Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 134 of 171
Found at i:41687379 original size:17 final size:17
Alignment explanation
Indices: 41687353--41687449 Score: 117
Period size: 17 Copynumber: 5.8 Consensus size: 17
41687343 AATCATTTTA
*
41687353 AAATTCATTTTAAAATT
1 AAATTTATTTTAAAATT
41687370 AAATTTATTTTAAAATT
1 AAATTTATTTTAAAATT
* *
41687387 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAAATT
*
41687404 AAATTTATTTTAAATTT
1 AAATTTATTTTAAAATT
* *
41687421 AGATTTA--TTAAATTT
1 AAATTTATTTTAAAATT
*
41687436 AAATTTAATTTAAA
1 AAATTTATTTTAAA
41687450 TTTAGAATTA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
15 14 0.20
17 57 0.80
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTATTTTAAAATT
Found at i:41687386 original size:12 final size:12
Alignment explanation
Indices: 41687345--41687369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41687335 GCCAGCCAAA
41687345 TCATTTTAAAAT
1 TCATTTTAAAAT
41687357 TCATTTTAAAAT
1 TCATTTTAAAAT
41687369 T
1 T
41687370 AAATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:41687416 original size:11 final size:11
Alignment explanation
Indices: 41687368--41687453 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
41687358 CATTTTAAAA
*
41687368 TTAAATTTATT
1 TTAAATTTAAT
*
41687379 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
41687391 TTATGTTAAAG
1 TTAAATTTAAT
*
41687402 TTAAATTTATT
1 TTAAATTTAAT
41687413 TTAAATTTAGAT
1 TTAAATTTA-AT
*
41687425 TT--ATTAAAT
1 TTAAATTTAAT
41687434 TTAAATTTAAT
1 TTAAATTTAAT
41687445 TTAAATTTA
1 TTAAATTTA
41687454 GAATTAATGT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
9 4 0.07
10 4 0.07
11 38 0.66
12 12 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:41687421 original size:6 final size:6
Alignment explanation
Indices: 41687361--41687458 Score: 68
Period size: 6 Copynumber: 17.3 Consensus size: 6
41687351 TAAAATTCAT
* * * *
41687361 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
41687407 TTT-AT TTTAAA TTTAGA TTT--A -TTAAA TTTAAA TTT-AA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
41687450 TTTAGAA TT
1 TTTA-AA TT
41687459 AATGTAAATT
Statistics
Matches: 71, Mismatches: 11, Indels: 19
0.70 0.11 0.19
Matches are distributed among these distances:
3 2 0.03
4 3 0.04
5 16 0.23
6 45 0.63
7 5 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:41687450 original size:17 final size:17
Alignment explanation
Indices: 41687361--41687489 Score: 115
Period size: 17 Copynumber: 7.6 Consensus size: 17
41687351 TAAAATTCAT
* *
41687361 TTTAAAATTAAATTTAT
1 TTTAAATTTAAATTTAA
*
41687378 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
* *
41687394 TGTTAAAGTTAAATTTAT
1 T-TTAAATTTAAATTTAA
*
41687412 TTTAAATTTAGATTT-A
1 TTTAAATTTAAATTTAA
41687428 -TTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
41687444 TTTAAATTTAGAA-TTAA
1 TTTAAATTTA-AATTTAA
* *
41687461 TGTAAATTTTAAAATT-A
1 TTTAAA-TTTAAATTTAA
41687478 TTATAAATTTAA
1 TT-TAAATTTAA
41687490 TAGAGTGTCC
Statistics
Matches: 95, Mismatches: 9, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
15 13 0.14
16 2 0.02
17 67 0.71
18 13 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:41689041 original size:30 final size:29
Alignment explanation
Indices: 41689005--41689088 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 29
41688995 CCTTAGAGAT
*
41689005 CCCTAAACTATCCAAAAATTATATTTTGAC
1 CCCTAAACTATCCAAAAATTACATTTT-AC
*
41689035 CCCTAAACTTTTCC-AAAATTACATTTTAC
1 CCCTAAAC-TATCCAAAAATTACATTTTAC
*
41689064 CCC-AAA-TATTCC-AAAATTCCATTTT
1 CCCTAAACTA-TCCAAAAATTACATTTT
41689089 TAACCCCGAT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
26 1 0.02
27 15 0.31
28 3 0.06
29 5 0.10
30 20 0.42
31 4 0.08
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (29 bp):
CCCTAAACTATCCAAAAATTACATTTTAC
Found at i:41689134 original size:58 final size:57
Alignment explanation
Indices: 41689047--41689292 Score: 275
Period size: 58 Copynumber: 4.3 Consensus size: 57
41689037 CTAAACTTTT
* * * *
41689047 CCAAAATTA-CATTTTACCC-CAAA-TATTCCAAAATTC-CATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTCACCCTCAAACT-TTCCAAAATTCTC-GTTTTGA-CCCAATTTCA
*
41689103 CCAAAATTACCATTTCACCCTCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTTAA
1 CCAAAATTACCATTTCACCCTCAAACTTTCCAAAATTCTCGTTTTGACCCAA-TTTCA
* * * *** *
41689161 CCAAAAATTACCATTTTACCCTCGAACCTTCCAAAATTCAATTTTTGACCTCGATTTCA
1 CC-AAAATTACCATTTCACCCTCAAACTTTCCAAAATTCTCGTTTTGACC-CAATTTCA
* *
41689220 CCAAAATTACCATTTCACCCCCGAACTTTCCAAAATTCTCGTTTTGACCCAATTTCAA
1 CCAAAATTACCATTTCACCCTCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTC-A
41689278 CCAAAATTACCATTT
1 CCAAAATTACCATTT
41689293 TGCCTCCCGG
Statistics
Matches: 162, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
56 9 0.06
57 19 0.12
58 83 0.51
59 49 0.30
60 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (57 bp):
CCAAAATTACCATTTCACCCTCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTCA
Found at i:41689197 original size:29 final size:29
Alignment explanation
Indices: 41689044--41689256 Score: 114
Period size: 29 Copynumber: 7.4 Consensus size: 29
41689034 CCCCTAAACT
*
41689044 TTTCCAAAATTA-CATTTTACCC-C-AAA
1 TTTCCAAAATTACCATTTTACCCTCGAAC
41689070 TATTCCAAAATT-CCATTTTTAACCC-CG-A-
1 T-TTCCAAAATTACCA-TTTT-ACCCTCGAAC
* *
41689098 TTTCACCAAAATTACCATTTCACCCTCAAAC
1 TTT--CCAAAATTACCATTTTACCCTCGAAC
* *
41689129 TTTCCAAAATT-CTCGTTTTGA-CC-C-AAT
1 TTTCCAAAATTAC-CATTTT-ACCCTCGAAC
41689156 TTTAACCAAAAATTACCATTTTACCCTCGAAC
1 TTT--CC-AAAATTACCATTTTACCCTCGAAC
* *
41689188 CTTCCAAAATT-CAATTTTTGA-CCTCG-A-
1 TTTCCAAAATTACCA-TTTT-ACCCTCGAAC
* *
41689215 TTTCACCAAAATTACCATTTCACCCCCGAAC
1 TTT--CCAAAATTACCATTTTACCCTCGAAC
41689246 TTTCCAAAATT
1 TTTCCAAAATT
41689257 CTCGTTTTGA
Statistics
Matches: 146, Mismatches: 13, Indels: 53
0.69 0.06 0.25
Matches are distributed among these distances:
26 1 0.01
27 21 0.14
28 15 0.10
29 73 0.50
30 24 0.16
31 8 0.05
32 4 0.03
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTCCAAAATTACCATTTTACCCTCGAAC
Found at i:41689219 original size:117 final size:115
Alignment explanation
Indices: 41689047--41689293 Score: 388
Period size: 117 Copynumber: 2.1 Consensus size: 115
41689037 CTAAACTTTT
* *
41689047 CCAAAATTA-CATTTTACCCCAAATATTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATT
1 CCAAAATTACCATTTTACCCCAAACATTCCAAAATTCAATTTTTAACCCCGATTTCACCAAAATT
* *
41689111 ACCATTTCACCCTCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTTAA
66 ACCATTTCACCCCCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTCAA
* * * *
41689161 CCAAAAATTACCATTTTACCCTCGAACCTTCCAAAATTCAATTTTTGACCTCGATTTCACCAAAA
1 CC-AAAATTACCATTTTACCC-CAAACATTCCAAAATTCAATTTTTAACCCCGATTTCACCAAAA
*
41689226 TTACCATTTCACCCCCGAACTTTCCAAAATTCTCGTTTTGACCCAATTTCAA
64 TTACCATTTCACCCCCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTCAA
41689278 CCAAAATTACCATTTT
1 CCAAAATTACCATTTT
41689294 GCCTCCCGGG
Statistics
Matches: 121, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
114 2 0.02
115 7 0.06
116 24 0.20
117 88 0.73
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.34
Consensus pattern (115 bp):
CCAAAATTACCATTTTACCCCAAACATTCCAAAATTCAATTTTTAACCCCGATTTCACCAAAATT
ACCATTTCACCCCCAAACTTTCCAAAATTCTCGTTTTGACCCAATTTCAA
Found at i:41700981 original size:33 final size:33
Alignment explanation
Indices: 41700939--41701006 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
41700929 TCAAATGTCA
41700939 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
41700972 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
41701005 AT
1 AT
41701007 AACGAATCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.43
Consensus pattern (33 bp):
ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGG
Found at i:41701129 original size:92 final size:92
Alignment explanation
Indices: 41700972--41701581 Score: 1112
Period size: 92 Copynumber: 6.6 Consensus size: 92
41700962 GTAAAGTTGG
41700972 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
41701037 AAGAGCAAGATGAATTTTCAAATGTCA
66 AAGAGCAAGATGAATTTTCAAATGTCA
*
41701064 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAGTCTTTATCTCTCTGAAGTTATAGT
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
41701129 AAGAGCAAGATGAATTTTCAAATGTCA
66 AAGAGCAAGATGAATTTTCAAATGTCA
*
41701156 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAGTCTTTATCTCTCTGAAGTTATAGT
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
*
41701221 AAGAGCAAGATGAGTTTTCAAATGTCA
66 AAGAGCAAGATGAATTTTCAAATGTCA
*
41701248 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGGATCTTTATCTCTCTGAAGTTATAGT
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
* *
41701313 AAGAACAAGATGAGTTTTCAAATGTCA
66 AAGAGCAAGATGAATTTTCAAATGTCA
*
41701340 AATCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
*
41701405 AAGAGCAAGATGAATTTTCAAATGCCA
66 AAGAGCAAGATGAATTTTCAAATGTCA
*
41701432 ATTCTTATCCTCTTGAAATTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
*
41701497 AAGAACAAGATGAATTTTCAAATGTCA
66 AAGAGCAAGATGAATTTTCAAATGTCA
* *
41701524 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAATGAACCTTTATCTCTCTGAAG
1 ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAG
41701582 ATAAAACCTC
Statistics
Matches: 501, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
92 501 1.00
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (92 bp):
ATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAATCTTTATCTCTCTGAAGTTATAGT
AAGAGCAAGATGAATTTTCAAATGTCA
Found at i:41701874 original size:17 final size:17
Alignment explanation
Indices: 41701848--41701924 Score: 109
Period size: 17 Copynumber: 4.5 Consensus size: 17
41701838 AATCATTTTA
*
41701848 AAATTCATTTTAAAATT
1 AAATTTATTTTAAAATT
41701865 AAATTTATTTTAAAATT
1 AAATTTATTTTAAAATT
* *
41701882 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAAATT
*
41701899 AAATTTATTTTAAATTT
1 AAATTTATTTTAAAATT
*
41701916 AGATTTATT
1 AAATTTATT
41701925 AGATTTAAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 54 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (17 bp):
AAATTTATTTTAAAATT
Found at i:41701881 original size:12 final size:12
Alignment explanation
Indices: 41701840--41701864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41701830 GCCAGCCAAA
41701840 TCATTTTAAAAT
1 TCATTTTAAAAT
41701852 TCATTTTAAAAT
1 TCATTTTAAAAT
41701864 T
1 T
41701865 AAATTTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (12 bp):
TCATTTTAAAAT
Found at i:41701916 original size:6 final size:6
Alignment explanation
Indices: 41701856--41701953 Score: 62
Period size: 6 Copynumber: 16.3 Consensus size: 6
41701846 TAAAATTCAT
* * * *
41701856 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
41701902 TTT-AT TTTAAA TTTAGA TTTATTAGA TTTAAA TTT-AA TTTAAA TTTAGAA
1 TTTAAA TTTAAA TTTAAA TTTA--A-A TTTAAA TTTAAA TTTAAA TTTA-AA
41701952 TT
1 TT
41701954 AATGTAAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
4 2 0.03
5 15 0.21
6 42 0.60
7 6 0.09
9 5 0.07
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:41701943 original size:11 final size:11
Alignment explanation
Indices: 41701863--41701948 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
41701853 CATTTTAAAA
*
41701863 TTAAATTTATT
1 TTAAATTTAAT
*
41701874 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
41701886 TTATGTTAAAG
1 TTAAATTTAAT
*
41701897 TTAAATTTATT
1 TTAAATTTAAT
41701908 TTAAATTTAGAT
1 TTAAATTTA-AT
41701920 TT--A-TTAGAT
1 TTAAATTTA-AT
41701929 TTAAATTTAAT
1 TTAAATTTAAT
41701940 TTAAATTTA
1 TTAAATTTA
41701949 GAATTAATGT
Statistics
Matches: 59, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
9 8 0.14
10 1 0.02
11 35 0.59
12 15 0.25
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:41701955 original size:17 final size:17
Alignment explanation
Indices: 41701907--41701983 Score: 63
Period size: 17 Copynumber: 4.6 Consensus size: 17
41701897 TTAAATTTAT
*
41701907 TTTAAATTTAG-ATTTA
1 TTTAAATTTAGAATTAA
*
41701923 -TTAGATTTA-AATTTAA
1 TTTAAATTTAGAA-TTAA
41701939 TTTAAATTTAGAATTAA
1 TTTAAATTTAGAATTAA
* *
41701956 TGTAAATTTTAAAATT-A
1 TTTAAA-TTTAGAATTAA
41701973 TTATAAATTTA
1 TT-TAAATTTA
41701984 ATAGAGTGTC
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
15 9 0.18
16 3 0.06
17 23 0.47
18 14 0.29
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TTTAAATTTAGAATTAA
Found at i:41701966 original size:18 final size:18
Alignment explanation
Indices: 41701928--41701982 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
41701918 ATTTATTAGA
* *
41701928 TTTAAATTTAATTTAAA-
1 TTTAAAATTAATATAAAT
* *
41701945 TTTAGAATTAATGTAAAT
1 TTTAAAATTAATATAAAT
*
41701963 TTTAAAATTATTATAAAT
1 TTTAAAATTAATATAAAT
41701981 TT
1 TT
41701983 AATAGAGTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
17 14 0.45
18 17 0.55
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (18 bp):
TTTAAAATTAATATAAAT
Found at i:41703671 original size:58 final size:59
Alignment explanation
Indices: 41703580--41703825 Score: 337
Period size: 58 Copynumber: 4.3 Consensus size: 59
41703570 CCAAACTTTT
* *
41703580 CCAAAATTA-CATTTTA-CCCCGAACCTTCCAAAATTC-CATTTTTGACCTCGATTTC-A
1 CCAAAATTACCATTTCACCCCCGAACCTTCCAAAATTCTCATTTTTGACC-CAATTTCAA
* *
41703636 CCAAAATTACCATTTCACCCCCGAACTTTCCAAAATTCTC-GTTTTGACCCAATTTCAA
1 CCAAAATTACCATTTCACCCCCGAACCTTCCAAAATTCTCATTTTTGACCCAATTTCAA
* * *
41703694 CCAAAAATTACCATTTTACCTCCGAACCTTCCAAAATTC-CATTTTTGACCCCGATTTC-A
1 CC-AAAATTACCATTTCACCCCCGAACCTTCCAAAATTCTCATTTTTGA-CCCAATTTCAA
*
41703753 CCAAAATTACCATTTCACCCCCGAACTTTCCAAAATTCTCA-TTTTGACCCAATTTCAA
1 CCAAAATTACCATTTCACCCCCGAACCTTCCAAAATTCTCATTTTTGACCCAATTTCAA
41703811 CCAAAATTACCATTT
1 CCAAAATTACCATTT
41703826 TGCCCCCCGG
Statistics
Matches: 168, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
56 9 0.05
57 20 0.12
58 86 0.51
59 45 0.27
60 8 0.05
ACGTcount: A:0.32, C:0.32, G:0.04, T:0.32
Consensus pattern (59 bp):
CCAAAATTACCATTTCACCCCCGAACCTTCCAAAATTCTCATTTTTGACCCAATTTCAA
Found at i:41703728 original size:30 final size:29
Alignment explanation
Indices: 41703513--41703787 Score: 127
Period size: 30 Copynumber: 9.4 Consensus size: 29
41703503 GAGATCCCTA
* * *
41703513 AACTATCCAAAAATTA-TATTTTGACCCCTA
1 AACTTTCCAAAAATTACCATTTT-ACCCC-G
* *
41703543 AACTTTTCC-AAAATTA-TATTTTAACCCCCA
1 AAC-TTTCCAAAAATTACCATTTT-A-CCCCG
41703573 AACTTTTCC-AAAATTA-CATTTTACCCCG
1 AAC-TTTCCAAAAATTACCATTTTACCCCG
* *
41703601 AACCTTCC-AAAATT-CCATTTTTGACCTCG
1 AACTTTCCAAAAATTACCA-TTTT-ACCCCG
* *
41703630 -A-TTTCACCAAAATTACCATTTCACCCCCG
1 AACTTTC-CAAAAATTACCATTTTA-CCCCG
*
41703659 AACTTTCC-AAAATT-CTCGTTTTGA-CCC-
1 AACTTTCCAAAAATTAC-CATTTT-ACCCCG
41703686 AA-TTTCAACCAAAAATTACCATTTTACCTCCG
1 AACTTT---CCAAAAATTACCATTTTACC-CCG
*
41703718 AACCTTCC-AAAATT-CCATTTTTGACCCCG
1 AACTTTCCAAAAATTACCA-TTTT-ACCCCG
* *
41703747 -A-TTTCACCAAAATTACCATTTCACCCCCG
1 AACTTTC-CAAAAATTACCATTTTA-CCCCG
41703776 AACTTTCCAAAA
1 AACTTTCCAAAA
41703788 TTCTCATTTT
Statistics
Matches: 199, Mismatches: 16, Indels: 60
0.72 0.06 0.22
Matches are distributed among these distances:
26 3 0.02
27 20 0.10
28 24 0.12
29 59 0.30
30 70 0.35
31 19 0.10
32 2 0.01
33 2 0.01
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (29 bp):
AACTTTCCAAAAATTACCATTTTACCCCG
Found at i:41703735 original size:117 final size:115
Alignment explanation
Indices: 41703580--41703831 Score: 452
Period size: 117 Copynumber: 2.2 Consensus size: 115
41703570 CCAAACTTTT
*
41703580 CCAAAATTA-CATTTTACCCCGAACCTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAATT
1 CCAAAATTACCATTTTACCCCGAACCTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAATT
*
41703644 ACCATTTCACCCCCGAACTTTCCAAAATTCTCGTTTTGACCCAATTTCAA
66 ACCATTTCACCCCCGAACTTTCCAAAATTCTCATTTTGACCCAATTTCAA
41703694 CCAAAAATTACCATTTTACCTCCGAACCTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAA
1 CC-AAAATTACCATTTTACC-CCGAACCTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAA
41703759 TTACCATTTCACCCCCGAACTTTCCAAAATTCTCATTTTGACCCAATTTCAA
64 TTACCATTTCACCCCCGAACTTTCCAAAATTCTCATTTTGACCCAATTTCAA
*
41703811 CCAAAATTACCATTTTGCCCC
1 CCAAAATTACCATTTTACCCC
41703832 CCGGGTATCC
Statistics
Matches: 132, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
114 2 0.02
115 9 0.07
116 25 0.19
117 96 0.73
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.32
Consensus pattern (115 bp):
CCAAAATTACCATTTTACCCCGAACCTTCCAAAATTCCATTTTTGACCCCGATTTCACCAAAATT
ACCATTTCACCCCCGAACTTTCCAAAATTCTCATTTTGACCCAATTTCAA
Found at i:41703827 original size:29 final size:28
Alignment explanation
Indices: 41703607--41703832 Score: 123
Period size: 29 Copynumber: 7.8 Consensus size: 28
41703597 CCCGAACCTT
* *
41703607 CCAAAATTCCATTTTTGACCTCGATTTCA
1 CCAAAATTCCA-TTTTGACCCCAATTTCA
*
41703636 CCAAAATTACCA-TTTCACCCCCGAACTTT--
1 CCAAAATT-CCATTTTGA-CCCC-AA-TTTCA
*
41703665 CCAAAATTCTCGTTTTGA-CCCAATTTCAA
1 CCAAAATTC-CATTTTGACCCCAATTTC-A
*
41703694 CCAAAAATTACCATTTT-ACCTCCGAACCTT--
1 CC-AAAATT-CCATTTTGACC-CC-AA-TTTCA
*
41703724 CCAAAATTCCATTTTTGACCCCGATTTCA
1 CCAAAATTCCA-TTTTGACCCCAATTTCA
*
41703753 CCAAAATTACCA-TTTCACCCCCGAACTTT--
1 CCAAAATT-CCATTTTGA-CCCC-AA-TTTCA
41703782 CCAAAATTCTCATTTTGA-CCCAATTTCAA
1 CCAAAATTC-CATTTTGACCCCAATTTC-A
*
41703811 CCAAAATTACCATTTTGCCCCC
1 CCAAAATT-CCATTTTGACCCC
41703833 CGGGTATCCA
Statistics
Matches: 154, Mismatches: 13, Indels: 59
0.68 0.06 0.26
Matches are distributed among these distances:
26 6 0.04
27 6 0.04
28 20 0.13
29 72 0.47
30 37 0.24
31 9 0.06
32 2 0.01
33 2 0.01
ACGTcount: A:0.31, C:0.33, G:0.05, T:0.32
Consensus pattern (28 bp):
CCAAAATTCCATTTTGACCCCAATTTCA
Found at i:41704798 original size:16 final size:15
Alignment explanation
Indices: 41704760--41704800 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
41704750 ATATTAAGAT
41704760 AATTATAT-AAAAAA
1 AATTATATAAAAAAA
*
41704774 ATTTA-ATAAATAAAA
1 AATTATATAAA-AAAA
41704789 AATTATATAAAA
1 AATTATATAAAA
41704801 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
13 2 0.09
14 6 0.27
15 9 0.41
16 5 0.23
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATTATATAAAAAAA
Found at i:41709052 original size:75 final size:76
Alignment explanation
Indices: 41708973--41709137 Score: 183
Period size: 76 Copynumber: 2.2 Consensus size: 76
41708963 TATAAAATAT
* *
41708973 GTTTTCAAGAAAT-ATGTCGAGCCTTGAG-ATTGCTGTAGAGGT-CTTTCAATTTTCATTTTATC
1 GTTTTCAAGAAATGA-GTCAAG-CTTGAGAATTGCTGTAGAGGTCCTTTCAATTATCATTTTATC
41709035 AAAAATCGAATTC
64 AAAAATCGAATTC
* * * * * *
41709048 GTTTTCAAGAAATGAGTTAAGTTTTAGAATTGCTGTTGATGTCCTTTTAATTATCATTTTATCAA
1 GTTTTCAAGAAATGAGTCAAGCTTGAGAATTGCTGTAGAGGTCCTTTCAATTATCATTTTATCAA
* * * *
41709113 AATTTGATTTT
66 AAATCGAATTC
41709124 GTTTTCAAGAAATG
1 GTTTTCAAGAAATG
41709138 GGTCGAACCT
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
74 4 0.05
75 29 0.39
76 42 0.56
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (76 bp):
GTTTTCAAGAAATGAGTCAAGCTTGAGAATTGCTGTAGAGGTCCTTTCAATTATCATTTTATCAA
AAATCGAATTC
Found at i:41713227 original size:23 final size:23
Alignment explanation
Indices: 41713192--41713291 Score: 139
Period size: 23 Copynumber: 4.4 Consensus size: 23
41713182 ACCAATTATT
41713192 ATTAT-TTTGTAACTCTCCTGCC
1 ATTATGTTTGTAACTCTCCTGCC
** *
41713214 ATTATGTTTGTAACTCTTTTGTC
1 ATTATGTTTGTAACTCTCCTGCC
*
41713237 ATTATGTTTGTAACTCTCCTACC
1 ATTATGTTTGTAACTCTCCTGCC
*
41713260 ATTATGTTTGTAACTCTCTTGCC
1 ATTATGTTTGTAACTCTCCTGCC
*
41713283 ATAATGTTT
1 ATTATGTTT
41713292 TGTTTTAAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
22 5 0.07
23 62 0.93
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (23 bp):
ATTATGTTTGTAACTCTCCTGCC
Found at i:41713262 original size:46 final size:46
Alignment explanation
Indices: 41713192--41713291 Score: 157
Period size: 46 Copynumber: 2.2 Consensus size: 46
41713182 ACCAATTATT
* * *
41713192 ATTAT-TTTGTAACTCTCCTGCCATTATGTTTGTAACTCTTTTGTC
1 ATTATGTTTGTAACTCTCCTACCATTATGTTTGTAACTCTCTTGCC
41713237 ATTATGTTTGTAACTCTCCTACCATTATGTTTGTAACTCTCTTGCC
1 ATTATGTTTGTAACTCTCCTACCATTATGTTTGTAACTCTCTTGCC
*
41713283 ATAATGTTT
1 ATTATGTTT
41713292 TGTTTTAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 5 0.10
46 45 0.90
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (46 bp):
ATTATGTTTGTAACTCTCCTACCATTATGTTTGTAACTCTCTTGCC
Found at i:41714291 original size:21 final size:23
Alignment explanation
Indices: 41714267--41714321 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
41714257 CCTATAACTT
*
41714267 CTACCGATACAAGTATGC-A-AA
1 CTACCGATACAACTATGCAATAA
*
41714288 CTACCGATACATCTATGCATATAA
1 CTACCGATACAACTATGCA-ATAA
41714312 CTACCGATAC
1 CTACCGATAC
41714322 TCACAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.55
23 1 0.03
24 12 0.41
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (23 bp):
CTACCGATACAACTATGCAATAA
Found at i:41714922 original size:59 final size:61
Alignment explanation
Indices: 41714845--41714962 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 61
41714835 CCTCAACTCG
* *
41714845 CATTTGATACTCATGATGACACA-AGTCATCGGACC-CTTAATCCGT-AATGGAATTCATTT
1 CATTTAATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAT-GAATTCATTT
* *
41714904 CATTTAATACTCACGATGACATATAGTCATCGGACCTCTTATTCCGTAAATGAATTCAT
1 CATTTAATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAATGAATTCAT
41714963 ATACTCACAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
59 20 0.38
60 12 0.23
61 17 0.33
62 3 0.06
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (61 bp):
CATTTAATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAATGAATTCATTT
Found at i:41715030 original size:52 final size:52
Alignment explanation
Indices: 41714911--41715096 Score: 232
Period size: 52 Copynumber: 3.6 Consensus size: 52
41714901 TTTCATTTAA
* * * *
41714911 TACTCACGATGACA-TATAGTCATCGGACCTCT-TATTCCGTAAATGAATTCATA
1 TACTCACGATGACACT-TAGTCATCGGACCT-TATAATCCGTGAA-GGATTCATG
*
41714964 TACTCACAATGACACTTAGTCATCGGACCTTATAATCCGTGAAGGATTCATG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTGAAGGATTCATG
* * * * *
41715016 TACTCACGATGACACTAAATCATCAGACCTTATAATCCGTGAACGATTCAAG
1 TACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTGAAGGATTCATG
*
41715068 TACTCACGATGACACTTAGGCATCGGACC
1 TACTCACGATGACACTTAGTCATCGGACC
41715097 CTTTTTCATT
Statistics
Matches: 116, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
52 79 0.68
53 36 0.31
54 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (52 bp):
TACTCACGATGACACTTAGTCATCGGACCTTATAATCCGTGAAGGATTCATG
Found at i:41716001 original size:20 final size:21
Alignment explanation
Indices: 41715958--41716001 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
41715948 ACTTTCATCA
* *
41715958 TTAAGCTTTAATTAAACATTT
1 TTAACCTTTAATTAAACATAT
*
41715979 TTAACCTTT-ATTAAACCTAT
1 TTAACCTTTAATTAAACATAT
41715999 TTA
1 TTA
41716002 TAATCAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (21 bp):
TTAACCTTTAATTAAACATAT
Found at i:41719212 original size:23 final size:23
Alignment explanation
Indices: 41719178--41719239 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
41719168 TATTTTGTTG
*
41719178 TCCTGCTATTATGTTTGTAACTC
1 TCCTGCCATTATGTTTGTAACTC
* *
41719201 TTCTGTCATTATGTTTGTAACTC
1 TCCTGCCATTATGTTTGTAACTC
*
41719224 TCCTGCCATAATGTTT
1 TCCTGCCATTATGTTT
41719240 TGTTTTAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (23 bp):
TCCTGCCATTATGTTTGTAACTC
Found at i:41720159 original size:31 final size:31
Alignment explanation
Indices: 41720121--41720184 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
41720111 TGCTGGGGAC
41720121 TTGAAGAGTCAAACTTATCCATTATTTTGAT
1 TTGAAGAGTCAAACTTATCCATTATTTTGAT
41720152 TTGAAGAGTCAAACTTATCCATTATTTTGAT
1 TTGAAGAGTCAAACTTATCCATTATTTTGAT
41720183 TT
1 TT
41720185 AAAATGATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (31 bp):
TTGAAGAGTCAAACTTATCCATTATTTTGAT
Found at i:41723856 original size:38 final size:37
Alignment explanation
Indices: 41723790--41723892 Score: 93
Period size: 38 Copynumber: 2.8 Consensus size: 37
41723780 TTTTACAATG
* * *
41723790 TTTTAGAATTTCTTAATAACA-TTAATAATGATTATATTT
1 TTTTACAATTT-TTAATAA-ATTTTATAATGATAAT-TTT
* *
41723829 TTTTACCATTTTTAATAAATTTTATAATTATAATTTT
1 TTTTACAATTTTTAATAAATTTTATAATGATAATTTT
* * *
41723866 TTTTATAAATTTTAAT-ATTTTTATAAT
1 TTTTACAATTTTTAATAAATTTTATAAT
41723893 ATTTTGAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
36 10 0.19
37 17 0.31
38 18 0.33
39 9 0.17
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (37 bp):
TTTTACAATTTTTAATAAATTTTATAATGATAATTTT
Found at i:41723881 original size:19 final size:18
Alignment explanation
Indices: 41723838--41723897 Score: 59
Period size: 18 Copynumber: 3.2 Consensus size: 18
41723828 TTTTTACCAT
*
41723838 TTTTAATAAATTTTAT-AA
1 TTTTAAT-ATTTTTATAAA
* *
41723856 TTATAATTTTTTTTATAAA
1 TTTTAA-TATTTTTATAAA
41723875 TTTTAATATTTTTATAATA
1 TTTTAATATTTTTATAA-A
41723894 TTTT
1 TTTT
41723898 GAAATATGTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAATATTTTTATAAA
Found at i:41728421 original size:21 final size:21
Alignment explanation
Indices: 41728395--41728452 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
41728385 CGACGCAGAT
*
41728395 TTCTACCGGTACATGTACT-AG
1 TTCTACCGATACATGTA-TAAG
* *
41728416 TTCTACCGATACAAGTATAAT
1 TTCTACCGATACATGTATAAG
41728437 TTCTACCGATACATGT
1 TTCTACCGATACATGT
41728453 CATGCATCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (21 bp):
TTCTACCGATACATGTATAAG
Found at i:41729251 original size:52 final size:52
Alignment explanation
Indices: 41729168--41729411 Score: 319
Period size: 52 Copynumber: 4.7 Consensus size: 52
41729158 CATTTCGCTC
* * * ** *
41729168 ATATACTCACGATGACACATAGCCACCAGACCT-TATAATCCACAAGGGATTA
1 ATATACTCACGATGACACTTAGTCATCAGACCTCT-TAATCCGTAAAGGATTA
* *
41729220 ATATACTCACGATGACACTTAGTCATTAGACCTCTTAATCCGTAAAGGATTC
1 ATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGATTA
* * *
41729272 ATATACTCACGATGACACTTAGTCATCGGATCTCTTAATCCGTGAAGGATTA
1 ATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGATTA
* ** * *
41729324 ATATACTCATGATGACACTTAGTCATTGGACCTCTTAATCTGTAAAGGATTC
1 ATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGATTA
*
41729376 ATATACTCACGATGACACTTAGTCATCGGACCTCTT
1 ATATACTCACGATGACACTTAGTCATCAGACCTCTT
41729412 CGTTTATGAC
Statistics
Matches: 170, Mismatches: 21, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
52 169 0.99
53 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (52 bp):
ATATACTCACGATGACACTTAGTCATCAGACCTCTTAATCCGTAAAGGATTA
Found at i:41729346 original size:104 final size:104
Alignment explanation
Indices: 41729166--41729411 Score: 370
Period size: 104 Copynumber: 2.4 Consensus size: 104
41729156 TTCATTTCGC
* * * *
41729166 TCATATACTCACGATGACACATAGCCACCAGACCT-TATAATCCACAAGGGATTAATATACTCAC
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCT-TAATCCACAAGGGATTAATATACTCAC
41729230 GATGACACTTAGTCATTAGACCTCTTAATCCGTAAAGGAT
65 GATGACACTTAGTCATTAGACCTCTTAATCCGTAAAGGAT
* ** *
41729270 TCATATACTCACGATGACACTTAGTCATCGGATCTCTTAATCCGTGAA-GGATTAATATACTCAT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCC-ACAAGGGATTAATATACTCAC
* *
41729334 GATGACACTTAGTCATTGGACCTCTTAATCTGTAAAGGAT
65 GATGACACTTAGTCATTAGACCTCTTAATCCGTAAAGGAT
41729374 TCATATACTCACGATGACACTTAGTCATCGGACCTCTT
1 TCATATACTCACGATGACACTTAGTCATCGGACCTCTT
41729412 CGTTTATGAC
Statistics
Matches: 129, Mismatches: 11, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
104 126 0.98
105 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (104 bp):
TCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCACAAGGGATTAATATACTCACG
ATGACACTTAGTCATTAGACCTCTTAATCCGTAAAGGAT
Found at i:41735706 original size:21 final size:21
Alignment explanation
Indices: 41735673--41735730 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 21
41735663 CGGCGCAAAT
* * *
41735673 TTCTACTAGTACATGTACCAG
1 TTCTACCAATACATGTACAAG
* * *
41735694 TTCTACCAATACAAGTATAAT
1 TTCTACCAATACATGTACAAG
*
41735715 TTCTACCGATACATGT
1 TTCTACCAATACATGT
41735731 CATGCATCTA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.34
Consensus pattern (21 bp):
TTCTACCAATACATGTACAAG
Found at i:41736485 original size:61 final size:57
Alignment explanation
Indices: 41736375--41736537 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 57
41736365 CGCATTTGAC
** * * *
41736375 ACTCACGATGACACAAAGTTATCGGACCT-TTAATCCGTAATGGATTTCATTTCCTTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGA-TTCA--T--TTCATAT
*
41736436 ACTCACGATGACACTTAGTCATCGGACCTCTTAATCTATAAAGG----A-TTCATAT
1 ACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCATTTCATAT
* *
41736488 ACTCACGATGACACTTAGTCATCGGGCCTCTTAATCCATAAAAGATTCAT
1 ACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCAT
41736538 ATACTCACGA
Statistics
Matches: 87, Mismatches: 9, Indels: 16
0.78 0.08 0.14
Matches are distributed among these distances:
52 48 0.55
56 1 0.01
57 1 0.01
61 26 0.30
62 11 0.13
ACGTcount: A:0.31, C:0.24, G:0.13, T:0.31
Consensus pattern (57 bp):
ACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCATTTCATAT
Found at i:41736507 original size:52 final size:52
Alignment explanation
Indices: 41736429--41736556 Score: 220
Period size: 52 Copynumber: 2.5 Consensus size: 52
41736419 TTTCATTTCC
* *
41736429 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCTATAAAGGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAAGA
*
41736481 TTCATATACTCACGATGACACTTAGTCATCGGGCCTCTTAATCCATAAAAGA
1 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAAGA
*
41736533 TTCATATACTCACGATAACACTTA
1 TTCATATACTCACGATGACACTTA
41736557 CAGTACGTTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (52 bp):
TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAAGA
Found at i:41736594 original size:16 final size:16
Alignment explanation
Indices: 41736572--41736627 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
41736562 CGTTTGGTTC
41736572 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
41736588 ACTGTAATGGAATATA
1 GCTGTAATGGAATAGA
41736604 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
41736620 GCTGTAAT
1 GCTGTAAT
41736628 CAGTAATTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.38, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:41736866 original size:58 final size:56
Alignment explanation
Indices: 41736797--41736942 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
41736787 AATTTTAATG
*
41736797 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
41736855 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
41736913 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
41736943 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:41737652 original size:26 final size:26
Alignment explanation
Indices: 41737616--41737666 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
41737606 TAACTATATC
41737616 TGGATCTTAGGCCTATCCTTTACATT
1 TGGATCTTAGGCCTATCCTTTACATT
41737642 TGGATCTTAGGCCTATCCTTTACAT
1 TGGATCTTAGGCCTATCCTTTACAT
41737667 CTTCCTCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.41
Consensus pattern (26 bp):
TGGATCTTAGGCCTATCCTTTACATT
Found at i:41739011 original size:15 final size:15
Alignment explanation
Indices: 41738987--41739026 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
41738977 AGAAAAAGGC
41738987 CAAAACAGAGAGTAT
1 CAAAACAGAGAGTAT
*
41739002 CAAAATAGAGAGTAT
1 CAAAACAGAGAGTAT
41739017 CAAAACAGAG
1 CAAAACAGAG
41739027 GGAGAGCTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.12, G:0.20, T:0.12
Consensus pattern (15 bp):
CAAAACAGAGAGTAT
Found at i:41743385 original size:4 final size:4
Alignment explanation
Indices: 41743376--41743404 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41743366 ATAATAAGGA
41743376 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
41743405 TTATGCCGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:41744567 original size:12 final size:12
Alignment explanation
Indices: 41744550--41744589 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
41744540 TCCAAGCCGT
41744550 AAAAATAACAAC
1 AAAAATAACAAC
*
41744562 AAAAATAACAGC
1 AAAAATAACAAC
* *
41744574 AAAAACAACATC
1 AAAAATAACAAC
41744586 AAAA
1 AAAA
41744590 TAATAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.72, C:0.17, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:41744609 original size:21 final size:21
Alignment explanation
Indices: 41744585--41744633 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
41744575 AAAACAACAT
*
41744585 CAAAATAATAAAAAATTGCAC
1 CAAAATAATAAAAAATAGCAC
* * *
41744606 CAAAACAGTAAAAAATAGTAC
1 CAAAATAATAAAAAATAGCAC
41744627 CAAAATA
1 CAAAATA
41744634 GCAACCAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.63, C:0.14, G:0.06, T:0.16
Consensus pattern (21 bp):
CAAAATAATAAAAAATAGCAC
Found at i:41755832 original size:29 final size:27
Alignment explanation
Indices: 41755585--41756038 Score: 221
Period size: 30 Copynumber: 15.6 Consensus size: 27
41755575 TCTCACGGGT
* *
41755585 AAAATGGTAA-TTTTGAAAGGTTCGGGGTC
1 AAAAT-GTAATTTTTGGAA-GTTTGGGG-C
* * *
41755614 AAGAATGGAATTTTTGGACA-TTCGAGGGT
1 AA-AATGTAATTTTTGGA-AGTTTG-GGGC
** *
41755643 AAAATGGTAATTTTTAAAAGTTTCGAGGTC
1 AAAAT-GTAATTTTTGGAAGTTT-G-GGGC
41755673 AAAAATGGTAATTTTTGGAAGTTTGGGGGC
1 -AAAAT-GTAATTTTTGGAAGTTT-GGGGC
* *
41755703 AAAATGTAATGTTTGGAAAAGTTTGAGGTC
1 AAAATGTAATTTTTGG--AAGTTTG-GGGC
* *
41755733 AAAAATGCAA-TTTTGGAAGTTTGGGGGT
1 -AAAATGTAATTTTTGGAAGTTT-GGGGC
* * * ***
41755761 AAAACGTTATTTTTGGAAAGTTTAAAGTTA
1 AAAATGTAATTTTTGG-AAGTTT--GGGGC
* * *
41755791 AAAATGCAATTTTAGGACGTTTGGGGC
1 AAAATGTAATTTTTGGAAGTTTGGGGC
* *
41755818 AAAAATGTAATTTTTGTAAAGTTCGGGTGTC
1 -AAAATGTAATTTTTG-GAAGTTTGGG-G-C
* * *
41755849 AAAATGTAGTTTTTGGAAAATTTGAGGTC
1 AAAATGTAATTTTTGG-AAGTTTG-GGGC
* *
41755878 AAAATGTAATTTTAGGAAGTTTGGGGGA
1 AAAATGTAATTTTTGGAAGTTT-GGGGC
* *
41755906 AAAATGTAATTTTTGTGAAGTTCGAGGGTT
1 AAAATGTAATTTTTG-GAAGTTTG-GGG-C
* *
41755936 AAAATGCAATTTTTTGGAAAGTTTGGGATC
1 AAAATGTAA-TTTTTGG-AAGTTTGGG-GC
* ** *
41755966 AAAATGTAATTTTAGGAAGTTCAAGGGA
1 AAAATGTAATTTTTGGAAGTT-TGGGGC
*
41755994 AAAATGTAATTTTTGTGAAGTTAGAGGGTC
1 AAAATGTAATTTTTG-GAAGTTTG-GGG-C
41756024 AAAATGTAATTTTTG
1 AAAATGTAATTTTTG
41756039 AAAACTTCAT
Statistics
Matches: 325, Mismatches: 67, Indels: 65
0.71 0.15 0.14
Matches are distributed among these distances:
27 7 0.02
28 83 0.26
29 89 0.27
30 100 0.31
31 46 0.14
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (27 bp):
AAAATGTAATTTTTGGAAGTTTGGGGC
Found at i:41755853 original size:58 final size:56
Alignment explanation
Indices: 41755584--41756038 Score: 276
Period size: 58 Copynumber: 7.8 Consensus size: 56
41755574 TTCTCACGGG
* *
41755584 TAAAATGGTAA-TTTTGAAAGGTTCGGGGTCAAGAATGGAATTTTTGGACA-TTCGAGGG-
1 TAAAAT-GTAATTTTTGAAA-GTTCGGGGTCAA-AATGTAATTTTTGGA-AGTTTG-GGGC
* *
41755642 TAAAATGGTAATTTTTAAAAGTTTCGAGGTCAAAAATGGTAATTTTTGGAAGTTTGGGGGC
1 TAAAAT-GTAATTTTTGAAAG-TTCGGGGTC-AAAAT-GTAATTTTTGGAAGTTT-GGGGC
* * * * *
41755703 -AAAATGTAATGTTTGGAAAAGTTTGAGGTCAAAAATGCAA-TTTTGGAAGTTTGGGGG
1 TAAAATGTAAT-TTTTG-AAAGTTCGGGGTC-AAAATGTAATTTTTGGAAGTTTGGGGC
* * *** * * * * *
41755760 TAAAACGTTATTTTTGGAAAGTTTAAAGTTAAAAATGCAATTTTAGGACGTTTGGGGC
1 TAAAATGTAATTTTT-GAAAG-TTCGGGGTCAAAATGTAATTTTTGGAAGTTTGGGGC
* * * *
41755818 AAAAATGTAATTTTTGTAAAGTTCGGGTGTCAAAATGTAGTTTTTGGAAAATTTGAGG-
1 TAAAATGTAATTTTTG-AAAGTTCGGG-GTCAAAATGTAATTTTTGG-AAGTTTGGGGC
* * * ** * *
41755876 TCAAAATGTAATTTTAGGAAGTTTGGGGGAAAAATGTAATTTTTGTGAAGTTCGAGGGT
1 T-AAAATGTAATTTTTGAAAGTTCGGGGTCAAAATGTAATTTTTG-GAAGTTTG-GGGC
* * * * **
41755935 TAAAATGCAATTTTTTGGAAAGTTTGGGATCAAAATGTAATTTTAGGAAGTTCAAGGG-
1 TAAAATGTAA-TTTTT-GAAAGTTCGGGGTCAAAATGTAATTTTTGGAAGTT-TGGGGC
* * *
41755993 AAAAATGTAATTTTTGTGAAGTTAGAGGGTCAAAATGTAATTTTTG
1 TAAAATGTAATTTTTG-AAAGTTCG-GGGTCAAAATGTAATTTTTG
41756039 AAAACTTCAT
Statistics
Matches: 314, Mismatches: 58, Indels: 50
0.74 0.14 0.12
Matches are distributed among these distances:
56 1 0.00
57 55 0.18
58 127 0.40
59 62 0.20
60 64 0.20
61 5 0.02
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (56 bp):
TAAAATGTAATTTTTGAAAGTTCGGGGTCAAAATGTAATTTTTGGAAGTTTGGGGC
Found at i:41755865 original size:88 final size:86
Alignment explanation
Indices: 41755664--41756038 Score: 368
Period size: 88 Copynumber: 4.3 Consensus size: 86
41755654 TTTTAAAAGT
* **
41755664 TTCGA-GGTCAAAAATGGTAATTTTTGG-AAGTTTGGGGGCAAAATGTAATGTTT-GGAAAAGTT
1 TTCGAGGGTC-AAAAT-GTAATTTTTGGAAAGTTTGAGATCAAAATGTAAT-TTTAGG--AAGTT
* *
41755726 TGAGGTCAAAAATGCAA-TTTTG-GAAG
61 TG-GG-GAAAAATGTAATTTTTGTGAAG
* * * * * * * * *
41755752 TTTGGGGGT-AAAACGTTATTTTTGGAAAGTTTAAAGTTAAAAATGCAATTTTAGGACGTTTGGG
1 TTCGAGGGTCAAAATGTAATTTTTGGAAAGTTT-GAGATCAAAATGTAATTTTAGGAAGTTTGGG
*
41755816 GCAAAAATGTAATTTTTGTAAAG
65 G-AAAAATGTAATTTTTGTGAAG
* * *
41755839 TTCG-GGTGTCAAAATGTAGTTTTTGGAAAATTTGAGGTCAAAATGTAATTTTAGGAAGTTTGGG
1 TTCGAGG-GTCAAAATGTAATTTTTGGAAAGTTTGAGATCAAAATGTAATTTTAGGAAGTTT-GG
41755903 GGAAAAATGTAATTTTTGTGAAG
64 GGAAAAATGTAATTTTTGTGAAG
* * * **
41755926 TTCGAGGGTTAAAATGCAATTTTTTGGAAAGTTTGGGATCAAAATGTAATTTTAGGAAGTTCAAG
1 TTCGAGGGTCAAAATGTAA-TTTTTGGAAAGTTTGAGATCAAAATGTAATTTTAGGAAGTT-TGG
41755991 GGAAAAATGTAATTTTTGTGAAG
64 GGAAAAATGTAATTTTTGTGAAG
*
41756014 TTAGAGGGTCAAAATGTAATTTTTG
1 TTCGAGGGTCAAAATGTAATTTTTG
41756039 AAAACTTCAT
Statistics
Matches: 238, Mismatches: 36, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
85 11 0.05
86 23 0.10
87 83 0.35
88 118 0.50
89 3 0.01
ACGTcount: A:0.34, C:0.05, G:0.26, T:0.35
Consensus pattern (86 bp):
TTCGAGGGTCAAAATGTAATTTTTGGAAAGTTTGAGATCAAAATGTAATTTTAGGAAGTTTGGGG
AAAAATGTAATTTTTGTGAAG
Found at i:41757642 original size:15 final size:15
Alignment explanation
Indices: 41757622--41757665 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
41757612 AGAGGGGTCC
41757622 TTGGGCAGAGGAGCA
1 TTGGGCAGAGGAGCA
*
41757637 TTGGGCAGAGGAACA
1 TTGGGCAGAGGAGCA
41757652 TTGGGCAGAGGAGC
1 TTGGGCAGAGGAGC
41757666 GGTCAACGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.45, T:0.14
Consensus pattern (15 bp):
TTGGGCAGAGGAGCA
Found at i:41757724 original size:11 final size:11
Alignment explanation
Indices: 41757708--41757739 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
41757698 TTGATGTGGC
41757708 GATGACATGGT
1 GATGACATGGT
41757719 GATGACATGGT
1 GATGACATGGT
*
41757730 GCTGACATGG
1 GATGACATGG
41757740 CATGCTGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (11 bp):
GATGACATGGT
Found at i:41757747 original size:13 final size:13
Alignment explanation
Indices: 41757721--41757754 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41757711 GACATGGTGA
41757721 TGACATGG--TGC
1 TGACATGGCATGC
41757732 TGACATGGCATGC
1 TGACATGGCATGC
41757745 TGACATGGCA
1 TGACATGGCA
41757755 ACGATGGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
13 13 0.62
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.24
Consensus pattern (13 bp):
TGACATGGCATGC
Found at i:41757849 original size:14 final size:14
Alignment explanation
Indices: 41757827--41757878 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
41757817 TTGGGCTTGT
*
41757827 ATGGGTTTTTGTAA
1 ATGGATTTTTGTAA
*
41757841 ATGGTTTTTTGTAA
1 ATGGATTTTTGTAA
* *
41757855 ATGGACTATTGTAA
1 ATGGATTTTTGTAA
*
41757869 ATGGACTTTT
1 ATGGATTTTT
41757879 AAGTAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.25, C:0.04, G:0.23, T:0.48
Consensus pattern (14 bp):
ATGGATTTTTGTAA
Found at i:41758449 original size:98 final size:99
Alignment explanation
Indices: 41758347--41758888 Score: 673
Period size: 98 Copynumber: 5.5 Consensus size: 99
41758337 TTTCCTTCCA
* * *
41758347 TATCTTCGTGGTATTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
*
41758412 GGTTCGTCATTGCGAC-TAAACCTTTCCCTTTTG
66 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTG
* * *
41758445 TATCTTCGTGGTACTGGATTCGCCATTGCAGCTTAAATCTTTCCCTTCATGCTTTCGAGGTACAA
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
* *
41758510 GGTTCGTCGTTGTGACTTAAACCCTTCCCTTTTG
66 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTG
* * * * *
41758544 TATCTTCGTGGTATTGGATTCACCGTTACGACTTAAATCTTTCCCTTCATGCTTCCAAGGTACAA
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
**
41758609 GGTTCGTCGTTGCGACTTAAACCTTTCCC-TTCA
66 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTG
* ** * * *
41758642 AATCTTTATGGT-GTCGGA-TCTGCCGTTGCGGCTTAAATCTTTCCCTTCCTGCTT-TGAGGTAC
1 TATCTTCGTGGTACT-GGATTC-GCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTAC
** *
41758704 AAGGTTCACCGTTGTGACTTAAACCTTTCCCTTTTG
64 AAGGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTG
* * * * **
41758740 TATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTTTCCCTTTATGCTTCCGAGGTATGA
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
* *
41758805 GGTTCGTCATTGCGACTTAAACCTTTCCC-TTCG
66 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTG
* * * * * *
41758838 TATTTTAGCGGTACTGGATTCGTCATCGCGGCTTAAATCTTTCCCTTCATG
1 TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATG
41758889 GTAATGAAAC
Statistics
Matches: 376, Mismatches: 61, Indels: 14
0.83 0.14 0.03
Matches are distributed among these distances:
97 37 0.10
98 204 0.54
99 135 0.36
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (99 bp):
TATCTTCGTGGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
GGTTCGTCGTTGCGACTTAAACCTTTCCCTTTTG
Found at i:41758472 original size:49 final size:50
Alignment explanation
Indices: 41758414--41758884 Score: 192
Period size: 49 Copynumber: 9.6 Consensus size: 50
41758404 AGGTACAAGG
*
41758414 TTCGTCATTGCGAC-TAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGA
* * * * *
41758463 TTCGCCATTGC-AGCTTAAATCTTTCCCTTCATG-CT-TTCGAGGTACAAGG-
1 TTCGCCATTGCGA-CTTAAACCTTTCCCTT-TTGTATCTTCGTGGTAC-TGGA
* * * * *
41758512 TTCGTCGTTGTGACTTAAACCCTTCCCTTTTGTATCTTCGTGGTATTGGA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGA
* * * * * ** *
41758562 TTCACCGTTACGACTTAAATCTTTCCC--TT-CATGCTTCCAAGGTACAAGG-
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTAT-CTT-CGTGGTAC-TGGA
* * *** ** *
41758611 TTCGTCGTTGCGACTTAAACCTTTCCC-TTCAAATCTTTATGGT-GTCGGA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACT-GGA
* * * * * * *
41758660 -TCTGCCGTTGCGGCTTAAATCTTTCCCTTCCTG---CTTTGAGGTACAAGG-
1 TTC-GCCATTGCGACTTAAACCTTTCCCTT-TTGTATCTTCGTGGTAC-TGGA
* * * *
41758708 TTCACCGTTGTGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACTAGA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGA
* * * * * * *
41758758 TTCGTCGTTGTGGCTTAAATCTTTCCC--TT-TATGCTTCCGAGGTA-TGAGG
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTAT-CTT-CGTGGTACTG-GA
* * * * *
41758807 TTCGTCATTGCGACTTAAACCTTTCCC-TTCGTATTTTAGCGGTACTGGA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGA
* * * *
41758856 TTCGTCATCGCGGCTTAAATCTTTCCCTT
1 TTCGCCATTGCGACTTAAACCTTTCCCTT
41758885 CATGGTAATG
Statistics
Matches: 315, Mismatches: 75, Indels: 63
0.70 0.17 0.14
Matches are distributed among these distances:
47 7 0.02
48 47 0.15
49 163 0.52
50 91 0.29
51 7 0.02
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (50 bp):
TTCGCCATTGCGACTTAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGA
Found at i:41758871 original size:196 final size:196
Alignment explanation
Indices: 41758347--41758888 Score: 761
Period size: 196 Copynumber: 2.8 Consensus size: 196
41758337 TTTCCTTCCA
41758347 TATCTTCGTGGTATTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
1 TATCTTCGTGGTATTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
* * * *
41758412 GGTTCGTCATTGCGAC-TAAACCTTTCCCTTTTGTATCTTCGTGGTACTGGATTCGCCATTGCAG
66 GGTTCGTCATTGCGACTTAAACCTTTCCC-TTCGTATTTTAG-GGTACTGGATTCGCCATTGCGG
**
41758476 CTTAAATCTTTCCCTTCATGCTTTCGAGGTACAAGGTTCGTCGTTGTGACTTAAACCCTTCCCTT
129 CTTAAATCTTTCCCTTCATGCTTTCGAGGTACAAGGTTCACCGTTGTGACTTAAACCCTTCCCTT
41758541 TTG
194 TTG
** * *
41758544 TATCTTCGTGGTATTGGATTCACCGTTACGACTTAAATCTTTCCCTTCATGCTTCCAAGGTACAA
1 TATCTTCGTGGTATTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
* ** *
41758609 GGTTCGTCGTTGCGACTTAAACCTTTCCCTTCAAATCTTTATGGTGT-C-GGA-TCTGCCGTTGC
66 GGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTAT-TTTA-GG-GTACTGGATTC-GCCATTGC
* *
41758671 GGCTTAAATCTTTCCCTTCCTGCTTT-GAGGTACAAGGTTCACCGTTGTGACTTAAACCTTTCCC
127 GGCTTAAATCTTTCCCTTCATGCTTTCGAGGTACAAGGTTCACCGTTGTGACTTAAACCCTTCCC
41758735 TTTTG
192 TTTTG
* * ** * **
41758740 TATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTTTCCCTTTATGCTTCCGAGGTATGA
1 TATCTTCGTGGTATTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
* *
41758805 GGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTATTTTAGCGGTACTGGATTCGTCATCGCGGC
66 GGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTATTTTAG-GGTACTGGATTCGCCATTGCGGC
41758870 TTAAATCTTTCCCTTCATG
130 TTAAATCTTTCCCTTCATG
41758889 GTAATGAAAC
Statistics
Matches: 302, Mismatches: 34, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
194 3 0.01
195 6 0.02
196 158 0.52
197 116 0.38
198 16 0.05
199 3 0.01
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (196 bp):
TATCTTCGTGGTATTGGATTCACCGTTGTGGCTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
GGTTCGTCATTGCGACTTAAACCTTTCCCTTCGTATTTTAGGGTACTGGATTCGCCATTGCGGCT
TAAATCTTTCCCTTCATGCTTTCGAGGTACAAGGTTCACCGTTGTGACTTAAACCCTTCCCTTTT
G
Found at i:41759337 original size:15 final size:15
Alignment explanation
Indices: 41759313--41759343 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41759303 AACTATTACC
*
41759313 AAATATTTACAAGGA
1 AAATAATTACAAGGA
41759328 AAATAATTACAAGGA
1 AAATAATTACAAGGA
41759343 A
1 A
41759344 CAGTATCAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.13, T:0.23
Consensus pattern (15 bp):
AAATAATTACAAGGA
Found at i:41765857 original size:14 final size:14
Alignment explanation
Indices: 41765838--41765879 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
41765828 CTTGTATAGG
*
41765838 TTTTTGTAAATGGT
1 TTTTTGTAAATGGA
41765852 TTTTTGTAAATGGA
1 TTTTTGTAAATGGA
* *
41765866 CTCTTGTAAATGGA
1 TTTTTGTAAATGGA
41765880 GTAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (14 bp):
TTTTTGTAAATGGA
Found at i:41766178 original size:30 final size:30
Alignment explanation
Indices: 41766137--41766284 Score: 106
Period size: 30 Copynumber: 5.0 Consensus size: 30
41766127 ATAAGGAAAA
* *
41766137 AGGGGTAAAAATAAAAATTTTGGAAAGTTT
1 AGGGGTCAAAATATAAATTTTGGAAAGTTT
* * * *
41766167 AGGGGTTAAAATGTAATTTTTAGAAAGTTT
1 AGGGGTCAAAATATAAATTTTGGAAAGTTT
* * *
41766197 -GGGGTTAAAGTATAATTTTTAGG-AAGTTT
1 AGGGGTCAAAATATAAATTTT-GGAAAGTTT
* **
41766226 AAGGGTCAAAAT-CGAATTTCTGGAAAGTTT
1 AGGGGTCAAAATATAAATTT-TGGAAAGTTT
* * *
41766256 GGGGGTCAAAAT-TAGATTTTTGGGAAGTT
1 AGGGGTCAAAATATA-AATTTTGGAAAGTT
41766285 CGGTGTCAAA
Statistics
Matches: 93, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
29 30 0.32
30 59 0.63
31 4 0.04
ACGTcount: A:0.36, C:0.03, G:0.26, T:0.35
Consensus pattern (30 bp):
AGGGGTCAAAATATAAATTTTGGAAAGTTT
Found at i:41766200 original size:29 final size:30
Alignment explanation
Indices: 41766154--41766276 Score: 117
Period size: 30 Copynumber: 4.1 Consensus size: 30
41766144 AAAATAAAAA
* *
41766154 TTTTGGAAAGTTTAGGGGTTAAAATGTAAT
1 TTTTAGAAAGTTTAGGGGTCAAAATGTAAT
* * *
41766184 TTTTAGAAAGTTT-GGGGTTAAAGTATAAT
1 TTTTAGAAAGTTTAGGGGTCAAAATGTAAT
* *
41766213 TTTTAGGAAGTTTAAGGGTCAAAATCG-AAT
1 TTTTAGAAAGTTTAGGGGTCAAAAT-GTAAT
* * *
41766243 TTCTGGAAAGTTTGGGGGTCAAAAT-TAGAT
1 TTTTAGAAAGTTTAGGGGTCAAAATGTA-AT
41766273 TTTT
1 TTTT
41766277 GGGAAGTTCG
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
29 27 0.36
30 48 0.64
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (30 bp):
TTTTAGAAAGTTTAGGGGTCAAAATGTAAT
Found at i:41767091 original size:4 final size:4
Alignment explanation
Indices: 41767082--41767107 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41767072 CAAGATATCT
41767082 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
41767108 TTGAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:41768090 original size:46 final size:47
Alignment explanation
Indices: 41768002--41768090 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
41767992 TGAGATGGTA
* * *
41768002 GCTTTAATCTGCCCTTCTTGATTTTAGGGGTAAAAGATTGGATAGTG
1 GCTTCAATCTGCCCTTCTTGATCTTAAGGGTAAAAGATTGGATAGTG
41768049 GCTTCAATCTGCCCTTCTTGA-CTTAAGGGTAAAAGATTGGAT
1 GCTTCAATCTGCCCTTCTTGATCTTAAGGGTAAAAGATTGGAT
41768091 GACTTCAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 19 0.49
47 20 0.51
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.36
Consensus pattern (47 bp):
GCTTCAATCTGCCCTTCTTGATCTTAAGGGTAAAAGATTGGATAGTG
Found at i:41768150 original size:42 final size:41
Alignment explanation
Indices: 41768028--41768492 Score: 473
Period size: 42 Copynumber: 11.3 Consensus size: 41
41768018 CTTGATTTTA
* * * *
41768028 GGGGTAAAAGATTGGATAGTGGCTTCAATCTGCCCTTCTTGACTTA
1 GGGGTAAGAGATTGGATA-TGTCTTCAATCTGCCC--CATGA--TC
* * * * *
41768074 AGGGTAAAAGATTGG--ATGACTTCAATTTGCCCCATGATT
1 GGGGTAAGAGATTGGATATGTCTTCAATCTGCCCCATGATC
* *
41768113 GGGGCAAGAGATTGGATAATGTCTTCAATCTGTCCCATGATC
1 GGGGTAAGAGATTGGAT-ATGTCTTCAATCTGCCCCATGATC
* *
41768155 GGGGTAAGAGATTGG--ATGGCTTCAATCTACCCCATGATC
1 GGGGTAAGAGATTGGATATGTCTTCAATCTGCCCCATGATC
* *
41768194 GGGGTAAGAGATTGGAT-GGTCTTCAATCTACCCCATGATC
1 GGGGTAAGAGATTGGATATGTCTTCAATCTGCCCCATGATC
* * * * *
41768234 GGGGTAAGGGATTGAATGATGTCTTTAATCTACCCTATGATC
1 GGGGTAAGAGATTGGAT-ATGTCTTCAATCTGCCCCATGATC
*
41768276 GGGGTAAGAGATTGG--ATGATCTTCAATCTGCCCCATGATT
1 GGGGTAAGAGATTGGATATG-TCTTCAATCTGCCCCATGATC
* *
41768316 GGGGTAAGAGATTGGATGATTTCTTCAATTTGCCCCATGATC
1 GGGGTAAGAGATTGGAT-ATGTCTTCAATCTGCCCCATGATC
*
41768358 GGGGTAAGAGATTGGAT-GGTCTTCAATCTGCCCCATGATC
1 GGGGTAAGAGATTGGATATGTCTTCAATCTGCCCCATGATC
* * *
41768398 GGGATAAGAGATTGGATGATGTCTTCAATTTTCCCCATGATC
1 GGGGTAAGAGATTGGAT-ATGTCTTCAATCTGCCCCATGATC
* * *
41768440 GAGGTAAAAGATTGGAT-GGTCTTCAATCTG-CCCATTGATC
1 GGGGTAAGAGATTGGATATGTCTTCAATCTGCCCCA-TGATC
* *
41768480 AGGGTAAAAGATT
1 GGGGTAAGAGATT
41768493 AGTGTAGCTT
Statistics
Matches: 358, Mismatches: 47, Indels: 34
0.82 0.11 0.08
Matches are distributed among these distances:
39 56 0.16
40 130 0.36
41 4 0.01
42 137 0.38
43 16 0.04
44 1 0.00
46 14 0.04
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (41 bp):
GGGGTAAGAGATTGGATATGTCTTCAATCTGCCCCATGATC
Found at i:41768293 original size:82 final size:82
Alignment explanation
Indices: 41768075--41768492 Score: 544
Period size: 82 Copynumber: 5.1 Consensus size: 82
41768065 CTTGACTTAA
* * * * * *
41768075 GGGTAAAAGATTGGATGA---CTTCAATTTGCCCCATGATTGGGGCAAGAGATTGGATAATGTCT
1 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGAT--GGTCT
*
41768137 TCAATCTGTCCCATGATCG
64 TCAATCTGCCCCATGATCG
41768156 GGGTAAGAGATTGGATG--G-CTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
*
41768218 AATCTACCCCATGATCG
66 AATCTGCCCCATGATCG
* * * * *
41768235 GGGTAAGGGATTGAATGATGTCTTTAATCTACCCTATGATCGGGGTAAGAGATTGGATGATCTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
*
41768300 AATCTGCCCCATGATTG
66 AATCTGCCCCATGATCG
* * *
41768317 GGGTAAGAGATTGGATGATTTCTTCAATTTGCCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
41768382 AATCTGCCCCATGATCG
66 AATCTGCCCCATGATCG
* * * * *
41768399 GGATAAGAGATTGGATGATGTCTTCAATTTTCCCCATGATCGAGGTAAAAGATTGGATGGTCTTC
1 GGGTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
*
41768464 AATCTG-CCCATTGATCA
66 AATCTGCCCCA-TGATCG
*
41768481 GGGTAAAAGATT
1 GGGTAAGAGATT
41768493 AGTGTAGCTT
Statistics
Matches: 300, Mismatches: 32, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
79 36 0.12
81 54 0.18
82 210 0.70
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (82 bp):
GGGTAAGAGATTGGATGATGTCTTCAATCTACCCCATGATCGGGGTAAGAGATTGGATGGTCTTC
AATCTGCCCCATGATCG
Found at i:41768773 original size:99 final size:99
Alignment explanation
Indices: 41768587--41769075 Score: 550
Period size: 99 Copynumber: 4.9 Consensus size: 99
41768577 CGAGGTAGAG
* *
41768587 GATTCGCCGTTACGGCCTCAAT-CTTCCCTATCACATCTTCTAAGGTACCAGGTTCATCGTTGCG
1 GATTCGCCGTTACGGCCTCAATCCTT-CCTATCACATCTTCTAAGGTACCGGGTTCATCGTTGTG
*
41768651 GCCTCAACCTTTCCCTTCATATCTTCATGGTACCA
65 GCCTCAACCTTTCCCTTCATATCTTCATGGTACTA
* * * * * * *
41768686 AATTCACCGTTATGGCCTCAATCCTTCCTATCGCATCTTATAAGGTACCGGGTTCGTCATTGTGG
1 GATTCGCCGTTACGGCCTCAATCCTTCCTATCACATCTTCTAAGGTACCGGGTTCATCGTTGTGG
* * *
41768751 CCTCAACCTTTCTCTTCGTATCTTCATGGTACTG
66 CCTCAACCTTTCCCTTCATATCTTCATGGTACTA
* * * * * ** ** * *
41768785 GATTCGTCGTTGCGGCCTTAATCCTTCCCATCTCATCTTCTAAGGTACTTGGTTCCCCATCGTGG
1 GATTCGCCGTTACGGCCTCAATCCTTCCTATCACATCTTCTAAGGTACCGGGTTCATCGTTGTGG
* *
41768850 CCTCTACCTTTCCCTTCGTATCTTCATGGTACTA
66 CCTCAACCTTTCCCTTCATATCTTCATGGTACTA
* * * **
41768884 GATTCGTCGTTACGGCCTCAATCCATCCTATCACATCTTCTAAGGTACCGGGTTCACCGTTGCAG
1 GATTCGCCGTTACGGCCTCAATCCTTCCTATCACATCTTCTAAGGTACCGGGTTCATCGTTGTGG
* *
41768949 CCTCAACCTTTCTCTTCATATCTTCATGGTACTG
66 CCTCAACCTTTCCCTTCATATCTTCATGGTACTA
* * * * * * * * * * *
41768983 GATACGCCATT-GGGAACTCAATCCTTCCCATCACATCTTCCAAGGTATCGGATTCGTTGTTGTA
1 GATTCGCCGTTACGG-CCTCAATCCTTCCTATCACATCTTCTAAGGTACCGGGTTCATCGTTGTG
41769047 GCCTCAACCTTTCCCTTCATATCTTCATG
65 GCCTCAACCTTTCCCTTCATATCTTCATG
41769076 TTCCCTCGGT
Statistics
Matches: 327, Mismatches: 61, Indels: 4
0.83 0.16 0.01
Matches are distributed among these distances:
98 2 0.01
99 322 0.98
100 3 0.01
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (99 bp):
GATTCGCCGTTACGGCCTCAATCCTTCCTATCACATCTTCTAAGGTACCGGGTTCATCGTTGTGG
CCTCAACCTTTCCCTTCATATCTTCATGGTACTA
Found at i:41768802 original size:49 final size:49
Alignment explanation
Indices: 41768586--41769075 Score: 250
Period size: 50 Copynumber: 9.9 Consensus size: 49
41768576 TCGAGGTAGA
* * * * * *
41768586 GGATTCGCCGTTACGGCCTCAATC-TTCCCTATCACATCTTCTAAGGTACCA
1 GGATTCGTCGTTGCGGCCTCAACCTTTCCCT-TCATATCTTC-ATGGTA-CT
* *
41768637 GG-TTCATCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACC
1 GGATTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACT
** ** ** ** *
41768685 AAATTCACCGTTATGGCCTCAATCC-TT-CCTATCGCATCTT-ATAAGGTACC
1 GGATTCGTCGTTGCGGCCTCAA-CCTTTCCCT-TCATATCTTCAT--GGTACT
* * * * *
41768735 GGGTTCGTCATTGTGGCCTCAACCTTTCTCTTCGTATCTTCATGGTACT
1 GGATTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACT
* * *
41768784 GGATTCGTCGTTGCGGCCTTAATCC-TTCCCATC-TCATCTTCTAAGGTACTT
1 GGATTCGTCGTTGCGGCCTCAA-CCTTTCCCTTCAT-ATCTTC-ATGGTAC-T
** * * * * *
41768835 GG-TTCCCCATCGTGGCCTCTACCTTTCCCTTCGTATCTTCATGGTACT
1 GGATTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACT
* * * * * *
41768883 AGATTCGTCGTTACGGCCTCAATCC-AT-CCTATCACATCTTCTAAGGTACC
1 GGATTCGTCGTTGCGGCCTCAA-CCTTTCCCT-TCATATCTTC-ATGGTACT
* ** * *
41768933 GGGTTCACCGTTGCAGCCTCAACCTTTCTCTTCATATCTTCATGGTACT
1 GGATTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACT
* * * * * * *
41768982 GGATACGCCATTG-GGAACTCAATCC-TTCCCATCACATCTTCCAAGGTA-T
1 GGATTCGTCGTTGCGG-CCTCAA-CCTTTCCCTTCATATCTT-CATGGTACT
* **
41769031 CGGATTCGTTGTTGTAGCCTCAACCTTTCCCTTCATATCTTCATG
1 -GGATTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATG
41769076 TTCCCTCGGT
Statistics
Matches: 329, Mismatches: 83, Indels: 56
0.70 0.18 0.12
Matches are distributed among these distances:
48 13 0.04
49 136 0.41
50 161 0.49
51 19 0.06
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.34
Consensus pattern (49 bp):
GGATTCGTCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACT
Found at i:41775009 original size:29 final size:30
Alignment explanation
Indices: 41774978--41775138 Score: 134
Period size: 30 Copynumber: 5.4 Consensus size: 30
41774968 AAAATTGAAA
*
41774978 TTTTGGAAAGTTTAAAGGTTAAAATGTAAT
1 TTTTGGAAAGTTTAAGGGTTAAAATGTAAT
*** *
41775008 TTTCAAAAAGTTTAGGGGTTAAAATGTAAT
1 TTTTGGAAAGTTTAAGGGTTAAAATGTAAT
* * ***
41775038 TTTTAGAAAGTTT-GGGGTTAAAACAAAAT
1 TTTTGGAAAGTTTAAGGGTTAAAATGTAAT
*
41775067 TTTTAGG-AAGTTTTAGGGTTAAAAT-TAAAT
1 TTTT-GGAAAGTTTAAGGGTTAAAATGT-AAT
* *
41775097 TTTTGGAAAGTTT-AGGGATCAAAAT-CAGAT
1 TTTTGGAAAGTTTAAGGG-TTAAAATGTA-AT
41775127 TTTTGGAAAGTT
1 TTTTGGAAAGTT
41775139 CGGGGCTCAA
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
29 30 0.28
30 79 0.72
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (30 bp):
TTTTGGAAAGTTTAAGGGTTAAAATGTAAT
Found at i:41775149 original size:30 final size:30
Alignment explanation
Indices: 41775094--41775163 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
41775084 GTTAAAATTA
*
41775094 AATTTTTGGAAAGTTTAGGGATCAAAATC-
1 AATTTTTGGAAAGTTCAGGGATCAAAATCG
* * *
41775123 AGATTTTTGGAAAGTTCGGGGCTCAAATTCG
1 A-ATTTTTGGAAAGTTCAGGGATCAAAATCG
41775154 AATTTTTGGA
1 AATTTTTGGA
41775164 TAAAACAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.03
30 33 0.94
31 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (30 bp):
AATTTTTGGAAAGTTCAGGGATCAAAATCG
Found at i:41777494 original size:3 final size:3
Alignment explanation
Indices: 41777486--41777525 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
41777476 CTGCTCAAAG
41777486 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41777526 TCATTCACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41780645 original size:25 final size:26
Alignment explanation
Indices: 41780617--41780671 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
41780607 TAATATTTTG
*
41780617 AAAAATATATA-AAATAGAAATTTAT
1 AAAAATACATACAAATAGAAATTTAT
* * *
41780642 AAAAATGCATACAATTATAAATTTAT
1 AAAAATACATACAAATAGAAATTTAT
41780668 AAAA
1 AAAA
41780672 TCTTATAGTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAATACATACAAATAGAAATTTAT
Found at i:41780910 original size:12 final size:12
Alignment explanation
Indices: 41780893--41780918 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41780883 AAATTTATGA
41780893 ATTTATAAATAT
1 ATTTATAAATAT
41780905 ATTTATAAATAT
1 ATTTATAAATAT
41780917 AT
1 AT
41780919 GAAATCATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTATAAATAT
Found at i:41784550 original size:19 final size:19
Alignment explanation
Indices: 41784522--41784565 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
41784512 AATTTTGAAA
*
41784522 AATTTAGGGG-TAAAATGGT
1 AATTTTGGGGTTAAAAT-GT
41784541 AATTTTGGGGTTAAAATGT
1 AATTTTGGGGTTAAAATGT
41784560 AATTTT
1 AATTTT
41784566 CAAGAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.25, T:0.41
Consensus pattern (19 bp):
AATTTTGGGGTTAAAATGT
Found at i:41784613 original size:60 final size:60
Alignment explanation
Indices: 41784543--41784665 Score: 210
Period size: 60 Copynumber: 2.0 Consensus size: 60
41784533 AAAATGGTAA
* * *
41784543 TTTTGGGGTTAAAATGTAATTTTCAAGAAGTTTTGGGGTCAAAATATAATTTCTAGAAAG
1 TTTTGAGGTTAAAATATAATTTTCAAAAAGTTTTGGGGTCAAAATATAATTTCTAGAAAG
*
41784603 TTTTGAGGTTAAAATATAATTTTCAAAAAGTTTTGGGGTCAAAATATAATTTTTAGAAAG
1 TTTTGAGGTTAAAATATAATTTTCAAAAAGTTTTGGGGTCAAAATATAATTTCTAGAAAG
41784663 TTT
1 TTT
41784666 AGGGACCTAC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (60 bp):
TTTTGAGGTTAAAATATAATTTTCAAAAAGTTTTGGGGTCAAAATATAATTTCTAGAAAG
Found at i:41784663 original size:30 final size:30
Alignment explanation
Indices: 41784543--41784665 Score: 160
Period size: 30 Copynumber: 4.1 Consensus size: 30
41784533 AAAATGGTAA
* *
41784543 TTTTGGGGTTAAAATGTAATTTTCA-AGAAG
1 TTTTGGGGTCAAAATATAATTTTCAGA-AAG
41784573 TTTTGGGGTCAAAATATAA-TTTCTAGAAAG
1 TTTTGGGGTCAAAATATAATTTTC-AGAAAG
* * *
41784603 TTTTGAGGTTAAAATATAATTTTCAAAAAG
1 TTTTGGGGTCAAAATATAATTTTCAGAAAG
*
41784633 TTTTGGGGTCAAAATATAATTTTTAGAAAG
1 TTTTGGGGTCAAAATATAATTTTCAGAAAG
41784663 TTT
1 TTT
41784666 AGGGACCTAC
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
29 4 0.05
30 72 0.89
31 5 0.06
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.41
Consensus pattern (30 bp):
TTTTGGGGTCAAAATATAATTTTCAGAAAG
Found at i:41785476 original size:17 final size:17
Alignment explanation
Indices: 41785434--41785476 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
41785424 TTAAAACAAC
41785434 AATTTCAAATCTGGAAA
1 AATTTCAAATCTGGAAA
** *
41785451 AATCCCAAATTTGGAAA
1 AATTTCAAATCTGGAAA
41785468 AATTTCAAA
1 AATTTCAAA
41785477 GTCTTTCCTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.28
Consensus pattern (17 bp):
AATTTCAAATCTGGAAA
Found at i:41786547 original size:33 final size:33
Alignment explanation
Indices: 41786510--41786586 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
41786500 AATAATATTA
* * *
41786510 AATTTGAATTAAATTCAAG-TTCAAATTAAATTG
1 AATTTAAAATAAATTCAAGATT-AAAGTAAATTG
* *
41786543 AATTTAAAATAAATTTAAGATTAAAGTAAATTT
1 AATTTAAAATAAATTCAAGATTAAAGTAAATTG
41786576 AATTTCAAAAT
1 AATTT-AAAAT
41786587 GGTTTAGGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 30 0.81
34 7 0.19
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (33 bp):
AATTTAAAATAAATTCAAGATTAAAGTAAATTG
Found at i:41786552 original size:17 final size:17
Alignment explanation
Indices: 41786516--41786567 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
41786506 ATTAAATTTG
*
41786516 AATTAAATTCAAGTTCA
1 AATTAAATTCAAGTTAA
* *
41786533 AATTAAATTGAATTTAA
1 AATTAAATTCAAGTTAA
*
41786550 AA-TAAATTTAAGATTAA
1 AATTAAATTCAAG-TTAA
41786567 A
1 A
41786568 GTAAATTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (17 bp):
AATTAAATTCAAGTTAA
Found at i:41786747 original size:46 final size:46
Alignment explanation
Indices: 41786680--41786771 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
41786670 TCATCGGTAA
41786680 GCAATATATGTAGTTGTAAACTTGAAATTTCCATTAATTAATTACT
1 GCAATATATGTAGTTGTAAACTTGAAATTTCCATTAATTAATTACT
41786726 GCAATATATGTAGTTGTAAACTTGAAATTTCCATTAATTAATTACT
1 GCAATATATGTAGTTGTAAACTTGAAATTTCCATTAATTAATTACT
41786772 CTAATAGTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (46 bp):
GCAATATATGTAGTTGTAAACTTGAAATTTCCATTAATTAATTACT
Found at i:41788993 original size:18 final size:18
Alignment explanation
Indices: 41788967--41789028 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
41788957 CATATAACAT
*
41788967 TTTAT-AAAGAATAGAAA
1 TTTATAAAAGAATAAAAA
* **
41788984 TTTATAAAAGTATTTAAA
1 TTTATAAAAGAATAAAAA
* *
41789002 TATATAAAGGAAATAAAAA
1 TTTATAAAAG-AATAAAAA
41789021 TTTATAAA
1 TTTATAAA
41789029 TTTATAAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
17 5 0.15
18 17 0.50
19 12 0.35
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.34
Consensus pattern (18 bp):
TTTATAAAAGAATAAAAA
Found at i:41795048 original size:27 final size:27
Alignment explanation
Indices: 41795022--41795072 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
41795012 TTACTGTTAC
41795022 CTTTTT-TCTCCATGGTTTTTATTTTA
1 CTTTTTGTCTCCATGGTTTTTATTTTA
41795048 CTTTTTGTCTCCATGGTTTTTATTT
1 CTTTTTGTCTCCATGGTTTTTATTT
41795073 ATATTATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.10, C:0.16, G:0.10, T:0.65
Consensus pattern (27 bp):
CTTTTTGTCTCCATGGTTTTTATTTTA
Found at i:41800002 original size:36 final size:36
Alignment explanation
Indices: 41799947--41800039 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
41799937 ATGGCCTTAT
*
41799947 GCTCTAACCGAGACATAAGCAATCACTTAGCATTAC
1 GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
* ** *
41799983 GCTCTAACTGAGATGTAAGCAATCACATAGCATTAT
1 GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
* *
41800019 GCTCTAACCAAGACGTAAGCA
1 GCTCTAACCGAGACATAAGCA
41800040 TTCCATCGAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 49 1.00
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (36 bp):
GCTCTAACCGAGACATAAGCAATCACATAGCATTAC
Found at i:41803252 original size:197 final size:194
Alignment explanation
Indices: 41802866--41803255 Score: 468
Period size: 197 Copynumber: 2.0 Consensus size: 194
41802856 AAATATGCTA
* * *
41802866 TCTAAATAAGTAATTTATTATTTATTTAAACTTAAATTAATTAATATTTAAAAATAGAATTTACA
1 TCTAAATAAGTAATTTATAATTTATTTAAACTTAAATTAATTAATATTTAAAAATACAATTCACA
* *
41802931 ATATATTAATCTACTTCAAAATTAATAAATTTAAATCTAAAAATTTAATTAGATTTTTCAAAATT
66 ATATATTAATCTACTTCAAAATTAATAAATTTAAATCAAAAAATTTAATCAGATTTTTCAAAATT
* *** * * * *
41802996 TCAAATTTAATAATGTTTATGTATTTAAGTATAAAAAAATCAGTTCAATTTAATTAAAATATAGT
131 TCAAAATTAAT-ATGTTTACCAATTTAAATATAAAAAAATAAATTAAATTTAATTAAAATATAGT
*
41803061 TCTAAATAAGTAATTTTATAATTTTATTTAAACTTAAATTAATTAATATTTAAAATTACAATTCA
1 TCTAAATAAGTAA-TTTATAA-TTTATTTAAACTTAAATTAATTAATATTTAAAAATACAATTCA
* * *
41803126 CATTATATTAATCTACTTCAAAATTAATAATTTTAAAT-AAAAAATTTAATCA-ATTTCGTT-TA
64 CAATATATTAATCTACTTCAAAATTAATAAATTTAAATCAAAAAATTTAATCAGATTT--TTCAA
* * *
41803188 AATTT-AAAATTAAT-T-TTTCCCAATTTAAATATATTAAAAATAAAATAAATAAATTTAGTTAA
127 AATTTCAAAATTAATATGTTTACCAATTTAAATATA-AAAAAAT-AAAT---TAAATTTAATTAA
41803250 AATATA
187 AATATA
41803256 TTTCATTAAT
Statistics
Matches: 166, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
192 13 0.08
193 7 0.04
194 2 0.01
195 25 0.15
196 24 0.14
197 95 0.57
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (194 bp):
TCTAAATAAGTAATTTATAATTTATTTAAACTTAAATTAATTAATATTTAAAAATACAATTCACA
ATATATTAATCTACTTCAAAATTAATAAATTTAAATCAAAAAATTTAATCAGATTTTTCAAAATT
TCAAAATTAATATGTTTACCAATTTAAATATAAAAAAATAAATTAAATTTAATTAAAATATAGT
Found at i:41803684 original size:27 final size:26
Alignment explanation
Indices: 41803646--41803707 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
41803636 TTTTTTGTGA
41803646 TTTTATATATTTATAAATTTATAA-AT
1 TTTTATATATTTATAAATTTA-AATAT
* * *
41803672 TTTTATTTCATTTCTATATTTAAATAT
1 TTTTATAT-ATTTATAAATTTAAATAT
*
41803699 TTTTTTATA
1 TTTTATATA
41803708 AATTTCTATT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (26 bp):
TTTTATATATTTATAAATTTAAATAT
Found at i:41803820 original size:25 final size:25
Alignment explanation
Indices: 41803758--41803814 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 25
41803748 ATACCATAAG
*
41803758 ATTTTTATAAATTTGTAATTGTATGC
1 ATTTTTATAAATTTGTAATTATAT-C
41803784 ATTTTTATAAATTTGTAAATTATAT-
1 ATTTTTATAAATTTGT-AATTATATC
41803809 ATTTTT
1 ATTTTT
41803815 CAAAATATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 6 0.21
26 16 0.55
27 7 0.24
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (25 bp):
ATTTTTATAAATTTGTAATTATATC
Found at i:41804988 original size:16 final size:17
Alignment explanation
Indices: 41804957--41805001 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
41804947 ATTTCATTTA
* *
41804957 AATTTAAATTTATTTTTTT
1 AATTTAAA-TT-TTTTCTC
41804976 AATTTAAATTTTTTCTC
1 AATTTAAATTTTTTCTC
41804993 AATTTAAAT
1 AATTTAAAT
41805002 ATATTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.58
18 2 0.08
19 8 0.33
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
AATTTAAATTTTTTCTC
Found at i:41805367 original size:2 final size:2
Alignment explanation
Indices: 41805312--41805354 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
41805302 TAAGCATGAT
41805312 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
41805354 T
1 T
41805355 CTTCTTTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41805472 original size:25 final size:25
Alignment explanation
Indices: 41805417--41805472 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
41805407 ATACCATAAG
* *
41805417 ATTTTTATAAATTTGTAATTGTATGC
1 ATTTTTATAAATTTATAATTATAT-C
41805443 A-TTTTATAAATTTATAATATATAT-
1 ATTTTTATAAATTTATAAT-TATATC
41805467 ATTTTT
1 ATTTTT
41805473 CAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.04
25 20 0.77
26 5 0.19
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (25 bp):
ATTTTTATAAATTTATAATTATATC
Found at i:41826751 original size:52 final size:52
Alignment explanation
Indices: 41826670--41826859 Score: 310
Period size: 52 Copynumber: 3.7 Consensus size: 52
41826660 TTCCCATTTA
* *
41826670 ATACTCACGATGACACAAAGTCATCGGACCTTA-AATCTGTAAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGT-AAAGGATCCAT
*
41826722 ATGCTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATCCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATCCAT
* * *
41826774 ATACTCATGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATCCAT
41826826 ATACTCACGATGACACATAGTCATCGGACCTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCAT
41826860 TCATTTACGG
Statistics
Matches: 129, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
52 122 0.95
53 7 0.05
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCTGTAAAGGATCCAT
Found at i:41831629 original size:11 final size:11
Alignment explanation
Indices: 41831613--41831639 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
41831603 AAAATGTATC
41831613 AATTATATTAA
1 AATTATATTAA
41831624 AATTATATTAA
1 AATTATATTAA
41831635 AATTA
1 AATTA
41831640 AAATAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTATATTAA
Found at i:41832210 original size:19 final size:19
Alignment explanation
Indices: 41832186--41832224 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
41832176 CGTCATGCCT
41832186 AAGAAGACCTTGAAACACC
1 AAGAAGACCTTGAAACACC
41832205 AAGAAGACCTTGAAACACC
1 AAGAAGACCTTGAAACACC
41832224 A
1 A
41832225 TTAATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.26, G:0.15, T:0.10
Consensus pattern (19 bp):
AAGAAGACCTTGAAACACC
Found at i:41850933 original size:20 final size:21
Alignment explanation
Indices: 41850885--41850941 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 21
41850875 CAAGATAGGC
41850885 AATCTTAGAAGATTTGATCCTTGT
1 AATCTTAG-AGATTTGA--CTTGT
*
41850909 GATCTTAGAGATTTGA-TTGT
1 AATCTTAGAGATTTGACTTGT
41850929 AATCTTAGAGATT
1 AATCTTAGAGATT
41850942 CTTTTTGTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.52
23 8 0.26
24 7 0.23
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (21 bp):
AATCTTAGAGATTTGACTTGT
Found at i:41856998 original size:17 final size:18
Alignment explanation
Indices: 41856967--41857046 Score: 92
Period size: 17 Copynumber: 4.4 Consensus size: 18
41856957 TAAATTGATC
41856967 TAAATTTATTTTTAAATT
1 TAAATTTATTTTTAAATT
*
41856985 TAAATTTA-TTTTAATTT
1 TAAATTTATTTTTAAATT
41857002 TAAATTTATCTTTTTAAATT
1 TAAATTTA--TTTTTAAATT
** *
41857022 TAAATTT-GCTTTAACTT
1 TAAATTTATTTTTAAATT
41857039 TAAATTTA
1 TAAATTTA
41857047 ATTAAATTCG
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
17 30 0.57
18 8 0.15
20 15 0.28
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (18 bp):
TAAATTTATTTTTAAATT
Found at i:41857021 original size:37 final size:35
Alignment explanation
Indices: 41856967--41857046 Score: 115
Period size: 37 Copynumber: 2.2 Consensus size: 35
41856957 TAAATTGATC
* *
41856967 TAAATTTATTTTTAAATTTAAATTTATTTTAATTT
1 TAAATTTATTTTTAAATTTAAATTTACTTTAACTT
*
41857002 TAAATTTATCTTTTTAAATTTAAATTTGCTTTAACTT
1 TAAATTTA--TTTTTAAATTTAAATTTACTTTAACTT
41857039 TAAATTTA
1 TAAATTTA
41857047 ATTAAATTCG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 8 0.20
37 32 0.80
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.59
Consensus pattern (35 bp):
TAAATTTATTTTTAAATTTAAATTTACTTTAACTT
Found at i:41858960 original size:29 final size:29
Alignment explanation
Indices: 41858874--41859088 Score: 125
Period size: 30 Copynumber: 7.2 Consensus size: 29
41858864 CCAAAAATGG
*
41858874 CATTTTGACCCCAAAACTTTCTAGAAATTA
1 CATTTTAACCCCAAAACTTTCTA-AAATTA
* * * *
41858904 CAATTTAACACTAAAACTTTTTGAAAATTA
1 CATTTTAACCCCAAAACTTTCT-AAAATTA
* *
41858934 CATTTTAACCCCAAAACATTCTAAAATTC
1 CATTTTAACCCCAAAACTTTCTAAAATTA
* * * *
41858963 CATTTTTGA-CCC-TAATTTTACCAAAAATTA
1 CA-TTTTAACCCCAAAACTTT--CTAAAATTA
* * *
41858993 CCATTTT-ACCCTC-GAACTTTCCAAAATTC
1 -CATTTTAACCC-CAAAACTTTCTAAAATTA
*** *
41859022 CATTTTAACCCCAATTTTTATCCAAAATTA
1 CATTTTAACCCCAAAACTT-TCTAAAATTA
* *
41859052 CCATTTT-ACCCCTAAACTTTCTAAAATTT
1 -CATTTTAACCCCAAAACTTTCTAAAATTA
41859081 CAATTTTA
1 C-ATTTTA
41859089 TCCCTAATTT
Statistics
Matches: 140, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
28 12 0.09
29 38 0.27
30 75 0.54
31 15 0.11
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (29 bp):
CATTTTAACCCCAAAACTTTCTAAAATTA
Found at i:41859019 original size:59 final size:58
Alignment explanation
Indices: 41858927--41859351 Score: 305
Period size: 59 Copynumber: 7.2 Consensus size: 58
41858917 AAACTTTTTG
* * *
41858927 AAAATTA-CATTTTAACCC-CAAAACATTCTAAAATTCCATTTTTGACCCTAATTTTACCA
1 AAAATTACCATTTT-ACCCTC-GAACTTTCTAAAATT-CATTTTTAACCCTAATTTTACCA
* *
41858986 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCA-TTTTAACCCCAATTTTTATCC-
1 AAAATTACCATTTTACCCTCGAACTTTCTAAAATT-CATTTTTAACCCTAA-TTTTA-CCA
* * *
41859045 AAAATTACCATTTTACCC-CTAAACTTTCTAAAATTTCAATTTTATCCCTAATTTTACCA
1 AAAATTACCATTTTACCCTC-GAACTTTCTAAAA-TTCATTTTTAACCCTAATTTTACCA
* * * *
41859104 AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCAATTTTAAACCTCGATTTCACCA
1 AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCATTTTTAACCCT-AATTTTACCA
* * * * * * * *
41859163 AAAATTACCATTTTACCACT-GAA-TATCTAAAATATAACTTTTGACCTTGATTTCATC-
1 AAAATTACCATTTTACC-CTCGAACTTTCTAAAAT-TCATTTTTAACCCTAATTTTACCA
* * * * * * * * * *
41859220 AAAATTACCATTTTACCCCCGGA-TGTCCAAAAATCCTATTTTTGATCCCGATTTTTTCTA
1 AAAATTACCATTTTACCCTCGAACT-TTCTAAAATTC-ATTTTT-AACCCTAATTTTACCA
* * * * * *
41859280 AAAATTACCGTTTTACCCTC-AAGTGTCTAAAATATCATTTTTAACTACAAATTTTTCC-
1 AAAATTACCATTTTACCCTCGAACTTTCTAAAAT-TCATTTTTAAC-CCTAATTTTACCA
41859338 AAAATTACCATTTT
1 AAAATTACCATTTT
41859352 GCCCCTGAGA
Statistics
Matches: 294, Mismatches: 52, Indels: 41
0.76 0.13 0.11
Matches are distributed among these distances:
56 1 0.00
57 20 0.07
58 69 0.23
59 160 0.54
60 44 0.15
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTTCTAAAATTCATTTTTAACCCTAATTTTACCA
Found at i:41859074 original size:118 final size:117
Alignment explanation
Indices: 41858927--41859351 Score: 391
Period size: 118 Copynumber: 3.6 Consensus size: 117
41858917 AAACTTTTTG
* *
41858927 AAAATTA-CATTTTAACCCCAAAACATTCTAAAAT-TCCATTTTTGACCCTAATTTTACCAAAAA
1 AAAATTACCATTTT-ACCCCTAAACTTTCTAAAATAT-CATTTTTGACCCTAATTTTACC-AAAA
*
41858990 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCAATTTTTATCC
63 TTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCGATTTTTATCC
* *
41859045 AAAATTACCATTTTACCCCTAAACTTTCTAAAATTTCAATTTT-ATCCCTAATTTTACCAAAAAT
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATATCATTTTTGA-CCCTAATTTTACC-AAAAT
* * * *
41859109 TACCATTTTACCCTCGAACTTTCTAAAATTCAATTTTAAACCTCGA-TTTCA-CC
64 TACCATTTTACCCTCGAACTTTCCAAAATTCCATTTT-AACCCCGATTTTTATCC
* * * * * * * * *
41859162 AAAAATTACCATTTTACCACTGAA-TATCTAAAATATAACTTTTGACCTTGATTTCATCAAAATT
1 -AAAATTACCATTTTACCCCTAAACTTTCTAAAATATCATTTTTGACCCTAATTTTACCAAAATT
* * * * * * *
41859226 ACCATTTTACCCCCGGA-TGTCCAAAAATCCTATTTTTGATCCCGATTTTT-TCTA
65 ACCATTTTACCCTCGAACTTTCCAAAATTCC-A-TTTTAACCCCGATTTTTATC-C
* * * * * * * *
41859280 AAAATTACCGTTTTA-CCCTCAAGTGTCTAAAATATCATTTTTAACTACAAATTTTTCCAAAATT
1 AAAATTACCATTTTACCCCTAAACTTTCTAAAATATCATTTTTGAC-CCTAATTTTACCAAAATT
41859344 ACCATTTT
65 ACCATTTT
41859352 GCCCCTGAGA
Statistics
Matches: 251, Mismatches: 43, Indels: 26
0.78 0.13 0.08
Matches are distributed among these distances:
115 9 0.04
116 32 0.13
117 67 0.27
118 130 0.52
119 13 0.05
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (117 bp):
AAAATTACCATTTTACCCCTAAACTTTCTAAAATATCATTTTTGACCCTAATTTTACCAAAATTA
CCATTTTACCCTCGAACTTTCCAAAATTCCATTTTAACCCCGATTTTTATCC
Found at i:41859093 original size:29 final size:27
Alignment explanation
Indices: 41858888--41859146 Score: 110
Period size: 30 Copynumber: 8.9 Consensus size: 27
41858878 TTGACCCCAA
* *
41858888 AACTTTCTAGAAATTACAATTTAACACT
1 AACTTTCTA-AAATTACAATTTTACCCT
* *
41858916 AAAACTTTTTGAAAATTAC-ATTTTAACCCCAA
1 --AACTTTCT-AAAATTACAATTTT-A-CCC-T
* * *
41858948 AACATTCTAAAATTCCATTTTTGACCCT
1 AACTTTCTAAAATTACAATTTT-ACCCT
* * *
41858976 AATTTTACCAAAAATTACCATTTTACCCT
1 AACTTT--CTAAAATTACAATTTTACCCT
* * *
41859005 CGAACTTTCCAAAATT-CCATTTTAACCCC
1 --AACTTTCTAAAATTACAATTTT-ACCCT
* * *
41859034 AATTTTTATCCAAAATTACCATTTTACCCCT
1 AA--CTT-TCTAAAATTACAATTTTA-CCCT
*
41859065 AAACTTTCTAAAATTTCAATTTTATCCCT
1 -AACTTTCTAAAATTACAATTTTA-CCCT
* * *
41859094 AATTTTACCAAAAATTACCATTTTACCCT
1 AACTTT--CTAAAATTACAATTTTACCCT
41859123 CGAACTTTCTAAAATT-CAATTTTA
1 --AACTTTCTAAAATTACAATTTTA
41859147 AACCTCGATT
Statistics
Matches: 176, Mismatches: 33, Indels: 42
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.01
28 23 0.13
29 62 0.35
30 64 0.36
31 23 0.13
32 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (27 bp):
AACTTTCTAAAATTACAATTTTACCCT
Found at i:41859476 original size:28 final size:28
Alignment explanation
Indices: 41859423--41859497 Score: 73
Period size: 28 Copynumber: 2.6 Consensus size: 28
41859413 CTCGATTCTT
41859423 TCAAAAATTACCATTTTACCCATAAACA
1 TCAAAAATTACCATTTTACCCATAAACA
* *
41859451 TCAAAAA-TGCCATTTCTAACCC-TAAATCTT
1 TCAAAAATTACCATTT-T-ACCCATAAA-C-A
*
41859481 TCCAAAATTACCATTTT
1 TCAAAAATTACCATTTT
41859498 GCCCTCGGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 7 0.18
28 12 0.32
29 5 0.13
30 7 0.18
31 7 0.18
ACGTcount: A:0.40, C:0.25, G:0.01, T:0.33
Consensus pattern (28 bp):
TCAAAAATTACCATTTTACCCATAAACA
Found at i:41859514 original size:146 final size:145
Alignment explanation
Indices: 41859219--41859501 Score: 349
Period size: 146 Copynumber: 1.9 Consensus size: 145
41859209 TTGATTTCAT
* *
41859219 CAAAATTACCATTTTACCCCCGGATGTCCAAAAATCCTATTTTTGATCCCGATTTTTTCTAAAAA
1 CAAAATTACCATTTTACCCCCGGA-GTCCAAAAATCCCATTTTTGATCCCGATTCTTTCTAAAAA
* *** * * * *
41859284 TTACCGTTTTACCCTCAAGTGTCTAAAATATCATTTTTAACTACAAATTTTTCCAAAATTACCAT
65 TTACCATTTTACCCTCAAACATCAAAAATACCATTTCTAACTACAAATCTTTCCAAAATTACCAT
41859349 TTTGCCCCTGAGAGTC
130 TTTGCCCCTGAGAGTC
* * *
41859365 CAAAATTACCATTTTACCCTC-GAGCATCCAAAAAGTCCCATTTTTTATCTCGATTCTTTC-AAA
1 CAAAATTACCATTTTACCCCCGGAG--TCCAAAAA-TCCCATTTTTGATCCCGATTCTTTCTAAA
* *
41859428 AATTACCATTTTACCCAT-AAACATCAAAAATGCCATTTCTAAC-CCTAAATCTTTCCAAAATTA
63 AATTACCATTTTACCC-TCAAACATCAAAAATACCATTTCTAACTAC-AAATCTTTCCAAAATTA
41859491 CCATTTTGCCC
126 CCATTTTGCCC
41859502 TCGGGTATCC
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
144 1 0.01
145 3 0.03
146 91 0.78
147 22 0.19
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (145 bp):
CAAAATTACCATTTTACCCCCGGAGTCCAAAAATCCCATTTTTGATCCCGATTCTTTCTAAAAAT
TACCATTTTACCCTCAAACATCAAAAATACCATTTCTAACTACAAATCTTTCCAAAATTACCATT
TTGCCCCTGAGAGTC
Found at i:41863768 original size:43 final size:43
Alignment explanation
Indices: 41863707--41863829 Score: 167
Period size: 43 Copynumber: 2.9 Consensus size: 43
41863697 ACCCGTGTGT
* * *
41863707 GTATACTATTTGGAGGCACACAGGTTGACACATGGGCATGAGA
1 GTATACTGTTTTGAGGCACACAGGTTGACACACGGGCATGAGA
* *
41863750 GTATACTGTTTTGAGGCACACAGGTTGACACACGGTCATGTGA
1 GTATACTGTTTTGAGGCACACAGGTTGACACACGGGCATGAGA
* *
41863793 GTATACTGTTTTGAGGCACATAAGG-TGGCACACGGGC
1 GTATACTGTTTTGAGGCACA-CAGGTTGACACACGGGC
41863830 GTGTGTCAGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
43 68 0.96
44 3 0.04
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (43 bp):
GTATACTGTTTTGAGGCACACAGGTTGACACACGGGCATGAGA
Found at i:41864447 original size:55 final size:53
Alignment explanation
Indices: 41864363--41864465 Score: 125
Period size: 55 Copynumber: 1.9 Consensus size: 53
41864353 TAAGTTGCAA
* * *
41864363 GAGGCACATGTGCTGGCACACAGACGTGTGTCAGGGTGTGTATGTATACTGTTTG
1 GAGGCACACGAGCTGGCACACAGACGTGTGTCAGGATGTG--TGTATACTGTTTG
** * *
41864418 GAGGCACACGAGCTGGCACATGGGCGTGTGTTAGGATGTGTGTATACT
1 GAGGCACACGAGCTGGCACACAGACGTGTGTCAGGATGTGTGTATACT
41864466 ATTTTGAGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
53 8 0.20
55 33 0.80
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (53 bp):
GAGGCACACGAGCTGGCACACAGACGTGTGTCAGGATGTGTGTATACTGTTTG
Found at i:41865715 original size:33 final size:32
Alignment explanation
Indices: 41865661--41865729 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
41865651 AAGAAAGATA
* * *
41865661 AATTCTATTAGGATTTGAAAAGGAGTAGTTTG
1 AATTCTATTAAGATTTAAAAAGGAGTAATTTG
*
41865693 AATTCTAGTTAAGATTTAAAAAGGATTAATTTG
1 AATTCTA-TTAAGATTTAAAAAGGAGTAATTTG
41865726 AATT
1 AATT
41865730 TCAAATTGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 7 0.22
33 25 0.78
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (32 bp):
AATTCTATTAAGATTTAAAAAGGAGTAATTTG
Found at i:41867142 original size:42 final size:43
Alignment explanation
Indices: 41867096--41867275 Score: 199
Period size: 42 Copynumber: 4.3 Consensus size: 43
41867086 TCAAGTCATA
* *
41867096 AGTCTTCCTTTAATCATATTCTCATTCTTATCCT-GAGACATG
1 AGTCTTCCTTTAATCATATTCTCATGCTCATCCTCGAGACATG
* * *
41867138 AGTCTTCTTTTAATCATAATCTCATTCTCAT-CTCGAGACATG
1 AGTCTTCCTTTAATCATATTCTCATGCTCATCCTCGAGACATG
* * * **
41867180 AGTCTTCCTTTAATCATATTTTCATGCTCATTC-CGAGTCGCG
1 AGTCTTCCTTTAATCATATTCTCATGCTCATCCTCGAGACATG
* *
41867222 AGTCTTCCATTT-ATACAAATTCTCATGCTCA-ACTCGAGACATG
1 AGTCTTCC-TTTAAT-CATATTCTCATGCTCATCCTCGAGACATG
41867265 AGTCTTCCTTT
1 AGTCTTCCTTT
41867276 TTATACATCA
Statistics
Matches: 117, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.02
42 83 0.71
43 32 0.27
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (43 bp):
AGTCTTCCTTTAATCATATTCTCATGCTCATCCTCGAGACATG
Found at i:41867275 original size:85 final size:84
Alignment explanation
Indices: 41867096--41867275 Score: 222
Period size: 84 Copynumber: 2.1 Consensus size: 84
41867086 TCAAGTCATA
* * * *
41867096 AGTCTTCCTTTAATCATATTCTCATTCTTATCCTGAGACATGAGTCTTCTTTTAATCATAATCTC
1 AGTCTTCCTTTAATCATATTCTCATGCTCATCCTGAGACACGAGTCTTCATTTAATCATAATCTC
* *
41867161 ATTCTCATCTCGAGACATG
66 ATGCTCAACTCGAGACATG
* * *
41867180 AGTCTTCCTTTAATCATATTTTCATGCTCATTCC-GAGTCGCGAGTCTTCCATTT-ATACA-AAT
1 AGTCTTCCTTTAATCATATTCTCATGCTCA-TCCTGAGACACGAGTCTT-CATTTAAT-CATAA-
41867242 TCTCATGCTCAACTCGAGACATG
62 TCTCATGCTCAACTCGAGACATG
41867265 AGTCTTCCTTT
1 AGTCTTCCTTT
41867276 TTATACATCA
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
84 42 0.51
85 41 0.49
ACGTcount: A:0.24, C:0.25, G:0.11, T:0.40
Consensus pattern (84 bp):
AGTCTTCCTTTAATCATATTCTCATGCTCATCCTGAGACACGAGTCTTCATTTAATCATAATCTC
ATGCTCAACTCGAGACATG
Found at i:41869665 original size:26 final size:26
Alignment explanation
Indices: 41869631--41869682 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
41869621 TTTGCAAAAG
41869631 ACTAGCGTAGGCCCATTTTTGCCATT
1 ACTAGCGTAGGCCCATTTTTGCCATT
41869657 ACTAGCGTAGGCCCATTTTTGCCATT
1 ACTAGCGTAGGCCCATTTTTGCCATT
41869683 CTTTGCATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (26 bp):
ACTAGCGTAGGCCCATTTTTGCCATT
Found at i:41873119 original size:21 final size:24
Alignment explanation
Indices: 41873075--41873121 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
41873065 TAACGTATAC
*
41873075 CAACAACATTTGGTTATTCATCTT
1 CAACAAAATTTGGTTATTCATCTT
41873099 CAACAAAATTT-GTT-TTC-TCTT
1 CAACAAAATTTGGTTATTCATCTT
41873120 CA
1 CA
41873122 CTTGAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 3 0.14
23 3 0.14
24 10 0.45
ACGTcount: A:0.30, C:0.21, G:0.06, T:0.43
Consensus pattern (24 bp):
CAACAAAATTTGGTTATTCATCTT
Found at i:41878003 original size:35 final size:36
Alignment explanation
Indices: 41877940--41878014 Score: 134
Period size: 35 Copynumber: 2.1 Consensus size: 36
41877930 GCTTTTAGGA
41877940 TTATATACCATAAATTATTATAATATCAAAGTGTAG
1 TTATATACCATAAATTATTATAATATCAAAGTGTAG
*
41877976 TTATATACCAT-AATTTTTATAATATCAAAGTGTAG
1 TTATATACCATAAATTATTATAATATCAAAGTGTAG
41878011 TTAT
1 TTAT
41878015 GCTTTTAGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 27 0.71
36 11 0.29
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.43
Consensus pattern (36 bp):
TTATATACCATAAATTATTATAATATCAAAGTGTAG
Found at i:41878014 original size:19 final size:19
Alignment explanation
Indices: 41877957--41878014 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
41877947 CCATAAATTA
41877957 TTATAATATCAAAGTGTAG
1 TTATAATATCAAAGTGTAG
* *
41877976 TTAT-ATACCATAA-T-T-T
1 TTATAATATCA-AAGTGTAG
41877992 TTATAATATCAAAGTGTAG
1 TTATAATATCAAAGTGTAG
41878011 TTAT
1 TTAT
41878015 GCTTTTAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 10
0.68 0.09 0.23
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 7 0.23
19 10 0.33
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (19 bp):
TTATAATATCAAAGTGTAG
Found at i:41889120 original size:3 final size:3
Alignment explanation
Indices: 41889112--41889147 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
41889102 TACATCCCAA
41889112 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
41889148 GAATAGAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41890218 original size:20 final size:20
Alignment explanation
Indices: 41890193--41890234 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
41890183 GTTTTTCAAA
*
41890193 AAAGTCAACGGTCAACGGTC
1 AAAGTCAACGATCAACGGTC
41890213 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGGTC
41890233 AA
1 AA
41890235 CCAACACCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.14
Consensus pattern (20 bp):
AAAGTCAACGATCAACGGTC
Found at i:41890233 original size:14 final size:14
Alignment explanation
Indices: 41890197--41890250 Score: 56
Period size: 14 Copynumber: 3.9 Consensus size: 14
41890187 TTCAAAAAAG
*
41890197 TCAACGGTCAACGG
1 TCAACGGTCAACGA
*
41890211 TCAA-AGTCAACGA
1 TCAACGGTCAACGA
*
41890224 TCAACGGTCAACCA
1 TCAACGGTCAACGA
* *
41890238 ACACCGGTCAACG
1 TCAACGGTCAACG
41890251 GTCGGTCAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.35, C:0.31, G:0.20, T:0.13
Consensus pattern (14 bp):
TCAACGGTCAACGA
Found at i:41890253 original size:7 final size:7
Alignment explanation
Indices: 41890196--41890235 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
41890186 TTTCAAAAAA
41890196 GTCAACG
1 GTCAACG
41890203 GTCAACG
1 GTCAACG
*
41890210 GTCAA-A
1 GTCAACG
41890216 GTCAACG
1 GTCAACG
*
41890223 ATCAACG
1 GTCAACG
41890230 GTCAAC
1 GTCAAC
41890236 CAACACCGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.15
Consensus pattern (7 bp):
GTCAACG
Found at i:41890347 original size:15 final size:15
Alignment explanation
Indices: 41890327--41890362 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41890317 GGTTCATTTG
41890327 GTTTGGTTCAAATGA
1 GTTTGGTTCAAATGA
*
41890342 GTTTGGTTTAAATGA
1 GTTTGGTTCAAATGA
*
41890357 ATTTGG
1 GTTTGG
41890363 GTTTGGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.28, T:0.44
Consensus pattern (15 bp):
GTTTGGTTCAAATGA
Found at i:41890368 original size:21 final size:22
Alignment explanation
Indices: 41890342--41890385 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
41890332 GTTCAAATGA
41890342 GTTTGGTTTAAAT-GAATTTGG
1 GTTTGGTTTAAATAGAATTTGG
41890363 GTTTGGTTTAAATAGAATTTGG
1 GTTTGGTTTAAATAGAATTTGG
41890385 G
1 G
41890386 CTTAATGGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (22 bp):
GTTTGGTTTAAATAGAATTTGG
Found at i:41890789 original size:11 final size:11
Alignment explanation
Indices: 41890756--41890830 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
41890746 AAGTGTGATT
*
41890756 AAAAGAGGAAG
1 AAAAGAGAAAG
*
41890767 AAAATAGAAAAG
1 AAAAGAG-AAAG
41890779 AAAAGAGAAAG
1 AAAAGAGAAAG
41890790 AAATA-AGAAATG
1 AAA-AGAGAAA-G
* *
41890802 AATGAGAAAAAG
1 AA-AAGAGAAAG
41890814 AAAAGAGAAAG
1 AAAAGAGAAAG
*
41890825 GAAAGA
1 AAAAGA
41890831 TGAGAGGCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 30 0.59
12 17 0.33
13 4 0.08
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:41890798 original size:23 final size:23
Alignment explanation
Indices: 41890756--41890828 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
41890746 AAGTGTGATT
*
41890756 AAAAGAGGAAGAAAATAGAAAAG
1 AAAAGAGAAAGAAAATAGAAAAG
*
41890779 AAAAGAGAAAG-AAATAAGAAATG
1 AAAAGAGAAAGAAAAT-AGAAAAG
* * * *
41890802 AATGAGAAAAAGAAAAGAGAAAGG
1 AA-AAGAGAAAGAAAATAGAAAAG
41890826 AAA
1 AAA
41890829 GATGAGAGGC
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
22 4 0.10
23 18 0.45
24 15 0.38
25 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.25, T:0.05
Consensus pattern (23 bp):
AAAAGAGAAAGAAAATAGAAAAG
Found at i:41891360 original size:18 final size:18
Alignment explanation
Indices: 41891330--41891390 Score: 79
Period size: 18 Copynumber: 3.4 Consensus size: 18
41891320 ACATAACTGA
*
41891330 GAGCTCACTTAAACATGC
1 GAGCTCACCTAAACATGC
* *
41891348 AAGCTCTA-CTAAAGATGC
1 GAGCTC-ACCTAAACATGC
41891366 GAGCTCACCTAAACATGC
1 GAGCTCACCTAAACATGC
41891384 GAGCTCA
1 GAGCTCA
41891391 ACCAAATATA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 1 0.03
18 34 0.94
19 1 0.03
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.20
Consensus pattern (18 bp):
GAGCTCACCTAAACATGC
Found at i:41891410 original size:36 final size:36
Alignment explanation
Indices: 41891330--41891410 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
41891320 ACATAACTGA
* * * *
41891330 GAGCTCACTTAAACATGCAAGCTCTACTAAAGATGC
1 GAGCTCACCTAAACATGCAAGCTCAACCAAAGATAC
* * *
41891366 GAGCTCACCTAAACATGCGAGCTCAACCAAATATAT
1 GAGCTCACCTAAACATGCAAGCTCAACCAAAGATAC
*
41891402 GAGTTCACC
1 GAGCTCACC
41891411 AAGATTATGA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.16, T:0.21
Consensus pattern (36 bp):
GAGCTCACCTAAACATGCAAGCTCAACCAAAGATAC
Found at i:41895249 original size:32 final size:32
Alignment explanation
Indices: 41895213--41895273 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
41895203 CCAAGATTCT
*
41895213 CAAGTTGCAAAAGTTATAACTTTTTTTTACTC
1 CAAGTTGCAAAACTTATAACTTTTTTTTACTC
41895245 CAAGTTGCAAAACTTATAACTTTTTTTTA
1 CAAGTTGCAAAACTTATAACTTTTTTTTA
41895274 ATGTAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.08, T:0.44
Consensus pattern (32 bp):
CAAGTTGCAAAACTTATAACTTTTTTTTACTC
Found at i:41903486 original size:53 final size:53
Alignment explanation
Indices: 41903350--41903559 Score: 210
Period size: 53 Copynumber: 3.9 Consensus size: 53
41903340 AAGTTGGAGG
* * * * * * * *
41903350 AGGCAAATGGGCTGGCACATGGGCGTGTGTTAGGGTGTGTGTGTATGCTGTTTTG
1 AGGCACATGGGCTGACACATAGGAGTGTGTCA-GG-GTGTGTGTATACTGTTCTA
** * * * *
41903405 AGGCACACAGGTTGGCACACA-GACGTGTGTCAGGGTGTGTGTATATTGTTCTA
1 AGGCACATGGGCTGACACATAGGA-GTGTGTCAGGGTGTGTGTATACTGTTCTA
41903458 AGGCACATGGGCTGACACATAGGAGTGTGTCAGGGTGTGTGTATACTGTTCTA
1 AGGCACATGGGCTGACACATAGGAGTGTGTCAGGGTGTGTGTATACTGTTCTA
* * *
41903511 AGG-ATATGGGCTAACACATGAGCA-TGTGTCAGGGTGTGTGTATACTGTT
1 AGGCACATGGGCTGACACAT-AGGAGTGTGTCAGGGTGTGTGTATACTGTT
41903560 TTCAGACACA
Statistics
Matches: 131, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
52 39 0.30
53 65 0.50
54 5 0.04
55 22 0.17
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.30
Consensus pattern (53 bp):
AGGCACATGGGCTGACACATAGGAGTGTGTCAGGGTGTGTGTATACTGTTCTA
Done.