Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 163 of 199
Found at i:53355777 original size:42 final size:43
Alignment explanation
Indices: 53355694--53355799 Score: 162
Period size: 42 Copynumber: 2.5 Consensus size: 43
53355684 CTAAAGATCA
* *
53355694 TGTTCTTTAGCGGCGCTT-TAGAAGAAAACGCCTCTAAAAGTAG
1 TGTTCTTTAGCGGCGCTTGT-TAAGAAAACGCCGCTAAAAGTAG
*
53355737 TGTTCTTTAGCGGCGCTTGTTCA-AAAACGCCGCTAAAAGTAG
1 TGTTCTTTAGCGGCGCTTGTTAAGAAAACGCCGCTAAAAGTAG
53355779 TGTTCTTTAGCGGCGCTTGTT
1 TGTTCTTTAGCGGCGCTTGTT
53355800 TCACAAATGC
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
42 39 0.66
43 19 0.32
44 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGCTTGTTAAGAAAACGCCGCTAAAAGTAG
Found at i:53356248 original size:12 final size:12
Alignment explanation
Indices: 53356233--53356258 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
53356223 TTTCTATCGT
53356233 TGCTTCTCTCGC
1 TGCTTCTCTCGC
53356245 TGCTTCTCTCGC
1 TGCTTCTCTCGC
53356257 TG
1 TG
53356259 TGGCCTCTGC
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:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (12 bp):
TGCTTCTCTCGC
Found at i:53356312 original size:21 final size:21
Alignment explanation
Indices: 53356244--53356300 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
53356234 GCTTCTCTCG
*
53356244 CTGCTTCTCTCGCTGTGGCCT
1 CTGCTTCTCTCGCTGTAGCCT
*
53356265 CTGCTTCTCTCACTGTAGCCT
1 CTGCTTCTCTCGCTGTAGCCT
*
53356286 CTGCTTCCCTCGCTG
1 CTGCTTCTCTCGCTG
53356301 CCGCCTGTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.04, C:0.40, G:0.19, T:0.37
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGTAGCCT
Found at i:53361790 original size:9 final size:9
Alignment explanation
Indices: 53361776--53362026 Score: 194
Period size: 9 Copynumber: 29.8 Consensus size: 9
53361766 AAGTTATTTA
53361776 TTATGTAAG
1 TTATGTAAG
53361785 TTATGTAAG
1 TTATGTAAG
*
53361794 TTGTGTAAG
1 TTATGTAAG
53361803 TTATGTAAG
1 TTATGTAAG
* *
53361812 CTGTGTAAG
1 TTATGTAAG
*
53361821 TTGTGT-A-
1 TTATGTAAG
* *
53361828 TTATGAAAC
1 TTATGTAAG
53361837 TTATGTAAG
1 TTATGTAAG
*
53361846 TTGTGT-A-
1 TTATGTAAG
53361853 TTATGTAAG
1 TTATGTAAG
*
53361862 TTATGTCAG
1 TTATGTAAG
*
53361871 TTGTGT-A-
1 TTATGTAAG
* *
53361878 TTATGAAAC
1 TTATGTAAG
53361887 TTATGTAAG
1 TTATGTAAG
*
53361896 TTATGT--C
1 TTATGTAAG
53361903 TTATGTAAG
1 TTATGTAAG
*
53361912 TTATGTAAA
1 TTATGTAAG
53361921 TTATGT-A-
1 TTATGTAAG
53361928 TTATGTAAG
1 TTATGTAAG
*
53361937 TTATGTCAG
1 TTATGTAAG
*
53361946 TTGTGT-A-
1 TTATGTAAG
*
53361953 TTATGTAAA
1 TTATGTAAG
53361962 TTATGT-A-
1 TTATGTAAG
53361969 TTATGTAAG
1 TTATGTAAG
*
53361978 TTATGTAAT
1 TTATGTAAG
*
53361987 TTGTGT-A-
1 TTATGTAAG
*
53361994 TTATGTAAC
1 TTATGTAAG
* *
53362003 TTATTTAAT
1 TTATGTAAG
53362012 TTATGTAAG
1 TTATGTAAG
53362021 -TATGTA
1 TTATGTA
53362027 TTATTATGTA
Statistics
Matches: 196, Mismatches: 30, Indels: 33
0.76 0.12 0.13
Matches are distributed among these distances:
7 41 0.21
8 20 0.10
9 135 0.69
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:53361794 original size:25 final size:25
Alignment explanation
Indices: 53361765--53362073 Score: 261
Period size: 25 Copynumber: 12.2 Consensus size: 25
53361755 GATTTAGGAA
* *
53361765 TAAGTTATTTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
53361790 TAAGTTGTGTAAGTTATGTAAGCTGTG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* *
53361817 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
53361842 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* * *
53361867 TCAGTTGTGTATTATGAAACTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
53361892 TAAGTTATGTCTTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
53361917 TAAATTATGTATTATGTAAGTTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* *
53361942 TCAGTTGTGTATTATGTAAATTATG
1 TAAGTTGTGTATTATGTAAGTTATG
* * *
53361967 T-A-TTATGTAAGTTATGTAATTTGTG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* * *
53361992 T-A-TTATGTAACTTATTTAATTTATG
1 TAAGTTGTGT-A-TTATGTAAGTTATG
* *
53362017 TAAGTATGTATTATTATGTAATTTAT-
1 TAAGT-TGT-GTATTATGTAAGTTATG
* * *
53362043 TATGTAG-GATATTATCTAAGTTATG
1 TAAGTTGTG-TATTATGTAAGTTATG
53362068 TAAGTT
1 TAAGTT
53362074 TTTTTTTTTT
Statistics
Matches: 234, Mismatches: 40, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
23 5 0.02
24 15 0.06
25 168 0.72
26 7 0.03
27 35 0.15
28 3 0.01
29 1 0.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (25 bp):
TAAGTTGTGTATTATGTAAGTTATG
Found at i:53361856 original size:16 final size:16
Alignment explanation
Indices: 53361765--53361984 Score: 138
Period size: 16 Copynumber: 13.7 Consensus size: 16
53361755 GATTTAGGAA
*
53361765 TAAGTTATTTATTATG
1 TAAGTTATGTATTATG
*
53361781 TAAGTTATGTAAGTTGTG
1 TAAGTTATGT-A-TTATG
* *
53361799 TAAGTTATGTAAGCTGTG
1 TAAGTTATGT-A-TTATG
*
53361817 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
53361833 -AA---A---CTTATG
1 TAAGTTATGTATTATG
*
53361842 TAAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
53361858 TAAGTTATGTCAGTTGTG
1 TAAGTTATGT-A-TTATG
*
53361876 T-A-TTATGAAACTTATG
1 TAAGTTATG-TA-TTATG
*
53361892 TAAGTTATGTCTTATG
1 TAAGTTATGTATTATG
53361908 TAAGTTATGTAAATTATG
1 TAAGTTATGT--ATTATG
53361926 T-A-TTATGTAAGTTATG
1 TAAGTTATGT-A-TTATG
* *
53361942 TCAGTTGTGTATTATG
1 TAAGTTATGTATTATG
*
53361958 TAAATTATGTATTATG
1 TAAGTTATGTATTATG
53361974 TAAGTTATGTA
1 TAAGTTATGTA
53361985 ATTTGTGTAT
Statistics
Matches: 162, Mismatches: 23, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.03
10 2 0.01
15 4 0.02
16 92 0.57
17 8 0.05
18 51 0.31
ACGTcount: A:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (16 bp):
TAAGTTATGTATTATG
Found at i:53361882 original size:41 final size:41
Alignment explanation
Indices: 53361837--53362025 Score: 200
Period size: 41 Copynumber: 4.8 Consensus size: 41
53361827 ATTATGAAAC
* *
53361837 TTATGTAAGTTGTGTATTATGTAAGTTATGTCAGTTGTGTA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
53361878 TTATG--AA--A---CTTATGTAAGTTATGTC--TTATGTAA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGT-A
53361911 GTTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
1 -TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
53361953 TTATGTAAATTATGTATTATGTAAGTTATGTAATTTGTGTA
1 TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
* *
53361994 TTATGTAACTTATTTAATTTATGTAAG-TATGT
1 TTATGTAAATTATGT-A-TTATGTAAGTTATGT
53362026 ATTATTATGT
Statistics
Matches: 125, Mismatches: 10, Indels: 25
0.78 0.06 0.16
Matches are distributed among these distances:
32 5 0.04
33 1 0.01
34 21 0.17
36 2 0.02
38 1 0.01
39 1 0.01
41 73 0.58
42 7 0.06
43 14 0.11
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (41 bp):
TTATGTAAATTATGTATTATGTAAGTTATGTCAGTTGTGTA
Found at i:53362161 original size:24 final size:26
Alignment explanation
Indices: 53362118--53362172 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
53362108 TTATGTACGG
* *
53362118 TATGTGTTATTATGTAAGTTCTTTAT
1 TATGTGTTATTATGTAAGTTATGTAT
*
53362144 TATGT-TTGTTATGT-AGTTATGTAT
1 TATGTGTTATTATGTAAGTTATGTAT
53362168 TATGT
1 TATGT
53362173 AGGATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 13 0.50
25 8 0.31
26 5 0.19
ACGTcount: A:0.22, C:0.02, G:0.18, T:0.58
Consensus pattern (26 bp):
TATGTGTTATTATGTAAGTTATGTAT
Found at i:53362366 original size:15 final size:15
Alignment explanation
Indices: 53362346--53362378 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
53362336 ATAATTATTT
*
53362346 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
53362361 ATAAATTTAATACTA
1 ATAAATTTAATACTA
53362376 ATA
1 ATA
53362379 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:53364847 original size:266 final size:265
Alignment explanation
Indices: 53364430--53365207 Score: 1278
Period size: 266 Copynumber: 3.0 Consensus size: 265
53364420 ATATTTTACT
* * *
53364430 TTTTTACGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATATATCGAGACCAAAACGGTGCATT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
*
53364495 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACAAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
53364560 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTGAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
*
53364625 CGACGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATTAAAACTACGCGTTTTAGTT
196 CGGCGTTTTCTAGTAAGCGCCACTAATATAA-TATACATCAAAATTAAAACTACGCGTTTTAGTT
53364690 AAGATA
260 AAGATA
53364696 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
53364761 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
53364826 ACACTGCGTTTTGTTAAGATA--------CG--TT--A-C-A--G-CGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
53364874 CGGCGTTTTCTAGTAAGCGCCAC-----TAATATA-ATCAAAATTAAAACTACGCGTTTTAGTTA
196 CGGCGTTTTCTAGTAAGCGCCACTAATATAATATACATCAAAATTAAAACTACGCGTTTTAGTTA
53364933 AGATA
261 AGATA
*
53364938 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGATGCGTT
1 TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
*
53365003 TTGGTTCAGATTTTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
66 TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
*
53365068 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGCTCAAGCGCCGCTAAAGCTATTCTTTAA
131 ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
* *
53365133 CGGCGTTTTCTAGTAAGCGCCAGTAATATAAATATACATCAAAATTAAAACTACGCGTTTTAGTA
196 CGGCGTTTTCTAGTAAGCGCCACTAATAT-AATATACATCAAAATTAAAACTACGCGTTTTAGTT
53365198 AAGATA
260 AAGATA
53365204 TTTT
1 TTTT
53365208 ACGGCGCTTT
Statistics
Matches: 477, Mismatches: 11, Indels: 48
0.89 0.02 0.09
Matches are distributed among these distances:
242 183 0.38
243 4 0.01
244 3 0.01
249 40 0.08
250 3 0.01
252 3 0.01
253 1 0.00
254 1 0.00
255 1 0.00
256 3 0.01
258 3 0.01
259 41 0.09
264 1 0.00
265 6 0.01
266 184 0.39
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (265 bp):
TTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACATCGAGACCAAAACGGTGCGTT
TTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAATGTAACATAGCTTAAGACCAA
ACACTGCGTTTTGTTAAGATACGTTGCGGCGCTTTGGATCAAGCGCCGCTAAAGCTATTCTTTAA
CGGCGTTTTCTAGTAAGCGCCACTAATATAATATACATCAAAATTAAAACTACGCGTTTTAGTTA
AGATA
Found at i:53364940 original size:242 final size:245
Alignment explanation
Indices: 53364606--53365092 Score: 881
Period size: 242 Copynumber: 2.0 Consensus size: 245
53364596 GATCAAGCGC
*
53364606 CGCTGAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCACTAATATAAGTATACATCAAAATT
1 CGCTAAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCAC----ATAAGTATACATCAAAATT
53364671 AAAACTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTA
62 AAAACTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTA
*
53364736 TACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCAC
127 TACATCGAGACCAAAACGATGCGTTTTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCAC
53364801 TAAATGTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTTACAG
192 TAAATGTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTTACAG
*
53364855 CGCTAAAGCTATTCTTTAACGGCGTTTTCTAGTAAGCGCCAC-TAA-TATA-ATCAAAATTAAAA
1 CGCTAAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCACATAAGTATACATCAAAATTAAAA
53364917 CTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACA
66 CTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACA
*
53364982 TCGAGACCAAAACGATGCGTTTTGGTTCAGATTTTTTGCGGCGTTTTCCTATAAGCGCCACTAAA
131 TCGAGACCAAAACGATGCGTTTTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAA
53365047 TGTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTT
196 TGTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTT
53365093 GCGGCGCTTT
Statistics
Matches: 234, Mismatches: 4, Indels: 7
0.96 0.02 0.03
Matches are distributed among these distances:
242 187 0.80
243 4 0.02
244 3 0.01
249 40 0.17
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (245 bp):
CGCTAAAGCTATTCTTTAACGACGTTTTCTAGTAAGCGCCACATAAGTATACATCAAAATTAAAA
CTACGCGTTTTAGTTAAGATATTTTTGCGGCGTTTTAACGTCAGCGCCACTAATTGAAGTATACA
TCGAGACCAAAACGATGCGTTTTGGTTCAGATATTTTGCGGCGTTTTCCTATAAGCGCCACTAAA
TGTAACATAGCTTAAGACCAAACACTGCGTTTTGTTAAGATACGTTACAG
Found at i:53365412 original size:113 final size:112
Alignment explanation
Indices: 53365262--53365576 Score: 359
Period size: 113 Copynumber: 2.8 Consensus size: 112
53365252 GCATATCACA
* * * *
53365262 AAGCGCCACTAAATCTAGGATACATCAACACCAAAAACGATGCGTTTTGGTTAAGATATTTTGCG
1 AAGCGCCACTAATTCTAGGATACATCAACA-CAAAAACGATGCGTTTTGGTTAGGAAATTTTACG
* *
53365327 GCGCATATCGTAAAACGCCGCTAAGACGCTTTCAG-GGCGT-TTTTTTAG
65 GCGCATATTGTAAAACGCCGCTAAGACACTTT-AGCGGCGTGTTTTTT-G
* *
53365375 AAGCGACACTAATTCTAGGATACATCAACACTAAAAACGATGCGTTTTGGTTAGGAGAA-ATTAC
1 AAGCGCCACTAATTCTAGGATACATCAACAC-AAAAACGATGCGTTTTGGTTAGGA-AATTTTAC
* * * *
53365439 GGCGCGTTGTTGTAAAGCACCGCTAAGACACTTTAGCGGCGTGTTTTTTG
64 GGCGC-ATATTGTAAAACGCCGCTAAGACACTTTAGCGGCGTGTTTTTTG
* * * * * * *
53365489 AAGCGCCACTAATTCTTGCATACATAAAGACGAAAACGTTGCGTTTTGGATAGGAAATTTTACGG
1 AAGCGCCACTAATTCTAGGATACATCAACACAAAAACGATGCGTTTTGGTTAGGAAATTTTACGG
*
53365554 CGCGTAGTTGT-AAACGCCGCTAA
66 CGCATA-TTGTAAAACGCCGCTAA
53365577 TGATGTTCTT
Statistics
Matches: 170, Mismatches: 25, Indels: 15
0.81 0.12 0.07
Matches are distributed among these distances:
112 14 0.08
113 95 0.56
114 55 0.32
115 6 0.04
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (112 bp):
AAGCGCCACTAATTCTAGGATACATCAACACAAAAACGATGCGTTTTGGTTAGGAAATTTTACGG
CGCATATTGTAAAACGCCGCTAAGACACTTTAGCGGCGTGTTTTTTG
Found at i:53365751 original size:16 final size:18
Alignment explanation
Indices: 53365724--53365756 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53365714 TAGAATTGGG
53365724 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
53365741 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
53365757 GTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:53368789 original size:6 final size:6
Alignment explanation
Indices: 53368778--53368803 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
53368768 CTACGCCGCT
53368778 GGCGGA GGCGGA GGCGGA GGCGGA GG
1 GGCGGA GGCGGA GGCGGA GGCGGA GG
53368804 AGGAAGGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.69, T:0.00
Consensus pattern (6 bp):
GGCGGA
Found at i:53378766 original size:9 final size:9
Alignment explanation
Indices: 53378716--53378782 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
53378706 AAGGAAGAAG
53378716 AAAAATAGAA
1 AAAAATA-AA
*
53378726 AAAAA-AAG
1 AAAAATAAA
*
53378734 AAAGATAAA
1 AAAAATAAA
* *
53378743 TAATATAAA
1 AAAAATAAA
53378752 ATAAAATAAA
1 A-AAAATAAA
53378762 AAAAATAAA
1 AAAAATAAA
* *
53378771 AGAATTAAA
1 AAAAATAAA
53378780 AAA
1 AAA
53378783 TATTTTTTAA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
8 5 0.11
9 27 0.60
10 13 0.29
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (9 bp):
AAAAATAAA
Found at i:53380698 original size:9 final size:9
Alignment explanation
Indices: 53380684--53380774 Score: 132
Period size: 9 Copynumber: 10.2 Consensus size: 9
53380674 AGTCCTTTTG
53380684 TTATT-TTA
1 TTATTATTA
*
53380692 TTTATT-TTC
1 -TTATTATTA
*
53380701 TTATTCTTA
1 TTATTATTA
*
53380710 TTCTTATTA
1 TTATTATTA
53380719 TTATTATTA
1 TTATTATTA
53380728 TTATTATTA
1 TTATTATTA
53380737 TTATTATTA
1 TTATTATTA
53380746 TTATTATTA
1 TTATTATTA
53380755 TTATTATTA
1 TTATTATTA
53380764 TTATTATTA
1 TTATTATTA
53380773 TT
1 TT
53380775 GCTAACATTG
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
8 5 0.07
9 71 0.93
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (9 bp):
TTATTATTA
Found at i:53380709 original size:6 final size:6
Alignment explanation
Indices: 53380684--53380774 Score: 132
Period size: 6 Copynumber: 15.3 Consensus size: 6
53380674 AGTCCTTTTG
* * *
53380684 TTATT- TTATTTA TT-TTC TTATTC TTATTC TTATTA TTATTA TTATTA
1 TTATTA TTA-TTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA
53380731 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
1 TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TTATTA TT
53380775 GCTAACATTG
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
5 7 0.09
6 72 0.89
7 2 0.02
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (6 bp):
TTATTA
Found at i:53380960 original size:17 final size:17
Alignment explanation
Indices: 53380938--53380970 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
53380928 TTCTTTCATT
53380938 TTTA-TTATTATTATTTA
1 TTTATTTATT-TTATTTA
53380955 TTTATTTATTTTATTT
1 TTTATTTATTTTATTT
53380971 TTTCTTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTATTTATTTTATTTA
Found at i:53380974 original size:44 final size:43
Alignment explanation
Indices: 53380898--53380982 Score: 111
Period size: 44 Copynumber: 1.9 Consensus size: 43
53380888 CTATTAGTAA
53380898 TATTATTATTATCCTTATTTCATTTATGTTTTCTTTCATTTTTAT
1 TATTATTATTAT-CTTATTTCATTTATGTTTTCTTTC-TTTTTAT
*
53380943 TATTATTATTTAT-TTATTT-ATTTTATTTTTTCTTTCTTTT
1 TATTATTA-TTATCTTATTTCA-TTTATGTTTTCTTTCTTTT
53380983 CTAAAAGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
43 5 0.14
44 20 0.54
45 8 0.22
46 4 0.11
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (43 bp):
TATTATTATTATCTTATTTCATTTATGTTTTCTTTCTTTTTAT
Found at i:53381123 original size:24 final size:24
Alignment explanation
Indices: 53381072--53381127 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 24
53381062 ATCTTTATAT
53381072 TTTATTTTTTTTATATATAGACATA
1 TTTATTTTTTTTATATATA-ACATA
53381097 TTTATGTTTTTTTATAT-T-ACATAA
1 TTTAT-TTTTTTTATATATAACAT-A
53381121 TTTATTT
1 TTTATTT
53381128 ACCTACACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 6 0.21
24 6 0.21
25 6 0.21
26 11 0.38
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (24 bp):
TTTATTTTTTTTATATATAACATA
Found at i:53382753 original size:16 final size:16
Alignment explanation
Indices: 53382732--53382762 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53382722 TGAATTACTG
53382732 ATTACAGTTCTATTAT
1 ATTACAGTTCTATTAT
*
53382748 ATTACAGTTTTATTA
1 ATTACAGTTCTATTA
53382763 CTATCAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTACAGTTCTATTAT
Found at i:53387042 original size:43 final size:43
Alignment explanation
Indices: 53386968--53387293 Score: 424
Period size: 43 Copynumber: 7.6 Consensus size: 43
53386958 CGCCATTGTC
* * * * *
53386968 AACGCCGCTATAG-TCAGGACCTTTAGTGGCACATTTTCCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
*
53387010 AACGCCGCTATAGATCATGACCTTTAGCGGCAC-TTTTACACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
* *
53387052 AACGCCGCTATAGATCATAACCTTTAGCGTCGCTTTTTACACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
*
53387095 AACGCCGCTATAGATCATGACCTTTAGCGGTGCTTTTTACACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
* * *
53387138 AACGCCGCTATAGATCAAGATCTTTAGCGGCGCTTTTTTCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
* * * *
53387181 AATGCCGCTATAGATCAAGACCTTTAGCGGC-ATTTTTCCCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTT-ACACA
* * *
53387224 AACGCCGCTATAGATCATGATCTTTAGCGACGCTTTTTCCACA
1 AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
* * *
53387267 AACGCCACTATAGCTCAAGACCTTTAG
1 AACGCCGCTATAGATCATGACCTTTAG
53387294 TGACGCTTCA
Statistics
Matches: 254, Mismatches: 26, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
42 56 0.22
43 193 0.76
44 5 0.02
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (43 bp):
AACGCCGCTATAGATCATGACCTTTAGCGGCGCTTTTTACACA
Found at i:53387334 original size:86 final size:83
Alignment explanation
Indices: 53387001--53387340 Score: 310
Period size: 86 Copynumber: 4.0 Consensus size: 83
53386991 TAGTGGCACA
* * *
53387001 TTTTCCACAAACGCCGCTATAGATCATGACCTTTAGCGGCACTT-TTACACAAACGCCGCTATAG
1 TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATT--ACAAACGCCGCTATAG
* *
53387065 AT-CATAACCTTTAGCGTCGCT
64 ATCCAT--TCTTTAGCGACGCT
* * *
53387086 TTTTACACAAACGCCGCTATAGATCATGACCTTTAGCGGTGCTTTTTACACAAACGCCGCTATAG
1 TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATT--ACAAACGCCGCTATAG
* * *
53387151 ATCAAGATCTTTAGCGGCGCT
64 ATCCA-TTCTTTAGCGACGCT
* * * *
53387172 TTTTTCACAAATGCCGCTATAGATCAAGACCTTTAGCGGC-ATTTTTCCCACAAACGCCGCTATA
1 TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATT---ACAAACGCCGCTATA
53387236 GAT-CATGATCTTTAGCGACGCT
63 GATCCAT--TCTTTAGCGACGCT
* * * * * * *
53387258 TTTTCCACAAACGCCACTATAGCTCAAGACCTTTAGTGACGCTTCAATTACAAACGCCGCTAAAA
1 TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTT--ATTACAAACGCCGCTATAG
*
53387323 ATACCATTCTTTGGCGAC
64 AT-CCATTCTTTAGCGAC
53387341 ATTTATGGAA
Statistics
Matches: 217, Mismatches: 27, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
85 47 0.22
86 162 0.75
87 3 0.01
88 3 0.01
89 2 0.01
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.29
Consensus pattern (83 bp):
TTTTACACAAACGCCGCTATAGATCAAGACCTTTAGCGGCGCTTATTACAAACGCCGCTATAGAT
CCATTCTTTAGCGACGCT
Found at i:53387410 original size:16 final size:16
Alignment explanation
Indices: 53387391--53387424 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
53387381 AAATATTAAA
*
53387391 TATTAAAATCAAACAT
1 TATTAAAATAAAACAT
*
53387407 TATTAATATAAAACAT
1 TATTAAAATAAAACAT
53387423 TA
1 TA
53387425 ATTAGTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTAAAATAAAACAT
Found at i:53393056 original size:16 final size:17
Alignment explanation
Indices: 53393020--53393061 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
53393010 CACTATAATC
53393020 ATTATTTTAATATATTAA
1 ATTA-TTTAATATATTAA
53393038 ATTATTTAATATA-TAA
1 ATTATTTAATATATTAA
53393054 ATTATTTA
1 ATTATTTA
53393062 TAAATAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 11 0.46
17 9 0.38
18 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTATTTAATATATTAA
Found at i:53393184 original size:7 final size:7
Alignment explanation
Indices: 53393168--53393349 Score: 59
Period size: 7 Copynumber: 26.0 Consensus size: 7
53393158 ACTAATTAAT
53393168 CTAAACC
1 CTAAACC
*
53393175 CTAAATC
1 CTAAACC
53393182 CTAAACC
1 CTAAACC
*
53393189 CT-AACT
1 CTAAACC
*
53393195 CTTAACC
1 CTAAACC
*
53393202 CTCAACCC
1 CT-AAACC
53393210 CT-AACC
1 CTAAACC
53393216 ACTAAACC
1 -CTAAACC
*
53393224 TTAAACC
1 CTAAACC
*
53393231 C-CAACC
1 CTAAACC
* *
53393237 CTTAA-T
1 CTAAACC
53393243 CTATAACC
1 CTA-AACC
*
53393251 TTAAACC
1 CTAAACC
* *
53393258 ATAAACT
1 CTAAACC
* *
53393265 GTAACCC
1 CTAAACC
*
53393272 CTAAACA
1 CTAAACC
* *
53393279 TTAAACT
1 CTAAACC
*
53393286 GTAAACC
1 CTAAACC
* *
53393293 ATAACCC
1 CTAAACC
53393300 CTAAA-C
1 CTAAACC
53393306 CTATAATCC
1 CTA-AA-CC
*
53393315 ATAAACC
1 CTAAACC
* *
53393322 TTAAACT
1 CTAAACC
*
53393329 CTATACC
1 CTAAACC
* *
53393336 ATATACC
1 CTAAACC
53393343 CTAAACC
1 CTAAACC
53393350 AAAAACCTTA
Statistics
Matches: 125, Mismatches: 40, Indels: 20
0.68 0.22 0.11
Matches are distributed among these distances:
6 19 0.15
7 90 0.72
8 13 0.10
9 3 0.02
ACGTcount: A:0.41, C:0.35, G:0.01, T:0.23
Consensus pattern (7 bp):
CTAAACC
Found at i:53393757 original size:41 final size:41
Alignment explanation
Indices: 53393670--53393826 Score: 253
Period size: 41 Copynumber: 3.9 Consensus size: 41
53393660 AAATATTTTT
* * *
53393670 GCGGCGCTTTTACAAAAACGTCGCTAAAG-GCTGAGCATTA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGAGCATTA
* *
53393710 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGAGCATTA
*
53393751 GCGGCGCTTCTCCAAAAACGCCGCTAAAGCCCTGAGCATTA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGAGCATTA
53393792 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
1 GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGA
53393827 AAGGTAAGAA
Statistics
Matches: 110, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
40 27 0.25
41 83 0.75
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTCTACAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:53393911 original size:40 final size:40
Alignment explanation
Indices: 53393866--53393994 Score: 129
Period size: 40 Copynumber: 3.2 Consensus size: 40
53393856 GGCTTTTTGA
* *
53393866 GGCGTTTTTACAAAAAACGCCGCTAATACTC-ATTATTAGC
1 GGCGTTTTTACATAAAGCGCCGCTAATACTCGATT-TTAGC
* * * *
53393906 GGCG-TTTTCCTTAAAGCGCCACTAATACTCGATCTTTAGT
1 GGCGTTTTTACATAAAGCGCCGCTAATACTCGAT-TTTAGC
* * *
53393946 GGC-ATTTTATATAAAGCGCCGCTAATGCTCGATTTTTAGC
1 GGCGTTTTTACATAAAGCGCCGCTAATACTCGA-TTTTAGC
53393986 GGCGTTTTT
1 GGCGTTTTT
53393995 TATGCAAACG
Statistics
Matches: 71, Mismatches: 13, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
39 21 0.30
40 44 0.62
41 6 0.08
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.35
Consensus pattern (40 bp):
GGCGTTTTTACATAAAGCGCCGCTAATACTCGATTTTAGC
Found at i:53401761 original size:5 final size:5
Alignment explanation
Indices: 53401753--53401777 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
53401743 TTATATATCC
53401753 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
53401778 GGTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:53403094 original size:24 final size:24
Alignment explanation
Indices: 53403066--53403113 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
53403056 GGGTTACAAT
*
53403066 AAGATAAAATGTGAAGA-GTTAAGG
1 AAGATAAAAGGTGAA-ATGTTAAGG
*
53403090 AAGATGAAAGGTGAAATGTTAAGG
1 AAGATAAAAGGTGAAATGTTAAGG
53403114 GTTGATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.48, C:0.00, G:0.31, T:0.21
Consensus pattern (24 bp):
AAGATAAAAGGTGAAATGTTAAGG
Found at i:53403631 original size:15 final size:15
Alignment explanation
Indices: 53403594--53403632 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
53403584 TAATTTTAAA
53403594 TAATATTATTCAATAC
1 TAATATT-TTCAATAC
53403610 TAATATTTT-AATAC
1 TAATATTTTCAATAC
53403624 TAAATATTT
1 T-AATATTT
53403633 ATTACAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 9 0.41
16 7 0.32
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.49
Consensus pattern (15 bp):
TAATATTTTCAATAC
Found at i:53403631 original size:28 final size:27
Alignment explanation
Indices: 53403557--53403631 Score: 64
Period size: 28 Copynumber: 2.7 Consensus size: 27
53403547 ATTTAAATTT
*
53403557 TATTTTAATAGTAAAT-TTTAAAAATAA
1 TATTTTAATA-TAAATATTCAAAAATAA
* *
53403584 TAATTTTAA-ATAATATTATTCAATACTAA
1 T-ATTTTAATATAA-A-TATTCAAAAATAA
53403613 TATTTTAATACTAAATATT
1 TATTTTAATA-TAAATATT
53403632 TATTACAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
26 3 0.08
27 3 0.08
28 19 0.49
29 11 0.28
30 3 0.08
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (27 bp):
TATTTTAATATAAATATTCAAAAATAA
Found at i:53404114 original size:14 final size:14
Alignment explanation
Indices: 53404092--53404130 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
53404082 TCGGAAAAGT
53404092 AAGTCATTTTCCAGA
1 AAGTCATTTTCC-GA
53404107 AA-TCATTTTCCGA
1 AAGTCATTTTCCGA
53404120 AAGTCATTTTC
1 AAGTCATTTTC
53404131 AGTGAAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 17 0.74
15 2 0.09
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (14 bp):
AAGTCATTTTCCGA
Found at i:53404489 original size:25 final size:27
Alignment explanation
Indices: 53404458--53404513 Score: 89
Period size: 25 Copynumber: 2.1 Consensus size: 27
53404448 CAGGTTTGAT
*
53404458 AAAATAAATTA-TTAAAAATTCAA-AA
1 AAAATAAATTATTTAAAAATTAAATAA
53404483 AAAATAAATTATTTAAAAATTAAATAA
1 AAAATAAATTATTTAAAAATTAAATAA
53404510 AAAA
1 AAAA
53404514 CCGGTTCAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 11 0.39
26 11 0.39
27 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAATAAATTATTTAAAAATTAAATAA
Found at i:53406823 original size:17 final size:17
Alignment explanation
Indices: 53406797--53406831 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53406787 CAATTTTACT
53406797 ATAATGACAAAAGAATGA
1 ATAATGACAAAAG-ATGA
53406815 ATAAT-ACAAAAGATGA
1 ATAATGACAAAAGATGA
53406831 A
1 A
53406832 GACAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 7 0.41
18 5 0.29
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (17 bp):
ATAATGACAAAAGATGA
Found at i:53407006 original size:24 final size:24
Alignment explanation
Indices: 53406979--53407030 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
53406969 TTTGTAGGTG
*
53406979 AAATAAATTATACA-AATAAATGCT
1 AAATAAATTATA-ATAATAAATACT
*
53407003 AAATATATTATAATAATAAATACT
1 AAATAAATTATAATAATAAATACT
53407027 AAAT
1 AAAT
53407031 CTTCTACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAATTATAATAATAAATACT
Found at i:53412291 original size:26 final size:26
Alignment explanation
Indices: 53412241--53412291 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
53412231 TAAAATTAGC
* * *
53412241 ATTATACAATCATTCATATTTAATAT
1 ATTATACAATCACTCAAATTAAATAT
*
53412267 ATTATATAATCACTCAAATTAAATA
1 ATTATACAATCACTCAAATTAAATA
53412292 AATCTCATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (26 bp):
ATTATACAATCACTCAAATTAAATAT
Found at i:53422537 original size:26 final size:26
Alignment explanation
Indices: 53422508--53422557 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
53422498 TTATTTTATT
*
53422508 TTTAAAAAATATATTTTCTAATTCGA
1 TTTAAAAAATATATTCTCTAATTCGA
***
53422534 TTTATTTAATATATTCTCTAATTC
1 TTTAAAAAATATATTCTCTAATTC
53422558 AACTTAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.52
Consensus pattern (26 bp):
TTTAAAAAATATATTCTCTAATTCGA
Found at i:53426950 original size:18 final size:18
Alignment explanation
Indices: 53426881--53426955 Score: 64
Period size: 18 Copynumber: 4.2 Consensus size: 18
53426871 ATAATAGTTC
* *
53426881 TATTTTTAAATAAATAAAA
1 TATTTTTAAATATAT-AAT
*
53426900 TATTTTTAACTA-ATAAT
1 TATTTTTAAATATATAAT
* **
53426917 TGTAAATTAAAT-TATAAT
1 TAT-TTTTAAATATATAAT
53426935 TATTTTTAAATATATAAT
1 TATTTTTAAATATATAAT
53426953 TAT
1 TAT
53426956 CACAACTTTT
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 10 0.23
18 23 0.52
19 11 0.25
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (18 bp):
TATTTTTAAATATATAAT
Found at i:53431681 original size:19 final size:18
Alignment explanation
Indices: 53431657--53431694 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
53431647 ATATCTCTCA
53431657 GGCAAAGTAGAGTGATAAT
1 GGCAAA-TAGAGTGATAAT
*
53431676 GGCAAATGGAGTGATAAT
1 GGCAAATAGAGTGATAAT
53431694 G
1 G
53431695 TCCGGCCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.39, C:0.05, G:0.34, T:0.21
Consensus pattern (18 bp):
GGCAAATAGAGTGATAAT
Found at i:53435590 original size:113 final size:112
Alignment explanation
Indices: 53435434--53436052 Score: 503
Period size: 113 Copynumber: 5.4 Consensus size: 112
53435424 AAATCTCAAG
* * *
53435434 ACCAACACGCAGCA-TTCTGGTCTTGATGTATATTAGAATTAGTGGCGCTTACGAACAAACGCTG
1 ACCAAAACGCAG-AGTT-TGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAA-AAACGCCG
* * *
53435498 GTAATGCATAGTATTAGCGGCGCTTAGCGGAAACGCCGCAAAAGATGTTA
63 CTAATGCATAGTATTAGCGGCGCTTAGTGGAAACGCCGCAAAAGATCTTA
* * * *
53435548 ACCAAAACGCAGAGTTTGGTCTTGATTTATATTACAAGTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTAT-GA-AAAACGCCGC
* * * * *
53435613 TAATGTATAGTATTAGCGGCGCTGAGTGTTAAACACCGCAAAACATCTTA
64 TAATGCATAGTATTAGCGGCGCTTAGTG-GAAACGCCGCAAAAGATCTTA
* * * ** * * *
53435663 ACCAAAACGCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGCATTTAAGGAAAACGCCACT
1 ACCAAAACGCAGAG-TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAAAAACGCCGCT
* * * ** * * * *
53435728 AAAGCATAGTAATAGCAGCATTTGGTGGTAAGCGCCTCAAAATATCTTA
65 AATGCATAGTATTAGCGGCGCTTAGTGG-AAACGCCGCAAAAGATCTTA
* * *
53435777 ACCAAAACGCGGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTATTGGAAAACGCCGCT
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTA-TGAAAAACGCCGCT
* * * *
53435842 AA-ACTATAGTAGTAGCGGCG-TTTGTGGAAAGCGCCGC-AAAGTATCCTA
65 AATGC-ATAGTATTAGCGGCGCTTAGTGGAAA-CGCCGCAAAAG-ATCTTA
* * ** *
53435890 ACCAAAACGCAGAGTTTGGCCTTGACGTATATTA-AAGTTAGTGGCGCTTATTTCAAAACGCTGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAA-TTAGTGGCGCTTA-TGAAAAACGCCGC
* * * * * * * *
53435954 TAATGCTTACTAGTT-GCGGTGCTTTGTGGTAAGCGCCACCAAAAGGTATTA
64 TAATGCATAGTA-TTAGCGGCGCTTAGTGG-AAACGCC-GCAAAAGATCTTA
* ** * * * *
53436005 ACGAAAATACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGGCGC
1 ACCAAAACGCAGAGTTT-GGTCTTGATGTATATTAGAATTAGTGGCGC
53436053 ACACAGGAAA
Statistics
Matches: 404, Mismatches: 82, Indels: 36
0.77 0.16 0.07
Matches are distributed among these distances:
112 7 0.02
113 147 0.36
114 142 0.35
115 50 0.12
116 56 0.14
117 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (112 bp):
ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATGAAAAACGCCGCTA
ATGCATAGTATTAGCGGCGCTTAGTGGAAACGCCGCAAAAGATCTTA
Found at i:53435617 original size:114 final size:114
Alignment explanation
Indices: 53435434--53436052 Score: 504
Period size: 114 Copynumber: 5.4 Consensus size: 114
53435424 AAATCTCAAG
* ** * *
53435434 ACCAACACGCAGCA-TTCTGGTCTTGATGTATATTAGAATTAGTGGCGCTTACGAA-CAAACGCT
1 ACCAAAACGCAG-AGTT-TGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAAGAAAACGCC
* * *
53435497 GGTAATGCATAGTATTAGCGGCGCTTAGCGGAAACGCCGCAAAAGATGTTA
64 GCTAATGCATAGTATTAGCGGCGCTTAGTGGAAACGCCGCAAAAGATCTTA
* * *
53435548 ACCAAAACGCAGAGTTTGGTCTTGATTTATATTACAAGTAGTGGCGCTTATAAAGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAAGAAAACGCCGC
* * * * *
53435613 TAATGTATAGTATTAGCGGCGCTGAGTGTTAAACACCGCAAAACATCTTA
66 TAATGCATAGTATTAGCGGCGCTTAGTG-GAAACGCCGCAAAAGATCTTA
* * * * * *
53435663 ACCAAAACGCAGCGTTTTGGTCTTGATGTATACTATAATTAGTGGC-ATT-TAAGGAAAACGCCA
1 ACCAAAACGCAGAG-TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAAGAAAACGCCG
* * * ** * * * *
53435726 CTAAAGCATAGTAATAGCAGCATTTGGTGGTAAGCGCCTCAAAATATCTTA
65 CTAATGCATAGTATTAGCGGCGCTTAGTGG-AAACGCCGCAAAAGATCTTA
* * **
53435777 ACCAAAACGCGGAGTTTGGTCTTGAGGTATATTAGAATTAGTGGCGCTTAT-TGGAAAACGCCGC
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAAGAAAACGCCGC
* * * *
53435841 TAA-ACTATAGTAGTAGCGGCG-TTTGTGGAAAGCGCCGC-AAAGTATCCTA
66 TAATGC-ATAGTATTAGCGGCGCTTAGTGGAAA-CGCCGCAAAAG-ATCTTA
* * *** *
53435890 ACCAAAACGCAGAGTTTGGCCTTGACGTATATTA-AAGTTAGTGGCGCTTAT-TTCAAAACGCTG
1 ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAA-TTAGTGGCGCTTATAAAGAAAACGCCG
* * * * * * * *
53435953 CTAATGCTTACTAGTT-GCGGTGCTTTGTGGTAAGCGCCACCAAAAGGTATTA
65 CTAATGCATAGTA-TTAGCGGCGCTTAGTGG-AAACGCC-GCAAAAGATCTTA
* ** * * * *
53436005 ACGAAAATACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTGGCGC
1 ACCAAAACGCAGAGTTT-GGTCTTGATGTATATTAGAATTAGTGGCGC
53436053 ACACAGGAAA
Statistics
Matches: 407, Mismatches: 79, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
112 7 0.02
113 146 0.36
114 147 0.36
115 52 0.13
116 53 0.13
117 2 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (114 bp):
ACCAAAACGCAGAGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTATAAAGAAAACGCCGC
TAATGCATAGTATTAGCGGCGCTTAGTGGAAACGCCGCAAAAGATCTTA
Found at i:53436218 original size:18 final size:18
Alignment explanation
Indices: 53436197--53436232 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
53436187 TCATTTTATA
53436197 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
53436215 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
53436233 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:53436611 original size:7 final size:7
Alignment explanation
Indices: 53436599--53436628 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
53436589 TATGGTTTAA
53436599 GGGTTAG
1 GGGTTAG
53436606 GGGTTAG
1 GGGTTAG
53436613 GGGTTAG
1 GGGTTAG
53436620 GGGTTAG
1 GGGTTAG
53436627 GG
1 GG
53436629 ATTTGGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.60, T:0.27
Consensus pattern (7 bp):
GGGTTAG
Found at i:53437136 original size:15 final size:15
Alignment explanation
Indices: 53437118--53437159 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
53437108 TGGTTTTGAC
*
53437118 TTTTAGTGTTTGGGG
1 TTTTAGGGTTTGGGG
*
53437133 TTTTGGGGTTTGGGG
1 TTTTAGGGTTTGGGG
*
53437148 -TTTGGGGTTTGG
1 TTTTAGGGTTTGG
53437160 TTTTTGAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.02, C:0.00, G:0.48, T:0.50
Consensus pattern (15 bp):
TTTTAGGGTTTGGGG
Found at i:53437139 original size:8 final size:7
Alignment explanation
Indices: 53437125--53437159 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
53437115 GACTTTTAGT
53437125 GTTTGGG
1 GTTTGGG
53437132 GTTTTGGG
1 G-TTTGGG
53437140 GTTTGGG
1 GTTTGGG
53437147 GTTTGGG
1 GTTTGGG
53437154 GTTTGG
1 GTTTGG
53437160 TTTTTGAGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 20 0.74
8 7 0.26
ACGTcount: A:0.00, C:0.00, G:0.54, T:0.46
Consensus pattern (7 bp):
GTTTGGG
Found at i:53437165 original size:14 final size:14
Alignment explanation
Indices: 53437125--53437171 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
53437115 GACTTTTAGT
53437125 GTTTGGGGTTTTGGG
1 GTTT-GGGTTTTGGG
*
53437140 GTTTGGGGTTTGGG
1 GTTTGGGTTTTGGG
* *
53437154 GTTTGGTTTTTGAG
1 GTTTGGGTTTTGGG
53437168 GTTT
1 GTTT
53437172 AAGATTTAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 24 0.86
15 4 0.14
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (14 bp):
GTTTGGGTTTTGGG
Found at i:53437960 original size:44 final size:44
Alignment explanation
Indices: 53437883--53437970 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 44
53437873 GAGCGACTGC
*
53437883 GTTTTGACTTATAGTTAGTGGCGCTTAGTTTAAAACGCCGCAAA
1 GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
* * *
53437927 GTTTTGACTTATAGTTTGTGGTGCTTTGCTTAAAACGCCGCAAA
1 GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
53437971 AATGTTTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (44 bp):
GTTTTGACTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAAA
Found at i:53439442 original size:16 final size:16
Alignment explanation
Indices: 53439421--53439456 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
53439411 GTATTTATAA
*
53439421 TTATCGATTTTCAATT
1 TTATCGATTTACAATT
53439437 TTATCGATTTACAATT
1 TTATCGATTTACAATT
53439453 TTAT
1 TTAT
53439457 TTCAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATCGATTTACAATT
Found at i:53440255 original size:18 final size:18
Alignment explanation
Indices: 53440234--53440307 Score: 50
Period size: 18 Copynumber: 4.3 Consensus size: 18
53440224 CGATTTAACT
53440234 TGTTTTAGTTATTTATAG
1 TGTTTTAGTTATTTATAG
53440252 TG-TTTA-TT-TTCTA-A-
1 TGTTTTAGTTATT-TATAG
* * * **
53440266 TGGTTTAATTCATTGATCT
1 TGTTTTAGTT-ATTTATAG
53440285 TGTTTTAGTTATTTATAG
1 TGTTTTAGTTATTTATAG
53440303 TGTTT
1 TGTTT
53440308 ATTTTCTAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 14
0.67 0.11 0.22
Matches are distributed among these distances:
14 2 0.05
15 7 0.17
16 6 0.14
17 5 0.12
18 14 0.33
19 8 0.19
ACGTcount: A:0.20, C:0.04, G:0.15, T:0.61
Consensus pattern (18 bp):
TGTTTTAGTTATTTATAG
Found at i:53440293 original size:51 final size:51
Alignment explanation
Indices: 53440232--53440333 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
53440222 TACGATTTAA
53440232 CTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTCATTGAT
1 CTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTCATTGAT
53440283 CTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTCATTGAT
1 CTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTCATTGAT
53440334 TGTAATGCGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.59
Consensus pattern (51 bp):
CTTGTTTTAGTTATTTATAGTGTTTATTTTCTAATGGTTTAATTCATTGAT
Found at i:53440744 original size:21 final size:21
Alignment explanation
Indices: 53440714--53440763 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
53440704 CTACAACTTA
* * *
53440714 AAGCAAAGGCGGCAGCGAGGG
1 AAGCAGAGGCGACAGCGAGAG
*
53440735 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCGACAGCGAGAG
*
53440756 AAGTAGAG
1 AAGCAGAG
53440764 CAGAGCAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGACAGCGAGAG
Found at i:53441157 original size:42 final size:42
Alignment explanation
Indices: 53441079--53441324 Score: 357
Period size: 42 Copynumber: 5.8 Consensus size: 42
53441069 GTTTTTGTAT
* ** *
53441079 AAAAGCGCCGCTAAAGATAATGTTCTTTAGCAGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
53441121 AAAAACGCCGCTAAAGACCATGCTCTTCAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
53441163 AGAAACGCCGCTAAAGACCATGTTCTTTAGCGGCCCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * * *
53441205 AATAAATGCCCCGAAAGACCATGTTCTTTAGCGGCGCTTAGTA
1 AA-AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
53441248 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
53441290 ATAAACGCCGCTAAAGACCATGTTCTTTAGAGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
53441325 TTTCTTTCTA
Statistics
Matches: 181, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
42 144 0.80
43 37 0.20
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:53441341 original size:42 final size:42
Alignment explanation
Indices: 53441084--53441369 Score: 322
Period size: 42 Copynumber: 6.8 Consensus size: 42
53441074 TGTATAAAAG
** * * *
53441084 CGCCGCTAAAGATAATGTTCTTTAGCAGCGCTTAGAAAAAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAATAAA
* * * *
53441126 CGCCGCTAAAGACCATGCTCTTCAGCGGCGCTTAGAAAGAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAATAAA
**
53441168 CGCCGCTAAAGACCATGTTCTTTAGCGGCCCTTAGAAAATAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAG-AAATAAA
* * * *
53441211 TGCCCCGAAAGACCATGTTCTTTAGCGGCGCTTAGTAAA-AAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAG-AAATAAA
*
53441253 CGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAA
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAATAAA
* ***** *
53441295 CGCCGCTAAAGACCATGTTCTTTAGAGGCGTTTCTTTCTAAG
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAATAAA
* *
53441337 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
1 CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTT
53441370 TTGTTTGTAA
Statistics
Matches: 213, Mismatches: 29, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
41 3 0.01
42 170 0.80
43 40 0.19
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (42 bp):
CGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTAGAAATAAA
Found at i:53441345 original size:84 final size:84
Alignment explanation
Indices: 53441079--53441366 Score: 362
Period size: 84 Copynumber: 3.4 Consensus size: 84
53441069 GTTTTTGTAT
* ** * * *
53441079 AAAAGCGCCGCTAAAGATAATGTTCTTTAGCAGCGCTTAGAAAAAAACGCCGCTAAAGACCATGC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGACCATGT
*
53441144 TCTTCAGCGGCGCTTAG-A
66 TCTTTAGCGGCGCTTAGTA
* * * *
53441162 AAGAAACGCCGCTAAAGACCATGTTCTTTAGCGGCCCTTAGAAAATAAATGCCCCGAAAGACCAT
1 AA-AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAG-AAATAAACGCCGCTAAAGACCAT
53441227 GTTCTTTAGCGGCGCTTAGTA
64 GTTCTTTAGCGGCGCTTAGTA
53441248 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGACCATGT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGACCATGT
* * ** *
53441313 TCTTTAGAGGCGTTTCTTT
66 TCTTTAGCGGCGCTTAGTA
** * * *
53441332 CTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
53441367 TTTTTGTTTG
Statistics
Matches: 177, Mismatches: 25, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
83 2 0.01
84 99 0.56
85 73 0.41
86 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAATAAACGCCGCTAAAGACCATGT
TCTTTAGCGGCGCTTAGTA
Found at i:53441751 original size:17 final size:17
Alignment explanation
Indices: 53441723--53441757 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
53441713 TAATTTTACT
53441723 ATAATGACAAAAGACTGA
1 ATAATGACAAAAGA-TGA
53441741 ATAAT-ACAAAAGATGA
1 ATAATGACAAAAGATGA
53441757 A
1 A
53441758 GACAAAAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 8 0.47
18 5 0.29
ACGTcount: A:0.60, C:0.09, G:0.14, T:0.17
Consensus pattern (17 bp):
ATAATGACAAAAGATGA
Found at i:53447794 original size:50 final size:49
Alignment explanation
Indices: 53447734--53447978 Score: 163
Period size: 50 Copynumber: 4.9 Consensus size: 49
53447724 GATTTGGAAC
* *
53447734 TTGTAACTTTAATCTGCTTAACTGTGATGTCGGGGAAGCAAGATTCGCCA
1 TTGTAGCTTTAATCTG-TTAACTGTAATGTCGGGGAAGCAAGATTCGCCA
* ** * * * *
53447784 TTGTAGCTTTAATCTGTT-CCCCTACACTGTCAGGGAAGTAAGATTTGCTA
1 TTGTAGCTTTAATCTGTTAACTGTA-A-TGTCGGGGAAGCAAGATTCGCCA
* * * * *
53447834 TTGTAGCTTCAATCTTTTAACTGTAATGCCGTGGAAGCAAGATTCGCCG
1 TTGTAGCTTTAATCTGTTAACTGTAATGTCGGGGAAGCAAGATTCGCCA
* * * * * ** * **
53447883 TTGT-GACTTCAATCTTTTCCACTG-CATCGACTAGGAAGTAAGATTCGCTG
1 TTGTAG-CTTTAATCTGTT-AACTGTAAT-GTCGGGGAAGCAAGATTCGCCA
* * *
53447933 CTGTAGCTTCAATCTTTTGAACTGTAATGTCGGGGAAGCAAGATTC
1 TTGTAGCTTTAATCTGTT-AACTGTAATGTCGGGGAAGCAAGATTC
53447979 ATCGTTGTGA
Statistics
Matches: 151, Mismatches: 36, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
48 3 0.02
49 37 0.25
50 105 0.70
51 6 0.04
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (49 bp):
TTGTAGCTTTAATCTGTTAACTGTAATGTCGGGGAAGCAAGATTCGCCA
Found at i:53447922 original size:99 final size:99
Alignment explanation
Indices: 53447751--53448031 Score: 370
Period size: 99 Copynumber: 2.8 Consensus size: 99
53447741 TTTAATCTGC
* * * * * *
53447751 TTAACTGTGATGTCGGGGAAGCAAGATTCGCCATTGT-AGCTTTAATCTGTTCCCCTACA-CTGT
1 TTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGA-CTTCAATCTATTCCACTGCATC-GT
* *
53447814 C-AGGGAAGTAAGATTTGCTATTGTAGCTTCAATCTT
64 CTA-GGAAGTAAGATTCGCTACTGTAGCTTCAATCTT
* * * *
53447850 TTAACTGTAATGCCGTGGAAGCAAGATTCGCCGTTGTGACTTCAATCTTTTCCACTGCATCGACT
1 TTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGACTTCAATCTATTCCACTGCATCGTCT
*
53447915 AGGAAGTAAGATTCGCTGCTGTAGCTTCAATCTT
66 AGGAAGTAAGATTCGCTACTGTAGCTTCAATCTT
**
53447949 TTGAACTGTAATGTCGGGGAAGCAAGATTCATCGTTGTGACTTCAATCTATTCCACTGCATCGTC
1 TT-AACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGACTTCAATCTATTCCACTGCATCGTC
53448014 TAGGAAGTAAGATTCGCT
65 TAGGAAGTAAGATTCGCT
53448032 GTCTTCGATC
Statistics
Matches: 160, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
99 83 0.52
100 77 0.48
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (99 bp):
TTAACTGTAATGTCGGGGAAGCAAGATTCGCCGTTGTGACTTCAATCTATTCCACTGCATCGTCT
AGGAAGTAAGATTCGCTACTGTAGCTTCAATCTT
Found at i:53447993 original size:50 final size:48
Alignment explanation
Indices: 53447840--53447997 Score: 140
Period size: 50 Copynumber: 3.2 Consensus size: 48
53447830 GCTATTGTAG
* *
53447840 CTTCAATCTTTTAACTGTAATGCCGTGGAAGCAAGATTCGCCGTTGTGA
1 CTTCAATCTTTTAACTGTAATGACGAGGAAGCAAGATTC-CCGTTGTGA
* * * * * *
53447889 CTTCAATCTTTTCCACTG-CATCGACTAGGAAGTAAGATTCGCTGCTGT-A
1 CTTCAATCTTTT-AACTGTAAT-GACGAGGAAGCAAGATTC-CCGTTGTGA
* * *
53447938 GCTTCAATCTTTTGAACTGTAATGTCGGGGAAGCAAGATTCATCGTTGTGA
1 -CTTCAATCTTTT-AACTGTAATGACGAGGAAGCAAGATTC-CCGTTGTGA
53447989 CTTCAATCT
1 CTTCAATCT
53447998 ATTCCACTGC
Statistics
Matches: 85, Mismatches: 19, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
49 15 0.18
50 67 0.79
51 3 0.04
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.34
Consensus pattern (48 bp):
CTTCAATCTTTTAACTGTAATGACGAGGAAGCAAGATTCCCGTTGTGA
Found at i:53448020 original size:50 final size:49
Alignment explanation
Indices: 53447866--53448028 Score: 159
Period size: 50 Copynumber: 3.3 Consensus size: 49
53447856 GTAATGCCGT
*
53447866 GGAAGCAAGATTCGCCGTTGTGACTTCAATCTTTTCCACTGCATCGACTA
1 GGAAGCAAGATTC-CCGTTGTGACTTCAATCTTTTCCACTGCATCGTCTA
* * * ** * **
53447916 GGAAGTAAGATTCGCTGCTGT-AGCTTCAATCTTTTGAACTGTAAT-GTCGG
1 GGAAGCAAGATTC-CCGTTGTGA-CTTCAATCTTTTCCACTG-CATCGTCTA
* *
53447966 GGAAGCAAGATTCATCGTTGTGACTTCAATCTATTCCACTGCATCGTCTA
1 GGAAGCAAGATTC-CCGTTGTGACTTCAATCTTTTCCACTGCATCGTCTA
*
53448016 GGAAGTAAGATTC
1 GGAAGCAAGATTC
53448029 GCTGTCTTCG
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
49 3 0.03
50 82 0.93
51 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (49 bp):
GGAAGCAAGATTCCCGTTGTGACTTCAATCTTTTCCACTGCATCGTCTA
Found at i:53448243 original size:44 final size:44
Alignment explanation
Indices: 53448021--53449072 Score: 285
Period size: 44 Copynumber: 24.1 Consensus size: 44
53448011 GTCTAGGAAG
* * * ** *
53448021 TAAGATTCGCTGTCTTCGATCTGTTCCACTACTGCTTAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * * *
53448065 TAAGATCTT-TAATTTTCAACCTACTCCACTACTGTTTAAGGAGA
1 TAAGAT-TTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * * * *
53448109 TAATG-TCTACAATCTTCAACCTATTCCACTGCT-ATCTAGAGAGA
1 TAA-GATTTGCAGTCTTCAATCTACTCCACTACTGCTC-AGGGAGA
* * * * * * *
53448153 TAGGGTTTG-TGGCTTAAATCTACTTCC-CTACTCCT-GGGGAAGA
1 TAAGATTTGCAGTCTTCAATCTAC-TCCACTACTGCTCAGGG-AGA
* * * *
53448196 TAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * *
53448240 TAAGATATGCAATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * * * * * *
53448284 TAAGGTCTACAATCTTCAACCTATTCTATTGCTG-TCCAGAGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCT-CAGGGAGA
* * * * * *
53448328 TAGGGTTTG-TGGCTTAAATCTACTTCC-CTACT-CTCGGGGAAGA
1 TAAGATTTGCAGTCTTCAATCTAC-TCCACTACTGCTCAGGG-AGA
* * * * *
53448371 TAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * *
53448415 TAAGATCTGCAATTTTTAACCTACTCCACTGCTGCTCAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * * * *
53448459 TAAGGTCTACAATCTTCAACCTATTCCACTGCTG-TCCAGAGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCT-CAGGGAGA
* * * * * *
53448503 TAGGATTTG-TGGCTTAAATCTACTTCC-CTACTCCT-GGGGAAGA
1 TAAGATTTGCAGTCTTCAATCTAC-TCCACTACTGCTCAGGG-AGA
* * * ** * * * *
53448546 TAAGATTCGAACTCTTTGATTTGCTCCACTATTGCTTAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * *
53448590 TAAGATCTGCAATTTTCAACCTACTCCACTACTGCTCAGAGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * *
53448634 T-AGAGTTTG-TGGCTTAAATCTACTTCC-CTACTCCT-GGGGAAGA
1 TAAGA-TTTGCAGTCTTCAATCTAC-TCCACTACTGCTCAGGG-AGA
* * * * * *
53448677 TAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * *
53448721 TAAGATCTGCAATTTTCAACCTACTCCACTGCTGCTCAAGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * * *
53448765 TAAGA-CT--AGTCTTTAACCTATTCCAATGCTG-TCCAAGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCT-CAGGGAGA
* * * * * **
53448806 TAGGATTTG-TGGCTTAAATCTGCTTCC-CTACT-CTTGGGGAAGA
1 TAAGATTTGCAGTCTTCAATCTAC-TCCACTACTGCTCAGGG-AGA
* * * * * *
53448849 TAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
* * * * * *
53448893 TAAGATCTGTAATTTTCAACCTACTCCACTGA-TGCTCAAGGAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACT-ACTGCTCAGGGAGA
* * * * * * ** *
53448937 TAAGGTCTACAATCTTCAACCTACTCCAATGTTG-TCCAGGAAGA
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCT-CAGGGAGA
* * * * * *
53448981 TAGGATTTG-TGGCTTAAATCTGCTTCC-CTACTCCT-AGGGAAGA
1 TAAGATTTGCAGTCTTCAATCTAC-TCCACTACTGCTCAGGG-AGA
* * ** * * *
53449024 TAAGATTCGCCGTCTTTGATCTGCTCCACTACTACTTAGGGA-A
1 TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
53449067 TAAGAT
1 TAAGAT
53449073 CTACAATTCC
Statistics
Matches: 722, Mismatches: 236, Indels: 101
0.68 0.22 0.10
Matches are distributed among these distances:
40 1 0.00
41 31 0.04
42 15 0.02
43 165 0.23
44 483 0.67
45 27 0.04
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
TAAGATTTGCAGTCTTCAATCTACTCCACTACTGCTCAGGGAGA
Found at i:53448327 original size:175 final size:175
Alignment explanation
Indices: 53448016--53448635 Score: 994
Period size: 175 Copynumber: 3.5 Consensus size: 175
53448006 GCATCGTCTA
* * **
53448016 GGAAG-TAAGATTCGCTGTCTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTTTAATTT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
* * * * *
53448080 TCAACCTACTCCACTACTGTTTAAGGAGATAATGTCTACAATCTTCAACCTATTCCACTGCTATC
66 TCAACCTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
*
53448145 TAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
131 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
* *
53448190 GGAAGATAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATATGCAATTT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
* * *
53448255 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCTATTGCTGTC
66 TCAACCTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
53448320 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACT-CTCGG
131 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCT-GG
53448365 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
* *
53448430 TTAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
66 TCAACCTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
*
53448495 CAGAGAGATAGGATTTGTGGCTTAAATCTACTTCCCTACTCCTGG
131 CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
* * * *
53448540 GGAAGATAAGATTCGAAC-TCTTTGATTTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATT
1 GGAAGATAAGATTCG-CCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATT
*
53448604 TTCAACCTACTCCACTACTGCTCAGAGAGATA
65 TTCAACCTACTCCACTACTGCTCAGGGAGATA
53448636 GAGTTTGTGG
Statistics
Matches: 414, Mismatches: 28, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
174 7 0.02
175 404 0.98
176 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (175 bp):
GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTT
TCAACCTACTCCACTACTGCTCAGGGAGATAAGGTCTACAATCTTCAACCTATTCCACTGCTGTC
CAGAGAGATAGGGTTTGTGGCTTAAATCTACTTCCCTACTCCTGG
Found at i:53448534 original size:131 final size:130
Alignment explanation
Indices: 53448412--53448766 Score: 466
Period size: 131 Copynumber: 2.7 Consensus size: 130
53448402 CTGCTTAGGG
* * * * * * * * *
53448412 AGATAAGATCTGCAATTTTTAACCTACTCCACTGCTGCTCAGGGAGATAAGGTCTACAATCTTCA
1 AGATAAGAT-TGCAATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCA
*
53448477 ACCTATTCCACTGCTG-TCCAGAGAGATAG-GATTTGTGGCTTAAATCTACTTCCCTACTCCTGG
65 ACCTACTCCACTGCTGCT-CAGAGAGATAGAG-TTTGTGGCTTAAATCTACTTCCCTACTCCTGG
53448540 GGA
128 GGA
* *
53448543 AGATAAGATT-CGAACTCTTTGATTTGCTCCACTATTGCTTAGGGAGATAAGATCTGCAATTTTC
1 AGATAAGATTGC-AA-TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTC
*
53448607 AACCTACTCCACTACTGCTCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGG
64 AACCTACTCCACTGCTGCTCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGG
53448672 GA
129 GA
** * *
53448674 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATTTTCA
1 AGATAAGATT-GCAATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCA
53448739 ACCTACTCCACTGCTGCTCA-AGGAGATA
65 ACCTACTCCACTGCTGCTCAGA-GAGATA
53448767 AGACTAGTCT
Statistics
Matches: 197, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
129 1 0.01
130 4 0.02
131 189 0.96
132 2 0.01
133 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (130 bp):
AGATAAGATTGCAATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGCAATTTTCAA
CCTACTCCACTGCTGCTCAGAGAGATAGAGTTTGTGGCTTAAATCTACTTCCCTACTCCTGGGGA
Found at i:53448834 original size:172 final size:173
Alignment explanation
Indices: 53448604--53449080 Score: 739
Period size: 172 Copynumber: 2.8 Consensus size: 173
53448594 ATCTGCAATT
* * *
53448604 TTCAACCTACTCCACTACTG-CTCAGAGAGATA-GAGTTTGTGGCTTAAATCTACTTCCCTACTC
1 TTCAACCTACTCCAATGCTGTC-CAG-GAGATAGGA-TTTGTGGCTTAAATCTGCTTCCCTACTC
53448667 CTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCA
63 CTGGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCA
* *
53448732 ATTTTCAACCTACTCCACTGCTGCTCAAGGAGATAA-GACT-AGTC
128 ATTTTCAACCTACTCCACTGATGCTCAAGGAGATAAGGACTAAATC
* * *
53448776 TTTAACCTATTCCAATGCTGTCCAAGGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCTT
1 TTCAACCTACTCCAATGCTGTCC-AGGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCT
*
53448841 GGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTAAT
65 GGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAT
*
53448906 TTTCAACCTACTCCACTGATGCTCAAGGAGATAAGGTCTACAATC
130 TTTCAACCTACTCCACTGATGCTCAAGGAGATAAGGACTA-AATC
*
53448951 TTCAACCTACTCCAATGTTGTCCAGGAAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCT
1 TTCAACCTACTCCAATGCTGTCCAGG-AGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCT
* * *
53449016 AGGGAAGATAAGATTCGCCGTCTTTGATCTGCTCCACTACTACTTAGGGA-ATAAGATCTACAAT
65 GGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAAT
53449080 T
130 T
53449081 CCATTAATCT
Statistics
Matches: 280, Mismatches: 18, Indels: 12
0.90 0.06 0.04
Matches are distributed among these distances:
172 148 0.53
173 8 0.03
174 16 0.06
175 108 0.39
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (173 bp):
TTCAACCTACTCCAATGCTGTCCAGGAGATAGGATTTGTGGCTTAAATCTGCTTCCCTACTCCTG
GGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGCAATT
TTCAACCTACTCCACTGATGCTCAAGGAGATAAGGACTAAATC
Found at i:53459152 original size:103 final size:104
Alignment explanation
Indices: 53458973--53459237 Score: 417
Period size: 103 Copynumber: 2.6 Consensus size: 104
53458963 AACCGTTATT
* * * *
53458973 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
53459038 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
53459076 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
53459140 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
53459180 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
53459238 TTATGTACAA
Statistics
Matches: 149, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
102 1 0.01
103 82 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:53459599 original size:30 final size:29
Alignment explanation
Indices: 53459565--53459629 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
53459555 TAATCCACCA
53459565 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
53459595 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
53459625 CCCAA
1 CCCAA
53459630 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:53459603 original size:31 final size:30
Alignment explanation
Indices: 53459572--53459629 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53459562 CCACCCAACT
53459572 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
53459602 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
53459630 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:53466626 original size:26 final size:26
Alignment explanation
Indices: 53466596--53466645 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
53466586 CCAATGAACT
*
53466596 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACATAGCAACCCCTC
53466622 GGGGAATCAGCACATAGCAACCCC
1 GGGGAATCAGCACATAGCAACCCC
53466646 CTTTCACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.34, G:0.24, T:0.12
Consensus pattern (26 bp):
GGGGAATCAGCACATAGCAACCCCTC
Found at i:53466657 original size:103 final size:102
Alignment explanation
Indices: 53466460--53466723 Score: 404
Period size: 103 Copynumber: 2.6 Consensus size: 102
53466450 AACCGTTATT
* * * *
53466460 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC-TCGGGGA
** *
53466525 ATCAGCACATAGCAACCCCCTTTTTATTTCAGAGATAC
65 ATCAGCACATAGCAACCCCCTTTACATTTCAAAGATAC
53466563 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGA
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGA
53466627 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 ATCAGCACATAGCAACCCCCTTT-ACATTTCAAAGATAC
* **
53466666 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
53466724 TTATGTACAA
Statistics
Matches: 148, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
102 30 0.20
103 117 0.79
104 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (102 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGAA
TCAGCACATAGCAACCCCCTTTACATTTCAAAGATAC
Found at i:53467085 original size:30 final size:29
Alignment explanation
Indices: 53467051--53467115 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
53467041 TAATCCACCA
53467051 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
53467081 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
53467111 CCCAA
1 CCCAA
53467116 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:53467089 original size:31 final size:30
Alignment explanation
Indices: 53467058--53467115 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
53467048 CCACCCAACT
53467058 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
53467088 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
53467116 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:53473217 original size:5 final size:5
Alignment explanation
Indices: 53473201--53473289 Score: 115
Period size: 5 Copynumber: 17.8 Consensus size: 5
53473191 TTCATACTAG
* * * *
53473201 TCATA TCTTA TCATA TCATA ACGTA TCATA ACATA TCATA TCATA TCATA
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCATA
* * *
53473251 TCATA CCAAA TCATA TCATA TCATA TTATA TCATA TCAT
1 TCATA TCATA TCATA TCATA TCATA TCATA TCATA TCAT
53473290 TACATGTCCT
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 70 1.00
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.38
Consensus pattern (5 bp):
TCATA
Found at i:53473873 original size:49 final size:51
Alignment explanation
Indices: 53473818--53473964 Score: 135
Period size: 49 Copynumber: 3.0 Consensus size: 51
53473808 TACCCATACG
*
53473818 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACATGGCTAAGACACACA-A
1 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACAAGGCTAAGACACACATA
**** * * *
53473868 G-CTGTAAAAACACACACGG-CTGTGTGCTCTACACGGCCT---ACCCACATA
1 GTCTGTAAAGTTTCACACGGCCT-TGTGCTCCACAAGG-CTAAGACACACATA
* * *
53473916 GTCTGCAAAGTTTTACACGGCCTTGTGCTCCACAAGGCCAAGACACACA
1 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACAAGGCTAAGACACACA
53473965 GGTTGCAAAA
Statistics
Matches: 72, Mismatches: 17, Indels: 15
0.69 0.16 0.14
Matches are distributed among these distances:
47 6 0.08
48 5 0.07
49 50 0.69
50 5 0.07
51 6 0.08
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (51 bp):
GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACAAGGCTAAGACACACATA
Found at i:53473981 original size:98 final size:98
Alignment explanation
Indices: 53473818--53474004 Score: 257
Period size: 98 Copynumber: 1.9 Consensus size: 98
53473808 TACCCATACG
* * * * *
53473818 GTCTGTAAAGTTTCACACGGCCTTGTGCTCCACATGGCTAAGACACACAAGCTGTAAAAACACAC
1 GTCTGCAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAAGCTGCAAAAAAACAC
* * *
53473883 ACGGCTGTGTGCTCTACACGGCCTACCCACATA
66 ACGACCGTGTGCTCCACACGGCCTACCCACATA
* * *
53473916 GTCTGCAAAGTTTTACACGGCCTTGTGCTCCACAAGGCCAAGACACACAGGTTGCAAAAAAACAC
1 GTCTGCAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAAGCTGCAAAAAAACAC
* *
53473981 ATGACCGTGTGCTCCGCACGGCCT
66 ACGACCGTGTGCTCCACACGGCCT
53474005 GACACACGGC
Statistics
Matches: 76, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
98 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.20
Consensus pattern (98 bp):
GTCTGCAAAGTTTCACACGGCCTTGTGCTCCACAAGGCCAAGACACACAAGCTGCAAAAAAACAC
ACGACCGTGTGCTCCACACGGCCTACCCACATA
Found at i:53481048 original size:17 final size:16
Alignment explanation
Indices: 53481028--53481077 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
53481018 TTATTTTTAA
53481028 AATTTTTATATTATTTT
1 AATTTTTATATT-TTTT
*
53481045 AA-TTTAATATTTTTT
1 AATTTTTATATTTTTT
53481060 -ATTTATTGATATTTTTT
1 AATTT-TT-ATATTTTTT
53481077 A
1 A
53481078 TATAGTCAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 1 0.04
15 6 0.22
16 9 0.33
17 11 0.41
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
AATTTTTATATTTTTT
Found at i:53481151 original size:7 final size:7
Alignment explanation
Indices: 53481141--53481182 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
53481131 TGTTATAAAT
53481141 TATATAA
1 TATATAA
53481148 TATATAA
1 TATATAA
53481155 -ATATAA
1 TATATAA
*
53481161 TATAAAA
1 TATATAA
*
53481168 TATAAAA
1 TATATAA
53481175 TATTATAA
1 TA-TATAA
53481183 ACTTAAAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
6 6 0.19
7 21 0.68
8 4 0.13
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
TATATAA
Found at i:53484597 original size:16 final size:16
Alignment explanation
Indices: 53484576--53484607 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
53484566 TTAGCTAGCT
53484576 AGGGATCTTGACATTA
1 AGGGATCTTGACATTA
53484592 AGGGATCTTGACATTA
1 AGGGATCTTGACATTA
53484608 CTGAGTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.25, T:0.31
Consensus pattern (16 bp):
AGGGATCTTGACATTA
Found at i:53493206 original size:16 final size:17
Alignment explanation
Indices: 53493149--53493201 Score: 106
Period size: 17 Copynumber: 3.1 Consensus size: 17
53493139 ATTTCCTTTC
53493149 TTTCATTTTTTTAGTTA
1 TTTCATTTTTTTAGTTA
53493166 TTTCATTTTTTTAGTTA
1 TTTCATTTTTTTAGTTA
53493183 TTTCATTTTTTTAGTTA
1 TTTCATTTTTTTAGTTA
53493200 TT
1 TT
53493202 AATTTGCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.72
Consensus pattern (17 bp):
TTTCATTTTTTTAGTTA
Found at i:53505627 original size:175 final size:175
Alignment explanation
Indices: 53505336--53505709 Score: 606
Period size: 175 Copynumber: 2.1 Consensus size: 175
53505326 ACAGATCAGT
***
53505336 GAAGAATTACAGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCCAGTAATCCTATTT
1 GAAGAATTACAGATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCCAGTAATCCTATTT
53505401 CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
66 CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
*
53505466 GATCGCATCAGGTCTTTTCTCCCTAAGATTACAGTGGAATAGACC
131 GATCGCATCAGGTCTTATCTCCCTAAGATTACAGTGGAATAGACC
* * *
53505511 GAAGAATTATAGTTCTTATCTCCCTGAGATTACAGCAAAGCATATTGAAGCCAGTAATCCTATTT
1 GAAGAATTACAGATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCCAGTAATCCTATTT
* * * *
53505576 CCCTGAGATTATAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTA
66 CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
* *
53505641 GATCGCATCAGGTCTTATCTCCCTGAGATTATAGTGGAATAGACC
131 GATCGCATCAGGTCTTATCTCCCTAAGATTACAGTGGAATAGACC
* *
53505686 GAAGAATTA-AGATCCTGTCTCCCT
1 GAAGAATTACAGATCTTATCTCCCT
53505710 AAGCAGTAGC
Statistics
Matches: 183, Mismatches: 16, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
174 12 0.07
175 171 0.93
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (175 bp):
GAAGAATTACAGATCTTATCTCCCTGAGATTACAGCAAAGCAGATTGAAGCCAGTAATCCTATTT
CCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGCA
GATCGCATCAGGTCTTATCTCCCTAAGATTACAGTGGAATAGACC
Found at i:53505674 original size:85 final size:85
Alignment explanation
Indices: 53505400--53505679 Score: 285
Period size: 85 Copynumber: 3.2 Consensus size: 85
53505390 TAATCCTATT
*
53505400 TCCCTGAGATTACAATGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
1 TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
*
53505465 AGATCGCATCAGGTCTTTTC
66 AGATCGCATCAGGTCTTATC
* * ** * * * *
53505485 TCCCTAAGATTACAGTGGAATAGACCGAAGAATTATA-GTTCTTATCTCCCTG-AGATTACAGCA
1 TCCCTGAGATTACAGTGGAACAGA-TTAA-AA-TAAAGGATCTTATCTCTCTGAAG-TTACAGTA
* * * * * * * *
53505548 AAGCATATTGAAGCCAGTAATCCTATT
62 GAGCAGATCGCA-TCAG--GTCTTATC
* * *
53505575 TCCCTGAGATTATAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGT
1 TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
53505640 AGATCGCATCAGGTCTTATC
66 AGATCGCATCAGGTCTTATC
*
53505660 TCCCTGAGATTATAGTGGAA
1 TCCCTGAGATTACAGTGGAA
53505680 TAGACCGAAG
Statistics
Matches: 149, Mismatches: 37, Indels: 18
0.73 0.18 0.09
Matches are distributed among these distances:
85 46 0.31
86 4 0.03
87 36 0.24
88 35 0.23
89 4 0.03
90 24 0.16
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (85 bp):
TCCCTGAGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGC
AGATCGCATCAGGTCTTATC
Found at i:53505874 original size:44 final size:44
Alignment explanation
Indices: 53505780--53505874 Score: 154
Period size: 44 Copynumber: 2.2 Consensus size: 44
53505770 TTAAGCCGCG
* *
53505780 AGTCCTATCTCCCTGACCAGCAGTGGAATAGGTTGAAGATCGCA
1 AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATCACA
* *
53505824 ATTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATTACA
1 AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATCACA
53505868 AGTCCTA
1 AGTCCTA
53505875 ACCCGCAGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.25
Consensus pattern (44 bp):
AGTCCTATCTCCCTGACCAACAGTGGAATAGGTTGAAGATCACA
Found at i:53511128 original size:105 final size:104
Alignment explanation
Indices: 53510900--53511381 Score: 547
Period size: 105 Copynumber: 4.6 Consensus size: 104
53510890 AGATAAGTTG
* * * * * *
53510900 TTAGGATTTGTGATCATAAATTAGCTAACTCAAATAAACTTAGGTTATGATCTTAAATCAACTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
** ** *
53510965 CCTT-TAATATCAGTTGTGAATGTAGGTCAGTGAGCTAT
66 CCTTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * *
53511003 TTAGGAGTT-ACGATCTTAAATAAACTAACTCAAATAAATTTGGGTTACGATCTTAAATCAGCTA
1 TTAGGAGTTGA-GATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTA
* * * * *
53511067 ACCTTTATAATATTAGCTGTGAACGTAGGTCAGCAAGCTGT
65 ACC-TTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * *
53511108 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAGACTTAGGTTTCAATCTTAAATCAATTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
* * *
53511173 CCTTATAATATTAATTCTGAACATAGGTCAGCGAGCTAT
66 CCTTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * * ** *
53511212 TTAGAAGTTGCGATCTTAAAT-AGCTAAGTCAAATAAACTTAGGTCGCGATCTTAAATCAGCTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
* * *
53511276 CCTTTAAAATATCAACCGTGAACATAGGTCAGTGAGCTAT
66 CC-TTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
* * * *
53511316 TTAAGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCGATATTAAATCAACTAA
1 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
53511381 C
66 C
53511382 TCAAATAAAC
Statistics
Matches: 319, Mismatches: 54, Indels: 10
0.83 0.14 0.03
Matches are distributed among these distances:
103 94 0.29
104 101 0.32
105 123 0.39
106 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (104 bp):
TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAAACTTAGGTTACGATCTTAAATCAACTAA
CCTTATAATATCAACTGTGAACATAGGTCAGCGAGCTAT
Found at i:53511306 original size:208 final size:208
Alignment explanation
Indices: 53510900--53511381 Score: 635
Period size: 208 Copynumber: 2.3 Consensus size: 208
53510890 AGATAAGTTG
* * * *
53510900 TTAGGATTTGTGATCATAAATTAGCTAACTCAAATAAACTTAGGTTAT-GATCTTAAATCAACTA
1 TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTT-TCGATCTTAAATCAACTA
* * ** * *
53510964 ACCTTTAATATCAGTTGTGAATGTAGGTCAGTGAGCTATTTAGGAGTTACGATCTTAAATAAACT
65 ACCTTTAATATCAATTCTGAACATAGGTCAGCGAGCTATTTAGAAGTTACGATCTTAAATAAACT
* * * * * * * *
53511029 AACTCAAATAAATTTGGGTTACGATCTTAAATCAGCTAACCTTTATAATATTAGCTGTGAACGTA
130 AACTCAAATAAACTTAGGTCACGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATA
*
53511094 GGTCAGCAAGCTGT
195 GGTCAGCAAGCTAT
* * * *
53511108 TTAGGAGTTGAGATCTTAAATCAACTAACTCAAATAGACTTAGGTTTCAATCTTAAATCAATTAA
1 TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAACTAA
* * *
53511173 CCTTATAATATTAATTCTGAACATAGGTCAGCGAGCTATTTAGAAGTTGCGATCTTAAAT-AGCT
66 CCTT-TAATATCAATTCTGAACATAGGTCAGCGAGCTATTTAGAAGTTACGATCTTAAATAAACT
* *
53511237 AAGTCAAATAAACTTAGGTCGCGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATA
130 AACTCAAATAAACTTAGGTCACGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATA
**
53511302 GGTCAGTGAGCTAT
195 GGTCAGCAAGCTAT
* * *
53511316 TTAAGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCGATATTAAATCAACTAA
1 TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAACTAA
53511381 C
66 C
53511382 TCAAATAAAC
Statistics
Matches: 235, Mismatches: 37, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
207 1 0.00
208 187 0.80
209 47 0.20
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (208 bp):
TTAGGAGTTGTGATCTTAAATCAACTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAACTAA
CCTTTAATATCAATTCTGAACATAGGTCAGCGAGCTATTTAGAAGTTACGATCTTAAATAAACTA
ACTCAAATAAACTTAGGTCACGATCTTAAATCAGCTAACCTTTAAAATATCAACCGTGAACATAG
GTCAGCAAGCTAT
Found at i:53511418 original size:37 final size:37
Alignment explanation
Indices: 53511328--53511410 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
53511318 AAGAGTTGTG
*
53511328 ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCG
1 ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCA
* *
53511365 ATATTAAATCAACTAACTCAAATAAACTTAGGTTTCA
1 ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCA
53511402 ATCTTAAAT
1 ATCTTAAAT
53511411 TAGCTAACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (37 bp):
ATCTTAAATCAACTAACTCAAATAAACTTAGGTTCCA
Found at i:53511496 original size:142 final size:142
Alignment explanation
Indices: 53511222--53511644 Score: 537
Period size: 142 Copynumber: 3.0 Consensus size: 142
53511212 TTAGAAGTTG
* * ** *
53511222 CGATCTTAAAT-AGCTAAGTCAAATAAACTTAGGTCGCGATCTTAAATCAGCTAACCTTTAAAAT
1 CGATATTAAATCAGCTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAGCTAACCTTTATAAT
* * * * * * *
53511286 ATCA-ACCGTGAACATAGGTCAGTGAGCTATTTAAGAGTTGTGATCTTAAATCAACTAACTCAAA
66 ATTAGA-TGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAA
53511350 TAAACTTAGGTTC
130 TAAACTTAGGTTC
* * * * *
53511363 CGATATTAAATCAACTAACTCAAATAAACTTAGGTTTCAATCTTAAATTAGCTAACCTATATAAC
1 CGATATTAAATCAGCTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAGCTAACCTTTATAAT
* * * * **
53511428 ATTAGTTGTGAACATAGGTTAGCAAGTTGTTTAGGAGTTGCGATTTTAAATCAGGTAACTCAAAT
66 ATTAGATGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAAT
*
53511493 AAACTTAGGTTG
131 AAACTTAGGTTC
* * *
53511505 CGATATTAAATCAGCTAACTCAAATTAACTTAGGTTGT-GATCTAAAATCAACTAACCTTTATAA
1 CGATATTAAATCAGCTAACTCAAATAAACTTAGGTT-TCGATCTTAAATCAGCTAACCTTTATAA
* * *
53511569 TATTAGATGTGAACGTAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATTAACTAATTCAAA
65 TATTAGATGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAA
53511634 TAAACTTAGGT
130 TAAACTTAGGT
53511645 ATGAACATTT
Statistics
Matches: 238, Mismatches: 41, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
141 10 0.04
142 227 0.95
143 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (142 bp):
CGATATTAAATCAGCTAACTCAAATAAACTTAGGTTTCGATCTTAAATCAGCTAACCTTTATAAT
ATTAGATGTGAACATAGGTTAGCGAGCTGTTTAGGAGTTGCGATCTTAAATCAACTAACTCAAAT
AAACTTAGGTTC
Found at i:53511514 original size:37 final size:37
Alignment explanation
Indices: 53511464--53511560 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
53511454 TTGTTTAGGA
* *
53511464 GTTGCGATTTTAAATCAGGTAACTCAAATAAACTTAG
1 GTTGCGATATTAAATCAGCTAACTCAAATAAACTTAG
*
53511501 GTTGCGATATTAAATCAGCTAACTCAAATTAACTTAG
1 GTTGCGATATTAAATCAGCTAACTCAAATAAACTTAG
* * * *
53511538 GTTGTGATCTAAAATCAACTAAC
1 GTTGCGATATTAAATCAGCTAAC
53511561 CTTTATAATA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.32
Consensus pattern (37 bp):
GTTGCGATATTAAATCAGCTAACTCAAATAAACTTAG
Found at i:53511711 original size:10 final size:10
Alignment explanation
Indices: 53511696--53511726 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
53511686 ATCTTTCATA
53511696 CATTATATTT
1 CATTATATTT
53511706 CATTATATTT
1 CATTATATTT
53511716 CATTATATTT
1 CATTATATTT
53511726 C
1 C
53511727 TTCAGATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (10 bp):
CATTATATTT
Found at i:53522255 original size:69 final size:70
Alignment explanation
Indices: 53522123--53522255 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
53522113 TAGTTTATTA
* * * * *
53522123 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
53522188 CTTAG
66 CTTAG
53522193 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
53522256 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:53523796 original size:47 final size:47
Alignment explanation
Indices: 53523719--53524280 Score: 836
Period size: 47 Copynumber: 12.0 Consensus size: 47
53523709 TTAGGATTTT
** *
53523719 ATGTGATGAATGTGAATGTGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * **
53523766 ATTTGATAAATGTGAGCATGCATATGTGTGATAAGGTTGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53523813 ATGTGGTGAATATGAACATGTATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53523860 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53523907 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53523954 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53524001 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
53524048 ATGTGGTGAATATGAACATGCATATATGTGATAAGGCCGAATGGCCT
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
53524095 ATGTGATGAATGTGAACATGCATATATGTGATGAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53524142 ATGTGATGAATGTGAGCATGCATATATATGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
53524189 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * *
53524236 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGC
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGC
53524281 TAGTGTGAAA
Statistics
Matches: 460, Mismatches: 55, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 460 1.00
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:53523915 original size:25 final size:25
Alignment explanation
Indices: 53523840--53523915 Score: 63
Period size: 23 Copynumber: 3.2 Consensus size: 25
53523830 ATGTATATAT
53523840 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
* * * *
53523865 ATGA-ATGTG-AGCAT-G-CATATGT-
1 GTGATAAG-GCCGAATGGCCA-ATGTG
53523887 GTGATAAGGCCGAATGGCCAATGTG
1 GTGATAAGGCCGAATGGCCAATGTG
53523912 GTGA
1 GTGA
53523916 ATATGAACAT
Statistics
Matches: 36, Mismatches: 8, Indels: 14
0.62 0.14 0.24
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.34, T:0.24
Consensus pattern (25 bp):
GTGATAAGGCCGAATGGCCAATGTG
Found at i:53524244 original size:25 final size:25
Alignment explanation
Indices: 53524170--53524244 Score: 61
Period size: 23 Copynumber: 3.1 Consensus size: 25
53524160 TGCATATATA
*
53524170 TGATAAGGCCGAATGGCCAATGTGA
1 TGATAAGGCCGAATGGCCAATGTGG
* * *
53524195 TGA-ATGTG-AGCAT-G-CATATGT-G
1 TGATAAG-GCCGAATGGCCA-ATGTGG
53524217 TGATAAGGCCGAATGGCCAATGTGG
1 TGATAAGGCCGAATGGCCAATGTGG
53524242 TGA
1 TGA
53524245 ATATGAACAT
Statistics
Matches: 36, Mismatches: 7, Indels: 14
0.63 0.12 0.25
Matches are distributed among these distances:
22 6 0.17
23 10 0.28
24 10 0.28
25 10 0.28
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.24
Consensus pattern (25 bp):
TGATAAGGCCGAATGGCCAATGTGG
Found at i:53524493 original size:37 final size:37
Alignment explanation
Indices: 53524443--53524594 Score: 232
Period size: 37 Copynumber: 4.1 Consensus size: 37
53524433 GGAAATATAT
* * *
53524443 TCCGGGTGAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
53524480 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* *
53524517 CCCGGGTAAGACCCGATGACTACGTGTAGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
* * *
53524554 TCCGGGTAAGACCCGATAACTTCGTGTGGAGATTTCG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
53524591 TCCG
1 TCCG
53524595 AGCTAAAGGT
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 105 1.00
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTTTG
Found at i:53526343 original size:41 final size:41
Alignment explanation
Indices: 53526294--53526374 Score: 144
Period size: 41 Copynumber: 2.0 Consensus size: 41
53526284 ATTACGAAGT
53526294 TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAAC
1 TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAAC
**
53526335 TAGTATGAAAAATATATTAAAGATCGGTTAAGTAATTAAA
1 TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAA
53526375 TTGAGAAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.32
Consensus pattern (41 bp):
TAGTATGAAAAATATATTAAAGATCAATTAAGTAATTAAAC
Found at i:53529385 original size:15 final size:14
Alignment explanation
Indices: 53529365--53529394 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
53529355 CTTCATGTAG
53529365 TTGATTTGTCATAAT
1 TTGATTTGTCA-AAT
53529380 TTGATTTGTCAAAT
1 TTGATTTGTCAAAT
53529394 T
1 T
53529395 AGGCTTCCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (14 bp):
TTGATTTGTCAAAT
Found at i:53531243 original size:7 final size:7
Alignment explanation
Indices: 53531231--53531287 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
53531221 TAGTTTACAT
53531231 TTTTTTA
1 TTTTTTA
53531238 TTTTTTA
1 TTTTTTA
53531245 -TTTTTA
1 TTTTTTA
**
53531251 TAATTTA
1 TTTTTTA
53531258 TTTTTATAA
1 TTTTT-T-A
*
53531267 TTTTTAA
1 TTTTTTA
53531274 TTTTTTA
1 TTTTTTA
53531281 TTATTTT
1 TT-TTTT
53531288 TAAATTATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
6 6 0.15
7 23 0.57
8 5 0.12
9 6 0.15
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTA
Found at i:53531259 original size:20 final size:20
Alignment explanation
Indices: 53531234--53531301 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
53531224 TTTACATTTT
53531234 TTTATTTTTTATTTTTATAA
1 TTTATTTTTTATTTTTATAA
*
53531254 TTTATTTTTATAATTTT-TAA
1 TTTATTTTT-TATTTTTATAA
*
53531274 TTT-TTTATTATTTTTA-AA
1 TTTATTTTTTATTTTTATAA
53531292 -TTATTTTTTA
1 TTTATTTTTTA
53531302 ATGTAACATA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
17 2 0.05
18 14 0.34
19 4 0.10
20 15 0.37
21 6 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTATTTTTTATTTTTATAA
Found at i:53531277 original size:36 final size:36
Alignment explanation
Indices: 53531231--53531303 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
53531221 TAGTTTACAT
* *
53531231 TTTTTTATTTTTTATT-TTTATAATTTATTTTTATAA
1 TTTTTAATTTTTTATTATTTATAAATTATTTTT-TAA
*
53531267 TTTTTAATTTTTTATTATTTTTAAATTATTTTTTAA
1 TTTTTAATTTTTTATTATTTATAAATTATTTTTTAA
53531303 T
1 T
53531304 GTAACATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
36 19 0.58
37 14 0.42
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (36 bp):
TTTTTAATTTTTTATTATTTATAAATTATTTTTTAA
Found at i:53531279 original size:18 final size:19
Alignment explanation
Indices: 53531256--53531303 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
53531246 TTTTATAATT
53531256 TATTTTTATAATTTTT-AA
1 TATTTTTATAATTTTTAAA
*
53531274 T-TTTTTATTATTTTTAAA
1 TATTTTTATAATTTTTAAA
53531292 TTATTTTT-TAAT
1 -TATTTTTATAAT
53531304 GTAACATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 13 0.52
18 3 0.12
19 4 0.16
20 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TATTTTTATAATTTTTAAA
Found at i:53535677 original size:6 final size:7
Alignment explanation
Indices: 53535611--53535646 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
53535601 TGCCCTGTCG
53535611 TTAGGGT
1 TTAGGGT
53535618 TTAGGGT
1 TTAGGGT
53535625 TTAGGGT
1 TTAGGGT
53535632 TTAGGGT
1 TTAGGGT
53535639 TTAGGGT
1 TTAGGGT
53535646 T
1 T
53535647 AAGGTTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:53538835 original size:21 final size:21
Alignment explanation
Indices: 53538809--53538850 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
53538799 CCAGCTTCCA
* *
53538809 GCGGGGGTTCTAGTTGCTCCG
1 GCGGGGATTCTAGTTCCTCCG
53538830 GCGGGGATTCTAGTTCCTCCG
1 GCGGGGATTCTAGTTCCTCCG
53538851 ATAGGGGATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.26, G:0.38, T:0.29
Consensus pattern (21 bp):
GCGGGGATTCTAGTTCCTCCG
Found at i:53540449 original size:11 final size:11
Alignment explanation
Indices: 53540417--53540473 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
53540407 TTTTTTAAAT
* *
53540417 AGGAATTTGAA
1 AGGAAATTGAG
53540428 AGGAAATTGAG
1 AGGAAATTGAG
53540439 AGGAAATTGAG
1 AGGAAATTGAG
53540450 A-GAATATT-AG
1 AGGAA-ATTGAG
53540460 AGAGAAATTGAG
1 AG-GAAATTGAG
53540472 AG
1 AG
53540474 AAAGGATTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 6 0.15
11 27 0.68
12 7 0.17
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:53540472 original size:10 final size:10
Alignment explanation
Indices: 53540430--53540476 Score: 67
Period size: 11 Copynumber: 4.4 Consensus size: 10
53540420 AATTTGAAAG
53540430 GAAATTGAGA
1 GAAATTGAGA
53540440 GGAAATTGAGA
1 -GAAATTGAGA
53540451 GAATATTAGAGA
1 GAA-ATT-GAGA
53540463 GAAATTGAGA
1 GAAATTGAGA
53540473 GAAA
1 GAAA
53540477 GGATTAAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
10 11 0.32
11 16 0.47
12 7 0.21
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (10 bp):
GAAATTGAGA
Found at i:53548945 original size:5 final size:5
Alignment explanation
Indices: 53548935--53548971 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
53548925 AATTTAGTAC
*
53548935 TTATA TTATA TTATA TTATA TTACA TTATA TT-TA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
53548972 AAATAGTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 4 0.14
5 25 0.86
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:53556961 original size:45 final size:45
Alignment explanation
Indices: 53556887--53557002 Score: 160
Period size: 45 Copynumber: 2.6 Consensus size: 45
53556877 CTACGTGTAG
* * * **
53556887 CGAGTATCACTGATTATAAAGGTGGTTGCTATGTGTTGATTCCAC
1 CGAGTACCATTGATTATAAAGGTGGTTGCTATCTACTGATTCCAC
*
53556932 CGGGTACCATTGATTATAAAGGTGGTTGCTATCTACTGATTCCAC
1 CGAGTACCATTGATTATAAAGGTGGTTGCTATCTACTGATTCCAC
* *
53556977 CGAGTATCATTGATTATAAGGGTGGT
1 CGAGTACCATTGATTATAAAGGTGGT
53557003 GTTGTGTGCT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (45 bp):
CGAGTACCATTGATTATAAAGGTGGTTGCTATCTACTGATTCCAC
Found at i:53564598 original size:80 final size:80
Alignment explanation
Indices: 53564465--53564622 Score: 316
Period size: 80 Copynumber: 2.0 Consensus size: 80
53564455 AATTATATCA
53564465 ACCGAGTGATTACAAAACAACGTAGGCTTACATAACTTTACCTCAATATAGAAAATCTAGTATCA
1 ACCGAGTGATTACAAAACAACGTAGGCTTACATAACTTTACCTCAATATAGAAAATCTAGTATCA
53564530 GGAGTGAAGTCTTCT
66 GGAGTGAAGTCTTCT
53564545 ACCGAGTGATTACAAAACAACGTAGGCTTACATAACTTTACCTCAATATAGAAAATCTAGTATCA
1 ACCGAGTGATTACAAAACAACGTAGGCTTACATAACTTTACCTCAATATAGAAAATCTAGTATCA
53564610 GGAGTGAAGTCTT
66 GGAGTGAAGTCTT
53564623 GAGAATTACT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.27
Consensus pattern (80 bp):
ACCGAGTGATTACAAAACAACGTAGGCTTACATAACTTTACCTCAATATAGAAAATCTAGTATCA
GGAGTGAAGTCTTCT
Found at i:53568393 original size:21 final size:21
Alignment explanation
Indices: 53568334--53568393 Score: 50
Period size: 21 Copynumber: 2.9 Consensus size: 21
53568324 TAGGATCTCG
*
53568334 AACCCTGAACTCAAAACCTAA
1 AACCCTGAACTCATAACCTAA
** * **
53568355 AACCCAAAACAC-TAAACCTGC
1 AACCCTGAACTCAT-AACCTAA
53568376 AACCCTGAACTCATAACC
1 AACCCTGAACTCATAACC
53568394 CATAACTCAT
Statistics
Matches: 28, Mismatches: 9, Indels: 4
0.68 0.22 0.10
Matches are distributed among these distances:
21 27 0.96
22 1 0.04
ACGTcount: A:0.45, C:0.37, G:0.05, T:0.13
Consensus pattern (21 bp):
AACCCTGAACTCATAACCTAA
Found at i:53568509 original size:27 final size:27
Alignment explanation
Indices: 53568470--53568522 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
53568460 AAACTTGACC
53568470 CTTAAACCCCAAA-CACAAACCCTAAAT
1 CTTAAACCCCAAATC-CAAACCCTAAAT
* * *
53568497 CTTAAATCTCAAATCCAAACCTTAAA
1 CTTAAACCCCAAATCCAAACCCTAAA
53568523 CCTCATAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (27 bp):
CTTAAACCCCAAATCCAAACCCTAAAT
Found at i:53571772 original size:127 final size:125
Alignment explanation
Indices: 53571621--53571848 Score: 411
Period size: 127 Copynumber: 1.8 Consensus size: 125
53571611 TATTATGCTT
53571621 AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAATAAAAAATATTAA
1 AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAAT-AAAAATATTAA
* *
53571686 TATATATATAATTTTTTTCATATATAAATTTTGAAATTTATATATATAAATTAATATTTTTA
65 TATATAAATAATTTTTTT-ATATATAAATTTTAAAATTTATATATATAAATTAATATTTTTA
*
53571748 AATTTTTAGTTATTTTTAATACATACTTATAGTTTAATTTGTACTTTCTTAATAAAAATATTAAT
1 AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAATAAAAATATTAAT
53571813 ATATAAATAATTTTTTTATATATAAATTTTAAAATT
66 ATATAAATAATTTTTTTATATATAAATTTTAAAATT
53571849 ATTAAGGCAA
Statistics
Matches: 98, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
125 18 0.18
126 28 0.29
127 52 0.53
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (125 bp):
AATTTTTAGTTATTTTTAATACATACTTATAGTATAATTTGTACTTTCTTAATAAAAATATTAAT
ATATAAATAATTTTTTTATATATAAATTTTAAAATTTATATATATAAATTAATATTTTTA
Found at i:53574550 original size:51 final size:51
Alignment explanation
Indices: 53574460--53574595 Score: 137
Period size: 51 Copynumber: 2.7 Consensus size: 51
53574450 CAATGAGATG
* * * * *
53574460 AGATTCGTTGCCTTCAACTTTAATCTGCTCCGCTACAACGCCAGGGAAATA
1 AGATTCGCTGCCTTCAGCTTTAATCTACTCCACTACAACGCCAAGGAAATA
* * *
53574511 AGATTCGCTGCCTTCAGCTTTAATCTATTCCACTGCAACGCCAAGGAGATA
1 AGATTCGCTGCCTTCAGCTTTAATCTACTCCACTACAACGCCAAGGAAATA
* * * ** * *
53574562 GGATTTGCAGTATTCAGCTTTAATCCACTGCACT
1 AGATTCGCTGCCTTCAGCTTTAATCTACTCCACT
53574596 TCAGCTTTAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (51 bp):
AGATTCGCTGCCTTCAGCTTTAATCTACTCCACTACAACGCCAAGGAAATA
Found at i:53574616 original size:21 final size:21
Alignment explanation
Indices: 53574574--53574616 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
53574564 ATTTGCAGTA
*
53574574 TTCAGCTTTAATCCACTGCAC
1 TTCAGCTTTAATCCACTCCAC
*
53574595 TTCAGCTTTAATCCATTCCAC
1 TTCAGCTTTAATCCACTCCAC
53574616 T
1 T
53574617 GCAATGCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.07, T:0.37
Consensus pattern (21 bp):
TTCAGCTTTAATCCACTCCAC
Found at i:53574797 original size:45 final size:45
Alignment explanation
Indices: 53574741--53574837 Score: 122
Period size: 45 Copynumber: 2.2 Consensus size: 45
53574731 GTCTTCTTCA
* * * * * *
53574741 ATCTGCTTCGCTGTCAGTACAAGAAGGCAAGATCTGCTATCCTCG
1 ATCTACTTCGCTGCCAATACAAGAAGACAAGATATACTATCCTCG
* *
53574786 ATCTACTTCGCTGCCAATACAGGAAGACAAGATATACTATCTTCG
1 ATCTACTTCGCTGCCAATACAAGAAGACAAGATATACTATCCTCG
53574831 ATCTACT
1 ATCTACT
53574838 CCACTGCTAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (45 bp):
ATCTACTTCGCTGCCAATACAAGAAGACAAGATATACTATCCTCG
Found at i:53574988 original size:129 final size:132
Alignment explanation
Indices: 53574810--53575172 Score: 536
Period size: 132 Copynumber: 2.8 Consensus size: 132
53574800 CAATACAGGA
* * * * * * *
53574810 AGACAAGATATACTATCTTCGATCTACTCCACTGCTACTCAGGGAGATAGGACTAGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
* *
53574875 TCTGCTTCCCTACTACCTTGGAAAGATAATG-TTCGCC-T-TT-GATCTGCTCCACTACTGCTTA
66 TCTGCTTCCCTACTACCTTGGGAAGATAA-GATTCACCATCTTCGATCTGCTCCACTACTGCTTA
53574936 GGG
130 GGG
* * *
53574939 AGACGGGATCTACATTCTTCAACCTACTCCACTGCTGCTTAGGGAGATAGGACTGGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
53575004 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAG
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAG
53575069 GG
131 GG
* *
53575071 AGACAGGATCTACAATCTTCAACCTAATCCACTGTTGCTCAGGGAGATAGGACTGGTGGCTTAAA
1 AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
* * *
53575136 TCTGTTTCCCTACTTCTTTGGGAAGATAAGATTCACC
66 TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACC
53575173 GCCTTCTTCA
Statistics
Matches: 210, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
128 1 0.00
129 88 0.42
130 1 0.00
131 2 0.01
132 118 0.56
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (132 bp):
AGACAGGATCTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAA
TCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAG
GG
Found at i:53575102 original size:44 final size:44
Alignment explanation
Indices: 53574921--53575122 Score: 133
Period size: 44 Copynumber: 4.6 Consensus size: 44
53574911 CTTTGATCTG
** *
53574921 CTCCACTACTGCTTAGGGAGACGGGATCTACATTCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCAACCTA
* ***** * * *
53574965 CTCCACTGCTGCTTAGGGAGATAGGA-CTGGTGGCTTAAATCTG
1 CTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCAACCTA
* * * * * *
53575008 CTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACCATCTTCGATCTG
1 C-TCCACTACT-GCTTAGGG-AGATAGGATCT-ACAATCTTCAACCTA
*
53575053 CTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCAACCTA
* ** *
53575097 ATCCACTGTTGCTCAGGGAGATAGGA
1 CTCCACTACTGCTTAGGGAGATAGGA
53575123 CTGGTGGCTT
Statistics
Matches: 117, Mismatches: 33, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
43 17 0.15
44 82 0.70
45 18 0.15
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.27
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAGGATCTACAATCTTCAACCTA
Found at i:53576183 original size:18 final size:18
Alignment explanation
Indices: 53576162--53576196 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
53576152 TTCTAGGGAC
53576162 AACAAGTTCAATATAAAA
1 AACAAGTTCAATATAAAA
53576180 AACAAGTTCAATATAAA
1 AACAAGTTCAATATAAA
53576197 TAGTATGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (18 bp):
AACAAGTTCAATATAAAA
Found at i:53578267 original size:11 final size:10
Alignment explanation
Indices: 53578251--53578284 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
53578241 CGTGCTTTTT
*
53578251 AAAAAAATTC
1 AAAAAAATAC
53578261 AAAAAAATAC
1 AAAAAAATAC
53578271 AAAAAAATA-
1 AAAAAAATAC
53578280 AAAAA
1 AAAAA
53578285 TTGCATTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.82, C:0.06, G:0.00, T:0.12
Consensus pattern (10 bp):
AAAAAAATAC
Found at i:53578316 original size:30 final size:28
Alignment explanation
Indices: 53578281--53578396 Score: 101
Period size: 30 Copynumber: 4.0 Consensus size: 28
53578271 AAAAAAATAA
* *
53578281 AAAATTGCATTTTGA-CCCATAAATTTTCCT
1 AAAATTACATTTTAAGCCC-TAAATTTT--T
*
53578311 AAAATTATATTTTAAGCCCTAAACTATTTT
1 AAAATTACATTTTAAGCCCTAAA-T-TTTT
* * *
53578341 GAAATTACATTTTGA-CCCATCAACTTTTT
1 AAAATTACATTTTAAGCCC-T-AAATTTTT
53578370 AAAATTACATTTTAAGCCCTAAATTTT
1 AAAATTACATTTTAAGCCCTAAATTTT
53578397 CTTGAAATTA
Statistics
Matches: 70, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
28 6 0.09
29 21 0.30
30 34 0.49
31 6 0.09
32 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.41
Consensus pattern (28 bp):
AAAATTACATTTTAAGCCCTAAATTTTT
Found at i:53578387 original size:59 final size:59
Alignment explanation
Indices: 53578282--53578427 Score: 179
Period size: 59 Copynumber: 2.4 Consensus size: 59
53578272 AAAAAATAAA
* *
53578282 AAATTGCATTTTGACCCATAAATTTTCCTAAAATTATATTTTAAGCCCTAAACTATT-TTG
1 AAATTACATTTTGACCCATAAATTTT-CTAAAATTACATTTTAAGCCCTAAA-TATTCTTG
* *
53578342 AAATTACATTTTGACCCATCAACTTTT-TAAAATTACATTTTAAGCCCTAAATTTTCTTG
1 AAATTACATTTTGACCCAT-AAATTTTCTAAAATTACATTTTAAGCCCTAAATATTCTTG
** *
53578401 AAATTATGTTTTGACCCTATAAGTTTT
1 AAATTACATTTTGACCC-ATAAATTTT
53578428 GCTACATTTG
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
58 3 0.04
59 47 0.62
60 20 0.26
61 6 0.08
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.43
Consensus pattern (59 bp):
AAATTACATTTTGACCCATAAATTTTCTAAAATTACATTTTAAGCCCTAAATATTCTTG
Found at i:53578789 original size:13 final size:12
Alignment explanation
Indices: 53578765--53578794 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
53578755 TTTGAGGAAG
53578765 AAGAAGAAGAAA
1 AAGAAGAAGAAA
53578777 AAGAAGAAAGAAA
1 AAGAAG-AAGAAA
53578790 AAGAA
1 AAGAA
53578795 AAAAAGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGAAA
Found at i:53578929 original size:22 final size:22
Alignment explanation
Indices: 53578880--53578933 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
53578870 CAGCCCAATC
*
53578880 AAAAAAAAAAGAAATTAAGCCA
1 AAAAAAAAAAGAAATAAAGCCA
53578902 AAAAAAAAAAGAAA-AAAG-CA
1 AAAAAAAAAAGAAATAAAGCCA
53578922 ACACAAAAAAAA
1 A-A-AAAAAAAA
53578934 TAGCCCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 22 0.76
ACGTcount: A:0.80, C:0.09, G:0.07, T:0.04
Consensus pattern (22 bp):
AAAAAAAAAAGAAATAAAGCCA
Found at i:53591625 original size:69 final size:68
Alignment explanation
Indices: 53591552--53591765 Score: 191
Period size: 69 Copynumber: 3.1 Consensus size: 68
53591542 ACCTCAAACT
*
53591552 CTTGAACCATAAATCAAAATCCTAACCCCCAAACTTAAAACACATAACCCCAAACCATTGAACCT
1 CTTGAACCATAAATCAAAACCCTAA-CCCCAAACTTAAAACACATAACCCCAAACCATTGAACCT
*
53591617 TAAG
65 TAAA
* ** * ** * * * **
53591621 CTTGAACC-TCGAATCCCGAACCCGAACCCCAAACCCAAAACTC-GAACACCAAACCCGT-AACC
1 CTTGAACCAT-AAAT-CAAAACCCTAACCCCAAACTTAAAACACATAACCCCAAACCATTGAACC
* *
53591683 TCGAACT
64 T-TAA-A
* * *
53591690 CTTGAATCATAAATCAAAACCCTAAACCCCAAACTTATAACACATAACCCCAAACTATTGAACCT
1 CTTGAACCATAAATCAAAACCCT-AACCCCAAACTTAAAACACATAACCCCAAACCATTGAACCT
53591755 TAAA
65 TAAA
53591759 CTTGAAC
1 CTTGAAC
53591766 TTCAAACCCC
Statistics
Matches: 106, Mismatches: 31, Indels: 16
0.69 0.20 0.10
Matches are distributed among these distances:
67 5 0.05
68 20 0.19
69 56 0.53
70 20 0.19
71 5 0.05
ACGTcount: A:0.42, C:0.34, G:0.06, T:0.18
Consensus pattern (68 bp):
CTTGAACCATAAATCAAAACCCTAACCCCAAACTTAAAACACATAACCCCAAACCATTGAACCTT
AAA
Done.