Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
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: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 145 of 175
Found at i:44367630 original size:40 final size:40
Alignment explanation
Indices: 44367556--44367679 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 40
44367546 ACAAACGTCA
* *
44367556 CAAAAGATC-ACTATTAGCGGCACA-TATGTAAAAAACGCCG
1 CAAAAGATCAACCATTAGCGGCGCATTATG--AAAAACGCCG
* *
44367596 CAAAAGATCAAGCATTAGCGGCGC-TTCTTGAAAAACGCCG
1 CAAAAGATCAACCATTAGCGGCGCATT-ATGAAAAACGCCG
* * * * *
44367636 CTATAGGTCGACCATTAGCGGTGCATTATGAAAAACGCCG
1 CAAAAGATCAACCATTAGCGGCGCATTATGAAAAACGCCG
44367676 CAAA
1 CAAA
44367680 TAAAATAAGC
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
40 51 0.76
41 14 0.21
42 2 0.03
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (40 bp):
CAAAAGATCAACCATTAGCGGCGCATTATGAAAAACGCCG
Found at i:44367774 original size:38 final size:40
Alignment explanation
Indices: 44367722--44367825 Score: 149
Period size: 38 Copynumber: 2.6 Consensus size: 40
44367712 AGCTTTAATG
* * *
44367722 GCATTAGCGACGCTTTTGGAAAAACTCCGCTATAGA-T-A
1 GCATTAGCGGCGCTTTTAGAAAAACGCCGCTATAGATTAA
*
44367760 GCATTAGCGGCGCTTTTATAAAAACGCCGCTATAGATTAA
1 GCATTAGCGGCGCTTTTAGAAAAACGCCGCTATAGATTAA
*
44367800 GCATTAGCGGCGCTTTTTGAAAAACG
1 GCATTAGCGGCGCTTTTAGAAAAACG
44367826 TCGCAAAAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 32 0.55
39 1 0.02
40 25 0.43
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTAGAAAAACGCCGCTATAGATTAA
Found at i:44367907 original size:7 final size:7
Alignment explanation
Indices: 44367878--44368012 Score: 53
Period size: 7 Copynumber: 19.4 Consensus size: 7
44367868 ATTATTGTCA
*
44367878 TTAGAGT
1 TTAGGGT
44367885 TTATGGG-
1 TTA-GGGT
*
44367892 TTATGGT
1 TTAGGGT
44367899 TTAGGGT
1 TTAGGGT
**
44367906 TTATAGT
1 TTAGGGT
* **
44367913 TAATAGT
1 TTAGGGT
* *
44367920 TTAGAGC
1 TTAGGGT
*
44367927 TTAGAGT
1 TTAGGGT
44367934 TTAGGGT
1 TTAGGGT
*
44367941 TTATGGT
1 TTAGGGT
**
44367948 TTATAGT
1 TTAGGGT
**
44367955 TTATAGT
1 TTAGGGT
*
44367962 TT-GAGAT
1 TTAG-GGT
*
44367969 TTATGGT
1 TTAGGGT
44367976 TTAGGGT
1 TTAGGGT
44367983 TTAGGGT
1 TTAGGGT
*
44367990 TT-GAGAT
1 TTAG-GGT
44367997 TTAGGG-
1 TTAGGGT
44368003 TTAGGGT
1 TTAGGGT
44368010 TTA
1 TTA
44368013 AGGATAAATA
Statistics
Matches: 100, Mismatches: 21, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
6 9 0.09
7 88 0.88
8 3 0.03
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (7 bp):
TTAGGGT
Found at i:44367909 original size:14 final size:14
Alignment explanation
Indices: 44367878--44368012 Score: 62
Period size: 14 Copynumber: 9.7 Consensus size: 14
44367868 ATTATTGTCA
* *
44367878 TTAGAGTTTATGGG
1 TTAGGGTTTATGGT
* *
44367892 TTATGGTTTAGGGT
1 TTAGGGTTTATGGT
** * *
44367906 TTATAGTTAATAGT
1 TTAGGGTTTATGGT
* *
44367920 TTAGAGCTTA-GAGT
1 TTAGGGTTTATG-GT
44367934 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
** *
44367948 TTATAGTTTATAGT
1 TTAGGGTTTATGGT
*
44367962 TT-GAGATTTATGGT
1 TTAG-GGTTTATGGT
*
44367976 TTAGGGTTTAGGGT
1 TTAGGGTTTATGGT
* *
44367990 TT-GAGATTTA-GGG
1 TTAG-GGTTTATGGT
44368003 TTAGGGTTTA
1 TTAGGGTTTA
44368013 AGGATAAATA
Statistics
Matches: 89, Mismatches: 26, Indels: 13
0.70 0.20 0.10
Matches are distributed among these distances:
13 10 0.11
14 77 0.87
15 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.30, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:44367942 original size:42 final size:42
Alignment explanation
Indices: 44367885--44367991 Score: 137
Period size: 42 Copynumber: 2.5 Consensus size: 42
44367875 TCATTAGAGT
* *
44367885 TTATGGGTTATGGTTTAGGGTTTATAGTTAATAGTTT-AGAGC
1 TTATGGTTTAGGGTTTAGGGTTTATAGTTAATAGTTTGAGA-C
* * *
44367927 TTA-GAGTTTAGGGTTTATGGTTTATAGTTTATAGTTTGAGAT
1 TTATG-GTTTAGGGTTTAGGGTTTATAGTTAATAGTTTGAGAC
44367969 TTATGGTTTAGGGTTTAGGGTTT
1 TTATGGTTTAGGGTTTAGGGTTT
44367992 GAGATTTAGG
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
41 1 0.02
42 51 0.91
43 4 0.07
ACGTcount: A:0.21, C:0.01, G:0.29, T:0.49
Consensus pattern (42 bp):
TTATGGTTTAGGGTTTAGGGTTTATAGTTAATAGTTTGAGAC
Found at i:44367977 original size:35 final size:35
Alignment explanation
Indices: 44367897--44367985 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
44367887 ATGGGTTATG
* *
44367897 GTTTAGGGTTTATAGTTAATAGTTTAGAGCTTAGA
1 GTTTAGGGTTTATGGTTTATAGTTTAGAGCTTAGA
* *
44367932 GTTTAGGGTTTATGGTTTATAGTTTATAG-TTTGA
1 GTTTAGGGTTTATGGTTTATAGTTTAGAGCTTAGA
* *
44367966 GATTTATGGTTTAGGGTTTA
1 G-TTTAGGGTTTATGGTTTA
44367986 GGGTTTGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 5 0.11
35 42 0.89
ACGTcount: A:0.24, C:0.01, G:0.27, T:0.48
Consensus pattern (35 bp):
GTTTAGGGTTTATGGTTTATAGTTTAGAGCTTAGA
Found at i:44367984 original size:28 final size:28
Alignment explanation
Indices: 44367918--44368012 Score: 95
Period size: 28 Copynumber: 3.4 Consensus size: 28
44367908 ATAGTTAATA
* * *
44367918 GTTTAGAGCTTAGAGTTT-AGGGTTTATG
1 GTTTAGGGTTTAGAGTTTGA-GATTTATG
** *
44367946 GTTTATAGTTTATAGTTTGAGATTTATG
1 GTTTAGGGTTTAGAGTTTGAGATTTATG
*
44367974 GTTTAGGGTTTAGGGTTTGAGATTTA-G
1 GTTTAGGGTTTAGAGTTTGAGATTTATG
*
44368001 GGTTAGGGTTTA
1 GTTTAGGGTTTA
44368013 AGGATAAATA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 12 0.21
28 44 0.77
29 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.46
Consensus pattern (28 bp):
GTTTAGGGTTTAGAGTTTGAGATTTATG
Found at i:44368458 original size:21 final size:21
Alignment explanation
Indices: 44368404--44368460 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 21
44368394 TTTATGGTGT
*
44368404 ATGTTTA-AGGTT-GGAGTTA
1 ATGTTTAGAGGTTAGGGGTTA
44368423 ATGTTTAGAGGTTAGGGGTTA
1 ATGTTTAGAGGTTAGGGGTTA
*
44368444 A-GTTTAGGGGTTTAGGG
1 ATGTTTAGAGG-TTAGGG
44368461 CTTAGAGATC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.21
20 13 0.39
21 13 0.39
ACGTcount: A:0.23, C:0.00, G:0.39, T:0.39
Consensus pattern (21 bp):
ATGTTTAGAGGTTAGGGGTTA
Found at i:44369035 original size:113 final size:115
Alignment explanation
Indices: 44368858--44369268 Score: 464
Period size: 113 Copynumber: 3.6 Consensus size: 115
44368848 ATGACATCGT
* * *
44368858 TTTTTTTGGATTTTTAGTGGCGTTTTAGGTTAAATCGCCGCAATAGG-TTG-ATTTAGTGGCGCT
1 TTTTTATGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCATTTAGCGGCGCT
*
44368921 AGGTTATAAACGCCACTAATGGTTATCT-TGTTTATATCAAAACGGTGTAG
66 AGGATATAAACGCCACTAATGGTTAT-TATGTTTATATCAAAACGGTGTAG
44368971 TTTTTATGGATTTTTAGTGGCGTTTT-GGTTAAAACGCCGCAATAGGTTTG-ATTTAGCGGCGCT
1 TTTTTATGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCATTTAGCGGCGCT
* *
44369034 AGGGTATAAACGCCACTAATGGTTATTATGTTTATATCAAAATGGTGTAG
66 AGGATATAAACGCCACTAATGGTTATTATGTTTATATCAAAACGGTGTAG
* * * * * **
44369084 -TTTTATTGGATTTTTAGT-GC-ATTTAGGGTAAAATGCCGTAATAGTTTTGCCCTTAGCGGCGC
1 TTTTTA-TGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCATTTAGCGGCGC
* * * * * **
44369146 TTGGAGATAAAACGCCACTAAAT-GTTATTCTGTTTATGTGAAAACGCCGTCGTTT
65 TAGGATAT-AAACGCCACT-AATGGTTATTATGTTTATATCAAAACG--GT-GTAG
* * * *
44369201 TTTTTTTGGATTTTTAGTGGTGTTTTAGGGTT-AAACGCCGCAATAGATTTGCCTTTAGCGGCGC
1 TTTTTATGGATTTTTAGTGGCGTTTTA-GGTTAAAACGCCGCAATAGGTTTGCATTTAGCGGCGC
44369265 TAGG
65 TAGG
44369269 GTTTATTTTG
Statistics
Matches: 254, Mismatches: 30, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
111 3 0.01
112 47 0.19
113 113 0.44
114 29 0.11
115 3 0.01
116 2 0.01
117 14 0.06
118 5 0.02
119 35 0.14
120 3 0.01
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (115 bp):
TTTTTATGGATTTTTAGTGGCGTTTTAGGTTAAAACGCCGCAATAGGTTTGCATTTAGCGGCGCT
AGGATATAAACGCCACTAATGGTTATTATGTTTATATCAAAACGGTGTAG
Found at i:44369281 original size:101 final size:97
Alignment explanation
Indices: 44369170--44369363 Score: 237
Period size: 97 Copynumber: 2.0 Consensus size: 97
44369160 CCACTAAATG
* * * *
44369170 TTATTCTGTTTATGTGAAAACGCCGTCGTTTTTTTTTTGGATTTTTAGTGGTGTTTTAGGGTT-A
1 TTATTCTGTTTATATCAAAACGCCGTCG--TTTTGTTTGG-TTTTTAGTGGCG-TTTA-GGTTAA
44369234 AACGCCGCAATAGATTTGCCTTTAGCGGCGCTAGGGT
61 AACGCCGCAATAGATTTGCCTTTAGCGGCGCTAGGGT
* * * *
44369271 TTATTTTGTTTATATCAAAACGGCGTCGTTTTGTTTGGTTTTTAGTGGCGTTTATGTTAAAATGC
1 TTATTCTGTTTATATCAAAACGCCGTCGTTTTGTTTGGTTTTTAGTGGCGTTTAGGTTAAAACGC
* * *
44369336 CGTAATTGGTTTGCCTTTAGCGGCGCTA
66 CGCAATAGATTTGCCTTTAGCGGCGCTA
44369364 AGAGAAAACA
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
96 3 0.04
97 34 0.42
98 11 0.14
99 9 0.11
101 24 0.30
ACGTcount: A:0.18, C:0.13, G:0.25, T:0.44
Consensus pattern (97 bp):
TTATTCTGTTTATATCAAAACGCCGTCGTTTTGTTTGGTTTTTAGTGGCGTTTAGGTTAAAACGC
CGCAATAGATTTGCCTTTAGCGGCGCTAGGGT
Found at i:44372092 original size:17 final size:18
Alignment explanation
Indices: 44372060--44372093 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
44372050 TGATATGAAC
*
44372060 TAAAATTATTAAAAAAAT
1 TAAAATTATAAAAAAAAT
44372078 TAAAA-TATAAAAAAAA
1 TAAAATTATAAAAAAAA
44372094 AATCAGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAATTATAAAAAAAAT
Found at i:44372369 original size:21 final size:22
Alignment explanation
Indices: 44372343--44372386 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
44372333 AAAAGGTATC
*
44372343 TACAAATTAAATC-TCTAAGAT
1 TACAAATCAAATCTTCTAAGAT
*
44372364 TACAAATCATATCTTCTAAGAT
1 TACAAATCAAATCTTCTAAGAT
44372386 T
1 T
44372387 GCATATCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCAAATCTTCTAAGAT
Found at i:44372384 original size:22 final size:22
Alignment explanation
Indices: 44372343--44372399 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
44372333 AAAAGGTATC
* *
44372343 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
44372364 TACAAATCATATCTTCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
44372386 TGCATATCATATCT
1 TACAAATCATATCT
44372400 AAGATTGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 11 0.35
22 20 0.65
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:44372414 original size:18 final size:19
Alignment explanation
Indices: 44372378--44372462 Score: 135
Period size: 18 Copynumber: 4.7 Consensus size: 19
44372368 AATCATATCT
44372378 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
44372397 TCTAAGATTGCA-ATCATA
1 TCTAAGATTGCATATCATA
44372415 TCTAAGATTG--TATCATA
1 TCTAAGATTGCATATCATA
44372432 TCTAAGA-TGCATATCATA
1 TCTAAGATTGCATATCATA
44372450 T-TAAGATTGCATA
1 TCTAAGATTGCATA
44372463 CATTGAAGAT
Statistics
Matches: 62, Mismatches: 0, Indels: 9
0.87 0.00 0.13
Matches are distributed among these distances:
16 2 0.03
17 18 0.29
18 30 0.48
19 12 0.19
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:44372434 original size:35 final size:36
Alignment explanation
Indices: 44372371--44372458 Score: 123
Period size: 35 Copynumber: 2.5 Consensus size: 36
44372361 GATTACAAAT
44372371 CATATC-T-TCTAAGATTGCATATCATATCTAAGATTG
1 CATATCATATCTAAGATTG-ATATCATATCTAAGA-TG
44372407 CA-ATCATATCTAAGATTG-TATCATATCTAAGATG
1 CATATCATATCTAAGATTGATATCATATCTAAGATG
44372441 CATATCATAT-TAAGATTG
1 CATATCATATCTAAGATTG
44372459 CATACATTGA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
34 12 0.24
35 24 0.49
36 3 0.06
37 10 0.20
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (36 bp):
CATATCATATCTAAGATTGATATCATATCTAAGATG
Found at i:44373601 original size:49 final size:50
Alignment explanation
Indices: 44373493--44373601 Score: 116
Period size: 51 Copynumber: 2.2 Consensus size: 50
44373483 AAAAGTGTAA
* * * *
44373493 TTAAATATTATCAGATTTAAAATGTTTATTTTTATTTTTTGCTTTAATGTAT
1 TTAAATATTATCAGATTTAAAATGATTATTTATATTTTTT-CATCAA-GTAT
*
44373545 TTCAATATTATCA-ATTTAAAATGATTATTTATATTTAATTT-ATCAA-TAT
1 TTAAATATTATCAGATTTAAAATGATTATTTATATTT--TTTCATCAAGTAT
44373594 TTAAATAT
1 TTAAATAT
44373602 ATTTCAATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
49 10 0.20
51 24 0.49
52 12 0.24
53 3 0.06
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (50 bp):
TTAAATATTATCAGATTTAAAATGATTATTTATATTTTTTCATCAAGTAT
Found at i:44373604 original size:25 final size:25
Alignment explanation
Indices: 44373574--44373621 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
44373564 AATGATTATT
*
44373574 TATATTT-AATTTATCAATATTTAAA
1 TATATTTCAATAT-TCAATATTTAAA
44373599 TATATTTCAATATTCAATATTTA
1 TATATTTCAATATTCAATATTTA
44373622 TCAATTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (25 bp):
TATATTTCAATATTCAATATTTAAA
Found at i:44373928 original size:25 final size:23
Alignment explanation
Indices: 44373900--44373973 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 23
44373890 CATATTTTGG
44373900 ATTAATCAGGACACAATTTTTTTAA
1 ATTAATCA-GACACAA-TTTTTTAA
**
44373925 ATT-AT--GACACAAATTTTGCAA
1 ATTAATCAGACAC-AATTTTTTAA
*
44373946 TTTAATCACGACACAATTTTTTAA
1 ATTAATCA-GACACAATTTTTTAA
44373970 ATTA
1 ATTA
44373974 CATATTTGGA
Statistics
Matches: 38, Mismatches: 6, Indels: 11
0.69 0.11 0.20
Matches are distributed among these distances:
21 13 0.34
22 4 0.11
24 13 0.34
25 8 0.21
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.39
Consensus pattern (23 bp):
ATTAATCAGACACAATTTTTTAA
Found at i:44374091 original size:17 final size:16
Alignment explanation
Indices: 44374069--44374100 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
44374059 ATCATATAAT
44374069 AACTTACATAACTACAA
1 AACTTACATAA-TACAA
44374086 AACTTACATAATACA
1 AACTTACATAATACA
44374101 TAAATATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (16 bp):
AACTTACATAATACAA
Found at i:44374117 original size:13 final size:13
Alignment explanation
Indices: 44374099--44374178 Score: 71
Period size: 13 Copynumber: 6.3 Consensus size: 13
44374089 TTACATAATA
44374099 CATAAATATATAT
1 CATAAATATATAT
44374112 CATAAATATA-AT
1 CATAAATATATAT
* *
44374124 -ATATATA-ATTAC
1 CATAAATATA-TAT
*
44374136 CAACTAACTA-ATA-
1 C-A-TAAATATATAT
44374149 CATAAATATATAT
1 CATAAATATATAT
44374162 CATAAATATATAT
1 CATAAATATATAT
44374175 CATA
1 CATA
44374179 TACTAACTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 1 0.02
11 11 0.20
12 7 0.13
13 28 0.51
14 3 0.05
15 5 0.09
ACGTcount: A:0.54, C:0.11, G:0.00, T:0.35
Consensus pattern (13 bp):
CATAAATATATAT
Found at i:44374165 original size:101 final size:103
Alignment explanation
Indices: 44374054--44374291 Score: 267
Period size: 105 Copynumber: 2.3 Consensus size: 103
44374044 TAATGTTTAT
44374054 TATATATCATATAATAACTTACATAACTACAAAACTTACATAATACATAAATATATATCATAAAT
1 TATATATCATATAATAACTTACATAACTACAAAAC-TACATAATACATAAATATATA-CATAAAT
44374119 ATA-AT-ATATATAA-TTAC-CAACTA-ACTAATACATAAA
64 ATATATCATATATAACTTACACAACTACA-TAATACATAAA
* * *
44374155 TATATATCATAAATATATATCATATAC-TAACTTACACAACTACATAATACATAAATATATACGT
1 TATATATCAT--ATA-ATAAC-T-TACATAAC-TACAAAACTACATAATACATAAATATATACAT
* *
44374219 AAATATATATCTTATCTAACTTACACAACTACATAATACATAAA
60 AAATATATATCATATATAACTTACACAACTACATAATACATAAA
* * *
44374263 TATA-ATCATATCATAA-ATACATACCTACA
1 TATATATCATATAATAACTTACATAACTACA
44374292 TAAATGTATC
Statistics
Matches: 116, Mismatches: 9, Indels: 24
0.78 0.06 0.16
Matches are distributed among these distances:
101 17 0.15
102 3 0.03
103 3 0.03
104 16 0.14
105 30 0.26
106 16 0.14
107 9 0.08
108 21 0.18
109 1 0.01
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (103 bp):
TATATATCATATAATAACTTACATAACTACAAAACTACATAATACATAAATATATACATAAATAT
ATATCATATATAACTTACACAACTACATAATACATAAA
Found at i:44374239 original size:53 final size:54
Alignment explanation
Indices: 44374077--44374272 Score: 273
Period size: 53 Copynumber: 3.7 Consensus size: 54
44374067 ATAACTTACA
* *
44374077 TAAC-TACAAAACTTACATAATACATAAATATATATCATAAATATA-AT-ATATA
1 TAACTTACACAAC-TACATAATACATAAATATATATCATAAATATATATCATATC
44374129 TAA-TTAC-CAACTA-ACTAATACATAAATATATATCATAAATATATATCATATAC
1 TAACTTACACAACTACA-TAATACATAAATATATATCATAAATATATATCATAT-C
* *
44374182 TAACTTACACAACTACATAATACATAAATATATA-CGTAAATATATATCTTATC
1 TAACTTACACAACTACATAATACATAAATATATATCATAAATATATATCATATC
44374235 TAACTTACACAACTACATAATACATAAATATA-ATCATA
1 TAACTTACACAACTACATAATACATAAATATATATCATA
44374273 TCATAAATAC
Statistics
Matches: 130, Mismatches: 5, Indels: 17
0.86 0.03 0.11
Matches are distributed among these distances:
49 1 0.01
50 30 0.23
51 5 0.04
52 11 0.08
53 39 0.30
54 20 0.15
55 23 0.18
56 1 0.01
ACGTcount: A:0.52, C:0.15, G:0.01, T:0.33
Consensus pattern (54 bp):
TAACTTACACAACTACATAATACATAAATATATATCATAAATATATATCATATC
Found at i:44374312 original size:34 final size:33
Alignment explanation
Indices: 44374255--44374319 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
44374245 AACTACATAA
*
44374255 TACATAAATATAATCATATCATAAATACATACC
1 TACATAAATATAATCATAACATAAATACATACC
* * *
44374288 TACATAAATGTATCTCATAACATAACTACATA
1 TACATAAATATA-ATCATAACATAAATACATA
44374320 ACTTACAAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 11 0.41
34 16 0.59
ACGTcount: A:0.49, C:0.18, G:0.02, T:0.31
Consensus pattern (33 bp):
TACATAAATATAATCATAACATAAATACATACC
Found at i:44386220 original size:17 final size:17
Alignment explanation
Indices: 44386198--44386235 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
44386188 GTATATTAAC
*
44386198 TTATAATTATT-TAATTA
1 TTATAATAATTCT-ATTA
44386215 TTATAATAATTCTATTA
1 TTATAATAATTCTATTA
44386232 TTAT
1 TTAT
44386236 TGTTGCCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATAATAATTCTATTA
Found at i:44388401 original size:10 final size:10
Alignment explanation
Indices: 44388387--44388435 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
44388377 TTGGTAAATA
44388387 ATTTTTTA-T
1 ATTTTTTAGT
44388396 ATTTTTTAGT
1 ATTTTTTAGT
44388406 ATTTTTTA-T
1 ATTTTTTAGT
44388415 -TTCTTTT-GT
1 ATT-TTTTAGT
44388424 ATTATTTTAGT
1 ATT-TTTTAGT
44388435 A
1 A
44388436 AAAAACCCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
8 2 0.06
9 14 0.41
10 15 0.44
11 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.71
Consensus pattern (10 bp):
ATTTTTTAGT
Found at i:44388411 original size:19 final size:18
Alignment explanation
Indices: 44388387--44388432 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 18
44388377 TTGGTAAATA
44388387 ATTTTTTATATT-TTTTAGT
1 ATTTTTTAT-TTCTTTT-GT
44388406 ATTTTTTATTTCTTTTGT
1 ATTTTTTATTTCTTTTGT
44388424 ATTATTTTA
1 ATT-TTTTA
44388433 GTAAAAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (18 bp):
ATTTTTTATTTCTTTTGT
Found at i:44390931 original size:22 final size:22
Alignment explanation
Indices: 44390896--44390937 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
44390886 CTTCTTCACT
44390896 TTTCTTCTTCGATTTTTCGCGA
1 TTTCTTCTTCGATTTTTCGCGA
* *
44390918 TTTCTTGTTGGATTTTTCGC
1 TTTCTTCTTCGATTTTTCGC
44390938 AGTCAATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.19, G:0.17, T:0.57
Consensus pattern (22 bp):
TTTCTTCTTCGATTTTTCGCGA
Found at i:44397216 original size:22 final size:21
Alignment explanation
Indices: 44397188--44397247 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
44397178 AATACATGTT
44397188 CATAATATATAAACATAATATA
1 CATAATATATAAACAT-ATATA
* *
44397210 TATAATAT-TAAAACAT-TTTA
1 CATAATATAT-AAACATATATA
*
44397230 CATAATATATACACATAT
1 CATAATATATAAACATAT
44397248 GATTTCAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
20 15 0.48
21 3 0.10
22 13 0.42
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (21 bp):
CATAATATATAAACATATATA
Found at i:44397628 original size:24 final size:21
Alignment explanation
Indices: 44397585--44397650 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
44397575 CATAATATAA
* *
44397585 TAATGATAATAATAACAATAT
1 TAATGATATTAATAACAATAG
44397606 TAATGATATTAATAATTCAAATAG
1 TAATGATATTAATAA--C-AATAG
* *
44397630 TGATGATATTTAATAAAAATA
1 TAATGATA-TTAATAACAATA
44397651 ACAAAGAGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
21 14 0.38
22 4 0.11
23 1 0.03
24 11 0.30
25 7 0.19
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (21 bp):
TAATGATATTAATAACAATAG
Found at i:44399778 original size:68 final size:67
Alignment explanation
Indices: 44399670--44399955 Score: 227
Period size: 70 Copynumber: 4.0 Consensus size: 67
44399660 CATAATACGA
44399670 AAACAGAAATGGAAATACCTCGGTGTGACTGAGGCTCACTCACCTCTCGCAATATGAGTTGATTT
1 AAACAGAAATGGAAATACCTCGGTGTGACTGAGGCTCACTCACCTCTCGCAATATGAGTTGATTT
44399735 TG
66 TG
* * **
44399737 AAACAGAAATTGAAATTACCTCAGCGTGT-CCT-AGGCTCACTCATTTCTCGCAATATGAGTTGA
1 AAACAGAAATGGAAA-TACCTC-G-GTGTGACTGAGGCTCACTCACCTCTCGCAATATGAGTTGA
*
44399800 TTCTTTCAAAA
63 -T-TTT----G
* *
44399811 ATATGACGAAAACAGAATGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATAT
1 A-A--AC---A-GA-AATGGAAATACCTCGGTGTGA-CTGAGGCTC-ACTCACCTCTCGCAATAT
44399876 GAGTTGATTTTG
56 GAGTTGATTTTG
* * * **
44399888 AAAACAGAAATTGAATTACCTCAGCGTGT-CCTGAGGCTCAACTCATTTCTCGCAATATGAGTTT
1 -AAACAGAAATGGAAATACCTC-G-GTGTGACTGAGGCTC-ACTCACCTCTCGCAATATGAG-TT
44399952 GATT
61 GATT
44399956 CTTTCAAAAC
Statistics
Matches: 175, Mismatches: 19, Indels: 46
0.73 0.08 0.19
Matches are distributed among these distances:
67 14 0.08
68 35 0.20
69 4 0.02
70 47 0.27
71 8 0.05
72 5 0.03
74 1 0.01
75 3 0.02
77 3 0.02
78 1 0.01
79 4 0.02
80 2 0.01
81 12 0.07
82 13 0.07
83 23 0.13
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (67 bp):
AAACAGAAATGGAAATACCTCGGTGTGACTGAGGCTCACTCACCTCTCGCAATATGAGTTGATTT
TG
Found at i:44400028 original size:85 final size:83
Alignment explanation
Indices: 44399886--44400196 Score: 306
Period size: 86 Copynumber: 3.8 Consensus size: 83
44399876 GAGTTGATTT
* * * **
44399886 TGAAAACAGAAATTGAATTACCTCAGCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 TGAAAACAGAAATGGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAG-T
44399951 TGATTCTTTCAAAACATAA
65 TGATTCTTTCAAAACATAA
* *
44399970 TGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TGAAAACAGAAATGG-AAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
*
44400035 TGA-T-TTTGAAAAC---A
65 TGATTCTTTCAAAACATAA
** * * **
44400049 -G-AAATTGAAAT-----TACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 TGAAAACAGAAATGGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
44400107 GATTCTTTC-AAACATAA
66 GATTCTTTCAAAACATAA
* * * * *
44400124 TGACGAAAATAGAAAAGGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATG
1 T---GAAAACAGAAATGG-AAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATG
44400189 AGTTGATT
62 AGTTGATT
44400197 TAGAAAACAG
Statistics
Matches: 186, Mismatches: 24, Indels: 32
0.77 0.10 0.13
Matches are distributed among these distances:
71 43 0.23
72 5 0.03
73 3 0.02
75 1 0.01
77 8 0.04
78 1 0.01
79 2 0.01
80 8 0.04
82 8 0.04
83 1 0.01
84 18 0.10
85 42 0.23
86 46 0.25
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (83 bp):
TGAAAACAGAAATGGAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTCTTTCAAAACATAA
Found at i:44400086 original size:71 final size:71
Alignment explanation
Indices: 44399970--44400110 Score: 210
Period size: 71 Copynumber: 2.0 Consensus size: 71
44399960 CAAAACATAA
* *
44399970 TGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
1 TGAAAACAGAAATGGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
44400035 TGATTT
66 TGATTT
* * * * **
44400041 TGAAAACAGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGT
1 TGAAAACAGAAATGGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
44400106 TGATT
66 TGATT
44400111 CTTTCAAACA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (71 bp):
TGAAAACAGAAATGGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGT
TGATTT
Found at i:44400336 original size:309 final size:297
Alignment explanation
Indices: 44399521--44400652 Score: 1112
Period size: 301 Copynumber: 3.7 Consensus size: 297
44399511 TTTGAAAAGC
* * **
44399521 AGAAATTGAAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTT
1 AGAAA-TGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG-ATTT
* * * **
44399586 TG-AAACAG--AAATTGAATTACCTCA-ATGTGTCTTG-GGCTCAACTTATTTCTCGCAATATGA
64 TGAAAACAGCAAAATTGAAATA-CTCACACGTGTC-CGAGGCTCAAC-TCCTTCTCGCAATATGA
* *
44399646 GTTGATTTTTCAAACATAATACGAAAACAGAAA-TGGAAATACCTCGGTGTGA-CTGAGGCTCAC
126 GTTGATTTTT------T--T--G-AAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCAC
44399709 TCACCTCTCGCAATATGAGTTGATTTTG--AAACAGAAATTGAAATTACCTCAGCGTGTCCT-AG
180 TCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGT-CTGAG
*
44399771 GCTC-ACTCATTTCTCGCAATATGAGTTGATTCTTTCAAAAAT-ATGACGAAAA
244 GCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTCAAACATAATGACGAAAA
* * *
44399823 CAG-AATGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 -AGAAATGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
* * *
44399887 GAAAACAG--AAATTGAATTACCTCA-GCGTGTCCTGAGGCTCAACTCATTTCTCGCAATATGAG
65 GAAAACAGCAAAATTGAAATA-CTCACACGTGTCC-GAGGCTCAACTC-CTTCTCGCAATATGAG
* *
44399949 TTTGATTCTTTCAAAACATAATGAAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAA
127 -TTGATT-TTT-------T--TG-AAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTC-A
44400014 CTCACCTCTCGCAATATGAGTTGATTTTG-AAAACAGAAATTGAAATTACCTCAGCGTGTCTTGA
179 CTCACCTCTCGCAATATGAGTTGATTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTC-TGA
44400078 GGCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTCAAACATAATGACGAAAA
243 GGCTCAACTCATTTCTCGCAATATGAGTTGATTCTTTCAAACATAATGACGAAAA
* * *
44400133 TAGAAAAGGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTT
1 -AG-AAATGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * *
44400198 AGAAAACAGACATAAAACAAAATTGAAAGTGACTCAACACGTGAGCCAAGGCTCAACTACCTTCT
64 TGAAAACAG--------CAAAATTGAAA-T-ACTC-ACACGTG-TCCGAGGCTCAACT-CCTTCT
*
44400263 CGCAATAT-AGTTGATTTTTTTGAAA-AGAAATTGAAAATACCTC-GCGTG-CCCGAGGCTCAAC
116 CGCAATATGAGTTGATTTTTTTGAAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTC-AC
44400324 TCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAA-TACCTCAGCGTGTCTGAG
180 TCACCTCTCGCAATATGAGTTGA-TTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCTGAG
** * *
44400388 GCTCAACTCACCTCTCGCAATATGAGTTGATT-TTTGAAAACA-AAT--TG---A
244 GCTCAACTCATTTCTCGCAATATGAGTTGATTCTTT-CAAACATAATGACGAAAA
* * * *
44400436 ACAAATTAAAATACCTCAACGTGTCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTT
1 AGAAATGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTT
* * *
44400500 G-AAA-AGCAGAAATTGAAATAC-CTCA-GTGTCTTGAGGCTCAACT-CATCTCGCAATATGAGT
65 GAAAACAGCA-AAATTGAAATACTCACACGTGTC-CGAGGCTCAACTCCTTCTCGCAATATGAGT
* * * *
44400560 TGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCACTCACCTCTAGCA
128 TGATTTTTTTGA-AACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCACTCACCTCTCGCA
*
44400624 ATATGAGTTGATTTTGAAAAACAAAAATT
192 ATATGAGTTGATTTTGAAAAACAGAAATT
44400653 AAAAGCTTAA
Statistics
Matches: 733, Mismatches: 52, Indels: 104
0.82 0.06 0.12
Matches are distributed among these distances:
285 20 0.03
286 9 0.01
287 47 0.06
288 31 0.04
289 10 0.01
290 2 0.00
291 3 0.00
292 9 0.01
299 2 0.00
300 27 0.04
301 113 0.15
302 27 0.04
303 20 0.03
304 20 0.03
305 18 0.02
306 32 0.04
307 30 0.04
308 12 0.02
309 111 0.15
310 35 0.05
311 33 0.05
312 65 0.09
313 2 0.00
315 1 0.00
322 11 0.02
323 10 0.01
324 4 0.01
325 26 0.04
326 3 0.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (297 bp):
AGAAATGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTG
AAAACAGCAAAATTGAAATACTCACACGTGTCCGAGGCTCAACTCCTTCTCGCAATATGAGTTGA
TTTTTTTGAAACAGAAATTGAAAATACCTCGGCGTGACCTGAGGCTCACTCACCTCTCGCAATAT
GAGTTGATTTTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCTGAGGCTCAACTCATTTCTCG
CAATATGAGTTGATTCTTTCAAACATAATGACGAAAA
Found at i:44400393 original size:71 final size:71
Alignment explanation
Indices: 44400246--44400652 Score: 505
Period size: 71 Copynumber: 5.7 Consensus size: 71
44400236 ACGTGAGCCA
***
44400246 AGGCTCAACT-ACCTTCTCGCAATAT-AGTTGATTTTTTTGAAA-AGAAATTGAAAATACCTC-G
1 AGGCTCAACTCACC-TCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AAATACCTCAG
* *
44400307 CGTGCCCG
64 CGTGTCTG
44400315 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCG
44400380 TGTCTG
66 TGTCTG
* *
44400386 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACAAATTGAACAAATTAAAATACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-ACA--G---AAATTGAAATACC
*
44400451 TCAACGTGTCTTG
60 TCAGCGTGTC-TG
*
44400464 AGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAATACCTCA--G
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCG
44400526 TGTCTTG
66 TGTC-TG
*
44400533 AGGCTCAACTCA--TCTCGCAATATGAGTTGATTTTTTG-ACAACAGAAATTGAAATTACCTCAG
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAACAGAAATTGAAA-TACCTCAG
44400595 CGTGTCCTG
64 CGTGT-CTG
* *
44400604 AGGCTC-ACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
44400653 AAAAGCTTAA
Statistics
Matches: 303, Mismatches: 16, Indels: 36
0.85 0.05 0.10
Matches are distributed among these distances:
68 32 0.11
69 54 0.18
70 36 0.12
71 94 0.31
72 20 0.07
74 2 0.01
76 1 0.00
77 50 0.17
78 14 0.05
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (71 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACCTCAGCG
TGTCTG
Found at i:44400422 original size:140 final size:141
Alignment explanation
Indices: 44400246--44400652 Score: 539
Period size: 140 Copynumber: 2.9 Consensus size: 141
44400236 ACGTGAGCCA
44400246 AGGCTCAACT-ACCTTCTCGCAATAT-AGTTGATTTTTTTGAAAAGAAATTGAAAATACCTC-GC
1 AGGCTCAACTCACC-TCTCGCAATATGAGTTGA-TTTTTTGAAAAGAAATTGAAAATACCTCAGC
*
44400308 GTG-CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATA
64 GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATA
44400372 CCTCAGCGTGTC-TG
129 CCTCA--GTGTCTTG
*
44400386 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAAATTGAACAAATTAAAATAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGAAATTG--------AAAATAC
* * *
44400450 CTCAACGTGTCTTGAGGCTCAACTCA-CTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATT
58 CTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
44400514 GAAATACCTCAGTGTCTTG
123 GAAATACCTCAGTGTCTTG
*
44400533 AGGCTCAACTCA--TCTCGCAATATGAGTTGATTTTTTGACAACAGAAATTGAAATTACCTCAGC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGA-AA-AGAAATTGAAAATACCTCAGC
* *
44400596 GTGTCCTGAGGCTC-ACTCACCTCTAGCAATATGAGTTGA-TTTTGAAAAACAAAAATT
64 GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT
44400653 AAAAGCTTAA
Statistics
Matches: 238, Mismatches: 12, Indels: 35
0.84 0.04 0.12
Matches are distributed among these distances:
139 37 0.16
140 63 0.26
141 9 0.04
145 18 0.08
146 12 0.05
147 26 0.11
148 59 0.25
149 14 0.06
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (141 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAGAAATTGAAAATACCTCAGCGT
GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAATACC
TCAGTGTCTTG
Found at i:44400537 original size:527 final size:504
Alignment explanation
Indices: 44399401--44400638 Score: 1236
Period size: 527 Copynumber: 2.4 Consensus size: 504
44399391 AACATGTGAA
* *
44399401 CTGAGGCTCAACTCACTTTTCGCAATATGAGTTGATTTTTTTGACAA-CAGAAATTGAAATTACC
1 CTGAGGCTCAACTCAC-TCTCGCAATATGAGTTGA--TTTTTGAAAAGCAGAAATTGAAA-TACC
44399465 TCAGCGTGTCCT-AGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAAAGCAGAAATTG
62 TCA--GTGTCCTGAGGCTCAACTCA--TCTCGCAATATGAGTTG-ATTTTGAAAA-CAGAAATTG
* * * *
44399529 AAAATACCTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGAATTTTGAAACAG
121 AAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTCAAACAG
* * ** * * ** ***
44399594 AAATTGAATTACCTCAATGTGTCTTGGGCTCAACTTATTTCTCGCAATATGAGTTGATTTTTCAA
186 AAATGGAAATACCTCAACATGTCCTGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAAA
* * * * **
44399659 ACATAATACGAAAACAGAAATGGAAATACCTCGGTGTGACTGAGGCTCACTCACCTCTCGCAATA
251 ACAGAATA--AAAACAGAAATGGAAATACCACCGTGAGACCAAGGCTCACTCACCTCTCGCAATA
* * * **
44399724 TGAGTTGATTTTGAAACAGAAATTGAAATTACCTCAGCGTGTCCTAGGCTCACTCATTTCTCGCA
314 TGAGTTGATTTTGAAACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCACTCACCTCTCGCA
* *
44399789 ATATGAGTTGATTCTTTCAAAAATATGACGAAAACAGAATGAAAATACCTCGGTGTGACCTGAGG
379 ATATGAGTTGATTCTTT-AAAAATA-GAC-AAAACAGAATGAAAATACCTCAGCGTGACCTGAGG
* * *
44399854 CTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAATTACCTCAGCGTGTC
441 CTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAACAGAAATTAAAATACCTCAACGTGTC
* *
44399918 CTGAGGCTCAACTCATTTCTCGCAATATGAGTTTGATTCTTTCAAAACATAATGAAAACAGAAAT
1 CTGAGGCTCAACTCA-CTCTCGCAATATGAG-TTGATT-TTT---GA-A-AA-G----CAGAAAT
* *
44399983 GGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTGAAAAC
53 TG-AAATACCTCAGTGT--CCTGAGGCTCAACTCA--TCTCGCAATATGAGTTGATTTTGAAAAC
44400048 AGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTCT
113 AGAAATTGAAATTACCTCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATT-T
*
44400113 TTCAAACATAATGACGAAAATAGAAAAGGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCT
177 TTCAAAC------A-G-AAAT------GG-AAATACCTCAACATGTCCTG-GGCTCAACTCACCT
* *
44400178 CTTGCAATATGAGTTGATTTAGAAAACAGACAT-AAAACA-AAATTGAAAGTGACTCAACACGTG
226 CTCGCAATATGAGTTGATTTAGAAAACAGA-ATAAAAACAGAAATGGAAA-T-AC-C-AC-CGTG
44400241 AG-CCAAGGCTCAACT-ACCTTCTCGCAATAT-AGTTGATTTTTTTGAAA-AGAAATTGAAAATA
285 AGACCAAGGCTC-ACTCACC-TCTCGCAATATGAGTTGA---TTTTGAAACAGAAATTGAAAATA
* *
44400302 CCTC-GCGTGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATT-TTT-GAAA-A-AC-AG
345 CCTCAGCGTGCCCGAGGCTC-ACTCACCTCTCGCAATATGAGTTGATTCTTTAAAAATAGACAAA
* *
44400361 A-A-ATTG-AAATACCTCAGCGTG-TCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
409 ACAGAATGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTT
44400422 TGAAAACAAATTGAACAAATTAAAATACCTCAACGTGTC
473 TGAAAAC--A--G---AAATTAAAATACCTCAACGTGTC
*
44400461 TTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAATACCTCAG
1 CTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAATACCTCAG
* *
44400526 TGTCTTGAGGCTCAACTCATCTCGCAATATGAGTTGATTTTTTGACAACAGAAATTGAAATTACC
66 TGTCCTGAGGCTCAACTCATCTCGCAATATGAGTTGA--TTTTGAAAACAGAAATTGAAATTACC
* ** *
44400591 TCAGCGTGTCCTGAGGCTC-ACTCACCTCTAGCAATATGAGTTGATTTT
129 TCAGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTT
44400639 GAAAAACAAA
Statistics
Matches: 607, Mismatches: 57, Indels: 106
0.79 0.07 0.14
Matches are distributed among these distances:
516 2 0.00
517 31 0.05
518 4 0.01
520 1 0.00
522 2 0.00
525 20 0.03
526 28 0.05
527 119 0.20
528 34 0.06
529 45 0.07
530 8 0.01
534 2 0.00
535 38 0.06
536 28 0.05
537 4 0.01
538 2 0.00
539 2 0.00
540 4 0.01
541 16 0.03
542 22 0.04
543 52 0.09
544 40 0.07
545 19 0.03
546 34 0.06
547 42 0.07
548 8 0.01
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (504 bp):
CTGAGGCTCAACTCACTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAATTGAAATACCTCAG
TGTCCTGAGGCTCAACTCATCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTC
AGCGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTCAAACAGAAATGGAAAT
ACCTCAACATGTCCTGGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAGAAAACAGAATAAA
AACAGAAATGGAAATACCACCGTGAGACCAAGGCTCACTCACCTCTCGCAATATGAGTTGATTTT
GAAACAGAAATTGAAAATACCTCAGCGTGCCCGAGGCTCACTCACCTCTCGCAATATGAGTTGAT
TCTTTAAAAATAGACAAAACAGAATGAAAATACCTCAGCGTGACCTGAGGCTCAACTCACCTCTC
GCAATATGAGTTGATTTTGAAAACAGAAATTAAAATACCTCAACGTGTC
Found at i:44401695 original size:17 final size:17
Alignment explanation
Indices: 44401657--44401697 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
44401647 GCCCTGATCC
**
44401657 CCTTTTTTTTTTTTTTT
1 CCTTTTTTTTTTTTTCA
*
44401674 TCTTTTTTTTTTTTTCA
1 CCTTTTTTTTTTTTTCA
44401691 CCTTTTT
1 CCTTTTT
44401698 ATGTCTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.02, C:0.15, G:0.00, T:0.83
Consensus pattern (17 bp):
CCTTTTTTTTTTTTTCA
Found at i:44401708 original size:1 final size:1
Alignment explanation
Indices: 44401659--44401688 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
44401649 CCTGATCCCC
*
44401659 TTTTTTTTTTTTTTTTCTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
44401689 CACCTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:44413328 original size:3 final size:3
Alignment explanation
Indices: 44413320--44413346 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44413310 TGTGTTCAAA
44413320 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
44413347 GTAGATAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44414652 original size:23 final size:21
Alignment explanation
Indices: 44414600--44414657 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
44414590 GGGTTTGTAA
* *
44414600 ATTGGGCTCAGGTAGTTTTAGG
1 ATTGGGCT-AGGTTGGTTTAGG
44414622 ATTGGGCTAGGTTGGTTTAGGG
1 ATTGGGCTAGGTTGGTTTA-GG
44414644 TATTGGGCTAGGTT
1 -ATTGGGCTAGGTT
44414658 AGTTGGGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 9 0.28
22 10 0.31
23 13 0.41
ACGTcount: A:0.16, C:0.07, G:0.40, T:0.38
Consensus pattern (21 bp):
ATTGGGCTAGGTTGGTTTAGG
Found at i:44414898 original size:41 final size:41
Alignment explanation
Indices: 44414852--44414999 Score: 251
Period size: 41 Copynumber: 3.6 Consensus size: 41
44414842 CAGGCTTAGC
44414852 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
* * *
44414893 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATTAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
*
44414934 GCCTAGCAGGCTAAGTGCCGGTGAACTGACTCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
*
44414975 GCCTAGCAGGCTAAGTGCAGGTGAA
1 GCCTAGCAGGCTAAGTGCCGGTGAA
44415000 TCTGTTTAAA
Statistics
Matches: 99, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 99 1.00
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAA
Found at i:44414980 original size:82 final size:83
Alignment explanation
Indices: 44414852--44415003 Score: 279
Period size: 82 Copynumber: 1.8 Consensus size: 83
44414842 CAGGCTTAGC
*
44414852 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCCGGTG-
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCAGGTGA
44414916 ATCTGAATTAGGCTATAA
66 ATCTGAATTAGGCTATAA
*
44414934 GCCTAGCAGGCTAAGTGCCGGTGAACTGACTCAGGTTATAAGCCTAGCAGGCTAAGTGCAGGTGA
1 GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCAGGTGA
44414999 ATCTG
66 ATCTG
44415004 TTTAAATTAA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 62 0.93
83 5 0.07
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (83 bp):
GCCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGTTATAAGCCTAGCAGGCTAAGTGCAGGTGA
ATCTGAATTAGGCTATAA
Found at i:44421589 original size:44 final size:43
Alignment explanation
Indices: 44421447--44421632 Score: 196
Period size: 43 Copynumber: 4.3 Consensus size: 43
44421437 AAGCACCATT
* * *
44421447 AAAACGTCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCTCA
1 AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCA
* * * * *
44421490 CAAACGCCGCTAAAAACCAAGACCTTTAGTGGCACTTTTCCTA
1 AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCA
* *
44421533 AAAATGCCGCTAAAGACCAAGACCTTTAGCAGCGCTTTTTCCCA
1 AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCCCA
* * * * *
44421577 AAAACGCTGCTAAAGAACATGATCTTTAGCGACGCTTTAT--CA
1 AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTT-TCCCA
*
44421619 CAAACGCCGCTAAA
1 AAAACGCCGCTAAA
44421633 AGTACAATTC
Statistics
Matches: 117, Mismatches: 24, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
42 14 0.12
43 67 0.57
44 36 0.31
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (43 bp):
AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCA
Found at i:44423753 original size:40 final size:40
Alignment explanation
Indices: 44423690--44423774 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
44423680 TAGCTTGAAC
* * *
44423690 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
44423730 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
44423770 ATCAA
1 ATCAA
44423775 TCTTACAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:44423948 original size:86 final size:85
Alignment explanation
Indices: 44423850--44424037 Score: 252
Period size: 86 Copynumber: 2.2 Consensus size: 85
44423840 GGCATTAGGG
* * * * * *
44423850 CTAAATCTTCAATTTCTATAACGATTTATATGCGACAAATTAACAAAAATCAATGGTTCAAGTTC
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAACAAAAATAAATGGATCAAGTTC
* *
44423915 ATGTATTTACCAAAAATCAGA
65 ATGCATTTACCAAAAAGCAGA
*
44423936 CT-AATTTGTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGATCAAGTT
1 CTAAATTT-TCAAT-TTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGATCAAGTT
*
44424000 CATGCATTTACCAACAAGCAGA
64 CATGCATTTACCAAAAAGCAGA
44424022 CTAAATTTTCAATTTT
1 CTAAATTTTCAATTTT
44424038 CAATTTTTAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
85 7 0.08
86 75 0.84
87 7 0.08
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (85 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGATCAAGTTCA
TGCATTTACCAAAAAGCAGA
Found at i:44424300 original size:86 final size:87
Alignment explanation
Indices: 44424133--44424302 Score: 207
Period size: 86 Copynumber: 2.0 Consensus size: 87
44424123 ATTTCAGCAA
* * * * * * * *
44424133 TTTACATGCAAAAAATTAGCAAAAATTAACAGTTCATGTATAATGTATTTACCAAAAACCGGACC
1 TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACC
*
44424198 AACTTGTCAATTTTTATAACAT
66 AAATTGTCAATTTTTATAACAT
* * * *
44424220 TTTAAATGCAACAAATTAACACAAATTAACAATACAAGT-TCATATATTCACCAAAAACCAGACT
1 TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACC
*
44424284 AAATTTTCAATTTTTATAA
66 AAATTGTCAATTTTTATAA
44424303 AATAAGAGGA
Statistics
Matches: 69, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
86 37 0.54
87 32 0.46
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.32
Consensus pattern (87 bp):
TTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACCAGACC
AAATTGTCAATTTTTATAACAT
Found at i:44427471 original size:10 final size:10
Alignment explanation
Indices: 44427423--44427483 Score: 61
Period size: 10 Copynumber: 5.8 Consensus size: 10
44427413 AAAATAAAAG
44427423 TTTAAAATCTT
1 TTTAAAATC-T
* *
44427434 TTTTAAATTT
1 TTTAAAATCT
44427444 TTTAAAAAT-T
1 TTT-AAAATCT
44427454 TTTAAAATCT
1 TTTAAAATCT
44427464 TTTAAAATTCAT
1 TTTAAAA-TC-T
44427476 TTTAAAAT
1 TTTAAAAT
44427484 TTTAAATCAC
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
9 5 0.12
10 16 0.37
11 14 0.33
12 8 0.19
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (10 bp):
TTTAAAATCT
Found at i:44428404 original size:7 final size:7
Alignment explanation
Indices: 44428392--44428486 Score: 66
Period size: 7 Copynumber: 13.3 Consensus size: 7
44428382 AACACTTAAC
44428392 CCCTAAA
1 CCCTAAA
44428399 CCCTAAA
1 CCCTAAA
*
44428406 CCTTAAA
1 CCCTAAA
* *
44428413 CCGTTAA
1 CCCTAAA
*
44428420 CCATAAA
1 CCCTAAA
*
44428427 CCTTAAAA
1 CCCT-AAA
44428435 CCCTAAA
1 CCCTAAA
*
44428442 CTC-ATAA
1 CCCTA-AA
*
44428449 CCCTCAA
1 CCCTAAA
*
44428456 CCCTTAA
1 CCCTAAA
*
44428463 CCTCTAAC
1 CC-CTAAA
*
44428471 CCCTAAC
1 CCCTAAA
44428478 CCCTAAA
1 CCCTAAA
44428485 CC
1 CC
44428487 TTATTTAATA
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
6 1 0.01
7 58 0.83
8 11 0.16
ACGTcount: A:0.38, C:0.41, G:0.01, T:0.20
Consensus pattern (7 bp):
CCCTAAA
Found at i:44429129 original size:41 final size:41
Alignment explanation
Indices: 44429084--44429277 Score: 162
Period size: 41 Copynumber: 4.7 Consensus size: 41
44429074 ATATGTTTTT
44429084 GCGGCGCTTTACAAAAAACGCCGCTAAAGGTCTACGCATTA
1 GCGGCGCTTTACAAAAAACGCCGCTAAAGGTCTACGCATTA
* * * * *
44429125 GCGGCGCTTCATGAAAAAACGCCGCTAAAGGTTTGCACATTA
1 GCGGCGCTTTA-CAAAAAACGCCGCTAAAGGTCTACGCATTA
* * * * * *
44429167 ACGGCG-ATTCCTTACAAACGCCGCTAAAGGTC-AGTGCATTA
1 GCGGCGCTTTAC-AAAAAACGCCGCTAAAGGTCTA-CGCATTA
* * *
44429208 GCGGCGC-TTCCTGAAAAACGCCGCTAAAGGTCCACGCATTA
1 GCGGCGCTTTAC-AAAAAACGCCGCTAAAGGTCTACGCATTA
* **
44429249 GCGACGCTTCT-TGAAAAACGCCGCTAAAG
1 GCGGCGCTT-TACAAAAAACGCCGCTAAAG
44429278 ACCCACAAGG
Statistics
Matches: 124, Mismatches: 22, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
41 90 0.73
42 33 0.27
43 1 0.01
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTACAAAAAACGCCGCTAAAGGTCTACGCATTA
Found at i:44429417 original size:40 final size:38
Alignment explanation
Indices: 44429373--44429449 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
44429363 GCTTTCCTAA
*
44429373 AAGCGCCGCTAATACTCGATCTTTAGCGGCGTTTTTTGTG
1 AAGCGCCGCTAATACTC-A-ATTTAGCGGCGTTTTTTGTG
* *
44429413 AAGCGCCGCTACTGCTCAATTTAGCGGCGTTTTTTGT
1 AAGCGCCGCTAATACTCAATTTAGCGGCGTTTTTTGT
44429450 ACAAACGCCA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 18 0.53
39 1 0.03
40 15 0.44
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (38 bp):
AAGCGCCGCTAATACTCAATTTAGCGGCGTTTTTTGTG
Found at i:44430521 original size:76 final size:76
Alignment explanation
Indices: 44430426--44430625 Score: 194
Period size: 78 Copynumber: 2.6 Consensus size: 76
44430416 GAAATTAGGG
* * *
44430426 ATGTATAT-ATTAGATTCGAATATGTATGAGTATACAAGTATAAGTTCATGTTTTGATTATAAG-
1 ATGTATATGA-TAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGA-AATAAGA
44430489 TATGTAA-TTATAT
64 TATG-AATTTATAT
* * * * * * *
44430502 ATGTATATGATAGACTCGAATATATAAATAAATATACATGTATAAATTCTTGTATTGAAATTAGA
1 ATGTATATGATAGATTCGAATATGT--ATGAGTATACATGTATAAGTTCATGTATTGAAATAAGA
44430567 TATGAATTTATAT
64 TATGAATTTATAT
* *
44430580 ATGTATATG-TGAGGTTCGAATGTGTATG-GTTATACATGTATAAGTT
1 ATGTATATGAT-AGATTCGAATATGTATGAG-TATACATGTATAAGTT
44430626 TTATATTGAA
Statistics
Matches: 100, Mismatches: 17, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
76 38 0.38
77 8 0.08
78 54 0.54
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (76 bp):
ATGTATATGATAGATTCGAATATGTATGAGTATACATGTATAAGTTCATGTATTGAAATAAGATA
TGAATTTATAT
Found at i:44431064 original size:41 final size:41
Alignment explanation
Indices: 44431018--44431169 Score: 241
Period size: 41 Copynumber: 3.7 Consensus size: 41
44431008 CAGGCTTAGC
44431018 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
* *
44431059 GCCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAA
1 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
* ** *
44431100 GCATAGCAGGCTAAGTGCTGGTGAACTGAATCAGGTTATAA
1 GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
44431141 GCCTAGCAGGCTAAGTGCCAGTGAATCTG
1 GCCTAGCAGGCTAAGTGCCAGTG-ATCTG
44431170 TTTAAATTAA
Statistics
Matches: 100, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 96 0.96
42 4 0.04
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (41 bp):
GCCTAGCAGGCTAAGTGCCAGTGATCTGAATCAGGTTATAA
Found at i:44431380 original size:36 final size:36
Alignment explanation
Indices: 44431340--44431435 Score: 101
Period size: 34 Copynumber: 2.7 Consensus size: 36
44431330 GTTGGATATA
* *
44431340 TATATATGTATGCATTCGACATATGTGGATT-ATAAG
1 TATATATGTATGCATTCGGCATATGTAG-TTGATAAG
44431376 TATATATG--TGCATTCGGCACT-TGTAGTTGATAAG
1 TATATATGTATGCATTCGGCA-TATGTAGTTGATAAG
* * *
44431410 TATAAATATATGCATTTGGCATATGT
1 TATATATGTATGCATTCGGCATATGT
44431436 TTTTGAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
33 2 0.04
34 25 0.50
35 2 0.04
36 21 0.42
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (36 bp):
TATATATGTATGCATTCGGCATATGTAGTTGATAAG
Found at i:44433451 original size:14 final size:14
Alignment explanation
Indices: 44433432--44433458 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44433422 TTCTAAAGGA
44433432 AAAAGAAAAAAATT
1 AAAAGAAAAAAATT
44433446 AAAAGAAAAAAAT
1 AAAAGAAAAAAAT
44433459 ATATTTTTTG
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:0.81, C:0.00, G:0.07, T:0.11
Consensus pattern (14 bp):
AAAAGAAAAAAATT
Found at i:44454535 original size:12 final size:12
Alignment explanation
Indices: 44454518--44454543 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
44454508 AATAAAACGA
44454518 AGCCAATAGTTT
1 AGCCAATAGTTT
44454530 AGCCAATAGTTT
1 AGCCAATAGTTT
44454542 AG
1 AG
44454544 TGACCATTTT
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:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (12 bp):
AGCCAATAGTTT
Found at i:44457986 original size:21 final size:21
Alignment explanation
Indices: 44457941--44458013 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
44457931 TGTTAAGTCA
* * * *
44457941 TATGAGTTTCTGTTTAACCTT
1 TATGGGTTTCCGTTCAACCCT
44457962 TATGGGTTTCCGTTCAACTCC-
1 TATGGGTTTCCGTTCAAC-CCT
* *
44457983 TATGAGCTTCCGTTCAACCCT
1 TATGGGTTTCCGTTCAACCCT
*
44458004 TACGGGTTTC
1 TATGGGTTTC
44458014 TGTTTAGCAC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.93
22 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TATGGGTTTCCGTTCAACCCT
Found at i:44461478 original size:25 final size:25
Alignment explanation
Indices: 44461446--44461498 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
44461436 ACTATTTTTC
44461446 TTAGATGCATTGTCAAAAAATAATT
1 TTAGATGCATTGTCAAAAAATAATT
44461471 TTAGATGCATTGTCAAAAAATAATT
1 TTAGATGCATTGTCAAAAAATAATT
44461496 TTA
1 TTA
44461499 AATTTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (25 bp):
TTAGATGCATTGTCAAAAAATAATT
Found at i:44472680 original size:13 final size:13
Alignment explanation
Indices: 44472662--44472686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44472652 ACAAACGATA
44472662 AAATTTTCACACG
1 AAATTTTCACACG
44472675 AAATTTTCACAC
1 AAATTTTCACAC
44472687 ACATAAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:44473117 original size:11 final size:11
Alignment explanation
Indices: 44473101--44473130 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
44473091 AGCAAGTAAA
44473101 TCTCATTCTCT
1 TCTCATTCTCT
44473112 TCTCATTCTCT
1 TCTCATTCTCT
44473123 TCTCATTC
1 TCTCATTC
44473131 CCATTCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.37, G:0.00, T:0.53
Consensus pattern (11 bp):
TCTCATTCTCT
Found at i:44476398 original size:33 final size:33
Alignment explanation
Indices: 44476356--44476614 Score: 130
Period size: 33 Copynumber: 7.6 Consensus size: 33
44476346 TAGATGCGGT
44476356 GGAATCAGCACTTAGCAACCACCAATGAATAGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
44476389 GGAATCAGCACTTAGCAACC-CC--TCG----GG
1 GGAATCAGCACTTAGCAACCACCAAT-GAATAGG
* *
44476416 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--T-GAATA-GG
*
44476458 TGGAATCAGCACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATAGG
** *
44476492 GGAATCAGCACACAGCAACC-CC--T---TGGG
1 GGAATCAGCACTTAGCAACCACCAATGAATAGG
* *
44476519 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA-CCAC---CA-A--T-GAATA-GG
* *
44476561 TGGAATCAGTACTTAGCAACCACCAATGAATCGG
1 -GGAATCAGCACTTAGCAACCACCAATGAATAGG
**
44476595 GGAATCAGCACACAGCAACC
1 GGAATCAGCACTTAGCAACC
44476615 CCTTTATATG
Statistics
Matches: 175, Mismatches: 18, Indels: 66
0.68 0.07 0.25
Matches are distributed among these distances:
27 39 0.22
28 4 0.02
29 2 0.01
30 2 0.01
31 1 0.01
32 6 0.03
33 55 0.31
34 4 0.02
35 6 0.03
36 2 0.01
37 2 0.01
38 2 0.01
39 4 0.02
41 1 0.01
42 10 0.06
43 35 0.20
ACGTcount: A:0.34, C:0.29, G:0.20, T:0.18
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATAGG
Found at i:44476494 original size:103 final size:103
Alignment explanation
Indices: 44476250--44476618 Score: 632
Period size: 103 Copynumber: 3.6 Consensus size: 103
44476240 TAACCGTTAT
* * *
44476250 CGGTGGATTCCGCACTTAGCAACCACCAATGAATCGGGGAATCAACACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
* * *
44476315 GAATCAGCACTTAGCAACCCCC-TTCACATTTTAGATG
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* ** *
44476352 CGGTGGAATCAGCACTTAGCAACCACCAATGAATAGGGGAATCAGCACTTAGCAACCCCTCGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
44476417 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
44476455 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
44476520 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
66 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
*
44476558 CGGTGGAATCAGTACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTT
44476619 TATATGCAAT
Statistics
Matches: 251, Mismatches: 15, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
102 80 0.32
103 171 0.68
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (103 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGG
GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:44489611 original size:18 final size:19
Alignment explanation
Indices: 44489578--44489615 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
44489568 AGACTCCAGG
*
44489578 TCTGATTATTTTCAATCAT
1 TCTGATTATCTTCAATCAT
44489597 TCTGATT-TCTTCAATCAT
1 TCTGATTATCTTCAATCAT
44489615 T
1 T
44489616 GCTTGCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (19 bp):
TCTGATTATCTTCAATCAT
Found at i:44496533 original size:13 final size:14
Alignment explanation
Indices: 44496504--44496532 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44496494 GGTCATATAA
44496504 TTGGTTGATATTTT
1 TTGGTTGATATTTT
44496518 TTGGTTGATATTTT
1 TTGGTTGATATTTT
44496532 T
1 T
44496533 GTGTGTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.21, T:0.66
Consensus pattern (14 bp):
TTGGTTGATATTTT
Found at i:44500749 original size:43 final size:43
Alignment explanation
Indices: 44500696--44501008 Score: 400
Period size: 43 Copynumber: 7.3 Consensus size: 43
44500686 TTATTTCTAA
* * *
44500696 AAACACCGCTAAAGACCATGACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
* * *
44500739 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTCTGCCAC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
* *
44500782 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTCTGCCGC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
**
44500825 AAACGCCGCTAAAGACCACGACCTTTAGCAACG-TTTCTGTCGC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTT-TGTCGC
*
44500868 AAATGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
* * * *
44500911 AAATGCCGTTAAAGACCACAACCTTTAGTGGCGCTTTTGTCGC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
* * * *
44500954 AAATGCCGCTATAGAACA-AACCTTTAGCGGCGC-TTT-TCGC
1 AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
44500994 AAAAACGCCGCTAAA
1 --AAACGCCGCTAAA
44501009 AACATATCAT
Statistics
Matches: 245, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
40 4 0.02
41 3 0.01
42 27 0.11
43 208 0.85
44 3 0.01
ACGTcount: A:0.27, C:0.31, G:0.20, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCACGACCTTTAGCGGCGCTTTTGTCGC
Found at i:44501064 original size:18 final size:19
Alignment explanation
Indices: 44501041--44501076 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44501031 TTTTAATCAA
*
44501041 ATAAATTTTAT-TTTTATG
1 ATAAATATTATGTTTTATG
44501059 ATAAATATTATGTTTTAT
1 ATAAATATTATGTTTTAT
44501077 TTTTTAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
ATAAATATTATGTTTTATG
Found at i:44501977 original size:43 final size:43
Alignment explanation
Indices: 44501914--44502076 Score: 238
Period size: 43 Copynumber: 3.8 Consensus size: 43
44501904 GCATCACTAA
*
44501914 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGACCAAGAC
*
44501957 CTTTAACGGCGCTTTACCCACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGACCAAGAC
* * * *
44502000 CTTTAGCGACGCTTTACCCACAAACGCCGCTAAAAATCATGAC
1 CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGACCAAGAC
* *
44502043 CTTTAGCGGCGCTTCTA-GCAAAAACGCCGCTAAA
1 CTTTAGCGGCGCTT-TACCCACAAACGCCGCTAAA
44502077 AATATAACCT
Statistics
Matches: 109, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 107 0.98
44 2 0.02
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGACCAAGAC
Found at i:44502261 original size:35 final size:35
Alignment explanation
Indices: 44502226--44502293 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
44502216 CTATGAAAAT
44502226 TTTAACTTTA-AAAGTAAATATAA-AAATTAATAAA
1 TTTAACTTTAGAAAGTAAA-ATAATAAATTAATAAA
* **
44502260 TTTAATTTTAGAATTTAAAATAATAAATTAATAA
1 TTTAACTTTAGAAAGTAAAATAATAAATTAATAA
44502294 CACAATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 13 0.45
35 16 0.55
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (35 bp):
TTTAACTTTAGAAAGTAAAATAATAAATTAATAAA
Found at i:44502822 original size:23 final size:23
Alignment explanation
Indices: 44502772--44502823 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
44502762 GTTAGGTGTC
* *
44502772 AGTATAAAGACATGTCAGATATG
1 AGTATGAAGACATGTCAGAGATG
* * *
44502795 GGTATGAAGGCATGTCTGAGATG
1 AGTATGAAGACATGTCAGAGATG
44502818 AGTATG
1 AGTATG
44502824 TTCAAAGTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.31, T:0.27
Consensus pattern (23 bp):
AGTATGAAGACATGTCAGAGATG
Found at i:44507526 original size:33 final size:33
Alignment explanation
Indices: 44507488--44507551 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
44507478 TAATCTAAAT
* * *
44507488 CCTAAACCCTAACCCGATCCTGAATCCCTAATC
1 CCTAAACCCTAACCCAACCCTGAACCCCTAATC
*
44507521 CCTAAACTCTAACCCAACCCTGAACCCCTAA
1 CCTAAACCCTAACCCAACCCTGAACCCCTAA
44507552 ACATTATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.33, C:0.44, G:0.05, T:0.19
Consensus pattern (33 bp):
CCTAAACCCTAACCCAACCCTGAACCCCTAATC
Found at i:44510424 original size:22 final size:23
Alignment explanation
Indices: 44510381--44510426 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
44510371 AGTTAAGTGA
**
44510381 TTTTATAAAATATTTTTATTATT
1 TTTTATAAAATAAATTTATTATT
*
44510404 TTTTATAAATTAAATTT-TTATT
1 TTTTATAAAATAAATTTATTATT
44510426 T
1 T
44510427 AAAAAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATAAAATAAATTTATTATT
Found at i:44510939 original size:21 final size:20
Alignment explanation
Indices: 44510914--44510966 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 20
44510904 CTAAATCTTA
* *
44510914 AACCCTAAATCCTTAACTCCT
1 AACCCTAAA-CCTTAAATCCC
44510935 AACCCTTAAACCTTAAATCCC
1 AACCC-TAAACCTTAAATCCC
*
44510956 AACCTTAAACC
1 AACCCTAAACC
44510967 ATAATCCCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 18 0.64
22 4 0.14
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (20 bp):
AACCCTAAACCTTAAATCCC
Found at i:44510996 original size:15 final size:15
Alignment explanation
Indices: 44510961--44510998 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
44510951 ATCCCAACCT
44510961 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
44510975 T-AATCCATAATCCC
1 TAAATCCATAATCCC
44510989 TAAATCCATA
1 TAAATCCATA
44510999 TATAATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:44511250 original size:7 final size:7
Alignment explanation
Indices: 44511238--44511385 Score: 95
Period size: 7 Copynumber: 21.0 Consensus size: 7
44511228 ACTAGTTAAT
44511238 CTAAACC
1 CTAAACC
44511245 CTAAACC
1 CTAAACC
*
44511252 ATAAA-C
1 CTAAACC
*
44511258 TTAAACC
1 CTAAACC
*
44511265 CTAAAATC
1 CT-AAACC
*
44511273 ATAAACC
1 CTAAACC
* *
44511280 CTTAACG
1 CTAAACC
44511287 C-ATAACC
1 CTA-AACC
44511294 TCTAAACC
1 -CTAAACC
*
44511302 TTAAACC
1 CTAAACC
*
44511309 CT-AGCC
1 CTAAACC
*
44511315 TTTAAACC
1 -CTAAACC
*
44511323 ATAAACC
1 CTAAACC
*
44511330 ATAAACC
1 CTAAACC
*
44511337 ATAAACC
1 CTAAACC
44511344 CTAAACC
1 CTAAACC
*
44511351 GTAAACC
1 CTAAACC
*
44511358 ATAAACC
1 CTAAACC
44511365 CTAAACC
1 CTAAACC
* *
44511372 ATATACC
1 CTAAACC
44511379 CTAAACC
1 CTAAACC
44511386 AAAAGCTCTA
Statistics
Matches: 109, Mismatches: 25, Indels: 14
0.74 0.17 0.09
Matches are distributed among these distances:
6 8 0.07
7 87 0.80
8 13 0.12
9 1 0.01
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:44511383 original size:21 final size:20
Alignment explanation
Indices: 44511239--44511385 Score: 106
Period size: 21 Copynumber: 7.3 Consensus size: 20
44511229 CTAGTTAATC
* *
44511239 TAAACCCTAAACCATAAACT
1 TAAACCCTAAACCATAACCA
44511259 TAAACCCTAAA--AT---CA
1 TAAACCCTAAACCATAACCA
* *
44511274 TAAACCCTTAACGCATAACCTC
1 TAAACCCTAAAC-CATAACC-A
* * * *
44511296 TAAACCTTAAACCCTAGCCTT
1 TAAACCCTAAACCATAACC-A
*
44511317 TAAACCATAAACCATAAACCA
1 TAAACCCTAAACCAT-AACCA
*
44511338 TAAACCCTAAACCGTAAACCA
1 TAAACCCTAAACCAT-AACCA
*
44511359 TAAACCCTAAACCATATACCC
1 TAAACCCTAAACCATA-ACCA
44511380 TAAACC
1 TAAACC
44511386 AAAAGCTCTA
Statistics
Matches: 102, Mismatches: 16, Indels: 17
0.76 0.12 0.13
Matches are distributed among these distances:
15 11 0.11
18 4 0.04
20 12 0.12
21 62 0.61
22 13 0.13
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.20
Consensus pattern (20 bp):
TAAACCCTAAACCATAACCA
Found at i:44511639 original size:22 final size:22
Alignment explanation
Indices: 44511611--44511654 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
44511601 TTAGAAAACG
*
44511611 CCGCTAAAAGCCCTGAGCATTA
1 CCGCTAAAAGCCATGAGCATTA
*
44511633 CCGCTAAAAGTCATGAGCATTA
1 CCGCTAAAAGCCATGAGCATTA
44511655 GCGGCGCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.20
Consensus pattern (22 bp):
CCGCTAAAAGCCATGAGCATTA
Found at i:44511738 original size:41 final size:41
Alignment explanation
Indices: 44511646--44511928 Score: 383
Period size: 41 Copynumber: 6.9 Consensus size: 41
44511636 CTAAAAGTCA
* *
44511646 TGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAGCCA
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCT-AAAGCCC
* ** *
44511688 TGAGCATTAGCGCCGCTTTCTTAAAAATGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
** *
44511729 TGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* *
44511770 TAAGCATTAGCGGCACTTTCCCAAAAACGCCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
*
44511811 TGAGCATTAGCGGCGC-TTCCCAAAAACGTCGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
* * *
44511851 TTAGCATTAGCGGCAC-TTCGCCAAAAACGCTGCTAAAGCCC
1 TGAGCATTAGCGGCGCTTTC-CCAAAAACGCCGCTAAAGCCC
44511892 TGAGCATTAGCGGCGC-TTCGCCAAAAACGCCGCTAAA
1 TGAGCATTAGCGGCGCTTTC-CCAAAAACGCCGCTAAA
44511929 TCCCCAAAAA
Statistics
Matches: 216, Mismatches: 24, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
40 40 0.19
41 147 0.68
42 29 0.13
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCC
Found at i:44511875 original size:81 final size:82
Alignment explanation
Indices: 44511646--44511928 Score: 392
Period size: 81 Copynumber: 3.5 Consensus size: 82
44511636 CTAAAAGTCA
* * * * * **
44511646 TGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAGCCATGAGCATTAGCGCCGCTTTCTTA
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCT-AAAGCCCTAAGCATTAGCGGCACTTTCCCA
*
44511711 AAAATGCCGCTAAAGCCC
65 AAAACGCCGCTAAAGCCC
** *
44511729 TGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAAGCCCTAAGCATTAGCGGCACTTTCCCAA
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCACTTTCCCAA
44511794 AAACGCCGCTAAAGCCC
66 AAACGCCGCTAAAGCCC
* *
44511811 TGAGCATTAGCGGCGC-TTCCCAAAAACGTCGCTAAAGCCCTTAGCATTAGCGGCAC-TTCGCCA
1 TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCACTTTC-CCA
*
44511874 AAAACGCTGCTAAAGCCC
65 AAAACGCCGCTAAAGCCC
44511892 TGAGCATTAGCGGCGC-TTCGCCAAAAACGCCGCTAAA
1 TGAGCATTAGCGGCGCTTTC-CCAAAAACGCCGCTAAA
44511929 TCCCCAAAAA
Statistics
Matches: 180, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
80 3 0.02
81 74 0.41
82 73 0.41
83 30 0.17
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (82 bp):
TGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCCTAAGCATTAGCGGCACTTTCCCAA
AAACGCCGCTAAAGCCC
Found at i:44511877 original size:122 final size:123
Alignment explanation
Indices: 44511648--44511928 Score: 397
Period size: 122 Copynumber: 2.3 Consensus size: 123
44511638 AAAAGTCATG
* **
44511648 AGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAGCCATGAGCATTAGCGCCGCTTTCTTAAA
1 AGCATTAGCGGCGCTTTCCCAAAAACGCCGCT-AAAGCCATGAGCATTAGCGCCGCTTTCCCAAA
* * **
44511713 AATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAAGCCCTA
65 AACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCCCAAAAACGCTGCTAAAGCCCTA
* * *
44511772 AGCATTAGCGGCACTTTCCCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGC-TTCCCAAAA
1 AGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCATGAGCATTAGCGCCGCTTTCCCAAAA
* * *
44511836 ACGTCGCTAAAGCCCTTAGCATTAGCGGCAC-TTCGCCAAAAACGCTGCTAAAGCCCTG
66 ACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTC-CCAAAAACGCTGCTAAAGCCCTA
44511894 AGCATTAGCGGCGC-TTCGCCAAAAACGCCGCTAAA
1 AGCATTAGCGGCGCTTTC-CCAAAAACGCCGCTAAA
44511929 TCCCCAAAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
121 6 0.04
122 84 0.60
123 21 0.15
124 30 0.21
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.20
Consensus pattern (123 bp):
AGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGCCATGAGCATTAGCGCCGCTTTCCCAAAA
ACGCCGCTAAAGCCCTGAGCATTAGCGGCACTTTCCCAAAAACGCTGCTAAAGCCCTA
Found at i:44519480 original size:30 final size:30
Alignment explanation
Indices: 44519446--44519510 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
44519436 AGATAGTAGC
44519446 AACTTGAGTAAATAAACTTATTCCACCTCT
1 AACTTGAGTAAATAAACTTATTCCACCTCT
44519476 AACTTGAGTAAATAAACTTATTCCACCTCT
1 AACTTGAGTAAATAAACTTATTCCACCTCT
*
44519506 GACTT
1 AACTT
44519511 TCATCATTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.35, C:0.23, G:0.08, T:0.34
Consensus pattern (30 bp):
AACTTGAGTAAATAAACTTATTCCACCTCT
Found at i:44531629 original size:21 final size:23
Alignment explanation
Indices: 44531574--44531630 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
44531564 GTACTTCAAA
44531574 TTTGTGAGATTATAATTGAATAATC
1 TTTGTGAGATTATAATT--ATAATC
* *
44531599 ATTG-GCGATTATAATT-TAAT-
1 TTTGTGAGATTATAATTATAATC
44531619 TTTGTGAGATTA
1 TTTGTGAGATTA
44531631 AGCTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
20 3 0.11
21 10 0.37
24 11 0.41
25 3 0.11
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (23 bp):
TTTGTGAGATTATAATTATAATC
Found at i:44536856 original size:507 final size:506
Alignment explanation
Indices: 44535904--44536922 Score: 2020
Period size: 507 Copynumber: 2.0 Consensus size: 506
44535894 TTTGTTTCTC
44535904 CTTCTCAATACCTCTTGCATCCACTTCTTTTTCTTTCATTTCATTTCATATAATCACCACAAAAT
1 CTTCTCAATACCTCTTGCATCCACTTCTTTTTCTTTCATTTCATTTCATATAATCACCACAAAAT
44535969 ATAAAAAAAATCAAAATACTCGTCAAATGACACTTTATACGGTTGTCGAAACCACCAAAACTAAA
66 ATAAAAAAAATCAAAATACTCGTCAAATGACACTTTATACGGTTGTCGAAACCACCAAAACTAAA
44536034 TTCCTAATTAAAAAGAAATTTACAGATAGCAGTGAATAGAGTTGAATCCACAGAGACCGATGATA
131 TTCCTAATTAAAAAGAAATTTACAGATAGCAGTGAATAGAGTTGAATCCACAGAGACCGATGATA
44536099 ATTCTATTTATTCAATAAATATTAATAAAATAAAAGATGAATGGGAGTTAAGAAAACTTAAAATT
196 ATTCTATTTATTCAATAAATATTAATAAAATAAAAGATGAATGGGAGTTAAGAAAACTTAAAATT
44536164 TAACCAAAACTAAAGAAAACTAAATTTAAAACTTAGCAAAAAAGCAATAATTAGAAGTTAAAAGA
261 TAACCAAAACTAAAGAAAACTAAATTTAAAACTTAGCAAAAAAGCAATAATTAGAAGTTAAAAGA
*
44536229 AAATCAATATGACAAATCTCTAGTTAAAAGTAATATCTTCGCTTGATTCGTGATTTTTATCACCA
326 AAATCAATATGACAAATCTCTAGCTAAAAGTAATATCTTCGCTTGATTCGTGATTTTTATCACCA
44536294 ATGAAAAGATAGTTTTTAGTGTTCTTTGATAAACTAGTTACAGTTGTCGATGTCGCACCTAACAA
391 ATGAAAAGATAGTTTTTAGTGTTCTTTGATAAACTAGTTACAGTTGTCGATGTCGCACCTAACAA
44536359 CCAATCTTTCATTATCATCTCGATAACCAAGGGGTAGCTCGTTTGAAATTA
456 CCAATCTTTCATTATCATCTCGATAACCAAGGGGTAGCTCGTTTGAAATTA
44536410 CTTCTCAATACCTCTTGCATCCACTTCTTTTTCTTTCATTTCATTTCATATAATCACCACAAAAT
1 CTTCTCAATACCTCTTGCATCCACTTCTTTTTCTTTCATTTCATTTCATATAATCACCACAAAAT
44536475 ATAAAAAAAAATCAAAATACTCGTCAAATGACACTTTATACGGTTGTCGAAACCACCAAAACTAA
66 AT-AAAAAAAATCAAAATACTCGTCAAATGACACTTTATACGGTTGTCGAAACCACCAAAACTAA
44536540 ATTCCTAATTAAAAAGAAATTTACAGATAGCAGTGAATAGAGTTGAATCCACAGAGACCGATGAT
130 ATTCCTAATTAAAAAGAAATTTACAGATAGCAGTGAATAGAGTTGAATCCACAGAGACCGATGAT
44536605 AATTCTATTTATTCAATAAATATTAATAAAATAAAAGATGAATGGGAGTTAAGAAAACTTAAAAT
195 AATTCTATTTATTCAATAAATATTAATAAAATAAAAGATGAATGGGAGTTAAGAAAACTTAAAAT
44536670 TTAACCAAAACTAAAGAAAACTAAATTTAAAACTTAGCAAAAAAGCAATAATTAGAAGTTAAAAG
260 TTAACCAAAACTAAAGAAAACTAAATTTAAAACTTAGCAAAAAAGCAATAATTAGAAGTTAAAAG
44536735 AAAATCAATATGACAAATCTCTAGCTAAAAGTAATATCTTCGCTTGATTCGTGATTTTTATCACC
325 AAAATCAATATGACAAATCTCTAGCTAAAAGTAATATCTTCGCTTGATTCGTGATTTTTATCACC
44536800 AATGAAAAGATAGTTTTTAGTGTTCTTTGATAAACTAGTTACAGTTGTCGATGTCGCACCTAACA
390 AATGAAAAGATAGTTTTTAGTGTTCTTTGATAAACTAGTTACAGTTGTCGATGTCGCACCTAACA
44536865 ACCAATCTTTCATTATCATCTCGATAACCAAGGGGTAGCTCGTTTGAAATTA
455 ACCAATCTTTCATTATCATCTCGATAACCAAGGGGTAGCTCGTTTGAAATTA
44536917 CTTCTC
1 CTTCTC
44536923 TTACTAATAA
Statistics
Matches: 511, Mismatches: 1, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
506 67 0.13
507 444 0.87
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (506 bp):
CTTCTCAATACCTCTTGCATCCACTTCTTTTTCTTTCATTTCATTTCATATAATCACCACAAAAT
ATAAAAAAAATCAAAATACTCGTCAAATGACACTTTATACGGTTGTCGAAACCACCAAAACTAAA
TTCCTAATTAAAAAGAAATTTACAGATAGCAGTGAATAGAGTTGAATCCACAGAGACCGATGATA
ATTCTATTTATTCAATAAATATTAATAAAATAAAAGATGAATGGGAGTTAAGAAAACTTAAAATT
TAACCAAAACTAAAGAAAACTAAATTTAAAACTTAGCAAAAAAGCAATAATTAGAAGTTAAAAGA
AAATCAATATGACAAATCTCTAGCTAAAAGTAATATCTTCGCTTGATTCGTGATTTTTATCACCA
ATGAAAAGATAGTTTTTAGTGTTCTTTGATAAACTAGTTACAGTTGTCGATGTCGCACCTAACAA
CCAATCTTTCATTATCATCTCGATAACCAAGGGGTAGCTCGTTTGAAATTA
Found at i:44538478 original size:10 final size:10
Alignment explanation
Indices: 44538449--44538507 Score: 57
Period size: 10 Copynumber: 5.6 Consensus size: 10
44538439 GTCCACGTAT
44538449 AATTTATAAAA
1 AATTTA-AAAA
*
44538460 AATAGTAAAAA
1 AAT-TTAAAAA
44538471 AATTTAAAAA
1 AATTTAAAAA
44538481 AA-TTAATAAA
1 AATTTAA-AAA
*
44538491 AACTTTTAAAA
1 AA-TTTAAAAA
44538502 AATTTA
1 AATTTA
44538508 TTCATGTTAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 4 0.10
10 16 0.40
11 15 0.38
12 5 0.12
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (10 bp):
AATTTAAAAA
Found at i:44538482 original size:21 final size:22
Alignment explanation
Indices: 44538449--44538503 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
44538439 GTCCACGTAT
*
44538449 AATTTATAAAAAA-TAGTAAAAA
1 AATTTA-AAAAAATTAATAAAAA
44538471 AATTTAAAAAAATTAATAAAAA
1 AATTTAAAAAAATTAATAAAAA
**
44538493 CTTTTAAAAAA
1 AATTTAAAAAA
44538504 TTTATTCATG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (22 bp):
AATTTAAAAAAATTAATAAAAA
Found at i:44538504 original size:21 final size:19
Alignment explanation
Indices: 44538449--44538505 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 19
44538439 GTCCACGTAT
44538449 AATTTATAAAAAATAGTAAAAA
1 AATTT-TAAAAAAT--TAAAAA
*
44538471 AATTTAAAAAAATTAATAAA
1 AATTTTAAAAAATTAA-AAA
44538491 AACTTTTAAAAAATT
1 AA-TTTTAAAAAATT
44538506 TATTCATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 3 0.10
20 5 0.16
21 18 0.58
22 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (19 bp):
AATTTTAAAAAATTAAAAA
Found at i:44539478 original size:21 final size:21
Alignment explanation
Indices: 44539448--44539488 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44539438 TTCGGGCTTC
*
44539448 TACTCAGCCTGGTTGATGGAA
1 TACTCAGCCTGATTGATGGAA
*
44539469 TACTCGGCCTGATTGATGGA
1 TACTCAGCCTGATTGATGGA
44539489 CAAGTCTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (21 bp):
TACTCAGCCTGATTGATGGAA
Found at i:44541050 original size:11 final size:11
Alignment explanation
Indices: 44541030--44541129 Score: 67
Period size: 11 Copynumber: 9.6 Consensus size: 11
44541020 ACAAAAATTA
44541030 AAAAAGTATTTT
1 AAAAA-TATTTT
44541042 AAAAATATTTT
1 AAAAATATTTT
44541053 --AAA-A--TT
1 AAAAATATTTT
* *
44541059 AAAAA-AATTA
1 AAAAATATTTT
44541069 AAAAAGTATTTT
1 AAAAA-TATTTT
44541081 AAAAATATTTT
1 AAAAATATTTT
44541092 --AAA-ATTTT
1 AAAAATATTTT
*
44541100 AAAAAT-TTTAA
1 AAAAATATTT-T
44541111 AAAAAGTATTTT
1 AAAAA-TATTTT
44541123 AAAAATA
1 AAAAATA
44541130 AAAAAATATT
Statistics
Matches: 71, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
6 2 0.03
8 10 0.14
9 6 0.08
10 12 0.17
11 19 0.27
12 19 0.27
13 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:44541074 original size:39 final size:39
Alignment explanation
Indices: 44541004--44541129 Score: 171
Period size: 39 Copynumber: 3.1 Consensus size: 39
44540994 ACCAAAAATT
44541004 TATTTTAAAAATTAAAACAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAGTATTTTAAAAA
44541047 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
**
44541086 TATTTTAAAATTTTAAAAATTTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAA--TTAAAAAAATT-AAAAAAGTATTTTAAAAA
44541128 TA
1 TA
44541130 AAAAAATATT
Statistics
Matches: 78, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
39 35 0.45
40 2 0.03
41 9 0.12
42 26 0.33
43 6 0.08
ACGTcount: A:0.60, C:0.01, G:0.02, T:0.37
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:44541106 original size:9 final size:9
Alignment explanation
Indices: 44541037--44541113 Score: 64
Period size: 9 Copynumber: 8.1 Consensus size: 9
44541027 TTAAAAAAGT
44541037 ATTTTAAAA
1 ATTTTAAAA
*
44541046 ATATTTTAAA
1 AT-TTTAAAA
**
44541056 ATTAAAAAA
1 ATTTTAAAA
**
44541065 ATTAAAAAA
1 ATTTTAAAA
44541074 GTATTTTAAAA
1 --ATTTTAAAA
*
44541085 ATATTTTAAA
1 AT-TTTAAAA
44541095 ATTTTAAAA
1 ATTTTAAAA
44541104 ATTTTAAAA
1 ATTTTAAAA
44541113 A
1 A
44541114 AAGTATTTTA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
9 33 0.59
10 16 0.29
11 7 0.12
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (9 bp):
ATTTTAAAA
Found at i:44541135 original size:31 final size:31
Alignment explanation
Indices: 44541061--44541141 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
44541051 TTAAAATTAA
* *
44541061 AAAAATTAAAAAAGTATTT-TAAAAATATTTT
1 AAAAA-TAAAAAAATATTTAAAAAAATATTTT
* **
44541092 AAAATTTTAAAAAT-TTTAAAAAAAGTATTTT
1 AAAAATAAAAAAATATTTAAAAAAA-TATTTT
44541123 AAAAATAAAAAAATATTTA
1 AAAAATAAAAAAATATTTA
44541142 TTATATTCGG
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
29 3 0.08
30 11 0.28
31 21 0.54
32 4 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
AAAAATAAAAAAATATTTAAAAAAATATTTT
Found at i:44541578 original size:20 final size:20
Alignment explanation
Indices: 44541553--44541593 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
44541543 TTAAAAGTCC
44541553 AAAAAATATATATATTTAAT
1 AAAAAATATATATATTTAAT
44541573 AAAAAATATATATATTTAAT
1 AAAAAATATATATATTTAAT
44541593 A
1 A
44541594 TATAATTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAAATATATATATTTAAT
Found at i:44550329 original size:24 final size:25
Alignment explanation
Indices: 44550297--44550343 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
44550287 AAATCAAACT
44550297 TAATCACTTTAA-TATTAAATTAATA
1 TAATCAC-TTAAGTATTAAATTAATA
*
44550322 TAAT-ACTTAAGTATTAGATTAA
1 TAATCACTTAAGTATTAAATTAA
44550344 ATTTAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (25 bp):
TAATCACTTAAGTATTAAATTAATA
Found at i:44552431 original size:19 final size:21
Alignment explanation
Indices: 44552409--44552454 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
44552399 TAATTAAAAC
44552409 AACTAAATA-A-GATTAATTA
1 AACTAAATACATGATTAATTA
*
44552428 AACTATATACATGATTAATTA
1 AACTAAATACATGATTAATTA
*
44552449 AGCTAA
1 AACTAA
44552455 TCATTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (21 bp):
AACTAAATACATGATTAATTA
Found at i:44572561 original size:32 final size:32
Alignment explanation
Indices: 44572525--44572591 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
44572515 ATGTATAATA
*
44572525 AAACAAAAT-AAAAGAAATAGAAAAAGAAAAAG
1 AAACAAAATGAAAAGAAACAGAAAAA-AAAAAG
* * *
44572557 AAACAAAGTGAAACGAAACAGAAAGAAAAAAG
1 AAACAAAATGAAAAGAAACAGAAAAAAAAAAG
44572589 AAA
1 AAA
44572592 GAAGGAGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.75, C:0.06, G:0.15, T:0.04
Consensus pattern (32 bp):
AAACAAAATGAAAAGAAACAGAAAAAAAAAAG
Found at i:44573292 original size:24 final size:24
Alignment explanation
Indices: 44573265--44573311 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
44573255 ATTGAAATAG
44573265 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
44573289 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
44573312 GATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:44573576 original size:40 final size:40
Alignment explanation
Indices: 44573531--44573607 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
44573521 AGGTACCAAT
** *
44573531 TTACTTCGGTTTAACCAATGAGACACTGGGTGTCAAATTA
1 TTACTTCGAATTAACCAATGAGACACTGGGTGCCAAATTA
* * *
44573571 TTACTTTGAATTATCCAATGAGGCACTGGGTGCCAAA
1 TTACTTCGAATTAACCAATGAGACACTGGGTGCCAAA
44573608 CTAGTGTGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (40 bp):
TTACTTCGAATTAACCAATGAGACACTGGGTGCCAAATTA
Found at i:44590947 original size:19 final size:19
Alignment explanation
Indices: 44590923--44590994 Score: 117
Period size: 19 Copynumber: 3.8 Consensus size: 19
44590913 AATCATATAT
44590923 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
44590942 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
*
44590961 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
44590980 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
44590995 TCTCAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.36, C:0.14, G:0.11, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:44596577 original size:46 final size:46
Alignment explanation
Indices: 44596510--44596740 Score: 347
Period size: 46 Copynumber: 5.0 Consensus size: 46
44596500 CATGGCAAAG
*
44596510 TGTGAAACGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
44596556 TGTGAAAAATAGGTATGGTATTTC-GATAAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAG-TGAAGAAAACCATACTGAGT
* *
44596602 TGTAAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* * * *
44596648 TGTGAAAAGTAGGTATGGTGTTTTAGTAAAAAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
* *
44596694 TGTGAAAAGTAGGTATGGTATTTCCGTGAAGCAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
44596740 T
1 T
44596741 ATAGCAATGT
Statistics
Matches: 166, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.01
46 164 0.99
47 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGT
Found at i:44599429 original size:27 final size:27
Alignment explanation
Indices: 44599391--44599448 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
44599381 TTTCGGACTT
44599391 GAAATCAAATGATTTAAAGTGTATTTA
1 GAAATCAAATGATTTAAAGTGTATTTA
*
44599418 GAAATCAAATGATTTAAAGTGTATTTC
1 GAAATCAAATGATTTAAAGTGTATTTA
44599445 GAAA
1 GAAA
44599449 CTAAAAGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (27 bp):
GAAATCAAATGATTTAAAGTGTATTTA
Found at i:44610123 original size:24 final size:24
Alignment explanation
Indices: 44610099--44610179 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
44610089 TTTTTATATT
*
44610099 ATTATTTATATAAATATATAAATTA
1 ATTATATATATAAATAT-TAAATTA
* *
44610124 ATTATAAAGTAT-ATTATTAAATTA
1 ATTATATA-TATAAATATTAAATTA
*
44610148 ATTATAT-TATAAATATTATATT-
1 ATTATATATATAAATATTAAATTA
44610170 ATTATATATA
1 ATTATATATA
44610180 AAAGAAACAA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 10 0.21
23 11 0.23
24 13 0.28
25 10 0.21
26 3 0.06
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (24 bp):
ATTATATATATAAATATTAAATTA
Found at i:44610131 original size:11 final size:11
Alignment explanation
Indices: 44610115--44610153 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
44610105 TATATAAATA
44610115 TATAAATTAAT
1 TATAAATTAAT
*
44610126 TATAAAGTATAT
1 TATAAATTA-AT
44610138 TATTAAATTAAT
1 TA-TAAATTAAT
44610150 TATA
1 TATA
44610154 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:44610155 original size:17 final size:15
Alignment explanation
Indices: 44610098--44610178 Score: 60
Period size: 15 Copynumber: 5.2 Consensus size: 15
44610088 ATTTTTATAT
44610098 TATTAT-TTATATAAA
1 TATTATATTAT-TAAA
*
44610113 TATATAAATTAATTATAA
1 TAT-TATATT-ATTA-AA
*
44610131 -AGTATATTATTAAA
1 TATTATATTATTAAA
44610145 TTAATTATATTA-TAAA
1 -T-ATTATATTATTAAA
*
44610161 TATTATATTATTATA
1 TATTATATTATTAAA
44610176 TAT
1 TAT
44610179 AAAAGAAACA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
14 11 0.21
15 14 0.26
16 11 0.21
17 13 0.25
18 4 0.08
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (15 bp):
TATTATATTATTAAA
Found at i:44610165 original size:14 final size:16
Alignment explanation
Indices: 44610133--44610171 Score: 55
Period size: 14 Copynumber: 2.5 Consensus size: 16
44610123 AATTATAAAG
44610133 TATATTATTAAATTAAT
1 TATATTA-TAAATTAAT
44610150 TATATTATAAA-T-AT
1 TATATTATAAATTAAT
44610164 TATATTAT
1 TATATTAT
44610172 TATATATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 4 0.18
17 7 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTATAAATTAAT
Found at i:44610489 original size:3 final size:3
Alignment explanation
Indices: 44610481--44610519 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
44610471 GTGAGGTAAG
44610481 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44610520 GAGTGGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44610703 original size:24 final size:27
Alignment explanation
Indices: 44610671--44610729 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
44610661 CGGATTAGTT
44610671 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
44610694 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
44610721 ATTGAATTG
1 ATTGAATTG
44610730 GGATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:44610933 original size:37 final size:39
Alignment explanation
Indices: 44610874--44610969 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
44610864 CGGATAGATT
* * * *
44610874 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
44610911 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
44610950 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
44610970 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:44616799 original size:3 final size:3
Alignment explanation
Indices: 44616791--44616829 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
44616781 GTGAGGTAAG
44616791 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
44616830 GAGTGGGAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:44617013 original size:24 final size:27
Alignment explanation
Indices: 44616981--44617039 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
44616971 CGGATTAGTT
44616981 ATTG-ATTGAAAG-GTG-GAAA-AATG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
**
44617004 ATTGAATTGAAAGTGTGAGAAAGTGTG
1 ATTGAATTGAAAGTGTGAGAAAGAATG
44617031 ATTGAATTG
1 ATTGAATTG
44617040 GGATTATATG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 4 0.13
24 8 0.27
25 3 0.10
26 4 0.13
27 11 0.37
ACGTcount: A:0.39, C:0.00, G:0.31, T:0.31
Consensus pattern (27 bp):
ATTGAATTGAAAGTGTGAGAAAGAATG
Found at i:44617243 original size:37 final size:39
Alignment explanation
Indices: 44617184--44617279 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
44617174 CGGATAGATT
* * * *
44617184 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
44617221 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
44617260 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
44617280 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:44619229 original size:41 final size:41
Alignment explanation
Indices: 44619173--44619283 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
44619163 TTTAACATAT
* ** *
44619173 TCACCGGCACTTAGCCTGCTAGGCTTATTGCCTGATTCATA
1 TCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
44619214 TCACCAGCA-TGTAGCCTGCTAGGTTTATAACCTGATTCCGA
1 TCACCAGCACT-TAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
44619255 TCACCGGCACTTAGCCTGCTAGACTTATA
1 TCACCAGCACTTAGCCTGCTAGGCTTATA
44619284 GTCTGAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 57 0.97
42 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.30
Consensus pattern (41 bp):
TCACCAGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:44621214 original size:13 final size:13
Alignment explanation
Indices: 44621196--44621220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44621186 CAATCAAATG
44621196 CACACAAAATAAA
1 CACACAAAATAAA
44621209 CACACAAAATAA
1 CACACAAAATAA
44621221 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:44622951 original size:22 final size:22
Alignment explanation
Indices: 44622925--44622966 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44622915 GAATAAGATA
44622925 TAAATTGGATTGAAA-TGAGTAT
1 TAAATTGGATT-AAATTGAGTAT
*
44622947 TAAATTGTATTAAATTGAGT
1 TAAATTGGATTAAATTGAGT
44622967 TAATTTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.40, C:0.00, G:0.19, T:0.40
Consensus pattern (22 bp):
TAAATTGGATTAAATTGAGTAT
Found at i:44633376 original size:9 final size:9
Alignment explanation
Indices: 44633282--44633375 Score: 134
Period size: 9 Copynumber: 10.4 Consensus size: 9
44633272 GTAGTGATTC
*
44633282 AATTTGGTT
1 AATTCGGTT
44633291 AATTCGGTT
1 AATTCGGTT
*
44633300 AATTCGGGT
1 AATTCGGTT
44633309 AATTCGGTT
1 AATTCGGTT
44633318 AATTCGGTT
1 AATTCGGTT
* *
44633327 AACTCGGGT
1 AATTCGGTT
*
44633336 AATTCGGGT
1 AATTCGGTT
44633345 AATTCGGTT
1 AATTCGGTT
44633354 AATTCGGTT
1 AATTCGGTT
*
44633363 AATTTGGTT
1 AATTCGGTT
44633372 AATT
1 AATT
44633376 TTTAACCAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 77 1.00
ACGTcount: A:0.23, C:0.10, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:44634272 original size:42 final size:42
Alignment explanation
Indices: 44634210--44634315 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
44634200 CTACGGGTCA
* * * *
44634210 CACCACAACACCACCTACCAATCTTCATACTCTTATGGACCC
1 CACCACAACACCACCCACCAATCTTCACACTCCTATAGACCC
* * *
44634252 CATCACAACACCACCCACCAATCTTCCCACTCCTATAGATCC
1 CACCACAACACCACCCACCAATCTTCACACTCCTATAGACCC
* *
44634294 CACCACAACACTATCCACCAAT
1 CACCACAACACCACCCACCAAT
44634316 TTAACGTCTC
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.33, C:0.45, G:0.03, T:0.19
Consensus pattern (42 bp):
CACCACAACACCACCCACCAATCTTCACACTCCTATAGACCC
Found at i:44639216 original size:17 final size:17
Alignment explanation
Indices: 44639176--44639220 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
44639166 TCTTAATCAC
44639176 ATTAATATTAAATTAAT
1 ATTAATATTAAATTAAT
* *
44639193 ATAAATATTAGATTAA-
1 ATTAATATTAAATTAAT
44639209 ATTTAATATTAA
1 A-TTAATATTAA
44639221 CTCTTATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
ATTAATATTAAATTAAT
Found at i:44639321 original size:25 final size:25
Alignment explanation
Indices: 44639267--44639321 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
44639257 AAACACTAAA
*
44639267 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
44639292 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
44639316 TATTAA
1 T-TTAA
44639322 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:44641461 original size:7 final size:7
Alignment explanation
Indices: 44641451--44641494 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
44641441 TTATTATTTA
44641451 TTAAATT
1 TTAAATT
44641458 TTAAATT
1 TTAAATT
44641465 TTAAATT
1 TTAAATT
*
44641472 TTAAAAT
1 TTAAATT
44641479 TTAAATT
1 TTAAATT
44641486 TTAAATT
1 TTAAATT
44641493 TT
1 TT
44641495 CAAGTATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TTAAATT
Found at i:44641504 original size:21 final size:21
Alignment explanation
Indices: 44641459--44641504 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
44641449 TATTAAATTT
*
44641459 TAAATTTTAAATTTTAAAATT
1 TAAATTTTAAATTTTAAAATA
* *
44641480 TAAATTTTAAATTTTCAAGTA
1 TAAATTTTAAATTTTAAAATA
44641501 TAAA
1 TAAA
44641505 GTTAAGAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAATTTTAAATTTTAAAATA
Found at i:44642230 original size:16 final size:16
Alignment explanation
Indices: 44642209--44642245 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
44642199 GCAACAACTC
* *
44642209 TTGTTTAGAATAATTT
1 TTGTTTAGAACAATTG
44642225 TTGTTTAGAACAATTG
1 TTGTTTAGAACAATTG
44642241 TTGTT
1 TTGTT
44642246 CAAGAATAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.03, G:0.16, T:0.54
Consensus pattern (16 bp):
TTGTTTAGAACAATTG
Found at i:44643716 original size:15 final size:15
Alignment explanation
Indices: 44643675--44643721 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
44643665 TAACAAAGAG
44643675 TGACCAAAATATAAA
1 TGACCAAAATATAAA
* *
44643690 CGATCTAAAATATAAA
1 TGA-CCAAAATATAAA
*
44643706 TGACCAAAATAAAAA
1 TGACCAAAATATAAA
44643721 T
1 T
44643722 AATCTAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 13 0.50
16 13 0.50
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (15 bp):
TGACCAAAATATAAA
Found at i:44665176 original size:16 final size:16
Alignment explanation
Indices: 44665139--44665176 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
44665129 GATAAAGTTT
*
44665139 TCAATTATTTTTTAAA
1 TCAATAATTTTTTAAA
*
44665155 AC-ATAATTTTTTAAA
1 TCAATAATTTTTTAAA
44665170 TCAATAA
1 TCAATAA
44665177 ATAAAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 2
0.78 0.13 0.09
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (16 bp):
TCAATAATTTTTTAAA
Done.