Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 163 of 214
Found at i:48317636 original size:28 final size:28
Alignment explanation
Indices: 48317621--48318299 Score: 696
Period size: 28 Copynumber: 24.3 Consensus size: 28
48317611 TTTTTAATTA
*
48317621 AATTAAATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGG-T----TT-TT
*
48317655 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
* *
48317683 AACTAAATTATG-TTAGGTTAGGGTATTT
1 AATTAAATTA-GATTAGGTTAGGGTTTTT
*
48317711 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48317739 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGATTA-GGTTAGGGTTTTT
* *
48317768 AATTAAATCAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGATTA-GGTTAGGGTTTTT
* * *
48317797 AACTAAATT--A-T--GTTACGATTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48317820 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
* *
48317848 AATTAAATTAAATTAGGTTAGGATTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
* *
48317876 AATTAAATTAGGTTATGGTTAGAG-TTTT
1 AATTAAATTAGATTA-GGTTAGGGTTTTT
* * *
48317904 CATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 AAT-TAAATTAGATTA-GGTTAGGGTTTTT
*
48317934 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48317962 AATTAAATTAGGTTAGGGTTAGGGTTTTT
1 AATTAAATTAGATTA-GGTTAGGGTTTTT
* *
48317991 -ATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 AAT-TAAATTAGATTA-GGTTAGGGTTTTT
*
48318020 AACTAAA-T-GA-T--GTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318043 AACTAAATT--A-T--GTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318066 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318094 AATTAAATTAGGTTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318122 AATTAAATTAAATTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318150 AACTAAATTATG-TTAGGTTAGGGTTTTT
1 AATTAAATTA-GATTAGGTTAGGGTTTTT
* *
48318178 AATTAAATTAGGTTAATGTTAGGG-TTTT
1 AATTAAATTAGATT-AGGTTAGGGTTTTT
* * *
48318206 CATGTAAAATAGGTTAGGGTTAGGGTTTTT
1 AAT-TAAATTAGATTA-GGTTAGGGTTTTT
* * *
48318236 AATTAAATTAAATTATGTTAGGATTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318264 AATTAAATTAGGTTAGGTTAGGGTTTTT
1 AATTAAATTAGATTAGGTTAGGGTTTTT
*
48318292 AATCAAAT
1 AATTAAAT
48318300 AATGTCAAAA
Statistics
Matches: 561, Mismatches: 58, Indels: 58
0.83 0.09 0.09
Matches are distributed among these distances:
23 59 0.11
24 1 0.00
25 2 0.00
26 4 0.01
27 2 0.00
28 297 0.53
29 159 0.28
30 13 0.02
33 1 0.00
34 23 0.04
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
AATTAAATTAGATTAGGTTAGGGTTTTT
Found at i:48317652 original size:62 final size:63
Alignment explanation
Indices: 48317537--48317692 Score: 208
Period size: 62 Copynumber: 2.4 Consensus size: 63
48317527 ATCCGCTGAG
**
48317537 TTATGTTAGGGTTTTTACATT-AATTAAATTAGGTTAGGGTTAGGGTTAGGGTTTTTAACTAAA
1 TTATGTTAGGGTTTTTA-ATTAAATTAAATTAAATTAGGGTTAGGGTTAGGGTTTTTAACTAAA
*
48317600 TTATGTTAGGGTTTTTAATTAAATTAAATTAAATTA-GGTTAGGGTTAGGGTTTTTAATTAAA
1 TTATGTTAGGGTTTTTAATTAAATTAAATTAAATTAGGGTTAGGGTTAGGGTTTTTAACTAAA
*
48317662 TTAAATTAGGTTAGGGTTTTTAACTAAATTA
1 TT--A-T--GTTAGGGTTTTTAATTAAATTA
48317693 TGTTAGGTTA
Statistics
Matches: 83, Mismatches: 4, Indels: 8
0.87 0.04 0.08
Matches are distributed among these distances:
62 30 0.36
63 30 0.36
64 1 0.01
65 1 0.01
67 21 0.25
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (63 bp):
TTATGTTAGGGTTTTTAATTAAATTAAATTAAATTAGGGTTAGGGTTAGGGTTTTTAACTAAA
Found at i:48317831 original size:86 final size:82
Alignment explanation
Indices: 48317642--48318299 Score: 560
Period size: 86 Copynumber: 8.0 Consensus size: 82
48317632 ATTAGGTTAG
* *
48317642 GGTTAGGGTTTTTAATTAAATT-AA-A-TTAGGTTAGGGTTTTTAACTAAATTATGTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
48317704 GGTATTTAATTAAATTAAATTA
66 GG--TTT--TT-AATTAAATTA
* *
48317726 GGTTAGGGTTTTTAATTAAATT--A-GGTTAGGGTTAGGGTTTTTAATTAAATCAGGTTAGGGTT
1 GGTTAGGGTTTTTAATTAAATTAAATAGTTA-GGTTAGGGTTTTTAATTAAATTAGGTTA-GGTT
*
48317788 AGGGTTTTTAACTAAATTA
64 AGGGTTTTTAATTAAATTA
* * * **
48317807 TGTTACGATTTTTAATTAAATT-AA-A-TTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
*
48317869 GATTTTTAATTAAATTA
66 GGTTTTTAATTAAATTA
* ** * ** **
48317886 GGTTATGG-TTAGAGTTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAG
1 GGTTAGGGTTTTTA-ATTAAAT-T-AAATA-GTTA-GGTTAGGGTTTTTAATTAAATTAGGTTAG
48317950 GTTAGGGTTTTTAATTAAATTA
61 GTTAGGGTTTTTAATTAAATTA
** * *
48317972 GGTTAGGGTTAGGGTTT--TTATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAA-T--G--A
1 GGTTAGGGTT----TTTAATTAAATTAAATA-GTTA-GGTTAGGGTTTTTAATTAAATTAGGTTA
* *
48318030 TGTTAGGGTTTTTAACTAAATTA
60 GGTTAGGGTTTTTAATTAAATTA
*
48318053 TGTTAGGGTTTTTAATTAAATT-AA-A-TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
1 GGTTAGGGTTTTTAATTAAATTAAATAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
48318115 GGTTTTTAATTAAATTAAATTA
66 GG--TTT--TT-AATTAAATTA
* *
48318137 GGTTAGGGTTTTTAACTAAATT--AT-GTTAGGTTAGGGTTTTTAATTAAATTAGGTTAATGTTA
1 GGTTAGGGTTTTTAATTAAATTAAATAGTTAGGTTAGGGTTTTTAATTAAATTAGGTT-AGGTTA
*
48318199 GGG-TTTTCATGTAAAATAGGTTA
65 GGGTTTTTAAT-T--AA-A--TTA
* *
48318222 GGGTTAGGGTTTTTAATTAAATT-AA-A-TTATGTTAGGATTTTTAATTAAATTAGGTTAGGTTA
1 -GGTTAGGGTTTTTAATTAAATTAAATAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTA
*
48318284 GGGTTTTTAATCAAAT
65 GGGTTTTTAATTAAAT
48318300 AATGTCAAAA
Statistics
Matches: 481, Mismatches: 51, Indels: 88
0.78 0.08 0.14
Matches are distributed among these distances:
74 19 0.04
75 4 0.01
77 5 0.01
78 5 0.01
79 44 0.09
80 30 0.06
81 65 0.14
82 10 0.02
83 8 0.02
84 87 0.18
85 48 0.10
86 150 0.31
87 2 0.00
88 3 0.01
91 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.45
Consensus pattern (82 bp):
GGTTAGGGTTTTTAATTAAATTAAATAGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAG
GGTTTTTAATTAAATTA
Found at i:48317841 original size:114 final size:109
Alignment explanation
Indices: 48317626--48318299 Score: 662
Period size: 114 Copynumber: 6.1 Consensus size: 109
48317616 AATTAAATTA
**
48317626 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAACTAAA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAA
**
48317690 TTATGTTAGGTTAGGGTATTTAATTAAATTAAATTAGGTTAGGGTTTTT
66 TTATGTTAGGTT--TTTA-TTAATTAAATT--ATTAGGTTAGGGTTTTT
*
48317739 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATCAGGTTAGGGTTAGGGTTTTTAACTAAA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAA
* *
48317804 TTATGTTACG-ATTT-TTAATTAAATTAAATTAGGTTAGGGTTTTT
66 TTATGTTAGGTTTTTATTAATTAAATT--ATTAGGTTAGGGTTTTT
** * * * * **
48317848 AATTAAATTAAATTA-GGTTAGGATTTTTAATTAAATTAGGTTATGGTTAGAGTTTTCATGTAAA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAA
* *
48317912 ATAGGTTAGGGTTAGGGTTT-TTAATTAAATTAAATTAGGTTAGGGTTTTT
66 TTATGTTA-GGTT----TTTATTAATTAAATT--ATTAGGTTAGGGTTTTT
*
48317962 AATTAAATTAGGTTAGGGTTAGGGTTTTT-ATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAACTAA
* * *
48318026 ATGATGTTAGG-GTTT-TTAACTAAATTA-T--GTTAGGGTTTTT
65 ATTATGTTAGGTTTTTATTAATTAAATTATTAGGTTAGGGTTTTT
** *
48318066 AATTAAATTAAATTA-GGTTAGGGTTTTTAATTAAATTAGGTTA-GGTTAGGGTTTTTAATTAAA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAA
** *
48318129 TTAAATTAGGTTAGGGTTT-TTAACTAAATTATGTTAGGTTAGGGTTTTT
66 TTATGTTAGGTT----TTTATTAATTAAATTA--TTAGGTTAGGGTTTTT
** * *
48318178 AATTAAATTAGGTTAATGTTAGGG-TTTTCATGTAAAATAGGTTAGGGTTAGGGTTTTTAATTAA
1 AATTAAATTAGGTTAGGGTTAGGGTTTTTAAT-TAAATTAGGTTAGGGTTAGGG--TTT--TT-A
* *
48318242 ATTAAATTATGTTAGG-ATTT-TTAATTAAATTAGGTTAGGTTAGGGTTTTT
60 ACTAAATTATGTTAGGTTTTTATTAATTAAATTA--TTAGGTTAGGGTTTTT
*
48318292 AATCAAAT
1 AATTAAAT
48318300 AATGTCAAAA
Statistics
Matches: 480, Mismatches: 53, Indels: 55
0.82 0.09 0.09
Matches are distributed among these distances:
102 26 0.05
103 24 0.05
104 27 0.06
106 1 0.00
107 16 0.03
108 48 0.10
109 57 0.12
110 1 0.00
111 1 0.00
112 31 0.06
113 59 0.12
114 125 0.26
115 44 0.09
116 3 0.01
118 2 0.00
119 15 0.03
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.45
Consensus pattern (109 bp):
AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAA
TTATGTTAGGTTTTTATTAATTAAATTATTAGGTTAGGGTTTTT
Found at i:48320462 original size:14 final size:15
Alignment explanation
Indices: 48320445--48320478 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
48320435 AATAAATATC
48320445 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
48320459 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
48320474 TAAAA
1 TAAAA
48320479 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:48320701 original size:22 final size:22
Alignment explanation
Indices: 48320666--48320717 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
48320656 TTTAATATGG
* *
48320666 ATTTG-GAGATTTTTTGAAGGA
1 ATTTGAGAGAATTTTGGAAGGA
48320687 ATTTGAGAGAATTTTGGAAGGA
1 ATTTGAGAGAATTTTGGAAGGA
48320709 ATTTGAGAG
1 ATTTGAGAG
48320718 TTTGAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.37
Consensus pattern (22 bp):
ATTTGAGAGAATTTTGGAAGGA
Found at i:48320724 original size:30 final size:30
Alignment explanation
Indices: 48320688--48320747 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
48320678 TTTGAAGGAA
*
48320688 TTTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTTGAGAGAATTTTGAAAGGAATTTGAGAG
48320718 TTTGAGAGAATTTTGAAAGGAATTTGAGAG
1 TTTGAGAGAATTTTGAAAGGAATTTGAGAG
48320748 AATTTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (30 bp):
TTTGAGAGAATTTTGAAAGGAATTTGAGAG
Found at i:48320732 original size:11 final size:10
Alignment explanation
Indices: 48320685--48320752 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 10
48320675 TTTTTTGAAG
48320685 GAATTTGAGA
1 GAATTTGAGA
48320695 GAATTTTG-GAA
1 GAA-TTTGAG-A
48320706 GGAATTTGAGA
1 -GAATTTGAGA
48320717 G--TTTGAGA
1 GAATTTGAGA
*
48320725 GAATTTTGAAA
1 GAA-TTTGAGA
48320736 GGAATTTGAGA
1 -GAATTTGAGA
48320747 GAATTT
1 GAATTT
48320753 TTGAAGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
8 8 0.17
10 11 0.23
11 22 0.46
12 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (10 bp):
GAATTTGAGA
Found at i:48320744 original size:22 final size:22
Alignment explanation
Indices: 48320718--48320766 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
48320708 AATTTGAGAG
48320718 TTTGAGAGAA-TTTTGAAAGGAA
1 TTTGAGAGAATTTTTG-AAGGAA
48320740 TTTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
48320762 ATTGA
1 TTTGA
48320767 TATTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.35
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:48330372 original size:37 final size:37
Alignment explanation
Indices: 48330311--48330456 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
48330301 TACGTATGAT
* *
48330311 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
48330346 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
48330383 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
48330420 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
48330457 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:48330473 original size:46 final size:46
Alignment explanation
Indices: 48330420--48330688 Score: 340
Period size: 46 Copynumber: 5.6 Consensus size: 46
48330410 TAAGTGTAGC
* **
48330420 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
48330466 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
48330512 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
48330564 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
48330610 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
48330662 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
48330689 AGTACTCAAA
Statistics
Matches: 199, Mismatches: 12, Indels: 24
0.85 0.05 0.10
Matches are distributed among these distances:
46 112 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:48330539 original size:52 final size:52
Alignment explanation
Indices: 48330463--48330682 Score: 299
Period size: 52 Copynumber: 4.3 Consensus size: 52
48330453 TAGCTAAAGC
* *
48330463 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
48330516 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
48330568 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
48330614 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
48330666 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
48330683 ATCAGAAGTA
Statistics
Matches: 148, Mismatches: 12, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 86 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:48330585 original size:98 final size:98
Alignment explanation
Indices: 48330420--48330688 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
48330410 TAAGTGTAGC
* * *
48330420 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
48330485 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
48330519 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
48330584 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
48330617 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
48330682 GATCAGA
66 GATCAGA
48330689 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 151 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:48334762 original size:27 final size:26
Alignment explanation
Indices: 48334727--48334781 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 26
48334717 TTCGGTATTT
*
48334727 TTCGGTAATTCGGTTAATTC-GGTTAA
1 TTCGGTAATTCGGGTAATTCAGG-TAA
48334753 TTCGGTTAATTCGGGTAATTCAGGTAA
1 TTCGG-TAATTCGGGTAATTCAGGTAA
48334780 TT
1 TT
48334782 TTTAACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 19 0.73
28 2 0.08
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (26 bp):
TTCGGTAATTCGGGTAATTCAGGTAA
Found at i:48334781 original size:9 final size:9
Alignment explanation
Indices: 48334727--48334773 Score: 78
Period size: 9 Copynumber: 5.3 Consensus size: 9
48334717 TTCGGTATTT
48334727 TTCGG-TAA
1 TTCGGTTAA
48334735 TTCGGTTAA
1 TTCGGTTAA
48334744 TTCGGTTAA
1 TTCGGTTAA
48334753 TTCGGTTAA
1 TTCGGTTAA
*
48334762 TTCGGGTAA
1 TTCGGTTAA
48334771 TTC
1 TTC
48334774 AGGTAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
8 5 0.14
9 32 0.86
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (9 bp):
TTCGGTTAA
Found at i:48334956 original size:12 final size:12
Alignment explanation
Indices: 48334939--48334963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48334929 AGTAATTTCG
48334939 GGTCGGTTAACC
1 GGTCGGTTAACC
48334951 GGTCGGTTAACC
1 GGTCGGTTAACC
48334963 G
1 G
48334964 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:48349326 original size:12 final size:12
Alignment explanation
Indices: 48349284--48349329 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
48349274 TATTTTTTAT
*
48349284 AAAAATAT-TTA
1 AAAAATATATAA
48349295 AAAAAT-TA-AA
1 AAAAATATATAA
48349305 AGAAAATATATAA
1 A-AAAATATATAA
48349318 AAAAATATATAA
1 AAAAATATATAA
48349330 TTTTTAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
10 3 0.10
11 11 0.37
12 13 0.43
13 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
AAAAATATATAA
Found at i:48349358 original size:27 final size:26
Alignment explanation
Indices: 48349307--48349369 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
48349297 AAATTAAAAG
*
48349307 AAAATATATAAAAAAATATATAATTTT
1 AAAA-ATATAAAAAAATATATAATTAT
*
48349334 TAAAATATAAAAGAAAT-TATAAATTAT
1 AAAAATATAAAA-AAATATAT-AATTAT
48349361 AAAAATATA
1 AAAAATATA
48349370 TGTGTCTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 11 0.35
27 20 0.65
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (26 bp):
AAAAATATAAAAAAATATATAATTAT
Found at i:48352779 original size:25 final size:26
Alignment explanation
Indices: 48352730--48352779 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
48352720 ATTTTTATTT
*
48352730 TTATTAAAATATATTTAATAATAACC
1 TTATTAAAATATATATAATAATAACC
*
48352756 TTATTAAAATTTA-ATAATAATAAC
1 TTATTAAAATATATATAATAATAAC
48352780 AATAATCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TTATTAAAATATATATAATAATAACC
Found at i:48354701 original size:16 final size:17
Alignment explanation
Indices: 48354680--48354726 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
48354670 ACCCTAACAA
48354680 CTCTATTCCATTACA-C
1 CTCTATTCCATTACAGC
** *
48354696 CTCTATTTAATTATAGC
1 CTCTATTCCATTACAGC
48354713 C-CTATTCCATTACA
1 CTCTATTCCATTACA
48354727 ATCAACCAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 22 0.92
17 2 0.08
ACGTcount: A:0.28, C:0.30, G:0.02, T:0.40
Consensus pattern (17 bp):
CTCTATTCCATTACAGC
Found at i:48355559 original size:26 final size:25
Alignment explanation
Indices: 48355519--48355567 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
48355509 ATGAACGCCC
48355519 TTCTTTGCTCTCTGCTCTCTGCTGG
1 TTCTTTGCTCTCTGCTCTCTGCTGG
*
48355544 TTCTTTGTTTCTCTGCTCTCTGCT
1 TTCTTTG-CTCTCTGCTCTCTGCT
48355568 ACGCTGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.00, C:0.31, G:0.16, T:0.53
Consensus pattern (25 bp):
TTCTTTGCTCTCTGCTCTCTGCTGG
Found at i:48355577 original size:31 final size:33
Alignment explanation
Indices: 48355519--48355581 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
48355509 ATGAACGCCC
* *
48355519 TTCTTTGCTCTCTGCTCTCTGCTGGTTCTTTGT
1 TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTGT
48355552 TTCTCTGCTCTCTGCT-AC-GCTGGTTCTTTG
1 TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTG
48355582 CCCTCATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.02, C:0.29, G:0.19, T:0.51
Consensus pattern (33 bp):
TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTGT
Found at i:48358576 original size:3 final size:3
Alignment explanation
Indices: 48358568--48358599 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
48358558 CTTAAAATGA
48358568 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
48358600 AGTTTAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48359801 original size:27 final size:26
Alignment explanation
Indices: 48359770--48359847 Score: 77
Period size: 28 Copynumber: 2.9 Consensus size: 26
48359760 CTAGACTACA
48359770 TTTTAATTCTTTTATAAATCTATAAAT
1 TTTTAATTCTTTTATAAAT-TATAAAT
* * *
48359797 TTTTAGTTCTTTTATATAAATTTTTAAT
1 TTTTAATTC-TTT-TATAAATTATAAAT
*
48359825 TTTTAATT-TTTGATAAATGTATA
1 TTTTAATTCTTTTATAAAT-TATA
48359848 TAATATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
25 6 0.15
26 5 0.12
27 8 0.20
28 15 0.37
29 7 0.17
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTTAATTCTTTTATAAATTATAAAT
Found at i:48359828 original size:19 final size:21
Alignment explanation
Indices: 48359790--48359829 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
48359780 TTTATAAATC
*
48359790 TATAAATTTTTAGTTCTTTTA
1 TATAAATTTTTAGATCTTTTA
48359811 TATAAATTTTTA-AT-TTTTA
1 TATAAATTTTTAGATCTTTTA
48359830 ATTTTTGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 1 0.06
21 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATAAATTTTTAGATCTTTTA
Found at i:48363537 original size:2 final size:2
Alignment explanation
Indices: 48363530--48363585 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
48363520 TTAGAACAAA
*
48363530 AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
48363572 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
48363586 TAGTGTATCC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
AG
Found at i:48366404 original size:42 final size:42
Alignment explanation
Indices: 48366333--48366418 Score: 129
Period size: 42 Copynumber: 2.0 Consensus size: 42
48366323 ACAAAAACGC
* *
48366333 CGCCGCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTT-TAAG
1 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTT-TTCTAAG
*
48366375 CGCCTCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
48366417 CG
1 CG
48366419 TCGGCACTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
41 2 0.05
42 38 0.95
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
Found at i:48366811 original size:21 final size:21
Alignment explanation
Indices: 48366746--48366813 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
48366736 TGCTCTGCTT
* * *
48366746 TGCTTCTCTCGCTGCAGCTTT
1 TGCTTCCCTCGCTGCAGCCTC
* *
48366767 TGCTTCCCTCGCTGCAGTCAC
1 TGCTTCCCTCGCTGCAGCCTC
*
48366788 TGCTTCCCTCGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
48366809 TGCTT
1 TGCTT
48366814 TAAGTTGTAG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.04, C:0.41, G:0.19, T:0.35
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:48372333 original size:25 final size:25
Alignment explanation
Indices: 48372303--48372407 Score: 133
Period size: 25 Copynumber: 4.2 Consensus size: 25
48372293 ATGATATAAT
*
48372303 TTATGTATTAAGTAAATTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
48372328 TTATGTACGTGT-A-TAAGTTATGTAAG
1 TTATGTA--T-TAAGTAAGTTATGTAAG
*
48372354 TTATGTATTAAGTAAGCTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
* *
48372379 TTGTGTATTATGTAAGTTATGTAAG
1 TTATGTATTAAGTAAGTTATGTAAG
48372404 TTAT
1 TTAT
48372408 CAAAGTAATG
Statistics
Matches: 69, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
23 1 0.01
24 2 0.03
25 44 0.64
26 19 0.28
27 2 0.03
28 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGTATTAAGTAAGTTATGTAAG
Found at i:48372353 original size:9 final size:9
Alignment explanation
Indices: 48372314--48372567 Score: 221
Period size: 9 Copynumber: 29.4 Consensus size: 9
48372304 TATGTATTAA
*
48372314 GTAAATTAT
1 GTAAGTTAT
48372323 GTAAGTTAT
1 GTAAGTTAT
*
48372332 GTACGTGTA-
1 GTAAGT-TAT
48372341 -TAAGTTAT
1 GTAAGTTAT
48372349 GTAAGTTAT
1 GTAAGTTAT
*
48372358 GT-A-TTAA
1 GTAAGTTAT
*
48372365 GTAAGCTAT
1 GTAAGTTAT
*
48372374 GTAAGTTGT
1 GTAAGTTAT
48372383 GT-A-TTAT
1 GTAAGTTAT
48372390 GTAAGTTAT
1 GTAAGTTAT
48372399 GTAAGTTAT
1 GTAAGTTAT
** *
48372408 CAAAGTAAT
1 GTAAGTTAT
*
48372417 GTATGTTAT
1 GTAAGTTAT
48372426 GTAAG-T-T
1 GTAAGTTAT
48372433 GTAAGTTAAAT
1 GTAAGTT--AT
48372444 GT-A-TTAT
1 GTAAGTTAT
*
48372451 GTAGGTTAT
1 GTAAGTTAT
*
48372460 GTAAGTTGT
1 GTAAGTTAT
*
48372469 GTAAGATAT
1 GTAAGTTAT
*
48372478 TTAAGTTAT
1 GTAAGTTAT
* *
48372487 GTGAGTTTT
1 GTAAGTTAT
48372496 GT-A-TTAT
1 GTAAGTTAT
48372503 GTAAGTTAT
1 GTAAGTTAT
48372512 GTAAGTTAT
1 GTAAGTTAT
*
48372521 GTAAGTTTT
1 GTAAGTTAT
48372530 GT-A-TTAT
1 GTAAGTTAT
48372537 GTAAGTTAT
1 GTAAGTTAT
*
48372546 GTAGGTTAT
1 GTAAGTTAT
*
48372555 GTAAGTTTT
1 GTAAGTTAT
48372564 GTAA
1 GTAA
48372568 TGTACAAGTG
Statistics
Matches: 195, Mismatches: 33, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
7 32 0.16
8 14 0.07
9 143 0.73
10 3 0.02
11 3 0.02
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:48372403 original size:34 final size:34
Alignment explanation
Indices: 48372318--48372566 Score: 145
Period size: 34 Copynumber: 7.0 Consensus size: 34
48372308 TATTAAGTAA
* *
48372318 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGT
1 ATTATGTAAGTTATGTAAGT-TATGTAAGTTGTGT
* *
48372351 AAGTTATGT-A-TTAAGTAAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTGTGT
** *
48372385 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGTAT
1 ATTATGTAAGTTATGTAAGTTATGTAAGT--TGTGT
* *
48372421 GTTATGTAAG-T-TGTAAGTTAAATGT-A-TTATGT
1 ATTATGTAAGTTATGTAAGTT--ATGTAAGTTGTGT
* * *
48372453 AGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTGAGTTTTGT
1 A--TTATGTAAGTTATGTAAGTTATGTAAG---T-T--G---TGT
*
48372498 ATTATGTAAGTTATGTAAGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTGTGT
* *
48372532 ATTATGTAAGTTATGTAGGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTGTGT
48372566 A
1 A
48372567 ATGTACAAGT
Statistics
Matches: 168, Mismatches: 23, Indels: 48
0.70 0.10 0.20
Matches are distributed among these distances:
32 11 0.07
33 9 0.05
34 84 0.50
35 10 0.06
36 22 0.13
39 2 0.01
40 2 0.01
43 24 0.14
45 4 0.02
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGTTGTGT
Found at i:48372483 original size:52 final size:52
Alignment explanation
Indices: 48372345--48372567 Score: 176
Period size: 52 Copynumber: 4.3 Consensus size: 52
48372335 CGTGTATAAG
* * * *
48372345 TTATGTAAGTTATGT-A-TTAAGTAAGCTATGTAAGTTGTGT-A-TTATGTAA
1 TTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTTATGT-A
** * * * *
48372394 GTTATGTAAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAAATGTA
1 -TTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTT--ATGTA
* * * *
48372447 TTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTGAGTTTTGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTTATGTA
*
48372499 TTATGTAAGTTATGTAAGTTATGTAAG-T-TTTGTA-TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTAAGTTATGTAAGATATTT-AAGTTATGTAAGTTATGTA
*
48372549 GGTTATGTAAGTTTTGTAA
1 --TTATGTAAGTTATGTAA
48372568 TGTACAAGTG
Statistics
Matches: 140, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
50 33 0.24
51 5 0.04
52 89 0.64
53 2 0.01
54 11 0.08
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (52 bp):
TTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTTATGTA
Found at i:48372560 original size:43 final size:43
Alignment explanation
Indices: 48372318--48372567 Score: 237
Period size: 43 Copynumber: 5.8 Consensus size: 43
48372308 TATTAAGTAA
*
48372318 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGT-TATGTAAGTTATGTAAGTTATGT
* * *
48372360 ATTAAGTAAGCTATGTAAGTTGTGT-A-TTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
** * *
48372401 AAGTTATCAAAGTAATGTATGTTATGTAAG-T-TGTAAGTTAAATGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTT--ATGT
* * * *
48372446 ATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* *
48372489 GAGTTTTGT-A-TTATGTAAGTTATGTAAGTTATGTAAGTTTTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* *
48372532 ATTATGTAAGTTATGTAGGTTATGTAAGTTTTGTAA
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAA
48372568 TGTACAAGTG
Statistics
Matches: 167, Mismatches: 27, Indels: 27
0.76 0.12 0.12
Matches are distributed among these distances:
41 21 0.13
42 21 0.13
43 104 0.62
44 5 0.03
45 16 0.10
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (43 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGTTATGTAAGTTATGT
Found at i:48372611 original size:25 final size:26
Alignment explanation
Indices: 48372583--48372631 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
48372573 AAGTGTCAGG
*
48372583 TTATTGTT-ATTAAATTTTAATAAGA
1 TTATTGTTAACTAAATTTTAATAAGA
*
48372608 TTATTGTTAACTATATTTTAATAA
1 TTATTGTTAACTAAATTTTAATAA
48372632 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
TTATTGTTAACTAAATTTTAATAAGA
Found at i:48372638 original size:6 final size:6
Alignment explanation
Indices: 48372627--48372656 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
48372617 ACTATATTTT
48372627 AATAAA AATAAA AATAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA
48372657 TAATTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AATAAA
Found at i:48372765 original size:12 final size:13
Alignment explanation
Indices: 48372743--48372780 Score: 55
Period size: 11 Copynumber: 3.2 Consensus size: 13
48372733 ATATAATTAT
48372743 TAATAATATTTAA
1 TAATAATATTTAA
48372756 TAATAA-ATTTAA
1 TAATAATATTTAA
48372768 T-ATAATA-TTAA
1 TAATAATATTTAA
48372779 TA
1 TA
48372781 TTATTATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.39
12 8 0.35
13 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:48372788 original size:12 final size:12
Alignment explanation
Indices: 48372718--48372797 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
48372708 AATATATAAT
*
48372718 TTAATAACATTA
1 TTAATAATATTA
*
48372730 CTAAT-ATAATTA
1 TTAATAAT-ATTA
48372742 TTAATAATA-T-
1 TTAATAATATTA
*
48372752 TTAATAATA-AA
1 TTAATAATATTA
*
48372763 TTTAAT-ATAATA
1 -TTAATAATATTA
*
48372775 TTAATATTATTA
1 TTAATAATATTA
*
48372787 TTAAGAATATT
1 TTAATAATATT
48372798 TCAATGCCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
10 9 0.17
11 10 0.19
12 32 0.60
13 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (12 bp):
TTAATAATATTA
Found at i:48373626 original size:31 final size:31
Alignment explanation
Indices: 48373584--48373667 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
48373574 GAGCTCTTAG
* *
48373584 CCAT-TTAGCAGCAGAAATCAATAGAAGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
48373614 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
*
48373645 CCATCTTAGCTGCAAAAACCAAT
1 CCATCTTAGCAGCAAAAACCAAT
48373668 TAAAATCCAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 4 0.08
31 46 0.92
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (31 bp):
CCATCTTAGCAGCAAAAACCAATAGAAGGTA
Found at i:48375962 original size:39 final size:38
Alignment explanation
Indices: 48375907--48375992 Score: 102
Period size: 38 Copynumber: 2.2 Consensus size: 38
48375897 CCAAATCCCT
*
48375907 AACCCATAACCCCTAAATCCAC-CTTAACCCTTAAAGCATA
1 AACCC-TAACCCCTAAATCC-CTC-TAACCCCTAAAGCATA
* *
48375947 AACCCTAACCTCTAAATCTCTCTAACCCCTAAAGCATA
1 AACCCTAACCCCTAAATCCCTCTAACCCCTAAAGCATA
*
48375985 ACCCCTAA
1 AACCCTAA
48375993 AAATTTTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 23 0.56
39 13 0.32
40 5 0.12
ACGTcount: A:0.38, C:0.38, G:0.02, T:0.21
Consensus pattern (38 bp):
AACCCTAACCCCTAAATCCCTCTAACCCCTAAAGCATA
Found at i:48376157 original size:21 final size:21
Alignment explanation
Indices: 48376132--48376176 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
48376122 AAATCCTCCT
*
48376132 TAACCCTTAAAGCATAAACCC
1 TAACCCCTAAAGCATAAACCC
*
48376153 TAACCCCTAAAGCATAACCCC
1 TAACCCCTAAAGCATAAACCC
48376174 TAA
1 TAA
48376177 AAATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.36, G:0.04, T:0.18
Consensus pattern (21 bp):
TAACCCCTAAAGCATAAACCC
Found at i:48376466 original size:14 final size:14
Alignment explanation
Indices: 48376449--48376478 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
48376439 TTACCGTTGA
48376449 AACCCTAAACCCCT
1 AACCCTAAACCCCT
*
48376463 AACCCTTAACCCCT
1 AACCCTAAACCCCT
48376477 AA
1 AA
48376479 ATCCTCCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.47, G:0.00, T:0.17
Consensus pattern (14 bp):
AACCCTAAACCCCT
Found at i:48377142 original size:112 final size:114
Alignment explanation
Indices: 48376855--48377166 Score: 346
Period size: 112 Copynumber: 2.8 Consensus size: 114
48376845 CGCTACACCT
* * * * * *
48376855 AAAACGCCGCTAAATCCCCGAAAGGCTAAGAAACAGTGTCATTGGGCTTAGGTTTTCTTGTGGTG
1 AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
*
48376920 CTTTTTTAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
66 CTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
* * * * * *
48376969 AAAACGCCGCTAAAT-CCTG-AAAGCACAAAAAACGGTGCCGTTGGGCTTAGTTTTTTTTTGCGG
1 AAAACGCCGCTAAATCCCCGAAAAGCTC-AGAAACGGTGTCGTTGGGCTTAG-GTTTTCTTGCGG
* * * * *
48377032 CGCTATTCCAAAAACGCCGCTAAATC-CT-TGCATTAGCGGCGCTTCTT-TA
64 CGCTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTT-TTAAA
* * * * *
48377081 GAAACGCCGCTAAATCCCCGAAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTTGCGGCG
1 AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
*
48377146 CTTTTTCAAAAACGCCACTAA
66 CTTTTTCAAAAACGCCGCTAA
48377167 TGACTCGAAA
Statistics
Matches: 161, Mismatches: 32, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
112 64 0.40
113 46 0.29
114 51 0.32
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (114 bp):
AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
CTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
Found at i:48377199 original size:186 final size:183
Alignment explanation
Indices: 48376955--48377293 Score: 445
Period size: 186 Copynumber: 1.8 Consensus size: 183
48376945 CTGAGCATTA
* * * *
48376955 GCGGCGCTTTTAAAAAAACGCCGCTAAATCCTGAAAGCACAAAAAACGGTGCCGTTGGGCTTAGT
1 GCGGCGCTTTTAAAAAAACGCCACTAAATACTGAAAGCACAAAAAACGGCGCCGTTGGGATTAG-
* *
48377020 TTTTTTTTGCGGCGCTATTC-CAAAAACGCCGCTAAA-TCCTTG-CATTAGCGGCGCTTCT-TTA
65 -ATTTTTTGCGGCGCT-TTCTCAAAAACGCCGCTAAAGGCC-TGACATTAGCGGCGCTT-TATTA
*
48377081 GAAACGCCGCTAAATCCCCGAAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTT
126 AAAACGCCGCTAAATCCCCG-AAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTT
** * * *
48377140 GCGGCGCTTTTTCAAAAACGCCACT-AATGACTCGAAAGCTCAGAAAACGGCGTCGTTGGGATTA
1 GCGGCGCTTTTAAAAAAACGCCACTAAAT-ACT-GAAAGCACAAAAAACGGCGCCGTTGGGATTA
*
48377204 GATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTAGCGGCGCTTTATTAAA
64 GATTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCTG-ACATTAGCGGCGCTTTATTAAA
48377269 AACGCCGCTAAATCCCCGAAAGCTC
128 AACGCCGCTAAATCCCCGAAAGCTC
48377294 GGTAAACGAC
Statistics
Matches: 134, Mismatches: 13, Indels: 14
0.83 0.08 0.09
Matches are distributed among these distances:
183 3 0.02
184 34 0.25
185 34 0.25
186 63 0.47
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (183 bp):
GCGGCGCTTTTAAAAAAACGCCACTAAATACTGAAAGCACAAAAAACGGCGCCGTTGGGATTAGA
TTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCTGACATTAGCGGCGCTTTATTAAAAAC
GCCGCTAAATCCCCGAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTT
Found at i:48377351 original size:113 final size:113
Alignment explanation
Indices: 48377140--48377344 Score: 272
Period size: 113 Copynumber: 1.8 Consensus size: 113
48377130 TGGTTTTCTT
* * *
48377140 GCGGCGCTTTTTCAAAAACGCCACTAATGACTCGAAAGCTCAGAAAACGGCGTCGTTGGGATTAG
1 GCGGCGCTTTTTCAAAAACGCCACTAATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATTAG
48377205 ATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
66 ATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
* * * * *
48377253 GCGGCGCTTTATT-AAAAACGCCGCTAAAT-CCCCGAAAGCTCGGTAAACGACGTCGTTCGGCTT
1 GCGGCGCTTT-TTCAAAAACGCCACT-AATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATT
* *
48377316 AGGTTTTTTGCGGTGCTTTCT-ATAAAACG
64 AGATTTTTTGCGGCGCTTTCTCA-AAAACG
48377345 CTGCTAATTC
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
112 1 0.01
113 73 0.92
114 5 0.06
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (113 bp):
GCGGCGCTTTTTCAAAAACGCCACTAATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATTAG
ATTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
Found at i:48390669 original size:18 final size:19
Alignment explanation
Indices: 48390642--48390685 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
48390632 CCCCCCCCCC
*
48390642 AAAA-AAAAGGAA-AAATG
1 AAAAGAAAAGGAATAAAAG
*
48390659 AAATGAAAAGGAATAAAAG
1 AAAAGAAAAGGAATAAAAG
48390678 AAAAGAAA
1 AAAAGAAA
48390686 CTACAAATCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 8 0.36
19 11 0.50
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAAGAAAAGGAATAAAAG
Found at i:48391304 original size:25 final size:25
Alignment explanation
Indices: 48391270--48391322 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
48391260 TAGAGCACTT
*
48391270 AGTGCCTTTAGGTCAGTACATC-CA
1 AGTGCCTTTAAGTCAGTACATCTCA
48391294 AGTGCTCTTTAAGTCAGTACATCTCA
1 AGTGC-CTTTAAGTCAGTACATCTCA
48391320 AGT
1 AGT
48391323 TGCAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
AGTGCCTTTAAGTCAGTACATCTCA
Found at i:48398769 original size:199 final size:199
Alignment explanation
Indices: 48398427--48398789 Score: 519
Period size: 199 Copynumber: 1.8 Consensus size: 199
48398417 CCCTTGGCAC
* *
48398427 TGCTAAGTTTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTATTGATCTAGTCAATG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
* * * * *
48398492 ATTAGTATAATGATGATGGGCCACTTCAAACTTTAGTAAGAGTTTGAAAGAATAACTCACCTACT
66 ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
* *
48398557 GATATACTTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
131 GACATAATTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
48398622 ACAT
196 ACAT
* * *
48398626 TGCTAAGTCTAAAGAAAAGTTAGAAGTAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAGTG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
* * * * * * * *
48398691 ATCAGTCTAATAATGATGGACCACTTTAACCTTTAGCAAGAGTTAGGAAGAATCACTTATCTATT
66 ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
** *
48398756 GACATAATTGGTGATGTTCATGATGGGATCAAAA
131 GACATAATTGGTGATAATCATGATAGGATCAAAA
48398790 TAAGGGGTAG
Statistics
Matches: 141, Mismatches: 23, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
199 141 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (199 bp):
TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTAGAAAGAATAACTCACCTACT
GACATAATTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
ACAT
Found at i:48400929 original size:30 final size:31
Alignment explanation
Indices: 48400890--48400949 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
48400880 AGAGGTGGGA
48400890 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
1 TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
* **
48400921 TGGG-AGGGAGTAAAAGTTTTTGGGGAAAA
1 TGGGAAGGGAATAAAAGTTTTAAGGGAAAA
48400950 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAGTTTTAAGGGAAAAG
Found at i:48401181 original size:9 final size:9
Alignment explanation
Indices: 48401163--48401199 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
48401153 TATAGTTTGA
48401163 TATTCGAAT
1 TATTCGAAT
*
48401172 TATTCAAAT
1 TATTCGAAT
*
48401181 TATTCGAGT
1 TATTCGAAT
48401190 TATTCGAAT
1 TATTCGAAT
48401199 T
1 T
48401200 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:48405381 original size:16 final size:16
Alignment explanation
Indices: 48405347--48405399 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
48405337 ATAGCATTAG
48405347 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
48405363 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
48405379 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
48405395 TCATG
1 TCATG
48405400 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:48408172 original size:3 final size:3
Alignment explanation
Indices: 48408166--48408192 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48408156 GACCACGATG
48408166 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
48408193 GAAACTATTA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48411116 original size:35 final size:35
Alignment explanation
Indices: 48411070--48411140 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
48411060 AGTAAAAGAT
48411070 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
1 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
48411105 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
1 AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
48411140 A
1 A
48411141 CAAACCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.08, G:0.20, T:0.28
Consensus pattern (35 bp):
AGAATCAAGATTTGAGATAAAGTATATTCCGTAAG
Found at i:48422424 original size:73 final size:73
Alignment explanation
Indices: 48422343--48422488 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
48422333 ATTCTGACAA
*
48422343 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTG
1 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
48422408 TGTAAAAC
66 TGTAAAAC
48422416 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
1 ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
48422481 TGTAAAAC
66 TGTAAAAC
48422489 TTATTATCTT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (73 bp):
ATAGAATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTA
TGTAAAAC
Found at i:48443881 original size:37 final size:37
Alignment explanation
Indices: 48443833--48443927 Score: 120
Period size: 37 Copynumber: 2.5 Consensus size: 37
48443823 TTAATGAATG
*
48443833 CATGATTAAGCATGCCATTGAGATTGTTAAACCAG-AAC
1 CATGA-TAAGCATGCCATTGAAATTGTTAAA-CAGAAAC
* * *
48443871 CATGATAAGCATGCCACTGAAATTGTTAAACTGAAAG
1 CATGATAAGCATGCCATTGAAATTGTTAAACAGAAAC
*
48443908 CATGATAAACATGCCATTGA
1 CATGATAAGCATGCCATTGA
48443928 TATTTTTACT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
36 2 0.04
37 43 0.86
38 5 0.10
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (37 bp):
CATGATAAGCATGCCATTGAAATTGTTAAACAGAAAC
Found at i:48444750 original size:72 final size:68
Alignment explanation
Indices: 48444674--48444811 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 68
48444664 TGATTAAACT
* * *
48444674 TAATCACTTTAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATT-AATTTAA
1 TAATCACTTTAATAGTAAATTAATAAAATA-TTAT-T--AAAATAAGTATT-AAATTAAATTTAA
48444738 TATTAAGC
61 TATTAAGC
*
48444746 TAATCACTTTAATAGTAAATTAATAAAATATTATTAAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATAGTAAATTAATAAAATATTATTAAAATAAGTATTAAATTAAATTTAATATTA
48444811 A
66 A
48444812 ATCTATTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
67 5 0.08
68 23 0.38
70 1 0.02
71 4 0.07
72 28 0.46
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (68 bp):
TAATCACTTTAATAGTAAATTAATAAAATATTATTAAAATAAGTATTAAATTAAATTTAATATTA
AGC
Found at i:48449550 original size:21 final size:21
Alignment explanation
Indices: 48449524--48449614 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 21
48449514 GTGTTTTACT
* *
48449524 TTCTGTTTAGCTCTTTCGAGC
1 TTCTGTTAAGCTCTTACGAGC
48449545 TTCTGTTAAGCTCTTACGAGC
1 TTCTGTTAAGCTCTTACGAGC
* * * *
48449566 TTCTATTCAA-TTCTTATGAGT
1 TTCTGTT-AAGCTCTTACGAGC
* * *
48449587 TTTTGTTCAGCTCTCACGAGC
1 TTCTGTTAAGCTCTTACGAGC
48449608 TTCTGTT
1 TTCTGTT
48449615 GGCGTGTTCA
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 51 0.94
22 2 0.04
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (21 bp):
TTCTGTTAAGCTCTTACGAGC
Found at i:48452581 original size:51 final size:52
Alignment explanation
Indices: 48452491--48452609 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
48452481 GTAGAAATTG
* *
48452491 TGAAAATGGAGAAATGAGAAACATTTGGAAATGATTGTGG-TTTTCTCCAAAA
1 TGAAAATGGAGAAATGAG-AACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
*
48452543 TGAAAATGGAGAAATGTAG-TCATTTGGAAATGAATGTGGTTTTTCTCAAAAA
1 TGAAAATGGAGAAATG-AGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
48452595 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
48452610 CTTGGAAATG
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 1 0.02
50 5 0.08
51 20 0.32
52 34 0.55
53 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
Found at i:48453543 original size:22 final size:22
Alignment explanation
Indices: 48453515--48453560 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
48453505 TATGATTTTT
*
48453515 AAAAAAA-AAGTTACTCTCTTGA
1 AAAAAAATAAATTAC-CTCTTGA
*
48453537 AAAAAAATAAATTTCCTCTTGA
1 AAAAAAATAAATTACCTCTTGA
48453559 AA
1 AA
48453561 GTTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (22 bp):
AAAAAAATAAATTACCTCTTGA
Found at i:48456025 original size:18 final size:18
Alignment explanation
Indices: 48455979--48456027 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
48455969 TAGAGTTATG
48455979 GGCCCACATGCCCGTGTA
1 GGCCCACATGCCCGTGTA
* *
48455997 GGCCTATATGCCCGTGTA
1 GGCCCACATGCCCGTGTA
48456015 GGCCCACATGCCC
1 GGCCCACATGCCC
48456028 ATATTGGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (18 bp):
GGCCCACATGCCCGTGTA
Found at i:48456026 original size:36 final size:32
Alignment explanation
Indices: 48455979--48456063 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 32
48455969 TAGAGTTATG
48455979 GGCCCACATGCCCGTGTAGGCCTATATGCCCGTGT
1 GGCCCACATGCCCGTGTAGGCC--T-TGCCCGTGT
* * * *
48456014 AGGCCCACATGCCCATATTGGCCTTGCTCGTGT
1 -GGCCCACATGCCCGTGTAGGCCTTGCCCGTGT
48456047 GGCCCACATGCCCGTGT
1 GGCCCACATGCCCGTGT
48456064 GGCATGATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 15 0.35
33 8 0.19
34 1 0.02
36 19 0.44
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (32 bp):
GGCCCACATGCCCGTGTAGGCCTTGCCCGTGT
Found at i:48460236 original size:20 final size:20
Alignment explanation
Indices: 48460211--48460249 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
48460201 TACTCGCTTC
48460211 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
48460231 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
48460250 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:48461044 original size:37 final size:37
Alignment explanation
Indices: 48460994--48461067 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
48460984 GAATGTTTTC
48460994 CCTTCTATGGCAACATCAAATTCCCACTCTAACACTT
1 CCTTCTATGGCAACATCAAATTCCCACTCTAACACTT
48461031 CCTTCTATGGCAACATCAAATTCCCACTCTAACACTT
1 CCTTCTATGGCAACATCAAATTCCCACTCTAACACTT
48461068 ATGAACATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (37 bp):
CCTTCTATGGCAACATCAAATTCCCACTCTAACACTT
Found at i:48462740 original size:21 final size:21
Alignment explanation
Indices: 48462711--48462753 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
48462701 ACACCGAAAC
* *
48462711 AGGCTTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCAGCGTTTTTT
48462732 AGGCCTTTAGCAGCGTTTTTT
1 AGGCCTTTAGCAGCGTTTTTT
48462753 A
1 A
48462754 ACGCCGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (21 bp):
AGGCCTTTAGCAGCGTTTTTT
Found at i:48462922 original size:62 final size:61
Alignment explanation
Indices: 48462844--48462963 Score: 159
Period size: 62 Copynumber: 2.0 Consensus size: 61
48462834 GTTTATGTGA
* * ** * * *
48462844 AAAAACGCTGCTAAAGATCATGGTCTTTAGCGGCGTTTTTTGCAAAAGCGCCGCTAAAGGTG
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCG-CTTTTACAAAAACGCCGCTAAAGGTG
*
48462906 AAAAGCGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAG
48462964 ATCACAAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
61 20 0.40
62 30 0.60
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (61 bp):
AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTACAAAAACGCCGCTAAAGGTG
Found at i:48462976 original size:42 final size:43
Alignment explanation
Indices: 48462906--48463092 Score: 157
Period size: 42 Copynumber: 4.3 Consensus size: 43
48462896 GCTAAAGGTG
* * *
48462906 AAAAGCGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTAC
1 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTAC
48462948 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTATC
1 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTA-C
* * * ** * * *
48462992 ACAAACACCGCTAAAGGTCATGATCTTTAGCGACGCTTTTTGCC
1 AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTT-AC
* * * * **
48463036 ACAAACGCCGCTATAA-A--ACAAGCCTTTAGCGTCACTTCTCGC
1 AAAAACGCCGCTA-AAGATCACAAG-CTTTAGCGGCGCTTTTTAC
48463078 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
48463093 AACATAACAT
Statistics
Matches: 118, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.02
42 48 0.41
43 18 0.15
44 48 0.41
45 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTAC
Found at i:48463020 original size:44 final size:43
Alignment explanation
Indices: 48462911--48463048 Score: 170
Period size: 44 Copynumber: 3.2 Consensus size: 43
48462901 AGGTGAAAAG
*
48462911 CGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTACAAAAA
1 CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTACACAAA
* *
48462953 CGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTATCACAAA
1 CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTA-CACAAA
* * * * * *
48462997 CACCGCTAAAGGTCATGATCTTTAGCGACGCTTTTTGCCACAAA
1 CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTT-ACACAAA
48463041 CGCCGCTA
1 CGCCGCTA
48463049 TAAAACAAGC
Statistics
Matches: 82, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
42 29 0.35
43 5 0.06
44 48 0.59
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGATCACGACCTTTAGCGGCGCTTTTTACACAAA
Found at i:48463139 original size:18 final size:19
Alignment explanation
Indices: 48463112--48463148 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
48463102 TTTAAAAAAA
*
48463112 TTTATTTAAATATT-TATT
1 TTTATATAAATATTATATT
48463130 TTTATATAAATATTATATT
1 TTTATATAAATATTATATT
48463149 ATGTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATAAATATTATATT
Found at i:48464144 original size:16 final size:16
Alignment explanation
Indices: 48464123--48464153 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48464113 AGTCCCAAAC
48464123 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
48464139 TATTGTAAACATCAG
1 TATTGTAAACATCAG
48464154 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:48465162 original size:20 final size:21
Alignment explanation
Indices: 48465137--48465176 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48465127 AAAATTTTAT
*
48465137 TTATTTT-TATTTGTTAAAAA
1 TTATTTTATATATGTTAAAAA
48465157 TTATTTTATATATGTTAAAA
1 TTATTTTATATATGTTAAAA
48465177 TGAGATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (21 bp):
TTATTTTATATATGTTAAAAA
Found at i:48467345 original size:41 final size:40
Alignment explanation
Indices: 48467299--48467493 Score: 216
Period size: 41 Copynumber: 4.8 Consensus size: 40
48467289 CCACAATTGC
48467299 CCTGAGCATTAGCGGCGCTTTCTAAAAAACGCCGCT-AATA
1 CCTGAGCATTAGCGGCGCTTT-TAAAAAACGCCGCTAAATA
* * *
48467339 CTCTGAGCATTAGCGGCGTTTTTTCAAAAACGCCGCTAAAGA
1 C-CTGAGCATTAGCGGCG-CTTTTAAAAAACGCCGCTAAATA
** * * *
48467381 CCCAATCATTAGTGGCGCTTTTTAAAAA-GCCGCTAAA-A
1 CCTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAATA
* *
48467419 CCCTGAGCATTAGCTGCGCATTTTAAAAAACGCCGATAAATA
1 -CCTGAGCATTAGCGGCGC-TTTTAAAAAACGCCGCTAAATA
*
48467461 CCTGAGCATTAGCGGCGCTTTACAAAAAACGCC
1 CCTGAGCATTAGCGGCGCTTT-TAAAAAACGCC
48467494 ACAAATCCCC
Statistics
Matches: 129, Mismatches: 18, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
38 1 0.01
39 22 0.17
40 22 0.17
41 76 0.59
42 8 0.06
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.24
Consensus pattern (40 bp):
CCTGAGCATTAGCGGCGCTTTTAAAAAACGCCGCTAAATA
Found at i:48467448 original size:80 final size:82
Alignment explanation
Indices: 48467303--48467493 Score: 235
Period size: 80 Copynumber: 2.4 Consensus size: 82
48467293 AATTGCCCTG
* * ** *
48467303 AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAATACTCTGAGCATTAGCGGCGTTTTTTCAAAA
1 AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCATTTTAAAAA
*
48467368 ACGCCGCTAAAGACCCA
66 ACGCCGATAAAGACCCA
* * * *
48467385 ATCATTAGTGGCGCTTT-TTAAAAA-GCCGCTAAAACCCTGAGCATTAGCTGCGCATTTTAAAAA
1 AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCATTTTAAAAA
* **
48467448 ACGCCGATAAATACCTG
66 ACGCCGATAAAGACCCA
48467465 AGCATTAGCGGCGCTTTAC-AAAAAACGCC
1 AGCATTAGCGGCGCTTT-CTAAAAAACGCC
48467494 ACAAATCCCC
Statistics
Matches: 90, Mismatches: 16, Indels: 6
0.80 0.14 0.05
Matches are distributed among these distances:
80 61 0.68
81 11 0.12
82 18 0.20
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (82 bp):
AGCATTAGCGGCGCTTTCTAAAAAACGCCGCTAAAACCCTGAGCATTAGCGGCGCATTTTAAAAA
ACGCCGATAAAGACCCA
Found at i:48467602 original size:39 final size:38
Alignment explanation
Indices: 48467549--48467668 Score: 125
Period size: 39 Copynumber: 3.1 Consensus size: 38
48467539 TTGCGGCGCC
* *
48467549 TTTTGAAAAA-CGCCGCTAATGCTCATTTTTAGCAGTG
1 TTTTCAAAAAGCGCCGCTAATGCTCATTTTTAGCGGTG
* * *
48467586 TTTTCCAAAAAGCGCCGCTAATACTCAATCTTTAGCGGCG
1 TTTT-CAAAAAGCGCCGCTAATGCTC-ATTTTTAGCGGTG
*** *
48467626 TTTTTTTAAAGCGCCGCTAATGCTTGATTTTTAGCGGTG
1 TTTTCAAAAAGCGCCGCTAATGC-TCATTTTTAGCGGTG
48467665 TTTT
1 TTTT
48467669 TTATCCAAAC
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
37 4 0.06
38 5 0.07
39 43 0.64
40 15 0.22
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (38 bp):
TTTTCAAAAAGCGCCGCTAATGCTCATTTTTAGCGGTG
Found at i:48478936 original size:33 final size:33
Alignment explanation
Indices: 48478899--48478967 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
48478889 TAAATAAAAT
48478899 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
1 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
48478932 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
1 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
48478965 AGT
1 AGT
48478968 CAAATTCTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (33 bp):
AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
Found at i:48479559 original size:23 final size:23
Alignment explanation
Indices: 48479533--48479586 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
48479523 GTTACTAAGC
* * *
48479533 ATATATTAATAATTAATATAATA
1 ATATAATAATAATTAAAATAAAA
*
48479556 ATATAATAATATTTAAAATAAAA
1 ATATAATAATAATTAAAATAAAA
*
48479579 ATAAAATA
1 ATATAATA
48479587 TAAATAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAATAATAATTAAAATAAAA
Found at i:48487112 original size:14 final size:15
Alignment explanation
Indices: 48487093--48487125 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
48487083 GGTATAAAAT
*
48487093 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
48487107 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
48487122 AAAT
1 AAAT
48487126 GCTAGATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:48489524 original size:33 final size:33
Alignment explanation
Indices: 48489464--48489533 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
48489454 CACAAAGATC
* *
48489464 CAAATGTTTATATGCTCATCAAATACATATAAA
1 CAAATGTTCATATACTCATCAAATACATATAAA
* * * *
48489497 CAAATGTTCATATACTTATCCATTACATATAAC
1 CAAATGTTCATATACTCATCAAATACATATAAA
48489530 CAAA
1 CAAA
48489534 ATCATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (33 bp):
CAAATGTTCATATACTCATCAAATACATATAAA
Found at i:48489650 original size:41 final size:42
Alignment explanation
Indices: 48489575--48489655 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 42
48489565 CTTAATTTAA
* * *
48489575 CAGATTCACCGGCACTTAGCTTGCTAGGCTTATAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATT
*
48489617 CAGA-TCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
48489656 ATAATTTCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 31 0.89
42 4 0.11
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.27
Consensus pattern (42 bp):
CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATT
Found at i:48491420 original size:51 final size:49
Alignment explanation
Indices: 48491365--48491822 Score: 285
Period size: 51 Copynumber: 9.8 Consensus size: 49
48491355 GAATTGTAAT
*
48491365 TTTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
** * * * *
48491416 TTTAATCTATTCCACTGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
* * * * *
48491467 TTTAATCTGTTCCACTGCAAATT-TAGAGAAATAAGA-TT-T-GCG-ATC
1 TTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCGTAGC
* * * * *
48491512 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
* * * *
48491563 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TT-T-GC-TATC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* * * **
48491608 TTCAATCTACTTCGTTGCAACTTC-AGGTAGATAAGATTTGTA---T--C
1 TTTAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGTAGCGTAGC
*
48491652 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TT-TA-C-TATC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* * *
48491697 TTCAATCTGCTCCACTTCAACCTT-AGGGAGA-AGAGATTTGTA--GT---
1 TTTAATCTGCTCCACTGCAA-CTTCAAGGAGATA-AGATTTGTAGCGTAGC
* * * *
48491741 TTTAATCTGCTCTATTGCAACTTCAGGGGGATAAGATTTGT---G--GC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* *
48491785 TTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATT
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
48491823 CTCCACGATG
Statistics
Matches: 327, Mismatches: 55, Indels: 57
0.74 0.13 0.13
Matches are distributed among these distances:
42 2 0.01
43 7 0.02
44 95 0.29
45 89 0.27
46 11 0.03
47 5 0.02
48 3 0.01
49 2 0.01
50 5 0.02
51 108 0.33
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.34
Consensus pattern (49 bp):
TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
Found at i:48491546 original size:45 final size:45
Alignment explanation
Indices: 48491336--48491822 Score: 362
Period size: 44 Copynumber: 10.5 Consensus size: 45
48491326 TGCAACCCAT
* * *
48491336 TGCAACTTCAGGG-GTATAGGAATTG-TAAT-TTTAATCTACTCCAC
1 TGCAACTTCAGGGAG-ATAAGATTTGCT-ATCTTTAATCTGCTCCAC
* * **
48491380 TGCAACTTCAAGGAGATAAGATTTGTAGCTTGTAGCTTTAATCTATTCCAC
1 TGCAACTTCAGGGAGATAAGA-TT-T-GC---TATCTTTAATCTGCTCCAC
* * * *
48491431 TGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGATTTG---C---TATCTTTAATCTGCTCCAC
* * * * * *
48491482 TGCAAATTTAGAGAAATAAGATTTGCGATCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * * *
48491527 TGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGATT--T-GC---TATCTTTAATCTGCTCCAC
* * * * **
48491578 TGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTACTTCGT
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
*
48491623 TGCAACTTCAGGTAGATAAGATTTG-TATCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * *
48491667 TGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * *
48491712 TTCAACCTT-AGGGAGA-AGAGATTTG-TAGT-TTTAATCTGCTCTAT
1 TGCAA-CTTCAGGGAGATA-AGATTTGCTA-TCTTTAATCTGCTCCAC
* **
48491756 TGCAACTTCAGGGGGATAAGATTTG-TGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
*
48491800 TACAACTTCAGGGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGATT
48491823 CTCCACGATG
Statistics
Matches: 356, Mismatches: 62, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
43 3 0.01
44 120 0.34
45 106 0.30
46 4 0.01
47 2 0.01
48 4 0.01
49 2 0.01
50 3 0.01
51 112 0.31
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
Found at i:48491556 original size:96 final size:95
Alignment explanation
Indices: 48491426--48491822 Score: 392
Period size: 96 Copynumber: 4.3 Consensus size: 95
48491416 TTTAATCTAT
* * * *
48491426 TCCACTGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTT
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
*
48491491 AGAGAAATAAGATTTGCGATCTTCAATCTGC
65 AGAGAAATAAGATTTGCTATCTTCAATCTGC
*
48491522 TCCACTGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
1 TCCACTGCAACTTCAGGGAGATAAGATT-GTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
* *
48491587 AGGGAAATAAGATTTGCTATCTTCAATCTAC
65 AGAGAAATAAGATTTGCTATCTTCAATCTGC
* ** * * *
48491618 TTCGTTGCAACTTCAGGTAGATAAGA---T---TTGTATCTTTAATCTGCTCCACTGCAACTTCA
1 TCCACTGCAACTTCAGGGAGATAAGATTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTCA
* *
48491677 -AGGAGATAAGATTTACTATCTTCAATCTGC
66 GA-GAAATAAGATTTGCTATCTTCAATCTGC
* * * * * *
48491707 TCCACTTCAACCTT-AGGGAG--AAGA--G--ATTTGTAGTTTTAATCTGCTCTATTGCAACTTC
1 TCCACTGCAA-CTTCAGGGAGATAAGATTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
* ** ** *
48491765 AGGGGGATAAGATTTG-TGGCTTTAATCTGC
65 AGAGAAATAAGATTTGCTATCTTCAATCTGC
*
48491795 TCCACTACAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
48491823 CTCCACGATG
Statistics
Matches: 254, Mismatches: 35, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
87 7 0.03
88 26 0.10
89 105 0.41
90 7 0.03
92 1 0.00
95 2 0.01
96 106 0.42
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (95 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTCA
GAGAAATAAGATTTGCTATCTTCAATCTGC
Found at i:48491734 original size:89 final size:88
Alignment explanation
Indices: 48491460--48491822 Score: 349
Period size: 89 Copynumber: 4.0 Consensus size: 88
48491450 AATTTGTAAC
* * * * * * *
48491460 TTGTAGCTTTAATCTGTTCCACTGCAAATTTAGAGAAATAAGATTTGCGATCTTCAATCTGCTCC
1 TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGCTCC
48491525 ACTGT-AACTTCAGGGAGATAAGATTCGT
65 ACT-TCAACTTCAGGGAGATAAGA----T
* * * *
48491553 AACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTAC
1 ---TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGC
* * *
48491618 TTC-GTTGCAACTTCAGGTAGATAAGAT
62 TCCACTT-CAACTTCAGGGAGATAAGAT
*
48491645 TTGTATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCTCC
1 TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGCTCC
48491710 ACTTCAACCTT-AGGGAGA-AGAGAT
65 ACTTCAA-CTTCAGGGAGATA-AGAT
* * * * ** *
48491734 TTGTAGT-TTTAATCTGCTCTATTGCAACTTCAGGGGGATAAGATTTGTGGCTTTAATCTGCTCC
1 TTGTA-TCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAATCTGCTCC
*
48491798 ACTACAACTTCAGGGAGATAAGAT
65 ACTTCAACTTCAGGGAGATAAGAT
48491822 T
1 T
48491823 CTCCACGATG
Statistics
Matches: 233, Mismatches: 26, Indels: 24
0.82 0.09 0.08
Matches are distributed among these distances:
87 3 0.01
88 33 0.14
89 112 0.48
90 6 0.03
92 1 0.00
94 1 0.00
95 1 0.00
96 76 0.33
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (88 bp):
TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAATCTGCTCCA
CTTCAACTTCAGGGAGATAAGAT
Found at i:48492409 original size:11 final size:11
Alignment explanation
Indices: 48492379--48492439 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
48492369 CCGGCCCATT
48492379 TTTTAATAAATA
1 TTTTAA-AAATA
**
48492391 TTAAAAAAATA
1 TTTTAAAAATA
48492402 TTTTAAAAATA
1 TTTTAAAAATA
*
48492413 ---AAAAAATA
1 TTTTAAAAATA
*
48492421 TTTTAAAAGTA
1 TTTTAAAAATA
48492432 TTTTAAAA
1 TTTTAAAA
48492440 TTAAAAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.18
11 28 0.72
12 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:48492416 original size:19 final size:19
Alignment explanation
Indices: 48492392--48492428 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
48492382 TAATAAATAT
48492392 TAAAAAAATATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
48492411 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
48492429 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:48492422 original size:30 final size:30
Alignment explanation
Indices: 48492386--48492446 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
48492376 ATTTTTTAAT
48492386 AAATATTAAAAAAATATTTTAAAAATAAAA
1 AAATATTAAAAAAATATTTTAAAAATAAAA
** * *
48492416 AAATATTTTAAAAGTATTTTAAAATTAAAA
1 AAATATTAAAAAAATATTTTAAAAATAAAA
48492446 A
1 A
48492447 TAAAAAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATATTAAAAAAATATTTTAAAAATAAAA
Found at i:48496700 original size:85 final size:85
Alignment explanation
Indices: 48496599--48496770 Score: 308
Period size: 85 Copynumber: 2.0 Consensus size: 85
48496589 AACCCACCCT
* * *
48496599 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTGTGCATAATTCGGGTAAAATCGAA
1 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
48496664 AAAATTTGGTTAACAGACCG
66 AAAATTTGGTTAACAGACCG
48496684 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
1 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
*
48496749 AAAATTTGGTTAACCGACCG
66 AAAATTTGGTTAACAGACCG
48496769 AA
1 AA
48496771 TTCGGTTAAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (85 bp):
AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGAGTAAAATCGAA
AAAATTTGGTTAACAGACCG
Found at i:48496951 original size:13 final size:13
Alignment explanation
Indices: 48496933--48496962 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
48496923 AGCCCAAACT
48496933 CAATTACCCAACC
1 CAATTACCCAACC
48496946 CAATTACCCAACC
1 CAATTACCCAACC
48496959 CAAT
1 CAAT
48496963 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:48497114 original size:9 final size:9
Alignment explanation
Indices: 48497102--48497169 Score: 84
Period size: 9 Copynumber: 7.4 Consensus size: 9
48497092 AAGATAAAAA
*
48497102 AATTCAGGT
1 AATTCGGGT
48497111 AATTCGGGT
1 AATTCGGGT
*
48497120 ATTTTTC-GGT
1 A--ATTCGGGT
*
48497130 AATTCGGTT
1 AATTCGGGT
48497139 AATTCGGGT
1 AATTCGGGT
48497148 AATTCGGGT
1 AATTCGGGT
48497157 AATTCGGGT
1 AATTCGGGT
48497166 AATT
1 AATT
48497170 TTTAACCAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
8 3 0.06
9 41 0.80
10 4 0.08
11 3 0.06
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (9 bp):
AATTCGGGT
Found at i:48497346 original size:12 final size:12
Alignment explanation
Indices: 48497329--48497353 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48497319 AGTAATTTCG
48497329 GGTCGGTTAACC
1 GGTCGGTTAACC
48497341 GGTCGGTTAACC
1 GGTCGGTTAACC
48497353 G
1 G
48497354 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:48499750 original size:16 final size:15
Alignment explanation
Indices: 48499731--48499764 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
48499721 AATAAGCAAG
48499731 TAAATAAATAAATGGA
1 TAAATAAATAAAT-GA
48499747 TAAATAAATAAATGA
1 TAAATAAATAAATGA
48499762 TAA
1 TAA
48499765 TAAGAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
TAAATAAATAAATGA
Found at i:48506316 original size:17 final size:19
Alignment explanation
Indices: 48506296--48506336 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
48506286 ATACTTCTTA
*
48506296 AAAAATAAAA-A-ATGTAT
1 AAAAATAAAATATATATAT
*
48506313 AAAAGTAAAATATATATAT
1 AAAAATAAAATATATATAT
48506332 AAAAA
1 AAAAA
48506337 ATTGATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATAAAATATATATAT
Found at i:48510968 original size:20 final size:20
Alignment explanation
Indices: 48510941--48510993 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
48510931 TATTATATTC
48510941 CCAATATATTATAGATAAAT
1 CCAATATATTATAGATAAAT
* * *
48510961 CGAATATATTAGAGATAAGT
1 CCAATATATTATAGATAAAT
*
48510981 CCAATACATTATA
1 CCAATATATTATA
48510994 TAAGCTCAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.09, T:0.32
Consensus pattern (20 bp):
CCAATATATTATAGATAAAT
Found at i:48511080 original size:18 final size:18
Alignment explanation
Indices: 48511046--48511079 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
48511036 AGAATGGGCT
48511046 TAAAAATATTATGAAAAC
1 TAAAAATATTATGAAAAC
48511064 TAAAAATATT-TGAAAA
1 TAAAAATATTATGAAAA
48511080 AAACTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAATATTATGAAAAC
Found at i:48512447 original size:17 final size:18
Alignment explanation
Indices: 48512427--48512464 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
48512417 TTTATATATT
*
48512427 ATATTAT-TTATTATAAA
1 ATATTATCTTACTATAAA
*
48512444 ATATTTTCTTACTATAAA
1 ATATTATCTTACTATAAA
48512462 ATA
1 ATA
48512465 AATTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATCTTACTATAAA
Found at i:48517217 original size:21 final size:21
Alignment explanation
Indices: 48517191--48517230 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
48517181 TAATGTCATA
48517191 TCAGTATTTTCATCTTGAATT
1 TCAGTATTTTCATCTTGAATT
*
48517212 TCAGTATTTTCATTTTGAA
1 TCAGTATTTTCATCTTGAA
48517231 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
TCAGTATTTTCATCTTGAATT
Found at i:48520926 original size:3 final size:3
Alignment explanation
Indices: 48520918--48520952 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
48520908 GTAACAACTT
48520918 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
48520953 TATTGTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:48521415 original size:24 final size:24
Alignment explanation
Indices: 48521388--48521439 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
48521378 AATCAAAGTC
* *
48521388 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
48521412 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
48521436 AAAT
1 AAAT
48521440 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:48525798 original size:24 final size:24
Alignment explanation
Indices: 48525771--48525817 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
48525761 AAACCTAATT
48525771 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
*
48525795 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTAAAATATATTAT
48525818 ATTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:48525833 original size:24 final size:24
Alignment explanation
Indices: 48525783--48525833 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
48525773 AATCAAAGTA
* **
48525783 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
48525807 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
48525831 AAA
1 AAA
48525834 CCTTCTAGAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.39
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:48527973 original size:22 final size:24
Alignment explanation
Indices: 48527948--48528013 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
48527938 TTGACATCCT
48527948 TTCTTGTTCTG-GTT-GAAATAGA
1 TTCTTGTTCTGTGTTAGAAATAGA
* *
48527970 TTCTTTTTGTGTGTTAGAAATAGA
1 TTCTTGTTCTGTGTTAGAAATAGA
* * *
48527994 TTCTTTTTGTGGGTTAGAAA
1 TTCTTGTTCTGTGTTAGAAA
48528014 AGTATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 9 0.23
23 3 0.08
24 27 0.69
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (24 bp):
TTCTTGTTCTGTGTTAGAAATAGA
Found at i:48527990 original size:24 final size:24
Alignment explanation
Indices: 48527958--48528013 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
48527948 TTCTTGTTCT
48527958 GGTT-GAAATAGATTCTTTTTGTG
1 GGTTAGAAATAGATTCTTTTTGTG
*
48527981 TGTTAGAAATAGATTCTTTTTGTG
1 GGTTAGAAATAGATTCTTTTTGTG
48528005 GGTTAGAAA
1 GGTTAGAAA
48528014 AGTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.45
Consensus pattern (24 bp):
GGTTAGAAATAGATTCTTTTTGTG
Found at i:48528460 original size:23 final size:23
Alignment explanation
Indices: 48528415--48528461 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
48528405 AACTTATATT
* *
48528415 TAAAATTCAAATATATATAAAAA
1 TAAAATTCAAATATAAACAAAAA
* *
48528438 TAAAATTCAAATTTAAACCAAAA
1 TAAAATTCAAATATAAACAAAAA
48528461 T
1 T
48528462 GATATTTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAATTCAAATATAAACAAAAA
Found at i:48538395 original size:25 final size:25
Alignment explanation
Indices: 48538361--48538410 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
48538351 AAATGAACTG
*
48538361 TTGAACAATTTGTTCGATCTTTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
48538386 TTGAACAATTTGTTCGATCTCTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
48538411 CAAACTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
TTGAACAATTTGTTCGATCTCTGCA
Found at i:48543771 original size:19 final size:19
Alignment explanation
Indices: 48543736--48543773 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
48543726 TCTAGTTTCA
**
48543736 GATAAAATTTATGGATCTT
1 GATAAAATTTACAGATCTT
48543755 GATAAAATTTACAGATCTT
1 GATAAAATTTACAGATCTT
48543774 AATTTGGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
GATAAAATTTACAGATCTT
Found at i:48556849 original size:15 final size:15
Alignment explanation
Indices: 48556829--48556860 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
48556819 CTATGAACCT
48556829 TAGTAAAATTCGGCC
1 TAGTAAAATTCGGCC
48556844 TAGTAAAATTCGGCC
1 TAGTAAAATTCGGCC
48556859 TA
1 TA
48556861 ACTATAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
TAGTAAAATTCGGCC
Found at i:48562530 original size:3 final size:3
Alignment explanation
Indices: 48562522--48562547 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48562512 TTCAAATTTA
48562522 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
48562548 GAGAAAGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:48570900 original size:20 final size:20
Alignment explanation
Indices: 48570877--48570916 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
48570867 TAACGGGACC
48570877 GCTGATGTGG-CAAGTTAACT
1 GCTGATGTGGCCAA-TTAACT
48570897 GCTGATGTGGCCAATTAACT
1 GCTGATGTGGCCAATTAACT
48570917 TGCCACGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
GCTGATGTGGCCAATTAACT
Found at i:48571100 original size:3 final size:3
Alignment explanation
Indices: 48571094--48571136 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
48571084 ATTTTTTTGC
48571094 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
48571137 GACTCTCTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:48571687 original size:3 final size:3
Alignment explanation
Indices: 48571658--48571724 Score: 59
Period size: 3 Copynumber: 23.3 Consensus size: 3
48571648 CTATTTTTTC
* * * *
48571658 TCT TCT CCT TCT TAT TCT TCT TAT TCT TCT TCT TCT TC- TCC TCT T-T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
* *
48571704 TTT TCT TCT TTT TC- TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT T
48571725 AAACCCTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 6 0.12
3 45 0.88
ACGTcount: A:0.03, C:0.30, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:48573092 original size:18 final size:16
Alignment explanation
Indices: 48573050--48573092 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 16
48573040 TGTCGTTCGT
48573050 TTTCAAAATATTATTCA
1 TTTC-AAATATTATTCA
48573067 TTTACAAATCATTATTCAA
1 TTT-CAAAT-ATTATTC-A
48573086 TTTCAAA
1 TTTCAAA
48573093 ACTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 7 0.30
18 12 0.52
19 4 0.17
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (16 bp):
TTTCAAATATTATTCA
Found at i:48574078 original size:17 final size:18
Alignment explanation
Indices: 48574047--48574080 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
48574037 CATAATGTTT
48574047 GCCCGTGTGAGCCCACAC
1 GCCCGTGTGAGCCCACAC
48574065 GCCCGTGT-AGCCCACA
1 GCCCGTGTGAGCCCACA
48574081 TGACCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.18, C:0.44, G:0.26, T:0.12
Consensus pattern (18 bp):
GCCCGTGTGAGCCCACAC
Found at i:48576817 original size:20 final size:21
Alignment explanation
Indices: 48576765--48576818 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
48576755 GAGGGGTCAA
48576765 CACAC-AT-GTGTGGAAGGAGG
1 CACACGATCGTGTGGAA-GAGG
*
48576785 CACAGGATCGTGTGGAA-AGG
1 CACACGATCGTGTGGAAGAGG
48576805 CACACG-TCAGTGTG
1 CACACGATC-GTGTG
48576819 CGCCAGGGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 2 0.07
20 17 0.59
21 2 0.07
22 8 0.28
ACGTcount: A:0.28, C:0.19, G:0.37, T:0.17
Consensus pattern (21 bp):
CACACGATCGTGTGGAAGAGG
Found at i:48578586 original size:31 final size:31
Alignment explanation
Indices: 48578542--48578600 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
48578532 TTTTTCTCAA
*
48578542 TTAAATTAAAATTAAAATTTTATATATACAT
1 TTAAATCAAAATTAAAATTTTATATATACAT
* *
48578573 TTAAATCATAATTAAAGTTTTATATATA
1 TTAAATCAAAATTAAAATTTTATATATA
48578601 ATTATACTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTAAATCAAAATTAAAATTTTATATATACAT
Found at i:48582968 original size:16 final size:17
Alignment explanation
Indices: 48582939--48582971 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
48582929 ATCACAATAA
48582939 AATAAAATTCTAATATT
1 AATAAAATTCTAATATT
*
48582956 AATAAACTT-TAATATT
1 AATAAAATTCTAATATT
48582972 TTGATATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAAATTCTAATATT
Found at i:48584316 original size:9 final size:9
Alignment explanation
Indices: 48584302--48584329 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
48584292 TTTTGTTACA
48584302 ACAATTAAT
1 ACAATTAAT
48584311 ACAATTAAT
1 ACAATTAAT
48584320 ACAATTAAT
1 ACAATTAAT
48584329 A
1 A
48584330 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:48584351 original size:68 final size:66
Alignment explanation
Indices: 48584272--48584413 Score: 248
Period size: 68 Copynumber: 2.1 Consensus size: 66
48584262 TCAAGTTTGT
*
48584272 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
48584337 AAA
64 AAA
48584340 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
*
48584405 T
66 A
48584406 TTTACTAA
1 TTTACTAA
48584414 CAATTAATTT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
66 27 0.38
67 1 0.01
68 44 0.61
ACGTcount: A:0.45, C:0.09, G:0.05, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
A
Found at i:48584423 original size:16 final size:16
Alignment explanation
Indices: 48584402--48584443 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
48584392 AATAATTTGA
*
48584402 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
48584418 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
48584434 TAGTTTTAAT
1 TAATTTTAAT
48584444 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:48584427 original size:22 final size:22
Alignment explanation
Indices: 48584417--48584477 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
48584407 TTACTAACAA
* * *
48584417 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
48584439 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
*
48584461 TTAATTTTAATTAAAAA
1 TTAATTTTAATAAAAAA
48584478 CGGGCCAGGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:48584432 original size:59 final size:66
Alignment explanation
Indices: 48584272--48584435 Score: 216
Period size: 68 Copynumber: 2.5 Consensus size: 66
48584262 TCAAGTTTGT
*
48584272 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTT-ATACAACAATTAATACAATTAATACAATTAATAATTTGAT
48584337 AAA
64 AAA
48584340 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAA-GTTAGATTTTA-TACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
48584403 AAT
64 AAA
*
48584406 TTTACTAA-C-AA-TTA-ATTTTA-ATAACAATTA
1 TTTACTAATCAAAGTTAGATTTTATACAACAATTA
48584436 GTTTTAATTT
Statistics
Matches: 92, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
59 9 0.10
61 6 0.07
62 3 0.03
64 2 0.02
65 1 0.01
66 27 0.29
67 1 0.01
68 43 0.47
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (66 bp):
TTTACTAATCAAAGTTAGATTTTATACAACAATTAATACAATTAATACAATTAATAATTTGATAA
A
Found at i:48590379 original size:37 final size:37
Alignment explanation
Indices: 48590337--48590522 Score: 300
Period size: 37 Copynumber: 5.0 Consensus size: 37
48590327 GGTAGTTTTA
* *
48590337 GCTACACTTATCTAATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
48590374 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
48590411 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
48590448 GTTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
48590485 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
48590522 G
1 G
48590523 TAGCTTTAGC
Statistics
Matches: 141, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 141 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:48590594 original size:45 final size:46
Alignment explanation
Indices: 48590485--48590608 Score: 191
Period size: 46 Copynumber: 2.8 Consensus size: 46
48590475 GTGATAAGTG
* *
48590485 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
*
48590531 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTGGTAGC-CTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
*
48590576 GCTACACTTATCTAATCAAG-GAC-AAGTGATAAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG
48590609 AGGTCATATG
Statistics
Matches: 73, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
43 10 0.14
44 2 0.03
45 21 0.29
46 40 0.55
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGCTCTA
Done.