Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold129
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: 3652842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 48564 characters in sequence are not A, C, G, or T
File 4 of 23
Found at i:431085 original size:13 final size:13
Alignment explanation
Indices: 431067--431092 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
431057 CAATTTTTTG
431067 TGTATCGATACAT
1 TGTATCGATACAT
431080 TGTATCGATACAT
1 TGTATCGATACAT
431093 ACTTGCTGTA
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:431177 original size:20 final size:20
Alignment explanation
Indices: 431152--431224 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
431142 CAACTTTTTT
431152 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
431172 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
431193 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
431213 ATGTATCGATAC
1 ATGTATCGATAC
431225 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:431190 original size:41 final size:41
Alignment explanation
Indices: 431132--431224 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
431122 TGCCAAGAAT
*
431132 TGTATCGATACAACTTTTTTATGTATCGATACATTGCAACA
1 TGTATCGATACAACTTTTTCATGTATCGATACATTGCAACA
*
431173 TGTATCGATACATCTTTTTCATGTATCGATACATTGCAACA
1 TGTATCGATACAACTTTTTCATGTATCGATACATTGCAACA
431214 TGTATCGATAC
1 TGTATCGATAC
431225 TTTGAATTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (41 bp):
TGTATCGATACAACTTTTTCATGTATCGATACATTGCAACA
Found at i:431206 original size:21 final size:21
Alignment explanation
Indices: 431132--431206 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
431122 TGCCAAGAAT
* *
431132 TGTATCGATACAACTTTTTTA
1 TGTATCGATACATCTTTTTCA
****
431153 TGTATCGATACAT-TGCAACA
1 TGTATCGATACATCTTTTTCA
431173 TGTATCGATACATCTTTTTCA
1 TGTATCGATACATCTTTTTCA
431194 TGTATCGATACAT
1 TGTATCGATACAT
431207 TGCAACATGT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
TGTATCGATACATCTTTTTCA
Found at i:432945 original size:101 final size:97
Alignment explanation
Indices: 432796--434119 Score: 1262
Period size: 101 Copynumber: 13.9 Consensus size: 97
432786 GAAGAATGCT
* * **
432796 AATGTGCTGTTTCAAGGCCAACGACATTGGGTTTTAAAGATGACGAAGGTGCCAATATGCTGATT
1 AATGTGCTGATTCAAGGCCAGCGACATT-GGACTT-AA-ATGA--AAGGTGCCAATATGCTGATT
*
432861 CAAGGCCAGCGATATTGGACTTAAAAATGAAGGAGCC
61 CAAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * * * * *
432898 AATGTGCTGATTCAAAGCCAGCAATAATGGACTTAAAGATGACGAAGGCGCTAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-ATGA--AAGGTGCCAATATGCTGATTC
* *
432963 AAGGCCAGCGATATTGGACTTAAAGATGAAGATGCC
62 AAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * *
432999 AATGTACTGATTCAAGGCCAGCAACATTGGACTTAAAGATGAAAAAGGCGCCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-ATG--AAAGGTGCCAATATGCTGATTC
*
433064 AAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCC
62 AAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * * *
433100 AATGTGCTAATTCAAGGCCAGCAACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTAATTC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-ATG--AAAGGTGCCAATATGCTGATTC
*
433165 AAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCC
62 AAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* *
433201 AATGTGCTGATTCAAGGCCAGCAACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-ATG--AAAGGTGCCAATATGCTGATTC
* *
433266 AAGGCCAGCGATATTGGATTTAAAGATGAAGGTGCC
62 AAGGCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* *
433302 AATGTGCTGATTCAAGGCCAGTGACATTGGACTTAGAGA-CAAAGGTGCCAATATGCTGATTCAA
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTA-A-ATGAAAGGTGCCAATATGCTGATTCAA
**
433366 GGCCAGCGATATTGGACTTAAAGGTG-AGGTGCC
64 GGCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * * *
433399 AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAT-----GTACCAATGTGCTGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCTGATTCAAGG
* * ** *
433459 CCAGCGACATTGGTCTTAAAAGACAAAGATGCC
66 CCAGCGATATTGGACTTAAAA-ATGAAGGTGCC
* * *
433492 AATATGCTGATTCAAGGCCAGCGATATTGGAC-T---T-AAAGGTGCCAATGTGCTGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCTGATTCAAGG
* *
433552 CCAGCGACATTGGTCTTAAAAATG-AGGTGCC
66 CCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * * * * * *
433583 AATATGCTGATTCAAGGTCAGCGATATTGGAC-----TGAAAGGTGCTAATGTACGGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCTGATTCAAGG
* *
433643 CCAGCGACATTGGTA-TTAAAAGATAAAGGTGCC
66 CCAGCGATATTGG-ACTTAAAA-ATGAAGGTGCC
* * *
433676 AATATGCTGATTCAAGGCCAGCGATATTGGAC-T---T-AAAGGTGCCAATGTG-TGGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCT-GATTCAAG
* *
433735 GCCAGCGACATTGGTCTT----A--AAGGTGCC
65 GCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * * *
433762 AATGTGCTGATTCAAGGCCAGCAACATTGGTC-T---T-AAAGGTGCCAATGTGATGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCTGATTCAAGG
* * **
433822 CCAGCGACATTGGTCTTAAAAGACAAAGGTGCC
66 CCAGCGATATTGGACTTAAAA-ATGAAGGTGCC
* * *
433855 AATATGCTGATTCAAGGCCAGCGATATTGGAC-T---T-AAAGGTGCCAATGTGCTGATTCAAGG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCTGATTCAAGG
* *
433915 CCAGCGACATTGGTCTT----A--AAGGTGCC
66 CCAGCGATATTGGACTTAAAAATGAAGGTGCC
* * * *
433941 AATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-GATGAGGTGCCAATATGCTGATTCATG
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGA-AAGGTGCCAATATGCTGATTCAAG
**
434005 GCCAGAAATATTGGACTT----A--AAGGTGCC
65 GCCAGCGATATTGGACTTAAAAATGAAGGTGCC
* ** *
434032 AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAAACAAAGGTGCTAATATGCTGATTCAA
1 AATGTGCTGATTCAAGGCCAGCGACATTGGACTT--AAATGAAAGGTGCCAATATGCTGATTCAA
434097 GGCCAGCGATATTGGACTTAAAA
64 GGCCAGCGATATTGGACTTAAAA
434120 GAAGATGCCA
Statistics
Matches: 1100, Mismatches: 84, Indels: 81
0.87 0.07 0.06
Matches are distributed among these distances:
86 117 0.11
87 2 0.00
88 2 0.00
89 1 0.00
90 2 0.00
91 195 0.18
92 4 0.00
93 275 0.25
94 2 0.00
95 1 0.00
96 1 0.00
97 39 0.04
98 47 0.04
100 1 0.00
101 388 0.35
102 22 0.02
103 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (97 bp):
AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAATGAAAGGTGCCAATATGCTGATTCAAGG
CCAGCGATATTGGACTTAAAAATGAAGGTGCC
Found at i:433458 original size:43 final size:43
Alignment explanation
Indices: 433244--434118 Score: 852
Period size: 43 Copynumber: 19.1 Consensus size: 43
433234 TAAAGATGAC
* * *
433244 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGATTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
433287 AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTT
1 ----A--AAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
433336 AGAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
433385 AAAGGTGAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AA----AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * *
433433 AAATGTACCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
433476 AAAAGACAAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -AAAG-----G-TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
433526 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
433569 AAAAATGAGGTGCCAATATGCTGATTCAAGGTCAGCGATATTGGACTG
1 ---AA--AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * * * *
433617 AAAGGTGCTAATGTACGGATTCAAGGCCAGCGACATTGGTATTAAAAGAT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGG-ACT------T
*
433667 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
433710 AAAGGTGCCAATGTG-TGGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCGACATTGGACTT
* * *
433753 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* * *
433796 AAAGGTGCCAATGTGATGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
433839 AAAAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
433889 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
*
433932 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* ** *
433975 AAAGATGAGGTGCCAATATGCTGATTCATGGCCAGAAATATTGGACTT
1 --A-A--AGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
434023 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
* *
434066 AAAAAACAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 -------AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
434116 AAA
1 AAA
434119 AGAAGATGCC
Statistics
Matches: 708, Mismatches: 72, Indels: 100
0.80 0.08 0.11
Matches are distributed among these distances:
42 1 0.00
43 342 0.48
44 9 0.01
45 4 0.01
46 4 0.01
47 3 0.00
48 113 0.16
49 83 0.12
50 146 0.21
51 3 0.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT
Found at i:433523 original size:93 final size:91
Alignment explanation
Indices: 433244--434118 Score: 985
Period size: 93 Copynumber: 9.5 Consensus size: 91
433234 TAAAGATGAC
* * * * *
433244 AAAGGCGCCAATATGCTGATTCAAGGCCAGCGATATTGGAT-TTAAAGATGAAGGTGCCAATGTG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGG-TCTTAAAGA-AAAGGTGCCAATATG
* *
433308 CTGATTCAAGGCCAGTGACATTGGACTT
64 CTGATTCAAGGCCAGCGATATTGGACTT
* * * ***
433336 AGAGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAGGTGCCAA
1 ------AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAA
433401 TATGCTGATTCAAGGCCAGCGATATTGGACTT
60 TATGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
433433 AAATGTACCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAAGACAAAGATGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGA-AAAGGTGCCAATATG
433498 CTGATTCAAGGCCAGCGATATTGGACTT
64 CTGATTCAAGGCCAGCGATATTGGACTT
*
433526 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA-AATGAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAA-AAGGTGCCAATATGC
* *
433590 TGATTCAAGGTCAGCGATATTGGACTG
65 TGATTCAAGGCCAGCGATATTGGACTT
* * * *
433617 AAAGGTGCTAATGTACGGATTCAAGGCCAGCGACATTGGTATTAAAAGATAAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGA-AAAGGTGCCAATATG
433682 CTGATTCAAGGCCAGCGATATTGGACTT
64 CTGATTCAAGGCCAGCGATATTGGACTT
*
433710 AAAGGTGCCAATGTG-TGGATTCAAGGCCAGCGACATTGGTCTT-----AAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCT-GATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGC
* * *
433769 TGATTCAAGGCCAGCAACATTGGTCTT
65 TGATTCAAGGCCAGCGATATTGGACTT
*
433796 AAAGGTGCCAATGTGATGATTCAAGGCCAGCGACATTGGTCTTAAAAGACAAAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-AAAGA-AAAGGTGCCAATATG
433861 CTGATTCAAGGCCAGCGATATTGGACTT
64 CTGATTCAAGGCCAGCGATATTGGACTT
433889 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT-----AAAGGTGCCAATATGCT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCT
* *
433949 GATTCAAGGCCAGCGACATTGGTCTT
66 GATTCAAGGCCAGCGATATTGGACTT
* * ** * *
433975 AAAGATGAGGTGCCAATATGCTGATTCATGGCCAGAAATATTGGACTT-----AAAGGTGCCAAT
1 --A-A--AGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAAT
* * *
434035 GTGCTGATTCAAGGCCAGCGACATTGGTCTT
61 ATGCTGATTCAAGGCCAGCGATATTGGACTT
* * * *
434066 AAAAAACAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 -------AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAA
434119 AGAAGATGCC
Statistics
Matches: 691, Mismatches: 57, Indels: 60
0.86 0.07 0.07
Matches are distributed among these distances:
86 121 0.18
87 1 0.00
88 1 0.00
89 1 0.00
90 1 0.00
91 193 0.28
92 10 0.01
93 277 0.40
94 1 0.00
95 1 0.00
96 2 0.00
97 38 0.05
98 44 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (91 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTT
Found at i:433936 original size:22 final size:22
Alignment explanation
Indices: 433911--433978 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
433901 GTGCTGATTC
433911 AAGGCCAGCGACATTGGTCTTA
1 AAGGCCAGCGACATTGGTCTTA
* * * * *
433933 AAGG--TGCCA-ATATGCTGATTC
1 AAGGCCAGCGACAT-TGGT-CTTA
433954 AAGGCCAGCGACATTGGTCTTA
1 AAGGCCAGCGACATTGGTCTTA
433976 AAG
1 AAG
433979 ATGAGGTGCC
Statistics
Matches: 31, Mismatches: 10, Indels: 10
0.61 0.20 0.20
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 6 0.19
22 9 0.29
23 6 0.19
24 2 0.06
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (22 bp):
AAGGCCAGCGACATTGGTCTTA
Found at i:434270 original size:31 final size:31
Alignment explanation
Indices: 434186--434361 Score: 141
Period size: 31 Copynumber: 5.8 Consensus size: 31
434176 TGAAAAGGAG
* *
434186 AAAGATGCCACGGAGTTGTGGAC-TT--A-A
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGA
* * * * *
434213 AAGGGTGCCACGGAGTTGTGGGCTTTGAAGA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGA
*
434244 AAAGATGCCACTGAGTCATGGACTTTGAA-A
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGA
* * *
434274 AGAGATTGCCACTGAGTTGTGGACTTTGGAGA
1 AAAGA-TGCCACTGAGTCGTGGACTTTGAAGA
* * * *
434306 AAAAATGCCACTGAGTCCTGGAATTTG-GGA
1 AAAGATGCCACTGAGTCGTGGACTTTGAAGA
*
434336 CAAA-ATGGCACTGAGTCGTGGACTTT
1 -AAAGATGCCACTGAGTCGTGGACTTT
434362 AAAAAGGTAT
Statistics
Matches: 120, Mismatches: 22, Indels: 11
0.78 0.14 0.07
Matches are distributed among these distances:
27 20 0.17
28 2 0.02
30 27 0.22
31 67 0.56
32 4 0.03
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (31 bp):
AAAGATGCCACTGAGTCGTGGACTTTGAAGA
Found at i:434292 original size:62 final size:60
Alignment explanation
Indices: 434186--434332 Score: 172
Period size: 62 Copynumber: 2.5 Consensus size: 60
434176 TGAAAAGGAG
* ** *
434186 AAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAGA
1 AAAGATGCCACTGAGTCATGGACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAGA
* * *
434244 AAAGATGCCACTGAGTCATGGACTTTGAAAAGAGATTGCCACTGAGTTGTGGACTTTGGAGA
1 AAAGATGCCACTGAGTCATGGACTTTGAAAAG-G-GTGCCACGGAGTTGTGGACTTTGAAGA
* * *
434306 AAAAATGCCACTGAGTCCTGGAATTTG
1 AAAGATGCCACTGAGTCATGGACTTTG
434333 GGACAAAATG
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
58 20 0.27
59 2 0.03
60 5 0.07
61 1 0.01
62 47 0.63
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (60 bp):
AAAGATGCCACTGAGTCATGGACTTTGAAAAGGGTGCCACGGAGTTGTGGACTTTGAAGA
Found at i:435402 original size:19 final size:19
Alignment explanation
Indices: 435361--435401 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
435351 CTCACCAAGA
435361 TTTTCTATTTTGTTTTTCT
1 TTTTCTATTTTGTTTTTCT
* *
435380 TTTTCTCTTTT-TTTTTGT
1 TTTTCTATTTTGTTTTTCT
435398 TTTT
1 TTTT
435402 TTTGTGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.02, C:0.10, G:0.05, T:0.83
Consensus pattern (19 bp):
TTTTCTATTTTGTTTTTCT
Found at i:439944 original size:25 final size:25
Alignment explanation
Indices: 439910--439961 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
439900 ACCCTACTAG
439910 CAATGTTTTGACTTAAAGTTGATTA
1 CAATGTTTTGACTTAAAGTTGATTA
439935 CAATGTTTTGACTTAAAGTTGATTA
1 CAATGTTTTGACTTAAAGTTGATTA
439960 CA
1 CA
439962 TTGATTTCGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (25 bp):
CAATGTTTTGACTTAAAGTTGATTA
Found at i:443113 original size:19 final size:20
Alignment explanation
Indices: 443089--443139 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
443079 TATTTTAGTG
*
443089 TGTATCGATACAATG-AACA
1 TGTATCGATACAAAGCAACA
*
443108 TGTATCGATACAAAGCAATA
1 TGTATCGATACAAAGCAACA
*
443128 TGTATCAATACA
1 TGTATCGATACA
443140 TCTGGGCGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (20 bp):
TGTATCGATACAAAGCAACA
Found at i:448555 original size:20 final size:20
Alignment explanation
Indices: 448505--448556 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
448495 TAATAGAAAA
*
448505 TGTATCGATACAATCACTTG
1 TGTATCGATACAATCACTGG
** *
448525 TGTATTAATACAATTACTGG
1 TGTATCGATACAATCACTGG
448545 TGTATCGATACA
1 TGTATCGATACA
448557 TTTTGGTCCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (20 bp):
TGTATCGATACAATCACTGG
Found at i:453118 original size:30 final size:30
Alignment explanation
Indices: 453084--453166 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
453074 ATACATTTTT
453084 CAATGTATCGATACATCTAGGTAAAAAAAA
1 CAATGTATCGATACATCTAGGTAAAAAAAA
* * *
453114 CAATGTATCGATACATCTGGGTAAAAGACA
1 CAATGTATCGATACATCTAGGTAAAAAAAA
* *
453144 GAATGTATCAATACATCTAGGTA
1 CAATGTATCGATACATCTAGGTA
453167 GAAATGTGAC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.25
Consensus pattern (30 bp):
CAATGTATCGATACATCTAGGTAAAAAAAA
Found at i:453963 original size:30 final size:32
Alignment explanation
Indices: 453905--453963 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
453895 TGCCACCAAC
*
453905 TTGTGTGGGCTTTAGAGAAAGTTGCCACTGAT
1 TTGTGTGGGCTTTAGAGAAAGATGCCACTGAT
*
453937 TTGTGTGGGCTTT-GA-AAGGATGCCACT
1 TTGTGTGGGCTTTAGAGAAAGATGCCACT
453964 TGTAGACACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 10 0.40
31 2 0.08
32 13 0.52
ACGTcount: A:0.20, C:0.14, G:0.32, T:0.34
Consensus pattern (32 bp):
TTGTGTGGGCTTTAGAGAAAGATGCCACTGAT
Found at i:454392 original size:50 final size:50
Alignment explanation
Indices: 454228--454412 Score: 217
Period size: 50 Copynumber: 3.7 Consensus size: 50
454218 TTCCACAATT
* * * * *
454228 TGTATCGATACATTATTCATTGTATTGATATATTCTAGATTTTACCCAAA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGA
* * * * *
454278 TGTATCGATACATTGTTCATTATACCGATATATTCTGGATTTTACCTAGA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGA
* * * *
454328 TGCATCGATACATTTTTCATTGTATTGATACATTTTGGGTTTTACCCAGA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGA
* * *
454378 TGTATCAATACATTTCTCAATGTATCGATACATTC
1 TGTATCGATACATTTTTCATTGTATCGATACATTC
454413 AAGCATTTTT
Statistics
Matches: 113, Mismatches: 22, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 113 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (50 bp):
TGTATCGATACATTTTTCATTGTATCGATACATTCTGGATTTTACCCAGA
Found at i:454407 original size:100 final size:100
Alignment explanation
Indices: 454231--454412 Score: 249
Period size: 100 Copynumber: 1.8 Consensus size: 100
454221 CACAATTTGT
* *
454231 ATCGATACATTATTCATTGTATTGATATATTCTAGATTTTACCCAAATGTATCGATACATTGTTC
1 ATCGATACATTATTCATTGTATTGATACATTCTAGATTTTACCCAAATGTATCAATACATTGTTC
* *
454296 ATTATACCGATATATTCTGGATTTTACCTAGATGC
66 AATATACCGATACATTCTGGATTTTACCTAGATGC
* * * * *
454331 ATCGATACATTTTTCATTGTATTGATACATTTTGGGTTTTACCCAGATGTATCAATACATT-TCT
1 ATCGATACATTATTCATTGTATTGATACATTCTAGATTTTACCCAAATGTATCAATACATTGT-T
* *
454395 CAATGTATCGATACATTC
65 CAATATACCGATACATTC
454413 AAGCATTTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
99 1 0.01
100 69 0.99
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.42
Consensus pattern (100 bp):
ATCGATACATTATTCATTGTATTGATACATTCTAGATTTTACCCAAATGTATCAATACATTGTTC
AATATACCGATACATTCTGGATTTTACCTAGATGC
Found at i:456839 original size:79 final size:78
Alignment explanation
Indices: 456754--457151 Score: 362
Period size: 79 Copynumber: 5.0 Consensus size: 78
456744 TTCATTCATG
* ** * *
456754 CCGTTATTTTCAAGGGGATACTCTAGGCCTGGTTTTATTTTCAAAACACCAATTTTCTACAATCG
1 CCGTTATTTTCGAGGGGATACTCTAACCCTGATTTTATTTCCAAAACACCAATTTT-TACAATCG
456819 GGGATACTCCAACC
65 GGGATACTCCAACC
** * ** * **
456833 ATGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACATCAATTTTTCACAATTA
1 CCGTTATTTTCGAGGGGATACTCTAACCCTGATTTTATTTCCAAAACACCAATTTTT-ACAATCG
*
456898 GGGATACTCTAACC
65 GGGATACTCCAACC
* * *
456912 CCGTTATTTTTGAGGGG--A---TAA-CCTCGGTTTTATTTCCAAAATACCAATTTTTTACAATC
1 CCGTTATTTTCGAGGGGATACTCTAACCCT-GATTTTATTTCCAAAACACCAA-TTTTTACAATC
456971 GGGGATACTCCAATCC
64 GGGGATACTCCAA-CC
* * * * * * *
456987 CC-TTGTTTTTGAAGGGATACTCTAACCCCGATTTTA-TTCCAAAACATCGATTTTTTATAATCG
1 CCGTTATTTTCGAGGGGATACTCTAACCCTGATTTTATTTCCAAAACA-CCAATTTTTACAATCG
457050 ATCATTTGGAGATACTCCAACC
65 -------GG-GATACTCCAACC
* **
457072 CCGTTATTTTCGAGGGGATACTCAAACCCTGATTTTATTTTGAAAACACCAATTTTTCACAATCG
1 CCGTTATTTTCGAGGGGATACTCTAACCCTGATTTTATTTCCAAAACACCAATTTTT-ACAATCG
457137 GGGATACTCCAACC
65 GGGATACTCCAACC
457151 C
1 C
457152 TAGGTTTATT
Statistics
Matches: 253, Mismatches: 44, Indels: 44
0.74 0.13 0.13
Matches are distributed among these distances:
73 2 0.01
74 48 0.19
75 9 0.04
76 1 0.00
77 1 0.00
78 21 0.08
79 101 0.40
80 4 0.02
85 6 0.02
86 46 0.18
87 14 0.06
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (78 bp):
CCGTTATTTTCGAGGGGATACTCTAACCCTGATTTTATTTCCAAAACACCAATTTTTACAATCGG
GGATACTCCAACC
Found at i:457006 original size:153 final size:162
Alignment explanation
Indices: 456754--457150 Score: 440
Period size: 153 Copynumber: 2.5 Consensus size: 162
456744 TTCATTCATG
* * ** *
456754 CCGTTATTTTCAAGGGGATACTCTAGGCCTGGTTTTATTTTCAAAACACCAATTTTCTACAATCG
1 CCGTTATTTTCGAGGGGA-ACT-AAACCCTGGTTTTATTTTCAAAACACCAATTTTTTACAATCG
** *
456819 GGGATACTCCAACCATGTTATTTTCGAGGGGATACTCCAACCCCAATTTTATTTCCAAAACATC-
64 GGGATACTCCAACCACCTTATTTTCGAAGGGATACTCCAACCCCAATTTTA-TTCCAAAACATCG
* *
456883 A-ATTTT-TCA-C-A-ATTAGG-GATACTCTAACC
128 ATATTTTATAATCGACATTAGGAGATACTCCAACC
* * *
456912 CCGTTATTTTTGAGGGG-A-T-AA-CCTCGGTTTTATTTCCAAAATACCAATTTTTTACAATCGG
1 CCGTTATTTTCGAGGGGAACTAAACCCT-GGTTTTATTTTCAAAACACCAATTTTTTACAATCGG
* * * *
456973 GGATACTCCAATCC-CCTTGTTTTTGAAGGGATACTCTAACCCCGATTTTATTCCAAAACATCGA
65 GGATACTCCAA-CCACCTTATTTTCGAAGGGATACTCCAACCCCAATTTTATTCCAAAACATCGA
* *
457037 TTTTTTATAATCGATCATTTGGAGATACTCCAACC
129 TATTTTATAATCGA-CATTAGGAGATACTCCAACC
* * *
457072 CCGTTATTTTCGAGGGGATACTCAAACCCTGATTTTATTTTGAAAACACCAATTTTTCACAATCG
1 CCGTTATTTTCGAGGGGA-ACT-AAACCCTGGTTTTATTTTCAAAACACCAATTTTTTACAATCG
457137 GGGATACTCCAACC
64 GGGATACTCCAACC
457151 CTAGGTTTAT
Statistics
Matches: 200, Mismatches: 23, Indels: 26
0.80 0.09 0.10
Matches are distributed among these distances:
152 15 0.08
153 75 0.38
154 6 0.03
155 3 0.01
156 2 0.01
157 1 0.00
158 15 0.08
159 5 0.03
160 27 0.14
162 1 0.00
163 1 0.00
164 2 0.01
165 44 0.22
166 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (162 bp):
CCGTTATTTTCGAGGGGAACTAAACCCTGGTTTTATTTTCAAAACACCAATTTTTTACAATCGGG
GATACTCCAACCACCTTATTTTCGAAGGGATACTCCAACCCCAATTTTATTCCAAAACATCGATA
TTTTATAATCGACATTAGGAGATACTCCAACC
Found at i:457151 original size:51 final size:51
Alignment explanation
Indices: 457085--457196 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
457075 TTATTTTCGA
* ** *
457085 GGGGATACTCAAACCCT-GATTTTATTTTGAAAACACCAATTTTTCACAATC
1 GGGGATACTCAAACCCTAG-GTTTATTTCCAAAACACCAATTTTCCACAATC
* * *
457136 GGGGATACTCCAACCCTAGGTTTATTTCCAAAACACTAATTTTCCACAATT
1 GGGGATACTCAAACCCTAGGTTTATTTCCAAAACACCAATTTTCCACAATC
457187 GGGGATACTC
1 GGGGATACTC
457197 TACCCCTGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.31
Consensus pattern (51 bp):
GGGGATACTCAAACCCTAGGTTTATTTCCAAAACACCAATTTTCCACAATC
Found at i:457325 original size:79 final size:78
Alignment explanation
Indices: 457136--457640 Score: 520
Period size: 79 Copynumber: 6.4 Consensus size: 78
457126 TTTCACAATC
* * * * * * *
457136 GGGGATACTCCAACCCTAGGTTTATTTCCAAAACACTAATTTTCCACAATTGGGGATACT-CTAC
1 GGGGATACTCTAACCCGA-TTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAAC
457200 CCCTGTTATTTTCGA
65 CCC-GTTATTTTCGA
* * * * *
457215 -GGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATATTCCAAC
1 GGGGATACTCTAACCCGA-TTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAAC
457279 CCCGTTATTTTCGA
65 CCCGTTATTTTCGA
* * * *
457293 GGGGATACTCTAACTTCGATTTTATTTCCAAAACATCGATTTTTCACAATC-AGGGATACTCCAA
1 GGGGATACTCTAAC-CCGATTTTATTTCCAAAACACCAATTTTCCACAATCGA-GGATACTCCAA
* *
457357 CCTCGTTATTTTTGA
64 CCCCGTTATTTTCGA
* *
457372 -GGGATACTTTAATCCCGACTTTATTTCCAAAACACCAATTTTCCACAATCG-GAGATACTCCAA
1 GGGGATACTCTAA-CCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAG-GATACTCCAA
*
457435 TCCCGTTATTTTCGA
64 CCCCGTTATTTTCGA
* * * *
457450 GGGGATACTCTAACCCTAGTTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCTAAC
1 GGGGATACTCTAACCCGA-TTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAAC
*
457515 CCCGTTATTTTTGA
65 CCCGTTATTTTCGA
* * * * * * *
457529 GGAGATACCCTAACCTCGGTTTTATTTTCAAAACACCAAATTTT-TATAATCGAGAATACTCCAA
1 GGGGATACTCTAACC-CGATTTTATTTCCAAAACACC-AATTTTCCACAATCGAGGATACTCCAA
* *
457593 CCCTGTTATTTTTGA
64 CCCCGTTATTTTCGA
* *
457608 GGGGATACT-TAAACCCTGGTTTTATCTCCAAAA
1 GGGGATACTCT-AACCC-GATTTTATTTCCAAAA
457641 TATTAAACTT
Statistics
Matches: 362, Mismatches: 50, Indels: 28
0.82 0.11 0.06
Matches are distributed among these distances:
77 1 0.00
78 133 0.37
79 218 0.60
80 10 0.03
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (78 bp):
GGGGATACTCTAACCCGATTTTATTTCCAAAACACCAATTTTCCACAATCGAGGATACTCCAACC
CCGTTATTTTCGA
Found at i:457349 original size:157 final size:155
Alignment explanation
Indices: 457136--457640 Score: 576
Period size: 157 Copynumber: 3.2 Consensus size: 155
457126 TTTCACAATC
* * * *
457136 GGGGATACTCCAACCCTAGGTTTATTTCCAAAACACTAATTTTCCACAATTGGGGATACTCTACC
1 GGGGATACTCTAACCCGAGTTTTATTTCCAAAACAC-AATTTTCCACAATCGGGGATACTCTACC
*
457201 CCTGTTATTTTCGAGGGATACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTTCACAATCG
65 CCTGTTATTTTTGAGGGATACTCCAACCCC-GTTTTATTTTCAAAACACCAATTTTTCACAATCG
*
457266 AGGATATTCCAACCCCGTTATTTTCGA
129 AGGATACTCCAACCCCGTTATTTTCGA
* * * * *
457293 GGGGATACTCTAACTTCGA-TTTTATTTCCAAAACATCGATTTTTCACAATCAGGGATACTCCA-
1 GGGGATACTCTAAC-CCGAGTTTTATTTCCAAAACA-CAATTTTCCACAATCGGGGATACTCTAC
* ** * * * *
457356 ACCTCGTTATTTTTGAGGGATACTTTAATCCCGACTTTATTTCCAAAACACCAATTTTCCACAAT
64 CCCT-GTTATTTTTGAGGGATACTCCAACCCCG-TTTTATTTTCAAAACACCAATTTTTCACAAT
*
457421 CG-GAGATACTCCAATCCCGTTATTTTCGA
127 CGAG-GATACTCCAACCCCGTTATTTTCGA
* *
457450 GGGGATACTCTAACCCTAGTTTTATTTCTAAAACACCAATTTTCCACAATCGGGGATACTCTAAC
1 GGGGATACTCTAACCCGAGTTTTATTTCCAAAACA-CAATTTTCCACAATCGGGGATACTCT-AC
* *
457515 CCC-GTTATTTTTGAGGAGATAC-CCTAACCTCGGTTTTATTTTCAAAACACCAAATTTTT-ATA
64 CCCTGTTATTTTTGAGG-GATACTCC-AACC-CCGTTTTATTTTCAAAACACC-AATTTTTCACA
* * *
457577 ATCGAGAATACTCCAACCCTGTTATTTTTGA
125 ATCGAGGATACTCCAACCCCGTTATTTTCGA
*
457608 GGGGATACT-TAAACCCTG-GTTTTATCTCCAAAA
1 GGGGATACTCT-AACCC-GAGTTTTATTTCCAAAA
457641 TATTAAACTT
Statistics
Matches: 290, Mismatches: 43, Indels: 29
0.80 0.12 0.08
Matches are distributed among these distances:
156 7 0.02
157 190 0.66
158 82 0.28
159 11 0.04
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (155 bp):
GGGGATACTCTAACCCGAGTTTTATTTCCAAAACACAATTTTCCACAATCGGGGATACTCTACCC
CTGTTATTTTTGAGGGATACTCCAACCCCGTTTTATTTTCAAAACACCAATTTTTCACAATCGAG
GATACTCCAACCCCGTTATTTTCGA
Found at i:457702 original size:236 final size:235
Alignment explanation
Indices: 457156--457640 Score: 541
Period size: 236 Copynumber: 2.1 Consensus size: 235
457146 CAACCCTAGG
* * ** * * * ***
457156 TTTATTTCCAAAACACTAATTTTCCACAATTGGGGATACT-CTACCCCTGTTATTTTCGAGGGAT
1 TTTATCTCCAAAACACAAATTTTCCACAAGCGGAGATACTCCAATCCC-GTTATCCCCGAGGGAT
* * * *
457220 ACTCCAACCCCAGTTTTATTTTCAAAACACCAATTTTTCACAATCGAGGATATTCCAACCCCGTT
65 ACTCTAACCCTAGTTTTATTTTCAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTT
* * * * * *
457285 ATTTTCGAGGGGATACTCTAACTTCGATTTTATTTCCAAAACATCGATTTTTCACAATCAGGGAT
130 ATTTTCGAGGAGATACCCTAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCAGGAAT
*
457350 ACTCCAACCTCGTTATTTTTGAGGGATACTTTAATCCCGAC
195 ACTCCAACCTCGTTATTTTTGAGGGATACTTTAAACCCGAC
* * * ***
457391 TTTATTTCCAAAACACCAATTTTCCACAATCGGAGATACTCCAATCCCGTTATTTTCGAGGGGAT
1 TTTATCTCCAAAACACAAATTTTCCACAAGCGGAGATACTCCAATCCCGTTATCCCCGA-GGGAT
* *
457456 ACTCTAACCCTAGTTTTA-TTTCTAAAACACCAATTTTCCACAATCGGGGATACTCTAACCCCGT
65 ACTCTAACCCTAGTTTTATTTTC-AAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGT
* * * *
457520 TATTTTTGAGGAGATACCCTAACCTCGGTTTTATTTTCAAAACACCAAATTTTT-ATAATC-GAG
129 TATTTTCGAGGAGATACCCTAACCTCGATTTTATTTCCAAAACACC-AATTTTTCACAATCAG-G
**
457583 AATACTCCAACC-CTGTTATTTTTGAGGGGATAC-TTAAACCCTGGT
192 AATACTCCAACCTC-GTTATTTTTGA-GGGATACTTTAAACCC-GAC
457628 TTTATCTCCAAAA
1 TTTATCTCCAAAA
457641 TATTAAACTT
Statistics
Matches: 217, Mismatches: 25, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
235 54 0.25
236 137 0.63
237 26 0.12
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (235 bp):
TTTATCTCCAAAACACAAATTTTCCACAAGCGGAGATACTCCAATCCCGTTATCCCCGAGGGATA
CTCTAACCCTAGTTTTATTTTCAAAACACCAATTTTCCACAATCGAGGATACTCCAACCCCGTTA
TTTTCGAGGAGATACCCTAACCTCGATTTTATTTCCAAAACACCAATTTTTCACAATCAGGAATA
CTCCAACCTCGTTATTTTTGAGGGATACTTTAAACCCGAC
Found at i:458633 original size:28 final size:28
Alignment explanation
Indices: 458602--458838 Score: 202
Period size: 28 Copynumber: 8.5 Consensus size: 28
458592 CACTAATTTA
*
458602 TGGGCTTCGAAAAGGTGCCACTGACTAG
1 TGGGCTTTGAAAAGGTGCCACTGACTAG
* *
458630 TGGGCTTTGAAAAGGTGCCATTGACGCA-
1 TGGGCTTTGAAAAGGTGCCACTGAC-TAG
* *
458658 TGGGCTTTG-AGAGGATGCCACTGACTTG
1 TGGGCTTTGAAAAGG-TGCCACTGACTAG
* * *
458686 TGGGCTTTGAGAAGGTGCTACTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTAG
* * *
458714 TGAGCTTTGAAAATGTGCCACTGACTTG
1 TGGGCTTTGAAAAGGTGCCACTGACTAG
*
458742 TGGG-TTTGGAAAGGTGCCACTGACTCA-
1 TGGGCTTTGAAAAGGTGCCACTGACT-AG
*
458769 TGGGCTTTAGAAGAA--TGCCACTGACTCG
1 TGGGCTTT-GAA-AAGGTGCCACTGACTAG
* * *
458797 TGTGCTTTG-GAAGGATGCCACTAACTTA-
1 TGGGCTTTGAAAAGG-TGCCACTGAC-TAG
458825 TGGGCTTATGAAAA
1 TGGGCTT-TGAAAA
458839 CTCAAGGAAT
Statistics
Matches: 168, Mismatches: 26, Indels: 28
0.76 0.12 0.13
Matches are distributed among these distances:
25 2 0.01
27 28 0.17
28 125 0.74
29 9 0.05
30 4 0.02
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.28
Consensus pattern (28 bp):
TGGGCTTTGAAAAGGTGCCACTGACTAG
Found at i:458732 original size:84 final size:83
Alignment explanation
Indices: 458601--458818 Score: 226
Period size: 84 Copynumber: 2.6 Consensus size: 83
458591 CCACTAATTT
* * * *
458601 ATGGGCTTCGAAAAGGTGCCACTGACTAGTGGGCTTTGAAAAGGTGCCATTGACGCATGGGCTTT
1 ATGGGCTTTGAGAAGGTGCCACTGACTAGTGAGCTTTGAAAAGGTGCCACTGACGCATGGG-TTT
* *
458666 -GAGAGGATGCCACTGACTT
65 GGAAAGG-TGCCACTGACTC
* * * * ***
458685 GTGGGCTTTGAGAAGGTGCTACTGACTTGTGAGCTTTGAAAATGTGCCACTGACTTGTGGGTTTG
1 ATGGGCTTTGAGAAGGTGCCACTGACTAGTGAGCTTTGAAAAGGTGCCACTGACGCATGGGTTTG
458750 GAAAGGTGCCACTGACTC
66 GAAAGGTGCCACTGACTC
* * * *
458768 ATGGGCTTT-AGAAGAATGCCACTGACTCGTGTGCTTTG-GAAGGATGCCACT
1 ATGGGCTTTGAGAAG-GTGCCACTGACTAGTGAGCTTTGAAAAGG-TGCCACT
458819 AACTTATGGG
Statistics
Matches: 111, Mismatches: 20, Indels: 7
0.80 0.14 0.05
Matches are distributed among these distances:
82 8 0.07
83 48 0.43
84 55 0.50
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (83 bp):
ATGGGCTTTGAGAAGGTGCCACTGACTAGTGAGCTTTGAAAAGGTGCCACTGACGCATGGGTTTG
GAAAGGTGCCACTGACTC
Found at i:458816 original size:83 final size:83
Alignment explanation
Indices: 458601--458828 Score: 219
Period size: 83 Copynumber: 2.7 Consensus size: 83
458591 CCACTAATTT
* * * * * * * **
458601 ATGGGCTTCGAAAAGGTGCCACTGACTAGTGGGCTTTGAAAAGGTGCCATTGACGCATGGGCTTT
1 ATGGGCTTTGAGAAGATGCCACTGACTCGTGAGCTTTGAAAAGGTGCCACTAACTTATGGG-TTT
* *
458666 -GAGAGGATGCCACTGACTT
65 GGAAAGG-TGCCACTGACTC
* * * * * * *
458685 GTGGGCTTTGAGAAGGTGCTACTGACTTGTGAGCTTTGAAAATGTGCCACTGACTTGTGGGTTTG
1 ATGGGCTTTGAGAAGATGCCACTGACTCGTGAGCTTTGAAAAGGTGCCACTAACTTATGGGTTTG
458750 GAAAGGTGCCACTGACTC
66 GAAAGGTGCCACTGACTC
* *
458768 ATGGGCTTT-AGAAGAATGCCACTGACTCGTGTGCTTTG-GAAGGATGCCACTAACTTATGGG
1 ATGGGCTTTGAGAAG-ATGCCACTGACTCGTGAGCTTTGAAAAGG-TGCCACTAACTTATGGG
458829 CTTATGAAAA
Statistics
Matches: 119, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
82 8 0.07
83 56 0.47
84 55 0.46
ACGTcount: A:0.23, C:0.18, G:0.32, T:0.28
Consensus pattern (83 bp):
ATGGGCTTTGAGAAGATGCCACTGACTCGTGAGCTTTGAAAAGGTGCCACTAACTTATGGGTTTG
GAAAGGTGCCACTGACTC
Found at i:459611 original size:13 final size:13
Alignment explanation
Indices: 459571--459622 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
459561 CCGTTATAAG
459571 CAATGTATCGATA
1 CAATGTATCGATA
459584 CAA--T-T-GAT-
1 CAATGTATCGATA
459592 C-ATGTATCGATA
1 CAATGTATCGATA
459604 CAATGTATCGATA
1 CAATGTATCGATA
459617 CAATGT
1 CAATGT
459623 CCTATGTATC
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 4 0.12
10 2 0.06
11 4 0.12
12 1 0.03
13 20 0.61
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:459613 original size:33 final size:33
Alignment explanation
Indices: 459571--459639 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
459561 CCGTTATAAG
459571 CAATGTATCGATACAATTGAT-C-ATGTATCGATA
1 CAATGTATCGATACAA-TG-TCCTATGTATCGATA
459604 CAATGTATCGATACAATGTCCTATGTATCGATA
1 CAATGTATCGATACAATGTCCTATGTATCGATA
459637 CAA
1 CAA
459640 ATAGTGGTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 1 0.03
32 3 0.09
33 30 0.88
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (33 bp):
CAATGTATCGATACAATGTCCTATGTATCGATA
Found at i:462278 original size:13 final size:13
Alignment explanation
Indices: 462245--462285 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
462235 ATAGTAACCC
462245 ATGTATCGATACA
1 ATGTATCGATACA
*
462258 TTTGTATCGATACA
1 -ATGTATCGATACA
462272 ATGTATCGATACA
1 ATGTATCGATACA
462285 A
1 A
462286 GGAATGTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.52
14 12 0.48
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:468400 original size:20 final size:20
Alignment explanation
Indices: 468370--468424 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
468360 TTTCAATGCA
*
468370 ATGTATTGATACAATTCATC
1 ATGTATCGATACAATTCATC
* *
468390 TTGTATCGATATAATTCATC
1 ATGTATCGATACAATTCATC
468410 ATGTATCGATACAAT
1 ATGTATCGATACAAT
468425 GTATCGATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACAATTCATC
Found at i:468428 original size:13 final size:13
Alignment explanation
Indices: 468410--468439 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
468400 ATAATTCATC
468410 ATGTATCGATACA
1 ATGTATCGATACA
468423 ATGTATCGATACA
1 ATGTATCGATACA
468436 ATGT
1 ATGT
468440 CCTATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:468433 original size:33 final size:33
Alignment explanation
Indices: 468391--468456 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
468381 CAATTCATCT
*
468391 TGTATCGATATAAT-TCATCATGTATCGATACAA
1 TGTATCGATACAATGTCAT-ATGTATCGATACAA
*
468424 TGTATCGATACAATGTCCTATGTATCGATACAA
1 TGTATCGATACAATGTCATATGTATCGATACAA
468457 ACAATGGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.90
34 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTCATATGTATCGATACAA
Found at i:468543 original size:13 final size:13
Alignment explanation
Indices: 468525--468551 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
468515 TACAGTGAAC
468525 ATGTATCGATACA
1 ATGTATCGATACA
468538 ATGTATCGATACA
1 ATGTATCGATACA
468551 A
1 A
468552 AGCATAATGT
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:468938 original size:28 final size:28
Alignment explanation
Indices: 468871--469152 Score: 357
Period size: 28 Copynumber: 10.0 Consensus size: 28
468861 TTAGAAAGGG
*
468871 TGCCACTGACTGGTGGGCTTTGAAAATGA
1 TGCCACTGACTCGTGGGCTTTGAAAA-GA
*
468900 TGCCACTGACTCATGGGCTTTGAAAAGA
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
* *
468928 TGCCACTGACTCATGGGCTTTGAAGAGA
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
** * * *
468956 TGCTGCTGACTCATGGGCTTTGGAAGGA
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
* *
468984 TGCCACTAACTCGTGGGCTTTGAAAGGA
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
* *
469012 TGCCACTGACTCATGGGCTTTGAAGAGA
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
* * * *
469040 TGCCACTGACTTGTGGGCTTAGAAAGGG
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
* *
469068 TGCCACTGACTGGTAGGCTTTGAAAATGA
1 TGCCACTGACTCGTGGGCTTTGAAAA-GA
* *
469097 TGCCACTGACTTGTGGGCTTTGAAAAGG
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
469125 TGCCACTGACTCGTGGGCTTTGAAAAGA
1 TGCCACTGACTCGTGGGCTTTGAAAAGA
469153 GATCGTATTG
Statistics
Matches: 219, Mismatches: 33, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
28 170 0.78
29 49 0.22
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (28 bp):
TGCCACTGACTCGTGGGCTTTGAAAAGA
Found at i:469214 original size:14 final size:14
Alignment explanation
Indices: 469195--469232 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
469185 CTAACGAACA
*
469195 TTCTTGACAATAAT
1 TTCTTGACAACAAT
*
469209 TTCTTGACAACCAT
1 TTCTTGACAACAAT
469223 TTCTTGACAA
1 TTCTTGACAA
469233 ATGGTGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (14 bp):
TTCTTGACAACAAT
Found at i:484151 original size:20 final size:20
Alignment explanation
Indices: 484126--484250 Score: 97
Period size: 20 Copynumber: 5.7 Consensus size: 20
484116 TTTTAACTAG
484126 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
484146 ATGTATCGATACATCTAGGTAAAAAGGCAGA
1 ATGTATCGATACAT-T--G----AA---A-A
* *
484177 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
* * *
484197 ATGTATCGATACATTCATAC
1 ATGTATCGATACATTGAAAA
484217 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
484237 ATGTATTGATACAT
1 ATGTATCGATACAT
484251 CTAGGTAAAA
Statistics
Matches: 83, Mismatches: 11, Indels: 22
0.72 0.09 0.19
Matches are distributed among these distances:
20 60 0.72
21 1 0.01
23 1 0.01
24 2 0.02
27 2 0.02
28 1 0.01
30 2 0.02
31 14 0.17
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:484269 original size:30 final size:30
Alignment explanation
Indices: 484234--484290 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
484224 GATACATTGA
**
484234 AAAATGTATTGATACATCTAGGTAAAAGAC
1 AAAATGTATCAATACATCTAGGTAAAAGAC
*
484264 AAAATGTATCAATACATCTGGGTAAAA
1 AAAATGTATCAATACATCTAGGTAAAA
484291 ATGTAACTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (30 bp):
AAAATGTATCAATACATCTAGGTAAAAGAC
Found at i:485548 original size:12 final size:12
Alignment explanation
Indices: 485531--485555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
485521 CATAAAGTGT
485531 TGTATCGATACA
1 TGTATCGATACA
485543 TGTATCGATACA
1 TGTATCGATACA
485555 T
1 T
485556 ATTTTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:485553 original size:32 final size:32
Alignment explanation
Indices: 485512--485574 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
485502 TCAACGATTG
485512 GTATCGATACATAAAGTGTTGTATCGATACAT
1 GTATCGATACATAAAGTGTTGTATCGATACAT
*** *
485544 GTATCGATACATATTTTTTTGTATCGATACA
1 GTATCGATACATAAAGTGTTGTATCGATACA
485575 ATTTAAGCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (32 bp):
GTATCGATACATAAAGTGTTGTATCGATACAT
Found at i:485635 original size:13 final size:13
Alignment explanation
Indices: 485617--485641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
485607 ATTACTCAAA
485617 TGTATCGATACAT
1 TGTATCGATACAT
485630 TGTATCGATACA
1 TGTATCGATACA
485642 CTGATCTTTG
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:485706 original size:52 final size:52
Alignment explanation
Indices: 485650--485778 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
485640 CACTGATCTT
*
485650 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
**
485702 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTCAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
485754 TGTATCGATACATGCAAGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
485779 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:490877 original size:13 final size:13
Alignment explanation
Indices: 490859--490884 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
490849 CAATTTTTTG
490859 TGTATCGATACAT
1 TGTATCGATACAT
490872 TGTATCGATACAT
1 TGTATCGATACAT
490885 ACTTGCTGTA
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:491603 original size:21 final size:21
Alignment explanation
Indices: 491562--491605 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
491552 CTCTCCTTTA
* *
491562 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
491583 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
491604 TC
1 TC
491606 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:493429 original size:13 final size:13
Alignment explanation
Indices: 493411--493436 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493401 ATAATCACCC
493411 TGTATCGATACAA
1 TGTATCGATACAA
493424 TGTATCGATACAA
1 TGTATCGATACAA
493437 AGAAAAATGT
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):
TGTATCGATACAA
Found at i:495537 original size:15 final size:15
Alignment explanation
Indices: 495517--495547 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
495507 ATTTCGTTTG
*
495517 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
495532 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
495547 G
1 G
495548 GACATTTTTA
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:499630 original size:13 final size:13
Alignment explanation
Indices: 499612--499637 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
499602 CAATTTTTTG
499612 TGTATCGATACAT
1 TGTATCGATACAT
499625 TGTATCGATACAT
1 TGTATCGATACAT
499638 ACTTGCTGTA
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:507461 original size:21 final size:21
Alignment explanation
Indices: 507428--507468 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
507418 CTAAGTAAAA
507428 ATACGTATTGTATCAATACAT
1 ATACGTATTGTATCAATACAT
*
507449 ATAC-TATTGGTATTAATACA
1 ATACGTATT-GTATCAATACA
507469 CAAGGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (21 bp):
ATACGTATTGTATCAATACAT
Found at i:507533 original size:20 final size:21
Alignment explanation
Indices: 507502--507560 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
507492 GACAAAACCC
* *
507502 TGAAAAGTATCGATACACATT
1 TGAATAGTATCGATACACAAT
507523 TGAAT-GTATCGATACA-AAT
1 TGAATAGTATCGATACACAAT
*
507542 TGCATAGTATCGATACACA
1 TGAATAGTATCGATACACA
507561 CAAATATGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.18
20 22 0.67
21 5 0.15
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (21 bp):
TGAATAGTATCGATACACAAT
Found at i:507631 original size:53 final size:53
Alignment explanation
Indices: 507548--507684 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
507538 AAATTGCATA
507548 GTATCGATACACACAAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
1 GTATCGATACACAC-AATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
507602 GTATCGATACACACAATATGTATCGATACAGGTCATTGGCAGTAGCCAAATTT
1 GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
*
507655 GTATCGATACACAAAATATGTATCGATACA
1 GTATCGATACACACAATATGTATCGATACA
507685 TTGGAAATAG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
53 67 0.83
54 14 0.17
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (53 bp):
GTATCGATACACACAATATGTATCGATACAGGACATTGGCAGTAGCCAAATTT
Found at i:507727 original size:10 final size:10
Alignment explanation
Indices: 507708--507738 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
507698 AATCTCATTT
507708 TCACTGTTCA
1 TCACTGTTCA
*
507718 TCACTATTCA
1 TCACTGTTCA
507728 TCACTGTTCA
1 TCACTGTTCA
507738 T
1 T
507739 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.23, C:0.29, G:0.06, T:0.42
Consensus pattern (10 bp):
TCACTGTTCA
Found at i:507760 original size:21 final size:21
Alignment explanation
Indices: 507726--507786 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
507716 CATCACTATT
507726 CATCACTGTTCATGTATCGATA
1 CATCACT-TTCATGTATCGATA
507748 CATCACTTTCATGTATCGATA
1 CATCACTTTCATGTATCGATA
507769 CATCACTTTCATGTATCG
1 CATCACTTTCATGTATCG
507787 TTAAAAATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
21 32 0.82
22 7 0.18
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (21 bp):
CATCACTTTCATGTATCGATA
Found at i:507828 original size:43 final size:43
Alignment explanation
Indices: 507708--507857 Score: 182
Period size: 43 Copynumber: 3.5 Consensus size: 43
507698 AATCTCATTT
* *
507708 TCACTGTTCATCACTATTCATCACTGTTCATGTATCG--ATACA
1 TCACTGTTCATCACTATTCATCACT-TTCATGTATCGTTAAAAA
* * *
507750 TCACT-TTCATGTATCGATACATCACTTTCATGTATCGTTAAAAA
1 TCACTGTTCAT-CA-CTATTCATCACTTTCATGTATCGTTAAAAA
*
507794 TCACTGTTCA-CACTGTTCATCACTATTCATGTATCGTTAAAAA
1 TCACTGTTCATCACTATTCATCACT-TTCATGTATCGTTAAAAA
507837 TCACTGTTCATCACTATTCAT
1 TCACTGTTCATCACTATTCAT
507858 GTATCGATAC
Statistics
Matches: 91, Mismatches: 10, Indels: 12
0.81 0.09 0.11
Matches are distributed among these distances:
41 5 0.05
42 26 0.29
43 39 0.43
44 17 0.19
45 4 0.04
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.39
Consensus pattern (43 bp):
TCACTGTTCATCACTATTCATCACTTTCATGTATCGTTAAAAA
Found at i:507895 original size:13 final size:13
Alignment explanation
Indices: 507877--507901 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
507867 CATATTTGTG
507877 TGTATCGATACAA
1 TGTATCGATACAA
507890 TGTATCGATACA
1 TGTATCGATACA
507902 TCATAAATAG
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:508443 original size:34 final size:35
Alignment explanation
Indices: 508380--508446 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
508370 CTAAGTGATT
508380 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
508416 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
508447 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:510991 original size:10 final size:10
Alignment explanation
Indices: 510968--511012 Score: 58
Period size: 10 Copynumber: 4.6 Consensus size: 10
510958 GGCGTCCTCC
510968 ACAAAA-AAA
1 ACAAAACAAA
510977 A-AAAACAAA
1 ACAAAACAAA
510986 ACAAAACAAA
1 ACAAAACAAA
*
510996 AAAAAACAAAA
1 ACAAAAC-AAA
511007 ACAAAA
1 ACAAAA
511013 AAAGGGGTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
8 4 0.13
9 5 0.16
10 14 0.45
11 8 0.26
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (10 bp):
ACAAAACAAA
Found at i:510996 original size:21 final size:21
Alignment explanation
Indices: 510973--511012 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
510963 CCTCCACAAA
510973 AAAAAAAAAC-AAAACAAAAC
1 AAAAAAAAACAAAAACAAAAC
510993 AAAAAAAAACAAAAACAAAA
1 AAAAAAAAACAAAAACAAAA
511013 AAAGGGGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAAAACAAAAACAAAAC
Found at i:511014 original size:16 final size:16
Alignment explanation
Indices: 510971--511015 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
510961 GTCCTCCACA
*
510971 AAAAAAAAAAACAAAAC
1 AAAAACAAAAA-AAAAC
510988 -AAAACAAAAAAAAAC
1 AAAAACAAAAAAAAAC
511003 AAAAACAAAAAAA
1 AAAAACAAAAAAA
511016 GGGGTCCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 21 0.81
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAACAAAAAAAAAC
Found at i:512461 original size:29 final size:30
Alignment explanation
Indices: 512422--512712 Score: 172
Period size: 30 Copynumber: 9.6 Consensus size: 30
512412 TCACCCTTCA
512422 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * * *
512451 AAAGCACACAAGTCAGTGTCATTTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCA-CTCTTTTTC
512482 AAAAGCCCACAAGTCAGTGGCAAC-C---TTC
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
* * *
512510 AAAGCCCACAAATCAGTGGCACCCTTTTTT
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
512540 GAAGCCCACAAGTCGGTGGCA-TCTTTTCC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * *
512569 AAAGTCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAAGTCAGTGGCACTCTTTTTC
* * * * *
512599 TTTTGTAAGCTCACAACTCTA-TAGCACTATTTTTC
1 -----AAAGCCCACAAGTC-AGTGGCACTCTTTTTC
* * *
512634 TTTTTAAGCCCACAAGTTAGTGGCAC-CCTTTTC
1 ----AAAGCCCACAAGTCAGTGGCACTCTTTTTC
*
512667 AAAAGCCCACAAGTCAGTGGCAAC-C--TTTA
1 -AAAGCCCACAAGTCAGTGGC-ACTCTTTTTC
512696 AAAGCCCACAAGTCAGT
1 AAAGCCCACAAGTCAGT
512713 AGCAACCTTC
Statistics
Matches: 208, Mismatches: 37, Indels: 35
0.74 0.13 0.12
Matches are distributed among these distances:
26 2 0.01
27 20 0.10
28 20 0.10
29 44 0.21
30 45 0.22
31 10 0.05
32 18 0.09
33 7 0.03
34 19 0.09
35 23 0.11
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACTCTTTTTC
Found at i:512475 original size:27 final size:28
Alignment explanation
Indices: 512422--512596 Score: 104
Period size: 29 Copynumber: 6.0 Consensus size: 28
512412 TCACCCTTCA
*
512422 AAAGCCCACAAGTCAGTGGCATCTTTTTC
1 AAAGCACACAAGTCAGTGGCA-CTTTTTC
* *
512451 AAAGCACACAAGTCAGTGTCATTTTTTTTTC
1 AAAGCACACAAGTCAGTGGCA---CTTTTTC
* *
512482 AAAAGCCCACAAGTCAGTGGCAAC--CTTC
1 -AAAGCACACAAGTCAGTGGC-ACTTTTTC
* * *
512510 AAAGCCCACAAATCAGTGGCACCCTTTTTT
1 AAAGCACACAAGTCAGTGGCA--CTTTTTC
* * * *
512540 GAAGCCCACAAGTCGGTGGCATCTTTTCC
1 AAAGCACACAAGTCAGTGGCA-CTTTTTC
* *
512569 AAAGTC-CACAACTCCGTGGCACTCTTTT
1 AAAG-CACACAAGTCAGTGGCACT-TTTT
512597 TCTTTTGTAA
Statistics
Matches: 116, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
26 1 0.01
27 19 0.16
28 6 0.05
29 43 0.37
30 21 0.18
31 7 0.06
32 18 0.16
33 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.27
Consensus pattern (28 bp):
AAAGCACACAAGTCAGTGGCACTTTTTC
Found at i:512572 original size:59 final size:59
Alignment explanation
Indices: 512421--512597 Score: 196
Period size: 59 Copynumber: 3.0 Consensus size: 59
512411 CTCACCCTTC
* * * * *
512421 AAAAGCCCACAAGTCAGTGGCATCTTTTTCAAAGCACACAAGTCAGTGTCATTTTTTTTT
1 AAAAGCCCACAAGTCAGTGGCATC-TTTTCAAAGCCCACAAATCAGTGGCACTCTTTTTT
* * *
512481 CAAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAGCCCACAAATCAGTGGCACCCTTTTTT
1 -AAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTTT
* * * * *
512540 -GAAGCCCACAAGTCGGTGGCATCTTTTCCAAAGTCCACAACTCCGTGGCACTCTTTTT
1 AAAAGCCCACAAGTCAGTGGCATCTTTT-CAAAGCCCACAAATCAGTGGCACTCTTTTT
512598 CTTTTGTAAG
Statistics
Matches: 98, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
57 20 0.20
58 2 0.02
59 53 0.54
61 23 0.23
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.27
Consensus pattern (59 bp):
AAAAGCCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAATCAGTGGCACTCTTTTTT
Found at i:512615 original size:35 final size:34
Alignment explanation
Indices: 512574--512648 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
512564 TTTCCAAAGT
* * *
512574 CCACAACTCCGTGGCACTCTTTTTCTTTTGTAAGC
1 CCACAACTCCATAGCACTATTTTTCTTTT-TAAGC
* *
512609 TCACAACTCTATAGCACTATTTTTCTTTTTAAGC
1 CCACAACTCCATAGCACTATTTTTCTTTTTAAGC
512643 CCACAA
1 CCACAA
512649 GTTAGTGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.37
Consensus pattern (34 bp):
CCACAACTCCATAGCACTATTTTTCTTTTTAAGC
Found at i:512707 original size:28 final size:29
Alignment explanation
Indices: 512639--512762 Score: 148
Period size: 28 Copynumber: 4.3 Consensus size: 29
512629 TTTTCTTTTT
* *
512639 AAGCCCACAAGTTAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
512669 AAGCCCACAAGTCAGTGGCAACCTTT-AA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
512697 AAGCCCACAAGTCAGTAGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
* *
512725 AAGCACACAAGT-TGAT-GCAAACCTTTCAA
1 AAGCCCACAAGTCAG-TGGC-AACCTTTCAA
512754 AAGCCCACA
1 AAGCCCACA
512763 CAAGTTGGTG
Statistics
Matches: 84, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
27 5 0.06
28 42 0.50
29 16 0.19
30 21 0.25
ACGTcount: A:0.37, C:0.30, G:0.15, T:0.18
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:512940 original size:43 final size:43
Alignment explanation
Indices: 512878--512967 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
512868 GCACCTTCAT
*
512878 CTTTAAGTCCAATGCAGCTGACCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATACAGCTGACCTTGAATCAGCACATTGGCAC
* * *
512921 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATACAGCTGACCTTGAATCAGCACATTGGCAC
512964 CTTT
1 CTTT
512968 TCCATCTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.30
Consensus pattern (43 bp):
CTTTAAGTCCAATACAGCTGACCTTGAATCAGCACATTGGCAC
Found at i:512959 original size:92 final size:95
Alignment explanation
Indices: 512782--513020 Score: 313
Period size: 92 Copynumber: 2.5 Consensus size: 95
512772 GGCGTCTCCT
* * * *
512782 TTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCCTGCCTTTAAGTCCAATATCGC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA--C--CCTTTAAGTCCAATATAGC
512847 TGGCCTTAAATCAGCATATTGGCACC-TT-CATC
62 TGGCCTTAAATCAGCATATTGGCACCTTTCCATC
* *
512879 TTTAAGTCCAATGCAGCTGACCTTGAATCAGCACATTGGCA-CCTTTAAGTCCAATATAGCTGGC
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTTAAGTCCAATATAGCTGGC
*
512943 CTTGAATCAGCATATTGGCACCTTTTCCATC
66 CTTAAATCAGCATATTGGCACC-TTTCCATC
* * * *
512974 TTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGACATCCTTT
1 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTT
513021 TTCTCATCTT
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
92 43 0.34
94 2 0.02
95 40 0.32
96 5 0.04
97 36 0.29
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (95 bp):
TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCCTTTAAGTCCAATATAGCTGGC
CTTAAATCAGCATATTGGCACCTTTCCATC
Found at i:512999 original size:52 final size:53
Alignment explanation
Indices: 512921--513074 Score: 184
Period size: 52 Copynumber: 2.9 Consensus size: 53
512911 ACATTGGCAC
*
512921 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTC-CAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
* * * *
512973 CTTTAAGTTCAATGTAGTTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCA-CC-TTTTCTCAT
* * * * * *
513028 CTTTAAGCCCAATATCGTTGGCCATGAATCAACATATTAGCATCTTT
1 CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTT
513075 ATCACTTTTC
Statistics
Matches: 84, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
52 37 0.44
53 5 0.06
54 6 0.07
55 36 0.43
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.36
Consensus pattern (53 bp):
CTTTAAGTCCAATATAGTTGGCCTTGAATCAGCATATTGGCACCTTTTCTCAT
Found at i:514251 original size:13 final size:13
Alignment explanation
Indices: 514233--514257 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
514223 CATAAAGTGT
514233 TGTATCGATACAA
1 TGTATCGATACAA
514246 TGTATCGATACA
1 TGTATCGATACA
514258 TATTTTTTTG
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:514338 original size:13 final size:13
Alignment explanation
Indices: 514320--514344 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
514310 ATTACTCAAA
514320 TGTATCGATACAT
1 TGTATCGATACAT
514333 TGTATCGATACA
1 TGTATCGATACA
514345 CTGATCTTTA
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:514395 original size:52 final size:51
Alignment explanation
Indices: 514333--514481 Score: 217
Period size: 52 Copynumber: 2.9 Consensus size: 51
514323 ATCGATACAT
** *
514333 TGTATCGATACACTGATCTTTATATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* * *
514385 TGTATCGATACATTATAAAATGTATCGATACATGTAGGCAAATTTGCCCAGA
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTTGCCCAGA
514437 TGTATCGATACACTATTCAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTA-TCAATGTATCGATACATGCAGGCAAATTT
514482 TCATATTTCG
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.97
53 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:523113 original size:20 final size:21
Alignment explanation
Indices: 523074--523113 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
523064 GCTTCGTATA
523074 AATGTTTTCAAGTCTTAAATCG
1 AATGTTTTCAAG-CTTAAATCG
523096 AATGTTTTCAAG-TTAAAT
1 AATGTTTTCAAGCTTAAAT
523114 TACTTCAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
22 12 0.67
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.42
Consensus pattern (21 bp):
AATGTTTTCAAGCTTAAATCG
Found at i:523230 original size:20 final size:20
Alignment explanation
Indices: 523205--523272 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
523195 TATCGACACA
523205 TTGTATCGATACATTATGCC
1 TTGTATCGATACATTATGCC
523225 TTGTATCGATAC---A----
1 TTGTATCGATACATTATGCC
523238 TTGTATCGATACATTATGCC
1 TTGTATCGATACATTATGCC
523258 TTGTATCGATACATT
1 TTGTATCGATACATT
523273 GTATCGATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 12 0.29
16 1 0.02
17 1 0.02
20 27 0.66
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.41
Consensus pattern (20 bp):
TTGTATCGATACATTATGCC
Found at i:523232 original size:33 final size:33
Alignment explanation
Indices: 523195--523303 Score: 175
Period size: 33 Copynumber: 3.3 Consensus size: 33
523185 CCCTTGAAAA
*
523195 TATCGACACATTGTATCGATACATTATGCCTTG
1 TATCGATACATTGTATCGATACATTATGCCTTG
523228 TATCGATACATTGTATCGATACATTATGCCTTG
1 TATCGATACATTGTATCGATACATTATGCCTTG
** *
523261 TATCGATACATTGTATCGATACATGCT-CATTG
1 TATCGATACATTGTATCGATACATTATGCCTTG
523293 TATCGATACAT
1 TATCGATACAT
523304 ACCCAATTGT
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 15 0.21
33 57 0.79
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (33 bp):
TATCGATACATTGTATCGATACATTATGCCTTG
Found at i:523243 original size:13 final size:13
Alignment explanation
Indices: 523225--523284 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
523215 ACATTATGCC
523225 TTGTATCGATACA
1 TTGTATCGATACA
523238 TTGTATCGATACA
1 TTGTATCGATACA
*
523251 -T-TAT-G---CC
1 TTGTATCGATACA
523258 TTGTATCGATACA
1 TTGTATCGATACA
523271 TTGTATCGATACA
1 TTGTATCGATACA
523284 T
1 T
523285 GCTCATTGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.08
10 2 0.05
11 3 0.08
12 1 0.03
13 28 0.72
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:523293 original size:19 final size:19
Alignment explanation
Indices: 523269--523324 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
523259 TGTATCGATA
*
523269 CATTGTATCGATACATGCT
1 CATTGTATCGATACATGCC
*
523288 CATTGTATCGATACATACC
1 CATTGTATCGATACATGCC
*
523307 CAATTGTTTCGATACATG
1 C-ATTGTATCGATACATG
523325 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (19 bp):
CATTGTATCGATACATGCC
Found at i:523391 original size:13 final size:13
Alignment explanation
Indices: 523373--523398 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
523363 CATAGGATAA
523373 TGTATCGATACAT
1 TGTATCGATACAT
523386 TGTATCGATACAT
1 TGTATCGATACAT
523399 GAAGAATTGT
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:528852 original size:15 final size:15
Alignment explanation
Indices: 528832--528862 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
528822 TAAAAATGTC
*
528832 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
528847 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
528862 C
1 C
528863 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:530892 original size:20 final size:20
Alignment explanation
Indices: 530867--530944 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 20
530857 AATGTCCAAA
530867 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATGTTTCT
* *
530887 ATGTATCGATACATCTGGAAATTCA
1 ATGTATCGATACA--T-G--TTTCT
*
530912 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATGTTTCT
*
530932 TTGTATCGATACA
1 ATGTATCGATACA
530945 GGGTGATTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
20 28 0.60
22 1 0.02
23 2 0.04
25 16 0.34
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATGTTTCT
Found at i:531108 original size:20 final size:20
Alignment explanation
Indices: 531065--531110 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
531055 AAATCTTTTG
531065 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
531086 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
531106 CAAAA
1 CAAAA
531111 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:533517 original size:20 final size:20
Alignment explanation
Indices: 533472--533523 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
533462 GTAGCCAAAC
* **
533472 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
533492 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
533511 TTGTATCGATACA
1 TTGTATCGATACA
533524 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:534858 original size:13 final size:13
Alignment explanation
Indices: 534840--534864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534830 ACCAAGATCA
534840 TGTATCGATACAG
1 TGTATCGATACAG
534853 TGTATCGATACA
1 TGTATCGATACA
534865 AAGCAATATG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:534861 original size:32 final size:32
Alignment explanation
Indices: 534820--534883 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
534810 ACAACTCGTT
*
534820 GTGTATCGATACCAAG-ATCATGTATCGATACA
1 GTGTATCGATACAAAGAAT-ATGTATCGATACA
534852 GTGTATCGATACAAAGCAATATGTATCGATAC
1 GTGTATCGATACAAAG-AATATGTATCGATAC
534884 TTCTGAGTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 15 0.52
33 12 0.41
34 2 0.07
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (32 bp):
GTGTATCGATACAAAGAATATGTATCGATACA
Found at i:537473 original size:13 final size:13
Alignment explanation
Indices: 537441--537476 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
537431 ATAGTGCCTT
* *
537441 TGTATCAATATAG
1 TGTATCGATATAA
537454 TGTATCGATATAA
1 TGTATCGATATAA
537467 TGTATCGATA
1 TGTATCGATA
537477 CTACAAACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.08, G:0.17, T:0.39
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:541992 original size:3 final size:3
Alignment explanation
Indices: 541984--542015 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
541974 TCAGTCAACT
*
541984 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
542016 TTTGATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:546611 original size:21 final size:21
Alignment explanation
Indices: 546585--546625 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
546575 TGATGAGATT
546585 GGACAACTAAGATTGCTAGTA
1 GGACAACTAAGATTGCTAGTA
546606 GGACAACTAAGATTGCTAGT
1 GGACAACTAAGATTGCTAGT
546626 GTAACAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (21 bp):
GGACAACTAAGATTGCTAGTA
Found at i:546632 original size:21 final size:21
Alignment explanation
Indices: 546587--546636 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
546577 ATGAGATTGG
*
546587 ACAACTAAGATTGCTAGTAGG
1 ACAACTAAGATTGCTAGTAGA
546608 ACAACTAAGATTGCTAGT-GTA
1 ACAACTAAGATTGCTAGTAG-A
546629 ACAACTAA
1 ACAACTAA
546637 TGATGGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 1 0.04
21 26 0.96
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.24
Consensus pattern (21 bp):
ACAACTAAGATTGCTAGTAGA
Found at i:548812 original size:62 final size:62
Alignment explanation
Indices: 548736--548859 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
548726 AAAACTTTAT
548736 AGAAATTTAAAAGAAATGCCTCTTTTTATTACAGCAAGTTAAGGTCATTAATAGTTGGCCTA
1 AGAAATTTAAAAGAAATGCCTCTTTTTATTACAGCAAGTTAAGGTCATTAATAGTTGGCCTA
548798 AGAAATTTAAAAGAAATGCCTCTTTTTATTACAGCAAGTTAAGGTCATTAATAGTTGGCCTA
1 AGAAATTTAAAAGAAATGCCTCTTTTTATTACAGCAAGTTAAGGTCATTAATAGTTGGCCTA
548860 CTTCACAATC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (62 bp):
AGAAATTTAAAAGAAATGCCTCTTTTTATTACAGCAAGTTAAGGTCATTAATAGTTGGCCTA
Found at i:552699 original size:20 final size:21
Alignment explanation
Indices: 552655--552708 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 21
552645 ACATGGTCTA
*
552655 GTATTGATACACTCACTTAAT
1 GTATTGATACATTCACTTAAT
552676 GTATTGATACATTCACTT-AT
1 GTATTGATACATTCACTTAAT
*
552696 GTATCGATACATT
1 GTATTGATACATT
552709 AACTGCTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (21 bp):
GTATTGATACATTCACTTAAT
Found at i:555358 original size:32 final size:33
Alignment explanation
Indices: 555316--555390 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
555306 TATATTATTA
* *
555316 ATTTAATTTTTTA-TATAAATATGA-TTTTAATT
1 ATTT-ATTTTTTAGCATAAATATAATTTTTAATT
555348 ATTTATTTTTTAGCATAAATATAATTTTTAATT
1 ATTTATTTTTTAGCATAAATATAATTTTTAATT
555381 ATTTATTTTT
1 ATTTATTTTT
555391 AATGTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
31 8 0.21
32 13 0.33
33 18 0.46
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (33 bp):
ATTTATTTTTTAGCATAAATATAATTTTTAATT
Found at i:555399 original size:32 final size:31
Alignment explanation
Indices: 555316--555401 Score: 102
Period size: 32 Copynumber: 2.7 Consensus size: 31
555306 TATATTATTA
* *
555316 ATTTAATTTTTTATATAAATATGATTTTAATT
1 ATTT-ATTTTTTATGTAAATATAATTTTAATT
555348 ATTTATTTTTTA-GCATAAATATAATTTTTAATT
1 ATTTATTTTTTATG--TAAATATAA-TTTTAATT
*
555381 ATTTATTTTTAATGTAAATAT
1 ATTTATTTTTTATGTAAATAT
555402 TGTAGGAAGT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
31 8 0.17
32 19 0.40
33 19 0.40
34 1 0.02
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.58
Consensus pattern (31 bp):
ATTTATTTTTTATGTAAATATAATTTTAATT
Found at i:555996 original size:33 final size:32
Alignment explanation
Indices: 555954--556018 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
555944 ACACACCTAG
*
555954 ATGTATCGATACAT-TATGCTTTGTATCGATACA
1 ATGTATCGATACATGT-T-CATTGTATCGATACA
*
555987 ATGTATCGATATATGTTCATTGTATCGATACA
1 ATGTATCGATACATGTTCATTGTATCGATACA
556019 TGGACAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 14 0.48
33 14 0.48
34 1 0.03
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.40
Consensus pattern (32 bp):
ATGTATCGATACATGTTCATTGTATCGATACA
Found at i:556030 original size:20 final size:20
Alignment explanation
Indices: 555984--556039 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
555974 TTGTATCGAT
* *
555984 ACAA-TGTATCGATATATGT
1 ACAATTGTATCGATACATGG
*
556003 TC-ATTGTATCGATACATGG
1 ACAATTGTATCGATACATGG
*
556022 ACAATTGTATCCATACAT
1 ACAATTGTATCGATACAT
556040 TAAACTGGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 14 0.47
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:556112 original size:32 final size:31
Alignment explanation
Indices: 556071--556133 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
556061 ACCACTGTTT
*
556071 GTATCGATACGTG-GCACATTGTATCGATACAA
1 GTATCGATACATGAG-A-ATTGTATCGATACAA
556103 GTATCGATACATGATGAATTGTATCGATACA
1 GTATCGATACATGA-GAATTGTATCGATACA
556134 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 26 0.93
33 1 0.04
34 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (31 bp):
GTATCGATACATGAGAATTGTATCGATACAA
Found at i:558268 original size:20 final size:20
Alignment explanation
Indices: 558243--558293 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
558233 CCACTGTTTA
*
558243 TATCGATACATGGT-ACATTG
1 TATCGATACATGATGA-ATTG
558263 TATCGATACATGATGAATTG
1 TATCGATACATGATGAATTG
558283 TATCGATACAT
1 TATCGATACAT
558294 TGCTTATAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (20 bp):
TATCGATACATGATGAATTG
Found at i:566347 original size:22 final size:22
Alignment explanation
Indices: 566319--566360 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
566309 AATAATTTTT
*
566319 TTTGATAAAGGGGGAGAAATGC
1 TTTGATAAAAGGGGAGAAATGC
566341 TTTGATAAAAGGGGAGAAAT
1 TTTGATAAAAGGGGAGAAAT
566361 ATGTTTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.33, T:0.24
Consensus pattern (22 bp):
TTTGATAAAAGGGGAGAAATGC
Found at i:566973 original size:13 final size:13
Alignment explanation
Indices: 566955--566981 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
566945 ACATTATGCT
566955 TTGTATCGATACA
1 TTGTATCGATACA
566968 TTGTATCGATACA
1 TTGTATCGATACA
566981 T
1 T
566982 GTTCATTGTA
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:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:567011 original size:20 final size:19
Alignment explanation
Indices: 566965--567021 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
566955 TTGTATCGAT
*
566965 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
566984 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
567003 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
567022 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:567075 original size:20 final size:20
Alignment explanation
Indices: 567050--567103 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
567040 CTACCACTAT
*
567050 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
567070 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
567090 TTGTATCGATACAT
1 TTGTATCGATACAT
567104 TGCTTATAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:571726 original size:19 final size:19
Alignment explanation
Indices: 571702--571767 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
571692 AGTAGCTTCA
571702 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
571721 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
*
571735 T-TGTATCGATACAGCACT
1 TATGTATCGATACAACACT
571753 TATGTATCGATACAA
1 TATGTATCGATACAA
571768 ATCGTTGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 9 0.23
14 1 0.03
16 5 0.13
18 1 0.03
19 23 0.59
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:571741 original size:13 final size:13
Alignment explanation
Indices: 571723--571747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
571713 ACAACACTTA
571723 TGTATCGATACAT
1 TGTATCGATACAT
571736 TGTATCGATACA
1 TGTATCGATACA
571748 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:571745 original size:32 final size:32
Alignment explanation
Indices: 571704--571766 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
571694 TAGCTTCATA
571704 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
571736 TGTATCGATACAGCACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
571767 AATCGTTGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:578095 original size:21 final size:23
Alignment explanation
Indices: 578055--578098 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 23
578045 TTTTAACCGA
*
578055 TTATCAAGGGGGAGAAATTTTTT
1 TTATCAAGAGGGAGAAATTTTTT
578078 TTATCAA-AGGGA-AAATTTTTT
1 TTATCAAGAGGGAGAAATTTTTT
578099 AACAAGAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 4 0.20
23 7 0.35
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (23 bp):
TTATCAAGAGGGAGAAATTTTTT
Found at i:582728 original size:43 final size:43
Alignment explanation
Indices: 582665--582758 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
582655 TACTTTTCAT
** *
582665 AATGTATCGATACATGCATTTGAAATTTATAGTCGTTGGGCTC
1 AATGTATCGATACATGCATTTGAAATTTATAACCATTGGGCTC
* *
582708 AATGTATTGATACATTCATTTGAAATTTATAACCATTGGGCTC
1 AATGTATCGATACATGCATTTGAAATTTATAACCATTGGGCTC
*
582751 AATATATC
1 AATGTATC
582759 AATATATTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (43 bp):
AATGTATCGATACATGCATTTGAAATTTATAACCATTGGGCTC
Found at i:592657 original size:21 final size:21
Alignment explanation
Indices: 592633--592677 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
592623 AAAATATTCG
592633 ATTTA-AAGCTCGAAAACATTT
1 ATTTATAA-CTCGAAAACATTT
* *
592654 ATTTATAATTCTAAAACATTT
1 ATTTATAACTCGAAAACATTT
592675 ATT
1 ATT
592678 GATATTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTTATAACTCGAAAACATTT
Found at i:592879 original size:33 final size:32
Alignment explanation
Indices: 592816--592879 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
592806 CTTTTCAAGG
*
592816 TGTATCAATACTATGAACATGTATCAATACAA
1 TGTATCAATACTAAGAACATGTATCAATACAA
* * *
592848 TGTATCGATACTAAGCAATATGTATCGATACA
1 TGTATCAATACTAAG-AACATGTATCAATACA
592880 TCTAGGTGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (32 bp):
TGTATCAATACTAAGAACATGTATCAATACAA
Found at i:600113 original size:3 final size:3
Alignment explanation
Indices: 600105--600139 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
600095 AGTCAACTTT
* *
600105 ATC ATC ATC ATC ACC ATC ATC ATC TTC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
600140 TAATGGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:601820 original size:19 final size:20
Alignment explanation
Indices: 601796--601844 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
601786 CTTTTCAGGG
*
601796 TGTATCGATACTATG-AACA
1 TGTATCGATACTAAGCAACA
*
601815 TGTATCGATACTAAGCAATA
1 TGTATCGATACTAAGCAACA
601835 TGTATCGATA
1 TGTATCGATA
601845 TATCTGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (20 bp):
TGTATCGATACTAAGCAACA
Found at i:603558 original size:51 final size:50
Alignment explanation
Indices: 603493--603670 Score: 149
Period size: 51 Copynumber: 3.5 Consensus size: 50
603483 TCTTTTGTTG
* * * *
603493 AAAATTGGGGTTGGAGTATCCCCAACAGTGAAAAATTGATATTTTAAAAAT
1 AAAAATGGGATTGGAGTATCCCCGAC-GTGAAAAATTGATATTTTAAAAGT
* * * **
603544 AAAAATGGGATTGGAGTATCCTCGATGGTGAAAAATTCATATTTTGGAAGT
1 AAAAATGGGATTGGAGTATCCCCGA-CGTGAAAAATTGATATTTTAAAAGT
* * * * * * *
603595 AAATACGGGGTTAGAGTATCCCTGACGATGGAAAATTTGATATTTTTAAGAGT
1 AAAAATGGGATTGGAGTATCCCCGACG-T-GAAAAATTGATA-TTTTAAAAGT
* *
603648 AAAGATGGTATTGGAGTATCCCC
1 AAAAATGGGATTGGAGTATCCCC
603671 TCAAAAATGA
Statistics
Matches: 96, Mismatches: 27, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
50 1 0.01
51 61 0.64
52 10 0.10
53 24 0.25
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (50 bp):
AAAAATGGGATTGGAGTATCCCCGACGTGAAAAATTGATATTTTAAAAGT
Found at i:606000 original size:20 final size:20
Alignment explanation
Indices: 605977--606050 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
605967 ACAATTCAAA
605977 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
605997 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
606018 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
606038 GTATCGATACATG
1 GTATCGATACATG
606051 AAAAAGTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:606021 original size:21 final size:21
Alignment explanation
Indices: 605995--606070 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
605985 ACATGTTGCA
605995 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
606016 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
606036 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
*
606057 TTGTATCGATACAT
1 ATGTATCGATACAT
606071 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:606028 original size:41 final size:41
Alignment explanation
Indices: 605977--606070 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
605967 ACAATTCAAA
605977 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
*
606018 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
606059 GTATCGATACAT
1 GTATCGATACAT
606071 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:606127 original size:13 final size:13
Alignment explanation
Indices: 606109--606134 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
606099 TACAGCAAGT
606109 ATGTATCGATACA
1 ATGTATCGATACA
606122 ATGTATCGATACA
1 ATGTATCGATACA
606135 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:608376 original size:21 final size:21
Alignment explanation
Indices: 608343--608387 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
608333 TTGCAAGTTG
*
608343 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
608365 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
608385 AAA
1 AAA
608388 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:612322 original size:13 final size:13
Alignment explanation
Indices: 612304--612339 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
612294 TTTTTCTTTT
612304 TATCGATACAATG
1 TATCGATACAATG
*
612317 TATCGATACACTG
1 TATCGATACAATG
612330 TATCGATACA
1 TATCGATACA
612340 GGGTGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.14, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:614813 original size:20 final size:20
Alignment explanation
Indices: 614790--614863 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
614780 ACAATTCAAA
614790 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
614810 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
614831 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
614851 GTATCGATACATG
1 GTATCGATACATG
614864 AAAAAGTTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:614834 original size:21 final size:21
Alignment explanation
Indices: 614808--614883 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
614798 ACATGTTGCA
614808 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
614829 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
614849 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
*
614870 TTGTATCGATACAT
1 ATGTATCGATACAT
614884 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:614841 original size:41 final size:41
Alignment explanation
Indices: 614790--614883 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
614780 ACAATTCAAA
614790 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
*
614831 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGTT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
614872 GTATCGATACAT
1 GTATCGATACAT
614884 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:614940 original size:13 final size:13
Alignment explanation
Indices: 614922--614947 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
614912 TACAGCAAGT
614922 ATGTATCGATACA
1 ATGTATCGATACA
614935 ATGTATCGATACA
1 ATGTATCGATACA
614948 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:616056 original size:20 final size:20
Alignment explanation
Indices: 616010--616047 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
616000 ACATTTTAAA
616010 CATGTATTGATACATTCACT
1 CATGTATTGATACATTCACT
616030 CATGTATTGATACATTCA
1 CATGTATTGATACATTCA
616048 TGTTTGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (20 bp):
CATGTATTGATACATTCACT
Found at i:616089 original size:17 final size:17
Alignment explanation
Indices: 616063--616104 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
616053 GTATCGATAC
*
616063 AAATTGTAGAAATTTGA
1 AAATTTTAGAAATTTGA
616080 AAATTTTAGAAATTTGA
1 AAATTTTAGAAATTTGA
616097 AAATTTTA
1 AAATTTTA
616105 ACCATTGGGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (17 bp):
AAATTTTAGAAATTTGA
Found at i:616880 original size:13 final size:13
Alignment explanation
Indices: 616862--616887 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
616852 TACAGCAAGT
616862 ATGTATCGATACA
1 ATGTATCGATACA
616875 ATGTATCGATACA
1 ATGTATCGATACA
616888 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
Done.