Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 82 of 126
Found at i:24918617 original size:36 final size:36
Alignment explanation
Indices: 24918570--24918805 Score: 235
Period size: 36 Copynumber: 6.6 Consensus size: 36
24918560 ATGGCCTTAT
* * *
24918570 GCTCTAACCGAGACATAAGCAGTCA-ATTAGCATTAC
1 GCTCTAACCGAGACGTAAGCAATCACA-TAGCAATAC
*
24918606 GCTCTAACCGAGACGTAAGCAATTACATAGCAATAC
1 GCTCTAACCGAGACGTAAGCAATCACATAGCAATAC
* * * * * *
24918642 ACTCTAATCGAGACGTATGAAATCACATTA-CAAAAT
1 GCTCTAACCGAGACGTAAGCAATCACA-TAGCAATAC
* * * *
24918678 GCTTTAACCAAGACGTAAGCAATCTC-TAAGCATTAC
1 GCTCTAACCGAGACGTAAGCAATCACAT-AGCAATAC
* ** *
24918714 GCTATAACTAAGACGTAAGCAATTACATAGCAATAC
1 GCTCTAACCGAGACGTAAGCAATCACATAGCAATAC
* * *
24918750 GCTCTAACCGAGACGTATGCATTCACATAGCATTAC
1 GCTCTAACCGAGACGTAAGCAATCACATAGCAATAC
24918786 GCTCTAACCGAGACGTAAGC
1 GCTCTAACCGAGACGTAAGC
24918806 TCTCCATGGA
Statistics
Matches: 161, Mismatches: 34, Indels: 10
0.79 0.17 0.05
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 155 0.96
37 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (36 bp):
GCTCTAACCGAGACGTAAGCAATCACATAGCAATAC
Found at i:24918794 original size:108 final size:108
Alignment explanation
Indices: 24918570--24918805 Score: 303
Period size: 108 Copynumber: 2.2 Consensus size: 108
24918560 ATGGCCTTAT
* * * * *
24918570 GCTCTAACCGAGACATAAGCAGTCAATTAGCATTACGCTCTAACCGAGACGTAAGCAATTACATA
1 GCTCTAACCGAGACGTAAGCAATCAATAAGCATTACGCTATAACCAAGACGTAAGCAATTACATA
* *
24918635 GCAATACACTCTAATCGAGACGTATGAAATCACATTACAAAAT
66 GCAATACACTCTAACCGAGACGTATGAAATCACATTACAAAAC
* * ** *
24918678 GCTTTAACCAAGACGTAAGCAATCTCTAAGCATTACGCTATAACTAAGACGTAAGCAATTACATA
1 GCTCTAACCGAGACGTAAGCAATCAATAAGCATTACGCTATAACCAAGACGTAAGCAATTACATA
* * * **
24918743 GCAATACGCTCTAACCGAGACGTATGCATTCACA-TAGCATTAC
66 GCAATACACTCTAACCGAGACGTATGAAATCACATTA-CAAAAC
24918786 GCTCTAACCGAGACGTAAGC
1 GCTCTAACCGAGACGTAAGC
24918806 TCTCCATGGA
Statistics
Matches: 108, Mismatches: 19, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
107 2 0.02
108 106 0.98
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (108 bp):
GCTCTAACCGAGACGTAAGCAATCAATAAGCATTACGCTATAACCAAGACGTAAGCAATTACATA
GCAATACACTCTAACCGAGACGTATGAAATCACATTACAAAAC
Found at i:24920363 original size:37 final size:37
Alignment explanation
Indices: 24920313--24920433 Score: 206
Period size: 37 Copynumber: 3.3 Consensus size: 37
24920303 TTACTACTAA
*
24920313 TGTCGCTGCATGAGCACTTCTAGATTGCACACAAAAT
1 TGTCGCCGCATGAGCACTTCTAGATTGCACACAAAAT
24920350 TGTCGCCGCATGAGCACTTCTAGATTGCACACAAAAT
1 TGTCGCCGCATGAGCACTTCTAGATTGCACACAAAAT
* *
24920387 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAAT
1 TGTCGCCGCATGAGCACTTCTAGATTGCACACAAAAT
*
24920424 TGTCACCGCA
1 TGTCGCCGCA
24920434 AGAATATTTC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 80 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (37 bp):
TGTCGCCGCATGAGCACTTCTAGATTGCACACAAAAT
Found at i:24920453 original size:37 final size:37
Alignment explanation
Indices: 24920327--24920457 Score: 118
Period size: 37 Copynumber: 3.5 Consensus size: 37
24920317 GCTGCATGAG
* * * * * *
24920327 CACTTCTAGATTGCACACAAAATTGTCGCCGCATGAG
1 CACTTCCAGAATGCACCCAAAATTGTCACCGCAAGAA
* * * * * *
24920364 CACTTCTAGATTGCACACAAAATTGTCGCCGCATGAG
1 CACTTCCAGAATGCACCCAAAATTGTCACCGCAAGAA
*
24920401 CACTTCCAGATTGCACCCAAAATTGTCACCGCAAGAA
1 CACTTCCAGAATGCACCCAAAATTGTCACCGCAAGAA
* * *
24920438 TATTTCCGGAATGCACCCAA
1 CACTTCCAGAATGCACCCAA
24920458 GACTGTCGCT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 85 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (37 bp):
CACTTCCAGAATGCACCCAAAATTGTCACCGCAAGAA
Found at i:24920453 original size:74 final size:74
Alignment explanation
Indices: 24920313--24920471 Score: 192
Period size: 74 Copynumber: 2.1 Consensus size: 74
24920303 TTACTACTAA
* * * * * *
24920313 TGTCGCTGCATGAGCACTTCTAGATTGCACACAAAATTGTCGCCGCATGAGCACTTCTAGATTGC
1 TGTCGCTGCATGAGCACTTCCAGATTGCACACAAAATTGTCACCGCAAGAACACTTCCAGAATGC
*
24920378 ACACAAAAT
66 ACACAAAAC
* * * * *
24920387 TGTCGCCGCATGAGCACTTCCAGATTGCACCCAAAATTGTCACCGCAAGAATATTTCCGGAATGC
1 TGTCGCTGCATGAGCACTTCCAGATTGCACACAAAATTGTCACCGCAAGAACACTTCCAGAATGC
* *
24920452 ACCCAAGAC
66 ACACAAAAC
24920461 TGTCGCTGCAT
1 TGTCGCTGCAT
24920472 AAATATTCTT
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
74 70 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.24
Consensus pattern (74 bp):
TGTCGCTGCATGAGCACTTCCAGATTGCACACAAAATTGTCACCGCAAGAACACTTCCAGAATGC
ACACAAAAC
Found at i:24921389 original size:16 final size:16
Alignment explanation
Indices: 24921368--24921398 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24921358 TTGTGGATCC
24921368 CATTTTATCTTTATTA
1 CATTTTATCTTTATTA
*
24921384 CATTTTGTCTTTATT
1 CATTTTATCTTTATT
24921399 TTACATTATT
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:0.19, C:0.13, G:0.03, T:0.65
Consensus pattern (16 bp):
CATTTTATCTTTATTA
Found at i:24925025 original size:56 final size:56
Alignment explanation
Indices: 24924943--24925053 Score: 143
Period size: 56 Copynumber: 2.0 Consensus size: 56
24924933 TTATTTTAAG
* * *
24924943 CAAGCTCTCTATGTGAGCTTAATGTGATAAGATCCTATGCAAGCTGCTTTACAAGC
1 CAAGCTCCCTATGTGAGCTTAATGTGATAAGATCCTATGCAAGCTCCTTCACAAGC
* * * *
24924999 CAAGCTCCCTATGTGAGCTCT-TTGTGATAAGTTTCTATGCATGCTCCTTCACAAG
1 CAAGCTCCCTATGTGAGCT-TAATGTGATAAGATCCTATGCAAGCTCCTTCACAAG
24925054 TCATGTTGGA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
56 46 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.32
Consensus pattern (56 bp):
CAAGCTCCCTATGTGAGCTTAATGTGATAAGATCCTATGCAAGCTCCTTCACAAGC
Found at i:24928089 original size:41 final size:41
Alignment explanation
Indices: 24928038--24928224 Score: 284
Period size: 41 Copynumber: 4.5 Consensus size: 41
24928028 ACTTGATGTA
* *
24928038 TAAATGGAAGACTAATGTCTCGAGATAAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
24928080 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* *
24928121 TAAAGGAAGACTCATGTCTCGAAATGAGCAAGAGATTATAT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
* *
24928162 TAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATA-T
* *
24928204 TAAAGGAAGACTTATGACTCG
1 TAAAGGAAGACTCATGTCTCG
24928225 GTAAAGCATA
Statistics
Matches: 133, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 110 0.83
42 23 0.17
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (41 bp):
TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
Found at i:24928233 original size:41 final size:40
Alignment explanation
Indices: 24928038--24928253 Score: 247
Period size: 41 Copynumber: 5.2 Consensus size: 40
24928028 ACTTGATGTA
*
24928038 TAAATGGAAGACTAATGTCTCGAGATAAGCATGAGATTATAT
1 TAAA-GGAAGACTCATGTCTCG-GATAAGCATGAGATTATAT
*
24928080 TAAAGGAAGACTCATGTCTCGAGATGAGCATGAGATTATAT
1 TAAAGGAAGACTCATGTCTCG-GATAAGCATGAGATTATAT
* * *
24928121 TAAAGGAAGACTCATGTCTCGAAATGAGCAAGAGATTATAT
1 TAAAGGAAGACTCATGTCTCG-GATAAGCATGAGATTATAT
* *
24928162 TAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGATTATATT
1 TAAAGGAAGACTCATGTCTC-GGATAAGCATGAGATTATA-T
* * * *
24928204 TAAAGGAAGACTTATGACTCGG-TAAAGCATAAGATTGT-T
1 TAAAGGAAGACTCATGTCTCGGAT-AAGCATGAGATTATAT
24928243 TAAAAGGAAGA
1 T-AAAGGAAGA
24928254 TCTACGACTC
Statistics
Matches: 157, Mismatches: 13, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
39 2 0.01
40 10 0.06
41 122 0.78
42 23 0.15
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (40 bp):
TAAAGGAAGACTCATGTCTCGGATAAGCATGAGATTATAT
Found at i:24934980 original size:46 final size:46
Alignment explanation
Indices: 24934919--24935010 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
24934909 TCACAAAGAA
24934919 AAAGGGTACATATTGGTTTTATTTATTTTACAAACGGTTTCAAAGT
1 AAAGGGTACATATTGGTTTTATTTATTTTACAAACGGTTTCAAAGT
24934965 AAAGGGTACATATTGGTTTTATTTATTTTACAAACGGTTTCAAAGT
1 AAAGGGTACATATTGGTTTTATTTATTTTACAAACGGTTTCAAAGT
24935011 TTATCACACC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.41
Consensus pattern (46 bp):
AAAGGGTACATATTGGTTTTATTTATTTTACAAACGGTTTCAAAGT
Found at i:24941168 original size:33 final size:33
Alignment explanation
Indices: 24941096--24941170 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
24941086 AAAATTATAT
* *
24941096 TGCTGTTTTGGTGTTATTTTTTGTGCAGTTTTT
1 TGCTGTTTTGGTGCTATTTTTTGTGCAGTTTTG
* **
24941129 TACTGTTTTGGTGCTATTTTTT-TGTTGTTTTCG
1 TGCTGTTTTGGTGCTATTTTTTGTGCAGTTTT-G
24941162 TGCTGTTTT
1 TGCTGTTTT
24941171 TTTATTGTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
32 7 0.20
33 28 0.80
ACGTcount: A:0.05, C:0.08, G:0.23, T:0.64
Consensus pattern (33 bp):
TGCTGTTTTGGTGCTATTTTTTGTGCAGTTTTG
Found at i:24941193 original size:22 final size:22
Alignment explanation
Indices: 24941109--24941185 Score: 88
Period size: 22 Copynumber: 3.6 Consensus size: 22
24941099 TGTTTTGGTG
*
24941109 TTATT-TTTT-GTGCAG-TTTT
1 TTATTGTTTTGGTGCTGTTTTT
* *
24941128 TTACTGTTTTGGTGCTATTTTT
1 TTATTGTTTTGGTGCTGTTTTT
* *
24941150 TTGTTGTTTTCGTGCTGTTTTT
1 TTATTGTTTTGGTGCTGTTTTT
24941172 TTATTGTTTTGGTG
1 TTATTGTTTTGGTG
24941186 ATGCTTTTGC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 4 0.09
20 4 0.09
21 4 0.09
22 34 0.74
ACGTcount: A:0.06, C:0.06, G:0.21, T:0.66
Consensus pattern (22 bp):
TTATTGTTTTGGTGCTGTTTTT
Found at i:24941257 original size:22 final size:22
Alignment explanation
Indices: 24941232--24941280 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
24941222 TTTTTGCTGC
* *
24941232 TGTTTTGATTGTT-TTTTTTTG
1 TGTTTTGAATGTTATTTTTATG
24941253 T-TGTTTGAATGTTATTTTTATG
1 TGT-TTTGAATGTTATTTTTATG
24941275 TGTTTT
1 TGTTTT
24941281 TATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 11 0.48
23 1 0.04
ACGTcount: A:0.10, C:0.00, G:0.18, T:0.71
Consensus pattern (22 bp):
TGTTTTGAATGTTATTTTTATG
Found at i:24941259 original size:21 final size:21
Alignment explanation
Indices: 24941235--24941279 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24941225 TTGCTGCTGT
* *
24941235 TTTGATTGTT-TTTTTTTGTTG
1 TTTGAATGTTATTTTTATG-TG
24941256 TTTGAATGTTATTTTTATGTG
1 TTTGAATGTTATTTTTATGTG
24941277 TTT
1 TTT
24941280 TTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.11, C:0.00, G:0.18, T:0.71
Consensus pattern (21 bp):
TTTGAATGTTATTTTTATGTG
Found at i:24948801 original size:23 final size:23
Alignment explanation
Indices: 24948786--24948836 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
24948776 TTCACTCAAT
24948786 TTTCTCTTTAAATTTCACATAAA
1 TTTCTCTTTAAATTTCACATAAA
* *
24948809 TTTCTCTTTAAAATTCTCA-AAA
1 TTTCTCTTTAAATTTCACATAAA
24948831 -TTCTCT
1 TTTCTCT
24948837 AAAATTTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 6 0.23
22 3 0.12
23 17 0.65
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTCTCTTTAAATTTCACATAAA
Found at i:24948842 original size:10 final size:9
Alignment explanation
Indices: 24948818--24948852 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
24948808 ATTTCTCTTT
24948818 AAAATTCTC
1 AAAATTCTC
24948827 AAAATTCTC
1 AAAATTCTC
*
24948836 TAAAATTTTC
1 -AAAATTCTC
24948846 AAAATTC
1 AAAATTC
24948853 ATTTAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.46, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
AAAATTCTC
Found at i:24948871 original size:14 final size:14
Alignment explanation
Indices: 24948854--24948898 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
24948844 TCAAAATTCA
24948854 TTTAATTTAATTAT
1 TTTAATTTAATTAT
* *
24948868 TTTATTTTTATT-T
1 TTTAATTTAATTAT
24948881 TTATAATTTAATTAT
1 TT-TAATTTAATTAT
24948896 TTT
1 TTT
24948899 TTAACAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.12
14 19 0.76
15 3 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTAATTTAATTAT
Found at i:24948892 original size:28 final size:28
Alignment explanation
Indices: 24948856--24948947 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
24948846 AAAATTCATT
*
24948856 TAATTTAATTATTTTATTTTTATTTTTA
1 TAATTTAATTATTTTATTTTTATTTCTA
* *
24948884 TAATTTAATTA---T-TTTTTA--ACAA
1 TAATTTAATTATTTTATTTTTATTTCTA
*
24948906 T-ATTTAATTATTTTATTTTTATTTGTA
1 TAATTTAATTATTTTATTTTTATTTCTA
24948933 TAATTTAATTATTTT
1 TAATTTAATTATTTT
24948948 TAATAATATT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
21 9 0.18
22 2 0.04
24 7 0.14
25 7 0.14
27 2 0.04
28 24 0.47
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (28 bp):
TAATTTAATTATTTTATTTTTATTTCTA
Found at i:24948911 original size:49 final size:48
Alignment explanation
Indices: 24948858--24948963 Score: 185
Period size: 49 Copynumber: 2.2 Consensus size: 48
24948848 AATTCATTTA
*
24948858 ATTTAATTATTTTATTTTTATTTTTATAATTTAATTATTTTTTAACAAT
1 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTA-TTTTTAACAAT
*
24948907 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAATAAT
1 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAACAAT
24948955 ATTTAATTA
1 ATTTAATTA
24948964 ATCTATCTCG
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
48 19 0.35
49 36 0.65
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (48 bp):
ATTTAATTATTTTATTTTTATTTGTATAATTTAATTATTTTTAACAAT
Found at i:24948944 original size:23 final size:23
Alignment explanation
Indices: 24948869--24948949 Score: 65
Period size: 23 Copynumber: 3.4 Consensus size: 23
24948859 TTTAATTATT
*
24948869 TTATTTTTATTTTTATAATTTAA
1 TTATTTTTATTTATATAATTTAA
** * *
24948892 TTATTTTTTAACAATATTTAA-TTATT
1 TTA-TTTTT-A-TTTATATAATTTA-A
*
24948918 TTATTTTTATTTGTATAATTTAA
1 TTATTTTTATTTATATAATTTAA
24948941 TTATTTTTA
1 TTATTTTTA
24948950 ATAATATTTA
Statistics
Matches: 43, Mismatches: 10, Indels: 10
0.68 0.16 0.16
Matches are distributed among these distances:
23 17 0.40
24 9 0.21
25 9 0.21
26 8 0.19
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (23 bp):
TTATTTTTATTTATATAATTTAA
Found at i:24948951 original size:10 final size:10
Alignment explanation
Indices: 24948858--24948963 Score: 53
Period size: 10 Copynumber: 10.9 Consensus size: 10
24948848 AATTCATTTA
24948858 ATTTAATTAT
1 ATTTAATTAT
* *
24948868 -TTTATTTTT
1 ATTTAATTAT
24948877 ATTT--TTAT
1 ATTTAATTAT
24948885 AATTTAATTATT
1 -ATTTAATTA-T
* **
24948897 TTTTAACAAT
1 ATTTAATTAT
24948907 ATTTAATTAT
1 ATTTAATTAT
* *
24948917 -TTTATTTTT
1 ATTTAATTAT
*
24948926 ATTT--GTAT
1 ATTTAATTAT
24948934 AATTTAATTAT
1 -ATTTAATTAT
* *
24948945 TTTTAATAAT
1 ATTTAATTAT
24948955 ATTTAATTA
1 ATTTAATTA
24948964 ATCTATCTCG
Statistics
Matches: 69, Mismatches: 18, Indels: 18
0.66 0.17 0.17
Matches are distributed among these distances:
8 5 0.07
9 22 0.32
10 29 0.42
11 12 0.17
12 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (10 bp):
ATTTAATTAT
Found at i:24952525 original size:29 final size:29
Alignment explanation
Indices: 24952493--24952579 Score: 70
Period size: 28 Copynumber: 3.0 Consensus size: 29
24952483 AAACAAAAGC
24952493 CATCTCGTCAAATTAATTTTTTCAAAACA
1 CATCTCGTCAAATTAATTTTTTCAAAACA
* * * * * *
24952522 CATCACGCCAATTTTA-TTTTTCAGAACC
1 CATCTCGTCAAATTAATTTTTTCAAAACA
* *
24952550 CATCTTC-TCAAAATCATTTTTTCCAAAACA
1 CATC-TCGTCAAATTAATTTTTT-CAAAACA
24952580 ATTCCATTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 5
0.70 0.22 0.08
Matches are distributed among these distances:
28 19 0.45
29 18 0.43
30 5 0.12
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.37
Consensus pattern (29 bp):
CATCTCGTCAAATTAATTTTTTCAAAACA
Found at i:24952731 original size:21 final size:22
Alignment explanation
Indices: 24952707--24952759 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
24952697 TTAAAATACC
*
24952707 AAACCCTAATTTTAATAA-CCT
1 AAACCCTAATTTTAAAAACCCT
24952728 AAACCCCTAA-TTTAAAAACCCT
1 AAA-CCCTAATTTTAAAAACCCT
24952750 AAA-CCTAATT
1 AAACCCTAATT
24952760 AAAACAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 5 0.18
21 11 0.39
22 12 0.43
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.28
Consensus pattern (22 bp):
AAACCCTAATTTTAAAAACCCT
Found at i:24953185 original size:33 final size:33
Alignment explanation
Indices: 24953148--24953213 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
24953138 GAACACTCTC
24953148 GTACCCTTTGTAAAAGAAACCGATAATAAAATA
1 GTACCCTTTGTAAAAGAAACCGATAATAAAATA
24953181 GTACCCTTTGTAAAAGAAACCGATAATAAAATA
1 GTACCCTTTGTAAAAGAAACCGATAATAAAATA
24953214 AAAAGAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.24
Consensus pattern (33 bp):
GTACCCTTTGTAAAAGAAACCGATAATAAAATA
Found at i:24954569 original size:2 final size:2
Alignment explanation
Indices: 24954562--24954596 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
24954552 GTACTAACTA
24954562 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24954597 AGACATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:24955094 original size:17 final size:18
Alignment explanation
Indices: 24955072--24955107 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
24955062 TAAATGAGTT
24955072 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
24955089 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
24955107 A
1 A
24955108 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:24959542 original size:21 final size:21
Alignment explanation
Indices: 24959504--24959543 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24959494 AGTTCTGTTT
*
24959504 CTTCCTTCTCTTCTTCCTTTC
1 CTTCCTTCTCTTCATCCTTTC
* *
24959525 CTTCCTTGTCTTGATCCTT
1 CTTCCTTCTCTTCATCCTT
24959544 CTCTTGATTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.38, G:0.05, T:0.55
Consensus pattern (21 bp):
CTTCCTTCTCTTCATCCTTTC
Found at i:24983745 original size:36 final size:35
Alignment explanation
Indices: 24983704--24983895 Score: 188
Period size: 36 Copynumber: 5.3 Consensus size: 35
24983694 CATACATCTC
* *
24983704 GGTTAGAGCATCTAGCTATGAAGTTGCGTATGTCTT
1 GGTTAGAGCATATA-CTATGAAGTTGCATATGTCTT
24983740 GGTTAGAGCATATCACTATGAAGTTGCATATGTCTT
1 GGTTAGAGCATAT-ACTATGAAGTTGCATATGTCTT
* * * *
24983776 GGTTAGAGCATATTACGATGATGCTGCATATATCTT
1 GGTTAGAGCATA-TACTATGAAGTTGCATATGTCTT
* * * * *
24983812 GATTAGAGCATATTGCTATGATGTTGCATACGTCTC
1 GGTTAGAGCATA-TACTATGAAGTTGCATATGTCTT
* * *
24983848 GGTTAGAGCGTATTATTATGATA-TTGCATACGTCTT
1 GGTTAGAGCATA-TACTATGA-AGTTGCATATGTCTT
*
24983884 AGTTAGAGCATA
1 GGTTAGAGCATA
24983896 ATGTTAAGTG
Statistics
Matches: 132, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
36 130 0.98
37 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (35 bp):
GGTTAGAGCATATACTATGAAGTTGCATATGTCTT
Found at i:24994803 original size:44 final size:40
Alignment explanation
Indices: 24994742--24994874 Score: 133
Period size: 40 Copynumber: 3.2 Consensus size: 40
24994732 AGAATGTGAT
* *
24994742 AAAGGAAGACTCATGACTCAAAAGGAGCGTGAGAATATTGTTAA
1 AAAGGAAGACTTATGACTCAAAA-GAGC---AGAAGATTGTTAA
** *
24994786 AAAGGAAGACTTATGACTCAGTAGAGCATAAGATTGTTAA
1 AAAGGAAGACTTATGACTCAAAAGAGCAGAAGATTGTTAA
* * * * *
24994826 AAGGGAAGACTTATGACTCGATAGAGCATAATATTGTT-A
1 AAAGGAAGACTTATGACTCAAAAGAGCAGAAGATTGTTAA
24994865 AAAGGAAGAC
1 AAAGGAAGAC
24994875 ACATGAACTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.13
40 45 0.57
43 4 0.05
44 20 0.25
ACGTcount: A:0.43, C:0.11, G:0.24, T:0.23
Consensus pattern (40 bp):
AAAGGAAGACTTATGACTCAAAAGAGCAGAAGATTGTTAA
Found at i:24994833 original size:40 final size:39
Alignment explanation
Indices: 24994778--24994874 Score: 151
Period size: 40 Copynumber: 2.4 Consensus size: 39
24994768 GCGTGAGAAT
24994778 ATTGTTAAAAAGGAAGACTTATGACTC-AGTAGAGCATAAG
1 ATTGTT-AAAAGGAAGACTTATGACTCGA-TAGAGCATAAG
*
24994818 ATTGTTAAAAGGGAAGACTTATGACTCGATAGAGCATAAT
1 ATTGTTAAAA-GGAAGACTTATGACTCGATAGAGCATAAG
24994858 ATTGTTAAAAGGAAGAC
1 ATTGTTAAAAGGAAGAC
24994875 ACATGAACTT
Statistics
Matches: 54, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
39 11 0.20
40 42 0.78
41 1 0.02
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.26
Consensus pattern (39 bp):
ATTGTTAAAAGGAAGACTTATGACTCGATAGAGCATAAG
Found at i:24995493 original size:21 final size:24
Alignment explanation
Indices: 24995426--24995503 Score: 80
Period size: 21 Copynumber: 3.5 Consensus size: 24
24995416 CTAACTTGGG
24995426 TTGTATCGGTAG-TT-GTGTA-G-
1 TTGTATCGGTAGTTTAGTGTATGC
* *
24995446 TGGGTATCGGTAGTTTTGTGTATGC
1 T-TGTATCGGTAGTTTAGTGTATGC
24995471 TTGTATCGGTAG-TTAG-G-ATGC
1 TTGTATCGGTAGTTTAGTGTATGC
24995492 TTGTATCGGTAG
1 TTGTATCGGTAG
24995504 AAGTTGTAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
20 1 0.02
21 26 0.52
22 3 0.06
23 8 0.16
24 11 0.22
25 1 0.02
ACGTcount: A:0.15, C:0.08, G:0.35, T:0.42
Consensus pattern (24 bp):
TTGTATCGGTAGTTTAGTGTATGC
Found at i:25007175 original size:66 final size:66
Alignment explanation
Indices: 25007069--25007201 Score: 232
Period size: 66 Copynumber: 2.0 Consensus size: 66
25007059 TTTCTCGAAA
* *
25007069 AGTTCATTCAATTTCAGGTTCCACTGGGAGTAAGTCGATAATTTC-GTTGATACTCATAAACACC
1 AGTTCATTCAATTTCAGGGTCCACTGGCAGTAAGTCGATAA-TTCGGTTGATACTCATAAACACC
25007133 TG
65 TG
25007135 AGTTCATTCAATTTCAGGGTCCACTGGCAGTAAGTCGATAATTCGGTTGATACTCATAAACACCT
1 AGTTCATTCAATTTCAGGGTCCACTGGCAGTAAGTCGATAATTCGGTTGATACTCATAAACACCT
25007200 G
66 G
25007201 A
1 A
25007202 AATAATCAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 3 0.05
66 61 0.95
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (66 bp):
AGTTCATTCAATTTCAGGGTCCACTGGCAGTAAGTCGATAATTCGGTTGATACTCATAAACACCT
G
Found at i:25007518 original size:15 final size:15
Alignment explanation
Indices: 25007475--25007512 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
25007465 TATGAAGGAT
*
25007475 ATTAATCTAAAGT--
1 ATTAATCTAAACTAA
25007488 ATTAATCTAAACTAA
1 ATTAATCTAAACTAA
25007503 ATTAATCTAA
1 ATTAATCTAA
25007513 GTTAAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.55
15 10 0.45
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (15 bp):
ATTAATCTAAACTAA
Found at i:25012243 original size:16 final size:17
Alignment explanation
Indices: 25012210--25012243 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25012200 ATGAGTTAGA
*
25012210 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
25012227 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
25012243 A
1 A
25012244 GGGTTTAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:25022640 original size:83 final size:82
Alignment explanation
Indices: 25022499--25022740 Score: 317
Period size: 83 Copynumber: 2.9 Consensus size: 82
25022489 GTTACTGTCC
25022499 CGTGTAAAATAATATTGTTGTAGCAAATGTGCAAGTGTACACAACATTCAAGTAATAAAGTGATA
1 CGTGTAAAATAATATTGTTGTAGC--ATGTGCAAGTGTACACAAC-TTCAAGTAATAAAGTGATA
*
25022564 AGTAGAGTATTGTACTATCG
63 AGTAGAGTATCGTACTATCG
* * *
25022584 CGTGTAAAATAATATTGTTGTAGCATGTGCAAGTGTACACAACGTTTAAGTAATAAAGTAACAAG
1 CGTGTAAAATAATATTGTTGTAGCATGTGCAAGTGTACACAAC-TTCAAGTAATAAAGTGATAAG
25022649 TAGAGTATCGTACTATCG
65 TAGAGTATCGTACTATCG
* * * * *
25022667 TGTGTAAAATAATATTGCAATCGTA-AATGTGCAAGTGTACACAA-TGCAAGTAATATAGTGATA
1 CGTGTAAAATAATATTG---TTGTAGCATGTGCAAGTGTACACAACTTCAAGTAATAAAGTGATA
*
25022730 AGTAAAGTATC
63 AGTAGAGTATC
25022741 AATCCCATAG
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
83 94 0.67
85 42 0.30
86 4 0.03
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (82 bp):
CGTGTAAAATAATATTGTTGTAGCATGTGCAAGTGTACACAACTTCAAGTAATAAAGTGATAAGT
AGAGTATCGTACTATCG
Found at i:25024497 original size:18 final size:18
Alignment explanation
Indices: 25024474--25024509 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
25024464 TATTTCTTCA
25024474 GCTAAGTTTTTCACTTAC
1 GCTAAGTTTTTCACTTAC
25024492 GCTAAGTTTTTCACTTAC
1 GCTAAGTTTTTCACTTAC
25024510 TTTGCTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (18 bp):
GCTAAGTTTTTCACTTAC
Found at i:25024772 original size:15 final size:16
Alignment explanation
Indices: 25024736--25024766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
25024726 CTAAAAAAAT
*
25024736 ATTTTTCTTTTTACAA
1 ATTTTTCTTTTAACAA
25024752 ATTTTTCTTTTAACA
1 ATTTTTCTTTTAACA
25024767 TTTTTTTTCT
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:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTCTTTTAACAA
Found at i:25024772 original size:16 final size:17
Alignment explanation
Indices: 25024736--25024778 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
25024726 CTAAAAAAAT
*
25024736 ATTTTTCTTTTTACA-A
1 ATTTTTCTTTTAACATA
*
25024752 ATTTTTCTTTTAACATT
1 ATTTTTCTTTTAACATA
*
25024769 TTTTTTCTTT
1 ATTTTTCTTT
25024779 CTAAGCACTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.19, C:0.12, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTCTTTTAACATA
Found at i:25034839 original size:125 final size:123
Alignment explanation
Indices: 25034683--25035050 Score: 562
Period size: 125 Copynumber: 3.0 Consensus size: 123
25034673 GATTTCGTTA
*
25034683 AATATTAAAAAC-TGGAAGTTAATATCCTTTTGGAAAGGATATAATATTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
*
25034747 ATATTTCTTTAAAGGAATATTTAAATTTTAATATGAGATATTATATAAAAGGAAATTG
66 ATATTTCTTTAAAGGAATATTTACATTTTAATATGAGATATTATATAAAAGGAAATTG
* * * *
25034805 AATATTAAAAAACCATGGAAGTTAATATCTTTTTGGAAATGATATAATGTTTTAATAAATCTTCT
1 AATATT-AAAAA-CATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCC
* * *
25034870 ATATATTTCTTTAATGGAATATTTCCATTTAAATATGAGATATTATATAAAAGGAAATTG
64 ATATATTTCTTTAAAGGAATATTTACATTTTAATATGAGATATTATATAAAAGGAAATTG
*
25034930 AATATTAAAAACATGGAAGTTAATATCCTTTAGGAAAGGATATAATGTTTTAATAAACCTTCCAT
1 AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
* * *
25034995 ATATTTCTCTAAA-G-ATATATTATCATTTTAATATGAGATATTAAATAAAAAGAAAT
66 ATATTTCTTTAAAGGAATAT-TTA-CATTTTAATATGAGATATTATATAAAAGGAAAT
25035051 ATAGCAGAAC
Statistics
Matches: 221, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
121 4 0.02
122 9 0.04
123 95 0.43
124 6 0.03
125 107 0.48
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (123 bp):
AATATTAAAAACATGGAAGTTAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCAT
ATATTTCTTTAAAGGAATATTTACATTTTAATATGAGATATTATATAAAAGGAAATTG
Found at i:25040200 original size:127 final size:123
Alignment explanation
Indices: 25039973--25040275 Score: 444
Period size: 127 Copynumber: 2.4 Consensus size: 123
25039963 TGTTCCATTG
*
25039973 TAAACACATTATATCCTTTCCAAAAGGATATTAACTTTCATGTTTTTAATATTCAATTTCCTTTT
1 TAAA-ACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCCTTTT
*
25040038 ATATAATATCTCATATTTAAATGGAAATATTCCTTTAAAGAAATATATAGAAGGTTTAT
65 ATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATAGAAGGTTTAT
* * *
25040097 TAAAACATTATATCCTTTTCAAAAGGATATTAACTTCCATGTTTTTTTTTAATCTTCAGTTTCCT
1 TAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATG----TTTTTAATATTCAATTTCCT
* * *
25040162 TTTATATAATATCTCATATTAAAATTGAAATATTCCTTTAAAGAAATATATGGAATGTTTAT
62 TTTATATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATAGAAGGTTTAT
*** * *
25040224 TAAAACATTATAAAATTTCCAAAAGGATATTAACTTCCAGGTCTTTAATATT
1 TAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATT
25040276 TAATGAATCT
Statistics
Matches: 160, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
123 44 0.28
124 4 0.03
127 112 0.70
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (123 bp):
TAAAACATTATATCCTTTCCAAAAGGATATTAACTTCCATGTTTTTAATATTCAATTTCCTTTTA
TATAATATCTCATATTAAAATGGAAATATTCCTTTAAAGAAATATATAGAAGGTTTAT
Found at i:25043599 original size:19 final size:19
Alignment explanation
Indices: 25043575--25043619 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
25043565 TCCTCAAGCA
25043575 AAATAAAAACAAGAAAAGT
1 AAATAAAAACAAGAAAAGT
* *
25043594 AAAT-AAAGCAGGAAAAGT
1 AAATAAAAACAAGAAAAGT
*
25043612 AAACAAAA
1 AAATAAAA
25043620 GGAGCTTGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.71, C:0.07, G:0.13, T:0.09
Consensus pattern (19 bp):
AAATAAAAACAAGAAAAGT
Found at i:25049102 original size:27 final size:27
Alignment explanation
Indices: 25049058--25049110 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
25049048 AAACTGAAAT
* *
25049058 TAAACAAAGAAAAGAAATAATAAAAAG
1 TAAACAAAGAAAAAAAATAACAAAAAG
25049085 TAAACAAA-AAAATAAAATAACAAAAA
1 TAAACAAAGAAAA-AAAATAACAAAAA
25049111 AAAATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (27 bp):
TAAACAAAGAAAAAAAATAACAAAAAG
Found at i:25052219 original size:15 final size:15
Alignment explanation
Indices: 25052181--25052220 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
25052171 TGTGAAGGAG
25052181 AAACCAAAGACCCCA
1 AAACCAAAGACCCCA
**
25052196 AAAGTAAAGACCCCA
1 AAACCAAAGACCCCA
*
25052211 ACACCAAAGA
1 AAACCAAAGA
25052221 AGATTGCCAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.55, C:0.33, G:0.10, T:0.03
Consensus pattern (15 bp):
AAACCAAAGACCCCA
Found at i:25055117 original size:24 final size:28
Alignment explanation
Indices: 25055084--25055136 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
25055074 GCATGATGAG
*
25055084 AATTAATGCAA-A-C-ACATAAAAACAA
1 AATTAATGCAATATCAAAATAAAAACAA
25055109 AATT-ATGCAATATCAAAATAAAAACAA
1 AATTAATGCAATATCAAAATAAAAACAA
25055136 A
1 A
25055137 TGCAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 5 0.21
26 1 0.04
27 12 0.50
ACGTcount: A:0.64, C:0.13, G:0.04, T:0.19
Consensus pattern (28 bp):
AATTAATGCAATATCAAAATAAAAACAA
Found at i:25063143 original size:52 final size:53
Alignment explanation
Indices: 25063044--25063175 Score: 142
Period size: 52 Copynumber: 2.5 Consensus size: 53
25063034 ATTTTCTGGT
* * *
25063044 GTTTTGGGACACTGATAGTCGATACCAACTTTATCAAATATAATTTTT-TTTTA
1 GTTTTGGGACACTGAT-GGCGACACCAACTTTATCAAATATAATTTTTCGTTTA
* * * *
25063097 -TTTTGGGACACTGATGGCAGACACCAACTTTATTAGATTTATTTTTTCGTTTA
1 GTTTTGGGACACTGATGGC-GACACCAACTTTATCAAATATAATTTTTCGTTTA
*
25063150 GTTTTTGGGACACTAATGGCCGACAC
1 G-TTTTGGGACACTGATGG-CGACAC
25063176 AAATAAATTC
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
51 2 0.03
52 38 0.58
53 4 0.06
55 21 0.32
56 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (53 bp):
GTTTTGGGACACTGATGGCGACACCAACTTTATCAAATATAATTTTTCGTTTA
Found at i:25063230 original size:2 final size:2
Alignment explanation
Indices: 25063223--25063254 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25063213 GACCCAGTAC
25063223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25063255 AGTGTTTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25066392 original size:75 final size:75
Alignment explanation
Indices: 25066309--25066578 Score: 218
Period size: 86 Copynumber: 3.4 Consensus size: 75
25066299 TAGGATTTAT
*
25066309 AATTTATAATAAATAAAATTTAAAATTAAAAGTTGAAATTGAAATGAAATGAAAATGAAATTTAA
1 AATTTATAATAAATAAAATTTAAAATTAAAAATTGAAATTGAAATGAAATGAAAATGAAATTTAA
*
25066374 ATAAAAGTAA
66 ATAAAAGTGA
* * * * *
25066384 AATTTATAATAAATAGAATTTATAATTTATAATAAATAAAATTTAAAAGTTGAAATTG-AAATGA
1 AATTTATAATAAATAAAATTTA-AAATTA-AA-AATTGAAA-TTGAAA--TGAAA-TGAAAATGA
*
25066448 AATTTAAATAAAAGTTGG
59 AATTTAAATAAAAG-TGA
* * *
25066466 AACTTATAATAAATAGAATTTATAATTTATAATAAATAAAATTTGGAATTGAAATGAAATGAAAA
1 AATTTATAATAAATAAAATTTA-AA---AT--T--A-AAAA-TTGAAATTGAAATGAAATGAAAA
* *
25066531 TGAAATTTAATTAAAATTTGA
56 TGAAATTTAAATAAAA-GTGA
* * *
25066552 AATTTATACTAAATAGAATTTATAATT
1 AATTTATAATAAATAAAATTTAAAATT
25066579 TATAATAAAT
Statistics
Matches: 157, Mismatches: 20, Indels: 31
0.75 0.10 0.15
Matches are distributed among these distances:
75 21 0.13
76 5 0.03
77 2 0.01
78 5 0.03
79 5 0.03
80 1 0.01
81 25 0.16
82 29 0.18
85 4 0.03
86 45 0.29
87 1 0.01
88 7 0.04
89 7 0.04
ACGTcount: A:0.55, C:0.01, G:0.09, T:0.36
Consensus pattern (75 bp):
AATTTATAATAAATAAAATTTAAAATTAAAAATTGAAATTGAAATGAAATGAAAATGAAATTTAA
ATAAAAGTGA
Found at i:25066412 original size:23 final size:23
Alignment explanation
Indices: 25066371--25066428 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
25066361 AAATGAAATT
* *
25066371 TAAATAAAA-GTAAAATTTATAA
1 TAAATAAAATTTATAATTTATAA
*
25066393 TAAATAGAATTTATAATTTATAA
1 TAAATAAAATTTATAATTTATAA
25066416 TAAATAAAATTTA
1 TAAATAAAATTTA
25066429 AAAGTTGAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 8 0.26
23 23 0.74
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (23 bp):
TAAATAAAATTTATAATTTATAA
Found at i:25066428 original size:16 final size:17
Alignment explanation
Indices: 25066360--25066409 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
25066350 AAATGAAATG
*
25066360 AAAATGAAATTTA-AAT
1 AAAATAAAATTTATAAT
25066376 AAAAGTAAAATTTATAAT
1 AAAA-TAAAATTTATAAT
*
25066394 -AAATAGAATTTATAAT
1 AAAATAAAATTTATAAT
25066410 TTATAATAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 16 0.53
17 11 0.37
18 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (17 bp):
AAAATAAAATTTATAAT
Found at i:25066495 original size:23 final size:23
Alignment explanation
Indices: 25066469--25066588 Score: 78
Period size: 23 Copynumber: 5.5 Consensus size: 23
25066459 AAGTTGGAAC
25066469 TTATAATAAATAGAATTTATAAT
1 TTATAATAAATAGAATTTATAAT
* **
25066492 TTATAATAAATAAAATTTGGAAT
1 TTATAATAAATAGAATTTATAAT
* * *
25066515 TGA-AATGAAAT-GAA--AATGAAA
1 TTATAAT-AAATAGAATTTAT-AAT
*
25066536 TT-TAAT---TAAAATTTGA-AAT
1 TTATAATAAATAGAATTT-ATAAT
*
25066555 TTATACTAAATAGAATTTATAAT
1 TTATAATAAATAGAATTTATAAT
25066578 TTATAATAAAT
1 TTATAATAAAT
25066589 TAAATTTGAA
Statistics
Matches: 69, Mismatches: 16, Indels: 24
0.63 0.15 0.22
Matches are distributed among these distances:
17 1 0.01
18 2 0.03
19 4 0.06
20 3 0.04
21 7 0.10
22 6 0.09
23 46 0.67
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (23 bp):
TTATAATAAATAGAATTTATAAT
Found at i:25066594 original size:23 final size:23
Alignment explanation
Indices: 25066539--25066602 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 23
25066529 AATGAAATTT
*
25066539 AATTAAAATTTGAAATTTATACTA
1 AATT-AAATTTGAAATTTATAATA
25066563 AA-TAGAATTT-ATAATTTATAATA
1 AATTA-AATTTGA-AATTTATAATA
25066586 AATTAAATTTGAAATTT
1 AATTAAATTTGAAATTT
25066603 GAAATTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
22 2 0.06
23 28 0.80
24 5 0.14
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (23 bp):
AATTAAATTTGAAATTTATAATA
Found at i:25066612 original size:6 final size:6
Alignment explanation
Indices: 25066585--25066781 Score: 79
Period size: 6 Copynumber: 34.5 Consensus size: 6
25066575 AATTTATAAT
*
25066585 AAATT- AAATTTG AAATTTG AAATTG AAA-TG AAA-TG AAAATG AAATT-
1 AAATTG AAA-TTG AAA-TTG AAATTG AAATTG AAATTG AAATTG AAATTG
* * * *
25066631 TAATTA AAAGTTT AAATTT ATAA-T- AAA-T- AAATTTTG AAATTTG AAATTG
1 AAATTG AAA-TTG AAATTG A-AATTG AAATTG AAA--TTG AAA-TTG AAATTG
* * *
25066680 AAA-TG AAA-TG AAAATG AAATT- TAATTA AAAGTTG AAATT- AAA-TG
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAA-TTG AAATTG AAATTG
* * * *
25066724 AAATTG AAA-TG AAA-TG AAAATG AAATT- TAA-TG AAAATG AAATTC
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG AAATTG
*
25066768 AAATTC AAA-TG AAA
1 AAATTG AAATTG AAA
25066782 AACATAGGAA
Statistics
Matches: 160, Mismatches: 14, Indels: 36
0.76 0.07 0.17
Matches are distributed among these distances:
4 8 0.05
5 56 0.35
6 63 0.39
7 30 0.19
8 3 0.02
ACGTcount: A:0.55, C:0.01, G:0.12, T:0.32
Consensus pattern (6 bp):
AAATTG
Found at i:25066654 original size:70 final size:70
Alignment explanation
Indices: 25066570--25066766 Score: 273
Period size: 70 Copynumber: 2.9 Consensus size: 70
25066560 CTAAATAGAA
25066570 TTTATAATTTATAATAAATTAAATTTGAAATTTGAAATTGAAATGAAATGAAAATGAAATTTAAT
1 TTTA-AATTTATAATAAATTAAATTTGAAATTTGAAATTGAAATGAAATGAAAATGAAATTTAAT
25066635 TAAAAG
65 TAAAAG
25066641 TTTAAATTTATAATAAA-TAAATTTTGAAATTTGAAATTGAAATGAAATGAAAATGAAATTTAAT
1 TTTAAATTTATAATAAATTAAA-TTTGAAATTTGAAATTGAAATGAAATGAAAATGAAATTTAAT
25066705 TAAAAG
65 TAAAAG
* * **
25066711 TTGAAA-TTA-AATGAAATTGAAA--TGAAA--TGAAAATGAAATTTAATGAAAATGAAATT
1 TTTAAATTTATAAT-AAATT-AAATTTGAAATTTGAAATTGAAATGAAATGAAAATGAAATT
25066767 CAAATTCAAA
Statistics
Matches: 118, Mismatches: 4, Indels: 13
0.87 0.03 0.10
Matches are distributed among these distances:
66 26 0.22
68 8 0.07
69 10 0.08
70 67 0.57
71 7 0.06
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (70 bp):
TTTAAATTTATAATAAATTAAATTTGAAATTTGAAATTGAAATGAAATGAAAATGAAATTTAATT
AAAAG
Found at i:25066672 original size:93 final size:86
Alignment explanation
Indices: 25066434--25066664 Score: 306
Period size: 86 Copynumber: 2.6 Consensus size: 86
25066424 ATTTAAAAGT
* ** *
25066434 TGAAATTG-AAATGAAATTTAAATAAAAGTTGGAACTTATAATAAATAGAATTTATAATTTATAA
1 TGAAA-TGAAAATGAAATTTAATTAAAAGTTTAAATTTATAATAAATAGAATTTATAATTTATAA
*
25066498 TAAATAAAATTTGGAATTGAAA
65 TAAATAAAATTTGAAATTGAAA
*
25066520 TGAAATGAAAATGAAATTTAATTAAAA-TTTGAAATTTATACTAAATAGAATTTATAATTTATAA
1 TGAAATGAAAATGAAATTTAATTAAAAGTTT-AAATTTATAATAAATAGAATTTATAATTTATAA
25066584 TAAATTAAATTTGAAATTTGAAATTGAAA
65 TAAA-T--A----AAATTTGAAATTGAAA
25066613 TGAAATGAAAATGAAATTTAATTAAAAGTTTAAATTTATAATAAATA-AATTT
1 TGAAATGAAAATGAAATTTAATTAAAAGTTTAAATTTATAATAAATAGAATTT
25066665 TGAAATTTGA
Statistics
Matches: 128, Mismatches: 7, Indels: 14
0.86 0.05 0.09
Matches are distributed among these distances:
85 4 0.03
86 57 0.45
87 1 0.01
89 1 0.01
92 5 0.04
93 57 0.45
94 3 0.02
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (86 bp):
TGAAATGAAAATGAAATTTAATTAAAAGTTTAAATTTATAATAAATAGAATTTATAATTTATAAT
AAATAAAATTTGAAATTGAAA
Found at i:25066697 original size:16 final size:16
Alignment explanation
Indices: 25066672--25066781 Score: 112
Period size: 16 Copynumber: 6.7 Consensus size: 16
25066662 TTTTGAAATT
* *
25066672 TGAAATTGAAATGAAA
1 TGAAAATGAAATTAAA
*
25066688 TGAAAATGAAATTTAA
1 TGAAAATGAAATTAAA
*
25066704 TTAAAAGTTGAAATTAAA
1 TGAAAA--TGAAATTAAA
* *
25066722 TGAAATTGAAATGAAA
1 TGAAAATGAAATTAAA
*
25066738 TGAAAATGAAATTTAA
1 TGAAAATGAAATTAAA
25066754 TGAAAATGAAATTCAAA
1 TGAAAATGAAATT-AAA
**
25066771 TTCAAATGAAA
1 TGAAAATGAAA
25066782 AACATAGGAA
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
16 53 0.69
17 11 0.14
18 13 0.17
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (16 bp):
TGAAAATGAAATTAAA
Found at i:25066730 original size:50 final size:49
Alignment explanation
Indices: 25066672--25066771 Score: 166
Period size: 50 Copynumber: 2.0 Consensus size: 49
25066662 TTTTGAAATT
*
25066672 TGAAATTGAAATGAAATGAAAATGAAATTTAATTAAAAGTTGAAATT-AAA
1 TGAAATTGAAATGAAATGAAAATGAAATTTAATGAAAA--TGAAATTCAAA
25066722 TGAAATTGAAATGAAATGAAAATGAAATTTAATGAAAATGAAATTCAAA
1 TGAAATTGAAATGAAATGAAAATGAAATTTAATGAAAATGAAATTCAAA
25066771 T
1 T
25066772 TCAAATGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
48 7 0.15
49 4 0.08
50 37 0.77
ACGTcount: A:0.56, C:0.01, G:0.14, T:0.29
Consensus pattern (49 bp):
TGAAATTGAAATGAAATGAAAATGAAATTTAATGAAAATGAAATTCAAA
Found at i:25070492 original size:18 final size:17
Alignment explanation
Indices: 25070467--25070500 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25070457 TATTCTTTTT
25070467 CTAACTTTTATTGATTA
1 CTAACTTTTATTGATTA
*
25070484 CTAATCTTTTGTTGATT
1 CTAA-CTTTTATTGATT
25070501 TTCTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (17 bp):
CTAACTTTTATTGATTA
Found at i:25076191 original size:24 final size:25
Alignment explanation
Indices: 25076155--25076202 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
25076145 TGTTATTGCA
*
25076155 ATTTTTCTGTTAATTT-TTGTCTTTT
1 ATTTTACTGTTAATTTGTT-TCTTTT
25076180 ATTTTACT-TTAATTTGTTTCTTT
1 ATTTTACTGTTAATTTGTTTCTTT
25076203 AGTTTTTGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.15, C:0.08, G:0.06, T:0.71
Consensus pattern (25 bp):
ATTTTACTGTTAATTTGTTTCTTTT
Found at i:25078857 original size:21 final size:20
Alignment explanation
Indices: 25078831--25078881 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
25078821 TTTTTGGTAT
*
25078831 CGGTAGATGCATGACTTGTAC
1 CGGTAGATCCAT-ACTTGTAC
* *
25078852 CGGTAGAAACCATACTTGTAT
1 CGGTAG-ATCCATACTTGTAC
25078873 CGGTAGATC
1 CGGTAGATC
25078882 TAGCACAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 19 0.76
22 4 0.16
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (20 bp):
CGGTAGATCCATACTTGTAC
Found at i:25080867 original size:17 final size:17
Alignment explanation
Indices: 25080820--25080857 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
25080810 TTTTCTCTAG
*
25080820 TTGTCAGTACATTTTAA
1 TTGTCACTACATTTTAA
*
25080837 TTGTCACTGCATTTTAA
1 TTGTCACTACATTTTAA
25080854 TTGT
1 TTGT
25080858 TCTCACATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.50
Consensus pattern (17 bp):
TTGTCACTACATTTTAA
Found at i:25090278 original size:88 final size:88
Alignment explanation
Indices: 25090129--25090300 Score: 274
Period size: 88 Copynumber: 2.0 Consensus size: 88
25090119 GTCGGGTTCA
*
25090129 CAAATCGGGTCACTAATCCGGGTTAGGTTCAAAGGGTATTTGGTCACAAAATTTGGGCCTCAAAC
1 CAAATCGGGTCACTAATCCGGGTTAGGTTCAAAGGGTATTGGGTCACAAAATTTGGGCCTCAAAC
* *
25090194 ACTTGGGTTTTGGTTTTGGTTTG
66 ACTTGGGTTTCGGCTTTGGTTTG
*
25090217 CAAATCGAGG-CACTAATCTGGGTTAGGTTCAAAGGGTATTGGGTCACAAAATTTGGGCCTCAAA
1 CAAATCG-GGTCACTAATCCGGGTTAGGTTCAAAGGGTATTGGGTCACAAAATTTGGGCCTCAAA
* *
25090281 CATTTGTGTTTCGGCTTTGG
65 CACTTGGGTTTCGGCTTTGG
25090301 GTATATGATT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 75 0.97
89 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.33
Consensus pattern (88 bp):
CAAATCGGGTCACTAATCCGGGTTAGGTTCAAAGGGTATTGGGTCACAAAATTTGGGCCTCAAAC
ACTTGGGTTTCGGCTTTGGTTTG
Found at i:25096406 original size:7 final size:7
Alignment explanation
Indices: 25096394--25096421 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
25096384 AAATCAAAAT
25096394 GTGTTGA
1 GTGTTGA
25096401 GTGTTGA
1 GTGTTGA
25096408 GTGTTGA
1 GTGTTGA
25096415 GTGTTGA
1 GTGTTGA
25096422 ATATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (7 bp):
GTGTTGA
Found at i:25097875 original size:13 final size:14
Alignment explanation
Indices: 25097859--25097892 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
25097849 ATAGCAATAA
25097859 TTTTTTTTTC-TTC
1 TTTTTTTTTCTTTC
*
25097872 TTTTCTTTTCTTTC
1 TTTTTTTTTCTTTC
25097886 TTTTTTT
1 TTTTTTT
25097893 CTCATTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTCTTTC
Found at i:25097877 original size:8 final size:8
Alignment explanation
Indices: 25097861--25097894 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
25097851 AGCAATAATT
25097861 TTTTTTTC
1 TTTTTTTC
*
25097869 TTCTTTTC
1 TTTTTTTC
25097877 TTTTCTTTC
1 TTTT-TTTC
25097886 TTTTTTTC
1 TTTTTTTC
25097894 T
1 T
25097895 CATTTTGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTTC
Found at i:25097885 original size:17 final size:17
Alignment explanation
Indices: 25097860--25097894 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25097850 TAGCAATAAT
*
25097860 TTTTTTTTCTTCTTTTC
1 TTTTCTTTCTTCTTTTC
*
25097877 TTTTCTTTCTTTTTTTC
1 TTTTCTTTCTTCTTTTC
25097894 T
1 T
25097895 CATTTTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTCTTTCTTCTTTTC
Found at i:25098601 original size:6 final size:6
Alignment explanation
Indices: 25098590--25098615 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
25098580 GCTACCTTTG
25098590 TTTTCT TTTTCT TTTTCT TTTTCT TT
1 TTTTCT TTTTCT TTTTCT TTTTCT TT
25098616 GGGCGCTCAC
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:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTCT
Found at i:25110317 original size:21 final size:20
Alignment explanation
Indices: 25110273--25110334 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
25110263 AGAAGTTTAG
* *
25110273 GTTGTATCAGTAGAATCCAGA
1 GTTGTATCGGTAGAATCC-CA
25110294 GTTGTATCGGTAGAACTCCCA
1 GTTGTATCGGTAGAA-TCCCA
* *
25110315 GTTCTATCGATAGAAGTCCC
1 GTTGTATCGGTAGAA-TCCC
25110335 TCAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 32 0.91
22 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (20 bp):
GTTGTATCGGTAGAATCCCA
Found at i:25120254 original size:21 final size:21
Alignment explanation
Indices: 25120228--25120275 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
25120218 ATGACCATCT
*
25120228 GAAGGAAAAGGAAGAA-GAAGA
1 GAAGGAAAAAG-AGAATGAAGA
25120249 GAAGGAAAAAGAGAATGAAGA
1 GAAGGAAAAAGAGAATGAAGA
25120270 GAAGGA
1 GAAGGA
25120276 CCTTGCCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAGAATGAAGA
Found at i:25120733 original size:17 final size:18
Alignment explanation
Indices: 25120711--25120748 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25120701 AGTTTTCATG
*
25120711 CATTTT-TATTGTCATTA
1 CATTTTATATTGTCACTA
*
25120728 CATTTTATTTTGTCACTA
1 CATTTTATATTGTCACTA
25120746 CAT
1 CAT
25120749 CCCTTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.24, C:0.16, G:0.05, T:0.55
Consensus pattern (18 bp):
CATTTTATATTGTCACTA
Found at i:25135829 original size:11 final size:11
Alignment explanation
Indices: 25135800--25135829 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
25135790 AACTCGTGCA
25135800 TCCAAAAACAC
1 TCCAAAAACAC
25135811 TCCTAAAAACAC
1 TCC-AAAAACAC
25135823 TCCAAAA
1 TCCAAAA
25135830 CCCTCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.53, C:0.33, G:0.00, T:0.13
Consensus pattern (11 bp):
TCCAAAAACAC
Found at i:25137579 original size:18 final size:19
Alignment explanation
Indices: 25137553--25137590 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
25137543 CGGTTGGTTC
*
25137553 GAGGGACAA-GAAAAGAAA
1 GAGGCACAAGGAAAAGAAA
*
25137571 GAGGCACAAGGGAAAGAAA
1 GAGGCACAAGGAAAAGAAA
25137590 G
1 G
25137591 TGAAGAAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.37, T:0.00
Consensus pattern (19 bp):
GAGGCACAAGGAAAAGAAA
Found at i:25146509 original size:294 final size:287
Alignment explanation
Indices: 25145948--25146527 Score: 946
Period size: 294 Copynumber: 2.0 Consensus size: 287
25145938 CGTAAACACA
*
25145948 AAATTCTTCAAAAGTTTTATGACTTCTAATCTTTAATGCGTGTATTTTCTAAGATTGTAAAAGAG
1 AAATTCTTCAAAAGTTTTATGACTTCTAATCTTTAATGCGTGTATTTTATAAGATTGTAAAAGAG
* *
25146013 CCTATTTATAAGCTAAATTTATAGGTCAGATAATAATAAAATAACCTAGACTAATCAGCGTTTGA
66 CCTATTTATAAGCTAAATTTATAGGTCAAATAATAATAAAATAACCTAGACTAATCAGCATTTGA
* *
25146078 CTGAAATAAATAAACAGAGTTTAATTGGAAGATTATTTATCAAATTTGACTGAATTATTAGGCAT
131 CTGAAATAAATAAACAGAGTTTAATTGGAAGATTATTTATCAAATTTGACTGAAATATGAGGCAT
**
25146143 ACTCAATAGTGGATTTTCTAAAAACAAAGTGAAATAGGAAATATCAGTGCAATATAGGAATTATA
196 ACTCAATAACGGATTTTCTAAAAACAAAGTGAAATAGGAAATATCAGTGCAATATAGGAATTATA
25146208 AGTTAGCCTAAACTGCAAAACAAAAAG
261 AGTTAGCCTAAACTGCAAAACAAAAAG
* *
25146235 AAATTCTTCAAAA-TTTTATGAGTTCTAATCTTTAATGCGTGTATTTTATAATATTGTAAAAGAG
1 AAATTCTTCAAAAGTTTTATGACTTCTAATCTTTAATGCGTGTATTTTATAAGATTGTAAAAGAG
**
25146299 CCTATTTATAAGCTAAATTTATAGGTCAAATAATAATAAAATAATTTAGACTAATCAGCATTTGA
66 CCTATTTATAAGCTAAATTTATAGGTCAAATAATAATAAAATAACCTAGACTAATCAGCATTTGA
* * *
25146364 CTGAAATAAATAAATAAATAAATAGATTTTAATTTGAAGATTATTTATCAAATTTGACTGAAATA
131 CTG--------AAATAAATAAACAGAGTTTAATTGGAAGATTATTTATCAAATTTGACTGAAATA
25146429 TGAGGCATACTCAATAACGGATTTTCTAAAAACAAAGTGAAATAGGAAATATCAGTGCAATATAG
188 TGAGGCATACTCAATAACGGATTTTCTAAAAACAAAGTGAAATAGGAAATATCAGTGCAATATAG
*
25146494 GAATTATAGGTTAGCCTAAACTGCAAAACAAAAA
253 GAATTATAAGTTAGCCTAAACTGCAAAACAAAAA
25146528 CAAAAATACA
Statistics
Matches: 270, Mismatches: 15, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
286 112 0.41
287 13 0.05
294 145 0.54
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (287 bp):
AAATTCTTCAAAAGTTTTATGACTTCTAATCTTTAATGCGTGTATTTTATAAGATTGTAAAAGAG
CCTATTTATAAGCTAAATTTATAGGTCAAATAATAATAAAATAACCTAGACTAATCAGCATTTGA
CTGAAATAAATAAACAGAGTTTAATTGGAAGATTATTTATCAAATTTGACTGAAATATGAGGCAT
ACTCAATAACGGATTTTCTAAAAACAAAGTGAAATAGGAAATATCAGTGCAATATAGGAATTATA
AGTTAGCCTAAACTGCAAAACAAAAAG
Found at i:25148872 original size:17 final size:17
Alignment explanation
Indices: 25148850--25148884 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
25148840 CAAAATTAAA
*
25148850 TTTTTAAAAATGTTTAT
1 TTTTTAAAAATGCTTAT
*
25148867 TTTTTAAATATGCTTAT
1 TTTTTAAAAATGCTTAT
25148884 T
1 T
25148885 ATATTATACG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.60
Consensus pattern (17 bp):
TTTTTAAAAATGCTTAT
Found at i:25149891 original size:14 final size:14
Alignment explanation
Indices: 25149872--25149899 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25149862 ATAATTTTTA
25149872 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
25149886 ATTTTTTTAAAAAT
1 ATTTTTTTAAAAAT
25149900 TTTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTTTTTAAAAAT
Found at i:25153644 original size:6 final size:6
Alignment explanation
Indices: 25153635--25153714 Score: 67
Period size: 6 Copynumber: 13.7 Consensus size: 6
25153625 TAAAATGATT
* * *
25153635 TTTAAA TTT-AT TTCTAAA ATTAAA TTT-AC TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TT-TAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
25153682 TTCATT TTTAAA TTTAAA TTT-AT TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA
25153715 GTTTCAATTT
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
5 11 0.20
6 43 0.77
7 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:25153644 original size:24 final size:24
Alignment explanation
Indices: 25153611--25153703 Score: 73
Period size: 24 Copynumber: 3.7 Consensus size: 24
25153601 TTTGGGTCAA
* *
25153611 TTTT-AATTTAAGTTTAAAATGAT
1 TTTTAAATTTAAATTTAAAATAAT
*
25153634 TTTTAAATTT-ATTTCTAAAATTAAATT
1 TTTTAAATTTAAATT-TAAAA-T-AA-T
* *
25153661 TACTTTAAATTTAAATTTAAATTCAT
1 T--TTTAAATTTAAATTTAAAATAAT
25153687 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
25153704 TTTTAAATTT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
23 7 0.12
24 26 0.46
25 1 0.02
26 3 0.05
27 3 0.05
28 1 0.02
29 13 0.23
30 3 0.05
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTAAATTTAAATTTAAAATAAT
Found at i:25153668 original size:41 final size:41
Alignment explanation
Indices: 25153623--25153710 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
25153613 TTAATTTAAG
** *
25153623 TTTAAAATGATTTTTAAATTTATTTCTAAAATTAAATTTAC
1 TTTAAAATGAAATTTAAATTCATTTCTAAAATTAAATTTAC
* * * * *
25153664 TTTAAATTTAAATTTAAATTCATTTTTAAATTTAAATTTAT
1 TTTAAAATGAAATTTAAATTCATTTCTAAAATTAAATTTAC
25153705 TTTAAA
1 TTTAAA
25153711 TTTAGTTTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.53
Consensus pattern (41 bp):
TTTAAAATGAAATTTAAATTCATTTCTAAAATTAAATTTAC
Found at i:25153674 original size:17 final size:18
Alignment explanation
Indices: 25153635--25153679 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
25153625 TAAAATGATT
*
25153635 TTTAAATTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
25153653 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
25153670 TTTAAATTTA
1 TTTAAATTTA
25153680 AATTCATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 13 0.54
18 11 0.46
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:25153710 original size:11 final size:11
Alignment explanation
Indices: 25153654--25153724 Score: 51
Period size: 11 Copynumber: 6.7 Consensus size: 11
25153644 ATTTCTAAAA
*
25153654 TTAAATTTACT
1 TTAAATTTATT
*
25153665 TTAAATTTAAAT
1 TTAAATTT-ATT
*
25153677 TTAAATTCATT
1 TTAAATTTATT
*
25153688 TTTAA---A-T
1 TTAAATTTATT
25153695 TTAAATTTATT
1 TTAAATTTATT
*
25153706 TTAAATTTAGT
1 TTAAATTTATT
*
25153717 TTCAATTT
1 TTAAATTT
25153725 GAAATAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
7 5 0.10
8 1 0.02
10 1 0.02
11 32 0.67
12 9 0.19
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.56
Consensus pattern (11 bp):
TTAAATTTATT
Found at i:25153711 original size:41 final size:41
Alignment explanation
Indices: 25153635--25153714 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
25153625 TAAAATGATT
*
25153635 TTTAAATTTATTTCTAAAATTAAATTTACTTTAAATTTAAA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
* * *
25153676 TTTAAATTCATTTTTAAATTTAAATTTATTTTAAATTTA
1 TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTA
25153715 GTTTCAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (41 bp):
TTTAAATTCATTTCTAAAATTAAATTTACTTTAAATTTAAA
Found at i:25153724 original size:18 final size:18
Alignment explanation
Indices: 25153634--25153729 Score: 74
Period size: 18 Copynumber: 5.4 Consensus size: 18
25153624 TTAAAATGAT
25153634 TTTTAAATTT-ATTTCTAA
1 TTTTAAATTTAATTTC-AA
** *
25153652 AATTAAATTTACTTT-AA
1 TTTTAAATTTAATTTCAA
* * *
25153669 ATTTAAATTTAAATTCAT
1 TTTTAAATTTAATTTCAA
25153687 TTTTAAATTTAAATTT--A
1 TTTTAAATTT-AATTTCAA
*
25153704 TTTTAAATTTAGTTTCAA
1 TTTTAAATTTAATTTCAA
*
25153722 TTTGAAAT
1 TTTTAAAT
25153730 AATTTTAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 10
0.73 0.14 0.12
Matches are distributed among these distances:
16 4 0.07
17 24 0.39
18 26 0.43
19 7 0.11
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (18 bp):
TTTTAAATTTAATTTCAA
Found at i:25154765 original size:15 final size:15
Alignment explanation
Indices: 25154745--25154778 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25154735 CCAAAACAAG
* *
25154745 TAAAATAAAGAGTTT
1 TAAAATAAAAAGATT
25154760 TAAAATAAAAAGATT
1 TAAAATAAAAAGATT
25154775 TAAA
1 TAAA
25154779 GAAAAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (15 bp):
TAAAATAAAAAGATT
Found at i:25155696 original size:59 final size:58
Alignment explanation
Indices: 25155633--25155830 Score: 238
Period size: 58 Copynumber: 3.4 Consensus size: 58
25155623 CCTGGACTAT
** *
25155633 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTCAACCCTGATTTTA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCC-TTTTTGACCCTGATTTCA
25155692 CC-AAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCTTTTTGA-CCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCTTTTTGACCCT-GATTTCA
* * * * * *
25155749 CCAAAAATTACTATTTTGCCCTCGAATTTTCCAAAATTCCCTTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATT-CCTTTTTGACCCTGATTTCA
* * * *
25155808 TCGAAAGTTACCATTTTGCCCCC
1 CCAAAAATTACCATTTTACCCCC
25155831 GCGAGTCAAA
Statistics
Matches: 121, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
56 3 0.02
57 13 0.11
58 67 0.55
59 36 0.30
60 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.05, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCTTTTTGACCCTGATTTCA
Found at i:25155724 original size:29 final size:29
Alignment explanation
Indices: 25155636--25155728 Score: 118
Period size: 29 Copynumber: 3.2 Consensus size: 29
25155626 GGACTATCCA
25155636 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCCCAAACTTTCC
* ** *
25155665 AAAATT-CCATTTT-CAACCCTGATTTTACC
1 AAAATTACCATTTTAC-CCCCAAACTTT-CC
25155694 AAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTACCATTTTACCCCCAAACTTTCC
25155723 AAAATT
1 AAAATT
25155729 CCTTTTTGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
27 1 0.02
28 14 0.27
29 22 0.42
30 14 0.27
31 1 0.02
ACGTcount: A:0.35, C:0.30, G:0.01, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCAAACTTTCC
Found at i:25155755 original size:29 final size:28
Alignment explanation
Indices: 25155721--25155807 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 28
25155711 CCCAAACTTT
25155721 CCAAAATTCCTTTTTGACCTCGATTTCA
1 CCAAAATTCCTTTTTGACCTCGATTTCA
* * *
25155749 CCAAAAATTACTATTTTGCCCTCGAATTT-T
1 CC-AAAATTCCT-TTTTGACCTCG-ATTTCA
*
25155779 CCAAAATTCCCTTTTTGACCCCGATTTCA
1 CCAAAATT-CCTTTTTGACCTCGATTTCA
25155808 TCGAAAGTTA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 6 0.13
29 23 0.49
30 14 0.30
31 4 0.09
ACGTcount: A:0.26, C:0.29, G:0.07, T:0.38
Consensus pattern (28 bp):
CCAAAATTCCTTTTTGACCTCGATTTCA
Found at i:25170802 original size:76 final size:76
Alignment explanation
Indices: 25170500--25170891 Score: 545
Period size: 76 Copynumber: 5.0 Consensus size: 76
25170490 TCAATCGAAC
* * *
25170500 ATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATT---
25170565 GAAGTAAGAGCAAG
63 GAAGTAAGAGCAAG
* *
25170579 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAG-TTGGATAACAAGTCTTTATCTCTGAAATT--
25170644 AGAAGTAAGAGCAAG
63 -GAAGTAAGAGCAAG
* ** * *
25170659 ATCATTTCCTATCTTC-TGAAA-TGAAATAAGTAAAACTAGATATCAAGTCTTTATCTCTGAAAT
1 ATCATTTCCTATCCTCTTGAAATTG----AAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAAT
*
25170722 TGAAGTAAGAGCAAC
62 TGAAGTAAGAGCAAG
*
25170737 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
25170802 GTAAGAGCAAG
66 GTAAGAGCAAG
*
25170813 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTTGAAATTGA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTC-TGAAATTGA
25170878 AGTAAGAGCAAG
65 AGTAAGAGCAAG
25170890 AT
1 AT
25170892 GAAGCCTCGA
Statistics
Matches: 289, Mismatches: 16, Indels: 18
0.89 0.05 0.06
Matches are distributed among these distances:
76 98 0.34
77 23 0.08
78 30 0.10
79 41 0.14
80 62 0.21
81 28 0.10
82 7 0.02
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:25171217 original size:11 final size:11
Alignment explanation
Indices: 25171201--25171271 Score: 60
Period size: 11 Copynumber: 6.7 Consensus size: 11
25171191 ATTTCTAAAA
*
25171201 TTAAATTTACT
1 TTAAATTTAAT
25171212 TTAAATTTAAAT
1 TTAAATTT-AAT
*
25171224 TTAAA-TTCAT
1 TTAAATTTAAT
*
25171234 TT---TTAAAT
1 TTAAATTTAAT
*
25171242 TTAAATTTATT
1 TTAAATTTAAT
*
25171253 TTAAATTTAGT
1 TTAAATTTAAT
25171264 TTAAATTT
1 TTAAATTT
25171272 GAAATAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
8 5 0.10
10 4 0.08
11 32 0.67
12 7 0.15
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.56
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:25171220 original size:6 final size:6
Alignment explanation
Indices: 25171196--25171297 Score: 70
Period size: 6 Copynumber: 17.7 Consensus size: 6
25171186 ATTTTATTTC
* * * **
25171196 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* * * *
25171243 TAAATT T-ATTT TAAATT T-AGTT TAAATT TGAAA-- TAATTT TAAAAT
1 TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT TAAATT
*
25171288 TAAAAT TAAA
1 TAAATT TAAA
25171298 AAGCCCAAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 12
0.73 0.16 0.12
Matches are distributed among these distances:
4 2 0.03
5 13 0.18
6 56 0.76
7 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (6 bp):
TAAATT
Found at i:25171221 original size:17 final size:18
Alignment explanation
Indices: 25171196--25171297 Score: 70
Period size: 17 Copynumber: 5.9 Consensus size: 18
25171186 ATTTTATTTC
* *
25171196 TAAAATTAAATTT-ACTT
1 TAAATTTAAATTTAAATT
25171213 TAAATTTAAATTTAAATT
1 TAAATTTAAATTTAAATT
* **
25171231 CATTTTTAAATTTAAATT
1 TAAATTTAAATTTAAATT
* *
25171249 T-ATTTTAAATTT-AGTT
1 TAAATTTAAATTTAAATT
*
25171265 TAAATTTGAAA--TAATTT
1 TAAATTT-AAATTTAAATT
* *
25171282 TAAAATTAAAATTAAA
1 TAAATTTAAATTTAAA
25171298 AAGCCCAAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 11
0.74 0.13 0.12
Matches are distributed among these distances:
16 8 0.12
17 35 0.52
18 24 0.36
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TAAATTTAAATTTAAATT
Found at i:25171256 original size:41 final size:40
Alignment explanation
Indices: 25171191--25171270 Score: 115
Period size: 41 Copynumber: 2.0 Consensus size: 40
25171181 TTAAAATTTT
25171191 ATTTCTAAAATTAAATTTACTTTAAATTTAAATTTAAATTC
1 ATTTCTAAAATTAAATTTACTTTAAATTT-AATTTAAATTC
* * * *
25171232 ATTTTTAAATTTAAATTTATTTTAAATTTAGTTTAAATT
1 ATTTCTAAAATTAAATTTACTTTAAATTTAATTTAAATT
25171271 TGAAATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
40 9 0.26
41 26 0.74
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (40 bp):
ATTTCTAAAATTAAATTTACTTTAAATTTAATTTAAATTC
Found at i:25172311 original size:15 final size:15
Alignment explanation
Indices: 25172291--25172324 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
25172281 CCAAAACAAG
* *
25172291 TAAAATAAAGAGTTT
1 TAAAATAAAAAGATT
25172306 TAAAATAAAAAGATT
1 TAAAATAAAAAGATT
25172321 TAAA
1 TAAA
25172325 GAAAAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (15 bp):
TAAAATAAAAAGATT
Found at i:25173238 original size:59 final size:59
Alignment explanation
Indices: 25173173--25173432 Score: 317
Period size: 59 Copynumber: 4.4 Consensus size: 59
25173163 CCTGGACTAT
* ** *** *
25173173 CCAAAAATTACCATTTTACCCCCGAACTTTCTGAAATAGTATTTTTAGCCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAGCCTCGATTTCA
* * *
25173232 TCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAGCCTCGATTTCA
*
25173291 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTT-GACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAG-CCTCGATTTCA
* ** * * *
25173350 CCAAAAATTACTATTTTACCCTTAAATTTTCCAAAATTCCCTTTTT-GACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAG-CCTCGATTTCA
* *
25173409 CCGAAAGTTACCATTTTACCCCCA
1 CCAAAAATTACCATTTTACCCCCA
25173433 CGAGTCCAAA
Statistics
Matches: 176, Mismatches: 24, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
59 176 1.00
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAGCCTCGATTTCA
Found at i:25173267 original size:30 final size:29
Alignment explanation
Indices: 25173233--25173385 Score: 106
Period size: 30 Copynumber: 5.2 Consensus size: 29
25173223 CCGATTTCAT
25173233 CAAAAATTACCATTTTACCCTCAAACTTTC
1 CAAAAATTACCATTTTACCCTCAAA-TTTC
* *
25173263 C-AAAATT-CCATTTTTAACCTC-GATTTCAC
1 CAAAAATTACCA-TTTTACCCTCAAATTT--C
25173292 CAAAAATTACCATTTTACCC-CTAAACTTTC
1 CAAAAATTACCATTTTACCCTC-AAA-TTTC
*
25173322 C-AAAATT-CCATTTTTGA-CCTC-GATTTCAC
1 CAAAAATTACCA-TTTT-ACCCTCAAATTT--C
* *
25173351 CAAAAATTACTATTTTACCCTTAAATTTTC
1 CAAAAATTACCATTTTACCCTCAAA-TTTC
25173381 CAAAA
1 CAAAA
25173386 TTCCCTTTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 36
0.69 0.06 0.26
Matches are distributed among these distances:
27 6 0.06
28 8 0.08
29 33 0.34
30 37 0.38
31 7 0.07
32 6 0.06
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCTCAAATTTC
Found at i:25173277 original size:29 final size:28
Alignment explanation
Indices: 25173235--25173400 Score: 94
Period size: 29 Copynumber: 5.6 Consensus size: 28
25173225 GATTTCATCA
25173235 AAAATTACCA-TTTTACCCTCAAACTTTCC
1 AAAATT-CCATTTTTACCCTCAAA-TTTCC
* *
25173264 AAAATTCCATTTTTAACCTC-GATTTCACC
1 AAAATTCCATTTTTACCCTCAAATTT--CC
25173293 AAAAATTACCA-TTTTACCC-CTAAACTTTCC
1 -AAAATT-CCATTTTTACCCTC-AAA-TTTCC
*
25173323 AAAATTCCATTTTTGA-CCTC-GATTTCACC
1 AAAATTCCATTTTT-ACCCTCAAATTT--CC
* *
25173352 AAAAATTAC-TATTTTACCCTTAAATTTTCC
1 -AAAATTCCAT-TTTTACCCTCAAA-TTTCC
*
25173382 AAAATTCCCTTTTTGACCC
1 AAAATTCCATTTTT-ACCC
25173401 CGATTTCACC
Statistics
Matches: 108, Mismatches: 9, Indels: 39
0.69 0.06 0.25
Matches are distributed among these distances:
27 6 0.06
28 8 0.07
29 45 0.42
30 38 0.35
31 5 0.05
32 6 0.06
ACGTcount: A:0.33, C:0.28, G:0.02, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCTCAAATTTCC
Found at i:25173381 original size:118 final size:118
Alignment explanation
Indices: 25173173--25173432 Score: 351
Period size: 118 Copynumber: 2.2 Consensus size: 118
25173163 CCTGGACTAT
* ** ** *
25173173 CCAAAAATTACCATTTTACCCCCGAACTTTCTGAAATAGTATTTTTAGCCCCGATTTCATCAAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTTAGCCCCGATTTCACCAAAA
*
25173238 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
66 ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
25173291 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTT-GACCTCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTTAG-CCCCGATTTCACCAAA
* * * * *
25173355 AATTACTATTTTACCCTTAAATTTTCCAAAATTCCCTTTTTGACCCCGATTTCA
65 AATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* *
25173409 CCGAAAGTTACCATTTTACCCCCA
1 CCAAAAATTACCATTTTACCCCCA
25173433 CGAGTCCAAA
Statistics
Matches: 123, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
117 1 0.01
118 122 0.99
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATACCATTTTTAGCCCCGATTTCACCAAAA
ATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:25175904 original size:15 final size:15
Alignment explanation
Indices: 25175884--25175923 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
25175874 TAATTTGGTA
*
25175884 TGAAAAATTAAGTGT
1 TGAAAAATTAAGTAT
25175899 TGAAAAATTAAGTAT
1 TGAAAAATTAAGTAT
*
25175914 TGAAAGATTA
1 TGAAAAATTA
25175924 TGGGAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (15 bp):
TGAAAAATTAAGTAT
Found at i:25179553 original size:686 final size:686
Alignment explanation
Indices: 25178241--25179574 Score: 2352
Period size: 686 Copynumber: 1.9 Consensus size: 686
25178231 AAAATTTGTC
* *
25178241 TTCAACCAATTCATCGAGATCCGACCACCTTCGAATTGGTTTGGGATCTTCCCCAACAGTGTCTC
1 TTCAACCAATTCATCGAGATCCGACCACCTTCGAACTGGTTCGGGATCTTCCCCAACAGTGTCTC
* * *
25178306 GCAAAGGGTCACTTTACCGACAACGATCGATGCTCTCGTGAAGATTGACCCATTAATCGATAAAC
66 GCAAAGGGTCACTTTACCGACAACGACCGATGCTCCCGTGAAGATTGACCCATCAATCGATAAAC
25178371 AGAGTTGTAGCGCTACGTCTTCGAGTGTGATTGTACACTCGCCGCATGAAAGGTGGAAATATTGT
131 AGAGTTGTAGCGCTACGTCTTCGAGTGTGATTGTACACTCGCCGCATGAAAGGTGGAAATATTGT
* *
25178436 GTTTCGGTCCTCCATCTTTCTACCAACGTGCTGATTAGTTGGAAATCAAGTTTGCAGCCCCCAAA
196 GTTTCGGGCCTCCATCTTTCTACCAACATGCTGATTAGTTGGAAATCAAGTTTGCAGCCCCCAAA
*
25178501 CATGTGATACTCATGTAAGAATCCAGCCGGTTGCAAGTAGTTGCGAATTTCAAGGATCAGAGGCT
261 CATGTGATACTCATGTAAGAATCCAGCCGGTTGCAAGTAGTCGCGAATTTCAAGGATCAGAGGCT
25178566 TTCCCATATTATTAATGAAGCCCTCCAAAACACGATCATCAGCTTATTTACAAAAAATATATATT
326 TTCCCATATTATTAATGAAGCCCTCCAAAACACGATCATCAGCTTATTTACAAAAAATATATATT
25178631 AAAATTAATAAAAATAAATTTAACAGTATTCAAAGTAACGAAATTTAAATTTTCGTACTACCATT
391 AAAATTAATAAAAATAAATTTAACAGTATTCAAAGTAACGAAATTTAAATTTTCGTACTACCATT
**
25178696 GATAATTGGACATCGGAAATATGATCGACGTCGCATCGGATTAGAGAAGCGGGCATTTTTTAAAA
456 GATAATTGGACATCAAAAATATGATCGACGTCGCATCGGATTAGAGAAGCGGGCATTTTTTAAAA
*
25178761 TCGAGTTAAAAATTTGAGATTTTAAAAAATATTATTTTTAAATAAAAATATCGAAAATAATTAAA
521 TCGAGTTAAAAATTTGAGATTTTAAAAAATATTATTTTAAAATAAAAATATCGAAAATAATTAAA
* *
25178826 ACGAGAAAATAACGAGATTAATAGCGGATTTGAGAGAGTTGAGAGAGCTGAGAGGGATATGAGTG
586 ACGAGAAAATAACGAGATTAATAGCGGATTTGAGAGAGTTGAGAAAGCTGAGAAGGATATGAGTG
25178891 AAAAAGAATGAAAAACGAAGGGGTATTTGTAGGGTT
651 AAAAAGAATGAAAAACGAAGGGGTATTTGTAGGGTT
25178927 TTCAACCAATTCATCGAGATCCGACCACCTTCGAACTGGTTCGGGATCTTCCCCAACAGTGTCTC
1 TTCAACCAATTCATCGAGATCCGACCACCTTCGAACTGGTTCGGGATCTTCCCCAACAGTGTCTC
** * * *
25178992 GCAAAGGGTCACTTTATTGATAACGACCGATGCTCCCGTGACGATTGATCCATCAATCGATAAAT
66 GCAAAGGGTCACTTTACCGACAACGACCGATGCTCCCGTGAAGATTGACCCATCAATCGATAAA-
*
25179057 C-GAGTTGTAGCGCTACGTCTTCGAGTGTGATTGTACACTCGCCTCATGAAAGGTGGAAAT-TGT
130 CAGAGTTGTAGCGCTACGTCTTCGAGTGTGATTGTACACTCGCCGCATGAAAGGTGGAAATAT-T
*
25179120 GTGTTTCGGGCCTCCATCTTTCTACCAACATGCTGATTAGTTGGAAATCAAGTTTGTAGCCCCCA
194 GTGTTTCGGGCCTCCATCTTTCTACCAACATGCTGATTAGTTGGAAATCAAGTTTGCAGCCCCCA
*
25179185 AACATGTGATACTTATGTAAGAATCCAGCCGGTTGCAAGTAGTCGCGAATTTCAAGGATCAGAGG
259 AACATGTGATACTCATGTAAGAATCCAGCCGGTTGCAAGTAGTCGCGAATTTCAAGGATCAGAGG
*
25179250 CTTTCCCATATTATTAATGAAGCCCTCCAAAACACGATCATTAGCTTATTTACAAAAAA-ATATA
324 CTTTCCCATATTATTAATGAAGCCCTCCAAAACACGATCATCAGCTTATTTACAAAAAATATATA
*
25179314 TTAAAATTAATAAAAATAAATTTAACAGTATTCAAAGTAACGAAATTTAAATTTTCGTATTACCA
389 TTAAAATTAATAAAAATAAATTTAACAGTATTCAAAGTAACGAAATTTAAATTTTCGTACTACCA
25179379 TTGATAATTGGACATCAAAAATATGATCGACGTCGCATCGGATTAGAGAAGCGGGCATTTTTTAA
454 TTGATAATTGGACATCAAAAATATGATCGACGTCGCATCGGATTAGAGAAGCGGGCATTTTTTAA
*
25179444 AATCGAGTTAAAAA-TTGAGATTTTAAACAAAATATTATTTTAAAATAAAAATATTGAAAATAAT
519 AATCGAGTTAAAAATTTGAGATTTT-AA-AAAATATTATTTTAAAATAAAAATATCGAAAATAAT
* * * *
25179508 TAAAATGAGAAAATAACGAGATTAGTAGTGGATTTGAGAGAGTTGAGAAAGCTGAGAAGGATTTG
582 TAAAACGAGAAAATAACGAGATTAATAGCGGATTTGAGAGAGTTGAGAAAGCTGAGAAGGATATG
25179573 AG
647 AG
25179575 AGAGTTGAGA
Statistics
Matches: 616, Mismatches: 28, Indels: 8
0.94 0.04 0.01
Matches are distributed among these distances:
684 10 0.02
685 149 0.24
686 456 0.74
687 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (686 bp):
TTCAACCAATTCATCGAGATCCGACCACCTTCGAACTGGTTCGGGATCTTCCCCAACAGTGTCTC
GCAAAGGGTCACTTTACCGACAACGACCGATGCTCCCGTGAAGATTGACCCATCAATCGATAAAC
AGAGTTGTAGCGCTACGTCTTCGAGTGTGATTGTACACTCGCCGCATGAAAGGTGGAAATATTGT
GTTTCGGGCCTCCATCTTTCTACCAACATGCTGATTAGTTGGAAATCAAGTTTGCAGCCCCCAAA
CATGTGATACTCATGTAAGAATCCAGCCGGTTGCAAGTAGTCGCGAATTTCAAGGATCAGAGGCT
TTCCCATATTATTAATGAAGCCCTCCAAAACACGATCATCAGCTTATTTACAAAAAATATATATT
AAAATTAATAAAAATAAATTTAACAGTATTCAAAGTAACGAAATTTAAATTTTCGTACTACCATT
GATAATTGGACATCAAAAATATGATCGACGTCGCATCGGATTAGAGAAGCGGGCATTTTTTAAAA
TCGAGTTAAAAATTTGAGATTTTAAAAAATATTATTTTAAAATAAAAATATCGAAAATAATTAAA
ACGAGAAAATAACGAGATTAATAGCGGATTTGAGAGAGTTGAGAAAGCTGAGAAGGATATGAGTG
AAAAAGAATGAAAAACGAAGGGGTATTTGTAGGGTT
Found at i:25179569 original size:29 final size:29
Alignment explanation
Indices: 25179537--25179603 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
25179527 GATTAGTAGT
25179537 GGATTTGAGAGAGTTGAGAAAGCTGAGAA
1 GGATTTGAGAGAGTTGAGAAAGCTGAGAA
25179566 GGATTTGAGAGAGTTGAGAAAGCTGAGAA
1 GGATTTGAGAGAGTTGAGAAAGCTGAGAA
25179595 GGATTTGAG
1 GGATTTGAG
25179604 TGAAAAAGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.36, C:0.03, G:0.39, T:0.22
Consensus pattern (29 bp):
GGATTTGAGAGAGTTGAGAAAGCTGAGAA
Found at i:25188863 original size:52 final size:52
Alignment explanation
Indices: 25188686--25188878 Score: 260
Period size: 52 Copynumber: 3.7 Consensus size: 52
25188676 AATGAAAAAG
** * * *
25188686 GGTCCGATGATTAAGTGTCATCGTGAGTATATGAATCCTTCACGAATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
* * * *
25188738 GGACTGATGGCTATGTGTCATCTTGAGCATATGAATCCTTTACGGATTTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGA-TTATGA
* * *
25188791 GGTTCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTATGGGTTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
*
25188843 GGTCCGGTGGCTATGTGTCATCGTGAGTATATGAAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAAT
25188879 GAAATGAAAT
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
52 77 0.63
53 45 0.37
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGA
Found at i:25191272 original size:25 final size:24
Alignment explanation
Indices: 25191244--25191299 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 24
25191234 GATCTTAAAT
*
25191244 AGAATATGTGTATATGGA-ATATGTG
1 AGAA-ATGTGT-TATAGACATATGTG
25191269 AGAAATGTGTTATAGACTATATGTG
1 AGAAATGTGTTATAGAC-ATATGTG
25191294 AGAAAT
1 AGAAAT
25191300 AATTTATGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 17 0.61
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (24 bp):
AGAAATGTGTTATAGACATATGTG
Found at i:25193010 original size:15 final size:15
Alignment explanation
Indices: 25192998--25193027 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25192988 TCATCCTGAG
25192998 TATATGAATCCTGTA
1 TATATGAATCCTGTA
25193013 TATATGAATCCTGTA
1 TATATGAATCCTGTA
25193028 CGGATTATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (15 bp):
TATATGAATCCTGTA
Found at i:25193054 original size:67 final size:67
Alignment explanation
Indices: 25192946--25193076 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 67
25192936 TCATCGTGAG
*
25192946 TATATGAATCCTTTACGAATTATGAGGTCCGATGGCTATGTGTCATCCTGAGTATATGAATCCTG
1 TATATGAATCCTGTACGAATTATGAGGTCCGATGGCTATGTGTCATCCTGAGTATATGAATCCTG
25193011 TA
66 TA
* * *
25193013 TATATGAATCCTGTACGGATTATGAGGTCCGATGGCTATGTGTCATCGTTAGTATATGAATCCT
1 TATATGAATCCTGTACGAATTATGAGGTCCGATGGCTATGTGTCATCCTGAGTATATGAATCCT
25193077 TTACGGATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (67 bp):
TATATGAATCCTGTACGAATTATGAGGTCCGATGGCTATGTGTCATCCTGAGTATATGAATCCTG
TA
Found at i:25193230 original size:52 final size:52
Alignment explanation
Indices: 25193013--25193216 Score: 356
Period size: 52 Copynumber: 3.9 Consensus size: 52
25193003 GAATCCTGTA
* *
25193013 TATATGAATCCTGTACGGATTATGAGGTCCGATGGCTATGTGTCATC-GTTAG
1 TATATGAATCCTTTACGGATTATGAGGTCCGATGGCTATGTGTCATCAG-GAG
25193065 TATATGAATCCTTTACGGATTTATGAGGTCCGATGGCTATGTGTCATCAGGAG
1 TATATGAATCCTTTACGGA-TTATGAGGTCCGATGGCTATGTGTCATCAGGAG
25193118 TATATGAATCCTTTACGGATTATGAGGTCCGATGGCTATGTGTCATCAGGAG
1 TATATGAATCCTTTACGGATTATGAGGTCCGATGGCTATGTGTCATCAGGAG
*
25193170 TATATGAATCCTTTACGGATTATGAGGTCCGGTGGCTATGTGTCATC
1 TATATGAATCCTTTACGGATTATGAGGTCCGATGGCTATGTGTCATC
25193217 GTGAATTAAT
Statistics
Matches: 147, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
52 97 0.66
53 49 0.33
54 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (52 bp):
TATATGAATCCTTTACGGATTATGAGGTCCGATGGCTATGTGTCATCAGGAG
Found at i:25194548 original size:52 final size:52
Alignment explanation
Indices: 25194456--25194696 Score: 358
Period size: 52 Copynumber: 4.6 Consensus size: 52
25194446 AATGAAAAAG
* *
25194456 GGTCCGATGTCTAAGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* * *
25194508 GATCTGATGGCTATGTGTCATCCTGAGTATATGAATCCTTTAC-GAATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAG-ATTATGA
*
25194560 GGTCCAATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGA-TTATGA
* *
25194613 GGTCCGATGGCTATGTGTCATCGTAAGTATATGAATCCTTTACGGATTATGA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
* * *
25194665 GTTCCGGTGGCTATGTGTCATCATGAGTATAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATAT
25194697 TAATGAAATG
Statistics
Matches: 170, Mismatches: 16, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
51 1 0.01
52 119 0.70
53 50 0.29
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (52 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGA
Found at i:25194652 original size:105 final size:104
Alignment explanation
Indices: 25194456--25194696 Score: 374
Period size: 105 Copynumber: 2.3 Consensus size: 104
25194446 AATGAAAAAG
* * *
25194456 GGTCCGATGTCTAAGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGATCTGATGGCTA
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGATCCGATGGCTA
*
25194521 TGTGTCATCCTGAGTATATGAATCCTTTACGAATTATGA
66 TGTGTCATCCTAAGTATATGAATCCTTTACGAATTATGA
* *
25194560 GGTCCAATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTTATGAGGTCCGATGGCT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGA-TTATGAGATCCGATGGCT
* *
25194625 ATGTGTCATCGTAAGTATATGAATCCTTTACGGATTATGA
65 ATGTGTCATCCTAAGTATATGAATCCTTTACGAATTATGA
* * *
25194665 GTTCCGGTGGCTATGTGTCATCATGAGTATAT
1 GGTCCGATGGCTATGTGTCATCGTGAGTATAT
25194697 TAATGAAATG
Statistics
Matches: 124, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
104 43 0.35
105 81 0.65
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (104 bp):
GGTCCGATGGCTATGTGTCATCGTGAGTATATGAATCCTTTACAGATTATGAGATCCGATGGCTA
TGTGTCATCCTAAGTATATGAATCCTTTACGAATTATGA
Found at i:25198412 original size:17 final size:18
Alignment explanation
Indices: 25198392--25198438 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
25198382 ATTCAATTAC
25198392 ATTAATGATTTTTTAT-T-
1 ATTAAT-ATTTTTTATATA
25198409 ATTATATAATTTTTTATATA
1 ATTA-AT-ATTTTTTATATA
25198429 ATTAATATTT
1 ATTAATATTT
25198439 AAAAATTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 4 0.15
18 15 0.58
19 3 0.12
20 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
ATTAATATTTTTTATATA
Found at i:25198776 original size:23 final size:24
Alignment explanation
Indices: 25198744--25198794 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
25198734 TTGTGACACA
*
25198744 TTTTTCCTCTGTCTTATAGCACGC
1 TTTTTCCTCTATCTTATAGCACGC
* * *
25198768 TTTTT-CTCTATTTTGTGGCACGC
1 TTTTTCCTCTATCTTATAGCACGC
25198791 TTTT
1 TTTT
25198795 GCCTTATGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.10, C:0.24, G:0.14, T:0.53
Consensus pattern (24 bp):
TTTTTCCTCTATCTTATAGCACGC
Found at i:25199141 original size:26 final size:25
Alignment explanation
Indices: 25199112--25199166 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
25199102 TGATCTGATG
*
25199112 TTTAGTTTT-CTATTTTTTAATTTAT
1 TTTA-TTTTGCTATTTTTTAATATAT
*
25199137 CTTTATTTTGTTATTTTTTAATATAT
1 -TTTATTTTGCTATTTTTTAATATAT
25199163 TTTA
1 TTTA
25199167 ATTTCGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.22, C:0.04, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTATTTTGCTATTTTTTAATATAT
Found at i:25201532 original size:16 final size:17
Alignment explanation
Indices: 25201504--25201542 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
25201494 CAATTCGATT
25201504 AAAAATATAAAAAT-TC
1 AAAAATATAAAAATCTC
25201520 AACAAAT-TAAAAATCTC
1 AA-AAATATAAAAATCTC
25201537 AAAAAT
1 AAAAAT
25201543 CTCGGTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAATATAAAAATCTC
Found at i:25202386 original size:58 final size:58
Alignment explanation
Indices: 25202274--25202387 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
25202264 AAAAATTAGA
* * * * *
25202274 TAAATTTTTTTTAAGTCTCTTAAAAGTTGGTAAAAATAATTTTTGGGCCCTTAAAAGC
1 TAAATTTTTTTTAAGACCCTTAAAACTTAGTAAAAATAATTTTTGAGCCCTTAAAAGC
* *
25202332 TAAATTTTTTTTGAA-ACCCTTAAAACTTAGTAAAAATAATTTTTTAGCCTTTAAAA
1 TAAATTTTTTTT-AAGACCCTTAAAACTTAGTAAAAATAATTTTTGAGCCCTTAAAA
25202388 ATTAAAAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
58 46 0.96
59 2 0.04
ACGTcount: A:0.38, C:0.11, G:0.10, T:0.42
Consensus pattern (58 bp):
TAAATTTTTTTTAAGACCCTTAAAACTTAGTAAAAATAATTTTTGAGCCCTTAAAAGC
Found at i:25202395 original size:28 final size:28
Alignment explanation
Indices: 25202362--25202434 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
25202352 TAAAACTTAG
* *
25202362 TAAAAATAATTTTTTAGC-CTTTAAAAAT
1 TAAAAA-AATTTTTTAACTCTTTAAAAAC
* *
25202390 TAAAAAAATATTTAAACTCTTTAAAAAC
1 TAAAAAAATTTTTTAACTCTTTAAAAAC
25202418 TAAAAAAATTATTTTAA
1 TAAAAAAATT-TTTTAA
25202435 ACCTCTCTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
27 8 0.22
28 24 0.65
29 5 0.14
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.38
Consensus pattern (28 bp):
TAAAAAAATTTTTTAACTCTTTAAAAAC
Found at i:25203560 original size:19 final size:20
Alignment explanation
Indices: 25203538--25203584 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
25203528 AATCGATACC
25203538 AAAATTTT-TAAT-ATTATTT
1 AAAATTTTCTAATCATTA-TT
25203557 AAAATTTTCTAATGCATTATT
1 AAAATTTTCTAAT-CATTATT
25203578 AAAATTT
1 AAAATTT
25203585 CTGAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 9 0.36
22 4 0.16
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (20 bp):
AAAATTTTCTAATCATTATT
Found at i:25203585 original size:20 final size:19
Alignment explanation
Indices: 25203538--25203591 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
25203528 AATCGATACC
*
25203538 AAAATTTTTAATATTATTT
1 AAAATTTCTAATATTATTT
25203557 AAAATTTTCTAATGCATTA-TT
1 AAAA-TTTCTAAT--ATTATTT
25203578 AAAATTTCTGAATA
1 AAAATTTCT-AATA
25203592 ATATCAATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 9 0.30
22 4 0.13
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.48
Consensus pattern (19 bp):
AAAATTTCTAATATTATTT
Found at i:25203665 original size:20 final size:20
Alignment explanation
Indices: 25203637--25203699 Score: 65
Period size: 20 Copynumber: 3.2 Consensus size: 20
25203627 AGTATCTAAT
*
25203637 ATTTTTAACATAATATCAAA
1 ATTTCTAACATAATATCAAA
* * *
25203657 ATTTCTAACA-AATACCGAT
1 ATTTCTAACATAATATCAAA
* *
25203676 ATTTCTTACATGATATCAAA
1 ATTTCTAACATAATATCAAA
25203696 ATTT
1 ATTT
25203700 TTAATTAATA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (20 bp):
ATTTCTAACATAATATCAAA
Found at i:25205376 original size:17 final size:17
Alignment explanation
Indices: 25205354--25205424 Score: 60
Period size: 17 Copynumber: 4.4 Consensus size: 17
25205344 CAAGATAAAC
*
25205354 ATTAAATTAAATTTAAT
1 ATTAAATTAAATATAAT
*
25205371 ATTAAATT-AATAAAAT
1 ATTAAATTAAATATAAT
*
25205387 ACT--ATTAAA-ATAATT
1 ATTAAATTAAATATAA-T
* *
25205402 ATTAAATTAAATTTATT
1 ATTAAATTAAATATAAT
25205419 ATTAAA
1 ATTAAA
25205425 CTATTAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
14 6 0.14
15 5 0.12
16 8 0.19
17 21 0.50
18 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTAAATTAAATATAAT
Found at i:25205380 original size:11 final size:11
Alignment explanation
Indices: 25205354--25205411 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 11
25205344 CAAGATAAAC
25205354 ATTAA-ATTAA
1 ATTAATATTAA
25205364 ATTTAATATTAA
1 A-TTAATATTAA
25205376 ATTAATA--AA
1 ATTAATATTAA
*
25205385 A-TACTATTAA
1 ATTAATATTAA
*
25205395 AATAATTATTAA
1 ATTAA-TATTAA
25205407 ATTAA
1 ATTAA
25205412 ATTTATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 3 0.08
10 4 0.10
11 12 0.31
12 16 0.41
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:25214089 original size:102 final size:102
Alignment explanation
Indices: 25213948--25214172 Score: 342
Period size: 102 Copynumber: 2.2 Consensus size: 102
25213938 CGAGTCCTCG
* * *
25213948 ACAGCTCGTTTGAGCAGCATCGTGACTCGAAAAAGAGATATGGATCCTATATGGATTATAGGTCC
1 ACAGCTCGTGTGAGCAGCATCGTGACTCGAAAAAGAGATATGGATCCTATATGGATTACAAGTCC
* *
25214013 TACGATGGCTGGGACTTATGCTTTACACATACTCCCG
66 TACGATGGCTGGGACTCATGCTTTACACATACTCCCA
* * *
25214050 TCAGCTCGTGTGAGCAGTATTGTGACTCGAAAAAGAGATATGGATCCTATATGGATTACAAGTCC
1 ACAGCTCGTGTGAGCAGCATCGTGACTCGAAAAAGAGATATGGATCCTATATGGATTACAAGTCC
* **
25214115 TACGATGGCTGGGAGTCATGCTTTACGTATACTCCCA
66 TACGATGGCTGGGACTCATGCTTTACACATACTCCCA
*
25214152 ACAGCTCGTGTGAGCAACATC
1 ACAGCTCGTGTGAGCAGCATC
25214173 ATTAGGAAAC
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
102 108 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (102 bp):
ACAGCTCGTGTGAGCAGCATCGTGACTCGAAAAAGAGATATGGATCCTATATGGATTACAAGTCC
TACGATGGCTGGGACTCATGCTTTACACATACTCCCA
Found at i:25226436 original size:20 final size:20
Alignment explanation
Indices: 25226413--25226453 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
25226403 AGAAGGTCCA
*
25226413 AAAATAAATAA-ATAAATTAT
1 AAAAT-AATAACATAAAATAT
25226433 AAAATAATAACATAAAATAT
1 AAAATAATAACATAAAATAT
25226453 A
1 A
25226454 TAGTATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATAATAACATAAAATAT
Found at i:25226569 original size:29 final size:30
Alignment explanation
Indices: 25226513--25226570 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
25226503 AAAGTGATAG
* *
25226513 GGTTAAAGTGTGAATATTCAAAAGTTGAAA
1 GGTTAAAGTATAAATATTCAAAAGTTGAAA
*
25226543 GGTTAAAGTATAAAT-TTGAAAAGTTGAA
1 GGTTAAAGTATAAATATTCAAAAGTTGAA
25226571 GGACTAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.45, C:0.02, G:0.22, T:0.31
Consensus pattern (30 bp):
GGTTAAAGTATAAATATTCAAAAGTTGAAA
Found at i:25235095 original size:23 final size:23
Alignment explanation
Indices: 25235043--25235122 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
25235033 CCTACAACTT
*
25235043 CTACCGATACAAGCAT-C-CTAA
1 CTACCGATACAAGCATACACAAA
* *
25235064 CTACTGATACAAGTATACACAAA
1 CTACCGATACAAGCATACACAAA
25235087 CTACCGATACAAGCATACACAAAA
1 CTACCGATACAAGCATACAC-AAA
25235111 CTACCGATACAA
1 CTACCGATACAA
25235123 CCCAAGTCAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
21 14 0.27
22 1 0.02
23 21 0.41
24 15 0.29
ACGTcount: A:0.45, C:0.29, G:0.09, T:0.17
Consensus pattern (23 bp):
CTACCGATACAAGCATACACAAA
Done.