Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold152
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: 2945013
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 18 of 18
Found at i:2794781 original size:13 final size:13
Alignment explanation
Indices: 2794763--2794788 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2794753 ACATTTTTCT
2794763 TTGTATCGATACA
1 TTGTATCGATACA
2794776 TTGTATCGATACA
1 TTGTATCGATACA
2794789 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2797353 original size:13 final size:13
Alignment explanation
Indices: 2797335--2797360 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2797325 TACACCAAGT
2797335 ATGTATCGATACA
1 ATGTATCGATACA
2797348 ATGTATCGATACA
1 ATGTATCGATACA
2797361 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2799662 original size:93 final size:88
Alignment explanation
Indices: 2799561--2799751 Score: 231
Period size: 88 Copynumber: 2.1 Consensus size: 88
2799551 CAATTATGAT
* *
2799561 ATTTACAATCAATCAACTTTTCTACTTTTCTATATAAAAAAAATCTAATTCTCAAATAT-ATTCT
1 ATTTACAATCAATCAAC-ATT-T--TTTT-TACATAAAAAAAATCTAATTCTCAAATATAATTC-
* * * *
2799625 TTGCATTAGTCTAGTCCTTATAGTCTGAC
60 ATGCATTAATCTAATCCTTATAGTCTAAC
* *
2799654 ATTTACAATCAATCAACATTTTTTTTACCTAAAAAAAATCTAATTCTCAGATATAATTCATGCAT
1 ATTTACAATCAATCAACATTTTTTTTACATAAAAAAAATCTAATTCTCAAATATAATTCATGCAT
* *
2799719 TAATCTAATCCTTGTAGTCTAAT
66 TAATCTAATCCTTATAGTCTAAC
2799742 ATTTACAATC
1 ATTTACAATC
2799752 CATGCATTAT
Statistics
Matches: 87, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
88 59 0.68
89 8 0.09
91 1 0.01
92 2 0.02
93 17 0.20
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.41
Consensus pattern (88 bp):
ATTTACAATCAATCAACATTTTTTTTACATAAAAAAAATCTAATTCTCAAATATAATTCATGCAT
TAATCTAATCCTTATAGTCTAAC
Found at i:2799845 original size:69 final size:68
Alignment explanation
Indices: 2799752--2799888 Score: 177
Period size: 68 Copynumber: 2.0 Consensus size: 68
2799742 ATTTACAATC
* * *
2799752 CATGCATTATTTTTATCAATTTTTTTTTCATATTAGAA-GAAATTTGATTCCTATAAAAAATCTA
1 CATGCATTAGTTTTATCAA-CTTTTTTTCATATTAGAATG-AATCTGATTCCTATAAAAAATCTA
2799816 TGCAT
64 TGCAT
* * * * *
2799821 CATGCATTGGTTTTATTAACTTTTTTTCGTATTAGAATGAATCTGATTCCTATCAATAATCTATG
1 CATGCATTAGTTTTATCAACTTTTTTTCATATTAGAATGAATCTGATTCCTATAAAAAATCTATG
2799886 CAT
66 CAT
2799889 TAATCATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 3
0.84 0.11 0.04
Matches are distributed among these distances:
68 42 0.71
69 17 0.29
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.46
Consensus pattern (68 bp):
CATGCATTAGTTTTATCAACTTTTTTTCATATTAGAATGAATCTGATTCCTATAAAAAATCTATG
CAT
Found at i:2800044 original size:160 final size:164
Alignment explanation
Indices: 2799833--2800247 Score: 428
Period size: 160 Copynumber: 2.5 Consensus size: 164
2799823 TGCATTGGTT
* * * * * * *
2799833 TTATTAACTTTTTTTCGTATTAGAATGAATCTGATTCCTATCAATAATCTATGCATTAATCATAT
1 TTATTAACTTATTTT-ATATTAGAAAGAATCTGATTCCCATTAAAAATCTATGCATTTATCATAT
* * ** * * * *
2799898 TTATTTC-AAAACAGAATTTATGTATTAGTCTTATTTTTCAAATTTTAATCCATGCATTAATCTA
65 TTA-TTCAAAAACAGAATTTATGCATTAATCCCATTTTGCAAACTCTAATCCATACATTAATCTA
* * *
2799962 TTCATCGCT-GTTTGACATTTAC-A-AT-CATTAGTC
129 TTCAT-GATAGTCTAACATTTACAACATACATTAGTC
* * * *
2799995 TTATTAACTTCTTTTATATT-GAAAGAATATGATTCCCATTAAAAATCTATACTTTTATCATATT
1 TTATTAACTTATTTTATATTAGAAAGAATCTGATTCCCATTAAAAATCTATGCATTTATCATATT
* * ** * *
2800059 TATTCAAAAACAGAATCTATGCATTAATCCCATTTTGCGAACTCTAATTTATATATTAGTCTATT
66 TATTCAAAAACAGAATTTATGCATTAATCCCATTTTGCAAACTCTAATCCATACATTAATCTATT
* *
2800124 CCTTATAGTCTAACATTTACAAACATACATTAGTC
131 CATGATAGTCTAACATTTAC-AACATACATTAGTC
* * * * *
2800159 TTATCAACTTATTTCATATTAGAAAAAATCTGATTCCCATTAAGAATATATGCATTTATCATATT
1 TTATTAACTTATTTTATATTAGAAAGAATCTGATTCCCATTAAAAATCTATGCATTTATCATATT
*
2800224 TATTCAAAAACAGAATTCATGCAT
66 TATTCAAAAACAGAATTTATGCAT
2800248 CACATCTATT
Statistics
Matches: 206, Mismatches: 40, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
159 4 0.02
160 96 0.47
161 4 0.02
162 15 0.07
163 2 0.01
164 25 0.12
165 60 0.29
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.42
Consensus pattern (164 bp):
TTATTAACTTATTTTATATTAGAAAGAATCTGATTCCCATTAAAAATCTATGCATTTATCATATT
TATTCAAAAACAGAATTTATGCATTAATCCCATTTTGCAAACTCTAATCCATACATTAATCTATT
CATGATAGTCTAACATTTACAACATACATTAGTC
Found at i:2800312 original size:39 final size:39
Alignment explanation
Indices: 2800269--2800378 Score: 123
Period size: 38 Copynumber: 2.8 Consensus size: 39
2800259 TTTGAATTTT
* * ***
2800269 AATAAAAAATTTATATATTAATCAGATCTTTTATGTTCC
1 AATAAAAAATTTATACATTAATCATATCTTTTAAAATCC
* * * *
2800308 AATAAATAATTTATACATTACTAATAT-TTTTAAAATCT
1 AATAAAAAATTTATACATTAATCATATCTTTTAAAATCC
*
2800346 AATAAAAAATTTATGCATTAATCATATCTTTTA
1 AATAAAAAATTTATACATTAATCATATCTTTTA
2800379 GATTTCAGTT
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
38 30 0.53
39 27 0.47
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.44
Consensus pattern (39 bp):
AATAAAAAATTTATACATTAATCATATCTTTTAAAATCC
Found at i:2800669 original size:16 final size:15
Alignment explanation
Indices: 2800648--2800686 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2800638 ATACATACGT
2800648 AAAAATATATATTTCA
1 AAAAATATAT-TTTCA
*
2800664 AAAAATAT-TTTTTA
1 AAAAATATATTTTCA
2800678 AAAAATATA
1 AAAAATATA
2800687 AAAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AAAAATATATTTTCA
Found at i:2800843 original size:14 final size:15
Alignment explanation
Indices: 2800824--2800853 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
2800814 AAAAATTTAC
2800824 ATATTTTT-TTATTT
1 ATATTTTTATTATTT
2800838 ATATTTTTATTATTT
1 ATATTTTTATTATTT
2800853 A
1 A
2800854 AAATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
ATATTTTTATTATTT
Found at i:2800902 original size:20 final size:19
Alignment explanation
Indices: 2800865--2800908 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2800855 AATATTATAA
2800865 ATATTT-TTTTATGTTTTT
1 ATATTTATTTTATGTTTTT
*
2800883 ATATTTATTTTTTGTATTTT
1 ATATTTATTTTATGT-TTTT
2800903 AT-TTTA
1 ATATTTA
2800909 ATTAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 11 0.48
20 6 0.26
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (19 bp):
ATATTTATTTTATGTTTTT
Found at i:2800905 original size:18 final size:18
Alignment explanation
Indices: 2800865--2800907 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
2800855 AATATTATAA
*
2800865 ATATTTTTTTATGTTTTT
1 ATATTTTTTTATGTATTT
*
2800883 ATATTTATTTTTTGTATTT
1 ATATTT-TTTTATGTATTT
2800902 -TATTTT
1 ATATTTT
2800908 AATTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 11 0.50
19 10 0.45
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (18 bp):
ATATTTTTTTATGTATTT
Found at i:2801805 original size:17 final size:18
Alignment explanation
Indices: 2801779--2801820 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
2801769 TTAACTTCAA
2801779 ATTT-AATTATATAAA-AT
1 ATTTAAATTATA-AAATAT
2801796 -TTTAAATTATAAAATAT
1 ATTTAAATTATAAAATAT
2801813 ATTTAAAT
1 ATTTAAAT
2801821 AAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
ATTTAAATTATAAAATAT
Found at i:2801895 original size:26 final size:27
Alignment explanation
Indices: 2801836--2801895 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
2801826 ATAATTATTT
*
2801836 AATA-TAATTTAATTTAAATTTTTATA
1 AATATTAATTTAATTTAAATATTTATA
*
2801862 ATTATTAATTTAA-TTAAATATTTATA
1 AATATTAATTTAATTTAAATATTTATA
*
2801888 AATGTTAA
1 AATATTAA
2801896 AAATTTTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.72
27 8 0.28
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
AATATTAATTTAATTTAAATATTTATA
Found at i:2802627 original size:2 final size:2
Alignment explanation
Indices: 2802620--2802646 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2802610 TGAATACACA
2802620 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 A
2802647 ACTTGAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2823782 original size:13 final size:13
Alignment explanation
Indices: 2823764--2823815 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
2823754 AGCTTCGTAG
2823764 CGATACATTGTAT
1 CGATACATTGTAT
2823777 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
2823796 CGATACATTGTAT
1 CGATACATTGTAT
2823809 CGATACA
1 CGATACA
2823816 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:2823796 original size:19 final size:19
Alignment explanation
Indices: 2823772--2823836 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
2823762 AGCGATACAT
2823772 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
2823791 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
2823804 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
2823823 TGTATCGACACAAA
1 TGTATCGATACAAA
2823837 TCATTGAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:2823805 original size:32 final size:32
Alignment explanation
Indices: 2823764--2823830 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
2823754 AGCTTCGTAG
2823764 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
2823796 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
2823828 CGA
1 CGA
2823831 CACAAATCAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:2824741 original size:20 final size:20
Alignment explanation
Indices: 2824716--2824785 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
2824706 ACTCAAATTA
2824716 TATCGATATAATAAGAAATG
1 TATCGATATAATAAGAAATG
* *
2824736 TATCGATACAATTTTAA-ACATG
1 TATCGATATAA---TAAGAAATG
* * *
2824758 TATCGATATATTTAGTAATG
1 TATCGATATAATAAGAAATG
2824778 TATCGATA
1 TATCGATA
2824786 CATTTTCTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 2 0.05
20 21 0.54
22 13 0.33
23 3 0.08
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (20 bp):
TATCGATATAATAAGAAATG
Found at i:2824790 original size:20 final size:19
Alignment explanation
Indices: 2824731--2824790 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 19
2824721 ATATAATAAG
2824731 AAATGTATCGATACAATTTTA
1 AAATGTATCGATAC-A-TTTA
*
2824752 AACATGTATCGATATATTTA
1 AA-ATGTATCGATACATTTA
*
2824772 GTAATGTATCGATACATTT
1 -AAATGTATCGATACATTT
2824791 TCTTGGCAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 19 0.56
21 4 0.12
22 11 0.32
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (19 bp):
AAATGTATCGATACATTTA
Found at i:2825739 original size:52 final size:51
Alignment explanation
Indices: 2825596--2825833 Score: 149
Period size: 52 Copynumber: 4.6 Consensus size: 51
2825586 GATGAGAAAA
* * * * * * *
2825596 ATGATAAAGATG-CAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAAAT
1 ATGAGAAAGATGCCAATATGCTAATTCAAGGCCAGCGACATTAGACTT-AAG
* * *
2825647 ATGCG-AAGAATGCCAATATGCTAATTCATGACCAGCGACATTAGACTTGAAG
1 ATGAGAAAG-ATGCCAATATGCTAATTCAAGGCCAGCGACATTAGACTT-AAG
* * * * * *
2825699 ATGAG-AAGAATGCCAATGTGCTGATTCAAGGTCAGTGACATTGGGCTTAAG
1 ATGAGAAAG-ATGCCAATATGCTAATTCAAGGCCAGCGACATTAGACTTAAG
** * * * * * *
2825750 AATGTTAAATATGCCAATACGCTGATTCAAGGCCAGCGATATCAGATTTAAAG
1 -ATGAGAAAGATGCCAATATGCTAATTCAAGGCCAGCGACATTAGACTT-AAG
* * * *
2825803 ATGATAAAGGTGCCAATGTGCTAATCCAAGG
1 ATGAGAAAGATGCCAATATGCTAATTCAAGG
2825834 TCAACAACAT
Statistics
Matches: 143, Mismatches: 39, Indels: 9
0.75 0.20 0.05
Matches are distributed among these distances:
50 3 0.02
51 9 0.06
52 126 0.88
53 5 0.03
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (51 bp):
ATGAGAAAGATGCCAATATGCTAATTCAAGGCCAGCGACATTAGACTTAAG
Found at i:2825804 original size:104 final size:104
Alignment explanation
Indices: 2825596--2825846 Score: 258
Period size: 104 Copynumber: 2.4 Consensus size: 104
2825586 GATGAGAAAA
* * * *
2825596 ATGATAAAGATG-CAATATGCTGATTCAAGGCCAGCAATATTGGGCTTAAATATGCGAAGAATGC
1 ATGAGAAAGATGCCAATGTGCTGATTCAAGGTCAGCAACATTGGGCTTAAATATGCGAAGAATGC
* * * *
2825660 CAATATGCTAATTCATGACCAGCGACATTAGACTTGAAG
66 CAATACGCTAATTCAAGACCAGCGACATCAGACTTAAAG
** **
2825699 ATGAG-AAGAATGCCAATGTGCTGATTCAAGGTCAGTGACATTGGGCTTAAGA-ATGTTAA-ATA
1 ATGAGAAAG-ATGCCAATGTGCTGATTCAAGGTCAGCAACATTGGGCTTAA-ATATGCGAAGA-A
* * * *
2825761 TGCCAATACGCTGATTCAAGGCCAGCGATATCAGATTTAAAG
63 TGCCAATACGCTAATTCAAGACCAGCGACATCAGACTTAAAG
* * * * *
2825803 ATGATAAAGGTGCCAATGTGCTAATCCAAGGTCAACAACATTGG
1 ATGAGAAAGATGCCAATGTGCTGATTCAAGGTCAGCAACATTGG
2825847 AACAAAAGAT
Statistics
Matches: 120, Mismatches: 23, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
102 3 0.03
103 8 0.07
104 105 0.88
105 4 0.03
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (104 bp):
ATGAGAAAGATGCCAATGTGCTGATTCAAGGTCAGCAACATTGGGCTTAAATATGCGAAGAATGC
CAATACGCTAATTCAAGACCAGCGACATCAGACTTAAAG
Found at i:2827112 original size:8 final size:8
Alignment explanation
Indices: 2827099--2827151 Score: 61
Period size: 8 Copynumber: 6.1 Consensus size: 8
2827089 TTTTCTTTGT
2827099 TTTTTTTA
1 TTTTTTTA
2827107 TTTTTTTA
1 TTTTTTTA
2827115 TTGTTTTTTTGA
1 ---TTTTTTT-A
2827127 TTTTTTTA
1 TTTTTTTA
*
2827135 TTATTTTA
1 TTTTTTTA
2827143 TTTTTTTA
1 TTTTTTTA
2827151 T
1 T
2827152 GTATGAAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
8 24 0.62
9 7 0.18
11 7 0.18
12 1 0.03
ACGTcount: A:0.13, C:0.00, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTTA
Found at i:2827112 original size:21 final size:20
Alignment explanation
Indices: 2827095--2827146 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
2827085 ATCTTTTTCT
2827095 TTGTTTTTTTTATTTTTTTA
1 TTGTTTTTTTTATTTTTTTA
*
2827115 TTGTTTTTTTGATTTTTTTA
1 TTGTTTTTTTTATTTTTTTA
*
2827135 TTATTTTATTTT
1 TTGTTTT-TTTT
2827147 TTTATGTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.83
Consensus pattern (20 bp):
TTGTTTTTTTTATTTTTTTA
Found at i:2827130 original size:28 final size:27
Alignment explanation
Indices: 2827083--2827149 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 27
2827073 CATCTAGACA
* *
2827083 TTATCTTTTTCTTTGTTTTTTTTATTTTT
1 TTAT-TTTTT-TTTGATTTTTTTATTATT
2827112 TTATTGTTTTTTTGATTTTTTTATTATT
1 TTATT-TTTTTTTGATTTTTTTATTATT
2827140 TTATTTTTTT
1 TTATTTTTTT
2827150 ATGTATGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 5 0.14
28 22 0.63
29 8 0.23
ACGTcount: A:0.10, C:0.03, G:0.04, T:0.82
Consensus pattern (27 bp):
TTATTTTTTTTTGATTTTTTTATTATT
Found at i:2839155 original size:13 final size:13
Alignment explanation
Indices: 2839137--2839162 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2839127 CATTTTTGGG
2839137 TGTATCGATACAT
1 TGTATCGATACAT
2839150 TGTATCGATACAT
1 TGTATCGATACAT
2839163 ATTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2839177 original size:32 final size:33
Alignment explanation
Indices: 2839117--2839180 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2839107 TACAAGCCAA
*
2839117 TGTATCGATACATTTTTGGGTGTATCGATACAT
1 TGTATCGATACATTATTGGGTGTATCGATACAT
*
2839150 TGTATCGATACA-TATTGTGTGTATCGATACA
1 TGTATCGATACATTATTGGGTGTATCGATACA
2839181 AATTTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATTGGGTGTATCGATACAT
Found at i:2839260 original size:20 final size:20
Alignment explanation
Indices: 2839213--2839267 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
2839203 GCCAATGACT
**
2839213 TGTATCGATACATTCTTTTC
1 TGTATCGATACATTCTGGTC
2839233 TAGTATCGATACATT-TGGTC
1 T-GTATCGATACATTCTGGTC
2839253 ATGTATCGATACATT
1 -TGTATCGATACATT
2839268 GTATCCATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTATCGATACATTCTGGTC
Found at i:2841309 original size:21 final size:21
Alignment explanation
Indices: 2841280--2841329 Score: 57
Period size: 20 Copynumber: 2.3 Consensus size: 21
2841270 CTGCTAGTGT
*
2841280 GGGGCTGCCCGATTGCGACCTC
1 GGGG-TGCCCGATCGCGACCTC
*
2841302 GGGGTG-CCGATCGCGACCTG
1 GGGGTGCCCGATCGCGACCTC
2841322 GTGGGTGC
1 G-GGGTGC
2841330 TGCCTAAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 13 0.54
21 7 0.29
22 4 0.17
ACGTcount: A:0.08, C:0.30, G:0.44, T:0.18
Consensus pattern (21 bp):
GGGGTGCCCGATCGCGACCTC
Found at i:2841781 original size:13 final size:13
Alignment explanation
Indices: 2841763--2841787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2841753 ATAAACCCCT
2841763 TGTATCGATACAC
1 TGTATCGATACAC
2841776 TGTATCGATACA
1 TGTATCGATACA
2841788 GAGAATGCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:2847974 original size:13 final size:13
Alignment explanation
Indices: 2847956--2847981 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2847946 CATTTTTGGG
2847956 TGTATCGATACAT
1 TGTATCGATACAT
2847969 TGTATCGATACAT
1 TGTATCGATACAT
2847982 ATTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2847996 original size:32 final size:33
Alignment explanation
Indices: 2847936--2847999 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
2847926 TACAGGCCAA
*
2847936 TGTATCGATACATTTTTGGGTGTATCGATACAT
1 TGTATCGATACATTATTGGGTGTATCGATACAT
*
2847969 TGTATCGATACA-TATTGTGTGTATCGATACA
1 TGTATCGATACATTATTGGGTGTATCGATACA
2848000 AATTTAACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.41
Consensus pattern (33 bp):
TGTATCGATACATTATTGGGTGTATCGATACAT
Found at i:2848083 original size:20 final size:22
Alignment explanation
Indices: 2848032--2848086 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
2848022 GCCAATGACC
**
2848032 TGTATCGATACATTCTTTTCCA
1 TGTATCGATACATTCTGGTCCA
*
2848054 -GTATCAATACATT-TGGT-CA
1 TGTATCGATACATTCTGGTCCA
2848073 TGTATCGATACATT
1 TGTATCGATACATT
2848087 GTATCGATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 14 0.50
21 12 0.43
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (22 bp):
TGTATCGATACATTCTGGTCCA
Found at i:2851321 original size:20 final size:21
Alignment explanation
Indices: 2851296--2851389 Score: 88
Period size: 20 Copynumber: 4.6 Consensus size: 21
2851286 TGTCTGCATA
2851296 TATCGATACATTGAAG-AATG
1 TATCGATACATTGAAGAAATG
*
2851316 TATCGATACAATG-AGAAATG
1 TATCGATACATTGAAGAAATG
* *
2851336 TATCGATACAATTTTAAG-CATG
1 TATCGATAC-A-TTGAAGAAATG
* *
2851358 TATCGATACATT-TAGTAATG
1 TATCGATACATTGAAGAAATG
*
2851378 TATTGATACATT
1 TATCGATACATT
2851390 TCCTTGGTAG
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
19 4 0.06
20 41 0.66
21 2 0.03
22 13 0.21
23 2 0.03
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (21 bp):
TATCGATACATTGAAGAAATG
Found at i:2851364 original size:42 final size:41
Alignment explanation
Indices: 2851296--2851387 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 41
2851286 TGTCTGCATA
2851296 TATCGATAC-ATTGAAGAATGTATCGATACAATGAGAAATG
1 TATCGATACAATTGAAGAATGTATCGATACAATGAGAAATG
* * * * *
2851336 TATCGATACAATTTTAAGCATGTATCGATACATTTAGTAATG
1 TATCGATACAA-TTGAAGAATGTATCGATACAATGAGAAATG
*
2851378 TATTGATACA
1 TATCGATACA
2851388 TTTCCTTGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
40 9 0.20
41 1 0.02
42 34 0.77
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (41 bp):
TATCGATACAATTGAAGAATGTATCGATACAATGAGAAATG
Found at i:2851432 original size:13 final size:13
Alignment explanation
Indices: 2851414--2851439 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2851404 CAGGGTAGTT
2851414 TTATATCGATACA
1 TTATATCGATACA
2851427 TTATATCGATACA
1 TTATATCGATACA
2851440 AAACTTACGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (13 bp):
TTATATCGATACA
Found at i:2852221 original size:59 final size:59
Alignment explanation
Indices: 2852158--2852328 Score: 189
Period size: 59 Copynumber: 2.9 Consensus size: 59
2852148 TTTGGATCAC
* * * * *
2852158 ATAAAACAACCTAAATTACCCTAAAATGCATGGAATTTACAAAATGGTCTTTAGATTAT
1 ATAAAATAACCTAAATAACCCTAAAATGCATGAAAATTACAAAATGGTCTCTAGATTAT
* * * ** * *
2852217 ATAAAATAACCTAAACAACCTTAAAATGTATGAAAATTACAAAATAATCCCTAGATTTT
1 ATAAAATAACCTAAATAACCCTAAAATGCATGAAAATTACAAAATGGTCTCTAGATTAT
** * * *
2852276 GGAAAATAACCTAAGTGACTCTAAAATGCATGAAAATTACAAAATGGTCTCTA
1 ATAAAATAACCTAAATAACCCTAAAATGCATGAAAATTACAAAATGGTCTCTA
2852329 TATGCATGAA
Statistics
Matches: 89, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
59 89 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (59 bp):
ATAAAATAACCTAAATAACCCTAAAATGCATGAAAATTACAAAATGGTCTCTAGATTAT
Found at i:2853901 original size:32 final size:33
Alignment explanation
Indices: 2853839--2853903 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
2853829 CACACCCAGA
2853839 TGTATCGATACATATTGCTTAGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
* * *
2853872 TGTATCGATACTTGTT-CTTGGTATCGATACAT
1 TGTATCGATACATATTGCTTAGTATCGATACAT
2853904 ATTAAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATATTGCTTAGTATCGATACAT
Found at i:2857829 original size:15 final size:16
Alignment explanation
Indices: 2857809--2857841 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2857799 AGAGTAGATA
*
2857809 TTGAAA-TTATCAAAG
1 TTGAAACTTATAAAAG
2857824 TTGAAACTTATAAAAG
1 TTGAAACTTATAAAAG
2857840 TT
1 TT
2857842 TTGTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.36
Consensus pattern (16 bp):
TTGAAACTTATAAAAG
Found at i:2862178 original size:13 final size:13
Alignment explanation
Indices: 2862160--2862184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2862150 TTCCATAATT
2862160 TGTATCGATACAA
1 TGTATCGATACAA
2862173 TGTATCGATACA
1 TGTATCGATACA
2862185 TTCTGGGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2862250 original size:50 final size:50
Alignment explanation
Indices: 2862170--2862287 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
2862160 TGTATCGATA
* * *
2862170 CAATGTATCGATACATTCTGGGTTTCACCTAGATATATTGATACA-TTCTT
1 CAATGTATCGATACATTTTGGGTTTCACCTAAATATATCGATACATTTC-T
* * *
2862220 CATTGTATCGATACATTTTGGGTTTTACCTAAATGTATCGATACATTTCT
1 CAATGTATCGATACATTTTGGGTTTCACCTAAATATATCGATACATTTCT
*
2862270 GAATGTATCGATACATTT
1 CAATGTATCGATACATTT
2862288 AGGCATTTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
50 56 0.95
51 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (50 bp):
CAATGTATCGATACATTTTGGGTTTCACCTAAATATATCGATACATTTCT
Found at i:2862770 original size:19 final size:19
Alignment explanation
Indices: 2862737--2862793 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
2862727 TTGTATCGAT
** *
2862737 ACATTGTATTAATACATGT
1 ACATTGTATCGATACATGC
*
2862756 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
2862775 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
2862794 AAACTGGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:2867387 original size:15 final size:15
Alignment explanation
Indices: 2867369--2867398 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2867359 CCAAATTGAG
2867369 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
2867384 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
2867399 ATTGATGAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:2867394 original size:16 final size:16
Alignment explanation
Indices: 2867358--2867398 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
2867348 GACAAAAGTG
* *
2867358 TCCAAATTGAGGAAGC
1 TCCAAAATGAAGAAGC
2867374 T-CAAAATGAAGAAGC
1 TCCAAAATGAAGAAGC
2867389 TCC-AAATGAA
1 TCCAAAATGAA
2867399 ATTGATGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 20 0.91
16 2 0.09
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (16 bp):
TCCAAAATGAAGAAGC
Found at i:2869483 original size:13 final size:13
Alignment explanation
Indices: 2869465--2869503 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
2869455 ACATTTTTCT
2869465 TTGTATCGATACA
1 TTGTATCGATACA
2869478 TTGTATCGATACA
1 TTGTATCGATACA
*
2869491 CTGTATCGATACA
1 TTGTATCGATACA
2869504 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:2869667 original size:20 final size:20
Alignment explanation
Indices: 2869624--2869669 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
2869614 AAATCTTTTG
2869624 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
2869645 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
2869665 CAAAA
1 CAAAA
2869670 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:2881523 original size:20 final size:20
Alignment explanation
Indices: 2881470--2881523 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
2881460 CTACCACTGT
*
2881470 TTGTATCGATACACGGCATA
1 TTGTATCGATACATGGCATA
*
2881490 TTGTATCGATACATGGTGA-A
1 TTGTATCGATACATGG-CATA
2881510 TTGTATCGATACAT
1 TTGTATCGATACAT
2881524 TACTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGTATCGATACATGGCATA
Found at i:2884522 original size:51 final size:50
Alignment explanation
Indices: 2884467--2884565 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 50
2884457 TTTCATTGAT
2884467 GTTTTATTTCTAAAA-TATCGATTTTTCACAATCGAGGATACTCCAACCCTG
1 GTTTTATTTCTAAAACT-TC-ATTTTTCACAATCGAGGATACTCCAACCCTG
* *
2884518 GTTTTATTTCTAAAACGTTCATTTTTCACCATCGGGGATACTCCAACC
1 GTTTTATTTCTAAAAC-TTCATTTTTCACAATCGAGGATACTCCAACC
2884566 TCGTTATTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 41 0.93
52 2 0.05
53 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.37
Consensus pattern (50 bp):
GTTTTATTTCTAAAACTTCATTTTTCACAATCGAGGATACTCCAACCCTG
Found at i:2884600 original size:79 final size:78
Alignment explanation
Indices: 2884500--2884723 Score: 247
Period size: 79 Copynumber: 2.8 Consensus size: 78
2884490 TTTCACAATC
*
2884500 GAGGATACTCCAACCCTGGTTTTATTTCTAAAACGTTC-ATTTTTCACCATCGGGGATACTCCAA
1 GAGGATACTCCAACCC-GGTTTTATTTCTAAAACG-TCAATTTTCCACCATCGGGGATACTCCAA
* *
2884564 CCTCGTTATTTT-TGA
64 CCTCATT-TTTTCCGA
* ** * * *
2884579 -AGGGATACTCTAACCTCGGTTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAA
1 GA-GGATACTCCAACC-CGGTTTTATTTCTAAAACGTCAATTTTCCACCATCGGGGATACTCCAA
*
2884643 CCTTATTTTTTCCGA
64 CCTCATTTTTTCCGA
* * * *
2884658 GAGGATACTCCAACCCCAGTTTTATTTTTAAAATGTCAATTTTCCACCATCGGGGATACTTCAAC
1 GAGGATACTCCAA-CCCGGTTTTATTTCTAAAACGTCAATTTTCCACCATCGGGGATACTCCAAC
2884723 C
65 C
2884724 CCAATTTTAT
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
78 6 0.05
79 110 0.92
80 4 0.03
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (78 bp):
GAGGATACTCCAACCCGGTTTTATTTCTAAAACGTCAATTTTCCACCATCGGGGATACTCCAACC
TCATTTTTTCCGA
Found at i:2884714 original size:130 final size:130
Alignment explanation
Indices: 2884580--2884854 Score: 358
Period size: 130 Copynumber: 2.1 Consensus size: 130
2884570 TATTTTTGAA
* **
2884580 GGGATACTCTAACCTCGGTTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACC
1 GGGATACTCTAACCCCAATTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACC
** * * * **
2884645 TTATTTTTTCCGAGA-GGATACTCCAACCCCAGTTTTATTTTTAAAA-TGTCAATTTTCCACCAT
66 CCATTATTTCCGA-ATGGACACTCCAACCCCAGTTTTATTTCTAAAACACT-AATTTTCCACCAT
2884708 CG
129 CG
* *
2884710 GGGATACT-TCAACCCCAATTTTATTTCTGAAACACCGATTTTCCACCATCGAGGATACTCCAAC
1 GGGATACTCT-AACCCCAATTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAAC
** * *
2884774 CCCATTATTTCCGAATGGACACTCCAACCCTGGTTTTATTTCTAAAACACTGATTTTTCACCATC
65 CCCATTATTTCCGAATGGACACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCCACCATC
2884839 G
130 G
2884840 GGGATACTCTAACCC
1 GGGATACTCTAACCC
2884855 TATTATTTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
129 2 0.02
130 121 0.97
131 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (130 bp):
GGGATACTCTAACCCCAATTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACC
CCATTATTTCCGAATGGACACTCCAACCCCAGTTTTATTTCTAAAACACTAATTTTCCACCATCG
Found at i:2884723 original size:51 final size:51
Alignment explanation
Indices: 2884658--2884777 Score: 159
Period size: 51 Copynumber: 2.4 Consensus size: 51
2884648 TTTTTTCCGA
* * ***
2884658 GAGGATACTCCAACCCCAGTTTTATTTTTAAAATGTCAATTTTCCACCATC
1 GAGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTCCACCATC
* * * *
2884709 GGGGATACTTCAACCCCAATTTTATTTCTGAAACACCGATTTTCCACCATC
1 GAGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTCCACCATC
2884760 GAGGATACTCCAACCCCA
1 GAGGATACTCCAACCCCA
2884778 TTATTTCCGA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (51 bp):
GAGGATACTCCAACCCCAATTTTATTTCTAAAACACCAATTTTCCACCATC
Found at i:2884838 original size:209 final size:209
Alignment explanation
Indices: 2884467--2884894 Score: 529
Period size: 209 Copynumber: 2.0 Consensus size: 209
2884457 TTTCATTGAT
* * ***
2884467 GTTTTATTTCTAAAATATCGATTTTTCACAATCGAGGATACTCCAACCCTGGTTTTATTTCTAAA
1 GTTTTATTTCTAAAATATCAATTTTCCACAATCGAGGATACTCCAACCCCAATTTTATTTCTAAA
** * * * * ** * *
2884532 ACGTTCATTTTTCACCATCGGGGATACTCCAACCTCGTTATTTTTGAAGGGATACTCTAACCTCG
66 ACGACCATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCCGAAGGGACACTCCAACCTCG
* *
2884597 GTTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACCTTATT-TTTTCCGAGAG
131 GTTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACCCTATTATTTT-CAAGAG
2884661 GATACTCCAACCCCA
195 GATACTCCAACCCCA
* * * * * *
2884676 GTTTTATTTTTAAAATGTCAATTTTCCACCATCGGGGATACTTCAACCCCAATTTTATTTCTGAA
1 GTTTTATTTCTAAAATATCAATTTTCCACAATCGAGGATACTCCAACCCCAATTTTATTTCTAAA
*
2884741 AC-ACCGATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCCGAATGGACACTCCAACC-C
66 ACGACC-ATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCCGAAGGGACACTCCAACCTC
* ** * *
2884804 TGGTTTTATTTCTAAAACACTGATTTTTCACCATCGGGGATACTCTAACCCTATTATTTTCAAGA
130 -GGTTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACCCTATTATTTTCAAGA
*
2884869 GGATACTTCAACCCCA
194 GGATACTCCAACCCCA
*
2884885 ATTTTATTTC
1 GTTTTATTTC
2884895 CATAACATTG
Statistics
Matches: 184, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
208 2 0.01
209 178 0.97
210 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (209 bp):
GTTTTATTTCTAAAATATCAATTTTCCACAATCGAGGATACTCCAACCCCAATTTTATTTCTAAA
ACGACCATTTTCCACCATCGAGGATACTCCAACCCCATTATTTCCGAAGGGACACTCCAACCTCG
GTTTTATTTCTAAAACACCGATTTACCACCATCGAGGATACTCCAACCCTATTATTTTCAAGAGG
ATACTCCAACCCCA
Found at i:2885011 original size:78 final size:79
Alignment explanation
Indices: 2884710--2885056 Score: 403
Period size: 79 Copynumber: 4.4 Consensus size: 79
2884700 TCCACCATCG
* ** * * *
2884710 GGGATACTTCAACCCCAATTTTATTTCTGAAACACCGATTTTCCACCATCGAGGATACTCCAACC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTCCAACC
2884775 CCATTATTTCCGAA
66 CCATTATTTCCGAA
* * *** * *
2884789 TGGACACTCCAACCCTGGTTTTATTTCTAAAACA-CTGATTTTTCACCATCGGGGATACTCTAAC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATC-GATTTTTCACCATCGGGGATACTCCAAC
* *
2884853 CCTATTATTTTC-AA
65 CCCATTATTTCCGAA
* * * * *
2884867 GAGGATACTTCAACCCCAATTTTATTTCCATAACATTGATTTTTCACCATCGGTGATACTCTAAC
1 G-GGATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTCCAAC
* *
2884932 CCCGTTATTTTCGAA
65 CCCATTATTTCCGAA
* *
2884947 GGGATACTCCAACCTCAA-TTTATTTCCAAAACATCAATTTTTCACCATCGGGGATACTCCAACC
1 GGGATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTCCAACC
*
2885011 CCATTATTTCCGAT
66 CCATTATTTCCGAA
* * *
2885025 GGGATACTCCAATCCCATTTTTATCTCCAAAA
1 GGGATACTCCAACCCCAATTTTATTTCCAAAA
2885057 TATTAAATTT
Statistics
Matches: 225, Mismatches: 38, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
78 70 0.31
79 152 0.68
80 3 0.01
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.33
Consensus pattern (79 bp):
GGGATACTCCAACCCCAATTTTATTTCCAAAACATCGATTTTTCACCATCGGGGATACTCCAACC
CCATTATTTCCGAA
Found at i:2888574 original size:20 final size:21
Alignment explanation
Indices: 2888547--2888603 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
2888537 GTGAAAAACC
2888547 AGAATGTATCAATACAATG-A
1 AGAATGTATCAATACAATGCA
* * *
2888567 ATAATGTATCGATACATTGCA
1 AGAATGTATCAATACAATGCA
*
2888588 AGCATGTATCAATACA
1 AGAATGTATCAATACA
2888604 TTCACTTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AGAATGTATCAATACAATGCA
Found at i:2888616 original size:20 final size:20
Alignment explanation
Indices: 2888549--2888623 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
2888539 GAAAAACCAG
* *
2888549 AATGTATCAATACAATGAAT
1 AATGTATCAATACATTCAAT
* *
2888569 AATGTATCGATACATTGCAAG
1 AATGTATCAATACATT-CAAT
* *
2888590 CATGTATCAATACATTCACT
1 AATGTATCAATACATTCAAT
* *
2888610 TATGTATCGATACA
1 AATGTATCAATACA
2888624 ATTTTTTTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (20 bp):
AATGTATCAATACATTCAAT
Found at i:2888692 original size:20 final size:20
Alignment explanation
Indices: 2888664--2888721 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
2888654 ACATGGTCCA
2888664 GTATCGATACATTCACTTAT
1 GTATCGATACATTCACTTAT
*
2888684 GTATTGATACATTCACTTAT
1 GTATCGATACATTCACTTAT
*
2888704 GTATCGATACATTAACTT
1 GTATCGATACATTCACTT
2888722 GTTGTATCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
GTATCGATACATTCACTTAT
Found at i:2891454 original size:13 final size:13
Alignment explanation
Indices: 2891436--2891460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2891426 CATAAAGTGT
2891436 TGTATCGATACAA
1 TGTATCGATACAA
2891449 TGTATCGATACA
1 TGTATCGATACA
2891461 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2891476 original size:32 final size:33
Alignment explanation
Indices: 2891416--2891481 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
2891406 TTCAATGATT
2891416 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*
2891449 TGTATCGATACAT-AAGTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
2891481 T
1 T
2891482 TTAAGCTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.59
33 13 0.41
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:2891540 original size:13 final size:13
Alignment explanation
Indices: 2891522--2891546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2891512 ATTACTCAAA
2891522 TGTATCGATACAT
1 TGTATCGATACAT
2891535 TGTATCGATACA
1 TGTATCGATACA
2891547 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2898911 original size:12 final size:13
Alignment explanation
Indices: 2898894--2898925 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2898884 ATCTTCACAA
2898894 AAAAAAAC-AAAC
1 AAAAAAACAAAAC
2898906 AAAAAAACAAAAC
1 AAAAAAACAAAAC
2898919 AAAAAAA
1 AAAAAAA
2898926 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:2898911 original size:13 final size:14
Alignment explanation
Indices: 2898893--2898926 Score: 54
Period size: 12 Copynumber: 2.6 Consensus size: 14
2898883 AATCTTCACA
2898893 AAAAAAAAC-AAAC
1 AAAAAAAACAAAAC
2898906 -AAAAAAACAAAAC
1 AAAAAAAACAAAAC
2898919 AAAAAAAA
1 AAAAAAAA
2898927 AAGGAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.42
13 4 0.21
14 7 0.37
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:2898934 original size:17 final size:17
Alignment explanation
Indices: 2898892--2898928 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
2898882 TAATCTTCAC
2898892 AAAAA-AAAACAAACAA
1 AAAAACAAAACAAACAA
2898908 AAAAACAAAACAAA-AA
1 AAAAACAAAACAAACAA
2898924 AAAAA
1 AAAAA
2898929 GGAAAAACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 8 0.40
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAACAAAACAAACAA
Found at i:2899764 original size:9 final size:9
Alignment explanation
Indices: 2899750--2899776 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2899740 TCATGACACC
2899750 ATAACATCA
1 ATAACATCA
2899759 ATAACATCA
1 ATAACATCA
2899768 ATAACATCA
1 ATAACATCA
2899777 TTATTTGCAT
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:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAACATCA
Found at i:2899953 original size:36 final size:34
Alignment explanation
Indices: 2899870--2900412 Score: 325
Period size: 34 Copynumber: 17.0 Consensus size: 34
2899860 TCTTCAAATA
*
2899870 CCTTCTTAAAGTCCACCACTCCGTGGCACC---TT
1 CCTT-TTAAAGTCCACAACTCCGTGGCACCTTTTT
* *
2899902 -CTTTTCAAAGCCCACAACTCCGTGGCACTATTTTT
1 CCTTTT-AAAGTCCACAACTCCGTGGCAC-CTTTTT
2899937 CCCTTTTAAAGTCCACAACTCCGTGGCA-C-----
1 -CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* *
2899966 CATTTT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC-CTTTTT
* *
2900000 CCTTCT-AAGTCCACAACTTCGTGGCACCTTTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* *
2900033 -CTTTTCAAAGCCCACAACTCCGTGACACTCTTTTT
1 CCTTTT-AAAGTCCACAACTCCGTGGCAC-CTTTTT
* *
2900068 CCCTTTTAAAGTCCACAACCCCGTGGCACCTTGTT
1 -CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* *
2900103 CCTTTT-AAGTCCACGACTCCGCGGCACC---TT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* * * **
2900133 CCTTTCAAAGTCCGCGACTGTGTGGCA-C-----
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* * * * *
2900161 CCTTTT-AAGCCCACAACTCAGTGGTATCTCTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* * * *
2900194 CC----AAAGTCCACGACTCAGTGCCATC-TTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* * *
2900223 -C-TCTAAAGCCCACAACTCCGTGGCACTCTCTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC-CTTTTT
*
2900256 CCTTCT-AAGTCCACAACTCCGTGGCACC----T
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
*
2900285 --TTTT-AAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC-CTTTTT
*
2900317 CCTTCT-AAGTCCACAACTCCGTGGCA-C-----
1 CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
* *
2900344 CCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCAC-CTTTTT
*
2900379 CCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
1 -CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
2900413 AAGTCCACAA
Statistics
Matches: 405, Mismatches: 56, Indels: 98
0.72 0.10 0.18
Matches are distributed among these distances:
27 61 0.15
28 31 0.08
29 5 0.01
30 29 0.07
31 56 0.14
32 7 0.02
33 31 0.08
34 95 0.23
35 35 0.09
36 45 0.11
37 10 0.02
ACGTcount: A:0.20, C:0.36, G:0.13, T:0.31
Consensus pattern (34 bp):
CCTTTTAAAGTCCACAACTCCGTGGCACCTTTTT
Found at i:2899981 original size:27 final size:28
Alignment explanation
Indices: 2899940--2899992 Score: 90
Period size: 27 Copynumber: 1.9 Consensus size: 28
2899930 TATTTTTCCC
*
2899940 TTTTAAAGTCCACAACTCCGTGGCACCA
1 TTTTAAAGCCCACAACTCCGTGGCACCA
2899968 TTTT-AAGCCCACAACTCCGTGGCAC
1 TTTTAAAGCCCACAACTCCGTGGCAC
2899993 TCTTTTTCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (28 bp):
TTTTAAAGCCCACAACTCCGTGGCACCA
Found at i:2899999 original size:28 final size:27
Alignment explanation
Indices: 2899938--2899999 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
2899928 ACTATTTTTC
* *
2899938 CCTTTTAAAGTCCACAACTCCGTGGCA
1 CCTTTTTAAGCCCACAACTCCGTGGCA
*
2899965 CCATTTTAAGCCCACAACTCCGTGGCA
1 CCTTTTTAAGCCCACAACTCCGTGGCA
2899992 CTCTTTTT
1 C-CTTTTT
2900000 CCTTCTAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.31
Consensus pattern (27 bp):
CCTTTTTAAGCCCACAACTCCGTGGCA
Found at i:2900291 original size:27 final size:27
Alignment explanation
Indices: 2900261--2900437 Score: 147
Period size: 27 Copynumber: 6.0 Consensus size: 27
2900251 TCTTTCCTTC
2900261 TAAGTCCACAACTCCGTGGCACCTTTT
1 TAAGTCCACAACTCCGTGGCACCTTTT
*
2900288 TAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
1 TAAGTCCACAACTCCGTGGCAC-C---TT--TT
2900321 CTAAGTCCACAACTCCGTGGCACCCTTTT
1 -TAAGTCCACAACTCCGTGGCA-CCTTTT
* * *
2900350 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
1 TAAGTCCACAACTCCGTGGCAC-C----T---TTT
*
2900385 TAAGTCCACAACTCCGTGGCACCCTTT
1 TAAGTCCACAACTCCGTGGCACCTTTT
* *
2900412 TAAGTCCACAACTCTGTGGCATCTTT
1 TAAGTCCACAACTCCGTGGCACCTTT
2900438 CTCCTTTTCA
Statistics
Matches: 122, Mismatches: 12, Indels: 32
0.73 0.07 0.19
Matches are distributed among these distances:
27 48 0.39
28 20 0.16
29 2 0.02
31 4 0.03
32 1 0.01
33 2 0.02
34 22 0.18
35 23 0.19
ACGTcount: A:0.21, C:0.34, G:0.14, T:0.31
Consensus pattern (27 bp):
TAAGTCCACAACTCCGTGGCACCTTTT
Found at i:2900293 original size:61 final size:61
Alignment explanation
Indices: 2899878--2900443 Score: 520
Period size: 61 Copynumber: 9.0 Consensus size: 61
2899868 TACCTTCTTA
* * *
2899878 AAGTCCACCACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTATTTTTCCCTTT
1 AAGTCCACAACTCCGTGGCACC-T-TTTT--AAGCCCACAACTCCGTGGCACTCTTTTT-CCTTC
2899943 T
61 T
*
2899944 AAAGTCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 -AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
* *
2900006 AAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCC
1 AAGTCCACAACTCCGTGGCACC----T-TTTT--AAGCCCACAACTCCGTGGCACTCTTTTT-CC
*
2900071 TTTT
58 TTCT
* * * *
2900075 AAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGCGGCAC-C---TTCCT
1 -AAGTCCACAACTCCGTGGCACC----T--TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCC-
*
2900136 TTCA
58 TTCT
* * ** * * * * *
2900140 AAGTCCGCGACTGTGTGGCACCCTTTTAAGCCCACAACTCAGTGGTA-TCTCTTT-C--CA
1 AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * * * *
2900197 AAGTCCACGACTCAGTGCCATCTTTTCTCTAAAGCCCACAACTCCGTGGCACTCTCTTTCCTTCT
1 AAGTCCACAACTCCGTGGCA-CCTTT-T-T-AAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
2900262 AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
* * *
2900323 AAGTCCACAACTCCGTGGCACCCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 AAGTCCACAACTCCGTGGCA-CCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTCT
* * * *
2900386 AAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCTGTGGCA-TCTTTCTCCTT
1 AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTT
2900444 TTCAAAAGCC
Statistics
Matches: 425, Mismatches: 49, Indels: 57
0.80 0.09 0.11
Matches are distributed among these distances:
57 18 0.04
58 23 0.05
59 1 0.00
60 6 0.01
61 100 0.24
62 70 0.16
63 54 0.13
64 23 0.05
65 26 0.06
66 4 0.01
67 21 0.05
68 28 0.07
69 22 0.05
70 24 0.06
71 5 0.01
ACGTcount: A:0.20, C:0.35, G:0.13, T:0.31
Consensus pattern (61 bp):
AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
Found at i:2900404 original size:35 final size:36
Alignment explanation
Indices: 2900343--2900412 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
2900333 CTCCGTGGCA
* *
2900343 CCCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTT
*
2900379 CCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT
1 CCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTT
2900413 AAGTCCACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 24 0.77
36 7 0.23
ACGTcount: A:0.19, C:0.36, G:0.11, T:0.34
Consensus pattern (36 bp):
CCCTTTTAAAGCCCACAACTCCGTGGCACCCTTTTT
Found at i:2900477 original size:33 final size:33
Alignment explanation
Indices: 2900440--2901065 Score: 935
Period size: 33 Copynumber: 19.1 Consensus size: 33
2900430 GCATCTTTCT
*
2900440 CCTTTTCAAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
2900473 CCTTTTC-AAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* * *
2900505 CTTTTTCTAAAGTCCACACAAGTCAGTGGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
2900537 CCTTCTCTAAAGCCCACACAAATCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900570 CTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900603 CTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900636 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
2900668 CCTTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTT-TCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900702 CTTTTTCTAAAGCCCACACAAGTCGGTGGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900734 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
2900767 CTTTTTCTAAGGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
2900800 CCTTCTCTAAAGCCCACACAAGTTGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900833 CTTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900866 CCTTCTCTAAAGCCCACACAAGTCGGTGGCAA-
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
2900898 CCTTTCTCTAAAGCCCACACAAGTCGGTGGCAA-
1 CCTTT-TCTAAAGCCCACACAAGTCGGTGGCAAC
*
2900931 CTTTCTTCTAAAGCCCACACAAGTCGGTGGCAAC
1 CCTT-TTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
2900965 TCTTCTC-AAAGCCCACACAAGTCGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* *
2900997 CC-TCTCTAAAGCCCACACAAGTTGGTGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
* * **
2901029 CATTCTCTAAAGCCCACACAAGTCAATGGCAAC
1 CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
2901062 CCTT
1 CCTT
2901066 CTAAGCCCAA
Statistics
Matches: 542, Mismatches: 41, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
31 4 0.01
32 147 0.27
33 384 0.71
34 7 0.01
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (33 bp):
CCTTTTCTAAAGCCCACACAAGTCGGTGGCAAC
Found at i:2900519 original size:317 final size:311
Alignment explanation
Indices: 2899876--2900554 Score: 795
Period size: 317 Copynumber: 2.1 Consensus size: 311
2899866 AATACCTTCT
* * * *
2899876 TAAAGTCCACCACTCCGTGGCACCTTCTTTTCAAAGCCCACAACTCCGTGGCACTATTTTTCCCT
1 TAAAGTCCACCACTCAGTGCCACCTTCTTCTCAAAGCCCACAACTCCGTGGCACTATCTTTCCCT
*
2899941 TTTAAAGTCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
66 TCTAAAGTCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
*
2900006 AAGTCCACAACTTCGTGGCACCTTTTTCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCC
131 AAGTCCACAACTCCGTGGCACC----TCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCC
*
2900071 TTTTAAAGTCCACAACCCCGTGGCACCTTGTTCCTTTTAAGTCCACGACTCCGCGGCACCTTCCT
192 TTTTAAAGTCCACAACCCCGTGGCACC----TCCTTTTAAGTCCACAACTCCGCGGCACCTTCCT
* * * * *
2900136 TTCAAAGTCCGCGACTGTGTGGCACCCTTTTAAGCCCACAACTCAGTGGTATCTCTTTC
253 TTCAAAGCCCACGACAGTGTGGCACCCTTTTAAGCCCACAACTCAGTGGAACCTCTTTC
* * * *
2900195 CAAAGTCCACGACTCAGTGCCATCTT-TTCTCTAAAGCCCACAACTCCGTGGCACTCTCTTT-CC
1 TAAAGTCCACCACTCAGTGCCACCTTCTTCTC-AAAGCCCACAACTCCGTGGCACTATCTTTCCC
*
2900258 TTCT-AAGTCCACAACTCCGTGGCACCTTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
65 TTCTAAAGTCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTC
* *
2900322 TAAGTCCACAACTCCGTGGCACC-CTTTT-AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
130 TAAGTCCACAACTCCGTGGCACCTCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCCTTT
* * * *
2900385 T-AAGTCCACAACTCCGTGGCA-C-CCTTTTAAGTCCACAACTCTGTGGCATCTTTCTCCTTTTC
195 TAAAGTCCACAACCCCGTGGCACCTCCTTTTAAGTCCACAACTCCGCGGCA-C-CT-TCC-TTTC
* * *
2900447 AAAAGCCCAC-ACAAGTCGGTGGCAACCCTTTTCAAAGCCCACACAAGTCGGTGGCAACCTTTTT
256 -AAAGCCCACGAC-AGT--GTGGC-ACCCTTTT--AAG-CC-CACAACTCAGTGG-AACCTCTTT
2900511 C
311 C
* *
2900512 TAAAGTCCACACAAGTCAGTGGCAACCTTC-TCT-AAAGCCCACA
1 TAAAGTCCAC-C-ACTCAGT-GCCACCTTCTTCTCAAAGCCCACA
2900555 CAAATCGGTG
Statistics
Matches: 310, Mismatches: 31, Indels: 39
0.82 0.08 0.10
Matches are distributed among these distances:
304 23 0.07
305 1 0.00
306 1 0.00
307 3 0.01
308 6 0.02
309 10 0.03
310 19 0.06
311 39 0.13
312 13 0.04
314 3 0.01
315 2 0.01
316 11 0.04
317 97 0.31
318 19 0.06
319 54 0.17
320 9 0.03
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (311 bp):
TAAAGTCCACCACTCAGTGCCACCTTCTTCTCAAAGCCCACAACTCCGTGGCACTATCTTTCCCT
TCTAAAGTCCACAACTCCGTGGCACCATTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
AAGTCCACAACTCCGTGGCACCTCTTTTCAAAGCCCACAACTCCGTGACACTCTTTTTCCCTTTT
AAAGTCCACAACCCCGTGGCACCTCCTTTTAAGTCCACAACTCCGCGGCACCTTCCTTTCAAAGC
CCACGACAGTGTGGCACCCTTTTAAGCCCACAACTCAGTGGAACCTCTTTC
Found at i:2900695 original size:197 final size:196
Alignment explanation
Indices: 2900448--2901067 Score: 1030
Period size: 197 Copynumber: 3.2 Consensus size: 196
2900438 CTCCTTTTCA
*
2900448 AAAGCCCACACAAGTCGGTGGCAACCCTTTTC-AAAGCCCACACAAGTCGGTGGCAACCTTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
* * *
2900512 TAAAGTCCACACAAGTCAGTGGCAACCTTCTCTAAAGCCCACACAAATCGGTGGCAACCTTTTTC
66 TAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
* * *
2900577 TAAAGCCCACACAAGTCGGTGGCAACCTTTTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCT
131 TAAAGCCCACACAAGTCGGTGGCAACC-TTCTCTAAAGCCCACACAAGTTGGTGGCAACCATTCT
2900642 CT
195 CT
*
2900644 AAAGCCCACACAAGTCGGTGGCAACCTTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
2900709 TAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
66 TAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
* * *
2900774 TAAGGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCTTTTT
131 TAAAGCCCACACAAGTCGGTGGCAA-CCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCATTCT
2900839 CT
195 CT
*
2900841 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTCTC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
* *
2900906 TAAAGCCCACACAAGTCGGTGGCAACTTTCTTCTAAAGCCCACACAAGTCGGTGGCAA-C-TCTT
66 TAAAGCCCACACAAGTCGGTGGCAACCTTC-TCTAAAGCCCACACAAGTCGGTGGCAACCTTTTT
*
2900969 CTCAAAGCCCACACAAGTCGGTGGCAACCCTCTCTAAAGCCCACACAAGTTGGTGGCAACCATTC
130 CT-AAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCATTC
2901034 TCT
194 TCT
**
2901037 AAAGCCCACACAAGTCAATGGCAACCCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCT
2901068 AAGCCCAATA
Statistics
Matches: 400, Mismatches: 20, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
196 102 0.25
197 269 0.67
198 29 0.07
ACGTcount: A:0.28, C:0.33, G:0.18, T:0.21
Consensus pattern (196 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
TAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTCGGTGGCAACCTTTTTC
TAAAGCCCACACAAGTCGGTGGCAACCTTCTCTAAAGCCCACACAAGTTGGTGGCAACCATTCTC
T
Found at i:2901157 original size:49 final size:48
Alignment explanation
Indices: 2901067--2901531 Score: 459
Period size: 43 Copynumber: 9.9 Consensus size: 48
2901057 GCAACCCTTC
* * * *
2901067 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGACACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TTATCTT
* *
2901116 TAAGTCTAATGTAGCTGGCCTTGAATCAGCACATCGGCA-C----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* * * * *
2901159 TAAGTCCAATATCGCTAGCCTTGAATTAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
*
2901208 TAAGTCCAATGTAGCTGGCCTTGAATCAACACATTGGCA-C----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* *
2901251 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
2901300 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* * *
2901343 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT-ATCTT
2901392 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C----CTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
* * * *
2901435 TAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTCATCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT-ATCTT
* * * *
2901490 TAAGTCCAATATTG-TTGCCTTGAATCAGCATATTGGCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
2901532 CATCATCTTT
Statistics
Matches: 349, Mismatches: 37, Indels: 61
0.78 0.08 0.14
Matches are distributed among these distances:
43 151 0.43
44 3 0.01
48 7 0.02
49 148 0.42
50 2 0.01
54 23 0.07
55 15 0.04
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.31
Consensus pattern (48 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTATCTT
Found at i:2901229 original size:92 final size:92
Alignment explanation
Indices: 2901062--2901531 Score: 726
Period size: 92 Copynumber: 5.0 Consensus size: 92
2901052 CAATGGCAAC
* * * *
2901062 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGACACCTTTATCTTTAAGTCTAATG
1 CCTT-TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATG
*
2901127 TAGCTGGCCTTGAATCAGCACATCGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
* * *
2901155 CCTTTAAGTCCAATATCGCTAGCCTTGAATTAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
*
2901220 AGCTGGCCTTGAATCAACACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
2901247 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
2901312 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
*
2901339 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
2901404 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
2901431 CCTTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTCATCTTCATCTTTAAGTC
1 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--CTTCATCTTTAAGTC
* * * *
2901496 CAATATTG-TTGCCTTGAATCAGCATATTGGCA
60 CAATGTAGCTGGCCTTGAATCAGCACATTGGCA
2901528 CCTT
1 CCTT
2901532 CATCATCTTT
Statistics
Matches: 350, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
92 298 0.85
93 4 0.01
96 1 0.00
97 26 0.07
98 21 0.06
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (92 bp):
CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:2901272 original size:22 final size:22
Alignment explanation
Indices: 2901205--2901272 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
2901195 GCACCTTCAT
*
2901205 CTTTAAGTCCAATGTAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
* * * *
2901227 CTTGAA-T-CAACACA-TTGGCAC
1 CTTTAAGTCCAATATAGCTGG--C
2901248 CTTTAAGTCCAATATAGCTGGC
1 CTTTAAGTCCAATATAGCTGGC
2901270 CTT
1 CTT
2901273 GAATCAGCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 3 0.09
20 4 0.12
21 7 0.22
22 10 0.31
23 5 0.16
24 3 0.09
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (22 bp):
CTTTAAGTCCAATATAGCTGGC
Found at i:2901519 original size:54 final size:55
Alignment explanation
Indices: 2901432--2901535 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 55
2901422 ACATTGGCAC
2901432 CTTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTCATCTTCAT
1 CTTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTCATCTTCAT
* * * *
2901487 CTTTAAGTCCAATATTG-TTGCCTTGAATCAGCATATTGGCACCTTCATC
1 CTTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTCATC
2901536 ATCTTTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
54 30 0.67
55 15 0.33
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (55 bp):
CTTTAAGCCCAATATAGCTAGCCTTGAATCAGCATATTGGCACCCTCATCTTCAT
Found at i:2902352 original size:13 final size:13
Alignment explanation
Indices: 2902334--2902390 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
2902324 CATAAAGTGT
2902334 TGTATCGATACAA
1 TGTATCGATACAA
2902347 TGTATCGATACATAA
1 TGTATCGATAC--AA
2902362 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
2902379 TGTATCGATACA
1 TGTATCGATACA
2902391 TAAGTTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2902369 original size:32 final size:32
Alignment explanation
Indices: 2902314--2902411 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
2902304 TTCAACGATT
2902314 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
2902347 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
2902379 TGTATCGATACATAAGTTTTATATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
2902411 T
1 T
2902412 TTAAGCTACT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 50 0.79
33 13 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:2902371 original size:19 final size:18
Alignment explanation
Indices: 2902312--2902409 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
2902302 ATTTCAACGA
2902312 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
2902331 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2902347 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
2902363 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
2902379 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
2902395 TTTTATATCGATACA
1 -TTTGTATCGATACA
2902410 ATTTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:2902470 original size:13 final size:13
Alignment explanation
Indices: 2902452--2902476 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2902442 ATTACTTAAA
2902452 TGTATCGATACAT
1 TGTATCGATACAT
2902465 TGTATCGATACA
1 TGTATCGATACA
2902477 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2902529 original size:52 final size:52
Alignment explanation
Indices: 2902485--2902613 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
2902475 CACTGATCTT
*
2902485 TGTATCGATACATGTAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
2902537 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
2902589 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
2902614 TCATATTTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:2907998 original size:19 final size:19
Alignment explanation
Indices: 2907974--2908017 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
2907964 ACAAGAGAGC
*
2907974 AAAAAGATA-CAAACACAGA
1 AAAAAGAAAGCAAACACA-A
*
2907993 AAAAAGAAAGCAAACAGAA
1 AAAAAGAAAGCAAACACAA
2908012 AAAAAG
1 AAAAAG
2908018 GAAAAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.73, C:0.11, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAAAGAAAGCAAACACAA
Found at i:2909187 original size:20 final size:19
Alignment explanation
Indices: 2909162--2909213 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2909152 GTTATGGGTG
2909162 AGAAAGAAAAAAGAAGAAGA
1 AGAAAGAAAAAAGAAGAA-A
**
2909182 AGAAAGAATGAAGAAGAAA
1 AGAAAGAAAAAAGAAGAAA
*
2909201 ATAAAAGAAAAAA
1 A-GAAAGAAAAAA
2909214 AATCAAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (19 bp):
AGAAAGAAAAAAGAAGAAA
Found at i:2909776 original size:7 final size:7
Alignment explanation
Indices: 2909764--2909797 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2909754 AGTTTCCACA
2909764 AAAAAAT
1 AAAAAAT
*
2909771 AAAAAAG
1 AAAAAAT
*
2909778 AATAAAT
1 AAAAAAT
2909785 AAAAAAT
1 AAAAAAT
2909792 AAAAAA
1 AAAAAA
2909798 GTATAAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:2909781 original size:10 final size:10
Alignment explanation
Indices: 2909763--2909807 Score: 56
Period size: 10 Copynumber: 4.5 Consensus size: 10
2909753 TAGTTTCCAC
2909763 AAAAA-AATA
1 AAAAAGAATA
2909772 AAAAAGAATA
1 AAAAAGAATA
*
2909782 AATAAAAAATA
1 AA-AAAGAATA
*
2909793 AAAAAGTATA
1 AAAAAGAATA
2909803 AAAAA
1 AAAAA
2909808 ATATTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 5 0.16
10 17 0.55
11 9 0.29
ACGTcount: A:0.82, C:0.00, G:0.04, T:0.13
Consensus pattern (10 bp):
AAAAAGAATA
Found at i:2909790 original size:21 final size:20
Alignment explanation
Indices: 2909763--2909808 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 20
2909753 TAGTTTCCAC
2909763 AAAAAAATAAAAAAGAATAA
1 AAAAAAATAAAAAAGAATAA
*
2909783 ATAAAAAATAAAAAAGTATAA
1 A-AAAAAATAAAAAAGAATAA
2909804 AAAAA
1 AAAAA
2909809 TATTAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (20 bp):
AAAAAAATAAAAAAGAATAA
Found at i:2923559 original size:62 final size:62
Alignment explanation
Indices: 2923458--2924006 Score: 656
Period size: 62 Copynumber: 8.9 Consensus size: 62
2923448 ACACTTTTTT
* * * * * *
2923458 AGTCCTCAAAGAGTAGGACGTCTTTTTCTTTTAAAGCCCACATAAGTTGGTTGAACCTGTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* * * * * * *
2923520 AGTTCTCAAAGAGCAAGACGCTTTTTTCTTTTAAAGCCCATACATGTTGGTGGCACTCATTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
** * *
2923582 AGTCCTCAAAGAGCAAAACGTCTTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTCGTTC
1 AGTCCTCAAAGAGCAGGACG-CCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* *
2923645 AGTCCTCAAAGAGCAGGACGCCTTTTTCATTTAAAGCCCATACAAGTTGGTGGCACCCGTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* * ** * * * * * *
2923707 AGTCTTCAAAGAGCGGGATTCCATTTTCATTCAAAGCCCACACAAGTTAGTGGTACCTGTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* **
2923769 AGTCCTCAAAGAGTAGGGTGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* * * *
2923831 AGTCCTCAAAAAGCAGGACG---TCTACTTTTAAAGCCCACACAAGTTGCTGGCACCCGTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* * * * * *
2923890 AGTCCTCAAAAAGCAAGATGCCTTTTTCGTTTAAAGCTCACATAAGTTGGTGGCACCCGTTC
1 AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* *
2923952 AGTCCTCAAAAAGCAGGATG-CTTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCA
1 AGTCCTCAAAGAGCAGGACGCCTTT-TTCTTTTAAAGCCCACACAAGTTGGTGGCA
2924007 ACCCTCTTTA
Statistics
Matches: 418, Mismatches: 64, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
59 54 0.13
61 4 0.01
62 303 0.72
63 57 0.14
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (62 bp):
AGTCCTCAAAGAGCAGGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
Found at i:2923990 original size:245 final size:245
Alignment explanation
Indices: 2923458--2924009 Score: 710
Period size: 245 Copynumber: 2.2 Consensus size: 245
2923448 ACACTTTTTT
* * * *
2923458 AGTCCTCAAAGAGTAGGACGTCTTTTTCTTTTAAAGCCCACATAAGTTGGTTGAACCTGTTCAGT
1 AGTCCTCAAAGAGCAGGATG-CTTTTTCTTTTAAAGCCCACACAAGTTGGTGGAACCTGTTCAGT
* * * * *
2923523 TCTCAAAGAGCAAGACGCTTTTTTCTTTTAAAGCCCATACATGTTGGTGGCACTCATTCAGTCCT
65 CCTCAAAGAGCAAGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCT
* * * *
2923588 CAAAGAGCAAAACGTCTTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACTCGTTCAGTCCTCA
130 CAAAAAGCAAAACGTC---TTACTTTTAAAGCCCACACAAGTTGCTGGCACCCGTTCAGTCCTCA
* * *
2923653 AAGAGCAGGACGCCTTTTTCATTTAAAGCCCATACAAGTTGGTGGCACCCGTTC
192 AAAAGCAAGACGCCTTTTTCATTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
* * * * * * * *
2923707 AGTCTTCAAAGAGCGGGATTCCATTTTCATTCAAAGCCCACACAAGTTAGTGGTACCTGTTCAGT
1 AGTCCTCAAAGAGCAGGA-TGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGAACCTGTTCAGT
* * ** *
2923772 CCTCAAAGAGTAGGGTGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCGTTCAGTCCT
65 CCTCAAAGAGCAAGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCT
**
2923837 CAAAAAGCAGGACGTC-TACTTTTAAAGCCCACACAAGTTGCTGGCACCCGTTCAGTCCTCAAAA
130 CAAAAAGCAAAACGTCTTACTTTTAAAGCCCACACAAGTTGCTGGCACCCGTTCAGTCCTCAAAA
* * * *
2923901 AGCAAGATGCCTTTTTCGTTTAAAGCTCACATAAGTTGGTGGCACCCGTTC
195 AGCAAGACGCCTTTTTCATTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
*
2923952 AGTCCTCAAAAAGCAGGATGCTTTCTTCTTTTAAAGCCCACACAAGTTGGTGGCAACC
1 AGTCCTCAAAGAGCAGGATGCTTT-TTCTTTTAAAGCCCACACAAGTTGGTGG-AACC
2924010 CTCTTTAAAG
Statistics
Matches: 256, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
244 4 0.02
245 129 0.50
246 3 0.01
249 120 0.47
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (245 bp):
AGTCCTCAAAGAGCAGGATGCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGAACCTGTTCAGTC
CTCAAAGAGCAAGACGCCTTTTTCTTTTAAAGCCCACACAAGTTGGTGGCACCCATTCAGTCCTC
AAAAAGCAAAACGTCTTACTTTTAAAGCCCACACAAGTTGCTGGCACCCGTTCAGTCCTCAAAAA
GCAAGACGCCTTTTTCATTTAAAGCCCACACAAGTTGGTGGCACCCGTTC
Found at i:2924025 original size:32 final size:31
Alignment explanation
Indices: 2923981--2924122 Score: 135
Period size: 32 Copynumber: 4.4 Consensus size: 31
2923971 GCTTTCTTCT
2923981 TTTAAAGCCCACACAAGTTGGTGGCAACCCTC
1 TTTAAAG-CCACACAAGTTGGTGGCAACCCTC
* *
2924013 TTTAAAGTCCACACAAGTCGATGGCAACCCTC
1 TTTAAAG-CCACACAAGTTGGTGGCAACCCTC
* * * *
2924045 TTTAAAGCCTACACAAGTTAGTGG-TA-TCTT
1 TTTAAAGCC-ACACAAGTTGGTGGCAACCCTC
* *
2924075 TTTCAAAGCTCACACAAGTTGGTGGTAACCCTT
1 TTT-AAAGC-CACACAAGTTGGTGGCAACCCTC
2924108 TTCTAAAGTCCACAC
1 TT-TAAAG-CCACAC
2924123 CAGTCGATGG
Statistics
Matches: 91, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
30 5 0.05
31 21 0.23
32 49 0.54
33 14 0.15
34 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (31 bp):
TTTAAAGCCACACAAGTTGGTGGCAACCCTC
Found at i:2926924 original size:13 final size:13
Alignment explanation
Indices: 2926906--2926930 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2926896 ATGGGTAAGA
2926906 AAAAAGGAAGAAG
1 AAAAAGGAAGAAG
2926919 AAAAAGGAAGAA
1 AAAAAGGAAGAA
2926931 AGAAGAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAGAAG
Found at i:2926949 original size:20 final size:20
Alignment explanation
Indices: 2926902--2926951 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
2926892 GGTTATGGGT
2926902 AAGAAA-AAAGGAAGAAGAAA
1 AAGAAAGAAA-GAAGAAGAAA
*
2926922 AAGGAAGAAAGAAGAA-AAA
1 AAGAAAGAAAGAAGAAGAAA
2926941 AATGAAAGAAA
1 AA-GAAAGAAA
2926952 AAAAACTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 5 0.19
20 18 0.69
21 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (20 bp):
AAGAAAGAAAGAAGAAGAAA
Found at i:2930777 original size:156 final size:155
Alignment explanation
Indices: 2930266--2930773 Score: 575
Period size: 156 Copynumber: 3.3 Consensus size: 155
2930256 ACTTTCATAC
* * *
2930266 CGAAAGTATACCTTAGAGG-CATTTTCGTAATTTTTT-AAAACTAAGTCCTAGGATGTCACT-AG
1 CGAAAGTAT-CCTTA-AGGACATTTTCATAATTTTTTCAAAACGAAGTCCTAGGTTGTCACTAAG
* **
2930328 ATCCGTTTTTATGTAAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGT
64 -TCCGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGT
*
2930393 CCTTT-AGCGGTATTGGGCA-TTTCTAAGT
128 CCTTTAAG-GGTATTGAGCACTTT-TAAGT
* * * * *
2930421 CGAAGGTGATTCC-TAAGGACATTTTCATAATTTTTTCAAAACCAAGTCCTAGGTTGTTACCAAA
1 CGAAAGT-A-TCCTTAAGGACATTTTCATAATTTTTTCAAAACGAAGTCCTAGGTTGTCACTAAG
* * * *
2930485 TCCGCTTTTATGCCAAAAGTGGGCATTTAGGATAGGTTCATCCTATTTATAATTCTTTTTAAGTC
64 TCCGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTC
* *
2930550 CTTTAGGGGTATTTGA-CACTTCTAAGT
129 CTTTAAGGGTA-TTGAGCACTTTTAAGT
* *
2930577 CGAAGGTATCCTCTAAGGACATTTTCGTAATTTTTTCAAAATCGAA-TCCTAGGTTGTCACTAAG
1 CGAAAGTATCCT-TAAGGACATTTTCATAATTTTTTCAAAA-CGAAGTCCTAGGTTGTCACTAAG
* * ** **
2930641 TCTGCTTTCATGCCAAAGGTAAGTATTTAAAATAGGTTCATCCCATCTATAA-TCTTTTTTAAGT
64 TCCGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTC-TTTTTAAGT
*
2930705 CCTTTAAGGGTATCGAGCACTTTTAAGT
128 CCTTTAAGGGTATTGAGCACTTTTAAGT
* **
2930733 TGAAAGTATCCCTTAAGGGTATTTTCATAATTTTTTCAAAA
1 CGAAAGTAT-CCTTAAGGACATTTTCATAATTTTTTCAAAA
2930774 TCGAGCCTTA
Statistics
Matches: 299, Mismatches: 40, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
154 6 0.02
155 30 0.10
156 249 0.83
157 14 0.05
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (155 bp):
CGAAAGTATCCTTAAGGACATTTTCATAATTTTTTCAAAACGAAGTCCTAGGTTGTCACTAAGTC
CGCTTTTATGCCAAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATTCTTTTTAAGTCCT
TTAAGGGTATTGAGCACTTTTAAGT
Found at i:2934216 original size:78 final size:79
Alignment explanation
Indices: 2934027--2934239 Score: 225
Period size: 78 Copynumber: 2.7 Consensus size: 79
2934017 AAAATACCAA
* * * *
2934027 ATTT-TCACAATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTA
1 ATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTA
*
2934091 TTCCCAAAATATTG
66 TTCCCAAAATATCG
* * * * *
2934105 ATTTCTCATAATTGGGGATACTCCAACCTCGTTATTTTCGAGGGGATACTCCAATCCC-GATTTT
1 ATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTA
** *
2934169 TTTTC-TAATCATCG
66 TTCCCAAAAT-ATCG
* * * * * *
2934183 ATTTCTCACAACCGGGGATACTCGAGCCCCGTTATTTTCAAGGGAACACTCCAACCC
1 ATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCC
2934240 TGTTATTATC
Statistics
Matches: 110, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
77 3 0.03
78 61 0.55
79 46 0.42
ACGTcount: A:0.25, C:0.29, G:0.16, T:0.30
Consensus pattern (79 bp):
ATTTCTCACAATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGGATTTA
TTCCCAAAATATCG
Found at i:2935734 original size:23 final size:25
Alignment explanation
Indices: 2935707--2935757 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
2935697 TACACAAAAA
2935707 TTCTCTC-CTCGTTG-TTCTTCTTC
1 TTCTCTCACTCGTTGTTTCTTCTTC
*
2935730 TTCTCTCTACTCTTTGTTTCTTCTTC
1 TTCTCTC-ACTCGTTGTTTCTTCTTC
2935756 TT
1 TT
2935758 TGCTATCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
25 6 0.25
26 11 0.46
ACGTcount: A:0.02, C:0.31, G:0.06, T:0.61
Consensus pattern (25 bp):
TTCTCTCACTCGTTGTTTCTTCTTC
Found at i:2935757 original size:26 final size:25
Alignment explanation
Indices: 2935708--2935757 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2935698 ACACAAAAAT
*
2935708 TCTCTCCTCGTTGTTCTTCTTCTTC
1 TCTCTACTCGTTGTTCTTCTTCTTC
*
2935733 TCTCTACTCTTTGTTTCTTCTTCTT
1 TCTCTACTCGTTG-TTCTTCTTCTT
2935758 TGCTATCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.50
26 11 0.50
ACGTcount: A:0.02, C:0.32, G:0.06, T:0.60
Consensus pattern (25 bp):
TCTCTACTCGTTGTTCTTCTTCTTC
Found at i:2941240 original size:3 final size:3
Alignment explanation
Indices: 2941232--2941266 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2941222 TGAAACTAGA
2941232 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2941267 AGAAGTTATT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Done.