Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 9 of 187
Found at i:3210329 original size:18 final size:18
Alignment explanation
Indices: 3210306--3210341 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3210296 TTAATATATT
3210306 ATTTTG-TATTTAAATTTA
1 ATTTTGATATTT-AATTTA
3210324 ATTTTGATATTTAATTTA
1 ATTTTGATATTTAATTTA
3210342 GTAGTTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (18 bp):
ATTTTGATATTTAATTTA
Found at i:3212581 original size:20 final size:20
Alignment explanation
Indices: 3212556--3212738 Score: 90
Period size: 22 Copynumber: 8.8 Consensus size: 20
3212546 TTTAGATTAG
*
3212556 AATTTTGTATGAATATTTTA
1 AATTTTGTATGAATATTATA
3212576 AATTTTTTGTATGAATATTATA
1 AA--TTTTGTATGAATATTATA
* * *
3212598 ATTTTTTTATGAATATTGT-
1 AATTTTGTATGAATATTATA
* *
3212617 AATGTTGTATGAATATTGTA
1 AATTTTGTATGAATATTATA
* * *
3212637 ATTATTTTATAATTAA-ATT-TG
1 A--ATTTTGT-ATGAATATTATA
* * *
3212658 TATTTATAGTTTTG--GATTAGTA
1 AATTT-T-G-TATGAATATTA-TA
* *
3212680 ATTTTTTGTATGAATATTGT-
1 A-ATTTTGTATGAATATTATA
3212700 AATTTTGTATGAATATTATA
1 AATTTTGTATGAATATTATA
3212720 AATTTTTTGTATGAATATT
1 AA--TTTTGTATGAATATT
3212739 GTAATATTAT
Statistics
Matches: 122, Mismatches: 23, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
19 36 0.30
20 28 0.23
21 4 0.03
22 47 0.39
23 7 0.06
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (20 bp):
AATTTTGTATGAATATTATA
Found at i:3212745 original size:49 final size:49
Alignment explanation
Indices: 3212692--3212942 Score: 373
Period size: 49 Copynumber: 5.2 Consensus size: 49
3212682 TTTTTGTATG
*
3212692 AATATTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* * **
3212741 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* * *
3212790 AATTTTGTAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
* *
3212839 AATATTATAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
*
3212888 AATTTTGTAATTTTGTATGAATATTATAA--TTTTT-TATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
*
3212934 AATGTTGTA
1 AATATTGTA
3212943 TGAATATTGT
Statistics
Matches: 181, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
46 20 0.11
47 5 0.03
49 156 0.86
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTATAATTTTTTTGTATGAATATTGT
Found at i:3212760 original size:27 final size:26
Alignment explanation
Indices: 3212724--3213031 Score: 253
Period size: 27 Copynumber: 12.8 Consensus size: 26
3212714 ATTATAAATT
3212724 TTTTGTATGAATATTGTAATATTATA
1 TTTTGTATGAATATTGTAATATTATA
*
3212750 GTTTTGTATGAATATTG-CA-ATT-T-
1 -TTTTGTATGAATATTGTAATATTATA
* *
3212773 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTAT-A
*
3212800 TTTTGTATGAATA-T-T-ATATT-TT
1 TTTTGTATGAATATTGTAATATTATA
*
3212822 TTTTGAATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTAT-A
3212849 TTTTGTATGAATATTGT-A-ATT-T-
1 TTTTGTATGAATATTGTAATATTATA
* *
3212871 TTTTGTATGAATATTGTAATTTTGTAA
1 TTTTGTATGAATATTGTAATATTAT-A
3212898 TTTTGTATGAATA-T-T-ATA--AT-
1 TTTTGTATGAATATTGTAATATTATA
3212918 TTTT-TATGAATATTGT------A-A
1 TTTTGTATGAATATTGTAATATTATA
*
3212936 TGTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATATTAT-A
*
3212963 TTTTGTATGAATATTG-CA-ATT-T-
1 TTTTGTATGAATATTGTAATATTATA
*
3212985 TTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATATTAT-A
*
3213012 TTTTGTATGAATATTATAAT
1 TTTTGTATGAATATTGTAAT
3213032 GTGGGGATAT
Statistics
Matches: 233, Mismatches: 16, Indels: 64
0.74 0.05 0.20
Matches are distributed among these distances:
18 4 0.02
19 20 0.09
20 5 0.02
21 1 0.00
22 62 0.27
23 5 0.02
24 17 0.07
25 20 0.09
26 6 0.03
27 93 0.40
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (26 bp):
TTTTGTATGAATATTGTAATATTATA
Found at i:3212804 original size:98 final size:98
Alignment explanation
Indices: 3212696--3212936 Score: 416
Period size: 98 Copynumber: 2.5 Consensus size: 98
3212686 TGTATGAATA
*
3212696 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
3212761 ATATTGCAATTTTTTTGTATGAATATTGTAATT
66 ATATTGCAATTTTTTTGTATGAATATTGTAATT
** *
3212794 TTGTAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
*
3212859 ATATTGTAATTTTTTTGTATGAATATTGTAATT
66 ATATTGCAATTTTTTTGTATGAATATTGTAATT
3212892 TTGTAATTTTGTATGAATATTAT-AA-TTTTT-TATGAATATTGTAAT
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAAT
3212937 GTTGTATGAA
Statistics
Matches: 135, Mismatches: 8, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
95 14 0.10
96 5 0.04
98 116 0.86
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.55
Consensus pattern (98 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
ATATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:3212953 original size:49 final size:48
Alignment explanation
Indices: 3212699--3212985 Score: 354
Period size: 49 Copynumber: 6.0 Consensus size: 48
3212689 ATGAATATTG
*
3212699 TAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTA
1 TAATTTTGTATGAATATTAT-AATTTTTTGTATGAATATTGTAATTTTA
* ** *
3212748 TAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATTTTG
1 TAATTTTGTATGAATATTATAA-TTTTTTGTATGAATATTGTAATTTTA
* * *
3212797 TAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGTAATATTA
1 TAATTTTGTATGAATATTATA-ATTTTTTGTATGAATATTGTAATTTTA
* *
3212846 TAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATTTTG
1 TAATTTTGTATGAATATTATAA-TTTTTTGTATGAATATTGTAATTTTA
3212895 TAATTTTGTATGAATATTATAA-TTTTT-TATGAATATTGTAATGTTGTA
1 TAATTTTGTATGAATATTATAATTTTTTGTATGAATATTGTAAT-TT-TA
* *
3212943 TGAATATTG--T-AATATTATAA--TTTTGTATGAATATTGCAATTTT
1 T-AATTTTGTATGAATATTATAATTTTTTGTATGAATATTGTAATTTT
3212986 TTTGTATGAA
Statistics
Matches: 210, Mismatches: 21, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
44 1 0.00
45 6 0.03
46 39 0.19
47 8 0.04
48 4 0.02
49 152 0.72
ACGTcount: A:0.32, C:0.01, G:0.13, T:0.54
Consensus pattern (48 bp):
TAATTTTGTATGAATATTATAATTTTTTGTATGAATATTGTAATTTTA
Found at i:3212953 original size:98 final size:91
Alignment explanation
Indices: 3212696--3213079 Score: 375
Period size: 98 Copynumber: 4.0 Consensus size: 91
3212686 TGTATGAATA
* *
3212696 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTAT-AA-TTTTT-TATGAATATTGTAATATTATAATATTG--T-A
*
3212761 ATATTGCAATTTTTTTGTATGAATATTGTAATT
60 ATATTGTAA-TTTTTTGTATGAATATTGTAATT
* *
3212794 TTGTAATTTTGTATGAATATTATATTTTTTTTGAATGAATATTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATA-ATTTTTT--ATGAATATTGTAATATTATAATATTG--T-A
3212859 ATATTGTAATTTTTTTGTATGAATATTGTAATT
60 ATATTGTAA-TTTTTTGTATGAATATTGTAATT
*
3212892 TTGTAATTTTGTATGAATATTATAATTTTTTATGAATATTGTAATGTTGTATGAATATTGTAATA
1 TTGTAATTTTGTATGAATATTATAATTTTTTATGAATATTGTAAT-AT-TAT-AATATTGTAATA
* *
3212957 TTATAA--TTTTGTATGAATATTGCAATT
63 TTGTAATTTTTTGTATGAATATTGTAATT
* * * * *
3212984 TT-T--TTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTATAATGTGGGGAT-ATATT
1 TTGTAATT-T-TG--TA-TG-AATATTATAATTTTTTATGAATATTGTAATAT---TATAATATT
3213045 GTAATATTGTAATTTTTTGTATGAATATTGTAATT
57 GTAATATTGTAATTTTTTGTATGAATATTGTAATT
3213080 ATTTTATAAT
Statistics
Matches: 255, Mismatches: 15, Indels: 34
0.84 0.05 0.11
Matches are distributed among these distances:
89 2 0.01
90 1 0.00
91 3 0.01
92 22 0.09
93 2 0.01
94 19 0.07
95 50 0.20
96 26 0.10
97 15 0.06
98 115 0.45
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (91 bp):
TTGTAATTTTGTATGAATATTATAATTTTTTATGAATATTGTAATATTATAATATTGTAATATTG
TAATTTTTTGTATGAATATTGTAATT
Found at i:3212995 original size:49 final size:49
Alignment explanation
Indices: 3212724--3213084 Score: 220
Period size: 49 Copynumber: 7.5 Consensus size: 49
3212714 ATTATAAATT
*
3212724 TTTTGTATGAATATTGTAATATTATAGTTTTGTATGAATATTG-CA-ATT-T--
1 TTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAATATTATAA
*
3212773 TTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATA-T-T-ATATT-T-T
1 TTTTGTATGAATATTGTAA--TT-T--TTTTGTATGAATATTGTAATATTATAA
*
3212822 TTTTGAATGAATATTGTAATATTATAATTTTGTATGAATATTGT-A-ATT-T--
1 TTTTGTATGAATATTGT-A-ATT-T--TTTTGTATGAATATTGTAATATTATAA
3212871 TTTTGTATGAATATTGTAATTTTGTAATT-T-TG--TA-TG-AATATTATAA
1 TTTTGTATGAATATTGTAATTTT-T--TTGTATGAATATTGTAATATTATAA
* *
3212917 TTTTTTATGAATATTGTAA---TGTTGTATGAATATTGTAATATTATAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
* *
3212963 TTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
* * ** * *
3213012 TTTTGTATGAATATTATAA--TGTGGGGAT--ATATTGTAATATTGTAA
1 TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
*
3213057 TTTTTTGTATGAATATTGTAATTATTTT
1 --TTTTGTATGAATATTGTAATTTTTTT
3213085 ATAATTAATT
Statistics
Matches: 260, Mismatches: 22, Indels: 60
0.76 0.06 0.18
Matches are distributed among these distances:
40 2 0.01
41 1 0.00
42 5 0.02
43 6 0.02
44 4 0.02
45 22 0.08
46 47 0.18
47 30 0.12
48 7 0.03
49 127 0.49
50 6 0.02
51 3 0.01
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
TTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGTAATATTATAA
Found at i:3213026 original size:19 final size:19
Alignment explanation
Indices: 3212556--3212955 Score: 170
Period size: 19 Copynumber: 22.2 Consensus size: 19
3212546 TTTAGATTAG
*
3212556 AATTTTGTATGAATATTTT
1 AATTTTGTATGAATATTGT
*
3212575 AAATTTTTTGTATGAATATTAT
1 -AA--TTTTGTATGAATATTGT
*
3212597 AATTTTTTTATGAATATTGT
1 AA-TTTTGTATGAATATTGT
*
3212617 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
3212636 AATTATTTTAT-AATTAAATTTGT
1 AATT-TTGTATGAA-T--A-TTGT
* * *
3212659 -ATTTATAGTTTTGGAT-TAGT
1 AATTT-T-G-TATGAATATTGT
3212679 AATTTTTTGTATGAATATTGT
1 AA--TTTTGTATGAATATTGT
*
3212700 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
3212719 AAATTTT-T-TG--TA-TG-
1 -AATTTTGTATGAATATTGT
* *
3212733 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
* *
3212749 AGTTTTGTATGAATATTGC
1 AATTTTGTATGAATATTGT
*
3212768 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
3212782 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
*
3212798 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
* *
3212817 -ATTTTTTTTG-A-A-TG-
1 AATTTTGTATGAATATTGT
* *
3212831 AATATTG--T-AATATTAT
1 AATTTTGTATGAATATTGT
3212847 AATTTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
3212866 AATTTT-TTTG--TA-TG-
1 AATTTTGTATGAATATTGT
* *
3212880 AATATTG--T-AATTTTGT
1 AATTTTGTATGAATATTGT
*
3212896 AATTTTGTATGAATATTAT
1 AATTTTGTATGAATATTGT
*
3212915 AATTTTTTATGAATATTGT
1 AATTTTGTATGAATATTGT
*
3212934 AATGTTGTATGAATATTGT
1 AATTTTGTATGAATATTGT
3212953 AAT
1 AAT
3212956 ATTATAATTT
Statistics
Matches: 285, Mismatches: 47, Indels: 97
0.66 0.11 0.23
Matches are distributed among these distances:
13 10 0.04
14 15 0.05
15 16 0.06
16 30 0.11
17 1 0.00
18 20 0.07
19 110 0.39
20 40 0.14
21 10 0.04
22 22 0.08
23 7 0.02
24 3 0.01
25 1 0.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (19 bp):
AATTTTGTATGAATATTGT
Found at i:3213162 original size:27 final size:27
Alignment explanation
Indices: 3213131--3213263 Score: 203
Period size: 27 Copynumber: 4.9 Consensus size: 27
3213121 ATATTTTGTT
3213131 CACCATTGGCGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
*
3213158 CACCATTGGTGCCTCCCAAATAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
3213185 CACCATTGGCGCCTCCGAAGTAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
3213212 CACCATTGGCGCCTCCGAAGTAGGCAC
1 CACCATTGGCGCCTCCCAAATAGGCAC
* *
3213239 CACCATTGGCGCCTTCCAGATAGGC
1 CACCATTGGCGCCTCCCAAATAGGC
3213264 GCCAATACTA
Statistics
Matches: 98, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 98 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.17
Consensus pattern (27 bp):
CACCATTGGCGCCTCCCAAATAGGCAC
Found at i:3220189 original size:20 final size:20
Alignment explanation
Indices: 3220164--3220206 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
3220154 TGTAGCTTTG
3220164 GTTTCTTTTAAAGCAGTTTA
1 GTTTCTTTTAAAGCAGTTTA
3220184 GTTTCTTTTAAAGCAGTTTA
1 GTTTCTTTTAAAGCAGTTTA
3220204 GTT
1 GTT
3220207 AATCATTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.51
Consensus pattern (20 bp):
GTTTCTTTTAAAGCAGTTTA
Found at i:3222496 original size:16 final size:17
Alignment explanation
Indices: 3222475--3222507 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3222465 TTTATTAATT
3222475 ATTTAAT-GTTAAAATA
1 ATTTAATGGTTAAAATA
3222491 ATTTAATGGTTAAAATA
1 ATTTAATGGTTAAAATA
3222508 TTTTGCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
ATTTAATGGTTAAAATA
Found at i:3222510 original size:16 final size:15
Alignment explanation
Indices: 3222474--3222510 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
3222464 TTTTATTAAT
3222474 TATTTAATGTTAAAA
1 TATTTAATGTTAAAA
3222489 TAATTTAATGGTTAAAA
1 T-ATTTAAT-GTTAAAA
3222506 TATTT
1 TATTT
3222511 TGCTAATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 11 0.55
17 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (15 bp):
TATTTAATGTTAAAA
Found at i:3230310 original size:15 final size:15
Alignment explanation
Indices: 3230290--3230318 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3230280 GAACTATTAG
3230290 TTTTTTCTATTAATA
1 TTTTTTCTATTAATA
3230305 TTTTTTCTATTAAT
1 TTTTTTCTATTAAT
3230319 TCCTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTTTTCTATTAATA
Found at i:3233677 original size:6 final size:6
Alignment explanation
Indices: 3233647--3233691 Score: 63
Period size: 6 Copynumber: 7.3 Consensus size: 6
3233637 AGTACCTGAT
* *
3233647 CAGTAAA CAGTAA CGGTAG CAGTAA CAGTAA CAGTAA CAGTAA CA
1 CAGT-AA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CAGTAA CA
3233692 ATATTCGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
6 30 0.88
7 4 0.12
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (6 bp):
CAGTAA
Found at i:3235234 original size:2 final size:2
Alignment explanation
Indices: 3235227--3235284 Score: 53
Period size: 2 Copynumber: 33.5 Consensus size: 2
3235217 CTTTCTTTTG
3235227 AT AT AT AT AT AT AT AT AT A- AT AT A- AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3235265 AT -T A- AT A- AT A- AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3235285 AAAACATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
1 9 0.19
2 38 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3235251 original size:5 final size:5
Alignment explanation
Indices: 3235229--3235312 Score: 77
Period size: 5 Copynumber: 16.6 Consensus size: 5
3235219 TTCTTTTGAT
3235229 ATATA TATATA TATATA ATATA ATATA ATATA ATAT- AT-TA ATAATA
1 ATATA -ATATA -ATATA ATATA ATATA ATATA ATATA ATATA AT-ATA
* *
3235275 ATATA ATATA A-A-A ACATA ATCATTA CTATA ATATA ATA
1 ATATA ATATA ATATA ATATA AT-A-TA ATATA ATATA ATA
3235313 ATATTTTTTA
Statistics
Matches: 68, Mismatches: 3, Indels: 15
0.79 0.03 0.17
Matches are distributed among these distances:
3 3 0.04
4 6 0.09
5 39 0.57
6 17 0.25
7 3 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3235316 original size:8 final size:9
Alignment explanation
Indices: 3235227--3235284 Score: 61
Period size: 8 Copynumber: 6.6 Consensus size: 9
3235217 CTTTCTTTTG
3235227 ATATATAT-
1 ATATATATA
3235235 ATATATAT-
1 ATATATATA
3235243 ATA-ATATA
1 ATATATATA
3235251 ATATAATATA
1 ATAT-ATATA
3235261 ATATAT-TA
1 ATATATATA
3235269 ATAATAATATA
1 AT-AT-ATATA
3235280 ATATA
1 ATATA
3235285 AAAACATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.09
8 18 0.41
9 5 0.11
10 13 0.30
11 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
ATATATATA
Found at i:3241601 original size:9 final size:9
Alignment explanation
Indices: 3241583--3241623 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
3241573 TGGCTGAAGC
3241583 TCTTCCTCT
1 TCTTCCTCT
*
3241592 TCTTCATCT
1 TCTTCCTCT
*
3241601 TCTTCCTCC
1 TCTTCCTCT
3241610 TCTTCCTCT
1 TCTTCCTCT
3241619 TCTTC
1 TCTTC
3241624 TTCACCTTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.02, C:0.44, G:0.00, T:0.54
Consensus pattern (9 bp):
TCTTCCTCT
Found at i:3241649 original size:3 final size:3
Alignment explanation
Indices: 3241643--3241674 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3241633 CTCGCCATCA
*
3241643 TCG TCG TCG TCG TCG TCG TCG TCA TCG TCG TC
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TC
3241675 ATCATCTTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.28, T:0.34
Consensus pattern (3 bp):
TCG
Found at i:3241675 original size:9 final size:9
Alignment explanation
Indices: 3241638--3241677 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
3241628 CCTTCCTCGC
*
3241638 CATCATCGT
1 CATCGTCGT
*
3241647 CGTCGTCGT
1 CATCGTCGT
*
3241656 CGTCGTCGT
1 CATCGTCGT
3241665 CATCGTCGT
1 CATCGTCGT
3241674 CATC
1 CATC
3241678 ATCTTCGTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.10, C:0.35, G:0.23, T:0.33
Consensus pattern (9 bp):
CATCGTCGT
Found at i:3241679 original size:12 final size:12
Alignment explanation
Indices: 3241638--3241686 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
3241628 CCTTCCTCGC
3241638 CATCATCGTCGT
1 CATCATCGTCGT
* *
3241650 CGTCGTCGTCGT
1 CATCATCGTCGT
*
3241662 CGTCATCGTCGT
1 CATCATCGTCGT
*
3241674 CATCATCTTCGT
1 CATCATCGTCGT
3241686 C
1 C
3241687 CTCTTCTCCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.10, C:0.35, G:0.20, T:0.35
Consensus pattern (12 bp):
CATCATCGTCGT
Found at i:3241802 original size:21 final size:21
Alignment explanation
Indices: 3241778--3241817 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3241768 ATCTTCCTCC
3241778 TCACCTGCAT-CTTCATCTTGA
1 TCACCTGC-TGCTTCATCTTGA
3241799 TCACCTGCTGCTTCATCTT
1 TCACCTGCTGCTTCATCTT
3241818 CCTCATCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.15, C:0.35, G:0.10, T:0.40
Consensus pattern (21 bp):
TCACCTGCTGCTTCATCTTGA
Found at i:3241825 original size:24 final size:24
Alignment explanation
Indices: 3241767--3241825 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
3241757 TCACCTGATC
*
3241767 CATCTTCCTCCTCACCTGCATCTT
1 CATCTTCCTCATCACCTGCATCTT
*
3241791 CATC-T--TGATCACCTGC-TGCTT
1 CATCTTCCTCATCACCTGCAT-CTT
3241812 CATCTTCCTCATCA
1 CATCTTCCTCATCA
3241826 TCATTGTCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 16 0.57
22 1 0.04
23 1 0.04
24 9 0.32
ACGTcount: A:0.15, C:0.41, G:0.07, T:0.37
Consensus pattern (24 bp):
CATCTTCCTCATCACCTGCATCTT
Found at i:3245602 original size:100 final size:101
Alignment explanation
Indices: 3245415--3245653 Score: 372
Period size: 100 Copynumber: 2.4 Consensus size: 101
3245405 AATTCATCAT
* *
3245415 TTACATTCATAATGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAACCCAGCTATGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAACCCAGCTATGGT
* ** *
3245480 CTTACATATAAACATTGTCATGGTCCAAATATGGCC
66 CTTACATATAAACACTACCATGGTCCAAACATGGCC
* * *
3245516 TTACGTTCATAGTGCCATAACCCAGTT-TGGTCTTATCATCAGAATGCCATAGCCCAGCTATGGT
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAACCCAGCTATGGT
* *
3245580 CTTACATATAAACACTACCATGGTCCAACCATGGTC
66 CTTACATATAAACACTACCATGGTCCAAACATGGCC
3245616 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATC
1 TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATC
3245654 CGTCAATTCA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
100 91 0.73
101 34 0.27
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (101 bp):
TTACGTTCATAGTGTCATAACCCAGTTATGGTCTTATCATCAGAACGCCATAACCCAGCTATGGT
CTTACATATAAACACTACCATGGTCCAAACATGGCC
Found at i:3252033 original size:35 final size:35
Alignment explanation
Indices: 3251952--3252033 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
3251942 ATATATACAC
*
3251952 TAAA-TAAAATAATAATAAAATAATATTTAAAAAT
1 TAAATTAAAATATTAATAAAATAATATTTAAAAAT
* **
3251986 TAAATTAAAATATTAATAAACTAATATTTATTTAAT
1 TAAATTAAAATATTAATAAAATAATATTTA-AAAAT
3252022 T-AATTAAAATAT
1 TAAATTAAAATAT
3252034 CTCCAACATC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 4 0.10
35 34 0.81
36 4 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (35 bp):
TAAATTAAAATATTAATAAAATAATATTTAAAAAT
Found at i:3270397 original size:28 final size:28
Alignment explanation
Indices: 3270357--3270427 Score: 142
Period size: 28 Copynumber: 2.5 Consensus size: 28
3270347 ATTACATATT
3270357 AACAAATATAAACATTTTTTTGGAAAGC
1 AACAAATATAAACATTTTTTTGGAAAGC
3270385 AACAAATATAAACATTTTTTTGGAAAGC
1 AACAAATATAAACATTTTTTTGGAAAGC
3270413 AACAAATATAAACAT
1 AACAAATATAAACAT
3270428 ACTAAACTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (28 bp):
AACAAATATAAACATTTTTTTGGAAAGC
Found at i:3273111 original size:75 final size:75
Alignment explanation
Indices: 3272882--3273179 Score: 324
Period size: 75 Copynumber: 4.0 Consensus size: 75
3272872 TGGGTATGAT
* * * * *
3272882 GTATGAATATGGA-G-GT-GAACACTGAATTGCTACCATATCTTATAGAAGATTCTACAAGTCCT
1 GTATGAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTCCT
3272944 AAAGAGATGG
66 AAAGAGATGG
* * * *
3272954 GTAAGACTATGGA-GA-T-GAACATTGAATTGTTACCAAAGCCTTATAGAAGATTCTACAAGTCC
1 GTATGAATATGGAGGAGTGGAACATTGAATTGATATCAAAG-CTTATAGAAGATTCTACAAGTCC
3273016 TAAAGAGATGG
65 TAAAGAGATGG
* * * *
3273027 GTCAT-AATATGGAGGAGTGGAGCATCGAATTGATATCAAAGCTTATAGAAGATTCTCCAAGTAC
1 GT-ATGAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTCC
*
3273091 TAAAGAGATAG
65 TAAAGAGATGG
* * * * * * *
3273102 ATATGAATATTGAGGAG-GAGAACGTTGAATTGATGTCAAAGCTTATAGAAGATTCTTCAAATGC
1 GTATGAATATGGAGGAGTG-GAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTCC
3273166 TAAAGAGATGG
65 TAAAGAGATGG
3273177 GTA
1 GTA
3273180 AGGATGTGGC
Statistics
Matches: 192, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
72 31 0.16
73 43 0.22
74 6 0.03
75 94 0.49
76 18 0.09
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (75 bp):
GTATGAATATGGAGGAGTGGAACATTGAATTGATATCAAAGCTTATAGAAGATTCTACAAGTCCT
AAAGAGATGG
Found at i:3277553 original size:19 final size:19
Alignment explanation
Indices: 3277529--3277578 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
3277519 TTGTTTGATA
3277529 AAATTAATCTTATTTTATT
1 AAATTAATCTTATTTTATT
*
3277548 AAATTAA--TTA-TTTCTT
1 AAATTAATCTTATTTTATT
3277564 AAATCTAATCTTATT
1 AAAT-TAATCTTATT
3277579 AATATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 9 0.35
17 6 0.23
19 10 0.38
20 1 0.04
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
AAATTAATCTTATTTTATT
Found at i:3281599 original size:26 final size:25
Alignment explanation
Indices: 3281569--3281620 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3281559 GTCAACTCTC
3281569 TTTTATAACCAAATATAAAATATTAA
1 TTTTATAA-CAAATATAAAATATTAA
* * *
3281595 TTTTATAACTATTATAAAATTTTAA
1 TTTTATAACAAATATAAAATATTAA
3281620 T
1 T
3281621 AATTTATTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTATAACAAATATAAAATATTAA
Found at i:3286817 original size:14 final size:14
Alignment explanation
Indices: 3286798--3286836 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
3286788 CATTACATAT
3286798 TAAAATGTTTTCCG
1 TAAAATGTTTTCCG
* *
3286812 TAAAATGATTTCTG
1 TAAAATGTTTTCCG
*
3286826 GAAAATGTTTT
1 TAAAATGTTTT
3286837 ACTTTTCTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.15, T:0.44
Consensus pattern (14 bp):
TAAAATGTTTTCCG
Found at i:3291131 original size:12 final size:12
Alignment explanation
Indices: 3291114--3291139 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3291104 CTTGTAACCC
3291114 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3291126 TGTTTGAGTTCA
1 TGTTTGAGTTCA
3291138 TG
1 TG
3291140 CCTCACACGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.08, G:0.27, T:0.50
Consensus pattern (12 bp):
TGTTTGAGTTCA
Found at i:3292280 original size:15 final size:15
Alignment explanation
Indices: 3292260--3292297 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
3292250 ACCTCCTCCT
3292260 ACCGCAGCTGCTGCC
1 ACCGCAGCTGCTGCC
3292275 ACCGCAGCTGCTGCC
1 ACCGCAGCTGCTGCC
*
3292290 GCCGCAGC
1 ACCGCAGC
3292298 CGCGTCGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.47, G:0.29, T:0.11
Consensus pattern (15 bp):
ACCGCAGCTGCTGCC
Found at i:3296520 original size:3 final size:3
Alignment explanation
Indices: 3296512--3296551 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
3296502 TTTCATCCAA
3296512 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3296552 TCAATTTCAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3298342 original size:14 final size:14
Alignment explanation
Indices: 3298305--3298357 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
3298295 TATATTTAAA
3298305 AAAATATAAAAACTT
1 AAAATATAAAAA-TT
* * *
3298320 TATACATAAAAATT
1 AAAATATAAAAATT
*
3298334 AAAATATAAAAACT
1 AAAATATAAAAATT
*
3298348 AAAATTTAAA
1 AAAATATAAA
3298358 TTTTAAAAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
14 21 0.70
15 9 0.30
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATATAAAAATT
Found at i:3316426 original size:19 final size:18
Alignment explanation
Indices: 3316382--3316427 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
3316372 ACCAAACATT
3316382 TATTTTGATTTTTTATACA
1 TATTTT-ATTTTTTATACA
3316401 T-TTTTATTTTATTATGA-A
1 TATTTTATTTT-TTAT-ACA
3316419 TATTTTATT
1 TATTTTATT
3316428 ATCTCCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 5 0.21
18 10 0.42
19 9 0.38
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.67
Consensus pattern (18 bp):
TATTTTATTTTTTATACA
Found at i:3321636 original size:22 final size:22
Alignment explanation
Indices: 3321577--3321638 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
3321567 AAAACCAACT
**
3321577 TACTAAGCTCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
*
3321599 TACTAAGCTCTCATGTTTCACG
1 TACTAAGCTCTCATGTTTAACG
3321621 TACTAAGCTCTCATGTTT
1 TACTAAGCTCTCATGTTT
3321639 GAACAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:3335134 original size:17 final size:17
Alignment explanation
Indices: 3335102--3335154 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
3335092 ATATTACGAA
*
3335102 TTAAAAATAGATATATAT
1 TTAATAATA-ATATATAT
*
3335120 TTAATAATAATATATAA
1 TTAATAATAATATATAT
* *
3335137 TAAATAATAAAATATAT
1 TTAATAATAATATATAT
3335154 T
1 T
3335155 ATTTTAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 22 0.73
18 8 0.27
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAATAATAATATATAT
Found at i:3335216 original size:23 final size:24
Alignment explanation
Indices: 3335171--3335216 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
3335161 AATTAATTAT
*
3335171 TAATAACATATGAAATATGTATAA
1 TAATAACATATGAAATATATATAA
3335195 TAATAA-ATATGAAACTA-ATATA
1 TAATAACATATGAAA-TATATATA
3335217 GTGTGCATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (24 bp):
TAATAACATATGAAATATATATAA
Found at i:3353694 original size:38 final size:38
Alignment explanation
Indices: 3353645--3353777 Score: 158
Period size: 38 Copynumber: 3.3 Consensus size: 38
3353635 TCCTTCTAGC
3353645 TTTTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
1 TTTTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
* *
3353683 TTTTGCTGATTTGCTCCCTCTGTTCCTCTGTTTATTTTCTTTTT
1 TTTTGCCGATTTGCTCCCTCTGTT--TCT-TTTCTTTTC---TT
*
3353727 TTTCTGCCGATTTGCTCCCTCTGTTTCTTTTCCTTTCTT
1 TTT-TGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
* *
3353766 TTCTGTCGATTT
1 TTTTGCCGATTT
3353778 CCTCAGTTTC
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
38 31 0.38
39 4 0.05
40 3 0.04
41 8 0.10
42 7 0.09
43 3 0.04
44 5 0.06
45 20 0.25
ACGTcount: A:0.04, C:0.26, G:0.11, T:0.59
Consensus pattern (38 bp):
TTTTGCCGATTTGCTCCCTCTGTTTCTTTTCTTTTCTT
Found at i:3353711 original size:46 final size:46
Alignment explanation
Indices: 3353661--3353769 Score: 154
Period size: 45 Copynumber: 2.5 Consensus size: 46
3353651 CGATTTGCTC
* *
3353661 CCTCTGTTTCTTTTCTTTTCTTTTTTGCTGATTTGCTCCCTCTGTT
1 CCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGCTCCCTCTGTT
*
3353707 CCTCTGTTTATTTTCTTTT-TTTTCTGCCGATTTGCTCCCTCTGTT
1 CCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGCTCCCTCTGTT
*
3353752 --TCT-TTTCCTTTCTTTTCT
1 CCTCTGTTTCTTTTCTTTTCT
3353770 GTCGATTTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
42 11 0.19
43 4 0.07
45 24 0.42
46 18 0.32
ACGTcount: A:0.03, C:0.27, G:0.09, T:0.61
Consensus pattern (46 bp):
CCTCTGTTTCTTTTCTTTTCTTTTCTGCCGATTTGCTCCCTCTGTT
Found at i:3354300 original size:23 final size:23
Alignment explanation
Indices: 3354270--3354316 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
3354260 TGTGTGATCA
3354270 TGGACTGGGACATATGCTTAATT
1 TGGACTGGGACATATGCTTAATT
3354293 TGGACTGGGACATATGCTTAATT
1 TGGACTGGGACATATGCTTAATT
3354316 T
1 T
3354317 AAGCCCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.36
Consensus pattern (23 bp):
TGGACTGGGACATATGCTTAATT
Found at i:3355877 original size:16 final size:16
Alignment explanation
Indices: 3355856--3355900 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
3355846 TTATTAAATT
*
3355856 ATATATTTTAATTATA
1 ATATATTTTAATAATA
3355872 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
*
3355887 ATTATATTTAAATA
1 A-TATATTTTAATA
3355901 TGATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 9 0.36
17 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:3355906 original size:16 final size:16
Alignment explanation
Indices: 3355857--3355897 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3355847 TATTAAATTA
*
3355857 TATATTTTAATTATAA-
1 TATA-TTTAATAATAAT
3355873 TATATTTAATAATAAT
1 TATATTTAATAATAAT
3355889 TATATTTAA
1 TATATTTAA
3355898 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTAATAATAAT
Found at i:3356096 original size:16 final size:16
Alignment explanation
Indices: 3356072--3356104 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
3356062 TTGATTTGCT
*
3356072 ATTATGCCTCTATTCC
1 ATTACGCCTCTATTCC
3356088 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
3356104 A
1 A
3356105 ATACAGCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.33, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:3358299 original size:29 final size:30
Alignment explanation
Indices: 3358264--3358335 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
3358254 TAATTTAAGT
*
3358264 TTCATGTGTATAATTGC-ACTAAATCAAAG
1 TTCATGTGTATAATTGCAACTAAACCAAAG
* *
3358293 TTCATGTAGCA-AATTGCATATTAAACCAAAG
1 TTCATGT-GTATAATTGCA-ACTAAACCAAAG
*
3358324 TTCATGTATATA
1 TTCATGTGTATA
3358336 TTTGATATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
29 13 0.38
30 3 0.09
31 18 0.53
ACGTcount: A:0.39, C:0.14, G:0.12, T:0.35
Consensus pattern (30 bp):
TTCATGTGTATAATTGCAACTAAACCAAAG
Found at i:3364120 original size:2 final size:2
Alignment explanation
Indices: 3364113--3364141 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3364103 TGAAATATTT
3364113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3364142 CAGGTTTATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3368036 original size:16 final size:17
Alignment explanation
Indices: 3368009--3368045 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
3367999 AATTAAGTCA
3368009 ATAATAATATAAAATTT
1 ATAATAATATAAAATTT
*
3368026 ATAAT-ATATAACATTT
1 ATAATAATATAAAATTT
3368042 ATAA
1 ATAA
3368046 GTAAGGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATAATATAAAATTT
Found at i:3368811 original size:118 final size:118
Alignment explanation
Indices: 3368585--3368818 Score: 321
Period size: 118 Copynumber: 2.0 Consensus size: 118
3368575 ATTATTGTGC
*
3368585 AATTACATGCAATTAAATCCAAATCCAATTACTTGGTGGCTTTCCAAATACTATTGAATTCAAGA
1 AATTACATGCAATTAAATCCAAATCCAATTACTTGGTGACTTTCCAAATACTATTGAATTCAAGA
* * *
3368650 AAAAAGTAATTTAATATCATGTTCATTTTTATAACGGCATAATGATAATTTGT
66 AAAAAGTAATTTAATATCATGTTCATTCTCATAAAGGCATAATGATAATTTGT
* * * *
3368703 AATTACATGCAATTACA-CCAAATCGAATTA-TTAGGTGACTTTCTAGATACTATTGAATTCAAG
1 AATTACATGCAATTAAATCCAAATCCAATTACTT-GGTGACTTTCCAAATACTATTGAATTCAAG
** *
3368766 AAAAAAAAGTAATTT-ATATCATGTTTGTTCTCGTAAAGGCATAATGATAATTT
65 --AAAAAAGTAATTTAATATCATGTTCATTCTCATAAAGGCATAATGATAATTT
3368819 TAACCTTCAA
Statistics
Matches: 102, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
116 2 0.02
117 39 0.38
118 48 0.47
119 13 0.13
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.36
Consensus pattern (118 bp):
AATTACATGCAATTAAATCCAAATCCAATTACTTGGTGACTTTCCAAATACTATTGAATTCAAGA
AAAAAGTAATTTAATATCATGTTCATTCTCATAAAGGCATAATGATAATTTGT
Found at i:3373923 original size:2 final size:2
Alignment explanation
Indices: 3373911--3373942 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3373901 TCGATCTAAA
3373911 AT AT A- AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3373943 TTATTGAACG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3378128 original size:42 final size:43
Alignment explanation
Indices: 3378028--3378137 Score: 141
Period size: 42 Copynumber: 2.6 Consensus size: 43
3378018 CAATGTCAAC
* * **
3378028 GTCCCAGACGTGGTCTTACATGTAATCAAATAACGATGTCACT
1 GTCCCAGACATGGTCTTACACGTAATCAAATAACGACATCACT
* * * *
3378071 GTCCCAGACAGGGTCTTACACGTAATCATAT-ATGACATCAGT
1 GTCCCAGACATGGTCTTACACGTAATCAAATAACGACATCACT
3378113 GTCCCAGACATGGTCTTACACGTAA
1 GTCCCAGACATGGTCTTACACGTAA
3378138 ATCTTAAACC
Statistics
Matches: 58, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
42 31 0.53
43 27 0.47
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACACGTAATCAAATAACGACATCACT
Found at i:3381594 original size:18 final size:18
Alignment explanation
Indices: 3381571--3381609 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3381561 ACATTGCTTC
3381571 TCAAAAGTACTTTTAAAG
1 TCAAAAGTACTTTTAAAG
* *
3381589 TCAAAAGTATTTTTGAAG
1 TCAAAAGTACTTTTAAAG
3381607 TCA
1 TCA
3381610 GAGGCAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (18 bp):
TCAAAAGTACTTTTAAAG
Found at i:3384937 original size:6 final size:7
Alignment explanation
Indices: 3384920--3384944 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3384910 TAAATTTTCA
3384920 AAAAAAT
1 AAAAAAT
3384927 AAAAAAT
1 AAAAAAT
3384934 AAAAAAT
1 AAAAAAT
3384941 AAAA
1 AAAA
3384945 CTTTTTTACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:3401303 original size:30 final size:30
Alignment explanation
Indices: 3401267--3401328 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
3401257 ACTTATTTTA
* *
3401267 TTGTTAATTTTTTTATTATTTTAAAGAGAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
3401297 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
3401327 TT
1 TT
3401329 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.02, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:3402164 original size:29 final size:28
Alignment explanation
Indices: 3402114--3402183 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
3402104 AATAAACACT
* *
3402114 AAAAATTTATTTAAAAAATAAATAATAA
1 AAAAATATATTTAAAAAATAAAAAATAA
* *
3402142 AAAAAGTAT-TTTAAAAATTTAAAAAATTA
1 AAAAA-TATATTTAAAAA-ATAAAAAATAA
3402171 AAAAATATATTTA
1 AAAAATATATTTA
3402184 TTTATTATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 16 0.46
29 19 0.54
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
AAAAATATATTTAAAAAATAAAAAATAA
Found at i:3405023 original size:19 final size:19
Alignment explanation
Indices: 3404986--3405024 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3404976 TTTTTTCCTA
*
3404986 TTTTATTTTTTTCACCTTT
1 TTTTATTTTTTTCAACTTT
* *
3405005 TTTTTTTTTTTTTAACTTT
1 TTTTATTTTTTTCAACTTT
3405024 T
1 T
3405025 AGAGCATTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTTTTTCAACTTT
Found at i:3432057 original size:6 final size:6
Alignment explanation
Indices: 3432046--3432076 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3432036 TCACCCACAA
3432046 AAACAC AAACAC AAACAC AAACAC AAACAC A
1 AAACAC AAACAC AAACAC AAACAC AAACAC A
3432077 CAGAGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACAC
Found at i:3433212 original size:133 final size:133
Alignment explanation
Indices: 3432974--3433218 Score: 357
Period size: 133 Copynumber: 1.8 Consensus size: 133
3432964 TTGTGTATAT
* * * *
3432974 ATATGTGGTGTAACGGTCTTGATTCCTCCTAAAGGGAATTGCTGTATAACGATCTTGATTCCTCC
1 ATATGCGGTGTAACGGTCTTGATTCCTCCTAAAGGAAATTGCGGGATAACGATCTTGATTCCTCC
* * * **
3433039 TAAGGGGGATCGCATGAGCTGCATTTAAGTGAGTGTCTATCTACACGCGTGCTAGTCTTTTTCTG
66 TAAAGGGAATCACATGAGCTGCATTTAAGTGAGCATCTATCTACACGCGTGCTAGTCTTTTTCTG
3433104 TCC
131 TCC
*
3433107 ATATGCGGTGTAACGGTTTTGATTCCTCCTAAAGGAAATTGCGGCGA-AACGATCTTGATTCCTC
1 ATATGCGGTGTAACGGTCTTGATTCCTCCTAAAGGAAATTGCGG-GATAACGATCTTGATTCCTC
* **
3433171 CTAAATGGAATCACATGATTTGCATTTAAGTGAGCATCTATCTACACG
65 CTAAAGGGAATCACATGAGCTGCATTTAAGTGAGCATCTATCTACACG
3433219 TGCGTGAGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
133 97 0.99
134 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (133 bp):
ATATGCGGTGTAACGGTCTTGATTCCTCCTAAAGGAAATTGCGGGATAACGATCTTGATTCCTCC
TAAAGGGAATCACATGAGCTGCATTTAAGTGAGCATCTATCTACACGCGTGCTAGTCTTTTTCTG
TCC
Found at i:3438752 original size:78 final size:78
Alignment explanation
Indices: 3438653--3438891 Score: 406
Period size: 78 Copynumber: 3.1 Consensus size: 78
3438643 GTAGATCAGT
* *
3438653 TGATGGCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGATACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
3438718 CCAAATCCAAGGA
66 CCAAATCCAAGGA
*
3438731 TGATGTCGCTTCAAAAATAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
*
3438796 CCAAATCCGAGGA
66 CCAAATCCAAGGA
* * *
3438809 GGATGTCACTTCAAAAGTAGGCAACAAATCCAAAAATGGGGACACTGGTGACACACCCAAGTCTA
1 TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
*
3438874 CCAAATCCAAGAA
66 CCAAATCCAAGGA
3438887 TGATG
1 TGATG
3438892 ACAATGTTAA
Statistics
Matches: 150, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 150 1.00
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (78 bp):
TGATGTCGCTTCAAAAGTAGGCAACAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTA
CCAAATCCAAGGA
Found at i:3438802 original size:42 final size:42
Alignment explanation
Indices: 3438677--3438894 Score: 111
Period size: 42 Copynumber: 5.5 Consensus size: 42
3438667 AAGTAGGCAA
*
3438677 CAAATCCAAAAATGAGGACACTGGTGATACACCCAAGTCTAC
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
** * * * ** * *
3438719 CAAATCCAAGGATGATGTCGCT--T--CA-A-AAATAGGC-AA
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCA-AGTCTAC
3438755 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
* ** * * * **** * *
3438797 CAAATCCGAGGAGGATGTCACT--T--CA-AAAGTAGGC-AA
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
*
3438833 CAAATCCAAAAATGGGGACACTGGTGACACACCCAAGTCTAC
1 CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
* *
3438875 CAAATCCAAGAATGATGACA
1 CAAATCCAAAAATGAGGACA
3438895 ATGTTAAGCC
Statistics
Matches: 115, Mismatches: 47, Indels: 28
0.61 0.25 0.15
Matches are distributed among these distances:
36 35 0.30
37 8 0.07
38 5 0.04
40 6 0.05
41 8 0.07
42 53 0.46
ACGTcount: A:0.41, C:0.24, G:0.19, T:0.16
Consensus pattern (42 bp):
CAAATCCAAAAATGAGGACACTGGTGACACACCCAAGTCTAC
Found at i:3442210 original size:2 final size:2
Alignment explanation
Indices: 3442203--3442236 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
3442193 ATAGATTTAA
* *
3442203 AT AT AT AT AT AT AT AT AT AT AT AT CT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3442237 TGTTCTGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3444084 original size:19 final size:19
Alignment explanation
Indices: 3444055--3444091 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3444045 GTCGTTTTCT
3444055 TTAAAATTATAAT-TGAGA
1 TTAAAATTATAATGTGAGA
3444073 TTAAATATTATAATGTGAG
1 TTAAA-ATTATAATGTGAG
3444092 GTAAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 8 0.47
20 4 0.24
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.41
Consensus pattern (19 bp):
TTAAAATTATAATGTGAGA
Found at i:3444096 original size:19 final size:18
Alignment explanation
Indices: 3444056--3444097 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
3444046 TCGTTTTCTT
*
3444056 TAAAATTATAATTGAGAT
1 TAAAATTATAATTGAGAG
3444074 TAAATATTATAATGTGAG-G
1 TAAA-ATTATAAT-TGAGAG
3444093 TAAAA
1 TAAAA
3444098 AAGAGTGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (18 bp):
TAAAATTATAATTGAGAG
Found at i:3447490 original size:26 final size:26
Alignment explanation
Indices: 3447467--3447526 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
3447457 GTCTCGATAT
3447467 ATGGCTCTTTATGAGCTTCCCGATTA
1 ATGGCTCTTTATGAGCTTCCCGATTA
* * *
3447493 AAGGCTCTTTGTGAGCTTCCTGATTA
1 ATGGCTCTTTATGAGCTTCCCGATTA
3447519 ATGGCTCT
1 ATGGCTCT
3447527 CCGGATTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (26 bp):
ATGGCTCTTTATGAGCTTCCCGATTA
Found at i:3452734 original size:28 final size:25
Alignment explanation
Indices: 3452702--3452759 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
3452692 TATAGTTACA
*
3452702 ATAAAATTTTTAATTATTTATTAATTTC
1 ATAAAATTTTTAA--A-ATATTAATTTC
*
3452730 ATAAATTTTTTAAAATATTAATTTC
1 ATAAAATTTTTAAAATATTAATTTC
3452755 ATAAA
1 ATAAA
3452760 TGTTAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 15 0.54
26 1 0.04
28 12 0.43
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
ATAAAATTTTTAAAATATTAATTTC
Found at i:3458368 original size:4 final size:4
Alignment explanation
Indices: 3458359--3458403 Score: 90
Period size: 4 Copynumber: 11.2 Consensus size: 4
3458349 TTGGTTTTTG
3458359 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
3458404 AACACACACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3466766 original size:14 final size:15
Alignment explanation
Indices: 3466731--3466767 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
3466721 CACTCTCCTC
*
3466731 TTTGCTCCTCTTCGT
1 TTTGCTTCTCTTCGT
3466746 TTT-CTTCTCTT-GT
1 TTTGCTTCTCTTCGT
3466759 TTTGCTTCT
1 TTTGCTTCT
3466768 TTGAGCGACG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 12 0.60
15 3 0.15
ACGTcount: A:0.00, C:0.27, G:0.11, T:0.62
Consensus pattern (15 bp):
TTTGCTTCTCTTCGT
Found at i:3470476 original size:109 final size:107
Alignment explanation
Indices: 3470282--3470514 Score: 340
Period size: 109 Copynumber: 2.1 Consensus size: 107
3470272 TACGCATACT
* * *
3470282 AATATCCTTTTAAAAAAAATTTCAAAATGAGACAATGTTTTGTGTTTGGAAATTCGAGAAAACGT
1 AATATCCTTTT---AAAAACTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGT
* *
3470347 GCCCTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATGGCCA
63 GCCCTAATGTGCTAGGTTTCGA--TTTCTCGTTCGACCAAATAGCCA
*
3470394 AATATCCTTTTAAAAACTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAAACTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
3470459 CTAATGTGCTAGGTTTCGATTTCTCGTTGGACCAAATAGCCG
66 CTAATGTGCTAGGTTTCGATTTCTCGTTCGACCAAATAGCCA
*
3470501 AATATCCTCTTAAA
1 AATATCCTTTTAAA
3470515 TCTTAATCCA
Statistics
Matches: 112, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
107 33 0.29
109 68 0.61
112 11 0.10
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (107 bp):
AATATCCTTTTAAAAACTTCAAAATAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
CTAATGTGCTAGGTTTCGATTTCTCGTTCGACCAAATAGCCA
Found at i:3474157 original size:29 final size:28
Alignment explanation
Indices: 3474124--3474180 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
3474114 CAATTTAGGA
*
3474124 TTTAAATAATATA-AATTATTTGTTATAAC
1 TTTAAA-AATACACAATTATTT-TTATAAC
3474153 TTTAAAAATACACCAATTATTTTTATAA
1 TTTAAAAATACA-CAATTATTTTTATAA
3474181 TATAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 12 0.48
30 8 0.32
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTAAAAATACACAATTATTTTTATAAC
Found at i:3476773 original size:27 final size:27
Alignment explanation
Indices: 3476734--3476787 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
3476724 ATTTGTTATG
3476734 TTTTTTTCAGAGAAAATTGATAGTGTT
1 TTTTTTTCAGAGAAAATTGATAGTGTT
** *
3476761 TTTTTTTTTGAGAAAATTGATGGTGTT
1 TTTTTTTCAGAGAAAATTGATAGTGTT
3476788 AACGGCAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (27 bp):
TTTTTTTCAGAGAAAATTGATAGTGTT
Found at i:3479600 original size:22 final size:23
Alignment explanation
Indices: 3479575--3479619 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
3479565 TCGTAATGAC
*
3479575 ATATGAAATTAACAATA-TAAAT
1 ATATCAAATTAACAATACTAAAT
*
3479597 ATATCAAATTAATAATACTAAAT
1 ATATCAAATTAACAATACTAAAT
3479620 GTATTACATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (23 bp):
ATATCAAATTAACAATACTAAAT
Found at i:3484275 original size:3 final size:3
Alignment explanation
Indices: 3484267--3484292 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3484257 TTTTAAGCTT
3484267 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
3484293 TTAATATGAG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:3491842 original size:2 final size:2
Alignment explanation
Indices: 3491837--3491872 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3491827 CTTGATATTT
3491837 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3491873 AAACTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3492461 original size:34 final size:35
Alignment explanation
Indices: 3492385--3492514 Score: 135
Period size: 34 Copynumber: 3.7 Consensus size: 35
3492375 GGCCCATTTT
*
3492385 TATTTT-AAAA-ATTTTAAAATTAAAAAAATTAAAAAAG
1 TATTTTAAAAATATTTTAAAA--ATAAAAA-T-AAAAAG
*
3492422 TATTTTAAAAATATTTTAAAAATAAAAA-ATAAAG
1 TATTTTAAAAATATTTTAAAAATAAAAATAAAAAG
3492456 TATTTTAAAAATATTTTAAATTAA-AAAAATTAAAAAG
1 TATTTTAAAAATATTTTAAA--AATAAAAA-TAAAAAG
*
3492493 TA-TGTAAAAATATTTTAAAAAT
1 TATTTTAAAAATATTTTAAAAAT
3492515 CATTTTTTCT
Statistics
Matches: 82, Mismatches: 4, Indels: 16
0.80 0.04 0.16
Matches are distributed among these distances:
34 27 0.33
35 5 0.06
36 18 0.22
37 19 0.23
38 4 0.05
39 9 0.11
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (35 bp):
TATTTTAAAAATATTTTAAAAATAAAAATAAAAAG
Found at i:3492519 original size:12 final size:11
Alignment explanation
Indices: 3492416--3492520 Score: 61
Period size: 11 Copynumber: 9.0 Consensus size: 11
3492406 AAAAAAATTA
3492416 AAAAAGTATTTT
1 AAAAA-TATTTT
3492428 AAAAATATTTT
1 AAAAATATTTT
***
3492439 AAAAATA-AAA
1 AAAAATATTTT
3492449 AATAAAGTATTTT
1 AA-AAA-TATTTT
3492462 AAAAATATTTT
1 AAAAATATTTT
* **
3492473 AAATTAAAAAAATT
1 -AA--AAATATTTT
*
3492487 AAAAAGTA-TGT
1 AAAAA-TATTTT
3492498 AAAAATATTTT
1 AAAAATATTTT
3492509 AAAAATCATTTT
1 AAAAAT-ATTTT
3492521 TTCTTCTTCC
Statistics
Matches: 71, Mismatches: 13, Indels: 18
0.70 0.13 0.18
Matches are distributed among these distances:
10 4 0.06
11 39 0.55
12 18 0.25
13 4 0.06
14 6 0.08
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:3493309 original size:13 final size:14
Alignment explanation
Indices: 3493293--3493322 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
3493283 GGACTGTTTA
3493293 TTTATTTA-TTGGT
1 TTTATTTATTTGGT
3493306 TTTATTTATTTGGT
1 TTTATTTATTTGGT
3493320 TTT
1 TTT
3493323 GGGCCCGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (14 bp):
TTTATTTATTTGGT
Found at i:3493739 original size:32 final size:32
Alignment explanation
Indices: 3493702--3493764 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
3493692 GACGATCGTG
*
3493702 GCCGCGGTAGAGCAACGACGGCCTAGTGGCCA
1 GCCGCGGCAGAGCAACGACGGCCTAGTGGCCA
*
3493734 GCCGCGGCAGAGCAACGGCGGCCTAGTGGCC
1 GCCGCGGCAGAGCAACGACGGCCTAGTGGCC
3493765 GGACTCAGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.33, G:0.40, T:0.08
Consensus pattern (32 bp):
GCCGCGGCAGAGCAACGACGGCCTAGTGGCCA
Found at i:3496838 original size:305 final size:305
Alignment explanation
Indices: 3496287--3496854 Score: 852
Period size: 305 Copynumber: 1.9 Consensus size: 305
3496277 GTTACATGCA
*
3496287 ATTACTAGTCTTATACTATTCATACAATTGTAGATTTAGTCCATATTCTCCAATTGGATCATTCT
1 ATTACTAGTCTTATACTATTCATACAATTGTAGATTTACTCCATATTCTCCAATTGGATCATTCT
* * * * * *
3496352 AAATCTCTGTATTTTTTGGATTTTGAAATTTCAGTATTAACGTAAAATGAATTTTGTTAATCCAT
66 AAATCTCTATACTTTTCGAATTTTAAAATTTCAATATTAACGTAAAATGAATTTTGTTAATCCAT
* * *
3496417 TAATTGGATTTTAGTGAGTAATATATGAAAAATAATAATCTAACATGACATTACACATATAATAA
131 TAACTGAATTTTAATGAGTAATATATGAAAAATAATAATCTAACATGACATTACACATATAATAA
* * * * ** **
3496482 AATGTTTGACGCATTAGATTTTGGAAATGGTAAAATTTTACTTAACGGTTTTAACAATTTATTAT
196 AATATATGACACATTAAATTTTAAAAATAATAAAATTTTACTTAACGGTTTTAACAATTTATTAT
3496547 TTGACGAATATTGAAAATTTAAAAAAAAAAGACTAAAAATGACCC
261 TTGACGAATATTGAAAATTTAAAAAAAAAAGACTAAAAATGACCC
* * * * * *
3496592 ATTACTAGTCTTGTACTATTCATACAGTTGTAGATTTACTCTATATTTTCTATTTGGATCATTCT
1 ATTACTAGTCTTATACTATTCATACAATTGTAGATTTACTCCATATTCTCCAATTGGATCATTCT
*
3496657 AAATCTCTATACTTTTCGAATTTTAAAATTTCAATCTTAACGTAAAAT-AATTTTTGTTAATCCA
66 AAATCTCTATACTTTTCGAATTTTAAAATTTCAATATTAACGTAAAATGAA-TTTTGTTAATCCA
* *
3496721 TTAACTGAATTTTAATGAGTAATATGTAGAAAAA-AATAATCTAACATGACATTACATATATAAT
130 TTAACTGAATTTTAATGAGTAATATAT-GAAAAATAATAATCTAACATGACATTACACATATAAT
*
3496785 AAAATATATGACACATTAAATTTTAAAAATAATAAATTTTTACTTAACGGTTTTAACAATTTATT
194 AAAATATATGACACATTAAATTTTAAAAATAATAAAATTTTACTTAACGGTTTTAACAATTTATT
3496850 ATTTG
259 ATTTG
3496855 GTGAGAATTA
Statistics
Matches: 233, Mismatches: 28, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
304 2 0.01
305 225 0.97
306 6 0.03
ACGTcount: A:0.39, C:0.11, G:0.10, T:0.40
Consensus pattern (305 bp):
ATTACTAGTCTTATACTATTCATACAATTGTAGATTTACTCCATATTCTCCAATTGGATCATTCT
AAATCTCTATACTTTTCGAATTTTAAAATTTCAATATTAACGTAAAATGAATTTTGTTAATCCAT
TAACTGAATTTTAATGAGTAATATATGAAAAATAATAATCTAACATGACATTACACATATAATAA
AATATATGACACATTAAATTTTAAAAATAATAAAATTTTACTTAACGGTTTTAACAATTTATTAT
TTGACGAATATTGAAAATTTAAAAAAAAAAGACTAAAAATGACCC
Found at i:3500451 original size:49 final size:48
Alignment explanation
Indices: 3500374--3500473 Score: 116
Period size: 47 Copynumber: 2.1 Consensus size: 48
3500364 ATATTTTAAA
*
3500374 ATTATTTTATGGTACAAATAAATTATAAAAATAAACTTAAA-TTAAAATAT
1 ATTATTTTATGGTACAAATAAATAAT-AAAA-AAA-TTAAATTTAAAATAT
* *
3500424 ATTATTTT-TTGTACAAATAACA-AATAAAAACATTAAATTTAAAATAT
1 ATTATTTTATGGTACAAATAA-ATAATAAAAAAATTAAATTTAAAATAT
3500471 ATT
1 ATT
3500474 TTTAAATTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
46 5 0.11
47 14 0.31
48 4 0.09
49 13 0.29
50 9 0.20
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (48 bp):
ATTATTTTATGGTACAAATAAATAATAAAAAAATTAAATTTAAAATAT
Found at i:3504029 original size:4 final size:4
Alignment explanation
Indices: 3504020--3504053 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
3504010 CGTCCAGCCC
3504020 AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AA
3504054 CAAAGCAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:3508438 original size:101 final size:98
Alignment explanation
Indices: 3508256--3508453 Score: 315
Period size: 101 Copynumber: 2.0 Consensus size: 98
3508246 ATATAATAAA
*
3508256 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
3508321 CCTGTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTGTAGAATCCCAAACTCGGAATATTTCCTTT
*
3508354 ACTTTAAAAGAACATCCAGTACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACA
1 ACTTTAAAAGAACATCC---ACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACA
* * * *
3508419 ATTCCTTTAGGATCTCAAACTCGGAATATTTCCTT
63 ATCCCTGTAGAATCCCAAACTCGGAATATTTCCTT
3508454 CATGATTTTT
Statistics
Matches: 91, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
98 17 0.19
101 74 0.81
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTGTAGAATCCCAAACTCGGAATATTTCCTTT
Found at i:3511641 original size:59 final size:52
Alignment explanation
Indices: 3511594--3511764 Score: 203
Period size: 52 Copynumber: 3.4 Consensus size: 52
3511584 GATCAAGTGA
*
3511594 CAAGTGGA-AAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
1 CAAGT-GACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
*
3511646 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
* * **
3511698 CAAGAGAC------AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGAT
1 CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
* *
3511744 CAAGAGACAAAGTGATAAGTG
1 CAAGTGAC-AAGTGAAAAGTG
3511765 GCTACACTTA
Statistics
Matches: 103, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
46 42 0.41
51 2 0.02
52 54 0.52
53 5 0.05
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.26
Consensus pattern (52 bp):
CAAGTGACAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGAT
Found at i:3511737 original size:46 final size:46
Alignment explanation
Indices: 3511660--3511763 Score: 172
Period size: 46 Copynumber: 2.3 Consensus size: 46
3511650 TGACAAGTGA
* * *
3511660 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGAC
*
3511706 AAAGTGATAAGTAATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGAC
3511752 AAAGTGATAAGT
1 AAAGTGATAAGT
3511764 GGCTACACTT
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTAATAGCTTCAGCTACACTTATCTGATCAAGAGAC
Found at i:3512582 original size:22 final size:22
Alignment explanation
Indices: 3512554--3512706 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
3512544 TTTATTGTTC
*
3512554 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
3512576 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
3512598 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
3512620 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
3512642 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
*
3512664 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
3512686 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
3512707 ACTATCAACA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:3516360 original size:21 final size:21
Alignment explanation
Indices: 3516334--3516386 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
3516324 AGCTGAGGCG
*
3516334 GTGAGATTAGTTACAGTAGCA
1 GTGAGATTAGATACAGTAGCA
* * **
3516355 GTGAGATTGGATACTGTAGTG
1 GTGAGATTAGATACAGTAGCA
3516376 GTGAGATTAGA
1 GTGAGATTAGA
3516387 AACAATGGTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.06, G:0.34, T:0.30
Consensus pattern (21 bp):
GTGAGATTAGATACAGTAGCA
Found at i:3520024 original size:16 final size:16
Alignment explanation
Indices: 3520003--3520035 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3519993 AATCTTAATG
3520003 GAGCATGCATTGGAAA
1 GAGCATGCATTGGAAA
3520019 GAGCATGCATTGGAAA
1 GAGCATGCATTGGAAA
3520035 G
1 G
3520036 CTATGGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.12, G:0.33, T:0.18
Consensus pattern (16 bp):
GAGCATGCATTGGAAA
Found at i:3520535 original size:27 final size:27
Alignment explanation
Indices: 3520497--3520549 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3520487 AACTGAGAAG
3520497 TGAATAGAAAACACAGAATATCTTATT
1 TGAATAGAAAACACAGAATATCTTATT
* *
3520524 TGAATAGAAAACACATAATATGTTAT
1 TGAATAGAAAACACAGAATATCTTAT
3520550 AGTTTCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (27 bp):
TGAATAGAAAACACAGAATATCTTATT
Found at i:3524647 original size:21 final size:23
Alignment explanation
Indices: 3524615--3524659 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3524605 AATAATATAA
3524615 TTAATTATAAATATAAAA-TATT
1 TTAATTATAAATATAAAATTATT
*
3524637 TTAATTA-AAATTTAAAATTATT
1 TTAATTATAAATATAAAATTATT
3524659 T
1 T
3524660 ATGAGAAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTAATTATAAATATAAAATTATT
Found at i:3528631 original size:4 final size:4
Alignment explanation
Indices: 3528622--3528670 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
3528612 AAAAGAAGGT
3528622 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
3528670 A
1 A
3528671 GAGGGAGAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:3529546 original size:15 final size:15
Alignment explanation
Indices: 3529526--3529577 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 15
3529516 AGTGAATTGG
3529526 AAATAAAAATATATT
1 AAATAAAAATATATT
3529541 AAATAAAAACTA-ATTT
1 AAATAAAAA-TATA-TT
3529557 ATTAATAAAATATATATT
1 A--AATAAAA-ATATATT
3529575 AAA
1 AAA
3529578 ATGATTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
15 10 0.32
16 7 0.23
18 12 0.39
19 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
AAATAAAAATATATT
Found at i:3530316 original size:112 final size:112
Alignment explanation
Indices: 3530073--3530378 Score: 296
Period size: 112 Copynumber: 2.7 Consensus size: 112
3530063 TACCATAACA
* *
3530073 CGCCGC-AAAATCTCAAGACCAAAACACATCGTTTTGGTCTTGATGTATACTAGAATTAGTGGCG
1 CGCCGCAAAAATCT-TA-ACCAAAACACATCGTTTT-GTCTTGATGTATATTAGAATTAGTGGCG
* * * * *
3530137 ATTATGATAAAACGCCGCTAAAGGAAGTATTAACGGCGCATTGTCGAAAG
63 CTTACGATAAAACGCCGCTAAAGCAAGTATTAACGGCGCATTGACAAAAG
* * * *
3530187 CGCCGCAAAAATCTTAACGAAAACGCATCGTTTTGTCTTGCTGTATATTAGCATTAGTGGCGCTT
1 CGCCGCAAAAATCTTAACCAAAACACATCGTTTTGTCTTGATGTATATTAGAATTAGTGGCGCTT
* * *
3530252 ACGA-AAACCCGCCGTTAAAGCAAGTATTAGCGGCGC-TT-ACAAAAAG
66 ACGATAAA-ACGCCGCTAAAGCAAGTATTAACGGCGCATTGAC-AAAAG
* * * ** * * * *
3530298 CGCCGCAGTATATGTTAACCAAAACACAGAGTTTGGTCTAGAGGTATATTAGAATTTGTGGCGCT
1 CGCCGCA-AAAATCTTAACCAAAACACATCGTTTTGTCTTGATGTATATTAGAATTAGTGGCGCT
* **
3530363 TATGGGAAAACGCCGC
65 TACGATAAAACGCCGC
3530379 AAAATATCCT
Statistics
Matches: 156, Mismatches: 31, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
110 1 0.01
111 16 0.10
112 106 0.68
113 19 0.12
114 7 0.04
115 7 0.04
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (112 bp):
CGCCGCAAAAATCTTAACCAAAACACATCGTTTTGTCTTGATGTATATTAGAATTAGTGGCGCTT
ACGATAAAACGCCGCTAAAGCAAGTATTAACGGCGCATTGACAAAAG
Found at i:3530511 original size:190 final size:186
Alignment explanation
Indices: 3530182--3530548 Score: 448
Period size: 190 Copynumber: 2.0 Consensus size: 186
3530172 GCGCATTGTC
* * * *
3530182 GAAAGCGCCGCAAAAATCTTAACGAAAACGCATCGTTTTGTCTTGCTGTATATTAGCATTAGTGG
1 GAAAACGCCGCAAAAATCCTAACCAAAACGCACCGTTTTGTCTTGCTGTATATTAGCATTAGTGG
* * * * * ** *
3530247 CGCTTACGAAAACCCGCCGTTAAAGCAAGTATTAGCGGCGCTTACAAAAAGCGCCGCAGTATATG
66 CGCTTAAGAAAACACGCCGCTAAAGCAAATATTAGCAGCGCTTACAAAAAGCGCCGCAAAATATC
* *
3530312 TTAACCAAAACACAGAGTTTGGTCTAGAGGTATATTAGAATTTGTGGCGCTTATGG
131 TTAACCAAAACACAGAGTTTGGTCTAGAGGTATACTAGAATTAGTGGCGCTTATGG
* * *
3530368 GAAAACGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTGGTGTATGTTA-CAGTTAG
1 GAAAACGCCGCAAAA-ATCCTAACCAAAACGCACCGTTTT-GTCTTGCTGTATATTAGCA-TTAG
** * *** *
3530432 TGGCGCTTAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGTTTTGTGAGAAGCGCCGCAAA
63 TGGCGCTTAAGAAAACACGCCGCTAAAGCA-AATATTAGCAGCG-CTTACAAAAAGCGCCGCAAA
* *
3530497 ATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGG
126 ATATCTTAACCAAAACACAGAGTTTGGTCTAGAGGTATACTAGAATTAGTGG
3530549 TGCAAAGGGA
Statistics
Matches: 150, Mismatches: 26, Indels: 6
0.82 0.14 0.03
Matches are distributed among these distances:
186 14 0.09
187 22 0.15
188 43 0.29
189 11 0.07
190 60 0.40
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (186 bp):
GAAAACGCCGCAAAAATCCTAACCAAAACGCACCGTTTTGTCTTGCTGTATATTAGCATTAGTGG
CGCTTAAGAAAACACGCCGCTAAAGCAAATATTAGCAGCGCTTACAAAAAGCGCCGCAAAATATC
TTAACCAAAACACAGAGTTTGGTCTAGAGGTATACTAGAATTAGTGGCGCTTATGG
Found at i:3530576 original size:113 final size:114
Alignment explanation
Indices: 3530373--3530665 Score: 344
Period size: 113 Copynumber: 2.6 Consensus size: 114
3530363 TATGGGAAAA
* * ** * *
3530373 CGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTG-GTGTATGTTACAGTTAGTGGCG
1 CGCCGCAAAATATCCTAACCAAAACGCA-AGTTTTGGTCTTGAG-GTATACTAGAATTAGTGGCG
* *
3530437 CTTAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCG-TTTTGTGAGAAG
64 CTAAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGCGTTTG-GAGAAG
* *
3530488 CGCCGCAAAATATCTTAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTAGAATTAGTGGTGC
1 CGCCGCAAAATATCCTAACCAAAACGCA-AGTTTTGGTCTTGAGGTATACTAGAATTAGTGGCGC
* * *
3530552 -AAAGGGAACACGCCGCTAAGGCATACTATTAGCGGCGCGTTTGGAGAAG
65 TAAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGCGTTTGGAGAAG
* * * *
3530601 CGCCGCAAAATTTCGTAACCAAAACGCAACGTTTTTGTCTTGATGTATAC-AGTAATTAGTGGCG
1 CGCCGCAAAATATCCTAACCAAAACGCAA-GTTTTGGTCTTGAGGTATACTAG-AATTAGTGGCG
3530665 C
64 C
3530666 ATAAGCGCCG
Statistics
Matches: 154, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
112 1 0.01
113 68 0.44
114 57 0.37
115 28 0.18
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (114 bp):
CGCCGCAAAATATCCTAACCAAAACGCAAGTTTTGGTCTTGAGGTATACTAGAATTAGTGGCGCT
AAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGCGTTTGGAGAAG
Found at i:3530702 original size:183 final size:184
Alignment explanation
Indices: 3530485--3530848 Score: 518
Period size: 184 Copynumber: 2.0 Consensus size: 184
3530475 GTTTTGTGAG
**
3530485 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGGT
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGAC
* *
3530550 GC-AAAGGGA-ACACGCCGCTAAGGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAAATT
66 GCTAAAGGGAGA-ACGCCGCTAAAGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAAATA
* * ** *
3530613 TCGTAACCAAAACGCAACGTTTTTGTCTTGATGTATACAGTAATTAGTGGCGCAT
130 TAGTAACCAAAACACAACGTTTAAGTCTTGATGTATACAGGAATTAGTGGCGCAT
* * *
3530668 AAGCGCCGCAAAATATGC-TCACCAAAACGCAGAGTTTTGTCTTGAGGTATATTAGAATTAGTGA
1 AAGCGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGA
* * * *
3530732 CGCTTATGGGAGAACGCTGCTAAAGCATACTATTAGCGGCGCGTTTTGAGAAGCGCCGCAAAATA
65 CGCTAAAGGGAGAACGCCGCTAAAGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAAATA
* * *
3530797 TATTAACCAAAACACAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCG
130 TAGTAACCAAAACACAACGTTTAAGTCTTGATGTATACAGGAATTAGTGGCG
3530849 TCCACGAGAA
Statistics
Matches: 159, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
183 60 0.38
184 98 0.62
185 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (184 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAGAATTAGTGAC
GCTAAAGGGAGAACGCCGCTAAAGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAAATAT
AGTAACCAAAACACAACGTTTAAGTCTTGATGTATACAGGAATTAGTGGCGCAT
Found at i:3530795 original size:297 final size:300
Alignment explanation
Indices: 3530373--3530940 Score: 738
Period size: 297 Copynumber: 1.9 Consensus size: 300
3530363 TATGGGAAAA
* * * * *
3530373 CGCCGCAAAATATCCTAACCAAAGCGCACCGTTTTGGTCTTGGTGTATGTTACAGTTAGTGGCGC
1 CGCCGCAAAATATCCTAACCAAAACGCACAGTTTTGGTCTTGGTGTATATTACAATTAGTGACGC
* *
3530438 TTAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGTTTTGTGAGAAGCGCCGCAAAATATCT
66 TTAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGGTTTGTGAGAAGCGCCGCAAAATATAT
* * * *
3530503 TAACCAAAACGCAGAGTTT-GGTCTTGAGGTATACTAGAATTAGTGGTG-CAAAGGGAACA-CGC
131 TAACCAAAACACAGAGTTTAAGTCTTGAGGTATACTAGAATTAGTGGCGTCAAAGAGAA-ATCGC
* * *
3530565 CGCTAAGGCATACTATTAGCGGCGCGTTTGGAGAAGCGCCGCAAAATTTCGTAACCAAAACGCA-
195 CGCTAAAGCATACTATTAGCGGCACGTTTGGAGAAGCGCCGCAAAATATCGTAACCAAAACGCAG
*
3530629 ACGTTTTTGTCTTGATGTATACAGTAATTAGTGGCGCATAAG
260 A-GTTTTGGTCTTGATGTATACAGTAATTAGTGGCGCATAAG
* * * *
3530671 CGCCGCAAAATATGCTCACCAAAACGCAGAGTTTT-GTCTTGAG-GTATATTAGAATTAGTGACG
1 CGCCGCAAAATATCCTAACCAAAACGCACAGTTTTGGTCTTG-GTGTATATTACAATTAGTGACG
* * * *
3530734 CTTATGGGAGA-ACGCTGCTAAAGCATACTATTAGCGGCGCGTTT-TGAGAAGCGCCGCAAAATA
65 CTTAAGGGA-ACACGCCGCTAAAGCATAATATTAGCAGCG-GTTTGTGAGAAGCGCCGCAAAATA
* * * * *
3530797 TATTAACCAAAACACAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGGCGTCCACGAGAAATC
128 TATTAACCAAAACACAGAGTTTAAGTCTTGAGGTATACTAGAATTAGTGGCGTCAAAGAGAAATC
* * * * *
3530862 GCCGCTAAAGCATATTATTAGCGGCACTTTTTGAGAAGCGCCGGAAAATATCTTAACCAAAACGC
193 GCCGCTAAAGCATACTATTAGCGGCACGTTTGGAGAAGCGCCGCAAAATATCGTAACCAAAACGC
3530927 AGAGTTTTGGTCTT
258 AGAGTTTTGGTCTT
3530941 AACCATGCAT
Statistics
Matches: 230, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
297 93 0.40
298 61 0.27
299 75 0.33
300 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (300 bp):
CGCCGCAAAATATCCTAACCAAAACGCACAGTTTTGGTCTTGGTGTATATTACAATTAGTGACGC
TTAAGGGAACACGCCGCTAAAGCATAATATTAGCAGCGGTTTGTGAGAAGCGCCGCAAAATATAT
TAACCAAAACACAGAGTTTAAGTCTTGAGGTATACTAGAATTAGTGGCGTCAAAGAGAAATCGCC
GCTAAAGCATACTATTAGCGGCACGTTTGGAGAAGCGCCGCAAAATATCGTAACCAAAACGCAGA
GTTTTGGTCTTGATGTATACAGTAATTAGTGGCGCATAAG
Found at i:3530940 original size:115 final size:114
Alignment explanation
Indices: 3530668--3530940 Score: 327
Period size: 115 Copynumber: 2.4 Consensus size: 114
3530658 AGTGGCGCAT
* *
3530668 AAGCGCCGCAAAATATGC-TCACCAAAACGCAGAGTTTTGTCTTGAGGTATATTAGAATTAGTGA
1 AAGCGCCGCAAAATAT-CTTAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGA
* * * * *
3530732 CGCTTATGGGAGAACGCTGCTAAAGCATACTATTAGCGGCGCGTTTTGAG
65 CGCTCACGAGAGAACGCCGCTAAAGCATACTATTAGCGGCACGTTTTGAG
* * * * * * *
3530782 AAGCGCCGCAAAATATATTAACCAAAACACAGCGTTTAAGTCTTGATGTATACTGGAATTAGTGG
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTT-TGTCTTGAGGTATACTAGAATTAGTGA
* *
3530847 CG-TCCACGAGA-AATCGCCGCTAAAGCATATTATTAGCGGCACTTTTTGAG
65 CGCT-CACGAGAGAA-CGCCGCTAAAGCATACTATTAGCGGCACGTTTTGAG
*
3530897 AAGCGCCGGAAAATATCTTAACCAAAACGCAGAGTTTTGGTCTT
1 AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTT-GTCTT
3530941 AACCATGCAT
Statistics
Matches: 133, Mismatches: 21, Indels: 9
0.82 0.13 0.06
Matches are distributed among these distances:
114 35 0.26
115 98 0.74
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (114 bp):
AAGCGCCGCAAAATATCTTAACCAAAACGCAGAGTTTTGTCTTGAGGTATACTAGAATTAGTGAC
GCTCACGAGAGAACGCCGCTAAAGCATACTATTAGCGGCACGTTTTGAG
Found at i:3531022 original size:21 final size:21
Alignment explanation
Indices: 3530998--3531037 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3530988 TTTGGTCTAT
*
3530998 GGTTTATGGTTTAAAGGTTGG
1 GGTTTAAGGTTTAAAGGTTGG
*
3531019 GGTTTAAGGTTTAGAGGTT
1 GGTTTAAGGTTTAAAGGTT
3531038 ATGTGTTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAAGGTTTAAAGGTTGG
Found at i:3533871 original size:21 final size:21
Alignment explanation
Indices: 3533845--3533895 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
3533835 CTACAACTTA
*
3533845 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
*
3533866 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
3533887 AAGCAGAGG
1 AAGCAGAGG
3533896 TTCAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.18, G:0.47, T:0.02
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:3534815 original size:116 final size:117
Alignment explanation
Indices: 3534609--3534853 Score: 339
Period size: 116 Copynumber: 2.1 Consensus size: 117
3534599 TTTGGTGTAG
* ** * * *
3534609 TGAGTCCGAAATTGAGAACTAGTAAGATGCATTCCTTCAACTGTTGCTCTTCTAAACAGTTTCAC
1 TGAGTCCAAAATTGAGAACTAGTAAGACACATTCCCTCAACTGATGCTCTTCTAAACAGTCTCAC
** * * *
3534674 TAGTGAAAATGCGGTGAGATAGAGAATAAATTGTATTGATGGCCTTAAATCC
66 TAGTGAAAATAAGGTGAGATAGAGAATAAATTGTACTGATGCCCTTAAACCC
* * *
3534726 TGAGTCCAAAATTGAGAACTGGTGAGACACGTTCCCTCAACTGATGCTCTTC-AAACAGTCTCAC
1 TGAGTCCAAAATTGAGAACTAGTAAGACACATTCCCTCAACTGATGCTCTTCTAAACAGTCTCAC
* *
3534790 TAGTGAAAATAAGGTGAGATGGAGAATAAATTGTACTGATGCCCTTTAACCC
66 TAGTGAAAATAAGGTGAGATAGAGAATAAATTGTACTGATGCCCTTAAACCC
3534842 TGAGTCCAAAAT
1 TGAGTCCAAAAT
3534854 AAAAGTCAAC
Statistics
Matches: 112, Mismatches: 16, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
116 68 0.61
117 44 0.39
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (117 bp):
TGAGTCCAAAATTGAGAACTAGTAAGACACATTCCCTCAACTGATGCTCTTCTAAACAGTCTCAC
TAGTGAAAATAAGGTGAGATAGAGAATAAATTGTACTGATGCCCTTAAACCC
Found at i:3544561 original size:9 final size:9
Alignment explanation
Indices: 3544549--3544730 Score: 74
Period size: 9 Copynumber: 19.8 Consensus size: 9
3544539 TTTTGGATTT
3544549 TTTTTATAA
1 TTTTTATAA
3544558 TTTTTATAA
1 TTTTTATAA
3544567 GTTTTTA-AGA
1 -TTTTTATA-A
3544577 TTTTTTTATAAA
1 --TTTTTAT-AA
* *
3544589 ATTTTAAATA
1 TTTTTATA-A
3544599 TATTTTATTAA
1 T-TTTTA-TAA
*
3544610 -TTTTATTA
1 TTTTTATAA
3544618 TTTTT-TAA
1 TTTTTATAA
*
3544626 --TATAT-A
1 TTTTTATAA
* *
3544632 TTTTTAGAT
1 TTTTTATAA
3544641 TTTTTATAA
1 TTTTTATAA
**
3544650 TACTTATAA
1 TTTTTATAA
* *
3544659 GTTATTATTA
1 -TTTTTATAA
*
3544669 TTGTTATAA
1 TTTTTATAA
3544678 TTTTTATAA
1 TTTTTATAA
*
3544687 GTTTATT-CAA
1 -TTT-TTATAA
*
3544697 TTTTAAT-A
1 TTTTTATAA
*
3544705 TATTTATAA
1 TTTTTATAA
3544714 TTTTTTATAA
1 -TTTTTATAA
3544724 TTTTTAT
1 TTTTTAT
3544731 GAGAAAATAT
Statistics
Matches: 127, Mismatches: 27, Indels: 38
0.66 0.14 0.20
Matches are distributed among these distances:
6 3 0.02
7 1 0.01
8 14 0.11
9 60 0.47
10 32 0.25
11 14 0.11
12 2 0.02
13 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:3544571 original size:19 final size:18
Alignment explanation
Indices: 3544549--3544730 Score: 74
Period size: 19 Copynumber: 9.9 Consensus size: 18
3544539 TTTTGGATTT
3544549 TTTTTATAATTTTTATAA
1 TTTTTATAATTTTTATAA
3544567 GTTTTTA-AGATTTTTTTATAAA
1 -TTTTTATA-A--TTTTTAT-AA
* *
3544589 ATTTTAAATATATTTTATTAA
1 TTTTTATA-AT-TTTTA-TAA
*
3544610 -TTTTATTATTTTT-TAA
1 TTTTTATAATTTTTATAA
* * *
3544626 --TATAT-ATTTTTAGAT
1 TTTTTATAATTTTTATAA
**
3544641 TTTTTATAATACTTATAA
1 TTTTTATAATTTTTATAA
* * *
3544659 GTTATTATTATTGTTATAA
1 -TTTTTATAATTTTTATAA
*
3544678 TTTTTATAAGTTTATT-CAA
1 TTTTTATAA-TTT-TTATAA
* *
3544697 TTTTAAT-ATATTTATAA
1 TTTTTATAATTTTTATAA
3544714 TTTTTTATAATTTTTAT
1 -TTTTTATAATTTTTAT
3544731 GAGAAAATAT
Statistics
Matches: 121, Mismatches: 25, Indels: 34
0.67 0.14 0.19
Matches are distributed among these distances:
14 6 0.05
15 5 0.04
16 5 0.04
17 8 0.07
18 25 0.21
19 40 0.33
20 8 0.07
21 19 0.16
22 5 0.04
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTTATAATTTTTATAA
Found at i:3544593 original size:21 final size:21
Alignment explanation
Indices: 3544558--3544649 Score: 64
Period size: 21 Copynumber: 4.4 Consensus size: 21
3544548 TTTTTTATAA
**
3544558 TTTTTATAAGTTTTTAAGATT
1 TTTTTATAAAATTTTAAGATT
3544579 TTTTTATAAAATTTTAA-ATAT
1 TTTTTATAAAATTTTAAGAT-T
* * **
3544600 ATTTTAT-TAATTTTATTATT
1 TTTTTATAAAATTTTAAGATT
* * *
3544620 TTTTAATATATATTTTTAGA-T
1 TTTTTATA-AAATTTTAAGATT
3544641 TTTTTATAA
1 TTTTTATAA
3544650 TACTTATAAG
Statistics
Matches: 54, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
20 16 0.30
21 32 0.59
22 6 0.11
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (21 bp):
TTTTTATAAAATTTTAAGATT
Found at i:3544633 original size:14 final size:14
Alignment explanation
Indices: 3544590--3544636 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
3544580 TTTTATAAAA
3544590 TTTTAA-ATATATT
1 TTTTAATATATATT
*
3544603 TTATTAATTTTATTATT
1 TT-TTAA-TATA-TATT
3544620 TTTTAATATATATT
1 TTTTAATATATATT
3544634 TTT
1 TTT
3544637 AGATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 3 0.11
16 6 0.21
17 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTTAATATATATT
Found at i:3550898 original size:18 final size:19
Alignment explanation
Indices: 3550872--3550915 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
3550862 AATATCGATA
*
3550872 AAATCGAGTTAATTC-ATC
1 AAATCGAGTCAATTCAATC
*
3550890 AAATTGAGTCAATTCAATC
1 AAATCGAGTCAATTCAATC
3550909 AAATCGA
1 AAATCGA
3550916 ATCAGTTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (19 bp):
AAATCGAGTCAATTCAATC
Found at i:3551224 original size:13 final size:13
Alignment explanation
Indices: 3551206--3551232 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3551196 ACTATCAGGA
3551206 TATTTACATCAAT
1 TATTTACATCAAT
3551219 TATTTACATCAAT
1 TATTTACATCAAT
3551232 T
1 T
3551233 TGTTATTCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTACATCAAT
Found at i:3561745 original size:12 final size:12
Alignment explanation
Indices: 3561724--3561753 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3561714 AAATAAACTC
*
3561724 AAATATTAATTA
1 AAATAATAATTA
3561736 AAATAATAATTA
1 AAATAATAATTA
3561748 AAATAA
1 AAATAA
3561754 ATTATAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATAATAATTA
Found at i:3568234 original size:18 final size:21
Alignment explanation
Indices: 3568203--3568250 Score: 75
Period size: 19 Copynumber: 2.4 Consensus size: 21
3568193 TTTGCCAGTC
3568203 GAAAGAGAGAAAGAAGAA-GA
1 GAAAGAGAGAAAGAAGAAGGA
3568223 -AAAGAGAG-AAGAAGAAGGA
1 GAAAGAGAGAAAGAAGAAGGA
3568242 GAAAGAGAG
1 GAAAGAGAG
3568251 GGCGGGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.31
19 10 0.38
20 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (21 bp):
GAAAGAGAGAAAGAAGAAGGA
Found at i:3568237 original size:21 final size:18
Alignment explanation
Indices: 3568203--3568250 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 18
3568193 TTTGCCAGTC
3568203 GAAAGAGAGAAAGAAGAA
1 GAAAGAGAGAAAGAAGAA
*
3568221 GAAAAGAGAGAAGAAGAAGGA
1 G-AAAGAGAG-A-AAGAAGAA
3568242 GAAAGAGAG
1 GAAAGAGAG
3568251 GGCGGGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 8 0.31
20 9 0.35
21 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (18 bp):
GAAAGAGAGAAAGAAGAA
Found at i:3569600 original size:2 final size:2
Alignment explanation
Indices: 3569593--3569632 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3569583 GGTATGTTAT
3569593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3569633 TTTAAACCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3570036 original size:11 final size:11
Alignment explanation
Indices: 3570009--3570099 Score: 59
Period size: 11 Copynumber: 8.5 Consensus size: 11
3569999 ATTAATCCTT
*
3570009 TCTCAATTATTC
1 TCTCAATT-TCC
3570021 TCTCAATTTCC
1 TCTCAATTTCC
*
3570032 TCTCAATTTGC
1 TCTCAATTTCC
*
3570043 TATCAATTTCC
1 TCTCAATTTCC
3570054 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
3570065 TCTCAA-ATCC
1 TCTCAATTTCC
* *
3570075 -AT--ATTTGC
1 TCTCAATTTCC
3570083 TCTCAATTTCC
1 TCTCAATTTCC
3570094 TCTCAA
1 TCTCAA
3570100 ATTTATCTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 17
0.69 0.11 0.19
Matches are distributed among these distances:
7 1 0.02
8 2 0.03
9 3 0.05
10 4 0.07
11 37 0.61
12 14 0.23
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:3570051 original size:22 final size:23
Alignment explanation
Indices: 3570009--3570054 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
3569999 ATTAATCCTT
* *
3570009 TCTCAATTATTCTCTCAATTTCC
1 TCTCAATTATGCTATCAATTTCC
3570032 TCTCAATT-TGCTATCAATTTCC
1 TCTCAATTATGCTATCAATTTCC
3570054 T
1 T
3570055 TCCAAATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.22, C:0.28, G:0.02, T:0.48
Consensus pattern (23 bp):
TCTCAATTATGCTATCAATTTCC
Found at i:3570070 original size:22 final size:21
Alignment explanation
Indices: 3570009--3570099 Score: 66
Period size: 22 Copynumber: 4.3 Consensus size: 21
3569999 ATTAATCCTT
3570009 TCTCAATTATTCTCTCAATTTCC
1 TCTCAA-T-TTCTCTCAATTTCC
*
3570032 TCTCAATTTGCTATCAATTTCC
1 TCTCAATTT-CTCTCAATTTCC
*
3570054 T-TCCAAATTTCTCTCAA-ATCC
1 TCT-C-AATTTCTCTCAATTTCC
*
3570075 -AT--ATTTGCTCTCAATTTCC
1 TCTCAATTT-CTCTCAATTTCC
3570094 TCTCAA
1 TCTCAA
3570100 ATTTATCTTA
Statistics
Matches: 54, Mismatches: 5, Indels: 19
0.69 0.06 0.24
Matches are distributed among these distances:
17 4 0.07
18 7 0.13
19 3 0.06
20 1 0.02
21 7 0.13
22 21 0.39
23 11 0.20
ACGTcount: A:0.24, C:0.30, G:0.02, T:0.44
Consensus pattern (21 bp):
TCTCAATTTCTCTCAATTTCC
Found at i:3570080 original size:17 final size:18
Alignment explanation
Indices: 3570055--3570088 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3570045 TCAATTTCCT
3570055 TCCAAATTT-CTCTCAAA
1 TCCAAATTTGCTCTCAAA
*
3570072 TCCATATTTGCTCTCAA
1 TCCAAATTTGCTCTCAA
3570089 TTTCCTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.29, G:0.03, T:0.38
Consensus pattern (18 bp):
TCCAAATTTGCTCTCAAA
Found at i:3570089 original size:40 final size:40
Alignment explanation
Indices: 3570037--3570120 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 40
3570027 TTTCCTCTCA
*
3570037 ATTTGCTATCAATTTCCT-TCCAAATTTCTCTCAAATCCAT
1 ATTTGCTATCAATTTCCTCT-CAAATTTATCTCAAATCCAT
* * *
3570077 ATTTGCTCTCAATTTCCTCTCAAATTTATCTTAAATCCCT
1 ATTTGCTATCAATTTCCTCTCAAATTTATCTCAAATCCAT
3570117 ATTT
1 ATTT
3570121 TTAATTATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 38 0.97
41 1 0.03
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.45
Consensus pattern (40 bp):
ATTTGCTATCAATTTCCTCTCAAATTTATCTCAAATCCAT
Found at i:3571279 original size:7 final size:7
Alignment explanation
Indices: 3571267--3571292 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
3571257 TAGTCGATTG
3571267 GTATTTA
1 GTATTTA
3571274 GTATTTA
1 GTATTTA
3571281 GTATTTA
1 GTATTTA
3571288 GTATT
1 GTATT
3571293 ATATATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:3571982 original size:18 final size:18
Alignment explanation
Indices: 3571941--3571975 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3571931 GCCAGGTGCG
*
3571941 TATCCTAACCCTTTTATA
1 TATCCTAACCCTTATATA
3571959 TATCCTAACCCTTATAT
1 TATCCTAACCCTTATAT
3571976 GTTTCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (18 bp):
TATCCTAACCCTTATATA
Found at i:3572485 original size:34 final size:33
Alignment explanation
Indices: 3572411--3572505 Score: 85
Period size: 34 Copynumber: 2.9 Consensus size: 33
3572401 ATTTTGATCT
* *
3572411 TATTTAATGTAATAAAATAGAAA-TTCTTTTATA
1 TATTTTATGT-ATAAAATAGAAATTTCTTTTACA
3572444 TTATTTTATGTACTAAAATAGAAATTTACTTTTACA
1 -TATTTTATGTA-TAAAATAGAAATTT-CTTTTACA
*
3572480 -CTTTTA---ATAAAATAGAAA-TTCTTTTA
1 TATTTTATGTATAAAATAGAAATTTCTTTTA
3572506 AATAAGGCAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
28 6 0.11
29 2 0.04
30 11 0.20
31 1 0.02
33 1 0.02
34 25 0.45
35 2 0.04
36 7 0.13
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.46
Consensus pattern (33 bp):
TATTTTATGTATAAAATAGAAATTTCTTTTACA
Found at i:3576234 original size:26 final size:27
Alignment explanation
Indices: 3576198--3576256 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 27
3576188 TAAATAAATA
3576198 TTTTTATTC-TTTAATTTTAAAATATT
1 TTTTTATTCTTTTAATTTTAAAATATT
*
3576224 TTTTTATTCTTTTTATTTTTAAAATATT
1 TTTTTATTC-TTTTAATTTTAAAATATT
3576252 TTTTT
1 TTTTT
3576257 GTGTTTATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 9 0.30
28 21 0.70
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (27 bp):
TTTTTATTCTTTTAATTTTAAAATATT
Found at i:3578003 original size:14 final size:14
Alignment explanation
Indices: 3577984--3578018 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3577974 TGACTTTTTT
*
3577984 TTCTAATGATACTA
1 TTCTAACGATACTA
3577998 TTCTAACGATACTA
1 TTCTAACGATACTA
3578012 TTCTAAC
1 TTCTAAC
3578019 ATGTAATTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:3579052 original size:49 final size:48
Alignment explanation
Indices: 3578980--3579098 Score: 175
Period size: 49 Copynumber: 2.5 Consensus size: 48
3578970 TTATTTATTT
* * **
3578980 AATTAGATTAATTGCAACATTAAAACTTGGAATAAACTTTGTGGTCACA
1 AATTAGATTAATTGCAACATTAAAACTTGAAACAAACTTTGTAAT-ACA
* *
3579029 AATTAGATTATTTGCAACATTAAAACTTGAAACAAACTTTGTAATATA
1 AATTAGATTAATTGCAACATTAAAACTTGAAACAAACTTTGTAATACA
3579077 AATTAGATTAATTGCAACATTA
1 AATTAGATTAATTGCAACATTA
3579099 CAATATTACA
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
48 23 0.37
49 40 0.63
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (48 bp):
AATTAGATTAATTGCAACATTAAAACTTGAAACAAACTTTGTAATACA
Done.