Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 172 of 204
Found at i:51428360 original size:7 final size:7
Alignment explanation
Indices: 51428348--51428372 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
51428338 TTTTAAAGTT
51428348 AAAAATA
1 AAAAATA
51428355 AAAAATA
1 AAAAATA
51428362 AAAAATA
1 AAAAATA
51428369 AAAA
1 AAAA
51428373 TATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:51430088 original size:128 final size:129
Alignment explanation
Indices: 51429846--51430170 Score: 463
Period size: 128 Copynumber: 2.5 Consensus size: 129
51429836 CGCACTTTTA
* * ***
51429846 ATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
* ** * * *
51429911 AGATGAAAGCTACTAATCCTATCTCCCTGAAGTTGTAGTAGAGCGGATTAAAACCACAGATCTT
66 AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCACAGATCTT
* * *
51429975 ATCTCTCTGAAGTTGCAGTAGAGTAAATCGCATCAAGTCTTATCTCCCT-AAGCAATAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
* *
51430039 AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTT
66 AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCACAGATCTT
* * **
51430103 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCATGAAGTTACAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
51430168 AGA
66 AGA
51430171 TCAAAACCAC
Statistics
Matches: 172, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
128 112 0.65
129 60 0.35
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (129 bp):
ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGCAACAGTGGAGC
AGACGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTAGAGCAGATTAAAACCACAGATCTT
Found at i:51430156 original size:85 final size:85
Alignment explanation
Indices: 51429846--51430254 Score: 332
Period size: 85 Copynumber: 4.8 Consensus size: 85
51429836 CGCACTTTTA
*
51429846 ATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
* * * *
51429911 AGATGAAAGCTAC-TAATCCT
66 AGATTAAAACCACAT-ATCTT
* * * *** * *
51429931 ATCTCCCTGAAGTTGTAGTAGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGT--
1 ATCTCTCTGAAGTTGCAGTAGAGCAGA-TCGCATC-CAG-TCTTATCTCCCTGAAGTTGCAGTGG
*
51429994 AG-AG--TAAATCGCATCA-AGTCTT
63 AGCAGATTAAAAC-CA-CATA-TCTT
* **** * * * * *
51430016 ATCTCCCT-AAGCAATAGTGGAGCAGA-CGAAAGAAACCAATCCTATCTCCCTGAAGTTGCAGTG
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATC----GCATCCAGTCTTATCTCCCTGAAGTTGCAGTG
51430079 GAGCAGATTAAAACCACATATCTT
62 GAGCAGATTAAAACCACATATCTT
* * *
51430103 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCTAGTCTTATCTCCATGAAGTTACAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
* *
51430168 AGATCAAAACCACAGATCTT
66 AGATTAAAACCACATATCTT
* * * * * **
51430188 ATCTCTCTGAACTTGCAGTAAAGCAGATCGCATCAAGCCATATCTCCCTGAAGTTATAGTGGAGC
1 ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
51430253 AG
66 AG
51430255 GTTGAAGATA
Statistics
Matches: 260, Mismatches: 45, Indels: 38
0.76 0.13 0.11
Matches are distributed among these distances:
83 4 0.02
84 36 0.14
85 147 0.57
86 11 0.04
87 18 0.07
88 38 0.15
89 6 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (85 bp):
ATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGC
AGATTAAAACCACATATCTT
Found at i:51430216 original size:44 final size:44
Alignment explanation
Indices: 51429846--51430216 Score: 266
Period size: 44 Copynumber: 8.7 Consensus size: 44
51429836 CGCACTTTTA
* * *
51429846 ATCTCTCTGAAGTTGCAGTAGAGCAGATC-ACATC-CAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * * * *
51429887 ATCTCCCTGAAGTTGCAGTGGAGCAGATGAAAGCTACTA-ATCCT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCAC-AGATCTT
* * *
51429931 ATCTCCCTGAAGTTGTAGTAGAGCGGATTAAAACCACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * * ** *
51429975 ATCTCTCTGAAGTTGCAGTAGAGTAAATC-GCATCA-AG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
**** * * *
51430016 ATCTCCCT-AAGCAATAGTGGAGCAGA-CGAAAGA-AACCA-ATCCT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATC-AAA-ACCA-CAGATCTT
* * *
51430059 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACATATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* ** * *
51430103 ATCTCTCTGAAGTTGCAGTAGAGCAGATC-GCATC-TAG-TCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * *
51430144 ATCTCCATGAAGTTACAGTGGAGCAGATCAAAACCACAGATCTT
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
* * *
51430188 ATCTCTCTGAACTTGCAGTAAAGCAGATC
1 ATCTCCCTGAAGTTGCAGTAGAGCAGATC
51430217 GCATCAAGCC
Statistics
Matches: 247, Mismatches: 65, Indels: 33
0.72 0.19 0.10
Matches are distributed among these distances:
39 1 0.00
40 11 0.04
41 67 0.27
42 7 0.03
43 24 0.10
44 137 0.55
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (44 bp):
ATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGATCTT
Found at i:51431678 original size:3 final size:3
Alignment explanation
Indices: 51431667--51431727 Score: 61
Period size: 3 Copynumber: 19.0 Consensus size: 3
51431657 TATTTAGCTA
*
51431667 ATT AGTT ATT ATT ATT ATT ATT ATT ATT ATT ATT -GT ATTT ATT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT
51431713 ACTT ACCTT ATT ATT
1 A-TT A--TT ATT ATT
51431728 TTTTTATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 1 0.02
3 38 0.75
4 8 0.16
5 4 0.08
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:51433095 original size:27 final size:27
Alignment explanation
Indices: 51433042--51433097 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
51433032 ATATATATTC
* *
51433042 AATTATAAAAATGCAACACGCACTTTT
1 AATTATAAAAATACAACACACACTTTT
* * *
51433069 AATTATAAAAATATAACACATATTTTT
1 AATTATAAAAATACAACACACACTTTT
51433096 AA
1 AA
51433098 GCACTAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.04, T:0.34
Consensus pattern (27 bp):
AATTATAAAAATACAACACACACTTTT
Found at i:51433255 original size:11 final size:11
Alignment explanation
Indices: 51433239--51433300 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
51433229 CTTACTTTTC
51433239 TATTTTAAAAA
1 TATTTTAAAAA
51433250 TATTTT--AAA
1 TATTTTAAAAA
51433259 -ATTTTAAAAA
1 TATTTTAAAAA
* *
51433269 -AATTAAAAAA
1 TATTTTAAAAA
* *
51433279 GTATGTAAAAAA
1 -TATTTTAAAAA
51433291 TATTTTAAAA
1 TATTTTAAAA
51433301 TTAAAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 5 0.12
9 3 0.07
10 11 0.27
11 14 0.34
12 8 0.20
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:51436111 original size:27 final size:29
Alignment explanation
Indices: 51436077--51436148 Score: 103
Period size: 27 Copynumber: 2.5 Consensus size: 29
51436067 AATACATATA
*
51436077 TTTAATTATAAAAATGCAATAC-ACTTTT
1 TTTAATTATAAAAATGCAATACAAATTTT
*
51436105 TTT-ATTATAAAAATGTAATACATAATTTT
1 TTTAATTATAAAAATGCAATACA-AATTTT
51436134 TTTAATTATAAAAAT
1 TTTAATTATAAAAAT
51436149 ATAACACATA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 17 0.44
28 3 0.08
29 8 0.21
30 11 0.28
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (29 bp):
TTTAATTATAAAAATGCAATACAAATTTT
Found at i:51436142 original size:30 final size:30
Alignment explanation
Indices: 51436077--51436164 Score: 119
Period size: 30 Copynumber: 3.0 Consensus size: 30
51436067 AATACATATA
*
51436077 TTTAATTATAAAAATGCAATAC--ACTTTT
1 TTTAATTATAAAAATGTAATACATACTTTT
*
51436105 TTT-ATTATAAAAATGTAATACATAATTTT
1 TTTAATTATAAAAATGTAATACATACTTTT
* *
51436134 TTTAATTATAAAAATATAACACATACTTTT
1 TTTAATTATAAAAATGTAATACATACTTTT
51436164 T
1 T
51436165 AAGCACTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
27 17 0.33
28 3 0.06
29 8 0.15
30 24 0.46
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.45
Consensus pattern (30 bp):
TTTAATTATAAAAATGTAATACATACTTTT
Found at i:51436459 original size:13 final size:13
Alignment explanation
Indices: 51436441--51436468 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
51436431 AGTAGATTCA
51436441 TTTATAATTAATG
1 TTTATAATTAATG
51436454 TTTATAATTAATG
1 TTTATAATTAATG
51436467 TT
1 TT
51436469 GAATTTTTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (13 bp):
TTTATAATTAATG
Found at i:51439526 original size:19 final size:19
Alignment explanation
Indices: 51439502--51439540 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51439492 TTTTGTAAAT
51439502 TATATAATGTA-TGATGAAA
1 TATAT-ATGTATTGATGAAA
*
51439521 TATATATTTATTGATGAAA
1 TATATATGTATTGATGAAA
51439540 T
1 T
51439541 GAGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.44
Consensus pattern (19 bp):
TATATATGTATTGATGAAA
Found at i:51439713 original size:45 final size:46
Alignment explanation
Indices: 51439621--51439732 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
51439611 TGATCAGTGA
*
51439621 CAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGATAGCTCTAGCTACACTTATCTGAT
*
51439667 CAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGAT
1 CAAGTGACAAAGTGATAAGTGATAGCTCTAGCTACACTTATCTGAT
*
51439712 C-AGGGACAAA-TGATAAGTGAT
1 CAAGTGACAAAGTGATAAGTGAT
51439733 CATACGTAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 10 0.16
44 8 0.13
45 19 0.31
46 25 0.40
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (46 bp):
CAAGTGACAAAGTGATAAGTGATAGCTCTAGCTACACTTATCTGAT
Found at i:51441038 original size:2 final size:2
Alignment explanation
Indices: 51441031--51441070 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
51441021 ATACTAATTA
*
51441031 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
51441071 GAAAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:51441518 original size:19 final size:19
Alignment explanation
Indices: 51441463--51441520 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
51441453 ATAACAAAAA
51441463 CAAAATAATTTTCAAAAATT
1 CAAAATAATTTT-AAAAATT
*
51441483 CAAAATAATTTTTAAAATT
1 CAAAATAATTTTAAAAATT
51441502 CAAAAT-ATTTATAAAAATT
1 CAAAATAATTT-TAAAAATT
51441521 ATATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 4 0.11
19 19 0.54
20 12 0.34
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
CAAAATAATTTTAAAAATT
Found at i:51441535 original size:18 final size:18
Alignment explanation
Indices: 51441509--51441551 Score: 77
Period size: 18 Copynumber: 2.3 Consensus size: 18
51441499 ATTCAAAATA
51441509 TTTATAAAAATTATATTTT
1 TTTA-AAAAATTATATTTT
51441528 TTTAAAAAATTATATTTT
1 TTTAAAAAATTATATTTT
51441546 TTTAAA
1 TTTAAA
51441552 TAAAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 20 0.83
19 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAAAAAATTATATTTT
Found at i:51443561 original size:41 final size:41
Alignment explanation
Indices: 51443504--51443586 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
51443494 TTGGGCAACC
*
51443504 ACTTTCCCTTCAACCAACACAACTAAAATAAAAGGATTTGA
1 ACTTTCCCTTCAACCAACACAACTAAAACAAAAGGATTTGA
*
51443545 ACTTTCCCTTCAACCAACACAACTAAAACAAAGGGATTTGA
1 ACTTTCCCTTCAACCAACACAACTAAAACAAAAGGATTTGA
51443586 A
1 A
51443587 TTTTTTATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.43, C:0.25, G:0.08, T:0.23
Consensus pattern (41 bp):
ACTTTCCCTTCAACCAACACAACTAAAACAAAAGGATTTGA
Found at i:51446423 original size:25 final size:25
Alignment explanation
Indices: 51446358--51446411 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
51446348 GTTATTAGGG
* *
51446358 TTACCGATTC-CAGCTCTTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
51446382 TTACCGATACTCAGCTCGTATGAGC
1 TTACCGATACTCAGCTCGTATGAGC
51446407 TTACC
1 TTACC
51446412 ATTATTTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (25 bp):
TTACCGATACTCAGCTCGTATGAGC
Found at i:51452024 original size:34 final size:34
Alignment explanation
Indices: 51451985--51452053 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
51451975 TTATTATGAG
*
51451985 TTATAATTTGTATGGTTAGAATCCTTAATGAGTA
1 TTATAATTTATATGGTTAGAATCCTTAATGAGTA
51452019 TTATAATTTATATGGTTAGAATCCTTAATGAGTA
1 TTATAATTTATATGGTTAGAATCCTTAATGAGTA
51452053 T
1 T
51452054 ATTTTCAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.45
Consensus pattern (34 bp):
TTATAATTTATATGGTTAGAATCCTTAATGAGTA
Found at i:51463848 original size:5 final size:5
Alignment explanation
Indices: 51463838--51463870 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
51463828 TGATAAGTGG
51463838 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATT
51463871 AATAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:51476771 original size:12 final size:12
Alignment explanation
Indices: 51476756--51476785 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
51476746 AAAAATTATA
51476756 AAAAAAAAACAT
1 AAAAAAAAACAT
*
51476768 AAAAAAAAACGT
1 AAAAAAAAACAT
51476780 AAAAAA
1 AAAAAA
51476786 GAAGAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (12 bp):
AAAAAAAAACAT
Found at i:51483745 original size:21 final size:20
Alignment explanation
Indices: 51483721--51483790 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
51483711 TTTATTTTTA
51483721 CTTTTTTATTAACTTTTATCT
1 CTTTTTTATTAA-TTTTATCT
* *
51483742 CTTTTTTTTTAATTTT-TTT
1 CTTTTTTATTAATTTTATCT
51483761 C-TTTTT-TTAAGTTTTATCT
1 CTTTTTTATTAA-TTTTATCT
*
51483780 TTTTTCTTATT
1 CTTTT-TTATT
51483791 TTATTTTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
17 4 0.10
18 9 0.22
19 5 0.12
20 7 0.17
21 13 0.32
22 2 0.05
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.74
Consensus pattern (20 bp):
CTTTTTTATTAATTTTATCT
Found at i:51483767 original size:17 final size:17
Alignment explanation
Indices: 51483745--51483784 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
51483735 TTTATCTCTT
* *
51483745 TTTTTTTAATTTTTTTC
1 TTTTTTTAAGTTTTATC
51483762 TTTTTTTAAGTTTTATC
1 TTTTTTTAAGTTTTATC
51483779 TTTTTT
1 TTTTTT
51483785 CTTATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (17 bp):
TTTTTTTAAGTTTTATC
Found at i:51483776 original size:38 final size:36
Alignment explanation
Indices: 51483707--51483797 Score: 98
Period size: 38 Copynumber: 2.5 Consensus size: 36
51483697 CCTTCTTTTA
51483707 TTTTTTTATTTTTACTTTTTTATTAACTTTTATCTCTT
1 TTTTTTTATTTTTA-TTTTTTATTAACTTTTATCT-TT
* *
51483745 TTTTTTTAATTTTT-TTCTTTTTTTAAGTTTTATC-TT
1 TTTTTTT-ATTTTTATT-TTTTATTAACTTTTATCTTT
*
51483781 TTTTCTTA-TTTTATTTT
1 TTTTTTTATTTTTATTTT
51483798 GTTTATTTAT
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
34 6 0.13
35 3 0.06
36 8 0.17
37 2 0.04
38 22 0.47
39 6 0.13
ACGTcount: A:0.14, C:0.08, G:0.01, T:0.77
Consensus pattern (36 bp):
TTTTTTTATTTTTATTTTTTATTAACTTTTATCTTT
Found at i:51483784 original size:9 final size:8
Alignment explanation
Indices: 51483702--51483821 Score: 68
Period size: 8 Copynumber: 14.9 Consensus size: 8
51483692 GACACCCTTC
51483702 TTTTATTT
1 TTTTATTT
51483710 TTTTA--T
1 TTTTATTT
*
51483716 TTTTACTT
1 TTTTATTT
*
51483724 TTTTATTAAC
1 TTTTATT--T
*
51483734 TTTTATCT
1 TTTTATTT
*
51483742 CTTT-TTT
1 TTTTATTT
*
51483749 TTTAATTT
1 TTTTATTT
*
51483757 TTTTCTTT
1 TTTTATTT
**
51483765 TTTTA-AG
1 TTTTATTT
51483772 TTTTATCTT
1 TTTTAT-TT
* *
51483781 TTTTCTTA
1 TTTTATTT
51483789 TTTTATTT
1 TTTTATTT
51483797 TGTTTATTT
1 T-TTTATTT
*
51483806 ATTTATTT
1 TTTTATTT
51483814 TATTTATT
1 T-TTTATT
51483822 GTTATTAATT
Statistics
Matches: 82, Mismatches: 21, Indels: 17
0.68 0.17 0.14
Matches are distributed among these distances:
6 6 0.07
7 9 0.11
8 43 0.52
9 18 0.22
10 6 0.07
ACGTcount: A:0.16, C:0.06, G:0.02, T:0.77
Consensus pattern (8 bp):
TTTTATTT
Found at i:51483792 original size:17 final size:17
Alignment explanation
Indices: 51483707--51483794 Score: 54
Period size: 17 Copynumber: 4.9 Consensus size: 17
51483697 CCTTCTTTTA
*
51483707 TTTTTTTATTTTTA-CT
1 TTTTTTTAGTTTTATCT
*
51483723 TTTTTATTAACTTTTATCTCTT
1 TTTTT-TT-AGTTTTA--TC-T
* *
51483745 TTTTTTTAATTTTTTTCT
1 TTTTTTT-AGTTTTATCT
*
51483763 TTTTTTAAGTTTTATCT
1 TTTTTTTAGTTTTATCT
51483780 TTTTTCTTA-TTTTAT
1 TTTTT-TTAGTTTTAT
51483795 TTTGTTTATT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
16 5 0.09
17 21 0.36
18 15 0.26
19 2 0.03
21 9 0.16
22 6 0.10
ACGTcount: A:0.15, C:0.08, G:0.01, T:0.76
Consensus pattern (17 bp):
TTTTTTTAGTTTTATCT
Found at i:51483901 original size:21 final size:21
Alignment explanation
Indices: 51483868--51483960 Score: 98
Period size: 20 Copynumber: 4.3 Consensus size: 21
51483858 AATGTTTTGT
51483868 AATATATATTTTTTAAAATTTTA
1 AATAT-TA-TTTTTAAAATTTTA
*
51483891 AATATTATTTTT-AAATTTTG
1 AATATTATTTTTAAAATTTTA
*
51483911 AAGATTATTTTTAAAATTTTA
1 AATATTATTTTTAAAATTTTA
* * *
51483932 AATATATATTATTAATAATATAA
1 AATAT-TATTTTTAA-AATTTTA
51483955 AATATT
1 AATATT
51483961 TAAATATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
20 18 0.30
21 16 0.27
22 11 0.18
23 15 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
AATATTATTTTTAAAATTTTA
Found at i:51483961 original size:41 final size:42
Alignment explanation
Indices: 51483877--51483978 Score: 106
Period size: 41 Copynumber: 2.5 Consensus size: 42
51483867 TAATATATAT
* * * *
51483877 TTTTTAAAATTTTAAATAT-TATTTTTAAATTTTGAAGATTA
1 TTTTTAAAATTTTAAATATATATTATTAAAATATGAAGAATA
51483918 TTTTTAAAATTTTAAATATATATTATTAATAATAT-AA-AATA
1 TTTTTAAAATTTTAAATATATATTATTAA-AATATGAAGAATA
*
51483959 --TTTAAATATTTTAAAGATAT
1 TTTTTAAA-ATTTTAAATATAT
51483979 GACCTTTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
39 6 0.11
40 12 0.23
41 22 0.42
42 10 0.19
43 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (42 bp):
TTTTTAAAATTTTAAATATATATTATTAAAATATGAAGAATA
Found at i:51484029 original size:31 final size:29
Alignment explanation
Indices: 51483987--51484052 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 29
51483977 ATGACCTTTC
51483987 AAATT-TATAATTAGTTTT-TAAATATTTTT
1 AAATTATATAATTAGTTTTAT-AATA-TTTT
*
51484016 AATATTATATAATTTGTTTTATAATATTTT
1 AA-ATTATATAATTAGTTTTATAATATTTT
51484046 AAATTAT
1 AAATTAT
51484053 GATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.21
30 9 0.27
31 16 0.48
32 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
AAATTATATAATTAGTTTTATAATATTTT
Found at i:51484051 original size:29 final size:30
Alignment explanation
Indices: 51483987--51484052 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 30
51483977 ATGACCTTTC
51483987 AAATT-TATAATTAGTTTTTAAATATTTTT
1 AAATTATATAATTAGTTTTTAAATATTTTT
*
51484016 AATATTATATAATTTG-TTTTATAATA-TTTT
1 AA-ATTATATAATTAGTTTTTA-AATATTTTT
51484046 AAATTAT
1 AAATTAT
51484053 GATTTTTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 7 0.21
30 14 0.42
31 12 0.36
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (30 bp):
AAATTATATAATTAGTTTTTAAATATTTTT
Found at i:51491516 original size:85 final size:84
Alignment explanation
Indices: 51491398--51491710 Score: 398
Period size: 85 Copynumber: 3.7 Consensus size: 84
51491388 ACGTCGCTAA
* * * *
51491398 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAAT
1 CTTTAGCGGCGCTTA-TG-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA-
51491463 AAACGCCGCTAAAGATCATGTT
63 AAACGCCGCTAAAGATCATGTT
* *
51491485 CTTTAGCGGCACTTATGAAAAAACGCCGCTAAAGATCACGTTCTTTAGCGGCGCTTAGGAAAAAA
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
51491550 CGCCGCTAAAGATCATGTT
66 CGCCGCTAAAGATCATGTT
* * * *
51491569 CTTTAGCGGCGCTTAGGAAAAAGCGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGGAGAAA
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAGGAAAAA
*
51491634 ACGCCGCTAAA-AGTAATGTT
65 ACGCCGCTAAAGA-TCATGTT
* * ** *
51491654 CTATAGCGGCGCTTGTTCAAAAACGCCGCTAATAG-T-AGTGTTCTTTAGCGACGCTTA
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTA
51491711 TTTCACAAAC
Statistics
Matches: 201, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
84 76 0.38
85 109 0.54
86 3 0.01
87 13 0.06
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (84 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAAAA
CGCCGCTAAAGATCATGTT
Found at i:51491522 original size:42 final size:42
Alignment explanation
Indices: 51491398--51491711 Score: 377
Period size: 42 Copynumber: 7.4 Consensus size: 42
51491388 ACGTCGCTAA
* *
51491398 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-TG-AAAAAACGCCGCTAAAGATCATGTT
*
51491442 CTTTAGCGGCGC-TAAGAAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATG-AAA-AAACGCCGCTAAAGATCATGTT
* *
51491485 CTTTAGCGGCACTTATGAAAAAACGCCGCTAAAGATCACGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
*
51491527 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
* *
51491569 CTTTAGCGGCGCTTAGGAAAAAGCGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
* *
51491611 CTTTAGCGGCGCTT-TGGGAGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT--GAAAAAACGCCGCTAAAGA-TCATGTT
* * **
51491654 CTATAGCGGCGCTTGTTCAAAAACGCCGCTAATAG-T-AGTGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAA-AGATCA-TGTT
*
51491696 CTTTAGCGACGCTTAT
1 CTTTAGCGGCGCTTAT
51491712 TTCACAAACG
Statistics
Matches: 242, Mismatches: 19, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
41 1 0.00
42 153 0.63
43 73 0.30
44 15 0.06
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
Found at i:51491709 original size:127 final size:127
Alignment explanation
Indices: 51491403--51491710 Score: 394
Period size: 127 Copynumber: 2.4 Consensus size: 127
51491393 GCTAACTTTT
* *
51491403 GCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGAAAATAAACG
1 GCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAATAAACG
* *
51491468 CCGCTAAAGATCATGTTCTTTAGCGGCACTTATGAAAAAACGCCGCTAAAGATCACGTTCTTTA
64 CCGCTAAAGATCATGTTCTTTAGCGGCACTTATGAAAAAACGCCGCTAAAGATAACGTTCTATA
* *
51491532 GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAA-AAGCGCC
1 GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAATAAACGCC
* * *
51491596 GCTAAAGATCATGTTCTTTAGCGGCGCTT-TGGGAGAAAACGCCGCTAAA-AGTAATGTTCTATA
66 GCTAAAGATCATGTTCTTTAGCGGCACTTAT--GAAAAAACGCCGCTAAAGA-TAACGTTCTATA
** *
51491659 GCGGCGCTT-GTTCAAAAACGCCGCTAATAG-T-AGTGTTCTTTAGCGACGCTTA
1 GCGGCGCTTAG-GAAAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTA
51491711 TTTCACAAAC
Statistics
Matches: 161, Mismatches: 12, Indels: 14
0.86 0.06 0.07
Matches are distributed among these distances:
125 1 0.01
126 37 0.23
127 112 0.70
128 2 0.01
129 9 0.06
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (127 bp):
GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAATAAACGCC
GCTAAAGATCATGTTCTTTAGCGGCACTTATGAAAAAACGCCGCTAAAGATAACGTTCTATA
Found at i:51492168 original size:12 final size:12
Alignment explanation
Indices: 51492136--51492171 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
51492126 TTTTGAACCT
*
51492136 CTGCTTCTATCG
1 CTGCTTCTCTCG
51492148 CTGCTTCTCTCG
1 CTGCTTCTCTCG
51492160 CTGCTTCTCTCG
1 CTGCTTCTCTCG
51492172 ATGTGGCCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.03, C:0.39, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:51492186 original size:21 final size:21
Alignment explanation
Indices: 51492160--51492208 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
51492150 GCTTCTCTCG
*
51492160 CTGCTTCTCTCGATGTGGCCT
1 CTGCTTCTCTCGATGTAGCCT
*
51492181 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGATGTAGCCT
51492202 CTGCTTC
1 CTGCTTC
51492209 CCTCCCTGCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.37, G:0.20, T:0.39
Consensus pattern (21 bp):
CTGCTTCTCTCGATGTAGCCT
Found at i:51498376 original size:7 final size:7
Alignment explanation
Indices: 51498366--51498418 Score: 70
Period size: 7 Copynumber: 7.0 Consensus size: 7
51498356 ATATATATTT
51498366 TTATGTA
1 TTATGTA
51498373 TTATGTAA
1 TTATGT-A
51498381 GTTATGTAA
1 -TTATGT-A
51498390 GTTATGTA
1 -TTATGTA
51498398 TTATGTA
1 TTATGTA
51498405 TTATGTA
1 TTATGTA
51498412 TTATGTA
1 TTATGTA
51498419 AGTACTGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
7 27 0.61
8 2 0.05
9 15 0.34
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (7 bp):
TTATGTA
Found at i:51498387 original size:9 final size:9
Alignment explanation
Indices: 51498373--51498957 Score: 539
Period size: 9 Copynumber: 65.2 Consensus size: 9
51498363 TTTTTATGTA
51498373 TTATGTAAG
1 TTATGTAAG
51498382 TTATGTAAG
1 TTATGTAAG
51498391 TTATGT-A-
1 TTATGTAAG
51498398 TTATGT-A-
1 TTATGTAAG
51498405 TTATGT-A-
1 TTATGTAAG
51498412 TTATGTAAG
1 TTATGTAAG
51498421 -TACTGTAAG
1 TTA-TGTAAG
51498430 -TACTGTAAG
1 TTA-TGTAAG
51498439 TTATGTAAG
1 TTATGTAAG
* *
51498448 TTATTTAAT
1 TTATGTAAG
*
51498457 TTATGTAGG
1 TTATGTAAG
51498466 TTATGTAAG
1 TTATGTAAG
*
51498475 TTATGTAGG
1 TTATGTAAG
51498484 TTATGTAAG
1 TTATGTAAG
* *
51498493 TTATTTAAT
1 TTATGTAAG
*
51498502 TTATGTAGG
1 TTATGTAAG
51498511 TTATGTAAG
1 TTATGTAAG
* * *
51498520 TCATTTAAT
1 TTATGTAAG
*
51498529 TTATGCAAG
1 TTATGTAAG
51498538 TTTATGTAAG
1 -TTATGTAAG
51498548 TTATGTAAG
1 TTATGTAAG
*
51498557 TTACT-TAAT
1 TTA-TGTAAG
51498566 TTATGTAAG
1 TTATGTAAG
51498575 TTATGTAAG
1 TTATGTAAG
* *
51498584 TTATTTAAT
1 TTATGTAAG
*
51498593 TTATGTAGG
1 TTATGTAAG
51498602 TTATGTAAG
1 TTATGTAAG
* *
51498611 TTATTTAAT
1 TTATGTAAG
*
51498620 TTATGTAGG
1 TTATGTAAG
51498629 TTATGTAAG
1 TTATGTAAG
51498638 TTATGTAAG
1 TTATGTAAG
* *
51498647 TTATTTAAT
1 TTATGTAAG
*
51498656 TTATGTAGG
1 TTATGTAAG
51498665 TTATGTAAG
1 TTATGTAAG
*
51498674 -TCTG-ACCAGG
1 TTATGTA--A-G
*
51498684 TATATTGTCA-
1 T-TA-TGTAAG
** * *
51498694 TGCTCTAAT
1 TTATGTAAG
*
51498703 TTATGTAGG
1 TTATGTAAG
51498712 TTATGTAAG
1 TTATGTAAG
51498721 TTATGTAAG
1 TTATGTAAG
* *
51498730 TTATTTAAT
1 TTATGTAAG
*
51498739 TTATGTAGG
1 TTATGTAAG
51498748 TTATGTAAG
1 TTATGTAAG
51498757 TTATGTAAG
1 TTATGTAAG
51498766 TTATGTAAG
1 TTATGTAAG
* *
51498775 TTATTTAAT
1 TTATGTAAG
*
51498784 TTATGTAGG
1 TTATGTAAG
51498793 TTATGTAAG
1 TTATGTAAG
* *
51498802 TTATTTAAT
1 TTATGTAAG
*
51498811 TTATGTAGG
1 TTATGTAAG
51498820 TTATGTAAG
1 TTATGTAAG
*
51498829 TTATTTAA-
1 TTATGTAAG
51498837 TTAATGTAAG
1 TT-ATGTAAG
51498847 TTATGTAAG
1 TTATGTAAG
* *
51498856 TTATTTAAA
1 TTATGTAAG
*
51498865 TTATGCAAG
1 TTATGTAAG
*
51498874 TTTATGCAAG
1 -TTATGTAAG
* *
51498884 TTATTTAAT
1 TTATGTAAG
51498893 TTATGTAAG
1 TTATGTAAG
51498902 TTATGTAAG
1 TTATGTAAG
* *
51498911 TTATTTAAT
1 TTATGTAAG
51498920 TTATGTAAG
1 TTATGTAAG
51498929 TTATGTAAG
1 TTATGTAAG
*
51498938 TTTTGTAAG
1 TTATGTAAG
* *
51498947 ATATGTGAG
1 TTATGTAAG
51498956 TT
1 TT
51498958 TCTATATATG
Statistics
Matches: 464, Mismatches: 94, Indels: 36
0.78 0.16 0.06
Matches are distributed among these distances:
7 21 0.05
8 13 0.03
9 402 0.87
10 24 0.05
12 2 0.00
13 2 0.00
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (9 bp):
TTATGTAAG
Found at i:51498999 original size:8 final size:8
Alignment explanation
Indices: 51498986--51499038 Score: 52
Period size: 8 Copynumber: 6.0 Consensus size: 8
51498976 TTGTATGTTA
51498986 GTTATTAT
1 GTTATTAT
51498994 GTTATTAT
1 GTTATTAT
51499002 GTTAATATAT
1 GTT-AT-TAT
*
51499012 AAGTTATTTAA
1 --GTTA-TTAT
51499023 GTTATTAT
1 GTTATTAT
51499031 GTTATTAT
1 GTTATTAT
51499039 ATAAAGTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 22 0.58
9 6 0.16
10 3 0.08
11 3 0.08
12 4 0.11
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (8 bp):
GTTATTAT
Found at i:51499026 original size:29 final size:29
Alignment explanation
Indices: 51498985--51499091 Score: 117
Period size: 29 Copynumber: 3.6 Consensus size: 29
51498975 ATTGTATGTT
*
51498985 AGTTAT-TATGTTATTATGTTAATATATA
1 AGTTATGTAAGTTATTATGTTAATATATA
* *
51499013 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATTATGTTAATATAT-A
* *
51499043 AGTATTATGTAATTTATTATGTTATTATATGTA
1 AG--TTATGTAAGTTATTATGTTA--ATATATA
51499076 AGTTATGTAAGTTATT
1 AGTTATGTAAGTTATT
51499092 TAATTTGTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
28 6 0.09
29 19 0.29
30 3 0.05
31 13 0.20
32 18 0.27
33 3 0.05
34 4 0.06
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (29 bp):
AGTTATGTAAGTTATTATGTTAATATATA
Found at i:51499058 original size:37 final size:37
Alignment explanation
Indices: 51498985--51499058 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
51498975 ATTGTATGTT
* * *
51498985 AGTTATTATGTTATTATGTTAATATATAAGTTATTTA
1 AGTTATTATGTTATTATATAAATATATAAGTAATTTA
*
51499022 AGTTATTATGTTATTATATAAAGTAT-TATGTAATTTA
1 AGTTATTATGTTATTATATAAA-TATATAAGTAATTTA
51499059 TTATGTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.91
38 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (37 bp):
AGTTATTATGTTATTATATAAATATATAAGTAATTTA
Found at i:51499065 original size:32 final size:29
Alignment explanation
Indices: 51498985--51499091 Score: 126
Period size: 32 Copynumber: 3.6 Consensus size: 29
51498975 ATTGTATGTT
* *
51498985 AGTTAT-TATGTTATTATGTTAATATATA
1 AGTTATGTAAGTTATTATGTTATTATATA
*
51499013 AGTTATTTAAGTTATTATGTTATTATATAA
1 AGTTATGTAAGTTATTATGTTATTATAT-A
*
51499043 AGTATTATGTAATTTATTATGTTATTATATGTA
1 AG--TTATGTAAGTTATTATGTTATTATA--TA
51499076 AGTTATGTAAGTTATT
1 AGTTATGTAAGTTATT
51499092 TAATTTGTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
28 6 0.09
29 19 0.28
30 3 0.04
31 13 0.19
32 23 0.34
33 3 0.04
34 1 0.01
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (29 bp):
AGTTATGTAAGTTATTATGTTATTATATA
Found at i:51499068 original size:20 final size:20
Alignment explanation
Indices: 51498995--51499091 Score: 70
Period size: 21 Copynumber: 4.7 Consensus size: 20
51498985 AGTTATTATG
* * * *
51498995 TTATTATGTTAATATATAAG
1 TTATTAAGTTATTATGTAAT
*
51499015 TTATTTAAGTTATTATGTTAT
1 TTA-TTAAGTTATTATGTAAT
*
51499036 TATATAAAG-TATTATGTAAT
1 T-TATTAAGTTATTATGTAAT
* *
51499056 TTATTATGTTATTATATGTAAG
1 TTATTAAGTTA-T-TATGTAAT
51499078 TTATGTAAGTTATT
1 TTAT-TAAGTTATT
51499092 TAATTTGTGT
Statistics
Matches: 60, Mismatches: 11, Indels: 11
0.73 0.13 0.13
Matches are distributed among these distances:
19 5 0.08
20 16 0.27
21 19 0.32
22 14 0.23
23 6 0.10
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (20 bp):
TTATTAAGTTATTATGTAAT
Found at i:51499076 original size:22 final size:23
Alignment explanation
Indices: 51499048--51499091 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
51499038 TATAAAGTAT
* *
51499048 TATGTAATTTAT-TATGTTATTA
1 TATGTAAGTTATGTAAGTTATTA
51499070 TATGTAAGTTATGTAAGTTATT
1 TATGTAAGTTATGTAAGTTATT
51499092 TAATTTGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.55
Consensus pattern (23 bp):
TATGTAAGTTATGTAAGTTATTA
Found at i:51499084 original size:9 final size:9
Alignment explanation
Indices: 51499070--51499132 Score: 54
Period size: 9 Copynumber: 6.7 Consensus size: 9
51499060 TATGTTATTA
51499070 TATGTAAGT
1 TATGTAAGT
51499079 TATGTAAGT
1 TATGTAAGT
* *
51499088 TATTTAATT
1 TATGTAAGT
*
51499097 TGTGTAAGT
1 TATGTAAGT
*
51499106 TATGCAAGCT
1 TATGTAAG-T
*
51499116 TATATACAAGT
1 TATGT--AAGT
51499127 TATGTA
1 TATGTA
51499133 TTATAACATA
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
9 29 0.71
10 4 0.10
11 5 0.12
12 3 0.07
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:51499369 original size:15 final size:15
Alignment explanation
Indices: 51499349--51499389 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
51499339 GAAAATGAAG
* *
51499349 TAAATTTACTACTAA
1 TAAATTTAATACAAA
51499364 TAAATTTTAATACAAA
1 TAAA-TTTAATACAAA
51499380 TAAATTTAAT
1 TAAATTTAAT
51499390 TAACTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAATTTAATACAAA
Found at i:51499418 original size:17 final size:17
Alignment explanation
Indices: 51499396--51499428 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
51499386 TAATTAACTT
51499396 ATTTAGAAAACTTATAA
1 ATTTAGAAAACTTATAA
51499413 ATTTAGAAAACTTATA
1 ATTTAGAAAACTTATA
51499429 TAGATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (17 bp):
ATTTAGAAAACTTATAA
Found at i:51504346 original size:113 final size:113
Alignment explanation
Indices: 51504162--51504776 Score: 640
Period size: 113 Copynumber: 5.4 Consensus size: 113
51504152 TTTTTGTAAT
* ** *
51504162 ACGCCGCTAAT-ACTGTTC-TTTAGCGGCGTTTTATCGTAAATGCCACTAATTCTAATATACCTC
1 ACGCCACTAATGA-TGTTCTTTTA-CGGCGTTTT-TAATAAACGCCACTAATTCTAATATACCTC
*
51504225 AAAGCCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
63 AAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
* * ** * **
51504276 ACGCCACTAATGATGTTCTTTTACGGAGTTTTTAATAAGCGCCACTAAAACTAATCTACCTCAGG
1 ACGCCACTAATGATGTTCTTTTACGGCGTTTTTAATAAACGCCACTAATTCTAATATACCTCAAA
* * * * ****
51504341 ACCAAACGGTGCGTTTTGGTTAAGATA-TTTGTGACGCTT-TTTGTAA
66 ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
* ** *
51504387 TACGCCGCTAAT-ACTGTTC-TTTAGCGGCGTTTTATCGTAAACGCCACTAATTCTAATATATCT
1 -ACGCCACTAATGA-TGTTCTTTTA-CGGCGTTTT-TAATAAACGCCACTAATTCTAATATACCT
*
51504450 CAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGATTACAAATAA
62 CAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
* ** *
51504502 ACGCCACTAATGATGTTCTTTTACGGCGTTTTTTAATAAGCGCCACTAACACTAATCTACCTCAA
1 ACGCCACTAATGATGTTCTTTTACGGCG-TTTTTAATAAACGCCACTAATTCTAATATACCTCAA
* * * * ****
51504567 GACTAAACGGTGCGTTTTGGTTAAGATA-TTTGCGGCGCTT-TTTGTAA
65 AACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
* ** *
51504614 TACGCCGCTAAT-ACTGTTC-TTTAGCGGCGTTTTATCGTAAATGCCACTAATTCTAATATACCT
1 -ACGCCACTAATGA-TGTTCTTTTA-CGGCGTTTT-TAATAAACGCCACTAATTCTAATATACCT
51504677 CAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
62 CAAAACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
* *
51504729 ATGCCACTAATGATGTTCTTTTACGGTGTTTTTTTAAT-AACGCCACTA
1 ACGCCACTAATGATGTTCTTTTACGGCG--TTTTTAATAAACGCCACTA
51504777 GTTGTTCGGG
Statistics
Matches: 401, Mismatches: 79, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
111 8 0.02
112 45 0.11
113 177 0.44
114 140 0.35
115 27 0.07
116 4 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (113 bp):
ACGCCACTAATGATGTTCTTTTACGGCGTTTTTAATAAACGCCACTAATTCTAATATACCTCAAA
ACCAAACGCTGCGTTTTGGTTAAGGTATTTTGCGGCGCTTACAAATAA
Found at i:51504653 original size:227 final size:227
Alignment explanation
Indices: 51504126--51504776 Score: 1171
Period size: 227 Copynumber: 2.9 Consensus size: 227
51504116 AAAACGAAAC
51504126 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
1 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
*
51504191 TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAGCCAAACGCTGCGTTTTGGTTAAGGTAT
66 TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
51504256 TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAG-TTTTTAATAAGCGCCA
131 TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTTAATAAGCGCCA
*
51504320 CTAAAACTAATCTACCTCAGGACCAAACGGTG
196 CTAAAACTAATCTACCTCAAGACCAAACGGTG
*
51504352 CGTTTTGGTTAAGATATTTGTGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
1 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
* *
51504417 TTTATCGTAAACGCCACTAATTCTAATATATCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
66 TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
* *
51504482 TTTGCGGCGATTACAAATAAACGCCACTAATGATGTTCTTTTACGGCGTTTTTTAATAAGCGCCA
131 TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTTAATAAGCGCCA
* *
51504547 CTAACACTAATCTACCTCAAGACTAAACGGTG
196 CTAAAACTAATCTACCTCAAGACCAAACGGTG
*
51504579 CGTTTTGGTTAAGATATTTGCGGCGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
1 CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
51504644 TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
66 TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
* *
51504709 TTTGCGGCGCTTACAAATAAATGCCACTAATGATGTTCTTTTACGGTGTTTTTTTAATAA-CGCC
131 TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAG-TTTTTTAATAAGCGCC
51504773 ACTA
195 ACTA
51504777 GTTGTTCGGG
Statistics
Matches: 407, Mismatches: 16, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
226 172 0.42
227 224 0.55
228 11 0.03
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (227 bp):
CGTTTTGGTTAAGATATTTGCGACGCTTTTTGTAATACGCCGCTAATACTGTTCTTTAGCGGCGT
TTTATCGTAAATGCCACTAATTCTAATATACCTCAAAACCAAACGCTGCGTTTTGGTTAAGGTAT
TTTGCGGCGCTTACAAATAAACGCCACTAATGATGTTCTTTTACGGAGTTTTTTAATAAGCGCCA
CTAAAACTAATCTACCTCAAGACCAAACGGTG
Found at i:51508295 original size:30 final size:30
Alignment explanation
Indices: 51508259--51508391 Score: 176
Period size: 30 Copynumber: 4.4 Consensus size: 30
51508249 GTCGCAGAGC
* * * *
51508259 AGTTCATATCACTCGGACATTGCCGGTTCA
1 AGTTCATATCACCCAGACATAGGCGGTTCA
51508289 AGTTCATATCACCCAGACATAGGCGGTTCA
1 AGTTCATATCACCCAGACATAGGCGGTTCA
**
51508319 AGTTCATATCACCCAGACATAGGCAATTCA
1 AGTTCATATCACCCAGACATAGGCGGTTCA
* *
51508349 AGTTCATATCACCTAGACATAGGCGGTTCG
1 AGTTCATATCACCCAGACATAGGCGGTTCA
* *
51508379 AGTTTATTTCACC
1 AGTTCATATCACC
51508392 AAGAGCAACC
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 91 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (30 bp):
AGTTCATATCACCCAGACATAGGCGGTTCA
Found at i:51511783 original size:12 final size:13
Alignment explanation
Indices: 51511729--51511783 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 13
51511719 AAACGTTTGA
51511729 ATATCTTTAAAATT
1 ATAT-TTTAAAATT
51511743 A-ATTTTAAAATT
1 ATATTTTAAAATT
51511755 AATAATTTATAAAAATT
1 -AT-ATTT-T-AAAATT
51511772 ATA-TTTAAAATT
1 ATATTTTAAAATT
51511784 TAAAAAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
12 15 0.42
13 4 0.11
14 3 0.08
15 5 0.14
16 3 0.08
17 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTTTAAAATT
Found at i:51511797 original size:11 final size:11
Alignment explanation
Indices: 51511781--51511815 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
51511771 TATATTTAAA
51511781 ATTTAAAAAAT
1 ATTTAAAAAAT
51511792 ATTTAAAAAATAT
1 ATTT-AAAAA-AT
51511805 ATTTAAAAAAT
1 ATTTAAAAAAT
51511816 TATAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.27
12 10 0.45
13 6 0.27
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTTAAAAAAT
Found at i:51511806 original size:13 final size:13
Alignment explanation
Indices: 51511781--51511815 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
51511771 TATATTTAAA
51511781 ATTT-AAAAA-AT
1 ATTTAAAAAATAT
51511792 ATTTAAAAAATAT
1 ATTTAAAAAATAT
51511805 ATTTAAAAAAT
1 ATTTAAAAAAT
51511816 TATAAAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.18
12 5 0.23
13 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAAAAATAT
Found at i:51511815 original size:33 final size:34
Alignment explanation
Indices: 51511759--51511822 Score: 89
Period size: 33 Copynumber: 1.9 Consensus size: 34
51511749 AAAATTAATA
51511759 ATTTATAAAAATTATATTTAAAATT-TAAAAAAT
1 ATTTATAAAAATTATATTTAAAATTATAAAAAAT
51511792 ATTTA-AAAAA-TATATTTAAAAAATTATAAAA
1 ATTTATAAAAATTATATTT--AAAATTATAAAA
51511823 CAAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 7 0.25
32 5 0.18
33 11 0.39
34 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
ATTTATAAAAATTATATTTAAAATTATAAAAAAT
Found at i:51511881 original size:24 final size:24
Alignment explanation
Indices: 51511850--51511945 Score: 147
Period size: 24 Copynumber: 3.9 Consensus size: 24
51511840 AGGTCATATC
* *
51511850 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATCATA-ATTTAAAATAA
51511875 TTTAAAAATCATAATTTAAAATAA
1 TTTAAAAATCATAATTTAAAATAA
51511899 TTTAAAAATCATAATTTAAAATAA
1 TTTAAAAATCATAATTTAAAATAA
*
51511923 TTTAAAAATTATAATTATAAAAT
1 TTTAAAAATCATAATT-TAAAAT
51511946 TATAAAACAA
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
24 49 0.73
25 18 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TTTAAAAATCATAATTTAAAATAA
Found at i:51511888 original size:14 final size:13
Alignment explanation
Indices: 51511871--51511950 Score: 73
Period size: 14 Copynumber: 6.3 Consensus size: 13
51511861 TATATTTTAA
51511871 ATAATTTAAAAAT
1 ATAATTTAAAAAT
51511884 CATAATTT--AAA-
1 -ATAATTTAAAAAT
51511895 ATAATTTAAAAAT
1 ATAATTTAAAAAT
51511908 CATAATTT--AAA-
1 -ATAATTTAAAAAT
51511919 ATAATTTAAAAATT
1 ATAATTTAAAAA-T
*
51511933 ATAATTATAAAATT
1 ATAATT-TAAAAAT
51511947 ATAA
1 ATAA
51511951 AACAAATTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
10 14 0.25
12 12 0.21
14 25 0.45
15 5 0.09
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATTTAAAAAT
Found at i:51511900 original size:10 final size:10
Alignment explanation
Indices: 51511885--51511929 Score: 54
Period size: 10 Copynumber: 4.1 Consensus size: 10
51511875 TTTAAAAATC
51511885 ATAATTTAAA
1 ATAATTTAAA
51511895 ATAATTTAAAAA
1 ATAATTT--AAA
51511907 TCATAATTTAAA
1 --ATAATTTAAA
51511919 ATAATTTAAA
1 ATAATTTAAA
51511929 A
1 A
51511930 ATTATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 18 0.58
12 6 0.19
14 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATTTAAA
Found at i:51512005 original size:21 final size:20
Alignment explanation
Indices: 51511981--51512043 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 20
51511971 TAAATGTTTT
51511981 ATATTATTAAAAATATATTTA
1 ATATT-TTAAAAATATATTTA
51512002 ATA-TTTATAAAATAATATTTA
1 ATATTTTA-AAAAT-ATATTTA
*
51512023 AAATTTTAAACAATA-ATTTA
1 ATATTTTAAA-AATATATTTA
51512043 A
1 A
51512044 AAATAATATT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
19 3 0.08
20 12 0.32
21 15 0.41
22 7 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATATTTTAAAAATATATTTA
Found at i:51512013 original size:20 final size:20
Alignment explanation
Indices: 51511990--51512045 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
51511980 TATATTATTA
*
51511990 AAAAT-ATATTTAATATTTAT
1 AAAATAATATTTAAAATTT-T
51512010 AAAATAATATTTAAAATTTT
1 AAAATAATATTTAAAATTTT
*
51512030 -AAACAATAATTTAAAA
1 AAAATAAT-ATTTAAAA
51512046 ATAATATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.19
20 14 0.44
21 12 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAATAATATTTAAAATTTT
Found at i:51512047 original size:33 final size:33
Alignment explanation
Indices: 51512004--51512118 Score: 144
Period size: 33 Copynumber: 3.3 Consensus size: 33
51511994 TATATTTAAT
51512004 ATTTATAAAATAATATTTAAAATTT-TAAACAATA
1 ATTTA-AAAATAATATTTAAAATTTATAAA-AATA
51512038 ATTTAAAAATAATATTTAAAATTTATAAAAATA
1 ATTTAAAAATAATATTTAAAATTTATAAAAATA
*
51512071 ATTTCAAAAATATATATTTAAAAATTA-AAAAATA
1 ATTT-AAAAATA-ATATTTAAAATTTATAAAAATA
51512105 TATATTATAAAATA
1 -AT-TTA-AAAATA
51512119 TTTCAAATAT
Statistics
Matches: 74, Mismatches: 1, Indels: 10
0.87 0.01 0.12
Matches are distributed among these distances:
33 27 0.36
34 23 0.31
35 16 0.22
36 8 0.11
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (33 bp):
ATTTAAAAATAATATTTAAAATTTATAAAAATA
Found at i:51512084 original size:20 final size:22
Alignment explanation
Indices: 51512041--51512086 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
51512031 AACAATAATT
* *
51512041 TAAAAATAATATTTAAAATTTA
1 TAAAAATAATATTCAAAATATA
51512063 TAAAAATAAT-TTCAAAAATATA
1 TAAAAATAATATTC-AAAATATA
51512085 TA
1 TA
51512087 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAAAATAATATTCAAAATATA
Found at i:51512481 original size:19 final size:20
Alignment explanation
Indices: 51512443--51512487 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
51512433 AATATATTTA
*
51512443 ATATTTAAAGTTAAAAAAAT
1 ATATTTAAAATTAAAAAAAT
*
51512463 ATATTTAAAATT-TAAAAAT
1 ATATTTAAAATTAAAAAAAT
51512482 ATATTT
1 ATATTT
51512488 TTGAAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATTTAAAATTAAAAAAAT
Found at i:51512494 original size:21 final size:21
Alignment explanation
Indices: 51512443--51512495 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
51512433 AATATATTTA
*
51512443 ATATTT-AAAGTTAAAAAAAT
1 ATATTTAAAATTTAAAAAAAT
*
51512463 ATATTTAAAATTTAAAAATAT
1 ATATTTAAAATTTAAAAAAAT
* *
51512484 ATTTTTGAAATT
1 ATATTTAAAATT
51512496 ATTTTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 6 0.21
21 22 0.79
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
ATATTTAAAATTTAAAAAAAT
Found at i:51512584 original size:36 final size:36
Alignment explanation
Indices: 51512525--51512615 Score: 89
Period size: 36 Copynumber: 2.5 Consensus size: 36
51512515 TATATTTAAA
* *
51512525 ATTTAAAATTTAGAAAAATTAATTT-CAAATATATAT
1 ATTTAAAATTTAGAAAAATTAATTTAAAAAAATA-AT
* * *
51512561 TTTTAAAATTTATAAGACA-TAATTTAAAAAAATAAT
1 ATTTAAAATTTAGAA-AAATTAATTTAAAAAAATAAT
51512597 ATTTAAAATTTTA-AAAAAT
1 ATTTAAAA-TTTAGAAAAAT
51512616 ATATATTATA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
35 2 0.05
36 30 0.68
37 12 0.27
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (36 bp):
ATTTAAAATTTAGAAAAATTAATTTAAAAAAATAAT
Found at i:51512609 original size:23 final size:24
Alignment explanation
Indices: 51512581--51512628 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 24
51512571 TATAAGACAT
*
51512581 AATTTAAAAAAATA-ATATT-TAA
1 AATTTTAAAAAATATATATTATAA
51512603 AATTTTAAAAAATATATATTATAA
1 AATTTTAAAAAATATATATTATAA
51512627 AA
1 AA
51512629 CGTTTCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.57
23 5 0.22
24 5 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AATTTTAAAAAATATATATTATAA
Found at i:51512747 original size:25 final size:25
Alignment explanation
Indices: 51512713--51512761 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
51512703 TAAAACTTAA
* * *
51512713 AAAAGAAAAATTTAAAGAAAAAGAC
1 AAAAGAAAAAGTAAAAAAAAAAGAC
*
51512738 AAAAGTAAAAGTAAAAAAAAAAGA
1 AAAAGAAAAAGTAAAAAAAAAAGA
51512762 AAGTAAAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (25 bp):
AAAAGAAAAAGTAAAAAAAAAAGAC
Found at i:51513125 original size:34 final size:36
Alignment explanation
Indices: 51513087--51513159 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
51513077 ACAGCCCCTC
* *
51513087 ATTATTATTGTTT-TAA-GTTTTGTACCTAAATTCA
1 ATTATTATTCTTTCCAAGGTTTTGTACCTAAATTCA
* *
51513121 ATTATTATTCTTTCCAAGGTTTTTTAGCTAAATTCA
1 ATTATTATTCTTTCCAAGGTTTTGTACCTAAATTCA
51513157 ATT
1 ATT
51513160 CTAGCAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 12 0.36
35 2 0.06
36 19 0.58
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (36 bp):
ATTATTATTCTTTCCAAGGTTTTGTACCTAAATTCA
Found at i:51516209 original size:19 final size:19
Alignment explanation
Indices: 51516187--51516224 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51516177 TATAAATTTA
*
51516187 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
51516206 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
51516225 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:51516482 original size:27 final size:28
Alignment explanation
Indices: 51516444--51516520 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 28
51516434 CCAGCCCGGC
*
51516444 CCATTGGCGCCTCTCAGAAT-GGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
*
51516471 CCATTGGCGCCTCCCAG-GTAGGCACCA
1 CCATTGGCGCCTCCCAGAATAGGCACCA
51516498 CCATTGGCGCCTCCCAG-ATAGGC
1 CCATTGGCGCCTCCCAGAATAGGC
51516521 GCCAATACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (28 bp):
CCATTGGCGCCTCCCAGAATAGGCACCA
Found at i:51535756 original size:34 final size:34
Alignment explanation
Indices: 51535715--51535798 Score: 118
Period size: 34 Copynumber: 2.5 Consensus size: 34
51535705 GGTTTTTTTA
*
51535715 AAAATTAATTAAATTA-GATTTTTGGGGTTTTAA-
1 AAAATTAATTAAATTAGGATTTAT-GGGTTTTAAG
*
51535748 ATAAATTAATTAAATTAGGATTTATGGTTTTTAAG
1 A-AAATTAATTAAATTAGGATTTATGGGTTTTAAG
51535783 AAAATTAATTAAATTA
1 AAAATTAATTAAATTA
51535799 TGGTTTAGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
33 1 0.02
34 38 0.83
35 7 0.15
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (34 bp):
AAAATTAATTAAATTAGGATTTATGGGTTTTAAG
Found at i:51536096 original size:126 final size:127
Alignment explanation
Indices: 51535870--51536141 Score: 381
Period size: 126 Copynumber: 2.1 Consensus size: 127
51535860 CTTTTGTTTT
* *
51535870 TTTTTCTACAGTAGTT-TCTAAAAAAATTAATTTTGAGAAGACAGTTCTGAAAATATAATGTAAA
1 TTTTTCTACAGTAGTTCT-TAAAAAAATTAAATTTGAGAAGACAGTTCTGAAAAAATAATGTAAA
* *
51535934 AAACGTTTCAATCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTC
65 AAACGCTTCAATCAAGATGCACTGTCAGCAAAATTACGGAAAAAAGCTCCCACGTGGACGCTC
* * *
51535997 TTTTTCTACAGTAGTTCTTAAAAAAA-TAAATTTGAGAAGACGGTTCT-AAACAAATAGTGTTAA
1 TTTTTCTACAGTAGTTCTTAAAAAAATTAAATTTGAGAAGACAGTTCTGAAA-AAATAATGTAAA
* * * * *
51536060 AAATGCTTCAAGT-AGGATTCACTGTCAGCAAAATTACGGAAAAAAGCTCTCATGTGGACGCTC
65 AAACGCTTCAA-TCAAGATGCACTGTCAGCAAAATTACGGAAAAAAGCTCCCACGTGGACGCTC
51536123 TTTTTCTACAGTAGTTCTT
1 TTTTTCTACAGTAGTTCTT
51536142 GTTTGGCCTT
Statistics
Matches: 130, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
125 3 0.02
126 101 0.78
127 25 0.19
128 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (127 bp):
TTTTTCTACAGTAGTTCTTAAAAAAATTAAATTTGAGAAGACAGTTCTGAAAAAATAATGTAAAA
AACGCTTCAATCAAGATGCACTGTCAGCAAAATTACGGAAAAAAGCTCCCACGTGGACGCTC
Found at i:51539093 original size:9 final size:9
Alignment explanation
Indices: 51539070--51539100 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
51539060 ATTTCTATTT
51539070 TATTAAAAA
1 TATTAAAAA
51539079 TA-TAAAAA
1 TATTAAAAA
51539087 TATTAAAAA
1 TATTAAAAA
51539096 TATTA
1 TATTA
51539101 CCTTATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (9 bp):
TATTAAAAA
Found at i:51539177 original size:24 final size:24
Alignment explanation
Indices: 51539121--51539177 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
51539111 AAGAACTTCT
51539121 ATTTTATTAAAAATATAAAAATAA
1 ATTTTATTAAAAATATAAAAATAA
*
51539145 ATTACTATT-AAAATATTAAAAATAA
1 ATT-TTATTAAAAATA-TAAAAATAA
*
51539170 CTTTTATT
1 ATTTTATT
51539178 TTATTAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 13 0.46
25 15 0.54
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (24 bp):
ATTTTATTAAAAATATAAAAATAA
Found at i:51539179 original size:54 final size:54
Alignment explanation
Indices: 51539062--51539185 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
51539052 GTTGCATTAT
*** *
51539062 TTCTATTTTATTAAAAATATAAAAATATTAAAAATATTACCTTATTCAAAAGAAC
1 TTCTATTTTATTAAAAATATAAAAATA-TAAAAATATTAAAATATTAAAAAGAAC
* * *
51539117 TTCTATTTTATTAAAAATATAAAAATA-AATTACTATTAAAATATTAAAAATAAC
1 TTCTATTTTATTAAAAATATAAAAATATAA-AAATATTAAAATATTAAAAAGAAC
*
51539171 TTTTATTTTATTAAA
1 TTCTATTTTATTAAA
51539186 TGAAACAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
53 2 0.03
54 31 0.52
55 27 0.45
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (54 bp):
TTCTATTTTATTAAAAATATAAAAATATAAAAATATTAAAATATTAAAAAGAAC
Found at i:51539253 original size:93 final size:92
Alignment explanation
Indices: 51539125--51539313 Score: 360
Period size: 93 Copynumber: 2.0 Consensus size: 92
51539115 ACTTCTATTT
*
51539125 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTTATTTTATTAAATGAA
1 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGAA
51539190 ACAATATAAAAATAGTTTGTACAAATA
66 ACAATATAAAAATAGTTTGTACAAATA
51539217 TATTAAAAATATAAAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGA
1 TATTAAAAATAT-AAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGA
51539282 AACAATATAAAAATAGTTTGTACAAATA
65 AACAATATAAAAATAGTTTGTACAAATA
51539310 TATT
1 TATT
51539314 TAATAAATCA
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 12 0.13
93 83 0.87
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (92 bp):
TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAACAACTTTTATTTTATTAAATGAA
ACAATATAAAAATAGTTTGTACAAATA
Found at i:51544582 original size:7 final size:7
Alignment explanation
Indices: 51544546--51544573 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
51544536 GTATTGATAC
51544546 TTAAAAA
1 TTAAAAA
51544553 TTAAAAA
1 TTAAAAA
51544560 TTAAAAA
1 TTAAAAA
51544567 TTAAAAA
1 TTAAAAA
51544574 AACTTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
TTAAAAA
Found at i:51549059 original size:26 final size:25
Alignment explanation
Indices: 51549029--51549125 Score: 83
Period size: 26 Copynumber: 3.9 Consensus size: 25
51549019 GGACTCACCA
51549029 CAGCTCGTATGAGCTTACCGATATAT
1 CAGCTCGTATGAGCTTACCGATAT-T
** *
51549055 CAGCTTTTATGAGCTTA-CAAT-TT
1 CAGCTCGTATGAGCTTACCGATATT
* *
51549078 CAGCTCG-ATAGAGCTTACCGTTCTT
1 CAGCTCGTAT-GAGCTTACCGATATT
* *
51549103 CAACTCAGAATGAGCTTACCGAT
1 CAGCTC-GTATGAGCTTACCGAT
51549126 CATAGCTCGA
Statistics
Matches: 57, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
22 2 0.04
23 13 0.23
24 3 0.05
25 10 0.18
26 27 0.47
27 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (25 bp):
CAGCTCGTATGAGCTTACCGATATT
Found at i:51556126 original size:9 final size:9
Alignment explanation
Indices: 51556109--51556454 Score: 128
Period size: 9 Copynumber: 40.9 Consensus size: 9
51556099 TAAGTATAAT
*
51556109 TAAGCTATG
1 TAAGTTATG
51556118 TAAGTTATG
1 TAAGTTATG
*
51556127 TAAGTTATA
1 TAAGTTATG
*
51556136 TAAGTTGTG
1 TAAGTTATG
*
51556145 T-A-TGATG
1 TAAGTTATG
51556152 TAAGTTATG
1 TAAGTTATG
*
51556161 AAAGTTATG
1 TAAGTTATG
51556170 T-A-TTATG
1 TAAGTTATG
*
51556177 TAAGTTATT
1 TAAGTTATG
*
51556186 TAAGTTGTG
1 TAAGTTATG
51556195 T-A-TTATG
1 TAAGTTATG
*
51556202 TAAGTCATG
1 TAAGTTATG
* *
51556211 TAGGCTATG
1 TAAGTTATG
51556220 T-A-TTATG
1 TAAGTTATG
51556227 TAAGTTA--
1 TAAGTTATG
*
51556234 TAA--TAAG
1 TAAGTTATG
51556241 TAAGTTATG
1 TAAGTTATG
* *
51556250 AAAGTTATATA
1 TAAG-T-TATG
*
51556261 TAAGTTTATATA
1 TAAG--T-TATG
51556273 TAAGTTATG
1 TAAGTTATG
51556282 TAAGTTA--
1 TAAGTTATG
51556289 T-A--TATG
1 TAAGTTATG
51556295 TAAGTTATG
1 TAAGTTATG
*
51556304 T--GTTGTG
1 TAAGTTATG
*
51556311 TAAGTTTATATA
1 TAAG--T-TATG
*
51556323 TAAATTTTAT-
1 T-AA-GTTATG
51556333 TCAAGTTATG
1 T-AAGTTATG
51556343 --A---ATG
1 TAAGTTATG
51556347 TAAGTTATG
1 TAAGTTATG
*
51556356 TAAGTTGTG
1 TAAGTTATG
*
51556365 T--GTAATG
1 TAAGTTATG
51556372 TAAGTTATG
1 TAAGTTATG
51556381 T-A-TTATG
1 TAAGTTATG
*
51556388 TAAGTTATT
1 TAAGTTATG
* *
51556397 TAAATTATT
1 TAAGTTATG
*
51556406 TAAGTTGTG
1 TAAGTTATG
51556415 T-A-TTATG
1 TAAGTTATG
*
51556422 TAAGTCATG
1 TAAGTTATG
* *
51556431 TAGGCTATG
1 TAAGTTATG
51556440 T--GTTATG
1 TAAGTTATG
51556447 TAAGTTAT
1 TAAGTTAT
51556455 TATAAGAAAG
Statistics
Matches: 251, Mismatches: 45, Indels: 82
0.66 0.12 0.22
Matches are distributed among these distances:
4 5 0.02
5 2 0.01
6 3 0.01
7 57 0.23
8 11 0.04
9 141 0.56
10 5 0.02
11 10 0.04
12 15 0.06
13 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:51556156 original size:25 final size:25
Alignment explanation
Indices: 51556122--51556460 Score: 152
Period size: 25 Copynumber: 13.7 Consensus size: 25
51556112 GCTATGTAAG
*
51556122 TTATGTAAGTTATATAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTATGTA
*
51556147 TGATGTAAGTTATGA-AAGTTATGTA
1 TTATGTAAGTTAT-ATAAGTTATGTA
* *
51556172 TTATGTAAGTTATTTAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTATGTA
* * * *
51556197 TTATGTAAGTCATGTAGGCTATGTA
1 TTATGTAAGTTATATAAGTTATGTA
*
51556222 TTATGTAAGTTATAATAAG-TAAG--
1 TTATGTAAGTTAT-ATAAGTTATGTA
*
51556245 TTATGAAAGTTATATATAAG-T-T-TA
1 TTATGTAAG-T-TATATAAGTTATGTA
* *
51556269 -TATATAAGTTATGTAAGTTA--TA
1 TTATGTAAGTTATATAAGTTATGTA
* ** * *
51556291 -TATGTAAGTTATGTGTTGTGTAAGTT
1 TTATGTAAGTTATAT-AAGT-TATGTA
* * *
51556317 TATATATAAATTTTATTCAAGTTATG-A
1 T-TATGTAAGTTATA-T-AAGTTATGTA
* * *
51556344 --ATGTAAGTTATGTAAGTTGTGTG
1 TTATGTAAGTTATATAAGTTATGTA
* *
51556367 TAATGTAAGTTATGT-A-TTATGTAA
1 TTATGTAAGTTATATAAGTTATGT-A
* * * *
51556391 GTTATTTAAATTATTTAAGTTGTGTA
1 -TTATGTAAGTTATATAAGTTATGTA
* * * * *
51556417 TTATGTAAGTCATGTAGGCTATGTG
1 TTATGTAAGTTATATAAGTTATGTA
51556442 TTATGTAAGTTATTATAAG
1 TTATGTAAGTTA-TATAAG
51556461 AAAGTTATAT
Statistics
Matches: 234, Mismatches: 56, Indels: 47
0.69 0.17 0.14
Matches are distributed among these distances:
21 7 0.03
22 24 0.10
23 22 0.09
24 18 0.08
25 132 0.56
26 11 0.05
27 5 0.02
28 12 0.05
29 3 0.01
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATGTAAGTTATATAAGTTATGTA
Found at i:51556177 original size:50 final size:50
Alignment explanation
Indices: 51556110--51556241 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
51556100 AAGTATAATT
*
51556110 AAGCTATGTAAGTTATGTAAGTTATATAAGTTGTGTATGATGTAAGTTATGA
1 AAGCTATGT-A-TTATGTAAGTTATATAAGTTGTGTATGATGTAAGTCATGA
* * * *
51556162 AAGTTATGTATTATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGT
1 AAGCTATGTATTATGTAAGTTATATAAGTTGTGTATGATGTAAGTCATGA
*
51556212 AGGCTATGTATTATGTAAGTTATAATAAGT
1 AAGCTATGTATTATGTAAGTTAT-ATAAGT
51556242 AAGTTATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
50 57 0.80
51 6 0.08
52 8 0.11
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.43
Consensus pattern (50 bp):
AAGCTATGTATTATGTAAGTTATATAAGTTGTGTATGATGTAAGTCATGA
Found at i:51556265 original size:34 final size:34
Alignment explanation
Indices: 51556226--51556302 Score: 97
Period size: 32 Copynumber: 2.3 Consensus size: 34
51556216 TATGTATTAT
51556226 GTAAGTTATA-ATAAGTAAGTTATGAAAGTTATATA
1 GTAAGTTATATAT-A-TAAGTTATGAAAGTTATATA
*
51556261 -TAAGTT-TATATATAAGTTATGTAAGTTATATA
1 GTAAGTTATATATATAAGTTATGAAAGTTATATA
51556293 TGTAAGTTAT
1 -GTAAGTTAT
51556303 GTGTTGTGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
32 19 0.51
33 3 0.08
34 14 0.38
35 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.43
Consensus pattern (34 bp):
GTAAGTTATATATATAAGTTATGAAAGTTATATA
Found at i:51556272 original size:10 final size:11
Alignment explanation
Indices: 51556251--51556293 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
51556241 TAAGTTATGA
51556251 AAGTTATATAT
1 AAGTTATATAT
51556262 AAGTTTATATAT
1 AAG-TTATATAT
*
51556274 AAG-T-TATGT
1 AAGTTATATAT
51556283 AAGTTATATAT
1 AAGTTATATAT
51556294 GTAAGTTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
11 7 0.26
12 11 0.41
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.47
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:51556296 original size:13 final size:13
Alignment explanation
Indices: 51556278--51556302 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
51556268 ATATATAAGT
51556278 TATGTAAGTTATA
1 TATGTAAGTTATA
51556291 TATGTAAGTTAT
1 TATGTAAGTTAT
51556303 GTGTTGTGTA
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:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
TATGTAAGTTATA
Found at i:51556348 original size:52 final size:51
Alignment explanation
Indices: 51556222--51556365 Score: 141
Period size: 52 Copynumber: 2.7 Consensus size: 51
51556212 AGGCTATGTA
* * * *
51556222 TTATGTAAGTTATAATAAGTAAGTTATGAAAGTTATATATAAGTTTATATATAAG
1 TTATGTAAGTTAT-ATATGTAAGTTATG-TAG-T-TGTGTAAGTTTATATATAAG
*
51556277 TTATGTAAGTTATATATGTAAGTTATGT-GTTGTGTAAGTTTATATATAAATT
1 TTATGTAAGTTATATATGTAAGTTATGTAGTTGTGTAAGTTTATATAT-AA-G
51556329 TTAT-TCAAGTTATGA-ATGTAAGTTATGTAAGTTGTGT
1 TTATGT-AAGTTAT-ATATGTAAGTTATGT-AGTTGTGT
51556366 GTAATGTAAG
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
50 15 0.19
51 4 0.05
52 25 0.32
53 1 0.01
54 20 0.26
55 13 0.17
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (51 bp):
TTATGTAAGTTATATATGTAAGTTATGTAGTTGTGTAAGTTTATATATAAG
Found at i:51556374 original size:16 final size:16
Alignment explanation
Indices: 51556353--51556432 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
51556343 AATGTAAGTT
* *
51556353 ATGTAAGTTGTGTGTA
1 ATGTAAGTTATGTATA
*
51556369 ATGTAAGTTATGTATT
1 ATGTAAGTTATGTATA
* *
51556385 ATGTAAGTTATTTAAATT
1 ATGTAAGTTATGT--ATA
* * *
51556403 ATTTAAGTTGTGTATT
1 ATGTAAGTTATGTATA
*
51556419 ATGTAAGTCATGTA
1 ATGTAAGTTATGTA
51556433 GGCTATGTGT
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 39 0.75
18 13 0.25
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.47
Consensus pattern (16 bp):
ATGTAAGTTATGTATA
Found at i:51556483 original size:10 final size:11
Alignment explanation
Indices: 51556462--51556491 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
51556452 TATTATAAGA
51556462 AAGTTATATAT
1 AAGTTATATAT
51556473 AAGTTTATATAT
1 AAG-TTATATAT
51556485 AAGTTAT
1 AAGTTAT
51556492 GTAAGTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (11 bp):
AAGTTATATAT
Found at i:51556923 original size:19 final size:19
Alignment explanation
Indices: 51556901--51556941 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
51556891 GATATGATTG
*
51556901 ATAAATTTTTCAA-ATATAT
1 ATAAAATTTT-AATATATAT
51556920 ATAAAATTTTAATATATAT
1 ATAAAATTTTAATATATAT
51556939 ATA
1 ATA
51556942 TTAAAACTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
ATAAAATTTTAATATATAT
Found at i:51556940 original size:21 final size:22
Alignment explanation
Indices: 51556912--51556966 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
51556902 TAAATTTTTC
* *
51556912 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAACTGTATAT
*
51556933 ATATATATATTAAAACTGTATAT
1 AAATATATA-TAAAACTGTATAT
51556956 AAATATATATA
1 AAATATATATA
51556967 TCAAAGATGT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 8 0.29
22 10 0.36
23 10 0.36
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATATATAAAACTGTATAT
Found at i:51556961 original size:23 final size:22
Alignment explanation
Indices: 51556912--51556965 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
51556902 TAAATTTTTC
* *
51556912 AAATATATA-TAAAATTTTAAT
1 AAATATATATTAAAACTGTAAT
*
51556933 ATATATATATTAAAACTGTATAT
1 AAATATATATTAAAACTGTA-AT
51556956 AAATATATAT
1 AAATATATAT
51556966 ATCAAAGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.30
22 8 0.30
23 11 0.41
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATATATATTAAAACTGTAAT
Found at i:51556984 original size:25 final size:25
Alignment explanation
Indices: 51556926--51556987 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
51556916 ATATATAAAA
* *
51556926 TTTTAATATATATATATTAAAACTG
1 TTTTAAAATATATATATCAAAACTG
*
51556951 -TATATAAATATATATATCAAAGA-TG
1 TTTTA-AAATATATATATCAAA-ACTG
51556976 TTTTAAAATATA
1 TTTTAAAATATA
51556988 ACTTTGAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 3 0.10
25 23 0.77
26 4 0.13
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (25 bp):
TTTTAAAATATATATATCAAAACTG
Found at i:51559673 original size:21 final size:21
Alignment explanation
Indices: 51559607--51559673 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
51559597 TATGTTTCAT
51559607 TAAAA-TTTTAAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
51559629 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
51559649 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
51559670 TAAA
1 TAAA
51559674 TTTTAGTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.41
21 7 0.19
22 6 0.16
23 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:51560374 original size:8 final size:8
Alignment explanation
Indices: 51560361--51560429 Score: 81
Period size: 8 Copynumber: 8.9 Consensus size: 8
51560351 ACCCTTGACA
51560361 CCCTAAAC
1 CCCTAAAC
51560369 CCCTAAAC
1 CCCTAAAC
51560377 CCCT-AAC
1 CCCTAAAC
*
51560384 ACCTAAATC
1 CCCTAAA-C
51560393 CCCTAAAC
1 CCCTAAAC
*
51560401 CCCTAAAT
1 CCCTAAAC
51560409 CCCT-AAC
1 CCCTAAAC
*
51560416 CTCT-AAC
1 CCCTAAAC
51560423 CCCTAAA
1 CCCTAAA
51560430 TCTCGATCCC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
7 17 0.33
8 28 0.54
9 7 0.13
ACGTcount: A:0.36, C:0.46, G:0.00, T:0.17
Consensus pattern (8 bp):
CCCTAAAC
Found at i:51560699 original size:88 final size:89
Alignment explanation
Indices: 51560594--51560758 Score: 296
Period size: 89 Copynumber: 1.9 Consensus size: 89
51560584 TCCCAAACCC
* *
51560594 CTAACCACTAACCCCTAAATATTATTTAATATATAAATT-AAAAACACTAATTAATCTAAATCCT
1 CTAACCACTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCT
51560658 AAACCCTAACCCGACCCCGAATCA
66 AAACCCTAACCCGACCCCGAATCA
*
51560682 CTAACCCCTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCT
1 CTAACCACTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCT
51560747 AAACCCTAACCC
66 AAACCCTAACCC
51560759 CTAAATATTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
88 36 0.49
89 37 0.51
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (89 bp):
CTAACCACTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCT
AAACCCTAACCCGACCCCGAATCA
Found at i:51560819 original size:63 final size:63
Alignment explanation
Indices: 51560682--51560820 Score: 224
Period size: 63 Copynumber: 2.2 Consensus size: 63
51560672 CCCCGAATCA
* * *
51560682 CTAACCCCTAAACCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATC
1 CTAAACCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
* *
51560745 CTAAACCCTAACCCCTAAATATTATTTAATATATAAATTAAAATACACTAATTAATCTAAACC
1 CTAAACCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
*
51560808 CTAAACTCTAACC
1 CTAAACCCTAACC
51560821 TAACACCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 70 1.00
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.30
Consensus pattern (63 bp):
CTAAACCCTAACCCCTAAACATTATTTAATATATAAATTAAAAAACACTAATTAATCTAAACC
Found at i:51560874 original size:14 final size:14
Alignment explanation
Indices: 51560857--51560890 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
51560847 TCCTAACTTT
* *
51560857 TAACCACTAACCCC
1 TAACCCCTAACCAC
51560871 TAACCCCTAACCAC
1 TAACCCCTAACCAC
51560885 TAACCC
1 TAACCC
51560891 ATAAACCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (14 bp):
TAACCCCTAACCAC
Found at i:51560938 original size:14 final size:15
Alignment explanation
Indices: 51560921--51560952 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
51560911 CTTAAATCAA
51560921 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
51560935 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
51560950 AAT
1 AAT
51560953 ATATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:51561336 original size:42 final size:42
Alignment explanation
Indices: 51561290--51561373 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
51561280 ATTTTAATTA
51561290 ATATAAATAAACAAATTACATAGCAAATAGACAGATAAAATG
1 ATATAAATAAACAAATTACATAGCAAATAGACAGATAAAATG
51561332 ATATAAATAAACAAATTACATAGCAAATAGACAGATAAAATG
1 ATATAAATAAACAAATTACATAGCAAATAGACAGATAAAATG
51561374 TTTTTGCGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (42 bp):
ATATAAATAAACAAATTACATAGCAAATAGACAGATAAAATG
Found at i:51561439 original size:41 final size:41
Alignment explanation
Indices: 51561379--51561653 Score: 279
Period size: 41 Copynumber: 6.7 Consensus size: 41
51561369 AAATGTTTTT
51561379 GCGGCGCTTTT-TCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCT-AAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
51561420 GCGGCGCTTTTCTATAAACGCTGCTAAAGATTTGAGTATT-
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* * ** **
51561460 GCGACGATTTTGGAAAAAACGCCAATAAAGATCTGAGCATTA
1 GCGGCGCTTTT-CTAAAAACGCCGCTAAAGATCTGAGCATTA
* *
51561502 GCGGCGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
51561543 G-GACGCTTCTCAAAAAAACGCTGCTAAAGATCTGAGCATTA
1 GCGGCGCTTTTC-TAAAAACGCCGCTAAAGATCTGAGCATTA
* *
51561584 GCGGCGCTTTTAC-AAAAACGTCGCTAAAGATCTGGGCATTA
1 GCGGCGCTTTT-CTAAAAACGCCGCTAAAGATCTGAGCATTA
* * * *
51561625 GCGACGTTTTTTTTTAAAACGCCGCTAAA
1 GCGGCG-CTTTTCTAAAAACGCCGCTAAA
51561654 TCCCCGAAAG
Statistics
Matches: 192, Mismatches: 34, Indels: 15
0.80 0.14 0.06
Matches are distributed among these distances:
40 18 0.09
41 140 0.73
42 33 0.17
43 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.25
Consensus pattern (41 bp):
GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:51561601 original size:123 final size:122
Alignment explanation
Indices: 51561379--51561627 Score: 322
Period size: 123 Copynumber: 2.0 Consensus size: 122
51561369 AAATGTTTTT
* * * * * *
51561379 GCGGCGCTTTTTCAAAAACGCCGCTAAAGATCTGAGCATTAGCGGCGCTTTTCTATAAACGCTGC
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGACGCTTCTCAAAAAACGCTGC
* *
51561444 TAAAGATTTGAGTATTGCGACGATTTTGGAAAAAACGCCAATAAAGATCTGAGCATTA
66 TAAAGATCTGAGCATTGCGACGATTTT-GAAAAAACGCCAATAAAGATCTGAGCATTA
51561502 GCGGCGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTAG-GACGCTTCTCAAAAAAACGCTG
1 GCGGCGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGACGCTTCTC-AAAAAACGCTG
* * * ** *
51561566 CTAAAGATCTGAGCATTAGCGGCGCTTTT-ACAAAAACGTCGCTAAAGATCTGGGCATTA
65 CTAAAGATCTGAGCATT-GCGACGATTTTGA-AAAAACGCCAATAAAGATCTGAGCATTA
51561625 GCG
1 GCG
51561628 ACGTTTTTTT
Statistics
Matches: 109, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
122 9 0.08
123 91 0.83
124 9 0.08
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.24
Consensus pattern (122 bp):
GCGGCGCTTCTCCAAAAACGCCGCTAAAGATCTGAGCATTAGCGACGCTTCTCAAAAAACGCTGC
TAAAGATCTGAGCATTGCGACGATTTTGAAAAAACGCCAATAAAGATCTGAGCATTA
Found at i:51561734 original size:39 final size:41
Alignment explanation
Indices: 51561691--51561785 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 41
51561681 GGTCTTAGGT
* *
51561691 TTTTTTGCGGCGTTTTGGAAAAAAA-CGCCG-TAATGCAC-A
1 TTTTTAGCGGCGTTTT-CAAAAAAATCGCCGCTAATGCACGA
* * *
51561730 TTTTTAGCGGCG-ATTCAAAAAAATCGCTGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCAAAAAAATCGCCGCTAATGCACGA
51561770 TTTTTAGCGGCGTTTT
1 TTTTTAGCGGCGTTTT
51561786 TTATTCAACA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
37 7 0.15
38 6 0.13
39 18 0.39
40 13 0.28
41 2 0.04
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTCAAAAAAATCGCCGCTAATGCACGA
Found at i:51566086 original size:15 final size:14
Alignment explanation
Indices: 51566066--51566095 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
51566056 AGCTTCTTGG
51566066 TTTCTTCTACTTGTT
1 TTTCTTCTAC-TGTT
51566081 TTTCTTCTACTGTT
1 TTTCTTCTACTGTT
51566095 T
1 T
51566096 CCCATAACCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.07, C:0.20, G:0.07, T:0.67
Consensus pattern (14 bp):
TTTCTTCTACTGTT
Found at i:51569710 original size:34 final size:34
Alignment explanation
Indices: 51569667--51569732 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
51569657 AGTAAAATAT
51569667 TTTTCGTAAAATAATTT-CGGGAAAATATTTTAC
1 TTTTCGTAAAATAATTTACGGGAAAATATTTTAC
* *
51569700 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATAATTTACGGGAAAATATTTT
51569733 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 11 0.38
35 13 0.45
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATAATTTACGGGAAAATATTTTAC
Found at i:51570875 original size:24 final size:21
Alignment explanation
Indices: 51570844--51570887 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
51570834 TTTATTATTT
51570844 AAATTTAATTATAAAAATATATA
1 AAATTTAA-T-TAAAAATATATA
51570867 AAATATTAATTAAAAATATAT
1 AAAT-TTAATTAAAAATATAT
51570888 TTTTTAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 5 0.25
24 4 0.20
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTAATTAAAAATATATA
Found at i:51578019 original size:26 final size:25
Alignment explanation
Indices: 51577990--51578045 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
51577980 AAAATAAATA
51577990 AATAAA-TAAAAATGGAATGTATATAT
1 AATAAAGTAAAAATGGAA-GTATA-AT
*
51578016 AATAAAGTAAACATGGAAGTATAAT
1 AATAAAGTAAAAATGGAAGTATAAT
51578041 AATAA
1 AATAA
51578046 TAATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 7 0.25
26 11 0.39
27 10 0.36
ACGTcount: A:0.59, C:0.02, G:0.12, T:0.27
Consensus pattern (25 bp):
AATAAAGTAAAAATGGAAGTATAAT
Found at i:51578044 original size:3 final size:3
Alignment explanation
Indices: 51578036--51578096 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
51578026 ACATGGAAGT
51578036 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51578084 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
51578097 AAGGACCAAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51578179 original size:3 final size:3
Alignment explanation
Indices: 51578171--51578273 Score: 97
Period size: 3 Copynumber: 35.3 Consensus size: 3
51578161 ATAACAATGG
* * *
51578171 ATA ATA ATA GTA ATA ATA A-A ATA ATA ATA TTA GTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
51578218 ATA CTT ATA ATA ATT GTA ATA A-A ATA ATA ATA ATA ATGA CT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
51578262 ATA ATA A-A ATA A
1 ATA ATA ATA ATA A
51578274 AAATGCTAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
2 7 0.09
3 71 0.89
4 2 0.03
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:51578263 original size:53 final size:52
Alignment explanation
Indices: 51578171--51578272 Score: 136
Period size: 53 Copynumber: 1.9 Consensus size: 52
51578161 ATAACAATGG
* *
51578171 ATAATAATAGTAATAATAAAATAATAATATTAGTAATAATAATAATAATACTT
1 ATAATAATAGTAATAATAAAATAATAATATGACTAATAATAATAA-AATACTT
*
51578224 ATAATAATTGTAATAA-AATAATAATAATAATGACT-ATAATAATAAAATA
1 ATAATAATAGTAATAATAA-AATAATAAT-ATGACTAATAATAATAAAATA
51578273 AAAATGCTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
52 6 0.14
53 34 0.77
54 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (52 bp):
ATAATAATAGTAATAATAAAATAATAATATGACTAATAATAATAAAATACTT
Found at i:51578277 original size:35 final size:35
Alignment explanation
Indices: 51578205--51578275 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
51578195 TAATATTAGT
**
51578205 AATAATAATAATAATACTTATAATAATTGTAATAA
1 AATAATAATAATAATACTTATAATAATTAAAATAA
51578240 AATAATAATAATAATGAC-TATAATAA-TAAAATAA
1 AATAATAATAATAAT-ACTTATAATAATTAAAATAA
51578274 AA
1 AA
51578276 ATGCTAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
34 8 0.24
35 23 0.70
36 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (35 bp):
AATAATAATAATAATACTTATAATAATTAAAATAA
Found at i:51581427 original size:42 final size:42
Alignment explanation
Indices: 51581356--51581463 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
51581346 AGTATAACAA
51581356 GATCACCACATGCCCCAATCTGATTGAAATTTGAGCTACTCT
1 GATCACCACATGCCCCAATCTGATTGAAATTTGAGCTACTCT
**
51581398 GATCATCC-CATGCCCCTTTCTG-TTCGAAATTTGAGCTACTCT
1 GATCA-CCACATGCCCCAATCTGATT-GAAATTTGAGCTACTCT
* * *
51581440 GATCACCTCATGCCCTATTCTGAT
1 GATCACCACATGCCCCAATCTGAT
51581464 CAATATTTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
41 4 0.07
42 51 0.88
43 3 0.05
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.32
Consensus pattern (42 bp):
GATCACCACATGCCCCAATCTGATTGAAATTTGAGCTACTCT
Found at i:51581562 original size:6 final size:6
Alignment explanation
Indices: 51581551--51581594 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
51581541 TTGGCCTCTC
* *
51581551 CTTTTT CTTTTT CTTTTT C-TTTT CCTTCT CTTTTT C-TTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
51581595 CATCATTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:51581573 original size:11 final size:11
Alignment explanation
Indices: 51581553--51581594 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
51581543 GGCCTCTCCT
51581553 TTTTCTTTTTC
1 TTTTCTTTTTC
*
51581564 TTTTTCTTTTCC
1 -TTTTCTTTTTC
*
51581576 TTCTCTTTTTC
1 TTTTCTTTTTC
51581587 TTTTCTTT
1 TTTTCTTT
51581595 CATCATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:51581603 original size:18 final size:18
Alignment explanation
Indices: 51581565--51581621 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
51581555 TTCTTTTTCT
* *
51581565 TTTTCTTTTCCTTC-TCT
1 TTTTCTTTTCTTTCATCA
51581582 TTTTCTTTTCTTTCATCA
1 TTTTCTTTTCTTTCATCA
*
51581600 TTTTCATTT-TTTCATTCA
1 TTTTCTTTTCTTTCA-TCA
51581618 TTTT
1 TTTT
51581622 TTTATTTTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 18 0.51
18 17 0.49
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTCTTTTCTTTCATCA
Found at i:51581614 original size:17 final size:19
Alignment explanation
Indices: 51581582--51581621 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
51581572 TTCCTTCTCT
*
51581582 TTTTCTTTTCTTTCA-TCA
1 TTTTCATTTCTTTCATTCA
51581600 TTTTCATTT-TTTCATTCA
1 TTTTCATTTCTTTCATTCA
51581618 TTTT
1 TTTT
51581622 TTTATTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTTCATTTCTTTCATTCA
Found at i:51585009 original size:18 final size:18
Alignment explanation
Indices: 51584970--51585013 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
51584960 AGACTTGAAC
*
51584970 AAATAAAGCAAATATAGCA
1 AAATGAAGCAAATATA-CA
51584989 AAATGAAGCAAACTATA-A
1 AAATGAAGCAAA-TATACA
51585007 AAATGAA
1 AAATGAA
51585014 ATGCAACGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (18 bp):
AAATGAAGCAAATATACA
Found at i:51585967 original size:26 final size:25
Alignment explanation
Indices: 51585920--51585975 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 25
51585910 AAAATAAATA
*
51585920 AATAAATAAAAATGGAATGTATATAT
1 AATAAATAAAAATGGAAAGTAT-TAT
*
51585946 AATAAAGTAAACAT-GAAAGTATTAT
1 AATAAA-TAAAAATGGAAAGTATTAT
51585971 AATAA
1 AATAA
51585976 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 8 0.30
26 13 0.48
27 6 0.22
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.29
Consensus pattern (25 bp):
AATAAATAAAAATGGAAAGTATTAT
Found at i:51585977 original size:3 final size:3
Alignment explanation
Indices: 51585969--51586017 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
51585959 TGAAAGTATT
51585969 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
51586017 A
1 A
51586018 GTAACAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51586126 original size:3 final size:3
Alignment explanation
Indices: 51586118--51586226 Score: 127
Period size: 3 Copynumber: 37.3 Consensus size: 3
51586108 ATAACAATGG
* * *
51586118 ATA ATA ATA GTA ATA TTA A-A GTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
51586165 ATA ATA ATA ATA ATA ATA ATA ATT GTA ATA A-A ATA ATA ATA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
*
51586210 CT- ATA ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA ATA A
51586227 AAATGCTAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
2 6 0.07
3 81 0.91
4 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:51587458 original size:41 final size:37
Alignment explanation
Indices: 51587401--51587499 Score: 135
Period size: 41 Copynumber: 2.6 Consensus size: 37
51587391 GGAGATAAAG
* *
51587401 AAAAGTCATAATCATTGCATCAATTCCACTACAAAAAAAAA
1 AAAAGTCATAGTCATTGCATCAATTCCACGAC----AAAAA
*
51587442 AAAAGTCATAGTCATTGCATCCATTCCACGACAAAAA
1 AAAAGTCATAGTCATTGCATCAATTCCACGACAAAAA
51587479 AAAAGTCATAGTCATTGCATC
1 AAAAGTCATAGTCATTGCATC
51587500 CATTTTGATT
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
37 26 0.47
41 29 0.53
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.23
Consensus pattern (37 bp):
AAAAGTCATAGTCATTGCATCAATTCCACGACAAAAA
Found at i:51587487 original size:37 final size:38
Alignment explanation
Indices: 51587401--51587503 Score: 145
Period size: 37 Copynumber: 2.7 Consensus size: 38
51587391 GGAGATAAAG
* * *
51587401 AAAAGTCATAATCATTGCATCAATTCCACTACAAAAAAAAA
1 AAAAGTCATAGTCATTGCATCCATTCCACGAC---AAAAAA
51587442 AAAAGTCATAGTCATTGCATCCATTCCACGAC-AAAAA
1 AAAAGTCATAGTCATTGCATCCATTCCACGACAAAAAA
51587479 AAAAGTCATAGTCATTGCATCCATT
1 AAAAGTCATAGTCATTGCATCCATT
51587504 TTGATTTGAA
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
37 30 0.51
41 29 0.49
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.24
Consensus pattern (38 bp):
AAAAGTCATAGTCATTGCATCCATTCCACGACAAAAAA
Found at i:51588004 original size:19 final size:20
Alignment explanation
Indices: 51587979--51588026 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
51587969 AATGATAAAA
51587979 AATAAAAATCAATAAAATTT
1 AATAAAAATCAATAAAATTT
* * *
51587999 -ATAAAAATTATTAAATTTT
1 AATAAAAATCAATAAAATTT
51588018 AATAAAAAT
1 AATAAAAAT
51588027 ATAAGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
AATAAAAATCAATAAAATTT
Found at i:51588069 original size:28 final size:27
Alignment explanation
Indices: 51587989--51588070 Score: 74
Period size: 29 Copynumber: 2.9 Consensus size: 27
51587979 AATAAAAATC
* *
51587989 AATAAAATTTATAAAAATTATTAAATTTT
1 AATAAAAATTA-AAAAA-TATTATATTTT
* *
51588018 AATAAAAATATAAGAAATATTTATTTTTT
1 AATAAAAAT-TAAAAAATA-TTATATTTT
*
51588047 ATTAAAAATTAGAAAAATATTATA
1 AATAAAAATTA-AAAAATATTATA
51588071 AAAATCGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
28 8 0.19
29 33 0.77
30 2 0.05
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (27 bp):
AATAAAAATTAAAAAATATTATATTTT
Found at i:51588073 original size:10 final size:10
Alignment explanation
Indices: 51588060--51588130 Score: 51
Period size: 9 Copynumber: 7.3 Consensus size: 10
51588050 AAAAATTAGA
51588060 AAAATATTAT
1 AAAATATTAT
**
51588070 AAAA-ATCGT
1 AAAATATTAT
51588079 AAAA-ATTAT
1 AAAATATTAT
51588088 AAAATA-TAT
1 AAAATATTAT
*
51588097 AGAAATA-TAG
1 A-AAATATTAT
*
51588107 AAAAAATATAT
1 AAAATAT-TAT
*
51588118 AAAATTTTAT
1 AAAATATTAT
51588128 AAA
1 AAA
51588131 GTCATAAGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
9 22 0.46
10 19 0.40
11 7 0.15
ACGTcount: A:0.63, C:0.01, G:0.04, T:0.31
Consensus pattern (10 bp):
AAAATATTAT
Done.