Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006083.1 Hibiscus syriacus cultivar Beakdansim tig00014415_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 319407
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:6866 original size:17 final size:17
Alignment explanation
Indices: 6844--6880 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6834 CGATTTTGAG
6844 CTCGATTCAAGCTCGAA
1 CTCGATTCAAGCTCGAA
*
6861 CTCGATTCATGCTCGAA
1 CTCGATTCAAGCTCGAA
6878 CTC
1 CTC
6881 AAACTCGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.32, G:0.16, T:0.27
Consensus pattern (17 bp):
CTCGATTCAAGCTCGAA
Found at i:9505 original size:7 final size:7
Alignment explanation
Indices: 9493--9562 Score: 99
Period size: 7 Copynumber: 10.3 Consensus size: 7
9483 ATGTATAAAT
*
9493 TAAACCA
1 TAAACCC
9500 TAAACCC
1 TAAACCC
9507 TAAA-CC
1 TAAACCC
9513 TAAA-CC
1 TAAACCC
9519 TAAACCC
1 TAAACCC
9526 TAAACCC
1 TAAACCC
9533 TAAACCC
1 TAAACCC
*
9540 TAAAACC
1 TAAACCC
*
9547 TAAACCA
1 TAAACCC
9554 TAAACCC
1 TAAACCC
9561 TA
1 TA
9563 TCACATAATT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
6 12 0.21
7 45 0.79
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:9510 original size:19 final size:19
Alignment explanation
Indices: 9493--9559 Score: 89
Period size: 20 Copynumber: 3.3 Consensus size: 19
9483 ATGTATAAAT
9493 TAAACCATAAACCCTAAACC
1 TAAACC-TAAACCCTAAACC
9513 TAAACCTAAACCCTAAACCC
1 TAAACCTAAACCCTAAA-CC
*
9533 TAAACCCTAAAACCTAAACC
1 TAAA-CCTAAACCCTAAACC
9553 ATAAACC
1 -TAAACC
9560 CTATCACATA
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
19 11 0.26
20 16 0.37
21 16 0.37
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.15
Consensus pattern (19 bp):
TAAACCTAAACCCTAAACC
Found at i:9659 original size:14 final size:14
Alignment explanation
Indices: 9640--9669 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
9630 TATAATTATC
*
9640 AATAATGTATTTTT
1 AATAATGTAATTTT
9654 AATAATGTAATTTT
1 AATAATGTAATTTT
9668 AA
1 AA
9670 AATATCTAAA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:11088 original size:16 final size:15
Alignment explanation
Indices: 11067--11097 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
11057 TTAATATGTA
11067 CATATAAATTGAAGCT
1 CATATAAATT-AAGCT
11083 CATATAAATTAAGCT
1 CATATAAATTAAGCT
11098 TCGTGGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.32
Consensus pattern (15 bp):
CATATAAATTAAGCT
Found at i:11276 original size:20 final size:20
Alignment explanation
Indices: 11251--11297 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
11241 GGCAATGAAT
11251 CGACTGGGAACAGGTAGAAC
1 CGACTGGGAACAGGTAGAAC
* *
11271 CGACTGAGAACCGGTAGAAC
1 CGACTGGGAACAGGTAGAAC
*
11291 CGGCTGG
1 CGACTGG
11298 AAACCAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.23, G:0.36, T:0.11
Consensus pattern (20 bp):
CGACTGGGAACAGGTAGAAC
Found at i:17544 original size:81 final size:81
Alignment explanation
Indices: 17377--18111 Score: 1098
Period size: 81 Copynumber: 9.1 Consensus size: 81
17367 AGCATTTAGC
* * * ** * * * * * *
17377 CTTTTACCCAAAGGTATATAGCCTTTCATCTAA-TTTCATGATTAACACCTTCCTATCCAATACA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
* *
17441 AAGCTAGGCCATTAAT
66 CAGCTAGGCTATTAAT
* ** *
17457 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCCTAATTGACATTTTTCTTTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
17522 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * *
17538 CTTTTACTCAAAGGTATTTAACCTTTCATATAACTGGCATAATTGACACCTCTCTGTCATATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
17603 CAACTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* *
17619 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCAAAATTGACACATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
17684 CAACTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * * *
17700 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-ACATAAATGACACCTTTCTGTCAAAGGAA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
17764 CAGCTAGGCTACTAAT
66 CAGCTAGGCTATTAAT
*
17780 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACACCTTTGTTGTCAAATGC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTT-CTGTCAAATGC
*
17844 ACAGCTAGACTATTAAT
65 ACAGCTAGGCTATTAAT
*
17861 CTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACCTTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
17926 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* *
17942 CTTTTACTCAAAGATATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
*
18007 CAACTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
* * *
18023 CTTTTACTCATAGGTGTTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
18088 CAGCTAGGCTATTAAT
66 CAGCTAGGCTATTAAT
18104 CTTTTACT
1 CTTTTACT
18112 TTGGAATAGT
Statistics
Matches: 595, Mismatches: 57, Indels: 5
0.91 0.09 0.01
Matches are distributed among these distances:
80 117 0.20
81 461 0.77
82 17 0.03
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCA
CAGCTAGGCTATTAAT
Found at i:17878 original size:323 final size:324
Alignment explanation
Indices: 17442--18111 Score: 1110
Period size: 323 Copynumber: 2.1 Consensus size: 324
17432 TCCAATACAA
* * **
17442 AGCTAGGCCATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCCTAATTGACATT
1 AGCTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACC
*
17507 TTTCTTTCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATATAAC
66 TTTCTTTCAAATGCACAGCTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATATAAC
* *
17572 TGGCATAATTGACACCTCTCTGTCATATGCACAACTAGGCTATTAATCTTTTACTCAAAGGTATT
131 TGGCATAATTGACACCTCTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGATATT
*
17637 TAACCTTTCATCTAACTGGCAAAATTGACACATTTCTGTCAAATGCACAACTAGGCTATTAATCT
196 TAACCTTTCATCTAACTGGCAAAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATCT
*
17702 TTTACTCAAAGGTATTTAACCTTTCATCTAACT-ACATAAATGACACCTTTCTGTCAAAGGAAC
261 TTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAAATGACACCTTTATGTCAAAGGAAC
*
17765 AGCTAGGCTACTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACT-GCATAATTGACACC
1 AGCTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACC
* *
17829 TTTGTTGTCAAATGCACAGCTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAA
66 TTTCTT-TCAAATGCACAGCTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATATAA
* * *
17894 TTGGCATAATTGACACCTTTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTACTCAAAGATAT
130 CTGGCATAATTGACACCTCTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGATAT
* *
17959 TTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCACAACTAGGCTATTAATC
195 TTAACCTTTCATCTAACTGGCAAAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATC
* * * * * *
18024 TTTTACTCATAGGTGTTTAACCTTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCAC
260 TTTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAAATGACACCTTTATGTCAAAGGAAC
18089 AGCTAGGCTATTAATCTTTTACT
1 AGCTAGGCTATTAATCTTTTACT
18112 TTGGAATAGT
Statistics
Matches: 321, Mismatches: 24, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
322 16 0.05
323 258 0.80
324 47 0.15
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.36
Consensus pattern (324 bp):
AGCTAGGCTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACC
TTTCTTTCAAATGCACAGCTAGACTATTAATCTTTTACTCAAAGGTATTTAACCTTTCATATAAC
TGGCATAATTGACACCTCTCTGTCAAATGCACAACTAGGCTATTAATCTTTTACTCAAAGATATT
TAACCTTTCATCTAACTGGCAAAATTGACACATTTCTATCAAATGCACAACTAGGCTATTAATCT
TTTACTCAAAGGTATTTAACCTTTCATCTAACTGACATAAATGACACCTTTATGTCAAAGGAAC
Found at i:18297 original size:53 final size:53
Alignment explanation
Indices: 18239--18355 Score: 153
Period size: 55 Copynumber: 2.2 Consensus size: 53
18229 TTTACGTGGG
* * * *
18239 TTGCACACATTACTAATACAGAAATTCATAAACTTATTTTGAATTTATTATTT
1 TTGCACACAGTACCAATACAGAAATTCATAAACTTATTATGAATTTATTAGTT
* * *
18292 TTGCACACAAAGTGCCCATACAGAAATTCATAAACTTATTATGAATTTTTTAGTT
1 TTGCACAC--AGTACCAATACAGAAATTCATAAACTTATTATGAATTTATTAGTT
18347 TTGCACACA
1 TTGCACACA
18356 CAGTTCCATT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
53 9 0.16
55 46 0.84
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (53 bp):
TTGCACACAGTACCAATACAGAAATTCATAAACTTATTATGAATTTATTAGTT
Found at i:18733 original size:22 final size:21
Alignment explanation
Indices: 18695--18738 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
18685 TCGATACCCC
* *
18695 TACCATGATATCGATACTACTA
1 TACCATGATACCAATAC-ACTA
18717 TACCATGATACCAATACACTA
1 TACCATGATACCAATACACTA
18738 T
1 T
18739 TACGGTACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.39, C:0.25, G:0.07, T:0.30
Consensus pattern (21 bp):
TACCATGATACCAATACACTA
Found at i:21709 original size:90 final size:92
Alignment explanation
Indices: 21544--21719 Score: 257
Period size: 90 Copynumber: 1.9 Consensus size: 92
21534 CCTAACACAC
* * * *
21544 CCTTTTTTAGCCAAGGTACCCTAGTCATATTAGGGTTTTTATTATTATTTCAAATTAATTAAAGC
1 CCTTTTATAGCCAAGGTACCCTAATCATATCAGGG-TATTATTATTATTTCAAATTAATTAAAGC
*
21609 TATATTTAATTAATTGGAATTTAACAAT
65 TATATTTAATTAATTGAAATTTAACAAT
* * *
21637 CCTTTTATATCCAAGTTACCCTAATCATATCAGGG-ATT-TTATTATTTCAAATTAATTAAATCT
1 CCTTTTATAGCCAAGGTACCCTAATCATATCAGGGTATTATTATTATTTCAAATTAATTAAAGCT
21700 ATATTTAATTAATTGAAATT
66 ATATTTAATTAATTGAAATT
21720 AAATATTCGG
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
90 43 0.57
91 2 0.03
93 30 0.40
ACGTcount: A:0.35, C:0.12, G:0.09, T:0.44
Consensus pattern (92 bp):
CCTTTTATAGCCAAGGTACCCTAATCATATCAGGGTATTATTATTATTTCAAATTAATTAAAGCT
ATATTTAATTAATTGAAATTTAACAAT
Found at i:24957 original size:81 final size:80
Alignment explanation
Indices: 24864--25275 Score: 567
Period size: 81 Copynumber: 5.1 Consensus size: 80
24854 AGCATTTAGC
* * * * * *
24864 CTTTTACCCAAAGGCATATAACCTTTCATCTAATGTGCATGATTGACACATTCCTGTCTAATACA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAATG-GCATAATTGACACATTTCTGTCAAATACA
* *
24929 CAACTATGCCATTAAT
65 CAACTAGGCTATTAAT
*
24945 CTTTTACTCAAAGGTATTTAACCTTTTATCTAACT-GCATAATTGACACATTTCTGTCAAA-AGC
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TGGCATAATTGACACATTTCTGTCAAATA-C
* *
25008 ACATCCAGGCTATTAAT
64 ACAACTAGGCTATTAAT
*
25025 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TGGCATAATTGACACATTTCTGTCAAATACA
25090 CAACTAGGCTATTAAT
65 CAACTAGGCTATTAAT
* *
25106 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATACG
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAA-TGGCATAATTGACACATTTCTGTCAAATACA
* *
25171 TAGCTAGGCTATTAAT
65 CAACTAGGCTATTAAT
* * * *
25187 CTTTTACTGAAAGGTATTTAACCTTTCATCTAGCTGGCATAATTGACACATTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTA-ATGGCATAATTGACACATTTCTGTCAAATACA
*
25252 CACCTAGGCTATTAAT
65 CAACTAGGCTATTAAT
25268 CTTTTACT
1 CTTTTACT
25276 TTGGAATAGT
Statistics
Matches: 298, Mismatches: 28, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
79 1 0.00
80 70 0.23
81 226 0.76
82 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (80 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAATGGCATAATTGACACATTTCTGTCAAATACAC
AACTAGGCTATTAAT
Found at i:25890 original size:22 final size:22
Alignment explanation
Indices: 25863--25921 Score: 100
Period size: 22 Copynumber: 2.7 Consensus size: 22
25853 ATACCTCTAG
*
25863 CATGGTATCGATATTAATATAC
1 CATGGTATCGATACTAATATAC
*
25885 CATGGTATCGATACTATTATAC
1 CATGGTATCGATACTAATATAC
25907 CATGGTATCGATACT
1 CATGGTATCGATACT
25922 CTAACGGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Consensus pattern (22 bp):
CATGGTATCGATACTAATATAC
Found at i:28146 original size:2 final size:2
Alignment explanation
Indices: 28139--28176 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28129 GCCAGAAAAG
28139 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28177 GACATCATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30829 original size:81 final size:81
Alignment explanation
Indices: 30604--31177 Score: 790
Period size: 81 Copynumber: 7.1 Consensus size: 81
30594 AGCATTTAGC
* * * * * * * * * * * * *
30604 CTTTTACCCAAAGGCATATAGCCTTTCATCTAATTTGCATGATTGCCTCCTTCCTGTCCAATACA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
*
30669 CAACTAGGCCATTAAT
66 CAACTAGGCTATTAAT
*
30685 CTTTTACTCAAAGATATTTAACC-TTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
*
30749 CAACTAGGCTCTTAAT
66 CAACTAGGCTATTAAT
* * * *
30765 CTTTTACTCAATGGTATTTAACCTTTCATATAACTGGCATAATGGACACCTTTCTATCTAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
* *
30830 CAGCTAAGCTATTAAT
66 CAACTAGGCTATTAAT
* * *
30846 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGCCATAATTGACACCTTTCTGTCAATTGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
30911 CAACTAGGCTATTAAT
66 CAACTAGGCTATTAAT
* * * *
30927 ATTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATAATTGACACATTTATATCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
30992 CAACTAGGCTATTAAT
66 CAACTAGGCTATTAAT
* * * * **
31008 CTTTTACTCAAAGGTATTTAACCTTTCATCTATCTGGCATAGTTGACACCTTTTTGTCAAATATA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
*
31073 CAGCTAGGCTATTAAT
66 CAACTAGGCTATTAAT
* * *
31089 CTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACCTTTATGTCAAATGCA
1 CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
31154 CAACTAGGCTATTAAT
66 CAACTAGGCTATTAAT
31170 CTTTTACT
1 CTTTTACT
31178 TTGGATTAGT
Statistics
Matches: 435, Mismatches: 57, Indels: 2
0.88 0.12 0.00
Matches are distributed among these distances:
80 67 0.15
81 368 0.85
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (81 bp):
CTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTATCAAATGCA
CAACTAGGCTATTAAT
Found at i:31890 original size:21 final size:21
Alignment explanation
Indices: 31864--31918 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
31854 ATCCTCATAG
*
31864 TATCGATACTACTTGCGTCAA
1 TATCGATACTACTTGCATCAA
31885 TATCGATACTACTTGCATCAA
1 TATCGATACTACTTGCATCAA
31906 TATCGATACTACT
1 TATCGATACTACT
31919 CAGCTGATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.11, T:0.35
Consensus pattern (21 bp):
TATCGATACTACTTGCATCAA
Found at i:36526 original size:81 final size:81
Alignment explanation
Indices: 36441--36908 Score: 589
Period size: 81 Copynumber: 5.8 Consensus size: 81
36431 GGCATATAGT
* * * ** * * * * *
36441 CTTTCATCTAATTTGCATGATTTCCACCTTCCTGTCCAATACACAGCTAGGATATTAATCTTTTA
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
36506 CTCAAAGGTATTTAAC
66 CTCAAAGGTATTTAAC
* *
36522 CTTTCATCTAACTGGCATAATTGACACCTTTCTTTCAAATGTACAACT-GGACTATTAATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGG-CTATTAATCTTTT
36586 ACTCAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
* * * * *
36603 ATTTCATCTAATTGGCATAATTGACACCTCTCTGTCAAATGCACAGCTAGGCTATTAATCTTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
*
36668 CTCAAATGTATTTAAC
66 CTCAAAGGTATTTAAC
* * *
36684 CTTTCATCTAAATGGCATAATTTACA-CTTGTCTGTCAAATGCTCAACTAGGCTATTAATCTTTT
1 CTTTCATCTAACTGGCATAATTGACACCTT-TCTGTCAAATGCACAACTAGGCTATTAATCTTTT
36748 ACTCAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
* * * * *
36765 CTTTCATTTAGCTGGCATAATTGACACTTTTCTTCTCAAATGCACAACTAGGCTATTAATATTTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTC-TGTCAAATGCACAACTAGGCTATTAATCTTTT
36830 ACTCAAAGGTATTTAAC
65 ACTCAAAGGTATTTAAC
* * ** * * * *
36847 CTTTCATTTAACTGACATAATTGATGCTTTTATGTCAAATGCACATCTAAGCTATTAATCTT
1 CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTT
36909 ATACCTTTCA
Statistics
Matches: 337, Mismatches: 45, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.01
81 256 0.76
82 77 0.23
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (81 bp):
CTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAATGCACAACTAGGCTATTAATCTTTTA
CTCAAAGGTATTTAAC
Found at i:36951 original size:66 final size:66
Alignment explanation
Indices: 36845--36974 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 66
36835 AAGGTATTTA
** *
36845 ACCTTTCATTTAACTGACATAATTGATGCTTTTATGTCAAATGCACATCTAAGCTATTAATCTTA
1 ACCTTTCATTTAACTGACATAATTGACACCTTTATGTCAAATGCACATCTAAGCTATTAATCTTA
36910 T
66 T
* *
36911 ACCTTTCATTTAACTTG-CATAATTGACACCTTTGTGTCAAATGCACATCTAGGCTATTAATCTT
1 ACCTTTCATTTAAC-TGACATAATTGACACCTTTATGTCAAATGCACATCTAAGCTATTAATCTT
36975 TTACTTTGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
66 56 0.97
67 2 0.03
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (66 bp):
ACCTTTCATTTAACTGACATAATTGACACCTTTATGTCAAATGCACATCTAAGCTATTAATCTTA
T
Found at i:42927 original size:16 final size:17
Alignment explanation
Indices: 42906--42944 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
42896 TTATAGAGTT
42906 AAAAAAGG-GAAAAAAG
1 AAAAAAGGTGAAAAAAG
*
42922 AAAAAAGGTGAAAAAGG
1 AAAAAAGGTGAAAAAAG
42939 AAAAAA
1 AAAAAA
42945 ATAATAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (17 bp):
AAAAAAGGTGAAAAAAG
Found at i:52289 original size:17 final size:17
Alignment explanation
Indices: 52263--52303 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
52253 TCAGCTACAT
*
52263 CATCAACATTGTCACAA
1 CATCAGCATTGTCACAA
*
52280 CATCAGCATTTTCACAA
1 CATCAGCATTGTCACAA
52297 CATCAGC
1 CATCAGC
52304 GTATCGAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.37, C:0.32, G:0.07, T:0.24
Consensus pattern (17 bp):
CATCAGCATTGTCACAA
Found at i:54235 original size:45 final size:45
Alignment explanation
Indices: 54164--54253 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
54154 GCGTACTCCC
54164 AAGTCGTTACATTCAAAGATGCAAGTATGAATAGCATTATAATGT
1 AAGTCGTTACATTCAAAGATGCAAGTATGAATAGCATTATAATGT
* *
54209 AAGTTGTTACATTCAAAGATGGAAGTATGAATAGCATTATAATGT
1 AAGTCGTTACATTCAAAGATGCAAGTATGAATAGCATTATAATGT
54254 CTTAACGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.32
Consensus pattern (45 bp):
AAGTCGTTACATTCAAAGATGCAAGTATGAATAGCATTATAATGT
Found at i:54246 original size:25 final size:25
Alignment explanation
Indices: 54173--54246 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 25
54163 CAAGTCGTTA
54173 CATTCAAAGATGCAAGTATGAATAG
1 CATTCAAAGATGCAAGTATGAATAG
* * *
54198 CATT-ATA-ATGTAAGT-TG-TTA-
1 CATTCAAAGATGCAAGTATGAATAG
*
54218 CATTCAAAGATGGAAGTATGAATAG
1 CATTCAAAGATGCAAGTATGAATAG
54243 CATT
1 CATT
54247 ATAATGTCTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
20 4 0.11
21 4 0.11
22 9 0.24
23 9 0.24
24 4 0.11
25 8 0.21
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (25 bp):
CATTCAAAGATGCAAGTATGAATAG
Found at i:69368 original size:22 final size:22
Alignment explanation
Indices: 69343--69386 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
69333 TGGTTATTAC
*
69343 ATATATGATTTTTATAATGAAT
1 ATATATGATGTTTATAATGAAT
*
69365 ATATATGATGTTTATTATGAAT
1 ATATATGATGTTTATAATGAAT
69387 GTTACTTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATGATGTTTATAATGAAT
Found at i:76870 original size:22 final size:24
Alignment explanation
Indices: 76838--76884 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
76828 TAATTTTAAC
76838 ATTCATAATAA-ATATA-ATATAT
1 ATTCATAATAATATATATATATAT
*
76860 ATTCATGATAATATATATATATAT
1 ATTCATAATAATATATATATATAT
76884 A
1 A
76885 ATAACAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 5 0.23
24 7 0.32
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTCATAATAATATATATATATAT
Found at i:83243 original size:22 final size:22
Alignment explanation
Indices: 83211--83256 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
83201 CCGAAGTAAC
*
83211 ATTCATAATAAACATCATATAT
1 ATTCATAATAAAAATCATATAT
*
83233 ATTCATGATAAAAATCATATAT
1 ATTCATAATAAAAATCATATAT
83255 AT
1 AT
83257 AATAACGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.37
Consensus pattern (22 bp):
ATTCATAATAAAAATCATATAT
Found at i:94353 original size:34 final size:34
Alignment explanation
Indices: 94310--94393 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
94300 TACTGAAGGG
*
94310 AATGTATCGATACCGTTTCAAAATAGATTGCAAA
1 AATGTATCGATACCATTTCAAAATAGATTGCAAA
94344 AATGTATCGATACCATTTCAAAATAGATTGCAAA
1 AATGTATCGATACCATTTCAAAATAGATTGCAAA
94378 AATGTATCGATACCAT
1 AATGTATCGATACCAT
94394 AGCATAGTAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (34 bp):
AATGTATCGATACCATTTCAAAATAGATTGCAAA
Found at i:94405 original size:19 final size:19
Alignment explanation
Indices: 94381--94421 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
94371 TTGCAAAAAT
94381 GTATCGATACCATAGCATA
1 GTATCGATACCATAGCATA
* *
94400 GTATCGGTACCATAGTATA
1 GTATCGATACCATAGCATA
94419 GTA
1 GTA
94422 GTATCGATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (19 bp):
GTATCGATACCATAGCATA
Found at i:94864 original size:55 final size:55
Alignment explanation
Indices: 94777--95148 Score: 494
Period size: 55 Copynumber: 6.8 Consensus size: 55
94767 CTAAGTGTAC
*
94777 TACATGCACTCTGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
1 TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
* * *
94832 TACATGCACTATGTGTGCAAATCCACGGAATTCATCATGTGTTGATGAATAGTCG
1 TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
* * * *
94887 TACAGGTACTATGTGTGAAAATCCACGAAATTCATCATGAGTTGATGAATAGCAG
1 TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
* * * *
94942 TATAGGCACTATGTGTGCAAATCCACAGAAA-TCATCATGAGTTGATGAATTGTCG
1 TACATGCACTATGTGTGCAAATCCAC-GAAATTCATCATGAGTTGATGAATAGCCG
*
94997 TACATGCACTATGTGTGCAAATCCACGAAATTCATCTTGAGTTGATGAATAGCCG
1 TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
* * * ** *
95052 TACACGCATTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAATCA
1 TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
* * * * * * *
95107 TATAAGCACTATCTTTACAAAACCACAAAATTCATCATGAGT
1 TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGT
95149 GGATAAATTA
Statistics
Matches: 277, Mismatches: 38, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
54 4 0.01
55 269 0.97
56 4 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.29
Consensus pattern (55 bp):
TACATGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAGCCG
Found at i:101220 original size:20 final size:19
Alignment explanation
Indices: 101193--101245 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
101183 TGATTCAATT
101193 AGTATCGATACCGAAAGGGGA
1 AGTATCGATACC-AAA-GGGA
101214 A-TATCGATACCAAAGGGA
1 AGTATCGATACCAAAGGGA
101232 AGGTATCGATACCA
1 A-GTATCGATACCA
101246 TTTCAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.17
19 3 0.10
20 21 0.70
21 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:101320 original size:22 final size:22
Alignment explanation
Indices: 101269--101327 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 22
101259 TGCAAAAATG
101269 GTATCGATACCATAGCT-TAGTA
1 GTATCGATACCATAG-TATAGTA
*
101291 -T-T-GGTACCATAGTATAGTA
1 GTATCGATACCATAGTATAGTA
*
101310 GTATCGATACCATGGTAT
1 GTATCGATACCATAGTAT
101328 GGGTATCACT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
18 1 0.03
19 14 0.47
20 2 0.07
21 2 0.07
22 11 0.37
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (22 bp):
GTATCGATACCATAGTATAGTA
Found at i:101752 original size:55 final size:55
Alignment explanation
Indices: 101668--101921 Score: 330
Period size: 55 Copynumber: 4.6 Consensus size: 55
101658 AAAGTACTAC
*
101668 AGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAGTCGTAA
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGTCGTAA
* * * * **
101723 AGGCACAATGTGTGCAAATCCACAAAATTCATCATAAGTTGATGAATAGCCGTTC
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGTCGTAA
* * * * *
101778 AGGAACTATGTGTACAAATCCACAAAATTCATCATGATTTGATGAATAGTCGTAC
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGTCGTAA
* * * **
101833 AGACACTATGCGTACAAATCCATGGAATTCATCATGAGTTGATGAATAGTCGTACA
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGTCGTA-A
*
101889 A-GCACTATGTGTGCAAATCCACAGAATTTATCA
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCA
101922 CACCCCAACT
Statistics
Matches: 170, Mismatches: 28, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
55 169 0.99
56 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (55 bp):
AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGTCGTAA
Found at i:102717 original size:13 final size:13
Alignment explanation
Indices: 102699--102724 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
102689 AGTAAACTCG
102699 TTGACTTTGACCA
1 TTGACTTTGACCA
102712 TTGACTTTGACCA
1 TTGACTTTGACCA
102725 AAAAGTTAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:112277 original size:25 final size:24
Alignment explanation
Indices: 112232--112279 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 24
112222 GGATTTACAG
112232 AAATACCCTAAATTGTAAATGACCA
1 AAATACCCTAAA-TGTAAATGACCA
112257 AAATACCCCTAAA-GTATAATGAC
1 AAATA-CCCTAAATGTA-AATGAC
112280 TTAAAGTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 3 0.14
25 11 0.52
26 7 0.33
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (24 bp):
AAATACCCTAAATGTAAATGACCA
Found at i:133683 original size:14 final size:15
Alignment explanation
Indices: 133664--133692 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
133654 GGGTAAAACT
133664 GGGTCAAA-CGGGTC
1 GGGTCAAACCGGGTC
133678 GGGTCAAACCGGGTC
1 GGGTCAAACCGGGTC
133693 AACTACCCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.24, G:0.41, T:0.14
Consensus pattern (15 bp):
GGGTCAAACCGGGTC
Found at i:138385 original size:41 final size:41
Alignment explanation
Indices: 138106--138412 Score: 289
Period size: 41 Copynumber: 7.5 Consensus size: 41
138096 ATCGAGTTCG
* * ** * **
138106 ATCATGGCAACATGCACTAATTTACAATTTGA-TTCAATTCA
1 ATCATGGCAACATGCAATAATTCACAATTCAACTT-GATTTT
* * * * * **
138147 ATCATGGCATCATGGAATAATTCATAA-TAAACTTAATTCA
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
* * * ** **
138187 ATAATGG-AAGCATGCAATAATTCCCAATTTGAA-TCAATTCA
1 ATCATGGCAA-CATGCAATAATTCACAA-TTCAACTTGATTTT
**
138228 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTT
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
**
138269 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTT
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
* * *
138310 ATCATGGCATCATGCAATAATTCGCAATTGAACTTGATTTT
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
138351 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
* *
138392 ATCATGGCAGCATGTAATAAT
1 ATCATGGCAACATGCAATAAT
138413 CAATAATTCA
Statistics
Matches: 228, Mismatches: 32, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.00
40 32 0.14
41 191 0.84
42 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (41 bp):
ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
Found at i:138423 original size:41 final size:41
Alignment explanation
Indices: 138147--138412 Score: 311
Period size: 41 Copynumber: 6.5 Consensus size: 41
138137 ATTCAATTCA
* * * * * **
138147 ATCATGGCATCATGGAATAATTCATAA-TAAACTTAATTCA
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTGATTTT
* * * * ** **
138187 ATAATGGAAGCATGCAATAATTCCCAATTTGAA-TCAATTCA
1 ATCATGGCAGCATGCAATAATTCACAA-TTCAACTTGATTTT
*
138228 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTT
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTGATTTT
*
138269 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTT
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTGATTTT
* * *
138310 ATCATGGCATCATGCAATAATTCGCAATTGAACTTGATTTT
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTGATTTT
*
138351 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTT
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTGATTTT
*
138392 ATCATGGCAGCATGTAATAAT
1 ATCATGGCAGCATGCAATAAT
138413 CAATAATTCA
Statistics
Matches: 197, Mismatches: 26, Indels: 5
0.86 0.11 0.02
Matches are distributed among these distances:
40 25 0.13
41 169 0.86
42 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (41 bp):
ATCATGGCAGCATGCAATAATTCACAATTCAACTTGATTTT
Found at i:138423 original size:123 final size:123
Alignment explanation
Indices: 138106--138412 Score: 341
Period size: 123 Copynumber: 2.5 Consensus size: 123
138096 ATCGAGTTCG
* * ** * ** * *
138106 ATCATGGCAACATGCACTAATTTACAATTTGA-TTCAATTCAATCATGGCATCATGGAATAATTC
1 ATCATGGCAACATGCAATAATTCACAATTCAACTT-GATTTTATCATGGCAGCATGCAATAATTC
* * * ** * * *
138170 ATAA-TAAACTTAATTCAATAATGGAAGCATGCAATAATTCCCAATTTGAATCAATTCA
65 ACAATTCAACTTGATTTTATCATGGCATCATGCAATAATTCCCAATTTGAATCAATTCA
** *
138228 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGTATGCAATAATTCA
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGCAATAATTCA
* ** **
138293 CAATTCAACTTGATTTTATCATGGCATCATGCAATAATTCGCAA-TTGAACTTGATTTT
66 CAATTCAACTTGATTTTATCATGGCATCATGCAATAATTCCCAATTTGAA-TCAATTCA
*
138351 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGTAATAAT
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGCAATAAT
138413 CAATAATTCA
Statistics
Matches: 153, Mismatches: 29, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
122 57 0.37
123 96 0.63
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (123 bp):
ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGCAATAATTCA
CAATTCAACTTGATTTTATCATGGCATCATGCAATAATTCCCAATTTGAATCAATTCA
Found at i:138443 original size:82 final size:82
Alignment explanation
Indices: 138228--138459 Score: 281
Period size: 82 Copynumber: 2.8 Consensus size: 82
138218 AATCAATTCA
* * * **
138228 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGTATGCAATAATTCA
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTAATTTTATCATAGCAACATGCAATAATTCA
138293 CAATTCAACTTGATTTT
66 CAATTCAACTTGATTTT
* * * * *
138310 ATCATGGCATCATGCAATAATTCGCAATTGAACTTGATTTTATCATGGCAACATGCAATAATTCA
1 ATCATGGCAGCATGCAATAATTCACAATTCAACTTAATTTTATCATAGCAACATGCAATAATTCA
138375 CAATTCAACTTGATTTT
66 CAATTCAACTTGATTTT
* * * * *
138392 ATCATGGCAGCATGTAATAA-TCAATAATTCAA-TTCAATTTGT-TCATAGCAACATTCATTTAT
1 ATCATGGCAGCATGCAATAATTC-ACAATTCAACTT-AATTT-TATCATAGCAACATGCAATAAT
138454 TCACAA
63 TCACAA
138460 ACCAATTCAA
Statistics
Matches: 131, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
81 4 0.03
82 126 0.96
83 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.36
Consensus pattern (82 bp):
ATCATGGCAGCATGCAATAATTCACAATTCAACTTAATTTTATCATAGCAACATGCAATAATTCA
CAATTCAACTTGATTTT
Found at i:138477 original size:123 final size:123
Alignment explanation
Indices: 138228--138486 Score: 283
Period size: 123 Copynumber: 2.1 Consensus size: 123
138218 AATCAATTCA
** *
138228 ATCATGGCAGTATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGTATGCAATAATTCA
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGCAATAATTCA
* * * * *** * * *
138293 CAATTCAACTTGATTTTATCATGGCATCATGCAATAATTCGCAATTGAACTTGATTTT
66 CAATTCAACTTAATTTTATCATAGCAACATGCAATAATTCACAAACCAACTTAAGTAT
*
138351 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGTAATAA-TCA
1 ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGCAATAATTC-
* * * *
138415 ATAATTCAA-TTCAATTTGT-TCATAGCAACATTCATTTATTCACAAACCAA-TTCAAGTAT
65 ACAATTCAACTT-AATTT-TATCATAGCAACATGCAATAATTCACAAACCAACTT-AAGTAT
*
138474 ATCATGGTAACAT
1 ATCATGGCAACAT
138487 CTTTTAATTC
Statistics
Matches: 113, Mismatches: 19, Indels: 8
0.81 0.14 0.06
Matches are distributed among these distances:
122 6 0.05
123 106 0.94
124 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (123 bp):
ATCATGGCAACATGCAATAATTCACAATTCAACTTGATTTTATCATGGCAGCATGCAATAATTCA
CAATTCAACTTAATTTTATCATAGCAACATGCAATAATTCACAAACCAACTTAAGTAT
Found at i:143728 original size:2 final size:2
Alignment explanation
Indices: 143721--143761 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
143711 TTTCGTAAAT
143721 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
143762 TGTAGATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:153078 original size:29 final size:26
Alignment explanation
Indices: 153035--153094 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 26
153025 TTGACAAATC
*
153035 TATTTACATGTTTATACGTTATTATATGA
1 TATTTACATGTTTAT--GAT-TTATATGA
153064 TATTTACA-GTATTATGATTTATATGA
1 TATTTACATGT-TTATGATTTATATGA
153090 TATTT
1 TATTT
153095 TATATTGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 13 0.45
27 2 0.07
28 2 0.07
29 12 0.41
ACGTcount: A:0.32, C:0.05, G:0.10, T:0.53
Consensus pattern (26 bp):
TATTTACATGTTTATGATTTATATGA
Found at i:161113 original size:14 final size:14
Alignment explanation
Indices: 161096--161134 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
161086 GACATCATTT
161096 CTTACATCATCATC
1 CTTACATCATCATC
*
161110 CTTACATCATAATC
1 CTTACATCATCATC
*
161124 CCTACATCATC
1 CTTACATCATC
161135 CATGAACTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (14 bp):
CTTACATCATCATC
Found at i:169114 original size:35 final size:37
Alignment explanation
Indices: 169047--169127 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 37
169037 ATATCACATA
** *
169047 ATATAATATAAGCATATAATATATATGTCCACATG-C
1 ATATAATATAAGCATATAATATATATACCCACACGCC
* *
169083 ATATAATATAA-TATATAATATATGTACCCACACGCC
1 ATATAATATAAGCATATAATATATATACCCACACGCC
169119 A-ATAATATA
1 ATATAATATA
169128 TACATTTAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
35 26 0.67
36 13 0.33
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (37 bp):
ATATAATATAAGCATATAATATATATACCCACACGCC
Found at i:169465 original size:36 final size:38
Alignment explanation
Indices: 169396--169470 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 38
169386 ATGAGAGGTA
*
169396 ATCTACTCCACTACAACTTCAAGGTAGGTCAGAT-TTG
1 ATCTACTCCACTACAACTTCAAGGTAGGCCAGATCTTG
* * * *
169433 ATCTACTCCACTGC-TCTTCAGGGTATGCCAGATCTTG
1 ATCTACTCCACTACAACTTCAAGGTAGGCCAGATCTTG
169470 A
1 A
169471 AACTTTGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
36 15 0.47
37 17 0.53
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (38 bp):
ATCTACTCCACTACAACTTCAAGGTAGGCCAGATCTTG
Found at i:169680 original size:132 final size:132
Alignment explanation
Indices: 169529--169768 Score: 322
Period size: 132 Copynumber: 1.8 Consensus size: 132
169519 TTTACTACAC
* * * * *
169529 TACTCTTCATGGTAGGTCAAATCTT-AAAAAAAGTATTTGCTCCATTTCTCTTCAAGGTAGGTCA
1 TACTCTTCAGGGTAAGTCAAAT-TTGAAAAAAAGGATTTGCTCCACTGCTCTTCAAGGTAGGTCA
* * * *
169593 GATCTAT-GAAACTCGGATTCACTCCGCTGCTCGTCAGGGAGAATTAGATCGAGGTTTATTTGCT
65 GATCT-TGGAAACACAGATTCACTCCACTGCTCATCAGGGAGAATTAGATCGAGGTTTATTTGCT
169657 CCAG
129 CCAG
** *
169661 TACTCTTCAGGGTAAGTCAAATTTGAAAAATGGGATTTGCTCCACTGCTCTTCAGGGTAGGTCAG
1 TACTCTTCAGGGTAAGTCAAATTTGAAAAAAAGGATTTGCTCCACTGCTCTTCAAGGTAGGTCAG
* *
169726 ATCTTGGAAACACATATTCACTCCATTGCTCATCAGGGAGAAT
66 ATCTTGGAAACACAGATTCACTCCACTGCTCATCAGGGAGAAT
169769 ACATGTTGAT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
131 3 0.03
132 89 0.97
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (132 bp):
TACTCTTCAGGGTAAGTCAAATTTGAAAAAAAGGATTTGCTCCACTGCTCTTCAAGGTAGGTCAG
ATCTTGGAAACACAGATTCACTCCACTGCTCATCAGGGAGAATTAGATCGAGGTTTATTTGCTCC
AG
Found at i:170278 original size:74 final size:74
Alignment explanation
Indices: 170092--170379 Score: 371
Period size: 74 Copynumber: 3.9 Consensus size: 74
170082 TAATGTTTTC
* * * * * *
170092 ATGAATACGGTAATGTGATTCATGCATATTCTTACTCTTTGAGGAGTGTCCACATGAAAGGTGAG
1 ATGAATGCAGTAATGCGATTCATGCATATTCTTACTCCTTGAGGAGTGTCCTCATGAGAGGTGA-
*
170157 AAAGGTCTGA
65 AAAAGTCTGA
* * *
170167 ATGAATGCAGTAAAGTGATTCATGCATATTCTTACTCCTTAAGGAGTGTCCTCATGAGAGGTGAA
1 ATGAATGCAGTAATGCGATTCATGCATATTCTTACTCCTTGAGGAGTGTCCTCATGAGAGGTGAA
*
170232 AAAGTCTAA
66 AAAGTCTGA
* * * * * *
170241 ATGAATGTAGTAATGCGATTCTTGCATATCCTTACTCCTTGGGGTGTGTCCTTATGAGAGGTGAA
1 ATGAATGCAGTAATGCGATTCATGCATATTCTTACTCCTTGAGGAGTGTCCTCATGAGAGGTGAA
170306 AAAGTCTGA
66 AAAGTCTGA
* * *
170315 ATGAATACGGTAATACGATTCATGCATATT-TGTACTCCTTGAGGAGTGTCCTCATGAGAGGTGA
1 ATGAATGCAGTAATGCGATTCATGCATATTCT-TACTCCTTGAGGAGTGTCCTCATGAGAGGTGA
170379 A
65 A
170380 TGCAGTAATG
Statistics
Matches: 184, Mismatches: 28, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
73 1 0.01
74 126 0.68
75 57 0.31
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (74 bp):
ATGAATGCAGTAATGCGATTCATGCATATTCTTACTCCTTGAGGAGTGTCCTCATGAGAGGTGAA
AAAGTCTGA
Found at i:170794 original size:34 final size:32
Alignment explanation
Indices: 170734--170803 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
170724 CCTTACAAAC
*
170734 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
170766 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
170800 TCCC
1 TCCC
170804 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.29, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:171112 original size:21 final size:21
Alignment explanation
Indices: 171086--171127 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
171076 CCAGAATCGG
*
171086 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
171107 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
171128 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:171318 original size:36 final size:35
Alignment explanation
Indices: 171240--171361 Score: 199
Period size: 35 Copynumber: 3.5 Consensus size: 35
171230 AAACCATGCA
*
171240 GGGGGAATCTGTACCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
* * *
171275 GGAGGAATCTGTTCCCAGGGAATCGATACCCCCCCG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCCTG
171311 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
171346 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
171362 CATGGGGGGG
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
35 47 0.59
36 32 0.41
ACGTcount: A:0.19, C:0.30, G:0.33, T:0.19
Consensus pattern (35 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCCTG
Found at i:171352 original size:20 final size:20
Alignment explanation
Indices: 171327--171387 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
171317 ATCTGTTCCC
171327 GGGGAATCGATACCCCCTGG
1 GGGGAATCGATACCCCCTGG
* *
171347 GGGGAATCTG-TTCCCCATGGG
1 GGGGAATC-GATACCCCCT-GG
*
171368 GGGGAATCTATACCCCCTGG
1 GGGGAATCGATACCCCCTGG
171388 ACAATCTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.18, C:0.28, G:0.34, T:0.20
Consensus pattern (20 bp):
GGGGAATCGATACCCCCTGG
Found at i:173343 original size:3 final size:3
Alignment explanation
Indices: 173335--173372 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
173325 TACGTCTTTA
* *
173335 TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
173373 CCTTTCTTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.00, C:0.29, G:0.03, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:174360 original size:30 final size:30
Alignment explanation
Indices: 174324--174382 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
174314 ATTCACTAAT
174324 TTGTTCTTTCTTTTGAGGATAAAGAGTAAA
1 TTGTTCTTTCTTTTGAGGATAAAGAGTAAA
174354 TTGTTCTTTCTTTTGAGGATAAAGAGTAA
1 TTGTTCTTTCTTTTGAGGATAAAGAGTAA
174383 CCTTACAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.29, C:0.07, G:0.20, T:0.44
Consensus pattern (30 bp):
TTGTTCTTTCTTTTGAGGATAAAGAGTAAA
Found at i:174771 original size:21 final size:21
Alignment explanation
Indices: 174745--174786 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
174735 CCAGAATCGG
*
174745 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
174766 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
174787 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:174920 original size:15 final size:16
Alignment explanation
Indices: 174899--174948 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 16
174889 AAACCATGCA
174899 GGGGGAATCTGTACCC
1 GGGGGAATCTGTACCC
174915 -GGGGAAT-TGATACCCC
1 GGGGGAATCTG-TA-CCC
174931 TGGGGGGAATCTGTACCC
1 --GGGGGAATCTGTACCC
174949 CCTGGACAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.07
15 9 0.32
16 3 0.11
18 3 0.11
19 9 0.32
20 2 0.07
ACGTcount: A:0.20, C:0.24, G:0.36, T:0.20
Consensus pattern (16 bp):
GGGGGAATCTGTACCC
Found at i:180286 original size:61 final size:61
Alignment explanation
Indices: 180211--180333 Score: 210
Period size: 61 Copynumber: 2.0 Consensus size: 61
180201 ACACATGATA
* * *
180211 TCTATTTCTTAGGCATTTATTCGAATGGTAAAATTATTCAACCAAAGATGCATAAAATCAT
1 TCTATTTCTTAGGCAATTATTCGAATAGTAAAATTAATCAACCAAAGATGCATAAAATCAT
*
180272 TCTATTTCTTAGGCAATTATTCGAATAGTAGAATTAATCAACCAAAGATGCATAAAATCAT
1 TCTATTTCTTAGGCAATTATTCGAATAGTAAAATTAATCAACCAAAGATGCATAAAATCAT
180333 T
1 T
180334 TCCTTGAGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (61 bp):
TCTATTTCTTAGGCAATTATTCGAATAGTAAAATTAATCAACCAAAGATGCATAAAATCAT
Found at i:185235 original size:2 final size:2
Alignment explanation
Indices: 185228--185292 Score: 112
Period size: 2 Copynumber: 32.5 Consensus size: 2
185218 TACTTTTGAG
*
185228 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
185270 AT AT AT AT TT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
185293 AGTGGTATAG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:188051 original size:2 final size:2
Alignment explanation
Indices: 188039--188118 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
188029 GTTGCATGTG
*
188039 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
188081 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
188119 GATTTGTTAT
Statistics
Matches: 76, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:203366 original size:31 final size:30
Alignment explanation
Indices: 203313--203389 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
203303 TTATTTACAT
*
203313 AACTTTTTAAAA-TTACACTTTAATCC-CTA
1 AACTTTTCAAAATTTACACTTTAA-CCACTA
* *
203342 AACTTTTCCAAAATTTATACTTTAACCACTT
1 AACTTTT-CAAAATTTACACTTTAACCACTA
203373 AAC-TTTCAAAATTTACA
1 AACTTTTCAAAATTTACA
203390 TTTTGGTCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 17 0.41
30 9 0.22
31 15 0.37
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (30 bp):
AACTTTTCAAAATTTACACTTTAACCACTA
Found at i:205435 original size:27 final size:28
Alignment explanation
Indices: 205380--205444 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
205370 TCTAGGGCTT
*
205380 AGGGGTATTTTAGGTTATTTCACACTTC
1 AGGGGTATTTTAGGTCATTTCACACTTC
* *
205408 AGGGGTATTTT-GGTCATTTTACAGTTC
1 AGGGGTATTTTAGGTCATTTCACACTTC
*
205435 AAGGGTATTT
1 AGGGGTATTT
205445 CAGTCCTTCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
27 22 0.67
28 11 0.33
ACGTcount: A:0.22, C:0.11, G:0.25, T:0.43
Consensus pattern (28 bp):
AGGGGTATTTTAGGTCATTTCACACTTC
Found at i:206331 original size:15 final size:13
Alignment explanation
Indices: 206310--206350 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 13
206300 CTTTTTGGTT
206310 AATGTCAAAGTCA
1 AATGTCAAAGTCA
206323 ACGATGTCAAAGTCA
1 A--ATGTCAAAGTCA
206338 AA-GTCAAAGTCA
1 AATGTCAAAGTCA
206350 A
1 A
206351 TGGTCGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 11 0.42
13 2 0.08
15 13 0.50
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (13 bp):
AATGTCAAAGTCA
Found at i:207314 original size:35 final size:34
Alignment explanation
Indices: 207274--207339 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
207264 GGTGTGACAT
207274 GAGTTA-AGAAATTTATGAGATATTGAAGAGCTTTA
1 GAGTTAGAG-AATTTATGAGA-ATTGAAGAGCTTTA
* *
207309 GAGTTAGAGAGTTTATGAGAATTTAAGAGCT
1 GAGTTAGAGAATTTATGAGAATTGAAGAGCT
207340 ACATAGGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 10 0.36
35 16 0.57
36 2 0.07
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (34 bp):
GAGTTAGAGAATTTATGAGAATTGAAGAGCTTTA
Found at i:207358 original size:37 final size:35
Alignment explanation
Indices: 207285--207369 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 35
207275 AGTTAAGAAA
*
207285 TTTATGAGATATTGAAGAGCTTTAGAGTTAGAGAG
1 TTTATGAGATATTGAAGAGCTATAGAGTTAGAGAG
* *
207320 TTTATGAGA-ATTTAAGAGCTACATAGGAGTTAGTGAG
1 TTTATGAGATATTGAAGAGCT--ATA-GAGTTAGAGAG
* *
207357 TTAATGAGTTATT
1 TTTATGAGATATT
207370 TATTCTCCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
34 10 0.24
35 9 0.22
36 2 0.05
37 17 0.41
38 3 0.07
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (35 bp):
TTTATGAGATATTGAAGAGCTATAGAGTTAGAGAG
Found at i:208282 original size:2 final size:2
Alignment explanation
Indices: 208275--208329 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
208265 TTCTTATCAC
208275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
208317 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
208330 CTACTTAGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:214005 original size:40 final size:40
Alignment explanation
Indices: 213950--214031 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
213940 TGCAGGTTTA
213950 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
213990 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
214030 TA
1 TA
214032 GCACTACGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:214486 original size:41 final size:41
Alignment explanation
Indices: 214429--214549 Score: 242
Period size: 41 Copynumber: 3.0 Consensus size: 41
214419 TTTTCATGCT
214429 TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAACCG
1 TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAACCG
214470 TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAACCG
1 TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAACCG
214511 TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAAC
1 TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAAC
214550 GACATCAAGC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.55, C:0.09, G:0.21, T:0.15
Consensus pattern (41 bp):
TAGGTAAAAAGCAAAGAATAAGAATAAAGAGTTCAGAACCG
Found at i:215933 original size:19 final size:19
Alignment explanation
Indices: 215909--215947 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
215899 GAAGAGGAGG
215909 TTAGGTTTTCATGTTTTAA
1 TTAGGTTTTCATGTTTTAA
215928 TTAGGTTTTCATGTTTTAA
1 TTAGGTTTTCATGTTTTAA
215947 T
1 T
215948 CTTAGATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.15, T:0.59
Consensus pattern (19 bp):
TTAGGTTTTCATGTTTTAA
Found at i:216286 original size:22 final size:22
Alignment explanation
Indices: 216260--216316 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
216250 TTCTAAAAGC
216260 TTTAGAA-TGTTGTTTGAACCAA
1 TTTAGAAGT-TTGTTTGAACCAA
216282 TTTAGAAGTTTGTTTGAACCAA
1 TTTAGAAGTTTGTTTGAACCAA
*
216304 TTTTGAAGTTTGT
1 TTTAGAAGTTTGT
216317 AACAGCTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
22 32 0.97
23 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.19, T:0.46
Consensus pattern (22 bp):
TTTAGAAGTTTGTTTGAACCAA
Found at i:216371 original size:19 final size:20
Alignment explanation
Indices: 216345--216413 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
216335 TCACTTAATT
216345 TTGAAAAAATGGGTCTAAAG
1 TTGAAAAAATGGGTCTAAAG
216365 TTGAAAAAATGGGTCTAAAG
1 TTGAAAAAATGGGTCTAAAG
216385 TTGAAAAAATGGGTCTAAAG
1 TTGAAAAAATGGGTCTAAAG
216405 -TGAAAAAAT
1 TTGAAAAAAT
216414 ATGTACAATG
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
19 9 0.18
20 40 0.82
ACGTcount: A:0.48, C:0.04, G:0.23, T:0.25
Consensus pattern (20 bp):
TTGAAAAAATGGGTCTAAAG
Found at i:217261 original size:25 final size:22
Alignment explanation
Indices: 217207--217263 Score: 60
Period size: 25 Copynumber: 2.4 Consensus size: 22
217197 GATTGATGAT
*
217207 ATATTTGATTATTTTAAATAAA
1 ATATTTTATTATTTTAAATAAA
217229 ATAAATTTTATCTATTTTCAAATAAA
1 AT--ATTTTAT-TATTTT-AAATAAA
217255 GATATTTTA
1 -ATATTTTA
217264 AATATTTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 2 0.07
24 6 0.21
25 12 0.41
26 7 0.24
27 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
ATATTTTATTATTTTAAATAAA
Found at i:217269 original size:25 final size:24
Alignment explanation
Indices: 217216--217270 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
217206 TATATTTGAT
**
217216 TATTTTAAATAAAATAAATTTTATC
1 TATTTTAAATAAAAT-AATTTTAAA
217241 TATTTTCAAATAAAGAT-ATTTTAAA
1 TATTTT-AAATAAA-ATAATTTTAAA
217266 TATTT
1 TATTT
217271 AGTGTGATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 17 0.65
26 7 0.27
27 2 0.08
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTTTAAATAAAATAATTTTAAA
Found at i:218005 original size:182 final size:182
Alignment explanation
Indices: 217537--218390 Score: 1214
Period size: 182 Copynumber: 4.7 Consensus size: 182
217527 TGTCGGTTTA
* * *
217537 TGTCGATACTTTATAAAAATGTATCGATCCACATCAATATAACAGGAAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * * * * *
217602 GTCACGAAAAGACAAAATCGGTAAAGCGCTACTAGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAGGACAAAACCGGTAAAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATA
* *
217667 AGTATCAACACTTTGTGAATTTAAAAGAGAAGCATTTTTAGCG-C-ATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
** * **
217717 TGTCGATACTTTATAAAAATGTATCGATCCATGATGATATAACATGAAAAAAATATGAC-AAACC
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACA-GGTAAAAATATGACAAAACC
* * * *
217781 GATCTCTAAAGGACAAAACCGGTAAAGCGCTACCAAATATATTGAAAGTCTCGATACTTTAATAT
65 GGTCTCTAAAGGACAAAACCGGTAAAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATAT
**
217846 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGTTCCTATAAAG
130 AAGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
* * * *
217899 TGTGGATACTTTATAACAATGTATCAATCCACAACGATATAACAGGTAAAAATATGACAAAACCA
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * *
217964 GTCTCTAAAGGATAAAACCGGTATAGAGCGATCATATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAGGACAAAACCGGTAAAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATA
* *
218029 AGTATCGACACTTTTTGAATTTAAAAGAGAAGCAATTTTAGCGCTTATAAAG
131 AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
* * *
218081 TGTCGATACTTTGTAACAATGTATCGATCCACAATGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
*
218146 GTCTCTAAAGGACAAAACCGGTATAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCTAAAGGACAAAACCGGTAAAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATA
*
218211 AGTATAGACACTTAT-TGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
131 AGTATCGACACTT-TGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
* *
218263 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACATGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * ** *
218328 GTCT-TGAAATGAAAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATATTTTAATA
66 GTCTCT-AAAGGACAAAACCGGTAAAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATA
218391 AGTACGCATA
Statistics
Matches: 606, Mismatches: 62, Indels: 10
0.89 0.09 0.01
Matches are distributed among these distances:
180 141 0.23
181 27 0.04
182 437 0.72
183 1 0.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
TGTCGATACTTTATAAAAATGTATCGATCCACAACGATATAACAGGTAAAAATATGACAAAACCG
GTCTCTAAAGGACAAAACCGGTAAAGAGCGACCAAATATATTGAAAGTGTCGATACTTTAATATA
AGTATCGACACTTTGTGAATTTAAAAGAGAAGCAATTTTAGCGCCTATAAAG
Found at i:220770 original size:21 final size:21
Alignment explanation
Indices: 220746--220786 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
220736 AAGACAATCA
220746 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
220767 AGAGTCGAAGAGACACTTGA
1 AGAGTCGAAGAGAAACTTGA
220787 TAAGCATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.12, G:0.32, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:220879 original size:25 final size:25
Alignment explanation
Indices: 220826--220881 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
220816 TAGATGGAGT
* *
220826 GGTGAAAGGAGTTGAGGGGTGAAGT
1 GGTGAAAGAAGTTGAGGGGTGAAGG
*
220851 GGTGAAAGAAGTTGAGGTGTTG-AGG
1 GGTGAAAGAAGTTGAGG-GGTGAAGG
220876 GGTGAA
1 GGTGAA
220882 CTTAAGATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 24 0.89
26 3 0.11
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (25 bp):
GGTGAAAGAAGTTGAGGGGTGAAGG
Found at i:221088 original size:18 final size:18
Alignment explanation
Indices: 221065--221121 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
221055 GAAAAAATAT
221065 GAAGAAGAAAAGTGGGAG
1 GAAGAAGAAAAGTGGGAG
*
221083 GAAGAAGAAAAGAGGGAG
1 GAAGAAGAAAAGTGGGAG
*
221101 AAAGAAGAAAAGAT-GGAG
1 GAAGAAGAAAAG-TGGGAG
221119 GAA
1 GAA
221122 ATGAGGAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.56, C:0.00, G:0.40, T:0.04
Consensus pattern (18 bp):
GAAGAAGAAAAGTGGGAG
Found at i:222699 original size:19 final size:19
Alignment explanation
Indices: 222675--222742 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
222665 AATGCAGGGT
222675 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
222694 TAATTTTGTATACA-ATTTA
1 TAATTTTGTATA-AGATTTA
*
222713 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
222732 TAATTTTGTAT
1 TAATTTTGTAT
222743 GTGAATGTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
19 45 0.98
20 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:223383 original size:199 final size:199
Alignment explanation
Indices: 223103--224831 Score: 2101
Period size: 199 Copynumber: 8.8 Consensus size: 199
223093 CATATGTGCA
* *
223103 GATACATTTATAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* ** * * *
223168 TTTTGTAATCTAACCGGTATAAATATACCGAATTTATGTGAGAATAGGTCTACATAATGTATAGA
66 ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
* * * * ** * *
223233 CACTTTCTCATTTTGTGTCGATACTTTTTGTCCAAAATAAATGCAAAAAATGATGAACGCAT-AT
131 CACTTT-TGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAA
223297 GTGTC
195 GTGTC
* *
223302 GATACATTTATAAAAAGTATCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* ** * * * *
223367 TTTTGTAGTATAACCGGTATAAATATACCGGA-TTTATGTGAGAATAGGTTTACATAATGTATCT
66 ATTTACAATGTAACCGGTATAAATATACC-GATTTTATGTGAGAATAGGTCTACATAATGTATCG
* * * * * * *
223431 ACAATTTCTCATTTTGTGTCGATACTTTTTGTCCAGAATAAATGCCCAAAATGATGAACCCAT-T
130 ACACTTT-TGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAA
*
223495 TGTGTC
194 AGTGTC
* * * *
223501 GATACATTTATAAAAAAGTATCGATCCCAGAAACATCAAAACCCATAAATATAATGTAATAGGTA
1 GATACATTTAT-AAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
** * * * *
223566 AATTTACAATGTAATAGGTATAACTATACCGGTTTTATGAGAAAATAGGTCTACATAATGTATCG
65 AATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCG
* * * * * * *
223631 ACACGTATGGAATTTGTGTCGATACTGTTTGTCCAGAACGAATGCCCAAAAGGGTGCACCCATAA
130 ACAC-TTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAA
223696 AGTGTC
194 AGTGTC
* * * ** *
223702 GATAAATTTAATAAAAAGTGTCGATCCCAAAAACATCAAAACCCCTTATTATAATGTAATAGGTA
1 GATACATTT-ATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* ** * * *
223767 ATTTTGTAATATAACTGGTA-AAATATACCGATTTTTTGTGAGAATAGG--T-C--------T--
65 AATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCG
* *
223818 AC-C---T-AA--TGTGTCGACACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACACATAAA
130 ACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAA
223876 GTGTC
195 GTGTC
* *
223881 GATATATTTATAAAAATTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * *
223946 ATTTACAATGTAAACGGTATAAATATACCGATTTTATGTGAGAATTGGTCTACATAATGTGTCGA
66 ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
* *
224011 CACTTTTGAATTTGTGTCGATACTTTTTTTCCAGAATGAATGCCCAATATGGTGAACGCATAAAG
131 CACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAG
224076 TGTC
196 TGTC
* * * *
224080 GATACATATATAAAAAGTATCGATCCAAAAAACATTGAAACCGATAATTATAATCTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
224145 ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
66 ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
* * *
224210 CAATTTTGAATTTGTGTCGATACTTTTTGTCCCGAATGATTGCCCAAAATGGTGAACGCATAAAG
131 CACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAG
224275 TGTC
196 TGTC
* * * *
224279 AATACATTTATAAAAACTATCGATTCCAAAAACATCAAAACCGATAATTATAATGTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * * ** *
224344 ATTTACAATGTAACCGGTATAAATGTACCG-TTTTATGAGAAAATAGGTGAACATAATGTGTCGA
66 ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
* *
224408 CACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCTAAAATGGTGAACGCATAAA
131 CAC-TTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAA
224473 GTGTC
195 GTGTC
*
224478 GATACATTTATAAAAATTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
** * * * * * ** *
224543 ATTTACAATGTAACATGTATAAATGTACTGGTTTTATGAGAAAATAGGTGAACATAACGTATCGA
66 ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
* * * * *
224608 CACGTTTT-AGATTTGTGTCGTTACTTTTTGTCCAAAATGAATG-CCAAAAGGGTTGCATGCATA
131 CAC-TTTTGA-ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGG-TGAACGCATA
*
224671 AAGTGGC
193 AAGTGTC
* * * *
224678 GATATATTTTTAAAAAGAATTGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
1 GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * * * *
224743 ATTTACAATGTAACCGATATAAATATACC-AGTTTTATGAGAGAATATGTGTACATAATGTGTCG
66 ATTTACAATGTAACCGGTATAAATATACCGA-TTTTATGTGAGAATAGGTCTACATAATGTATCG
*
224807 ACACTTTTGGATTTTGTGTCGATAC
130 ACACTTTT-GAATTTGTGTCGATAC
224832 ATTTAAATAA
Statistics
Matches: 1342, Mismatches: 154, Indels: 67
0.86 0.10 0.04
Matches are distributed among these distances:
178 63 0.05
179 85 0.06
181 3 0.00
182 1 0.00
186 1 0.00
187 2 0.00
189 1 0.00
190 1 0.00
192 2 0.00
193 1 0.00
196 1 0.00
197 3 0.00
198 32 0.02
199 681 0.51
200 385 0.29
201 78 0.06
202 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
GATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
ATTTACAATGTAACCGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAATGTATCGA
CACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAG
TGTC
Found at i:223876 original size:179 final size:179
Alignment explanation
Indices: 223645--224017 Score: 534
Period size: 179 Copynumber: 2.1 Consensus size: 179
223635 GTATGGAATT
* * * *
223645 TGTGTCGATACTGTTTGTCCAGAACGAATGCCCAAAAGGGTGCACCCATAAAGTGTCGATAAATT
1 TGTGTCGACACTTTTTGTCCAGAACGAATGCCCAAAAGGGTGAACACATAAAGTGTCGATAAATT
* * * * **
223710 TAATAAAAAGTGTCGATCCCAAAAACATCAAAACCCCTTATTATAATGTAATAGGTAATTTTGTA
66 T-ATAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACA
* *
223775 ATAT-AACTGGTA-AAATATACCGATTTTTTGTGAGAATAGGTCTACCTAA
130 ATATAAAC-GGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAA
* * *
223824 TGTGTCGACACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACACATAAAGTGTCGATATATT
1 TGTGTCGACACTTTTTGTCCAGAACGAATGCCCAAAAGGGTGAACACATAAAGTGTCGATAAATT
* * *
223889 TATAAAAATTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAA
66 TATAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAA
* *
223954 TGTAAACGGTATAAATATACCGATTTTATGTGAGAATTGGTCTACATAA
131 TATAAACGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAA
224003 TGTGTCGACACTTTT
1 TGTGTCGACACTTTT
224018 GAATTTGTGT
Statistics
Matches: 172, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
178 61 0.35
179 111 0.65
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (179 bp):
TGTGTCGACACTTTTTGTCCAGAACGAATGCCCAAAAGGGTGAACACATAAAGTGTCGATAAATT
TATAAAAAGTATCGATCCCAAAAACATCAAAACCCATAATTATAATGTAATAGGTAAATTTACAA
TATAAACGGTATAAATATACCGATTTTATGTGAGAATAGGTCTACATAA
Found at i:236130 original size:34 final size:36
Alignment explanation
Indices: 236091--236165 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 36
236081 CCAACCTAAA
* * *
236091 ACCCAACCATAAACCAACTTAAA-A-CCCAAACAAG
1 ACCCAACCAGAAACCAACCTAAATAGCCAAAACAAG
* *
236125 CCCCAACCAGAACCCAACCTAAATAGCCAAAACAAG
1 ACCCAACCAGAAACCAACCTAAATAGCCAAAACAAG
236161 ACCCA
1 ACCCA
236166 GACCTGGAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
34 19 0.58
35 1 0.03
36 13 0.39
ACGTcount: A:0.49, C:0.39, G:0.05, T:0.07
Consensus pattern (36 bp):
ACCCAACCAGAAACCAACCTAAATAGCCAAAACAAG
Found at i:254611 original size:20 final size:20
Alignment explanation
Indices: 254562--254615 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 20
254552 TATCGAAAGG
*
254562 GGGTATCGATACCATAGTAT
1 GGGTATCGATACCATAGTAA
*
254582 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGTAA
254604 GGGTATCGATAC
1 GGGTATCGATAC
254616 TAGGAAACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.40
22 18 0.60
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.28
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:254657 original size:95 final size:95
Alignment explanation
Indices: 254487--254690 Score: 273
Period size: 95 Copynumber: 2.1 Consensus size: 95
254477 AAATTAGCTA
* * **
254487 AGTAGTATCGATACCATGGTAAGGGTATTGATACCAAGCATTATCAAAACTAAAATTGGTATCGA
1 AGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAACTAAAATTGGTATCGA
* *
254552 TATCGAAAGGGGGTATCGATACCATAGTAT
66 TACCGAAAGGGGGTATCGACACCATAGTAT
* * * * * *
254582 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAACATCGAACCTAAATTTGGTATCGA
1 AGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAACTAAAATTGGTATCGA
* *
254647 TACCGGAAGGGGGTATCGACACCATATTAT
66 TACCGAAAGGGGGTATCGACACCATAGTAT
*
254677 AGAAGTATCGATAC
1 AGTAGTATCGATAC
254691 TAGGGTAGCA
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (95 bp):
AGTAGTATCGATACCATGGTAAGGGTATCGATACCAAGAAACATCAAAACTAAAATTGGTATCGA
TACCGAAAGGGGGTATCGACACCATAGTAT
Found at i:254980 original size:30 final size:30
Alignment explanation
Indices: 254910--254980 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
254900 AATGGATTTA
* *
254910 TTTAGTGACCAAATTATAAATTTGGTAAAG
1 TTTAGTGACCAAAGTATAAATTTGGAAAAG
254940 TTT-GATGACCAAAGTATAAACTTT-GAAAAG
1 TTTAG-TGACCAAAGTATAAA-TTTGGAAAAG
*
254970 TTTAGGGACCA
1 TTTAGTGACCA
254981 TAATGTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 1 0.03
30 30 0.86
31 4 0.11
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.32
Consensus pattern (30 bp):
TTTAGTGACCAAAGTATAAATTTGGAAAAG
Found at i:256005 original size:31 final size:30
Alignment explanation
Indices: 255946--256006 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
255936 TAGAAACCTC
* *
255946 AGGGACCATTTTTTAATTTTTAAAAAGTTG
1 AGGGACCAATTTGTAATTTTTAAAAAGTTG
255976 AGGGACCAATTTGT-ATTTTTGGAAAAAGTTG
1 AGGGACCAATTTGTAATTTTT--AAAAAGTTG
256007 GGAATGGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 6 0.22
30 12 0.44
31 9 0.33
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (30 bp):
AGGGACCAATTTGTAATTTTTAAAAAGTTG
Found at i:256800 original size:18 final size:18
Alignment explanation
Indices: 256759--256800 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
256749 CCGGGTTAGT
* *
256759 AAAAAATAAATAAATAAA
1 AAAAAAGAAATAAAGAAA
*
256777 ACAAAAGAAATAAAGAAA
1 AAAAAAGAAATAAAGAAA
256795 AAAAAA
1 AAAAAA
256801 AAGTTTAAAG
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:0.83, C:0.02, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAAAAGAAATAAAGAAA
Found at i:258651 original size:17 final size:18
Alignment explanation
Indices: 258615--258670 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
258605 AGTATCCTCT
*
258615 TTCATTCAA-TAAAGCTAG
1 TTCACTCAATTAAA-CTAG
258633 TTCACT-AATTAAACTAG
1 TTCACTCAATTAAACTAG
* *
258650 TTCATTCATTTAAACTAG
1 TTCACTCAATTAAACTAG
258668 TTC
1 TTC
258671 TTTATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.33
18 22 0.67
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (18 bp):
TTCACTCAATTAAACTAG
Found at i:260368 original size:16 final size:16
Alignment explanation
Indices: 260347--260380 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
260337 ATGTTTATGT
260347 TAGTAAAATACTAACA
1 TAGTAAAATACTAACA
260363 TAGTAAAATACTAACA
1 TAGTAAAATACTAACA
260379 TA
1 TA
260381 TGTATCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.06, T:0.26
Consensus pattern (16 bp):
TAGTAAAATACTAACA
Found at i:261139 original size:45 final size:45
Alignment explanation
Indices: 261050--261361 Score: 446
Period size: 45 Copynumber: 6.9 Consensus size: 45
261040 GTAACCATAC
* * *
261050 AAATAAACTTATGAGCTTATGGAAT-AATGGTAAATATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
261094 AAATAAGCTTACGAGCTTATTGAATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
261139 AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTAGAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
261184 AAATAAGCTTACGAGCTCATGGCATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
261229 AAATAAGCTTACGAACTTATGGCATAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* * *
261274 AAATAAGCTTACAAGCTTATGAAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
261319 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTG
261362 ATAGGAAATT
Statistics
Matches: 241, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
44 22 0.09
45 201 0.83
46 18 0.07
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:263982 original size:2 final size:2
Alignment explanation
Indices: 263975--264000 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
263965 ATAAAAGCTA
263975 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
264001 GAAAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264032 original size:14 final size:13
Alignment explanation
Indices: 264004--264119 Score: 76
Period size: 14 Copynumber: 8.5 Consensus size: 13
263994 TATATATGAA
264004 AAAAAACAGAAAAG
1 AAAAAACA-AAAAG
264018 AATAAAACAAAAAG
1 AA-AAAACAAAAAG
* *
264032 AAAGAATAAAAAG
1 AAAAAACAAAAAG
264045 AAAAAGA-AGAAAAG
1 AAAAA-ACA-AAAAG
*
264059 -AAAAAGAAAAAG
1 AAAAAACAAAAAG
*
264071 AAAAAAAAGAAAAG
1 AAAAAACA-AAAAG
*
264085 AAAATAAGAAAACA-
1 AAAA-AACAAAA-AG
*
264099 AAAAGGAAAAAAAAG
1 AAAA--AACAAAAAG
264114 AAAAAA
1 AAAAAA
264120 GAAGAAGAAG
Statistics
Matches: 85, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
12 6 0.07
13 27 0.32
14 32 0.38
15 20 0.24
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (13 bp):
AAAAAACAAAAAG
Found at i:264048 original size:6 final size:6
Alignment explanation
Indices: 264021--264172 Score: 89
Period size: 6 Copynumber: 24.5 Consensus size: 6
264011 AGAAAAGAAT
* *
264021 AAAACA AAAAGA AAGAATA AAAAGA AAAAGAA GAAAAGA AAAAGA AAAAGAA
1 AAAAGA AAAAGA AA-AAGA AAAAGA AAAAG-A -AAAAGA AAAAGA AAAAG-A
* * *
264073 AAAAAA GAAAAGA AAATA-A GAAAACA AAAAG- GAAA-A AAAAGAA AAAAGA
1 AAAAGA -AAAAGA AAA-AGA -AAAAGA AAAAGA AAAAGA AAAAG-A AAAAGA
* * * * *
264122 AGAAGA AGAAGA AGAAGA AGAAGA ATTATAGA AAAAG- AAAAG- AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA A--AAAGA AAAAGA AAAAGA AAAAGA
264170 AAA
1 AAA
264173 GAAGGAAAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
5 16 0.13
6 67 0.56
7 28 0.23
8 9 0.08
ACGTcount: A:0.78, C:0.01, G:0.18, T:0.03
Consensus pattern (6 bp):
AAAAGA
Found at i:264084 original size:34 final size:35
Alignment explanation
Indices: 264003--264140 Score: 137
Period size: 34 Copynumber: 4.1 Consensus size: 35
263993 ATATATATGA
* *
264003 AAAAAAACAGAAAAGAATAA-AACAAAAAG--AAAG
1 AAAAAAA-AGAAAAGAAGAAGAAGAAAAAGAAAAAG
*
264036 AATAAAAAGAAAAAGAAGAA-AAGAAAAAGAAAAAG
1 AAAAAAAAG-AAAAGAAGAAGAAGAAAAAGAAAAAG
* *
264071 AAAAAAAAGAAAAGAA-AATAAGAAAACA-AAAAGG
1 AAAAAAAAGAAAAGAAGAAGAAGAAAA-AGAAAAAG
* *
264105 AAAAAAAAGAAAA-AAGAAGAAGAAGAAGAAGAAG
1 AAAAAAAAGAAAAGAAGAAGAAGAAAAAGAAAAAG
264139 AA
1 AA
264141 GAAGAATTAT
Statistics
Matches: 89, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
32 2 0.02
33 28 0.31
34 46 0.52
35 13 0.15
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (35 bp):
AAAAAAAAGAAAAGAAGAAGAAGAAAAAGAAAAAG
Found at i:264124 original size:3 final size:3
Alignment explanation
Indices: 264118--264176 Score: 61
Period size: 3 Copynumber: 20.0 Consensus size: 3
264108 AAAAAGAAAA
* *
264118 AAG AAG AAG AAG AAG AAG AAG AAG AAG AATT ATAG AAA AAG AA- AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G A-AG AAG AAG AAG AAG
264164 AA- AAG AA- AAG AAG
1 AAG AAG AAG AAG AAG
264177 GAAAAAATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
2 6 0.13
3 38 0.81
4 2 0.04
5 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:264130 original size:9 final size:9
Alignment explanation
Indices: 264042--264176 Score: 72
Period size: 9 Copynumber: 15.7 Consensus size: 9
264032 AAAGAATAAA
*
264042 AAGAAAAAG
1 AAGAAGAAG
264051 AAGAA-AAG
1 AAGAAGAAG
* *
264059 AAAAAGAAA
1 AAGAAGAAG
* *
264068 AAGAAAAAA
1 AAGAAGAAG
264077 AAGAA-AAG
1 AAGAAGAAG
*
264085 AA-AATAAG
1 AAGAAGAAG
* *
264093 AA-AACAAA
1 AAGAAGAAG
* *
264101 AAGGAAAAAA
1 AA-GAAGAAG
264111 AAGAA-AA-
1 AAGAAGAAG
264118 AAGAAGAAG
1 AAGAAGAAG
264127 AAGAAGAAG
1 AAGAAGAAG
264136 AAGAAGAAG
1 AAGAAGAAG
* *
264145 AATTATAGAAA
1 AA-GA-AGAAG
264156 AAGAA-AAG
1 AAGAAGAAG
264164 AA-AAGAA-
1 AAGAAGAAG
264171 AAGAAG
1 AAGAAG
264177 GAAAAAATGA
Statistics
Matches: 104, Mismatches: 12, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
7 11 0.11
8 35 0.34
9 43 0.41
10 9 0.09
11 6 0.06
ACGTcount: A:0.76, C:0.01, G:0.20, T:0.03
Consensus pattern (9 bp):
AAGAAGAAG
Found at i:268207 original size:45 final size:45
Alignment explanation
Indices: 268117--268383 Score: 351
Period size: 45 Copynumber: 5.9 Consensus size: 45
268107 GTAACCATAC
* * *
268117 AAATAAGCTTATGATCTTATGGAAT-AATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTGGTA
*
268161 AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTGGTA
* *
268206 AAATAAGCTTACGAGCTTATTGCATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTGGTA
268251 AAATAAGCTTACGAGCTTATGGCATAAAAT-GTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGCAT-AAATGGTAAGTATATTGGTA
** *
268296 AAATAAGCTTAC-ATGCTTATGTAATAAATGGTAAGTATGTTGGTA
1 AAATAAGCTTACGA-GCTTATGGCATAAATGGTAAGTATATTGGTA
*** * * *
268341 AAATATTATTATGAGCTTATGGGATTAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTATGGCA-TAAATGGTAAGTATATTG
268384 ATAAGAAATT
Statistics
Matches: 199, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
44 27 0.14
45 151 0.76
46 21 0.11
ACGTcount: A:0.39, C:0.07, G:0.19, T:0.34
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGCATAAATGGTAAGTATATTGGTA
Found at i:269581 original size:54 final size:54
Alignment explanation
Indices: 269171--269579 Score: 505
Period size: 54 Copynumber: 7.6 Consensus size: 54
269161 TTACCAAATA
* *
269171 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
* * *
269225 GACACTAAGTGTGCATTTCACAGAATTCATCTTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
*** * * * *
269279 ATTACTAAGTATGCATTTCATGGAATTCATCATTTGTGGATGAATAATCC-TTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAA-CCATTTC
* * *
269333 GGCACTAAGTGTGCATTTCACGAAATTCATCCTATCTAGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
* * * * *
269387 GGCACTAAGTGTGCATTTCACGAAATTAATCCTATATGGATGAATGATCATTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
* * * **
269441 GGTACTAAGTGTGCTTTTCACGGAATTCTTCCTATGTGGATGAATAACTGTTTC
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
* * * *
269495 GGCACTAAGTTTGCATTTTACGGAATTCATCATATGTGGATGAATAACCATTTT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
* * * *
269549 AGCACTAAGTGTGAAATCCACGGAATTCATC
1 GGCACTAAGTGTGCATTTCACGGAATTCATC
269580 ATGAGTTGAT
Statistics
Matches: 300, Mismatches: 53, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
53 2 0.01
54 296 0.99
55 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCATTTC
Found at i:269892 original size:81 final size:81
Alignment explanation
Indices: 269756--270089 Score: 499
Period size: 81 Copynumber: 4.1 Consensus size: 81
269746 TAGTCCAAAA
*
269756 TAAAAGAATAATGGCCTAACT-TGCAATTGGTAGAAAGGTTCCAATTATGCCAGTTAGATGAACG
1 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACG
269820 GTTAAACACCGTTGAG
66 GTTAAACACCGTTGAG
* **
269836 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCTAGTTAGATGAATA
1 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACG
*
269901 GATAAACACCGTTGAG
66 GTTAAACACCGTTGAG
** *
269917 TAAAAGAATAATGGCCTAACTGTATAATTGGTAGAAAGGTGCCAATTAGGCCAGTTAGATGAACG
1 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACG
*
269982 ATTAAACACCGTTGAG
66 GTTAAACACCGTTGAG
* * * * * *
269998 TAAAATAATAATGGCTTAATTGTGAAATTGGTAGAAAAGTGCCAATTATGCTAGTTAGATGAACG
1 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACG
* *
270063 GTTAAAAACTGTTGAG
66 GTTAAACACCGTTGAG
*
270079 TAAAATAATAA
1 TAAAAGAATAA
270090 GGGATTAGTT
Statistics
Matches: 229, Mismatches: 24, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
80 21 0.09
81 208 0.91
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (81 bp):
TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGGTGCCAATTATGCCAGTTAGATGAACG
GTTAAACACCGTTGAG
Found at i:270129 original size:81 final size:81
Alignment explanation
Indices: 269796--270141 Score: 255
Period size: 81 Copynumber: 4.3 Consensus size: 81
269786 TAGAAAGGTT
* * * * * * ** * *
269796 CCAATTATGCCAGTTAGATGAACGGTTAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGTGC
1 CCAAATATGCAAGTTAGATGAACGATTAAAAACCGTTGAGTAAAATAATAAGGGATTAATTGTGA
** * *
269861 AATTGGTAGAAAGGTG
66 AATTGACAAAAAAGTG
* * * * * * ** *
269877 CCAATTATGCTAGTTAGATGAATAGA-TAAACACCGTTGAGTAAAAGAATAATGGCCTAACTGT-
1 CCAAATATGCAAGTTAGATGAA-CGATTAAAAACCGTTGAGTAAAATAATAAGGGATTAATTGTG
** * *
269940 ATAATTGGTAGAAAGGTG
65 A-AATTGACAAAAAAGTG
* * * * * *
269958 CCAATTAGGCCAGTTAGATGAACGATTAAACACCGTTGAGTAAAATAATAATGGCTTAATTGTGA
1 CCAAATATGCAAGTTAGATGAACGATTAAAAACCGTTGAGTAAAATAATAAGGGATTAATTGTGA
** *
270023 AATTGGTAGAAAAGTG
66 AATTGACAAAAAAGTG
* * * * * *
270039 CCAATTATGCTAGTTAGATGAACGGTTAAAAACTGTTGAGTAAAATAATAAGGGATTAGTTGTGC
1 CCAAATATGCAAGTTAGATGAACGATTAAAAACCGTTGAGTAAAATAATAAGGGATTAATTGTGA
*
270104 ATTTGACAAAAAAGTG
66 AATTGACAAAAAAGTG
* *
270120 TCAAATATGCAAGTTAAATGAA
1 CCAAATATGCAAGTTAGATGAA
270142 AAGCTAAATA
Statistics
Matches: 233, Mismatches: 28, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
80 2 0.01
81 229 0.98
82 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.27
Consensus pattern (81 bp):
CCAAATATGCAAGTTAGATGAACGATTAAAAACCGTTGAGTAAAATAATAAGGGATTAATTGTGA
AATTGACAAAAAAGTG
Found at i:271539 original size:21 final size:21
Alignment explanation
Indices: 271482--271549 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
271472 CACAAAAATG
*
271482 ATCGATCCCTTAGGGCAAAGT
1 ATCGATCCCTTAGGGGAAAGT
271503 ATCGATCCCTTAGGGGAAAGT
1 ATCGATCCCTTAGGGGAAAGT
*
271524 ATCGATCCCTTAGGGG-AAGG
1 ATCGATCCCTTAGGGGAAAGT
271544 ATCGAT
1 ATCGAT
271550 ATGTAGGCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 9 0.20
21 36 0.80
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (21 bp):
ATCGATCCCTTAGGGGAAAGT
Found at i:274629 original size:15 final size:15
Alignment explanation
Indices: 274609--274647 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
274599 GAAAATCAAG
274609 AATAAAGATTAAGAC
1 AATAAAGATTAAGAC
* *
274624 AATAAAGACTAAGAT
1 AATAAAGATTAAGAC
*
274639 ATTAAAGAT
1 AATAAAGAT
274648 AAATAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.13, T:0.23
Consensus pattern (15 bp):
AATAAAGATTAAGAC
Found at i:278537 original size:7 final size:7
Alignment explanation
Indices: 278527--278576 Score: 70
Period size: 7 Copynumber: 7.6 Consensus size: 7
278517 GTTTTTTATT
278527 TTTTTCC
1 TTTTTCC
278534 TTTTTCC
1 TTTTTCC
278541 TTTTTCC
1 TTTTTCC
278548 TTTTT-C
1 TTTTTCC
278554 TTTTT--
1 TTTTTCC
278559 TTTTTCC
1 TTTTTCC
*
278566 TTTTTTC
1 TTTTTCC
278573 TTTT
1 TTTT
278577 ATTTTCAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
5 5 0.12
6 6 0.15
7 29 0.73
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
TTTTTCC
Found at i:278582 original size:18 final size:18
Alignment explanation
Indices: 278542--278582 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
278532 CCTTTTTCCT
*
278542 TTTTCCTTTTTCTTTTTT
1 TTTTCCTTTTTCTTTTTA
278560 TTTTCCTTTTT-TCTTTTA
1 TTTTCCTTTTTCT-TTTTA
278578 TTTTC
1 TTTTC
278583 AATAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCCTTTTTCTTTTTA
Found at i:278947 original size:15 final size:15
Alignment explanation
Indices: 278927--278965 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
278917 GAAAATTAGG
278927 AATAAATATTAAGAT
1 AATAAATATTAAGAT
* *
278942 AATAAAGACTAAGAT
1 AATAAATATTAAGAT
*
278957 ATTAAATAT
1 AATAAATAT
278966 AAATAAAGAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.31
Consensus pattern (15 bp):
AATAAATATTAAGAT
Found at i:281546 original size:24 final size:24
Alignment explanation
Indices: 281505--281563 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
281495 TATCGAAGTG
*
281505 CCGCGTAGAAATTTGTCCCGAAGGA
1 CCGCATAG-AATTTGTCCCGAAGGA
*
281530 CCGCATAGAATTTGTCCCGAATGA
1 CCGCATAGAATTTGTCCCGAAGGA
*
281554 CCACATAGAA
1 CCGCATAGAA
281564 AAATTCCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 24 0.77
25 7 0.23
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.20
Consensus pattern (24 bp):
CCGCATAGAATTTGTCCCGAAGGA
Found at i:294328 original size:4 final size:4
Alignment explanation
Indices: 294319--294405 Score: 102
Period size: 4 Copynumber: 21.8 Consensus size: 4
294309 TCAATCTACA
* * * * *
294319 ATAT ATAT ATAT ATAT ATAT TTAT TTAT ATTT ATTT ATAT ATCT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
294367 TTAT ACAT GTAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATA
294406 ATTTTCGAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 71 1.00
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (4 bp):
ATAT
Found at i:294330 original size:6 final size:6
Alignment explanation
Indices: 294319--294405 Score: 102
Period size: 6 Copynumber: 14.5 Consensus size: 6
294309 TCAATCTACA
* * * * *
294319 ATATAT ATATAT ATATAT ATTTAT TTATAT TTATTT ATATAT CTATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
294367 TTATAC ATGTAT ATATAT ATATAT ATATAT ATATAT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
294406 ATTTTCGAAA
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 68 1.00
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (6 bp):
ATATAT
Found at i:294334 original size:10 final size:10
Alignment explanation
Indices: 294319--294405 Score: 102
Period size: 10 Copynumber: 8.7 Consensus size: 10
294309 TCAATCTACA
294319 ATATATATAT
1 ATATATATAT
294329 ATATATATAT
1 ATATATATAT
* *
294339 TTATTTATAT
1 ATATATATAT
* *
294349 TTATTTATAT
1 ATATATATAT
* *
294359 ATCTATATTT
1 ATATATATAT
* *
294369 ATACATGTAT
1 ATATATATAT
294379 ATATATATAT
1 ATATATATAT
294389 ATATATATAT
1 ATATATATAT
294399 ATATATA
1 ATATATA
294406 ATTTTCGAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 65 1.00
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (10 bp):
ATATATATAT
Found at i:294703 original size:85 final size:85
Alignment explanation
Indices: 294494--294687 Score: 343
Period size: 85 Copynumber: 2.3 Consensus size: 85
294484 TGTCAAGCAG
*
294494 ATTTATGACAGTGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
1 ATTTATGACAGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
294559 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
** *
294579 ATTTATGATGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATATATTTATGACG
1 ATTTATGACAGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
294644 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
*
294664 ATTTATGACAGGGGCTTTAATGAC
1 ATTTATGACAGGGGCTTCAATGAC
294688 ACTCAAAGAA
Statistics
Matches: 102, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 102 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.32
Consensus pattern (85 bp):
ATTTATGACAGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
CACAAATGTGTGTCATCTTA
Found at i:294716 original size:85 final size:85
Alignment explanation
Indices: 294494--294720 Score: 287
Period size: 85 Copynumber: 2.7 Consensus size: 85
294484 TGTCAAGCAG
* * * * *
294494 ATTTATGACAGTGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACG
1 ATTTATGACAGGGGCTTCAATGACACGCAAAGTAAGTCATACATGAGCGTCATAAATTTATGACG
294559 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
** * * * * *
294579 ATTTATGATGGGGGCTTCAATGACGCGCAATGTAAGTCATACATGCGTGTCATATATTTATGACG
1 ATTTATGACAGGGGCTTCAATGACACGCAAAGTAAGTCATACATGAGCGTCATAAATTTATGACG
294644 CACAAATGTGTGTCATCTTA
66 CACAAATGTGTGTCATCTTA
* * *
294664 ATTTATGACAGGGGCTTTAATGACACTCAAAG-AACGTCATTA-ATTAGCGTCATAAAT
1 ATTTATGACAGGGGCTTCAATGACACGCAAAGTAA-GTCA-TACATGAGCGTCATAAAT
294721 GCGTGTCATA
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
84 2 0.02
85 122 0.97
86 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (85 bp):
ATTTATGACAGGGGCTTCAATGACACGCAAAGTAAGTCATACATGAGCGTCATAAATTTATGACG
CACAAATGTGTGTCATCTTA
Found at i:296338 original size:25 final size:25
Alignment explanation
Indices: 296292--296367 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
296282 CTTATATAAA
* * *
296292 TTGCACCGAAGTGCCGCATAGAGTT
1 TTGCACCGAAGTGCCACGTAGAATT
296317 TTGCACCGAAGTGCCACGTAGAAATT
1 TTGCACCGAAGTGCCACGTAG-AATT
*
296343 TTTC-CCGAAG-GACCACGTAGAATT
1 TTGCACCGAAGTG-CCACGTAGAATT
296367 T
1 T
296368 GTCTCGAAGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
24 6 0.13
25 33 0.73
26 6 0.13
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (25 bp):
TTGCACCGAAGTGCCACGTAGAATT
Found at i:296375 original size:24 final size:24
Alignment explanation
Indices: 296322--296388 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
296312 GAGTTTTGCA
*
296322 CCGAAGTG-CCACGTAGAAATTTTTC
1 CCGAAG-GACCACGTAG-AATTTGTC
296347 CCGAAGGACCACGTAGAATTTGTC
1 CCGAAGGACCACGTAGAATTTGTC
* * *
296371 TCGAAGGACTACATAGAA
1 CCGAAGGACCACGTAGAA
296389 AAGTTCCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
24 23 0.62
25 14 0.38
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (24 bp):
CCGAAGGACCACGTAGAATTTGTC
Found at i:300459 original size:13 final size:13
Alignment explanation
Indices: 300441--300466 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300431 TATGGTTGGC
300441 ATGATCAACCTCA
1 ATGATCAACCTCA
300454 ATGATCAACCTCA
1 ATGATCAACCTCA
300467 TATGGACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
ATGATCAACCTCA
Found at i:305718 original size:54 final size:54
Alignment explanation
Indices: 305660--306228 Score: 811
Period size: 54 Copynumber: 10.5 Consensus size: 54
305650 GAATTTATAA
* ** * *
305660 TATGTTGATGAATTACCGTTTCACCACTAAGTGTGTATTTCAC-AGAATTCATCA
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCG
* * *
305714 TATGTTGATGAATCACCATTTCGGCACTAAGTGTGCATTTCACGGAATTCATCA
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* * * *
305768 TATGTTGATGAATCACCATTTCGGCACTAAGTCTGAATTTCAC-AGAATTCATCA
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCG
* * * *
305822 TATGTTGATGAATCACCATTTCAGCACTAAGTATGCAATTCACGAAATTCATCG
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* * *
305876 TATGTTGATGAATCACTGTTTCGGAACTAAGTGTGCAATTCAC-AGAATTCATCG
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGA-AATTCATCG
*
305930 TATGTTGATGAATCACCGTTTCAGCACTAAGTGTGCATTTCACGAAATTCATCG
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
*
305984 TATGTTGATGAATCACCGTTTCGGCACTAAGTGCGCATTTCACGAAATTCATCG
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
*
306038 TATGTTGATGAATCACCGTTTCGGCACTAAGTGCGCATTTCACGAAATTCATCG
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* * *
306092 TATGTTGATGAATAACCATTTCGGCACTAAGTGTGCATTTCACGAAATTCATCA
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* * * *
306146 TATATTGATGAATCACCGTTTCAGCACTAAGTGTGCAATTCACGAAAGTCATCG
1 TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
* *
306200 TATATTGATGAATCACTGTTTCGGCACTA
1 TATGTTGATGAATCACCGTTTCGGCACTA
306229 TGTATGCAAA
Statistics
Matches: 472, Mismatches: 38, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
53 1 0.00
54 469 0.99
55 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (54 bp):
TATGTTGATGAATCACCGTTTCGGCACTAAGTGTGCATTTCACGAAATTCATCG
Found at i:305729 original size:27 final size:26
Alignment explanation
Indices: 305699--305891 Score: 74
Period size: 27 Copynumber: 7.2 Consensus size: 26
305689 AGTGTGTATT
305699 TCACAGAATTCATCATATGTTGATGAA
1 TCAC-GAATTCATCATATGTTGATGAA
* * ** * *
305726 TCACCATTTCGGCACTAAG-TG-TGCATT
1 TCACGAATTCATCA-TATGTTGATG-A-A
305753 TCACGGAATTCATCATATGTTGATGAA
1 TCAC-GAATTCATCATATGTTGATGAA
* * ** * *
305780 TCACCATTTCGGCACTAAGTCTGA--ATT
1 TCACGAATTCATCA-TATGT-TGATGA-A
305807 TCACAGAATTCATCATATGTTGATGAA
1 TCAC-GAATTCATCATATGTTGATGAA
* * * *
305834 TCACCATTTCAGCACTAAG-T-ATGCAA
1 TCACGAATTCATCA-TATGTTGATG-AA
*
305860 TTCACGAAATTCATCGTATGTTGATGAA
1 -TCACG-AATTCATCATATGTTGATGAA
305888 TCAC
1 TCAC
305892 TGTTTCGGAA
Statistics
Matches: 115, Mismatches: 33, Indels: 36
0.62 0.18 0.20
Matches are distributed among these distances:
25 5 0.04
26 29 0.25
27 48 0.42
28 28 0.24
29 5 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (26 bp):
TCACGAATTCATCATATGTTGATGAA
Found at i:307430 original size:36 final size:36
Alignment explanation
Indices: 307346--307567 Score: 229
Period size: 36 Copynumber: 6.3 Consensus size: 36
307336 ATAGTTTCAT
** *
307346 GTGAGATAAAAAATTTTTTAAG-AAAACAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* * * *
307381 GTGATATATAATCTTCTTTAAGAAAAATAATTTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* ***
307417 GTGAGAAAAAATCTTGAGT--GAAAAACAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* *
307451 GTGAGATAAAATCTGCTTTAAGAAAAGCAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* *
307487 GTGAGACAAAATCTCCTTTAAGAAAAACAATCTCAA
1 GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
* * *
307523 GGGAGATAAAAT-TTGTTTTAATAAAAACAATCTCAA
1 GTGAGATAAAATCTT-CTTTAAGAAAAACAATCTCAA
*
307559 -TGACATAAA
1 GTGAGATAAA
307568 TTTTGAGTGA
Statistics
Matches: 152, Mismatches: 31, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
34 27 0.18
35 25 0.16
36 100 0.66
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.27
Consensus pattern (36 bp):
GTGAGATAAAATCTTCTTTAAGAAAAACAATCTCAA
Found at i:307453 original size:17 final size:16
Alignment explanation
Indices: 307402--307464 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
307392 TCTTCTTTAA
*
307402 GAAAAATAATTTCAAGT
1 GAAAAA-AATCTCAAGT
**
307419 GAGAAAAAATCTTGAGT
1 GA-AAAAAATCTCAAGT
307436 GAAAAACAATCTCAAGT
1 GAAAAA-AATCTCAAGT
*
307453 GAGATAAAATCT
1 GA-AAAAAATCT
307465 GCTTTAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
16 4 0.11
17 26 0.70
18 7 0.19
ACGTcount: A:0.51, C:0.10, G:0.16, T:0.24
Consensus pattern (16 bp):
GAAAAAAATCTCAAGT
Found at i:307453 original size:70 final size:70
Alignment explanation
Indices: 307368--307579 Score: 232
Period size: 70 Copynumber: 3.0 Consensus size: 70
307358 ATTTTTTAAG
* * * * *
307368 AAAACAATCTCAAGTGATATATAATCTTCTTTAAGAAAAATAATTTCAAGTGAGAAAAAATCTTG
1 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGAAAAAATCTTG
307433 AGTGA
66 AGTGA
* *
307438 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAGCAATCTCAAGTGAGACAAAATCTCC
1 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGA-AAAA-AT-C
* *
307503 TTTA-AGA
63 TTGAGTGA
* * * * * * *
307510 AAAACAATCTCAAGGGAGATAAAATTTGTTTTAATAAAAACAATCTCAA-TGA-CATAAATTTTG
1 AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGAAAAAATCTTG
307573 AGTGA
66 AGTGA
307578 AA
1 AA
307580 TGATATGAGT
Statistics
Matches: 118, Mismatches: 20, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
67 3 0.03
68 5 0.04
69 3 0.03
70 49 0.42
71 7 0.06
72 47 0.40
73 4 0.03
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.27
Consensus pattern (70 bp):
AAAACAATCTCAAGTGAGATAAAATCTGCTTTAAGAAAAACAATCTCAAGTGAGAAAAAATCTTG
AGTGA
Found at i:307501 original size:17 final size:17
Alignment explanation
Indices: 307413--307501 Score: 65
Period size: 17 Copynumber: 5.1 Consensus size: 17
307403 AAAAATAATT
307413 TCAAGTGAGAAAAAATC
1 TCAAGTGAGAAAAAATC
**
307430 TTGAGTGA-AAAACAATC
1 TCAAGTGAGAAAA-AATC
*
307447 TCAAGTGAGATAAAATC
1 TCAAGTGAGAAAAAATC
** *
307464 TGC-TTTAAGAAAAGCAATC
1 T-CAAGTGAGAAAA--AATC
*
307483 TCAAGTGAGACAAAATC
1 TCAAGTGAGAAAAAATC
307500 TC
1 TC
307502 CTTTAAGAAA
Statistics
Matches: 53, Mismatches: 13, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
16 4 0.08
17 33 0.62
18 5 0.09
19 11 0.21
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (17 bp):
TCAAGTGAGAAAAAATC
Found at i:309278 original size:11 final size:11
Alignment explanation
Indices: 309262--309295 Score: 59
Period size: 11 Copynumber: 3.0 Consensus size: 11
309252 TATCATTTTA
309262 AAAACACACTT
1 AAAACACACTT
309273 AAAACACACTTT
1 AAAACACAC-TT
309285 AAAACACACTT
1 AAAACACACTT
309296 CTTCCCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAACACACTT
Found at i:311502 original size:21 final size:21
Alignment explanation
Indices: 311476--311515 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
311466 CAGAACCCCA
*
311476 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
311497 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
311516 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Done.