Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004983.1 Kokia drynarioides strain JFW-HI SEQ_118728, 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: 365800
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 102 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:358 original size:21 final size:21
Alignment explanation
Indices: 334--383 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
324 AGTTTTTAGC
* *
334 ATCGGTAGAAGTAAGACTTGT
1 ATCGGTAGAACTAACACTTGT
* *
355 ATCGATAGAACTATCACTTGT
1 ATCGGTAGAACTAACACTTGT
376 ATCGGTAG
1 ATCGGTAG
384 GAGTCTGCAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.30
Consensus pattern (21 bp):
ATCGGTAGAACTAACACTTGT
Found at i:7117 original size:21 final size:21
Alignment explanation
Indices: 7091--7137 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
7081 TTTTAGTGTT
*
7091 GGTAGAAGTAAAACTTGTATC
1 GGTAGAACTAAAACTTGTATC
**
7112 GGTAGAACTATTACTTGTATC
1 GGTAGAACTAAAACTTGTATC
*
7133 AGTAG
1 GGTAG
7138 GAGTCTGCAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.11, G:0.23, T:0.32
Consensus pattern (21 bp):
GGTAGAACTAAAACTTGTATC
Found at i:8075 original size:4 final size:4
Alignment explanation
Indices: 8059--8101 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
8049 AAAAAGAGGT
* * *
8059 AAGA AAAA AAGA AAGA AAGA AAGA AAAA AAAA AAGA AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA
8102 TGATAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:8097 original size:12 final size:12
Alignment explanation
Indices: 8062--8099 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
8052 AAGAGGTAAG
*
8062 AAAAAAAGAAAG
1 AAAAAAAGAAAA
*
8074 AAAGAAAGAAAA
1 AAAAAAAGAAAA
8086 AAAAAAAGAAAA
1 AAAAAAAGAAAA
8098 AA
1 AA
8100 GATGATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:8109 original size:23 final size:22
Alignment explanation
Indices: 8048--8112 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 22
8038 ACGTGTTATC
* *
8048 AAAAAAGAGGTAAGAAAAAAAG
1 AAAAAAGAGATAAAAAAAAAAG
8070 AAAGAAAGAAAGA-AAAAAAAAAAG
1 AAA-AAAG--AGATAAAAAAAAAAG
8094 AAAAAAGATGATAAAAAAA
1 AAAAAAGA-GATAAAAAAA
8113 CCGCAAAGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
21 1 0.03
22 5 0.14
23 15 0.42
24 13 0.36
25 2 0.06
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAAAAGAGATAAAAAAAAAAG
Found at i:11424 original size:49 final size:49
Alignment explanation
Indices: 11354--11514 Score: 177
Period size: 49 Copynumber: 3.3 Consensus size: 49
11344 GGAGGGAAAG
* **
11354 ATTGAAGCCGCAATGGTGAATCTTATACCCTGAAGATGTAAAGAAGCAT
1 ATTGAAGCCGCAAAGACGAATCTTATACCCTGAAGATGTAAAGAAGCAT
* ** *
11403 ATTGAAGCCGTAAAGACGAATCTTATACCCT-AGAGCATAG-AGGGAA--AG
1 ATTGAAGCCGCAAAGACGAATCTTATACCCTGA-AG-AT-GTAAAGAAGCAT
* *
11451 ATTGAAGCCGCAATGGCGAATCTTATACCCTGAAGATGTAAAGAAGCAT
1 ATTGAAGCCGCAAAGACGAATCTTATACCCTGAAGATGTAAAGAAGCAT
*
11500 ATTGAAGCCTCAAAG
1 ATTGAAGCCGCAAAG
11515 GCAAATCTCA
Statistics
Matches: 90, Mismatches: 15, Indels: 14
0.76 0.13 0.12
Matches are distributed among these distances:
46 1 0.01
47 6 0.07
48 32 0.36
49 44 0.49
50 6 0.07
51 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.22
Consensus pattern (49 bp):
ATTGAAGCCGCAAAGACGAATCTTATACCCTGAAGATGTAAAGAAGCAT
Found at i:11464 original size:97 final size:97
Alignment explanation
Indices: 11323--11508 Score: 354
Period size: 97 Copynumber: 1.9 Consensus size: 97
11313 AGGGAACATT
* *
11323 GAATCTTATACCCTAGAGCATGGAGGGAAAGATTGAAGCCGCAATGGTGAATCTTATACCCTGAA
1 GAATCTTATACCCTAGAGCATAGAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTGAA
11388 GATGTAAAGAAGCATATTGAAGCCGTAAAGAC
66 GATGTAAAGAAGCATATTGAAGCCGTAAAGAC
11420 GAATCTTATACCCTAGAGCATAGAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTGAA
1 GAATCTTATACCCTAGAGCATAGAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTGAA
11485 GATGTAAAGAAGCATATTGAAGCC
66 GATGTAAAGAAGCATATTGAAGCC
11509 TCAAAGGCAA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (97 bp):
GAATCTTATACCCTAGAGCATAGAGGGAAAGATTGAAGCCGCAATGGCGAATCTTATACCCTGAA
GATGTAAAGAAGCATATTGAAGCCGTAAAGAC
Found at i:11471 original size:48 final size:47
Alignment explanation
Indices: 11323--11481 Score: 187
Period size: 48 Copynumber: 3.3 Consensus size: 47
11313 AGGGAACATT
*
11323 GAATCTTATACCCTAGAGCATGGAGGGAAAGATTGAAGCCGCAATGGT
1 GAATCTTATACCCTAGAGCAT-GAGGGAAAGATTGAAGCCGCAATGGC
** * * * *
11371 GAATCTTATACCCT-GAAG-ATGTAAAGAAGCATATTGAAGCCGTAAAGAC
1 GAATCTTATACCCTAG-AGCATG-AGGGAA--AGATTGAAGCCGCAATGGC
11420 GAATCTTATACCCTAGAGCATAGAGGGAAAGATTGAAGCCGCAATGGC
1 GAATCTTATACCCTAGAGCAT-GAGGGAAAGATTGAAGCCGCAATGGC
11468 GAATCTTATACCCT
1 GAATCTTATACCCT
11482 GAAGATGTAA
Statistics
Matches: 91, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
46 1 0.01
47 7 0.08
48 45 0.49
49 30 0.33
50 7 0.08
51 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (47 bp):
GAATCTTATACCCTAGAGCATGAGGGAAAGATTGAAGCCGCAATGGC
Found at i:11840 original size:75 final size:75
Alignment explanation
Indices: 11628--11840 Score: 266
Period size: 75 Copynumber: 2.8 Consensus size: 75
11618 TCAAAATTAT
** * * *
11628 AGTGAAACTTCAAACCTTATCTT-ATTGATGAGATGTAGAGAAGTGAACCAAAATAATGAAGCAA
1 AGTGAAACTTCAAACCCCATCTTCA-TGATGAGATATAGAGAAGTGAACCAAAACAATGAAGCGA
11692 AACTCAATGTG
65 AACTCAATGTG
* * * *
11703 AGTGAAACTTCAAACTCCATCTTCATAATGAGATACAGAGAAGTGGACCAAAACAATGAAGCGAA
1 AGTGAAACTTCAAACCCCATCTTCATGATGAGATATAGAGAAGTGAACCAAAACAATGAAGCGAA
**
11768 GTTCAATGTG
66 ACTCAATGTG
* * * * *
11778 AGTGAAACTTTAAACCCCGTCTTCCTGATGAGATATAAAGAAGTGAATCAAAACAATGAAGCG
1 AGTGAAACTTCAAACCCCATCTTCATGATGAGATATAGAGAAGTGAACCAAAACAATGAAGCG
11841 GTCATCTTCT
Statistics
Matches: 117, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
75 116 0.99
76 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.19, T:0.23
Consensus pattern (75 bp):
AGTGAAACTTCAAACCCCATCTTCATGATGAGATATAGAGAAGTGAACCAAAACAATGAAGCGAA
ACTCAATGTG
Found at i:11855 original size:48 final size:48
Alignment explanation
Indices: 11797--11984 Score: 250
Period size: 48 Copynumber: 3.9 Consensus size: 48
11787 TTAAACCCCG
*
11797 TCTTCCTGATGAGATATAAAGAAGTGAATCAAAACAATGAAGCGGTCA
1 TCTTCCTGATGAGATATAAAGAAGTGAACCAAAACAATGAAGCGGTCA
* * * *
11845 TCTTCTTGATGAGATATAGAGAAGTGAACCAAAACAATGAAACGGTTA
1 TCTTCCTGATGAGATATAAAGAAGTGAACCAAAACAATGAAGCGGTCA
* * * * *
11893 TCTTCCTGATTAGATACAAAGAAGTGGACCAAAACAATAAAGTGGTCA
1 TCTTCCTGATGAGATATAAAGAAGTGAACCAAAACAATGAAGCGGTCA
** * *
11941 TCTTTTTGATGAGATATAAAGAAGTGGACCAAAATAATGAAGCG
1 TCTTCCTGATGAGATATAAAGAAGTGAACCAAAACAATGAAGCG
11985 AAATGTGAGT
Statistics
Matches: 119, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 119 1.00
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.24
Consensus pattern (48 bp):
TCTTCCTGATGAGATATAAAGAAGTGAACCAAAACAATGAAGCGGTCA
Found at i:11964 original size:96 final size:96
Alignment explanation
Indices: 11797--11981 Score: 280
Period size: 96 Copynumber: 1.9 Consensus size: 96
11787 TTAAACCCCG
* * *
11797 TCTTCCTGATGAGATATAAAGAAGTGAATCAAAACAATGAAGCGGTCATCTTCTTGATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATAAAGCGGTCATCTTCTTGATGAGATAT
*
11862 AGAGAAGTGAACCAAAACAATGAAACGGTTA
66 AAAGAAGTGAACCAAAACAATGAAACGGTTA
* * * *
11893 TCTTCCTGATTAGATACAAAGAAGTGGACCAAAACAATAAAGTGGTCATCTTTTTGATGAGATAT
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATAAAGCGGTCATCTTCTTGATGAGATAT
* *
11958 AAAGAAGTGGACCAAAATAATGAA
66 AAAGAAGTGAACCAAAACAATGAA
11982 GCGAAATGTG
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
96 79 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (96 bp):
TCTTCCTGATGAGATACAAAGAAGTGAACCAAAACAATAAAGCGGTCATCTTCTTGATGAGATAT
AAAGAAGTGAACCAAAACAATGAAACGGTTA
Found at i:12164 original size:96 final size:94
Alignment explanation
Indices: 11989--12369 Score: 383
Period size: 96 Copynumber: 4.0 Consensus size: 94
11979 GAAGCGAAAT
* * * *
11989 GTGAGTGAAACTTCAAACCCATCTTTTCC-GATGAGATACAGAGAAGTGGATCAAAACAATAAAG
1 GTGAGCGAAACTTCAAACCCATC--TTCCTGATGAGATACAAAGAAGTAGATCAAAACAATGAAG
* *
12053 CAAAGCTCAACATCCCTAAGGTTACAGTGGA
64 CAAAGCTCAATATCCCTGAGGTTACAGTGGA
** * * * *
12084 GTAGATTGAAACTTCAAACCCTATCTTCCTGAGGAGATATAAAAAAGTAGATCAAAACAATGAGG
1 GT-GAGCGAAACTTCAAACCC-ATCTTCCTGATGAGATACAAAGAAGTAGATCAAAACAATGAAG
* * *
12149 AAAATCTTAATATCCCTGAGGTTACAGTGGA
64 CAAAGCTCAATATCCCTGAGGTTACAGTGGA
* * * * * * *
12180 ATGGAGCAAAACTTCAAACCTTATCTTCCTAATGAGATATAGAGAAGT-GAATCAAAATAATGAA
1 GT-GAGCGAAACTTCAAACC-CATCTTCCTGATGAGATACAAAGAAGTAG-ATCAAAACAATGAA
* *
12244 GCAGAGCTCAATGTCCCTGAGGTTACAGTGGA
63 GCAAAGCTCAATATCCCTGAGGTTACAGTGGA
* *
12276 GTGAAGCGAAACTTCAAACCCATCTTCCTGATGAGATACAAAGAAGTAGGTCAAAAC-AGGTAA-
1 GTG-AGCGAAACTTCAAACCCATCTTCCTGATGAGATACAAAGAAGTAGATCAAAACAATG-AAG
* * * *
12339 CAAATCTCAATGTCCTTGAGGCTACAGTGGA
64 CAAAGCTCAATATCCCTGAGGTTACAGTGGA
12370 ATGAAGTAAA
Statistics
Matches: 235, Mismatches: 43, Indels: 17
0.80 0.15 0.06
Matches are distributed among these distances:
94 29 0.12
95 39 0.17
96 164 0.70
97 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (94 bp):
GTGAGCGAAACTTCAAACCCATCTTCCTGATGAGATACAAAGAAGTAGATCAAAACAATGAAGCA
AAGCTCAATATCCCTGAGGTTACAGTGGA
Found at i:12742 original size:84 final size:83
Alignment explanation
Indices: 12647--12874 Score: 294
Period size: 84 Copynumber: 2.7 Consensus size: 83
12637 AAACCATCAT
*
12647 CCAATCTTTTACCCTTAAGTCAAAAGGGGCAAATTGAAGACATCATCCAATCTTTTACCTCGATC
1 CCAATC-TTTACCCTTAAGTCAAAA-GGGCAGATTGAAGACATCATCCAATCTTTTACCTCGATC
*
12712 ATGTGGCAGATTGAAGCCAC
64 ATGGGGCAGATTGAAGCCAC
* * * * * * * *
12732 CCAATGTTTACCTTTAAGTCAGGAAGGGCAGATTAAAGTCATCATCTAATCTCTTATCTCGATCA
1 CCAATCTTTACCCTTAAGTCA-AAAGGGCAGATTGAAGACATCATCCAATCTTTTACCTCGATCA
*
12797 TGGGGCAGATTGAAGCCAT
65 TGGGGCAGATTGAAGCCAC
* * *
12816 CCAATCTTTACCCTTAAGTTAAGAAGGGCAGATTGAAGCCATCATCCAATATTTTACCT
1 CCAATCTTTACCCTTAAGTCAA-AAGGGCAGATTGAAGACATCATCCAATCTTTTACCT
12875 TTAAGTCAAG
Statistics
Matches: 120, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
84 113 0.94
85 7 0.06
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (83 bp):
CCAATCTTTACCCTTAAGTCAAAAGGGCAGATTGAAGACATCATCCAATCTTTTACCTCGATCAT
GGGGCAGATTGAAGCCAC
Found at i:12775 original size:130 final size:130
Alignment explanation
Indices: 12535--12783 Score: 331
Period size: 130 Copynumber: 1.9 Consensus size: 130
12525 CAATCTTAGG
* * * * *
12535 GTCAAGAGAGGCAGATTAAAGACATTATCCCATCTTTTACCCTGATCATGGGGTAGATTGAAGCC
1 GTCAAAAGAGGCAAATTAAAGACATCATCCAATCTTTTACCCTGATCATGGGGCAGATTGAAGCC
** *
12600 ATGCAATCTTTACCTTTAAGTCAAGAAGGGTAGATTTAAACCATCATCCAATCTTTTACCCTTAA
66 ACCCAATCTTTACCTTTAAGTCAAGAAGGGCAGATTTAAACCATCATCCAATCTTTTACCCTTAA
* * *
12665 GTCAAAAGGGGCAAATTGAAGACATCATCCAATCTTTTA-CCTCGATCATGTGGCAGATTGAAGC
1 GTCAAAAGAGGCAAATTAAAGACATCATCCAATCTTTTACCCT-GATCATGGGGCAGATTGAAGC
* * * *
12729 CACCCAATGTTTACCTTTAAGTCAGGAAGGGCAGA-TTAAAGTCATCATCTAATCT
65 CACCCAATCTTTACCTTTAAGTCAAGAAGGGCAGATTTAAA-CCATCATCCAATCT
12784 CTTATCTCGA
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
129 8 0.08
130 94 0.92
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (130 bp):
GTCAAAAGAGGCAAATTAAAGACATCATCCAATCTTTTACCCTGATCATGGGGCAGATTGAAGCC
ACCCAATCTTTACCTTTAAGTCAAGAAGGGCAGATTTAAACCATCATCCAATCTTTTACCCTTAA
Found at i:12887 original size:46 final size:46
Alignment explanation
Indices: 12603--12895 Score: 235
Period size: 46 Copynumber: 6.7 Consensus size: 46
12593 TGAAGCCATG
* * *
12603 CAATC-TTTACCTTTAAGTCAAGAAGGGTAGATTTAAACCATCATC
1 CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGCCATCATC
* * *
12648 CAATCTTTTACCCTTAAGTCAA-AAGGGGCAAATTGAAGACATCATC
1 CAATCTTTTACCTTTAAGTCAAGAA-GGGCAGATTGAAGCCATCATC
** * *
12694 CAATCTTTTACC-TCGA-TCATG--TGGCAGATTGAAGCCA-C--C
1 CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGCCATCATC
* * * *
12733 CAAT-GTTTACCTTTAAGTCAGGAAGGGCAGATTAAAGTCATCATC
1 CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGCCATCATC
* * * ** *
12778 TAATCTCTTATC-TCGA-TCATG--GGGCAGATTGAAG-C--CATC
1 CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGCCATCATC
* *
12817 CAATC-TTTACCCTTAAGTTAAGAAGGGCAGATTGAAGCCATCATC
1 CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGCCATCATC
* *
12862 CAATATTTTACCTTTAAGTCAAGAAGGACAGATT
1 CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATT
12896 AAAGTCATTC
Statistics
Matches: 191, Mismatches: 38, Indels: 37
0.72 0.14 0.14
Matches are distributed among these distances:
38 10 0.05
39 17 0.09
40 7 0.04
41 2 0.01
42 51 0.27
43 2 0.01
44 7 0.04
45 23 0.12
46 72 0.38
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (46 bp):
CAATCTTTTACCTTTAAGTCAAGAAGGGCAGATTGAAGCCATCATC
Found at i:12940 original size:39 final size:39
Alignment explanation
Indices: 12897--12999 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 39
12887 GGACAGATTA
*
12897 AAGTCATTCAATCTCTTACCCCGGCCATGAGGCAAATTG
1 AAGTCATTCAATCTCTTACCCCGACCATGAGGCAAATTG
** *
12936 AAGTCATCATCCAATCTCTTACCTTGACCATGAGGCGAATTG
1 AAGTCAT--T-CAATCTCTTACCCCGACCATGAGGCAAATTG
* * *
12978 AAGTCATCCAATTTTTTACCCC
1 AAGTCATTCAATCTCTTACCCC
13000 TAATCGAGAG
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
39 17 0.33
41 1 0.02
42 34 0.65
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (39 bp):
AAGTCATTCAATCTCTTACCCCGACCATGAGGCAAATTG
Found at i:12947 original size:130 final size:126
Alignment explanation
Indices: 12716--12958 Score: 312
Period size: 130 Copynumber: 1.9 Consensus size: 126
12706 TCGATCATGT
* *
12716 GGCAGATTGAAGCCACCCAATGTTTACCTTTAAGTCAGGAAGGGCAGATTAAAGTCATCATCTAA
1 GGCAGATTGAAGCCACCCAATGTTTACCTTTAAGTCAAGAAGGACAGATTAAAGTCAT-ATCTAA
* * * * *
12781 TCTCTTATCTCGATCATGGGGCAGATTGAAGCCATCCAATCT-TTACCCTTAAGTTAAGAAG
65 TCTCTTACCCCGACCATGAGGCAAATTGAAGCCATCCAATCTCTTACCCTTAAGTTAAGAAG
*
12842 GGCAGATTGAAGCCATCATCCAATATTTTACCTTTAAGTCAAGAAGGACAGATTAAAGTCAT-TC
1 GGCAGATTGAAGCCA-C--CCAAT-GTTTACCTTTAAGTCAAGAAGGACAGATTAAAGTCATATC
*
12906 -AATCTCTTACCCCGGCCATGAGGCAAATTGAAGTCATCATCCAATCTCTTACC
62 TAATCTCTTACCCCGACCATGAGGCAAATTGAAG-C--CATCCAATCTCTTACC
12959 TTGACCATGA
Statistics
Matches: 100, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
126 15 0.15
127 28 0.28
128 3 0.03
129 5 0.05
130 44 0.44
131 5 0.05
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.28
Consensus pattern (126 bp):
GGCAGATTGAAGCCACCCAATGTTTACCTTTAAGTCAAGAAGGACAGATTAAAGTCATATCTAAT
CTCTTACCCCGACCATGAGGCAAATTGAAGCCATCCAATCTCTTACCCTTAAGTTAAGAAG
Found at i:12953 original size:42 final size:42
Alignment explanation
Indices: 12900--12985 Score: 127
Period size: 42 Copynumber: 2.0 Consensus size: 42
12890 CAGATTAAAG
* *
12900 TCATTCAATCTCTTACCCCGGCCATGAGGCAAATTGAAGTCA
1 TCATCCAATCTCTTACCCCGACCATGAGGCAAATTGAAGTCA
** *
12942 TCATCCAATCTCTTACCTTGACCATGAGGCGAATTGAAGTCA
1 TCATCCAATCTCTTACCCCGACCATGAGGCAAATTGAAGTCA
12984 TC
1 TC
12986 CAATTTTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (42 bp):
TCATCCAATCTCTTACCCCGACCATGAGGCAAATTGAAGTCA
Found at i:15035 original size:148 final size:147
Alignment explanation
Indices: 14756--15022 Score: 326
Period size: 147 Copynumber: 1.8 Consensus size: 147
14746 TTTGACCCTA
* * * * *
14756 TTTTTTTTTATTTTTGTTATTTTCACTTAAAACTTTATTTTCTTTTTAATTTAATCCTTAAACCT
1 TTTTTTTGTATTTTTGTTATTTTCACCTAAAACTTTATTTCCCTTTTAATTTAATCCTTAAACAT
* *
14821 TTTTTCTTTTCAATTTTCCTCAATATATTTTTTGATTTTACAAATAGGCCCTAAACTCTTCAAAA
66 TTTTTCTTTTCAATTTTCCTCAATATATTTTTCGATTTTACAAATAGGCCATAAACTCTTCAAAA
14886 TTACATTTTTGGCAATG
131 TTACATTTTTGGCAATG
* * *
14903 TTTTTTTGTATTTTAT-TATATTTT-ACCTAAAATTTTATTTCCCTTTTAATTTAGTCCTTATAC
1 TTTTTTTGTATTTT-TGT-TATTTTCACCTAAAACTTTATTTCCCTTTTAATTTAATCCTTAAAC
* * * *
14966 ATTTATTTCTTTTTAATTTTATCTCGAT-TA-TTTTCGAATTTTATAAATTAGGCCATA
64 ATTT-TTTCTTTTCAATTTT-CCTCAATATATTTTTCG-ATTTTACAAA-TAGGCCATA
15023 CATTTTTAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
147 55 0.55
148 32 0.32
149 13 0.13
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (147 bp):
TTTTTTTGTATTTTTGTTATTTTCACCTAAAACTTTATTTCCCTTTTAATTTAATCCTTAAACAT
TTTTTCTTTTCAATTTTCCTCAATATATTTTTCGATTTTACAAATAGGCCATAAACTCTTCAAAA
TTACATTTTTGGCAATG
Found at i:18672 original size:10 final size:10
Alignment explanation
Indices: 18657--18701 Score: 54
Period size: 10 Copynumber: 4.2 Consensus size: 10
18647 TTGTCCTCTC
18657 CTTTTTTTTT
1 CTTTTTTTTT
18667 CTTTTTTTTT
1 CTTTTTTTTT
18677 CCCTTTTTCTTTT
1 --CTTTTT-TTTT
*
18690 CTTTTCTTTT
1 CTTTTTTTTT
18700 CT
1 CT
18702 CTCTCTTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
10 16 0.52
11 5 0.16
12 6 0.19
13 4 0.13
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:29532 original size:23 final size:23
Alignment explanation
Indices: 29506--29552 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
29496 TTTTCTTCTA
29506 GTTTTT-ATCTGCCTTTGTGACAT
1 GTTTTTCATCTGCC-TTGTGACAT
*
29529 GTTTTTCCTCTGCCTTGTGACAT
1 GTTTTTCATCTGCCTTGTGACAT
29552 G
1 G
29553 CTTCTGCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (23 bp):
GTTTTTCATCTGCCTTGTGACAT
Found at i:35495 original size:67 final size:67
Alignment explanation
Indices: 35421--35556 Score: 245
Period size: 67 Copynumber: 2.0 Consensus size: 67
35411 AAAAACACAA
* *
35421 TATAGTAATGCGTGATGATTAAAGTTAAATATAATTAAACTAAATGCAAATGATCCTTAATGCAA
1 TATAGTAATGAGTGATGATTAAAGTTAAATATAATTAAACTAAATGCAAATGATCCCTAATGCAA
35486 TT
66 TT
*
35488 TATAGTAATGAGTGATGATTAAAGTTAAATGTAATTAAACTAAATGCAAATGATCCCTAATGCAA
1 TATAGTAATGAGTGATGATTAAAGTTAAATATAATTAAACTAAATGCAAATGATCCCTAATGCAA
35553 TT
66 TT
35555 TA
1 TA
35557 ACCTAAGTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (67 bp):
TATAGTAATGAGTGATGATTAAAGTTAAATATAATTAAACTAAATGCAAATGATCCCTAATGCAA
TT
Found at i:52743 original size:21 final size:22
Alignment explanation
Indices: 52717--52761 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
52707 CAATGGAATC
*
52717 AAAAGTT-AATTTTTTTTGGTG
1 AAAAGTTAAATTTTTTTTGATG
52738 AAAAGTTAAATTTTTTTTGATG
1 AAAAGTTAAATTTTTTTTGATG
52760 AA
1 AA
52762 TTATAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (22 bp):
AAAAGTTAAATTTTTTTTGATG
Found at i:53095 original size:17 final size:15
Alignment explanation
Indices: 53073--53114 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 15
53063 GCAACACAAA
53073 AGAAAAGAAAAAGAG
1 AGAAAAGAAAAAGAG
*
53088 AGGAAAAAAAAAAAGAG
1 A-G-AAAAGAAAAAGAG
53105 AGAAAAGAAA
1 AGAAAAGAAA
53115 TGGCTTCATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 8 0.35
16 2 0.09
17 13 0.57
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAGAG
Found at i:53715 original size:5 final size:5
Alignment explanation
Indices: 53705--53734 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
53695 ATTTACCTCT
53705 TACCA TACCA TACCA TACCA TACCA TACCA
1 TACCA TACCA TACCA TACCA TACCA TACCA
53735 CCACCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (5 bp):
TACCA
Found at i:56044 original size:40 final size:40
Alignment explanation
Indices: 55991--56067 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
55981 AGATGAACTT
**
55991 AAATAGTTGATTTTTATCAATTTGTTGCATAAAAATTGTC
1 AAATAGTTGATTTTTATCAATTCCTTGCATAAAAATTGTC
* * * *
56031 AAATGGTTTATTTTTATTAATTCCTTGCATATAAATT
1 AAATAGTTGATTTTTATCAATTCCTTGCATAAAAATT
56068 ACAAAACTGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.34, C:0.08, G:0.10, T:0.48
Consensus pattern (40 bp):
AAATAGTTGATTTTTATCAATTCCTTGCATAAAAATTGTC
Found at i:59841 original size:3 final size:3
Alignment explanation
Indices: 59833--59897 Score: 54
Period size: 3 Copynumber: 23.3 Consensus size: 3
59823 TGTGGGTATT
59833 GAA GAA GAA G-A GAA -AA G-A GAA GAA GAA GGAA G-A GAA G-A GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA GAA GAA GAA
*
59874 GGAA -AA -AA AAA GAA GAA GAA GAA G
1 -GAA GAA GAA GAA GAA GAA GAA GAA G
59898 TTGTTCCGAC
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
2 14 0.26
3 33 0.62
4 6 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59855 original size:12 final size:13
Alignment explanation
Indices: 59833--59897 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 13
59823 TGTGGGTATT
59833 GAAGAAGAAGAGAA
1 GAAG-AGAAGAGAA
59847 -AAGAGAAGAAGAA
1 GAAGAGAAG-AGAA
59860 GGAAGAGAAGAGAA
1 -GAAGAGAAGAGAA
* * *
59874 GGAAAAAAAAAGAA
1 -GAAGAGAAGAGAA
59888 GAAGAAGAAG
1 GAAG-AGAAG
59898 TTGTTCCGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
12 5 0.12
13 10 0.24
14 18 0.44
15 8 0.20
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (13 bp):
GAAGAGAAGAGAA
Found at i:68204 original size:38 final size:39
Alignment explanation
Indices: 68162--68256 Score: 126
Period size: 38 Copynumber: 2.5 Consensus size: 39
68152 TTACCAATTG
*
68162 CATGTTTAA-CAT-TCCTATTATTACTGTTGAACTGAATA
1 CATGTTTAAGCATGT-CTATTACTACTGTTGAACTGAATA
* *
68200 CATG-TTAAGCATGTCTATTGCTACTGTTGAATTGAATA
1 CATGTTTAAGCATGTCTATTACTACTGTTGAACTGAATA
68238 CATG-TTAAGCATGTCTATT
1 CATGTTTAAGCATGTCTATT
68257 GTTTTATATG
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
37 4 0.08
38 47 0.90
39 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (39 bp):
CATGTTTAAGCATGTCTATTACTACTGTTGAACTGAATA
Found at i:68257 original size:38 final size:38
Alignment explanation
Indices: 68183--68257 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 38
68173 TTCCTATTAT
68183 TACTGTTGAACTGAATACATGTTAAGCATGTCTATTGC
1 TACTGTTGAACTGAATACATGTTAAGCATGTCTATTGC
*
68221 TACTGTTGAATTGAATACATGTTAAGCATGTCTATTG
1 TACTGTTGAACTGAATACATGTTAAGCATGTCTATTG
68258 TTTTATATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (38 bp):
TACTGTTGAACTGAATACATGTTAAGCATGTCTATTGC
Found at i:71777 original size:33 final size:33
Alignment explanation
Indices: 71735--71833 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
71725 TCCCAACCAG
* *
71735 CTTCTGCCACCGCCCA-TTCTTCCTCCAAACCCA
1 CTTCTGCCACC-CCCACTACTCCCTCCAAACCCA
*
71768 CTTCTGCCACCTCCACTACTCCCTCCAAACCCA
1 CTTCTGCCACCCCCACTACTCCCTCCAAACCCA
* *
71801 CTTATGCCACCCCCACTGCTCCCTCCAAACCCA
1 CTTCTGCCACCCCCACTACTCCCTCCAAACCCA
71834 TTTCAGCCGC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
32 3 0.05
33 56 0.95
ACGTcount: A:0.20, C:0.54, G:0.05, T:0.21
Consensus pattern (33 bp):
CTTCTGCCACCCCCACTACTCCCTCCAAACCCA
Found at i:71864 original size:36 final size:36
Alignment explanation
Indices: 71824--71988 Score: 276
Period size: 36 Copynumber: 4.6 Consensus size: 36
71814 CACTGCTCCC
* * *
71824 TCCAAACCCATTTCAGCCGCCACCAGCTCCACTAGT
1 TCCAGACCCATTGCAGCCTCCACCAGCTCCACTAGT
*
71860 TCCAAACCCATTGCAGCCTCCACCAGCTCCACTAGT
1 TCCAGACCCATTGCAGCCTCCACCAGCTCCACTAGT
71896 TCCAGACCCATTGCAGCCTCCACCAGCTCCACTAGT
1 TCCAGACCCATTGCAGCCTCCACCAGCTCCACTAGT
* *
71932 TCCAGACCCCTTGCAGCCTCCACCAGCTCCACCAGT
1 TCCAGACCCATTGCAGCCTCCACCAGCTCCACTAGT
71968 TCCAGACCCATTGCAGCCTCC
1 TCCAGACCCATTGCAGCCTCC
71989 TCTAGCACCT
Statistics
Matches: 123, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 123 1.00
ACGTcount: A:0.22, C:0.46, G:0.13, T:0.19
Consensus pattern (36 bp):
TCCAGACCCATTGCAGCCTCCACCAGCTCCACTAGT
Found at i:72841 original size:26 final size:26
Alignment explanation
Indices: 72790--72848 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
72780 TACCCTTAGC
* *
72790 AAAAGTTTGACGATTTTACCTTTGAT
1 AAAATTTTGACGATTTTACCTGTGAT
*
72816 AAAATTTTGACGATTTT-TCTCGTGAT
1 AAAATTTTGACGATTTTACCT-GTGAT
72842 AAAATTT
1 AAAATTT
72849 CGGGGATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 2 0.07
26 27 0.93
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (26 bp):
AAAATTTTGACGATTTTACCTGTGAT
Found at i:76178 original size:32 final size:32
Alignment explanation
Indices: 76142--76203 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
76132 ATACAAGTTG
*
76142 TTCCAAACAATAATTATTCTAAAC-ATAGTTAT
1 TTCCAAACAACAA-TATTCTAAACAATAGTTAT
* *
76174 TTCCAAACCACCATATTCTAAACAATAGTT
1 TTCCAAACAACAATATTCTAAACAATAGTT
76204 GTTTTGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (32 bp):
TTCCAAACAACAATATTCTAAACAATAGTTAT
Found at i:77051 original size:16 final size:16
Alignment explanation
Indices: 77030--77081 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
77020 AATGTCATTA
77030 TTCTAAACTAGAGTTG
1 TTCTAAACTAGAGTTG
**
77046 TTCTAAACTTCAGTTG
1 TTCTAAACTAGAGTTG
*
77062 TTCTCAA-TAGGAGTTG
1 TTCTAAACTA-GAGTTG
77078 TTCT
1 TTCT
77082 CAAATAACAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
15 1 0.03
16 29 0.97
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (16 bp):
TTCTAAACTAGAGTTG
Found at i:79582 original size:13 final size:12
Alignment explanation
Indices: 79563--79615 Score: 54
Period size: 13 Copynumber: 4.3 Consensus size: 12
79553 ATTCCTGTAG
79563 AAAATTAAAGAA
1 AAAATTAAAGAA
*
79575 ACAAATTAAA-AT
1 A-AAATTAAAGAA
*
79587 AAAATAAAAGACA
1 AAAATTAAAGA-A
*
79600 AAAATTAAACAA
1 AAAATTAAAGAA
79612 AAAA
1 AAAA
79616 ATTGCAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 7 0.21
12 9 0.27
13 17 0.52
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (12 bp):
AAAATTAAAGAA
Found at i:79614 original size:24 final size:24
Alignment explanation
Indices: 79563--79608 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
79553 ATTCCTGTAG
*
79563 AAAATTAAAGAAACAAATTAAAAT
1 AAAATAAAAGAAACAAATTAAAAT
79587 AAAATAAAAGACAA-AAATTAAA
1 AAAATAAAAGA-AACAAATTAAA
79609 CAAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 18 0.90
25 2 0.10
ACGTcount: A:0.74, C:0.04, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAATAAAAGAAACAAATTAAAAT
Found at i:87779 original size:32 final size:31
Alignment explanation
Indices: 87704--87781 Score: 102
Period size: 32 Copynumber: 2.5 Consensus size: 31
87694 TTGGTTCAAT
* * *
87704 TTGGTACTCAAACTTGACACTTTTTCTTAAT
1 TTGGTACTTAAACTTGACACTTTTTATTAAG
* *
87735 TTGATACCTAAACTTGACACTTTTTTATTAAG
1 TTGGTACTTAAACTTGACAC-TTTTTATTAAG
87767 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
87782 TTTGGGGTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 17 0.44
32 22 0.56
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTATTAAG
Found at i:87829 original size:31 final size:31
Alignment explanation
Indices: 87645--87836 Score: 120
Period size: 31 Copynumber: 6.4 Consensus size: 31
87635 AATATAATAA
* * *
87645 TTGGTACCTGAACTAGACACGTTTTCCTAAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAAT
**
87676 TTGGTACCTAAACTT-----TTTTTGGTTCAAT
1 TTGGTACCTAAACTTGACACTTTTT-CCT-AAT
*
87704 TTGGTA-CTCAAACTTGACACTTTTTCTTAAT
1 TTGGTACCT-AAACTTGACACTTTTTCCTAAT
* ** *
87735 TTGATACCTAAACTTGACACTTTTTTATTAAG
1 TTGGTACCTAAACTTGACAC-TTTTTCCTAAT
* *
87767 TTGGTACTTAAACTT-----TTTGGGGTCC-AAT
1 TTGGTACCTAAACTTGACACTTT---TTCCTAAT
*
87795 TTGGTACCTAAACTTGACTCTTTTTCCTAAT
1 TTGGTACCTAAACTTGACACTTTTTCCTAAT
87826 TTGGTACCTAA
1 TTGGTACCTAA
87837 TCTTTTTTAA
Statistics
Matches: 125, Mismatches: 17, Indels: 38
0.69 0.09 0.21
Matches are distributed among these distances:
26 7 0.06
27 3 0.02
28 31 0.25
29 1 0.01
30 3 0.02
31 46 0.37
32 26 0.21
33 8 0.06
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (31 bp):
TTGGTACCTAAACTTGACACTTTTTCCTAAT
Found at i:87844 original size:60 final size:60
Alignment explanation
Indices: 87732--87843 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 60
87722 ACTTTTTCTT
* *
87732 AATTTGATACCTAAACTTGACACTTTTTTATTAAGTTGGTACTTAAACTTTTTGGGGTCC
1 AATTTGATACCTAAACTTGACACTTTTTTACTAAGTTGGTACCTAAACTTTTTGGGGTCC
* * * * *
87792 AATTTGGTACCTAAACTTGACTC-TTTTTCCTAATTTGGTACCTAATCTTTTT
1 AATTTGATACCTAAACTTGACACTTTTTTACTAAGTTGGTACCTAAACTTTTT
87844 TAATCTTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 24 0.53
60 21 0.47
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (60 bp):
AATTTGATACCTAAACTTGACACTTTTTTACTAAGTTGGTACCTAAACTTTTTGGGGTCC
Found at i:87855 original size:59 final size:61
Alignment explanation
Indices: 87728--87856 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 61
87718 TGACACTTTT
* * **
87728 TCTTAATTTGATACCTAAACTTGACACTTTTTTATTAAGTTGGTACTTAAACTTTTTGGGG
1 TCTTAATTTGATACCTAAACTTGACACTTTTTTACTAAGTTGGTACCTAAACTTTTTGGAA
* * * * * * *
87789 TC-CAATTTGGTACCTAAACTTGACTC-TTTTTCCTAATTTGGTACCTAATCTTTTT-TAA
1 TCTTAATTTGATACCTAAACTTGACACTTTTTTACTAAGTTGGTACCTAAACTTTTTGGAA
87847 TCTTAATTTG
1 TCTTAATTTG
87857 TTAAGCATAG
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
58 2 0.04
59 30 0.55
60 21 0.38
61 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (61 bp):
TCTTAATTTGATACCTAAACTTGACACTTTTTTACTAAGTTGGTACCTAAACTTTTTGGAA
Found at i:88080 original size:58 final size:59
Alignment explanation
Indices: 88002--88148 Score: 201
Period size: 59 Copynumber: 2.5 Consensus size: 59
87992 ATTGAATCTA
** *
88002 AAAAAAAACTTAGGTACCAAATTAGGAAAAA-TGCCAAGTTC-TGGTACCAAATTGGGTTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTACCAAGTTCAT-GTACCAAATTGGG-TC
*
88061 -AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTATCAAGTTCATGTACCAAATTGGGTC
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTACCAAGTTCATGTACCAAATTGGGTC
* *
88119 AAAAAAAGTTCATGTACCAAATTAGGAAAA
1 AAAAAAAGTTTAGGTACCAAATTAGGAAAA
88149 GGTGTCAAAT
Statistics
Matches: 79, Mismatches: 6, Indels: 6
0.87 0.07 0.07
Matches are distributed among these distances:
58 30 0.38
59 48 0.61
60 1 0.01
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAAAAAGTTTAGGTACCAAATTAGGAAAAAGTACCAAGTTCATGTACCAAATTGGGTC
Found at i:88108 original size:31 final size:27
Alignment explanation
Indices: 88002--88148 Score: 100
Period size: 28 Copynumber: 5.1 Consensus size: 27
87992 ATTGAATCTA
* *
88002 AAAAAAAACTT-AGGTACCAAATTAGG
1 AAAAAAAAGTTCATGTACCAAATTAGG
* *
88028 AAAAATGCCAAGTTC-TGGTACCAAATTGGG
1 AAAAA---AAAGTTCAT-GTACCAAATTAGG
** * *
88058 TTCAAAAAAGTTTAGGTACCAAATTAGG
1 -AAAAAAAAGTTCATGTACCAAATTAGG
*
88086 AAAAAGTATCAAGTTCATGTACCAAATTGGG
1 AAAAA--A--AAGTTCATGTACCAAATTAGG
*
88117 TCAAAAAAAGTTCATGTACCAAATTAGG
1 -AAAAAAAAGTTCATGTACCAAATTAGG
88145 AAAA
1 AAAA
88149 GGTGTCAAAT
Statistics
Matches: 91, Mismatches: 18, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
26 5 0.05
27 6 0.07
28 37 0.41
29 5 0.05
30 13 0.14
31 21 0.23
32 4 0.04
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.24
Consensus pattern (27 bp):
AAAAAAAAGTTCATGTACCAAATTAGG
Found at i:88109 original size:59 final size:58
Alignment explanation
Indices: 87984--88148 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 58
87974 AATAAATTTA
** ** *
87984 GGTACCAAATTGAATCTAAAAAAAAACTTAGGTACCAAATTAGGAAAAATGCCAAGTTCT
1 GGTACCAAATTGGGTC--AAAAAAAGTTTAGGTACCAAATTAGGAAAAATACCAAGTTCT
*
88044 GGTACCAAATTGGGTTC-AAAAAAGTTTAGGTACCAAATTAGGAAAAAGTATCAAGTTCAT
1 GGTACCAAATTGGG-TCAAAAAAAGTTTAGGTACCAAATTAGGAAAAA-TACCAAGTTC-T
* *
88104 -GTACCAAATTGGGTCAAAAAAAGTTCATGTACCAAATTAGGAAAA
1 GGTACCAAATTGGGTCAAAAAAAGTTTAGGTACCAAATTAGGAAAA
88149 GGTGTCAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
58 30 0.32
59 48 0.52
60 13 0.14
61 2 0.02
ACGTcount: A:0.45, C:0.13, G:0.18, T:0.24
Consensus pattern (58 bp):
GGTACCAAATTGGGTCAAAAAAAGTTTAGGTACCAAATTAGGAAAAATACCAAGTTCT
Found at i:93643 original size:19 final size:19
Alignment explanation
Indices: 93619--93659 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
93609 ATTTTTAAAG
* *
93619 ATTCTAATTAGGATATATT
1 ATTCTAATTAAGAGATATT
*
93638 ATTCTATTTAAGAGATATT
1 ATTCTAATTAAGAGATATT
93657 ATT
1 ATT
93660 TCCTTAGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.49
Consensus pattern (19 bp):
ATTCTAATTAAGAGATATT
Found at i:95828 original size:52 final size:52
Alignment explanation
Indices: 95750--95979 Score: 322
Period size: 52 Copynumber: 4.4 Consensus size: 52
95740 AAGGTCTGAA
*
95750 GACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGAGGCCCGAT
1 GACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGCCCGAT
* *
95802 GACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATTATAAGGTCCC-AT
1 GACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGG-CCCGAT
* * *
95854 GACTATGTGTCATCGTGAGTATATGAATTCTTTATGAAAATTATGAGGTCCGAT
1 GACTATGTGTCATCGTGAGTATATGAATCCTTTATG--GATTATGAGGCCCGAT
* * * *
95908 GACTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTAAGAGGTCCGAT
1 GACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGCCCGAT
95960 GACTA--TGTCATCGTGAGTAT
1 GACTATGTGTCATCGTGAGTAT
95980 TAAATGAAAT
Statistics
Matches: 161, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
50 15 0.09
52 98 0.61
53 5 0.03
54 43 0.27
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
GACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTATGAGGCCCGAT
Found at i:95939 original size:106 final size:104
Alignment explanation
Indices: 95750--95979 Score: 340
Period size: 106 Copynumber: 2.2 Consensus size: 104
95740 AAGGTCTGAA
* *
95750 GACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTATGAGGCCCGATGACTATGTGTCAT
1 GACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGCCCGATGACTATGTGTCAT
* *
95815 TGTGAGTATATGAATCCTTTATGGATTATA-AGGTCCCAT
66 CGTGAGTATATGAATCCTTTACGGATTA-AGAGGTCCCAT
* *
95854 GACTATGTGTCATCGTGAGTATATGAATTCTTTATGAAAATTATGAGGTCCGATGACTATGTGTC
1 GACTATGTGTCATCGTGAGTATATGAATCCTTTATG--AATTATGAGGCCCGATGACTATGTGTC
* *
95919 ATCGTGAGTATATGATTCCTTTACGGATTAAGAGGTCCGAT
64 ATCGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCCAT
95960 GACTA--TGTCATCGTGAGTAT
1 GACTATGTGTCATCGTGAGTAT
95980 TAAATGAAAT
Statistics
Matches: 115, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
104 49 0.43
105 1 0.01
106 65 0.57
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (104 bp):
GACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTATGAGGCCCGATGACTATGTGTCAT
CGTGAGTATATGAATCCTTTACGGATTAAGAGGTCCCAT
Found at i:100960 original size:13 final size:13
Alignment explanation
Indices: 100942--100975 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
100932 TTCCTGGTAA
*
100942 GAAATTTCGGGAT
1 GAAATTTCGGAAT
100955 GAAATTTCGGAAT
1 GAAATTTCGGAAT
100968 GAAATTTC
1 GAAATTTC
100976 CCTAAGGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (13 bp):
GAAATTTCGGAAT
Found at i:101799 original size:20 final size:21
Alignment explanation
Indices: 101774--101812 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
101764 GCTGGTATTG
101774 ATTTTGT-AAAAAAATGGGTA
1 ATTTTGTAAAAAAAATGGGTA
101794 ATTTTGTAAAAAAAATGGG
1 ATTTTGTAAAAAAAATGGG
101813 GGTGTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.21, T:0.33
Consensus pattern (21 bp):
ATTTTGTAAAAAAAATGGGTA
Found at i:102262 original size:52 final size:52
Alignment explanation
Indices: 102187--102477 Score: 359
Period size: 52 Copynumber: 5.5 Consensus size: 52
102177 AAAAGGTCTA
* *
102187 ATGACTATGTGTCATCGTAAGTATATGAATCCTTTAAGGATTATGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
*
102239 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGTGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
* * * * **
102291 ATGACTATATGTCATCATGAGTATATGAATTCTTTACGGATTATAAGGTCTA
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
* * *
102343 ATGACTATGTGTCATCGTGAGTATATGATTCCTTTATGGATTAAGAGGTCCG
1 ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
* * *
102395 ATGACTATGTGTCATCGTGTGTATTAAATGAAATGAATCCATTACGGATTA-AAGGTCCG
1 ATGACTATGTGTCATC--GTG-AGT--AT---ATGAATCCTTTACGGATTATGAGGTCCG
*
102454 ATGACTCTGTGTCATCGTGAGTAT
1 ATGACTATGTGTCATCGTGAGTAT
102478 CAAATGCAAA
Statistics
Matches: 205, Mismatches: 26, Indels: 14
0.84 0.11 0.06
Matches are distributed among these distances:
52 153 0.75
54 5 0.02
55 2 0.01
56 2 0.01
57 5 0.02
59 22 0.11
60 16 0.08
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
ATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCG
Found at i:104443 original size:13 final size:12
Alignment explanation
Indices: 104424--104453 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
104414 TTAATATATT
104424 TATTTATTACTG
1 TATTTATTACTG
104436 TCATTTATTACTG
1 T-ATTTATTACTG
104449 TATTT
1 TATTT
104454 TTTTCTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.23, C:0.10, G:0.07, T:0.60
Consensus pattern (12 bp):
TATTTATTACTG
Found at i:105399 original size:59 final size:60
Alignment explanation
Indices: 105274--105445 Score: 172
Period size: 59 Copynumber: 2.9 Consensus size: 60
105264 TGAAAAAAAG
* *
105274 GACCCTTAAACTTTTTAAAAATTATATTTTGA-CCCTCAAACTTCTTCAAAATTAAAATTT
1 GACCC-TAAACTTTTTAAAAATTATATTTTAACCCCTCAAACTTCTCCAAAATTAAAATTT
* * *
105334 GACCCTAAACTTTTTAAAAATTACATCTTTAACCCCT-AAACTTC-CCAAAATTATATTTT
1 GACCCTAAACTTTTTAAAAATTATAT-TTTAACCCCTCAAACTTCTCCAAAATTAAAATTT
** * ** * * * *
105393 TTCCCTAATCTTTCCAAAACTTATATTTTAACCCC-CGAACTTTTACAAAATTA
1 GACCCTAAACTTTTTAAAAATTATATTTTAACCCCTCAAACTTCTCCAAAATTA
105446 TGTTTTAACC
Statistics
Matches: 93, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
58 14 0.15
59 59 0.63
60 16 0.17
61 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (60 bp):
GACCCTAAACTTTTTAAAAATTATATTTTAACCCCTCAAACTTCTCCAAAATTAAAATTT
Found at i:105409 original size:28 final size:29
Alignment explanation
Indices: 105367--105421 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
105357 CATCTTTAAC
105367 CCCTAAACTTCCCAAAA-TTATATTTTTT
1 CCCTAAACTTCCCAAAACTTATATTTTTT
* *
105395 CCCTAATCTTTCCAAAACTTATATTTT
1 CCCTAAACTTCCCAAAACTTATATTTT
105422 AACCCCCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.31, C:0.25, G:0.00, T:0.44
Consensus pattern (29 bp):
CCCTAAACTTCCCAAAACTTATATTTTTT
Found at i:105472 original size:30 final size:30
Alignment explanation
Indices: 105291--105472 Score: 140
Period size: 30 Copynumber: 6.1 Consensus size: 30
105281 AAACTTTTTA
* *
105291 AAAATTATATTTTGA-CCCTCAAACTTCTTC
1 AAAATTATATTTTAACCCCT-AAACTTCTCC
* * * * **
105321 AAAATTAAAATTTGA-CCCTAAACTTTTTA
1 AAAATTATATTTTAACCCCTAAACTTCTCC
*
105350 AAAATTACATCTTTAACCCCTAAACTTC-CC
1 AAAATTATAT-TTTAACCCCTAAACTTCTCC
** *
105380 AAAATTATATTTT-TTCCCTAATCTT-TCC
1 AAAATTATATTTTAACCCCTAAACTTCTCC
** * *
105408 AAAACTTATATTTTAACCCCCGAACTTTTAC
1 AAAA-TTATATTTTAACCCCTAAACTTCTCC
* *
105439 AAAATTATGTTTTAACCCCTAAAATTCTCC
1 AAAATTATATTTTAACCCCTAAACTTCTCC
105469 AAAA
1 AAAA
105473 CTTCATTTTT
Statistics
Matches: 120, Mismatches: 26, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
28 15 0.12
29 28 0.23
30 61 0.51
31 16 0.13
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTATATTTTAACCCCTAAACTTCTCC
Found at i:109648 original size:15 final size:15
Alignment explanation
Indices: 109628--109662 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
109618 ACCCTGAAGA
109628 TAATGTCACAAATTT
1 TAATGTCACAAATTT
*
109643 TAATGTCCCAAATTT
1 TAATGTCACAAATTT
*
109658 CAATG
1 TAATG
109663 AAATGATGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (15 bp):
TAATGTCACAAATTT
Found at i:116442 original size:39 final size:39
Alignment explanation
Indices: 116390--116508 Score: 113
Period size: 38 Copynumber: 3.1 Consensus size: 39
116380 TATTTCACCT
*
116390 AAAAAATA-ATCGAGATG-AACCCGTAAAGGGCGTCTCGA
1 AAAAAAGAGATCGAGATGAAACCCGTAAAGGGCGTCT-GA
*
116428 AAAAAAGAGATCGAGATGAAAACCCATAAAAGGG-GTCT-A
1 AAAAAAGAGATCGAGATG-AAACCCGT-AAAGGGCGTCTGA
* * *
116467 AAAAAAG-GATCGAAATGAAAACTCGCAAAGGGCGTCTTGA
1 AAAAAAGAGATCGAGATG-AAACCCGTAAAGGGCGTC-TGA
116507 AA
1 AA
116509 CCAAAGGGAT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
37 6 0.09
38 25 0.37
39 18 0.26
40 3 0.04
41 10 0.15
42 6 0.09
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.14
Consensus pattern (39 bp):
AAAAAAGAGATCGAGATGAAACCCGTAAAGGGCGTCTGA
Found at i:117724 original size:85 final size:85
Alignment explanation
Indices: 117579--117746 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 85
117569 CAAACTCCCA
* * * *
117579 CCTTCCTGATGAGAAACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTTTTGATGAGTTAC
1 CCTTCCTGATGAGAAACAAAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCTTGATGAGATAC
*
117644 AGAGAAGTAGATCAAATCTG
66 AGAGAAGTAGACCAAATCTG
* * * * *
117664 CCTTCCTGATGA-AATACAAAGAATTGGATTAAATCAATGAAGCGATTATCTTCCTT-ATGAGAT
1 CCTTCCTGATGAGAA-ACAAAGAAGTGGATCAAAGCAATAAAGCGATCATCTT-CTTGATGAGAT
117727 ACAGAGAAGTAGACCAAATC
64 ACAGAGAAGTAGACCAAATC
117747 AATGAAACAA
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
84 2 0.03
85 67 0.94
86 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (85 bp):
CCTTCCTGATGAGAAACAAAGAAGTGGATCAAAGCAATAAAGCGATCATCTTCTTGATGAGATAC
AGAGAAGTAGACCAAATCTG
Found at i:117888 original size:37 final size:37
Alignment explanation
Indices: 117838--117908 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
117828 AGGCGGTCAT
*
117838 CTTCCTAATGAGATACAGAGAAGTGGATCAAATCTGC
1 CTTCCTAATGAGATACAAAGAAGTGGATCAAATCTGC
* *
117875 CTTCCTGATGAGATACAAAGAAGTGGATTAAATC
1 CTTCCTAATGAGATACAAAGAAGTGGATCAAATC
117909 AATGAAGCGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.37, C:0.17, G:0.21, T:0.25
Consensus pattern (37 bp):
CTTCCTAATGAGATACAAAGAAGTGGATCAAATCTGC
Found at i:117934 original size:85 final size:85
Alignment explanation
Indices: 117790--117956 Score: 246
Period size: 85 Copynumber: 2.0 Consensus size: 85
117780 AACCCCCCAT
* * *
117790 CTTCCTGGTAAGATACAGAGAAGTGGGTCAAAGCAATAAGGCGGTCATCTTCCTAATGAGATACA
1 CTTCCTGATAAGATACAAAGAAGTGGATCAAAGCAATAAGGCGGTCATCTTCCTAATGAGATACA
*
117855 GAGAAGTGGATCAAATCTGC
66 GAGAAGTAGATCAAATCTGC
* * * *
117875 CTTCCTGATGAGATACAAAGAAGTGGATTAAATCAATGAA-GCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATAAGATACAAAGAAGTGGATCAAAGCAAT-AAGGCGGTCATCTTCCTAATGAGATAC
117939 AGAGAAGTAGATCAAATC
65 AGAGAAGTAGATCAAATC
117957 AATGAAGCAA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
85 71 0.97
86 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.23
Consensus pattern (85 bp):
CTTCCTGATAAGATACAAAGAAGTGGATCAAAGCAATAAGGCGGTCATCTTCCTAATGAGATACA
GAGAAGTAGATCAAATCTGC
Found at i:118153 original size:85 final size:84
Alignment explanation
Indices: 117998--118164 Score: 217
Period size: 85 Copynumber: 2.0 Consensus size: 84
117988 TAAACCCCCA
* * * *
117998 TCTTCTTGATAGATATAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTTCTGATAAGATACA
1 TCTTCCTGATAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATACA
*
118063 AAGAAGTGGACCAAATCCG
66 AAGAAGTAGACCAAATCCG
* * * * * *
118082 TCTTCCTGATGAGATACAGAGACGTGGATTAAATCAATGAAGCGGTCATCTTCCTGATGAGATAT
1 TCTTCCTGAT-AGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATAC
*
118147 AGAGAAGTAGACCAAATC
65 AAAGAAGTAGACCAAATC
118165 AATGAAGAAA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
84 9 0.13
85 61 0.87
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (84 bp):
TCTTCCTGATAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTCCTGATAAGATACA
AAGAAGTAGACCAAATCCG
Found at i:118360 original size:209 final size:209
Alignment explanation
Indices: 117500--118372 Score: 1126
Period size: 209 Copynumber: 4.2 Consensus size: 209
117490 ACTTCAAACG
* * ** * * * ***
117500 TCATCTTCCTGATGAGATACAAAGAAGTAAACCAAAAGAATGAAGCAAATCCCAATGTGAACAAA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATGTGAGTGAA
* * * *
117565 ACTTCAAACTCCCACCTTCCTGATGAGAAACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCT
66 ACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCT
* * * * * * *
117630 TTTTGATGAGTTACAGAGAAGTAGATCAAATCTGCCTTCCTGATGAAATACAAAGAATTGGATTA
131 TCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGATTA
117695 AATCAATGAAGCGA
196 AATCAATGAAGCGA
* * *
117709 TTATCTTCCTTATGAGATACAGAGAAGTAGACCAAATCAATGAA-ACAAAACTCAATGTGAGTGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGA-AAAGCTCAATGTGAGTGA
* * *
117773 AACTTCAAACCCCCCATCTTCCTGGTAAGATACAGAGAAGTGGGTCAAAGCAATAAGGCGGTCAT
65 AACTTCAAA-CCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCAT
* * * *
117838 CTTCCTAATGAGATACAGAGAAGTGGATCAAATCTGCCTTCCTGATGAGATACAAAGAAGTGGAT
129 CTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGAT
*
117903 TAAATCAATGAAGCGG
194 TAAATCAATGAAGCGA
* *
117919 TCATCTTCCTGATGAGATACAGAGAAGTAGATCAAATCAATGAAGCAAAGCGT-AATGTGAGTGA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGC-TCAATGTGAGTGA
* * *
117983 AACTTTAAACCCCCATCTTCTTGAT-AGATATAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATC
65 AACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATC
* * * * *
118047 TT-TCTGATAAGATACAAAGAAGTGGACCAAATCCGTCTTCCTGATGAGATACAGAGACGTGGAT
130 TTCT-TGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGAT
*
118111 TAAATCAATGAAGCGG
194 TAAATCAATGAAGCGA
*
118127 TCATCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATGTGAGTGAA
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATGTGAGTGAA
* * * * *
118192 ACTTCAAACCCCCATCTTTCTGATGAGATACAAAGGAGTGGGTCAAAGCAATGAAGCAGTCATCT
66 ACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCT
** * * *
118257 TCTTGATGAGATACAGAGAAGTGGACCAAATCCGTTTTCCTGATGAGATATAGAGAAGTGGATCA
131 TCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGAT-T
* *
118322 AAAT-AATAAAACGA
195 AAATCAATGAAGCGA
** * *
118336 TCATCTTCCCAATGAGACATAGAGAAGTAGACCAAAT
1 TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAAT
118373 TCATCTTCCT
Statistics
Matches: 586, Mismatches: 69, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
207 1 0.00
208 188 0.32
209 206 0.35
210 190 0.32
211 1 0.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.23
Consensus pattern (209 bp):
TCATCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGAAAAGCTCAATGTGAGTGAA
ACTTCAAACCCCCATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCT
TCTTGATGAGATACAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGATACAAAGAAGTGGATTA
AATCAATGAAGCGA
Found at i:118499 original size:85 final size:85
Alignment explanation
Indices: 118211--118504 Score: 345
Period size: 85 Copynumber: 3.5 Consensus size: 85
118201 CCCCATCTTT
* * * * *
118211 CTGATGAGATACAAAGGAGTGGGTCAAAGCAATGAAGCAGTCATCTTCTTGATGAGATACAGAGA
1 CTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAGAGA
118276 AGTGGACCAAATCCGTTTTC
66 AGTGGACCAAATCCGTTTTC
* * * * * * ** * *
118296 CTGATGAGATATAGAGAAGTGGATCAAAATAATAAAACGATCATCTTCCCAATGAGACATAGAGA
1 CTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAGAGA
* * * *
118361 AGTAGACCAAATTCATCTTC
66 AGTGGACCAAATCCGTTTTC
* * *
118381 CTGATGAGATATAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCCTGATGAGATACAGAGA
1 CTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAGAGA
*
118446 AATGGACCAAATCCGTTTTC
66 AGTGGACCAAATCCGTTTTC
* * * *
118466 CTAATGAGATACAAAGAAGTAGACCAAACCAATGAAGCG
1 CTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCG
118505 AAGCTCAACG
Statistics
Matches: 169, Mismatches: 40, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
85 169 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (85 bp):
CTGATGAGATACAAAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCCTGATGAGATACAGAGA
AGTGGACCAAATCCGTTTTC
Found at i:120460 original size:28 final size:28
Alignment explanation
Indices: 120406--120511 Score: 122
Period size: 28 Copynumber: 3.6 Consensus size: 28
120396 ACCATACAGT
* *
120406 TTCCAAAAATTACATATTTGACTCCTAAAC
1 TTCCAAAAATTATATTTTTG-C-CCTAAAC
*
120436 TTCCCAAAATTATATTTTTGCCCTAAAC
1 TTCCAAAAATTATATTTTTGCCCTAAAC
* * *
120464 TTCCCAAAATTATATTTTTGCCCCAAATT
1 TTCCAAAAATTATATTTTTGCCCTAAA-C
120493 TTCCAAAAACTTATATTTT
1 TTCCAAAAA-TTATATTTT
120512 AACCCCGAAC
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 33 0.49
29 9 0.13
30 26 0.38
ACGTcount: A:0.35, C:0.23, G:0.03, T:0.40
Consensus pattern (28 bp):
TTCCAAAAATTATATTTTTGCCCTAAAC
Found at i:120529 original size:31 final size:29
Alignment explanation
Indices: 120405--120540 Score: 89
Period size: 28 Copynumber: 4.7 Consensus size: 29
120395 GACCATACAG
* * *
120405 TTTCCAAAAATTACATATTTGACTCCTAAA-
1 TTTCCAAAAATTATAT-TTTAAC-CCCAAAT
* * ** *
120435 CTTCCCAAAATTATATTTTTGCCCTAAA-
1 TTTCCAAAAATTATATTTTAACCCCAAAT
* * **
120463 CTTCCCAAAATTATATTTTTGCCCCAAAT
1 TTTCCAAAAATTATATTTTAACCCCAAAT
*
120492 TTTCCAAAAACTTATATTTTAACCCCGAACT
1 TTTCCAAAAA-TTATATTTTAACCCC-AAAT
*
120523 TTTCC-AAAATTATTTTTT
1 TTTCCAAAAATTATATTTT
120541 GACTTCAGAA
Statistics
Matches: 91, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
28 33 0.36
29 20 0.22
30 30 0.33
31 8 0.09
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
TTTCCAAAAATTATATTTTAACCCCAAAT
Found at i:123615 original size:18 final size:18
Alignment explanation
Indices: 123592--123641 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
123582 AAAATGCTGG
** *
123592 AAATGATGTTAACGTTTT
1 AAATGATGTTAACACTTC
123610 AAATGATGTTAACACTTC
1 AAATGATGTTAACACTTC
123628 AAATGATGTTAACA
1 AAATGATGTTAACA
123642 TTGATGGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (18 bp):
AAATGATGTTAACACTTC
Found at i:124167 original size:72 final size:72
Alignment explanation
Indices: 124075--124270 Score: 365
Period size: 72 Copynumber: 2.7 Consensus size: 72
124065 CAATGCTAAA
* *
124075 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTAAGTTTGGTTTTTGGATATTGAATTTATGTTCTACTAATTTAT
124140 GTGTAAT
66 GTGTAAT
124147 CTAGTTTTATCAATAGTTGTTTAAGTTTGGTTTTTGGATATTGAATTTATGTTCTACTAATTTAT
1 CTAGTTTTATCAATAGTTGTTTAAGTTTGGTTTTTGGATATTGAATTTATGTTCTACTAATTTAT
124212 GTGTAAT
66 GTGTAAT
*
124219 CTAGTTTTATCAATAGTTGTTTAGGTTTGGTTTTTGGATATTGAATTTATGT
1 CTAGTTTTATCAATAGTTGTTTAAGTTTGGTTTTTGGATATTGAATTTATGT
124271 GTAATTTAGT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 121 1.00
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTAAGTTTGGTTTTTGGATATTGAATTTATGTTCTACTAATTTAT
GTGTAAT
Found at i:124299 original size:31 final size:31
Alignment explanation
Indices: 124207--124308 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 31
124197 GTTCTACTAA
*
124207 TTTATGTGTAATCTAGTTTTATCAATAGTTG
1 TTTATGTGTAATTTAGTTTTATCAATAGTTG
* **
124238 TTTA-G-G---TTTGGTTTT-TGGATA-TTG
1 TTTATGTGTAATTTAGTTTTATCAATAGTTG
124262 AATTTATGTGTAATTTAGTTTTATCAATAGTTG
1 --TTTATGTGTAATTTAGTTTTATCAATAGTTG
* *
124295 TTTATATTTAATTT
1 TTTATGTGTAATTT
124309 TGGATATAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 18
0.66 0.11 0.22
Matches are distributed among these distances:
24 3 0.06
25 4 0.08
26 11 0.21
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 24 0.45
32 4 0.08
33 3 0.06
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.56
Consensus pattern (31 bp):
TTTATGTGTAATTTAGTTTTATCAATAGTTG
Found at i:136804 original size:13 final size:12
Alignment explanation
Indices: 136780--136813 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
136770 TGACAAACAA
136780 TATTTCTTTTTTT
1 TATTT-TTTTTTT
*
136793 TATTTTTATTTT
1 TATTTTTTTTTT
136805 TATTTTTTT
1 TATTTTTTT
136814 GATAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (12 bp):
TATTTTTTTTTT
Found at i:139983 original size:2 final size:2
Alignment explanation
Indices: 139978--140008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
139968 TATGTGTGTG
139978 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 T
140009 TTGTTACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140191 original size:2 final size:2
Alignment explanation
Indices: 140184--140208 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
140174 ATACTAACCT
140184 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 T
140209 GATTTAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:141100 original size:29 final size:29
Alignment explanation
Indices: 141044--141119 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
141034 TAAATAAGTC
* *
141044 AAATATGCCAATTTTGAAAATTAATTAGGC
1 AAATAGGCCAATTTT-AAAATTAATTAGGA
** *
141074 ATTTAGGCCAATTTTAAAATTATTTAGGA
1 AAATAGGCCAATTTTAAAATTAATTAGGA
*
141103 AAATAGGCCGATTTTAA
1 AAATAGGCCAATTTTAA
141120 GGGAAAGCGC
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 26 0.68
30 12 0.32
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (29 bp):
AAATAGGCCAATTTTAAAATTAATTAGGA
Found at i:150719 original size:28 final size:28
Alignment explanation
Indices: 150687--150770 Score: 123
Period size: 28 Copynumber: 3.0 Consensus size: 28
150677 TTGGTAACAT
*
150687 GCATGACTTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
* * *
150715 GCATGACCTTTGAGTCAAAAGGAAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
*
150743 GCATGACCTTTGGGTCAACAGAGAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
150771 ATCGAATGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (28 bp):
GCATGACCTTTGGGTCAACAGGGAGTAA
Found at i:151514 original size:21 final size:21
Alignment explanation
Indices: 151490--151543 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
151480 AGCTTCACTT
*
151490 GTATCGGTAAAACTGTCATAA
1 GTATCGGTAAAACTATCATAA
* *
151511 GTATCGATAAAACTATCATAG
1 GTATCGGTAAAACTATCATAA
151532 GTATCGGTAAAA
1 GTATCGGTAAAA
151544 GTCTGCATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.28
Consensus pattern (21 bp):
GTATCGGTAAAACTATCATAA
Found at i:158339 original size:18 final size:18
Alignment explanation
Indices: 158316--158365 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
158306 AGACTCAAGC
158316 TCCTTTGTTTGCTTTTCT
1 TCCTTTGTTTGCTTTTCT
* *
158334 TCCTTTATTTACTTTTCT
1 TCCTTTGTTTGCTTTTCT
**
158352 TGTTTTGTTTGCTT
1 TCCTTTGTTTGCTT
158366 GGGGACAAGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.04, C:0.18, G:0.10, T:0.68
Consensus pattern (18 bp):
TCCTTTGTTTGCTTTTCT
Found at i:165202 original size:62 final size:62
Alignment explanation
Indices: 165072--165212 Score: 198
Period size: 62 Copynumber: 2.3 Consensus size: 62
165062 TAAAAAATTT
* * * *
165072 TGAATTGTTCAATGACTTAAATGAGAACTTTTGAATAGTTCAATGACTTAAATGAGAACTTT
1 TGAATAGTTCAATGACTTAAATGAGAACTTTTGAATAGTTCAATGACTAAAATGAAAACTTC
165134 TGAATAGTTCAATGACTTAAATGAGAACTTTTGAATAGTTCAATGACTAAAAT-ATAAACTTAC
1 TGAATAGTTCAATGACTTAAATGAGAACTTTTGAATAGTTCAATGACTAAAATGA-AAACTT-C
*
165197 T-AATAGTT-ATTGACTT
1 TGAATAGTTCAATGACTT
165213 TGGGTGTAAT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
61 8 0.11
62 63 0.88
63 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (62 bp):
TGAATAGTTCAATGACTTAAATGAGAACTTTTGAATAGTTCAATGACTAAAATGAAAACTTC
Found at i:165204 original size:31 final size:31
Alignment explanation
Indices: 165055--165186 Score: 219
Period size: 31 Copynumber: 4.3 Consensus size: 31
165045 CAAACTAGTA
* * * *
165055 ACTTAAATAAAAAATTTTGAATTGTTCAATG
1 ACTTAAATGAGAACTTTTGAATAGTTCAATG
165086 ACTTAAATGAGAACTTTTGAATAGTTCAATG
1 ACTTAAATGAGAACTTTTGAATAGTTCAATG
165117 ACTTAAATGAGAACTTTTGAATAGTTCAATG
1 ACTTAAATGAGAACTTTTGAATAGTTCAATG
165148 ACTTAAATGAGAACTTTTGAATAGTTCAATG
1 ACTTAAATGAGAACTTTTGAATAGTTCAATG
*
165179 ACTAAAAT
1 ACTTAAAT
165187 ATAAACTTAC
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 96 1.00
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.36
Consensus pattern (31 bp):
ACTTAAATGAGAACTTTTGAATAGTTCAATG
Found at i:173686 original size:20 final size:20
Alignment explanation
Indices: 173663--173705 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
173653 GATTTTCTTT
173663 TGCATCTAGAAGATTTCTAG
1 TGCATCTAGAAGATTTCTAG
173683 TGCATCTAGAAGATTTCTAG
1 TGCATCTAGAAGATTTCTAG
173703 TGC
1 TGC
173706 TGACGTAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (20 bp):
TGCATCTAGAAGATTTCTAG
Found at i:185274 original size:106 final size:106
Alignment explanation
Indices: 185128--185339 Score: 345
Period size: 106 Copynumber: 2.0 Consensus size: 106
185118 ACTAATCTGG
* *
185128 CTCGGTTGAGTTATAAATTGCTTTATGCATGTGATTGGTAACTAATTTTAAACTCTTCGAACTTA
1 CTCGGTTGAGTTATAAATTGATTTATGCATGTGATTGGTAACTAATTTTAAACTCTTCAAACTTA
* * * *
185193 CTAAGCTATGAAGC-TTACTAGTGATATCATTGTTGTTTTGT
66 CTAAGATATGAA-CTTTACCAGTGATATCATTGCTATTTTGT
185234 CTCGGTTGAGTTATAAATTGATTTATGCATGTGATTGGTAACTAATTTTAAACTCTTCAAACTTA
1 CTCGGTTGAGTTATAAATTGATTTATGCATGTGATTGGTAACTAATTTTAAACTCTTCAAACTTA
*
185299 CTAAGATATGAACTTTACCAGTGATATTATTGCTATTTTGT
66 CTAAGATATGAACTTTACCAGTGATATCATTGCTATTTTGT
185340 AGATTTTATT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
105 1 0.01
106 97 0.99
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (106 bp):
CTCGGTTGAGTTATAAATTGATTTATGCATGTGATTGGTAACTAATTTTAAACTCTTCAAACTTA
CTAAGATATGAACTTTACCAGTGATATCATTGCTATTTTGT
Found at i:191436 original size:11 final size:11
Alignment explanation
Indices: 191420--191451 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
191410 CATAAAAATG
191420 TATGACATCAC
1 TATGACATCAC
191431 TATGACATCAC
1 TATGACATCAC
*
191442 TTTGACATCA
1 TATGACATCA
191452 TTTATGCCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.31
Consensus pattern (11 bp):
TATGACATCAC
Found at i:192468 original size:29 final size:29
Alignment explanation
Indices: 192419--192476 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
192409 CCACTTCTCT
* *
192419 CAGATTGGTACCTATAATTTTTTTTGTCC
1 CAGATTGGTACCCATAATTTTTTTCGTCC
192448 CAGATTGGTACCCA-AACTTTTTTTCGTCC
1 CAGATTGGTACCCATAA-TTTTTTTCGTCC
192477 ACTGGTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 24 0.92
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (29 bp):
CAGATTGGTACCCATAATTTTTTTCGTCC
Found at i:194188 original size:23 final size:23
Alignment explanation
Indices: 194161--194206 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
194151 TGTCACCATG
194161 ACAATATTATTCTGCCACGTGTC
1 ACAATATTATTCTGCCACGTGTC
194184 ACAATATTATTCTGCCACGTGTC
1 ACAATATTATTCTGCCACGTGTC
194207 TCAAACTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (23 bp):
ACAATATTATTCTGCCACGTGTC
Found at i:197709 original size:42 final size:42
Alignment explanation
Indices: 197662--197750 Score: 151
Period size: 42 Copynumber: 2.1 Consensus size: 42
197652 CTGTAACATA
197662 TGGCACACCATTTCTTAATGGTCATTTGCATCAAAATATTAT
1 TGGCACACCATTTCTTAATGGTCATTTGCATCAAAATATTAT
* * *
197704 TGGCACACTATTTCTTGATGGTCATTTGCATCAAATTATTAT
1 TGGCACACCATTTCTTAATGGTCATTTGCATCAAAATATTAT
197746 TGGCA
1 TGGCA
197751 ATCTACTGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (42 bp):
TGGCACACCATTTCTTAATGGTCATTTGCATCAAAATATTAT
Found at i:207752 original size:34 final size:34
Alignment explanation
Indices: 207705--207784 Score: 106
Period size: 34 Copynumber: 2.4 Consensus size: 34
207695 CGAACTATGA
* * *
207705 ACTGCGAGCTCATCAAGTGTGTGAGCTCACCAAG
1 ACTGCGAGCTCATCAAATGTATGAACTCACCAAG
*
207739 ACTGCGAGGTCATCAAATGTATGAACTCACCAAG
1 ACTGCGAGCTCATCAAATGTATGAACTCACCAAG
* *
207773 ACTACAAGCTCA
1 ACTGCGAGCTCA
207785 CTAAACATGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.20
Consensus pattern (34 bp):
ACTGCGAGCTCATCAAATGTATGAACTCACCAAG
Found at i:208552 original size:14 final size:14
Alignment explanation
Indices: 208533--208559 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
208523 AATATTTCAA
208533 TTAATATTTTAGTG
1 TTAATATTTTAGTG
208547 TTAATATTTTAGT
1 TTAATATTTTAGT
208560 ATTAGTCGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (14 bp):
TTAATATTTTAGTG
Found at i:209097 original size:18 final size:20
Alignment explanation
Indices: 209074--209112 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
209064 ACCTAAAATG
*
209074 ATGATT-TTTA-TTATATAT
1 ATGATTATTTACTTAAATAT
209092 ATGATTATTTACTTAAATAT
1 ATGATTATTTACTTAAATAT
209112 A
1 A
209113 ATGGTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (20 bp):
ATGATTATTTACTTAAATAT
Found at i:211667 original size:13 final size:13
Alignment explanation
Indices: 211649--211673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
211639 TATCACTTTT
211649 ACACTTTCACATA
1 ACACTTTCACATA
211662 ACACTTTCACAT
1 ACACTTTCACAT
211674 GCTTTATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (13 bp):
ACACTTTCACATA
Found at i:216844 original size:17 final size:17
Alignment explanation
Indices: 216824--216881 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
216814 CCCTTGACTT
216824 TTAACCTTCCATCTTCC
1 TTAACCTTCCATCTTCC
216841 TTAACC-TCC-T-TTGACC
1 TTAACCTTCCATCTT--CC
* *
216857 TTTAACTTTCCATCTTCT
1 -TTAACCTTCCATCTTCC
216875 TTAACCT
1 TTAACCT
216882 CTCTGGACCT
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 2 0.06
15 1 0.03
16 5 0.16
17 17 0.53
18 4 0.12
19 1 0.03
20 2 0.06
ACGTcount: A:0.19, C:0.34, G:0.02, T:0.45
Consensus pattern (17 bp):
TTAACCTTCCATCTTCC
Found at i:216861 original size:34 final size:34
Alignment explanation
Indices: 216816--216915 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 34
216806 TTTAATTTCC
* * *
216816 CTTGACTTTTAACCTTCCATCTTCCTTAACCTC-
1 CTTGACCTTTAACTTTCCATCTTCTTTAACCTCT
216849 CTTTGACCTTTAACTTTCCATCTTCTTTAACCTCT
1 C-TTGACCTTTAACTTTCCATCTTCTTTAACCTCT
* *
216884 CTGGACCTTTAATTTTCCATCTTCTTTAACCT
1 CTTGACCTTTAACTTTCCATCTTCTTTAACCT
216916 TTCATATTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
33 1 0.02
34 58 0.97
35 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.04, T:0.46
Consensus pattern (34 bp):
CTTGACCTTTAACTTTCCATCTTCTTTAACCTCT
Found at i:217440 original size:33 final size:34
Alignment explanation
Indices: 217379--217442 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
217369 TGTTATATTA
* * *
217379 TGCTTGCAAGTTTTGTTAAGGGATTACTTATGTT
1 TGCTTGAAAGTTTTGTTAAAGGACTACTTATGTT
217413 TGCTTGAAAG-TTTGTTAAAGGACTACTTAT
1 TGCTTGAAAGTTTTGTTAAAGGACTACTTAT
217443 ATTTATATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 18 0.67
34 9 0.33
ACGTcount: A:0.25, C:0.09, G:0.22, T:0.44
Consensus pattern (34 bp):
TGCTTGAAAGTTTTGTTAAAGGACTACTTATGTT
Found at i:218171 original size:18 final size:18
Alignment explanation
Indices: 218118--218172 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
218108 CACACTAGTA
* **
218118 GTCGTGGTCGAGGACATG
1 GTCGCGGTCGAGGATGTG
*
218136 GTCGCGGTC-ATGGTTGTG
1 GTCGCGGTCGA-GGATGTG
218154 GTCGCGGTCGAGGATGTG
1 GTCGCGGTCGAGGATGTG
218172 G
1 G
218173 ATGTGAACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 1 0.03
18 28 0.93
19 1 0.03
ACGTcount: A:0.11, C:0.16, G:0.47, T:0.25
Consensus pattern (18 bp):
GTCGCGGTCGAGGATGTG
Found at i:220042 original size:141 final size:141
Alignment explanation
Indices: 219788--220074 Score: 565
Period size: 141 Copynumber: 2.0 Consensus size: 141
219778 GTTTTGGATG
219788 TGCTGTATATGTTCCGATTGCTGCACCACAACACTCTAAGATGGGTCCTCAAAGGAGGTTAGGAA
1 TGCTGTATATGTTCCGATTGCTGCACCACAACACTCTAAGATGGGTCCTCAAAGGAGGTTAGGAA
*
219853 TGTATGTTGGATATGAATCTCCATCAATAATTAAATATCTTGAGCCATTAACGGGGAATTTATTT
66 TATATGTTGGATATGAATCTCCATCAATAATTAAATATCTTGAGCCATTAACGGGGAATTTATTT
219918 ACGACTCGATT
131 ACGACTCGATT
219929 TGCTGTATATGTTCCGATTGCTGCACCACAACACTCTAAGATGGGTCCTCAAAGGAGGTTAGGAA
1 TGCTGTATATGTTCCGATTGCTGCACCACAACACTCTAAGATGGGTCCTCAAAGGAGGTTAGGAA
219994 TATATGTTGGATATGAATCTCCATCAATAATTAAATATCTTGAGCCATTAACGGGGAATTTATTT
66 TATATGTTGGATATGAATCTCCATCAATAATTAAATATCTTGAGCCATTAACGGGGAATTTATTT
220059 ACGACTCGATT
131 ACGACTCGATT
220070 TGCTG
1 TGCTG
220075 ACTATCATTT
Statistics
Matches: 145, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
141 145 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (141 bp):
TGCTGTATATGTTCCGATTGCTGCACCACAACACTCTAAGATGGGTCCTCAAAGGAGGTTAGGAA
TATATGTTGGATATGAATCTCCATCAATAATTAAATATCTTGAGCCATTAACGGGGAATTTATTT
ACGACTCGATT
Found at i:223188 original size:16 final size:16
Alignment explanation
Indices: 223167--223197 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
223157 TTTTTAAAAA
223167 GATTGAAAGTATTAAT
1 GATTGAAAGTATTAAT
223183 GATTGAAAGTATTAA
1 GATTGAAAGTATTAA
223198 AAGTAAGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.19, T:0.35
Consensus pattern (16 bp):
GATTGAAAGTATTAAT
Found at i:228261 original size:3 final size:3
Alignment explanation
Indices: 228253--228283 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
228243 GCTTAAAAAG
*
228253 GAA GAA GAA GAA GGA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
228284 TTAAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:234430 original size:25 final size:25
Alignment explanation
Indices: 234380--234430 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
234370 GGTTCTCCAT
* **
234380 GAAAGTTTTTTTAATTTCTCTTGGA
1 GAAAGTTTTTCTAATTTCTCACGGA
234405 GAAAGTTTTTCTAATTTCTCACGGA
1 GAAAGTTTTTCTAATTTCTCACGGA
234430 G
1 G
234431 GTTCATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.45
Consensus pattern (25 bp):
GAAAGTTTTTCTAATTTCTCACGGA
Found at i:239104 original size:10 final size:11
Alignment explanation
Indices: 239076--239125 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 11
239066 GAAAATTTAA
239076 ATTAAATAAATT
1 ATTAAA-AAATT
239088 ATT-AAAAATT
1 ATTAAAAAATT
239098 -TTAAAAAATT
1 ATTAAAAAATT
*
239108 ATTAAATAATT
1 ATTAAAAAATT
239119 -TTAAAAA
1 ATTAAAAA
239126 TTGATTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 18 0.53
11 11 0.32
12 3 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:239108 original size:20 final size:21
Alignment explanation
Indices: 239077--239125 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
239067 AAAATTTAAA
239077 TTAAATAAATTATTAAA-AATT
1 TTAAA-AAATTATTAAATAATT
239098 TTAAAAAATTATTAAATAATT
1 TTAAAAAATTATTAAATAATT
239119 TTAAAAA
1 TTAAAAA
239126 TTGATTTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TTAAAAAATTATTAAATAATT
Found at i:239136 original size:21 final size:21
Alignment explanation
Indices: 239077--239136 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
239067 AAAATTTAAA
*
239077 TTAAATAAATTA-TTAAAAATT
1 TTAAA-AAATTATTTAATAATT
*
239098 TTAAAAAATTATTAAATAATT
1 TTAAAAAATTATTTAATAATT
239119 TT-AAAAATTGATTTAATA
1 TTAAAAAATT-ATTTAATA
239137 GTCAATTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.38
21 21 0.62
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAAAAAATTATTTAATAATT
Found at i:241554 original size:22 final size:23
Alignment explanation
Indices: 241512--241565 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
241502 GCTCTCCGTT
241512 ATTTAGCACGTATAGTGCTCTCC
1 ATTTAGCACGTATAGTGCTCTCC
*
241535 ATTTAGCACGT-TTGTGCTCTCC
1 ATTTAGCACGTATAGTGCTCTCC
*
241557 GTTTAGCAC
1 ATTTAGCAC
241566 CTCGATGCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 18 0.62
23 11 0.38
ACGTcount: A:0.19, C:0.26, G:0.19, T:0.37
Consensus pattern (23 bp):
ATTTAGCACGTATAGTGCTCTCC
Found at i:241574 original size:22 final size:22
Alignment explanation
Indices: 241499--241581 Score: 60
Period size: 22 Copynumber: 3.6 Consensus size: 22
241489 GGGACCCTAG
*
241499 CGTGCTCTCCGTTATTTAGCACGTAT
1 CGTGCTCTCCG---TTTAGCACG-CT
* * *
241525 AGTGCTCTCCATTTAGCACGTT
1 CGTGCTCTCCGTTTAGCACGCT
*
241547 TGTGCTCTCCGTTTAGCAC-CT
1 CGTGCTCTCCGTTTAGCACGCT
*
241568 CGATGCTCTTCGTT
1 CG-TGCTCTCCGTT
241582 CATTAGTGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 2 0.04
22 28 0.58
23 9 0.19
26 9 0.19
ACGTcount: A:0.13, C:0.29, G:0.19, T:0.39
Consensus pattern (22 bp):
CGTGCTCTCCGTTTAGCACGCT
Found at i:245026 original size:12 final size:12
Alignment explanation
Indices: 244966--245064 Score: 72
Period size: 12 Copynumber: 8.0 Consensus size: 12
244956 TGCAACAATC
244966 ATATATATGTAT
1 ATATATATGTAT
*
244978 ACATATATGTAT
1 ATATATATGTAT
* *
244990 GTATGTATGTAT
1 ATATATATGTAT
* **
245002 ATGTATACATAT
1 ATATATATGTAT
*
245014 ATACATATGTAT
1 ATATATATGTAT
*
245026 ATATACATAATATAT
1 ATAT--AT-ATGTAT
* *
245041 GTATATATGCAT
1 ATATATATGTAT
*
245053 ATGTATATGTAT
1 ATATATATGTAT
245065 TTATGTATTG
Statistics
Matches: 63, Mismatches: 21, Indels: 6
0.70 0.23 0.07
Matches are distributed among these distances:
12 51 0.81
13 2 0.03
14 2 0.03
15 8 0.13
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.44
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:245046 original size:8 final size:8
Alignment explanation
Indices: 244967--245054 Score: 50
Period size: 8 Copynumber: 10.6 Consensus size: 8
244957 GCAACAATCA
244967 TATATATG
1 TATATATG
* *
244975 TATACATA
1 TATATATG
*
244983 TATGTATG
1 TATATATG
*
244991 TATGTATG
1 TATATATG
* *
244999 TATATGTA
1 TATATATG
* *
245007 TACATATA
1 TATATATG
*
245015 TACATATG
1 TATATATG
*
245023 TATATATACA
1 TATATAT--G
245033 TAATATATG
1 T-ATATATG
245042 TATATATG
1 TATATATG
*
245050 CATAT
1 TATAT
245055 GTATATGTAT
Statistics
Matches: 62, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
8 54 0.87
9 1 0.02
10 1 0.02
11 6 0.10
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.44
Consensus pattern (8 bp):
TATATATG
Found at i:253867 original size:33 final size:33
Alignment explanation
Indices: 253825--253891 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
253815 TATGTTTTAA
253825 AGATTGCTTTTATTAATTATTATTATTTTCTTT
1 AGATTGCTTTTATTAATTATTATTATTTTCTTT
* *
253858 AGATTGCTTTTATTATTTCTTATTATTTTCTTT
1 AGATTGCTTTTATTAATTATTATTATTTTCTTT
253891 A
1 A
253892 AGGATGCGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.07, G:0.06, T:0.64
Consensus pattern (33 bp):
AGATTGCTTTTATTAATTATTATTATTTTCTTT
Found at i:256833 original size:16 final size:16
Alignment explanation
Indices: 256814--256873 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
256804 CTGATTATAG
256814 CTCTATTCCATTACAA
1 CTCTATTCCATTACAA
*
256830 CTCTATTGCATTACAA
1 CTCTATTCCATTACAA
* *
256846 CTCTATTTCATTACAG
1 CTCTATTCCATTACAA
*
256862 CCCTATTCCATT
1 CTCTATTCCATT
256874 CCCCTCCACC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.27, C:0.30, G:0.03, T:0.40
Consensus pattern (16 bp):
CTCTATTCCATTACAA
Found at i:257564 original size:2 final size:2
Alignment explanation
Indices: 257559--257613 Score: 65
Period size: 2 Copynumber: 27.5 Consensus size: 2
257549 ACATCATATA
* * * *
257559 TG TG TG TG TG TG TG TG TG TG TG TG TG CG CG CG TG TG TG AG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
257601 TG TG TG TG AG TG T
1 TG TG TG TG TG TG T
257614 CGGACTAGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.04, C:0.05, G:0.49, T:0.42
Consensus pattern (2 bp):
TG
Found at i:259248 original size:19 final size:20
Alignment explanation
Indices: 259224--259263 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
259214 TCTTTATCCT
*
259224 TTTATTT-CCTTATTTTTTA
1 TTTATTTACCTTAGTTTTTA
*
259243 TTTATTTACTTTAGTTTTTA
1 TTTATTTACCTTAGTTTTTA
259263 T
1 T
259264 AATTTGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTATTTACCTTAGTTTTTA
Found at i:263205 original size:10 final size:10
Alignment explanation
Indices: 263190--263215 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
263180 ATTATAAGTC
263190 AAAAAAATAA
1 AAAAAAATAA
263200 AAAAAAATAA
1 AAAAAAATAA
263210 AAAAAA
1 AAAAAA
263216 GTGAAAAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:263537 original size:56 final size:54
Alignment explanation
Indices: 263430--263552 Score: 138
Period size: 56 Copynumber: 2.2 Consensus size: 54
263420 ATGTACCTAC
* * * * *
263430 TCACCTAATTATTAATATATTTTTTTCATTTAACTATGAAATGATATAAAATGG
1 TCACCCAATTATTAATATATTTTTTTCATTTAACTATAAAAAGATACAAAATAG
* * * *
263484 TCACTCAATTATTAGTATTTTTTTTGGTCATTTAACTATAAAAAGTTACAAAATAG
1 TCACCCAATTATTAATATATTTTTT--TCATTTAACTATAAAAAGATACAAAATAG
*
263540 TCACCCAACTATT
1 TCACCCAATTATT
263553 TATTTTGTCT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 21 0.38
56 35 0.62
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.42
Consensus pattern (54 bp):
TCACCCAATTATTAATATATTTTTTTCATTTAACTATAAAAAGATACAAAATAG
Found at i:264622 original size:12 final size:12
Alignment explanation
Indices: 264607--264641 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
264597 AATTTTTTAT
*
264607 AAAATTGTAAAA
1 AAAATTATAAAA
264619 AAAATTAT-AAA
1 AAAATTATAAAA
264630 AAAATTATAAAA
1 AAAATTATAAAA
264642 TCAAATAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (12 bp):
AAAATTATAAAA
Found at i:265065 original size:10 final size:10
Alignment explanation
Indices: 265050--265190 Score: 53
Period size: 10 Copynumber: 14.3 Consensus size: 10
265040 GAAACTGTAA
265050 TTTTTATAAT
1 TTTTTATAAT
*
265060 TTTTTAT-TT
1 TTTTTATAAT
* *
265069 TTCTTTACATT
1 TT-TTTATAAT
265080 TTTTTATAAGT
1 TTTTTATAA-T
* *
265091 TTCTTATAAA
1 TTTTTATAAT
*
265101 TTTATA-AAGT
1 TTTTTATAA-T
*
265111 TTTATT-T-TT
1 TTT-TTATAAT
265120 TTTTTAT-A-
1 TTTTTATAAT
*
265128 TTTCTAT-AT
1 TTTTTATAAT
*
265137 ATTTTATAAT
1 TTTTTATAAT
* *
265147 TCTTTATGAT
1 TTTTTATAAT
**
265157 TTTTATATTTT
1 TTTT-TATAAT
*
265168 TTTTTCTAAT
1 TTTTTATAAT
*
265178 TTTTAATAAT
1 TTTTTATAAT
265188 TTT
1 TTT
265191 CAAATACTTA
Statistics
Matches: 95, Mismatches: 26, Indels: 20
0.67 0.18 0.14
Matches are distributed among these distances:
8 9 0.09
9 15 0.16
10 49 0.52
11 22 0.23
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:265143 original size:17 final size:19
Alignment explanation
Indices: 265120--265166 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
265110 TTTTATTTTT
265120 TTTTTATATTTCTATAT-A
1 TTTTTATATTTCTATATGA
* *
265138 -TTTTATAATTCTTTATGA
1 TTTTTATATTTCTATATGA
265156 TTTTTATATTT
1 TTTTTATATTT
265167 TTTTTTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 14 0.58
18 1 0.04
19 9 0.38
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (19 bp):
TTTTTATATTTCTATATGA
Found at i:265168 original size:8 final size:8
Alignment explanation
Indices: 265120--265168 Score: 53
Period size: 8 Copynumber: 5.6 Consensus size: 8
265110 TTTTATTTTT
265120 TTTTTATA
1 TTTTTATA
*
265128 TTTCTATA
1 TTTTTATA
265136 TATTTTATAA
1 T-TTTTAT-A
265146 TTCTTTATGA
1 TT-TTTAT-A
265156 TTTTTATA
1 TTTTTATA
265164 TTTTT
1 TTTTT
265169 TTTTCTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
8 14 0.40
9 11 0.31
10 10 0.29
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:265667 original size:3 final size:3
Alignment explanation
Indices: 265659--265683 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
265649 TTTTTACCTC
265659 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
265684 ATGGATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:267353 original size:20 final size:19
Alignment explanation
Indices: 267303--267356 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
267293 AGCAGTCTGC
*
267303 AACTTAGTTGTTTCGGTAG
1 AACTTAGTTGTATCGGTAG
* *
267322 AAGCATACTTGTATCGGTAG
1 AA-CTTAGTTGTATCGGTAG
267342 AACTGTAGTTGTATC
1 AACT-TAGTTGTATC
267357 AATAGAAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (19 bp):
AACTTAGTTGTATCGGTAG
Found at i:267601 original size:20 final size:20
Alignment explanation
Indices: 267578--267624 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
267568 AAGGTATCGA
*
267578 TAGAAGTGAAGTTATATCAG
1 TAGAAGTGAAGTTATACCAG
* * *
267598 TAGAAGTGGAGTTCTACCGG
1 TAGAAGTGAAGTTATACCAG
267618 TAGAAGT
1 TAGAAGT
267625 CTCACTAGAG
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:0.34, C:0.09, G:0.30, T:0.28
Consensus pattern (20 bp):
TAGAAGTGAAGTTATACCAG
Found at i:276772 original size:17 final size:17
Alignment explanation
Indices: 276752--276784 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
276742 TAGTAAACAA
*
276752 ATTTTAAATTTAAATTT
1 ATTTTAAATGTAAATTT
276769 ATTTTAAATGTAAATT
1 ATTTTAAATGTAAATT
276785 GCCCAATACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTTAAATGTAAATTT
Found at i:276832 original size:42 final size:44
Alignment explanation
Indices: 276751--276838 Score: 126
Period size: 43 Copynumber: 2.0 Consensus size: 44
276741 TTAGTAAACA
**
276751 AATTTTAAATTTAAATTTATTTTAAATGTAAATTGCCCAA-TAC
1 AATTTTAAATTTAAATTTATTTTAAATGTAAAAGGCCCAATTAC
* *
276794 AATTTTAAATTTAAATTTA-TTTAAGTTTAAAAGGCCCAATTAC
1 AATTTTAAATTTAAATTTATTTTAAATGTAAAAGGCCCAATTAC
276837 AA
1 AA
276839 ACCCAACGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 16 0.40
43 24 0.60
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (44 bp):
AATTTTAAATTTAAATTTATTTTAAATGTAAAAGGCCCAATTAC
Found at i:278370 original size:30 final size:28
Alignment explanation
Indices: 278347--278541 Score: 160
Period size: 30 Copynumber: 6.6 Consensus size: 28
278337 TTTTGACCTG
*
278347 TAAATTTCTCTAAAATTACATTTTAGCCAC
1 TAAATTT-TCTAAAATTACATTTTAACC-C
*
278377 ATAAATCTTTC-AAAATTATATTTTAACCCC
1 -TAAAT-TTTCTAAAATTACATTTTAA-CCC
* *
278407 TAAACTTCTCCAAAATTACA-TTTAACCC
1 TAAA-TTTTCTAAAATTACATTTTAACCC
*
278435 TAAAATTTTATAAAATTACATTTTAACCC
1 T-AAATTTTCTAAAATTACATTTTAACCC
* * * *
278464 ATAAACTTTTATAAAATTACATATTATCCT
1 -TAAA-TTTTCTAAAATTACATTTTAACCC
* *
278494 TCAAACTTTTCAAAAATTACATTTTGACCC
1 T-AAA-TTTTCTAAAATTACATTTTAACCC
*
278524 TAAATTTTTTTAAAATTA
1 TAAA-TTTTCTAAAATTA
278542 TGTTTTGACC
Statistics
Matches: 136, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
28 16 0.12
29 41 0.30
30 68 0.50
31 9 0.07
32 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.41
Consensus pattern (28 bp):
TAAATTTTCTAAAATTACATTTTAACCC
Found at i:278416 original size:60 final size:59
Alignment explanation
Indices: 278322--278485 Score: 172
Period size: 58 Copynumber: 2.8 Consensus size: 59
278312 ACCCTCGAAC
* * ** * *
278322 TCTTTTAAAATTGTATTTTGACCTGTAAATTTCTCTAAAATTACATTTTAGCCAC-ATAAA
1 TCTTTTAAAATTATATTTTAACCCATAAACTTCTCTAAAATTACATTTTAACC-CTA-AAA
* * *
278382 TCTTTCAAAATTATATTTTAACCCCTAAACTTCTCCAAAATTACA-TTTAACCCTAAAA
1 TCTTTTAAAATTATATTTTAACCCATAAACTTCTCTAAAATTACATTTTAACCCTAAAA
* * *
278440 T-TTTATAAAATTACATTTTAACCCATAAACTTTTATAAAATTACAT
1 TCTTT-TAAAATTATATTTTAACCCATAAACTTCTCTAAAATTACAT
278486 ATTATCCTTC
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
57 3 0.03
58 39 0.45
59 7 0.08
60 38 0.44
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.41
Consensus pattern (59 bp):
TCTTTTAAAATTATATTTTAACCCATAAACTTCTCTAAAATTACATTTTAACCCTAAAA
Found at i:278463 original size:58 final size:60
Alignment explanation
Indices: 278379--278527 Score: 164
Period size: 58 Copynumber: 2.5 Consensus size: 60
278369 TTAGCCACAT
* *
278379 AAATCTTTC-AAAATTATATTTTAACCCCTAAACTTCTCCAAAATTACAT-TTAACCCT-A
1 AAAT-TTTCAAAAATTACATTTTAACCCCTAAACTTCTACAAAATTACATATTAACCCTCA
* * * * *
278437 AAATTTT-ATAAAATTACATTTTAACCCATAAACTTTTATAAAATTACATATTATCCTTCA
1 AAATTTTCA-AAAATTACATTTTAACCCCTAAACTTCTACAAAATTACATATTAACCCTCA
* *
278497 AACTTTTCAAAAATTACATTTTGA-CCCTAAA
1 AAATTTTCAAAAATTACATTTTAACCCCTAAA
278528 TTTTTTTAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
57 3 0.04
58 39 0.51
59 12 0.16
60 21 0.28
61 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.01, T:0.38
Consensus pattern (60 bp):
AAATTTTCAAAAATTACATTTTAACCCCTAAACTTCTACAAAATTACATATTAACCCTCA
Found at i:278480 original size:88 final size:89
Alignment explanation
Indices: 278348--278541 Score: 216
Period size: 88 Copynumber: 2.2 Consensus size: 89
278338 TTTGACCTGT
* * * *
278348 AAATTTCTCTAAAATTACATTTTAGCCACATAAATCTTTCAAAATTATATTTTAACCCCT-AAAC
1 AAATTT-TATAAAATTACATTTTAACCACATAAATCTTTCAAAATTACATATT-ACCCCTCAAAC
*
278412 TTCTCCAAAATTACA-TTTAACCCTA
64 TTCTCAAAAATTACATTTTAACCCTA
* * *
278437 AAATTTTATAAAATTACATTTTAACC-CATAAA-CTTTTATAAAATTACATATTATCCTTCAAAC
1 AAATTTTATAAAATTACATTTTAACCACATAAATC-TTT-CAAAATTACATATTACCCCTCAAAC
* *
278500 TTTTCAAAAATTACATTTTGACCCTA
64 TTCTCAAAAATTACATTTTAACCCTA
* *
278526 AATTTTTTTAAAATTA
1 AAATTTTATAAAATTA
278542 TGTTTTGACC
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
86 1 0.01
87 13 0.15
88 46 0.52
89 29 0.33
ACGTcount: A:0.41, C:0.18, G:0.01, T:0.40
Consensus pattern (89 bp):
AAATTTTATAAAATTACATTTTAACCACATAAATCTTTCAAAATTACATATTACCCCTCAAACTT
CTCAAAAATTACATTTTAACCCTA
Done.