Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 150 of 193
Found at i:46757146 original size:119 final size:118
Alignment explanation
Indices: 46756817--46757164 Score: 387
Period size: 119 Copynumber: 2.9 Consensus size: 118
46756807 CTTAATCAGA
* * * * * * * *
46756817 GGGCAGATTAAAGACCATTCAATTTTTTACCTTAATCAGAGGGCAGATTAAAGACCATTCAATCT
1 GGGCAGATTGAAG-CAATCCAATCTTTTACCTTAACCAGAGGGCAGATTGAAGACCATCCGATCT
* *
46756882 TTTACCCTAAC-TAGAGGGTAGATTGAAGCCATCCAATCTCTTACCCCGACCATG
65 CTTACCCGAACAT-GAGGGTAGATTGAAGCCATCCAATCTCTTACCCCGACCATG
* * * *
46756936 GGGCAGATTGAAGCAGTCCAATCTTTTACCTTAACTAGAGGGCAGATTGAAAACCATCCGATCGC
1 GGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGATTGAAGACCATCCGATCTC
* * * * **
46757001 TTACCCCGATCA-AAGGGCAGATTGAAGACCATCCGATCTCTTACCTTGACCATG
66 TTA-CCCGAACATGAGGGTAGATTGAAG-CCATCCAATCTCTTACCCCGACCATG
*
46757055 GGGTAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGATTGAAGACCATCCGATCTC
1 GGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGATTGAAGACCATCCGATCTC
* * * * * *
46757120 TTATCTCGACCATGA-GGTAGACTGAAGCAATTCAATCTTTTACCC
66 TTA-CCCGAACATGAGGGTAGATTGAAGCCATCCAATCTCTTACCC
46757165 TAACTAGAGG
Statistics
Matches: 189, Mismatches: 36, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
118 69 0.37
119 119 0.63
120 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (118 bp):
GGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGATTGAAGACCATCCGATCTC
TTACCCGAACATGAGGGTAGATTGAAGCCATCCAATCTCTTACCCCGACCATG
Found at i:46758277 original size:67 final size:64
Alignment explanation
Indices: 46758165--46758333 Score: 237
Period size: 67 Copynumber: 2.7 Consensus size: 64
46758155 TTCTTATTAT
46758165 TTTTATTCATTTA-TTATTATT-TTTATGAATATAAATAAAT--A-TAAAATAATATTAATTTTG
1 TTTTATT-ATTTATTTATTATTATTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTG
46758225 TTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTT
1 TTTTATTATTTATTTA-TTATTATT-TATGAATATAAATAAATAAAT-TAAAATAATATTAATTT
46758290 TG
63 TG
*
46758292 TTTTATTATTTATTTA-T-TT-TTTATGAATATAGATAAATAAAT
1 TTTTATTATTTATTTATTATTATTTATGAATATAAATAAATAAAT
46758334 AACGAACCCA
Statistics
Matches: 100, Mismatches: 1, Indels: 14
0.87 0.01 0.12
Matches are distributed among these distances:
59 5 0.05
60 10 0.10
61 5 0.05
62 22 0.22
63 19 0.19
64 2 0.02
65 2 0.02
67 35 0.35
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.54
Consensus pattern (64 bp):
TTTTATTATTTATTTATTATTATTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTG
Found at i:46761495 original size:22 final size:22
Alignment explanation
Indices: 46761470--46761513 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
46761460 AATTAACTAC
*
46761470 ACATAT-CTCCAAAATATATGCA
1 ACATATCCTCC-AAATAAATGCA
46761492 ACATATCCTCCAAATAAATGCA
1 ACATATCCTCCAAATAAATGCA
46761514 TTATTTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.45, C:0.25, G:0.05, T:0.25
Consensus pattern (22 bp):
ACATATCCTCCAAATAAATGCA
Found at i:46767305 original size:27 final size:27
Alignment explanation
Indices: 46767254--46767305 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
46767244 GTTAATAAAA
**
46767254 TTCTCTTTGAGTTTTTTTTTTAAGAAT
1 TTCTCTTTGAGTTTTTTTTAAAAGAAT
46767281 TTCTC-TTGAGTTTTCTTTTAAAAGA
1 TTCTCTTTGAGTTTT-TTTTAAAAGA
46767306 GTTTTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.58
Consensus pattern (27 bp):
TTCTCTTTGAGTTTTTTTTAAAAGAAT
Found at i:46768451 original size:3 final size:3
Alignment explanation
Indices: 46768438--46768482 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
46768428 TTTTAAAATG
46768438 TTA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
46768483 TCTGGTCAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46769483 original size:6 final size:6
Alignment explanation
Indices: 46769463--46769538 Score: 63
Period size: 6 Copynumber: 13.0 Consensus size: 6
46769453 TTAAATTGGT
* *
46769463 TTTAAA TTT-AT TTTAAA TTTAAA TTTATCTAA -TTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA
*
46769511 TTTAAG TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
46769539 AATAAAATCA
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 36 0.63
8 3 0.05
9 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:46769483 original size:17 final size:17
Alignment explanation
Indices: 46769463--46769538 Score: 100
Period size: 17 Copynumber: 4.4 Consensus size: 17
46769453 TTAAATTGGT
46769463 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
46769480 TTTAAATTTATCTAATTAAA
1 TTTAAATTTAT-T--TTAAA
*
46769500 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
46769517 TTTAAATTTA-ATTAAA
1 TTTAAATTTATTTTAAA
46769533 TTTAAA
1 TTTAAA
46769539 AATAAAATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
16 10 0.19
17 25 0.47
18 1 0.02
19 1 0.02
20 16 0.30
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:46770350 original size:17 final size:17
Alignment explanation
Indices: 46770330--46770364 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
46770320 AATATTTATT
46770330 AATAATTAATAATAATA
1 AATAATTAATAATAATA
*
46770347 AATATTTAATAATAATA
1 AATAATTAATAATAATA
46770364 A
1 A
46770365 TATTAGTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATAATTAATAATAATA
Found at i:46777476 original size:50 final size:50
Alignment explanation
Indices: 46777138--46777495 Score: 181
Period size: 50 Copynumber: 7.1 Consensus size: 50
46777128 AAAACACGAC
* * * **
46777138 GAGAAAGATCTAAGACCACAACGACGGATCCAGTACCGCAAAGATACAAAA
1 GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATA-TGAA
* * * * * * * * *
46777189 GGGAAA-A-GTAACGATCGTAACGG-TGAACCTTA-TACCTCAAAGACATGAC
1 GAGAAAGATCTAA-GACCGCAACGGCGGATCC--AGTACCACAAAGATATGAA
* * * * **
46777238 GGGAAAGATCTAAGACCACAACGGCGGATCCAGTACCGCAAAGAGACAAAA
1 GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATA-TGAA
* * * * ** * * * * * *
46777289 GGGAAAGGTTTGAG-TTGCAAAGGCGGA-CCGTGTACCTCAGAAGACACGAC
1 GAGAAAGATCTAAGACCGCAACGGCGGATCC-AGTACCACA-AAGATATGAA
* * ** **
46777339 GAGAAAGATCTAAGACAGCAACGGCGGATCCAGTATCGTAAAGATACAAAA
1 GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATA-TGAA
* * *
46777390 GGGAAAGATCTAAG-CCGTAACGGCGGATCCAATACCACAAAGATATGAA
1 GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATATGAA
* * * *
46777439 GAGAAAGATCTAAGACCGCGACGGTGGATCCAGTACCACGAAGATTTGAA
1 GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATATGAA
*
46777489 GGGAAAG
1 GAGAAAG
46777496 GTTTAAGTAG
Statistics
Matches: 224, Mismatches: 69, Indels: 29
0.70 0.21 0.09
Matches are distributed among these distances:
49 32 0.14
50 131 0.58
51 59 0.26
52 2 0.01
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.13
Consensus pattern (50 bp):
GAGAAAGATCTAAGACCGCAACGGCGGATCCAGTACCACAAAGATATGAA
Found at i:46777483 original size:100 final size:100
Alignment explanation
Indices: 46777135--46777475 Score: 384
Period size: 100 Copynumber: 3.4 Consensus size: 100
46777125 CATAAAACAC
* *
46777135 GACGAGAAAGATCTAAGACCACAACGACGGATCCAGTACCGCAAAGATACAAAAGGGAAA-A-GT
1 GACGAGAAAGATCTAAGACCACAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCT
* * *
46777198 AACGATCGTAACGGTGAACCTTATACCTCAAAGACAT
66 AA-G-TCGTAACGGCGGACCGTATACCTCAAAGACAT
* * * *
46777235 GACGGGAAAGATCTAAGACCACAACGGCGGATCCAGTACCGCAAAGAGACAAAAGGGAAAGGTTT
1 GACGAGAAAGATCTAAGACCACAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCT
* * * * * *
46777300 GAGTTGCAAAGGCGGACCGTGTACCTCAGAAGACAC
66 AAGTCGTAACGGCGGACCGTATACCTCA-AAGACAT
* *
46777336 GACGAGAAAGATCTAAGA-CAGCAACGGCGGATCCAGTATCGTAAAGATACAAAAGGGAAAGATC
1 GACGAGAAAGATCTAAGACCA-CAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATC
* * * *
46777400 TAAGCCGTAACGGCGGATCC-AATACCACAAAGATAT
65 TAAGTCGTAACGGCGGA-CCGTATACCTCAAAGACAT
* * * *
46777436 GAAGAGAAAGATCTAAGACCGCGACGGTGGATCCAGTACC
1 GACGAGAAAGATCTAAGACCACAACGGCGGATCCAGTACC
46777476 ACGAAGATTT
Statistics
Matches: 200, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
100 115 0.57
101 81 0.41
102 4 0.02
ACGTcount: A:0.40, C:0.21, G:0.26, T:0.13
Consensus pattern (100 bp):
GACGAGAAAGATCTAAGACCACAACGGCGGATCCAGTACCGCAAAGATACAAAAGGGAAAGATCT
AAGTCGTAACGGCGGACCGTATACCTCAAAGACAT
Found at i:46777812 original size:39 final size:39
Alignment explanation
Indices: 46777755--46778056 Score: 140
Period size: 39 Copynumber: 7.7 Consensus size: 39
46777745 ATGAAGATTC
* *
46777755 TGATCTCTTGGCCC-GAGCCAGGGACAGATTGAAGCCATT
1 TGATCTCTT-ACCCTGAGCCAGGGGCAGATTGAAGCCATT
* * * *
46777794 TGATCTCTTACCCTGAGCCTGGGGCAGATCAT-TA-TCAAT
1 TGATCTCTTACCCTGAGCCAGGGGCAGAT--TGAAGCCATT
** * *
46777833 CAATCTCTTACCTTGAGCCAGGGGCAGATTGCAGCCATT
1 TGATCTCTTACCCTGAGCCAGGGGCAGATTGAAGCCATT
* * * * *
46777872 TGATCTTTTACCCCGAGCCTGGGGCAGATCATCATCAACCA--
1 TGATCTCTTACCCTGAGCCAGGGGCAGAT--TGA--AGCCATT
*
46777913 --ATCTCTTACCCTAAGCCAGGGGCAGATTGCAA-CCATT
1 TGATCTCTTACCCTGAGCCAGGGGCAGATTG-AAGCCATT
* * * * * * *
46777950 CGACCTTTTACCCCGAGCCTA-GGGCAGATCAT-CA-TCAAT
1 TGATCTCTTACCCTGAGCC-AGGGGCAGAT--TGAAGCCATT
** * * *
46777989 CAATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATT
1 TGATCTCTTACCCTGAGCCAGGGGCAGATTGAAGCCATT
* * **
46778028 TGATCTTTTACCCTAAGCTTGGGGCAGAT
1 TGATCTCTTACCCTGAGCCAGGGGCAGAT
46778057 CATCATCAAC
Statistics
Matches: 195, Mismatches: 48, Indels: 40
0.69 0.17 0.14
Matches are distributed among these distances:
35 3 0.02
36 1 0.01
37 3 0.02
38 8 0.04
39 171 0.88
40 2 0.01
41 3 0.02
43 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
TGATCTCTTACCCTGAGCCAGGGGCAGATTGAAGCCATT
Found at i:46777968 original size:156 final size:156
Alignment explanation
Indices: 46777770--46778306 Score: 844
Period size: 156 Copynumber: 3.4 Consensus size: 156
46777760 TCTTGGCCCG
* * * * * * *
46777770 AGCCAGGGACAGATTG-AAGCCATTTGATCTCTTACCCTGAGCCTGGGGCAGATCATTATCAATC
1 AGCCAGGGGCAGATTGCAA-CCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATC
* ** *
46777834 AATCTCTTACCTTGAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTACCCCGAGCCTGGGGCAG
65 AATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAG
46777899 ATCATCATCAACCAATCTCTTACCCTA
130 ATCATCATCAACCAATCTCTTACCCTA
46777926 AGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
1 AGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
46777991 ATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
66 ATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
46778056 TCATCATCAACCAATCTCTTACCCTA
131 TCATCATCAACCAATCTCTTACCCTA
46778082 AGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
1 AGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
* * *
46778147 ATCTCTTACCTTGGGCTAGCGACAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
66 ATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
**
46778212 TCATCATCAACCAATCTCTTACCCCG
131 TCATCATCAACCAATCTCTTACCCTA
* * * * * *
46778238 ACCCAGGGGCAGATTGCAACCATCCGACCTTTTACTCCAAG-CTTGGAGCAGATCATCATCAACC
1 AGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGG-GCAGATCATCATCAATC
46778302 AATCT
65 AATCT
46778307 TCTACCCCAA
Statistics
Matches: 357, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
155 4 0.01
156 351 0.98
157 2 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (156 bp):
AGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
ATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
TCATCATCAACCAATCTCTTACCCTA
Found at i:46778078 original size:39 final size:39
Alignment explanation
Indices: 46777796--46778251 Score: 252
Period size: 39 Copynumber: 11.7 Consensus size: 39
46777786 AAGCCATTTG
*
46777796 ATCTCTTACCCTGAGCCTGGGGCAGATCATTATCAATCA
1 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
* * * * **
46777835 ATCTCTTACCTTGAGCCAGGGGCAGAT--TGCAGCCATTTG
1 ATCTCTTACCCTGAGCCTGGGGCAGATCAT-CA-TCAATCA
* * *
46777874 ATCTTTTACCCCGAGCCTGGGGCAGATCATCATCAACCA
1 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
* * * * *
46777913 ATCTCTTACCCTAAGCCAGGGGCAGAT--TGCAACCATTCG
1 ATCTCTTACCCTGAGCCTGGGGCAGATCAT-C-ATCAATCA
* * * *
46777952 ACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
1 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
* * * **
46777991 ATCTCTTACCTTGAG-CTAGGGGCAGAT--TGCAGCCATTTG
1 ATCTCTTACCCTGAGCCT-GGGGCAGATCAT-CA-TCAATCA
* * * *
46778030 ATCTTTTACCCTAAGCTTGGGGCAGATCATCATCAACCA
1 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
* * * * *
46778069 ATCTCTTACCCTAAGCCAGGGGCAGAT--TGCAACCATTCG
1 ATCTCTTACCCTGAGCCTGGGGCAGATCAT-C-ATCAATCA
* * * *
46778108 ACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
1 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
* * * * * * **
46778147 ATCTCTTACCTTG-GGCTAGCGACAGAT--TGCAGCCATTTG
1 ATCTCTTACCCTGAGCCT-GGGGCAGATCAT-CA-TCAATCA
* * * *
46778186 ATCTTTTACCCTAAGCTTGGGGCAGATCATCATCAACCA
1 ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
* * *
46778225 ATCTCTTACCCCGACCCAGGGGCAGAT
1 ATCTCTTACCCTGAGCCTGGGGCAGAT
46778252 TGCAACCATC
Statistics
Matches: 296, Mismatches: 97, Indels: 48
0.67 0.22 0.11
Matches are distributed among these distances:
37 5 0.02
38 12 0.04
39 263 0.89
40 11 0.04
41 5 0.02
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.26
Consensus pattern (39 bp):
ATCTCTTACCCTGAGCCTGGGGCAGATCATCATCAATCA
Found at i:46778175 original size:234 final size:234
Alignment explanation
Indices: 46777757--46778306 Score: 733
Period size: 234 Copynumber: 2.4 Consensus size: 234
46777747 GAAGATTCTG
** * * * * *
46777757 ATCTCTTGGCCCGAGCCAGGGACAGATTGAAGCCATTTGATCTCTTACCCTGAGCCTGGGGCAGA
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
* * * * * * *
46777822 TCATTATCAATCAATCTCTTACCTTGAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTACCCCG
66 TCATCATCAACCAATCTCTTACCCTAAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCG
* * *
46777887 AGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCTAAGCCAGGGGCAGATTGCAACCATTCG
131 AGCCTAGGGCAGATCATCATCAACCAATCTCTTACCCTAAGCCAGCGACAGATTGCAACCATTCG
* *
46777952 ACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATCA
196 ACCTTTTACCCCAAGCCTAGGGCAGATCATCATCAACCA
** *
46777991 ATCTCTTACCTTGAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
46778056 TCATCATCAACCAATCTCTTACCCTAAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCG
66 TCATCATCAACCAATCTCTTACCCTAAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCG
* * ** * * *
46778121 AGCCTAGGGCAGATCATCATCAATCAATCTCTTACCTTGGGCTAGCGACAGATTGCAGCCATTTG
131 AGCCTAGGGCAGATCATCATCAACCAATCTCTTACCCTAAGCCAGCGACAGATTGCAACCATTCG
* * * *
46778186 ATCTTTTACCCTAAGCTTGGGGCAGATCATCATCAACCA
196 ACCTTTTACCCCAAGCCTAGGGCAGATCATCATCAACCA
* * ** * *
46778225 ATCTCTTACCCCGACCCAGGGGCAGATTGCAACCATCCGACCTTTTACTCC-AAGCTTGGAGCAG
1 ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTAC-CCTAAGCTTGGGGCAG
46778289 ATCATCATCAACCAATCT
65 ATCATCATCAACCAATCT
46778307 TCTACCCCAA
Statistics
Matches: 273, Mismatches: 42, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
234 271 0.99
235 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (234 bp):
ATCTCTTACCCCGAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGA
TCATCATCAACCAATCTCTTACCCTAAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCG
AGCCTAGGGCAGATCATCATCAACCAATCTCTTACCCTAAGCCAGCGACAGATTGCAACCATTCG
ACCTTTTACCCCAAGCCTAGGGCAGATCATCATCAACCA
Found at i:46778314 original size:78 final size:78
Alignment explanation
Indices: 46777769--46778306 Score: 655
Period size: 78 Copynumber: 6.9 Consensus size: 78
46777759 CTCTTGGCCC
* * * * ** * * *
46777769 GAGCCAGGGACAGATTG-AAGCCATTTGATCTCTTACCCTGAGCCTGGGGCAGATCATTATCAAT
1 GAGCCAGGGGCAGATTGCAA-CCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAAC
*
46777833 CAATCTCTTACCTT
65 CAATCTCTTACCCT
* * * * *
46777847 GAGCCAGGGGCAGATTGCAGCCATTTGATCTTTTACCCCGAGCCTGGGGCAGATCATCATCAACC
1 GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
46777912 AATCTCTTACCCT
66 AATCTCTTACCCT
* * * * *
46777925 AAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATC
1 GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
*
46777990 AATCTCTTACCTT
66 AATCTCTTACCCT
* * * * *
46778003 GAGCTAGGGGCAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGATCATCATCAACC
1 GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
46778068 AATCTCTTACCCT
66 AATCTCTTACCCT
* * * * *
46778081 AAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCGAGCCTAGGGCAGATCATCATCAATC
1 GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
*
46778146 AATCTCTTACCTT
66 AATCTCTTACCCT
* * * * * * * *
46778159 GGGCTAGCGACAGATTGCAGCCATTTGATCTTTTACCCTAAGCTTGGGGCAGATCATCATCAACC
1 GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
*
46778224 AATCTCTTACCCC
66 AATCTCTTACCCT
* * * *
46778237 GACCCAGGGGCAGATTGCAACCATCCGACCTTTTACTCCAAGCTTGGAGCAGATCATCATCAACC
1 GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
46778302 AATCT
66 AATCT
46778307 TCTACCCCAA
Statistics
Matches: 396, Mismatches: 63, Indels: 2
0.86 0.14 0.00
Matches are distributed among these distances:
78 395 1.00
79 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (78 bp):
GAGCCAGGGGCAGATTGCAACCATTCGACCTTTTACCCCAAGCTTGGGGCAGATCATCATCAACC
AATCTCTTACCCT
Found at i:46778696 original size:206 final size:206
Alignment explanation
Indices: 46778337--46779209 Score: 1278
Period size: 206 Copynumber: 4.3 Consensus size: 206
46778327 GATTACGATG
** ** * *
46778337 ATTGAAACAAACGATGCGACCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCTAG
1 ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
* *
46778402 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGCA
66 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
*
46778467 ATAAAATGGTTAGCTTTCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACA
131 ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACA
46778532 CAGAGAAGCGA
196 CAGAGAAGCGA
* *
46778543 ATTGAAACAAGTGATGCGATCATCTTCCTGATGAGACACTAAGAAGAAGACCAAATCAAACCCAG
1 ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
* *
46778608 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCA
66 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
* *
46778673 ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGATCAAATTCGTCTTCCTGATGAAACA
131 ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACA
46778738 CAGAGAAGCGA
196 CAGAGAAGCGA
*
46778749 ATTGAAACAAGTGATGTGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
1 ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
46778814 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
66 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
* * *
46778879 ATAAAATGGTTAGCTTCTTGATGAGATACAAAGAAGTGGACCAAATTCAG-CTTCCTGATGAGAT
131 ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTC-GTCTTCCTGATGAGAC
*
46778943 ACAGAGGAGCGA
195 ACAGAGAAGCGA
* * * * * * *
46778955 ATTGAAACAAATGAGGCGGTCATCTTCCTGATGAGAAACAGAGAAGATG-CCAACTC-GA--C--
1 ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
* * * * * *
46779014 GCTCGATATGAGCAAATCTTCGAACCTCAGCTTTCTGATGAGATACTGAGAAACAGGTCAAAGCA
66 GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
* * *
46779079 ATAAAATGGTTGGCTTCCTGAAGAGATACTA-AGAAGTGGACCAAATTCGTCTTCCTGAGGAGAT
131 ATAAAATGGTTAGCTTCCTGATGAGATAC-AGAGAAGTGGACCAAATTCGTCTTCCTGATGAGA-
46779143 C-CAGAGAAGCGA
194 CACAGAGAAGCGA
* * * * * *
46779155 ATTAAAACAAGTAACGCGGTCATCTTCCTGATGAAATACTGAGAAGAAGGCCAAA
1 ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAA
46779210 CCAATGAAAC
Statistics
Matches: 611, Mismatches: 51, Indels: 15
0.90 0.08 0.02
Matches are distributed among these distances:
199 1 0.00
200 165 0.27
201 5 0.01
202 1 0.00
204 1 0.00
205 6 0.01
206 431 0.71
207 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (206 bp):
ATTGAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCAG
GCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCAAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGATGAGACA
CAGAGAAGCGA
Found at i:46779582 original size:6 final size:6
Alignment explanation
Indices: 46779562--46779637 Score: 63
Period size: 6 Copynumber: 13.0 Consensus size: 6
46779552 TTAAATTGGT
* *
46779562 TTTAAA TTT-AT TTTAAA TTTAAA TTTATCTAA -TTAAA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA---AA TTTAAA TTTAAA TTTAAA
*
46779610 TTTAAG TTTAAA TTT-AA -TTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
46779638 ATAGTATTAA
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
4 2 0.04
5 14 0.25
6 36 0.63
8 3 0.05
9 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:46779582 original size:17 final size:17
Alignment explanation
Indices: 46779562--46779637 Score: 91
Period size: 17 Copynumber: 4.4 Consensus size: 17
46779552 TTAAATTGGT
46779562 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
46779579 TTTAAATTTATCTAATTAAA
1 TTTAAATTTAT-T--TTAAA
* *
46779599 TTTAAATTTACTTTAAG
1 TTTAAATTTATTTTAAA
*
46779616 TTTAAATTTA-ATTAAA
1 TTTAAATTTATTTTAAA
46779632 TTTAAA
1 TTTAAA
46779638 ATAGTATTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
16 10 0.19
17 25 0.48
18 1 0.02
19 1 0.02
20 15 0.29
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:46779613 original size:11 final size:11
Alignment explanation
Indices: 46779562--46779636 Score: 61
Period size: 10 Copynumber: 7.0 Consensus size: 11
46779552 TTAAATTGGT
*
46779562 TTTAAATTTAT
1 TTTAAATTTAA
46779573 TTTAAATTTAAA
1 TTTAAATTT-AA
*
46779585 TTT--ATCTAA
1 TTTAAATTTAA
46779594 -TTAAATTTAAA
1 TTTAAATTT-AA
*
46779605 TTT-ACTTTAA
1 TTTAAATTTAA
46779615 GTTTAAATTTAA
1 -TTTAAATTTAA
46779627 -TTAAATTTAA
1 TTTAAATTTAA
46779637 AATAGTATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 15
0.72 0.07 0.21
Matches are distributed among these distances:
8 2 0.04
9 2 0.04
10 18 0.35
11 18 0.35
12 12 0.23
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:46779654 original size:33 final size:33
Alignment explanation
Indices: 46779591--46779654 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
46779581 TAAATTTATC
* **
46779591 TAATTAAATTTAAATTTACTTTAAGTTTAAATT
1 TAATTAAATTTAAATATACTTTAAACTTAAATT
*
46779624 TAATTAAATTTAAA-ATAGTATTAAACTTAAA
1 TAATTAAATTTAAATATACT-TTAAACTTAAA
46779655 AATAAAATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
32 3 0.12
33 23 0.88
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (33 bp):
TAATTAAATTTAAATATACTTTAAACTTAAATT
Found at i:46780461 original size:13 final size:13
Alignment explanation
Indices: 46780443--46780471 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
46780433 GCATTGAATG
46780443 AATATTTATTAAT
1 AATATTTATTAAT
46780456 AATATTTATTAAT
1 AATATTTATTAAT
46780469 AAT
1 AAT
46780472 TAATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTTATTAAT
Found at i:46781700 original size:58 final size:58
Alignment explanation
Indices: 46781607--46781803 Score: 213
Period size: 58 Copynumber: 3.4 Consensus size: 58
46781597 CCTAAATTAC
*
46781607 CCAAAAATTACATTTTTACCCCTAAACTTCTAAAAATTACATTTTTAACCCGAAACTT
1 CCAAAAATTACATTTTTACCCCCAAACTTCTAAAAATTACATTTTTAACCCGAAACTT
* * * *
46781665 CCAAAAATTATATTTTTACCCCCGAACTT-TCAAAAATTACATTTTTGA-TCGCAAACTT
1 CCAAAAATTACATTTTTACCCCCAAACTTCT-AAAAATTACATTTTTAACCCG-AAACTT
* * * * * *
46781723 CCAAAAATTCCATTTTTCACCCTCAAACTTCTAAAAATTCCGTTTTTTACCTCAAAACTT
1 CCAAAAATTACATTTTT-ACCCCCAAACTTCTAAAAATTACATTTTTAACC-CGAAACTT
*
46781783 CC-GAAATTACCA-TTTTACCCC
1 CCAAAAATTA-CATTTTTACCCC
46781804 TAGATGTCCA
Statistics
Matches: 115, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
57 3 0.03
58 67 0.58
59 33 0.29
60 11 0.10
61 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACATTTTTACCCCCAAACTTCTAAAAATTACATTTTTAACCCGAAACTT
Found at i:46781752 original size:30 final size:28
Alignment explanation
Indices: 46781607--46781803 Score: 182
Period size: 29 Copynumber: 6.8 Consensus size: 28
46781597 CCTAAATTAC
46781607 CCAAAAATTACATTTTTACCCCTAAACTT
1 CCAAAAATTACATTTTTACCCC-AAACTT
* *
46781636 CTAAAAATTACATTTTTAACCCGAAACTT
1 CCAAAAATTACATTTTT-ACCCCAAACTT
* *
46781665 CCAAAAATTATATTTTTACCCCCGAACTT
1 CCAAAAATTACATTTTTA-CCCCAAACTT
* * *
46781694 TCAAAAATTACATTTTTGATCGCAAACTT
1 CCAAAAATTACATTTTT-ACCCCAAACTT
*
46781723 CCAAAAATTCCATTTTTCACCCTCAAACTT
1 CCAAAAATTACATTTTT-ACCC-CAAACTT
* * * *
46781753 CTAAAAATTCCGTTTTTTACCTCAAAACTT
1 CCAAAAATTAC-ATTTTTACC-CCAAACTT
*
46781783 CC-GAAATTACCA-TTTTACCCC
1 CCAAAAATTA-CATTTTTACCCC
46781804 TAGATGTCCA
Statistics
Matches: 137, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
27 1 0.01
28 8 0.06
29 89 0.65
30 33 0.24
31 6 0.04
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (28 bp):
CCAAAAATTACATTTTTACCCCAAACTT
Found at i:46786563 original size:2 final size:2
Alignment explanation
Indices: 46786548--46786579 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
46786538 AAAATGCAAA
46786548 AT AT -T AT A- 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
46786580 TAAGAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46786658 original size:3 final size:3
Alignment explanation
Indices: 46786652--46786698 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
46786642 CTAATAATAC
46786652 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
46786699 GAAGCAGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:46803877 original size:18 final size:18
Alignment explanation
Indices: 46803854--46803897 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
46803844 TTTTAGAAAA
46803854 TTTTTAAAA-TTTTATATT
1 TTTTTAAAATTTTTA-ATT
*
46803872 TTTTTAGAATTTTTAATT
1 TTTTTAAAATTTTTAATT
46803890 TTTTTAAA
1 TTTTTAAA
46803898 TTTAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTAAAATTTTTAATT
Found at i:46803944 original size:19 final size:18
Alignment explanation
Indices: 46803897--46803936 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
46803887 ATTTTTTTAA
*
46803897 ATTT-AAATTTTGAAAAT
1 ATTTGAAATTTTAAAAAT
46803914 ATTTGAAATTTTAAAAATT
1 ATTTGAAATTTTAAAAA-T
46803933 ATTT
1 ATTT
46803937 TGAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 4 0.20
18 11 0.55
19 5 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
ATTTGAAATTTTAAAAAT
Found at i:46816671 original size:31 final size:31
Alignment explanation
Indices: 46816635--46816751 Score: 111
Period size: 31 Copynumber: 3.9 Consensus size: 31
46816625 TACCACTTAT
*
46816635 AATATAACAATACATTATATTTAAATAATTG
1 AATATAACAATACATTATATTTAAATAATTA
46816666 AATATATA-AA-ACATTATA---AAA-AATTA
1 AATATA-ACAATACATTATATTTAAATAATTA
** * * * *
46816692 AATATAATGACAAATAATATTTAAATAATTT
1 AATATAACAATACATTATATTTAAATAATTA
46816723 AATATAACAATACATTATATTTAATATAA
1 AATATAACAATACATTATATTTAA-ATAA
46816752 ATAAGTGTAT
Statistics
Matches: 68, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
25 1 0.01
26 11 0.16
27 9 0.13
30 11 0.16
31 31 0.46
32 5 0.07
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (31 bp):
AATATAACAATACATTATATTTAAATAATTA
Found at i:46818708 original size:6 final size:6
Alignment explanation
Indices: 46818669--46818696 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46818659 GAAAATTTAA
46818669 GCAGCT GCAGCT GCAGCT GCAGCT GCAG
1 GCAGCT GCAGCT GCAGCT GCAGCT GCAG
46818697 TTCAGGTGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.36, T:0.14
Consensus pattern (6 bp):
GCAGCT
Found at i:46826395 original size:15 final size:16
Alignment explanation
Indices: 46826374--46826419 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
46826364 AATACGAAGC
*
46826374 AATATAATAAGCAGAT
1 AATATAATATGCAGAT
*
46826390 AA-ATAATATGC-GAA
1 AATATAATATGCAGAT
46826404 AATATAATATGCAGAT
1 AATATAATATGCAGAT
46826420 GCAAATAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
14 4 0.16
15 17 0.68
16 4 0.16
ACGTcount: A:0.54, C:0.07, G:0.13, T:0.26
Consensus pattern (16 bp):
AATATAATATGCAGAT
Found at i:46826410 original size:30 final size:30
Alignment explanation
Indices: 46826374--46826434 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
46826364 AATACGAAGC
46826374 AATATAATAAGCAGAT-AAATAATATGCGAA
1 AATATAATAAGCAGATCAAATAA-ATGCGAA
*
46826404 AATATAATATGCAGATGCAAATAAATGCGAA
1 AATATAATAAGCAGAT-CAAATAAATGCGAA
46826435 TATTGGTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 15 0.54
31 7 0.25
32 6 0.21
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (30 bp):
AATATAATAAGCAGATCAAATAAATGCGAA
Found at i:46826657 original size:30 final size:30
Alignment explanation
Indices: 46826612--46826973 Score: 511
Period size: 30 Copynumber: 12.1 Consensus size: 30
46826602 TTTGGCAAAA
*
46826612 TTGGGGTCAAAAATGTAATATTGGAAAAGTT
1 TTGGGGTC-AAAATGTAATTTTGGAAAAGTT
* *
46826643 TTGGGGTCAAAATGTAATATTAGAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
* *
46826673 TTGGGGTTAAAATGTGATTTTGGAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
*
46826703 TTGGGGTTAAAATGTAATTTTGG-AAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
*
46826732 TTGGGGTCAAAATGTAATTTTAGAAAAGCTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAG-TT
*
46826763 TT-GGGTCAAAATGTAATTTTGAAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
* *
46826792 TTGGGGTTAAAATGTCATTTTGG-AAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
46826821 TTGGGGTCAAAATGTAATTTT-GAAAATGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAA-GTT
*
46826851 TTGGGGTCAAAATGTAATTTTTG-AAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
* *
46826880 TTGGGATCAAAATGTAATTTTGAAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
*
46826910 TTGGGGTTAAAATGTAATTTTGGAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTT
*
46826940 TTGGGGTCAAAATGTAATTTT-TATAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGA-AAAGTT
46826970 TTGG
1 TTGG
46826974 AACCTACAGA
Statistics
Matches: 300, Mismatches: 23, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
28 1 0.00
29 83 0.28
30 203 0.68
31 13 0.04
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (30 bp):
TTGGGGTCAAAATGTAATTTTGGAAAAGTT
Found at i:46826738 original size:89 final size:89
Alignment explanation
Indices: 46826612--46826973 Score: 516
Period size: 89 Copynumber: 4.0 Consensus size: 89
46826602 TTTGGCAAAA
* * *
46826612 TTGGGGTCAAAAATGTAATATTGGAAAAGTTTTGGGGTCAAAATGTAATATTAGAAAAGTTTTGG
1 TTGGGGT-TAAAATGTAATTTTGG-AAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTGG
* *
46826677 GGTTAAAATGTGATTTTGGAAAAGTT
64 GGTCAAAATGTAATTTTGGAAAAGTT
46826703 TTGGGGTTAAAATGTAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGCTTTT-GG
1 TTGGGGTTAAAATGTAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAG-TTTTGGG
*
46826767 GTCAAAATGTAATTTTGAAAAAGTT
65 GTCAAAATGTAATTTTGGAAAAGTT
*
46826792 TTGGGGTTAAAATGTCATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTT-GAAAATGTTTTGGG
1 TTGGGGTTAAAATGTAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAA-GTTTTGGG
*
46826856 GTCAAAATGTAATTTTTG-AAAGTT
65 GTCAAAATGTAATTTTGGAAAAGTT
* * * * *
46826880 TTGGGATCAAAATGTAATTTTGAAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGG
1 TTGGGGTTAAAATGTAATTTTG-GAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTGGG
*
46826945 GTCAAAATGTAATTTT-TATAAAGTT
65 GTCAAAATGTAATTTTGGA-AAAGTT
46826970 TTGG
1 TTGG
46826974 AACCTACAGA
Statistics
Matches: 249, Mismatches: 15, Indels: 15
0.89 0.05 0.05
Matches are distributed among these distances:
88 34 0.14
89 175 0.70
90 33 0.13
91 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (89 bp):
TTGGGGTTAAAATGTAATTTTGGAAAGTTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGG
TCAAAATGTAATTTTGGAAAAGTT
Found at i:46826758 original size:59 final size:59
Alignment explanation
Indices: 46826612--46826973 Score: 523
Period size: 59 Copynumber: 6.1 Consensus size: 59
46826602 TTTGGCAAAA
* *
46826612 TTGGGGTCAAAAATGTAATATTGGAAAAGTTTTGGGGTCAAAATGTAATATTAGAAAAGTT
1 TTGGGGTC-AAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAAT-TTTGAAAAGTT
* * * *
46826673 TTGGGGTTAAAATGTGATTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTTGGAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGAAAAGTT
*
46826732 TTGGGGTCAAAATGTAATTTTAGAAAAGCTTTT-GGGTCAAAATGTAATTTTGAAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAG-TTTTGGGGTCAAAATGTAATTTTG-AAAAGTT
* *
46826792 TTGGGGTTAAAATGTCATTTTGG-AAAGTTTTGGGGTCAAAATGTAATTTTGAAAATGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGAAAA-GTT
* *
46826851 TTGGGGTCAAAATGTAATTTTTG-AAAGTTTTGGGATCAAAATGTAATTTTGAAAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTG-AAAAGTT
* *
46826910 TTGGGGTTAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTTATAAAGTT
1 TTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGA-AAAGTT
46826970 TTGG
1 TTGG
46826974 AACCTACAGA
Statistics
Matches: 272, Mismatches: 22, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
58 8 0.03
59 150 0.55
60 107 0.39
61 7 0.03
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.39
Consensus pattern (59 bp):
TTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATGTAATTTTGAAAAGTT
Found at i:46828062 original size:18 final size:19
Alignment explanation
Indices: 46828020--46828069 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
46828010 AAAGTTATTA
*
46828020 TTATCATTATTAAAATACAT
1 TTATTATTATT-AAATACAT
*
46828040 TTATTATTATTAAA-ACCT
1 TTATTATTATTAAATACAT
46828058 TTATTATTATTA
1 TTATTATTATTA
46828070 TTATCATTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 15 0.54
19 3 0.11
20 10 0.36
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (19 bp):
TTATTATTATTAAATACAT
Found at i:46828475 original size:24 final size:24
Alignment explanation
Indices: 46828442--46828488 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
46828432 GCGTGTTTAA
*
46828442 ATTTTTAGAACAAGGG-TCGTATTG
1 ATTTTCAGAA-AAGGGTTCGTATTG
*
46828466 ATTTTCAGAATAGGGTTCGTATT
1 ATTTTCAGAAAAGGGTTCGTATT
46828489 AGAACAGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (24 bp):
ATTTTCAGAAAAGGGTTCGTATTG
Found at i:46853517 original size:86 final size:86
Alignment explanation
Indices: 46853372--46853534 Score: 226
Period size: 86 Copynumber: 1.9 Consensus size: 86
46853362 TTTAAGTTCA
* *
46853372 GTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTAGGATATGGATTCATTAAGAGTA
1 GTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTAGGATATGAATTCATTAAAAGTA
46853437 ATAAACTCAACCTCTCATGTCG
66 A-AAACTCAACCTCTCATGTCG
*
46853459 GTGAATTCATCAAGTCTC-TCTCAATA-GACCACCCAAA-TCTTGGGATATGAACTT-ATTAAAA
1 GTGAATTCATCAAGTC-CGTCTCAATAGGACCACCCAAACTC-TAGGATATGAA-TTCATTAAAA
*
46853520 GTGAAAACTCAACCT
63 GTAAAAACTCAACCT
46853535 TATGCATGTA
Statistics
Matches: 69, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
85 13 0.19
86 29 0.42
87 26 0.38
88 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.27
Consensus pattern (86 bp):
GTGAATTCATCAAGTCCGTCTCAATAGGACCACCCAAACTCTAGGATATGAATTCATTAAAAGTA
AAAACTCAACCTCTCATGTCG
Found at i:46861370 original size:13 final size:14
Alignment explanation
Indices: 46861337--46861372 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
46861327 TCATATCTCA
46861337 AAAATCGAGCTAGT
1 AAAATCGAGCTAGT
*
46861351 AAAATCGAGTTAGT
1 AAAATCGAGCTAGT
46861365 -AAATCGAG
1 AAAATCGAG
46861373 GGTTTGCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (14 bp):
AAAATCGAGCTAGT
Found at i:46863687 original size:17 final size:18
Alignment explanation
Indices: 46863646--46863687 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
46863636 CCCAATGAGA
46863646 TAAATTTAGTTTTAAAAT
1 TAAATTTAGTTTTAAAAT
* * *
46863664 TAGATTTA-TTTTGAATT
1 TAAATTTAGTTTTAAAAT
46863681 TAAATTT
1 TAAATTT
46863688 GCATAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
TAAATTTAGTTTTAAAAT
Found at i:46863719 original size:23 final size:23
Alignment explanation
Indices: 46863646--46863719 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
46863636 CCCAATGAGA
** *
46863646 TAAATTTAGTTTTAAAATTAGAT
1 TAAATTTAAATTTAAAATTAAAT
* * * * **
46863669 TTATTTTGAATTTAAATTTGCAT
1 TAAATTTAAATTTAAAATTAAAT
*
46863692 AAAATTTAAATTTAAAATTAAAT
1 TAAATTTAAATTTAAAATTAAAT
46863715 TAAAT
1 TAAAT
46863720 GTCCAAAGTC
Statistics
Matches: 35, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATTAAAT
Found at i:46865563 original size:29 final size:28
Alignment explanation
Indices: 46865530--46865887 Score: 122
Period size: 29 Copynumber: 12.2 Consensus size: 28
46865520 CAAAAATTAT
*
46865530 ATTTTTGACCCCAACTTTCCAAAATTCC
1 ATTTTTTACCCCAACTTTCCAAAATTCC
* *
46865558 ATTTTTTAACCTCGA-TTTCACCAAAAATTACC
1 ATTTTTT-ACCCCAACTTT--CC-AAAATT-CC
46865590 A--TTTTACCCCTAAACTTTCCAAAATTCC
1 ATTTTTTACCCC--AACTTTCCAAAATTCC
* * *
46865618 ATTTTTAACCTCGA-TTTCACCAAAAATTACC
1 ATTTTTTACCCCAACTTT--CC-AAAATT-CC
*
46865649 A--TTTTACCCCCAAACTTTCCAAAATTCT
1 ATTTTTTA-CCCC-AACTTTCCAAAATTCC
* *
46865677 ATTTTTAACCCCAA-TTTCACTAAAAAAATACC
1 ATTTTTTACCCCAACTTTC-C----AAAATTCC
46865709 A--TTTTACCCCTAAACTTTCCAAAATTCC
1 ATTTTTTACCCC--AACTTTCCAAAATTCC
*
46865737 A-TTTTAACCCC-A-TTTGCACCCAAAATTACC
1 ATTTTTTACCCCAACTTT----CCAAAATT-CC
*
46865767 A--TTTTACCCCAAACTTTCCAAAATCCC
1 ATTTTTTACCCC-AACTTTCCAAAATTCC
* * *
46865794 A-TTTTAACCTCGA-TTTCACCAAAAATTACC
1 ATTTTTTACCCCAACTTT--CC-AAAATT-CC
*
46865824 A--TTTTACCCCTGAACTTTCCAAAATCCC
1 ATTTTTTACCCC--AACTTTCCAAAATTCC
* * *
46865852 ATTTTTAACCCCGAATTTTCCCAAAATTAC
1 ATTTTTTACCCC-AACTTT-CCAAAATTCC
46865882 ATTTTT
1 ATTTTT
46865888 GCCCCTAAGA
Statistics
Matches: 251, Mismatches: 32, Indels: 92
0.67 0.09 0.25
Matches are distributed among these distances:
25 3 0.01
26 4 0.02
27 11 0.04
28 45 0.18
29 78 0.31
30 68 0.27
31 13 0.05
32 25 0.10
33 4 0.02
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.35
Consensus pattern (28 bp):
ATTTTTTACCCCAACTTTCCAAAATTCC
Found at i:46865627 original size:59 final size:59
Alignment explanation
Indices: 46865542--46865895 Score: 488
Period size: 59 Copynumber: 6.0 Consensus size: 59
46865532 TTTTGACCCC
46865542 AACTTTCCAAAATTCCATTTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTA
1 AACTTTCCAAAATTCCA-TTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTA
*
46865602 AACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCA
1 AACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTA
* * * * *
46865661 AACTTTCCAAAATTCTATTTTTAACCCCAATTTCACTAAAAAAATACCATTTTACCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC-CAAAAATTACCATTTTACCCCTA
* *
46865721 AACTTTCCAAAATTCCA-TTTTAACC-CCATTTGCACCCAAAATTACCATTTTACCCC-A
1 AACTTTCCAAAATTCCATTTTTAACCTCGATTT-CACCAAAAATTACCATTTTACCCCTA
* *
46865778 AACTTTCCAAAATCCCA-TTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTG
1 AACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTA
* * *
46865836 AACTTTCCAAAATCCCATTTTTAACCCCGAATTTTC-CC-AAAATTA-CATTTTTGCCCCTA
1 AACTTTCCAAAATTCCATTTTTAACCTCG-A-TTTCACCAAAAATTACCA-TTTTACCCCTA
46865895 A
1 A
46865896 GAGTCAAAAA
Statistics
Matches: 267, Mismatches: 19, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
57 48 0.18
58 47 0.18
59 112 0.42
60 56 0.21
61 4 0.01
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (59 bp):
AACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCTA
Found at i:46872558 original size:41 final size:38
Alignment explanation
Indices: 46872458--46872561 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
46872448 TTCGAAGCAA
* *
46872458 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
46872495 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
46872533 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
46872562 CTCGAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:46873464 original size:13 final size:12
Alignment explanation
Indices: 46873394--46873475 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
46873384 TTCATATACA
*
46873394 TATATATATTAGT
1 TATA-ATATTAAT
*
46873407 TAATAATAATAA-
1 T-ATAATATTAAT
*
46873419 TATAATACTAAT
1 TATAATATTAAT
*
46873431 TA-AATAATAATT
1 TATAATATTAA-T
*
46873443 TATATTATTATAT
1 TATAATATTA-AT
46873456 TATAATATTAAT
1 TATAATATTAAT
46873468 TAATAATA
1 T-ATAATA
46873476 AATTTAAAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:46873938 original size:22 final size:22
Alignment explanation
Indices: 46873913--46873954 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46873903 GTCGCGACTC
*
46873913 CAAGGATTTGTTGTCACGATGT
1 CAAGGATTTGTCGTCACGATGT
*
46873935 CAAGGTTTTGTCGTCACGAT
1 CAAGGATTTGTCGTCACGAT
46873955 ATGACAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (22 bp):
CAAGGATTTGTCGTCACGATGT
Found at i:46880687 original size:22 final size:23
Alignment explanation
Indices: 46880636--46880707 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 23
46880626 ACTCTAAGCC
*
46880636 ATTTCTTGTCGCGACGTCAGAGG
1 ATTTGTTGTCGCGACGTCAGAGG
*
46880659 -TTCGTTGTCGCGAC-TCCA-AGG
1 ATTTGTTGTCGCGACGT-CAGAGG
* *
46880680 ATTTGTTGTCACGATGTCA-AGG
1 ATTTGTTGTCGCGACGTCAGAGG
*
46880702 TTTTGT
1 ATTTGT
46880708 CGTCACGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
21 4 0.10
22 35 0.88
23 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (23 bp):
ATTTGTTGTCGCGACGTCAGAGG
Found at i:46880712 original size:22 final size:22
Alignment explanation
Indices: 46880675--46880716 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46880665 GTCGCGACTC
*
46880675 CAAGGATTTGTTGTCACGATGT
1 CAAGGATTTGTCGTCACGATGT
*
46880697 CAAGGTTTTGTCGTCACGAT
1 CAAGGATTTGTCGTCACGAT
46880717 ATGACAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (22 bp):
CAAGGATTTGTCGTCACGATGT
Found at i:46880988 original size:15 final size:15
Alignment explanation
Indices: 46880968--46880998 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46880958 TATGAACATA
46880968 TTCAAGCACAATTTC
1 TTCAAGCACAATTTC
*
46880983 TTCAAGCACATTTTC
1 TTCAAGCACAATTTC
46880998 T
1 T
46880999 AAAAGATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
TTCAAGCACAATTTC
Found at i:46881673 original size:17 final size:17
Alignment explanation
Indices: 46881632--46881663 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46881622 AGTTTAGGAT
46881632 TTTATTTCAATATTAAG
1 TTTATTTCAATATTAAG
46881649 TTTATTTCAAT-TTAA
1 TTTATTTCAATATTAA
46881664 TCTTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTATTTCAATATTAAG
Found at i:46894153 original size:22 final size:23
Alignment explanation
Indices: 46894102--46894173 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 23
46894092 ACTCTAAGCC
*
46894102 ATTTCTTGTCGCGACGTCAGAGG
1 ATTTGTTGTCGCGACGTCAGAGG
*
46894125 -TTCGTTGTCGCGAC-TCCA-AGG
1 ATTTGTTGTCGCGACGT-CAGAGG
* *
46894146 ATTTGTTGTCACGATGTCA-AGG
1 ATTTGTTGTCGCGACGTCAGAGG
*
46894168 TTTTGT
1 ATTTGT
46894174 CGTCACGATA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
21 4 0.10
22 35 0.88
23 1 0.03
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (23 bp):
ATTTGTTGTCGCGACGTCAGAGG
Found at i:46894178 original size:22 final size:22
Alignment explanation
Indices: 46894141--46894182 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46894131 GTCGCGACTC
*
46894141 CAAGGATTTGTTGTCACGATGT
1 CAAGGATTTGTCGTCACGATGT
*
46894163 CAAGGTTTTGTCGTCACGAT
1 CAAGGATTTGTCGTCACGAT
46894183 ATGACAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (22 bp):
CAAGGATTTGTCGTCACGATGT
Found at i:46894454 original size:15 final size:15
Alignment explanation
Indices: 46894434--46894464 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
46894424 TATGAACATA
46894434 TTCAAGCACAATTTC
1 TTCAAGCACAATTTC
*
46894449 TTCAAGCACATTTTC
1 TTCAAGCACAATTTC
46894464 T
1 T
46894465 AAAAGATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.39
Consensus pattern (15 bp):
TTCAAGCACAATTTC
Found at i:46895139 original size:17 final size:17
Alignment explanation
Indices: 46895098--46895129 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46895088 AGTTTAGGAT
46895098 TTTATTTCAATATTAAG
1 TTTATTTCAATATTAAG
46895115 TTTATTTCAAT-TTAA
1 TTTATTTCAATATTAA
46895130 TCTTATTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTATTTCAATATTAAG
Found at i:46897328 original size:30 final size:30
Alignment explanation
Indices: 46897293--46897432 Score: 107
Period size: 30 Copynumber: 4.7 Consensus size: 30
46897283 TAAACCTTTT
46897293 AAAATTCCATTTTTAACCTCGAAACTTCCA
1 AAAATTCCATTTTTAACCTCGAAACTTCCA
* * *
46897323 AAAATTGCCA-TTTTACCCTCGAACCTT-CT
1 AAAATT-CCATTTTTAACCTCGAAACTTCCA
* *
46897352 AAAATTCCATTTTT-AGCTCCG--GCTTCACCA
1 AAAATTCCATTTTTAACCT-CGAAACTT--CCA
* *
46897382 AAAATTACCA-TTTTACCCCCG-AACTTTCC-
1 AAAATT-CCATTTTTAACCTCGAAAC-TTCCA
46897411 AAAATTCCATTTTTAACCTCGA
1 AAAATTCCATTTTTAACCTCGA
46897433 TTTCACCAAA
Statistics
Matches: 85, Mismatches: 13, Indels: 24
0.70 0.11 0.20
Matches are distributed among these distances:
27 3 0.04
28 8 0.09
29 28 0.33
30 36 0.42
31 8 0.09
32 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.34
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCTCGAAACTTCCA
Found at i:46897494 original size:58 final size:59
Alignment explanation
Indices: 46897293--46897729 Score: 460
Period size: 59 Copynumber: 7.5 Consensus size: 59
46897283 TAAACCTTTT
* * * * * *
46897293 AAAATTCCATTTTTAACCTCGAAACTT--CCAAAAATTGCCATTTTACCCTCGAACCTTCT
1 AAAATTCCATTTTTAACCCCG--ATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * **
46897352 AAAATTCCATTTTTAGCTCCGGCTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
*
46897411 AAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCA-TTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * * * **
46897469 AAAATTCCATTTTTCACCCCTATTTCACCAAAAATTACCATTTTACCCCCAAATTTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
** **
46897528 AAAATTCCATTTTTAA-CCTTAGTTTCACCAAAAATTACCATTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTTAACCCCGA-TTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * *
46897587 AAAATTCCATTTTTAACCCCGATTTCATC-AAAATTACCATTTTTACCCTCGAAGC-CT-C
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCA-TTTTACCCCCGAA-CTTTCC
* * * ** *
46897645 AAAAATCTATTTTTAACCCCGATTTCACC-AAAATTACCATTTTGCCCCCG-GGTATCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* * *
46897702 AAAAGTCCCGTTTTCAACCCCGATTTCA
1 AAAA-TTCCATTTTTAACCCCGATTTCA
46897730 TCGGTTCTTA
Statistics
Matches: 322, Mismatches: 46, Indels: 21
0.83 0.12 0.05
Matches are distributed among these distances:
56 1 0.00
57 17 0.05
58 124 0.39
59 176 0.55
60 4 0.01
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
Found at i:46897502 original size:117 final size:116
Alignment explanation
Indices: 46897288--46897694 Score: 468
Period size: 117 Copynumber: 3.5 Consensus size: 116
46897278 AATCCTAAAC
* * * * *
46897288 CTTTTAAAATTCCATTTTTAACCTCGAAACTT--CCAAAAATTGCCATTTTACCCTCGAACCTTC
1 CTTTCAAAATTCCATTTTTAACCTCG--ATTTCACCAAAAATTACCATTTTACCCCCGAACTTTC
* * **
46897351 TAAAATTCCATTTTTAGCTCCGGCTTCACCAAAAATTACCATTTTACCCCCGAA
64 CAAAATTCCATTTTTA-CCCCGATTTCACCAAAAATTACCATTTTACCCCCGAA
46897405 CTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCA-TTTACCCCCGAACTTTCC
1 CTTT-CAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCC
* *
46897469 AAAATTCCATTTTTCACCCCTATTTCACCAAAAATTACCATTTTACCCCCAAA
65 AAAATTCCATTTTT-ACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAA
* * * **
46897522 TTTTTTAAAATTCCATTTTTAACCT-TAGTTTCACCAAAAATTACCATTTTACCCCTAAACTTTC
1 -CTTTCAAAATTCCATTTTTAACCTCGA-TTTCACCAAAAATTACCATTTTACCCCCGAACTTTC
* *
46897586 CAAAATTCCATTTTTAACCCCGATTTCATC-AAAATTACCATTTTTACCCTCGAA
64 CAAAATTCCATTTTT-ACCCCGATTTCACCAAAAATTACCA-TTTTACCCCCGAA
* * * * *
46897640 GC-CTCAAAAATCTATTTTTAACCCCGATTTCACC-AAAATTACCATTTTGCCCCCG
1 -CTTTCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCG
46897695 GGTATCCAAA
Statistics
Matches: 249, Mismatches: 32, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
116 22 0.09
117 136 0.55
118 91 0.37
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.35
Consensus pattern (116 bp):
CTTTCAAAATTCCATTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAACTTTCCA
AAATTCCATTTTTACCCCGATTTCACCAAAAATTACCATTTTACCCCCGAA
Found at i:46909920 original size:39 final size:40
Alignment explanation
Indices: 46909813--46909924 Score: 112
Period size: 37 Copynumber: 2.9 Consensus size: 40
46909803 CAGACCAAAC
* *
46909813 AAGATCATTTCCAATCCGCTTGAAATTGAAGTAGAGTGGA
1 AAGATCATTTCCAATCCGCTTGAAATTGAAGTAGAGAGCA
* *
46909853 TA-A-CAAGTCTT-C-AT-CTC-TGAAATTGAAGTAG-GAGCA
1 AAGATC-A-T-TTCCAATCCGCTTGAAATTGAAGTAGAGAGCA
46909889 AAGATCATTTCCAATCCGCTTGAAATTGAAGTAGAG
1 AAGATCATTTCCAATCCGCTTGAAATTGAAGTAGAG
46909925 TGGATAACAC
Statistics
Matches: 56, Mismatches: 6, Indels: 20
0.68 0.07 0.24
Matches are distributed among these distances:
35 2 0.04
36 6 0.11
37 18 0.32
38 6 0.11
39 18 0.32
40 4 0.07
41 2 0.04
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (40 bp):
AAGATCATTTCCAATCCGCTTGAAATTGAAGTAGAGAGCA
Found at i:46910013 original size:68 final size:68
Alignment explanation
Indices: 46909902--46910728 Score: 1160
Period size: 68 Copynumber: 11.9 Consensus size: 68
46909892 ATCATTTCCA
* * *
46909902 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
*
46909967 GTA
66 GTC
* * * *
46909970 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGCAAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
46910035 GATC
66 G-TC
* **
46910039 ATTTCCAATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTAATTATCTCTGAAATTGAAGTAA
1 A--T-C---CC-CTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAA
46910104 GAGCAACGTC
59 GAGCAACGTC
*
46910114 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
46910179 GTC
66 GTC
* *
46910182 ATCCCCTTGAAATTGAAGTAGAGTGGATAATACA-TATTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACA-AGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
46910246 CGTC
65 CGTC
*
46910250 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
46910315 GTC
66 GTC
*
46910318 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
46910383 GTC
66 GTC
46910386 AT-CCCTTGAAATTGAAGTAGAGTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACA-AGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
46910449 CGTC
65 CGTC
* *
46910453 ATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
46910518 GTC
66 GTC
*
46910521 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACA-AGTCTTTATCTCTGAAATTGAAGTAAGAGCA
*
46910585 ATGTC
64 ACGTC
* * * * *
46910590 ATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAATTTGAAGTAAGAGC-AG
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
46910654 GATC
66 G-TC
* * *
46910658 ATTTCCTATCCTCCTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAG
1 A--TCC---CCT--TGAAATTGAAGTAGAG-TGGATAACAAGTCTTTAT--CTCTGAAATTGAAG
46910723 TAAGAG
56 TAAGAG
46910729 TAAGATGAAG
Statistics
Matches: 690, Mismatches: 42, Indels: 44
0.89 0.05 0.06
Matches are distributed among these distances:
67 68 0.10
68 435 0.63
69 69 0.10
70 3 0.00
71 1 0.00
72 2 0.00
73 3 0.00
75 20 0.03
76 70 0.10
78 19 0.03
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:46910087 original size:144 final size:136
Alignment explanation
Indices: 46909826--46910652 Score: 1282
Period size: 136 Copynumber: 6.0 Consensus size: 136
46909816 ATCATTTCCA
* *
46909826 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGCAAA
1 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
46909891 GATCATTTCCAATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAA
66 G-TCA--T-C---CC-CTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAA
*
46909956 GTAAGAGCAACGTA
123 GTAAGAGCAACGTC
* *
46909970 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGCAAA
1 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
*
46910035 GATCATTTCCAATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTAATTATCTCTGAAATTGAA
66 G-TCA--T-C---CC-CTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAA
46910100 GTAAGAGCAACGTC
123 GTAAGAGCAACGTC
*
46910114 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
* *
46910179 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAATACATATTTATCTCTGAAATTGAAGTAAGAGC
66 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGC
46910244 AACGTC
131 AACGTC
*
46910250 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
*
46910315 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGC
66 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGC
46910380 AACGTC
131 AACGTC
*
46910386 ATCC-CTTGAAATTGAAGTAGAGTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCGCTTGAAATTGAAGTAGAGTGGATAACA-AGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
* *
46910449 CGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
65 CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAG
46910514 CAACGTC
130 CAACGTC
*
46910521 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCGCTTGAAATTGAAGTAGAG-TGGATAACA-AGTCTTCATCTCTGAAATTGAAGTAAGAGCA
* * ** *
46910585 ATGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAATTTGAAGTAAGA
64 ACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGA
46910650 GCA
129 GCA
46910653 GGATCATTTC
Statistics
Matches: 662, Mismatches: 18, Indels: 13
0.96 0.03 0.02
Matches are distributed among these distances:
135 131 0.20
136 216 0.33
137 105 0.16
140 1 0.00
141 1 0.00
143 3 0.00
144 205 0.31
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (136 bp):
ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGC
AACGTC
Found at i:46910256 original size:136 final size:136
Alignment explanation
Indices: 46909826--46910728 Score: 1274
Period size: 144 Copynumber: 6.4 Consensus size: 136
46909816 ATCATTTCCA
* * *
46909826 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGCAAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
46909891 GATCATTTCCAATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAA
66 G-TCA--T-C---CC-CTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAA
*
46909956 GTAAGAGCAACGTA
123 GTAAGAGCAACGTC
* * *
46909970 ATCCGCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAGGAGCAAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
*
46910035 GATCATTTCCAATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTAATTATCTCTGAAATTGAA
66 G-TCA--T-C---CC-CTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAA
46910100 GTAAGAGCAACGTC
123 GTAAGAGCAACGTC
46910114 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
* *
46910179 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAATACATATTTATCTCTGAAATTGAAGTAAGAGC
66 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGC
46910244 AACGTC
131 AACGTC
46910250 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
*
46910315 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGC
66 GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGC
46910380 AACGTC
131 AACGTC
*
46910386 AT-CCCTTGAAATTGAAGTAGAGTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACA-AGTCTTCATCTCTGAAATTGAAGTAAGAGCAA
* *
46910449 CGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG
65 CGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAG
46910514 CAACGTC
130 CAACGTC
* *
46910521 ATCCGCTTGAAATTGAAGTAGAGTTGGATAACACA-TCTTTATCTCTGAAATTGAAGTAAGAGCA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACA-AGTCTTCATCTCTGAAATTGAAGTAAGAGCA
* * ** *
46910585 ATGTCATCCTCTTGAAATTGAAGTAGAGTGGATAACACGCCTTTATCTCTGAATTTGAAGTAAGA
64 ACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGA
*
46910650 GC-AGGATC
129 GCAACG-TC
* * **
46910658 ATTTCCTATCCTCCTGAAATTGAAGTAGAGCTGGATATCAAGCCTTTGTCCCTCTGAAATTGAAG
1 A--TCC---CCT--TGAAATTGAAGTAGAG-TGGATAACAAGTCTTCAT--CTCTGAAATTGAAG
46910723 TAAGAG
56 TAAGAG
46910729 TAAGATGAAG
Statistics
Matches: 720, Mismatches: 25, Indels: 26
0.93 0.03 0.03
Matches are distributed among these distances:
135 131 0.18
136 217 0.30
137 107 0.15
139 3 0.00
140 1 0.00
141 1 0.00
142 2 0.00
143 4 0.01
144 234 0.32
146 20 0.03
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (136 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGCAAC
GTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTATTTATCTCTGAAATTGAAGTAAGAGC
AACGTC
Found at i:46911082 original size:6 final size:6
Alignment explanation
Indices: 46911046--46911149 Score: 78
Period size: 6 Copynumber: 18.0 Consensus size: 6
46911036 GACTTTGATT
* * * *
46911046 TTTAAG TTTAAA -TTAAT TTTAAA TTT-TA TTTAGA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
46911090 TCTTAAA TTTAAA TTTATTTA TTTAAA TTT-AC TTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTA--AA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
46911139 -TTAAA TTTAAA
1 TTTAAA TTTAAA
46911150 AATAATATTA
Statistics
Matches: 78, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
4 4 0.05
5 18 0.23
6 49 0.63
7 2 0.03
8 5 0.06
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:46911083 original size:17 final size:16
Alignment explanation
Indices: 46911058--46911149 Score: 116
Period size: 17 Copynumber: 5.7 Consensus size: 16
46911048 TAAGTTTAAA
*
46911058 TTAATTTTAAATTTTAT
1 TTAAATTTAAA-TTTAT
*
46911075 TTAGATTTAAATTTAT
1 TTAAATTTAAATTTAT
46911091 CTTAAATTTAAATTTAT
1 -TTAAATTTAAATTTAT
46911108 TT--ATTTAAATTTACT
1 TTAAATTTAAATTTA-T
*
46911123 TTAAATTTAAATTTAA
1 TTAAATTTAAATTTAT
46911139 TTAAATTTAAA
1 TTAAATTTAAA
46911150 AATAATATTA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
14 11 0.16
15 3 0.04
16 18 0.27
17 35 0.52
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TTAAATTTAAATTTAT
Found at i:46911140 original size:11 final size:11
Alignment explanation
Indices: 46911046--46911149 Score: 68
Period size: 11 Copynumber: 9.0 Consensus size: 11
46911036 GACTTTGATT
46911046 TTTAAGTTTAAA
1 TTTAA-TTTAAA
46911058 -TTAATTTTAAA
1 TTTAA-TTTAAA
* *
46911069 TTTTATTTAGA
1 TTTAATTTAAA
**
46911080 TTTAAATTTATC
1 TTT-AATTTAAA
*
46911092 TTAAATTTAAA
1 TTTAATTTAAA
46911103 TTTATTTATTTAAA
1 TTTA---ATTTAAA
*
46911117 TTTACTTTAAA
1 TTTAATTTAAA
46911128 TTTAAATTT-AA
1 TTT-AATTTAAA
*
46911139 TTAAATTTAAA
1 TTTAATTTAAA
46911150 AATAATATTA
Statistics
Matches: 72, Mismatches: 13, Indels: 15
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.07
11 42 0.58
12 14 0.19
14 11 0.15
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:46913108 original size:161 final size:162
Alignment explanation
Indices: 46912767--46913108 Score: 553
Period size: 161 Copynumber: 2.1 Consensus size: 162
46912757 AATTAGTTTT
* **
46912767 CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCATTTTTTGGCTTATTTA
1 CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTCAGGCTTATTTA
* *
46912832 TTCATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATTAACTTTTATTTAATT
66 TGCATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATTAACTTTTACTTAATT
* *
46912897 ACAAAATTGGCCCAATAATTTTTCAAGGTTTA
131 ACAAAATTGGCCCAAGAATTTTTCAAGATTTA
* * *
46912929 TAAATTAGTCCTTTGACTGTTTGACTGCACCAG-GGACTGCCACGTGTCACTTTCAGGCTTATTT
1 CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGG-CTGCCACGTGTCACTTTCAGGCTTATTT
46912993 ATGCATTTAGTCCCTGACATTTTT-ATTTGTTTTAATTTAATCCCTAAATTAACTTTTACTTAAT
65 ATGCATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATTAACTTTTACTTAAT
*
46913057 TACGAAATTGGCCCAAGAATTTTTCAAGATTTA
130 TACAAAATTGGCCCAAGAATTTTTCAAGATTTA
*
46913090 CAATTTAATCCCTTGACTG
1 CAATTTAATCCTTTGACTG
46913109 CTGGATGCCT
Statistics
Matches: 164, Mismatches: 15, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
161 86 0.52
162 78 0.48
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (162 bp):
CAATTTAATCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTCAGGCTTATTTA
TGCATTTAGTCCCTGACATTTTTAATTTGTTTTAATTTAATCCCTAAATTAACTTTTACTTAATT
ACAAAATTGGCCCAAGAATTTTTCAAGATTTA
Found at i:46913243 original size:30 final size:28
Alignment explanation
Indices: 46913172--46913280 Score: 105
Period size: 29 Copynumber: 3.8 Consensus size: 28
46913162 TAGGTCCTCG
*
46913172 AAACTTCCAAAATTACCATTTTACCCCTA
1 AAACTTCTAAAATTACCATTTTACCCC-A
* *
46913201 AACCTTTTAAAATT-CCATTTTTAACCCCA
1 AAACTTCTAAAATTACCA-TTTT-ACCCCA
* *
46913230 AAACTTCCAAAAATTACCATTTTACTCCCG
1 AAACTT-CTAAAATTACCATTTTAC-CCCA
*
46913260 AACCTTCTAAAATT-CCATTTT
1 AAACTTCTAAAATTACCATTTT
46913281 TAACTCCGGT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
28 10 0.15
29 30 0.45
30 23 0.35
31 3 0.05
ACGTcount: A:0.36, C:0.28, G:0.01, T:0.35
Consensus pattern (28 bp):
AAACTTCTAAAATTACCATTTTACCCCA
Found at i:46913330 original size:58 final size:58
Alignment explanation
Indices: 46913178--46913640 Score: 530
Period size: 58 Copynumber: 8.0 Consensus size: 58
46913168 CTCGAAACTT
* * * *
46913178 CCAAAATTACCATTTTACCCCTAAACCTTT-TAAAATTCCATTTTTAACCCCAAAACTTC-
1 CCAAAATTACCATTTTACCCCTGAA-CTTTCCAAAATTCCATTTTTAACCCC--GATTTCA
* * * * *
46913237 CAAAAATTACCATTTTACTCCC-GAACCTTCTAAAATTCCATTTTTAACTCCGGTTTCA
1 CCAAAATTACCATTTTAC-CCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
46913295 CCAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCA-TTTTAACCTCGATTTCA
1 CCAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
*
46913352 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTTA
1 CC-AAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
46913410 CCAAAAATTACCATTTTACCCCTGAATTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CC-AAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
46913469 CCAAAAATTACCTTTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCTGATTTCA
1 CC-AAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
46913528 TCAAAATTACCATTTTA-CCCTCGAAGC-CT-CAAAAATCCATTTTTAACCCCGATTTCA
1 CCAAAATTACCATTTTACCCCT-GAA-CTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * ** * * *
46913585 CCAAAATTACCATTTTGCCCCCG-GGTATCCAAAATTCCCGTTTTCAACCCCGATTT
1 CCAAAATTACCATTTTACCCCTGAACTTTCCAAAATT-CCATTTTTAACCCCGATTT
46913641 TATCGGTTCT
Statistics
Matches: 352, Mismatches: 40, Indels: 25
0.84 0.10 0.06
Matches are distributed among these distances:
56 1 0.00
57 73 0.21
58 164 0.47
59 111 0.32
60 3 0.01
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:46913587 original size:233 final size:232
Alignment explanation
Indices: 46913180--46913642 Score: 600
Period size: 233 Copynumber: 2.0 Consensus size: 232
46913170 CGAAACTTCC
46913180 AAAATTACCATTTTACCCCTAAACCTTTTAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATT
1 AAAATTACCATTTTACCCCTAAACCTTTTAAAATTCCATTTTTAACCCC-AAACTTCCAAAAATT
* * *
46913245 ACCATTTTACTCCCGAACCTTCTAAAATTCCATTTTTAACTCCGGTTTCACCAAAATTACCATTT
65 ACCATTTTACTCCCAAACCTTCCAAAATTCCATTTTTAACTCCGATTTCACCAAAATTACCATTT
* * * * *
46913310 TACCCTTGAACTTTCCAAAATTCCATTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCT
130 TACCCTCGAACTCTCCAAAAATCCATTTTAACCCCGATTTCACC-AAAATTACCATTTTACCCCC
*
46913375 GAACTTTCCAAAATT-CCATTTT-AACCCCGATTTTACCA
194 G-ACTATCCAAAATTCCCATTTTCAACCCCGATTTTACCA
* * * *
46913413 AAAATTACCATTTTACCCCTGAA-TTTTCTAAAATTCCATTTTTAACCCC-GATTTCACCAAAAA
1 AAAATTACCATTTTACCCCTAAACCTTT-TAAAATTCCATTTTTAACCCCAAACTT--CCAAAAA
* * *
46913476 TTACCTTTTTAC-CCCTAAACTTTCCAAAATTCCATTTTTAAC-CCTGATTTCATCAAAATTACC
63 TTACCATTTTACTCCC-AAACCTTCCAAAATTCCATTTTTAACTCC-GATTTCACCAAAATTACC
*
46913539 ATTTTACCCTCGAAGC-CT-CAAAAATCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTG
126 ATTTTACCCTCGAA-CTCTCCAAAAATCCA-TTTTAACCCCGATTTCACCAAAATTACCATTTTA
** *
46913602 CCCCCGGGTATCCAAAATTCCCGTTTTCAACCCCGATTTTA
189 CCCCCGACTATCCAAAATTCCCATTTTCAACCCCGATTTTA
46913643 TCGGTTCTTA
Statistics
Matches: 201, Mismatches: 20, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
231 13 0.06
232 42 0.21
233 145 0.72
234 1 0.00
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (232 bp):
AAAATTACCATTTTACCCCTAAACCTTTTAAAATTCCATTTTTAACCCCAAACTTCCAAAAATTA
CCATTTTACTCCCAAACCTTCCAAAATTCCATTTTTAACTCCGATTTCACCAAAATTACCATTTT
ACCCTCGAACTCTCCAAAAATCCATTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCCGA
CTATCCAAAATTCCCATTTTCAACCCCGATTTTACCA
Found at i:46913606 original size:29 final size:29
Alignment explanation
Indices: 46913268--46913607 Score: 206
Period size: 29 Copynumber: 11.7 Consensus size: 29
46913258 CGAACCTTCT
* * *
46913268 AAAATT-CCATTTTTAACTCCGGTTTCACC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
**
46913297 AAAATTACCATTTTACCCTTGAACTTT--CC
1 AAAATTACCATTTTACCCCCG-A-TTTCACC
* *
46913326 AAAATT-CCATTTTAACCTCGATTTCACC
1 AAAATTACCATTTTACCCCCGATTTCACC
*
46913354 AAAAATTACCATTTTACCCCTGAACTTT--CC
1 -AAAATTACCATTTTACCCCCG-A-TTTCACC
* *
46913384 AAAATT-CCATTTTAACCCCGATTTTACC
1 AAAATTACCATTTTACCCCCGATTTCACC
* * *
46913412 AAAAATTACCATTTTACCCCTGAATTT-TCT
1 -AAAATTACCATTTTACCCCCG-ATTTCACC
*
46913442 AAAATT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
* **
46913471 AAAAATTACCTTTTTACCCCTAAACTTT--CC
1 -AAAATTACCATTTTACCCC-CGA-TTTCACC
* * *
46913501 AAAATT-CCATTTTTAACCCTGATTTCATC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
* **
46913530 AAAATTACCATTTTACCCTCGA-AGC-CTC
1 AAAATTACCATTTTACCCCCGATTTCAC-C
* *
46913558 AAAAAT-CCATTTTTAACCCCGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
*
46913587 AAAATTACCATTTTGCCCCCG
1 AAAATTACCATTTTACCCCCG
46913608 GGTATCCAAA
Statistics
Matches: 239, Mismatches: 43, Indels: 58
0.70 0.13 0.17
Matches are distributed among these distances:
26 6 0.03
27 8 0.03
28 55 0.23
29 101 0.42
30 52 0.22
31 11 0.05
32 6 0.03
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGATTTCACC
Found at i:46918066 original size:31 final size:29
Alignment explanation
Indices: 46918028--46918086 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
46918018 ACTCTTTGAA
*
46918028 GAAGTTGTTAGGTAGGACTCTTAGAATAAAG
1 GAAGTTGTT--GTAGGACTCTTAAAATAAAG
*
46918059 GAAGTTGTTTTAGGACTCTTAAAATAAA
1 GAAGTTGTTGTAGGACTCTTAAAATAAA
46918087 AATAGTACTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 17 0.65
31 9 0.35
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (29 bp):
GAAGTTGTTGTAGGACTCTTAAAATAAAG
Found at i:46921510 original size:25 final size:23
Alignment explanation
Indices: 46921469--46921514 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
46921459 CTAATTAGGG
46921469 AATTATTATTTAGATTTAATTCA
1 AATTATTATTTAGATTTAATTCA
*
46921492 AATTATCTTTTTAGAATTTAATT
1 AATTAT-TATTTAG-ATTTAATT
46921515 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (23 bp):
AATTATTATTTAGATTTAATTCA
Found at i:46929133 original size:15 final size:14
Alignment explanation
Indices: 46929115--46929162 Score: 53
Period size: 16 Copynumber: 3.3 Consensus size: 14
46929105 TATTATTTAG
46929115 AAAAAAGTTGAAAA
1 AAAAAAGTTGAAAA
*
46929129 GAAAAAA-ATGAAAA
1 -AAAAAAGTTGAAAA
46929143 AAAAAAGAATTGAAAA
1 AAAAAAG--TTGAAAA
46929159 AAAA
1 AAAA
46929163 TTGAGAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 6 0.21
14 6 0.21
15 6 0.21
16 10 0.36
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.10
Consensus pattern (14 bp):
AAAAAAGTTGAAAA
Found at i:46929136 original size:16 final size:14
Alignment explanation
Indices: 46929115--46929162 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 14
46929105 TATTATTTAG
*
46929115 AAAAAAGTTGAAAA
1 AAAAAAATTGAAAA
46929129 GAAAAAAA-TGAAAAA
1 -AAAAAAATTG-AAAA
46929144 AAAAAGAATTGAAAA
1 AAAAA-AATTGAAAA
46929159 AAAA
1 AAAA
46929163 TTGAGAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
14 7 0.24
15 20 0.69
16 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.10
Consensus pattern (14 bp):
AAAAAAATTGAAAA
Found at i:46943265 original size:32 final size:32
Alignment explanation
Indices: 46943204--46943266 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
46943194 CTTTCTAAAA
** *
46943204 TTACTCCTAAAATCATGCCCCAAACACTTAAC
1 TTACTCCTAAAATCATGCAACAAAAACTTAAC
* *
46943236 TTACTTCTAAAATCATGTAACAAAAACTTAA
1 TTACTCCTAAAATCATGCAACAAAAACTTAA
46943267 AAATTAAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.29
Consensus pattern (32 bp):
TTACTCCTAAAATCATGCAACAAAAACTTAAC
Found at i:46946981 original size:6 final size:6
Alignment explanation
Indices: 46946921--46947018 Score: 53
Period size: 6 Copynumber: 16.3 Consensus size: 6
46946911 TAAAATTCAT
* * * *
46946921 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* * *
46946967 TTT-AT TTTAAA TTTAGATT TGTTAAA TTTAAA TCT-AA TTTAAA TTTAGAA
1 TTTAAA TTTAAA TTTA-A-A T-TTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
46947017 TT
1 TT
46947019 AATGTAAATT
Statistics
Matches: 68, Mismatches: 14, Indels: 19
0.67 0.14 0.19
Matches are distributed among these distances:
4 2 0.03
5 14 0.21
6 40 0.59
7 7 0.10
8 2 0.03
9 3 0.04
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:46946986 original size:17 final size:17
Alignment explanation
Indices: 46946913--46947049 Score: 118
Period size: 17 Copynumber: 8.1 Consensus size: 17
46946903 AATCGTTTTA
* *
46946913 AAATTCATTTTAAAATT
1 AAATTTATTTTAAATTT
*
46946930 AAATTTATTTTAAAATT
1 AAATTTATTTTAAATTT
* *
46946947 AAATTTATGTTAAAGTT
1 AAATTTATTTTAAATTT
46946964 AAATTTATTTTAAATTT
1 AAATTTATTTTAAATTT
* *
46946981 AGA-TT-TGTTAAATTT
1 AAATTTATTTTAAATTT
* *
46946996 AAATCTAATTTAAATTT
1 AAATTTATTTTAAATTT
* *
46947013 AGAA-TTAATGTAAATTTT
1 A-AATTTATTTTAAA-TTT
* *
46947031 AAAATTATTATAAATTT
1 AAATTTATTTTAAATTT
46947048 AA
1 AA
46947050 TAGAGTGTCC
Statistics
Matches: 100, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
15 11 0.11
16 3 0.03
17 72 0.72
18 14 0.14
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (17 bp):
AAATTTATTTTAAATTT
Found at i:46947036 original size:18 final size:18
Alignment explanation
Indices: 46946996--46947047 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
46946986 TGTTAAATTT
*
46946996 AAATCTAATTTAAA-TTTA
1 AAAT-TAATATAAATTTTA
* *
46947014 GAATTAATGTAAATTTTA
1 AAATTAATATAAATTTTA
*
46947032 AAATTATTATAAATTT
1 AAATTAATATAAATTT
46947048 AATAGAGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
17 8 0.29
18 20 0.71
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
AAATTAATATAAATTTTA
Found at i:46949139 original size:58 final size:59
Alignment explanation
Indices: 46948988--46949175 Score: 179
Period size: 58 Copynumber: 3.2 Consensus size: 59
46948978 TCCAGAAATC
* * * *
46948988 ACCATTTTACCGCCGAATC-TTCCAAAATTCCATTTTTTA-CCCCGATTTCACCAAAATTT
1 ACCATTTTACCCCCCAAACTTTCCAAAATTCCA-TTTTGAGCCCCGATTTCA-CAAAATTT
* * * * * * * **
46949047 ACCGTTTT-GCCTCCGAACTTTCCAAAATTTCATTTTGA-CCTCGTTTTTGCTAAAATTT
1 ACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTGAGCCCCGATTTCAC-AAAATTT
* *
46949105 ACCATTTTACCCCCCAAACTTTCC-AAATTCCATTTTTAGCCCCGATTTCACAAAAATT
1 ACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTGAGCCCCGATTTCACAAAATTT
46949163 ACCATTTTACCCC
1 ACCATTTTACCCC
46949176 TAAAAGCCCA
Statistics
Matches: 101, Mismatches: 24, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
57 1 0.01
58 61 0.60
59 39 0.39
ACGTcount: A:0.27, C:0.30, G:0.06, T:0.37
Consensus pattern (59 bp):
ACCATTTTACCCCCCAAACTTTCCAAAATTCCATTTTGAGCCCCGATTTCACAAAATTT
Found at i:46950945 original size:196 final size:196
Alignment explanation
Indices: 46950625--46951055 Score: 702
Period size: 196 Copynumber: 2.2 Consensus size: 196
46950615 TCACATGAAT
*
46950625 TGTCGAGGACTCGTAAC-CTATGCGGTACCCCAGCCATCGGTACGGTGTCTATCTGTACTATAAA
1 TGTCGAGGACTCGCAACAC-ATGCGGTACCCCAGCCATCGGTACGGTGTCTATCTGTACTATAAA
* * *
46950689 CTGTTTCCTAATGATGCTACTCACACTAGCTATCAAGAGTATGCATAAAGTATAAGTCCCAACCA
65 CTGTTTCCTAACGATGCTACTCACACGAGCTATCAAGAGTATGCATAAAGCATAAGTCCCAACCA
*
46950754 TCGTAAGACCTATAATCCATATAGGATCCATATCTCTTTTCCGAGTCACGATACTGCTCACACAA
130 TCGTAAGACCTATAATCCATATAGGATCCATATCTCTTTTCCAAGTCACGATACTGCTCACACAA
46950819 GC
195 GC
*
46950821 TGTCGAGGACTCGCAACACATGCGGTACCCCAGCCATCGGTACGGTGTCTATCTGTACTGTAAAC
1 TGTCGAGGACTCGCAACACATGCGGTACCCCAGCCATCGGTACGGTGTCTATCTGTACTATAAAC
* * * * *
46950886 TGTTTCCTAACGATGCTGCTCATACGAGTTGTCAAGAGTATGCATAAAGCATAAGTCCCAGCCAT
66 TGTTTCCTAACGATGCTACTCACACGAGCTATCAAGAGTATGCATAAAGCATAAGTCCCAACCAT
* * * *
46950951 CGTAAGACCTGTAATCCATATAGGATCCATATCTCTTTTTCAAGTCACGATGCTGCTCACACGAG
131 CGTAAGACCTATAATCCATATAGGATCCATATCTCTTTTCCAAGTCACGATACTGCTCACACAAG
46951016 C
196 C
*
46951017 TGTCGAGGACTCGCAACACTTGCGGTACCCCAGCCATCG
1 TGTCGAGGACTCGCAACACATGCGGTACCCCAGCCATCG
46951056 TGTCGGTACT
Statistics
Matches: 218, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
196 217 1.00
197 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (196 bp):
TGTCGAGGACTCGCAACACATGCGGTACCCCAGCCATCGGTACGGTGTCTATCTGTACTATAAAC
TGTTTCCTAACGATGCTACTCACACGAGCTATCAAGAGTATGCATAAAGCATAAGTCCCAACCAT
CGTAAGACCTATAATCCATATAGGATCCATATCTCTTTTCCAAGTCACGATACTGCTCACACAAG
C
Found at i:46951858 original size:2 final size:2
Alignment explanation
Indices: 46951851--46951886 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
46951841 TTTTAATTTC
46951851 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
46951887 GGCAAACTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46958154 original size:18 final size:18
Alignment explanation
Indices: 46958127--46958164 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
46958117 TTAAGCATAT
46958127 ATGACATGAATTTAAACA
1 ATGACATGAATTTAAACA
* *
46958145 ATGACCTGAATTTAATCA
1 ATGACATGAATTTAAACA
46958163 AT
1 AT
46958165 CAGTTTCCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.13, G:0.11, T:0.32
Consensus pattern (18 bp):
ATGACATGAATTTAAACA
Found at i:46962578 original size:18 final size:18
Alignment explanation
Indices: 46962555--46962597 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
46962545 GAATAATTTT
46962555 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
46962573 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
46962591 TTAATTA
1 TTAATTA
46962598 TAATTGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:46963506 original size:21 final size:22
Alignment explanation
Indices: 46963461--46963503 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
46963451 AGTTTAATTT
*
46963461 TTTTTAATTAATAATATTAAAA
1 TTTTTAATTAATAAAATTAAAA
46963483 TTTTTAATT-ATGAAAATTAAA
1 TTTTTAATTAAT-AAAATTAAA
46963504 TTTATGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TTTTTAATTAATAAAATTAAAA
Found at i:46968112 original size:205 final size:206
Alignment explanation
Indices: 46967743--46968115 Score: 457
Period size: 205 Copynumber: 1.8 Consensus size: 206
46967733 AATAGCCATG
* * * * *
46967743 AAACTTATAAACTTGTGTTGATAGCTTGGCGGTGAAGGATACCATTAAAGGATGATGTGGGCCTC
1 AAACTTATAAACTTGTATTGATAGCCT-G-GGAGAAGGACACCATTAAAAGATGATGTGGGCCTC
* * ** * * * * * *
46967808 CAAAGATAAGAAGAGAGGTTGTGGGACGTGGAAAGTGGTCCTTTGAGGCGCCTCCAACGCCTTAG
64 CAAAGATAAAAAGAGAGATAATGAGACGTGCAAAGTGGTCCCTTGAGACGCCTCCAACACCTTAA
* * *
46967873 TCAATGTTTTAGGTTCAATCAATCTGACAATTTGATTATGTGAATCATAAAAAAATTTATTCCGT
129 TCAATATTTTAGGTTCAAACAATCTAACAATTTGATTATGTGAATCATAAAAAAATTTATTCCGT
46967938 ATGCAAGAAAAAT
194 ATGCAAGAAAAAT
* *
46967951 AAACTTATAAACTTGTATTGATAGCCT-GGAGATGGACACCATTAAAAGATGATGTGGGCCTGCA
1 AAACTTATAAACTTGTATTGATAGCCTGGGAGAAGGACACCATTAAAAGATGATGTGGGCCTCCA
* *
46968015 AAGATAAAAAGAGAGATAATGAGATGT-CAAATGTGGTCCCTTGAGACGCCTCCGACACCTTAAT
66 AAGATAAAAAGAGAGATAATGAGACGTGCAAA-GTGGTCCCTTGAGACGCCTCCAACACCTTAAT
* *
46968079 CAATATTTT-GGATTCAAACGATAC-AATAATTTGATTA
130 CAATATTTTAGG-TTCAAACAAT-CTAACAATTTGATTA
46968116 CGTAAATTTA
Statistics
Matches: 138, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
204 5 0.04
205 107 0.78
206 1 0.01
208 25 0.18
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (206 bp):
AAACTTATAAACTTGTATTGATAGCCTGGGAGAAGGACACCATTAAAAGATGATGTGGGCCTCCA
AAGATAAAAAGAGAGATAATGAGACGTGCAAAGTGGTCCCTTGAGACGCCTCCAACACCTTAATC
AATATTTTAGGTTCAAACAATCTAACAATTTGATTATGTGAATCATAAAAAAATTTATTCCGTAT
GCAAGAAAAAT
Found at i:46969225 original size:8 final size:8
Alignment explanation
Indices: 46969212--46969241 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
46969202 TTATTTTTTT
46969212 AAAATTTA
1 AAAATTTA
46969220 AAAATTTA
1 AAAATTTA
*
46969228 AAAATATA
1 AAAATTTA
46969236 AAAATT
1 AAAATT
46969242 ATTTTTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (8 bp):
AAAATTTA
Found at i:46977634 original size:26 final size:27
Alignment explanation
Indices: 46977586--46977637 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
46977576 GGTTACGTTG
*
46977586 TTGATTTTTTTTATATTAATATTTTGTT
1 TTGATTTTTTTTAGATT-ATATTTTGTT
46977614 TTGATTTTTTTTAGATT-TATTTTG
1 TTGATTTTTTTTAGATTATATTTTG
46977638 ATAAAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
28 16 0.70
ACGTcount: A:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (27 bp):
TTGATTTTTTTTAGATTATATTTTGTT
Found at i:46979559 original size:21 final size:21
Alignment explanation
Indices: 46979533--46979604 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
46979523 ACAAAACATT
46979533 ATGTTTGTAACTCTCCTCATA
1 ATGTTTGTAACTCTCCTCATA
* * *
46979554 ATGTTTGTAACTTTTCTCAAA
1 ATGTTTGTAACTCTCCTCATA
* *
46979575 ATATTTTGTAACTCTCCTCATT
1 AT-GTTTGTAACTCTCCTCATA
46979597 ATGTTTGT
1 ATGTTTGT
46979605 TTTAAATTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 25 0.61
22 16 0.39
ACGTcount: A:0.24, C:0.18, G:0.10, T:0.49
Consensus pattern (21 bp):
ATGTTTGTAACTCTCCTCATA
Found at i:46982218 original size:22 final size:22
Alignment explanation
Indices: 46982190--46982243 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
46982180 TGTAAGTCAG
**
46982190 ATTTTATTTTGGGAATTTTGGT
1 ATTTTATTTTGGGAATTTAAGT
* *
46982212 ATTTTATTTTGGGAGTTTAATT
1 ATTTTATTTTGGGAATTTAAGT
46982234 ATTTTATTTT
1 ATTTTATTTT
46982244 AAATAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.17, T:0.63
Consensus pattern (22 bp):
ATTTTATTTTGGGAATTTAAGT
Found at i:46997569 original size:16 final size:17
Alignment explanation
Indices: 46997545--46997584 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
46997535 TCTATCATAC
*
46997545 ATTTGTTTATTGAG-AA
1 ATTTTTTTATTGAGTAA
46997561 ATTTTTTTATTGAGTAA
1 ATTTTTTTATTGAGTAA
46997578 ATTTTTT
1 ATTTTTT
46997585 AAAATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (17 bp):
ATTTTTTTATTGAGTAA
Found at i:46997804 original size:27 final size:27
Alignment explanation
Indices: 46997766--46997821 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
46997756 ATACAAACTT
46997766 TAATGATCAAATTTATCATTAAGCCTA
1 TAATGATCAAATTTATCATTAAGCCTA
46997793 TAATGATCAAATTTATCATTAAGCCTA
1 TAATGATCAAATTTATCATTAAGCCTA
46997820 TA
1 TA
46997822 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (27 bp):
TAATGATCAAATTTATCATTAAGCCTA
Found at i:47001613 original size:13 final size:13
Alignment explanation
Indices: 47001595--47001646 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
47001585 AGTTTAGCAT
*
47001595 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
*
47001608 TGCTTTGGAAAAG
1 TGCTTTTGAAAAG
* * *
47001621 TGATTTTAAAAAT
1 TGCTTTTGAAAAG
*
47001634 TACTTTTGAAAAG
1 TGCTTTTGAAAAG
47001647 CTTGATTTAA
Statistics
Matches: 29, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:47015190 original size:31 final size:32
Alignment explanation
Indices: 47015155--47015224 Score: 115
Period size: 31 Copynumber: 2.2 Consensus size: 32
47015145 TTTTTGTTTC
47015155 AGTTAAATTTGACCCTCAATTTTTT-AAAAAA
1 AGTTAAATTTGACCCTCAATTTTTTGAAAAAA
* *
47015186 AGTTAAATTTGACTCTCAATTTTTTGAAAAAG
1 AGTTAAATTTGACCCTCAATTTTTTGAAAAAA
47015218 AGTTAAA
1 AGTTAAA
47015225 ATGATGTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (32 bp):
AGTTAAATTTGACCCTCAATTTTTTGAAAAAA
Found at i:47021871 original size:13 final size:13
Alignment explanation
Indices: 47021853--47021890 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
47021843 TTAACAAACC
*
47021853 ACATTTTTTCACA
1 ACATTTTTTCAAA
47021866 ACA-TTTTTCAAAA
1 ACATTTTTTC-AAA
47021879 ACATTTTTTCAA
1 ACATTTTTTCAA
47021891 CTCAAGCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 6 0.27
13 10 0.45
14 6 0.27
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (13 bp):
ACATTTTTTCAAA
Found at i:47030269 original size:15 final size:15
Alignment explanation
Indices: 47030251--47030294 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
47030241 GTAGGAGGCT
47030251 GAGCAATTGGTGGAG
1 GAGCAATTGGTGGAG
* * *
47030266 GAGCCATAGGTGGCG
1 GAGCAATTGGTGGAG
*
47030281 GAGCAAGTGGTGGA
1 GAGCAATTGGTGGA
47030295 AGGGCTGAGG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.25, C:0.11, G:0.48, T:0.16
Consensus pattern (15 bp):
GAGCAATTGGTGGAG
Found at i:47035155 original size:15 final size:15
Alignment explanation
Indices: 47035135--47035186 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
47035125 ACTACAAAAC
47035135 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
47035150 ATTTATAATTATAATAAAT
1 ATTTATTA-T-TAAT--AT
*
47035169 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
47035184 ATT
1 ATT
47035187 AATATTGAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:47035172 original size:19 final size:19
Alignment explanation
Indices: 47035148--47035184 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
47035138 TATTATTAAT
*
47035148 ATATTTATAATTATAATAA
1 ATATTTATAATTAAAATAA
*
47035167 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
47035185 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:47035911 original size:2 final size:2
Alignment explanation
Indices: 47035904--47035959 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
47035894 TACACTCACA
47035904 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
47035946 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
47035960 GTGTGTCTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47037313 original size:31 final size:29
Alignment explanation
Indices: 47037248--47037313 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
47037238 ATTTTAATAT
* * *
47037248 TTTTATAATTTTTAAAAGATTAAATTAAA
1 TTTTATAATTTTTAAAAAATCAAAATAAA
*
47037277 TTTTATTATTTTTAAAAAAATCAAAATATAA
1 TTTTATAATTTTT-AAAAAATCAAAATA-AA
47037308 TTTTAT
1 TTTTAT
47037314 GACTATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.39
30 11 0.35
31 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (29 bp):
TTTTATAATTTTTAAAAAATCAAAATAAA
Found at i:47037387 original size:22 final size:20
Alignment explanation
Indices: 47037349--47037395 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
47037339 TATAAAGTGC
*
47037349 TTAAATTAAAAATTTACCAT
1 TTAAATTAAAAAATTACCAT
47037369 TTAATATTAAAAAAATTACCAT
1 TTAA-ATT-AAAAAATTACCAT
*
47037391 CTAAA
1 TTAAA
47037396 AAGAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 15 0.65
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (20 bp):
TTAAATTAAAAAATTACCAT
Found at i:47037628 original size:3 final size:3
Alignment explanation
Indices: 47037613--47037652 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
47037603 ATATATACCA
* * *
47037613 ATC ATC ATG ATC ATC ATC ATC ATG ATC ATC ATT ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
47037653 CTGAAGCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:47037633 original size:15 final size:15
Alignment explanation
Indices: 47037613--47037650 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
47037603 ATATATACCA
47037613 ATCATCATGATCATC
1 ATCATCATGATCATC
47037628 ATCATCATGATCATC
1 ATCATCATGATCATC
*
47037643 ATTATCAT
1 ATCATCAT
47037651 CACTGAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (15 bp):
ATCATCATGATCATC
Found at i:47044424 original size:24 final size:26
Alignment explanation
Indices: 47044378--47044425 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
47044368 TATTATAACT
*
47044378 TTTTATTTTTAATTTAAATTTAATAA
1 TTTTATTTTTAATATAAATTTAATAA
47044404 TTTTA-TTTTAA-ATAAATTTAAT
1 TTTTATTTTTAATATAAATTTAAT
47044426 TATCATGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 10 0.48
25 6 0.29
26 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTATTTTTAATATAAATTTAATAA
Found at i:47044856 original size:25 final size:24
Alignment explanation
Indices: 47044803--47044856 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
47044793 TTATAATATA
**
47044803 TATAATTATAAATTTTGAAAAGTC
1 TATAATTATAAAAATTGAAAAGTC
*
47044827 AATAATATATAAAAATTGAAAATGT-
1 TATAAT-TATAAAAATTGAAAA-GTC
47044852 TATAA
1 TATAA
47044857 AAATTAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 5 0.21
25 17 0.71
26 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (24 bp):
TATAATTATAAAAATTGAAAAGTC
Found at i:47044993 original size:18 final size:16
Alignment explanation
Indices: 47044955--47045002 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 16
47044945 ATTAAAAATA
*
47044955 TTTTTAAATATTTTTAT
1 TTTTTACAT-TTTTTAT
47044972 TTTTTACATTTTTTAT
1 TTTTTACATTTTTTAT
47044988 AGTTTTTACATTTTT
1 --TTTTTACATTTTT
47045003 AATAATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 7 0.25
17 8 0.29
18 13 0.46
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTTACATTTTTTAT
Found at i:47048087 original size:96 final size:96
Alignment explanation
Indices: 47047910--47048093 Score: 230
Period size: 96 Copynumber: 1.9 Consensus size: 96
47047900 GAGAAGGGTG
* ** * * * *
47047910 TTTGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCGCAAATTTTCATAACCGA
1 TTTGATTATCTCGATTGGAAGAAAAATCGCACCTAGTGAGTTAAGGCACAAAGTTTCAAAACCGA
47047975 AGATAAGAAAACATTGCCTCGATTAAGGATA
66 AGATAAGAAAACATTGCCTCGATTAAGGATA
* *
47048006 TTTGATTATTTCGATTGGAAGAAAAATCGCACCTAGT-ATGTTAAGGTACAAAGTTTCAAAACTC
1 TTTGATTATCTCGATTGGAAGAAAAATCGCACCTAGTGA-GTTAAGGCACAAAGTTTCAAAAC-C
*
47048070 GAA-ATAA-AAGAATATTGCCTCGAT
64 GAAGATAAGAA-AACATTGCCTCGAT
47048094 ATTAAAGTTT
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 3 0.04
96 68 0.91
97 4 0.05
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (96 bp):
TTTGATTATCTCGATTGGAAGAAAAATCGCACCTAGTGAGTTAAGGCACAAAGTTTCAAAACCGA
AGATAAGAAAACATTGCCTCGATTAAGGATA
Found at i:47048411 original size:30 final size:28
Alignment explanation
Indices: 47048375--47048591 Score: 173
Period size: 30 Copynumber: 7.3 Consensus size: 28
47048365 TGGAGACTTG
*
47048375 GAAAGTTTAAGGGTAAAAATGTAATCTTTA
1 GAAAGTTT-AGGGTCAAAATGTAAT-TTTA
* *
47048405 GAAAGTTTTGGGATCAAAATATAATTTTA
1 GAAAGTTTAGGG-TCAAAATGTAATTTTA
* * *
47048434 AAGAAGTTTGGGGGCCAAAATGTAATTTATA
1 GA-AAGTTT-AGGGTCAAAATGTAATTT-TA
* * * *
47048465 GAAAGTTTTGGAGTTAAAATATAATTTTG
1 GAAAGTTTAGG-GTCAAAATGTAATTTTA
* *
47048494 GAAAAGTTCATGGGTCAAAATGTAATTTACA
1 G-AAAGTTTA-GGGTCAAAATGTAATTT-TA
* *
47048525 GAAAGTTTAGGGTCAAAATATAATTTTG
1 GAAAGTTTAGGGTCAAAATGTAATTTTA
*
47048553 GAAAAGTTTAGAGGTTAAAATGTAATTTTCA
1 G-AAAGTTTAG-GGTCAAAATGTAATTTT-A
*
47048584 AAAAGTTT
1 GAAAGTTT
47048592 TGGGGTTAAA
Statistics
Matches: 149, Mismatches: 27, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
28 1 0.01
29 37 0.25
30 102 0.68
31 9 0.06
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (28 bp):
GAAAGTTTAGGGTCAAAATGTAATTTTA
Found at i:47048457 original size:60 final size:60
Alignment explanation
Indices: 47048372--47048625 Score: 261
Period size: 60 Copynumber: 4.3 Consensus size: 60
47048362 AAATGGAGAC
* *
47048372 TTGG-AAAGTTTAAGGGTAAAAATGTAATCTT-TAGAAAGTTTTGGGATCAAAATATAATT
1 TTGGAAAAGTTTAGGGGTCAAAATGTAAT-TTATAGAAAGTTTTGGGATCAAAATATAATT
* * * *
47048431 TT-AAAGAAGTTTGGGGGCCAAAATGTAATTTATAGAAAGTTTT-GGAGTTAAAATATAATT
1 TTGGAA-AAGTTTAGGGGTCAAAATGTAATTTATAGAAAGTTTTGGGA-TCAAAATATAATT
* * * *
47048491 TTGGAAAAGTTCATGGGTCAAAATGTAATTTACAGAAAGTTTAGGG-TCAAAATATAATT
1 TTGGAAAAGTTTAGGGGTCAAAATGTAATTTATAGAAAGTTTTGGGATCAAAATATAATT
* * * * * *
47048550 TTGGAAAAGTTTAGAGGTTAAAATGTAATTT-TCAAAAAGTTTTGGGGTTAAAATACTATTT
1 TTGGAAAAGTTTAGGGGTCAAAATGTAATTTAT-AGAAAGTTTTGGGATCAAAATA-TAATT
*
47048611 TTGG-ATAGTTTAGGG
1 TTGGAAAAGTTTAGGG
47048626 ACTTTCAGGG
Statistics
Matches: 161, Mismatches: 25, Indels: 17
0.79 0.12 0.08
Matches are distributed among these distances:
59 58 0.36
60 91 0.57
61 12 0.07
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (60 bp):
TTGGAAAAGTTTAGGGGTCAAAATGTAATTTATAGAAAGTTTTGGGATCAAAATATAATT
Found at i:47048573 original size:119 final size:121
Alignment explanation
Indices: 47048372--47048615 Score: 302
Period size: 119 Copynumber: 2.0 Consensus size: 121
47048362 AAATGGAGAC
* * *
47048372 TTGG-AAAGTTTAAGGGTAAAAATGTAATCTTTAGAAAGTTTTGGGATCAAAATATAATTTTAAA
1 TTGGAAAAGTTCAAGGGTAAAAATGTAATCTTCAGAAAGTTTAGGGATCAAAATATAATTTTAAA
* * *
47048436 GAAGTTTGGGGGCCAAAATGTAATTTAT-AGAAAGTTTTGGAGTTAAAATA-TAATT
66 GAAGTTTAGAGGCCAAAATGTAATTT-TCAAAAAGTTTTGGAGTTAAAATACTAATT
* * *
47048491 TTGGAAAAGTTCATGGGTCAAAATGTAAT-TTACAGAAAGTTTAGGG-TCAAAATATAATTTTGG
1 TTGGAAAAGTTCAAGGGTAAAAATGTAATCTT-CAGAAAGTTTAGGGATCAAAATATAATTTT-A
** * *
47048554 AA-AAGTTTAGAGGTTAAAATGTAATTTTCAAAAAGTTTTGGGGTTAAAATACTATTT
64 AAGAAGTTTAGAGGCCAAAATGTAATTTTCAAAAAGTTTTGGAGTTAAAATACTAATT
47048611 TTGGA
1 TTGGA
47048616 TAGTTTAGGG
Statistics
Matches: 107, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
118 1 0.01
119 62 0.58
120 44 0.41
ACGTcount: A:0.39, C:0.04, G:0.21, T:0.36
Consensus pattern (121 bp):
TTGGAAAAGTTCAAGGGTAAAAATGTAATCTTCAGAAAGTTTAGGGATCAAAATATAATTTTAAA
GAAGTTTAGAGGCCAAAATGTAATTTTCAAAAAGTTTTGGAGTTAAAATACTAATT
Found at i:47048611 original size:30 final size:30
Alignment explanation
Indices: 47048477--47048612 Score: 96
Period size: 30 Copynumber: 4.5 Consensus size: 30
47048467 AAGTTTTGGA
* ** *
47048477 GTTAAAATATAATTTTGGAAAAGTTCATG-G
1 GTTAAAATCTAATTTTCAAAAAGTTTA-GAG
* * * *
47048507 GTCAAAATGTAATTTACAGAAAGTTTAG-G
1 GTTAAAATCTAATTTTCAAAAAGTTTAGAG
* * **
47048536 GTCAAAATATAATTTTGGAAAAGTTTAGAG
1 GTTAAAATCTAATTTTCAAAAAGTTTAGAG
* * *
47048566 GTTAAAATGTAATTTTCAAAAAGTTTTGGG
1 GTTAAAATCTAATTTTCAAAAAGTTTAGAG
*
47048596 GTTAAAATACTATTTTT
1 GTTAAAAT-CTAATTTT
47048613 GGATAGTTTA
Statistics
Matches: 84, Mismatches: 20, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
29 25 0.30
30 53 0.63
31 6 0.07
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (30 bp):
GTTAAAATCTAATTTTCAAAAAGTTTAGAG
Found at i:47049601 original size:3 final size:3
Alignment explanation
Indices: 47049595--47049649 Score: 74
Period size: 3 Copynumber: 17.7 Consensus size: 3
47049585 AGACTAATAT
**
47049595 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA CTTA ACA GTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA
47049642 TTA TTA TT
1 TTA TTA TT
47049650 CAATGTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
3 42 0.91
4 4 0.09
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:47050405 original size:7 final size:6
Alignment explanation
Indices: 47050378--47050432 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
47050368 TATATAAGTC
** *
47050378 TAAATT TAAA-T TAAATT TAAATTT TAAAAC AAAATT TAAATT TAAAATT
1 TAAATT TAAATT TAAATT TAAA-TT TAAATT TAAATT TAAATT T-AAATT
47050427 TAAATT
1 TAAATT
47050433 CAAAAATCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 5 0.12
6 23 0.57
7 12 0.30
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:47050424 original size:13 final size:13
Alignment explanation
Indices: 47050378--47050437 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
47050368 TATATAAGTC
47050378 TAAATTT-AAA-T
1 TAAATTTAAAATT
*
47050389 TAAATTTAAATTT
1 TAAATTTAAAATT
**
47050402 TAAA-ACAAAATT
1 TAAATTTAAAATT
47050414 TAAATTTAAAATT
1 TAAATTTAAAATT
*
47050427 TAAATTCAAAA
1 TAAATTTAAAA
47050438 ATCAATTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 7 0.18
12 11 0.28
13 21 0.54
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:47050431 original size:19 final size:18
Alignment explanation
Indices: 47050378--47050432 Score: 67
Period size: 19 Copynumber: 3.0 Consensus size: 18
47050368 TATATAAGTC
47050378 TAAATTT-AAATTAAATT
1 TAAATTTAAAATTAAATT
**
47050395 TAAATTTTAAAACAAAATT
1 TAAA-TTTAAAATTAAATT
47050414 TAAATTTAAAATTTAAATT
1 TAAATTTAAAA-TTAAATT
47050433 CAAAAATCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 4 0.13
18 10 0.32
19 17 0.55
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTAAAATTAAATT
Found at i:47056593 original size:16 final size:16
Alignment explanation
Indices: 47056573--47056625 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
47056563 AAAAATTATG
* *
47056573 TTTTCCAGCCTTCTAG
1 TTTTCCACCCTTCTAA
*
47056589 TTTTCTACCCCTTC-AA
1 TTTTCCA-CCCTTCTAA
*
47056605 TTTTCCATCCTTCTAA
1 TTTTCCACCCTTCTAA
47056621 TTTTC
1 TTTTC
47056626 TTTCCACTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 20 0.67
17 5 0.17
ACGTcount: A:0.15, C:0.32, G:0.04, T:0.49
Consensus pattern (16 bp):
TTTTCCACCCTTCTAA
Found at i:47064723 original size:16 final size:18
Alignment explanation
Indices: 47064697--47064729 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
47064687 GATACGAACT
47064697 AATTGAATTGAA-TAAAA
1 AATTGAATTGAACTAAAA
47064714 AATT-AATTGAACTAAA
1 AATTGAATTGAACTAAA
47064730 CAGATGAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (18 bp):
AATTGAATTGAACTAAAA
Found at i:47066937 original size:20 final size:20
Alignment explanation
Indices: 47066909--47066948 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
47066899 CTCTAATTAG
*
47066909 AATCTCTAAAAATTAGCTAT
1 AATCCCTAAAAATTAGCTAT
*
47066929 AATCCCTAAAGATTAGCTAT
1 AATCCCTAAAAATTAGCTAT
47066949 TCAATGCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (20 bp):
AATCCCTAAAAATTAGCTAT
Found at i:47083057 original size:2 final size:2
Alignment explanation
Indices: 47083052--47083077 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
47083042 GCACGCCTGT
47083052 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
47083078 TCTTTGTCTC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:47088491 original size:134 final size:134
Alignment explanation
Indices: 47088230--47088479 Score: 306
Period size: 134 Copynumber: 1.9 Consensus size: 134
47088220 CGATACCAAG
*
47088230 AGAAATTTATTAATACCAAATAAAAGTGATCGATATCGTATCAATACTTGATAAATACTTTGAAA
1 AGAAATTTATTAATACCAAATAAAAGTGATCGATACCGTATCAATACTTGATAAATACTTTGAAA
** ** * * * *
47088295 GTTAGAATACCAATTTCATATTGATACCAAAAAAAGTATTGATAAAAGTGTACCGCTATCGATAC
66 AATAGAATACCAATTTCATATCAATACCAAAAAAAGTATCGACAAAACTGTACAGCTATCGATAC
47088360 TTGA
131 TTGA
** *
47088364 AGAAATTTATTAATATTAAGCA-AAAAGT-ATTGATACCGTATCAATACTTGATAAATACTTTGA
1 AGAAATTTATTAATACCAA--ATAAAAGTGATCGATACCGTATCAATACTTGATAAATACTTTGA
** * ** *
47088427 AAAATAGAATGTCATTTTTGTATCAATACCAAAAAAGGTATCGACAAAACTGT
64 AAAATAGAATACCAATTTCATATCAATACCAAAAAAAGTATCGACAAAACTGT
47088480 GAATCTATCG
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
134 90 0.93
135 6 0.06
136 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (134 bp):
AGAAATTTATTAATACCAAATAAAAGTGATCGATACCGTATCAATACTTGATAAATACTTTGAAA
AATAGAATACCAATTTCATATCAATACCAAAAAAAGTATCGACAAAACTGTACAGCTATCGATAC
TTGA
Found at i:47089761 original size:23 final size:23
Alignment explanation
Indices: 47089735--47089778 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
47089725 CACTTATTGG
47089735 TAATTAATTATGTTTATATTTGT
1 TAATTAATTATGTTTATATTTGT
*
47089758 TAATTAGTTATGTTTATATTT
1 TAATTAATTATGTTTATATTT
47089779 TTTCAGTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
TAATTAATTATGTTTATATTTGT
Found at i:47090965 original size:28 final size:30
Alignment explanation
Indices: 47090920--47090976 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
47090910 AAATTAATAA
*
47090920 TGATAAAATTAT-ATTTTA-ATTTTAAAAG
1 TGATAAAATTATAATTTAATATTTTAAAAG
47090948 TGATAAAAATT-TAATTTAATATTTTAAAA
1 TGAT-AAAATTATAATTTAATATTTTAAAA
47090977 ATTATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 11 0.44
30 9 0.36
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (30 bp):
TGATAAAATTATAATTTAATATTTTAAAAG
Found at i:47091226 original size:24 final size:27
Alignment explanation
Indices: 47091198--47091255 Score: 72
Period size: 25 Copynumber: 2.3 Consensus size: 27
47091188 TTTATTTATT
47091198 AATATTAA-A-TTTATGTTATTT-TTGC
1 AATATTAACATTTTATGTT-TTTGTTGC
47091223 -ATA-TAACATTTTATGTTTTTGTTGC
1 AATATTAACATTTTATGTTTTTGTTGC
47091248 AATATTAA
1 AATATTAA
47091256 TTCATTTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
23 3 0.11
24 7 0.25
25 12 0.43
26 3 0.11
27 3 0.11
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (27 bp):
AATATTAACATTTTATGTTTTTGTTGC
Done.