Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 21 of 198
Found at i:6112901 original size:20 final size:21
Alignment explanation
Indices: 6112880--6112920 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
6112870 AGTTTTTCTG
6112880 AAAAA-TTATAGAATTTTATGA
1 AAAAATTTA-AGAATTTTATGA
6112901 AAAAATTTAAGAATTTTATG
1 AAAAATTTAAGAATTTTATG
6112921 TTTTTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (21 bp):
AAAAATTTAAGAATTTTATGA
Found at i:6128541 original size:23 final size:23
Alignment explanation
Indices: 6128497--6128541 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
6128487 TCTTATTTTG
* *
6128497 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
6128520 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
6128542 CAAAAATCCT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:6128903 original size:36 final size:37
Alignment explanation
Indices: 6128828--6128903 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 37
6128818 CATACATACG
* *
6128828 TTTTATAATATATACATATACATACACATTTTTTAAT
1 TTTTATAATATATACATATACACACACATTTTATAAT
* *
6128865 TTTTATAA-ATATATATATACACATAC-TTTTATATAT
1 TTTTATAATATATACATATACACACACATTTTATA-AT
6128901 TTT
1 TTT
6128904 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 6 0.18
36 20 0.59
37 8 0.24
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTTATAATATATACATATACACACACATTTTATAAT
Found at i:6130699 original size:18 final size:19
Alignment explanation
Indices: 6130653--6130699 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 19
6130643 CAATAAAACA
6130653 TTTCTTCATATGTATAATT
1 TTTCTTCATATGTATAATT
* *
6130672 TTT-TTTATATTTAT-ATT
1 TTTCTTCATATGTATAATT
6130689 TTTCTTCATAT
1 TTTCTTCATAT
6130700 AACTTTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 6 0.25
18 15 0.62
19 3 0.12
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTCTTCATATGTATAATT
Found at i:6130897 original size:30 final size:29
Alignment explanation
Indices: 6130863--6130953 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 29
6130853 CCACCACTAT
6130863 CTCCATGTCCACCACTGCCACCATGTCCTC
1 CTCCATG-CCACCACTGCCACCATGTCCTC
* * * *
6130893 CTCCACCGCCACCACTGCCTCCTTTTCCTC
1 CTCCA-TGCCACCACTGCCACCATGTCCTC
* * * *
6130923 CACCATGCCCGCCACTACCGCCATGTCCTC
1 CTCCATG-CCACCACTGCCACCATGTCCTC
6130953 C
1 C
6130954 ACTACCACTA
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
29 1 0.02
30 46 0.96
31 1 0.02
ACGTcount: A:0.14, C:0.54, G:0.10, T:0.22
Consensus pattern (29 bp):
CTCCATGCCACCACTGCCACCATGTCCTC
Found at i:6130903 original size:21 final size:21
Alignment explanation
Indices: 6130874--6130915 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6130864 TCCATGTCCA
*
6130874 CCACTGCCACCA-TGTCCTCCT
1 CCACCGCCACCACTG-CCTCCT
6130895 CCACCGCCACCACTGCCTCCT
1 CCACCGCCACCACTGCCTCCT
6130916 TTTCCTCCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.14, C:0.57, G:0.10, T:0.19
Consensus pattern (21 bp):
CCACCGCCACCACTGCCTCCT
Found at i:6132722 original size:21 final size:21
Alignment explanation
Indices: 6132698--6132753 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
6132688 TCCACCATGC
*
6132698 CCACCACTGCCTCCACCACTA
1 CCACCACTGCCTCCACCACCA
*
6132719 CCACCA-TGTCCTCCGCCACCA
1 CCACCACTG-CCTCCACCACCA
*
6132740 CCACCACTACCTCC
1 CCACCACTGCCTCC
6132754 CTGCCCTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.21, C:0.59, G:0.05, T:0.14
Consensus pattern (21 bp):
CCACCACTGCCTCCACCACCA
Found at i:6132792 original size:72 final size:72
Alignment explanation
Indices: 6132671--6132868 Score: 315
Period size: 72 Copynumber: 2.8 Consensus size: 72
6132661 CCATGTTCCG
* * * *
6132671 CCACTGCCTCTCTGTCCTCCACCATGCCCACCACTGCCTCCACCACTACCACCATGTCCTCCGCC
1 CCACTACCTCCCTGTCCTCCACCATGCCCACCACTGCCGCCACCACTACCACCATGACCTCCGCC
6132736 ACCACCA
66 ACCACCA
* *
6132743 CCACTACCTCCCTGCCCTCCACCATGCCCACCACTGCCGCCACCGCTACCACCATGACCTCCGCC
1 CCACTACCTCCCTGTCCTCCACCATGCCCACCACTGCCGCCACCACTACCACCATGACCTCCGCC
6132808 ACCACCA
66 ACCACCA
* * *
6132815 CCACTACCTCCTTGTCCTCCACCATGCCCACCACTACCGCCACCACTACTACCA
1 CCACTACCTCCCTGTCCTCCACCATGCCCACCACTGCCGCCACCACTACCACCA
6132869 CCACCATGTC
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 115 1.00
ACGTcount: A:0.20, C:0.56, G:0.08, T:0.16
Consensus pattern (72 bp):
CCACTACCTCCCTGTCCTCCACCATGCCCACCACTGCCGCCACCACTACCACCATGACCTCCGCC
ACCACCA
Found at i:6132897 original size:66 final size:66
Alignment explanation
Indices: 6132827--6132987 Score: 279
Period size: 66 Copynumber: 2.4 Consensus size: 66
6132817 ACTACCTCCT
*
6132827 TGTCCTCCACCATGC-CCACCACTACCGCCACCACTACTACCACCACCATGTCCGCCACTGCCAC
1 TGTCCTCCACCA-CCACCACCACTACCGCCACCACTACTACCACCACCATGTCCGCCACTGCCAC
6132891 CA
65 CA
* *
6132893 TGTCCTCCGCCACCACCGCCACTACCGCCACCACTACTACCACCACCATGTCCGCCACTGCCACC
1 TGTCCTCCACCACCACCACCACTACCGCCACCACTACTACCACCACCATGTCCGCCACTGCCACC
6132958 A
66 A
6132959 TGTCCTCCACCACCACCACCACTACCGCC
1 TGTCCTCCACCACCACCACCACTACCGCC
6132988 TTGTCCTCCA
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
65 1 0.01
66 88 0.99
ACGTcount: A:0.22, C:0.55, G:0.09, T:0.14
Consensus pattern (66 bp):
TGTCCTCCACCACCACCACCACTACCGCCACCACTACTACCACCACCATGTCCGCCACTGCCACC
A
Found at i:6132923 original size:15 final size:15
Alignment explanation
Indices: 6132902--6132940 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6132892 ATGTCCTCCG
*
6132902 CCACCACCGCCACTA
1 CCACCACCACCACTA
* *
6132917 CCGCCACCACTACTA
1 CCACCACCACCACTA
6132932 CCACCACCA
1 CCACCACCA
6132941 TGTCCGCCAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.28, C:0.59, G:0.05, T:0.08
Consensus pattern (15 bp):
CCACCACCACCACTA
Found at i:6132974 original size:18 final size:18
Alignment explanation
Indices: 6132865--6132976 Score: 74
Period size: 18 Copynumber: 6.6 Consensus size: 18
6132855 CACCACTACT
*
6132865 ACCACCACCATGTCCGCC
1 ACCACCACCATGTCCTCC
**
6132883 ACTGCCACCATGTCCTCC
1 ACCACCACCATGTCCTCC
* * *
6132901 GCCACCACC--G-CCACT
1 ACCACCACCATGTCCTCC
* * *
6132916 ACCGCCACCA-CTACT--
1 ACCACCACCATGTCCTCC
*
6132931 ACCACCACCATGTCCGCC
1 ACCACCACCATGTCCTCC
**
6132949 ACTGCCACCATGTCCTCC
1 ACCACCACCATGTCCTCC
6132967 ACCACCACCA
1 ACCACCACCA
6132977 CCACTACCGC
Statistics
Matches: 67, Mismatches: 22, Indels: 10
0.68 0.22 0.10
Matches are distributed among these distances:
15 19 0.28
16 3 0.04
17 1 0.01
18 44 0.66
ACGTcount: A:0.22, C:0.54, G:0.10, T:0.13
Consensus pattern (18 bp):
ACCACCACCATGTCCTCC
Found at i:6133017 original size:30 final size:30
Alignment explanation
Indices: 6132794--6133018 Score: 94
Period size: 30 Copynumber: 7.1 Consensus size: 30
6132784 ACCGCTACCA
* * * *
6132794 CCATGACCTCCGCCACCACCACCACTACCT
1 CCATGTCCTCCACCACCACCACCACTGCCG
* * *
6132824 CCTTGTCCTCCACCATGC-CCACCACTACCG
1 CCATGTCCTCCACCA-CCACCACCACTGCCG
** * * *
6132854 CCACCACTACTACCACCACCATGTCCGCCACTGCCA
1 CCA--TGTCCT-CCACCACCA---CCACCACTGCCG
* * *
6132890 CCATGTCCTCCGCCACCACCGCCACTACCG
1 CCATGTCCTCCACCACCACCACCACTGCCG
** * * *
6132920 CCACCACTACTACCACCACCATGTCCGCCACTGCCA
1 CCA--TGTCCT-CCACCACCA---CCACCACTGCCG
*
6132956 CCATGTCCTCCACCACCACCACCACTACCG
1 CCATGTCCTCCACCACCACCACCACTGCCG
* * *
6132986 CCTTGTCCTCCACCATGC-CTACCACTGCCG
1 CCATGTCCTCCACCA-CCACCACCACTGCCG
6133016 CCA
1 CCA
6133019 CCGCTACCAC
Statistics
Matches: 144, Mismatches: 36, Indels: 30
0.69 0.17 0.14
Matches are distributed among these distances:
30 73 0.51
31 2 0.01
32 7 0.05
33 31 0.22
34 6 0.04
36 25 0.17
ACGTcount: A:0.21, C:0.54, G:0.09, T:0.16
Consensus pattern (30 bp):
CCATGTCCTCCACCACCACCACCACTGCCG
Found at i:6133032 original size:72 final size:72
Alignment explanation
Indices: 6132953--6133234 Score: 363
Period size: 72 Copynumber: 4.1 Consensus size: 72
6132943 TCCGCCACTG
* * *
6132953 CCACCATGTCCTCCACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCTACCACTGCCGCC
1 CCACCATGACCTCCACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCCACCACTACCGCC
6133018 ACCGCTA
66 ACCGCTA
* * * *
6133025 CCACCATGACCTCCGCCACCACCACCACTACCTCCTTGCCCTCCACCATGCCCGCCACTACCGCC
1 CCACCATGACCTCCACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCCACCACTACCGCC
6133090 ACCG---
66 ACCGCTA
*
6133094 ----C-T-A-CT--ACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCCACCACTGCCGCC
1 CCACCATGACCTCCACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCCACCACTACCGCC
6133150 ACCGCTA
66 ACCGCTA
* * *
6133157 CCACCATGACCTCCGCCACCACCGCCACTACCTCCTTGTCCTCCACCATGCCCACCACTACCGCC
1 CCACCATGACCTCCACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCCACCACTACCGCC
*
6133222 ACCACTA
66 ACCGCTA
*
6133229 CTACCA
1 CCACCA
6133235 CCACCATGTC
Statistics
Matches: 180, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
60 50 0.28
62 2 0.01
63 1 0.01
64 1 0.01
65 1 0.01
67 1 0.01
68 1 0.01
69 1 0.01
70 2 0.01
72 120 0.67
ACGTcount: A:0.20, C:0.55, G:0.09, T:0.15
Consensus pattern (72 bp):
CCACCATGACCTCCACCACCACCACCACTACCGCCTTGTCCTCCACCATGCCCACCACTACCGCC
ACCGCTA
Found at i:6133080 original size:132 final size:132
Alignment explanation
Indices: 6132935--6133240 Score: 472
Period size: 132 Copynumber: 2.3 Consensus size: 132
6132925 ACTACTACCA
* * *
6132935 CCACCATGTCCGCCACTGCCACCA-TGTCCT-CCACCACCACCACCACTACCGCCTTGTCCTCCA
1 CCACCATGCCCGCCACTACCACCACCG--CTACCACCACCACCACCACTACCGCCTTGTCCTCCA
*
6132998 CCATGCCTACCACTGCCGCCACCGCTACCACCATGACCTCCGCCACCACCACCACTACCTCCTTG
64 CCATGCCCACCACTGCCGCCACCGCTACCACCATGACCTCCGCCACCACCACCACTACCTCCTTG
6133063 CCCT
129 CCCT
* *
6133067 CCACCATGCCCGCCACTACCGCCACCGCTACTACCACCACCACCACTACCGCCTTGTCCTCCACC
1 CCACCATGCCCGCCACTACCACCACCGCTACCACCACCACCACCACTACCGCCTTGTCCTCCACC
* *
6133132 ATGCCCACCACTGCCGCCACCGCTACCACCATGACCTCCGCCACCACCGCCACTACCTCCTTGTC
66 ATGCCCACCACTGCCGCCACCGCTACCACCATGACCTCCGCCACCACCACCACTACCTCCTTGCC
6133197 CT
131 CT
* * * *
6133199 CCACCATGCCCACCACTACCGCCACCACTACTACCACCACCA
1 CCACCATGCCCGCCACTACCACCACCGCTACCACCACCACCA
6133241 TGTCCGCCAC
Statistics
Matches: 162, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
131 2 0.01
132 159 0.98
133 1 0.01
ACGTcount: A:0.20, C:0.55, G:0.09, T:0.15
Consensus pattern (132 bp):
CCACCATGCCCGCCACTACCACCACCGCTACCACCACCACCACCACTACCGCCTTGTCCTCCACC
ATGCCCACCACTGCCGCCACCGCTACCACCATGACCTCCGCCACCACCACCACTACCTCCTTGCC
CT
Found at i:6133099 original size:15 final size:15
Alignment explanation
Indices: 6133076--6133119 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
6133066 TCCACCATGC
6133076 CCGCCACTACCGCCA
1 CCGCCACTACCGCCA
* *
6133091 CCGCTACTACCACCA
1 CCGCCACTACCGCCA
*
6133106 CCACCACTACCGCC
1 CCGCCACTACCGCC
6133120 TTGTCCTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.23, C:0.59, G:0.09, T:0.09
Consensus pattern (15 bp):
CCGCCACTACCGCCA
Found at i:6133140 original size:30 final size:30
Alignment explanation
Indices: 6133046--6133149 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
6133036 TCCGCCACCA
* *
6133046 CCACCACTACCTCCTTGCCCTCCACCATGC
1 CCACCACTACCGCCTTGTCCTCCACCATGC
* ** *
6133076 CCGCCACTACCGCCACCGCTACTACCACCA---
1 CCACCACTACCGCC-TTG-TCCT-CCACCATGC
6133106 CCACCACTACCGCCTTGTCCTCCACCATGC
1 CCACCACTACCGCCTTGTCCTCCACCATGC
*
6133136 CCACCACTGCCGCC
1 CCACCACTACCGCC
6133150 ACCGCTACCA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
27 6 0.11
28 3 0.05
29 1 0.02
30 38 0.67
31 1 0.02
32 2 0.04
33 6 0.11
ACGTcount: A:0.18, C:0.57, G:0.10, T:0.15
Consensus pattern (30 bp):
CCACCACTACCGCCTTGTCCTCCACCATGC
Found at i:6133161 original size:30 final size:30
Alignment explanation
Indices: 6133067--6133164 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 30
6133057 TCCTTGCCCT
*
6133067 CCACCATGCCCGCCACTACCGCCACCGCTA
1 CCACCATGCCCACCACTACCGCCACCGCTA
* * **
6133097 CTACCA-CCACCACCACTACCGCC-TTGTCCT-
1 CCACCATGC-CCACCACTACCGCCACCG--CTA
*
6133127 CCACCATGCCCACCACTGCCGCCACCGCTA
1 CCACCATGCCCACCACTACCGCCACCGCTA
6133157 CCACCATG
1 CCACCATG
6133165 ACCTCCGCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
29 4 0.08
30 44 0.85
31 4 0.08
ACGTcount: A:0.20, C:0.55, G:0.11, T:0.13
Consensus pattern (30 bp):
CCACCATGCCCACCACTACCGCCACCGCTA
Found at i:6133305 original size:42 final size:42
Alignment explanation
Indices: 6133253--6133338 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
6133243 TCCGCCACTG
* ** *
6133253 CCACCATGTCCTCTGCCACCACCGCCACTACCGCCTTGTCCT
1 CCACCATGTCCACCACCACCACCGCCACTACCGCCATGTCCT
* *
6133295 CCACCATGTCCACCACTACCGCCGCCACTACCGCCATGTCCT
1 CCACCATGTCCACCACCACCACCGCCACTACCGCCATGTCCT
6133337 CC
1 CC
6133339 GCCACCACTA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.16, C:0.53, G:0.12, T:0.19
Consensus pattern (42 bp):
CCACCATGTCCACCACCACCACCGCCACTACCGCCATGTCCT
Found at i:6133311 original size:30 final size:30
Alignment explanation
Indices: 6133181--6133317 Score: 85
Period size: 30 Copynumber: 4.4 Consensus size: 30
6133171 GCCACCACCG
* *
6133181 CCACTACCTCCTTGTCCTCCACCATGCCCA
1 CCACTACCGCCTTGTCCTCCACCATGTCCA
** * *
6133211 CCACTACCGCCACCACTACTACCACCACCATGTCCG
1 CCACTACCG----C-CTTGT-CCTCCACCATGTCCA
* * * ** *** *
6133247 CCACTGCCACCATGTCCTCTGCCACCACCG
1 CCACTACCGCCTTGTCCTCCACCATGTCCA
6133277 CCACTACCGCCTTGTCCTCCACCATGTCCA
1 CCACTACCGCCTTGTCCTCCACCATGTCCA
6133307 CCACTACCGCC
1 CCACTACCGCC
6133318 GCCACTACCG
Statistics
Matches: 75, Mismatches: 26, Indels: 12
0.66 0.23 0.11
Matches are distributed among these distances:
30 49 0.65
31 2 0.03
32 1 0.01
34 1 0.01
35 3 0.04
36 19 0.25
ACGTcount: A:0.19, C:0.53, G:0.09, T:0.18
Consensus pattern (30 bp):
CCACTACCGCCTTGTCCTCCACCATGTCCA
Found at i:6133320 original size:72 final size:70
Alignment explanation
Indices: 6133244--6133455 Score: 204
Period size: 72 Copynumber: 3.0 Consensus size: 70
6133234 ACCACCATGT
* *
6133244 CCGCCACTGCCACCATGTCCTCTGCCACCACCGCCACTACCGCCTTGTCCTCCACCATGTCCACC
1 CCGCCACTACCACCATGTCCTCT-CCACCACC-CCACTACCACCTTGTCCTCCACCATGTCCACC
6133309 ACTACCG
64 ACTACCG
* * * *
6133316 CCGCCACTACCGCCATGT-C-CTCCGCCA--CCACTACCACCCTGTCCTCCGCC-TCCG-CCACC
1 CCGCCACTACCACCATGTCCTCTCCACCACCCCACTACCACCTTGTCCTCCACCAT--GTCCACC
* *
6133375 ACTTCCA
64 ACTACCG
* * *
6133382 CCGCCACTACCAGCGTGTCCTC-CACTTCCACCACCACTACCACCTTGTCCTCCACCATGTCCAC
1 CCGCCACTACCACCATGTCCTCTC-C-ACCACC-CCACTACCACCTTGTCCTCCACCATGTCCAC
*
6133446 CACTGCCG
63 CACTACCG
6133454 CC
1 CC
6133456 TTGTCCTCCG
Statistics
Matches: 113, Mismatches: 16, Indels: 22
0.75 0.11 0.15
Matches are distributed among these distances:
65 1 0.01
66 45 0.40
67 3 0.03
68 2 0.02
69 8 0.07
70 2 0.02
71 2 0.02
72 49 0.43
73 1 0.01
ACGTcount: A:0.17, C:0.54, G:0.11, T:0.18
Consensus pattern (70 bp):
CCGCCACTACCACCATGTCCTCTCCACCACCCCACTACCACCTTGTCCTCCACCATGTCCACCAC
TACCG
Found at i:6133340 original size:24 final size:24
Alignment explanation
Indices: 6133313--6133365 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
6133303 TCCACCACTA
* *
6133313 CCGCCGCCACTACCGCCATGTCCT
1 CCGCCACCACTACCACCATGTCCT
*
6133337 CCGCCACCACTACCACCCTGTCCT
1 CCGCCACCACTACCACCATGTCCT
6133361 CCGCC
1 CCGCC
6133366 TCCGCCACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.58, G:0.13, T:0.15
Consensus pattern (24 bp):
CCGCCACCACTACCACCATGTCCT
Found at i:6133375 original size:24 final size:24
Alignment explanation
Indices: 6133313--6133376 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 24
6133303 TCCACCACTA
* * * *
6133313 CCGCCGCCACTACCGCCATGTCCT
1 CCGCCACCACCACCACCCTGTCCT
*
6133337 CCGCCACCACTACCACCCTGTCCT
1 CCGCCACCACCACCACCCTGTCCT
* *
6133361 CCGCCTCCGCCACCAC
1 CCGCCACCACCACCAC
6133377 TTCCACCGCC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.59, G:0.12, T:0.14
Consensus pattern (24 bp):
CCGCCACCACCACCACCCTGTCCT
Found at i:6133377 original size:96 final size:93
Alignment explanation
Indices: 6133136--6133365 Score: 280
Period size: 96 Copynumber: 2.4 Consensus size: 93
6133126 TCCACCATGC
** * * *
6133136 CCACCACTGCCGCCACCGCTACCACCATGACCTCCGCCACCACCGCCACTACCTCCTTGTCCTCC
1 CCACCACCACCGCCACCACTACCACCATGTCCTCCGCCACCACCGCCACTACCGCCTTGTCCTCC
6133201 ACCATGCCCACCACTACCGCCACCACTA
66 ACCATGCCCACCACTACCGCCACCACTA
* * * *
6133229 CTACCACCACCATGTCCGCCACTGCCACCATGTCCTCTGCCACCACCGCCACTACCGCCTTGTCC
1 CCACCACCACC--G-CCACCACTACCACCATGTCCTCCGCCACCACCGCCACTACCGCCTTGTCC
* *
6133294 TCCACCATGTCCACCACTACCGCCGCCACTA
63 TCCACCATGCCCACCACTACCGCCACCACTA
* * *
6133325 CCGCCATGTCCTCCGCCACCACTACCACCCTGTCCTCCGCC
1 CCACCA---CCACCGCCACCACTACCACCATGTCCTCCGCC
6133366 TCCGCCACCA
Statistics
Matches: 113, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
93 8 0.07
95 1 0.01
96 99 0.88
97 1 0.01
99 4 0.04
ACGTcount: A:0.18, C:0.55, G:0.11, T:0.16
Consensus pattern (93 bp):
CCACCACCACCGCCACCACTACCACCATGTCCTCCGCCACCACCGCCACTACCGCCTTGTCCTCC
ACCATGCCCACCACTACCGCCACCACTA
Found at i:6133389 original size:42 final size:42
Alignment explanation
Indices: 6133343--6133425 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
6133333 TCCTCCGCCA
* * *
6133343 CCACTACCACCCTGTCCTCCGCCTCCGCCACCACTTCCACCG
1 CCACTACCACCCTGTCCTCCACCTCCACCACCACTACCACCG
* * *
6133385 CCACTACCAGCGTGTCCTCCACTTCCACCACCACTACCACC
1 CCACTACCACCCTGTCCTCCACCTCCACCACCACTACCACC
6133426 TTGTCCTCCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.18, C:0.57, G:0.08, T:0.17
Consensus pattern (42 bp):
CCACTACCACCCTGTCCTCCACCTCCACCACCACTACCACCG
Found at i:6133407 original size:30 final size:30
Alignment explanation
Indices: 6133373--6133436 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
6133363 GCCTCCGCCA
* *
6133373 CCACTTCCACCGCCACTACCAGCGTGTCCT
1 CCACTTCCACCACCACTACCACCGTGTCCT
*
6133403 CCACTTCCACCACCACTACCACCTTGTCCT
1 CCACTTCCACCACCACTACCACCGTGTCCT
6133433 CCAC
1 CCAC
6133437 CATGTCCACC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.19, C:0.53, G:0.08, T:0.20
Consensus pattern (30 bp):
CCACTTCCACCACCACTACCACCGTGTCCT
Found at i:6133446 original size:30 final size:30
Alignment explanation
Indices: 6133412--6133483 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
6133402 TCCACTTCCA
6133412 CCACCACTACCACCTTGTCCTCCACCATGT
1 CCACCACTACCACCTTGTCCTCCACCATGT
* * *
6133442 CCACCACTGCCGCCTTGTCCTCCGCCATGT
1 CCACCACTACCACCTTGTCCTCCACCATGT
*
6133472 CCTCCACTACCA
1 CCACCACTACCA
6133484 TTTCCTAGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.17, C:0.51, G:0.10, T:0.22
Consensus pattern (30 bp):
CCACCACTACCACCTTGTCCTCCACCATGT
Found at i:6135385 original size:19 final size:18
Alignment explanation
Indices: 6135361--6135396 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
6135351 ACATCAAAAT
6135361 AAAATTTACAAAAGTAATC
1 AAAATTTACAAAA-TAATC
*
6135380 AAAATTTTCAAAATAAT
1 AAAATTTACAAAATAAT
6135397 ATTTAAGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.08, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAATTTACAAAATAATC
Found at i:6135505 original size:17 final size:17
Alignment explanation
Indices: 6135485--6135525 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
6135475 AAACTATTCT
6135485 TATTAAATGCAAATCAA
1 TATTAAATGCAAATCAA
*
6135502 TATTAAATGCAAATTAA
1 TATTAAATGCAAATCAA
6135519 T-TTAAAT
1 TATTAAAT
6135526 ATTCAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 6 0.26
17 17 0.74
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (17 bp):
TATTAAATGCAAATCAA
Found at i:6135543 original size:22 final size:21
Alignment explanation
Indices: 6135512--6135554 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
6135502 TATTAAATGC
6135512 AAATTAATTTAAATATTCAAAA
1 AAATTAATTTAAATATT-AAAA
* *
6135534 AAATTTATTTTAATATTAAAA
1 AAATTAATTTAAATATTAAAA
6135555 TGAAGGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTAATTTAAATATTAAAA
Found at i:6143597 original size:25 final size:25
Alignment explanation
Indices: 6143565--6143619 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
6143555 GGAATCTCCT
*
6143565 TTTA-CAAAGTAAATTAGTACAAAC
1 TTTATCAAAGTAAAATAGTACAAAC
6143589 TTTATCAAAGTAAAATAGTACAAAC
1 TTTATCAAAGTAAAATAGTACAAAC
6143614 TTTATC
1 TTTATC
6143620 TATTTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (25 bp):
TTTATCAAAGTAAAATAGTACAAAC
Found at i:6144636 original size:60 final size:60
Alignment explanation
Indices: 6144563--6144733 Score: 235
Period size: 60 Copynumber: 2.9 Consensus size: 60
6144553 GTGAGTTAGG
*
6144563 TGGCACATTTGTTGAAAGGAAGTGGAGAGTTTGACACAATATCTTCTCTTTTTTTTTCAC-
1 TGGCACATTTGTTGAAAGGAAGTGGAGAGTTTGACACAATGTCTT-TCTTTTTTTTTCACA
6144623 TGGCACATTTGTTGAAAGGAAGTGGAGAGTTTGACACAATGTC-TTCTTTTTTTTTCACA
1 TGGCACATTTGTTGAAAGGAAGTGGAGAGTTTGACACAATGTCTTTCTTTTTTTTTCACA
* ** * * *
6144682 T-ACGGA-GTGTTGAAAGAAAGTGGAGAGTTTGACACAATGTCTTT-TTTGTTTT
1 TGGCACATTTGTTGAAAGGAAGTGGAGAGTTTGACACAATGTCTTTCTTTTTTTT
6144734 GGGAAGATGA
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
57 40 0.39
58 18 0.18
59 2 0.02
60 42 0.41
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (60 bp):
TGGCACATTTGTTGAAAGGAAGTGGAGAGTTTGACACAATGTCTTTCTTTTTTTTTCACA
Found at i:6150813 original size:20 final size:20
Alignment explanation
Indices: 6150788--6150836 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
6150778 ATTTGATTAC
* *
6150788 TTTAATTTCACTAGATCAAA
1 TTTAATTTCACAAAATCAAA
*
6150808 TTTAATTTTCCCAAAATCAAA
1 TTTAA-TTTCACAAAATCAAA
6150829 TTTAATTT
1 TTTAATTT
6150837 TCCCAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTAATTTCACAAAATCAAA
Found at i:6150848 original size:22 final size:21
Alignment explanation
Indices: 6150802--6150844 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6150792 ATTTCACTAG
6150802 ATCAAATTTAATTTTCCCAAA
1 ATCAAATTTAATTTTCCCAAA
6150823 ATCAAATTTAATTTTCCCAAA
1 ATCAAATTTAATTTTCCCAAA
6150844 A
1 A
6150845 ATCACTTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (21 bp):
ATCAAATTTAATTTTCCCAAA
Found at i:6150857 original size:21 final size:20
Alignment explanation
Indices: 6150809--6150858 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
6150799 TAGATCAAAT
*
6150809 TTAATTTTCCCAAAATCAAAT
1 TTAATTTTCCCAAAATC-AAC
6150830 TTAATTTTCCCAAAAATC-AC
1 TTAATTTTCCC-AAAATCAAC
6150850 TTAGATTTT
1 TTA-ATTTT
6150859 TCAAATTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 16 0.62
22 6 0.23
ACGTcount: A:0.38, C:0.18, G:0.02, T:0.42
Consensus pattern (20 bp):
TTAATTTTCCCAAAATCAAC
Found at i:6153965 original size:24 final size:25
Alignment explanation
Indices: 6153917--6153966 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
6153907 ATACATTATC
* *
6153917 TTATTATATATTATCATTTTGATTT
1 TTATTATATATTATCATTATAATTT
*
6153942 TTATT-TATATTATTATTATAATTT
1 TTATTATATATTATCATTATAATTT
6153966 T
1 T
6153967 ATAATGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (25 bp):
TTATTATATATTATCATTATAATTT
Found at i:6158640 original size:2 final size:2
Alignment explanation
Indices: 6158633--6158670 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6158623 TTATTGACTT
6158633 TA 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 TA
6158671 AGCGTGTGAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6162745 original size:2 final size:2
Alignment explanation
Indices: 6162738--6162766 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6162728 TGCTTATAAC
6162738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6162767 CAAAAACCCT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6166241 original size:33 final size:33
Alignment explanation
Indices: 6166204--6166353 Score: 119
Period size: 33 Copynumber: 4.5 Consensus size: 33
6166194 ATAACTCAGT
6166204 TATGGTCTTA-TTATCAGAATGCCATAGCCCAGC
1 TATGGTCTTACTTAT-AGAATGCCATAGCCCAGC
* * * * * *
6166237 TATGGTCTTACATATAAACAATGTCATGGTCCAAC
1 TATGGTCTTAC-T-TATAGAATGCCATAGCCCAGC
* * * *
6166272 CATGGTCTTACGTTTATAG--TGTCATAACCCAGT
1 TATGGTCTTAC--TTATAGAATGCCATAGCCCAGC
6166305 TATGGTCTTA-TTATTAGAATGCCATAGCCCAGC
1 TATGGTCTTACTTA-TAGAATGCCATAGCCCAGC
*
6166338 TATGGTCTTACATATA
1 TATGGTCTTACTTATA
6166354 AACACTACCA
Statistics
Matches: 89, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
30 3 0.03
31 3 0.03
33 51 0.57
34 2 0.02
35 27 0.30
36 3 0.03
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (33 bp):
TATGGTCTTACTTATAGAATGCCATAGCCCAGC
Found at i:6169706 original size:14 final size:14
Alignment explanation
Indices: 6169687--6169715 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6169677 ACCAATAAAT
6169687 AAATTATAACAATC
1 AAATTATAACAATC
6169701 AAATTATAACAATC
1 AAATTATAACAATC
6169715 A
1 A
6169716 CCTATCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATTATAACAATC
Found at i:6187001 original size:27 final size:27
Alignment explanation
Indices: 6186971--6187032 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
6186961 CCTATCAGGT
6186971 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
* *
6186998 AGGCACCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
6187025 AGGCGCCA
1 AGGCGCCA
6187033 TTACTAGACC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.31, C:0.23, G:0.32, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:6188032 original size:49 final size:48
Alignment explanation
Indices: 6187960--6188099 Score: 178
Period size: 49 Copynumber: 2.9 Consensus size: 48
6187950 NNNNNNNNNN
*
6187960 AATATTGTAATATTATAATTTTGTATGAATATTGCAATTTTTTTGTAT
1 AATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTGTAT
* **
6188008 GAATATTGTAATATTATAATTTTGTATGAATATTGTAA--TGTCGGTAT
1 -AATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTGTAT
* *
6188055 -ATATTGTAATATTGTAATTTTTTGTATGAATATTGTAATTATTTT
1 AATATTGTAATATTATAA--TTTTGTATGAATATTGTAATTTTTTT
6188100 ATAATTAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
45 16 0.21
47 25 0.32
49 37 0.47
ACGTcount: A:0.33, C:0.01, G:0.13, T:0.53
Consensus pattern (48 bp):
AATATTGTAATATTATAATTTTGTATGAATATTGTAATTTTTTTGTAT
Found at i:6188038 original size:27 final size:27
Alignment explanation
Indices: 6187960--6188046 Score: 130
Period size: 27 Copynumber: 3.4 Consensus size: 27
6187950 NNNNNNNNNN
6187960 AATATTGTAATATTATAATTTTGTATG
1 AATATTGTAATATTATAATTTTGTATG
*
6187987 AATATTG-CA-ATT-T--TTTTGTATG
1 AATATTGTAATATTATAATTTTGTATG
6188009 AATATTGTAATATTATAATTTTGTATG
1 AATATTGTAATATTATAATTTTGTATG
6188036 AATATTGTAAT
1 AATATTGTAAT
6188047 GTCGGTATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
22 16 0.30
23 1 0.02
24 4 0.08
25 4 0.08
26 1 0.02
27 27 0.51
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (27 bp):
AATATTGTAATATTATAATTTTGTATG
Found at i:6188164 original size:19 final size:19
Alignment explanation
Indices: 6188142--6188179 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6188132 TATAAATTTA
*
6188142 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
6188161 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
6188180 AAATTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:6202349 original size:5 final size:5
Alignment explanation
Indices: 6202339--6202371 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
6202329 AAAGCTCATA
6202339 AAAAT AAAAT AAAAT AAAAT AAAAT AAATAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AA
6202372 CTAGTGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 23 0.85
6 4 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
AAAAT
Found at i:6208941 original size:3 final size:3
Alignment explanation
Indices: 6208929--6208966 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
6208919 CATTATTATT
*
6208929 TGC TGT TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
6208967 AAATGGTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.29, G:0.34, T:0.37
Consensus pattern (3 bp):
TGC
Found at i:6221675 original size:13 final size:15
Alignment explanation
Indices: 6221647--6221679 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
6221637 AGGTGGAGAA
6221647 ATAAATATTTGACAT
1 ATAAATATTTGACAT
6221662 ATAAAT-TTTG-CAT
1 ATAAATATTTGACAT
6221675 ATAAA
1 ATAAA
6221680 GAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 4 0.22
15 6 0.33
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
ATAAATATTTGACAT
Found at i:6239941 original size:45 final size:45
Alignment explanation
Indices: 6239810--6239943 Score: 198
Period size: 45 Copynumber: 3.0 Consensus size: 45
6239800 CATGTTTTCA
** * * *
6239810 CATGATGCCATAATGTCTTTCAACTAT-AGTCTTACTTATTTATAT
1 CATGATGCCATAACATCTTTCAGCTATGA-TCTTACTCATTTTTAT
*
6239855 CATGATGCCATAGCATCTTTCAGCTATGATCTTACTCATTTTTAT
1 CATGATGCCATAACATCTTTCAGCTATGATCTTACTCATTTTTAT
6239900 CATGATGCCATAACATCTTTCAGCTATGATCTTACTCATTTTTA
1 CATGATGCCATAACATCTTTCAGCTATGATCTTACTCATTTTTA
6239944 GACGTATAGC
Statistics
Matches: 81, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
45 80 0.99
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.43
Consensus pattern (45 bp):
CATGATGCCATAACATCTTTCAGCTATGATCTTACTCATTTTTAT
Found at i:6244710 original size:20 final size:19
Alignment explanation
Indices: 6244657--6244715 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
6244647 AGTAATGAAT
*
6244657 CTGTTCACCAAGAGATATAA
1 CTGTTCA-CAAGAGATACAA
* *
6244677 TTGTTCA-AA-TGATACAA
1 CTGTTCACAAGAGATACAA
*
6244694 CTGTTCATCAAGAGATAGAA
1 CTGTTCA-CAAGAGATACAA
6244714 CT
1 CT
6244716 ATTGTTTAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
17 12 0.40
18 2 0.07
19 2 0.07
20 14 0.47
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (19 bp):
CTGTTCACAAGAGATACAA
Found at i:6252883 original size:20 final size:19
Alignment explanation
Indices: 6252858--6252922 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
6252848 TTAGTAACTC
6252858 AAAATATTATAAAAACTTAA
1 AAAATATTATAAAAA-TTAA
* *
6252878 AAAATA-CATAAAAGTTCAA
1 AAAATATTATAAAAATT-AA
* *
6252897 AAAAAATTATAAATATTAA
1 AAAATATTATAAAAATTAA
6252916 AATAATA
1 AA-AATA
6252923 CATGAAAATT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.06
19 17 0.49
20 16 0.46
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATATTATAAAAATTAA
Found at i:6252906 original size:39 final size:40
Alignment explanation
Indices: 6252858--6252945 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 40
6252848 TTAGTAACTC
*
6252858 AAAATATTATAAAAACTTAAAA-AATACAT-AAAAGTT-CAA
1 AAAAAATTATAAAAA-TTAAAATAATACATGAAAA-TTACAA
* *
6252897 AAAAAATTATAAATATTAAAATAATACATGAAAATTATAA
1 AAAAAATTATAAAAATTAAAATAATACATGAAAATTACAA
6252937 AAAAAATTA
1 AAAAAATTA
6252946 AAATGTTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
38 6 0.14
39 22 0.51
40 15 0.35
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (40 bp):
AAAAAATTATAAAAATTAAAATAATACATGAAAATTACAA
Found at i:6262450 original size:68 final size:69
Alignment explanation
Indices: 6262336--6262469 Score: 198
Period size: 68 Copynumber: 2.0 Consensus size: 69
6262326 GCAAAAGTAA
* *
6262336 TAGTTTTTGATGTATCAATTTATAGATAGATAAGTCAAATGCTAGTGTG-AAACAACTCTGGTGT
1 TAGTTTTTGATGCATCAATCTATAGATAGATAAGTCAAATGCTAGTGTGTAAACAACTCTGGTGT
6262400 TGTT
66 TGTT
* * * * *
6262404 TAGTTTTTGATGCATCAGTCTATCGATAGATAAGTCAAATGTTAGTGTGTGAACAACTCTGTTGT
1 TAGTTTTTGATGCATCAATCTATAGATAGATAAGTCAAATGCTAGTGTGTAAACAACTCTGGTGT
6262469 T
66 T
6262470 TTAACCAGAG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
68 44 0.76
69 14 0.24
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (69 bp):
TAGTTTTTGATGCATCAATCTATAGATAGATAAGTCAAATGCTAGTGTGTAAACAACTCTGGTGT
TGTT
Found at i:6266638 original size:17 final size:18
Alignment explanation
Indices: 6266602--6266638 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
6266592 TCAGGCGTAA
6266602 TATGTCTTGGCAGTGACT
1 TATGTCTTGGCAGTGACT
6266620 TATGT-TTGGC-GTGATCT
1 TATGTCTTGGCAGTGA-CT
6266637 TA
1 TA
6266639 AAGACAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 9 0.50
18 5 0.28
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.43
Consensus pattern (18 bp):
TATGTCTTGGCAGTGACT
Found at i:6273122 original size:17 final size:16
Alignment explanation
Indices: 6273096--6273160 Score: 51
Period size: 17 Copynumber: 3.9 Consensus size: 16
6273086 AATATTTCAC
*
6273096 TAAGAGTCAATATTTGT
1 TAAGAATCAATATTT-T
*
6273113 TAAGAATCAAATAAATTT
1 TAAGAATC-AAT-ATTTT
* *
6273131 TAA-AGTCTATATTTAT
1 TAAGAATCAATATTT-T
6273147 TAAGAATCAATATT
1 TAAGAATCAATATT
6273161 ATATTATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
15 3 0.08
16 6 0.16
17 18 0.49
18 7 0.19
19 3 0.08
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.40
Consensus pattern (16 bp):
TAAGAATCAATATTTT
Found at i:6273655 original size:16 final size:19
Alignment explanation
Indices: 6273622--6273659 Score: 55
Period size: 16 Copynumber: 2.2 Consensus size: 19
6273612 AAAAAATCAA
6273622 ATAATAAATATGTAATTAT
1 ATAATAAATATGTAATTAT
6273641 ATAATAAA-A-GT-ATTAT
1 ATAATAAATATGTAATTAT
6273657 ATA
1 ATA
6273660 TATCACATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 2 0.11
18 1 0.05
19 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
ATAATAAATATGTAATTAT
Found at i:6278191 original size:18 final size:18
Alignment explanation
Indices: 6278152--6278193 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
6278142 ATTCTAATTT
*
6278152 TTTTATAATTATTAAGTA
1 TTTTATAATTATTAAGGA
*
6278170 TTTTA-AATTATTTAGGA
1 TTTTATAATTATTAAGGA
6278187 GTTTTAT
1 -TTTTAT
6278194 GTTAATAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (18 bp):
TTTTATAATTATTAAGGA
Found at i:6303129 original size:19 final size:20
Alignment explanation
Indices: 6303105--6303146 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
6303095 ACATTTGTCG
*
6303105 GTGAAAT-TGATGATTTAAT
1 GTGAAATATAATGATTTAAT
6303124 GTGAAATAATAATGATTTAAT
1 GTGAAAT-ATAATGATTTAAT
6303145 GT
1 GT
6303147 ACACTTTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (20 bp):
GTGAAATATAATGATTTAAT
Found at i:6306188 original size:3 final size:3
Alignment explanation
Indices: 6306182--6306213 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6306172 GAAGAAGAAA
6306182 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AG
6306214 AATAAGAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:6306673 original size:65 final size:65
Alignment explanation
Indices: 6306604--6306728 Score: 189
Period size: 65 Copynumber: 1.9 Consensus size: 65
6306594 TGTTGTTGGT
* * *
6306604 ATATTGTTGCTTATGTTGTTATACATGGCTG-CTTGTATACATGGCTAACCAACTTATGTTTTGT
1 ATATTGTTACTTATGTTGTTATACATGCCTGTC-GGTATACATGGCTAACCAACTTATGTTTTGT
6306668 A
65 A
**
6306669 ATATTGTTACTTATGTTGTTATACATGCCTGTCGGTATACATGGCTAACCAGTTTATGTT
1 ATATTGTTACTTATGTTGTTATACATGCCTGTCGGTATACATGGCTAACCAACTTATGTT
6306729 GTTGCTTACA
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 53 0.98
66 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.44
Consensus pattern (65 bp):
ATATTGTTACTTATGTTGTTATACATGCCTGTCGGTATACATGGCTAACCAACTTATGTTTTGTA
Found at i:6307487 original size:21 final size:21
Alignment explanation
Indices: 6307463--6307517 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
6307453 GGCAACCTCC
* *
6307463 TGCTAAGTTGGGGTATACTCT
1 TGCTGAGTTGGGGTAGACTCT
* * *
6307484 TGCTGATTTGGGGTAGCCTGT
1 TGCTGAGTTGGGGTAGACTCT
6307505 TGCTGAGTTGGGG
1 TGCTGAGTTGGGG
6307518 CAACCACTTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.36
Consensus pattern (21 bp):
TGCTGAGTTGGGGTAGACTCT
Found at i:6308388 original size:82 final size:81
Alignment explanation
Indices: 6308285--6308602 Score: 421
Period size: 82 Copynumber: 4.0 Consensus size: 81
6308275 ACGCATACAC
* * *
6308285 ACCTAAAAAATAGTCATTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
1 ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
6308350 CAATCTTATACACACAT
66 CAATC-TATACACACAT
6308367 ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
1 ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
*
6308432 CAATCATATACATACAT
66 CAATC-TATACACACAT
6308449 ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
1 ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
* *
6308514 CAATC-ATACACAGAC
66 CAATCTATACACACAT
** * * * * * * * * *
6308529 AAAT-TAAAA-AA-CACTACATGCATATTAAAAAACAATCAACAGCATGTGACTAGCCTCACCAA
1 ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
*
6308591 CAAT-TAGACACA
66 CAATCTATACACA
6308603 GAAAAATTAA
Statistics
Matches: 215, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
77 53 0.25
78 2 0.01
79 4 0.02
80 9 0.04
82 147 0.68
ACGTcount: A:0.47, C:0.26, G:0.06, T:0.20
Consensus pattern (81 bp):
ACCTAAAAAACAATCACTGCATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAA
CAATCTATACACACAT
Found at i:6308602 original size:77 final size:77
Alignment explanation
Indices: 6308304--6308637 Score: 308
Period size: 82 Copynumber: 4.2 Consensus size: 77
6308294 ATAGTCATTG
* * * * * * *
6308304 CATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAACAATCTTATACACACATAC
1 CATGCATATTAAAAAACAATCAACAACATATGACCAGCCCCACCAACAATC--AGACACAGAAAA
* * *
6308369 CTAAAAAACAATCACTG
64 AT-TAAAA-AA-CACTA
* * * * * * *
6308386 CATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAACAATCATATACATACATAC
1 CATGCATATTAAAAAACAATCAACAACATATGACCAGCCCCACCAACAATCAGACACAGA-A-AA
* * *
6308451 CTAAAAAACAATCACTG
64 AT-TAAAA-AA-CACTA
* * * * *
6308468 CATGCATATTAAAAAATAGTCAACAACATATGACCATCCCCACCAACAATCATACACAGACAAAT
1 CATGCATATTAAAAAACAATCAACAACATATGACCAGCCCCACCAACAATCAGACACAGAAAAAT
6308533 TAAAAAACACTA
66 TAAAAAACACTA
* * * * *
6308545 CATGCATATTAAAAAACAATCAACAGCATGTGACTAGCCTCACCAACAATTAGACACAGAAAAAT
1 CATGCATATTAAAAAACAATCAACAACATATGACCAGCCCCACCAACAATCAGACACAGAAAAAT
6308610 TAAAAAACACTA
66 TAAAAAACACTA
6308622 CATGCATATTAAAAAA
1 CATGCATATTAAAAAA
6308638 ACTCACTAAA
Statistics
Matches: 230, Mismatches: 20, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
77 87 0.38
78 2 0.01
79 4 0.02
80 9 0.04
82 128 0.56
ACGTcount: A:0.49, C:0.25, G:0.06, T:0.20
Consensus pattern (77 bp):
CATGCATATTAAAAAACAATCAACAACATATGACCAGCCCCACCAACAATCAGACACAGAAAAAT
TAAAAAACACTA
Found at i:6311509 original size:21 final size:22
Alignment explanation
Indices: 6311469--6311509 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
6311459 GTAATTTACT
*
6311469 TTAAAATATTTTGAAAGTTGGA
1 TTAAAATATGTTGAAAGTTGGA
6311491 TTAAAATATGTTG-AAGTTG
1 TTAAAATATGTTGAAAGTTG
6311510 AAGGCATGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.39, C:0.00, G:0.20, T:0.41
Consensus pattern (22 bp):
TTAAAATATGTTGAAAGTTGGA
Found at i:6320985 original size:27 final size:27
Alignment explanation
Indices: 6320954--6321095 Score: 194
Period size: 27 Copynumber: 5.3 Consensus size: 27
6320944 ATAGGTCAAT
6320954 AAATGACCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
6320981 AAATGACCAAAATTCCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
** * * *
6321008 AAATGATAGAAATGCCCCTATAAGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
6321035 AAATGACCGAAATACCCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
6321062 AAATGACCGAAATACCCCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
6321089 AAATGAC
1 AAATGAC
6321096 TGTTATACCT
Statistics
Matches: 97, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 97 1.00
ACGTcount: A:0.43, C:0.22, G:0.17, T:0.18
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:6321289 original size:26 final size:26
Alignment explanation
Indices: 6321259--6321365 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
6321249 TGGAGGAAGT
6321259 ATACTATTACTGGCAACTTTGCTGCG
1 ATACTATTACTGGCAACTTTGCTGCG
* *
6321285 ATACTGTTACTGGCAACTTTGTTGCG
1 ATACTATTACTGGCAACTTTGCTGCG
* * *
6321311 ATACTGTTACTGGCAGCTTTGCTGCA
1 ATACTATTACTGGCAACTTTGCTGCG
* *
6321337 ATACTACTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAACTTTGCTGCG
6321363 ATA
1 ATA
6321366 TTGGTGTGTT
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAACTTTGCTGCG
Found at i:6330421 original size:20 final size:19
Alignment explanation
Indices: 6330371--6330421 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
6330361 CGCGCTTGTA
6330371 CATGATTTGCACTTCGGTGC
1 CATGA-TTGCACTTCGGTGC
* *
6330391 TATGTTTGCACTTCGGTGCC
1 CATGATTGCACTTCGGTG-C
*
6330411 CCTGATTGCAC
1 CATGATTGCAC
6330422 ATTTGTGCCT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.14, C:0.27, G:0.24, T:0.35
Consensus pattern (19 bp):
CATGATTGCACTTCGGTGC
Found at i:6335294 original size:2 final size:2
Alignment explanation
Indices: 6335282--6335331 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
6335272 TTAATTGTGC
*
6335282 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6335324 AT AT AT AT
1 AT AT AT AT
6335332 TATTTTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6339978 original size:29 final size:30
Alignment explanation
Indices: 6339936--6340001 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
6339926 AACAACTCAG
* *
6339936 TGACTAAAATGTAACAT-TTTAAACATAAA
1 TGACTAAAATGTAACATATGTAAACAAAAA
*
6339965 TGACTAAAATGTAATATAATGTAAACAAAAA
1 TGACTAAAATGTAACAT-ATGTAAACAAAAA
6339996 TGACTA
1 TGACTA
6340002 TTTTGATAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
29 16 0.50
31 16 0.50
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (30 bp):
TGACTAAAATGTAACATATGTAAACAAAAA
Found at i:6340197 original size:2 final size:2
Alignment explanation
Indices: 6340190--6340228 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
6340180 AGCAAAGTTC
6340190 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6340229 GTAGTAGTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6346341 original size:2 final size:2
Alignment explanation
Indices: 6346328--6346359 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6346318 CTTAAGTTTA
*
6346328 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6346360 TAAAATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6348543 original size:19 final size:20
Alignment explanation
Indices: 6348516--6348553 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
6348506 TCATTATAAA
* *
6348516 TATAGAAAATTAATGAAATC
1 TATAGAAAACTAATAAAATC
6348536 TATA-AAAACTAATAAAAT
1 TATAGAAAACTAATAAAAT
6348554 TAGGATAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.61, C:0.05, G:0.05, T:0.29
Consensus pattern (20 bp):
TATAGAAAACTAATAAAATC
Found at i:6350800 original size:23 final size:22
Alignment explanation
Indices: 6350757--6350801 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
6350747 TAAAGACGAA
* *
6350757 AAAAATGTAATTTAATTCTTTT
1 AAAAATGTAAATTAATACTTTT
*
6350779 AAAATTGTAAATTATATACTTTT
1 AAAAATGTAAATTA-ATACTTTT
6350802 TGAACTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
AAAAATGTAAATTAATACTTTT
Found at i:6365753 original size:52 final size:53
Alignment explanation
Indices: 6365696--6365816 Score: 122
Period size: 53 Copynumber: 2.2 Consensus size: 53
6365686 AAATGATATT
*
6365696 ATATTAATATTAAATACATAAAAT-ATATTATTCACTATT-AAAT-TTTTTAATA
1 ATATTAATATTAAATA-ATAAAATGATATTATTCA-TATTAAAATATTATTAATA
* * * * *
6365748 ATATTAGTTTTTAAATATTAAAATGATATTATTTATATTAAAATAATTATTATTA
1 ATATTA-ATATTAAATAATAAAATGATATTATTCATATTAAAAT-ATTATTAATA
6365803 ATATTTAATATTAA
1 ATA-TTAATATTAA
6365817 TATTTTAGAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
52 16 0.29
53 21 0.38
55 15 0.27
56 3 0.05
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (53 bp):
ATATTAATATTAAATAATAAAATGATATTATTCATATTAAAATATTATTAATA
Found at i:6365787 original size:20 final size:21
Alignment explanation
Indices: 6365761--6365807 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
6365751 TTAGTTTTTA
*
6365761 AATATTAAAATGA-TATTATT
1 AATATTAAAATAATTATTATT
*
6365781 TATATTAAAATAATTATTATT
1 AATATTAAAATAATTATTATT
6365802 AATATT
1 AATATT
6365808 TAATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (21 bp):
AATATTAAAATAATTATTATT
Found at i:6365792 original size:28 final size:27
Alignment explanation
Indices: 6365679--6365789 Score: 93
Period size: 25 Copynumber: 4.1 Consensus size: 27
6365669 TCCATATAGC
*
6365679 AATATTTAAATGATATTATATTAATATTA
1 AATATTAAAATGATATTAT-TT-ATATTA
* *
6365708 AATACATAAAAT-ATATTATTCACTATTA
1 AATA-TTAAAATGATATTATTTA-TATTA
* ** * *
6365736 AATTTTTTAATAATATTAGTT-T-TTA
1 AATATTAAAATGATATTATTTATATTA
6365761 AATATTAAAATGATATTATTTATATTA
1 AATATTAAAATGATATTATTTATATTA
6365788 AA
1 AA
6365790 ATAATTATTA
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
25 19 0.30
26 2 0.03
27 10 0.16
28 16 0.25
29 11 0.17
30 5 0.08
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (27 bp):
AATATTAAAATGATATTATTTATATTA
Found at i:6365815 original size:80 final size:83
Alignment explanation
Indices: 6365679--6365842 Score: 187
Period size: 80 Copynumber: 2.0 Consensus size: 83
6365669 TCCATATAGC
* * * *
6365679 AATATTTAAATGATATTATATTAATATTAAATACATAAAATATATTATTCACTATTAAATTTTTT
1 AATATTAAAATGATATTATATTAATATTAAATACATAAAATATAATATTCAATATT-AATATTTT
*
6365744 A-ATAATATTAGTTT-TTA
65 AGATAATAATAGTTTATTA
* * *
6365761 AATATTAAAATGATATTAT-TT-ATATTAAAATA-AT-TATTATTAATATTTAATATTAATATTT
1 AATATTAAAATGATATTATATTAATATT-AAATACATAAAATA-TAATATTCAATATTAATATTT
6365822 TAGATAATAATAGTTTATTA
64 TAGATAATAATAGTTTATTA
6365842 A
1 A
6365843 TATCAAAGTA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
79 11 0.16
80 30 0.43
81 11 0.16
82 18 0.26
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (83 bp):
AATATTAAAATGATATTATATTAATATTAAATACATAAAATATAATATTCAATATTAATATTTTA
GATAATAATAGTTTATTA
Found at i:6373214 original size:26 final size:26
Alignment explanation
Indices: 6373178--6373229 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
6373168 TGTGGACGGG
*
6373178 AGGTCGGATCAACTTGCAGAATCACA
1 AGGTCGGATCAACTCGCAGAATCACA
*
6373204 AGGTTGGATCAACTCGCAGAATCACA
1 AGGTCGGATCAACTCGCAGAATCACA
6373230 CTATCTTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (26 bp):
AGGTCGGATCAACTCGCAGAATCACA
Found at i:6377952 original size:16 final size:17
Alignment explanation
Indices: 6377925--6377957 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6377915 TCAAATGAAT
6377925 AAAAACTCTATTATTAA
1 AAAAACTCTATTATTAA
*
6377942 AAAAACT-TATTTTTAA
1 AAAAACTCTATTATTAA
6377958 TGTCAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAAACTCTATTATTAA
Found at i:6378077 original size:21 final size:20
Alignment explanation
Indices: 6378051--6378107 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 20
6378041 AATAGATAGG
6378051 TAAAATTCTAAAAAAAACAC
1 TAAAATTCTAAAAAAAACAC
** **
6378071 TAAAAATTCTACCAAAAATTC
1 T-AAAATTCTAAAAAAAACAC
6378092 TAAAATT-TAAAAAAAA
1 TAAAATTCTAAAAAAAA
6378108 ATTAAAATCA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 7 0.23
20 7 0.23
21 16 0.53
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (20 bp):
TAAAATTCTAAAAAAAACAC
Found at i:6393541 original size:29 final size:29
Alignment explanation
Indices: 6393507--6393574 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
6393497 GGGTTTTTTA
* *
6393507 ATAAAAATAATATTAAAAATAAATTAATT
1 ATAAAAATAAGATGAAAAATAAATTAATT
* * *
6393536 ATAAAAATAGGGTGAGAAATAAATTAATT
1 ATAAAAATAAGATGAAAAATAAATTAATT
*
6393565 ACAAAAATAA
1 ATAAAAATAA
6393575 AGTGTTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.63, C:0.01, G:0.07, T:0.28
Consensus pattern (29 bp):
ATAAAAATAAGATGAAAAATAAATTAATT
Found at i:6393791 original size:28 final size:28
Alignment explanation
Indices: 6393756--6393828 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
6393746 GATTTTAGAG
6393756 ATTAAATGTAGGGAAAATGCATTAAGGC
1 ATTAAATGTAGGGAAAATGCATTAAGGC
* * *
6393784 ATTAAATGTAAGGAAACTGTATTAAGGC
1 ATTAAATGTAGGGAAAATGCATTAAGGC
*
6393812 ATTAAATGTAGAGAAAA
1 ATTAAATGTAGGGAAAA
6393829 GGTTATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.47, C:0.05, G:0.22, T:0.26
Consensus pattern (28 bp):
ATTAAATGTAGGGAAAATGCATTAAGGC
Found at i:6396566 original size:3 final size:3
Alignment explanation
Indices: 6396524--6396550 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
6396514 TTCTGATTGT
6396524 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
6396551 CCGCTTCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:6402791 original size:88 final size:88
Alignment explanation
Indices: 6402628--6403029 Score: 538
Period size: 88 Copynumber: 4.6 Consensus size: 88
6402618 AACAGATCAG
* * * * * *
6402628 TGAAGATAGTAGATCTTACCTTCCTGTAGT-GACAGTGAAGCAGATCAAAGACACAAGCCCTACC
1 TGAAGATAGCAGATCTTGCCTTCCTGCA-TCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCC
* *
6402692 TACCTCAGTTGTAGTGGAGCAGGT
65 TCCCTCGGTTGTAGTGGAGCAGGT
* * * * * *
6402716 TAAAGGTAGCAGATCTTGCCTTCCTACATCGATAGTGAAGTAGATTGAAGACACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
* *
6402781 CTCTCGGTTGTAGTGGAGTAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * *
6402804 TGAAGATAGCAGATCTTGCCTT-TTGGCATGGACAGTGAAGCAGATTGAAGACACAAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCT-GCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCC
6402868 TCCCTCGGTTGTAGTGGAGCAGGT
65 TCCCTCGGTTGTAGTGGAGCAGGT
* * * *
6402892 TGAAGATAGCAGATCTTGCCTTCTTGCATCGACAGTGAAGTAGATCGAAGACACAAGTCTTGCGT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
6402957 CCCTCGGTTGTAGTGGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * *
6402980 TGAAGATAGCAGGTCTTGTCTTTCTGCATCGACAGTGAAGCAGATCGAAG
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAG
6403030 CCAATGGTCC
Statistics
Matches: 276, Mismatches: 35, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
87 2 0.01
88 272 0.99
89 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.26
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
CCCTCGGTTGTAGTGGAGCAGGT
Found at i:6402801 original size:43 final size:43
Alignment explanation
Indices: 6402748--6402985 Score: 144
Period size: 43 Copynumber: 5.4 Consensus size: 43
6402738 CCTACATCGA
* *
6402748 TAGTGAAGTAGATTGAAGACACAAGCCTTGCCTCTCTCGGTTG
1 TAGTGAAGCAGATTGAAGACACAAGTCTTGCCTCTCTCGGTTG
* * * * * *
6402791 TAGTGGAGTAGGTTGAAGATAGC-AGATCTTGCCT-T-TTGGCATGG
1 TAGTGAAGCAGATTGAAGACA-CAAG-TCTTGCCTCTCTCGG--TTG
* * *
6402835 ACAGTGAAGCAGATTGAAGACACAAGCCTTGCCTCCCTCGGTTG
1 -TAGTGAAGCAGATTGAAGACACAAGTCTTGCCTCTCTCGGTTG
* * * * * *
6402879 TAGTGGAGCAGGTTGAAGATAGC-AGATCTTGCCT-TCTTGCATCG
1 TAGTGAAGCAGATTGAAGACA-CAAG-TCTTGCCTCTCTCG-GTTG
* * * * *
6402923 ACAGTGAAGTAGATCGAAGACACAAGTCTTGCGTCCCTCGGTTG
1 -TAGTGAAGCAGATTGAAGACACAAGTCTTGCCTCTCTCGGTTG
* *
6402967 TAGTGGAGCAGGTTGAAGA
1 TAGTGAAGCAGATTGAAGA
6402986 TAGCAGGTCT
Statistics
Matches: 141, Mismatches: 40, Indels: 28
0.67 0.19 0.13
Matches are distributed among these distances:
42 3 0.02
43 57 0.40
44 40 0.28
45 38 0.27
46 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGTGAAGCAGATTGAAGACACAAGTCTTGCCTCTCTCGGTTG
Found at i:6402997 original size:44 final size:44
Alignment explanation
Indices: 6402694--6402997 Score: 154
Period size: 44 Copynumber: 6.9 Consensus size: 44
6402684 GCCCTACCTA
* * * * *
6402694 CCTCAGTTGTAGTGGAGCAGGTTAAAGGTAGCAGATCTTGCCTT
1 CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
* * * * * * * *
6402738 CCTAC-ATCGATAGTGAAGTAGATTGAAGACA-CAAGCCTTGCCTC
1 CCT-CGGTTG-TAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
* * *
6402782 TCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCT-
1 CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
* * * * * * * * *
6402825 -TTTGGCATGGACAGTGAAGCAGATTGAAGACA-CAAGCCTTGCCTC
1 CCTCGG--TTG-TAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
*
6402870 CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCT-
1 CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
* * * * * * * * * * * *
6402913 TCTTGCATCGACAGTGAAGTAGATCGAAGACA-CAAGTCTTGCGTC
1 CCTCG-GTTG-TAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
6402958 CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTG
1 CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTG
6402998 TCTTTCTGCA
Statistics
Matches: 180, Mismatches: 66, Indels: 28
0.66 0.24 0.10
Matches are distributed among these distances:
42 3 0.02
43 54 0.30
44 70 0.39
45 50 0.28
46 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (44 bp):
CCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGTCTTGCCTC
Found at i:6404479 original size:3 final size:3
Alignment explanation
Indices: 6404429--6404463 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
6404419 TGGCCTTCTG
*
6404429 ATT ATTT ATT ATT ATT ATT ATT AAT ATT ATT ATT A
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6404464 CCGCTTCGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:6407412 original size:2 final size:2
Alignment explanation
Indices: 6407405--6407446 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
6407395 ATGCTTAACA
6407405 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6407447 TACTCATAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6415958 original size:28 final size:28
Alignment explanation
Indices: 6415900--6415962 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
6415890 GGCTTAACCG
* * *
6415900 GAACAGAACAACACCACAATACTTATTA
1 GAACAAAACAACACCACAATACATATCA
* *
6415928 GAACAAAACAACACCATAATGCATATCA
1 GAACAAAACAACACCACAATACATATCA
6415956 GAACAAA
1 GAACAAA
6415963 GAGTGCGCTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.54, C:0.24, G:0.08, T:0.14
Consensus pattern (28 bp):
GAACAAAACAACACCACAATACATATCA
Found at i:6417646 original size:35 final size:35
Alignment explanation
Indices: 6417606--6417676 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
6417596 AAAGAAGTAC
6417606 AGACAAGATTCATTATTGAGGGTAAAAGGTGAAGA
1 AGACAAGATTCATTATTGAGGGTAAAAGGTGAAGA
6417641 AGACAAGATTCATTATTGAGGGTAAAAGGTGAAGA
1 AGACAAGATTCATTATTGAGGGTAAAAGGTGAAGA
6417676 A
1 A
6417677 TCTATCTCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.28, T:0.23
Consensus pattern (35 bp):
AGACAAGATTCATTATTGAGGGTAAAAGGTGAAGA
Found at i:6419077 original size:61 final size:60
Alignment explanation
Indices: 6418977--6419097 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 60
6418967 TATAAAAAGT
* ** *
6418977 TCAACAAATTTAGTCCTCAATGTTTACAAAATTTGTCATTTTTAGTTTGAATTCTAAAAAA
1 TCAACAAATTTAGCCCTCAATGTTTACAAAATTTGTCA-TTTTAACTTGAATCCTAAAAAA
* ** *
6419038 TCAATAAATTTAGCCCTCAATGTTTACAATTTTTTTCATTTTAACTTGAATCCTAAAAAA
1 TCAACAAATTTAGCCCTCAATGTTTACAAAATTTGTCATTTTAACTTGAATCCTAAAAAA
6419098 GTTAATTCTA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
60 19 0.37
61 33 0.63
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.41
Consensus pattern (60 bp):
TCAACAAATTTAGCCCTCAATGTTTACAAAATTTGTCATTTTAACTTGAATCCTAAAAAA
Found at i:6422091 original size:6 final size:6
Alignment explanation
Indices: 6422075--6422104 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
6422065 GGCTTTGGTG
6422075 GAAGG- GAAGGA GAAGGA GAAGGA GAAGGA G
1 GAAGGA GAAGGA GAAGGA GAAGGA GAAGGA G
6422105 CAGAAGCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GAAGGA
Found at i:6425191 original size:14 final size:14
Alignment explanation
Indices: 6425172--6425204 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6425162 AAAGTATTTT
*
6425172 AAAAATTCAAATTA
1 AAAAATTAAAATTA
6425186 AAAAATTAAAATTA
1 AAAAATTAAAATTA
6425200 AAAAA
1 AAAAA
6425205 AAGAGCATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATTAAAATTA
Found at i:6426881 original size:102 final size:102
Alignment explanation
Indices: 6426700--6426904 Score: 365
Period size: 102 Copynumber: 2.0 Consensus size: 102
6426690 AGAATGTCAC
*
6426700 ATCATTGAACTTTGATTATTTTTCGAAGTTCAAAGAGTAAAATAAATCTAATTGTCAGCTTCAAA
1 ATCATTGAACTTTGATTATTTTTCGAAGTTCAAAGAGTAAAATAAATCTAATTGTCAACTTCAAA
*
6426765 TACTAAAGTGGATAAAAGAATATAGGTACCAAACTAG
66 TACTAAAGTAGATAAAAGAATATAGGTACCAAACTAG
* * *
6426802 ATCATTGAATTTTGATTATTTTTCGAAGTTCAAAGATTAAAATGAATCTAATTGTCAACTTCAAA
1 ATCATTGAACTTTGATTATTTTTCGAAGTTCAAAGAGTAAAATAAATCTAATTGTCAACTTCAAA
6426867 TACTAAAGTAGATAAAAGAATATAGGTACCAAACTAG
66 TACTAAAGTAGATAAAAGAATATAGGTACCAAACTAG
6426904 A
1 A
6426905 ATTATGGTGG
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 98 1.00
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (102 bp):
ATCATTGAACTTTGATTATTTTTCGAAGTTCAAAGAGTAAAATAAATCTAATTGTCAACTTCAAA
TACTAAAGTAGATAAAAGAATATAGGTACCAAACTAG
Found at i:6431345 original size:17 final size:17
Alignment explanation
Indices: 6431325--6431371 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
6431315 CACATTTTAT
6431325 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
6431342 ATTATTTAGTCA-TATTGA
1 ATTATTTA-T-ATTATTGA
6431360 A-TATTTATATTA
1 ATTATTTATATTA
6431372 AAATTGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 3 0.11
17 14 0.52
18 8 0.30
19 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.55
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:6435005 original size:16 final size:17
Alignment explanation
Indices: 6434974--6435006 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6434964 AAATCATTAT
6434974 TTATAAATGCAATAAATC
1 TTATAAAT-CAATAAATC
6434992 TTATAAAT-AATAAAT
1 TTATAAATCAATAAAT
6435007 AATATTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
TTATAAATCAATAAATC
Found at i:6440952 original size:32 final size:32
Alignment explanation
Indices: 6440916--6441259 Score: 343
Period size: 32 Copynumber: 10.8 Consensus size: 32
6440906 TATATAAATT
* *
6440916 CATATACAAATCAATTCGGCAACATAAGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
*
6440948 CATATACAATTCAATTCGGAAATATATAGGTATA
1 CATATACAATTCAATTCGGCAATATA-A-GTATA
* *
6440982 CATATACAATTCAATTCGACAATA-AGTGTATA
1 CATATACAATTCAATTCGGCAATATA-AGTATA
* *
6441014 CCTATACAATTCAATTTGGCAATATAAGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* ***
6441046 CATATACAATTCAATTCGACAATAGGTGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* *
6441078 CCTATACAATTCAATTCGGCAACATAAGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* * ***
6441110 CATATACAATTCAATTTGACAATAGGTGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* * * ***
6441142 CCTATACAATTCAATTTGACAATAGGTGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* ***
6441174 CCTATACAATTCAATTCGGCAATAGGTGTATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* * *
6441206 CCTATATAATTTAATTCGGCAATAT-A-TATA
1 CATATACAATTCAATTCGGCAATATAAGTATA
* *
6441236 CGTATACAAATCAATTCGGCAATA
1 CATATACAATTCAATTCGGCAATA
6441260 CATAAAATAT
Statistics
Matches: 268, Mismatches: 41, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
30 24 0.09
32 214 0.80
33 3 0.01
34 27 0.10
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (32 bp):
CATATACAATTCAATTCGGCAATATAAGTATA
Found at i:6441050 original size:64 final size:64
Alignment explanation
Indices: 6440916--6441259 Score: 440
Period size: 64 Copynumber: 5.4 Consensus size: 64
6440906 TATATAAATT
* * * *** * *
6440916 CATATACAAATCAATTCGGCAACATAAGTATACATATACAATTCAATTCGGAAATATATAGGTAT
1 CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATA-A-GTAT
6440981 A
64 A
* *
6440982 CATATACAATTCAATTCGACAATAAGTGTATACCTATACAATTCAATTTGGCAATATAAGTATA
1 CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATA
*
6441046 CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAACATAAGTATA
1 CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATA
* * * ***
6441110 CATATACAATTCAATTTGACAATAGGTGTATACCTATACAATTCAATTTGACAATAGGTGTATA
1 CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATA
* * * *
6441174 CCTATACAATTCAATTCGGCAATAGGTGTATACCTATATAATTTAATTCGGCAATAT-A-TATA
1 CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATA
* * *
6441236 CGTATACAAATCAATTCGGCAATA
1 CATATACAATTCAATTCGACAATA
6441260 CATAAAATAT
Statistics
Matches: 248, Mismatches: 30, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
62 26 0.10
64 172 0.69
65 1 0.00
66 49 0.20
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (64 bp):
CATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTATA
Found at i:6441127 original size:96 final size:95
Alignment explanation
Indices: 6440916--6441259 Score: 383
Period size: 96 Copynumber: 3.6 Consensus size: 95
6440906 TATATAAATT
* * **
6440916 CATATACAAATCAATTCGGCAACATAAGTATACATATACAATTCAATTCGGA-AATATATAGGTA
1 CATATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTC-GACAATAGGT--GTA
* *
6440980 TACATATACAATTCAATTCGAC-AATAAGTGTATA
63 TACCTATACAATTCAATTCGGCAAATAA--GTATA
* *
6441014 CCTATACAATTCAATTTGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGTATAC
1 CATATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGTATAC
6441079 CTATACAATTCAATTCGGCAACATAAGTATA
66 CTATACAATTCAATTCGGCAA-ATAAGTATA
* * *** * *
6441110 CATATACAATTCAATTTGACAATAGGTGTATACCTATACAATTCAATTTGACAATAGGTGTATAC
1 CATATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGTATAC
*
6441175 CTATACAATTCAATTCGGC-AATAGGTGTATA
66 CTATACAATTCAATTCGGCAAATA--AGTATA
* * * * * *
6441206 CCTATATAATTTAATTCGGCAATAT-A-TATACGTATACAAATCAATTCGGCAATA
1 CATATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATA
6441260 CATAAAATAT
Statistics
Matches: 214, Mismatches: 27, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
94 27 0.13
95 1 0.00
96 129 0.60
97 3 0.01
98 54 0.25
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (95 bp):
CATATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGTATAC
CTATACAATTCAATTCGGCAAATAAGTATA
Found at i:6441494 original size:29 final size:30
Alignment explanation
Indices: 6441462--6441519 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
6441452 AAAAATACCT
* *
6441462 ATTTGGACATTT-TTCACTTTAGCCCCTAA
1 ATTTGCACATTTATTCAATTTAGCCCCTAA
* *
6441491 ATTTTCACATTTATTCAATTTAGTCCCTA
1 ATTTGCACATTTATTCAATTTAGCCCCTA
6441520 TTTCATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.45
Consensus pattern (30 bp):
ATTTGCACATTTATTCAATTTAGCCCCTAA
Found at i:6446183 original size:22 final size:22
Alignment explanation
Indices: 6446158--6446201 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6446148 TCTCGAAACT
6446158 TCTTTGATGCTGACTGAAATGA
1 TCTTTGATGCTGACTGAAATGA
6446180 TCTTTGATGCTGACTGAAATGA
1 TCTTTGATGCTGACTGAAATGA
6446202 CTTACTCGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (22 bp):
TCTTTGATGCTGACTGAAATGA
Found at i:6447647 original size:32 final size:32
Alignment explanation
Indices: 6447606--6448207 Score: 681
Period size: 32 Copynumber: 18.8 Consensus size: 32
6447596 CAATATATAA
* *
6447606 ATACATATACAATTCAATTCGACAACATAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* ***
6447638 ATACATATACAATTCAATTCGACAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
*
6447670 ATACCTATACAATTCAATTCGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* ***
6447702 ATACATATACAATTCAATTCGACAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
*
6447734 ATACCTATACAATTCAATTCGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* ***
6447766 ATACATATACAATTCAATTCGACAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* *
6447798 ATACCTATACAATTCAATTTGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* ***
6447830 ATACATACACAATTCAATTCGGCAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
*
6447862 ATACCTATACAATTCAATTCGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* * ***
6447894 ATACATATACAATTCGATTCGACAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
*
6447926 ATACCTATACAATTCAATTCGGCAATATAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* **
6447958 ATACATATACAATTCAATTCGACAATAATGTGT
1 ATACATATACAATTCAATTCGGCAAT-ATAAGT
6447991 ATATC-TATACAATTCAATTCGGCAATATAAGT
1 ATA-CATATACAATTCAATTCGGCAATATAAGT
* ***
6448023 ATACATATACAATTCAATTCGACAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* * * *
6448055 ATACCTGTACAATTTAATTCGGCAATACAAGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
***
6448087 ATACATATACAATTCAATTCGGCAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* ***
6448119 ATACCTATACAATTCAATTCGGCAATAGGTGT
1 ATACATATACAATTCAATTCGGCAATATAAGT
* *
6448151 ATATC-TGTACAATTCAATTCGGAAATAT-A-T
1 ATA-CATATACAATTCAATTCGGCAATATAAGT
* * *
6448181 ATACGTATACAAATCAATTCGACAATA
1 ATACATATACAATTCAATTCGGCAATA
6448208 CATAAAATAT
Statistics
Matches: 479, Mismatches: 86, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
29 1 0.00
30 22 0.05
31 1 0.00
32 426 0.89
33 28 0.06
34 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (32 bp):
ATACATATACAATTCAATTCGGCAATATAAGT
Found at i:6447679 original size:64 final size:64
Alignment explanation
Indices: 6447606--6448207 Score: 960
Period size: 64 Copynumber: 9.4 Consensus size: 64
6447596 CAATATATAA
* * *
6447606 ATACATATACAATTCAATTCGACAACATAAGTATACATATACAATTCAATTCGACAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
6447670 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
6447734 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
* * *
6447798 ATACCTATACAATTCAATTTGGCAATATAAGTATACATACACAATTCAATTCGGCAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
*
6447862 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCGATTCGACAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
*
6447926 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAATGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAAT-AGGTGT
*
6447991 ATATCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
* * * *
6448055 ATACCTGTACAATTTAATTCGGCAATACAAGTATACATATACAATTCAATTCGGCAATAGGTGT
1 ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
*** * *
6448119 ATACCTATACAATTCAATTCGGCAATAGGTGTATATC-TGTACAATTCAATTCGGA-AATA--TA
1 ATACCTATACAATTCAATTCGGCAATATAAGTATA-CATATACAATTCAATTC-GACAATAGGTG
6448180 T
64 T
* * *
6448181 ATACGTATACAAATCAATTCGACAATA
1 ATACCTATACAATTCAATTCGGCAATA
6448208 CATAAAATAT
Statistics
Matches: 505, Mismatches: 30, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
62 26 0.05
64 415 0.82
65 64 0.13
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (64 bp):
ATACCTATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
Found at i:6447715 original size:96 final size:96
Alignment explanation
Indices: 6447606--6448207 Score: 760
Period size: 96 Copynumber: 6.3 Consensus size: 96
6447596 CAATATATAA
* * *
6447606 ATACATATACAATTCAATTCGACAACATAAGTATACATATACAATTCAATTCGACAATAGGTGTA
1 ATACATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGTA
6447671 TACCTATACAATTCAATTCGGCAATATAAGT
66 TACCTATACAATTCAATTCGGCAATATAAGT
** * ***
6447702 ATACATATACAATTCAATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTA
1 ATACATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGTA
* * ***
6447767 TACATATACAATTCAATTCGACAATAGGTGT
66 TACCTATACAATTCAATTCGGCAATATAAGT
* * * * *
6447798 ATACCTATACAATTCAATTTGGCAATATAAGTATACATACACAATTCAATTCGGCAATAGGTGTA
1 ATACATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGTA
6447863 TACCTATACAATTCAATTCGGCAATATAAGT
66 TACCTATACAATTCAATTCGGCAATATAAGT
* ** * ***
6447894 ATACATATACAATTCGATTCGACAATAGGTGTATACCTATACAATTCAATTCGGCAATATAAGTA
1 ATACATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGTA
* * **
6447959 TACATATACAATTCAATTCGACAATAATGTGT
66 TACCTATACAATTCAATTCGGCAAT-ATAAGT
* * *
6447991 ATATC-TATACAATTCAATTCGGCAATATAAGTATACATATACAATTCAATTCGACAATAGGTGT
1 ATA-CATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGT
* * *
6448055 ATACCTGTACAATTTAATTCGGCAATACAAGT
65 ATACCTATACAATTCAATTCGGCAATATAAGT
* ** *
6448087 ATACATATACAATTCAATTCGGCAATAGGTGTATACCTATACAATTCAATTCGGCAATAGGTGTA
1 ATACATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGTA
* * *
6448152 TATCTGTACAATTCAATTCGGAAATAT-A-T
66 TACCTATACAATTCAATTCGGCAATATAAGT
* *
6448181 ATACGTATACAAATCAATTCGACAATA
1 ATACATATACAATTCAATTCGACAATA
6448208 CATAAAATAT
Statistics
Matches: 428, Mismatches: 75, Indels: 8
0.84 0.15 0.02
Matches are distributed among these distances:
94 25 0.06
95 2 0.00
96 322 0.75
97 78 0.18
98 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (96 bp):
ATACATATACAATTCAATTCGACAATAGAAGTATACATATACAATTCAATTCGGCAATAGGTGTA
TACCTATACAATTCAATTCGGCAATATAAGT
Found at i:6449232 original size:11 final size:11
Alignment explanation
Indices: 6449218--6449243 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
6449208 GTAAACACCA
6449218 AAAATAATTTT
1 AAAATAATTTT
6449229 AAAATAATTTT
1 AAAATAATTTT
6449240 AAAA
1 AAAA
6449244 CCTCAGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:6454688 original size:26 final size:26
Alignment explanation
Indices: 6454635--6454690 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
6454625 AATTTTAAAA
* * *
6454635 TATTTTTCAAATACTTTTTTATTTTT
1 TATTTTTAAAATAATTTTTTATTGTT
6454661 TATTTTTAAAATAATTTTTT-TGTGTT
1 TATTTTTAAAATAATTTTTTAT-TGTT
6454687 TATT
1 TATT
6454691 AAAAAATGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 1 0.04
26 25 0.96
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (26 bp):
TATTTTTAAAATAATTTTTTATTGTT
Found at i:6459519 original size:56 final size:56
Alignment explanation
Indices: 6459458--6459608 Score: 203
Period size: 56 Copynumber: 2.7 Consensus size: 56
6459448 TTTTATATAA
* *
6459458 TGCCATGGGTCTTGACCACATGGTATTACATACATTCATTCAATCATATCATATCT
1 TGCCATGGGTCTTAACCTCATGGTATTACATACATTCATTCAATCATATCATATCT
* * * * * *
6459514 TGCCATGGGTTTTAACCTCATGATTTTACATACATACATTCAGTCATTTCATATCT
1 TGCCATGGGTCTTAACCTCATGGTATTACATACATTCATTCAATCATATCATATCT
* * *
6459570 TGCCATGGGTCTTAACCTCATGGTCTTACAAATATTCAT
1 TGCCATGGGTCTTAACCTCATGGTATTACATACATTCAT
6459609 GTATCGCGAT
Statistics
Matches: 81, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 81 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (56 bp):
TGCCATGGGTCTTAACCTCATGGTATTACATACATTCATTCAATCATATCATATCT
Found at i:6467731 original size:22 final size:23
Alignment explanation
Indices: 6467690--6467737 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 23
6467680 GTAGTCTTTG
*
6467690 CTTTACTTTTGTTAATTTAT-CA
1 CTTTACTTTTGTTAAATTATGCA
6467712 CTTTA-TTTTGTTAACATTATGCA
1 CTTTACTTTTGTTAA-ATTATGCA
6467735 CTT
1 CTT
6467738 AGTTTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.23, C:0.15, G:0.06, T:0.56
Consensus pattern (23 bp):
CTTTACTTTTGTTAAATTATGCA
Found at i:6486266 original size:16 final size:16
Alignment explanation
Indices: 6486225--6486267 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
6486215 CGTTTTGTAC
*
6486225 TCTTCCTTTTCTTTCTT
1 TCTT-CTTTTTTTTCTT
6486242 TCTAT-TTTTTTTTCTT
1 TCT-TCTTTTTTTTCTT
6486258 TCTTCTTTTT
1 TCTTCTTTTT
6486268 ACTTCTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 1 0.04
16 18 0.78
17 3 0.13
18 1 0.04
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (16 bp):
TCTTCTTTTTTTTCTT
Found at i:6487154 original size:42 final size:42
Alignment explanation
Indices: 6487094--6487183 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
6487084 ACATGAGCGT
* * *
6487094 GTGTGGGCCACACAGGCAAGGACATGGGCGTGTGCCCAGGCC
1 GTGTGAGCCACACAGGCAAGGACATAGGCATGTGCCCAGGCC
* *
6487136 GTGTGAGCCACACGGGCAAGGACATAGGCATGTGTCCAGGCC
1 GTGTGAGCCACACAGGCAAGGACATAGGCATGTGCCCAGGCC
6487178 GTGTGA
1 GTGTGA
6487184 CGTATATAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.21, C:0.26, G:0.39, T:0.14
Consensus pattern (42 bp):
GTGTGAGCCACACAGGCAAGGACATAGGCATGTGCCCAGGCC
Found at i:6492877 original size:43 final size:43
Alignment explanation
Indices: 6492827--6492984 Score: 203
Period size: 43 Copynumber: 3.7 Consensus size: 43
6492817 TAATAATGTC
* * * *
6492827 ATATCCCAGATATGGTCTTACA-TATAATCTCGTATCGATTCCA
1 ATATCCCAGACATGGTCTTACACGA-AATCTCATATCGATGCCA
* *
6492870 ATATCCCAGCCATGGTCTTACACGAAATCACATATCGATGCCA
1 ATATCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCA
* *
6492913 ATATCCCAGACATGGTCTTACACGAAGTCTCATATCAATGCC-
1 ATATCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCA
* *
6492955 ATATCCCAGATATGGTCTTACACGTAATCT
1 ATATCCCAGACATGGTCTTACACGAAATCT
6492985 TGGTAACCCT
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
42 27 0.27
43 73 0.72
44 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.13, T:0.29
Consensus pattern (43 bp):
ATATCCCAGACATGGTCTTACACGAAATCTCATATCGATGCCA
Found at i:6497140 original size:42 final size:43
Alignment explanation
Indices: 6497019--6497140 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 43
6497009 CTTTAAAACT
* * *
6497019 ACACGGGAAAGGATATGGGTATGT-TCCTAGGCCGTGTAAGCT
1 ACACGGGAAAGGACATGGGTATGTGTCCTAGGCCGTGTGAGCC
* *
6497061 ACAAGGGCAAGGACATGGGTATGTG-CCTAGGCCGTGTGAGCC
1 ACACGGGAAAGGACATGGGTATGTGTCCTAGGCCGTGTGAGCC
* * *
6497103 ACACGGGTAAGGACATAGGCATGTGTCC-AGGCCGTGTG
1 ACACGGGAAAGGACATGGGTATGTGTCCTAGGCCGTGTG
6497141 GCGTATAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 67 0.97
43 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.36, T:0.20
Consensus pattern (43 bp):
ACACGGGAAAGGACATGGGTATGTGTCCTAGGCCGTGTGAGCC
Found at i:6513366 original size:22 final size:23
Alignment explanation
Indices: 6513319--6513369 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
6513309 ACTCTTTTAA
* *
6513319 TAATTGTTTAATTTATTCTTATT
1 TAATTGTTTAATTTATTATTAGT
6513342 TAATT-TTTAGATTTA-TATTAGT
1 TAATTGTTTA-ATTTATTATTAGT
6513364 TAATTG
1 TAATTG
6513370 AATTCTCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (23 bp):
TAATTGTTTAATTTATTATTAGT
Found at i:6516871 original size:2 final size:2
Alignment explanation
Indices: 6516864--6516893 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6516854 CATAGCTTGC
6516864 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6516894 CTGCATAGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6519081 original size:38 final size:38
Alignment explanation
Indices: 6519034--6519170 Score: 177
Period size: 38 Copynumber: 3.6 Consensus size: 38
6519024 CTAGCATTTT
** *
6519034 TTGTAGATTCTTGGGTAATATAACGAGATCTAGCCTTA
1 TTGTAGATTCTCAGGTAATATAACGAGATCTAGCCTTG
*
6519072 TTGTAGATTCTC-GAGTAATATAATGAGATCTAGCCTTG
1 TTGTAGATTCTCAG-GTAATATAACGAGATCTAGCCTTG
* *
6519110 TTGTAGATTCTTAGGTACTATAACGAGATCTAGCTCTTG
1 TTGTAGATTCTCAGGTAATATAACGAGATCTAGC-CTTG
* *
6519149 TCGTGGATTCTCAGGTAATATA
1 TTGTAGATTCTCAGGTAATATA
6519171 TAACATAGGT
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
37 1 0.01
38 62 0.72
39 23 0.27
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (38 bp):
TTGTAGATTCTCAGGTAATATAACGAGATCTAGCCTTG
Found at i:6523946 original size:21 final size:22
Alignment explanation
Indices: 6523922--6523964 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
6523912 ATTTAAGTAT
*
6523922 AATTTATAAAAAT-TTTAAAAA
1 AATTAATAAAAATATTTAAAAA
6523943 AATTAATAAAAATATTTAAAAA
1 AATTAATAAAAATATTTAAAAA
6523965 TTTAACAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATTAATAAAAATATTTAAAAA
Found at i:6523969 original size:21 final size:21
Alignment explanation
Indices: 6523922--6523969 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
6523912 ATTTAAGTAT
6523922 AATTT-ATAAAAATTTTAAAA
1 AATTTAATAAAAATTTTAAAA
*
6523942 AAATTAATAAAAATATTT-AAA
1 AATTTAATAAAAAT-TTTAAAA
6523963 AATTTAA
1 AATTTAA
6523970 CAAATTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 4 0.17
21 17 0.71
22 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTTAATAAAAATTTTAAAA
Found at i:6526931 original size:20 final size:19
Alignment explanation
Indices: 6526892--6526936 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
6526882 ATTTTTTTTC
6526892 ATTTTTATTATTTAAATAT
1 ATTTTTATTATTTAAATAT
**
6526911 AATTTTTATTATTTATCTAT
1 -ATTTTTATTATTTAAATAT
6526931 ATTTTT
1 ATTTTT
6526937 CTAAAATTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTATTATTTAAATAT
Found at i:6528685 original size:45 final size:46
Alignment explanation
Indices: 6528631--6528733 Score: 172
Period size: 46 Copynumber: 2.2 Consensus size: 46
6528621 TACAAAGATA
*
6528631 AAAACCAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATT
1 AAAA-CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
6528677 AAAACAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
1 AAAACAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
*
6528723 AAAAGAAAATA
1 AAAACAAAATA
6528734 GATATACACA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
45 19 0.35
46 35 0.65
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (46 bp):
AAAACAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATT
Found at i:6533246 original size:45 final size:46
Alignment explanation
Indices: 6533197--6533294 Score: 171
Period size: 46 Copynumber: 2.2 Consensus size: 46
6533187 AGATAGAAAC
*
6533197 CAAAATATTATCTCTTAAAC-TTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
6533242 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
1 CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
*
6533288 GAAAATA
1 CAAAATA
6533295 GATATACACA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 19 0.38
46 31 0.62
ACGTcount: A:0.44, C:0.19, G:0.03, T:0.34
Consensus pattern (46 bp):
CAAAATATTATCTCCTAAACTTTAGCATCTAATCTCCTAATTAAAA
Found at i:6537999 original size:33 final size:33
Alignment explanation
Indices: 6537955--6538053 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 33
6537945 GTGGACTTTA
*
6537955 TCTGTGTTTACTATCCTAACAGATTGTCTTTGT
1 TCTGTGTTTACTATCCTAACAGATTATCTTTGT
* * * * *
6537988 TTTGTGTTTACTATTCGAGCGGATTATCTTTGT
1 TCTGTGTTTACTATCCTAACAGATTATCTTTGT
*
6538021 TCTGTGTTTACTATCCTAGA-AGACTATCTTTGT
1 TCTGTGTTTACTATCCTA-ACAGATTATCTTTGT
6538054 AGATGCCATA
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.18, C:0.16, G:0.17, T:0.48
Consensus pattern (33 bp):
TCTGTGTTTACTATCCTAACAGATTATCTTTGT
Found at i:6539257 original size:30 final size:30
Alignment explanation
Indices: 6539221--6539277 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
6539211 ACCAAGGAAG
6539221 CCTTGAGAACTAGTAGAAAAACCTTGAGCC
1 CCTTGAGAACTAGTAGAAAAACCTTGAGCC
* * *
6539251 CCTTGAGCAGTAGTAGGAAAACCTTGA
1 CCTTGAGAACTAGTAGAAAAACCTTGA
6539278 AAACCTTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.21
Consensus pattern (30 bp):
CCTTGAGAACTAGTAGAAAAACCTTGAGCC
Done.