Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
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: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 247 of 297
Found at i:84462136 original size:20 final size:20
Alignment explanation
Indices: 84462087--84462159 Score: 62
Period size: 21 Copynumber: 3.7 Consensus size: 20
84462077 TTTTTAATAC
*
84462087 TTTTA-AGACTTTTTAT-AT
1 TTTTATAGAATTTTTATGAT
** *
84462105 TTTTCCATAATTTTTATGAT
1 TTTTATAGAATTTTTATGAT
84462125 TTTTATAGAATTTTAATATG-T
1 TTTTATAGAATTTT--TATGAT
*
84462146 TTTTATAAAATTTT
1 TTTTATAGAATTTT
84462160 AAATATTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 4 0.09
19 9 0.20
20 13 0.30
21 14 0.32
22 4 0.09
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTTATAGAATTTTTATGAT
Found at i:84462160 original size:31 final size:31
Alignment explanation
Indices: 84462115--84462194 Score: 69
Period size: 30 Copynumber: 2.6 Consensus size: 31
84462105 TTTTCCATAA
* * *
84462115 TTTTTATGATTTTTATAGA-ATTTTAATATGT-
1 TTTTTATAAATTTTATA-ATATTTTAA-ATATG
84462146 TTTTATA-AAATTTTA-AATATTTTAAATATG
1 TTTT-TATAAATTTTATAATATTTTAAATATG
*
84462176 TTTTTATTAATTTTATAAT
1 TTTTTATAAATTTTATAAT
84462195 TTATTAGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
29 6 0.15
30 19 0.47
31 13 0.32
32 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (31 bp):
TTTTTATAAATTTTATAATATTTTAAATATG
Found at i:84462164 original size:22 final size:22
Alignment explanation
Indices: 84462119--84462168 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
84462109 CCATAATTTT
*
84462119 TATGATTTTTATAGAATTTTAA
1 TATGATTTTTATAAAATTTTAA
84462141 TATG-TTTTTATAAAATTTTAA
1 TATGATTTTTATAAAATTTTAA
84462162 -AT-ATTTT
1 TATGATTTT
84462169 AAATATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (22 bp):
TATGATTTTTATAAAATTTTAA
Found at i:84462221 original size:10 final size:9
Alignment explanation
Indices: 84462096--84462285 Score: 90
Period size: 9 Copynumber: 20.2 Consensus size: 9
84462086 CTTTTAAGAC
84462096 TTTTTAT-A
1 TTTTTATAA
84462104 TTTTTCCATAA
1 TTTTT--ATAA
*
84462115 TTTTTATGA
1 TTTTTATAA
84462124 TTTTTATAGAA
1 TTTTTAT--AA
* *
84462135 TTTTAATATG
1 TTTTTATA-A
84462145 TTTTTATAAA
1 TTTTTAT-AA
*
84462155 ATTTTA-AA
1 TTTTTATAA
*
84462163 TATTTTAAATATG
1 T-TTTT--ATA-A
84462176 TTTTTATTAA
1 TTTTTA-TAA
84462186 -TTTTATAA
1 TTTTTATAA
*
84462194 TTTATTAGAA
1 TTT-TTATAA
84462204 -TTTTAT-A
1 TTTTTATAA
84462211 -TTTTATAA
1 TTTTTATAA
*
84462219 TATTTTATAG
1 T-TTTTATAA
84462229 TTTTTAATAA
1 TTTTT-ATAA
84462239 TTTTTAT-A
1 TTTTTATAA
*
84462247 TTTTTGATAC
1 TTTTT-ATAA
*
84462257 TTTTT-TATT
1 TTTTTATA-A
84462266 TTTTTATAA
1 TTTTTATAA
*
84462275 TTTTTCTAA
1 TTTTTATAA
84462284 TT
1 TT
84462286 ATTCTGGGTT
Statistics
Matches: 141, Mismatches: 18, Indels: 45
0.69 0.09 0.22
Matches are distributed among these distances:
7 7 0.05
8 22 0.16
9 47 0.33
10 42 0.30
11 17 0.12
12 5 0.04
13 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:84462260 original size:17 final size:16
Alignment explanation
Indices: 84462185--84462268 Score: 71
Period size: 17 Copynumber: 4.8 Consensus size: 16
84462175 GTTTTTATTA
84462185 ATTTTATAATTTATTAGA-
1 ATTTTAT-ATTT-TTA-AT
84462203 ATTTTATATTTTATAAT
1 ATTTTATATTTT-TAAT
84462220 ATTTTATAGTTTTTAAT
1 ATTTTATA-TTTTTAAT
*
84462237 AATTTTTATATTTTTGAT
1 -A-TTTTATATTTTTAAT
*
84462255 ACTTTTTTATTTTT
1 A-TTTTATATTTTT
84462269 TTATAATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.03
17 30 0.52
18 19 0.33
19 7 0.12
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (16 bp):
ATTTTATATTTTTAAT
Found at i:84462269 original size:36 final size:36
Alignment explanation
Indices: 84462204--84462279 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
84462194 TTTATTAGAA
84462204 TTTTATATTTTATAATATTTTATAGTTTTTAATAAT
1 TTTTATATTTTATAATATTTTATAGTTTTTAATAAT
* * * *
84462240 TTTTATATTTT-TGATACTTTTTTATTTTTTTATAAT
1 TTTTATATTTTATAATA-TTTTATAGTTTTTAATAAT
84462276 TTTT
1 TTTT
84462280 CTAATTATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 4 0.11
36 31 0.89
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (36 bp):
TTTTATATTTTATAATATTTTATAGTTTTTAATAAT
Found at i:84462320 original size:19 final size:18
Alignment explanation
Indices: 84462204--84462321 Score: 64
Period size: 19 Copynumber: 6.3 Consensus size: 18
84462194 TTTATTAGAA
* *
84462204 TTTTATA-TTTTATAATA
1 TTTTATATTTTTATTATT
* *
84462221 TTTTATAGTTTTTAATAAT
1 TTTTATA-TTTTTATTATT
84462240 TTTTATATTTTTGA-TACTT
1 TTTTATATTTTT-ATTA-TT
* *
84462259 TTTTATTTTTTTATAATT
1 TTTTATATTTTTATTATT
*
84462277 TTTCTA-ATTATTCTGGGTT-TT
1 TTT-TATATT-TT-T--ATTATT
84462298 TTTTATAGTTTTTATTATT
1 TTTTATA-TTTTTATTATT
84462317 TTTTA
1 TTTTA
84462322 ATCATTTTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
17 7 0.09
18 17 0.22
19 38 0.49
20 4 0.05
21 8 0.10
22 3 0.04
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTATATTTTTATTATT
Found at i:84463340 original size:11 final size:11
Alignment explanation
Indices: 84463324--84463349 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
84463314 AAAAATGGCC
84463324 TAAACAAACTT
1 TAAACAAACTT
84463335 TAAACAAACTT
1 TAAACAAACTT
84463346 TAAA
1 TAAA
84463350 AATAGTAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAACAAACTT
Found at i:84466741 original size:43 final size:42
Alignment explanation
Indices: 84466679--84466770 Score: 139
Period size: 43 Copynumber: 2.1 Consensus size: 42
84466669 AATGCCCCAC
*
84466679 AAAAGATCATAACTTTTAGTGGCATTTGTGGGGAAAGCGCCGCT
1 AAAAG-TCATAACTTTTAGTGGCATTTGTGGGG-AAGAGCCGCT
* *
84466723 AAAAGTCATGACTTTTAGTGGCATTTTTGGGGAAGAGCCGCT
1 AAAAGTCATAACTTTTAGTGGCATTTGTGGGGAAGAGCCGCT
84466765 AAAAGT
1 AAAAGT
84466771 TGCTTTTGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 15 0.33
43 25 0.56
44 5 0.11
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (42 bp):
AAAAGTCATAACTTTTAGTGGCATTTGTGGGGAAGAGCCGCT
Found at i:84467674 original size:14 final size:13
Alignment explanation
Indices: 84467655--84467686 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
84467645 AATCAAATTG
84467655 AATTAAACCATTAT
1 AATTAAA-CATTAT
84467669 AATTAAACATTAT
1 AATTAAACATTAT
84467682 AATTA
1 AATTA
84467687 TTTATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTAAACATTAT
Found at i:84467711 original size:51 final size:51
Alignment explanation
Indices: 84467602--84467704 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
84467592 CTACTAATGA
84467602 TGAATTAAACCATTATAATTAAAAATTATAATTATTTATAATAAATCAAAT
1 TGAATTAAACCATTATAATTAAAAATTATAATTATTTATAATAAATCAAAT
*
84467653 TGAATTAAACCATTATAATTAAACATTATAATTATTTATAATAAATCAAAT
1 TGAATTAAACCATTATAATTAAAAATTATAATTATTTATAATAAATCAAAT
84467704 T
1 T
84467705 TTATTAAGTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (51 bp):
TGAATTAAACCATTATAATTAAAAATTATAATTATTTATAATAAATCAAAT
Found at i:84472799 original size:9 final size:9
Alignment explanation
Indices: 84472785--84472947 Score: 61
Period size: 9 Copynumber: 18.1 Consensus size: 9
84472775 AAGTGAGCTT
84472785 TGTAAGTTA
1 TGTAAGTTA
84472794 TGTAAGTTA
1 TGTAAGTTA
* *
84472803 TGTTA-TGA
1 TGTAAGTTA
* *
84472811 TATACATTTA
1 TGTA-AGTTA
* *
84472821 TATAAGGTA
1 TGTAAGTTA
84472830 TGTAAGTTA
1 TGTAAGTTA
* *
84472839 TGATATGATA
1 TG-TAAGTTA
* *
84472849 TAT-ATTTA
1 TGTAAGTTA
84472857 TGT-A-TTA
1 TGTAAGTTA
*
84472864 TGTAAGTTG
1 TGTAAGTTA
84472873 TGTAAGTTA
1 TGTAAGTTA
* *
84472882 TGATATGATA
1 TG-TAAGTTA
* *
84472892 TAT-ATTTA
1 TGTAAGTTA
*
84472900 TGATATATATTTA
1 TG---TA-AGTTA
84472913 TGT-A-TTA
1 TGTAAGTTA
*
84472920 TGTAAGTTT
1 TGTAAGTTA
84472929 TGTAAGTTA
1 TGTAAGTTA
84472938 TGTAAGTTA
1 TGTAAGTTA
84472947 T
1 T
84472948 TATATGATAT
Statistics
Matches: 114, Mismatches: 27, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
7 12 0.11
8 15 0.13
9 60 0.53
10 19 0.17
11 1 0.01
13 7 0.06
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (9 bp):
TGTAAGTTA
Found at i:84472839 original size:36 final size:36
Alignment explanation
Indices: 84472787--84472857 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
84472777 GTGAGCTTTG
* *
84472787 TAAGTTATGTAAGTTATGTTATGATATACATTTATA
1 TAAGGTATGTAAGTTATGATATGATATACATTTATA
*
84472823 TAAGGTATGTAAGTTATGATATGATATATATTTAT
1 TAAGGTATGTAAGTTATGATATGATATACATTTAT
84472858 GTATTATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.37, C:0.01, G:0.15, T:0.46
Consensus pattern (36 bp):
TAAGGTATGTAAGTTATGATATGATATACATTTATA
Found at i:84472858 original size:27 final size:27
Alignment explanation
Indices: 84472828--84473018 Score: 126
Period size: 27 Copynumber: 7.1 Consensus size: 27
84472818 TTATATAAGG
84472828 TATGTAAGTTATGATATGATATATATT
1 TATGTAAGTTATGATATGATATATATT
* * * * *
84472855 TATGT-A-TTATG-TAAGTTGTGTAAGT
1 TATGTAAGTTATGATATGATATAT-ATT
*
84472880 TATGATATGATATAT-ATTTATGATATATATT
1 TATG-TAAG-T-TATGA--TATGATATATATT
* * * * *
84472911 TATGT-A-TTATG-TAAGTTTTGTAAGT
1 TATGTAAGTTATGATATGATATAT-ATT
*
84472936 TATGTAAGTTATTATATGATATATATT
1 TATGTAAGTTATGATATGATATATATT
* *
84472963 TATGTGAGTTATTATATGATATATATT
1 TATGTAAGTTATGATATGATATATATT
* *
84472990 TATGTAATTTATTATATGATATATATT
1 TATGTAAGTTATGATATGATATATATT
84473017 TA
1 TA
84473019 ACATTAAGAT
Statistics
Matches: 124, Mismatches: 26, Indels: 28
0.70 0.15 0.16
Matches are distributed among these distances:
24 12 0.10
25 18 0.15
26 6 0.05
27 65 0.52
28 6 0.05
29 1 0.01
30 4 0.03
31 6 0.05
32 6 0.05
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (27 bp):
TATGTAAGTTATGATATGATATATATT
Found at i:84472907 original size:56 final size:52
Alignment explanation
Indices: 84472823--84473018 Score: 218
Period size: 56 Copynumber: 3.7 Consensus size: 52
84472813 TACATTTATA
* *
84472823 TAAGGTATGTAAGTTATGATATGATATATATTTATGTATTATGTAAGTTGTG
1 TAAGTTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGTTGTG
* * *
84472875 TAAGTTATGATATGATATATATTTATGATATATATTTATGTATTATGTAAGTTTTG
1 TAAGTTATG-TAAG-T-TAT-TATATGATATATATTTATGTATTATGTAAGTTGTG
*
84472931 TAAGTTATGTAAGTTATTATATGATATATATTTATGTGAGTTAT-T-A-TATGATA
1 TAAGTTATGTAAGTTATTATATGATATATATTTATGT-A-TTATGTAAGT-TG-TG
* *
84472984 TATATTTATGTAATTTATTATATGATATATATTTA
1 TA-AGTTATGTAAGTTATTATATGATATATATTTA
84473019 ACATTAAGAT
Statistics
Matches: 124, Mismatches: 11, Indels: 16
0.82 0.07 0.11
Matches are distributed among these distances:
51 1 0.01
52 29 0.23
53 11 0.09
54 36 0.29
55 6 0.05
56 41 0.33
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.51
Consensus pattern (52 bp):
TAAGTTATGTAAGTTATTATATGATATATATTTATGTATTATGTAAGTTGTG
Found at i:84473216 original size:14 final size:14
Alignment explanation
Indices: 84473197--84473224 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
84473187 TGACAATGTG
84473197 AAAAATCACATGAA
1 AAAAATCACATGAA
84473211 AAAAATCACATGAA
1 AAAAATCACATGAA
84473225 TAAATTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.07, T:0.14
Consensus pattern (14 bp):
AAAAATCACATGAA
Found at i:84475097 original size:19 final size:20
Alignment explanation
Indices: 84475066--84475111 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
84475056 TTTTGATTCT
84475066 GGGAAATATTTAGGGATTAG
1 GGGAAATATTTAGGGATTAG
*
84475086 GGGAAA-ATTTAGGGATTTG
1 GGGAAATATTTAGGGATTAG
84475105 GGGAAAT
1 GGGAAAT
84475112 TTGGGTGGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.35, C:0.00, G:0.37, T:0.28
Consensus pattern (20 bp):
GGGAAATATTTAGGGATTAG
Found at i:84476314 original size:21 final size:21
Alignment explanation
Indices: 84476290--84476334 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
84476280 AGCTCATGAG
84476290 TTATGATTTAAGGG-TTAGGCT
1 TTAT-ATTTAAGGGTTTAGGCT
* *
84476311 TTATATTTTAGGGTTTAGGGT
1 TTATATTTAAGGGTTTAGGCT
84476332 TTA
1 TTA
84476335 AGGTTTTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.22, C:0.02, G:0.27, T:0.49
Consensus pattern (21 bp):
TTATATTTAAGGGTTTAGGCT
Found at i:84476327 original size:7 final size:7
Alignment explanation
Indices: 84476317--84476372 Score: 60
Period size: 7 Copynumber: 8.0 Consensus size: 7
84476307 GGCTTTATAT
84476317 TTTAGGG
1 TTTAGGG
84476324 TTTAGGG
1 TTTAGGG
*
84476331 TTTAAGG
1 TTTAGGG
*
84476338 TTTTGGG
1 TTTAGGG
*
84476345 ATTT-GGC
1 -TTTAGGG
*
84476352 TTTAGAG
1 TTTAGGG
84476359 TTTAGGG
1 TTTAGGG
84476366 TTTAGGG
1 TTTAGGG
84476373 GCTAAAATTC
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
6 3 0.08
7 34 0.85
8 3 0.08
ACGTcount: A:0.16, C:0.02, G:0.38, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:84477055 original size:81 final size:82
Alignment explanation
Indices: 84476922--84477151 Score: 336
Period size: 81 Copynumber: 2.8 Consensus size: 82
84476912 CGTTTGGACC
* * * *
84476922 AAAAACGCCACTATTTCTCAGTTTTTCGCGGAGTTTTGGACAAAAACGCCACTATTGCTCAGTTT
1 AAAAACGCCACTATTGCTCAGTTTTTTGCGGCGTTTTGGATAAAAACGCCACTATTGCTCAGTTT
**
84476987 TTCACGGTGTTTTGGAT
66 TTCACGACGTTTTGGAT
*
84477004 AAAAACGCCACT-TTGCTCAGTTTTTTGCGGCGTTTTGGATAAAAACTCCACTATTGCTCAGTTT
1 AAAAACGCCACTATTGCTCAGTTTTTTGCGGCGTTTTGGATAAAAACGCCACTATTGCTCAGTTT
*
84477068 TTCGCGACGTTTTGGAT
66 TTCACGACGTTTTGGAT
* * * * *
84477085 AAAAACGCCACTACTGCTCAATTTTTTGCAGCGTTTTGCATAAAGACGCCACTATTGCTCAGTTT
1 AAAAACGCCACTATTGCTCAGTTTTTTGCGGCGTTTTGGATAAAAACGCCACTATTGCTCAGTTT
84477150 TT
66 TT
84477152 TGCCGCGTTT
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
81 73 0.55
82 60 0.45
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (82 bp):
AAAAACGCCACTATTGCTCAGTTTTTTGCGGCGTTTTGGATAAAAACGCCACTATTGCTCAGTTT
TTCACGACGTTTTGGAT
Found at i:84477121 original size:122 final size:124
Alignment explanation
Indices: 84476904--84477163 Score: 357
Period size: 122 Copynumber: 2.1 Consensus size: 124
84476894 TAGCTCAACC
* *
84476904 TTTTGTGGCG-TTTGGACCAAAAACGCCACTATTTCTCAGTTTTTCGCGGAGTTTTGGACAAAAA
1 TTTTGCGGCGTTTTGGACCAAAAACGCCACTATTGCTCAGTTTTTCGCGGAGTTTTGGACAAAAA
* * * * *
84476968 CGCCACTATTGCTCAGTTTTTCACGGTGTTTTGGATAAAAACGCCACT-TTGCTCAGTT
66 CGCCACTACTGCTCAATTTTTCACAGCGTTTTGCATAAAAACGCCACTATTGCTCAGTT
* * *
84477026 TTTTGCGGCGTTTTGGA-TAAAAACTCCACTATTGCTCAGTTTTTCGC-GACGTTTTGGATAAAA
1 TTTTGCGGCGTTTTGGACCAAAAACGCCACTATTGCTCAGTTTTTCGCGGA-GTTTTGGACAAAA
** *
84477089 ACGCCACTACTGCTCAATTTTTTGCAGCGTTTTGCATAAAGACGCCACTATTGCTCAGTT
65 ACGCCACTACTGCTCAATTTTTCACAGCGTTTTGCATAAAAACGCCACTATTGCTCAGTT
*
84477149 TTTTGCCGCGTTTTG
1 TTTTGCGGCGTTTTG
84477164 TTTCAAACGC
Statistics
Matches: 121, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
121 2 0.02
122 89 0.74
123 30 0.25
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.37
Consensus pattern (124 bp):
TTTTGCGGCGTTTTGGACCAAAAACGCCACTATTGCTCAGTTTTTCGCGGAGTTTTGGACAAAAA
CGCCACTACTGCTCAATTTTTCACAGCGTTTTGCATAAAAACGCCACTATTGCTCAGTT
Found at i:84477152 original size:41 final size:41
Alignment explanation
Indices: 84476922--84477163 Score: 333
Period size: 41 Copynumber: 5.9 Consensus size: 41
84476912 CGTTTGGACC
* * *
84476922 AAAAACGCCACTATTTCTCAGTTTTTCGCGGAGTTTTGGAC
1 AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTGGAT
* *
84476963 AAAAACGCCACTATTGCTCAGTTTTTCACGGTGTTTTGGAT
1 AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTGGAT
*
84477004 AAAAACGCCACT-TTGCTCAGTTTTTTGCGGCGTTTTGGAT
1 AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTGGAT
* *
84477044 AAAAACTCCACTATTGCTCAGTTTTTCGCGACGTTTTGGAT
1 AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTGGAT
* * * * *
84477085 AAAAACGCCACTACTGCTCAATTTTTTGCAGCGTTTTGCAT
1 AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTGGAT
* * *
84477126 AAAGACGCCACTATTGCTCAGTTTTTTGCCGCGTTTTG
1 AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTG
84477164 TTTCAAACGC
Statistics
Matches: 179, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
40 36 0.20
41 143 0.80
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (41 bp):
AAAAACGCCACTATTGCTCAGTTTTTCGCGGCGTTTTGGAT
Found at i:84479068 original size:10 final size:10
Alignment explanation
Indices: 84479053--84479127 Score: 63
Period size: 9 Copynumber: 8.0 Consensus size: 10
84479043 TATTTTACAT
84479053 ATAAAATATA
1 ATAAAATATA
*
84479063 ATAAAATAAAA
1 ATAAAAT-ATA
*
84479074 ATAAAA-AAA
1 ATAAAATATA
84479083 ATAAAA-ATA
1 ATAAAATATA
*
84479092 A-AAAATAGA
1 ATAAAATATA
84479101 AT-AAATAT-
1 ATAAAATATA
*
84479109 AT-ATATATA
1 ATAAAATATA
84479118 ATAAAATATA
1 ATAAAATATA
84479128 TAATAAAAGA
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
8 11 0.20
9 22 0.41
10 13 0.24
11 8 0.15
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.25
Consensus pattern (10 bp):
ATAAAATATA
Found at i:84479070 original size:5 final size:5
Alignment explanation
Indices: 84479053--84479141 Score: 58
Period size: 5 Copynumber: 17.4 Consensus size: 5
84479043 TATTTTACAT
* * *
84479053 ATAAA ATATA ATAAA ATAAAA ATAAA A-AAA ATAAA A-ATA A-AAA ATAGA
1 ATAAA ATAAA ATAAA AT-AAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
* * *
84479101 ATAAA TATATAT ATATA ATAAA ATATATA ATAAA AGAAA AT
1 ATAAA -ATA-AA ATAAA ATAAA ATA-A-A ATAAA ATAAA AT
84479142 TTTTTAAAAA
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
4 10 0.15
5 37 0.57
6 13 0.20
7 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (5 bp):
ATAAA
Found at i:84479128 original size:12 final size:12
Alignment explanation
Indices: 84479058--84479135 Score: 51
Period size: 12 Copynumber: 6.9 Consensus size: 12
84479048 TACATATAAA
84479058 ATATAATAAAAT
1 ATATAATAAAAT
*
84479070 A-AAAATAAAA-
1 ATATAATAAAAT
84479080 A-A-AATAAAAAT
1 ATATAAT-AAAAT
* * *
84479091 AAAAAATAGAAT
1 ATATAATAAAAT
* *
84479103 AAAT-AT-ATAT
1 ATATAATAAAAT
84479113 ATATAATAAAAT
1 ATATAATAAAAT
84479125 ATATAATAAAA
1 ATATAATAAAA
84479136 GAAAATTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
9 3 0.06
10 11 0.21
11 13 0.25
12 23 0.43
13 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (12 bp):
ATATAATAAAAT
Found at i:84480628 original size:15 final size:15
Alignment explanation
Indices: 84480605--84480635 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
84480595 ATAAATGGAC
*
84480605 TTTATTTTTTTATTT
1 TTTACTTTTTTATTT
84480620 TTTACTTTTTTATTT
1 TTTACTTTTTTATTT
84480635 T
1 T
84480636 AGTTTAAGGC
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:0.03, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTACTTTTTTATTT
Found at i:84481061 original size:86 final size:85
Alignment explanation
Indices: 84480968--84481418 Score: 301
Period size: 87 Copynumber: 5.2 Consensus size: 85
84480958 ATGCCAAATC
* *
84480968 ATCTTGGATCTACTTCAGTAAAATCATCTTAAGGTTAGATCTGCTATGTATCTGCTCTCTGTTGA
1 ATCTTGGATCTGCTTCAGTAAAA-CATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTTGA
84481033 AATGGAGATGCCAGATCTGTT
65 AATGGAGATGCCAGATCTGTT
* * * * * * * * * *
84481054 ATCTTGGATCTGCTTCGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCT-TCGATTTGTTC
1 ATCTTGGATCTGCTTC--AGT-AAAACATCTGAAGGTTAGATCTGCTATGTATCT-GCTCT-CT-
* *** *
84481118 CTTGTAAACACAAGAATGCCAAATC----
60 GTTG-AAA-TGGAG-ATGCCAGATCTGTT
*
84481143 ATCTTGGATCTGCTTCAGTATAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGA
1 ATCTTGGATCTGCTTCAGTA-AAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTTGA
84481208 AATGGAGATGCCAGATCTGTT
65 AATGGAGATGCCAGATCTGTT
** * * * * * * * * *
84481229 ATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCT-TCGATTTGTTC
1 ATCTTGGATCTGC-TT-CAGT-AAAACATCTGAAGGTTAGATCTGCTATGTATCT-GCTCT-CT-
* *** *
84481293 CTTGTAAACACAAGAATGCCAAATC----
60 GTTG-AAA-TGGAG-ATGCCAGATCTGTT
* * *
84481318 ATCTTGGATCTGCTTCAGTGAAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGA
1 ATCTTGGATCTGCTTCAGT-AAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTTGA
*
84481383 AATGGAAATGCCAGATCTGTT
65 AATGGAGATGCCAGATCTGTT
84481404 ATCTTGGATCTGCTT
1 ATCTTGGATCTGCTT
84481419 TGGTGTGAGA
Statistics
Matches: 266, Mismatches: 70, Indels: 58
0.68 0.18 0.15
Matches are distributed among these distances:
82 18 0.07
83 3 0.01
84 6 0.02
85 4 0.02
86 45 0.17
87 63 0.24
88 59 0.22
89 35 0.13
90 5 0.02
91 6 0.02
92 4 0.02
93 18 0.07
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (85 bp):
ATCTTGGATCTGCTTCAGTAAAACATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTTGAA
ATGGAGATGCCAGATCTGTT
Found at i:84481108 original size:175 final size:175
Alignment explanation
Indices: 84480910--84481463 Score: 959
Period size: 175 Copynumber: 3.2 Consensus size: 175
84480900 CGTAACACAT
* * * * *
84480910 GAAAGCCAAATCTACTGTGTCTTCGATTTGCTCCTTGTGAACACAA-AGATGCCAAATCATCTTG
1 GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGA-ATGCCAAATCATCTTG
* * *
84480974 GATCTACTTCAGTAAAATCATCTTAAGGTTAGATCTGCTATGTATCTGCTCTCTGTTGAAATGGA
65 GATCTGCTTCAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGA
*
84481039 GATGCCAGATCTGTTATCTTGGATCTGCTTCGGTGTGAGAACATCC
130 GATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
84481085 GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
1 GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
84481150 ATCTGCTTCAGTATAAA-CATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGA
66 ATCTGCTTCAGTA-AAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGA
84481214 GATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
130 GATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
84481260 GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
1 GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
* * *
84481325 ATCTGCTTCAGTGAAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCCGTCGAAATGGAA
66 ATCTGCTTCAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGAG
84481390 ATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
131 ATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
*
84481435 GAAAGTCAGATCTGCTATGTCTTCGATTT
1 GAAAGTCAAATCTGCTATGTCTTCGATTT
84481464 CCTCATCGTC
Statistics
Matches: 363, Mismatches: 13, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
174 3 0.01
175 356 0.98
176 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (175 bp):
GAAAGTCAAATCTGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGAATGCCAAATCATCTTGG
ATCTGCTTCAGTAAAATCATCTGAAGGTTAGATCTGCTATGTATCTGCTCTCTGTCGAAATGGAG
ATGCCAGATCTGTTATCTTGGATCTGCTTTGGTGTGAGAACATCC
Found at i:84481158 original size:89 final size:89
Alignment explanation
Indices: 84481054--84481333 Score: 310
Period size: 89 Copynumber: 3.2 Consensus size: 89
84481044 CAGATCTGTT
84481054 ATCTTGGATCTGCTTCGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCC
1 ATCTTGGATCTGCTTCGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCC
84481119 TTGTAAACACAAGAATGCCAAATC
66 TTGTAAACACAAGAATGCCAAATC
* * * * * * * *
84481143 ATCTTGGATCTGCTTCAGTAT-A-AACATCTGAAGGTTAGATCTGCTATG---T--ATCTGCT-C
1 ATCTTGGATCTGCTTCGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCC
* ** *
84481200 TCTGTCGAA-A-TGGAGATGCCAGATC
66 T-TGT-AAACACAAGA-ATGCCAAATC
*
84481225 TGTTATCTTGGATCTGCTTTGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTG
1 ----ATCTTGGATCTGCTTCGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTG
84481290 TTCCTTGTAAACACAAGAATGCCAAATC
62 TTCCTTGTAAACACAAGAATGCCAAATC
84481318 ATCTTGGATCTGCTTC
1 ATCTTGGATCTGCTTC
84481334 AGTGAAATCA
Statistics
Matches: 148, Mismatches: 26, Indels: 34
0.71 0.12 0.16
Matches are distributed among these distances:
81 4 0.03
82 18 0.12
83 2 0.01
84 1 0.01
86 18 0.12
87 23 0.16
88 23 0.16
89 34 0.23
91 1 0.01
92 2 0.01
93 18 0.12
94 4 0.03
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (89 bp):
ATCTTGGATCTGCTTCGGTGTGAGAACATCCGAAAGTCAAATCTGCTATGTCTTCGATTTGTTCC
TTGTAAACACAAGAATGCCAAATC
Found at i:84493519 original size:6 final size:6
Alignment explanation
Indices: 84493508--84493540 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
84493498 AAAATATAAT
*
84493508 AAAATA AAAATA AAAA-A GAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
84493541 ACAGAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (6 bp):
AAAATA
Found at i:84493531 original size:17 final size:17
Alignment explanation
Indices: 84493509--84493541 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
84493499 AAATATAATA
84493509 AAATAAAAATAAAAAAG
1 AAATAAAAATAAAAAAG
84493526 AAATAAAAATAAAAAA
1 AAATAAAAATAAAAAA
84493542 CAGAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (17 bp):
AAATAAAAATAAAAAAG
Found at i:84493540 original size:18 final size:18
Alignment explanation
Indices: 84493509--84493550 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
84493499 AAATATAATA
84493509 AAATAAAAATAAAAA-AG
1 AAATAAAAATAAAAACAG
84493526 AAATAAAAATAAAAAACAG
1 AAATAAAAAT-AAAAACAG
84493545 -AATAAA
1 AAATAAA
84493551 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.43
18 11 0.48
19 2 0.09
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (18 bp):
AAATAAAAATAAAAACAG
Found at i:84493569 original size:12 final size:12
Alignment explanation
Indices: 84493554--84493578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
84493544 GAATAAATAT
84493554 ATATATAATAAA
1 ATATATAATAAA
84493566 ATATATAATAAA
1 ATATATAATAAA
84493578 A
1 A
84493579 GATTTTTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATATAATAAA
Found at i:84508575 original size:15 final size:15
Alignment explanation
Indices: 84508552--84508583 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
84508542 TTGCTTCACA
*
84508552 CACTGTGTTATCAAG
1 CACTATGTTATCAAG
84508567 CACTATGTTATCAAG
1 CACTATGTTATCAAG
84508582 CA
1 CA
84508584 ACAATACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (15 bp):
CACTATGTTATCAAG
Found at i:84514899 original size:23 final size:23
Alignment explanation
Indices: 84514873--84514919 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
84514863 TAAACTACGC
* *
84514873 TTACAACTGAAAAGAAACCTAAA
1 TTACAACTAAAAAGAAAACTAAA
* *
84514896 TTACAAGTAAAAATAAAACTAAA
1 TTACAACTAAAAAGAAAACTAAA
84514919 T
1 T
84514920 AGAAAATGGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (23 bp):
TTACAACTAAAAAGAAAACTAAA
Found at i:84528807 original size:41 final size:43
Alignment explanation
Indices: 84528712--84528831 Score: 122
Period size: 42 Copynumber: 2.8 Consensus size: 43
84528702 ATCAAGTACA
* * *
84528712 ATGCCGACGTCCCAGAAGTGGTCTTACATGTAATTCAATATCG
1 ATGCCGATGTCCCAGAAGTGGTCTTACACGTAAATCAATATCG
** *
84528755 ATGCCTCTGTCCCAGTAG-GGTCTTACACG-AAATCAGATA-CG
1 ATGCCGATGTCCCAGAAGTGGTCTTACACGTAAATCA-ATATCG
* *
84528796 ATGCCGATGTCCTAGACA-TGGTCTTATACGTAAATC
1 ATGCCGATGTCCCAGA-AGTGGTCTTACACGTAAATC
84528832 TCAATCAAGG
Statistics
Matches: 62, Mismatches: 11, Indels: 8
0.77 0.14 0.10
Matches are distributed among these distances:
41 19 0.31
42 24 0.39
43 19 0.31
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (43 bp):
ATGCCGATGTCCCAGAAGTGGTCTTACACGTAAATCAATATCG
Found at i:84534695 original size:17 final size:18
Alignment explanation
Indices: 84534657--84534695 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
84534647 TTTAGGGTTT
84534657 TTTAATATAGTAAAATAA
1 TTTAATATAGTAAAATAA
*
84534675 -TTAAT-TATTAAAATAA
1 TTTAATATAGTAAAATAA
84534691 TTTAA
1 TTTAA
84534696 AGTTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTAATATAGTAAAATAA
Found at i:84541562 original size:7 final size:7
Alignment explanation
Indices: 84541550--84541575 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
84541540 GACTAAATCG
84541550 AATTTAA
1 AATTTAA
84541557 AATTTAA
1 AATTTAA
84541564 AATTTAA
1 AATTTAA
84541571 AATTT
1 AATTT
84541576 TACCTTAATT
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:84546251 original size:25 final size:25
Alignment explanation
Indices: 84546214--84546274 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
84546204 GCAAATGTGC
* * *
84546214 TAATCAGATAGCACTAGCGTGCTAA
1 TAATCAGAGAGCACTAACATGCTAA
*
84546239 TAATCGGAGAGCACTAACATGCTAA
1 TAATCAGAGAGCACTAACATGCTAA
84546264 TAATCAGAGAG
1 TAATCAGAGAG
84546275 AGCGCTAAGG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAGCACTAACATGCTAA
Found at i:84565029 original size:39 final size:40
Alignment explanation
Indices: 84564826--84565045 Score: 232
Period size: 40 Copynumber: 5.5 Consensus size: 40
84564816 TATTCGAATG
* * *
84564826 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGC-GAGTGACT
* * *
84564867 ATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * * *
84564907 ATATTCGGGCCAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* * * *
84564947 ATATCCGGGCTAAGTCCCGAAGGCATTTATGC-TGTGACC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
* **
84564986 ATATCCGGGCTAAGACCCGAAGGC-CTTGTGCGAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
84565025 ATATCC-GGCTAA-ATCCCGAAG
1 ATATCCGGGCTAAGA-CCCGAAG
84565046 ATACTTGGGT
Statistics
Matches: 148, Mismatches: 29, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
37 1 0.01
38 18 0.12
39 36 0.24
40 65 0.44
41 28 0.19
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGACT
Found at i:84571035 original size:15 final size:15
Alignment explanation
Indices: 84570962--84571039 Score: 88
Period size: 15 Copynumber: 5.2 Consensus size: 15
84570952 AGAAAATCGA
84570962 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
84570977 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
84570991 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
*
84571006 AATAAAGAGATCCAAG
1 -ATAAAGAAATCCAAG
*
84571022 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
84571037 ATA
1 ATA
84571040 CGATACTATG
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.07
15 46 0.85
16 4 0.07
ACGTcount: A:0.58, C:0.15, G:0.15, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:84580577 original size:11 final size:11
Alignment explanation
Indices: 84580561--84580585 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
84580551 ATATTTAGAA
84580561 TTCTCTTCATT
1 TTCTCTTCATT
84580572 TTCTCTTCATT
1 TTCTCTTCATT
84580583 TTC
1 TTC
84580586 ATCAGCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:84582687 original size:48 final size:47
Alignment explanation
Indices: 84582618--84582742 Score: 144
Period size: 47 Copynumber: 2.6 Consensus size: 47
84582608 GTGCGAGTTA
** ***
84582618 TACCTTGATTTGGCTTTGGGCCATGGTATAGGT-ATTTTGGAGAGGAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTGATCCAGGAGA--AGT
* *
84582666 TACCTTGATTTGGCTACGGGCCATGGTATAGGTGCTCCAGGATAAGT
1 TACCTTGATTTGGCTACGGGCCATGGTATAGGTGATCCAGGAGAAGT
* *
84582713 TACCTTGCTTTGGCTACGAGCCATGGTATA
1 TACCTTGATTTGGCTACGGGCCATGGTATA
84582743 AGTACTCATC
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
47 31 0.46
48 31 0.46
49 5 0.07
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.34
Consensus pattern (47 bp):
TACCTTGATTTGGCTACGGGCCATGGTATAGGTGATCCAGGAGAAGT
Found at i:84583223 original size:19 final size:19
Alignment explanation
Indices: 84583199--84583239 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
84583189 TTAAATTGTT
*
84583199 TTATAATATGAAATGAATA
1 TTATAATATGAAAGGAATA
*
84583218 TTATAATATTAAAGGAATA
1 TTATAATATGAAAGGAATA
84583237 TTA
1 TTA
84583240 ATATTATAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (19 bp):
TTATAATATGAAAGGAATA
Found at i:84589149 original size:11 final size:11
Alignment explanation
Indices: 84589133--84589254 Score: 84
Period size: 11 Copynumber: 10.7 Consensus size: 11
84589123 AAATGTCTTT
84589133 TAAAATAATAA
1 TAAAATAATAA
84589144 TAAAATTAATAA
1 TAAAA-TAATAA
**
84589156 TAAAATAATTT
1 TAAAATAATAA
* * *
84589167 TTATATAATATT
1 TAAAATAATA-A
84589179 TAAATAATAATAA
1 T-AA-AATAATAA
* *
84589192 TAAAATAGTAG
1 TAAAATAATAA
* *
84589203 TAATATAATAT
1 TAAAATAATAA
*
84589214 TAAAATAATAG
1 TAAAATAATAA
*
84589225 TAAAATAGAGAA
1 TAAAATA-ATAA
84589237 -AAAATAATAA
1 TAAAATAATAA
*
84589247 AAAAATAA
1 TAAAATAA
84589255 CATAAAAAAA
Statistics
Matches: 87, Mismatches: 18, Indels: 12
0.74 0.15 0.10
Matches are distributed among these distances:
10 3 0.03
11 59 0.68
12 17 0.20
13 2 0.02
14 6 0.07
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (11 bp):
TAAAATAATAA
Found at i:84589153 original size:12 final size:12
Alignment explanation
Indices: 84589133--84589161 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
84589123 AAATGTCTTT
84589133 TAAAA-TAATAA
1 TAAAATTAATAA
84589144 TAAAATTAATAA
1 TAAAATTAATAA
84589156 TAAAAT
1 TAAAAT
84589162 AATTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTAATAA
Found at i:84589196 original size:36 final size:36
Alignment explanation
Indices: 84589137--84589223 Score: 106
Period size: 36 Copynumber: 2.5 Consensus size: 36
84589127 GTCTTTTAAA
* ** *
84589137 ATAATAATAAAAT--TAATAATAAAATAATTTTTAT
1 ATAATATTAAAATAATAATAATAAAATAATAGTAAT
* *
84589171 ATAATATTTAAATAATAATAATAAAATAGTAGTAAT
1 ATAATATTAAAATAATAATAATAAAATAATAGTAAT
84589207 ATAATATTAAAATAATA
1 ATAATATTAAAATAATA
84589224 GTAAAATAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 11 0.25
36 33 0.75
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (36 bp):
ATAATATTAAAATAATAATAATAAAATAATAGTAAT
Found at i:84589375 original size:13 final size:13
Alignment explanation
Indices: 84589357--84589382 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84589347 TTTTGTCCAT
84589357 TCCTATTTTTCAA
1 TCCTATTTTTCAA
84589370 TCCTATTTTTCAA
1 TCCTATTTTTCAA
84589383 GCCAATATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (13 bp):
TCCTATTTTTCAA
Found at i:84606712 original size:27 final size:27
Alignment explanation
Indices: 84606665--84606728 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
84606655 AAATATTCTC
*
84606665 TAAATTAAT-AAATATTAATTTATCGA
1 TAAATTAATAAAATATTAATTTATCCA
*
84606691 TAAATTAATAAAATATTCATTTATCCA
1 TAAATTAATAAAATATTAATTTATCCA
*
84606718 TAAACTAATAA
1 TAAATTAATAA
84606729 CCTTGATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 9 0.26
27 25 0.74
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.39
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATTTATCCA
Found at i:84607056 original size:18 final size:19
Alignment explanation
Indices: 84607011--84607058 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
84607001 GACCAATATT
* *
84607011 AATAAATAATATTTTTTAAA
1 AATATATAA-ATTTATTAAA
84607031 AATATATAAATTTATTAAA
1 AATATATAAATTTATTAAA
84607050 AAT-TATAAA
1 AATATATAAA
84607059 AGATTATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 6 0.23
19 12 0.46
20 8 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATATAAATTTATTAAA
Found at i:84607200 original size:15 final size:16
Alignment explanation
Indices: 84607163--84607202 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
84607153 TTAATTGCAC
84607163 AAATATCAAAGTACAT
1 AAATATCAAAGTACAT
84607179 AAA-ATCAAA-TAC-T
1 AAATATCAAAGTACAT
84607192 AACATATCAAA
1 AA-ATATCAAA
84607203 ATTTCACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 3 0.14
14 4 0.18
15 12 0.55
16 3 0.14
ACGTcount: A:0.60, C:0.15, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATATCAAAGTACAT
Found at i:84613420 original size:34 final size:33
Alignment explanation
Indices: 84613356--84613421 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 33
84613346 AGATTTGTAA
* *
84613356 AAAATTATAAATATATTTAAAAATATAAAATTG
1 AAAATTATAAATATAATTAAAAATAAAAAATTG
*
84613389 AAAATTATATATTATAATTAAATAA-AAAAAATT
1 AAAATTATA-AATATAATTAAA-AATAAAAAATT
84613422 TGAACAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 9 0.32
34 17 0.61
35 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (33 bp):
AAAATTATAAATATAATTAAAAATAAAAAATTG
Found at i:84618514 original size:13 final size:13
Alignment explanation
Indices: 84618498--84618523 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
84618488 AAAAAATATA
84618498 TATGCATAATACT
1 TATGCATAATACT
84618511 TATGCATAATACT
1 TATGCATAATACT
84618524 AATCATAAAT
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:0.08, T:0.38
Consensus pattern (13 bp):
TATGCATAATACT
Found at i:84619899 original size:24 final size:24
Alignment explanation
Indices: 84619872--84619917 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
84619862 TAAAGTTATT
*
84619872 AGAGTTCGACTAGGAAAAGATAGC
1 AGAGTTCAACTAGGAAAAGATAGC
*
84619896 AGAGTTTAACTAGGAAAAGATA
1 AGAGTTCAACTAGGAAAAGATA
84619918 CTCATTTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.09, G:0.26, T:0.20
Consensus pattern (24 bp):
AGAGTTCAACTAGGAAAAGATAGC
Found at i:84624362 original size:16 final size:16
Alignment explanation
Indices: 84624341--84624373 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
84624331 ATGGAACATT
84624341 ACACCGAAAACACCGC
1 ACACCGAAAACACCGC
84624357 ACACCGAAAACACCGC
1 ACACCGAAAACACCGC
84624373 A
1 A
84624374 AAAGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.42, G:0.12, T:0.00
Consensus pattern (16 bp):
ACACCGAAAACACCGC
Found at i:84628471 original size:25 final size:26
Alignment explanation
Indices: 84628422--84628473 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
84628412 TGAATGATGG
84628422 AAATTCAGTATATTTTTTCTTTTGTTTT
1 AAATTCAGTATA--TTTTCTTTTGTTTT
84628450 AAATTCAGTATA-TTTCTTTTGTTT
1 AAATTCAGTATATTTTCTTTTGTTT
84628474 CTTTTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
28 12 0.50
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (26 bp):
AAATTCAGTATATTTTCTTTTGTTTT
Found at i:84628929 original size:31 final size:31
Alignment explanation
Indices: 84628894--84628955 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
84628884 AGAAGTTTCA
84628894 AAGATTTTAGTTTTAGAAGAAAGTATATACT
1 AAGATTTTAGTTTTAGAAGAAAGTATATACT
*
84628925 AAGATTTTAGTTTTAGAAGAAAGTATGTACT
1 AAGATTTTAGTTTTAGAAGAAAGTATATACT
84628956 GTAGTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.39
Consensus pattern (31 bp):
AAGATTTTAGTTTTAGAAGAAAGTATATACT
Found at i:84629730 original size:11 final size:11
Alignment explanation
Indices: 84629714--84629755 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
84629704 CTCTCACAAC
*
84629714 AATTCTCTCTA
1 AATTCTCTCCA
*
84629725 AATTCTTTCCA
1 AATTCTCTCCA
84629736 AATTCTC-CCA
1 AATTCTCTCCA
84629746 AATTTCTCTC
1 AA-TTCTCTC
84629756 AATTTTTGTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 5 0.19
11 20 0.77
12 1 0.04
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (11 bp):
AATTCTCTCCA
Found at i:84630947 original size:7 final size:7
Alignment explanation
Indices: 84630935--84630967 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
84630925 TAGTCGTTTC
84630935 GTATTTA
1 GTATTTA
84630942 GTATTTA
1 GTATTTA
84630949 GTATTTA
1 GTATTTA
84630956 GTATTTA
1 GTATTTA
84630963 GTATT
1 GTATT
84630968 ACCTATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:84631515 original size:30 final size:30
Alignment explanation
Indices: 84631464--84631524 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
84631454 GATGACGACA
* * * *
84631464 CGGGTCCATCAGCAGCGCCTACACAATCAC
1 CGGGCCCATCAACAGCACCTACACAACCAC
84631494 CGGGCCCATCAACAGCACCTACACAACCAC
1 CGGGCCCATCAACAGCACCTACACAACCAC
84631524 C
1 C
84631525 TGGGTCAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.44, G:0.16, T:0.10
Consensus pattern (30 bp):
CGGGCCCATCAACAGCACCTACACAACCAC
Found at i:84633266 original size:41 final size:42
Alignment explanation
Indices: 84633203--84633314 Score: 158
Period size: 41 Copynumber: 2.7 Consensus size: 42
84633193 ATCGTTAGTG
* *
84633203 ACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGA-
1 ACAT-ATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAC
84633245 A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAC
1 ACA-TATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAC
*
84633287 ACAT-TTCGGACTATAAGTCTAGCAGGCT
1 ACATATTCAGACTATAAGTCTAGCAGGCT
84633315 AAGAGCCGGT
Statistics
Matches: 64, Mismatches: 3, Indels: 7
0.86 0.04 0.09
Matches are distributed among these distances:
41 59 0.92
42 4 0.06
43 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (42 bp):
ACATATTCAGACTATAAGTCTAGCAGGCTTAATGCCGGTGAC
Found at i:84633585 original size:33 final size:32
Alignment explanation
Indices: 84633529--84633592 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
84633519 ATAGATATGT
84633529 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
84633561 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
84633593 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:84633609 original size:33 final size:33
Alignment explanation
Indices: 84633536--84633609 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
84633526 TGTATATATA
* * **
84633536 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
84633568 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
84633601 TGTATGTAT
1 TATATGTAT
84633610 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:84634983 original size:9 final size:9
Alignment explanation
Indices: 84634969--84635000 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
84634959 TTGACTACGG
84634969 TAATATTTT
1 TAATATTTT
84634978 TAATATTTT
1 TAATATTTT
*
84634987 TTATATTTT
1 TAATATTTT
84634996 TAATA
1 TAATA
84635001 AAATATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (9 bp):
TAATATTTT
Found at i:84638241 original size:125 final size:125
Alignment explanation
Indices: 84638036--84638375 Score: 540
Period size: 125 Copynumber: 2.7 Consensus size: 125
84638026 TAAGGCCTTT
* * *
84638036 TCAGATACTACTGTAGTAAAAGAGCGTCCACGTGAGAGATTTTTCCCGTAATTTTCCTGAAAGTG
1 TCAGATACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCTTTTT-CCGTAATTTTGCTGAAAGTG
*
84638101 CATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATTTTCTCAAAATTATTTTA
65 CATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTA
*
84638162 TCAGATACTACTGTAGCAAAA-AGCGTCCACGTGGGAGCTCTTTTCCGTAATTTTGCTGAAAGTG
1 TCAGATACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCT-TTTTCCGTAATTTTGCTGAAAGTG
* * * *
84638226 CATCCTTCTTAAAGCGTTTTTGATATTATTTGTTCAGAAACATCTTCTCAAATTTATTTTA
65 CATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTA
* *
84638287 TCAGATACTAC-ATAGTAAAAGAGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTGACAGTG
1 TCAGATACTACTGTAGTAAAAGAGCGTCCACGTGGGAGC-TTTTTCCGTAATTTTGCTGAAAGTG
84638351 CATCCTTCTTGAAGCGTTTTTGACA
65 CATCCTTCTTGAAGCGTTTTTGACA
84638376 AGCGTCGACG
Statistics
Matches: 197, Mismatches: 14, Indels: 7
0.90 0.06 0.03
Matches are distributed among these distances:
124 7 0.04
125 165 0.84
126 25 0.13
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (125 bp):
TCAGATACTACTGTAGTAAAAGAGCGTCCACGTGGGAGCTTTTTCCGTAATTTTGCTGAAAGTGC
ATCCTTCTTGAAGCGTTTTTGACACTATTTGTTCAGAAACATCTTCTCAAAATTATTTTA
Found at i:84638424 original size:68 final size:68
Alignment explanation
Indices: 84638308--84638439 Score: 219
Period size: 68 Copynumber: 1.9 Consensus size: 68
84638298 ATAGTAAAAG
* * *
84638308 AGCGTCCACGTGGGAGCTTTTTTCCGTAATTTTGCTGACAGTGCATCCTTCTTGAAGCGTTTTTG
1 AGCGTCCACGTAGGAGCTTTTTTCCGTAATTTTGCTGAAAGTGCATCCTTCTTAAAGCGTTTTTG
84638373 ACA
66 ACA
* *
84638376 AGCGTCGACGTAGGAGCTTTTTTCCGTAATTTTGCTGAAAGTGTATCCTTCTTAAAGCGTTTTT
1 AGCGTCCACGTAGGAGCTTTTTTCCGTAATTTTGCTGAAAGTGCATCCTTCTTAAAGCGTTTTT
84638440 TACCCTATTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.39
Consensus pattern (68 bp):
AGCGTCCACGTAGGAGCTTTTTTCCGTAATTTTGCTGAAAGTGCATCCTTCTTAAAGCGTTTTTG
ACA
Found at i:84638683 original size:18 final size:17
Alignment explanation
Indices: 84638658--84638713 Score: 85
Period size: 17 Copynumber: 3.2 Consensus size: 17
84638648 CCCTTAAAAA
84638658 CACTAAAAACCCTAAAC
1 CACTAAAAACCCTAAAC
*
84638675 CACTAAAAACCTTAAAC
1 CACTAAAAACCCTAAAC
*
84638692 CACCAAAAAACCCTAAAC
1 CA-CTAAAAACCCTAAAC
84638710 CACT
1 CACT
84638714 GAGCCCTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 19 0.56
18 15 0.44
ACGTcount: A:0.52, C:0.36, G:0.00, T:0.12
Consensus pattern (17 bp):
CACTAAAAACCCTAAAC
Found at i:84638931 original size:164 final size:164
Alignment explanation
Indices: 84638717--84639457 Score: 614
Period size: 164 Copynumber: 4.4 Consensus size: 164
84638707 AACCACTGAG
84638717 CCCTAATTTAATT-AATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
1 CCCTAATTTAATTGAATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
84638781 GTGTTCATTAATTTTTTTCCTTAAAAATACTAAAAACTCTAAACCACTAAAACCCTAACCCTAAA
66 GTGTTCATTAATTTTTTTCCTTAAAAATACTAAAAACTCTAAACCACTAAAACCCTAACCCTAAA
*
84638846 ACAATAAAAAACCCTAA-TCCTAAAAAACTTTAAA
131 ACAATAAAAAACCCTAACT-CTAAAAAACCTTAAA
* *
84638880 CCCTAATTTAATTGATTTTTTTTTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
1 CCCTAATTTAATTGAATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
84638945 GTGTTCATTAATTTTTTTCCTTAAAAATACTAAAAACTCTAAACCACTAAAACCCTAACCCTAAA
66 GTGTTCATTAATTTTTTTCCTTAAAAATACTAAAAACTCTAAACCACTAAAACCCTAACCCTAAA
* *
84639010 ACAATCAAAAATCCTAACTCTAAAAAACCTTAAA
131 ACAATAAAAAACCCTAACTCTAAAAAACCTTAAA
* * * ** * * * *
84639044 CCCTAATTTAATTGCTAA-GTGTTCATTAATTTTTC-T-CTTAA-AAAACCTTAA-AAACCCTAA
1 CCCTAATTTAATTG--AATTTTTTC-TT-A-TTTTCATAGTTAATTTAA--TTAATTAGCCATCA
* *** * * *** * * * * *
84639104 ACCACTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACC-CT
59 A-CTCTAAGTGTTCA-TTAATT--TTTTTCCTTA--AAAATA-CTAA--AAACT-CTAAACCACT
* * ** ** ** * ** *** * *
84639168 -CAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACCTTAAAAAC-CCTAAACCACTAAG
114 AAAACCCTAA-----CCCTAA---AAC-AATAAAAAACCCT-AACTCTAAAAAACC-TTAAA
* * *
84639228 CCCTAATTTAATTG-ATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTCCAA
1 CCCTAATTTAATTGAATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
* * * * *
84639292 GTGGTCGTTAA-TTTTTCCCTTTAAAAACACTAAAAACCCTAAACCACTAAAACCCTAACCCTAA
66 GTGTTCATTAATTTTTTTCC-TTAAAAATACTAAAAACTCTAAACCACTAAAACCCTAACCCTAA
84639356 AACAATAAAAAACCCTAA-TCTTAAAAAACCTTAAA
130 AACAATAAAAAACCCTAACTC-TAAAAAACCTTAAA
*
84639391 CCCTAATTTAATTG-A-TTTTT-TTATTTTCATAGTTAATTTAATTAATTAACCATCAACTCTAA
1 CCCTAATTTAATTGAATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
84639453 GTGTT
66 GTGTT
84639458 TAAAAATCCC
Statistics
Matches: 446, Mismatches: 92, Indels: 82
0.72 0.15 0.13
Matches are distributed among these distances:
161 44 0.10
162 6 0.01
163 33 0.07
164 172 0.39
165 7 0.02
166 13 0.03
167 14 0.03
168 15 0.03
170 9 0.02
171 5 0.01
172 7 0.02
173 10 0.02
174 10 0.02
175 7 0.02
176 10 0.02
177 3 0.01
178 1 0.00
179 13 0.03
180 12 0.03
181 15 0.03
182 7 0.02
183 13 0.03
184 20 0.04
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.38
Consensus pattern (164 bp):
CCCTAATTTAATTGAATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAGCCATCAACTCTAA
GTGTTCATTAATTTTTTTCCTTAAAAATACTAAAAACTCTAAACCACTAAAACCCTAACCCTAAA
ACAATAAAAAACCCTAACTCTAAAAAACCTTAAA
Found at i:84639196 original size:115 final size:115
Alignment explanation
Indices: 84639058--84639341 Score: 507
Period size: 115 Copynumber: 2.5 Consensus size: 115
84639048 AATTTAATTG
84639058 CTAAGTGTTCATTAATTTTTCTCTTAAAAAACCTTAAAAACCCTAAACCACTAAGCCCTAATTTA
1 CTAAGTGTTCATTAATTTTTCTCTTAAAAAACCTTAAAAACCCTAAACCACTAAGCCCTAATTTA
84639123 ATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
66 ATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
84639173 CTAAGTGTTCATTAATTTTTCTCTTAAAAAACCTTAAAAACCCTAAACCACTAAGCCCTAATTTA
1 CTAAGTGTTCATTAATTTTTCTCTTAAAAAACCTTAAAAACCCTAAACCACTAAGCCCTAATTTA
84639238 ATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
66 ATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
* * * * *
84639288 CCAAGTGGTCGTTAATTTTTCCCTTTAAAAACAC-TAAAAACCCTAAACCACTAA
1 CTAAGTGTTCATTAATTTTTCTCTTAAAAAAC-CTTAAAAACCCTAAACCACTAA
84639342 AACCCTAACC
Statistics
Matches: 163, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
115 162 0.99
116 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.05, T:0.39
Consensus pattern (115 bp):
CTAAGTGTTCATTAATTTTTCTCTTAAAAAACCTTAAAAACCCTAAACCACTAAGCCCTAATTTA
ATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACT
Found at i:84639343 original size:16 final size:15
Alignment explanation
Indices: 84639319--84639358 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
84639309 CCTTTAAAAA
84639319 CACTAAAAACCCTAAAC
1 CACT-AAAACCCT-AAC
84639336 CACTAAAACCCTAAC
1 CACTAAAACCCTAAC
84639351 C-CTAAAAC
1 CACTAAAAC
84639359 AATAAAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 8 0.35
17 4 0.17
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (15 bp):
CACTAAAACCCTAAC
Found at i:84639519 original size:82 final size:81
Alignment explanation
Indices: 84639376--84639537 Score: 261
Period size: 82 Copynumber: 2.0 Consensus size: 81
84639366 AACCCTAATC
*
84639376 TTAAAAAACCTTAAACCCTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAATTAAC
1 TTAAAAAACCCTAAACCCTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAATTAAC
*
84639441 CATCAACTCTAAGTGT
66 CATCAACTCCAAGTGT
* * *
84639457 TTAAAAATCCCTAAACCCTAATTTAATTAGTTTTTTTTATTTTTATAGTTAATTTAATTAATTAA
1 TTAAAAAACCCTAAACCCTAATTTAATT-GATTTTTTTATTTTCATAGTTAATTTAATTAATTAA
*
84639522 CCCTCAACTCCAAGTG
65 CCATCAACTCCAAGTG
84639538 GTCGTTAATT
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
81 26 0.35
82 48 0.65
ACGTcount: A:0.36, C:0.15, G:0.05, T:0.44
Consensus pattern (81 bp):
TTAAAAAACCCTAAACCCTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAATTAAC
CATCAACTCCAAGTGT
Found at i:84639588 original size:16 final size:15
Alignment explanation
Indices: 84639562--84639601 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
84639552 CCTTTAAAGA
84639562 CACTAAAAACCCTAAAC
1 CACT-AAAACCCT-AAC
84639579 CACTAAAACCCTAAC
1 CACTAAAACCCTAAC
84639594 C-CTAAAAC
1 CACTAAAAC
84639602 AATCAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 8 0.35
17 4 0.17
ACGTcount: A:0.50, C:0.38, G:0.00, T:0.12
Consensus pattern (15 bp):
CACTAAAACCCTAAC
Found at i:84639790 original size:115 final size:113
Alignment explanation
Indices: 84639636--84639860 Score: 371
Period size: 115 Copynumber: 2.0 Consensus size: 113
84639626 ACCCTAAACA
*
84639636 CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTT
1 CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTGTT
* *
84639701 CATTAATTTTTCTCTTAAAAAAC-CTTAAAAACCCTAAGCCACTAAGCC
66 CATTAATTTTTCCCTTAAAAAACAC-TAAAAACCCTAAACCACTAAGCC
84639749 CTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTG
1 CTAATTTAATTGA-TTTTT-TTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTG
* *
84639814 TTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAA
64 TTCATTAATTTTTCCCTTAAAAAACACTAAAAACCCTAAACCACTAA
84639861 AACCCTAACC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
113 13 0.12
114 5 0.05
115 85 0.82
116 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (113 bp):
CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTGTT
CATTAATTTTTCCCTTAAAAAACACTAAAAACCCTAAACCACTAAGCC
Found at i:84639792 original size:276 final size:276
Alignment explanation
Indices: 84639467--84640428 Score: 1811
Period size: 276 Copynumber: 3.5 Consensus size: 276
84639457 TTAAAAATCC
* * *
84639467 CTAAACCCTAATTTAATT-AGTTTTTT-TTATTTTTATAGTTAATTTAATTAATTAACCCTCAAC
1 CTAAGCCCTAATTTAATTGA-TTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAAC
* * ** * * *
84639530 TCCAAGTGGTCGTTAATTTTTCCCTTTAAAGACACTAAAAACCCTAAACCACTAAAACCCTAACC
65 TCTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACC
84639595 CTAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTT
130 CTAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTT
84639660 TCATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACC
195 TCATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACC
84639725 TTAAAAACCCTAAGCCA
260 TTAAAAACCCTAAGCCA
84639742 CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
1 CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
84639807 CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
66 CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
84639872 TAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTTT
131 TAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTTT
84639937 CATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACCT
196 CATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACCT
84640002 TAAAAACCCTAAGCCA
261 TAAAAACCCTAAGCCA
84640018 CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
1 CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
84640083 CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
66 CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
84640148 TAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTTT
131 TAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTTT
84640213 CATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACCT
196 CATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACCT
84640278 TAAAAACCCTAAGCCA
261 TAAAAACCCTAAGCCA
84640294 CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
1 CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
84640359 CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
66 CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
84640424 TAAAA
131 TAAAA
84640429 TTCAGAGAAA
Statistics
Matches: 675, Mismatches: 10, Indels: 3
0.98 0.01 0.00
Matches are distributed among these distances:
275 23 0.03
276 652 0.97
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (276 bp):
CTAAGCCCTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACT
CTAAGTGTTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAAAACCCTAACCC
TAAAACAATCAAAAAACTTAACTCTAAAAAACCCTAAACACTAATTTAATTGATTTTTTTATTTT
CATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTTCATTAATTTTTCTCTTAAAAAACCT
TAAAAACCCTAAGCCA
Found at i:84640079 original size:115 final size:113
Alignment explanation
Indices: 84639912--84640136 Score: 371
Period size: 115 Copynumber: 2.0 Consensus size: 113
84639902 ACCCTAAACA
*
84639912 CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTT
1 CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTGTT
* *
84639977 CATTAATTTTTCTCTTAAAAAAC-CTTAAAAACCCTAAGCCACTAAGCC
66 CATTAATTTTTCCCTTAAAAAACAC-TAAAAACCCTAAACCACTAAGCC
84640025 CTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTG
1 CTAATTTAATTGA-TTTTT-TTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTG
* *
84640090 TTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAA
64 TTCATTAATTTTTCCCTTAAAAAACACTAAAAACCCTAAACCACTAA
84640137 AACCCTAACC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
113 13 0.12
114 5 0.05
115 85 0.82
116 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (113 bp):
CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTGTT
CATTAATTTTTCCCTTAAAAAACACTAAAAACCCTAAACCACTAAGCC
Found at i:84640355 original size:115 final size:113
Alignment explanation
Indices: 84640188--84640412 Score: 371
Period size: 115 Copynumber: 2.0 Consensus size: 113
84640178 ACCCTAAACA
*
84640188 CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAATTAACCCTCAACTCTAAGTGTT
1 CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTGTT
* *
84640253 CATTAATTTTTCTCTTAAAAAAC-CTTAAAAACCCTAAGCCACTAAGCC
66 CATTAATTTTTCCCTTAAAAAACAC-TAAAAACCCTAAACCACTAAGCC
84640301 CTAATTTAATTGATTTTTTCTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTG
1 CTAATTTAATTGA-TTTTT-TTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTG
* *
84640366 TTTATTAATTTTTCCCTTAAAAAACACTAAAAACCTTAAACCACTAA
64 TTCATTAATTTTTCCCTTAAAAAACACTAAAAACCCTAAACCACTAA
84640413 AACCCTAACC
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
113 13 0.12
114 5 0.05
115 85 0.82
116 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (113 bp):
CTAATTTAATTGATTTTTTTATTTTCATAGTTAATTTAATTAACTAACCCTCAACTCTAAGTGTT
CATTAATTTTTCCCTTAAAAAACACTAAAAACCCTAAACCACTAAGCC
Found at i:84647075 original size:31 final size:30
Alignment explanation
Indices: 84647040--84647099 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
84647030 AATAACATTT
* *
84647040 GTAAATAATCTTTAAACAATTTAATATAATG
1 GTAAATAATATATAAA-AATTTAATATAATG
* *
84647071 GTAAATTATATATAAATATTTAATATAAT
1 GTAAATAATATATAAAAATTTAATATAAT
84647100 CATGCATAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (30 bp):
GTAAATAATATATAAAAATTTAATATAATG
Found at i:84647926 original size:13 final size:13
Alignment explanation
Indices: 84647910--84647986 Score: 50
Period size: 14 Copynumber: 5.8 Consensus size: 13
84647900 AACTTCGAAT
84647910 TCAAACCCAAATC
1 TCAAACCCAAATC
*
84647923 TCAAATCCTAAATC
1 TCAAA-CCCAAATC
* * *
84647937 TCGAA-CCTAACC
1 TCAAACCCAAATC
**
84647949 TTGAACCCAAA-C
1 TCAAACCCAAATC
*
84647961 TTTAAACCCTAAATC
1 -TCAAACCC-AAATC
84647976 TCAAACCCAAA
1 TCAAACCCAAA
84647987 CTGAACCCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
12 9 0.18
13 19 0.38
14 21 0.42
15 1 0.02
ACGTcount: A:0.43, C:0.34, G:0.03, T:0.21
Consensus pattern (13 bp):
TCAAACCCAAATC
Found at i:84648143 original size:34 final size:34
Alignment explanation
Indices: 84648078--84648143 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
84648068 TTGAGATCAT
*
84648078 AGTTTAGGGTTTGAGGGTTTGAGATTTGAGTTCG
1 AGTTTAGGGTTTGAGGGTTCGAGATTTGAGTTCG
*
84648112 AGTTTAGTGTTT-AGGGTTCGAGATTTAGAGTT
1 AGTTTAGGGTTTGAGGGTTCGAGATTT-GAGTT
84648144 TGAGGTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.20, C:0.03, G:0.35, T:0.42
Consensus pattern (34 bp):
AGTTTAGGGTTTGAGGGTTCGAGATTTGAGTTCG
Found at i:84648144 original size:21 final size:21
Alignment explanation
Indices: 84648102--84648163 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
84648092 GGGTTTGAGA
*
84648102 TTTGA-GTTCGAG-TTTAGTG
1 TTTGAGGTTCGAGATTTAGAG
84648121 TTT-AGGGTTCGAGATTTAGAG
1 TTTGA-GGTTCGAGATTTAGAG
*
84648142 TTTGAGGTTCAAGATTTAGAG
1 TTTGAGGTTCGAGATTTAGAG
84648163 T
1 T
84648164 CTATAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 1 0.03
19 3 0.08
20 7 0.19
21 25 0.68
22 1 0.03
ACGTcount: A:0.23, C:0.05, G:0.31, T:0.42
Consensus pattern (21 bp):
TTTGAGGTTCGAGATTTAGAG
Found at i:84648392 original size:30 final size:30
Alignment explanation
Indices: 84648356--84648437 Score: 155
Period size: 30 Copynumber: 2.7 Consensus size: 30
84648346 CAAACACAAG
84648356 CCAAAATAGCTCAGACCCGTTACAGCAAAC
1 CCAAAATAGCTCAGACCCGTTACAGCAAAC
84648386 CCAAAATAGCTCAGACCCGTTACAGCAAAC
1 CCAAAATAGCTCAGACCCGTTACAGCAAAC
*
84648416 CCAAAATAGCCCAGACCCGTTA
1 CCAAAATAGCTCAGACCCGTTA
84648438 TACACACACC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.39, C:0.34, G:0.13, T:0.13
Consensus pattern (30 bp):
CCAAAATAGCTCAGACCCGTTACAGCAAAC
Found at i:84651522 original size:7 final size:7
Alignment explanation
Indices: 84651510--84651535 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
84651500 AAGAGAGAAT
84651510 GATGAGG
1 GATGAGG
84651517 GATGAGG
1 GATGAGG
84651524 GATGAGG
1 GATGAGG
84651531 GATGA
1 GATGA
84651536 TTAGGAATGG
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:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:84654744 original size:18 final size:18
Alignment explanation
Indices: 84654721--84654756 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
84654711 CATCTTGCAT
84654721 AGTCAAATTAGCATAGAA
1 AGTCAAATTAGCATAGAA
84654739 AGTCAAATTAGCATAGAA
1 AGTCAAATTAGCATAGAA
84654757 TTCTTGAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.22
Consensus pattern (18 bp):
AGTCAAATTAGCATAGAA
Found at i:84670938 original size:25 final size:26
Alignment explanation
Indices: 84670861--84670945 Score: 127
Period size: 26 Copynumber: 3.3 Consensus size: 26
84670851 TGAGTGTCCC
*
84670861 ATTATATGGCTCTTTGTGAGCTTCCCG
1 ATTA-ATGGCTCTTTGTGAGCTTCCTG
*
84670888 ATTAAAGGCTCTTTGTGAGCTTCCTG
1 ATTAATGGCTCTTTGTGAGCTTCCTG
*
84670914 ATTAATGGCTCTCTG-GAGCTTCCTG
1 ATTAATGGCTCTTTGTGAGCTTCCTG
84670939 ATTAATG
1 ATTAATG
84670946 CCTTTTCGGA
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 17 0.31
26 33 0.61
27 4 0.07
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (26 bp):
ATTAATGGCTCTTTGTGAGCTTCCTG
Found at i:84670956 original size:25 final size:25
Alignment explanation
Indices: 84670861--84670958 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 25
84670851 TGAGTGTCCC
*
84670861 ATTATATGGCTCTTT-GTGAGCTTCCCG
1 ATTA-ATGGCT-TTTCG-GAGCTTCCTG
*
84670888 ATTAAAGGCTCTTT-GTGAGCTTCCTG
1 ATTAATGGCT-TTTCG-GAGCTTCCTG
*
84670914 ATTAATGGC-TCTCTGGAGCTTCCTG
1 ATTAATGGCTTTTC-GGAGCTTCCTG
*
84670939 ATTAATGCCTTTTCGGAGCT
1 ATTAATGGCTTTTCGGAGCT
84670959 ACCCTTATTG
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
24 2 0.03
25 24 0.39
26 32 0.52
27 4 0.06
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.39
Consensus pattern (25 bp):
ATTAATGGCTTTTCGGAGCTTCCTG
Found at i:84673766 original size:16 final size:16
Alignment explanation
Indices: 84673701--84673769 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
84673691 AAAATAATTT
*
84673701 TATTTTAATATATTTAA
1 TATTTTATTA-ATTTAA
** *
84673718 TATTAAATTAAATTAAA
1 TATTTTATT-AATTTAA
*
84673735 TATTTATCTTAA--TAA
1 TATTT-TATTAATTTAA
84673750 TATTTTATTAATTTAA
1 TATTTTATTAATTTAA
84673766 TATT
1 TATT
84673770 GAAGTGATTG
Statistics
Matches: 39, Mismatches: 9, Indels: 9
0.68 0.16 0.16
Matches are distributed among these distances:
14 5 0.13
15 7 0.18
16 7 0.18
17 17 0.44
18 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTATTAATTTAA
Found at i:84675093 original size:32 final size:32
Alignment explanation
Indices: 84675033--84675093 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
84675023 TAGTCCGTCG
* * *
84675033 GGATAGTAAACACATGATAGATATAGTTCACT
1 GGATAGTAAACACATAATAGAAAAAGTTCACT
84675065 GGATAGTAAACACATAATAGAAAAAGTTC
1 GGATAGTAAACACATAATAGAAAAAGTTC
84675094 GTTGGACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.18, T:0.25
Consensus pattern (32 bp):
GGATAGTAAACACATAATAGAAAAAGTTCACT
Found at i:84678032 original size:40 final size:39
Alignment explanation
Indices: 84677977--84678111 Score: 157
Period size: 40 Copynumber: 3.4 Consensus size: 39
84677967 ACCAGTTTGG
*
84677977 CACCCAGTACCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAA-TTGA
* * **
84678017 CACCCAGTGTCTCATCGGCTAAACCGAAGT-A-AATTGA
1 CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTGA
*
84678054 CACCCAGTGCCTCATCGAATATATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATA-ATTCGAAGTAAT-AATTGA
* *
84678095 CACCTAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
84678112 ACTCGAAGTC
Statistics
Matches: 79, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
37 22 0.28
38 9 0.11
39 2 0.03
40 25 0.32
41 21 0.27
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTGA
Found at i:84678109 original size:41 final size:40
Alignment explanation
Indices: 84677977--84678112 Score: 152
Period size: 37 Copynumber: 3.5 Consensus size: 40
84677967 ACCAGTTTGG
** * *
84677977 CACCCAGTACCTCATCGGATAATTCGAAGTAATAAGTTGA
1 CACCCAGTGTCTCATCGAATAATTCGAAGTAATAAATTGA
** **
84678017 CACCCAGTGTCTCATCGGCTAAACCGAAG---TAAATTGA
1 CACCCAGTGTCTCATCGAATAATTCGAAGTAATAAATTGA
*
84678054 CACCCAGTGCCTCATCGAATATATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATA-ATTCGAAGTAATAAATTGA
*
84678095 CACCTAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
84678113 CTCGAAGTCG
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 25 0.32
38 6 0.08
40 24 0.30
41 24 0.30
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
CACCCAGTGTCTCATCGAATAATTCGAAGTAATAAATTGA
Found at i:84679026 original size:16 final size:16
Alignment explanation
Indices: 84679000--84679032 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
84678990 AAACCTTAAT
84679000 TTTTCCTTTCTTCTTTC
1 TTTTCCTTTCTT-TTTC
84679017 TTTT-CTTTCTTTTTC
1 TTTTCCTTTCTTTTTC
84679032 T
1 T
84679033 CCCTGTTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTCCTTTCTTTTTC
Found at i:84679656 original size:22 final size:22
Alignment explanation
Indices: 84679628--84679704 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
84679618 GAACTAATAT
*
84679628 AACAGTAGGCATCGAAGTGCAA
1 AACAGTAAGCATCGAAGTGCAA
* **
84679650 AACAGTAAGCATTGAAGTGCGG
1 AACAGTAAGCATCGAAGTGCAA
* *
84679672 AAC-GATAAGCACCGAAGTGCGA
1 AACAG-TAAGCATCGAAGTGCAA
*
84679694 AACAATAAGCA
1 AACAGTAAGCA
84679705 CTAAAGCGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.43, C:0.18, G:0.26, T:0.13
Consensus pattern (22 bp):
AACAGTAAGCATCGAAGTGCAA
Found at i:84679705 original size:22 final size:22
Alignment explanation
Indices: 84679640--84679705 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
84679630 CAGTAGGCAT
* * *
84679640 CGAAGTGCAAAACAGTAAGCAT
1 CGAAGTGCGAAACAATAAGCAC
* * *
84679662 TGAAGTGCGGAACGATAAGCAC
1 CGAAGTGCGAAACAATAAGCAC
84679684 CGAAGTGCGAAACAATAAGCAC
1 CGAAGTGCGAAACAATAAGCAC
84679706 TAAAGCGTAA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.42, C:0.20, G:0.26, T:0.12
Consensus pattern (22 bp):
CGAAGTGCGAAACAATAAGCAC
Found at i:84679748 original size:22 final size:22
Alignment explanation
Indices: 84679698--84679749 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
84679688 GTGCGAAACA
* *
84679698 ATAAGCACTAAAGCGTAAGACG
1 ATAAGCGCTAAAGCGCAAGACG
84679720 ATAAGCGCTAAAGCGCAAGACG
1 ATAAGCGCTAAAGCGCAAGACG
84679742 ATAAGCGC
1 ATAAGCGC
84679750 ACTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (22 bp):
ATAAGCGCTAAAGCGCAAGACG
Found at i:84688103 original size:6 final size:6
Alignment explanation
Indices: 84688083--84688144 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
84688073 AAAATTTTTC
* * *
84688083 TCCCCTT TCCTCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCTT TCCCTT
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT
* *
84688132 TTCTCT TCCCCT T
1 TCCCCT TCCCCT T
84688145 GGGTTGCAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
6 43 0.91
7 4 0.09
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (6 bp):
TCCCCT
Found at i:84688532 original size:21 final size:21
Alignment explanation
Indices: 84688508--84688550 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
84688498 TTGGTTCAAT
84688508 CCTCATCTTATTCTCAAGGTA
1 CCTCATCTTATTCTCAAGGTA
*
84688529 CCTCATTTTATTCTCAAGGTA
1 CCTCATCTTATTCTCAAGGTA
84688550 C
1 C
84688551 GCTTACTCTT
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:0.23, C:0.28, G:0.09, T:0.40
Consensus pattern (21 bp):
CCTCATCTTATTCTCAAGGTA
Found at i:84691248 original size:23 final size:23
Alignment explanation
Indices: 84691221--84691265 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
84691211 TATGTTAAGT
84691221 ATAATTTGACTTCAAAAATTTTA
1 ATAATTTGACTTCAAAAATTTTA
84691244 ATAATTTGACTTCAAAAATTTT
1 ATAATTTGACTTCAAAAATTTT
84691266 CTCAAGGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (23 bp):
ATAATTTGACTTCAAAAATTTTA
Found at i:84691627 original size:16 final size:16
Alignment explanation
Indices: 84691591--84691630 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
84691581 TAAAAATAAT
* *
84691591 TTAAAATATAAATTTA
1 TTAATATATAAACTTA
84691607 TTAATATATAAACTTA
1 TTAATATATAAACTTA
84691623 TTAATATA
1 TTAATATA
84691631 AATCTACCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATATATAAACTTA
Found at i:84698152 original size:23 final size:23
Alignment explanation
Indices: 84698116--84698159 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
84698106 AACAAAGATA
*
84698116 AATTTAATTAAAGATATTTATGT
1 AATTTAATTAAAGAAATTTATGT
* *
84698139 AATTTAGTTTAAGAAATTTAT
1 AATTTAATTAAAGAAATTTAT
84698160 TTCCGATAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
AATTTAATTAAAGAAATTTATGT
Found at i:84699558 original size:23 final size:23
Alignment explanation
Indices: 84699531--84699575 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
84699521 AAATTGAATT
84699531 CTAAAATTT-TGAAGATATAAAAG
1 CTAAAATTTATGAA-ATATAAAAG
*
84699554 CTAAATTTTATGAAATATAAAA
1 CTAAAATTTATGAAATATAAAA
84699576 AAAAATCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.53, C:0.04, G:0.09, T:0.33
Consensus pattern (23 bp):
CTAAAATTTATGAAATATAAAAG
Found at i:84713142 original size:10 final size:10
Alignment explanation
Indices: 84713127--84713160 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
84713117 CCTAACATTG
84713127 ACTATATTAA
1 ACTATATTAA
*
84713137 ACTATATT-G
1 ACTATATTAA
84713146 ACTATATTAA
1 ACTATATTAA
84713156 ACTAT
1 ACTAT
84713161 CATTCTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (10 bp):
ACTATATTAA
Found at i:84713147 original size:19 final size:19
Alignment explanation
Indices: 84713123--84713160 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
84713113 TTACCCTAAC
84713123 ATTGACTATATTAAACTAT
1 ATTGACTATATTAAACTAT
84713142 ATTGACTATATTAAACTAT
1 ATTGACTATATTAAACTAT
84713161 CATTCTGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (19 bp):
ATTGACTATATTAAACTAT
Found at i:84718764 original size:49 final size:48
Alignment explanation
Indices: 84718662--84718787 Score: 157
Period size: 49 Copynumber: 2.6 Consensus size: 48
84718652 TCATGAGAGC
* * *
84718662 CAGTGTAAGACATGTCTAGGACAT-GCATCGGCCTCGAGATATACAAG
1 CAGTGTAAGACCTGTCTGGGACATGGCATCCGCCTCGAGATATACAAG
* **
84718709 CTAGTGTAAGACCTGTCTGGGATATGGCATCCGCCTCGTTATATGA-AAG
1 C-AGTGTAAGACCTGTCTGGGACATGGCATCCGCCTCGAGATAT-ACAAG
84718758 TCAGTGTAAGACCTGTCTGGGACATGGCAT
1 -CAGTGTAAGACCTGTCTGGGACATGGCAT
84718788 TGACTTGATG
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
47 1 0.01
48 20 0.29
49 45 0.66
50 2 0.03
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (48 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCCGCCTCGAGATATACAAG
Found at i:84719273 original size:17 final size:16
Alignment explanation
Indices: 84719242--84719275 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
84719232 TTCATCCACC
84719242 GAAAACAAAAACAAAA
1 GAAAACAAAAACAAAA
*
84719258 GAAAAGAAACAACAAAA
1 GAAAACAAA-AACAAAA
84719275 G
1 G
84719276 CTAGGTTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (16 bp):
GAAAACAAAAACAAAA
Found at i:84721198 original size:11 final size:11
Alignment explanation
Indices: 84721184--84721228 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
84721174 AGATAAATAT
84721184 TATTTTATTAA
1 TATTTTATTAA
*
84721195 TATTTTAATAATA
1 TATTTT-ATTA-A
*
84721208 TATTTTATTAT
1 TATTTTATTAA
84721219 TATTTTATTA
1 TATTTTATTA
84721229 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:84721211 original size:24 final size:24
Alignment explanation
Indices: 84721179--84721234 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
84721169 TAATTAGATA
84721179 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
84721204 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
84721228 AGTATAT
1 AATATAT
84721235 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:84723408 original size:46 final size:46
Alignment explanation
Indices: 84723351--84723494 Score: 184
Period size: 46 Copynumber: 3.2 Consensus size: 46
84723341 ATGAAATGTG
*
84723351 TAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAA-GAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAA
*
84723397 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
* ** * * * *
84723443 TAAGACCATAGTTGAAAGATATTATGGCATCATGTCA-AAGATAAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
84723488 TAAGACC
1 TAAGACC
84723495 GTGGATGGGA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
45 17 0.20
46 70 0.80
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (46 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAA
Found at i:84729383 original size:12 final size:11
Alignment explanation
Indices: 84729361--84729394 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
84729351 TAAACTATTA
84729361 TTAAACATAAT
1 TTAAACATAAT
84729372 TTAAATCATAAT
1 TTAAA-CATAAT
*
84729384 TTAAACTTAAT
1 TTAAACATAAT
84729395 CAAATTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAACATAAT
Found at i:84731293 original size:42 final size:41
Alignment explanation
Indices: 84731239--84731380 Score: 149
Period size: 42 Copynumber: 3.4 Consensus size: 41
84731229 CAAGCATAGC
**
84731239 GCATCATTGGATAAACTGAAGCACATATACTGGCACGTAAGT
1 GCATCATTGGATAAACTGAAGCA-ATATACTGGCATATAAGT
* * ** * * *
84731281 GTATCATCGGATATCCGGAAGCAATTATATTGGTATATAAGT
1 GCATCATTGGATAAACTGAAGCAA-TATACTGGCATATAAGT
* *
84731323 GCATCATTGGATAAACTGAAGTAAATATACTAGCATATAAGT
1 GCATCATTGGATAAACTGAAG-CAATATACTGGCATATAAGT
*
84731365 GCATCATTGGCTAAAC
1 GCATCATTGGATAAAC
84731381 CAAAGTATAA
Statistics
Matches: 79, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
41 1 0.01
42 76 0.96
43 2 0.03
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (41 bp):
GCATCATTGGATAAACTGAAGCAATATACTGGCATATAAGT
Found at i:84747434 original size:34 final size:34
Alignment explanation
Indices: 84747394--84747459 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
84747384 CAATATTTTA
* * *
84747394 AAAAATTACAAAGTTATAAAT-TTAGAAAAAAATT
1 AAAAATTAAAAACTGATAAATCTT-GAAAAAAATT
84747428 AAAAATTAAAAACTGATAAATCTTGAAAAAAA
1 AAAAATTAAAAACTGATAAATCTTGAAAAAAA
84747460 ATACAAACAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.64, C:0.05, G:0.06, T:0.26
Consensus pattern (34 bp):
AAAAATTAAAAACTGATAAATCTTGAAAAAAATT
Found at i:84760295 original size:53 final size:53
Alignment explanation
Indices: 84760238--84760537 Score: 258
Period size: 53 Copynumber: 5.7 Consensus size: 53
84760228 ACTGGGGTAC
* * *
84760238 CGACCATCAGTGTTCCAACACCCCAATCTTTTTTAAATTTAGTACTAAGGTGT
1 CGACCATCAGTGTCCCAACACCCCAATTTTTTTTAAATTTGGTACTAAGGTGT
* ** *
84760291 CGACCATTAGTGTCCCAACACCCTTA-TTTTTTTAAATTTTGGTACTAGGGTGT
1 CGACCATCAGTGTCCCAACACCCCAATTTTTTTTAAA-TTTGGTACTAAGGTGT
** * * *
84760344 CGTTCATCAGTGTCCCAGCA-CCCAATTTTTTTTTAAATTTGGTA-T-TGGAG-
1 CGACCATCAGTGTCCCAACACCCCAA-TTTTTTTTAAATTTGGTACTAAGGTGT
* * * * *
84760394 CGCCAGCCATAAGTGTCCCAGCACCCTAATTTTTTTTAAAATCTGGTACTAGGGTGT
1 CG--A-CCATCAGTGTCCCAACACCCCAATTTTTTTT-AAATTTGGTACTAAGGTGT
* * * * *
84760451 CGACCATCAGTGTCTCAACA-TCCATTTTTTTTTAAAATCTGGTGC-AAGAGTGT
1 CGACCATCAGTGTCCCAACACCCCAATTTTTTTT-AAATTTGGTACTAAG-GTGT
*
84760504 CGACCATCAGTGTCCCAACA-TCC-ATTTTTTTTAA
1 CGACCATCAGTGTCCCAACACCCCAATTTTTTTTAA
84760538 TTTTAAAAGG
Statistics
Matches: 203, Mismatches: 32, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
50 2 0.01
51 5 0.02
52 23 0.11
53 129 0.64
54 37 0.18
55 2 0.01
56 3 0.01
57 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (53 bp):
CGACCATCAGTGTCCCAACACCCCAATTTTTTTTAAATTTGGTACTAAGGTGT
Found at i:84760336 original size:106 final size:104
Alignment explanation
Indices: 84760212--84760534 Score: 298
Period size: 106 Copynumber: 3.1 Consensus size: 104
84760202 AAAATATTTA
* * * ** *
84760212 TTTTTTAAAATATAGTACTGGGGTACCGACCATCAGTGTTCCAACACCCCAATCTTTTTTAAATT
1 TTTTTTAAAATTTGGTACTAGGGTGTCGACCATCAGTGTTCCAACA-CCCAATTTTTTTTAAATT
* *
84760277 TAGTACTAAGGTGTCGACCATTAGTGTCCCAACACCCTTAT
65 TGGTACTAAGGTGTCGACCATAAGTGTCCCAACACCC-TAT
* ** * *
84760318 TTTTTTAAATTTTGGTACTAGGGTGTCGTTCATCAGTGTCCCAGCACCCAATTTTTTTTTAAATT
1 TTTTTTAAAATTTGGTACTAGGGTGTCGACCATCAGTGTTCCAACACCCAA-TTTTTTTTAAATT
* * *
84760383 TGGTA-T-TGGAG-CGCCAGCCATAAGTGTCCCAGCACCCTAATT
65 TGGTACTAAGGTGTCG--A-CCATAAGTGTCCCAACACCCT-A-T
* * *
84760425 TTTTTTAAAATCTGGTACTAGGGTGTCGACCATCAGTG-TCTCAACATCCATTTTTTTTTAAAAT
1 TTTTTTAAAATTTGGTACTAGGGTGTCGACCATCAGTGTTC-CAACACCCAATTTTTTTT-AAAT
* * * *
84760489 CTGGTGC-AAGAGTGTCGACCATCAGTGTCCCAACATCC-AT
64 TTGGTACTAAG-GTGTCGACCATAAGTGTCCCAACACCCTAT
84760529 TTTTTT
1 TTTTTT
84760535 TAATTTTAAA
Statistics
Matches: 174, Mismatches: 31, Indels: 26
0.75 0.13 0.11
Matches are distributed among these distances:
103 2 0.01
104 10 0.06
105 9 0.05
106 80 0.46
107 67 0.39
108 2 0.01
109 2 0.01
110 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (104 bp):
TTTTTTAAAATTTGGTACTAGGGTGTCGACCATCAGTGTTCCAACACCCAATTTTTTTTAAATTT
GGTACTAAGGTGTCGACCATAAGTGTCCCAACACCCTAT
Found at i:84760514 original size:160 final size:158
Alignment explanation
Indices: 84760241--84760535 Score: 376
Period size: 160 Copynumber: 1.9 Consensus size: 158
84760231 GGGGTACCGA
* * * *
84760241 CCATCAGTGTTCCAACACCCCAATCTTTTTTAAATTTAGTACTAAGGTGTCGACCATTAGTGTCC
1 CCATAAGTGTCCCAACACCCCAATCTTTTTTAAATCTAGTACTAAGGTGTCGACCATCAGTGTCC
* * * * * ** *
84760306 CAACACCCTTATTTTTTTAAATTTTGGTACTAGGGTGTCGTTCATCAGTGTCCCAGCACCCAATT
66 CAACACCATTATTTTTTTAAAATCTGGTACAAGAGTGTCGACCATCAGTGTCCCAACACCC-ATT
84760371 TTTTTTTAAATTTGGTATTGGAGCGCCAG
130 TTTTTTTAAATTTGGTATTGGAGCGCCAG
* * * * *
84760400 CCATAAGTGTCCCAGCACCCTAATTTTTTTTAAAATCTGGTACTAGGGTGTCGACCATCAGTGTC
1 CCATAAGTGTCCCAACACCCCAATCTTTTTT-AAATCTAGTACTAAGGTGTCGACCATCAGTGTC
* * *
84760465 TCAACATCCATT-TTTTTTTAAAATCTGGTGCAAGAGTGTCGACCATCAGTGTCCCAACATCCAT
65 CCAACA-CCATTATTTTTTTAAAATCTGGTACAAGAGTGTCGACCATCAGTGTCCCAACACCCAT
84760529 TTTTTTT
129 TTTTTTT
84760536 AATTTTAAAA
Statistics
Matches: 114, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
159 35 0.31
160 75 0.66
161 4 0.04
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (158 bp):
CCATAAGTGTCCCAACACCCCAATCTTTTTTAAATCTAGTACTAAGGTGTCGACCATCAGTGTCC
CAACACCATTATTTTTTTAAAATCTGGTACAAGAGTGTCGACCATCAGTGTCCCAACACCCATTT
TTTTTTAAATTTGGTATTGGAGCGCCAG
Found at i:84763952 original size:59 final size:60
Alignment explanation
Indices: 84763884--84764000 Score: 155
Period size: 62 Copynumber: 1.9 Consensus size: 60
84763874 ATCACTTTAG
* * *
84763884 TATTAAATTAATATAATACTTATC-AAGATAAATATTAGATTAAATTCAATATTAAATAT
1 TATTAAATTAATAGAATACTTATCTAAGATAAACATTAAATTAAATTCAATATTAAATAT
* * *
84763943 TATTAAATTAATAGAATATTTATCTATAAGATAAACATTAAATTAACTTTAATATTAA
1 TATTAAATTAATAGAATACTTATC--TAAGATAAACATTAAATTAAATTCAATATTAA
84764001 GATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 22 0.45
62 27 0.55
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTATCTAAGATAAACATTAAATTAAATTCAATATTAAATAT
Found at i:84765621 original size:11 final size:11
Alignment explanation
Indices: 84765583--84765624 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
84765573 GCAAAATATG
84765583 AAAG-AATAAA
1 AAAGAAATAAA
*
84765593 AAAGAAATAAT
1 AAAGAAATAAA
**
84765604 AGTGAAATAAA
1 AAAGAAATAAA
84765615 AAAGAAATAA
1 AAAGAAATAA
84765625 CTGTGGAACG
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
10 4 0.16
11 21 0.84
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (11 bp):
AAAGAAATAAA
Found at i:84768660 original size:30 final size:30
Alignment explanation
Indices: 84768626--84768686 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
84768616 TCCTTAACTC
84768626 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
84768656 AAACTTTTGTATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
84768686 A
1 A
84768687 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.39
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:84777189 original size:49 final size:47
Alignment explanation
Indices: 84777117--84777432 Score: 224
Period size: 47 Copynumber: 6.7 Consensus size: 47
84777107 ATAAGTTGTC
* *
84777117 GATGCCATGTCCCAGACATGGTCTTATACTGGCTAGCATCATCGAGGCT
1 GATG-CATGTCCCAGACATGGTCTTACACTGGC-ATCATCATCGAGGCT
* * * *
84777166 GATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCGTAT-ATACG-TGCT
1 GATG-CATGTCCCAGACATGGTCTTACACTGGC-ATC--ATCAT-CGAGGCT
* * * *
84777216 GATGCATGTCCCAGACAT-GTCTTACACTAGCA-CAAC-TCTTAGCCT
1 GATGCATGTCCCAGACATGGTCTTACACTGGCATCATCATC-GAGGCT
* * *
84777261 -ATGCGTGTCCCAGACA-CGTCTTACACTGGCTATCATCATCGAGGCC
1 GATGCATGTCCCAGACATGGTCTTACACTGGC-ATCATCATCGAGGCT
* * *
84777307 AATGCATGTCCCAGACAT-GTCTTACACTGGCACTCATC-TCTACG-T
1 GATGCATGTCCCAGACATGGTCTTACACTGGCA-TCATCATCGAGGCT
* * * * *
84777352 CGATGCCATGTTCCAGACATGGTCTTATACTGGCACTCATAAT-GTGGCC
1 -GATG-CATGTCCCAGACATGGTCTTACACTGGCA-TCATCATCGAGGCT
* *
84777401 GATGCATGTCCCAGACAT-ATCTTACATTGGCA
1 GATGCATGTCCCAGACATGGTCTTACACTGGCA
84777433 CACAAGAAAT
Statistics
Matches: 217, Mismatches: 32, Indels: 39
0.75 0.11 0.14
Matches are distributed among these distances:
43 1 0.00
44 29 0.13
45 3 0.01
46 26 0.12
47 61 0.28
48 35 0.16
49 49 0.23
50 9 0.04
51 4 0.02
ACGTcount: A:0.24, C:0.28, G:0.20, T:0.28
Consensus pattern (47 bp):
GATGCATGTCCCAGACATGGTCTTACACTGGCATCATCATCGAGGCT
Found at i:84777411 original size:141 final size:141
Alignment explanation
Indices: 84777116--84777431 Score: 336
Period size: 141 Copynumber: 2.2 Consensus size: 141
84777106 GATAAGTTGT
* * **
84777116 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTAGCATCATCGAGGCTGATGCCATGTCCCAG
1 CGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAGCATCATCGAGGCCAATGCCATGTCCCAG
* * *
84777181 ACATGGTCTTATACTAGCTCTCGTATATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAG
64 ACATGGTCTTACACTAGCACTCATATATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAG
* *
84777246 CACAACTCTTAGC
129 CACAAATCGTAGC
* * *
84777259 CTATGCGTGTCCCAGACACGTCTTACACTGGCTATCATCATCGAGGCCAATG-CATGTCCCAGAC
1 CGATGCATGTCCCAGACACGTCTTACACTGGCTAGCATCATCGAGGCCAATGCCATGTCCCAGAC
* * * * * *
84777323 AT-GTCTTACACTGGCACTCATCTCTACGT-C-GATGCCATGTTCCAGACATGGTCTTATACTGG
66 ATGGTCTTACACTAGCACTCATATATACGTGCTGATG-CATGTCCCAGACAT-GTCTTACACTAG
*
84777385 CACTCATAAT-GTGGC
129 CA--CA-AATCGTAGC
** *
84777400 CGATGCATGTCCCAGACATATCTTACATTGGC
1 CGATGCATGTCCCAGACACGTCTTACACTGGC
84777432 ACACAAGAAA
Statistics
Matches: 144, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
137 4 0.03
138 14 0.10
139 33 0.23
140 14 0.10
141 61 0.42
142 14 0.10
143 4 0.03
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (141 bp):
CGATGCATGTCCCAGACACGTCTTACACTGGCTAGCATCATCGAGGCCAATGCCATGTCCCAGAC
ATGGTCTTACACTAGCACTCATATATACGTGCTGATGCATGTCCCAGACATGTCTTACACTAGCA
CAAATCGTAGC
Found at i:84777424 original size:94 final size:93
Alignment explanation
Indices: 84777116--84777433 Score: 281
Period size: 94 Copynumber: 3.4 Consensus size: 93
84777106 GATAAGTTGT
* * * * *
84777116 CGATGCCATGTCCCAGACATGGTCTTATACTGGCTAGCATCATC-GAGGCTGATGCCATGTCCCA
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ACCAAC-TCTTA-GCCGATGCCATGTCCCA
* * *
84777180 GACATGGTCTTATACTAGCTCTCGTATATACGT-GC
61 GACATGGTCTTATACTGGCACTC--ATA-ATGTGGC
* * * *
84777215 TGATGCATGTCCCAGACATGTCTTACACTAGCA-CAACTCTTAGCCTATG-CGTGTCCCAGACA-
1 CGATGCATGTCCCAGACATGTCTTACACTGGCACCAACTCTTAGCCGATGCCATGTCCCAGACAT
* * * *
84777277 CGTCTTACACTGGCTA-TCATCATCGAGGC
66 GGTCTTATACTGGC-ACTCATAAT-GTGGC
* * * *
84777306 CAATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTC-TACGTCGATGCCATGTTCCAGAC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCAC-CAACTCTTA-GCCGATGCCATGTCCCAGAC
84777370 ATGGTCTTATACTGGCACTCATAATGTGGC
64 ATGGTCTTATACTGGCACTCATAATGTGGC
* *
84777400 CGATGCATGTCCCAGACATATCTTACATTGGCAC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCAC
84777434 ACAAGAAATT
Statistics
Matches: 179, Mismatches: 30, Indels: 25
0.76 0.13 0.11
Matches are distributed among these distances:
89 1 0.01
90 3 0.02
91 32 0.18
92 15 0.08
93 22 0.12
94 54 0.30
95 22 0.12
96 1 0.01
97 11 0.06
98 14 0.08
99 4 0.02
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (93 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCACCAACTCTTAGCCGATGCCATGTCCCAGACAT
GGTCTTATACTGGCACTCATAATGTGGC
Found at i:84781354 original size:144 final size:144
Alignment explanation
Indices: 84781094--84781377 Score: 550
Period size: 144 Copynumber: 2.0 Consensus size: 144
84781084 TTGCTTAAAA
84781094 GACCATAAAATTCCTATTAGAATCCCCATTACAAATAGCTTACTATTATTCAATCATATGTGACC
1 GACCATAAAATTCCTATTAGAATCCCCATTACAAATAGCTTACTATTATTCAATCATATGTGACC
84781159 CCCCAAGCAGGGCTTTTCACTCATGCCCTACTGTTCTCACATCCTTTGACATCCTTGCTATTTGA
66 CCCCAAGCAGGGCTTTTCACTCATGCCCTACTGTTCTCACATCCTTTGACATCCTTGCTATTTGA
84781224 TAGTTGTAACTCAT
131 TAGTTGTAACTCAT
*
84781238 GACCATAAAATTCCTATTAGAATCCCCATTACAGATAGCTTACTATTATTCAATCATATGTGACC
1 GACCATAAAATTCCTATTAGAATCCCCATTACAAATAGCTTACTATTATTCAATCATATGTGACC
*
84781303 CCCCAAGCAGGGCTTTTCACTCATGCCCTACTGTTCTTACATCCTTTGACATCCTTGCTATTTGA
66 CCCCAAGCAGGGCTTTTCACTCATGCCCTACTGTTCTCACATCCTTTGACATCCTTGCTATTTGA
84781368 TAGTTGTAAC
131 TAGTTGTAAC
84781378 GTATAGAGTT
Statistics
Matches: 138, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
144 138 1.00
ACGTcount: A:0.27, C:0.27, G:0.12, T:0.34
Consensus pattern (144 bp):
GACCATAAAATTCCTATTAGAATCCCCATTACAAATAGCTTACTATTATTCAATCATATGTGACC
CCCCAAGCAGGGCTTTTCACTCATGCCCTACTGTTCTCACATCCTTTGACATCCTTGCTATTTGA
TAGTTGTAACTCAT
Found at i:84783233 original size:21 final size:21
Alignment explanation
Indices: 84783209--84783248 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
84783199 CAGAATTGCA
*
84783209 GATATACTACCAAAATGTGTG
1 GATATACCACCAAAATGTGTG
84783230 GATATACCACCAAAATGTG
1 GATATACCACCAAAATGTG
84783249 CTGATCATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.25
Consensus pattern (21 bp):
GATATACCACCAAAATGTGTG
Done.