Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 26 of 226
Found at i:11809042 original size:20 final size:21
Alignment explanation
Indices: 11808997--11809045 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
11808987 AGAATTGTAA
*
11808997 TATTAAAT-ATTTATTAAAAT
1 TATTAAATAAATTATTAAAAT
* *
11809017 TTTTAAATAAATTATT-ATAT
1 TATTAAATAAATTATTAAAAT
11809037 TATTAAATA
1 TATTAAATA
11809046 TATGTTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TATTAAATAAATTATTAAAAT
Found at i:11810051 original size:28 final size:27
Alignment explanation
Indices: 11810015--11810068 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
11810005 TTATTATTGT
*
11810015 ATTATTATTAAATATTATAAGTATTATC
1 ATTATTATTAAAGA-TATAAGTATTATC
11810043 ATTATTATTAAAGATATAAGTATTAT
1 ATTATTATTAAAGATATAAGTATTAT
11810069 TATTCAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTATTATTAAAGATATAAGTATTATC
Found at i:11813137 original size:46 final size:46
Alignment explanation
Indices: 11812981--11813231 Score: 418
Period size: 46 Copynumber: 5.5 Consensus size: 46
11812971 CTTACGTATG
*
11812981 ACCACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
11813024 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AAGGCT
* *
11813071 ATCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
11813117 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
* *
11813163 ACCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTGAGGCT
1 ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
*
11813209 ACCACTTATCACTTCGTCACTTG
1 ACCACTTATCACTTTGTCACTTG
11813232 TCACTGGTCA
Statistics
Matches: 195, Mismatches: 9, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
43 12 0.06
44 5 0.03
45 20 0.10
46 115 0.59
47 43 0.22
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (46 bp):
ACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCT
Found at i:11815709 original size:29 final size:30
Alignment explanation
Indices: 11815650--11815707 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11815640 TCCGAGCCTT
*
11815650 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
11815680 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
11815708 AGAGTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:11824278 original size:26 final size:27
Alignment explanation
Indices: 11824249--11824299 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
11824239 TTTAGTGAAA
11824249 ATTAAAAAAAT-ATTTATT-ATAATTCT
1 ATTAAAAAAATAATTT-TTAATAATTCT
*
11824275 ATTAAAAATATAATTTTTAATAATT
1 ATTAAAAAAATAATTTTTAATAATT
11824300 TTAAGTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTAAAAAAATAATTTTTAATAATTCT
Found at i:11824303 original size:24 final size:23
Alignment explanation
Indices: 11824276--11824335 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
11824266 TATAATTCTA
11824276 TTAAAAATATAATTTTTAATAATT
1 TTAAAAATATAATTTTTAAT-ATT
*
11824300 TTAAGTAA-ATAA-TTTTAATATT
1 TTAA-AAATATAATTTTTAATATT
*
11824322 TT-AAAATTTAATTT
1 TTAAAAATATAATTT
11824336 GAATATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
20 2 0.07
21 4 0.13
22 7 0.23
23 7 0.23
24 8 0.27
25 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAAAATATAATTTTTAATATT
Found at i:11825379 original size:30 final size:32
Alignment explanation
Indices: 11825344--11825403 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
11825334 AAAATGATAA
*
11825344 AATTTTAGT-AATGTACTTTTCAA-TTTGATT
1 AATTTTAATCAATGTACTTTTCAACTTTGATT
* *
11825374 AATTTTAATCATTGTACTTTTTAACTTTGA
1 AATTTTAATCAATGTACTTTTCAACTTTGA
11825404 AATTTCATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 8 0.32
31 12 0.48
32 5 0.20
ACGTcount: A:0.30, C:0.08, G:0.08, T:0.53
Consensus pattern (32 bp):
AATTTTAATCAATGTACTTTTCAACTTTGATT
Found at i:11837631 original size:43 final size:42
Alignment explanation
Indices: 11837553--11837669 Score: 157
Period size: 43 Copynumber: 2.8 Consensus size: 42
11837543 GAAACAAATA
* *
11837553 AAAATTATAAAATAT-AAAATATATATATGTGTATATA-CAT
1 AAAATTATAAAATATAAAAATATATGTATGTATATATATCAT
**
11837593 AAAATTATAAAAATATGAAAAATATATGTATGTATATATATTTT
1 AAAATTAT-AAAATAT-AAAAATATATGTATGTATATATATCAT
*
11837637 AAAATTATAAAATATAAAAATATATGTAAGTAT
1 AAAATTATAAAATATAAAAATATATGTATGTAT
11837670 GTGTATATAC
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
40 8 0.12
41 7 0.10
42 17 0.25
43 27 0.40
44 9 0.13
ACGTcount: A:0.56, C:0.01, G:0.06, T:0.38
Consensus pattern (42 bp):
AAAATTATAAAATATAAAAATATATGTATGTATATATATCAT
Found at i:11837713 original size:84 final size:83
Alignment explanation
Indices: 11837550--11837834 Score: 190
Period size: 84 Copynumber: 3.4 Consensus size: 83
11837540 AAGGAAACAA
*
11837550 ATAAAAATTATAAAATAT-AAAATATA-TATATGTGTATATACATAAAATTATAAAAATATGAAA
1 ATAAAAATTATAAAATATAAAAATATATTATATGTGTATATACATAAAAGTATAAAAATAT--AA
11837613 AATATATGTATGTATATATAT
64 AATATATGTA-GTATATATAT
* * * *
11837634 TTTAAAATTATAAAATATAAAAATATATGTAAGTATGTGTATATACATATATAGGTATATAAAT-
1 ATAAAAATTATAAAATATAAAAATATAT-T-A-TATGTGTATATACATA-A-AAGTATAAAAATA
*
11837698 T-AAA-ATATGTA-TATATGTAT
61 TAAAATATATGTAGTATATATAT
* * * * * * * * * * ** *
11837718 ATAAAAAATATGAATTATAAAAAAATATATACAAGTATTTATATATATATTTATAAAAATTTTAA
1 ATAAAAATTATAAAATATAAAAATATAT-TATATGTGTATATACATAAAAGTATAAAAA-TAT-A
* *
11837783 AAATGTATATAG-ATATATAT
63 AAATATATGTAGTATATATAT
** *
11837803 ATGTATA-TATAAAATATAAAAATATATATATA
1 ATAAAAATTATAAAATATAAAAATATAT-TATA
11837835 AAATACATAT
Statistics
Matches: 156, Mismatches: 32, Indels: 26
0.73 0.15 0.12
Matches are distributed among these distances:
80 8 0.05
81 1 0.01
82 12 0.08
83 1 0.01
84 71 0.46
85 24 0.15
86 7 0.04
87 4 0.03
88 1 0.01
89 16 0.10
90 2 0.01
91 9 0.06
ACGTcount: A:0.54, C:0.01, G:0.06, T:0.39
Consensus pattern (83 bp):
ATAAAAATTATAAAATATAAAAATATATTATATGTGTATATACATAAAAGTATAAAAATATAAAA
TATATGTAGTATATATAT
Found at i:11837823 original size:39 final size:37
Alignment explanation
Indices: 11837758--11837870 Score: 99
Period size: 37 Copynumber: 3.0 Consensus size: 37
11837748 ACAAGTATTT
* *
11837758 ATATATATATTTATAAAAATTTTAAAAATGTATATAG
1 ATATATATATTTATAAAAATTATAAAAATATATATAG
*
11837795 ATATATATATGTATATATAAAA-TATAAAAATATATATATAAA
1 ATATATATAT-T-TATA-AAAATTAT-AAAA-ATATATAT-AG
*
11837837 ATACATATATTT-T-AAAA-TATAAAATATATATATA
1 ATATATATATTTATAAAAATTATAAAA-ATATATATA
11837871 AGTATGTATA
Statistics
Matches: 66, Mismatches: 4, Indels: 14
0.79 0.05 0.17
Matches are distributed among these distances:
35 1 0.02
36 13 0.20
37 17 0.26
38 1 0.02
39 7 0.11
40 9 0.14
41 8 0.12
42 10 0.15
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.41
Consensus pattern (37 bp):
ATATATATATTTATAAAAATTATAAAAATATATATAG
Found at i:11837889 original size:37 final size:36
Alignment explanation
Indices: 11837789--11837893 Score: 108
Period size: 37 Copynumber: 2.9 Consensus size: 36
11837779 TTAAAAATGT
*
11837789 ATATAGATATATATATGTATAT-A-TAAAATATAAAA
1 ATATATATATA-ATATGTATATAATTAAAATATAAAA
* ** *
11837824 ATATATATATAAAATACATATATTTTAAAATAT-AAA
1 ATATATATATAATATGTATATA-ATTAAAATATAAAA
11837860 ATATATATATAAGTATGTATATAAATTAAAATAT
1 ATATATATATAA-TATGTATAT-AATTAAAATAT
11837894 GTATATATAT
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
34 7 0.12
35 10 0.18
36 15 0.27
37 23 0.41
38 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (36 bp):
ATATATATATAATATGTATATAATTAAAATATAAAA
Found at i:11837976 original size:3 final size:3
Alignment explanation
Indices: 11837968--11838026 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
11837958 TAAATGAGTA
11837968 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
11838016 AAT AAT AAT AA
1 AAT AAT AAT AA
11838027 CAACAACAGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11840168 original size:51 final size:51
Alignment explanation
Indices: 11840092--11840256 Score: 260
Period size: 51 Copynumber: 3.3 Consensus size: 51
11840082 ACTTTTGATC
*
11840092 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATGTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* *
11840143 AGTGACAAGTGATAAGTAGTAGCTTCAGTTGCACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
* * *
11840194 AGTGGCAAGTGATAAGTGGTAGCTT-AGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
*
11840244 AGTGATAAGTGAT
1 AGTGACAAGTGAT
11840257 CATACGTAAG
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 33 0.32
51 71 0.68
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTAGTAGCTTCAGCTACACTTATCTGATCAGTGACA
Found at i:11843064 original size:75 final size:75
Alignment explanation
Indices: 11842939--11843102 Score: 231
Period size: 75 Copynumber: 2.2 Consensus size: 75
11842929 ATTCATGTAT
* * **
11842939 GCTCATACGAACTGAATAACGGGAAGCTCATGCGAGCTAAATAACGGGAAACTCATGTGAGCTGT
1 GCTCATACGAGCTGAATAACGGGAAGCTCATGCGAGCTAAATAACAGGAAACTCATGTGAGCTAA
11843004 ATAAT-GGGAA
66 AT-ATCGGGAA
* * * *
11843014 GCTCATACGAGCTGAGTATCGGGAAGCTCATGCGAGCTAAGTATCAGGAAACTCATGTGAGCTAA
1 GCTCATACGAGCTGAATAACGGGAAGCTCATGCGAGCTAAATAACAGGAAACTCATGTGAGCTAA
11843079 ATATCGGGAA
66 ATATCGGGAA
*
11843089 GCTCATAAGAGCTG
1 GCTCATACGAGCTG
11843103 TGGTGTATCC
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 2 0.03
75 77 0.97
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (75 bp):
GCTCATACGAGCTGAATAACGGGAAGCTCATGCGAGCTAAATAACAGGAAACTCATGTGAGCTAA
ATATCGGGAA
Found at i:11843101 original size:25 final size:25
Alignment explanation
Indices: 11842939--11843094 Score: 152
Period size: 25 Copynumber: 6.2 Consensus size: 25
11842929 ATTCATGTAT
* * * *
11842939 GCTCATACGAACTGAATAACGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
*
11842964 GCTCATGCGAGCTAAATAACGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
* * **
11842989 ACTCATGTGAGCTGTATAAT-GGGAA
1 GCTCATGCGAGCTAAAT-ATCGGGAA
* * *
11843014 GCTCATACGAGCTGAGTATCGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
* *
11843039 GCTCATGCGAGCTAAGTATCAGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
* *
11843064 ACTCATGTGAGCTAAATATCGGGAA
1 GCTCATGCGAGCTAAATATCGGGAA
11843089 GCTCAT
1 GCTCAT
11843095 AAGAGCTGTG
Statistics
Matches: 108, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
24 2 0.02
25 105 0.97
26 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (25 bp):
GCTCATGCGAGCTAAATATCGGGAA
Found at i:11845068 original size:18 final size:17
Alignment explanation
Indices: 11845043--11845086 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
11845033 ATATACATAC
* *
11845043 ATACTTATATTTTTTAT
1 ATACTTATAATTATTAT
11845060 ATACTTTATAATTATTAT
1 ATAC-TTATAATTATTAT
*
11845078 ATACATATA
1 ATACTTATA
11845087 TATATACACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (17 bp):
ATACTTATAATTATTAT
Found at i:11851164 original size:34 final size:34
Alignment explanation
Indices: 11851121--11851189 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
11851111 AGATTTGCAC
11851121 ATGTGGGTCTGCGGTTTTAGGAAGTGGGTGTTGA
1 ATGTGGGTCTGCGGTTTTAGGAAGTGGGTGTTGA
11851155 ATGTGGGTCTGCGGTTTTAGGAAGTGGGTGTTGA
1 ATGTGGGTCTGCGGTTTTAGGAAGTGGGTGTTGA
11851189 A
1 A
11851190 GCTCAAGTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.16, C:0.06, G:0.43, T:0.35
Consensus pattern (34 bp):
ATGTGGGTCTGCGGTTTTAGGAAGTGGGTGTTGA
Found at i:11852164 original size:5 final size:5
Alignment explanation
Indices: 11852156--11852185 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
11852146 ATCAAATCAG
11852156 TCACC TCACC TCACC TCACC TCACC TCACC
1 TCACC TCACC TCACC TCACC TCACC TCACC
11852186 CCATCTCATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
TCACC
Found at i:11852193 original size:15 final size:15
Alignment explanation
Indices: 11852157--11852193 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
11852147 TCAAATCAGT
*
11852157 CACCTCACCTCACCT
1 CACCTCACCTCACCC
11852172 CACCTCACCTCACCC
1 CACCTCACCTCACCC
*
11852187 CATCTCA
1 CACCTCA
11852194 TTTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.59, G:0.00, T:0.19
Consensus pattern (15 bp):
CACCTCACCTCACCC
Found at i:11853277 original size:21 final size:22
Alignment explanation
Indices: 11853238--11853278 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
11853228 TTACTAAATA
11853238 ATTTAAATATATGAAATATGCC
1 ATTTAAATATATGAAATATGCC
*
11853260 ATTTAAGTATAT-AAATATG
1 ATTTAAATATATGAAATATG
11853279 GGAGAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (22 bp):
ATTTAAATATATGAAATATGCC
Found at i:11858013 original size:2 final size:2
Alignment explanation
Indices: 11858006--11858044 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
11857996 AAAGAAAAGG
11858006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11858045 ATCTGTAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11870598 original size:22 final size:23
Alignment explanation
Indices: 11870568--11870627 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
11870558 TTTTCAGGTA
* *
11870568 CTTCAATTTTTT-TTCAATGTTC
1 CTTCTATTTTTTGTTCAATGTGC
*
11870590 CTTCTATTTCTTTGTTGAATGTGC
1 CTTCTATTT-TTTGTTCAATGTGC
*
11870614 CCTCT-TTTTTTGTT
1 CTTCTATTTTTTGTT
11870628 TTTTTTAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 14 0.44
23 6 0.19
24 12 0.38
ACGTcount: A:0.12, C:0.18, G:0.10, T:0.60
Consensus pattern (23 bp):
CTTCTATTTTTTGTTCAATGTGC
Found at i:11876852 original size:16 final size:17
Alignment explanation
Indices: 11876831--11876864 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11876821 ATGTCTAGAT
11876831 AAATT-ATTAATTGAGG
1 AAATTAATTAATTGAGG
11876847 AAATTAGATTAATTGAGG
1 AAATTA-ATTAATTGAGG
11876865 GGTTAATTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
18 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (17 bp):
AAATTAATTAATTGAGG
Found at i:11878310 original size:46 final size:45
Alignment explanation
Indices: 11878244--11878359 Score: 180
Period size: 46 Copynumber: 2.6 Consensus size: 45
11878234 TTTGAGTACT
* * *
11878244 TCTGATCAGTGGCAAAGTGATAAGTGGTTGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
11878289 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
11878335 TCTGATCAGGGAC-AAGTGATAAGTG
1 TCTGATCAGTGACAAAGTGATAAGTG
11878360 ATCATACGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
44 12 0.18
45 12 0.18
46 42 0.64
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (45 bp):
TCTGATCAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:11879559 original size:29 final size:29
Alignment explanation
Indices: 11879522--11879588 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
11879512 ATATAAAATT
* *
11879522 ATATATTTATGATTTTTATA-AATATATAA
1 ATATTTTTATGATTTTAATAGAAT-TATAA
* *
11879551 ATATTTTTATTATTTTAATAGAATTATAT
1 ATATTTTTATGATTTTAATAGAATTATAA
*
11879580 ATTTTTTTA
1 ATATTTTTA
11879589 AAATTAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (29 bp):
ATATTTTTATGATTTTAATAGAATTATAA
Found at i:11879959 original size:40 final size:40
Alignment explanation
Indices: 11879884--11880170 Score: 273
Period size: 40 Copynumber: 7.2 Consensus size: 40
11879874 ATTTTATGAC
* *
11879884 TTTACCAAAATATTTAACAA-TTACCAATAATTCTAAAGA
1 TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
* * *
11879923 TTTATCAAAATATTTAACAATTTACCAATAATTCTAAGGA
1 TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
** * *
11879963 TTTACCAAAATATCTAATGATTTACCAATATTTCTAAGGA
1 TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
* * * *
11880003 TATACCAATATATCTAACAATTTGCCAA-AATTTTTAACGA
1 TTTACCAAAATATCTAACAATTTACCAATAA-TTCTAACGA
11880043 TTTACCAATAAT-TCTAACAATTTACCAA-AATATCTAACGA
1 TTTACCAA-AATATCTAACAATTTACCAATAAT-TCTAACGA
* ** * *
11880083 TTTACCAATAAT-TTTAAGGATTTATCAA-AATATCTAACGC
1 TTTACCAA-AATATCTAACAATTTACCAATAAT-TCTAACGA
* ** *
11880123 TTTACCAAAATTTCTAATGATTTATCAA-AATATCTAACGA
1 TTTACCAAAATATCTAACAATTTACCAATAAT-TCTAACGA
11880163 TTTACCAA
1 TTTACCAA
11880171 TATTTATGAG
Statistics
Matches: 216, Mismatches: 27, Indels: 9
0.86 0.11 0.04
Matches are distributed among these distances:
39 24 0.11
40 190 0.88
41 2 0.01
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (40 bp):
TTTACCAAAATATCTAACAATTTACCAATAATTCTAACGA
Found at i:11879965 original size:20 final size:19
Alignment explanation
Indices: 11879884--11880170 Score: 243
Period size: 20 Copynumber: 14.4 Consensus size: 19
11879874 ATTTTATGAC
*
11879884 TTTACCAAAATATTTAAC-A
1 TTTACCAAAAT-TCTAACGA
* *
11879903 ATTACCAATAATTCTAAAGA
1 TTTACCAA-AATTCTAACGA
* * *
11879923 TTTATCAAAATATTTAACAA
1 TTTACCAAAAT-TCTAACGA
*
11879943 TTTACCAATAATTCTAAGGA
1 TTTACCAA-AATTCTAACGA
*
11879963 TTTACCAAAATATCTAATGA
1 TTTACCAAAAT-TCTAACGA
* *
11879983 TTTACCAATATTTCTAAGGA
1 TTTACCAA-AATTCTAACGA
* * *
11880003 TATACCAATATATCTAACAA
1 TTTACCAAAAT-TCTAACGA
* *
11880023 TTTGCCAAAATTTTTAACGA
1 TTTACCAAAA-TTCTAACGA
*
11880043 TTTACCAATAATTCTAACAA
1 TTTACCAA-AATTCTAACGA
11880063 TTTACCAAAATATCTAACGA
1 TTTACCAAAAT-TCTAACGA
* *
11880083 TTTACCAATAATTTTAAGGA
1 TTTACCAA-AATTCTAACGA
* *
11880103 TTTATCAAAATATCTAACGC
1 TTTACCAAAAT-TCTAACGA
*
11880123 TTTACCAAAATTTCTAATGA
1 TTTACCAAAA-TTCTAACGA
*
11880143 TTTATCAAAATATCTAACGA
1 TTTACCAAAAT-TCTAACGA
11880163 TTTACCAA
1 TTTACCAA
11880171 TATTTATGAG
Statistics
Matches: 213, Mismatches: 41, Indels: 27
0.76 0.15 0.10
Matches are distributed among these distances:
19 25 0.12
20 176 0.83
21 12 0.06
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTACCAAAATTCTAACGA
Found at i:11880314 original size:20 final size:19
Alignment explanation
Indices: 11880289--11880373 Score: 64
Period size: 20 Copynumber: 4.3 Consensus size: 19
11880279 TATCTAAAAC
11880289 TTTACCAATAGTTTTATGGA
1 TTTACCAATA-TTTTATGGA
* * *
11880309 TTTACCAAAATATCTA-AGA
1 TTTACCAATAT-TTTATGGA
* *
11880328 CTTTGCCAATATTTTTATTGA
1 -TTTACCAATA-TTTTATGGA
*
11880349 TTTACCAGTATTTATATGGA
1 TTTACCAATATTT-TATGGA
11880369 TTTAC
1 TTTAC
11880374 TTTACTAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
19 6 0.12
20 41 0.82
21 3 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTACCAATATTTTATGGA
Found at i:11880318 original size:40 final size:40
Alignment explanation
Indices: 11880274--11880355 Score: 128
Period size: 40 Copynumber: 2.0 Consensus size: 40
11880264 GCGAATTTGT
11880274 CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
1 CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
* * * *
11880314 CAAAATATCTAAGACTTTGCCAATATTTTTATTGATTTAC
1 CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
11880354 CA
1 CA
11880356 GTATTTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (40 bp):
CAAAATATCTAAAACTTTACCAATAGTTTTATGGATTTAC
Found at i:11880533 original size:21 final size:20
Alignment explanation
Indices: 11880503--11880573 Score: 90
Period size: 21 Copynumber: 3.5 Consensus size: 20
11880493 AATTTATACA
11880503 TTTATCAAAATATCTAACATT
1 TTTATCAAAATATCTAACA-T
* *
11880524 TTTATTAAAATATATAACA-
1 TTTATCAAAATATCTAACAT
* *
11880543 ATTATCAAAATATCTAATAT
1 TTTATCAAAATATCTAACAT
11880563 TTTATCAAAAT
1 TTTATCAAAAT
11880574 TTTTAAAACT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 15 0.36
20 10 0.24
21 17 0.40
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (20 bp):
TTTATCAAAATATCTAACAT
Found at i:11887893 original size:17 final size:16
Alignment explanation
Indices: 11887860--11887890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
11887850 TACTACTTTA
11887860 ATTTTATAATTTTAAT
1 ATTTTATAATTTTAAT
*
11887876 ATTTTTTAATTTTAA
1 ATTTTATAATTTTAA
11887891 ATAATAGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTTATAATTTTAAT
Found at i:11888774 original size:16 final size:15
Alignment explanation
Indices: 11888740--11888775 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
11888730 AGTTTTGAAG
11888740 AAAAATGAATATTGT
1 AAAAATGAATATTGT
* *
11888755 AAAAATGTATGTTGT
1 AAAAATGAATATTGT
11888770 AAAAAT
1 AAAAAT
11888776 ATTGATTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:11892770 original size:3 final size:3
Alignment explanation
Indices: 11892762--11892810 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
11892752 AGTATGAAAT
11892762 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11892810 T
1 T
11892811 CTTGATCATC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11909645 original size:29 final size:29
Alignment explanation
Indices: 11909603--11909661 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
11909593 GAGTTAAGTC
11909603 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
1 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
11909632 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
1 AGTCGTGAGCTTGAGAGGCGATGGAAGAA
11909661 A
1 A
11909662 AGGACAAGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.10, G:0.41, T:0.17
Consensus pattern (29 bp):
AGTCGTGAGCTTGAGAGGCGATGGAAGAA
Found at i:11915735 original size:3 final size:3
Alignment explanation
Indices: 11915721--11915750 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
11915711 TAATTTGGTC
*
11915721 ATT ATT ACT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
11915751 TGATGGTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11928567 original size:19 final size:18
Alignment explanation
Indices: 11928531--11928577 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
11928521 ATTTTTGTAG
*
11928531 TATAAATAATTTTAAGTA
1 TATAAAAAATTTTAAGTA
11928549 CTATAAAAAATTATT-AGTA
1 -TATAAAAAATT-TTAAGTA
11928568 TGATAAAAAA
1 T-ATAAAAAA
11928578 AATTCTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.88
20 2 0.08
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.36
Consensus pattern (18 bp):
TATAAAAAATTTTAAGTA
Found at i:11929369 original size:18 final size:20
Alignment explanation
Indices: 11929331--11929371 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
11929321 CTTCTTAGCC
11929331 ATAATATTTACAACATTTTT
1 ATAATATTTACAACATTTTT
*
11929351 ATAATATTT-CAA-TTTTTT
1 ATAATATTTACAACATTTTT
11929369 ATA
1 ATA
11929372 GTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (20 bp):
ATAATATTTACAACATTTTT
Found at i:11937612 original size:27 final size:27
Alignment explanation
Indices: 11937582--11937643 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
11937572 CCTATCAGGT
11937582 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
11937609 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
11937636 AGGCGCCA
1 AGGCGCCA
11937644 TTACTAGACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:11938589 original size:19 final size:19
Alignment explanation
Indices: 11938567--11938604 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11938557 TATAAATTTA
*
11938567 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
11938586 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
11938605 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:11943607 original size:23 final size:23
Alignment explanation
Indices: 11943537--11943622 Score: 101
Period size: 21 Copynumber: 4.0 Consensus size: 23
11943527 CTTGATTAGT
11943537 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
11943558 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
11943578 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
*
11943601 ATACGACACATAAAGTGTCTGA
1 ATACGACACATAAAGTGCCTGA
11943623 TCAGCAAAGT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:11943623 original size:44 final size:41
Alignment explanation
Indices: 11943537--11943623 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 41
11943527 CTTGATTAGT
* *
11943537 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
* *
11943578 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGTCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
11943622 AT
1 AT
11943624 CAGCAAAGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 11 0.28
42 10 0.26
43 1 0.03
44 17 0.44
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:11943895 original size:14 final size:13
Alignment explanation
Indices: 11943876--11943915 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
11943866 TATTCATAAA
11943876 TTAATTCATTTTAT
1 TTAATTCATTTT-T
*
11943890 TTAATTCATATTT
1 TTAATTCATTTTT
*
11943903 TAAATTCATTTTT
1 TTAATTCATTTTT
11943916 CAATCAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (13 bp):
TTAATTCATTTTT
Found at i:11944239 original size:3 final size:3
Alignment explanation
Indices: 11944231--11944276 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
11944221 ACATTAATTT
11944231 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11944277 AATTTCTATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:11944636 original size:16 final size:16
Alignment explanation
Indices: 11944615--11944666 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
11944605 TTTGGTTCGC
*
11944615 TGTATTGGTTTAGAGG
1 TGTATTGGATTAGAGG
11944631 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* * * *
11944647 CGTAATGGAATAGAGA
1 TGTATTGGATTAGAGG
11944663 TGTA
1 TGTA
11944667 ATAGCAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.29, C:0.02, G:0.35, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:11944713 original size:45 final size:44
Alignment explanation
Indices: 11944648--11944737 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 44
11944638 GATTAGAGGC
*
11944648 GTAATGGAATAGAGATGTAATAGCAAATCAACTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAG-AAATCAACTGTTTGGTTGAAT
* * ***
11944693 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGACGTAATAGAAATCAACTGTTTGGTTGAAT
11944737 G
1 G
11944738 GAATAGCATA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 18 0.46
45 21 0.54
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (44 bp):
GTAATGGAATAGAGACGTAATAGAAATCAACTGTTTGGTTGAAT
Found at i:11945138 original size:15 final size:15
Alignment explanation
Indices: 11945110--11945150 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
11945100 ATAAAATATA
11945110 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
11945125 TATTAAATATATTAT
1 AATTAAATATATTAT
11945140 AATTAAA-ATAT
1 AATTAAATATAT
11945151 CACAGAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:11947412 original size:6 final size:6
Alignment explanation
Indices: 11947398--11947439 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
11947388 TCCAAATTTG
* * *
11947398 AGCACA AGCAAA AGCAAA AGCAAA A-CAAA ATCAAA ATCAAA A
1 AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA AGCAAA A
11947440 TCGATTTTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.67, C:0.19, G:0.10, T:0.05
Consensus pattern (6 bp):
AGCAAA
Found at i:11947432 original size:17 final size:17
Alignment explanation
Indices: 11947406--11947439 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11947396 TGAGCACAAG
11947406 CAAAAGCAAAAGCAAAA
1 CAAAAGCAAAAGCAAAA
* *
11947423 CAAAATCAAAATCAAAA
1 CAAAAGCAAAAGCAAAA
11947440 TCGATTTTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.18, G:0.06, T:0.06
Consensus pattern (17 bp):
CAAAAGCAAAAGCAAAA
Found at i:11947534 original size:19 final size:18
Alignment explanation
Indices: 11947510--11947552 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
11947500 AAATCTGGAG
11947510 AAAAGAAAATG-GAGAAAAT
1 AAAAGAAAATGTGAG--AAT
11947529 AAAAG-AAATGTGAGAAT
1 AAAAGAAAATGTGAGAAT
11947546 AAAAGAA
1 AAAAGAA
11947553 GCGTACCGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.36
18 6 0.27
19 8 0.36
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (18 bp):
AAAAGAAAATGTGAGAAT
Found at i:11949361 original size:18 final size:19
Alignment explanation
Indices: 11949338--11949377 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
11949328 CAAACCAAAA
11949338 AAACAACACATTTA-CAAT
1 AAACAACACATTTAGCAAT
*
11949356 AAACAACATATTTAGCAAT
1 AAACAACACATTTAGCAAT
11949375 AAA
1 AAA
11949378 GAAGAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.57, C:0.17, G:0.03, T:0.23
Consensus pattern (19 bp):
AAACAACACATTTAGCAAT
Found at i:11950184 original size:21 final size:22
Alignment explanation
Indices: 11950136--11950193 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
11950126 CTTTTAACAA
*
11950136 TTTATATTTATTTTAAGATTTAT
1 TTTA-ATTTATTTTAAGAATTAT
11950159 TTTAATTT-TTTT-AGAATTAT
1 TTTAATTTATTTTAAGAATTAT
*
11950179 TGTTAA-TAATTTTAA
1 T-TTAATTTATTTTAA
11950194 AAAAATCAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
20 9 0.30
21 12 0.40
22 5 0.17
23 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTAATTTATTTTAAGAATTAT
Found at i:11954504 original size:14 final size:16
Alignment explanation
Indices: 11954467--11954501 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
11954457 AAGAGATTTT
11954467 TTTTAAAAAATTATATA
1 TTTT-AAAAATTATATA
11954484 TTTTAAAAATTAT-TA
1 TTTTAAAAATTATATA
11954499 TTT
1 TTT
11954502 AAACTCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 9 0.50
17 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAAAATTATATA
Found at i:11958438 original size:18 final size:17
Alignment explanation
Indices: 11958412--11958446 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
11958402 AATTATTTCT
11958412 AAAAAAAAAAAGAAAAG
1 AAAAAAAAAAAGAAAAG
*
11958429 AAAAACAAAATAGAAAAG
1 AAAAA-AAAAAAGAAAAG
11958447 GAGATATGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (17 bp):
AAAAAAAAAAAGAAAAG
Found at i:11959267 original size:30 final size:31
Alignment explanation
Indices: 11959215--11959279 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
11959205 AACAACCTAG
**
11959215 TGACTTAAATAAAAACTTTTGAATTGTTCAA
1 TGACTTAAATAAAAACTTTTGAATAATTCAA
* *
11959246 TGACTTAAAT-GAAATTTTTGAATAATTCAA
1 TGACTTAAATAAAAACTTTTGAATAATTCAA
11959276 TGAC
1 TGAC
11959280 CACTTTATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.42, C:0.09, G:0.11, T:0.38
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTGAATAATTCAA
Found at i:11970659 original size:46 final size:46
Alignment explanation
Indices: 11970588--11970772 Score: 307
Period size: 46 Copynumber: 4.0 Consensus size: 46
11970578 CATGGCAAAG
11970588 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
* *
11970634 TGTAAAAAGTAGGTATGATGTTTCGGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
* *
11970680 TATGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
* * *
11970726 TGTGAAAAGTAGGCATGGTATTTCCGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
11970772 T
1 T
11970773 ATAGCAATGT
Statistics
Matches: 129, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 129 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTGTTTCGGTGAAGAAAACCATACTGAGT
Found at i:11994107 original size:20 final size:20
Alignment explanation
Indices: 11994080--11994121 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
11994070 ACATATAAAT
*
11994080 ATTTTAAATATATATATATAA
1 ATTTAAAAT-TATATATATAA
11994101 ATTTAAAATTATATATATAA
1 ATTTAAAATTATATATATAA
11994121 A
1 A
11994122 AAATTATTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTAAAATTATATATATAA
Found at i:11994296 original size:22 final size:22
Alignment explanation
Indices: 11994252--11994296 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11994242 ACAATCATTT
* *
11994252 TTTATTTTTATATATTTTTAAA
1 TTTATTATTATATATTTTGAAA
11994274 TTTATTATTATAT-TTTTGGAAA
1 TTTATTATTATATATTTT-GAAA
11994296 T
1 T
11994297 ATTTATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTATTATTATATATTTTGAAA
Found at i:12002783 original size:15 final size:15
Alignment explanation
Indices: 12002763--12002791 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12002753 CAAAGAACCT
12002763 GAGGAAGATTGCCCC
1 GAGGAAGATTGCCCC
12002778 GAGGAAGATTGCCC
1 GAGGAAGATTGCCC
12002792 TTCCAGTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.24, G:0.34, T:0.14
Consensus pattern (15 bp):
GAGGAAGATTGCCCC
Found at i:12007338 original size:21 final size:21
Alignment explanation
Indices: 12007308--12007360 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
12007298 CGTTGTTTCT
*
12007308 AATCTTACCGCTACAGTACCC
1 AATCTCACCGCTACAGTACCC
12007329 AATCTCACCGCTACAGTACCC
1 AATCTCACCGCTACAGTACCC
12007350 AATCTCACCGC
1 AATCTCACCGC
12007361 CACCGCTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.42, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTACCC
Found at i:12020828 original size:2 final size:2
Alignment explanation
Indices: 12020784--12020817 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12020774 ACTAAGCGTG
12020784 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12020818 ACTTTATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12025581 original size:27 final size:26
Alignment explanation
Indices: 12025521--12025582 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
12025511 TTATTTCTAA
12025521 AAAATAATTTGAAAGAATTTTAATATT
1 AAAA-AATTTGAAAGAATTTTAATATT
** *
12025548 ACTAAATTTGAAAAGAGTTTTAA-ATAT
1 AAAAAATTTG-AAAGAATTTTAATAT-T
12025575 AAAAAATT
1 AAAAAATT
12025583 AATCAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (26 bp):
AAAAAATTTGAAAGAATTTTAATATT
Found at i:12026497 original size:26 final size:24
Alignment explanation
Indices: 12026468--12026516 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
12026458 TATATATTTA
12026468 TTATATAATATAAAATATAGATATAT
1 TTATATAATATAAAA-ATA-ATATAT
*
12026494 TTATATAATTTAAAAATAATATA
1 TTATATAATATAAAAATAATATA
12026517 AAATAAATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 3 0.14
26 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATATAATATAAAAATAATATAT
Found at i:12027050 original size:37 final size:37
Alignment explanation
Indices: 12026971--12027075 Score: 107
Period size: 37 Copynumber: 3.0 Consensus size: 37
12026961 TATATTTTTT
*
12026971 ATATCATTATATTAAATTATTTAAATA-C---CAT--
1 ATATCATTATATTAAATTATTCAAATATCATTCATAA
* * *
12027002 TTATCATTATATTAATTTACTT-AAATATTATTCATAA
1 ATATCATTATATTAAATTA-TTCAAATATCATTCATAA
*
12027039 ATATCGTTATATTAAATTATTCAAATATCATTCATAA
1 ATATCATTATATTAAATTATTCAAATATCATTCATAA
12027076 TTAGGTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
31 22 0.37
32 2 0.03
35 3 0.05
36 2 0.03
37 30 0.51
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.47
Consensus pattern (37 bp):
ATATCATTATATTAAATTATTCAAATATCATTCATAA
Found at i:12027094 original size:68 final size:68
Alignment explanation
Indices: 12026971--12027099 Score: 154
Period size: 68 Copynumber: 1.9 Consensus size: 68
12026961 TATATTTTTT
* * * * *
12026971 ATATCATTATATTAAATTATTTAAATACCATTTATCATTATATTAATTTACTT-AAATATTATTC
1 ATATCATTATATTAAATTATTCAAATACCATTCATAATTATATAAAATTA-TTAAAATATTATTC
12027035 ATAA
65 ATAA
* *
12027039 ATATCGTTATATTAAATTATTCAAATATCATTCATAATTAGGTATAAAATT-TTAAAATATT
1 ATATCATTATATTAAATTATTCAAATACCATTCATAATTA--TATAAAATTATTAAAATATT
12027100 TTATTTTTGT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
68 37 0.73
69 7 0.14
70 7 0.14
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (68 bp):
ATATCATTATATTAAATTATTCAAATACCATTCATAATTATATAAAATTATTAAAATATTATTCA
TAA
Found at i:12029144 original size:46 final size:46
Alignment explanation
Indices: 12029061--12029243 Score: 266
Period size: 46 Copynumber: 4.0 Consensus size: 46
12029051 CATGGAAAAA
* *
12029061 TTGTGAAAAGTAGG--TA-TGTTTCAGTGAAGAAAGCCATACTAAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
12029104 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
* *
12029150 TTGTGAAAAGTAGGTATGGTGTTTCAATGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
* * *
12029196 TTGTGAAAAGTAGGTATGGTATTCCAGTGAATG-AAACCATACTGAG
1 TTGTGAAAAGTAGGTATAGTGTTTCAGTGAA-GAAAACCATACTGAG
12029242 TT
1 TT
12029244 ATAGCATTGT
Statistics
Matches: 129, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
43 14 0.11
45 2 0.02
46 112 0.87
47 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.26, T:0.29
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATAGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:12033414 original size:19 final size:19
Alignment explanation
Indices: 12033390--12033427 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12033380 ATTTACCAAT
12033390 ATATAATACGAAAATATAA
1 ATATAATACGAAAATATAA
* *
12033409 ATATAATATGAATATATAA
1 ATATAATACGAAAATATAA
12033428 TTTTTTATTT
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:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATATAATACGAAAATATAA
Found at i:12046242 original size:22 final size:22
Alignment explanation
Indices: 12046217--12046260 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12046207 ATAAAACTCG
*
12046217 TTTT-AAAAATCATTAAAATTAT
1 TTTTAAAAAAT-ATAAAAATTAT
12046239 TTTTAAAAAATATAAAAATTAT
1 TTTTAAAAAATATAAAAATTAT
12046261 ATAAAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTTAAAAAATATAAAAATTAT
Found at i:12054887 original size:40 final size:40
Alignment explanation
Indices: 12054843--12054918 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
12054833 CCCATCCATG
*
12054843 ACATGACACGGCATCAACCAAAGTTCCAAATTTTTTTAAT
1 ACATGACACGACATCAACCAAAGTTCCAAATTTTTTTAAT
12054883 ACATGACACGACATCAACCAAAGTTCCAAATTTTTT
1 ACATGACACGACATCAACCAAAGTTCCAAATTTTTT
12054919 AATCAGTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.24, G:0.09, T:0.29
Consensus pattern (40 bp):
ACATGACACGACATCAACCAAAGTTCCAAATTTTTTTAAT
Found at i:12057776 original size:4 final size:4
Alignment explanation
Indices: 12057767--12057792 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
12057757 ATGTCGACCC
12057767 ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT AT
12057793 CAAATTTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:12058078 original size:20 final size:22
Alignment explanation
Indices: 12058041--12058080 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
12058031 AATATTTAAT
12058041 TATTTATTAAATATTAAAAAAA
1 TATTTATTAAATATTAAAAAAA
12058063 TATTT-TTAAA-ATTAAAAA
1 TATTTATTAAATATTAAAAA
12058081 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTTATTAAATATTAAAAAAA
Found at i:12058125 original size:26 final size:26
Alignment explanation
Indices: 12058060--12058127 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
12058050 AATATTAAAA
* *
12058060 AAATATTTTTAAAATTAAAAATTATT
1 AAATATTTTTAAAATTAAAAATAAGT
* *
12058086 AAA-ATGTATGAAAATTATAAAA-AAGT
1 AAATAT-TTTTAAAATTA-AAAATAAGT
12058112 AAATATTTTTAAAATT
1 AAATATTTTTAAAATT
12058128 TTTAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
25 2 0.06
26 25 0.76
27 6 0.18
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
AAATATTTTTAAAATTAAAAATAAGT
Found at i:12063962 original size:27 final size:28
Alignment explanation
Indices: 12063930--12063988 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
12063920 AAGAGAACCC
*
12063930 CGTGCCAAAA-ATGGCAGACTAAAGAGA
1 CGTGCCAAAATACGGCAGACTAAAGAGA
12063957 CGTGCCAAAATACGGCAGACTAAAGAGA
1 CGTGCCAAAATACGGCAGACTAAAGAGA
12063985 CGTG
1 CGTG
12063989 GCTTTCTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (28 bp):
CGTGCCAAAATACGGCAGACTAAAGAGA
Found at i:12070861 original size:49 final size:51
Alignment explanation
Indices: 12070796--12070891 Score: 151
Period size: 49 Copynumber: 1.9 Consensus size: 51
12070786 AATCCCATAG
*
12070796 TAATTCTCAACGATGAATTAACC-AA-ACTACACTCCTGGAGCTCCATATA
1 TAATTCTCAACAATGAATTAACCAAACACTACACTCCTGGAGCTCCATATA
* *
12070845 TAATTCTCAACAATGAATTAACCAAACACTACACTCTTTGAGCTCCA
1 TAATTCTCAACAATGAATTAACCAAACACTACACTCCTGGAGCTCCA
12070892 ACAGTAATAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 22 0.52
50 2 0.05
51 18 0.43
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.27
Consensus pattern (51 bp):
TAATTCTCAACAATGAATTAACCAAACACTACACTCCTGGAGCTCCATATA
Found at i:12085905 original size:14 final size:14
Alignment explanation
Indices: 12085869--12085907 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12085859 GCTTAATAAA
12085869 TTATGACATATGCT
1 TTATGACATATGCT
* * *
12085883 TAATAACATATGGT
1 TTATGACATATGCT
12085897 TTATGACATAT
1 TTATGACATAT
12085908 AAACTAATGA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (14 bp):
TTATGACATATGCT
Found at i:12086188 original size:20 final size:21
Alignment explanation
Indices: 12086151--12086200 Score: 84
Period size: 20 Copynumber: 2.4 Consensus size: 21
12086141 ATATAATAAT
12086151 AATTATATTAAGAATTTTATTA
1 AATTATA-TAAGAATTTTATTA
12086173 AATTATATAA-AATTTTATTA
1 AATTATATAAGAATTTTATTA
12086193 AATTATAT
1 AATTATAT
12086201 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.64
21 3 0.11
22 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AATTATATAAGAATTTTATTA
Found at i:12086201 original size:10 final size:10
Alignment explanation
Indices: 12086151--12086235 Score: 61
Period size: 10 Copynumber: 8.6 Consensus size: 10
12086141 ATATAATAAT
12086151 AATTATATTAA
1 AATTATATT-A
*
12086162 GAATTTTATTA
1 -AATTATATTA
*
12086173 AATTATATAA
1 AATTATATTA
*
12086183 AATTTTATTA
1 AATTATATTA
*
12086193 AATTATATTT
1 AATTATATTA
12086203 AA-TA-A-T-
1 AATTATATTA
*
12086209 AATTATGTTA
1 AATTATATTA
*
12086219 AAATATAGTTA
1 AATTATA-TTA
12086230 AATTAT
1 AATTAT
12086236 TTATTATTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 11
0.72 0.14 0.14
Matches are distributed among these distances:
6 2 0.04
7 3 0.05
8 1 0.02
9 3 0.05
10 31 0.54
11 9 0.16
12 8 0.14
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (10 bp):
AATTATATTA
Found at i:12086206 original size:58 final size:59
Alignment explanation
Indices: 12086127--12086282 Score: 171
Period size: 58 Copynumber: 2.7 Consensus size: 59
12086117 TTATATTATG
*
12086127 ATTTTAGTAAATTCATA--TAATAATAATTATATTAAGAATTTTA-TTAAATTATATA-AA
1 ATTTTATTAAATT-ATATTTAATAATAATTATATTAA-AATTTTAGTTAAATTATATATAA
* * * *
12086184 ATTTTATTAAATTATATTTAATAATAATTATGTTAAAA-TATAGTTAAATTATTTATTA
1 ATTTTATTAAATTATATTTAATAATAATTATATTAAAATTTTAGTTAAATTATATATAA
* * *
12086242 TTTTTATTAAATCATTTTTAATAATAATCT-TATTAAAATTT
1 ATTTTATTAAATTATATTTAATAATAAT-TATATTAAAATTT
12086283 AATAACAATA
Statistics
Matches: 83, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
56 6 0.07
57 25 0.30
58 50 0.60
59 2 0.02
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.51
Consensus pattern (59 bp):
ATTTTATTAAATTATATTTAATAATAATTATATTAAAATTTTAGTTAAATTATATATAA
Found at i:12086428 original size:44 final size:45
Alignment explanation
Indices: 12086374--12086480 Score: 137
Period size: 45 Copynumber: 2.4 Consensus size: 45
12086364 ATTACAACAT
* *
12086374 CATTCTATTCAACCAAACACA-AGAA-TACTGTTACAGCTCTATTC
1 CATTCCATTCAACCAAACA-ATAGAATTACTATTACAGCTCTATTC
*
12086418 CATTCCATTCAACCAAACAATTGAATTACTATTACAGCTCTATTC
1 CATTCCATTCAACCAAACAATAGAATTACTATTACAGCTCTATTC
* * *
12086463 CATTACAGTGAACCAAAC
1 CATTCCATTCAACCAAAC
12086481 GTACCATTAC
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.02
44 21 0.38
45 33 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.29
Consensus pattern (45 bp):
CATTCCATTCAACCAAACAATAGAATTACTATTACAGCTCTATTC
Found at i:12088553 original size:31 final size:32
Alignment explanation
Indices: 12088495--12088571 Score: 84
Period size: 31 Copynumber: 2.4 Consensus size: 32
12088485 TTGATATTTA
* * * * *
12088495 ATTTTTTTAATTACAAATGGTATTTAAATTAT
1 ATTTTATTACTTACAAATAGTACTTAAACTAT
12088527 ATTTTATTACTTA-AAATAGTACTTAAACTAT
1 ATTTTATTACTTACAAATAGTACTTAAACTAT
*
12088558 ATTCTATTATCTTA
1 ATTTTATTA-CTTA
12088572 GTTATTAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 23 0.61
32 15 0.39
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.51
Consensus pattern (32 bp):
ATTTTATTACTTACAAATAGTACTTAAACTAT
Found at i:12089781 original size:61 final size:62
Alignment explanation
Indices: 12089703--12089825 Score: 151
Period size: 61 Copynumber: 2.0 Consensus size: 62
12089693 ATTTTTTAAC
* * ** * * * *
12089703 TTTTAGAGTTAGGACTAAATTGATAAATTTTGTAAA-ATTTGAGGGTTAAATTTATTA-ATTT
1 TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACA-TTAAGGGCTAAATTTATTATATTT
12089764 TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACATTAAGGGCTAAATTTATTATATTT
1 TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACATTAAGGGCTAAATTTATTATATTT
12089826 AGGATCAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
61 47 0.90
62 5 0.10
ACGTcount: A:0.40, C:0.04, G:0.14, T:0.42
Consensus pattern (62 bp):
TTTTAGAATTAGAACTAAAAGGACAAATTTTATAAACATTAAGGGCTAAATTTATTATATTT
Found at i:12102660 original size:4 final size:4
Alignment explanation
Indices: 12102651--12102681 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
12102641 CATAATATTA
12102651 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGT
12102682 ATGTATGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.23, G:0.26, T:0.52
Consensus pattern (4 bp):
TGTC
Found at i:12105244 original size:2 final size:2
Alignment explanation
Indices: 12105237--12105265 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12105227 GGTAAGTGGT
12105237 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12105266 TCGTTTAGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12109354 original size:2 final size:2
Alignment explanation
Indices: 12109347--12109372 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12109337 ATTAATGAAA
12109347 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
12109373 TATACTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12114170 original size:20 final size:20
Alignment explanation
Indices: 12114111--12114171 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
12114101 AAAAATAAAA
* * *
12114111 TAAATAAATAATACATTAAAT
1 TAAAAAAATAACACA-TAATT
* *
12114132 TAAAAAAATAACTCCTAATT
1 TAAAAAAATAACACATAATT
12114152 TAAAGAAAATAA-ACATAATT
1 TAAA-AAAATAACACATAATT
12114172 ATCTAAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (20 bp):
TAAAAAAATAACACATAATT
Found at i:12126732 original size:23 final size:28
Alignment explanation
Indices: 12126700--12126751 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
12126690 TTGAATAAAT
12126700 TAATATTTTAA-AA-A-TA-TTTATATA
1 TAATATTTTAATAAGATTATTTTATATA
12126724 TAAT-TTTTAATAAGATTATTTTATATA
1 TAATATTTTAATAAGATTATTTTATATA
12126751 T
1 T
12126752 TCATAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.25
24 6 0.25
25 1 0.04
26 2 0.08
27 9 0.38
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TAATATTTTAATAAGATTATTTTATATA
Found at i:12127959 original size:61 final size:60
Alignment explanation
Indices: 12127887--12128004 Score: 150
Period size: 61 Copynumber: 1.9 Consensus size: 60
12127877 AAGTTAGAAC
* * * *
12127887 TAAATTGATAAA-TTTCGTAAATATTGA-AGGTTAAGTTTATTGAATTTTTTAGAATTAAAAT
1 TAAAATGATAAAGTTT-GTAAACATTGAGA-GCTAAATTTATTGAATTTTTTAG-ATTAAAAT
*
12127948 TAAAATGATAAAGTTTGTAAACATTGAGAGCTAAATTTGTTGAATTTTTTAGATTAA
1 TAAAATGATAAAGTTTGTAAACATTGAGAGCTAAATTTATTGAATTTTTTAGATTAA
12128005 TACAATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
60 5 0.10
61 41 0.82
62 4 0.08
ACGTcount: A:0.41, C:0.03, G:0.14, T:0.42
Consensus pattern (60 bp):
TAAAATGATAAAGTTTGTAAACATTGAGAGCTAAATTTATTGAATTTTTTAGATTAAAAT
Found at i:12133199 original size:2 final size:2
Alignment explanation
Indices: 12133192--12133217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12133182 CTAATATCCC
12133192 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12133218 ATGTGCCTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12135858 original size:10 final size:10
Alignment explanation
Indices: 12135843--12135867 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12135833 TCATAAAGTT
12135843 GGAGCGGGTC
1 GGAGCGGGTC
12135853 GGAGCGGGTC
1 GGAGCGGGTC
12135863 GGAGC
1 GGAGC
12135868 AAGATCACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.20, G:0.60, T:0.08
Consensus pattern (10 bp):
GGAGCGGGTC
Found at i:12141199 original size:2 final size:2
Alignment explanation
Indices: 12141186--12141228 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
12141176 TAATTACATC
*
12141186 AT AT AT AC 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
12141228 A
1 A
12141229 ACTTTTCATC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12141712 original size:17 final size:18
Alignment explanation
Indices: 12141687--12141720 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12141677 TTGATATTTT
12141687 ATATATTTA-TATTTAAA
1 ATATATTTATTATTTAAA
*
12141704 ATATTTTTATTATTTAA
1 ATATATTTATTATTTAA
12141721 TTTAAATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
ATATATTTATTATTTAAA
Found at i:12142115 original size:43 final size:43
Alignment explanation
Indices: 12142066--12142150 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
12142056 TAAAACCACT
12142066 TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTAC
1 TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTAC
*
12142109 TTTTTATAAAAGAAAACATGATAAGTGCATGATAATTACCTA
1 TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTA
12142151 TTCTTCTCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (43 bp):
TTTTTATAAAAGAAAACATGATAAGTACATGATAATTACCTAC
Found at i:12143047 original size:130 final size:125
Alignment explanation
Indices: 12142760--12143099 Score: 484
Period size: 130 Copynumber: 2.7 Consensus size: 125
12142750 GATAAAATCA
* * * * *
12142760 AAGCAGGATGCTTTATCAGAAGAATTTCTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
** *
12142825 AGGTCCTTCAA-AAATAATTTCGAGTTGACGTTTCTGAGAAATAGTATAAAAAACGCTTC
66 AGGTCCTAGAAGAAATAATTTCGAGTTGACATTTCTGAGAAATAGTATAAAAAACGCTTC
*
12142884 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGTGCTTTTGCTACAGT
1 AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* * * *
12142949 AGGTCCTGGAAGAAATAATTTCGATTTGACATTTCTGAGCAAATAGTATAAAACATGCTTC
66 AGGTCCTAGAAGAAATAATTTCGAGTTGACATTTCTGAG-AAATAGTATAAAAAACGCTTC
* *
12143010 AGGCAGGCAGGATGCTTTGTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTA
1 A---A-GCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTA
*
12143075 CAGTAGGTTCTAGAAGAAATAATTT
62 CAGTAGGTCCTAGAAGAAATAATTT
12143100 GAAGAACGTA
Statistics
Matches: 193, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
124 68 0.35
125 25 0.13
126 20 0.10
129 1 0.01
130 79 0.41
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (125 bp):
AAGCAGGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTAGAAGAAATAATTTCGAGTTGACATTTCTGAGAAATAGTATAAAAAACGCTTC
Found at i:12143786 original size:11 final size:11
Alignment explanation
Indices: 12143772--12143809 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
12143762 AAGAAATTTA
12143772 AGAGGAAATTG
1 AGAGGAAATTG
*
12143783 AGAGCAAATTG
1 AGAGGAAATTG
12143794 AGAGGAAATTTG
1 AGAGGAAA-TTG
12143806 AGAG
1 AGAG
12143810 AGGATTAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.45, C:0.03, G:0.34, T:0.18
Consensus pattern (11 bp):
AGAGGAAATTG
Found at i:12145278 original size:9 final size:9
Alignment explanation
Indices: 12145260--12145335 Score: 98
Period size: 9 Copynumber: 8.4 Consensus size: 9
12145250 TTTGGTTAAA
12145260 AATTAACCG
1 AATTAACCG
*
12145269 AATTACCCG
1 AATTAACCG
12145278 AATTAACCG
1 AATTAACCG
*
12145287 AATTACCCG
1 AATTAACCG
12145296 AATTAACCG
1 AATTAACCG
* *
12145305 AATTACCCA
1 AATTAACCG
*
12145314 AATTAACCA
1 AATTAACCG
*
12145323 AATTAACCA
1 AATTAACCG
12145332 AATT
1 AATT
12145336 GAATCACTAC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 60 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:12145332 original size:18 final size:18
Alignment explanation
Indices: 12145259--12145335 Score: 118
Period size: 18 Copynumber: 4.3 Consensus size: 18
12145249 TTTTGGTTAA
12145259 AAATTAACCGAATTACCC
1 AAATTAACCGAATTACCC
*
12145277 GAATTAACCGAATTACCC
1 AAATTAACCGAATTACCC
*
12145295 GAATTAACCGAATTACCC
1 AAATTAACCGAATTACCC
* *
12145313 AAATTAACCAAATTAACC
1 AAATTAACCGAATTACCC
12145331 AAATT
1 AAATT
12145336 GAATCACTAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 55 1.00
ACGTcount: A:0.45, C:0.25, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATTAACCGAATTACCC
Found at i:12145481 original size:18 final size:18
Alignment explanation
Indices: 12145439--12145485 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
12145429 ATTTAATTTT
*
12145439 ATGATTGGGTTGGGTCGG
1 ATGATTGGGTTGGGTCGA
* * *
12145457 GTAATTGGGTTGGGTTGA
1 ATGATTGGGTTGGGTCGA
12145475 ATGATTGGGTT
1 ATGATTGGGTT
12145486 TAGATTGGGT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.02, G:0.45, T:0.38
Consensus pattern (18 bp):
ATGATTGGGTTGGGTCGA
Found at i:12146856 original size:15 final size:15
Alignment explanation
Indices: 12146832--12146887 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
12146822 CTTCCCTCCT
*
12146832 TTTTTTATTTTAAAA
1 TTTTTAATTTTAAAA
* *
12146847 TTTTTAATTTTTATA
1 TTTTTAATTTTAAAA
**
12146862 TTTCAAATTTTAAAA
1 TTTTTAATTTTAAAA
12146877 --TTTAATTTTAA
1 TTTTTAATTTTAA
12146888 TTATTAGTAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 9 0.28
15 23 0.72
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAATTTTAAAA
Found at i:12146859 original size:21 final size:21
Alignment explanation
Indices: 12146833--12146887 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
12146823 TTCCCTCCTT
*
12146833 TTTTTATTTTAAAATTTTTAA
1 TTTTTATTTTAAAATTTTAAA
*
12146854 TTTTTATATTTCAAATTTTAAA
1 TTTTTAT-TTTAAAATTTTAAA
* *
12146876 ATTTAATTTTAA
1 TTTTTATTTTAA
12146888 TTATTAGTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
21 11 0.39
22 17 0.61
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTATTTTAAAATTTTAAA
Found at i:12157749 original size:14 final size:14
Alignment explanation
Indices: 12157732--12157765 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12157722 GAGAGATTTT
12157732 AGAAAAGAGAAAAA
1 AGAAAAGAGAAAAA
*
12157746 AGAAGAGAGAAAAA
1 AGAAAAGAGAAAAA
12157760 A-AAAAG
1 AGAAAAG
12157766 CGAGAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAAAAGAGAAAAA
Found at i:12159060 original size:27 final size:29
Alignment explanation
Indices: 12159030--12159084 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
12159020 TAAAATAGAT
12159030 AATA-AAATTACATTTT-A-ACTCTAAAAA
1 AATATAAATTA-ATTTTGACACTCTAAAAA
*
12159057 AATATAATTTAATTTTGACACTCTAAAA
1 AATATAAATTAATTTTGACACTCTAAAA
12159085 TAGTTTCACC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 9 0.38
28 6 0.25
29 9 0.38
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (29 bp):
AATATAAATTAATTTTGACACTCTAAAAA
Found at i:12165027 original size:33 final size:33
Alignment explanation
Indices: 12164982--12165049 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
12164972 CAGATTTCAT
12164982 TGTTACCATTATTCATTCGGTTGAAAAATGTGG
1 TGTTACCATTATTCATTCGGTTGAAAAATGTGG
*
12165015 TGTTACCGTTATTCATTCGGTTGAAAAATGTGG
1 TGTTACCATTATTCATTCGGTTGAAAAATGTGG
12165048 TG
1 TG
12165050 AAGAAATGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.40
Consensus pattern (33 bp):
TGTTACCATTATTCATTCGGTTGAAAAATGTGG
Found at i:12165222 original size:20 final size:22
Alignment explanation
Indices: 12165176--12165224 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
12165166 TGTAGCATAA
*
12165176 AATATATGTATTTAATTATTAT
1 AATATATGTAGTTAATTATTAT
*
12165198 -TTATAT-TAGTTAA-TATTAT
1 AATATATGTAGTTAATTATTAT
12165217 AATATATG
1 AATATATG
12165225 AGATATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
19 6 0.27
20 11 0.50
21 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (22 bp):
AATATATGTAGTTAATTATTAT
Found at i:12167513 original size:50 final size:50
Alignment explanation
Indices: 12167429--12167669 Score: 274
Period size: 50 Copynumber: 4.8 Consensus size: 50
12167419 ATTTGGGTAA
** *
12167429 AGAGATCCCATGTAAGACCATGTCTGGGGTATGGCATTGGCACCGAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
12167479 AGAGGTCCCACGTAAGACCATGTTTGGGACATGGCATTGGCATCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
12167529 AGAGGTCCC-TCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGATCCCAT-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
12167579 AGA-ACTCCCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACATG
1 AGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* * *
12167628 AAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12167670 TGTTATTATC
Statistics
Matches: 163, Mismatches: 23, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 39 0.24
50 122 0.75
51 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:12168954 original size:9 final size:9
Alignment explanation
Indices: 12168940--12168988 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
12168930 ATTGGTTAAA
*
12168940 AATTAACTG
1 AATTAACCG
*
12168949 AATTAACTG
1 AATTAACCG
*
12168958 AATTACCCG
1 AATTAACCG
12168967 AATTAACCG
1 AATTAACCG
12168976 AATTAACCG
1 AATTAACCG
12168985 AATT
1 AATT
12168989 GAATCACTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:12169131 original size:18 final size:18
Alignment explanation
Indices: 12169091--12169134 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12169081 AATTTTTATG
**
12169091 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
12169109 ATTGGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
12169127 TTTGGGTT
1 ATTGGGTT
12169135 TGTTAGGTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:12172005 original size:30 final size:30
Alignment explanation
Indices: 12171969--12172031 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
12171959 ATTTATTTTA
12171969 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
* *
12171999 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
12172029 TTG
1 TTG
12172032 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:12172135 original size:18 final size:18
Alignment explanation
Indices: 12172114--12172153 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12172104 GAAATATTTA
*
12172114 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
12172132 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
12172150 TTTT
1 TTTT
12172154 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:12172176 original size:12 final size:12
Alignment explanation
Indices: 12172155--12172188 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12172145 TATATTTTTT
*
12172155 AAAATTATATAA
1 AAAATAATATAA
12172167 AAAATAATATAA
1 AAAATAATATAA
*
12172179 AAATTAATAT
1 AAAATAATAT
12172189 GGACAGGCCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATAATATAA
Found at i:12172846 original size:70 final size:70
Alignment explanation
Indices: 12172770--12172910 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
12172760 CATGTAAGTG
12172770 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
1 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
12172835 CCCGA
66 CCCGA
12172840 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
1 TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
12172905 CCCGA
66 CCCGA
12172910 T
1 T
12172911 TCGTAGAACA
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (70 bp):
TGATGGGTTGTGGATCAAAGCCCATGACAAATGCACACATAACGTTCTATGAAGATGTGAATTGA
CCCGA
Found at i:12174583 original size:20 final size:20
Alignment explanation
Indices: 12174560--12174601 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
12174550 TTTTTTGGAA
12174560 TTTTCTAATATTTTT-AGATT
1 TTTTCTAAT-TTTTTAAGATT
* *
12174580 TTTTTTCATTTTTTAAGATT
1 TTTTCTAATTTTTTAAGATT
12174600 TT
1 TT
12174602 AACAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (20 bp):
TTTTCTAATTTTTTAAGATT
Found at i:12174590 original size:28 final size:27
Alignment explanation
Indices: 12174540--12174601 Score: 70
Period size: 28 Copynumber: 2.3 Consensus size: 27
12174530 AGATATTTTT
12174540 AGATTTTTAGTTTTTTGGAATTTTCTA
1 AGATTTTTAGTTTTTTGGAATTTTCTA
* *** *
12174567 ATATTTTTAGATTTTTTTTCATTTTTTA
1 AGATTTTTAG-TTTTTTGGAATTTTCTA
12174595 AGATTTT
1 AGATTTT
12174602 AACAATTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 9 0.32
28 19 0.68
ACGTcount: A:0.23, C:0.03, G:0.10, T:0.65
Consensus pattern (27 bp):
AGATTTTTAGTTTTTTGGAATTTTCTA
Found at i:12196986 original size:22 final size:22
Alignment explanation
Indices: 12196958--12197074 Score: 162
Period size: 22 Copynumber: 5.3 Consensus size: 22
12196948 TTTATTGTTC
*
12196958 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
12196980 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
12197002 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
12197024 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
12197046 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
12197068 AAACATG
1 AAACATG
12197075 TGTTTTTGGG
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 84 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:12206737 original size:15 final size:15
Alignment explanation
Indices: 12206719--12206748 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12206709 CCACCAACAC
12206719 CAACAACAACAATAA
1 CAACAACAACAATAA
12206734 CAACAACAACAATAA
1 CAACAACAACAATAA
12206749 TAATAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.27, G:0.00, T:0.07
Consensus pattern (15 bp):
CAACAACAACAATAA
Found at i:12211863 original size:3 final size:3
Alignment explanation
Indices: 12211849--12211898 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
12211839 AAATGACATT
* * *
12211849 TTA TTA TT- TTA TTA TTA TTG TTA TTA TTA ATA TTA TTG TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12211895 TTA T
1 TTA T
12211899 GAAATAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 4 0.10
3 35 0.90
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12211884 original size:18 final size:18
Alignment explanation
Indices: 12211852--12211893 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
12211842 TGACATTTTA
*
12211852 TTATT-TTATTATTATTG
1 TTATTATTAATATTATTG
12211869 TTATTATTAATATTATTG
1 TTATTATTAATATTATTG
12211887 TTATTAT
1 TTATTAT
12211894 ATTATGAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TTATTATTAATATTATTG
Found at i:12212180 original size:24 final size:24
Alignment explanation
Indices: 12212153--12212206 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
12212143 TACATTTGTA
*
12212153 ATATATG-TATTATTTATTAGTTAG
1 ATATATGTTATTA-TTATTAATTAG
* *
12212177 ATATTTGTTATTATTATTAATTAT
1 ATATATGTTATTATTATTAATTAG
12212201 ATATAT
1 ATATAT
12212207 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (24 bp):
ATATATGTTATTATTATTAATTAG
Found at i:12214190 original size:25 final size:25
Alignment explanation
Indices: 12214161--12214208 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
12214151 AAACTCCAAA
12214161 CCAACCACATACTACTACATTTTTC
1 CCAACCACATACTACTACATTTTTC
12214186 CCAACCACATACTACTACATTTT
1 CCAACCACATACTACTACATTTT
12214209 CCTCAAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.31
Consensus pattern (25 bp):
CCAACCACATACTACTACATTTTTC
Found at i:12224990 original size:23 final size:23
Alignment explanation
Indices: 12224962--12225025 Score: 60
Period size: 23 Copynumber: 2.7 Consensus size: 23
12224952 ATAACATATG
12224962 AAATATGTTATTATTAATAGT-AT
1 AAATATGTTATTATTAAT-GTAAT
* * *
12224985 AAATATATGATTGATGAATGTAAT
1 AAATATGTTATT-ATTAATGTAAT
12225009 AAATATG-TATATATTAA
1 AAATATGTTAT-TATTAA
12225026 AACAGAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (23 bp):
AAATATGTTATTATTAATGTAAT
Found at i:12225844 original size:27 final size:26
Alignment explanation
Indices: 12225814--12225898 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
12225804 TCTCAAATTT
*
12225814 TATATTTTTATAAATGATCTAAGTTTA
1 TATATTTTTATAAAT-TTCTAAGTTTA
* *
12225841 TATATTTTTGA-AAATTTTTAAGGTTTT
1 TATATTTTT-ATAAATTTCTAA-GTTTA
* *
12225868 TAAATTTTTATAAATTTCTAAATTTA
1 TATATTTTTATAAATTTCTAAGTTTA
12225894 TATAT
1 TATAT
12225899 ATTTGAAATA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
26 12 0.26
27 34 0.72
28 1 0.02
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (26 bp):
TATATTTTTATAAATTTCTAAGTTTA
Found at i:12225889 original size:18 final size:18
Alignment explanation
Indices: 12225868--12225902 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12225858 TTAAGGTTTT
*
12225868 TAAATTTTTATAAATTTC
1 TAAATTTATATAAATTTC
*
12225886 TAAATTTATATATATTT
1 TAAATTTATATAAATTT
12225903 GAAATATTTT
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:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (18 bp):
TAAATTTATATAAATTTC
Done.