
967510 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
967566 TTCAAAGCCCACAAGTCAGTGACACCATTTCAAAACACACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
967622 TTCAAAGCCCGCGTAAGTTAGTGGCACCCTTTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCAC--AAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
967680 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAATGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-C-TTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
967737 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCATGCAAGTTAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCA--CAAGTCAGTGGCACCCT
* * * *
967795 TTCAAAGCCCACAAGTTAGTGGCACTTTTCTCAAAGCCCGCAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT-TCAAAGCCCACAAGTCAGTGGCACCCT
** *
967852 TTCAAAGCCCACAAGTTGGTGGCACTCTTTTCAGAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-C-TTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
967909 TTCAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCCACAAGTCAGTAGCAGTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACC-TTTCAAAGCCCACAAGTCAGTGGCA-CCCT
* * *
967966 TTCAAAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
968022 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* *
968078 TTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * * * *
968135 TTTAAAGCCCACAAGTCAGTGGCTTCTTTTCAAAGCCCACAAGGT-AGTGGTAACTCAT
1 TTCAAAGCCCACAAGTCAGTGGC-ACCTTTCAAAGCCCACAA-GTCAGTGG-CAC-CCT
* * *
968193 TTCAAAGCCCACACGAGTCGGTGACAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-C-TTTCAAAG-CC-CACAAGTCAGTGGCACC
968253 TTTTTTTTTT
Statistics
Matches: 698, Mismatches: 75, Indels: 49
0.85 0.09 0.06
Matches are distributed among these distances:
55 3 0.00
56 213 0.31
57 326 0.47
58 111 0.16
59 11 0.02
60 9 0.01
62 9 0.01
63 6 0.01
64 10 0.01
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (55 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:967541 original size:85 final size:84
Alignment explanation
Indices: 967396--968255 Score: 1082
Period size: 85 Copynumber: 10.0 Consensus size: 84
967386 CATTCATCTC
* * *
967396 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTAAAGCCCATAAGTCAATGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
**
967461 CCACAAGCCAGTGGCACACT
66 CCACAAGTTAGTGGCAC-CT
* * * *
967481 TTCAAAGCCCACAAGTCAATGGCACTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAG
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
967545 CCCACAAGTTAGTGGCATCCT
65 CCCACAAGTTAGTGGCA-CCT
* * * *
967566 TTCAAAGCCCACAAGTCAGTGACACCATTTCAAAACACACAAGTCAGTGGCAC-CTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
*
967630 CCGCGTAAGTTAGTGGCACCCT
66 CCAC--AAGTTAGTGGCA-CCT
* * *
967652 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAATGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
967717 CCACAAGTTAGTGGCATCCT
66 CCACAAGTTAGTGGCA-CCT
* *
967737 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCATGCAAGTTAGTGGCAC-CTTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAA
*
967801 GCCCACAAGTTAGTGGCACTTT
64 GCCCACAAGTTAGTGGCAC-CT
* * ** *
967823 TCTCAAAGCCCGCAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTGGTGGCACTCTTTTCAGAG
1 T-TCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAG
*
967888 CCCACAAGTCAGTGGCACCCT
65 CCCACAAGTTAGTGGCA-CCT
* * * *
967909 TTCAAAGCCCACAAGTCAGTGACACCTTTTCAAAGCCCACAAGTCAGTAGCAGTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
967974 CCACAAGTTAGTGGCATCCT
66 CCACAAGTTAGTGGCA-CCT
* * *
967994 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
*
968058 CCACAAGTCAGTGGCACCCT
66 CCACAAGTTAGTGGCA-CCT
* * *
968078 TTCAAAGCCCACAAGTCAGTGGCATCCTTTTAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
968143 CCACAAGTCAGTGGCTTCTT
66 CCACAAGTTAGTGGC-ACCT
* * * *
968163 TTCAAAGCCCACAAGGT-AGTGGTAACTCATTTCAAAGCCCACACGAGTCGGTGACAACTCTTTT
1 TTCAAAGCCCACAA-GTCAGTGG-CAC-CCTTTCAAAGCCCACA--AGTCAGTGGC-ACTCTTTT
968227 CAAAGCCCACACAAGTTAGTGGCACCT
60 CAAAG-CC-CACAAGTTAGTGGCACCT
968254 TT
1 TT
968256 TTTTTTTAAA
Statistics
Matches: 679, Mismatches: 74, Indels: 38
0.86 0.09 0.05
Matches are distributed among these distances:
84 113 0.17
85 306 0.45
86 143 0.21
87 78 0.11
89 8 0.01
90 12 0.02
91 6 0.01
92 13 0.02
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
CCACAAGTTAGTGGCACCT
Found at i:969162 original size:20 final size:20
Alignment explanation
Indices: 969120--969165 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
969110 AAGTACCCAG
* *
969120 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATCA
*
969140 ATGTATCGATACATGTATGA
1 ATGTATCGATACATGTATCA
969160 ATGTAT
1 ATGTAT
969166 GAAAAGTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTATCA
Found at i:969289 original size:13 final size:13
Alignment explanation
Indices: 969271--969295 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
969261 TCAACACTTA
969271 TGTATCGATACAT
1 TGTATCGATACAT
969284 TGTATCGATACA
1 TGTATCGATACA
969296 GCACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:970141 original size:53 final size:52
Alignment explanation
Indices: 970075--970817 Score: 316
Period size: 43 Copynumber: 15.6 Consensus size: 52
970065 TGAGAAGAAT
* * *
970075 GCCAATGTGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGCTGACGAGGGC
1 GCCAATATGCTGATTCAAGGCCAACGACATT-GGTCTTAAAGATGACGAGGGC
* *
970128 GCCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGCTGACGAGGGC
1 GCCAATATGCTGATTCAAGGCCAACGACATT-GGTCTTAAAGATGACGAGGGC
* * * * *
970181 GCCAATATGCTGATTCAAGGCCAGCGATACTGGTCTTAAAGATGA--A-AGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * * *
970230 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGACCTAAAGATGACAAAGGC
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * * *
970282 GCCAATATGCTGATTCAATGCCAGCAATATTGGACTT----A--A--A-GGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* ** * *
970325 GCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTT-AA-A-GAC-AAGGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * *
970373 GCCAATATGCTGATTCAAGGCTAGCGACATTGGTCTT-AA-A-GAC-AAGGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * *
970421 GCCAATATGCTGATTCAA-G-C-A--ATATTGGACTT--A-A--A----GGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * *
970459 GCCAATGTGCTGATTTAAGGCCAGCGACATTGGTCTT-AA-A-GAC-AAGGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * *
970507 GCCAATATGCTGATTCAAGGCCAACAATATTGGAC-T-----T-A--A-GGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * *
970549 GCCAATGTGCTGATTCAAGGCCAATGACATTGGTCTTAAAGATGACAAAGGC
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * * * *
970601 ACCAATATGCTAATTCAAGGCCAGCAATATTGGACTT----A--A--A-GGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * *
970644 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACAAAGGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * *
970693 GCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT----A--A--A-GGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* * * * * *
970736 GCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACAAAGGT
1 GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
* *
970785 GCCAATATGCTGATTCAAGGCCAGCGATATTGG
1 GCCAATATGCTGATTCAAGGCCAACGACATTGG
970818 ACCTAAAGGT
Statistics
Matches: 571, Mismatches: 78, Indels: 86
0.78 0.11 0.12
Matches are distributed among these distances:
38 19 0.03
39 1 0.00
40 1 0.00
41 1 0.00
42 35 0.06
43 121 0.21
44 6 0.01
45 4 0.01
46 6 0.01
47 4 0.01
48 103 0.18
49 111 0.19
50 1 0.00
51 2 0.00
52 76 0.13
53 80 0.14
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.24
Consensus pattern (52 bp):
GCCAATATGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATGACGAGGGC
Found at i:970337 original size:43 final size:43
Alignment explanation
Indices: 970276--970867 Score: 512
Period size: 43 Copynumber: 13.1 Consensus size: 43
970266 TAAAGATGAC
* * *
970276 AAAGGCGCCAATATGCTGATTCAATGCCAGCAATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
970319 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
970362 AAAGACAAGGTGCCAATATGCTGATTCAAGGCTAGCGACATTGGTCTT
1 ----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
970410 AAAGACAAGGTGCCAATATGCTGATTCAA-G-CA---ATATTGGACTT
1 ----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
970453 AAAGGTGCCAATGTGCTGATTTAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
970496 AAAGACAAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTT
1 ----A-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* ** * *
970544 -AAGGTGCCAATGTGCTGATTCAAGGCCAATGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
970586 AAAGATGACAAAGGCACCAATATGCTAATTCAAGGCCAGCAATATTGGACTT
1 AAAG--G-----TG--CCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
970638 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
970681 AAAGACAAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
970730 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
970773 AAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACCT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
*
970822 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
970865 AAA
1 AAA
970868 AGAAGATGCC
Statistics
Matches: 454, Mismatches: 58, Indels: 74
0.77 0.10 0.13
Matches are distributed among these distances:
38 21 0.05
39 2 0.00
40 2 0.00
42 37 0.08
43 170 0.37
45 2 0.00
46 1 0.00
47 3 0.01
48 104 0.23
49 77 0.17
50 2 0.00
52 33 0.07
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:970365 original size:95 final size:95
Alignment explanation
Indices: 970128--970439 Score: 344
Period size: 101 Copynumber: 3.2 Consensus size: 95
970118 TGACGAGGGC
* * * * *
970128 GCCAATATGCTGATTCAAGGCCAACGACATTGGGTTTTAAAGCTGACGAGGGCGCCAATATGCTG
1 GCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGATGAC-AAGGCGCCAATATGCTG
*
970193 ATTCAAGGCCAGCGATACTGGTCTTAAAGATGAAAGT
64 ATTCAAGGCCAGCGATATTGGTCTT-AA-A-G--AGT
* *
970230 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGACCTAAAGATGACAAAGGCGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGAC-AAGGCGCCAATATGCTGA
* * *
970295 TTCAATGCCAGCAATATTGGACTTAAAG-GT
65 TTCAAGGCCAGCGATATTGGTCTTAAAGAGT
* *
970325 GCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTT-AA-A-GACAAGGTGCCAATATGCTGAT
1 GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAGGCGCCAATATGCTGAT
* *
970387 TCAAGGCTAGCGACATTGGTCTTAAAGACAAGGT
66 TCAAGGCCAGCGATATTGGTCTTAAAG---A-GT
*
970421 GCCAATATGCTGATTCAAG
1 GCCAATGTGCTGATTCAAG
970440 CAATATTGGA
Statistics
Matches: 183, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
91 40 0.22
92 3 0.02
93 1 0.01
94 2 0.01
95 36 0.20
96 20 0.11
98 1 0.01
99 1 0.01
100 2 0.01
101 48 0.26
102 29 0.16
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (95 bp):
GCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGACAAGGCGCCAATATGCTGAT
TCAAGGCCAGCGATATTGGTCTTAAAGAGT
Found at i:970731 original size:92 final size:92
Alignment explanation
Indices: 970319--970867 Score: 790
Period size: 92 Copynumber: 6.0 Consensus size: 92
970309 TATTGGACTT
* * * * *
970319 AAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGTCTTAAAGACAAGGTGCCAATATGCT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATGTGCT
*
970384 GATTCAAGGCTAGCGACATTGGTCTTAAAGAC
61 GATTCAAGGCCAGCGACATTGGTCTTAAAGAC
*
970416 -AAGGTGCCAATATGCTGATTCAA-G-CA---ATATTGGACTTAAAGGTGCCAATGTGCTGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
970475 AAGGCCAGCGACATTGGTCTTAAAGAC
66 AAGGCCAGCGACATTGGTCTTAAAGAC
* *
970502 -AAGGTGCCAATATGCTGATTCAAGGCCAACAATATTGGACTT-AAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
**
970565 AAGGCCAATGACATTGGTCTTAAAGATGAC
66 AAGGCCAGCGACATTGGTCTT-AA-A-GAC
** * *
970595 AAAGGCACCAATATGCTAATTCAAGGCCAGCAATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
970660 AAGGCCAGCGACATTGGTCTTAAAGAC
66 AAGGCCAGCGACATTGGTCTTAAAGAC
* *
970687 AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGTTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
970752 AAGGCCAGCGACATTGGTCTTAAAGAC
66 AAGGCCAGCGACATTGGTCTTAAAGAC
*
970779 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACCTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
* *
970844 AAGGCCAGCGATATTGGACTTAAA
66 AAGGCCAGCGACATTGGTCTTAAA
970868 AGAAGATGCC
Statistics
Matches: 418, Mismatches: 24, Indels: 25
0.90 0.05 0.05
Matches are distributed among these distances:
86 68 0.16
87 2 0.00
88 2 0.00
90 39 0.09
91 22 0.05
92 176 0.42
93 4 0.01
94 42 0.10
95 41 0.10
96 22 0.05
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
AAGGCCAGCGACATTGGTCTTAAAGAC
Found at i:971071 original size:30 final size:30
Alignment explanation
Indices: 971020--971119 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
971010 CCATGGCGTT
*
971020 GTGGACTTTGGAGAAAAAATGCCACTAAGTC
1 GTGGACTTTGG-GAAAAAATGCCACTGAGTC
*
971051 GTGGACTTTGGGACAAAATGCCACTGAGTC
1 GTGGACTTTGGGAAAAAATGCCACTGAGTC
* *
971081 GTGGGCTTTGGGATAAAATGCCACTGAGTC
1 GTGGACTTTGGGAAAAAATGCCACTGAGTC
971111 GTGGACTTT
1 GTGGACTTT
971120 AAGAAAGTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 53 0.83
31 11 0.17
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.26
Consensus pattern (30 bp):
GTGGACTTTGGGAAAAAATGCCACTGAGTC
Found at i:983229 original size:23 final size:23
Alignment explanation
Indices: 983202--983246 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
983192 GCATTCAACC
*
983202 TTGGGTTACAATCTCTT-AAGAGT
1 TTGGGATACAAT-TCTTGAAGAGT
*
983225 TTGGGATATAATTCTTGAAGAG
1 TTGGGATACAATTCTTGAAGAG
983247 ATTGTGAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (23 bp):
TTGGGATACAATTCTTGAAGAGT
Found at i:983629 original size:32 final size:32
Alignment explanation
Indices: 983550--983673 Score: 153
Period size: 32 Copynumber: 3.8 Consensus size: 32
983540 CAGAAGGAGA
983550 TGCCACCAACTTGTGTGGGCTTTAGAGGGAC-AGT
1 TGCCACCAACTTGTGTGGGCTTTAGA---ACAAGT
* * *
983584 TGCCACCAGCTTGTATGGGCTTTAGAACAAGG
1 TGCCACCAACTTGTGTGGGCTTTAGAACAAGT
983616 TGCCACCAACTTGTGTGGGCTTTAGAA-AACGT
1 TGCCACCAACTTGTGTGGGCTTTAGAACAA-GT
* *
983648 TTCCACCAGCTTGTGTGGGCTTTAGA
1 TGCCACCAACTTGTGTGGGCTTTAGA
983674 GGGGGTGTCA
Statistics
Matches: 80, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
31 4 0.05
32 52 0.65
34 24 0.30
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTAGAACAAGT
Found at i:983632 original size:66 final size:64
Alignment explanation
Indices: 983550--983673 Score: 194
Period size: 64 Copynumber: 1.9 Consensus size: 64
983540 CAGAAGGAGA
**
983550 TGCCACCAACTTGTGTGGGCTTTAGAGGGACAGTTGCCACCAGCTTGTATGGGCTTTAGAACAAG
1 TGCCACCAACTTGTGTGGGCTTTAGA-AAAC-GTTGCCACCAGCTTGTATGGGCTTTAGAACAAG
983615 G
64 G
* *
983616 TGCCACCAACTTGTGTGGGCTTTAGAAAACGTTTCCACCAGCTTGTGTGGGCTTTAGA
1 TGCCACCAACTTGTGTGGGCTTTAGAAAACGTTGCCACCAGCTTGTATGGGCTTTAGA
983674 GGGGGTGTCA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
64 26 0.48
65 2 0.04
66 26 0.48
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (64 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAACGTTGCCACCAGCTTGTATGGGCTTTAGAACAAGG
Found at i:983738 original size:28 final size:28
Alignment explanation
Indices: 983682--984115 Score: 208
Period size: 28 Copynumber: 14.8 Consensus size: 28
983672 GAGGGGGTGT
983682 CACTAACTTGTGCGGGCTTT-AAAAGGATGC
1 CACTAACTTGT--GGGCTTTGAAAA-GATGC
*
983712 CACTAACTTGTAGGCTTTGAAAAGATGC
1 CACTAACTTGTGGGCTTTGAAAAGATGC
* * *
983740 CACTGACTTGTGGGCTTTGAAAGGCTGC
1 CACTAACTTGTGGGCTTTGAAAAGATGC
* * *
983768 CACTGACTTGTGGGCTTT-AAAAGGGTGT
1 CACTAACTTGTGGGCTTTGAAAA-GATGC
* * **
983796 AACTGACTCATGGGCTTTGAAAAGAAGATGC
1 CACTAACTTGTGGGCTTTG--AA-AAGATGC
* * ** *
983827 CACCAACTTGTGTGGGTTTGAAGGGGGTTGC
1 CACTAACTTGTG-GGCTTTGAA--AAGATGC
* * *
983858 CACTGACCTGTGTGGACTTTGAAAAAGGTTGC
1 CACT-AACT-TGTGGGCTTTG-AAAA-GATGC
** * * *
983890 CACCGACTTCTGTAGCCTTTAGAGAAAGGTGC
1 CACTAAC-T-TGTGGGCTTT-GA-AAAGATGC
* *
983922 CACTAACTTGTGGGCTTTGAAAGGGTGC
1 CACTAACTTGTGGGCTTTGAAAAGATGC
* ** *
983950 CAC-AGAGTTGTGGGCTTAAAAAATATGC
1 CACTA-ACTTGTGGGCTTTGAAAAGATGC
* * * * *
983978 CACTGATTTTTGGACTTTGAAAGGATGC
1 CACTAACTTGTGGGCTTTGAAAAGATGC
* * *
984006 CACTGACTTGTGGTCTTTGAAAAGGTGC
1 CACTAACTTGTGGGCTTTGAAAAGATGC
** ** ** *
984034 CACTGCCTTGTGAACTTTGAATGGGTGC
1 CACTAACTTGTGGGCTTTGAAAAGATGC
*
984062 CACTAACTCGTGGGCTTTGAAAAAAAGATGC
1 CACTAACTTGTGGGCTTTG---AAAAGATGC
*
984093 CACCAACTTGTGTGGGCTTTGAA
1 CACTAAC-T-TGTGGGCTTTGAA
984116 GGGGGTTGCT
Statistics
Matches: 308, Mismatches: 74, Indels: 44
0.72 0.17 0.10
Matches are distributed among these distances:
27 4 0.01
28 177 0.57
29 6 0.02
30 23 0.07
31 34 0.11
32 44 0.14
33 20 0.06
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.28
Consensus pattern (28 bp):
CACTAACTTGTGGGCTTTGAAAAGATGC
Found at i:983757 original size:56 final size:56
Alignment explanation
Indices: 983677--984084 Score: 289
Period size: 56 Copynumber: 7.0 Consensus size: 56
983667 CTTTAGAGGG
* * * *
983677 GGTGTCACTAACTTGTGCGGGCTTTAAAAGGATGCCACTAACTTGTAGGCTTTGAAAA
1 GGTGCCACTGACTTGT--GGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
* * *
983735 GATGCCACTGACTTGTGGGCTTTGAAAGGCTGCCACTGACTTGTGGGCTTT-AAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
** ** * * **
983790 GGGTGTAACTGACTCATGGGCTTTGAAAAGAAGATGCCACCAACTTGTGTGGGTTTGAAGGG
1 -GGTGCCACTGACTTGTGGGCTTTG-AAAG--GATGCCACTAACTTGTG-GGCTTTGAA-AA
* * ** * *
983852 GGTTGCCACTGACCTGTGTGGACTTTGAAAAAGGTTGCCACCGACTTCTGTAGCCTTTAGAGAAA
1 GG-TGCCACTGA-CT-TGTGGGCTTTG--AAAGGATGCCACTAAC-T-TGTGGGCTTT-GA-AAA
* * * **
983917 GGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCAC-AGAGTTGTGGGCTTAAAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTA-ACTTGTGGGCTTTGAAAA
** * * * * *
983973 TATGCCACTGATTTTTGGACTTTGAAAGGATGCCACTGACTTGTGGTCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
* ** * * *
984029 GGTGCCACTGCCTTGTGAACTTTGAATGGGTGCCACTAACTCGTGGGCTTTGAAAA
1 GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
984085 AAAGATGCCA
Statistics
Matches: 271, Mismatches: 62, Indels: 36
0.73 0.17 0.10
Matches are distributed among these distances:
55 4 0.01
56 141 0.52
57 5 0.02
58 20 0.07
59 15 0.06
60 17 0.06
61 4 0.01
62 17 0.06
63 14 0.05
64 21 0.08
65 12 0.04
66 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (56 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTAACTTGTGGGCTTTGAAAA
Found at i:984217 original size:27 final size:28
Alignment explanation
Indices: 984157--984224 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
984147 AAAGGGTTAG
* *
984157 AGAAGGGTGCCATTGACTTGTGGGCTTT
1 AGAAGGGTGCCACTGAATTGTGGGCTTT
984185 AGAAGGGTGCCACT-AATTGTGGG-TTT
1 AGAAGGGTGCCACTGAATTGTGGGCTTT
*
984211 TGAAAGGGTGCCAC
1 AG-AAGGGTGCCAC
984225 GGAGTTATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 4 0.11
27 19 0.53
28 13 0.36
ACGTcount: A:0.22, C:0.15, G:0.35, T:0.28
Consensus pattern (28 bp):
AGAAGGGTGCCACTGAATTGTGGGCTTT
Found at i:984247 original size:27 final size:27
Alignment explanation
Indices: 984217--984380 Score: 184
Period size: 27 Copynumber: 6.1 Consensus size: 27
984207 GTTTTGAAAG
984217 GGTGCCACGGAGTTATGGACTTAAAAA
1 GGTGCCACGGAGTTATGGACTTAAAAA
984244 GGTGCCACGGAGTTATGGACTTAAAAA
1 GGTGCCACGGAGTTATGGACTTAAAAA
* * *
984271 GATGCCACGGAGTTGTGGACTTAAAAG
1 GGTGCCACGGAGTTATGGACTTAAAAA
* ** * * *
984298 GGTACCACAAAGTTGTGGATTTAAAAG
1 GGTGCCACGGAGTTATGGACTTAAAAA
* * ** **
984325 GGTGCCACGAAGTTGTGGAAATAAATG
1 GGTGCCACGGAGTTATGGACTTAAAAA
*
984352 GGTGCCACGGAGTTATGAACTTAAAAA
1 GGTGCCACGGAGTTATGGACTTAAAAA
984379 GG
1 GG
984381 GAAGGTGCCA
Statistics
Matches: 117, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 117 1.00
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (27 bp):
GGTGCCACGGAGTTATGGACTTAAAAA
Found at i:984396 original size:32 final size:32
Alignment explanation
Indices: 984352--984531 Score: 145
Period size: 32 Copynumber: 5.7 Consensus size: 32
984342 GAAATAAATG
* *
984352 GGTGCCACGGAGTTATGAACTTAAAAAGGGAA
1 GGTGCCATGGAGTTGTGAACTTAAAAAGGGAA
984384 GGTGCCATGGAG-T-TG-ACTT-AAAAGGGAA
1 GGTGCCATGGAGTTGTGAACTTAAAAAGGGAA
* *** * *
984412 GATGCCACAAAGTTGTGGACTTTAAAAGGGAA
1 GGTGCCATGGAGTTGTGAACTTAAAAAGGGAA
* * * * *
984444 GCTGCCATTGAGTTGT-AGACTTTAATAGGAAAA
1 GGTGCCATGGAGTTGTGA-ACTTAAAAAGG-GAA
* *
984477 GGTTGCCATGGAGTTGTGGACTTAAAAAAGGAA
1 GG-TGCCATGGAGTTGTGAACTTAAAAAGGGAA
* *
984510 GGTGCTATGGAGTTGTGGACTT
1 GGTGCCATGGAGTTGTGAACTT
984532 TAACAGAAAA
Statistics
Matches: 120, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
28 17 0.14
29 5 0.04
30 4 0.03
31 5 0.04
32 61 0.51
33 7 0.06
34 21 0.17
ACGTcount: A:0.32, C:0.11, G:0.32, T:0.25
Consensus pattern (32 bp):
GGTGCCATGGAGTTGTGAACTTAAAAAGGGAA
Found at i:984491 original size:34 final size:34
Alignment explanation
Indices: 984422--984571 Score: 157
Period size: 34 Copynumber: 4.5 Consensus size: 34
984412 GATGCCACAA
* * *
984422 AGTTGTGGACTTTAAAAGG-GAA-GCTGCCATTG
1 AGTTGTGGACTTTAAAAGGAAAAGGTTGCCATGG
* *
984454 AGTTGTAGACTTTAATAGGAAAAGGTTGCCATGG
1 AGTTGTGGACTTTAAAAGGAAAAGGTTGCCATGG
* *
984488 AGTTGTGGACTTAAAAAAGG--AAGG-TGCTATGG
1 AGTTGTGGACTT-TAAAAGGAAAAGGTTGCCATGG
* * *
984520 AGTTGTGGACTTTAACAGAAAAAGGTTGCCACGG
1 AGTTGTGGACTTTAAAAGGAAAAGGTTGCCATGG
984554 AGTTGTGGACTTTGAAAA
1 AGTTGTGGACTTT-AAAA
984572 AAAATGCCAC
Statistics
Matches: 96, Mismatches: 15, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
31 4 0.04
32 36 0.38
33 10 0.10
34 38 0.40
35 8 0.08
ACGTcount: A:0.32, C:0.10, G:0.31, T:0.27
Consensus pattern (34 bp):
AGTTGTGGACTTTAAAAGGAAAAGGTTGCCATGG
Found at i:984493 original size:66 final size:66
Alignment explanation
Indices: 984422--984572 Score: 212
Period size: 66 Copynumber: 2.3 Consensus size: 66
984412 GATGCCACAA
* * * * *
984422 AGTTGTGGACTTTAAAAGGGAAGCTGCCATTGAGTTGTAGACTTTAATAGGAAAAGGTTGCCATG
1 AGTTGTGGACTTTAAAAAGGAAGCTGCCATGGAGTTGTAGACTTTAACAGAAAAAGGTTGCCACG
984487 G
66 G
* * * *
984488 AGTTGTGGACTTAAAAAAGGAAGGTGCTATGGAGTTGTGGACTTTAACAGAAAAAGGTTGCCACG
1 AGTTGTGGACTTTAAAAAGGAAGCTGCCATGGAGTTGTAGACTTTAACAGAAAAAGGTTGCCACG
984553 G
66 G
984554 AGTTGTGGACTTTGAAAAA
1 AGTTGTGGACTTT-AAAAA
984573 AAATGCCACT
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
66 69 0.93
67 5 0.07
ACGTcount: A:0.32, C:0.10, G:0.30, T:0.27
Consensus pattern (66 bp):
AGTTGTGGACTTTAAAAAGGAAGCTGCCATGGAGTTGTAGACTTTAACAGAAAAAGGTTGCCACG
G
Found at i:992127 original size:166 final size:166
Alignment explanation
Indices: 991947--992315 Score: 433
Period size: 165 Copynumber: 2.2 Consensus size: 166
991937 AAAATTTAAT
* ****
991947 TCATTTTCATGAGTTTTTGATTTTTTTCCTTGCAATTTTTTTATTTTTGAAATACGGAGTTTTCC
1 TCATTTTCATGAGTTTTTGATTTTTTTCCTTGAAATTCCCCTATTTTTGAAATACGGAGTTTTCC
* ** *
992012 ACCCCATAAATTTTTTGGGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAATATTATT
66 ACCCCATAAATTTTTTGGGAGGAACTTTCTTGGCTTTTAATTTTTAAAATTCATCAAATATTATT
* * * * *
992077 CTTTATTTCATATT-AAGCTAGTTTTTAAAAATTTA-
131 ATTTATTTAATATTCAAGC-AGGTTTCAAAAATTCAC
* * * *
992112 TGAGTTTTTATGAGTTTTTGA-ATTTTTCCTT-AACATTCCCCTATTTTTGAAATATGGAGTTTT
1 TCA-TTTTCATGAGTTTTTGATTTTTTTCCTTGAA-ATTCCCCTATTTTTGAAATACGGAGTTTT
** **** *
992175 TTACTTTGTAAATTTTTTGGGAGGAACTTTCTTGGCTTTTAATTTTTAAAATTCATCAAATATTG
64 CCACCCCATAAATTTTTTGGGAGGAACTTTCTTGGCTTTTAATTTTTAAAATTCATCAAATATTA
*
992240 TTATTTATTTAATATTCAATCAGGTTTCAAAAATTCAC
129 TTATTTATTTAATATTCAAGCAGGTTTCAAAAATTCAC
*
992278 TCATTTTCATGAGTTTTTAATTTTTTT-CTTGAAATTCC
1 TCATTTTCATGAGTTTTTGATTTTTTTCCTTGAAATTCC
992316 TTTTTTCCCG
Statistics
Matches: 168, Mismatches: 30, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
164 1 0.01
165 139 0.83
166 28 0.17
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.52
Consensus pattern (166 bp):
TCATTTTCATGAGTTTTTGATTTTTTTCCTTGAAATTCCCCTATTTTTGAAATACGGAGTTTTCC
ACCCCATAAATTTTTTGGGAGGAACTTTCTTGGCTTTTAATTTTTAAAATTCATCAAATATTATT
ATTTATTTAATATTCAAGCAGGTTTCAAAAATTCAC
Found at i:995055 original size:13 final size:13
Alignment explanation
Indices: 995037--995062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
995027 TACAGCAAGT
995037 ATGTATCGATACA
1 ATGTATCGATACA
995050 ATGTATCGATACA
1 ATGTATCGATACA
995063 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:997322 original size:21 final size:22
Alignment explanation
Indices: 997276--997320 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
997266 TTGCAAGTTG
997276 AAATAAAGAAGTTAGCTAATGA
1 AAATAAAGAAGTTAGCTAATGA
*
997298 AAATAATG-AGTTAGCTAA-GA
1 AAATAAAGAAGTTAGCTAATGA
997318 AAA
1 AAA
997321 ATGAAAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 10 0.45
22 7 0.32
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (22 bp):
AAATAAAGAAGTTAGCTAATGA
Found at i:999144 original size:15 final size:15
Alignment explanation
Indices: 999124--999154 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
999114 TAAAAATGTC
*
999124 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
999139 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
999154 C
1 C
999155 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1001239 original size:20 final size:20
Alignment explanation
Indices: 1001168--1001245 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
1001158 AATGTCCAAA
*
1001168 ATGTATCGATACATATTTCT
1 ATGTATCGATACATTTTTCT
* *
1001188 GTGTATCGATACATTTGGAAATTCA
1 ATGTATCGATACATTT-----TTCT
1001213 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1001233 TTGTATCGATACA
1 ATGTATCGATACA
1001246 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 29 0.62
25 18 0.38
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1001409 original size:20 final size:20
Alignment explanation
Indices: 1001366--1001411 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1001356 AAATCTTTTG
1001366 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1001387 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1001407 CAAAA
1 CAAAA
1001412 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1005554 original size:20 final size:19
Alignment explanation
Indices: 1005529--1005619 Score: 76
Period size: 20 Copynumber: 4.6 Consensus size: 19
1005519 ACCCTTGAAA
1005529 GTATCGATACATATCCAGAT
1 GTATCGATACATATCCA-AT
* * **
1005549 GTATCGATATATAATGCTTT
1 GTATCGATACAT-ATCCAAT
* * *
1005569 GTATCGATACATGTTCATT
1 GTATCGATACATATCCAAT
1005588 GTATCGATACATA-CTCAATT
1 GTATCGATACATATC-CAA-T
1005608 GTATCGATACAT
1 GTATCGATACAT
1005620 GAAAGTGGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
19 18 0.32
20 36 0.63
21 3 0.05
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
GTATCGATACATATCCAAT
Found at i:1005591 original size:19 final size:20
Alignment explanation
Indices: 1005567--1005620 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
1005557 ATATAATGCT
*
1005567 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGCTCAA
*
1005586 TTGTATCGATACATACTCAA
1 TTGTATCGATACATGCTCAA
1005606 TTGTATCGATACATG
1 TTGTATCGATACATG
1005621 AAAGTGGTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
TTGTATCGATACATGCTCAA
Found at i:1013359 original size:19 final size:20
Alignment explanation
Indices: 1013335--1013384 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1013325 GATTCAATGC
1013335 ATCGATACATGCTC-ATTGT
1 ATCGATACATGCTCAATTGT
***
1013354 ATCGATACGCACTCAATTGT
1 ATCGATACATGCTCAATTGT
*
1013374 ATTGATACATG
1 ATCGATACATG
1013385 AAACTATCAG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (20 bp):
ATCGATACATGCTCAATTGT
Found at i:1015122 original size:13 final size:13
Alignment explanation
Indices: 1015104--1015130 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1015094 TATAAGGAAC
1015104 ATGTATCGATACA
1 ATGTATCGATACA
1015117 ATGTATCGATACA
1 ATGTATCGATACA
1015130 A
1 A
1015131 AGCATAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1017680 original size:20 final size:20
Alignment explanation
Indices: 1017655--1017710 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
1017645 TTTTTCAGAT
1017655 TGTATCGATACATTCTTCAA
1 TGTATCGATACATTCTTCAA
1017675 TGTATCGATACATTCTTCAA
1 TGTATCGATACATTCTTCAA
1017695 TGTATCGATACATTCT
1 TGTATCGATACATTCT
1017711 GGAAAATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATTCTTCAA
Found at i:1019987 original size:34 final size:32
Alignment explanation
Indices: 1019944--1020008 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
1019934 TACAAGCCAA
1019944 TGTATCGATACAAT-TTGGTCATGTATCGATACAT
1 TGTATCGATAC-ATCTT-GT-ATGTATCGATACAT
1019978 TGTATCGATACATCTTGTATGTATCGATACA
1 TGTATCGATACATCTTGTATGTATCGATACA
1020009 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 13 0.43
33 4 0.13
34 13 0.43
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATCTTGTATGTATCGATACAT
Found at i:1019997 original size:15 final size:13
Alignment explanation
Indices: 1019965--1019990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1019955 AATTTGGTCA
1019965 TGTATCGATACAT
1 TGTATCGATACAT
1019978 TGTATCGATACAT
1 TGTATCGATACAT
1019991 CTTGTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1020108 original size:13 final size:13
Alignment explanation
Indices: 1020090--1020114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1020080 ACATTTGGTC
1020090 ATGTATCAATACA
1 ATGTATCAATACA
1020103 ATGTATCAATAC
1 ATGTATCAATAC
1020115 TGTGCATTAT
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:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (13 bp):
ATGTATCAATACA
Found at i:1020649 original size:24 final size:23
Alignment explanation
Indices: 1020617--1020678 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 23
1020607 CATTTTCCTT
1020617 TTCTCTCCCCCTTAATCAAAAAAA
1 TTCTCTCCCCCTTAAT-AAAAAAA
*
1020641 TTCTCT-CCCCTT--TAATAAAA
1 TTCTCTCCCCCTTAATAAAAAAA
1020661 TT-TCTCCCCCTTAATAAA
1 TTCTCTCCCCCTTAATAAA
1020679 CAATTTCCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 3 0.09
20 14 0.42
21 1 0.03
22 3 0.09
23 6 0.18
24 6 0.18
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (23 bp):
TTCTCTCCCCCTTAATAAAAAAA
Found at i:1020668 original size:19 final size:20
Alignment explanation
Indices: 1020617--1020678 Score: 72
Period size: 19 Copynumber: 3.0 Consensus size: 20
1020607 CATTTTCCTT
1020617 TTCTCTCCCCCTTAATCAAAAAAA
1 TTCTCTCCCCCTTAAT----AAAA
*
1020641 TTCTCTCCCCTTTAATAAAA
1 TTCTCTCCCCCTTAATAAAA
1020661 TT-TCTCCCCCTTAATAAA
1 TTCTCTCCCCCTTAATAAA
1020679 CAATTTCCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 15 0.42
20 6 0.17
24 15 0.42
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (20 bp):
TTCTCTCCCCCTTAATAAAA
Found at i:1022084 original size:21 final size:21
Alignment explanation
Indices: 1022055--1022095 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1022045 TGTGAGTGTG
*
1022055 GGGGCTGCCCGGTTGCGACCTA
1 GGGGCTG-CCGGTCGCGACCTA
1022077 GGGG-TGCCGGTCGCGACCT
1 GGGGCTGCCGGTCGCGACCT
1022096 GGTGAGTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 2 0.11
22 4 0.22
ACGTcount: A:0.07, C:0.32, G:0.44, T:0.17
Consensus pattern (21 bp):
GGGGCTGCCGGTCGCGACCTA
Found at i:1029369 original size:13 final size:13
Alignment explanation
Indices: 1029351--1029407 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1029341 CATAAAATGT
1029351 TGTATCGATACAA
1 TGTATCGATACAA
1029364 TGTATCGATACATAA
1 TGTATCGATAC--AA
1029379 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1029396 TGTATCGATACA
1 TGTATCGATACA
1029408 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1029388 original size:19 final size:18
Alignment explanation
Indices: 1029364--1029426 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1029354 ATCGATACAA
1029364 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1029383 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1029396 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1029415 TGTATCGATACA
1 TGTATCGATACA
1029427 ATGTAAGCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1029389 original size:32 final size:32
Alignment explanation
Indices: 1029331--1029431 Score: 166
Period size: 32 Copynumber: 3.1 Consensus size: 32
1029321 TTCAACGATT
* *
1029331 TGTATTGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1029364 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1029396 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1029428 TGTA
1 TGTA
1029432 AGCTACTACC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 53 0.82
33 12 0.18
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1029487 original size:13 final size:13
Alignment explanation
Indices: 1029469--1029493 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1029459 ATTACTCAAA
1029469 TGTATCGATACAT
1 TGTATCGATACAT
1029482 TGTATCGATACA
1 TGTATCGATACA
1029494 CTGATCCTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1029544 original size:52 final size:52
Alignment explanation
Indices: 1029502--1029682 Score: 317
Period size: 52 Copynumber: 3.5 Consensus size: 52
1029492 CACTGATCCT
*
1029502 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATTGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1029554 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1029606 TGTATCGATACATGCAGGCAAATTTACCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
1029658 TGTATCGATACATGCAAGCGAATTT
1 TGTATCGATACATGCAGGCAAATTT
1029683 TCATATTTCG
Statistics
Matches: 124, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 124 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1045043 original size:29 final size:29
Alignment explanation
Indices: 1044976--1045150 Score: 210
Period size: 30 Copynumber: 6.0 Consensus size: 29
1044966 TCACCCTTCA
1044976 AAAGCCCACAAGTCAGTGGCATCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTT-C
1045006 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1045035 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
1045062 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
1045092 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1045121 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1045151 TTTTGTAAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
27 22 0.18
28 1 0.01
29 45 0.36
30 56 0.45
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Found at i:1045078 original size:86 final size:87
Alignment explanation
Indices: 1044970--1045141 Score: 258
Period size: 86 Copynumber: 2.0 Consensus size: 87
1044960 CATTCCTCAC
* * *
1044970 CCTTCAAAAGCCCACAAGTCAGTGGCA-TCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTT
1 CCTTCAAAAGCCCACAAATCAGTGGCACCCTTTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTC
*
1045034 CAAAGTCCACAAGTCAGTGGCAA
65 CAAAGTCCACAACTCAGTGGCAA
* *
1045057 CCTTC-AAAGCCCACAAATCAGTGGCACCCTTTTTCGAAGCCCACAAGTCGGTGGCATCTTTTCC
1 CCTTCAAAAGCCCACAAATCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCC
*
1045121 AAAGTCCACAACTCCGTGGCA
66 AAAGTCCACAACTCAGTGGCA
1045142 CTCTTTTTCT
Statistics
Matches: 77, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
86 66 0.86
87 11 0.14
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.23
Consensus pattern (87 bp):
CCTTCAAAAGCCCACAAATCAGTGGCACCCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCC
AAAGTCCACAACTCAGTGGCAA
Found at i:1045167 original size:35 final size:34
Alignment explanation
Indices: 1045126--1045199 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 34
1045116 TTTCCAAAGT
** *
1045126 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCGTAACACTCTTTTTCCTTT-TAAGC
*
1045161 TCACAACTCCGTAACACTCTTTTTCCTTTTAAGC
1 CCACAACTCCGTAACACTCTTTTTCCTTTTAAGC
1045195 CCACA
1 CCACA
1045200 CAAGTCGGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.22, C:0.34, G:0.09, T:0.35
Consensus pattern (34 bp):
CCACAACTCCGTAACACTCTTTTTCCTTTTAAGC
Found at i:1045296 original size:33 final size:33
Alignment explanation
Indices: 1045191--1045379 Score: 246
Period size: 33 Copynumber: 5.8 Consensus size: 33
1045181 TTTTCCTTTT
1045191 AAGCCCACACAAGTCGGTGGCAACCCTTCTT--A
1 AAGCCCACACAAGTCGGTGGCAACCCTT-TTCCA
**
1045223 AAGCCCACACAAGTTAGTGGCAACCC--TTCCAA
1 AAGCCCACACAAGTCGGTGGCAACCCTTTTCC-A
1045255 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
1 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
* *
1045288 AAGCCCACACAAGTCGGTGGCAACCC--CTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
* * * *
1045319 AAGCCCACACAAGTTGGTGGCAACCATTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
1045352 AAGCCCACACAAGTCGGTGGCAACCCTT
1 AAGCCCACACAAGTCGGTGGCAACCCTT
1045380 CTAAGCCCAA
Statistics
Matches: 140, Mismatches: 10, Indels: 13
0.86 0.06 0.08
Matches are distributed among these distances:
29 2 0.01
31 27 0.19
32 49 0.35
33 58 0.41
34 4 0.03
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.17
Consensus pattern (33 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
Found at i:1045312 original size:97 final size:97
Alignment explanation
Indices: 1045191--1045379 Score: 326
Period size: 97 Copynumber: 1.9 Consensus size: 97
1045181 TTTTCCTTTT
* *
1045191 AAGCCCACACAAGTCGGTGGCAACCCTTCTTAAAGCCCACACAAGTTAGTGGCAACCCTTC-CAA
1 AAGCCCACACAAGTCGGTGGCAACCCCTC-TAAAGCCCACACAAGTTAGTGGCAACCATTCTCAA
1045255 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
65 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCA
* *
1045288 AAGCCCACACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTTGGTGGCAACCATTCTCTAA
1 AAGCCCACACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTTAGTGGCAACCATTCTCAAA
1045353 AGCCCACACAAGTCGGTGGCAACCCTT
66 AGCCCACACAAGTCGGTGGCAACCCTT
1045380 CTAAGCCCAA
Statistics
Matches: 87, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
96 29 0.33
97 58 0.67
ACGTcount: A:0.30, C:0.35, G:0.19, T:0.17
Consensus pattern (97 bp):
AAGCCCACACAAGTCGGTGGCAACCCCTCTAAAGCCCACACAAGTTAGTGGCAACCATTCTCAAA
AGCCCACACAAGTCGGTGGCAACCCTTTTCCA
Found at i:1045383 original size:64 final size:64
Alignment explanation
Indices: 1045191--1045388 Score: 301
Period size: 64 Copynumber: 3.1 Consensus size: 64
1045181 TTTTCCTTTT
** *
1045191 AAGCCCACACAAGTCGGTGGCAACCCTTCT-TAAAGCCCACACAAGTTAGTGGCAACCCTTCCAA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTT-CTA
* * *
1045255 AAGCCCACACAAGTCGGTGGCAACCCTTTTCCAAAGCCCACACAAGTCGGTGGCAACCCCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTA
* *
1045319 AAGCCCACACAAGTTGGTGGCAACCATTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT-
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTA
1045382 AAGCCCA
1 AAGCCCA
1045389 ATATCGCTGG
Statistics
Matches: 122, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
63 7 0.06
64 89 0.73
65 26 0.21
ACGTcount: A:0.30, C:0.35, G:0.18, T:0.17
Consensus pattern (64 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCTA
Found at i:1045492 original size:43 final size:44
Alignment explanation
Indices: 1045386--1046172 Score: 559
Period size: 43 Copynumber: 16.8 Consensus size: 44
1045376 CCTTCTAAGC
* *
1045386 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCTTCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--CATC---AAGT
* *
1045435 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCC-TCAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
* *
1045478 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-----CATC---AAGT
* * *
1045530 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA--CATTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCA-TCAAGT
*
1045573 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCAC-----CCATC---AAGT
* * * * *
1045625 CCAATGTAGCTGGCCTTGAATTAGCACATTGGTA-CCTTCAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
* *
1045668 CCAATATCGCTGGCCTTGAATCAACATATTGG-AGCCTTTATCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-----CATC---AAGT
* * * *
1045720 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
* *
1045763 CCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTTCCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C----CCATC---AAGT
* * *
1045815 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTCAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
* *
1045858 CCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-----CATC---AAGT
* * * *
1045910 CCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-CCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
*
1045953 CCAATATAGCTGGCCTTGAATCAGCATATTAGCACCTTCATCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--CATC---AAGT
* * * * *
1046002 CCAATGTAGCTGGCATTGAATCAGCACATTGGCA-CCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
* * *
1046045 CCAATATTGCTGGCCTTGAATCAGCATATTGGCAACTTCATCTTTAGGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGC-AC-CCATC---AAGT
* * * * * * *
1046094 TCAATGTAGCTAGCCTTGAATCAGTACATTGGCA-CCTTTAAGT
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
1046137 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1 CCAATATAGCTGGCCTTGAATCAGCATATTGGCACC
1046173 TTTTCCATCT
Statistics
Matches: 586, Mismatches: 90, Indels: 129
0.73 0.11 0.16
Matches are distributed among these distances:
42 1 0.00
43 270 0.46
44 5 0.01
45 2 0.00
46 23 0.04
47 1 0.00
48 3 0.01
49 109 0.19
50 2 0.00
51 2 0.00
52 167 0.28
53 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (44 bp):
CCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCATCAAGT
Found at i:1045548 original size:95 final size:94
Alignment explanation
Indices: 1045376--1046228 Score: 1342
Period size: 95 Copynumber: 9.1 Consensus size: 94
1045366 CGGTGGCAAC
* *
1045376 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TTCTTCTTTAAGTCCAA
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAA
1045439 TGTAGCTGGCCTTGAATCAGCACATTGGCA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1045469 CCCTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCTTTAAGTCCAA
1045534 TGTAGCTGGCCTTGAATCAGCACATTGGCA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1045564 CATTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTT-CATCTTTAAGTCCAA
* *
1045629 TGTAGCTGGCCTTGAATTAGCACATTGGTA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1045659 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAACATATTGG-AGCCTTTATCATCTTTAAGTCCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTT-TCATCTTTAAGTCCA
1045723 ATGTAGCTGGCCTTGAATCAGCACATTGGCA
64 ATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
1045754 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTTCCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTT-CATCTTTAAGTCCAA
1045819 TGTAGCTGGCCTTGAATCAGCACATTGGCA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1045849 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCTTTAAGTCCAA
1045914 TGTAGCTGGCCTTGAATCAGCACATTGGCA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1045944 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTAGCACC--TTCATCTTTAAGTCCAAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAAT
*
1046007 GTAGCTGGCATTGAATCAGCACATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
1046036 CCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCAAC--TTCATCTTTAGGTTCAAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAAT
* *
1046099 GTAGCTAGCCTTGAATCAGTACATTGGCA
66 GTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1046128 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTT-CATCTTTAAGTCCAA
*
1046193 TGTAGCTGGCCTTGAATCAGCACATTGACA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
1046223 TCCTTT
1 -CCTTT
1046229 TTCTCATCTT
Statistics
Matches: 705, Mismatches: 42, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
92 210 0.30
93 4 0.01
94 6 0.01
95 477 0.68
96 8 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (94 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1046264 original size:54 final size:52
Alignment explanation
Indices: 1046129--1046265 Score: 177
Period size: 52 Copynumber: 2.6 Consensus size: 52
1046119 ACATTGGCAC
* *
1046129 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
* *
1046181 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACA-CC-TTTTC-CAT
* * *
1046236 CTTTAAG-CCAATATCGTTGGCCATGAATCA
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCA
1046266 ACATATTGGC
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
52 38 0.52
53 2 0.03
54 23 0.32
55 10 0.14
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (52 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACACCTTTTCCAT
Found at i:1047125 original size:32 final size:32
Alignment explanation
Indices: 1047079--1047173 Score: 136
Period size: 32 Copynumber: 2.9 Consensus size: 32
1047069 ATTTATATCG
**
1047079 ATACATAAAGTGTTGTATCGATACAATGTGTCA
1 ATACAT-AAGTGTTGTATCGATACAATGTAACA
*
1047112 ATACATAAGTGTTGTATCGATACAATGTAACG
1 ATACATAAGTGTTGTATCGATACAATGTAACA
* *
1047144 ATACATAAGTTTTGTATTGATACAATGTAA
1 ATACATAAGTGTTGTATCGATACAATGTAA
1047174 GCTACTGCCA
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 51 0.89
33 6 0.11
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.35
Consensus pattern (32 bp):
ATACATAAGTGTTGTATCGATACAATGTAACA
Found at i:1059458 original size:29 final size:29
Alignment explanation
Indices: 1059388--1059560 Score: 201
Period size: 29 Copynumber: 6.0 Consensus size: 29
1059378 TTCCTCACCC
1059388 TTCAAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTT
1059417 TTCCAAAGCCCACAAGTCAGTGGCATCTTT
1 TT-CAAAGCCCACAAGTCAGTGGCATCTTT
* * *
1059447 TTCAAAGTCCACAAGTCAGTGGCAAC--C
1 TTCAAAGCCCACAAGTCAGTGGCATCTTT
* *
1059474 TTCAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCTTT
* *
1059504 TT-GAAGCCCACAAGTCGGTGGCATCTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTT
* * * *
1059532 TCCAAAGTCCACAACTCCGTGGCA-CTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCTTT
1059560 T
1 T
1059561 CTTTTGTAAG
Statistics
Matches: 123, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
27 22 0.18
28 11 0.09
29 59 0.48
30 31 0.25
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCATCTTT
Found at i:1059515 original size:56 final size:58
Alignment explanation
Indices: 1059388--1059560 Score: 192
Period size: 56 Copynumber: 3.0 Consensus size: 58
1059378 TTCCTCACCC
* * * *
1059388 TTCAAAGCCCACAAGTCAGTGGCATCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAGCCCACAAGTCAGTGGCAAC-TCTTCCAAAGCCCACAAATCAGTGGCACCTTT
*
1059447 TTCAAAGTCCACAAGTCAGTGGCAAC-CTT-CAAAGCCCACAAATCAGTGGCACCCTTT
1 TTCAAAGCCCACAAGTCAGTGGCAACTCTTCCAAAGCCCACAAATCAGTGGCA-CCTTT
* * * * * * *
1059504 TT-GAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCA-CTTT
1 TTCAAAGCCCACAAGTCAGTGGCAACTCTTCCAAAGCCCACAAATCAGTGGCACCTTT
1059560 T
1 T
1059561 CTTTTGTAAG
Statistics
Matches: 98, Mismatches: 13, Indels: 9
0.82 0.11 0.08
Matches are distributed among these distances:
56 45 0.46
57 10 0.10
58 19 0.19
59 24 0.24
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (58 bp):
TTCAAAGCCCACAAGTCAGTGGCAACTCTTCCAAAGCCCACAAATCAGTGGCACCTTT
Found at i:1059532 original size:85 final size:85
Alignment explanation
Indices: 1059386--1059555 Score: 252
Period size: 85 Copynumber: 2.0 Consensus size: 85
1059376 CATTCCTCAC
* * *
1059386 CCTTCAAAGCCCACAAGTCAGTGGCATCTTTTTCCAAAGCCCACAAGTCAGTGGCATCTTTTTCA
1 CCTTCAAAGCCCACAAATCAGTGGCACCTTTTT-CAAAGCCCACAAGTCAGTGGCATCTTTTCCA
*
1059451 AAGTCCACAAGTCAGTGGCAA
65 AAGTCCACAACTCAGTGGCAA
* *
1059472 CCTTCAAAGCCCACAAATCAGTGGCACCCTTTTT-GAAGCCCACAAGTCGGTGGCATCTTTTCCA
1 CCTTCAAAGCCCACAAATCAGTGGCA-CCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCA
*
1059536 AAGTCCACAACTCCGTGGCA
65 AAGTCCACAACTCAGTGGCA
1059556 CTTTTCTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
85 45 0.59
86 25 0.33
87 6 0.08
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.24
Consensus pattern (85 bp):
CCTTCAAAGCCCACAAATCAGTGGCACCTTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAA
AGTCCACAACTCAGTGGCAA
Found at i:1059663 original size:32 final size:32
Alignment explanation
Indices: 1059602--1059799 Score: 221
Period size: 32 Copynumber: 6.2 Consensus size: 32
1059592 TTTTCCTTTT
*
1059602 AAGCCCACACCAGTCGGTGGGGCAACCCTTCTTA
1 AAGCCCACACAAGTCGGT--GGCAACCCTTCTTA
** **
1059636 AAGCCCACACAAGTTAGTGGCAACCCTTCCAA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTTA
1059668 AAG-CCACACACAGTCGGTGGCAACCCTT-TTCCA
1 AAGCCCACACA-AGTCGGTGGCAACCCTTCTT--A
*
1059701 AAGCCCACACAAGTCGGTGGCAACCCCTC-TA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTTA
* *
1059732 AAGCCCACACAAGTTGGTGGC-ACCATTCTCTA
1 AAGCCCACACAAGTCGGTGGCAACCCTTCT-TA
1059764 AAGCCCACAC-AGTCGGTGGCAACCCTTC-T-
1 AAGCCCACACAAGTCGGTGGCAACCCTTCTTA
1059793 AAGCCCA
1 AAGCCCA
1059800 ATATCGCTGG
Statistics
Matches: 141, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
29 7 0.05
30 6 0.04
31 37 0.26
32 48 0.34
33 21 0.15
34 22 0.16
ACGTcount: A:0.28, C:0.36, G:0.19, T:0.17
Consensus pattern (32 bp):
AAGCCCACACAAGTCGGTGGCAACCCTTCTTA
Found at i:1059708 original size:65 final size:64
Alignment explanation
Indices: 1059606--1059791 Score: 213
Period size: 65 Copynumber: 2.9 Consensus size: 64
1059596 CCTTTTAAGC
**
1059606 CCACAC-CAGTCGGTGGGGCAACCCTTCTT-AAAGCCCACACAAGTTAGTGGCAACCCTTCCAAA
1 CCACACACAGTCGGT--GGCAACCCTT-TTCAAAGCCCACACAAGTCGGTGGCAACCCTTCCAAA
1059669 AG
63 AG
* *
1059671 CCACACACAGTCGGTGGCAACCCTTTTCCAAAGCCCACACAAGTCGGTGGCAACCCCT-CTAAAG
1 CCACACACAGTCGGTGGCAACCCTTTT-CAAAGCCCACACAAGTCGGTGGCAACCCTTCCAAAAG
* * *
1059735 CC-CACACAAGTTGGTGGC-ACCATTCTCTAAAGCCCACAC-AGTCGGTGGCAACCCTTC
1 CCACACAC-AGTCGGTGGCAACCCTTTTC-AAAGCCCACACAAGTCGGTGGCAACCCTTC
1059792 TAAGCCCAAT
Statistics
Matches: 107, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
62 17 0.16
63 24 0.22
64 26 0.24
65 32 0.30
66 8 0.07
ACGTcount: A:0.27, C:0.36, G:0.19, T:0.17
Consensus pattern (64 bp):
CCACACACAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCCTTCCAAAAG
Found at i:1060229 original size:94 final size:94
Alignment explanation
Indices: 1059787--1060629 Score: 1106
Period size: 94 Copynumber: 9.1 Consensus size: 94
1059777 CGGTGGCAAC
* *
1059787 CCTTCTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--TTCTTCTTTAAGTCCAA
1 CCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAA
*
1059850 TGTAGCTGGCCTTGAATCAGCACATTGGCC
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1059880 CCCTCAA-TCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCC-A
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCTTTAAGTCCAA
1059943 TGTAGCTGGCCTTGAATCAGCACAATTGGCA
65 TGTAGCTGGCCTTGAATCAGCAC-ATTGGCA
* *
1059974 CATTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACATTTTCCATC-TTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTT-CATCTTTAAGTCCAA
* *
1060038 TGTAG-TGGCCTTGAATTAGCACATTGGTA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* * * *
1060067 CCTTCAAGTCCAATATCGCTGGCCTTGAATCAACATATTGG-AGCTTTCTAATC-TTAAGTCCCA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCTTTAAGT-CCA
1060130 ATGTAGCTGGCCTTGAATCAGCACATTGGCA
64 ATGTAGCTGGCCTTGAATCAGCACATTGGCA
*
1060161 CCTTTAA-TCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTTTCCATCTTTAAGTCC-
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTTT-CATCTTTAAGTCCA
1060224 ATGTAGCTGGCCTTGAATCAGCACATTGGCAA
64 ATGTAGCTGGCCTTGAATCAGCACATTGGC-A
*
1060256 CC-TTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-TCATCTTTAAGTCCAA
1060320 TGT-GCTGGCCTTGAATCAGCACATTGGCA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
* * *
1060349 CCTTTAAGTCC-ATATAGCTTGCCTTGCAATCAGC--ATTAGCACC--TTCATC-TTAAGTCCAA
1 CCTTTAAGTCCAATATCGCTGGCCTTG-AATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAA
*
1060408 TGTAGCTGGCATTGAATCAGCACAATTGGCA
65 TGTAGCTGGCCTTGAATCAGCAC-ATTGGCA
* * *
1060439 CCTTTAAGTCCAATATTGCTGGCCTTG-ATCAGCATATTGGCA-C--TTCATCTTTAGGTTCAAT
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAA-
* *
1060500 GTAGTAGCTAGCCTTGAATCAGTACATTGGCA
65 -T-GTAGCTGGCCTTGAATCAGCACATTGGCA
* *
1060532 CCTTTAAGTCCAATATAGCT-GCCTTGAATCAGC-TATTGGCACCTTTTCCATCTTTAAGT-TAA
1 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTT-CATCTTTAAGTCCAA
*
1060594 TGTAGCTGGCCTTGAATCAGCACATTGACA
65 TGTAGCTGGCCTTGAATCAGCACATTGGCA
1060624 TCCTTT
1 -CCTTT
1060630 TCTCATCTTT
Statistics
Matches: 669, Mismatches: 46, Indels: 70
0.85 0.06 0.09
Matches are distributed among these distances:
88 13 0.02
89 29 0.04
90 26 0.04
91 62 0.09
92 62 0.09
93 170 0.25
94 188 0.28
95 103 0.15
96 16 0.02
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (94 bp):
CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTTCATCTTTAAGTCCAAT
GTAGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1060240 original size:52 final size:50
Alignment explanation
Indices: 1060162--1060680 Score: 256
Period size: 52 Copynumber: 10.9 Consensus size: 50
1060152 ACATTGGCAC
* * *
1060162 CTTTAA-TCCAATATCGCTGGCCTTGAATCAGCATATTGGTACCTTTTTCCAT
1 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCACATTGGCACC-TTTT-CAT
1060214 CTTTAAGTCC-ATGTAGCTGGCCTTGAATCAGCACATTGGCA-------A-
1 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * * *
1060256 CCTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCACATTGGCACCTTT-TCAT
1060308 CTTTAAGTCCAATGTGCTGGCCTTGAATCAGCACATTGGCA------C--
1 CTTTAAGTCCAATGTGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * *
1060350 CTTTAAGTCCATAT-AGCTTGCCTTGCAATCAG--CATTAGCACC--TTCAT
1 CTTTAAGTCCA-ATGTGCTGGCCTTG-AATCAGCACATTGGCACCTTTTCAT
*
1060397 C-TTAAGTCCAATGTAGCTGGCATTGAATCAGCACAATTGGCA------C--
1 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCAC-ATTGGCACCTTTTCAT
* *
1060440 CTTTAAGTCCAATATTGCTGGCCTTG-ATCAGCATATTGGCA-C--TTCAT
1 CTTTAAGTCCAAT-GTGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* * * *
1060487 CTTTAGGTTCAATGTAGTAGCTAGCCTTGAATCAGTACATTGGCA------C--
1 CTTTAAGTCCAA--T-GT-GCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
* *
1060533 CTTTAAGTCCAATATAGCT-GCCTTGAATCAGC-TATTGGCACCTTTTCCAT
1 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCACATTGGCACCTTTT-CAT
* *
1060583 CTTTAAGT-TAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTCTCAT
1 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCACATTGGCA-CC-TTT-TCAT
* * * *
1060636 CTTTAAGCCCATATCGT--TGGCCATGAATCAAC-CATTGGCAGCTTT
1 CTTTAAGTCCA-AT-GTGCTGGCCTTGAATCAGCACATTGGCACCTTT
1060681 ACACTTTTCT
Statistics
Matches: 371, Mismatches: 44, Indels: 106
0.71 0.08 0.20
Matches are distributed among these distances:
41 14 0.04
42 48 0.13
43 49 0.13
44 22 0.06
45 6 0.02
46 25 0.07
47 19 0.05
48 3 0.01
49 17 0.05
50 33 0.09
51 45 0.12
52 55 0.15
53 29 0.08
54 2 0.01
55 2 0.01
56 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (50 bp):
CTTTAAGTCCAATGTGCTGGCCTTGAATCAGCACATTGGCACCTTTTCAT
Found at i:1060373 original size:42 final size:43
Alignment explanation
Indices: 1060308--1060577 Score: 248
Period size: 42 Copynumber: 6.1 Consensus size: 43
1060298 CCTTTGTCAT
*
1060308 CTTTAAGTCCAATGT-GCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
* *
1060350 CTTTAAGTCC-ATATAGCTTGCCTTGCAATCAG--CATTAGCACC
1 CTTTAAGTCCAATATAGCTGGCCTTG-AATCAGCACATTGGCA-C
* *
1060392 TTCATCTTAAGTCCAATGTAGCTGGCATTGAATCAGCACAATTGGCAC
1 --C-T-TTAAGTCCAATATAGCTGGCCTTGAATCAGCAC-ATTGGCAC
* *
1060440 CTTTAAGTCCAATATTGCTGGCCTTG-ATCAGCATATTGGCACTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---C
* * * *
1060485 ATCTTTAGGTTCAATGTAGTAGCTAGCCTTGAATCAGTACATTGGCAC
1 --CTTTAAGTCCAA--TA-TAGCTGGCCTTGAATCAGCACATTGGCAC
*
1060533 CTTTAAGTCCAATATAGCT-GCCTTGAATCAGC-TATTGGCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
1060574 CTTT
1 CTTT
1060578 TCCATCTTTA
Statistics
Matches: 187, Mismatches: 21, Indels: 41
0.75 0.08 0.16
Matches are distributed among these distances:
41 22 0.12
42 39 0.21
43 18 0.10
44 24 0.13
45 3 0.02
46 25 0.13
47 22 0.12
48 3 0.02
49 8 0.04
50 10 0.05
51 13 0.07
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (43 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:1073921 original size:29 final size:29
Alignment explanation
Indices: 1073854--1074028 Score: 210
Period size: 30 Copynumber: 6.0 Consensus size: 29
1073844 TCACCCTTCA
1073854 AAAGCCCACAAGTCAGTGGCATCTTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTT-C
1073884 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1073913 AAAGTCCACAAGTCAGTGGCAAC--CTTC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* *
1073940 AAAGCCCACAAATCAGTGGCACCCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
* * *
1073970 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCATCTTTTTC
* * *
1073999 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1074029 TTTTGTAAGC
Statistics
Matches: 124, Mismatches: 17, Indels: 8
0.83 0.11 0.05
Matches are distributed among these distances:
27 22 0.18
28 1 0.01
29 45 0.36
30 56 0.45
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (29 bp):
AAAGCCCACAAGTCAGTGGCATCTTTTTC
Done.