Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 40 of 206
Found at i:11433209 original size:30 final size:28
Alignment explanation
Indices: 11433175--11433263 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 28
11433165 TGGAGCTGGA
*
11433175 GGTGGCTTCGGTGGAGGAGGTGGGTTTGGC
1 GGTGGC-T-GGTGCAGGAGGTGGGTTTGGC
*
11433205 GGTGGAGCTGGTGCAGGTGGTGGGTTTGGC
1 GGT-G-GCTGGTGCAGGAGGTGGGTTTGGC
* * *
11433235 GGTGGAGCCGGTGCAGGTGGTGGGCTTGG
1 GGT-G-GCTGGTGCAGGAGGTGGGTTTGG
11433264 AGGAGGATTG
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
30 49 0.92
31 2 0.04
32 2 0.04
ACGTcount: A:0.07, C:0.11, G:0.57, T:0.25
Consensus pattern (28 bp):
GGTGGCTGGTGCAGGAGGTGGGTTTGGC
Found at i:11433211 original size:18 final size:18
Alignment explanation
Indices: 11433139--11433211 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 18
11433129 TGGTGCTGGC
11433139 GGTGGGTTTGGAGGTGGA
1 GGTGGGTTTGGAGGTGGA
* * *
11433157 GCTGGAG-GTGGAGCTGGA
1 GGTGG-GTTTGGAGGTGGA
* * * *
11433175 GGTGGCTTCGGTGGAGGA
1 GGTGGGTTTGGAGGTGGA
*
11433193 GGTGGGTTTGGCGGTGGA
1 GGTGGGTTTGGAGGTGGA
11433211 G
1 G
11433212 CTGGTGCAGG
Statistics
Matches: 39, Mismatches: 14, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
18 38 0.97
19 1 0.03
ACGTcount: A:0.11, C:0.07, G:0.59, T:0.23
Consensus pattern (18 bp):
GGTGGGTTTGGAGGTGGA
Found at i:11434040 original size:19 final size:19
Alignment explanation
Indices: 11434016--11434053 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
11434006 TCAAATTTTG
*
11434016 AAAATAATTTTTA-AAATTC
1 AAAAT-ATTTATAGAAATTC
11434035 AAAATATTTATAGAAATTC
1 AAAATATTTATAGAAATTC
11434054 TAAACTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (19 bp):
AAAATATTTATAGAAATTC
Found at i:11434112 original size:19 final size:19
Alignment explanation
Indices: 11434090--11434129 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
11434080 AATTTTTTAA
11434090 AAAAATATAA-AAAATATAT
1 AAAAATATAATAAAATA-AT
*
11434109 AAAAATTTAATAAAATAAT
1 AAAAATATAATAAAATAAT
11434128 AA
1 AA
11434130 TTTTGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATATAATAAAATAAT
Found at i:11436823 original size:17 final size:18
Alignment explanation
Indices: 11436796--11436831 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
11436786 ATTGTAGTAG
11436796 TTACAAAAGTTCAGGGAC
1 TTACAAAAGTTCAGGGAC
11436814 TTAC-AAAGTTCAGGGAC
1 TTACAAAAGTTCAGGGAC
11436831 T
1 T
11436832 ATTATGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (18 bp):
TTACAAAAGTTCAGGGAC
Found at i:11438106 original size:18 final size:18
Alignment explanation
Indices: 11438069--11438106 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
11438059 AAAAAATTAC
*
11438069 ATTTTTTAGATTTAATAT
1 ATTTTTTAGATTTAAAAT
11438087 ATTTTTTA-ATTTCAAAAT
1 ATTTTTTAGATTT-AAAAT
11438105 AT
1 AT
11438107 ATAGAGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (18 bp):
ATTTTTTAGATTTAAAAT
Found at i:11438681 original size:32 final size:35
Alignment explanation
Indices: 11438644--11438722 Score: 128
Period size: 36 Copynumber: 2.3 Consensus size: 35
11438634 TTGAAGTAAT
11438644 TATTTGAAATA-TTTTACATAT-AAA-AATAATGA
1 TATTTGAAATATTTTTACATATAAAATAATAATGA
11438676 TATTTGAAATATTTTTACATATAAAAATAATAATGA
1 TATTTGAAATATTTTTACATAT-AAAATAATAATGA
11438712 TATTTGAAATA
1 TATTTGAAATA
11438723 ATTATTTGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
32 11 0.26
33 10 0.23
35 3 0.07
36 19 0.44
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (35 bp):
TATTTGAAATATTTTTACATATAAAATAATAATGA
Found at i:11438951 original size:29 final size:29
Alignment explanation
Indices: 11438893--11438957 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
11438883 AATATAATGA
* * * *
11438893 TATTTGAAATAATTATTTGATTTTATAGT
1 TATTTGAAAAAATAATTTGATTTCAAAGT
11438922 TATTTGAAAAAATAATTTCG-TTTCAAAGT
1 TATTTGAAAAAATAATTT-GATTTCAAAGT
11438951 T-TTTGAA
1 TATTTGAA
11438958 GCTTTTACAG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 6 0.19
29 24 0.77
30 1 0.03
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (29 bp):
TATTTGAAAAAATAATTTGATTTCAAAGT
Found at i:11439525 original size:24 final size:22
Alignment explanation
Indices: 11439454--11439531 Score: 59
Period size: 24 Copynumber: 3.3 Consensus size: 22
11439444 ACTGCCCATA
* *
11439454 TTATTTTTTTTATTTTTTTGAAAA
1 TTATATTTTTTA--TTTTTGAAAT
*
11439478 TTATATTTATATTATTTTT-TAAT
1 TTATATTT-T-TTATTTTTGAAAT
11439501 TTAATATTTTTTATTTATTGAAAT
1 TT-ATATTTTTTATTT-TTGAAAT
11439525 TTCATAT
1 TT-ATAT
11439532 AGTCATCTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
22 6 0.14
23 7 0.16
24 27 0.61
25 1 0.02
26 3 0.07
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (22 bp):
TTATATTTTTTATTTTTGAAAT
Found at i:11447616 original size:96 final size:95
Alignment explanation
Indices: 11447455--11448366 Score: 517
Period size: 96 Copynumber: 9.7 Consensus size: 95
11447445 AAACTTATAC
* * *
11447455 CCCTGAAGTTGCAGTGG-GACAGATTGAAGTCATCGTGGCGAATCTTATTTCTCTGAAGTTGCAG
1 CCCTGAAGTTGCAGTGGAG-CAGATTGAA-T-A---TAGCAAATCTTATTTCCCTGAAGTTGCAG
* *
11447519 TGGAACAGATTAAAGTTACAAGTTACAAATATTATCT
60 TGGAACAGATTAAAGCTA-AAGTTACAAATCTTATCT
* * ** * *
11447556 CCTTGAAGTTGTAGTGGAGCAGATTGAATATAGTGAATCTTATTTCCCTAAAGTTACAGTGGAAC
1 CCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAAC
11447621 AGATTAAAGCTACAAGTTACAAATCTTATCT
66 AGATTAAAGCTA-AAGTTACAAATCTTATCT
* * * * *
11447652 CCCTAAAGTTGTAGTGGAGCAGATTGAATATAACGAATCTTATTTCCCTGAAGCTGCAGTGGAAC
1 CCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAAC
* * * *
11447717 AGATTGAAG--ATAG---CGAATCTTATTT
66 AGATTAAAGCTAAAGTTACAAATCTTATCT
* * * * * * * * *
11447742 CCCTGAAGTTGTAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCTCCCTAAAGTTGTAA
1 CCCTGAAGTTGCAGTGGAGCAGATTGAA--TA-TAG---CAAATCTTATTTCCCTGAAGTTGCAG
* * * * *
11447807 TGGAGCAGATTGAAGATAACG--AC---TATTATCT
60 TGGAACAGATTAAAGCTAAAGTTACAAATCTTATCT
* * * * *
11447838 CCCTGAAGTTGCAGTGGAGTAGATTGAAGATAACAAATATTATTTTCCTGAAGTTGCAGTGGAAC
1 CCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAAC
* * * *
11447903 AGATTGAAGCTGTAAGTTATAAATCTTATTT
66 AGATTAAAGCT-AAAGTTACAAATCTTATCT
* * * * * *
11447934 CTCTGAAGTTGCAGTGGAGCAGATTGAAGAT-GCAAATATTATTTTCCTGAAGTTGTAGTGGAAT
1 CCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAAC
11447998 AGATTAAAGCTATAAGTTACAAATCTTATCT
66 AGATTAAAGCTA-AAGTTACAAATCTTATCT
* * * * * * * *
11448029 CCTTGGAGTTGCAGTGGAGCATATTGAAGT-TA-CAAGTCTTATCTCCCTGAAGTAGTAGTGGAG
1 CCCTGAAGTTGCAGTGGAGCAGATTGAA-TATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAA
* * *
11448092 TAGATTGAAGC----G--ACAAATCCTATAC-
65 CAGATTAAAGCTAAAGTTACAAATCTTAT-CT
* * * * * * * * * * *
11448117 CTCTGAAGTTGCAATAGA-TAGGATTAAATCTACCATTGTAAGTCTTATCTCCTTAAAGTTGCAT
1 CCCTGAAGTTGCAGTGGAGCA-GATTGAATATAGCA----AA-TCTTATTTCCCTGAAGTTGCAG
* * * * *
11448181 TGGAATAGACTAAGGCTACAAGCTACAAATGTTAT-T
60 TGGAACAGATTAAAGCTA-AAGTTACAAATCTTATCT
* * * *
11448217 CCCCTGAAGTTACAGT-GAACAGATTGAA-AT-GACAAGTCTTATTTCCCTGAAGTTACAGT-GA
1 -CCCTGAAGTTGCAGTGGAGCAGATTGAATATAG-CAAATCTTATTTCCCTGAAGTTGCAGTGGA
* *
11448278 AGCA-AGTTGAAGC---A---ACAAATCTTGTCT
64 A-CAGA-TTAAAGCTAAAGTTACAAATCTTATCT
** * ** * *
11448305 TTCTGAATTTGCAGTGGAGCAGATTGAAGCTA-CAAGTCTTATCTCCCTGAAGTTGCAGTGGA
1 CCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGA
11448367 GTAAATTGAA
Statistics
Matches: 638, Mismatches: 127, Indels: 104
0.73 0.15 0.12
Matches are distributed among these distances:
87 22 0.03
88 67 0.11
89 6 0.01
90 71 0.11
91 2 0.00
92 2 0.00
93 10 0.02
94 54 0.08
95 117 0.18
96 223 0.35
98 2 0.00
99 6 0.01
100 9 0.01
101 46 0.07
102 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (95 bp):
CCCTGAAGTTGCAGTGGAGCAGATTGAATATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAAC
AGATTAAAGCTAAAGTTACAAATCTTATCT
Found at i:11447625 original size:45 final size:45
Alignment explanation
Indices: 11447455--11448002 Score: 315
Period size: 45 Copynumber: 11.6 Consensus size: 45
11447445 AAACTTATAC
* *
11447455 CCCTGAAGTTGCAGTGGGACAGATTGAAGTCATCGTGGCGAATCTTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAA-T-A---TAGCGAATCTTATTT
* * * * * *
11447505 CTCTGAAGTTGCAGTGGAACAGATTAAAGTTACAAGTTACAAATATTATCT
1 CCCTGAAGTTGCAGTGGAACAGATTGAA--TA-TAG---CGAATCTTATTT
* * * *
11447556 CCTTGAAGTTGTAGTGGAGCAGATTGAATATAGTGAATCTTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
* * * * * *
11447601 CCCTAAAGTTACAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAACAGATTGAA--TA-TAG---CGAATCTTATTT
* * * *
11447652 CCCTAAAGTTGTAGTGGAGCAGATTGAATATAACGAATCTTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
* *
11447697 CCCTGAAGCTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
* * * ** *
11447742 CCCTGAAGTTGTAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCT
1 CCCTGAAGTTGCAGTGGAACAGATTGAA--TA-TAG---CGAATCTTATTT
* * * * * * * * *
11447793 CCCTAAAGTTGTAATGGAGCAGATTGAAGATAACGACTATTATCT
1 CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
** * * * *
11447838 CCCTGAAGTTGCAGTGGAGTAGATTGAAGATAACAAATATTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
* * **
11447883 TCCTGAAGTTGCAGTGGAACAGATTGAAGCTGTAAGTTATAAATCTTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAA--TAT-AG---CGAATCTTATTT
* * * * *
11447934 CTCTGAAGTTGCAGTGGAGCAGATTGAAGAT-GCAAATATTATTT
1 CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
* * *
11447978 TCCTGAAGTTGTAGTGGAATAGATT
1 CCCTGAAGTTGCAGTGGAACAGATT
11448003 AAAGCTATAA
Statistics
Matches: 386, Mismatches: 90, Indels: 50
0.73 0.17 0.10
Matches are distributed among these distances:
44 30 0.08
45 175 0.45
47 5 0.01
48 10 0.03
49 6 0.02
50 26 0.07
51 134 0.35
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.32
Consensus pattern (45 bp):
CCCTGAAGTTGCAGTGGAACAGATTGAATATAGCGAATCTTATTT
Found at i:11447736 original size:141 final size:141
Alignment explanation
Indices: 11447546--11448002 Score: 601
Period size: 141 Copynumber: 3.2 Consensus size: 141
11447536 ACAAGTTACA
* * * * * *
11447546 AATATTATCTCCTTGAAGTTGTAGTGGAGCAGATTGAATATAGTGAATCTTATTTCCCTAAAGTT
1 AATATTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
* *
11447611 ACAGTGGAACAGATTAAAGCTACAAGTTACAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
66 GCAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
*
11447676 TGAATATAACG
131 TGAAGATAACG
* * *
11447687 AATCTTATTTCCCTGAAGCTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
1 AATATTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
* *
11447752 GTAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCTCCCTAAAGTTGTAATGGAGCAGAT
66 GCAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
11447817 TGAAGATAACG
131 TGAAGATAACG
* ** * * * *
11447828 ACTATTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAACAAATATTATTTTCCTGAAGTT
1 AATATTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
* ** * * * *
11447893 GCAGTGGAACAGATTGAAGCTGTAAGTTATAAATCTTATTTCTCTGAAGTTGCAGTGGAGCAGAT
66 GCAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
* *
11447958 TGAAGAT-GCA
131 TGAAGATAACG
* * * *
11447968 AATATTATTTTCCTGAAGTTGTAGTGGAATAGATT
1 AATATTATCTCCCTGAAGTTGCAGTGGAACAGATT
11448003 AAAGCTATAA
Statistics
Matches: 276, Mismatches: 40, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
140 31 0.11
141 245 0.89
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.32
Consensus pattern (141 bp):
AATATTATCTCCCTGAAGTTGCAGTGGAACAGATTGAAGATAGCGAATCTTATTTCCCTGAAGTT
GCAGTGGAACAGATTAAAGCTACAAGTTATAAATCTTATCTCCCTAAAGTTGTAGTGGAGCAGAT
TGAAGATAACG
Found at i:11448074 original size:44 final size:44
Alignment explanation
Indices: 11448011--11448110 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 44
11448001 TTAAAGCTAT
* * * *
11448011 AAGTTACAAATCTTATCTCCTTGGAGTTGCAGTGGAGCATATTG
1 AAGTTACAAATCTTATCTCCCTGAAGTAGCAGTGGAGCAGATTG
* * *
11448055 AAGTTACAAGTCTTATCTCCCTGAAGTAGTAGTGGAGTAGATTG
1 AAGTTACAAATCTTATCTCCCTGAAGTAGCAGTGGAGCAGATTG
**
11448099 AAGCGACAAATC
1 AAGTTACAAATC
11448111 CTATACCTCT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (44 bp):
AAGTTACAAATCTTATCTCCCTGAAGTAGCAGTGGAGCAGATTG
Found at i:11448409 original size:44 final size:44
Alignment explanation
Indices: 11448218--11448409 Score: 147
Period size: 44 Copynumber: 4.4 Consensus size: 44
11448208 AATGTTATTC
* * * * *
11448218 CCCTGAAGTTACAGT-GAACAGATTGAAA-TGACAAGTCTTATTT
1 CCCTGAAGTTGCAGTGGAGCAAATTGAAACT-ACAAGTCCTATCT
* * * * * * * *
11448261 CCCTGAAGTTACAGTGAAGCAAGTTGAAGCAACAAATCTTGTCT
1 CCCTGAAGTTGCAGTGGAGCAAATTGAAACTACAAGTCCTATCT
** * * * *
11448305 TTCTGAATTTGCAGTGGAGCAGATTGAAGCTACAAGTCTTATCT
1 CCCTGAAGTTGCAGTGGAGCAAATTGAAACTACAAGTCCTATCT
* **
11448349 CCCTGAAGTTGCAGTGGAGTAAATTGAAACTACATTTCCTATAC-
1 CCCTGAAGTTGCAGTGGAGCAAATTGAAACTACAAGTCCTAT-CT
11448393 CCCTGAAGTTGCAGTGG
1 CCCTGAAGTTGCAGTGG
11448410 GCTGGAATGA
Statistics
Matches: 118, Mismatches: 28, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
43 15 0.13
44 102 0.86
45 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (44 bp):
CCCTGAAGTTGCAGTGGAGCAAATTGAAACTACAAGTCCTATCT
Found at i:11448943 original size:18 final size:17
Alignment explanation
Indices: 11448920--11448957 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
11448910 GGTTTTTTTT
*
11448920 AAAAATAGAAATCAAATA
1 AAAAATAGAAA-AAAATA
11448938 AAAAATAGAAAAAAATA
1 AAAAATAGAAAAAAATA
11448955 AAA
1 AAA
11448958 TACAGAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (17 bp):
AAAAATAGAAAAAAATA
Found at i:11449018 original size:13 final size:13
Alignment explanation
Indices: 11448991--11449024 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
11448981 ATTTTTTATC
11448991 TTTTATATCTATTA
1 TTTT-TATCTATTA
*
11449005 TTTTTATCTTTTA
1 TTTTTATCTATTA
11449018 TTTTTAT
1 TTTTTAT
11449025 AAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTTATCTATTA
Found at i:11450056 original size:3 final size:3
Alignment explanation
Indices: 11450048--11450073 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11450038 TCTCTTTTAT
11450048 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
11450074 TCTCCTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11462307 original size:16 final size:16
Alignment explanation
Indices: 11462286--11462319 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
11462276 GTTCTAAATG
11462286 TTCATTTATCATTGAA
1 TTCATTTATCATTGAA
*
11462302 TTCATTTATCATTTAA
1 TTCATTTATCATTGAA
11462318 TT
1 TT
11462320 GAATTTAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (16 bp):
TTCATTTATCATTGAA
Found at i:11462483 original size:42 final size:42
Alignment explanation
Indices: 11462421--11462586 Score: 176
Period size: 42 Copynumber: 4.0 Consensus size: 42
11462411 ACTGAGATGT
* * * *
11462421 GATTACGTGTAAGACTATGTCTGGGACATTGGCATCGTTATGT
1 GATT-CGTGTAAAACCATGTCTGGGACATTGGCATCGATATGA
* * * *
11462464 GATTCTTGTAAAATCATGTCTGGGATATTGGCATTGATATGA
1 GATTCGTGTAAAACCATGTCTGGGACATTGGCATCGATATGA
* * *
11462506 GATTCGTGTAAGACCATGTCTAGGACTTTGGCATCGATATGA
1 GATTCGTGTAAAACCATGTCTGGGACATTGGCATCGATATGA
*
11462548 GATTCGTGTAAGACCATAG-CT-GG-CTATTGGCATCGATAT
1 GATTCGTGTAAAACCAT-GTCTGGGAC-ATTGGCATCGATAT
11462587 ATGATAGCAT
Statistics
Matches: 105, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
40 1 0.01
41 15 0.14
42 84 0.80
43 5 0.05
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.34
Consensus pattern (42 bp):
GATTCGTGTAAAACCATGTCTGGGACATTGGCATCGATATGA
Found at i:11462600 original size:42 final size:41
Alignment explanation
Indices: 11462491--11462622 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 41
11462481 GTCTGGGATA
* * *
11462491 TTGGCATTGATATGAGATTCGTGTAAGACCAT-GTCTAGGACT
1 TTGGCATCGATATGAGATGCATGTAAGACCATAG-CT-GGACT
* *
11462533 TTGGCATCGATATGAGATTCGTGTAAGACCATAGCTGG-CT
1 TTGGCATCGATATGAGATGCATGTAAGACCATAGCTGGACT
* *
11462573 ATTGGCATCGATAT-ATGATAGCATGTAAGACCATATCTGGAGT
1 -TTGGCATCGATATGA-GAT-GCATGTAAGACCATAGCTGGACT
*
11462616 ATGGCAT
1 TTGGCAT
11462623 TGTGCGAGTT
Statistics
Matches: 79, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
40 3 0.04
41 18 0.23
42 56 0.71
43 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (41 bp):
TTGGCATCGATATGAGATGCATGTAAGACCATAGCTGGACT
Found at i:11462600 original size:84 final size:84
Alignment explanation
Indices: 11462428--11462606 Score: 202
Period size: 84 Copynumber: 2.1 Consensus size: 84
11462418 TGTGATTACG
* * * * * *
11462428 TGTAAGACTATGTCTGGGACATTGGCATCGTTATGTGATTCTTGTAAAATCATGTCTGGGATATT
1 TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTCGTGTAAAACCATGTCTGGGATATT
* * *
11462493 GGCATTGATATGAGATTCG
66 GGCATCGATATGAGATGCA
* * *
11462512 TGTAAGACCATGTCTAGGACTTTGGCATCGATATGAGATTCGTGTAAGACCATAG-CT-GGCTAT
1 TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTCGTGTAAAACCAT-GTCTGGGATAT
11462575 TGGCATCGATAT-ATGATAGCA
65 TGGCATCGATATGA-GAT-GCA
11462596 TGTAAGACCAT
1 TGTAAGACCAT
11462607 ATCTGGAGTA
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
82 1 0.01
83 19 0.24
84 59 0.74
85 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (84 bp):
TGTAAGACCATGTCTAGGACATTGGCATCGATATGAGATTCGTGTAAAACCATGTCTGGGATATT
GGCATCGATATGAGATGCA
Found at i:11469138 original size:16 final size:16
Alignment explanation
Indices: 11469117--11469170 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
11469107 GTGGAGGAAA
11469117 GAAAATTGAAAAGATG
1 GAAAATTGAAAAGATG
*
11469133 GAAAATTGAAAGGATG
1 GAAAATTGAAAAGATG
11469149 GAAAATT-AGAAAGATG
1 GAAAATTGA-AAAGATG
*
11469165 AAAAAT
1 GAAAAT
11469171 ATAAATTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 1 0.03
16 33 0.97
ACGTcount: A:0.57, C:0.00, G:0.24, T:0.19
Consensus pattern (16 bp):
GAAAATTGAAAAGATG
Found at i:11481996 original size:2 final size:2
Alignment explanation
Indices: 11481989--11482016 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11481979 AGATGAGGCG
11481989 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
11482017 AAGCAGTTAA
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11483483 original size:89 final size:89
Alignment explanation
Indices: 11483332--11483510 Score: 340
Period size: 89 Copynumber: 2.0 Consensus size: 89
11483322 CCGAACTTCA
11483332 AATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCTTTTT
1 AATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCTTTTT
11483397 TTCAGGCAATTTCAGTTTTCTACG
66 TTCAGGCAATTTCAGTTTTCTACG
* *
11483421 AATGTTACACGGTCAACTCCAAACTATTATCGATCAAACTAGATATTCACTCAATAACCCTTTTT
1 AATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCTTTTT
11483486 TTCAGGCAATTTCAGTTTTCTACG
66 TTCAGGCAATTTCAGTTTTCTACG
11483510 A
1 A
11483511 TTCTAAAACC
Statistics
Matches: 88, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.34
Consensus pattern (89 bp):
AATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCTTTTT
TTCAGGCAATTTCAGTTTTCTACG
Found at i:11486899 original size:20 final size:21
Alignment explanation
Indices: 11486874--11486923 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
11486864 TGTGCCTTCT
*
11486874 TCCACATGGGCGTG-TGTCCC
1 TCCACATGGGCGTGTTGACCC
*
11486894 TCCACATGGGCTTGTTGACCC
1 TCCACATGGGCGTGTTGACCC
*
11486915 CCCACATGG
1 TCCACATGG
11486924 CTGTGTGGCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.14, C:0.36, G:0.26, T:0.24
Consensus pattern (21 bp):
TCCACATGGGCGTGTTGACCC
Found at i:11486921 original size:21 final size:20
Alignment explanation
Indices: 11486875--11486923 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
11486865 GTGCCTTCTT
* *
11486875 CCACATGGGCGTGTGTCCCT
1 CCACATGGGCGTGTGACCCC
*
11486895 CCACATGGGCTTGTTGACCCC
1 CCACATGGGCGTG-TGACCCC
11486916 CCACATGG
1 CCACATGG
11486924 CTGTGTGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.14, C:0.37, G:0.27, T:0.22
Consensus pattern (20 bp):
CCACATGGGCGTGTGACCCC
Found at i:11487517 original size:87 final size:87
Alignment explanation
Indices: 11487367--11487543 Score: 212
Period size: 87 Copynumber: 2.0 Consensus size: 87
11487357 AATTCTGATT
* * * * **
11487367 TGATCTGGCAGTTTAACTGCAACTTATTTGTATAGCGGTTTACCACACTGTATCGTATATACGTC
1 TGATCTGGCAGTTTAACTGCAACTTATTCGTACAGCGATTTACCACACTGTACCACATATACGTC
* * *
11487432 AGTTTTGCTGCGTATTATTATC
66 AGCTCTGCTGCGTATTAATATC
* * * * *
11487454 TGATCTGGCAGTTTTACTGCAACTTATTCGTACATCGATTTATCC-TATTGTACCACATGTACGT
1 TGATCTGGCAGTTTAACTGCAACTTATTCGTACAGCGATTTA-CCACACTGTACCACATATACGT
11487518 CAGCTCTGCTGCGTATTAATATC
65 CAGCTCTGCTGCGTATTAATATC
11487541 TGA
1 TGA
11487544 GTGGTTTAGT
Statistics
Matches: 75, Mismatches: 14, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
87 73 0.97
88 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (87 bp):
TGATCTGGCAGTTTAACTGCAACTTATTCGTACAGCGATTTACCACACTGTACCACATATACGTC
AGCTCTGCTGCGTATTAATATC
Found at i:11493033 original size:21 final size:22
Alignment explanation
Indices: 11493004--11493047 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
11492994 TTTCTAATTG
*
11493004 TTTTCAAACT-ATTTTTAAGGTC
1 TTTTCAAACTCA-ATTTAAGGTC
11493026 TTTT-AAACTCAATTTAAGGTC
1 TTTTCAAACTCAATTTAAGGTC
11493047 T
1 T
11493048 ATAAGTGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.48
Consensus pattern (22 bp):
TTTTCAAACTCAATTTAAGGTC
Found at i:11496177 original size:27 final size:31
Alignment explanation
Indices: 11496110--11496171 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 31
11496100 TCCTTTAACA
11496110 ATAAACATAACTATTTAATAGATGTCTACTTG
1 ATAAACATAACTATTTAATAGA-GTCTACTTG
*
11496142 AATAAACATAATTATTTAATAGA-TC-ACTTG
1 -ATAAACATAACTATTTAATAGAGTCTACTTG
11496172 TAACATTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 5 0.18
31 2 0.07
33 21 0.75
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
ATAAACATAACTATTTAATAGAGTCTACTTG
Found at i:11497718 original size:3 final size:3
Alignment explanation
Indices: 11497710--11497772 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
11497700 TGTCATTAGA
11497710 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
11497758 TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT
11497773 ATTGTAGTCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11497860 original size:9 final size:9
Alignment explanation
Indices: 11497846--11497872 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
11497836 TTAAATGTTG
11497846 ATACTATTA
1 ATACTATTA
11497855 ATACTATTA
1 ATACTATTA
11497864 ATACTATTA
1 ATACTATTA
11497873 GTATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
ATACTATTA
Found at i:11500741 original size:41 final size:41
Alignment explanation
Indices: 11500683--11500832 Score: 237
Period size: 41 Copynumber: 3.7 Consensus size: 41
11500673 TTTAACATAT
* * *
11500683 TCACCGGCATTTAGCCTGCTAAGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * *
11500724 TCACCGACACTTTGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
11500765 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
*
11500806 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
11500833 AAGTCCGAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:11502486 original size:13 final size:13
Alignment explanation
Indices: 11502468--11502492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11502458 CAATCAAATG
11502468 CACACAAAATAAA
1 CACACAAAATAAA
11502481 CACACAAAATAA
1 CACACAAAATAA
11502493 TATTAAATTA
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:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:11511315 original size:16 final size:16
Alignment explanation
Indices: 11511290--11511326 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
11511280 CAAATGCACT
*
11511290 AAAAACGAATGATGCC
1 AAAAACGAATGATGAC
*
11511306 AAAAATGAATGATGAC
1 AAAAACGAATGATGAC
11511322 AAAAA
1 AAAAA
11511327 GGTTCGCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.14
Consensus pattern (16 bp):
AAAAACGAATGATGAC
Found at i:11512967 original size:23 final size:23
Alignment explanation
Indices: 11512932--11513191 Score: 234
Period size: 23 Copynumber: 11.1 Consensus size: 23
11512922 ACACTAAAAT
*
11512932 TTGGACAGCATATATACAAC-AA
1 TTGGGCAGCATATATACAACAAA
11512954 TCTGGGCAGCATATATACAACAAA
1 T-TGGGCAGCATATATACAACAAA
* * * *
11512978 TTGAGCAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
* *
11513003 TTGGACAGCATATATATAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
11513026 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
11513049 TTGAGCAGCATTTTTACATCAAAA
1 TTGGGCAGCATATATACAAC-AAA
* * *
11513073 TTCGACAGCATATATACAACAAT
1 TTGGGCAGCATATATACAACAAA
* *
11513096 TTGGACAGCATAAATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* * * *
11513119 TTGAGCAGCATTTTTACACCAAAAA
1 TTGGGCAGCATATATACA--ACAAA
*
11513144 TTGGACAGCATATATACAACAAA
1 TTGGGCAGCATATATACAACAAA
* *
11513167 TTGGGCAGCATATATATACCAAA
1 TTGGGCAGCATATATACAACAAA
11513190 TT
1 TT
11513192 CAAACCAAAA
Statistics
Matches: 189, Mismatches: 42, Indels: 13
0.77 0.17 0.05
Matches are distributed among these distances:
22 1 0.01
23 133 0.70
24 20 0.11
25 35 0.19
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (23 bp):
TTGGGCAGCATATATACAACAAA
Found at i:11512987 original size:71 final size:71
Alignment explanation
Indices: 11512912--11513191 Score: 420
Period size: 71 Copynumber: 4.0 Consensus size: 71
11512902 CCAAACTAGA
* * *
11512912 CAGCATTTTCACACTAAAATTTGGACAGCATATATACAAC-AATCTGGGCAGCATATATACAACA
1 CAGCATTTTTACACCAAAAATTGGACAGCATATATACAACAAAT-TGGGCAGCATATATACAACA
11512976 AATTGAG
65 AATTGAG
* * *
11512983 CAGCATTTTTACACCAAAAATTGGACAGCATATATATAACAAATTGGGCAGCATATATATACCAA
1 CAGCATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
11513048 ATTGAG
66 ATTGAG
* * * * *
11513054 CAGCATTTTTACATC-AAAATTCGACAGCATATATACAACAATTTGGACAGCATAAATACAACAA
1 CAGCATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
11513118 ATTGAG
66 ATTGAG
* *
11513124 CAGCATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATATACCAA
1 CAGCATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
11513189 ATT
66 ATT
11513192 CAAACCAAAA
Statistics
Matches: 186, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
70 62 0.33
71 121 0.65
72 3 0.02
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (71 bp):
CAGCATTTTTACACCAAAAATTGGACAGCATATATACAACAAATTGGGCAGCATATATACAACAA
ATTGAG
Found at i:11513121 original size:141 final size:142
Alignment explanation
Indices: 11512873--11513191 Score: 493
Period size: 141 Copynumber: 2.3 Consensus size: 142
11512863 GGACAGCTCT
* * * * *
11512873 TATACATCAATTTGGACAGCA-ATTATATACCAAACTAGACAGCATTTTCACACTAAAATTTGGA
1 TATACAACAAATTGGGCAGCATA-TATATACCAAATTAGACAGCATTTTCACACTAAAATTTCGA
* *
11512937 CAGCATATATACAACAATCTGGGCAGCATATATACAACAAATTGAGCAGCATTTTTACACCAAAA
65 CAGCATATATACAACAATCTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAA
11513002 ATTGGACAGCATA
130 ATTGGACAGCATA
* *
11513015 TATATAACAAATTGGGCAGCATATATATACCAAATT-GAGCAGCATTTTTACA-TCAAAA-TTCG
1 TATACAACAAATTGGGCAGCATATATATACCAAATTAGA-CAGCATTTTCACACT-AAAATTTCG
*
11513077 ACAGCATATATACAACAATTTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
64 ACAGCATATATACAACAATCTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAA
11513142 AATTGGACAGCATA
129 AATTGGACAGCATA
11513156 TATACAACAAATTGGGCAGCATATATATACCAAATT
1 TATACAACAAATTGGGCAGCATATATATACCAAATT
11513192 CAAACCAAAA
Statistics
Matches: 163, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
141 117 0.72
142 45 0.28
143 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.13, T:0.26
Consensus pattern (142 bp):
TATACAACAAATTGGGCAGCATATATATACCAAATTAGACAGCATTTTCACACTAAAATTTCGAC
AGCATATATACAACAATCTGGACAGCATAAATACAACAAATTGAGCAGCATTTTTACACCAAAAA
TTGGACAGCATA
Found at i:11513881 original size:28 final size:28
Alignment explanation
Indices: 11513849--11513916 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
11513839 ATAAGTTCGT
* *
11513849 ACACTTAGTGCTTAATAATCAATCTCGC
1 ACACTTAGTGCTTAACAATCAAACTCGC
* *
11513877 ACACTTAGTGCTTTACAATTAAACTCGC
1 ACACTTAGTGCTTAACAATCAAACTCGC
11513905 ACACTTAGTGCT
1 ACACTTAGTGCT
11513917 AATCTCATTA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (28 bp):
ACACTTAGTGCTTAACAATCAAACTCGC
Found at i:11515489 original size:138 final size:138
Alignment explanation
Indices: 11515126--11515496 Score: 410
Period size: 138 Copynumber: 2.7 Consensus size: 138
11515116 GGCTGTTACA
* * * * *
11515126 GCAGTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAAGTTGCAGTGAATCGGATTGAAGCT
1 GCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCTTAAAGTTGCAGAGGATCGGATTGAAGCT
* * * *
11515191 ACAATTTCTATAGCCATGAAGTTACAATGGGTTGGAATGAAACTACGACAACGAATCTTATCTCC
66 ACAATTTCTATACCCCTGAAGTTGCAGTGGGTTGGAATGAAACTACGACAACGAATCTTATCTCC
11515256 CTGAAGTT
131 CTGAAGTT
* ** * * * *
11515264 GCAATGG-GTTAGAATGAAGCTAAGAATCTTATATCCTTGAAGTTGTAGTA-GATCGGATTGAAG
1 GCAGTGGAGCAAG-ATGAAGCTACGAATCCTATATCCTTAAAGTTGCAG-AGGATCGGATTGAAG
* * ****
11515327 CCACAATTTCTATACCCCTAAAGTTGCAGTGGGTTGGAATGAAACTACGATGGTGAATCTTATCT
64 CTACAATTTCTATACCCCTGAAGTTGCAGTGGGTTGGAATGAAACTACGACAACGAATCTTATCT
11515392 CCCT-AGAGTT
129 CCCTGA-AGTT
* * *
11515402 GCAGTGGAGCAAGATGAAGCTACGAATCCTAAATCCTTAAAGTGGCAGAGGATCAGG-TTGAAGT
1 GCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCTTAAAGTTGCAGAGGATC-GGATTGAAGC
* * *
11515466 TATAA-ATCTTATATCCCTGAAGTTGCAGTGG
65 TACAATTTC-TATACCCCTGAAGTTGCAGTGG
11515497 ATCAGATTAA
Statistics
Matches: 189, Mismatches: 37, Indels: 14
0.79 0.15 0.06
Matches are distributed among these distances:
137 7 0.04
138 177 0.94
139 5 0.03
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (138 bp):
GCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCTTAAAGTTGCAGAGGATCGGATTGAAGCT
ACAATTTCTATACCCCTGAAGTTGCAGTGGGTTGGAATGAAACTACGACAACGAATCTTATCTCC
CTGAAGTT
Found at i:11515501 original size:44 final size:44
Alignment explanation
Indices: 11515398--11515586 Score: 123
Period size: 44 Copynumber: 4.3 Consensus size: 44
11515388 ATCTCCCTAG
* * * * * * * *
11515398 AGTTGCAGTGGAGCAAGATGAAGCTACGAATCCTAAATCCTTAA
1 AGTTGCAGTGGATCAGGTTGAAGTTACAAATCCTATATCCCTGA
* * * *
11515442 AGTGGCAGAGGATCAGGTTGAAGTTATAAATCTTATATCCCTGA
1 AGTTGCAGTGGATCAGGTTGAAGTTACAAATCCTATATCCCTGA
* * * * *
11515486 AGTTGCAGTGGATCAGATTAAATTTACAATTCCTATACCCCTGA
1 AGTTGCAGTGGATCAGGTTGAAGTTACAAATCCTATATCCCTGA
* * ** * *
11515530 AGTTACAGTGTG-TTAGAAT-AAGGCTACAAAT-CTATCAGCCCTGA
1 AGTTGCAGTG-GATCAGGTTGAA-GTTACAAATCCTAT-ATCCCTGA
11515574 AGTTGCAGTGGAT
1 AGTTGCAGTGGAT
11515587 TGGATTGAAA
Statistics
Matches: 112, Mismatches: 29, Indels: 8
0.75 0.19 0.05
Matches are distributed among these distances:
43 7 0.06
44 104 0.93
45 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (44 bp):
AGTTGCAGTGGATCAGGTTGAAGTTACAAATCCTATATCCCTGA
Found at i:11517285 original size:3 final size:3
Alignment explanation
Indices: 11517277--11517345 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
11517267 TGTCATTAGA
11517277 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
11517325 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
11517346 GTTATAGTCA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:11517432 original size:9 final size:9
Alignment explanation
Indices: 11517418--11517444 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
11517408 TTAAATGTTG
11517418 ATACTATTA
1 ATACTATTA
11517427 ATACTATTA
1 ATACTATTA
11517436 ATACTATTA
1 ATACTATTA
11517445 GTATATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (9 bp):
ATACTATTA
Found at i:11517561 original size:22 final size:22
Alignment explanation
Indices: 11517528--11517574 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
11517518 ATTAATTGAA
11517528 TATTTTTCATTATTGTTATT-AT
1 TATTTTTCATTATTG-TATTCAT
11517550 TATTTCTT-ATTATTGTATTCAT
1 TATTT-TTCATTATTGTATTCAT
11517572 TAT
1 TAT
11517575 AGTATCGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 17 0.74
23 2 0.09
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (22 bp):
TATTTTTCATTATTGTATTCAT
Found at i:11531523 original size:33 final size:34
Alignment explanation
Indices: 11531449--11531523 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 34
11531439 ACATCGGGCC
* * **
11531449 GAAATTCAATTTAAATAATAAAATATATTTTTTA
1 GAAATTAAATTTAAATAATAAAATATATATAATA
* *
11531483 G-ACTTAAATTT-AATTATAAAATATATATAATA
1 GAAATTAAATTTAAATAATAAAATATATATAATA
11531515 GAAATTAAA
1 GAAATTAAA
11531524 AAAAATATTT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
32 18 0.55
33 14 0.42
34 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.04, T:0.40
Consensus pattern (34 bp):
GAAATTAAATTTAAATAATAAAATATATATAATA
Found at i:11533575 original size:42 final size:42
Alignment explanation
Indices: 11533451--11533646 Score: 158
Period size: 42 Copynumber: 4.7 Consensus size: 42
11533441 GACTGTCAAT
* * * * * * *
11533451 GCCACACGGCCAGGGACATGAGCATGTGCCCAAGCTGTGTGA
1 GCCACACGGGCAAGGACATGGGCGTGTGCCTAGGCCGTGTGA
* * * * ** * *
11533493 GCCACACGAGCAAGGATATAGACGCCTGCCCAAGCCGTGTGA
1 GCCACACGGGCAAGGACATGGGCGTGTGCCTAGGCCGTGTGA
* * *** *
11533535 TCCACACGGGCAAGGACATGGGTGTGTGCCTAGTTTGTGTGG
1 GCCACACGGGCAAGGACATGGGCGTGTGCCTAGGCCGTGTGA
* * * *
11533577 GACACACGGGTAAGGACATAGGCGTGTGCCTAGGCCATGTGA
1 GCCACACGGGCAAGGACATGGGCGTGTGCCTAGGCCGTGTGA
*
11533619 GCCACACGGGCAAGGACATGGTCGTGTG
1 GCCACACGGGCAAGGACATGGGCGTGTG
11533647 TCCAAGCCGT
Statistics
Matches: 115, Mismatches: 39, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
42 115 1.00
ACGTcount: A:0.23, C:0.25, G:0.35, T:0.17
Consensus pattern (42 bp):
GCCACACGGGCAAGGACATGGGCGTGTGCCTAGGCCGTGTGA
Found at i:11535158 original size:17 final size:16
Alignment explanation
Indices: 11535107--11535160 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
11535097 CCATTTCTTA
* *
11535107 AAAAAAAATGAAATTT
1 AAAAAAAATCAAATCT
11535123 AAAGAAAAATGCAAA-CT
1 AAA-AAAAAT-CAAATCT
11535140 AAAAAAAATCAAAATCT
1 AAAAAAAATC-AAATCT
11535157 AAAA
1 AAAA
11535161 CAGCTTGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 1 0.03
16 12 0.38
17 16 0.50
18 3 0.09
ACGTcount: A:0.70, C:0.07, G:0.06, T:0.17
Consensus pattern (16 bp):
AAAAAAAATCAAATCT
Found at i:11539326 original size:23 final size:21
Alignment explanation
Indices: 11539299--11539348 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
11539289 TATGCGTATT
11539299 TTTCTATATAGTATATAGACATA
1 TTTCTATATA-TA-ATAGACATA
* *
11539322 TTTCTTTATATAATATACATA
1 TTTCTATATATAATAGACATA
11539343 TATTCT
1 T-TTCT
11539349 TAAACCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 6 0.25
23 9 0.38
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (21 bp):
TTTCTATATATAATAGACATA
Found at i:11547744 original size:1 final size:1
Alignment explanation
Indices: 11547738--11547777 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
11547728 TTCTTTTCTA
* * *
11547738 TTTTTTTGTTTTTTTTTTTGTTTTTTTTTTGTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
11547778 GAATCTGAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:11547749 original size:20 final size:20
Alignment explanation
Indices: 11547726--11547764 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11547716 GGCCTCTCCA
11547726 TTTTCTTTTCTATTTTTTTG
1 TTTTCTTTTCTATTTTTTTG
* * *
11547746 TTTTTTTTTTTGTTTTTTT
1 TTTTCTTTTCTATTTTTTT
11547765 TTTGTTTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.05, G:0.05, T:0.87
Consensus pattern (20 bp):
TTTTCTTTTCTATTTTTTTG
Found at i:11547753 original size:12 final size:12
Alignment explanation
Indices: 11547738--11547777 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
11547728 TTCTTTTCTA
11547738 TTTTTTTGTTTT
1 TTTTTTTGTTTT
11547750 TTTTTTTG-TTT
1 TTTTTTTGTTTT
11547761 TTTTTTTGTTTT
1 TTTTTTTGTTTT
11547773 TTTTT
1 TTTTT
11547778 GAATCTGAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (12 bp):
TTTTTTTGTTTT
Found at i:11547754 original size:11 final size:11
Alignment explanation
Indices: 11547738--11547777 Score: 71
Period size: 11 Copynumber: 3.5 Consensus size: 11
11547728 TTCTTTTCTA
11547738 TTTTTTTGTTTT
1 TTTTTTTG-TTT
11547750 TTTTTTTGTTT
1 TTTTTTTGTTT
11547761 TTTTTTTGTTT
1 TTTTTTTGTTT
11547772 TTTTTT
1 TTTTTT
11547778 GAATCTGAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:11551667 original size:17 final size:18
Alignment explanation
Indices: 11551624--11551670 Score: 62
Period size: 16 Copynumber: 2.7 Consensus size: 18
11551614 ATATGTGTAT
*
11551624 ATATATAAATATGAGAAAA
1 ATATAT-AATATGAAAAAA
11551643 ATAT-TAAT-TGAAAAAA
1 ATATATAATATGAAAAAA
11551659 ATATATAATATG
1 ATATATAATATG
11551671 TACATATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 11 0.44
17 7 0.28
18 3 0.12
19 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
ATATATAATATGAAAAAA
Found at i:11551746 original size:25 final size:25
Alignment explanation
Indices: 11551653--11551749 Score: 72
Period size: 25 Copynumber: 3.6 Consensus size: 25
11551643 ATATTAATTG
11551653 AAAAAAATAT-ATAATATGTACATATAT
1 AAAAAAA-ATGATAATA--TACATATAT
* * *
11551680 ATAAAAAATAATTATATACATATAT
1 AAAAAAAATGATAATATACATATAT
*
11551705 AGATTATAAAAACGATAAT-TACATATAT
1 A-A--A-AAAAATGATAATATACATATAT
11551733 ACAAAAAAATGATAATA
1 A-AAAAAAATGATAATA
11551750 ATTAAATTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
25 21 0.38
26 3 0.05
27 11 0.20
28 12 0.21
29 9 0.16
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (25 bp):
AAAAAAAATGATAATATACATATAT
Found at i:11553397 original size:12 final size:11
Alignment explanation
Indices: 11553374--11553407 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
11553364 TTTTATGCGT
*
11553374 AGAAAAAGAAA
1 AGAAAAAAAAA
11553385 AGAAAAACAAAA
1 AGAAAAA-AAAA
11553397 AGAAAAAAAAA
1 AGAAAAAAAAA
11553408 CCACGAATCG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.85, C:0.03, G:0.12, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:11553398 original size:17 final size:16
Alignment explanation
Indices: 11553376--11553408 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
11553366 TTATGCGTAG
11553376 AAAAAGAAAAGAAAAAC
1 AAAAAGAAAA-AAAAAC
11553393 AAAAAGAAAAAAAAAC
1 AAAAAGAAAAAAAAAC
11553409 CACGAATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAAC
Found at i:11579944 original size:45 final size:44
Alignment explanation
Indices: 11579894--11580077 Score: 246
Period size: 45 Copynumber: 4.1 Consensus size: 44
11579884 TAACGGTAGT
* *
11579894 AGTAACAGTATTCAACACACAAAGTGATGAATCTGTAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAACAGTAAC
* *
11579939 GGTAACAATATTCGACACACAAAGTGCCT-AATCGATAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTG-CTGAATCG-TAACAGTAAC
*
11579984 AGTAACAGTATTCGACACACAAAGTG-TCGAGTCGGTAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCT-GAATC-GTAACAGTAAC
*
11580029 AGTAACAGTATTCGACACACAAAGTGCCGAATCAGTAACAGTAAC
1 AGTAACAGTATTCGACACACAAAGTGCTGAATC-GTAACAGTAAC
11580074 AGTA
1 AGTA
11580078 GTCGGTACAT
Statistics
Matches: 123, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
43 1 0.01
44 1 0.01
45 119 0.97
46 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (44 bp):
AGTAACAGTATTCGACACACAAAGTGCTGAATCGTAACAGTAAC
Found at i:11580022 original size:90 final size:90
Alignment explanation
Indices: 11579878--11580077 Score: 287
Period size: 90 Copynumber: 2.2 Consensus size: 90
11579868 AGTATACAGT
* ** * *
11579878 AATCAGTAACGGTAGTAGTAACAGTATTCAACACACAAAGTGATGAATCTGTAACAGTAACGGTA
1 AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGATGAATCGGTAACAGTAACAGTA
*
11579943 ACAATATTCGACACACAAAGTGCCT
66 ACAATATTCGACACACAAAGTGCCG
* *
11579968 AATC-GATAACAGTAACAGTAACAGTATTCGACACACAAAGTG-TCGAGTCGGTAACAGTAACAG
1 AATCAG-TAACAGTAACAGTAACAGTATTCAACACACAAAGTGAT-GAATCGGTAACAGTAACAG
*
11580031 TAACAGTATTCGACACACAAAGTGCCG
64 TAACAATATTCGACACACAAAGTGCCG
11580058 AATCAGTAACAGTAACAGTA
1 AATCAGTAACAGTAACAGTA
11580078 GTCGGTACAT
Statistics
Matches: 98, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
89 2 0.02
90 95 0.97
91 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (90 bp):
AATCAGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGATGAATCGGTAACAGTAACAGTA
ACAATATTCGACACACAAAGTGCCG
Found at i:11580101 original size:38 final size:39
Alignment explanation
Indices: 11579932--11580104 Score: 125
Period size: 45 Copynumber: 4.2 Consensus size: 39
11579922 GAATCTGTAA
* * * *
11579932 CAGTAACGGTAACAATATTCGACACACAAAGTGCCTAATCGATAA
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTG-C----CGA-AT
*
11579977 CAGTAACAGTAACAGTATTCGACACACAAAGTGTCGAGTCGGTAA-
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTG-C----C-G-AAT
*
11580022 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAAT
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
** * *
11580061 CAGTAACAGTAACAGTAGTCGGTACA-TAAGTGCCTAAT
1 CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
11580099 CAGTAA
1 CAGTAA
11580105 GCCGGCAAAT
Statistics
Matches: 115, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
38 18 0.16
39 24 0.21
40 1 0.01
44 1 0.01
45 68 0.59
46 2 0.02
47 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.20
Consensus pattern (39 bp):
CAGTAACAGTAACAGTAGTCGACACACAAAGTGCCGAAT
Found at i:11587269 original size:24 final size:23
Alignment explanation
Indices: 11587210--11587263 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
11587200 AAAAATAAAA
11587210 TAAAAAATAATTCTTTATTTTTT
1 TAAAAAATAATTCTTTATTTTTT
11587233 TAAAAAATAATTCTTTATTTTTT
1 TAAAAAATAATTCTTTATTTTTT
*
11587256 TTAAAAAT
1 TAAAAAAT
11587264 GTATTCATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
TAAAAAATAATTCTTTATTTTTT
Found at i:11587786 original size:29 final size:28
Alignment explanation
Indices: 11587709--11587786 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
11587699 ACAATTAGAT
*
11587709 CTAAATTTTTAAATAAAAAATAAAAAGA
1 CTAAATTTTAAAATAAAAAATAAAAAGA
* **
11587737 CTACATTCTTAAAA-ATAAAAATACGAAGA
1 CTAAATT-TTAAAATA-AAAAATAAAAAGA
11587766 CTAAATTTTAAATATAAAAAA
1 CTAAATTTTAAA-ATAAAAAA
11587787 ATAATCACCT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
28 12 0.29
29 28 0.68
30 1 0.02
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (28 bp):
CTAAATTTTAAAATAAAAAATAAAAAGA
Found at i:11588655 original size:25 final size:24
Alignment explanation
Indices: 11588627--11588679 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
11588617 AAATAATATT
*
11588627 ATTTTAAGAAAATGTATTAGTAAAA
1 ATTTTAAGAAAATGGATTAG-AAAA
* *
11588652 ATTTTAAGGAAATGGATTAGAATA
1 ATTTTAAGAAAATGGATTAGAAAA
11588676 ATTT
1 ATTT
11588680 AATATTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.47, C:0.00, G:0.15, T:0.38
Consensus pattern (24 bp):
ATTTTAAGAAAATGGATTAGAAAA
Found at i:11589359 original size:4 final size:4
Alignment explanation
Indices: 11589350--11589374 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
11589340 TTGTTATTGA
11589350 GTAT GTAT GTAT GTAT GTAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT G
11589375 CAAACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:11592957 original size:50 final size:50
Alignment explanation
Indices: 11592829--11593118 Score: 296
Period size: 50 Copynumber: 5.7 Consensus size: 50
11592819 ATTTGGGTAA
*
11592829 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAAATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--G--A-CATG
* * * * * *
11592885 AGAGGGCCTATGGAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * *
11592935 AGGGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** * * *
11592985 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** * * *
11593035 AGAACTCCCATGTAAGACCATATCTGGAATATGGCATTGGCA--GTACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-ACATG
* **
11593084 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
11593119 TTTAGCATGT
Statistics
Matches: 198, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
48 1 0.01
49 32 0.16
50 125 0.63
51 1 0.01
53 1 0.01
55 2 0.01
56 36 0.18
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:11595601 original size:17 final size:17
Alignment explanation
Indices: 11595579--11595616 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
11595569 AAGATGTAAG
11595579 AAGCTTCTTTCGTGTTT
1 AAGCTTCTTTCGTGTTT
11595596 AAGCTTCTTTCGTGTTT
1 AAGCTTCTTTCGTGTTT
11595613 AAGC
1 AAGC
11595617 CACTACCCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.16, C:0.18, G:0.18, T:0.47
Consensus pattern (17 bp):
AAGCTTCTTTCGTGTTT
Found at i:11611898 original size:27 final size:25
Alignment explanation
Indices: 11611849--11611945 Score: 76
Period size: 26 Copynumber: 3.8 Consensus size: 25
11611839 TTAATCCTTT
*
11611849 AATTTGTTATTTATTTATTTTGTTTA
1 AATTT-TTATATATTTATTTTGTTTA
11611875 AATTTTTATATATATTATTATTG-TTA
1 AATTTTTATATAT-TTATT-TTGTTTA
* *
11611901 ACA-GTTTACAT-TTTATTTAT-TTTA
1 A-ATTTTTATATATTTATTT-TGTTTA
11611925 AATTTTATATATATATTATTT
1 AATTTT-TATATAT-TTATTT
11611946 ATATTAAACT
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
23 2 0.04
24 12 0.21
25 12 0.21
26 21 0.37
27 10 0.18
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (25 bp):
AATTTTTATATATTTATTTTGTTTA
Found at i:11611973 original size:51 final size:52
Alignment explanation
Indices: 11611871--11612001 Score: 153
Period size: 52 Copynumber: 2.5 Consensus size: 52
11611861 ATTTATTTTG
* * *
11611871 TTTAAATTTTTATATATATTA-TTATTGTTAACAGTTTACATTTTATTTA-T
1 TTTAAATTTTTATATATATTATTTATTGTAAACAGTTTACATATTATCTATT
* *
11611921 TTTAAATTTTATATATATATTATTTATAT-TAAACTGTTT-GATATTATCTATT
1 TTTAAATTTT-TATATATATTATTTAT-TGTAAACAGTTTACATATTATCTATT
11611973 TTTAAATTGTTTCATATATATTATTTATT
1 TTTAAATT-TTT-ATATATATTATTTATT
11612002 TTGAGTTGCT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
50 10 0.14
51 19 0.27
52 23 0.33
53 18 0.26
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (52 bp):
TTTAAATTTTTATATATATTATTTATTGTAAACAGTTTACATATTATCTATT
Found at i:11611983 original size:25 final size:25
Alignment explanation
Indices: 11611933--11611998 Score: 71
Period size: 25 Copynumber: 2.5 Consensus size: 25
11611923 TAAATTTTAT
*
11611933 ATATATATTATTTATATTAAACTGTTTG
1 ATATATATTA-TT-T-TTAAACTGTTTC
*
11611961 ATAT-TATCTATTTTTAAATTGTTTC
1 ATATATAT-TATTTTTAAACTGTTTC
11611986 ATATATATTATTT
1 ATATATATTATTT
11611999 ATTTTGAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
25 19 0.56
26 4 0.12
27 5 0.15
28 6 0.18
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.58
Consensus pattern (25 bp):
ATATATATTATTTTTAAACTGTTTC
Found at i:11612023 original size:26 final size:26
Alignment explanation
Indices: 11611974--11612053 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
11611964 TTATCTATTT
*
11611974 TTAAATTG-TTTCATATATATTATTTATT
1 TTAAATTGCTTT-ATA-A-ATTATTTATC
* * *
11612002 TTGAGTTGCTTTATACATTATTTTATC
1 TTAAATTGCTTTATAAATTA-TTTATC
*
11612029 TTAAATTGTTTTATAAATTATTTAT
1 TTAAATTGCTTTATAAATTATTTAT
11612054 ATTAGATTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
26 9 0.21
27 21 0.50
28 9 0.21
29 3 0.07
ACGTcount: A:0.30, C:0.05, G:0.06, T:0.59
Consensus pattern (26 bp):
TTAAATTGCTTTATAAATTATTTATC
Found at i:11612071 original size:106 final size:106
Alignment explanation
Indices: 11611907--11612117 Score: 234
Period size: 106 Copynumber: 2.0 Consensus size: 106
11611897 GTTAACAGTT
* * *
11611907 TACATTTTATTTATTTTAAATTTTATATATATATTATTTATATTAAACTGTTTGATATTATCTA-
1 TACATTATATTTATCTTAAATTTTATATATAAATTATTTATATTAAACTGTTTGATATT-T-TAT
* * *
11611971 T-TTTTAAATTGTTTCATATATATTATTTATTTTGAGTTGCTTTA
64 TCTTTTAAATTCTTT--TATATATTATTTATTTTAAATTGCTTTA
* * * *
11612015 TACATTAT-TTTATCTTAAATTGTT-T-TATAAATTATTTATATTAGATTTTTTTATATTTTATT
1 TACATTATATTTATCTTAAATT-TTATATATAAATTATTTATATTAAACTGTTTGATATTTTATT
* *
11612077 CTTTTAAATTCTTTTATGTATTGTTTATTTTAAATTGCTTT
65 CTTTTAAATTCTTTTATATATTATTTATTTTAAATTGCTTT
11612118 GAATTATTTA
Statistics
Matches: 88, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
104 25 0.28
105 2 0.02
106 39 0.44
107 13 0.15
108 9 0.10
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (106 bp):
TACATTATATTTATCTTAAATTTTATATATAAATTATTTATATTAAACTGTTTGATATTTTATTC
TTTTAAATTCTTTTATATATTATTTATTTTAAATTGCTTTA
Found at i:11612075 original size:26 final size:26
Alignment explanation
Indices: 11611913--11612113 Score: 106
Period size: 26 Copynumber: 7.7 Consensus size: 26
11611903 AGTTTACATT
* *
11611913 TTATTTATTTTAAATT-TTATATATATA
1 TTATTTATATTAAATTGTT-T-TATAAA
* *
11611940 TTATTTATATTAAACTGTTTGAT--A
1 TTATTTATATTAAATTGTTTTATAAA
* * *
11611964 TTATCTATTTTTAAATTGTTTCATATATA
1 TTATTTA-TATTAAATTGTTT--TATAAA
* * * * *
11611993 TTATTTATTTTGAGTTGCTTTATACA
1 TTATTTATATTAAATTGTTTTATAAA
*
11612019 TTATTTTATCTTAAATTGTTTTATAAA
1 TTA-TTTATATTAAATTGTTTTATAAA
* * **
11612046 TTATTTATATTAGATTTTTTTATATT
1 TTATTTATATTAAATTGTTTTATAAA
* **
11612072 TTATTCT-T-TTAAATTCTTTTATGTA
1 TTATT-TATATTAAATTGTTTTATAAA
* *
11612097 TTGTTTATTTTAAATTG
1 TTATTTATATTAAATTG
11612114 CTTTGAATTA
Statistics
Matches: 136, Mismatches: 28, Indels: 21
0.74 0.15 0.11
Matches are distributed among these distances:
24 8 0.06
25 29 0.21
26 41 0.30
27 39 0.29
28 12 0.09
29 7 0.05
ACGTcount: A:0.29, C:0.04, G:0.05, T:0.61
Consensus pattern (26 bp):
TTATTTATATTAAATTGTTTTATAAA
Found at i:11612076 original size:53 final size:52
Alignment explanation
Indices: 11611862--11612113 Score: 178
Period size: 53 Copynumber: 4.8 Consensus size: 52
11611852 TTGTTATTTA
* ** *
11611862 TTTATTTTGTTTAAATT-TTTATATATATTA-TTATTGTTA-ACAG-TTTACAT
1 TTTATTTT-TTTAAATTGTTTATATATATTATTTA-TATTAGATTGTTTTATAT
* * *
11611912 TTTATTTATTTTAAATT-TTATATATATATTATTTATATTAAACTGTTTGATAT
1 TTTATTT-TTTTAAATTGTT-TATATATATTATTTATATTAGATTGTTTTATAT
* * * * * *
11611965 TATCTATTTTTAAATTGTTTCATATATATTATTTAT-TTTGAGTTGCTTTATAC
1 TTTATTTTTTTAAATTGTTT-ATATATATTATTTATATTAGA-TTGTTTTATAT
* * *
11612018 ATTATTTTATCTTAAATTGTTT-TATAAATTATTTATATTAGATTTTTTTATAT
1 TTTATTTT-T-TTAAATTGTTTATATATATTATTTATATTAGATTGTTTTATAT
* * * * * *
11612071 TTTATTCTTTTAAATTCTTT-TATGTATTGTTTATTTTAAATTG
1 TTTATTTTTTTAAATTGTTTATATATATTATTTATATTAGATTG
11612114 CTTTGAATTA
Statistics
Matches: 160, Mismatches: 31, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
50 17 0.11
51 43 0.27
52 20 0.12
53 64 0.40
54 5 0.03
55 11 0.07
ACGTcount: A:0.29, C:0.04, G:0.06, T:0.61
Consensus pattern (52 bp):
TTTATTTTTTTAAATTGTTTATATATATTATTTATATTAGATTGTTTTATAT
Found at i:11620378 original size:61 final size:61
Alignment explanation
Indices: 11620278--11620394 Score: 191
Period size: 61 Copynumber: 1.9 Consensus size: 61
11620268 ATGCAAATTC
*
11620278 TGTAACACTCCTTACCCGAGACCGTCGCCGGAATCGAGTACGAGATGCTATCCAATCTAAA
1 TGTAACACTCCTTACCCGAGACCGTCACCGGAATCGAGTACGAGATGCTATCCAATCTAAA
* *
11620339 TGTAACAGC-CCTTACCCGAGACCGTCACCGGAATTGAGTACGAGATGTTATCCAAT
1 TGTAACA-CTCCTTACCCGAGACCGTCACCGGAATCGAGTACGAGATGCTATCCAAT
11620395 TTAACTTACC
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 51 0.98
62 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (61 bp):
TGTAACACTCCTTACCCGAGACCGTCACCGGAATCGAGTACGAGATGCTATCCAATCTAAA
Found at i:11625670 original size:34 final size:35
Alignment explanation
Indices: 11625615--11625681 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11625605 CAAACACCAG
*
11625615 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
11625650 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11625682 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11626995 original size:19 final size:20
Alignment explanation
Indices: 11626960--11627001 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
11626950 ATAATTGATA
11626960 TATTAATAAATAAATAA-AT
1 TATTAATAAATAAATAATAT
*
11626979 TATTAACTAAA-ATATAATAT
1 TATTAA-TAAATAAATAATAT
11626999 TAT
1 TAT
11627002 AATTGTAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
TATTAATAAATAAATAATAT
Found at i:11627980 original size:15 final size:16
Alignment explanation
Indices: 11627960--11627993 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11627950 ATTGAAAATA
11627960 TTAA-TTTTCAATGAT
1 TTAATTTTTCAATGAT
*
11627975 TTAATTTTTCAATGGT
1 TTAATTTTTCAATGAT
11627991 TTA
1 TTA
11627994 CCAATGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.56
Consensus pattern (16 bp):
TTAATTTTTCAATGAT
Found at i:11628632 original size:36 final size:36
Alignment explanation
Indices: 11628533--11628611 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
11628523 TAACAATAAT
* *
11628533 TTTA-AATAATATTATTAAT-ATA-TA-TTAAAAATA
1 TTTATAATAATATT-TTAATAATACAATTTATAAATA
*
11628566 TTTATATTAATATTTTAATAATACAATTTATAAATA
1 TTTATAATAATATTTTAATAATACAATTTATAAATA
11628602 TTTATAATAA
1 TTTATAATAA
11628612 ATCTTTTATA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
33 9 0.24
34 11 0.29
35 1 0.03
36 17 0.45
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (36 bp):
TTTATAATAATATTTTAATAATACAATTTATAAATA
Found at i:11630584 original size:2 final size:2
Alignment explanation
Indices: 11630577--11630619 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
11630567 TACTAAGGAG
11630577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11630619 A
1 A
11630620 AAGTGTTGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:11630939 original size:65 final size:66
Alignment explanation
Indices: 11630870--11631007 Score: 217
Period size: 66 Copynumber: 2.1 Consensus size: 66
11630860 TCAAGATTAA
* *
11630870 AATTTTAAAATTC-AAAAAATTAGTGACTTGGAATGATCTAATA-AGAGAATATGAGCTAAATCT
1 AATTTTAAAATTCGAAAAAATTAGAGACTTCGAATGATCTAATAGA-AGAATATGAGCTAAATCT
11630933 TC
65 TC
* *
11630935 AATTTTAAAATTCGAAAAATTTAGAGACTTCGAATGATCTAATTGAAGAATATGAGCTAAATCTT
1 AATTTTAAAATTCGAAAAAATTAGAGACTTCGAATGATCTAATAGAAGAATATGAGCTAAATCTT
11631000 C
66 C
11631001 AATTTTA
1 AATTTTA
11631008 CTGTAACACC
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
65 13 0.19
66 53 0.79
67 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.34
Consensus pattern (66 bp):
AATTTTAAAATTCGAAAAAATTAGAGACTTCGAATGATCTAATAGAAGAATATGAGCTAAATCTT
C
Found at i:11633430 original size:25 final size:24
Alignment explanation
Indices: 11633398--11633445 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
11633388 CAAGCCCTCT
11633398 CAAGCTTCCCGTTATAGTGCTCTTG
1 CAAGCTTCCCGTTA-AGTGCTCTTG
*
11633423 CAAGCTTCCCGTTAATTGCTCTT
1 CAAGCTTCCCGTTAAGTGCTCTT
11633446 CTGAGAATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.17, C:0.29, G:0.17, T:0.38
Consensus pattern (24 bp):
CAAGCTTCCCGTTAAGTGCTCTTG
Found at i:11633602 original size:24 final size:25
Alignment explanation
Indices: 11633560--11633607 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
11633550 TCCGGTGCTC
* *
11633560 TCTGTTAAAGTGCTTTTCGGAGCTT
1 TCTGTTAAAGTACTCTTCGGAGCTT
11633585 TCTGTT-AAGTACTCTTCGGAGCT
1 TCTGTTAAAGTACTCTTCGGAGCT
11633608 ACCCGATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.42
Consensus pattern (25 bp):
TCTGTTAAAGTACTCTTCGGAGCTT
Found at i:11636422 original size:20 final size:20
Alignment explanation
Indices: 11636397--11636484 Score: 72
Period size: 20 Copynumber: 4.4 Consensus size: 20
11636387 AGATGCAAAA
*
11636397 CAGGGGCACTAAAGTGCAAT
1 CAGGGGCACTAAAGTGCATT
* **
11636417 CAGGGGCATTGGAGTGCATT
1 CAGGGGCACTAAAGTGCATT
*
11636437 CAGGGGCA-TGAATGTGC-TGT
1 CAGGGGCACT-AAAGTGCAT-T
* *
11636457 CAGGGGCACCAGAGTGCATT
1 CAGGGGCACTAAAGTGCATT
*
11636477 TAGGGGCA
1 CAGGGGCA
11636485 TAGTTGTGCA
Statistics
Matches: 53, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.04
20 50 0.94
21 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.19
Consensus pattern (20 bp):
CAGGGGCACTAAAGTGCATT
Found at i:11636441 original size:40 final size:40
Alignment explanation
Indices: 11636397--11636485 Score: 99
Period size: 40 Copynumber: 2.2 Consensus size: 40
11636387 AGATGCAAAA
***
11636397 CAGGGGCACT-AAAGTGCAATCAGGGGCATTGGAGTGCATT
1 CAGGGGCA-TGAAAGTGCAATCAGGGGCACCAGAGTGCATT
* **
11636437 CAGGGGCATGAATGTGCTGTCAGGGGCACCAGAGTGCATT
1 CAGGGGCATGAAAGTGCAATCAGGGGCACCAGAGTGCATT
*
11636477 TAGGGGCAT
1 CAGGGGCAT
11636486 AGTTGTGCAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.02
40 40 0.98
ACGTcount: A:0.25, C:0.18, G:0.37, T:0.20
Consensus pattern (40 bp):
CAGGGGCATGAAAGTGCAATCAGGGGCACCAGAGTGCATT
Found at i:11640311 original size:124 final size:126
Alignment explanation
Indices: 11639994--11640345 Score: 548
Period size: 126 Copynumber: 2.8 Consensus size: 126
11639984 TAATTTCGAG
** *
11639994 TTGACGTTTCTGATAAAATAATATAAAATCGCTTCTAGCAGGATGATATTTGAGAAGAATTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* *
11640059 AAATCGAGCCCTCGTGGACGCGCTTCTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* *
11640120 TTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAACTTGTG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
* * * * *
11640185 AAATTGCGGCCTCGT-CAGCGCGCTTTTGCTACAGTAGGTCATGTAAGAAATAA-T-TTTTT
66 AAATCGCGCCCTCGTGGA-CGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
* *
11640244 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTCAGAAGAATTTATG
1 TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
11640309 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
66 AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
11640346 CATGTTTGGG
Statistics
Matches: 205, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
124 98 0.48
125 3 0.01
126 104 0.51
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (126 bp):
TTGACGTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTG
AAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTT
Found at i:11643384 original size:43 final size:43
Alignment explanation
Indices: 11643337--11643647 Score: 222
Period size: 43 Copynumber: 7.3 Consensus size: 43
11643327 GCGCCGGAGA
*
11643337 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCGC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCAC
* * * *
11643380 AAACGCCGTTAAATG-CTAAGACCTTTA-CGGCGCTTCT-CCAGC
1 AAACGCCGCTAAA-GACCAAGACCTTTAGCAGCGCTTTTCCCA-C
* * * *
11643422 AAACGCCGCTATAGACCACGCCCTTTAGCAACGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCAC
* * * * * * * **
11643465 AAACGCTGTTATAGACCACGATCTTTAGCGGCGTTTTTAGCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCAC
* * * * **
11643508 AAACGCCGCTATAGACCATGACTTTTAGCGGCGCTTTTAGCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCAC
* * * **
11643551 AAACGCCGCCAAAGATCATA-ATCTTTAGC-GACGCTTTTATCAC
1 AAACGCCGCTAAAGACCA-AGACCTTTAGCAG-CGCTTTTCCCAC
* * * ** *
11643594 AAACGCCGCTAAAAAAC-A-ACCTTTAGCAGCACTTTTCGTAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCAC
11643635 AAACGCCGCTAAA
1 AAACGCCGCTAAA
11643648 AATATAACCT
Statistics
Matches: 216, Mismatches: 44, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
41 32 0.15
42 31 0.14
43 149 0.69
44 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCAC
Found at i:11643536 original size:86 final size:86
Alignment explanation
Indices: 11643337--11643630 Score: 276
Period size: 86 Copynumber: 3.5 Consensus size: 86
11643327 GCGCCGGAGA
* * *
11643337 AAACGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTCCCGCAAACGCCGTTAAATG-CTAAGA
1 AAACGCCGCTATAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGTTAAA-GACCAAGA
* *
11643401 CCTTTA-CGGCGCTTCT-CCAGC
65 TCTTTAGCGGCGCTTTTACCA-C
* * * * * *
11643422 AAACGCCGCTATAGACCACGCCCTTTAGCAACGCTTTTCCCACAAACGCTGTTATAGACCACGAT
1 AAACGCCGCTATAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGTTAAAGACCAAGAT
* *
11643487 CTTTAGCGGCGTTTTTAGCAC
66 CTTTAGCGGCGCTTTTACCAC
* * * ** ** *
11643508 AAACGCCGCTATAGACCATGACTTTTAGCGGCGCTTTTAGCACAAACGCCGCCAAAGATCATA-A
1 AAACGCCGCTATAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGTTAAAGACCA-AGA
* *
11643572 TCTTTAGCGACGCTTTTATCAC
65 TCTTTAGCGGCGCTTTTACCAC
* * * *
11643594 AAACGCCGCTAAAAAAC-A-ACCTTTAGCAGCACTTTTC
1 AAACGCCGCTATAGACCAAGACCTTTAGCAGCGCTTTTC
11643631 GTAAAAACGC
Statistics
Matches: 168, Mismatches: 37, Indels: 9
0.79 0.17 0.04
Matches are distributed among these distances:
84 16 0.10
85 58 0.35
86 92 0.55
87 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.24
Consensus pattern (86 bp):
AAACGCCGCTATAGACCAAGACCTTTAGCAGCGCTTTTCCCACAAACGCCGTTAAAGACCAAGAT
CTTTAGCGGCGCTTTTACCAC
Found at i:11647175 original size:16 final size:16
Alignment explanation
Indices: 11647154--11647188 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
11647144 AATAAGAAAG
* *
11647154 CAGCATGTATAAATAC
1 CAGCATATATAAAGAC
11647170 CAGCATATATAAAGAC
1 CAGCATATATAAAGAC
11647186 CAG
1 CAG
11647189 AACCTGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.20, G:0.14, T:0.20
Consensus pattern (16 bp):
CAGCATATATAAAGAC
Found at i:11647992 original size:20 final size:21
Alignment explanation
Indices: 11647963--11648007 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
11647953 AAATTATAAA
*
11647963 TTTTAGTTTTTTTATTTTATT
1 TTTTAGTTTTTGTATTTTATT
11647984 TTTTA-TTTTTGTATTTTATT
1 TTTTAGTTTTTGTATTTTATT
11648004 TTTT
1 TTTT
11648008 CTTATAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.82
Consensus pattern (21 bp):
TTTTAGTTTTTGTATTTTATT
Found at i:11648006 original size:13 final size:11
Alignment explanation
Indices: 11647969--11648007 Score: 51
Period size: 12 Copynumber: 3.3 Consensus size: 11
11647959 TAAATTTTAG
11647969 TTTTTTTATTT
1 TTTTTTTATTT
11647980 TATTTTTTATTT
1 T-TTTTTTATTT
11647992 TTGTATTTTATTT
1 TT-T-TTTTATTT
11648005 TTT
1 TTT
11648008 CTTATAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 2 0.08
12 13 0.52
13 10 0.40
ACGTcount: A:0.13, C:0.00, G:0.03, T:0.85
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:11648374 original size:7 final size:7
Alignment explanation
Indices: 11648364--11648401 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
11648354 CTCTAACTCT
11648364 TAACCCC
1 TAACCCC
11648371 TAACCCC
1 TAACCCC
*
11648378 TAACCCT
1 TAACCCC
*
11648385 TTACCCC
1 TAACCCC
11648392 TAACCCC
1 TAACCCC
11648399 TAA
1 TAA
11648402 ATCTCAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.50, G:0.00, T:0.21
Consensus pattern (7 bp):
TAACCCC
Found at i:11648380 original size:21 final size:21
Alignment explanation
Indices: 11648356--11648401 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
11648346 CCCTAAATCT
*
11648356 CTAACTCTTAACCCCTAACCC
1 CTAACCCTTAACCCCTAACCC
*
11648377 CTAACCCTTTACCCCTAACCC
1 CTAACCCTTAACCCCTAACCC
11648398 CTAA
1 CTAA
11648402 ATCTCAAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.28, C:0.48, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACCCTTAACCCCTAACCC
Found at i:11648637 original size:26 final size:24
Alignment explanation
Indices: 11648591--11648646 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 24
11648581 TATATGAAAT
11648591 TATTTAATATATAAATTAAAAACA
1 TATTTAATATATAAATTAAAAACA
*
11648615 TATTTAGA-ATATAAATTAAAAAAA
1 TATTTA-ATATATAAATTAAAAACA
*
11648639 TAATTAAT
1 TATTTAAT
11648647 CTAAACCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 1 0.04
24 26 0.93
25 1 0.04
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
TATTTAATATATAAATTAAAAACA
Found at i:11648750 original size:21 final size:21
Alignment explanation
Indices: 11648720--11648800 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
11648710 ACAAACCCCT
11648720 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCTTAAATCCC
* *
11648741 AACCCTTAAACCAT-AATCCC
1 AACCCCTAAACCTTAAATCCC
* * * *
11648761 TAATCCATAATCCCTAAAT-CC
1 -AACCCCTAAACCTTAAATCCC
11648782 ATACTCCCTAAACCTTAAA
1 A-AC-CCCTAAACCTTAAA
11648801 ATAGTAATGT
Statistics
Matches: 46, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
20 7 0.15
21 25 0.54
22 14 0.30
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCCCTAAACCTTAAATCCC
Found at i:11648768 original size:14 final size:14
Alignment explanation
Indices: 11648751--11648792 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
11648741 AACCCTTAAA
11648751 CCATAATCCCTAAT
1 CCATAATCCCTAAT
11648765 CCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
11648780 CCATACTCCCTAA
1 CCATAATCCCTAA
11648793 ACCTTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 13 0.50
15 13 0.50
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:11648780 original size:15 final size:15
Alignment explanation
Indices: 11648747--11648793 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
11648737 TCCCAACCCT
11648747 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
11648761 T-AATCCATAATCCC
1 TAAATCCATAATCCC
*
11648775 TAAATCCATACTCCC
1 TAAATCCATAATCCC
11648790 TAAA
1 TAAA
11648794 CCTTAAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 2 0.07
14 12 0.40
15 16 0.53
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:11649421 original size:19 final size:19
Alignment explanation
Indices: 11649367--11649439 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
11649357 ACGATTTAAA
* *
11649367 AAACACGGAAATTTTTTTT
1 AAACACAGAAATTTTTTTG
* *
11649386 AAAAACACG-AATATTTTTG
1 AAACACA-GAAATTTTTTTG
11649405 AAACACAGAAA-TTTTTTG
1 AAACACAGAAATTTTTTTG
*
11649423 AAAACACGAAAAATTTT
1 -AAACAC-AGAAATTTT
11649440 GAAAAAATGG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
18 7 0.17
19 27 0.64
20 5 0.12
21 3 0.07
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.33
Consensus pattern (19 bp):
AAACACAGAAATTTTTTTG
Found at i:11649439 original size:18 final size:18
Alignment explanation
Indices: 11649241--11649444 Score: 124
Period size: 18 Copynumber: 11.6 Consensus size: 18
11649231 ACGAAAGTTT
* *
11649241 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
11649259 TTTTTGAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
11649277 --TTTGTAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* *
11649293 TTTTAG-AAACGCGAAAA
1 TTTTTGAAAACACGAAAA
*
11649310 TTTTTAGAAGA-ACGAAAA
1 TTTTT-GAAAACACGAAAA
**
11649328 TTTTT-AAAACACGACATTT
1 TTTTTGAAAACACGA-A-AA
11649347 TTTTTG-AAACACG---A
1 TTTTTGAAAACACGAAAA
** *
11649361 -TTTAAAAAACACGGAAATTT
1 TTTTTGAAAACAC-GAAA--A
* *
11649381 TTTTTAAAAACACGAATA
1 TTTTTGAAAACACGAAAA
*
11649399 TTTTTG-AAACACAGAAAT
1 TTTTTGAAAACAC-GAAAA
11649417 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
11649435 ATTTTGAAAA
1 TTTTTGAAAA
11649445 AATGGAATTT
Statistics
Matches: 145, Mismatches: 23, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
13 3 0.02
14 6 0.04
15 1 0.01
16 17 0.12
17 24 0.17
18 60 0.41
19 20 0.14
20 3 0.02
21 11 0.08
ACGTcount: A:0.46, C:0.11, G:0.12, T:0.31
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:11649461 original size:21 final size:22
Alignment explanation
Indices: 11649435--11649476 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
11649425 AACACGAAAA
11649435 ATTTTGAAAAAATG-GAATTTT
1 ATTTTGAAAAAATGAGAATTTT
*
11649456 ATTTTGAAAACATGAGAATTT
1 ATTTTGAAAAAATGAGAATTT
11649477 CGAAAGACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (22 bp):
ATTTTGAAAAAATGAGAATTTT
Found at i:11649802 original size:19 final size:18
Alignment explanation
Indices: 11649748--11649802 Score: 56
Period size: 21 Copynumber: 2.8 Consensus size: 18
11649738 AACACGAAAA
*
11649748 TTTGAAATACGTAAATTTT
1 TTTGAAACACG-AAATTTT
11649767 TTTGAAAACACGGGAAATTTTT
1 TTTG-AAACAC--GAAA-TTTT
11649789 TTTGAAACACGAAA
1 TTTGAAACACGAAA
11649803 ACATGAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
19 8 0.26
20 5 0.16
21 9 0.29
22 9 0.29
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (18 bp):
TTTGAAACACGAAATTTT
Found at i:11649821 original size:17 final size:17
Alignment explanation
Indices: 11649799--11649914 Score: 85
Period size: 17 Copynumber: 6.6 Consensus size: 17
11649789 TTTGAAACAC
11649799 GAAAACATGAAAATTTT
1 GAAAACATGAAAATTTT
* *
11649816 GAAAACACGGAAATTTTTTT
1 GAAAACA-TGAAA--ATTTT
*
11649836 GAAAACACGAAAATTTTT
1 GAAAACATGAAAA-TTTT
*
11649854 G-AAACATGAGAAGTTTTT
1 GAAAACATGA-AA-ATTTT
* *
11649872 G-ACAC-TAAAAATTTT
1 GAAAACATGAAAATTTT
* *
11649887 GAAAACACGAAAATTTC
1 GAAAACATGAAAATTTT
11649904 GAAAACATGAA
1 GAAAACATGAA
11649915 TTTTTTTTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
15 5 0.06
16 5 0.06
17 33 0.43
18 19 0.25
19 4 0.05
20 11 0.14
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (17 bp):
GAAAACATGAAAATTTT
Found at i:11649833 original size:18 final size:18
Alignment explanation
Indices: 11649807--11649857 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 18
11649797 ACGAAAACAT
*
11649807 GAAAATTTTGAAAACACG
1 GAAATTTTTGAAAACACG
11649825 GAAATTTTTTTGAAAACACG
1 GAAA--TTTTTGAAAACACG
*
11649845 AAAATTTTTGAAA
1 GAAATTTTTGAAA
11649858 CATGAGAAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 13 0.45
20 16 0.55
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (18 bp):
GAAATTTTTGAAAACACG
Found at i:11649991 original size:17 final size:18
Alignment explanation
Indices: 11649977--11650015 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
11649967 ACGAAAACAT
11649977 AAAAATTTTGAAAACACG
1 AAAAATTTTGAAAACACG
*
11649995 AAAATTTTTG-AAACACG
1 AAAAATTTTGAAAACACG
11650012 AAAA
1 AAAA
11650016 CACGAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.23
Consensus pattern (18 bp):
AAAAATTTTGAAAACACG
Found at i:11650003 original size:18 final size:18
Alignment explanation
Indices: 11649799--11650015 Score: 115
Period size: 18 Copynumber: 11.7 Consensus size: 18
11649789 TTTGAAACAC
*
11649799 GAAAACATGAAAA-TTTT
1 GAAAACACGAAAATTTTT
*
11649816 GAAAACACGGAAATTTTTTT
1 GAAAACAC-GAAA-ATTTTT
11649836 GAAAACACGAAAATTTTT
1 GAAAACACGAAAATTTTT
* *
11649854 G-AAACATGAGAAGTTTTT
1 GAAAACACGA-AAATTTTT
* *
11649872 G---ACACTAAAAATTTT
1 GAAAACACGAAAATTTTT
*
11649887 GAAAACACGAAAA-TTTC
1 GAAAACACGAAAATTTTT
* **
11649904 GAAAACATGAATTTTTTT
1 GAAAACACGAAAATTTTT
** * ***
11649922 TTAAATACGATTTTTTTTT
1 GAAAACACGA-AAATTTTT
*
11649941 AAAAACACGAGAAAGTTTTT
1 GAAAACACGA-AAA-TTTTT
11649961 GAAAACACGAAAACATAAAAATTTT
1 GAAAACACG-AAA-AT-----TTTT
11649986 GAAAACACGAAAATTTTT
1 GAAAACACGAAAATTTTT
11650004 G-AAACACGAAAA
1 GAAAACACGAAAA
11650016 CACGAAAATT
Statistics
Matches: 155, Mismatches: 28, Indels: 34
0.71 0.13 0.16
Matches are distributed among these distances:
15 7 0.05
16 4 0.03
17 38 0.25
18 40 0.26
19 18 0.12
20 28 0.18
21 2 0.01
23 2 0.01
24 3 0.02
25 13 0.08
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.30
Consensus pattern (18 bp):
GAAAACACGAAAATTTTT
Found at i:11650036 original size:45 final size:45
Alignment explanation
Indices: 11649933--11650060 Score: 145
Period size: 45 Copynumber: 2.8 Consensus size: 45
11649923 TAAATACGAT
*
11649933 TTTTTTTTAAAAACACGAGAAAGTTTTTGAAAACACGAAAACATAAAA
1 TTTTTTTT-AAAACACGA-AAA-TTTTTGAAAACACGAAAACAGAAAA
* *
11649981 --ATTTTGAAAACACGAAAATTTTTG-AAACACGAAAACACGAAAA
1 TTTTTTTTAAAACACGAAAATTTTTGAAAACACGAAAACA-GAAAA
***
11650024 TTTTTTTTAAAACACGGGGATTTTTGAAAACACGAAA
1 TTTTTTTTAAAACACGAAAATTTTTGAAAACACGAAA
11650061 TTTTTTTATT
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
42 13 0.19
43 10 0.15
44 3 0.04
45 28 0.41
46 14 0.21
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (45 bp):
TTTTTTTTAAAACACGAAAATTTTTGAAAACACGAAAACAGAAAA
Found at i:11650063 original size:17 final size:17
Alignment explanation
Indices: 11650011--11650099 Score: 54
Period size: 18 Copynumber: 5.0 Consensus size: 17
11650001 TTTGAAACAC
11650011 GAAAACACGAAAATTTTTTT
1 GAAAACACG-AAA--TTTTT
* **
11650031 TAAAACACGGGGATTTTT
1 GAAAACAC-GAAATTTTT
11650049 GAAAACACGAAATTTTT
1 GAAAACACGAAATTTTT
** **
11650066 TTATTCACGAAAATTTTT
1 GAAAACACG-AAATTTTT
*
11650084 G-AAACACGGAATTTTT
1 GAAAACACGAAATTTTT
11650100 TTTAAAGAAA
Statistics
Matches: 53, Mismatches: 14, Indels: 8
0.71 0.19 0.11
Matches are distributed among these distances:
16 7 0.13
17 17 0.32
18 20 0.38
20 8 0.15
21 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (17 bp):
GAAAACACGAAATTTTT
Found at i:11650065 original size:18 final size:18
Alignment explanation
Indices: 11650011--11650100 Score: 60
Period size: 17 Copynumber: 5.0 Consensus size: 18
11650001 TTTGAAACAC
11650011 GAAAACACGAAAATTTTTTT
1 GAAAACACG-AAA-TTTTTT
* **
11650031 TAAAACACGGGGA-TTTTT
1 GAAAACAC-GAAATTTTTT
11650049 GAAAACACGAAATTTTTT
1 GAAAACACGAAATTTTTT
* ** *
11650067 -TATTCACGAAAATTTTT
1 GAAAACACGAAATTTTTT
*
11650084 G-AAACACGGAATTTTTT
1 GAAAACACGAAATTTTTT
11650101 TTAAAGAAAG
Statistics
Matches: 53, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
17 27 0.51
18 17 0.32
20 8 0.15
21 1 0.02
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (18 bp):
GAAAACACGAAATTTTTT
Found at i:11650067 original size:20 final size:20
Alignment explanation
Indices: 11650011--11650067 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
11650001 TTTGAAACAC
11650011 GAAAACACGAAAATTTTTTTT
1 GAAAACACG-AAATTTTTTTT
**
11650032 -AAAACACGGGGA---TTTTT
1 GAAAACAC-GAAATTTTTTTT
11650049 GAAAACACGAAATTTTTTT
1 GAAAACACGAAATTTTTTT
11650068 ATTCACGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 11
0.64 0.10 0.26
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
20 12 0.44
21 1 0.04
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
GAAAACACGAAATTTTTTTT
Found at i:11650196 original size:18 final size:17
Alignment explanation
Indices: 11650157--11650202 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
11650147 TATTATTATT
11650157 ATTTTGAAACATGAGAA
1 ATTTTGAAACATGAGAA
*
11650174 ATTTTGAAGATATGA-AA
1 ATTTTGAA-ACATGAGAA
11650191 ATTTTTGAAACA
1 A-TTTTGAAACA
11650203 CGATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (17 bp):
ATTTTGAAACATGAGAA
Found at i:11651007 original size:19 final size:20
Alignment explanation
Indices: 11650979--11651018 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11650969 GGGTCGTGGG
11650979 TCGGGCCGGGCCGG-CCGGT
1 TCGGGCCGGGCCGGCCCGGT
* *
11650998 TCGGGTCGGGTCGGCCCGGT
1 TCGGGCCGGGCCGGCCCGGT
11651018 T
1 T
11651019 TTTGAATCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.00, C:0.33, G:0.50, T:0.17
Consensus pattern (20 bp):
TCGGGCCGGGCCGGCCCGGT
Found at i:11651039 original size:11 final size:11
Alignment explanation
Indices: 11651025--11651085 Score: 61
Period size: 11 Copynumber: 5.4 Consensus size: 11
11651015 GGTTTTTGAA
*
11651025 TCTTTTTTTCC
1 TCTTTTTTTCT
11651036 TCTTTTTTTTCT
1 TC-TTTTTTTCT
*
11651048 TCTTTCTTTCT
1 TCTTTTTTTCT
11651059 TCTTTCTTCTTCT
1 TCTTT-TT-TTCT
*
11651072 TC-CTTTTTCT
1 TCTTTTTTTCT
11651082 TCTT
1 TCTT
11651086 CCTTCTTCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 6 0.15
11 17 0.41
12 12 0.29
13 6 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TCTTTTTTTCT
Found at i:11651050 original size:3 final size:3
Alignment explanation
Indices: 11651044--11651096 Score: 52
Period size: 3 Copynumber: 16.0 Consensus size: 3
11651034 CCTCTTTTTT
*
11651044 TTC TTC TTTC TTTC TTC TTTC TTC TTC TTCC TTT TTC TTC TTCC TTC
1 TTC TTC -TTC -TTC TTC -TTC TTC TTC TT-C TTC TTC TTC TT-C TTC
11651091 TTC TTC
1 TTC TTC
11651097 AAAGTTTAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
3 28 0.64
4 16 0.36
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:11651080 original size:23 final size:23
Alignment explanation
Indices: 11651029--11651096 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
11651019 TTTGAATCTT
* * *
11651029 TTTTTCCTCTTT-TTTTTCTTCT
1 TTTTTCTTCTTTCTTCTTCTTCC
11651051 TTCTTTCTTCTTTCTTCTTCTTCC
1 TT-TTTCTTCTTTCTTCTTCTTCC
*
11651075 TTTTTCTTCTTCCTTCTTCTTC
1 TTTTTCTTCTTTCTTCTTCTTC
11651097 AAAGTTTAGT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 2 0.05
23 28 0.70
24 10 0.25
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTCTTCTTTCTTCTTCTTCC
Found at i:11651241 original size:15 final size:16
Alignment explanation
Indices: 11651216--11651245 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11651206 TGGCAAAGCT
11651216 TTTTCTCTTTTTTTTG
1 TTTTCTCTTTTTTTTG
11651232 TTTT-TCTTTTTTTT
1 TTTTCTCTTTTTTTT
11651246 TGAAATCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (16 bp):
TTTTCTCTTTTTTTTG
Found at i:11651242 original size:16 final size:17
Alignment explanation
Indices: 11651215--11651247 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
11651205 TTGGCAAAGC
11651215 TTTTTCTCTTTTTTTTG
1 TTTTTCTCTTTTTTTTG
11651232 TTTTTCT-TTTTTTTTG
1 TTTTTCTCTTTTTTTTG
11651248 AAATCTCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (17 bp):
TTTTTCTCTTTTTTTTG
Found at i:11651446 original size:30 final size:29
Alignment explanation
Indices: 11651410--11651509 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
11651400 AAATACAGTA
*
11651410 AAAGTTTTAGGGCTGAAACGTAATTTAGAG
1 AAAG-TTTAGGGCTGAAATGTAATTTAGAG
* *
11651440 AAAGTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGCT-GAAATGTAATTTAGAG
* *
11651469 AAAGTTTAGGGGTTGAAATGTAATTTCGAG
1 AAAGTTTA-GGGCTGAAATGTAATTTAGAG
*
11651499 AAAGTATAGGG
1 AAAGTTTAGGG
11651510 GTCAAAATGC
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
29 32 0.53
30 28 0.47
ACGTcount: A:0.38, C:0.04, G:0.28, T:0.30
Consensus pattern (29 bp):
AAAGTTTAGGGCTGAAATGTAATTTAGAG
Found at i:11651486 original size:59 final size:59
Alignment explanation
Indices: 11651409--11651524 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
11651399 TAAATACAGT
* *
11651409 AAAAGTTTTAGGGCTGAAACGTAATTTAGAGAAAGTTTAGGGGTCAAAATGTAATTTAG
1 AAAAGTTTTAGGGCTGAAACGTAATTTAGAGAAAGTATAGGGGTCAAAATGCAATTTAG
* * *
11651468 AAAAG-TTTAGGGGTTGAAATGTAATTTCGAGAAAGTATAGGGGTCAAAATGCAATTT
1 AAAAGTTTTA-GGGCTGAAACGTAATTTAGAGAAAGTATAGGGGTCAAAATGCAATTT
11651525 TTTAATTTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 4 0.08
59 47 0.92
ACGTcount: A:0.39, C:0.05, G:0.26, T:0.30
Consensus pattern (59 bp):
AAAAGTTTTAGGGCTGAAACGTAATTTAGAGAAAGTATAGGGGTCAAAATGCAATTTAG
Found at i:11651510 original size:30 final size:30
Alignment explanation
Indices: 11651410--11651511 Score: 127
Period size: 30 Copynumber: 3.4 Consensus size: 30
11651400 AAATACAGTA
* *
11651410 AAAGTTTTA-GGGCTGAAACGTAATTTAGAG
1 AAAG-TTTAGGGGTTGAAATGTAATTTAGAG
**
11651440 AAAGTTTAGGGGTCAAAATGTAATTTAGA-
1 AAAGTTTAGGGGTTGAAATGTAATTTAGAG
*
11651469 AAAGTTTAGGGGTTGAAATGTAATTTCGAG
1 AAAGTTTAGGGGTTGAAATGTAATTTAGAG
*
11651499 AAAGTATAGGGGT
1 AAAGTTTAGGGGT
11651512 CAAAATGCAA
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 30 0.48
30 32 0.52
ACGTcount: A:0.37, C:0.04, G:0.28, T:0.30
Consensus pattern (30 bp):
AAAGTTTAGGGGTTGAAATGTAATTTAGAG
Found at i:11651518 original size:30 final size:30
Alignment explanation
Indices: 11651429--11651524 Score: 140
Period size: 30 Copynumber: 3.2 Consensus size: 30
11651419 GGGCTGAAAC
11651429 GTAATTTAGAGAAAGTTTAGGGGTCAAAAT
1 GTAATTTAGAGAAAGTTTAGGGGTCAAAAT
**
11651459 GTAATTTAGA-AAAGTTTAGGGGTTGAAAT
1 GTAATTTAGAGAAAGTTTAGGGGTCAAAAT
* *
11651488 GTAATTTCGAGAAAGTATAGGGGTCAAAAT
1 GTAATTTAGAGAAAGTTTAGGGGTCAAAAT
*
11651518 GCAATTT
1 GTAATTT
11651525 TTTAATTTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 26 0.45
30 32 0.55
ACGTcount: A:0.39, C:0.04, G:0.26, T:0.31
Consensus pattern (30 bp):
GTAATTTAGAGAAAGTTTAGGGGTCAAAAT
Found at i:11651544 original size:13 final size:13
Alignment explanation
Indices: 11651526--11651551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11651516 ATGCAATTTT
11651526 TTAATTTTTTTAA
1 TTAATTTTTTTAA
11651539 TTAATTTTTTTAA
1 TTAATTTTTTTAA
11651552 CACAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTAATTTTTTTAA
Found at i:11652006 original size:41 final size:40
Alignment explanation
Indices: 11651924--11652162 Score: 253
Period size: 41 Copynumber: 5.8 Consensus size: 40
11651914 TAAAATGTTT
* **
11651924 TTAGCGGCGCTTTTCAAAAACGCCGCTAAATCCCCTTGCA
1 TTAGCGGCGCTTTTCAAAAACGCCGCTAAAGCCCCCAGCA
* *
11651964 TTAGCGGCGCTTTTCCAAAAATGCTGCTAAAGCCCCCAGCA
1 TTAGCGGCGCTTTT-CAAAAACGCCGCTAAAGCCCCCAGCA
* *
11652005 TTAGCGGCGCTTTCCAAAAAACGCCGCTAAATCCCCCAGCA
1 TTAGCGGCGCTTTTC-AAAAACGCCGCTAAAGCCCCCAGCA
* * * *
11652046 TTAGCGGCGCTTTTCAAGAAACGTCGCTAAAACACCGAGCA
1 TTAGCGGCGCTTTTCAA-AAACGCCGCTAAAGCCCCCAGCA
* * *** *
11652087 TTAGCGACGCTTTTTTAAAAACGCCGCTAAAGCCTTGAGAA
1 TTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGCCCCCAGCA
* **
11652128 TTAGCGGCACTTTTTTGAAAACGCCGCTAAAGCCC
1 TTAGCGGCGC-TTTTCAAAAACGCCGCTAAAGCCC
11652163 AAAAGGTAAG
Statistics
Matches: 169, Mismatches: 26, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
40 17 0.10
41 146 0.86
42 6 0.04
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (40 bp):
TTAGCGGCGCTTTTCAAAAACGCCGCTAAAGCCCCCAGCA
Found at i:11652149 original size:123 final size:122
Alignment explanation
Indices: 11651924--11652158 Score: 290
Period size: 123 Copynumber: 1.9 Consensus size: 122
11651914 TAAAATGTTT
* * ** * * *
11651924 TTAGCGGCGCTTTTCAAAAACGCCGCTAAATCCCCTTGCATTAGCGGCGCTTTTCCAAAAATGCT
1 TTAGCGGCGCTTTTCAAAAACGCCGCTAAAACACCGAGCATTAGCGACGCTTTTCCAAAAACGCC
* *
11651989 GCTAAAGCCCCCAGCATTAGCGGCGCTTTCCAAAAAACGCCGCTAAATCCCCCAGCA
66 GCTAAAGCCCCCAGAATTAGCGGCACTTTCCAAAAAACGCCGCTAAATCCCCCAGCA
* **
11652046 TTAGCGGCGCTTTTCAAGAAACGTCGCTAAAACACCGAGCATTAGCGACGCTTTTTTAAAAACGC
1 TTAGCGGCGCTTTTCAA-AAACGCCGCTAAAACACCGAGCATTAGCGACGCTTTTCCAAAAACGC
*** ****
11652111 CGCTAAAGCCTTGAGAATTAGCGGCACTTTTTTGAAAACGCCGCTAAA
65 CGCTAAAGCCCCCAGAATTAGCGGCACTTTCCAAAAAACGCCGCTAAA
11652159 GCCCAAAAGG
Statistics
Matches: 93, Mismatches: 19, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
122 17 0.18
123 76 0.82
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (122 bp):
TTAGCGGCGCTTTTCAAAAACGCCGCTAAAACACCGAGCATTAGCGACGCTTTTCCAAAAACGCC
GCTAAAGCCCCCAGAATTAGCGGCACTTTCCAAAAAACGCCGCTAAATCCCCCAGCA
Done.