Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 2 of 25
Found at i:123122 original size:13 final size:13
Alignment explanation
Indices: 123104--123128 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
123094 GTCAACGAGT
123104 TGTATCGATACAA
1 TGTATCGATACAA
123117 TGTATCGATACA
1 TGTATCGATACA
123129 TAAGTGTTGT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:123205 original size:13 final size:13
Alignment explanation
Indices: 123187--123214 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
123177 ATACATTACT
123187 CATTGTATCGATA
1 CATTGTATCGATA
123200 CATTGTATCGATA
1 CATTGTATCGATA
123213 CA
1 CA
123215 CTGATCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:123212 original size:33 final size:33
Alignment explanation
Indices: 123170--123235 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
123160 GCTAAGGAAA
*
123170 TGTATCGATACA-TTACTCATTGTATCGATACAT
1 TGTATCGATACACTGA-TCATTGTATCGATACAT
*
123203 TGTATCGATACACTGATCTTTGTATCGATACAT
1 TGTATCGATACACTGATCATTGTATCGATACAT
123236 GCAGGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACACTGATCATTGTATCGATACAT
Found at i:137129 original size:26 final size:27
Alignment explanation
Indices: 137100--137165 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
137090 CGTCCTCCGC
*
137100 AAAAA-AAAAAAGAAGAAAAAAGAAAA
1 AAAAACAAAAAAGAACAAAAAAGAAAA
* *
137126 AAAAACAACAAA-AACAAAACAGAAAA
1 AAAAACAAAAAAGAACAAAAAAGAAAA
137152 AAAAACAACAAAAG
1 AAAAACAA-AAAAG
137166 GGGTCCGGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 25 0.76
27 8 0.24
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (27 bp):
AAAAACAAAAAAGAACAAAAAAGAAAA
Found at i:137138 original size:12 final size:12
Alignment explanation
Indices: 137123--137164 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
137113 AGAAAAAAGA
137123 AAAAAAAACAAC
1 AAAAAAAACAAC
137135 AAAAACAAAACAGA-
1 -AAAA-AAAACA-AC
137149 AAAAAAAACAAC
1 AAAAAAAACAAC
137161 AAAA
1 AAAA
137165 GGGGTCCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 1 0.04
12 10 0.38
13 8 0.31
14 6 0.23
15 1 0.04
ACGTcount: A:0.83, C:0.14, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAC
Found at i:137138 original size:20 final size:20
Alignment explanation
Indices: 137102--137139 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
137092 TCCTCCGCAA
* *
137102 AAAAAAAAAGAAGAAAAAAG
1 AAAAAAAAACAACAAAAAAG
137122 AAAAAAAAACAACAAAAA
1 AAAAAAAAACAACAAAAA
137140 CAAAACAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.87, C:0.05, G:0.08, T:0.00
Consensus pattern (20 bp):
AAAAAAAAACAACAAAAAAG
Found at i:138588 original size:29 final size:29
Alignment explanation
Indices: 138555--138899 Score: 198
Period size: 29 Copynumber: 11.6 Consensus size: 29
138545 TTCCTTACCC
138555 TTCAAAAGCCCACAAGTCAGTGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* *
138584 TTCAAAAGCCCACAAATCAATGGCATCTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* **
138613 TTCAAAAGCCCACAAGTCAATGATATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATC-TT
* * *
138643 TTC-AAAGTCCACAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* * *
138670 TTC-AAAGCTCACAAATCAGTGGCACCCTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA---TCTT
* *
138701 TTC-GAAGCCCACAAGTCAGTGGCATTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* * * *
138729 TTCTAAAGTCCACAACTCCGTGGCACTCCTTTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-T-C---TT
*** * * *
138763 TTGGTAAGCCCACAACTCCGTAGCACTCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCA-TC-TT
** * * * *
138794 TTCCTTTTAAGCCCGCAAGTTAGTGGTACCCTT
1 TT-C--AAAAGCCCACAAGTCAGTGGCA-TCTT
* *
138827 TTCAAAAGCCCACAAGTCAGTGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
* * *
138855 TTCAAAAGCCCACAAGTCAATGGCAAC-C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTT
*
138883 TTCAAAAGCACACAAGT
1 TTCAAAAGCCCACAAGT
138900 TGATGCAACC
Statistics
Matches: 254, Mismatches: 48, Indels: 29
0.77 0.15 0.09
Matches are distributed among these distances:
27 21 0.08
28 50 0.20
29 87 0.34
30 23 0.09
31 26 0.10
32 1 0.00
33 5 0.02
34 41 0.16
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.26
Consensus pattern (29 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTT
Found at i:138682 original size:27 final size:27
Alignment explanation
Indices: 138643--138698 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
138633 TGATATCTTT
*
138643 TTCAAAGTCCACAAGTCAGTGGCAACC
1 TTCAAAGTCCACAAATCAGTGGCAACC
*
138670 TTCAAAG-CTCACAAATCAGTGGCACCC
1 TTCAAAGTC-CACAAATCAGTGGCAACC
138697 TT
1 TT
138699 TTTTCGAAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.21
Consensus pattern (27 bp):
TTCAAAGTCCACAAATCAGTGGCAACC
Found at i:138709 original size:87 final size:87
Alignment explanation
Indices: 138559--138753 Score: 218
Period size: 87 Copynumber: 2.2 Consensus size: 87
138549 TTACCCTTCA
* * *
138559 AAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCCCACAAATCAATGGCATCTTTTCAAAAGCCC
1 AAAGTCCACAAGTCAGTGGCAACTCTTCAAAAGCCCACAAATCAATGGCATCTTTTCAAAAGCCC
*
138624 ACAAGTCAATGATATCTTTTTC-
66 ACAAGTCAATGACAT-TTTTTCT
* * * *
138646 AAAGTCCACAAGTCAGTGGCAAC-CTTC-AAAGCTCACAAATCAGTGGCACCCTTTTTTC-GAAG
1 AAAGTCCACAAGTCAGTGGCAACTCTTCAAAAGCCCACAAATCAATGGCA---TCTTTTCAAAAG
* *
138708 CCCACAAGTCAGTGGCATTTTTTCT
63 CCCACAAGTCAATGACATTTTTTCT
* *
138733 AAAGTCCACAACTCCGTGGCA
1 AAAGTCCACAAGTCAGTGGCA
138754 CTCCTTTTTT
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
85 19 0.21
86 9 0.10
87 58 0.63
88 6 0.07
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (87 bp):
AAAGTCCACAAGTCAGTGGCAACTCTTCAAAAGCCCACAAATCAATGGCATCTTTTCAAAAGCCC
ACAAGTCAATGACATTTTTTCT
Found at i:138867 original size:28 final size:28
Alignment explanation
Indices: 138827--138925 Score: 130
Period size: 28 Copynumber: 3.5 Consensus size: 28
138817 TGGTACCCTT
138827 TTCAAAAGCCCACAAGTCAGTGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
*
138855 TTCAAAAGCCCACAAGTCAATGGCAACC
1 TTCAAAAGCCCACAAGTCAGTGGCAACC
* *
138883 TTCAAAAGCACACAAGT-TGAT-GCAACCC
1 TTCAAAAGCCCACAAGTCAG-TGGCAA-CC
138911 TTTCAAAAGCCCACA
1 -TTCAAAAGCCCACA
138926 CAAGTTGGTG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 46 0.73
29 13 0.21
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.16
Consensus pattern (28 bp):
TTCAAAAGCCCACAAGTCAGTGGCAACC
Found at i:139088 original size:93 final size:88
Alignment explanation
Indices: 138948--139163 Score: 218
Period size: 93 Copynumber: 2.4 Consensus size: 88
138938 GTCTTTTTCT
* * *** ***
138948 AAGTCCGATATCGCTGGCCTTGAACCAGCATATTGGGGCCTTTATCTTTTAA-ACCCAATATCGC
1 AAGTCCGATATCGTTGGCCTTGAATCAGCATATTGACACCGGCATC-TTTAAGA-CCAATATCGC
* *
139012 TGGCCTTGAATAAGCATATTAACACC
64 TGGCCTTGAATAAGCACATCAACA-C
* *
139038 TTGAAGTCCGATATCGTTGGCCTTGAATCAGCATATTGACACCGGCATCTTTAAGACCAATGTTG
1 ---AAGTCCGATATCGTTGGCCTTGAATCAGCATATTGACACCGGCATCTTTAAGACCAATATCG
* **
139103 CTGGCCTTGAATCAGCACATCGGCAC
63 CTGGCCTTGAATAAGCACATCAACAC
* *
139129 AAGTCCAATATCGTTGGCCGTGAATCAGCATATTG
1 AAGTCCGATATCGTTGGCCTTGAATCAGCATATTG
139164 GCATCTTTAT
Statistics
Matches: 105, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
88 33 0.31
91 1 0.01
92 32 0.30
93 39 0.37
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (88 bp):
AAGTCCGATATCGTTGGCCTTGAATCAGCATATTGACACCGGCATCTTTAAGACCAATATCGCTG
GCCTTGAATAAGCACATCAACAC
Found at i:145055 original size:21 final size:20
Alignment explanation
Indices: 145009--145061 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
144999 GTAGCCAAAC
**
145009 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
145029 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
145049 TTGTATCGATACA
1 TTGTATCGATACA
145062 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:151235 original size:12 final size:13
Alignment explanation
Indices: 151218--151254 Score: 67
Period size: 12 Copynumber: 2.9 Consensus size: 13
151208 CATTTTTCTT
151218 TGTATCGATACA-
1 TGTATCGATACAC
151230 TGTATCGATACAC
1 TGTATCGATACAC
151243 TGTATCGATACA
1 TGTATCGATACA
151255 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:151250 original size:45 final size:45
Alignment explanation
Indices: 151151--151254 Score: 118
Period size: 45 Copynumber: 2.3 Consensus size: 45
151141 AAATGTCCAA
* *
151151 AATGTATCGATACATGTTTCTGTGTATCGATACATCTGGAAATTC
1 AATGTATCGATACATGTTTCTGTGTATCGATACATCTAGAAATAC
* * * * ***
151196 AATGAATCGATACATTTTTCTTTGTATCGATACATGTATCGATAC
1 AATGTATCGATACATGTTTCTGTGTATCGATACATCTAGAAATAC
*
151241 ACTGTATCGATACA
1 AATGTATCGATACA
151255 GGGGGATTAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (45 bp):
AATGTATCGATACATGTTTCTGTGTATCGATACATCTAGAAATAC
Found at i:155684 original size:13 final size:13
Alignment explanation
Indices: 155666--155691 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
155656 TACAGCAAGT
155666 ATGTATCGATACA
1 ATGTATCGATACA
155679 ATGTATCGATACA
1 ATGTATCGATACA
155692 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:157942 original size:21 final size:21
Alignment explanation
Indices: 157909--157953 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
157899 TTGCAAGTTG
*
157909 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
157931 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
157951 AAA
1 AAA
157954 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:159777 original size:15 final size:15
Alignment explanation
Indices: 159757--159787 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
159747 TAAAAATGTC
*
159757 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
159772 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
159787 C
1 C
159788 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:161888 original size:13 final size:13
Alignment explanation
Indices: 161866--161904 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
161856 ACATTTTTCT
161866 TTGTATCGATACA
1 TTGTATCGATACA
*
161879 TTGTACCGATACA
1 TTGTATCGATACA
161892 TTGTATCGATACA
1 TTGTATCGATACA
161905 GGGTGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:170875 original size:24 final size:24
Alignment explanation
Indices: 170843--170890 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
170833 GACCAAGGTG
170843 CCGATTCTTTCGATTTTTCCTTTC
1 CCGATTCTTTCGATTTTTCCTTTC
170867 CCGATTCTTTCGATTTTTCCTTTC
1 CCGATTCTTTCGATTTTTCCTTTC
170891 AAGTTGTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.08, C:0.29, G:0.08, T:0.54
Consensus pattern (24 bp):
CCGATTCTTTCGATTTTTCCTTTC
Found at i:172096 original size:15 final size:15
Alignment explanation
Indices: 172076--172108 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
172066 AGTCAACTTT
172076 ATCATTATCATCATC
1 ATCATTATCATCATC
*
172091 ATCATTATCTTCATC
1 ATCATTATCATCATC
172106 ATC
1 ATC
172109 TTTGATGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.27, G:0.00, T:0.42
Consensus pattern (15 bp):
ATCATTATCATCATC
Found at i:173734 original size:13 final size:13
Alignment explanation
Indices: 173716--173745 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
173706 ACAATTCTTC
173716 ATGTATCGATACA
1 ATGTATCGATACA
*
173729 ATGTATGGATACA
1 ATGTATCGATACA
173742 ATGT
1 ATGT
173746 GTCATGTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:173743 original size:33 final size:33
Alignment explanation
Indices: 173693--173762 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
173683 AGCCGTTGGG
*
173693 ACAATGTATCGAAACAAT-TCTTCATGTATCGAT
1 ACAATGTATCGAAACAATGT-GTCATGTATCGAT
* *
173726 ACAATGTATGGATACAATGTGTCATGTATCGAT
1 ACAATGTATCGAAACAATGTGTCATGTATCGAT
173759 ACAA
1 ACAA
173763 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (33 bp):
ACAATGTATCGAAACAATGTGTCATGTATCGAT
Found at i:173864 original size:20 final size:19
Alignment explanation
Indices: 173792--173864 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
173782 TGCCAGTTTT
173792 ATGTATCGATACAATTGTG-C
1 ATGTATCGATAC-ATTG-GAC
* *
173812 ATGTATCGATACAATGAAC
1 ATGTATCGATACATTGGAC
*
173831 ATGTATCGATACATCTGGAT
1 ATGTATCGATACAT-TGGAC
173851 ATGTATCGATACAT
1 ATGTATCGATACAT
173865 ATAAGGGTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 29 0.63
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (19 bp):
ATGTATCGATACATTGGAC
Found at i:181406 original size:20 final size:21
Alignment explanation
Indices: 181374--181412 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
181364 AGCCTTTGAC
*
181374 CATGCATTTTTTATTATGTTT
1 CATGCATTTTTTAATATGTTT
181395 CATGCA-TTTTTAATATGT
1 CATGCATTTTTTAATATGT
181413 CCAGCATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.10, G:0.10, T:0.56
Consensus pattern (21 bp):
CATGCATTTTTTAATATGTTT
Found at i:183864 original size:31 final size:31
Alignment explanation
Indices: 183810--183920 Score: 90
Period size: 31 Copynumber: 3.7 Consensus size: 31
183800 AATCTTTTTC
* * *
183810 CTTCTTCAAAGTCTACGATTCAGTGGCATCT
1 CTTCTTAAAAGTCTACGACTCAGTGGCATAT
* *
183841 CTTCTTAAAATTCTATGACTCAGTGGCATAT
1 CTTCTTAAAAGTCTACGACTCAGTGGCATAT
* * *
183872 CTT-TTTAAAGTCCT-TGACTCTA-TGGCACA-
1 CTTCTTAAAAGT-CTACGACTC-AGTGGCATAT
183901 CTTC-T-AAAGTCTACGACTCA
1 CTTCTTAAAAGTCTACGACTCA
183921 CTGACATCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
27 3 0.04
28 10 0.15
29 4 0.06
30 18 0.27
31 32 0.48
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (31 bp):
CTTCTTAAAAGTCTACGACTCAGTGGCATAT
Found at i:184094 original size:61 final size:64
Alignment explanation
Indices: 184044--184168 Score: 168
Period size: 66 Copynumber: 2.0 Consensus size: 64
184034 TCACAGCTTC
*
184044 GTGGCACCC-TTTC-AT-AGTCCACAACTTCGTGGCACCTTATTCTTTTAAAGTCCACAACTCT
1 GTGGCACCCTTTTCTATCAGTCCACAACTTCGTGGCACATTATTCTTTTAAAGTCCACAACTCT
* * *
184105 GTGGCACCCTTTTCTTTTCGAGTCCACAACTTCGTGGCACATTTTTCTTTT-AACTCCACAACTC
1 GTGGCACCCTTTTC-TATC-AGTCCACAACTTCGTGGCACATTATTCTTTTAAAGTCCACAACTC
184169 CATGCACCTT
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
61 9 0.16
62 4 0.07
64 1 0.02
65 12 0.22
66 29 0.53
ACGTcount: A:0.21, C:0.31, G:0.13, T:0.35
Consensus pattern (64 bp):
GTGGCACCCTTTTCTATCAGTCCACAACTTCGTGGCACATTATTCTTTTAAAGTCCACAACTCT
Found at i:184101 original size:33 final size:32
Alignment explanation
Indices: 184059--184215 Score: 165
Period size: 33 Copynumber: 4.8 Consensus size: 32
184049 ACCCTTTCAT
*
184059 AGTCCACAACTTCGTGGCACCTTATTCTTTTAA
1 AGTCCACAACTTCGTGGCACCTTTTTCTTTT-A
* *
184092 AGTCCACAAC-TCTGTGGCACCCTTTTCTTTTCG
1 AGTCCACAACTTC-GTGGCACCTTTTTCTTTT-A
*
184125 AGTCCACAACTTCGTGGCACATTTTTCTTTTA
1 AGTCCACAACTTCGTGGCACCTTTTTCTTTTA
* * *
184157 ACTCCACAACTCCAT-GCACCTTTTTCTTTTTTA
1 AGTCCACAACTTCGTGGCACCTTTTTC--TTTTA
* * *
184190 AGTCTACAACTTCGTAGCACCCTTTT
1 AGTCCACAACTTCGTGGCACCTTTTT
184216 AAGTCCAAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
31 10 0.10
32 14 0.14
33 68 0.66
34 11 0.11
ACGTcount: A:0.21, C:0.30, G:0.11, T:0.38
Consensus pattern (32 bp):
AGTCCACAACTTCGTGGCACCTTTTTCTTTTA
Found at i:184141 original size:66 final size:65
Alignment explanation
Indices: 184053--184210 Score: 192
Period size: 65 Copynumber: 2.4 Consensus size: 65
184043 CGTGGCACCC
* **
184053 TTTCATAGTCCACAACTTCGTGGCACCTTATTCTTTTAAAGTCCACAACTCTGTGGCACCCTTTT
1 TTTCA-AGTCCACAACTTCGTGGCACCTTATTCTTTT-AACTCCACAACTCCAT-GCACCCTTTT
184118 C-T
63 CTT
* * * *
184120 TTTCGAGTCCACAACTTCGTGGCACATTTTTCTTTTAACTCCACAACTCCATGCACCTTTTTCTT
1 TTTCAAGTCCACAACTTCGTGGCACCTTATTCTTTTAACTCCACAACTCCATGCACCCTTTTCTT
* * *
184185 TTTTAAGTCTACAACTTCGTAGCACC
1 TTTCAAGTCCACAACTTCGTGGCACC
184211 CTTTTAAGTC
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 10 0.13
65 35 0.45
66 29 0.37
67 4 0.05
ACGTcount: A:0.22, C:0.30, G:0.11, T:0.38
Consensus pattern (65 bp):
TTTCAAGTCCACAACTTCGTGGCACCTTATTCTTTTAACTCCACAACTCCATGCACCCTTTTCTT
Found at i:184381 original size:33 final size:33
Alignment explanation
Indices: 184241--184835 Score: 571
Period size: 33 Copynumber: 18.5 Consensus size: 33
184231 TGGCACCTTT
* * *
184241 CCCTTTTAAAGCCCACATAAGTTGGTGGCAA--
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
*
184272 CCCTTCTAAAGCCCACATAAGTCGGTGGCAA--
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* **
184303 CCCTTCTAAAGCCCACACAGGTTAGTGGCAA-C
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
** *
184335 ATCTTCTAAAGCCCACACAAGTCAGTGGCAACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* *
184368 CCCCTCTAAAGCCCACACAAGTTGGTGGCAACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * *
184401 CCCCTCTAAAGCCCACAAAAGTCGATGG-AACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * *
184433 CCCTTCTAAAGCCCATACAAGTCTGTAGCAACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * *
184466 CCTTTCTAAAGCTCACATAAGTCGATGGCAA--
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * *
184497 CCCTTCTAAAACCCACATAAGTCAGTGGCAA--
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * *
184528 CGCTTCTATAAAGCCCACACAATTTGCTGGCAA-C
1 CCCTTC--TAAAGCCCACACAAGTCGGTGGCAACC
* * *
184562 CTCTTCTAAAGCTCACACAAGTAGGTGGCAATCC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAA-CC
* * * * *
184596 CAC-TCTAAAGTCCACACAAATTGGTGGCAA-T
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * *
184627 CTCTTCTAAAGCCCATACAAGTTGGTGGCAACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
*
184660 CCCTTTTAAAGCCCACACAAGTCGGTGGCAACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* *
184693 CCCCTCTAAAGCCCACATAAGTCGGTGGCAACC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
184726 CTCC-TCTAAAGCCCACACAAGTCGGTGGCAATCC
1 C-CCTTCTAAAGCCCACACAAGTCGGTGGCAA-CC
*
184760 CCC-TCTAAAGCCCACACAAATCGGTGGCAA--
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
* * * *
184790 CCTTTCTAAAGCCCACACAAATTGGTGGC-ATC
1 CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
*
184822 TCCTTCT-AAGCCCA
1 CCCTTCTAAAGCCCA
184836 ATGTCGTTGA
Statistics
Matches: 477, Mismatches: 72, Indels: 30
0.82 0.12 0.05
Matches are distributed among these distances:
30 3 0.01
31 120 0.25
32 103 0.22
33 238 0.50
34 13 0.03
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.20
Consensus pattern (33 bp):
CCCTTCTAAAGCCCACACAAGTCGGTGGCAACC
Found at i:184433 original size:65 final size:65
Alignment explanation
Indices: 184241--184835 Score: 562
Period size: 65 Copynumber: 9.2 Consensus size: 65
184231 TGGCACCTTT
* * * *
184241 CCCTTTTAAAGCCCACATAAGTTGGTGGCAA--CCCTTCTAAAGCCCACATAAGTCGGTGGCAA-
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAAC
* * ** * *
184303 CCCTTCTAAAGCCCACACAGGTTAGTGGCAA-CATCTTCTAAAGCCCACACAAGTCAGTGGCAAC
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAA-
184367 C
65 C
* * *
184368 CCCCTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACAAAAGTCGATGG-AAC
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAA-
184432 C
65 C
* * ** * * *
184433 CCCTTCTAAAGCCCATACAAGTCT-GTAGCAACCCCTTTCTAAAGCTCACATAAGTCGATGGCAA
1 CCCTTCTAAAGCCCACACAAGT-TGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAA
184497 -
65 C
* * ** * ** * * * *
184497 CCCTTCTAAAACCCACATAAGTCAGTGGCAACGCTTCTATAAAGCCCACACAATTTGCTGGCAAC
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAAC
* * * * * * * * *
184562 CTCTTCTAAAGCTCACACAAGTAGGTGGCAATCCCACTCTAAAGTCCACACAAATTGGTGGCAAT
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAAC
* * * *
184627 CTCTTCTAAAGCCCATACAAGTTGGTGGCAACCCCCTTTTAAAGCCCACACAAGTCGGTGGCAAC
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAA-
184692 C
65 C
* * * *
184693 CCCCTCTAAAGCCCACATAAGTCGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCGGTGGCAAT
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAA-
184758 C
65 C
* * * ** * * *
184759 CCCCTCTAAAGCCCACACAAATCGGTGGCAA--CCTTTCTAAAGCCCACACAAATTGGTGGCATC
1 CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAAC
*
184822 TCCTTCT-AAGCCCA
1 CCCTTCTAAAGCCCA
184836 ATGTCGTTGA
Statistics
Matches: 441, Mismatches: 83, Indels: 18
0.81 0.15 0.03
Matches are distributed among these distances:
62 34 0.08
63 33 0.07
64 74 0.17
65 188 0.43
66 112 0.25
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.20
Consensus pattern (65 bp):
CCCTTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:184604 original size:194 final size:192
Alignment explanation
Indices: 184241--184835 Score: 643
Period size: 194 Copynumber: 3.1 Consensus size: 192
184231 TGGCACCTTT
* * *
184241 CCCTTTTAAAGCCCACATAAGTTGGTGGCAA-CCC-TTCTAAAGCCCACATAAGTCGGTGGCAAC
1 CCCTTCTAAAGCCCATACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACATAAGTCGGTGGCAAC
* * * * *
184304 CCTTCTAAAGCCCACACAGGTTAGTGGCAACATCTTC-TAAAGCCCACACAAGTCAGTGGCAACC
66 CCTTCTAAAGCCCACATAAGTCAGTGGCAAC-CCTTCTTAAAGCCCACACAA-TTAGTGGCAACC
* *
184368 CCCCTCTAAAGCCCACACAAGTTGGTGGCAACCCCCCTCTAAAGCCCACA-AAAGTCGATGG-AA
129 CCCCTCTAAAGCCCACACAAGTAGGTGGCAA-CCCACTCTAAAGCCCACACAAA-TCGATGGCAA
184431 CC
192 -C
* * *
184433 CCCTTCTAAAGCCCATACAAGTCT-GTAGCAACCCCTTTCTAAAGCTCACATAAGTCGATGGCAA
1 CCCTTCTAAAGCCCATACAAGT-TGGTGGCAACCCCTTTCTAAAGCCCACATAAGTCGGTGGCAA
* * *
184497 CCCTTCTAAAACCCACATAAGTCAGTGGCAACGCTTCTATAAAGCCCACACAATTTGCTGGCAA-
65 CCCTTCTAAAGCCCACATAAGTCAGTGGCAACCCTTCT-TAAAGCCCACACAATTAG-TGGCAAC
* * * * * *
184561 CCTCTTCTAAAGCTCACACAAGTAGGTGGCAATCCCACTCTAAAGTCCACACAAATTGGTGGCAA
128 CCCCCTCTAAAGCCCACACAAGTAGGTGGCAA-CCCACTCTAAAGCCCACACAAATCGATGGCAA
*
184626 T
192 C
* *
184627 CTCTTCTAAAGCCCATACAAGTTGGTGGCAACCCCCTTT-TAAAGCCCACACAAGTCGGTGGCAA
1 CCCTTCTAAAGCCCATACAAGTTGGTGGCAA-CCCCTTTCTAAAGCCCACATAAGTCGGTGGCAA
* * * **
184691 CCCCCCTCTAAAGCCCACATAAGTCGGTGGCAACCCTCCTCTAAAGCCCACACAAGTCGGTGGCA
65 --CCCTTCTAAAGCCCACATAAGTCAGTGGCAACCCTTCT-TAAAGCCCACACAA-TTAGTGGCA
* * * ** * *
184756 ATCCCCCTCTAAAGCCCACACAAATCGGTGGCAA-CCTTTCTAAAGCCCACACAAATTGGTGGCA
126 ACCCCCCTCTAAAGCCCACACAAGTAGGTGGCAACCCACTCTAAAGCCCACACAAATCGATGGCA
*
184820 TC
191 AC
*
184822 TCCTTCT-AAGCCCA
1 CCCTTCTAAAGCCCA
184836 ATGTCGTTGA
Statistics
Matches: 341, Mismatches: 48, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
192 25 0.07
193 9 0.03
194 161 0.47
195 64 0.19
196 53 0.16
197 29 0.09
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.20
Consensus pattern (192 bp):
CCCTTCTAAAGCCCATACAAGTTGGTGGCAACCCCTTTCTAAAGCCCACATAAGTCGGTGGCAAC
CCTTCTAAAGCCCACATAAGTCAGTGGCAACCCTTCTTAAAGCCCACACAATTAGTGGCAACCCC
CCTCTAAAGCCCACACAAGTAGGTGGCAACCCACTCTAAAGCCCACACAAATCGATGGCAAC
Found at i:185034 original size:69 final size:71
Alignment explanation
Indices: 184948--185087 Score: 248
Period size: 69 Copynumber: 2.0 Consensus size: 71
184938 TTAAGTCTAA
184948 TATCACTGGCCTTGAATTAGCATATTGGCACCTTTG-T-TCTTTAAGTCAATATCGCTGGCCTTG
1 TATCACTGGCCTTGAATTAGCATATTGGCACCTTTGTTATCTTTAAGTCAATATCGCTGGCCTTG
*
185011 TATCAG
66 AATCAG
*
185017 TATCACTGGCCTTGAATTAGCATATTGGCACCTTTGTTATCTTTAAGTCAATATCGTTGGCCTTG
1 TATCACTGGCCTTGAATTAGCATATTGGCACCTTTGTTATCTTTAAGTCAATATCGCTGGCCTTG
185082 AATCAG
66 AATCAG
185088 CATGGTCCTT
Statistics
Matches: 67, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
69 36 0.54
70 1 0.01
71 30 0.45
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.38
Consensus pattern (71 bp):
TATCACTGGCCTTGAATTAGCATATTGGCACCTTTGTTATCTTTAAGTCAATATCGCTGGCCTTG
AATCAG
Found at i:185110 original size:47 final size:48
Alignment explanation
Indices: 185047--185138 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
185037 CATATTGGCA
* * ** *
185047 CCTTTGTTATCTTTAAG-TCAATATCGTTGGCCTTGAATCAGCATGGT
1 CCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATCAGCATGGT
185094 CCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATCAGCAT
1 CCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATCAGCAT
185139 ATTGGCACCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
47 16 0.41
48 23 0.59
ACGTcount: A:0.24, C:0.24, G:0.15, T:0.37
Consensus pattern (48 bp):
CCTTTGTCATCTTTAAGCCCAATATCACTAGCCTTGAATCAGCATGGT
Found at i:185193 original size:58 final size:57
Alignment explanation
Indices: 185122--185322 Score: 195
Period size: 52 Copynumber: 3.5 Consensus size: 57
185112 CCAATATCAC
*
185122 TAGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCCAATGT
1 TAGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGT-CAATAT
* * * * *
185180 TAGCCTTGAATCAGCACATTGGCACCTTTGTCA-TCTT-TAAGC-CCAA-T--ATCAT
1 TAGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCAAT-AT
* *
185232 TAGTCTTGAATCAACATATTGGCACCTTTATC-TTCTTCTCATCTTCAAG-CATGATAT
1 TAGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCA--ATAT
185289 CACTAG-CTGTGAATCAGCATATTGGCACCTTTAT
1 ---TAGCCT-TGAATCAGCATATTGGCACCTTTAT
185323 TCTTCGCATG
Statistics
Matches: 116, Mismatches: 14, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
51 2 0.02
52 33 0.28
53 3 0.03
54 4 0.03
55 3 0.03
56 3 0.03
57 6 0.05
58 33 0.28
59 2 0.02
60 27 0.23
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (57 bp):
TAGCCTTGAATCAGCATATTGGCACCTTTATCATTCTTCTCATCTTCAAGTCAATAT
Found at i:189091 original size:13 final size:13
Alignment explanation
Indices: 189073--189098 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
189063 ACATTTTGGG
189073 ATGTATCGATACA
1 ATGTATCGATACA
189086 ATGTATCGATACA
1 ATGTATCGATACA
189099 TATTGTGTGT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:189093 original size:33 final size:32
Alignment explanation
Indices: 189051--189118 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 32
189041 CGTTACAAGC
*
189051 CAATGTATCGATACATTTTGGGATGTATCGATA
1 CAATGTATCGATACATATTGGG-TGTATCGATA
*
189084 CAATGTATCGATACATATTGTGTGTATCGATA
1 CAATGTATCGATACATATTGGGTGTATCGATA
189116 CAA
1 CAA
189119 ACAGTTAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
CAATGTATCGATACATATTGGGTGTATCGATA
Found at i:189223 original size:20 final size:20
Alignment explanation
Indices: 189200--189263 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
189190 CATTTGGTCA
189200 TGTATCGATACTATGCAATC
1 TGTATCGATACTATGCAATC
189220 TGTATCG--A-TA--CAA--
1 TGTATCGATACTATGCAATC
189233 TGTATCGATACTATGCAATC
1 TGTATCGATACTATGCAATC
189253 TGTATCGATAC
1 TGTATCGATAC
189264 ATTTAAAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 7 0.19
15 4 0.11
16 2 0.05
17 2 0.05
18 4 0.11
20 18 0.49
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (20 bp):
TGTATCGATACTATGCAATC
Found at i:189241 original size:33 final size:33
Alignment explanation
Indices: 189199--189264 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
189189 ACATTTGGTC
189199 ATGTATCGATACTATGCAATCTGTATCGATACA
1 ATGTATCGATACTATGCAATCTGTATCGATACA
189232 ATGTATCGATACTATGCAATCTGTATCGATACA
1 ATGTATCGATACTATGCAATCTGTATCGATACA
189265 TTTAAAGGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACTATGCAATCTGTATCGATACA
Found at i:189951 original size:20 final size:21
Alignment explanation
Indices: 189928--189984 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
189918 ACAATTCAAA
* *
189928 GTATCGATACATGTTACA-AT
1 GTATCGATACATGTAAAATAT
*
189948 GTATCGATACATGAAAAATAT
1 GTATCGATACATGTAAAATAT
189969 GTATCGATACATGTAA
1 GTATCGATACATGTAA
189985 TTGGGAATTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.47
21 17 0.53
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (21 bp):
GTATCGATACATGTAAAATAT
Found at i:189972 original size:21 final size:20
Alignment explanation
Indices: 189928--189981 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
189918 ACAATTCAAA
** *
189928 GTATCGATACATGTTACAAT
1 GTATCGATACATGAAAAAAT
189948 GTATCGATACATGAAAAATAT
1 GTATCGATACATGAAAAA-AT
189969 GTATCGATACATG
1 GTATCGATACATG
189982 TAATTGGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGAAAAAAT
Found at i:190057 original size:21 final size:20
Alignment explanation
Indices: 190011--190063 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
190001 GTAGCCAAAC
**
190011 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
190031 -TGTATCGATACACCAAAAAA
1 TTGTATCGATACACC-AAAAA
190051 TTGTATCGATACA
1 TTGTATCGATACA
190064 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 14 0.48
20 3 0.10
21 12 0.41
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:190565 original size:34 final size:35
Alignment explanation
Indices: 190502--190568 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
190492 CTGAGTGATT
190502 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
190538 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
190569 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:193735 original size:13 final size:13
Alignment explanation
Indices: 193717--193741 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
193707 TTTTCCAGAT
193717 TGTATCGATACAA
1 TGTATCGATACAA
193730 TGTATCGATACA
1 TGTATCGATACA
193742 TTACTTCAGT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:196137 original size:34 final size:35
Alignment explanation
Indices: 196074--196140 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
196064 CTGAGTGATT
196074 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
196110 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
196141 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:198480 original size:13 final size:13
Alignment explanation
Indices: 198462--198499 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
198452 ATAAACCCTT
*
198462 TGTATCGATACAC
1 TGTATCGATACAA
198475 TGTATCGATACAA
1 TGTATCGATACAA
198488 TGTATCGATACA
1 TGTATCGATACA
198500 GAGAATGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:203031 original size:3 final size:3
Alignment explanation
Indices: 203023--203053 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
203013 TCTGAGTCAC
*
203023 CAT CAT CAT CAT CAT CAT CAT CTT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
203054 CTTGATGGTT
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:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:204584 original size:19 final size:20
Alignment explanation
Indices: 204539--204590 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
204529 TTACAAGCCA
*
204539 ATGTATCGATACATTTTGGG
1 ATGTATCGATACATATTGGG
*
204559 ATGTATCGATACATATTGTG
1 ATGTATCGATACATATTGGG
204579 -TGTATCGATACA
1 ATGTATCGATACA
204591 AACAGTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.29, C:0.12, G:0.21, T:0.38
Consensus pattern (20 bp):
ATGTATCGATACATATTGGG
Found at i:207452 original size:13 final size:13
Alignment explanation
Indices: 207434--207458 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
207424 ACCAAGAACA
207434 TGTATCGATACAT
1 TGTATCGATACAT
207447 TGTATCGATACA
1 TGTATCGATACA
207459 AAGCAATGTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:207478 original size:33 final size:32
Alignment explanation
Indices: 207415--207479 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
207405 CAATTTGCTG
* *
207415 TGTATCGATACCAAGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCAATACAT
**
207447 TGTATCGATACAAAGCAATGTGTATCAATACAT
1 TGTATCGATACAAAG-AACATGTATCAATACAT
207480 CTGGGCCTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.29
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCAATACAT
Found at i:214622 original size:3 final size:3
Alignment explanation
Indices: 214616--214652 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
214606 GTCAACTTCT
*
214616 TCA TCA TCA TCA TCA TC- TCA TCA TCA TCT TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
214653 TTTGATGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:214638 original size:17 final size:17
Alignment explanation
Indices: 214616--214649 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
214606 GTCAACTTCT
214616 TCATCATCATCATCATC
1 TCATCATCATCATCATC
*
214633 TCATCATCATCTTCATC
1 TCATCATCATCATCATC
214650 ATCTTTGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.38
Consensus pattern (17 bp):
TCATCATCATCATCATC
Found at i:214641 original size:20 final size:20
Alignment explanation
Indices: 214616--214653 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
214606 GTCAACTTCT
214616 TCATCATCATCATCATCTCA
1 TCATCATCATCATCATCTCA
*
214636 TCATCATCTTCATCATCT
1 TCATCATCATCATCATCT
214654 TTGATGGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.39
Consensus pattern (20 bp):
TCATCATCATCATCATCTCA
Found at i:215177 original size:210 final size:209
Alignment explanation
Indices: 214816--215241 Score: 719
Period size: 210 Copynumber: 2.0 Consensus size: 209
214806 AGCTTCCCAT
* * *
214816 GATTTTGAAAGACTATTGAGAAGCTTCTTCACCATCTCTTTGTTGGGAAAGGTTTTCCTAAGAGC
1 GATTTTGAAAGACTATTGAAAAGCTTCTTCACCATCTCTTTGTTAGGAAAGGTTTTCCCAAGAGC
* * * *
214881 TTTCAACCCATTGCTAATATTGGTAAACCAATTGAGCATCTCTTTGATGCTTTCATCGATTTTCA
66 TTTCAACCCATTGCTAATATCGATAAACCAATTGAGCATCTCTTTAATGCTTTCATCAATTTTCA
214946 TCTTGAAGAGCTCATAGTCAAGGGTGAGCATGCTAATTTTTGATTCCTTGACTTGTGTTGTTCCT
131 TCTTGAAGAGCTCATAGTCAAGGGTGAGCATGCTAATTTTTGATTCCTTGACTTGTGTTGTTCCT
215011 TCATGTGTTGTGGC
196 TCATGTGTTGTGGC
* *
215025 GATTTTGGAAGACTATTGAAAAGCTTCTTCACCATCCTCTTTGTTAGGAAAGGTTTTCCCGAGAG
1 GATTTTGAAAGACTATTGAAAAGCTTCTTCACCAT-CTCTTTGTTAGGAAAGGTTTTCCCAAGAG
*
215090 CTTTCAACCCATTGCTAATATCGATAAATCAATT-AGGCATCTCTTTAATGCTTTCATCAATTTT
65 CTTTCAACCCATTGCTAATATCGATAAACCAATTGA-GCATCTCTTTAATGCTTTCATCAATTTT
*
215154 CATCTTGAAGAGCTCATAGTCAAGGGTGAGCATGCTAATTTTTTATTCCTTGACTTGTGTTGTTC
129 CATCTTGAAGAGCTCATAGTCAAGGGTGAGCATGCTAATTTTTGATTCCTTGACTTGTGTTGTTC
215219 CTTCATGTGTTGTGGC
194 CTTCATGTGTTGTGGC
*
215235 GAGTTTG
1 GATTTTG
215242 TCCCATATTT
Statistics
Matches: 203, Mismatches: 12, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
209 34 0.17
210 169 0.83
ACGTcount: A:0.23, C:0.18, G:0.19, T:0.39
Consensus pattern (209 bp):
GATTTTGAAAGACTATTGAAAAGCTTCTTCACCATCTCTTTGTTAGGAAAGGTTTTCCCAAGAGC
TTTCAACCCATTGCTAATATCGATAAACCAATTGAGCATCTCTTTAATGCTTTCATCAATTTTCA
TCTTGAAGAGCTCATAGTCAAGGGTGAGCATGCTAATTTTTGATTCCTTGACTTGTGTTGTTCCT
TCATGTGTTGTGGC
Found at i:217817 original size:13 final size:13
Alignment explanation
Indices: 217799--217824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
217789 TACACAAAGT
217799 ATGTATCGATACA
1 ATGTATCGATACA
217812 ATGTATCGATACA
1 ATGTATCGATACA
217825 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:217822 original size:32 final size:33
Alignment explanation
Indices: 217781--217844 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
217771 TAGCCAAACT
**
217781 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
217813 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
217845 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:221935 original size:16 final size:16
Alignment explanation
Indices: 221899--221935 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
221889 GATAAAAATG
*
221899 TCCAAATTGAAGAAGC
1 TCCAAAATGAAGAAGC
221915 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
221930 TCCAAA
1 TCCAAA
221936 CGAAATCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:224045 original size:13 final size:13
Alignment explanation
Indices: 224013--224048 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
224003 TATTTTTCTT
* *
224013 TGTATCAATACAT
1 TGTATCGATACAC
224026 TGTATCGATACAC
1 TGTATCGATACAC
224039 TGTATCGATA
1 TGTATCGATA
224049 TAGGGGGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:224205 original size:20 final size:20
Alignment explanation
Indices: 224162--224207 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
224152 AAATCTTTTG
224162 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
224183 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
224203 CAAAA
1 CAAAA
224208 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:225956 original size:39 final size:40
Alignment explanation
Indices: 225899--225979 Score: 94
Period size: 39 Copynumber: 2.0 Consensus size: 40
225889 TTTAATAAAA
* *
225899 GGGGAGAATGCATAAATTTGCTAAATTTA-TCTTA-TTAAG
1 GGGGAGAATGCACAAATTTGCTAAAATTACT-TTAGTTAAG
* * *
225938 GGGGAGAATGTACGAATTTGTTAAAATTACTTTAGTTAAG
1 GGGGAGAATGCACAAATTTGCTAAAATTACTTTAGTTAAG
225978 GG
1 GG
225980 AGAAAGAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
39 27 0.77
40 8 0.23
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.35
Consensus pattern (40 bp):
GGGGAGAATGCACAAATTTGCTAAAATTACTTTAGTTAAG
Found at i:226566 original size:21 final size:21
Alignment explanation
Indices: 226540--226596 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
226530 ACATGTTGCA
226540 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
226561 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
226582 ATGTATCGATACATG
1 ATGTATCGATACATG
226597 TCATTGGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:226663 original size:13 final size:13
Alignment explanation
Indices: 226645--226670 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
226635 TACACAAAGT
226645 ATGTATCGATACA
1 ATGTATCGATACA
226658 ATGTATCGATACA
1 ATGTATCGATACA
226671 CAAAAAATTG
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:226668 original size:32 final size:33
Alignment explanation
Indices: 226627--226690 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
226617 TAGCCAAACT
**
226627 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
226659 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
226691 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:231021 original size:52 final size:52
Alignment explanation
Indices: 230888--231028 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
230878 TGAAAAGTTA
230888 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
230940 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
230992 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
231029 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:231035 original size:13 final size:13
Alignment explanation
Indices: 231017--231041 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
231007 CAAAAATCAG
231017 TGTATCGATACAA
1 TGTATCGATACAA
231030 TGTATCGATACA
1 TGTATCGATACA
231042 TGTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:231124 original size:13 final size:13
Alignment explanation
Indices: 231106--231130 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
231096 CAAAAAAATA
231106 TGTATCGATACAT
1 TGTATCGATACAT
231119 TGTATCGATACA
1 TGTATCGATACA
231131 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:231126 original size:33 final size:33
Alignment explanation
Indices: 231084--231150 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
231074 AGTAGCTTAA
231084 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
231117 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
231150 A
1 A
231151 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:231229 original size:21 final size:21
Alignment explanation
Indices: 231188--231229 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
231178 GTTGGGACCT
*
231188 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
231209 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
231230 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:232144 original size:171 final size:168
Alignment explanation
Indices: 231949--232333 Score: 611
Period size: 171 Copynumber: 2.3 Consensus size: 168
231939 TTTTAGAGAT
231949 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAA-GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
232014 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
* *
232079 TGTCAACGTGCTGATTCAAGGCCAGC-TACATTGAACT-TAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTA-A-AG-A-TGGAAA
* * *
232120 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATGATGATGAGAAAA
1 GATGAAG-TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
232185 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
65 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
232250 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
130 TGTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
*
232289 -AT---GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
232334 GTGCCAATGT
Statistics
Matches: 203, Mismatches: 8, Indels: 13
0.91 0.04 0.06
Matches are distributed among these distances:
164 40 0.20
165 1 0.00
168 3 0.01
169 4 0.02
170 2 0.01
171 151 0.74
172 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (168 bp):
GATGAAGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAAG
TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGAT
GTCAACGTGCTGATTCAAGGCCAGCTTAAAGATGGAAA
Found at i:232166 original size:49 final size:49
Alignment explanation
Indices: 232020--232178 Score: 147
Period size: 49 Copynumber: 3.1 Consensus size: 49
232010 AAAAGTGATA
* * * * *
232020 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT--G
* ** * * *
232071 AAAAAGGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG
1 ---AA-GATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
232124 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAAATG
1 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
*
232173 ATGATG
1 AAGATG
232179 AGAAAAGTGA
Statistics
Matches: 85, Mismatches: 19, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
49 45 0.53
50 2 0.02
53 1 0.01
54 2 0.02
55 35 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (49 bp):
AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG
Found at i:232281 original size:45 final size:42
Alignment explanation
Indices: 232229--232361 Score: 126
Period size: 43 Copynumber: 3.1 Consensus size: 42
232219 ACGATATTGG
* *
232229 GCTTAAAGATGAGAAAAAGGATGTCAACGTGCTGATTCAAGGCCA
1 GCTTAAAGATG-G-AAAAGG-TGCCAACATGCTGATTCAAGGCCA
* *
232274 GCTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCA
1 GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
* * **
232316 GC-TATA-TTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCA
1 GCTTAAAGATGGA---AAAGGTGCCAACATGCTGATTCAAGGCCA
232359 GCT
1 GCT
232362 ACATTGGACT
Statistics
Matches: 76, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
40 4 0.05
41 3 0.04
42 23 0.30
43 34 0.45
44 1 0.01
45 11 0.14
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (42 bp):
GCTTAAAGATGGAAAAGGTGCCAACATGCTGATTCAAGGCCA
Found at i:232310 original size:42 final size:42
Alignment explanation
Indices: 232258--232453 Score: 157
Period size: 43 Copynumber: 4.5 Consensus size: 42
232248 GATGTCAACG
*
232258 TGCTGATTCAAGGCCAGCTTAAAGATGGA-AAATGTGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAA-ATGGATAAAGGTGCCAATA
* * *
232300 TGCTGATTCAAGGCCAGC-TATATTGGACTTAAAGGTGCCAATG
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--TAAAGGTGCCAATA
* *
232343 TGCTGATTCAAGGCCAGC-TACATTGGACTTAAAGATGAAGATGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--T-AA-A-G--G-TGCCAATA
* * *
232392 TGCTGATTCAAGGCCAGC-GATATTGGACTTAAAGGTGCCAATA
1 TGCTGATTCAAGGCCAGCTTAAAATGGA--TAAAGGTGCCAATA
*
232435 TGCTGAGTCAAGGCCAGCT
1 TGCTGATTCAAGGCCAGCT
232454 ACATTGGACT
Statistics
Matches: 135, Mismatches: 9, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
40 4 0.03
41 3 0.02
42 18 0.13
43 65 0.48
44 3 0.02
45 1 0.01
46 2 0.01
47 1 0.01
48 3 0.02
49 35 0.26
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (42 bp):
TGCTGATTCAAGGCCAGCTTAAAATGGATAAAGGTGCCAATA
Found at i:232390 original size:49 final size:49
Alignment explanation
Indices: 232291--233497 Score: 1658
Period size: 49 Copynumber: 24.8 Consensus size: 49
232281 GATGGAAAAT
* *
232291 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
232334 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * *
232383 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * *
232426 GTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
232475 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * * *
232524 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * * * *
232573 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAATGGTGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* *
232622 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * * *
232671 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
232720 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAG
* *
232771 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * *
232820 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGTG-GG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
232868 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
232917 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * *
232966 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
233015 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAG
* * *
233066 GTGCCAATATGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * *
233115 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAATGGTG-GG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
233163 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
233212 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * *
233261 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
233310 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAG
* *
233361 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
*
233410 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* *
233458 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
233498 GAGGGGTTGC
Statistics
Matches: 1033, Mismatches: 105, Indels: 47
0.87 0.09 0.04
Matches are distributed among these distances:
43 75 0.07
45 1 0.00
47 2 0.00
48 139 0.13
49 682 0.66
51 119 0.12
52 15 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (49 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
Found at i:232561 original size:98 final size:98
Alignment explanation
Indices: 232291--233497 Score: 1838
Period size: 98 Copynumber: 12.4 Consensus size: 98
232281 GATGGAAAAT
*
232291 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCAATGTGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
232350 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * *
232383 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATATGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
*
232442 TCAAGGCCAGCTACATTGGACTTAAAGATAAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * * * *
232475 GTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
* * *
232540 TCAAGGCCAGCGATATTGGACTTAAAGATGATG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * * *
232573 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
*
232638 TCAAGGCCAGCTACATTGGACTTAAAGATGATG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * *
232671 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
232736 TCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAG
232771 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
* * *
232836 TCAAGGCCAGCTACATTGGACTTAATGGTG-GG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * *
232868 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
232933 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* *
232966 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
233031 TCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAG
*
233066 GTGCCAATATGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
* * *
233131 TCAAGGCCAGCTACATTGGACTTAATGGTG-GG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* * *
233163 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
233228 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* *
233261 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
233326 TCAAGGCCAGCTACATTGGACTT-AAGATGGAAAAG
66 TCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAG
233361 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
233426 TCAAGGCCAGCTACATTGGACTTAAAGATG-AG
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
* *
233458 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
233498 GAGGGGTTGC
Statistics
Matches: 1026, Mismatches: 69, Indels: 35
0.91 0.06 0.03
Matches are distributed among these distances:
92 121 0.12
96 1 0.00
97 236 0.23
98 390 0.38
100 267 0.26
101 11 0.01
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (98 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAG
TCAAGGCCAGCTACATTGGACTTAAAGATGAAG
Found at i:232955 original size:295 final size:295
Alignment explanation
Indices: 232291--233497 Score: 2030
Period size: 295 Copynumber: 4.1 Consensus size: 295
232281 GATGGAAAAT
* *
232291 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGAT
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
232350 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
*
232415 TGGACTT----A--AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAA-A--GAT
131 TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGA-
* * * * *
232471 AAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
195 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
* * * *
232536 TGATTCAAGGCCAGCGATATTGGACTTAAAGATGATG
260 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-GG
* * * * * *
232573 ATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAATGGTGAAGGTGCCAATGTGCTGAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
*
232638 TCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATTCAAGGCCAGCGATAT
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
*
232703 TGGACTTAAAGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
131 TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
232768 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
196 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* *
232833 GAGTCAAGGCCAGCTACATTGGACTTAATGGTGGG
261 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGG
*
232868 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
232933 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
232998 TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
131 TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
*
233063 AAGGTGCCAATATGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
196 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
* *
233128 GAGTCAAGGCCAGCTACATTGGACTTAATGGTGGG
261 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGG
*
233163 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
233228 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
66 TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
233293 TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
131 TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
233358 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
196 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
*
233423 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGAG
261 GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGG
*
233458 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTA
233498 GAGGGGTTGC
Statistics
Matches: 876, Mismatches: 34, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
282 35 0.04
283 1 0.00
288 90 0.10
294 43 0.05
295 616 0.70
296 89 0.10
297 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.25
Consensus pattern (295 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAG
TCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATAT
TGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAGATGGAA
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCT
GAGTCAAGGCCAGCTACATTGGACTTAAAGATGGG
Found at i:233539 original size:33 final size:34
Alignment explanation
Indices: 233502--233566 Score: 114
Period size: 33 Copynumber: 1.9 Consensus size: 34
233492 GGCTTAGAGG
*
233502 GGTTGCCACCGACTTGTGTTGGCTTT-GGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
233535 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG
233567 GGAGAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 25 0.83
34 5 0.17
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.29
Consensus pattern (34 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGGAAGAA
Found at i:233609 original size:34 final size:33
Alignment explanation
Indices: 233571--234103 Score: 341
Period size: 34 Copynumber: 16.6 Consensus size: 33
233561 AGGAAGGGAG
*
233571 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAA-GGAA
*
233605 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
233640 GAAGGTGCCACGGAGTTGTGGGCTTTAAA-G--
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
*
233670 --AG-TGCCACGGAGTCGTGGGCTTTAAAAGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
233701 AAAGGGTGCCACGGAGTTATGGGCTTAGAAGGAA
1 AAA-GATGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
233735 AAAGAGTGCCACAGAGTTGTGGGCTTTTAA--AA
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
233767 AAAG-TGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * *
233800 GAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
233834 GAAGGTGCCACGGAGTTGTGGGCTTAAAGATGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAA-AGGAA
*
233868 AAA-AGTGCCACGGAATTGTGGGCTTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
233900 ---G-TGCCACGGAGTTGTGGGCTTTAAAGG-A
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* **
233928 AAAGGTGCCACGGAGTTGTGGGCTTTGAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
** * * * *
233960 AAA-ATGCCATTGAGTCGTGGACCTT--GA-GAC
1 AAAGATGCCACGGAGTTGTGG-GCTTAAAAGGAA
* * * *
233990 AAA-ATGCCACTGAGTCGTGGACTTTAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * ** *
234021 AAAGATGCCACTGAGTCGTGGACTT-TGA-GAC
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
234052 AAA-ATGCCACTGAGTCGTGGACTTTAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
234083 AAAGATGCCACTGAGTCGTGG
1 AAAGATGCCACGGAGTTGTGG
234104 ACTTTGAGCA
Statistics
Matches: 423, Mismatches: 44, Indels: 66
0.79 0.08 0.12
Matches are distributed among these distances:
27 24 0.06
28 24 0.06
29 4 0.01
30 60 0.14
31 35 0.08
32 77 0.18
33 21 0.05
34 128 0.30
35 44 0.10
36 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:233744 original size:96 final size:96
Alignment explanation
Indices: 233571--233953 Score: 432
Period size: 96 Copynumber: 4.0 Consensus size: 96
233561 AGGAAGGGAG
* *
233571 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAAAGGGTGCCACGGAGTTGTGGGCTTTAA
*
233634 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-
64 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
* * *
233666 AAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGGAAAAAGGGTGCCACGGAGTTATGGGC-TTAGA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-GAAAAAGGGTGCCACGGAGTTGTGGGCTTTAAA
* *
233730 AGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTTAA
65 AAGAAAAAG-GTGCCACGGAGTTGTGGGC-TTT-A
* *
233765 AAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAA-GGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAGGGTGCCACGGAGTTGTGGGCTTTAAA
*
233829 AAGAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGATGA
65 AAGAAAAAGGTGCCACGGAGTTGTGGGCTT-----T-A
* *
233867 AAAAAGTGCCACGGAATTGTGGGCTTT------AAAAGGGTGCCACGGAGTTGTGGGCTTT--AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAA
*
233924 AGGAAAAGGTGCCACGGAGTTGTGGGCTTT
66 AGAAAAAGGTGCCACGGAGTTGTGGGCTTT
233954 GAAGAAAAAA
Statistics
Matches: 253, Mismatches: 21, Indels: 34
0.82 0.07 0.11
Matches are distributed among these distances:
89 1 0.00
94 29 0.11
95 19 0.08
96 83 0.33
97 11 0.04
98 37 0.15
99 41 0.16
100 4 0.02
102 28 0.11
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (96 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAA
AGAAAAAGGTGCCACGGAGTTGTGGGCTTTA
Found at i:233788 original size:160 final size:156
Alignment explanation
Indices: 233603--233953 Score: 442
Period size: 160 Copynumber: 2.2 Consensus size: 156
233593 CTTAAAAGGG
*
233603 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-A
1 AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
* *
233667 -AAG-A-GTGCCACGGAGTCGTGGGCTTTAAA-AGGAAAAAGGGTGCCACGGAGTTATGGGCTTA
66 GAAGAAGGTGCCACGGAGTCGTGGGC-TTAAAGAGGAAAAA-AGTGCCACGGAATTATGGGCTT-
233728 GAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTT
128 -----AAAAAGAGTGCCACAGAGTTGTGGGC-TTT
*
233763 AAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
1 AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT--
* * *
233828 AAAGAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTT
64 -AAGAAGAAGGTGCCACGGAGTCGTGGGCTTAAAGAGGAAAAAAGTGCCACGGAATTATGGGCTT
* * *
233893 TAAAAGGGTGCCACGGAGTTGTGGGCTTT
128 AAAAAGAGTGCCACAGAGTTGTGGGCTTT
233922 AAAGGAAAAGGTGCCACGGAGTTGTGGGCTTT
1 AAA--AAAA-GTGCCACGGAGTTGTGGGCTTT
233954 GAAGAAAAAA
Statistics
Matches: 170, Mismatches: 10, Indels: 20
0.85 0.05 0.10
Matches are distributed among these distances:
159 6 0.04
160 84 0.49
161 4 0.02
162 22 0.13
164 1 0.01
165 3 0.02
166 25 0.15
167 25 0.15
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (156 bp):
AAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAA
GAAGAAGGTGCCACGGAGTCGTGGGCTTAAAGAGGAAAAAAGTGCCACGGAATTATGGGCTTAAA
AAGAGTGCCACAGAGTTGTGGGCTTT
Found at i:233826 original size:194 final size:188
Alignment explanation
Indices: 233571--233968 Score: 502
Period size: 194 Copynumber: 2.0 Consensus size: 188
233561 AGGAAGGGAG
233571 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAG-TGCCACGGAGTTGTGGACTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
* *
233636 AGAAGAAGGTGCCACGGAGTTGTGGGCTT-T-AAAGAGTGCCACGGAGTCGTGGGCTTTAAAAGG
64 AGAAGAAGGTGCCACGGAGTTGTGGGCTTATAAAAAAGTGCCACGGAATCGTGGGCTTT------
*
233699 AAAAAGGGTGCCACGGAGTTATGGGC-TTAGAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTT
123 -AAAAGGGTGCCACGGAGTTATGGGCTTTA-AAGG-AAAAG-GTGCCACAGAGTTGTGGGCTTTG
233763 AA-AA
184 AAGAA
* *
233767 AAAGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
*
233830 AGAAGAAGGTGCCACGGAGTTGTGGGCTTAAAGATGAAAAAAGTGCCACGGAATTGTGGGCTTTA
64 AGAAGAAGGTGCCACGGAGTTGTGGGCTT----AT-AAAAAAGTGCCACGGAATCGTGGGCTTTA
* *
233895 AAAGGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAA
124 AAAGGGTGCCACGGAGTTATGGGCTTTAAAGGAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAA
*
233960 AAAATGCCA
1 AAAGTGCCA
233969 TTGAGTCGTG
Statistics
Matches: 182, Mismatches: 9, Indels: 25
0.84 0.04 0.12
Matches are distributed among these distances:
192 23 0.13
193 15 0.08
194 83 0.46
195 26 0.14
196 6 0.03
197 4 0.02
199 1 0.01
201 24 0.13
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.21
Consensus pattern (188 bp):
AAAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
AAGAAGGTGCCACGGAGTTGTGGGCTTATAAAAAAGTGCCACGGAATCGTGGGCTTTAAAAGGGT
GCCACGGAGTTATGGGCTTTAAAGGAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAA
Found at i:234039 original size:62 final size:62
Alignment explanation
Indices: 233933--234139 Score: 319
Period size: 62 Copynumber: 3.3 Consensus size: 62
233923 AAGGAAAAGG
* * * * * *
233933 TGCCACGGAGTTGTGGGCTTTGAAGAAAAA-ATGCCATTGAGTCGTGGACCTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
233994 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
*
234056 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAG-CAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACA-A-AA
234119 TGCCACTGAGTCGTGGACTTT
1 TGCCACTGAGTCGTGGACTTT
234140 TTTTTTTTTT
Statistics
Matches: 136, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
61 28 0.21
62 86 0.63
63 22 0.16
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (62 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAAGATGCCACTGAGTCGTGGACTTTGAGACAAAA
Found at i:235187 original size:15 final size:15
Alignment explanation
Indices: 235167--235200 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
235157 CTCACCGAGA
*
235167 TTTTCTGTTTTGTTT
1 TTTTCTGTTTTCTTT
*
235182 TTTTCTTTTTTCTTT
1 TTTTCTGTTTTCTTT
235197 TTTT
1 TTTT
235201 TGTGTTTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTCTGTTTTCTTT
Found at i:242525 original size:52 final size:52
Alignment explanation
Indices: 242392--242532 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
242382 TGAAAAGTTA
242392 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
242444 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
**
242496 CTGCATGTATCGATACA-AAAATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTTAAT-AGTGTATCGATACA
242533 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:242539 original size:13 final size:13
Alignment explanation
Indices: 242521--242545 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242511 CAAAAATCAG
242521 TGTATCGATACAA
1 TGTATCGATACAA
242534 TGTATCGATACA
1 TGTATCGATACA
242546 TGTGAGTAAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:242628 original size:13 final size:13
Alignment explanation
Indices: 242610--242634 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
242600 CAAAAAAATA
242610 TGTATCGATACAT
1 TGTATCGATACAT
242623 TGTATCGATACA
1 TGTATCGATACA
242635 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:242630 original size:33 final size:33
Alignment explanation
Indices: 242588--242654 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
242578 AGTAGCTTAA
242588 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
242621 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
242654 A
1 A
242655 AATCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:242733 original size:21 final size:21
Alignment explanation
Indices: 242692--242733 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
242682 GTTGGGACCT
*
242692 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
242713 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
242734 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:247480 original size:20 final size:20
Alignment explanation
Indices: 247423--247480 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
247413 CAAAAACTCA
*
247423 AAATGTATCGATACATTCCC
1 AAATGTATCGATACATTTCC
* **
247443 AAATGTATCAATACATTTGG
1 AAATGTATCGATACATTTCC
*
247463 GAATGTATCGATACATTT
1 AAATGTATCGATACATTT
247481 ACTCATGTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (20 bp):
AAATGTATCGATACATTTCC
Found at i:251153 original size:20 final size:20
Alignment explanation
Indices: 251128--251167 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
251118 ACAAGGATTG
251128 GATAATGTAATAAACATGAA
1 GATAATGTAATAAACATGAA
*
251148 GATAATGTAATAAACTTGAA
1 GATAATGTAATAAACATGAA
251168 ACTAAGTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.28
Consensus pattern (20 bp):
GATAATGTAATAAACATGAA
Found at i:251519 original size:157 final size:156
Alignment explanation
Indices: 251326--251607 Score: 438
Period size: 157 Copynumber: 1.8 Consensus size: 156
251316 TGGAAAATAT
* * *
251326 TTTCTTAAATGGTTTAGGAAATATTACATGCTAAATGGTTGGTACAAATTAAGACAAAGTTATCT
1 TTTCCTAAATGATTTAGGAAATATTAAATGCTAAATGGTTGGTACAAATTAAGACAAAGTTATCT
* * *
251391 AAAAGTTAGATAATGTTTTAATTAAGACAAACAACCTAAAAGTTAGGTAATCTTCGATTTATTGT
66 AAAAGTTAGATAATG-TCTAATTAAGACAAACAACCTAAAAGTTAGATAATCTTCAATTTATTGT
251456 CTTAAAATATTGTTTTTGAAAAACAAG
130 CTTAAAATATTGTTTTTGAAAAACAAG
* * * *
251483 TTTCCTAAATGATTTGGGAAATATTAAATGCTAAATGGTTTGTCCATATTAAGACAAAGTTATCT
1 TTTCCTAAATGATTTAGGAAATATTAAATGCTAAATGGTTGGTACAAATTAAGACAAAGTTATCT
* * *
251548 AAAAGTTAGATAATGTCTAATTATGACAAACAATCTAAAAGTTAGATAATGTTCAATTTA
66 AAAAGTTAGATAATGTCTAATTAAGACAAACAACCTAAAAGTTAGATAATCTTCAATTTA
251608 AGACAAACTT
Statistics
Matches: 112, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
156 39 0.35
157 73 0.65
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.36
Consensus pattern (156 bp):
TTTCCTAAATGATTTAGGAAATATTAAATGCTAAATGGTTGGTACAAATTAAGACAAAGTTATCT
AAAAGTTAGATAATGTCTAATTAAGACAAACAACCTAAAAGTTAGATAATCTTCAATTTATTGTC
TTAAAATATTGTTTTTGAAAAACAAG
Found at i:251613 original size:37 final size:36
Alignment explanation
Indices: 251530--251615 Score: 111
Period size: 36 Copynumber: 2.3 Consensus size: 36
251520 GTTTGTCCAT
**
251530 ATTAAGACAAAGTTATCTAAAAGTTAGATAATGTCTA
1 ATTAAGACAAA-CAATCTAAAAGTTAGATAATGTCTA
*
251567 ATTATGACAAACAATCTAAAAGTTAGATAATGT-TCA
1 ATTAAGACAAACAATCTAAAAGTTAGATAATGTCT-A
251603 ATTTAAGACAAAC
1 A-TTAAGACAAAC
251616 TTCCTGAAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 1 0.02
36 22 0.51
37 20 0.47
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (36 bp):
ATTAAGACAAACAATCTAAAAGTTAGATAATGTCTA
Found at i:251626 original size:37 final size:35
Alignment explanation
Indices: 251530--251628 Score: 101
Period size: 37 Copynumber: 2.7 Consensus size: 35
251520 GTTTGTCCAT
*
251530 ATTAAGACAAAGTTATCTAAAAGTTAGATAATGTCTA
1 ATTAAGACAAA-CT-TCTAAAAGTTAGATAATGTCTA
* *
251567 ATTATGACAAACAATCTAAAAGTTAGATAATGT-TCA
1 ATTAAGACAAAC-TTCTAAAAGTTAGATAATGTCT-A
*
251603 ATTTAAGACAAACTTCCTGAAAGTTA
1 A-TTAAGACAAACTT-CTAAAAGTTA
251629 AAAATTTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
35 1 0.02
36 22 0.42
37 29 0.56
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.31
Consensus pattern (35 bp):
ATTAAGACAAACTTCTAAAAGTTAGATAATGTCTA
Found at i:252907 original size:19 final size:19
Alignment explanation
Indices: 252885--252947 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
252875 TAGCCAAACT
252885 TGTATCGATACACCAAGTA
1 TGTATCGATACACCAAGTA
252904 TGTATCGAT--A-C-A--A
1 TGTATCGATACACCAAGTA
252917 TGTATCGATACACCAAGTA
1 TGTATCGATACACCAAGTA
252936 TGTATCGATACA
1 TGTATCGATACA
252948 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 2 0.05
17 2 0.05
19 22 0.58
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACCAAGTA
Found at i:252921 original size:13 final size:13
Alignment explanation
Indices: 252903--252960 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
252893 TACACCAAGT
252903 ATGTATCGATACA
1 ATGTATCGATACA
252916 ATGTATCGATACACCAA
1 ATGTATCGAT--A-C-A
252933 GTATGTATCGATACA
1 --ATGTATCGATACA
252948 ATGTATCGATACA
1 ATGTATCGATACA
252961 CCAAAAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
15 2 0.05
16 2 0.05
17 2 0.05
19 10 0.26
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:252926 original size:32 final size:32
Alignment explanation
Indices: 252885--252964 Score: 160
Period size: 32 Copynumber: 2.5 Consensus size: 32
252875 TAGCCAAACT
252885 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAGTATGTATCGATACAA
252917 TGTATCGATACACCAAGTATGTATCGATACAA
1 TGTATCGATACACCAAGTATGTATCGATACAA
252949 TGTATCGATACACCAA
1 TGTATCGATACACCAA
252965 AAAATTGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACCAAGTATGTATCGATACAA
Found at i:259146 original size:13 final size:13
Alignment explanation
Indices: 259128--259153 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
259118 ACATTTTTCT
259128 TTGTATCGATACA
1 TTGTATCGATACA
259141 TTGTATCGATACA
1 TTGTATCGATACA
259154 GGGGGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:261747 original size:13 final size:13
Alignment explanation
Indices: 261729--261754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
261719 TACACCAAGT
261729 ATGTATCGATACA
1 ATGTATCGATACA
261742 ATGTATCGATACA
1 ATGTATCGATACA
261755 CCAAAAAATT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:266041 original size:7 final size:8
Alignment explanation
Indices: 266022--266132 Score: 78
Period size: 8 Copynumber: 14.6 Consensus size: 8
266012 TATGTAAATT
266022 TTAATATA
1 TTAATATA
266030 TTAATA-A
1 TTAATATA
*
266037 TTAATATT
1 TTAATATA
*
266045 TATAAAAT-
1 T-TAATATA
266053 TTAATATA
1 TTAATATA
266061 TT--TATA
1 TTAATATA
*
266067 -TAA-ATT
1 TTAATATA
*
266073 TTAATATG
1 TTAATATA
266081 TTAATATA
1 TTAATATA
266089 TTAATATA
1 TTAATATA
*
266097 TATAA-ATT
1 T-TAATATA
266105 TTAATATA
1 TTAATATA
*
266113 TTTATATAA
1 TTAATAT-A
266122 TT-ATAT-
1 TTAATATA
266128 TTAAT
1 TTAAT
266133 TAATATTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 23
0.72 0.08 0.20
Matches are distributed among these distances:
5 1 0.01
6 8 0.10
7 20 0.24
8 43 0.52
9 11 0.13
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (8 bp):
TTAATATA
Found at i:266063 original size:18 final size:18
Alignment explanation
Indices: 266040--266123 Score: 77
Period size: 18 Copynumber: 4.8 Consensus size: 18
266030 TTAATAATTA
266040 ATATTTATAAAATTTAAT
1 ATATTTATAAAATTTAAT
*
266058 ATATTTATATAAATTTTA-
1 ATATTTATA-AAATTTAAT
* *
266076 ATATGT-TAATATATTAAT
1 ATATTTATAAAAT-TTAAT
*
266094 ATA--TATAAATTTTAAT
1 ATATTTATAAAATTTAAT
*
266110 ATATTTATATAATT
1 ATATTTATAAAATT
266124 ATATTTAATT
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
16 12 0.23
17 9 0.17
18 24 0.46
19 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (18 bp):
ATATTTATAAAATTTAAT
Found at i:266068 original size:20 final size:20
Alignment explanation
Indices: 266045--266121 Score: 62
Period size: 20 Copynumber: 4.2 Consensus size: 20
266035 AATTAATATT
266045 TATAAAATTTAATATATTTA
1 TATAAAATTTAATATATTTA
* *
266065 TATAAATTTTAATAT-GTTA
1 TATAAAATTTAATATATTTA
*
266084 -AT-ATA-TT-A-ATA--TA
1 TATAAAATTTAATATATTTA
*
266097 TATAAATTTTAATATATTTA
1 TATAAAATTTAATATATTTA
266117 TATAA
1 TATAA
266122 TTATATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 16
0.66 0.09 0.25
Matches are distributed among these distances:
13 2 0.05
14 4 0.09
15 2 0.05
16 4 0.09
17 2 0.05
18 5 0.12
19 3 0.07
20 21 0.49
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (20 bp):
TATAAAATTTAATATATTTA
Found at i:266089 original size:10 final size:9
Alignment explanation
Indices: 266021--266152 Score: 70
Period size: 8 Copynumber: 15.3 Consensus size: 9
266011 TTATGTAAAT
266021 TTTAATATA
1 TTTAATATA
266030 -TTAATA-A
1 TTTAATATA
266037 -TTAATAT-
1 TTTAATATA
266044 TTATAA-A-A
1 TT-TAATATA
266052 TTTAATATA
1 TTTAATATA
*
266061 TTTATATAAA
1 TTTA-ATATA
266071 TTTTAATAT-
1 -TTTAATATA
*
266080 GTTAATATA
1 TTTAATATA
266089 -TTAATATA
1 TTTAATATA
*
266097 TATAA-AT-
1 TTTAATATA
266104 TTTAATATA
1 TTTAATATA
266113 TTT-ATATA
1 TTTAATATA
* *
266121 ATTATATTTA
1 TTTA-ATATA
* *
266131 ATTAATATT
1 TTTAATATA
*
266140 TTTTATATTA
1 TTTAATA-TA
266150 TTT
1 TTT
266153 TAATTTTTTT
Statistics
Matches: 96, Mismatches: 12, Indels: 29
0.70 0.09 0.21
Matches are distributed among these distances:
7 14 0.15
8 37 0.39
9 22 0.23
10 19 0.20
11 4 0.04
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (9 bp):
TTTAATATA
Found at i:266114 original size:52 final size:51
Alignment explanation
Indices: 266011--266121 Score: 177
Period size: 52 Copynumber: 2.2 Consensus size: 51
266001 TGCAGTTAAA
* *
266011 TTATGTAAATTTTAATATATTAATAATTAATATTTATAAAATTTAATATAT
1 TTATATAAATTTTAATATATTAATAATTAATATATATAAAATTTAATATAT
* *
266062 TTATATAAATTTTAATATGTTAATATATTAATATATATAAATTTTAATATAT
1 TTATATAAATTTTAATATATTAATA-ATTAATATATATAAAATTTAATATAT
266114 TTATATAA
1 TTATATAA
266122 TTATATTTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
51 23 0.42
52 32 0.58
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (51 bp):
TTATATAAATTTTAATATATTAATAATTAATATATATAAAATTTAATATAT
Found at i:268203 original size:41 final size:41
Alignment explanation
Indices: 268146--268231 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
268136 AAATAATCAG
* *
268146 ATTAGTCAAAGGTACTACTTCATAGCACAAGCATGCATGAA
1 ATTAGTAAAAGGTACTACTTCATAGCACAAGCACGCATGAA
* *
268187 ATTAGTAAAATGTACTACTTCATAGCACAAGCACGCATGTA
1 ATTAGTAAAAGGTACTACTTCATAGCACAAGCACGCATGAA
268228 ATTA
1 ATTA
268232 AAACTTATCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (41 bp):
ATTAGTAAAAGGTACTACTTCATAGCACAAGCACGCATGAA
Found at i:273069 original size:18 final size:17
Alignment explanation
Indices: 273041--273112 Score: 74
Period size: 18 Copynumber: 4.0 Consensus size: 17
273031 ATAAATTATC
273041 TTAAGTTAATTTTAATTTT
1 TTAA-TTAA-TTTAATTTT
273060 TTAATTAATTTAATTTT
1 TTAATTAATTTAATTTT
* *
273077 ATTAATCTGA-TTGATTTT
1 -TTAAT-TAATTTAATTTT
273095 TTAAATTAATTTAATTTT
1 TT-AATTAATTTAATTTT
273113 CAATCTTATG
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
17 13 0.29
18 26 0.58
19 6 0.13
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (17 bp):
TTAATTAATTTAATTTT
Found at i:273885 original size:22 final size:21
Alignment explanation
Indices: 273839--273911 Score: 60
Period size: 22 Copynumber: 3.4 Consensus size: 21
273829 ATTAAAAATT
* *
273839 TATT-ATATATTTTATTTATA
1 TATTAATAAATTTTATATATA
273859 TTATTAATAAATTTTATATATTA
1 -TATTAATAAATTTTATATA-TA
* *
273882 TATTTAA-AGATATTTATAAATA
1 TA-TTAATAAAT-TTTATATATA
273904 TATTAATA
1 TATTAATA
273912 TTGATTCACA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
21 8 0.19
22 22 0.51
23 13 0.30
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TATTAATAAATTTTATATATA
Found at i:274108 original size:33 final size:32
Alignment explanation
Indices: 274056--274135 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
274046 AATATTAAAT
* * *
274056 TTAATAATTTATATTTTTATATTATATTT-ATA
1 TTAAAAATTTATATATTTATATAAT-TTTAATA
274088 TTAAAAATATTATATATTTATATAATTTTAATA
1 TTAAAAAT-TTATATATTTATATAATTTTAATA
274121 TATAAATAATTTATA
1 T-TAAA-AATTTATA
274136 AAATAAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 10 0.24
33 19 0.46
34 9 0.22
35 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTAAAAATTTATATATTTATATAATTTTAATA
Found at i:274110 original size:41 final size:41
Alignment explanation
Indices: 274052--274177 Score: 123
Period size: 50 Copynumber: 2.9 Consensus size: 41
274042 TTAAAATATT
*
274052 AAATTTAATA-ATTTATATTTTTATATTATATTTATATTAA
1 AAATTTAATATATTTATATTTTTATATTATATTTATAATAA
274092 AAATATT-ATATATTTATATAATTTTAATATATAAATAATTTATAAAATAA
1 AAAT-TTAATATATTTATAT--TTTT-ATAT-T--AT-ATTTAT--AATAA
*
274142 AAATTTAATATATTTATATATTTATATTAT-TTTATA
1 AAATTTAATATATTTATATTTTTATATTATATTTATA
274178 CTTTCATAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 24
0.73 0.02 0.24
Matches are distributed among these distances:
40 8 0.11
41 10 0.14
42 5 0.07
43 4 0.06
44 6 0.08
45 1 0.01
46 1 0.01
47 6 0.08
48 9 0.12
49 2 0.03
50 20 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (41 bp):
AAATTTAATATATTTATATTTTTATATTATATTTATAATAA
Found at i:274120 original size:24 final size:24
Alignment explanation
Indices: 274078--274161 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
274068 ATTTTTATAT
274078 TATATTTATAT--TAAAAATATTA
1 TATATTTATATAATAAAAATATTA
***
274100 TATATTTATATAATTTTAATATATA
1 TATATTTATATAATAAAAATAT-TA
* *
274125 AATAATTTATAAAATAAAAAT-TTAA
1 TAT-ATTTATATAATAAAAATATT-A
274150 TATATTTATATA
1 TATATTTATATA
274162 TTTATATTAT
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
22 11 0.23
24 15 0.32
25 8 0.17
26 13 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TATATTTATATAATAAAAATATTA
Found at i:274538 original size:13 final size:14
Alignment explanation
Indices: 274516--274549 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
274506 TTTAATGTAT
*
274516 TTTATTTAAAA-TA
1 TTTATATAAAATTA
274529 TTTATATAAAATTA
1 TTTATATAAAATTA
274543 TTTATAT
1 TTTATAT
274550 TATAAATAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTATATAAAATTA
Found at i:274584 original size:18 final size:18
Alignment explanation
Indices: 274563--274597 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
274553 AAATAAGTTA
274563 AATATTATTAAATTAAAT
1 AATATTATTAAATTAAAT
*
274581 AATATTATTTAATTAAA
1 AATATTATTAAATTAAA
274598 ATTAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
AATATTATTAAATTAAAT
Found at i:274604 original size:23 final size:22
Alignment explanation
Indices: 274572--274637 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 22
274562 AAATATTATT
* *
274572 AAATTAAATAATATTATTTAATTA
1 AAATT-AATAA-ATTATTAAATCA
274596 AAATTAATAAAAATTATTAAATCA
1 AAATTAAT--AAATTATTAAATCA
*
274620 AAA-TAATAAATTAATAAA
1 AAATTAATAAATTATTAAA
274638 AATATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 10 0.27
23 7 0.19
24 18 0.49
25 2 0.05
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (22 bp):
AAATTAATAAATTATTAAATCA
Found at i:274611 original size:24 final size:23
Alignment explanation
Indices: 274584--274629 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
274574 ATTAAATAAT
* *
274584 ATTATTTAATTAAAATTAATAAAA
1 ATTATTAAATCAAAA-TAATAAAA
274608 ATTATTAAATCAAAATAATAAA
1 ATTATTAAATCAAAATAATAAA
274630 TTAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (23 bp):
ATTATTAAATCAAAATAATAAAA
Found at i:275114 original size:16 final size:16
Alignment explanation
Indices: 275071--275155 Score: 53
Period size: 16 Copynumber: 4.9 Consensus size: 16
275061 CTATAATAAA
*
275071 AAATATATTATTTAATT
1 AAATAT-TTATTTTATT
* * *
275088 AGATGTATATTTTATT
1 AAATATTTATTTTATT
*
275104 AAATATTTATTATATTT
1 AAATATTTATTTTA-TT
*
275121 AATTATTTATTTAATATT
1 AAATATTTATTT--TATT
*
275139 AAAGTTATTTAATTTAT
1 AAA--TATTTATTTTAT
275156 ATTTAATTTT
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
16 18 0.35
17 16 0.31
18 7 0.14
19 2 0.04
20 8 0.16
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (16 bp):
AAATATTTATTTTATT
Found at i:275131 original size:21 final size:21
Alignment explanation
Indices: 275093--275167 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
275083 TAATTAGATG
* **
275093 TATATTTTATTAAATATTTAT
1 TATATTTAATTATTTATTTAT
275114 TATATTTAATTATTTATTTA-
1 TATATTTAATTATTTATTTAT
* *
275134 -ATATTAAAGTTATTTA-AT-T
1 TATATTTAA-TTATTTATTTAT
275153 TATATTTAATT-TTTA
1 TATATTTAATTATTTA
275168 AATAAATAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 4 0.09
19 10 0.22
20 14 0.31
21 17 0.38
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.61
Consensus pattern (21 bp):
TATATTTAATTATTTATTTAT
Found at i:275861 original size:32 final size:32
Alignment explanation
Indices: 275759--275862 Score: 86
Period size: 32 Copynumber: 3.2 Consensus size: 32
275749 CATTTAAGTT
* * * *
275759 TTATTTATAATTGTCCATAATAATGTTAAATG
1 TTATTTATAATTATACAAAATAATGTTAAATA
* * *
275791 TTATTT-T-TTTATACAAAAGACATGGTTTTAAATT
1 TTATTTATAATTATACAAAATA-AT-G--TTAAATA
*
275825 TTATTTATAATTATTCAAAATAATGTTAAATA
1 TTATTTATAATTATACAAAATAATGTTAAATA
275857 TTATTT
1 TTATTT
275863 TTAAGTACAA
Statistics
Matches: 56, Mismatches: 10, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
30 8 0.14
31 3 0.05
32 19 0.34
34 13 0.23
35 3 0.05
36 10 0.18
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (32 bp):
TTATTTATAATTATACAAAATAATGTTAAATA
Found at i:275872 original size:66 final size:66
Alignment explanation
Indices: 275751--275874 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
275741 AATCATCACA
* * * * *
275751 TTTAAGTTTTATTTATAATTGTCCATAATAATGTTAAATGTTATTTTTTTATACAAAAGACATGG
1 TTTAAATTTTATTTATAATTATCCAAAATAATGTTAAATATTATTTTTTAATACAAAAGACATGG
275816 T
66 T
*
275817 TTTAAATTTTATTTATAATTATTCAAAATAATGTTAAATATTA-TTTTTAAGTACAAAA
1 TTTAAATTTTATTTATAATTATCCAAAATAATGTTAAATATTATTTTTTAA-TACAAAA
275875 AATATAGCTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
65 6 0.12
66 45 0.88
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (66 bp):
TTTAAATTTTATTTATAATTATCCAAAATAATGTTAAATATTATTTTTTAATACAAAAGACATGG
T
Found at i:276050 original size:14 final size:16
Alignment explanation
Indices: 276031--276063 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
276021 ATGAAATAAA
276031 TAATTTTTA-AATT-T
1 TAATTTTTATAATTAT
276045 TAATTTTTATAATTAT
1 TAATTTTTATAATTAT
276061 TAA
1 TAA
276064 ATAATATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTTTTATAATTAT
Found at i:276093 original size:42 final size:39
Alignment explanation
Indices: 276015--276099 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 39
276005 ATTAATAAAA
276015 ATAATTATGAAATAAATAATTTTTAAATTTTAATTTTT-
1 ATAATTATGAAATAAATAATTTTTAAATTTTAATTTTTG
* *
276053 ATAATTATTAAATAATATAATTATATTTAATATTTAATTTTTG
1 ATAATTATGAAATAA-ATAATT-T-TTAAAT-TTTAATTTTTG
276096 ATAA
1 ATAA
276100 CATACGAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
38 14 0.35
39 6 0.15
40 1 0.03
41 5 0.12
42 10 0.25
43 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (39 bp):
ATAATTATGAAATAAATAATTTTTAAATTTTAATTTTTG
Found at i:276160 original size:25 final size:25
Alignment explanation
Indices: 276106--276161 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
276096 ATAACATACG
*
276106 AATTT-ATTTTTTAATAAAAATTTA
1 AATTTAATTTTTTAACAAAAATTTA
* * *
276130 ATATTTAATTTTTTAACACAATTTTC
1 A-ATTTAATTTTTTAACAAAAATTTA
276156 AATTTA
1 AATTTA
276162 TAAAAAAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 1 0.04
25 9 0.35
26 16 0.62
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (25 bp):
AATTTAATTTTTTAACAAAAATTTA
Found at i:280939 original size:10 final size:10
Alignment explanation
Indices: 280921--280955 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
280911 TTTGAAAATG
*
280921 TAGCTGTTAC
1 TAGCCGTTAC
280931 TAGCCGTTAC
1 TAGCCGTTAC
280941 TAGCCGTTAC
1 TAGCCGTTAC
*
280951 AAGCC
1 TAGCC
280956 AATGTATCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (10 bp):
TAGCCGTTAC
Found at i:280995 original size:13 final size:13
Alignment explanation
Indices: 280977--281002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
280967 ACATTTGGTC
280977 ATGTATCGATACA
1 ATGTATCGATACA
280990 ATGTATCGATACA
1 ATGTATCGATACA
281003 TCTTGTATGT
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:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Done.