Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 180 of 325
Found at i:55424431 original size:27 final size:28
Alignment explanation
Indices: 55424399--55424452 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
55424389 CTAATACTAA
*
55424399 TTCTG-TAATAGGCTTAGGCCCACCTGG
1 TTCTGTTAATAGGCTAAGGCCCACCTGG
*
55424426 TTCTGTTAATGGGCTAAGGCCCACCTG
1 TTCTGTTAATAGGCTAAGGCCCACCTG
55424453 ATACTGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (28 bp):
TTCTGTTAATAGGCTAAGGCCCACCTGG
Found at i:55424459 original size:28 final size:28
Alignment explanation
Indices: 55424404--55424460 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
55424394 ACTAATTCTG
* * *
55424404 TAATAGGCTTAGGCCCACCTGGTTCTGT
1 TAATAGGCTAAGGCCCACCTGATACTGT
*
55424432 TAATGGGCTAAGGCCCACCTGATACTGT
1 TAATAGGCTAAGGCCCACCTGATACTGT
55424460 T
1 T
55424461 TCTGTGATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.25, T:0.30
Consensus pattern (28 bp):
TAATAGGCTAAGGCCCACCTGATACTGT
Found at i:55427468 original size:30 final size:30
Alignment explanation
Indices: 55427432--55427562 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
55427422 GACAAGATTG
* * * * *
55427432 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
55427462 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
55427490 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
55427520 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
55427549 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55427563 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:55427523 original size:58 final size:58
Alignment explanation
Indices: 55427432--55427562 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
55427422 GACAAGATTG
* * * * * *
55427432 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
55427490 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
55427549 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55427563 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:55435426 original size:30 final size:30
Alignment explanation
Indices: 55435390--55435520 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
55435380 GACAAGATTG
* * * * *
55435390 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
55435420 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
55435448 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
55435478 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
55435507 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55435521 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:55435481 original size:58 final size:58
Alignment explanation
Indices: 55435390--55435520 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
55435380 GACAAGATTG
* * * * * *
55435390 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
55435448 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
55435507 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
55435521 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:55439624 original size:42 final size:42
Alignment explanation
Indices: 55439507--55439712 Score: 247
Period size: 42 Copynumber: 4.9 Consensus size: 42
55439497 TACCATACCA
* * * *
55439507 ATGCTATATCCTAGATATGGTCTTACATGTAA-TCTCGTA-TCG
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCATACT-G
* * * *
55439549 ATGCCAATAGCCCTGGTATGGTCTTACATGAAGTCTCATACTG
1 ATGCC-ATATCCCAGATATGGTCTTACACGAAGTCTCATACTG
55439592 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATACTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATACTG
* * *
55439634 ATGCCATATCCCAGATATAGTCTTACACAAAGTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATACTG
*
55439676 ATGCCATATCCTAGATATGGTCTTACACGTAA-TCTCA
1 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCA
55439713 ATAACCCTAA
Statistics
Matches: 144, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
42 109 0.76
43 34 0.24
44 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTCTCATACTG
Found at i:55439683 original size:84 final size:85
Alignment explanation
Indices: 55439507--55439712 Score: 274
Period size: 84 Copynumber: 2.4 Consensus size: 85
55439497 TACCATACCA
* * * * * *
55439507 ATGCTATATCCTAGATATGGTCTTACATGTAATCTCGTATCGATGCCAATAGCCCTGGTATGGTC
1 ATGCCATATCCTAGATATGGTCTTACACGTAATCTCATATCGATGCCAATAGCCCAGATATAGTC
**
55439572 TTACATGAAGTCTCATACTG
66 TTACACAAAGTCTCATACTG
* *
55439592 ATGCCATATCCCAGATATGGTCTTACACG-AAGTCTCATA-CTGATGCC-ATATCCCAGATATAG
1 ATGCCATATCCTAGATATGGTCTTACACGTAA-TCTCATATC-GATGCCAATAGCCCAGATATAG
*
55439654 TCTTACACAAAGTCTCATATTG
64 TCTTACACAAAGTCTCATACTG
55439676 ATGCCATATCCTAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCTAGATATGGTCTTACACGTAATCTCA
55439713 ATAACCCTAA
Statistics
Matches: 106, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
84 66 0.62
85 40 0.38
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (85 bp):
ATGCCATATCCTAGATATGGTCTTACACGTAATCTCATATCGATGCCAATAGCCCAGATATAGTC
TTACACAAAGTCTCATACTG
Found at i:55445154 original size:27 final size:29
Alignment explanation
Indices: 55445110--55445186 Score: 88
Period size: 27 Copynumber: 2.8 Consensus size: 29
55445100 AAGACGTTTC
* *
55445110 CTTT-TAGAGATTTTCCACAAAGGCAT-T
1 CTTTATAGAGGTTTGCCACAAAGGCATAT
55445137 CTTTAT-GAGGTTTGCCACAAAGGCATAT
1 CTTTATAGAGGTTTGCCACAAAGGCATAT
* * *
55445165 CTTTCTAGAGTTTTTCCACAAA
1 CTTTATAGAGGTTTGCCACAAA
55445187 TGTTTCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
27 22 0.52
28 7 0.17
29 13 0.31
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (29 bp):
CTTTATAGAGGTTTGCCACAAAGGCATAT
Found at i:55445609 original size:53 final size:53
Alignment explanation
Indices: 55445492--55445698 Score: 249
Period size: 52 Copynumber: 3.9 Consensus size: 53
55445482 AAACTTCCCC
* * *
55445492 ATATGATGTCATAACCCACCAGTTATGGTCTTACATG-TATGGTCTTCTTTCT
1 ATATGATGTCATAACCCACCAATTACGGTCTTACACGATATGGTCTTCTTTCT
* *
55445544 ATATGATGTCATAACCCACTAGTTACGGTCTTACACGATATGGTCTTCTTTCT
1 ATATGATGTCATAACCCACCAATTACGGTCTTACACGATATGGTCTTCTTTCT
*** * * *
55445597 ATATGATGTCAT-ACCCACCAATTATAATCTTACACGATATAGACTT-TTTCCC
1 ATATGATGTCATAACCCACCAATTACGGTCTTACACGATATGGTCTTCTTT-CT
* * * *
55445649 ATATGATGTTATAACCCATCAATTACTGTCTTACAAGATATGGTCTTCTT
1 ATATGATGTCATAACCCACCAATTACGGTCTTACACGATATGGTCTTCTT
55445699 CAGTGCTATG
Statistics
Matches: 132, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
51 3 0.02
52 73 0.55
53 54 0.41
54 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (53 bp):
ATATGATGTCATAACCCACCAATTACGGTCTTACACGATATGGTCTTCTTTCT
Found at i:55445680 original size:105 final size:105
Alignment explanation
Indices: 55445492--55445698 Score: 267
Period size: 105 Copynumber: 2.0 Consensus size: 105
55445482 AAACTTCCCC
* ** * * * *
55445492 ATATGATGTCATAACCCACCAGTTATGGTCTTACATGTATGGTCTTCTTTCTATATGATGTCATA
1 ATATGATGTCATAACCCACCAATTATAATCTTACACGTATAGACTTCTTTCCATATGATGTCATA
* *
55445557 ACCCACTAGTTACGGTCTTACACGATATGGTCTTCTTTCT
66 ACCCACTAATTACGGTCTTACAAGATATGGTCTTCTTTCT
*
55445597 ATATGATGTCAT-ACCCACCAATTATAATCTTACACGATATAGACTT-TTTCCCATATGATGTTA
1 ATATGATGTCATAACCCACCAATTATAATCTTACACG-TATAGACTTCTTT-CCATATGATGTCA
*
55445660 TAACCCA-TCAATTACTGTCTTACAAGATATGGTCTTCTT
64 TAACCCACT-AATTACGGTCTTACAAGATATGGTCTTCTT
55445699 CAGTGCTATG
Statistics
Matches: 88, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
104 24 0.27
105 64 0.73
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.38
Consensus pattern (105 bp):
ATATGATGTCATAACCCACCAATTATAATCTTACACGTATAGACTTCTTTCCATATGATGTCATA
ACCCACTAATTACGGTCTTACAAGATATGGTCTTCTTTCT
Found at i:55446285 original size:42 final size:41
Alignment explanation
Indices: 55446177--55446333 Score: 156
Period size: 43 Copynumber: 3.7 Consensus size: 41
55446167 TTCCGATATG
* ** *
55446177 TGATTTCGTGTAAAACCACGTCTGGGATGTTGCCATCG-ATT
1 TGATTTCGTGTAAGACCACGTCTGGGA-CATGGCATCGTATT
*
55446218 TGAGATTTACGTGTAAGACCATGTCTGGGACATCGGCATCGTATT
1 T--GATTT-CGTGTAAGACCACGTCTGGGACAT-GGCATCGTATT
*
55446263 TGATTTCGTGTAAGACC-CTGTCTGGGACAGTGGCATCTATATT
1 TGATTTCGTGTAAGACCAC-GTCTGGGACA-TGGCATC-GTATT
* *
55446306 TGATTACATGTAAGACCACGTCTGGGAC
1 TGATTTCGTGTAAGACCACGTCTGGGAC
55446334 GTTGGCATTG
Statistics
Matches: 98, Mismatches: 9, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
41 1 0.01
42 27 0.28
43 40 0.41
44 26 0.27
45 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (41 bp):
TGATTTCGTGTAAGACCACGTCTGGGACATGGCATCGTATT
Found at i:55450167 original size:23 final size:22
Alignment explanation
Indices: 55450141--55450183 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
55450131 TTATGAAACA
*
55450141 TATGTTTTGATATGACTTTGGCT
1 TATGATTTGATATGA-TTTGGCT
*
55450164 TATGATTTGGTATGATTTGG
1 TATGATTTGATATGATTTGG
55450184 TATGAATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.19, C:0.05, G:0.26, T:0.51
Consensus pattern (22 bp):
TATGATTTGATATGATTTGGCT
Found at i:55450179 original size:10 final size:10
Alignment explanation
Indices: 55450141--55450188 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
55450131 TTATGAAACA
* *
55450141 TATGTTTTGA
1 TATGATTTGG
55450151 TATGACTTTGG
1 TATGA-TTTGG
55450162 CTTATGATTTGG
1 --TATGATTTGG
55450174 TATGATTTGG
1 TATGATTTGG
55450184 TATGA
1 TATGA
55450189 ATTATAAGCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 19 0.58
11 4 0.12
12 5 0.15
13 5 0.15
ACGTcount: A:0.21, C:0.04, G:0.25, T:0.50
Consensus pattern (10 bp):
TATGATTTGG
Found at i:55459561 original size:47 final size:47
Alignment explanation
Indices: 55459502--55459895 Score: 590
Period size: 47 Copynumber: 8.4 Consensus size: 47
55459492 GATGTACAAG
* * *
55459502 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
55459549 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * *
55459596 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
55459643 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * *
55459690 GTGTGTATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
55459737 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* * * * * * *
55459784 GTGTATATTTGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
*
55459831 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
* *
55459878 GCGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
55459896 TCCCGAAGGG
Statistics
Matches: 311, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 311 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAA
Found at i:55459618 original size:94 final size:94
Alignment explanation
Indices: 55459499--55459895 Score: 677
Period size: 94 Copynumber: 4.2 Consensus size: 94
55459489 ATTGATGTAC
55459499 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
55459564 AAGGCCGAATGGCCAATGTGATGAATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
55459593 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
55459658 AAGGCCGAATGGCCAATGTGATGAATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
*
55459687 AAGGTGTGTATATGTGATAAGGCCTAATGGTCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
55459752 AAGGCCGAATGGCCAATGTGATGAATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
* * * * * * *
55459781 AAAGTGTATATTTGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
*
55459846 AAGGCCGAATGGCCAATGTGATGGATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
* * * *
55459875 AAAGCGTATAAATGTGATAAG
1 AAGGTGTGTATATGTGATAAG
55459896 TCCCGAAGGG
Statistics
Matches: 289, Mismatches: 14, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
94 289 1.00
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (94 bp):
AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
AAGGCCGAATGGCCAATGTGATGAATGTG
Found at i:55461822 original size:40 final size:40
Alignment explanation
Indices: 55461761--55462114 Score: 530
Period size: 40 Copynumber: 8.9 Consensus size: 40
55461751 TTCAGTATGT
*
55461761 TATATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
55461801 TGTATCCGGGCTAAGTCCCGAAGAGCATTCGTACTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
55461841 TATATCCGGACTAGGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
55461881 TATATCCGGACTAGGTCCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
55461921 TGTATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* * *
55461961 TGTATCCGGGCTATGTTCCGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
55462001 TATACCCGGGCTAAGTCCCAAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* *
55462041 TATACCCGGGCTAAGTCCTGAAGAGCATTCGTGCTGGTGA
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
* * *
55462081 TGTATCCGGGCTAAGCCCCAAAG-GCATTCGTGCT
1 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
55462115 TGGACAAAAT
Statistics
Matches: 290, Mismatches: 24, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
39 11 0.04
40 279 0.96
ACGTcount: A:0.22, C:0.23, G:0.30, T:0.26
Consensus pattern (40 bp):
TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGA
Found at i:55465931 original size:47 final size:47
Alignment explanation
Indices: 55465872--55466265 Score: 599
Period size: 47 Copynumber: 8.4 Consensus size: 47
55465862 GATGTACAAG
* *
55465872 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * *
55465919 GTGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAG
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
55465966 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
55466013 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAG
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
55466060 GTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
*
55466107 GTGTATATATGTGATAAGGCCAAATGGCCAATGTGATGAATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* * * * *
55466154 GTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAG
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
55466201 GTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGGATGTGAAA
1 GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
* *
55466248 GCGTATAAATGTGATAAG
1 GTGTATATATGTGATAAG
55466266 TCCCGAAGGG
Statistics
Matches: 313, Mismatches: 34, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 313 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (47 bp):
GTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAA
Found at i:55466030 original size:94 final size:94
Alignment explanation
Indices: 55465869--55466265 Score: 677
Period size: 94 Copynumber: 4.2 Consensus size: 94
55465859 ATTGATGTAC
*
55465869 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGCATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
55465934 AAGGCCGAATGGCCAATGTGATGAATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
55465963 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
55466028 AAGGCCGAATGGCCAATGTGATGAATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
55466057 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
*
55466122 AAGGCCAAATGGCCAATGTGATGAATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
* * * * * *
55466151 AAAGTGTATATATGAGATAAGACCTAATGGCCGATGTGATGGATGTGAAGGTGTATATATGTGAT
1 AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
*
55466216 AAGGCCGAATGGCCAATGTGATGGATGTG
66 AAGGCCGAATGGCCAATGTGATGAATGTG
* * * *
55466245 AAAGCGTATAAATGTGATAAG
1 AAGGTGTGTATATGTGATAAG
55466266 TCCCGAAGGG
Statistics
Matches: 290, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 290 1.00
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.28
Consensus pattern (94 bp):
AAGGTGTGTATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGAT
AAGGCCGAATGGCCAATGTGATGAATGTG
Found at i:55467517 original size:42 final size:42
Alignment explanation
Indices: 55467449--55467588 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 42
55467439 GTTACAATGT
55467449 TGGCATCG-ATTTGAGATTTACGTGTAAGACCATGTCTGGGACA-
1 TGGCATCGTATTT--GATTT-CGTGTAAGACCATGTCTGGGACAG
*
55467492 TCGGCATCGTATTTGATTTCGTGTAAGACCCTGTCTGGGACAG
1 T-GGCATCGTATTTGATTTCGTGTAAGACCATGTCTGGGACAG
* ** *
55467535 TGGCATCGATATTTGATTACACGTAAGACCACGTCTGGGAC-G
1 TGGCATCG-TATTTGATTTCGTGTAAGACCATGTCTGGGACAG
*
55467577 TTGGCATTGTAT
1 -TGGCATCGTAT
55467589 GAGTTTTTCG
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
42 33 0.39
43 41 0.48
44 7 0.08
45 4 0.05
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (42 bp):
TGGCATCGTATTTGATTTCGTGTAAGACCATGTCTGGGACAG
Found at i:55468273 original size:23 final size:22
Alignment explanation
Indices: 55468242--55468284 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
55468232 TTGTGAAACA
*
55468242 TATGTTTTGGTATGACTTTGGCT
1 TATGATTTGGTATGA-TTTGGCT
55468265 TATGATTTGGTATGATTTGG
1 TATGATTTGGTATGATTTGG
55468285 TATGAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.16, C:0.05, G:0.28, T:0.51
Consensus pattern (22 bp):
TATGATTTGGTATGATTTGGCT
Found at i:55468280 original size:10 final size:10
Alignment explanation
Indices: 55468242--55468289 Score: 60
Period size: 10 Copynumber: 4.5 Consensus size: 10
55468232 TTGTGAAACA
*
55468242 TATGTTTTGG
1 TATGATTTGG
55468252 TATGACTTTGG
1 TATGA-TTTGG
55468263 CTTATGATTTGG
1 --TATGATTTGG
55468275 TATGATTTGG
1 TATGATTTGG
55468285 TATGA
1 TATGA
55468290 ATTATAAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 19 0.56
11 5 0.15
12 5 0.15
13 5 0.15
ACGTcount: A:0.19, C:0.04, G:0.27, T:0.50
Consensus pattern (10 bp):
TATGATTTGG
Found at i:55478422 original size:28 final size:27
Alignment explanation
Indices: 55478384--55478440 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
55478374 ATATATTCTT
55478384 AATAAATTTATCTAAATAATTATCTAAAC
1 AATAAATTTATCTAAATAATT-T-TAAAC
*
55478413 AATAAA-TTATCTAAGTAATTTTAAAC
1 AATAAATTTATCTAAATAATTTTAAAC
55478439 AA
1 AA
55478441 ATTATCATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 7 0.26
27 1 0.04
28 13 0.48
29 6 0.22
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.37
Consensus pattern (27 bp):
AATAAATTTATCTAAATAATTTTAAAC
Found at i:55480116 original size:9 final size:9
Alignment explanation
Indices: 55480104--55480155 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
55480094 TTTAATTATT
55480104 TTTTTACAA
1 TTTTTACAA
*
55480113 TTTTTTTGATAA
1 --TTTTT-ACAA
*
55480125 TTTTTATAA
1 TTTTTACAA
55480134 TTTTTACAA
1 TTTTTACAA
55480143 TATTTTACAA
1 T-TTTTACAA
55480153 TTT
1 TTT
55480156 CTAGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 15 0.41
10 14 0.38
11 5 0.14
12 3 0.08
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (9 bp):
TTTTTACAA
Found at i:55480116 original size:10 final size:10
Alignment explanation
Indices: 55480103--55480204 Score: 61
Period size: 10 Copynumber: 10.5 Consensus size: 10
55480093 TTTTAATTAT
*
55480103 TTTTTTACAA
1 TTTTTTATAA
55480113 TTTTTTTGATAA
1 -TTTTTT-ATAA
55480125 -TTTTTATAA
1 TTTTTTATAA
*
55480134 -TTTTTACAA
1 TTTTTTATAA
* *
55480143 TATTTTACAA
1 TTTTTTATAA
* *
55480153 ---TTTCTAG
1 TTTTTTATAA
55480160 TTTTTTATAA
1 TTTTTTATAA
* *
55480170 TTTTTGATAG
1 TTTTTTATAA
*
55480180 TTTTTTATTA
1 TTTTTTATAA
*
55480190 TTTTTTACAA
1 TTTTTTATAA
55480200 TTTTT
1 TTTTT
55480205 AAAAATTCTA
Statistics
Matches: 71, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
7 4 0.06
9 12 0.17
10 46 0.65
11 6 0.08
12 3 0.04
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:55480172 original size:57 final size:56
Alignment explanation
Indices: 55480103--55480214 Score: 138
Period size: 57 Copynumber: 2.0 Consensus size: 56
55480093 TTTTAATTAT
* *
55480103 TTTTTTACAATTTTTTTGATA-ATTTTTA-TAATTTTTACAATATTTTACAATTTCTAG
1 TTTTTTACAA--TTTTTGATAGATTTTTATTAATTTTTACAAT-TTTTAAAAATTCTAG
* * *
55480160 TTTTTTATAATTTTTGATAGTTTTTTATTATTTTTTACAATTTTTAAAAATTCTA
1 TTTTTTACAATTTTTGATAGATTTTTATTAATTTTTACAATTTTTAAAAATTCTA
55480215 ACATATTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
55 9 0.19
56 18 0.38
57 21 0.44
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (56 bp):
TTTTTTACAATTTTTGATAGATTTTTATTAATTTTTACAATTTTTAAAAATTCTAG
Found at i:55480196 original size:47 final size:46
Alignment explanation
Indices: 55480114--55480202 Score: 117
Period size: 47 Copynumber: 1.9 Consensus size: 46
55480104 TTTTTACAAT
55480114 TTTTTTGATAATTTTTATAATTTTTACAATATTTTACAATTTCTAG
1 TTTTTTGATAATTTTTATAATTTTTACAATATTTTACAATTTCTAG
* ** *
55480160 TTTTTT-ATAATTTTTGATAGTTTTTTATTATTTTTTACAATTT
1 TTTTTTGATAATTTTT-ATA-ATTTTTACAATATTTTACAATTT
55480203 TTAAAAATTC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 9 0.24
46 9 0.24
47 19 0.51
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (46 bp):
TTTTTTGATAATTTTTATAATTTTTACAATATTTTACAATTTCTAG
Found at i:55480251 original size:29 final size:30
Alignment explanation
Indices: 55480188--55480244 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55480178 AGTTTTTTAT
* *
55480188 TATTTTTTACAATTTTTAAAAATTCTAACA
1 TATTTTTTACAATTTTCAAAAATTATAACA
55480218 TATTTTTTA-AATTTTCAAACAATTATA
1 TATTTTTTACAATTTTCAAA-AATTATA
55480245 TATATTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTTTTACAATTTTCAAAAATTATAACA
Found at i:55480870 original size:16 final size:15
Alignment explanation
Indices: 55480837--55480872 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
55480827 AAGTAGAGTT
*
55480837 TAAATAATTATTTAA
1 TAAATAATTATATAA
55480852 TAAATAATATATATAA
1 TAAATAAT-TATATAA
55480868 TAAAT
1 TAAAT
55480873 TACTAGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAATAATTATATAA
Found at i:55482383 original size:9 final size:9
Alignment explanation
Indices: 55482369--55482431 Score: 63
Period size: 9 Copynumber: 6.8 Consensus size: 9
55482359 TTCACATCCT
55482369 TCTCTCAAC
1 TCTCTCAAC
*
55482378 TCTCTCAAT
1 TCTCTCAAC
*
55482387 TCTCTCAAAT
1 TCTCTC-AAC
55482397 TCTCTCAAAC
1 TCTCTC-AAC
* *
55482407 CCTCTCAAG
1 TCTCTCAAC
*
55482416 TCTCTCATC
1 TCTCTCAAC
55482425 TCTCTCA
1 TCTCTCA
55482432 TTTCTAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
9 29 0.63
10 17 0.37
ACGTcount: A:0.22, C:0.40, G:0.02, T:0.37
Consensus pattern (9 bp):
TCTCTCAAC
Found at i:55482419 original size:29 final size:28
Alignment explanation
Indices: 55482368--55482422 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
55482358 TTTCACATCC
* *
55482368 TTCTCTCAACTCTCTCAATTCTCTCAAA
1 TTCTCTCAACCCTCTCAAGTCTCTCAAA
55482396 TTCTCTCAAACCCTCTCAAGTCTCTCA
1 TTCTCTC-AACCCTCTCAAGTCTCTCA
55482423 TCTCTCTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.24, C:0.38, G:0.02, T:0.36
Consensus pattern (28 bp):
TTCTCTCAACCCTCTCAAGTCTCTCAAA
Found at i:55489335 original size:2 final size:2
Alignment explanation
Indices: 55489328--55489375 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
55489318 TTATGTATGG
55489328 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
55489370 TA TA TA
1 TA TA TA
55489376 GGGCATTGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55489745 original size:24 final size:24
Alignment explanation
Indices: 55489710--55489758 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 24
55489700 AATAAAAACC
55489710 ATAATAAAAAAAACCCTAACCTTA
1 ATAATAAAAAAAACCCTAACCTTA
55489734 ATAA-AAATAAAAACCCTAACCTTA
1 ATAATAAA-AAAAACCCTAACCTTA
55489758 A
1 A
55489759 GAGAGAGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.12
24 21 0.88
ACGTcount: A:0.59, C:0.20, G:0.00, T:0.20
Consensus pattern (24 bp):
ATAATAAAAAAAACCCTAACCTTA
Found at i:55492743 original size:19 final size:21
Alignment explanation
Indices: 55492697--55492746 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
55492687 AACGAGAGTT
55492697 TGTCTCTACCATAAGTTAAGG
1 TGTCTCTACCATAAGTTAAGG
55492718 TGTCTCTACCATAAGTTAAGG
1 TGTCTCTACCATAAGTTAAGG
*
55492739 TCTCTCTA
1 TGTCTCTA
55492747 AAAGACTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (21 bp):
TGTCTCTACCATAAGTTAAGG
Found at i:55497286 original size:67 final size:67
Alignment explanation
Indices: 55497204--55497340 Score: 274
Period size: 67 Copynumber: 2.0 Consensus size: 67
55497194 ATAAGAAAAG
55497204 ATTGCTCAAAGGAAATGTTTTGGTTCAAAAAATAAATTGAACCGAAGAAAAGAAAATTCATTTTC
1 ATTGCTCAAAGGAAATGTTTTGGTTCAAAAAATAAATTGAACCGAAGAAAAGAAAATTCATTTTC
55497269 TA
66 TA
55497271 ATTGCTCAAAGGAAATGTTTTGGTTCAAAAAATAAATTGAACCGAAGAAAAGAAAATTCATTTTC
1 ATTGCTCAAAGGAAATGTTTTGGTTCAAAAAATAAATTGAACCGAAGAAAAGAAAATTCATTTTC
55497336 TA
66 TA
55497338 ATT
1 ATT
55497341 CACGCCAAAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 70 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.31
Consensus pattern (67 bp):
ATTGCTCAAAGGAAATGTTTTGGTTCAAAAAATAAATTGAACCGAAGAAAAGAAAATTCATTTTC
TA
Found at i:55499692 original size:3 final size:3
Alignment explanation
Indices: 55499686--55499781 Score: 183
Period size: 3 Copynumber: 31.7 Consensus size: 3
55499676 GATGAACACG
55499686 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
55499734 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATGA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA
55499780 AT
1 AT
55499782 CTAAATTTTG
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 89 0.97
4 3 0.03
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:55501755 original size:44 final size:44
Alignment explanation
Indices: 55501700--55502204 Score: 266
Period size: 44 Copynumber: 11.1 Consensus size: 44
55501690 CTCGCGTCTA
* * * *
55501700 CAATCTGCTCCACTATAACCTCAGGGAGATGAGATTTGTAACTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTT
* * * ***
55501744 CAACCTACTCCACTGCAACTTCAGGGAGATAAGGTTTGTGGTTTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGT-AACTT
* * * *
55501789 C-ATCTACTCCACTATAACTTTAGGGAGATAAGATTAGTGACTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTT
* * *
55501832 CAATTTGCTCTACTGTAACTTCAGGGAGATAAGATTTGCTATA-TT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTG-TA-ACTT
* * * * * * *
55501877 CGATATGCTCCACTGCAACTTCAGGGAGATGAGACTTGTACCTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTT
* * * **
55501921 CAA-CTTGCTCCATTGCAACTTCAGGGAGATAA-AGTTTGCTATTTT
1 CAATC-TACTCCACTGTAACTTCAGGGAGATAAGA-TTTG-TAACTT
* * ** *
55501966 CAATCTATTCTACACTAACTTTAGGGAGATAAGATTTGTAGCTCGTAGCTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGTA------A-CTT
* * * * *
55502017 TAATCTATTCCACTGTAACTTCAGGGAGATAATACTTGCTATAGTGGAT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTG-TA-ACT---T
* * **
55502066 CTAATCCGAC-CCACTGTAACTTCAGAGG-TATAAGATTTGTCGCTT
1 C-AAT-CTACTCCACTGTAACTTCAG-GGAGATAAGATTTGTAACTT
* * ** * **
55502111 CAATCTGCTGCACTACAACTTCAGGGAGATAAGGTTTGCTATTTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTG-TAACTT
* * * * * *
55502156 CAATCTGCTCCATTGTAACTTTAGGGAGATGAGACTTGTATCTT
1 CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTT
55502200 CAATC
1 CAATC
55502205 GTCTTCACTA
Statistics
Matches: 349, Mismatches: 85, Indels: 54
0.72 0.17 0.11
Matches are distributed among these distances:
43 9 0.03
44 163 0.47
45 103 0.30
46 4 0.01
47 2 0.01
48 1 0.00
49 2 0.01
50 26 0.07
51 37 0.11
52 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (44 bp):
CAATCTACTCCACTGTAACTTCAGGGAGATAAGATTTGTAACTT
Found at i:55502216 original size:89 final size:89
Alignment explanation
Indices: 55501700--55502231 Score: 355
Period size: 89 Copynumber: 5.9 Consensus size: 89
55501690 CTCGCGTCTA
* * * * * * *
55501700 CAATCTGCTCCACTATAACCTCAGGGAGATGAGATTTGTAACTTCAACCTACTCCACTGCAACTT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATGAGACTTGTAGCTTCAATCTGCTTCACTGCAACTT
*
55501765 CAGGGAGATAAGGTTTG-TGGTTTT
66 CAGGGAGATAAGGTTTGCT-ATTTT
* * * * * *
55501789 C-ATCTACTCCACTATAACTTTAGGGAGATAAGA-TTAGT-GACTTCAATTTGC-TCTACTGTAA
1 CAATCTGCTCCACTGTAACTTCAGGGAGATGAGACTT-GTAG-CTTCAATCTGCTTC-ACTGCAA
* *
55501850 CTTCAGGGAGATAAGATTTGCTATATT
63 CTTCAGGGAGATAAGGTTTGCTATTTT
* * * * * *
55501877 CGATATGCTCCACTGCAACTTCAGGGAGATGAGACTTGTACCTTCAA-CTTGCTCCATTGCAACT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATGAGACTTGTAGCTTCAATC-TGCTTCACTGCAACT
*
55501941 TCAGGGAGATAAAGTTTGCTATTTT
65 TCAGGGAGATAAGGTTTGCTATTTT
** * ** * * * *
55501966 CAATCTATTCTACACTAACTTTAGGGAGATAAGATTTGTAGCTCGTAGCTTTAATCT-ATTCCAC
1 CAATCTGCTCCACTGTAACTTCAGGGAGAT--GA---G-A-CTTGTAGCTTCAATCTGCTT-CAC
* *** *
55502030 TGTAACTTCAGGGAGATAATACTTGCTATAGTGGAT
58 TGCAACTTCAGGGAGATAAGGTTTGCTAT--T--TT
* * * * * * *
55502066 CTAATCCGAC-CCACTGTAACTTCAGAGG-TATAAGATTTGTCGCTTCAATCTGCTGCACTACAA
1 C-AATCTG-CTCCACTGTAACTTCAG-GGAGATGAGACTTGTAGCTTCAATCTGCTTCACTGCAA
55502129 CTTCAGGGAGATAAGGTTTGCTATTTT
63 CTTCAGGGAGATAAGGTTTGCTATTTT
* * * *
55502156 CAATCTGCTCCATTGTAACTTTAGGGAGATGAGACTTGTATCTTCAATC-GTCTTCACTACAACT
1 CAATCTGCTCCACTGTAACTTCAGGGAGATGAGACTTGTAGCTTCAATCTG-CTTCACTGCAACT
* *
55502220 TTAGGAAGATAA
65 TCAGGGAGATAA
55502232 AATTTGTGGT
Statistics
Matches: 335, Mismatches: 79, Indels: 58
0.71 0.17 0.12
Matches are distributed among these distances:
87 3 0.01
88 71 0.21
89 146 0.44
90 5 0.01
91 2 0.01
92 1 0.00
94 40 0.12
95 4 0.01
96 39 0.12
97 1 0.00
98 1 0.00
99 1 0.00
100 2 0.01
101 17 0.05
102 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (89 bp):
CAATCTGCTCCACTGTAACTTCAGGGAGATGAGACTTGTAGCTTCAATCTGCTTCACTGCAACTT
CAGGGAGATAAGGTTTGCTATTTT
Found at i:55502306 original size:24 final size:24
Alignment explanation
Indices: 55502269--55502322 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
55502259 TCCACTGTAA
*
55502269 CTTCAGAGAAATAAGATTCGCTAT
1 CTTCAAAGAAATAAGATTCGCTAT
* * *
55502293 CTTCAAAGAGATAAGATTTGCTTT
1 CTTCAAAGAAATAAGATTCGCTAT
55502317 CTTCAA
1 CTTCAA
55502323 TCTACTCCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (24 bp):
CTTCAAAGAAATAAGATTCGCTAT
Found at i:55502471 original size:47 final size:45
Alignment explanation
Indices: 55502419--55502533 Score: 133
Period size: 45 Copynumber: 2.5 Consensus size: 45
55502409 TATCTTCAGT
*
55502419 CTGCTCCACTGCAACTTCAGGGACATAAGACTTGTTG-TAACTTCAAC
1 CTGCTCCACTGCAACTTCAGGGACATAAG--GT-TTGCTAACTTCAAC
* * ** *
55502466 CTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAAT
1 CTGCTCCACTGCAACTTCAGGGACATAAGGTTTGCTAACTTCAAC
*
55502511 CTGCTTCACTGCAACTTCAGGGA
1 CTGCTCCACTGCAACTTCAGGGA
55502534 GATGAGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 3 0.05
45 29 0.49
47 27 0.46
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGACATAAGGTTTGCTAACTTCAAC
Found at i:55502562 original size:44 final size:45
Alignment explanation
Indices: 55502382--55502583 Score: 165
Period size: 44 Copynumber: 4.5 Consensus size: 45
55502372 AATCTATTCT
* * * * * *
55502382 ACTAAAACTTCAGGGAAATTAG-ATCGCTATCTTCAGTCTGCTCC
1 ACTACAACTTCAGGGAGATAAGAATCGCTATTTTCAATCTGCTTC
* * * * * ** * *
55502426 ACTGCAACTTCAGGGACATAAGACTTGTTGTAACTTCAACCTGCTCC
1 ACTACAACTTCAGGGAGATAAGAATCG--CTATTTTCAATCTGCTTC
** *
55502473 ACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAATCTGCTTC
1 ACTACAACTTCAGGGAGATAAGAATCGCTATTTTCAATCTGCTTC
* * * *
55502518 ACTGCAACTTCAGGGAGATGAGAATCG-TATTTTTAATCTTCTTC
1 ACTACAACTTCAGGGAGATAAGAATCGCTATTTTCAATCTGCTTC
*
55502562 ACTACAACTTCAGGAAGATAAG
1 ACTACAACTTCAGGGAGATAAG
55502584 CTTTGTGGTT
Statistics
Matches: 126, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
44 52 0.41
45 37 0.29
47 37 0.29
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (45 bp):
ACTACAACTTCAGGGAGATAAGAATCGCTATTTTCAATCTGCTTC
Found at i:55502592 original size:351 final size:352
Alignment explanation
Indices: 55502108--55502811 Score: 1122
Period size: 351 Copynumber: 2.0 Consensus size: 352
55502098 AGATTTGTCG
* * * *
55502108 CTTCAATCTGCTGCACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAATCTGCTCCATTGTA
1 CTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAATCTGCTCCACTGCA
* * * *
55502173 ACTTTAGGGAGATGAGACTTGTATCTTCAATCGTCTTCACTACAACTTTAGGAAGATAAAATTTG
66 ACTTCAGGGAGATGAGAATCGTATCTTCAATCGTCTTCACTACAACTTCAGGAAGATAAAATTTG
*
55502238 TGGTTTGTAGCTTTAATCTGTTCCACTGTAACTTCAGAGAAATAAGATTCGCTATCTTCAAAGAG
131 TGGTTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGAGAAATAAGATTCGCTATCTTCAAAGAG
* *
55502303 ATAAGATTTGCTTTCTTCAATCTACTCCATTGCAACTTCAGAGAGATCAGATTTGTAATTTGTAG
196 ATAAGATTTGCTTTCTTCAATCTACTCCACTGCAACTTCAGAGAGATCAGATTTGTAATTTATAG
* * *
55502368 CTTTAATCTATTCTACTAAAACTTCAGGGAAATTAGAT-CGCTATCTTCAGTCTGCTCCACTGCA
261 CTTTAATCTATTCCACTAAAACTTCAGAGAAATAAGATCCGCTATCTTCAGTCTGCTCCACTGCA
55502432 ACTTCAGGGACATAAGACTTGTTGTAA
326 ACTTCAGGGACATAAGACTTGTTGTAA
*
55502459 CTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAATCTGCTTCACTGCA
1 CTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAATCTGCTCCACTGCA
* * * **
55502524 ACTTCAGGGAGATGAGAATCGTATTTTTAATCTTCTTCACTACAACTTCAGGAAGATAAGCTTTG
66 ACTTCAGGGAGATGAGAATCGTATCTTCAATCGTCTTCACTACAACTTCAGGAAGATAAAATTTG
* *
55502589 TGGTTTGTAGCTTTAATCTGTTCCATTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAAAGAG
131 TGGTTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGAGAAATAAGATTCGCTATCTTCAAAGAG
* * *
55502654 ATAAGATTTGCTTTCTTCAATCTACTCTACTGCAACTTCAGGGAGATCAGATTTGTATTTTATAG
196 ATAAGATTTGCTTTCTTCAATCTACTCCACTGCAACTTCAGAGAGATCAGATTTGTAATTTATAG
* * * * *
55502719 CTTTAATTTGTTCCACTGAAACTTTAGAGAAATAAGATCCGCTATCTTCAGTCTGCTCCATTGCA
261 CTTTAATCTATTCCACTAAAACTTCAGAGAAATAAGATCCGCTATCTTCAGTCTGCTCCACTGCA
*
55502784 ACTTCAGGGAGATAAGACTTGTTGTAA
326 ACTTCAGGGACATAAGACTTGTTGTAA
55502811 C
1 C
55502812 AATACCCACC
Statistics
Matches: 321, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
351 269 0.84
352 52 0.16
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (352 bp):
CTTCAACCTGCTCCACTACAACTTCAGGGAGATAAGGTTTGCTATTTTCAATCTGCTCCACTGCA
ACTTCAGGGAGATGAGAATCGTATCTTCAATCGTCTTCACTACAACTTCAGGAAGATAAAATTTG
TGGTTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGAGAAATAAGATTCGCTATCTTCAAAGAG
ATAAGATTTGCTTTCTTCAATCTACTCCACTGCAACTTCAGAGAGATCAGATTTGTAATTTATAG
CTTTAATCTATTCCACTAAAACTTCAGAGAAATAAGATCCGCTATCTTCAGTCTGCTCCACTGCA
ACTTCAGGGACATAAGACTTGTTGTAA
Found at i:55504650 original size:22 final size:22
Alignment explanation
Indices: 55504625--55504678 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
55504615 TTGGCTCGTT
*
55504625 TTATTTATTTAATTTT-TTGCCC
1 TTATTTATTTAATTTTATT-CCA
*
55504647 TTA-TTATTGTTATTTTATTCCA
1 TTATTTATT-TAATTTTATTCCA
55504669 TTATTTATTT
1 TTATTTATTT
55504679 GTTTATTACT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 5 0.19
22 15 0.56
23 7 0.26
ACGTcount: A:0.20, C:0.09, G:0.04, T:0.67
Consensus pattern (22 bp):
TTATTTATTTAATTTTATTCCA
Found at i:55504778 original size:3 final size:3
Alignment explanation
Indices: 55504712--55504758 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
55504702 CAAACTTTAG
55504712 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
55504759 CGTGTTCATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:55507509 original size:17 final size:17
Alignment explanation
Indices: 55507453--55507510 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
55507443 CTTTCACCAT
*
55507453 ATTAATGAAAAA-TAAA
1 ATTAATAAAAAATTAAA
* *
55507469 ATTATATAATAAATT--T
1 ATTA-ATAAAAAATTAAA
*
55507485 ATTTATAAAAAATTAAA
1 ATTAATAAAAAATTAAA
55507502 ATTAATAAA
1 ATTAATAAA
55507511 TAAAGTTTTG
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
15 9 0.29
16 7 0.23
17 14 0.45
18 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTAATAAAAAATTAAA
Found at i:55507847 original size:14 final size:14
Alignment explanation
Indices: 55507837--55507866 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55507827 TGAAAATGTC
55507837 TTTC-GGAAAATGA
1 TTTCTGGAAAATGA
55507850 TTTCTGGAAAATGA
1 TTTCTGGAAAATGA
55507864 TTT
1 TTT
55507867 ATTTTTCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
TTTCTGGAAAATGA
Found at i:55508343 original size:15 final size:15
Alignment explanation
Indices: 55508323--55508376 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
55508313 ATGCTAAAAA
55508323 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
55508338 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
55508355 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
55508372 ATATT
1 ATATT
55508377 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:55508426 original size:15 final size:16
Alignment explanation
Indices: 55508406--55508435 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55508396 AATAAAATTA
55508406 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
55508421 TTTAAAATTTATTAT
1 TTTAAAATTTATTAT
55508436 GAAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:55508940 original size:2 final size:2
Alignment explanation
Indices: 55508933--55508972 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
55508923 TCTTTTACAC
55508933 AT AT AT 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 AT AT AT
55508973 TTGTTTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55509480 original size:22 final size:23
Alignment explanation
Indices: 55509455--55509499 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55509445 TTAAGAAGTA
*
55509455 TATTTTTT-AATTATTTTAATTT
1 TATTTTTTAAATAATTTTAATTT
55509477 TATTTTTTAAATAATTTTAATTT
1 TATTTTTTAAATAATTTTAATTT
55509500 ACTTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTTAAATAATTTTAATTT
Found at i:55509505 original size:22 final size:23
Alignment explanation
Indices: 55509457--55509506 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
55509447 AAGAAGTATA
* * *
55509457 TTTTTTAATTATTTTAATTTTAT
1 TTTTTAAATAATTTTAATTTTAC
55509480 TTTTTAAATAATTTTAA-TTTAC
1 TTTTTAAATAATTTTAATTTTAC
55509502 TTTTT
1 TTTTT
55509507 CTTTTACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTAAATAATTTTAATTTTAC
Found at i:55511768 original size:27 final size:28
Alignment explanation
Indices: 55511711--55511780 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
55511701 AAAATTGTAC
**
55511711 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
55511739 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
55511766 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55511781 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:55515113 original size:29 final size:29
Alignment explanation
Indices: 55515081--55515153 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
55515071 CTTCGAGCTC
*
55515081 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55515110 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55515139 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
55515154 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:55523167 original size:29 final size:29
Alignment explanation
Indices: 55523135--55523207 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
55523125 CTTCGAGCTC
*
55523135 GCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55523164 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
55523193 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
55523208 ATCTCGTCAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:55525007 original size:24 final size:24
Alignment explanation
Indices: 55524977--55525195 Score: 375
Period size: 24 Copynumber: 9.1 Consensus size: 24
55524967 GAATGTGACT
* *
55524977 ATAGCAAATCGCACACATAGTGCT
1 ATAGTAAATCGCACACATAGTGCC
*
55525001 ATAGCAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
55525025 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
55525049 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
55525073 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
55525097 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
55525121 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
*
55525145 ATAGTGAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
55525169 ATAGTAAATCGCACACATAGTGCC
1 ATAGTAAATCGCACACATAGTGCC
55525193 ATA
1 ATA
55525196 TGGTCTTTGC
Statistics
Matches: 189, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 189 1.00
ACGTcount: A:0.36, C:0.25, G:0.18, T:0.21
Consensus pattern (24 bp):
ATAGTAAATCGCACACATAGTGCC
Found at i:55528206 original size:22 final size:23
Alignment explanation
Indices: 55528181--55528225 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
55528171 TTAAGAAGTA
*
55528181 TATTTTTT-AATTATTTTAATTT
1 TATTTTTTAAATAATTTTAATTT
55528203 TATTTTTTAAATAATTTTAATTT
1 TATTTTTTAAATAATTTTAATTT
55528226 ACTTTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TATTTTTTAAATAATTTTAATTT
Found at i:55528231 original size:22 final size:23
Alignment explanation
Indices: 55528183--55528232 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
55528173 AAGAAGTATA
* * *
55528183 TTTTTTAATTATTTTAATTTTAT
1 TTTTTAAATAATTTTAATTTTAC
55528206 TTTTTAAATAATTTTAA-TTTAC
1 TTTTTAAATAATTTTAATTTTAC
55528228 TTTTT
1 TTTTT
55528233 CTTTTACATC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTTAAATAATTTTAATTTTAC
Found at i:55530495 original size:27 final size:28
Alignment explanation
Indices: 55530438--55530507 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
55530428 AAAATTGTAC
**
55530438 AGCACTAAGTGTGCGAATTTGATTATAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
* *
55530466 AGCACTATGTGTGCG-AGCTGATTTTAT
1 AGCACTAAGTGTGCGAAGCTGATTATAT
55530493 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
55530508 GATTCACTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 23 0.62
28 14 0.38
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.33
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAAGCTGATTATAT
Found at i:55533858 original size:29 final size:29
Alignment explanation
Indices: 55533818--55533874 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
55533808 CCCAGTGCCG
55533818 ATATTTCCAGCATGCACACTTAGTGCCAT
1 ATATTTCCAGCATGCACACTTAGTGCCAT
55533847 ATATTTCCAGCATGCACACTTAGTGCCA
1 ATATTTCCAGCATGCACACTTAGTGCCA
55533875 ATCTCGTCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (29 bp):
ATATTTCCAGCATGCACACTTAGTGCCAT
Found at i:55540310 original size:39 final size:39
Alignment explanation
Indices: 55540228--55540390 Score: 245
Period size: 39 Copynumber: 4.2 Consensus size: 39
55540218 TATGGTAACC
* * *
55540228 CGCACAAATGCCTTCGGGACTTAACCCAGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
55540268 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAGCT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
55540307 CGCACCATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
55540346 CGTACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
55540385 CGCACA
1 CGCACA
55540391 TTCATACACA
Statistics
Matches: 111, Mismatches: 12, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
39 94 0.85
40 17 0.15
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.23
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:55548184 original size:25 final size:25
Alignment explanation
Indices: 55548110--55548187 Score: 76
Period size: 25 Copynumber: 3.2 Consensus size: 25
55548100 CTCGGCCCTG
55548110 TCACATATATACACCTTCACATTCA
1 TCACATATATACACCTTCACATTCA
** *
55548135 TCACAT-T-GGCTA--TTCAGCCTT-A
1 TCACATATATAC-ACCTTCA-CATTCA
55548157 TCACATATATACACCTTCACATTCA
1 TCACATATATACACCTTCACATTCA
55548182 TCACAT
1 TCACAT
55548188 CTGCCATTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 11 0.28
23 6 0.15
24 6 0.15
25 17 0.43
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.33
Consensus pattern (25 bp):
TCACATATATACACCTTCACATTCA
Found at i:55548233 original size:49 final size:47
Alignment explanation
Indices: 55548059--55548375 Score: 433
Period size: 47 Copynumber: 6.7 Consensus size: 47
55548049 CCCTTCGGGA
* * * * * *
55548059 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACCTTCACATTCATCACATTGGCCATTAGGC
* * *
55548106 CCTGTCACATATATACACCTTCACATTCATCACATTGGCTATTCA-GC
1 CTTATCACATATATACACCTTCACATTCATCACATTGGCCATT-AGGC
55548153 CTTATCACATATATACACCTTCACATTCATCACATCT-GCCATTAGGC
1 CTTATCACATATATACACCTTCACATTCATCACAT-TGGCCATTAGGC
* *
55548200 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACCTTCACATTCATCACATTGGCCATTAGGC
55548249 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCA-GC
1 CTTATCACATATATACAC-C-TTCACATTCATCACATTGGCCATT-AGGC
*
55548298 CTTATCACATATATACACCTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACCTTCACATTCATCACATTGGCCATTAGGC
*
55548345 CTTATCACATATATACACATTCACATTCATC
1 CTTATCACATATATACACCTTCACATTCATC
55548376 GCGTAAAATC
Statistics
Matches: 242, Mismatches: 18, Indels: 20
0.86 0.06 0.07
Matches are distributed among these distances:
46 2 0.01
47 150 0.62
48 2 0.01
49 87 0.36
50 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACCTTCACATTCATCACATTGGCCATTAGGC
Found at i:55548256 original size:96 final size:94
Alignment explanation
Indices: 55548059--55548375 Score: 442
Period size: 96 Copynumber: 3.3 Consensus size: 94
55548049 CCCTTCGGGA
* * * * * * * *
55548059 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACAC
1 CTTATCACATATATACACCTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
* *
55548124 CTTCACATTCATCACATTGGCTATTCA-GC
66 CTTCACATTCATCACATCGGCCATT-AGGC
55548153 CTTATCACATATATACACCTTCACATTCATCACATCT-GCCATTAGGCCTTATCACATATATATA
1 CTTATCACATATATACACCTTCACATTCATCACAT-TGGCCATTAGGCCTTATCAC--ATATATA
*
55548217 CACTTTCACATTCATCACATCGGCCATTAGGC
63 CACCTTCACATTCATCACATCGGCCATTAGGC
55548249 CTTATCACATATATACACACTTTCACATTCATCACATTGGCCATTCA-GCCTTATCACATATATA
1 CTTATCACATATATACAC-C-TTCACATTCATCACATTGGCCATT-AGGCCTTATCACATATATA
55548313 CACCTTCACATTCATCACATCGGCCATTAGGC
63 CACCTTCACATTCATCACATCGGCCATTAGGC
*
55548345 CTTATCACATATATACACATTCACATTCATC
1 CTTATCACATATATACACCTTCACATTCATC
55548376 GCGTAAAATC
Statistics
Matches: 202, Mismatches: 13, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
94 57 0.28
95 2 0.01
96 108 0.53
97 2 0.01
98 32 0.16
99 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.07, T:0.32
Consensus pattern (94 bp):
CTTATCACATATATACACCTTCACATTCATCACATTGGCCATTAGGCCTTATCACATATATACAC
CTTCACATTCATCACATCGGCCATTAGGC
Found at i:55551908 original size:80 final size:80
Alignment explanation
Indices: 55551802--55551964 Score: 213
Period size: 80 Copynumber: 2.0 Consensus size: 80
55551792 GTAATTATAT
* *
55551802 CGGGTTAAGACCCGAAGGCAATTGTGCTAG-CG-ACTACATCCGGGCTAAGACCCAAAGGCATTC
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGTACT--ATCCGGGCTAAGACCCAAAGGCATTC
*
55551865 GTGCAAGTTGTTAAATC
64 GTGCAAGTGGTTAAATC
* * * *
55551882 CGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTCTATCCGGGCTAAGACCCGAAGGCATTCGT
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGTACTATCCGGGCTAAGACCCAAAGGCATTCGT
* *
55551947 GCATGTGGTTATATC
66 GCAAGTGGTTAAATC
55551962 CGG
1 CGG
55551965 TTGTATTCTG
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
80 68 0.94
81 2 0.03
82 2 0.03
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (80 bp):
CGGGCTAAGACCCGAAGGCAATTGTGCAAGTCGTACTATCCGGGCTAAGACCCAAAGGCATTCGT
GCAAGTGGTTAAATC
Found at i:55551962 original size:40 final size:40
Alignment explanation
Indices: 55551758--55551964 Score: 179
Period size: 40 Copynumber: 5.2 Consensus size: 40
55551748 CAATTGAATG
* * ** **
55551758 ATATCCGGGCTAAGTCCCGAAGACATTTATGC-TAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAT-GTGGTT
* * **
55551798 ATAT-CGGGTTAAGACCCGAAGGCAATT-GTGC-TAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAT-GTGGTT
* * * *
55551837 ACATCCGGGCTAAGACCCAAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
* * * * *
55551877 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
*
55551917 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
55551957 ATATCCGG
1 ATATCCGG
55551965 TTGTATTCTG
Statistics
Matches: 136, Mismatches: 27, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
39 30 0.22
40 106 0.78
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
Found at i:55559961 original size:40 final size:40
Alignment explanation
Indices: 55559902--55560109 Score: 209
Period size: 40 Copynumber: 5.2 Consensus size: 40
55559892 CAATTGAATG
* * * *
55559902 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * ** *
55559942 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55559982 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
55560022 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
55560062 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
55560102 ATATCCGG
1 ATATCCGG
55560110 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 28, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 140 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:55560040 original size:80 final size:80
Alignment explanation
Indices: 55559903--55560109 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
55559893 AATTGAATGA
* * ** * * *
55559903 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
55559968 TTGTGCTAG-CG-AC
66 TTGTGCAAGTCGTAC
* * *
55559981 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
55560046 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
55560063 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
55560110 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 104 0.95
81 2 0.02
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:55564019 original size:7 final size:7
Alignment explanation
Indices: 55563985--55564086 Score: 64
Period size: 7 Copynumber: 14.4 Consensus size: 7
55563975 AAACATAATC
55563985 CCCT-AA
1 CCCTAAA
*
55563991 CCCTTAA
1 CCCTAAA
*
55563998 CCCTTAAC
1 CCC-TAAA
55564006 CCCTAAA
1 CCCTAAA
*
55564013 CCTTAAA
1 CCCTAAA
*
55564020 CCCCAATA
1 CCCTAA-A
55564028 CCCTAAA
1 CCCTAAA
* *
55564035 ACTTAAA
1 CCCTAAA
55564042 CCCT-AA
1 CCCTAAA
* *
55564048 CCTTTAA
1 CCCTAAA
55564055 CCCATAAA
1 CCC-TAAA
*
55564063 CCATAAA
1 CCCTAAA
* *
55564070 CCATAAT
1 CCCTAAA
55564077 CCCTAAA
1 CCCTAAA
55564084 CCC
1 CCC
55564087 ATGATACATA
Statistics
Matches: 73, Mismatches: 18, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
6 9 0.12
7 48 0.66
8 16 0.22
ACGTcount: A:0.39, C:0.40, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAA
Found at i:55564021 original size:22 final size:21
Alignment explanation
Indices: 55563984--55564049 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 21
55563974 AAAACATAAT
*
55563984 CCCCTAACCCTT-AACCCTTAA
1 CCCCTAAACCTTAAACCC-TAA
*
55564005 CCCCTAAACCTTAAACCCCAA
1 CCCCTAAACCTTAAACCCTAA
* *
55564026 TACCCTAAAACTTAAACCCTAA
1 -CCCCTAAACCTTAAACCCTAA
55564048 CC
1 CC
55564050 TTTAACCCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.36, C:0.44, G:0.00, T:0.20
Consensus pattern (21 bp):
CCCCTAAACCTTAAACCCTAA
Found at i:55564351 original size:40 final size:39
Alignment explanation
Indices: 55564301--55564404 Score: 111
Period size: 40 Copynumber: 2.6 Consensus size: 39
55564291 TTTTGTGGCA
* *
55564301 TTTTTCAAAAAACGCCGCTAAAGATCGAGC-ACTAGCGGCG
1 TTTTTTAAAAAACGCCGCTAAAGATAGA-CTA-TAGCGGCG
* * *
55564341 TTTTTTAAAAAGCGCCGCTAAAGGTATACTTATAGCGGCG
1 TTTTTTAAAAAACGCCGCTAAAGATAGAC-TATAGCGGCG
*
55564381 TTTCTTAAAAAAGCGCCGCTAAAG
1 TTTTTTAAAAAA-CGCCGCTAAAG
55564405 CCACTAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
39 1 0.02
40 41 0.76
41 12 0.22
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (39 bp):
TTTTTTAAAAAACGCCGCTAAAGATAGACTATAGCGGCG
Found at i:55564717 original size:39 final size:40
Alignment explanation
Indices: 55564638--55564729 Score: 123
Period size: 39 Copynumber: 2.3 Consensus size: 40
55564628 GGTGTACATA
55564638 TAGCGGCGTTTTTGAAAAAGCGCCGCTAAAACTCAATCTT
1 TAGCGGCGTTTTTGAAAAAGCGCCGCTAAAACTCAATCTT
** ** *
55564678 TAGCGGCGTTTTTG-GGAAGCGCCGCTAATGCTCATTCTT
1 TAGCGGCGTTTTTGAAAAAGCGCCGCTAAAACTCAATCTT
*
55564717 TAGTGGCGTTTTT
1 TAGCGGCGTTTTT
55564730 CATTCAAACG
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 32 0.70
40 14 0.30
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (40 bp):
TAGCGGCGTTTTTGAAAAAGCGCCGCTAAAACTCAATCTT
Found at i:55575235 original size:44 final size:47
Alignment explanation
Indices: 55575026--55575343 Score: 249
Period size: 47 Copynumber: 6.7 Consensus size: 47
55575016 TTTCTTGTGT
* * *
55575026 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCC-ACATTATAAGT-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGATGATGA-TA
* * * * *
55575072 GCCAATGTAAGACCATGCCTGGGACATGACATCGACGTAGAT-ATGAGA
1 GCCAGTGTAAGA-CATGTCTGGGACATG-CATCGGCCTAGATGATGATA
*
55575120 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGATGATGATA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGATGATGATA
* * *
55575167 GCCAGTGTAAGA-AGTGTCTAGGACATGCATCGG-CTA-A-GA-GTCTC
1 GCCAGTGTAAGACA-TGTCTGGGACATGCATCGGCCTAGATGATG-ATA
* * ** * ** *
55575211 GCTAGTGTAAGACATGTCCGGGACATGCATCAACACGTATAT-ACAAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-C-TAGATGATGATA
* * *
55575259 GCTAGTATAAGACCATGTCTGGGACATAGCATCGGCCTCGATGATGATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTAGATGATGATA
* *
55575308 ACCTGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
55575344 AACGAGAAGT
Statistics
Matches: 215, Mismatches: 40, Indels: 31
0.75 0.14 0.11
Matches are distributed among these distances:
43 1 0.00
44 29 0.13
45 2 0.01
46 25 0.12
47 65 0.30
48 36 0.17
49 51 0.24
50 6 0.03
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTAGATGATGATA
Found at i:55581304 original size:2 final size:2
Alignment explanation
Indices: 55581297--55581336 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
55581287 TGGAGATGTA
**
55581297 TG TG TG TG TG TG TG TG TG TG TG TG TG TG CA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
55581337 CTAATGGCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.03, C:0.03, G:0.47, T:0.47
Consensus pattern (2 bp):
TG
Found at i:55588306 original size:14 final size:17
Alignment explanation
Indices: 55588249--55588299 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
55588239 TTTAGTTTTT
*
55588249 TATTGATTAATACTTAATG
1 TATT-ATTAATA-TTAATC
*
55588268 TTTCTATTAATATTAATC
1 TAT-TATTAATATTAATC
55588286 TATTATTAATATTA
1 TATTATTAATATTA
55588300 TTATATTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 11 0.39
18 7 0.25
19 9 0.32
20 1 0.04
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (17 bp):
TATTATTAATATTAATC
Found at i:55588306 original size:17 final size:17
Alignment explanation
Indices: 55588249--55588306 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
55588239 TTTAGTTTTT
*
55588249 TATTGATTAATACTTAATG
1 TATT-ATTAATA-TTAATA
* *
55588268 TTTCTATTAATATTAATC
1 TAT-TATTAATATTAATA
*
55588286 TATTATTAATATTATTA
1 TATTATTAATATTAATA
55588303 TATT
1 TATT
55588307 TATATCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 16 0.48
18 7 0.21
19 9 0.27
20 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.55
Consensus pattern (17 bp):
TATTATTAATATTAATA
Found at i:55590276 original size:31 final size:31
Alignment explanation
Indices: 55590236--55590381 Score: 213
Period size: 31 Copynumber: 4.7 Consensus size: 31
55590226 TTAGTCTTGA
* *
55590236 CATAT-ACTAGGCTGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
* *
55590266 CATATCACTAGCCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
* *
55590297 CATATCACTGGGCTGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
55590328 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
55590359 CACATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
55590382 ACTGTAAACG
Statistics
Matches: 107, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 5 0.05
31 102 0.95
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:55590464 original size:42 final size:42
Alignment explanation
Indices: 55590405--55590538 Score: 223
Period size: 42 Copynumber: 3.2 Consensus size: 42
55590395 TGGCCCTTAG
** * *
55590405 GCCCATTTCAATATCACACATAATGTCAATGGATGTATACAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
55590447 GCCCATTTCAATATCACATGTAATATCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
55590489 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
55590531 GCCCATTT
1 GCCCATTT
55590539 GGGGAGACTA
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 86 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:55591545 original size:27 final size:27
Alignment explanation
Indices: 55591515--55591579 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
55591505 GGGCATATTC
*
55591515 GTCATTTTACCATACAAGGG-TATTACG
1 GTCATTTTACCATACAAGGGCT-TTACA
* *
55591542 GTCACTTTACCCTACAAGGGCTTTACA
1 GTCATTTTACCATACAAGGGCTTTACA
*
55591569 GTCTTTTTACC
1 GTCATTTTACC
55591580 TATTAGGGGT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
27 31 0.97
28 1 0.03
ACGTcount: A:0.25, C:0.25, G:0.15, T:0.35
Consensus pattern (27 bp):
GTCATTTTACCATACAAGGGCTTTACA
Found at i:55591872 original size:81 final size:81
Alignment explanation
Indices: 55591696--55591874 Score: 177
Period size: 81 Copynumber: 2.2 Consensus size: 81
55591686 AGAAAGTCAA
* ** * *
55591696 GGGTATTTCTGTAATTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTTAG
1 GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAGGGTAGTTTAG
55591761 TAATTTCACAAACCAG
66 TAATTTCACAAACCAG
* * * * *
55591777 TGTTGTTTCGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAGCTAG-GGGTAGTTT
1 GGGTATTTCAGTAATTTTACAAATC-AGGGGTATTTTGGTAATTTTACAA-ATAGAGGGTAGTTT
* **
55591840 GGTAA-TTCTATCCTA-CAG
64 AGTAATTTC-A-CAAACCAG
55591858 GGGTATTTCAGTAATTT
1 GGGTATTTCAGTAATTT
55591875 CATAATCGAG
Statistics
Matches: 78, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
80 4 0.05
81 70 0.90
82 4 0.05
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.41
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAATAGAGGGTAGTTTAG
TAATTTCACAAACCAG
Found at i:55592052 original size:27 final size:27
Alignment explanation
Indices: 55591630--55592064 Score: 148
Period size: 27 Copynumber: 16.1 Consensus size: 27
55591620 TTGGTAAATC
* *
55591630 TACAAACCAAGGGTATTTCAGTAATTT
1 TACAAATCGAGGGTATTTCAGTAATTT
** *
55591657 TGTAAA-CGAATGGTATTTCTA-TAATTTT
1 TACAAATCG-AGGGTATTTC-AGTAA-TTT
* * *
55591685 TAGAAAGTCAAGGGTATTTCTGTAATTT
1 TACAAA-TCGAGGGTATTTCAGTAATTT
** **
55591713 TGTAAATC-AGGGGTATTTTGGTAATTT
1 TACAAATCGA-GGGTATTTCAGTAATTT
* *
55591740 TACAAATTGAGGGTATTTTAGTAATTT
1 TACAAATCGAGGGTATTTCAGTAATTT
* * * * *
55591767 CACAAA-CCAGTGTTGTTTCGGTAATTT
1 TACAAATCGAG-GGTATTTCAGTAATTT
* **
55591794 TACAAA-CTAGGGGTATTTTGGTAATTT
1 TACAAATCGA-GGGTATTTCAGTAATTT
* * * *
55591821 TAC-AAGCTAGGGGTAGTTT-GGTAATTC
1 TACAAATCGA-GGGTA-TTTCAGTAATTT
**
55591848 TATCCTA-C-AGGGGTATTTCAGTAA-TT
1 TA-CAAATCGA-GGGTATTTCAGTAATTT
** *
55591874 T-CATAATCGAGGGTAAAAT-GGTAATTT
1 TACA-AATCGAGGGT-ATTTCAGTAATTT
** * ** *
55591901 TGTAAATTGAGGGTAAAAT-GGTAATTT
1 TACAAATCGAGGGT-ATTTCAGTAATTT
* * *** *
55591928 CATAAATCGAGGGTAAAAC-GATAATTC
1 TACAAATCGAGGGTATTTCAG-TAATTT
*
55591955 TATAAATCGAGGGTATTTTCA-TAATTT
1 TACAAATCGAGGGTA-TTTCAGTAATTT
*
55591982 TACAAGTCGAGGGTATTTCAGTAATTT
1 TACAAATCGAGGGTATTTCAGTAATTT
*
55592009 TGCAAA-CTGAGGGTATTTTC-GTAATTT
1 TACAAATC-GAGGGTA-TTTCAGTAATTT
** *
55592036 TACAAATCGAGATTATTTCGGTAATTT
1 TACAAATCGAGGGTATTTCAGTAATTT
55592063 TA
1 TA
55592065 GAAACCGGGG
Statistics
Matches: 321, Mismatches: 57, Indels: 60
0.73 0.13 0.14
Matches are distributed among these distances:
24 1 0.00
25 1 0.00
26 34 0.11
27 242 0.75
28 29 0.09
29 13 0.04
30 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
TACAAATCGAGGGTATTTCAGTAATTT
Found at i:55594174 original size:31 final size:31
Alignment explanation
Indices: 55594127--55594272 Score: 258
Period size: 31 Copynumber: 4.7 Consensus size: 31
55594117 TTAATCTTGA
55594127 CATAT-ACTGGGCCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
55594157 CATATCACTGGGTCGAAGCCTTTCCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
55594188 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
*
55594219 CATATCACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTCCATAAAT
55594250 CATATCACTGGGCCGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
55594273 ACTGTAAACG
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
30 5 0.04
31 107 0.96
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTCCATAAAT
Found at i:55594343 original size:42 final size:42
Alignment explanation
Indices: 55594296--55594424 Score: 240
Period size: 42 Copynumber: 3.1 Consensus size: 42
55594286 TGGCCCTTAG
*
55594296 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
*
55594338 GCCCATTTCAATATCACATGTAATGTCGATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
55594380 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
55594422 GCC
1 GCC
55594425 TATTAGGGGA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.30
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGTAATGTCAATGAATGTATGCAA
Found at i:55594605 original size:25 final size:25
Alignment explanation
Indices: 55594577--55594646 Score: 106
Period size: 25 Copynumber: 2.8 Consensus size: 25
55594567 CTCTTTTAAT
*
55594577 AACTGGGGCAAAGCCC-TTTCTGATA
1 AACTAGGGCAAAGCCCTTTTC-GATA
55594602 AACTAGGGCAAAGCCCTTTTCGATA
1 AACTAGGGCAAAGCCCTTTTCGATA
*
55594627 AACTAGGGCAGAGCCCTTTT
1 AACTAGGGCAAAGCCCTTTT
55594647 AGCACTTCCT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
25 38 0.90
26 4 0.10
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (25 bp):
AACTAGGGCAAAGCCCTTTTCGATA
Found at i:55595474 original size:27 final size:27
Alignment explanation
Indices: 55595443--55595502 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
55595433 TACGGAACAT
*
55595443 AAGGGCA-TATTCGTCATTTTACCATAC
1 AAGGGCATTA-TCGTCACTTTACCATAC
* * *
55595470 AAGGGTATTATGGTCACTTTACCCTAC
1 AAGGGCATTATCGTCACTTTACCATAC
55595497 AAGGGC
1 AAGGGC
55595503 TTTACAGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (27 bp):
AAGGGCATTATCGTCACTTTACCATAC
Found at i:55595676 original size:27 final size:27
Alignment explanation
Indices: 55595636--55595786 Score: 191
Period size: 27 Copynumber: 5.6 Consensus size: 27
55595626 AGAAAGTCAA
** *
55595636 GGGTATTTCT-GTAATTTTGTAAATTAG
1 GGGTATTT-TGGTAATTTTACAAACTAG
*
55595663 GGGTATTTTGGTAATTTTACAAA-TTG
1 GGGTATTTTGGTAATTTTACAAACTAG
*
55595689 AGGGTATTTTGGTAATTTCACAAACTAG
1 -GGGTATTTTGGTAATTTTACAAACTAG
*
55595717 TGGTATTTCT-GTAATTTTACAAACTAG
1 GGGTATTT-TGGTAATTTTACAAACTAG
*
55595744 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACTAG
55595771 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
55595787 CTATCCTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
26 4 0.04
27 103 0.94
28 3 0.03
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACTAG
Found at i:55595722 original size:54 final size:54
Alignment explanation
Indices: 55595661--55595819 Score: 189
Period size: 54 Copynumber: 2.9 Consensus size: 54
55595651 TTTGTAAATT
* *
55595661 AGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTTGGTAATTTCACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACTAG-GGGTATTTTGGTAATTTCACAAACC
* *
55595715 AGTGGTATTTCT-GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTT-TGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTCACAAACC
* ** * *
55595769 AGGGGTATTTTGGTAATTCTATCCTAC-AGGGGCATTTTAGTAATTTCACAA
1 AGGGGTATTTTGGTAATTTTA-CAAACTAGGGGTATTTTGGTAATTTCACAA
55595820 TCGAGGGTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
53 1 0.01
54 83 0.92
55 6 0.07
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.40
Consensus pattern (54 bp):
AGGGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTCACAAACC
Found at i:55595752 original size:81 final size:81
Alignment explanation
Indices: 55595637--55595786 Score: 239
Period size: 81 Copynumber: 1.9 Consensus size: 81
55595627 GAAAGTCAAG
** * **
55595637 GGTATTTCTGTAATTTTGTAAATTAGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTTGG
1 GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTTTGG
55595701 TAATTTCACAAACTAGT
65 TAATTTCACAAACTAGT
55595718 GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGT
1 GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGT
55595783 AATT
66 AATT
55595787 CTATCCTACA
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
81 62 0.98
82 1 0.02
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.43
Consensus pattern (81 bp):
GGTATTTCTGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGT
AATTTCACAAACTAGT
Found at i:55595826 original size:27 final size:27
Alignment explanation
Indices: 55595661--55595826 Score: 151
Period size: 27 Copynumber: 6.1 Consensus size: 27
55595651 TTTGTAAATT
* *
55595661 AGGGGTATTTTGGTAATTTTACAAATTG
1 AGGGGTATTTTGGTAATTTCACAAA-CG
*
55595689 A-GGGTATTTTGGTAATTTCACAAACT
1 AGGGGTATTTTGGTAATTTCACAAACG
* * *
55595715 AGTGGTATTTCT-GTAATTTTACAAACT
1 AGGGGTATTT-TGGTAATTTCACAAACG
* *
55595742 AGGGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTCACAAACG
**
55595769 AGGGGTATTTTGGTAA-TTCTATCCTAC-
1 AGGGGTATTTTGGTAATTTC-A-CAAACG
* * *
55595796 AGGGGCATTTTAGTAATTTCACAATCG
1 AGGGGTATTTTGGTAATTTCACAAACG
55595823 AGGG
1 AGGG
55595827 TAAAACGGTA
Statistics
Matches: 116, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
26 6 0.05
27 102 0.88
28 8 0.07
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTCACAAACG
Found at i:55595840 original size:26 final size:26
Alignment explanation
Indices: 55595808--55595909 Score: 84
Period size: 27 Copynumber: 3.8 Consensus size: 26
55595798 GGGCATTTTA
*
55595808 GTAATTTCACAATCGAGGGTAAAACG
1 GTAATTTTACAATCGAGGGTAAAACG
* *
55595834 GTAATTTTGC-ATGCTGAGGGTAAAATG
1 GTAATTTTACAAT-C-GAGGGTAAAACG
*
55595861 GTAATTTTTTA-AATTGAGGGTAAAACG
1 GTAA--TTTTACAATCGAGGGTAAAACG
*
55595888 ATAATTCTATA-AATCGAGGGTA
1 GTAATT-T-TACAATCGAGGGTA
55595910 CTTTGATAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
25 4 0.07
26 10 0.16
27 41 0.67
29 6 0.10
ACGTcount: A:0.36, C:0.09, G:0.24, T:0.31
Consensus pattern (26 bp):
GTAATTTTACAATCGAGGGTAAAACG
Found at i:55595917 original size:27 final size:26
Alignment explanation
Indices: 55595887--55596033 Score: 118
Period size: 27 Copynumber: 5.5 Consensus size: 26
55595877 AGGGTAAAAC
* *
55595887 GATAATTCTATAAATCGAGGGTACTTT
1 GATAATTTTACAAATCGAGGGTA-TTT
* *
55595914 GATAATTTGACAAGTCGAGGGTATTT
1 GATAATTTTACAAATCGAGGGTATTT
* *
55595940 TAGTAATTTTGCAAA-CTGAGGGTATTT
1 GA-TAATTTTACAAATC-GAGGGTATTT
* *
55595967 CGGTAATTTTACAAATCGAGGATATTT
1 -GATAATTTTACAAATCGAGGGTATTT
* * *
55595994 GGGTAATTTTATAAACCG-GGGTACTTT
1 -GATAATTTTACAAATCGAGGGTA-TTT
*
55596021 GGTAATTTTACAA
1 GATAATTTTACAA
55596034 GTGGGGTATT
Statistics
Matches: 98, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
26 21 0.21
27 76 0.78
28 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (26 bp):
GATAATTTTACAAATCGAGGGTATTT
Found at i:55595947 original size:54 final size:53
Alignment explanation
Indices: 55595889--55596053 Score: 176
Period size: 54 Copynumber: 3.1 Consensus size: 53
55595879 GGTAAAACGA
* * * *
55595889 TAATTCTATAAATCGAGGGTACTTTGATAATTTGACAAGTCGAGGGTATTTTAG
1 TAATTTTATAAA-CGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAG
** * * **
55595943 TAATTTTGCAAACTGAGGGTA-TTTCGGTAATTTTACAAATCGAGGATATTTGGG
1 TAATTTTATAAAC-GAGGGTACTTT-GGTAATTTTACAAGTCGAGGGTATTTCAG
55595997 TAATTTTATAAACCG-GGGTACTTTGGTAATTTTACAAGT-G-GGGTATTTCAG
1 TAATTTTATAAA-CGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAG
55596048 TAATTT
1 TAATTT
55596054 GGTAAACTAA
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
51 14 0.15
52 1 0.01
53 23 0.25
54 53 0.58
55 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (53 bp):
TAATTTTATAAACGAGGGTACTTTGGTAATTTTACAAGTCGAGGGTATTTCAG
Found at i:55598345 original size:40 final size:40
Alignment explanation
Indices: 55598286--55598438 Score: 252
Period size: 40 Copynumber: 3.8 Consensus size: 40
55598276 CATGAGCATT
55598286 TGAATGATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
1 TGAAT-ATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
*
55598327 TGAATATACCCGGACTAAGTCCCGAAGGCATTTATGCTAG
1 TGAATATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
*
55598367 TGAATATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
1 TGAATATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
* * *
55598407 TGATTATATCCGGGCTAAGACCCGAAGGCATT
1 TGAATATACCCGGGCTAAGTCCCGAAGGCATT
55598439 CGTGCGAGTT
Statistics
Matches: 107, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
40 102 0.95
41 5 0.05
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (40 bp):
TGAATATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAG
Found at i:55598431 original size:80 final size:82
Alignment explanation
Indices: 55598285--55598479 Score: 263
Period size: 80 Copynumber: 2.4 Consensus size: 82
55598275 ACATGAGCAT
* * *
55598285 TTGAATGATACCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATACCCGGACTAAGTCCC
1 TTGAATCATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATACCCGGACTAAGACCC
* *
55598350 GAAGGCATTTATGCTAG
66 GAAGGCATTCATGCGAG
* * *
55598367 -TGAAT-ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCC
1 TTGAATCATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATACCCGGACTAAGACCC
*
55598430 GAAGGCATTCGTGCGAG
66 GAAGGCATTCATGCGAG
* *
55598447 TTG--TCATATCCGGGCTAAGACTCGAAGGCATTT
1 TTGAATCATATCCGGGCTAAGTCCCGAAGGCATTT
55598480 GTGCAAGATA
Statistics
Matches: 101, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
79 1 0.01
80 93 0.92
81 7 0.07
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.26
Consensus pattern (82 bp):
TTGAATCATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAATATACCCGGACTAAGACCC
GAAGGCATTCATGCGAG
Found at i:55598456 original size:40 final size:39
Alignment explanation
Indices: 55598296--55598523 Score: 190
Period size: 40 Copynumber: 5.7 Consensus size: 39
55598286 TGAATGATAC
* * * *
55598296 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGAAT-ATAC
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTG--TCATAT
* * * *
55598336 CCGGACTAAGTCCCGAAGGCATTTATGCTAGTGAAT-ATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTG--TCATAT
* * * *
55598376 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTG-TCATAT
* *
55598416 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGTCATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGTCATAT
* ** *
55598456 CCGGGCTAAGACTCGAAGGCATTTGTGCAAGATACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCAAG-TGTCATAT
* * *
55598496 CCAGGTTAAGACCCGAAGGCAATTGTGC
1 CCGGGCTAAGACCCGAAGGCATTTGTGC
55598524 TTGTGGTTAT
Statistics
Matches: 167, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
39 2 0.01
40 163 0.98
41 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTGTCATAT
Found at i:55598536 original size:80 final size:80
Alignment explanation
Indices: 55598296--55598543 Score: 227
Period size: 80 Copynumber: 3.1 Consensus size: 80
55598286 TGAATGATAC
* * * * * *
55598296 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGA--ATATACCCGGACTAAGTCCCGAAGGCATT
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAAT-CCAGG-CTAAGACCCGAAGGCAAT
* **
55598359 TATGCTAGTGAATATAT
64 TGTGCTAGTGGTTATAT
* * ** * *
55598376 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCCGGGCTAAGACCCGAAGGC-ATTC
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCAGGCTAAGACCCGAAGGCAATT-
* * *
55598440 GTGCGAGTTGTCATAT
65 GTGCTAGTGGTTATAT
* * *
55598456 CCGGGCTAAGACTCGAAGGCATTTGTGCAAGAT-ACCAAATCCAGGTTAAGACCCGAAGGCAATT
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAG-TGACCAAATCCAGGCTAAGACCCGAAGGCAATT
*
55598520 GTGCTTGTGGTTATAT
65 GTGCTAGTGGTTATAT
55598536 CC-GGCTAA
1 CCGGGCTAA
55598544 ATTCCAAAGA
Statistics
Matches: 141, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
79 8 0.06
80 121 0.86
81 8 0.06
82 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAATCCAGGCTAAGACCCGAAGGCAATTG
TGCTAGTGGTTATAT
Found at i:55601645 original size:29 final size:29
Alignment explanation
Indices: 55601586--55601643 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
55601576 TAAATAGCCG
* *
55601586 AAGCTAGTTAAATCGTACACTTAATGCCC
1 AAGCTAGTTAAAACGCACACTTAATGCCC
* *
55601615 AAGCTAGTTTAAAACGCACATTTAGTGCC
1 AAGCTAG-TTAAAACGCACACTTAATGCC
55601644 AAAACTTCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 7 0.29
30 17 0.71
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (29 bp):
AAGCTAGTTAAAACGCACACTTAATGCCC
Found at i:55602953 original size:25 final size:25
Alignment explanation
Indices: 55602914--55603148 Score: 229
Period size: 25 Copynumber: 9.4 Consensus size: 25
55602904 GCCATTATTA
* *
55602914 CGATAATACGATCGGTACAAAGCCAT
1 CGATAACA-GATCGGCACAAAGCCAT
* *
55602940 CGATAACAGATCGGTACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * *
55602965 CAATATCATATCGGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * *
55602990 CCATAACAGATTGGCACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * * *
55603015 CAATATCATATCAGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* *
55603040 CGATAATAGATCGGCACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * * *
55603065 CAATATCATATCAGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
*
55603090 CGATAACAGAT-GGCACATAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
* * * *
55603114 CAATATCATATTGGCACAAAGCCAT
1 CGATAACAGATCGGCACAAAGCCAT
55603139 CGATAACAGA
1 CGATAACAGA
55603149 ATAATTGGCT
Statistics
Matches: 166, Mismatches: 42, Indels: 3
0.79 0.20 0.01
Matches are distributed among these distances:
24 19 0.11
25 140 0.84
26 7 0.04
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.20
Consensus pattern (25 bp):
CGATAACAGATCGGCACAAAGCCAT
Found at i:55602999 original size:50 final size:50
Alignment explanation
Indices: 55602924--55603148 Score: 371
Period size: 50 Copynumber: 4.5 Consensus size: 50
55602914 CGATAATACG
* *
55602924 ATCGGTACAAAGCCATCGATAACAGATCGGTACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
* *
55602974 ATCGGCACAAAGCCATCCATAACAGATTGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
* *
55603024 ATCAGCACAAAGCCATCGATAATAGATCGGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
*
55603074 ATCAGCACAAAGCCATCGATAACAGAT-GGCACATAGCCATCAATATCAT
1 ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
*
55603123 ATTGGCACAAAGCCATCGATAACAGA
1 ATCGGCACAAAGCCATCGATAACAGA
55603149 ATAATTGGCT
Statistics
Matches: 164, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 46 0.28
50 118 0.72
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.20
Consensus pattern (50 bp):
ATCGGCACAAAGCCATCGATAACAGATCGGCACATAGCCATCAATATCAT
Found at i:55603410 original size:41 final size:41
Alignment explanation
Indices: 55603288--55603410 Score: 165
Period size: 41 Copynumber: 3.0 Consensus size: 41
55603278 TAAAAACCAC
* * * * *
55603288 CGGTGGAACTACGGTCGTCAAGCAACCATGCGATCATTAAC
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
* *
55603329 CGGTGGATCCACGTTCATCAAGCAACCATGCGATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
* *
55603370 CGGTGGATCCATGGTCGTCAAGCAACCATGCAATCCTCAAT
1 CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
55603411 TTCTTCCTCC
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (41 bp):
CGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
Found at i:55603828 original size:81 final size:81
Alignment explanation
Indices: 55603732--55603936 Score: 184
Period size: 81 Copynumber: 2.5 Consensus size: 81
55603722 TGTAAGTATG
** ** ** *
55603732 GGGTATTTTTGTAATTTTCCAAATCAAGGGTATTTCAGTAATTTTCCAAATTATGGGTATTTTGG
1 GGGTATTTCAGTAATTTTCCAAATCAAGGGTATTTCAGTAATTTTAAAAACAAGGGGTATTTTGG
* *
55603797 TAATTTTACAAATCGA
66 CAATTTTACAAATCAA
** *
55603813 GGGTATTTC-GATAA-TTTCACAAATC-AGGGATATTTTGGTATTTTTAAAAACAAGGGGTATTT
1 GGGTATTTCAG-TAATTTTC-CAAATCAAGGG-TATTTCAGTAATTTTAAAAACAAGGGGTATTT
* *
55603875 TGGCAATTTTGCTAATCAA
63 TGGCAATTTTACAAATCAA
* * * *
55603894 GGGTATTTCAGTAATTCT-AAAATACAGGGGCATTTCAGTAATT
1 GGGTATTTCAGTAATTTTCCAAAT-CAAGGGTATTTCAGTAATT
55603937 CTACCCTACA
Statistics
Matches: 97, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
80 13 0.13
81 78 0.80
82 6 0.06
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.40
Consensus pattern (81 bp):
GGGTATTTCAGTAATTTTCCAAATCAAGGGTATTTCAGTAATTTTAAAAACAAGGGGTATTTTGG
CAATTTTACAAATCAA
Found at i:55603909 original size:27 final size:27
Alignment explanation
Indices: 55603648--55603901 Score: 192
Period size: 27 Copynumber: 9.4 Consensus size: 27
55603638 TTTCACCCTA
* * * *
55603648 AAGGGTGTTTTGGTAAATCTACAAACC
1 AAGGGTATTTTGGTAATTTTACAAATC
**
55603675 AAGGGTATTTTGGTAATTTTTTAAAGTC
1 AAGGGTATTTTGGTAATTTTACAAA-TC
* ** *
55603703 AATGGTATTTCT-GTAATTTTGTAAGT-
1 AAGGGTATTT-TGGTAATTTTACAAATC
* * *
55603729 ATGGGGTATTTTTGTAATTTTCCAAATC
1 A-AGGGTATTTTGGTAATTTTACAAATC
** * *
55603757 AAGGGTATTTCAGTAATTTTCCAAATT
1 AAGGGTATTTTGGTAATTTTACAAATC
*
55603784 ATGGGTATTTTGGTAATTTTACAAATC
1 AAGGGTATTTTGGTAATTTTACAAATC
* * * *
55603811 GAGGGTATTTCGATAATTTCACAAATC
1 AAGGGTATTTTGGTAATTTTACAAATC
* *
55603838 -AGGGATATTTTGGTATTTTTA-AAAAC
1 AAGGG-TATTTTGGTAATTTTACAAATC
* * *
55603864 AAGGGGTATTTTGGCAATTTTGCTAATC
1 AA-GGGTATTTTGGTAATTTTACAAATC
55603892 AAGGGTATTT
1 AAGGGTATTT
55603902 CAGTAATTCT
Statistics
Matches: 180, Mismatches: 38, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
26 10 0.06
27 139 0.77
28 30 0.17
29 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
AAGGGTATTTTGGTAATTTTACAAATC
Found at i:55603928 original size:27 final size:27
Alignment explanation
Indices: 55603898--55604028 Score: 181
Period size: 27 Copynumber: 4.9 Consensus size: 27
55603888 AATCAAGGGT
***
55603898 ATTTCAGTAATTCTAAAATACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
55603925 ATTTCAGTAATTCTACCCTACAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
* *
55603952 ATTTCAGTAATTCTATCCTATAGGGGC
1 ATTTCAGTAATTCTACCCTACAGGGGC
*
55603979 ATTTCAGTAATTCTACCCTACAGGGGT
1 ATTTCAGTAATTCTACCCTACAGGGGC
* * *
55604006 ATGTCAGTAATACTAGCCTACAG
1 ATTTCAGTAATTCTACCCTACAG
55604029 ATATGAGATT
Statistics
Matches: 93, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCCTACAGGGGC
Found at i:55606869 original size:25 final size:25
Alignment explanation
Indices: 55606836--55606999 Score: 123
Period size: 25 Copynumber: 6.6 Consensus size: 25
55606826 CGATTGGCAT
* *
55606836 AAAGCCATCGATAACAGATCGGCAG
1 AAAGCCATCGATAACAGATCAGCAC
* * * * * *
55606861 ATAGTCATCAATACCATATCAGTAC
1 AAAGCCATCGATAACAGATCAGCAC
*
55606886 AAAGCCATCGATAACAGATCAACAC
1 AAAGCCATCGATAACAGATCAGCAC
* * * *
55606911 ATAGCCATCAATATCATATC-GCAAC
1 AAAGCCATCGATAACAGATCAGC-AC
**
55606936 AAAGCCATCGATAACAGATCAATAC
1 AAAGCCATCGATAACAGATCAGCAC
* * * * **
55606961 ATAGCCATCAATATCATATTGGCAC
1 AAAGCCATCGATAACAGATCAGCAC
55606986 AAAGCCATCGATAA
1 AAAGCCATCGATAA
55607000 TAGAATAATT
Statistics
Matches: 100, Mismatches: 37, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
24 1 0.01
25 99 0.99
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.20
Consensus pattern (25 bp):
AAAGCCATCGATAACAGATCAGCAC
Found at i:55606895 original size:50 final size:49
Alignment explanation
Indices: 55606836--55606999 Score: 220
Period size: 50 Copynumber: 3.3 Consensus size: 49
55606826 CGATTGGCAT
** * * * *
55606836 AAAGCCATCGATAACAGATCGGCAGATAGTCATCAATACCATATCAGTAC
1 AAAGCCATCGATAACAGATCAACACATAGCCATCAATATCATATC-GAAC
55606886 AAAGCCATCGATAACAGATCAACACATAGCCATCAATATCATATCGCAAC
1 AAAGCCATCGATAACAGATCAACACATAGCCATCAATATCATATCG-AAC
* * *
55606936 AAAGCCATCGATAACAGATCAATACATAGCCATCAATATCATATTGGCAC
1 AAAGCCATCGATAACAGATCAACACATAGCCATCAATATCATA-TCGAAC
55606986 AAAGCCATCGATAA
1 AAAGCCATCGATAA
55607000 TAGAATAATT
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
49 1 0.01
50 100 0.97
51 2 0.02
ACGTcount: A:0.43, C:0.25, G:0.13, T:0.20
Consensus pattern (49 bp):
AAAGCCATCGATAACAGATCAACACATAGCCATCAATATCATATCGAAC
Found at i:55607199 original size:41 final size:41
Alignment explanation
Indices: 55607142--55607265 Score: 194
Period size: 41 Copynumber: 3.0 Consensus size: 41
55607132 CTTAAAAGCC
* *
55607142 ACCGGTGGATCCACGGTCGTCAAGCAACCATGTGATCCTTA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
55607183 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
* * * *
55607224 ATCGGTGGATCCATGGTCGTTAAGCAACCATGCAATCCTCA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
55607265 A
1 A
55607266 TTTCTTCCTC
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 77 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (41 bp):
ACCGGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCA
Found at i:55607567 original size:28 final size:26
Alignment explanation
Indices: 55607531--55607818 Score: 142
Period size: 27 Copynumber: 10.7 Consensus size: 26
55607521 ATCTACAAAC
55607531 CAAGGGTATTTCAGTAATTTTTGAAAGT
1 CAAGGGTATTTCAGTAATTTTT-AAA-T
*
55607559 CAATGGTATTTCTA-TAATTTTATAAAT
1 CAAGGGTATTTC-AGTAATTTT-TAAAT
* * *
55607586 CAGGGGTATTTCTGTAATTTTCCAAAT
1 CAAGGGTATTTCAGTAATTTT-TAAAT
* **
55607613 CAAGGGTATTT-TGATAATGTTCCAAAT
1 CAAGGGTATTTCAG-TAAT-TTTTAAAT
** *
55607640 C-AGGCGTATTTTGGTAATTTTACAAAT
1 CAAGG-GTATTTCAGTAATTTT-TAAAT
* **
55607667 CGAGGGTATTTC-GATAATTTCACAAAT
1 CAAGGGTATTTCAG-TAATTT-TTAAAT
* * * *
55607694 TAAGGGTATTT-TGTAATTTTACAAAC
1 CAAGGGTATTTCAGTAATTTT-TAAAT
* **
55607720 CAGGGGTATTTTGGTAATTTTGCT-AAT
1 CAAGGGTATTTCAGTAATTTT--TAAAT
* **
55607747 CGAGGGTATTTTGGTAATTTTGTAAA-
1 CAAGGGTATTTCAGTAATTTT-TAAAT
*
55607773 CAAAGGGTATTT-AGTAATTTTGTAAAC
1 C-AAGGGTATTTCAGTAATTTT-TAAAT
*
55607800 CAAGGGTATTTTAGTAATT
1 CAAGGGTATTTCAGTAATT
55607819 CTACCATACA
Statistics
Matches: 214, Mismatches: 27, Indels: 39
0.76 0.10 0.14
Matches are distributed among these distances:
26 52 0.24
27 133 0.62
28 27 0.13
29 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (26 bp):
CAAGGGTATTTCAGTAATTTTTAAAT
Found at i:55607593 original size:27 final size:26
Alignment explanation
Indices: 55607563--55607848 Score: 159
Period size: 27 Copynumber: 10.7 Consensus size: 26
55607553 GAAAGTCAAT
*
55607563 GGTATTTCTATAATTTTATAAATCAGG
1 GGTATTT-TATAATTTTACAAATCAGG
* * *
55607590 GGTATTTCTGTAATTTTCCAAATCAAG
1 GGTATTT-TATAATTTTACAAATCAGG
* *
55607617 GGTATTTTGATAATGTTCCAAATCAGG
1 GGTATTTT-ATAATTTTACAAATCAGG
* *
55607644 CGTATTTTGGTAATTTTACAAATC-GAG
1 GGTATTTT-ATAATTTTACAAATCAG-G
* * * *
55607671 GGTATTTCGATAATTTCACAAATTAAG
1 GGTATTT-TATAATTTTACAAATCAGG
* *
55607698 GGTATTTTGTAATTTTACAAACCAGG
1 GGTATTTTATAATTTTACAAATCAGG
* * *
55607724 GGTATTTTGGTAATTTTGCTAATC-GAG
1 GGTATTTT-ATAATTTTACAAATCAG-G
* ** *
55607751 GGTATTTTGGTAATTTTGTAAA-CAAAG
1 GGTATTTT-ATAATTTTACAAATC-AGG
** * *
55607778 GGTA-TTTAGTAATTTTGTAAACCAAG
1 GGTATTTTA-TAATTTTACAAATCAGG
* *
55607804 GGTATTTTAGTAATTCTAC-CATACAGG
1 GGTATTTTA-TAATTTTACAAAT-CAGG
*
55607831 GGCATTTTAGTAATTTTA
1 GGTATTTTA-TAATTTTA
55607849 TCTTACAAGT
Statistics
Matches: 209, Mismatches: 38, Indels: 24
0.77 0.14 0.09
Matches are distributed among these distances:
26 48 0.23
27 161 0.77
ACGTcount: A:0.31, C:0.10, G:0.19, T:0.41
Consensus pattern (26 bp):
GGTATTTTATAATTTTACAAATCAGG
Found at i:55607640 original size:54 final size:53
Alignment explanation
Indices: 55607534--55607818 Score: 220
Period size: 54 Copynumber: 5.3 Consensus size: 53
55607524 TACAAACCAA
* ** * **
55607534 GGGTATTTCAGTAATTTTTGAAAGTCAATGGTATTTCT-ATAATTTTATAAATCAG
1 GGGTATTT-TGTAATTTTACAAA-TCAAGGGTATTT-TGATAATTTTCCAAATCAG
* *
55607589 GGGTATTTCTGTAATTTTCCAAATCAAGGGTATTTTGATAATGTTCCAAATCAG
1 GGGTATTT-TGTAATTTTACAAATCAAGGGTATTTTGATAATTTTCCAAATCAG
* * * * *
55607643 GCGTATTTTGGTAATTTTACAAATCGAGGGTATTTCGATAA-TTTCACAAATTAA
1 GGGTATTTT-GTAATTTTACAAATCAAGGGTATTTTGATAATTTTC-CAAATCAG
* * * * *
55607697 GGGTATTTTGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCTAATC-G
1 GGGTATTTTGTAATTTTACAAATCAAGGGTATTTTGATAATTTTCCAAATCAG
** * ** * *
55607749 AGGGTATTTTGGTAATTTTGTAAA-CAAAGGGTATTTAG-TAATTTTGTAAACCAA
1 -GGGTATTTT-GTAATTTTACAAATC-AAGGGTATTTTGATAATTTTCCAAATCAG
55607803 GGGTATTTTAGTAATT
1 GGGTATTTT-GTAATT
55607819 CTACCATACA
Statistics
Matches: 189, Mismatches: 33, Indels: 18
0.79 0.14 0.08
Matches are distributed among these distances:
53 71 0.38
54 98 0.52
55 20 0.11
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (53 bp):
GGGTATTTTGTAATTTTACAAATCAAGGGTATTTTGATAATTTTCCAAATCAG
Found at i:55607765 original size:80 final size:79
Alignment explanation
Indices: 55607573--55607818 Score: 253
Period size: 80 Copynumber: 3.1 Consensus size: 79
55607563 GGTATTTCTA
* * * *
55607573 TAATTTTATAAATC-AGGGGTATTTCT-GTAATTTTCCAAATCAAGGGTATTTTGATAATGTTCC
1 TAATTTTACAAATCGA-GGGTATTT-TGGTAA-TTTCCAAATAAAGGGTATTTTG-TAATTTTAC
* *
55607636 AAATCAGGCGTATTTTGG
62 AAACCAGGGGTATTTTGG
* * *
55607654 TAATTTTACAAATCGAGGGTATTTCGATAATTTCACAAATTAAGGGTATTTTGTAATTTTACAAA
1 TAATTTTACAAATCGAGGGTATTTTGGTAATTTC-CAAATAAAGGGTATTTTGTAATTTTACAAA
55607719 CCAGGGGTATTTTGG
65 CCAGGGGTATTTTGG
* * ** * * **
55607734 TAATTTTGCTAATCGAGGGTATTTTGGTAATTTTGTAAACAAAGGGTATTTAGTAATTTTGTAAA
1 TAATTTTACAAATCGAGGGTATTTTGGTAA-TTTCCAAATAAAGGGTATTTTGTAATTTTACAAA
* *
55607799 CCAAGGGTATTTTAG
65 CCAGGGGTATTTTGG
55607814 TAATT
1 TAATT
55607819 CTACCATACA
Statistics
Matches: 140, Mismatches: 21, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
80 95 0.68
81 44 0.31
82 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (79 bp):
TAATTTTACAAATCGAGGGTATTTTGGTAATTTCCAAATAAAGGGTATTTTGTAATTTTACAAAC
CAGGGGTATTTTGG
Found at i:55607838 original size:80 final size:80
Alignment explanation
Indices: 55607695--55607847 Score: 184
Period size: 80 Copynumber: 1.9 Consensus size: 80
55607685 TTCACAAATT
* * * * * * * *
55607695 AAGGGTATTTTGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGCTAATCGAGGGTATTTTG
1 AAGGGTATTTAGTAATTTTACAAACCAAGGGTATTTTAGTAATTCTACCAATCGAGGGCATTTTA
55607760 GTAATTTTGTAAACA
66 GTAATTTTGTAAACA
**
55607775 AAGGGTATTTAGTAATTTTGTAAACCAAGGGTATTTTAGTAATTCTACC-ATAC-AGGGGCATTT
1 AAGGGTATTTAGTAATTTTACAAACCAAGGGTATTTTAGTAATTCTACCAAT-CGA-GGGCATTT
55607838 TAGTAATTTT
64 TAGTAATTTT
55607848 ATCTTACAAG
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
79 3 0.05
80 58 0.95
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (80 bp):
AAGGGTATTTAGTAATTTTACAAACCAAGGGTATTTTAGTAATTCTACCAATCGAGGGCATTTTA
GTAATTTTGTAAACA
Found at i:55607855 original size:27 final size:27
Alignment explanation
Indices: 55607807--55607898 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
55607797 AACCAAGGGT
* * *
55607807 ATTTTAGTAATTCTACCATACAGGGGC
1 ATTTCAGTAATTCTACCTTACAGGGGA
* * * * *
55607834 ATTTTAGTAATTTTATCTTACAAGTGA
1 ATTTCAGTAATTCTACCTTACAGGGGA
*
55607861 ATTTCAGTAATTCTACCTTACAGGGGT
1 ATTTCAGTAATTCTACCTTACAGGGGA
55607888 ATTTCAGTAAT
1 ATTTCAGTAAT
55607899 ACTAGCCTAC
Statistics
Matches: 53, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.40
Consensus pattern (27 bp):
ATTTCAGTAATTCTACCTTACAGGGGA
Found at i:55607910 original size:54 final size:54
Alignment explanation
Indices: 55607807--55607910 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
55607797 AACCAAGGGT
* * ** * *
55607807 ATTTTAGTAATTCTACCATACAGGGGCATTTTAGTAATTTTATCTTACAAGTGA
1 ATTTCAGTAATTCTACCATACAGGGGCATTTCAGTAATACTAGCCTACAAGTGA
* *
55607861 ATTTCAGTAATTCTACCTTACAGGGGTATTTCAGTAATACTAGCCTACAA
1 ATTTCAGTAATTCTACCATACAGGGGCATTTCAGTAATACTAGCCTACAA
55607911 ATATGAGATT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (54 bp):
ATTTCAGTAATTCTACCATACAGGGGCATTTCAGTAATACTAGCCTACAAGTGA
Found at i:55612046 original size:28 final size:28
Alignment explanation
Indices: 55611979--55612048 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
55611969 ATAGTGAATC
* * *
55611979 CGCACACTTAGTGCTATATATTTTCAGCT
1 CGCACACTTAGTGCTATAGA-TATCAACT
55612008 CGCACACTTAGTGCTATAGA-ATCAAACT
1 CGCACACTTAGTGCTATAGATATC-AACT
55612036 CGCACACTTAGTG
1 CGCACACTTAGTG
55612049 TTGTACAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 16 0.43
29 19 0.51
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAGATATCAACT
Found at i:55615583 original size:25 final size:25
Alignment explanation
Indices: 55615549--55615599 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
55615539 GCTTTTAGAT
55615549 TTGTGTGATTAAACTGTTTCAAACC
1 TTGTGTGATTAAACTGTTTCAAACC
55615574 TTGTGTGATTAAACTGTTTCAAACC
1 TTGTGTGATTAAACTGTTTCAAACC
55615599 T
1 T
55615600 AACACGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (25 bp):
TTGTGTGATTAAACTGTTTCAAACC
Found at i:55629317 original size:68 final size:70
Alignment explanation
Indices: 55629245--55629442 Score: 267
Period size: 71 Copynumber: 2.8 Consensus size: 70
55629235 ACACCCTGTA
* * * * *
55629245 GTAGCTAGGTCACATGCGTGATA-CGAGATGTA-TC-CCATGTAGACAAGATAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAG-TGAAGACACCATGTAGACAAGAGAGCTACGTGAAAG
55629307 ATAAAT
65 ATAAAT
*
55629313 GTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGTGAAAG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGAA-GACACCATGTAGACAAGAGAGCTACGTGAAAG
55629378 ATAAAT
65 ATAAAT
* * *
55629384 GTAGCTGGGTCGCATGCGTGATTCCAAGTGACGGACACCATGTAGACAAGAGAGCTACG
1 GTAGCTAGGTCGCATGCGTGATACCAAGTGA-AGACACCATGTAGACAAGAGAGCTACG
55629443 AGACAAATCG
Statistics
Matches: 117, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
68 24 0.21
69 3 0.03
70 1 0.01
71 89 0.76
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (70 bp):
GTAGCTAGGTCGCATGCGTGATACCAAGTGAAGACACCATGTAGACAAGAGAGCTACGTGAAAGA
TAAAT
Found at i:55629369 original size:71 final size:71
Alignment explanation
Indices: 55629279--55629442 Score: 301
Period size: 71 Copynumber: 2.3 Consensus size: 71
55629269 GAGATGTATC
*
55629279 CCATGTAGACAAGATAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55629344 AGGACA
66 AGGACA
*
55629350 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTGGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
*
55629415 CGGACA
66 AGGACA
55629421 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
55629443 AGACAAATCG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 90 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:55635390 original size:41 final size:41
Alignment explanation
Indices: 55635345--55635462 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
55635335 TGAAAGATAA
55635345 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
55635386 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
55635416 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
55635457 ATGTAG
1 ATGTAG
55635463 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:55635401 original size:71 final size:71
Alignment explanation
Indices: 55635313--55635476 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
55635303 GAGATGTATC
55635313 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55635378 AGGACA
66 AGGACA
55635384 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55635449 AGGACA
66 AGGACA
55635455 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
55635477 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:55642965 original size:41 final size:41
Alignment explanation
Indices: 55642920--55643037 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
55642910 TGAAAGATAA
55642920 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
55642961 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
55642991 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
55643032 ATGTAG
1 ATGTAG
55643038 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:55642976 original size:71 final size:71
Alignment explanation
Indices: 55642888--55643051 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
55642878 GAGATGTATC
55642888 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55642953 AGGACA
66 AGGACA
55642959 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
55643024 AGGACA
66 AGGACA
55643030 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
55643052 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Done.