Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_pilon, whole genome shotgun sequence
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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 18
Found at i:2550037 original size:20 final size:22
Alignment explanation
Indices: 2550014--2550078 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
2550004 AGTTACATAT
2550014 ATAGTTTATATA-ACATGTA-A
1 ATAGTTTATATATACATGTACA
* *
2550034 ATAGATTGTATATATACATATACT
1 ATAG-TT-TATATATACATGTACA
*
2550058 ATAGGTTATATATACATGTAC
1 ATAGTTTATATATACATGTAC
2550079 TATAAGTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 4 0.11
21 2 0.05
22 20 0.54
23 7 0.19
24 4 0.11
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (22 bp):
ATAGTTTATATATACATGTACA
Found at i:2550094 original size:24 final size:22
Alignment explanation
Indices: 2550042--2550093 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
2550032 AAATAGATTG
*
2550042 TATATATACATATACTATAGGT
1 TATATATACATATACTATAAGT
*
2550064 TATATATACATGTACTATAAGT
1 TATATATACATATACTATAAGT
*
2550086 TACATATA
1 TATATATA
2550094 TAGTTTACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (22 bp):
TATATATACATATACTATAAGT
Found at i:2550911 original size:65 final size:64
Alignment explanation
Indices: 2550861--2551008 Score: 212
Period size: 64 Copynumber: 2.3 Consensus size: 64
2550851 ACACTAATTA
* *
2550861 CATTCGATGTTTCAA-AAGAGCCA-AGAGTGCATCGATGCATGGTCTGTGCATCGGTACATCAAA
1 CATTCGATGTTTCAATAA-A-ACATAGAGT-CATCGATACATGGTCTGTGCATCGGTACATCAAA
2550924 AG
63 AG
*
2550926 CATTCGATGTTTCAATAAAACATGGAGTCATCGATACATGGTCTGTGCATCGGTACATCAAAAG
1 CATTCGATGTTTCAATAAAACATAGAGTCATCGATACATGGTCTGTGCATCGGTACATCAAAAG
*
2550990 CATTCGATG-TTCAAGAAAA
1 CATTCGATGTTTCAATAAAA
2551009 TTAGGTGTGT
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
63 9 0.12
64 46 0.60
65 20 0.26
66 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (64 bp):
CATTCGATGTTTCAATAAAACATAGAGTCATCGATACATGGTCTGTGCATCGGTACATCAAAAG
Found at i:2551024 original size:64 final size:64
Alignment explanation
Indices: 2550885--2551008 Score: 214
Period size: 64 Copynumber: 1.9 Consensus size: 64
2550875 AAAGAGCCAA
*
2550885 GAGTGCATCGATGCATGGTCTGTGCATCGGTACATCAAAAGCATTCGATGTTTCAATAAAACATG
1 GAGT-CATCGATGCATGGTCTGTGCATCGGTACATCAAAAGCATTCGATGTTTCAAGAAAACATG
*
2550950 GAGTCATCGATACATGGTCTGTGCATCGGTACATCAAAAGCATTCGATG-TTCAAGAAAA
1 GAGTCATCGATGCATGGTCTGTGCATCGGTACATCAAAAGCATTCGATGTTTCAAGAAAA
2551009 TTAGGTGTGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
63 9 0.16
64 44 0.77
65 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (64 bp):
GAGTCATCGATGCATGGTCTGTGCATCGGTACATCAAAAGCATTCGATGTTTCAAGAAAACATG
Found at i:2552594 original size:43 final size:44
Alignment explanation
Indices: 2552492--2552596 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
2552482 CGATGCACTG
* * *
2552492 CATAGTGTATCGATGGACATTCAAGGCATGCATCGGTGCACCTT
1 CATAGTGTATCGATGCACATTCAAGGCATACATCGGTACACCTT
* * * *
2552536 CATAGTGCATCGATGCATATTTAA-GCGATACATCGGTACACTTT
1 CATAGTGTATCGATGCACATTCAAGGC-ATACATCGGTACACCTT
2552580 C-TAGTGTATCGATGCAC
1 CATAGTGTATCGATGCAC
2552597 GTTGCAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
43 16 0.31
44 35 0.69
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (44 bp):
CATAGTGTATCGATGCACATTCAAGGCATACATCGGTACACCTT
Found at i:2558366 original size:19 final size:19
Alignment explanation
Indices: 2558342--2558395 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2558332 ATAAGACTTA
2558342 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
2558361 GTGCATCGGTACACTAGGG
1 GTGCATCGGTACACTAGGG
*
2558380 GTGCATCAGTACACTA
1 GTGCATCGGTACACTA
2558396 ATTACATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.31, T:0.22
Consensus pattern (19 bp):
GTGCATCGGTACACTAGGG
Found at i:2558477 original size:65 final size:65
Alignment explanation
Indices: 2558423--2558548 Score: 218
Period size: 65 Copynumber: 2.0 Consensus size: 65
2558413 AAAAGAGCCA
2558423 GGAGTGCATCAATGCATGGTATGTGCATCGATACATCAAAAGCATTCGATGTTTCAATAAAACAT
1 GGAGTGCATCAATGCATGGTATGTGCATCGATACATCAAAAGCATTCGATGTTTCAATAAAACAT
** *
2558488 GGAGTGCATTGATGCATGGTCTGTGCATCGATACATCAAAAGCATTCGATG-TTCAATAAAA
1 GGAGTGCATCAATGCATGGTATGTGCATCGATACATCAAAAGCATTCGATGTTTCAATAAAA
2558549 TTAGGTGTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
64 10 0.17
65 48 0.83
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (65 bp):
GGAGTGCATCAATGCATGGTATGTGCATCGATACATCAAAAGCATTCGATGTTTCAATAAAACAT
Found at i:2558921 original size:21 final size:21
Alignment explanation
Indices: 2558865--2558923 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
2558855 TATGCATAGT
2558865 GTTTAGGGTTTAAGG-TTTATG
1 GTTTAGGG-TTAAGGTTTTATG
* *** *
2558886 CTTTACAATTTAGGTTTTATG
1 GTTTAGGGTTAAGGTTTTATG
2558907 GTTTAGGGTTAAGGTTT
1 GTTTAGGGTTAAGGTTT
2558924 CTATAAACTA
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
20 5 0.19
21 22 0.81
ACGTcount: A:0.20, C:0.03, G:0.27, T:0.49
Consensus pattern (21 bp):
GTTTAGGGTTAAGGTTTTATG
Found at i:2558949 original size:12 final size:12
Alignment explanation
Indices: 2558932--2558958 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2558922 TTCTATAAAC
2558932 TATATATTTTAT
1 TATATATTTTAT
2558944 TATATATTTTAT
1 TATATATTTTAT
2558956 TAT
1 TAT
2558959 TTTATAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATATATTTTAT
Found at i:2559028 original size:2 final size:2
Alignment explanation
Indices: 2559021--2559052 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2559011 ATATGGTTTT
2559021 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2559053 ATTTATACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2559214 original size:18 final size:18
Alignment explanation
Indices: 2559191--2559225 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2559181 GTTTATATAA
2559191 AATTATAAACTATATATG
1 AATTATAAACTATATATG
* *
2559209 AATTATCAACTGTATAT
1 AATTATAAACTATATAT
2559226 ACATATATAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (18 bp):
AATTATAAACTATATATG
Found at i:2560867 original size:19 final size:19
Alignment explanation
Indices: 2560843--2560896 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 19
2560833 AACGGTCGGG
2560843 TCAGACCGGTCAAACCAGT
1 TCAGACCGGTCAAACCAGT
*
2560862 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCAGT
2560881 TCTA-ACCGGTCGAAAC
1 TC-AGACCGGTC-AAAC
2560897 GGGTCAGAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 27 0.84
20 5 0.16
ACGTcount: A:0.30, C:0.31, G:0.22, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCAGT
Found at i:2560880 original size:9 final size:9
Alignment explanation
Indices: 2560841--2560919 Score: 68
Period size: 10 Copynumber: 8.3 Consensus size: 9
2560831 TCAACGGTCG
*
2560841 GGTCAGACC
1 GGTCAAACC
2560850 GGTCAAACC
1 GGTCAAACC
* *
2560859 AGTTCAGACC
1 -GGTCAAACC
2560869 GGTCAAACC
1 GGTCAAACC
*
2560878 GGTTCTAACC
1 GG-TCAAACC
*
2560888 GGTCGAAACG
1 GGTC-AAACC
2560898 GGTCAGAACC
1 GGTCA-AACC
*
2560908 GGTTAAACC
1 GGTCAAACC
2560917 GGT
1 GGT
2560920 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
9 27 0.48
10 29 0.52
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:2568892 original size:40 final size:40
Alignment explanation
Indices: 2568848--2568979 Score: 108
Period size: 40 Copynumber: 3.1 Consensus size: 40
2568838 TTAGTTATAC
2568848 ATATATATACTATATTAATATAATTTATAATTTATAAACT
1 ATATATATACTATATTAATATAATTTATAATTTATAAACT
* * *
2568888 ATATATTTTA-TATAGCTT-ATA-CATATATAATTTATATACATACAT
1 ATATA-TATACTATA--TTAATATAATTTATAA-TT-TATA-A-AC-T
* *
2568933 ACATATATATACTATATTAATATAAATTATAGTTTATAAACT
1 --ATATATATACTATATTAATATAATTTATAATTTATAAACT
2568975 ATATA
1 ATATA
2568980 CTTTTTATAG
Statistics
Matches: 71, Mismatches: 8, Indels: 26
0.68 0.08 0.25
Matches are distributed among these distances:
40 21 0.30
41 8 0.11
42 7 0.10
43 3 0.04
44 3 0.04
45 7 0.10
46 8 0.11
47 14 0.20
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (40 bp):
ATATATATACTATATTAATATAATTTATAATTTATAAACT
Found at i:2568916 original size:47 final size:47
Alignment explanation
Indices: 2568865--2569010 Score: 132
Period size: 47 Copynumber: 3.3 Consensus size: 47
2568855 TACTATATTA
2568865 ATATAATTTATAATTTATAAACTATATATTTTATATAGCTTATACAT
1 ATATAATTTATAATTTATAAACTATATATTTTATATAGCTTATACAT
* * * *
2568912 ATATAATTTAT-A--TACATAC-ATACA-TATATATA-CTATATTA-AT
1 ATATAATTTATAATTTATAAACTATATATTTTATATAGCT-TA-TACAT
* *
2568954 ATA-AA-TTATAGTTTATAAACTATATACTTTT-TATAGTTTATACAT
1 ATATAATTTATAATTTATAAACTATATA-TTTTATATAGCTTATACAT
*
2568999 ATATAGTTTATA
1 ATATAATTTATA
2569011 TACATAGTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
40 4 0.05
41 4 0.05
42 14 0.18
43 11 0.14
44 11 0.14
45 11 0.14
46 5 0.07
47 16 0.21
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (47 bp):
ATATAATTTATAATTTATAAACTATATATTTTATATAGCTTATACAT
Found at i:2568946 original size:87 final size:87
Alignment explanation
Indices: 2568844--2569016 Score: 294
Period size: 87 Copynumber: 2.0 Consensus size: 87
2568834 TATATTAGTT
*
2568844 ATACATATATATACTATATTAATATAATTTATAATTTATAAACTATATA-TTTTATATAGCTTAT
1 ATACATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTTTT-TATAGCTTAT
2568908 ACATATATAATTTATATACATAC
65 ACATATATAATTTATATACATAC
* *
2568931 ATACATATATATACTATATTAATATAAATTATAGTTTATAAACTATATACTTTTTATAGTTTATA
1 ATACATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGCTTATA
*
2568996 CATATATAGTTTATATACATA
66 CATATATAATTTATATACATA
2569017 GTTTATATAT
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 77 0.95
88 4 0.05
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (87 bp):
ATACATATATATACTATATTAATATAAATTATAATTTATAAACTATATACTTTTTATAGCTTATA
CATATATAATTTATATACATAC
Found at i:2569017 original size:13 final size:13
Alignment explanation
Indices: 2568985--2569064 Score: 79
Period size: 13 Copynumber: 5.8 Consensus size: 13
2568975 ATATACTTTT
2568985 TATAGTTTATACATA
1 TATAGTTTAT--ATA
2569000 TATAGTTTATATA
1 TATAGTTTATATA
*
2569013 CATAGTTTATATA
1 TATAGTTTATATA
*
2569026 TATAGTTCATATAAA
1 TATAGTT--TATATA
* *
2569041 CATAATTTATATA
1 TATAGTTTATATA
*
2569054 TATAGCTTATA
1 TATAGTTTATA
2569065 AGAATTATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
13 34 0.63
15 20 0.37
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.46
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:2569020 original size:28 final size:26
Alignment explanation
Indices: 2568986--2569065 Score: 97
Period size: 28 Copynumber: 2.9 Consensus size: 26
2568976 TATACTTTTT
*
2568986 ATAGTTTATACATATATAGTTTATATAC
1 ATAGTTTAT--ATATATAGTTTATAAAC
2569014 ATAGTTTATATATATAGTTCATATAAAC
1 ATAGTTTATATATATAGTT--TATAAAC
* *
2569042 ATAATTTATATATATAGCTTATAA
1 ATAGTTTATATATATAGTTTATAA
2569066 GAATTATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 15 0.32
28 32 0.68
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (26 bp):
ATAGTTTATATATATAGTTTATAAAC
Found at i:2569446 original size:19 final size:20
Alignment explanation
Indices: 2569419--2569460 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
2569409 TATGTGTGTT
2569419 ATTTAATTTAT-ATTTTAAA
1 ATTTAATTTATAATTTTAAA
* * *
2569438 ATTTTATTTGTAATTTTACA
1 ATTTAATTTATAATTTTAAA
2569458 ATT
1 ATT
2569461 CTTCAAGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTAATTTATAATTTTAAA
Found at i:2571840 original size:8 final size:8
Alignment explanation
Indices: 2571794--2571843 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
2571784 TTGTTAGTGT
*
2571794 TATGTATG
1 TATGTATA
2571802 TATGTATA
1 TATGTATA
2571810 TAT-TATA
1 TATGTATA
2571817 TCATGT-TA
1 T-ATGTATA
2571825 TA-GATATA
1 TATG-TATA
2571833 TATGTATA
1 TATGTATA
2571841 TAT
1 TAT
2571844 TTATTTAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
6 1 0.03
7 7 0.19
8 26 0.72
9 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (8 bp):
TATGTATA
Found at i:2572528 original size:16 final size:17
Alignment explanation
Indices: 2572497--2572530 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2572487 AGAACAAATC
*
2572497 AATTTTTTTGTCTTAAA
1 AATTATTTTGTCTTAAA
2572514 AATTATTTT-TCTTAAA
1 AATTATTTTGTCTTAAA
2572530 A
1 A
2572531 TTGTTTAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (17 bp):
AATTATTTTGTCTTAAA
Found at i:2574906 original size:18 final size:18
Alignment explanation
Indices: 2574883--2574923 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
2574873 AGGCATTTGA
*
2574883 TCCTCTAATTGTGCTTGT
1 TCCTCTAATCGTGCTTGT
**
2574901 TCCTCTGCTCGTGCTTGT
1 TCCTCTAATCGTGCTTGT
2574919 TCCTC
1 TCCTC
2574924 GTGTTGTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.32, G:0.17, T:0.46
Consensus pattern (18 bp):
TCCTCTAATCGTGCTTGT
Found at i:2576547 original size:23 final size:23
Alignment explanation
Indices: 2576465--2576547 Score: 84
Period size: 23 Copynumber: 3.7 Consensus size: 23
2576455 CAGAACCTCC
* *
2576465 AGGGGGTATCGA-TTCCCCTAC-
1 AGGGGGAATCGAGTTCCCCTTCA
*
2576486 AGAGGGAATC-AGTTCCCCTTCAA
1 AGGGGGAATCGAGTTCCCCTTC-A
2576509 AGGGGGAATCG-GTTCCCCTTCA
1 AGGGGGAATCGAGTTCCCCTTCA
* *
2576531 AGGGGGTATCGATTTCC
1 AGGGGGAATCGAGTTCC
2576548 TCTGCCCTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 16 0.31
22 11 0.22
23 23 0.45
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGAGTTCCCCTTCA
Found at i:2587572 original size:20 final size:20
Alignment explanation
Indices: 2587547--2587593 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
2587537 GTTAAGAAAA
*
2587547 ATATATAAGCAAA-AGTATAT
1 ATATATAAACAAACA-TATAT
2587567 ATATATAAACAAACATATAT
1 ATATATAAACAAACATATAT
2587587 ATATATA
1 ATATATA
2587594 TATGTATGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (20 bp):
ATATATAAACAAACATATAT
Found at i:2592390 original size:14 final size:14
Alignment explanation
Indices: 2592350--2592403 Score: 63
Period size: 14 Copynumber: 3.7 Consensus size: 14
2592340 AACACCAATC
*
2592350 TTTTTCTTCTTTATA
1 TTTTT-TTCTTTTTA
*
2592365 TTTTCTTCTTTTTA
1 TTTTTTTCTTTTTA
*
2592379 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTA
2592393 TTTCTTTTCTT
1 TTT-TTTTCTT
2592404 GATCTTCTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 23 0.68
15 11 0.32
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTTTTTA
Found at i:2593974 original size:23 final size:23
Alignment explanation
Indices: 2593928--2593976 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
2593918 CGGTACCACC
*
2593928 ACTAAGAGTATCAATATTATTAT
1 ACTAAGAGTATCAATACTATTAT
*
2593951 ACTAAGTAGTATCGATACTATATAT
1 ACTAAG-AGTATCAATACTAT-TAT
2593976 A
1 A
2593977 GTATCGGTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 12 0.55
25 4 0.18
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (23 bp):
ACTAAGAGTATCAATACTATTAT
Found at i:2595114 original size:10 final size:10
Alignment explanation
Indices: 2595096--2595129 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2595086 TTTTATACGT
*
2595096 TTTAACATTC
1 TTTATCATTC
2595106 TTTATCATTC
1 TTTATCATTC
2595116 TTTA-CATTC
1 TTTATCATTC
2595125 TTTAT
1 TTTAT
2595130 TATTTTTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.24, C:0.18, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTATCATTC
Found at i:2596758 original size:7 final size:7
Alignment explanation
Indices: 2596748--2596833 Score: 100
Period size: 7 Copynumber: 12.0 Consensus size: 7
2596738 AAAAGGAAAG
2596748 GAAAAAA
1 GAAAAAA
2596755 GAAAAAA
1 GAAAAAA
*
2596762 GAAACAA
1 GAAAAAA
*
2596769 GAAACAA
1 GAAAAAA
*
2596776 GAAACAA
1 GAAAAAA
*
2596783 GAAACAA
1 GAAAAAA
*
2596790 GAAACAA
1 GAAAAAA
*
2596797 GAAACAA
1 GAAAAAA
2596804 GAAAAAA
1 GAAAAAA
2596811 GAAAAAAA
1 G-AAAAAA
2596819 GAAAAGAA
1 GAAAA-AA
2596827 GAAAAAA
1 GAAAAAA
2596834 ATAATTTAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
7 61 0.81
8 14 0.19
ACGTcount: A:0.78, C:0.07, G:0.15, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:2596897 original size:23 final size:23
Alignment explanation
Indices: 2596845--2596898 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
2596835 TAATTTAAAA
* *
2596845 AAATAAAAAAAATAAAAGAAATG
1 AAATGAAAAAAATAAAAGAAAGG
2596868 AAATGAAAAAAATAAAA-AAAGG
1 AAATGAAAAAAATAAAAGAAAGG
2596890 AAATTGAAA
1 AAA-TGAAA
2596899 GGAGAGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 7 0.25
23 21 0.75
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (23 bp):
AAATGAAAAAAATAAAAGAAAGG
Found at i:2599145 original size:67 final size:67
Alignment explanation
Indices: 2599016--2599203 Score: 243
Period size: 68 Copynumber: 2.8 Consensus size: 67
2599006 ATTGTCTGTC
* **
2599016 ACCTTTGAGATTATTTCTCTTGAAATAAA-TTTTGTCTCGCTTAAGACAGTTTCTCTTAAAACAT
1 ACCTTTGAGATTGTTTCTCTCAAAATAAAGTTTTGTCTCGCTTAAGACAGTTTCTCTTAAAACAT
2599080 AA
66 AA
* * * *
2599082 ACCTTTGAGATTGTTTCTCTCAAAATAAAGTTTTGTCTCGTTTGAGACAGTTTCTTTTGAAACAT
1 ACCTTTGAGATTGTTTCTCTCAAAATAAAGTTTTGTCTCGCTTAAGACAGTTTCTCTTAAAACAT
2599147 AA
66 AA
* * * * * *
2599149 ACCTATCGAGAGTGTTTTTCTCAAAACAAAGTTTCGTCTCGCTTAAGACAATTTC
1 ACCT-TTGAGATTGTTTCTCTCAAAATAAAGTTTTGTCTCGCTTAAGACAGTTTC
2599204 CCTTGAAGCC
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 26 0.25
67 37 0.35
68 42 0.40
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (67 bp):
ACCTTTGAGATTGTTTCTCTCAAAATAAAGTTTTGTCTCGCTTAAGACAGTTTCTCTTAAAACAT
AA
Found at i:2600924 original size:2 final size:2
Alignment explanation
Indices: 2600902--2600965 Score: 87
Period size: 2 Copynumber: 32.5 Consensus size: 2
2600892 TTTATGTATG
*
2600902 TA TA TA T- TA TA TCA TG T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2600943 TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
2600966 TTATCTAATA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.04
2 52 0.93
3 2 0.04
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2609831 original size:2 final size:2
Alignment explanation
Indices: 2609824--2609882 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
2609814 TAAGAAACTA
2609824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2609866 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
2609883 GGGTTAGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2610189 original size:102 final size:102
Alignment explanation
Indices: 2610010--2610195 Score: 237
Period size: 102 Copynumber: 1.8 Consensus size: 102
2610000 TATCATCTCA
* * * * **
2610010 TTTCCTACTGTTAATTTCAGCTATCTATTTTCACTCATCTAGTTATCCTAAATATCTGTAAAACT
1 TTTCCTACTGTTAATCTCAACCATCTATTTTCACTCATCCAACTATCCTAAATATCTGTAAAACT
2610075 AAAAAAAATTTACATTGTGTAACATGATCATATCATT
66 AAAAAAAATTTACATTGTGTAACATGATCATATCATT
* * * * * *
2610112 TTTCCTACTGTTAATCTCAACCATCTATTTTCACTTATCCAACTGTTCTAAATTTGTGTAAAATT
1 TTTCCTACTGTTAATCTCAACCATCTATTTTCACTCATCCAACTATCCTAAATATCTGTAAAACT
* **
2610177 AAAAGAGTTTTACATTGTG
66 AAAAAAAATTTACATTGTG
2610196 CAAGTGGATC
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
102 69 1.00
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (102 bp):
TTTCCTACTGTTAATCTCAACCATCTATTTTCACTCATCCAACTATCCTAAATATCTGTAAAACT
AAAAAAAATTTACATTGTGTAACATGATCATATCATT
Found at i:2613933 original size:21 final size:21
Alignment explanation
Indices: 2613891--2613934 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2613881 ATTTTACTTT
* *
2613891 TTTTTATTTTTTTATTTGAAA
1 TTTTAATTTTTTTAATTGAAA
2613912 TTTTAATTTTTTTAAATT-AAA
1 TTTTAATTTTTTT-AATTGAAA
2613933 TT
1 TT
2613935 GTTTAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTTTAATTTTTTTAATTGAAA
Found at i:2616352 original size:21 final size:21
Alignment explanation
Indices: 2616328--2616367 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2616318 TGCATCTTTG
2616328 CATTAGCAT-ATATACATTGTA
1 CATTA-CATGATATACATTGTA
*
2616349 CATTACATGGTATACATTG
1 CATTACATGATATACATTG
2616368 CATCTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
CATTACATGATATACATTGTA
Found at i:2618146 original size:21 final size:21
Alignment explanation
Indices: 2618122--2618161 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2618112 TGCATCTTTG
2618122 CATTAGCAT-ATATACATTGTA
1 CATTA-CATGATATACATTGTA
*
2618143 CATTACATGGTATACATTG
1 CATTACATGATATACATTG
2618162 CATCTCAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
CATTACATGATATACATTGTA
Found at i:2619565 original size:4 final size:4
Alignment explanation
Indices: 2619558--2619640 Score: 70
Period size: 4 Copynumber: 21.2 Consensus size: 4
2619548 CTTAAAAAAG
* *
2619558 AGAA AGAAA AGAA AGAA AG-A AGGA A-AA AGAA TGAA A-AA AGAA A-AA
1 AGAA AG-AA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
2619603 AGAA A-AA AGAAA AGTAAA AGAA AGAA AG-A AGAA AGAA A
1 AGAA AGAA AG-AA AG--AA AGAA AGAA AGAA AGAA AGAA A
2619641 ATCGATCAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 18
0.76 0.03 0.20
Matches are distributed among these distances:
3 17 0.25
4 37 0.55
5 8 0.12
6 5 0.07
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:2619587 original size:18 final size:18
Alignment explanation
Indices: 2619564--2619633 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 18
2619554 AAAGAGAAAG
2619564 AAAAGAAAGAAAGAAGGA
1 AAAAGAAAGAAAGAAGGA
* * *
2619582 AAAAGAATGAAAAAAGAA
1 AAAAGAAAGAAAGAAGGA
* *
2619600 AAAAGAAA-AAAGAAAAGT
1 AAAAGAAAGAAAG-AAGGA
2619618 AAAAGAAAGAAAGAAG
1 AAAAGAAAGAAAGAAG
2619634 AAAGAAAATC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
17 3 0.07
18 34 0.83
19 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (18 bp):
AAAAGAAAGAAAGAAGGA
Found at i:2619602 original size:7 final size:7
Alignment explanation
Indices: 2619590--2619641 Score: 56
Period size: 7 Copynumber: 7.7 Consensus size: 7
2619580 GAAAAAGAAT
2619590 GAAAAAA
1 GAAAAAA
2619597 GAAAAAA
1 GAAAAAA
2619604 GAAAAAA
1 GAAAAAA
2619611 G--AAAA
1 GAAAAAA
*
2619616 G-TAAAA
1 GAAAAAA
2619622 GAAAGAAA
1 GAAA-AAA
*
2619630 GAAGAAA
1 GAAAAAA
2619637 GAAAA
1 GAAAA
2619642 TCGATCAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
5 5 0.13
6 5 0.13
7 23 0.59
8 6 0.15
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:2619609 original size:25 final size:24
Alignment explanation
Indices: 2619551--2619641 Score: 89
Period size: 25 Copynumber: 3.8 Consensus size: 24
2619541 AAAAAAACTT
*
2619551 AAAAAAG-AGAAAGAAAAG-AAAG
1 AAAAAAGAAAAAAGAAAAGAAAAG
* *
2619573 AAAGAAGGAAAAAGAATGAA-AAAAG
1 AAAAAAGAAAAAAGAA--AAGAAAAG
2619598 AAAAAAGAAAAAAGAAAAGTAAAAG
1 AAAAAAGAAAAAAGAAAAG-AAAAG
*
2619623 AAAGAAAGAAGAAAGAAAA
1 AAA-AAAGAAAAAAGAAAA
2619642 TCGATCAAAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
22 6 0.11
23 9 0.16
25 28 0.49
26 14 0.25
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (24 bp):
AAAAAAGAAAAAAGAAAAGAAAAG
Found at i:2619622 original size:36 final size:36
Alignment explanation
Indices: 2619564--2619636 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
2619554 AAAGAGAAAG
* *
2619564 AAAAGAAAGAAAGAAGGAAAAAGAATGAAAAAAGAA
1 AAAAGAAAGAAAGAAAGAAAAAGAAAGAAAAAAGAA
* *
2619600 AAAAGAAA-AAAGAAAAGTAAAAGAAAGAAAGAAGAA
1 AAAAGAAAGAAAG-AAAGAAAAAGAAAGAAAAAAGAA
2619636 A
1 A
2619637 GAAAATCGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (36 bp):
AAAAGAAAGAAAGAAAGAAAAAGAAAGAAAAAAGAA
Found at i:2619636 original size:29 final size:29
Alignment explanation
Indices: 2619551--2619636 Score: 101
Period size: 29 Copynumber: 3.1 Consensus size: 29
2619541 AAAAAAACTT
2619551 AAAAAAGAGAAAG-AAAAGAAAGAAAGAAG
1 AAAAAAGA-AAAGTAAAAGAAAGAAAGAAG
* * *
2619580 GAAAAAG--AA-TGAAA-AAAGAAAAAAG
1 AAAAAAGAAAAGTAAAAGAAAGAAAGAAG
2619605 AAAAAAGAAAAGTAAAAGAAAGAAAGAAG
1 AAAAAAGAAAAGTAAAAGAAAGAAAGAAG
2619634 AAA
1 AAA
2619637 GAAAATCGAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
25 16 0.35
26 5 0.11
27 2 0.04
28 4 0.09
29 19 0.41
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (29 bp):
AAAAAAGAAAAGTAAAAGAAAGAAAGAAG
Found at i:2621758 original size:56 final size:56
Alignment explanation
Indices: 2621609--2621880 Score: 280
Period size: 58 Copynumber: 4.8 Consensus size: 56
2621599 CAAAAGAATT
* * * *
2621609 TTTAAAGAAA-CTAAGCATGATTTTTAGGGGTTTCTTGATGATGATTTTC-AATGAA
1 TTTAAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAAAT-AA
* * *
2621664 TTCTTAAAAGAAGCTAAGCGTAATTTTTAGGGGTTTCTTGATGATGGTTTCCAAATAA
1 -T-TTAAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAAATAA
* *
2621722 -TTAAAAAAATGTTAAGCCTAATTTTTAGGGGTTTCTTGATGATGGTTTCCAAATAA
1 TTTAAAAAAA-GCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAAATAA
* * * * * * *
2621778 TTAAAAAAAAAAGTTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCCAAAGAAA
1 TT--TAAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAAA-TAA
* *
2621837 TTTTAAAATGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGA
1 -TTTAAAA-AAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGA
2621881 CAACTGAAAA
Statistics
Matches: 184, Mismatches: 22, Indels: 17
0.83 0.10 0.08
Matches are distributed among these distances:
55 8 0.04
56 45 0.24
57 8 0.04
58 79 0.43
59 42 0.23
60 2 0.01
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (56 bp):
TTTAAAAAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAAATAA
Found at i:2621820 original size:114 final size:116
Alignment explanation
Indices: 2621601--2621880 Score: 300
Period size: 114 Copynumber: 2.4 Consensus size: 116
2621591 GATATTTTCA
* * * * * *
2621601 AAAGAATTTTTAAAGAAA-CTAAGCATGATTTTTAGGGGTTTCTTGATGATGATTTTCAATGAAT
1 AAAGAAATTTAAAATAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAATGAAT
*** * * * * *
2621665 TCTTAAAAGAAGCTAAGCGTAATTTTTAGGGGTTTCTTGATGATGGTTTCC
66 TAAAAAAAAAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATCTCC
* * *
2621716 AAA-TAA-TTAAAA-AAATGTTAAGCCTAATTTTTAGGGGTTTCTTGATGATGGTTTCCAAAT-A
1 AAAGAAATTTAAAATAAA-GCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCC-AATGA
* * *
2621777 ATTAAAAAAAAAAGTTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
64 ATTAAAAAAAAAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATCTCC
* *
2621830 AAAGAAATTTTAAAATGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGA
1 AAAGAAA-TTTAAAATAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGA
2621881 CAACTGAAAA
Statistics
Matches: 135, Mismatches: 23, Indels: 12
0.79 0.14 0.07
Matches are distributed among these distances:
112 3 0.02
113 5 0.04
114 81 0.60
115 8 0.06
117 36 0.27
118 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (116 bp):
AAAGAAATTTAAAATAAAGCTAAGCCTAATTTTTAGGGGTTTCTTGATGATGATTTCCAATGAAT
TAAAAAAAAAAGCTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATCTCC
Found at i:2623793 original size:22 final size:23
Alignment explanation
Indices: 2623738--2623799 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
2623728 TTTTGCCGTA
*
2623738 CTTTTGCAATTTGGTCCTTCGTG
1 CTTTTGCAGTTTGGTCCTTCGTG
*
2623761 CTTTTGCAGTTTGGTCCTTCTTG
1 CTTTTGCAGTTTGGTCCTTCGTG
**
2623784 -TTTTTTAGTTTGGTCC
1 CTTTTGCAGTTTGGTCC
2623800 CTGAAGGGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 14 0.40
23 21 0.60
ACGTcount: A:0.06, C:0.19, G:0.21, T:0.53
Consensus pattern (23 bp):
CTTTTGCAGTTTGGTCCTTCGTG
Found at i:2626206 original size:31 final size:31
Alignment explanation
Indices: 2626163--2626227 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
2626153 TAAAAAAGAC
* * *
2626163 TTTAGGCACCTAAAGTTAACTTTATTTATAG
1 TTTAAGCACCTAAAATTAACTTTATGTATAG
*
2626194 TTTAAGCACCTAAAATTAGCTTTATGTATAG
1 TTTAAGCACCTAAAATTAACTTTATGTATAG
2626225 TTT
1 TTT
2626228 GTGCGCCTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (31 bp):
TTTAAGCACCTAAAATTAACTTTATGTATAG
Found at i:2630929 original size:46 final size:48
Alignment explanation
Indices: 2630876--2630971 Score: 178
Period size: 46 Copynumber: 2.0 Consensus size: 48
2630866 AATGTTATGC
2630876 AACCAACCTAAAATGTTAAATGTTTTGACAACATT-CG-TTGTAACTT
1 AACCAACCTAAAATGTTAAATGTTTTGACAACATTACGATTGTAACTT
2630922 AACCAACCTAAAATGTTAAATGTTTTGACAACATTACGATTGTAACTT
1 AACCAACCTAAAATGTTAAATGTTTTGACAACATTACGATTGTAACTT
2630970 AA
1 AA
2630972 AATGTTACGT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
46 35 0.73
47 2 0.04
48 11 0.23
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (48 bp):
AACCAACCTAAAATGTTAAATGTTTTGACAACATTACGATTGTAACTT
Found at i:2631335 original size:24 final size:24
Alignment explanation
Indices: 2631303--2631359 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
2631293 TAAATGTGGT
2631303 TCAATACTTGTTTCATGATAAGTA
1 TCAATACTTGTTTCATGATAAGTA
2631327 TCAATACTTGTTTCATGATAAGTA
1 TCAATACTTGTTTCATGATAAGTA
*
2631351 TCGATACTT
1 TCAATACTT
2631360 AACTAAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (24 bp):
TCAATACTTGTTTCATGATAAGTA
Found at i:2631368 original size:18 final size:18
Alignment explanation
Indices: 2631345--2631397 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
2631335 TGTTTCATGA
2631345 TAAGTATCGATACTTAAC-
1 TAAGTATCGATACTT-ACG
*
2631363 TAAGTATCAATACTTACG
1 TAAGTATCGATACTTACG
2631381 TACAAGTATCGATACTT
1 T--AAGTATCGATACTT
2631398 TCCGGGATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 2 0.07
18 15 0.50
20 13 0.43
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TAAGTATCGATACTTACG
Found at i:2633545 original size:2 final size:2
Alignment explanation
Indices: 2633540--2633567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2633530 ATTTTTTTTC
2633540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2633568 TGTATGGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2635664 original size:14 final size:14
Alignment explanation
Indices: 2635629--2635665 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
2635619 GTTTTTTTTT
2635629 AAAAAAAAATTTCA
1 AAAAAAAAATTTCA
2635643 AAATAAAAAATTTCA
1 AAA-AAAAAATTTCA
2635658 AAAAAAAA
1 AAAAAAAA
2635666 TATGAGGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAAAAAATTTCA
Found at i:2636348 original size:87 final size:87
Alignment explanation
Indices: 2636202--2636377 Score: 352
Period size: 87 Copynumber: 2.0 Consensus size: 87
2636192 TATCTTTCAG
2636202 TAGCTTCATCCCTTGTTATGGTTCGTTTGTCGATGGAGTCAGATATATTAGCATCTATATTTTGT
1 TAGCTTCATCCCTTGTTATGGTTCGTTTGTCGATGGAGTCAGATATATTAGCATCTATATTTTGT
2636267 TCGAGTTTTTTAGATGAGATTT
66 TCGAGTTTTTTAGATGAGATTT
2636289 TAGCTTCATCCCTTGTTATGGTTCGTTTGTCGATGGAGTCAGATATATTAGCATCTATATTTTGT
1 TAGCTTCATCCCTTGTTATGGTTCGTTTGTCGATGGAGTCAGATATATTAGCATCTATATTTTGT
2636354 TCGAGTTTTTTAGATGAGATTT
66 TCGAGTTTTTTAGATGAGATTT
2636376 TA
1 TA
2636378 ACATTTTCCT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.21, C:0.12, G:0.20, T:0.46
Consensus pattern (87 bp):
TAGCTTCATCCCTTGTTATGGTTCGTTTGTCGATGGAGTCAGATATATTAGCATCTATATTTTGT
TCGAGTTTTTTAGATGAGATTT
Found at i:2639567 original size:3 final size:3
Alignment explanation
Indices: 2639547--2639590 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
2639537 CAAAAAGTAA
*
2639547 AAT AAT ATT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AA
2639591 ATAGTTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2639602 original size:23 final size:23
Alignment explanation
Indices: 2639547--2639590 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2639537 CAAAAAGTAA
*
2639547 AATAATATTAATAAAATAATAAT
1 AATAATAATAATAAAATAATAAT
2639570 AATAATAATAAT-AAATAATAA
1 AATAATAATAATAAAATAATAA
2639591 ATAGTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAATAATAATAAAATAATAAT
Found at i:2640104 original size:29 final size:30
Alignment explanation
Indices: 2640071--2640184 Score: 92
Period size: 29 Copynumber: 3.8 Consensus size: 30
2640061 GAGACAAAAT
*
2640071 TTGTTTCAAGGGAAA-TGACTCAAAGATAA
1 TTGTTTCAAGAGAAACTGACTCAAAGATAA
* *
2640100 TTGTTTCAAGAGAAACTGTCT-AAGAGACAAAA
1 TTGTTTCAAGAGAAACTGACTCAA-AG--ATAA
* * * *
2640132 TTTATTTTAAGGGAAAC-GACTCAAATATAA
1 -TTGTTTCAAGAGAAACTGACTCAAAGATAA
*
2640162 -TGTTTCAAGAGAAACTGTCTCAA
1 TTGTTTCAAGAGAAACTGACTCAA
2640185 GAGAGACAAA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
28 12 0.18
29 22 0.34
30 9 0.14
32 7 0.11
33 15 0.23
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (30 bp):
TTGTTTCAAGAGAAACTGACTCAAAGATAA
Found at i:2640232 original size:64 final size:64
Alignment explanation
Indices: 2640051--2640240 Score: 235
Period size: 62 Copynumber: 3.0 Consensus size: 64
2640041 CAAAGATGAT
* * *
2640051 TGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAATGACTCAAAGATAATTGTTTCAAGAGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAAGACTCAAAGAT-TTTGTTTCAAGAGAAAC
* * * **
2640116 TGTCT--A-AGAGACAAAATTTATTTTAAGGGAAACGACTCAAATATAATGTTTCAAGAGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAAGACTCAAAGATTTTGTTTCAAGAGAAAC
* * *
2640177 TGTCTCAAGAGAGACAAAATTTGTTTTGA-GAAAAAGACTCAAAGATTTGTGTTTCAAGGGAAAC
1 TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAAGACTCAAAGATTT-TGTTTCAAGAGAAAC
2640241 AATTTCAAAT
Statistics
Matches: 108, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
61 21 0.19
62 34 0.31
63 16 0.15
64 32 0.30
65 5 0.05
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (64 bp):
TGTCTCAAGAGAGACAAAATTTGTTTTAAGGGAAAAGACTCAAAGATTTTGTTTCAAGAGAAAC
Found at i:2640453 original size:35 final size:36
Alignment explanation
Indices: 2640365--2640453 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 36
2640355 TATTCCGAGG
*
2640365 GAAAATGTCTCAAGGGAGACAAAATTTGTTTTAAGA
1 GAAAATGTCTCAAGCGAGACAAAATTTGTTTTAAGA
* *
2640401 GAAAACTGTCTCCAGCGAGACAACATTTGTTTTTAA-A
1 GAAAA-TGTCTCAAGCGAGACAAAATTTG-TTTTAAGA
*
2640438 -AAAATGTCTCTAGCGA
1 GAAAATGTCTCAAGCGA
2640454 TAAGACACTT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 11 0.23
36 9 0.19
37 21 0.45
38 6 0.13
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (36 bp):
GAAAATGTCTCAAGCGAGACAAAATTTGTTTTAAGA
Found at i:2644032 original size:27 final size:28
Alignment explanation
Indices: 2643997--2644049 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 28
2643987 AGAATGAAAA
*
2643997 GATGCAAATGCAGATGC-AACAAAATGTT
1 GATGCAAATGCA-ATGCGAAAAAAATGTT
2644025 GATG-AAATGCAATGCGAAAAAAATG
1 GATGCAAATGCAATGCGAAAAAAATG
2644050 ACACAAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 15 0.65
28 4 0.17
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (28 bp):
GATGCAAATGCAATGCGAAAAAAATGTT
Found at i:2647502 original size:3 final size:3
Alignment explanation
Indices: 2647479--2647523 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
2647469 CAAAAAGTAA
* *
2647479 AAT AAT ATT AAT AA- AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2647524 TTATTATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2647505 original size:23 final size:22
Alignment explanation
Indices: 2647470--2647515 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
2647460 TGGGTCTACC
* *
2647470 AAAAAGTAAAATAATATTAATA
1 AAAAAATAAAATAATAATAATA
2647492 AAAAAATAATAATAATAATAATA
1 AAAAAATAA-AATAATAATAATA
2647515 A
1 A
2647516 TAATAATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (22 bp):
AAAAAATAAAATAATAATAATA
Found at i:2649027 original size:2 final size:2
Alignment explanation
Indices: 2649011--2649050 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2649001 CTTAAATTTT
*
2649011 TA TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2649051 TTGTTGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:2651390 original size:15 final size:15
Alignment explanation
Indices: 2651357--2651397 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
2651347 TAATGGAAGT
* *
2651357 AATCCCTGCA-AATA
1 AATCTCTGCATAAAA
2651371 AATCTCTGCATAAAA
1 AATCTCTGCATAAAA
2651386 AATCTCTGCATA
1 AATCTCTGCATA
2651398 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.27
Consensus pattern (15 bp):
AATCTCTGCATAAAA
Found at i:2651689 original size:15 final size:15
Alignment explanation
Indices: 2651669--2651715 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2651659 TCCTGGTTTT
2651669 AATATGAATGATTAA
1 AATATGAATGATTAA
* *
2651684 AATATGATTAATTTAA
1 AATATGAATGA-TTAA
2651700 AA-ATTGAATGATTAA
1 AATA-TGAATGATTAA
2651715 A
1 A
2651716 TTAAAAGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (15 bp):
AATATGAATGATTAA
Found at i:2653698 original size:20 final size:19
Alignment explanation
Indices: 2653675--2653720 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2653665 ATCTAATTGA
* *
2653675 AATGAATTTTAGGATAAATC
1 AATGAA-TTTAAGAGAAATC
2653695 AATGCAATTTAAGAGAAATC
1 AATG-AATTTAAGAGAAATC
2653715 AATGAA
1 AATGAA
2653721 AGTCATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (19 bp):
AATGAATTTAAGAGAAATC
Found at i:2658727 original size:3 final size:3
Alignment explanation
Indices: 2658719--2658757 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
2658709 TTTTGCCGGG
* *
2658719 TTA TTA TTA ATA TTA TTA TTA TTA TTA TTA AT- TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2658758 CATTTTTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 30 0.97
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2660108 original size:36 final size:36
Alignment explanation
Indices: 2660059--2660131 Score: 130
Period size: 36 Copynumber: 2.0 Consensus size: 36
2660049 TTTCATCTCG
2660059 AATGATAAGTTGGTCTATTTATGATTGTAGT-CCTA
1 AATGATAAGTTGGTCTATTTATGATTGTAGTGCCTA
2660094 AATGATAAAGTTGGTCTATTTATGATTGTAGTGCCTA
1 AATGAT-AAGTTGGTCTATTTATGATTGTAGTGCCTA
2660131 A
1 A
2660132 CAAGTAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 6 0.17
36 25 0.69
37 5 0.14
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (36 bp):
AATGATAAGTTGGTCTATTTATGATTGTAGTGCCTA
Found at i:2660702 original size:14 final size:15
Alignment explanation
Indices: 2660681--2660718 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
2660671 AACGCAGATC
*
2660681 ATTTTTTTTTCTTTA
1 ATTTTTTTTTCTTAA
2660696 ATTTTTTTTTCTTAA
1 ATTTTTTTTTCTTAA
2660711 ATTATTTT
1 ATT-TTTT
2660719 AAAAGGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (15 bp):
ATTTTTTTTTCTTAA
Found at i:2662607 original size:18 final size:17
Alignment explanation
Indices: 2662579--2662612 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2662569 AAATATGATA
2662579 AGAGAAAGAGAGAAAAG
1 AGAGAAAGAGAGAAAAG
2662596 AGAGATAAGAGAGAAAA
1 AGAGA-AAGAGAGAAAA
2662613 TGTCCATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (17 bp):
AGAGAAAGAGAGAAAAG
Found at i:2662608 original size:11 final size:9
Alignment explanation
Indices: 2662579--2662612 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
2662569 AAATATGATA
2662579 AGAG-AAAG
1 AGAGAAAAG
2662587 AGAGAAAAG
1 AGAGAAAAG
*
2662596 AGAGATAAG
1 AGAGAAAAG
2662605 AGAGAAAA
1 AGAGAAAA
2662613 TGTCCATGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.65, C:0.00, G:0.32, T:0.03
Consensus pattern (9 bp):
AGAGAAAAG
Found at i:2671982 original size:31 final size:31
Alignment explanation
Indices: 2671944--2672008 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
2671934 AAGAGTCGAG
2671944 GGTTACCTATGTCCTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
*
2671975 GGTTACCTATGTCCTTCGGGACATATGGATA
1 GGTTACCTATGTCCTTCGGGACATATGGACA
2672006 GGT
1 GGT
2672009 CCTTGGCGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGGACATATGGACA
Found at i:2672033 original size:21 final size:20
Alignment explanation
Indices: 2671985--2672063 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 20
2671975 GGTTACCTAT
*
2671985 GTCCTTCGGGACATATGGAT-AG
1 GTCCTT-GGGACATAT--ATGAC
2672007 GTCCTTGGCGACATATATGAC
1 GTCCTTGG-GACATATATGAC
2672028 GTCCTTTGGGACATATATGAC
1 GTCC-TTGGGACATATATGAC
2672049 GTCCTTCGGGACATA
1 GTCCTT-GGGACATA
2672064 GATTTCACAT
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
20 4 0.08
21 31 0.60
22 17 0.33
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (20 bp):
GTCCTTGGGACATATATGAC
Found at i:2672536 original size:6 final size:6
Alignment explanation
Indices: 2672525--2672564 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
2672515 TCTCGTCTCG
* *
2672525 GGTCGT GGTCGT GGTCGT GGTCAT GGTCAT GGTCGT GGTC
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTC
2672565 ATACGTGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.05, C:0.17, G:0.45, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2672696 original size:42 final size:42
Alignment explanation
Indices: 2672637--2672944 Score: 544
Period size: 42 Copynumber: 7.3 Consensus size: 42
2672627 CGTTGCGATT
2672637 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
2672679 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
2672721 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
2672763 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* * *
2672805 TTCGACTATCACAACGAACTTGGAATAAATCACAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
2672847 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
2672889 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
2672931 TTGGACTATCGCAA
1 TTGGACTATCGCAA
2672945 TGCGAATATG
Statistics
Matches: 250, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 250 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:2677300 original size:256 final size:257
Alignment explanation
Indices: 2676693--2677386 Score: 1002
Period size: 256 Copynumber: 2.7 Consensus size: 257
2676683 AGTTGTTTTG
* * * *
2676693 AAAATGAGAAAACGAATTCCAAAGTTTCTCATTTAACTCTTTTCTGAAAATGAAATTTTTGAAAA
1 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAA-TGTTTTCAGAAAATGAAATTTTTGAAAA
*
2676758 GTAAGAAAGCGATTTCCAAAGTTT-TTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTTGG
65 GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGG
* *
2676822 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATATATCAGTCTTTCGAGCA
130 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAAT-CTTCGGGTCATCTATCAATCTTTCGAGCA
* * * **
2676887 AGATGATAAGTCATTCGGGCCATCCATAAGTCCTTCGGGCAGGATGTTTCTATATGATTTTTGA
194 AGATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTCTACATGATTTTCAA
2676951 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATG-AATTTTTGGAAAA
1 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTT-GAAAA
* * * * *
2677015 GAAAGAAAGTGATTTCCAATGTATCTTACCCAATAAATTATTTCCAAAATTAGAAAGTCCTTCGG
65 GTAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGG
* * *
2677080 GCCATCAGTAAGTCTTTTGAGCATGATGATTAAATCTTTGGGTCATCTGTCAATCTTTCGAGCAA
130 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTATCAATCTTTCGAGCAA
* * * * *
2677145 GATGTTAAGTCCTTCGGGCCGTCTATAAGACC-TCGAGCAGGATATTT-TCACATGATTTTCAA
195 GATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTCT-ACATGATTTTCAA
* * * * *
2677207 AAAATAAGAAAGTGATTTCCAAAGTTTCTTATTTAATGTTTACAGAAAATGAAAATTTTGAAAAG
1 AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAG
* *
2677272 TAAGAAAGCGACTTCCAAAGTTTCTTACCCAGTAAATTATTTCCAAAATTAGTAAGTCCTTCGGG
66 TAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGGG
* *
2677337 CCATCAGTAA-TCTTTCAAGCATGATGATTAAATTCTTCGGGTTATCTATC
131 CCATCAGTAAGTCTTTCGAGCATGATGATTAAA-TCTTCGGGTCATCTATC
2677387 GGTCTCACTT
Statistics
Matches: 389, Mismatches: 42, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
255 21 0.05
256 165 0.42
257 97 0.25
258 106 0.27
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Consensus pattern (257 bp):
AAAATAAGAAAGCGAATTCCAAAGTTTCTCATTTAATGTTTTCAGAAAATGAAATTTTTGAAAAG
TAAGAAAGCGATTTCCAAAGTTTCTTACCCAATAAATTATTTCCAAAATTAGTAAGTCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTCGGGTCATCTATCAATCTTTCGAGCAAG
ATGATAAGTCATTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTCTACATGATTTTCAA
Found at i:2677523 original size:3 final size:3
Alignment explanation
Indices: 2677515--2677568 Score: 56
Period size: 3 Copynumber: 17.7 Consensus size: 3
2677505 TTTGTCCAGG
* * *
2677515 TTA TTA TTA ATA TTTA ATA TTA TTA TTA TTGA -TA TTG TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
2677561 TTA TTA TT
1 TTA TTA TT
2677569 TTTTATAGTC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
2 1 0.02
3 38 0.90
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:2677843 original size:30 final size:30
Alignment explanation
Indices: 2677809--2677869 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
2677799 GCCGCCGCGC
2677809 TGCCATGTTCTGGCCATCGGTGCTCGACAA
1 TGCCATGTTCTGGCCATCGGTGCTCGACAA
2677839 TGCCATGTTCTGGCCATCGGTGCTCGACAA
1 TGCCATGTTCTGGCCATCGGTGCTCGACAA
2677869 T
1 T
2677870 TCCAACATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.30, G:0.26, T:0.28
Consensus pattern (30 bp):
TGCCATGTTCTGGCCATCGGTGCTCGACAA
Found at i:2680709 original size:41 final size:43
Alignment explanation
Indices: 2680648--2680735 Score: 135
Period size: 41 Copynumber: 2.1 Consensus size: 43
2680638 TTGGAGGAAG
2680648 TTTCTGAAGGCTCATATGTTGTGTG-CAAGG-AGACCTTACCA
1 TTTCTGAAGGCTCATATGTTGTGTGCCAAGGAAGACCTTACCA
* *
2680689 TTTCTGAAGGCTCCTCTGTTGTGTGCCAAGGTAAGACCTTACCA
1 TTTCTGAAGGCTCATATGTTGTGTGCCAAGG-AAGACCTTACCA
2680733 TTT
1 TTT
2680736 GCTATGTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
41 23 0.55
42 5 0.12
44 14 0.33
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.34
Consensus pattern (43 bp):
TTTCTGAAGGCTCATATGTTGTGTGCCAAGGAAGACCTTACCA
Found at i:2680793 original size:71 final size:71
Alignment explanation
Indices: 2680673--2680806 Score: 241
Period size: 71 Copynumber: 1.9 Consensus size: 71
2680663 ATGTTGTGTG
*
2680673 CAAGGAGACCTTACCATTTCTGAAGGCTCCTCTGTTGTGTGCCAAGGTAAGACCTTACCATTTGC
1 CAAGGAGACCTTACCATTTCTGAAGGCTCCTCTGTTATGTGCCAAGGTAAGACCTTACCATTTGC
2680738 TATGTA
66 TATGTA
* *
2680744 CAAGGAGACCTTACCATTTCTGAAGGCTCCTTTGTTATGTGCCAGGGTAAGACCTTACCATTT
1 CAAGGAGACCTTACCATTTCTGAAGGCTCCTCTGTTATGTGCCAAGGTAAGACCTTACCATTT
2680807 CCGCAGGCAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (71 bp):
CAAGGAGACCTTACCATTTCTGAAGGCTCCTCTGTTATGTGCCAAGGTAAGACCTTACCATTTGC
TATGTA
Found at i:2680829 original size:44 final size:45
Alignment explanation
Indices: 2680749--2680846 Score: 119
Period size: 44 Copynumber: 2.2 Consensus size: 45
2680739 ATGTACAAGG
* * * *
2680749 AGACCTTACCATTTCTGAAGGCTCCTTTGTTATGTGC-CAGGGTA
1 AGACCTTACCATTTCCGAAGGCACCTTGGTTATGTGCTCAGGATA
*
2680793 AGACCTTACCATTTCCGCAGGCACCTTGGCTT-TGTGCTCAGGATA
1 AGACCTTACCATTTCCGAAGGCACCTTGG-TTATGTGCTCAGGATA
*
2680838 AGTCCTTAC
1 AGACCTTAC
2680847 TGCATGCTCC
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
44 30 0.65
45 16 0.35
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (45 bp):
AGACCTTACCATTTCCGAAGGCACCTTGGTTATGTGCTCAGGATA
Found at i:2685324 original size:53 final size:53
Alignment explanation
Indices: 2685244--2685370 Score: 218
Period size: 53 Copynumber: 2.4 Consensus size: 53
2685234 AAAAATTACA
* **
2685244 ATCTCTTGAAAGCTCTTACAAGGTATAGAAGTTTTATGCCTAGGCATCAGACC
1 ATCTCTTGAAAGCTCTTACAAGGTATAGAAGTGTTACACCTAGGCATCAGACC
2685297 ATCTCTTGAAAGCTCTTACAAGGTATAGAAGTGTTACACCTAGGCATCAGACC
1 ATCTCTTGAAAGCTCTTACAAGGTATAGAAGTGTTACACCTAGGCATCAGACC
*
2685350 ATCTCTCGAAAGCTCTTACAA
1 ATCTCTTGAAAGCTCTTACAA
2685371 TGAAAAGGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 70 1.00
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (53 bp):
ATCTCTTGAAAGCTCTTACAAGGTATAGAAGTGTTACACCTAGGCATCAGACC
Found at i:2688776 original size:32 final size:32
Alignment explanation
Indices: 2688737--2688802 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
2688727 TTTAATATAT
2688737 TACATGTTGAATATTAAATAACCTATAGTTTA
1 TACATGTTGAATATTAAATAACCTATAGTTTA
2688769 TACATGTTGAATATTAAATAACCTATAGTTTA
1 TACATGTTGAATATTAAATAACCTATAGTTTA
2688801 TA
1 TA
2688803 TATTTAACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (32 bp):
TACATGTTGAATATTAAATAACCTATAGTTTA
Found at i:2690218 original size:8 final size:9
Alignment explanation
Indices: 2690194--2690222 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
2690184 TCAAAACATA
2690194 AAGAAAAAG
1 AAGAAAAAG
2690203 AAGAAAAAG
1 AAGAAAAAG
2690212 AAGAAAAAG
1 AAGAAAAAG
2690221 AA
1 AA
2690223 ATTCAAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (9 bp):
AAGAAAAAG
Found at i:2697088 original size:113 final size:108
Alignment explanation
Indices: 2696943--2697164 Score: 390
Period size: 112 Copynumber: 2.0 Consensus size: 108
2696933 CTATCTACTT
2696943 TAATGCATTTGCTAGAAATCTTGTGTCCTAACACAATTCATTCGGTTACCATAAAATGACATTTT
1 TAATGCATTTGCTAGAAATCTTGTGTCCTAACACAATTCATTCGGTTA-CATAAAATGACATTTT
2697008 CCCAGTTTAACACCAGTTAGATTTTCGCATCGCTTCAACACTTTATA
65 CCCAGTTTAACACCAG--A-ATTTTCGCATCGCTTCAACACTTTATA
2697055 TAATGCATTTGGCTAGAAATCTTGTGTCCTAACACAATTCATTCGGTTACATAAAATGACATTTT
1 TAATGCATTT-GCTAGAAATCTTGTGTCCTAACACAATTCATTCGGTTACATAAAATGACATTTT
*
2697120 CCCAGTTTAACACCAGATTTTTCGCATCGCTTCAACACTTTATA
65 CCCAGTTTAACACCAGAATTTTCGCATCGCTTCAACACTTTATA
2697164 T
1 T
2697165 TTGCCAAATC
Statistics
Matches: 108, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
109 27 0.25
110 1 0.01
112 42 0.39
113 38 0.35
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (108 bp):
TAATGCATTTGCTAGAAATCTTGTGTCCTAACACAATTCATTCGGTTACATAAAATGACATTTTC
CCAGTTTAACACCAGAATTTTCGCATCGCTTCAACACTTTATA
Found at i:2703247 original size:2 final size:2
Alignment explanation
Indices: 2703240--2703275 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2703230 GACGTATTTA
*
2703240 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2703276 GTTTCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2714566 original size:20 final size:20
Alignment explanation
Indices: 2714541--2714579 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2714531 TACATGCATA
*
2714541 CAGTTACAAGCTACTAACAT
1 CAGTTACAAACTACTAACAT
2714561 CAGTTACAAACTACTAACA
1 CAGTTACAAACTACTAACA
2714580 ATCCTAACCA
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:0.44, C:0.26, G:0.08, T:0.23
Consensus pattern (20 bp):
CAGTTACAAACTACTAACAT
Found at i:2717592 original size:23 final size:23
Alignment explanation
Indices: 2717566--2717634 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
2717556 CACCACAGCT
*
2717566 CGTATAATTGCACCGAAGTGCCA
1 CGTAAAATTGCACCGAAGTGCCA
* **
2717589 CGTAAAATTGCACCGGAGTGCTG
1 CGTAAAATTGCACCGAAGTGCCA
* * *
2717612 CGTAGAATTACACCGTAGTGCCA
1 CGTAAAATTGCACCGAAGTGCCA
2717635 TATAATAATG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAAAATTGCACCGAAGTGCCA
Found at i:2717821 original size:103 final size:103
Alignment explanation
Indices: 2717653--2717867 Score: 376
Period size: 103 Copynumber: 2.1 Consensus size: 103
2717643 TGTCCATAAG
* *
2717653 GACCACATATCATTCCTTAAAAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
2717718 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAAAATACATATATGTCCCGAAA
* *
2717756 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
2717821 TTCACACATGTTCCAAAAAATACATATATGTCCCGAAG
66 TTCACACATGTTCCAAAAAATACATATATGTCCCGAAA
2717859 GACCACATA
1 GACCACATA
2717868 GACCATCGAC
Statistics
Matches: 106, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.38, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAAAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAAAATACATATATGTCCCGAAA
Found at i:2725497 original size:19 final size:19
Alignment explanation
Indices: 2725475--2725520 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
2725465 AATAATTTTA
*
2725475 TGATTTATATTTTTTTATT
1 TGATTTAGATTTTTTTATT
* *
2725494 TGATTTGGGTTTTTTTATT
1 TGATTTAGATTTTTTTATT
2725513 TGAGTTTA
1 TGA-TTTA
2725521 AAATTAATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.17, C:0.00, G:0.15, T:0.67
Consensus pattern (19 bp):
TGATTTAGATTTTTTTATT
Found at i:2725630 original size:14 final size:14
Alignment explanation
Indices: 2725611--2725644 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
2725601 TGGACTAAAT
2725611 ATAAACAAATGAAC
1 ATAAACAAATGAAC
2725625 ATAAACAAATGAAC
1 ATAAACAAATGAAC
2725639 ATAAAC
1 ATAAAC
2725645 GATCGATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.06, T:0.15
Consensus pattern (14 bp):
ATAAACAAATGAAC
Found at i:2735180 original size:24 final size:24
Alignment explanation
Indices: 2735149--2735255 Score: 76
Period size: 24 Copynumber: 4.5 Consensus size: 24
2735139 AGAACATGAT
2735149 GATGGTAGAAGAGAAGATGA-GGAA
1 GATGGTAGAAGAGAAGATGATGG-A
* * *
2735173 GATGGTAGATGTGAAGTTGATGGA
1 GATGGTAGAAGAGAAGATGATGGA
* **
2735197 GATGGTAGAAGTGAATG-TGATAAA
1 GATGGTAGAAGAGAA-GATGATGGA
* * *
2735221 TATGGTAGATGTGAAG-TAGATGGA
1 GATGGTAGAAGAGAAGAT-GATGGA
*
2735245 GATGATAGAAG
1 GATGGTAGAAG
2735256 TTGAGATAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.03
24 62 0.93
25 3 0.04
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.23
Consensus pattern (24 bp):
GATGGTAGAAGAGAAGATGATGGA
Found at i:2736572 original size:41 final size:41
Alignment explanation
Indices: 2736479--2736608 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 41
2736469 ATATTTGTAA
* ** *
2736479 TTTAGTGGCGTTTTAATATAAACACCGCTAAAGAC-TATAC
1 TTTAGTGGTGTTTTTCTACAAACACCGCTAAAGACTTATAC
* * *
2736519 TTTAGTGTTGTTTTTCTACAAACGCCGCTAAAGACTTGTAC
1 TTTAGTGGTGTTTTTCTACAAACACCGCTAAAGACTTATAC
* *
2736560 TTTAGTGGTG--TTTCTACATAAACACCGCAAAAGACTAATAC
1 TTTAGTGGTGTTTTTCTAC--AAACACCGCTAAAGACTTATAC
2736601 TTTAGTGG
1 TTTAGTGG
2736609 CATTTTTTGA
Statistics
Matches: 75, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
39 7 0.09
40 29 0.39
41 39 0.52
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.35
Consensus pattern (41 bp):
TTTAGTGGTGTTTTTCTACAAACACCGCTAAAGACTTATAC
Found at i:2737286 original size:5 final size:5
Alignment explanation
Indices: 2737269--2737307 Score: 60
Period size: 5 Copynumber: 7.6 Consensus size: 5
2737259 AAAAAAAATA
*
2737269 ATTTT ATTCT ATTTT ATTTT ATTTT GATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT ATT
2737308 ATTAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 26 0.84
6 5 0.16
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:2737300 original size:16 final size:15
Alignment explanation
Indices: 2737269--2737307 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2737259 AAAAAAAATA
2737269 ATTTTATTCTATTTT
1 ATTTTATTCTATTTT
*
2737284 ATTTTATTTTGATTTT
1 ATTTTATTCT-ATTTT
2737300 ATTTTATT
1 ATTTTATT
2737308 ATTAATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
ATTTTATTCTATTTT
Found at i:2738896 original size:31 final size:31
Alignment explanation
Indices: 2738848--2738911 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
2738838 GTTTGCAAGG
*
2738848 TTATCACATATCGACTTATTTTCAACAGAAA
1 TTATCACATATCAACTTATTTTCAACAGAAA
*
2738879 TTATCACGTATCAACTTATTTTCAACAGAAA
1 TTATCACATATCAACTTATTTTCAACAGAAA
2738910 TT
1 TT
2738912 CTCTCATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (31 bp):
TTATCACATATCAACTTATTTTCAACAGAAA
Found at i:2739554 original size:35 final size:35
Alignment explanation
Indices: 2739480--2739591 Score: 145
Period size: 35 Copynumber: 3.2 Consensus size: 35
2739470 CTATTATCAT
* * **
2739480 TTTTC-AACAAATATCTACCAAACTTTGAAAACTGT
1 TTTTCAAAGAAATATTTACCAAACTTTGAAAAC-AA
*
2739515 TTTTCAAAGAAATATTTACCAAACTTTGAAAACCA
1 TTTTCAAAGAAATATTTACCAAACTTTGAAAACAA
* *
2739550 TTTTCAAAGAAACATTTACCAAACTTTGAATACAA
1 TTTTCAAAGAAATATTTACCAAACTTTGAAAACAA
2739585 TTTTCAA
1 TTTTCAA
2739592 CACTAGTCTG
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
35 44 0.64
36 25 0.36
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.34
Consensus pattern (35 bp):
TTTTCAAAGAAATATTTACCAAACTTTGAAAACAA
Found at i:2754760 original size:23 final size:23
Alignment explanation
Indices: 2754734--2754797 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
2754724 CAGCTCGTGT
2754734 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
2754757 AATTGCACC-AGAGTGCCGCGTAG
1 AATTGCACCGA-AGTGCCACGTAG
*
2754780 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
2754798 TATAATAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:2754984 original size:103 final size:103
Alignment explanation
Indices: 2754816--2755128 Score: 547
Period size: 103 Copynumber: 3.0 Consensus size: 103
2754806 TGTCCATAAG
* * *
2754816 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
*
2754881 TTCACACATGTTCCATAGAATACATATATGTCCCGAAA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
2754919 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
* *
2754984 TTCACACATGTTCCAAAGAATACATATATGTTCTG-AA
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
2755021 GAACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGA
1 G-ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGA
*
2755086 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
65 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
2755125 GACC
1 GACC
2755129 GCGTAGACCC
Statistics
Matches: 199, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
102 3 0.02
103 194 0.97
104 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
Found at i:2759179 original size:20 final size:19
Alignment explanation
Indices: 2759132--2759179 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
2759122 AATGATTTTC
* * *
2759132 TTTTGAAAGCTAAAATGGA
1 TTTTGAAAACCAAAATGAA
*
2759151 TTTTCAAAACCAAAATGAAA
1 TTTTGAAAACCAAAATG-AA
2759171 TTTTGAAAA
1 TTTTGAAAA
2759180 AGGATTTAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (19 bp):
TTTTGAAAACCAAAATGAA
Found at i:2762324 original size:19 final size:19
Alignment explanation
Indices: 2762297--2762347 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
2762287 GAAATTAGAG
* *
2762297 TTTTCAAAGTTTTAGTTTT
1 TTTTAAAAGTTTTAATTTT
2762316 TTTTAAAAGTTTTAATTTT
1 TTTTAAAAGTTTTAATTTT
*
2762335 TTTAAAAAGTTTT
1 TTTTAAAAGTTTT
2762348 TTGGAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTAAAAGTTTTAATTTT
Found at i:2763613 original size:18 final size:18
Alignment explanation
Indices: 2763578--2763622 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2763568 CAACTCAAGA
* *
2763578 AAAATAAAATAGTGAAAT
1 AAAATAAAATAATCAAAT
*
2763596 AAAATTAAATAATCAAAT
1 AAAATAAAATAATCAAAT
*
2763614 CAAATAAAA
1 AAAATAAAA
2763623 GAAAAAGATG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.22
Consensus pattern (18 bp):
AAAATAAAATAATCAAAT
Found at i:2769594 original size:41 final size:41
Alignment explanation
Indices: 2769529--2769642 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 41
2769519 TTGCATTTCG
*
2769529 CGTTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTAC-AATGT
1 CGTTGCGATTTTCCAAATT--CGTTGCGATAGTCTACGAATGT
* * * **
2769570 TGTTGCGATTTTTTCAAATTCGTTGCGAAAGTCTACGGTTGT
1 CGTTGCGA-TTTTCCAAATTCGTTGCGATAGTCTACGAATGT
2769612 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
2769643 TAAAAAAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
41 43 0.70
42 15 0.25
43 3 0.05
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.40
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACGAATGT
Found at i:2769733 original size:6 final size:6
Alignment explanation
Indices: 2769722--2769748 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2769712 GACACGTATT
2769722 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
2769749 TGAGATGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:2770264 original size:6 final size:6
Alignment explanation
Indices: 2770234--2770311 Score: 126
Period size: 6 Copynumber: 13.5 Consensus size: 6
2770224 GTCCGTCTCG
*
2770234 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGG GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
2770279 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2770312 AATACGTGTC
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
5 15 0.21
6 55 0.79
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:2770445 original size:22 final size:22
Alignment explanation
Indices: 2770409--2770484 Score: 63
Period size: 22 Copynumber: 3.6 Consensus size: 22
2770399 AATTTGGAAA
2770409 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTGTAGACT
**
2770431 ATCGCAACGCGAACTG--GAAA
1 ATCGCAACGCGAACTGTAGACT
* *
2770451 ATCGCAACGCG-ATTTTCA-ACT
1 ATCGCAACGCGAACTGT-AGACT
2770472 ATCGCAACGCGAA
1 ATCGCAACGCGAA
2770485 ATGGAAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 13 0.30
22 15 0.35
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.17
Consensus pattern (22 bp):
ATCGCAACGCGAACTGTAGACT
Found at i:2770456 original size:20 final size:20
Alignment explanation
Indices: 2770403--2770503 Score: 87
Period size: 20 Copynumber: 4.9 Consensus size: 20
2770393 ACAACGAATT
2770403 TGGAAAATCGCAACGAC-AAC
1 TGGAAAATCGCAACG-CGAAC
**
2770423 TGTAGACTATCGCAACGCGAAC
1 TG--GAAAATCGCAACGCGAAC
**
2770445 TGGAAAATCGCAACGCGATT
1 TGGAAAATCGCAACGCGAAC
** * *
2770465 TTCAACTATCGCAACGCGAAA
1 TGGAA-AATCGCAACGCGAAC
2770486 TGGAAAATCGCAACGCGA
1 TGGAAAATCGCAACGCGA
2770504 TTTTCAACTA
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
20 31 0.49
21 16 0.25
22 16 0.25
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (20 bp):
TGGAAAATCGCAACGCGAAC
Found at i:2770473 original size:41 final size:41
Alignment explanation
Indices: 2770428--2770522 Score: 181
Period size: 41 Copynumber: 2.3 Consensus size: 41
2770418 ACAACTGTAG
*
2770428 ACTATCGCAACGCGAACTGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2770469 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2770510 ACTATCGCAACGC
1 ACTATCGCAACGC
2770523 AATTTTCAAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:2770477 original size:21 final size:21
Alignment explanation
Indices: 2770451--2770545 Score: 120
Period size: 21 Copynumber: 4.6 Consensus size: 21
2770441 GAACTGGAAA
2770451 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
2770472 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
2770492 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* *
2770513 ATCGCAACGCAATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
2770534 ATCGCAACGCGA
1 ATCGCAACGCGA
2770546 ATTTGCGATA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:2778038 original size:17 final size:18
Alignment explanation
Indices: 2778006--2778040 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2777996 TGACCGGTCA
2778006 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
2778024 CGACCCGA-TCGTTGACC
1 CGACCCGACCCGTTGACC
2778041 GTTGACCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:2778187 original size:29 final size:29
Alignment explanation
Indices: 2778048--2778187 Score: 217
Period size: 29 Copynumber: 4.8 Consensus size: 29
2778038 ACCGTTGACC
* *
2778048 GGTGCTATTCTGGTAAATAATTCAGTTTC
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2778077 GATGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2778106 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
2778135 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
* *
2778164 TGTGCTATTCTGGTAATTAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
2778188 AAATGGTGCT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 101 1.00
ACGTcount: A:0.23, C:0.11, G:0.21, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:2785286 original size:29 final size:28
Alignment explanation
Indices: 2785245--2785406 Score: 191
Period size: 29 Copynumber: 5.7 Consensus size: 28
2785235 ATCGTTGACC
* *
2785245 GGTGTTATTCTGGTAAATAATTCGGCTTC
1 GGTGCTATTCTGGTAAATAATTCGG-TTT
* *
2785274 GGTGCTGTTCTGGTAAATAATTTGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGG-TTT
*
2785303 GGTGCTATTCTGGTAAATAATTCAGTGTT
1 GGTGCTATTCTGGTAAATAATTCGGT-TT
2785332 GGTGCTATTCTGGTAAATAATTCGGTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTT
* * ** *
2785360 GGTGCTATGCTGGTAATTAATTCGAAATG
1 GGTGCTATTCTGGTAAATAATTCG-GTTT
2785389 GGTGCTATT-TGGTAAATA
1 GGTGCTATTCTGGTAAATA
2785407 TTTTAAAAAG
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
28 33 0.29
29 82 0.71
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.41
Consensus pattern (28 bp):
GGTGCTATTCTGGTAAATAATTCGGTTT
Found at i:2785393 original size:57 final size:57
Alignment explanation
Indices: 2785274--2785406 Score: 173
Period size: 57 Copynumber: 2.3 Consensus size: 57
2785264 ATTCGGCTTC
* * * *
2785274 GGTGCTGTTCTGGTAAATAATTTGGTTTTGGTGCTATTCTGGTAAATAATTCAGTGTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATGCTGGTAAATAATTCAATG-T
*
2785332 GGTGCTATTCTGGTAAATAATTCGG-TTTGGTGCTATGCTGGTAATTAATTCGAAATG-
1 GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATGCTGGTAAATAATTC--AATGT
2785389 GGTGCTATT-TGGTAAATA
1 GGTGCTATTCTGGTAAATA
2785407 TTTTAAAAAG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
56 9 0.13
57 33 0.49
58 23 0.34
59 3 0.04
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.41
Consensus pattern (57 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTTGGTGCTATGCTGGTAAATAATTCAATGT
Found at i:2785401 original size:28 final size:28
Alignment explanation
Indices: 2785303--2785434 Score: 99
Period size: 28 Copynumber: 4.6 Consensus size: 28
2785293 ATTTGGTTTT
*
2785303 GGTGCTATTCTGGTAAATAATTC--AGTG
1 GGTGCTATT-TGGTAAATAATTCGAAATG
** *
2785330 TTGGTGCTATTCTGGTAAATAATTCG-GTTT
1 --GGTGCTATT-TGGTAAATAATTCGAAATG
* *
2785360 GGTGCTATGCTGGTAATTAATTCGAAATG
1 GGTGCTAT-TTGGTAAATAATTCGAAATG
* ** *
2785389 GGTGCTATTTGGTAAATATTTTAAAAAG
1 GGTGCTATTTGGTAAATAATTCGAAATG
2785417 GGTGCTATTTGTGTAAAT
1 GGTGCTATTTG-GTAAAT
2785435 GTTCAATTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
28 46 0.54
29 38 0.45
30 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (28 bp):
GGTGCTATTTGGTAAATAATTCGAAATG
Found at i:2787142 original size:65 final size:63
Alignment explanation
Indices: 2786943--2787152 Score: 221
Period size: 65 Copynumber: 3.3 Consensus size: 63
2786933 TGCACTAAGA
* * ** *
2786943 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGG-TT
* *
2787007 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATCGGTGCATGGT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGATGCATGGT
2787070 AT
63 -T
* *
2787072 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
*
2787136 GATGCATCGGTGCATCA
1 G-TGCATCGATGCATCA
2787153 CTCTGAAAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 53 0.43
65 62 0.50
67 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTT
Found at i:2787548 original size:56 final size:59
Alignment explanation
Indices: 2787488--2787605 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 59
2787478 AGAAATTTAG
2787488 ATTTTGAAG-GA-AT-AATTTATAATTTCTTAAAGTTCAAAGCCACATCTATGTATTTC
1 ATTTTGAAGAGATATAAATTTATAATTTCTTAAAGTTCAAAGCCACATCTATGTATTTC
2787544 ATTTTGAAGAAATGAGTTATAAATTTATAATTTCTTAAAGTTCAAAGCCACATCTATGTATT
1 ATTTTGAAG--A-GA--TATAAATTTATAATTTCTTAAAGTTCAAAGCCACATCTATGTATT
2787606 CCATCGACTA
Statistics
Matches: 54, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
56 9 0.17
60 2 0.04
63 2 0.04
64 41 0.76
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (59 bp):
ATTTTGAAGAGATATAAATTTATAATTTCTTAAAGTTCAAAGCCACATCTATGTATTTC
Found at i:2791205 original size:12 final size:12
Alignment explanation
Indices: 2791188--2791214 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2791178 AATTAACAGT
2791188 AAACAGCTTCCC
1 AAACAGCTTCCC
2791200 AAACAGCTTCCC
1 AAACAGCTTCCC
2791212 AAA
1 AAA
2791215 ATCGATCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.37, G:0.07, T:0.15
Consensus pattern (12 bp):
AAACAGCTTCCC
Found at i:2793492 original size:54 final size:54
Alignment explanation
Indices: 2793429--2794180 Score: 802
Period size: 54 Copynumber: 13.9 Consensus size: 54
2793419 AATATGAAAA
* * * * * * *
2793429 TTCACAAACTCATTTTGAAATCCTTGGGGTGCACA-TATAGTGCCGATACAGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACT-TAGTGCCGATACGGTCG
* * * * * * ***
2793483 TTCACAAACTCATTGTGAATTTCGTAGGTTGCACACATAGTGCCAATACGGAAA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * *
2793537 TTCATAAACTCATTATGAATTTCGTGGGTTGCACACTTAATGCCGATATGGTCG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* ** *
2793591 TTCATACACAT-ATTATGAATTTTGTGGGTTGCACACTTAGTGCCGACACGGTCG
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * *
2793645 TTCATAAACAT-ATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATATGGTCA
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
** *
2793699 TTCATAAACAT-ATTATGAATTCTATGGGTTGCACACTTAGTGCCGATACAGTCG
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * ** * *
2793753 TTCATAAATTCATTATGAATTCTGTGGGTTGCACA-TATAGTATCGAAACGGTCA
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACT-TAGTGCCGATACGGTCG
*
2793807 TTCATAAACTCATTATGAATTCCGTGGGTTGTACACTTAGTGCCGATACGGTCG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * ***
2793861 TTCATAAACAT-ATTATGAATTCCATGGGTTGCACACTTAGTGTCGATATAATCG
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * *
2793915 TTCATAAACTCATTATGAATTACGTGGGTTGCACACTTAGTGCTGATACAGTCG
1 TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
** * *
2793969 TTCATAAACAT-ATTATGAATTTTGTGGGTTGCACACTTAGTGTCGATACAGTCG
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * * * * * *
2794023 TTGATAAA-TGTATTATGAATTCTGTGGGTTGAACACTTAGTTCTGGTACGGTCG
1 TTCATAAACT-CATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
* * *
2794077 TTGATAAACAT-ATTACGAATCCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
1 TTCATAAAC-TCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
*
2794131 TTCATAAACTCATTATGAATTTCGTGGAGGGTTGCACACTTAGTGCCGAT
1 TTCATAAACTCATTATGAATTCCGT---GGGTTGCACACTTAGTGCCGAT
2794181 TCATAAACAT
Statistics
Matches: 594, Mismatches: 88, Indels: 29
0.84 0.12 0.04
Matches are distributed among these distances:
52 1 0.00
53 4 0.01
54 562 0.95
55 4 0.01
56 1 0.00
57 22 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (54 bp):
TTCATAAACTCATTATGAATTCCGTGGGTTGCACACTTAGTGCCGATACGGTCG
Found at i:2794195 original size:49 final size:46
Alignment explanation
Indices: 2794131--2794223 Score: 127
Period size: 49 Copynumber: 2.0 Consensus size: 46
2794121 GATACGGTCG
2794131 TTCATAAACTCATTATGAATT-TCGTGGAGGGTTGCACACTTAGTGCCGA
1 TTCATAAACTCATTATGAATTAT-GT---GGGTTGCACACTTAGTGCCGA
2794180 TTCATAAACAT-ATTATGAATTATGTGGGTTGCACACTTAGTGCC
1 TTCATAAAC-TCATTATGAATTATGTGGGTTGCACACTTAGTGCC
2794224 AATAGTATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
46 19 0.45
49 21 0.50
50 2 0.05
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.34
Consensus pattern (46 bp):
TTCATAAACTCATTATGAATTATGTGGGTTGCACACTTAGTGCCGA
Found at i:2799391 original size:161 final size:162
Alignment explanation
Indices: 2799096--2799458 Score: 511
Period size: 161 Copynumber: 2.2 Consensus size: 162
2799086 CCTACAAAAC
* * * **
2799096 CATATTATGAATTCCATGGGTTGCGCACTTAGTGCCGATACGGTCGTTCATAAACTCATTATGAA
1 CATATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATAAAGTCGTTCATAAACTCATTATGAA
* ** * *
2799161 TTCTGTGGGTTGCACACTTAGTGTTGATACGGTCGTTCATAAACATATTATGAATTCTGTGGGTT
66 TTATGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTAGATT
**
2799226 GCACACTTAGTGAC-GATACGGTCGTTCATAAA
131 GCACACTTAGT-ACTGATACAATCGTTCATAAA
*
2799258 CATATTATGAATTCTGTGGGTT-CACACTTAGTGTCGATAAAGTCGTTCATAAACAT-ATTATGA
1 CATATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATAAAGTCGTTCATAAAC-TCATTATGA
2799321 ATTATGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAAC-TCATTATGAATT-TCGTAG
65 ATTATGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACAT-ATTATGAATTCT-GTAG
2799384 ATTGCACACTTAGTACTGATACAATCGTTCATAAA
128 ATTGCACACTTAGTACTGATACAATCGTTCATAAA
* * *
2799419 CATATTATGAATTCCGTTGGTTGCACATTTAGTGTTGATA
1 CATATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATA
2799459 GTACACATAG
Statistics
Matches: 179, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
160 4 0.02
161 139 0.78
162 36 0.20
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (162 bp):
CATATTATGAATTCCGTGGGTTGCACACTTAGTGTCGATAAAGTCGTTCATAAACTCATTATGAA
TTATGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCTGTAGATT
GCACACTTAGTACTGATACAATCGTTCATAAA
Found at i:2799458 original size:54 final size:54
Alignment explanation
Indices: 2799096--2799452 Score: 488
Period size: 54 Copynumber: 6.6 Consensus size: 54
2799086 CCTACAAAAC
** *
2799096 CATATTATGAATTCCATGGGTTGCGCACTTAGTGCCGATACGGTCGTTCATAAA
1 CATATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
**
2799150 C-TCATTATGAATTCTGTGGGTTGCACACTTAGTGTTGATACGGTCGTTCATAAA
1 CAT-ATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
*
2799204 CATATTATGAATTCTGTGGGTTGCACACTTAGTGACGATACGGTCGTTCATAAA
1 CATATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
* **
2799258 CATATTATGAATTCTGTGGGTT-CACACTTAGTGTCGATAAAGTCGTTCATAAA
1 CATATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
*
2799311 CATATTATGAATTATGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
1 CATATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
* * * * **
2799365 C-TCATTATGAATT-TCGTAGATTGCACACTTAGTACTGATACAATCGTTCATAAA
1 CAT-ATTATGAATTCT-GTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
* * *
2799419 CATATTATGAATTCCGTTGGTTGCACATTTAGTG
1 CATATTATGAATTCTGTGGGTTGCACACTTAGTG
2799453 TTGATAGTAC
Statistics
Matches: 271, Mismatches: 25, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
53 52 0.19
54 217 0.80
55 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (54 bp):
CATATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAA
Found at i:2802187 original size:15 final size:15
Alignment explanation
Indices: 2802167--2802195 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2802157 GAATAATCAT
2802167 GGTAACGGTGATGAC
1 GGTAACGGTGATGAC
2802182 GGTAACGGTGATGA
1 GGTAACGGTGATGA
2802196 TGAAATGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.10, G:0.41, T:0.21
Consensus pattern (15 bp):
GGTAACGGTGATGAC
Done.