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 164 of 171
Found at i:48654391 original size:321 final size:322
Alignment explanation
Indices: 48653797--48654445 Score: 943
Period size: 321 Copynumber: 2.0 Consensus size: 322
48653787 ATACAAGAAA
48653797 ATGTGAAAATGAAAAACAAATATTGGAACGATCAGAAACACAGATTTGAGAATTTGAAAGCAGAA
1 ATGTGAAAATGAAAAACAAATATTGGAACGATCAGAAACACAGATTTGAGAATTTGAAAGCAGAA
48653862 AACACTTAGTAGTTCACTTTGGATGAAGAAAACACAATGGGAAGTGGTTGGTTTAACTCTAAAAT
66 AACACTTA-TAGTTCACTTTGGATGAAGAAAACACAATGGGAAGTGGTTGGTTTAACTCTAAAAT
* *
48653927 GTTTTGTTCATCATTAGTTTCATTTGTTATTTAGTGGATGATAAATAAAGACCCTATTTTAAACC
130 GTTTTGTTCATCATTAGTTTCATTTGTTATTTAGTGGATGACAAATAAAAACCCTATTTTAAACC
* * ** * * * * *
48653992 GTGTGTGATTTGAATTCGAATCGTTTCAATTAATTTATTGTTAAAATGTTATATTTTTTTATAAT
195 ATATGTGACCTGAATTCGAATCG-TTCAATCAAGTTATTATTAAAATGTTACATTTTCTTATAAT
** * * *
48654057 TCATCAAAAATAAAATAAATAAAG-CGCTATTTTTTATCCACATTTCATAGTCTGCTCCACCAC
259 TCAAAAAAAATAAAATAAATAAAGACCCTACTTTTTATCCACATTTCAAAGTCTGCTCCACCAC
48654120 ATGTGAAAACTGAAAAACAAATATTGGAACGATCAGAAACACAGATTTGAGAATTTGAAAGCAGA
1 ATGTGAAAA-TGAAAAACAAATATTGGAACGATCAGAAACACAGATTTGAGAATTTGAAAGCAGA
48654185 AAACAC-T-TAGTTCACTTTGGATGAAGAAAACACAATGGGAAGTGGTTGGTTTAACTCTAAAAT
65 AAACACTTATAGTTCACTTTGGATGAAGAAAACACAATGGGAAGTGGTTGGTTTAACTCTAAAAT
*
48654248 GTTTTGTTCATCATTAGTTTCATTTGTTATTTAGTGGATGACAAATAAAAACCC-ACTTTTAATC
130 GTTTTGTTCATCATTAGTTTCATTTGTTATTTAGTGGATGACAAATAAAAACCCTA-TTTTAAAC
* * * * * *
48654312 TATATGTGACCTGAATTTGAATATCG-TCAATCACGTTGTTATTAGAACT-TTACATTTTCCTTG
194 CATATGTGACCTGAATTCG-A-ATCGTTCAATCAAGTTATTATTA-AAATGTTACATTTT-CTTA
* * *
48654375 T-ATTTAAAAAAAATAAAATAAATAAAGACCCTGCTTTTTATCCACCTTTCAAAGTCTGCTCCAC
255 TAATTCAAAAAAAATAAAATAAATAAAGACCCTACTTTTTATCCACATTTCAAAGTCTGCTCCAC
48654439 CAC
320 CAC
48654442 ATGT
1 ATGT
48654446 CCTATGCCCT
Statistics
Matches: 293, Mismatches: 26, Indels: 15
0.88 0.08 0.04
Matches are distributed among these distances:
320 1 0.00
321 172 0.59
322 45 0.15
323 14 0.05
324 61 0.21
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (322 bp):
ATGTGAAAATGAAAAACAAATATTGGAACGATCAGAAACACAGATTTGAGAATTTGAAAGCAGAA
AACACTTATAGTTCACTTTGGATGAAGAAAACACAATGGGAAGTGGTTGGTTTAACTCTAAAATG
TTTTGTTCATCATTAGTTTCATTTGTTATTTAGTGGATGACAAATAAAAACCCTATTTTAAACCA
TATGTGACCTGAATTCGAATCGTTCAATCAAGTTATTATTAAAATGTTACATTTTCTTATAATTC
AAAAAAAATAAAATAAATAAAGACCCTACTTTTTATCCACATTTCAAAGTCTGCTCCACCAC
Found at i:48655272 original size:16 final size:16
Alignment explanation
Indices: 48655251--48655285 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
48655241 TTTAAATCAA
* *
48655251 ATTTATTTAATTAATT
1 ATTTATTAAATTAAAT
48655267 ATTTATTAAATTAAAT
1 ATTTATTAAATTAAAT
48655283 ATT
1 ATT
48655286 GACTAAATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTATTAAATTAAAT
Found at i:48656348 original size:96 final size:96
Alignment explanation
Indices: 48656231--48656424 Score: 388
Period size: 96 Copynumber: 2.0 Consensus size: 96
48656221 TTACAACCAA
48656231 TAGGGAAATTTTGACTAATGTAAACTTTTGAATTGATTATTTTTATTAAATTAACAATAGATTAA
1 TAGGGAAATTTTGACTAATGTAAACTTTTGAATTGATTATTTTTATTAAATTAACAATAGATTAA
48656296 TGTTGGCATGGGAGCTTGGGTTAATCCAGCT
66 TGTTGGCATGGGAGCTTGGGTTAATCCAGCT
48656327 TAGGGAAATTTTGACTAATGTAAACTTTTGAATTGATTATTTTTATTAAATTAACAATAGATTAA
1 TAGGGAAATTTTGACTAATGTAAACTTTTGAATTGATTATTTTTATTAAATTAACAATAGATTAA
48656392 TGTTGGCATGGGAGCTTGGGTTAATCCAGCT
66 TGTTGGCATGGGAGCTTGGGTTAATCCAGCT
48656423 TA
1 TA
48656425 CTTGTCTAGT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 98 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (96 bp):
TAGGGAAATTTTGACTAATGTAAACTTTTGAATTGATTATTTTTATTAAATTAACAATAGATTAA
TGTTGGCATGGGAGCTTGGGTTAATCCAGCT
Found at i:48657169 original size:69 final size:69
Alignment explanation
Indices: 48657091--48657229 Score: 278
Period size: 69 Copynumber: 2.0 Consensus size: 69
48657081 ATAGATGTCA
48657091 AATATCCTCAATTATCTAGTCTTGGGATTATCATGTAATTATCACTTAAATCATCATCCATATCA
1 AATATCCTCAATTATCTAGTCTTGGGATTATCATGTAATTATCACTTAAATCATCATCCATATCA
48657156 AAAT
66 AAAT
48657160 AATATCCTCAATTATCTAGTCTTGGGATTATCATGTAATTATCACTTAAATCATCATCCATATCA
1 AATATCCTCAATTATCTAGTCTTGGGATTATCATGTAATTATCACTTAAATCATCATCCATATCA
48657225 AAAT
66 AAAT
48657229 A
1 A
48657230 CATGAAATAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.37
Consensus pattern (69 bp):
AATATCCTCAATTATCTAGTCTTGGGATTATCATGTAATTATCACTTAAATCATCATCCATATCA
AAAT
Found at i:48657853 original size:43 final size:42
Alignment explanation
Indices: 48657801--48657881 Score: 126
Period size: 43 Copynumber: 1.9 Consensus size: 42
48657791 GTCAAATAGC
48657801 ATATACTAGACCTAGTTACACCCCATTAACTAACTTAATATT
1 ATATACTAGACCTAGTTACACCCCATTAACTAACTTAATATT
** *
48657843 ATATGACTAGACCTAGTTACATGCCATTAACTAATTTAA
1 ATAT-ACTAGACCTAGTTACACCCCATTAACTAACTTAA
48657882 GACAAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 4 0.11
43 31 0.89
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.33
Consensus pattern (42 bp):
ATATACTAGACCTAGTTACACCCCATTAACTAACTTAATATT
Found at i:48659450 original size:29 final size:28
Alignment explanation
Indices: 48659377--48659450 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
48659367 GTTTCTACGT
48659377 ACATGCGAGCCTATATGCAAACCCTAGA
1 ACATGCGAGCCTATATGCAAACCCTAGA
* * * *
48659405 ACTTGAGAGCCTATATGCGAACCCTAGGT
1 ACATGCGAGCCTATATGCAAACCCTA-GA
*
48659434 GCATGCGAGCCTATATG
1 ACATGCGAGCCTATATG
48659451 ATCATGTCAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.22
Consensus pattern (28 bp):
ACATGCGAGCCTATATGCAAACCCTAGA
Found at i:48660379 original size:95 final size:92
Alignment explanation
Indices: 48660239--48660426 Score: 297
Period size: 95 Copynumber: 2.0 Consensus size: 92
48660229 ATTATTTTTA
* * *
48660239 TGATGAATAATTAATTACCAAGAGTTCACCACTTTTGCCAGTGGAATAGGCATTGTTGATGTATT
1 TGATGAATAATTAAGTAACAAGAGTTCACCACTTTTGCCAGTGGAATAGGCATTGTTGATGAATT
48660304 ACTTGTTATTATTTTTATGATGAATAAT
66 ACTT-TTATTATTTTTATGATGAATAAT
*
48660332 TGATGAATAATTAAGTAAGAAGAGTCTTCACCACTTTTGCTC-GTGGAATAGGCATTGTTGATGA
1 TGATGAATAATTAAGTAACAAGAG--TTCACCACTTTTGC-CAGTGGAATAGGCATTGTTGATGA
48660396 ATTACTTTTATTATTTTTATGATGAATAAT
63 ATTACTTTTATTATTTTTATGATGAATAAT
48660426 T
1 T
48660427 AAGCATGAAG
Statistics
Matches: 88, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
93 21 0.24
94 24 0.27
95 42 0.48
96 1 0.01
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (92 bp):
TGATGAATAATTAAGTAACAAGAGTTCACCACTTTTGCCAGTGGAATAGGCATTGTTGATGAATT
ACTTTTATTATTTTTATGATGAATAAT
Found at i:48660472 original size:83 final size:83
Alignment explanation
Indices: 48660332--48660484 Score: 270
Period size: 83 Copynumber: 1.8 Consensus size: 83
48660322 GATGAATAAT
* *
48660332 TGATGAATAATTAAGTAAGAAGAGTCTTCACCACTTTTGCTCGTGGAATAGGCATTGTTGATGAA
1 TGATGAATAATTAAGCAAGAAGAGTCTTCACCACTTTTGCTAGTGGAATAGGCATTGTTGATGAA
48660397 TTACTTTTATTATTTTTA
66 TTACTTTTATTATTTTTA
* *
48660415 TGATGAATAATTAAGCATGAAGAGTCTTCACCACTTTTGCTAGTGGAATAGGTATTGTTGATGAA
1 TGATGAATAATTAAGCAAGAAGAGTCTTCACCACTTTTGCTAGTGGAATAGGCATTGTTGATGAA
48660480 TTACT
66 TTACT
48660485 AACGTTGTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 66 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (83 bp):
TGATGAATAATTAAGCAAGAAGAGTCTTCACCACTTTTGCTAGTGGAATAGGCATTGTTGATGAA
TTACTTTTATTATTTTTA
Found at i:48661747 original size:21 final size:21
Alignment explanation
Indices: 48661721--48661763 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
48661711 TGTTACTAGG
48661721 TATCATTCCGGTGTCTATTGC
1 TATCATTCCGGTGTCTATTGC
48661742 TATCATTCCGGTGTCTATTGC
1 TATCATTCCGGTGTCTATTGC
48661763 T
1 T
48661764 CCCTATCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (21 bp):
TATCATTCCGGTGTCTATTGC
Found at i:48665168 original size:23 final size:21
Alignment explanation
Indices: 48665134--48665180 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
48665124 CAAATTTTAA
* *
48665134 TATTTATATTTTTTGAATTTT
1 TATTTATATTTTTTAAAATTT
48665155 TATTTATAATTTTTTTAAAATTT
1 TATTTAT-A-TTTTTTAAAATTT
48665178 TAT
1 TAT
48665181 AATCAAGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTTATATTTTTTAAAATTT
Found at i:48666993 original size:21 final size:23
Alignment explanation
Indices: 48666969--48667023 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
48666959 TGCGTTGTTG
48666969 TTAAAAAAATTATTTAT-A-TTT
1 TTAAAAAAATTATTTATAATTTT
***
48666990 TTAAAATTTTTATTTATAATTTT
1 TTAAAAAAATTATTTATAATTTT
*
48667013 TTTAAAAAATT
1 TTAAAAAAATT
48667024 TATAATCAAG
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
21 14 0.56
22 1 0.04
23 10 0.40
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAAAAATTATTTATAATTTT
Found at i:48669489 original size:82 final size:79
Alignment explanation
Indices: 48669390--48669639 Score: 272
Period size: 84 Copynumber: 3.0 Consensus size: 79
48669380 ATTAGAAAAT
* * *
48669390 AATTTTTTTCGTGATTTATTTCCGTCGTTTAACAGATTTTATTCTATTTTGATTTTATTTCCAAA
1 AATTTTTTT-G-GATTTATTCCCATCGTTTAACAGATTTTATTCTATTTTGATTTTGTTTCCAAA
48669455 -ACGAGAATAAGTTGAATA
64 TA--A-AATAAGTTGAATA
** *
48669473 AATTTTTTTGGAATTTATTCCCCCCGTTCAACAGATTTTATTCTATATTTGGATTTTGGTTT-CA
1 AATTTTTTTGG-ATTTATTCCCATCGTTTAACAGATTTTATTCTAT-TTT-GATTTT-GTTTCCA
* *
48669537 AATAATAATTAAG-TAAATT
62 AATAA-AA-TAAGTTGAATA
* *
48669556 AATTTGTTTCGGGATTTATTCCCATCGTTTAACAGATTTTATTCTAATTTGATTTTGTTTCCAAA
1 AATTT-TTT-TGGATTTATTCCCATCGTTTAACAGATTTTATTCTATTTTGATTTTGTTTCCAAA
48669621 TAAAATAAGTTGAATA
64 TAAAATAAGTTGAATA
48669637 AAT
1 AAT
48669640 CCGTTTCGAG
Statistics
Matches: 142, Mismatches: 15, Indels: 22
0.79 0.08 0.12
Matches are distributed among these distances:
80 4 0.03
81 14 0.10
82 44 0.31
83 27 0.19
84 47 0.33
85 6 0.04
ACGTcount: A:0.30, C:0.11, G:0.12, T:0.47
Consensus pattern (79 bp):
AATTTTTTTGGATTTATTCCCATCGTTTAACAGATTTTATTCTATTTTGATTTTGTTTCCAAATA
AAATAAGTTGAATA
Found at i:48669573 original size:84 final size:82
Alignment explanation
Indices: 48669390--48669694 Score: 307
Period size: 82 Copynumber: 3.7 Consensus size: 82
48669380 ATTAGAAAAT
* * * * *
48669390 AATTTTTTTCGTGATTTATTTCCGTCGTTTAACAGATTTTATTCTAT-TTTGATTTTATTTCCAA
1 AATTTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCTATATTTGATTTTGTTTCCAA
48669454 A-ACGAGAATAAGTTGAATA
66 ATA--A-AATAAGTTGAATA
* * * *
48669473 AATTT-TTTTGGAATTTATTCCCCCCGTTCAACAGATTTTATTCTATATTTGGATTTTGGTTT-C
1 AATTTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCTATATTT-GATTTT-GTTTCC
* *
48669536 AAATAATAATTAAG-TAAATT
64 AAATAA-AA-TAAGTTGAATA
**
48669556 AATTTGTTTCGGGATTTATTCCCATCGTTTAACAGATTTTATTCTA-ATTTGATTTTGTTTCCAA
1 AATTTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCTATATTTGATTTTGTTTCCAA
48669620 ATAAAATAAGTTGAATA
66 ATAAAATAAGTTGAATA
** * ** * * *
48669637 AATCCGTTTCGAGATTTATTCTTGCCGATTAACAAATTATATTCTATATTTGGATTTT
1 AATTTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCTATATTT-GATTTT
48669695 ATAATAATTA
Statistics
Matches: 184, Mismatches: 28, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
80 4 0.02
81 46 0.25
82 51 0.28
83 30 0.16
84 49 0.27
85 4 0.02
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (82 bp):
AATTTGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTCTATATTTGATTTTGTTTCCAA
ATAAAATAAGTTGAATA
Found at i:48669669 original size:81 final size:83
Alignment explanation
Indices: 48669390--48669694 Score: 286
Period size: 81 Copynumber: 3.7 Consensus size: 83
48669380 ATTAGAAAAT
* * * ** *
48669390 AATTTTTTTCGTGATTTATTTCCGTCGTTTAACAGATTTTATTCTAT-TTT-GATTTTATTTCCA
1 AATTTGTTTCGAGATTTATTCCCACCG-TTAACAGATTTTATTCTATATTTGGATTTTGTTTCCA
48669453 AA-ACGAGAATAAGTTGAATA
65 AATA--AGAATAAGTTGAATA
* * *
48669473 AATTTTTTTGGA-ATTTATTCCCCCCGTTCAACAGATTTTATTCTATATTTGGATTTTGGTTT-C
1 AATTTGTTTCGAGATTTATTCCCACCGTT-AACAGATTTTATTCTATATTTGGATTTT-GTTTCC
* * *
48669536 AAATAATAATTAAG-TAAATT
64 AAATAAGAA-TAAGTTGAATA
* *
48669556 AATTTGTTTCGGGATTTATTCCCATCGTTTAACAGATTTTATTCTA-ATTT-GATTTTGTTTCCA
1 AATTTGTTTCGAGATTTATTCCCACCG-TTAACAGATTTTATTCTATATTTGGATTTTGTTTCCA
48669619 AATAA-AATAAGTTGAATA
65 AATAAGAATAAGTTGAATA
** *** * *
48669637 AATCCGTTTCGAGATTTATTCTTGCCGATTAACAAATTATATTCTATATTTGGATTTT
1 AATTTGTTTCGAGATTTATTCCCACCG-TTAACAGATTTTATTCTATATTTGGATTTT
48669695 ATAATAATTA
Statistics
Matches: 184, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
80 4 0.02
81 48 0.26
82 45 0.24
83 39 0.21
84 42 0.23
85 6 0.03
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.47
Consensus pattern (83 bp):
AATTTGTTTCGAGATTTATTCCCACCGTTAACAGATTTTATTCTATATTTGGATTTTGTTTCCAA
ATAAGAATAAGTTGAATA
Found at i:48669842 original size:11 final size:11
Alignment explanation
Indices: 48669826--48669850 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48669816 GTTCAACAAA
48669826 TTTGATTTAAT
1 TTTGATTTAAT
48669837 TTTGATTTAAT
1 TTTGATTTAAT
48669848 TTT
1 TTT
48669851 CAAGCAAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTGATTTAAT
Found at i:48676423 original size:11 final size:11
Alignment explanation
Indices: 48676393--48676417 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
48676383 AATGTGTTAA
48676393 TGGAAAAAGAT
1 TGGAAAAAGAT
48676404 TGGAAAAAGAT
1 TGGAAAAAGAT
48676415 TGG
1 TGG
48676418 GCAAAGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (11 bp):
TGGAAAAAGAT
Found at i:48687631 original size:301 final size:300
Alignment explanation
Indices: 48687081--48687664 Score: 1017
Period size: 301 Copynumber: 1.9 Consensus size: 300
48687071 TAAAAAAGAT
** *
48687081 CAATTTGGTTTAAAATGGTGAACTTCTCTTGATTAATTCACACTGGGTAATAATTGATAGATGAG
1 CAATTTGGTTTAAAATGGTGAACTTCTCTTGATTAATTCACACTGGACAACAATTGATAGATGAG
48687146 CCGTATGTATTTTCTTCTCAAGTCAAACAAGTTTTTTACTCAAAAGATCCAACTGATAAGGGTTG
66 CCGTATGTATTTTCTTCTCAAGTCAAACAAGTTTTTTACTCAAAAGATCCAACTGATAAGGGTTG
*
48687211 GTATGTTGTACTCCGTAACACCCATAAAGACTTGTTTGACATGGGAAATGGAAGTAAAGATGACA
131 GTACGTTGTACTCCGTAACACCCATAAAGACTTGTTTGACATGGGAAATGGAAGTAAAGATGACA
* * * * *
48687276 TGGACGAAAGATTAGAAACTTTATCTTTTCTAGAACAAAACTTAAATGAAACTATCCCTAGTACT
196 TGGACGAAAGATCAGAAACTTTACCTTTTCCAGAACAAAACTTAAATAAAACTATCCCTAATACT
48687341 AGTACACAATTTCAATGGGTTCGTCATCCCTAGTAGTACA
261 AGTACACAATTTCAATGGGTTCGTCATCCCTAGTAGTACA
*
48687381 CAATTTGGTTTTAAAATGGTGAACTTCTCTTGATTAATTCTCACTGGACAACAATTGATAGATGA
1 CAATTTGG-TTTAAAATGGTGAACTTCTCTTGATTAATTCACACTGGACAACAATTGATAGATGA
*
48687446 -CTCGTATGTATTTTCTTCTCAAGTTAAACAAGTTTTTTACTCAAAAGATCCAACTGATAAGGGT
65 GC-CGTATGTATTTTCTTCTCAAGTCAAACAAGTTTTTTACTCAAAAGATCCAACTGATAAGGGT
* *
48687510 TGGTACGTTGTACTCCGTAACACCCATAGAGACTTGTTTGACATGGGCAATGGAAGTAAAGATGA
129 TGGTACGTTGTACTCCGTAACACCCATAAAGACTTGTTTGACATGGGAAATGGAAGTAAAGATGA
*
48687575 CATGGACGAAAGATCAGAAATTTTACCTTTTCCAGAACAAAACTTAAATAAAACTATCCCTAATA
194 CATGGACGAAAGATCAGAAACTTTACCTTTTCCAGAACAAAACTTAAATAAAACTATCCCTAATA
48687640 CTAGTACACAATTTCAATGGGTTCG
259 CTAGTACACAATTTCAATGGGTTCG
48687665 CCAGGATGTG
Statistics
Matches: 268, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
300 9 0.03
301 259 0.97
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (300 bp):
CAATTTGGTTTAAAATGGTGAACTTCTCTTGATTAATTCACACTGGACAACAATTGATAGATGAG
CCGTATGTATTTTCTTCTCAAGTCAAACAAGTTTTTTACTCAAAAGATCCAACTGATAAGGGTTG
GTACGTTGTACTCCGTAACACCCATAAAGACTTGTTTGACATGGGAAATGGAAGTAAAGATGACA
TGGACGAAAGATCAGAAACTTTACCTTTTCCAGAACAAAACTTAAATAAAACTATCCCTAATACT
AGTACACAATTTCAATGGGTTCGTCATCCCTAGTAGTACA
Found at i:48689429 original size:21 final size:21
Alignment explanation
Indices: 48689405--48689455 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
48689395 TTCAAAGCGG
*
48689405 AGGCAACAACGAGGGAAGCAA
1 AGGCAACAACAAGGGAAGCAA
* * * *
48689426 AGGCAGCAGCAAGGGCAGCAG
1 AGGCAACAACAAGGGAAGCAA
48689447 AGGCAACAA
1 AGGCAACAA
48689456 GAAAGTATGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.22, G:0.35, T:0.00
Consensus pattern (21 bp):
AGGCAACAACAAGGGAAGCAA
Found at i:48689814 original size:43 final size:43
Alignment explanation
Indices: 48689757--48690179 Score: 366
Period size: 43 Copynumber: 10.1 Consensus size: 43
48689747 TAATGTTAGT
* * * *
48689757 GGCGTTTGTAGGAAAAGTGCCTCTAAAGATCATGTTCTATAGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
* * * * *
48689800 GGCGCTTATGGGAAAAACGCCGCTAAAGATCATGATCTATAAC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
* * * *
48689843 --C--------CACAAA-CGCCGCTAAAGACCATGTTTTGTAGC
1 GGCGTTTGTGGGA-AAAGCGCCGCTAAAGATCATGTTCTATAGC
* * * * *
48689876 GACGTTTGTGAGAAAAGCGCTGCTAAAGACCATGTTCTGTAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
* **
48689919 GGCATTTGTGGGAAAAATGCCGCTAAAGATCATGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
* *
48689962 AGCATTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
* * * * *
48690005 GGTGTTTGTGAGAAGAA-CACCGCTAAAAATTATGTTCTATAGC
1 GGCGTTTGTGGGAA-AAGCGCCGCTAAAGATCATGTTCTATAGC
* *
48690048 GGCGTATGTGGGAAAAGCGCTGCTAAAGATCATGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
* * * ** * * *
48690091 GACGTTTATGAGAAAAGCGTAGTTAAAGATCATGTTCTATTGT
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
** **
48690134 GGCGTTTGTGGGAAAAGCATCATTAAAGATCATGTTCTATAGC
1 GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
48690177 GGC
1 GGC
48690180 ATTTTCTCAC
Statistics
Matches: 306, Mismatches: 60, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
33 22 0.07
34 3 0.01
35 1 0.00
41 1 0.00
42 5 0.02
43 272 0.89
44 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
GGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGTTCTATAGC
Found at i:48690689 original size:41 final size:41
Alignment explanation
Indices: 48690622--48690998 Score: 302
Period size: 41 Copynumber: 9.2 Consensus size: 41
48690612 AAACGACGCA
48690622 AAAGGT-AGAGCAATAG-GGACGCTTATGGAAAAGCGCAGCT
1 AAAGGTCAGAGCAATAGCGG-CGCTTATGGAAAAGCGCAGCT
* * * *
48690662 AAAGGTCAGAGTAATAGCAGCGTTTAT-GAGAAAGCACCA-CT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGA-AAAGC-GCAGCT
* * * *
48690703 AAAGATCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGTT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCAGCT
* * * * *
48690744 AAAGGTTAGAGCAATAGCAGTGCTTTTTGAAAAGCGTC-GCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCG-CAGCT
* * * *
48690785 AAAGGTCAGAGCAATAGCCGCACTTAT-GAGTAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGA-AAAGCGCAGCT
* * * *
48690826 AAAGGTCAGTGTAATAGCGACGCTTATGGGAAAGCGCCA-CT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCG-CAGCT
* * ** **
48690867 AAAGGTTAGAGCAATAGCGGCACTTATGGGCAAGCGCCTCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCAGCT
* * * * *
48690908 AAAGATCAAAGCAATAGCGACGCTTAAGGACAAGCGCCA-CT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCG-CAGCT
** * *
48690949 AAAGGTCAGAGCAATAGCGGCGCTTATAAAAAAGCACCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCAGCT
*
48690990 AAAAGTCAG
1 AAAGGTCAG
48690999 TGTAATATTA
Statistics
Matches: 264, Mismatches: 59, Indels: 27
0.75 0.17 0.08
Matches are distributed among these distances:
40 14 0.05
41 242 0.92
42 8 0.03
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCAGCT
Found at i:48690778 original size:82 final size:82
Alignment explanation
Indices: 48690622--48690998 Score: 368
Period size: 82 Copynumber: 4.6 Consensus size: 82
48690612 AAACGACGCA
* * *
48690622 AAAGGT-AGAGCAATAG-GGACGCTTATGGAAAAGCGCAGCTAAAGGTCAGAGTAATAGC-A-GC
1 AAAGGTCAGAGCAATAGCGG-CGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGC
* * *
48690683 GTTTATGAGAAAGCACCACT
65 -TTAAGGA-AAAGCGCCACT
* * * *
48690703 AAAGATCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGTTAAAGGTTAGAGCAATAGC-AGTGC
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGA-CGC
*** * *
48690767 TTTTTGAAAAGCGTCGCT
65 TTAAGGAAAAGCGCCACT
* * * * * *
48690785 AAAGGTCAGAGCAATAGCCGCACTTATGAGTAAGCGCCGCTAAAGGTCAGTGTAATAGCGACGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
* *
48690850 TATGGGAAAGCGCCACT
66 TAAGGAAAAGCGCCACT
* * * * * *
48690867 AAAGGTTAGAGCAATAGCGGCACTTATGGGCAAGCGCCTCTAAAGATCAAAGCAATAGCGACGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
*
48690932 TAAGGACAAGCGCCACT
66 TAAGGAAAAGCGCCACT
*** * *
48690949 AAAGGTCAGAGCAATAGCGGCGCTTATAAAAAAGCACCGCTAAAAGTCAG
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAG
48690999 TGTAATATTA
Statistics
Matches: 243, Mismatches: 48, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
81 5 0.02
82 227 0.93
83 9 0.04
84 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (82 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCAATAGCGACGCT
TAAGGAAAAGCGCCACT
Found at i:48690786 original size:123 final size:121
Alignment explanation
Indices: 48690622--48690975 Score: 390
Period size: 123 Copynumber: 2.9 Consensus size: 121
48690612 AAACGACGCA
* * * *
48690622 AAAGG-TAGAGCAATAG-GGACGCTTATGGAAAAGCGCAGCTAAAGGTCAGAGTAATAGCAGCGT
1 AAAGGTTAGAGCAATAGCAG-CACTTATGGAAAAGCGC-GCTAAAGGTCAGAGCAATAGC-GCGC
* * **
48690685 TTATGAGAAAGCACCACTAAAGATCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCGTT
63 TTATGAGAAAGCGCCACTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCACT
** * * *
48690744 AAAGGTTAGAGCAATAGCAGTGCTTTTTGAAAAGCGTCGCTAAAGGTCAGAGCAATAGCCGCACT
1 AAAGGTTAGAGCAATAGCAGCACTTATGGAAAAGCG-CGCTAAAGGTCAGAGCAATAG-CGCGCT
* * * * *
48690809 TATGAGTAAGCGCCGCTAAAGGTCAGTGTAATAGCGACGCTTATGGGAAAGCGCCACT
64 TATGAGAAAGCGCCACTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCACT
* ** * * *
48690867 AAAGGTTAGAGCAATAGCGGCACTTATGGGCAAGCGCCTCTAAAGATCAAAGCAATAGCGACGCT
1 AAAGGTTAGAGCAATAGCAGCACTTATGGAAAAGCG-CGCTAAAGGTCAGAGCAATAGCG-CGCT
*
48690932 TAAG-GACAAGCGCCACTAAAGGTCAGAGCAATAGCGGCGCTTAT
64 TATGAGA-AAGCGCCACTAAAGGTCAGAGCAATAGCGGCGCTTAT
48690976 AAAAAAGCAC
Statistics
Matches: 192, Mismatches: 34, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
122 8 0.04
123 181 0.94
124 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.28, T:0.18
Consensus pattern (121 bp):
AAAGGTTAGAGCAATAGCAGCACTTATGGAAAAGCGCGCTAAAGGTCAGAGCAATAGCGCGCTTA
TGAGAAAGCGCCACTAAAGGTCAGAGCAATAGCGGCGCTTATGGGAAAGCGCCACT
Found at i:48695291 original size:19 final size:20
Alignment explanation
Indices: 48695263--48695313 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
48695253 TAAAATAGAG
*
48695263 AAAATTATAAAAATAATA-A-
1 AAAATCATAAAAAT-ATACAT
*
48695282 AAAATCATAAATATATACAT
1 AAAATCATAAAAATATACAT
48695302 AAAA-CATAAAAA
1 AAAATCATAAAAA
48695314 ATTAACAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 3 0.11
19 20 0.74
20 4 0.15
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATCATAAAAATATACAT
Found at i:48696970 original size:43 final size:43
Alignment explanation
Indices: 48696905--48697132 Score: 325
Period size: 43 Copynumber: 5.3 Consensus size: 43
48696895 ATTTGTTAAT
*
48696905 TTTAGTGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCAT-TCTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGT-TC
* * * *
48696948 TTTAGCGGTGTTTGTGAAAAAAGCGCCGCTAAAGACCATGTTT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGTTC
* *
48696991 TTTAGCGGCGTTTGTGGGAAAAGCGCCACTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGTTC
* *
48697034 TTTAGCGGCGTTTGTGAGAAAATCGTCGCTAAAGA-CTATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATC-ATGTTC
* *
48697077 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGATCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGTTC
48697120 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
48697133 TTCCAAATAA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
42 1 0.01
43 160 0.98
44 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCATGTTC
Found at i:48703814 original size:11 final size:11
Alignment explanation
Indices: 48703800--48703895 Score: 65
Period size: 11 Copynumber: 8.8 Consensus size: 11
48703790 ACTTTGGATT
*
48703800 TTAAATTTATA
1 TTAAATTTAAA
48703811 TTAAATTTAAA
1 TTAAATTTAAA
**
48703822 TTAGTTTTAAA
1 TTAAATTTAAA
* *
48703833 TT-TA-TT-CA
1 TTAAATTTAAA
48703841 -TAAATTTAAA
1 TTAAATTTAAA
* *
48703851 TTTATTTTAAA
1 TTAAATTTAAA
48703862 TTTAAATTTAAA
1 -TTAAATTTAAA
*
48703874 TTAATCTTTAAA
1 TTAA-ATTTAAA
48703886 TTTAAATTTA
1 -TTAAATTTA
48703896 GTTTAAATTC
Statistics
Matches: 64, Mismatches: 14, Indels: 13
0.70 0.15 0.14
Matches are distributed among these distances:
7 1 0.02
8 2 0.03
9 4 0.06
10 1 0.02
11 33 0.52
12 19 0.30
13 4 0.06
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:48703821 original size:17 final size:17
Alignment explanation
Indices: 48703799--48703904 Score: 80
Period size: 17 Copynumber: 6.5 Consensus size: 17
48703789 AACTTTGGAT
48703799 TTTAAATTTATATTAAA
1 TTTAAATTTATATTAAA
*
48703816 TTTAAA-TTAGTTTTAAA
1 TTTAAATTTA-TATTAAA
*
48703833 TTT--A-TT-CA-TAAA
1 TTTAAATTTATATTAAA
*
48703845 TTTAAATTTATTTTAAA
1 TTTAAATTTATATTAAA
* *
48703862 TTTAAATTTAAATTAATC
1 TTTAAATTTATATTAA-A
* * *
48703880 TTTAAATTTAAATTTAG
1 TTTAAATTTATATTAAA
48703897 TTTAAATT
1 TTTAAATT
48703905 CGGAATGATT
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
12 7 0.10
14 1 0.01
15 5 0.07
16 3 0.04
17 41 0.57
18 15 0.21
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATATTAAA
Found at i:48703852 original size:29 final size:28
Alignment explanation
Indices: 48703797--48703875 Score: 99
Period size: 29 Copynumber: 2.8 Consensus size: 28
48703787 TCAACTTTGG
48703797 ATTTTAAATTTATATTAAATTTAAA-TT
1 ATTTTAAATTTATATTAAATTTAAATTT
48703824 AGTTTTAAATTTAT-TCATAAATTTAAATTT
1 A-TTTTAAATTTATAT--TAAATTTAAATTT
*
48703854 ATTTTAAATTTAAATTTAAATT
1 ATTTTAAATTTATA-TTAAATT
48703876 AATCTTTAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
27 2 0.04
28 12 0.27
29 27 0.60
30 3 0.07
31 1 0.02
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTAAATTTATATTAAATTTAAATTT
Found at i:48703877 original size:5 final size:6
Alignment explanation
Indices: 48703799--48703904 Score: 82
Period size: 6 Copynumber: 18.3 Consensus size: 6
48703789 AACTTTGGAT
* **
48703799 TTTAAA TTTATA -TTAAA TTTAAA -TTAGT TTTAAA TTT--A TTCATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT--TAAA
* *
48703845 TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA -TTAATC TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA
*
48703892 TTT-AG TTTAAA TT
1 TTTAAA TTTAAA TT
48703905 CGGAATGATT
Statistics
Matches: 78, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
4 3 0.04
5 19 0.24
6 49 0.63
7 4 0.05
8 3 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:48703901 original size:24 final size:24
Alignment explanation
Indices: 48703841--48703895 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
48703831 AATTTATTCA
*
48703841 TAAATTTAAATTTAT-TTTAAATT
1 TAAATTTAAATTAATCTTTAAATT
48703864 TAAATTTAAATTAATCTTTAAATT
1 TAAATTTAAATTAATCTTTAAATT
48703888 TAAATTTA
1 TAAATTTA
48703896 GTTTAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATTTAAATTAATCTTTAAATT
Found at i:48703901 original size:35 final size:35
Alignment explanation
Indices: 48703811--48703904 Score: 88
Period size: 35 Copynumber: 2.7 Consensus size: 35
48703801 TAAATTTATA
48703811 TTAAATTTAAA-TTAGTTTTAAATTTATTCATAAAT
1 TTAAATTTAAATTTAG-TTTAAATTTATTCATAAAT
* * **
48703846 TTAAATTT-ATTTTAAATTTAAATTTAAATT-A-ATCT
1 TTAAATTTAAATTT-AGTTTAAATTT--ATTCATAAAT
48703881 TTAAATTTAAATTTAGTTTAAATT
1 TTAAATTTAAATTTAGTTTAAATT
48703905 CGGAATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 10
0.75 0.09 0.16
Matches are distributed among these distances:
34 1 0.02
35 38 0.79
36 6 0.12
37 3 0.06
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (35 bp):
TTAAATTTAAATTTAGTTTAAATTTATTCATAAAT
Found at i:48704002 original size:15 final size:15
Alignment explanation
Indices: 48703982--48704012 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
48703972 AATTACAAAA
48703982 TCCAAAATGTACAAT
1 TCCAAAATGTACAAT
48703997 TCCAAAATGTACAAT
1 TCCAAAATGTACAAT
48704012 T
1 T
48704013 GGGTTGGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.29
Consensus pattern (15 bp):
TCCAAAATGTACAAT
Found at i:48704717 original size:24 final size:22
Alignment explanation
Indices: 48704675--48704734 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
48704665 GCCTTATTAT
48704675 TAATATTAATAATAATAATGAA
1 TAATATTAATAATAATAATGAA
** *
48704697 TGTAATATTAATAATGGTAATTAA
1 --TAATATTAATAATAATAATGAA
48704721 TAACTATTAATAAT
1 TAA-TATTAATAAT
48704735 TATTAGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.09
23 10 0.31
24 19 0.59
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (22 bp):
TAATATTAATAATAATAATGAA
Found at i:48705904 original size:30 final size:29
Alignment explanation
Indices: 48705858--48706256 Score: 278
Period size: 29 Copynumber: 13.7 Consensus size: 29
48705848 CCCTAAATTG
*
48705858 TCCAAAAATCACATTTTTACCCCTCAAACTT
1 TCCAAAAATTACATTTTTA-CCCTCAAAC-T
* * *
48705889 TGC-AAAATTATATTTTTGACCCT-GAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACT
*
48705917 TCCAAAAATTACATTTTTACCC-CTGAACT
1 TCCAAAAATTACATTTTTACCCTC-AAACT
* * * * *
48705946 CCCAAAAATAACAATTTTAACCTTGAAACT
1 TCCAAAAATTAC-ATTTTTACCCTCAAACT
* **
48705976 TCCAAAAATTATATTTTTACCCCTCGGACT
1 TCCAAAAATTACATTTTTA-CCCTCAAACT
* *
48706006 TTCAAAAATTACATTTTTGACCCTGAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACT
* *
48706036 TCCAAAAATTACATTTTTACCTTCAGACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
**
48706065 TCCAAAAATTACATTTTTGACATTCAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACT
** *
48706095 AT-TGAAAATTACATTTTTACCCTCTAACT
1 -TCCAAAAATTACATTTTTACCCTCAAACT
*** *
48706124 TTTGAAAATTACATTTTTACCCTGAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
* * *
48706153 T-CTAGAATTACATTTTTATCC-CAAA-T
1 TCCAAAAATTACATTTTTACCCTCAAACT
** *
48706179 ATCCAAAAATCCCATTTTGACCC-CAAAACT
1 -TCCAAAAATTACATTTTTACCCTC-AAACT
** *
48706209 TTTAAAAATTACCA-TTTTACCCTCGAA-T
1 TCCAAAAATTA-CATTTTTACCCTCAAACT
* *
48706237 ATCCAAAAACTCCATTTTTA
1 -TCCAAAAATTACATTTTTA
48706257 AGCTTGAAAC
Statistics
Matches: 290, Mismatches: 59, Indels: 40
0.75 0.15 0.10
Matches are distributed among these distances:
26 1 0.00
27 4 0.01
28 42 0.14
29 128 0.44
30 110 0.38
31 5 0.02
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCTCAAACT
Found at i:48706075 original size:59 final size:59
Alignment explanation
Indices: 48705858--48706316 Score: 325
Period size: 59 Copynumber: 7.8 Consensus size: 59
48705848 CCCTAAATTG
* * * *
48705858 TCCAAAAATCACATTTTTACCCCTCAAACTTTGC-AAAATTATATTTTTGACCCTG-AACT
1 TCCAAAAATTACATTTTTA-CCCTCAGAC-TTCCAAAAATTACATTTTTGACCCTGAAACT
* * * * * *
48705917 TCCAAAAATTACATTTTTACCC-CTGAACTCCCAAAAATAACAATTTTAACCTTGAAACT
1 TCCAAAAATTACATTTTTACCCTCAG-ACTTCCAAAAATTACATTTTTGACCCTGAAACT
* * *
48705976 TCCAAAAATTATATTTTTACCCCTCGGACTTTCAAAAATTACATTTTTGACCCTGAAACT
1 TCCAAAAATTACATTTTTA-CCCTCAGACTTCCAAAAATTACATTTTTGACCCTGAAACT
* ** *
48706036 TCCAAAAATTACATTTTTACCTTCAGACTTCCAAAAATTACATTTTTGACATTCAAACT
1 TCCAAAAATTACATTTTTACCCTCAGACTTCCAAAAATTACATTTTTGACCCTGAAACT
** ***
48706095 AT-TGAAAATTACATTTTTACCCTCTA-ACTTTTGAAAATTACATTTTT-ACCCTGAAACT
1 -TCCAAAAATTACATTTTTACCCTC-AGACTTCCAAAAATTACATTTTTGACCCTGAAACT
* * * * ** **
48706153 T-CTAGAATTACATTTTTATCC-CA-AATATCCAAAAATCCCA-TTTTGACCCCAAAACT
1 TCCAAAAATTACATTTTTACCCTCAGACT-TCCAAAAATTACATTTTTGACCCTGAAACT
** * * * * * *
48706209 TTTAAAAATTACCA-TTTTACCCTC-GAATATCCAAAAACTCCATTTTTAAGCTTGAAACT
1 TCCAAAAATTA-CATTTTTACCCTCAGACT-TCCAAAAATTACATTTTTGACCCTGAAACT
** * * * *
48706268 TTTAAAAATTAC-TATGTTACCC-CCGAATGTCCAAAAATTTCATTTTTGA
1 TCCAAAAATTACAT-TTTTACCCTCAGACT-TCCAAAAATTACATTTTTGA
48706317 TCCCGATTTC
Statistics
Matches: 321, Mismatches: 62, Indels: 34
0.77 0.15 0.08
Matches are distributed among these distances:
55 7 0.02
56 19 0.06
57 33 0.10
58 49 0.15
59 161 0.50
60 50 0.16
61 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (59 bp):
TCCAAAAATTACATTTTTACCCTCAGACTTCCAAAAATTACATTTTTGACCCTGAAACT
Found at i:48712116 original size:14 final size:12
Alignment explanation
Indices: 48712039--48712122 Score: 66
Period size: 12 Copynumber: 6.8 Consensus size: 12
48712029 GAGTCACGTG
*
48712039 GCTGATGTGG-T
1 GCTGACGTGGAT
48712050 GCTGACGTGGAT
1 GCTGACGTGGAT
48712062 GCTGACGTGG-T
1 GCTGACGTGGAT
*
48712073 AG-TGACATGGCAGT
1 -GCTGACGTGG-A-T
*
48712087 GCTTACGTGGAT
1 GCTGACGTGGAT
48712099 GCTGACGTGGTAAT
1 GCTGACGTGG--AT
*
48712113 GCTGATGTGG
1 GCTGACGTGG
48712123 CGATGCTGAT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
11 17 0.29
12 22 0.37
13 2 0.03
14 18 0.31
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (12 bp):
GCTGACGTGGAT
Found at i:48713061 original size:48 final size:47
Alignment explanation
Indices: 48712912--48713080 Score: 159
Period size: 48 Copynumber: 3.6 Consensus size: 47
48712902 TACTGGATTT
* * *
48712912 GCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTACAAGGTTC
1 GCCGTTGCGGCTTAAA-CCTTCCCTTCATTTTTC-GAGGTACAAGGTTC
* * *
48712961 GCCGTTGTGGCTT-AA--TTCCCTTGACA-TTTTCGTGGTAC-TGGATTC
1 GCCGTTGCGGCTTAAACCTTCCCTT--CATTTTTCGAGGTACAAGG-TTC
*
48713006 ACCGTTGCGGCTTAAATCCTTCCCTTCATTTTTCGAGGTACAAGGTTC
1 GCCGTTGCGGCTTAAA-CCTTCCCTTCATTTTTCGAGGTACAAGGTTC
* *
48713054 GCTGTTGCGGCTTGAACCTTTCCCTTC
1 GCCGTTGCGGCTTAAACC-TTCCCTTC
48713081 CTGCTCCATG
Statistics
Matches: 98, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
44 2 0.02
45 27 0.28
46 5 0.05
47 6 0.06
48 37 0.38
49 21 0.21
ACGTcount: A:0.15, C:0.27, G:0.22, T:0.37
Consensus pattern (47 bp):
GCCGTTGCGGCTTAAACCTTCCCTTCATTTTTCGAGGTACAAGGTTC
Found at i:48722043 original size:23 final size:22
Alignment explanation
Indices: 48722001--48722043 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
48721991 AATTTTGTTT
* *
48722001 TTTTAAATTAAGTTTGAATTGA
1 TTTTAAATTAAATTTAAATTGA
48722023 TTTTAAATGTAAATTTAAATT
1 TTTTAAAT-TAAATTTAAATT
48722044 TAAATACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTAAATTAAATTTAAATTGA
Found at i:48724072 original size:31 final size:29
Alignment explanation
Indices: 48724018--48724191 Score: 120
Period size: 30 Copynumber: 5.7 Consensus size: 29
48724008 GGAGGTCCCT
*
48724018 AAACTATCCAAAAATTATA-TTTTGACCCCC
1 AAACT-TCC-AAAATTACATTTTTGACCCCC
* * *
48724048 AAACTCCTCCAAAATTACATTTTTGAGCTCA
1 AAACT--TCCAAAATTACATTTTTGACCCCC
*
48724079 AAACTTCCATAAATTACATTTTT-ACCCTC
1 AAACTTCCA-AAATTACATTTTTGACCCCC
* * * * *
48724108 GAGCTTCCAAAAAATTCCAATTTTGACCCCA
1 AAACTTCC--AAAATTACATTTTTGACCCCC
*
48724139 AAACTTTCAAATATTACCATTTTT-ACCCCC
1 AAACTTCCAAA-ATTA-CATTTTTGACCCCC
*
48724169 AAACTTTCAAAAATTACCATTTT
1 AAAC-TTCCAAAATTA-CATTTT
48724192 ACCCCCGGAT
Statistics
Matches: 112, Mismatches: 23, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
29 15 0.13
30 60 0.54
31 37 0.33
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAATTACATTTTTGACCCCC
Found at i:48724181 original size:60 final size:59
Alignment explanation
Indices: 48724018--48724196 Score: 157
Period size: 60 Copynumber: 3.0 Consensus size: 59
48724008 GGAGGTCCCT
* * * * * * * * *
48724018 AAACTATCCAAAAATTATATTTTGACCCCCAAACTCCTCCAAAATTACATTTTTGAGCTCA
1 AAACT-TCCATAAATTACATTTTTACCCCCAAACT-TTCAAAAATTCCAATTTTGACCCCA
* * * *
48724079 AAACTTCCATAAATTACATTTTTACCCTCGAGCTTCCAAAAAATTCCAATTTTGACCCCA
1 AAACTTCCATAAATTACATTTTTACCCCCAAACTTTC-AAAAATTCCAATTTTGACCCCA
*
48724139 AAACTTTCA-AATATTACCATTTTTACCCCCAAACTTTCAAAAATTACC-ATTTT-ACCCC
1 AAACTTCCATAA-ATTA-CATTTTTACCCCCAAACTTTCAAAAATT-CCAATTTTGACCCC
48724197 CGGATATCCA
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
59 8 0.08
60 64 0.67
61 24 0.25
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (59 bp):
AAACTTCCATAAATTACATTTTTACCCCCAAACTTTCAAAAATTCCAATTTTGACCCCA
Found at i:48724183 original size:90 final size:89
Alignment explanation
Indices: 48724022--48724220 Score: 203
Period size: 90 Copynumber: 2.2 Consensus size: 89
48724012 GTCCCTAAAC
* * *
48724022 TATCCAAAAATT--ATATTTTGACCCCCAAACTCCTCCAAAATTACATTTTTGAGCTCAAAACTT
1 TATCCAAAAATTCCA-ATTTTGACCCCAAAACT-CTCCAAAATTACATTTTTGACCCCAAAACTT
* * *
48724085 CCATAAATTA-CATTTTTACCCTCGAGC
64 CCAAAAATTACCA-TTTTACCCCCG-GA
* *
48724112 T-TCCAAAAAATTCCAATTTTGACCCCAAAACT-TTCAAATATTACCATTTTT-ACCCCCAAACT
1 TATCC-AAAAATTCCAATTTTGACCCCAAAACTCTCCAAA-ATTA-CATTTTTGACCCCAAAACT
*
48724174 TTCAAAAATTACCATTTTACCCCCGGA
63 TCCAAAAATTACCATTTTACCCCCGGA
*
48724201 TATCCAAAAATTCCATTTTT
1 TATCCAAAAATTCCAATTTT
48724221 TATCCCAATT
Statistics
Matches: 92, Mismatches: 10, Indels: 15
0.79 0.09 0.13
Matches are distributed among these distances:
89 24 0.26
90 42 0.46
91 25 0.27
92 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (89 bp):
TATCCAAAAATTCCAATTTTGACCCCAAAACTCTCCAAAATTACATTTTTGACCCCAAAACTTCC
AAAAATTACCATTTTACCCCCGGA
Found at i:48724327 original size:28 final size:28
Alignment explanation
Indices: 48724292--48724354 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
48724282 TCAAAACTTT
*
48724292 TCCAAAATTACCATTTTGCCCCCGAGAA
1 TCCAAAATTAACATTTTGCCCCCGAGAA
* *
48724320 TTCAAAATTAACATTTTGCCCCCGAGTA
1 TCCAAAATTAACATTTTGCCCCCGAGAA
48724348 TCCAAAA
1 TCCAAAA
48724355 AGTCTCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.35, C:0.29, G:0.10, T:0.27
Consensus pattern (28 bp):
TCCAAAATTAACATTTTGCCCCCGAGAA
Found at i:48729299 original size:18 final size:19
Alignment explanation
Indices: 48729278--48729320 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
48729268 ACTCACCAAC
48729278 TATTTAATA-TTATTTAAT
1 TATTTAATATTTATTTAAT
* *
48729296 TA-TTATTATTTTTTTAAT
1 TATTTAATATTTATTTAAT
48729314 TATTTAA
1 TATTTAA
48729321 CTTTCGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 5 0.25
18 12 0.60
19 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTAATATTTATTTAAT
Found at i:48729950 original size:19 final size:20
Alignment explanation
Indices: 48729923--48729966 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
48729913 AAGGTAAATA
48729923 TAAAAATATTTAAT-ATTTT
1 TAAAAATATTTAATAATTTT
* *
48729942 TAAATATATTTTATAATTTT
1 TAAAAATATTTAATAATTTT
48729962 TAAAA
1 TAAAA
48729967 TTTGAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAAAATATTTAATAATTTT
Found at i:48731078 original size:96 final size:96
Alignment explanation
Indices: 48730907--48731088 Score: 217
Period size: 96 Copynumber: 1.9 Consensus size: 96
48730897 AAGGATGTTT
** * * *
48730907 GATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAAGCACAAATTTTCATAACCGAAGA
1 GATTATCTCGATTTGAAGAAAACTCGCACCTAGTAAATTAAAGCACAAAATTTCATAACCGAAGA
*
48730972 TAAGGAAATATTGCCTCGATTAAGGGTATTC
66 TAAAGAAATATTGCCTCGATTAAGGGTATTC
* * * *
48731003 GATTATTTCGTTTTGAAGAAAACTCGCACCTAGTAAATTAAGGCGCAAAATTTCGA-AACTCGAA
1 GATTATCTCGATTTGAAGAAAACTCGCACCTAGTAAATTAAAGCACAAAATTTC-ATAAC-CGAA
*
48731067 -ATAAA-AGAATATTGCCTTGATT
64 GATAAAGA-AATATTGCCTCGATT
48731089 TTAAAATTTT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
95 1 0.01
96 66 0.92
97 5 0.07
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAAGAAAACTCGCACCTAGTAAATTAAAGCACAAAATTTCATAACCGAAGA
TAAAGAAATATTGCCTCGATTAAGGGTATTC
Found at i:48731342 original size:30 final size:29
Alignment explanation
Indices: 48731300--48731400 Score: 80
Period size: 31 Copynumber: 3.4 Consensus size: 29
48731290 ACCCGAGGGT
48731300 AAAATGGTAATTTTTAGTAAAATTTGGGTTA
1 AAAATGG-AATTTTT-GTAAAATTTGGGTTA
* * *
48731331 AAAATGGAA-TTTTGGAAAGTTTGGGGGT-
1 AAAATGGAATTTTTGTAAAATTT-GGGTTA
* ** *
48731359 AAAATGATAATTTTTGGTAAAATCGGGGTCA
1 AAAATG-GAATTTTT-GTAAAATTTGGGTTA
48731390 AAAATGGAATT
1 AAAATGGAATT
48731401 CTGGGAAGTT
Statistics
Matches: 54, Mismatches: 11, Indels: 11
0.71 0.14 0.14
Matches are distributed among these distances:
28 13 0.24
29 10 0.19
30 13 0.24
31 18 0.33
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGGAATTTTTGTAAAATTTGGGTTA
Found at i:48731362 original size:28 final size:30
Alignment explanation
Indices: 48731296--48731381 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 30
48731286 GGACACCCGA
*
48731296 GGGTAAAATGGTAATTTTTAGTAAAATTTG
1 GGGTAAAATGGTAATTTTTAGGAAAATTTG
* *
48731326 GGTTAAAAATGG-AA-TTTT-GGAAAGTTTGG
1 GGGT-AAAATGGTAATTTTTAGGAAAATTT-G
*
48731355 GGGTAAAATGATAATTTTT-GGTAAAAT
1 GGGTAAAATGGTAATTTTTAGG-AAAAT
48731382 CGGGGTCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
28 13 0.29
29 10 0.22
30 11 0.24
31 11 0.24
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTAGGAAAATTTG
Found at i:48731373 original size:59 final size:57
Alignment explanation
Indices: 48731296--48731629 Score: 198
Period size: 59 Copynumber: 5.6 Consensus size: 57
48731286 GGACACCCGA
*
48731296 GGGTAAAATGGTAATTTTTAGTAAAATTTGGGTTAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAAT-GTAATTTTTAG-AAAATTTGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* ** * * * * *
48731355 GGGTAAAATGATAATTTTTGGTAAAATCGGGGTCAAAAATGGAATTCTGGGAAGTTCAA
1 GGGTAAAATG-TAATTTTTAG-AAAATTTGGGTTAAAAATGGAATTTTGGAAAGTTTAG
* * * ** * *
48731414 GGGTAAAATGGTAATTCTT-GATAAAATCGAGG-CCAAAATGGAATTTTAGAATA-CTTAG
1 GGGTAAAAT-GTAATTTTTAGA-AAATTTG-GGTTAAAAATGGAATTTTGGAA-AGTTTAG
* *
48731472 GGGTAAAGATGTAATTTTTAGAAAGTTTTAGGGTTAAAATAT--AATTTTGGAGAAATTTAG
1 GGGTAAA-ATGTAATTTTTAGAAA-ATTT-GGGTTAAAA-ATGGAATTTTGGA-AAGTTTAG
* * * * *
48731532 GGTTAGAATGTAATTTTCA-AAAAGTTTTGAGGTTAAAATAT--AATTTTTAGAAAGTTTTG
1 GGGTAAAATGTAATTTTTAGAAAA--TTTG-GGTTAAAA-ATGGAA-TTTTGGAAAGTTTAG
* *
48731591 GGGTTAAAATATAATTTTTAGAAAGTTTTGGGGTTAAAA
1 GGG-TAAAATGTAATTTTTAGAAA-ATTT-GGGTTAAAA
48731630 TACCATTTTT
Statistics
Matches: 214, Mismatches: 40, Indels: 41
0.73 0.14 0.14
Matches are distributed among these distances:
57 1 0.00
58 44 0.21
59 118 0.55
60 45 0.21
61 6 0.03
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (57 bp):
GGGTAAAATGTAATTTTTAGAAAATTTGGGTTAAAAATGGAATTTTGGAAAGTTTAG
Found at i:48731531 original size:29 final size:29
Alignment explanation
Indices: 48731468--48731650 Score: 179
Period size: 30 Copynumber: 6.1 Consensus size: 29
48731458 TTTAGAATAC
* *
48731468 TTAGGGGTAAAGATGTAATTTTTAGAAAGTT
1 TTAGGGTTAAA-ATATAATTTTTAGAAAG-T
*
48731499 TTAGGGTTAAAATATAATTTTGGAGAAA-T
1 TTAGGGTTAAAATATAATTTT-TAGAAAGT
* * * *
48731528 TTAGGGTTAGAATGTAATTTTCAAAAAGT
1 TTAGGGTTAAAATATAATTTTTAGAAAGT
*
48731557 TTTGAGGTTAAAATATAATTTTTAGAAAGTT
1 TTAG-GGTTAAAATATAATTTTTAGAAAG-T
*
48731588 TTGGGGTTAAAATATAATTTTTAGAAAGTT
1 TTAGGGTTAAAATATAATTTTTAGAAAG-T
* ** * *
48731618 TTGGGGTTAAAATACCATTTTTGGACAGT
1 TTAGGGTTAAAATATAATTTTTAGAAAGT
48731647 TTAG
1 TTAG
48731651 AGACTTCCAG
Statistics
Matches: 130, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
28 4 0.03
29 28 0.22
30 79 0.61
31 19 0.15
ACGTcount: A:0.36, C:0.02, G:0.21, T:0.40
Consensus pattern (29 bp):
TTAGGGTTAAAATATAATTTTTAGAAAGT
Found at i:48731648 original size:30 final size:30
Alignment explanation
Indices: 48731483--48731631 Score: 203
Period size: 30 Copynumber: 5.0 Consensus size: 30
48731473 GGTAAAGATG
*
48731483 TAATTTTTAGAAAGTTTTAGGGTTAAAATA
1 TAATTTTTAGAAAGTTTTGGGGTTAAAATA
* * * *
48731513 TAATTTTGGAGAAA--TTTAGGGTTAGAATG
1 TAATTTT-TAGAAAGTTTTGGGGTTAAAATA
* * *
48731542 TAATTTTCAAAAAGTTTTGAGGTTAAAATA
1 TAATTTTTAGAAAGTTTTGGGGTTAAAATA
48731572 TAATTTTTAGAAAGTTTTGGGGTTAAAATA
1 TAATTTTTAGAAAGTTTTGGGGTTAAAATA
48731602 TAATTTTTAGAAAGTTTTGGGGTTAAAATA
1 TAATTTTTAGAAAGTTTTGGGGTTAAAATA
48731632 CCATTTTTGG
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
28 4 0.04
29 20 0.19
30 75 0.72
31 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (30 bp):
TAATTTTTAGAAAGTTTTGGGGTTAAAATA
Found at i:48733513 original size:17 final size:16
Alignment explanation
Indices: 48733491--48733550 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 16
48733481 TTATATTTTA
48733491 TTAAATTTACAATAAAT
1 TTAAATTTA-AATAAAT
48733508 TTAAATTTAAATTAAATTTAT
1 TTAAATTTAAA-T-AA---AT
48733529 TTAAATTTAAAATAAAT
1 TTAAATTT-AAATAAAT
48733546 TTAAA
1 TTAAA
48733551 ATGGTTTGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.05
17 17 0.46
18 2 0.05
20 2 0.05
21 11 0.30
22 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAATTTAAATAAAT
Found at i:48733522 original size:11 final size:11
Alignment explanation
Indices: 48733503--48733550 Score: 62
Period size: 11 Copynumber: 4.4 Consensus size: 11
48733493 AAATTTACAA
48733503 TAAATTTAAATT
1 TAAA-TTAAATT
48733515 TAAATTAAATT
1 TAAATTAAATT
*
48733526 T-ATTTAAATT
1 TAAATTAAATT
*
48733536 TAAAATAAATT
1 TAAATTAAATT
48733547 TAAA
1 TAAA
48733551 ATGGTTTGGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 9 0.28
11 19 0.59
12 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
TAAATTAAATT
Found at i:48733532 original size:21 final size:21
Alignment explanation
Indices: 48733506--48733548 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
48733496 TTTACAATAA
*
48733506 ATTTAAATTTAAATTAAATTT
1 ATTTAAATTTAAAATAAATTT
48733527 ATTTAAATTTAAAATAAATTT
1 ATTTAAATTTAAAATAAATTT
48733548 A
1 A
48733549 AAATGGTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTTAAATTTAAAATAAATTT
Found at i:48739817 original size:16 final size:16
Alignment explanation
Indices: 48739798--48739841 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
48739788 ATTTAGATTC
*
48739798 TTTAAAAATTAATTTT
1 TTTAAAAATTAAATTT
48739814 TTTAAAAATATAAATTT
1 TTTAAAAAT-TAAATTT
* *
48739831 GTAAAAAATTA
1 TTTAAAAATTA
48739842 TTAAAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 13 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (16 bp):
TTTAAAAATTAAATTT
Found at i:48740832 original size:22 final size:21
Alignment explanation
Indices: 48740796--48740837 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
48740786 GATGTTTGGA
48740796 AGGAATTCAACTTGGTAGATAT
1 AGGAATTCAACTTGGT-GATAT
* *
48740818 AGGAATTCCATTTGGTGATA
1 AGGAATTCAACTTGGTGATA
48740838 ATCAACACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (21 bp):
AGGAATTCAACTTGGTGATAT
Found at i:48744537 original size:22 final size:21
Alignment explanation
Indices: 48744499--48744545 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
48744489 AATAATTTTC
*
48744499 TAAAATATAATTAAAATTACAT
1 TAAAATAAAATTAAAA-TACAT
*
48744521 TAAAATAAAA-TATAAATATAT
1 TAAAATAAAATTA-AAATACAT
48744542 TAAA
1 TAAA
48744546 GCGTAACATC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAATAAAATTAAAATACAT
Found at i:48754453 original size:13 final size:13
Alignment explanation
Indices: 48754425--48754466 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
48754415 TATTCAACTG
* *
48754425 AAATTAAACTTGA
1 AAATTAAAATTAA
48754438 AAATTAAAATTAA
1 AAATTAAAATTAA
*
48754451 AAA-TAAAAATAA
1 AAATTAAAATTAA
48754463 AAAT
1 AAAT
48754467 AAATTTGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (13 bp):
AAATTAAAATTAA
Found at i:48755200 original size:10 final size:10
Alignment explanation
Indices: 48755187--48755215 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
48755177 TAAAAAATTA
48755187 TATATAAAAG
1 TATATAAAAG
48755197 TATATAAAAG
1 TATATAAAAG
48755207 TATATAAAA
1 TATATAAAA
48755216 TTTGCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (10 bp):
TATATAAAAG
Found at i:48757522 original size:21 final size:21
Alignment explanation
Indices: 48757484--48757523 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
48757474 CTTTAGACCA
* *
48757484 CGTTGTGTATAAATCACTTAT
1 CGTTGTGGATAAACCACTTAT
*
48757505 CGTTGTGGATGAACCACTT
1 CGTTGTGGATAAACCACTT
48757524 GTAATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (21 bp):
CGTTGTGGATAAACCACTTAT
Found at i:48758722 original size:56 final size:56
Alignment explanation
Indices: 48758620--48758730 Score: 141
Period size: 56 Copynumber: 2.0 Consensus size: 56
48758610 TGCTAATTCC
* * * * *
48758620 CAAAATAGTATGCAAACACGGTCTGACCCACGCCCGTGTGCCTAGCCCATGTGTCA
1 CAAAATAGTATGCAAACACGATCTGACACACGCCCATGGGCATAGCCCATGTGTCA
* * * *
48758676 CAAAATAGTATGCACACACGATCTGGCACACGCTCATGGGCATAGCCCGTGTGTC
1 CAAAATAGTATGCAAACACGATCTGACACACGCCCATGGGCATAGCCCATGTGTC
48758731 TCCTATAGCT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.20
Consensus pattern (56 bp):
CAAAATAGTATGCAAACACGATCTGACACACGCCCATGGGCATAGCCCATGTGTCA
Found at i:48762641 original size:23 final size:24
Alignment explanation
Indices: 48762615--48762659 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
48762605 ATCTCATTCC
48762615 CTCTCACC-TCCTTATT-TCTCCTT
1 CTCTCACCTTCCTT-TTCTCTCCTT
48762638 CTCTCACCTTCCTTTTCTCTCC
1 CTCTCACCTTCCTTTTCTCTCC
48762660 ACTTAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.07, C:0.47, G:0.00, T:0.47
Consensus pattern (24 bp):
CTCTCACCTTCCTTTTCTCTCCTT
Found at i:48763440 original size:5 final size:6
Alignment explanation
Indices: 48763425--48763453 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
48763415 CATCAGAAAC
48763425 AAAAAT AAAAAT -AAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
48763454 GCAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:48763442 original size:11 final size:11
Alignment explanation
Indices: 48763426--48763451 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48763416 ATCAGAAACA
48763426 AAAATAAAAAT
1 AAAATAAAAAT
48763437 AAAATAAAAAT
1 AAAATAAAAAT
48763448 AAAA
1 AAAA
48763452 ATGCAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:48770258 original size:22 final size:22
Alignment explanation
Indices: 48770232--48770282 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
48770222 TCAATAACGG
48770232 CCACATAATTGCACATAAACTA
1 CCACATAATTGCACATAAACTA
* * * *
48770254 TCACATAATTGTAGATGAACTA
1 CCACATAATTGCACATAAACTA
48770276 CCACATA
1 CCACATA
48770283 TCTTCCTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (22 bp):
CCACATAATTGCACATAAACTA
Found at i:48771790 original size:24 final size:24
Alignment explanation
Indices: 48771763--48771816 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
48771753 AGGGGTTCGA
*
48771763 AATGCACAATTCGTAAGAACTCAC
1 AATGCACAATTCGCAAGAACTCAC
* **
48771787 AATGCACAGTTCGCAAGAGTTCAC
1 AATGCACAATTCGCAAGAACTCAC
48771811 AATGCA
1 AATGCA
48771817 TAGTTCACAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (24 bp):
AATGCACAATTCGCAAGAACTCAC
Found at i:48771821 original size:24 final size:24
Alignment explanation
Indices: 48771783--48771829 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
48771773 TCGTAAGAAC
*
48771783 TCACAATGCACAGTTCGCAAGAGT
1 TCACAATGCACAGTTCACAAGAGT
*
48771807 TCACAATGCATAGTTCACAAGAG
1 TCACAATGCACAGTTCACAAGAG
48771830 CTTGTGTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (24 bp):
TCACAATGCACAGTTCACAAGAGT
Found at i:48772679 original size:19 final size:19
Alignment explanation
Indices: 48772652--48772690 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
48772642 TAGGAGTTGG
48772652 CATAAATAA-TCTGCATGTA
1 CATAAATAATTCT-CATGTA
*
48772671 CATATATAATTCTCATGTA
1 CATAAATAATTCTCATGTA
48772690 C
1 C
48772691 CTAGGGTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (19 bp):
CATAAATAATTCTCATGTA
Found at i:48774202 original size:14 final size:13
Alignment explanation
Indices: 48774176--48774209 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
48774166 TTATTTTTTT
*
48774176 ATAATTATGATGG
1 ATAATTAAGATGG
48774189 ATAATTAAGTATGG
1 ATAATTAAG-ATGG
48774203 ATAATTA
1 ATAATTA
48774210 TTTGACGTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.18, T:0.38
Consensus pattern (13 bp):
ATAATTAAGATGG
Found at i:48774500 original size:23 final size:23
Alignment explanation
Indices: 48774469--48774544 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 23
48774459 ATAACAATTC
*
48774469 ATAAGTTAAAAGTTGTGATTTAA
1 ATAACTTAAAAGTTGTGATTTAA
**** * *
48774492 ATAACTT-AAA-TAACAAATT-C
1 ATAACTTAAAAGTTGTGATTTAA
*
48774512 ATAAGTTAAAAGTTGTGATTTAA
1 ATAACTTAAAAGTTGTGATTTAA
48774535 ATAACTTAAA
1 ATAACTTAAA
48774545 TAACAGATTG
Statistics
Matches: 35, Mismatches: 15, Indels: 6
0.62 0.27 0.11
Matches are distributed among these distances:
20 6 0.17
21 7 0.20
22 7 0.20
23 15 0.43
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.36
Consensus pattern (23 bp):
ATAACTTAAAAGTTGTGATTTAA
Found at i:48774519 original size:43 final size:43
Alignment explanation
Indices: 48774459--48774549 Score: 175
Period size: 43 Copynumber: 2.1 Consensus size: 43
48774449 TCTCATGCAT
48774459 ATAAC-AATTCATAAGTTAAAAGTTGTGATTTAAATAACTTAA
1 ATAACAAATTCATAAGTTAAAAGTTGTGATTTAAATAACTTAA
48774501 ATAACAAATTCATAAGTTAAAAGTTGTGATTTAAATAACTTAA
1 ATAACAAATTCATAAGTTAAAAGTTGTGATTTAAATAACTTAA
48774544 ATAACA
1 ATAACA
48774550 GATTGGTGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
42 5 0.10
43 43 0.90
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (43 bp):
ATAACAAATTCATAAGTTAAAAGTTGTGATTTAAATAACTTAA
Found at i:48776505 original size:12 final size:12
Alignment explanation
Indices: 48776488--48776522 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
48776478 AACCCACTCT
48776488 TTTAAATTTAAG
1 TTTAAATTTAAG
**
48776500 TTTAAATTTATT
1 TTTAAATTTAAG
48776512 TTTAAATTTAA
1 TTTAAATTTAA
48776523 AATTATTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TTTAAATTTAAG
Found at i:48776515 original size:18 final size:18
Alignment explanation
Indices: 48776494--48776540 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
48776484 CTCTTTTAAA
* *
48776494 TTTAAGTTTAAATTTATT
1 TTTAAATTTAAAATTATT
48776512 TTTAAATTTAAAATTA-T
1 TTTAAATTTAAAATTATT
*
48776529 TCTAAATTTAAA
1 TTTAAATTTAAA
48776541 TAAATAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTAAAATTATT
Found at i:48776536 original size:17 final size:18
Alignment explanation
Indices: 48776500--48776540 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
48776490 TAAATTTAAG
* *
48776500 TTTAAATTTATTTTTAAA
1 TTTAAAATTATTTCTAAA
48776518 TTTAAAATTA-TTCTAAA
1 TTTAAAATTATTTCTAAA
48776535 TTTAAA
1 TTTAAA
48776541 TAAATAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAAATTATTTCTAAA
Found at i:48776655 original size:24 final size:23
Alignment explanation
Indices: 48776625--48776671 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 23
48776615 ATGACCCAAA
48776625 ATACCCCAAGCCCAAATACTAACC
1 ATACCCCAAGCCCAAATAC-AACC
48776649 ATACCCCAAGCCCAAATACAACC
1 ATACCCCAAGCCCAAATACAACC
48776672 CAAACTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.43, C:0.43, G:0.04, T:0.11
Consensus pattern (23 bp):
ATACCCCAAGCCCAAATACAACC
Found at i:48777668 original size:23 final size:23
Alignment explanation
Indices: 48777641--48777693 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
48777631 CAAGTTATTT
48777641 AAATTAATCAAAATTAAAAT-TAA
1 AAATTAAT-AAAATTAAAATATAA
* *
48777664 AAATTAATTAAATTAAAGTATAA
1 AAATTAATAAAATTAAAATATAA
48777687 AAATTAA
1 AAATTAA
48777694 ATATGCAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (23 bp):
AAATTAATAAAATTAAAATATAA
Found at i:48778386 original size:17 final size:17
Alignment explanation
Indices: 48778343--48778380 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
48778333 TTAAATAGAT
*
48778343 TTTAAATTTATTTTAAA
1 TTTAAATTTACTTTAAA
48778360 TTTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
48778377 TTTA
1 TTTA
48778381 GGTTTAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:48780398 original size:59 final size:59
Alignment explanation
Indices: 48780265--48780800 Score: 772
Period size: 59 Copynumber: 9.1 Consensus size: 59
48780255 CCTAGACTGT
* *
48780265 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCA-TTTTAACCTCGGTTTCA
1 CCAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
48780323 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTGCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
48780382 CCAAAAATTACCATTTTACCCCTTGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCC-TGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
48780442 CCAAAAATTACCATTTAACCCCTAAACATTCC-AAATTCTATTTTTAACCCCAATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
48780500 TCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCTATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * **
48780559 CTAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTTTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
48780618 CCAAAAATTACCATTTTACCACTAAACATTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * * *
48780677 TCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATCTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
48780736 CCAAAAATTACCATTTTACCCCTTGAACTTTCCAAAATTCCATTTTTAGCCCCGATTTCA
1 CCAAAAATTACCATTTTACCCC-TGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
48780796 CCAAA
1 CCAAA
48780801 GTTTCCAAAA
Statistics
Matches: 427, Mismatches: 46, Indels: 8
0.89 0.10 0.02
Matches are distributed among these distances:
58 86 0.20
59 250 0.59
60 91 0.21
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:48780819 original size:38 final size:38
Alignment explanation
Indices: 48780764--48780838 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
48780754 CCCCTTGAAC
* *
48780764 TTTCCAAAATTCCATTTTTAGCCCCGATTTCACCAAAG
1 TTTCCAAAATTCCATTTTTAACCCCGATTTAACCAAAG
*
48780802 TTTCCAAAATTCTATTTTTAACCCCGATTTAACCAAA
1 TTTCCAAAATTCCATTTTTAACCCCGATTTAACCAAA
48780839 AATTAGCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (38 bp):
TTTCCAAAATTCCATTTTTAACCCCGATTTAACCAAAG
Found at i:48790789 original size:42 final size:42
Alignment explanation
Indices: 48790742--48790825 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 42
48790732 AAAATGAGTT
*
48790742 GTTTATGAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTA
1 GTTTATGAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTA
*
48790784 GTTTATGAGTGTTTTTGAAGAATGAAATTATATTTGGGTTTA
1 GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
48790826 AAAATATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 3 0.08
42 36 0.92
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.48
Consensus pattern (42 bp):
GTTTATGAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
Found at i:48792779 original size:3 final size:3
Alignment explanation
Indices: 48792766--48792810 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
48792756 TTATGATATC
*
48792766 GAA GCA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
48792811 AGGGATGACC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:48795345 original size:48 final size:49
Alignment explanation
Indices: 48795289--48795408 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 49
48795279 TGAACCCCAG
* *
48795289 CTTCCTGATGAGATACTGAGAAGCAGG-TCGAAGCAA-TAAAGCGGTTAC
1 CTTCCTGATGAGATACTGAGAAG-AGGATCAAAGCAAGTAAAGCGGTCAC
* * * * * *
48795337 CTTCCTGATGAGACACAGAGAAGTGGATCAAAGCAAGTGATGCGGTCAT
1 CTTCCTGATGAGATACTGAGAAGAGGATCAAAGCAAGTAAAGCGGTCAC
*
48795386 CTTCTTGATGAGATACTGAGAAG
1 CTTCCTGATGAGATACTGAGAAG
48795409 TAGACCAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
47 2 0.03
48 29 0.49
49 28 0.47
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.23
Consensus pattern (49 bp):
CTTCCTGATGAGATACTGAGAAGAGGATCAAAGCAAGTAAAGCGGTCAC
Found at i:48795461 original size:172 final size:172
Alignment explanation
Indices: 48795165--48795705 Score: 868
Period size: 172 Copynumber: 3.1 Consensus size: 172
48795155 CCAAATCCGT
* * * *
48795165 CTTCCTAATGAGACACA-AGGAAATGGATTAAAACAAGTGATGCAATCATCTTCCTGATGAGATA
1 CTTCCTGATGAGACACAGA-GAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATA
*
48795229 CTGAGAAGTAGACCAAATCAAATCAACCAGACTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCC
65 CTGAGAAGTAGACCAAATCAAATCAACCAGGCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCC
48795294 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTAC
130 TGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTAC
* * *
48795337 CTTCCTGATGAGACACAGAGAAGTGGATCAAAGCAAGTGATGCGGTCATCTTCTTGATGAGATAC
1 CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATAC
* * *
48795402 TGAGAAGTAGACCAAATCAAATCAACTAGGCTCAAAGTGAGCAAATCTTCGAGCCCCAGCTTCCT
66 TGAGAAGTAGACCAAATCAAATCAACCAGGCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCCT
* *
48795467 GATGAGATACTGAGAAGCAAGTCGAAGCAATAAAGCGATTAC
131 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTAC
* * * * *
48795509 CTTCCTGATGAGATACAGAGAACTAGATCAAAACAAGTGATGCAGTTATCTTCCTAATGAGATAC
1 CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATAC
*
48795574 TGAGAAGTAGACCAACTCAAATCAACCAGGCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCCT
66 TGAGAAGTAGACCAAATCAAATCAACCAGGCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCCT
* *
48795639 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGTGGTCAC
131 GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTAC
*
48795681 CTTCCTGATGAGATACAGAGAAGTG
1 CTTCCTGATGAGACACAGAGAAGTG
48795706 AACCAGATCT
Statistics
Matches: 337, Mismatches: 31, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
172 336 1.00
173 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (172 bp):
CTTCCTGATGAGACACAGAGAAGTGGATCAAAACAAGTGATGCAGTCATCTTCCTGATGAGATAC
TGAGAAGTAGACCAAATCAAATCAACCAGGCTCAAAGTGAGCAAATCTTTGAACCCCAGCTTCCT
GATGAGATACTGAGAAGCAGGTCGAAGCAATAAAGCGGTTAC
Found at i:48796303 original size:17 final size:17
Alignment explanation
Indices: 48796281--48796359 Score: 86
Period size: 17 Copynumber: 4.6 Consensus size: 17
48796271 CCACTCTTTC
* *
48796281 AAATTTAAACTTGTTTT
1 AAATTTAAATTTATTTT
*
48796298 AAATTTAAATTTAATTT
1 AAATTTAAATTTATTTT
*
48796315 AAGTTTAAATTTATTTTT
1 AAATTTAAATTTA-TTTT
* * *
48796333 AAATTTAAAATTACTCT
1 AAATTTAAATTTATTTT
48796350 AAATTTAAAT
1 AAATTTAAAT
48796360 AAATAAAAGT
Statistics
Matches: 51, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
17 37 0.73
18 14 0.27
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:48796306 original size:6 final size:6
Alignment explanation
Indices: 48796295--48796359 Score: 62
Period size: 6 Copynumber: 11.2 Consensus size: 6
48796285 TTAAACTTGT
* **
48796295 TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
48796342 ATT-AC TCTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA T
48796360 AAATAAAAGT
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
5 7 0.16
6 38 0.84
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:48820106 original size:24 final size:24
Alignment explanation
Indices: 48820078--48820123 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
48820068 GGTAGGAAAC
* *
48820078 TGCATCTGATTTTGTTTCTGAACT
1 TGCATCTGATTATGTATCTGAACT
48820102 TGCATCTGATTATGTATCTGAA
1 TGCATCTGATTATGTATCTGAA
48820124 ATGTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (24 bp):
TGCATCTGATTATGTATCTGAACT
Found at i:48823148 original size:146 final size:145
Alignment explanation
Indices: 48822877--48823188 Score: 364
Period size: 146 Copynumber: 2.1 Consensus size: 145
48822867 CTTTGGATAC
*
48822877 CCGAGGGTAAAATGGTAATTTTTGACTTTCGAGGACATAATGGTAATTCTGGAAAATTTTAGGGT
1 CCGAGGGTAAAATGGTAATTTTGGACTTTCGAGGACATAATGGTAATTCTGGAAAATTTTAGGGT
* * * * * * ** *
48822942 TAAACACGATATCTTGGATACTTAAGGGTGAAATGGTAATTTTCGAAAGAATCGAGATC-AAAAT
66 TAAAAACGATATCTTAGACAATCAAGGGTAAAACAGTAATTTTAGAAAGAATCGAGATCAAAAAT
**
48823006 GAGACTTTTTAGATGT
131 GAGA-TTTTTAGACAT
** *
48823022 TTGAGGGTAAAATGGTAATTTTGGACTTTCAGAGG-CA-ATATGGTAATTTTGGGAAAATTTTAG
1 CCGAGGGTAAAATGGTAATTTTGGACTTTC-GAGGACATA-ATGGTAATTCT-GGAAAATTTTAG
* * *
48823085 GGTTAAAAATGATATTTTAGACAATCGAGGGTAAAACAGTAATTTTTAGAAA-AATC-AGAATCA
63 GGTTAAAAACGATATCTTAGACAATCAAGGGTAAAACAGTAA-TTTTAGAAAGAATCGAG-ATCA
*
48823148 AAAATGAGATTTTTGGACAT
126 AAAATGAGATTTTTAGACAT
48823168 CCGAGGGTAAAATGGTAATTT
1 CCGAGGGTAAAATGGTAATTT
48823189 CAAGAGTTTC
Statistics
Matches: 140, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
144 1 0.01
145 41 0.29
146 81 0.58
147 17 0.12
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.32
Consensus pattern (145 bp):
CCGAGGGTAAAATGGTAATTTTGGACTTTCGAGGACATAATGGTAATTCTGGAAAATTTTAGGGT
TAAAAACGATATCTTAGACAATCAAGGGTAAAACAGTAATTTTAGAAAGAATCGAGATCAAAAAT
GAGATTTTTAGACAT
Found at i:48823286 original size:59 final size:59
Alignment explanation
Indices: 48823205--48823404 Score: 240
Period size: 59 Copynumber: 3.4 Consensus size: 59
48823195 TTTCAAGGTC
* * * * * *
48823205 AAAAATGT-ATTTTGGGAGGTTTTGAGGTTAAAAATGGAGTTTTTGAAAGTTCGAGGGT
1 AAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGT
* * * ** *
48823263 AAAAATGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGAAATTTTGGGAGTTCGGGGGC
1 AAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGT
* *
48823322 GAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTGGAGAAGTTCGGGGGT
1 AAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGA-AAGTTCGGGGGT
*
48823382 CAAAATATAATTTTTGGACAGTT
1 AAAAATATAATTTTTGGA-AGTT
48823405 AAGGGACCTT
Statistics
Matches: 120, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
58 8 0.07
59 81 0.68
60 27 0.22
61 4 0.03
ACGTcount: A:0.33, C:0.04, G:0.29, T:0.34
Consensus pattern (59 bp):
AAAAATATAATTTTTGGAAGTTTTGAGGTCAAAAATGGAATTTTTGAAAGTTCGGGGGT
Found at i:48823299 original size:30 final size:30
Alignment explanation
Indices: 48823201--48823404 Score: 157
Period size: 30 Copynumber: 6.9 Consensus size: 30
48823191 AGAGTTTCAA
* * *
48823201 GGTCAAAAATGT-ATTTTGGGAGGTTTTGA
1 GGTCAAAAATGTAATTTTTGGAAGTTTTGG
* * * * *
48823230 GGTTAAAAATGGAGTTTTTGAAAG-TTCGAG
1 GGTCAAAAATGTAATTTTTGGAAGTTTTG-G
48823260 GGT-AAAAATGTAATTTTTGGAAGTTTTGG
1 GGTCAAAAATGTAATTTTTGGAAGTTTTGG
* * * *
48823289 GGTCAAAAATGGAAATTTTGGGAG-TTCGG
1 GGTCAAAAATGTAATTTTTGGAAGTTTTGG
* * * *
48823318 GGGCGAAAATATAATTTTTGGAAGTTTTGA
1 GGTCAAAAATGTAATTTTTGGAAGTTTTGG
* * **
48823348 GGTCAAAAATGGAATTTTGGAGAAGTTCGGG
1 GGTCAAAAATGTAATTTTTG-GAAGTTTTGG
*
48823379 GGTC-AAAATATAATTTTTGGACAGTT
1 GGTCAAAAATGTAATTTTTGGA-AGTT
48823405 AAGGGACCTT
Statistics
Matches: 133, Mismatches: 35, Indels: 13
0.73 0.19 0.07
Matches are distributed among these distances:
29 58 0.44
30 64 0.48
31 11 0.08
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.34
Consensus pattern (30 bp):
GGTCAAAAATGTAATTTTTGGAAGTTTTGG
Found at i:48824555 original size:3 final size:3
Alignment explanation
Indices: 48824529--48824581 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
48824519 TTTTTTAAAT
* * * *
48824529 TTA TTAA TTA ATA TTA TTA GTA TTA TTAA TTA GTA TTA TTA TTA TTG
1 TTA TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
48824576 TTA TTA
1 TTA TTA
48824582 AATATTATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
3 34 0.85
4 6 0.15
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:48824555 original size:22 final size:22
Alignment explanation
Indices: 48824529--48824589 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
48824519 TTTTTTAAAT
48824529 TTATTAATTAATATTATTAGTA
1 TTATTAATTAATATTATTAGTA
* *
48824551 TTATTAATTAGTATTATTATTA
1 TTATTAATTAATATTATTAGTA
*
48824573 TTGTT-ATTAAATATTAT
1 TTATTAATT-AATATTAT
48824590 AATGAACTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 3 0.09
22 31 0.91
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (22 bp):
TTATTAATTAATATTATTAGTA
Found at i:48825325 original size:17 final size:17
Alignment explanation
Indices: 48825300--48825386 Score: 88
Period size: 17 Copynumber: 5.1 Consensus size: 17
48825290 TATTTAAATC
*
48825300 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* *
48825317 ATTCAAATTTAACATAA
1 ATTTAAATTTAAAATAA
*
48825334 ATTTAAATTCT-AAATGA
1 ATTTAAATT-TAAAATAA
48825351 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
48825368 A-CTAAGATTTAAAAATAA
1 ATTTAA-ATTT-AAAATAA
48825386 A
1 A
48825387 AAGTTGGGTT
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
16 4 0.07
17 45 0.78
18 9 0.16
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:48825727 original size:39 final size:39
Alignment explanation
Indices: 48825684--48825794 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
48825674 TGCCCCAAGT
*
48825684 TCGGGGTAAGAGATTGATTGATGGTGATCTG-CTCCGGGC
1 TCGGGGTAAGAGATTGATTGATGGTGATCTGCCT-CAGGC
* ** * * *
48825723 TCGGGGTAAAAGATCAAATGGCT-GTAATCTGCCTCAGGC
1 TCGGGGTAAGAGAT-TGATTGATGGTGATCTGCCTCAGGC
* * *
48825762 TCGGGGTAAGAGATTGGTTGGTGATGATCTGCC
1 TCGGGGTAAGAGATTGATTGATGGTGATCTGCC
48825795 CCAAGTTCGA
Statistics
Matches: 54, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
38 3 0.06
39 45 0.83
40 6 0.11
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (39 bp):
TCGGGGTAAGAGATTGATTGATGGTGATCTGCCTCAGGC
Found at i:48826012 original size:30 final size:30
Alignment explanation
Indices: 48825976--48826035 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
48825966 ACTTTACTGC
**
48825976 AACTTCAAGAGGATAGGAAATGATGTTTGA
1 AACTTCAAGAAAATAGGAAATGATGTTTGA
*
48826006 AACTTCAAGAAAATAGGAATTGATGTTTGA
1 AACTTCAAGAAAATAGGAAATGATGTTTGA
48826036 TGCTTCGTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (30 bp):
AACTTCAAGAAAATAGGAAATGATGTTTGA
Found at i:48826216 original size:92 final size:92
Alignment explanation
Indices: 48826006--48828830 Score: 4807
Period size: 92 Copynumber: 30.7 Consensus size: 92
48825996 TGATGTTTGA
** * *
48826006 AACTTCAAGAAAATAGGAATTGATGTTTGATGCTTCGTCTTGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48826071 TAAAAGACTTGCTATCCAACTTTATTAC
66 T-AAAGACTTGCTATCCAACTTTACTAC
*
48826099 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48826164 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48826191 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCAAAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48826256 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* * * *
48826283 AACTTCAAGAGGATAGGAATTGATGTTTGATTCTTCATCTTGCTCTTACTATAACTTCAAAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48826348 TAAAAACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* * *
48826375 AACTTCAAGAGGATAGGAATTGATGTTTAATGCTTCATCTTGCTCTTACTACAACTTCAAAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48826440 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* * *
48826467 AACTTCAAAAGGATAGGAATTAATGTTTAATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48826532 TAAAGA-TCTGCTATCCAACTTTACTAC
66 TAAAGACT-TGCTATCCAACTTTACTAC
* * *
48826559 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTATTATAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48826624 TAAAAACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48826651 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTGCTCTTACTACAACTTCA-AAAGG
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGA-G
48826715 ATAAAGACTTGCTATCCAACTTTACTAC
65 ATAAAGACTTGCTATCCAACTTTACTAC
* *
48826743 AACTTCAAGAGGATAGGAATTAATGTTTAATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
* * *
48826808 TAAAGGCCTGCTATCCAACTTTACTGC
66 TAAAGACTTGCTATCCAACTTTACTAC
*
48826835 AACTTCAAGAGGATAAGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48826900 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48826927 AACTTCAAGAGAATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGG
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48826992 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48827019 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48827084 TAAAAGACTTACTATCCAACTTTACTAC
66 T-AAAGACTTGCTATCCAACTTTACTAC
* *
48827112 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48827177 TAAAGACTTGCTATCCAACTTTAATAC
66 TAAAGACTTGCTATCCAACTTTACTAC
48827204 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
* *
48827269 TAAA-ATTTGGTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48827295 AACTTTAAGATGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
* * *
48827360 TAAAGGCCTGCTATCCAACTTTACTGC
66 TAAAGACTTGCTATCCAACTTTACTAC
*
48827387 AACTTCAAGAGGATAAGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48827452 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48827479 AACTTCAAGAGAATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGG
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48827544 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48827571 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48827636 TAAAAGACTTACTATCCAACTTTACTAC
66 T-AAAGACTTGCTATCCAACTTTACTAC
* *
48827664 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48827729 TAAAGACTTGCTATCCAACTTTAATAC
66 TAAAGACTTGCTATCCAACTTTACTAC
48827756 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
* *
48827821 TAAA-ATTTGGTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48827847 AACTTTAAGATGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
* * *
48827912 TAAAGGCCTGCTATCCAACTTTACTGC
66 TAAAGACTTGCTATCCAACTTTACTAC
*
48827939 AACTTCAAGAGGATAAGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48828004 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48828031 AACTTCAAGAGAATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGG
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48828096 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48828123 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48828188 TAAAAGACTTACTATCCAACTTTACTAC
66 T-AAAGACTTGCTATCCAACTTTACTAC
* *
48828216 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48828281 TAAAGACTTGCTATCCAACTTTAATAC
66 TAAAGACTTGCTATCCAACTTTACTAC
48828308 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48828373 TAAA-ATTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48828399 AACTTTAAGATGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48828464 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
*
48828491 AACTTCAAGAGGATAGGAATTGATGTTTGACGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
*
48828556 TAAAGACTTGCTATCCAACTTTACCAC
66 TAAAGACTTGCTATCCAACTTTACTAC
* *
48828583 AACTTCAAGAGGATAGAAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAAAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48828648 TAAAAGACTTGCTATCCAACTTTACTAC
66 T-AAAGACTTGCTATCCAACTTTACTAC
* *
48828676 AACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAACTCTTACTACAACTTCAGAGAGA
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
48828741 TAAAGACTTGCTATCCAACTTTACTAC
66 TAAAGACTTGCTATCCAACTTTACTAC
**
48828768 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTTCTCTTACTACAACTTCA-AGAG
1 AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAG
48828831 GATAGGAAAT
Statistics
Matches: 2589, Mismatches: 132, Indels: 24
0.94 0.05 0.01
Matches are distributed among these distances:
91 266 0.10
92 1899 0.73
93 424 0.16
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (92 bp):
AACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTCAGAGAGA
TAAAGACTTGCTATCCAACTTTACTAC
Found at i:48828673 original size:41 final size:41
Alignment explanation
Indices: 48828628--48828774 Score: 136
Period size: 41 Copynumber: 3.3 Consensus size: 41
48828618 CATCTAGCTC
48828628 TTACTACAACTTCAGAAAGATAAAAGACTTGCTATCCAACT
1 TTACTACAACTTCAGAAAGATAAAAGACTTGCTATCCAACT
* * *
48828669 TTACTACAACTTCA-AGAGGATAGGAAATGATGTTTGATGCTTCATCTAACT
1 TTACTACAACTTCAGA-AAGATA--AAA-GA---CT--TGC-T-ATCCAACT
*
48828720 CTTACTACAACTTCAGAGAGAT-AAAGACTTGCTATCCAACT
1 -TTACTACAACTTCAGAAAGATAAAAGACTTGCTATCCAACT
48828761 TTACTACAACTTCA
1 TTACTACAACTTCA
48828775 AGAGGATAGG
Statistics
Matches: 86, Mismatches: 7, Indels: 27
0.72 0.06 0.22
Matches are distributed among these distances:
40 15 0.17
41 26 0.30
42 1 0.01
43 6 0.07
44 2 0.02
45 1 0.01
47 1 0.01
48 2 0.02
49 6 0.07
50 1 0.01
51 7 0.08
52 17 0.20
53 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (41 bp):
TTACTACAACTTCAGAAAGATAAAAGACTTGCTATCCAACT
Found at i:48828844 original size:52 final size:52
Alignment explanation
Indices: 48828761--48828975 Score: 222
Period size: 52 Copynumber: 4.3 Consensus size: 52
48828751 CTATCCAACT
* **
48828761 TTACTACAACTTCAAGAGGATAGGAATTGATGTTTGATGCTTCATCTTTCTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTC
48828813 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTC
* * *
48828865 TTACTACAACTTCAA-AGAGAT---AAA-GA---CT--TGC-T-ATCCAACT-
1 TTACTACAACTTCAAGAG-GATAGGAAATGATGTTTGATGCTTCATCTAGCTC
* * * *
48828905 TTACTACAACTTTAAGAGGATAGGAATTGATGTTTGATGCTTTATCTTGCTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTC
*
48828957 TTACTACAATTTCAGAGAG
1 TTACTACAACTTCA-AGAG
48828976 ATAAAGACTT
Statistics
Matches: 134, Mismatches: 14, Indels: 29
0.76 0.08 0.16
Matches are distributed among these distances:
40 17 0.13
41 8 0.06
42 1 0.01
43 5 0.04
44 2 0.01
45 1 0.01
47 1 0.01
48 2 0.01
49 6 0.04
50 1 0.01
51 7 0.05
52 79 0.59
53 4 0.03
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTC
Found at i:48828929 original size:144 final size:144
Alignment explanation
Indices: 48828669--48828975 Score: 551
Period size: 144 Copynumber: 2.1 Consensus size: 144
48828659 CTATCCAACT
48828669 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAACTCTTACTACAACTTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAACTCTTACTACAACTTC
*
48828734 AGAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAT
66 AAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAT
*
48828799 GCTTCATCTTTCTC
131 GCTTCATCTTGCTC
*
48828813 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAACTCTTACTACAACTTC
*
48828878 AAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTTAAGAGGATAGGAATTGATGTTTGAT
66 AAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAT
*
48828943 GCTTTATCTTGCTC
131 GCTTCATCTTGCTC
*
48828957 TTACTACAATTTCAGAGAG
1 TTACTACAACTTCA-AGAG
48828976 ATAAAGACTT
Statistics
Matches: 156, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
144 152 0.97
145 4 0.03
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (144 bp):
TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAACTCTTACTACAACTTC
AAAGAGATAAAGACTTGCTATCCAACTTTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAT
GCTTCATCTTGCTC
Found at i:48828976 original size:92 final size:92
Alignment explanation
Indices: 48828813--48828985 Score: 292
Period size: 92 Copynumber: 1.9 Consensus size: 92
48828803 CATCTTTCTC
48828813 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTC
48828878 AAAGAGATAAAGACTTGCTATCCAACT
66 AAAGAGATAAAGACTTGCTATCCAACT
* * * * *
48828905 TTACTACAACTTTAAGAGGATAGGAATTGATGTTTGATGCTTTATCTTGCTCTTACTACAATTTC
1 TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTC
*
48828970 AGAGAGATAAAGACTT
66 AAAGAGATAAAGACTT
48828986 TTGCCTTTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 75 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (92 bp):
TTACTACAACTTCAAGAGGATAGGAAATGATGTTTGATGCTTCATCTAGCTCTTACTACAACTTC
AAAGAGATAAAGACTTGCTATCCAACT
Found at i:48830343 original size:27 final size:27
Alignment explanation
Indices: 48830313--48830364 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
48830303 TCGACCTCTC
48830313 CTTTACTTTTTTTT-TTCTTTTTTTCCA
1 CTTTACTTTTTTTTCTT-TTTTTTTCCA
*
48830340 CTTTTCTTTTTTTTCTTTTTTTTTC
1 CTTTACTTTTTTTTCTTTTTTTTTC
48830365 TTTTTGATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 21 0.91
28 2 0.09
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (27 bp):
CTTTACTTTTTTTTCTTTTTTTTTCCA
Found at i:48835954 original size:28 final size:28
Alignment explanation
Indices: 48835923--48836116 Score: 85
Period size: 28 Copynumber: 6.8 Consensus size: 28
48835913 TTTAGATACC
48835923 CGAGGGCAAAATGGTAATTTTAGACTTT
1 CGAGGGCAAAATGGTAATTTTAGACTTT
** * *
48835951 CGAGGATAAAATGGTAATTTTGGAAAATTT
1 CGAGGGCAAAATGGTAATTTT--AGACTTT
* * * *
48835981 TG-GGGTTAAAAATGAT-ATTTTAGACACTT
1 CGAGGG--CAAAATGGTAATTTTAGAC-TTT
* * * ***
48836010 -AAGGGTAAAATGGTAATTTTTGAAAGAAT
1 CGAGGGCAAAATGGTAA-TTTT-AGACTTT
* *
48836039 CG-GGATCAAAATGAG-ACTTTTTAGA-TGTT
1 CGAGG-GCAAAATG-GTAAT-TTTAGACT-TT
*
48836068 CGAGGGCAAAATGGTATTTTTAGACTTT
1 CGAGGGCAAAATGGTAATTTTAGACTTT
*
48836096 TGAGGGCAAAATGGTAATTTT
1 CGAGGGCAAAATGGTAATTTT
48836117 GGGAAAATTT
Statistics
Matches: 120, Mismatches: 29, Indels: 34
0.66 0.16 0.19
Matches are distributed among these distances:
27 7 0.06
28 50 0.42
29 30 0.25
30 25 0.21
31 8 0.07
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.34
Consensus pattern (28 bp):
CGAGGGCAAAATGGTAATTTTAGACTTT
Found at i:48836078 original size:29 final size:28
Alignment explanation
Indices: 48836056--48836116 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
48836046 AAAATGAGAC
48836056 TTTTTAGA-TGTTCGAGGGCAAAATGGTA
1 TTTTTAGACT-TTCGAGGGCAAAATGGTA
*
48836084 TTTTTAGACTTTTGAGGGCAAAATGGTA
1 TTTTTAGACTTTCGAGGGCAAAATGGTA
*
48836112 ATTTT
1 TTTTT
48836117 GGGAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.41
Consensus pattern (28 bp):
TTTTTAGACTTTCGAGGGCAAAATGGTA
Found at i:48836159 original size:58 final size:59
Alignment explanation
Indices: 48836097--48836237 Score: 142
Period size: 58 Copynumber: 2.4 Consensus size: 59
48836087 TTAGACTTTT
* * * * * *
48836097 GAGGGCAAAATGGTAATTTTGGGAAAATTTAGGGTTAAAAATGACA-TTTTAGATAAT-C
1 GAGGGTAAAATGGTAATTTTGAGAAAAATCAGGATCAAAAATGACATTTTTAGA-AATCC
* * * * * *
48836155 GAGGGTAAAACGATAATTTTTAGAAAAATCAGGATCAAAAATGAGATTTTTGGACATCC
1 GAGGGTAAAATGGTAATTTTGAGAAAAATCAGGATCAAAAATGACATTTTTAGAAATCC
*
48836214 GAGGGTAAAATGGTAATTTCGAGA
1 GAGGGTAAAATGGTAATTTTGAGA
48836238 GTTTCGGGGC
Statistics
Matches: 65, Mismatches: 16, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
58 38 0.58
59 27 0.42
ACGTcount: A:0.40, C:0.07, G:0.24, T:0.28
Consensus pattern (59 bp):
GAGGGTAAAATGGTAATTTTGAGAAAAATCAGGATCAAAAATGACATTTTTAGAAATCC
Found at i:48836190 original size:145 final size:145
Alignment explanation
Indices: 48835913--48836267 Score: 412
Period size: 145 Copynumber: 2.4 Consensus size: 145
48835903 AAATGGGACC
* * *
48835913 TTTAGATACCCGAGGGCAAAATGGTAATTTTAGACTTTCGAGGATAAAATGGTAATTTTGGAAAA
1 TTTAGACATCCGAGGGCAAAATGGTAATTTTAGACTTTCGAGGACAAAATGGTAATTTTGGAAAA
* * * * * * *
48835978 TTTTGGGGTTAAAAATGATATTTTAGACACTTAAGGGTAAAATGGTAATTTTTGAAAGAATCGGG
66 TTTTAGGGTTAAAAATGACATTTTAGACAATCAAGGGTAAAACGATAATTTTTGAAAGAATCAGG
48836043 ATC-AAAATGAGACTT
131 ATCAAAAATGAGA-TT
** * * * *
48836058 TTTAGATGTTCGAGGGCAAAATGGTATTTTTAGACTTTTGAGGGCAAAATGGTAATTTTGGGAAA
1 TTTAGACATCCGAGGGCAAAATGGTAATTTTAGACTTTCGAGGACAAAATGGTAATTTT-GGAAA
* *
48836123 A-TTTAGGGTTAAAAATGACATTTTAGATAATCGAGGGTAAAACGATAATTTTTAGAAA-AATCA
65 ATTTTAGGGTTAAAAATGACATTTTAGACAATCAAGGGTAAAACGATAATTTTT-GAAAGAATCA
48836186 GGATCAAAAATGAGATT
129 GGATCAAAAATGAGATT
* * * * * * *
48836203 TTTGGACATCCGAGGGTAAAATGGTAATTTCGAGAGTTTCGGGGCCAAAAATGG-AATTTTTGAA
1 TTTAGACATCCGAGGGCAAAATGGTAATTT-TAGACTTTCGAGGAC-AAAATGGTAATTTTGGAA
48836267 A
64 A
48836268 GTTCAAGGTC
Statistics
Matches: 177, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
145 135 0.76
146 35 0.20
147 7 0.04
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.32
Consensus pattern (145 bp):
TTTAGACATCCGAGGGCAAAATGGTAATTTTAGACTTTCGAGGACAAAATGGTAATTTTGGAAAA
TTTTAGGGTTAAAAATGACATTTTAGACAATCAAGGGTAAAACGATAATTTTTGAAAGAATCAGG
ATCAAAAATGAGATT
Found at i:48836280 original size:29 final size:29
Alignment explanation
Indices: 48836248--48836444 Score: 202
Period size: 29 Copynumber: 6.8 Consensus size: 29
48836238 GTTTCGGGGC
*
48836248 CAAAAATGGAATTTTTGAAAGTTCAAGGT
1 CAAAAATGGAATTTTTGGAAGTTCAAGGT
48836277 CAAAAATGGAATTTTTGGAAGTTCAAGGT
1 CAAAAATGGAATTTTTGGAAGTTCAAGGT
* ** *
48836306 CAAAAATGAAATTTTTGGAA-TTTTAGGG
1 CAAAAATGGAATTTTTGGAAGTTCAAGGT
* * * ***
48836334 CAAAAAT-GTAGTTTTGAAAGTTTTGGAGT
1 CAAAAATGGAATTTTTGGAAGTTCAAG-GT
** *
48836363 CAAAAATGGAATTTTTGGAAGTTCGGGGG
1 CAAAAATGGAATTTTTGGAAGTTCAAGGT
* * *
48836392 CAAAAATGTAATTTTTGGAAGTTTTAGGGT
1 CAAAAATGGAATTTTTGGAAG-TTCAAGGT
48836422 C-AAAATGGAATTTTTGGAAGTTC
1 CAAAAATGGAATTTTTGGAAGTTC
48836445 GGGGACAAAT
Statistics
Matches: 141, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
27 8 0.06
28 19 0.13
29 94 0.67
30 20 0.14
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.34
Consensus pattern (29 bp):
CAAAAATGGAATTTTTGGAAGTTCAAGGT
Found at i:48836290 original size:58 final size:59
Alignment explanation
Indices: 48836237--48836532 Score: 243
Period size: 58 Copynumber: 5.1 Consensus size: 59
48836227 TAATTTCGAG
* * * *
48836237 AGTTTCGGGGCCAAAAATGGAATTTTTGAAAGTTCAAGGTCAAAAATGGAATTTTTGGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGA
* * ** * * *
48836296 AG-TTCAAGGTCAAAAATGAAATTTTTGGAA-TTTTAGGGCAAAAAT-GTAGTTTTGAA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGA
* ** *
48836352 AGTTT-TGGAGTCAAAAATGGAATTTTTGGAAGTTCGGGGGCAAAAATGTAATTTTTGGA
1 AGTTTCAGG-GTCAAAAATGGAATTTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGA
* * * * *
48836411 AGTTTTAGGGTC-AAAATGGAATTTTTGGAAGTTC--GGGGACAAATGTAATTTGTT-AA
1 AGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGCAAAAATGGAATTT-TTGGA
** * **
48836467 AGTTTTGGGGTCAAAAATGGAATTTTAGAGAAGTTTGAGGGTCAAAATAT--AATTTTTGGA
1 AGTTTCAGGGTCAAAAATGGAATTTTTG-GAAGTTCAAGGG-CAAAA-ATGGAATTTTTGGA
48836527 CAGTTT
1 -AGTTT
48836533 AAGGACCTTC
Statistics
Matches: 192, Mismatches: 31, Indels: 26
0.77 0.12 0.10
Matches are distributed among these distances:
56 38 0.20
57 51 0.27
58 63 0.33
59 19 0.10
60 11 0.06
61 8 0.04
62 2 0.01
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (59 bp):
AGTTTCAGGGTCAAAAATGGAATTTTTGGAAGTTCAAGGGCAAAAATGGAATTTTTGGA
Found at i:48836396 original size:115 final size:113
Alignment explanation
Indices: 48836248--48836536 Score: 339
Period size: 115 Copynumber: 2.5 Consensus size: 113
48836238 GTTTCGGGGC
* ** *
48836248 CAAAAATGGAATTTTTGAAAGTTCAAGGTCAAAAATGGAATTTTTGGAAGTTCAAGGTCAAAAAT
1 CAAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAAT-GAATTTTTGGAAGTTTAAGGTC-AAAAT
* *
48836313 GAAATTTTTGGAATTTTAGGGCAAAAATGTAGTTT-TGAAAGTTTTGGAGT
64 GAAATTTTTGGAA-GTTAGGGCAAAAATGTAATTTGTGAAAGTTTTGGAGT
* *
48836363 CAAAAATGGAATTTTTGGAAGTTCGGGGGCAAAAATGTAATTTTTGGAAGTTTTAGGGTCAAAAT
1 CAAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATG-AATTTTTGGAAG-TTTAAGGTCAAAAT
* * * * * *
48836428 GGAATTTTTGGAAGTTCGGGGACAAATGTAATTTGTTAAAGTTTTGGGGT
64 GAAATTTTTGGAAGTTAGGGCAAAAATGTAATTTGTGAAAGTTTTGGAGT
* *
48836478 CAAAAATGGAATTTTAGAGAAGTTTGAGGGTCAAAATAT-AATTTTTGGACAGTTTAAGG
1 CAAAAATGGAATTTTTG-GAAGTTCG-GGGTCAAAA-ATGAATTTTTGGA-AGTTTAAGG
48836537 ACCTTCATGG
Statistics
Matches: 149, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
114 17 0.11
115 90 0.60
116 30 0.20
117 10 0.07
118 2 0.01
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (113 bp):
CAAAAATGGAATTTTTGGAAGTTCGGGGTCAAAAATGAATTTTTGGAAGTTTAAGGTCAAAATGA
AATTTTTGGAAGTTAGGGCAAAAATGTAATTTGTGAAAGTTTTGGAGT
Found at i:48838318 original size:13 final size:13
Alignment explanation
Indices: 48838309--48838333 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48838299 CAATTGGGCT
48838309 TGTAAATTGGACA
1 TGTAAATTGGACA
48838322 TGTAAATTGGAC
1 TGTAAATTGGAC
48838334 TTTATATAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (13 bp):
TGTAAATTGGACA
Found at i:48838396 original size:17 final size:17
Alignment explanation
Indices: 48838371--48838441 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
48838361 TATTTAAATC
*
48838371 ATTTTAATTCAAAATAA
1 ATTTAAATTCAAAATAA
* * *
48838388 ATTCAAATTTAACATAA
1 ATTTAAATTCAAAATAA
* *
48838405 ATTTAAATTCTAAATGA
1 ATTTAAATTCAAAATAA
48838422 ATTTAAATTTC-AAATAA
1 ATTTAAA-TTCAAAATAA
48838439 ATT
1 ATT
48838442 AAGATTTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 40 0.93
18 3 0.07
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (17 bp):
ATTTAAATTCAAAATAA
Found at i:48838430 original size:34 final size:34
Alignment explanation
Indices: 48838371--48838441 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
48838361 TATTTAAATC
*
48838371 ATTTTAATTCAAAATAAATTCAAATTT-AACATAA
1 ATTTAAATTCAAAATAAATTCAAATTTCAA-ATAA
* * *
48838405 ATTTAAATTCTAAATGAATTTAAATTTCAAATAA
1 ATTTAAATTCAAAATAAATTCAAATTTCAAATAA
48838439 ATT
1 ATT
48838442 AAGATTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 30 0.94
35 2 0.06
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.41
Consensus pattern (34 bp):
ATTTAAATTCAAAATAAATTCAAATTTCAAATAA
Found at i:48838448 original size:17 final size:16
Alignment explanation
Indices: 48838382--48838448 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 16
48838372 TTTTAATTCA
48838382 AAATAAATTCAAATTT-
1 AAATAAATT-AAATTTC
48838398 AACATAAATTTAAA-TTC
1 AA-ATAAA-TTAAATTTC
*
48838415 TAAATGAATTTAAATTTC
1 -AAAT-AAATTAAATTTC
48838433 AAATAAATTAAGATTT
1 AAATAAATTAA-ATTT
48838449 AAAAATTAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
16 10 0.24
17 23 0.55
18 9 0.21
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
AAATAAATTAAATTTC
Found at i:48841989 original size:4 final size:4
Alignment explanation
Indices: 48841980--48842007 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
48841970 TATGAGTATT
48841980 CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA
48842008 TTTCAAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:48843526 original size:27 final size:27
Alignment explanation
Indices: 48843423--48843530 Score: 62
Period size: 27 Copynumber: 3.9 Consensus size: 27
48843413 ATATTGTTTT
*
48843423 TTTAGTTTTTAAGGGGCTCAAAAAAGT--
1 TTTAGCTTTTAAGGGGC-CAAAAAA-TAA
* * * *
48843450 TTTACCTTTTAA-AGGCCCAAAAACAA
1 TTTAGCTTTTAAGGGGCCAAAAAATAA
* * *
48843476 TTTACCAACTTTTAATGAGCCAAAAAATAA
1 TTT---AGCTTTTAAGGGGCCAAAAAATAA
48843506 TTTAGCTTTTAA-GGGCTCAAAAAAT
1 TTTAGCTTTTAAGGGGC-CAAAAAAT
48843531 TTTTTTACCA
Statistics
Matches: 62, Mismatches: 12, Indels: 14
0.70 0.14 0.16
Matches are distributed among these distances:
25 6 0.10
26 9 0.15
27 26 0.42
29 8 0.13
30 13 0.21
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (27 bp):
TTTAGCTTTTAAGGGGCCAAAAAATAA
Found at i:48844016 original size:28 final size:28
Alignment explanation
Indices: 48843932--48844022 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
48843922 TTTTTTTAGT
*
48843932 TTTTAAGGGGCCCAAAAAA-A-ATTAAC
1 TTTTAAGGGGCCCAAAAAATATTTTAAC
* *
48843958 TTTTAA-AGG-CCAAACAAAT-TTTACCAAC
1 TTTTAAGGGGCCCAAA-AAATATTT--TAAC
*
48843986 TTTTAAGGGGCCCAAAAAATATTTTAGC
1 TTTTAAGGGGCCCAAAAAATATTTTAAC
48844014 TTTTAAGGG
1 TTTTAAGGG
48844023 TTCAAAAACT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
24 5 0.10
25 5 0.10
26 7 0.14
28 20 0.39
29 6 0.12
30 8 0.16
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (28 bp):
TTTTAAGGGGCCCAAAAAATATTTTAAC
Found at i:48845499 original size:53 final size:53
Alignment explanation
Indices: 48845441--48845560 Score: 159
Period size: 53 Copynumber: 2.2 Consensus size: 53
48845431 ATTAATTTTT
* * *
48845441 TTGCTCATTTTTCCAATTACATGTGGAACACGATTGGAGAGTTAATCAAATTG
1 TTGCTCATTTTTCCAACTACATCTGGAACACGATTGAAGAGTTAATCAAATTG
* * * *
48845494 TTGCTCATTTTTCCAACTACATCTGGACCATGGTTGAAGATTTAATCAAATTG
1 TTGCTCATTTTTCCAACTACATCTGGAACACGATTGAAGAGTTAATCAAATTG
*
48845547 TTGCACTATTTTTC
1 TTGCTC-ATTTTTC
48845561 AACAATTTAA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
53 51 0.88
54 7 0.12
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (53 bp):
TTGCTCATTTTTCCAACTACATCTGGAACACGATTGAAGAGTTAATCAAATTG
Found at i:48846272 original size:18 final size:18
Alignment explanation
Indices: 48846251--48846289 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
48846241 AATAATGATA
*
48846251 ATTTAGCCCTTAATGTTT
1 ATTTAGCCCCTAATGTTT
48846269 ATTTAGCCCCTAATGTTT
1 ATTTAGCCCCTAATGTTT
48846287 ATT
1 ATT
48846290 CATTTTGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (18 bp):
ATTTAGCCCCTAATGTTT
Found at i:48846484 original size:19 final size:19
Alignment explanation
Indices: 48846460--48846502 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
48846450 CATAAAAATT
48846460 AAAAAATCAAAAAATTTT-A
1 AAAAAAT-AAAAAATTTTCA
*
48846479 AAAAAATAAAATATTTTCA
1 AAAAAATAAAAAATTTTCA
48846498 AAAAA
1 AAAAA
48846503 GTTGATAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAAATAAAAAATTTTCA
Found at i:48849135 original size:51 final size:51
Alignment explanation
Indices: 48849043--48849141 Score: 128
Period size: 51 Copynumber: 1.9 Consensus size: 51
48849033 AATATTGCAA
** *
48849043 ACTAAATTTGTTAAATCGGGATCAAATTGACAAATTGTGTAAAAGTTGTGG
1 ACTAAATTTGTTAAATAAGGATCAAATTGACAAATTATGTAAAAGTTGTGG
* * *
48849094 ACTAAATTTGTTAAATAAGTATGAAATTGACATAA-TATGTAAATGTTG
1 ACTAAATTTGTTAAATAAGGATCAAATTGACA-AATTATGTAAAAGTTG
48849142 AGGTGAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 39 0.95
52 2 0.05
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.35
Consensus pattern (51 bp):
ACTAAATTTGTTAAATAAGGATCAAATTGACAAATTATGTAAAAGTTGTGG
Found at i:48854568 original size:53 final size:53
Alignment explanation
Indices: 48854483--48854613 Score: 163
Period size: 53 Copynumber: 2.5 Consensus size: 53
48854473 GATTTAATCA
* * * * * *
48854483 GATTGAAGATTCAATTAATTTTTTTGCTCATTTTTCCAATTACATGTGGAACAC
1 GATTGAAGATTTAATCAA-ATTGTTGCTCATTTTTCCAACTACATCTGGAACAC
* * *
48854537 GATTGGAGATTTAATCAAATTGTTGCTCATTTTTCCAACTACATCTGGACCAT
1 GATTGAAGATTTAATCAAATTGTTGCTCATTTTTCCAACTACATCTGGAACAC
*
48854590 GGTTGAAGATTTAATCAAATTGTT
1 GATTGAAGATTTAATCAAATTGTT
48854614 TCACTATTTT
Statistics
Matches: 66, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 51 0.77
54 15 0.23
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (53 bp):
GATTGAAGATTTAATCAAATTGTTGCTCATTTTTCCAACTACATCTGGAACAC
Found at i:48858585 original size:9 final size:9
Alignment explanation
Indices: 48858559--48858589 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
48858549 TTTTAATCAT
48858559 TTTATTAAA
1 TTTATTAAA
48858568 TTATATTAAA
1 TT-TATTAAA
48858578 TTTATTAAA
1 TTTATTAAA
48858587 TTT
1 TTT
48858590 TTTGTGAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTATTAAA
Found at i:48880252 original size:16 final size:16
Alignment explanation
Indices: 48880227--48880260 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48880217 AACATAATAT
*
48880227 ATTATTAATTTAAAAA
1 ATTATAAATTTAAAAA
*
48880243 ATTATAAATTTATAAA
1 ATTATAAATTTAAAAA
48880259 AT
1 AT
48880261 CACTTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTATAAATTTAAAAA
Found at i:48881968 original size:6 final size:6
Alignment explanation
Indices: 48881950--48882057 Score: 82
Period size: 6 Copynumber: 18.0 Consensus size: 6
48881940 TTAAATTGAT
* *
48881950 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTTAAATA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AA-A TTTAAA
* ** *
48881997 TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAA TTTAACA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAA-A
48882046 -TTATAA TTTAAA
1 TTTA-AA TTTAAA
48882058 AGTCCAAATA
Statistics
Matches: 83, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 53 0.64
7 14 0.17
8 4 0.05
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (6 bp):
TTTAAA
Done.