Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 35 of 352
Found at i:11224793 original size:21 final size:20
Alignment explanation
Indices: 11224769--11224808 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
11224759 ATTTCACCCA
11224769 TCAATTGAACTATTTT-TTTTC
1 TCAATT-AAC-ATTTTATTTTC
11224790 TCAATTAACATTTTATTTT
1 TCAATTAACATTTTATTTT
11224809 ATCATTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 7 0.39
21 6 0.33
ACGTcount: A:0.28, C:0.12, G:0.03, T:0.57
Consensus pattern (20 bp):
TCAATTAACATTTTATTTTC
Found at i:11228682 original size:14 final size:14
Alignment explanation
Indices: 11228663--11228691 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11228653 TGGATTTGTG
11228663 GTTCTGAAACCACT
1 GTTCTGAAACCACT
11228677 GTTCTGAAACCACT
1 GTTCTGAAACCACT
11228691 G
1 G
11228692 AAAACGGACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (14 bp):
GTTCTGAAACCACT
Found at i:11230622 original size:2 final size:2
Alignment explanation
Indices: 11230615--11230647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
11230605 AAATAGTAAA
11230615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
11230648 ATAGAGGAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11237498 original size:43 final size:43
Alignment explanation
Indices: 11237450--11237604 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 43
11237440 TGCTCTCATA
11237450 TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTTCGAG
1 TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTTCGAG
* * * * * *
11237493 GAAGACCATGTCTGCGACATCGGCATCG-TAATTGTGA-TTCGTG
1 TAAGACCACGTCTGGGACGTTGGCATCGAT-A-TGTGATTTCGAG
* * *
11237536 TAAGACC-CTGTCTGGGACAG-TGGAATCGACATGTGATTAC-ATG
1 TAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTTCGA-G
*
11237579 TAAGACCACGTCTAGGACGTTGGCAT
1 TAAGACCACGTCTGGGACGTTGGCAT
11237605 TGTACGATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 18
0.71 0.14 0.15
Matches are distributed among these distances:
42 7 0.08
43 73 0.85
44 6 0.07
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.26
Consensus pattern (43 bp):
TAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTTCGAG
Found at i:11239836 original size:46 final size:46
Alignment explanation
Indices: 11239769--11239943 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
11239759 TGTAACCCGC
11239769 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
11239815 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C--GTTCGCAT
* * * * ** *
11239865 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGAACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
*
11239908 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
11239944 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.58
47 25 0.23
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
Found at i:11239885 original size:93 final size:93
Alignment explanation
Indices: 11239777--11239947 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
11239767 GCCCATAAGT
* ** *
11239777 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
11239842 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
11239870 GAACTCAGACTCAACTCAACGAGTTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
11239935 CGAGTTCGGATGC
66 CGAGCTCGGATGC
11239948 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGAACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:11240525 original size:19 final size:19
Alignment explanation
Indices: 11240499--11240535 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11240489 GCAACTCATA
11240499 ATTTCAACT-ATTTTACAT
1 ATTTCAACTCATTTTACAT
11240517 ATTTACAACTCATTTTACA
1 ATTT-CAACTCATTTTACA
11240536 ACTTAGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (19 bp):
ATTTCAACTCATTTTACAT
Found at i:11243037 original size:24 final size:22
Alignment explanation
Indices: 11242980--11243037 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 22
11242970 TCGTTTTTGA
*
11242980 TTTTATTAA-AAATTTTAGAAG
1 TTTTATTAATAAATGTTAGAAG
* *
11243001 TTTTCATTGATAAATGTTAGATG
1 TTTT-ATTAATAAATGTTAGAAG
11243024 TTTTTGATTAATAA
1 -TTTT-ATTAATAA
11243038 CATGGATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 4 0.14
22 4 0.14
23 10 0.34
24 11 0.38
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (22 bp):
TTTTATTAATAAATGTTAGAAG
Found at i:11257434 original size:52 final size:51
Alignment explanation
Indices: 11257362--11257475 Score: 149
Period size: 52 Copynumber: 2.2 Consensus size: 51
11257352 CCCTTTTAAA
* ** *
11257362 ATTAAAAAAAA-TGGATGTTGGGACATTGATGGCCGACACCCTTATACTAG
1 ATTAAAAAAAATTGGATGTTGGGACACTGATGGCCGACACCCCAATACCAG
* *
11257412 ATTAAAAAAAATTAGGGTGTTGGGACACTGATGGCCGGCACCCCAATACCAG
1 ATTAAAAAAAATT-GGATGTTGGGACACTGATGGCCGACACCCCAATACCAG
*
11257464 ATTTAAAAAAAT
1 ATTAAAAAAAAT
11257476 AATGTTGAGA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 11 0.20
51 1 0.02
52 43 0.78
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.24
Consensus pattern (51 bp):
ATTAAAAAAAATTGGATGTTGGGACACTGATGGCCGACACCCCAATACCAG
Found at i:11260926 original size:17 final size:17
Alignment explanation
Indices: 11260890--11260923 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
11260880 TTCTTTTTTA
11260890 TATGTTATCTGTTATAT
1 TATGTTATCTGTTATAT
11260907 TATGTTA-CTGTTATAT
1 TATGTTATCTGTTATAT
11260923 T
1 T
11260924 TATAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (17 bp):
TATGTTATCTGTTATAT
Found at i:11261111 original size:15 final size:14
Alignment explanation
Indices: 11261087--11261116 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
11261077 ATAGTATATG
11261087 TATTATTAATATTT
1 TATTATTAATATTT
11261101 TATTAATTAATATTT
1 TATT-ATTAATATTT
11261116 T
1 T
11261117 CTAATGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTATTAATATTT
Found at i:11263331 original size:47 final size:47
Alignment explanation
Indices: 11263257--11263350 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
11263247 AATTAAGGAA
*
11263257 AAGGGTGAGAGTAAGTGCGTTCTGTGGGGAGCTTTGAAAGATTTGAT
1 AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
11263304 AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
1 AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
11263351 CCAGACACAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.26, C:0.07, G:0.38, T:0.29
Consensus pattern (47 bp):
AAGGGTGAGAGTAAGTGCGTTCCGTGGGGAGCTTTGAAAGATTTGAT
Found at i:11273297 original size:206 final size:206
Alignment explanation
Indices: 11272936--11273830 Score: 1345
Period size: 206 Copynumber: 4.4 Consensus size: 206
11272926 CATTTGACAC
* * * * *
11272936 ACATAGCAGATCTGGCCTTCAGATGATTAGACTGAAGTAGATCCAAGATGATTTGGCATTCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
* *
11273001 GTTTACAAGCAGCAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
66 GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
11273066 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
* *
11273131 GGAGAGTAGAT
196 GAAGAGCAGAT
* *
11273142 ACATAGTAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
*
11273207 GCTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
66 GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
* *
11273272 TAAGATGATTTGGCATCTTTGTATTGTCAGAGAACAAATCGAATTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
11273337 GAAGAGCAGAT
196 GAAGAGCAGAT
* * *
11273348 ACATAGCAGATCTGATCTTCAGATGTTTATACTGAAGCAGAACCAAGATGGTTTGGCATCCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
* * * *
11273413 GCTTACAAGGAACAAATCGAAATCATAGCTGAATTGGCTTTCACGTGTTTACGATGAAGCAAATA
66 GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
*
11273478 TAAGATGATTTGGCATCTTTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
*
11273543 GGAGAGCAGAT
196 GAAGAGCAGAT
* * **
11273554 ACATAGCAGATCTGGTCTTCAGATGTTTATATTGAAGTAGATTTAAGATGATTTGGCATCCTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
* * *
11273619 GTTTATAAGGAACAAATC-AAAGACATAGCTGATTTGAC-TT----T-C--ACG-T-----AAAT
66 GTTTACAAGGAACAAATCGAAA-TCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAAT
* *
11273669 CTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCAT-TTCGA
130 CTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGA
11273733 CGAAGAGCAGAT
195 CGAAGAGCAGAT
*** *
11273745 ACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATACTTGT
1 ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
11273810 GTTTACAAGGAACAAATCGAA
66 GTTTACAAGGAACAAATCGAA
11273831 GAAGCAGATT
Statistics
Matches: 638, Mismatches: 49, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
191 90 0.14
192 61 0.10
197 1 0.00
198 3 0.00
201 1 0.00
205 5 0.01
206 477 0.75
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (206 bp):
ACATAGCAGATCTGGTCTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
GTTTACAAGGAACAAATCGAAATCATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGAC
GAAGAGCAGAT
Found at i:11275652 original size:17 final size:17
Alignment explanation
Indices: 11275616--11275649 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
11275606 TTCTTTTTCA
*
11275616 TATGTTATCTGTTATAT
1 TATGTTATCTATTATAT
11275633 TATGTTA-CTATTATAT
1 TATGTTATCTATTATAT
11275649 T
1 T
11275650 TATAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (17 bp):
TATGTTATCTATTATAT
Found at i:11277562 original size:29 final size:28
Alignment explanation
Indices: 11277530--11277601 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
11277520 GAGATTTTTA
* *
11277530 ATTTATTTTATTTATTTAAATATTTCTTT
1 ATTTACTTTAATTATTTAAATA-TTCTTT
* *
11277559 ATTTACTTTAATTCTTTAATTATTCTTT
1 ATTTACTTTAATTATTTAAATATTCTTT
* * *
11277587 TTTTAATTAAATTAT
1 ATTTACTTTAATTAT
11277602 ATTCTTTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
28 17 0.49
29 18 0.51
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (28 bp):
ATTTACTTTAATTATTTAAATATTCTTT
Found at i:11277599 original size:28 final size:29
Alignment explanation
Indices: 11277544--11277599 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
11277534 ATTTTATTTA
* *
11277544 TTTAAATATTTCTTTATTTACTTTAATTC
1 TTTAAATATTTCTTTATTTAATTAAATTC
* *
11277573 TTTAATTA-TTCTTTTTTTAATTAAATT
1 TTTAAATATTTCTTTATTTAATTAAATT
11277600 ATATTCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.29, C:0.07, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTAAATATTTCTTTATTTAATTAAATTC
Found at i:11277743 original size:74 final size:74
Alignment explanation
Indices: 11277619--11277758 Score: 164
Period size: 74 Copynumber: 1.9 Consensus size: 74
11277609 TAAATTTAAA
*
11277619 TTTATTCCTTTATATTATTCTTTTAATTAAATTCGATTGTTTATTTTTTATTTC-TTTAAA-TAT
1 TTTATTCCTTTATATTATTCTTTTAATTAAATTC-A-TGTTCATTTTTTA-TTCATTTAAATTAT
11277682 TTCTTTACTTAG
63 TTCTTTACTTAG
*
11277694 TTTATTTCTTTA-ATTATT-TTTTAAATTAAATTC-TGTTCATTTAAATTTATTCATTTAAATTA
1 TTTATTCCTTTATATTATTCTTTT-AATTAAATTCATGTTCATTT---TTTATTCATTTAAATTA
11277756 TTT
62 TTT
11277759 TTATTAAACT
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
71 8 0.14
73 7 0.12
74 26 0.46
75 16 0.28
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (74 bp):
TTTATTCCTTTATATTATTCTTTTAATTAAATTCATGTTCATTTTTTATTCATTTAAATTATTTC
TTTACTTAG
Found at i:11277748 original size:14 final size:15
Alignment explanation
Indices: 11277719--11277754 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
11277709 ATTTTTTAAA
*
11277719 TTAAATTCTGTTCAT
1 TTAAATTCTATTCAT
11277734 TTAAATT-TATTCAT
1 TTAAATTCTATTCAT
11277748 TTAAATT
1 TTAAATT
11277755 ATTTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 13 0.65
15 7 0.35
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.56
Consensus pattern (15 bp):
TTAAATTCTATTCAT
Found at i:11279812 original size:53 final size:51
Alignment explanation
Indices: 11279732--11279883 Score: 160
Period size: 53 Copynumber: 2.9 Consensus size: 51
11279722 CCATGGCAAC
* * * * **
11279732 AAGTGATAAGCGATATCCGTATAAGACCATAGTTGGGCTATGGCTTCAGATTA
1 AAGTGATAAGTG--ATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
*
11279785 AAGTGATACAAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCGGAGAA
1 AAGTGAT--AAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
* * * *
11279838 AAGTGATAAGTGCTCTCGTGTAAGACCATATCTAGGATATGGCATC
1 AAGTGATAAGTGATC-CGTATAAGACCATAGCTAGGCTATGGCATC
11279884 GGTATGATAT
Statistics
Matches: 85, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
51 7 0.08
52 27 0.32
53 47 0.55
55 4 0.05
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (51 bp):
AAGTGATAAGTGATCCGTATAAGACCATAGCTAGGCTATGGCATCAGAGAA
Found at i:11283234 original size:22 final size:23
Alignment explanation
Indices: 11283209--11283254 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11283199 CAACCAAACT
11283209 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
11283231 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
11283254 A
1 A
11283255 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:11283260 original size:23 final size:23
Alignment explanation
Indices: 11283216--11283260 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11283206 ACTAATTCAA
*
11283216 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
11283239 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
11283261 CACATACCCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:11290871 original size:22 final size:23
Alignment explanation
Indices: 11290846--11290891 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
11290836 CAACCAAACC
11290846 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
11290868 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
11290891 A
1 A
11290892 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:11290897 original size:23 final size:23
Alignment explanation
Indices: 11290853--11290897 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
11290843 ACCAATTCAA
*
11290853 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
11290876 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
11290898 CACATACCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:11292633 original size:18 final size:18
Alignment explanation
Indices: 11292610--11292647 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11292600 CTACTGCTGC
11292610 TGTCCAATATTGTTTTAG
1 TGTCCAATATTGTTTTAG
11292628 TGTCCAATATTGTTTTAG
1 TGTCCAATATTGTTTTAG
11292646 TG
1 TG
11292648 CAAGCTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (18 bp):
TGTCCAATATTGTTTTAG
Found at i:11294397 original size:25 final size:25
Alignment explanation
Indices: 11294320--11294467 Score: 174
Period size: 25 Copynumber: 6.0 Consensus size: 25
11294310 AATCTCTTTA
* * **
11294320 ATGAGCTTCCTGATATATGGCTTTC
1 ATGAGCTTCCCGTTATATGGCTCAC
* *
11294345 -TGGAGCTTCTCGATAT-TGGCTCAC
1 AT-GAGCTTCCCGTTATATGGCTCAC
* ** *
11294369 ATGAGCTTCCTGTTATACAGCTCAA
1 ATGAGCTTCCCGTTATATGGCTCAC
*
11294394 ATGAGCTTCTCGTTATATGGCTCAC
1 ATGAGCTTCCCGTTATATGGCTCAC
11294419 ATGAGCTTCCCGTTATATGGCTCAC
1 ATGAGCTTCCCGTTATATGGCTCAC
11294444 ATGAGCTTCCCGTTATATGGCTCA
1 ATGAGCTTCCCGTTATATGGCTCA
11294468 AGAGAGAGCT
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
24 18 0.17
25 86 0.83
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGCTCAC
Found at i:11294467 original size:75 final size:76
Alignment explanation
Indices: 11294347--11294499 Score: 195
Period size: 75 Copynumber: 2.0 Consensus size: 76
11294337 TGGCTTTCTG
* * *
11294347 GAGCTTCTCGATATTGGCTCACATGAGCTTCCTGTTATACAGCTCAA-A-TGAGCTTCTCGTTAT
1 GAGCTTCCCGATATTGGCTCACATGAGCTTCCCGTTATACAGCTCAAGAGAGAGCTTCTCGTT-T
11294410 ATG-GCTCACAT
65 ATGTGCTCACAT
* ** *
11294421 GAGCTTCCCGTTATATGGCTCACATGAGCTTCCCGTTATATGGCTCAAGAGAGAGCTTCTTGTTT
1 GAGCTTCCCGATAT-TGGCTCACATGAGCTTCCCGTTATACAGCTCAAGAGAGAGCTTCTCGTTT
*
11294486 ATGTGCTCATAT
65 ATGTGCTCACAT
11294498 GA
1 GA
11294500 ACATTCCTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
74 12 0.18
75 30 0.45
76 5 0.07
77 20 0.30
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (76 bp):
GAGCTTCCCGATATTGGCTCACATGAGCTTCCCGTTATACAGCTCAAGAGAGAGCTTCTCGTTTA
TGTGCTCACAT
Found at i:11296649 original size:18 final size:18
Alignment explanation
Indices: 11296626--11296661 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11296616 TCCCCATAGT
11296626 CTCCTTGTGATCTTTCTC
1 CTCCTTGTGATCTTTCTC
11296644 CTCCTTGTGATCTTTCTC
1 CTCCTTGTGATCTTTCTC
11296662 TCTTGATGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.33, G:0.11, T:0.50
Consensus pattern (18 bp):
CTCCTTGTGATCTTTCTC
Found at i:11298524 original size:46 final size:46
Alignment explanation
Indices: 11298261--11298524 Score: 368
Period size: 46 Copynumber: 5.7 Consensus size: 46
11298251 TACCATAGTG
** * * *
11298261 TCTTTCAATTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
** * * *
11298307 TCTTTCAACCATGGTCTTATTCTTTTCATGTCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
** *
11298353 TCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
11298399 TCTTTCAACTATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
11298445 TCTTTCAACCGTGGTCTTACACATTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
*
11298491 TCTTTCAACCATGGTATTACACATTTCATATCAG
1 TCTTTCAACCATGGTCTTACACATTTCATATCAG
11298525 AGAGCACACT
Statistics
Matches: 202, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 198 0.98
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTA
Found at i:11300670 original size:11 final size:11
Alignment explanation
Indices: 11300654--11300696 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
11300644 CTTTATATAC
11300654 TAATAAAATAT
1 TAATAAAATAT
11300665 TAATAAAATATAT
1 TAAT-AAA-ATAT
*
11300678 TATTAAAATAT
1 TAATAAAATAT
11300689 TAATAAAA
1 TAATAAAA
11300697 AAATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:11300684 original size:24 final size:24
Alignment explanation
Indices: 11300648--11300696 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
11300638 TTCTTTCTTT
11300648 ATATACTAATAAAATATTAATAAA
1 ATATACTAATAAAATATTAATAAA
* *
11300672 ATATATTATTAAAATATTAATAAA
1 ATATACTAATAAAATATTAATAAA
11300696 A
1 A
11300697 AAATATTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATACTAATAAAATATTAATAAA
Found at i:11300698 original size:13 final size:13
Alignment explanation
Indices: 11300658--11300703 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 13
11300648 ATATACTAAT
11300658 AAAATATTAATAA
1 AAAATATTAATAA
* *
11300671 AATATATT-AT-T
1 AAAATATTAATAA
11300682 AAAATATTAATAAA
1 AAAATATTAAT-AA
11300696 AAAATATT
1 AAAATATT
11300704 TATCTAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
11 7 0.27
12 4 0.15
13 7 0.27
14 8 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATATTAATAA
Found at i:11304463 original size:14 final size:15
Alignment explanation
Indices: 11304441--11304473 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
11304431 ACAAGGTGAC
11304441 TAAAAATTTAAT-AT
1 TAAAAATTTAATAAT
*
11304455 TAAACATTTAATAAT
1 TAAAAATTTAATAAT
11304470 TAAA
1 TAAA
11304474 TAAAAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
TAAAAATTTAATAAT
Found at i:11304926 original size:18 final size:18
Alignment explanation
Indices: 11304903--11304941 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
11304893 TATTAAATTT
*
11304903 AAAAAATAAATTTAGTTA
1 AAAAAATAAATCTAGTTA
*
11304921 AAAAAATAAATCTATTTA
1 AAAAAATAAATCTAGTTA
11304939 AAA
1 AAA
11304942 TATGAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAAATAAATCTAGTTA
Found at i:11313244 original size:21 final size:21
Alignment explanation
Indices: 11313220--11313263 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11313210 CGATGACGTG
11313220 ATTATTGAGAAATTATA-AAAA
1 ATTATT-AGAAATTATATAAAA
**
11313241 ATTATTTTAAATTATATAAAA
1 ATTATTAGAAATTATATAAAA
11313262 AT
1 AT
11313264 GTAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (21 bp):
ATTATTAGAAATTATATAAAA
Found at i:11313297 original size:29 final size:30
Alignment explanation
Indices: 11313229--11313297 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
11313219 GATTATTGAG
11313229 AAATTATAAAAAATTATTTTAAATTATATAA
1 AAATTA-AAAAAATTATTTTAAATTATATAA
*
11313260 AAATGTAAAAAAA-TA-TTTAAATTATTTAAA
1 AAAT-TAAAAAAATTATTTTAAATTATAT-AA
11313290 AAATTAAA
1 AAATTAAA
11313298 TGTTGTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 15 0.43
30 8 0.23
31 10 0.29
32 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (30 bp):
AAATTAAAAAAATTATTTTAAATTATATAA
Found at i:11313325 original size:10 final size:10
Alignment explanation
Indices: 11313303--11313387 Score: 52
Period size: 10 Copynumber: 8.5 Consensus size: 10
11313293 TTAAATGTTG
11313303 TAAATAGTTAT
1 TAAATA-TTAT
11313314 TAAATATTAT
1 TAAATATTAT
11313324 TAAAATATT-T
1 T-AAATATTAT
*
11313334 TGAA-ATTAT
1 TAAATATTAT
* *
11313343 TAAAAATCAT
1 TAAATATTAT
* *
11313353 AAAAGATTATT
1 TAAATATTA-T
11313364 TAAA-ATT-T
1 TAAATATTAT
*
11313372 GTAAAAATTAT
1 -TAAATATTAT
11313383 TAAAT
1 TAAAT
11313388 GTTGTGAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
8 4 0.07
9 10 0.17
10 27 0.46
11 18 0.31
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (10 bp):
TAAATATTAT
Found at i:11313693 original size:20 final size:20
Alignment explanation
Indices: 11313668--11313712 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
11313658 AATAATTTGT
*
11313668 TAATTATTTAT-ATTTTTTAA
1 TAATTATTTATGA-TATTTAA
11313688 TAATTATTTATGATATTTAA
1 TAATTATTTATGATATTTAA
11313708 TAATT
1 TAATT
11313713 TTAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TAATTATTTATGATATTTAA
Found at i:11313809 original size:9 final size:9
Alignment explanation
Indices: 11313795--11313853 Score: 59
Period size: 9 Copynumber: 6.6 Consensus size: 9
11313785 ACATATTTAT
11313795 TTTTTACAA
1 TTTTTACAA
*
11313804 TTTTTATATA
1 TTTTTACA-A
11313814 TTTTTA-AA
1 TTTTTACAA
*
11313822 TATTTTACTA
1 T-TTTTACAA
*
11313832 TTTTTA-AT
1 TTTTTACAA
11313840 TTTTTACAA
1 TTTTTACAA
11313849 TTTTT
1 TTTTT
11313854 TTATTTGGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 8 0.20
9 24 0.59
10 9 0.22
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTACAA
Found at i:11313819 original size:19 final size:18
Alignment explanation
Indices: 11313736--11313837 Score: 68
Period size: 19 Copynumber: 5.6 Consensus size: 18
11313726 AATTTTATAA
*
11313736 TAATTTTTTTACAATTTT
1 TAATATTTTTACAATTTT
* * * *
11313754 AAAACATTTTAACAATATT
1 -TAATATTTTTACAATTTT
*
11313773 TAATAATTATTTAC-ATATT
1 TAAT-ATT-TTTACAATTTT
11313792 T-AT-TTTTTACAATTTT
1 TAATATTTTTACAATTTT
11313808 TATATATTTTTA-AATATTT
1 TA-ATATTTTTACAAT-TTT
*
11313827 TACTATTTTTA
1 TAATATTTTTA
11313838 ATTTTTTACA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
15 5 0.08
16 7 0.11
18 17 0.26
19 33 0.50
20 4 0.06
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (18 bp):
TAATATTTTTACAATTTT
Found at i:11313844 original size:17 final size:18
Alignment explanation
Indices: 11313795--11313853 Score: 68
Period size: 17 Copynumber: 3.3 Consensus size: 18
11313785 ACATATTTAT
11313795 TTTTTACAATTTTTATA-TA
1 TTTTTA-AATTTTT-TACTA
*
11313814 TTTTTAAATATTTTACTA
1 TTTTTAAATTTTTTACTA
*
11313832 TTTTT-AATTTTTTACAA
1 TTTTTAAATTTTTTACTA
11313849 TTTTT
1 TTTTT
11313854 TTATTTGGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 17 0.47
18 13 0.36
19 6 0.17
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTTTAAATTTTTTACTA
Found at i:11313854 original size:18 final size:18
Alignment explanation
Indices: 11313793--11313859 Score: 55
Period size: 17 Copynumber: 3.7 Consensus size: 18
11313783 TTACATATTT
* *
11313793 ATTTTTTACAATTTTTATA
1 ATTTTTTA-ATTTTTTACA
* * *
11313812 TATTTTTAAATATTTTACT
1 -ATTTTTTAATTTTTTACA
11313831 A-TTTTTAATTTTTTACA
1 ATTTTTTAATTTTTTACA
*
11313848 ATTTTTTTATTT
1 ATTTTTTAATTT
11313860 GGCCAACAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
17 14 0.38
18 10 0.27
19 6 0.16
20 7 0.19
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTTAATTTTTTACA
Found at i:11314413 original size:15 final size:17
Alignment explanation
Indices: 11314379--11314415 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
11314369 GTCTGTCTCC
*
11314379 TTATTTATTCACTTTTT
1 TTATTTATTCACTTTAT
11314396 TTATTT-TTC-CTTTAT
1 TTATTTATTCACTTTAT
11314411 TTATT
1 TTATT
11314416 ATTTGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 3 0.16
17 6 0.32
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (17 bp):
TTATTTATTCACTTTAT
Found at i:11316126 original size:40 final size:40
Alignment explanation
Indices: 11316040--11316130 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
11316030 TGTTATCTAT
* * *
11316040 CAGGCTTTGTGTCGGTGTATTTATCGGGCTTTGTACCTAG
1 CAGGCTTTGTGCCAGTATATTTATCGGGCTTTGTACCTAG
* * **
11316080 CGGGCTTTGTGCCAGTATGTTTATCGGGCTTTGTGTCTAG
1 CAGGCTTTGTGCCAGTATATTTATCGGGCTTTGTACCTAG
*
11316120 TAGGCTTTGTG
1 CAGGCTTTGTG
11316131 TCGGTGTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.11, C:0.16, G:0.32, T:0.41
Consensus pattern (40 bp):
CAGGCTTTGTGCCAGTATATTTATCGGGCTTTGTACCTAG
Found at i:11316149 original size:25 final size:25
Alignment explanation
Indices: 11316134--11316191 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
11316124 CTTTGTGTCG
11316134 GTGTTATCTATCAGGCCTTGAGCTA
1 GTGTTATCTATCAGGCCTTGAGCTA
** *
11316159 GTGTTATCTATCAAACCTTGAGCTG
1 GTGTTATCTATCAGGCCTTGAGCTA
11316184 GTGATTAT
1 GTG-TTAT
11316192 TTAGTAGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 25 0.86
26 4 0.14
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (25 bp):
GTGTTATCTATCAGGCCTTGAGCTA
Found at i:11319006 original size:11 final size:11
Alignment explanation
Indices: 11318990--11319014 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
11318980 TTCAACCGAT
11318990 GAAAATGAAGA
1 GAAAATGAAGA
11319001 GAAAATGAAGA
1 GAAAATGAAGA
11319012 GAA
1 GAA
11319015 TTCTCGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.28, T:0.08
Consensus pattern (11 bp):
GAAAATGAAGA
Found at i:11322147 original size:16 final size:17
Alignment explanation
Indices: 11322117--11322149 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
11322107 TTCATAAGTA
11322117 TATATCAATTATTTCAT
1 TATATCAATTATTTCAT
11322134 TATATCAA-TATTTCAT
1 TATATCAATTATTTCAT
11322150 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATCAATTATTTCAT
Found at i:11322495 original size:46 final size:46
Alignment explanation
Indices: 11322430--11322886 Score: 598
Period size: 46 Copynumber: 10.0 Consensus size: 46
11322420 TTATCTTTGA
* * * * * *
11322430 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
* * *** *
11322476 CAGGTTGCCATGGTATCTTTCAACCATGGTTTTTTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* ** * ** * *
11322522 TACATTGCCATAGTATCTTTCAACCATGGTCTTATTCATTCCCGT-T
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATT-TCATAT
*
11322568 -ATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11322613 CCTGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
* * * *
11322659 CATGTTGCCATGGTATCTTACAACCATAGTTTTACACATTTTATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11322705 CATGTTGCCATGGTGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
11322751 CATGTTGCCATGG-AGTCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTA-TCTTTCAACCATGGTCTTACACATTTCATAT
*
11322797 CATTTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
*
11322843 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACATATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
11322887 TTCAGAAAGT
Statistics
Matches: 365, Mismatches: 40, Indels: 12
0.88 0.10 0.03
Matches are distributed among these distances:
44 1 0.00
45 39 0.11
46 322 0.88
47 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
Found at i:11325612 original size:38 final size:38
Alignment explanation
Indices: 11325561--11325715 Score: 220
Period size: 38 Copynumber: 3.9 Consensus size: 38
11325551 ATATGAATTA
11325561 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTG
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTG
11325599 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAATG
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--------TG
* *
11325645 TGTAAGACCATGGTTGAAAGATACCATGTCAACTTGTG
1 TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTG
11325683 TGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 TGTAAGACCATGGTTGAAAGATACCATGGCAAC
11325716 GTGACATGAA
Statistics
Matches: 106, Mismatches: 3, Indels: 16
0.85 0.02 0.13
Matches are distributed among these distances:
38 70 0.66
46 36 0.34
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.25
Consensus pattern (38 bp):
TGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTG
Found at i:11325664 original size:46 final size:46
Alignment explanation
Indices: 11325597--11325805 Score: 229
Period size: 46 Copynumber: 4.7 Consensus size: 46
11325587 TGGCAACCTG
*
11325597 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATAAAA
* *
11325643 TGTGTAAGACCATGGTTGAAAGATACCATGTCAA-CT----T---G
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATAAAA
*
11325681 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACAT-AAAA
** * * *
11325728 -GAATAAGCCCATGGTTGAAAGATACCATGGCAACATGACAGAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATAAAA
* * * *
11325773 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
11325806 TCACGTCAAA
Statistics
Matches: 138, Mismatches: 15, Indels: 20
0.80 0.09 0.12
Matches are distributed among these distances:
38 33 0.24
39 1 0.01
41 1 0.01
43 1 0.01
45 6 0.04
46 96 0.70
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATAAAA
Found at i:11325688 original size:84 final size:84
Alignment explanation
Indices: 11325547--11325761 Score: 324
Period size: 84 Copynumber: 2.6 Consensus size: 84
11325537 GAGTGTGCTC
* * *
11325547 CCTGATATGAATTATGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
11325612 TTGAAAGATACCATGGCAA
66 TTGAAAGATACCATGGCAA
* *
11325631 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGTCAACTTGTGTGTAAGACCATGG
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
11325696 TTGAAAGATACCATGGCAA
66 TTGAAAGATACCATGGCAA
* * ** *
11325715 CGTGACATGAAAA-GAATAAGCCCATGGTTGAAAGATACCATGGCAAC
1 CCTGATAT-AAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
11325762 ATGACAGAAA
Statistics
Matches: 119, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
84 115 0.97
85 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.23, T:0.24
Consensus pattern (84 bp):
CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGG
TTGAAAGATACCATGGCAA
Found at i:11326111 original size:23 final size:25
Alignment explanation
Indices: 11326066--11326112 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
11326056 AATAAATATA
*
11326066 CATAAAATATATGGAAATGATGAAG
1 CATAAAATATATGGAAATAATGAAG
*
11326091 CATAAAATAT-T-GATATAATGAA
1 CATAAAATATATGGAAATAATGAA
11326113 ATGAATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 1 0.05
25 10 0.50
ACGTcount: A:0.53, C:0.04, G:0.15, T:0.28
Consensus pattern (25 bp):
CATAAAATATATGGAAATAATGAAG
Found at i:11330053 original size:6 final size:6
Alignment explanation
Indices: 11330035--11330109 Score: 82
Period size: 6 Copynumber: 12.3 Consensus size: 6
11330025 AAGAAACATT
* *
11330035 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAAA ATCAGA ATCAGA ATCAGT
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA
*
11330083 ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCA-G-A ATCAGA ATCAGA ATCAGA AT
11330110 GTGAATGCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 3 0.05
6 50 0.86
7 4 0.07
8 1 0.02
ACGTcount: A:0.51, C:0.16, G:0.15, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:11330594 original size:54 final size:54
Alignment explanation
Indices: 11330531--11330638 Score: 164
Period size: 54 Copynumber: 2.0 Consensus size: 54
11330521 AAGGTATCTC
*
11330531 GGTAATTCTACCTTAC-AGGAGTATTTCAGTAATTCTACCTTACAGGGGTATTTT
1 GGTAATTCTACCTTACAAGG-GTATTTCAGTAATTCTACCCTACAGGGGTATTTT
* * *
11330585 GGTATTTCTACCTTACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTT
11330639 AATAATTTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
54 46 0.94
55 3 0.06
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (54 bp):
GGTAATTCTACCTTACAAGGGTATTTCAGTAATTCTACCCTACAGGGGTATTTT
Found at i:11330645 original size:27 final size:27
Alignment explanation
Indices: 11330523--11330637 Score: 140
Period size: 27 Copynumber: 4.3 Consensus size: 27
11330513 ACCCCACAAA
* *
11330523 GGTATCTCGGTAATTCTACCTTACAGG
1 GGTATTTCAGTAATTCTACCTTACAGG
*
11330550 AGTATTTCAGTAATTCTACCTTACAGG
1 GGTATTTCAGTAATTCTACCTTACAGG
** * *
11330577 GGTATTTTGGTATTTCTACCTTACAAG
1 GGTATTTCAGTAATTCTACCTTACAGG
* * *
11330604 GGTATTTCGGTAATTCTACCCTATAGG
1 GGTATTTCAGTAATTCTACCTTACAGG
11330631 GGTATTT
1 GGTATTT
11330638 TAATAATTTC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 75 1.00
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
GGTATTTCAGTAATTCTACCTTACAGG
Found at i:11330661 original size:54 final size:54
Alignment explanation
Indices: 11330544--11330672 Score: 136
Period size: 54 Copynumber: 2.4 Consensus size: 54
11330534 AATTCTACCT
* * * ** **
11330544 TACAGGAGTATTTCAGTAATTCTACCTTACAGGGGTATTTTGGTATTTCTACCT
1 TACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAATATTTCTACAA
* *
11330598 TACAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTTAATAATTTC-ACAA
1 TACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAAT-ATTTCTACAA
*
11330652 -ATCAGGGGTATTTTGGTAATT
1 TA-CAGGGGTATTTCGGTAATT
11330673 TTACAAACCA
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
53 1 0.02
54 56 0.90
55 5 0.08
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.40
Consensus pattern (54 bp):
TACAGGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTTAATATTTCTACAA
Found at i:11330742 original size:27 final size:27
Alignment explanation
Indices: 11330630--11331176 Score: 297
Period size: 27 Copynumber: 20.6 Consensus size: 27
11330620 TACCCTATAG
** * * * *
11330630 GGGTATTTTAATAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11330657 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
** * *
11330684 GGGTATTTTGGTAATTTTATTGATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*
11330711 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* *** * * *
11330738 AGGTATTTCAATAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** * **
11330765 GGGTAAAATGGTAATTCTATAAATTAA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** * * * * *
11330792 GGGTAAAATAGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
*** *
11330819 GGGTAAAATGATAATTTTAT----C--
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * * * *
11330840 --TTATTTCGATAATTTTACAAATCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * * *
11330865 GGATATTTGGGTAATTTTATAAATCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* * ** *
11330892 GGGTACTTTGGTAATTTTACAAGTCGA
1 GGGTATTTTGGTAATTTTATAAACCAA
** * * * *
11330919 GGGTATTTCAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
11330946 GGGTATTTTGATAATTTTATAAACTAG
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11330973 GGGTATTTTGATAATTTTACAAA-C-A
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
11330998 GTGGTGTTTTGGTAATTTTACAAACTAA
1 G-GGTATTTTGGTAATTTTATAAACCAA
* * *
11331026 TGGTATTTTGATAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11331053 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTATAAACCAA
*
11331080 GGGTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTATAAACCAA
* * *
11331107 GAGTATTTTAGTAATTTTACAAACC-A
1 GGGTATTTTGGTAATTTTATAAACCAA
* *
11331133 GGAGTATTTTGGTAATTTTGTAAATCAA
1 GG-GTATTTTGGTAATTTTATAAACCAA
11331161 GGGTATTTTGGTAATT
1 GGGTATTTTGGTAATT
11331177 CTATCCTACA
Statistics
Matches: 405, Mismatches: 102, Indels: 26
0.76 0.19 0.05
Matches are distributed among these distances:
19 12 0.03
23 2 0.00
25 1 0.00
26 22 0.05
27 364 0.90
28 4 0.01
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTATAAACCAA
Found at i:11330743 original size:81 final size:81
Alignment explanation
Indices: 11330630--11331176 Score: 346
Period size: 81 Copynumber: 6.9 Consensus size: 81
11330620 TACCCTATAG
** * * * * *
11330630 GGGTATTTTAATAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGG
** *
11330695 TAATTTTATTGATCGA
66 TAATTTTATAAATCAA
* * *** ** ***
11330711 GGGTATTTTGGTAATTTTGTAAACCAAAGGTATTTCAATAATTTTGTAAATC-GAGGGTAAAATG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAG-GGGTATTTTG
* *
11330775 GTAATTCTATAAATTAA
65 GTAATTTTATAAATCAA
*** * * * * * *** * * * *
11330792 GGGTAAAATAGTAATTCTGTAAATCGAGGGTAAAATGATAATTTT----ATC----TTATTTCGA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGG
* *
11330849 TAATTTTACAAATCGA
66 TAATTTTATAAATCAA
* * * * * * **
11330865 GGATATTTGGGTAATTTTATAAATCAGGGGTACTTTGGTAATTTTACAAGTC-GAGGGTATTTCA
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAG-GGGTATTTTG
* * *
11330929 GTAATTTCACAAATCAG
65 GTAATTTTATAAATCAA
* * * * * *
11330946 GGGTATTTTGATAATTTTATAAACTAGGGGTATTTTGATAATTTTACAAA-CAGTGGTGTTTTGG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGG
*
11331010 TAATTTTACAAA-CTAA
66 TAATTTTATAAATC-AA
* * * *
11331026 TGGTATTTTGATAATTTTGTAAACCAAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGG
1 GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGG
* *
11331091 TGATTTTATAAACCAA
66 TAATTTTATAAATCAA
* * * ** *
11331107 GAGTATTTTAGTAATTTTACAAACC-AGGAGTATTTTGGTAATTTTGTAAATCAAGGGTATTTTG
1 GGGTATTTTGGTAATTTTATAAACCAAGG-GTATTTTGGTAATTTTACAAATCAGGGGTATTTTG
11331171 GTAATT
65 GTAATT
11331177 CTATCCTACA
Statistics
Matches: 352, Mismatches: 100, Indels: 28
0.73 0.21 0.06
Matches are distributed among these distances:
73 46 0.13
77 5 0.01
79 1 0.00
80 69 0.20
81 230 0.65
82 1 0.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTGGTAATTTTACAAATCAGGGGTATTTTGG
TAATTTTATAAATCAA
Found at i:11331175 original size:54 final size:53
Alignment explanation
Indices: 11330849--11331176 Score: 327
Period size: 54 Copynumber: 6.1 Consensus size: 53
11330839 CTTATTTCGA
* * * * *
11330849 TAATTTTACAAATCGAGGATATTTGGGTAATTTTATAAATCAGGGGTACTTTGG
1 TAATTTTACAAA-CCAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGG
* * ** * * * *
11330903 TAATTTTACAAGTCGAGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGA
1 TAATTTTACAA-ACCAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGG
* * * * *
11330957 TAATTTTATAAACTAGGGGTATTTTGATAATTTTACAAA-C-AGTGGTGTTTTGG
1 TAATTTTACAAACCA-GGGTATTTTGGTAATTTTATAAATCAAG-GGTATTTTGG
* * * * *
11331010 TAATTTTACAAACTAATGGTATTTTGATAATTTTGTAAACCAAGGGTATTTTGG
1 TAATTTTACAAAC-CAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGG
* * * *
11331064 TAATTTTACAAACCAGGGGTATTTTGGTGATTTTATAAACCAAGAGTATTTTAG
1 TAATTTTACAAACCA-GGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGG
*
11331118 TAATTTTACAAACCAGGAGTATTTTGGTAATTTTGTAAATCAAGGGTATTTTGG
1 TAATTTTACAAACCAGG-GTATTTTGGTAATTTTATAAATCAAGGGTATTTTGG
11331172 TAATT
1 TAATT
11331177 CTATCCTACA
Statistics
Matches: 230, Mismatches: 36, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
52 1 0.00
53 46 0.20
54 181 0.79
55 2 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (53 bp):
TAATTTTACAAACCAGGGTATTTTGGTAATTTTATAAATCAAGGGTATTTTGG
Found at i:11348347 original size:9 final size:9
Alignment explanation
Indices: 11348328--11348391 Score: 85
Period size: 9 Copynumber: 7.2 Consensus size: 9
11348318 TCGGGTATTT
11348328 TTCGG-TAA
1 TTCGGTTAA
*
11348336 TTCGATTAA
1 TTCGGTTAA
11348345 TTCGGTTAA
1 TTCGGTTAA
11348354 TTCGGTTAA
1 TTCGGTTAA
*
11348363 TTCGGGTAA
1 TTCGGTTAA
*
11348372 TTCGGGTAA
1 TTCGGTTAA
*
11348381 TTCGGGTAA
1 TTCGGTTAA
11348390 TT
1 TT
11348392 TTTAACCAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
8 4 0.08
9 48 0.92
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.41
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:11348356 original size:18 final size:18
Alignment explanation
Indices: 11348331--11348391 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
11348321 GGTATTTTTC
*
11348331 GGTAATTCGATTAATTCG
1 GGTAATTCGGTTAATTCG
*
11348349 GTTAATTCGGTTAATTCG
1 GGTAATTCGGTTAATTCG
*
11348367 GGTAATTCGGGTAATTCG
1 GGTAATTCGGTTAATTCG
11348385 GGTAATT
1 GGTAATT
11348392 TTTAACCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.25, C:0.10, G:0.26, T:0.39
Consensus pattern (18 bp):
GGTAATTCGGTTAATTCG
Found at i:11349981 original size:27 final size:27
Alignment explanation
Indices: 11349923--11349974 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
11349913 TTTATACAAA
* *
11349923 TAATTCGGTTAATTCGGTTAATTTGCG
1 TAATTCGGGTAATTCGATTAATTTGCG
11349950 TAATTCGGGTAATTCGATTAATTTG
1 TAATTCGGGTAATTCGATTAATTTG
11349975 GTTAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.21, T:0.44
Consensus pattern (27 bp):
TAATTCGGGTAATTCGATTAATTTGCG
Found at i:11349982 original size:9 final size:9
Alignment explanation
Indices: 11349923--11349981 Score: 66
Period size: 9 Copynumber: 6.6 Consensus size: 9
11349913 TTTATACAAA
11349923 TAATTCGGT
1 TAATTCGGT
11349932 TAATTCGGT
1 TAATTCGGT
*
11349941 TAATTTGCG-
1 TAATTCG-GT
*
11349950 TAATTCGGG
1 TAATTCGGT
*
11349959 TAATTCGAT
1 TAATTCGGT
*
11349968 TAATTTGGT
1 TAATTCGGT
11349977 TAATT
1 TAATT
11349982 TTATACTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
8 1 0.02
9 40 0.95
10 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (9 bp):
TAATTCGGT
Found at i:11350401 original size:20 final size:20
Alignment explanation
Indices: 11350373--11350447 Score: 51
Period size: 20 Copynumber: 3.5 Consensus size: 20
11350363 CAACATAGGG
11350373 GTATCGATACCTAAGCCTAT
1 GTATCGATACCTAAGCCTAT
* * * * *
11350393 GTATTGATATCAATACAACATAGG
1 GTATCGATA-C-CTA-AGCCTA-T
11350417 GGTATCGATACCTAAGCCTAT
1 G-TATCGATACCTAAGCCTAT
*
11350438 GTATTGATAC
1 GTATCGATAC
11350448 ATTAGTGCTA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
20 16 0.41
21 2 0.05
22 6 0.15
23 6 0.15
24 2 0.05
25 7 0.18
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (20 bp):
GTATCGATACCTAAGCCTAT
Found at i:11350419 original size:45 final size:45
Alignment explanation
Indices: 11350355--11350446 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
11350345 ACTCGTATGG
11350355 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
1 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
11350400 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
1 TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
11350445 TA
1 TA
11350447 CATTAGTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (45 bp):
TATCAATACAACATAGGGGTATCGATACCTAAGCCTATGTATTGA
Found at i:11359084 original size:93 final size:93
Alignment explanation
Indices: 11358925--11359110 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 93
11358915 AAGGGTCCAC
*
11358925 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTAGATG
1 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTACATG
11358990 GATATGATATTTAGACTACTAATACATT
66 GATATGATATTTAGACTACTAATACATT
* * *
11359018 AAAAAATACAAGATAGCTTAAGTACTTATGACGCTTACATGTACAAGTTTAATTATTATTACATG
1 AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTACATG
11359083 GATATGATATTTAGACTACTAATACATT
66 GATATGATATTTAGACTACTAATACATT
11359111 GAGAAAGCAA
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.34
Consensus pattern (93 bp):
AAAAAATACAAGATAGCTTAAGTACTTATGACACTTACAAGTACAAGTTTAAATATTATTACATG
GATATGATATTTAGACTACTAATACATT
Found at i:11365787 original size:24 final size:24
Alignment explanation
Indices: 11365719--11365800 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
11365709 CGAGCAATAA
**
11365719 AATGGGAAGCTCATGTGAGCCATGT
1 AATGGGAAGCTCATAAGAGCCAT-T
**
11365744 AACAGGAAGCTC-TAGAGAGCCATT
1 AATGGGAAGCTCATA-AGAGCCATT
* *
11365768 AATGGGAAGCTCATACGAGCCAAT
1 AATGGGAAGCTCATAAGAGCCATT
11365792 AATGGGAAG
1 AATGGGAAG
11365801 GTTCAAGCGA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
24 28 0.60
25 19 0.40
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.18
Consensus pattern (24 bp):
AATGGGAAGCTCATAAGAGCCATT
Found at i:11365817 original size:25 final size:24
Alignment explanation
Indices: 11365719--11365828 Score: 80
Period size: 25 Copynumber: 4.5 Consensus size: 24
11365709 CGAGCAATAA
** *
11365719 AATGGGAAGCTCATGTGAGCCATGT
1 AATGGGAAGCTCATACGAGCCA-AT
** * *
11365744 AACAGGAAGCTC-TAGAGAGCCATT
1 AATGGGAAGCTCATA-CGAGCCAAT
11365768 AATGGGAAGCTCATACGAGCCAAT
1 AATGGGAAGCTCATACGAGCCAAT
*
11365792 AATGGGAAGGTTCA-AGCGAGCCAAT
1 AATGGGAA-GCTCATA-CGAGCCAAT
* *
11365817 ATTGGAAAGCTC
1 AATGGGAAGCTC
11365829 CGAAGAGCTT
Statistics
Matches: 68, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
24 31 0.46
25 37 0.54
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (24 bp):
AATGGGAAGCTCATACGAGCCAAT
Found at i:11365851 original size:25 final size:24
Alignment explanation
Indices: 11365823--11365888 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 24
11365813 CAATATTGGA
*
11365823 AAGCTCCGAAGAGCTTTTAATCGGG
1 AAGCTCCGAAGAGCTTTT-ATCGAG
*
11365848 AAGCTCATGAAAGAGCCTTTTATCGAG
1 AAGCTC-CG-AAGAG-CTTTTATCGAG
*
11365875 AAGCTTCGAAGAGC
1 AAGCTCCGAAGAGC
11365889 CATATATCGG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
24 1 0.03
25 11 0.32
26 2 0.06
27 15 0.44
28 5 0.15
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.23
Consensus pattern (24 bp):
AAGCTCCGAAGAGCTTTTATCGAG
Found at i:11369614 original size:43 final size:43
Alignment explanation
Indices: 11369565--11369674 Score: 139
Period size: 43 Copynumber: 2.6 Consensus size: 43
11369555 CTGACATTTC
** * * *
11369565 GCCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGTATTATA
1 GCCTGCTAGGCCCGAAGCCCGATATAATCTCACCGGCATTATA
*
11369608 GCCTGCTAGGCCCGAAGCCCGATATAATCTCACTGGCATTATA
1 GCCTGCTAGGCCCGAAGCCCGATATAATCTCACCGGCATTATA
* * *
11369651 GCCTACAAGGCCCAAAGCCCGATA
1 GCCTGCTAGGCCCGAAGCCCGATA
11369675 ATATTATTCA
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (43 bp):
GCCTGCTAGGCCCGAAGCCCGATATAATCTCACCGGCATTATA
Found at i:11371627 original size:14 final size:15
Alignment explanation
Indices: 11371598--11371627 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
11371588 AAAAATTTAG
11371598 ACATGATACTTTCAC
1 ACATGATACTTTCAC
11371613 ACATGATAC-TTCAC
1 ACATGATACTTTCAC
11371627 A
1 A
11371628 TATAATAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.37, C:0.27, G:0.07, T:0.30
Consensus pattern (15 bp):
ACATGATACTTTCAC
Found at i:11378238 original size:3 final size:3
Alignment explanation
Indices: 11378230--11378266 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
11378220 GTGTTCTTAA
*
11378230 AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
11378267 CATATTAGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:11383531 original size:48 final size:48
Alignment explanation
Indices: 11383473--11383568 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
11383463 AGAGATTAAG
11383473 CTATCCTGGTTTCAAAAATACCAAAATTACTAAAAACGGGACAAGGAA
1 CTATCCTGGTTTCAAAAATACCAAAATTACTAAAAACGGGACAAGGAA
*
11383521 CTATCTTGGTTTCAAAAATACCAAAATTACTAAAAACGGGACAAGGAA
1 CTATCCTGGTTTCAAAAATACCAAAATTACTAAAAACGGGACAAGGAA
11383569 ACTTACTCAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.46, C:0.18, G:0.15, T:0.22
Consensus pattern (48 bp):
CTATCCTGGTTTCAAAAATACCAAAATTACTAAAAACGGGACAAGGAA
Found at i:11384310 original size:2 final size:2
Alignment explanation
Indices: 11384303--11384374 Score: 54
Period size: 2 Copynumber: 36.0 Consensus size: 2
11384293 ATAATCTATT
* * * * * * *
11384303 GA GA GA GA GA GT GA GA GT GA GT GA GA GA GA GT GA GT GT GT GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
11384345 GT GA GA GA GA GA GA GA AA GA AA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
11384375 CCACTCATGG
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.42, C:0.00, G:0.47, T:0.11
Consensus pattern (2 bp):
GA
Found at i:11388237 original size:66 final size:66
Alignment explanation
Indices: 11388155--11388288 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
11388145 GAAAGAAAAA
11388155 TAAAAATAAAATCGAGGGTGAAAAACACTAGTTGAAGGATCATATTCACGAACCTTCAACTTGTA
1 TAAAAATAAAATCGAGGGTGAAAAACACTAGTTGAAGGATCATATTCACGAACCTTCAACTTGTA
11388220 T
66 T
11388221 TAAAAATAAAATCGAGGGTGAAAAACACTAGTTGAAGGATCATATTCACGAACCTTCAACTTGTA
1 TAAAAATAAAATCGAGGGTGAAAAACACTAGTTGAAGGATCATATTCACGAACCTTCAACTTGTA
11388286 T
66 T
11388287 TA
1 TA
11388289 CTCTTACTAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (66 bp):
TAAAAATAAAATCGAGGGTGAAAAACACTAGTTGAAGGATCATATTCACGAACCTTCAACTTGTA
T
Found at i:11389593 original size:27 final size:27
Alignment explanation
Indices: 11389547--11389696 Score: 210
Period size: 27 Copynumber: 5.5 Consensus size: 27
11389537 CGTGTGAGGT
*
11389547 AGCCTTTGTGGCGATCTATGAAAAGGA
1 AGCCTTTGTGGCGATTTATGAAAAGGA
* *
11389574 AGCATTTGTAGCGATTTATGAAAAAGGA
1 AGCCTTTGTGGCGATTTATG-AAAAGGA
11389602 AGCCTTTGTGGCGATTTATGAAAAAGGA
1 AGCCTTTGTGGCGATTTATG-AAAAGGA
*
11389630 AGCCTTTGTGGCGATTTATGAAAAAGA
1 AGCCTTTGTGGCGATTTATGAAAAGGA
* * *
11389657 AGCCTTTATGGCGATCTATGAAAAAGA
1 AGCCTTTGTGGCGATTTATGAAAAGGA
*
11389684 AGCATTTGTGGCG
1 AGCCTTTGTGGCG
11389697 CACTTTAAAA
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
27 59 0.53
28 53 0.47
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (27 bp):
AGCCTTTGTGGCGATTTATGAAAAGGA
Found at i:11389609 original size:28 final size:28
Alignment explanation
Indices: 11389547--11389696 Score: 225
Period size: 28 Copynumber: 5.5 Consensus size: 28
11389537 CGTGTGAGGT
*
11389547 AGCCTTTGTGGCGATCTATG-AAAAGGA
1 AGCCTTTGTGGCGATTTATGAAAAAGGA
* *
11389574 AGCATTTGTAGCGATTTATGAAAAAGGA
1 AGCCTTTGTGGCGATTTATGAAAAAGGA
11389602 AGCCTTTGTGGCGATTTATGAAAAAGGA
1 AGCCTTTGTGGCGATTTATGAAAAAGGA
11389630 AGCCTTTGTGGCGATTTATGAAAAA-GA
1 AGCCTTTGTGGCGATTTATGAAAAAGGA
* *
11389657 AGCCTTTATGGCGATCTATGAAAAA-GA
1 AGCCTTTGTGGCGATTTATGAAAAAGGA
*
11389684 AGCATTTGTGGCG
1 AGCCTTTGTGGCG
11389697 CACTTTAAAA
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 55 0.49
28 58 0.51
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (28 bp):
AGCCTTTGTGGCGATTTATGAAAAAGGA
Found at i:11389659 original size:55 final size:56
Alignment explanation
Indices: 11389547--11389696 Score: 243
Period size: 55 Copynumber: 2.7 Consensus size: 56
11389537 CGTGTGAGGT
*
11389547 AGCCTTTGTGGCGATCTATG-AAAAGGAAGCATTTGTAGCGATTTATGAAAAAGGA
1 AGCCTTTGTGGCGATCTATGAAAAAGGAAGCATTTGTGGCGATTTATGAAAAAGGA
* *
11389602 AGCCTTTGTGGCGATTTATGAAAAAGGAAGCCTTTGTGGCGATTTATGAAAAA-GA
1 AGCCTTTGTGGCGATCTATGAAAAAGGAAGCATTTGTGGCGATTTATGAAAAAGGA
*
11389657 AGCCTTTATGGCGATCTATGAAAAA-GAAGCATTTGTGGCG
1 AGCCTTTGTGGCGATCTATGAAAAAGGAAGCATTTGTGGCG
11389697 CACTTTAAAA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
54 14 0.16
55 44 0.50
56 30 0.34
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (56 bp):
AGCCTTTGTGGCGATCTATGAAAAAGGAAGCATTTGTGGCGATTTATGAAAAAGGA
Found at i:11390060 original size:24 final size:24
Alignment explanation
Indices: 11390033--11390103 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
11390023 AGCTTGGCAC
11390033 TTGTCTAAGCGTCAAACAACATCA
1 TTGTCTAAGCGTCAAACAACATCA
* *
11390057 TTGT-T-A--GT-ATACTTGACA-C-
1 TTGTCTAAGCGTCAAAC--AACATCA
11390076 TTGTCTAAGCGTCAAACAACATCA
1 TTGTCTAAGCGTCAAACAACATCA
11390100 TTGT
1 TTGT
11390104 TAGTATACTT
Statistics
Matches: 34, Mismatches: 4, Indels: 18
0.61 0.07 0.32
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 4 0.12
22 4 0.12
23 4 0.12
24 11 0.32
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (24 bp):
TTGTCTAAGCGTCAAACAACATCA
Found at i:11390078 original size:43 final size:43
Alignment explanation
Indices: 11390025--11390114 Score: 171
Period size: 43 Copynumber: 2.1 Consensus size: 43
11390015 CAATCAATAG
*
11390025 CTTGGCACTTGTCTAAGCGTCAAACAACATCATTGTTAGTATA
1 CTTGACACTTGTCTAAGCGTCAAACAACATCATTGTTAGTATA
11390068 CTTGACACTTGTCTAAGCGTCAAACAACATCATTGTTAGTATA
1 CTTGACACTTGTCTAAGCGTCAAACAACATCATTGTTAGTATA
11390111 CTTG
1 CTTG
11390115 CACATATTTC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 46 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (43 bp):
CTTGACACTTGTCTAAGCGTCAAACAACATCATTGTTAGTATA
Found at i:11390663 original size:46 final size:47
Alignment explanation
Indices: 11390603--11390783 Score: 244
Period size: 46 Copynumber: 3.9 Consensus size: 47
11390593 TTTAACATGA
* * * *
11390603 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
* * * *
11390649 TGCCATGGTATCTTTCAACCATGATCTTATTC-TTTTCATGTCACAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
11390695 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
*
11390741 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCA
11390784 GAGAGCACAC
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
45 5 0.04
46 115 0.96
ACGTcount: A:0.22, C:0.24, G:0.12, T:0.42
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCATATCACGT
Found at i:11392884 original size:11 final size:11
Alignment explanation
Indices: 11392868--11392917 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
11392858 ATACTAATAA
11392868 AATAATAAAAT
1 AATAATAAAAT
11392879 AATAATAAAAT
1 AATAATAAAAT
*
11392890 ATATTATTAAAAT
1 A-A-TAATAAAAT
*
11392903 ATTAATAAAAT
1 AATAATAAAAT
11392914 AATA
1 AATA
11392918 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 23 0.70
12 1 0.03
13 9 0.27
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:11392900 original size:24 final size:25
Alignment explanation
Indices: 11392873--11392919 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
11392863 AATAAAATAA
11392873 TAAAATAATAATAAAAT-ATATTAT
1 TAAAATAATAATAAAATAATATTAT
*
11392897 TAAAATATTAATAAAATAATATT
1 TAAAATAATAATAAAATAATATT
11392920 TATCTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
TAAAATAATAATAAAATAATATTAT
Found at i:11392901 original size:32 final size:32
Alignment explanation
Indices: 11392856--11392953 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 32
11392846 TTCTTTCTTT
11392856 ATATACTAATAAAATAATAA-AATAATAATAAA
1 ATATACTAATAAAATAATAATAA-AATAATAAA
* * * *
11392888 ATATATTATTAAAATATTAATAAAATAAT-AT
1 ATATACTAATAAAATAATAATAAAATAATAAA
* * *
11392919 TTAT-CTAATTAAATAATTATAAAAT-ATCAAA
1 ATATACTAATAAAATAATAATAAAATAAT-AAA
11392950 ATAT
1 ATAT
11392954 CTCTAGCATC
Statistics
Matches: 51, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
29 2 0.04
30 16 0.31
31 8 0.16
32 23 0.45
33 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (32 bp):
ATATACTAATAAAATAATAATAAAATAATAAA
Found at i:11395338 original size:17 final size:16
Alignment explanation
Indices: 11395318--11395372 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 16
11395308 GTGTGTTGAA
11395318 ATTTATACGGTTTAAAG
1 ATTTATA-GGTTTAAAG
**
11395335 ATTTAT-TTTTCTAAA-
1 ATTTATAGGTT-TAAAG
11395350 ATTTATAAGGTTTAAAG
1 ATTTAT-AGGTTTAAAG
11395367 ATTTAT
1 ATTTAT
11395373 TTTTCTCTCG
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
15 8 0.27
16 8 0.27
17 14 0.47
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (16 bp):
ATTTATAGGTTTAAAG
Found at i:11395353 original size:32 final size:32
Alignment explanation
Indices: 11395316--11395378 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
11395306 TTGTGTGTTG
*
11395316 AAATTTATACGGTTTAAAGATTTATTTTTCTA
1 AAATTTATAAGGTTTAAAGATTTATTTTTCTA
11395348 AAATTTATAAGGTTTAAAGATTTATTTTTCT
1 AAATTTATAAGGTTTAAAGATTTATTTTTCT
11395379 CTCGCTTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.51
Consensus pattern (32 bp):
AAATTTATAAGGTTTAAAGATTTATTTTTCTA
Found at i:11396110 original size:24 final size:24
Alignment explanation
Indices: 11396083--11396133 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
11396073 ATTCTTACTA
* **
11396083 CATCAATATCCATTTCATGCATTT
1 CATCAATAACCATTTCATAAATTT
11396107 CATCAATAACCATTTCATAAATTT
1 CATCAATAACCATTTCATAAATTT
11396131 CAT
1 CAT
11396134 TTCTATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.39
Consensus pattern (24 bp):
CATCAATAACCATTTCATAAATTT
Found at i:11396865 original size:44 final size:44
Alignment explanation
Indices: 11396777--11396869 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 44
11396767 GATTAAACCA
*
11396777 AAGTAACAGTACGACACACAAGGTGCCTCATCGACTTAAAGTCG
1 AAGTAACAGTACGACACACAAGGTGCCTCATCGACTCAAAGTCG
** *
11396821 AAGTAACAGTACGACACTTATA-GTGCCTCATCGGA-TCAAGGTCG
1 AAGTAACAGTACGACACACA-AGGTGCCTCATC-GACTCAAAGTCG
11396865 AAGTA
1 AAGTA
11396870 TCCCTGAACA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 40 0.93
45 3 0.07
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (44 bp):
AAGTAACAGTACGACACACAAGGTGCCTCATCGACTCAAAGTCG
Found at i:11397341 original size:15 final size:15
Alignment explanation
Indices: 11397321--11397349 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11397311 AAACACTTTT
11397321 AAATCAATATCATTC
1 AAATCAATATCATTC
11397336 AAATCAATATCATT
1 AAATCAATATCATT
11397350 ATTTCAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATCAATATCATTC
Found at i:11398240 original size:31 final size:28
Alignment explanation
Indices: 11398205--11398272 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
11398195 TGTTTATCTC
*
11398205 ATAAAAATCTTATAATTTAATTAATTATCAA
1 ATAAAAATCTT-TAATTTAA-TAATAAT-AA
* *
11398236 ATAAACATCTTTTATTTAATAATAATAA
1 ATAAAAATCTTTAATTTAATAATAATAA
11398264 ATAATAAAT
1 ATAA-AAAT
11398273 ATCTATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 6 0.19
29 9 0.28
30 7 0.22
31 10 0.31
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (28 bp):
ATAAAAATCTTTAATTTAATAATAATAA
Found at i:11400393 original size:42 final size:43
Alignment explanation
Indices: 11400320--11400402 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 43
11400310 GAATTGAGTA
* **
11400320 CTTCGTTTACTCGATGTCATAGTTCAACTATGGTCTTACACAT
1 CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACACAT
*
11400363 CTTCATTTA-TCGATGTCATAGCCCAGCTATGGTCTTACAC
1 CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACAC
11400403 GAATCACATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.78
43 8 0.22
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.37
Consensus pattern (43 bp):
CTTCATTTACTCGATGTCATAGCCCAACTATGGTCTTACACAT
Found at i:11400444 original size:46 final size:47
Alignment explanation
Indices: 11400373--11400491 Score: 127
Period size: 46 Copynumber: 2.6 Consensus size: 47
11400363 CTTCATTTAT
* * * *
11400373 CGATGTCATAGCCCAGCTATGGTCTTACACGAATCA-CATATCTCA-A-
1 CGATGCCATATCCCAGATATGGTCTTACAC-AAT-AGCATATATCATAC
* * *
11400419 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCATAC
1 CGATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCATAC
*
11400466 CGATACCATATCCCAGATATGGTCTT
1 CGATGCCATATCCCAGATATGGTCTT
11400492 GTACGAAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 1 0.02
45 10 0.16
46 26 0.43
47 24 0.39
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (47 bp):
CGATGCCATATCCCAGATATGGTCTTACACAATAGCATATATCATAC
Found at i:11400549 original size:31 final size:31
Alignment explanation
Indices: 11400514--11400662 Score: 208
Period size: 31 Copynumber: 4.8 Consensus size: 31
11400504 CTTGTCACTT
*
11400514 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * *
11400545 GTAGCTGGAGCTACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * *
11400576 GTAGTCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
11400607 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
11400638 GTAGCCGAAACTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
11400663 TGTCATTTGT
Statistics
Matches: 104, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:11400737 original size:50 final size:51
Alignment explanation
Indices: 11400638--11400766 Score: 179
Period size: 50 Copynumber: 2.5 Consensus size: 51
11400628 CACTGATCAG
* * * * * *
11400638 GTAGCCGAAACTACCACTTTTCACTTGTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAAATAAGT
*
11400689 GTAGCCGAAGCTATTACTTATCACTT-TCACTTATCCTTGATCAAATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAAATAAGT
*
11400739 GCAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
11400767 TGCTATGGTC
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 45 0.66
51 23 0.34
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTATCCTTGATCAAATAAGT
Found at i:11404002 original size:16 final size:17
Alignment explanation
Indices: 11403973--11404005 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
11403963 ATTTGTTGGA
11403973 TTCTTTTATTTCTTTTC
1 TTCTTTTATTTCTTTTC
11403990 TTCTTTT-TTTCTTTTC
1 TTCTTTTATTTCTTTTC
11404006 CTTTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTCTTTTATTTCTTTTC
Found at i:11406394 original size:18 final size:20
Alignment explanation
Indices: 11406360--11406396 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
11406350 TTTTATTTAA
11406360 ATTTATTAAATTAATATTTG
1 ATTTATTAAATTAATATTTG
11406380 ATTT-TTAAA-TAATATTT
1 ATTTATTAAATTAATATTT
11406397 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (20 bp):
ATTTATTAAATTAATATTTG
Found at i:11422454 original size:23 final size:23
Alignment explanation
Indices: 11422424--11422470 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
11422414 TAGGGTTTAG
11422424 GATTTCTGCAAGAATAATTCTAA
1 GATTTCTGCAAGAATAATTCTAA
11422447 GATTTCTGCAAGAATAATTCTAA
1 GATTTCTGCAAGAATAATTCTAA
11422470 G
1 G
11422471 TAGACATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (23 bp):
GATTTCTGCAAGAATAATTCTAA
Found at i:11422994 original size:127 final size:126
Alignment explanation
Indices: 11422459--11423101 Score: 777
Period size: 126 Copynumber: 5.0 Consensus size: 126
11422449 TTTCTGCAAG
* * *
11422459 AATAATTCTAAGTAGACATTTCTGAACAAATAGTGTCGAAAAACACTTTAAAGTTTAAACAGGAT
1 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTC-AAAAACGC-TTCAAG------CAGGAT
* * *
11422524 GCACTGTCAGCAAAATTTTTG-GAAAAAGCTCTCACGTTGG-CGCTCTTTTGCTACAGTAGTTCG
58 GCACTGTCAGCAAAA-TTTCGAAAAAAAGCTCCCACG-TGGACGCTCTTTTGCTACAGTAGTTCG
*
11422587 GAGAAA
121 TAGAAA
* * * * * * *
11422593 AATAATTTTGAGTAGATATTTCTGAACAGATAGTGTCGAAAACACTTCAATCAGGATGCACTATC
1 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTC
* * * * * *
11422658 AACAAAATTTCTAGAGAAAGCTCCCACGTGAACGCTCTTTTGCTATAGTAGTTCGTAGAAA
66 AGCAAAATTTCGAAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * * *
11422719 AATAATTCTGAGCAGACGTTTCTGAACAAATAGTGTCGAAAATGCTTCAAGCAGGATGCACTGTC
1 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTC
* * *
11422784 AGTAAAATTTCGAAAAAAAGCTCCTACGTGGACGCTCTTTTGCTACAATAGTTCGTAGAAA
66 AGCAAAATTTCGAAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
** * *
11422845 AATAATTCTGAGTAGATGTTTCTGAACAAATAGTGTCAAAAATGCTTCAAGCAGGATGCACTATC
1 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTC
** *
11422910 AGCAAAATTTCGAAAAAAAAGCTCCCACGTAAACGCTCTTTTGCTACAATAGTTCGTAGAAA
66 AGCAAAATTTCG-AAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
* * * *
11422972 AATAATTCTGAGTAGACATTTCTAAACAAATGGTGTCAAAAAACGCTTCAAACATGATGCACTGT
1 AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTC-AAAAACGCTTCAAGCAGGATGCACTGT
* * * * *
11423037 CAGCAAAATTTAGAAAAAAAGCTCTCATGTGGATGCTCTTTTGCTATAGTAGTTCGTAGAAA
65 CAGCAAAATTTCGAAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
11423099 AAT
1 AAT
11423102 GAGGCTATAA
Statistics
Matches: 447, Mismatches: 58, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
125 5 0.01
126 239 0.53
127 124 0.28
128 35 0.08
132 4 0.01
133 7 0.02
134 33 0.07
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (126 bp):
AATAATTCTGAGTAGACATTTCTGAACAAATAGTGTCAAAAACGCTTCAAGCAGGATGCACTGTC
AGCAAAATTTCGAAAAAAAGCTCCCACGTGGACGCTCTTTTGCTACAGTAGTTCGTAGAAA
Found at i:11426564 original size:18 final size:18
Alignment explanation
Indices: 11426523--11426564 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
11426513 GACTAGAAAA
* *
11426523 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
*
11426541 AAGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
11426559 AGGATA
1 AGGATA
11426565 TGCACATGGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.07, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:11427160 original size:7 final size:7
Alignment explanation
Indices: 11427148--11427172 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11427138 CATTACTTAT
11427148 ATACATA
1 ATACATA
11427155 ATACATA
1 ATACATA
11427162 ATACATA
1 ATACATA
11427169 ATAC
1 ATAC
11427173 TAAATATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACATA
Found at i:11427178 original size:7 final size:7
Alignment explanation
Indices: 11427168--11427207 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
11427158 CATAATACAT
11427168 AATACTA
1 AATACTA
*
11427175 AATATTA
1 AATACTA
11427182 AATACTA
1 AATACTA
11427189 AATACTA
1 AATACTA
11427196 AATACTA
1 AATACTA
11427203 AATAC
1 AATAC
11427208 GAAACGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (7 bp):
AATACTA
Found at i:11427178 original size:14 final size:15
Alignment explanation
Indices: 11427148--11427207 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
11427138 CATTACTTAT
11427148 ATACAT-AATAC-ATA
1 ATACATAAATACTA-A
11427162 ATACAT-AATACTAA
1 ATACATAAATACTAA
*
11427176 ATA-TTAAATACTAA
1 ATACATAAATACTAA
11427190 ATAC-TAAATACTAA
1 ATACATAAATACTAA
11427204 ATAC
1 ATAC
11427208 GAAACGACTA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
13 1 0.02
14 40 0.95
15 1 0.02
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (15 bp):
ATACATAAATACTAA
Found at i:11427178 original size:21 final size:22
Alignment explanation
Indices: 11427161--11427207 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
11427151 CATAATACAT
*
11427161 AATACAT-AATACTAAATATTA
1 AATACATAAATACTAAATACTA
11427182 AATAC-TAAATACTAAATACTA
1 AATACATAAATACTAAATACTA
11427203 AATAC
1 AATAC
11427208 GAAACGACTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (22 bp):
AATACATAAATACTAAATACTA
Found at i:11428199 original size:48 final size:46
Alignment explanation
Indices: 11428143--11428278 Score: 148
Period size: 48 Copynumber: 2.8 Consensus size: 46
11428133 ATGCAAACAT
*
11428143 CATAAATGAAAAAAAAATCAAGCAGTATTGAAATTGTAATTATAA-TTG
1 CATAAATGAAAAAAAAATCAA-TAGTATTGAAATT-TAATTA-AATTTG
* *
11428191 CATAAATGAATAAAATATCAAATAGTATTGCAAATTTAATTAAATTTG
1 CATAAATGAAAAAAAAATC-AATAGTATTG-AAATTTAATTAAATTTG
* *
11428239 TATAAATTAAAAAAAATATCGAATAGTATTGAAAATTTAA
1 CATAAATGAAAAAAAA-ATC-AATAGTATTG-AAATTTAA
11428279 AATTATCACT
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
47 2 0.03
48 45 0.60
49 28 0.37
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (46 bp):
CATAAATGAAAAAAAAATCAATAGTATTGAAATTTAATTAAATTTG
Found at i:11428264 original size:49 final size:47
Alignment explanation
Indices: 11428143--11428278 Score: 143
Period size: 49 Copynumber: 2.8 Consensus size: 47
11428133 ATGCAAACAT
* *
11428143 CATAAATGAAAAAAAA-ATCAAGCAGTATTGAAATTGTAATTATAATTG
1 CATAAATTAAAAAAAATATCAA-TAGTATTGAAATT-TAATTATAATTG
* *
11428191 CATAAA-TGAATAAAATATCAAATAGTATTGCAAATTTAATTA-AATTTG
1 CATAAATTAAAAAAAATATC-AATAGTATTG-AAATTTAATTATAA-TTG
*
11428239 TATAAATTAAAAAAAATATCGAATAGTATTGAAAATTTAA
1 CATAAATTAAAAAAAATATC-AATAGTATTG-AAATTTAA
11428279 AATTATCACT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
47 8 0.11
48 30 0.41
49 36 0.49
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (47 bp):
CATAAATTAAAAAAAATATCAATAGTATTGAAATTTAATTATAATTG
Found at i:11428431 original size:11 final size:11
Alignment explanation
Indices: 11428415--11428473 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
11428405 AACAAACAAA
11428415 TTTGATAGAAT
1 TTTGATAGAAT
11428426 TTTGATAGAAT
1 TTTGATAGAAT
* *
11428437 TTTGAGAAAAT
1 TTTGATAGAAT
** *
11428448 TTCAAT-GAAA
1 TTTGATAGAAT
*
11428458 TTTGATAGATT
1 TTTGATAGAAT
11428469 TTTGA
1 TTTGA
11428474 AGGGAATATT
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
10 6 0.17
11 30 0.83
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (11 bp):
TTTGATAGAAT
Found at i:11432865 original size:34 final size:35
Alignment explanation
Indices: 11432827--11432893 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
11432817 CAGTAAAATA
*
11432827 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
11432861 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
11432894 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:11432867 original size:20 final size:20
Alignment explanation
Indices: 11432842--11432881 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
11432832 CGTAAAATGA
*
11432842 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
11432862 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
11432882 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:11432897 original size:14 final size:15
Alignment explanation
Indices: 11432821--11432897 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
11432811 GATTGCCAGT
* *
11432821 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
11432835 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
11432849 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
11432869 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
11432884 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
11432898 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:11444942 original size:18 final size:19
Alignment explanation
Indices: 11444901--11444950 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
11444891 ATATTAGAAT
*
11444901 TTTTTCATAATTATTAATAG
1 TTTTT-ATAATTTTTAATAG
11444921 -TTTTATAATTTTTAA-AG
1 TTTTTATAATTTTTAATAG
*
11444938 TTTTTTTAATTTT
1 TTTTTATAATTTT
11444951 GTATTCATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 2 0.07
18 21 0.78
19 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTTATAATTTTTAATAG
Found at i:11446650 original size:23 final size:23
Alignment explanation
Indices: 11446624--11446668 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11446614 TATATATGTA
*
11446624 ATTTTAACTTTCCTTCTTTTTTT
1 ATTTTAACTTTCATTCTTTTTTT
**
11446647 ATTTTATTTTTCATTCTTTTTT
1 ATTTTAACTTTCATTCTTTTTT
11446669 GCTTTTCCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.73
Consensus pattern (23 bp):
ATTTTAACTTTCATTCTTTTTTT
Found at i:11446674 original size:23 final size:24
Alignment explanation
Indices: 11446632--11446692 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
11446622 TAATTTTAAC
* *
11446632 TTTCCTTCTTTTTTTATTTT-ATT
1 TTTCATTCTTTTTTGATTTTCATT
*
11446655 TTTCATTCTTTTTTGCTTTTCCATT
1 TTTCATTCTTTTTTGATTTT-CATT
*
11446680 CTTCATTTCTTTT
1 TTTCA-TTCTTTT
11446693 AATGTAGCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 17 0.55
25 7 0.23
26 7 0.23
ACGTcount: A:0.08, C:0.18, G:0.02, T:0.72
Consensus pattern (24 bp):
TTTCATTCTTTTTTGATTTTCATT
Found at i:11451877 original size:21 final size:21
Alignment explanation
Indices: 11451851--11451893 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
11451841 GTTCCTGGAG
11451851 TTTGAAGGCACCATTTTTATT
1 TTTGAAGGCACCATTTTTATT
11451872 TTTGAAGGCACCATTTTTATT
1 TTTGAAGGCACCATTTTTATT
11451893 T
1 T
11451894 CTGATGTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (21 bp):
TTTGAAGGCACCATTTTTATT
Found at i:11452306 original size:3 final size:3
Alignment explanation
Indices: 11452298--11452323 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11452288 ATCACATGTT
11452298 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
11452324 TGGATGTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:11456214 original size:78 final size:78
Alignment explanation
Indices: 11456081--11456232 Score: 250
Period size: 78 Copynumber: 1.9 Consensus size: 78
11456071 GAGTCACATC
** *
11456081 TCATGTAACTGTAGTGAATCAAGATTACCTTTTCAGGTCAAATCCTATCCACCTTAGGTTACCAT
1 TCATGTAACTGTAGCAAATCAAGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
11456146 AATGAATCATATA
66 AATGAATCATATA
* *
11456159 TCATGTAACTGTAGCAAATCAGGATTACCTTTTCAGGTCAAATCCTATCCGCCTTAAGTTACCAT
1 TCATGTAACTGTAGCAAATCAAGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
*
11456224 AGTGAATCA
66 AATGAATCA
11456233 GGAATAAATC
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 68 1.00
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (78 bp):
TCATGTAACTGTAGCAAATCAAGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCAT
AATGAATCATATA
Found at i:11456245 original size:40 final size:40
Alignment explanation
Indices: 11456197--11456338 Score: 140
Period size: 40 Copynumber: 3.5 Consensus size: 40
11456187 CTTTTCAGGT
* * *
11456197 CAAATCCTATCCGCCTTAAGTTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACCTTAAATTACCATAGTGAATCAAGAA
* * *
11456237 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAAGAA
1 CAAATCCTATCCACCTTAAATTACCATAGTGAATCAAGAA
* ** * ** **
11456277 CAAATCCTATCTATTTTGAGGTATTATAGTGAATCAAGAA
1 CAAATCCTATCCACCTTAAATTACCATAGTGAATCAAGAA
* *
11456317 CGAATCCTATCCACTTTAAATT
1 CAAATCCTATCCACCTTAAATT
11456339 CTCGAGAAGG
Statistics
Matches: 81, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.37, C:0.20, G:0.11, T:0.32
Consensus pattern (40 bp):
CAAATCCTATCCACCTTAAATTACCATAGTGAATCAAGAA
Found at i:11460297 original size:15 final size:14
Alignment explanation
Indices: 11460278--11460321 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
11460268 ATGTTGATAA
*
11460278 TATTTTATAATTAT
1 TATTTTATAAATAT
*
11460292 TAATTTGATAAATAT
1 T-ATTTTATAAATAT
*
11460307 TATTTTATTAATAT
1 TATTTTATAAATAT
11460321 T
1 T
11460322 TTAATAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TATTTTATAAATAT
Found at i:11460347 original size:26 final size:26
Alignment explanation
Indices: 11460276--11460347 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
11460266 TGATGTTGAT
* * *
11460276 AATATTTTATAATTATTAATTTGATA
1 AATATTTTATTATTATTATTTTAATA
*
11460302 AATATTATT-TTATTAATATTTTAATA
1 AATATT-TTATTATTATTATTTTAATA
11460328 AGATATTTTATTATT-TTATT
1 A-ATATTTTATTATTATTATT
11460348 ATTATTTATT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 26 0.68
27 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (26 bp):
AATATTTTATTATTATTATTTTAATA
Found at i:11469685 original size:42 final size:42
Alignment explanation
Indices: 11469623--11469785 Score: 157
Period size: 42 Copynumber: 3.7 Consensus size: 42
11469613 TTCGTTTTCT
**
11469623 TGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TGATGCCATAGCCCAACTATGGTCTTACACATCTTCACATAA
* * *
11469665 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATAT-A
1 TGATGCCATAGCCCAACTATGGTCTTACACATCTTCACATAA
* ** *
11469706 TCGATGCCATAGCCCAATTATCATCTTACACGTAATCACATATCACATAT
1 T-GATGCCATAGCCCAACTATGGTCTTACAC---AT--C-T-TCACATAA
*
11469756 TGATGCCATAGCCCAGCTATGGTCTTACAC
1 TGATGCCATAGCCCAACTATGGTCTTACAC
11469786 GAATCACATA
Statistics
Matches: 96, Mismatches: 16, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
41 2 0.02
42 60 0.62
45 2 0.02
48 1 0.01
49 30 0.31
50 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (42 bp):
TGATGCCATAGCCCAACTATGGTCTTACACATCTTCACATAA
Found at i:11469765 original size:49 final size:48
Alignment explanation
Indices: 11469692--11469797 Score: 140
Period size: 49 Copynumber: 2.2 Consensus size: 48
11469682 TATGGTCTTA
* *
11469692 CACATATTCATATATCGATGCCATAGCCCAATTATCATCTTACACGTAAT
1 CACATA-TCACATATCGATGCCATAGCCCAACTATCATCTTACACG-AAT
* * **
11469742 CACATATCACATATTGATGCCATAGCCCAGCTATGGTCTTACACGAAT
1 CACATATCACATATCGATGCCATAGCCCAACTATCATCTTACACGAAT
11469790 CACATATC
1 CACATATC
11469798 TCACTGATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
48 11 0.22
49 33 0.66
50 6 0.12
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.29
Consensus pattern (48 bp):
CACATATCACATATCGATGCCATAGCCCAACTATCATCTTACACGAAT
Found at i:11469823 original size:46 final size:46
Alignment explanation
Indices: 11469729--11469873 Score: 164
Period size: 47 Copynumber: 3.1 Consensus size: 46
11469719 CCAATTATCA
* * *
11469729 TCTTACACGTAATCACATATCACATATTGATGCCATAGCCCAGCTATGG
1 TCTTACACG-AATCACATATCAC--ACTGATGCCATATCCCAGATATGG
*
11469778 TCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATATGG
1 TCTTACACGAATCACATATCACACTGATGCCATATCCCAGATATGG
* * * * * *
11469824 TCTTATACAGTAGCATATATCACACCGATGTCATATCCCAGATATGG
1 TCTTACAC-GAATCACATATCACACTGATGCCATATCCCAGATATGG
11469871 TCT
1 TCT
11469874 AATACGAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
46 28 0.33
47 35 0.42
48 12 0.14
49 9 0.11
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (46 bp):
TCTTACACGAATCACATATCACACTGATGCCATATCCCAGATATGG
Done.