Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 145 of 208
Found at i:44145312 original size:77 final size:76
Alignment explanation
Indices: 44145136--44145418 Score: 256
Period size: 79 Copynumber: 3.7 Consensus size: 76
44145126 GAAAATTACA
* * * * *
44145136 TAAAGGTTGCTTTAAACCTTAAAATATCTTTAAGAAATTAAGTAATT-TCTACATCAGGAAAAAA
1 TAAAGGTTACTTAAAACCTTAAAGTGT-TTTAAGAAATTAAGTAATTCT-TAAATCAGG--AAAA
44145200 AAATACTTAATTTAT
62 AAATACTTAATTTAT
* * *
44145215 GAAGGGTTACTTAAAACCTTAAAGTGTGTTTAAGAAATTAAGTAATTCTTAAATCACGG-GAAAA
1 TAAAGGTTACTTAAAACCTTAAAGTGT-TTTAAGAAATTAAGTAATTCTTAAATCA-GGAAAAAA
44145279 ATACTTAATTTAT
64 ATACTTAATTTAT
* * * * *
44145292 TAAAGGTTACTTAAAACCTTAAAGAGTTTTAAGGAATTAAGTAATTCCTAAACCAAGAAAAAAA-
1 TAAAGGTTACTTAAAACCTTAAAGTGTTTTAAGAAATTAAGTAATTCTTAAATCAGGAAAAAAAT
* * *
44145356 A-ATACTCTA-
66 ACTTAATTTAT
* * * * * *
44145365 -AGA-GTTACTTAAAACCTTAATGGGACTTTAAGAAATTAAGCAATTCCTAAATCA
1 TAAAGGTTACTTAAAACCTTAAAGTG-TTTTAAGAAATTAAGTAATTCTTAAATCA
44145419 TGAGAAAATT
Statistics
Matches: 173, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
71 19 0.11
72 27 0.16
74 5 0.03
75 2 0.01
76 30 0.17
77 41 0.24
79 46 0.27
80 3 0.02
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (76 bp):
TAAAGGTTACTTAAAACCTTAAAGTGTTTTAAGAAATTAAGTAATTCTTAAATCAGGAAAAAAAT
ACTTAATTTAT
Found at i:44149956 original size:22 final size:22
Alignment explanation
Indices: 44149911--44149973 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 22
44149901 TATGTATATG
44149911 TTTATAAAATGTATTATAATTTATAA
1 TTTATAAAAT-T-TTAT-ATTTAT-A
*
44149937 TTTATAAAATTTTAT-TTTATG
1 TTTATAAAATTTTATATTTATA
44149958 TTT-TAAAATTTT-TATT
1 TTTATAAAATTTTATATT
44149974 CATTTCGATT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.31
21 3 0.09
22 5 0.14
24 4 0.11
25 1 0.03
26 10 0.29
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (22 bp):
TTTATAAAATTTTATATTTATA
Found at i:44153880 original size:40 final size:40
Alignment explanation
Indices: 44153790--44153886 Score: 124
Period size: 40 Copynumber: 2.5 Consensus size: 40
44153780 ATACTCTTTA
* * *
44153790 TCTGTTGTGTTTCGATTAGATTAGCTCTTATGAGCTTCTG
1 TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTG
* * * *
44153830 TCTAGCGTGTTTCGGTTGGATTAGCTCTTGTGAGCTTCTT
1 TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTG
44153870 TCTGGTGTG-TTCGGTTG
1 TCTGGTGTGTTTCGGTTG
44153887 ATCTGGCGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
39 8 0.17
40 40 0.83
ACGTcount: A:0.10, C:0.15, G:0.28, T:0.46
Consensus pattern (40 bp):
TCTGGTGTGTTTCGGTTGGATTAGCTCTTATGAGCTTCTG
Found at i:44155710 original size:17 final size:18
Alignment explanation
Indices: 44155676--44155711 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
44155666 TACAAAATAC
44155676 AAATTTATTTCGCAATTT
1 AAATTTATTTCGCAATTT
44155694 AAATTTATTTC-CAATTT
1 AAATTTATTTCGCAATTT
44155711 A
1 A
44155712 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.36, C:0.11, G:0.03, T:0.50
Consensus pattern (18 bp):
AAATTTATTTCGCAATTT
Found at i:44161541 original size:25 final size:25
Alignment explanation
Indices: 44161513--44161560 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
44161503 ACAGCCACAC
44161513 AATAAACCCAATACCCAACACCCAA
1 AATAAACCCAATACCCAACACCCAA
*
44161538 AATAAATCCAATACCCAACACCC
1 AATAAACCCAATACCCAACACCC
44161561 CACAAGCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (25 bp):
AATAAACCCAATACCCAACACCCAA
Found at i:44166087 original size:16 final size:18
Alignment explanation
Indices: 44166053--44166093 Score: 59
Period size: 16 Copynumber: 2.4 Consensus size: 18
44166043 AAAATACAAA
44166053 TTTATTTCCCAATTTTAT
1 TTTATTTCCCAATTTTAT
44166071 TTTATTT-CCAA-TTTAT
1 TTTATTTCCCAATTTTAT
*
44166087 TTAATTT
1 TTTATTT
44166094 TTATGCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 4 0.18
18 7 0.32
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTATTTCCCAATTTTAT
Found at i:44166753 original size:77 final size:77
Alignment explanation
Indices: 44166608--44166759 Score: 180
Period size: 77 Copynumber: 2.0 Consensus size: 77
44166598 TTCTTCAACA
* **
44166608 TTACTCAAAACATTAAAAGGCTTTTAAGAAATTAACTAATTCAAAAATAATGAGAAAATTACTTA
1 TTACTCAAAACATTAAAAGGCTTTTAAGAAATTAACTAATTCAAAAATAATGAGAAAATGACAAA
44166673 ATTTCTTAAATG
66 ATTTCTTAAATG
* * * ** ** * *
44166685 TTACTTAAAACATTAAAAGAGCTTTTAAGAAATTGAGTAATTCTCAAATCTTGA-ATAATGAGAA
1 TTACTCAAAACATTAAAAG-GCTTTTAAGAAATTAACTAATTCAAAAATAATGAGAAAATGACAA
44166749 AATTTCTTAAA
65 AATTTCTTAAA
44166760 GGTCCTGAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
77 34 0.55
78 28 0.45
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (77 bp):
TTACTCAAAACATTAAAAGGCTTTTAAGAAATTAACTAATTCAAAAATAATGAGAAAATGACAAA
ATTTCTTAAATG
Found at i:44172589 original size:45 final size:45
Alignment explanation
Indices: 44172538--44172637 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 45
44172528 ATGTCATGCT
44172538 ATCTTTCAACCA-GGATCTTACTCATTTATATCATGACACCATAGC
1 ATCTTTCAACCATGG-TCTTACTCATTTATATCATGACACCATAGC
* * * **
44172583 ATCTTTCAGCCATGGTCTTACTCATTTTTATTATGATGCCATAGC
1 ATCTTTCAACCATGGTCTTACTCATTTATATCATGACACCATAGC
* *
44172628 GTTTTTCAAC
1 ATCTTTCAAC
44172638 TATAGTTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 44 0.96
46 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.11, T:0.39
Consensus pattern (45 bp):
ATCTTTCAACCATGGTCTTACTCATTTATATCATGACACCATAGC
Found at i:44182561 original size:17 final size:17
Alignment explanation
Indices: 44182539--44182571 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
44182529 TAGAATTGGG
*
44182539 TTGAGAAAATTATTTAA
1 TTGAGAAAAATATTTAA
44182556 TTGAGAAAAATATTTA
1 TTGAGAAAAATATTTA
44182572 TTTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TTGAGAAAAATATTTAA
Found at i:44183356 original size:40 final size:40
Alignment explanation
Indices: 44183301--44183392 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
44183291 TAGTAGAAAA
* *
44183301 GGACTAAATTGTGGAATTAATTGTTTATTTTGAGTAATAT
1 GGACTAAATTGTGGAATTAATTGTTAATTTTGAGCAATAT
44183341 GGACTAAATTGTGGAATTAATTGTTAATTTTGAGCAATAT
1 GGACTAAATTGTGGAATTAATTGTTAATTTTGAGCAATAT
44183381 GGACTAAATTGT
1 GGACTAAATTGT
44183393 TAAAATTTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.41
Consensus pattern (40 bp):
GGACTAAATTGTGGAATTAATTGTTAATTTTGAGCAATAT
Found at i:44184249 original size:18 final size:18
Alignment explanation
Indices: 44184226--44184273 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
44184216 ATGGAAAAGT
*
44184226 TGAGAAATGAACATGAGA
1 TGAGAAATGAACATGAAA
*
44184244 TGAGAAATGAAATATGAAA
1 TGAGAAATG-AACATGAAA
44184263 TGATGAAATGA
1 TGA-GAAATGA
44184274 GATATGAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 9 0.35
19 11 0.42
20 6 0.23
ACGTcount: A:0.52, C:0.02, G:0.25, T:0.21
Consensus pattern (18 bp):
TGAGAAATGAACATGAAA
Found at i:44185728 original size:48 final size:48
Alignment explanation
Indices: 44185652--44185744 Score: 143
Period size: 48 Copynumber: 1.9 Consensus size: 48
44185642 TCAAGAGGGA
* * *
44185652 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAGCAAAG
1 ATAAATAGTGATAAAAGTGTAGAAAGTGGAAAACCAAGTTTAGCAAAG
44185700 ATAAATA-TGGATAAAAGTGTAGAAAGTGGAAAACCAAGTTTAGCA
1 ATAAATAGT-GATAAAAGTGTAGAAAGTGGAAAACCAAGTTTAGCA
44185745 TTGCATAGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.22
Consensus pattern (48 bp):
ATAAATAGTGATAAAAGTGTAGAAAGTGGAAAACCAAGTTTAGCAAAG
Found at i:44187267 original size:9 final size:9
Alignment explanation
Indices: 44187255--44187289 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
44187245 TAACTTAACT
44187255 TAATTAATC
1 TAATTAATC
44187264 TAATTAATC
1 TAATTAATC
44187273 T-ATTAAATC
1 TAATT-AATC
44187282 TAATTAAT
1 TAATTAAT
44187290 GGTAACTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 3 0.12
9 18 0.75
10 3 0.12
ACGTcount: A:0.46, C:0.09, G:0.00, T:0.46
Consensus pattern (9 bp):
TAATTAATC
Found at i:44189997 original size:24 final size:24
Alignment explanation
Indices: 44189965--44190012 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
44189955 ATTTAAAAGT
44189965 TAAAATATGCTCTAAGTCCCTATA
1 TAAAATATGCTCTAAGTCCCTATA
*
44189989 TAAAATATGCTTTAAGTCCCTATA
1 TAAAATATGCTCTAAGTCCCTATA
44190013 CACTCTGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (24 bp):
TAAAATATGCTCTAAGTCCCTATA
Found at i:44190327 original size:7 final size:7
Alignment explanation
Indices: 44190315--44190376 Score: 106
Period size: 7 Copynumber: 8.6 Consensus size: 7
44190305 GAAATAGTTA
44190315 AGGGTTT
1 AGGGTTT
44190322 AGGGTTT
1 AGGGTTT
44190329 AGGGTTT
1 AGGGTTT
44190336 AGGGTTTT
1 AGGG-TTT
44190344 AGGGTTT
1 AGGGTTT
44190351 AGGGTTT
1 AGGGTTT
44190358 AGGGTTTT
1 AGGG-TTT
44190366 AGGGTTT
1 AGGGTTT
44190373 AGGG
1 AGGG
44190377 CAATATTGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
7 39 0.74
8 14 0.26
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.42
Consensus pattern (7 bp):
AGGGTTT
Found at i:44190346 original size:15 final size:14
Alignment explanation
Indices: 44190315--44190376 Score: 106
Period size: 15 Copynumber: 4.3 Consensus size: 14
44190305 GAAATAGTTA
44190315 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
44190329 AGGGTTTAGGGTTTT
1 AGGGTTTAGGG-TTT
44190344 AGGGTTTAGGGTTT
1 AGGGTTTAGGGTTT
44190358 AGGGTTTTAGGGTTT
1 AGGG-TTTAGGGTTT
44190373 AGGG
1 AGGG
44190377 CAATATTGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
14 18 0.39
15 28 0.61
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.42
Consensus pattern (14 bp):
AGGGTTTAGGGTTT
Found at i:44190347 original size:22 final size:22
Alignment explanation
Indices: 44190315--44190376 Score: 117
Period size: 22 Copynumber: 2.9 Consensus size: 22
44190305 GAAATAGTTA
44190315 AGGG-TTTAGGGTTTAGGGTTT
1 AGGGTTTTAGGGTTTAGGGTTT
44190336 AGGGTTTTAGGGTTTAGGGTTT
1 AGGGTTTTAGGGTTTAGGGTTT
44190358 AGGGTTTTAGGGTTTAGGG
1 AGGGTTTTAGGGTTTAGGG
44190377 CAATATTGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
21 4 0.10
22 36 0.90
ACGTcount: A:0.15, C:0.00, G:0.44, T:0.42
Consensus pattern (22 bp):
AGGGTTTTAGGGTTTAGGGTTT
Found at i:44190991 original size:63 final size:63
Alignment explanation
Indices: 44190918--44191046 Score: 240
Period size: 63 Copynumber: 2.0 Consensus size: 63
44190908 CGTGTGAAAA
44190918 AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
1 AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
* *
44190981 AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACATGCCTGTGTGATAG
1 AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
44191044 AGT
1 AGT
44191047 TACACAGCCT
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.28, C:0.21, G:0.33, T:0.19
Consensus pattern (63 bp):
AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
Found at i:44191024 original size:21 final size:20
Alignment explanation
Indices: 44190928--44191045 Score: 94
Period size: 21 Copynumber: 5.7 Consensus size: 20
44190918 AGTGACATAC
*
44190928 CCGTGTGAAAGAGGCACACGG
1 CCGTGTGATAGAGGCACAC-G
* *
44190949 CCGTGTGGTAGAGACACACG
1 CCGTGTGATAGAGGCACACG
* *
44190969 CCTGTATGATAGAGTGACATAC-
1 CC-GTGTGATAGAG-G-CACACG
*
44190991 CCGTGTGAAAGAGGCACACGG
1 CCGTGTGATAGAGGCACAC-G
* * *
44191012 CCGTGTGGTAGAGACACATG
1 CCGTGTGATAGAGGCACACG
44191032 CCTGTGTGATAGAG
1 CC-GTGTGATAGAG
44191046 TTACACAGCC
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
19 4 0.05
20 7 0.09
21 59 0.78
22 2 0.03
23 4 0.05
ACGTcount: A:0.27, C:0.21, G:0.34, T:0.18
Consensus pattern (20 bp):
CCGTGTGATAGAGGCACACG
Found at i:44191061 original size:63 final size:63
Alignment explanation
Indices: 44190918--44191061 Score: 225
Period size: 63 Copynumber: 2.3 Consensus size: 63
44190908 CGTGTGAAAA
*
44190918 AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
1 AGTGACACACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
* * *
44190981 AGTGACATACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACATGCCTGTGTGATAG
1 AGTGACACACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
* * *
44191044 AGTTACACAGCCTTGTGA
1 AGTGACACACCCGTGTGA
44191062 GTAGCCCGTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 75 1.00
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (63 bp):
AGTGACACACCCGTGTGAAAGAGGCACACGGCCGTGTGGTAGAGACACACGCCTGTATGATAG
Found at i:44193214 original size:51 final size:51
Alignment explanation
Indices: 44193139--44193306 Score: 329
Period size: 51 Copynumber: 3.3 Consensus size: 51
44193129 TTAGATCATG
44193139 ATTA-GGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
1 ATTAGGGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
44193189 ATTAGGGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
1 ATTAGGGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
44193240 ATTAGGGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
1 ATTAGGGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
44193291 ATTAGGGACTAAATTG
1 ATTAGGGACTAAATTG
44193307 AATAAATGAA
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
50 4 0.03
51 113 0.97
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.39
Consensus pattern (51 bp):
ATTAGGGACTAAATTGTAAAGTTAGTTAAGCTTGTTAGTTAACTTTGTAAC
Found at i:44221482 original size:45 final size:45
Alignment explanation
Indices: 44221408--44221493 Score: 109
Period size: 45 Copynumber: 1.9 Consensus size: 45
44221398 TCTTCCACCG
* *
44221408 AGTATAAATAATTAACAATAAATACTATGTGATTTACTTAAATTT
1 AGTATAAATAATTAACAATAAATAATATGTAATTTACTTAAATTT
* * * * *
44221453 AGTATAAATAATTTATAGTATATAATATGTAATTTAGTTAA
1 AGTATAAATAATTAACAATAAATAATATGTAATTTACTTAA
44221494 TTAGACAGTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.42
Consensus pattern (45 bp):
AGTATAAATAATTAACAATAAATAATATGTAATTTACTTAAATTT
Found at i:44221832 original size:2 final size:2
Alignment explanation
Indices: 44221825--44221855 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
44221815 CAAACATGCC
44221825 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
44221856 ATTACATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44222443 original size:19 final size:20
Alignment explanation
Indices: 44222407--44222444 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
44222397 TAAAAATTTT
*
44222407 AAAAATTAATAAATCAATTA
1 AAAAATTAATAAACCAATTA
*
44222427 AAAAATT-ATAACCCAATT
1 AAAAATTAATAAACCAATT
44222445 CAACCACTAA
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:0.61, C:0.11, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATTAATAAACCAATTA
Found at i:44229052 original size:42 final size:42
Alignment explanation
Indices: 44228993--44229118 Score: 130
Period size: 43 Copynumber: 3.0 Consensus size: 42
44228983 TTCCGATATG
44228993 TGATTTACGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
1 TGATTT-CGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
* * * * * *
44229036 TGATTAT-GTGTAAGACCTTGTTTGGGATAGTGACA-CTGTTATT
1 TGATT-TCGTGTAAGACCATGTCTGGGACATTGGCATC-G-TATA
* *
44229079 TGATTTCATGTAAGACCACGTCTGGGACATTGGCATCGTA
1 TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTA
44229119 CGAGCTTTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
41 1 0.02
42 27 0.42
43 35 0.54
44 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACATTGGCATCGTATA
Found at i:44235070 original size:22 final size:22
Alignment explanation
Indices: 44235045--44235089 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
44235035 TTGAGATTGT
44235045 TTTGTATAAAGGGTTGGAGAGA
1 TTTGTATAAAGGGTTGGAGAGA
44235067 TTTGTATAAAGGGTTGGAGAGA
1 TTTGTATAAAGGGTTGGAGAGA
44235089 T
1 T
44235090 CCAACTGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (22 bp):
TTTGTATAAAGGGTTGGAGAGA
Found at i:44235324 original size:19 final size:19
Alignment explanation
Indices: 44235302--44235348 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
44235292 CTGGCACATA
*
44235302 AAGTGTATATTGGCATACG
1 AAGTGTATATTGGCACACG
*
44235321 AAGTGTATCTTGGCACACG
1 AAGTGTATATTGGCACACG
*
44235340 AATTGTATA
1 AAGTGTATA
44235349 AACCCATACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.32, C:0.13, G:0.23, T:0.32
Consensus pattern (19 bp):
AAGTGTATATTGGCACACG
Found at i:44236594 original size:17 final size:17
Alignment explanation
Indices: 44236557--44236605 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
44236547 AATTTAGTTC
* *
44236557 ATTTGTTTATTTATCGTT
1 ATTTATTTATTT-TTGTT
* *
44236575 ATTTTTTTCTTTTTGTT
1 ATTTATTTATTTTTGTT
44236592 ATTTATTTATTTTT
1 ATTTATTTATTTTT
44236606 ATTCCTCTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 16 0.62
18 10 0.38
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (17 bp):
ATTTATTTATTTTTGTT
Found at i:44238799 original size:9 final size:9
Alignment explanation
Indices: 44238785--44238814 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
44238775 ATTAAAATAT
44238785 TAATTAAAC
1 TAATTAAAC
*
44238794 TAATTAAAT
1 TAATTAAAC
44238803 TAATTAAAC
1 TAATTAAAC
44238812 TAA
1 TAA
44238815 AATAACCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAC
Found at i:44240734 original size:23 final size:23
Alignment explanation
Indices: 44240708--44240762 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
44240698 ACAATAATCC
44240708 AAAAAATTAA-AGAAAATATTTTT
1 AAAAAATTAATAGAAAATA-TTTT
**
44240731 AAAAAATTAATTTAAAATATTTT
1 AAAAAATTAATAGAAAATATTTT
*
44240754 AAATAATTA
1 AAAAAATTA
44240763 TTAGTGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAAATTAATAGAAAATATTTT
Found at i:44244323 original size:13 final size:13
Alignment explanation
Indices: 44244305--44244331 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
44244295 AATTAGTAGC
44244305 TTAATTGATTATT
1 TTAATTGATTATT
44244318 TTAATTGATTATT
1 TTAATTGATTATT
44244331 T
1 T
44244332 ATGGTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (13 bp):
TTAATTGATTATT
Found at i:44251350 original size:38 final size:38
Alignment explanation
Indices: 44251308--44251464 Score: 208
Period size: 38 Copynumber: 4.2 Consensus size: 38
44251298 TTGTCTATAA
* * * *
44251308 GGTGTTATCGGGCTATATGCCTAGTAGGCCTTTGTGCC
1 GGTGTTATCGGGCTATGTGCCTAGCAAGCCTTCGTGCC
* **
44251346 GGTGTTTTTAGGCTATGTGCCTAGCAAGCCTTCGTGCC
1 GGTGTTATCGGGCTATGTGCCTAGCAAGCCTTCGTGCC
* * *
44251384 GGTGTTATTGGGCTATGTACCTAGCAAGCCTTCATGCC
1 GGTGTTATCGGGCTATGTGCCTAGCAAGCCTTCGTGCC
*
44251422 GGTGTTATCGGGCTATGTGCCTAGC-AGGCTTCGTGCC
1 GGTGTTATCGGGCTATGTGCCTAGCAAGCCTTCGTGCC
44251459 GGTGTT
1 GGTGTT
44251465 TAACGGGACT
Statistics
Matches: 104, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
37 16 0.15
38 88 0.85
ACGTcount: A:0.13, C:0.22, G:0.31, T:0.33
Consensus pattern (38 bp):
GGTGTTATCGGGCTATGTGCCTAGCAAGCCTTCGTGCC
Found at i:44253064 original size:24 final size:24
Alignment explanation
Indices: 44253011--44253064 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
44253001 ATTAATTTAC
* *
44253011 TATTACTATTATTATGATCATTGT
1 TATTATTAATATTATGATCATTGT
44253035 TATTATTAATATTATTGAT-ATTGT
1 TATTATTAATATTA-TGATCATTGT
44253059 TATTAT
1 TATTAT
44253065 ACTAGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (24 bp):
TATTATTAATATTATGATCATTGT
Found at i:44253301 original size:18 final size:18
Alignment explanation
Indices: 44253275--44253318 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44253265 ATTATTGCTC
* *
44253275 TTATGTGTATGGTATTGT
1 TTATTTGTATGGTATTGA
**
44253293 TTATTTGTATTTTATTGA
1 TTATTTGTATGGTATTGA
44253311 TTATTTGT
1 TTATTTGT
44253319 CATTCATTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (18 bp):
TTATTTGTATGGTATTGA
Found at i:44260472 original size:50 final size:50
Alignment explanation
Indices: 44260394--44260995 Score: 590
Period size: 50 Copynumber: 12.2 Consensus size: 50
44260384 AGCCACAAAC
** * * *
44260394 CTTACTTCCCCGGTATTACAGTGAAACAGATTGAAGCTACAACAGTGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* ** * *
44260444 ATTACTTCCCTAGCATTGCAGTGGAACAGATTAAAGCTACAACAGCGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * * *
44260494 CTTACTTCCCCGGTGTGGTAGTGAAACAGATTAAAGCTACAACAACGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * ** **
44260544 CTTACTT------CATTGACAGTGCAATGGAACAAA-CTA-AACAGCGAAT
1 CTTACTTCCCCGGCGTTG-CAGTGAAACAGATTAAAGCTACAACAGCGAAT
* *
44260587 CTTACTTCCCCGGTGTTGCGGTGAAACAGATTAAAGCTACAACAGCGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * * * *
44260637 CTTACTTCCCCGGCATTGCAATGAAATATATTAAAGCTACAATAGCGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * *
44260687 CTTACTTCCCCGGCATGGCAGTGAAACAGATTAAAGCTACAACAACGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * * *
44260737 CTTATTTCCCCGGCGGTGCAGTGGAACAGATTAAAGCTACAACAGTGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * * * * *
44260787 CTTACTTCCCCGACATTGCAATGAAACATATTAACGCTACAACAGTGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
* * * * **
44260837 CCTACTTCCCCGGTGTTGCACTGAAATAGATTAAAGCTACAACAAAGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
** * * * * * *
44260887 CTTACTTCCATGGTGGTGCAGTGGAACTGATCAAAGCTACAAAAGCGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
** * * * *
44260937 CTTACTTCCATGGCGGTGCAGTGGAACCGATTAAAGCTACAAAAGCGAAT
1 CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
*
44260987 CTTAGTTCC
1 CTTACTTCC
44260996 TTACAGACAC
Statistics
Matches: 454, Mismatches: 89, Indels: 18
0.81 0.16 0.03
Matches are distributed among these distances:
43 16 0.04
44 5 0.01
45 11 0.02
48 11 0.02
49 6 0.01
50 405 0.89
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (50 bp):
CTTACTTCCCCGGCGTTGCAGTGAAACAGATTAAAGCTACAACAGCGAAT
Found at i:44261009 original size:50 final size:50
Alignment explanation
Indices: 44260869--44261011 Score: 128
Period size: 50 Copynumber: 2.9 Consensus size: 50
44260859 GAAATAGATT
* ** *** *
44260869 AAAGCTACAACAA-AGAATCTTACTTCCATGGTGGTGCAGTGGAACTGATC
1 AAAGCTACAA-AAGCGAATCTTACTTCCATGACGACACAGTGGAACCGATC
* *** *
44260919 AAAGCTACAAAAGCGAATCTTACTTCCATGGCGGTGCAGTGGAACCGATT
1 AAAGCTACAAAAGCGAATCTTACTTCCATGACGACACAGTGGAACCGATC
* *
44260969 AAAGCTACAAAAGCGAATCTTAGTTCC-TTACAGACACAGTGGA
1 AAAGCTACAAAAGCGAATCTTACTTCCATGAC-GACACAGTGGA
44261012 TTGGAGCAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
49 4 0.05
50 77 0.95
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (50 bp):
AAAGCTACAAAAGCGAATCTTACTTCCATGACGACACAGTGGAACCGATC
Found at i:44262067 original size:24 final size:24
Alignment explanation
Indices: 44262014--44262067 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
44262004 ATTAATTTAC
* *
44262014 TATTACTATTATTATGATCATTGT
1 TATTATTAATATTATGATCATTGT
44262038 TATTATTAATATTATTGAT-ATTGT
1 TATTATTAATATTA-TGATCATTGT
44262062 TATTAT
1 TATTAT
44262068 ACTAGTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.57
Consensus pattern (24 bp):
TATTATTAATATTATGATCATTGT
Found at i:44262328 original size:18 final size:18
Alignment explanation
Indices: 44262302--44262345 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
44262292 ATTATTGCTC
* *
44262302 TTATGTGTATGGTATTGT
1 TTATTTGTATGGTATTGA
**
44262320 TTATTTGTATTTTATTGA
1 TTATTTGTATGGTATTGA
44262338 TTATTTGT
1 TTATTTGT
44262346 CATTCATTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.64
Consensus pattern (18 bp):
TTATTTGTATGGTATTGA
Found at i:44268820 original size:25 final size:25
Alignment explanation
Indices: 44268792--44268854 Score: 83
Period size: 25 Copynumber: 2.5 Consensus size: 25
44268782 ATGTGAGCTA
*
44268792 TATAACGAGAAGCTTAT-TCGGGCTG
1 TATAACGAGAAGCTTATCT-AGGCTG
* *
44268817 TATAACGGGAAACTTATCTAGGCTG
1 TATAACGAGAAGCTTATCTAGGCTG
44268842 TATAACGAGAAGC
1 TATAACGAGAAGC
44268855 CCATAAAGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 31 0.97
26 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (25 bp):
TATAACGAGAAGCTTATCTAGGCTG
Found at i:44268929 original size:25 final size:25
Alignment explanation
Indices: 44268901--44269041 Score: 87
Period size: 25 Copynumber: 5.6 Consensus size: 25
44268891 AATAACAGGT
44268901 AGCTCCGAAGAGCCATTAATCGGGA
1 AGCTCCGAAGAGCCATTAATCGGGA
* *
44268926 AGCTCCGGATAGCCA-TATATCGGGA
1 AGCTCCGAAGAGCCATTA-ATCGGGA
* * * *
44268951 AG-TTC-AAGCGAGCTA-T-ATTGGAA
1 AGCTCCGAA--GAGCCATTAATCGGGA
* *
44268974 AGCT-CTAGAGAGCCATTAATCAGGA
1 AGCTCCGA-AGAGCCATTAATCGGGA
* *
44268999 AGCTCACAAAGAGCCTTTAATCGGGA
1 AGCTC-CGAAGAGCCATTAATCGGGA
*
44269025 AGCTCATGAAGAGCCAT
1 AGCTC-CGAAGAGCCAT
44269042 ATATAGGGAC
Statistics
Matches: 88, Mismatches: 18, Indels: 19
0.70 0.14 0.15
Matches are distributed among these distances:
23 14 0.16
24 7 0.08
25 36 0.41
26 29 0.33
27 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.20
Consensus pattern (25 bp):
AGCTCCGAAGAGCCATTAATCGGGA
Found at i:44268999 original size:26 final size:25
Alignment explanation
Indices: 44268982--44269041 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
44268972 AAAGCTCTAG
44268982 AGAGCCATTAATCAGGAAGCTCACAA
1 AGAGCCATTAATC-GGAAGCTCACAA
* **
44269008 AGAGCCTTTAATCGGGAAGCTCATGA
1 AGAGCCATTAATC-GGAAGCTCACAA
44269034 AGAGCCAT
1 AGAGCCAT
44269042 ATATAGGGAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (25 bp):
AGAGCCATTAATCGGAAGCTCACAA
Found at i:44288640 original size:28 final size:30
Alignment explanation
Indices: 44288571--44288646 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 30
44288561 GAAAATTTTG
*
44288571 AAATAAATAATATATATGTACATATAAATTTA
1 AAATAAATAATATATA-GTACATAT-AATTCA
** *
44288603 AAATGGATAATGTATA-TACATAT-ATTCA
1 AAATAAATAATATATAGTACATATAATTCA
*
44288631 AAATAAATAACATATA
1 AAATAAATAATATATA
44288647 TAAAAAAGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 16 0.44
30 7 0.19
32 13 0.36
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (30 bp):
AAATAAATAATATATAGTACATATAATTCA
Found at i:44290341 original size:44 final size:45
Alignment explanation
Indices: 44290263--44290600 Score: 206
Period size: 44 Copynumber: 7.7 Consensus size: 45
44290253 TAATCTGCTG
* * **
44290263 CACTGCAACTTCAGGGAGATAGGA-TTAGCAACTTCTGTCTACTC
1 CACTGCAACTTCAGGGAGATAAGACTTGGTTACTTCTGTCTACTC
* *** *
44290307 CACTACAACTTCAGGGAGATAAGACTT-GTTACTTCAACCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGGTTACTTCTGTCTACTC
* * ** * *
44290351 TACTGCAACTTCAGAGAGATAAGGTTTGTGGCTT-CTTTTGTCTGCTC
1 CACTGCAACTTCAGGGAGATAA-GACT-TGG-TTACTTCTGTCTACTC
*
44290398 CACTGCAACTTCAGGGAGATAAGAC-TGG--A--TGTGATCTACTC
1 CACTGCAACTTCAGGGAGATAAGACTTGGTTACTTCTG-TCTACTC
* * * *
44290439 TACTACAACTTCAGAGAGATAAGATCTGTGGTT--TTAAT-TC-ACTC
1 CACTGCAACTTCAGGGAGATAAGA-CT-TGGTTACTT-CTGTCTACTC
* * * *
44290483 CACTGCAACTTTAGGGAGATAGGA-TTGGTTTCTTCTGTCTGCTC
1 CACTGCAACTTCAGGGAGATAAGACTTGGTTACTTCTGTCTACTC
* ** *
44290527 CACTGCAACTTCAGAGAGATAAGATCTGTGGTT--TT-AATCCACTC
1 CACTGCAACTTCAGGGAGATAAGA-CT-TGGTTACTTCTGTCTACTC
* *
44290571 CACTACAACTTCAGGGAGATAGGA-TTGGTT
1 CACTGCAACTTCAGGGAGATAAGACTTGGTT
44290601 TATTTAATCT
Statistics
Matches: 229, Mismatches: 44, Indels: 45
0.72 0.14 0.14
Matches are distributed among these distances:
40 3 0.01
41 37 0.16
42 4 0.02
43 4 0.02
44 131 0.57
45 8 0.03
46 4 0.02
47 36 0.16
48 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (45 bp):
CACTGCAACTTCAGGGAGATAAGACTTGGTTACTTCTGTCTACTC
Found at i:44290612 original size:88 final size:87
Alignment explanation
Indices: 44290303--44290622 Score: 324
Period size: 88 Copynumber: 3.6 Consensus size: 87
44290293 ACTTCTGTCT
* *
44290303 ACTCCACTACAACTTCAGGGAGATAAGACTT-GTTACTTCAACCTGCTCTACTGCAACTTCAGAG
1 ACTCCACTACAACTTCAGGGAGATAAGA-TTGGTTA-TTTAATCTGCTCTACTGCAACTTCAGAG
* * ** *
44290367 AGATAAGGTTTGTGGCTTCTTTTGTCT
64 AGATAAGATCTGTGG--T-TTTAATCC
* * * * * * *
44290394 GCTCCACTGCAACTTCAGGGAGATAAGACTGG--ATGTGATCTACTCTACTACAACTTCAGAGAG
1 ACTCCACTACAACTTCAGGGAGATAAGATTGGTTATTTAATCTGCTCTACTGCAACTTCAGAGAG
*
44290457 ATAAGATCTGTGGTTTTAATTC
66 ATAAGATCTGTGGTTTTAATCC
* * * ** *
44290479 ACTCCACTGCAACTTTAGGGAGATAGGATTGGTT-TCTTCTGTCTGCTCCACTGCAACTTCAGAG
1 ACTCCACTACAACTTCAGGGAGATAAGATTGGTTAT-TT-AATCTGCTCTACTGCAACTTCAGAG
44290543 AGATAAGATCTGTGGTTTTAATCC
64 AGATAAGATCTGTGGTTTTAATCC
* * *
44290567 ACTCCACTACAACTTCAGGGAGATAGGATTGGTTTATTTAATCTGCTTTTCTGCAA
1 ACTCCACTACAACTTCAGGGAGATAAGATTGG-TTATTTAATCTGCTCTACTGCAA
44290623 ACTATGGTGT
Statistics
Matches: 189, Mismatches: 33, Indels: 17
0.79 0.14 0.07
Matches are distributed among these distances:
85 32 0.17
86 2 0.01
87 1 0.01
88 120 0.63
89 5 0.03
90 2 0.01
91 27 0.14
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (87 bp):
ACTCCACTACAACTTCAGGGAGATAAGATTGGTTATTTAATCTGCTCTACTGCAACTTCAGAGAG
ATAAGATCTGTGGTTTTAATCC
Found at i:44290621 original size:132 final size:131
Alignment explanation
Indices: 44290303--44290622 Score: 337
Period size: 132 Copynumber: 2.4 Consensus size: 131
44290293 ACTTCTGTCT
* *
44290303 ACTCCACTACAACTTCAGGGAGATAAGACTTG-TTACTTCAACCTGCTCTACTGCAACTTCAGAG
1 ACTCCACTACAACTTCAGGGAGATAAGA-TTGTTTA-TTTAATCTGCTCTACTGCAACTTCAGAG
* * * *
44290367 AGATAAGGTTTGTGGCTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTGA
64 AGATAAGGTATGTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGTAA
*
44290432 TCT
129 TCC
* * * * * * *
44290435 ACTCTACTACAACTTCAGAGAGATAAGATCTGTGGT-TTTAAT-TCACTCCACTGCAACTTTAGG
1 ACTCCACTACAACTTCAGGGAGATAAGAT-TGT-TTATTTAATCT-GCTCTACTGCAACTTCAGA
* *
44290498 GAGAT-AGG-AT-TGGTTTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTT
63 GAGATAAGGTATGTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-C--TGGAT
*
44290560 TTAATCC
125 GTAATCC
* * *
44290567 ACTCCACTACAACTTCAGGGAGATAGGATTGGTTTATTTAATCTGCTTTTCTGCAA
1 ACTCCACTACAACTTCAGGGAGATAAGATT-GTTTATTTAATCTGCTCTACTGCAA
44290623 ACTATGGTGT
Statistics
Matches: 153, Mismatches: 25, Indels: 20
0.77 0.13 0.10
Matches are distributed among these distances:
129 40 0.26
130 2 0.01
131 7 0.05
132 102 0.67
133 1 0.01
134 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (131 bp):
ACTCCACTACAACTTCAGGGAGATAAGATTGTTTATTTAATCTGCTCTACTGCAACTTCAGAGAG
ATAAGGTATGTGGCTTCTTCTGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTGGATGTAATC
C
Found at i:44290745 original size:44 final size:45
Alignment explanation
Indices: 44290627--44290845 Score: 185
Period size: 44 Copynumber: 4.9 Consensus size: 45
44290617 CTGCAAACTA
* *
44290627 TGGTGTCTTCGATTTGCTTCGCTGTCAGTACAGGAAGGCAAAATC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAAAGC
* * * * * * *
44290672 TGCTATCTT-TAGTCTGCTTCACTGTCAGTACAAGAAGG-TAAGGC
1 TGGTGTCTTCGA-TCTGCTTCGCTGTCAGTACAGGAAGGCAAAAGC
* * *
44290716 TGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATC
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAAAGC
** * * * * * *
44290761 TTCTATCTTCAATCTAC-TCTGCTGGCAGTACAGGAAGGC-AATGA
1 TGGTGTCTTCGATCTGCTTC-GCTGTCAGTACAGGAAGGCAAAAGC
* * *
44290805 TGGTGTCTTCGATTTACTTCACTGTCAGTACAGGAAGGCAA
1 TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAA
44290846 GATCTGCTAT
Statistics
Matches: 131, Mismatches: 37, Indels: 12
0.73 0.21 0.07
Matches are distributed among these distances:
44 66 0.50
45 65 0.50
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.31
Consensus pattern (45 bp):
TGGTGTCTTCGATCTGCTTCGCTGTCAGTACAGGAAGGCAAAAGC
Found at i:44290790 original size:89 final size:89
Alignment explanation
Indices: 44290626--44290860 Score: 319
Period size: 89 Copynumber: 2.6 Consensus size: 89
44290616 TCTGCAAACT
* * * *
44290626 ATGGTGTCTTCGATTTGCTTCGCTGTCAGTACAGGAAGGCAAAATCTGCTATCTTTAGTCTGCTT
1 ATGGTGTCTTCGATTTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTT
* *
44290691 CACTGTCAGTACAAGAAGGTAAGG
66 CACTGGCAGTACAAGAAGGCAAGG
* * * *
44290715 CTGGTGTCTTCGATCTGCTTCGTTGTCAGTACAGGAAGGCAAGATCTTCTATCTTCAATCTAC-T
1 ATGGTGTCTTCGATTTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTT
* * *
44290779 CTGCTGGCAGTACAGGAAGGCAATG
66 C-ACTGGCAGTACAAGAAGGCAAGG
* *
44290804 ATGGTGTCTTCGATTTACTTCACTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCA
1 ATGGTGTCTTCGATTTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCA
44290861 GTGATCTGTT
Statistics
Matches: 126, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
88 2 0.02
89 124 0.98
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (89 bp):
ATGGTGTCTTCGATTTGCTTCGCTGTCAGTACAGGAAGGCAAGATCTGCTATCTTCAATCTACTT
CACTGGCAGTACAAGAAGGCAAGG
Found at i:44292965 original size:3 final size:3
Alignment explanation
Indices: 44292957--44293043 Score: 106
Period size: 3 Copynumber: 28.7 Consensus size: 3
44292947 TAATCACTTA
* * *
44292957 ATT ATT ATT ATT ATT -TGCT ATT ATT -TT TTT ACT ATTT ATT ATT GTT
1 ATT ATT ATT ATT ATT AT--T ATT ATT ATT ATT ATT A-TT ATT ATT ATT
44293003 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44293044 ATTTGATTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
2 3 0.04
3 67 0.91
4 3 0.04
5 1 0.01
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:44293349 original size:2 final size:2
Alignment explanation
Indices: 44293342--44293371 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
44293332 TGAAAATCTC
*
44293342 AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44293372 TATTTGCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44294791 original size:7 final size:7
Alignment explanation
Indices: 44294770--44294824 Score: 53
Period size: 7 Copynumber: 8.1 Consensus size: 7
44294760 CCTTGGCCTC
44294770 TCTTTCT
1 TCTTTCT
44294777 TCTTT-T
1 TCTTTCT
44294783 TC-TTCTT
1 TCTTTC-T
44294790 TCTTTCT
1 TCTTTCT
*
44294797 TTTTTCT
1 TCTTTCT
*
44294804 TTTTTCT
1 TCTTTCT
44294811 TCTTT-T
1 TCTTTCT
*
44294817 CCTTTCT
1 TCTTTCT
44294824 T
1 T
44294825 TTCTCTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 2 0.05
6 8 0.20
7 27 0.68
8 3 0.08
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TCTTTCT
Found at i:44294821 original size:27 final size:25
Alignment explanation
Indices: 44294770--44294835 Score: 89
Period size: 27 Copynumber: 2.6 Consensus size: 25
44294760 CCTTGGCCTC
*
44294770 TCTTTCTTC-TTTTTCTTCTTTCTT
1 TCTTTTTTCTTTTTTCTTCTTTCTT
44294794 TCTTTTTTCTTTTTTCTTCTTTTCCTT
1 TCTTTTTTCTTTTTTCTTC-TTT-CTT
*
44294821 TCTTTTCTCTTTTTT
1 TCTTTTTTCTTTTTT
44294836 TTAAATATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
24 8 0.22
25 9 0.24
26 3 0.08
27 17 0.46
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (25 bp):
TCTTTTTTCTTTTTTCTTCTTTCTT
Found at i:44294836 original size:20 final size:20
Alignment explanation
Indices: 44294799--44294835 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44294789 TTCTTTCTTT
*
44294799 TTTCTTTTTTCTTCTTTTCC
1 TTTCTTTTCTCTTCTTTTCC
44294819 TTTCTTTTCTCTT-TTTT
1 TTTCTTTTCTCTTCTTTT
44294836 TTAAATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTCTTCTTTTCC
Found at i:44297555 original size:11 final size:11
Alignment explanation
Indices: 44297539--44297567 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
44297529 CAGTCGTTCC
44297539 TGCATCTGTCT
1 TGCATCTGTCT
44297550 TGCATCTGTCT
1 TGCATCTGTCT
44297561 TGCATCT
1 TGCATCT
44297568 CTTTTTGCAA
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:0.10, C:0.28, G:0.17, T:0.45
Consensus pattern (11 bp):
TGCATCTGTCT
Found at i:44297736 original size:24 final size:25
Alignment explanation
Indices: 44297709--44297761 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
44297699 GGCTCTTTCG
* *
44297709 TGAAATTTAATGCAAATG-ATGTAA
1 TGAAATGTAATGCAAATGAATGGAA
*
44297733 TGAAATGTAATGCAGATGAATGGAA
1 TGAAATGTAATGCAAATGAATGGAA
44297758 TGAA
1 TGAA
44297762 TGCAAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.28
Consensus pattern (25 bp):
TGAAATGTAATGCAAATGAATGGAA
Found at i:44300036 original size:28 final size:30
Alignment explanation
Indices: 44299967--44300041 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 30
44299957 GAAAATTTTG
*
44299967 AAATAAATAATATATATGTACATATAAATTTA
1 AAATAAATAATATATA-GTACATAT-AATTCA
**
44299999 AAATGGATAATATATA-TACATAT-ATTCA
1 AAATAAATAATATATAGTACATATAATTCA
*
44300027 AAATAAATAACATAT
1 AAATAAATAATATAT
44300042 GTAAAAAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
28 16 0.43
30 7 0.19
32 14 0.38
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (30 bp):
AAATAAATAATATATAGTACATATAATTCA
Found at i:44301320 original size:9 final size:9
Alignment explanation
Indices: 44301306--44301332 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
44301296 GTTTAGGTTG
44301306 TGGGCCACT
1 TGGGCCACT
44301315 TGGGCCACT
1 TGGGCCACT
44301324 TGGGCCACT
1 TGGGCCACT
44301333 AGGTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.33, G:0.33, T:0.22
Consensus pattern (9 bp):
TGGGCCACT
Found at i:44304895 original size:29 final size:29
Alignment explanation
Indices: 44304853--44304920 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
44304843 TACCGAAGGG
44304853 ATTGGCGATTTTATTGCATATTATAAGTT
1 ATTGGCGATTTTATTGCATATTATAAGTT
44304882 ATTGGCGATTTTATTGCATATTATAAGTT
1 ATTGGCGATTTTATTGCATATTATAAGTT
44304911 ATTGGCGATT
1 ATTGGCGATT
44304921 ATATCGCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.26, C:0.07, G:0.19, T:0.47
Consensus pattern (29 bp):
ATTGGCGATTTTATTGCATATTATAAGTT
Found at i:44312215 original size:17 final size:16
Alignment explanation
Indices: 44312193--44312226 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
44312183 AAATAACTCA
*
44312193 ATCGAATATAATTAATT
1 ATCGAAT-TAAATAATT
44312210 ATCGAATTAAATAATT
1 ATCGAATTAAATAATT
44312226 A
1 A
44312227 GGGATTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.38
Consensus pattern (16 bp):
ATCGAATTAAATAATT
Found at i:44314104 original size:22 final size:22
Alignment explanation
Indices: 44314074--44314115 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
44314064 CCAACGATGT
*
44314074 AATATCCCGAAAATTACTACTG
1 AATACCCCGAAAATTACTACTG
44314096 AATACCCCGAAAATTACTAC
1 AATACCCCGAAAATTACTAC
44314116 AGTAAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (22 bp):
AATACCCCGAAAATTACTACTG
Found at i:44314314 original size:30 final size:31
Alignment explanation
Indices: 44314280--44314337 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
44314270 TAAATACTCG
* *
44314280 AAATTTGAGGGAATAA-AGTGTAAATATGAA
1 AAATTTGAAGGAACAATAGTGTAAATATGAA
*
44314310 AAATTTGAAGGACCAATAGTGTAAATAT
1 AAATTTGAAGGAACAATAGTGTAAATAT
44314338 TTTAAGAGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.28
Consensus pattern (31 bp):
AAATTTGAAGGAACAATAGTGTAAATATGAA
Found at i:44322058 original size:33 final size:33
Alignment explanation
Indices: 44322016--44322079 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
44322006 GTAGACTAGC
44322016 TCTGTGTTTACTATCCCAATGGACTATCTCTAT
1 TCTGTGTTTACTATCCCAATGGACTATCTCTAT
* * *
44322049 TCTGTGTTTACTGTCCTAGTGGACTATCTCT
1 TCTGTGTTTACTATCCCAATGGACTATCTCT
44322080 TCTGTGCGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.23, G:0.16, T:0.44
Consensus pattern (33 bp):
TCTGTGTTTACTATCCCAATGGACTATCTCTAT
Found at i:44328849 original size:22 final size:20
Alignment explanation
Indices: 44328795--44328874 Score: 88
Period size: 20 Copynumber: 3.9 Consensus size: 20
44328785 CACAACACGT
44328795 AGCCTATGTTGAGCCATAAC
1 AGCCTATGTTGAGCCATAAC
*
44328815 AGCCTATGTTGAGCCATAAT
1 AGCCTATGTTGAGCCATAAC
* *
44328835 AGCTCTTGTGTTGAGCCATAGC
1 AGC-C-TATGTTGAGCCATAAC
* * *
44328857 AACATATGTTGAGTCATA
1 AGCCTATGTTGAGCCATA
44328875 GCCTGAAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 34 0.68
21 1 0.02
22 15 0.30
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (20 bp):
AGCCTATGTTGAGCCATAAC
Found at i:44328983 original size:9 final size:9
Alignment explanation
Indices: 44328969--44328993 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
44328959 TTAGTATCGA
44328969 GGGCATATC
1 GGGCATATC
44328978 GGGCATATC
1 GGGCATATC
44328987 GGGCATA
1 GGGCATA
44328994 AAGTGTACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (9 bp):
GGGCATATC
Found at i:44330551 original size:16 final size:16
Alignment explanation
Indices: 44330530--44330584 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
44330520 TCTAGGTATG
44330530 TGAAGAGACTTGAAAA
1 TGAAGAGACTTGAAAA
*
44330546 TGAAGAG--TTAGAAATG
1 TGAAGAGACTT-GAAA-A
*
44330562 TGAAGAGACTTGAAGA
1 TGAAGAGACTTGAAAA
44330578 TGAAGAG
1 TGAAGAG
44330585 TTACACACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.06
15 4 0.12
16 21 0.66
17 3 0.09
18 2 0.06
ACGTcount: A:0.45, C:0.04, G:0.31, T:0.20
Consensus pattern (16 bp):
TGAAGAGACTTGAAAA
Found at i:44330568 original size:32 final size:32
Alignment explanation
Indices: 44330527--44330587 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
44330517 GTTTCTAGGT
44330527 ATGTGAAGAGACTTGAAAATGAAGAGTTAGAA
1 ATGTGAAGAGACTTGAAAATGAAGAGTTAGAA
*
44330559 ATGTGAAGAGACTTGAAGATGAAGAGTTA
1 ATGTGAAGAGACTTGAAAATGAAGAGTTA
44330588 CACACATGCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.44, C:0.03, G:0.30, T:0.23
Consensus pattern (32 bp):
ATGTGAAGAGACTTGAAAATGAAGAGTTAGAA
Found at i:44330665 original size:39 final size:39
Alignment explanation
Indices: 44330601--44330692 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 39
44330591 ACATGCATGT
* * *
44330601 AGATGAATACTCACAACTCCTATAGCATTTAAATGATGA
1 AGATGAATAGTCACAACTCCTATAGCACTGAAATGATGA
* * *
44330640 AGATAAATAGTCACAACTCCTATAGCACTGAAGTGATGT
1 AGATGAATAGTCACAACTCCTATAGCACTGAAATGATGA
44330679 AGATGAATAGTCAC
1 AGATGAATAGTCAC
44330693 TTACAACTCC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.26
Consensus pattern (39 bp):
AGATGAATAGTCACAACTCCTATAGCACTGAAATGATGA
Found at i:44335016 original size:32 final size:32
Alignment explanation
Indices: 44334965--44335025 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
44334955 GTTTCTAAGT
*
44334965 ATGTAAAGAGACTTGAAGATGAAGAGTTAGAA
1 ATGTAAAGAAACTTGAAGATGAAGAGTTAGAA
*
44334997 ATGTGAAGAAACTTGAAGATGAAGAGTTA
1 ATGTAAAGAAACTTGAAGATGAAGAGTTA
44335026 CACACATGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.46, C:0.03, G:0.28, T:0.23
Consensus pattern (32 bp):
ATGTAAAGAAACTTGAAGATGAAGAGTTAGAA
Found at i:44335093 original size:39 final size:39
Alignment explanation
Indices: 44335039--44335130 Score: 157
Period size: 39 Copynumber: 2.4 Consensus size: 39
44335029 ACATGCATGT
* *
44335039 AGATGAATAGTCACAACTCCTATAGCATTTAAGTGATGA
1 AGATGAATAGTCACAACTCCTATAGCACTGAAGTGATGA
*
44335078 AGATGAATAGTCACAACTCCTATAGCACTGAAGTGATGT
1 AGATGAATAGTCACAACTCCTATAGCACTGAAGTGATGA
44335117 AGATGAATAGTCAC
1 AGATGAATAGTCAC
44335131 TTACAACTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.26
Consensus pattern (39 bp):
AGATGAATAGTCACAACTCCTATAGCACTGAAGTGATGA
Found at i:44337341 original size:30 final size:30
Alignment explanation
Indices: 44337305--44337365 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
44337295 GAAGTAAGCG
44337305 AGTTTGGCTTGAGGTGCGGTAGTCACTACC
1 AGTTTGGCTTGAGGTGCGGTAGTCACTACC
*
44337335 AGTTTGGCTTGAGGTGCGGTAGTCCCTACC
1 AGTTTGGCTTGAGGTGCGGTAGTCACTACC
44337365 A
1 A
44337366 ACCGAAGTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.33, T:0.30
Consensus pattern (30 bp):
AGTTTGGCTTGAGGTGCGGTAGTCACTACC
Found at i:44340796 original size:2 final size:2
Alignment explanation
Indices: 44340789--44340814 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44340779 TTTATAAACC
44340789 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
44340815 GCTTACAGAG
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44348630 original size:257 final size:252
Alignment explanation
Indices: 44348178--44348692 Score: 772
Period size: 257 Copynumber: 2.0 Consensus size: 252
44348168 CAGAGAAGAT
* * *
44348178 AATTTTGTAAATATTTCAAACGGGTAGAATGAGTTTAGACTCGATTTAAAAAAAAATAACTTCCT
1 AATTTTGTAAATATTTCAAACAGGTAGAACGAGTTTAGACTCGATTTAAAAAAAAAAAACTTCCT
44348243 TCCTCTCAAACTTAATTTAAAAAAAAAAGAAATTCAACTCTAACAAATCCAATCGAATGAAACCA
66 TCCTCTCAAACTTAATTTAAAAAAAAAAGAAATTCAACTCTAACAAATCCAATCGAATGAAACCA
*
44348308 ATTGGTTTCAATTTTTTTATCATATCTATTGGTAATTACCATTACAAATAAATTGAGTTTGATTC
131 ATTGATTTCAATTTTTTTATCATATCTATTGGTAATTACCATTACAAATAAATTGAGTTTGATTC
44348373 TACTCTATTA-TTTGTTCGTCCATTAACTAATGCAAGTTTAATCACTATTTACAAGTA
196 TACTCTATTAGTTT-TTCGTCCATTAACTAATGCAAGTTTAATCACTATTTACAAGTA
*
44348430 GATTTTGTAAATATTTCAAACAGGTAGAACGAGTTTAGACTCGATTTTAAAAAAAAAAATACTTC
1 AATTTTGTAAATATTTCAAACAGGTAGAACGAGTTTAGACTCGA-TTTAAAAAAAAAAA-ACTTC
* * * * *
44348495 C-TCCATTTCAAACTTAATTT-TAAAAAACA-AAATTCCAACTCTATCAAATCCGATCGAATGAA
64 CTTCC-TCTCAAACTTAATTTAAAAAAAAAAGAAATT-CAACTCTAACAAATCCAATCGAATG-A
*
44348557 AACCAATCT-ATTTCAATTTTTTTTTTATCATATCTATCT-GTAATTACTATTACAAATAAATTG
126 AACCAAT-TGATTTCAA---TTTTTTTATCATATCTAT-TGGTAATTACCATTACAAATAAATTG
* *
44348620 AGTTTGATTCTACTCTATTAGTTTTTCGTCCATTAACTAATGCATGTTTAATCACTATTTACGAG
186 AGTTTGATTCTACTCTATTAGTTTTTCGTCCATTAACTAATGCAAGTTTAATCACTATTTACAAG
44348685 TA
251 TA
44348687 AATTTT
1 AATTTT
44348693 TCACATTTAA
Statistics
Matches: 238, Mismatches: 14, Indels: 17
0.88 0.05 0.06
Matches are distributed among these distances:
252 46 0.19
253 46 0.19
254 34 0.14
255 1 0.00
257 107 0.45
258 4 0.02
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (252 bp):
AATTTTGTAAATATTTCAAACAGGTAGAACGAGTTTAGACTCGATTTAAAAAAAAAAAACTTCCT
TCCTCTCAAACTTAATTTAAAAAAAAAAGAAATTCAACTCTAACAAATCCAATCGAATGAAACCA
ATTGATTTCAATTTTTTTATCATATCTATTGGTAATTACCATTACAAATAAATTGAGTTTGATTC
TACTCTATTAGTTTTTCGTCCATTAACTAATGCAAGTTTAATCACTATTTACAAGTA
Found at i:44349803 original size:3 final size:3
Alignment explanation
Indices: 44349795--44349828 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
44349785 ATTTTTAGAA
44349795 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
44349829 TTGCATAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:44349968 original size:40 final size:40
Alignment explanation
Indices: 44349924--44350051 Score: 122
Period size: 40 Copynumber: 3.2 Consensus size: 40
44349914 AGCGGCATTT
*
44349924 TTAGCGGCG-TTTGGGAAAAAACGCCACTAAAAATCAAGCA
1 TTAGCGGCGCTTT-GGAAAAAACGCCGCTAAAAATCAAGCA
* * **
44349964 TTAGCAGCGCTTT-TATAAAAACGCCGCTAAAGGTCAAGCA
1 TTAGCGGCGCTTTGGA-AAAAACGCCGCTAAAAATCAAGCA
* *
44350004 TCAGCGGCGCTTTTTGG--AAAACGCTGCTAAAAAT-AAGCA
1 TTAGCGGCGC--TTTGGAAAAAACGCCGCTAAAAATCAAGCA
44350043 TTAGCGGCG
1 TTAGCGGCG
44350052 TTTTTTGTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
39 14 0.20
40 51 0.72
41 3 0.04
42 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTTGGAAAAAACGCCGCTAAAAATCAAGCA
Found at i:44350057 original size:39 final size:40
Alignment explanation
Indices: 44349940--44350067 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
44349930 GCGTTTGGGA
* * *
44349940 AAAAACGCCACTAAAAATCAAGCATTAGCAGCGCTTTTAT-
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCG-TTTTTTG
** * *
44349980 AAAAACGCCGCTAAAGGTCAAGCATCAGCGGCGCTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTTTG
* *
44350020 GAAAACGCTGCTAAAAAT-AAGCATTAGCGGCGTTTTTTG
1 AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTTTG
*
44350059 TAAAACGCC
1 AAAAACGCC
44350068 ACAAAAAGCC
Statistics
Matches: 72, Mismatches: 15, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 30 0.42
40 42 0.58
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.23
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCAAGCATTAGCGGCGTTTTTTG
Found at i:44350160 original size:41 final size:41
Alignment explanation
Indices: 44350103--44350511 Score: 498
Period size: 41 Copynumber: 10.0 Consensus size: 41
44350093 CTATTTTTTG
* *
44350103 GGGCCTTTAGCGGCATTTTTGAAAAAGTGCTGCTAATGCTC
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
*
44350144 GGGCCTTTAGCGGCATTTTTAAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* *
44350185 GGGCCTTTAGC-GCATTTTTAAAAAAGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* *
44350225 GGGCCTTTAGCGGCATTTTTTATAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* ** * *
44350266 GGGTCTTTAGCGGTGTTTTTGATAAAGGGCCGCTAATGCTC
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* * * * *
44350307 GGGTCTTTAGCGACGTTTTTGATAAAGCACCGCTAATGCTC
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* * ** * *
44350348 GGGCCTTTAGCGACGTTTTTGGTAAAGCGTCGCTAATGCTG
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* *
44350389 GGGCCTTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCC-TTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
* *
44350431 GGCCCTTTAGCGGCATTTTTGAAGAAGCGCCGCTAATGGC-C
1 GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAAT-GCTC
* * * *
44350472 GGCCCTTTAGCGACGTTTTTTTAAAAAGCGCCGCTAATGC
1 GGGCCTTTAGCGGC-ATTTTTGAAAAAGCGCCGCTAATGC
44350512 CCTTTTTTTT
Statistics
Matches: 331, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
40 39 0.12
41 236 0.71
42 56 0.17
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:44350768 original size:14 final size:15
Alignment explanation
Indices: 44350740--44350772 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
44350730 AAGGTTTATA
44350740 GATTATGGAATTAGG
1 GATTATGGAATTAGG
44350755 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
44350769 GATT
1 GATT
44350773 TTGATTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:44351101 original size:28 final size:29
Alignment explanation
Indices: 44351038--44351109 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
44351028 ATATATTAAA
* *
44351038 TAAGGTTTAGGGGTTAGCGGTTAGGAGTT
1 TAAGGTTTAGGGGTTAACAGTTAGGAGTT
**
44351067 TGGGGTTT-GGGGTTAACAGTTAGTGA-TT
1 TAAGGTTTAGGGGTTAACAGTTAG-GAGTT
*
44351095 TAAGGTTTAGAGGTT
1 TAAGGTTTAGGGGTT
44351110 CGGGGTCAGA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
28 21 0.62
29 13 0.38
ACGTcount: A:0.21, C:0.03, G:0.39, T:0.38
Consensus pattern (29 bp):
TAAGGTTTAGGGGTTAACAGTTAGGAGTT
Found at i:44355370 original size:2 final size:2
Alignment explanation
Indices: 44355363--44355390 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44355353 CTGTGTAATT
44355363 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44355391 AATTTAAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44357696 original size:30 final size:31
Alignment explanation
Indices: 44357657--44357716 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
44357647 GGAGGTGGGA
* *
44357657 TGGGAAGGGAATAAAAGTTTTAGTGGAAAAG
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
* *
44357688 TGGG-AGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTTAGGGGAAAA
44357717 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:44357886 original size:30 final size:30
Alignment explanation
Indices: 44357825--44357886 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
44357815 GGAGGGGAGG
* * **
44357825 GGAGTAAAAGTTTTGGGGGGAAAGTGGAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
44357855 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
1 GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
44357885 GG
1 GG
44357887 CTTGGGAGTT
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:0.42, C:0.00, G:0.39, T:0.19
Consensus pattern (30 bp):
GGAGTAAAAGTTTTGAGGGAAAAGTAAAAA
Found at i:44357942 original size:9 final size:9
Alignment explanation
Indices: 44357928--44357964 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
44357918 TATAGTTTGA
44357928 TATTCGAAT
1 TATTCGAAT
44357937 TATTCGAAT
1 TATTCGAAT
*
44357946 TATTCGAGT
1 TATTCGAAT
44357955 TATTCGAAT
1 TATTCGAAT
44357964 T
1 T
44357965 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44358033 original size:9 final size:9
Alignment explanation
Indices: 44358016--44358046 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44358006 TCGAGTTGAT
44358016 TCGAATAAC
1 TCGAATAAC
*
44358025 TCGATTAAC
1 TCGAATAAC
44358034 TCGAATAAC
1 TCGAATAAC
44358043 TCGA
1 TCGA
44358047 TTCGTTTAAC
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:44358172 original size:19 final size:19
Alignment explanation
Indices: 44358150--44358215 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
44358140 TAATTTGATA
44358150 AATTTTATGTATGGTGTTT
1 AATTTTATGTATGGTGTTT
* * *
44358169 AATTTTTTGTTACTGTCTGTGT
1 AATTTTATG-TA-TG-GTGTTT
*
44358191 AATTTTATGTGTGGTGTTT
1 AATTTTATGTATGGTGTTT
44358210 AATTTT
1 AATTTT
44358216 TCGTTACTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 18 0.49
20 4 0.11
21 3 0.08
22 12 0.32
ACGTcount: A:0.18, C:0.03, G:0.20, T:0.59
Consensus pattern (19 bp):
AATTTTATGTATGGTGTTT
Found at i:44358190 original size:24 final size:24
Alignment explanation
Indices: 44358163--44358241 Score: 64
Period size: 25 Copynumber: 3.5 Consensus size: 24
44358153 TTTATGTATG
44358163 GTGTTTAATTTTTTGTTACTGTCT
1 GTGTTTAATTTTTTGTTACTGTCT
* *
44358187 GTG--TAATTTTATG----TGT-G
1 GTGTTTAATTTTTTGTTACTGTCT
* *
44358204 GTGTTTAATTTTTCGTTACTCTCT
1 GTGTTTAATTTTTTGTTACTGTCT
44358228 GTGTTTTAATTTTT
1 GTG-TTTAATTTTT
44358242 CATATGTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 15
0.66 0.10 0.24
Matches are distributed among these distances:
17 3 0.07
18 3 0.07
19 8 0.20
22 9 0.22
23 2 0.05
24 6 0.15
25 10 0.24
ACGTcount: A:0.14, C:0.08, G:0.18, T:0.61
Consensus pattern (24 bp):
GTGTTTAATTTTTTGTTACTGTCT
Found at i:44358195 original size:41 final size:41
Alignment explanation
Indices: 44358150--44358231 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
44358140 TAATTTGATA
* *
44358150 AATTTTATGTATGGTGTTTAATTTTTTGTTACTGTCTGTGT
1 AATTTTATGTATGGTGTTTAATTTTTCGTTACTCTCTGTGT
*
44358191 AATTTTATGTGTGGTGTTTAATTTTTCGTTACTCTCTGTGT
1 AATTTTATGTATGGTGTTTAATTTTTCGTTACTCTCTGTGT
44358232 TTTAATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.16, C:0.07, G:0.20, T:0.57
Consensus pattern (41 bp):
AATTTTATGTATGGTGTTTAATTTTTCGTTACTCTCTGTGT
Found at i:44358692 original size:43 final size:43
Alignment explanation
Indices: 44358555--44358819 Score: 291
Period size: 43 Copynumber: 6.2 Consensus size: 43
44358545 AGGTTATATT
* * * *
44358555 TTTAGCGGCGTTT-TTGCAATAAGCGTCGCTAAAGGT-TTGTTC
1 TTTAGCGGCGTTTGTGGCAA-AAGCGCCGCTAAAGGTCATGGTC
* * * * *
44358597 TTTAGCGGTGTTTGTGACAGAAGCGTCGCTAAAAAGTCATGGTC
1 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCT-AAAGGTCATGGTC
* * * *
44358641 TATAGCGGCGTTTATGGTAAAAGCGCCGCTAAAGGACATGGTC
1 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGGTC
* * **
44358684 TTTAGCGGCGTTTGTGGGAAAAGCACCGCTAAAGGTCCCGGTC
1 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGGTC
*
44358727 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGGTC
* * * * *
44358770 TTTAGCGACGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGCC
1 TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGGTC
44358813 TTTAGCG
1 TTTAGCG
44358820 ACGCATTCTT
Statistics
Matches: 189, Mismatches: 31, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
42 22 0.12
43 140 0.74
44 27 0.14
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGCAAAAGCGCCGCTAAAGGTCATGGTC
Found at i:44358881 original size:22 final size:22
Alignment explanation
Indices: 44358855--44358896 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
44358845 CGGCACTTAT
*
44358855 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
44358877 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
44358897 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:44361821 original size:7 final size:7
Alignment explanation
Indices: 44361796--44361851 Score: 94
Period size: 7 Copynumber: 8.0 Consensus size: 7
44361786 CATAATTGAA
44361796 TAATAAT
1 TAATAAT
*
44361803 TAATTAT
1 TAATAAT
*
44361810 AAATAAT
1 TAATAAT
44361817 TAATAAT
1 TAATAAT
44361824 TAATAAT
1 TAATAAT
44361831 TAATAAT
1 TAATAAT
44361838 TAATAAT
1 TAATAAT
44361845 TAATAAT
1 TAATAAT
44361852 ATTTATTTAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATAAT
Found at i:44362779 original size:16 final size:16
Alignment explanation
Indices: 44362760--44362795 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
44362750 TTTGAATTCA
*
44362760 AGAAAATTTAAATTAG
1 AGAAAATTTAAATAAG
*
44362776 AGAAAATTTGAATAAG
1 AGAAAATTTAAATAAG
44362792 AGAA
1 AGAA
44362796 GTTCGACCCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (16 bp):
AGAAAATTTAAATAAG
Found at i:44365273 original size:28 final size:28
Alignment explanation
Indices: 44365233--44365288 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
44365223 TGATTGATAG
44365233 TTTGGATCTTAAAAATAAATTAACAGAC
1 TTTGGATCTTAAAAATAAATTAACAGAC
44365261 TTTGGATCTTAAAAATAAATTAACAGAC
1 TTTGGATCTTAAAAATAAATTAACAGAC
44365289 CAAGCATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (28 bp):
TTTGGATCTTAAAAATAAATTAACAGAC
Found at i:44366771 original size:57 final size:58
Alignment explanation
Indices: 44366698--44366811 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
44366688 TTTTCATGTC
* *
44366698 ATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATT-CGATTTCTCTATTTTA
1 ATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCGATTTCTCCATTTTA
* * * *
44366755 ATTTTCATTTTTGAGAAAACCATAATCATTTCCAAATGTTTCCTATTTCTCCATTTT
1 ATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCGATTTCTCCATTTT
44366812 CACCATTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 37 0.74
58 13 0.26
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.46
Consensus pattern (58 bp):
ATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCGATTTCTCCATTTTA
Found at i:44367905 original size:4 final size:4
Alignment explanation
Indices: 44367896--44367922 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
44367886 AGAGGACTAA
44367896 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
44367923 GATAAACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:44370493 original size:39 final size:39
Alignment explanation
Indices: 44370450--44370590 Score: 210
Period size: 39 Copynumber: 3.6 Consensus size: 39
44370440 CATGTTCATT
* *
44370450 TTTAAGCATATATCACATTACACATATAATCACATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* * *
44370489 TTTAAGGATATGTCACAATACTCATATAATCATATAACA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
* *
44370528 TTTAAGCATATACCACAATACTCATATAATCACATAAAA
1 TTTAAGCATATATCACAATACTCATATAATCACATAACA
*
44370567 TTCAAGCATATATCACAATACTCA
1 TTTAAGCATATATCACAATACTCA
44370591 AAAACATGTT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 90 1.00
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.30
Consensus pattern (39 bp):
TTTAAGCATATATCACAATACTCATATAATCACATAACA
Found at i:44371118 original size:23 final size:24
Alignment explanation
Indices: 44371084--44371128 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
44371074 CATCTCAGTT
44371084 CACATATTCACAA-AT-ACATAAG
1 CACATATTCACAAGATAACATAAG
44371106 CACATAGTTCACAAGATAACATA
1 CACATA-TTCACAAGATAACATA
44371129 GGTATGAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 2 0.10
25 5 0.25
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (24 bp):
CACATATTCACAAGATAACATAAG
Found at i:44371227 original size:52 final size:52
Alignment explanation
Indices: 44371164--44371268 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
44371154 TTTAGAGTAG
44371164 GGGTCTAGGCTACTACTAAATTCTCAAATAATGCATTGAATTATTTCCACAA
1 GGGTCTAGGCTACTACTAAATTCTCAAATAATGCATTGAATTATTTCCACAA
44371216 GGGTCTAGGCTACTACTAAATTCTCAAATAATGCATTGAATTATTTCCACAA
1 GGGTCTAGGCTACTACTAAATTCTCAAATAATGCATTGAATTATTTCCACAA
44371268 G
1 G
44371269 CAATTAATCC
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.32
Consensus pattern (52 bp):
GGGTCTAGGCTACTACTAAATTCTCAAATAATGCATTGAATTATTTCCACAA
Found at i:44376872 original size:39 final size:39
Alignment explanation
Indices: 44376832--44376967 Score: 218
Period size: 39 Copynumber: 3.5 Consensus size: 39
44376822 ATACAGTTTT
* * *
44376832 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
**
44376871 AAGGTTATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
44376910 AAGCATATATCACAATACTCATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
44376949 AAGCATACATCACAATACT
1 AAGCATATATCACAATACT
44376968 TAAAAATATG
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 89 1.00
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.29
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:44376901 original size:17 final size:17
Alignment explanation
Indices: 44376879--44376940 Score: 54
Period size: 17 Copynumber: 3.4 Consensus size: 17
44376869 TTAAGGTTAT
44376879 ATCACAATACTCATATA
1 ATCACAATACTCATATA
*
44376896 ATCAC-ATAACATTCAAGCATA
1 ATCACAAT-AC--TC-A-TATA
44376917 TATCACAATACTCATATA
1 -ATCACAATACTCATATA
44376935 ATCACA
1 ATCACA
44376941 TAACATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
16 2 0.06
17 13 0.36
18 3 0.08
19 3 0.08
20 3 0.08
21 3 0.08
22 7 0.19
23 2 0.06
ACGTcount: A:0.47, C:0.24, G:0.02, T:0.27
Consensus pattern (17 bp):
ATCACAATACTCATATA
Found at i:44376923 original size:22 final size:22
Alignment explanation
Indices: 44376890--44376962 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 22
44376880 TCACAATACT
44376890 CATATAATCACATAACATTCAAG
1 CATAT-ATCACATAACATTCAAG
44376913 CATATATCACA-ATAC--TC-A-
1 CATATATCACATA-ACATTCAAG
*
44376931 TATA-ATCACATAACATTCAAG
1 CATATATCACATAACATTCAAG
*
44376952 CATACATCACA
1 CATATATCACA
44376963 ATACTTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 15
0.71 0.03 0.26
Matches are distributed among these distances:
17 8 0.20
18 4 0.10
19 3 0.07
20 3 0.07
21 4 0.10
22 14 0.34
23 5 0.12
ACGTcount: A:0.47, C:0.25, G:0.03, T:0.26
Consensus pattern (22 bp):
CATATATCACATAACATTCAAG
Found at i:44377907 original size:17 final size:18
Alignment explanation
Indices: 44377872--44377912 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
44377862 GAAATTTCAT
44377872 TTAAAAGACTAGATAAAA
1 TTAAAAGACTAGATAAAA
44377890 TTAAAA-ACTA-ATAGAAA
1 TTAAAAGACTAGATA-AAA
44377907 TATAAA
1 T-TAAA
44377913 TGGTTACCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.14
17 8 0.38
18 10 0.48
ACGTcount: A:0.63, C:0.05, G:0.07, T:0.24
Consensus pattern (18 bp):
TTAAAAGACTAGATAAAA
Found at i:44379074 original size:28 final size:25
Alignment explanation
Indices: 44379026--44379102 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 25
44379016 ATTAGTACAG
* *
44379026 TGTGGGCCTTAGCCTATTACAGTAA
1 TGTGGGCCTTAGCCCAATACAGTAA
* *
44379051 TAGTATGGGTCTTAGCCCAATACACT-A
1 T-G--TGGGCCTTAGCCCAATACAGTAA
*
44379078 TGTGGGCCTTAGCCCAGTACAGTAA
1 TGTGGGCCTTAGCCCAATACAGTAA
44379103 ACAGTACAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
24 18 0.44
25 2 0.05
26 2 0.05
27 2 0.05
28 17 0.41
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.29
Consensus pattern (25 bp):
TGTGGGCCTTAGCCCAATACAGTAA
Found at i:44379706 original size:27 final size:27
Alignment explanation
Indices: 44379442--44379715 Score: 241
Period size: 27 Copynumber: 10.2 Consensus size: 27
44379432 TATATCAGTC
* * *
44379442 ATTTTACCCTAT-GGGGGTATTTAG-TC
1 ATTTTACCCT-TCGAGGGTATTTCGATA
* * * *
44379468 ATTTTATCCTTCGAGGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * * *
44379495 ATTTTACCCTTCGGGGGTATTTTGGTC
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
44379522 ATTTTATCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
44379549 ATTTTATCCTAT-GGGGGTATTTCGATA
1 ATTTTACCCT-TCGAGGGTATTTCGATA
*
44379576 ATTTTACCCTTTGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* *
44379603 ATTTTACCCGTCGAGGATATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* * *
44379630 TTTTTACCCTTCGAAGGTATTTCGGTA
1 ATTTTACCCTTCGAGGGTATTTCGATA
* ** *
44379657 AGTTTACCCTTTTAGTGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTCGATA
**
44379684 ATTTTAAACTTCGAGGGTATTTC-AGTA
1 ATTTTACCCTTCGAGGGTATTTCGA-TA
44379711 ATTTT
1 ATTTT
44379716 TTAGCCCAAG
Statistics
Matches: 209, Mismatches: 34, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
25 1 0.00
26 21 0.10
27 186 0.89
28 1 0.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.45
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTCGATA
Found at i:44386848 original size:26 final size:26
Alignment explanation
Indices: 44386774--44386850 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
44386764 ACACCAATAT
* * *
44386774 CGCAGCAAAGCTGCCAGTAATAATAA
1 CGCAGCAAAGTTGCCAGTAACAGTAA
* * *
44386800 TGCAGCAGAGCTT-CCAATAACAGTAA
1 CGCAGCAAAG-TTGCCAGTAACAGTAA
*
44386826 CGTAGCAAAGTTGCCAGTAACAGTA
1 CGCAGCAAAGTTGCCAGTAACAGTA
44386851 TTTGTGGTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
25 2 0.05
26 36 0.92
27 1 0.03
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.18
Consensus pattern (26 bp):
CGCAGCAAAGTTGCCAGTAACAGTAA
Found at i:44387083 original size:27 final size:27
Alignment explanation
Indices: 44387029--44387249 Score: 227
Period size: 27 Copynumber: 8.2 Consensus size: 27
44387019 TATATCAATC
*
44387029 ATTTTACCCTAT-G-GGGTATTTT-AGTC
1 ATTTTACCCT-TCGAGGGTATTTTGA-TA
* *
44387055 ATTTTACCCTTCGGGGGTATTTTGATC
1 ATTTTACCCTTCGAGGGTATTTTGATA
* * *
44387082 ATTTTACCCTGCGAAGGGTATATT-AGTC
1 ATTTTACCCTTCG-AGGGTATTTTGA-TA
*
44387110 ATTTTACCCTTCGAGGGTATTTTGGTA
1 ATTTTACCCTTCGAGGGTATTTTGATA
* * *
44387137 ATTTTTCCCTATAG-GGGTATTTTGGTA
1 ATTTTACCCT-TCGAGGGTATTTTGATA
* * *
44387164 ATTTTACCATTCGATGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTGATA
*
44387191 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTGATA
*
44387218 ATTTTACCCTTCGAGGGTATTTCGATA
1 ATTTTACCCTTCGAGGGTATTTTGATA
44387245 ATTTT
1 ATTTT
44387250 TTAGCCTAAG
Statistics
Matches: 170, Mismatches: 17, Indels: 15
0.84 0.08 0.07
Matches are distributed among these distances:
25 1 0.01
26 13 0.08
27 131 0.77
28 25 0.15
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTTACCCTTCGAGGGTATTTTGATA
Found at i:44392442 original size:127 final size:127
Alignment explanation
Indices: 44392216--44392469 Score: 508
Period size: 127 Copynumber: 2.0 Consensus size: 127
44392206 CATAGCATAA
44392216 CAAGCAAATCAATTTCTATAAAGAATTACTATAAAAATTCTTTATAAAACAATCTAATAATAGCA
1 CAAGCAAATCAATTTCTATAAAGAATTACTATAAAAATTCTTTATAAAACAATCTAATAATAGCA
44392281 GAAGATGGAGGAAAGACAGAAAGACCTTCTGAGAATTTTATGTATGTCTTCTGAATGAGATC
66 GAAGATGGAGGAAAGACAGAAAGACCTTCTGAGAATTTTATGTATGTCTTCTGAATGAGATC
44392343 CAAGCAAATCAATTTCTATAAAGAATTACTATAAAAATTCTTTATAAAACAATCTAATAATAGCA
1 CAAGCAAATCAATTTCTATAAAGAATTACTATAAAAATTCTTTATAAAACAATCTAATAATAGCA
44392408 GAAGATGGAGGAAAGACAGAAAGACCTTCTGAGAATTTTATGTATGTCTTCTGAATGAGATC
66 GAAGATGGAGGAAAGACAGAAAGACCTTCTGAGAATTTTATGTATGTCTTCTGAATGAGATC
44392470 TCGCTCCTAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 127 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (127 bp):
CAAGCAAATCAATTTCTATAAAGAATTACTATAAAAATTCTTTATAAAACAATCTAATAATAGCA
GAAGATGGAGGAAAGACAGAAAGACCTTCTGAGAATTTTATGTATGTCTTCTGAATGAGATC
Found at i:44392587 original size:22 final size:22
Alignment explanation
Indices: 44392561--44392602 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
44392551 TTAAAAGAGA
* *
44392561 CATAATTATTCGACTAATATCT
1 CATAACTATTCAACTAATATCT
*
44392583 CATAACTATTCAAGTAATAT
1 CATAACTATTCAACTAATAT
44392603 TAATTATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (22 bp):
CATAACTATTCAACTAATATCT
Found at i:44403170 original size:23 final size:24
Alignment explanation
Indices: 44403144--44403192 Score: 59
Period size: 22 Copynumber: 2.1 Consensus size: 24
44403134 CCATGACATC
*
44403144 ATTTTCGTA-ATACTTATAATC-AA
1 ATTTTCCTATATA-TTATAATCGAA
44403167 A-TTTCCTATATATTATAATCGAA
1 ATTTTCCTATATATTATAATCGAA
44403190 ATT
1 ATT
44403193 CTTCAATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
22 14 0.64
23 7 0.32
24 1 0.05
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTTCCTATATATTATAATCGAA
Found at i:44409292 original size:26 final size:26
Alignment explanation
Indices: 44409212--44409349 Score: 71
Period size: 26 Copynumber: 5.3 Consensus size: 26
44409202 TGTAAATGTT
* *
44409212 GAAAGTCTGCATGGACTATCT-ATTG
1 GAAAGTCTGCACGGACTATCTAATAG
* ** * * * *
44409237 AAAAAGTCCACAAGGACCATCTGATGG
1 -GAAAGTCTGCACGGACTATCTAATAG
***
44409264 GAAAGTCTGTTGGGACTATCTAATAG
1 GAAAGTCTGCACGGACTATCTAATAG
* * * *
44409290 GAAGGTCCGCACTGACTATCTAATGG
1 GAAAGTCTGCACGGACTATCTAATAG
* * *
44409316 GAAAGTCTGCAAGGACCATTTAATAAG
1 GAAAGTCTGCACGGACTATCTAAT-AG
*
44409343 GGAAGTC
1 GAAAGTC
44409350 CATTGAGACT
Statistics
Matches: 80, Mismatches: 30, Indels: 3
0.71 0.27 0.03
Matches are distributed among these distances:
26 70 0.88
27 10 0.12
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.24
Consensus pattern (26 bp):
GAAAGTCTGCACGGACTATCTAATAG
Found at i:44409444 original size:25 final size:26
Alignment explanation
Indices: 44409416--44409470 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
44409406 GAATGGACTA
44409416 TCTACGT-GGAAGTCTGCCAGAACTG
1 TCTACGTGGGAAGTCTGCCAGAACTG
* * * *
44409441 TCTATGTGGGAAGTCTTCCAGGATTG
1 TCTACGTGGGAAGTCTGCCAGAACTG
44409467 TCTA
1 TCTA
44409471 TGTGAGAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (26 bp):
TCTACGTGGGAAGTCTGCCAGAACTG
Found at i:44409456 original size:26 final size:26
Alignment explanation
Indices: 44409423--44409474 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
44409413 CTATCTACGT
44409423 GGAAGTCTGCCAGAACTGTCTATGTG
1 GGAAGTCTGCCAGAACTGTCTATGTG
* * *
44409449 GGAAGTCTTCCAGGATTGTCTATGTG
1 GGAAGTCTGCCAGAACTGTCTATGTG
44409475 AGAGGTCCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (26 bp):
GGAAGTCTGCCAGAACTGTCTATGTG
Found at i:44423141 original size:17 final size:17
Alignment explanation
Indices: 44423119--44423152 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
44423109 TTAAACATGA
44423119 ATCAAAAAAATATTATT
1 ATCAAAAAAATATTATT
44423136 ATCAAAAAAATATTATT
1 ATCAAAAAAATATTATT
44423153 GAATTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (17 bp):
ATCAAAAAAATATTATT
Found at i:44428372 original size:4 final size:4
Alignment explanation
Indices: 44428363--44428408 Score: 51
Period size: 4 Copynumber: 11.8 Consensus size: 4
44428353 TACAAAGTGT
* *
44428363 TTTA TTTA -TTA TTTTA GTTA TTTA TTTA TTCA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
44428409 CTTCAACCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 6 0.17
4 26 0.74
5 3 0.09
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:44428383 original size:16 final size:16
Alignment explanation
Indices: 44428364--44428409 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
44428354 ACAAAGTGTT
*
44428364 TTATTTATTATTTTAG
1 TTATTTATTATTTCAG
*
44428380 TTATTTATT-TATTCAT
1 TTATTTATTAT-TTCAG
44428396 TTATTTATTATTTC
1 TTATTTATTATTTC
44428410 TTCAACCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 24 0.92
17 1 0.04
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (16 bp):
TTATTTATTATTTCAG
Found at i:44435203 original size:44 final size:44
Alignment explanation
Indices: 44435135--44435305 Score: 209
Period size: 44 Copynumber: 3.9 Consensus size: 44
44435125 AATCGTAGTA
* * ** *
44435135 AATCGTATCTCCCTAAAGTTACAGTGGAATAGATTGAAGCTATG
1 AATCTTATCTCCATAAAGTTACAGTGGAGCAGATTGAAGCTACG
* *
44435179 AATCTTATCTCTC-TAAAGTTACAGTGGAGTAGATTAAAGCTACG
1 AATCTTATCTC-CATAAAGTTACAGTGGAGCAGATTGAAGCTACG
* * *
44435223 AATCTTATCTCCATGAAGTTGCAGTGGAGCAGATTGAAGCTACA
1 AATCTTATCTCCATAAAGTTACAGTGGAGCAGATTGAAGCTACG
* * *
44435267 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAG
1 AATCTTATCTCCATAAAGTTACAGTGGAGCAGATTGAAG
44435306 ATAGAAAATC
Statistics
Matches: 115, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
43 1 0.01
44 113 0.98
45 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCATAAAGTTACAGTGGAGCAGATTGAAGCTACG
Found at i:44436588 original size:4 final size:4
Alignment explanation
Indices: 44436579--44436633 Score: 69
Period size: 4 Copynumber: 13.8 Consensus size: 4
44436569 TACAAACTAT
*
44436579 TTTA TTTA -TTA TTTTA TTTTA TTTA TTTA TTTA TTCA TTTA TTTA TTTA
1 TTTA TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
44436628 -TTA TTT
1 TTTA TTT
44436634 CTTCAACCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
3 6 0.13
4 32 0.70
5 8 0.17
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:44436598 original size:17 final size:18
Alignment explanation
Indices: 44436576--44436626 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 18
44436566 TTTTACAAAC
44436576 TATTTTATTTA-TTATTT
1 TATTTTATTTATTTATTT
44436593 TATTTTATTTATTTA-TT
1 TATTTTATTTATTTATTT
*
44436610 TA-TTCATTTATTTATTT
1 TATTTTATTTATTTATTT
44436627 ATTATTTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 11 0.35
17 17 0.55
18 3 0.10
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTTTATTTATTTATTT
Found at i:44445080 original size:53 final size:55
Alignment explanation
Indices: 44445005--44445110 Score: 173
Period size: 53 Copynumber: 2.0 Consensus size: 55
44444995 ATTTGGAGAT
*
44445005 AAATAGATATACATATAATATTAAATTTAAATATTTTAAAAGTAAAAATAATGAAC
1 AAATAGATATACATATAATATTAAATTTAAATATTTT-AAAGTAAAAAGAATGAAC
44445061 AAATAGATA-A-A-ATAATATTAAATTTAAATATTTTAAAGTAAAAAGAATGA
1 AAATAGATATACATATAATATTAAATTTAAATATTTTAAAGTAAAAAGAATGA
44445111 TAAATTGATA
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
52 15 0.31
53 23 0.47
54 1 0.02
55 1 0.02
56 9 0.18
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (55 bp):
AAATAGATATACATATAATATTAAATTTAAATATTTTAAAGTAAAAAGAATGAAC
Found at i:44446813 original size:44 final size:44
Alignment explanation
Indices: 44446765--44446983 Score: 147
Period size: 45 Copynumber: 5.0 Consensus size: 44
44446755 TTCTCCGCTG
* *
44446765 TAACTTCAGAGAGATAAGGTTTATACCTTTAATCTACTCTACTA
1 TAACTTCAGAGAGATAAGATTTATACCTTCAATCTACTCTACTA
* * * * *
44446809 TAACTTCAGAAAGATAAGATTTGCTATCTTCGATCTACTCCACTA
1 TAACTTCAGAGAGATAAGATTT-ATACCTTCAATCTACTCTACTA
* * * * * * *
44446854 TAACTTTAGGGAAATAAGATCTATACCATCAATCT-GTCTCACTG
1 TAACTTCAGAGAGATAAGATTTATACCTTCAATCTACTCT-ACTA
* * * * * * * *
44446898 CAACTTCAG-G-GGTAAGGTTTATAACTTTAATATGCTCTACTG
1 TAACTTCAGAGAGATAAGATTTATACCTTCAATCTACTCTACTA
* * * * *
44446940 CAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCTCTACT
1 TAACTTCAGAGAGATAAGATTT-ATACCTTCAATCTACTCTACT
44446984 GCAACTTTGG
Statistics
Matches: 132, Mismatches: 37, Indels: 11
0.73 0.21 0.06
Matches are distributed among these distances:
42 28 0.21
43 6 0.05
44 47 0.36
45 51 0.39
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.34
Consensus pattern (44 bp):
TAACTTCAGAGAGATAAGATTTATACCTTCAATCTACTCTACTA
Found at i:44446987 original size:45 final size:45
Alignment explanation
Indices: 44446715--44447109 Score: 184
Period size: 44 Copynumber: 8.8 Consensus size: 45
44446705 TTAATTCGAC
* * * *
44446715 CTACTGCAACTTTAG-AAGTATAGGACTT-ATCAT-TTCAATCTTCT
1 CTACTGCAACTTCAGAAAG-ATAAGATTTGAT-ATCTTCAATCTGCT
** * * * * * *
44446759 CCGCTGTAACTTCAGAGAGATAAGGTTT-ATACCTTTAATCTACT
1 CTACTGCAACTTCAGAAAGATAAGATTTGATATCTTCAATCTGCT
** * * *
44446803 CTACTATAACTTCAGAAAGATAAGATTTGCTATCTTCGATCTACT
1 CTACTGCAACTTCAGAAAGATAAGATTTGATATCTTCAATCTGCT
* ** * * * * *
44446848 CCACTATAACTTTAGGGAA-ATAAGATCT-ATACCATCAATCTG-T
1 CTACTGCAACTTCA-GAAAGATAAGATTTGATATCTTCAATCTGCT
* * * * * *
44446891 CTCACTGCAACTTCAG--GGGTAAGGTTT-ATAACTTTAATATGCT
1 CT-ACTGCAACTTCAGAAAGATAAGATTTGATATCTTCAATCTGCT
*
44446934 CTACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGCT
1 CTACTGCAACTTCAGAAAGATAAGATTTGATATCTTCAATCTGCT
* *** * * *
44446979 CTACTGCAACTT-TGGGGGTATAAGATTTGTGGTTTGTAGCTTTAATCTGCT
1 CTACTGCAACTTCAGAAAG-ATAAGA-TT-T-G---ATATCTTCAATCTGCT
* *
44447030 CTACTGCAACTTCA-TAAGATAAGATTTGTTATCTTCAATCTGCT
1 CTACTGCAACTTCAGAAAGATAAGATTTGATATCTTCAATCTGCT
* * ** * *
44447074 CAACTGTAACTTCAGGGAGATAAGATTAGCTATCTT
1 CTACTGCAACTTCAGAAAGATAAGATTTGATATCTT
44447110 GTAGCTTTAG
Statistics
Matches: 264, Mismatches: 68, Indels: 37
0.72 0.18 0.10
Matches are distributed among these distances:
42 29 0.11
43 7 0.03
44 104 0.39
45 81 0.31
46 5 0.02
47 2 0.01
48 2 0.01
49 2 0.01
50 6 0.02
51 26 0.10
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (45 bp):
CTACTGCAACTTCAGAAAGATAAGATTTGATATCTTCAATCTGCT
Found at i:44447085 original size:95 final size:96
Alignment explanation
Indices: 44446913--44447085 Score: 276
Period size: 95 Copynumber: 1.8 Consensus size: 96
44446903 TCAGGGGTAA
44446913 GGTTTATAACTTTAATATGCTCTACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGC
1 GGTTTATAACTTTAATATGCTCTACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGC
*
44446978 TCTACTGCAACTTTGGGGGTATAAGATTTGT
66 TCAACTGCAACTTTGGGGGTATAAGATTTGT
* * * * *
44447009 GGTTTGTAGCTTTAATCTGCTCTACTGCAACTTCA-TAAGATAAGATTTGTTATCTTCAATCTGC
1 GGTTTATAACTTTAATATGCTCTACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGC
*
44447073 TCAACTGTAACTT
66 TCAACTGCAACTT
44447086 CAGGGAGATA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
95 38 0.54
96 32 0.46
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (96 bp):
GGTTTATAACTTTAATATGCTCTACTGCAACTTCAGAAAGATAAGATTTGCTATCTTCAATCTGC
TCAACTGCAACTTTGGGGGTATAAGATTTGT
Found at i:44447257 original size:44 final size:43
Alignment explanation
Indices: 44447209--44447334 Score: 144
Period size: 44 Copynumber: 2.9 Consensus size: 43
44447199 GATTTTTTGT
* * *
44447209 TTCAATATGCTCCACCGAAACTTCAAGGAGATAAGATTAATGGC
1 TTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT-ATGGC
* * * *
44447253 TTCAATCTTCTCCATTGCAACTTCAAAGAGATAAGGATTGTGGC
1 TTCAATCTGCTCCACTGCAACTTCAAGGAGATAA-GATTATGGC
* * *
44447297 TTTAATCTGCTCCACTGCAACTTCAGGGTGATAAGATT
1 TTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
44447335 CACCATGGTA
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
43 4 0.06
44 60 0.88
45 4 0.06
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (43 bp):
TTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTATGGC
Done.