Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold30
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: 2650045
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.30
Warning! 144233 characters in sequence are not A, C, G, or T
File 12 of 17
Found at i:1853320 original size:240 final size:236
Alignment explanation
Indices: 1853027--1853682 Score: 707
Period size: 240 Copynumber: 2.7 Consensus size: 236
1853017 TTGTGGACTT
*
1853027 AAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAGGGTG
1 AAAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAGGGTG
** ** * *
1853092 TTATGGAGTTGTGGAC-TTAAAAGGGTGCCA-GAAAGTTGTGGACTTTGAAAAGAAAAAGGTGCT
65 CCACAGAGTTGTGGACTTTAAAAGAGTGCCACG-AAGTTGTGGAC-TT-AAAAG-----GGTGCC
** * *
1853155 ATGGAGTTATGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTT-AAAAG-GGTGCCA
122 ACAGAGTTATGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAGAAGTGCCA
* **
1853218 CGGAGTTATGGGCTTTAAAAGGGTGCCACGGAGTTATAGACTTAAAAGAA
187 CGGAATTATGGGCTTTAAAAGGGTGCCACAAAGTTATAGACTTAAAAGAA
* * *
1853268 AAAAGAGTGCCACGGAGTTGTAGACTTAAAAGGGTGCCACGAAGTTGTGGGCTTTAAAAGGGTGC
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGC
* *
1853333 CACAGAGTTGTGGGCTTTAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTA
66 CACAGAGTTGTGGACTTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTA
*
1853398 TGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCACGGAA
131 TGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAG----AAGTGCCACGGAA
* * *
1853463 TTGTGGGCTTTAAAAGGGTGCCACAAAGTTATGGACTTAAAAGGA
192 TTATGGGCTTTAAAAGGGTGCCACAAAGTTATAGACTTAAAAGAA
* * *
1853508 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTATGGAC-TTAAAAGGAAAA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAA-G----
* * * *
1853572 AGAGTGCCACAAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCAC-AGAGTTGTGGGCTTAAAAGG
61 -G-GTGCCACAGAGTTGTGGACTT------TAAAAGAGTGCCACGA-AGTTGTGGACTTAAAAGG
* *
1853636 GTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACAGAGTT
117 GTGCCACAGAGTTATGGACTTTGAAAA-GAAAAAG-GTGCCACGGAGTT
1853683 GTGGACTTAA
Statistics
Matches: 356, Mismatches: 35, Indels: 37
0.83 0.08 0.09
Matches are distributed among these distances:
234 52 0.15
235 5 0.01
239 11 0.03
240 148 0.42
241 45 0.13
242 1 0.00
245 1 0.00
246 20 0.06
250 4 0.01
251 9 0.03
252 60 0.17
ACGTcount: A:0.33, C:0.12, G:0.32, T:0.22
Consensus pattern (236 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTTAAAAGGGTGC
CACAGAGTTGTGGACTTTAAAAGAGTGCCACGAAGTTGTGGACTTAAAAGGGTGCCACAGAGTTA
TGGACTTTGAAAAGAAAAAGGTGCCACGGAGTTATGGGCTTTGAAAAGAAGTGCCACGGAATTAT
GGGCTTTAAAAGGGTGCCACAAAGTTATAGACTTAAAAGAA
Found at i:1853668 original size:34 final size:34
Alignment explanation
Indices: 1853630--1853753 Score: 173
Period size: 34 Copynumber: 3.7 Consensus size: 34
1853620 TTGTGGGCTT
1853630 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
*
1853664 AAAAGAGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* *
1853698 ATAAGGG-GCCACAGAGTTATGGACTTTGAAAA-GA
1 AAAAGGGTGCCACAGAGTTGTGGAC-TT-AAAAGGA
*
1853732 AAAA-GGTGCCACAGAGTCGTGG
1 AAAAGGGTGCCACAGAGTTGTGG
1853754 CCTTTGGGAA
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
33 18 0.22
34 58 0.73
35 4 0.05
ACGTcount: A:0.38, C:0.13, G:0.31, T:0.18
Consensus pattern (34 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1853696 original size:61 final size:61
Alignment explanation
Indices: 1853569--1853753 Score: 221
Period size: 61 Copynumber: 2.9 Consensus size: 61
1853559 CTTAAAAGGA
* * * *
1853569 AAAAGAGTGCCACAAAGTTGTGGGCTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
1853630 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
* * *
1853691 AAAAGGAATAAGGGGCCACAGAGTTATGGACTTTGAAAA-GAAAAAG-GTGCCACAGAGTCGTGG
1 AAAA-G-----GGTGCCACAGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACAGAGTTGTGG
1853754 CCTTTGGGAA
Statistics
Matches: 109, Mismatches: 7, Indels: 10
0.87 0.06 0.08
Matches are distributed among these distances:
61 61 0.56
62 1 0.01
67 34 0.31
68 9 0.08
69 4 0.04
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.18
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGACTT
Found at i:1853782 original size:31 final size:31
Alignment explanation
Indices: 1853740--1853798 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1853730 GAAAAAGGTG
* *
1853740 CCACAGAGTCGTGGCCTTTGGGAAGAGATTA
1 CCACAGAGTCGTGGACTTTGAGAAGAGATTA
*
1853771 CCACTGAGTCGTGGACTTTGAGAAGAGA
1 CCACAGAGTCGTGGACTTTGAGAAGAGA
1853799 GATTTGAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.22
Consensus pattern (31 bp):
CCACAGAGTCGTGGACTTTGAGAAGAGATTA
Found at i:1855083 original size:22 final size:22
Alignment explanation
Indices: 1855058--1855113 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1855048 TGATTTTGCC
*
1855058 TTTGCACTTTTTTTGTGTTT-TT
1 TTTG-ACTTTTTTTGTGTTTAAT
**
1855080 TTTGTTTTGTTTTTGTGTTTAAT
1 TTTGACTT-TTTTTGTGTTTAAT
1855103 TTTGACTTTTT
1 TTTGACTTTTT
1855114 CATCATTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
21 2 0.07
22 18 0.67
23 7 0.26
ACGTcount: A:0.07, C:0.05, G:0.14, T:0.73
Consensus pattern (22 bp):
TTTGACTTTTTTTGTGTTTAAT
Found at i:1855105 original size:13 final size:11
Alignment explanation
Indices: 1855065--1855184 Score: 74
Period size: 11 Copynumber: 11.2 Consensus size: 11
1855055 GCCTTTGCAC
1855065 TTTTTTTGTGT
1 TTTTTTTGTGT
1855076 TTTTTTTGT-T
1 TTTTTTTGTGT
1855086 TTGTTTTTGTGT
1 TT-TTTTTGTGT
** *
1855098 TTAATTT-TGA
1 TTTTTTTGTGT
* ** **
1855108 CTTTTTCATCA
1 TTTTTTTGTGT
1855119 TTTTTTT-TG-
1 TTTTTTTGTGT
1855128 -TTTTTTGT-T
1 TTTTTTTGTGT
*
1855137 TTTTTTTGTTT
1 TTTTTTTGTGT
1855148 TTGTTTTTGT-T
1 TT-TTTTTGTGT
1855159 TTTTTTGTGTTGT
1 TTTTTT-TG-TGT
1855172 TTTTTTTGTGT
1 TTTTTTTGTGT
1855183 TT
1 TT
1855185 GCACTTTTGA
Statistics
Matches: 87, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
8 6 0.07
9 1 0.01
10 21 0.24
11 39 0.45
12 13 0.15
13 7 0.08
ACGTcount: A:0.04, C:0.03, G:0.14, T:0.79
Consensus pattern (11 bp):
TTTTTTTGTGT
Found at i:1855177 original size:29 final size:29
Alignment explanation
Indices: 1855122--1855185 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
1855112 TTCATCATTT
*
1855122 TTTTTGTTTTTTGTTTTTTTTTGTTTTTG
1 TTTTTGTTTTTTGTTTTTGTTTGTTTTTG
1855151 TTTTTGTTTTTT-TTGTGTTGTTT-TTTTTG
1 TTTTTGTTTTTTGTT-T-TTGTTTGTTTTTG
*
1855180 TGTTTG
1 TTTTTG
1855186 CACTTTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 2 0.06
29 24 0.77
30 5 0.16
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (29 bp):
TTTTTGTTTTTTGTTTTTGTTTGTTTTTG
Found at i:1855178 original size:17 final size:16
Alignment explanation
Indices: 1855065--1855177 Score: 77
Period size: 16 Copynumber: 6.4 Consensus size: 16
1855055 GCCTTTGCAC
1855065 TTTTTTTGTGTTTT-TT
1 TTTTTTTGT-TTTTGTT
*
1855081 TTGTTTTGTTTTTGTGT
1 TTTTTTTGTTTTTGT-T
* *
1855098 TTAATTTTGACTTTTTCATCAT
1 TT-TTTTTG--TTTTT-GT--T
1855120 TTTTTTTGTTTTTTGTT
1 TTTTTTTG-TTTTTGTT
1855137 TTTTTTTGTTTTTGTT
1 TTTTTTTGTTTTTGTT
1855153 TTTGTTTT-TTTTGTGTT
1 TTT-TTTTGTTTT-TGTT
1855170 GTTTTTTT
1 -TTTTTTT
1855178 TGTGTTTGCA
Statistics
Matches: 80, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
15 4 0.05
16 24 0.30
17 24 0.30
18 8 0.10
19 1 0.01
20 10 0.12
21 6 0.08
22 3 0.04
ACGTcount: A:0.04, C:0.03, G:0.13, T:0.80
Consensus pattern (16 bp):
TTTTTTTGTTTTTGTT
Found at i:1855183 original size:14 final size:13
Alignment explanation
Indices: 1855119--1855180 Score: 74
Period size: 14 Copynumber: 4.8 Consensus size: 13
1855109 TTTTTCATCA
1855119 TTTTTTTTGTTT-
1 TTTTTTTTGTTTG
*
1855131 TTTGTTTTTTTTTG
1 TTT-TTTTTGTTTG
*
1855145 TTTTTGTT-TTTG
1 TTTTTTTTGTTTG
1855157 TTTTTTTTGTGTTG
1 TTTTTTTTGT-TTG
1855171 TTTTTTTTGT
1 TTTTTTTTGT
1855181 GTTTGCACTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
12 14 0.33
13 13 0.30
14 16 0.37
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (13 bp):
TTTTTTTTGTTTG
Found at i:1862185 original size:20 final size:20
Alignment explanation
Indices: 1862132--1862186 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1862122 AAATTCCCAG
**
1862132 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
1862152 ATGTATCGATACATTGAGT-A
1 ATGTATCGATACATTGA-TCA
1862172 ATGTATCGATACATT
1 ATGTATCGATACATT
1862187 TCCTTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:1862570 original size:20 final size:19
Alignment explanation
Indices: 1862545--1862613 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
1862535 ATCGATATAA
1862545 TGTATCGATACATATTTTTT
1 TGTATCGATACA-ATTTTTT
1862565 TGTATCGATACAA------
1 TGTATCGATACAATTTTTT
1862578 TGTATCGATACATATTTTTT
1 TGTATCGATACA-ATTTTTT
*
1862598 TGTGTCGATACAATTT
1 TGTATCGATACAATTT
1862614 AAGCTACTGC
Statistics
Matches: 41, Mismatches: 1, Indels: 15
0.72 0.02 0.26
Matches are distributed among these distances:
13 12 0.29
14 1 0.02
19 5 0.12
20 23 0.56
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.48
Consensus pattern (19 bp):
TGTATCGATACAATTTTTT
Found at i:1862583 original size:13 final size:13
Alignment explanation
Indices: 1862565--1862589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1862555 CATATTTTTT
1862565 TGTATCGATACAA
1 TGTATCGATACAA
1862578 TGTATCGATACA
1 TGTATCGATACA
1862590 TATTTTTTTG
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:1862592 original size:33 final size:33
Alignment explanation
Indices: 1862512--1862611 Score: 146
Period size: 33 Copynumber: 3.0 Consensus size: 33
1862502 TTCAATGATT
*** * *
1862512 TGTATCGATACATAAAATGTTGTATCGATATAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1862545 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
*
1862578 TGTATCGATACATATTTTTTTGTGTCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1862611 T
1 T
1862612 TTAAGCTACT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 61 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATATTTTTTTGTATCGATACAA
Found at i:1862670 original size:13 final size:13
Alignment explanation
Indices: 1862652--1862676 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1862642 ATTACTCAAA
1862652 TGTATCGATACAT
1 TGTATCGATACAT
1862665 TGTATCGATACA
1 TGTATCGATACA
1862677 CTGATCTCTG
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:1862741 original size:52 final size:52
Alignment explanation
Indices: 1862685--1862804 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
1862675 CACTGATCTC
* *
1862685 TGTATCGATACATGCAGGGAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1862737 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1862789 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1862805 AACAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1866956 original size:11 final size:12
Alignment explanation
Indices: 1866941--1866992 Score: 72
Period size: 11 Copynumber: 4.4 Consensus size: 12
1866931 AAGTGATGAA
1866941 AAAAAAACAAAC
1 AAAAAAACAAAC
*
1866953 AAAAAAAACACAC
1 -AAAAAAACAAAC
1866966 AAAAAAA-AAAC
1 AAAAAAACAAAC
1866977 AAAAAAACAAA-
1 AAAAAAACAAAC
1866988 AAAAA
1 AAAAA
1866993 CAGAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
11 15 0.42
12 10 0.28
13 11 0.31
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:1866956 original size:13 final size:13
Alignment explanation
Indices: 1866940--1866992 Score: 69
Period size: 12 Copynumber: 4.4 Consensus size: 13
1866930 AAAGTGATGA
1866940 AAAAAAAACAAAC
1 AAAAAAAACAAAC
*
1866953 AAAAAAAACACAC
1 AAAAAAAACAAAC
1866966 -AAAAAAA-AAAC
1 AAAAAAAACAAAC
1866977 -AAAAAAACAAA-
1 AAAAAAAACAAAC
1866988 AAAAA
1 AAAAA
1866993 CAGAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
11 10 0.28
12 14 0.39
13 12 0.33
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAACAAAC
Found at i:1866970 original size:28 final size:28
Alignment explanation
Indices: 1866940--1867003 Score: 85
Period size: 28 Copynumber: 2.3 Consensus size: 28
1866930 AAAGTGATGA
* *
1866940 AAAAAAAACAAACAAAA-AAAACACACAA
1 AAAAAAAACAAA-AAAACAAAAAAAACAA
*
1866968 AAAAAAAACAAAAAAACAAAAAAAACAG
1 AAAAAAAACAAAAAAACAAAAAAAACAA
1866996 AAAAAAAA
1 AAAAAAAA
1867004 TGCAAAGGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
27 4 0.12
28 28 0.88
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (28 bp):
AAAAAAAACAAAAAAACAAAAAAAACAA
Found at i:1866985 original size:32 final size:30
Alignment explanation
Indices: 1866939--1867003 Score: 94
Period size: 32 Copynumber: 2.1 Consensus size: 30
1866929 AAAAGTGATG
*
1866939 AAAAAAAAACAAACAAAAAAAACACACAAAA
1 AAAAAAAAAAAAACAAAAAAAACACA-AAAA
*
1866970 AAAAAACAAAAAAACAAAAAAAACAGAAAAA
1 AAAAAA-AAAAAAACAAAAAAAACACAAAAA
1867001 AAA
1 AAA
1867004 TGCAAAGGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAACAAAAAAAACACAAAAA
Found at i:1866999 original size:11 final size:10
Alignment explanation
Indices: 1866942--1867003 Score: 65
Period size: 11 Copynumber: 5.9 Consensus size: 10
1866932 AGTGATGAAA
1866942 AAAAAACAAAC
1 AAAAAA-AAAC
1866953 AAAAAAAACAC
1 AAAAAAAA-AC
1866964 ACAAAAAAAA-
1 A-AAAAAAAAC
1866974 AACAAAAAAAC
1 AA-AAAAAAAC
1866985 -AAAAAAAAC
1 AAAAAAAAAC
1866994 AGAAAAAAAA
1 A-AAAAAAAA
1867004 TGCAAAGGCA
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.20
10 11 0.24
11 18 0.40
12 7 0.16
ACGTcount: A:0.85, C:0.13, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:1867001 original size:13 final size:13
Alignment explanation
Indices: 1866939--1867003 Score: 69
Period size: 14 Copynumber: 4.7 Consensus size: 13
1866929 AAAAGTGATG
1866939 AAAAAAAAACAAA
1 AAAAAAAAACAAA
*
1866952 CAAAAAAAACACACA
1 -AAAAAAAA-ACAAA
1866967 AAAAAAAAACAAA
1 AAAAAAAAACAAA
1866980 AAAACAAAAA-AAA
1 AAAA-AAAAACAAA
1866993 CAGAAAAAAAA
1 -A-AAAAAAAA
1867004 TGCAAAGGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 11 0.24
14 27 0.60
15 7 0.16
ACGTcount: A:0.86, C:0.12, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAAAACAAA
Found at i:1867265 original size:20 final size:21
Alignment explanation
Indices: 1867240--1867302 Score: 85
Period size: 20 Copynumber: 3.1 Consensus size: 21
1867230 GTTCTTTTCC
1867240 AAAAAAAGAAACAAAACA-AA
1 AAAAAAAGAAACAAAACAGAA
* *
1867260 AAAAAAAGAAAAAAAAGAGAA
1 AAAAAAAGAAACAAAACAGAA
*
1867281 AAGAAAA-AAACAAAACAGAA
1 AAAAAAAGAAACAAAACAGAA
1867301 AA
1 AA
1867303 GCTCGATAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 29 0.78
21 8 0.22
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (21 bp):
AAAAAAAGAAACAAAACAGAA
Found at i:1867281 original size:31 final size:29
Alignment explanation
Indices: 1867240--1867302 Score: 56
Period size: 31 Copynumber: 2.1 Consensus size: 29
1867230 GTTCTTTTCC
* *
1867240 AAAAAAAGAAACAAAACAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAACAAAAAAAAAAGA
* *
1867269 AAAAAAAGAGAAAAGAAAA-AAACAAAACAGA
1 AAAAAAA-A-AAAA-AAAACAAAAAAAAAAGA
1867300 AAA
1 AAA
1867303 GCTCGATAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
29 7 0.26
31 16 0.59
32 4 0.15
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAAAAAACAAAAAAAAAAGA
Found at i:1868378 original size:31 final size:31
Alignment explanation
Indices: 1868309--1868458 Score: 167
Period size: 31 Copynumber: 4.7 Consensus size: 31
1868299 CTTTTTAAGT
* *
1868309 CCACGACTCAGTGGCATTTTGTC-TCAAAGT
1 CCACGACTCAGTGGCATTTTTTCTTCAAAGC
*
1868339 CCATGACTCAGTGGCATTTTTTCTTCAAAGC
1 CCACGACTCAGTGGCATTTTTTCTTCAAAGC
1868370 CCACGACTCAGTGGCATTTTTTCTTCAAAGC
1 CCACGACTCAGTGGCATTTTTTCTTCAAAGC
* * * *
1868401 CCACAACTCTGTGGCACACTTTTTCTTTTTAAAGC
1 CCACGACTCAGTGG--CA-TTTTT-TCTTCAAAGC
* *
1868436 CCACAACTCTGTGGCACTTTTTT
1 CCACGACTCAGTGGCA-TTTTTT
1868459 TTCCCTTTTC
Statistics
Matches: 107, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.20
31 48 0.45
32 1 0.01
33 10 0.09
34 5 0.05
35 22 0.21
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (31 bp):
CCACGACTCAGTGGCATTTTTTCTTCAAAGC
Found at i:1868507 original size:34 final size:35
Alignment explanation
Indices: 1868365--1868744 Score: 375
Period size: 38 Copynumber: 10.8 Consensus size: 35
1868355 TTTTTTCTTC
* * *
1868365 AAAGCCCACGACTCAGTGGCA-T-TTTTTC--TTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* *
1868396 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* * *
1868431 AAAGCCCACAACTCTGTGGCACTTTTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCAC-TCTTTTT--CTTTTT
1868469 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* * *
1868503 AAAGCCCGCAACTCTGTGGCACTCTTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCACTC-TTTTT--CTTTTT
*
1868541 AAAGCCCATAACTCCGTGGCAC-CTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* *
1868575 AAAGCCCACAACTCTGTGGCACTCTTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCACTC-TTTTT--CTTTTT
* *
1868613 AAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
1868648 -AAGCCCACAACTCCGTGGCACTCTTTTTTTTCCTTTTT
1 AAAGCCCACAACTCCGTGGCACTC---TTTTT-CTTTTT
** * *
1868686 AAAGCCCACAACTCTATGGCAC-CTTGTTCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
* *
1868720 -AAGTCCACAACTTCGTGGCA-TCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTT
1868745 CACCCTCTCT
Statistics
Matches: 293, Mismatches: 35, Indels: 40
0.80 0.10 0.11
Matches are distributed among these distances:
31 19 0.06
33 25 0.09
34 78 0.27
35 33 0.11
36 25 0.09
37 11 0.04
38 83 0.28
39 19 0.06
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.36
Consensus pattern (35 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTTT
Found at i:1868515 original size:72 final size:72
Alignment explanation
Indices: 1868393--1868744 Score: 514
Period size: 72 Copynumber: 4.9 Consensus size: 72
1868383 GCATTTTTTC
* *
1868393 TTCAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTTTTT
1 TTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTT
1868458 TTTCCCTT
65 TTTCCCTT
*
1868466 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCGCAACTCTGTGGCACTCTTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1868531 TTCCCTT
66 TTCCCTT
*
1868538 TTCAAAGCCCATAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
1868603 TTCCCTT
66 TTCCCTT
* * *
1868610 TTCAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT-AAGCCCACAACTCCGTGGCACTCTTT
1 TTCAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTC-TT
*
1868674 TTTTTCCTT
64 TTTTCCCTT
* ** * * *
1868683 TTTAAAGCCCACAACTCTATGGCACCTTGTTCCTTTT-AAGTCCACAACT-TCGTGGCA-TCTTT
1 TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCT-GTGGCACTCTTT
1868745 CACCCTCTCT
Statistics
Matches: 259, Mismatches: 17, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
70 3 0.01
71 2 0.01
72 188 0.73
73 66 0.25
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.37
Consensus pattern (72 bp):
TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTT
TTCCCTT
Found at i:1868793 original size:34 final size:32
Alignment explanation
Indices: 1868746--1868849 Score: 172
Period size: 33 Copynumber: 3.2 Consensus size: 32
1868736 GGCATCTTTC
1868746 ACCCTCTCTAAAGCCCACACAAGTCGGTGGCAA
1 ACCCTCTCTAAAGCCCACACAAGTCGGTGGC-A
1868779 ACCCTTCTCTAAAGCCCACACAAGTCGGTGGCA
1 ACCC-TCTCTAAAGCCCACACAAGTCGGTGGCA
*
1868812 ACCACTCTCTAAAGCCCACACAAGTCGGTGGCG
1 ACC-CTCTCTAAAGCCCACACAAGTCGGTGGCA
1868845 ACCCT
1 ACCCT
1868850 TTAAGTCCAA
Statistics
Matches: 68, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
32 2 0.03
33 38 0.56
34 28 0.41
ACGTcount: A:0.28, C:0.38, G:0.18, T:0.16
Consensus pattern (32 bp):
ACCCTCTCTAAAGCCCACACAAGTCGGTGGCA
Found at i:1868971 original size:49 final size:49
Alignment explanation
Indices: 1868848--1869576 Score: 936
Period size: 49 Copynumber: 15.2 Consensus size: 49
1868838 GGTGGCGACC
* * *
1868848 CTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-C--CTTCAT
* * * *
1868900 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * * *
1868949 CATTAAGTCTAATATAGTTGGCCTTGAATCAACATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1868998 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--CA-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
*
1869043 --TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1869090 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
*
1869139 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1869188 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C--CA-
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1869233 --TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1869280 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1869329 CTTTAAGTCCAATATAGTTGGCCTTGAATCAACATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* *
1869378 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1869421 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * * *
1869470 CTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
* * *
1869519 CATTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCCCCTTCAC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
1869568 CTTTAAGTC
1 CTTTAAGTC
1869577 TAGTGTGGCA
Statistics
Matches: 586, Mismatches: 73, Indels: 39
0.84 0.10 0.06
Matches are distributed among these distances:
43 114 0.19
44 1 0.00
46 4 0.01
48 2 0.00
49 427 0.73
51 1 0.00
52 37 0.06
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.32
Consensus pattern (49 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCAT
Found at i:1869157 original size:141 final size:142
Alignment explanation
Indices: 1868897--1869610 Score: 835
Period size: 141 Copynumber: 5.0 Consensus size: 142
1868887 GCACCTTCTT
* *
1868897 CACC-TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCTAA
1 CACCATTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAA
* * *
1868961 TATAGTTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAA
66 TATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAA
1869026 TCAGCACATTGG
131 TCAGCACATTGG
* * * * *
1869038 CACCA-TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAA
1 CACCATTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAA
* * * *
1869102 TGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAA
66 TATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAA
*
1869167 TCAGCATATTGG
131 TCAGCACATTGG
1869179 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG------CACCATTAAG
1 CACC---A--TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
* *
1869238 TCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGCTGGCC
61 TCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCC
*
1869303 TTGACTCAGCACATTGG
126 TTGAATCAGCACATTGG
* * * * * * *
1869320 CACCTTCATCTTTAAGTCCAATATAGTTGGCCTTGAATCAACATATTGGCACCTTTATCTTTAAG
1 CA-C--CA--TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
* * * *
1869385 TCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATCGCTGGCC
61 TCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCC
* *
1869444 TTGAATCAGTATATTGG
126 TTGAATCAGCACATTGG
*
1869461 CACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAG
1 CACC---A--TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAG
* * * * * *
1869526 TCCAATATAGCTGGCCTTGAATCAGCATATTGGCCCCTTCACCTTTAAGTCTAGTGTGGCAGGCC
61 TCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCC
* *
1869591 TTGAATCTGCACAGTGG
126 TTGAATCAGCACATTGG
1869608 CAC
1 CAC
1869611 ATTGCAAAAC
Statistics
Matches: 485, Mismatches: 63, Indels: 44
0.82 0.11 0.07
Matches are distributed among these distances:
138 1 0.00
140 1 0.00
141 369 0.76
142 1 0.00
144 2 0.00
145 1 0.00
147 110 0.23
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (142 bp):
CACCATTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTCACCATTAAGTCCAA
TATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAGCTGGCCTTGAA
TCAGCACATTGG
Found at i:1869177 original size:190 final size:190
Alignment explanation
Indices: 1868850--1869610 Score: 1270
Period size: 190 Copynumber: 4.0 Consensus size: 190
1868840 TGGCGACCCT
* * *
1868850 TTAAGTCCAATATCGCTGGCCTTGAATCAACATATTGGCACCTTCTTCACCTTTAAGTCCAATGT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-T-TT-ATCTTTAAGTCCAATGT
* *
1868915 AGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCTAATATAGTTGGCCTTGAATCA
63 AGCTGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCA
1868980 ACATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
128 ACATATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
1869043 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
* * *
1869108 TGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
66 TGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAACA
1869173 TATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
131 TATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
*
1869233 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
* * *
1869298 TGGCCTTGACTCAGCACATTGGCACCTTCATCTTTAAGTCCAATATAGTTGGCCTTGAATCAACA
66 TGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAACA
*
1869363 TATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
131 TATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
* *
1869423 TTAAGTCCAATATCGCTGGCCTTGAATCAGTATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
*
1869488 TGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAGCA
66 TGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAACA
* * * * * * * * *
1869553 TATTGGCCCCTTCACCTTTAAGTCTAGTGTGGCAGGCCTTGAATCTGCACAGTGGCAC
131 TATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1869611 ATTGCAAAAC
Statistics
Matches: 540, Mismatches: 28, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
190 497 0.92
191 2 0.00
192 1 0.00
193 40 0.07
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (190 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
TGGCCTTGACTCAGCACATTGGCACCTTCACCATTAAGTCCAATATAGCTGGCCTTGAATCAACA
TATTGGCACCTTTATCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCA
Found at i:1870186 original size:33 final size:33
Alignment explanation
Indices: 1870149--1870248 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
1870139 TTCAATGATT
*** *
1870149 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1870182 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1870215 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATATTTTTTTGTATCGATACAA
1870248 T
1 T
1870249 TTAAGCTACT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATTTTTTTGTATCGATACAA
Found at i:1870187 original size:13 final size:13
Alignment explanation
Indices: 1870169--1870226 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 13
1870159 CATAAAATGT
1870169 TGTATCGATACAA
1 TGTATCGATACAA
1870182 TGTATCGATACATA
1 TGTATCGATACA-A
1870196 TTTTTTTGTATCGATACAA
1 ------TGTATCGATACAA
1870215 TGTATCGATACA
1 TGTATCGATACA
1870227 TATTTTTTTG
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 24 0.63
14 1 0.03
19 1 0.03
20 12 0.32
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1870207 original size:20 final size:19
Alignment explanation
Indices: 1870182--1870250 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1870172 ATCGATACAA
1870182 TGTATCGATACATATTTTTT
1 TGTATCGATACA-ATTTTTT
1870202 TGTATCGATACAA------
1 TGTATCGATACAATTTTTT
1870215 TGTATCGATACATATTTTTT
1 TGTATCGATACA-ATTTTTT
1870235 TGTATCGATACAATTT
1 TGTATCGATACAATTT
1870251 AAGCTACTGC
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
13 12 0.29
14 1 0.02
19 5 0.12
20 24 0.57
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (19 bp):
TGTATCGATACAATTTTTT
Found at i:1870307 original size:13 final size:13
Alignment explanation
Indices: 1870289--1870313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1870279 ATTACTCAAA
1870289 TGTATCGATACAT
1 TGTATCGATACAT
1870302 TGTATCGATACA
1 TGTATCGATACA
1870314 CTGATCTCTG
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:1870378 original size:52 final size:52
Alignment explanation
Indices: 1870322--1870441 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
1870312 CACTGATCTC
* *
1870322 TGTATCGATACATGCAGGGAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1870374 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1870426 TGTATCGATACATGCA
1 TGTATCGATACATGCA
1870442 AACAACTTTT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1883889 original size:13 final size:13
Alignment explanation
Indices: 1883871--1883895 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1883861 TACAAAGATC
1883871 AATGTATCGATAT
1 AATGTATCGATAT
1883884 AATGTATCGATA
1 AATGTATCGATA
1883896 CATTGAATAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (13 bp):
AATGTATCGATAT
Found at i:1883894 original size:33 final size:33
Alignment explanation
Indices: 1883852--1883915 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
1883842 AAATTCTGAG
1883852 ATGTATCGATACAAAG-ATCAATGTATCGATATA
1 ATGTATCGATACAAAGAAT-AATGTATCGATATA
**
1883885 ATGTATCGATACATTGAATAATGTATCGATA
1 ATGTATCGATACAAAGAATAATGTATCGATA
1883916 CATTGAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATATA
Found at i:1883907 original size:20 final size:20
Alignment explanation
Indices: 1883882--1883939 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
1883872 ATGTATCGAT
1883882 ATAATGTATCGATACATTGA
1 ATAATGTATCGATACATTGA
1883902 ATAATGTATCGATACATTGA
1 ATAATGTATCGATACATTGA
1883922 ATAATGTATCGATACATT
1 ATAATGTATCGATACATT
1883940 TCCTTGGCAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
ATAATGTATCGATACATTGA
Found at i:1890011 original size:4 final size:4
Alignment explanation
Indices: 1890002--1890028 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1889992 AAAACAAAAC
1890002 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1890029 CACCTCAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1892215 original size:79 final size:80
Alignment explanation
Indices: 1892118--1892301 Score: 239
Period size: 79 Copynumber: 2.3 Consensus size: 80
1892108 GGTGTTTTGA
* * * * *
1892118 AAATAAAATCAGGGTTGGAGTATCCCCTA-TAAAATAACAGGGTTGGAGTATCTCCGATTGTAGA
1 AAATAAAATCGGGGTTGGAGTATCCCC-ACGAAAATAACAGGGTTGAAGTATCCCCGATTGTAAA
1892182 AA-ATCGA-TGCTTTAG
65 AAGAT-GAGTGCTTTAG
**
1892197 AAATAAGGTCGGGGTTGGAGTATCCCCACGAAAATAACAGGGTTGAAGTATCCCCGATTGTAAAA
1 AAATAAAATCGGGGTTGGAGTATCCCCACGAAAATAACAGGGTTGAAGTATCCCCGATTGTAAAA
* *
1892262 AGATTAGTGTTTTAG
66 AGATGAGTGCTTTAG
*
1892277 AAATAAAATTGGGGTTGGAGTATCC
1 AAATAAAATCGGGGTTGGAGTATCC
1892302 ACGATTGTGA
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
78 1 0.01
79 58 0.64
80 31 0.34
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.27
Consensus pattern (80 bp):
AAATAAAATCGGGGTTGGAGTATCCCCACGAAAATAACAGGGTTGAAGTATCCCCGATTGTAAAA
AGATGAGTGCTTTAG
Found at i:1894680 original size:20 final size:20
Alignment explanation
Indices: 1894654--1894708 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1894644 GTAAACCCAG
1894654 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
1894674 CATGTATCGATACAATGAAC
1 AATGTATCGATACAATGAAC
*
1894694 AATGTATTGATACAA
1 AATGTATCGATACAA
1894709 ATTGTGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.27
Consensus pattern (20 bp):
AATGTATCGATACAATGAAC
Found at i:1895037 original size:10 final size:11
Alignment explanation
Indices: 1895014--1895042 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1895004 AAATTCCCCA
1895014 TTTTTGAGATT
1 TTTTTGAGATT
1895025 TTTTTGAGATT
1 TTTTTGAGATT
1895036 TTTTTGA
1 TTTTTGA
1895043 AAAACTAGGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (11 bp):
TTTTTGAGATT
Found at i:1895743 original size:166 final size:163
Alignment explanation
Indices: 1895438--1896284 Score: 662
Period size: 166 Copynumber: 5.1 Consensus size: 163
1895428 TCAAACGTCT
** * * ** ** *
1895438 TCAAATATTATCATTTAATTCCCATCAAATCAGTTTTGAAAATTTTCTTTTATTTT-ATGAGTTA
1 TCAAATATTATCA-TTAATTCATATTAAATCAGTTCT-AAAAAATTAATTCATTTTCATGAGTT-
* * * * **
1895502 TTG-A--TTTTCTTTTAGAATTCTCTCTATTTTC-AAAATACAGAATTTTCTACTCCGTAAATAT
63 TTGAATTTTTTCTTTGA-AATTCTC-CT-TTTTCGAAAA-ATAGAGTTTTCTACTCCATAAATGC
*
1895563 TTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTTAAATTCA
124 TTTCGGG-GGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * * * * * * *
1895604 TCAAATATTATTACTTAATTCATGTTAAATTAGTT-TCCAAAAATTCATTTATTTTAATAAATTT
1 TCAAATATTATCA-TTAATTCATATTAAATCAGTTCT-AAAAAATTAATTCATTTTCAT-GAGTT
* * * * ** *
1895668 TTCAATTTTTTCCTTGAAAATCTCCTATTTTCGAAATATAGAGTTTTCTACTCTGTAAAT-TTTT
63 TTGAATTTTTTCTTTGAAATTCTCCT-TTTTCGAAAAATAGAGTTTTCTACTCCATAAATGCTTT
* ** * *
1895732 TGAGGGGATTTTTCTCAGTTTTCAATTTGTAAAATTCA
127 CG-GGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * *
1895770 TCAAATATAACCATTTATTCTATATTAAATCAGTTCTAAAAAATTAAATCATTTTCATGAGTTTT
1 TCAAATATTATCATTAATTC-ATATTAAATCAGTTCTAAAAAATTAATTCATTTTCATGAGTTTT
* * **
1895835 AAATTTTTTCTTTGACATTC-CCTTTTCCTTC-AAAAACCGAGTTTTCTACTCCATAAATGCTTT
65 GAATTTTTTCTTTGAAATTCTCC-TTT--TTCGAAAAATAGAGTTTTCTACTCCATAAATGCTTT
*
1895898 CGGGGGGATTTTTCTTGGTTTCTAATTTTTAAAATTCA
127 C-GGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
* * * *
1895936 TCAAATATCATCATTTAACTTGC--ATTAAATCAGTTCTGAAAAATTAATTCATTTTTATGCA-C
1 TCAAATATTATCA-TTAA-TT-CATATTAAATCAGTTCTAAAAAATTAATTCATTTTCATG-AGT
* * * * *
1895998 TTTGAATTTTTTTTCTTTGAAATTCT-CTTTTCCTGGAAAATTGAATTTTTTACTCCATAAATGC
62 TTTGAA--TTTTTTCTTTGAAATTCTCCTTTTTC-GAAAAATAGAGTTTTCTACTCCATAAATGC
*
1896062 TTTCGGGGGATTTTT-TTAGGTTTTTAATTTTTAAAATTTA
124 TTTCGGGGGATTTTTCTT-GGTTTTTAATTTTTAAAATTCA
* * * * *
1896102 TTAAATATTATCATTTAACTCATATTAAATTAGTTTTAAAAAATTAATTTATTTTCATGAGTTTT
1 TCAAATATTATCA-TTAATTCATATTAAATCAGTTCTAAAAAATTAATTCATTTTCATGAGTTTT
* * * * **
1896167 GAATTTTGTTTTTTGAAATTTTCCTGTTTCTGAAAAACTA-AGTTTTCTATTCCATAAATATTTT
65 GAATTTT-TTCTTTGAAATTCTCCTTTTTC-GAAAAA-TAGAGTTTTCTACTCCATAAATGCTTT
* * ** *
1896231 CAGGGGATTTTTCTTGATTTAAAATTTTTAAAATTTA
127 CGGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
*
1896268 TCAAATATTATTATTAA
1 TCAAATATTATCATTAA
1896285 ACTCCCATTA
Statistics
Matches: 550, Mismatches: 100, Indels: 63
0.77 0.14 0.09
Matches are distributed among these distances:
164 9 0.02
165 87 0.16
166 343 0.62
167 74 0.13
168 28 0.05
169 9 0.02
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (163 bp):
TCAAATATTATCATTAATTCATATTAAATCAGTTCTAAAAAATTAATTCATTTTCATGAGTTTTG
AATTTTTTCTTTGAAATTCTCCTTTTTCGAAAAATAGAGTTTTCTACTCCATAAATGCTTTCGGG
GGATTTTTCTTGGTTTTTAATTTTTAAAATTCA
Found at i:1896073 original size:332 final size:332
Alignment explanation
Indices: 1895530--1896327 Score: 814
Period size: 332 Copynumber: 2.4 Consensus size: 332
1895520 TCTCTCTATT
* * * *
1895530 TTCAAAATACAGAATTTTCTACTCCGTAAATATTTTCGGGAGGATTTTTCTTGGTTTTTAATTTT
1 TTCAAAA-ACAGAGTTTTCTACTCCATAAATATTTTCGGGGGGATTTTTCTTGGTTTATAATTTT
* * * * *
1895595 TTAAATTCATCAAATATTATTACTTAA-TTCATGTTAAATTAGTTTCCAAAAATTCATTTATTTT
65 TAAAATTCATCAAATATTATTATTTAACTTCA--TTAAATCAGTTT-GAAAAATTAATTTATTTT
* * * **
1895659 AATAAATTTTTCAATTTTTTCCTTGAAAATCTCCTATTTTCGAAATATAGAGTTTTCTACTCTGT
127 TATAAATCTTTCAATTTTTTCCTTGAAAATCTCCTATTTTCGAAATATAGAATTTTCTACTCCAT
* *
1895724 AAATTTTTTGAGGGGATTTTTCTCA-GTTTTCAATTTGTAAAATTCATCAAATATAACCATTT-A
192 AAATCTTTCGAGGGGATTTTT-TCAGGTTTTCAATTTGTAAAATTCATCAAATATAACCATTTAA
* *
1895787 TTCTATATTAAATCAGTTCTAAAAAATTAAATCATTTTCATGAGTTTTAAATTTT-TTCTTTGAC
256 CTC-ATATTAAATCAGTTCTAAAAAATTAAATCATTTTCATGAGTTTTAAATTTTGTTCTTTGAA
1895851 A-TTCCCT-TTTCC
320 ATTTCCCTGTTT-C
* ** *
1895863 TTCAAAAACCGAGTTTTCTACTCCATAAATGCTTTCGGGGGGATTTTTCTTGGTTTCTAATTTTT
1 TTCAAAAACAGAGTTTTCTACTCCATAAATATTTTCGGGGGGATTTTTCTTGGTTTATAATTTTT
* * *
1895928 AAAATTCATCAAATATCATCATTTAACTTGCATTAAATCAGTTCTGAAAAATTAATTCATTTTTA
66 AAAATTCATCAAATATTATTATTTAACTT-CATTAAATCAGTT-TGAAAAATTAATTTATTTTTA
** * * * * * *
1895993 TGCA-CTTTGAATTTTTTTTCTTTGAAATTCT-CT-TTTCCTGGAAA-ATTGAATTTTTTACTCC
129 TAAATCTTTCAA--TTTTTTCCTTGAAAATCTCCTATTT--TCGAAATATAGAATTTTCTACTCC
* * * * * * *
1896054 ATAAATGCTTTCG-GGGGATTTTTTTAGGTTTTTAATTTTTAAAATTTATTAAATATTATCATTT
190 ATAAAT-CTTTCGAGGGGATTTTTTCAGGTTTTCAATTTGTAAAATTCATCAAATATAACCATTT
* * * * * *
1896118 AACTCATATTAAATTAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTGAATTTTGTTTTTTGA
254 AACTCATATTAAATCAGTTCTAAAAAATTAAATCATTTTCATGAGTTTTAAATTTTGTTCTTTGA
*
1896183 AATTTTCCTGTTTC
319 AATTTCCCTGTTTC
* * * * *
1896197 -TGAAAAACTA-AGTTTTCTATTCCATAAATATTTTC-AGGGGATTTTTCTTGATTTAAAATTTT
1 TTCAAAAAC-AGAGTTTTCTACTCCATAAATATTTTCGGGGGGATTTTTCTTGGTTTATAATTTT
* * * * *
1896259 TAAAATTTATCAAATATTATTATTAAACTCCCATTAAATCAATTTTGCAAAATTCAATTTATTTC
65 TAAAATTCATCAAATATTATTATTTAACT-TCATTAAATC-AGTTTGAAAAATT-AATTTATTT-
1896324 TTAT
126 TTAT
1896328 CTTTTGATTT
Statistics
Matches: 384, Mismatches: 63, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
331 10 0.03
332 273 0.71
333 86 0.22
334 12 0.03
335 3 0.01
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (332 bp):
TTCAAAAACAGAGTTTTCTACTCCATAAATATTTTCGGGGGGATTTTTCTTGGTTTATAATTTTT
AAAATTCATCAAATATTATTATTTAACTTCATTAAATCAGTTTGAAAAATTAATTTATTTTTATA
AATCTTTCAATTTTTTCCTTGAAAATCTCCTATTTTCGAAATATAGAATTTTCTACTCCATAAAT
CTTTCGAGGGGATTTTTTCAGGTTTTCAATTTGTAAAATTCATCAAATATAACCATTTAACTCAT
ATTAAATCAGTTCTAAAAAATTAAATCATTTTCATGAGTTTTAAATTTTGTTCTTTGAAATTTCC
CTGTTTC
Found at i:1896297 original size:166 final size:164
Alignment explanation
Indices: 1895544--1896322 Score: 685
Period size: 166 Copynumber: 4.7 Consensus size: 164
1895534 AAATACAGAA
* *
1895544 TTTTCTACTCCGTAAATATTTTCGGGAGGATTTTTCTTGGTTTTTAATTTTTTAAATTCATCAAA
1 TTTTCTACTCCATAAATATTTTCGGG-GGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
* * * * ** * * * * *
1895609 TATTATTACTTAATTCATGTTAAATTAGTTTCCAAAAATTCATTTATTTTAATAAATTTTTCAAT
65 TATTATCA-TTAACTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCAT-GAGTTTTGAAT
* * * *
1895674 TTTTTCCTTGAAAATCTCCTATTTTC-GAAATA-TAGAG
128 TTTTTCTTTGAAATTCTCCT-TTTCCTGAAAAACTA-AG
** * ** * *
1895711 TTTTCTACTCTGTAAAT-TTTTTGAGGGGATTTTTCTCAGTTTTCAATTTGTAAAATTCATCAAA
1 TTTTCTACTCCATAAATATTTTCG-GGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
* * * * * * * *
1895775 TATAACCATTTATTCTATATTAAATCAGTTCTAAAAAATTAAATCATTTTCATGAGTTTTAAATT
65 TATTATCATTAACTC-ATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTGAATT
* * **
1895840 TTTTCTTTGACATTC-CCTTTTCCTTCAAAAACCGAG
129 TTTTCTTTGAAATTCTCCTTTTCC-TGAAAAACTAAG
** *
1895876 TTTTCTACTCCATAAATGCTTTCGGGGGGATTTTTCTTGGTTTCTAATTTTTAAAATTCATCAAA
1 TTTTCTACTCCATAAATATTTTC-GGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAA
* *** * * * * *
1895941 TATCATCATTTAACTTGCATTAAATCAGTTCTGAAAAATTAATTCATTTTTATGCA-CTTTGAAT
65 TATTATCA-TTAACTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATG-AGTTTTGAA-
* *
1896005 TTTTTTTCTTTGAAATTCT-CTTTTCCTGGAAAATTGAA-
127 -TTTTTTCTTTGAAATTCTCCTTTTCCTGAAAAACT-AAG
* ** * *
1896043 TTTTTTACTCCATAAATGCTTTCGGGGGATTTTT-TTAGGTTTTTAATTTTTAAAATTTATTAAA
1 TTTTCTACTCCATAAATATTTTCGGGGGATTTTTCTT-GGTTTTTAATTTTTAAAATTCATCAAA
*
1896107 TATTATCATTTAACTCATATTAAATTAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTGAATT
65 TATTATCA-TTAACTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTGAATT
* *
1896172 TTGTTTTTTGAAATTTTCCTGTTT-CTGAAAAACTAAG
129 TT-TTCTTTGAAATTCTCCT-TTTCCTGAAAAACTAAG
* * * ** *
1896209 TTTTCTATTCCATAAATATTTTCAGGGGATTTTTCTTGATTTAAAATTTTTAAAATTTATCAAAT
1 TTTTCTACTCCATAAATATTTTCGGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAAT
* ** * **
1896274 ATTATTATTAAACTCCCATTAAATCAATTTTGCAAAATTCAATTTATTT
66 ATTATCATT-AACTCATATTAAATCAGTTTTAAAAAATT-AATTTATTT
1896323 CTTATCTTTT
Statistics
Matches: 498, Mismatches: 92, Indels: 44
0.79 0.15 0.07
Matches are distributed among these distances:
163 4 0.01
164 7 0.01
165 67 0.13
166 331 0.66
167 65 0.13
168 24 0.05
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.48
Consensus pattern (164 bp):
TTTTCTACTCCATAAATATTTTCGGGGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATCAAAT
ATTATCATTAACTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTTGAATTTT
TTCTTTGAAATTCTCCTTTTCCTGAAAAACTAAG
Found at i:1898989 original size:79 final size:79
Alignment explanation
Indices: 1898899--1899072 Score: 253
Period size: 79 Copynumber: 2.2 Consensus size: 79
1898889 AGTAAAATCA
* * * *
1898899 GGGTTAAAGTATCCCCG-TTGGTGGAAAATTGGTGTTTTGGAAATAAAACTGGGGTTAG-AGTAT
1 GGGTTAGAGTATCCCCGATT-GTGGAAAATTGATGTTTTGAAAATAAAACTGAGGTT-GTAGTAT
*
1898962 CCCCTCGAAAATAATG
64 CCCCTCGAAAATAACG
* *
1898978 GGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTGAAAATAAAATTGAGGTTGTAGTATCC
1 GGGTTAGAGTATCCCCGATTGTGGAAAATTGATGTTTTGAAAATAAAACTGAGGTTGTAGTATCC
1899043 CCTCGAAAATAACG
66 CCTCGAAAATAACG
1899057 GGGTTAGAGTATCCCC
1 GGGTTAGAGTATCCCC
1899073 TCGAAAATAA
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
78 1 0.01
79 82 0.96
80 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (79 bp):
GGGTTAGAGTATCCCCGATTGTGGAAAATTGATGTTTTGAAAATAAAACTGAGGTTGTAGTATCC
CCTCGAAAATAACG
Found at i:1899044 original size:130 final size:130
Alignment explanation
Indices: 1898776--1899026 Score: 317
Period size: 130 Copynumber: 1.9 Consensus size: 130
1898766 ATGGGGCTGG
* *
1898776 AGTATCCCCGATTGTGAAAAATCGATGTTTCGAAAATAAAATCGGGATTTGAGTATCCCCTTGAA
1 AGTATCCCCGATTGTGAAAAATCGATGTTTCGAAAATAAAATCGGGATTAGAGTATCCCCTCGAA
* *
1898841 AATAACAGGGTTGGAGTATCCTCGATTGTAGAAAATCAATGTTCTCAAAGTAAAATCAGGGTTAA
66 AATAACAGGGTTGGAGTATCCCCGATTGTAGAAAATCAATGTTCTCAAAATAAAATCAGGGTTAA
* * * * * *
1898906 AGTATCCCCG-TTGGTGGAAAATTGGTGTTTTGGAAATAAAA-CTGGGGTTAGAGTATCCCCTCG
1 AGTATCCCCGATT-GTGAAAAATCGATGTTTCGAAAATAAAATC-GGGATTAGAGTATCCCCTCG
** * ** * *
1898969 AAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTTTTGAAAATAAAAT
64 AAAATAACAGGGTTGGAGTATCCCCGATTGTAGAAAATCAATGTTCTCAAAATAAAAT
1899027 TGAGGTTGTA
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
129 3 0.03
130 99 0.97
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (130 bp):
AGTATCCCCGATTGTGAAAAATCGATGTTTCGAAAATAAAATCGGGATTAGAGTATCCCCTCGAA
AATAACAGGGTTGGAGTATCCCCGATTGTAGAAAATCAATGTTCTCAAAATAAAATCAGGGTTAA
Found at i:1899054 original size:31 final size:30
Alignment explanation
Indices: 1899016--1899100 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 30
1899006 TTGATGTTTT
*
1899016 GAAAATAAAATTGAGGTT-GTAGTATCCCCTC
1 GAAAATAAAA-CGAGGTTAG-AGTATCCCCTC
*
1899047 GAAAAT--AACGGGGTTAGAGTATCCCCTC
1 GAAAATAAAACGAGGTTAGAGTATCCCCTC
* *
1899075 GAAAATAATA-G-GGTTGGAGTATCCCC
1 GAAAATAAAACGAGGTTAGAGTATCCCC
1899101 GATTGTGAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
28 36 0.77
29 4 0.09
30 1 0.02
31 6 0.13
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.25
Consensus pattern (30 bp):
GAAAATAAAACGAGGTTAGAGTATCCCCTC
Found at i:1899067 original size:28 final size:28
Alignment explanation
Indices: 1899036--1899100 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
1899026 TTGAGGTTGT
*
1899036 AGTATCCCCTCGAAAATAACGGGGTTAG
1 AGTATCCCCTCGAAAATAACAGGGTTAG
* *
1899064 AGTATCCCCTCGAAAATAATAGGGTTGG
1 AGTATCCCCTCGAAAATAACAGGGTTAG
1899092 AGTATCCCC
1 AGTATCCCC
1899101 GATTGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
AGTATCCCCTCGAAAATAACAGGGTTAG
Found at i:1899089 original size:107 final size:107
Alignment explanation
Indices: 1898949--1899268 Score: 471
Period size: 107 Copynumber: 3.0 Consensus size: 107
1898939 AAATAAAACT
1898949 GGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTT
1 GGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTT
* * * *
1899014 TTGAAAATAAAATTGAGGTTGTAGTATCCCCTCGAAAATAAC
66 TTGAAAACAAAATCGAGGTTGGAGTATCCCCTCGGAAATAAC
* *
1899056 GGGGTTAGAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCCCCGATTGTGAAAAATTGATGTT
1 GGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTT
*
1899121 TTGAAAACAAAATCG-GCGTTGGAGTATCCACTCGGAAATAAC
66 TTGAAAACAAAATCGAG-GTTGGAGTATCCCCTCGGAAATAAC
* * * * * *
1899163 AGGATTTGAGTATCCCCTTGGAAATAACGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTT
1 GGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTT
* * * *
1899228 TTGGAAACAAAACCAAGGTTGGAGTATCCCCTTGGAAATAA
66 TTGAAAACAAAATCGAGGTTGGAGTATCCCCTCGGAAATAA
1899269 AAACATGAAT
Statistics
Matches: 191, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
106 1 0.01
107 189 0.99
108 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (107 bp):
GGGGTTAGAGTATCCCCTCGAAAATAATGGGGTTGGAGTATCCCCGATTGTGGAAAATTGATGTT
TTGAAAACAAAATCGAGGTTGGAGTATCCCCTCGGAAATAAC
Found at i:1899206 original size:28 final size:28
Alignment explanation
Indices: 1899138--1899207 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
1899128 CAAAATCGGC
*
1899138 GTTGGAGTATCCACTCGGAAATAACAGG
1 GTTGGAGTATCCCCTCGGAAATAACAGG
* * * *
1899166 ATTTGAGTATCCCCTTGGAAATAACGGG
1 GTTGGAGTATCCCCTCGGAAATAACAGG
1899194 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
1899208 GATTGTGGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (28 bp):
GTTGGAGTATCCCCTCGGAAATAACAGG
Found at i:1899782 original size:6 final size:6
Alignment explanation
Indices: 1899771--1899800 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1899761 TCACCCAGGT
1899771 TTTTTG TTTTTG TTTTTG TTTTT- TTTTTG T
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG T
1899801 AGAAGAGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTTG
Found at i:1905114 original size:79 final size:79
Alignment explanation
Indices: 1904946--1905116 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 79
1904936 ATAAAGACGA
* * * * *
1904946 GGTTGGAGTAGCCCCTCAGAAATAATGGGGCTGGAGTATCCCCGATTGTGAAAAATTGGTGTTCC
1 GGTTGGAGTATCCCCTCAAAAATAATGGGGCTGGAGTATCCCCGATTGTGAAAAATCGATATTCC
1905011 AGAAATAAAATCGG
66 AGAAATAAAATCGG
* * *
1905025 GGTTGGAGTATCCCCTCAAAAATAATGGGGTTGGAGTATTCCCGATT-TTAGAAAATCGATATTC
1 GGTTGGAGTATCCCCTCAAAAATAATGGGGCTGGAGTATCCCCGATTGTGA-AAAATCGATATTC
* *
1905089 TAGAAATAAAATTGG
65 CAGAAATAAAATCGG
1905104 GGTTGGAGTATCC
1 GGTTGGAGTATCC
1905117 TCGATGGTGA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 2 0.02
79 79 0.98
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCAAAAATAATGGGGCTGGAGTATCCCCGATTGTGAAAAATCGATATTCC
AGAAATAAAATCGG
Found at i:1905131 original size:51 final size:50
Alignment explanation
Indices: 1905050--1905168 Score: 123
Period size: 51 Copynumber: 2.3 Consensus size: 50
1905040 TCAAAAATAA
* *
1905050 TGGGGTTGGAGTATTCCCGATTTTAGAAAATCGATATTCTAGAAATAAAAT
1 TGGGGTTGGAGTA-TCCCGATGTGAGAAAATCGATATTCTAGAAATAAAAT
* * * * *
1905101 TGGGGTTGGAGTATCCTCGATGGTGA-AAAATTGGTGTTTTGGAAATAAAAT
1 TGGGGTTGGAGTATCC-CGAT-GTGAGAAAATCGATATTCTAGAAATAAAAT
* *
1905152 CGGGGTTTGAGTATCCC
1 TGGGGTTGGAGTATCCC
1905169 CTTAAAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
50 4 0.07
51 51 0.89
52 2 0.04
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.33
Consensus pattern (50 bp):
TGGGGTTGGAGTATCCCGATGTGAGAAAATCGATATTCTAGAAATAAAAT
Found at i:1905186 original size:79 final size:77
Alignment explanation
Indices: 1905103--1905274 Score: 200
Period size: 78 Copynumber: 2.2 Consensus size: 77
1905093 AATAAAATTG
* * * * * * *
1905103 GGGTTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGGTTTGAGTATCC
1 GGGTTGGAGTATCC-CGATGGTGAAAAATCGATATTTTGAAAAT-AAACCAGGGTTGGAGTATCC
*
1905168 CCTTAAAAATAACA
64 CCTCAAAAATAACA
* * *
1905182 GGGTTGGAGTATGCCCGATTGTGAAAAATCGATATTTTGAAAATAAACCAGGGTTGGAGTTTTCC
1 GGGTTGGAGTAT-CCCGATGGTGAAAAATCGATATTTTGAAAATAAACCAGGGTTGGAGTATCCC
*
1905247 CTCGAAAATAACA
65 CTCAAAAATAACA
*
1905260 GGGTTAGAGTATCCC
1 GGGTTGGAGTATCCC
1905275 CTCAAAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
77 3 0.04
78 38 0.48
79 36 0.46
80 2 0.03
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (77 bp):
GGGTTGGAGTATCCCGATGGTGAAAAATCGATATTTTGAAAATAAACCAGGGTTGGAGTATCCCC
TCAAAAATAACA
Found at i:1905228 original size:130 final size:130
Alignment explanation
Indices: 1904971--1905217 Score: 370
Period size: 130 Copynumber: 1.9 Consensus size: 130
1904961 TCAGAAATAA
*
1904971 TGGGGCTGGAGTATCCCCGATTGTGAAAAATTGGTGTTCCAGAAATAAAATCGGGGTTGGAGTAT
1 TGGGGCTGGAGTATCCCCGATGGTGAAAAATTGGTGTTCCAGAAATAAAATCGGGGTTGGAGTAT
** * *
1905036 CCCCTCAAAAATAATGGGGTTGGAGTATTCCCGATTTTAGAAAATCGATATTCTAGAAATAAAAT
66 CCCCTCAAAAATAACAGGGTTGGAGTATGCCCGATTTGAGAAAATCGATATTCTAGAAATAAAAT
* * *** *
1905101 TGGGGTTGGAGTATCCTCGATGGTGAAAAATTGGTGTTTTGGAAATAAAATCGGGGTTTGAGTAT
1 TGGGGCTGGAGTATCCCCGATGGTGAAAAATTGGTGTTCCAGAAATAAAATCGGGGTTGGAGTAT
*
1905166 CCCCTTAAAAATAACAGGGTTGGAGTATGCCCGATTGTGA-AAAATCGATATT
66 CCCCTCAAAAATAACAGGGTTGGAGTATGCCCGATT-TGAGAAAATCGATATT
1905218 TTGAAAATAA
Statistics
Matches: 104, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
130 102 0.98
131 2 0.02
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (130 bp):
TGGGGCTGGAGTATCCCCGATGGTGAAAAATTGGTGTTCCAGAAATAAAATCGGGGTTGGAGTAT
CCCCTCAAAAATAACAGGGTTGGAGTATGCCCGATTTGAGAAAATCGATATTCTAGAAATAAAAT
Found at i:1905269 original size:28 final size:28
Alignment explanation
Indices: 1905220--1905302 Score: 103
Period size: 28 Copynumber: 2.9 Consensus size: 28
1905210 TCGATATTTT
* * *
1905220 GAAAATAAACCAGGGTTGGAGTTTTCCCTC
1 GAAAAT-AA-CAGGGTTAGAGTATCCCCTC
1905250 GAAAATAACAGGGTTAGAGTATCCCCTC
1 GAAAATAACAGGGTTAGAGTATCCCCTC
* *
1905278 AAAAATAACAAGGTTAGAGTATCCC
1 GAAAATAACAGGGTTAGAGTATCCC
1905303 TGATTGTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 40 0.83
29 2 0.04
30 6 0.12
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (28 bp):
GAAAATAACAGGGTTAGAGTATCCCCTC
Found at i:1905370 original size:28 final size:28
Alignment explanation
Indices: 1905338--1905400 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1905328 AAACAAAACT
1905338 GGGGTTGGAGTATCCTCTCGAAAATAAC
1 GGGGTTGGAGTATCCTCTCGAAAATAAC
* * *
1905366 GGGGTTTGAGTATCCTCTTGGAAATAAC
1 GGGGTTGGAGTATCCTCTCGAAAATAAC
1905394 GGGGTTG
1 GGGGTTG
1905401 AAATATCTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (28 bp):
GGGGTTGGAGTATCCTCTCGAAAATAAC
Found at i:1905391 original size:107 final size:104
Alignment explanation
Indices: 1905152--1905461 Score: 372
Period size: 107 Copynumber: 2.9 Consensus size: 104
1905142 GAAATAAAAT
* *
1905152 CGGGGTTTGAGTATCCCCTTAAAAATAACAGGGTTGGAGTATGCCCGATTGTGAAAAATCGATAT
1 CGGGGTTTGAGTATCCCCTTAAAAATAACAGGGTT-GAGTAT-CCCGATTGTGAAAAATTGATGT
* *
1905217 TTT-GAAA-ATAAACCAGGGTTGGAGTTTTCCCTCGAAAATAA
64 TTTGGAAACA-AAACCGGGGTTGGAG-TATCCCTCGAAAATAA
* * * *
1905258 CAGGGTTAGAGTATCCCCTCAAAAATAACAAGGTTAGAGTATCCCTGATTGTGAAAAATTGATGT
1 CGGGGTTTGAGTATCCCCTTAAAAATAACAGGGTT-GAGTATCCC-GATTGTGAAAAATTGATGT
*
1905323 TTTGGAAACAAAACTGGGGTTGGAGTATCCTCTCGAAAATAA
64 TTTGGAAACAAAACCGGGGTTGGAGTATCC-CTCGAAAATAA
* ** * * * *
1905365 CGGGGTTTGAGTATCCTCTTGGAAATAACGGGGTTGAAATATCTCCGATTGGGGAAAATTGATGT
1 CGGGGTTTGAGTATCCCCTTAAAAATAACAGGGTTG-AGTATC-CCGATTGTGAAAAATTGATGT
*
1905430 TTTGGAAACAAAACCGGGGTTGAAGTATCCCT
64 TTTGGAAACAAAACCGGGGTTGGAGTATCCCT
1905462 TTGGAAATAA
Statistics
Matches: 175, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
105 3 0.02
106 64 0.37
107 105 0.60
108 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (104 bp):
CGGGGTTTGAGTATCCCCTTAAAAATAACAGGGTTGAGTATCCCGATTGTGAAAAATTGATGTTT
TGGAAACAAAACCGGGGTTGGAGTATCCCTCGAAAATAA
Found at i:1906003 original size:10 final size:9
Alignment explanation
Indices: 1905975--1906001 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1905965 GATAAAAATT
1905975 TTCAAAAAA
1 TTCAAAAAA
1905984 TTCAAAAAA
1 TTCAAAAAA
1905993 TTCAAAAAA
1 TTCAAAAAA
1906002 ATCTTTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (9 bp):
TTCAAAAAA
Found at i:1908933 original size:157 final size:157
Alignment explanation
Indices: 1908755--1909207 Score: 522
Period size: 157 Copynumber: 2.9 Consensus size: 157
1908745 CTACTATTAT
* * * * *
1908755 GTTGTCACTGGGTCTGCTTTTATGTCGAAGGTGGGTATTTAGGATAGGTTCATCCTATCTTTAAT
1 GTTGTCACTAGATCCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTTTAAT
* * * * * *
1908820 ATTTTAAAGTCCTTTAGGGTTACTGAGATACTTTTACGTTGAAGGCATACCTGTAAGGGCATTTT
66 ATTTTTAAGTCCTTTAGGGTTACCGAGATACTTTCACATCGAAGGCATACCTATAAGGGCATTTT
* *
1908885 AGTAATTTTTCTAAAATCAAGTCCTAA
131 AGTAAATTTTATAAAATCAAGTCCTAA
* *
1908912 GTTGTCACTAGATCCGCTTTTATGCCGAAAGTGGGTATTTAGGATAGGTTCATCCCATCTCTAAT
1 GTTGTCACTAGATCCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTTTAAT
* * * *
1908977 ATTTTTAAGTCTTTTAGGGTTACCGAGATACTTTCACATCGAAGGTATACTTATAGGGGCATTTT
66 ATTTTTAAGTCCTTTAGGGTTACCGAGATACTTTCACATCGAAGGCATACCTATAAGGGCATTTT
* *
1909042 AGTAAATTTTATAGAATCGAGTCCTAA
131 AGTAAATTTTATAAAATCAAGTCCTAA
* * * * *
1909069 GTTGTCA-TCGAGTTCGCTTTTATGCCAAAGGTGGATACTTAGGATAGGTTCATCCCAT-TTATA
1 GTTGTCACTAGA-TCCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTT-TA
* * * *
1909132 ATTCTTTTTAAGTCCTTTAGAGG-TATCGAG-TA-TTTCTACATCGAAAGCAT-CCCATAAGGGC
64 A-TATTTTTAAGTCCTTTAG-GGTTACCGAGATACTTTC-ACATCGAAGGCATACCTATAAGGGC
* * *
1909193 TTTTTTGTAATTTTT
126 ATTTTAGTAAATTTT
1909208 CTTGAACTTA
Statistics
Matches: 252, Mismatches: 39, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
156 28 0.11
157 200 0.79
158 22 0.09
159 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (157 bp):
GTTGTCACTAGATCCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTTTAAT
ATTTTTAAGTCCTTTAGGGTTACCGAGATACTTTCACATCGAAGGCATACCTATAAGGGCATTTT
AGTAAATTTTATAAAATCAAGTCCTAA
Found at i:1909977 original size:7 final size:7
Alignment explanation
Indices: 1909967--1909992 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1909957 ATAAGGTACC
1909967 AATATCA
1 AATATCA
1909974 AATATCA
1 AATATCA
1909981 AATATCA
1 AATATCA
1909988 AATAT
1 AATAT
1909993 TGAAACCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.31
Consensus pattern (7 bp):
AATATCA
Found at i:1912401 original size:6 final size:6
Alignment explanation
Indices: 1912386--1912450 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 6
1912376 ATTTTTTTTA
* *
1912386 TAATTAT TAATTT TAATTT T-CTTT TAATTT TGAGTTT T-ATTT T-ATTT
1 TAATT-T TAATTT TAATTT TAATTT TAATTT T-AATTT TAATTT TAATTT
1912433 T-ATTT TACATTT T-ATTT T
1 TAATTT TA-ATTT TAATTT T
1912451 TTACTAGTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
5 23 0.46
6 12 0.24
7 15 0.30
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (6 bp):
TAATTT
Found at i:1912412 original size:17 final size:17
Alignment explanation
Indices: 1912392--1912439 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
1912382 TTTATAATTA
*
1912392 TTAATTTTAATTTTCTT
1 TTAATTTTAATTTTATT
*
1912409 TTAATTTTGAGTTTTATT
1 TTAATTTT-AATTTTATT
1912427 TT-ATTTT-ATTTTA
1 TTAATTTTAATTTTA
1912440 CATTTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 5 0.19
17 13 0.48
18 9 0.33
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (17 bp):
TTAATTTTAATTTTATT
Found at i:1913597 original size:21 final size:21
Alignment explanation
Indices: 1913564--1913610 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
1913554 AAAAAATTAA
1913564 AAAAATCAAAAAATCAAAAAT
1 AAAAATCAAAAAATCAAAAAT
1913585 AAAAA-CAAGAAAATCAAAAAT
1 AAAAATCAA-AAAATCAAAAAT
1913606 AAAAA
1 AAAAA
1913611 AAATTGGATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.79, C:0.09, G:0.02, T:0.11
Consensus pattern (21 bp):
AAAAATCAAAAAATCAAAAAT
Found at i:1914354 original size:76 final size:75
Alignment explanation
Indices: 1914193--1914462 Score: 236
Period size: 76 Copynumber: 3.5 Consensus size: 75
1914183 TATGTTGTGA
* * *
1914193 CTATTGATGGGAAAATTTTAGAAACCACATATTCCCTATCATGCTCTTTTTCTTTAGCTTGTCAT
1 CTATTGATGGG-AAATTATA-AAACCACATATTCCC-ATCATGCTCTTTTTCTTCAACTTGTCAT
** *
1914258 CGGTTTGTTTTAG
63 CAATTTATTTTAG
* * * * **
1914271 CTGTTGATGGGAAATTATAAAATCGCATATTCCTCATCATGCTTTTTTTCTTCAACTTGTTGTCA
1 CTATTGATGGGAAATTATAAAACCACATATTCC-CATCATGCTCTTTTTCTTCAACTTGTCATCA
1914336 ATTTATTTCT-G
65 ATTTATTT-TAG
* * * * * * * * *
1914347 CTATTGATGGGAGATTGTAAAACCACATATTTCCCATCATGATCATCTACTCCAGCTTGTTATCA
1 CTATTGATGGGAAATTATAAAACCACATA-TTCCCATCATGCTCTTTTTCTTCAACTTGTCATCA
*
1914412 ATTTGTTTTAG
65 ATTTATTTTAG
* * * *
1914423 CTGTTGGTGGGAAATTGTAAAACCACAAATTTCCCATCAT
1 CTATTGATGGGAAATTATAAAACCACATA-TTCCCATCAT
1914463 TATCATCTAC
Statistics
Matches: 158, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
75 1 0.01
76 134 0.85
77 13 0.08
78 10 0.06
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (75 bp):
CTATTGATGGGAAATTATAAAACCACATATTCCCATCATGCTCTTTTTCTTCAACTTGTCATCAA
TTTATTTTAG
Found at i:1914468 original size:76 final size:76
Alignment explanation
Indices: 1914323--1914514 Score: 251
Period size: 76 Copynumber: 2.5 Consensus size: 76
1914313 TTTTTTTCTT
* * * *
1914323 CAACTTGTTGTCAATTTATTTCTGCTATTGATGGGAGATTGTAAAACCACATATTTCCCATCATG
1 CAACTTGTTATCAATTTGTTTCTGCTATTGATGGGAAATTGTAAAACCACAAATTTCCCATCATG
1914388 ATCATCTACTC
66 ATCATCTACTC
* * *
1914399 CAGCTTGTTATCAATTTGTTT-TAGCTGTTGGTGGGAAATTGTAAAACCACAAATTTCCCATCAT
1 CAACTTGTTATCAATTTGTTTCT-GCTATTGATGGGAAATTGTAAAACCACAAATTTCCCATCAT
*
1914463 TATCATCTACTC
65 GATCATCTACTC
* * * * *
1914475 TAACTTGTTATCAGTTTGTTTCAGCCATTGATGAGAAATT
1 CAACTTGTTATCAATTTGTTTCTGCTATTGATGGGAAATT
1914515 ATAGAATTAC
Statistics
Matches: 98, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.01
76 97 0.99
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.39
Consensus pattern (76 bp):
CAACTTGTTATCAATTTGTTTCTGCTATTGATGGGAAATTGTAAAACCACAAATTTCCCATCATG
ATCATCTACTC
Found at i:1915136 original size:66 final size:65
Alignment explanation
Indices: 1915030--1915262 Score: 274
Period size: 66 Copynumber: 3.6 Consensus size: 65
1915020 CAAGTGTCAC
* * * **
1915030 TCAACCTTATTTCGAATTAGGTTTTGTCCTACTTGCTTTTAGTTGACTTTATCGATTTTGTCCTA
1 TCAACCTTATTTCGACTTAGGTTTTATCCTAATCACTTTTAGTTGACTTTATCGATTTTG-CCTA
*
1915095 A
65 G
*
1915096 TCAACCTTATTTTGACTTAGGTTTTATCCTAATCACTTTTAGTTGACTTTATCGATTTTGCCCTA
1 TCAACCTTATTTCGACTTAGGTTTTATCCTAATCACTTTTAGTTGACTTTATCGATTTTG-CCTA
1915161 G
65 G
** * * * * *
1915162 TCAACCCCATTTCAACTTAGGTTCTATTCTAGTCACTTTTAGTTGAC-TTATCGGTTTTGCCTTA
1 TCAACCTTATTTCGACTTAGGTTTTATCCTAATCACTTTTAGTTGACTTTATCGATTTTGCC-TA
1915226 G
65 G
*
1915227 TCAACC-T-TTCCTGACTTAGGTTTTATCCTAATCACT
1 TCAACCTTATTTC-GACTTAGGTTTTATCCTAATCACT
1915263 CTTTCTTGAC
Statistics
Matches: 143, Mismatches: 22, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 22 0.15
65 20 0.14
66 98 0.69
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (65 bp):
TCAACCTTATTTCGACTTAGGTTTTATCCTAATCACTTTTAGTTGACTTTATCGATTTTGCCTAG
Found at i:1915439 original size:105 final size:106
Alignment explanation
Indices: 1915239--1915440 Score: 237
Period size: 106 Copynumber: 1.9 Consensus size: 106
1915229 AACCTTTCCT
* * * * * *
1915239 GACTTAGGTTTTATCCTAATCACTCTTTCTTGACTTGTCAGTTTCCTCTCAGTCAACCTCTTAAA
1 GACTTAAGTTTTATCCTAATCACTCTTTCTTGACTTCTCAATTTCATCTCAATCAACCCCTTAAA
* * *
1915304 CTAGTTGACTTATCGATTTCACCTTGGTTAACCTCTTTTTA
66 CTAGTTGACTTATAGATTTCACCCTAGTTAACCTCTTTTTA
* * * *
1915345 GACTTAAGTTTTATCTTAGTCACTTTTTGTTGACTTCTCAATTTCATC-CAATCAACCCCTTAAA
1 GACTTAAGTTTTATCCTAATCACTCTTTCTTGACTTCTCAATTTCATCTCAATCAACCCCTTAAA
* * *
1915409 TTTGTTGACTTATTAG-TTTCGCCCTAGTTAAC
66 CTAGTTGACTTA-TAGATTTCACCCTAGTTAAC
1915441 TTAGGTTTTA
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
105 37 0.47
106 42 0.53
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (106 bp):
GACTTAAGTTTTATCCTAATCACTCTTTCTTGACTTCTCAATTTCATCTCAATCAACCCCTTAAA
CTAGTTGACTTATAGATTTCACCCTAGTTAACCTCTTTTTA
Found at i:1915517 original size:63 final size:65
Alignment explanation
Indices: 1915437--1915592 Score: 178
Period size: 65 Copynumber: 2.4 Consensus size: 65
1915427 TCGCCCTAGT
1915437 TAACTTAGGTTTTATCCTAGTCACCCTT-GTTGACT-TATC-GATTTCACCCTAGTCAACCCTTT
1 TAACTTAGGTTTTATCCTAGTCACCCTTGGTTGACTAT-TCAGATTTCACCCTAGTCAACCCTTT
1915499 C
65 C
** ** * *
1915500 TAACTTTA-GTTTTATCCTAG-CTATGCTTGGTTGACTATTCAGATTTTGCCTTAGTCAACTCTT
1 TAAC-TTAGGTTTTATCCTAGTC-ACCCTTGGTTGACTATTCAGATTTCACCCTAGTCAACCCTT
1915563 TC
64 TC
* *
1915565 TGACTTAGGTCTTATCCTAGTCACCCTT
1 TAACTTAGGTTTTATCCTAGTCACCCTT
1915593 TTTACCTTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
62 1 0.01
63 20 0.26
64 15 0.20
65 39 0.51
66 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.13, T:0.42
Consensus pattern (65 bp):
TAACTTAGGTTTTATCCTAGTCACCCTTGGTTGACTATTCAGATTTCACCCTAGTCAACCCTTTC
Found at i:1919284 original size:13 final size:13
Alignment explanation
Indices: 1919266--1919290 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1919256 TAGTAACCCA
1919266 TGTATCGATACAT
1 TGTATCGATACAT
1919279 TGTATCGATACA
1 TGTATCGATACA
1919291 AAGAACATTG
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:1924103 original size:13 final size:13
Alignment explanation
Indices: 1924085--1924111 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1924075 ACATGTTGCT
1924085 TTGTATCGATACA
1 TTGTATCGATACA
1924098 TTGTATCGATACA
1 TTGTATCGATACA
1924111 T
1 T
1924112 GTTCATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1924109 original size:33 final size:32
Alignment explanation
Indices: 1924067--1924130 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1924057 ACACCCAGAC
* *
1924067 GTATCGATACATGTTGCTTTGTATCGATACATT
1 GTATCGATACATGTT-CATTATATCGATACATT
1924100 GTATCGATACATGTTCATTATATCGATACAT
1 GTATCGATACATGTTCATTATATCGATACAT
1924131 GGCCAAATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (32 bp):
GTATCGATACATGTTCATTATATCGATACATT
Found at i:1924146 original size:21 final size:19
Alignment explanation
Indices: 1924096--1924152 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1924086 TGTATCGATA
**
1924096 CATTGTATCGATACATGTT
1 CATTGTATCGATACATGGC
*
1924115 CATTATATCGATACATGGC
1 CATTGTATCGATACATGGC
1924134 CAAATTGTATCGATACATG
1 C--ATTGTATCGATACATG
1924153 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 17 0.53
21 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
CATTGTATCGATACATGGC
Found at i:1930394 original size:13 final size:13
Alignment explanation
Indices: 1930376--1930404 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1930366 ACAACATTCC
1930376 TTGTATCGATACA
1 TTGTATCGATACA
1930389 TTGTATCGATACA
1 TTGTATCGATACA
1930402 TTG
1 TTG
1930405 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1932293 original size:17 final size:17
Alignment explanation
Indices: 1932267--1932321 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1932257 AAGATAATCA
1932267 TTTAAGGGGGAGAATTT
1 TTTAAGGGGGAGAATTT
* **
1932284 TTT-AGAGGGGATAATCG
1 TTTAAG-GGGGAGAATTT
1932301 TTTAAGGGGGAGAATATT
1 TTTAAGGGGGAGAAT-TT
1932319 TTT
1 TTT
1932322 TTAAGGGGAG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 2 0.07
17 22 0.76
18 5 0.17
ACGTcount: A:0.29, C:0.02, G:0.33, T:0.36
Consensus pattern (17 bp):
TTTAAGGGGGAGAATTT
Found at i:1932990 original size:20 final size:21
Alignment explanation
Indices: 1932940--1932991 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1932930 TTTCACTATT
* *
1932940 TGTATCGATACATGGTACAAT
1 TGTATCGATACATGGAACAAA
* *
1932961 TGTATTGATACAT-GAAGAAA
1 TGTATCGATACATGGAACAAA
1932981 TGTATCGATAC
1 TGTATCGATAC
1932992 CTAGCGTGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TGTATCGATACATGGAACAAA
Found at i:1938770 original size:52 final size:52
Alignment explanation
Indices: 1938661--1938777 Score: 146
Period size: 52 Copynumber: 2.2 Consensus size: 52
1938651 AGTTGCTTGC
* * * ***
1938661 ATGTATCGATACATTTGGGCAAATTTTCCTGCATGTATCGATATATTTTATA
1 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
*
1938713 ATGTATCGATACATCTGGGTAAATTTGCCTGCATGTATCGATACA-AAGATCA
1 ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGAT-A
*
1938765 GTGTATCGATACA
1 ATGTATCGATACA
1938778 ATGTATCGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
51 2 0.04
52 54 0.96
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (52 bp):
ATGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATAAGATA
Found at i:1938784 original size:13 final size:13
Alignment explanation
Indices: 1938766--1938790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1938756 CAAAGATCAG
1938766 TGTATCGATACAA
1 TGTATCGATACAA
1938779 TGTATCGATACA
1 TGTATCGATACA
1938791 TTTGAGTAAT
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:1938858 original size:20 final size:20
Alignment explanation
Indices: 1938829--1938886 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1938819 GCAGTAGCTT
1938829 AAAT-TGTATCGATACAAAA
1 AAATATGTATCGATACAAAA
*
1938848 AAATATGTATCGATACAACA
1 AAATATGTATCGATACAAAA
***
1938868 CTTTATGTATCGATACAAA
1 AAATATGTATCGATACAAA
1938887 TCGTTGAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 4 0.12
20 29 0.88
ACGTcount: A:0.47, C:0.14, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATATGTATCGATACAAAA
Found at i:1941166 original size:20 final size:20
Alignment explanation
Indices: 1941141--1941219 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1941131 ACTGCCAAGG
1941141 AAATGTATCGATACATTGAT
1 AAATGTATCGATACATTGAT
* *
1941161 AAATGTATCAATACA-TGCTT
1 AAATGTATCGATACATTG-AT
**
1941181 CAAATTGTATCGATACATTTCT
1 -AAA-TGTATCGATACATTGAT
* *
1941203 CATTGTATCGATACATT
1 AAATGTATCGATACATT
1941220 CTAGGTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.04
20 29 0.60
21 4 0.08
22 12 0.25
23 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTGAT
Found at i:1942330 original size:49 final size:49
Alignment explanation
Indices: 1942169--1942767 Score: 682
Period size: 49 Copynumber: 12.7 Consensus size: 49
1942159 AAAAGGATGT
* *
1942169 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTTAATGATGGAA-AAAGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TTAA--A--GAAGAAGGTGC
* *
1942222 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1942265 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
1942314 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--AGAAG--GGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
1942359 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * **
1942408 CAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
1942457 CAATGTGCTGATTCAAGGCCAGCTACATTGGGCGTAAAGATG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
1942505 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-AAG--GG-GC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* *
1942548 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * *
1942597 CAATATGCTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
1942640 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * *
1942689 CAATATACTGATTCAAGGCCAGCGATATTGGACTT-----A-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
1942732 CAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1942768 GAAGGGTTGC
Statistics
Matches: 472, Mismatches: 51, Indels: 55
0.82 0.09 0.10
Matches are distributed among these distances:
43 149 0.32
44 2 0.00
45 41 0.09
46 3 0.01
47 9 0.02
48 38 0.08
49 198 0.42
52 2 0.00
53 30 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
Found at i:1942339 original size:92 final size:92
Alignment explanation
Indices: 1942160--1942767 Score: 975
Period size: 92 Copynumber: 6.5 Consensus size: 92
1942150 AAGATGAGAA
* * * *
1942160 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTTAATGATGGAAAAAGTGCCAA
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TTAAAGAT-G--AAGGTGCCAA
*
1942225 TATGCTGATTCAAGGCCAGCTATATTGGACTT
61 TATGCTGATTCAAGGCCAGCGATATTGGACTT
*
1942257 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
1942322 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
1942349 AGAAGGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
1 A-AA-GGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATAT
1942414 GCTGATTCAAGGCCAGCGATATTGGACTT
64 GCTGATTCAAGGCCAGCGATATTGGACTT
* *
1942443 AAAGGTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCGTAAAGATG-AGGTGCCA
1 --A----AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCA
1942507 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
60 ATATGCTGATTCAAGGCCAGCGATATTGGACTT
* *
1942540 AAAGGGGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1942605 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
1942632 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATAC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1942697 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCGATATTGGACTT
*
1942724 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGGCTTA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1942768 GAAGGGTTGC
Statistics
Matches: 486, Mismatches: 17, Indels: 21
0.93 0.03 0.04
Matches are distributed among these distances:
91 46 0.09
92 214 0.44
93 2 0.00
94 88 0.18
95 7 0.01
96 35 0.07
97 46 0.09
98 45 0.09
99 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCGATATTGGACTT
Found at i:1942930 original size:33 final size:33
Alignment explanation
Indices: 1942767--1942929 Score: 240
Period size: 33 Copynumber: 4.9 Consensus size: 33
1942757 CATTGGGCTT
*
1942767 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAA
* * * *
1942800 AGAATGGTTGCCACCAACCTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAA
1942833 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-AA
1942867 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTGAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-AA
*
1942900 AGAA-GGTTGCCACCGACTTATGTGGGCTTT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTT
1942930 GGGAAGGGAG
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
33 115 0.96
34 5 0.04
ACGTcount: A:0.21, C:0.19, G:0.33, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAA
Found at i:1942995 original size:71 final size:70
Alignment explanation
Indices: 1942920--1943271 Score: 398
Period size: 71 Copynumber: 5.2 Consensus size: 70
1942910 CACCGACTTA
** * *
1942920 TGTGGGCTTTGGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTGAAAAGGGA-AAAGATGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAGAGTGCC
1942984 ACGGAGT
64 ACGGAGT
*
1942991 TGTGGGCTTT----A---AAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCAC
1 TGTGGGCTTTGAAAAGGGAAAAGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGAGTGCCAC
1943048 GGAGT
66 GGAGT
*
1943053 TGTGGGCTTTGAAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-AGTGCC
1 TGTGGGCTTTG-AAAAGGGAAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGAGTGCC
1943117 ACGGAGT
64 ACGGAGT
* * * *
1943124 GGTGGGC-TT-AAAA-GGAACAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTGAAAAGGGAA-AAGATGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAAGAGTGCC
1943185 ACGGAGT
64 ACGGAGT
*
1943192 TGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG--AAA-A-TGCC
1 TGTGGGCTTTGAAAAGGG-AAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGAGTGCC
1943253 ACGGAGT
64 ACGGAGT
*
1943260 CGTGGGCTTTGA
1 TGTGGGCTTTGA
1943272 GAAGAGATTT
Statistics
Matches: 246, Mismatches: 15, Indels: 43
0.81 0.05 0.14
Matches are distributed among these distances:
62 22 0.09
63 28 0.11
64 7 0.03
66 6 0.02
67 28 0.11
68 47 0.19
69 3 0.01
70 14 0.06
71 65 0.26
72 20 0.08
73 6 0.02
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (70 bp):
TGTGGGCTTTGAAAAGGGAAAAGATGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGAGTGCCAC
GGAGT
Found at i:1943091 original size:37 final size:36
Alignment explanation
Indices: 1943001--1943269 Score: 377
Period size: 37 Copynumber: 7.8 Consensus size: 36
1942991 TGTGGGCTTT
1943001 AAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAA-G
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
1943035 AAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAAGG
1943071 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA-G
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
*
1943106 AAAAA-AGTGCCACGGAGTGGTGGGC-TT-AAAAGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
* * *
1943139 AACAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
1943173 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGGG
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA-GG
1943210 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA-G
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
*
1943245 --AAA-A-TGCCACGGAGTCGTGGGCTTT
1 AAAAAGAGTGCCACGGAGTTGTGGGCTTT
1943270 GAGAAGAGAT
Statistics
Matches: 217, Mismatches: 9, Indels: 21
0.88 0.04 0.09
Matches are distributed among these distances:
31 20 0.09
32 5 0.02
33 29 0.13
34 57 0.26
35 30 0.14
36 18 0.08
37 58 0.27
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (36 bp):
AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGG
Found at i:1943219 original size:139 final size:134
Alignment explanation
Indices: 1942920--1943268 Score: 464
Period size: 139 Copynumber: 2.6 Consensus size: 134
1942910 CACCGACTTA
** * * *
1942920 TGTGGGCTTTG-GGAAGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTG
1 TGTGGGCTTTGAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-AGAAAAA-AGTG
* * *
1942982 CCACGGAGTTGTGGGCTTTAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCA
64 CCACGGAGTCGTGGGCTTAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCA
1943047 CGGAGT
129 CGGAGT
1943053 TGTGGGCTTTGAAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCC
1 TGTGGGCTTTGAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCC
* *
1943117 ACGGAGTGGTGGGCTTAAAAGGAACAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAG
66 ACGGAGTCGTGGGCTT--AA--AA-AAGGTGCCACGGAGTTGTGGACTTTAAAA-AGAAAAAG-G
1943181 TGCCACGGAGT
124 TGCCACGGAGT
1943192 TGTGGGCTTT-AAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG--AAAA-TGCC
1 TGTGGGCTTTGAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCC
1943253 ACGGAGTCGTGGGCTT
66 ACGGAGTCGTGGGCTT
1943269 TGAGAAGAGA
Statistics
Matches: 195, Mismatches: 10, Indels: 19
0.87 0.04 0.08
Matches are distributed among these distances:
133 40 0.21
134 25 0.13
135 7 0.04
136 19 0.10
137 12 0.06
138 33 0.17
139 59 0.30
ACGTcount: A:0.33, C:0.12, G:0.35, T:0.20
Consensus pattern (134 bp):
TGTGGGCTTTGAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCC
ACGGAGTCGTGGGCTTAAAAAAGGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACG
GAGT
Found at i:1945761 original size:32 final size:33
Alignment explanation
Indices: 1945718--1945782 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
1945708 TAGCCAAACT
*
1945718 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCAATACACAAAAATATGTATCGATACAA
1945750 TGTATCAATACACAAAAAATATGTATCGATACA
1 TGTATCAATACAC-AAAAATATGTATCGATACA
1945783 TTGGCTTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.40
34 18 0.60
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (33 bp):
TGTATCAATACACAAAAATATGTATCGATACAA
Found at i:1948015 original size:21 final size:21
Alignment explanation
Indices: 1947982--1948031 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1947972 TTGCAAGTTG
*
1947982 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1948004 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1948025 AAATAAA
1 AAATAAA
1948032 AATTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1951213 original size:13 final size:13
Alignment explanation
Indices: 1951195--1951220 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1951185 CAATTTTTTA
1951195 TGTATCGATACAT
1 TGTATCGATACAT
1951208 TGTATCGATACAT
1 TGTATCGATACAT
1951221 ACTTGCTGTA
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):
TGTATCGATACAT
Found at i:1951968 original size:21 final size:21
Alignment explanation
Indices: 1951927--1951970 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1951917 CTCCCCTTTA
* *
1951927 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1951948 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1951969 TC
1 TC
1951971 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1953783 original size:13 final size:13
Alignment explanation
Indices: 1953765--1953803 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1953755 ATAATCACCC
1953765 TGTATCGATACAA
1 TGTATCGATACAA
1953778 TGTATCGATACAA
1 TGTATCGATACAA
1953791 TGTATCGATACAA
1 TGTATCGATACAA
1953804 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1955885 original size:15 final size:15
Alignment explanation
Indices: 1955865--1955895 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1955855 ATTTCGTTTG
*
1955865 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1955880 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1955895 G
1 G
1955896 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1957582 original size:21 final size:21
Alignment explanation
Indices: 1957553--1957597 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1957543 AAGTTTTCAT
*
1957553 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1957573 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1957595 TTT
1 TTT
1957598 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1959830 original size:13 final size:13
Alignment explanation
Indices: 1959812--1959837 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1959802 CAATTTTTTA
1959812 TGTATCGATACAT
1 TGTATCGATACAT
1959825 TGTATCGATACAT
1 TGTATCGATACAT
1959838 ACTTGCTGTA
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):
TGTATCGATACAT
Found at i:1961736 original size:13 final size:13
Alignment explanation
Indices: 1961718--1961755 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1961708 CATTTTTCTT
1961718 TGTATCGATACAA
1 TGTATCGATACAA
*
1961731 TGTATCGATACAC
1 TGTATCGATACAA
1961744 TGTATCGATACA
1 TGTATCGATACA
1961756 GGGGGATTAT
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:1964285 original size:19 final size:19
Alignment explanation
Indices: 1964261--1964325 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
1964251 TAGCCAAACT
1964261 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
1964280 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
1964293 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
1964314 TGTATCGATACA
1 TGTATCGATACA
1964326 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:1964297 original size:13 final size:13
Alignment explanation
Indices: 1964279--1964304 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1964269 TACACAAAAT
1964279 ATGTATCGATACA
1 ATGTATCGATACA
1964292 ATGTATCGATACA
1 ATGTATCGATACA
1964305 CAAAAAATAT
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:1964302 original size:32 final size:33
Alignment explanation
Indices: 1964261--1964325 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
1964251 TAGCCAAACT
1964261 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
1964293 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
1964326 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:1971200 original size:52 final size:52
Alignment explanation
Indices: 1971115--1971239 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1971105 ATATGAAAAG
* *
1971115 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1971167 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1971219 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1971240 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1971252 original size:52 final size:51
Alignment explanation
Indices: 1971115--1971259 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
1971105 ATATGAAAAG
*
1971115 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
1971167 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
1971219 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1971260 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:1971266 original size:13 final size:13
Alignment explanation
Indices: 1971248--1971272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1971238 CAAAGATCAG
1971248 TGTATCGATACAA
1 TGTATCGATACAA
1971261 TGTATCGATACA
1 TGTATCGATACA
1971273 TTTGAGTAAT
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:1971353 original size:33 final size:33
Alignment explanation
Indices: 1971316--1971379 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1971306 AGCTTAAATA
1971316 GTATCGATACAAAAAAATATGTATCGATACATC
1 GTATCGATACAAAAAAATATGTATCGATACATC
* ***
1971349 GTATCGATACAACACTTTATGTATCGATACA
1 GTATCGATACAAAAAAATATGTATCGATACA
1971380 AATCGTTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (33 bp):
GTATCGATACAAAAAAATATGTATCGATACATC
Found at i:1973669 original size:20 final size:20
Alignment explanation
Indices: 1973644--1973722 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1973634 ACTGCCAAGG
1973644 AAATGTATCGATACATTGAT
1 AAATGTATCGATACATTGAT
* *
1973664 AAATGTATCAATACA-TGCTT
1 AAATGTATCGATACATTG-AT
**
1973684 CAAATTGTATCGATACATTTCT
1 -AAA-TGTATCGATACATTGAT
* *
1973706 CATTGTATCGATACATT
1 AAATGTATCGATACATT
1973723 CTAGGTTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.04
20 29 0.60
21 4 0.08
22 12 0.25
23 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.38
Consensus pattern (20 bp):
AAATGTATCGATACATTGAT
Found at i:1980319 original size:152 final size:154
Alignment explanation
Indices: 1980129--1980497 Score: 348
Period size: 153 Copynumber: 2.4 Consensus size: 154
1980119 ATTTTTGTGT
** ** ** ** **
1980129 CTTTTAGGTTTATTTAGATATTTTCATGTCGAAAGTATA-CTTAGGGGTTTTTTGTAATTTTTTT
1 CTTTTAGG-TTATCAAGATATTTTCATGTCGAAAGTATACCCAAGGGAATTTTCATAATTTCCTT
* * * * *
1980193 AAAATCAACTCCTAGGTCATCATCGAGTCACTTTTATGCCAAAGGTGTGTATTTAGGATATGTTT
65 AAAATCAACTCCTAGATCATCATCGAGTCACTTTTATGCCAAAGGTGTGCACTTAGGATAGGTTC
* *
1980258 GTCCTTTTAATAATTTTTTCAT-AC
130 ATCCTTTTAATAATCTTTTCATGAC
* * * *
1980282 CTTTTAGGTTATCGAGATACTTTCATGTTGAAGGTATACCCAAGGGAATTTTCATAATTTCCTTA
1 CTTTTAGGTTATCAAGATATTTTCATGTCGAAAGTATACCCAAGGGAATTTTCATAATTTCCTTA
* ** * * * **
1980347 GAATTGAGTCCTAGATTATCATTGAGTCGTTTTTATGCCAAAGGTGTGCACTTAGGATAGGTTCA
66 AAATCAACTCCTAGATCATCATCGAGTCACTTTTATGCCAAAGGTGTGCACTTAGGATAGGTTCA
* * *
1980412 TCTTTTTATTAATCTTTTCATGTC
131 TCCTTTTAATAATCTTTTCATGAC
* ** * **
1980436 CTTTAAGGTTATCAAGATATTTTCACATC-AAAGGTATACCCTAGGGATATTTTGGTAATTTC
1 CTTTTAGGTTATCAAGATATTTTCATGTCGAAA-GTATACCCAAGGGA-ATTTTCATAATTTC
1980498 TCTAGACCCA
Statistics
Matches: 171, Mismatches: 41, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
152 25 0.15
153 97 0.57
154 37 0.22
155 12 0.07
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.43
Consensus pattern (154 bp):
CTTTTAGGTTATCAAGATATTTTCATGTCGAAAGTATACCCAAGGGAATTTTCATAATTTCCTTA
AAATCAACTCCTAGATCATCATCGAGTCACTTTTATGCCAAAGGTGTGCACTTAGGATAGGTTCA
TCCTTTTAATAATCTTTTCATGAC
Found at i:1982338 original size:224 final size:225
Alignment explanation
Indices: 1981947--1982391 Score: 865
Period size: 224 Copynumber: 2.0 Consensus size: 225
1981937 TGAGTTTTTT
1981947 GCCATTCTTTTCGAAAATATGTCAGGATATCCTCTAAATCTAGAAATATCCTTTTCAAATGTCAA
1 GCCATTCTTTTCGAAAATATGTCAGGATATCCTCTAAATCTAGAAATATCCTTTTCAAATGTCAA
*
1982012 ACTTGAAAAATAGATTTAAACATAATGAAAATTGTATGTTCGACCAAATTTTTAGCAAACAGAAA
66 ACTTGAAAAATAGATTTAAACATAATGAAAATTGTATGTTCGACCAAATTTTTAGCAAACAAAAA
*
1982077 ATTTTGAATTCATAAAACCATGTTGTTTATTTAAAACTCATTATAGCATTTTAAGGAATCATGAT
131 ATTTTGAATTCATAAAACCACGTTGTTTATTTAAAACTCATTATAGCATTTTAAGGAATCATGAT
1982142 TAAATATCAAAATTAAAACCGTGAAATTTC
196 TAAATATCAAAATTAAAACCGTGAAATTTC
1982172 GCCATTCTTTTCGAAAATATGTCAGGATA-CCTCTAAATCTAGAAATATCCTTTTCAAATGTCAA
1 GCCATTCTTTTCGAAAATATGTCAGGATATCCTCTAAATCTAGAAATATCCTTTTCAAATGTCAA
1982236 ACTTGAAAAATAGATTTAAACATAATGAAAATTGTATGTTCGACCAAATTTTTAGCAAACAAAAA
66 ACTTGAAAAATAGATTTAAACATAATGAAAATTGTATGTTCGACCAAATTTTTAGCAAACAAAAA
1982301 ATTTTGAATTCATAAAACCACGTTGTTTATTTAAAACTCATTATAGCATTTTAAGGAATCATGAT
131 ATTTTGAATTCATAAAACCACGTTGTTTATTTAAAACTCATTATAGCATTTTAAGGAATCATGAT
1982366 TAAATATCAAAATTAAAACCGTGAAA
196 TAAATATCAAAATTAAAACCGTGAAA
1982392 CTTAATATAT
Statistics
Matches: 218, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
224 189 0.87
225 29 0.13
ACGTcount: A:0.42, C:0.14, G:0.11, T:0.34
Consensus pattern (225 bp):
GCCATTCTTTTCGAAAATATGTCAGGATATCCTCTAAATCTAGAAATATCCTTTTCAAATGTCAA
ACTTGAAAAATAGATTTAAACATAATGAAAATTGTATGTTCGACCAAATTTTTAGCAAACAAAAA
ATTTTGAATTCATAAAACCACGTTGTTTATTTAAAACTCATTATAGCATTTTAAGGAATCATGAT
TAAATATCAAAATTAAAACCGTGAAATTTC
Found at i:1983169 original size:22 final size:22
Alignment explanation
Indices: 1983120--1983180 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
1983110 AATAATAAAG
* *
1983120 GAGCATCCAAATACCTTGGTTT
1 GAGCATCTAAATGCCTTGGTTT
1983142 GAGCATCTAAATGCCTT-GTTT
1 GAGCATCTAAATGCCTTGGTTT
*
1983163 GGGGCATCTAAATGCCTT
1 -GAGCATCTAAATGCCTT
1983181 AGTACAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 4 0.11
22 31 0.89
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
GAGCATCTAAATGCCTTGGTTT
Found at i:1984192 original size:40 final size:40
Alignment explanation
Indices: 1984131--1984207 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
1984121 TTATTTCTAA
* * * *
1984131 ATATTTGTAAAATGTTAAAATTTTTAGCATGGAGATTTAG
1 ATATTTGTAAAATGCTAAAATTTATACCATGAAGATTTAG
*
1984171 ATATTTGTAAAATGCTGAAATTTATACCATGAAGATT
1 ATATTTGTAAAATGCTAAAATTTATACCATGAAGATT
1984208 CGAACCTTGG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.40
Consensus pattern (40 bp):
ATATTTGTAAAATGCTAAAATTTATACCATGAAGATTTAG
Found at i:1984811 original size:15 final size:15
Alignment explanation
Indices: 1984793--1984821 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1984783 AGTAAATATT
1984793 TATGTAATATAATAA
1 TATGTAATATAATAA
1984808 TATGTAATATAATA
1 TATGTAATATAATA
1984822 TATCAATAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
TATGTAATATAATAA
Found at i:1984829 original size:20 final size:21
Alignment explanation
Indices: 1984797--1984839 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1984787 AATATTTATG
*
1984797 TAATATAATAATATGTA-ATA
1 TAATATAATAATAGGTATATA
1984817 TAATAT-ATCAATAGGTATATA
1 TAATATAAT-AATAGGTATATA
1984838 TA
1 TA
1984840 TGTATAGTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 13 0.65
21 5 0.25
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (21 bp):
TAATATAATAATAGGTATATA
Found at i:1989315 original size:162 final size:162
Alignment explanation
Indices: 1988962--1989328 Score: 389
Period size: 162 Copynumber: 2.2 Consensus size: 162
1988952 TGGATATGTA
* * * *
1988962 ATTTTGATATATTTGATGTTTAATTTTGTGTTTTAATTATATAAGGATCAAGTTGTAATGTTAGA
1 ATTTTAATATATTTGATGTTTAATTTTGTGTTTT-A--AT-TAAGGACCAAATTGTAATGTTAAA
* * *
1989027 AAGTTTAAGAGTTTATTTGTAAATATGTAAAAATTTTGTTCCAAGGCCAAAAGTACTTGGCCAAA
62 AAGTTTAAAAGTTTATTTGCAAATATGTAAAAATTTTGTTCCAAGGCCAAAAGTACTTGACCAAA
* * * * *
1989092 TTTTTCTTTTAATTTTTGAATCTGATATTTATGTTG
127 TCTTTCTTGTAACTTATGAATATGATATTTATGTTG
* * * * *
1989128 ATTTGAATATATTTGGTGCTTAATTTTGTGTTTTAATTAAGGGCCAAATTGTAATTTTAAAAAGT
1 ATTTTAATATATTTGATGTTTAATTTTGTGTTTTAATTAAGGACCAAATTGTAATGTTAAAAAGT
* * * *
1989193 TTAAAAGTTTATTTGCACATAT-TGGAAAA-TTTGTTCCAAGGCC-AAAGTTACTTGATCGAATC
66 TTAAAAGTTTATTTGCAAATATGT-AAAAATTTTGTTCCAAGGCCAAAAG-TACTTGACCAAATC
** * * * *
1989255 TTTCTTGTGGCTTATGTATATGATTTTTGGTGTTT
129 TTTCTTGTAACTTATGAATATGATATTT-ATGTTG
* *
1989290 ATTTTAATACATTTAATGTTTAATTTTGTGTTTTAATTA
1 ATTTTAATATATTTGATGTTTAATTTTGTGTTTTAATTA
1989329 TATAGGGACT
Statistics
Matches: 166, Mismatches: 32, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
160 4 0.02
161 45 0.27
162 84 0.51
163 2 0.01
165 1 0.01
166 30 0.18
ACGTcount: A:0.30, C:0.07, G:0.16, T:0.47
Consensus pattern (162 bp):
ATTTTAATATATTTGATGTTTAATTTTGTGTTTTAATTAAGGACCAAATTGTAATGTTAAAAAGT
TTAAAAGTTTATTTGCAAATATGTAAAAATTTTGTTCCAAGGCCAAAAGTACTTGACCAAATCTT
TCTTGTAACTTATGAATATGATATTTATGTTG
Found at i:1990671 original size:13 final size:13
Alignment explanation
Indices: 1990655--1990681 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1990645 ACAATTCATC
1990655 ATGTATCGATACA
1 ATGTATCGATACA
1990668 ATGTATCGATACA
1 ATGTATCGATACA
1990681 A
1 A
1990682 ACAGTGGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1990767 original size:13 final size:15
Alignment explanation
Indices: 1990734--1990773 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 15
1990724 ATTGTCCATT
1990734 TATCGATACAATGATG
1 TATCGATACAATGA-G
1990750 TATCGATACAA-G-G
1 TATCGATACAATGAG
1990763 TATCGATACAA
1 TATCGATACAA
1990774 AGCATAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 12 0.50
15 1 0.04
16 11 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (15 bp):
TATCGATACAATGAG
Found at i:1997896 original size:19 final size:19
Alignment explanation
Indices: 1997872--1997932 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
1997862 TTTGAATTTT
1997872 AAACAGTTTGTATCGATAC
1 AAACAGTTTGTATCGATAC
**
1997891 AAACAGAAAATGTATCGATAC
1 AAACAG--TTTGTATCGATAC
*
1997912 ATA-AGTGTTGTATCGATAC
1 AAACAGT-TTGTATCGATAC
1997931 AA
1 AA
1997933 TGTATCGATA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
19 18 0.55
20 2 0.06
21 13 0.39
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (19 bp):
AAACAGTTTGTATCGATAC
Found at i:1997938 original size:13 final size:13
Alignment explanation
Indices: 1997920--1997944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1997910 ACATAAGTGT
1997920 TGTATCGATACAA
1 TGTATCGATACAA
1997933 TGTATCGATACA
1 TGTATCGATACA
1997945 TAAGTTTTGT
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:1997940 original size:32 final size:32
Alignment explanation
Indices: 1997899--1997971 Score: 137
Period size: 32 Copynumber: 2.3 Consensus size: 32
1997889 ACAAACAGAA
1997899 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
1997931 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
1997963 AATGTATCG
1 AATGTATCG
1997972 CTATGAACCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:1997957 original size:19 final size:18
Alignment explanation
Indices: 1997901--1997963 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1997891 AAACAGAAAA
1997901 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
1997920 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
1997933 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
1997952 TGTATCGATACA
1 TGTATCGATACA
1997964 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:1998014 original size:21 final size:21
Alignment explanation
Indices: 1997988--1998030 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1997978 ACCTACTACC
1997988 AAGGAAATGTATCAATACATT
1 AAGGAAATGTATCAATACATT
*
1998009 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCAATACATT
1998030 A
1 A
1998031 TATCGATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (21 bp):
AAGGAAATGTATCAATACATT
Found at i:2000509 original size:52 final size:52
Alignment explanation
Indices: 2000421--2000520 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
2000411 CGGGGAACCC
* ** *
2000421 CGATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCCAACTT
1 CGATTTTATTTCCAAAACACCAATTTTCCTACAATCGAGGATACTCCAACTT
*
2000473 CGATTTTATTTCCAAAAACACCAATTTTTC-ACAATCGAGGATACTCCA
1 CGATTTTATTTCC-AAAACACCAATTTTCCTACAATCGAGGATACTCCA
2000521 TCCTCGTTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
52 27 0.64
53 15 0.36
ACGTcount: A:0.32, C:0.24, G:0.09, T:0.35
Consensus pattern (52 bp):
CGATTTTATTTCCAAAACACCAATTTTCCTACAATCGAGGATACTCCAACTT
Found at i:2003904 original size:19 final size:19
Alignment explanation
Indices: 2003880--2003945 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 19
2003870 TTTCAACGAT
2003880 TTGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
2003899 TTGTATCTATAC--AA---
1 TTGTATCGATACATAAGTG
2003913 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
2003931 TTGTATCGATACATA
1 TTGTATCGATACATA
2003946 TAAAGCTACT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
17 2 0.05
19 25 0.64
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Done.