Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 143 of 205
Found at i:43365092 original size:15 final size:16
Alignment explanation
Indices: 43365063--43365105 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
43365053 TATTGCAATG
*
43365063 ATTTATTTATAAAT-AA
1 ATTT-TTTATTAATAAA
43365079 ATTTTTTATTAATAAA
1 ATTTTTTATTAATAAA
43365095 AGTTTTTTATT
1 A-TTTTTTATT
43365106 CTAATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 7 0.29
17 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
ATTTTTTATTAATAAA
Found at i:43368474 original size:25 final size:26
Alignment explanation
Indices: 43368446--43368494 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
43368436 AGAAGAGAAG
*
43368446 ATGAAGAACAGAAAAAGAA-AAAGGA
1 ATGAAAAACAGAAAAAGAAGAAAGGA
* *
43368471 ATGAAAAACGGAAGAAGAAGAAAG
1 ATGAAAAACAGAAAAAGAAGAAAG
43368495 AGCCTTACCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.65, C:0.04, G:0.27, T:0.04
Consensus pattern (26 bp):
ATGAAAAACAGAAAAAGAAGAAAGGA
Found at i:43368578 original size:18 final size:18
Alignment explanation
Indices: 43368555--43368592 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
43368545 TTTGCAATCC
43368555 AAGGGGAAGGGAAAAGGG
1 AAGGGGAAGGGAAAAGGG
*
43368573 AAGGGGAAGGGAAAGGGG
1 AAGGGGAAGGGAAAAGGG
43368591 AA
1 AA
43368593 AGGGTAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGAAAAGGG
Found at i:43368605 original size:24 final size:24
Alignment explanation
Indices: 43368555--43368606 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
43368545 TTTGCAATCC
* **
43368555 AAGGGGAAGGGAAAAGGGAAGGGG
1 AAGGGAAAGGGAAAAGGGAAGAAG
* *
43368579 AAGGGAAAGGGGAAAGGGTAGAAG
1 AAGGGAAAGGGAAAAGGGAAGAAG
43368603 AAGG
1 AAGG
43368607 CATCATTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.54, T:0.02
Consensus pattern (24 bp):
AAGGGAAAGGGAAAAGGGAAGAAG
Found at i:43377342 original size:42 final size:43
Alignment explanation
Indices: 43377137--43377408 Score: 300
Period size: 43 Copynumber: 6.3 Consensus size: 43
43377127 ACGTCGCTAA
* * * * *
43377137 CTTTTGCGGCGCTTACAGAAAAAAACGTCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTA-GGAAAAAAACGCCGCTAAAAGTAATGTT
* * *
43377181 CTTTAGCGGCGCTTAGGAAAAAGACGCCGCTAATTA-TCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAA-AAGTAATGTT
* ** * *
43377224 CTTTAGCAGCGCTTAGGAAAAAAACATCGCT-AATGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAG-TAATGTT
* *
43377267 CTTTAGCAGTGCTTAGGAAAAAAACGCCGCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAATGTT
* *
43377310 CTATAGCGGCGCTT-GGTAAAAAACGCCGCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAATGTT
* *
43377352 CTATAGCGGCGCTT-GGTAAAAAACGCCGCTAAAAGTAATGTT
1 CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAATGTT
* *
43377394 TTTTAACGGCGCTTA
1 CTTTAGCGGCGCTTA
43377409 TTTCACAAAC
Statistics
Matches: 199, Mismatches: 24, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
42 81 0.41
43 101 0.51
44 17 0.09
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTAGGAAAAAAACGCCGCTAAAAGTAATGTT
Found at i:43382903 original size:25 final size:25
Alignment explanation
Indices: 43382875--43382934 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
43382865 TGTATTATGT
* *
43382875 AAGTTGTGTATAATGTTAGTTATCA
1 AAGTTATGTATAATGTAAGTTATCA
* **
43382900 AAGTTATGTATTATGTAAGTTATTT
1 AAGTTATGTATAATGTAAGTTATCA
43382925 AAGTTATGTA
1 AAGTTATGTA
43382935 AGTTGTGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (25 bp):
AAGTTATGTATAATGTAAGTTATCA
Found at i:43382922 original size:9 final size:9
Alignment explanation
Indices: 43382857--43383008 Score: 92
Period size: 9 Copynumber: 17.8 Consensus size: 9
43382847 NNNNNNNNNN
*
43382857 GTAAGTAAT
1 GTAAGTTAT
43382866 GT-A-TTAT
1 GTAAGTTAT
*
43382873 GTAAGTTGT
1 GTAAGTTAT
*
43382882 GT-A-TAAT
1 GTAAGTTAT
*
43382889 GTTAGTTAT
1 GTAAGTTAT
**
43382898 CAAAGTTAT
1 GTAAGTTAT
43382907 GT-A-TTAT
1 GTAAGTTAT
43382914 GTAAGTTAT
1 GTAAGTTAT
*
43382923 TTAAGTTAT
1 GTAAGTTAT
*
43382932 GTAAGTTGT
1 GTAAGTTAT
43382941 GT-A-TTAT
1 GTAAGTTAT
43382948 GTAAGTTAT
1 GTAAGTTAT
* *
43382957 GTAGGCTAT
1 GTAAGTTAT
43382966 GT-A-TTAT
1 GTAAGTTAT
43382973 GTAAGTTAT
1 GTAAGTTAT
*
43382982 -TATGTTATTAT
1 GTAAG---TTAT
43382993 GTAAGTTAT
1 GTAAGTTAT
*
43383002 GCAAGTT
1 GTAAGTT
43383009 TATATATAAG
Statistics
Matches: 108, Mismatches: 21, Indels: 28
0.69 0.13 0.18
Matches are distributed among these distances:
7 25 0.23
8 12 0.11
9 64 0.59
11 4 0.04
12 3 0.03
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.47
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:43382930 original size:34 final size:34
Alignment explanation
Indices: 43382892--43382956 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
43382882 GTATAATGTT
43382892 AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
1 AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
** *
43382926 AGTTATGTAAGTTGTGTATTATGTAAGTTAT
1 AGTTATCAAAGTTATGTATTATGTAAGTTAT
43382957 GTAGGCTATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (34 bp):
AGTTATCAAAGTTATGTATTATGTAAGTTATTTA
Found at i:43382947 original size:25 final size:25
Alignment explanation
Indices: 43382919--43383008 Score: 100
Period size: 25 Copynumber: 3.8 Consensus size: 25
43382909 ATTATGTAAG
*
43382919 TTATTTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
* * *
43382944 TTATGTAAGTTATGTAGGCTATGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
43382969 TTATGTAAGTTAT-T-A--TGT-TA
1 TTATGTAAGTTATGTAAGTTGTGTA
*
43382989 TTATGTAAGTTATGCAAGTT
1 TTATGTAAGTTATGTAAGTT
43383009 TATATATAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
20 15 0.28
21 2 0.04
22 1 0.02
24 2 0.04
25 34 0.63
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTTGTGTA
Found at i:43382955 original size:59 final size:59
Alignment explanation
Indices: 43382869--43382982 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
43382859 AAGTAATGTA
* *
43382869 TTATGTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAG
1 TTATGTAAGTTGTGTATAATGTAAGTTATCAAAGCTATGTATTATGTAAGTTATTTAAG
* ** *
43382928 TTATGTAAGTTGTGTATTATGTAAGTTATGTAGGCTATGTATTATGTAAGTTATT
1 TTATGTAAGTTGTGTATAATGTAAGTTATCAAAGCTATGTATTATGTAAGTTATT
43382983 ATGTTATTAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 49 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (59 bp):
TTATGTAAGTTGTGTATAATGTAAGTTATCAAAGCTATGTATTATGTAAGTTATTTAAG
Found at i:43382967 original size:34 final size:34
Alignment explanation
Indices: 43382900--43382975 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
43382890 TTAGTTATCA
* *
43382900 AAGTTATGTATTATGTAAGTTATTTAAGTTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
* *
43382934 AAGTTGTGTATTATGTAAGTTATGTAGGCTATGT
1 AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
43382968 -A-TTATGTA
1 AAGTTATGTA
43382976 AGTTATTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 6 0.16
33 1 0.03
34 30 0.81
ACGTcount: A:0.30, C:0.01, G:0.21, T:0.47
Consensus pattern (34 bp):
AAGTTATGTATTATGTAAGTTATGTAAGCTATGT
Found at i:43382992 original size:20 final size:19
Alignment explanation
Indices: 43382903--43383001 Score: 73
Period size: 25 Copynumber: 5.1 Consensus size: 19
43382893 GTTATCAAAG
43382903 TTATGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
*
43382922 TT-T-AAGTTATGTAAG---
1 TTATGTA-TTATGTAAGTTA
*
43382937 TTGTGTATTATGTAAGTTA
1 TTATGTATTATGTAAGTTA
43382956 TGTAGGCTATGTATTATGTAAGTTA
1 --T----TATGTATTATGTAAGTTA
43382981 TTATGTTATTATGTAAGTTA
1 TTATG-TATTATGTAAGTTA
43383001 T
1 T
43383002 GCAAGTTTAT
Statistics
Matches: 64, Mismatches: 3, Indels: 25
0.70 0.03 0.27
Matches are distributed among these distances:
15 2 0.03
16 10 0.16
17 2 0.03
18 10 0.16
19 6 0.09
20 15 0.23
21 1 0.02
23 1 0.02
25 17 0.27
ACGTcount: A:0.29, C:0.01, G:0.19, T:0.51
Consensus pattern (19 bp):
TTATGTATTATGTAAGTTA
Found at i:43383273 original size:2 final size:2
Alignment explanation
Indices: 43383268--43383296 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43383258 TTTTAAATAA
43383268 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
43383297 AATTTTAAGT
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:43383359 original size:17 final size:17
Alignment explanation
Indices: 43383298--43383387 Score: 81
Period size: 17 Copynumber: 4.9 Consensus size: 17
43383288 ATATATATAA
43383298 ATTTTAAGTAATGTAATAT
1 ATTTT-AGTAA-GTAATAT
*
43383317 ATTTAAGTAATGTAAGTTAT
1 ATTTTAGTAA-GTAA--TAT
*
43383337 AAATTTTTGTAAGTAATAT
1 --ATTTTAGTAAGTAATAT
* *
43383356 ATTTAAGTAATTAATAT
1 ATTTTAGTAAGTAATAT
43383373 ATTTTAGTAAGTAAT
1 ATTTTAGTAAGTAAT
43383388 GTAAGTAATG
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
17 27 0.46
18 10 0.17
19 7 0.12
20 3 0.05
21 4 0.07
22 8 0.14
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (17 bp):
ATTTTAGTAAGTAATAT
Found at i:43383377 original size:34 final size:37
Alignment explanation
Indices: 43383297--43383479 Score: 131
Period size: 39 Copynumber: 4.8 Consensus size: 37
43383287 TATATATATA
43383297 AATTTTAAGTAATGTAATATATTTAAGTAATGTAAGTTAT
1 AATTTT-AGTAA-GTAATATATTTAAGTAATGTAAG-TAT
*
43383337 AAATTTTTGTAAGTAATATATTTAAGTAAT-TAA-TAT
1 -AATTTTAGTAAGTAATATATTTAAGTAATGTAAGTAT
* ** * * *
43383373 -ATTTTAGTAAGTAATGTAAGTAATGTAATATATACTTT
1 AATTTTAGTAAGTAATATATTTAA-GTAATGTA-AGTAT
* * *
43383411 AATTTTAGTAAGTCATGTATTTAAGTAATATATTTAAGTA-
1 AATTTTAGTAAGTAATATATTTAAG---TA-ATGTAAGTAT
* * *
43383451 AATTCTAGTAAGTAATGTATTTAATTAAT
1 AATTTTAGTAAGTAATATATTTAAGTAAT
43383480 ATATTTAAGT
Statistics
Matches: 118, Mismatches: 15, Indels: 23
0.76 0.10 0.15
Matches are distributed among these distances:
34 19 0.16
35 5 0.04
36 7 0.06
37 3 0.03
38 6 0.05
39 38 0.32
40 26 0.22
41 10 0.08
42 4 0.03
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.45
Consensus pattern (37 bp):
AATTTTAGTAAGTAATATATTTAAGTAATGTAAGTAT
Found at i:43383444 original size:13 final size:13
Alignment explanation
Indices: 43383428--43383492 Score: 71
Period size: 13 Copynumber: 4.9 Consensus size: 13
43383418 GTAAGTCATG
43383428 TATTTAAGTAATA
1 TATTTAAGTAATA
43383441 TATTTAAGTAA-A
1 TATTTAAGTAATA
*
43383453 T-TCTAGTAAGTAATG
1 TAT-T--TAAGTAATA
*
43383468 TATTTAATTAATA
1 TATTTAAGTAATA
43383481 TATTTAAGTAAT
1 TATTTAAGTAAT
43383493 GTAAGTTATA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
11 1 0.02
12 3 0.07
13 29 0.67
14 7 0.16
15 2 0.05
16 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:43384360 original size:13 final size:13
Alignment explanation
Indices: 43384342--43384371 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43384332 TTCACTTCAT
43384342 TATTAATACCAAA
1 TATTAATACCAAA
*
43384355 TATTAATATCAAA
1 TATTAATACCAAA
43384368 TATT
1 TATT
43384372 TAACAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTAATACCAAA
Found at i:43386816 original size:15 final size:15
Alignment explanation
Indices: 43386798--43386973 Score: 98
Period size: 15 Copynumber: 11.9 Consensus size: 15
43386788 ACCCTTGACA
*
43386798 CCCTAAACCTTAAAT
1 CCCTAAACCCTAAAT
*
43386813 CCCTAACCCCTAAAT
1 CCCTAAACCCTAAAT
* **
43386828 CTCTTAGCCCCTAAAT
1 C-CCTAAACCCTAAAT
* * *
43386844 TCCTAACCCCT-AAC
1 CCCTAAACCCTAAAT
* *
43386858 CCCT-AACCCTTAAC
1 CCCTAAACCCTAAAT
43386872 CCCTAAATCCCT-AA-
1 CCCTAAA-CCCTAAAT
*
43386886 CACCTAACCCCTAAAT
1 C-CCTAAACCCTAAAT
* *
43386902 CCCTAATCCCT-AAC
1 CCCTAAACCCTAAAT
* *
43386916 CCCTAAACCTTATAT
1 CCCTAAACCCTAAAT
*
43386931 CCC-AAACACCT-AAC
1 CCCTAAAC-CCTAAAT
43386945 CCCTAAATCCCT-AAT
1 CCCTAAA-CCCTAAAT
*
43386960 CCCTAACCCCTAAA
1 CCCTAAACCCTAAA
43386974 CCTTATATCC
Statistics
Matches: 127, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
13 5 0.04
14 40 0.31
15 64 0.50
16 18 0.14
ACGTcount: A:0.34, C:0.44, G:0.01, T:0.22
Consensus pattern (15 bp):
CCCTAAACCCTAAAT
Found at i:43386825 original size:22 final size:22
Alignment explanation
Indices: 43386798--43386922 Score: 90
Period size: 22 Copynumber: 5.6 Consensus size: 22
43386788 ACCCTTGACA
*
43386798 CCCTAAACCTTAAATCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
* * ** *
43386820 CCCTAAATCTCTTAGCCCCTAAAT
1 CCCTAAA-CCCTAAATCCCT-AAC
* * *
43386844 TCCTAACCCCT-AACCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
* *
43386865 CCTTAACCCCTAAATCCCTAAC
1 CCCTAAACCCTAAATCCCTAAC
* * *
43386887 ACCTAACCCCTAAATCCCTAAT
1 CCCTAAACCCTAAATCCCTAAC
*
43386909 CCCTAACCCCTAAA
1 CCCTAAACCCTAAA
43386923 CCTTATATCC
Statistics
Matches: 82, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
21 11 0.13
22 54 0.66
23 10 0.12
24 7 0.09
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (22 bp):
CCCTAAACCCTAAATCCCTAAC
Found at i:43386857 original size:7 final size:7
Alignment explanation
Indices: 43386845--43386972 Score: 112
Period size: 7 Copynumber: 17.7 Consensus size: 7
43386835 CCCCTAAATT
43386845 CCTAACC
1 CCTAACC
43386852 CCTAACC
1 CCTAACC
43386859 CCTAACC
1 CCTAACC
*
43386866 CTTAACC
1 CCTAACC
*
43386873 CCTAAATC
1 CCT-AACC
*
43386881 CCTAACA
1 CCTAACC
43386888 CCTAACC
1 CCTAACC
*
43386895 CCTAAATC
1 CCT-AACC
*
43386903 CCTAATC
1 CCTAACC
43386910 CCTAACC
1 CCTAACC
*
43386917 CCTAAAC
1 CCTAACC
* *
43386924 CTTATATC
1 CCTA-ACC
* *
43386932 CCAAACA
1 CCTAACC
43386939 CCTAACC
1 CCTAACC
*
43386946 CCTAAATC
1 CCT-AACC
*
43386954 CCTAATC
1 CCTAACC
43386961 CCTAACC
1 CCTAACC
43386968 CCTAA
1 CCTAA
43386973 ACCTTATATC
Statistics
Matches: 98, Mismatches: 19, Indels: 8
0.78 0.15 0.06
Matches are distributed among these distances:
7 76 0.78
8 22 0.22
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.20
Consensus pattern (7 bp):
CCTAACC
Found at i:43386891 original size:29 final size:28
Alignment explanation
Indices: 43386845--43386978 Score: 109
Period size: 29 Copynumber: 4.9 Consensus size: 28
43386835 CCCCTAAATT
*
43386845 CCTAACCCCTAACCCCTAACCCTTAACC
1 CCTAATCCCTAACCCCTAACCCTTAACC
* * *
43386873 CCTAAATCCCTAACACCTAACCCCTAAATC
1 CCT-AATCCCTAACCCCTAA-CCCTTAACC
*
43386903 CCTAATCCCTAACCCCTAAACCTT-A--
1 CCTAATCCCTAACCCCTAACCCTTAACC
* * * *
43386928 --T-ATCCCAAACACCTAACCCCTAAATC
1 CCTAATCCCTAACCCCTAA-CCCTTAACC
*
43386954 CCTAATCCCTAACCCCTAAACCTTA
1 CCTAATCCCTAACCCCTAACCCTTA
43386979 TATCCCAAAC
Statistics
Matches: 82, Mismatches: 15, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
22 13 0.16
23 4 0.05
24 1 0.01
27 1 0.01
28 11 0.13
29 42 0.51
30 10 0.12
ACGTcount: A:0.34, C:0.46, G:0.00, T:0.21
Consensus pattern (28 bp):
CCTAATCCCTAACCCCTAACCCTTAACC
Found at i:43386913 original size:51 final size:51
Alignment explanation
Indices: 43386851--43386993 Score: 207
Period size: 51 Copynumber: 2.8 Consensus size: 51
43386841 AATTCCTAAC
* * * *
43386851 CCCTAACCCCTAACCCTTAACCCCTAAATCCCTAACACCTAACCCCTAAAT
1 CCCTAATCCCTAACCCCTAAACCCTAAATCCCAAACACCTAACCCCTAAAT
* *
43386902 CCCTAATCCCTAACCCCTAAACCTTATATCCCAAACACCTAACCCCTAAAT
1 CCCTAATCCCTAACCCCTAAACCCTAAATCCCAAACACCTAACCCCTAAAT
* *
43386953 CCCTAATCCCTAACCCCTAAACCTTATATCCCAAAC-CCTAA
1 CCCTAATCCCTAACCCCTAAACCCTAAATCCCAAACACCTAA
43386994 TAGAGTACAT
Statistics
Matches: 86, Mismatches: 6, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
50 5 0.06
51 81 0.94
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (51 bp):
CCCTAATCCCTAACCCCTAAACCCTAAATCCCAAACACCTAACCCCTAAAT
Found at i:43386932 original size:22 final size:22
Alignment explanation
Indices: 43386836--43386973 Score: 124
Period size: 22 Copynumber: 6.3 Consensus size: 22
43386826 ATCTCTTAGC
* *
43386836 CCCTAAATTCCTAACCCCTAAC
1 CCCTAAATCCCTAACCCCTAAA
43386858 CCCT-AA-CCCTTAACCCCTAAA
1 CCCTAAATCCC-TAACCCCTAAA
43386879 TCCCT-AA-CACCTAACCCCTAAA
1 -CCCTAAATC-CCTAACCCCTAAA
43386901 TCCCT-AATCCCTAACCCCTAAA
1 -CCCTAAATCCCTAACCCCTAAA
* * * * *
43386923 CCTTATATCCCAAACACCTAAC
1 CCCTAAATCCCTAACCCCTAAA
* *
43386945 CCCTAAATCCCTAATCCCTAAC
1 CCCTAAATCCCTAACCCCTAAA
43386967 CCCTAAA
1 CCCTAAA
43386974 CCTTATATCC
Statistics
Matches: 99, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
20 2 0.02
21 15 0.15
22 79 0.80
23 3 0.03
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (22 bp):
CCCTAAATCCCTAACCCCTAAA
Found at i:43388182 original size:14 final size:14
Alignment explanation
Indices: 43388163--43388230 Score: 52
Period size: 15 Copynumber: 4.9 Consensus size: 14
43388153 ATGGCCGTTG
43388163 AAACCCTAAATCTC
1 AAACCCTAAATCTC
*
43388177 AAACCCCTAAACCTC
1 AAA-CCCTAAATCTC
*
43388192 TAACCCCTAAAT-T-
1 -AAACCCTAAATCTC
* *
43388205 -AACCTTAAATCCC
1 AAACCCTAAATCTC
*
43388218 AAACCTTAAATCT
1 AAACCCTAAATCT
43388231 ATACCCCGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
11 8 0.19
14 15 0.36
15 17 0.40
16 2 0.05
ACGTcount: A:0.41, C:0.35, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATCTC
Found at i:43388186 original size:15 final size:15
Alignment explanation
Indices: 43388166--43388203 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
43388156 GCCGTTGAAA
43388166 CCCTAAATCTCAAAC
1 CCCTAAATCTCAAAC
* *
43388181 CCCTAAACCTCTAAC
1 CCCTAAATCTCAAAC
43388196 CCCTAAAT
1 CCCTAAAT
43388204 TAACCTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.37, C:0.42, G:0.00, T:0.21
Consensus pattern (15 bp):
CCCTAAATCTCAAAC
Found at i:43388783 original size:41 final size:41
Alignment explanation
Indices: 43388721--43389054 Score: 391
Period size: 41 Copynumber: 8.1 Consensus size: 41
43388711 TTTTGTTACT
** * *
43388721 ATTAGCGGCGCTTC-GGCAAAAACGCCGCTAAAGGTAAGAGT
1 ATTAGCGGCGC-TCAGATAAAAACGCCGCTAAAGGTCAGAGC
* * *
43388762 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
* * * *
43388803 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGT
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
* * *
43388844 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
* * * *
43388885 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGT
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
* * *
43388926 ATTAGTGGCGCTCAGATAAAAACGCCGCTAAAGATCCGAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
* * * *
43388967 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGA
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
* ** *
43389008 ATTAGCGACGCTCAGATAAAAACGCCGCTAAATATCCGAGC
1 ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
43389049 ATTAGC
1 ATTAGC
43389055 TGTAACAACC
Statistics
Matches: 242, Mismatches: 50, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
40 2 0.01
41 240 0.99
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (41 bp):
ATTAGCGGCGCTCAGATAAAAACGCCGCTAAAGGTCAGAGC
Found at i:43388858 original size:82 final size:82
Alignment explanation
Indices: 43388721--43389054 Score: 578
Period size: 82 Copynumber: 4.1 Consensus size: 82
43388711 TTTTGTTACT
* ** * **
43388721 ATTAGCGGCGCTTCGGCAAAAACGCCGCTAAAGGTAAGAGTATTAGTGGCGCTCAGATAAAAACG
1 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
43388786 CCGCTAAAGATCCGAGC
66 CCGCTAAAGATCCGAGC
43388803 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
1 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
43388868 CCGCTAAAGATCCGAGC
66 CCGCTAAAGATCCGAGC
43388885 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
1 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
43388950 CCGCTAAAGATCCGAGC
66 CCGCTAAAGATCCGAGC
* * *
43388967 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGAATTAGCGACGCTCAGATAAAAACG
1 ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
*
43389032 CCGCTAAATATCCGAGC
66 CCGCTAAAGATCCGAGC
43389049 ATTAGC
1 ATTAGC
43389055 TGTAACAACC
Statistics
Matches: 242, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 242 1.00
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.18
Consensus pattern (82 bp):
ATTAGCGGCGCTTAGATAAAAATGCCGCTAAAGGCCAGAGTATTAGTGGCGCTCAGATAAAAACG
CCGCTAAAGATCCGAGC
Found at i:43398989 original size:40 final size:41
Alignment explanation
Indices: 43398893--43398990 Score: 96
Period size: 40 Copynumber: 2.5 Consensus size: 41
43398883 GCGCTTTATA
* * **
43398893 TAAAACGCCGCTAATTC-CTATTTTTAGCGGCGCTTCTTGG
1 TAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTCTTGG
* * *
43398933 -AAATCACTGCTGATGCTCTACCTTTAGCGGCGC-T-TTGG
1 TAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTCTTGG
43398971 CTAAATCGCCGCTAATGCTC
1 -TAAATCGCCGCTAATGCTC
43398991 GATTTTTTGT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
38 4 0.09
39 12 0.27
40 29 0.64
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (41 bp):
TAAATCGCCGCTAATGCTCTACCTTTAGCGGCGCTTCTTGG
Found at i:43402240 original size:382 final size:382
Alignment explanation
Indices: 43401534--43402298 Score: 1494
Period size: 382 Copynumber: 2.0 Consensus size: 382
43401524 CTCACTAGCT
43401534 TTATACCTTTAGATATTTGGACTAATGGTCCAAACACTCCACGAATTTAATTATACTTAAGTTCC
1 TTATACCTTTAGATATTTGGACTAATGGTCCAAACACTCCACGAATTTAATTATACTTAAGTTCC
*
43401599 GTCTTTCTATTTTGATCAGTTTATTCCATATCTATATTTCTCAATAAATTTATTCAAGATCATCC
66 GTCTTTCTATTTTGATCAGTTTATTCCATATCCATATTTCTCAATAAATTTATTCAAGATCATCC
43401664 TTTTATTTCGTTATTTCAACAATAATATTGCATGCAAAACCATTGTCAACCACTTTTATTATCAA
131 TTTTATTTCGTTATTTCAACAATAATATTGCATGCAAAACCATTGTCAACCACTTTTATTATCAA
43401729 TTCCATATTTTCTTGAATTGACATAACTTATCGAGATATCTTATTTTCACTATTTTAATATTCAG
196 TTCCATATTTTCTTGAATTGACATAACTTATCGAGATATCTTATTTTCACTATTTTAATATTCAG
43401794 TTTTAGGTACTTGAATCTCTTCTATAGTTTTACTTATTAGTTATGCCTTGGGTCTCTTCTGGAGC
261 TTTTAGGTACTTGAATCTCTTCTATAGTTTTACTTATTAGTTATGCCTTGGGTCTCTTCTGGAGC
43401859 ACCCACCTTCACTATATGATCATCTAAATTTATTGTTTTCTTGTATGAGAAATTTCA
326 ACCCACCTTCACTATATGATCATCTAAATTTATTGTTTTCTTGTATGAGAAATTTCA
* *
43401916 TTATACCTTTAGATATTTGGACTAATGGTCCAAACACTCTACGAATTTAATTATACTTAAGTTTC
1 TTATACCTTTAGATATTTGGACTAATGGTCCAAACACTCCACGAATTTAATTATACTTAAGTTCC
43401981 GTCTTTCTATTTTGATCAGTTTATTCCATATCCATATTTCTCAATAAATTTATTCAAGATCATCC
66 GTCTTTCTATTTTGATCAGTTTATTCCATATCCATATTTCTCAATAAATTTATTCAAGATCATCC
43402046 TTTTATTTCGTTATTTCAACAATAATATTGCATGCAAAACCATTGTCAACCACTTTTATTATCAA
131 TTTTATTTCGTTATTTCAACAATAATATTGCATGCAAAACCATTGTCAACCACTTTTATTATCAA
43402111 TTCCATATTTTCTTGAATTGACATAACTTATCGAGATATCTTATTTTCACTATTTTAATATTCAG
196 TTCCATATTTTCTTGAATTGACATAACTTATCGAGATATCTTATTTTCACTATTTTAATATTCAG
43402176 TTTTAGGTACTTGAATCTCTTCTATAGTTTTACTTATTAGTTATGCCTTGGGTCTCTTCTGGAGC
261 TTTTAGGTACTTGAATCTCTTCTATAGTTTTACTTATTAGTTATGCCTTGGGTCTCTTCTGGAGC
*
43402241 ACCCACCTTCACTATATGATCATCTAAATTTATTGTTTTCTTGTATGAGAATTTTCA
326 ACCCACCTTCACTATATGATCATCTAAATTTATTGTTTTCTTGTATGAGAAATTTCA
43402298 T
1 T
43402299 ATTTGGAACT
Statistics
Matches: 379, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
382 379 1.00
ACGTcount: A:0.28, C:0.18, G:0.10, T:0.44
Consensus pattern (382 bp):
TTATACCTTTAGATATTTGGACTAATGGTCCAAACACTCCACGAATTTAATTATACTTAAGTTCC
GTCTTTCTATTTTGATCAGTTTATTCCATATCCATATTTCTCAATAAATTTATTCAAGATCATCC
TTTTATTTCGTTATTTCAACAATAATATTGCATGCAAAACCATTGTCAACCACTTTTATTATCAA
TTCCATATTTTCTTGAATTGACATAACTTATCGAGATATCTTATTTTCACTATTTTAATATTCAG
TTTTAGGTACTTGAATCTCTTCTATAGTTTTACTTATTAGTTATGCCTTGGGTCTCTTCTGGAGC
ACCCACCTTCACTATATGATCATCTAAATTTATTGTTTTCTTGTATGAGAAATTTCA
Found at i:43406913 original size:20 final size:20
Alignment explanation
Indices: 43406890--43406929 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43406880 GTAGTAACTG
*
43406890 TTTTAACTAAATC-TTAACAA
1 TTTTAA-TAAAACTTTAACAA
43406910 TTTTAATAAAACTTTAACAA
1 TTTTAATAAAACTTTAACAA
43406930 ACTTAACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAATAAAACTTTAACAA
Found at i:43407378 original size:18 final size:18
Alignment explanation
Indices: 43407348--43407385 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
43407338 AATTCATAAA
43407348 GTTATTATCTTTCAAAAC
1 GTTATTATCTTTCAAAAC
43407366 GTTATTAAT-TTTCAAAAC
1 GTTATT-ATCTTTCAAAAC
43407384 GT
1 GT
43407386 CACTTATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.89
19 2 0.11
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.45
Consensus pattern (18 bp):
GTTATTATCTTTCAAAAC
Found at i:43420716 original size:22 final size:21
Alignment explanation
Indices: 43420690--43420741 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
43420680 GGGGGTCAAT
*
43420690 ACGCCCGTGTGGGAGGAGGTAC
1 ACGCCCGTGT-GGAGGAGGCAC
* *
43420712 ACGCCTGTGTGGATGAGGCAC
1 ACGCCCGTGTGGAGGAGGCAC
*
43420733 ATGCCCGTG
1 ACGCCCGTG
43420742 CGGATAAGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.17
Consensus pattern (21 bp):
ACGCCCGTGTGGAGGAGGCAC
Found at i:43428042 original size:55 final size:55
Alignment explanation
Indices: 43427956--43428065 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
43427946 GACCCTAATC
43427956 GGAACAATGGTTTCGGGACCACAAATCCGAGTAAAAAATATTTAAATATTATTAT
1 GGAACAATGGTTTCGGGACCACAAATCCGAGTAAAAAATATTTAAATATTATTAT
* * *
43428011 GGAACAGTGGTTTCGGGACCACAAGTTCGAGTAAAAAATATTTAAATATTATTAT
1 GGAACAATGGTTTCGGGACCACAAATCCGAGTAAAAAATATTTAAATATTATTAT
43428066 CTATGTTTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (55 bp):
GGAACAATGGTTTCGGGACCACAAATCCGAGTAAAAAATATTTAAATATTATTAT
Found at i:43434468 original size:55 final size:55
Alignment explanation
Indices: 43434384--43434510 Score: 200
Period size: 55 Copynumber: 2.3 Consensus size: 55
43434374 TTAATGAAAG
*
43434384 CAAGTCAATGAGTTACATGGGCTAGTCACAAAGGCGTGTTGCTAGCCGTATGACC
1 CAAGTCAATGAGTTACATGGGCTAGTCACAAAGGCGTGTGGCTAGCCGTATGACC
* * * * *
43434439 CAAGTCAATGAGTTACATGGGCTAGTCACACAGGGGTGTGGTTGGCCGTGTGACC
1 CAAGTCAATGAGTTACATGGGCTAGTCACAAAGGCGTGTGGCTAGCCGTATGACC
43434494 CAAGTCAATGAGTTACA
1 CAAGTCAATGAGTTACA
43434511 CGGGGTCAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 66 1.00
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (55 bp):
CAAGTCAATGAGTTACATGGGCTAGTCACAAAGGCGTGTGGCTAGCCGTATGACC
Found at i:43437623 original size:20 final size:19
Alignment explanation
Indices: 43437598--43437691 Score: 86
Period size: 20 Copynumber: 4.9 Consensus size: 19
43437588 ACTTCCTTAT
43437598 ATGTATGCAACATATCATAC
1 ATGTATGCAACATAT-ATAC
*
43437618 ATGTATGCAATATATATATC
1 ATGTATGCAACATATATA-C
* * *
43437638 GTG-A--CATGCTTATATAC
1 ATGTATGCA-ACATATATAC
43437655 ATGTATGCAACATATCATAC
1 ATGTATGCAACATAT-ATAC
*
43437675 ATGTATGCAATATATAT
1 ATGTATGCAACATATAT
43437692 CGTGACATAC
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
17 5 0.08
18 7 0.12
19 10 0.17
20 37 0.63
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (19 bp):
ATGTATGCAACATATATAC
Found at i:43437677 original size:57 final size:55
Alignment explanation
Indices: 43437598--43437710 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 55
43437588 ACTTCCTTAT
*
43437598 ATGTATGCAACATATCATACATGTATGCAATATATATATCGTGACATGCTTATATAC
1 ATGTATGCAACATATCATACATGTATGC-A-ATATATATCGTGACATACTTATATAC
43437655 ATGTATGCAACATATCATACATGTATGCAATATATATCGTGACATACTTATATAC
1 ATGTATGCAACATATCATACATGTATGCAATATATATCGTGACATACTTATATAC
43437710 A
1 A
43437711 GTCATACATA
Statistics
Matches: 55, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
55 26 0.47
56 1 0.02
57 28 0.51
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (55 bp):
ATGTATGCAACATATCATACATGTATGCAATATATATCGTGACATACTTATATAC
Found at i:43437689 original size:37 final size:37
Alignment explanation
Indices: 43437598--43437690 Score: 91
Period size: 37 Copynumber: 2.4 Consensus size: 37
43437588 ACTTCCTTAT
*
43437598 ATGTATGCAACATATCATACATGTATGCAATATATATATC
1 ATGTATGC-A-ATAT-ATACATGTATGCAACATATATATC
* * *
43437638 GTGACATGC-TTATATACATGTATGCAACATATCATA-C
1 ATG-TATGCAATATATACATGTATGCAACATAT-ATATC
43437675 ATGTATGCAATATATA
1 ATGTATGCAATATATA
43437691 TCGTGACATA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
36 4 0.09
37 27 0.63
38 6 0.14
40 2 0.05
41 4 0.09
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (37 bp):
ATGTATGCAATATATACATGTATGCAACATATATATC
Found at i:43437725 original size:57 final size:57
Alignment explanation
Indices: 43437598--43437718 Score: 185
Period size: 55 Copynumber: 2.2 Consensus size: 57
43437588 ACTTCCTTAT
* *
43437598 ATGTATGCAACATATCATACATGTATGCAATATATATATCGTGACATGCTTATATAC
1 ATGTATACAACATATCATACATGTATGCAATATATATATCGTGACATACTTATATAC
*
43437655 ATGTATGCAACATATCATACATGTATGC-A-ATATATATCGTGACATACTTATATAC
1 ATGTATACAACATATCATACATGTATGCAATATATATATCGTGACATACTTATATAC
43437710 A-GTCATACA
1 ATGT-ATACA
43437719 TAACATAAAG
Statistics
Matches: 61, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
54 2 0.03
55 30 0.49
56 1 0.02
57 28 0.46
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.34
Consensus pattern (57 bp):
ATGTATACAACATATCATACATGTATGCAATATATATATCGTGACATACTTATATAC
Found at i:43438848 original size:44 final size:44
Alignment explanation
Indices: 43438785--43438872 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
43438775 TGCCACCAAT
* * *
43438785 CGGGATAACCTCTCCAATCCCATAATTTTCTCTTAAAATGACTC
1 CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATCACTC
43438829 CGGGATAACCTC-CCTAATCCCATAATCTTCTCCTAAAATCACTC
1 CGGGATAACCTCTCC-AATCCCATAATCTTCTCCTAAAATCACTC
43438873 TAACCTTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
43 2 0.05
44 38 0.95
ACGTcount: A:0.30, C:0.33, G:0.08, T:0.30
Consensus pattern (44 bp):
CGGGATAACCTCTCCAATCCCATAATCTTCTCCTAAAATCACTC
Found at i:43446643 original size:23 final size:23
Alignment explanation
Indices: 43446617--43446660 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
43446607 AAGGTGACTG
43446617 TAATATCCC-GAAAATTACTACTA
1 TAATA-CCCTGAAAATTACTACTA
43446640 TAATACCCTGAAAATTACTAC
1 TAATACCCTGAAAATTACTAC
43446661 AGTAAGAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.30
Consensus pattern (23 bp):
TAATACCCTGAAAATTACTACTA
Found at i:43456328 original size:44 final size:44
Alignment explanation
Indices: 43456265--43456645 Score: 514
Period size: 44 Copynumber: 8.7 Consensus size: 44
43456255 GGTGAAACTA
* *
43456265 TAAGTTCTATCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
43456309 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * *
43456353 CATGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGACTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * * * *
43456397 CATGTCCTAGCTCCCTAAATAGCAGTGGAATAGGTGGAAAATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * *
43456441 TAAGTCCTATCTCCCTGAACAACAGTGGAATAGGTCGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
**
43456485 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTCAAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* *
43456529 CATGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* * * * *
43456573 CATGTCCTAGCTCCCTGAATAGTAGTGGAATAGGTGAAAGATTG
1 TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
* *
43456617 T-AGATCCTATCTCCCT-AAGCAGTAGTGGA
1 TAAG-TCCTAGCTCCCTGAA-CAGCAGTGGA
43456646 GTACATCGAA
Statistics
Matches: 304, Mismatches: 31, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
43 3 0.01
44 301 0.99
ACGTcount: A:0.30, C:0.19, G:0.27, T:0.24
Consensus pattern (44 bp):
TAAGTCCTAGCTCCCTGAACAGCAGTGGAATAGGTGGAAGATTG
Found at i:43461929 original size:36 final size:37
Alignment explanation
Indices: 43461866--43461935 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
43461856 GCTAACGAAC
43461866 CGACTGTGCAACCTTCCCAAAACATACAAAGCGGCCG
1 CGACTGTGCAACCTTCCCAAAACATACAAAGCGGCCG
43461903 CGACTGTGCAACCTT-CCAAAACATACAAAGCGG
1 CGACTGTGCAACCTTCCCAAAACATACAAAGCGG
43461936 TCGTCTTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.34, C:0.33, G:0.19, T:0.14
Consensus pattern (37 bp):
CGACTGTGCAACCTTCCCAAAACATACAAAGCGGCCG
Found at i:43467460 original size:16 final size:16
Alignment explanation
Indices: 43467441--43467471 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43467431 TTGAAAGAGT
43467441 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
43467457 TTTCAAATTTATATG
1 TTTCAAATATATATG
43467472 CTCCAAAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:43471908 original size:14 final size:14
Alignment explanation
Indices: 43471889--43471915 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
43471879 TGGGTATTTG
43471889 TGAAAAAAATGAAA
1 TGAAAAAAATGAAA
43471903 TGAAAAAAATGAA
1 TGAAAAAAATGAA
43471916 GTCCTAAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
TGAAAAAAATGAAA
Found at i:43484131 original size:121 final size:121
Alignment explanation
Indices: 43483917--43484157 Score: 376
Period size: 121 Copynumber: 2.0 Consensus size: 121
43483907 CCGACAATAC
* * *
43483917 TCTATGAGTTTATATTACAGGAGATTTAGCTTGGATTGGTAATCCCGCTGTAAGGATGAGGTTCG
1 TCTATGAGTTTATATTACAGGAGATTTAGCTTGGACTGGTAATCCCGCTATAAGGATGAGATTCG
* *
43483982 AGGGAGTGTGCTCTCTGAAATGGAAATGTGCACACATGAATATGAATTGACGGACT
66 AGGGAGTGTGCTATCTGAAATGAAAATGTGCACACATGAATATGAATTGACGGACT
* * *
43484038 TCTATGAGTTTATATTATAGGGGATTTAGCTT-GACCTGGTAATCCCGCTATAAGGATGAGATTT
1 TCTATGAGTTTATATTACAGGAGATTTAGCTTGGA-CTGGTAATCCCGCTATAAGGATGAGATTC
* *
43484102 GTGGGAGTGTGCTATCTGAAATGAAAATGTGCGCACATGAATATGAATTGACGGAC
65 GAGGGAGTGTGCTATCTGAAATGAAAATGTGCACACATGAATATGAATTGACGGAC
43484158 CAAGAATTGT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
120 2 0.02
121 107 0.98
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (121 bp):
TCTATGAGTTTATATTACAGGAGATTTAGCTTGGACTGGTAATCCCGCTATAAGGATGAGATTCG
AGGGAGTGTGCTATCTGAAATGAAAATGTGCACACATGAATATGAATTGACGGACT
Found at i:43486058 original size:17 final size:15
Alignment explanation
Indices: 43486018--43486068 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
43486008 ATTAAGGCTC
*
43486018 AGAAAGAAGCATAAA
1 AGAAAGAAGCAGAAA
*
43486033 AGAAGGAAGCAGAAGGA
1 AGAAAGAAGCAGAA--A
43486050 AGAAAGAAGCAG-AA
1 AGAAAGAAGCAGAAA
43486064 AGAAA
1 AGAAA
43486069 AGGCTTTGGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 6 0.19
15 12 0.39
16 1 0.03
17 12 0.39
ACGTcount: A:0.63, C:0.06, G:0.29, T:0.02
Consensus pattern (15 bp):
AGAAAGAAGCAGAAA
Found at i:43490168 original size:3 final size:3
Alignment explanation
Indices: 43490160--43490185 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43490150 ATTTGTCAAC
43490160 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
43490186 GGGGAATGAC
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):
TAA
Found at i:43495532 original size:22 final size:22
Alignment explanation
Indices: 43495502--43495544 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
43495492 ACACCAAAAC
*
43495502 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
43495524 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
43495545 AGCGCCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:43495728 original size:43 final size:42
Alignment explanation
Indices: 43495681--43495861 Score: 143
Period size: 43 Copynumber: 4.3 Consensus size: 42
43495671 CTTTTCCCTA
* * *
43495681 AAACGCTGCAAAAGACCCTGATCTATAGCGGCTCTTCGACCAC
1 AAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTC-ACCAC
* * * * *
43495724 AAACGCCACTAAAGAACCTAATCTTTAGCGGCGCTTCCCCAC
1 AAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTCACCAC
* * * * *
43495766 AAACACCGCTAAAGACCATGATCTTTAGGGGCG-TT--CCGC
1 AAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTCACCAC
* * * * * *
43495805 AAATGCCGCGAAAGACCCTTATCTTTAGCGGCGCTTTTACCAA
1 AAACGCCGCTAAAGACCCTGATCTATAGCGGCGC-TTCACCAC
*
43495848 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
43495862 GCCAACACCT
Statistics
Matches: 108, Mismatches: 26, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
39 30 0.28
41 4 0.04
42 31 0.29
43 43 0.40
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (42 bp):
AAACGCCGCTAAAGACCCTGATCTATAGCGGCGCTTCACCAC
Found at i:43495778 original size:42 final size:41
Alignment explanation
Indices: 43495659--43495840 Score: 138
Period size: 43 Copynumber: 4.4 Consensus size: 41
43495649 AAGATTAGGG
* * * *
43495659 TCTTTAGCGACGCTTTTCCCTA-AAACGCTGCAAAAGACCCTGA
1 TCTTTAGCGGCGC--TTCCC-ACAAACGCCGCTAAAGAACCTGA
* * * *
43495702 TCTATAGCGGCTCTTCGACCACAAACGCCACTAAAGAACCTAA
1 TCTTTAGCGGCGCTTC--CCACAAACGCCGCTAAAGAACCTGA
*
43495745 TCTTTAGCGGCGCTTCCCCACAAACACCGCTAAAG-ACCATGA
1 TCTTTAGCGGCGCTT-CCCACAAACGCCGCTAAAGAACC-TGA
* * * * * *
43495787 TCTTTAGGGGCG-TT-CCGCAAATGCCGCGAAAGACCCTTA
1 TCTTTAGCGGCGCTTCCCACAAACGCCGCTAAAGAACCTGA
43495826 TCTTTAGCGGCGCTT
1 TCTTTAGCGGCGCTT
43495841 TTACCAAAAA
Statistics
Matches: 111, Mismatches: 21, Indels: 17
0.74 0.14 0.11
Matches are distributed among these distances:
39 27 0.24
40 4 0.04
41 8 0.07
42 30 0.27
43 41 0.37
44 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.19, T:0.23
Consensus pattern (41 bp):
TCTTTAGCGGCGCTTCCCACAAACGCCGCTAAAGAACCTGA
Found at i:43496239 original size:21 final size:21
Alignment explanation
Indices: 43496213--43496325 Score: 109
Period size: 21 Copynumber: 5.4 Consensus size: 21
43496203 TTTGACGCTG
43496213 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* **
43496234 CTCTGCTTTCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
43496255 CTCTGCTTCCTTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * * *
43496276 CTGTACTTCTCTCACTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
43496297 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
43496318 ATCTGCTT
1 CTCTGCTT
43496326 TAAGCTACTG
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.05, C:0.42, G:0.17, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:43496386 original size:66 final size:66
Alignment explanation
Indices: 43496296--43496462 Score: 212
Period size: 66 Copynumber: 2.5 Consensus size: 66
43496286 CTCACTGCCG
* * *
43496296 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTACT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAG-TACTAGCTGGAGTTCTTCATATCTTT-GTT
43496359 GAA
64 GAA
** *
43496362 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATATCTTTGTTGA
43496427 A
66 A
* * * *
43496428 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGT
1 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGT
43496463 TGTGTAATTT
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 2 0.02
66 83 0.93
67 4 0.04
ACGTcount: A:0.14, C:0.28, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTAAGTACTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:43501789 original size:16 final size:16
Alignment explanation
Indices: 43501768--43501887 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
43501758 ATAATTAAGC
43501768 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
43501784 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
43501800 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
43501809 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
43501825 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
43501839 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
43501857 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
43501873 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
43501888 AGTTATTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 45 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:43501810 original size:25 final size:25
Alignment explanation
Indices: 43501782--43501936 Score: 129
Period size: 25 Copynumber: 6.2 Consensus size: 25
43501772 TAAGTTATGT
43501782 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
43501807 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
43501832 ATTATGCTATG-TA---AGTTATGTAA
1 ATTATG-TAAGTTATTTA-TTATGAAA
* * * * *
43501855 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATTTATTATGAAA
*
43501880 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATTTATTATGAAA
* *
43501905 ATTAAGTAAGTTATGTAATTTATGAATA
1 ATTATGTAAGTTAT-TTA-TTATGAA-A
43501933 ATTA
1 ATTA
43501937 AAAAAATGTA
Statistics
Matches: 105, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
22 4 0.04
23 12 0.11
25 71 0.68
26 6 0.06
27 7 0.07
28 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.15, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATTTATTATGAAA
Found at i:43501914 original size:34 final size:34
Alignment explanation
Indices: 43501808--43502640 Score: 320
Period size: 34 Copynumber: 24.5 Consensus size: 34
43501798 ATTATGAAAA
*
43501808 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTA----A-GTAAG
* * * *
43501847 TTATGTAAGTCATATAAGTTATG--TATTATGTAAG
1 TTATGTAAGTTATGT-A-TTATGAAAATTAAGTAAG
*
43501881 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
* ** *
43501915 TTATGTAATTTATGAATAATTAAAAAAATGTAAGT-TG
1 TTATGTAAGTTATG--T-ATTATGAAAAT-TAAGTAAG
* *
43501952 TGTAAGTTGTAAGTTATGTAAGTTATGTATAA-T-ATTAA-
1 T-T-A--TGTAAGTTATGT-A-TTATG-AAAATTAAGTAAG
**
43501990 TTAAT-TAAGTTATGTAATTTATGTATTGCATTAATGTAAG
1 TT-ATGTAAGTTATGT-A-TTATG-A--AAATTAA-GTAAG
* * * * **
43502030 TTATGTAATTTATGAATAATTAAAAAAAAGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
* * *
43502064 TTATGTAAGTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
* *
43502098 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAA-GTAAG
* * * * **
43502129 TTATGTAATTTATGAATAATTAAAAAAAAGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
* * *
43502163 TTATGTAAGTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
* *
43502197 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAA-GTAAG
* * * * **
43502228 TTATGTAATTTATGAATAATTAAAAAAAAGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
* * *
43502262 TTATGTAAGTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
* *
43502296 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAA-GTAAG
* * * * **
43502327 TTATGTAATTTATGAATAATTAAAAAAAAGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
* * *
43502361 TTATGTAAGTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
* *
43502395 TTATGTAATTTATGTA-T-TG--CATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAA-GTAAG
* * * * **
43502426 TTATGTAATTTATGAATAATTAAAAAAAAGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
* * *
43502460 TTATGTAAGTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
* **
43502494 TTATGTAATTTATGTA-T-T--CCATTAATGTAAG
1 TTATGTAAGTTATGTATTATGAAAATTAA-GTAAG
* * *
43502525 TTATGTAAGTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
* * * *
43502559 TCATGTAATTTATG---TAT-AATATTAATGCAAG
1 TTATGTAAGTTATGTATTATGAAAATTAA-GTAAG
* * * *
43502590 TTATGTAATTTATGTATAAT-ATTAATTAATTAAG
1 TTATGTAAGTTATGTATTATGA-AAATTAAGTAAG
*
43502624 TTATGTAATTTATGTAT
1 TTATGTAAGTTATGTAT
43502641 AATATTAATG
Statistics
Matches: 608, Mismatches: 125, Indels: 127
0.71 0.15 0.15
Matches are distributed among these distances:
30 30 0.05
31 114 0.19
32 10 0.02
33 11 0.02
34 327 0.54
35 26 0.04
36 2 0.00
37 16 0.03
38 13 0.02
39 27 0.04
40 14 0.02
41 18 0.03
ACGTcount: A:0.41, C:0.01, G:0.14, T:0.44
Consensus pattern (34 bp):
TTATGTAAGTTATGTATTATGAAAATTAAGTAAG
Found at i:43501964 original size:16 final size:16
Alignment explanation
Indices: 43501943--43501975 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43501933 ATTAAAAAAA
*
43501943 TGTAAGTTGTGTAAGT
1 TGTAAGTTATGTAAGT
43501959 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43501975 T
1 T
43501976 ATGTATAATA
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:0.27, C:0.00, G:0.27, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:43502076 original size:99 final size:99
Alignment explanation
Indices: 43501960--43502643 Score: 1162
Period size: 99 Copynumber: 6.9 Consensus size: 99
43501950 TGTGTAAGTT
43501960 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
43502025 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
66 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
43502059 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
43502124 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
66 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
43502158 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
43502223 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
66 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
43502257 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
43502322 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
66 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
43502356 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
43502421 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
66 GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
*
43502455 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTCCATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
* * * **
43502520 GTAAGTTATGTAAGTTATGTATAA-TATTAATTAA
66 GTAAGTTATGTAATTTATGAATAATTA-AAAAAAA
* * * ** **
43502554 TTAAGTCATGTAATTTATGTATAATATTAA-T--GCAAGTTATGTAATTTATGTATAATATTAAT
1 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATG--T-AT-TGCAT
*
43502616 TAAT-TAAGTTATGTAATTTATGTATAAT
62 TAATGTAAGTTATGTAATTTATGAATAAT
43502644 ATTAATGTAA
Statistics
Matches: 565, Mismatches: 14, Indels: 11
0.96 0.02 0.02
Matches are distributed among these distances:
96 17 0.03
98 4 0.01
99 537 0.95
100 7 0.01
ACGTcount: A:0.41, C:0.01, G:0.13, T:0.44
Consensus pattern (99 bp):
GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAAT
GTAAGTTATGTAATTTATGAATAATTAAAAAAAA
Found at i:43502679 original size:31 final size:29
Alignment explanation
Indices: 43502609--43502680 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
43502599 TTATGTATAA
* *
43502609 TATTAATTAATTAAGTTATGTAATTTATG
1 TATTAATTAATTAAGTTATGTAATTCAGG
* *
43502638 TATAATATTAATGTAAGTTATGTAATTCCGG
1 TATTA-ATTAAT-TAAGTTATGTAATTCAGG
43502669 TATTACATTAAT
1 TATTA-ATTAAT
43502681 ATTATACATA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 4 0.11
30 6 0.17
31 25 0.71
ACGTcount: A:0.38, C:0.04, G:0.11, T:0.47
Consensus pattern (29 bp):
TATTAATTAATTAAGTTATGTAATTCAGG
Found at i:43502679 original size:65 final size:65
Alignment explanation
Indices: 43501960--43502791 Score: 642
Period size: 65 Copynumber: 12.7 Consensus size: 65
43501950 TGTGTAAGTT
* * **
43501960 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAA-
1 GTAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATTATATTAAT
43502024 T--
63 TAA
* ** * * *
43502025 GTAAGTTATGTAATTTATGAATAATTAAAAAAAAGTAAGTTATGTAAGTTATGTATAATATTAAT
1 GTAAGTTATGTAATTTATGTATAA-T--ATTAATGTAAGTTATGTAATTTATGTATTATATTAAT
43502090 TAA
63 TAA
* *** * **
43502093 TTAAGTTATGTAATTTATGTATTGCATTAATGTAAGTTATGTAATTTATG-AATA-ATTAAAAAA
1 GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATTATATT--AATT
43502156 AA
64 AA
* * **
43502158 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAA-
1 GTAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATTATATTAAT
43502222 T--
63 TAA
* ** * * *
43502223 GTAAGTTATGTAATTTATGAATAATTAAAAAAAAGTAAGTTATGTAAGTTATGTATAATATTAAT
1 GTAAGTTATGTAATTTATGTATAA-T--ATTAATGTAAGTTATGTAATTTATGTATTATATTAAT
43502288 TAA
63 TAA
* *** * **
43502291 TTAAGTTATGTAATTTATGTATTGCATTAATGTAAGTTATGTAATTTATG-AATA-ATTAAAAAA
1 GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATTATATT--AATT
43502354 AA
64 AA
* * **
43502356 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATTGCATTAA-
1 GTAAGTTATGTAATTTATGTATAATATTAA-T--GTAAGTTATGTAATTTATGTATTATATTAAT
43502420 T--
63 TAA
* ** * * *
43502421 GTAAGTTATGTAATTTATGAATAATTAAAAAAAAGTAAGTTATGTAAGTTATGTATAATATTAAT
1 GTAAGTTATGTAATTTATGTATAA-T--ATTAATGTAAGTTATGTAATTTATGTATTATATTAAT
43502486 TAA
63 TAA
* *** * *
43502489 TTAAGTTATGTAATTTATGTATTCCATTAATGTAAGTTATGTAAGTTATGTATAATATTAATTAA
1 GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATTATATTAATTAA
* * * *
43502554 TTAAGTCATGTAATTTATGTATAATATTAATGCAAGTTATGTAATTTATGTATAATATTAATTAA
1 GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATTATATTAATTAA
* *** *
43502619 TTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTCCGGTATTACATTAATATT
1 GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATTATATT-A-ATT
43502684 ATA
64 A-A
* * ** * * ** * *
43502687 CATAAATTACATAACTTA---ATTA-ATTAAAATACCGGTTATGTAATTTATGTATAATATTAA-
1 -GTAAGTTATGTAATTTATGTATAATATTAATGTA--AGTTATGTAATTTATGTATTATATTAAT
43502747 T--
63 TAA
*
43502748 GTAAGTTATGTAATTTATGTTTAATATTAATGTAAGTTATGTAA
1 GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAA
43502792 GTTGTAAGTT
Statistics
Matches: 606, Mismatches: 119, Indels: 87
0.75 0.15 0.11
Matches are distributed among these distances:
60 12 0.02
62 9 0.01
63 8 0.01
64 12 0.02
65 397 0.66
66 13 0.02
67 23 0.04
68 110 0.18
69 16 0.03
70 6 0.01
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.44
Consensus pattern (65 bp):
GTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGTATTATATTAATTAA
Found at i:43502756 original size:31 final size:31
Alignment explanation
Indices: 43502721--43502791 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
43502711 TAAAATACCG
43502721 GTTATGTAATTTATGTATAATATTAATGTAA
1 GTTATGTAATTTATGTATAATATTAATGTAA
*
43502752 GTTATGTAATTTATGTTTAATATTAATGTAA
1 GTTATGTAATTTATGTATAATATTAATGTAA
43502783 GTTATGTAA
1 GTTATGTAA
43502792 GTTGTAAGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (31 bp):
GTTATGTAATTTATGTATAATATTAATGTAA
Found at i:43502760 original size:9 final size:9
Alignment explanation
Indices: 43502746--43502845 Score: 68
Period size: 9 Copynumber: 11.1 Consensus size: 9
43502736 TATAATATTA
43502746 ATGTAAGTT
1 ATGTAAGTT
*
43502755 ATGTAATTT
1 ATGTAAGTT
*
43502764 ATGTTTAATATT
1 ATG--TAA-GTT
43502776 AATGTAAGTT
1 -ATGTAAGTT
43502786 ATGTAAG-T
1 ATGTAAGTT
43502794 -TGTAAGTT
1 ATGTAAGTT
43502802 ATGTAAGTT
1 ATGTAAGTT
* *
43502811 ATATATA-AT
1 ATGTA-AGTT
43502820 AT-TAA-TT
1 ATGTAAGTT
43502827 AAT-TAAGTT
1 -ATGTAAGTT
43502836 ATGTAAGTT
1 ATGTAAGTT
43502845 A
1 A
43502846 ACTATTTTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 20
0.74 0.06 0.20
Matches are distributed among these distances:
7 8 0.11
8 11 0.15
9 42 0.56
10 3 0.04
11 6 0.08
12 2 0.03
13 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:43502799 original size:16 final size:16
Alignment explanation
Indices: 43502778--43502810 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43502768 TTAATATTAA
43502778 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43502794 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
43502810 T
1 T
43502811 ATATATAATA
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:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:43502801 original size:47 final size:49
Alignment explanation
Indices: 43502747--43502844 Score: 137
Period size: 47 Copynumber: 2.0 Consensus size: 49
43502737 ATAATATTAA
* * *
43502747 TGTAAGTTATGTAATTTATGTTTAATATTAA-T-GTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGTTATATATAATATTAATTAGTAAGTTATGTAAGT
*
43502794 TGTAAGTTATGTAAGTTATATATAATATTAATTAATTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGTTATATATAATATTAATT-AGTAAGTTATGTAAGT
43502844 T
1 T
43502845 AACTATTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
47 28 0.64
48 1 0.02
50 15 0.34
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (49 bp):
TGTAAGTTATGTAAGTTATATATAATATTAATTAGTAAGTTATGTAAGT
Found at i:43502930 original size:16 final size:16
Alignment explanation
Indices: 43502909--43502941 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
43502899 AACTCAATTA
*
43502909 TATCTTCGAACTTATT
1 TATCTTCAAACTTATT
43502925 TATCTTCAAACTTATT
1 TATCTTCAAACTTATT
43502941 T
1 T
43502942 CTACAAGTTT
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:0.27, C:0.18, G:0.03, T:0.52
Consensus pattern (16 bp):
TATCTTCAAACTTATT
Found at i:43503094 original size:38 final size:38
Alignment explanation
Indices: 43503043--43503121 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
43503033 CAACAGAAGA
43503043 ATGAAAATTTACCTTCCACGCCAAAGAATAGACGACTT
1 ATGAAAATTTACCTTCCACGCCAAAGAATAGACGACTT
43503081 ATGAAAATTTACCTTCCACGCCAAAGAATAGACGACTT
1 ATGAAAATTTACCTTCCACGCCAAAGAATAGACGACTT
43503119 ATG
1 ATG
43503122 CAGCGAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (38 bp):
ATGAAAATTTACCTTCCACGCCAAAGAATAGACGACTT
Found at i:43503914 original size:33 final size:33
Alignment explanation
Indices: 43503877--43503939 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
43503867 GAAAAATAAT
**
43503877 AATTAAACTATACAACTAAAATATAACCAAAAA
1 AATTAAACTATACAAAAAAAATATAACCAAAAA
43503910 AATTAAACTATACAAAAAAAATATAACCAA
1 AATTAAACTATACAAAAAAAATATAACCAA
43503940 CTTAAAGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.65, C:0.14, G:0.00, T:0.21
Consensus pattern (33 bp):
AATTAAACTATACAAAAAAAATATAACCAAAAA
Found at i:43503921 original size:20 final size:19
Alignment explanation
Indices: 43503893--43503931 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
43503883 ACTATACAAC
*
43503893 TAAAATATAACCAAAAAAAT
1 TAAAATAT-ACAAAAAAAAT
*
43503913 TAAACTATACAAAAAAAAT
1 TAAAATATACAAAAAAAAT
43503932 ATAACCAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (19 bp):
TAAAATATACAAAAAAAAT
Found at i:43504337 original size:38 final size:38
Alignment explanation
Indices: 43504293--43504382 Score: 155
Period size: 38 Copynumber: 2.4 Consensus size: 38
43504283 AATTTGTAAT
43504293 GATAAATGATAGGAAGTTGAAATTATTCAAACAAACCG
1 GATAAATGATAGGAAGTTGAAATTATTCAAACAAACCG
43504331 GATAAATGACT-GGAAGTTGAAATTATTCAAACAAACCG
1 GATAAATGA-TAGGAAGTTGAAATTATTCAAACAAACCG
*
43504369 GATAAATGACAGGA
1 GATAAATGATAGGA
43504383 TTATCTAAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
38 48 0.98
39 1 0.02
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (38 bp):
GATAAATGATAGGAAGTTGAAATTATTCAAACAAACCG
Found at i:43505506 original size:22 final size:22
Alignment explanation
Indices: 43505465--43505518 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
43505455 TTGTATTTTC
* *
43505465 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
43505488 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
43505509 -TAAAAGTTTT
1 ATTAAAGTTTT
43505519 TGATAAGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:43505566 original size:21 final size:20
Alignment explanation
Indices: 43505540--43505583 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
43505530 TAAATTTTAG
43505540 TTTTTTATTTCCTTT-TTATAT
1 TTTTTTATTT--TTTCTTATAT
43505561 TTTTTTATTTTTTCTTATAT
1 TTTTTTATTTTTTCTTATAT
43505581 TTT
1 TTT
43505584 GGTCCTGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 3 0.14
20 9 0.41
21 10 0.45
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTATTTTTTCTTATAT
Found at i:43511087 original size:9 final size:9
Alignment explanation
Indices: 43511073--43511240 Score: 129
Period size: 9 Copynumber: 19.3 Consensus size: 9
43511063 NNNNNNNNNN
43511073 TAACTTACA
1 TAACTTACA
43511082 TAACTTACA
1 TAACTTACA
*
43511091 TAATACATA-A
1 T-A-ACTTACA
43511101 TAACTTAC-
1 TAACTTACA
43511109 -AACTTACA
1 TAACTTACA
*
43511117 TAACATACA
1 TAACTTACA
* **
43511126 TTACTTTGA
1 TAACTTACA
43511135 TAACTTACA
1 TAACTTACA
* **
43511144 TTACTTTGA
1 TAACTTACA
43511153 TAACTTACA
1 TAACTTACA
43511162 TAACTTACA
1 TAACTTACA
43511171 T-AC-TACA
1 TAACTTACA
* *
43511178 CAACTTAAA
1 TAACTTACA
* *
43511187 TAGCTTACT
1 TAACTTACA
43511196 TAA--TACA
1 TAACTTACA
43511203 TAACTTACA
1 TAACTTACA
43511212 TAACTT--A
1 TAACTTACA
*
43511219 TACACGTACA
1 TA-ACTTACA
43511229 TAACTTACA
1 TAACTTACA
43511238 TAA
1 TAA
43511241 TTGACTTAAT
Statistics
Matches: 121, Mismatches: 26, Indels: 24
0.71 0.15 0.14
Matches are distributed among these distances:
7 20 0.17
8 11 0.09
9 80 0.66
10 6 0.05
11 4 0.03
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.34
Consensus pattern (9 bp):
TAACTTACA
Found at i:43511193 original size:25 final size:25
Alignment explanation
Indices: 43511174--43511253 Score: 54
Period size: 25 Copynumber: 3.2 Consensus size: 25
43511164 ACTTACATAC
* * *
43511174 TACACAACTTAAATAGCTTACTTAA
1 TACACAACTTACATAACTTACATAA
* * * *
43511199 TACATAACTTACATAACTTATACACG
1 TACACAACTTACATAACTTACATA-A
* *
43511225 TACATAACTTACATAA-TTGACTTAA
1 TACACAACTTACATAACTT-ACATAA
43511250 TACA
1 TACA
43511254 TGAATATATA
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
25 24 0.57
26 18 0.43
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.33
Consensus pattern (25 bp):
TACACAACTTACATAACTTACATAA
Found at i:43517767 original size:16 final size:17
Alignment explanation
Indices: 43517746--43517778 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43517736 TATGTTGATC
43517746 AGAAACA-TATATTATA
1 AGAAACAGTATATTATA
*
43517762 AGAAACAGTCTATTATA
1 AGAAACAGTATATTATA
43517779 CCTGATATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.09, G:0.09, T:0.30
Consensus pattern (17 bp):
AGAAACAGTATATTATA
Found at i:43526807 original size:36 final size:36
Alignment explanation
Indices: 43526761--43527193 Score: 848
Period size: 36 Copynumber: 12.0 Consensus size: 36
43526751 GGTAGCTTTA
*
43526761 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43526797 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43526833 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43526869 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43526905 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43526941 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43526977 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43527013 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43527049 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43527085 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43527121 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
*
43527157 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
43527193 G
1 G
43527194 GTAGCTTAGC
Statistics
Matches: 395, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
36 395 1.00
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTATACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:43534451 original size:46 final size:45
Alignment explanation
Indices: 43534399--43534550 Score: 182
Period size: 36 Copynumber: 3.6 Consensus size: 45
43534389 TTTGAGTACT
* *
43534399 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
*
43534445 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
43534481 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
*
43534526 TCTGATC-AGGGACAAA-TGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
43534551 ATCATACGTA
Statistics
Matches: 93, Mismatches: 4, Indels: 21
0.79 0.03 0.18
Matches are distributed among these distances:
36 28 0.30
38 1 0.01
39 2 0.02
40 4 0.04
41 2 0.02
42 2 0.02
43 12 0.13
44 8 0.09
45 12 0.13
46 22 0.24
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:43535861 original size:20 final size:20
Alignment explanation
Indices: 43535838--43535889 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
43535828 TTGTCTTTTA
*
43535838 TATTATTATATTATACCAT-T
1 TATTATTATATTAT-CAATAT
43535858 TATTCATT-TATTATCAATAT
1 TATT-ATTATATTATCAATAT
*
43535878 TATTACTATATT
1 TATTATTATATT
43535890 CCTAAGCACA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 5 0.19
20 19 0.70
21 3 0.11
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.56
Consensus pattern (20 bp):
TATTATTATATTATCAATAT
Found at i:43538037 original size:13 final size:13
Alignment explanation
Indices: 43538019--43538044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43538009 AAAGAGATTT
43538019 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
43538032 GTTTTCTAGTAAA
1 GTTTTCTAGTAAA
43538045 AAAATTGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTTTTCTAGTAAA
Found at i:43538115 original size:19 final size:20
Alignment explanation
Indices: 43538078--43538117 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
43538068 TCTTTTCGCA
* *
43538078 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
43538098 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
43538117 T
1 T
43538118 AAATACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:43540005 original size:18 final size:19
Alignment explanation
Indices: 43539965--43540004 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
43539955 GCAAATGTTC
43539965 TTTCATTCTTTATGATTTT
1 TTTCATTCTTTATGATTTT
43539984 TTTCATTCTTTCA-GATTTT
1 TTTCATTCTTT-ATGATTTT
43540003 TT
1 TT
43540005 CTGCCAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTCATTCTTTATGATTTT
Found at i:43540967 original size:7 final size:7
Alignment explanation
Indices: 43540943--43540990 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
43540933 TTGAGTCGTA
43540943 AAAAATG
1 AAAAATG
*
43540950 ATAATATG
1 A-AAAATG
43540958 AAAAATG
1 AAAAATG
43540965 AAAAAGTG
1 AAAAA-TG
43540973 -AAAATG
1 AAAAATG
*
43540979 AAAACTG
1 AAAAATG
43540986 AAAAA
1 AAAAA
43540991 ATGGAAAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 2 0.06
7 24 0.71
8 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.15, T:0.17
Consensus pattern (7 bp):
AAAAATG
Found at i:43540974 original size:15 final size:15
Alignment explanation
Indices: 43540943--43541004 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
43540933 TTGAGTCGTA
*
43540943 AAAAATGATAATA-TG
1 AAAAATGA-AAAAGTG
43540958 AAAAATGAAAAAGTG
1 AAAAATGAAAAAGTG
*
43540973 -AAAATG-AAAACTG
1 AAAAATGAAAAAGTG
*
43540986 AAAAAATGGAAAAGT-
1 -AAAAATGAAAAAGTG
43541001 AAAA
1 AAAA
43541005 CGGAGAGGCT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
13 6 0.15
14 13 0.32
15 16 0.40
16 5 0.12
ACGTcount: A:0.66, C:0.02, G:0.16, T:0.16
Consensus pattern (15 bp):
AAAAATGAAAAAGTG
Found at i:43541005 original size:22 final size:21
Alignment explanation
Indices: 43540942--43540998 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
43540932 TTTGAGTCGT
*
43540942 AAAAAATGATAATATGAAAAATG
1 AAAAAATGA-AA-ATGAAAACTG
*
43540965 AAAAAGTGAAAATGAAAACTG
1 AAAAAATGAAAATGAAAACTG
43540986 AAAAAATGGAAAA
1 AAAAAAT-GAAAA
43540999 GTAAAACGGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.50
22 7 0.23
23 8 0.27
ACGTcount: A:0.67, C:0.02, G:0.16, T:0.16
Consensus pattern (21 bp):
AAAAAATGAAAATGAAAACTG
Found at i:43542563 original size:163 final size:163
Alignment explanation
Indices: 43542257--43542564 Score: 422
Period size: 163 Copynumber: 1.9 Consensus size: 163
43542247 ATCTCTCTGG
* * * *
43542257 GCAGCAGTGGAATAAATTGAATATTACAGATCTTATCTCCCTAGGCAGTAGTGGAGTAGATCGAA
1 GCAGCAGTGGAATAAATTGAAGATTACAGACCTTATATCCCTAGGCAGTAGTGGAGCAGATCGAA
* * *
43542322 AATAGCAGATTTTACCTCCCTGAGGTTACAGTGAAATATATTGAAGCCAGTAATTCTATCTTCCT
66 AATAGCAGATTTTACCTCCCAGAGGTTACAGTGAAATACATTGAAGCCAATAATTCTATCTTCCT
* * *
43542387 GGTCGGTAGTGGAATCGATCGAAGAAAGTAGAA
131 GGGCAGCAGTGGAATCGATCGAAGAAAGTAGAA
* * *
43542420 GCAGCAGTGGAATAGATTGAAGATTACAGACCTTATATCCCTATGTAGTAGTGGAGCAGATC-AA
1 GCAGCAGTGGAATAAATTGAAGATTACAGACCTTATATCCCTAGGCAGTAGTGGAGCAGATCGAA
* ** * *
43542484 AGATGGTGGATTTTACCTCCCAGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATC-TCT
66 A-ATAGCAGATTTTACCTCCCAGAGGTTACAGTGAAATACATTGAAGCCAATAATTCTATCTTC-
43542548 CTGGGCAGCAGTGGAAT
129 CTGGGCAGCAGTGGAAT
43542565 AAATTGAATA
Statistics
Matches: 125, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
162 5 0.04
163 120 0.96
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (163 bp):
GCAGCAGTGGAATAAATTGAAGATTACAGACCTTATATCCCTAGGCAGTAGTGGAGCAGATCGAA
AATAGCAGATTTTACCTCCCAGAGGTTACAGTGAAATACATTGAAGCCAATAATTCTATCTTCCT
GGGCAGCAGTGGAATCGATCGAAGAAAGTAGAA
Found at i:43542657 original size:132 final size:130
Alignment explanation
Indices: 43542420--43542838 Score: 577
Period size: 132 Copynumber: 3.2 Consensus size: 130
43542410 GAAAGTAGAA
* * * *
43542420 GCAGCAGTGGAATAGATTGAAGATTACAGACCTTATATCCCTATGTAGTAGTGGAGCAGATCAAA
1 GCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTA-GCAGTAGTGGAGTAGATCAAA
* * * *
43542485 GATGGTGGATTTTACCTCCCAGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCTCT
65 GATGGTAGATTTTACCTCCCTGAGGTTACAGT-GAGTACATTGAAGCCAGTAATTCTATCTCCCT
43542550 GG
129 GG
* * *
43542552 GCAGCAGTGGAATAAATTGAATATTACAGATCTTATCTCCCTAGACAGTAGTGGAGTAGATCGAA
1 GCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAG-CAGTAGTGGAGTAGATCAAA
*
43542617 GATGGTAGATTTTACCTCTCTGAGGTTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCT
65 GATGGTAGATTTTACCTCCCTGAGGTTACAGT-GAGTACATTGAAGCCAGTAATTCTATCTCCCT
43542682 GG
129 GG
* *
43542684 GCAGCAGTGGAATAGATTGAAGATTACAGATTTTATCTCTCTAGGCAGTAGTGGAGTAGATCAAA
1 GCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTA-GCAGTAGTGGAGTAGATCAAA
* * * *
43542749 GATGGCAGATTTTACCTCCCTGAGGTTACAGTGAAATATATTGAAGCCAGTAATTCTATCTTCCT
65 GATGGTAGATTTTACCTCCCTGAGGTTACAGTG-AGTACATTGAAGCCAGTAATTCTATCTCCCT
43542814 GG
129 GG
* * * * *
43542816 TCGGTAGTGGAATCGATCGAAGA
1 GCAGCAGTGGAATAGATTGAAGA
43542839 AAGTAGATCT
Statistics
Matches: 256, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
131 2 0.01
132 253 0.99
133 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (130 bp):
GCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGCAGTAGTGGAGTAGATCAAAG
ATGGTAGATTTTACCTCCCTGAGGTTACAGTGAGTACATTGAAGCCAGTAATTCTATCTCCCTGG
Found at i:43542737 original size:44 final size:44
Alignment explanation
Indices: 43542541--43542762 Score: 146
Period size: 44 Copynumber: 5.0 Consensus size: 44
43542531 CCAATAATTC
* * * * * *
43542541 TATCTCTCTGGGCAGCAGTGGAATAAATTGAATATTACAGATCT
1 TATCTCTCTAGGCAGCAGTGGAGTAGATTGAAGATGACAGATTT
* * * * **
43542585 TATCTCCCTAGACAGTAGTGGAGTAGATCGAAGATGGTAGATTT
1 TATCTCTCTAGGCAGCAGTGGAGTAGATTGAAGATGACAGATTT
* * * * * *
43542629 TACCTCTCTGAGGTTA-CAGTAGAGTACATTG-A-A-GCCAGTAATTC
1 TATCTCTCT-AGG-CAGCAGTGGAGTAGATTGAAGATGACAG--ATTT
* * * *
43542673 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATTT
1 TATCTCTCTAGGCAGCAGTGGAGTAGATTGAAGATGACAGATTT
* ** *
43542717 TATCTCTCTAGGCAGTAGTGGAGTAGATCAAAGATGGCAGATTT
1 TATCTCTCTAGGCAGCAGTGGAGTAGATTGAAGATGACAGATTT
43542761 TA
1 TA
43542763 CCTCCCTGAG
Statistics
Matches: 129, Mismatches: 41, Indels: 16
0.69 0.22 0.09
Matches are distributed among these distances:
42 4 0.03
43 15 0.12
44 92 0.71
45 14 0.11
46 4 0.03
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (44 bp):
TATCTCTCTAGGCAGCAGTGGAGTAGATTGAAGATGACAGATTT
Found at i:43542880 original size:44 final size:44
Alignment explanation
Indices: 43542830--43542971 Score: 185
Period size: 44 Copynumber: 3.2 Consensus size: 44
43542820 TAGTGGAATC
*
43542830 GATCGAAGAAAGTAGATCTTGTCTTCATGTATTGGTGTGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTA
* *
43542874 GATCGAAGGAAGCAGATCTTGTCTTCATGTATTGGTATGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTA
* * *** * *
43542918 GATCAAAGAGAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTA
1 GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGT-GTGAAGTA
43542963 GATCGAAGA
1 GATCGAAGA
43542972 TACAAGTCTT
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
44 70 0.83
45 14 0.17
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (44 bp):
GATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTA
Found at i:43543044 original size:44 final size:44
Alignment explanation
Indices: 43542989--43543134 Score: 147
Period size: 44 Copynumber: 3.4 Consensus size: 44
43542979 CTTATCTCCC
*
43542989 TGAAGTAGCAGTGGAGCAGACAGAAGTAACCAATCCTATCTCTT
1 TGAAGTTGCAGTGGAGCAGACAGAAGTAACCAATCCTATCTCTT
* * * * * *
43543033 TGAAGTTGCAGTTGAGCAGATC-GCA-T--CCAGTCTTATCCCTC
1 TGAAGTTGCAGTGGAGCAGA-CAGAAGTAACCAATCCTATCTCTT
* * * * *
43543074 TGAAGTTGCAGAGGAGCAGACAGAAGAAATCGATCCTATCTCCT
1 TGAAGTTGCAGTGGAGCAGACAGAAGTAACCAATCCTATCTCTT
43543118 TGAAGTTGCAGTGGAGC
1 TGAAGTTGCAGTGGAGC
43543135 GGATTAAAAT
Statistics
Matches: 78, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
40 1 0.01
41 31 0.40
43 1 0.01
44 44 0.56
45 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGACAGAAGTAACCAATCCTATCTCTT
Found at i:43543121 original size:85 final size:85
Alignment explanation
Indices: 43542976--43543134 Score: 239
Period size: 85 Copynumber: 1.9 Consensus size: 85
43542966 CGAAGATACA
* * *
43542976 AGTCTTATCTCCCTGAAGTAGCAGTGGAGCAGACAGAAGTAACCAATCCTATCTCTTTGAAGTTG
1 AGTCTTATCTCCCTGAAGTAGCAGAGGAGCAGACAGAAGAAACCAATCCTATCTCCTTGAAGTTG
*
43543041 CAGTTGAGCAGATCGCATCC
66 CAGTGGAGCAGATCGCATCC
* * *
43543061 AGTCTTATC-CCTCTGAAGTTGCAGAGGAGCAGACAGAAGAAATCGATCCTATCTCCTTGAAGTT
1 AGTCTTATCTCC-CTGAAGTAGCAGAGGAGCAGACAGAAGAAACCAATCCTATCTCCTTGAAGTT
43543125 GCAGTGGAGC
65 GCAGTGGAGC
43543135 GGATTAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 2 0.03
85 64 0.97
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (85 bp):
AGTCTTATCTCCCTGAAGTAGCAGAGGAGCAGACAGAAGAAACCAATCCTATCTCCTTGAAGTTG
CAGTGGAGCAGATCGCATCC
Found at i:43546869 original size:21 final size:21
Alignment explanation
Indices: 43546845--43546893 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
43546835 TTTAACATTA
43546845 AGTATCAATACCTTGAATAAG
1 AGTATCAATACCTTGAATAAG
43546866 AGTATCAATACCTTGAATAAG
1 AGTATCAATACCTTGAATAAG
43546887 AGTATCA
1 AGTATCA
43546894 GTACTTAATC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
AGTATCAATACCTTGAATAAG
Found at i:43548878 original size:2 final size:2
Alignment explanation
Indices: 43548873--43548897 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
43548863 AACTCGTGGC
43548873 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 T
43548898 TTCTATTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:43555898 original size:31 final size:29
Alignment explanation
Indices: 43555830--43555901 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
43555820 CTCAGGTTAG
*
43555830 ATTTTAGTCACTTATATTTGAAATGTTAT
1 ATTTTAGTCACTTATATTTGAAATGTAAT
* ***
43555859 GTTTTAGTCACTTATATTATCGTGTTGTAAT
1 ATTTTAGTCACTTATATT-T-GAAATGTAAT
43555890 ATTTTAGTCACT
1 ATTTTAGTCACT
43555902 GAGTCGTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.49
30 1 0.03
31 17 0.49
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.51
Consensus pattern (29 bp):
ATTTTAGTCACTTATATTTGAAATGTAAT
Found at i:43559007 original size:33 final size:36
Alignment explanation
Indices: 43558930--43559005 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
43558920 TCTGTAAGAA
* *
43558930 ATTATTAATAATATTTTTAAATTATAATATATTAAT
1 ATTATTAATAATAGTTTTAAACTATAATATATTAAT
*
43558966 ATTATTAATAATAGTTTTAAACTATAATGTATTAAT
1 ATTATTAATAATAGTTTTAAACTATAATATATTAAT
43559002 ATTA
1 ATTA
43559006 ATATTTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (36 bp):
ATTATTAATAATAGTTTTAAACTATAATATATTAAT
Found at i:43559138 original size:17 final size:18
Alignment explanation
Indices: 43559097--43559139 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
43559087 AAATTAGTTA
43559097 AATATTTTTATTTACATT
1 AATATTTTTATTTACATT
43559115 AAT-TTTTTAATTTA-A-T
1 AATATTTTT-ATTTACATT
43559131 AATATTTTT
1 AATATTTTT
43559140 TGAAGAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 11 0.48
18 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
AATATTTTTATTTACATT
Found at i:43561539 original size:6 final size:7
Alignment explanation
Indices: 43561518--43561547 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
43561508 TGTATATCAA
43561518 TTTCTTT
1 TTTCTTT
43561525 TTTCTTT
1 TTTCTTT
43561532 TTTCTTT
1 TTTCTTT
43561539 TTTCATTT
1 TTTC-TTT
43561547 T
1 T
43561548 ACATATTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTCTTT
Found at i:43563897 original size:46 final size:46
Alignment explanation
Indices: 43563839--43563927 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
43563829 GTTAAACACA
* *
43563839 CTTTCTAGCCATGCTTCTTTATCTTTCTTTGGCTTCCCTATGTACT
1 CTTTCTACCCATGCTTCTTTATCTCTCTTTGGCTTCCCTATGTACT
43563885 CTTTCTACCCATGCTTCTTTATCTCTCTTTGGCTTCCCTATGT
1 CTTTCTACCCATGCTTCTTTATCTCTCTTTGGCTTCCCTATGT
43563928 TGCCATAACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.10, C:0.30, G:0.10, T:0.49
Consensus pattern (46 bp):
CTTTCTACCCATGCTTCTTTATCTCTCTTTGGCTTCCCTATGTACT
Found at i:43568793 original size:5 final size:6
Alignment explanation
Indices: 43568763--43568791 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43568753 AATGTAAATG
43568763 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
43568792 TATTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:43572452 original size:105 final size:105
Alignment explanation
Indices: 43572280--43572953 Score: 724
Period size: 105 Copynumber: 6.4 Consensus size: 105
43572270 GTCAGTTAAT
* * * * * * *
43572280 TGTTTAAGAATTGCGATCTTGAATCAGTTAACTCAAAGAAATTTAGGTTGCGATCTTAAATCAAC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
* * * *
43572345 TAACCTTTATAATTCCAATTGTGAACGTAGGTCAGGGACC
66 TAACCTTTATAATTCCAGTTGTGAACATAGGTCAGTGAGC
* * *
43572385 TGTTTAGGAGTTGCAATATTAAATCAGCTAACTCAAAGAAATTTAGGTTATGATCTTAAATCAAC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
* * * *
43572450 TAACCTTTATAATTCCAGCTGTGAATATAGGTTAGTGAGT
66 TAACCTTTATAATTCCAGTTGTGAACATAGGTCAGTGAGC
* * * * *
43572490 TGTTTAAGAGTTGCGATATTAAATCAGCTAACTTAACGAAATTTAGGTTGTGATATTAAATTAGC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
* * * *
43572555 TAACCTTTATAATTCCAGTTGTGAACACATGTTAGCGAGC
66 TAACCTTTATAATTCCAGTTGTGAACATAGGTCAGTGAGC
* * * * * *
43572595 TGTTTAGGAGTTGCGATCTTAAACCAGCTAACTCAAAGAAAATTGGGTTGCGATATTAAATCAGC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
* * * * ** ** *
43572660 TAACTTTTATAATTTCAGTGGTGAACGTAGGTTTGCAATC
66 TAACCTTTATAATTCCAGTTGTGAACATAGGTCAGTGAGC
* * * * * * *
43572700 TGTTTAGGAGTTGTGATATTAAATTAGCTAACTCAAAGAAATTTAGGCTATGATCTTAAATGAAT
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
** * *
43572765 TAACCTTTATAATTCCAACTGTAAATATAGGTCAGTGAGC
66 TAACCTTTATAATTCCAGTTGTGAACATAGGTCAGTGAGC
* * * * * *
43572805 TATTTAGGAGTTGTGATCTTAAATCAACTAACTC--AGAAACTTAGGTTGTGATATTAAATCAGC
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
* *
43572868 TAACCTTTATAATTCTAGTTGTG-ACTGTAGGTCAGTGAGC
66 TAACCTTTATAATTCCAGTTGTGAAC-ATAGGTCAGTGAGC
* ** * *
43572908 TGTTTAGAAGTTATGATCTTAAATCAGCTAACTCAAATAAATTTAG
1 TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAG
43572954 ACATGAAAAT
Statistics
Matches: 469, Mismatches: 97, Indels: 6
0.82 0.17 0.01
Matches are distributed among these distances:
102 1 0.00
103 84 0.18
105 384 0.82
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (105 bp):
TGTTTAGGAGTTGCGATATTAAATCAGCTAACTCAAAGAAATTTAGGTTGTGATATTAAATCAAC
TAACCTTTATAATTCCAGTTGTGAACATAGGTCAGTGAGC
Found at i:43581520 original size:142 final size:140
Alignment explanation
Indices: 43581226--43581546 Score: 473
Period size: 142 Copynumber: 2.3 Consensus size: 140
43581216 GGCGCTTCGA
* *
43581226 TCCACTGTAATCTCAGGGAGATAGAATTACTAGCTTCAATCTGCTTCGCTGTAATCTCAGGGAGA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAACCTGCTTCGCTGTAATCTCAGGGAGA
* * * * *
43581291 TAAGACCTGACCTCAATCTGATGCGATCTACTCTGCTGTAACTTTAGAGAGATAAGATCTTTTAT
66 TAAGACCTGACCTCAATCTGACGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTAT
43581356 TTTAATCCGC
131 TTTAATCCGC
*
43581366 TCCACTATAATCTCAGGGAGATAGGATTACTAGCTTCAACCTGC-TCTGCTGTAATCTCAGGGAG
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAACCTGCTTC-GCTGTAATCTCAGGGAG
* * *
43581430 ATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTT
65 ATAAGA--CCTGACCTCAATCTGACGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTT
*
43581495 TGTTTTAATCCGC
128 TATTTTAATCCGC
* * *
43581508 TCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAA
1 TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAA
43581547 TCTGACGCGA
Statistics
Matches: 162, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
139 2 0.01
140 64 0.40
142 96 0.59
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (140 bp):
TCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAACCTGCTTCGCTGTAATCTCAGGGAGA
TAAGACCTGACCTCAATCTGACGCGATCTACTCTACTATAACTTCAGAGAGATAAGATCCTTTAT
TTTAATCCGC
Found at i:43581538 original size:98 final size:98
Alignment explanation
Indices: 43581414--43581648 Score: 443
Period size: 98 Copynumber: 2.4 Consensus size: 98
43581404 ACCTGCTCTG
43581414 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
1 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
43581479 GAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
66 GAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
43581512 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
1 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
43581577 GAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
66 GAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
* * *
43581610 CTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTG
43581649 CTTCGCTGTA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
98 134 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (98 bp):
CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
GAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
Found at i:43581627 original size:142 final size:142
Alignment explanation
Indices: 43581501--43581818 Score: 573
Period size: 142 Copynumber: 2.2 Consensus size: 142
43581491 CCTTTGTTTT
*
43581501 AATCCGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTA
*
43581566 CTATAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
66 CTATAACTTAAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
43581631 ATTACTAGCTTC
131 ATTACTAGCTTC
* * *
43581643 AATCTGCTTCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTTTA
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTA
* *
43581708 CTGTAACTTAAGAGAGATAAGATCCTTTGTTTTAATTCGCTCCACTGTAATCTCAGGGAGATAGG
66 CTATAACTTAAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
43581773 ATTACTAGCTTC
131 ATTACTAGCTTC
43581785 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT
43581819 CTATAATTCC
Statistics
Matches: 167, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
142 167 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (142 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTA
CTATAACTTAAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
ATTACTAGCTTC
Found at i:43581726 original size:240 final size:240
Alignment explanation
Indices: 43581274--43581790 Score: 842
Period size: 240 Copynumber: 2.2 Consensus size: 240
43581264 ATCTGCTTCG
* * * * * * *
43581274 CTGTAATCTCAGGGAGATAAGA--CCTGACCTCAATCTGATGCGATCTACTCTGCTGTAACTTTA
1 CTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
*
43581337 GAGAGATAAGATCTTTTATTTTAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTT
66 GAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTT
43581402 CAACCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCT
131 CAACCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCT
*
43581467 ACTATAACTTCAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
196 ACTATAACTTAAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
*
43581512 CTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
1 CTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
* *
43581577 GAGAGATAAGATCCTTTGTTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTT
66 GAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTT
* *
43581642 CAATCTGCT-TCGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTT
131 CAACCTGCTCT-GCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTC
* *
43581706 TACTGTAACTTAAGAGAGATAAGATCCTTTGTTTTAATTCGCTCCA
195 TACTATAACTTAAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
* *
43581752 CTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTG
1 CTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTG
43581791 CTCCACTGTA
Statistics
Matches: 258, Mismatches: 18, Indels: 4
0.92 0.06 0.01
Matches are distributed among these distances:
238 22 0.09
239 1 0.00
240 235 0.91
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (240 bp):
CTGTAATCTCAGGGAGATAAGATTACTGGCTTCAATCTGACGCGATCTACTCTACTATAACTTCA
GAGAGATAAGATCCTTTATTTTAATCCGCTCCACTATAATCTCAGGGAGATAGGATTACTAGCTT
CAACCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTCAATCTGACGCGATCTACTCT
ACTATAACTTAAGAGAGATAAGATCCTTTGTTTTAATCCGCTCCA
Found at i:43601078 original size:20 final size:20
Alignment explanation
Indices: 43601032--43601070 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43601022 TTAGTGCCTT
43601032 GCTTGTACTTCAGTACCCCA
1 GCTTGTACTTCAGTACCCCA
*
43601052 GCTTGTACTTCGGTACCCC
1 GCTTGTACTTCAGTACCCC
43601071 TATTTGTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.36, G:0.18, T:0.31
Consensus pattern (20 bp):
GCTTGTACTTCAGTACCCCA
Found at i:43602407 original size:25 final size:25
Alignment explanation
Indices: 43602377--43602470 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
43602367 GTCACGACCC
*
43602377 ACAGCTCGTATGAGCATACTGATTT
1 ACAGCTCATATGAGCATACTGATTT
* *
43602402 ATAGCTCATGA-GAGCATATTGATCTT
1 ACAGCTCAT-ATGAGCATACTGAT-TT
* * *
43602428 -CAGCTCGAT-TGAGCATACCGGTTC
1 ACAGCTC-ATATGAGCATACTGATTT
43602452 ACAGCTCATATGAGCATAC
1 ACAGCTCATATGAGCATAC
43602471 ATGTACATAA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
24 3 0.05
25 47 0.85
26 5 0.09
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (25 bp):
ACAGCTCATATGAGCATACTGATTT
Found at i:43610612 original size:20 final size:18
Alignment explanation
Indices: 43610576--43610657 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 18
43610566 ACACTGTTTG
*
43610576 TACTTCGGTACCCCCTATT
1 TACTTCGATA-CCCCTATT
43610595 TATCATTCGATACCCCTAATT
1 TA-C-TTCGATACCCCT-ATT
*
43610616 GTACTTCGGTACCCCTATTT
1 -TACTTCGATACCCCTA-TT
* *
43610636 GTACTTCGGTACCCCTGTT
1 -TACTTCGATACCCCTATT
43610655 TAC
1 TAC
43610658 ACGTTCGTGC
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
18 3 0.05
19 5 0.09
20 35 0.64
21 10 0.18
22 2 0.04
ACGTcount: A:0.18, C:0.32, G:0.12, T:0.38
Consensus pattern (18 bp):
TACTTCGATACCCCTATT
Found at i:43619861 original size:15 final size:15
Alignment explanation
Indices: 43619822--43619901 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
43619812 GTATCTTGGG
*
43619822 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
43619837 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
43619852 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
43619867 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
43619882 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
43619896 TTTCTT
1 TTTCTT
43619902 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
14 10 0.19
15 41 0.77
16 2 0.04
ACGTcount: A:0.10, C:0.19, G:0.14, T:0.57
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:43619891 original size:30 final size:30
Alignment explanation
Indices: 43619813--43619900 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
43619803 CATAGTATCG
* * *
43619813 TATCTTGGGTTTCTTTA-TCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCC-GGATTTCTC
*
43619843 TAT-TCTGGATTTCTTTATTCCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCGGATTTCTC
*
43619873 TATCTTGGATTTCTTTATT-CGGTTTTCT
1 TATCTTGGATTTCTTTATTCCGGATTTCT
43619901 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 9 0.18
30 37 0.74
31 4 0.08
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCCGGATTTCTC
Found at i:43630783 original size:25 final size:25
Alignment explanation
Indices: 43630745--43630817 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
43630735 TCCTGTACAT
43630745 GTATGCTCATGCGAGC-GATGAATCG
1 GTATGCTCATGCGAGCTG-TGAATCG
43630770 GTATGCTC-TCGCGAGCTGTGAATCG
1 GTATGCTCAT-GCGAGCTGTGAATCG
* * *
43630795 GTAAGCTCATACGAGCTGAGAAT
1 GTATGCTCATGCGAGCTGTGAAT
43630818 TGGCAAGCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
24 1 0.02
25 39 0.93
26 2 0.05
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (25 bp):
GTATGCTCATGCGAGCTGTGAATCG
Found at i:43630825 original size:25 final size:25
Alignment explanation
Indices: 43630781--43630830 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
43630771 TATGCTCTCG
* *
43630781 CGAGCTGTGAATCGGTAAGCTCATA
1 CGAGCTGAGAATCGGCAAGCTCATA
*
43630806 CGAGCTGAGAATTGGCAAGCTCATA
1 CGAGCTGAGAATCGGCAAGCTCATA
43630831 AGAGTTGTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (25 bp):
CGAGCTGAGAATCGGCAAGCTCATA
Found at i:43635835 original size:31 final size:31
Alignment explanation
Indices: 43635792--43635850 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
43635782 AGGGTTACGA
43635792 AGCATTACCGGACTTACAATACAATTAATGG
1 AGCATTACCGGACTTACAATACAATTAATGG
*
43635823 AGCATTATCGGACTTACAATACAATTAA
1 AGCATTACCGGACTTACAATACAATTAA
43635851 ACATTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (31 bp):
AGCATTACCGGACTTACAATACAATTAATGG
Found at i:43643318 original size:40 final size:39
Alignment explanation
Indices: 43643253--43643338 Score: 118
Period size: 40 Copynumber: 2.2 Consensus size: 39
43643243 TTTATATATA
* *
43643253 TAGCCAAAGCTATCTCAAACTGCACACCAAGTGCCACTTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCA-TTT
* * *
43643293 TAGCCGAAGCTATTTCGAACCGCACACTAAGTGCCATTT
1 TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
43643332 TAGCCGA
1 TAGCCGA
43643339 TAAGTCGTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 10 0.24
40 31 0.76
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (39 bp):
TAGCCGAAGCTATCTCAAACCGCACACCAAGTGCCATTT
Found at i:43644356 original size:34 final size:34
Alignment explanation
Indices: 43644313--43644380 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
43644303 CAAAACGATA
43644313 AAATTTTTCAACGAAACTTTAATACCATCTTATT
1 AAATTTTTCAACGAAACTTTAATACCATCTTATT
*
43644347 AAATTTTTCAAGGAAACTTTAATACCATCTTATT
1 AAATTTTTCAACGAAACTTTAATACCATCTTATT
43644381 GCCACTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.41
Consensus pattern (34 bp):
AAATTTTTCAACGAAACTTTAATACCATCTTATT
Found at i:43648729 original size:40 final size:40
Alignment explanation
Indices: 43648650--43648817 Score: 187
Period size: 40 Copynumber: 4.2 Consensus size: 40
43648640 CGGATGATAA
* * * **
43648650 CCGGACTAAGATCTGAAGGCATTCGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * * *
43648690 CCGGGCTATGTCCCGAAGGCATTTATGCTAG-TGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTG-CTATAT
*
43648730 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
* * *
43648770 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
*
43648810 TC-GGCTAA
1 CCGGGCTAA
43648818 ATCCCAAAGA
Statistics
Matches: 109, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
39 8 0.07
40 99 0.91
41 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGTTGCTATAT
Found at i:43648808 original size:80 final size:80
Alignment explanation
Indices: 43648650--43648817 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
43648640 CGGATGATAA
* * * * *
43648650 CCGGACTAAGATCTGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
*
43648715 TGCTAGTGATTATAT
66 TGCAAGTGATTATAT
* *
43648730 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
43648795 TGCAAGTTG-TTATAT
66 TGCAAG-TGATTATAT
*
43648810 TC-GGCTAA
1 CCGGGCTAA
43648818 ATCCCAAAGA
Statistics
Matches: 78, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
79 6 0.08
80 70 0.90
81 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
TGCAAGTGATTATAT
Found at i:43649094 original size:22 final size:22
Alignment explanation
Indices: 43649054--43649095 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
43649044 GAATGTGCAT
*
43649054 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
43649076 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
43649096 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:43650630 original size:43 final size:44
Alignment explanation
Indices: 43650582--43650689 Score: 121
Period size: 43 Copynumber: 2.5 Consensus size: 44
43650572 TCCTAGATAT
* * *
43650582 GGTCTTACATGTTATCACATAT-CGATGCCACTGTCCCACACAG
1 GGTCTTACATGTAATCACATATACAATGCCAATGTCCCACACAG
* * * * *
43650625 GGTCTTACACGAAATCACA-ATACAATGCCAATGTCCTAGACAT
1 GGTCTTACATGTAATCACATATACAATGCCAATGTCCCACACAG
*
43650668 GGCCTTACATGTAATCACATAT
1 GGTCTTACATGTAATCACATAT
43650690 TGATTTGATG
Statistics
Matches: 52, Mismatches: 11, Indels: 3
0.79 0.17 0.05
Matches are distributed among these distances:
42 2 0.04
43 48 0.92
44 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (44 bp):
GGTCTTACATGTAATCACATATACAATGCCAATGTCCCACACAG
Found at i:43654284 original size:40 final size:40
Alignment explanation
Indices: 43654229--43654416 Score: 313
Period size: 40 Copynumber: 4.7 Consensus size: 40
43654219 GAGCATTGGA
43654229 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
43654269 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTA
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* * *
43654309 ATATGTCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
43654349 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
43654389 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
43654417 AGGTGTTTGC
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 137 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:43659014 original size:12 final size:12
Alignment explanation
Indices: 43658997--43659022 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43658987 TAGCTCCTCA
43658997 TAGTCTCTTTGT
1 TAGTCTCTTTGT
43659009 TAGTCTCTTTGT
1 TAGTCTCTTTGT
43659021 TA
1 TA
43659023 TCTTTCTCTC
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:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (12 bp):
TAGTCTCTTTGT
Found at i:43659214 original size:85 final size:85
Alignment explanation
Indices: 43659112--43659281 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
43659102 TGTAAAGAAA
*
43659112 GAAAATTTTTCTTTCTTCTCTTCTCTTCTAACGTGAATTGCATGGAAAAGATGGTGGGTTGGTTC
1 GAAAAATTTTCTTTCTTCTCTTCTCTTCTAACGTGAATTGCATGGAAAAGATGGTGGGTTGGTTC
43659177 CTTTTCATCTTTCTTTCCAC
66 CTTTTCATCTTTCTTTCCAC
43659197 GAAAAATTTTCTTTCTTCTCTTCTCTTCTAACGTGAATTGCATGGAAAAGATGGTGGGTTGGTTC
1 GAAAAATTTTCTTTCTTCTCTTCTCTTCTAACGTGAATTGCATGGAAAAGATGGTGGGTTGGTTC
43659262 CTTTTCATCTTTCTTTCCAC
66 CTTTTCATCTTTCTTTCCAC
43659282 TTATATATAC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.44
Consensus pattern (85 bp):
GAAAAATTTTCTTTCTTCTCTTCTCTTCTAACGTGAATTGCATGGAAAAGATGGTGGGTTGGTTC
CTTTTCATCTTTCTTTCCAC
Found at i:43660020 original size:66 final size:66
Alignment explanation
Indices: 43659949--43660110 Score: 288
Period size: 66 Copynumber: 2.5 Consensus size: 66
43659939 AGAGGCTCAA
* * * *
43659949 AGAAAATATGAAGAACTCCAGCTACAGCTTAAAGCGGAGGAAACAGCGAGGGAAGCAGAGCAAAG
1 AGAAAATATGATGTACTCCAGTTATAGCTTAAAGCGGAGGAAACAGCGAGGGAAGCAGAGCAAAG
43660014 C
66 C
43660015 AGAAAATATGATGTACTCCAGTTATAGCTTAAAGCGGAGGAAACAGCGAGGGAAGCAGAGCAAAG
1 AGAAAATATGATGTACTCCAGTTATAGCTTAAAGCGGAGGAAACAGCGAGGGAAGCAGAGCAAAG
43660080 C
66 C
43660081 AGAAAATATGATGTACTCCAGTTATAGCTT
1 AGAAAATATGATGTACTCCAGTTATAGCTT
43660111 CAGAATATGA
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 92 1.00
ACGTcount: A:0.41, C:0.16, G:0.27, T:0.16
Consensus pattern (66 bp):
AGAAAATATGATGTACTCCAGTTATAGCTTAAAGCGGAGGAAACAGCGAGGGAAGCAGAGCAAAG
C
Found at i:43660498 original size:42 final size:42
Alignment explanation
Indices: 43660441--43660553 Score: 163
Period size: 42 Copynumber: 2.7 Consensus size: 42
43660431 TTAGTAAAAT
* * * * *
43660441 CGCCGCTAAAGGTCATGTTCTTTAGTGGTGTTTTTGGGGAAG
1 CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
*
43660483 CGCCGCTAAAAGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
1 CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
*
43660525 CGCCGCTAAAGGTCATGTTCTATAACGGC
1 CGCCGCTAAAGGTCATGTTCTATAGCGGC
43660554 ATTTTTCCAC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.29
Consensus pattern (42 bp):
CGCCGCTAAAGGTCATGTTCTATAGCGGCGTTTGTGGGAAAG
Done.