Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 166 of 222
Found at i:53114280 original size:3 final size:3
Alignment explanation
Indices: 53114272--53114300 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
53114262 ACTATTTACC
53114272 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53114301 AATCCTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:53121005 original size:25 final size:25
Alignment explanation
Indices: 53120957--53121005 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
53120947 CATAATTGAA
* * *
53120957 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
53120982 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
53121006 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:53121465 original size:43 final size:43
Alignment explanation
Indices: 53121401--53121486 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
53121391 TCTGTGATTG
* *
53121401 ATATTGAAATGGCAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTAAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
* *
53121444 ATATTAAAATGGAAAATATGAGAAATGATTATGAGATGAGAAA
1 ATATTAAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
53121487 TGAAATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.52, C:0.01, G:0.23, T:0.23
Consensus pattern (43 bp):
ATATTAAAATGGAAAAGATGAGAAATGAATATGAGATGAGAAA
Found at i:53128547 original size:13 final size:13
Alignment explanation
Indices: 53128529--53128576 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
53128519 TTAGCAATGC
53128529 TTTGAAAAGTGCT
1 TTTGAAAAGTGCT
*
53128542 TTTGAAAACTG-T
1 TTTGAAAAGTGCT
*
53128554 TGTGGAAAAGTGCT
1 T-TTGAAAAGTGCT
53128568 TTTGAAAAG
1 TTTGAAAAG
53128577 GTTGGTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 2 0.07
13 25 0.86
14 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.35
Consensus pattern (13 bp):
TTTGAAAAGTGCT
Found at i:53128588 original size:26 final size:26
Alignment explanation
Indices: 53128532--53128580 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
53128522 GCAATGCTTT
*
53128532 GAAAAGTGCTTTTGAAAACTGTTGTG
1 GAAAAGTGCTTTTGAAAACGGTTGTG
53128558 GAAAAGTGCTTTTGAAAA-GGTTG
1 GAAAAGTGCTTTTGAAAACGGTTG
53128581 GTTTAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.33
Consensus pattern (26 bp):
GAAAAGTGCTTTTGAAAACGGTTGTG
Found at i:53131582 original size:95 final size:95
Alignment explanation
Indices: 53131421--53131812 Score: 446
Period size: 95 Copynumber: 4.1 Consensus size: 95
53131411 ACTCGAATAG
* * * *** * * *
53131421 GATTGTTGATGATAATAAACCAAATGAATTTAGGCTATGATATTAGATCAGCG-GACATATTAGA
1 GATTGTTCATGATAATAAATCAAATGAACTTAGGCTGCAATATTAAATCAGCGAGTCAT-TTGGA
* * * *
53131485 GCAACGATATTAAATCATCTAACTCGGATAG
65 GCAACGATATTAAATCAGCTAACTCAGAGAA
* **
53131516 GATTGTTCATGATAATAAATCAAATGAACTTAGGCTGCAATCTTAAATCAGCGACCCATTTGGAG
1 GATTGTTCATGATAATAAATCAAATGAACTTAGGCTGCAATATTAAATCAGCGAGTCATTTGGAG
*
53131581 CAACGATATTAAGTCAGCTAACTCAGAGAA
66 CAACGATATTAAATCAGCTAACTCAGAGAA
** *
53131611 GATTGTTCATGATAATAAATCAAATGAACTTA-GCTTGCAATCCTAAATTAGCGAGTCATTTGGA
1 GATTGTTCATGATAATAAATCAAATGAACTTAGGC-TGCAATATTAAATCAGCGAGTCATTTGGA
**
53131675 GCAGTGATATTAAATCAGCTAACTCAGAGAA
65 GCAACGATATTAAATCAGCTAACTCAGAGAA
* * * * * * *
53131706 AATCGTTCATGATAGTAAATCAAATGAGCTTAGGTTGCGATATTAAATCAGGGAGTCATTTGGAG
1 GATTGTTCATGATAATAAATCAAATGAACTTAGGCTGCAATATTAAATCAGCGAGTCATTTGGAG
* * * *
53131771 TAGCGATATTAAATCATCTAACTCAAAGAA
66 CAACGATATTAAATCAGCTAACTCAGAGAA
*
53131801 GATTTTTCATGA
1 GATTGTTCATGA
53131813 CAAATAAACT
Statistics
Matches: 254, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
94 2 0.01
95 248 0.98
96 4 0.02
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (95 bp):
GATTGTTCATGATAATAAATCAAATGAACTTAGGCTGCAATATTAAATCAGCGAGTCATTTGGAG
CAACGATATTAAATCAGCTAACTCAGAGAA
Found at i:53133656 original size:13 final size:13
Alignment explanation
Indices: 53133638--53133664 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53133628 AAAAGTTATA
53133638 TTTAATAATTCAT
1 TTTAATAATTCAT
53133651 TTTAATAATTCAT
1 TTTAATAATTCAT
53133664 T
1 T
53133665 AATAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTAATAATTCAT
Found at i:53139964 original size:17 final size:17
Alignment explanation
Indices: 53139926--53139964 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
53139916 TTTGCAATAA
* *
53139926 AAAAAGAAATTATATAC
1 AAAAAGAAATTAAAAAC
*
53139943 CAAAAGAAATTAAAAAC
1 AAAAAGAAATTAAAAAC
53139960 AAAAA
1 AAAAA
53139965 AACAAAATCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAAAGAAATTAAAAAC
Found at i:53144008 original size:16 final size:15
Alignment explanation
Indices: 53143985--53144014 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
53143975 ATGAAAACAG
53143985 AAAGGAAAGAAAGAA
1 AAAGGAAAGAAAGAA
53144000 AAAGAGAAAGAAAGA
1 AAAG-GAAAGAAAGA
53144015 CACAAGGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAGGAAAGAAAGAA
Found at i:53144718 original size:15 final size:15
Alignment explanation
Indices: 53144698--53144750 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
53144688 GATTGAATTG
53144698 ATATATATATTATGA
1 ATATATATATTATGA
53144713 ATATAT-TGATTATGA
1 ATATATAT-ATTATGA
* *
53144728 ATTGATTTATATAATGA
1 A-T-ATATATATTATGA
53144745 ATATAT
1 ATATAT
53144751 TGATTATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 1 0.03
15 17 0.55
16 2 0.06
17 10 0.32
18 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.47
Consensus pattern (15 bp):
ATATATATATTATGA
Found at i:53144745 original size:32 final size:35
Alignment explanation
Indices: 53144689--53144766 Score: 117
Period size: 32 Copynumber: 2.3 Consensus size: 35
53144679 GATTGAATGG
*
53144689 ATTGAATTGATATATATATTATGAATATATTGATT
1 ATTGAATTGATATATATATAATGAATATATTGATT
53144724 A-TGAATTGAT-T-TATATAATGAATATATTGATT
1 ATTGAATTGATATATATATAATGAATATATTGATT
53144756 ATTTGAATTGA
1 A-TTGAATTGA
53144767 AATGAATATA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
32 21 0.52
33 1 0.03
34 17 0.43
35 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (35 bp):
ATTGAATTGATATATATATAATGAATATATTGATT
Found at i:53148538 original size:41 final size:40
Alignment explanation
Indices: 53148474--53148613 Score: 110
Period size: 41 Copynumber: 3.5 Consensus size: 40
53148464 CAACTTTGAG
* *
53148474 TCGATGAGACACTGAGTGTCAATTTACTACTGCGGATTAAT
1 TCGATGAGACACTGGGTGCCAATTTACTACT-CGGATTAAT
*
53148515 TCGATGAGGCACTGGGTGCCAATTTACT--TC-GATTTAA-
1 TCGATGAGACACTGGGTGCCAATTTACTACTCGGA-TTAAT
* * * * *
53148552 TCGATGATACACTGGGTGTCAAATTATTACTTCGAATT-AT
1 TCGATGAGACACTGGGTGCCAATTTACTAC-TCGGATTAAT
* * * *
53148592 CCGATAAGGCACTAGGTGCCAA
1 TCGATGAGACACTGGGTGCCAA
53148614 ATTGGTTTGT
Statistics
Matches: 78, Mismatches: 15, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
37 25 0.32
38 5 0.06
39 2 0.03
40 20 0.26
41 26 0.33
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGCCAATTTACTACTCGGATTAAT
Found at i:53153219 original size:44 final size:44
Alignment explanation
Indices: 53153120--53153325 Score: 190
Period size: 43 Copynumber: 4.7 Consensus size: 44
53153110 TGGCATTACA
* * * *
53153120 TGATTTCGTATAAGACCATAGCTGGGCTATGGCATCGATATATG
1 TGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATATG
* * * * *
53153164 AGACTT-TGTGTAAAACCATATCTAGGATATGTCATCGATATATG
1 TGA-TTACGTGTAAGACCATATCTGGGATATGGCATCGATATATG
* * *
53153208 TGATTACGTGTAAGACCATGTATGGGACATTGGCATC-AT-TATG
1 TGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATATG
**
53153251 TGATTTTGTGTAAGACCATAGT-TGGGATATTGGCATCG--ATATG
1 TGATTACGTGTAAGACCATA-TCTGGGATA-TGGCATCGATATATG
* *
53153294 TGATAACATGTAAGACCATATCTGGGATATGG
1 TGATTACGTGTAAGACCATATCTGGGATATGG
53153326 AATTGTATGT
Statistics
Matches: 131, Mismatches: 24, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
42 4 0.03
43 64 0.49
44 55 0.42
45 8 0.06
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (44 bp):
TGATTACGTGTAAGACCATATCTGGGATATGGCATCGATATATG
Found at i:53153320 original size:86 final size:88
Alignment explanation
Indices: 53153130--53153325 Score: 217
Period size: 86 Copynumber: 2.3 Consensus size: 88
53153120 TGATTTCGTA
*
53153130 TAAGACCATAGCTGGG-CTATGGCATCGATATATGAGACTTTGTGTAAAACCATATCTAGGATAT
1 TAAGACCATATCTGGGACTATGGCATCGATATATGAGACTTTGTGTAAAACCATATCTAGGATAT
* * *
53153194 GTCATCGATATATGTGATTACGTG
66 GGCATCGA-ATATGTGATAACATG
* * * * * *
53153218 TAAGACCATGTATGGGAC-ATTGGCATC-AT-TATGTGATTTTGTGTAAGACCATAGT-TGGGAT
1 TAAGACCATATCTGGGACTA-TGGCATCGATATATGAGACTTTGTGTAAAACCATA-TCTAGGAT
53153279 ATTGGCATCG-ATATGTGATAACATG
64 A-TGGCATCGAATATGTGATAACATG
53153304 TAAGACCATATCTGGGA-TATGG
1 TAAGACCATATCTGGGACTATGG
53153326 AATTGTATGT
Statistics
Matches: 91, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
85 3 0.03
86 29 0.32
87 27 0.30
88 24 0.26
89 8 0.09
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.32
Consensus pattern (88 bp):
TAAGACCATATCTGGGACTATGGCATCGATATATGAGACTTTGTGTAAAACCATATCTAGGATAT
GGCATCGAATATGTGATAACATG
Found at i:53153876 original size:16 final size:16
Alignment explanation
Indices: 53153849--53153885 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
53153839 CTTGATGCAA
53153849 TTATTTGTAATAT-AG
1 TTATTTGTAATATGAG
53153864 TTATTTAGTAATATGAG
1 TTATTT-GTAATATGAG
53153881 TTATT
1 TTATT
53153886 ATATTACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 7 0.35
17 7 0.35
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (16 bp):
TTATTTGTAATATGAG
Found at i:53155840 original size:3 final size:3
Alignment explanation
Indices: 53155832--53155858 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
53155822 ATTATATTCC
53155832 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
53155859 TGAATTATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:53161269 original size:12 final size:12
Alignment explanation
Indices: 53161235--53161290 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
53161225 ATATTTATTG
*
53161235 TTATAATTATTAA
1 TTAT-ATTATTAT
*
53161248 TTACTATTATTGT
1 TTA-TATTATTAT
53161261 TTATATTATTAT
1 TTATATTATTAT
*
53161273 TTTTATTATTAT
1 TTATATTATTAT
53161285 ATTATA
1 -TTATA
53161291 GAATAAATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
12 19 0.53
13 16 0.44
14 1 0.03
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (12 bp):
TTATATTATTAT
Found at i:53161272 original size:15 final size:15
Alignment explanation
Indices: 53161228--53161284 Score: 53
Period size: 15 Copynumber: 3.7 Consensus size: 15
53161218 GAAATAGATA
* *
53161228 TTTATTGTTATAATT
1 TTTATTATTATTATT
* *
53161243 ATTAATTACTATTATT
1 -TTTATTATTATTATT
53161259 GTTTA-TATTATTATT
1 -TTTATTATTATTATT
53161274 TTTATTATTAT
1 TTTATTATTAT
53161285 ATTATAGAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
14 4 0.12
15 15 0.45
16 14 0.42
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTATTATTATTATT
Found at i:53170413 original size:25 final size:25
Alignment explanation
Indices: 53170385--53170539 Score: 104
Period size: 24 Copynumber: 6.2 Consensus size: 25
53170375 ATCCAGGCAA
*
53170385 TATAATGGGAAGCTCACAAAGAGCC
1 TATAACGGGAAGCTCACAAAGAGCC
* * *
53170410 TATAACAGGTAGCTC-CGAAGAGCAC
1 TATAACGGGAAGCTCACAAAGAGC-C
* * * *
53170435 T-TAACGGGTAGCAC-CGAATAGCC
1 TATAACGGGAAGCTCACAAAGAGCC
* * **
53170458 ATATAATGGGAAGTTCA-AGCGAG-C
1 -TATAACGGGAAGCTCACAAAGAGCC
* *
53170482 AATAACGGGAAGCTCACAAAAAGCC
1 TATAACGGGAAGCTCACAAAGAGCC
*
53170507 TTTAATCGGGAAGCTCACAAAGAGCC
1 TATAA-CGGGAAGCTCACAAAGAGCC
53170533 GTATAAC
1 -TATAAC
53170540 AAGACGCTCA
Statistics
Matches: 97, Mismatches: 25, Indels: 15
0.71 0.18 0.11
Matches are distributed among these distances:
23 14 0.14
24 30 0.31
25 29 0.30
26 20 0.21
27 4 0.04
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (25 bp):
TATAACGGGAAGCTCACAAAGAGCC
Found at i:53172942 original size:15 final size:15
Alignment explanation
Indices: 53172922--53172974 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 15
53172912 GATTGAATTG
53172922 ATATATATATTATGA
1 ATATATATATTATGA
53172937 ATATAT-TGATTATGA
1 ATATATAT-ATTATGA
*
53172952 ATTGATATATATAATGA
1 A-T-ATATATATTATGA
53172969 ATATAT
1 ATATAT
53172975 TGATTATTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
14 1 0.03
15 18 0.55
16 2 0.06
17 11 0.33
18 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (15 bp):
ATATATATATTATGA
Found at i:53172969 original size:32 final size:34
Alignment explanation
Indices: 53172913--53173004 Score: 125
Period size: 34 Copynumber: 2.6 Consensus size: 34
53172903 GATTGAATGG
53172913 ATTGAATTGATATATATATTATGAATATATTGATT
1 ATTGAATTGATATATATA-TATGAATATATTGATT
53172948 A-TGAATTGATATATATA-ATGAATATATTGATT
1 ATTGAATTGATATATATATATGAATATATTGATT
*
53172980 ATTTGAATTGAAATGAATATATATG
1 A-TTGAATTGATAT--ATATATATG
53173005 TGCAAATATG
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
32 16 0.31
34 26 0.51
35 1 0.02
36 5 0.10
37 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (34 bp):
ATTGAATTGATATATATATATGAATATATTGATT
Found at i:53175556 original size:25 final size:26
Alignment explanation
Indices: 53175485--53175556 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
53175475 AATTTTCTTG
* * *
53175485 AAATTTTAGCGGGGGTAAAATCATCA
1 AAATTTTACCGAGAGTAAAATCATCA
* *
53175511 AAATTTTACCGAGAGTAAAATCGTTA
1 AAATTTTACCGAGAGTAAAATCATCA
*
53175537 AAATTTTA-CTAGAGTAAAAT
1 AAATTTTACCGAGAGTAAAAT
53175557 TGAGATAAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 11 0.28
26 29 0.73
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (26 bp):
AAATTTTACCGAGAGTAAAATCATCA
Found at i:53182438 original size:24 final size:26
Alignment explanation
Indices: 53182388--53182440 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
53182378 GTATTATAAG
* *
53182388 AAAACATATCTATTCTTTTATACAAT
1 AAAACATATCTAATCTTTTATAAAAT
*
53182414 AAAAGATATCTAAT-TTTTA-AAAAT
1 AAAACATATCTAATCTTTTATAAAAT
53182438 AAA
1 AAA
53182441 TTCCATATCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 5 0.21
26 12 0.50
ACGTcount: A:0.51, C:0.09, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAACATATCTAATCTTTTATAAAAT
Found at i:53191653 original size:21 final size:21
Alignment explanation
Indices: 53191620--53191667 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
53191610 ATAAAAGTTA
53191620 AAAAAATTACATA-TAATTTTTT
1 AAAAAATTACATACT--TTTTTT
53191642 AAAAAATT-CATACTTTTTTT
1 AAAAAATTACATACTTTTTTT
53191662 AAAAAA
1 AAAAAA
53191668 AATGTCCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.48
21 4 0.16
22 9 0.36
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAAAATTACATACTTTTTTT
Found at i:53191668 original size:21 final size:22
Alignment explanation
Indices: 53191617--53191668 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
53191607 TTCATAAAAG
53191617 TTAAAAAAATTACATATAATTTT
1 TTAAAAAAATTACATAT-ATTTT
53191640 TT-AAAAAATT-CATACT-TTTT
1 TTAAAAAAATTACATA-TATTTT
53191660 TTAAAAAAA
1 TTAAAAAAA
53191669 ATGTCCATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 6 0.22
21 10 0.37
22 9 0.33
23 2 0.07
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAAAAAAATTACATATATTTT
Found at i:53194478 original size:87 final size:86
Alignment explanation
Indices: 53194324--53194483 Score: 203
Period size: 87 Copynumber: 1.8 Consensus size: 86
53194314 TTAAAATTAA
* * * * *
53194324 GTGAATTCATCAAGTCCGCCTCAATAGAACACCCAAACTCTGGGATATGAATTCATTTAGAGTAA
1 GTGAATTCATCAAGTCCACCTCAATAGAACACCCAAACTCTGGGATATGAACTCATTAAAAGCAA
53194389 AAAACTCAACCTCACACATCG
66 AAAACTCAACCTCACACATCG
* * * * * *
53194410 GTGAATTCATCAAGTTCATCTCACTAGGACCACCCAAACTTTGGGCTATGAACTCATTAAAAGCA
1 GTGAATTCATCAAGTCCACCTCAATA-GAACACCCAAACTCTGGGATATGAACTCATTAAAAGCA
*
53194475 AAAAGCTCA
65 AAAAACTCA
53194484 TCCTTATGCA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
86 22 0.36
87 39 0.64
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (86 bp):
GTGAATTCATCAAGTCCACCTCAATAGAACACCCAAACTCTGGGATATGAACTCATTAAAAGCAA
AAAACTCAACCTCACACATCG
Found at i:53198765 original size:16 final size:16
Alignment explanation
Indices: 53198744--53198791 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
53198734 AATAAGAATT
53198744 AGTTATGACCACCATA
1 AGTTATGACCACCATA
53198760 AGTTATGACCACCATA
1 AGTTATGACCACCATA
53198776 AGTTATGACCACCATA
1 AGTTATGACCACCATA
53198792 GCAAGCTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (16 bp):
AGTTATGACCACCATA
Found at i:53201925 original size:24 final size:24
Alignment explanation
Indices: 53201898--53202021 Score: 105
Period size: 24 Copynumber: 5.2 Consensus size: 24
53201888 TAAGCACATA
53201898 AACGGAAAGCTCTGGAGAGCCATT
1 AACGGAAAGCTCTGGAGAGCCATT
* *
53201922 AACGGGAAGCTCCGGAGAGCCATT
1 AACGGAAAGCTCTGGAGAGCCATT
*
53201946 AAC-GAGAAGCTCAT--ACGAGCCAAT
1 AACGGA-AAGCTC-TGGA-GAGCCATT
* *
53201970 ATC-GAGAAGCTCTGGAGATCCATT
1 AACGGA-AAGCTCTGGAGAGCCATT
**
53201994 AACAGG-AAGCTCCAGAGAGCCATT
1 AAC-GGAAAGCTCTGGAGAGCCATT
53202018 AACG
1 AACG
53202022 AGAAGGTCAT
Statistics
Matches: 81, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
23 4 0.05
24 75 0.93
25 1 0.01
26 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.27, T:0.15
Consensus pattern (24 bp):
AACGGAAAGCTCTGGAGAGCCATT
Found at i:53201979 original size:48 final size:47
Alignment explanation
Indices: 53201912--53202076 Score: 143
Period size: 48 Copynumber: 3.4 Consensus size: 47
53201902 GAAAGCTCTG
* * * *
53201912 GAGAGCCATTAACGGGAAGCTCCGGAGAGCCATTAACGAGAAGCTCA
1 GAGAGCCAATATCGAGAAGCTCTGGAGAGCCATTAACGAGAAGCTCA
* *
53201959 TACGAGCCAATATCGAGAAGCTCTGGAGATCCATTAAC-AGGAAGCTCCA
1 GA-GAGCCAATATCGAGAAGCTCTGGAGAGCCATTAACGA-GAAGCT-CA
* * * ** *
53202008 GAGAGCCATTAACGAGAAGGTCATAAAGAGCCTTTAATCGAGAAGCTCA
1 GAGAGCCAATATCGAGAAGCTC-TGGAGAGCCATTAA-CGAGAAGCTCA
53202057 CGAAGAGCCATATATCGAGA
1 -G-AGAGCCA-ATATCGAGA
53202077 CGTTCATAAG
Statistics
Matches: 93, Mismatches: 16, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
47 2 0.02
48 53 0.57
49 15 0.16
50 8 0.09
51 8 0.09
52 7 0.08
ACGTcount: A:0.36, C:0.22, G:0.25, T:0.16
Consensus pattern (47 bp):
GAGAGCCAATATCGAGAAGCTCTGGAGAGCCATTAACGAGAAGCTCA
Found at i:53202021 original size:72 final size:74
Alignment explanation
Indices: 53201904--53202055 Score: 227
Period size: 72 Copynumber: 2.1 Consensus size: 74
53201894 CATAAACGGA
* * *
53201904 AAGCTCTGGAGAGCCATTAACGGGAAGCTCCGGAGAGCCATTAACGAGAAGCTCAT-ACGAGCCA
1 AAGCTCTGGAGAGCCATTAACAGGAAGCTCCAGAGAGCCATTAACGAGAAGCTCATAAAGAGCCA
53201968 AT-ATCGAG
66 ATAATCGAG
* * *
53201976 AAGCTCTGGAGATCCATTAACAGGAAGCTCCAGAGAGCCATTAACGAGAAGGTCATAAAGAGCCT
1 AAGCTCTGGAGAGCCATTAACAGGAAGCTCCAGAGAGCCATTAACGAGAAGCTCATAAAGAGCCA
*
53202041 TTAATCGAG
66 ATAATCGAG
53202050 AAGCTC
1 AAGCTC
53202056 ACGAAGAGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
72 52 0.73
73 7 0.10
74 12 0.17
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (74 bp):
AAGCTCTGGAGAGCCATTAACAGGAAGCTCCAGAGAGCCATTAACGAGAAGCTCATAAAGAGCCA
ATAATCGAG
Found at i:53202026 original size:24 final size:24
Alignment explanation
Indices: 53201912--53202055 Score: 130
Period size: 24 Copynumber: 5.9 Consensus size: 24
53201902 GAAAGCTCTG
* *
53201912 GAGAGCCATTAACGGGAAGCTCCG
1 GAGAGCCATTAACGAGAAGCTCCA
53201936 GAGAGCCATTAACGAGAAGCT-CA
1 GAGAGCCATTAACGAGAAGCTCCA
* * * **
53201959 TACGAGCCAATATCGAGAAGCTCTG
1 GA-GAGCCATTAACGAGAAGCTCCA
*
53201984 GAGATCCATTAAC-AGGAAGCTCCA
1 GAGAGCCATTAACGA-GAAGCTCCA
* *
53202008 GAGAGCCATTAACGAGAAGGTCATA
1 GAGAGCCATTAACGAGAAGCTC-CA
* *
53202033 AAGAGCCTTTAATCGAGAAGCTC
1 GAGAGCCATTAA-CGAGAAGCTC
53202056 ACGAAGAGCC
Statistics
Matches: 95, Mismatches: 19, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
23 3 0.03
24 70 0.74
25 13 0.14
26 9 0.09
ACGTcount: A:0.35, C:0.22, G:0.26, T:0.17
Consensus pattern (24 bp):
GAGAGCCATTAACGAGAAGCTCCA
Found at i:53202062 original size:26 final size:25
Alignment explanation
Indices: 53201913--53202076 Score: 113
Period size: 24 Copynumber: 6.6 Consensus size: 25
53201903 AAAGCTCTGG
* **
53201913 AGAGCCATTAACGGGAAGCTC-CGG
1 AGAGCCATTAACGAGAAGCTCACAA
*
53201937 AGAGCCATTAACGAGAAGCTCA-TA
1 AGAGCCATTAACGAGAAGCTCACAA
* * * ***
53201961 CGAGCCAATATCGAGAAGCTC-TGG
1 AGAGCCATTAACGAGAAGCTCACAA
* *
53201985 AGATCCATTAAC-AGGAAGCTC-CAG
1 AGAGCCATTAACGA-GAAGCTCACAA
* *
53202009 AGAGCCATTAACGAGAAGGTCATAA
1 AGAGCCATTAACGAGAAGCTCACAA
* *
53202034 AGAGCCTTTAATCGAGAAGCTCACGA
1 AGAGCCATTAA-CGAGAAGCTCACAA
*
53202060 AGAGCCATATATCGAGA
1 AGAGCCAT-TAACGAGA
53202077 CGTTCATAAG
Statistics
Matches: 109, Mismatches: 24, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
23 1 0.01
24 71 0.65
25 12 0.11
26 23 0.21
27 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.16
Consensus pattern (25 bp):
AGAGCCATTAACGAGAAGCTCACAA
Found at i:53205125 original size:52 final size:53
Alignment explanation
Indices: 53205031--53205148 Score: 161
Period size: 52 Copynumber: 2.3 Consensus size: 53
53205021 TGTCCTAGTT
* *
53205031 ATATAAACATAAAAAATTAAAAAATTATTATTATTATTAACAACTTAATAAGG
1 ATATAAACATAAAAAATTAAAAAATTATTAATAATATTAACAACTTAATAAGG
* *
53205084 ATATAAACATAAAAATTTTAAAAAA-TA-TAATAATATTAACAACTTAATAATG
1 ATATAAACATAAAAA-ATTAAAAAATTATTAATAATATTAACAACTTAATAAGG
*
53205136 ATATTAAC-TAAAA
1 ATATAAACATAAAA
53205149 TAAAAATATT
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
51 5 0.08
52 29 0.49
53 17 0.29
54 8 0.14
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (53 bp):
ATATAAACATAAAAAATTAAAAAATTATTAATAATATTAACAACTTAATAAGG
Found at i:53205475 original size:14 final size:14
Alignment explanation
Indices: 53205456--53205494 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
53205446 ATTAATATAG
53205456 AAAATTGAGAGAAA
1 AAAATTGAGAGAAA
*
53205470 AAAATTTA-AGAAA
1 AAAATTGAGAGAAA
*
53205483 AAAAATGAGAGA
1 AAAATTGAGAGA
53205495 TTAGAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (14 bp):
AAAATTGAGAGAAA
Found at i:53207733 original size:25 final size:25
Alignment explanation
Indices: 53207704--53207753 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
53207694 TATTTTTTAA
53207704 AAATA-TATAAAATTTGAAACATTAT
1 AAATATTATAAAATTTGAAA-ATTAT
* *
53207729 AAATATTTTGAAATTTGAAAATTAT
1 AAATATTATAAAATTTGAAAATTAT
53207754 TTTGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (25 bp):
AAATATTATAAAATTTGAAAATTAT
Found at i:53209558 original size:31 final size:31
Alignment explanation
Indices: 53209520--53209582 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
53209510 AATGTTAGTC
53209520 ATTTGTGTATTTACAATATAAATATTGGGTT
1 ATTTGTGTATTTACAATATAAATATTGGGTT
53209551 ATTTGTGTATTTACAATATAAATATTGGGTT
1 ATTTGTGTATTTACAATATAAATATTGGGTT
53209582 A
1 A
53209583 AAAAAAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (31 bp):
ATTTGTGTATTTACAATATAAATATTGGGTT
Found at i:53214995 original size:29 final size:29
Alignment explanation
Indices: 53214939--53214996 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
53214929 TCAGCCAAAA
**
53214939 ACAGCCATAAGAAAGAGCTTAAGTTGGTT
1 ACAGCCATAAGAAAGAGCTTAACCTGGTT
**
53214968 ACAGCCATGGGAAAGAGCTTAACCTGGTT
1 ACAGCCATAAGAAAGAGCTTAACCTGGTT
53214997 TTTCATACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.22
Consensus pattern (29 bp):
ACAGCCATAAGAAAGAGCTTAACCTGGTT
Found at i:53217459 original size:20 final size:20
Alignment explanation
Indices: 53217421--53217460 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
53217411 AGGCAACCCA
*
53217421 CATTTATTTTTATTTATTTT
1 CATTTATTTTAATTTATTTT
53217441 CATTTA-TTTAATTTAATTTT
1 CATTTATTTTAATTT-ATTTT
53217461 GAATTCTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (20 bp):
CATTTATTTTAATTTATTTT
Found at i:53218445 original size:26 final size:29
Alignment explanation
Indices: 53218402--53218456 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
53218392 CATAAAACCC
53218402 AATTACAACCCAAACCC-AAGACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
* *
53218430 AATTA-AA-CCAAGCCCAAATACCCAACA
1 AATTACAACCCAAACCCAAAGACCCAACA
53218457 GACCCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 7 0.29
27 12 0.50
28 5 0.21
ACGTcount: A:0.51, C:0.36, G:0.04, T:0.09
Consensus pattern (29 bp):
AATTACAACCCAAACCCAAAGACCCAACA
Found at i:53218848 original size:10 final size:10
Alignment explanation
Indices: 53218825--53218859 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
53218815 GTTAAGATCT
* *
53218825 TTTTTTTTTG
1 TTTTTATTTA
53218835 TTTTTATTTA
1 TTTTTATTTA
53218845 TTTTTATTTA
1 TTTTTATTTA
53218855 TTTTT
1 TTTTT
53218860 CCCCCTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.03, T:0.86
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:53219559 original size:3 final size:3
Alignment explanation
Indices: 53219551--53219586 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
53219541 AATAATTTGA
*
53219551 TAT TAT TAT TAT TAT TAT TAT TAT CAT TATT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TA
53219587 GTTTTATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:53221536 original size:13 final size:13
Alignment explanation
Indices: 53221518--53221560 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
53221508 AAATTTGAAT
53221518 TATTTAGTGATAA
1 TATTTAGTGATAA
53221531 TATTTAG-GAT--
1 TATTTAGTGATAA
53221541 TATTTAGTGATAA
1 TATTTAGTGATAA
53221554 TATTTAG
1 TATTTAG
53221561 AAAAAATAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 3 0.11
13 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:53221542 original size:23 final size:23
Alignment explanation
Indices: 53221516--53221560 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
53221506 TAAAATTTGA
53221516 ATTATTTAGTGATAATATTTAGG
1 ATTATTTAGTGATAATATTTAGG
53221539 ATTATTTAGTGATAATATTTAG
1 ATTATTTAGTGATAATATTTAG
53221561 AAAAAATAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (23 bp):
ATTATTTAGTGATAATATTTAGG
Found at i:53227337 original size:12 final size:12
Alignment explanation
Indices: 53227320--53227349 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
53227310 GTTTATTTTT
53227320 TTAAAAAAATAG
1 TTAAAAAAATAG
*
53227332 TTAAAAGAATAG
1 TTAAAAAAATAG
53227344 TTAAAA
1 TTAAAA
53227350 TTTGTTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.10, T:0.27
Consensus pattern (12 bp):
TTAAAAAAATAG
Found at i:53231162 original size:116 final size:116
Alignment explanation
Indices: 53230958--53231192 Score: 443
Period size: 116 Copynumber: 2.0 Consensus size: 116
53230948 ATTCTCAGGT
53230958 ATTTCTTTAACTTCATTATCACAAAGGACTTGAGTAGGTTGTGCTTCATCCCAATCCCAAGTGTT
1 ATTTCTTTAACTTCATTATCACAAAGGACTTGAGTAGGTTGTGCTTCATCCCAATCCCAAGTGTT
* * *
53231023 CTCTTCATCAAGCACATCGTCTCAGCTAATCACGACCTTTTTTGTCACATG
66 CTCTTCATCAAACACATCATCTCAGCTAATCACGACCTTTTCTGTCACATG
53231074 ATTTCTTTAACTTCATTATCACAAAGGACTTGAGTAGGTTGTGCTTCATCCCAATCCCAAGTGTT
1 ATTTCTTTAACTTCATTATCACAAAGGACTTGAGTAGGTTGTGCTTCATCCCAATCCCAAGTGTT
53231139 CTCTTCATCAAACACATCATCTCAGCTAATCACGACCTTTTCTGTCACATG
66 CTCTTCATCAAACACATCATCTCAGCTAATCACGACCTTTTCTGTCACATG
53231190 ATT
1 ATT
53231193 GAACAATTTG
Statistics
Matches: 116, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.35
Consensus pattern (116 bp):
ATTTCTTTAACTTCATTATCACAAAGGACTTGAGTAGGTTGTGCTTCATCCCAATCCCAAGTGTT
CTCTTCATCAAACACATCATCTCAGCTAATCACGACCTTTTCTGTCACATG
Found at i:53239205 original size:33 final size:33
Alignment explanation
Indices: 53239162--53239228 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
53239152 CAAAATATTT
53239162 TCCACTATGGTGACATCCTTCATCTTCTCACCA
1 TCCACTATGGTGACATCCTTCATCTTCTCACCA
*
53239195 TCCATTATGGTGACATCCTTCATCTTCTCACCA
1 TCCACTATGGTGACATCCTTCATCTTCTCACCA
53239228 T
1 T
53239229 GGAACCACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.34, G:0.09, T:0.36
Consensus pattern (33 bp):
TCCACTATGGTGACATCCTTCATCTTCTCACCA
Found at i:53242469 original size:24 final size:24
Alignment explanation
Indices: 53242439--53242507 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
53242429 ACAAATAAAA
53242439 AATAATAATACAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
53242463 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
*
53242487 AATAATAATACACAATAATTT
1 AATAATAATACATAATAATTT
53242508 CAAAAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:53243407 original size:20 final size:21
Alignment explanation
Indices: 53243373--53243414 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
53243363 ACAGAAAATA
* *
53243373 AAAAAATCTGGAGAAAGAAAG
1 AAAAAATCTGAAGAAAAAAAG
53243394 AAAAAATC-GAAGAAAAAAAG
1 AAAAAATCTGAAGAAAAAAAG
53243414 A
1 A
53243415 TTGAATCACC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.69, C:0.05, G:0.19, T:0.07
Consensus pattern (21 bp):
AAAAAATCTGAAGAAAAAAAG
Found at i:53243948 original size:25 final size:26
Alignment explanation
Indices: 53243895--53243945 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
53243885 TAAGTTGGGT
* *
53243895 TTTGGGCTAGGCTTAATGGGTTTAGG
1 TTTGGGCTAGGCTTAATAGCTTTAGG
53243921 TTTGGGCTAGG-TTAATAAGCTTTAG
1 TTTGGGCTAGGCTTAAT-AGCTTTAG
53243946 TTTACTTGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.20, C:0.08, G:0.33, T:0.39
Consensus pattern (26 bp):
TTTGGGCTAGGCTTAATAGCTTTAGG
Found at i:53244426 original size:44 final size:43
Alignment explanation
Indices: 53244327--53244970 Score: 186
Period size: 44 Copynumber: 14.8 Consensus size: 43
53244317 AGACTTGATG
* * *
53244327 CAATCTACTCTACTGCAACATCAGAGAGATAAGATCTATTACTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGAT-TATGACTT
* * * * * *
53244371 TAATCTGCTCCACTACAACTTCTGGGAGATAGGATTATCGACTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTAT-GACTT
* *
53244415 CAATCTACTCCACTGCAACCTCAGGGAGATAAGATT-TGCTTCTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATG--ACTT
** * * ** * * * **
53244459 CGGTCTGCCCCACTGTGACTTCAGGGGGATAAGACT-TGTTTTCT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATG-ACT-T
* * * * ** *
53244503 CAGTCTGCTCCACTACAACCTCAGGGAGATAAGA-CCTGA-TG
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATGACTT
* * * * * *
53244544 CGATCCACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGA-TTATGACTT
* ** * * * *
53244588 TAATCCGCTCCACTGCAGCTTCAGGGAGATAGGATTATCGGCTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTAT-GACTT
* * * *
53244632 CCATCTGCTCCACTGCAACCTCAGAGAGATAAGATT-TGCCATCTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATG--A-CTT
* * * ** * ** *
53244677 CGATCT-GTCCCACTGTAAC-TTTGGAGGGATAAGACCTGCTTAC-T
1 CAATCTACT-CCACTGCAACATCAGG-GAGATAAGA--TTATGACTT
* * * * **
53244721 CAGTCTGCTCCGCTGCAACCTCAGGGAGATAAGA-CCTGA-TAT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATGACT-T
* * * * * *
53244763 -GATCCACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGA-TTATGACTT
* * * * * * *
53244806 TAATCTGCTCCACTACAACTTCA--GATATAGGATTATCGGCTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTAT-GACTT
* *
53244848 CAATCTGCTCCACTGCAACCTCAGGGAGATAAGATT-TGCCATCTT
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATG--A-CTT
* * * * ** *
53244893 CGATCT-GTCCCACTGCAACTTCAGGGGGATAAGACCTGCTTAC-T
1 CAATCTACT-CCACTGCAACATCAGGGAGATAAGA--TTATGACTT
* * *
53244937 CAATCTGCTCCACTGCAACCTTAGGGAGATAAGA
1 CAATCTACTCCACTGCAACATCAGGGAGATAAGA
53244971 CCTAATTTCC
Statistics
Matches: 443, Mismatches: 121, Indels: 72
0.70 0.19 0.11
Matches are distributed among these distances:
41 58 0.13
42 35 0.08
43 18 0.04
44 263 0.59
45 63 0.14
46 2 0.00
47 2 0.00
48 2 0.00
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (43 bp):
CAATCTACTCCACTGCAACATCAGGGAGATAAGATTATGACTT
Found at i:53244790 original size:218 final size:218
Alignment explanation
Indices: 53244333--53244973 Score: 1011
Period size: 218 Copynumber: 3.0 Consensus size: 218
53244323 GATGCAATCT
* * *
53244333 ACTCTACTGCAACATCAGAGAGATAAGATCTATTACTTTAATCTGCTCCACTACAACTTCTGGGA
1 ACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCTGCTCCACTACAACTTCAGGGA
* * * *
53244398 GATAGGATTATCGACTTCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTG-CTTCTTCGG
66 GATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
* * * * * *
53244462 TCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTTTTCTCAGTCTGCTCCACTACAACCTCAG
131 TCTGTCCCACTGTAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
*
53244527 GGAGATAAGACCTGATGCGATCC
196 GGAGATAAGACCTGATACGATCC
* * *
53244550 ACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCCGCTCCACTGCAGCTTCAGGGA
1 ACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCTGCTCCACTACAACTTCAGGGA
* *
53244615 GATAGGATTATCGGCTTCCATCTGCTCCACTGCAACCTCAGAGAGATAAGATTTGCCATCTTCGA
66 GATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
* *
53244680 TCTGTCCCACTGTAACTT-TGGAGGGATAAGACCTGCTTACTCAGTCTGCTCCGCTGCAACCTCA
131 TCTGTCCCACTGTAACTTCAGG-GGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCA
*
53244744 GGGAGATAAGACCTGATATGATCC
195 GGGAGATAAGACCTGATACGATCC
53244768 ACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCTGCTCCACTACAACTTCA--GA
1 ACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCTGCTCCACTACAACTTCAGGGA
*
53244831 TATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
66 GATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
* * *
53244896 TCTGTCCCACTGCAACTTCAGGGGGATAAGACCTGCTTACTCAATCTGCTCCACTGCAACCTTAG
131 TCTGTCCCACTGTAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
53244961 GGAGATAAGACCT
196 GGAGATAAGACCT
53244974 AATTTCCCAA
Statistics
Matches: 388, Mismatches: 33, Indels: 7
0.91 0.08 0.02
Matches are distributed among these distances:
216 134 0.35
217 114 0.29
218 140 0.36
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (218 bp):
ACTCTACTGCAACTTCAGAGAGATAAGATTTATTACTTTAATCTGCTCCACTACAACTTCAGGGA
GATAGGATTATCGGCTTCAATCTGCTCCACTGCAACCTCAGGGAGATAAGATTTGCCATCTTCGA
TCTGTCCCACTGTAACTTCAGGGGGATAAGACCTGCTTACTCAGTCTGCTCCACTGCAACCTCAG
GGAGATAAGACCTGATACGATCC
Found at i:53245127 original size:129 final size:129
Alignment explanation
Indices: 53244973--53245230 Score: 417
Period size: 129 Copynumber: 2.0 Consensus size: 129
53244963 AGATAAGACC
* * *
53244973 TAATTTCCCAACCTATTCTACTGCTGACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCATT
1 TAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATATGCTTCATT
* * * * *
53245038 ACACTTGAAGATAAGATTCGCCGTCTTCGATCCGCTCTGTTACTGCTTAGGAAGACAATATCTG
66 ACACTTGAAGATAAGATTCACCGTCTTCGATCCGCTCCGCTACTACTTAGGAAGACAAGATCTG
* *
53245102 TAATTTCCCGACCTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATATGCTTCCTT
1 TAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATATGCTTCATT
*
53245167 ACACTTGAAGATAAGATTCACCGTCTTCGATCCGCTCCGCTACTACTTAGGGAGACAAGATCTG
66 ACACTTGAAGATAAGATTCACCGTCTTCGATCCGCTCCGCTACTACTTAGGAAGACAAGATCTG
53245231 CTATATTTAC
Statistics
Matches: 118, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 118 1.00
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (129 bp):
TAATTTCCCAACCTATTCCACTGCTGACCAGGGATATAGGACTTATGGCTTAAATATGCTTCATT
ACACTTGAAGATAAGATTCACCGTCTTCGATCCGCTCCGCTACTACTTAGGAAGACAAGATCTG
Found at i:53251363 original size:24 final size:24
Alignment explanation
Indices: 53251333--53251401 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
53251323 ACAAATAAAA
53251333 AATAATAATACAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
53251357 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
*
53251381 AATAATAATACACAATAATTT
1 AATAATAATACATAATAATTT
53251402 CAAAAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:53252821 original size:25 final size:28
Alignment explanation
Indices: 53252775--53252831 Score: 84
Period size: 26 Copynumber: 2.1 Consensus size: 28
53252765 TTGGGCTAAG
*
53252775 TTAGGTTTTTGGCTAGGCTTAAT-GGGT
1 TTAGGTTTTGGGCTAGGCTTAATAGGGT
53252802 TTAGG-TTTGGGCTAGG-TTAATAGGGT
1 TTAGGTTTTGGGCTAGGCTTAATAGGGT
53252828 TTAG
1 TTAG
53252832 TTTACTGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 5 0.18
26 18 0.64
27 5 0.18
ACGTcount: A:0.18, C:0.05, G:0.35, T:0.42
Consensus pattern (28 bp):
TTAGGTTTTGGGCTAGGCTTAATAGGGT
Found at i:53256529 original size:5 final size:5
Alignment explanation
Indices: 53256519--53256552 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
53256509 AACTATTAAT
53256519 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
53256553 AGGGTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (5 bp):
ATATG
Found at i:53256649 original size:7 final size:7
Alignment explanation
Indices: 53256637--53256690 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
53256627 TAGTAGTATA
53256637 ATAATAT
1 ATAATAT
53256644 ATAATAT
1 ATAATAT
53256651 ATAATAT
1 ATAATAT
53256658 ATAATAT
1 ATAATAT
53256665 ATAATAT
1 ATAATAT
53256672 ATAATAT
1 ATAATAT
53256679 ATAATAT
1 ATAATAT
53256686 ATAAT
1 ATAAT
53256691 GTACTACTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
ATAATAT
Found at i:53259530 original size:208 final size:208
Alignment explanation
Indices: 53259165--53259581 Score: 780
Period size: 208 Copynumber: 2.0 Consensus size: 208
53259155 TAGAACACTT
*
53259165 AACCACTGAAGCATATATACATTTGTGTTAGATATTTACAGAAAAAAATAAATTATTCAAGGTGT
1 AACCACTAAAGCATATATACATTTGTGTTAGATATTTACAGAAAAAAATAAATTATTCAAGGTGT
*
53259230 TACAAATCTACCCTTAAAAGAAATTTCTACCTCGAAATTTACCTGATCAGAACAGACGAGGATTC
66 TACAAATCTACCCTTAAAAGAAATTTCTACCTCAAAATTTACCTGATCAGAACAGACGAGGATTC
*
53259295 TGCTGACGCATCGAGTCCTCGGGTTCCCACGTGGCTCCCTCAGTGCCATGATTCTGCCACAGAAC
131 TGCTGACGCATCGAGTCCTCAGGTTCCCACGTGGCTCCCTCAGTGCCATGATTCTGCCACAGAAC
53259360 CTTCACTAACGGG
196 CTTCACTAACGGG
* *
53259373 AACCACTAAAGCATCTATACATTTGTGTTAGATATTTATAGAAAAAAATAAATTATTCAAGGTGT
1 AACCACTAAAGCATATATACATTTGTGTTAGATATTTACAGAAAAAAATAAATTATTCAAGGTGT
53259438 TACAAATCTACCCTTAAAAGAAATTTCTACCTCAAAATTTACCTGATCAGAACAGACGAGGATTC
66 TACAAATCTACCCTTAAAAGAAATTTCTACCTCAAAATTTACCTGATCAGAACAGACGAGGATTC
*
53259503 TGCTGACGCATCGAGTTCTCAGGTTCCCACGTGGCTCCCTCAGTGCCATGATTCTGCCACAGAAC
131 TGCTGACGCATCGAGTCCTCAGGTTCCCACGTGGCTCCCTCAGTGCCATGATTCTGCCACAGAAC
53259568 CTTCACTAACGGG
196 CTTCACTAACGGG
53259581 A
1 A
53259582 TGGACTTCCT
Statistics
Matches: 203, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
208 203 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (208 bp):
AACCACTAAAGCATATATACATTTGTGTTAGATATTTACAGAAAAAAATAAATTATTCAAGGTGT
TACAAATCTACCCTTAAAAGAAATTTCTACCTCAAAATTTACCTGATCAGAACAGACGAGGATTC
TGCTGACGCATCGAGTCCTCAGGTTCCCACGTGGCTCCCTCAGTGCCATGATTCTGCCACAGAAC
CTTCACTAACGGG
Found at i:53265126 original size:13 final size:13
Alignment explanation
Indices: 53265108--53265146 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
53265098 ATTCCATCCC
53265108 AAATACAGATACA
1 AAATACAGATACA
* *
53265121 AAATACAGGTAAA
1 AAATACAGATACA
53265134 AAATACAGATACA
1 AAATACAGATACA
53265147 GGAATTACAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.10, T:0.15
Consensus pattern (13 bp):
AAATACAGATACA
Found at i:53266714 original size:14 final size:14
Alignment explanation
Indices: 53266678--53266716 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
53266668 CCAGAACCCC
53266678 AAATCTTGAA-CTT
1 AAATCTTGAACCTT
* *
53266691 GAACCTTGAACCTT
1 AAATCTTGAACCTT
53266705 AAATCTTGAACC
1 AAATCTTGAACC
53266717 CCGATGTTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (14 bp):
AAATCTTGAACCTT
Found at i:53266788 original size:21 final size:21
Alignment explanation
Indices: 53266764--53266864 Score: 68
Period size: 21 Copynumber: 4.8 Consensus size: 21
53266754 AGGGTCTATG
*
53266764 GTTATGGGTTTAGGGTTACAT
1 GTTATAGGTTTAGGGTTACAT
**
53266785 GTTATTTGTTTAGGGTT-CAT
1 GTTATAGGTTTAGGGTTACAT
* *
53266805 GGTTTAAAGATTTAGGGTTACGA-
1 -G-TTATAGGTTTAGGGTTAC-AT
53266828 GTT-T-GAGTTTAGGGTTTA-AT
1 GTTATAG-GTTTAGGG-TTACAT
*
53266848 GTTTTAGGTTTAGGGTT
1 GTTATAGGTTTAGGGTT
53266865 TGGAATTCTA
Statistics
Matches: 63, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
19 2 0.03
20 15 0.24
21 30 0.48
22 14 0.22
23 1 0.02
24 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.31, T:0.47
Consensus pattern (21 bp):
GTTATAGGTTTAGGGTTACAT
Found at i:53266831 original size:22 final size:20
Alignment explanation
Indices: 53266792--53266843 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
53266782 CATGTTATTT
*
53266792 GTTTAGGGTTCATGGTTTAAA
1 GTTTAGGGTTCACGGTTT-AA
*
53266813 GATTTAGGGTT-ACGAGTTTGA
1 G-TTTAGGGTTCACG-GTTTAA
53266834 GTTTAGGGTT
1 GTTTAGGGTT
53266844 TAATGTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 9 0.33
21 5 0.19
22 13 0.48
ACGTcount: A:0.21, C:0.04, G:0.33, T:0.42
Consensus pattern (20 bp):
GTTTAGGGTTCACGGTTTAA
Found at i:53269685 original size:134 final size:134
Alignment explanation
Indices: 53269445--53269978 Score: 924
Period size: 134 Copynumber: 4.0 Consensus size: 134
53269435 GAAAACTCAA
*
53269445 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACATACGCCCGTGTGGCCAGGC
1 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACACACGCCCGTGTGGCCAGGC
53269510 CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
66 CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
53269575 ACGG
131 ACGG
* *
53269579 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACATACGCCCTTGTGGCCAGGC
1 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACACACGCCCGTGTGGCCAGGC
** *
53269644 CGTGTGGTTCACATGGCTAAAAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
66 CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
53269709 ACGG
131 ACGG
* *
53269713 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAAGGACACACTCCCGTGTGGCCAGGC
1 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACACACGCCCGTGTGGCCAGGC
* *
53269778 CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGTCGTGTGGGCATTCGATGTAAGGC
66 CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
**
53269843 ATAG
131 ACGG
**
53269847 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTTTAAGGGACACACGCCCGTGTGGCCAGGC
1 AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACACACGCCCGTGTGGCCAGGC
* *
53269912 CGTGTGGTTCACAAGGCCGAGAGGCACGCCCGTGTCTTAGGTCGTGTGGGCATTCGATGTGAGGC
66 CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
53269977 AC
131 AC
53269979 ACGACCGTGT
Statistics
Matches: 378, Mismatches: 22, Indels: 0
0.94 0.05 0.00
Matches are distributed among these distances:
134 378 1.00
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (134 bp):
AGAATTTTTCCCAAAATTTTAAAATTTTCCTTAGGTGCAAGGGACACACGCCCGTGTGGCCAGGC
CGTGTGGTTCACATGGCCGAGAGGCACGCCCGTGTCTTAGGCCGTGTGGGCATTCGATGTGAGGC
ACGG
Found at i:53271169 original size:63 final size:63
Alignment explanation
Indices: 53271016--53271172 Score: 149
Period size: 63 Copynumber: 2.5 Consensus size: 63
53271006 GCCTGAAGGC
* * * * * *
53271016 TAAACAGAAGCACATAAGTGCTAAAC-AAAGACCCATAAGGGTTGAATGGAAACCCATAAGGAT
1 TAAACAAAAGCTCAAAAGTGCTAAACGGAA-ACCCATAAGGGTTGAACGAAAACCCATAAGGAT
* * * *
53271079 TAAACAAAAGCTCAAAAGAGCTGAACGGAAACCCATTAGGGTTGAACGAAAACTCAT-AGGAGT
1 TAAACAAAAGCTCAAAAGTGCTAAACGGAAACCCATAAGGGTTGAACGAAAACCCATAAGGA-T
***
53271142 TAAA-AAGAAGCTCGTGAGTGCTAAACGGAAA
1 TAAACAA-AAGCTCAAAAGTGCTAAACGGAAA
53271173 GTAAAAATGA
Statistics
Matches: 76, Mismatches: 15, Indels: 6
0.78 0.15 0.06
Matches are distributed among these distances:
62 6 0.08
63 68 0.89
64 2 0.03
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (63 bp):
TAAACAAAAGCTCAAAAGTGCTAAACGGAAACCCATAAGGGTTGAACGAAAACCCATAAGGAT
Found at i:53278795 original size:42 final size:42
Alignment explanation
Indices: 53278728--53278863 Score: 119
Period size: 42 Copynumber: 3.2 Consensus size: 42
53278718 AGGCTAAACA
* * * * *
53278728 GAAGCACATAAGTGCTAAACAAAAACCCGTAAGGGTTGAACG
1 GAAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTGAACG
* * * **
53278770 GAAGCTCATAAGAGCTGAACGAAAACCCAAAAGGATTAAAAA
1 GAAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTGAACG
* * * * * *
53278812 AAAGCTCAAAAGAGCTGAACGGAAACCTATTATGGTTGAACG
1 GAAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTGAACG
*
53278854 GAAACTCATA
1 GAAGCTCATA
53278864 GGAGTTAAAC
Statistics
Matches: 70, Mismatches: 24, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTGAACGAAAACCCATAAGGGTTGAACG
Found at i:53286094 original size:28 final size:27
Alignment explanation
Indices: 53286056--53286117 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
53286046 AATTGTAATT
*
53286056 TTTTATACAAAAAAACTATGAATTTTTTA
1 TTTT-TAC-AAAAAACTATAAATTTTTTA
* *
53286085 TTTTTACAAAACATTATAAATTTTTTA
1 TTTTTACAAAAAACTATAAATTTTTTA
53286112 TATTTT
1 T-TTTT
53286118 TATTATATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
27 18 0.62
28 7 0.24
29 4 0.14
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (27 bp):
TTTTTACAAAAAACTATAAATTTTTTA
Found at i:53310573 original size:30 final size:30
Alignment explanation
Indices: 53310512--53310574 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
53310502 ACTTATTTTA
* *
53310512 TTGTTAATTTTGTTATTATTTTAAATACAT
1 TTGTTAATTTTGTTATTATTTCAAAGACAT
*
53310542 TTGTTAATTTTGTTATTATTTCAAAGGCAT
1 TTGTTAATTTTGTTATTATTTCAAAGACAT
53310572 TTG
1 TTG
53310575 CTTTTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTCAAAGACAT
Found at i:53310678 original size:18 final size:18
Alignment explanation
Indices: 53310657--53310696 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
53310647 GAAATATTTA
*
53310657 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
53310675 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
53310693 TTTT
1 TTTT
53310697 TATAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:53323798 original size:18 final size:18
Alignment explanation
Indices: 53323772--53323811 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
53323762 GACTCGGAAA
* *
53323772 AGGATACATATAAGGGTT
1 AGGACACATATAACGGTT
53323790 AGGACACATATAACGGTT
1 AGGACACATATAACGGTT
53323808 AGGA
1 AGGA
53323812 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.23
Consensus pattern (18 bp):
AGGACACATATAACGGTT
Found at i:53325673 original size:51 final size:50
Alignment explanation
Indices: 53325625--53325724 Score: 112
Period size: 51 Copynumber: 1.9 Consensus size: 50
53325615 TTAAAATTAT
*
53325625 TTAAAAATAGAGATTTAAGAGAAATTTAAGAA-GAACTTGAGAGCAAATTGAAA
1 TTAAAAAT-G-GATTGAAGAGAAATTT-AGAAGGAACTTGAGAGCAAATT-AAA
* * * *
53325678 TTAAATATGGATTGGAGAGAAATTTTGAAGGAATTTGAGAGCAAATT
1 TTAAAAATGGATTGAAGAGAAATTTAGAAGGAACTTGAGAGCAAATT
53325725 GAGAGGAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
50 3 0.07
51 30 0.73
52 1 0.02
53 7 0.17
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.28
Consensus pattern (50 bp):
TTAAAAATGGATTGAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTAAA
Found at i:53325717 original size:22 final size:23
Alignment explanation
Indices: 53325692--53325756 Score: 64
Period size: 22 Copynumber: 2.8 Consensus size: 23
53325682 ATATGGATTG
*
53325692 GAGAGAAATTTTGA-AGGAATTT
1 GAGAGAAATTTTGAGAGGAAATT
53325714 GAGAGCAAA--TTGAGAGGAAATT
1 GAGAG-AAATTTTGAGAGGAAATT
*
53325736 GAGAGGAAATTTAAGAGAGGA
1 GAGA-GAAATTT-TGAGAGGA
53325757 TTAGTTTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
21 4 0.11
22 19 0.54
23 4 0.11
24 1 0.03
25 7 0.20
ACGTcount: A:0.45, C:0.02, G:0.32, T:0.22
Consensus pattern (23 bp):
GAGAGAAATTTTGAGAGGAAATT
Found at i:53325756 original size:14 final size:11
Alignment explanation
Indices: 53325702--53325746 Score: 65
Period size: 11 Copynumber: 4.2 Consensus size: 11
53325692 GAGAGAAATT
*
53325702 TTGA-AGGAAT
1 TTGAGAGGAAA
*
53325712 TTGAGAGCAAA
1 TTGAGAGGAAA
53325723 TTGAGAGGAAA
1 TTGAGAGGAAA
53325734 TTGAGAGGAAA
1 TTGAGAGGAAA
53325745 TT
1 TT
53325747 TAAGAGAGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 4 0.13
11 27 0.87
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:53328778 original size:19 final size:20
Alignment explanation
Indices: 53328756--53328801 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
53328746 AAAAAAATTA
*
53328756 GAATTTTTATAAA-TATTTT
1 GAATTTTTAAAAATTATTTT
*
53328775 GAA-TTTAAAAAATTATTTT
1 GAATTTTTAAAAATTATTTT
53328794 GAATTTTT
1 GAATTTTT
53328802 TTGTAAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
18 7 0.32
19 12 0.55
20 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (20 bp):
GAATTTTTAAAAATTATTTT
Found at i:53329401 original size:30 final size:30
Alignment explanation
Indices: 53329367--53329428 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
53329357 CTTAACAAGT
* *
53329367 AAATGTCTCTAAAATAATAACAAAATTAAC
1 AAATGCCTCTAAAACAATAACAAAATTAAC
* *
53329397 AAATGCCTTTAAAACAATAATAAAATTAAC
1 AAATGCCTCTAAAACAATAACAAAATTAAC
53329427 AA
1 AA
53329429 TAAAATAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.58, C:0.13, G:0.03, T:0.26
Consensus pattern (30 bp):
AAATGCCTCTAAAACAATAACAAAATTAAC
Found at i:53330502 original size:45 final size:45
Alignment explanation
Indices: 53330451--53330537 Score: 122
Period size: 45 Copynumber: 1.9 Consensus size: 45
53330441 CTACTAAATA
*
53330451 TTTAACTAAATTGCAT-GCAATTTATTATAAATTATTTAAATTAAT
1 TTTAACTAAATTACATAG-AATTTATTATAAATTATTTAAATTAAT
* * *
53330496 TTTAACTAAATTACATAGTATTTATTGTTAATTATTTAAATT
1 TTTAACTAAATTACATAGAATTTATTATAAATTATTTAAATT
53330538 TGATTAAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 36 0.97
46 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (45 bp):
TTTAACTAAATTACATAGAATTTATTATAAATTATTTAAATTAAT
Found at i:53340976 original size:4 final size:4
Alignment explanation
Indices: 53340967--53341010 Score: 88
Period size: 4 Copynumber: 11.0 Consensus size: 4
53340957 ATTATAGTTG
53340967 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
53341011 TTACCTCTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:53346500 original size:19 final size:20
Alignment explanation
Indices: 53346459--53346500 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
53346449 AGCGTTACTT
**
53346459 AAAATGTTAAAGAGATTTTA
1 AAAATGTTAAAGAGATTAGA
*
53346479 AAAATTTTAAAGA-ATTAGA
1 AAAATGTTAAAGAGATTAGA
53346498 AAA
1 AAA
53346501 TCATAGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.57, C:0.00, G:0.12, T:0.31
Consensus pattern (20 bp):
AAAATGTTAAAGAGATTAGA
Found at i:53346537 original size:78 final size:77
Alignment explanation
Indices: 53346438--53346643 Score: 236
Period size: 78 Copynumber: 2.6 Consensus size: 77
53346428 CTAGGGTAAG
* * *
53346438 TTAATTTTTTAAGCGTTACTTAAAATGTTAAAGAGATTTTAAAAATTTTAAAGAATTAGAAAATC
1 TTAATTTTTTAA-CGTTACTTAAAATATTAAAGAGATTTTAAAAAATTAAAAGAATTAGAAAATC
*
53346503 ATAGAAAAATCTA
65 ATAGAAAAATCAA
* * * * * *
53346516 TTAATTTTTTATACCTCACTTAAAACATTAAACGA-CTTTTAAAAAATTAAAAGAGTTCGAAAAT
1 TTAATTTTTTA-ACGTTACTTAAAATATTAAA-GAGATTTTAAAAAATTAAAAGAATTAGAAAAT
53346580 CATAGAAAAATCAA
64 CATAGAAAAATCAA
* * *
53346594 TTAATTTCTTAAATGTTACTTAAAATATTAAAGAG-CTTTAAACAAATTAA
1 TTAATTT-TTTAACGTTACTTAAAATATTAAAGAGATTTTAAA-AAATTAA
53346644 GTAACTCCTA
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
77 8 0.07
78 93 0.87
79 6 0.06
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.36
Consensus pattern (77 bp):
TTAATTTTTTAACGTTACTTAAAATATTAAAGAGATTTTAAAAAATTAAAAGAATTAGAAAATCA
TAGAAAAATCAA
Found at i:53352570 original size:23 final size:22
Alignment explanation
Indices: 53352544--53352619 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
53352534 TCGGAATTTT
53352544 CATATCATATAACATATCGAAA
1 CATATCATATAACATATCGAAA
* * * *
53352566 CCATATCGTTTAACAAATCAAAA
1 -CATATCATATAACATATCGAAA
* *
53352589 TTATATCATATAGCATAT-GAAA
1 -CATATCATATAACATATCGAAA
53352611 CATATCATA
1 CATATCATA
53352620 CCCTCATCTG
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
21 8 0.20
22 3 0.07
23 30 0.73
ACGTcount: A:0.47, C:0.17, G:0.05, T:0.30
Consensus pattern (22 bp):
CATATCATATAACATATCGAAA
Found at i:53354481 original size:38 final size:38
Alignment explanation
Indices: 53354439--53354526 Score: 131
Period size: 38 Copynumber: 2.3 Consensus size: 38
53354429 TTACTACCCT
* *
53354439 ATTGAGAACATGATAAGCATGTCTACTGTTAATGATGA
1 ATTGAGTACATGATAAACATGTCTACTGTTAATGATGA
** *
53354477 ATTGAGTACATCTTAAACATGTCTACTGTTAGTGATGA
1 ATTGAGTACATGATAAACATGTCTACTGTTAATGATGA
53354515 ATTGAGTACATG
1 ATTGAGTACATG
53354527 TTATTGTCTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (38 bp):
ATTGAGTACATGATAAACATGTCTACTGTTAATGATGA
Found at i:53360401 original size:13 final size:13
Alignment explanation
Indices: 53360383--53360409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53360373 CATATTTATA
53360383 TAATTAAAATATT
1 TAATTAAAATATT
53360396 TAATTAAAATATT
1 TAATTAAAATATT
53360409 T
1 T
53360410 GAACATTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATTAAAATATT
Found at i:53360464 original size:29 final size:29
Alignment explanation
Indices: 53360432--53360494 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
53360422 AAACATTTAT
*
53360432 AATATGAAATATTTGT-AAATTTTAATATA
1 AATAT-AAATATTTGTAAAATATTAATATA
** *
53360461 AATATATTTATTTTTAAAATATTAATATA
1 AATATAAATATTTGTAAAATATTAATATA
53360490 AATAT
1 AATAT
53360495 TTTAAATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
AATATAAATATTTGTAAAATATTAATATA
Found at i:53360481 original size:23 final size:23
Alignment explanation
Indices: 53360455--53360529 Score: 62
Period size: 23 Copynumber: 3.1 Consensus size: 23
53360445 TGTAAATTTT
53360455 AATATAAATATATTTATTTTTAA
1 AATATAAATATATTTATTTTTAA
* ** *
53360478 AATATTAATATAAATATTTTAAA
1 AATATAAATATATTTATTTTTAA
*
53360501 TAATATATTAAGA-ATATTATTTTTAA
1 -AATATA--AATATAT-TTATTTTTAA
53360527 AAT
1 AAT
53360530 TTATTATTAA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
23 19 0.49
24 5 0.13
25 4 0.10
26 11 0.28
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (23 bp):
AATATAAATATATTTATTTTTAA
Found at i:53360508 original size:14 final size:14
Alignment explanation
Indices: 53360450--53360509 Score: 52
Period size: 14 Copynumber: 4.2 Consensus size: 14
53360440 ATATTTGTAA
53360450 ATTTTAATATAAAT
1 ATTTTAATATAAAT
* *
53360464 ATATTTATTTTTAAA-
1 AT-TTTA-ATATAAAT
*
53360479 ATATTAATATAAAT
1 ATTTTAATATAAAT
53360493 ATTTTAA-ATAATAT
1 ATTTTAATATAA-AT
53360507 ATT
1 ATT
53360510 AAGAATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
13 9 0.25
14 16 0.44
15 6 0.17
16 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTTAATATAAAT
Found at i:53360539 original size:13 final size:14
Alignment explanation
Indices: 53360506--53360543 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
53360496 TTAAATAATA
53360506 TATTAAGAATATTAT
1 TATTAA-AATATTAT
*
53360521 TTTTAAAAT-TTAT
1 TATTAAAATATTAT
53360534 TATTAAAATA
1 TATTAAAATA
53360544 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
13 12 0.60
14 3 0.15
15 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (14 bp):
TATTAAAATATTAT
Found at i:53360574 original size:17 final size:18
Alignment explanation
Indices: 53360552--53360598 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
53360542 TAAAATTTTA
53360552 ATATTATATAATTTAT-C
1 ATATTATATAATTTATAC
*
53360569 ATATTAT-TAA-GTATAC
1 ATATTATATAATTTATAC
53360585 ATATTTATATAATT
1 ATA-TTATATAATT
53360599 ATTTATATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.12
16 7 0.29
17 11 0.46
18 3 0.12
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATTATATAATTTATAC
Found at i:53361056 original size:37 final size:36
Alignment explanation
Indices: 53361015--53361093 Score: 113
Period size: 37 Copynumber: 2.2 Consensus size: 36
53361005 ATAACTCCTA
* * *
53361015 TTCATTTTTGTTTTTGCTCTGCAGGGAATCACTATTG
1 TTCATTTTTGTCTTTACTCTACAGGGAATCAC-ATTG
*
53361052 TTCATTTTTGTCTTTACTCTACAGGGAATCTCATTG
1 TTCATTTTTGTCTTTACTCTACAGGGAATCACATTG
53361088 TTCATT
1 TTCATT
53361094 CTTGGTTGCT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
36 10 0.26
37 28 0.74
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.49
Consensus pattern (36 bp):
TTCATTTTTGTCTTTACTCTACAGGGAATCACATTG
Found at i:53364581 original size:10 final size:9
Alignment explanation
Indices: 53364562--53364600 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
53364552 AATAGACATG
53364562 AAAATAAAT
1 AAAATAAAT
53364571 AAAATTAAAT
1 AAAA-TAAAT
53364581 AAGAATAAAT
1 AA-AATAAAT
*
53364591 AAAAAAAAT
1 AAAATAAAT
53364600 A
1 A
53364601 TACAAGTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 11 0.41
10 14 0.52
11 2 0.07
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAATAAAT
Found at i:53365501 original size:151 final size:145
Alignment explanation
Indices: 53365153--53365593 Score: 489
Period size: 151 Copynumber: 3.0 Consensus size: 145
53365143 TAAAGTTTTC
* * * * * * *
53365153 TTTAAAAAAGATAATTAATTTTCTTAAAAATCAAAAC-ATAATTTCGAAATAATT-AAAAAAATC
1 TTTAAAAAA-A-AACTATTTTTCTTAAAGATTAAAACTTTTATTT-GAAATAGTTGAAAAAAATC
* * *
53365216 --AATTTTTTTTAAAATTTTAAATTTTCCTTTAAAATGACTTAAAAAACATATTTTTATTTTTCA
63 AAAATTTATTTTAAAATTTTAAACTTTCCTTTAAAATGAC-TAAAAAAAATATTTTTATTTTTCA
53365279 AAATCTAAACTTTCTCTTT
127 AAATCTAAACTTTCTCTTT
* *
53365298 TTTAAAAAAAAACTATTTTTCTTAAAGATTAAAGCTTTTATTTTAAAGTAGTTGAAAAAAATCAA
1 TTTAAAAAAAAACTATTTTTCTTAAAGATTAAAACTTTTATTTGAAA-TAGTTGAAAAAAATCAA
53365363 AACTTTATTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAAAAAAATAGATTTTTATTTTTCA
65 AA-TTTATTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAAAAAAAT--ATTTTTATTTTTCA
* *
53365428 AAATTTAAATTTTCTCCTTTT
127 AAATCTAAACTTTCT-C-TTT
* * *
53365449 TTTTAAAAAATATTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGGAAAAAAAT-A
1 TTTAAAAAAAAACTATTTTTCTTAAAGATTAAAACTTTTA-TTTGAAATAGTT-GAAAAAAATCA
* * * **
53365513 AAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAGAAAAAACATATATATTT-TTTAA
64 AAATTTATTTTAAAATTTTAAACTTTCCTTTAAAATGACTA-AAAAAA-ATAT-T-TTTATTTTT
*
53365577 AAAAATCTAAACTTTCT
125 CAAAATCTAAACTTTCT
53365594 TTAAAAAAAA
Statistics
Matches: 253, Mismatches: 27, Indels: 26
0.83 0.09 0.08
Matches are distributed among these distances:
143 23 0.09
144 10 0.04
145 18 0.07
147 11 0.04
148 34 0.13
149 27 0.11
150 38 0.15
151 72 0.28
152 20 0.08
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (145 bp):
TTTAAAAAAAAACTATTTTTCTTAAAGATTAAAACTTTTATTTGAAATAGTTGAAAAAAATCAAA
ATTTATTTTAAAATTTTAAACTTTCCTTTAAAATGACTAAAAAAAATATTTTTATTTTTCAAAAT
CTAAACTTTCTCTTT
Found at i:53365510 original size:52 final size:50
Alignment explanation
Indices: 53365453--53365599 Score: 127
Period size: 52 Copynumber: 2.8 Consensus size: 50
53365443 CCTTTTTTTT
* * ** *
53365453 AAAAAATATTATTTTTCTTAAAGATTAAAACTTTTACTTTGAAATAGTTGGA
1 AAAAAATATTATTTTT-TTAAAAATTAAAAC-TTTACTTTAAAATAACTAGA
** * *
53365505 AAAAAATAAAATTTGTTTTAAAAATTTAAACTTTCCTTTAAAATAACTAGA
1 AAAAAATATTATTT-TTTTAAAAATTAAAACTTTACTTTAAAATAACTAGA
*
53365556 AAAAACATATATATTTTTTAAAAAAATCT-AAACTTT-CTTTAAAA
1 AAAAA-ATAT-TATTTTTT-TAAAAAT-TAAAACTTTACTTTAAAA
53365600 AAAAAATCAA
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
51 20 0.26
52 38 0.49
53 19 0.24
54 1 0.01
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (50 bp):
AAAAAATATTATTTTTTTAAAAATTAAAACTTTACTTTAAAATAACTAGA
Found at i:53365623 original size:25 final size:24
Alignment explanation
Indices: 53365575--53365623 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53365565 TATATTTTTT
* **
53365575 AAAAAAATCTAAACTTTCTTTAAA
1 AAAAAAATCAAAACTTTCCCTAAA
53365599 AAAAAAATCAAAACTTTTCCCTAAA
1 AAAAAAATCAAAAC-TTTCCCTAAA
53365624 TCAAGCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (24 bp):
AAAAAAATCAAAACTTTCCCTAAA
Found at i:53369716 original size:23 final size:22
Alignment explanation
Indices: 53369690--53369738 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
53369680 TTACTCTTTA
*
53369690 TGGCTTGAGTAAGTATATGAATG
1 TGGCTT-ACTAAGTATATGAATG
*
53369713 TGGC-TCCTAAGTATATGAATG
1 TGGCTTACTAAGTATATGAATG
53369734 TGGCT
1 TGGCT
53369739 CTTAAGATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 18 0.78
22 1 0.04
23 4 0.17
ACGTcount: A:0.27, C:0.10, G:0.29, T:0.35
Consensus pattern (22 bp):
TGGCTTACTAAGTATATGAATG
Found at i:53369724 original size:21 final size:21
Alignment explanation
Indices: 53369699--53369744 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
53369689 ATGGCTTGAG
53369699 TAAGTATATGAATGTGGCTCC
1 TAAGTATATGAATGTGGCTCC
*
53369720 TAAGTATATGAATGTGGCTCT
1 TAAGTATATGAATGTGGCTCC
53369741 TAAG
1 TAAG
53369745 ATGACATCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (21 bp):
TAAGTATATGAATGTGGCTCC
Found at i:53372138 original size:11 final size:11
Alignment explanation
Indices: 53372122--53372150 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
53372112 ACCATTCAAA
53372122 GAATTTTCTAT
1 GAATTTTCTAT
53372133 GAATTTTCTAT
1 GAATTTTCTAT
53372144 GAATTTT
1 GAATTTT
53372151 ATGGGTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (11 bp):
GAATTTTCTAT
Found at i:53379535 original size:36 final size:36
Alignment explanation
Indices: 53379483--53379565 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
53379473 ATATATAATT
* * * * * * *
53379483 ATCACTTTTAAATATTACAACTATATCATTATGCCGA
1 ATCACTTAT-AATATTACAAATACACCAATATACCAA
53379520 ATCACTTATAATATTACAAATACACCAATATACCAA
1 ATCACTTATAATATTACAAATACACCAATATACCAA
53379556 ATCACTTATA
1 ATCACTTATA
53379566 TGCTCAATTT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 31 0.79
37 8 0.21
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.34
Consensus pattern (36 bp):
ATCACTTATAATATTACAAATACACCAATATACCAA
Found at i:53379836 original size:43 final size:44
Alignment explanation
Indices: 53379775--53379897 Score: 128
Period size: 43 Copynumber: 2.8 Consensus size: 44
53379765 ACAATGTCAA
* * * *
53379775 TGTCCCAGACATGGTCTTACATGTAATCACATATCGATGCC-AC
1 TGTCCTAGACAGGGTCTTACATGTAAACACATATCGATACCAAC
*
53379818 TGTCCTAGACAGGGTCTTACATGTAACCACA-AGTCGATACCAAC
1 TGTCCTAGACAGGGTCTTACATGTAAACACATA-TCGATACCAAC
* * *
53379862 -GTCTTAGAC-GTGGTCTTACACGAAAACACATATCGA
1 TGTCCTAGACAG-GGTCTTACATGTAAACACATATCGA
53379898 AATCCTATGT
Statistics
Matches: 68, Mismatches: 8, Indels: 8
0.81 0.10 0.10
Matches are distributed among these distances:
42 2 0.03
43 63 0.93
44 3 0.04
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (44 bp):
TGTCCTAGACAGGGTCTTACATGTAAACACATATCGATACCAAC
Found at i:53382365 original size:14 final size:15
Alignment explanation
Indices: 53382311--53382388 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
53382301 AAAGCTATGA
* *
53382311 ATATTTATATTATTT
1 ATATTTTTAATATTT
*
53382326 ATATTTAATAATATTT
1 ATATTT-TTAATATTT
*
53382342 CACA-TTTTAATATTT
1 -ATATTTTTAATATTT
53382357 -TATTTTTAATAATTT
1 ATATTTTTAAT-ATTT
*
53382372 AATATTTTTAAAATTT
1 -ATATTTTTAATATTT
53382388 A
1 A
53382389 AAATATTAGG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
13 1 0.02
14 7 0.13
15 19 0.37
16 14 0.27
17 11 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTTTTAATATTT
Found at i:53382371 original size:15 final size:15
Alignment explanation
Indices: 53382323--53382387 Score: 53
Period size: 17 Copynumber: 4.1 Consensus size: 15
53382313 ATTTATATTA
*
53382323 TTTATATTTAATAAT
1 TTTATTTTTAATAAT
*
53382338 ATTTCACATTTTAAT-AT
1 -TTT-A-TTTTTAATAAT
53382355 TTTATTTTTAATAAT
1 TTTATTTTTAATAAT
53382370 TTAATATTTTTAA-AAT
1 TT--TATTTTTAATAAT
53382386 TT
1 TT
53382388 AAAATATTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
14 7 0.17
15 5 0.12
16 11 0.27
17 12 0.29
18 6 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATTTTTAATAAT
Found at i:53382386 original size:16 final size:17
Alignment explanation
Indices: 53382346--53382389 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
53382336 ATATTTCACA
53382346 TTTTAAT-ATTT--TAT
1 TTTTAATAATTTAATAT
53382360 TTTTAATAATTTAATAT
1 TTTTAATAATTTAATAT
53382377 TTTTAA-AATTTAA
1 TTTTAATAATTTAA
53382390 AATATTAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.26
15 4 0.15
16 7 0.26
17 9 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTAATAATTTAATAT
Found at i:53384883 original size:25 final size:25
Alignment explanation
Indices: 53384849--53384899 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
53384839 TCTTGAAAAC
*
53384849 TTTAACCTTTTTAGAAACACAACGA
1 TTTAACCTTTTTAAAAACACAACGA
53384874 TTTAACCTTTTTAAAAACACAACGA
1 TTTAACCTTTTTAAAAACACAACGA
53384899 T
1 T
53384900 AATAATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (25 bp):
TTTAACCTTTTTAAAAACACAACGA
Found at i:53390732 original size:21 final size:21
Alignment explanation
Indices: 53390708--53390767 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
53390698 CTAATATTAC
*
53390708 ATGCAAACCCATATGTTATTT
1 ATGCGAACCCATATGTTATTT
* *
53390729 ATGCGAACCAATATATTATTT
1 ATGCGAACCCATATGTTATTT
*
53390750 ATGTGAACCCTATATGTT
1 ATGCGAACCC-ATATGTT
53390768 TGTGACATGC
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 26 0.81
22 6 0.19
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (21 bp):
ATGCGAACCCATATGTTATTT
Found at i:53393672 original size:17 final size:17
Alignment explanation
Indices: 53393650--53393699 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
53393640 TCTCAGATTT
53393650 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
53393667 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
53393684 TGATACCCATATCTTT
1 TGATACCCATATCTTT
53393700 GACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:53398210 original size:17 final size:17
Alignment explanation
Indices: 53398188--53398237 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
53398178 TCTCAGATTT
53398188 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
53398205 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
53398222 TGATACCCATATCTTT
1 TGATACCCATATCTTT
53398238 TACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:53398522 original size:28 final size:27
Alignment explanation
Indices: 53398456--53398523 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
53398446 TGTATTTAAT
* ***
53398456 TATAATATATATTTTTAAAATTTTATTT
1 TATAATA-ATATTTATAAAATTTTAAAA
*
53398484 TATTAAAAATATTTATAAAATTTTAAAAA
1 TA-TAATAATATTTATAAAATTTT-AAAA
53398513 TATAATAATAT
1 TATAATAATAT
53398524 ACATATTAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TATAATAATATTTATAAAATTTTAAAA
Found at i:53399171 original size:32 final size:31
Alignment explanation
Indices: 53399135--53399209 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 31
53399125 TAAAAATAAA
** *
53399135 AATTATAAATTATAAAAAATCTTAAAATTAGG
1 AATTATAAAAAATAAAAAA-CATAAAATTAGG
* *
53399167 AATTATAAAAAAATTAAAAAGATAAAATTAGG
1 AATTAT-AAAAAATAAAAAACATAAAATTAGG
53399199 AATTATAAAAA
1 AATTATAAAAA
53399210 TTTCAATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
31 5 0.14
32 22 0.59
33 10 0.27
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.29
Consensus pattern (31 bp):
AATTATAAAAAATAAAAAACATAAAATTAGG
Found at i:53399186 original size:25 final size:24
Alignment explanation
Indices: 53399126--53399186 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 24
53399116 ATTTAAAAAT
*
53399126 AAAAA-TAAAAATTATAAATTATA
1 AAAAATTAAAAATTAGAAATTATA
* *
53399149 AAAAATCTTAAAATTAGGAATTATAA
1 AAAAAT-TAAAAATTAGAAATTAT-A
53399175 AAAAATTAAAAA
1 AAAAATTAAAAA
53399187 GATAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
23 5 0.16
25 19 0.61
26 7 0.23
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (24 bp):
AAAAATTAAAAATTAGAAATTATA
Found at i:53400961 original size:21 final size:21
Alignment explanation
Indices: 53400918--53400961 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
53400908 CATGGACGTT
*
53400918 TGGCTACCCCACACGCCTATG
1 TGGCTACCCCACACGCCCATG
* * *
53400939 TGGCTACTCCACATGCCCCTG
1 TGGCTACCCCACACGCCCATG
53400960 TG
1 TG
53400962 CTCAGATCGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.20, T:0.23
Consensus pattern (21 bp):
TGGCTACCCCACACGCCCATG
Found at i:53426335 original size:19 final size:20
Alignment explanation
Indices: 53426298--53426335 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
53426288 AAGTTAATAA
*
53426298 AAATTTTGATTAAGGTGGAC
1 AAATTTTGATTAAGATGGAC
*
53426318 AAATTTT-ATTACGATGGA
1 AAATTTTGATTAAGATGGA
53426336 TGACAGTGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (20 bp):
AAATTTTGATTAAGATGGAC
Found at i:53426516 original size:5 final size:5
Alignment explanation
Indices: 53426506--53426530 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53426496 AAATTTTTTT
53426506 ATTCG ATTCG ATTCG ATTCG ATTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG
53426531 GTCGAATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:53427368 original size:24 final size:24
Alignment explanation
Indices: 53427336--53427383 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
53427326 GGTAACATAG
53427336 GAAATTTATGCTTTTTATTTGTAA
1 GAAATTTATGCTTTTTATTTGTAA
* *
53427360 GAAATTTATGTTTTTTTTTTGTAA
1 GAAATTTATGCTTTTTATTTGTAA
53427384 TTTTTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
GAAATTTATGCTTTTTATTTGTAA
Found at i:53429335 original size:11 final size:12
Alignment explanation
Indices: 53429308--53429337 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
53429298 TCTTATTTGT
53429308 AATTTTTATTTC
1 AATTTTTATTTC
53429320 AATTTTTATTTC
1 AATTTTTATTTC
53429332 -ATTTTT
1 AATTTTT
53429338 CGCAAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.33
12 12 0.67
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
AATTTTTATTTC
Found at i:53443051 original size:14 final size:15
Alignment explanation
Indices: 53443023--53443060 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
53443013 GTTTGGTAGT
53443023 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
53443037 AAAATGATTTT-TGG
1 AAAATGATTTTCTGG
53443051 AAAATGATTT
1 AAAATGATTT
53443061 ACTTTTCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 18 0.78
15 5 0.22
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:53445747 original size:13 final size:13
Alignment explanation
Indices: 53445729--53445754 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
53445719 CCATTATTCA
53445729 TATATCTCTCACT
1 TATATCTCTCACT
53445742 TATATCTCTCACT
1 TATATCTCTCACT
53445755 CATAACCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TATATCTCTCACT
Found at i:53446065 original size:15 final size:15
Alignment explanation
Indices: 53446041--53446070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
53446031 AAATGTTTTC
*
53446041 TGGAATCTTCAACAA
1 TGGAAGCTTCAACAA
53446056 TGGAAGCTTCAACAA
1 TGGAAGCTTCAACAA
53446071 ACAATTTGTA
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:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (15 bp):
TGGAAGCTTCAACAA
Found at i:53447580 original size:26 final size:26
Alignment explanation
Indices: 53447543--53447612 Score: 122
Period size: 26 Copynumber: 2.7 Consensus size: 26
53447533 TATTCCAACC
*
53447543 CACAGCTCGTGTGAGCATGCCCATTT
1 CACAACTCGTGTGAGCATGCCCATTT
*
53447569 CACAACTTGTGTGAGCATGCCCATTT
1 CACAACTCGTGTGAGCATGCCCATTT
53447595 CACAACTCGTGTGAGCAT
1 CACAACTCGTGTGAGCAT
53447613 TGATGTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (26 bp):
CACAACTCGTGTGAGCATGCCCATTT
Found at i:53447679 original size:48 final size:48
Alignment explanation
Indices: 53447624--53447719 Score: 149
Period size: 48 Copynumber: 2.0 Consensus size: 48
53447614 GATGTAAAAG
**
53447624 AAAGGTTA-TGTTTATATGTAAAGGCATGTTATGTGTGAGATTTCCCGA
1 AAAGGTTACT-TTTATATGTAAAGGCACATTATGTGTGAGATTTCCCGA
*
53447672 AAAGGTTACTTTTATATGTAAAGGCACATTATGTGTGAGCTTTCCCGA
1 AAAGGTTACTTTTATATGTAAAGGCACATTATGTGTGAGATTTCCCGA
53447720 GTATTCGAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.36
Consensus pattern (48 bp):
AAAGGTTACTTTTATATGTAAAGGCACATTATGTGTGAGATTTCCCGA
Found at i:53452106 original size:36 final size:36
Alignment explanation
Indices: 53451975--53452092 Score: 155
Period size: 36 Copynumber: 3.3 Consensus size: 36
53451965 ATTCCAACCA
* * *
53451975 AAACACACTAGATGCTCAAAAGAGCTAATCCATCCA
1 AAACACACCAGATGCTCAAAAGAGTTAATCCATCCG
* **
53452011 AAACACACCAGATGCTCAAAATAGTTAATCCATATG
1 AAACACACCAGATGCTCAAAAGAGTTAATCCATCCG
** *
53452047 AAATGCAACAGATGCTCAAAAGAGTTAATCCATCCG
1 AAACACACCAGATGCTCAAAAGAGTTAATCCATCCG
53452083 AAACACACCA
1 AAACACACCA
53452093 ATGGCTCCGA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.45, C:0.25, G:0.12, T:0.18
Consensus pattern (36 bp):
AAACACACCAGATGCTCAAAAGAGTTAATCCATCCG
Found at i:53458925 original size:28 final size:27
Alignment explanation
Indices: 53458861--53458934 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
53458851 TAATGAGATT
* **
53458861 AGCACTAAGTGTGTGAGTTTAATTGAA
1 AGCACTAAGTGTGTGAGTATAAGGGAA
*
53458888 ATGCAGTAAGTGTGTGAGTATAAGGGTAA
1 A-GCACTAAGTGTGTGAGTATAAGGG-AA
*
53458917 AGCACTAAGTGTGCGAGT
1 AGCACTAAGTGTGTGAGT
53458935 TTGATTACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 1 0.03
28 35 0.90
29 3 0.08
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.28
Consensus pattern (27 bp):
AGCACTAAGTGTGTGAGTATAAGGGAA
Found at i:53459803 original size:39 final size:39
Alignment explanation
Indices: 53459756--53459833 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
53459746 GGTATATTTT
53459756 TGTGTTATAAATTTAATGTATAATGCTGTCCAATTTTAA
1 TGTGTTATAAATTTAATGTATAATGCTGTCCAATTTTAA
53459795 TGTGTTATAAATTTAATGTATAATGCTGTCCAATTTTAA
1 TGTGTTATAAATTTAATGTATAATGCTGTCCAATTTTAA
53459834 GTATATTGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (39 bp):
TGTGTTATAAATTTAATGTATAATGCTGTCCAATTTTAA
Found at i:53459830 original size:22 final size:22
Alignment explanation
Indices: 53459804--53459877 Score: 96
Period size: 22 Copynumber: 3.2 Consensus size: 22
53459794 ATGTGTTATA
53459804 AATTTAATGTATAATGCTGTCC
1 AATTTAATGTATAATGCTGTCC
53459826 AATTTTAA-GTATATTGATGCTGTCC
1 AA-TTTAATGTATA---ATGCTGTCC
*
53459851 ATTTTAATGTATAATGCTGTCC
1 AATTTAATGTATAATGCTGTCC
53459873 AATTT
1 AATTT
53459878 TGAGTATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
22 20 0.44
23 5 0.11
24 5 0.11
25 15 0.33
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.45
Consensus pattern (22 bp):
AATTTAATGTATAATGCTGTCC
Found at i:53459851 original size:25 final size:24
Alignment explanation
Indices: 53459817--53459948 Score: 107
Period size: 25 Copynumber: 5.6 Consensus size: 24
53459807 TTAATGTATA
53459817 ATGCTGTCCAATTTTAAGTATATT
1 ATGCTGTCCAATTTTAAGTATATT
53459841 GATGCTGTCC-ATTTTAATGTATA--
1 -ATGCTGTCCAATTTTAA-GTATATT
*
53459864 ATGCTGTCCAATTTTGAGTATATTT
1 ATGCTGTCCAATTTTAAGTATA-TT
* * ** *
53459889 AAGCTGTCTAATTCGATGTATA--
1 ATGCTGTCCAATTTTAAGTATATT
*
53459911 ATGCTGTCC-A-TTTAGAGCATATT
1 ATGCTGTCCAATTTTA-AGTATATT
53459934 ATTGCTGTCCAATTT
1 A-TGCTGTCCAATTT
53459949 GATGAATAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
20 2 0.02
21 5 0.06
22 21 0.25
23 7 0.08
24 15 0.18
25 31 0.37
26 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (24 bp):
ATGCTGTCCAATTTTAAGTATATT
Done.