Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold488
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: 2093548
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 4 of 14
Found at i:459820 original size:52 final size:52
Alignment explanation
Indices: 459687--459825 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 52
459677 GAAAATTTAT
* *
459687 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATAAATCTGGGCAAATTTGC
*** *
459739 CTGCATGTATCGATACATTTTATAATGTATCGATAAATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATAAATCTGGGCAAATTTGC
*
459791 CTGCATGTATCGATACA-AAGATCGGTGTATCGATA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATA
459826 CAATGTATCG
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATAAATCTGGGCAAATTTGC
Found at i:459834 original size:13 final size:13
Alignment explanation
Indices: 459816--459840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
459806 CAAAGATCGG
459816 TGTATCGATACAA
1 TGTATCGATACAA
459829 TGTATCGATACA
1 TGTATCGATACA
459841 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:459918 original size:33 final size:33
Alignment explanation
Indices: 459881--459947 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
459871 AGTAGCTTAA
459881 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
459914 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
459947 A
1 A
459948 AATCATTGAA
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:459921 original size:13 final size:13
Alignment explanation
Indices: 459903--459927 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
459893 CAAAAAAATA
459903 TGTATCGATACAT
1 TGTATCGATACAT
459916 TGTATCGATACA
1 TGTATCGATACA
459928 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:460828 original size:52 final size:52
Alignment explanation
Indices: 460694--461829 Score: 1858
Period size: 52 Copynumber: 22.0 Consensus size: 52
460684 GAAAAGTGAT
* * * * * * *
460694 AAAGATGCCAATATGTTGATTCACGGCCAACAATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG-G-A
* * * * *
460748 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
460801 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* *
460853 AAAGGTGCCAATATGTTGATTTAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
460905 AAAGGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
460957 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461009 AAAGGTGCTAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* *
461061 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461113 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAATGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461165 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461217 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
461269 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461321 AAAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
461373 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* *
461425 AAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461477 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
461529 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
461581 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
461633 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* *
461685 AAAAGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* * * *
461728 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* * *
461780 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGCTTAGAGGTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG
461830 CCAATGTGCT
Statistics
Matches: 1021, Mismatches: 51, Indels: 22
0.93 0.05 0.02
Matches are distributed among these distances:
43 37 0.04
44 1 0.00
46 1 0.00
49 1 0.00
51 1 0.00
52 933 0.91
53 6 0.01
54 5 0.00
55 36 0.04
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
Found at i:461750 original size:43 final size:43
Alignment explanation
Indices: 461689--461871 Score: 186
Period size: 43 Copynumber: 4.0 Consensus size: 43
461679 GGTGGAAAAA
* *
461689 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
461732 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC-T-----T---AAAG
* * * *
461784 GTGCCAATATGTTGATTCAAGGCCAGCTATATTGGGCTTAGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* * *
461827 GTGCCAATGTGCTAATTCAAGGCTAGCTACATTGGACTTAGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA-AAG
461871 G
1 G
461872 GTTACCACCG
Statistics
Matches: 115, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
43 71 0.62
44 4 0.03
46 1 0.01
49 1 0.01
51 1 0.01
52 37 0.32
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:461757 original size:95 final size:95
Alignment explanation
Indices: 461633--461871 Score: 372
Period size: 95 Copynumber: 2.5 Consensus size: 95
461623 TAAAGGTGAA
* *
461633 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAA-GTGCCAAT
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGT-GAAAAAGGTGCCAAT
461697 ATGCTGATTCAAGGCCAGCGATATTGGACTT
65 ATGCTGATTCAAGGCCAGCGATATTGGACTT
*
461728 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAAAAGGTGCCAATA
* * *
461793 TGTTGATTCAAGGCCAGCTATATTGGGCTT
66 TGCTGATTCAAGGCCAGCGATATTGGACTT
* * *
461823 AGAGGTGCCAATGTGCTAATTCAAGGCTAGCTACATTGGACTTAGAAGG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA-AAGG
461872 GTTACCACCG
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
94 6 0.05
95 123 0.93
96 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.26
Consensus pattern (95 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAAAAGGTGCCAATA
TGCTGATTCAAGGCCAGCGATATTGGACTT
Found at i:461905 original size:32 final size:32
Alignment explanation
Indices: 461864--461932 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
461854 TACATTGGAC
461864 TTAGA-AGGGTTACCACCGACTTGTGTGGGCT
1 TTAGAGAGGGTTACCACCGACTTGTGTGGGCT
*
461895 TTAGAGAGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAGAGGGTTACCACCGACTTGTGTGGGCT
461927 TT-GAGA
1 TTAGAGA
461933 CGAAAAAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 9 0.25
32 27 0.75
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (32 bp):
TTAGAGAGGGTTACCACCGACTTGTGTGGGCT
Found at i:461976 original size:28 final size:27
Alignment explanation
Indices: 461936--461996 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
461926 TTTGAGACGA
* *
461936 AAAAGGTTACCACGGAATTGTGGGCTTT
1 AAAAGGGTACCACGGAATTGTGGAC-TT
*
461964 AAAAGGGTACCACGGAGTTGTGGACTT
1 AAAAGGGTACCACGGAATTGTGGACTT
461991 AAAAGG
1 AAAAGG
461997 AACAAGGTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 8 0.27
28 22 0.73
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (27 bp):
AAAAGGGTACCACGGAATTGTGGACTT
Found at i:462038 original size:34 final size:34
Alignment explanation
Indices: 461964--462088 Score: 180
Period size: 34 Copynumber: 3.7 Consensus size: 34
461954 TGTGGGCTTT
* * * *
461964 AAAAGGGTACCACGGAGTTGTGGAC-TTAAAAGG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
*
461997 AACAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
462031 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
**
462065 AAGGAGGTGCCACGGAGTTGTGGG
1 AAAAAGGTGCCACGGAGTTGTGGG
462089 ATTTGCAGAA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 21 0.25
34 62 0.75
ACGTcount: A:0.32, C:0.13, G:0.36, T:0.19
Consensus pattern (34 bp):
AAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAG
Found at i:462103 original size:34 final size:33
Alignment explanation
Indices: 461945--462167 Score: 135
Period size: 34 Copynumber: 6.9 Consensus size: 33
461935 AAAAAGGTTA
* *
461945 CCACGGAATTGTGGGCTTT---AAAA-G-GGTA
1 CCACGGAGTTGTGGGCTTTAAGAAAAGGAGGTG
* **
461973 CCACGGAGTTGTGGAC-TTAA-AAGGAACAAGGTG
1 CCACGGAGTTGTGGGCTTTAAGAA--AAGGAGGTG
* **
462006 CCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTG
1 CCACGGAGTTGTGGGCTTTAAGAA-AAGGAGGTG
*
462040 CCACGGAGTTGTGGGCTTTAAAAAGAAGGAGGTG
1 CCACGGAGTTGTGGGCTTTAAGAA-AAGGAGGTG
* *
462074 CCACGGAGTTGTGGGATTTGCAGAAAAGGA--TG
1 CCACGGAGTTGTGGGCTTT-AAGAAAAGGAGGTG
* * * * *
462106 CCACTGAGTCGTGGACTTTGAGACAAA--AGATG
1 CCACGGAGTTGTGGGCTTTAAGA-AAAGGAGGTG
* * *
462138 CCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 CCACGGAGTTGTGGGCTTT-AAGAAAAGGA
462168 TGTCACTGAG
Statistics
Matches: 163, Mismatches: 17, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.01
28 14 0.09
29 2 0.01
30 1 0.01
31 5 0.03
32 44 0.27
33 21 0.13
34 69 0.42
35 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.33, T:0.21
Consensus pattern (33 bp):
CCACGGAGTTGTGGGCTTTAAGAAAAGGAGGTG
Found at i:462138 original size:32 final size:32
Alignment explanation
Indices: 462028--462224 Score: 174
Period size: 32 Copynumber: 6.2 Consensus size: 32
462018 GGGCTTTAAA
* * * *
462028 AAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTTG
* *
462059 AA-AAAGAAGGAGGTGCCACGGAGTTGTGGGA-TTTG
1 AAGAAA-AA-GA--TGCCACTGAGTCGT-GGACTTTG
* *
462094 CAGAAAAGGATGCCACTGAGTCGTGGACTTTG
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTTG
462126 -AGACAAAAGATGCCACTGAGTCGTGGACTTTG
1 AAGA-AAAAGATGCCACTGAGTCGTGGACTTTG
* *
462158 AAGAAAAGGATGTCACTGAGTCGTGGACTTTG
1 AAGAAAAAGATGCCACTGAGTCGTGGACTTTG
* *
462190 -AG-AAGAGATTGCCACTGAGTCATGGACTTT-
1 AAGAAAAAGA-TGCCACTGAGTCGTGGACTTTG
462220 AAGAA
1 AAGAA
462225 GATATTTGAA
Statistics
Matches: 140, Mismatches: 13, Indels: 25
0.79 0.07 0.14
Matches are distributed among these distances:
30 7 0.05
31 33 0.24
32 71 0.51
33 3 0.02
34 19 0.14
35 4 0.03
36 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.22
Consensus pattern (32 bp):
AAGAAAAAGATGCCACTGAGTCGTGGACTTTG
Found at i:462164 original size:64 final size:63
Alignment explanation
Indices: 462072--462224 Score: 204
Period size: 64 Copynumber: 2.4 Consensus size: 63
462062 AAGAAGGAGG
* * *
462072 TGCCACGGAGTTGTGGGA-TTTGCAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGACAAAAGA
1 TGCCACTGAGTCGT-GGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAG--AAAAGA
462136 -
63 T
* *
462136 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGTCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGAAAAGAT
*
462199 TGCCACTGAGTCATGGACTTT-AAGAA
1 TGCCACTGAGTCGTGGACTTTGAAGAA
462225 GATATTTGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
62 10 0.12
63 23 0.28
64 48 0.59
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (63 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGGATGCCACTGAGTCGTGGACTTTGAGAAAAGAT
Found at i:462226 original size:31 final size:31
Alignment explanation
Indices: 462072--462224 Score: 177
Period size: 32 Copynumber: 4.9 Consensus size: 31
462062 AAGAAGGAGG
* * *
462072 TGCCACGGAGTTGTGGGA-TTTGCAGAAAAGGA
1 TGCCACTGAGTCGT-GGACTTTGAAGAAAA-GA
*
462104 TGCCACTGAGTCGTGGACTTTGAGACAAAAGA
1 TGCCACTGAGTCGTGGACTTTGA-AGAAAAGA
462136 TGCCACTGAGTCGTGGACTTTGAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAA-GA
* *
462168 TGTCACTGAGTCGTGGACTTTG-AGAAGAGA
1 TGCCACTGAGTCGTGGACTTTGAAGAAAAGA
*
462198 TTGCCACTGAGTCATGGACTTT-AAGAA
1 -TGCCACTGAGTCGTGGACTTTGAAGAA
462225 GATATTTGAA
Statistics
Matches: 107, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
30 2 0.02
31 36 0.34
32 64 0.60
33 5 0.05
ACGTcount: A:0.29, C:0.16, G:0.31, T:0.24
Consensus pattern (31 bp):
TGCCACTGAGTCGTGGACTTTGAAGAAAAGA
Found at i:462355 original size:16 final size:17
Alignment explanation
Indices: 462324--462361 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
462314 GATGCAAATA
* *
462324 ATGATGTTATTGATGTT
1 ATGATGTTAATGATGTC
462341 ATGATG-TAATGATGTC
1 ATGATGTTAATGATGTC
462357 ATGAT
1 ATGAT
462362 TACAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.29, C:0.03, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTTAATGATGTC
Found at i:463207 original size:17 final size:17
Alignment explanation
Indices: 463187--463220 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
463177 TCTTCTTCTT
*
463187 TTTTTTTTCCTTTTTTG
1 TTTTGTTTCCTTTTTTG
*
463204 TTTTGTTTCTTTTTTTG
1 TTTTGTTTCCTTTTTTG
463221 GAAAAGAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (17 bp):
TTTTGTTTCCTTTTTTG
Found at i:463488 original size:16 final size:16
Alignment explanation
Indices: 463467--463517 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
463457 TTTTTGTGTG
463467 TGTTTTTTGTTTTGTT
1 TGTTTTTTGTTTTGTT
**
463483 TGTTTTTTGACTT-TT
1 TGTTTTTTGTTTTGTT
463498 T-TTTTTTGACTTTTGTT
1 TGTTTTTTG--TTTTGTT
463515 TGT
1 TGT
463518 GTGTTTACTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 7 0.26
15 3 0.11
16 13 0.48
17 3 0.11
18 1 0.04
ACGTcount: A:0.04, C:0.04, G:0.16, T:0.76
Consensus pattern (16 bp):
TGTTTTTTGTTTTGTT
Found at i:463503 original size:13 final size:14
Alignment explanation
Indices: 463485--463511 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
463475 GTTTTGTTTG
463485 TTTTTTGACTTTTT
1 TTTTTTGACTTTTT
463499 TTTTTTGACTTTT
1 TTTTTTGACTTTT
463512 GTTTGTGTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTTTGACTTTTT
Found at i:463528 original size:32 final size:30
Alignment explanation
Indices: 463469--463529 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
463459 TTTGTGTGTG
*
463469 TTTTTTGTTTTGTTTGTTTTTTGACTTTTT
1 TTTTTTGTTTTGTTTGTTGTTTGACTTTTT
463499 TTTTTTGACTTTTGTTTGTGTGTTT-ACTTTT
1 TTTTTTG--TTTTGTTTGT-TGTTTGACTTTT
463530 GACTGTTCCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 7 0.26
32 16 0.59
33 4 0.15
ACGTcount: A:0.05, C:0.05, G:0.15, T:0.75
Consensus pattern (30 bp):
TTTTTTGTTTTGTTTGTTGTTTGACTTTTT
Found at i:470500 original size:52 final size:52
Alignment explanation
Indices: 470430--470550 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
470420 GAAAATTTAT
*
470430 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
470482 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
470534 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
470551 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:470563 original size:52 final size:51
Alignment explanation
Indices: 470430--470570 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
470420 GAAAATTTAT
470430 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
470482 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
470534 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
470571 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:470577 original size:13 final size:13
Alignment explanation
Indices: 470559--470583 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470549 CAAAGATCAG
470559 TGTATCGATACAA
1 TGTATCGATACAA
470572 TGTATCGATACA
1 TGTATCGATACA
470584 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:470661 original size:33 final size:33
Alignment explanation
Indices: 470624--470690 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
470614 AGTAGCTTAA
470624 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
470657 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
470690 A
1 A
470691 AATCATTGAA
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:470664 original size:13 final size:13
Alignment explanation
Indices: 470646--470670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
470636 CAAAAAAATA
470646 TGTATCGATACAT
1 TGTATCGATACAT
470659 TGTATCGATACA
1 TGTATCGATACA
470671 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:470932 original size:52 final size:52
Alignment explanation
Indices: 470867--471318 Score: 778
Period size: 52 Copynumber: 8.7 Consensus size: 52
470857 ATAAAAATCT
*
470867 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
* * * *
470919 AAAAGGTGTCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAATGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
*
470971 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTAAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
* * *
471023 AAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTAG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
471075 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
*
471127 AAAATGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
*
471179 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
* *
471231 AAAAGGTGCCAATATGCTGATTCAAGGCCATCTATATTGGACTTAAAGGTGG
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
*
471283 AAAAGGTGCCAATATACTGATTCAAGGCCAGCGATA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
471319 GAGATATAAA
Statistics
Matches: 376, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 376 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGG
Found at i:472053 original size:52 final size:52
Alignment explanation
Indices: 471918--472576 Score: 1084
Period size: 52 Copynumber: 12.6 Consensus size: 52
471908 GAAAAGTGAT
* * * * * * *
471918 AAAGATGCCAATACGTTGATTCACGGCCAACAATATTGGACTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTG-G-A
* * * * *
471972 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
472025 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
472077 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* *
472129 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
* *
472181 AAAGGTGTCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
472233 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
472285 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
472337 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGG-A
* *
472390 AAATGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
472442 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
*
472494 AAAGGTGCCAATATGCTGATTCAAGGCCATCTATATTGGACTTAAAGGTGGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
472546 AAAGGTGCCAATATGCTGATTCAAGGCCAGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGC
472577 AATAGAGATA
Statistics
Matches: 569, Mismatches: 34, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
52 472 0.83
53 56 0.10
54 5 0.01
55 36 0.06
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGA
Found at i:474798 original size:18 final size:18
Alignment explanation
Indices: 474759--474801 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
474749 TGCTTAAAAT
474759 ATTTTTTTATTTTTTCTC
1 ATTTTTTTATTTTTTCTC
474777 -TTTTCTTTATTTTTTC-C
1 ATTTT-TTTATTTTTTCTC
474794 ATTTTTTT
1 ATTTTTTT
474802 CAATTTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (18 bp):
ATTTTTTTATTTTTTCTC
Found at i:483262 original size:84 final size:83
Alignment explanation
Indices: 483174--483328 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 83
483164 AAACAACATA
* * * *
483174 GATAAGGTTGTCTTTAA-AAGACAATATCTAAAGTAGACATGTATTAAGATAAAATGGATAATCT
1 GATAAGGTTGTC-TTAATAAGACAATATCTAAAGTAGAAATGTATCAAGA-AAAATAGATAAGCT
*
483238 TTTTTTAATAACATAATATG
64 TGTTTTAATAACATAATATG
* * *
483258 GATAAGGTTGTCTTAATAAGACACTGTCTAAAGTAGAAATGTGTCAAGAAAAATAGATAAGCTTG
1 GATAAGGTTGTCTTAATAAGACAATATCTAAAGTAGAAATGTATCAAGAAAAATAGATAAGCTTG
483323 TTTTAA
66 TTTTAA
483329 AAAGACAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
83 23 0.37
84 39 0.63
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.34
Consensus pattern (83 bp):
GATAAGGTTGTCTTAATAAGACAATATCTAAAGTAGAAATGTATCAAGAAAAATAGATAAGCTTG
TTTTAATAACATAATATG
Found at i:487464 original size:30 final size:30
Alignment explanation
Indices: 487429--487500 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 30
487419 TAAACATAAA
*
487429 TATTTATATTTTAATAATACAA-TATAATAT
1 TATTTATATTTTAATAATA-AATTATAACAT
487459 TA-TT-TATTTTAATAATAAATTATAACAT
1 TATTTATATTTTAATAATAAATTATAACAT
**
487487 TATCAATATTTTAA
1 TATTTATATTTTAA
487501 ATTTTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.06
28 22 0.61
29 2 0.06
30 10 0.28
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTTATATTTTAATAATAAATTATAACAT
Found at i:487555 original size:24 final size:25
Alignment explanation
Indices: 487503--487561 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
487493 TATTTTAAAT
*
487503 TTTAAATAATATTTTTAATATTTTA
1 TTTAAATAATATTTTTAATATTCTA
*
487528 -TTAAA-ACTATTTTT-ATATTACTA
1 TTTAAATAATATTTTTAATATT-CTA
487551 TTTAAATAATA
1 TTTAAATAATA
487562 AATTTATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.18
23 10 0.36
24 10 0.36
25 3 0.11
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTAAATAATATTTTTAATATTCTA
Found at i:487816 original size:12 final size:12
Alignment explanation
Indices: 487786--487835 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
487776 AAAATTGTAA
*
487786 AATAAT-ATTTT
1 AATAATAATTAT
487797 AATAATAATTAT
1 AATAATAATTAT
*
487809 ATTAATAATT-T
1 AATAATAATTAT
*
487820 AATAAAAATTAT
1 AATAATAATTAT
487832 AATA
1 AATA
487836 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 15 0.45
12 18 0.55
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AATAATAATTAT
Found at i:487820 original size:23 final size:23
Alignment explanation
Indices: 487788--487832 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
487778 AATTGTAAAA
* *
487788 TAATATTTTAATAATAATTATAT
1 TAATAATTTAATAAAAATTATAT
487811 TAATAATTTAATAAAAATTATA
1 TAATAATTTAATAAAAATTATA
487833 ATATTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATAATTTAATAAAAATTATAT
Found at i:487834 original size:20 final size:22
Alignment explanation
Indices: 487787--487841 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
487777 AAATTGTAAA
*
487787 ATAATATTTTAATAATAATTAT
1 ATAATATTTTAATAATAAATAT
*
487809 ATTAATAATTTAATAA-AAAT-T
1 A-TAATATTTTAATAATAAATAT
487830 ATAATATTTTAA
1 ATAATATTTTAA
487842 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 4 0.14
23 13 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATAATATTTTAATAATAAATAT
Found at i:488806 original size:16 final size:16
Alignment explanation
Indices: 488784--488845 Score: 70
Period size: 16 Copynumber: 3.9 Consensus size: 16
488774 GATCTATCGG
*
488784 ATTTGAATTTTTTTTA
1 ATTTGAATTTTTTTAA
* **
488800 GTTTGAATCATTTTAA
1 ATTTGAATTTTTTTAA
**
488816 ATTCAAATTTTTTTAA
1 ATTTGAATTTTTTTAA
488832 ATTTGAATTTTTTT
1 ATTTGAATTTTTTT
488846 GCTCTCTAAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (16 bp):
ATTTGAATTTTTTTAA
Found at i:489707 original size:21 final size:22
Alignment explanation
Indices: 489656--489708 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
489646 AAAAATATTT
*
489656 AAAATTA-AAAAAATTATTGAC
1 AAAATTATAAAAAATTATTGAA
*
489677 TAAATT-TAAAAAATTATT-AA
1 AAAATTATAAAAAATTATTGAA
489697 AAAATTATAAAA
1 AAAATTATAAAA
489709 TAAAACTCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 6 0.22
21 21 0.78
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (22 bp):
AAAATTATAAAAAATTATTGAA
Found at i:495089 original size:18 final size:18
Alignment explanation
Indices: 495053--495091 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
495043 ATTTGAGGAT
*
495053 GATATATTTGAAGTGGAG
1 GATATATTTGAAGTAGAG
**
495071 GATATATTTGTGGTAGAG
1 GATATATTTGAAGTAGAG
495089 GAT
1 GAT
495092 CTAATTAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.33, T:0.36
Consensus pattern (18 bp):
GATATATTTGAAGTAGAG
Found at i:500209 original size:33 final size:33
Alignment explanation
Indices: 500152--500217 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
500142 GCCAAGGAAA
*
500152 TGTATCGATACATTATTCAATGTATTGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
**
500185 TGTATCGATACATTGA-TCTTTGTATCGATACAT
1 TGTATCGATACATT-ATTCAATGTATCGATACAT
500218 CTGGGAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:508665 original size:30 final size:31
Alignment explanation
Indices: 508485--509043 Score: 465
Period size: 30 Copynumber: 17.8 Consensus size: 31
508475 CAATTCTTCA
*
508485 AATCTCTTTTCTCAAAGTCCACGACTCAGT-G
1 AATCTC-TTCCTCAAAGTCCACGACTCAGTGG
* * * *
508516 ACATCTTTTTTCTTCAAAGTCCACAACTTAGTGG
1 A-ATC--TCTTCCTCAAAGTCCACGACTCAGTGG
*
508550 AATCTCTTTTCTCAAAGTCCACGACTCAGTGG
1 AATCTC-TTCCTCAAAGTCCACGACTCAGTGG
* *
508582 CAATCTTTTTTCTTCAAAGTCCACGACTCAGTGG
1 -AATC--TCTTCCTCAAAGTCCACGACTCAGTGG
* * *
508616 CAATCTTTTTTCTTCAAAGTCCACGACTCGGTGG
1 -AATC--TCTTCCTCAAAGTCCACGACTCAGTGG
*
508650 AATCTCTTCCT-AAAGTCCACAACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* * * *
508680 CATCTCTTCTTTAAAGTCCACAACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* * *
508711 CATCTCTT-TTCTAAGTCCACGACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* *
508741 AATCATTTTTC-CAAAGTCCAC-ACTCAGTGG
1 AATC-TCTTCCTCAAAGTCCACGACTCAGTGG
* * *
508771 CAATCTTTTTCTTCAAAGTCCACGACTCAATGG
1 -AATC-TCTTCCTCAAAGTCCACGACTCAGTGG
* * * *
508804 CAT-TTTTCTTCAAAGTCCACAACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* * * *
508834 CATCTCTT-TTCTAAGTCCATGACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* * * * *
508864 CATTCTTTTCTTCAAAGTCCACAACTTAGTGG
1 -AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* *
508896 CATCTCTT-TTCAAAGTCCACGACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
*
508926 TAATCTCTT-CTCAAAATCCACGACTCAGTGG
1 -AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* * * *
508957 CATCTTTTCTTCAAAGTCCACAACTCAGTGG
1 AATCTCTTCCTCAAAGTCCACGACTCAGTGG
508988 CAATCTCTT-CTCAAAGTCCACGACTCAGTGG
1 -AATCTCTTCCTCAAAGTCCACGACTCAGTGG
* * *
509019 CATCTCTTCC-AAAAGTCCATGACTC
1 AATCTCTTCCTCAAAGTCCACGACTC
509044 TATGGCACCT
Statistics
Matches: 442, Mismatches: 65, Indels: 43
0.80 0.12 0.08
Matches are distributed among these distances:
30 150 0.34
31 134 0.30
32 60 0.14
33 38 0.09
34 59 0.13
35 1 0.00
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.32
Consensus pattern (31 bp):
AATCTCTTCCTCAAAGTCCACGACTCAGTGG
Found at i:508835 original size:123 final size:124
Alignment explanation
Indices: 508485--509084 Score: 623
Period size: 123 Copynumber: 4.8 Consensus size: 124
508475 CAATTCTTCA
* * * *
508485 AATCTCTTTTCTCAAAGTCCACGACTCAGTGACATCTTTTTTCTTCAAAGTCCACAACTTAGTGG
1 AATCT-TTTTCTCAAAGTCCACGACTCAGTGGCATC--TCTTCTTCAAAGTCCACGACTCAGTGG
* * *
508550 AATCTCTTT-TCTCAAAGTCCACGACTCAGTGGCAATCTTTTTTCTTCAAAGTCCACGACTCAGT
63 CATCT-TTTCT-TCAAAGTCCACAACTCAGTGGC-ATCTCTTTTC-T--AAGTCCACGACTCAGT
508614 GGC
122 GGC
* * * *
508617 AATCTTTTTTCTTCAAAGTCCACGACTCGGTGGAATCTCTTCCT-AAAGTCCACAACTCAGTGGC
1 AATC-TTTTTC-TCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTCAGTGGC
* *
508681 ATCTCTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGG-
64 ATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGC
* *
508741 AATCATTTTTC-CAAAGTCCAC-ACTCAGTGGCAATCTTTTTCTTCAAAGTCCACGACTCAATGG
1 AATC-TTTTTCTCAAAGTCCACGACTCAGTGGC-ATC-TCTTCTTCAAAGTCCACGACTCAGTGG
*
508804 CAT-TTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCATGACTCAGTGGC
63 CATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGC
* * * *
508865 ATTC-TTTTCTTCAAAGTCCACAACTTAGTGGCATCTCTT-TTCAAAGTCCACGACTCAGTGGTA
1 AATCTTTTTC-TCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTCAGTGG-C
* * * * * *
508928 ATCTCTTC-TCAAAATCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGC
64 ATCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCAGTGGC
* *
508989 AATC-TCTTCTCAAAGTCCACGACTCAGTGGCATCTCTTC--CAAAAGTCCATGACTCTA-TGGC
1 AATCTTTTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTTC-AAAGTCCACGACTC-AGTGGC
* * * *
509050 ACCTTTTTCTTTTCAAAGTCGATAACTCTGTGGCA
64 ATC-TTTTC--TTCAAAGTCCACAACTCAGTGGCA
509085 CCCTTTTAAG
Statistics
Matches: 402, Mismatches: 46, Indels: 46
0.81 0.09 0.09
Matches are distributed among these distances:
121 8 0.02
122 42 0.10
123 137 0.34
124 78 0.19
125 27 0.07
126 18 0.04
127 1 0.00
128 9 0.02
129 22 0.05
130 23 0.06
131 5 0.01
132 9 0.02
133 23 0.06
ACGTcount: A:0.25, C:0.28, G:0.14, T:0.33
Consensus pattern (124 bp):
AATCTTTTTCTCAAAGTCCACGACTCAGTGGCATCTCTTCTTCAAAGTCCACGACTCAGTGGCAT
CTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGC
Found at i:508877 original size:62 final size:62
Alignment explanation
Indices: 508489--509151 Score: 549
Period size: 62 Copynumber: 10.6 Consensus size: 62
508479 TCTTCAAATC
* * * * * *
508489 TCTTTTC-TCAAAGTCCACGACTCAGTGACATCTTTTTTCTTCAAAGTCCACAACTTAGTGGAAT
1 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTC-T--AAGTCCACGACTCAGTGGCAT
* *
508553 CTCTTTTC-TCAAAGTCCACGACTCAGTGGCAATCTTTTTTCTTCAAAGTCCACGACTCAGTGGC
1 -TCTTTTCTTCAAAGTCCACAACTCAGTGGC-ATCTCTTTTC-T--AAGTCCACGACTCAGTGGC
508617 AAT
61 -AT
* * * * * *
508620 CTTTTTTCTTCAAAGTCCACGACTCGGTGGAATCTC-TTCCTAAAGTCCACAACTCAGTGGCA-
1 -TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCT-AAGTCCACGACTCAGTGGCAT
* * *
508682 TCTCTTCTTTAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGG-AA
1 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCAT
* *
508743 TCATTTT-TCCAAAGTCCAC-ACTCAGTGGCAATCT-TTTTCTTCAAAGTCCACGACTCAATGGC
1 TC-TTTTCTTCAAAGTCCACAACTCAGTGGC-ATCTCTTTTC-T--AAGTCCACGACTCAGTGGC
508805 A-
61 AT
*
508806 T-TTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCATGACTCAGTGGCAT
1 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCAT
* * * *
508867 TCTTTTCTTCAAAGTCCACAACTTAGTGGCATCTCTTTTCAAAGTCCACGACTCAGTGGTAA
1 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCAT
* * * * * * *
508929 TCTCTTC-TCAAAATCCACGACTCAGTGGCATCTTTTCTTCAAAGTCCACAACTCAGTGGCAA
1 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTT-TTCTAAGTCCACGACTCAGTGGCAT
* * * * *
508991 TCTCTTC-TCAAAGTCCACGACTCAGTGGCATCTC-TTCCAAAAGTCCATGACTCTA-TGGCACC
1 TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTC-TAAGTCCACGACTC-AGTGGCA--
509053 T
62 T
* * * * * * *
509054 T-TTTCTTTTCAAAGTCGATAACTCTGTGGCA-C-CCTTT-TAAGT-CACAACTCTGTGGCACT
1 TCTTT-TCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCA-T
* *
509113 T-TTTTCTTCTTAAAGCCCACAACTCTGTGGCA-CTCTTTT
1 TCTTTTCTTC--AAAGTCCACAACTCAGTGGCATCTCTTTT
509152 TCCTTTAAAG
Statistics
Matches: 511, Mismatches: 59, Indels: 60
0.81 0.09 0.10
Matches are distributed among these distances:
58 4 0.01
59 6 0.01
60 66 0.13
61 119 0.23
62 143 0.28
63 39 0.08
64 39 0.08
65 29 0.06
66 33 0.06
67 13 0.03
68 20 0.04
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.33
Consensus pattern (62 bp):
TCTTTTCTTCAAAGTCCACAACTCAGTGGCATCTCTTTTCTAAGTCCACGACTCAGTGGCAT
Found at i:509078 original size:34 final size:33
Alignment explanation
Indices: 509030--510058 Score: 696
Period size: 34 Copynumber: 31.8 Consensus size: 33
509020 ATCTCTTCCA
** *
509030 AAAGTCCATGACTCTATGGCACCTTTTTCTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
509063 CAAAGTCGATAACTCTGTGGCACC-----CTTTT
1 -AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
*
509092 -AAGT-CACAACTCTGTGGCACTTTTTTCTTCTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTT-TT
* *
509124 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTTCTTTT
509158 AAAG-CTCACAACTCTGTGGCACTCTTTTTCCTTTT
1 AAAGTC-CACAACTCTGTGGCAC-CTTTTT-CTTTT
* *
509193 -AAGTCCACAATTCTGTGGCACCTTGTTCTTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTC-TTTT
* *
509226 AAAGCCCACAACTCCGTGGCACACTTTTT-TCTTT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTTCT-TTT
*
509260 AAAGTCCACAACTCTATGGCACC-----CTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * *
509288 -AAGTCCACAACTCCGTAGCAATCTTTTTCCTTTT
1 AAAGTCCACAACTCTGTGGC-ACCTTTTT-CTTTT
**
509322 -AAGTCCACAACTCCATGGCACC-----CTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
509349 -AAGCCCACAACTCCGTGGCACTCTTTTTCCTTTT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
* *
509383 -AAGTCCACAACTCCGTCGCACCTTGGTTT-TTTT
1 AAAGTCCACAACTCTGTGGCACCTT--TTTCTTTT
*
509416 -AAGTCCACAACTCCGTGGCACC-TTTTCTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * *
509447 TAAGTCTACAACTCCGTGGCACCTTTTTCCTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTT-CTTTT
* * * *
509481 AAAGCCCACAACTCCGTGGCACTCTGTATCTTTT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTTCTTTT
* * ** *
509515 TAAGTCTACAACTCCATGGCAATCTTTTTCCTTTT
1 AAAGTCCACAACTCTGTGGC-ACCTTTTT-CTTTT
* *
509550 AAA-TCCATAACTCTGTGGCACCTTGTTCTTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTC-TTTT
* * *
509583 AAA-TCCCACAACTCCGTGGCACTCTTTTTCCTTC
1 AAAGT-CCACAACTCTGTGGCAC-CTTTTTCTTTT
*
509617 AAAGTCCACAACTCTGTGACACC-----CTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * *
509645 -AGGTCCACAACTCCGTGGCAATCTTTTTCCTTTT
1 AAAGTCCACAACTCTGTGGC-ACCTTTTT-CTTTT
509679 -AAGTCCACAACTCTGTGGCACC-----CTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * *
509706 -AAGCCCATAACTCCGTGGCACTCTTTTTCTTTT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTTCTTTT
* *
509739 TAAGTCCACAACTCTGTGGCACTCTTTTTCCTTCT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
* * **
509774 -AAGCCCATAACTCCATGGCACTCTTTTTCCTTTT
1 AAAGTCCACAACTCTGTGGCAC-CTTTTT-CTTTT
509808 -AAGTCCACAACT-TCGTGGCACC----T-TTTT
1 AAAGTCCACAACTCT-GTGGCACCTTTTTCTTTT
* * *
509835 -AAGTCCACAACTCTGGGGCATCTTGTTCCTTTT
1 AAAGTCCACAACTCTGTGGCACCTT-TTTCTTTT
*
509868 -AAGTCCACAACTCCGTGGCACC-TTTTCTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* * * *
509899 TAAGTCCACGACTCCGTGGCACCTTGTTCCTTTT
1 AAAGTCCACAACTCTGTGGCACCTT-TTTCTTTT
*
509933 -AAGTCCACAACTCCGTGGCA-CTTTTTCTTTT
1 AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
* *
509964 TAAGTCCACAACTCTTTGGCACCATTTTTCCCTTTT
1 AAAGTCCACAACTCTGTGGCACC-TTTTT--CTTTT
* * * * *
510000 -AAGCCCACACCTCCGTGGCATCCTTTTTTCCTGT
1 AAAGTCCACAACTCTGTGGCA-CC-TTTTTCTTTT
*
510034 -AAGTCCATAACTCTGTGGCACCTTT
1 AAAGTCCACAACTCTGTGGCACCTTT
510059 AAGTCCAATA
Statistics
Matches: 812, Mismatches: 107, Indels: 154
0.76 0.10 0.14
Matches are distributed among these distances:
26 14 0.02
27 105 0.13
28 13 0.02
29 7 0.01
30 3 0.00
31 21 0.03
32 72 0.09
33 118 0.15
34 388 0.48
35 59 0.07
36 12 0.01
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.36
Consensus pattern (33 bp):
AAAGTCCACAACTCTGTGGCACCTTTTTCTTTT
Found at i:509170 original size:68 final size:65
Alignment explanation
Indices: 509086--510058 Score: 808
Period size: 68 Copynumber: 15.0 Consensus size: 65
509076 TCTGTGGCAC
* * *
509086 CCTTTTAAGT-CACAACTCTGTGGCACTTTTTTCTTCTTAAAGCCCACAACTCTGTGGCACTCTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTT-TT-AAGTCCACAACTCCGTGGCAC-CTT
509150 TTT
63 TTT
* * * *
509153 CCTTTAAAG-CTCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAATTCTGTGGCACCTT
1 CCTTTTAAGTC-CACAACTCCGTGGCACT-TTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTT
*
509217 GTT
63 TTT
* * * **
509220 CTTTTTAAAGCCCACAACTCCGTGGCACACTTTTTTCTTTAAAGTCCACAACTCTATGGCA-C--
1 CCTTTT-AAGTCCACAACTCCGTGG--CACTTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT
509282 ---
63 TTT
* * *
509282 CCTTTTAAGTCCACAACTCCGTAGCAATCTTTTTCCTTTTAAGTCCACAACTCCATGGCA-C---
1 CCTTTTAAGTCCACAACTCCGTGGC-A-CTTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTT
509343 --
64 TT
* *
509343 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTCGCACCTTG
1 CCTTTTAAGTCCACAACTCCGTGGCACT-TTTTT-CTTTTAAGTCCACAACTCCGTGGCACCTT-
509408 GTTT
63 -TTT
* *
509412 --TTTTAAGTCCACAACTCCGTGGCAC-CTTTTCTTTTTAAGTCTACAACTCCGTGGCACCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTC-TTTTAAGTCCACAACTCCGTGGCACCTTTT
509474 T
65 T
* * * * * *
509475 CCTTTTAAAGCCCACAACTCCGTGGCACTCTGTATCTTTTTAAGTCTACAACTCCATGGCAATCT
1 CCTTTT-AAGTCCACAACTCCGTGGCACT-TTTTTC-TTTTAAGTCCACAACTCCGTGGC-ACCT
509540 TTTT
62 TTTT
* * * * * *
509544 CCTTTTAAATCCATAACTCTGTGGCACCTTGTTCTTTTTAAATCCCACAACTCCGTGGCACTCTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTC-TTTTAAGT-CCACAACTCCGTGGCAC-CTT
509609 TTT
63 TTT
** * * * * *
509612 CCTTCAAAGTCCACAACTCTGTGACAC-----CCTTTTAGGTCCACAACTCCGTGGCAATCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTAAGTCCACAACTCCGTGGC-ACCTTTT
509672 T
65 T
* * * *
509673 CCTTTTAAGTCCACAACTCTGTGGCAC-----CCTTTTAAGCCCATAACTCCGTGGCACTCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTAAGTCCACAACTCCGTGGCAC-CTTTT
509733 T
65 T
* * * * * *
509734 CTTTTTAAGTCCACAACTCTGTGGCACTCTTTTTCCTTCTAAGCCCATAACTCCATGGCACTCTT
1 CCTTTTAAGTCCACAACTCCGTGGCACT-TTTTT-CTTTTAAGTCCACAACTCCGTGGCAC-CTT
509799 TTT
63 TTT
* * * * * *
509802 CCTTTTAAGTCCACAACTTCGTGGCAC----CT-TTTTAAGTCCACAACTCTGGGGCATCTTGTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
* * *
509862 CCTTTTAAGTCCACAACTCCGTGGCAC-CTTTTCTTTTTAAGTCCACGACTCCGTGGCACCTTGT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTC-TTTTAAGTCCACAACTCCGTGGCACCTTTT
509926 T
65 T
**
509927 CCTTTTAAGTCCACAACTCCGTGGCAC-TTTTTCTTTTTAAGTCCACAACTCTTTGGCACCATTT
1 CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTC-TTTTAAGTCCACAACTCCGTGGCACC-TTT
509991 TT
64 TT
* * * * * *
509993 CCCTTTTAAGCCCACACCTCCGTGGCATCCTTTTTTCCTGTAAGTCCATAACTCTGTGGCACCTT
1 -CCTTTTAAGTCCACAACTCCGTGGCA--CTTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTT
510058 T
63 T
510059 AAGTCCAATA
Statistics
Matches: 766, Mismatches: 92, Indels: 95
0.80 0.10 0.10
Matches are distributed among these distances:
59 3 0.00
60 38 0.05
61 209 0.27
62 13 0.02
63 6 0.01
64 1 0.00
65 117 0.15
66 24 0.03
67 78 0.10
68 215 0.28
69 49 0.06
70 13 0.02
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.36
Consensus pattern (65 bp):
CCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:509294 original size:27 final size:27
Alignment explanation
Indices: 509256--509375 Score: 114
Period size: 27 Copynumber: 4.2 Consensus size: 27
509246 ACACTTTTTT
* *
509256 CTTTAAAGTCCACAACTCTATGGCACC
1 CTTTTAAGTCCACAACTCCATGGCACC
* *
509283 CTTTTAAGTCCACAACTCCGTAGCAATCTTTTTC
1 CTTTTAAGTCCACAACTCCATGGC-A-C-----C
509317 CTTTTAAGTCCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCATGGCACC
* * *
509344 CTTTTAAGCCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCATGGCACC
509371 CTTTT
1 CTTTT
509376 TCCTTTTAAG
Statistics
Matches: 77, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
27 50 0.65
28 1 0.01
29 1 0.01
32 1 0.01
33 1 0.01
34 23 0.30
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.32
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCATGGCACC
Found at i:509296 original size:61 final size:61
Alignment explanation
Indices: 509046--509474 Score: 302
Period size: 61 Copynumber: 6.8 Consensus size: 61
509036 CATGACTCTA
* * *
509046 TGGCAC-C-TTTTTCTTTTCAAAGTCGATAACTCTGTGGCACCCTTTTAAGT-CACAACTCTG
1 TGGCACACTTTTTTC-TTT-AAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCG
* *
509106 TGG--CACTTTTTTCTTCTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTAAAG-CTCACA
1 TGGCACACTTTTTTC-T-TTAAAGTCCACAACTCTGTGGCA--C-----CCTTTTAAGTC-CACA
*
509168 ACTCTG
56 ACTCCG
* * * * *
509174 TGGCACTCTTTTTCCTTTTAAGTCCACAATTCTGTGGCACCTTGTTCTTTTTAAAGCCCACAACT
1 TGGCACACTTTTTTCTTTAAAGTCCACAACTCTGTGGCACC-----C-TTTT-AAGTCCACAACT
509239 CCG
59 CCG
*
509242 TGGCACACTTTTTTCTTTAAAGTCCACAACTCTATGGCACCCTTTTAAGTCCACAACTCCG
1 TGGCACACTTTTTTCTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCG
* * * ** *
509303 TAGCA-ATCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCCTTTTAAGCCCACAACTCCG
1 TGGCACA-CTTTTTTCTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCG
* * * * * *
509364 TGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTCGCACCTTGGTTTTTTTAAGTCCACAACTC
1 TGGCACACTTTTTTCTTTAAAGTCCACAACTCTGTGGCACC------CTTTTAAGTCCACAACTC
509429 CG
60 CG
* * *
509431 TGGCAC-CTTTTCTT-TTT-AAGTCTACAACTCCGTGGCACCTTTTT
1 TGGCACACTTTT-TTCTTTAAAGTCCACAACTCTGTGGCACCCTTTT
509475 CCTTTTAAAG
Statistics
Matches: 307, Mismatches: 31, Indels: 63
0.77 0.08 0.16
Matches are distributed among these distances:
58 1 0.00
59 6 0.02
60 30 0.10
61 107 0.35
62 5 0.02
63 1 0.00
65 20 0.07
66 10 0.03
67 36 0.12
68 81 0.26
69 2 0.01
70 8 0.03
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.37
Consensus pattern (61 bp):
TGGCACACTTTTTTCTTTAAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCCG
Found at i:509528 original size:357 final size:356
Alignment explanation
Indices: 509086--509991 Score: 1191
Period size: 357 Copynumber: 2.6 Consensus size: 356
509076 TCTGTGGCAC
* * *
509086 CCTTTTAAGTCACAACTCTGTGGCACTTTTTTCTTCTTAAAGCCCACAACTCTGTGGCACTCTTT
1 CCTTTTAAGTCACAACTCCGTGGCACCTTTTTCTT-TTAAAGCCCACAACTCTGTGGCACTC-TG
* * *
509151 TTCCTTTAAAG-CTCACAACTCTGTGGCACTCTTTTTCCTTTTAAGTCCACAATTCTGTGGCACC
64 TTCCTTTTAAGTCT-ACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACC
509215 TTGTTCTTTTTAAAGCCCACAACTCCGTGGCACACTTTTTTCTTTAAAGTCCACAACTCTATGGC
128 TTGTTCTTTTTAAAGCCCACAACTCCGTGGCACACTTTTTTCTTTAAAGTCCACAACTCTATGGC
509280 ACCCTTTTAAGTCCACAACTCCGTAGCAATCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCC
193 ACCCTTTTAAGTCCACAACTCCGTAGCAATCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCC
509345 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTCGCAC-CTTGG
258 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTCGCACTCTT--
* * *
509409 TTT-TTTTAAGTCCACAACTCCGTGGCAC-C-TTTT
321 TTTCTTCTAAGCCCACAACTCCATGGCACTCTTTTT
* *
509442 CTTTTTAAGTCTACAACTCCGTGGCACCTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTG
1 CCTTTTAAGTC-ACAACTCCGTGGCACCTTTTT-CTTTTAAAGCCCACAACTCTGTGGCACTCTG
* * * * *
509507 TATCTTTTTAAGTCTACAACTCCATGGCAATCTTTTTCCTTTTAAATCCATAACTCTGTGGCACC
64 T-TCCTTTTAAGTCTACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACC
* * * * * *
509572 TTGTTCTTTTTAAATCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGTCCACAACTCTGTGAC
128 TTGTTCTTTTTAAAGCCCACAACTCCGTGGCACACTTTTTTCTTTAAAGTCCACAACTCTATGGC
* * **
509637 ACCCTTTTAGGTCCACAACTCCGTGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCC
193 ACCCTTTTAAGTCCACAACTCCGTAGCAATCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCC
* * * *
509702 TTTTAAGCCCATAACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGGCACTCTTTT
258 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTCGCACTCTTTT
*
509767 TCCTTCTAAGCCCATAACTCCATGGCACTCTTTTT
323 T-CTTCTAAGCCCACAACTCCATGGCACTCTTTTT
* * *
509802 CCTTTTAAGTCCACAACTTCGTGGCACC----T-TTTT-AAGTCCACAACTCTGGGGCA-TCTTG
1 CCTTTTAAGT-CACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTC-TG
* * * *
509860 TTCCTTTTAAGTCCACAACTCCGTGGCAC-C-TTTTCTTTTTAAGTCCACGACTCCGTGGCACCT
64 TTCCTTTTAAGTCTACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCT
* * * *
509923 TGTTCCTTTT-AAGTCCACAACTCCGTGG--CAC-TTTTTCTTTTTAAGTCCACAACTCTTTGGC
129 TGTTCTTTTTAAAGCCCACAACTCCGTGGCACACTTTTTTC-TTTAAAGTCCACAACTCTATGGC
*
509984 ACCATTTT
193 ACCCTTTT
509992 TCCCTTTTAA
Statistics
Matches: 483, Mismatches: 55, Indels: 33
0.85 0.10 0.06
Matches are distributed among these distances:
346 5 0.01
347 28 0.06
349 16 0.03
350 37 0.08
351 1 0.00
352 26 0.05
353 20 0.04
354 4 0.01
356 16 0.03
357 271 0.56
358 29 0.06
359 1 0.00
360 28 0.06
361 1 0.00
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.37
Consensus pattern (356 bp):
CCTTTTAAGTCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTGTT
CCTTTTAAGTCTACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTG
TTCTTTTTAAAGCCCACAACTCCGTGGCACACTTTTTTCTTTAAAGTCCACAACTCTATGGCACC
CTTTTAAGTCCACAACTCCGTAGCAATCTTTTTCCTTTTAAGTCCACAACTCCATGGCACCCTTT
TAAGCCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCCGTCGCACTCTTTTTCT
TCTAAGCCCACAACTCCATGGCACTCTTTTT
Found at i:509653 original size:61 final size:61
Alignment explanation
Indices: 509512--510026 Score: 462
Period size: 61 Copynumber: 8.1 Consensus size: 61
509502 CTCTGTATCT
* * * * *
509512 TTTTAAGTCTACAACTCCATGGCAATCTTTTTCCTTTTAAATCCATAACTCTGTGGCACCTTGTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACC-----
509577 C
61 C
* ** *
509578 TTTTTAAATCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGTCCACAACTCTGTGACACCC
1 -TTTTAAGT-CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCC
* *
509641 TTTTAGGTCCACAACTCCGTGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCC
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCC
* * *
509702 TTTTAAGCCCATAACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGGCACTCTTTT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA--C----
509767 TCC
60 -CC
* * * * *
509770 TTCTAAGCCCATAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACT-TCGTGGCACCT
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCT-GTGGCACCC
* * * *
509831 TTTTAAGTCCACAACTCTGGGGCA-TCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTC
1 TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACC----C
* * *
509895 TTTTTAAGTCCACGACTCCGTGGCAC-CTTGTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTT
1 -TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC-----
*
509959 CT
60 CC
** * * * *
509961 TTTTAAGTCCACAACTCTTTGGCAC-CATTTTTCCCTTTTAAGCCCACACCTCCGTGGCATCC
1 TTTTAAGTCCACAACTCCGTGGCACTC-TTTTT-CCTTTTAAGTCCACAACTCTGTGGCACCC
510023 TTTT
1 TTTT
510027 TTCCTGTAAG
Statistics
Matches: 380, Mismatches: 45, Indels: 51
0.80 0.09 0.11
Matches are distributed among these distances:
60 32 0.08
61 121 0.32
62 11 0.03
63 2 0.01
65 77 0.20
66 5 0.01
67 32 0.08
68 99 0.26
70 1 0.00
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (61 bp):
TTTTAAGTCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCC
Found at i:509664 original size:129 final size:122
Alignment explanation
Indices: 509512--510026 Score: 435
Period size: 129 Copynumber: 4.0 Consensus size: 122
509502 CTCTGTATCT
* * *
509512 TTTTAAGTCTACAACTCCATGGCAATCTTTTTCCTTTTAAATCCATAACTCTGTGGCACCTTGTT
1 TTTTAAGTCCACAACTCCATGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCA-C-----
**
509577 CTTTTTAAATCCCACAACTCCGTGGCACTCTTTTTCCTTCAAAGTCCACAACTCTGTGACACCC
60 CTTTTTAAAT-CCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACCC
* * *
509641 TTTTAGGTCCACAACTCCGTGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
1 TTTTAAGTCCACAACTCCATGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
** * * *
509706 AAGCCCATAACTCCGTGGCACTCTTTTTCTTTTTAAGTCCACAACTCTGTGGCACTCTTTTTCC
66 AAATCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGT-G-ACAC-----CC
* * * *
509770 TTCTAAGCCCATAACTCCATGGCACTCTTTTTCCTTTTAAGTCCACAACT-TCGTGGCACCTTTT
1 TTTTAAGTCCACAACTCCATGGCAATCTTTTTCCTTTTAAGTCCACAACTCT-GTGGCACCTTTT
* * * * * *
509834 TAAGTCCACAACTCTGGGGCA-TCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACCTTTTC
65 TAAATCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACC----C
* * * * *
509895 TTTTTAAGTCCACGACTCCGTGGC-ACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCACTTTTT
1 -TTTTAAGTCCACAACTCCATGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCAC-----
* ** * * * * *
509959 CTTTTTAAGTCCACAACTCTTTGGCAC-CATTTTTCCCTTTTAAGCCCACACCTCCGTGGCATCC
60 CTTTTTAAATCCACAACTCCGTGGCACTC-TTTTT-CCTTTTAAGTCCACAACTCTGTGACACCC
510023 TTTT
1 TTTT
510027 TTCCTGTAAG
Statistics
Matches: 320, Mismatches: 44, Indels: 46
0.78 0.11 0.11
Matches are distributed among these distances:
121 1 0.00
122 42 0.13
123 8 0.03
124 3 0.01
125 31 0.10
126 20 0.06
127 5 0.02
128 29 0.09
129 127 0.40
130 25 0.08
131 4 0.01
132 25 0.08
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (122 bp):
TTTTAAGTCCACAACTCCATGGCAATCTTTTTCCTTTTAAGTCCACAACTCTGTGGCACCTTTTT
AAATCCACAACTCCGTGGCACTCTTTTTCCTTTTAAGTCCACAACTCTGTGACACCC
Found at i:509670 original size:27 final size:27
Alignment explanation
Indices: 509620--509671 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
509610 TTCCTTCAAA
* *
509620 GTCCACAACTCTGTGACACCCTTTTAG
1 GTCCACAACTCCGTGACAACCTTTTAG
* *
509647 GTCCACAACTCCGTGGCAATCTTTT
1 GTCCACAACTCCGTGACAACCTTTT
509672 TCCTTTTAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (27 bp):
GTCCACAACTCCGTGACAACCTTTTAG
Found at i:509717 original size:27 final size:27
Alignment explanation
Indices: 509673--509732 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
509663 CAATCTTTTT
* *
509673 CCTTTTAAGTCCACAACTCTGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
509700 CCTTTTAAGCCCATAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAC
*
509727 TCTTTT
1 CCTTTT
509733 TCTTTTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.33
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAC
Found at i:510220 original size:91 final size:88
Alignment explanation
Indices: 510058--510326 Score: 342
Period size: 91 Copynumber: 3.0 Consensus size: 88
510048 GTGGCACCTT
* * * *
510058 TAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGACCAATGTCGCT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCCCTTTCATCTTTAAGACCAATGTCGCT
510123 GGCCTTGAATCAGCACATTGGTA
66 GGCCTTGAATCAGCACATTGGTA
* * *
510146 TAAGCCCAATATCGCTGGCCTTGAATTAGCATATCGGCGCCTTCGTCATCTTTAAGACCAATGTT
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGC-CCTT--TCATCTTTAAGACCAATGTC
*
510211 GCTGGCCTTGAATCAGCACATTGGCA
63 GCTGGCCTTGAATCAGCACATTGGTA
* * * * *
510237 CAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTGAA-CCCAATATC
1 TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGC-CCTTT--CATCTTTAAGACCAATGTC
* *
510301 GCTAGCCTTGAATCAGCATATTGGTA
63 GCTGGCCTTGAATCAGCACATTGGTA
510327 CCTTTATCTT
Statistics
Matches: 156, Mismatches: 20, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
88 34 0.22
89 4 0.03
90 29 0.19
91 89 0.57
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (88 bp):
TAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCCCTTTCATCTTTAAGACCAATGTCGCT
GGCCTTGAATCAGCACATTGGTA
Found at i:510317 original size:51 final size:49
Alignment explanation
Indices: 510238--510707 Score: 327
Period size: 49 Copynumber: 9.8 Consensus size: 49
510228 ACATTGGCAC
*
510238 AAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT---ATCTTG
* * *
510290 AA-CCCAATATCGCTAGCCTTGAATCAGCATATTGGTACCTTTATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTG
* * * *
510338 AAGACCAATATCGCTGGCTTTAAATCAACATATTGG---C---A---T-
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTG
* * * *
510377 AAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTATCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTG
* * * *
510429 AAGCCCAATGTCGCTGGCCTTGAAT---CA-A----CA-CATTAGCAT-
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTG
* * *
510468 AAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TT-T-ATCTTG
* * * *
510520 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTT-ATCTTG
* ** * *
510569 AAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCGCCTTCATCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-ATCTTG
* * * * * *
510621 AAGACCAATGTCGCTAGTCTTGAATCAGCATATTGGCACCTTCATCTTT
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTG
* * * *
510670 AAGTCCGATATCGTTGGCCTTGAATCAGTATATTGGCA
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCA
510708 TATTTAACAT
Statistics
Matches: 338, Mismatches: 50, Indels: 63
0.75 0.11 0.14
Matches are distributed among these distances:
39 53 0.16
40 4 0.01
41 1 0.00
42 4 0.01
43 3 0.01
44 1 0.00
46 1 0.00
47 2 0.01
48 10 0.03
49 109 0.32
50 6 0.02
51 42 0.12
52 102 0.30
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTG
Found at i:510403 original size:39 final size:39
Alignment explanation
Indices: 510337--510413 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 39
510327 CCTTTATCTT
* *
510337 TAAGACCAATATCGCTGGCTTTAAATCAACATATTGGCA
1 TAAGACCAATATCACTGGCCTTAAATCAACATATTGGCA
* * *
510376 TAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGC
1 TAAGACCAATATCACTGGCCTTAAATCAACATATTGGC
510414 GCCTTTATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (39 bp):
TAAGACCAATATCACTGGCCTTAAATCAACATATTGGCA
Found at i:510403 original size:139 final size:142
Alignment explanation
Indices: 510147--510455 Score: 435
Period size: 139 Copynumber: 2.2 Consensus size: 142
510137 ACATTGGTAT
* * * *
510147 AAGCCCAATATCGCTGGCCTTGAATTAGCATATCGGCGCCTTCGTCATCTTTAAGACCAATGTTG
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATCGGCACCTTC-TCATCTTTAAGACCAATATCG
* *
510212 CTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCAC
65 CTGGCCTTAAATCAACACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCAC
510277 CTTTACCATCTTG
130 CTTTACCATCTTG
* * *
510290 AA-CCCAATATCGCTAGCCTTGAATCAGCATATTGGTACCTT-T-ATCTTTAAGACCAATATCGC
1 AAGCCCAATATCGCTGGCCTTGAATCAGCATATCGGCACCTTCTCATCTTTAAGACCAATATCGC
* * * * *
510352 TGGCTTTAAATCAACATATTGGCATAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCC
66 TGGCCTTAAATCAACACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACC
* *
510417 TTTATCATCTTT
131 TTTACCATCTTG
*
510429 AAGCCCAATGTCGCTGGCCTTGAATCA
1 AAGCCCAATATCGCTGGCCTTGAATCA
510456 ACACATTAGC
Statistics
Matches: 147, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
139 88 0.60
140 23 0.16
142 34 0.23
143 2 0.01
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (142 bp):
AAGCCCAATATCGCTGGCCTTGAATCAGCATATCGGCACCTTCTCATCTTTAAGACCAATATCGC
TGGCCTTAAATCAACACATTGGCACAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACC
TTTACCATCTTG
Found at i:510469 original size:91 final size:91
Alignment explanation
Indices: 510293--510647 Score: 410
Period size: 91 Copynumber: 3.8 Consensus size: 91
510283 CATCTTGAAC
* * *
510293 CCAATATCGCTAGCCTTGAATCAGCATATTGGTACC-TT-T-ATCTTTAAGACCAATATCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGACCAATGTCGCTGG
* * * *
510355 CTTTAAATCAACATATTGGCATAAGT
66 CCTTGAATCAACACATTAGCATAAGT
* * *
510381 CCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTATCATCTTTAAGCCCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGACCAATGTCGCTGG
510446 CCTTGAATCAACACATTAGCATAAGT
66 CCTTGAATCAACACATTAGCATAAGT
* * *
510472 CTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTCGCTGG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGACCAATGTCGCTGG
* *
510537 CCTTGAATCAGCACATTGGCACTTTCATCTTTAAGT
66 CCTTGAATCA--ACA----CA--TT-AGC-ATAAGT
** * * *
510573 CCAATATCGCTGGCCTTGAATCAATATATTGGCGCCTTCATCATCTTTAAGACCAATGTCGCTAG
1 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGACCAATGTCGCTGG
*
510638 TCTTGAATCA
66 CCTTGAATCA
510648 GCATATTGGC
Statistics
Matches: 228, Mismatches: 26, Indels: 13
0.85 0.10 0.05
Matches are distributed among these distances:
88 32 0.14
89 2 0.01
90 1 0.00
91 113 0.50
93 3 0.01
97 2 0.01
99 2 0.01
100 2 0.01
101 71 0.31
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (91 bp):
CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCATCTTTAAGACCAATGTCGCTGG
CCTTGAATCAACACATTAGCATAAGT
Found at i:510487 original size:230 final size:231
Alignment explanation
Indices: 510063--510605 Score: 784
Period size: 230 Copynumber: 2.4 Consensus size: 231
510053 ACCTTTAAGT
* *
510063 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGACCAATGTCGCTGGCCT
1 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGCCT
* * * * * *
510128 TGAATCAGCACATTGGTATAAGCCCAATATCGCTGGCCTTGAATTAGCATATCGGCGCCTTCGTC
66 TGAATCAACATATTGGCATAAGCCCAATATCACTGGCCTTGAATCAGCATATCGGCGCCTTCATC
* * *
510193 ATCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCACTGGCCT
131 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTAGCACAAGCCCAATATCACTGGCCT
510258 TGAATCAGCATATTGGCACCTTTACCATCTTGAA-C
196 TGAATCAGCATATTGGCACCTTTACCATCTTGAAGC
* *
510293 CCAATATCGCTAGCCTTGAATCAGCATATTGGTACCTTTATCTTTAAGACCAATATCGCTGGCTT
1 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGCCT
* * * *
510358 TAAATCAACATATTGGCATAAGTCCAATATCACTGGCCTTGAATCAGCATATTGGCGCCTTTATC
66 TGAATCAACATATTGGCATAAGCCCAATATCACTGGCCTTGAATCAGCATATCGGCGCCTTCATC
* * * * *
510423 ATCTTTAAGCCCAATGTCGCTGGCCTTGAATCAACACATTAGCATAAGTCTAATATCGCTGGCCT
131 ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTAGCACAAGCCCAATATCACTGGCCT
** * *
510488 TGAATCAGCATATTGGCACCTTTGTCATCTTTAAGT
196 TGAATCAGCATATTGGCACCTTTACCATCTTGAAGC
* * * *
510524 CCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CTTTCATCTTTAAGTCCAATATCGCTGGCC
1 CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTT-ATCTTTAAGACCAATATCGCTGGCC
*
510588 TTGAATCAATATATTGGC
65 TTGAATCAACATATTGGC
510606 GCCTTCATCA
Statistics
Matches: 277, Mismatches: 34, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
230 208 0.75
231 69 0.25
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (231 bp):
CCAATATCGCTAGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGACCAATATCGCTGGCCT
TGAATCAACATATTGGCATAAGCCCAATATCACTGGCCTTGAATCAGCATATCGGCGCCTTCATC
ATCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTAGCACAAGCCCAATATCACTGGCCT
TGAATCAGCATATTGGCACCTTTACCATCTTGAAGC
Found at i:510643 original size:101 final size:101
Alignment explanation
Indices: 510467--510759 Score: 372
Period size: 101 Copynumber: 2.9 Consensus size: 101
510457 CACATTAGCA
* * ** *
510467 TAAGTCTAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTCATCATCTTTAAGACCAATGTC
* *
510532 GCTGGCCTTGAATCAGCACATTGGCACTTTCATCTT
66 GCTAGCCTTGAATCAGCACATTGGCACCTTCATCTT
* *
510568 TAAGTCCAATATCGCTGGCCTTGAATCAATATATTGGCGCCTTCATCATCTTTAAGACCAATGTC
1 TAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTCATCATCTTTAAGACCAATGTC
* *
510633 GCTAGTCTTGAATCAGCATATTGGCACCTTCATCTT
66 GCTAGCCTTGAATCAGCACATTGGCACCTTCATCTT
* * ** * * *
510669 TAAGTCCGATATCGTTGGCCTTGAATCAGTATATTGGCATATTTAACAT-TCTTAAGCCCAATGT
1 TAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTCATCATCT-TTAAGACCAATGT
* * **
510733 CACTGGCCTTGTCTCAGCACATTGGCA
65 CGCTAGCCTTGAATCAGCACATTGGCA
510760 TTCTTCTTCA
Statistics
Matches: 165, Mismatches: 26, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
100 1 0.01
101 164 0.99
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (101 bp):
TAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTCATCATCTTTAAGACCAATGTC
GCTAGCCTTGAATCAGCACATTGGCACCTTCATCTT
Found at i:517373 original size:42 final size:45
Alignment explanation
Indices: 517317--517402 Score: 108
Period size: 42 Copynumber: 2.0 Consensus size: 45
517307 CTTAATATGC
**
517317 TTATTTTTTAAATATATTAAAA-T-ATTAAA-AATAAAA-ATTTTA
1 TTATTTTAAAAATATATTAAAAGTAATTAAATAA-AAAAGATTTTA
*
517359 TTATTTTAAAAATATTTTAAAAGTAATTAAATAAAAAAGATTTT
1 TTATTTTAAAAATATATTAAAAGTAATTAAATAAAAAAGATTTT
517403 TATTCATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
42 19 0.51
43 1 0.03
44 10 0.27
45 7 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (45 bp):
TTATTTTAAAAATATATTAAAAGTAATTAAATAAAAAAGATTTTA
Found at i:518267 original size:2 final size:2
Alignment explanation
Indices: 518262--518287 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
518252 CACACACTGA
518262 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
518288 CGTGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:521011 original size:2 final size:2
Alignment explanation
Indices: 521004--521037 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
520994 ACAGTAATTG
521004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
521038 GCATATGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523226 original size:15 final size:17
Alignment explanation
Indices: 523206--523242 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
523196 AAATTTAAAA
523206 ATTAAATATAT-TT-AT
1 ATTAAATATATATTCAT
523221 ATTAAATATATATTCAT
1 ATTAAATATATATTCAT
523238 ATTAA
1 ATTAA
523243 TTTGAATCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAAATATATATTCAT
Found at i:523362 original size:2 final size:2
Alignment explanation
Indices: 523355--523389 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
523345 GGGTTTCAGA
523355 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
523390 AATTAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:523635 original size:19 final size:19
Alignment explanation
Indices: 523599--523636 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
523589 ATTTAAATTT
*
523599 AAATCTACTACATATTAAA
1 AAATCTACTAAATATTAAA
523618 AAATCTACTTAAAT-TTAAA
1 AAATCTAC-TAAATATTAAA
523637 CTATTTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATCTACTAAATATTAAA
Found at i:523988 original size:193 final size:196
Alignment explanation
Indices: 523730--524087 Score: 499
Period size: 198 Copynumber: 1.8 Consensus size: 196
523720 ACCCTGTAAA
* * * * *
523730 TTATGAATAATGAATTAAATTAATAAATTTGTCTTATTTAAATATATATTTTTTATTAATTCATT
1 TTATGAATAATAAATTAAATAAATAAATTTATCTTATTTAAATATATAATTTTTAATAATTCATT
* * *
523795 TAAATCAGCTAAATATTTTACTTAAAGAG-TA-TAATTAAACAATTTTAATTAAAATATACTGTA
66 TAAATCACCTAAATATTTTAATTAAAGAGATATTAATTAAACAATTTTAATTAAAATATACTATA
* * *
523858 TACTGTAAACCTGAA-TTATAAGGAGGTAATTATAATGCAGATTGTAAGTTTCAAAAACTCTATA
131 TACTCTAAACC-AAAGTTATAAGGAGATAATTATAATGCAGATTGTAAGTTTCAAAAACTCTATA
523922 AT
195 AT
*
523924 TTATGAATAATAAATTAAATAAATAAATTTATC-TATTTAAATATGTAATTTTTAATAATTCATT
1 TTATGAATAATAAATTAAATAAATAAATTTATCTTATTTAAATATATAATTTTTAATAATTCATT
* * * *
523988 TAAATCACCTGAATATTTTAATTAAATAGTATATTTTAATTAAACTATTTTAATTAAAATATATT
66 TAAATCACCTAAATATTTTAATTAAAGAG-ATA--TTAATTAAACAATTTTAATTAAAATATACT
*
524053 ATATTCTCTAAACCAAAGTTATAAGGAGATAATTA
128 ATATACTCTAAACCAAAGTTATAAGGAGATAATTA
524088 ATATAAATTA
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
193 53 0.38
194 30 0.21
195 2 0.01
197 2 0.01
198 54 0.38
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (196 bp):
TTATGAATAATAAATTAAATAAATAAATTTATCTTATTTAAATATATAATTTTTAATAATTCATT
TAAATCACCTAAATATTTTAATTAAAGAGATATTAATTAAACAATTTTAATTAAAATATACTATA
TACTCTAAACCAAAGTTATAAGGAGATAATTATAATGCAGATTGTAAGTTTCAAAAACTCTATAA
T
Found at i:524036 original size:14 final size:14
Alignment explanation
Indices: 524019--524045 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
524009 TTAAATAGTA
524019 TATTTTAATTAAAC
1 TATTTTAATTAAAC
524033 TATTTTAATTAAA
1 TATTTTAATTAAA
524046 ATATATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTTTAATTAAAC
Found at i:524561 original size:2 final size:2
Alignment explanation
Indices: 524554--524582 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
524544 TTCCTAATAC
524554 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
524583 GTGTCTAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:527362 original size:22 final size:23
Alignment explanation
Indices: 527331--527427 Score: 56
Period size: 22 Copynumber: 4.1 Consensus size: 23
527321 TAGCGTACAT
*
527331 ATTTCATAACATAATAATAAATA
1 ATTTAATAACATAATAATAAATA
* *
527354 ATTT-ATAACACACAAGTAA-AAATT
1 ATTTAAT-A-ACATAA-TAATAAATA
* *
527378 ATTATGAATAAAATAATAATAAATG
1 ATT-T-AATAACATAATAATAAATA
* * *
527403 ATAT-ACAGCATAATAATAAATA
1 ATTTAATAACATAATAATAAATA
527425 ATT
1 ATT
527428 GTTAATTAGC
Statistics
Matches: 56, Mismatches: 11, Indels: 15
0.68 0.13 0.18
Matches are distributed among these distances:
22 18 0.32
23 5 0.09
24 16 0.29
25 14 0.25
26 1 0.02
27 2 0.04
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.32
Consensus pattern (23 bp):
ATTTAATAACATAATAATAAATA
Found at i:527478 original size:21 final size:23
Alignment explanation
Indices: 527453--527498 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
527443 ATATTTGAAG
527453 ATAATAGT-AAATTTTATAA-TT
1 ATAATAGTAAAATTTTATAACTT
*
527474 ATAATTGTAAAATTTTATAACTT
1 ATAATAGTAAAATTTTATAACTT
527497 AT
1 AT
527499 TATTAAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
ATAATAGTAAAATTTTATAACTT
Found at i:528365 original size:17 final size:18
Alignment explanation
Indices: 528345--528386 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
528335 AAAAATGAAT
*
528345 AAAAAATTTATGTTTA-A
1 AAAAAATTAATGTTTATA
* *
528362 AAAAACTTAATTTTTATA
1 AAAAAATTAATGTTTATA
528380 AAAAAAT
1 AAAAAAT
528387 ATATAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
AAAAAATTAATGTTTATA
Found at i:530588 original size:14 final size:14
Alignment explanation
Indices: 530569--530596 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
530559 TTTATAATTC
530569 TTATTAGGTATATT
1 TTATTAGGTATATT
530583 TTATTAGGTATATT
1 TTATTAGGTATATT
530597 GACTTAGATT
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:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (14 bp):
TTATTAGGTATATT
Found at i:531049 original size:3 final size:3
Alignment explanation
Indices: 531041--531074 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
531031 AGTAAAATCC
531041 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
531075 CGAATTTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:531429 original size:21 final size:22
Alignment explanation
Indices: 531398--531474 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 22
531388 GTAATTATAA
*
531398 AATATAAATATTATA-AAAAAT
1 AATAAAAATATTATATAAAAAT
* *
531419 AATTAAAATATTTTATAAAAAT
1 AATAAAAATATTATATAAAAAT
* *
531441 TATAAAAATA-TAAAT-AAAAT
1 AATAAAAATATTATATAAAAAT
*
531461 ATATAAATATATTA
1 A-ATAAAAATATTA
531475 AAATTTATAT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
20 5 0.11
21 23 0.52
22 16 0.36
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAAATATTATATAAAAAT
Found at i:531469 original size:41 final size:39
Alignment explanation
Indices: 531392--531492 Score: 93
Period size: 40 Copynumber: 2.6 Consensus size: 39
531382 TGTAATGTAA
*
531392 TTATAAAATATAAATATTATAAAAAATAATTAAAATATT
1 TTATAAAATATAAATAATATAAAAAATAATTAAAATATT
*
531431 TTATAAAAATTATAAA-AATATAAATAA-AATATATAAATA-T
1 TTAT-AAAA-TATAAATAATATAAAAAATAAT-TA-AAATATT
* * *
531471 AT-TAAAATTTATATAATATAAA
1 TTATAAAATATAAATAATATAAA
531493 TTATTAATAT
Statistics
Matches: 52, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
37 4 0.08
38 12 0.23
39 8 0.15
40 17 0.33
41 11 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (39 bp):
TTATAAAATATAAATAATATAAAAAATAATTAAAATATT
Found at i:531489 original size:38 final size:33
Alignment explanation
Indices: 531448--531528 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 33
531438 AATTATAAAA
* *
531448 ATATAAATA-AAATATATAAATATATTAAAATTT
1 ATATAAATATAAAT-TATTAATATAATAAAATTT
531481 ATAT-AATATAAATTATTAATATAATAAAATTT
1 ATATAAATATAAATTATTAATATAATAAAATTT
*
531513 ATATAAATATATATTA
1 ATATAAATATAAATTA
531529 ATTTAAACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 25 0.58
33 18 0.42
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
ATATAAATATAAATTATTAATATAATAAAATTT
Found at i:531507 original size:21 final size:21
Alignment explanation
Indices: 531393--531507 Score: 60
Period size: 21 Copynumber: 5.4 Consensus size: 21
531383 GTAATGTAAT
531393 TATAA-AATAT-AAATATTATA
1 TATAATAATATAAAATATTA-A
* * *
531413 AAAAATAAT-TAAAATATT-T
1 TATAATAATATAAAATATTAA
* *
531432 TATAAAAATTATAAAAATATAAA
1 TATAATAA-TAT-AAAATATTAA
*
531455 TAAAAT-ATATAAATATATTAAAA
1 TATAATAATATAAA-ATATT--AA
* *
531478 TTTATATAATATAAATTATTAA
1 TATA-ATAATATAAAATATTAA
531500 TATAATAA
1 TATAATAA
531508 AATTTATATA
Statistics
Matches: 69, Mismatches: 15, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
19 5 0.07
20 8 0.12
21 22 0.32
22 13 0.19
23 8 0.12
24 6 0.09
25 7 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
TATAATAATATAAAATATTAA
Found at i:531518 original size:14 final size:14
Alignment explanation
Indices: 531467--531518 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
531457 AAATATATAA
*
531467 ATATATTAAAATTT
1 ATATAATAAAATTT
531481 ATATAATATAAATTATT
1 ATATAATA-AAA-T-TT
531498 AATATAATAAAATTT
1 -ATATAATAAAATTT
531513 ATATAA
1 ATATAA
531519 ATATATATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 13 0.39
15 5 0.15
16 2 0.06
17 5 0.15
18 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATAATAAAATTT
Found at i:531535 original size:27 final size:30
Alignment explanation
Indices: 531469--531535 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 30
531459 ATATATAAAT
531469 ATATTAAAATTTATATAATATAAATTATTA
1 ATATTAAAATTTATATAATATAAATTATTA
*
531499 ATATAATAAAATTTATATAA-ATATA-TATTA
1 ATAT--TAAAATTTATATAATATAAATTATTA
531529 AT-TTAAA
1 ATATTAAA
531536 CATAATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
27 4 0.12
29 1 0.03
30 11 0.32
31 4 0.12
32 14 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (30 bp):
ATATTAAAATTTATATAATATAAATTATTA
Found at i:532944 original size:13 final size:13
Alignment explanation
Indices: 532909--532970 Score: 58
Period size: 13 Copynumber: 4.8 Consensus size: 13
532899 ATAAATTAAA
*
532909 ATATTTAAATATAT
1 ATATTAAAATA-AT
*
532923 ATAGT-AAATAAT
1 ATATTAAAATAAT
532935 ATATTAAAATAAT
1 ATATTAAAATAAT
*
532948 AAATATAAAAT-AT
1 ATAT-TAAAATAAT
532961 -TATTAAAATA
1 ATATTAAAATA
532971 CATAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 6 0.15
12 8 0.20
13 17 0.41
14 10 0.24
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATTAAAATAAT
Found at i:532956 original size:26 final size:26
Alignment explanation
Indices: 532895--532976 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
532885 TTATATACTT
* * *
532895 ATAAATA-AATTAAAATATTTAAAT-
1 ATAAATATAAATAATATATTAAAATA
*
532919 ATATATAGTAAATAATATATTAAAATA
1 ATAAATA-TAAATAATATATTAAAATA
532946 ATAAATAT-AA-AATATTATTAAAATA
1 ATAAATATAAATAATA-TATTAAAATA
532971 CATAAA
1 -ATAAA
532977 AAAATTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 10 0.21
25 12 0.25
26 20 0.42
27 6 0.12
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (26 bp):
ATAAATATAAATAATATATTAAAATA
Found at i:532962 original size:22 final size:23
Alignment explanation
Indices: 532898--532962 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
532888 TATACTTATA
532898 AATAAAT-TAAAATATTTAAATAT
1 AATAAATATAAAATA-TTAAATAT
*
532921 ATATAGTAA-ATAATATATTAAA-AT
1 A-ATA--AATATAAAATATTAAATAT
532945 AATAAATATAAAATATTA
1 AATAAATATAAAATATTA
532963 TTAAAATACA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
21 2 0.06
22 10 0.29
23 4 0.11
24 6 0.17
25 5 0.14
26 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
AATAAATATAAAATATTAAATAT
Found at i:533656 original size:22 final size:23
Alignment explanation
Indices: 533617--533659 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
533607 ATCATTTAAT
533617 TTATTTAATAAATAAAAATATTA
1 TTATTTAATAAATAAAAATATTA
*
533640 TTATTTAA-ATATAAAAATAT
1 TTATTTAATAAATAAAAATAT
533660 ATAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TTATTTAATAAATAAAAATATTA
Found at i:534081 original size:20 final size:22
Alignment explanation
Indices: 534047--534139 Score: 72
Period size: 22 Copynumber: 4.3 Consensus size: 22
534037 GATTTATAAT
534047 TTATATATTCGTATATTTT-ATTA
1 TTATATATT--TATATTTTAATTA
534070 -TATATATTTATATTTTAAATTA
1 TTATATATTTATATTTT-AATTA
* *
534092 TTATATATTTA-ATATAAATT-
1 TTATATATTTATATTTTAATTA
* *
534112 TTAATATATTAATAATTT-A-TA
1 TT-ATATATTTATATTTTAATTA
534133 TTATATA
1 TTATATA
534140 AATTTTAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
20 16 0.28
21 15 0.26
22 17 0.29
23 10 0.17
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (22 bp):
TTATATATTTATATTTTAATTA
Found at i:534109 original size:21 final size:21
Alignment explanation
Indices: 534066--534125 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
534056 CGTATATTTT
*
534066 ATTA-TATATATTTATATTTTAA
1 ATTATTATATATTTA-A-TATAA
534088 ATTATTATATATTTAATATAA
1 ATTATTATATATTTAATATAA
534109 ATT-TTA-ATATATTAATA
1 ATTATTATATAT-TTAATA
534126 ATTTATATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 4 0.11
20 9 0.26
21 7 0.20
22 5 0.14
23 10 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
ATTATTATATATTTAATATAA
Found at i:534153 original size:32 final size:35
Alignment explanation
Indices: 534103--534174 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 35
534093 TATATATTTA
*
534103 ATATAAATTTTAATATA-TTA-ATAA-TTTATATT
1 ATATAAATTTTAAAATATTTATATAATTTTATATT
534135 ATATAAATTTTAAAATATTTATATAATTTTTATATT
1 ATATAAATTTTAAAATATTTATATAA-TTTTATATT
534171 ATAT
1 ATAT
534175 TTTAATATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
32 16 0.46
33 3 0.09
34 4 0.11
36 12 0.34
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
ATATAAATTTTAAAATATTTATATAATTTTATATT
Found at i:534174 original size:22 final size:22
Alignment explanation
Indices: 534128--534199 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
534118 TATTAATAAT
*
534128 TTATA-TTATATAAATTTTA-A
1 TTATATTTATATAATTTTTATA
*
534148 -AATATTTATATAATTTTTATA
1 TTATATTTATATAATTTTTATA
534169 TTATATTT-TA-ATATTTTTATTA
1 TTATATTTATATA-ATTTTTA-TA
*
534191 CTATATTTA
1 TTATATTTA
534200 ACATTATCAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 3 0.07
20 14 0.33
21 10 0.24
22 15 0.36
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (22 bp):
TTATATTTATATAATTTTTATA
Found at i:534177 original size:32 final size:31
Alignment explanation
Indices: 534072--534179 Score: 98
Period size: 32 Copynumber: 3.5 Consensus size: 31
534062 TTTTATTATA
* *
534072 TATATTTATATTTTAAATTATTATAT-A-TTT
1 TATA-TTAAATTTTAAAATATTATATAATTTT
* * *
534102 AATA-TAAATTTTAATATATTA-ATAATTTA
1 TATATTAAATTTTAAAATATTATATAATTTT
534131 TATTATATAAATTTTAAAATATTTATATAATTTT
1 TA-TAT-TAAATTTTAAAATA-TTATATAATTTT
*
534165 TATATTATATTTTAA
1 TATATTAAATTTTAA
534180 TATTTTTATT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
27 2 0.03
28 15 0.24
29 3 0.05
30 5 0.08
32 22 0.35
33 6 0.10
34 9 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TATATTAAATTTTAAAATATTATATAATTTT
Found at i:534199 original size:21 final size:21
Alignment explanation
Indices: 534149--534200 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
534139 AAATTTTAAA
*
534149 ATATTTATATAATTTTTATATT
1 ATATTTA-ATAATTTTTATACT
534171 ATATTTTAAT-ATTTTTATTACT
1 ATA-TTTAATAATTTTTA-TACT
534193 ATATTTAA
1 ATATTTAA
534201 CATTATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.44
22 11 0.41
23 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATATTTAATAATTTTTATACT
Found at i:536750 original size:43 final size:44
Alignment explanation
Indices: 536668--536755 Score: 160
Period size: 43 Copynumber: 2.0 Consensus size: 44
536658 CGTCGTCCCT
536668 TTGAAAGAACTGATAACAGATAAACAATGATACAAAACGTTAAGA
1 TTGAAAGAACTGATAACAGA-AAACAATGATACAAAACGTTAAGA
536713 TTGAAAGAACTGATAACAG-AAACAATGATACAAAACGTTAAGA
1 TTGAAAGAACTGATAACAGAAAACAATGATACAAAACGTTAAGA
536756 AGGTAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
43 24 0.56
45 19 0.44
ACGTcount: A:0.53, C:0.11, G:0.16, T:0.19
Consensus pattern (44 bp):
TTGAAAGAACTGATAACAGAAAACAATGATACAAAACGTTAAGA
Found at i:536765 original size:45 final size:44
Alignment explanation
Indices: 536671--536765 Score: 138
Period size: 43 Copynumber: 2.1 Consensus size: 44
536661 CGTCCCTTTG
* *
536671 AAAGAACTGATAACAGATAAACAATGATACAAAACGTTAAGATTG
1 AAAGAACTGATAACAGA-AAACAATGATACAAAACGTTAAGAGTA
536716 AAAGAACTGATAACAG-AAACAATGATACAAAACGTTAAGAAGGTA
1 AAAGAACTGATAACAGAAAACAATGATACAAAACGTTAAG-A-GTA
536761 AAAGA
1 AAAGA
536766 CAATGAACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 23 0.50
44 1 0.02
45 22 0.48
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (44 bp):
AAAGAACTGATAACAGAAAACAATGATACAAAACGTTAAGAGTA
Found at i:540643 original size:88 final size:87
Alignment explanation
Indices: 540522--540691 Score: 272
Period size: 88 Copynumber: 1.9 Consensus size: 87
540512 GCAGAACACA
*
540522 GTGGATTCTAGATTAAAAACCAAACAAGCAATGGTCCTAAACTAACATTGATCACAAACCAAGCA
1 GTGGATTCTAGATTAAAAACCAAACAAGCAATGGTCCCAAACTAACATTGATCACAAACCAAGCA
540587 ATGG-TCTAATCCACTTGATATCG
66 ATGGTTC-AATCCA-TTGATATCG
* *
540610 GTGGATTCTAGATTAAAAACCAAAC-AGATAATGGTCCCAAACTAATATTGATCACAAACCAAGC
1 GTGGATTCTAGATTAAAAACCAAACAAG-CAATGGTCCCAAACTAACATTGATCACAAACCAAGC
540674 AATGGTTCAATCCATTGA
65 AATGGTTCAATCCATTGA
540692 CATTAATGTC
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
87 6 0.08
88 69 0.90
89 2 0.03
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (87 bp):
GTGGATTCTAGATTAAAAACCAAACAAGCAATGGTCCCAAACTAACATTGATCACAAACCAAGCA
ATGGTTCAATCCATTGATATCG
Found at i:547280 original size:13 final size:13
Alignment explanation
Indices: 547262--547288 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
547252 ACATTATGCT
547262 TTGTATCGATACA
1 TTGTATCGATACA
547275 TTGTATCGATACA
1 TTGTATCGATACA
547288 T
1 T
547289 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:547318 original size:20 final size:19
Alignment explanation
Indices: 547272--547328 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
547262 TTGTATCGAT
*
547272 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
547291 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
547310 ACAATTGTATCGACACATG
1 AC-ATTGTATCGATACATG
547329 AAATTGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:547401 original size:20 final size:20
Alignment explanation
Indices: 547357--547410 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
547347 CTACCACTAT
*
547357 TTGTATCAATACATGATACA
1 TTGTATCGATACATGATACA
*
547377 ATGTATCGATACATGATGA-A
1 TTGTATCGATACATGAT-ACA
547397 TTGTATCGATACAT
1 TTGTATCGATACAT
547411 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGATACA
Found at i:553598 original size:13 final size:13
Alignment explanation
Indices: 553580--553605 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
553570 ATATAATATT
553580 CATTGTATCGATA
1 CATTGTATCGATA
553593 CATTGTATCGATA
1 CATTGTATCGATA
553606 TACAAGGTAC
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):
CATTGTATCGATA
Found at i:555539 original size:21 final size:21
Alignment explanation
Indices: 555500--555576 Score: 100
Period size: 22 Copynumber: 3.6 Consensus size: 21
555490 AGATTTGACA
*
555500 AAGGGGGAGAAATGCTTTGATT
1 AAGGGGGAGAAAT-TTTTGATT
555522 AAGGGGGAGAAATTTTTGATT
1 AAGGGGGAGAAATTTTTGATT
* * *
555543 AAAGGGGAAAAATTCTTTAATT
1 AAGGGGGAGAAATT-TTTGATT
555565 AAGGGGGAGAAA
1 AAGGGGGAGAAA
555577 AACGAAAAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 19 0.40
22 29 0.60
ACGTcount: A:0.39, C:0.03, G:0.32, T:0.26
Consensus pattern (21 bp):
AAGGGGGAGAAATTTTTGATT
Found at i:556139 original size:13 final size:13
Alignment explanation
Indices: 556121--556147 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
556111 ACATTATGCT
556121 TTGTATCGATACA
1 TTGTATCGATACA
556134 TTGTATCGATACA
1 TTGTATCGATACA
556147 T
1 T
556148 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:556156 original size:19 final size:19
Alignment explanation
Indices: 556131--556186 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
556121 TTGTATCGAT
*
556131 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
*
556150 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
*
556169 ACAATTATATCGATACAT
1 AC-ATTGTATCGATACAT
556187 AAAATTGGCA
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:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:556274 original size:33 final size:33
Alignment explanation
Indices: 556216--556284 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
556206 CTACCACTAT
* *
556216 TTGTATCGATACATGGTACAATGTATCGATATA
1 TTGTATCGATACATGATACAATGTATCGATACA
*
556249 TTGTATCGATACATGATGA-ATTGTATCGATACA
1 TTGTATCGATACATGAT-ACAATGTATCGATACA
556282 TTG
1 TTG
556285 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGTATCGATACATGATACAATGTATCGATACA
Found at i:557109 original size:57 final size:56
Alignment explanation
Indices: 557017--557170 Score: 184
Period size: 57 Copynumber: 2.6 Consensus size: 56
557007 TAAGCTTTCA
* *
557017 AACCTAAATGAACCCAACATACATAGAATTTCATAAAAGTCCCTAGATCATGAAAAAT
1 AACCTAAAT-AGCCCAATATACATA-AATTTCATAAAAGTCCCTAGATCATGAAAAAT
*
557075 AACCTAAATAGCCCAATATACATAAATTTGCATAAAAGTCCCTAGATCATGGAAAAT
1 AACCTAAATAGCCCAATATACATAAATTT-CATAAAAGTCCCTAGATCATGAAAAAT
** *
557132 GTCCTAAAT-GACCCAATCATACATGAAATTACATGAAAA
1 AACCTAAATAG-CCCAAT-ATACAT-AAATTTCAT-AAAA
557171 TTTTGGGATC
Statistics
Matches: 85, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
56 6 0.07
57 52 0.61
58 18 0.21
59 9 0.11
ACGTcount: A:0.47, C:0.20, G:0.10, T:0.23
Consensus pattern (56 bp):
AACCTAAATAGCCCAATATACATAAATTTCATAAAAGTCCCTAGATCATGAAAAAT
Found at i:558050 original size:22 final size:22
Alignment explanation
Indices: 558025--558068 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
558015 ATCACTTACC
558025 CATCTTTATATGGTTCATGTTA
1 CATCTTTATATGGTTCATGTTA
558047 CATCTTTATATGGTTCATGTTA
1 CATCTTTATATGGTTCATGTTA
558069 TATTTAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (22 bp):
CATCTTTATATGGTTCATGTTA
Found at i:560478 original size:21 final size:21
Alignment explanation
Indices: 560454--560509 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
560444 ACGTTCACTG
* *
560454 GTTGCATTGATATATCTTCAT
1 GTTGTATTGATACATCTTCAT
560475 GTTGTATTGATACATCTTCAT
1 GTTGTATTGATACATCTTCAT
560496 GTTGTATTGATACA
1 GTTGTATTGATACA
560510 AAGCTTGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.46
Consensus pattern (21 bp):
GTTGTATTGATACATCTTCAT
Found at i:565006 original size:15 final size:15
Alignment explanation
Indices: 564955--565008 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
564945 AATTTTACTG
564955 AACTCTTTTAGTAGA
1 AACTCTTTTAGTAGA
*
564970 AACTTTACTTTTACT-G-
1 AAC--T-CTTTTAGTAGA
564986 AACTCTTTTAGTAGA
1 AACTCTTTTAGTAGA
565001 AACTCTTT
1 AACTCTTT
565009 CTCTAAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
13 7 0.22
14 2 0.06
15 11 0.34
16 3 0.09
17 2 0.06
18 7 0.22
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.44
Consensus pattern (15 bp):
AACTCTTTTAGTAGA
Found at i:566869 original size:157 final size:151
Alignment explanation
Indices: 566584--567112 Score: 505
Period size: 157 Copynumber: 3.4 Consensus size: 151
566574 TACAATTATG
* * * *
566584 AAAATGCCCCTAGGAGATATCTTCGACGTAGAAGTACTTGATACTCCTAAAGGACTTAAAAAGGA
1 AAAATGCCTCTAAG-GATA-CTTCGACGTA-AAGTACTCGATACCCCTAAAGGACTTAAAAAGGA
* * * * * * *
566649 TTATAG-ATAGGACAAACCTATCCTAAATACCCACTTTCGACGTAAAAGTGGACCCAGTTATAAC
63 TTATGGAATAGG-GAAACCTATCCTAAATACACACTTT-GGCGTAAAAGTAGACCTAGTGATAAC
566713 CTAGGACTCGGTTCTAAAAAATTACA
126 CTAGGACTCGGTTCTAAAAAATTACA
* *
566739 AAAATGCCTTTAGAGGATAGCTTCGACGTGAAAGTA-TCCAAGTACCCCTAAAGGACTTAAAAAG
1 AAAATGCCTCTA-AGGATA-CTTCGACGT-AAAGTACT-CGA-TACCCCTAAAGGACTTAAAAAG
* * * *
566803 GATTATGGAATAGGGTAAACCTATCCTAAATACTCACCTTTGGCATAAAAGCAGACCTAATGATA
61 GATTATGGAATAGGG-AAACCTATCCTAAATACACA-CTTTGGCGTAAAAGTAGACCTAGTGATA
* * * *
566868 ACCTATGAGTTGGTTCTAAAAAATTACT
124 ACCTAGGACTCGGTTCTAAAAAATTACA
* * * **
566896 AAAATACCCCTAAGAGATACATTTGACGTAGAAGTACTCGATACCCCTAAAAAACTTAAAAAGGA
1 AAAATGCCTCTAAG-GATAC-TTCGACGTA-AAGTACTCGATACCCCTAAAGGACTTAAAAAGGA
* * * * ** * *
566961 -TGTGGAAT---G-AACCTATCCTAAATGCAGAACTTCGGCGTGGAAGTAGACCTGGTGATAACG
63 TTATGGAATAGGGAAACCTATCCTAAATACA-CACTTTGGCGTAAAAGTAGACCTAGTGATAACC
* *
567021 TAGGACTCGATTCTAGGAAAATTACA
127 TAGGACTCGGTTCTA-AAAAATTACA
567047 AAAATGCCTCTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAGGACTTAAAAAGGA
1 AAAATGCCTCTAA-GGATA-CTTCGACGT-AAAGTACTCGATACCCCTAAAGGACTTAAAAAGGA
567112 T
63 T
567113 ATAGATTGGA
Statistics
Matches: 306, Mismatches: 51, Indels: 37
0.78 0.13 0.09
Matches are distributed among these distances:
150 49 0.16
151 63 0.21
152 4 0.01
154 1 0.00
155 36 0.12
156 56 0.18
157 92 0.30
158 5 0.02
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.24
Consensus pattern (151 bp):
AAAATGCCTCTAAGGATACTTCGACGTAAAGTACTCGATACCCCTAAAGGACTTAAAAAGGATTA
TGGAATAGGGAAACCTATCCTAAATACACACTTTGGCGTAAAAGTAGACCTAGTGATAACCTAGG
ACTCGGTTCTAAAAAATTACA
Found at i:569299 original size:22 final size:23
Alignment explanation
Indices: 569268--569311 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
569258 TGCTGTTATT
569268 GCTTGCTTTGCTGTTG-TCTTCA
1 GCTTGCTTTGCTGTTGCTCTTCA
*
569290 GCTTGTTTTGCTGTTGCTCTTC
1 GCTTGCTTTGCTGTTGCTCTTC
569312 TTGCTGCTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.02, C:0.23, G:0.23, T:0.52
Consensus pattern (23 bp):
GCTTGCTTTGCTGTTGCTCTTCA
Found at i:569578 original size:14 final size:14
Alignment explanation
Indices: 569531--569593 Score: 51
Period size: 16 Copynumber: 4.4 Consensus size: 14
569521 TAATTCGTAC
*
569531 AATTATATTATAAA
1 AATTAAATTATAAA
569545 AATT-AA-TA-AAA
1 AATTAAATTATAAA
569556 GAGATTAAATTATAAA
1 -A-ATTAAATTATAAA
*
569572 AATTAAAATTTAAAAA
1 AATT-AAA-TTATAAA
569588 AATTAA
1 AATTAA
569594 GATAAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 13
0.73 0.04 0.24
Matches are distributed among these distances:
11 3 0.08
12 3 0.08
13 4 0.10
14 9 0.22
15 8 0.20
16 13 0.32
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
AATTAAATTATAAA
Found at i:569745 original size:7 final size:7
Alignment explanation
Indices: 569733--569763 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
569723 TCGTATGTGA
569733 AAAAAAT
1 AAAAAAT
569740 AAAAAAT
1 AAAAAAT
569747 AAAAAAT
1 AAAAAAT
569754 AAAAAAT
1 AAAAAAT
569761 AAA
1 AAA
569764 TTGAATTCTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:569982 original size:165 final size:164
Alignment explanation
Indices: 569811--570159 Score: 407
Period size: 164 Copynumber: 2.1 Consensus size: 164
569801 ACACTATTAA
* * * *
569811 ATGAATTTTAAAAATTTTAAGCCAAGAAAAATCTCTTTGAAAATATTTATGGAA-TAGAAAAC-T
1 ATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCTTTGAAAA-ATTTA-CGAAGTAGAAAACAC
* * * * * *
569874 TGATTTTTCGGGAAAGGAAAATTTCAACGAAAAAATTCAAAACTCATGAAAATAAATTATTTTTT
64 CG-TATTTCAGAAAAGGAAAATTTCAACGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTT
* * * *
569939 AATAACTGATTTAATATG-AATCAAATGATGATATTTG
128 AAGAACTGATTAAATATGAAAT-AAATAATAATATTTG
** *
569976 ATGAATTTTAAAAATTAAAAACCTAGAAAAATCCCTTTGAAAAATTTACGAAGTAGAAAACACCG
1 ATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCTTTGAAAAATTTACGAAGTAGAAAACACCG
* * * * * * *
570041 TATTTCAGAAAAGGAGAATTTCAAGGAAAAATTTGAAAATTTATGAAAATAAGTGAATTTTTAAG
66 TATTTCAGAAAAGGAAAATTTCAACGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTAAG
*
570106 AACTGATTAAATATGAAATGAATAATAATATTTG
131 AACTGATTAAATATGAAATAAATAATAATATTTG
*
570140 ATTAATTTTAAAAATTTTAA
1 ATGAATTTTAAAAATTTTAA
570160 CCCTATAAAA
Statistics
Matches: 153, Mismatches: 28, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
163 3 0.02
164 108 0.71
165 42 0.27
ACGTcount: A:0.48, C:0.07, G:0.12, T:0.33
Consensus pattern (164 bp):
ATGAATTTTAAAAATTTTAAACCAAGAAAAATCCCTTTGAAAAATTTACGAAGTAGAAAACACCG
TATTTCAGAAAAGGAAAATTTCAACGAAAAAATTCAAAACTCATGAAAATAAATGAATTTTTAAG
AACTGATTAAATATGAAATAAATAATAATATTTG
Found at i:570520 original size:16 final size:16
Alignment explanation
Indices: 570478--570521 Score: 63
Period size: 15 Copynumber: 2.8 Consensus size: 16
570468 AAAGTTCACC
*
570478 TTATGAAAATTCATAA
1 TTATGAAAATTCAAAA
*
570494 TT-TGCAAATTCAAAA
1 TTATGAAAATTCAAAA
570509 TTATGAAAATTCA
1 TTATGAAAATTCA
570522 CTTGTGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 13 0.54
16 11 0.46
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (16 bp):
TTATGAAAATTCAAAA
Found at i:571068 original size:15 final size:15
Alignment explanation
Indices: 571048--571077 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
571038 ATGTCTATAA
571048 TGACCTAAAAATTCT
1 TGACCTAAAAATTCT
*
571063 TGACCTAAATATTCT
1 TGACCTAAAAATTCT
571078 CCTCCTCGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (15 bp):
TGACCTAAAAATTCT
Found at i:572267 original size:17 final size:17
Alignment explanation
Indices: 572245--572277 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
572235 TTCAATAAAC
572245 ATATTACTTT-CAAAATG
1 ATATTA-TTTACAAAATG
572262 ATATTATTTACAAAAT
1 ATATTATTTACAAAAT
572278 CAGGTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (17 bp):
ATATTATTTACAAAATG
Found at i:572426 original size:38 final size:36
Alignment explanation
Indices: 572377--572475 Score: 117
Period size: 37 Copynumber: 2.7 Consensus size: 36
572367 CTGTAGCATA
* *
572377 GGTTAGAACAAAAACCACTATTCTAATCCGGTGGCAC
1 GGTTAGAACAAAAACCATTATTCTAAT-CGATGGCAC
* *
572414 GGTTCAGAACAAAAACTATTATTCTTATCGATGGCAC
1 GGTT-AGAACAAAAACCATTATTCTAATCGATGGCAC
* *
572451 GAGTTGGAACAAAAATCATTATTCT
1 G-GTTAGAACAAAAACCATTATTCT
572476 TATCTAGTGG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 30 0.57
38 23 0.43
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (36 bp):
GGTTAGAACAAAAACCATTATTCTAATCGATGGCAC
Found at i:572498 original size:31 final size:31
Alignment explanation
Indices: 572460--572518 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
572450 CGAGTTGGAA
* *
572460 CAAAAATCATTATTCTTATCTAGTGGCATTG
1 CAAAAATCACTATTCTTAACTAGTGGCATTG
*
572491 CAAAAATCACTATTCTTAACTGGTGGCA
1 CAAAAATCACTATTCTTAACTAGTGGCA
572519 CGGTTTGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.34
Consensus pattern (31 bp):
CAAAAATCACTATTCTTAACTAGTGGCATTG
Found at i:573373 original size:15 final size:15
Alignment explanation
Indices: 573344--573411 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
573334 AAATATTACG
573344 ACTATAAAATAATTT
1 ACTATAAAATAATTT
573359 ACTA-AAAATATATTT
1 ACTATAAAATA-ATTT
* ***
573374 ATTATGTCATAATTT
1 ACTATAAAATAATTT
573389 A--ATAAAATAATTT
1 ACTATAAAATAATTT
*
573402 AATA-AAAATA
1 ACTATAAAATA
573412 TACTTATTAT
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.24
14 12 0.29
15 17 0.40
16 3 0.07
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (15 bp):
ACTATAAAATAATTT
Found at i:573400 original size:13 final size:13
Alignment explanation
Indices: 573382--573408 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
573372 TTATTATGTC
573382 ATAATTTAATAAA
1 ATAATTTAATAAA
573395 ATAATTTAATAAA
1 ATAATTTAATAAA
573408 A
1 A
573409 ATATACTTAT
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:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATTTAATAAA
Found at i:573408 original size:43 final size:43
Alignment explanation
Indices: 573347--573438 Score: 166
Period size: 43 Copynumber: 2.1 Consensus size: 43
573337 TATTACGACT
* *
573347 ATAAAATAATTTACTAAAAATATATTTATTATGTCATAATTTA
1 ATAAAATAATTTAATAAAAATATACTTATTATGTCATAATTTA
573390 ATAAAATAATTTAATAAAAATATACTTATTATGTCATAATTTA
1 ATAAAATAATTTAATAAAAATATACTTATTATGTCATAATTTA
573433 ATAAAA
1 ATAAAA
573439 CTCAAATATT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.41
Consensus pattern (43 bp):
ATAAAATAATTTAATAAAAATATACTTATTATGTCATAATTTA
Found at i:577001 original size:21 final size:21
Alignment explanation
Indices: 576975--577027 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
576965 TTCAACAAAT
*
576975 TGTATCGATACAAT-AGGGTAA
1 TGTATCGATACAATAAGCG-AA
*
576996 TGTATCGATA-TATAAGCGAA
1 TGTATCGATACAATAAGCGAA
577016 TGTATCGATACA
1 TGTATCGATACA
577028 TGTCTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 14 0.52
21 13 0.48
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (21 bp):
TGTATCGATACAATAAGCGAA
Found at i:577202 original size:52 final size:51
Alignment explanation
Indices: 577084--577266 Score: 231
Period size: 52 Copynumber: 3.5 Consensus size: 51
577074 TCTGGAATAA
* * * *
577084 AAATGTATCGATACATTTTTTATTGTATCGATACATTCTGGGTTTTGACCT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTTTGGTTTTTGACCT
* *
577135 AAATGTATCGATACATTCTTCATTGTATTGATACATTTTAGCTTTTTGACCT
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTTT-GGTTTTTGACCT
* * *
577187 AAATGTATCTATACATTCTTCATTGTATCGATTCATTTTGGGTTTTTGACCC
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTTT-GGTTTTTGACCT
* * * *
577239 AAATATATCAATAGATTCTTCAATGTAT
1 AAATGTATCGATACATTCTTCATTGTAT
577267 ATATACATGC
Statistics
Matches: 115, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 35 0.30
52 80 0.70
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (51 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTTTGGTTTTTGACCT
Found at i:577216 original size:103 final size:104
Alignment explanation
Indices: 577084--577274 Score: 269
Period size: 104 Copynumber: 1.8 Consensus size: 104
577074 TCTGGAATAA
* * * * *
577084 AAATGTATCGATACATTTTTTATTGTATCGATACATTCTGGG-TTTTGACCTAAATGTATCGATA
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTTGACCCAAATATATCAATA
*
577148 CATTCTTCATTGTAT-TGATACATTTTAGCTTTTTGACCT
66 CATTCTTCAATGTATAT-ATACATTTTAGCTTTTTGACCT
* * *
577187 AAATGTATCTATACATTCTTCATTGTATCGATTCATTTTGGGTTTTTGACCCAAATATATCAATA
1 AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTTGACCCAAATATATCAATA
*
577252 GATTCTTCAATGTATATATACAT
66 CATTCTTCAATGTATATATACAT
577275 GCAAGCAATT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
103 37 0.49
104 38 0.50
105 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.45
Consensus pattern (104 bp):
AAATGTATCGATACATTCTTCATTGTATCGATACATTCTGGGTTTTTGACCCAAATATATCAATA
CATTCTTCAATGTATATATACATTTTAGCTTTTTGACCT
Found at i:578334 original size:13 final size:13
Alignment explanation
Indices: 578316--578341 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
578306 TACAGCAAGT
578316 ATGTATCGATACA
1 ATGTATCGATACA
578329 ATGTATCGATACA
1 ATGTATCGATACA
578342 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:580591 original size:21 final size:21
Alignment explanation
Indices: 580558--580602 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
580548 TTGCAAGTTG
*
580558 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
580580 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
580600 AAA
1 AAA
580603 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:584517 original size:13 final size:13
Alignment explanation
Indices: 584499--584536 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
584489 GGAAATTCTA
*
584499 TGTATCGATACAT
1 TGTATCGATACAC
584512 TGTATCGATACAC
1 TGTATCGATACAC
584525 TGTATCGATACA
1 TGTATCGATACA
584537 GTGTGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAC
Done.