Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 68 of 106
Found at i:12380278 original size:51 final size:51
Alignment explanation
Indices: 12380113--12380297 Score: 158
Period size: 51 Copynumber: 3.5 Consensus size: 51
12380103 AAGTAGGCCT
* * *
12380113 AAATGTTGGAGAATTTAGAAATTCTAAAAAAGGAAAATTTTCTAGATTGAACT-
1 AAATGGTGGAGAATTTAGAAATTCTAAAAAA-AAAAATTTT-TAAATTG-ACTC
* * * * *
12380166 AAATGGAGGA-AACTTTAGAAATTAAGATCAAAAAATAAAATAATTTCTAAATTGGCCC
1 AAATGGTGGAGAA-TTTAGAAA-T----TCTAAAAA-AAAA-AATTTTTAAATTGACTC
12380224 AAATGGTGGAGAATTTAGAAATTCTAAAAAAAAAAATTTTTAAATTGACTC
1 AAATGGTGGAGAATTTAGAAATTCTAAAAAAAAAAATTTTTAAATTGACTC
** *
12380275 AAATGGTAAAAAATTTAGAAATT
1 AAATGGTGGAGAATTTAGAAATT
12380298 AAGATCAAAA
Statistics
Matches: 106, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
51 34 0.32
52 6 0.06
53 23 0.22
54 1 0.01
57 2 0.02
58 32 0.30
59 8 0.08
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (51 bp):
AAATGGTGGAGAATTTAGAAATTCTAAAAAAAAAAATTTTTAAATTGACTC
Found at i:12380311 original size:109 final size:111
Alignment explanation
Indices: 12380086--12380401 Score: 358
Period size: 109 Copynumber: 2.8 Consensus size: 111
12380076 AAAAAAAAAG
* * * *
12380086 AAATAAAAAGAATT-TATAAGTAGGCCTAAATGTTGGAGAATTTAGAAATTCTAAAAAAGGAAAA
1 AAATAAAAAAAATTCTA-AA-TAGGCCCAAATGGTGGAGAATTTAGAAATTCTAAAAAAGAAAAA
* * *
12380150 TTTTCTAGATTGAACT-AAATGG-AGGAAACTTTAGAAATTAAGATCAAA
64 TTTT-TAAATTG-ACTCAAATGGTAGAAAAATTTAGAAATTAAGATCAAA
* * *
12380198 AAATAAAATAATTTCTAAATTGGCCCAAATGGTGGAGAATTTAGAAATTCTAAAAAA-AAAAATT
1 AAATAAAAAAAATTCTAAATAGGCCCAAATGGTGGAGAATTTAGAAATTCTAAAAAAGAAAAATT
12380262 TTTAAATTGACTCAAATGGTA-AAAAATTTAGAAATTAAGATCAAA
66 TTTAAATTGACTCAAATGGTAGAAAAATTTAGAAATTAAGATCAAA
* * * *
12380307 AAATAAAAAAAATTCTAAATAAGCCCAAATTGTGAAAAATTTAGAAATTC-AAAAAGAGAAAATA
1 AAATAAAAAAAATTCTAAATAGGCCCAAATGGTGGAGAATTTAGAAATTCTAAAAA-AGAAAA-A
* * * *
12380371 TTTCTAATTTGA-TCCAAATGGTGGAATAATT
64 TTTTTAAATTGACT-CAAATGGTAGAAAAATT
12380402 AGATATATTT
Statistics
Matches: 175, Mismatches: 21, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
108 8 0.05
109 78 0.45
110 14 0.08
111 54 0.31
112 19 0.11
113 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.14, T:0.28
Consensus pattern (111 bp):
AAATAAAAAAAATTCTAAATAGGCCCAAATGGTGGAGAATTTAGAAATTCTAAAAAAGAAAAATT
TTTAAATTGACTCAAATGGTAGAAAAATTTAGAAATTAAGATCAAA
Found at i:12384362 original size:18 final size:17
Alignment explanation
Indices: 12384335--12384368 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
12384325 AATGAATGGA
12384335 GAAAAATGAAAAAAAAT
1 GAAAAATGAAAAAAAAT
12384352 GAAACAATGAAAAAAAA
1 GAAA-AATGAAAAAAAA
12384369 AAAAGACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (17 bp):
GAAAAATGAAAAAAAAT
Found at i:12385844 original size:51 final size:50
Alignment explanation
Indices: 12385789--12386051 Score: 189
Period size: 51 Copynumber: 5.0 Consensus size: 50
12385779 AAAAAGAAAT
*
12385789 AAAAAGAATTTCTAAATAGGCGCAAATGATGAAGAATTTAGAAATTCTAAAA
1 AAAAAAAATTTCTAAATAGGC-CAAATGATGAAGAATTTAGAAATTCT-AAA
* * * *
12385841 AAAAAAAATTTCTAAATTGACCAAAATGGTGGAA-ACTTTAGAAA-T-TAAGA
1 AAAAAAAATTTCTAAATAGGCC-AAATGAT-GAAGAATTTAGAAATTCTAA-A
* *
12385891 TTAAAAAAATTTCTAAATAGGTCCAAAT-AGTGGAGAATTTAGAAATTCTAAA
1 -AAAAAAAATTTCTAAATAGG-CCAAATGA-TGAAGAATTTAGAAATTCTAAA
* * * *
12385943 AAAAAAAATTT-TAAATTGATCCAAATTATGAA-AATTTTAGAAATTAAGATAAAAAA
1 AAAAAAAATTTCTAAATAG-GCCAAATGATGAAGAA-TTTAGAAATT---CT---AAA
* * *
12385999 TAAAAAAAATTTCTAAATAGGTCCAAATGGTGAAAAATTTAAAAATTC-AAA
1 -AAAAAAAATTTCTAAATAGG-CCAAATGATGAAGAATTTAGAAATTCTAAA
12386050 AA
1 AA
12386052 GAGAATATAT
Statistics
Matches: 167, Mismatches: 22, Indels: 46
0.71 0.09 0.20
Matches are distributed among these distances:
49 4 0.02
50 31 0.19
51 47 0.28
52 37 0.22
53 7 0.04
56 3 0.02
57 11 0.07
58 25 0.15
59 2 0.01
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.28
Consensus pattern (50 bp):
AAAAAAAATTTCTAAATAGGCCAAATGATGAAGAATTTAGAAATTCTAAA
Found at i:12385948 original size:103 final size:102
Alignment explanation
Indices: 12385782--12386051 Score: 316
Period size: 108 Copynumber: 2.6 Consensus size: 102
12385772 CTTAAAAAAA
*
12385782 AAGAAATAAAAAGAATTTCTAAATAGG-CGCAAATGATGAAGAATTTAGAAATTCTAAAAAAAAA
1 AAGATATAAAAA-AATTTCTAAATAGGTC-CAAATG-TGAAGAATTTAGAAATTCTAAAAAAAAA
* *
12385846 AAATTTCTAAATTGA-CCAAAATGGTGGAAACTTTAGAAATT
63 AAATTT-TAAATTGATCC-AAATGATGAAAACTTTAGAAATT
*
12385887 AAGAT-TAAAAAAATTTCTAAATAGGTCCAAATAGTGGAGAATTTAGAAATTCT-AAAAAAAAAA
1 AAGATATAAAAAAATTTCTAAATAGGTCCAAAT-GTGAAGAATTTAGAAATTCTAAAAAAAAAAA
* *
12385950 ATTTTAAATTGATCCAAATTATGAAAATTTTAGAAATT
65 ATTTTAAATTGATCCAAATGATGAAAACTTTAGAAATT
* *
12385988 AAGATAAAAAATAAAAAAAATTTCTAAATAGGTCCAAATGGTGAAAAATTTAAAAATTC-AAAAA
1 AAGAT-----AT-AAAAAAATTTCTAAATAGGTCCAAAT-GTGAAGAATTTAGAAATTCTAAAAA
12386052 GAGAATATAT
Statistics
Matches: 144, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
101 32 0.22
102 16 0.11
103 37 0.26
104 8 0.06
105 4 0.03
107 1 0.01
108 46 0.32
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.27
Consensus pattern (102 bp):
AAGATATAAAAAAATTTCTAAATAGGTCCAAATGTGAAGAATTTAGAAATTCTAAAAAAAAAAAA
TTTTAAATTGATCCAAATGATGAAAACTTTAGAAATT
Found at i:12387057 original size:3 final size:3
Alignment explanation
Indices: 12387049--12387084 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
12387039 ATCCTATTTA
12387049 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
12387085 TCTTAATACG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:12387092 original size:14 final size:14
Alignment explanation
Indices: 12387049--12387085 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
12387039 ATCCTATTTA
12387049 AATAATAATAATAAT
1 AATAAT-ATAATAAT
12387064 AATAATATAATAAT
1 AATAATATAATAAT
12387078 AATAATAT
1 AATAATAT
12387086 CTTAATACGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:12388705 original size:3 final size:3
Alignment explanation
Indices: 12388699--12388736 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
12388689 CTATTTATCA
*
12388699 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12388737 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:12391675 original size:12 final size:12
Alignment explanation
Indices: 12391658--12391690 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
12391648 ACTCCATGAA
12391658 GATGCAAGACAT
1 GATGCAAGACAT
12391670 GATGCAAGACAT
1 GATGCAAGACAT
12391682 GATGCAAGA
1 GATGCAAGA
12391691 AATAGCAACG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.15, G:0.27, T:0.15
Consensus pattern (12 bp):
GATGCAAGACAT
Found at i:12397377 original size:21 final size:22
Alignment explanation
Indices: 12397333--12397377 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
12397323 AATCTTGATT
*
12397333 TAATGTCAGTAAAATTTTATTAA
1 TAATGTCA-TAAAATTTTAGTAA
*
12397356 TAATGTC-TAAAATTTTGGTAA
1 TAATGTCATAAAATTTTAGTAA
12397377 T
1 T
12397378 GAAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
23 7 0.35
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.44
Consensus pattern (22 bp):
TAATGTCATAAAATTTTAGTAA
Found at i:12403237 original size:22 final size:24
Alignment explanation
Indices: 12403200--12403254 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
12403190 AATAATTTTT
* *
12403200 TATATATAAA-TTTATTTAAAT-A
1 TATATAAAAATTTTATTAAAATAA
12403222 TAT-TAAAAATTTTATTAAAATAA
1 TATATAAAAATTTTATTAAAATAA
12403245 TATATAAAAA
1 TATATAAAAA
12403255 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 13 0.46
23 4 0.14
24 6 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TATATAAAAATTTTATTAAAATAA
Found at i:12405051 original size:26 final size:24
Alignment explanation
Indices: 12405022--12405082 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 24
12405012 ATTAATTAAA
*
12405022 ATTAATATATTTTTATTAAAAAATAT
1 ATTAATATATATTTA-TAAAAAAT-T
*
12405048 ATTAATTTATATTTATAAAAAATT
1 ATTAATATATATTTATAAAAAATT
12405072 ATTTAA-ATATA
1 A-TTAATATATA
12405083 CAACATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
24 6 0.19
25 12 0.39
26 13 0.42
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTAATATATATTTATAAAAAATT
Found at i:12405246 original size:17 final size:18
Alignment explanation
Indices: 12405218--12405251 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
12405208 GTATCCATTG
12405218 AATATAAATATAAAAATA
1 AATATAAATATAAAAATA
12405236 AATAT-AATATAAAAAT
1 AATATAAATATAAAAAT
12405252 TCAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATATAAATATAAAAATA
Found at i:12407634 original size:22 final size:22
Alignment explanation
Indices: 12407583--12407655 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 22
12407573 TTTTTTAGCT
*
12407583 AAAAATACCTTAAATAATCATGTTA
1 AAAAATACCTTAAATAATC---CTA
12407608 AAAAATACCTTAAATAATCCTA
1 AAAAATACCTTAAATAATCCTA
* *
12407630 AAAAA-A-ATT-AGTAATCCTA
1 AAAAATACCTTAAATAATCCTA
12407649 AAAAATA
1 AAAAATA
12407656 AATGCTAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 14 0.32
20 3 0.07
21 1 0.02
22 7 0.16
25 19 0.43
ACGTcount: A:0.58, C:0.12, G:0.03, T:0.27
Consensus pattern (22 bp):
AAAAATACCTTAAATAATCCTA
Found at i:12407635 original size:25 final size:25
Alignment explanation
Indices: 12407583--12407636 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
12407573 TTTTTTAGCT
***
12407583 AAAAATACCTTAAATAATCATGTTA
1 AAAAATACCTTAAATAATCATAAAA
*
12407608 AAAAATACCTTAAATAATCCTAAAA
1 AAAAATACCTTAAATAATCATAAAA
12407633 AAAA
1 AAAA
12407637 TTAGTAATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.59, C:0.13, G:0.02, T:0.26
Consensus pattern (25 bp):
AAAAATACCTTAAATAATCATAAAA
Found at i:12408212 original size:13 final size:15
Alignment explanation
Indices: 12408183--12408216 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
12408173 AAAATACATT
12408183 AAATAATCTCTTAAA
1 AAATAATCTCTTAAA
12408198 AAATAAT-TC-TAAA
1 AAATAATCTCTTAAA
12408211 AAATAA
1 AAATAA
12408217 ACAATAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
14 2 0.11
15 7 0.37
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAATCTCTTAAA
Found at i:12409128 original size:23 final size:21
Alignment explanation
Indices: 12409102--12409149 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 21
12409092 AAAAATTAAT
*
12409102 AAAAATTATTATAATATATATTA
1 AAAAATTATGATAAT-TAT-TTA
12409125 AAAAATTATGATAATTATTTA
1 AAAAATTATGATAATTATTTA
12409146 AAAA
1 AAAA
12409150 TTAATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 7 0.29
22 3 0.12
23 14 0.58
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (21 bp):
AAAAATTATGATAATTATTTA
Found at i:12412032 original size:14 final size:14
Alignment explanation
Indices: 12412009--12412048 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
12411999 ATTTTTTAAT
12412009 TAAAAA-ATATTTA
1 TAAAAATATATTTA
12412022 TAAAAATATATATT-
1 TAAAAATATAT-TTA
12412036 TAAAAAT-TATTTA
1 TAAAAATATATTTA
12412049 ATTATCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 2 0.08
13 9 0.38
14 11 0.46
15 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAAATATATTTA
Found at i:12412312 original size:69 final size:71
Alignment explanation
Indices: 12412149--12412330 Score: 183
Period size: 69 Copynumber: 2.5 Consensus size: 71
12412139 TAAAAAATGC
* * * * *
12412149 ATTTCTAAATAATATGAATATATATCTTTTTGAATTTAAAAAATTTCAAATGTATGATATATTAT
1 ATTTCTTAATAATATAAATATAT-TATTTTTAAATTTAAAAAATTTAAAATGTATGA-ATATTA-
*
12412214 TTTTAAAATAG
63 --TTAAAATAA
* *
12412225 GTTTCCTAATAATATAAATATATTATTTTTAAATTT-AAAAATTTAAAATGTAGTG-ATATTA-T
1 ATTTCTTAATAATATAAATATATTATTTTTAAATTTAAAAAATTTAAAATGTA-TGAATATTATT
12412287 AAAATAA
65 AAAATAA
*
12412294 ATTTCTTAATAATTTAAATATA-TATCATTTTAAATTT
1 ATTTCTTAATAATATAAATATATTAT--TTTTAAATTT
12412331 GAAATTTGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
68 3 0.03
69 26 0.28
70 10 0.11
73 6 0.07
74 15 0.16
75 13 0.14
76 19 0.21
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (71 bp):
ATTTCTTAATAATATAAATATATTATTTTTAAATTTAAAAAATTTAAAATGTATGAATATTATTA
AAATAA
Found at i:12412627 original size:14 final size:14
Alignment explanation
Indices: 12412608--12412637 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12412598 AATTACTTTA
*
12412608 ATTTTTTATATTTT
1 ATTTTTTAAATTTT
12412622 ATTTTTTAAATTTT
1 ATTTTTTAAATTTT
12412636 AT
1 AT
12412638 AATTAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTTAAATTTT
Found at i:12412698 original size:199 final size:199
Alignment explanation
Indices: 12412491--12412891 Score: 741
Period size: 199 Copynumber: 2.0 Consensus size: 199
12412481 ATATATATAT
12412491 ATATATATATATATTGAACATCTAAGGAATTAAATAATATTAAAGTATGAGAAAGAAAGATCAAA
1 ATATATATATATATTGAACATCTAAGGAATTAAATAATATTAAAGTATGAGAAAGAAAGATCAAA
*
12412556 CTTATAATCTTATGATTAATAATC-ATGTATTTTAATCGATTAAATTACTTTAATTTTTTATATT
66 CTTATAATCTTATGATTAATAA-CAATGTATTTTAATCGATTAAATTACTTCAATTTTTTATATT
*
12412620 TTATTTTTTAAATTTTATAATTAATGAAAAAATTATTTAAGACGTTTTTAGTAAAAAATTATCTT
130 TTATTTTTTAAATTTTATAATTAATGAAAAAATTATTTAAGACGTTTTTAGTAAAAAAATATCTT
12412685 AAATA
195 AAATA
* * *
12412690 ATATATATATATATTGAACATTTAAGGAATTAAATAATCTTAAAGTATGAGAAGGAAAGATCAAA
1 ATATATATATATATTGAACATCTAAGGAATTAAATAATATTAAAGTATGAGAAAGAAAGATCAAA
12412755 CTTATAATCTTATGATTAATAACAATGTATTTTAATCGATTAAATTACTTCAATTTTTTATATTT
66 CTTATAATCTTATGATTAATAACAATGTATTTTAATCGATTAAATTACTTCAATTTTTTATATTT
12412820 TATTTTTTAAATTTTATAATTAATGAAAAAATTATTTAAGACGTTTTTAGTAAAAAAATATCTTA
131 TATTTTTTAAATTTTATAATTAATGAAAAAATTATTTAAGACGTTTTTAGTAAAAAAATATCTTA
12412885 AATA
196 AATA
12412889 ATA
1 ATA
12412892 AGGTTCAAAA
Statistics
Matches: 196, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
198 1 0.01
199 195 0.99
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (199 bp):
ATATATATATATATTGAACATCTAAGGAATTAAATAATATTAAAGTATGAGAAAGAAAGATCAAA
CTTATAATCTTATGATTAATAACAATGTATTTTAATCGATTAAATTACTTCAATTTTTTATATTT
TATTTTTTAAATTTTATAATTAATGAAAAAATTATTTAAGACGTTTTTAGTAAAAAAATATCTTA
AATA
Found at i:12412826 original size:14 final size:14
Alignment explanation
Indices: 12412807--12412836 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12412797 AATTACTTCA
*
12412807 ATTTTTTATATTTT
1 ATTTTTTAAATTTT
12412821 ATTTTTTAAATTTT
1 ATTTTTTAAATTTT
12412835 AT
1 AT
12412837 AATTAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTTAAATTTT
Found at i:12413001 original size:62 final size:59
Alignment explanation
Indices: 12412846--12413002 Score: 134
Period size: 62 Copynumber: 2.5 Consensus size: 59
12412836 TAATTAATGA
* *
12412846 AAAAATTATTTAAGACGTTTTTAGTAAAAAAATATCTTAAATAATAAGGTTCAAAAAAGAG
1 AAAAATTATTTAAGACGTTTTTA-T-AAAAAATATATTAAATAATAAGCTTCAAAAAAGAG
* ** * *** * * *
12412907 AAATGTATTATTTAAGATATTTTTGATCAAAAATATATTAAATAATCTTCTTTAAAGAAATATT
1 AAA--AATTATTTAAGACGTTTTT-ATAAAAAATATATTAAATAATAAGCTTCAAA-AAAGA-G
12412971 AAAAATTATTTAAGACGTTTTTACTAAAAAAT
1 AAAAATTATTTAAGACGTTTTTA-TAAAAAAT
12413003 GATAAAAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 11
0.73 0.16 0.11
Matches are distributed among these distances:
61 4 0.05
62 45 0.61
63 21 0.28
64 4 0.05
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (59 bp):
AAAAATTATTTAAGACGTTTTTATAAAAAATATATTAAATAATAAGCTTCAAAAAAGAG
Found at i:12414662 original size:19 final size:18
Alignment explanation
Indices: 12414624--12414662 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
12414614 TGTTTTTGTT
* *
12414624 TTTTTTTAATTTTTATAA
1 TTTTTTTAATTATTAAAA
12414642 TTTTTTTAATTAATTAAAA
1 TTTTTTTAATT-ATTAAAA
12414661 TT
1 TT
12414663 GATAGGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTTAATTATTAAAA
Found at i:12417721 original size:18 final size:18
Alignment explanation
Indices: 12417698--12417743 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
12417688 TCTCTCATTT
12417698 TTTATTATTTA-TTCTTAA
1 TTTATTATTTAGTTCTT-A
*
12417716 TTTATTAATTAGTTCTTA
1 TTTATTATTTAGTTCTTA
12417734 TTTATTATTT
1 TTTATTATTT
12417744 CTTTTATAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTATTTAGTTCTTA
Found at i:12419131 original size:26 final size:27
Alignment explanation
Indices: 12419071--12419131 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
12419061 TTGTTTTTTT
12419071 TTTTTTTTGGTATCTTGTATTTTGATA
1 TTTTTTTTGGTATCTTGTATTTTGATA
12419098 TTTTTTTT-GTAT-TT-TATATTTGATAA
1 TTTTTTTTGGTATCTTGTAT-TTTGAT-A
12419124 TTTTTTTT
1 TTTTTTTT
12419132 TTTTCGGACA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 3 0.09
25 8 0.25
26 13 0.41
27 8 0.25
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.72
Consensus pattern (27 bp):
TTTTTTTTGGTATCTTGTATTTTGATA
Found at i:12420814 original size:16 final size:17
Alignment explanation
Indices: 12420781--12420815 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12420771 AATTTAATGA
12420781 ATTTTGATATAATTTTG
1 ATTTTGATATAATTTTG
*
12420798 ATTTTGATA-ACTTTTG
1 ATTTTGATATAATTTTG
12420814 AT
1 AT
12420816 AAAATTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (17 bp):
ATTTTGATATAATTTTG
Found at i:12420824 original size:21 final size:21
Alignment explanation
Indices: 12420798--12420959 Score: 100
Period size: 21 Copynumber: 7.8 Consensus size: 21
12420788 TATAATTTTG
*
12420798 ATTTTGATAACTTTTGATAAA
1 ATTTTGATAACTTTTGATATA
* * *
12420819 ATTTTGATAACCTTCGTTATA
1 ATTTTGATAACTTTTGATATA
* *
12420840 ATTTT-AGTAAC-TTTGATGTT
1 ATTTTGA-TAACTTTTGATATA
*
12420860 AGTTTGATAA-TTTATGATATA
1 ATTTTGATAACTTT-TGATATA
* ** *
12420881 ATTTTGGTAACCATTGATACA
1 ATTTTGATAACTTTTGATATA
* * *
12420902 A-ATTGGTAA-TCTTTGATAAA
1 ATTTTGATAACT-TTTGATATA
* *
12420922 ATTTTGATAACTACTTGATGTA
1 ATTTTGATAACT-TTTGATATA
*
12420944 ATTTTAATAACTTTTG
1 ATTTTGATAACTTTTG
12420960 TAGACATCAA
Statistics
Matches: 105, Mismatches: 28, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
20 30 0.29
21 56 0.53
22 19 0.18
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.47
Consensus pattern (21 bp):
ATTTTGATAACTTTTGATATA
Found at i:12420909 original size:20 final size:19
Alignment explanation
Indices: 12420884--12420924 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12420874 TGATATAATT
12420884 TTGGTAACCATTGATACAAA
1 TTGGTAACCATTGATA-AAA
* *
12420904 TTGGTAATCTTTGATAAAA
1 TTGGTAACCATTGATAAAA
12420923 TT
1 TT
12420925 TTGATAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (19 bp):
TTGGTAACCATTGATAAAA
Found at i:12420940 original size:22 final size:22
Alignment explanation
Indices: 12420914--12420955 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12420904 TTGGTAATCT
*
12420914 TTGATAAAATTTTGATAACTAC
1 TTGATAAAATTTTAATAACTAC
**
12420936 TTGATGTAATTTTAATAACT
1 TTGATAAAATTTTAATAACT
12420956 TTTGTAGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
TTGATAAAATTTTAATAACTAC
Found at i:12421141 original size:21 final size:22
Alignment explanation
Indices: 12421102--12421157 Score: 87
Period size: 21 Copynumber: 2.5 Consensus size: 22
12421092 AATTAAACAC
12421102 CAAAAAATAAAACAAACAAAAATA
1 CAAAAAA-AAAAC-AACAAAAATA
12421126 CAAAAAAAAAAC-ACAAAAATA
1 CAAAAAAAAAACAACAAAAATA
12421147 CAAAAAAAAAA
1 CAAAAAAAAAA
12421158 GCAGAAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.62
23 5 0.16
24 7 0.22
ACGTcount: A:0.82, C:0.12, G:0.00, T:0.05
Consensus pattern (22 bp):
CAAAAAAAAAACAACAAAAATA
Found at i:12422242 original size:33 final size:32
Alignment explanation
Indices: 12422204--12422279 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 32
12422194 TTTATTTTTT
*
12422204 ATTTTTTAAAATATT-TTATATATTATTTATATC
1 ATTTTTTAAAATATTATTAT-TATTATTTAT-GC
*
12422237 A-TTTTTAACATTATTATTATTATTATTTATGC
1 ATTTTTTAA-AATATTATTATTATTATTTATGC
*
12422269 ATGTTTTAAAA
1 ATTTTTTAAAA
12422280 CTTTTAGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
32 10 0.28
33 22 0.61
34 4 0.11
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (32 bp):
ATTTTTTAAAATATTATTATTATTATTTATGC
Found at i:12422350 original size:17 final size:18
Alignment explanation
Indices: 12422316--12422367 Score: 70
Period size: 17 Copynumber: 2.9 Consensus size: 18
12422306 TTGTTGTTTC
12422316 ATAACAATAATTAATAATA
1 ATAACAATAA-TAATAATA
12422335 ATAACAATAA-AATAATA
1 ATAACAATAATAATAATA
**
12422352 ATAACAGCAATAATAA
1 ATAACAATAATAATAA
12422368 AAATGATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 15 0.50
18 5 0.17
19 10 0.33
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (18 bp):
ATAACAATAATAATAATA
Found at i:12422362 original size:20 final size:20
Alignment explanation
Indices: 12422318--12422364 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12422308 GTTGTTTCAT
* *
12422318 AACAAT-AATTAATAATAAT
1 AACAATAAAATAATAATAAC
12422337 AACAATAAAATAATAATAAC
1 AACAATAAAATAATAATAAC
*
12422357 AGCAATAA
1 AACAATAA
12422365 TAAAAATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (20 bp):
AACAATAAAATAATAATAAC
Found at i:12422786 original size:13 final size:13
Alignment explanation
Indices: 12422768--12422844 Score: 64
Period size: 13 Copynumber: 5.5 Consensus size: 13
12422758 CCCTCAAAAT
12422768 CCTAAAACTAAAC
1 CCTAAAACTAAAC
*
12422781 CCTAAACCTTTCAAAC
1 CCTAAAAC--T-AAAC
12422797 CCTAAAACTAAAC
1 CCTAAAACTAAAC
*
12422810 CCTAAACATTTTAAAC
1 CCTAAA-A--CTAAAC
*
12422826 CTTAAAACTAAAC
1 CCTAAAACTAAAC
*
12422839 CATAAA
1 CCTAAA
12422845 CCCTTCAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
13 27 0.52
14 2 0.04
15 2 0.04
16 21 0.40
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (13 bp):
CCTAAAACTAAAC
Found at i:12422800 original size:29 final size:29
Alignment explanation
Indices: 12422768--12422861 Score: 134
Period size: 29 Copynumber: 3.2 Consensus size: 29
12422758 CCCTCAAAAT
12422768 CCTAAAACTAAACCCTAAACCTTTCAAAC
1 CCTAAAACTAAACCCTAAACCTTTCAAAC
* *
12422797 CCTAAAACTAAACCCTAAACATTTTAAAC
1 CCTAAAACTAAACCCTAAACCTTTCAAAC
* * *
12422826 CTTAAAACTAAACCATAAACCCTTCAAAC
1 CCTAAAACTAAACCCTAAACCTTTCAAAC
*
12422855 CCCAAAA
1 CCTAAAA
12422862 TCAAATCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 56 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (29 bp):
CCTAAAACTAAACCCTAAACCTTTCAAAC
Found at i:12422889 original size:35 final size:35
Alignment explanation
Indices: 12422835--12422901 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
12422825 CCTTAAAACT
*
12422835 AAACCATAAACCCTTCAAACCCCAAAATCAAATCA
1 AAACCATAAACCCTCCAAACCCCAAAATCAAATCA
* * *
12422870 AAACCCTAAATCCTCCAAACCCTAAAATCAAA
1 AAACCATAAACCCTCCAAACCCCAAAATCAAA
12422902 ACCCTAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (35 bp):
AAACCATAAACCCTCCAAACCCCAAAATCAAATCA
Found at i:12422912 original size:44 final size:44
Alignment explanation
Indices: 12422864--12422953 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
12422854 CCCCAAAATC
* *
12422864 AAATCAAAACCCTAAATCCTCCAAACCCTAAAATCAAAACCCTA
1 AAATCAAAACCCTAAACCCTACAAACCCTAAAATCAAAACCCTA
* ** * *
12422908 AAATCGAAACTTTAAACCCTACAAACCCTAAAATTAAGACCCTA
1 AAATCAAAACCCTAAACCCTACAAACCCTAAAATCAAAACCCTA
12422952 AA
1 AA
12422954 CCCTAAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (44 bp):
AAATCAAAACCCTAAACCCTACAAACCCTAAAATCAAAACCCTA
Found at i:12422923 original size:14 final size:14
Alignment explanation
Indices: 12422864--12422917 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
12422854 CCCCAAAATC
12422864 AAATCAAAACCCTA
1 AAATCAAAACCCTA
* *
12422878 AATCCTCCAAACCCTA
1 AA--ATCAAAACCCTA
12422894 AAATCAAAACCCTA
1 AAATCAAAACCCTA
*
12422908 AAATCGAAAC
1 AAATCAAAAC
12422918 TTTAAACCCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
14 21 0.64
16 12 0.36
ACGTcount: A:0.52, C:0.31, G:0.02, T:0.15
Consensus pattern (14 bp):
AAATCAAAACCCTA
Found at i:12422998 original size:15 final size:16
Alignment explanation
Indices: 12422973--12423008 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12422963 TTCCAAACCC
12422973 TAAAA-CTCTAG-CCT
1 TAAAATCTCTAGACCT
12422987 TAAAATCTCTAGACCT
1 TAAAATCTCTAGACCT
12423003 TAAAAT
1 TAAAAT
12423009 TGAAACCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 6 0.30
16 9 0.45
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (16 bp):
TAAAATCTCTAGACCT
Found at i:12423071 original size:16 final size:16
Alignment explanation
Indices: 12423018--12423079 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 16
12423008 TTGAAACCAT
*
12423018 AAACCCTAAAAT-C-A
1 AAACTCTAAAATCCAA
**
12423032 AAACTCT-AAA-CCCC
1 AAACTCTAAAATCCAA
*
12423046 AAACTCTAAAATTCAA
1 AAACTCTAAAATCCAA
*
12423062 AAACTGTAAAATCCAA
1 AAACTCTAAAATCCAA
12423078 AA
1 AA
12423080 TCCCAAACTC
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
13 4 0.11
14 13 0.35
15 3 0.08
16 17 0.46
ACGTcount: A:0.55, C:0.26, G:0.02, T:0.18
Consensus pattern (16 bp):
AAACTCTAAAATCCAA
Found at i:12424588 original size:22 final size:22
Alignment explanation
Indices: 12424563--12424657 Score: 61
Period size: 22 Copynumber: 4.4 Consensus size: 22
12424553 GATATACTGC
*
12424563 TAAATTATCAA-TAATTTATTAT
1 TAAATTAT-AATTAATTTACTAT
*
12424585 TAAATTATAATTGATTTACTAT
1 TAAATTATAATTAATTTACTAT
* * * *
12424607 TAATTTATGATTTA-TTACTAC
1 TAAATTATAATTAATTTACTAT
* * * *
12424628 TAAGTTATGAA-TGATTTACAAC
1 TAAATTAT-AATTAATTTACTAT
12424650 TAAATTAT
1 TAAATTAT
12424658 TGATGTTTAC
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
21 17 0.29
22 42 0.71
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.47
Consensus pattern (22 bp):
TAAATTATAATTAATTTACTAT
Found at i:12424722 original size:22 final size:21
Alignment explanation
Indices: 12424576--12424735 Score: 99
Period size: 22 Copynumber: 7.4 Consensus size: 21
12424566 ATTATCAATA
* *
12424576 ATTTATTATTAAATTATAATTG
1 ATTTACTATTAAATTATGA-TG
*
12424598 ATTTACTATTAATTTATGAT-
1 ATTTACTATTAAATTATGATG
* * *
12424618 TTATTACTACTAAGTTATGAATG
1 AT-TTACTATTAAATTATG-ATG
* *
12424641 ATTTACAACTAAATTATTGATG
1 ATTTACTATTAAATTA-TGATG
* * *
12424663 -TTTACTACTAAGTTACCGATG
1 ATTTACTATTAAATTA-TGATG
** * *
12424684 ATTTGTTATAAAATTATAACTG
1 ATTTACTATTAAATTATGA-TG
*
12424706 ATTTACTATTAATTTATTGATG
1 ATTTACTATTAAATTA-TGATG
12424728 ATTTACTA
1 ATTTACTA
12424736 CAAAGTTATC
Statistics
Matches: 106, Mismatches: 25, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.01
21 33 0.31
22 67 0.63
23 5 0.05
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.47
Consensus pattern (21 bp):
ATTTACTATTAAATTATGATG
Found at i:12424750 original size:22 final size:22
Alignment explanation
Indices: 12424621--12424757 Score: 73
Period size: 22 Copynumber: 6.3 Consensus size: 22
12424611 TTATGATTTA
* *
12424621 TTACTACTAAGTTATGAATGAT
1 TTACTACAAAGTTATCAATGAT
* **
12424643 TTACAACTAAA-TTATTGATG-T
1 TTACTAC-AAAGTTATCAATGAT
* * *
12424664 TTACTACTAAGTTACCGATGAT
1 TTACTACAAAGTTATCAATGAT
** * *
12424686 TTGTTATAAAATTAT-AACTGAT
1 TTACTACAAAGTTATCAA-TGAT
** * **
12424708 TTACTATTAATTTATTGATGAT
1 TTACTACAAAGTTATCAATGAT
12424730 TTACTACAAAGTTATCAATGAT
1 TTACTACAAAGTTATCAATGAT
*
12424752 TAACTA
1 TTACTA
12424758 ATTTACTACT
Statistics
Matches: 84, Mismatches: 26, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
20 2 0.02
21 15 0.18
22 64 0.76
23 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (22 bp):
TTACTACAAAGTTATCAATGAT
Found at i:12424782 original size:52 final size:52
Alignment explanation
Indices: 12424700--12424806 Score: 135
Period size: 52 Copynumber: 2.1 Consensus size: 52
12424690 TATAAAATTA
* * * * *
12424700 TAACTGATTTACTATTAATTTATTGATGATTTACTACAAAGTTATCAATGAT
1 TAACTAATTTACTACTAAATTATAGATGATTTACTACAAAGTTATCAATAAT
**
12424752 TAACTAATTTACTACTAAATTACTAG-TGATTTACTATTAAGTTATCAATAAT
1 TAACTAATTTACTACTAAATTA-TAGATGATTTACTACAAAGTTATCAATAAT
12424804 TAA
1 TAA
12424807 ATCTAAATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
52 45 0.96
53 2 0.04
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (52 bp):
TAACTAATTTACTACTAAATTATAGATGATTTACTACAAAGTTATCAATAAT
Found at i:12424849 original size:21 final size:18
Alignment explanation
Indices: 12424823--12424866 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
12424813 ATTATCAATG
12424823 ATTTACTATCATATTGTATAC
1 ATTTACTA-C-TATTGTAT-C
*
12424844 ATTTACTACTATTTTATC
1 ATTTACTACTATTGTATC
12424862 ATTTA
1 ATTTA
12424867 TTTACTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 1 0.05
21 8 0.36
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTTACTACTATTGTATC
Found at i:12427925 original size:14 final size:14
Alignment explanation
Indices: 12427906--12427965 Score: 50
Period size: 14 Copynumber: 4.3 Consensus size: 14
12427896 TTTCTGTTTG
*
12427906 ATTTTATTTTTCTT
1 ATTTTATTTTTATT
* *
12427920 ATTTTATTTATGTT
1 ATTTTATTTTTATT
* *
12427934 ATTTTGTTTATTTTT
1 ATTTTATTT-TTATT
*
12427949 A-TTTACTTTTATT
1 ATTTTATTTTTATT
12427962 ATTT
1 ATTT
12427966 CTTGTTTTAA
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
13 5 0.14
14 27 0.75
15 4 0.11
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (14 bp):
ATTTTATTTTTATT
Found at i:12427937 original size:23 final size:24
Alignment explanation
Indices: 12427909--12427974 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 24
12427899 CTGTTTGATT
12427909 TTATTTTTCTTATTTTATTTA-TG
1 TTATTTTTCTTATTTTATTTACTG
*
12427932 TTATTTTGT-TTATTTTTATTTACTT
1 TTATTTT-TCTTA-TTTTATTTACTG
*
12427957 TTATTATTTCTTGTTTTA
1 TTATT-TTTCTTATTTTA
12427975 AATTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
23 10 0.28
24 10 0.28
25 12 0.33
26 4 0.11
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (24 bp):
TTATTTTTCTTATTTTATTTACTG
Found at i:12428128 original size:16 final size:17
Alignment explanation
Indices: 12428100--12428131 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12428090 AACTATTGAA
12428100 GAATTTTTCATGGATTT
1 GAATTTTTCATGGATTT
12428117 GAATTTTT-ATGGATT
1 GAATTTTTCATGGATT
12428132 CTGTCAAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (17 bp):
GAATTTTTCATGGATTT
Found at i:12431218 original size:60 final size:59
Alignment explanation
Indices: 12431142--12431338 Score: 279
Period size: 59 Copynumber: 3.3 Consensus size: 59
12431132 AACATGAAAG
*
12431142 TTTTTATTCTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTAGAA
1 TTTTTATTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTAGAA
* * *
12431201 TTTTTATTTTTAAGAAAAATTAATACTTTCAACTTTTTTTTAAAAATA-ATTTTTTAGAA
1 TTTTTA-TTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTAGAA
* * * *
12431260 ATTTTATCTTCAAGGAAAATTGATACTTTCAATTTTTTCTCAAAAATATATATTTTTTAGAA
1 TTTTTAT-TTTAAGAAAAATTGATACTTTCAACTTTTTCTC-AAAA-ATATATTTTTTAGAA
12431322 TTTTTATTTTAAGAAAA
1 TTTTTATTTTAAGAAAA
12431339 TCATTAAAAA
Statistics
Matches: 119, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.01
59 49 0.41
60 41 0.34
61 11 0.09
62 17 0.14
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (59 bp):
TTTTTATTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTAGAA
Found at i:12432348 original size:22 final size:21
Alignment explanation
Indices: 12432314--12432377 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
12432304 GATATATTAA
**
12432314 TAGATAACCAAAAGAAAATAAT
1 TAGATAAATAAAA-AAAATAAT
*
12432336 TAGATAAATAAAAAATATTAA-
1 TAGATAAATAAAAAA-AATAAT
*
12432357 TAGATAAATAATAAAAATAAT
1 TAGATAAATAAAAAAAATAAT
12432378 AATCATAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.11
21 16 0.46
22 15 0.43
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.25
Consensus pattern (21 bp):
TAGATAAATAAAAAAAATAAT
Found at i:12432362 original size:21 final size:21
Alignment explanation
Indices: 12432307--12432372 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 21
12432297 ATAGATAGAT
**
12432307 ATATTAATAGATAACCAAAAGA
1 ATATTAATAGATAAATAAAA-A
*
12432329 A-AATAATTAGATAAATAAAAA
1 ATATTAA-TAGATAAATAAAAA
12432350 ATATTAATAGATAAATAATAAA
1 ATATTAATAGATAAATAA-AAA
12432372 A
1 A
12432373 ATAATAATCA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 17 0.46
22 20 0.54
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (21 bp):
ATATTAATAGATAAATAAAAA
Found at i:12432363 original size:17 final size:18
Alignment explanation
Indices: 12432328--12432369 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
12432318 TAACCAAAAG
12432328 AAAATAATTAGATAAATAA
1 AAAAT-ATTAGATAAATAA
*
12432347 AAAATATTA-ATAGATAA
1 AAAATATTAGATAAATAA
*
12432364 ATAATA
1 AAAATA
12432370 AAAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
18 4 0.19
19 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAATATTAGATAAATAA
Found at i:12432751 original size:41 final size:41
Alignment explanation
Indices: 12432675--12432870 Score: 243
Period size: 42 Copynumber: 4.7 Consensus size: 41
12432665 CTCCTTTAAA
* * *
12432675 CAGAGGCTCCACGACCTTG-AAAATAAATGGCTCATCTAAT
1 CAGAGGCTCAACGACTTTGAAAAATAAATGACTCATCTAAT
12432715 CAGAGGCTCAACGACTTTGAAAAATAAATGACTCATCTAAT
1 CAGAGGCTCAACGACTTTGAAAAATAAATGACTCATCTAAT
* * *
12432756 CAGAGGCTCAACGACTTTTGAAAAGTAAATGGCTCCTCTAAT
1 CAGAGGCTCAACGAC-TTTGAAAAATAAATGACTCATCTAAT
* * * *
12432798 CAGAGGCTCAACGATTTTGAAAAAATAAATAAAGCTCCTCTAAA
1 CAGAGGCTCAACGACTTTG-AAAAATAAAT-GA-CTCATCTAAT
12432842 CAGAGGCTCAACGACTTTTG-AAAATAAAT
1 CAGAGGCTCAACGAC-TTTGAAAAATAAAT
12432871 AAAGCTCCCC
Statistics
Matches: 138, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
40 17 0.12
41 39 0.28
42 46 0.33
43 9 0.07
44 23 0.17
45 4 0.03
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (41 bp):
CAGAGGCTCAACGACTTTGAAAAATAAATGACTCATCTAAT
Found at i:12432796 original size:42 final size:41
Alignment explanation
Indices: 12432664--12432870 Score: 258
Period size: 41 Copynumber: 5.0 Consensus size: 41
12432654 AATAAACAAA
* * * *
12432664 GCTCCTTTAAACAGAGGCTCCACGAC-CTTGAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAATG
*
12432704 GCTCATCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTTG-AAAATAAATG
* *
12432745 ACTCATCTAATCAGAGGCTCAACGACTTTTGAAAAGTAAATG
1 GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAA-TAAATG
*
12432787 GCTCCTCTAATCAGAGGCTCAACGA-TTTTGAAAAAATAAATAAA
1 GCTCCTCTAATCAGAGGCTCAACGACTTTTG--AAAATAAAT--G
*
12432831 GCTCCTCTAAACAGAGGCTCAACGACTTTTGAAAATAAAT
1 GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAAT
12432871 AAAGCTCCCC
Statistics
Matches: 149, Mismatches: 10, Indels: 13
0.87 0.06 0.08
Matches are distributed among these distances:
40 25 0.17
41 44 0.30
42 38 0.26
43 13 0.09
44 24 0.16
45 5 0.03
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAACGACTTTTGAAAATAAATG
Found at i:12432796 original size:83 final size:85
Alignment explanation
Indices: 12432631--12432870 Score: 335
Period size: 83 Copynumber: 2.8 Consensus size: 85
12432621 TCCTATAAGT
* * * * * *
12432631 AGAGGCTCAACAACTTTGAAAAAAATAAACAAAGCTCCTTTAAACAGAGGCTCCACGAC-CTTGA
1 AGAGGCTCAACGACTTTG-AAAAAATAAATAAAGCTCATCTAAACAGAGGCTCAACGACTTTTGA
12432695 AAATAAATGGCTCATCTAATC
65 AAATAAATGGCTCATCTAATC
* *
12432716 AGAGGCTCAACGACTTTG-AAAAATAAAT-GA-CTCATCTAATCAGAGGCTCAACGACTTTTGAA
1 AGAGGCTCAACGACTTTGAAAAAATAAATAAAGCTCATCTAAACAGAGGCTCAACGACTTTTGAA
*
12432778 AAGTAAATGGCTCCTCTAATC
66 AA-TAAATGGCTCATCTAATC
* *
12432799 AGAGGCTCAACGATTTTGAAAAAATAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTGAA
1 AGAGGCTCAACGACTTTGAAAAAATAAATAAAGCTCATCTAAACAGAGGCTCAACGACTTTTGAA
12432864 AATAAAT
66 AATAAAT
12432871 AAAGCTCCCC
Statistics
Matches: 137, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
81 21 0.15
82 8 0.06
83 43 0.31
84 10 0.07
85 23 0.17
86 32 0.23
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (85 bp):
AGAGGCTCAACGACTTTGAAAAAATAAATAAAGCTCATCTAAACAGAGGCTCAACGACTTTTGAA
AATAAATGGCTCATCTAATC
Found at i:12432902 original size:43 final size:42
Alignment explanation
Indices: 12432631--12432912 Score: 146
Period size: 42 Copynumber: 6.6 Consensus size: 42
12432621 TCCTATAAGT
* * **
12432631 AGAGGCTCAACAACTTTGAAAAAAATAAACAAAGCTCCTTTAAAC
1 AGAGGCGCAACAACTTTG---AAAATAAATAAAGCTCCCCTAAAC
* * * * * ** *
12432676 AGAGGCTCCACGACCTTGAAAATAAAT--GGCTCATCTAATC
1 AGAGGCGCAACAACTTTGAAAATAAATAAAGCTCCCCTAAAC
* * * ** *
12432716 AGAGGCTCAACGACTTTGAAAAATAAAT-GA-CTCATCTAATC
1 AGAGGCGCAACAACTTTG-AAAATAAATAAAGCTCCCCTAAAC
* * * * *
12432757 AGAGGCTCAACGACTTTTGAAAAGTAAAT--GGCTCCTCTAATC
1 AGAGGCGCAACAAC-TTTGAAAA-TAAATAAAGCTCCCCTAAAC
* * * *
12432799 AGAGGCTCAACGATTTTGAAAAAATAAATAAAGCTCCTCTAAAC
1 AGAGGCGCAACAACTTTG--AAAATAAATAAAGCTCCCCTAAAC
* *
12432843 AGAGGCTCAACGACTTTTGAAAATAAATAAAGCTCCCCTAAAC
1 AGAGGCGCAACAAC-TTTGAAAATAAATAAAGCTCCCCTAAAC
* *
12432886 TGAGGCAGCAA-AACTTTGAAAGTAAAT
1 AGAGGC-GCAACAACTTTGAAAATAAAT
12432913 GCTCCTTGAC
Statistics
Matches: 204, Mismatches: 22, Indels: 25
0.81 0.09 0.10
Matches are distributed among these distances:
40 25 0.12
41 42 0.21
42 57 0.28
43 34 0.17
44 27 0.13
45 19 0.09
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (42 bp):
AGAGGCGCAACAACTTTGAAAATAAATAAAGCTCCCCTAAAC
Found at i:12441083 original size:15 final size:15
Alignment explanation
Indices: 12441040--12441076 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
12441030 TTACTTTGTT
*
12441040 AAATGTAATGAATGA
1 AAATGCAATGAATGA
*
12441055 AGATGCAATGAATGA
1 AAATGCAATGAATGA
12441070 AAATGCA
1 AAATGCA
12441077 TGTAATGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (15 bp):
AAATGCAATGAATGA
Found at i:12444293 original size:60 final size:61
Alignment explanation
Indices: 12444209--12444347 Score: 192
Period size: 60 Copynumber: 2.3 Consensus size: 61
12444199 CAAAAAAACA
* * *
12444209 TGAAAGTTTTTA-TTCTAAAAAAAATTGATATTTTCAACTTTTCCTCAAAAATAT-TTTTTT
1 TGAAA-TTTTTATTTTTAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATATTTT
* * * *
12444269 TGAAATTTTTATTTTTAAAGAAAATTGATACTTTCAATTTTTTCTCGAAAATATATATTTT
1 TGAAATTTTTATTTTTAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATATTTT
12444330 TGAAATTTTTATTTTTAA
1 TGAAATTTTTATTTTTAA
12444348 GGAATTTTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
59 6 0.09
60 41 0.59
61 23 0.33
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.51
Consensus pattern (61 bp):
TGAAATTTTTATTTTTAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATATATTTT
Found at i:12444354 original size:78 final size:76
Alignment explanation
Indices: 12444272--12444424 Score: 211
Period size: 78 Copynumber: 2.0 Consensus size: 76
12444262 TTTTTTTTGA
* *
12444272 AATTTTTATTTTTAA-AGAAAATTGATACTTTCAATTTTTTCTCGAAAATATATATTTTTGA-AA
1 AATTTTTATTTTTAAGA-AAAAATGATACTTTCAACTTTTTCTC-AAAA-ATAT-TTTTTGATAA
* *
12444335 TTTTTATTTTTAAGG
62 ATTTTATCTTTAAGG
*
12444350 AATTTTTATTTTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATATTTTTTTATAAATTT
1 AATTTTTATTTTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATATTTTTTGATAAATTT
12444415 TATCTTTAAG
66 TATCTTTAAG
12444425 AAAAATTGAT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
75 6 0.09
76 18 0.26
77 4 0.06
78 39 0.57
79 1 0.01
ACGTcount: A:0.36, C:0.07, G:0.06, T:0.52
Consensus pattern (76 bp):
AATTTTTATTTTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATATTTTTTGATAAATTT
TATCTTTAAGG
Found at i:12444355 original size:17 final size:17
Alignment explanation
Indices: 12444333--12444365 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
12444323 ATATTTTTGA
12444333 AATTTTTATTTTTAAGG
1 AATTTTTATTTTTAAGG
12444350 AATTTTTATTTTTAAG
1 AATTTTTATTTTTAAG
12444366 AAAAAATGAT
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:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (17 bp):
AATTTTTATTTTTAAGG
Found at i:12444423 original size:59 final size:59
Alignment explanation
Indices: 12444339--12444487 Score: 210
Period size: 59 Copynumber: 2.5 Consensus size: 59
12444329 TTGAAATTTT
* *
12444339 TATTTTTAAGGAATTTTTATTTTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATA
1 TATTTTTTA-GAAATTTTA-TTTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATA
* * *
12444400 T-TTTTTTATAAATTTTATCTTTAAGAAAAATTGATATTTTCAACTTTTTCTCAAAAATA
1 TATTTTTTAGAAATTTTAT-TTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATA
*
12444459 TATTTTTTAGAATTTTTATTTTAAGAAAA
1 TATTTTTTAGAAATTTTATTTTAAGAAAA
12444488 TCATTATAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
58 1 0.01
59 56 0.71
60 21 0.27
61 1 0.01
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (59 bp):
TATTTTTTAGAAATTTTATTTTAAGAAAAAATGATACTTTCAACTTTTTCTCAAAAATA
Found at i:12444441 original size:137 final size:136
Alignment explanation
Indices: 12444215--12444480 Score: 380
Period size: 138 Copynumber: 1.9 Consensus size: 136
12444205 AACATGAAAG
*
12444215 TTTTTATTCTAAAAAAAATTGATATTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTTA
1 TTTTTATTCTAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTTA
* *
12444280 TTTTTAAAGAAAATTGATACTTTCAATTTTTTCTCGAAAATATATATTTTTGA-AATTTTTATTT
66 TCTTTAAAGAAAATTGATACTTTCAACTTTTTCTC-AAAA-ATATATTTTTGAGAATTTTTATTT
12444344 TTAAGGAA
129 TTAAGGAA
* *
12444352 TTTTTATTTTTAAGAAAAAA-TGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAT-AAA-TT
1 TTTTTA-TTCTAA-AAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT-TGAAATTT
* *
12444414 TTATCTTT-AAGAAAAATTGATATTTTCAACTTTTTCTCAAAAATATATTTTTTAGAATTTTTAT
63 TTATCTTTAAAG-AAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTGAGAATTTTTAT
12444478 TTT
127 TTT
12444481 AAGAAAATCA
Statistics
Matches: 117, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
135 11 0.09
136 19 0.16
137 39 0.33
138 41 0.35
139 7 0.06
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.52
Consensus pattern (136 bp):
TTTTTATTCTAAAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTGAAATTTTTA
TCTTTAAAGAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTGAGAATTTTTATTTTT
AAGGAA
Found at i:12445417 original size:22 final size:21
Alignment explanation
Indices: 12445380--12445454 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 21
12445370 ATAGATATAT
**
12445380 TAATAGATAACCAAAAGAA-AA
1 TAATAGATAAATAAAA-AATAA
*
12445401 TAATTAGATAAATAAAAAATAT
1 TAA-TAGATAAATAAAAAATAA
12445423 TAATAGATAAATAATAATAATAA
1 TAATAGATAAATAA-AA-AATAA
12445446 TAATA-ATAA
1 TAATAGATAA
12445455 TAATAATGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
21 16 0.35
22 21 0.46
23 9 0.20
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.27
Consensus pattern (21 bp):
TAATAGATAAATAAAAAATAA
Found at i:12445440 original size:3 final size:3
Alignment explanation
Indices: 12445418--12445473 Score: 67
Period size: 3 Copynumber: 17.7 Consensus size: 3
12445408 ATAAATAAAA
* *
12445418 AAT ATT AAT AGAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAAA
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
12445466 AAT AAT AA
1 AAT AAT AA
12445474 AATTAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
3 39 0.85
4 6 0.13
5 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:12449518 original size:17 final size:18
Alignment explanation
Indices: 12449498--12449541 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
12449488 AATTTTTTTG
12449498 TTATTATTT-TCTATTTA
1 TTATTATTTATCTATTTA
* *
12449515 TTATT-TTTATCTTTTTT
1 TTATTATTTATCTATTTA
12449532 TTATTATTTA
1 TTATTATTTA
12449542 AATGAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 4 0.17
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
TTATTATTTATCTATTTA
Found at i:12452207 original size:29 final size:31
Alignment explanation
Indices: 12452146--12452225 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
12452136 AATATGATGG
*
12452146 ATGATTTTTAAATTATAAAAAAATATTTAAT
1 ATGATATTTAAATTATAAAAAAATATTTAAT
**
12452177 ATGATATTTAAATT-TTTAAAAA-ATTTAAT
1 ATGATATTTAAATTATAAAAAAATATTTAAT
12452206 AT-ATTATTTAAAATTATAAA
1 ATGA-TATTT-AAATTATAAA
12452226 TTTATTAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
28 1 0.02
29 14 0.34
30 11 0.27
31 15 0.37
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (31 bp):
ATGATATTTAAATTATAAAAAAATATTTAAT
Found at i:12452393 original size:31 final size:29
Alignment explanation
Indices: 12452324--12452394 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
12452314 TGTTAATAAA
12452324 TTTATAATTTAGATATCACATTATAAATT
1 TTTATAATTTAGATATCACATTATAAATT
* *
12452353 TTTAAAATTTATATATCACATTA-AATATTTT
1 TTTATAATTTAGATATCACATTATAA-A--TT
12452384 TTTATAATTTA
1 TTTATAATTTA
12452395 AAAATTATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 2 0.06
29 22 0.61
31 12 0.33
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.52
Consensus pattern (29 bp):
TTTATAATTTAGATATCACATTATAAATT
Found at i:12454567 original size:2 final size:2
Alignment explanation
Indices: 12454560--12454589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12454550 GTCAGTTTTA
12454560 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
12454590 GTAGCCATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12457268 original size:2 final size:2
Alignment explanation
Indices: 12457261--12457290 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12457251 TTGCGACATG
12457261 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
12457291 GTCATAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12462486 original size:17 final size:16
Alignment explanation
Indices: 12462466--12462533 Score: 88
Period size: 17 Copynumber: 4.2 Consensus size: 16
12462456 TATCTATTAA
12462466 TATTTTTATTATTTATC
1 TATTTTT-TTATTTATC
12462483 TA--TTTTTATTTATC
1 TATTTTTTTATTTATC
12462497 TATTTCTTTTATTTATC
1 TATTT-TTTTATTTATC
12462514 TATTTTTTT-TGTTATC
1 TATTTTTTTAT-TTATC
12462530 TATT
1 TATT
12462534 AATATATTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
14 11 0.23
15 4 0.09
16 14 0.30
17 18 0.38
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.72
Consensus pattern (16 bp):
TATTTTTTTATTTATC
Found at i:12462493 original size:14 final size:14
Alignment explanation
Indices: 12462474--12462520 Score: 67
Period size: 14 Copynumber: 3.1 Consensus size: 14
12462464 AATATTTTTA
12462474 TTATTTATCTATTT
1 TTATTTATCTATTT
12462488 TTATTTATCTATTTCTT
1 TTATTTATCTA--T-TT
12462505 TTATTTATCTATTT
1 TTATTTATCTATTT
12462519 TT
1 TT
12462521 TTTGTTATCT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.50
15 1 0.03
16 1 0.03
17 13 0.43
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTTATCTATTT
Found at i:12462501 original size:31 final size:31
Alignment explanation
Indices: 12462466--12462554 Score: 96
Period size: 32 Copynumber: 2.9 Consensus size: 31
12462456 TATCTATTAA
12462466 TATTTTTATTATTTATCTATTTTTATTTATC
1 TATTTTTATTATTTATCTATTTTTATTTATC
*
12462497 TATTTCTT-TTATTTATCTATTTTTTTTGTTATC
1 TATTT-TTATTATTTATCTA-TTTTTAT-TTATC
**
12462530 TATTAATA-TATTTATC--TTTTTATTT
1 TATTTTTATTATTTATCTATTTTTATTT
12462555 TGATTAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
28 2 0.04
29 6 0.12
31 16 0.32
32 17 0.34
33 9 0.18
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (31 bp):
TATTTTTATTATTTATCTATTTTTATTTATC
Found at i:12463093 original size:14 final size:15
Alignment explanation
Indices: 12463074--12463102 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12463064 GAGCTTTTAG
12463074 AAAGAAAGG-AGAGA
1 AAAGAAAGGAAGAGA
12463088 AAAGAAAGGAAGAGA
1 AAAGAAAGGAAGAGA
12463103 GAGAGAGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (15 bp):
AAAGAAAGGAAGAGA
Found at i:12463381 original size:8 final size:8
Alignment explanation
Indices: 12463370--12463402 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
12463360 TTTTTATTTT
*
12463370 TTTATGTA
1 TTTATATA
12463378 TTTATATA
1 TTTATATA
12463386 TTTATATA
1 TTTATATA
12463394 TTTAT-TA
1 TTTATATA
12463401 TT
1 TT
12463403 ATTATAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
7 4 0.17
8 20 0.83
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (8 bp):
TTTATATA
Found at i:12463387 original size:20 final size:20
Alignment explanation
Indices: 12463346--12463388 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12463336 TTCCCAGGTC
* *
12463346 TTTTTTTATTTTATTTTTTA
1 TTTTTTTATTGTATTTTATA
12463366 TTTTTTTA-TGTATTTATATA
1 TTTTTTTATTGTATTT-TATA
12463386 TTT
1 TTT
12463389 ATATATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (20 bp):
TTTTTTTATTGTATTTTATA
Found at i:12463511 original size:13 final size:13
Alignment explanation
Indices: 12463462--12463512 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
12463452 GTTTGTTTAA
*
12463462 TATTTTATATTTT
1 TATTTTATTTTTT
12463475 TATTTTCATTTTTCCT
1 TATTTT-ATTTTT--T
12463491 T-TTTTATTTTTT
1 TATTTTATTTTTT
12463503 TATTTTATTT
1 TATTTTATTT
12463513 AAATAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
12 2 0.06
13 14 0.42
14 11 0.33
15 4 0.12
16 2 0.06
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (13 bp):
TATTTTATTTTTT
Found at i:12463593 original size:58 final size:58
Alignment explanation
Indices: 12463521--12463985 Score: 386
Period size: 58 Copynumber: 7.7 Consensus size: 58
12463511 TTAAATAAAA
* *
12463521 TTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATCTTCTTTGAAAAT-AAGCT
1 TTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT-TTCTTTAAAAATAAAGTT
* ** *
12463579 TTCCAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TT
1 TTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCTTTAAAAATAAAGTT
* * *
12463637 TTCAAAAAAAAAAATTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
1 TTC----AAAAAAA--TATTTTTGAGGAAAAGTTGAAAGTATCAATTTCT-TTAAAAATAAAGTT
* * * * * ** *
12463702 TTTAAAAAAGATTTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTT
1 TTCAAAAAA-A----TATTTTTGAGGAAAAGTTGAAAGTATCAA-TTTCTTTAAAAATAAAGTT
* ** *
12463766 TCCAAAAAAA-ATGCTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TT
1 TTCAAAAAAATAT--TTTTGAGGAAAAGTTGAAAGTATCAATTTCT-TTAAAAATAAAGTT
* * * * * * *
12463825 TTCAAAAAAGGTCTTTTTGGAGGAAAAGTTAAAAGTATAAATTTTTTTCGAAATTAAAGTT
1 TTCAAAAAA-ATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTCTTT-AAAAATAAAGTT
*
12463886 TTCAAAAAAATATTTTTG-GGAAAAAGTTGAAAGTATCAATTT-TTCTCAAAATTAAAGTT
1 TTCAAAAAAATATTTTTGAGG-AAAAGTTGAAAGTATCAATTTCTT-T-AAAAATAAAGTT
* *
12463945 TT-TAAAAAATAATTTTGAGGAAAAGTTGAAAGTATCAATTT
1 TTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTT
12463986 TTTCTGTATA
Statistics
Matches: 335, Mismatches: 47, Indels: 50
0.78 0.11 0.12
Matches are distributed among these distances:
58 89 0.27
59 59 0.18
60 68 0.20
61 18 0.05
62 7 0.02
63 4 0.01
64 83 0.25
65 7 0.02
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (58 bp):
TTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTCTTTAAAAATAAAGTT
Found at i:12463833 original size:60 final size:58
Alignment explanation
Indices: 12463513--12463987 Score: 429
Period size: 64 Copynumber: 7.9 Consensus size: 58
12463503 TATTTTATTT
* * * *
12463513 AAATAAA-ATTCAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAA-TCTTCTTTGA
1 AAATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTC-TTAA
** * * *
12463570 AAATAAGCTTTCCAAAAAATATTTTTGAAAAAAAGTTGAAAGTATCAATTTTCCTTAA
1 AAATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
* *
12463628 AAATAAATTTTCAAAAAAAAAAATTTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAATAAATTTTC----AAAAAAA--TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
* * * * **
12463692 AAATAAATTTTTTAAAAAAGATTTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTCCTCGA
1 AAATAAA-TTTTCAAAAAA-A----TATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
* * *
12463756 AATTAAAGTTTCCAAAAAAA-ATGCTTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTAA
1 AAATAAA-TTTTCAAAAAAATAT--TTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
* * * * * *
12463816 AAATAAATTTTCAAAAAAGGTCTTTTTGGAGGAAAAGTTAAAAGTATAAATTTTT-TTCGA
1 AAATAAATTTTCAAAAAA-ATATTTTT-GAGAAAAAGTTGAAAGTATCAATTTTTCTT-AA
* * *
12463876 AATTAAAGTTTTCAAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTTCTCAA
1 AAATAAA-TTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
* * * *
12463935 AATTAAAGTTTT-TAAAAAATAATTTTGAGGAAAAGTTGAAAGTATCAATTTTT
1 AAATAAA-TTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTT
12463988 TCTGTATAAA
Statistics
Matches: 345, Mismatches: 53, Indels: 39
0.79 0.12 0.09
Matches are distributed among these distances:
57 6 0.02
58 87 0.25
59 55 0.16
60 74 0.21
61 18 0.05
62 7 0.02
63 1 0.00
64 93 0.27
65 4 0.01
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.37
Consensus pattern (58 bp):
AAATAAATTTTCAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTAA
Found at i:12464010 original size:24 final size:24
Alignment explanation
Indices: 12463978--12464038 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
12463968 AGTTGAAAGT
*
12463978 ATCAATTTTTTCTGTATAAAAACA
1 ATCATTTTTTTCTGTATAAAAACA
12464002 ATCATTTTTTTCTGTATAAAAACA
1 ATCATTTTTTTCTGTATAAAAACA
12464026 ATCATTTTTTTCT
1 ATCATTTTTTTCT
12464039 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.34, C:0.13, G:0.03, T:0.49
Consensus pattern (24 bp):
ATCATTTTTTTCTGTATAAAAACA
Found at i:12468633 original size:42 final size:42
Alignment explanation
Indices: 12468587--12468891 Score: 262
Period size: 42 Copynumber: 7.2 Consensus size: 42
12468577 GTGTCTCTAT
12468587 TTAGAGGAGCAATTTACTTTTCAAAAGTCATTGAGCCTCTGA
1 TTAGAGGAGCAATTTACTTTTCAAAAGTCATTGAGCCTCTGA
* * * * * *
12468629 TTAGAAGAGTC-ATTTACTTTCCAAAAGTCATTAAACCTTTAA
1 TTAGAGGAG-CAATTTACTTTTCAAAAGTCATTGAGCCTCTGA
* * **
12468671 TTAGAGGAGCTTTAGTTA-TTTTC-AAAGTTGTTGAGCCTCTGA
1 TTAGAGGAGC--AATTTACTTTTCAAAAGTCATTGAGCCTCTGA
* * ** *
12468713 TTAGAGAAGCCATTTACTTTTC-AAAGTTGTTGAGCCTCTTA
1 TTAGAGGAGCAATTTACTTTTCAAAAGTCATTGAGCCTCTGA
* * * * *
12468754 TTAGAGAAGCCATTTATTTTTCTAAAGTCATCGAGCCTCTGA
1 TTAGAGGAGCAATTTACTTTTCAAAAGTCATTGAGCCTCTGA
*
12468796 TTAGAGGAG-ACATTTATTTTTTCAAAA-TCATTGAGCCTCTGA
1 TTAGAGGAGCA-ATTTA-CTTTTCAAAAGTCATTGAGCCTCTGA
** * * *
12468838 TTAGAGGAGCCTTGTTTATTTTTCAAAAGTCGTTGAGCATCTGA
1 TTAGAGGAG-C-AATTTACTTTTCAAAAGTCATTGAGCCTCTGA
*
12468882 TTAGATGAGC
1 TTAGAGGAGC
12468892 TTTCTTTATG
Statistics
Matches: 218, Mismatches: 33, Indels: 23
0.80 0.12 0.08
Matches are distributed among these distances:
40 4 0.02
41 45 0.21
42 115 0.53
43 25 0.11
44 29 0.13
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.37
Consensus pattern (42 bp):
TTAGAGGAGCAATTTACTTTTCAAAAGTCATTGAGCCTCTGA
Found at i:12468843 original size:167 final size:169
Alignment explanation
Indices: 12468553--12468886 Score: 419
Period size: 167 Copynumber: 2.0 Consensus size: 169
12468543 ATTGTCAATG
* * *
12468553 AGCCATTTATTTTCCAAAGTTGTGGTGTCTCTATTTAGAGGAGCAATTTACTTTTCAAAAGTCAT
1 AGCCATTTATTTTCCAAAGTTGTGGAGCCTCTATTTAGAGAAGCAATTTACTTTTCAAAAGTCAT
* * * *
12468618 TGAGCCTCTGATTAGAAGAGTCATTTACTTTCCAAAAGTCATTAAACCTTTAATTAGAGGAGCTT
66 CGAGCCTCTGATTAGAAGAGACATTTACTTTCCAAAAGTCATTAAACCTCTAATTAGAGGAGCCT
* *
12468683 TAG-TTA-TTTTC-AAAGTTGTTGAGCCTCTGATTAGAGA
131 T-GTTTATTTTTCAAAAGTCGTTGAGCATCTGATTAGAGA
* * * *
12468720 AGCCATTTACTTTT-CAAAGTTGTTGAGCCTCT-TATTAGAGAAGCCATTTATTTTTCTAAAGTC
1 AGCCATTTA-TTTTCCAAAGTTGTGGAGCCTCTAT-TTAGAGAAGCAATTTACTTTTCAAAAGTC
* * * * * *
12468783 ATCGAGCCTCTGATTAGAGGAGACATTTATTTTTTCAAAA-TCATTGAGCCTCTGATTAGAGGAG
64 ATCGAGCCTCTGATTAGAAGAGACATTTA-CTTTCCAAAAGTCATTAAACCTCTAATTAGAGGAG
12468847 CCTTGTTTATTTTTCAAAAGTCGTTGAGCATCTGATTAGA
128 CCTTGTTTATTTTTCAAAAGTCGTTGAGCATCTGATTAGA
12468887 TGAGCTTTCT
Statistics
Matches: 142, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
166 2 0.01
167 101 0.71
168 17 0.12
169 22 0.15
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (169 bp):
AGCCATTTATTTTCCAAAGTTGTGGAGCCTCTATTTAGAGAAGCAATTTACTTTTCAAAAGTCAT
CGAGCCTCTGATTAGAAGAGACATTTACTTTCCAAAAGTCATTAAACCTCTAATTAGAGGAGCCT
TGTTTATTTTTCAAAAGTCGTTGAGCATCTGATTAGAGA
Found at i:12468931 original size:45 final size:44
Alignment explanation
Indices: 12468599--12468939 Score: 178
Period size: 42 Copynumber: 8.0 Consensus size: 44
12468589 AGAGGAGCAA
* * *
12468599 TTTACTTTTCAAAAGTCATTGAGCCTCTGATTAGAAGAG---TC
1 TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAGAGCTTTC
* * * * * * * *
12468640 ATTTACTTTCCAAAAGTCATTAAACCTTTAATTAGAGGAGCTTTA
1 -TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAGAGCTTTC
* * *
12468685 GTTA-TTTTC-AAAGTTGTTGAGCCTCTGATTAG-AGAAGC---C
1 TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAG-AGCTTTC
* * * *
12468724 ATTTACTTTTC-AAAGTTGTTGAGCCTCTTATTAG-AGAAGC---C
1 -TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAG-AGCTTTC
* * ** * *
12468765 ATTTATTTTTCTAAAGTCATCGAGCCTCTGATTAGAGGAGACATT-
1 -TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAGAG-CTTTC
* * * * * *
12468810 TAT-TTTTTCAAAA-TCATTGAGCCTCTGATTAGAGGAGCCTTG
1 TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAGAGCTTTC
* * *
12468852 TTTATTTTTCAAAAGTCGTTGAGCATCTGATTAGATGAGCTTTC
1 TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAGAGCTTTC
*
12468896 TTTATGTTTCTC-AAAGTCGTTAAGCCTCTGTTTAGAAGAGCTTT
1 TTTAT-TTT-TCAAAAGTCGTTAAGCCTCTGATTAGAAGAGCTTT
12468940 GATCAAAATT
Statistics
Matches: 243, Mismatches: 39, Indels: 31
0.78 0.12 0.10
Matches are distributed among these distances:
40 3 0.01
41 48 0.20
42 99 0.41
43 25 0.10
44 34 0.14
45 32 0.13
46 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (44 bp):
TTTATTTTTCAAAAGTCGTTAAGCCTCTGATTAGAAGAGCTTTC
Found at i:12469251 original size:23 final size:24
Alignment explanation
Indices: 12469225--12469269 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
12469215 TATTTTTATT
12469225 TATTTTTATTTTTTATCTA-TTAA
1 TATTTTTATTTTTTATCTACTTAA
*
12469248 TATTTTTATTATTTATCTACTT
1 TATTTTTATTTTTTATCTACTT
12469270 TTATTTATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (24 bp):
TATTTTTATTTTTTATCTACTTAA
Found at i:12469256 original size:33 final size:33
Alignment explanation
Indices: 12469191--12469326 Score: 100
Period size: 32 Copynumber: 4.0 Consensus size: 33
12469181 AGCTTTTATT
* *
12469191 TTTATTTTTATTATTTA-ATA-TATATATTTTTA
1 TTTATTTTTATTTTTTATCTATTA-ATATTTTTA
12469223 TTTATTTTTATTTTTTATCTATTAATATTTTTA
1 TTTATTTTTATTTTTTATCTATTAATATTTTTA
** *
12469256 -TTATTTATCTACTTTTATTTATCTATTTCTTTTATTTA
1 TTTATTT-T-TA--TTT-TTTATCTATTAATATT-TTTA
* * * *
12469294 TCTATTTTT-TTTGTTCTCTATTAATATATTTA
1 TTTATTTTTATTTTTTATCTATTAATATTTTTA
12469326 T
1 T
12469327 CTTTTTATTT
Statistics
Matches: 83, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
32 27 0.33
33 22 0.27
34 7 0.08
36 3 0.04
37 14 0.17
38 5 0.06
39 5 0.06
ACGTcount: A:0.24, C:0.06, G:0.01, T:0.69
Consensus pattern (33 bp):
TTTATTTTTATTTTTTATCTATTAATATTTTTA
Found at i:12469274 original size:23 final size:22
Alignment explanation
Indices: 12469223--12469275 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 22
12469213 TATATTTTTA
*
12469223 TTTATTTTTATTTTTTATCTAT
1 TTTATTTTTATTATTTATCTAT
*
12469245 TAATATTTTTATTATTTATCTACT
1 T-TTATTTTTATTATTTATCTA-T
12469269 TTTATTT
1 TTTATTT
12469276 ATCTATTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 1 0.04
23 23 0.88
24 2 0.08
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATTTTTATTATTTATCTAT
Found at i:12469305 original size:17 final size:16
Alignment explanation
Indices: 12469184--12469305 Score: 77
Period size: 17 Copynumber: 7.2 Consensus size: 16
12469174 CTCAATGAGC
12469184 TTTTATTT-TTATTTT
1 TTTTATTTATTATTTT
* *
12469199 TATTATTTAATATATATAT
1 TTTTATTT-AT-TAT-TTT
*
12469218 TTTTATTTATTTTTATT
1 TTTTATTTATTATT-TT
* * *
12469235 TTTTATCTATTAATAT
1 TTTTATTTATTATTTT
**
12469251 TTTTA-TTATTTATCTAC
1 TTTTATTTA-TTAT-TTT
*
12469268 TTTTATTTATCTATTTC
1 TTTTATTTAT-TATTTT
12469285 TTTTATTTATCTATTTT
1 TTTTATTTAT-TATTTT
12469302 TTTT
1 TTTT
12469306 GTTCTCTATT
Statistics
Matches: 84, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
15 9 0.11
16 10 0.12
17 45 0.54
18 11 0.13
19 9 0.11
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTATTATTTT
Found at i:12470056 original size:14 final size:15
Alignment explanation
Indices: 12470020--12470056 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
12470010 TTTTTTTTTT
12470020 TTATATATTTATATA
1 TTATATATTTATATA
*
12470035 -TATATATTTATTTA
1 TTATATATTTATATA
12470049 TTAT-TATT
1 TTATATATT
12470057 ATTATCGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTATATATTTATATA
Found at i:12470126 original size:16 final size:17
Alignment explanation
Indices: 12470107--12470142 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
12470097 TCTATTTTCA
12470107 TTTATTTTC-CTTTATT
1 TTTATTTTCACTTTATT
*
12470123 TTTATTTTCATTTTATT
1 TTTATTTTCACTTTATT
12470140 TTT
1 TTT
12470143 TTATTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTATTTTCACTTTATT
Found at i:12470128 original size:26 final size:27
Alignment explanation
Indices: 12470091--12470141 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
12470081 ATTTTATATT
12470091 TTTATTTCTATTTTCA-TTTATTTTCC
1 TTTATTTCTATTTTCATTTTATTTTCC
*
12470117 TTTATTTTTATTTTCATTTTATTTT
1 TTTATTTCTATTTTCATTTTATTTT
12470142 TTTATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.16, C:0.10, G:0.00, T:0.75
Consensus pattern (27 bp):
TTTATTTCTATTTTCATTTTATTTTCC
Found at i:12470142 original size:6 final size:6
Alignment explanation
Indices: 12470080--12470152 Score: 53
Period size: 6 Copynumber: 12.0 Consensus size: 6
12470070 GTTTGTTTAA
* *
12470080 TATTTT ATATTTT TATTTC TATTTT CATTTAT T-TTCCTT TATTTT TATTTT
1 TATTTT -TATTTT TATTTT TATTTT TATTT-T TATT--TT TATTTT TATTTT
* *
12470131 CA-TTT TATTTT T-TTAT TATTTT
1 TATTTT TATTTT TATTTT TATTTT
12470153 ACTTTCTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
5 8 0.15
6 32 0.62
7 9 0.17
8 3 0.06
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (6 bp):
TATTTT
Found at i:12470150 original size:38 final size:39
Alignment explanation
Indices: 12470080--12470157 Score: 97
Period size: 38 Copynumber: 2.0 Consensus size: 39
12470070 GTTTGTTTAA
* *
12470080 TATTTTATATTTTTATTTCTATTTTCATTTATTTTCCTT
1 TATTTTATATTTTCATTTCTATTTTCATTTATTTTACTT
**
12470119 TATTTT-TATTTTCATTT-TATTTTTTTATTATTTTACTT
1 TATTTTATATTTTCATTTCTATTTTCAT-TTATTTTACTT
12470157 T
1 T
12470158 CTTTAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 7 0.21
38 21 0.62
39 6 0.18
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (39 bp):
TATTTTATATTTTCATTTCTATTTTCATTTATTTTACTT
Found at i:12470419 original size:60 final size:61
Alignment explanation
Indices: 12470170--12470695 Score: 442
Period size: 60 Copynumber: 8.8 Consensus size: 61
12470160 TTAAATAAAA
* * * **
12470170 TTCAAAAAA-A-TATTTTTGAGAAAAAGTTAAAAGTATCAA-TTTTCTTTGAAAAT-AAGCTT
1 TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TCAAAAATAAAG-TT
* * * * *
12470229 TTCAAAAAATA-TTTTTGT-A-GAAAAATTGAAAGTATCAA-TTTTCTTTAAAAATAAATTT
1 TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC-TCAAAAATAAAGTT
* * * * * *
12470287 TTAAAAAAATATTTTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTT
1 TTCAAAAAAGA----TTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTT
* * * *
12470352 TTTAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAATATCAA-TTTTCTCGAAATTAAAGTT
1 TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTT
* * * * *
12470412 TCCAAAAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TT
1 TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTT
* * * * * *
12470471 TTCAAAAAAGGTCTTTTTTGAAGAAAAATTGAAAGTATC-ATTTTTCCTTAAAAA-AAAATT
1 TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTT-CTCAAAAATAAAGTT
* * * *
12470531 TTCAAAAAAAATTTTTTTTTGA-GAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTT
1 TTCAAAAAAGA-TTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTT
* * * *
12470592 TTC-AAAAAGGTTTTTTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAG-T
1 TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTT
* ** *
12470651 TTCTAAAAA-A-TAATTTTG-GAAAAATGTTGAAAGTATCAATTTTTC
1 TTCAAAAAAGATTTTTTTTGAGGAAAA-GTTGAAAGTATCAATTTTTC
12470696 CTGTACAAAA
Statistics
Matches: 395, Mismatches: 52, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
57 6 0.02
58 67 0.17
59 71 0.18
60 149 0.38
61 50 0.13
63 6 0.02
64 1 0.00
65 40 0.10
66 5 0.01
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (61 bp):
TTCAAAAAAGATTTTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTCAAAAATAAAGTT
Found at i:12470464 original size:120 final size:119
Alignment explanation
Indices: 12470173--12470695 Score: 539
Period size: 120 Copynumber: 4.4 Consensus size: 119
12470163 AATAAAATTC
* * *
12470173 AAAAAAATATTTTT-GAGAAAAAGTTAAAAGTATCAA-TTTTCTTTGAAAATAAGCTTTTCAAAA
1 AAAAAAATATTTTTGGAG-AAAAGTTGAAAGTATCAATTTTTC-TTAAAAATAA-ATTTTCAAAA
* * ** *
12470236 AATA-TTTTTGT-A-GAAAAATTGAAAGTATCAATTTTCTTTAAAAATAAA-TTTTTA
63 AAGATTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTC-TCGAAAATAAAGTTTTCA
* ** *
12470290 AAAAAATATTTTTTTTTTTTTAGAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTTT
1 AAAAAA-A----TATTTTTGGAG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTC
* * * *
12470355 AAAAAAGATTTTTTTTGAGGAAAAGTTGAAAATATCAATTTTCTCGAAATTAAAGTTTCCA
59 AAAAAAGATTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCTCGAAAATAAAGTTTTCA
12470416 AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAG
1 AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAG
* * * * * * *
12470481 GTCTTTTTTGAAGAAAAATTGAAAGTATCATTTTTC-CTTAAAAAAAAATTTTCA
66 ATTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCTC-GAAAATAAAGTTTTCA
* * *
12470535 AAAAAAATTTTTTTTTGAGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAATTTTTC-AAAA
1 AAAAAAA-TATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAA-TTTTCAAAAA
* *
12470599 AGGTTTTTTTTGA-GAAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAG-TTTC-
64 AGATTTTTTTTGAGGAAAAA-TTGAAAGTATCAA-TTTTCTCGAAAATAAAGTTTTCA
* *
12470654 TAAAAAATAATTTTGGA-AAAATGTTGAAAGTATCAATTTTTC
1 AAAAAAATATTTTTGGAGAAAA-GTTGAAAGTATCAATTTTTC
12470696 CTGTACAAAA
Statistics
Matches: 343, Mismatches: 44, Indels: 37
0.81 0.10 0.09
Matches are distributed among these distances:
117 10 0.03
118 28 0.08
119 71 0.21
120 110 0.32
121 24 0.07
122 7 0.02
123 40 0.12
124 11 0.03
125 10 0.03
126 32 0.09
ACGTcount: A:0.44, C:0.06, G:0.10, T:0.40
Consensus pattern (119 bp):
AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAATTTTCAAAAAAG
ATTTTTTTTGAGGAAAAATTGAAAGTATCAATTTTCTCGAAAATAAAGTTTTCA
Found at i:12470539 original size:14 final size:13
Alignment explanation
Indices: 12470521--12470545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12470511 TTTTTCCTTA
12470521 AAAAAAAATTTTC
1 AAAAAAAATTTTC
12470534 AAAAAAAATTTT
1 AAAAAAAATTTT
12470546 TTTTTGAGAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAAAAAATTTTC
Found at i:12471731 original size:22 final size:22
Alignment explanation
Indices: 12471706--12471754 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
12471696 GAAAATTATA
12471706 TGTCTTCCTTTTGAATCATATT
1 TGTCTTCCTTTTGAATCATATT
*
12471728 TGTCTTCTTTTTGAATCATATT
1 TGTCTTCCTTTTGAATCATATT
12471750 TGTCT
1 TGTCT
12471755 ATAGCAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.57
Consensus pattern (22 bp):
TGTCTTCCTTTTGAATCATATT
Found at i:12472777 original size:5 final size:5
Alignment explanation
Indices: 12472769--12472825 Score: 69
Period size: 5 Copynumber: 10.8 Consensus size: 5
12472759 TTTATTATGT
* *
12472769 TATAA TATAA TATAA TATGA TATGA TATAA TATAA TATATA TATATA TATATA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATA-A TATA-A TATA-A
12472822 TATA
1 TATA
12472826 TGATTTGAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 32 0.65
6 17 0.35
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (5 bp):
TATAA
Found at i:12472810 original size:2 final size:2
Alignment explanation
Indices: 12472769--12472826 Score: 63
Period size: 2 Copynumber: 30.5 Consensus size: 2
12472759 TTTATTATGT
12472769 TA TA -A TA TA -A TA TA -A TA TGA TA TGA TA TA -A TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA TA TA
12472808 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
12472827 GATTTGAACA
Statistics
Matches: 49, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
1 5 0.10
2 40 0.82
3 4 0.08
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:12473022 original size:2 final size:2
Alignment explanation
Indices: 12473015--12473040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12473005 AGCTGTTACC
12473015 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
12473041 AACTTTTCGA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12477250 original size:2 final size:2
Alignment explanation
Indices: 12477245--12477280 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
12477235 ATCACAGTAC
*
12477245 AT AT AT AT TT 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
12477281 CACAGTGGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:12480489 original size:26 final size:27
Alignment explanation
Indices: 12480448--12480513 Score: 91
Period size: 26 Copynumber: 2.5 Consensus size: 27
12480438 AAATTTATTT
*
12480448 ATAA-AAATTAAATGAATATATTTTCTA
1 ATAATAAA-TAAATGAATATATTTTATA
*
12480475 AT-ATATATAAATGAATATATTTTATA
1 ATAATAAATAAATGAATATATTTTATA
12480501 ATAATAAATAAAT
1 ATAATAAATAAAT
12480514 CATAATCAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
26 21 0.62
27 13 0.38
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (27 bp):
ATAATAAATAAATGAATATATTTTATA
Found at i:12480633 original size:3 final size:3
Alignment explanation
Indices: 12480607--12480649 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
12480597 GATAAAAATA
* *
12480607 TAT TTT TAT TTT TAT T-T T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12480650 AAAACAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TAT
Found at i:12480783 original size:13 final size:13
Alignment explanation
Indices: 12480729--12480781 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
12480719 TATTTGTATT
12480729 TTATTCATTTAATAA
1 TTATT-ATTTAA-AA
*
12480744 ATA-TATTTAAAA
1 TTATTATTTAAAA
12480756 TTATTATTTAAAA
1 TTATTATTTAAAA
12480769 TTATTTATTTAAA
1 TTA-TTATTTAAA
12480782 TTTAATAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 4 0.12
13 18 0.53
14 10 0.29
15 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATTATTTAAAA
Found at i:12484075 original size:12 final size:12
Alignment explanation
Indices: 12484044--12484076 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
12484034 AAACCAAATT
*
12484044 TGCTGATCTGGG
1 TGCTGATTTGGG
12484056 TGCTGATTTGGG
1 TGCTGATTTGGG
12484068 TGCTGATTT
1 TGCTGATTT
12484077 CTTTGACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.12, G:0.36, T:0.42
Consensus pattern (12 bp):
TGCTGATTTGGG
Found at i:12491913 original size:3 final size:3
Alignment explanation
Indices: 12491905--12491929 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
12491895 AAGTACACGG
12491905 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
12491930 TGAGTCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:12493672 original size:2 final size:2
Alignment explanation
Indices: 12493665--12493692 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12493655 CACACGAGTG
12493665 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
12493693 TAAAGCAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:12494099 original size:15 final size:14
Alignment explanation
Indices: 12494074--12494125 Score: 68
Period size: 15 Copynumber: 3.6 Consensus size: 14
12494064 TGAGGAATCT
*
12494074 TTTCCTCTCTTTTCC
1 TTTCCTTTC-TTTCC
*
12494089 TTTCTTTTCTTTCC
1 TTTCCTTTCTTTCC
12494103 TTTCCTTTCCTTTCC
1 TTTCCTTT-CTTTCC
12494118 TTTCCTTT
1 TTTCCTTT
12494126 GGACTTTGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
14 12 0.36
15 21 0.64
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTCCTTTCTTTCC
Found at i:12494105 original size:10 final size:10
Alignment explanation
Indices: 12494074--12494125 Score: 70
Period size: 10 Copynumber: 5.3 Consensus size: 10
12494064 TGAGGAATCT
* *
12494074 TTTCCTCTCT
1 TTTCCTTTCC
12494084 TTTCCTTT-C
1 TTTCCTTTCC
*
12494093 TTTTCTTTCC
1 TTTCCTTTCC
12494103 TTTCCTTTCC
1 TTTCCTTTCC
12494113 TTTCCTTTCC
1 TTTCCTTTCC
12494123 TTT
1 TTT
12494126 GGACTTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
9 7 0.19
10 30 0.81
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (10 bp):
TTTCCTTTCC
Found at i:12494590 original size:16 final size:16
Alignment explanation
Indices: 12494559--12494609 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
12494549 ACAATTTTAA
12494559 AAAACAAATATATTTATC
1 AAAA-AAAT-TATTTATC
12494577 AAAAAAATTATTTAT-
1 AAAAAAATTATTTATC
12494592 AAATAAAATTATTTATC
1 AAA-AAAATTATTTATC
12494609 A
1 A
12494610 TTACTTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 3 0.10
16 19 0.61
17 5 0.16
18 4 0.13
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAAAATTATTTATC
Found at i:12495000 original size:27 final size:27
Alignment explanation
Indices: 12494970--12495023 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
12494960 TTTTGAAAAA
*
12494970 TAATCTATTTA-ATAAATTATTTAAATT
1 TAATATATTTAGAT-AATTATTTAAATT
*
12494997 TAATATTTTTAGATAATTATTTAAATT
1 TAATATATTTAGATAATTATTTAAATT
12495024 CAAATCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TAATATATTTAGATAATTATTTAAATT
Found at i:12495979 original size:19 final size:20
Alignment explanation
Indices: 12495952--12495991 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
12495942 GCAAATAAAT
* *
12495952 TGAAGAAAATATTTTT-TAA
1 TGAAAAAAAGATTTTTATAA
12495971 TGAAAAAAAGATTTTTATAA
1 TGAAAAAAAGATTTTTATAA
12495991 T
1 T
12495992 TCTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (20 bp):
TGAAAAAAAGATTTTTATAA
Found at i:12497220 original size:18 final size:17
Alignment explanation
Indices: 12497197--12497309 Score: 71
Period size: 18 Copynumber: 6.8 Consensus size: 17
12497187 TATATTAATA
12497197 AATAAATAATATTGTATT
1 AATAAATAATATT-TATT
* *
12497215 AATAAATCATATATTAATC
1 AATAAAT-A-ATATTTATT
* *
12497234 AATAATATTATAATATATT
1 AATAA-ATAAT-ATTTATT
*
12497253 AATAAATAATATACTATT
1 AATAAATAATAT-TTATT
12497271 AAT--ATAATA--TATT
1 AATAAATAATATTTATT
12497284 AAT--A-AATA-TTATT
1 AATAAATAATATTTATT
12497297 AATAAATAATATT
1 AATAAATAATATT
12497310 ATAATACATT
Statistics
Matches: 77, Mismatches: 8, Indels: 21
0.73 0.08 0.20
Matches are distributed among these distances:
12 4 0.05
13 15 0.19
15 1 0.01
16 10 0.13
17 3 0.04
18 20 0.26
19 17 0.22
20 7 0.09
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (17 bp):
AATAAATAATATTTATT
Found at i:12497250 original size:23 final size:24
Alignment explanation
Indices: 12497223--12497300 Score: 86
Period size: 23 Copynumber: 3.1 Consensus size: 24
12497213 TTAATAAATC
*
12497223 ATATATTAATCAATAATATTA-TA
1 ATATATTAATAAATAATATTATTA
12497246 ATATATTAATAAATAATATACTATTA
1 ATATATTAATAAATAATAT--TATTA
* *
12497272 ATATAATATATTAATAAATATTATTA
1 ATATATTA-ATAAAT-AATATTATTA
12497298 ATA
1 ATA
12497301 AATAATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
23 18 0.38
25 2 0.04
26 17 0.36
27 5 0.11
28 5 0.11
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
ATATATTAATAAATAATATTATTA
Found at i:12497271 original size:41 final size:40
Alignment explanation
Indices: 12497181--12497332 Score: 129
Period size: 38 Copynumber: 3.8 Consensus size: 40
12497171 TATAATTTAG
* * *
12497181 TAATATTATATTAATAAATAA-ATAATATTGTATTAATAAA
1 TAATA-TATATTAATAAATAATATTATAATATATTAATAAA
* *
12497221 T--CATATATTAATCAATAATATTATAATATATTAATAAA
1 TAATATATATTAATAAATAATATTATAATATATTAATAAA
12497259 TAATATACTATTAATATAAT-ATATTAATAAATATTATTAATAAA
1 TAATATA-TATTAATA-AATAATATT-AT-AATA-TATTAATAAA
* *
12497303 TAATAT-TA-TAATACATTAATA-AATAATATA
1 TAATATATATTAATA-AATAATATTATAATATA
12497333 AAAATAATAA
Statistics
Matches: 93, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
37 14 0.15
38 20 0.22
39 4 0.04
40 6 0.06
41 19 0.20
42 10 0.11
43 4 0.04
44 16 0.17
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (40 bp):
TAATATATATTAATAAATAATATTATAATATATTAATAAA
Found at i:12497341 original size:67 final size:68
Alignment explanation
Indices: 12497211--12497345 Score: 202
Period size: 67 Copynumber: 2.0 Consensus size: 68
12497201 AATAATATTG
* * ** *
12497211 TATTAATAAATCATATATTAATCAATAATATTATAATATATTAATAAATAATATACTATTAATAT
1 TATTAATAAATCATATATTAATAAATAATATTATAATACATTAATAAATAATATAAAAATAATA-
12497276 AATA
65 AATA
12497280 TATTAATAAAT-AT-TATTAATAAATAATATTATAATACATTAATAAATAATATAAAAATAATAA
1 TATTAATAAATCATATATTAATAAATAATATTATAATACATTAATAAATAATATAAAAATAATAA
12497343 ATA
66 ATA
12497346 GTTTTATTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
66 4 0.07
67 44 0.72
68 2 0.03
69 11 0.18
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (68 bp):
TATTAATAAATCATATATTAATAAATAATATTATAATACATTAATAAATAATATAAAAATAATAA
ATA
Found at i:12497342 original size:9 final size:10
Alignment explanation
Indices: 12497229--12497345 Score: 53
Period size: 11 Copynumber: 10.9 Consensus size: 10
12497219 AATCATATAT
*
12497229 TAATCAATAA
1 TAATAAATAA
*
12497239 TATTATAATATAT
1 TA--ATAA-ATAA
12497252 TAATAAATAA
1 TAATAAATAA
*
12497262 T-ATACTATTAA
1 TAATA--AATAA
*
12497273 T-ATAATATAT
1 TAATAA-ATAA
12497283 TAATAAATATTA
1 TAATAAATA--A
12497295 TTAATAAATAA
1 -TAATAAATAA
*
12497306 TATTATAATACA
1 TAATA-AATA-A
12497318 TTAATAAATAA
1 -TAATAAATAA
12497329 T-ATAAA-AA
1 TAATAAATAA
12497337 TAATAAATA
1 TAATAAATA
12497346 GTTTTATTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
8 3 0.04
9 14 0.17
10 18 0.22
11 22 0.27
12 8 0.10
13 18 0.22
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATAAATAA
Found at i:12497438 original size:15 final size:15
Alignment explanation
Indices: 12497418--12497458 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
12497408 TATAATTACT
*
12497418 TTTTAATATTAATAA
1 TTTTAATATAAATAA
12497433 TTTTAATAATAAATAA
1 TTTTAAT-ATAAATAA
*
12497449 TTTCAATATA
1 TTTTAATATA
12497459 TTTTAATAAT
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:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTTAATATAAATAA
Found at i:12497456 original size:25 final size:26
Alignment explanation
Indices: 12497428--12497495 Score: 104
Period size: 25 Copynumber: 2.7 Consensus size: 26
12497418 TTTTAATATT
12497428 AATAATTTTAATAATAAATAA-TTTC
1 AATAATTTTAATAATAAATAATTTTC
*
12497453 AATATATTTTAATAATAAATAATTTTT
1 AATA-ATTTTAATAATAAATAATTTTC
12497480 AAT-ATTTTAATAATAA
1 AATAATTTTAATAATAA
12497496 TATTAATATT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
25 17 0.43
26 17 0.43
27 6 0.15
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
AATAATTTTAATAATAAATAATTTTC
Found at i:12497461 original size:26 final size:26
Alignment explanation
Indices: 12497428--12497495 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
12497418 TTTTAATATT
12497428 AATA-ATTTTAATAATAAATAATTTC
1 AATATATTTTAATAATAAATAATTTC
*
12497453 AATATATTTTAATAATAAATAATTTT
1 AATATATTTTAATAATAAATAATTTC
*
12497479 TA-ATATTTTAATAATAA
1 AATATATTTTAATAATAA
12497496 TATTAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 19 0.47
26 21 0.52
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
AATATATTTTAATAATAAATAATTTC
Found at i:12497477 original size:16 final size:16
Alignment explanation
Indices: 12497418--12497483 Score: 56
Period size: 15 Copynumber: 4.5 Consensus size: 16
12497408 TATAATTACT
*
12497418 TTTTAAT-ATTAATAA
1 TTTTAATAATAAATAA
12497433 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
*
12497449 -TTT--CAAT--AT-A
1 TTTTAATAATAAATAA
12497459 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
12497475 TTTTTAATA
1 -TTTTAATA
12497484 TTTTAATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
10 1 0.03
11 5 0.12
13 6 0.15
15 12 0.30
16 8 0.20
17 8 0.20
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Done.