Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 130 of 182
Found at i:39935649 original size:33 final size:33
Alignment explanation
Indices: 39935607--39935673 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
39935597 CCAAGATGTA
*
39935607 TACAAAATCTACCAAAAGGATCCTAGGATAGTG
1 TACAAAATCTACCAAAAGGATCATAGGATAGTG
*
39935640 TACAAAATCTACCAAAAGGATCATCGGATAGTG
1 TACAAAATCTACCAAAAGGATCATAGGATAGTG
39935673 T
1 T
39935674 GATTCTTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (33 bp):
TACAAAATCTACCAAAAGGATCATAGGATAGTG
Found at i:39937023 original size:28 final size:27
Alignment explanation
Indices: 39936983--39937049 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
39936973 GCTAAAATGT
*
39936983 ATTAAAATTATGTAATAAGCTAAGACA-A
1 ATTAAAA-CATGTAATAA-CTAAGACATA
* *
39937011 ATTAACAACATGTATTAACTAGGACATA
1 ATTAA-AACATGTAATAACTAAGACATA
*
39937039 TTTAAAACATG
1 ATTAAAACATG
39937050 AATTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 13 0.39
28 18 0.55
29 2 0.06
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (27 bp):
ATTAAAACATGTAATAACTAAGACATA
Found at i:39945123 original size:45 final size:45
Alignment explanation
Indices: 39944955--39945123 Score: 128
Period size: 44 Copynumber: 3.8 Consensus size: 45
39944945 CTATACGCCT
** * *
39944955 AAAA-TGAGTAAGATAATAATTGAAAGATGCTATGACTTCA-GAA
1 AAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGACATCATGAA
* * * **
39944998 TAAAA-TAAGTAAGACCATAGTTGGAAGATGCTATAACATCATGGT
1 -AAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGACATCATGAA
* * * * ** *
39945043 AAAAGATGAATAAGACTACAGCTGAAAGACACTATGACATCATGAC
1 AAAAG-TGAGTAAGACCATAGTTGAAAGATGCTATGACATCATGAA
** *
39945089 GGAAGTGAGTAAGACCATGGTTGAAAGATGCTATG
1 AAAAGTGAGTAAGACCATAGTTGAAAGATGCTATG
39945124 GAATCCTTCG
Statistics
Matches: 93, Mismatches: 29, Indels: 5
0.73 0.23 0.04
Matches are distributed among these distances:
44 37 0.40
45 24 0.26
46 32 0.34
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.23
Consensus pattern (45 bp):
AAAAGTGAGTAAGACCATAGTTGAAAGATGCTATGACATCATGAA
Found at i:39970281 original size:4 final size:4
Alignment explanation
Indices: 39970272--39970300 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39970262 ATTGAATCTA
39970272 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
39970301 AACAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:39970335 original size:4 final size:4
Alignment explanation
Indices: 39970298--39970326 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
39970288 ATACATACAT
39970298 ACAA ACAA ACAA ACAA ACAA ACAA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA A
39970327 TACAAACAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:39972011 original size:17 final size:17
Alignment explanation
Indices: 39971989--39972026 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
39971979 ATCATAAGGT
39971989 CACAAGGCCAAAATATC
1 CACAAGGCCAAAATATC
39972006 CACAAGGCCAAAATATC
1 CACAAGGCCAAAATATC
39972023 CACA
1 CACA
39972027 TTATTATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.32, G:0.11, T:0.11
Consensus pattern (17 bp):
CACAAGGCCAAAATATC
Found at i:39980566 original size:19 final size:19
Alignment explanation
Indices: 39980531--39980569 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39980521 AATTATTGCA
*
39980531 ATGAATTGTTTTAGAAAGG
1 ATGAATTGTTTAAGAAAGG
39980550 ATGAATTG-TTAAGGAAAGG
1 ATGAATTGTTTAA-GAAAGG
39980569 A
1 A
39980570 GCTTGGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 3 0.17
19 15 0.83
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (19 bp):
ATGAATTGTTTAAGAAAGG
Found at i:39981782 original size:27 final size:27
Alignment explanation
Indices: 39981747--39981837 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
39981737 CACCAAAAAT
39981747 TGGAAGCCTTTGTGGCGATCTAAGAAA
1 TGGAAGCCTTTGTGGCGATCTAAGAAA
* * *
39981774 TGGAAGCCTTTGTGGCAATCCAAAAAA
1 TGGAAGCCTTTGTGGCGATCTAAGAAA
* * *
39981801 TGGAAGGCTTTGTGGCGAACTAAGAGA
1 TGGAAGCCTTTGTGGCGATCTAAGAAA
*
39981828 TGAAAGCCTT
1 TGGAAGCCTT
39981838 CATGGAAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.24
Consensus pattern (27 bp):
TGGAAGCCTTTGTGGCGATCTAAGAAA
Found at i:39984025 original size:13 final size:13
Alignment explanation
Indices: 39984007--39984031 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39983997 GATTAGATTA
39984007 GTAATTATTTTAT
1 GTAATTATTTTAT
39984020 GTAATTATTTTA
1 GTAATTATTTTA
39984032 ATAATAATTT
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:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
GTAATTATTTTAT
Found at i:39984261 original size:20 final size:20
Alignment explanation
Indices: 39984236--39984276 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39984226 TTTATACCTT
39984236 TACCCTTAGTGCTTGGGTAA
1 TACCCTTAGTGCTTGGGTAA
39984256 TACCCTTAGTGCTTGGGTAA
1 TACCCTTAGTGCTTGGGTAA
39984276 T
1 T
39984277 CCTTCCACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
TACCCTTAGTGCTTGGGTAA
Found at i:39990449 original size:22 final size:24
Alignment explanation
Indices: 39990424--39990474 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
39990414 TTATTTATAA
39990424 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
39990444 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
39990470 ATAAA
1 ATAAA
39990475 AGCAATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:39993138 original size:17 final size:15
Alignment explanation
Indices: 39993112--39993155 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
39993102 ACCAAACTCG
*
39993112 TATAAGAAAACTAATTA
1 TATAATAAAA-TAA-TA
39993129 TATAATAAAATAATA
1 TATAATAAAATAATA
*
39993144 AATAATAAAATA
1 TATAATAAAATA
39993156 TATTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.52
16 3 0.12
17 9 0.36
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (15 bp):
TATAATAAAATAATA
Found at i:39994929 original size:9 final size:9
Alignment explanation
Indices: 39994915--39994951 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
39994905 TATAGTTTGA
39994915 TATTCGAAT
1 TATTCGAAT
39994924 TATTCGAAT
1 TATTCGAAT
* *
39994933 TATTTGAGT
1 TATTCGAAT
39994942 TATTCGAAT
1 TATTCGAAT
39994951 T
1 T
39994952 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:39995021 original size:9 final size:9
Alignment explanation
Indices: 39995004--39995034 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
39994994 TCGAGTTGAT
39995004 TCGAATAAC
1 TCGAATAAC
*
39995013 TCGATTAAC
1 TCGAATAAC
39995022 TCGAATAAC
1 TCGAATAAC
39995031 TCGA
1 TCGA
39995035 TTTGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:39999339 original size:12 final size:12
Alignment explanation
Indices: 39999321--39999351 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
39999311 ACATTATTTT
39999321 GAAAAAAAAAT-
1 GAAAAAAAAATA
39999332 GAAAAAAAAATA
1 GAAAAAAAAATA
39999344 GAAAAAAA
1 GAAAAAAA
39999352 GAGGGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (12 bp):
GAAAAAAAAATA
Found at i:40015631 original size:27 final size:26
Alignment explanation
Indices: 40015600--40015777 Score: 142
Period size: 27 Copynumber: 6.6 Consensus size: 26
40015590 TAAATTGTAC
*
40015600 AGCACTAAGTGTGCGATTCTACTTTGT
1 AGCACTAAGTGTGCGATT-TACTATGT
* * * *
40015627 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTTACTATGT
* * *
40015653 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTTACTATGT
*
40015681 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTT-ACTATGT
* *
40015709 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTT-ACTATGT
* * *
40015736 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTTACTATGT
*
40015763 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40015778 GGCTCAATAT
Statistics
Matches: 125, Mismatches: 20, Indels: 12
0.80 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 100 0.80
28 24 0.19
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTTACTATGT
Found at i:40015661 original size:54 final size:54
Alignment explanation
Indices: 40015600--40015777 Score: 166
Period size: 54 Copynumber: 3.3 Consensus size: 54
40015590 TAAATTGTAC
* *
40015600 AGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-TACTTTGTAGCACTAAGTGTGCGAATTGAATATGAT
* ** ** * *
40015655 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATG-T
1 AGCACTAAGTGTGCG-ATTTACTTTGTAGCACTAAGTGTGCGA-ATTGAATATGAT
* * *
40015709 AGCACTAAGTGTGCGATTTGA-TTACGTAGCACTAAGTGTGCGAGTTGATTAT-AT
1 AGCACTAAGTGTGCGATTT-ACTT-TGTAGCACTAAGTGTGCGAATTGAATATGAT
*
40015763 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40015778 GGCTCAATAT
Statistics
Matches: 100, Mismatches: 17, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
54 59 0.59
55 41 0.41
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTTACTTTGTAGCACTAAGTGTGCGAATTGAATATGAT
Found at i:40015724 original size:55 final size:54
Alignment explanation
Indices: 40015628--40015777 Score: 167
Period size: 55 Copynumber: 2.8 Consensus size: 54
40015618 CTACTTTGTT
** * *
40015628 GCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGAATATGTA-GCACTAAGTGTGCGAATTGACCACGCA
* * ** *
40015682 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAG-TTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
* * *
40015737 GCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCG
40015778 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
54 37 0.45
55 44 0.54
56 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGTTGAATATGTAGCACTAAGTGTGCGAATTGACCACGCA
Found at i:40015724 original size:82 final size:81
Alignment explanation
Indices: 40015601--40015756 Score: 208
Period size: 82 Copynumber: 1.9 Consensus size: 81
40015591 AAATTGTACA
* * *
40015601 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
40015665 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
40015682 GCACTAAGTGTGCGAGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGT
1 GCACTAAGTGTGCGA-TTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGT
*
40015746 GTGCGAGTTGA
64 GTGCGAATTGA
40015757 TTATATAGCA
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
81 16 0.25
82 48 0.74
83 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:40015768 original size:82 final size:81
Alignment explanation
Indices: 40015597--40015777 Score: 204
Period size: 82 Copynumber: 2.2 Consensus size: 81
40015587 GATTAAATTG
* * *
40015597 TACAGCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
40015662 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
40015678 TGCGGCACTAAGTGTGCGAGTT-TGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCAC
1 TACAGCACTAAGTGTGCGA-TTCT-ACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCAC
* **
40015741 TAAGTGTGCGAGTTGATTA
63 TAAGTGTGCGAATTGACCA
* *
40015760 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
40015778 GGCTCAATAT
Statistics
Matches: 82, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 19 0.23
82 63 0.77
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCTACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:40015788 original size:27 final size:27
Alignment explanation
Indices: 40015682--40015788 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
40015672 TGACCATGCG
* * * *
40015682 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
40015710 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
40015737 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
40015764 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
40015789 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:40027402 original size:30 final size:31
Alignment explanation
Indices: 40027358--40027416 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
40027348 CCGAACTTTG
40027358 GGGAAAAAAATGTAAATATG-CAAAAGTTTA
1 GGGAAAAAAATGTAAATATGTCAAAAGTTTA
* * * *
40027388 GGGACAAAATTGTAATTTTGTCAAAAGTT
1 GGGAAAAAAATGTAAATATGTCAAAAGTT
40027417 GAGTCGAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 16 0.67
31 8 0.33
ACGTcount: A:0.46, C:0.05, G:0.20, T:0.29
Consensus pattern (31 bp):
GGGAAAAAAATGTAAATATGTCAAAAGTTTA
Found at i:40027964 original size:51 final size:50
Alignment explanation
Indices: 40027888--40028057 Score: 173
Period size: 51 Copynumber: 3.4 Consensus size: 50
40027878 TATAAACACG
* *
40027888 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGA-AGATAATGATCACA
* * * * *
40027939 TGTGTAGTACTATGTGCAGGCTACTACATGAACCGGAA-AGT-TTGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATC-GAAGA-TAATGATCACA
* * *
40027989 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAATAATTACA
1 TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAA-GATAATGATCACA
* * *
40028040 CGGGTGGTACTATGTGCA
1 TGTGTAGTACTATGTGCA
40028058 AACCACCGAA
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
49 3 0.03
50 38 0.40
51 52 0.55
52 2 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGCAGGCTACTACGTGTATCGAAGATAATGATCACA
Found at i:40035552 original size:51 final size:51
Alignment explanation
Indices: 40035472--40035659 Score: 229
Period size: 51 Copynumber: 3.7 Consensus size: 51
40035462 TGCCTATAAA
* *
40035472 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATC-GATA-GATAATGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGA-AGGAT-ATGGT
* * * *
40035523 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAGGATATGGT
* * * * *
40035574 CACGTGTGTAGTACTATGTGCAGGCTACTACATGAACCGGAAAG-TTTGAT
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAGGATATGGT
*
40035624 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTA
40035660 TCGAATGATA
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
50 38 0.32
51 78 0.65
52 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAAGGATATGGT
Found at i:40035659 original size:101 final size:102
Alignment explanation
Indices: 40035472--40035659 Score: 263
Period size: 101 Copynumber: 1.9 Consensus size: 102
40035462 TGCCTATAAA
* * * * *
40035472 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCGATAGATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGAACCGAAAGATAATGATCACATGTGTAGTAC
* *
40035537 TATGTGCAGGCTACTATGTGTACCGGAAGGCTTTGGT
66 TATGTGAAGGCTACTACGTGTACCGGAAGGCTTTGGT
* * *
40035574 CACGTGTGTAGTACTATGTGCAGGCTACTACATGAACCGGAAAG-T-TTGATCACGTGTGTAGTA
1 CACGTGTGTAGTACTAAGTGCAGGCTACTACATGAACC-GAAAGATAATGATCACATGTGTAGTA
40035637 CTATGTGAAGGCTACTACGTGTA
65 CTATGTGAAGGCTACTACGTGTA
40035660 TCGAATGATA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
101 36 0.48
102 35 0.47
103 4 0.05
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTAAGTGCAGGCTACTACATGAACCGAAAGATAATGATCACATGTGTAGTAC
TATGTGAAGGCTACTACGTGTACCGGAAGGCTTTGGT
Found at i:40041921 original size:23 final size:23
Alignment explanation
Indices: 40041895--40041942 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
40041885 ACAAGGTACG
*
40041895 AGGCATTATCGGACTGAAACATA
1 AGGCATTACCGGACTGAAACATA
40041918 AGGCATTACCGGACTGAAACATA
1 AGGCATTACCGGACTGAAACATA
40041941 AG
1 AG
40041943 CAATCATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.19
Consensus pattern (23 bp):
AGGCATTACCGGACTGAAACATA
Found at i:40050457 original size:120 final size:120
Alignment explanation
Indices: 40050244--40050467 Score: 396
Period size: 120 Copynumber: 1.9 Consensus size: 120
40050234 CCTTTGATAC
* *
40050244 GAGTCACAAAGGCCTAACCCAAGCCCAAGAATGTGATGGGCTCAAATTACCACAAGGCCCAATAA
1 GAGTCACAAAGGCCTAACCCAAGCCCAAGAACGTGATGGGCTCAAACTACCACAAGGCCCAATAA
*
40050309 CGAGATCAAAGGCCCGAAAAATGTGTTCCAAACTAAATGGGACTAGGAATTATAT
66 CGAGATCAAAGGCCCGAAAAATGCGTTCCAAACTAAATGGGACTAGGAATTATAT
40050364 GAGTCACAAAGG-CTGAACCCAAGCCCAAGAACGTGATGGGCTCAAACTACCACAAGGCCCAATA
1 GAGTCACAAAGGCCT-AACCCAAGCCCAAGAACGTGATGGGCTCAAACTACCACAAGGCCCAATA
*
40050428 ACGAGATCAAAGGCCCGACAAATGCGTTCCAAACTAAATG
65 ACGAGATCAAAGGCCCGAAAAATGCGTTCCAAACTAAATG
40050468 AGACCATTCA
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
119 2 0.02
120 97 0.98
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (120 bp):
GAGTCACAAAGGCCTAACCCAAGCCCAAGAACGTGATGGGCTCAAACTACCACAAGGCCCAATAA
CGAGATCAAAGGCCCGAAAAATGCGTTCCAAACTAAATGGGACTAGGAATTATAT
Found at i:40068314 original size:13 final size:13
Alignment explanation
Indices: 40068296--40068325 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40068286 AAACTAGATT
*
40068296 TTAACTAAGTAAA
1 TTAACTAAGAAAA
40068309 TTAACTAAGAAAA
1 TTAACTAAGAAAA
40068322 TTAA
1 TTAA
40068326 AAGATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:40070204 original size:38 final size:37
Alignment explanation
Indices: 40070175--40070469 Score: 155
Period size: 37 Copynumber: 8.0 Consensus size: 37
40070165 TTTATTGAAA
40070175 GGTTGGGAAAGACCTAGTCAAGGCCACCTTTAAAAAT
1 GGTTGGGAAAGACCTAGTCAAGGCCACCTTTAAAAAT
* * *
40070212 GGTTGGGATAGACCTAGTCAATGCCAACTTTTGAAAAA-
1 GGTTGGGAAAGACCTAGTCAAGGCC-ACCTTT-AAAAAT
* * *
40070250 GGTTAGGATAA-ACC-CGTCTAAGGCAACC-TTAAAAA-
1 GGTTGGGA-AAGACCTAGTC-AAGGCCACCTTTAAAAAT
* ***
40070285 GGTTGGGATAGACC-AGTCTAAGATAACCTTTTAAAAA-
1 GGTTGGGAAAGACCTAGTC-AAGGCCACC-TTTAAAAAT
* * * * *
40070322 AGTAGGGATAGACC-ATGTCTAAGGCAACCTTTAAAAAA
1 GGTTGGGAAAGACCTA-GTC-AAGGCCACCTTTAAAAAT
* * * * *
40070360 GATTGGGATAGA-ATCGTCTAAGGCAACC-TTAAAAAT
1 GGTTGGGAAAGACCTAGTC-AAGGCCACCTTTAAAAAT
* ** * *
40070396 -TTTGGGGTAGACCTTGTCTAAGGCCACCTTTAAAAAA
1 GGTTGGGAAAGACCTAGTC-AAGGCCACCTTTAAAAAT
* *
40070433 GGTTGGGATAGACC-AGTCTAAGGCAACCTTTTAAAAA
1 GGTTGGGAAAGACCTAGTC-AAGGCCACC-TTTAAAAA
40070470 ATTTGGGATA
Statistics
Matches: 210, Mismatches: 34, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
34 1 0.00
35 35 0.17
36 22 0.10
37 88 0.42
38 58 0.28
39 6 0.03
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (37 bp):
GGTTGGGAAAGACCTAGTCAAGGCCACCTTTAAAAAT
Found at i:40070284 original size:35 final size:35
Alignment explanation
Indices: 40070172--40070796 Score: 455
Period size: 35 Copynumber: 17.4 Consensus size: 35
40070162 ACCTTTATTG
* *
40070172 AAAGGTTGGGAAAGACCTAGTC-AAGGCCACCTTTAA
1 AAAGGTTGGGATAGACCT-GTCTAAGGCAACC-TTAA
* *
40070208 AAATGGTTGGGATAGACCTAGTC-AATGCCAACTTTTGAA
1 AAA-GGTTGGGATAGACCT-GTCTAA-GGCAAC-CTT-AA
* * *
40070247 AAAGGTTAGGATAAACCCGTCTAAGGCAACCTTAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
* **
40070282 AAAGGTTGGGATAGACCAGTCTAAGATAACCTTTTAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACC--TTAA
* *
40070319 AAAAGTAGGGATAGACCATGTCTAAGGCAACCTTTAAA
1 AAAGGTTGGGATAGACC-TGTCTAAGGCAACC-TT-AA
* *
40070357 AAAGATTGGGATAGA-ATCGTCTAAGGCAACCTTAA
1 AAAGGTTGGGATAGACCT-GTCTAAGGCAACCTTAA
** * *
40070392 AAATTTTGGGGTAGACCTTGTCTAAGGCCACCTTTAAA
1 AAAGGTTGGGATAGACC-TGTCTAAGGCAACC-TT-AA
*
40070430 AAAGGTTGGGATAGACCAGTCTAAGGCAACCTTTTAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACC--TTAA
** * *
40070467 AAAATTTGGGATAGACATTGTCTAAGGAAACCTTCAAA
1 AAAGGTTGGGATAGAC-CTGTCTAAGGCAACCTT--AA
* **
40070505 AAAGGTTAGGAT--A---G-CTAAAACAACCTTAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
* * * * *
40070534 AAAGGTAGGGATAGACTTCTCTATGGTAACCTTAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
* *
40070569 AAAGGTTGGGATAGACATTGTCTAAGGCAACTTTTAAA
1 AAAGGTTGGGATAGAC-CTGTCTAAGGCAAC-CTT-AA
* * * *
40070607 AAAGGTTTGGATCGACCCGTCTAAGACAACCTTAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
* * * *
40070642 AAATGTTGGGATAGACTTGTTTAAAGCAACCTT-A
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
* * *
40070676 AAAGGTTGGGATAGACCTTTTCCAAGGCAACCTAAA
1 AAAGGTTGGGATAGACC-TGTCTAAGGCAACCTTAA
** * * * *
40070712 AAATTTTGGCATAAACCCGTCTAAGGCAACCATAA
1 AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
* *
40070747 AAAGGTTAGGG-TA-AACTAGTCTAAGGCAAACTTAA
1 AAAGGTT-GGGATAGACCT-GTCTAAGGCAACCTTAA
40070782 AAAGGTTGGGATAGA
1 AAAGGTTGGGATAGA
40070797 TTTTTGTCTC
Statistics
Matches: 463, Mismatches: 93, Indels: 66
0.74 0.15 0.11
Matches are distributed among these distances:
29 12 0.03
31 11 0.02
32 1 0.00
34 21 0.05
35 150 0.32
36 53 0.11
37 107 0.23
38 103 0.22
39 5 0.01
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (35 bp):
AAAGGTTGGGATAGACCTGTCTAAGGCAACCTTAA
Found at i:40070295 original size:73 final size:72
Alignment explanation
Indices: 40070172--40070796 Score: 376
Period size: 73 Copynumber: 8.7 Consensus size: 72
40070162 ACCTTTATTG
* * * *
40070172 AAAGGTTGGGAAAGACCTAGTC-AAGGCCACCTTTAAAAATGGTTGGGATAGACCTAGTC-AATG
1 AAAGGTTAGGATAGACC-CGTCTAAGGCAACC-TTAAAAA-GGTTGGGATAGACCTAGTCTAA-G
*
40070235 CCAACTTTTGAA
62 GCAACTTTT-AA
* **
40070247 AAAGGTTAGGATAAACCCGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACC-AGTCTAAGATAA
1 AAAGGTTAGGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTAGTCTAAGGCAA
40070311 CCTTTTAA
66 -CTTTTAA
* * * * *
40070319 AAAAG-TAGGGATAGACCATGTCTAAGGCAACCTTTAAAAAAGATTGGGATAGA-ATCGTCTAAG
1 AAAGGTTA-GGATAGACC-CGTCTAAGGCAACC-TT-AAAAAGGTTGGGATAGACCTAGTCTAAG
*
40070382 GCAAC-CTTAA
62 GCAACTTTTAA
** * * * *
40070392 AAATTTTGGGGTAGACCTTGTCTAAGGCCACCTTTAAAAAAGGTTGGGATAGACC-AGTCTAAGG
1 AAAGGTTAGGATAGACC-CGTCTAAGGCAACC-TT-AAAAAGGTTGGGATAGACCTAGTCTAAGG
40070456 CAACCTTTTAA
63 CAA-CTTTTAA
** * ** * * *
40070467 AAAATTTGGGATAGACATTGTCTAAGGAAACCTTCAAAAAAGGTTAGGATAG--CTA----AA-A
1 AAAGGTTAGGATAGAC-CCGTCTAAGGCAACCTT--AAAAAGGTTGGGATAGACCTAGTCTAAGG
*
40070525 CAAC-CTTAA
63 CAACTTTTAA
* * * * *
40070534 AAAGG-TAGGGATAGACTTC-TCTATGGTAACCTTAAAAAGGTTGGGATAGACATTGTCTAAGGC
1 AAAGGTTA-GGATAGAC-CCGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTAGTCTAAGGC
40070597 AACTTTTAAA
64 AACTTTT-AA
* * * * * * *
40070607 AAAGGTTTGGATCGACCCGTCTAAGACAACCTTAAAAATGTTGGGATAGA-CTTGTTTAAAGCAA
1 AAAGGTTAGGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTAGTCTAAGGCAA
*
40070671 C-CTT-A
66 CTTTTAA
* ** * * ** * * *
40070676 AAAGGTTGGGATAGACCTTTTCCAAGGCAACCTAAAAAATTTTGGCATAAACC-CGTCTAAGGCA
1 AAAGGTTAGGATAGACC-CGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTAGTCTAAGGCA
**
40070740 AC-CATAA
65 ACTTTTAA
* * ** *
40070747 AAAGGTTAGGGTAAACTAGTCTAAGGCAAACTTAAAAAGGTTGGGATAGA
1 AAAGGTTAGGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGGGATAGA
40070797 TTTTTGTCTC
Statistics
Matches: 436, Mismatches: 84, Indels: 65
0.75 0.14 0.11
Matches are distributed among these distances:
64 15 0.03
66 14 0.03
67 16 0.04
68 1 0.00
69 19 0.04
70 65 0.15
71 23 0.05
72 36 0.08
73 135 0.31
74 19 0.04
75 93 0.21
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.25
Consensus pattern (72 bp):
AAAGGTTAGGATAGACCCGTCTAAGGCAACCTTAAAAAGGTTGGGATAGACCTAGTCTAAGGCAA
CTTTTAA
Found at i:40070330 original size:110 final size:109
Alignment explanation
Indices: 40070172--40070518 Score: 353
Period size: 110 Copynumber: 3.1 Consensus size: 109
40070162 ACCTTTATTG
* *
40070172 AAAGGTTGGGAAAGACCTAGTC-AAGGCCACCTTTAAAAATGGTTGGGATAGACCTAGTC-AATG
1 AAAGGTTGGGATAGACCTAGTCTAAGGCCACCTTTAAAAA-AGTTGGGATAGACC-AGTCTAA-G
* * *
40070235 CCAACTTTTGAAAAAGGTTAGGATA-AACCCGTCTAAGGCAACCTTAA
63 CCAACCTTTAAAAAAGATTAGGATAGAA-CCGTCTAAGGCAACCTTAA
*** * *
40070282 AAAGGTTGGGATAGACC-AGTCTAAGATAACCTTTTAAAAAAGTAGGGATAGACCATGTCTAAGG
1 AAAGGTTGGGATAGACCTAGTCTAAGGCCACC-TTTAAAAAAGTTGGGATAGACCA-GTCTAAGC
* *
40070346 CAACCTTTAAAAAAGATTGGGATAGAATCGTCTAAGGCAACCTTAA
64 CAACCTTTAAAAAAGATTAGGATAGAACCGTCTAAGGCAACCTTAA
** * * *
40070392 AAATTTTGGGGTAGACCTTGTCTAAGGCCACCTTTAAAAAAGGTTGGGATAGACCAGTCTAAGGC
1 AAAGGTTGGGATAGACCTAGTCTAAGGCCACCTTTAAAAAA-GTTGGGATAGACCAGTCTAAGCC
* * ** *
40070457 AACCTTTTAAAAAA-TTTGGGATAGACATTGTCTAAGGAAACCTTCAAA
65 AACC-TTTAAAAAAGATTAGGATAGA-ACCGTCTAAGGCAACCTT--AA
*
40070505 AAAGGTTAGGATAG
1 AAAGGTTGGGATAG
40070519 CTAAAACAAC
Statistics
Matches: 199, Mismatches: 27, Indels: 19
0.81 0.11 0.08
Matches are distributed among these distances:
109 5 0.03
110 122 0.61
111 60 0.30
113 12 0.06
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.24
Consensus pattern (109 bp):
AAAGGTTGGGATAGACCTAGTCTAAGGCCACCTTTAAAAAAGTTGGGATAGACCAGTCTAAGCCA
ACCTTTAAAAAAGATTAGGATAGAACCGTCTAAGGCAACCTTAA
Found at i:40070608 original size:102 final size:105
Alignment explanation
Indices: 40070265--40070796 Score: 298
Period size: 102 Copynumber: 5.0 Consensus size: 105
40070255 GGATAAACCC
* * * * *
40070265 GTCTAAGGCAACCTT--AAAAAGGTTGGGATAGACCAGTCTAAGATAACCTTTTAAAAAAGTAGG
1 GTCTAAGGCAACCTTCAAAAAAGGTTAGGAT-CA-C-GTCTAAAACAACC--TTAAAAAGGTAGG
* * * * *
40070328 GATAGACCATGTCTAAGGCAACCTTTAAAAAAGATTGGGATAGA-ATC
61 GATAGA-CTTCTCTAAAGCAACC-TT-AAAAAGGTTGGGATAGACATT
* * * ** ** * *
40070375 GTCTAAGGCAACCTT-AAAAATTTTGGGGTA-GACCTTGTCTAAGGCCACCTTTAAAAAAGGTTG
1 GTCTAAGGCAACCTTCAAAAA----AGGTTAGGATCACGTCTAAAACAACC-TT-AAAAAGGTAG
*** * **
40070438 GGATAGACCAGTCTAAGGCAACCTTTTAAAAAATTTGGGATAGACATT
60 GGATAGACTTCTCTAAAGCAACC--TTAAAAAGGTTGGGATAGACATT
*
40070486 GTCTAAGGAAACCTTCAAAAAAGGTTAGGAT-A-G-CTAAAACAACCTTAAAAAGGTAGGGATAG
1 GTCTAAGGCAACCTTCAAAAAAGGTTAGGATCACGTCTAAAACAACCTTAAAAAGGTAGGGATAG
** *
40070548 ACTTCTCTATGGTAACCTTAAAAAGGTTGGGATAGACATT
66 ACTTCTCTAAAGCAACCTTAAAAAGGTTGGGATAGACATT
* * * * * *
40070588 GTCTAAGGCAACTTTTAAAAAAGGTTTGGATCGACCCGTCTAAGACAACCTTAAAAATGTTGGGA
1 GTCTAAGGCAACCTTCAAAAAAGGTTAGGATC-A--CGTCTAAAACAACCTTAAAAAGGTAGGGA
* * *
40070653 TAGACTTGTTTAAAGCAACCTT-AAAAGGTTGGGATAGACCTT
63 TAGACTTCTCTAAAGCAACCTTAAAAAGGTTGGGATAGACATT
* * * * * ** *
40070695 TTCCAAGGCAACC-T-AAAAAA-TTTTGGCATAAACCCGTCTAAGGCAACCATAAAAAGGTTAGG
1 GTCTAAGGCAACCTTCAAAAAAGGTTAGG-AT---CACGTCTAAAACAACCTTAAAAAGG-TAGG
* ** * *
40070757 G-TAAACTAGTCTAAGGCAAACTTAAAAAGGTTGGGATAGA
61 GATAGACTTCTCTAAAGCAACCTTAAAAAGGTTGGGATAGA
40070797 TTTTTGTCTC
Statistics
Matches: 340, Mismatches: 60, Indels: 48
0.76 0.13 0.11
Matches are distributed among these distances:
102 48 0.14
104 33 0.10
105 47 0.14
106 29 0.09
107 31 0.09
108 45 0.13
109 2 0.01
110 47 0.14
111 48 0.14
112 5 0.01
114 2 0.01
115 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (105 bp):
GTCTAAGGCAACCTTCAAAAAAGGTTAGGATCACGTCTAAAACAACCTTAAAAAGGTAGGGATAG
ACTTCTCTAAAGCAACCTTAAAAAGGTTGGGATAGACATT
Found at i:40070781 original size:105 final size:107
Alignment explanation
Indices: 40070269--40070796 Score: 294
Period size: 110 Copynumber: 4.9 Consensus size: 107
40070259 AAACCCGTCT
* * * * * * * * *
40070269 AAGGCAAC-CTTAAAAAGGTTGGGATAGACCAGTCTAAGATAACCTTTTAAAAAAGTAGGGATAG
1 AAGGCAACTCTAAAAAAGGTTTGGATAAACCCGTCTAAGACAACC--ATAAAAAGGTTGGGATAA
* * * * * *
40070333 ACCATGTCTAAGGCAACCTTTAAAAAAGATTGGGATAGA-ATCGTCT
64 ACTA-GTCTAAAGCAAAC-TT-AAAAAGGTTGGGATAGACATTGTCC
* * * * * * * *
40070379 AAGGCAAC-CTTAAAAA-TTTTGGGGTAGACCTTGTCTAAGGCCACCTTTAAAAAAGGTTGGGAT
1 AAGGCAACTCTAAAAAAGGTTT-GGATAAACC-CGTCTAAGACAACC-AT-AAAAAGGTTGGGAT
* * * * ** *
40070442 AGACCAGTCTAAGGCAACCTTTTAAAAAATTTGGGATAGACATTGTCT
62 AAACTAGTCTAAAGCAAAC--TTAAAAAGGTTGGGATAGACATTGTCC
* * * * * *
40070490 AAGGAAAC-CTTCAAAAAAGGTTAGGAT--A---G-CTAAAACAACCTTAAAAAGGTAGGGATAG
1 AAGGCAACTC-T-AAAAAAGGTTTGGATAAACCCGTCTAAGACAACCATAAAAAGGTTGGGATAA
** ** * * *
40070548 ACTTCTCTATGGTAACCTTAAAAAGGTTGGGATAGACATTGTCT
64 ACTAGTCTAAAGCAAACTTAAAAAGGTTGGGATAGACATTGTCC
* ** * * *
40070592 AAGGCAACTTTTAAAAAAGGTTTGGATCGACCCGTCTAAGACAACCTTAAAAATGTTGGGATAGA
1 AAGGCAAC-TCTAAAAAAGGTTTGGATAAACCCGTCTAAGACAACCATAAAAAGGTTGGGATAAA
* * * * *
40070657 CTTGTTTAAAGCAACCTT-AAAAGGTTGGGATAGACCTTTTCC
65 CTAGTCTAAAGCAAACTTAAAAAGGTTGGGATAGACATTGTCC
* *
40070699 AAGGCAAC-CTAAAAAA-TTTTGGCATAAACCCGTCTAAGGCAACCATAAAAAGGTTAGGG-TAA
1 AAGGCAACTCTAAAAAAGGTTTGG-ATAAACCCGTCTAAGACAACCATAAAAAGGTT-GGGATAA
*
40070761 ACTAGTCTAAGGCAAACTTAAAAAGGTTGGGATAGA
64 ACTAGTCTAAAGCAAACTTAAAAAGGTTGGGATAGA
40070797 TTTTTGTCTC
Statistics
Matches: 345, Mismatches: 54, Indels: 42
0.78 0.12 0.10
Matches are distributed among these distances:
102 46 0.13
103 1 0.00
104 33 0.10
105 53 0.15
106 27 0.08
107 31 0.09
108 40 0.12
109 2 0.01
110 55 0.16
111 46 0.13
112 1 0.00
113 8 0.02
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (107 bp):
AAGGCAACTCTAAAAAAGGTTTGGATAAACCCGTCTAAGACAACCATAAAAAGGTTGGGATAAAC
TAGTCTAAAGCAAACTTAAAAAGGTTGGGATAGACATTGTCC
Found at i:40071063 original size:75 final size:75
Alignment explanation
Indices: 40070974--40071115 Score: 230
Period size: 75 Copynumber: 1.9 Consensus size: 75
40070964 TAGTAATTTA
* **
40070974 TATACAAAATCCTAATAGAAGCAGTCAACAAGTTGTGAACATATTGTCAACTTGTTTCACATGAC
1 TATACAAAATCCTAATAAAAGCAGTCAACAAGTTGCAAACATATTGTCAACTTGTTTCACATGAC
40071039 ATCAAAAACT
66 ATCAAAAACT
* * *
40071049 TATACAAAATCCTAATAAAAGCAGTCAACACGTTGCAAACATGTTGTCAACTTGTTTCTCATGAC
1 TATACAAAATCCTAATAAAAGCAGTCAACAAGTTGCAAACATATTGTCAACTTGTTTCACATGAC
40071114 AT
66 AT
40071116 TAGAAAATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 61 1.00
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (75 bp):
TATACAAAATCCTAATAAAAGCAGTCAACAAGTTGCAAACATATTGTCAACTTGTTTCACATGAC
ATCAAAAACT
Found at i:40079325 original size:20 final size:20
Alignment explanation
Indices: 40079300--40079344 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
40079290 CTTCATACTA
40079300 AATCTTTCGAATTAACTCTG
1 AATCTTTCGAATTAACTCTG
40079320 AATCTTTCGAATTAACTCTG
1 AATCTTTCGAATTAACTCTG
40079340 AATCT
1 AATCT
40079345 CTCGGTACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (20 bp):
AATCTTTCGAATTAACTCTG
Found at i:40082516 original size:40 final size:40
Alignment explanation
Indices: 40082372--40082503 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
40082362 GCTCCTCGTT
* * * *
40082372 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
*
40082412 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
* * *
40082451 CGAATGCCTTCGGGACTTAACCCGGAATTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
40082491 CAAATGCCTTCGG
1 CAAATGCCTTCGG
40082504 ATCTTAGTCC
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
39 34 0.41
40 48 0.59
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
Found at i:40082565 original size:41 final size:41
Alignment explanation
Indices: 40082488--40082565 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
40082478 TTAATAACTC
* * *
40082488 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
40082529 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
40082566 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:40083689 original size:13 final size:12
Alignment explanation
Indices: 40083661--40083697 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40083651 ACCACACACA
40083661 CATTTTTTTTT-
1 CATTTTTTTTTC
*
40083672 C-TTTTGTTTTC
1 CATTTTTTTTTC
40083683 CATTTTTTTTTC
1 CATTTTTTTTTC
40083695 CAT
1 CAT
40083698 AATTAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
10 8 0.36
11 2 0.09
12 12 0.55
ACGTcount: A:0.08, C:0.16, G:0.03, T:0.73
Consensus pattern (12 bp):
CATTTTTTTTTC
Found at i:40087450 original size:27 final size:28
Alignment explanation
Indices: 40087409--40087472 Score: 121
Period size: 27 Copynumber: 2.3 Consensus size: 28
40087399 GCATTTTTGT
40087409 TCGAAACTTTGGTACCTACCAGATAAGA
1 TCGAAACTTTGGTACCTACCAGATAAGA
40087437 TC-AAACTTTGGTACCTACCAGATAAGA
1 TCGAAACTTTGGTACCTACCAGATAAGA
40087464 TCGAAACTT
1 TCGAAACTT
40087473 GTCGAAAGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 27 0.77
28 8 0.23
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (28 bp):
TCGAAACTTTGGTACCTACCAGATAAGA
Found at i:40096496 original size:39 final size:39
Alignment explanation
Indices: 40096410--40096849 Score: 457
Period size: 39 Copynumber: 11.3 Consensus size: 39
40096400 CAAAATTGCA
*
40096410 ATCAGGGGTACCGAAGTACAACAGGGGGCACGTAAGTGTG
1 ATCAGGGGTACCGAAGTACAACA-GGGGCACGTAAGTGCG
* * * *
40096450 ATTAGGGGTACCGAAGTACAACAGAGGCATGTAAGTGTG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * **
40096489 ATCAGGGGTACCGAAGTACAATAGTGGCACGTAAGTGAA
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * * *
40096528 ATCAGGGCTACCAAAGTACAACAGGGGCACGTAGGTACG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * * *
40096567 ATTAGGGGTACCGAAGTACATCAGGGGCACGTAACTGTG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * *
40096606 ATCAGGGGTATCGAAGTACAACAGGGGCATGTAGGTGCG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * * *
40096645 ATCAAGGGTACCGAAGTACATCACGGGCACGTAAGTGCA
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * * * *
40096684 ATCAGGGGTACCGAAGTACAACAAGGGAATGTACGTGCA
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * * * * ** * *
40096723 ATCAGGGGTATCGAAGTGCAACACGAGAATATAGGTACG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * *
40096762 ATCAGGGGTACCGAAGTACATCAAGGGTACGTAAGTGCG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
* * * * *
40096801 ATAAAGGGTACCGAAGTACAATAGGGGCTCGTAAGTACG
1 ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
40096840 ATCAGGGGTA
1 ATCAGGGGTA
40096850 TAATTATAAA
Statistics
Matches: 327, Mismatches: 73, Indels: 1
0.82 0.18 0.00
Matches are distributed among these distances:
39 305 0.93
40 22 0.07
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (39 bp):
ATCAGGGGTACCGAAGTACAACAGGGGCACGTAAGTGCG
Found at i:40096789 original size:19 final size:20
Alignment explanation
Indices: 40096757--40096819 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
40096747 GAGAATATAG
*
40096757 GTACGATCAGGGGTACCGAA
1 GTACGATCAAGGGTACCGAA
40096777 GTAC-ATCAAGGGTA-CGTAA
1 GTACGATCAAGGGTACCG-AA
* *
40096796 GTGCGATAAAGGGTACCGAA
1 GTACGATCAAGGGTACCGAA
40096816 GTAC
1 GTAC
40096820 AATAGGGGCT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 2 0.06
19 14 0.39
20 18 0.50
21 2 0.06
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.17
Consensus pattern (20 bp):
GTACGATCAAGGGTACCGAA
Found at i:40099576 original size:25 final size:25
Alignment explanation
Indices: 40099498--40099581 Score: 84
Period size: 25 Copynumber: 3.4 Consensus size: 25
40099488 ACAACTTATG
* *
40099498 TGAGCATACCGATTTACAGCTCGTGA
1 TGAGCATACCGATTCACAGCTCAT-A
* *
40099524 -GAGCACACCGA-TCTACAACTCA-A
1 TGAGCATACCGATTC-ACAGCTCATA
40099547 GTGAGCATACCGATTCACAGCTCATA
1 -TGAGCATACCGATTCACAGCTCATA
40099573 TGAGCATAC
1 TGAGCATAC
40099582 ATGTACAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 42 0.89
26 3 0.06
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (25 bp):
TGAGCATACCGATTCACAGCTCATA
Found at i:40117038 original size:33 final size:33
Alignment explanation
Indices: 40116996--40117081 Score: 172
Period size: 33 Copynumber: 2.6 Consensus size: 33
40116986 AAGATATGGT
40116996 GGAATCAGCACTTAGCAACCACCAATGAATTGG
1 GGAATCAGCACTTAGCAACCACCAATGAATTGG
40117029 GGAATCAGCACTTAGCAACCACCAATGAATTGG
1 GGAATCAGCACTTAGCAACCACCAATGAATTGG
40117062 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
40117082 CCCTTCACAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATTGG
Found at i:40117115 original size:109 final size:103
Alignment explanation
Indices: 40116924--40117151 Score: 314
Period size: 109 Copynumber: 2.2 Consensus size: 103
40116914 ATCGGTGGAT
* **
40116924 TCAGCACTTAGCAACCACCAGTGATTGGGGGAATCAACACTTAGCAACCCTTTTCACATTCAAAG
1 TCAGCACTTAGCAACCACCAATGATTGGGGGAATCAACACTTAGCAACCCCCTTCACATTCAAAG
* *
40116989 ATATGGTGGAATCAGCACTTAGCAACCACCAATGAATTGGGGAA
66 ATACGGTGGAATCAGCACTTAGCAACC-CC--T---TGGGGGAA
* *
40117033 TCAGCACTTAGCAACCACCAATGAATT-GGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAA
1 TCAGCACTTAGCAACCACCAATG-ATTGGGGGAATCAACACTTAGCAACCCCCTTCACATTCAAA
*
40117097 GATACGTTGGAATCAGCACTTAGCAACCCCTTGGGGGAA
65 GATACGGTGGAATCAGCACTTAGCAACCCCTTGGGGGAA
40117136 TCAGCACTTAGCAACC
1 TCAGCACTTAGCAACC
40117152 CCCTTTATAT
Statistics
Matches: 110, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
103 23 0.21
106 1 0.01
108 2 0.02
109 81 0.74
110 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (103 bp):
TCAGCACTTAGCAACCACCAATGATTGGGGGAATCAACACTTAGCAACCCCCTTCACATTCAAAG
ATACGGTGGAATCAGCACTTAGCAACCCCTTGGGGGAA
Found at i:40117149 original size:70 final size:73
Alignment explanation
Indices: 40117029--40117233 Score: 283
Period size: 70 Copynumber: 2.8 Consensus size: 73
40117019 AATGAATTGG
*
40117029 GGAATCAGCACTTAGCAACCACCAATGAATTGGGGAATCAGCACTTAGCAACCCCCTTCACATTT
1 GGAATCAGCACTTAGCAACCACC-ATG--TCGGGGAATCAGCACTTAGCAACCCCCTTCACATTT
*
40117094 AAAGATACGTT
63 AAAGATACGGT
* * *
40117105 GGAATCAGCACTTAGCAACC-CC-T-TGGGGGAATCAGCACTTAGCAACCCCCTTTATATTTAAA
1 GGAATCAGCACTTAGCAACCACCATGTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAA
40117167 GATACGGT
66 GATACGGT
40117175 GGAATCAGCACTTAGCAACCACCAATGAGTCGGGGAATCAGCACTTAGCAA-CCCCTTCA
1 GGAATCAGCACTTAGCAACCACC-AT--GTCGGGGAATCAGCACTTAGCAACCCCCTTCA
40117234 TATTCAATGT
Statistics
Matches: 117, Mismatches: 6, Indels: 13
0.86 0.04 0.10
Matches are distributed among these distances:
70 63 0.54
71 2 0.02
73 2 0.02
75 9 0.08
76 41 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.21
Consensus pattern (73 bp):
GGAATCAGCACTTAGCAACCACCATGTCGGGGAATCAGCACTTAGCAACCCCCTTCACATTTAAA
GATACGGT
Found at i:40119187 original size:20 final size:20
Alignment explanation
Indices: 40119162--40119201 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
40119152 ATTTTAAAAT
*
40119162 CAAGTTAAAATGATTTTAAC
1 CAAGTTAAAATGATTCTAAC
40119182 CAAGTTAAAATGATTCTAAC
1 CAAGTTAAAATGATTCTAAC
40119202 ACATCAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (20 bp):
CAAGTTAAAATGATTCTAAC
Found at i:40119279 original size:22 final size:20
Alignment explanation
Indices: 40119253--40119292 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
40119243 TCAAGCCAAA
40119253 AAGTATCGATACCATTTTGGCC
1 AAGTATCGATA--ATTTTGGCC
*
40119275 AAGTATTGATAATTTTGG
1 AAGTATCGATAATTTTGG
40119293 AACTATCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (20 bp):
AAGTATCGATAATTTTGGCC
Found at i:40120499 original size:43 final size:40
Alignment explanation
Indices: 40120424--40120504 Score: 108
Period size: 43 Copynumber: 1.9 Consensus size: 40
40120414 ATAACTCTTG
* * *
40120424 AAAAGAATTTTAAAAAGGAAGATAATCTTGGGTTGTTGAA
1 AAAAGAATTTAAAAAAGGAAGATAAACATGGGTTGTTGAA
40120464 AAAAGAATTTAAAAAGAGGAGAAGATAAACATGGGTTGTTG
1 AAAAGAATTTAAAAA-A-G-GAAGATAAACATGGGTTGTTG
40120505 GATTTACCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
40 14 0.40
41 1 0.03
42 1 0.03
43 19 0.54
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.26
Consensus pattern (40 bp):
AAAAGAATTTAAAAAAGGAAGATAAACATGGGTTGTTGAA
Found at i:40122239 original size:19 final size:19
Alignment explanation
Indices: 40122217--40122267 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
40122207 AATGGTGTTT
40122217 GATTAGTGGAATTGTGTCA
1 GATTAGTGGAATTGTGTCA
* **
40122236 GATTAGTGGAACTGTGTGT
1 GATTAGTGGAATTGTGTCA
*
40122255 GATAAGTGGAATT
1 GATTAGTGGAATT
40122268 TTGTTTGCAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.27, C:0.04, G:0.33, T:0.35
Consensus pattern (19 bp):
GATTAGTGGAATTGTGTCA
Found at i:40129574 original size:24 final size:22
Alignment explanation
Indices: 40129534--40129594 Score: 61
Period size: 24 Copynumber: 2.7 Consensus size: 22
40129524 TCTTTATTTT
*
40129534 ATTTTATAATTTAATTTTGTTAG
1 ATTTTATAATTTAATTTTATT-G
* *
40129557 ATTTTAATTATTTTATTTTATTG
1 ATTTT-ATAATTTAATTTTATTG
*
40129580 ATTTT-TAAGTTAATT
1 ATTTTATAATTTAATT
40129595 ATATATTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
21 7 0.23
23 11 0.35
24 13 0.42
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
ATTTTATAATTTAATTTTATTG
Found at i:40131467 original size:21 final size:21
Alignment explanation
Indices: 40131431--40131494 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
40131421 ATAATGTTTG
40131431 TTTAAAATATTATTAAAATATAA
1 TTTAAAA-A-TATTAAAATATAA
**
40131454 TTTAAAAATATTAAAATACGA
1 TTTAAAAATATTAAAATATAA
40131475 TTTAAACAATA-TAAAATATA
1 TTTAAA-AATATTAAAATATA
40131495 CTAATATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 24 0.67
22 5 0.14
23 7 0.19
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (21 bp):
TTTAAAAATATTAAAATATAA
Found at i:40131668 original size:15 final size:15
Alignment explanation
Indices: 40131644--40131673 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40131634 CTTTTAATTA
40131644 AAATAAAATAATTTT
1 AAATAAAATAATTTT
*
40131659 AAATATAATAATTTT
1 AAATAAAATAATTTT
40131674 TTTTAACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAATAAAATAATTTT
Found at i:40131838 original size:14 final size:15
Alignment explanation
Indices: 40131819--40131848 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
40131809 TAAAAATAAA
40131819 AAAATTA-TTAATAT
1 AAAATTATTTAATAT
40131833 AAAATTATTTAATAT
1 AAAATTATTTAATAT
40131848 A
1 A
40131849 TTTTTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAATTATTTAATAT
Found at i:40132263 original size:13 final size:11
Alignment explanation
Indices: 40132243--40132285 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 11
40132233 TTATATCAGA
40132243 TTTTTTAAATAT
1 TTTTTTAAAT-T
40132255 TTTTGTTAAATT
1 TTTT-TTAAATT
40132267 TTTTTTAAAGTT
1 TTTTTTAAA-TT
40132279 TTATTTT
1 TT-TTTT
40132286 TAAAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 5 0.18
12 13 0.46
13 10 0.36
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (11 bp):
TTTTTTAAATT
Found at i:40132616 original size:2 final size:2
Alignment explanation
Indices: 40132609--40132634 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40132599 GGTACGCTAA
40132609 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
40132635 ATTCTTAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:40138509 original size:3 final size:3
Alignment explanation
Indices: 40138501--40138547 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
40138491 TCTGAATTGA
40138501 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40138548 CAAAAACAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40139910 original size:17 final size:17
Alignment explanation
Indices: 40139888--40139925 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
40139878 TTAATGGCAT
40139888 TAAAGTAAATTAGTAAA
1 TAAAGTAAATTAGTAAA
40139905 TAAAGTAAATTAGTAAA
1 TAAAGTAAATTAGTAAA
40139922 TAAA
1 TAAA
40139926 CATAGTTATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.29
Consensus pattern (17 bp):
TAAAGTAAATTAGTAAA
Found at i:40140708 original size:31 final size:31
Alignment explanation
Indices: 40140673--40141097 Score: 413
Period size: 31 Copynumber: 13.8 Consensus size: 31
40140663 TATATTGTCG
* **
40140673 AATTAATTCGTATATAATTATACATTGCTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
*
40140704 AATTAATTTGTATATGGTTATACATTGTTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
* *
40140735 AATTGAA-TTGTATATGGATATA-AGTTGTTG-
1 AATT-AATTTGTATATGGTTATACA-TTGCTGA
* *
40140765 AATTAATTCGTATATGGTTGTACATTGCTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
* *
40140796 AATTTATTTGTATATGGTTATACATTGTTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
* * *
40140827 AACTGAA-TTGTATATGGATATA-AGTTGTTG-
1 AA-TTAATTTGTATATGGTTATACA-TTGCTGA
*
40140857 AATTAATTTGTATATGGTTGTACATTGCTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
* **
40140888 AATTTATTTGTATATGGTTATACATTATTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
* * **** *
40140919 ATTTGATTTGTATATAAAGATA-AGTTGCCG-
1 AATTAATTTGTATATGGTTATACA-TTGCTGA
**
40140949 AATTAATTTGTATATAATTATACATTGCTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
*
40140980 AATTAATTTGTATATGGTTATACATTGTTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
*
40141011 AATTGAA-TTGTATATGGATATA-AGTTGCTG-
1 AATT-AATTTGTATATGGTTATACA-TTGCTGA
* * *
40141041 AATTAATTCGTATATGGTTGTAAATTGCTGA
1 AATTAATTTGTATATGGTTATACATTGCTGA
* *
40141072 AATTTATTTGTCTATGGTTATACATT
1 AATTAATTTGTATATGGTTATACATT
40141098 ATCGAAATTG
Statistics
Matches: 325, Mismatches: 51, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
29 7 0.02
30 90 0.28
31 222 0.68
32 6 0.02
ACGTcount: A:0.32, C:0.05, G:0.17, T:0.45
Consensus pattern (31 bp):
AATTAATTTGTATATGGTTATACATTGCTGA
Found at i:40140769 original size:92 final size:92
Alignment explanation
Indices: 40140671--40141173 Score: 641
Period size: 92 Copynumber: 5.5 Consensus size: 92
40140661 TATATATTGT
*
40140671 CGAATTAATTCGTATATAATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGTTGAA
1 CGAATTAATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
*
40140736 ATTGAATTGTATATGGATATAAGTTGT
66 ATTGAATTGTATATGGATATAAGTTGC
* ** *
40140763 TGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
1 CGAATTAATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
* *
40140828 ACTGAATTGTATATGGATATAAGTTGT
66 ATTGAATTGTATATGGATATAAGTTGC
* * ** * *
40140855 TGAATTAATTTGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTATTGAA
1 CGAATTAATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
* * ** *
40140920 TTTGATTTGTATATAAAGATAAGTTGC
66 ATTGAATTGTATATGGATATAAGTTGC
* *
40140947 CGAATTAATTTGTATATAATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGTTGAA
1 CGAATTAATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
40141012 ATTGAATTGTATATGGATATAAGTTGC
66 ATTGAATTGTATATGGATATAAGTTGC
* ** * * * * *
40141039 TGAATTAATTCGTATATGGTTGTAAATTGCTGAAATTTATTTGTCTATGGTTATACATTATCGAA
1 CGAATTAATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
** * *
40141104 ATTGGTTTGTATATGAAGATAAGTTGC
66 ATTGAATTGTATATGGATATAAGTTGC
* * * *
40141131 CGAATTTGATTCGTATATGAA-TATATATTGTTG-AATTGATTTG
1 CGAA-TTAATTCGTATAT-AATTATACATTGCTGAAATTTATTTG
40141174 AGCATTGGAT
Statistics
Matches: 361, Mismatches: 48, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
92 340 0.94
93 21 0.06
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (92 bp):
CGAATTAATTCGTATATAATTATACATTGCTGAAATTTATTTGTATATGGTTATACATTGTTGAA
ATTGAATTGTATATGGATATAAGTTGC
Found at i:40140981 original size:184 final size:184
Alignment explanation
Indices: 40140667--40141173 Score: 721
Period size: 184 Copynumber: 2.8 Consensus size: 184
40140657 GATATATATA
* ** * * *
40140667 TTGTCGAATTAATTCGTATATAATTATACATTGCTGAAATTAATTTGTATATGGTTATACATTGT
1 TTGTTGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
* * * ** ** *
40140732 TGAAATTGAATTGTATATGGATATAAGTTGTTGAATTAATTCGTATATGGTTGTACATTGCTGAA
66 TGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATATAATTATACATTGCTGAA
*
40140797 ATTTATTTGTATATGGTTATACATTGTTGAAACTGAATTGTATATGGATATAAG
131 ATTAATTTGTATATGGTTATACATTGTTGAAACTGAATTGTATATGGATATAAG
*
40140851 TTGTTGAATTAATTTGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
1 TTGTTGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
* * *
40140916 TGAATTTGATTTGTATATAAAGATAAGTTGCCGAATTAATTTGTATATAATTATACATTGCTGAA
66 TGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATATAATTATACATTGCTGAA
*
40140981 ATTAATTTGTATATGGTTATACATTGTTGAAATTGAATTGTATATGGATATAAG
131 ATTAATTTGTATATGGTTATACATTGTTGAAACTGAATTGTATATGGATATAAG
* * *
40141035 TTGCTGAATTAATTCGTATATGGTTGTAAATTGCTGAAATTTATTTGTCTATGGTTATACATTAT
1 TTGTTGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
* * * * *
40141100 CGAAATTGGTTTGTATATGAAGATAAGTTGCCGAATTTGATTCGTATATGAA-TATATATTGTTG
66 TGAAATTGATTTGTATATGAAGATAAGTTGCCGAA-TTAATTCGTATAT-AATTATACATTGCTG
*
40141164 -AATTGATTTG
129 AAATTAATTTG
40141174 AGCATTGGAT
Statistics
Matches: 288, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
184 265 0.92
185 21 0.07
186 2 0.01
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (184 bp):
TTGTTGAATTAATTCGTATATGGTTGTACATTGCTGAAATTTATTTGTATATGGTTATACATTAT
TGAAATTGATTTGTATATGAAGATAAGTTGCCGAATTAATTCGTATATAATTATACATTGCTGAA
ATTAATTTGTATATGGTTATACATTGTTGAAACTGAATTGTATATGGATATAAG
Found at i:40147377 original size:27 final size:26
Alignment explanation
Indices: 40147320--40147403 Score: 71
Period size: 27 Copynumber: 3.1 Consensus size: 26
40147310 TAAATCTAAA
* * *
40147320 GAATGGTAGGTATGGTAAACTCTGATA-
1 GAAT-GTACGTATGGTGAACTTTGA-AG
*
40147347 GAATGATATGTATGGTGAACTTTGAAG
1 GAATG-TACGTATGGTGAACTTTGAAG
* *
40147374 GAATTGTACATATGGCGAACTTTGAAG
1 GAA-TGTACGTATGGTGAACTTTGAAG
40147401 GAA
1 GAA
40147404 CGGTTCTGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 2 0.04
27 44 0.92
28 2 0.04
ACGTcount: A:0.35, C:0.07, G:0.29, T:0.30
Consensus pattern (26 bp):
GAATGTACGTATGGTGAACTTTGAAG
Found at i:40149000 original size:51 final size:51
Alignment explanation
Indices: 40148941--40149224 Score: 299
Period size: 51 Copynumber: 5.6 Consensus size: 51
40148931 TATCGATGAA
* * * *
40148941 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * * * * *
40148992 CACATGTGTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATGTTGGT
* ** *
40149043 CACGTGTGTAGTACTGTGTGAAGGCTACTACGT-AATTGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
* * * *
40149093 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATG--TTGGT
** *
40149144 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
*
40149194 CACGTGTGTAGTACTATGTGAAGGCCACTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTAC
40149225 ATGTATCGAA
Statistics
Matches: 189, Mismatches: 37, Indels: 15
0.78 0.15 0.06
Matches are distributed among these distances:
49 2 0.01
50 75 0.40
51 111 0.59
52 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATGTTGGT
Found at i:40149117 original size:101 final size:102
Alignment explanation
Indices: 40148941--40149179 Score: 426
Period size: 101 Copynumber: 2.4 Consensus size: 102
40148931 TATCGATGAA
40148941 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
*
40149006 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
**
40149043 CACGTGTGTAGTACTGTGTGAAGGCTACTACGT-AATTGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
*
40149107 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
*
40149144 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAA
40149180 CCGTAAAACT
Statistics
Matches: 131, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
101 96 0.73
102 35 0.27
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
Found at i:40149202 original size:101 final size:101
Alignment explanation
Indices: 40148941--40149223 Score: 415
Period size: 101 Copynumber: 2.8 Consensus size: 101
40148931 TATCGATGAA
*
40148941 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAA-CAGTAAATGATGGTCACATGTGTAGTAC
* *
40149006 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
**
40149043 CACGTGTGTAGTACTGTGTGAAGGCTACTACGT-AATTGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACAG-TAAATGATGGTCACATGTGTAGTAC
40149107 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
65 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * *** * *
40149144 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCACGTGTGTAGTACT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACAGTAAATGATGGTCACATGTGTAGTACT
* *
40149209 ATGTGAAGGCCACTA
66 AAGTGAAGGCTACTA
40149224 CATGTATCGA
Statistics
Matches: 164, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
101 128 0.78
102 36 0.22
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAACAGTAAATGATGGTCACATGTGTAGTACT
AAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Found at i:40149266 original size:152 final size:150
Alignment explanation
Indices: 40148948--40149266 Score: 335
Period size: 152 Copynumber: 2.1 Consensus size: 150
40148938 GAACACGTGT
*
40148948 GTAGTACTGTGTGAAGGCTACTACGTGAATCAATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCAATAAATGATGGTCACATGTGTAGTACTAAGTGA
* * * * * *
40149013 AGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTAA
66 AGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATGTGAAGGCCACTACGTAA
* * *
40149078 TTGATAAATGATGGTCACATGT
131 ATGATAAA-GA-GGTAACATGG
** * * * * * *
40149100 GTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAA-GCTTTGGTCACGTGTGTAGTACTATGT
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCAATAAATG--ATGGTCACATGTGTAGTACTAAGT
*
40149163 GAAGGCTACTACGTGAACCGTA-AAAC-TTGATCACGTGTGTAGTACTATGTGAAGGCCACTACA
64 GAAGGCTACAACGTGAACCG-AGAAACTTTGATCACGTGTGTAGTACTATGTGAAGGCCACTAC-
40149226 TGTATCGAATGATAAA-A-GTAACATGG
127 -GTA---AATGATAAAGAGGTAACATGG
40149252 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
40149267 AAACCCCAAA
Statistics
Matches: 138, Mismatches: 21, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
150 1 0.01
151 36 0.26
152 88 0.64
153 4 0.03
154 1 0.01
156 8 0.06
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.29
Consensus pattern (150 bp):
GTAGTACTGTGTGAAGGCTACTACGTGAACCAATAAATGATGGTCACATGTGTAGTACTAAGTGA
AGGCTACAACGTGAACCGAGAAACTTTGATCACGTGTGTAGTACTATGTGAAGGCCACTACGTAA
ATGATAAAGAGGTAACATGG
Found at i:40156007 original size:44 final size:44
Alignment explanation
Indices: 40155944--40156032 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
40155934 TAAATTTGCT
40155944 TATTTAGTTAACAAAACTAGTACAATAGAAGTGCTACATTGTTG
1 TATTTAGTTAACAAAACTAGTACAATAGAAGTGCTACATTGTTG
40155988 TATTTAGTTAACAAAACTAGTACAATAGAAGTGCTACATTGTTG
1 TATTTAGTTAACAAAACTAGTACAATAGAAGTGCTACATTGTTG
40156032 T
1 T
40156033 GGTGGCACTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (44 bp):
TATTTAGTTAACAAAACTAGTACAATAGAAGTGCTACATTGTTG
Found at i:40160717 original size:30 final size:30
Alignment explanation
Indices: 40160683--40160763 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
40160673 TGGTTGACAC
* *
40160683 ATCCCTTTTCGTAATTTGATAACTGAAGTT
1 ATCCCTTTTCATAATTTGATAACCGAAGTT
* *
40160713 ATCCCTTTTCATAGTTCT-ACAACCGAAGTT
1 ATCCCTTTTCATAATT-TGATAACCGAAGTT
40160743 ATCCCTTTTCATAATTTGATA
1 ATCCCTTTTCATAATTTGATA
40160764 GTCGTCACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
29 1 0.02
30 41 0.95
31 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (30 bp):
ATCCCTTTTCATAATTTGATAACCGAAGTT
Found at i:40160777 original size:30 final size:31
Alignment explanation
Indices: 40160743--40160936 Score: 145
Period size: 30 Copynumber: 6.5 Consensus size: 31
40160733 AACCGAAGTT
*
40160743 ATCCCTTTTCATAATTTGATAGTCGTCA-CC
1 ATCCCTTTTCATAATTTGATAGTCGTAAGCC
* * *
40160773 ATCCCTTTTCATAGTTTGATGGT-GTCA-CC
1 ATCCCTTTTCATAATTTGATAGTCGTAAGCC
* * * *
40160802 ATTCCTTTTTATAATTTGATAGCCG-AAGCT
1 ATCCCTTTTCATAATTTGATAGTCGTAAGCC
* **
40160832 ATCTCTTTTCATAGA-TTGATAG-CCAAAGCC
1 ATCCCTTTTCATA-ATTTGATAGTCGTAAGCC
* *
40160862 ATCCCTTTTTATAGA-TTGATAGCCG-AAGCC
1 ATCCCTTTTCATA-ATTTGATAGTCGTAAGCC
* * * * *
40160892 ATCCCTTTTCATAGTTCGATGGTCATCA-CC
1 ATCCCTTTTCATAATTTGATAGTCGTAAGCC
40160922 ATCCCTTTTCATAAT
1 ATCCCTTTTCATAAT
40160937 CGATAGCCGA
Statistics
Matches: 132, Mismatches: 25, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
29 26 0.20
30 103 0.78
31 3 0.02
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.39
Consensus pattern (31 bp):
ATCCCTTTTCATAATTTGATAGTCGTAAGCC
Found at i:40160882 original size:60 final size:59
Alignment explanation
Indices: 40160773--40160959 Score: 191
Period size: 60 Copynumber: 3.2 Consensus size: 59
40160763 AGTCGTCACC
* *** * *
40160773 ATCCCTTTTCATAGTTTGAT-GGTGTCACCATTCCTTTTTATAATTTGATAGCCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCCATAACCATCCCTTTTTATAA-TTGATAGCCGAAGCT
* *
40160832 ATCTCTTTTCATAGATT-GATAGCCA-AAGCCATCCCTTTTTATAGATTGATAGCCGAAGCC
1 ATCCCTTTTCATAG-TTCGATAGCCATAA-CCATCCCTTTTTATA-ATTGATAGCCGAAGCT
* * * * *
40160892 ATCCCTTTTCATAGTTCGATGGTCATCACCATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCCATAACCATCCCTTTTTATAATTGATAGCCGAAGCT
*
40160951 ATTCCTTTT
1 ATCCCTTTT
40160960 TATTCGTCGA
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
59 41 0.38
60 64 0.60
61 2 0.02
ACGTcount: A:0.24, C:0.24, G:0.14, T:0.38
Consensus pattern (59 bp):
ATCCCTTTTCATAGTTCGATAGCCATAACCATCCCTTTTTATAATTGATAGCCGAAGCT
Found at i:40162845 original size:22 final size:22
Alignment explanation
Indices: 40162803--40162846 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40162793 AACATGTATA
*
40162803 GGATGTTATGTAATAGTAATGT
1 GGATGTTATGTAATAGAAATGT
*
40162825 GGATGTTTATGTTAT-GAAATGT
1 GGATG-TTATGTAATAGAAATGT
40162847 ATGGTGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (22 bp):
GGATGTTATGTAATAGAAATGT
Found at i:40174556 original size:37 final size:37
Alignment explanation
Indices: 40174514--40174675 Score: 204
Period size: 37 Copynumber: 4.4 Consensus size: 37
40174504 GGCGGATGTA
40174514 TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
* *
40174551 TAGCTCTTATGAGCATTTGGTGTGTTTATGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
* ** * *
40174588 TAGCTCTTATGATCATTTGATAAG-GTAT-CGGTTGCAT
1 TAGCTCTTATGAGCATTTG--GCGTGTTTACGGTTGGAT
*
40174625 TAGCTCTTATGAGCATTTGGCGTG-TTATCGATTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTA-CGGTTGGAT
40174662 TAGCTCTTATGAGC
1 TAGCTCTTATGAGC
40174676 CACGTGTTAT
Statistics
Matches: 106, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
35 2 0.02
36 1 0.01
37 99 0.93
38 3 0.03
39 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.41
Consensus pattern (37 bp):
TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
Found at i:40175198 original size:37 final size:37
Alignment explanation
Indices: 40175153--40175338 Score: 225
Period size: 37 Copynumber: 5.1 Consensus size: 37
40175143 GGTGGGTGTA
*
40175153 TAGCTCTTATGAGCATTTGGTGTGTTTACGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
*
40175190 TAGCTCTTATGAGCATTTGGCGTGTTTATGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
* * ** * * *
40175227 TAGCTCTTATGATCATTCGATGAAGTAT-CAGTTGGAT
1 TAGCTCTTATGAGCATTTGGCG-TGTTTACGGTTGGAT
*
40175264 TAGCTCTTATGAGCATTCGGCGTG-TTATCGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTA-CGGTTGGAT
* *
40175301 TAGCTCTTATGAGCATTTGACGTGCTT-CGGTTGGAT
1 TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
40175337 TA
1 TA
40175339 CTTGTGTACT
Statistics
Matches: 127, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
35 1 0.01
36 12 0.09
37 109 0.86
38 5 0.04
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.40
Consensus pattern (37 bp):
TAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGAT
Found at i:40175231 original size:74 final size:73
Alignment explanation
Indices: 40175153--40175338 Score: 257
Period size: 74 Copynumber: 2.5 Consensus size: 73
40175143 GGTGGGTGTA
* *
40175153 TAGCTCTTATGAGCATTTGGTGTGTTTACGGTTGGATTAGCTCTTATGAGCATTTGGCGTGTTTA
1 TAGCTCTTATGAGCATTTGATGTGTTT-CGGTTGGATTAGCTCTTATGAGCATTCGGCGTG-TTA
40175218 T-GGTTGGAT
64 TCGGTTGGAT
* * * * *
40175227 TAGCTCTTATGATCATTCGATGAAGTATCAGTTGGATTAGCTCTTATGAGCATTCGGCGTGTTAT
1 TAGCTCTTATGAGCATTTGATG-TGTTTCGGTTGGATTAGCTCTTATGAGCATTCGGCGTGTTAT
40175292 CGGTTGGAT
65 CGGTTGGAT
* *
40175301 TAGCTCTTATGAGCATTTGACGTGCTTCGGTTGGATTA
1 TAGCTCTTATGAGCATTTGATGTGTTTCGGTTGGATTA
40175339 CTTGTGTACT
Statistics
Matches: 96, Mismatches: 14, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
73 16 0.17
74 77 0.80
75 3 0.03
ACGTcount: A:0.19, C:0.13, G:0.27, T:0.40
Consensus pattern (73 bp):
TAGCTCTTATGAGCATTTGATGTGTTTCGGTTGGATTAGCTCTTATGAGCATTCGGCGTGTTATC
GGTTGGAT
Found at i:40175668 original size:639 final size:639
Alignment explanation
Indices: 40174493--40175711 Score: 1948
Period size: 639 Copynumber: 1.9 Consensus size: 639
40174483 CTTATTGTAC
*
40174493 TGTGTTATGCGGGCGGATGTATAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGATTAGCTCT
1 TGTGTTATGAGGGCGGATGTATAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGATTAGCTCT
* * *
40174558 TATGAGCATTTGGTGTGTTTATGGTTGGATTAGCTCTTATGATCATTTGATAAGGTATCGGTTGC
66 TATGAGCATTTGGCGTGTTTATGGTTGGATTAGCTCTTATGATCATTCGATAAGGTATCAGTTGC
* *
40174623 ATTAGCTCTTATGAGCATTTGGCGTGTTATCGATTGGATTAGCTCTTATGAGCCACGTGTTATCA
131 ATTAGCTCTTATGAGCATTCGGCGTGTTATCGATTGGATTAGCTCTTATGAGCCACGTGCTATCA
* * *
40174688 GTTGGATTACTTGTGTACTCATATCTGTAAGTCGTTCATCAAATCGTAAATTATTGTACTATAAC
196 GTTGGATTACTTGTGTACTCATATCTATAAGCCATTCATCAAATCGTAAATTATTGTACTATAAC
*
40174753 TTATATAATGACTTTGAATAGTTTGACATGTAAATGATATCTAAAATTGAATCTATTGTGGACAT
261 TTATATAATGACTTTGAATAGTTTGACATCTAAATGATATCTAAAATTGAATCTATTGTGGACAT
* * * *
40174818 ATATATTTTCTTAGAGATTATTATTTGAATCTTAATTTGAATTATGCAATTTATCGGTTGACTTT
326 ATATATTTTCTCAAAGATTATTATTTGAATCTTAATTTGAATTATGCAATTCATCGGTTGACATT
* *
40174883 GTAGATGGTAGGAAACACAAGTAGTTGAGTTATTATTGAATGAATTGTTGTATTTACTTCGATAA
391 GTAGATGGCAGGAAACACAAGTAGTTGAGTTATTATTGAATGAATTGTTATATTTACTTCGATAA
* *
40174948 AATTTATTGTTTCTGTACGTCAAACTTACCAAGCTTTAATAAGCTTACTTACGTTAATTTTTGTT
456 AATTTATTGTTTCTGTACGTCAAACTTACCAAGCTTCAATAAGCTTACTTACGTTAATTTCTGTT
*
40175013 ACTGTAGATACTTTCGAAGGTTGGACGATCGGATCAGCACTCAAGTTACACTATCCATCCTGAGT
521 ACTGTAGATACTTTCGAAGGTTGGACGATCGGATCAGCACTCAAGTCACACTATCCATCCTGAGT
40175078 GTACTGAGGTTCAACATTTGTTACGAACTCTCATGTTGTACTATCTTGTTCTGG
586 GTACTGAGGTTCAACATTTGTTACGAACTCTCATGTTGTACTATCTTGTTCTGG
* * *
40175132 TGTGTTATGAGGGTGGGTGTATAGCTCTTATGAGCATTTGGTGTGTTTACGGTTGGATTAGCTCT
1 TGTGTTATGAGGGCGGATGTATAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGATTAGCTCT
40175197 TATGAGCATTTGGCGTGTTTATGGTTGGATTAGCTCTTATGATCATTCGATGAA-GTATCAGTTG
66 TATGAGCATTTGGCGTGTTTATGGTTGGATTAGCTCTTATGATCATTCGAT-AAGGTATCAGTTG
* * *
40175261 GATTAGCTCTTATGAGCATTCGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCATTTGACGTGC
130 CATTAGCTCTTATGAGCATTCGGCGTGTTATCGATTGGATTAGCTCTTATGAGC----CACGTGC
* * *
40175326 T-TCGGTTGGATTACTTGTGTACTCATATCTATATGCCATTCATCATATCGTAAATTATTGTACT
191 TATCAGTTGGATTACTTGTGTACTCATATCTATAAGCCATTCATCAAATCGTAAATTATTGTACT
* *
40175390 ATAACTTATATAATGACTTTGAATGGTTTGACATCTAAATGATATTTAAAATTGAATCTATTGTG
256 ATAACTTATATAATGACTTTGAATAGTTTGACATCTAAATGATATCTAAAATTGAATCTATTGTG
*
40175455 GACATATATATTTTCTCAAAGATTATTATTTGAATCTTGATTTGAATTATGCAATTCATCGGTTG
321 GACATATATATTTTCTCAAAGATTATTATTTGAATCTTAATTTGAATTATGCAATTCATCGGTTG
* * * *
40175520 ACATTGTGGATGGCATGAAACACATGTAGTTGAGTTATTATTGAATTAA-T-TTATATTTACTTC
386 ACATTGTAGATGGCAGGAAACACAAGTAGTTGAGTTATTATTGAATGAATTGTTATATTTACTTC
* * * * *
40175583 -AGTAAGATTTATTGTTTTTGTACGTCAAACTTACTAAGC-TCAATGAGCTTACTTGCGTTAATT
451 GA-TAAAATTTATTGTTTCTGTACGTCAAACTTACCAAGCTTCAATAAGCTTACTTACGTTAATT
* *
40175646 TCTGTT-CTTGTAGATGCTTTCGAAGGTTGGACGATCGGATCAGCACTCAAGTCACATTATCCAT
515 TCTGTTAC-TGTAGATACTTTCGAAGGTTGGACGATCGGATCAGCACTCAAGTCACACTATCCAT
40175710 CC
579 CC
40175712 GTATTTGGTA
Statistics
Matches: 531, Mismatches: 42, Indels: 14
0.90 0.07 0.02
Matches are distributed among these distances:
638 1 0.00
639 252 0.47
640 48 0.09
641 1 0.00
642 223 0.42
643 6 0.01
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.40
Consensus pattern (639 bp):
TGTGTTATGAGGGCGGATGTATAGCTCTTATGAGCATTTGGCGTGTTTACGGTTGGATTAGCTCT
TATGAGCATTTGGCGTGTTTATGGTTGGATTAGCTCTTATGATCATTCGATAAGGTATCAGTTGC
ATTAGCTCTTATGAGCATTCGGCGTGTTATCGATTGGATTAGCTCTTATGAGCCACGTGCTATCA
GTTGGATTACTTGTGTACTCATATCTATAAGCCATTCATCAAATCGTAAATTATTGTACTATAAC
TTATATAATGACTTTGAATAGTTTGACATCTAAATGATATCTAAAATTGAATCTATTGTGGACAT
ATATATTTTCTCAAAGATTATTATTTGAATCTTAATTTGAATTATGCAATTCATCGGTTGACATT
GTAGATGGCAGGAAACACAAGTAGTTGAGTTATTATTGAATGAATTGTTATATTTACTTCGATAA
AATTTATTGTTTCTGTACGTCAAACTTACCAAGCTTCAATAAGCTTACTTACGTTAATTTCTGTT
ACTGTAGATACTTTCGAAGGTTGGACGATCGGATCAGCACTCAAGTCACACTATCCATCCTGAGT
GTACTGAGGTTCAACATTTGTTACGAACTCTCATGTTGTACTATCTTGTTCTGG
Found at i:40180181 original size:33 final size:33
Alignment explanation
Indices: 40180136--40180198 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
40180126 GCTTCGTCAT
* *
40180136 ATGTGAGTGGGTCATCATCTTCCTGTTTGGAAA
1 ATGTGAGCGGGTCATCATCTTCCTATTTGGAAA
40180169 ATGTGAGCGGGTCATCATCTTCCTATTTGG
1 ATGTGAGCGGGTCATCATCTTCCTATTTGG
40180199 CAAACTCAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (33 bp):
ATGTGAGCGGGTCATCATCTTCCTATTTGGAAA
Found at i:40185692 original size:10 final size:10
Alignment explanation
Indices: 40185679--40185704 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
40185669 AATTATTATT
40185679 AAATATTTAA
1 AAATATTTAA
40185689 AAATATTTAA
1 AAATATTTAA
40185699 AAATAT
1 AAATAT
40185705 ATATAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAATATTTAA
Found at i:40185750 original size:37 final size:38
Alignment explanation
Indices: 40185673--40185750 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
40185663 TGATAAAATT
* * *
40185673 ATTATTAAATATTTAAAAATATTTAAAAATATATATAA
1 ATTACTAAATATTAAAAAATATTTAAAAATATAGATAA
*
40185711 ATTACTAAATATTAAAAATATATTTTAAAATAT-GA-AA
1 ATTACTAAATATTAAAAA-ATATTTAAAAATATAGATAA
40185748 ATT
1 ATT
40185751 GATATAAACC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 5 0.14
38 17 0.49
39 13 0.37
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (38 bp):
ATTACTAAATATTAAAAAATATTTAAAAATATAGATAA
Found at i:40185780 original size:11 final size:11
Alignment explanation
Indices: 40185764--40185821 Score: 61
Period size: 10 Copynumber: 5.6 Consensus size: 11
40185754 ATAAACCTAT
40185764 AAAATATTATA
1 AAAATATTATA
40185775 AAAATATTAT-
1 AAAATATTATA
*
40185785 -AGATATTATA
1 AAAATATTATA
*
40185795 AAAA-ATTCTA
1 AAAATATTATA
*
40185805 ATAA-ATTATA
1 AAAATATTATA
40185815 AAAATAT
1 AAAATAT
40185822 AGAATATATG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 8 0.21
10 16 0.42
11 14 0.37
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (11 bp):
AAAATATTATA
Found at i:40185792 original size:20 final size:19
Alignment explanation
Indices: 40185766--40185821 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
40185756 AAACCTATAA
40185766 AATATTATAAAAATATTAT
1 AATATTATAAAAATATTAT
*
40185785 AGATATTATAAAAA-ATTCT
1 A-ATATTATAAAAATATTAT
40185804 AATAAATTATAAAAATAT
1 AAT--ATTATAAAAATAT
40185822 AGAATATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 2 0.06
19 6 0.19
20 22 0.69
21 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
AATATTATAAAAATATTAT
Found at i:40186059 original size:6 final size:7
Alignment explanation
Indices: 40186023--40186065 Score: 50
Period size: 7 Copynumber: 5.6 Consensus size: 7
40186013 GGTTGAACCA
40186023 ATTTTTCT
1 ATTTTT-T
40186031 ATTTTTAAT
1 ATTTTT--T
40186040 ATGTTTTT
1 AT-TTTTT
40186048 ATTTTTT
1 ATTTTTT
40186055 ATTTTTT
1 ATTTTTT
40186062 ATTT
1 ATTT
40186066 AATTGAACTG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
7 16 0.50
8 9 0.28
9 3 0.09
10 4 0.12
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (7 bp):
ATTTTTT
Found at i:40186376 original size:28 final size:28
Alignment explanation
Indices: 40186325--40186509 Score: 89
Period size: 28 Copynumber: 6.5 Consensus size: 28
40186315 TTATGTTTGT
40186325 TTTTAATAATTTTTATAAGTTTATATCAA
1 TTTTAATAATTTTTATAAGTTTATAT-AA
*
40186354 TTTTAAT-ATTTTTATAA-TATTATATTA
1 TTTTAATAATTTTTATAAGT-TTATATAA
* * * * *
40186381 TTTTAAAAAATTCTCATACGTTTTTTTATAA
1 TTTT-AATAATTTTTATAAG--TTTATATAA
* *
40186412 TTTTAAATAA-TTTTAT-ATTTTTTATAA
1 TTTT-AATAATTTTTATAAGTTTATATAA
* * *
40186439 TTTCT--TAGATTTTTTTATGTTTTTATAA
1 TTT-TAATA-ATTTTTATAAGTTTATATAA
*
40186467 TATTT-ATAAGTTTTTATAATTTTA-ATAA
1 T-TTTAATAA-TTTTTATAAGTTTATATAA
*
40186495 GTTTATATCAATTTT
1 TTTTA-AT-AATTTT
40186510 AATATTTTAA
Statistics
Matches: 120, Mismatches: 20, Indels: 32
0.70 0.12 0.19
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 26 0.22
28 35 0.29
29 34 0.28
30 6 0.05
31 15 0.12
32 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (28 bp):
TTTTAATAATTTTTATAAGTTTATATAA
Found at i:40186441 original size:10 final size:10
Alignment explanation
Indices: 40186402--40186489 Score: 64
Period size: 10 Copynumber: 9.4 Consensus size: 10
40186392 TCTCATACGT
40186402 TTTTTTATAA
1 TTTTTTATAA
**
40186412 TTTTAAATAA
1 TTTTTTATAA
40186422 --TTTTAT-A
1 TTTTTTATAA
40186429 TTTTTTATAA
1 TTTTTTATAA
* *
40186439 TTTCTTA-GA
1 TTTTTTATAA
40186448 TTTTTT-T-A
1 TTTTTTATAA
40186456 TGTTTTTATAA
1 T-TTTTTATAA
*
40186467 -TATTTATAA
1 TTTTTTATAA
*
40186476 GTTTTTATAA
1 TTTTTTATAA
40186486 TTTT
1 TTTT
40186490 AATAAGTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
7 1 0.02
8 6 0.10
9 25 0.42
10 27 0.45
11 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:40186481 original size:19 final size:19
Alignment explanation
Indices: 40186457--40186549 Score: 74
Period size: 19 Copynumber: 5.0 Consensus size: 19
40186447 ATTTTTTTAT
40186457 GTTTTTATAATATTTATAA
1 GTTTTTATAATATTTATAA
40186476 GTTTTTATAAT-TTTAATAA
1 GTTTTTATAATATTT-ATAA
* *
40186495 GTTTATATCA-ATTT-TAA
1 GTTTTTATAATATTTATAA
40186512 -TATTTTA-AATATTTA-ATA
1 GT-TTTTATAATATTTATA-A
40186530 -TTATTTATATATATTTATAA
1 GTT-TTTATA-ATATTTATAA
40186550 TTGTTATGCT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
16 2 0.03
17 13 0.22
18 9 0.15
19 27 0.45
20 8 0.13
21 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (19 bp):
GTTTTTATAATATTTATAA
Found at i:40186509 original size:20 final size:19
Alignment explanation
Indices: 40186326--40186513 Score: 77
Period size: 19 Copynumber: 9.9 Consensus size: 19
40186316 TATGTTTGTT
*
40186326 TTTA-ATAATTTTTATAAG
1 TTTATATAATTTTAATAAG
40186344 TTTATATCAATTTTAAT-A-
1 TTTATAT-AATTTTAATAAG
* * * *
40186362 TTTTTATAATATTATATTAT
1 TTTATATAATTTTA-ATAAG
* * * * *
40186382 TTTAAAAAATTCTCATACG
1 TTTATATAATTTTAATAAG
*
40186401 TTTTTTTATAATTTTAAATAA-
1 --TTTATATAATTTT-AATAAG
* *
40186422 TTT-TATATTTTTTATAA-
1 TTTATATAATTTTAATAAG
* ** *
40186439 TTTCT-TAGATTTTTTTATG
1 TTTATATA-ATTTTAATAAG
*
40186458 TTTTTATAATATTT-ATAAG
1 TTTATATAAT-TTTAATAAG
*
40186477 TTTTTATAATTTTAATAAG
1 TTTATATAATTTTAATAAG
40186496 TTTATATCAATTTTAATA
1 TTTATAT-AATTTTAATA
40186514 TTTTAAATAT
Statistics
Matches: 128, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
17 15 0.12
18 31 0.24
19 39 0.30
20 31 0.24
21 9 0.07
22 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TTTATATAATTTTAATAAG
Found at i:40186547 original size:10 final size:9
Alignment explanation
Indices: 40186460--40186550 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 9
40186450 TTTTTATGTT
40186460 TTTATAATA
1 TTTATAATA
*
40186469 TTTATAAGTT
1 TTTATAA-TA
40186479 TTTATAAT-
1 TTTATAATA
*
40186487 TTTAATAA-G
1 TTT-ATAATA
40186496 TTTAT-ATCAA
1 TTTATAAT--A
40186506 TTT-TAATA
1 TTTATAATA
40186514 TTT-TAAATA
1 TTTAT-AATA
*
40186523 TTTAATATTA
1 TTT-ATAATA
40186533 TTTATATATA
1 TTTATA-ATA
40186543 TTTATAAT
1 TTTATAAT
40186551 TGTTATGCTT
Statistics
Matches: 67, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
7 1 0.01
8 10 0.15
9 28 0.42
10 27 0.40
11 1 0.01
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (9 bp):
TTTATAATA
Found at i:40189350 original size:10 final size:10
Alignment explanation
Indices: 40189337--40189379 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
40189327 AAATTTTAAA
40189337 TTTTAAATTT
1 TTTTAAATTT
*
40189347 TTTTAAAATACT
1 TTTT-AAAT-TT
40189359 TTTTAAATTT
1 TTTTAAATTT
*
40189369 TTTTTAATTT
1 TTTTAAATTT
40189379 T
1 T
40189380 AAAATATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
10 15 0.54
11 8 0.29
12 5 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:40189373 original size:12 final size:12
Alignment explanation
Indices: 40189308--40189375 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 12
40189298 ATTTTTTTAA
40189308 TTTTAAAATACTTT
1 TTTTAAAAT--TTT
40189322 TTTTAAAATTTT
1 TTTTAAAATTTT
40189334 AAATTTT-AAA-TTT
1 ---TTTTAAAATTTT
**
40189347 TTTTAAAATACT
1 TTTTAAAATTTT
40189359 TTTT-AAATTTT
1 TTTTAAAATTTT
40189370 TTTTAA
1 TTTTAA
40189376 TTTTAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
10 4 0.09
11 12 0.27
12 9 0.20
13 3 0.07
14 12 0.27
15 4 0.09
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:40189390 original size:40 final size:40
Alignment explanation
Indices: 40189308--40189429 Score: 133
Period size: 39 Copynumber: 3.0 Consensus size: 40
40189298 ATTTTTTTAA
* * *
40189308 TTTTAAAATACTTTTTTTAAA--ATTTTAAATTTT-AAATTT
1 TTTTAAAATAC--TTTTTAAATTTTTTTTAATTTTAAAATAT
40189347 TTTTAAAATACTTTTTAAATTTTTTTTAATTTTAAAATAT
1 TTTTAAAATACTTTTTAAATTTTTTTTAATTTTAAAATAT
*
40189387 TTTTAAAATACCTTTTTAAACTTTTGTCTTAATTTTTAAAATA
1 TTTTAAAATA-CTTTTTAAA-TTTT-TTTTAA-TTTTAAAATA
40189430 AATTTTTGGT
Statistics
Matches: 72, Mismatches: 4, Indels: 9
0.85 0.05 0.11
Matches are distributed among these distances:
37 8 0.11
39 21 0.29
40 15 0.21
41 9 0.12
42 4 0.06
43 5 0.07
44 10 0.14
ACGTcount: A:0.37, C:0.05, G:0.01, T:0.57
Consensus pattern (40 bp):
TTTTAAAATACTTTTTAAATTTTTTTTAATTTTAAAATAT
Found at i:40189402 original size:29 final size:29
Alignment explanation
Indices: 40189347--40189402 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
40189337 TTTTAAATTT
***
40189347 TTTTAAAATACTTTTTAAATTTTTTTTAA
1 TTTTAAAATACTTTTTAAATACCTTTTAA
40189376 TTTTAAAATA-TTTTTAAAATACCTTTT
1 TTTTAAAATACTTTTT-AAATACCTTTT
40189403 TAAACTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (29 bp):
TTTTAAAATACTTTTTAAATACCTTTTAA
Found at i:40190946 original size:22 final size:21
Alignment explanation
Indices: 40190921--40190961 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
40190911 TTTGAAGTTC
40190921 GTTGTCGCAACATTGAGTGGTG
1 GTTGTCGCAACATT-AGTGGTG
40190943 GTTGTCGCAACATTAGTGG
1 GTTGTCGCAACATTAGTGG
40190962 CTATATGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.20, C:0.15, G:0.34, T:0.32
Consensus pattern (21 bp):
GTTGTCGCAACATTAGTGGTG
Found at i:40193439 original size:26 final size:26
Alignment explanation
Indices: 40193373--40193439 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
40193363 CTTTACATAT
*
40193373 ATGCTCACACGAGCTATGAAAAGAGT
1 ATGCTCACACGAGCTATGAAAAGAGC
* * *
40193399 ATGCTCACACAAGCTATGAAATGGGC
1 ATGCTCACACGAGCTATGAAAAGAGC
* *
40193425 CTGCTCACATGAGCT
1 ATGCTCACACGAGCT
40193440 GTGGGTCAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (26 bp):
ATGCTCACACGAGCTATGAAAAGAGC
Found at i:40198267 original size:17 final size:17
Alignment explanation
Indices: 40198240--40198273 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
40198230 TGGTGAGGTA
40198240 TTTAATTTTC-TATTTT
1 TTTAATTTTCTTATTTT
40198256 TTTAACTTTTCTTATTTT
1 TTTAA-TTTTCTTATTTT
40198274 CAGTAAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 5 0.31
18 6 0.38
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTAATTTTCTTATTTT
Found at i:40198771 original size:21 final size:20
Alignment explanation
Indices: 40198747--40198827 Score: 73
Period size: 21 Copynumber: 4.2 Consensus size: 20
40198737 AAAAGAACTC
*
40198747 GAAAAAGAGATTGAAAAAGAA
1 GAAAAAGAAATTGAAAAAG-A
** *
40198768 GAAAAAGAAAAAGAAGAAAAA
1 GAAAAAGAAATTGAA-AAAGA
40198789 GAAAAAG-AA--GAAAAAGA
1 GAAAAAGAAATTGAAAAAGA
40198806 G--AAAGAAATTGAAAAAGA
1 GAAAAAGAAATTGAAAAAGA
40198824 GAAA
1 GAAA
40198828 GAAATCAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
15 4 0.08
16 2 0.04
17 5 0.10
18 12 0.24
20 3 0.06
21 20 0.41
22 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (20 bp):
GAAAAAGAAATTGAAAAAGA
Found at i:40198773 original size:9 final size:9
Alignment explanation
Indices: 40198726--40198809 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
40198716 TAATAAACTC
40198726 GAAAAAGAA
1 GAAAAAGAA
*
40198735 GGAAAAGAA
1 GAAAAAGAA
40198744 CTCGAAAAAGAGA
1 ---GAAAAAGA-A
40198757 TTGAAAAAGAA
1 --GAAAAAGAA
40198768 G--AAA-AA
1 GAAAAAGAA
40198774 GAAAAAGAA
1 GAAAAAGAA
40198783 G--AAA-AA
1 GAAAAAGAA
40198789 GAAAAAGAA
1 GAAAAAGAA
40198798 GAAAAAG-A
1 GAAAAAGAA
40198806 GAAA
1 GAAA
40198810 GAAATTGAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 21
0.72 0.03 0.24
Matches are distributed among these distances:
6 6 0.10
7 6 0.10
8 11 0.18
9 21 0.34
11 1 0.02
12 16 0.26
13 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.23, T:0.04
Consensus pattern (9 bp):
GAAAAAGAA
Found at i:40198777 original size:6 final size:6
Alignment explanation
Indices: 40198766--40198831 Score: 55
Period size: 6 Copynumber: 11.0 Consensus size: 6
40198756 ATTGAAAAAG
* *
40198766 AAGAAA AAGAAA AAGAAGA AA-AAGA AA-AAG AAGAAA AAGAGA AAGAAA
1 AAGAAA AAGAAA AAGAA-A AAGAA-A AAGAAA AAGAAA AAGAAA AAGAAA
** *
40198814 TTGAAA AAGAGA AAGAAA
1 AAGAAA AAGAAA AAGAAA
40198832 TCAAAAAAGA
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
5 2 0.04
6 43 0.90
7 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:40198777 original size:15 final size:15
Alignment explanation
Indices: 40198759--40198812 Score: 99
Period size: 15 Copynumber: 3.6 Consensus size: 15
40198749 AAAAGAGATT
40198759 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
40198774 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
40198789 GAAAAAGAAGAAAAA
1 GAAAAAGAAGAAAAA
*
40198804 GAGAAAGAA
1 GAAAAAGAA
40198813 ATTGAAAAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAGAAAAA
Found at i:40198819 original size:18 final size:18
Alignment explanation
Indices: 40198798--40198832 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
40198788 AGAAAAAGAA
40198798 GAAAAAGAGAAAGAAATT
1 GAAAAAGAGAAAGAAATT
40198816 GAAAAAGAGAAAGAAAT
1 GAAAAAGAGAAAGAAAT
40198833 CAAAAAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.09
Consensus pattern (18 bp):
GAAAAAGAGAAAGAAATT
Found at i:40198831 original size:30 final size:30
Alignment explanation
Indices: 40198750--40198853 Score: 76
Period size: 30 Copynumber: 3.6 Consensus size: 30
40198740 AGAACTCGAA
*
40198750 AAAGAGATTGAAAAAGAAGAAA-AAGAAAAAG
1 AAAGAAATTGAAAAAG-AGAAAGAA-AAAAAG
** *
40198781 -AAGAAAAAG-AAAA-AG-AAGAAAAAGAG
1 AAAGAAATTGAAAAAGAGAAAGAAAAAAAG
*
40198807 AAAGAAATTGAAAAAGAGAAAGAAATCAAA-
1 AAAGAAATTGAAAAAGAGAAAGAAA-AAAAG
* *
40198837 AAAGAATTTGAGAAAGA
1 AAAGAAATTGAAAAAGA
40198854 AGATAGTGAG
Statistics
Matches: 57, Mismatches: 10, Indels: 13
0.71 0.12 0.16
Matches are distributed among these distances:
26 7 0.12
27 11 0.19
28 4 0.07
29 6 0.11
30 27 0.47
31 2 0.04
ACGTcount: A:0.70, C:0.01, G:0.21, T:0.08
Consensus pattern (30 bp):
AAAGAAATTGAAAAAGAGAAAGAAAAAAAG
Found at i:40198838 original size:18 final size:18
Alignment explanation
Indices: 40198799--40198841 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
40198789 GAAAAAGAAG
**
40198799 AAAAAGAGAAAGAAATTG
1 AAAAAGAGAAAGAAATCA
40198817 AAAAAGAGAAAGAAATCA
1 AAAAAGAGAAAGAAATCA
40198835 AAAAAGA
1 AAAAAGA
40198842 ATTTGAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (18 bp):
AAAAAGAGAAAGAAATCA
Found at i:40203053 original size:6 final size:6
Alignment explanation
Indices: 40203035--40203090 Score: 60
Period size: 6 Copynumber: 9.2 Consensus size: 6
40203025 TGCAAATGTA
* *
40203035 TCATTT CTCATTT TCATTT TCATTT TCATTT CCATTT CCA-TT TCTATTT
1 TCATTT -TCATTT TCATTT TCATTT TCATTT TCATTT TCATTT TC-ATTT
*
40203084 CCATTT T
1 TCATTT T
40203091 GAGAAACCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
5 3 0.07
6 31 0.72
7 9 0.21
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (6 bp):
TCATTT
Found at i:40203065 original size:18 final size:18
Alignment explanation
Indices: 40203035--40203090 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
40203025 TGCAAATGTA
*
40203035 TCATTTCTCATTTTCATTT
1 TCATTT-TCATTTCCATTT
40203054 TCATTTTCATTTCCATTT
1 TCATTTTCATTTCCATTT
*
40203072 CCA-TTTCTATTTCCATTT
1 TCATTTTC-ATTTCCATTT
40203090 T
1 T
40203091 GAGAAACCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.12
18 23 0.70
19 6 0.18
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (18 bp):
TCATTTTCATTTCCATTT
Found at i:40207981 original size:25 final size:25
Alignment explanation
Indices: 40207947--40208096 Score: 170
Period size: 25 Copynumber: 6.3 Consensus size: 25
40207937 GTTTAGCGTA
* *
40207947 CTCTCTGATTTTTAGCACGTCCGTG
1 CTCTCTGATTATTAGCACGTCAGTG
* *
40207972 CTCTCTGATTATTTGCACATCAGTG
1 CTCTCTGATTATTAGCACGTCAGTG
*
40207997 CTCTCTGATTATTAACACGTCAGTG
1 CTCTCTGATTATTAGCACGTCAGTG
40208022 CTCTCTGATTATTAGCACGTC-GTG
1 CTCTCTGATTATTAGCACGTCAGTG
* *
40208046 CTCTCTAATTACTAGCACG-C--T-
1 CTCTCTGATTATTAGCACGTCAGTG
* *
40208067 CT-T-TGATTATTAGCACATTAGTG
1 CTCTCTGATTATTAGCACGTCAGTG
40208090 CTCTCTG
1 CTCTCTG
40208097 TTTAGCACAT
Statistics
Matches: 105, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
19 11 0.10
20 1 0.01
21 2 0.02
22 2 0.02
23 3 0.03
24 21 0.20
25 65 0.62
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.39
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACGTCAGTG
Found at i:40208102 original size:22 final size:22
Alignment explanation
Indices: 40208076--40208144 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
40208066 TCTTTGATTA
40208076 TTAGCACATTAGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCTGT
40208098 TTAGCACATTCA-TGCTCTCTGT
1 TTAGCACATT-AGTGCTCTCTGT
* * * *
40208120 ATAACACTTTAGTGCTCTCTAT
1 TTAGCACATTAGTGCTCTCTGT
40208142 TTA
1 TTA
40208145 ATAGTGCATA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
21 1 0.03
22 38 0.95
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCTGT
Found at i:40209544 original size:47 final size:47
Alignment explanation
Indices: 40209404--40209544 Score: 187
Period size: 47 Copynumber: 3.0 Consensus size: 47
40209394 CATGGCAATA
* *
40209404 TGTGATATGTGATTTTCGTGTAAGACCATATCTGGGATATCGCATCGG
1 TGTGATATGTGA-TTCCGTGTAAGACCATATCTGGGATATGGCATCGG
* * * *
40209452 TGTGATATGTGCTACTGTGTAAGACCATATCTGGGATATGACATCGG
1 TGTGATATGTGATTCCGTGTAAGACCATATCTGGGATATGGCATCGG
40209499 TGTGATATGTGATTCCGTGTAAGACCATAGT-T-GGACTATGGCATCG
1 TGTGATATGTGATTCCGTGTAAGACCATA-TCTGGGA-TATGGCATCG
40209545 AGAAAACGAA
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
46 3 0.04
47 66 0.81
48 12 0.15
ACGTcount: A:0.24, C:0.15, G:0.28, T:0.33
Consensus pattern (47 bp):
TGTGATATGTGATTCCGTGTAAGACCATATCTGGGATATGGCATCGG
Found at i:40211457 original size:156 final size:156
Alignment explanation
Indices: 40211173--40211485 Score: 626
Period size: 156 Copynumber: 2.0 Consensus size: 156
40211163 TTTATTTAAA
40211173 AAGTCTAAATTGACATGTGATCCCGAAAATTATTACAGTAAGAGAGTAGGTATTCTTGATATAGT
1 AAGTCTAAATTGACATGTGATCCCGAAAATTATTACAGTAAGAGAGTAGGTATTCTTGATATAGT
40211238 AAAACAAGGAAATTTCGAGGACGAAATTTCTTTTAAGGGGTAGAGAAATGTAATACCCCGAAAAT
66 AAAACAAGGAAATTTCGAGGACGAAATTTCTTTTAAGGGGTAGAGAAATGTAATACCCCGAAAAT
40211303 TTTTACAGTAAGATATTATCTTTGAT
131 TTTTACAGTAAGATATTATCTTTGAT
40211329 AAGTCTAAATTGACATGTGATCCCGAAAATTATTACAGTAAGAGAGTAGGTATTCTTGATATAGT
1 AAGTCTAAATTGACATGTGATCCCGAAAATTATTACAGTAAGAGAGTAGGTATTCTTGATATAGT
40211394 AAAACAAGGAAATTTCGAGGACGAAATTTCTTTTAAGGGGTAGAGAAATGTAATACCCCGAAAAT
66 AAAACAAGGAAATTTCGAGGACGAAATTTCTTTTAAGGGGTAGAGAAATGTAATACCCCGAAAAT
40211459 TTTTACAGTAAGATATTATCTTTGAT
131 TTTTACAGTAAGATATTATCTTTGAT
40211485 A
1 A
40211486 TAGTAAGGAA
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
156 157 1.00
ACGTcount: A:0.39, C:0.11, G:0.19, T:0.31
Consensus pattern (156 bp):
AAGTCTAAATTGACATGTGATCCCGAAAATTATTACAGTAAGAGAGTAGGTATTCTTGATATAGT
AAAACAAGGAAATTTCGAGGACGAAATTTCTTTTAAGGGGTAGAGAAATGTAATACCCCGAAAAT
TTTTACAGTAAGATATTATCTTTGAT
Found at i:40217658 original size:28 final size:27
Alignment explanation
Indices: 40217586--40217670 Score: 107
Period size: 27 Copynumber: 3.1 Consensus size: 27
40217576 ATCACATTAA
* *
40217586 GAAAGGAAAGTCTTTGTGGCGAAACAT
1 GAAAGAAAAGTCTTTGTGGCGAAATAT
* *
40217613 GAAAGAAAATTCTTTGTGGTGAAATAT
1 GAAAGAAAAGTCTTTGTGGCGAAATAT
* *
40217640 GAAAGAAAAAGCCTTTGTGGCGAATTAT
1 GAAAG-AAAAGTCTTTGTGGCGAAATAT
40217668 GAA
1 GAA
40217671 GGGATAACCT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 28 0.57
28 21 0.43
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (27 bp):
GAAAGAAAAGTCTTTGTGGCGAAATAT
Found at i:40220734 original size:42 final size:42
Alignment explanation
Indices: 40220602--40220827 Score: 153
Period size: 42 Copynumber: 5.4 Consensus size: 42
40220592 CTCGGTGGAT
* *
40220602 TCAGCACTTAGCAACCA-CATTAAATTCAGTGATACGGGGAA
1 TCAGCACATAGCAACCACCTTTAAATTCAGTGATACGGGGAA
* **
40220643 TCAGCAGATAGCAACC-CCTTTCACAA-TCAAAGATACGGTGGAA
1 TCAGCACATAGCAACCACCTTT-A-AATTCAGTGATACGG-GGAA
* * * * *
40220686 TCAGCACTTAGAAACCACCTTTATATTCAGTGATATGGAGAA
1 TCAGCACATAGCAACCACCTTTAAATTCAGTGATACGGGGAA
*
40220728 TCAGCACATAGCAA-C-CCTTTCACAA-TCAAAT-ATACGGTGGAA
1 TCAGCACATAGCAACCACCTTT-A-AATTC-AGTGATACGG-GGAA
* * * * **
40220770 TCAGCACTTAGCAACGACCTTTAGAA-TCAATAATTTGGGGAA
1 TCAGCACATAGCAACCACCTTTA-AATTCAGTGATACGGGGAA
* *
40220812 TCAACACTTAGCAACC
1 TCAGCACATAGCAACC
40220828 CCTCGGGGAA
Statistics
Matches: 146, Mismatches: 26, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
40 5 0.03
41 26 0.18
42 67 0.46
43 38 0.26
44 10 0.07
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (42 bp):
TCAGCACATAGCAACCACCTTTAAATTCAGTGATACGGGGAA
Found at i:40220739 original size:85 final size:85
Alignment explanation
Indices: 40220594--40220830 Score: 318
Period size: 84 Copynumber: 2.8 Consensus size: 85
40220584 ATCCGTTACT
* * * *
40220594 CGGTGGATTCAGCACTTAGCAACCA-CATTAAATTCAGTGATACGGGGAATCAGCAGATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATATGGGGAATCAGCACATAGCAAC
40220658 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* * *
40220678 CGGTGGAATCAGCACTTAGAAACCACCTTTATATTCAGTGATATGGAGAATCAGCACATAGCAA-
1 CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATATGGGGAATCAGCACATAGCAAC
*
40220742 CCCTTTCACAATCAAATATA
66 CCCTTTCACAATCAAAGATA
* * * * * *
40220762 CGGTGGAATCAGCACTTAGCAACGACCTTTAGAA-TCAATAATTTGGGGAATCAACACTTAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTA-AATTCAGTGATATGGGGAATCAGCACATAGCAA
40220826 CCCCT
65 CCCCT
40220831 CGGGGAATCT
Statistics
Matches: 133, Mismatches: 17, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
84 95 0.71
85 38 0.29
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (85 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTAAATTCAGTGATATGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:40220849 original size:26 final size:26
Alignment explanation
Indices: 40220806--40220856 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
40220796 TCAATAATTT
*
40220806 GGGGAATCAACACTTAGCAACCCCTC
1 GGGGAATCAACACATAGCAACCCCTC
** *
40220832 GGGGAATCTTCACATAGCGACCCCT
1 GGGGAATCAACACATAGCAACCCCT
40220857 TTTTATCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.27, C:0.33, G:0.22, T:0.18
Consensus pattern (26 bp):
GGGGAATCAACACATAGCAACCCCTC
Found at i:40227206 original size:18 final size:17
Alignment explanation
Indices: 40227183--40227230 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
40227173 GAAAAATACT
40227183 AACTAAGAAAAAATAAA
1 AACTAAGAAAAAATAAA
*
40227200 CACCTAA-AAAGAAATAAA
1 -AACTAAGAAA-AAATAAA
40227218 AACTAAAGAAAAA
1 AACT-AAGAAAAA
40227231 GAATTCCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 6 0.24
18 16 0.64
19 3 0.12
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.10
Consensus pattern (17 bp):
AACTAAGAAAAAATAAA
Found at i:40238997 original size:26 final size:26
Alignment explanation
Indices: 40238967--40239045 Score: 158
Period size: 26 Copynumber: 3.0 Consensus size: 26
40238957 ATATTTGGAG
40238967 TATGAATTGTTGATTTATTTAACATT
1 TATGAATTGTTGATTTATTTAACATT
40238993 TATGAATTGTTGATTTATTTAACATT
1 TATGAATTGTTGATTTATTTAACATT
40239019 TATGAATTGTTGATTTATTTAACATT
1 TATGAATTGTTGATTTATTTAACATT
40239045 T
1 T
40239046 GATAAAGGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.54
Consensus pattern (26 bp):
TATGAATTGTTGATTTATTTAACATT
Found at i:40258836 original size:8 final size:9
Alignment explanation
Indices: 40258809--40258834 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
40258799 ATTCTAAATT
40258809 TTAAAAAAA
1 TTAAAAAAA
40258818 TTAAAAAAA
1 TTAAAAAAA
40258827 TTAAAAAA
1 TTAAAAAA
40258835 TTCCATGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:40259223 original size:46 final size:45
Alignment explanation
Indices: 40259173--40259299 Score: 141
Period size: 43 Copynumber: 2.8 Consensus size: 45
40259163 ACGTAGGAAT
* * *
40259173 CAAATTACGAAAATATAATATCCTAAAATAATATCCTATTAGAAAA
1 CAAATTGCTAAAAGATAATATCCT-AAATAATATCCTATTAGAAAA
* * * *
40259219 CAAATTGCTAAGAGATAATAT-CT-TATAATATCCTATTAGGAAT
1 CAAATTGCTAAAAGATAATATCCTAAATAATATCCTATTAGAAAA
* *
40259262 CAAATTGCTAAAAGATAATATCTTATACTAATATCCTA
1 CAAATTGCTAAAAGATAATATCCTA-AATAATATCCTA
40259300 ACATCTCTCC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
43 37 0.55
44 1 0.01
45 2 0.03
46 27 0.40
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.32
Consensus pattern (45 bp):
CAAATTGCTAAAAGATAATATCCTAAATAATATCCTATTAGAAAA
Found at i:40259256 original size:43 final size:43
Alignment explanation
Indices: 40259200--40259288 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
40259190 ATATCCTAAA
*
40259200 ATAATATCCTATTAGAAAACAAATTGCTAAGAGATAATATCTT
1 ATAATATCCTATTAGAAAACAAATTGCTAAAAGATAATATCTT
* *
40259243 ATAATATCCTATTAGGAATCAAATTGCTAAAAGATAATATCTT
1 ATAATATCCTATTAGAAAACAAATTGCTAAAAGATAATATCTT
40259286 ATA
1 ATA
40259289 CTAATATCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (43 bp):
ATAATATCCTATTAGAAAACAAATTGCTAAAAGATAATATCTT
Found at i:40262433 original size:41 final size:41
Alignment explanation
Indices: 40262376--40262458 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
40262366 TATTGAATTC
*
40262376 TTTCTTTTATTGAAGAACACGTCAAAACCTAAATCCTAACA
1 TTTCTTTTATTGAAGAACACGTCAAAAACTAAATCCTAACA
*
40262417 TTTCTTTTATTGAAGAACATGTCAAAAACTAAATCCTAACA
1 TTTCTTTTATTGAAGAACACGTCAAAAACTAAATCCTAACA
40262458 T
1 T
40262459 ACTTCCATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.40, C:0.19, G:0.07, T:0.34
Consensus pattern (41 bp):
TTTCTTTTATTGAAGAACACGTCAAAAACTAAATCCTAACA
Found at i:40265302 original size:59 final size:60
Alignment explanation
Indices: 40265233--40265352 Score: 215
Period size: 59 Copynumber: 2.0 Consensus size: 60
40265223 AAAAGAAAAC
* *
40265233 TTTTTATAGTTCTATGTTTTGGTTCAATTGGTTCGAGCCCACACTTGAAGCAGTTCGTGG
1 TTTTTATAGTTCCATGTTTTGGTTCAATTGGTTCGAGCCCACACTTGAAGCAGCTCGTGG
40265293 TTTTT-TAGTTCCATGTTTTGGTTCAATTGGTTCGAGCCCACACTTGAAGCAGCTCGTGG
1 TTTTTATAGTTCCATGTTTTGGTTCAATTGGTTCGAGCCCACACTTGAAGCAGCTCGTGG
40265352 T
1 T
40265353 ACGAGAATAA
Statistics
Matches: 58, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 53 0.91
60 5 0.09
ACGTcount: A:0.17, C:0.18, G:0.23, T:0.41
Consensus pattern (60 bp):
TTTTTATAGTTCCATGTTTTGGTTCAATTGGTTCGAGCCCACACTTGAAGCAGCTCGTGG
Found at i:40269498 original size:6 final size:6
Alignment explanation
Indices: 40269479--40269529 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
40269469 AGGTTTCCAA
* * * * *
40269479 AAATCG AAACGG AAATGG AAATGG AAATGG AAATGA AAATGA AAATAG
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG
40269527 AAA
1 AAA
40269530 CTTACAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.59, C:0.04, G:0.24, T:0.14
Consensus pattern (6 bp):
AAATGG
Found at i:40270434 original size:18 final size:18
Alignment explanation
Indices: 40270413--40270451 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
40270403 ATCATATCTG
40270413 CAAGGCAATCCTATTCGC
1 CAAGGCAATCCTATTCGC
* *
40270431 CAA-GTAATTCTATTCGC
1 CAAGGCAATCCTATTCGC
40270448 CAAG
1 CAAG
40270452 TTATTTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (18 bp):
CAAGGCAATCCTATTCGC
Found at i:40288236 original size:21 final size:20
Alignment explanation
Indices: 40288193--40288237 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
40288183 GTTTGAAATT
* **
40288193 TGTTCAAAGTATTTTTTAAG
1 TGTTCAAAGTATTCTCAAAG
40288213 TGTTCAAAGTGATTCTCAAAG
1 TGTTCAAAGT-ATTCTCAAAG
40288234 TGTT
1 TGTT
40288238 TGAATTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (20 bp):
TGTTCAAAGTATTCTCAAAG
Done.