Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 41 of 150
Found at i:11378902 original size:15 final size:17
Alignment explanation
Indices: 11378884--11378921 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 17
11378874 TTTTTTCATA
11378884 TTTTAATTTT-TAAT-T
1 TTTTAATTTTCTAATAT
11378899 TTTTAATTTTCTAATAT
1 TTTTAATTTTCTAATAT
11378916 TTTTAA
1 TTTTAA
11378922 AAAAATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.48
16 4 0.19
17 7 0.33
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTAATTTTCTAATAT
Found at i:11381615 original size:20 final size:20
Alignment explanation
Indices: 11381564--11381615 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
11381554 TTCAACTATG
*
11381564 ATTAAACTTAATCGCTTTAAT
1 ATTAAA-TTAATCACTTTAAT
*
11381585 ATTAAGA-TAATCACTTTGAT
1 ATTAA-ATTAATCACTTTAAT
11381605 ATTAAATTAAT
1 ATTAAATTAAT
11381616 AAAATGTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 1 0.04
20 20 0.74
21 5 0.19
22 1 0.04
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (20 bp):
ATTAAATTAATCACTTTAAT
Found at i:11383173 original size:165 final size:165
Alignment explanation
Indices: 11382894--11383226 Score: 614
Period size: 165 Copynumber: 2.0 Consensus size: 165
11382884 CTTAGACTAC
* *
11382894 GAAAAAGAAACCCTAGAAGATTCAGGGGCCGCTCCTGGCCTCCATGCGTGTTGCGCCTCCGCGCG
1 GAAAAAAAAACCCTAGAAGATTCAGGGGCCGCTCCTGGCCTCCATGCGTGCTGCGCCTCCGCGCG
*
11382959 CGTGCGTTCCCTCCGAGCTTGTACCTGCACAACAAAAATGGCAACAAGCAAGAAAATCAGGAAAA
66 CGTGCATTCCCTCCGAGCTTGTACCTGCACAACAAAAATGGCAACAAGCAAGAAAATCAGGAAAA
11383024 TCACAAATCAAAAGCAACAAGCAAATAATGCATTT
131 TCACAAATCAAAAGCAACAAGCAAATAATGCATTT
*
11383059 GAAAAAAAAACCCTAGAAGATTC-GGGCGCCGCTCCTGGCCTTCATGCGTGCTGCGCCTCCGCGC
1 GAAAAAAAAACCCTAGAAGATTCAGGG-GCCGCTCCTGGCCTCCATGCGTGCTGCGCCTCCGCGC
11383123 GCGTGCATTCCCTCCGAGCTTGTACCTGCACAACAAAAATGGCAACAAGCAAGAAAATCAGGAAA
65 GCGTGCATTCCCTCCGAGCTTGTACCTGCACAACAAAAATGGCAACAAGCAAGAAAATCAGGAAA
11383188 ATCACAAATCAAAAGCAACAAGCAAATAATGCATTT
130 ATCACAAATCAAAAGCAACAAGCAAATAATGCATTT
11383224 GAA
1 GAA
11383227 GTTAGCTTTT
Statistics
Matches: 163, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
164 3 0.02
165 160 0.98
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (165 bp):
GAAAAAAAAACCCTAGAAGATTCAGGGGCCGCTCCTGGCCTCCATGCGTGCTGCGCCTCCGCGCG
CGTGCATTCCCTCCGAGCTTGTACCTGCACAACAAAAATGGCAACAAGCAAGAAAATCAGGAAAA
TCACAAATCAAAAGCAACAAGCAAATAATGCATTT
Found at i:11386240 original size:17 final size:17
Alignment explanation
Indices: 11386218--11386251 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
11386208 TTCTGGGATG
11386218 ACTATTCACCACTGAAA
1 ACTATTCACCACTGAAA
11386235 ACTATTCACCACTGAAA
1 ACTATTCACCACTGAAA
11386252 GAGATAGTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.29, G:0.06, T:0.24
Consensus pattern (17 bp):
ACTATTCACCACTGAAA
Found at i:11391301 original size:19 final size:19
Alignment explanation
Indices: 11391264--11391299 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
11391254 TTGAGCAGAT
11391264 ATTCCTTTGAGATTCTTTC
1 ATTCCTTTGAGATTCTTTC
*
11391283 ATTCTTTTGA-ATTCTTT
1 ATTCCTTTGAGATTCTTT
11391300 TCCAAATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.17, C:0.17, G:0.08, T:0.58
Consensus pattern (19 bp):
ATTCCTTTGAGATTCTTTC
Found at i:11396274 original size:45 final size:45
Alignment explanation
Indices: 11396212--11397057 Score: 306
Period size: 45 Copynumber: 18.8 Consensus size: 45
11396202 GATTAAAGTT
*
11396212 ACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * **
11396257 ACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACTGAAGATG
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * * **
11396302 ACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * * * * **
11396347 ATAATTC-TATCTCTCTG-AGTTTGCAGTAGAGCAGATTAAAG-TT
1 ACAAGTCTTATCTCCCTGAAG-TTGCAGTGGAGCAGACTGAAGAAA
* *
11396390 ACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGAAA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * *
11396435 GCAAGTCTTATCCCCCTGAAGTTGCAGTGG-GACAGACTGAATATGGA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG-CAGACTGAAGA--AA
* * * * **
11396482 A-AA-TCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTAAAGCCA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * * * **
11396524 ATAATTC-TATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAG-TT
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
** * * * *
11396567 ACAAGTCTTGCCTCCCTG-AGTTTGCAGCGAAGCAGACTGACGATA
1 ACAAGTCTTATCTCCCTGAAG-TTGCAGTGGAGCAGACTGAAGAAA
* * * * * * * * * * *
11396612 GC-AGATCTTGTCTTCTTGTACTAGCAGCGAAGTAGA-TCGAAG-AC
1 ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-GAAGAAA
* * ** * * *
11396656 ACTAGCCTTGCCTCCCTG-AGTTTGCAGCGGAGTAGACTGAAGATA
1 ACAAGTCTTATCTCCCTGAAG-TTGCAGTGGAGCAGACTGAAGAAA
* * * * * * **
11396701 AC-AGATCTTGTCTTCCT-AAATTGGCAGCGAAGTAGA-TCGAAG-TT
1 ACAAG-TCTTATCTCCCTGAAGTT-GCAGTGGAGCAGACT-GAAGAAA
* * * * *
11396745 ACAAGTCTTATCTCACTGAAGTTGCAGTAGAACAAACTGAAGATA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * *
11396790 GCGAA-TCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTTTAAA
1 AC-AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG----AAA
* ** * * **
11396839 TTAC-AGATCTTATCTCTCTGAAGTTGCAGTAAAGGAGA-TCATATCAA
1 --ACAAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AGAAA
* * * * ** **
11396886 AC----CTTATCTCCATAAAGTTGTAGTGGAACAGGTTGAAG-TT
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * * * *
11396926 GCAAATCTTATCTCCCTGAAGTTGCATTGGAGTAGACTAAAGATA
1 ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
* * * *
11396971 GCGAA-TCTTATTTCCTTGAAGTTGCAGTGGAGCAGATTGAAGTTATAA
1 AC-AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG--A-AA
* *
11397019 ATTATAGATCTTATCTCCCTGAAGTTGTAGTGGAGCAGA
1 A-CA-AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
11397058 TTAACCCTAT
Statistics
Matches: 598, Mismatches: 150, Indels: 100
0.71 0.18 0.12
Matches are distributed among these distances:
40 1 0.00
41 22 0.04
42 4 0.01
43 29 0.05
44 196 0.33
45 272 0.45
46 7 0.01
47 4 0.01
48 2 0.00
49 4 0.01
50 2 0.00
51 55 0.09
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (45 bp):
ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAA
Found at i:11396420 original size:178 final size:178
Alignment explanation
Indices: 11396117--11396606 Score: 700
Period size: 178 Copynumber: 2.8 Consensus size: 178
11396107 ATAGATTGAA
* * * * * *
11396117 GAAGATGGCTAATTTTATCTCCCTGAAGTTGTAGTAGAGTAGATTAAAGCCAATAATCCTATCTC
1 GAAGATGACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
* * * *
11396182 CCTAAAGTTT-CAGTGGAACGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTACAGTGGAGCA
66 CCT-GAGTTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCA
*
11396246 GACTGAAGAAAACAAGTCTTATCCCCCTGAAGTTGCAGTGGGGCAGACT
130 GACTGAAGAAAACAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACT
11396295 GAAGATGACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
1 GAAGATGACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
* * *
11396360 TCTGAGTTTGCAGTAGAGCAGATTAAAGTTACAAGTCTTATCTCCTTGAAGTTGCAGTGGAGCAG
66 CCTGAGTTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
* *
11396425 ATTGAAGAAAGCAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACT
131 ACTGAAGAAAACAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACT
* * * *
11396473 GAATATGGA-AAATCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTAAAGCCAATAATTCTATCT
1 GAAGAT-GACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATTCTATCT
* ** * *
11396536 CCCTGAGGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTGCCTCCCTG-AGTTTGCAGCGAAGC
65 CCCTGAGTTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAG-TTGCAGTGGAGC
11396600 AGACTGA
129 AGACTGA
11396607 CGATAGCAGA
Statistics
Matches: 280, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
176 2 0.01
177 95 0.34
178 181 0.65
179 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (178 bp):
GAAGATGACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCAATAATTCTATCTC
CCTGAGTTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
ACTGAAGAAAACAAGTCTTATCCCCCTGAAGTTGCAGTGGGACAGACT
Found at i:11396512 original size:133 final size:133
Alignment explanation
Indices: 11396217--11396560 Score: 335
Period size: 133 Copynumber: 2.6 Consensus size: 133
11396207 AAGTTACAAG
* * *
11396217 TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTGAAGAAAACAAGTCTTATCCCCCTGAAGTTGC
1 TCTTATCTCCCT-AAGTTACAGTGGAGCAGATTAAAGAAAACAAGTCTTATCTCCCTGAAGTTGC
* * * * * *
11396282 AGTGGGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCA
65 AGTGGAGCAGATTGAAGAAGACAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCA
11396347 ATAA
130 ATAA
* * * * ** *
11396351 T-TCTATCTCTCTGAGTTTGCAGTAGAGCAGATTAAAG-TTACAAGTCTTATCTCCTTGAAGTTG
1 TCT-TATCTCCCTAAG-TTACAGTGGAGCAGATTAAAGAAAACAAGTCTTATCTCCCTGAAGTTG
*
11396414 CAGTGGAGCAGATTGAAGAA-AGCAAGTCTTATCCCCCTGAAGTTGCAGTGG-GACAGACTGAAT
64 CAGTGGAGCAGATTGAAGAAGA-CAAATCTTATCCCCCTGAAGTTGCAGTGGAG-CAGA-TGAA-
*
11396477 ATG-GAA-AA
125 A-GCCAATAA
* ** * * *
11396485 TCTTATCTCCCTAAAGTT-CAGTGGAGCAAATTAAAGCCAATAATTC-TATCTCCCTGAGGTTGC
1 TCTTATCTCCCT-AAGTTACAGTGGAGCAGATTAAAGAAAACAAGTCTTATCTCCCTGAAGTTGC
11396548 AGTGGAGCAGATT
65 AGTGGAGCAGATT
11396561 AAAGTTACAA
Statistics
Matches: 172, Mismatches: 28, Indels: 21
0.78 0.13 0.10
Matches are distributed among these distances:
132 2 0.01
133 116 0.67
134 47 0.27
135 6 0.03
136 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (133 bp):
TCTTATCTCCCTAAGTTACAGTGGAGCAGATTAAAGAAAACAAGTCTTATCTCCCTGAAGTTGCA
GTGGAGCAGATTGAAGAAGACAAATCTTATCCCCCTGAAGTTGCAGTGGAGCAGATGAAAGCCAA
TAA
Found at i:11396771 original size:89 final size:89
Alignment explanation
Indices: 11396562--11396753 Score: 267
Period size: 89 Copynumber: 2.2 Consensus size: 89
11396552 GAGCAGATTA
* *
11396562 AAGTTACAAGTCTTGCCTCCCTGAGTTTGCAGCGAAGCAGACTGACGATAGCAGATCTTGTCTTC
1 AAGTTACAAGTCTTGCCTCCCTGAGTTTGCAGCGAAGCAGACTGAAGATAACAGATCTTGTCTTC
* **
11396627 TTGTACTAGCAGCGAAGTAGATCG
66 CTAAACTAGCAGCGAAGTAGATCG
** * * * *
11396651 AAGACACTAGCCTTGCCTCCCTGAGTTTGCAGCGGAGTAGACTGAAGATAACAGATCTTGTCTTC
1 AAGTTACAAGTCTTGCCTCCCTGAGTTTGCAGCGAAGCAGACTGAAGATAACAGATCTTGTCTTC
* *
11396716 CTAAATTGGCAGCGAAGTAGATCG
66 CTAAACTAGCAGCGAAGTAGATCG
11396740 AAGTTACAAGTCTT
1 AAGTTACAAGTCTT
11396754 ATCTCACTGA
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
89 86 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.27
Consensus pattern (89 bp):
AAGTTACAAGTCTTGCCTCCCTGAGTTTGCAGCGAAGCAGACTGAAGATAACAGATCTTGTCTTC
CTAAACTAGCAGCGAAGTAGATCG
Found at i:11396863 original size:96 final size:94
Alignment explanation
Indices: 11396750--11397045 Score: 286
Period size: 96 Copynumber: 3.2 Consensus size: 94
11396740 AAGTTACAAG
* * *
11396750 TCTTATCTCACTGAAGTTGCAGTAGAACAAACTGAAGATAGCGAATCTTATTTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTAGAA-AGACTGAAGATAGCGAATCTTATTTCCATGAAGTTGC
11396815 AGTGGAACAGATTGAAGCTTTAAATTACAGA
65 AGTGGAACAGATTGAAG-TTTAAATTACAGA
* * ** * * * * * *
11396846 TCTTATCTCTCTGAAGTTGCAGTA-AAGGA--GATCATATCAAACCTTATCTCCATAAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTAGAAAGACTGAAGATAGCGAATCTTATTTCCATGAAGTTGCA
* * *
11396908 GTGGAACAGGTTGAAG------TTGCAAA
66 GTGGAACAGATTGAAGTTTAAATTACAGA
* * * * *
11396931 TCTTATCTCCCTGAAGTTGCATTGGAGTAGACTAAAGATAGCGAATCTTATTTCCTTGAAGTTGC
1 TCTTATCTCCCTGAAGTTGCAGTAGA-AAGACTGAAGATAGCGAATCTTATTTCCATGAAGTTGC
* *
11396996 AGTGGAGCAGATTGAAGTTATAAATTATAGA
65 AGTGGAACAGATTGAAGTT-TAAATTACAGA
11397027 TCTTATCTCCCTGAAGTTG
1 TCTTATCTCCCTGAAGTTG
11397046 TAGTGGAGCA
Statistics
Matches: 154, Mismatches: 35, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
85 26 0.17
86 1 0.01
87 2 0.01
89 37 0.24
92 39 0.25
94 1 0.01
95 2 0.01
96 46 0.30
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (94 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAAAGACTGAAGATAGCGAATCTTATTTCCATGAAGTTGCA
GTGGAACAGATTGAAGTTTAAATTACAGA
Found at i:11404963 original size:29 final size:30
Alignment explanation
Indices: 11404904--11404961 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
11404894 TCCGAGCCTT
*
11404904 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
11404934 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
11404962 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:11405192 original size:13 final size:13
Alignment explanation
Indices: 11405174--11405204 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11405164 TTCCAGCAAC
11405174 TATGAATTTATTT
1 TATGAATTTATTT
11405187 TATGAATTTATTT
1 TATGAATTTATTT
*
11405200 GATGA
1 TATGA
11405205 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:11405374 original size:50 final size:50
Alignment explanation
Indices: 11405299--11405491 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
11405289 ATTTGGGTAA
11405299 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* *
11405349 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
11405399 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
11405449 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
11405492 TGTTATTATC
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
50 94 0.73
51 34 0.27
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.21
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:11408917 original size:14 final size:14
Alignment explanation
Indices: 11408898--11408927 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
11408888 ATTGTGTTCG
*
11408898 TAGTTAATTTAGAT
1 TAGTTAAATTAGAT
11408912 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
11408926 TA
1 TA
11408928 AAAACAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:11414589 original size:14 final size:14
Alignment explanation
Indices: 11414570--11414599 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
11414560 TTTGTGTTCG
11414570 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
11414584 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
11414598 TA
1 TA
11414600 AAAACAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:11418677 original size:2 final size:2
Alignment explanation
Indices: 11418670--11418696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
11418660 ATTTATTATC
11418670 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
11418697 CATTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11424137 original size:167 final size:168
Alignment explanation
Indices: 11423858--11424195 Score: 651
Period size: 167 Copynumber: 2.0 Consensus size: 168
11423848 TTTATGATTT
11423858 TCTACTAATGGTATTTTTATAGAAGATTTTTCTATAGATAACATAATTAAATTTTTATCAATAGA
1 TCTACTAATGGTATTTTTATAGAAGATTTTTCTATAG--AACATAATTAAATTTTTATCAATAGA
11423923 AAATGGTAAATATTGATATATAAAATTATTTCCTAATAATATATCTTCATGCATTGCAGGAAAAC
64 AAATGGTAAATATTGATATATAAAATTATTTCCTAATAATATATCTTCATGCATTGCAGGAAAAC
11423988 ATAAAATTTTTGGTATCACAAATCTTACATTATTTATGTA
129 ATAAAATTTTTGGTATCACAAATCTTACATTATTTATGTA
11424028 TCTACTAATGGTATTTTTATAGAAGATTTTTCTATAG-ACATAATTAAATTTTTATCAATAGAAA
1 TCTACTAATGGTATTTTTATAGAAGATTTTTCTATAGAACATAATTAAATTTTTATCAATAGAAA
11424092 ATGGTAAATATTGATATATAAAATTATTTCCTAATAATATATCTTCATGCATTGCAGGAAAACAT
66 ATGGTAAATATTGATATATAAAATTATTTCCTAATAATATATCTTCATGCATTGCAGGAAAACAT
11424157 AAAATTTTTGGTATCACAAATCTTACATTATTTATGTA
131 AAAATTTTTGGTATCACAAATCTTACATTATTTATGTA
11424195 T
1 T
11424196 AGTGCTATAT
Statistics
Matches: 168, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
167 131 0.78
170 37 0.22
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (168 bp):
TCTACTAATGGTATTTTTATAGAAGATTTTTCTATAGAACATAATTAAATTTTTATCAATAGAAA
ATGGTAAATATTGATATATAAAATTATTTCCTAATAATATATCTTCATGCATTGCAGGAAAACAT
AAAATTTTTGGTATCACAAATCTTACATTATTTATGTA
Found at i:11427146 original size:15 final size:16
Alignment explanation
Indices: 11427108--11427157 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 16
11427098 TTTTTATTTG
11427108 TAGAAGATGATTCTTC
1 TAGAAGATGATTCTTC
11427124 TGAAGAAGATGATTCTTC
1 T--AGAAGATGATTCTTC
* *
11427142 T-GAAGAAGTTTCTTC
1 TAGAAGATGATTCTTC
11427157 T
1 T
11427158 TCTTCTTCAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
15 13 0.43
16 1 0.03
18 16 0.53
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (16 bp):
TAGAAGATGATTCTTC
Found at i:11427160 original size:18 final size:18
Alignment explanation
Indices: 11427109--11427149 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
11427099 TTTTATTTGT
11427109 AGAAGATGATTCTTCTGA
1 AGAAGATGATTCTTCTGA
11427127 AGAAGATGATTCTTCTGA
1 AGAAGATGATTCTTCTGA
11427145 AGAAG
1 AGAAG
11427150 TTTCTTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (18 bp):
AGAAGATGATTCTTCTGA
Found at i:11428236 original size:34 final size:35
Alignment explanation
Indices: 11428181--11428247 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
11428171 CAAACACCAG
*
11428181 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
11428216 AAAACATTTTCCCG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
11428248 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:11437166 original size:43 final size:42
Alignment explanation
Indices: 11437110--11437216 Score: 128
Period size: 43 Copynumber: 2.5 Consensus size: 42
11437100 CCAGGCAGGT
* *
11437110 TCTTACACGAAATCATATA-CGATACCGATGTTCCAGACATGG
1 TCTTACACGAAATCATATATCGATACCAACG-TCCAGACATGG
* * *
11437152 TCTTACACGTAAATC-TCAAATCGATGCCAACGTCCAGACGTGG
1 TCTTACACG-AAATCAT-ATATCGATACCAACGTCCAGACATGG
11437195 TCTTACACGAAATCATATATCG
1 TCTTACACGAAATCATATATCG
11437217 GAATCCAATG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
42 20 0.36
43 27 0.49
44 8 0.15
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
TCTTACACGAAATCATATATCGATACCAACGTCCAGACATGG
Found at i:11438343 original size:13 final size:13
Alignment explanation
Indices: 11438325--11438349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
11438315 ACAAACGATA
11438325 AAATTTTCACACG
1 AAATTTTCACACG
11438338 AAATTTTCACAC
1 AAATTTTCACAC
11438350 ATAAATTAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:11445347 original size:41 final size:41
Alignment explanation
Indices: 11445301--11445412 Score: 125
Period size: 41 Copynumber: 2.7 Consensus size: 41
11445291 AATTTATATT
* *
11445301 AATGTATCAAGCATTATGCCTAGCAGGCTTTATGCCGGTGA
1 AATGTATCAAGCTTTATGCCTAGCAGGCTTCATGCCGGTGA
* * * * *
11445342 AATGTATTATGCTTTATGCTTAGCAGGCTACATGCCGGTGT
1 AATGTATCAAGCTTTATGCCTAGCAGGCTTCATGCCGGTGA
*** *
11445383 ACCCTATCAGGCTTTATGCCTAGCAGGCTT
1 AATGTATCAAGCTTTATGCCTAGCAGGCTT
11445413 GGTATCGGTG
Statistics
Matches: 57, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (41 bp):
AATGTATCAAGCTTTATGCCTAGCAGGCTTCATGCCGGTGA
Found at i:11452355 original size:29 final size:28
Alignment explanation
Indices: 11452308--11452363 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
11452298 AATTCCATTT
11452308 ATTTCACATTTCAACCCCTCAATTTGCAC
1 ATTTCACATTTCAACCCCT-AATTTGCAC
*
11452337 ATTTCACAATTT-AATCCCTAATTTGCA
1 ATTTCAC-ATTTCAACCCCTAATTTGCA
11452364 TTTTTATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 13 0.52
30 4 0.16
ACGTcount: A:0.30, C:0.29, G:0.04, T:0.38
Consensus pattern (28 bp):
ATTTCACATTTCAACCCCTAATTTGCAC
Found at i:11460833 original size:22 final size:21
Alignment explanation
Indices: 11460805--11460871 Score: 64
Period size: 22 Copynumber: 3.1 Consensus size: 21
11460795 AGCTGCCAAT
11460805 TAACAGAACGGCTAAAAGCCA
1 TAACAGAACGGCTAAAAGCCA
* * *
11460826 TAAGCAGAAAGGC-AGTAAGCCT
1 TAA-CAGAACGGCTA-AAAGCCA
*
11460848 TGAACAGAACGGCTACAAGCCA
1 T-AACAGAACGGCTAAAAGCCA
11460870 TA
1 TA
11460872 CACTTCCCCC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.14
22 28 0.78
23 3 0.08
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (21 bp):
TAACAGAACGGCTAAAAGCCA
Found at i:11460990 original size:25 final size:25
Alignment explanation
Indices: 11460962--11461025 Score: 65
Period size: 26 Copynumber: 2.5 Consensus size: 25
11460952 ATCATAGACA
11460962 AAATTGTCATTTAACCTCGAGGGGT
1 AAATTGTCATTTAACCTCGAGGGGT
* * **
11460987 AAATAGTCATTCTACCCTTTAGGGGT
1 AAATTGTCATT-TAACCTCGAGGGGT
*
11461013 ATATTCGTCATTT
1 AAATT-GTCATTT
11461026 TACCCATCGA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
25 10 0.32
26 15 0.48
27 6 0.19
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.38
Consensus pattern (25 bp):
AAATTGTCATTTAACCTCGAGGGGT
Found at i:11461029 original size:27 final size:26
Alignment explanation
Indices: 11460992--11461059 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
11460982 GGGGTAAATA
* *
11460992 GTCATTCTACCCTTTAG-GGGTATATTC
1 GTCATTTTACCC-ATAGAGGGTAT-TTC
*
11461019 GTCATTTTACCCATCGAGGGTATTTC
1 GTCATTTTACCCATAGAGGGTATTTC
11461045 GATCATTTTACCCAT
1 G-TCATTTTACCCAT
11461060 CGGTGGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
26 6 0.17
27 30 0.83
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.40
Consensus pattern (26 bp):
GTCATTTTACCCATAGAGGGTATTTC
Found at i:11461060 original size:27 final size:27
Alignment explanation
Indices: 11461022--11461138 Score: 101
Period size: 27 Copynumber: 4.3 Consensus size: 27
11461012 TATATTCGTC
* *
11461022 ATTTTACCCATCGAGGGTATTTCGATC
1 ATTTTACCCATCGAGGGTATTTAGATA
* * * *
11461049 ATTTTACCCATCG-GTGGTAATAAAATT
1 ATTTTACCCATCGAG-GGTATTTAGATA
* * * *
11461076 ATTTTACCCTTCGAAGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTATTTAGATA
* * *
11461103 ATTTTTCCCATCGGGGGTATTTAGGTA
1 ATTTTACCCATCGAGGGTATTTAGATA
11461130 ATTTTACCC
1 ATTTTACCC
11461139 TACAGGGGCA
Statistics
Matches: 69, Mismatches: 19, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
26 1 0.01
27 68 0.99
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTATTTAGATA
Found at i:11461134 original size:54 final size:54
Alignment explanation
Indices: 11461022--11461139 Score: 128
Period size: 54 Copynumber: 2.2 Consensus size: 54
11461012 TATATTCGTC
* * * * *
11461022 ATTTTACCCATCGAGGGTATTTCGATCATTTTACCCATCGGTGGTAATAAAATT
1 ATTTTACCCTTCGAAGGTATTTCGATAATTTTACCCATCGGGGGTAATAAAATA
* * * * * **
11461076 ATTTTACCCTTCGAAGGTATTTTGGTAATTTTTCCCATCGGGGGTATTTAGGTA
1 ATTTTACCCTTCGAAGGTATTTCGATAATTTTACCCATCGGGGGTAATAAAATA
11461130 ATTTTACCCT
1 ATTTTACCCT
11461140 ACAGGGGCAT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (54 bp):
ATTTTACCCTTCGAAGGTATTTCGATAATTTTACCCATCGGGGGTAATAAAATA
Found at i:11463326 original size:152 final size:152
Alignment explanation
Indices: 11463088--11463383 Score: 484
Period size: 152 Copynumber: 1.9 Consensus size: 152
11463078 GACATACTTT
* * *
11463088 TGTGCAAAGTATCCTAACCGTTCCCTTGCTCACGGTCCAATACTTCTAGGCCCAAATTCTGGGCC
1 TGTGCAAAGTATCCTAACAGTTCCCTTGCTCAAGGCCCAATACTTCTAGGCCCAAATTCTGGGCC
* * * *
11463153 GTTACAATTCTACCCCTTTAAAGAAATTTTGTCCTTGAAATTTTCAACTATCATAACAGTCGCAC
66 ATTACAATTCTACCCCCTTAAAGAAATTTCGTCCTCGAAATTTTCAACTATCATAACAGTCGCAC
*
11463218 ATCCTCGCCTCCCATACTACAC
131 ATCCTCACCTCCCATACTACAC
* * * *
11463240 TGTGCACAGTTTCCTAACAGTTCCCTTGCTCAAGGCCCAATACTTCTAGGCCCAAGTTCTGGGGC
1 TGTGCAAAGTATCCTAACAGTTCCCTTGCTCAAGGCCCAATACTTCTAGGCCCAAATTCTGGGCC
11463305 ATTACAATTCTACCCCCTTAAAGAAATTTCGTCCTCGAAATTTTCAACTATCATAACAGTCGCAC
66 ATTACAATTCTACCCCCTTAAAGAAATTTCGTCCTCGAAATTTTCAACTATCATAACAGTCGCAC
11463370 ATCCTCACCTCCCA
131 ATCCTCACCTCCCA
11463384 CACAATGCTC
Statistics
Matches: 132, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
152 132 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.29
Consensus pattern (152 bp):
TGTGCAAAGTATCCTAACAGTTCCCTTGCTCAAGGCCCAATACTTCTAGGCCCAAATTCTGGGCC
ATTACAATTCTACCCCCTTAAAGAAATTTCGTCCTCGAAATTTTCAACTATCATAACAGTCGCAC
ATCCTCACCTCCCATACTACAC
Found at i:11464686 original size:22 final size:21
Alignment explanation
Indices: 11464646--11464712 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
11464636 AGCTGCTAAT
* * *
11464646 TAACAGAACGACTAAAAGCCA
1 TAACAGAAAGGCTAGAAGCCA
*
11464667 TAAGCAGAAAGGC-AGTAAGCCT
1 TAA-CAGAAAGGCTAG-AAGCCA
*
11464689 TGAACAGAATGGCTAGAAGCCA
1 T-AACAGAAAGGCTAGAAGCCA
11464711 TA
1 TA
11464713 CACCTCCGTC
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
21 5 0.14
22 27 0.75
23 4 0.11
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (21 bp):
TAACAGAAAGGCTAGAAGCCA
Found at i:11464878 original size:27 final size:27
Alignment explanation
Indices: 11464848--11464961 Score: 113
Period size: 27 Copynumber: 4.2 Consensus size: 27
11464838 TACCATTTGG
* *
11464848 GGGTATATCCATTATTTTACCCATCGA
1 GGGTATATCGATCATTTTACCCATCGA
* * *
11464875 GGGTATTTCGATCATTTTACCTATCGG
1 GGGTATATCGATCATTTTACCCATCGA
* *
11464902 GGGTA-ATTTGATCATTTTACCCTTCGA
1 GGGTATA-TCGATCATTTTACCCATCGA
* * * *
11464929 GGGTATTTCAATAATTTTACCCTTCGA
1 GGGTATATCGATCATTTTACCCATCGA
11464956 GGGTAT
1 GGGTAT
11464962 TTTGGTAATT
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (27 bp):
GGGTATATCGATCATTTTACCCATCGA
Found at i:11464904 original size:54 final size:54
Alignment explanation
Indices: 11464846--11464949 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 54
11464836 TCTACCATTT
* * *
11464846 GGGGGT-ATATCCATTATTTTACCCATCGAGGGTATTTCGATCATTTTACCTATC
1 GGGGGTAAT-TCCATCATTTTACCCATCGAGGGTATTTCAATAATTTTACCTATC
** *
11464900 GGGGGTAATTTGATCATTTTACCCTTCGAGGGTATTTCAATAATTTTACC
1 GGGGGTAATTCCATCATTTTACCCATCGAGGGTATTTCAATAATTTTACC
11464950 CTTCGAGGGT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 41 0.95
55 2 0.05
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (54 bp):
GGGGGTAATTCCATCATTTTACCCATCGAGGGTATTTCAATAATTTTACCTATC
Found at i:11464962 original size:27 final size:27
Alignment explanation
Indices: 11464861--11464963 Score: 138
Period size: 27 Copynumber: 3.8 Consensus size: 27
11464851 TATATCCATT
*
11464861 ATTTTACCCATCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATC
*
11464888 ATTTTA-CCTATCGGGGGTAATTT-GATC
1 ATTTTACCCT-TCGAGGGT-ATTTCGATC
* *
11464915 ATTTTACCCTTCGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATC
11464942 ATTTTACCCTTCGAGGGTATTT
1 ATTTTACCCTTCGAGGGTATTT
11464964 TGGTAATTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
26 6 0.09
27 54 0.81
28 7 0.10
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.41
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATC
Found at i:11464970 original size:27 final size:27
Alignment explanation
Indices: 11464861--11465004 Score: 134
Period size: 27 Copynumber: 5.4 Consensus size: 27
11464851 TATATCCATT
* *
11464861 ATTTTACCCATCGAGGGTATTTCGATC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
11464888 ATTTTA-CCTATCGGGGGTAATTT-GATC
1 ATTTTACCCT-TCGAGGGT-ATTTCGATA
*
11464915 ATTTTACCCTTCGAGGGTATTTCAATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
11464942 ATTTTACCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * * *
11464969 ATTTT-GCCTAT-GGGGGTATTTAGGTA
1 ATTTTACCCT-TCGAGGGTATTTCGATA
11464995 ATTTTACCCT
1 ATTTTACCCT
11465005 ACAGGGGCAT
Statistics
Matches: 99, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
26 27 0.27
27 65 0.66
28 7 0.07
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:11467690 original size:18 final size:18
Alignment explanation
Indices: 11467664--11467699 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
11467654 AGAATTCAAA
* *
11467664 TTCTTTTATTTATTATTT
1 TTCTCTTATTAATTATTT
11467682 TTCTCTTATTAATTATTT
1 TTCTCTTATTAATTATTT
11467700 AGAGATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
TTCTCTTATTAATTATTT
Found at i:11468962 original size:21 final size:22
Alignment explanation
Indices: 11468926--11468967 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
11468916 TGGTTTATAA
11468926 ATTTTTATATTAAATTTGATAC
1 ATTTTTATATTAAATTTGATAC
*
11468948 ATTTTTAT-TTTAATTTGATA
1 ATTTTTATATTAAATTTGATA
11468968 AACTAATACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (22 bp):
ATTTTTATATTAAATTTGATAC
Found at i:11469022 original size:60 final size:61
Alignment explanation
Indices: 11468932--11469066 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 61
11468922 ATAAATTTTT
* *
11468932 ATATTAAATTTGAT--ACA-TTTTTATTTTAATTTGATAAACTAATACAAAATAGTTTCTAA
1 ATATT-AATTTGATAAACATTTTTTATTGTAATTTGATAAACTAATACAAAATAGTATCTAA
* * * *
11468991 ATATTAATTTGGTAAACATTTTTTA-TGTAATTTGGTAAACTAATACAAAGTAGTATGTAA
1 ATATTAATTTGATAAACATTTTTTATTGTAATTTGATAAACTAATACAAAATAGTATCTAA
11469051 ATATTAATTTGATAAA
1 ATATTAATTTGATAAA
11469067 AAAATAATGT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
58 7 0.11
59 5 0.08
60 48 0.73
61 6 0.09
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (61 bp):
ATATTAATTTGATAAACATTTTTTATTGTAATTTGATAAACTAATACAAAATAGTATCTAA
Found at i:11469129 original size:29 final size:29
Alignment explanation
Indices: 11469037--11469131 Score: 77
Period size: 29 Copynumber: 3.1 Consensus size: 29
11469027 AAACTAATAC
* *
11469037 AAAGTAGTATGTAAATATTAATTTGATAA
1 AAAGTAATATTTAAATATTAATTTGATAA
*
11469066 AAA--AATAATGTTAAATAATTACATTATCTAAATAA
1 AAAGTAAT-AT-TTAAAT-ATTA-A-T-T-T-GATAA
11469101 AAAGTAATATTTAAATATTAATTTGATAA
1 AAAGTAATATTTAAATATTAATTTGATAA
11469130 AA
1 AA
11469132 GAAAAAGTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
27 2 0.04
28 2 0.04
29 14 0.27
30 5 0.10
31 2 0.04
32 2 0.04
33 2 0.04
34 5 0.10
35 13 0.25
36 2 0.04
37 3 0.06
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
AAAGTAATATTTAAATATTAATTTGATAA
Found at i:11469139 original size:34 final size:32
Alignment explanation
Indices: 11469037--11469141 Score: 92
Period size: 34 Copynumber: 3.2 Consensus size: 32
11469027 AAACTAATAC
* *
11469037 AAAGTAGTATGTAAATATTAATTTGAT-AAAA
1 AAAGTAATATTTAAATATTAATTTGATAAAAA
* *
11469068 AAA-TAAT-GTTAAATAATTACATTAT-CTAAATAA
1 AAAGTAATATTTAAAT-ATTA-ATT-TGATAAA-AA
11469101 AAAGTAATATTTAAATATTAATTTGATAAAAGAA
1 AAAGTAATATTTAAATATTAATTTGAT-AAA-AA
11469135 AAAGTAA
1 AAAGTAA
11469142 ACTTGAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
29 5 0.09
30 7 0.12
31 7 0.12
32 4 0.07
33 9 0.16
34 20 0.34
35 6 0.10
ACGTcount: A:0.55, C:0.02, G:0.09, T:0.34
Consensus pattern (32 bp):
AAAGTAATATTTAAATATTAATTTGATAAAAA
Found at i:11469816 original size:22 final size:23
Alignment explanation
Indices: 11469773--11469816 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
11469763 TAATTTGATA
*
11469773 AAATAAAAAAATTACATTTTAAG
1 AAATAAAAAAATTACATCTTAAG
* *
11469796 AAATTAAAAAGTTA-ATCTTAA
1 AAATAAAAAAATTACATCTTAA
11469817 TTCCACATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
AAATAAAAAAATTACATCTTAAG
Found at i:11471265 original size:38 final size:38
Alignment explanation
Indices: 11471223--11471304 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
11471213 AGTAAAGTTT
*
11471223 CTTAACATATATTTGGTTCAATACTAACAATAAGCATG
1 CTTAACATATATTTAGTTCAATACTAACAATAAGCATG
* ** * *
11471261 CTTAACATGTATTTAGTTCAATGGTGACAATAGGCATG
1 CTTAACATATATTTAGTTCAATACTAACAATAAGCATG
11471299 C-TAACA
1 CTTAACA
11471305 GTAATACAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
37 5 0.13
38 33 0.87
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (38 bp):
CTTAACATATATTTAGTTCAATACTAACAATAAGCATG
Found at i:11473402 original size:30 final size:31
Alignment explanation
Indices: 11473375--11473434 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
11473365 ATAAATATTG
*
11473375 AATTT-ATACATGAATTTTGGTTTAATATAC
1 AATTTCATACATGAACTTTGGTTTAATATAC
* *
11473405 AATTTCATATATTAACTTTGGTTTAATATA
1 AATTTCATACATGAACTTTGGTTTAATATA
11473435 ATTATACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (31 bp):
AATTTCATACATGAACTTTGGTTTAATATAC
Found at i:11474850 original size:91 final size:89
Alignment explanation
Indices: 11474693--11474895 Score: 210
Period size: 91 Copynumber: 2.3 Consensus size: 89
11474683 ACACTCTAGT
* * * * * * *
11474693 TTGTGGATGAACCACCAGTG-TTGCAGGTTAATACGCTGCTATTAGTTGCAAATACACAACAGGT
1 TTGTGGATGAACCACTAGTGTTTGCAGGTTAATAAGCTACCAGTAGTTACAAATACACAACAAGT
**
11474757 TTGCGGATAAAAATTGCCAGTAAAAA
66 TTGCAAATAAAAATTGCCAGT--AAA
* ***
11474783 TTGTGGATGAACCACTAGTGTTTGTAGGTTAATAAGCTACCAGTAGTTATGGATACACAACAAGT
1 TTGTGGATGAACCACTAGTGTTTGCAGGTTAATAAGCTACCAGTAGTTACAAATACACAACAAGT
* * *
11474848 TTGTAAATAAAAATTTCCAGTAAG
66 TTGCAAATAAAAATTGCCAGTAAA
* *
11474872 TTCGTGGATAAACCACTAATGTTT
1 TT-GTGGATGAACCACTAGTGTTT
11474896 ACAGATAAAC
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
89 4 0.04
90 38 0.41
91 51 0.55
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (89 bp):
TTGTGGATGAACCACTAGTGTTTGCAGGTTAATAAGCTACCAGTAGTTACAAATACACAACAAGT
TTGCAAATAAAAATTGCCAGTAAA
Found at i:11476403 original size:6 final size:6
Alignment explanation
Indices: 11476392--11476425 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
11476382 GGATTGTAAG
*
11476392 TTTTCA TTTTCA TTTTCA TTTTCA TTTCCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
11476426 TTGAAACCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.68
Consensus pattern (6 bp):
TTTTCA
Found at i:11476531 original size:9 final size:10
Alignment explanation
Indices: 11476512--11476540 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
11476502 CATTTCTCTT
11476512 TTTCTATTCA
1 TTTCTATTCA
11476522 TTTC-ATTCA
1 TTTCTATTCA
11476531 TTTCTATTCA
1 TTTCTATTCA
11476541 AACAAGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTCTATTCA
Found at i:11478884 original size:20 final size:21
Alignment explanation
Indices: 11478861--11478935 Score: 54
Period size: 20 Copynumber: 3.8 Consensus size: 21
11478851 AAAATTTTCC
*
11478861 AAAAAAATCTT-GAAAATTCA
1 AAAAAAATATTAGAAAATTCA
* *
11478881 AAAAGAATATTAGAAAATTTA
1 AAAAAAATATTAGAAAATTCA
*
11478902 AGAAATAA-A-TA-AAAA--CA
1 A-AAAAAATATTAGAAAATTCA
11478919 AATAAAAATATTAGAAA
1 AA-AAAAATATTAGAAA
11478936 TATAAACATT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 1 0.02
19 6 0.14
20 14 0.33
21 10 0.23
22 5 0.12
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.23
Consensus pattern (21 bp):
AAAAAAATATTAGAAAATTCA
Found at i:11478898 original size:21 final size:19
Alignment explanation
Indices: 11478860--11478899 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
11478850 TAAAATTTTC
*
11478860 CAAAAAAATCTTGAAAATT
1 CAAAAAAATATTGAAAATT
11478879 CAAAAAGAATATTAGAAAATT
1 CAAAAA-AATATT-GAAAATT
11478900 TAAGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
20 5 0.28
21 7 0.39
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.25
Consensus pattern (19 bp):
CAAAAAAATATTGAAAATT
Found at i:11479744 original size:33 final size:35
Alignment explanation
Indices: 11479700--11479767 Score: 106
Period size: 33 Copynumber: 2.0 Consensus size: 35
11479690 TCATAATGAG
11479700 AAAATATAATATATT-ATATATAAATTTTA-ATTTT
1 AAAATATAATAT-TTGATATATAAATTTTACATTTT
11479734 AAAA-ATAATATTTGATATATAAATTTTACATTTT
1 AAAATATAATATTTGATATATAAATTTTACATTTT
11479768 GAGAAAAGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
32 2 0.06
33 21 0.66
34 9 0.28
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
AAAATATAATATTTGATATATAAATTTTACATTTT
Found at i:11480318 original size:31 final size:32
Alignment explanation
Indices: 11480283--11480343 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
11480273 TTATATTGAG
*
11480283 AATCATTTTTATAATAATTA-ATTATGAGAGA
1 AATCATATTTATAATAATTATATTATGAGAGA
* *
11480314 AATCATATTTATATTAATTATATTTTGAGA
1 AATCATATTTATAATAATTATATTATGAGA
11480344 AAACACTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 18 0.69
32 8 0.31
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (32 bp):
AATCATATTTATAATAATTATATTATGAGAGA
Found at i:11483293 original size:12 final size:12
Alignment explanation
Indices: 11483278--11483335 Score: 53
Period size: 12 Copynumber: 4.8 Consensus size: 12
11483268 GTTCTTAGTG
*
11483278 TTTTGGTGTTGT
1 TTTTGTTGTTGT
** *
11483290 TTTTACTGTTAT
1 TTTTGTTGTTGT
*
11483302 TTTTGTTATTGT
1 TTTTGTTGTTGT
* *
11483314 TATTGTTTTTGT
1 TTTTGTTGTTGT
11483326 TTTTGTTGTT
1 TTTTGTTGTT
11483336 TGGGTGTTAT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
12 35 1.00
ACGTcount: A:0.07, C:0.02, G:0.19, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:11487345 original size:3 final size:3
Alignment explanation
Indices: 11487337--11487388 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
11487327 ATATGTAGGT
* *
11487337 ATA ATA ATA ATA ATA TATA ATA AAA ATA ATA ATA ACA A-A ATTA ATA
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
11487383 A-A ATA A
1 ATA ATA A
11487389 ACTAAAAACC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
2 4 0.10
3 33 0.79
4 5 0.12
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:11487357 original size:16 final size:16
Alignment explanation
Indices: 11487336--11487382 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
11487326 TATATGTAGG
*
11487336 TATAATAATAATAATA
1 TATAATAAAAATAATA
11487352 TATAATAAAAATAATA
1 TATAATAAAAATAATA
* *
11487368 -ATAACAAAATTAATA
1 TATAATAAAAATAATA
11487383 AAATAAACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 13 0.46
16 15 0.54
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (16 bp):
TATAATAAAAATAATA
Found at i:11487833 original size:23 final size:22
Alignment explanation
Indices: 11487790--11487847 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
11487780 AAAGGGTATC
* *
11487790 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
11487811 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
11487834 TACATATCATATCT
1 TACAAATCATATCT
11487848 AAGATTGCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:11487850 original size:19 final size:20
Alignment explanation
Indices: 11487803--11487874 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
11487793 AAATTAAATC
*
11487803 TCTAAGATTACAAAATCATA
1 TCTAAGATTACAATATCATA
11487823 TCTTCTAAGATTAC-ATATCATA
1 ---TCTAAGATTACAATATCATA
* *
11487845 TCTAAGATTGCGTATATCATA
1 TCTAAGATTAC-AATATCATA
11487866 TCTAAGATT
1 TCTAAGATT
11487875 GCATATCCTC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 10 0.22
21 17 0.38
22 7 0.16
23 11 0.24
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (20 bp):
TCTAAGATTACAATATCATA
Found at i:11487863 original size:21 final size:21
Alignment explanation
Indices: 11487837--11487876 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
11487827 CTAAGATTAC
11487837 ATATCATATCTAAGATTGCGT
1 ATATCATATCTAAGATTGCGT
11487858 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
11487877 ATATCCTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCGT
Found at i:11496459 original size:20 final size:20
Alignment explanation
Indices: 11496419--11496483 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 20
11496409 AAAAATTGCA
* *
11496419 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAAAATATAT
*
11496439 AAAAATTTCAAAAAATATAT
1 AAAAAATTCAAAAAATATAT
*
11496459 ATTTTAAAAATTCTAAAAATATAT
1 A----AAAAATTCAAAAAATATAT
11496483 A
1 A
11496484 TATGAAGAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 18 0.50
24 18 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTCAAAAAATATAT
Found at i:11496486 original size:26 final size:26
Alignment explanation
Indices: 11496431--11496484 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 26
11496421 AAAATTCAAA
11496431 ATATTTATAAAAATTTCAAAAAATAT
1 ATATTTATAAAAATTTCAAAAAATAT
*
11496457 ATATTT-TAAAAA-TTCTAAAAATAT
1 ATATTTATAAAAATTTCAAAAAATAT
11496481 ATAT
1 ATAT
11496485 ATGAAGAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 15 0.56
25 6 0.22
26 6 0.22
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATTTATAAAAATTTCAAAAAATAT
Found at i:11496502 original size:26 final size:24
Alignment explanation
Indices: 11496428--11496505 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
11496418 AAAAAAATTC
*
11496428 AAAATAT-T-TAT-AAAAATTTCAA
1 AAAATATATATATGAAAAA-TTAAA
* * **
11496450 AAAATATATATTTTAAAAATTCTA
1 AAAATATATATATGAAAAATTAAA
11496474 AAAATATATATATGAAGAAAGTTAAA
1 AAAATATATATATGAA-AAA-TTAAA
11496500 AAAATA
1 AAAATA
11496506 AAAATTTTCT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
22 7 0.16
23 1 0.02
24 20 0.44
25 8 0.18
26 9 0.20
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATATATATATGAAAAATTAAA
Found at i:11497696 original size:22 final size:22
Alignment explanation
Indices: 11497671--11497713 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
11497661 TATCCAAACA
11497671 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
11497693 ATAATAGTAAAATGGTAGCAA
1 ATAACAATAAAATAGTAGCAA
11497714 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:11499403 original size:17 final size:17
Alignment explanation
Indices: 11499375--11499440 Score: 87
Period size: 17 Copynumber: 3.9 Consensus size: 17
11499365 TTCATGCATA
*
11499375 ATAATAGATCATTCAAT
1 ATAATAGTTCATTCAAT
* *
11499392 ATAGTAGTTCATACAAT
1 ATAATAGTTCATTCAAT
*
11499409 ATAACAGTTCATTCAAT
1 ATAATAGTTCATTCAAT
*
11499426 ATAATAATTCATTCA
1 ATAATAGTTCATTCA
11499441 TACAACATCA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.44, C:0.14, G:0.06, T:0.36
Consensus pattern (17 bp):
ATAATAGTTCATTCAAT
Found at i:11500108 original size:18 final size:18
Alignment explanation
Indices: 11500085--11500145 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
11500075 AATTTGACAA
11500085 ATTAATACAGTTCACCAT
1 ATTAATACAGTTCACCAT
** *
11500103 ATTAATACAAATCACCAA
1 ATTAATACAGTTCACCAT
*
11500121 ATTAACACAGTTCACCAT
1 ATTAATACAGTTCACCAT
*
11500139 AATAATA
1 ATTAATA
11500146 TAATTCGCCA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (18 bp):
ATTAATACAGTTCACCAT
Found at i:11500171 original size:36 final size:36
Alignment explanation
Indices: 11500082--11500163 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
11500072 CACAATTTGA
* *
11500082 CAAATTAATACAGTTCACCATATTAATACAAATCAC
1 CAAATTAACACAGTTCACCATAATAATACAAATCAC
* * *
11500118 CAAATTAACACAGTTCACCATAATAATATAATTCGC
1 CAAATTAACACAGTTCACCATAATAATACAAATCAC
*
11500154 CAAGTTAACA
1 CAAATTAACA
11500164 TGGTTCACAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (36 bp):
CAAATTAACACAGTTCACCATAATAATACAAATCAC
Found at i:11500466 original size:32 final size:30
Alignment explanation
Indices: 11500393--11500505 Score: 102
Period size: 29 Copynumber: 3.5 Consensus size: 30
11500383 ACAAAATCCT
* *
11500393 TATATATATTATATAAAACAAAACCCATATATGCA
1 TATATAT-TTATATATAACAAAACCC----ACGCA
*
11500428 TATATATTATATATATAATCAAGACCCACGCA
1 TATATATT-TATATATAA-CAAAACCCACGCA
*
11500460 TATATA-TTATATATAACAAAACCCATGCA
1 TATATATTTATATATAACAAAACCCACGCA
*
11500489 TATATATATTGTATATA
1 TATATAT-TTATATATA
11500506 TACACATACC
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
29 17 0.25
30 9 0.13
31 9 0.13
32 10 0.15
34 1 0.01
35 15 0.22
36 7 0.10
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (30 bp):
TATATATTTATATATAACAAAACCCACGCA
Found at i:11500503 original size:29 final size:31
Alignment explanation
Indices: 11500423--11500497 Score: 109
Period size: 29 Copynumber: 2.5 Consensus size: 31
11500413 AAACCCATAT
*
11500423 ATGCATATATATTATATATATAATCAAGACCC
1 ATGCATATATA-TATATATATAATCAAAACCC
*
11500455 ACGCATATATAT-TATATATAA-CAAAACCC
1 ATGCATATATATATATATATAATCAAAACCC
11500484 ATGCATATATATAT
1 ATGCATATATATAT
11500498 TGTATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 18 0.46
30 10 0.26
31 1 0.03
32 10 0.26
ACGTcount: A:0.45, C:0.16, G:0.05, T:0.33
Consensus pattern (31 bp):
ATGCATATATATATATATATAATCAAAACCC
Found at i:11505882 original size:25 final size:28
Alignment explanation
Indices: 11505820--11505883 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 28
11505810 AAATTTATTT
*
11505820 TTTTATATTATA-ATTATAGTATTTTAA
1 TTTTAGATTATATATTATAGTATTTTAA
11505847 -TTTAGGA-TATATATTA-A-TATTTTAA
1 TTTTA-GATTATATATTATAGTATTTTAA
11505872 TTTTA-ATTATAT
1 TTTTAGATTATAT
11505884 GTTGTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
24 1 0.03
25 13 0.41
26 13 0.41
27 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTTAGATTATATATTATAGTATTTTAA
Found at i:11506431 original size:22 final size:21
Alignment explanation
Indices: 11506402--11506446 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
11506392 AACTATATGT
* *
11506402 ATATATAGATATATTAGATTG
1 ATATATAGAAATATTAAATTG
*
11506423 ATATGATAGAAATTTTAAATTG
1 ATAT-ATAGAAATATTAAATTG
11506445 AT
1 AT
11506447 TAAAAAATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.42
Consensus pattern (21 bp):
ATATATAGAAATATTAAATTG
Found at i:11507515 original size:14 final size:14
Alignment explanation
Indices: 11507496--11507522 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
11507486 CAACACTTAT
11507496 AAAATTTAGTATTA
1 AAAATTTAGTATTA
11507510 AAAATTTAGTATT
1 AAAATTTAGTATT
11507523 TAATTTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (14 bp):
AAAATTTAGTATTA
Found at i:11517922 original size:10 final size:10
Alignment explanation
Indices: 11517907--11517948 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
11517897 CAACCTAATT
11517907 TTTATGTTTA
1 TTTATGTTTA
11517917 TTTATGTTTA
1 TTTATGTTTA
*
11517927 -TTATTTTTA
1 TTTATGTTTA
11517936 TTTA--TTTA
1 TTTATGTTTA
11517944 TTTAT
1 TTTAT
11517949 TTATTTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
8 8 0.28
9 8 0.28
10 13 0.45
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTATGTTTA
Found at i:11517939 original size:4 final size:4
Alignment explanation
Indices: 11517913--11517965 Score: 54
Period size: 4 Copynumber: 12.5 Consensus size: 4
11517903 AATTTTTATG
*
11517913 TTTA TTTA TGTTTA TTATT TTTA TTTA TTTA TTTA TTTA TTT- TATTA
1 TTTA TTTA --TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA T-TTA
11517960 TTTA TT
1 TTTA TT
11517966 GTCACTTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
3 1 0.02
4 33 0.79
5 4 0.10
6 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:11529449 original size:43 final size:43
Alignment explanation
Indices: 11529346--11529450 Score: 129
Period size: 43 Copynumber: 2.4 Consensus size: 43
11529336 TGTGATTTTG
* * * * *
11529346 TGTAAGACCATGTCTGAGACATTGGCATCGATATGAGATTACG
1 TGTAAGACCATGTCTGGGACAGTGACATCGATATGAGATAACA
* * *
11529389 TGTAAGACCCTGCCTGGGACAGTGACATCGATATGTGATAACA
1 TGTAAGACCATGTCTGGGACAGTGACATCGATATGAGATAACA
*
11529432 TGTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
11529451 TATGGCATTG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGACATCGATATGAGATAACA
Found at i:11538710 original size:15 final size:17
Alignment explanation
Indices: 11538685--11538721 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
11538675 ATGTGAATAA
11538685 TATTATTTAAAA-TTAC
1 TATTATTTAAAATTTAC
11538701 TATT-TTTAAAATTTAC
1 TATTATTTAAAATTTAC
11538717 TATTA
1 TATTA
11538722 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATTTAAAATTTAC
Found at i:11538745 original size:18 final size:18
Alignment explanation
Indices: 11538707--11538742 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
11538697 TTACTATTTT
*
11538707 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
11538725 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
11538743 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:11538756 original size:13 final size:13
Alignment explanation
Indices: 11538736--11538790 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
11538726 AAAATTTAAA
11538736 TATT-AAATAATT
1 TATTAAAATAATT
11538748 TATTAAAATAATT
1 TATTAAAATAATT
* * *
11538761 AATTATATTAATT
1 TATTAAAATAATT
11538774 ATATT--AATAATT
1 -TATTAAAATAATT
11538786 TATTA
1 TATTA
11538791 TATGACTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.11
12 10 0.29
13 18 0.51
14 3 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTAAAATAATT
Found at i:11550913 original size:16 final size:16
Alignment explanation
Indices: 11550892--11550934 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
11550882 CTCTCAACAT
11550892 TTAATTAAATTTGATA
1 TTAATTAAATTTGATA
* * *
11550908 TTAATTTAGTTTGATT
1 TTAATTAAATTTGATA
11550924 TTAATTTAAAT
1 TTAA-TTAAAT
11550935 GAAGATTAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (16 bp):
TTAATTAAATTTGATA
Found at i:11557983 original size:30 final size:30
Alignment explanation
Indices: 11557949--11558011 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
11557939 AGTTGCTCCG
11557949 AACTCTGATACAGCAACCTCATAAGTTTCC
1 AACTCTGATACAGCAACCTCATAAGTTTCC
11557979 AACTCTGATACAGCAACCTCATAAGTTTCC
1 AACTCTGATACAGCAACCTCATAAGTTTCC
11558009 AAC
1 AAC
11558012 AATTTCCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (30 bp):
AACTCTGATACAGCAACCTCATAAGTTTCC
Found at i:11573666 original size:19 final size:19
Alignment explanation
Indices: 11573642--11573682 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
11573632 ATGGCTTATT
11573642 TTATATTAATTTGAATATA
1 TTATATTAATTTGAATATA
11573661 TTATATTAATTTGAATATA
1 TTATATTAATTTGAATATA
11573680 TTA
1 TTA
11573683 CAAAACCGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (19 bp):
TTATATTAATTTGAATATA
Found at i:11587322 original size:31 final size:29
Alignment explanation
Indices: 11587258--11587326 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
11587248 ACGATAATGT
* *
11587258 AAGTGACTAAAATGTAACATTGCAAACAT
1 AAGTGACTAAAATGTAACATGGCAAACAA
* *
11587287 AAGTGACTAAAATGTAACCTGAGGTAAACAA
1 AAGTGACTAAAATGTAACAT--GGCAAACAA
11587318 AAGTGACTA
1 AAGTGACTA
11587327 TTTTGGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.48, C:0.13, G:0.17, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATGGCAAACAA
Found at i:11595034 original size:16 final size:16
Alignment explanation
Indices: 11594981--11595040 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
11594971 AATATGATTT
*
11594981 TCCCTAATTCAAATTA
1 TCCCTAATGCAAATTA
*
11594997 T-CCTAAGTATGC-AATGA
1 TCCCT-A--ATGCAAATTA
11595014 TCCCTAATGCAAATTA
1 TCCCTAATGCAAATTA
11595030 TCCCTAATGCA
1 TCCCTAATGCA
11595041 TTTAGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
15 7 0.19
16 17 0.47
17 6 0.17
18 6 0.17
ACGTcount: A:0.35, C:0.25, G:0.08, T:0.32
Consensus pattern (16 bp):
TCCCTAATGCAAATTA
Found at i:11598612 original size:24 final size:24
Alignment explanation
Indices: 11598596--11598647 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
11598586 AATCAAAATC
*
11598596 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATGCT
*
11598620 AAATATATTATACTAATAAATACT
1 AAATATATTATACTAATAAATGCT
11598644 AAAT
1 AAAT
11598648 CTTTTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATGCT
Found at i:11601540 original size:36 final size:36
Alignment explanation
Indices: 11601457--11601639 Score: 169
Period size: 36 Copynumber: 5.1 Consensus size: 36
11601447 AACTTAGATG
* ** *
11601457 GGTTGCCTTAGATGGGTCTATCCCAACTTTTTTTAAA
1 GGTTACCTTAGACAGGTCTATCCCAAC-CTTTTTAAA
*
11601494 GGTTGCCTTAGACAAGGTCTATCCCAACCTTTTT-AA
1 GGTTACCTTAGAC-AGGTCTATCCCAACCTTTTTAAA
* * * *
11601530 GGTTATCTTAGAC---TTTATACCAACATTTTTTAAA
1 GGTTACCTTAGACAGGTCTATCCCAAC-CTTTTTAAA
* * *
11601564 GGTTGCCTCAGGCAAGGTCTATCCCAACCTTTTT-AA
1 GGTTACCTTAGAC-AGGTCTATCCCAACCTTTTTAAA
*
11601600 GGTTACCTTAGACAGGTCTATCCCAACATTTTTTAAA
1 GGTTACCTTAGACAGGTCTATCCCAAC-CTTTTTAAA
11601637 GGT
1 GGT
11601640 ATGCCTTGAC
Statistics
Matches: 118, Mismatches: 19, Indels: 18
0.76 0.12 0.12
Matches are distributed among these distances:
32 9 0.08
33 5 0.04
34 11 0.09
35 14 0.12
36 30 0.25
37 27 0.23
38 22 0.19
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (36 bp):
GGTTACCTTAGACAGGTCTATCCCAACCTTTTTAAA
Found at i:11601559 original size:70 final size:71
Alignment explanation
Indices: 11601472--11601646 Score: 253
Period size: 70 Copynumber: 2.4 Consensus size: 71
11601462 CCTTAGATGG
* * *
11601472 GTCTATCCCAACTTTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTATC
1 GTCTATACCAACATTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACC
11601537 TTAGAC
66 TTAGAC
* * *
11601543 -TTTATACCAACATTTTTTAAAGGTTGCCTCAGGCAAGGTCTATCCCAACCTTTTTAAGGTTACC
1 GTCTATACCAACATTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACC
11601607 TTAGAC
66 TTAGAC
*
11601613 AGGTCTATCCCAACATTTTTTAAAGGTATGCCTT
1 --GTCTATACCAACATTTTTTAAAGGT-TGCCTT
11601647 GACTAAGTCT
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
70 64 0.70
73 22 0.24
74 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (71 bp):
GTCTATACCAACATTTTTTAAAGGTTGCCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTACC
TTAGAC
Found at i:11609152 original size:19 final size:21
Alignment explanation
Indices: 11609130--11609172 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
11609120 ATAAAAGACC
11609130 ATAAAAATA-TAGAAA-TTAT
1 ATAAAAATATTAGAAATTTAT
*
11609149 ATAAAATTATTAGAAATTTAT
1 ATAAAAATATTAGAAATTTAT
11609170 ATA
1 ATA
11609173 TATATTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAAAAATATTAGAAATTTAT
Found at i:11609157 original size:10 final size:11
Alignment explanation
Indices: 11609136--11609172 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
11609126 GACCATAAAA
11609136 ATATAGAAATT
1 ATATAGAAATT
11609147 ATATA-AAATT
1 ATATAGAAATT
11609157 AT-TAGAAATTT
1 ATATAGAAA-TT
11609168 ATATA
1 ATATA
11609173 TATATTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.09
10 10 0.43
11 9 0.39
12 2 0.09
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
ATATAGAAATT
Found at i:11609235 original size:22 final size:20
Alignment explanation
Indices: 11609186--11609254 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 20
11609176 ATTTGAATTT
11609186 TATTAAAAA-ATAGAAAAAC
1 TATTAAAAATATAGAAAAAC
*
11609205 TATTAAAAATATAGAAAAAT
1 TATTAAAAATATAGAAAAAC
* *
11609225 TATCTTAAAAATATAGGAAAAG
1 TA--TTAAAAATATAGAAAAAC
11609247 T-TTAAAAA
1 TATTAAAAA
11609255 AATATATAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.36
20 11 0.25
22 17 0.39
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (20 bp):
TATTAAAAATATAGAAAAAC
Found at i:11609351 original size:20 final size:20
Alignment explanation
Indices: 11609326--11609363 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
11609316 TGAAAACATG
*
11609326 ATAAAAAATAATTAAAATCA
1 ATAAAAAATAATAAAAATCA
11609346 ATAAAAAATAATAAAAAT
1 ATAAAAAATAATAAAAAT
11609364 ATTTTGAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (20 bp):
ATAAAAAATAATAAAAATCA
Found at i:11615645 original size:19 final size:19
Alignment explanation
Indices: 11615600--11615645 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
11615590 GCACAAAAAG
**
11615600 GAACAAAATTAAAATTAGA
1 GAACAAAATTAAAAGAAGA
*
11615619 -ACCAAAATTAAAAGAAGA
1 GAACAAAATTAAAAGAAGA
11615637 GAACAAAAT
1 GAACAAAAT
11615646 CAAACTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (19 bp):
GAACAAAATTAAAAGAAGA
Found at i:11617205 original size:101 final size:101
Alignment explanation
Indices: 11617020--11617207 Score: 238
Period size: 101 Copynumber: 1.9 Consensus size: 101
11617010 TTGGAAAGTA
* * *
11617020 AGATTCACCATTGTGGCTTTAATCTTTTTAGATGCAGTGTCAGAAAAGCAAGATTCACCGTTGCG
1 AGATTCACCATTGTGACTTTAATCCTTTTAGATGCAATGTCAGAAAAGCAAGATTCACCGTTGCG
*
11617085 GCTTTAACCTGCTCTACTGCACTGGATGAGTGAGTG
66 GCTTTAACCTGCTCCACTGCACTGGATGAGTGAGTG
* * *
11617121 AGATTCATCATTGTGACTTTAATCCTTTTA-ACTGCAAAT-TCGGGAAAGC-AGTATTCACCGTT
1 AGATTCACCATTGTGACTTTAATCCTTTTAGA-TGC-AATGTCAGAAAAGCAAG-ATTCACCGTT
* * *
11617183 GTGGCTTTAATCTGTTCCACTGCAC
63 GCGGCTTTAACCTGCTCCACTGCAC
11617208 CACTTGGGAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 3 0.04
101 69 0.93
102 2 0.03
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (101 bp):
AGATTCACCATTGTGACTTTAATCCTTTTAGATGCAATGTCAGAAAAGCAAGATTCACCGTTGCG
GCTTTAACCTGCTCCACTGCACTGGATGAGTGAGTG
Found at i:11617415 original size:44 final size:44
Alignment explanation
Indices: 11617323--11617560 Score: 167
Period size: 44 Copynumber: 5.2 Consensus size: 44
11617313 CCTTTATTTT
* * * * * *
11617323 AATCCGCTCCACTGTAATCTCAAGGAAATAGGATTACTAGCTTT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
**
11617367 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
* * * *
11617411 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATAAAATCCTT-TA-TTTT
1 AATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TTCTAGCTTC
** * * *
11617465 AATCCACTCCATTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
* *
11617509 AATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
11617553 AATCTGCT
1 AATCTGCT
11617561 GCGATCTACT
Statistics
Matches: 148, Mismatches: 30, Indels: 32
0.70 0.14 0.15
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 105 0.71
45 2 0.01
46 1 0.01
47 3 0.02
49 1 0.01
51 2 0.01
52 1 0.01
53 1 0.01
54 25 0.17
55 2 0.01
56 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTAGCTTC
Found at i:11617457 original size:142 final size:142
Alignment explanation
Indices: 11617279--11617601 Score: 547
Period size: 142 Copynumber: 2.3 Consensus size: 142
11617269 GACCTAATAT
*
11617279 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
* * *
11617344 AAGGAAATAGGATTACTAGCTTTAATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTAGCT
66 AAGGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTAGCT
11617409 TCAATCTGATGC
131 TCAATCTGATGC
* *
11617421 GATCTACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTTTAATCCACTCCATTGTAATCTC
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
* *
11617486 AGGGAGATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTAGCT
66 AAGGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTAGCT
*
11617551 TCAATCTGCTGC
131 TCAATCTGATGC
* *
11617563 GATCTACTCCACCGTAACTTCAGAGAGATAAGATCCTTT
1 GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTT
11617602 CTCAATCTGC
Statistics
Matches: 169, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 169 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (142 bp):
GATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTGTAATCTC
AAGGAAATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAAGGAGATAAGATTTCTAGCT
TCAATCTGATGC
Found at i:11617964 original size:87 final size:87
Alignment explanation
Indices: 11617818--11618608 Score: 1161
Period size: 87 Copynumber: 9.1 Consensus size: 87
11617808 ACTTGTAATC
* ** * * * * * *
11617818 TTCGATCTGCTTCACTGTCGACGCAGGAGGGCTAGATCTGCTATCTTCAACTAACTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
11617883 CCGATGGAGGGAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * * *
11617905 TTCGATCTGCTTCGCTATTAATGCAGGAAGGCAAGATCCGCTATCATTAACCAACTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
11617970 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* *
11617992 TTTGATCTGCTTCGCCGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
11618057 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
** * * * *
11618079 TTTTATCTACTTCGCCGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAACTCTACTGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
11618144 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
11618166 TTCGATCTGCTTCGCCGTTAACGCAGGAAGACAAGATCTGCTATCTTTAACTAGCTCCACTGTAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
11618231 CCGATGGAGACAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * *
11618253 TTCGATCTGCTTCACTGTTAACGCAGGAAGACAAGATCTGCTATCTTTAACCAGCTCCACAGCAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
*
11618318 CCGATGGAGGCCAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
11618340 TTCTATCTGCTTCGCTGTTAATGC-GAGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTGTA
1 TTCGATCTGCTTCGCTGTTAACGCAG-GAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCA
11618404 ACCGATGGAGGCAAGGCTTTGTT
65 ACCGATGGAGGCAAGGCTTTGTT
* * * * *
11618427 TTCGATCTGCTTTGCTGTTAATGTAGGAAGGCAAGATCTACTATCTTTAACCAGCTCCACTGTAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
11618492 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
* * * *
11618514 TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTGCTATCTTTAACAAGCTCCACTACAA
1 TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
11618579 CCGATGGAGGCAAGGCTTTGTT
66 CCGATGGAGGCAAGGCTTTGTT
11618601 TTCGATCT
1 TTCGATCT
11618609 TCACTAATCT
Statistics
Matches: 644, Mismatches: 58, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
86 1 0.00
87 642 1.00
88 1 0.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
TTCGATCTGCTTCGCTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTGCAA
CCGATGGAGGCAAGGCTTTGTT
Found at i:11618026 original size:43 final size:43
Alignment explanation
Indices: 11617977--11618113 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 43
11617967 CAACCGATGG
*
11617977 AGGCAAGGCTTTGTTTTTGATCTGCTTCGCCGTTAACGCAGGA
1 AGGCAAGGCTTTGTTTTTAATCTGCTTCGCCGTTAACGCAGGA
* * * * * * * *
11618020 AGGCAA-GATCTGCTATCTTTAACCAGCTCCACTG-CAAC-CGATGG-
1 AGGCAAGGCTTTG-T-T-TTTAATCTGCTTCGCCGTTAACGC-A-GGA
* *
11618064 AGGCAAGGCTTTGTTTTTTATCTACTTCGCCGTTAACGCAGGA
1 AGGCAAGGCTTTGTTTTTAATCTGCTTCGCCGTTAACGCAGGA
11618107 AGGCAAG
1 AGGCAAG
11618114 ATCTGCTATC
Statistics
Matches: 66, Mismatches: 19, Indels: 18
0.64 0.18 0.17
Matches are distributed among these distances:
42 16 0.24
43 20 0.30
44 13 0.20
45 17 0.26
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.28
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTTAATCTGCTTCGCCGTTAACGCAGGA
Found at i:11618287 original size:43 final size:43
Alignment explanation
Indices: 11618154--11618287 Score: 116
Period size: 43 Copynumber: 3.1 Consensus size: 43
11618144 CCGATGGAGG
* *
11618154 CAAGGCTTTGTTTTCGATCTGCTTCGCCGTTAACGCAGGAAGA
1 CAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAGGAAGA
* * * * *
11618197 CAA-GATCTGCTATCTT-TAACTAGCTCCACTG-TAAC-CGATGG-AGA
1 CAAGGCTTTG-T-T-TTCGATCT-GCTTCACTGTTAACGC-A-GGAAGA
11618241 CAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAGGAAGA
1 CAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAGGAAGA
11618284 CAAG
1 CAAG
11618288 ATCTGCTATC
Statistics
Matches: 68, Mismatches: 12, Indels: 22
0.67 0.12 0.22
Matches are distributed among these distances:
42 16 0.24
43 21 0.31
44 17 0.25
45 14 0.21
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (43 bp):
CAAGGCTTTGTTTTCGATCTGCTTCACTGTTAACGCAGGAAGA
Found at i:11618548 original size:43 final size:43
Alignment explanation
Indices: 11618412--11618548 Score: 111
Period size: 43 Copynumber: 3.2 Consensus size: 43
11618402 TAACCGATGG
*
11618412 AGGCAAGGCTTTGTTTTCGATCTGCTTTGCTGTTAATGTAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGTAGGA
* * * * * * * * *
11618455 AGGCAAGATCTACTATCTTT-AACCAGCTCCACTG-TAACCG-ATGG-
1 AGGCAAG-GCT-TTGT-TTTCGATCTGCTTCGCTGTTAA-TGTA-GGA
11618499 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGTAGGA
1 AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGTAGGA
11618542 AGGCAAG
1 AGGCAAG
11618549 ATCTGCTATC
Statistics
Matches: 66, Mismatches: 19, Indels: 18
0.64 0.18 0.17
Matches are distributed among these distances:
41 3 0.05
42 14 0.21
43 20 0.30
44 13 0.20
45 13 0.20
46 3 0.05
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (43 bp):
AGGCAAGGCTTTGTTTTCGATCTGCTTCGCTGTTAATGTAGGA
Found at i:11619840 original size:14 final size:14
Alignment explanation
Indices: 11619821--11619881 Score: 72
Period size: 13 Copynumber: 4.5 Consensus size: 14
11619811 TTAGCCTTTC
*
11619821 CATTTTTTATTTTT
1 CATTTTTCATTTTT
11619835 CA-TTTTCATTTTT
1 CATTTTTCATTTTT
* * *
11619848 TACTTTTCA-TTCT
1 CATTTTTCATTTTT
11619861 CATTTTTCATTTTT
1 CATTTTTCATTTTT
11619875 CATTTTT
1 CATTTTT
11619882 TTCATTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
13 21 0.54
14 18 0.46
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTTCATTTTT
Found at i:11619844 original size:20 final size:20
Alignment explanation
Indices: 11619821--11619880 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
11619811 TTAGCCTTTC
11619821 CATTTTTTATTTTTCATTTT
1 CATTTTTTATTTTTCATTTT
* *
11619841 CATTTTTTACTTTTCATTCT
1 CATTTTTTATTTTTCATTTT
*
11619861 CATTTTTCATTTTTCATTTT
1 CATTTTTTATTTTTCATTTT
11619881 TTTCATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTTTTATTTTTCATTTT
Found at i:11619890 original size:7 final size:7
Alignment explanation
Indices: 11619821--11619881 Score: 72
Period size: 7 Copynumber: 9.0 Consensus size: 7
11619811 TTAGCCTTTC
11619821 CATTTTT
1 CATTTTT
*
11619828 TATTTTT
1 CATTTTT
11619835 CA-TTTT
1 CATTTTT
11619841 CATTTTT
1 CATTTTT
* *
11619848 TACTTTT
1 CATTTTT
*
11619855 CA-TTCT
1 CATTTTT
11619861 CATTTTT
1 CATTTTT
11619868 CATTTTT
1 CATTTTT
11619875 CATTTTT
1 CATTTTT
11619882 TTCATTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 11 0.24
7 34 0.76
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:11620305 original size:24 final size:23
Alignment explanation
Indices: 11620278--11620328 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
11620268 TTGTTTTGAC
*
11620278 TTTGA-TTGATTTCTCTTTTTTTCT
1 TTTGACTTGATTT-T-TTCTTTTCT
11620302 TTTGACTTTGATTTTTTCTTTTCT
1 TTTGAC-TTGATTTTTTCTTTTCT
11620326 TTT
1 TTT
11620329 TTTGTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 16 0.67
25 1 0.04
26 7 0.29
ACGTcount: A:0.08, C:0.12, G:0.08, T:0.73
Consensus pattern (23 bp):
TTTGACTTGATTTTTTCTTTTCT
Found at i:11620321 original size:27 final size:26
Alignment explanation
Indices: 11620266--11620355 Score: 92
Period size: 27 Copynumber: 3.3 Consensus size: 26
11620256 TCTTTTCATA
*
11620266 TTTTGTTTTGACTTTGATTGATTTCTCTT
1 TTTTTTTTTGACTTTGATT--TTT-TCTT
11620295 TTTTTCTTTTGACTTTGATTTTTTCTT
1 TTTTT-TTTTGACTTTGATTTTTTCTT
** *
11620322 TTCTTTTTTTGTTTTTGATTTTGT-TT
1 TT-TTTTTTTGACTTTGATTTTTTCTT
11620348 TTTTTTTT
1 TTTTTTTT
11620356 GAATCTGAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
25 6 0.11
26 4 0.07
27 21 0.38
28 6 0.11
29 4 0.07
30 14 0.25
ACGTcount: A:0.07, C:0.08, G:0.10, T:0.76
Consensus pattern (26 bp):
TTTTTTTTTGACTTTGATTTTTTCTT
Found at i:11620349 original size:32 final size:32
Alignment explanation
Indices: 11620251--11620355 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 32
11620241 TTTTCTTTTC
* * * *
11620251 TTTTCTCTTTTCATATTTTGTTTTGACTTTGA
1 TTTTTTCTTTTCTTTTTTTCTTTTGACTTTGA
*
11620283 TTGATTTC---TCTTTTTTTCTTTTGACTTTGA
1 TT-TTTTCTTTTCTTTTTTTCTTTTGACTTTGA
* *
11620313 TTTTTTCTTTTCTTTTTTTGTTTTTGATTTTG-
1 TTTTTTCTTTTCTTTTTTT-CTTTTGACTTTGA
*
11620345 TTTTTTTTTTT
1 TTTTTTCTTTT
11620356 GAATCTGAAC
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
29 4 0.07
30 21 0.36
32 21 0.36
33 13 0.22
ACGTcount: A:0.08, C:0.10, G:0.09, T:0.74
Consensus pattern (32 bp):
TTTTTTCTTTTCTTTTTTTCTTTTGACTTTGA
Found at i:11620355 original size:12 final size:12
Alignment explanation
Indices: 11620313--11620356 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
11620303 TTGACTTTGA
*
11620313 TTTTTTCTTTTCT
1 TTTTTTGTTTT-T
11620326 TTTTTTGTTTTT
1 TTTTTTGTTTTT
**
11620338 GATTTTGTTTTT
1 TTTTTTGTTTTT
11620350 TTTTTTG
1 TTTTTTG
11620357 AATCTGAACC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.84
Consensus pattern (12 bp):
TTTTTTGTTTTT
Found at i:11628191 original size:19 final size:19
Alignment explanation
Indices: 11628146--11628191 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
11628136 GCACAAAAAT
**
11628146 GAACAAAATTAAAATTAGA
1 GAACAAAATTAAAAGAAGA
*
11628165 -ACCAAAATTAAAAGAAGA
1 GAACAAAATTAAAAGAAGA
11628183 GAACAAAAT
1 GAACAAAAT
11628192 CAAACTAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.65, C:0.09, G:0.11, T:0.15
Consensus pattern (19 bp):
GAACAAAATTAAAAGAAGA
Found at i:11631945 original size:19 final size:19
Alignment explanation
Indices: 11631921--11631993 Score: 137
Period size: 19 Copynumber: 3.8 Consensus size: 19
11631911 AATTTCTGAG
11631921 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
11631940 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
11631959 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
11631978 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
11631994 ATATATGATT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:11632567 original size:3 final size:3
Alignment explanation
Indices: 11632559--11632604 Score: 51
Period size: 3 Copynumber: 15.0 Consensus size: 3
11632549 TGTTAATGTA
11632559 ATT ATT ATT ATT ATT ATT ATT ATT -TT CA-T ATGT AATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT-T -ATT ATT ATT ATT
11632605 TTAGCTGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
2 3 0.08
3 31 0.82
4 2 0.05
5 2 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:11633212 original size:19 final size:20
Alignment explanation
Indices: 11633173--11633212 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11633163 TTTTAGGCGT
* *
11633173 TTGTAATATTTATTATTGCA
1 TTGTAATATTTAATATAGCA
11633193 TTGT-ATATTTAATATAGCA
1 TTGTAATATTTAATATAGCA
11633212 T
1 T
11633213 CACATCATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.53
Consensus pattern (20 bp):
TTGTAATATTTAATATAGCA
Found at i:11633574 original size:98 final size:98
Alignment explanation
Indices: 11633454--11633648 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
11633444 CTAAAAACAA
* *
11633454 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
11633519 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
11633552 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
11633617 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
11633649 ATTTTATTGT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:11640074 original size:23 final size:23
Alignment explanation
Indices: 11640038--11640088 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
11640028 AAGCATCCAA
11640038 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
11640061 TGTAATA-CCTCGAAAATTACTAC
1 TGTAATATCC-CGAAAATTACTAC
*
11640084 AGTAA
1 TGTAA
11640089 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:11669242 original size:21 final size:21
Alignment explanation
Indices: 11669210--11669262 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
11669200 AGACGTGTGT
*
11669210 TTTAACCACACAGCCATGT-A
1 TTTAGCCACACAGCCATGTCA
* *
11669230 TCTTAGTCACACAGGCATGTCA
1 T-TTAGCCACACAGCCATGTCA
11669252 TTTAGCCACAC
1 TTTAGCCACAC
11669263 GGCTGTGTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 1 0.04
21 24 0.89
22 2 0.07
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.26
Consensus pattern (21 bp):
TTTAGCCACACAGCCATGTCA
Found at i:11669966 original size:40 final size:38
Alignment explanation
Indices: 11669920--11669999 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
11669910 AGGTGTGTTT
* *
11669920 GGTTGG-ATGGGTCCATCAAACCTAATTATTAGTGTGTAGA
1 GGTTGGAAAGGGTCAAT-AAACC-AA-TATTAGTGTGTAGA
* *
11669960 GGTTGGAAAGGGTCAATAAACCCATATTAGTGTGTTGA
1 GGTTGGAAAGGGTCAATAAACCAATATTAGTGTGTAGA
11669998 GG
1 GG
11670000 GGATTGCTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
38 15 0.43
39 1 0.03
40 11 0.31
41 8 0.23
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (38 bp):
GGTTGGAAAGGGTCAATAAACCAATATTAGTGTGTAGA
Found at i:11671595 original size:14 final size:15
Alignment explanation
Indices: 11671576--11671609 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
11671566 TACAGTGCGC
11671576 AGCAAAA-GTGTGGT
1 AGCAAAATGTGTGGT
*
11671590 AGCAAAATGTGTGTT
1 AGCAAAATGTGTGGT
11671605 AGCAA
1 AGCAA
11671610 CTATTATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.38, C:0.09, G:0.29, T:0.24
Consensus pattern (15 bp):
AGCAAAATGTGTGGT
Found at i:11673475 original size:18 final size:18
Alignment explanation
Indices: 11673448--11673484 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11673438 TTTCCACGAC
* *
11673448 CGTCAGTATGTTCTCGAT
1 CGTCAATATGTCCTCGAT
11673466 CGTCAATATGTCCTCGAT
1 CGTCAATATGTCCTCGAT
11673484 C
1 C
11673485 TAAGACTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.27, G:0.19, T:0.35
Consensus pattern (18 bp):
CGTCAATATGTCCTCGAT
Found at i:11673611 original size:12 final size:12
Alignment explanation
Indices: 11673594--11673619 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
11673584 AAACCCAAAT
11673594 TCAATTGAATGA
1 TCAATTGAATGA
11673606 TCAATTGAATGA
1 TCAATTGAATGA
11673618 TC
1 TC
11673620 TATGGCTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (12 bp):
TCAATTGAATGA
Found at i:11675134 original size:21 final size:19
Alignment explanation
Indices: 11675089--11675136 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
11675079 TAAGTTTTCT
11675089 TGTCACACGGCCGAGGGTG
1 TGTCACACGGCCGAGGGTG
11675108 TGTCACACGGCCGAGGGTG
1 TGTCACACGGCCGAGGGTG
*
11675127 TGTCTCACGG
1 TGTCACACGG
11675137 GCTGGCCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.15, C:0.27, G:0.40, T:0.19
Consensus pattern (19 bp):
TGTCACACGGCCGAGGGTG
Found at i:11683867 original size:26 final size:26
Alignment explanation
Indices: 11683808--11683869 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
11683798 TACCTACAGT
* *
11683808 AGTTTCAAAATATCTTAACATATATC
1 AGTTTCAGAATATCATAACATATATC
* *
11683834 AGTTTCAGAATATCATAGCATGTATC
1 AGTTTCAGAATATCATAACATATATC
11683860 AGTTTCAGAA
1 AGTTTCAGAA
11683870 CACTTACAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATATCATAACATATATC
Found at i:11692096 original size:19 final size:19
Alignment explanation
Indices: 11692072--11692111 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
11692062 GAACCACTAA
11692072 TATATGCAAAATATTTATT
1 TATATGCAAAATATTTATT
*
11692091 TATATGTAAAATATTTATT
1 TATATGCAAAATATTTATT
11692110 TA
1 TA
11692112 ATAAATATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (19 bp):
TATATGCAAAATATTTATT
Found at i:11694640 original size:23 final size:23
Alignment explanation
Indices: 11694614--11694660 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
11694604 ATAAAAGAAG
*
11694614 TATAGTTCTATATGAATTTTACT
1 TATAGTTCTACATGAATTTTACT
11694637 TATAGTTCTACATGAATTTTACT
1 TATAGTTCTACATGAATTTTACT
11694660 T
1 T
11694661 GTATTTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (23 bp):
TATAGTTCTACATGAATTTTACT
Found at i:11699341 original size:188 final size:188
Alignment explanation
Indices: 11699007--11699383 Score: 454
Period size: 188 Copynumber: 2.0 Consensus size: 188
11698997 ATAGAGTGGC
* * * * *
11699007 ACCAAAGGGCAATATCATAACAGAATAGCACCGAATTGTTTTATCAAAATAGAGTGGCACCAAAG
1 ACCAAAGGGCAATATCAGAACAGAATAACACCAAATTGCTTTATCAAAACAGAGTGGCACCAAAG
* * * * * *
11699072 TGCATTAATAGAACTGAGAGCACATTGAATATTTCCTAATGGCATGCCATCTATATCCCTCTACT
66 TGCATTAACAGAAATGAGAGAACATTGAATATTTCCTAATGGCATACCATCTATATCCCACTAAT
*** * *
11699137 TTGTATCTTGTCTACTTGGGAA-AGTATACCAAAATTAGCTTCACATTTACATTTCAAA
131 TCACATATTGTCTACTTGAGAAGA-TATACCAAAATTAGCTTCACATTTACATTTCAAA
* ** * *
11699195 ACCAAAGTGCAATATTGGAACAGAATAACACCAAATTGCTTTATCATAACAGAGTGGCACTAAAG
1 ACCAAAGGGCAATATCAGAACAGAATAACACCAAATTGCTTTATCAAAACAGAGTGGCACCAAAG
* * *
11699260 TGCATTAACA-AAAT-AGAGAACGTGCTGAATGTTTCCTAATGGCATACCATCTATATCTCACTA
66 TGCATTAACAGAAATGAGAGAACAT--TGAATATTTCCTAATGGCATACCATCTATATCCCACTA
* ** *
11699323 ATTCACATATTTTCTACTTGAGAAGATATATTAAAATTAGCTTTACATTTACATTTCAAA
129 ATTCACATATTGTCTACTTGAGAAGATATACCAAAATTAGCTTCACATTTACATTTCAAA
11699383 A
1 A
11699384 TAGAGCTTAT
Statistics
Matches: 158, Mismatches: 28, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
186 7 0.04
187 3 0.02
188 147 0.93
189 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (188 bp):
ACCAAAGGGCAATATCAGAACAGAATAACACCAAATTGCTTTATCAAAACAGAGTGGCACCAAAG
TGCATTAACAGAAATGAGAGAACATTGAATATTTCCTAATGGCATACCATCTATATCCCACTAAT
TCACATATTGTCTACTTGAGAAGATATACCAAAATTAGCTTCACATTTACATTTCAAA
Found at i:11703247 original size:9 final size:9
Alignment explanation
Indices: 11703233--11703261 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
11703223 AATGACTAAA
11703233 TTGTAAAAG
1 TTGTAAAAG
11703242 TTGTAAAAG
1 TTGTAAAAG
11703251 TTGTAAAAG
1 TTGTAAAAG
11703260 TT
1 TT
11703262 CATTGCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (9 bp):
TTGTAAAAG
Found at i:11703400 original size:11 final size:10
Alignment explanation
Indices: 11703384--11703435 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
11703374 TTAAACTTAA
11703384 TTAATTAAAGG
1 TTAATTAAA-G
11703395 TTAATT-AAG
1 TTAATTAAAG
*
11703404 TTAATTAGGAG
1 TTAATTA-AAG
11703415 -TAATTATAAG
1 TTAATTA-AAG
11703425 TTAATTAAAG
1 TTAATTAAAG
11703435 T
1 T
11703436 ATATATGCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
9 7 0.20
10 14 0.40
11 14 0.40
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.40
Consensus pattern (10 bp):
TTAATTAAAG
Found at i:11716023 original size:27 final size:27
Alignment explanation
Indices: 11715989--11716131 Score: 189
Period size: 27 Copynumber: 5.3 Consensus size: 27
11715979 ATACCGTCGG
* *
11715989 GGGTAAAATGATCGAAATATCCTCGAA
1 GGGTAAAATGATCGAAATACCCCCGAA
*
11716016 GGGTAAAATGATCGAAATACCCCCAAA
1 GGGTAAAATGATCGAAATACCCCCGAA
* *
11716043 GGGTAAATTGACCGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATACCCCCGAA
*
11716070 GGGTAAAATGATTGAAATACCCCCGAA
1 GGGTAAAATGATCGAAATACCCCCGAA
* * *
11716097 GGGTAAAATGA-CATAAATACCCACAAA
1 GGGTAAAATGATC-GAAATACCCCCGAA
11716124 GGGTAAAA
1 GGGTAAAA
11716132 AGACTGTTAT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
27 102 1.00
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.17
Consensus pattern (27 bp):
GGGTAAAATGATCGAAATACCCCCGAA
Done.