Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009388.1 Kokia drynarioides strain JFW-HI SEQ_124095, whole genome shotgun sequence
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: 226929
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:6230 original size:23 final size:24
Alignment explanation
Indices: 6204--6248 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
6194 AATTTCATCA
6204 TTAAGCTTAATT-AACTCATTTTT
1 TTAAGCTTAATTAAACTCATTTTT
* *
6227 TTAATCTTGATTAAACTCATTT
1 TTAAGCTTAATTAAACTCATTT
6249 ATACTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.51
Consensus pattern (24 bp):
TTAAGCTTAATTAAACTCATTTTT
Found at i:15459 original size:72 final size:72
Alignment explanation
Indices: 15342--15485 Score: 288
Period size: 72 Copynumber: 2.0 Consensus size: 72
15332 CTCACTAGAT
15342 TTATGGGCTACCTGAGAGACTATTCATTGGCTGGTTGTCCAGCCATGTTTGCATGTTGCTTTGTC
1 TTATGGGCTACCTGAGAGACTATTCATTGGCTGGTTGTCCAGCCATGTTTGCATGTTGCTTTGTC
15407 TGGTCAC
66 TGGTCAC
15414 TTATGGGCTACCTGAGAGACTATTCATTGGCTGGTTGTCCAGCCATGTTTGCATGTTGCTTTGTC
1 TTATGGGCTACCTGAGAGACTATTCATTGGCTGGTTGTCCAGCCATGTTTGCATGTTGCTTTGTC
15479 TGGTCAC
66 TGGTCAC
15486 CAGTTAGTCA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (72 bp):
TTATGGGCTACCTGAGAGACTATTCATTGGCTGGTTGTCCAGCCATGTTTGCATGTTGCTTTGTC
TGGTCAC
Found at i:17725 original size:31 final size:31
Alignment explanation
Indices: 17690--17748 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
17680 ACTATGGGAC
17690 TTGAGCTAATATTGTCCTAATCTGACTGACT
1 TTGAGCTAATATTGTCCTAATCTGACTGACT
*
17721 TTGAGCTAATATTGTCTTAATCTGACTG
1 TTGAGCTAATATTGTCCTAATCTGACTG
17749 CCTTCATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (31 bp):
TTGAGCTAATATTGTCCTAATCTGACTGACT
Found at i:20696 original size:16 final size:16
Alignment explanation
Indices: 20675--20729 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
20665 CCTGCGAATA
20675 ACAAATGGTCATACGT
1 ACAAATGGTCATACGT
20691 ACAAATGGTCATACGT
1 ACAAATGGTCATACGT
20707 ACAAATGGTCATACGT
1 ACAAATGGTCATACGT
*
20723 GCAAATG
1 ACAAATG
20730 ACAACAACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (16 bp):
ACAAATGGTCATACGT
Found at i:27322 original size:20 final size:20
Alignment explanation
Indices: 27284--27335 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
27274 ACATAAGATC
*
27284 CAAATACAA-A-AAATGTCT
1 CAAATACAACATAAATATCT
*
27302 CATATACAACATAAATATCT
1 CAAATACAACATAAATATCT
*
27322 CAAATACATCATAA
1 CAAATACAACATAA
27336 TATGATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 8 0.29
19 1 0.04
20 19 0.68
ACGTcount: A:0.54, C:0.19, G:0.02, T:0.25
Consensus pattern (20 bp):
CAAATACAACATAAATATCT
Found at i:28661 original size:52 final size:52
Alignment explanation
Indices: 28583--28921 Score: 516
Period size: 52 Copynumber: 6.5 Consensus size: 52
28573 ATAGGTTCGG
* *
28583 TGACTATTTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCAGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
*
28635 TGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGTGGTCCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
* *
28687 TGACTATGTGTCATCGTGAGTATATGAATTCTTTACAGATTATGTGGTCCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
* * * *
28739 TAACTATGTGTTATCGTGAATATATGAATCCTTTACGGATTATGTGGTCTGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
* * * * *
28791 TGACTATGTGTCATCGTAAGTGTATGAATCCTTTACGGATAATGAGGTTCGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
* * *
28843 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGCTCTGA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
*
28895 TGGCTATGTGTCATCGTGAGTATATGA
1 TGACTATGTGTCATCGTGAGTATATGA
28922 TTCCCAATAC
Statistics
Matches: 259, Mismatches: 28, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 259 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (52 bp):
TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCGA
Found at i:28957 original size:104 final size:104
Alignment explanation
Indices: 28583--28969 Score: 506
Period size: 104 Copynumber: 3.7 Consensus size: 104
28573 ATAGGTTCGG
* ** *
28583 TGACTATTTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCAGATGACTATGTGTCA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
* *
28648 TCGTGAGTATATGAATCCTTTATGGATTATGTGGTCCGA
66 TCGTGAGTATATGAATCCTTTACGGATTATGTGGTCTGA
* * ** * *
28687 TGACTATGTGTCATCGTGAGTATATGAATTCTTTACAGATTATGTGGTCCGATAACTATGTGTTA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
*
28752 TCGTGAATATATGAATCCTTTACGGATTATGTGGTCTGA
66 TCGTGAGTATATGAATCCTTTACGGATTATGTGGTCTGA
* * * * *
28791 TGACTATGTGTCATCGTAAGTGTATGAATCCTTTACGGATAATGAGGTTCGATGACTATGTGTCA
1 TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
* *
28856 TCGTGAGTATATGAATCCTTTACGGATTATGAGCTCTGA
66 TCGTGAGTATATGAATCCTTTACGGATTATGTGGTCTGA
* * ** * * *
28895 TGGCTATGTGTCATCGTGAGTATATGATTCCCAATACGTATTA-AAGGTCCGATTACTCTGTGTC
1 TGACTATGTGTCATCGTGAGTATATGAAT-CCTTTACGGATTATAAGGTCCGATGACTATGTGTC
*
28959 ATCGTAAGTAT
65 ATCGTGAGTAT
28970 CAAATATGCA
Statistics
Matches: 248, Mismatches: 34, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
104 239 0.96
105 9 0.04
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.37
Consensus pattern (104 bp):
TGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
TCGTGAGTATATGAATCCTTTACGGATTATGTGGTCTGA
Found at i:29692 original size:21 final size:21
Alignment explanation
Indices: 29668--29714 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29658 TCATGTTTCA
*
29668 GTAGAAGAGACACTTGTATCG
1 GTAGAACAGACACTTGTATCG
* *
29689 GTAGAACTGACACTTGTATTG
1 GTAGAACAGACACTTGTATCG
29710 GTAGA
1 GTAGA
29715 TGTCTGCACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.28
Consensus pattern (21 bp):
GTAGAACAGACACTTGTATCG
Found at i:33583 original size:91 final size:92
Alignment explanation
Indices: 33427--33608 Score: 312
Period size: 91 Copynumber: 2.0 Consensus size: 92
33417 ATTTTAGTCC
33427 TTTAACAAAAAAAAATACTTTACAAGATCAGCAAATCTAACACTTAAGCTTATAAATCTCCTATA
1 TTTAACAAAAAAAAATACTTTACAAGATCAGCAAATCTAACACTTAAGCTTATAAATCTCCTATA
*
33492 AACTTTCAAGAGCAAGCTTATTCATCT
66 AACTTTCAAGAACAAGCTTATTCATCT
* * * *
33519 TTTAAC-AAAAAAATTACTTTACAAGATTATCAAATCTAACACTTAAGCTTATAAATCTCTTATA
1 TTTAACAAAAAAAAATACTTTACAAGATCAGCAAATCTAACACTTAAGCTTATAAATCTCCTATA
33583 AACTTTCAAGAACAAGCTTATTCATC
66 AACTTTCAAGAACAAGCTTATTCATC
33609 AATGTCAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
91 79 0.93
92 6 0.07
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.32
Consensus pattern (92 bp):
TTTAACAAAAAAAAATACTTTACAAGATCAGCAAATCTAACACTTAAGCTTATAAATCTCCTATA
AACTTTCAAGAACAAGCTTATTCATCT
Found at i:42053 original size:16 final size:16
Alignment explanation
Indices: 42032--42066 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42022 AAAATGTAAT
42032 TTTATTAT-TTTAATAA
1 TTTATTATATTT-ATAA
42048 TTTATTATATTTATAA
1 TTTATTATATTTATAA
42064 TTT
1 TTT
42067 TTAAAGGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTATATTTATAA
Found at i:42882 original size:387 final size:390
Alignment explanation
Indices: 42016--43174 Score: 1620
Period size: 387 Copynumber: 3.0 Consensus size: 390
42006 TTGGTAGTTC
* * *
42016 ATAATAAAAATGTAATTTTATTATTTTAATAATTTATTATATTTATAATTTTTAAAGGATTAAAT
1 ATAATAAAAATATAATTTTATTATTTTAATAATTTA-TATCTTTATAATTTTTAAAAGATTAAAT
* *
42081 TAAATTTTTATTATTTATTAA-GGAATCAAAGTGCTA-TCATTACTATTTTAAACTTTTATAAAT
65 CAAATTTTTATTATTT-TTAAGGGAATCAAAGTGCTACT-ATTACTAATTTAAACTTTTATAAAT
*
42144 CATAAAAAAGTCT--A-AA-TAA----T--TTTTTTTCATTTTAGGGATCCCTTTCAATTGTCAG
128 CATAAAAAAGCCTAAATAATTAATTTTTCATTTTTTTCATTTTAGGGATCCCTTTCAATTGTCAG
* * *
42199 TAAAATCTAATATATCTTAATGATTTCATATCAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCA
193 TAAAATCCAATATGTCTTAATGATTTCATATAAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCA
* * * *
42264 TTATTTGGGATTTAAATTTTAGGGTTTGAAAATTTATTTATTTTTGTTCAAATTAGACTTCAAAC
258 TTATTTGGGACTTAAATTTTAGGGCTTG-AAATTT-TTTATTTTTGTTCAAATTAGGCTCCAAAC
* * * *
42329 TTACTAACTGCTCTCACATCAAAACTTAAACTAGACAATTATTT-AACATTGAAGTTTGAAATTT
321 TTGCTAACTGCTCTCACATTAAAACTTGAACTAGACAATTATTTCAACATTGAAGCTTGAAATTT
42393 TTACG
386 TTACG
** * *
42398 ATAATAAAAATATAATTTTATTATTTTAATAGCTTATATCTTTATAGTCTTTAAAAGATTAAATC
1 ATAATAAAAATATAATTTTATTATTTTAATAATTTATATCTTTATAATTTTTAAAAGATTAAATC
* * *
42463 AAAATTTTATTATATTTAAGGGATTCAAAGTGCTACTATTACTAATTTAAACTTTTATAAATCAT
66 AAATTTTTATTATTTTTAAGGGAATCAAAGTGCTACTATTACTAATTTAAACTTTTATAAATCAT
* **
42528 AAAAAAGCCTAAATGAATTAATTTTTCATTTTTTTTATTTTAAGGGATCCCTGCCAATT-TCCAG
131 AAAAAAGCCTAAAT-AATTAATTTTTCATTTTTTTCATTTT-AGGGATCCCTTTCAATTGT-CAG
42592 TAAAATCCAATATGTCTTAATGATTTCATATAAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCA
193 TAAAATCCAATATGTCTTAATGATTTCATATAAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCA
*
42657 TTATTTGGGACTTAAATTTTAGGGCTTG-AA-TTTTT-TTTTTGTTTAAATTAGGCTCCAAACTT
258 TTATTTGGGACTTAAATTTTAGGGCTTGAAATTTTTTATTTTTGTTCAAATTAGGCTCCAAACTT
* * *
42719 GCT-A-TGCTTTCACATTAAAAATTGAACTAGACAACTATTTCAACATTGAAGCTTGAAATTTTT
323 GCTAACTGCTCTCACATTAAAACTTGAACTAGACAATTATTTCAACATTGAAGCTTGAAATTTTT
42782 ACG
388 ACG
42785 ATAATAAAAATATAATTTTATTATTTTAATAATTTATATCTTTATAATTTTTAAAAGATTAAATC
1 ATAATAAAAATATAATTTTATTATTTTAATAATTTATATCTTTATAATTTTTAAAAGATTAAATC
* ** *
42850 AAATTTTTATCATTTTTAAGGGGGTCAAAGTGCTACTATTACTAATTGAAACTTTTATAAATCAT
66 AAATTTTTATTATTTTTAAGGGAATCAAAGTGCTACTATTACTAATTTAAACTTTTATAAATCAT
* ** * *
42915 AAAAAGGCCTAAATAATTTTTTTTTCATTTTTTTCATTTTAGGGTGTCTCTTTCAATTGTCAGTA
131 AAAAAAGCCTAAATAATTAATTTTTCATTTTTTTCATTTTAGGG-ATCCCTTTCAATTGTCAGTA
* * *
42980 AAATCCAATATGTCTTAATGATTTCATATAAATTTATAGTAAATTCGTTTAAGGGTTAATTCATT
195 AAATCCAATATGTCTTAATGATTTCATATAAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCATT
* *
43045 ATTTGGGACTTGAATTTTAGGGCTTGAAATTTTATTTTATTTTTGTTCAAATTAGGCTCTAAACT
260 ATTTGGGACTTAAATTTTAGGGCTTGAAA--TT-TTTTATTTTTGTTCAAATTAGGCTCCAAACT
* * * * *
43110 TGCTAATTGCTCTCACATTAAAACTTGAATTAGACAATTGTTTCAACATTAAAACTTG-AATTTT
322 TGCTAACTGCTCTCACATTAAAACTTGAACTAGACAATTATTTCAACATTGAAGCTTGAAATTTT
43174 T
387 T
43175 CTTTGTCCAA
Statistics
Matches: 689, Mismatches: 62, Indels: 41
0.87 0.08 0.05
Matches are distributed among these distances:
380 4 0.01
381 87 0.13
382 34 0.05
383 1 0.00
385 6 0.01
386 158 0.23
387 161 0.23
388 26 0.04
389 3 0.00
390 4 0.01
391 6 0.01
392 41 0.06
393 114 0.17
394 44 0.06
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (390 bp):
ATAATAAAAATATAATTTTATTATTTTAATAATTTATATCTTTATAATTTTTAAAAGATTAAATC
AAATTTTTATTATTTTTAAGGGAATCAAAGTGCTACTATTACTAATTTAAACTTTTATAAATCAT
AAAAAAGCCTAAATAATTAATTTTTCATTTTTTTCATTTTAGGGATCCCTTTCAATTGTCAGTAA
AATCCAATATGTCTTAATGATTTCATATAAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCATTA
TTTGGGACTTAAATTTTAGGGCTTGAAATTTTTTATTTTTGTTCAAATTAGGCTCCAAACTTGCT
AACTGCTCTCACATTAAAACTTGAACTAGACAATTATTTCAACATTGAAGCTTGAAATTTTTACG
Found at i:43256 original size:386 final size:385
Alignment explanation
Indices: 42164--43174 Score: 1113
Period size: 386 Copynumber: 2.6 Consensus size: 385
42154 TCTAAATAAT
** * *
42164 TTTTTTTCATTTT-AGGGATCCCTTTCAATTGT-CAGTAAAATCTAATATATCTTAATGATTTCA
1 TTTTTTTCATTTTAAGGGATCCCTGCCAATT-TCCAGTAAAATCCAATATGTCTTAATGATTTCA
* * * * *
42227 TATCAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCATTATTTGGGATTTAAATTTTAGGGTTTG
65 TATAAATTTATAGTAAATTCGTTTAAGGGTTAAATCATTATTTGGGACTTAAATTTTAGGGCTTG
* * * * * *
42292 AAAATTTATTTATTTTTGTTCAAATTAGACTTCAAACTTACTAACTGCTCTCACATCAAAACTTA
130 --AA-TT-TTT-TTTTTGTTCAAATTAGGCTCCAAACTTGCT-A-TGCTCTCACATTAAAAATTG
* * ** *
42357 AACTAGACAATTATTT-AACATTGAAGTTTGAAATTTTTACGATAATAAAAATATAATTTTATTA
188 AACTAGACAACTATTTCAACATTAAAACTTGAAATTTTTACGATAATAAAAATATAATTCTATTA
* * * ** * **** * **
42421 TTTTAA-TAGCTTATATCTTTATAGTCTTTAAAAGATTAAATCAAAATT-TTATTATATTTAAGG
253 TCTTAACAATC-TATATCTGCATAATGAGGAAAAGATT-AAGC-AAATTCTTACAAT-TTTAAGG
* *
42484 GATTCAAAGTGCTACTATTACTAATTTAAACTTTTATAAATCATAAAAAAGCCTAAATGAATTAA
314 GAGTCAAAGTGCTACTATTACTAATTGAAACTTTTATAAATCATAAAAAAGCCTAAATGAATTAA
42549 TTTTTCA
379 TTTTTCA
*
42556 TTTTTTTTATTTTAAGGGATCCCTGCCAATTTCCAGTAAAATCCAATATGTCTTAATGATTTCAT
1 TTTTTTTCATTTTAAGGGATCCCTGCCAATTTCCAGTAAAATCCAATATGTCTTAATGATTTCAT
* *
42621 ATAAATTTTTAGTAAGTTCGTTTAAGGGTTAAATCATTATTTGGGACTTAAATTTTAGGGCTTGA
66 ATAAATTTATAGTAAATTCGTTTAAGGGTTAAATCATTATTTGGGACTTAAATTTTAGGGCTTGA
* *
42686 ATTTTTTTTTTGTTTAAATTAGGCTCCAAACTTGCTATGCTTTCACATTAAAAATTGAACTAGAC
131 ATTTTTTTTTTGTTCAAATTAGGCTCCAAACTTGCTATGCTCTCACATTAAAAATTGAACTAGAC
* * * * *
42751 AACTATTTCAACATTGAAGCTTGAAATTTTTACGATAATAAAAATATAATTTTATTATTTTAATA
196 AACTATTTCAACATTAAAACTTGAAATTTTTACGATAATAAAAATATAATTCTATTATCTTAACA
* ** **** * * * *
42816 ATTTATATCTTTATAATTTTTAAAAGATTAAATCAAATTTTTATCATTTTTAAGGGGGTCAAAGT
261 ATCTATATCTGCATAATGAGGAAAAGATT-AAGCAAATTCTTA-CAATTTTAAGGGAGTCAAAGT
* **
42881 GCTACTATTACTAATTGAAACTTTTATAAATCATAAAAAGGCCTAAAT-AATTTTTTTTTCA
324 GCTACTATTACTAATTGAAACTTTTATAAATCATAAAAAAGCCTAAATGAATTAATTTTTCA
* * **
42942 TTTTTTTCATTTT-AGGGTGTCTCTTTCAATTGT-CAGTAAAATCCAATATGTCTTAATGATTTC
1 TTTTTTTCATTTTAAGGG-ATCCCTGCCAATT-TCCAGTAAAATCCAATATGTCTTAATGATTTC
* *
43005 ATATAAATTTATAGTAAATTCGTTTAAGGGTTAATTCATTATTTGGGACTTGAATTTTAGGGCTT
64 ATATAAATTTATAGTAAATTCGTTTAAGGGTTAAATCATTATTTGGGACTTAAATTTTAGGGCTT
* *
43070 GAAATTTTATTTTATTTTTGTTCAAATTAGGCTCTAAACTTGCTAATTGCTCTCACATTAAAACT
129 G-AA---T-TTTT-TTTTTGTTCAAATTAGGCTCCAAACTTGCT-A-TGCTCTCACATTAAAAAT
* * *
43135 TGAATTAGACAATTGTTTCAACATTAAAACTTG-AATTTTT
186 TGAACTAGACAACTATTTCAACATTAAAACTTGAAATTTTT
43175 CTTTGTCCAA
Statistics
Matches: 553, Mismatches: 50, Indels: 31
0.87 0.08 0.05
Matches are distributed among these distances:
385 4 0.01
386 160 0.29
387 150 0.27
388 28 0.05
389 3 0.01
390 3 0.01
391 6 0.01
392 41 0.07
393 114 0.21
394 44 0.08
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.44
Consensus pattern (385 bp):
TTTTTTTCATTTTAAGGGATCCCTGCCAATTTCCAGTAAAATCCAATATGTCTTAATGATTTCAT
ATAAATTTATAGTAAATTCGTTTAAGGGTTAAATCATTATTTGGGACTTAAATTTTAGGGCTTGA
ATTTTTTTTTTGTTCAAATTAGGCTCCAAACTTGCTATGCTCTCACATTAAAAATTGAACTAGAC
AACTATTTCAACATTAAAACTTGAAATTTTTACGATAATAAAAATATAATTCTATTATCTTAACA
ATCTATATCTGCATAATGAGGAAAAGATTAAGCAAATTCTTACAATTTTAAGGGAGTCAAAGTGC
TACTATTACTAATTGAAACTTTTATAAATCATAAAAAAGCCTAAATGAATTAATTTTTCA
Found at i:43836 original size:3 final size:3
Alignment explanation
Indices: 43828--43857 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43818 TAAGAAGGGG
43828 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
43858 ATAAGACATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:43994 original size:56 final size:56
Alignment explanation
Indices: 43890--44001 Score: 170
Period size: 56 Copynumber: 2.0 Consensus size: 56
43880 TTTTCAAACA
*
43890 ATTCAATCTGTCCACAACAGAAAACAGAAAATCTGAAAAAGAATATGCAAGGCCAC
1 ATTCAATCTGTCCACAACAGAAAACAGAAAATCTGAAAAAGAAGATGCAAGGCCAC
* * * * *
43946 ATTCAATTTGTCCACAACAGAAAACAGAAAATCTGCATATGCAGATGCAAGGCCAC
1 ATTCAATCTGTCCACAACAGAAAACAGAAAATCTGAAAAAGAAGATGCAAGGCCAC
44002 CGATACAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.45, C:0.22, G:0.15, T:0.18
Consensus pattern (56 bp):
ATTCAATCTGTCCACAACAGAAAACAGAAAATCTGAAAAAGAAGATGCAAGGCCAC
Found at i:45775 original size:16 final size:16
Alignment explanation
Indices: 45731--45780 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
45721 CCTAAAGTAT
45731 TAAAATTTT-AA--TA
1 TAAAATTTTAAATTTA
45744 TAAAATTTTTATAATTTA
1 TAAAA-TTTTA-AATTTA
*
45762 TAAAATTTTAAATTGA
1 TAAAATTTTAAATTTA
45778 TAA
1 TAA
45781 TGATAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 5 0.16
14 4 0.13
16 10 0.32
17 5 0.16
18 7 0.23
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
TAAAATTTTAAATTTA
Found at i:47770 original size:21 final size:21
Alignment explanation
Indices: 47741--47780 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
47731 TTTTTCTTTT
*
47741 ACCTTAAACCTAAAACTCAGA
1 ACCTCAAACCTAAAACTCAGA
* *
47762 ACCTCAAACTTTAAACTCA
1 ACCTCAAACCTAAAACTCA
47781 AATCCTAAAT
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:0.45, C:0.30, G:0.03, T:0.23
Consensus pattern (21 bp):
ACCTCAAACCTAAAACTCAGA
Found at i:55574 original size:24 final size:24
Alignment explanation
Indices: 55547--55595 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
55537 TGGTGTGGCG
*
55547 AGCTGGGCTTCGTAGGAAGTAGTA
1 AGCTGGACTTCGTAGGAAGTAGTA
* *
55571 AGCTTGACTTCGTAGGAAGTTGTA
1 AGCTGGACTTCGTAGGAAGTAGTA
55595 A
1 A
55596 ACATCAGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.29
Consensus pattern (24 bp):
AGCTGGACTTCGTAGGAAGTAGTA
Found at i:56930 original size:17 final size:17
Alignment explanation
Indices: 56865--56922 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
56855 GCAAGGTAAG
56865 GAGCTCGCA-ATCTTGGT
1 GAGCTCGCACAT-TTGGT
* *
56882 GAGCTTGCACATTTGTT
1 GAGCTCGCACATTTGGT
*
56899 GAGCTCGCATATTTGGT
1 GAGCTCGCACATTTGGT
56916 GAGCTCG
1 GAGCTCG
56923 TAGATTTGTG
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 33 0.94
18 2 0.06
ACGTcount: A:0.17, C:0.21, G:0.29, T:0.33
Consensus pattern (17 bp):
GAGCTCGCACATTTGGT
Found at i:56930 original size:34 final size:34
Alignment explanation
Indices: 56865--56931 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 34
56855 GCAAGGTAAG
*
56865 GAGCTCGCAATCTTGGTGAGCTTGCACATTTGTT
1 GAGCTCGCAATCTTGGTGAGCTCGCACATTTGTT
* *
56899 GAGCTCGCATAT-TTGGTGAGCTCGTAGATTTGT
1 GAGCTCGCA-ATCTTGGTGAGCTCGCACATTTGT
56932 GTTCTGGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (34 bp):
GAGCTCGCAATCTTGGTGAGCTCGCACATTTGTT
Found at i:60432 original size:23 final size:26
Alignment explanation
Indices: 60391--60440 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 26
60381 AACCCTTTTA
60391 TTTTATTTTTGTTAAAATTTAA-CCC
1 TTTTATTTTTGTTAAAATTTAATCCC
60416 TTTTA-TTTT-TTAAAATTTAATCCC
1 TTTTATTTTTGTTAAAATTTAATCCC
60440 T
1 T
60441 CACTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.46
24 8 0.33
25 5 0.21
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTATTTTTGTTAAAATTTAATCCC
Found at i:60559 original size:18 final size:19
Alignment explanation
Indices: 60538--60582 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
60528 AAAATTTAAC
60538 TTTTTTTATT-TATTTG-A
1 TTTTTTTATTCTATTTGCA
60555 TTTTTTTATTCTATTTGCA
1 TTTTTTTATTCTATTTGCA
*
60574 TTTATTTAT
1 TTTTTTTAT
60583 CCATTGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 9 0.36
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTTTTATTCTATTTGCA
Found at i:66747 original size:17 final size:17
Alignment explanation
Indices: 66725--66765 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
66715 TAATTTACAA
66725 TGACAATGTAGATGCAG
1 TGACAATGTAGATGCAG
66742 TGACAATGTAGATGCAG
1 TGACAATGTAGATGCAG
66759 TGACAAT
1 TGACAAT
66766 AAAAATGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (17 bp):
TGACAATGTAGATGCAG
Found at i:66773 original size:17 final size:17
Alignment explanation
Indices: 66736--66774 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
66726 GACAATGTAG
** *
66736 ATGCAGTGACAATGTAG
1 ATGCAGTGACAATAAAA
66753 ATGCAGTGACAATAAAA
1 ATGCAGTGACAATAAAA
66770 ATGCA
1 ATGCA
66775 ATGGAAAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (17 bp):
ATGCAGTGACAATAAAA
Found at i:69121 original size:8 final size:9
Alignment explanation
Indices: 69103--69131 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
69093 CTTGAAACCC
69103 AAGGAAAAA
1 AAGGAAAAA
69112 AAGGAAAAA
1 AAGGAAAAA
69121 AAGGAAAAA
1 AAGGAAAAA
69130 AA
1 AA
69132 ATAAGAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGGAAAAA
Found at i:70733 original size:24 final size:24
Alignment explanation
Indices: 70697--70769 Score: 96
Period size: 24 Copynumber: 3.0 Consensus size: 24
70687 CCAGACAAAA
*
70697 ATTAGCTCATACGAGCCCAAATAG
1 ATTAGCTCTTACGAGCCCAAATAG
70721 ATTAGCTCTTACGAGCCCAAATA-
1 ATTAGCTCTTACGAGCCCAAATAG
*
70744 AGTTAGCTCATT-CGAGCCCAGATAG
1 A-TTAGCTC-TTACGAGCCCAAATAG
70769 A
1 A
70770 GTTTAACCAG
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
23 1 0.02
24 40 0.91
25 3 0.07
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (24 bp):
ATTAGCTCTTACGAGCCCAAATAG
Found at i:70761 original size:48 final size:50
Alignment explanation
Indices: 70672--70769 Score: 130
Period size: 48 Copynumber: 2.0 Consensus size: 50
70662 TTCTAGAGAT
70672 TTAGCTCATTCGAGCCCAGACAAAAATTAGCTCATACGAGCCCAAATAGA
1 TTAGCTCATTCGAGCCCAGACAAAAATTAGCTCATACGAGCCCAAATAGA
* * * *
70722 TTAGCTC-TTACGAGCCCA-A-ATAAGTTAGCTCATTCGAGCCCAGATAGA
1 TTAGCTCATT-CGAGCCCAGACAAAAATTAGCTCATACGAGCCCAAATAGA
70770 GTTTAACCAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 25 0.58
49 3 0.07
50 15 0.35
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (50 bp):
TTAGCTCATTCGAGCCCAGACAAAAATTAGCTCATACGAGCCCAAATAGA
Found at i:72890 original size:4 final size:4
Alignment explanation
Indices: 72881--72924 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
72871 TTCACTCAAA
*
72881 AAAG AAAG AAAAG AAAG AAA- AAAA AAAG AAAG AATAG AAAG AAA
1 AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AA-AG AAAG AAA
72925 ATAAAAAAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
3 3 0.08
4 25 0.69
5 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:72894 original size:9 final size:9
Alignment explanation
Indices: 72880--72947 Score: 63
Period size: 9 Copynumber: 7.9 Consensus size: 9
72870 TTTCACTCAA
72880 AAAAGAAAG
1 AAAAGAAAG
72889 AAAAGAAAG
1 AAAAGAAAG
72898 -AAA-AAA-
1 AAAAGAAAG
72904 AAAAGAAAG
1 AAAAGAAAG
*
72913 AATAGAAAG
1 AAAAGAAAG
*
72922 AAAATAAA-
1 AAAAGAAAG
* *
72930 AAAGGAAAA
1 AAAAGAAAG
72939 AAGAAGAAA
1 AA-AAGAAA
72948 AATGAGAGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
7 6 0.12
8 12 0.25
9 25 0.52
10 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:72910 original size:24 final size:24
Alignment explanation
Indices: 72878--72949 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
72868 AATTTCACTC
72878 AAAAAAGAAAGAAAAGAAAGAAAA
1 AAAAAAGAAAGAAAAGAAAGAAAA
*
72902 AAAAAAGAAAGAATAGAAAGAAAA
1 AAAAAAGAAAGAAAAGAAAGAAAA
*
72926 TAAAAAAGGAA-AAAAG-AAGAAAA
1 -AAAAAAGAAAGAAAAGAAAGAAAA
72949 A
1 A
72950 TGAGAGGTCG
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 7 0.16
24 27 0.61
25 9 0.20
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (24 bp):
AAAAAAGAAAGAAAAGAAAGAAAA
Found at i:73993 original size:49 final size:50
Alignment explanation
Indices: 73919--74192 Score: 183
Period size: 49 Copynumber: 5.7 Consensus size: 50
73909 ATTTCATACC
* * *
73919 CTAGAGATGTGAAGGGAAAGGTTGAAGCCACAACAG-TGAACCTTGTACA
1 CTAGAGATATGGAGGGAGAGGTTGAAGCCACAACAGATGAACCTTGTACA
* * * * ** *
73968 CTAGAAATATGGAGGGAGAGATTGAAGCCGCAAC-GATGAATCTCATACC
1 CTAGAGATATGGAGGGAGAGGTTGAAGCCACAACAGATGAACCTTGTACA
* * *
74017 CTAGAGATGT-GA---AG-GGTTGAAGTCATAACAG-TGAACCTTGTATC-
1 CTAGAGATATGGAGGGAGAGGTTGAAGCCACAACAGATGAACCTTGTA-CA
* * * * *
74061 CTAGAGATATGGAGGGAGAGTTTGAAGCCGCAAC-GATAAATCTTATACA
1 CTAGAGATATGGAGGGAGAGGTTGAAGCCACAACAGATGAACCTTGTACA
* * * * * ** ** *
74110 CTAAAGATGTGAAAGGAAAGGTTGAAGCCGTAA-AGACAAACCTTGTACC
1 CTAGAGATATGGAGGGAGAGGTTGAAGCCACAACAGATGAACCTTGTACA
** *
74159 CTAGAGATATGGAGGGAGAAATTGAAGTCACAAC
1 CTAGAGATATGGAGGGAGAGGTTGAAGCCACAAC
74193 GGCAAATTTT
Statistics
Matches: 165, Mismatches: 48, Indels: 23
0.70 0.20 0.10
Matches are distributed among these distances:
44 28 0.17
45 6 0.04
48 7 0.04
49 124 0.75
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.20
Consensus pattern (50 bp):
CTAGAGATATGGAGGGAGAGGTTGAAGCCACAACAGATGAACCTTGTACA
Found at i:74027 original size:98 final size:96
Alignment explanation
Indices: 73906--74185 Score: 354
Period size: 93 Copynumber: 2.9 Consensus size: 96
73896 GAGAAAATGT
* *
73906 TGAATTTCATACCCTAGAGATGTGAAGGGAAAGGTTGAAGCCACAACAGTGAACCTTGTACACTA
1 TGAATCTCATACCCTAGAGATGTGAA-GGAAAGGTTGAAGCCATAACAGTGAACCTTGTAC-CTA
*
73971 GAAATATGGAGGGAGAGATTGAAGCCGCAACGA
64 GAGATATGGAGGGAGAGATTGAAGCCGCAACGA
*
74004 TGAATCTCATACCCTAGAGATGTGAA-G---GGTTGAAGTCATAACAGTGAACCTTGTATCCTAG
1 TGAATCTCATACCCTAGAGATGTGAAGGAAAGGTTGAAGCCATAACAGTGAACCTTGTA-CCTAG
*
74065 AGATATGGAGGGAGAGTTTGAAGCCGCAACGA
65 AGATATGGAGGGAGAGATTGAAGCCGCAACGA
* * * * * **
74097 TAAATCTTATACACTAAAGATGTGAAAGGAAAGGTTGAAGCCGTAA-AGACAAACCTTGTACCCT
1 TGAATCTCATACCCTAGAGATGTG-AAGGAAAGGTTGAAGCCATAACAG-TGAACCTTGTA-CCT
*
74161 AGAGATATGGAGGGAGAAATTGAAG
63 AGAGATATGGAGGGAGAGATTGAAG
74186 TCACAACGGC
Statistics
Matches: 159, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
93 80 0.50
94 3 0.02
95 1 0.01
96 1 0.01
97 2 0.01
98 72 0.45
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.21
Consensus pattern (96 bp):
TGAATCTCATACCCTAGAGATGTGAAGGAAAGGTTGAAGCCATAACAGTGAACCTTGTACCTAGA
GATATGGAGGGAGAGATTGAAGCCGCAACGA
Found at i:74193 original size:98 final size:98
Alignment explanation
Indices: 73914--74235 Score: 350
Period size: 98 Copynumber: 3.3 Consensus size: 98
73904 GTTGAATTTC
* * * * * *
73914 ATACCCTAGAGATGTGAAGGGAAAGGTTGAAGCCACAACAGTGAACCTTGTACACTAGAAATATG
1 ATACACTAAAGATGTGAAAGGAAAGGTTGAAGCCATAACAGTGAACCTTGTACCCTAGAGATATG
* *
73979 GAGGGAGAGATTGAAGCCGCAACGATGAATCTC
66 GAGGGAGAGATTGAAGCCGCAACGATAAATCTT
* * * *
74012 ATACCCTAGAGATGTG-AA-G---GGTTGAAGTCATAACAGTGAACCTTGTATCCTAGAGATATG
1 ATACACTAAAGATGTGAAAGGAAAGGTTGAAGCCATAACAGTGAACCTTGTACCCTAGAGATATG
*
74072 GAGGGAGAGTTTGAAGCCGCAACGATAAATCTT
66 GAGGGAGAGATTGAAGCCGCAACGATAAATCTT
* **
74105 ATACACTAAAGATGTGAAAGGAAAGGTTGAAGCCGTAA-AGACAAACCTTGTACCCTAGAGATAT
1 ATACACTAAAGATGTGAAAGGAAAGGTTGAAGCCATAACAG-TGAACCTTGTACCCTAGAGATAT
* * * ** *
74169 GGAGGGAGAAATTGAAGTCACAACGGCAAATTTT
65 GGAGGGAGAGATTGAAGCCGCAACGATAAATCTT
* * * *
74203 ATACATTAGAAGTTATGAAAAGAAAGGTTGAAG
1 ATACACTA-AAGATGTGAAAGGAAAGGTTGAAG
74236 TCGCAACGGC
Statistics
Matches: 190, Mismatches: 27, Indels: 13
0.83 0.12 0.06
Matches are distributed among these distances:
93 80 0.42
94 2 0.01
95 1 0.01
96 1 0.01
97 3 0.02
98 82 0.43
99 21 0.11
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (98 bp):
ATACACTAAAGATGTGAAAGGAAAGGTTGAAGCCATAACAGTGAACCTTGTACCCTAGAGATATG
GAGGGAGAGATTGAAGCCGCAACGATAAATCTT
Found at i:74393 original size:90 final size:90
Alignment explanation
Indices: 74225--74442 Score: 249
Period size: 90 Copynumber: 2.4 Consensus size: 90
74215 TTATGAAAAG
* * * * * *
74225 AAAGGTTGAAGTCGCAACGGCGAACCTCATGCCTTAAAGATGTGATAGGAAAGATTGAAGCAACA
1 AAAGGTTGAAGCCGTAACGGCGAACCTTATACCTTAAAGACGTGATAGAAAAGATTGAAGCAACA
74290 ATAGCGAATCTTGTACCCTAAAGGA
66 ATAGCGAATCTTGTACCCTAAAGGA
** * * * *
74315 AAATTTTGACGCCGTAACGGCGAACCTTATACCTTAGAGACGTGAT-GCAAAAGATTGAAGCCAT
1 AAAGGTTGAAGCCGTAACGGCGAACCTTATACCTTAAAGACGTGATAG-AAAAGATTGAAGCAAC
* * *
74379 AATAGCGAATCTTGTACCGTAGAGGG
65 AATAGCGAATCTTGTACCCTAAAGGA
** * *
74405 AAAGGTTGAAGCCGTAACGATGAATCTTATACCCTAAA
1 AAAGGTTGAAGCCGTAACGGCGAACCTTATACCTTAAA
74443 AGGAAAGGTT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
89 1 0.01
90 103 0.99
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (90 bp):
AAAGGTTGAAGCCGTAACGGCGAACCTTATACCTTAAAGACGTGATAGAAAAGATTGAAGCAACA
ATAGCGAATCTTGTACCCTAAAGGA
Found at i:74506 original size:131 final size:132
Alignment explanation
Indices: 74295--74573 Score: 364
Period size: 131 Copynumber: 2.1 Consensus size: 132
74285 CAACAATAGC
* ** * * *
74295 GAATCTTGTACCCT-AAAGGAAAATTTTGACGCCGTAACGGCGAACCTTATACCTTAGAGACGTG
1 GAATCTTATACCCTAAAAGGAAAAGGTTGAAGCCGCAACAGCGAACCTTATACCTTAGAGACGTG
* * *
74359 ATGCAAAAGATTGAAGCCATAATAGCGAATCTTGTACCGTAGAGGGAAAGGTTGAAGCCGTAACG
66 ATGCAAAAGATTGAAGCCATAATAGCGAATATTGTACCCTAAAGGGAAAGGTTGAAGCCGTAACG
74424 AT
131 AT
* *
74426 GAATCTTATACCCTAAAAGG-AAAGGTTGAAGCCGCAACAGTGAACCTTATACCTTAGAGATGTG
1 GAATCTTATACCCTAAAAGGAAAAGGTTGAAGCCGCAACAGCGAACCTTATACCTTAGAGACGTG
** * * * *
74490 ATGGGAAATATTGAAGCCATAATGGTGAATATTGTACCCTAAAGGGAAAGGTTGAAGTCGTAACG
66 ATGCAAAAGATTGAAGCCATAATAGCGAATATTGTACCCTAAAGGGAAAGGTTGAAGCCGTAACG
*
74555 GT
131 AT
* *
74557 GAACCTTATACCTTAAA
1 GAATCTTATACCCTAAA
74574 GATGTGATGG
Statistics
Matches: 127, Mismatches: 20, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
131 122 0.96
132 5 0.04
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (132 bp):
GAATCTTATACCCTAAAAGGAAAAGGTTGAAGCCGCAACAGCGAACCTTATACCTTAGAGACGTG
ATGCAAAAGATTGAAGCCATAATAGCGAATATTGTACCCTAAAGGGAAAGGTTGAAGCCGTAACG
AT
Found at i:74518 original size:49 final size:48
Alignment explanation
Indices: 74444--75071 Score: 242
Period size: 49 Copynumber: 13.3 Consensus size: 48
74434 TACCCTAAAA
* ** *
74444 GGAAAGGTTGAAGCCGCAACAGTGAACCTTATACCTTAGAGATGTGATG
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGTGATG
* * ** * *
74493 GGAAATATTGAAGCCATAATGGTGAATATTGTACCCT-A-A----A-G
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTAAGATGTGATG
* * *
74534 GGAAAGGTTGAAGTCGTAACGGTGAACCTTATACCTTAAAGATGTGATG
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTT-AAGATGTGATG
*** * * * * *
74583 GGAAAGATTGAAGCCGCGACTGCGAATCTTGTACCCT---A---GA-G
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTAAGATGTGATG
* *** * ***
74624 GGAAAGGTTGAAGCTGCAATGACAAACCTTATACCTTAGAGATGTGATG
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGTGATG
* ** ** * * * *
74673 GGAAAGATTAAAATCGCAACGGCGAATCTTGTACCCT---A---GA-G
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTAAGATGTGATG
* * *
74714 GGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAGATGTTATG
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGTGATG
* * * * * *
74763 GGAAAGATGGAAACCGTAACGGCGAATCTTATACCCTAAAGATGTAGA-G
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATA-CCTTAAGATGT-GATG
* * * ** * *
74812 GAAAAGGTTGAAGTCGCAACGGTGAACCTTACACCTTAGAGATGTGATA
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGTGATG
* ** * * **
74861 GGAAAGATTGAGGCCGCAACGGCGAATCTTATACCCAAGAGATGTGGA-G
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGT-GATG
* * ** ** * * **
74910 GGAAAGGTTGAAGTCGCAACGGAAAACCTTATACCTTAGATATGTTAAA
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGTGATG
* * * *
74959 GGAAAGATTGAAGCCACAACGGTGAATCTTATACCCTAGAGATATAGA-G
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGT-GATG
* *** * *
75008 GGAAAGGTTGAAGCTGCAACGGCGAACCTTATACCTTAGAGATGTGAAG
1 GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTA-AGATGTGATG
75057 GGAAAGATTGAAGCC
1 GGAAAGATTGAAGCC
75072 GCAACAGCGA
Statistics
Matches: 427, Mismatches: 120, Indels: 64
0.70 0.20 0.10
Matches are distributed among these distances:
41 86 0.20
42 5 0.01
43 1 0.00
44 1 0.00
45 4 0.01
46 1 0.00
47 1 0.00
48 13 0.03
49 307 0.72
50 8 0.02
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (48 bp):
GGAAAGATTGAAGCCATAACGGTGAACCTTATACCTTAAGATGTGATG
Found at i:74559 original size:90 final size:90
Alignment explanation
Indices: 74402--75093 Score: 686
Period size: 90 Copynumber: 7.4 Consensus size: 90
74392 GTACCGTAGA
* * ** * * *
74402 GGGAAAGGTTGAAGCCGTAACGATGAATCTTATACCCTAAAAGGAAAGGTTGAAGCCGCAACAGT
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCTAAAGGGAAAGGTTGAAGTCGCAACGGT
74467 GAACCTTATACCTTAGAGATGTGAT
66 GAACCTTATACCTTAGAGATGTGAT
* ** * * * * *
74492 GGGAAATATTGAAGCCATAATGGTGAATATTGTACCCTAAAGGGAAAGGTTGAAGTCGTAACGGT
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCTAAAGGGAAAGGTTGAAGTCGCAACGGT
*
74557 GAACCTTATACCTTAAAGATGTGAT
66 GAACCTTATACCTTAGAGATGTGAT
* * * * * *
74582 GGGAAAGATTGAAGCCGCGACTGCGAATCTTGTACCCTAGAGGGAAAGGTTGAAG-CTGCAATGA
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCTAAAGGGAAAGGTTGAAGTC-GCAACGG
**
74646 CAAACCTTATACCTTAGAGATGTGAT
65 TGAACCTTATACCTTAGAGATGTGAT
* ** * * * *
74672 GGGAAAGATTAAAATCGCAACGGCGAATCTTGTACCCTAGAGGGAAAGGTTGAAGCCACAACGGT
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCTAAAGGGAAAGGTTGAAGTCGCAACGGT
*
74737 GAACCTTATACCTTAGAGATGTTAT
66 GAACCTTATACCTTAGAGATGTGAT
* * *
74762 GGGAAAGATGGAAACCGTAACGGCGAATCTTATACCCTAAAGATGTAGAGGAAAAGGTTGAAGTC
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCT--A-A---AG-GG-AAAGGTTGAAGTC
*
74827 GCAACGGTGAACCTTACACCTTAGAGATGTGAT
58 GCAACGGTGAACCTTATACCTTAGAGATGTGAT
* * *
74860 AGGAAAGATTGAGGCCGCAACGGCGAATCTTATACCCAAGAGATGTGGAGGGAAAGGTTGAAGTC
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCC--TA-A-----AGGGAAAGGTTGAAGTC
** * * *
74925 GCAACGGAAAACCTTATACCTTAGATATGTTAA
58 GCAACGGTGAACCTTATACCTTAGAGATGTGAT
* * *
74958 AGGAAAGATTGAAGCCACAACGGTGAATCTTATACCCTAGAGATATAGAGGGAAAGGTTGAAG-C
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCC------TA-A-AGGGAAAGGTTGAAGTC
* *
75022 TGCAACGGCGAACCTTATACCTTAGAGATGTGAA
58 -GCAACGGTGAACCTTATACCTTAGAGATGTGAT
*
75056 GGGAAAGATTGAAGCCGCAACAGCGAATCTTATACCCT
1 GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCT
75094 GAAGATGAGG
Statistics
Matches: 508, Mismatches: 75, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
89 1 0.00
90 261 0.51
91 1 0.00
92 2 0.00
96 2 0.00
97 3 0.01
98 229 0.45
99 2 0.00
100 4 0.01
102 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (90 bp):
GGGAAAGATTGAAGCCGCAACGGCGAATCTTATACCCTAAAGGGAAAGGTTGAAGTCGCAACGGT
GAACCTTATACCTTAGAGATGTGAT
Found at i:74610 original size:221 final size:220
Alignment explanation
Indices: 74220--74637 Score: 568
Period size: 221 Copynumber: 1.9 Consensus size: 220
74210 AGAAGTTATG
* * *
74220 AAAAGAAAGGTTGAAGTCGCAACGGCGAACCTCATGCCTTAAAGATGTGATAGGAAAGATTGAAG
1 AAAAGAAAGGTTGAAGCCGCAACAGCGAACCTCATACCTTAAAGATGTGATAGGAAAGATTGAAG
* ** *
74285 CAACAATAGCGAATCTTGTACCCTAAAGGAAAATTTTGACGCCGTAACGGCGAACCTTATACCTT
66 CAACAATAGCGAATATTGTACCCTAAAGGAAAAGGTTGAAGCCGTAACGGCGAACCTTATACCTT
* * *
74350 AGAGACGTGATGCAAAAGATTGAAGCCATAATAGCGAATCTTGTACCGTAGAGGGAAAGGTTGAA
131 AAAGACGTGATGCAAAAGATTGAAGCCAGAATAGCGAATCTTGTACCCTAGAGGGAAAGGTTGAA
74415 GCCGTAACGATGAATCTTATACCCT
196 GCCGTAACGATGAATCTTATACCCT
* * * * *
74440 AAAAGGAAAGGTTGAAGCCGCAACAGTGAACCTTATACCTTAGAGATGTGATGGGAAATATTGAA
1 AAAA-GAAAGGTTGAAGCCGCAACAGCGAACCTCATACCTTAAAGATGTGATAGGAAAGATTGAA
* * * * * * *
74505 GCCATAATGGTGAATATTGTACCCTAAAGGGAAAGGTTGAAGTCGTAACGGTGAACCTTATACCT
65 GCAACAATAGCGAATATTGTACCCTAAAGGAAAAGGTTGAAGCCGTAACGGCGAACCTTATACCT
* ** * *
74570 TAAAGATGTGATGGGAAAGATTGAAGCCGCGACT-GCGAATCTTGTACCCTAGAGGGAAAGGTTG
130 TAAAGACGTGATGCAAAAGATTGAAGCC-AGAATAGCGAATCTTGTACCCTAGAGGGAAAGGTTG
74634 AAGC
194 AAGC
74638 TGCAATGACA
Statistics
Matches: 169, Mismatches: 27, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
220 4 0.02
221 163 0.96
222 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.22
Consensus pattern (220 bp):
AAAAGAAAGGTTGAAGCCGCAACAGCGAACCTCATACCTTAAAGATGTGATAGGAAAGATTGAAG
CAACAATAGCGAATATTGTACCCTAAAGGAAAAGGTTGAAGCCGTAACGGCGAACCTTATACCTT
AAAGACGTGATGCAAAAGATTGAAGCCAGAATAGCGAATCTTGTACCCTAGAGGGAAAGGTTGAA
GCCGTAACGATGAATCTTATACCCT
Found at i:74819 original size:98 final size:98
Alignment explanation
Indices: 74709--75100 Score: 525
Period size: 98 Copynumber: 4.0 Consensus size: 98
74699 TCTTGTACCC
* * ** *
74709 TAGAGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAGATGTTATGGGAAAGATGGA
1 TAGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGA
* *
74774 AACCGTAACGGCGAATCTTATACCCTAAAGATG
66 AGCCGCAACGGCGAATCTTATACCCTAAAGATG
* * * *
74807 TAGAGGAAAAGGTTGAAGTCGCAACGGTGAACCTTACACCTTAGAGATGTGATAGGAAAGATTGA
1 TAGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGA
*
74872 GGCCGCAACGGCGAATCTTATACCC-AAGAGATG
66 AGCCGCAACGGCGAATCTTATACCCTAA-AGATG
* * ** * *
74905 TGGAGGGAAAGGTTGAAGTCGCAACGGAAAACCTTATACCTTAGATATGTTAAAGGAAAGATTGA
1 TAGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGA
* * * *
74970 AGCCACAACGGTGAATCTTATACCCTAGAGATA
66 AGCCGCAACGGCGAATCTTATACCCTAAAGATG
* * *
75003 TAGAGGGAAAGGTTGAAGCTGCAACGGCGAACCTTATACCTTAGAGATGTGAAGGGAAAGATTGA
1 TAGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGA
* *
75068 AGCCGCAACAGCGAATCTTATACCCTGAAGATG
66 AGCCGCAACGGCGAATCTTATACCCTAAAGATG
75101 AGGAGATTGA
Statistics
Matches: 255, Mismatches: 37, Indels: 4
0.86 0.12 0.01
Matches are distributed among these distances:
97 2 0.01
98 252 0.99
99 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (98 bp):
TAGAGGGAAAGGTTGAAGCCGCAACGGTGAACCTTATACCTTAGAGATGTGAAAGGAAAGATTGA
AGCCGCAACGGCGAATCTTATACCCTAAAGATG
Found at i:75100 original size:49 final size:49
Alignment explanation
Indices: 74712--75091 Score: 379
Period size: 49 Copynumber: 7.8 Consensus size: 49
74702 TGTACCCTAG
* * * *
74712 AGGGAAAGGTTGAAGCCACAACGGTGAACCTTATACCTTAGAGATGTTA
1 AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* * * * * * *
74761 TGGGAAAGATGGAAACCGTAACGGCGAATCTTATACCCTAAAGATGT-A
1 AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* * * * *
74809 GAGGAAAAGGTTGAAGTCGCAACGGTGAACCTTACACCTTAGAGATGTGA
1 -AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* * ** *
74859 TA-GGAAAGATTGAGGCCGCAACGGCGAATCTTATACCCAAGAGATGTGG
1 -AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* * ** * *
74908 AGGGAAAGGTTGAAGTCGCAACGGAAAACCTTATACCTTAGATATGTTA
1 AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* * * * * *
74957 AAGGAAAGATTGAAGCCACAACGGTGAATCTTATACCCTAGAGATAT-A
1 AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* *
75005 GAGGGAAAGGTTGAAGCTGCAACGGCGAACCTTATACCTTAGAGATGTGA
1 -AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
* *
75055 AGGGAAAGATTGAAGCCGCAACAGCGAATCTTATACC
1 AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACC
75092 CTGAAGATGA
Statistics
Matches: 260, Mismatches: 66, Indels: 10
0.77 0.20 0.03
Matches are distributed among these distances:
48 3 0.01
49 254 0.98
50 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.21
Consensus pattern (49 bp):
AGGGAAAGATTGAAGCCGCAACGGCGAACCTTATACCTTAGAGATGTGA
Found at i:77249 original size:23 final size:26
Alignment explanation
Indices: 77208--77257 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 26
77198 AACTCTTTTA
77208 TTTTATTTTTGTTAAAATTTAA-CCC
1 TTTTATTTTTGTTAAAATTTAATCCC
77233 TTTTA-TTTT-TTAAAATTTAATCCC
1 TTTTATTTTTGTTAAAATTTAATCCC
77257 T
1 T
77258 CACTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 11 0.46
24 8 0.33
25 5 0.21
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTATTTTTGTTAAAATTTAATCCC
Found at i:82004 original size:6 final size:6
Alignment explanation
Indices: 81995--82019 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
81985 TAAATTAAAA
81995 TATATT TATATT TATATT TATATT T
1 TATATT TATATT TATATT TATATT T
82020 TAAAATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATATT
Found at i:83154 original size:14 final size:14
Alignment explanation
Indices: 83132--83164 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
83122 GTGACTATTT
83132 TTTTA-TTTTACCC
1 TTTTATTTTTACCC
*
83145 TTTTATTTTTACCT
1 TTTTATTTTTACCC
83159 TTTTAT
1 TTTTAT
83165 CTAAGTTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTATTTTTACCC
Found at i:85389 original size:4 final size:4
Alignment explanation
Indices: 85382--85416 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
85372 AAATAATGTA
85382 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
85417 GCTACTATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:98812 original size:34 final size:34
Alignment explanation
Indices: 98769--98845 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
98759 CCGTATAACC
98769 TTCTACTTCGTTCCCACCTCATCAATCAATTACA
1 TTCTACTTCGTTCCCACCTCATCAATCAATTACA
98803 TTCTACTTCGTTCCCACCTCATCAATCAATTACA
1 TTCTACTTCGTTCCCACCTCATCAATCAATTACA
98837 TTCTACTTC
1 TTCTACTTC
98846 ATATACATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.25, C:0.35, G:0.03, T:0.38
Consensus pattern (34 bp):
TTCTACTTCGTTCCCACCTCATCAATCAATTACA
Found at i:98971 original size:31 final size:33
Alignment explanation
Indices: 98916--98981 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 33
98906 GTTTTAATAG
*
98916 TTTATAATTTTTTTAAAAGGTTAAA-T-TAATTT
1 TTTATAA-TTTTTTAAAAGATTAAAGTGTAATTT
98948 TTTATAA-TTTTTAAAGAGATTAAAGTGTAATTT
1 TTTATAATTTTTTAAA-AGATTAAAGTGTAATTT
98981 T
1 T
98982 ATTTTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 8 0.27
31 7 0.23
32 8 0.27
33 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (33 bp):
TTTATAATTTTTTAAAAGATTAAAGTGTAATTT
Found at i:99173 original size:31 final size:30
Alignment explanation
Indices: 99138--99217 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 30
99128 TTTTGGATCT
99138 TTAAAAGTCGAAAAAAATATTTTTAGACCCC
1 TTAAAAGTCGAAAAAAATATTTTTA-ACCCC
* * *
99169 TTAAAAGTTGGTAAAAAATATTTTTAAGCCC
1 TTAAAAG-TCGAAAAAAATATTTTTAACCCC
99200 TTAAAAG-CTGAAAAAAAT
1 TTAAAAGTC-GAAAAAAAT
99218 TTACCGCTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
30 8 0.19
31 18 0.43
32 16 0.38
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (30 bp):
TTAAAAGTCGAAAAAAATATTTTTAACCCC
Found at i:99544 original size:26 final size:26
Alignment explanation
Indices: 99493--99544 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
99483 ATCATAGTGG
* * * *
99493 TTGATTTGATCAATTAATTTTGTTAA
1 TTGATTTAATCAACTAATTCTATTAA
99519 TTGATTTAATCAACTAATTCTATTAA
1 TTGATTTAATCAACTAATTCTATTAA
99545 GTGTTTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (26 bp):
TTGATTTAATCAACTAATTCTATTAA
Found at i:102973 original size:21 final size:21
Alignment explanation
Indices: 102949--102992 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
102939 TGTTTAAAGG
102949 GTTTGGAAATGAAATTGAATT
1 GTTTGGAAATGAAATTGAATT
102970 GTTTGGAAATGAAATTGAATT
1 GTTTGGAAATGAAATTGAATT
102991 GT
1 GT
102993 AAGTAGTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (21 bp):
GTTTGGAAATGAAATTGAATT
Found at i:105420 original size:4 final size:4
Alignment explanation
Indices: 105407--105451 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
105397 AACGGGCACC
*
105407 AAAG -AAG AAAG AAAG AAAG AAGG AAA- AAA- AAAG AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
105452 TAGGAAGAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
3 9 0.24
4 28 0.76
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:105761 original size:12 final size:12
Alignment explanation
Indices: 105740--105791 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
105730 AATTAATAAT
*
105740 TTTCTCTCCTTC
1 TTTCTTTCCTTC
105752 TTTCTTTCCTCTC
1 TTTCTTTCCT-TC
* *
105765 TTTTTTTCATTC
1 TTTCTTTCCTTC
* *
105777 TTTTTTTCTTTC
1 TTTCTTTCCTTC
105789 TTT
1 TTT
105792 TCTGTGTCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
12 25 0.71
13 10 0.29
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTCTTTCCTTC
Found at i:105792 original size:12 final size:12
Alignment explanation
Indices: 105749--105792 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
105739 TTTTCTCTCC
*
105749 TTCTTTCTTTCCT
1 TTCTTT-TTTTCT
* *
105762 CTCTTTTTTTCA
1 TTCTTTTTTTCT
105774 TTCTTTTTTTCT
1 TTCTTTTTTTCT
105786 TTCTTTT
1 TTCTTTT
105793 CTGTGTCCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (12 bp):
TTCTTTTTTTCT
Found at i:108384 original size:10 final size:10
Alignment explanation
Indices: 108371--108523 Score: 58
Period size: 10 Copynumber: 15.8 Consensus size: 10
108361 CTTTATAAAA
108371 TTTTATAATT
1 TTTTATAATT
*
108381 TTTTCTATATT
1 TTTTATA-ATT
108392 TTTCTAT-A--
1 TTT-TATAATT
108400 TTTTATAA-T
1 TTTTATAATT
*
108409 TTTTACGAA-T
1 TTTTA-TAATT
*
108419 ATTTATAATT
1 TTTTATAATT
*
108429 TTTT-TCTATT
1 TTTTAT-AATT
* **
108439 TTTAATAAAA
1 TTTTATAATT
108449 TTTTATAATT
1 TTTTATAATT
108459 TTTCTAT-A-T
1 TTT-TATAATT
* *
108468 TTCTAT-ATA
1 TTTTATAATT
108477 TTTTATAA-T
1 TTTTATAATT
*
108486 TTTTACAGA-T
1 TTTTATA-ATT
*
108496 ATTTATAATT
1 TTTTATAATT
*
108506 TTTTCTAATT
1 TTTTATAATT
*
108516 TTTAATAA
1 TTTTATAA
108524 AATTTAAATA
Statistics
Matches: 105, Mismatches: 25, Indels: 26
0.67 0.16 0.17
Matches are distributed among these distances:
7 3 0.03
8 8 0.08
9 23 0.22
10 59 0.56
11 10 0.10
12 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTTATAATT
Found at i:108405 original size:39 final size:39
Alignment explanation
Indices: 108362--108484 Score: 128
Period size: 39 Copynumber: 3.2 Consensus size: 39
108352 TTCTTACGAC
108362 TTTATAAAATTTTATAATTTTTTCTATATTTTTCTATAT
1 TTTATAAAATTTTATAATTTTTTCTATATTTTTCTATAT
* * * * *
108401 TTTAT-AATTTTTACGAATATTTAT-AATTTTTTTCTAT-T
1 TTTATAAAATTTTA-TAAT-TTTTTCTATATTTTTCTATAT
* *
108439 TTTAATAAAATTTTATAA-TTTTTCTATATTTCTATATAT
1 TTT-ATAAAATTTTATAATTTTTTCTATATTTTTCTATAT
108478 TTTATAA
1 TTTATAA
108485 TTTTTACAGA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
37 4 0.06
38 24 0.36
39 27 0.41
40 11 0.17
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (39 bp):
TTTATAAAATTTTATAATTTTTTCTATATTTTTCTATAT
Found at i:108442 original size:19 final size:18
Alignment explanation
Indices: 108390--108519 Score: 64
Period size: 19 Copynumber: 6.8 Consensus size: 18
108380 TTTTTCTATA
108390 TTTTTCTATATTTTATAAT
1 TTTTTCTAT-TTTTATAAT
* * *
108409 TTTTACGAATATTTATAATT
1 TTTTTC-TATTTTTATAA-T
*
108429 TTTTTCTATTTTTAATAAA
1 TTTTTCTATTTTT-ATAAT
* * *
108448 ATTTTATAATTTTTCT-AT
1 TTTTTCT-ATTTTTATAAT
* *
108466 ATTTCTATATATTTTATAAT
1 -TTTTTCTAT-TTTTATAAT
* * *
108486 TTTTACAGATATTTATAAT
1 TTTTTC-TATTTTTATAAT
108505 TTTTTCTAATTTTTA
1 TTTTTCT-ATTTTTA
108520 ATAAAATTTA
Statistics
Matches: 80, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
18 3 0.04
19 55 0.69
20 22 0.28
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTTCTATTTTTATAAT
Found at i:108461 original size:28 final size:28
Alignment explanation
Indices: 108420--108489 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
108410 TTTACGAATA
* * *
108420 TTTATAATTTTTTTCTATTTTTAATAAAAT
1 TTTATAATTTTTCTATATTTCT-AT-AAAT
*
108450 TTTATAATTTTTCTATATTTCTATATAT
1 TTTATAATTTTTCTATATTTCTATAAAT
108478 TTTATAATTTTT
1 TTTATAATTTTT
108490 ACAGATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 15 0.42
29 2 0.06
30 19 0.53
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTATAATTTTTCTATATTTCTATAAAT
Found at i:108477 original size:77 final size:78
Alignment explanation
Indices: 108365--108528 Score: 271
Period size: 77 Copynumber: 2.1 Consensus size: 78
108355 TTACGACTTT
* *
108365 ATAAAATTTTATAATTTTTTCTATATTTTTCTATATTTTATAATTTTTAC-GAATATTTATAATT
1 ATAAAATTTTATAATTTTTTCTATATTTCTATATATTTTATAATTTTTACAG-ATATTTATAA-T
108429 TTTTTCT-ATTTTTA
64 TTTTTCTAATTTTTA
108443 ATAAAATTTTATAA-TTTTTCTATATTTCTATATATTTTATAATTTTTACAGATATTTATAATTT
1 ATAAAATTTTATAATTTTTTCTATATTTCTATATATTTTATAATTTTTACAGATATTTATAATTT
108507 TTTCTAATTTTTA
66 TTTCTAATTTTTA
108520 ATAAAATTT
1 ATAAAATTT
108529 AAATATTTTT
Statistics
Matches: 82, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
76 8 0.10
77 59 0.72
78 15 0.18
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (78 bp):
ATAAAATTTTATAATTTTTTCTATATTTCTATATATTTTATAATTTTTACAGATATTTATAATTT
TTTCTAATTTTTA
Found at i:108502 original size:28 final size:30
Alignment explanation
Indices: 108443--108519 Score: 81
Period size: 29 Copynumber: 2.7 Consensus size: 30
108433 TCTATTTTTA
* *
108443 ATAAAATTTTATAATTTTT-CTATATTTCT
1 ATAATATTTTATAATTTTTACGATATTTCT
108472 AT-ATATTTTATAATTTTTACAGATA-TT-T
1 ATAATATTTTATAATTTTTAC-GATATTTCT
* *
108500 ATAATTTTTTCTAATTTTTA
1 ATAATATTTTATAATTTTTA
108520 ATAAAATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
28 18 0.44
29 20 0.49
30 3 0.07
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (30 bp):
ATAATATTTTATAATTTTTACGATATTTCT
Found at i:115396 original size:2 final size:2
Alignment explanation
Indices: 115389--115432 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
115379 ATTCACAAAG
115389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
115431 AT
1 AT
115433 TAATCCTCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:121122 original size:21 final size:21
Alignment explanation
Indices: 121096--121172 Score: 77
Period size: 21 Copynumber: 3.7 Consensus size: 21
121086 GAAATTTTTA
*
121096 GTATCGGTAGAAG-CATGACTT
1 GTATCGGTAGAAGTC-TCACTT
*
121117 GTATCGGTAGATGTCTCACTT
1 GTATCGGTAGAAGTCTCACTT
* *
121138 GTATCGGTAGAACTGTCA-TAT
1 GTATCGGTAGAAGTCTCACT-T
*
121159 GTATCAGTAGAAGT
1 GTATCGGTAGAAGT
121173 TTGCACTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 1 0.02
21 45 0.96
22 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGTCTCACTT
Found at i:123615 original size:50 final size:50
Alignment explanation
Indices: 123556--123668 Score: 190
Period size: 50 Copynumber: 2.3 Consensus size: 50
123546 TTATGTACTT
* * *
123556 GTATCGGTAGAAGATGCAGGGTAGGGCTTCTTAGCTCTTTGGAGTTTTTA
1 GTATCGGTAGAAGATGCAGGGTAGGACTTCTTAGCTCTTTGAAGTTTTGA
*
123606 GTATCGGTAGAAGATGCAGTGTAGGACTTCTTAGCTCTTTGAAGTTTTGA
1 GTATCGGTAGAAGATGCAGGGTAGGACTTCTTAGCTCTTTGAAGTTTTGA
123656 GTATCGGTAGAAG
1 GTATCGGTAGAAG
123669 CATGACTTGT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 59 1.00
ACGTcount: A:0.23, C:0.12, G:0.31, T:0.35
Consensus pattern (50 bp):
GTATCGGTAGAAGATGCAGGGTAGGACTTCTTAGCTCTTTGAAGTTTTGA
Found at i:124792 original size:72 final size:72
Alignment explanation
Indices: 124675--124821 Score: 285
Period size: 72 Copynumber: 2.0 Consensus size: 72
124665 TCTAAGGCTA
*
124675 TTAACATCCTTCTATTAACATTATTACAATCACATCCCATTATTTAATTCTAGATCATCAGGTAT
1 TTAACATCCTTCTATTAACATTATTACAATCACATCCCATAATTTAATTCTAGATCATCAGGTAT
124740 ACTTAGC
66 ACTTAGC
124747 TTAACATCCTTCTATTAACATTATTACAATCACATCCCATAATTTAATTCTAGATCATCAGGTAT
1 TTAACATCCTTCTATTAACATTATTACAATCACATCCCATAATTTAATTCTAGATCATCAGGTAT
124812 ACTTAGC
66 ACTTAGC
124819 TTA
1 TTA
124822 GCAATTCAAC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (72 bp):
TTAACATCCTTCTATTAACATTATTACAATCACATCCCATAATTTAATTCTAGATCATCAGGTAT
ACTTAGC
Found at i:125736 original size:24 final size:24
Alignment explanation
Indices: 125704--125808 Score: 129
Period size: 24 Copynumber: 4.3 Consensus size: 24
125694 AGATGTAAGC
* *
125704 TCTTCCATTAAACAAATCATCAAG
1 TCTTCCATTAAAGAAATCACCAAG
* *
125728 TCTTCCATTAGAGATATCACCAAG
1 TCTTCCATTAAAGAAATCACCAAG
* *
125752 TCTTCCATTAAAGATAATTATCAAG
1 TCTTCCATTAAAGA-AATCACCAAG
**
125777 TCTTCCATTAAAGATGTCACCAAG
1 TCTTCCATTAAAGAAATCACCAAG
125801 TCTTCCAT
1 TCTTCCAT
125809 ATCATATAGT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 47 0.69
25 21 0.31
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (24 bp):
TCTTCCATTAAAGAAATCACCAAG
Found at i:125782 original size:49 final size:48
Alignment explanation
Indices: 125704--125808 Score: 165
Period size: 49 Copynumber: 2.2 Consensus size: 48
125694 AGATGTAAGC
*
125704 TCTTCCATTAAACAAATCATCAAGTCTTCCATTAGAGATATCACCAAG
1 TCTTCCATTAAACAAATCATCAAGTCTTCCATTAAAGATATCACCAAG
* * *
125752 TCTTCCATTAAAGATAATTATCAAGTCTTCCATTAAAGATGTCACCAAG
1 TCTTCCATTAAACA-AATCATCAAGTCTTCCATTAAAGATATCACCAAG
125801 TCTTCCAT
1 TCTTCCAT
125809 ATCATATAGT
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 13 0.25
49 39 0.75
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (48 bp):
TCTTCCATTAAACAAATCATCAAGTCTTCCATTAAAGATATCACCAAG
Found at i:131183 original size:19 final size:19
Alignment explanation
Indices: 131159--131208 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
131149 CAAGCTGACT
* * *
131159 CGAACCGTGTGAGCCGACC
1 CGAACCATGTGACCCAACC
131178 CGAACCATGTGACCCAACC
1 CGAACCATGTGACCCAACC
*
131197 CGAGCCAT-TGAC
1 CGAACCATGTGAC
131209 TTTGACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.26, C:0.38, G:0.24, T:0.12
Consensus pattern (19 bp):
CGAACCATGTGACCCAACC
Found at i:137895 original size:94 final size:94
Alignment explanation
Indices: 137734--137920 Score: 356
Period size: 94 Copynumber: 2.0 Consensus size: 94
137724 AAGTAATAAT
*
137734 GTATATCTACTAGTTTATTAAAATATCTTAACCAAATCCATAGATGTATGCAAAAAGGTATATCC
1 GTATATCTACTAGTTTATTAAAATATCTTAACCAAATCCATAGATGTATGCAAAAAGGTATAACC
137799 TAAAATAGAAAAGTCCCAAATTTAAATTG
66 TAAAATAGAAAAGTCCCAAATTTAAATTG
137828 GTATATCTACTAGTTTATTAAAATATCTTAACCAAATCCATAGATGTATGCAAAAAGGTATAACC
1 GTATATCTACTAGTTTATTAAAATATCTTAACCAAATCCATAGATGTATGCAAAAAGGTATAACC
*
137893 TAAAATAGCAAAGTCCCAAATTTAAATT
66 TAAAATAGAAAAGTCCCAAATTTAAATT
137921 TACACCACAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 91 1.00
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (94 bp):
GTATATCTACTAGTTTATTAAAATATCTTAACCAAATCCATAGATGTATGCAAAAAGGTATAACC
TAAAATAGAAAAGTCCCAAATTTAAATTG
Found at i:144218 original size:30 final size:29
Alignment explanation
Indices: 144159--144274 Score: 76
Period size: 30 Copynumber: 4.0 Consensus size: 29
144149 TAGTTTCGAG
* *
144159 AAAATTCGTGGTTAAAAAAGTGG-AA-TTTA
1 AAAATTCGAGGGT-AAAAA-TGGTAATTTTA
144188 AAACATTCGAGGGTAAAAATGGTAATTTTA
1 AAA-ATTCGAGGGTAAAAATGGTAATTTTA
** * * * *
144218 AGAGTTTCGAGGTTAAAAATGGGATTTTTG
1 A-AAATTCGAGGGTAAAAATGGTAATTTTA
* * *
144248 GAAGTTCGGGGGT-AAAATGGTAATTTT
1 AAAATTCGAGGGTAAAAATGGTAATTTT
144275 TTGAAGGTTC
Statistics
Matches: 68, Mismatches: 15, Indels: 9
0.74 0.16 0.10
Matches are distributed among these distances:
28 15 0.22
29 18 0.26
30 34 0.50
31 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATTCGAGGGTAAAAATGGTAATTTTA
Found at i:144255 original size:29 final size:28
Alignment explanation
Indices: 144193--144748 Score: 427
Period size: 29 Copynumber: 19.0 Consensus size: 28
144183 ATTTAAAACA
**
144193 TTCGAGGGTAAAAATGGTAATTTTAAG-AG
1 TTCGAGGGT-AAAATGG-AATTTTTGGAAG
* *
144222 TTTCGAGGTTAAAAATGGGATTTTTGGAAG
1 -TTCGAGGGT-AAAATGGAATTTTTGGAAG
* *
144252 TTCGGGGGTAAAATGGTAATTTTTTGAAGG
1 TTCGAGGGTAAAATGG-AATTTTTGGAA-G
144282 TTC-AGGGTCAAAAATGGAATTTTTGGAAG
1 TTCGAGGGT--AAAATGGAATTTTTGGAAG
144311 TTC-ACGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGA-GGGTAAAATGG-AATTTTTGGAA-G
* *
144341 TTCG-GGGTAAAAAATGGGATTTTTGGGAG
1 TTCGAGGGT--AAAATGGAATTTTTGGAAG
144370 TTCGAGGGTAAAATGGTAATTTTTGGAATG
1 TTCGAGGGTAAAATGG-AATTTTTGGAA-G
* * *
144400 GTC-AAGGTCAATAATGGGATTTTTGGAAG
1 TTCGAGGGT-AA-AATGGAATTTTTGGAAG
*
144429 TTCGGGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGGTAAAATGG-AATTTTTGGAA-G
* **
144459 TTCGAGGTTAAAAATGGGTTTTTTGGAAG
1 TTCGAGGGT-AAAATGGAATTTTTGGAAG
* *
144488 TTCGGGGGTAAATTGGTAATTTTTGGAAGG
1 TTCGAGGGTAAAATGG-AATTTTTGGAA-G
* *
144518 TTCG-GGGTCAAAAAT-AAGATTTTTGGGAG
1 TTCGAGGGT--AAAATGGA-ATTTTTGGAAG
*
144547 TT-TAGGGGTAAAATGGTAATTTTTGGAAG
1 TTCGA-GGGTAAAATGG-AATTTTTGGAAG
*
144576 TTCG-GGGTCAAAATGGGATTTTTGGAAG
1 TTCGAGGGT-AAAATGGAATTTTTGGAAG
144604 TTCGAGGGTAAAATGGTAATTTTTGGAAGG
1 TTCGAGGGTAAAATGG-AATTTTTGGAA-G
* *
144634 TTCGAGGTTAAAAATGGGATTTTTGGAAG
1 TTCGAGGGT-AAAATGGAATTTTTGGAAG
*
144663 TTCGGGGGTAAAATGGTAA-TTTTGGAAGG
1 TTCGAGGGTAAAATGG-AATTTTTGGAA-G
* * *
144692 TT-TAAGGTCAAAAATGGGATTTTTGGAAG
1 TTCGAGGGT--AAAATGGAATTTTTGGAAG
* *
144721 TT-TAGGGGT-AAATGGTAATTTTTTGAAG
1 TTCGA-GGGTAAAATGG-AATTTTTGGAAG
144749 GTTTAGGGAC
Statistics
Matches: 433, Mismatches: 51, Indels: 86
0.76 0.09 0.15
Matches are distributed among these distances:
27 6 0.01
28 91 0.21
29 155 0.36
30 144 0.33
31 37 0.09
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.34
Consensus pattern (28 bp):
TTCGAGGGTAAAATGGAATTTTTGGAAG
Found at i:144261 original size:59 final size:59
Alignment explanation
Indices: 144193--144751 Score: 754
Period size: 59 Copynumber: 9.5 Consensus size: 59
144183 ATTTAAAACA
* ** * *
144193 TTCGAGGGTAAAAATGGTAATTTTAAG-AGTTTCGAGGTTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGT-AAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
* *
144252 TTCGGGGGTAAAATGGTAATTTTTTGAAGGTTC-AGGGTCAAAAATGGAATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGA-GGTCAAAAATGGGATTTTTGGAAG
** * * *
144311 TTCACGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTAAAAAATGGGATTTTTGGGAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
* * *
144370 TTCGAGGGTAAAATGGTAATTTTTGGAATGG-TCAAGGTCAATAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAA-GGTTCGAGGTCAAAAATGGGATTTTTGGAAG
* *
144429 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGTTTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
* * ** *
144488 TTCGGGGGTAAATTGGTAATTTTTGGAAGGTTCGGGGTCAAAAATAAGATTTTTGGGAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
** *
144547 TTTAGGGGTAAAATGGTAATTTTTGGAA-GTTCGGGGTC-AAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
* *
144604 TTCGAGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTTAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
**
144663 TTCGGGGGTAAAATGGTAA-TTTTGGAAGGTTTAAGGTCAAAAATGGGATTTTTGGAAG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
** *
144721 TTTAGGGGT-AAATGGTAATTTTTTGAAGGTT
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTT
144752 TAGGGACCTT
Statistics
Matches: 442, Mismatches: 50, Indels: 17
0.87 0.10 0.03
Matches are distributed among these distances:
57 50 0.11
58 90 0.20
59 300 0.68
60 2 0.00
ACGTcount: A:0.30, C:0.04, G:0.32, T:0.35
Consensus pattern (59 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAG
Found at i:146581 original size:17 final size:16
Alignment explanation
Indices: 146559--146618 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 16
146549 TAATAAATTT
146559 TAAATTTAAATTTATAA
1 TAAATTTAAATTTA-AA
*
146576 TAAATTTAAATTTCAAC
1 TAAATTTAAATTT-AAA
* *
146593 CAAATTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
146610 TAAATTTAA
1 TAAATTTAA
146619 GCTGATTGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
17 35 0.97
18 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:146893 original size:17 final size:19
Alignment explanation
Indices: 146857--146894 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
146847 AATAACGTTA
146857 ATAATTTATTAATGAATTTT
1 ATAATTTATTAA-GAATTTT
146877 ATAATTT-TTAA-AATTTT
1 ATAATTTATTAAGAATTTT
146894 A
1 A
146895 AATATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
ATAATTTATTAAGAATTTT
Found at i:148532 original size:24 final size:24
Alignment explanation
Indices: 148498--148572 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
148488 ACTGACAACT
*
148498 TTAGCTCTTACTAGCCCAGAATGG
1 TTAGCTCTTACAAGCCCAGAATGG
* *
148522 TTAGCTTTTACGAA-CCCAAAATGG
1 TTAGCTCTTAC-AAGCCCAGAATGG
148546 TTAGCTCTTACAAGCCCAGAATGG
1 TTAGCTCTTACAAGCCCAGAATGG
148570 TTA
1 TTA
148573 ACCAATATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
23 2 0.05
24 41 0.93
25 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (24 bp):
TTAGCTCTTACAAGCCCAGAATGG
Found at i:171132 original size:18 final size:18
Alignment explanation
Indices: 171109--171151 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
171099 GAATAGATTT
171109 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
171127 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
171145 TTAATTA
1 TTAATTA
171152 CACCTTGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:172448 original size:12 final size:13
Alignment explanation
Indices: 172431--172460 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
172421 CATATTTAAT
172431 ATTTACGGACTC-
1 ATTTACGGACTCG
172443 ATTTACGGACTCG
1 ATTTACGGACTCG
172456 ATTTA
1 ATTTA
172461 TGAAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (13 bp):
ATTTACGGACTCG
Found at i:175962 original size:5 final size:6
Alignment explanation
Indices: 175901--175960 Score: 75
Period size: 6 Copynumber: 9.5 Consensus size: 6
175891 AATGCATAAT
* *
175901 AAAATA AAAATA AAAATA AAAATA AAAATG AAAATG AAAATGAA ATAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT--A A-AAATA
175952 AAAATA AAA
1 AAAATA AAA
175961 TATAGAACTA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
6 42 0.86
7 2 0.04
8 1 0.02
9 4 0.08
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:176311 original size:10 final size:10
Alignment explanation
Indices: 176296--176331 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
176286 ATATACTATT
176296 TTTTTTTGAA
1 TTTTTTTGAA
*
176306 TTTTTTT-AT
1 TTTTTTTGAA
176315 TTTTTTTGAA
1 TTTTTTTGAA
176325 TTTTTTT
1 TTTTTTT
176332 AAGATGACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:176311 original size:11 final size:11
Alignment explanation
Indices: 176295--176331 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
176285 AATATACTAT
176295 TTTTTTTTGAA
1 TTTTTTTTGAA
176306 -TTTTTTT--A
1 TTTTTTTTGAA
176314 TTTTTTTTGAA
1 TTTTTTTTGAA
176325 TTTTTTT
1 TTTTTTT
176332 AAGATGACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 1 0.04
9 7 0.30
10 7 0.30
11 8 0.35
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:176319 original size:19 final size:19
Alignment explanation
Indices: 176295--176332 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
176285 AATATACTAT
176295 TTTTTTTTGAATTTTTTTA
1 TTTTTTTTGAATTTTTTTA
176314 TTTTTTTTGAATTTTTTTA
1 TTTTTTTTGAATTTTTTTA
176333 AGATGACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.79
Consensus pattern (19 bp):
TTTTTTTTGAATTTTTTTA
Found at i:180127 original size:40 final size:40
Alignment explanation
Indices: 180072--180158 Score: 165
Period size: 40 Copynumber: 2.2 Consensus size: 40
180062 TCTAATGGTA
180072 TATGAATTATTAGCATAAAAATTATTATATAGGTACATAG
1 TATGAATTATTAGCATAAAAATTATTATATAGGTACATAG
*
180112 TATGAATTATTAGCATAAAAATTGTTATATAGGTACATAG
1 TATGAATTATTAGCATAAAAATTATTATATAGGTACATAG
180152 TATGAAT
1 TATGAAT
180159 ATATACAATG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.38
Consensus pattern (40 bp):
TATGAATTATTAGCATAAAAATTATTATATAGGTACATAG
Found at i:190096 original size:14 final size:14
Alignment explanation
Indices: 190077--190105 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
190067 AATAACCTCT
190077 CTTCCACACAACTA
1 CTTCCACACAACTA
190091 CTTCCACACAACTA
1 CTTCCACACAACTA
190105 C
1 C
190106 CCTAGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (14 bp):
CTTCCACACAACTA
Found at i:192914 original size:17 final size:19
Alignment explanation
Indices: 192875--192913 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
192865 TCTTATGCGG
192875 TTGAATTTTATTACTAAATT
1 TTGAATTTTATTAC-AAATT
192895 TTGAATTTTATTA-AAATT
1 TTGAATTTTATTACAAATT
192913 T
1 T
192914 GCCACCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (19 bp):
TTGAATTTTATTACAAATT
Found at i:193256 original size:12 final size:12
Alignment explanation
Indices: 193239--193272 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
193229 TTTTTGAATT
193239 AAAATTTAATAA
1 AAAATTTAATAA
193251 AAAATTTTAATAA
1 AAAA-TTTAATAA
*
193264 AAATTTTAA
1 AAAATTTAA
193273 CTTTAGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTTAATAA
Found at i:193261 original size:13 final size:12
Alignment explanation
Indices: 193239--193272 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
193229 TTTTTGAATT
193239 AAAA-TTTAATAA
1 AAAATTTTAAT-A
193251 AAAATTTTAATA
1 AAAATTTTAATA
193263 AAAATTTTAA
1 AAAATTTTAA
193273 CTTTAGTAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTTTAATA
Found at i:199426 original size:41 final size:41
Alignment explanation
Indices: 199364--199455 Score: 157
Period size: 41 Copynumber: 2.2 Consensus size: 41
199354 TTTATTTTAT
* *
199364 CAAGAATTCTAGTCACTCAATTCTAATAATCTCCACCTTAA
1 CAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTAA
*
199405 CAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTGA
1 CAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTAA
199446 CAAGAATTCT
1 CAAGAATTCT
199456 CTACGAACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.36, C:0.28, G:0.07, T:0.29
Consensus pattern (41 bp):
CAAGAATTCTAGTCACCCAATTCTAACAATCTCCACCTTAA
Found at i:203154 original size:28 final size:31
Alignment explanation
Indices: 203105--203174 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 31
203095 AATATACAAT
203105 AAAAAAATGACAAAAATAACAAA-C-AATATA
1 AAAAAAAT-ACAAAAATAACAAATCGAATATA
*
203135 AAAAAAATA-AATAAAT-ACAAATCGAATGTA
1 AAAAAAATACAA-AAATAACAAATCGAATATA
203165 AAAATAAATA
1 AAAA-AAATA
203175 GAGTGAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
28 7 0.20
29 6 0.17
30 17 0.49
31 5 0.14
ACGTcount: A:0.71, C:0.07, G:0.04, T:0.17
Consensus pattern (31 bp):
AAAAAAATACAAAAATAACAAATCGAATATA
Found at i:203255 original size:20 final size:19
Alignment explanation
Indices: 203213--203256 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
203203 AATATTAAAT
*
203213 TAAAAAGATATAAAAGGAC
1 TAAAAAGATATAAAAGGAA
203232 TAAAAA-ATATAAAAGCAGAA
1 TAAAAAGATATAAAAG--GAA
203252 TAAAA
1 TAAAA
203257 GCGTAACTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 9 0.41
19 6 0.27
20 7 0.32
ACGTcount: A:0.68, C:0.05, G:0.11, T:0.16
Consensus pattern (19 bp):
TAAAAAGATATAAAAGGAA
Found at i:203307 original size:31 final size:30
Alignment explanation
Indices: 203264--203386 Score: 103
Period size: 31 Copynumber: 4.0 Consensus size: 30
203254 AAAGCGTAAC
203264 TTTAAAAGAAATAAAAATAAAAAGG-TTAAAT
1 TTTAAAA-AAATAAAAAT-AAAAGGATTAAAT
*
203295 TTTAACAAAAATAAAAATAAAAGGATTTAA-
1 TTTAA-AAAAATAAAAATAAAAGGATTAAAT
* * *
203325 TTTAAAAAAA-AATAAATAAATGG-GTAAAA
1 TTTAAAAAAATAA-AAATAAAAGGATTAAAT
*
203354 TTTAAAAGGGAAA-AATAATAAAAGGATTAAAT
1 TTTAAAA---AAATAAAAATAAAAGGATTAAAT
203386 T
1 T
203387 CAAGTTGAAA
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
28 5 0.07
29 21 0.28
30 11 0.14
31 27 0.36
32 12 0.16
ACGTcount: A:0.63, C:0.01, G:0.11, T:0.26
Consensus pattern (30 bp):
TTTAAAAAAATAAAAATAAAAGGATTAAAT
Found at i:203377 original size:16 final size:16
Alignment explanation
Indices: 203332--203378 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
203322 TAATTTAAAA
*
203332 AAAAATAAATAAATGGG
1 AAAAAT-AATAAAAGGG
* *
203349 TAAAAT-TTAAAAGGG
1 AAAAATAATAAAAGGG
203364 AAAAATAATAAAAGG
1 AAAAATAATAAAAGG
203379 ATTAAATTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
15 12 0.50
16 7 0.29
17 5 0.21
ACGTcount: A:0.64, C:0.00, G:0.17, T:0.19
Consensus pattern (16 bp):
AAAAATAATAAAAGGG
Found at i:204999 original size:47 final size:46
Alignment explanation
Indices: 204887--205024 Score: 118
Period size: 47 Copynumber: 2.9 Consensus size: 46
204877 ATAAGATTTA
* * * * * *
204887 ATGTTATGACTTTAATCGGTCGCTCTGGATTTAGGGGTATATGATTTG
1 ATGTGATGACTTTAATCTGTC-CTCTAGATTT-GGGGTATAAGACTGG
* * *
204935 ATCTGGT-AGCTTCAATCTGCTCCTCTAGATTTGGGGTATAAGACTGG
1 ATGTGATGA-CTTTAATCTG-TCCTCTAGATTTGGGGTATAAGACTGG
*
204982 ATGTGATGACTTTAATCTGT-CTCTATGGATTTAGGGTATAAGA
1 ATGTGATGACTTTAATCTGTCCTCTA--GATTTGGGGTATAAGA
205025 TTGGTTGGAG
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
45 5 0.07
46 1 0.01
47 42 0.58
48 22 0.31
49 2 0.03
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.38
Consensus pattern (46 bp):
ATGTGATGACTTTAATCTGTCCTCTAGATTTGGGGTATAAGACTGG
Found at i:205082 original size:42 final size:41
Alignment explanation
Indices: 205036--205421 Score: 234
Period size: 40 Copynumber: 9.3 Consensus size: 41
205026 TGGTTGGAGG
* * *
205036 TTTCAATTTACCCACTAGTTGGGGTAAAAGATTAGATGGTC
1 TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
* * *
205077 TTTTCAATTTGCCCTCTAGTTAAGGTAAAAGATTGGTTGGTC
1 -TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
* * *
205119 -TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATT-GAATGATC
1 TTTCAATTTG-CCCTC-T-AGTTA-GGGTAAAAGATTAG-ATGGTC
*
205163 -TTCAATCTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
1 TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
* * * * * *
205203 -TTAAATCTGCCCATCATGACTTAGGGGTAAAAGACTGGATGATC
1 TTTCAATTTGCCC-TC-T-AGTTA-GGGTAAAAGATTAGATGGTC
* * * * * * * *
205247 -GTCAATTTGTCTTTTGGTTA-GGTAAAATATTGGATAGTC
1 TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
* * * **
205286 -TTCAATCTGCCCTTTAATTAGGGTAAAAGATTAGATAATC
1 TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
* * *
205326 -TTCAATTTGCCCCTCTTGACTTAGTGGTAAAAGATTGGATAGTC
1 TTTCAATTTG-CCCTC-T-AGTTAG-GGTAAAAGATTAGATGGTC
* * * * *
205370 TTT-AATATACCCTCTGGTTAGGGAAAAAGATTGGATGGTC
1 TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
*
205410 -TTCAATCTGCCC
1 TTTCAATTTGCCC
205422 ATCTTGACTT
Statistics
Matches: 275, Mismatches: 52, Indels: 36
0.76 0.14 0.10
Matches are distributed among these distances:
39 31 0.11
40 84 0.31
41 23 0.08
42 41 0.15
43 25 0.09
44 69 0.25
45 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (41 bp):
TTTCAATTTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTC
Found at i:205167 original size:84 final size:84
Alignment explanation
Indices: 205056--205496 Score: 382
Period size: 84 Copynumber: 5.2 Consensus size: 84
205046 CCCACTAGTT
* *
205056 GGGGTAAAAGATT-AGATGGTCTTTTCAATTTGCCCTCTAGTTAAGGTAAAAGATTGGTTGGTCT
1 GGGGTAAAAGATTGA-ATGATC--TTCAATTTGCCCTCTAGTTAAGGTAAAAGATTGGATGGTCT
205120 TCAATCTGCCCCTCTTGACTTA
63 TCAATCTGCCCCTCTTGACTTA
* * * *
205142 GGGGTAAAAGATTGAATGATCTTCAATCTGCCCTCTAGTTAGGGTAAAAGATTAGATGGTCTTAA
1 GGGGTAAAAGATTGAATGATCTTCAATTTGCCCTCTAGTTAAGGTAAAAGATTGGATGGTCTTCA
* *
205207 ATCTGCCCATCATGACTTA
66 ATCTGCCCCTCTTGACTTA
* * * * * * * * *
205226 GGGGTAAAAGACTGGATGATCGTCAATTTGTCTTTTGGTT-AGGTAAAATATTGGATAGTCTTCA
1 GGGGTAAAAGATTGAATGATCTTCAATTTGCCCTCTAGTTAAGGTAAAAGATTGGATGGTCTTCA
*
205290 ATCTG-CCCT-TT-AATTA
66 ATCTGCCCCTCTTGACTTA
* * * *
205306 -GGGTAAAAGATT-AGATAATCTTCAATTTGCCCCTCTTGACTTAGTGGTAAAAGATTGGATAGT
1 GGGGTAAAAGATTGA-ATGATCTTCAATTTG-CCCTC-T-AGTTA-AGGTAAAAGATTGGATGGT
* * * *
205369 CTTTAATAT-ACCCTC-TG-GTTA
61 CTTCAATCTGCCCCTCTTGACTTA
* * * * * *
205390 -GGGAAAAAGATTGGATGGTCTTCAATCTGCCCATCTTGACTTTAAGGTAAAAGTTTGGATGGTG
1 GGGGTAAAAGATTGAATGATCTTCAATTTGCCC-TC-T-A-GTTAAGGTAAAAGATTGGATGGT-
*
205454 ACTTCAATCTGCCCCTCTTGATTTA
61 -CTTCAATCTGCCCCTCTTGACTTA
205479 GGGGTAAAAGATTGAATG
1 GGGGTAAAAGATTGAATG
205497 GTGGCTGCAA
Statistics
Matches: 283, Mismatches: 53, Indels: 34
0.76 0.14 0.09
Matches are distributed among these distances:
79 24 0.08
80 6 0.02
81 2 0.01
82 5 0.02
83 27 0.10
84 165 0.58
85 3 0.01
86 25 0.09
87 6 0.02
88 2 0.01
89 3 0.01
90 15 0.05
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.34
Consensus pattern (84 bp):
GGGGTAAAAGATTGAATGATCTTCAATTTGCCCTCTAGTTAAGGTAAAAGATTGGATGGTCTTCA
ATCTGCCCCTCTTGACTTA
Found at i:205307 original size:123 final size:123
Alignment explanation
Indices: 205057--205489 Score: 365
Period size: 123 Copynumber: 3.4 Consensus size: 123
205047 CCACTAGTTG
* * * * * *
205057 GGGTAAAAGATTAGATGGTCTTTTCAATTTG-CCCTC-T-AGTTA-AGGTAAAAGATTGGTTGGT
1 GGGTAAAAGATTAGATGGTC--TTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGACTGGATAGT
* * * * * * *
205118 CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGATTGAATGATCTTCAATCTGCCCTCTAGTTA
64 CGTCAATAT-ACCCTC-TG-GTTA-GGGTAAAAGATTGGATG-TCTTCAATCTGCCCTTTAATTA
* * *
205183 GGGTAAAAGATTAGATGGTCTTAAATCTGCCCATCATGACTTAGGGGTAAAAGACTGGAT-GATC
1 GGGTAAAAGATTAGATGGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGACTGGATAG-TC
* ** * * *
205247 GTCAATTTGTCTTTTGGTTA-GGTAAAATATTGGATAGTCTTCAATCTGCCCTTTAATTA
65 GTCAATATACCCTCTGGTTAGGGTAAAAGATTGGAT-GTCTTCAATCTGCCCTTTAATTA
** * * * *
205306 GGGTAAAAGATTAGATAATCTTCAATTTGCCCCTCTTGACTTAGTGGTAAAAGATTGGATAGTCT
1 GGGTAAAAGATTAGATGGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGACTGGATAGTCG
* * *
205371 TTAATATACCCTCTGGTTAGGGAAAAAGATTGGATGGTCTTCAATCTGCCCATCTTGACTTTA
66 TCAATATACCCTCTGGTTAGGGTAAAAGATTGGAT-GTCTTCAATCTGCCC-T-TT-A-ATTA
* * * *
205434 AGGTAAAAGTTTGGATGGTGACTTCAATCTGCCCCTCTTGATTTAGGGGTAAAAGA
1 GGGTAAAAGATTAGATGGT--CTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGA
205490 TTGAATGGTG
Statistics
Matches: 248, Mismatches: 45, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
123 100 0.40
124 37 0.15
125 8 0.03
126 25 0.10
127 8 0.03
128 38 0.15
130 32 0.13
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (123 bp):
GGGTAAAAGATTAGATGGTCTTCAATCTGCCCCTCTTGACTTAGGGGTAAAAGACTGGATAGTCG
TCAATATACCCTCTGGTTAGGGTAAAAGATTGGATGTCTTCAATCTGCCCTTTAATTA
Found at i:205473 original size:46 final size:45
Alignment explanation
Indices: 205058--205541 Score: 258
Period size: 44 Copynumber: 11.3 Consensus size: 45
205048 CACTAGTTGG
* * *
205058 GGTAAAAGATTAGATGGT-CTTTTCAATTTGCCC-TC-T-AGTTA-A
1 GGTAAAAGATTGGATGGTGC--TTCAATCTGCCCATCTTGATTTAGA
* * * *
205100 GGTAAAAGATTGGTTGGT-CTTCAATCTGCCCCTCTTGACTTAGG
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
* * *
205144 GGTAAAAGATTGAATGAT-CTTCAATCTGCCC-TC-T-AGTTAG-
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
* * * * *
205184 GGTAAAAGATTAGATGGT-CTTAAATCTGCCCATCATGACTTAGG
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
* * * * * * *
205228 GGTAAAAGACTGGATGAT-CGTCAATTTG-TC-TTTTG-GTT--A
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
* * *
205267 GGTAAAATATTGGATAGT-CTTCAATCTGCCC-T-TT-AATTAG-
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
* ** * * * *
205307 GGTAAAAGATTAGATAAT-CTTCAATTTGCCCCTCTTGACTTAGT
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
* * * * *
205351 GGTAAAAGATTGGATAGT-CTTTAATATACCC-TC-TG-GTTAG-
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
*
205391 GGAAAAAGATTGGATGGT-CTTCAATCTGCCCATCTTGACTTTA-A
1 GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGA-TTTAGA
* * *
205435 GGTAAAAGTTTGGATGGTGACTTCAATCTGCCCCTCTTGATTTAGG
1 GGTAAAAGATTGGATGGTG-CTTCAATCTGCCCATCTTGATTTAGA
* * * * * * *
205481 GGTAAAAGATTGAATGGTGGCTGCAATCT-ACCACTTTTAACTTAGG
1 GGTAAAAGATTGGATGGT-GCTTCAATCTGCCCA-TCTTGATTTAGA
205527 GGTAAAAGATTGGAT
1 GGTAAAAGATTGGAT
205542 TTGGTGATGT
Statistics
Matches: 353, Mismatches: 63, Indels: 48
0.76 0.14 0.10
Matches are distributed among these distances:
39 26 0.07
40 93 0.26
41 18 0.05
42 29 0.08
43 19 0.05
44 95 0.27
45 6 0.02
46 66 0.19
47 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.34
Consensus pattern (45 bp):
GGTAAAAGATTGGATGGTGCTTCAATCTGCCCATCTTGATTTAGA
Found at i:205766 original size:99 final size:99
Alignment explanation
Indices: 205655--205891 Score: 271
Period size: 99 Copynumber: 2.4 Consensus size: 99
205645 GGTTTTGAAG
* * * * *
205655 CTTCACTCCATTCTACTGTAACCTCAGGGATATTAAGATATGCTTTTGGCTTTAATTTGACCTAC
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATATGCTTTTGGCTTTAATCTGACCCAC
** * *
205720 TGTAACTTC-GAGAGTATAGGATTTGGTGTTATAA
66 TACAACTTCAG-GAGTATAGGATTTAGTGCTATAA
* * * ** *
205754 CTTCACTCCATTCCACTATAACTTGAAAGACATTGAGATATGCTTTTGGCTTTAATCTGACCCAT
1 CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATATGCTTTTGGCTTTAATCTGACCCAC
* *
205819 TACAACTTCAGGGGTATAGGATTTAGTGCTGTAA
66 TACAACTTCAGGAGTATAGGATTTAGTGCTATAA
* *
205853 CTTCAAC-CTATTCCACCGTAACCTCAGGGACATTGAGAT
1 CTTC-ACTCCATTCCACTGTAACCTCAGGGACATTGAGAT
205892 CCGTTACATG
Statistics
Matches: 112, Mismatches: 24, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
99 109 0.97
100 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (99 bp):
CTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATATGCTTTTGGCTTTAATCTGACCCAC
TACAACTTCAGGAGTATAGGATTTAGTGCTATAA
Found at i:206413 original size:99 final size:99
Alignment explanation
Indices: 206216--206438 Score: 265
Period size: 99 Copynumber: 2.3 Consensus size: 99
206206 TCCACTGCAT
* ** *
206216 CTTCAAGGAGATAAGATTTTTTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGA
1 CTTCAAGGATATAAGATTTGGTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGA
*
206281 GATCTGCTTTTGGCTTTAATTCGACCAACTACAA
66 GATCTGCTTTTGACTTTAATTCGACCAACTACAA
* * * *
206315 CTTTAAGGGTGTAGGATTTGGTGTTGTAA-CTTCACTCCATTCCACTGTAACCTCAAGGACATTG
1 CTTCAAGGATATAAGATTTGGTGTTG-AAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTG
* * * *
206379 AGATCTG-TTACTT-ATTTTAA-TCTGATCTATTACAA
65 AGATCTGCTT--TTGACTTTAATTC-GACCAACTACAA
206414 CTTCAAGGATATAAGATTTGGTGTT
1 CTTCAAGGATATAAGATTTGGTGTT
206439 TCACTGGTCC
Statistics
Matches: 103, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
98 4 0.04
99 95 0.92
100 4 0.04
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (99 bp):
CTTCAAGGATATAAGATTTGGTGTTGAAGCTTCACTCCATTCCACTGTAACCTCAAGGACATTGA
GATCTGCTTTTGACTTTAATTCGACCAACTACAA
Found at i:207957 original size:18 final size:18
Alignment explanation
Indices: 207934--207968 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
207924 GCAAATAGAG
*
207934 TAAAAAAGGATTAAATTT
1 TAAAAAAAGATTAAATTT
*
207952 TAAAAAAATATTAAATT
1 TAAAAAAAGATTAAATT
207969 AAAAAGATAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (18 bp):
TAAAAAAAGATTAAATTT
Found at i:208075 original size:30 final size:28
Alignment explanation
Indices: 208000--208094 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 28
207990 AAATATAAAA
208000 AAAAATAAAAGGGTAATTTTAAAAGAAAT
1 AAAAATAAAAGGGTAA-TTTAAAAGAAAT
208029 AAAAATAAAA-GG---TTTAAAAGAAAT
1 AAAAATAAAAGGGTAATTTAAAAGAAAT
208053 AAAAATAAAAGGGTCAAATTTAACAA-AAAT
1 AAAAATAAAAGGGT--AATTTAA-AAGAAAT
208083 AAAAAATAAAAG
1 -AAAAATAAAAG
208095 AATTTAATTT
Statistics
Matches: 58, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
24 22 0.38
25 2 0.03
28 2 0.03
29 10 0.17
30 9 0.16
31 13 0.22
ACGTcount: A:0.66, C:0.02, G:0.12, T:0.20
Consensus pattern (28 bp):
AAAAATAAAAGGGTAATTTAAAAGAAAT
Found at i:211256 original size:20 final size:20
Alignment explanation
Indices: 211231--211269 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
211221 TATGATGAAA
211231 TGTGTAAAATTATTACATGG
1 TGTGTAAAATTATTACATGG
211251 TGTGTAAAATTATTACATG
1 TGTGTAAAATTATTACATG
211270 AAATGTAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
TGTGTAAAATTATTACATGG
Found at i:211276 original size:20 final size:20
Alignment explanation
Indices: 211233--211277 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
211223 TGATGAAATG
***
211233 TGTAAAATTATTACATGGTG
1 TGTAAAATTATTACATGAAA
211253 TGTAAAATTATTACATGAAA
1 TGTAAAATTATTACATGAAA
211273 TGTAA
1 TGTAA
211278 CATGTGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (20 bp):
TGTAAAATTATTACATGAAA
Found at i:211423 original size:4 final size:4
Alignment explanation
Indices: 211414--211449 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
211404 CAAAATTTTA
*
211414 TATT TATT TATT TATT TATC TATT TATT TA-T TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT T
211450 TATAAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:211944 original size:15 final size:14
Alignment explanation
Indices: 211917--211963 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
211907 GGTATACTGT
*
211917 TTTA-TTATATATA
1 TTTATTTATTTATA
211930 TTTATTCTATTTATA
1 TTTATT-TATTTATA
211945 TTTATTTATTT-TA
1 TTTATTTATTTATA
211958 -TTATTT
1 TTTATTT
211964 TTTCCTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 6 0.19
13 6 0.19
14 6 0.19
15 13 0.42
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTATTTATTTATA
Found at i:211945 original size:19 final size:19
Alignment explanation
Indices: 211921--211959 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
211911 TACTGTTTTA
211921 TTATATATATTTATTCTAT
1 TTATATATATTTATTCTAT
* *
211940 TTATATTTATTTATTTTAT
1 TTATATATATTTATTCTAT
211959 T
1 T
211960 ATTTTTTCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATATATTTATTCTAT
Found at i:214074 original size:20 final size:20
Alignment explanation
Indices: 214038--214087 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
214028 TAATTAAGCT
*
214038 TTAATTAACCACTTTTA-ATC
1 TTAATTAAACACTTTTATA-C
214058 TTAATTAAAC-CTATTTATAC
1 TTAATTAAACACT-TTTATAC
214078 TTAATATAAA
1 TTAAT-TAAA
214088 TCATATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 2 0.08
20 19 0.73
21 5 0.19
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACACTTTTATAC
Found at i:225717 original size:18 final size:18
Alignment explanation
Indices: 225694--225730 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
225684 ACAATTCATA
225694 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
225712 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
225730 T
1 T
225731 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Done.