Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008554.1 Hibiscus syriacus cultivar Beakdansim tig00111458_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3217407
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:687 original size:4 final size:4
Alignment explanation
Indices: 678--703 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
668 CTAACCTTTG
678 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
704 GTTCTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:1003 original size:16 final size:16
Alignment explanation
Indices: 978--1013 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
968 ATTTCTGCTA
*
978 TTTAACTTTATGCACT
1 TTTAAATTTATGCACT
*
994 TTTAAATTTATGCATT
1 TTTAAATTTATGCACT
1010 TTTA
1 TTTA
1014 TTTTCTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTAAATTTATGCACT
Found at i:1462 original size:18 final size:20
Alignment explanation
Indices: 1431--1469 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1421 ACAAATCGAA
1431 TTTATTTTACTAATT-AAATT
1 TTTATTTTA-TAATTCAAATT
1451 TTTATTTT-TAATTCAAATT
1 TTTATTTTATAATTCAAATT
1470 ATGCAATGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.28
19 5 0.28
20 8 0.44
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTATTTTATAATTCAAATT
Found at i:10211 original size:18 final size:18
Alignment explanation
Indices: 10184--10226 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
10174 AGTTTTTTTA
*
10184 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
10202 AAATAGAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
10220 AAATAAA
1 AAATAAA
10227 CAAATTAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:11061 original size:76 final size:76
Alignment explanation
Indices: 10850--11037 Score: 342
Period size: 76 Copynumber: 2.5 Consensus size: 76
10840 TCTTAAATCA
*
10850 TAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
*
10914 TATCCTAGAACT
65 TATCCTAAAACT
10926 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
10991 ATCCTAAAACT
66 ATCCTAAAACT
11002 TAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATAC
11038 AAAGATAAAA
Statistics
Matches: 109, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
75 5 0.05
76 104 0.95
ACGTcount: A:0.58, C:0.13, G:0.02, T:0.27
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCCTAAAACT
Found at i:12854 original size:11 final size:11
Alignment explanation
Indices: 12827--12869 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
12817 TAAAGTTCGC
12827 TGAAAATAAAA
1 TGAAAATAAAA
12838 TG-AAATAAAA
1 TGAAAATAAAA
*
12848 CGAAAATAAAA
1 TGAAAATAAAA
12859 TGAAAATAAAA
1 TGAAAATAAAA
12870 ACAAAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.31
11 20 0.69
ACGTcount: A:0.72, C:0.02, G:0.09, T:0.16
Consensus pattern (11 bp):
TGAAAATAAAA
Found at i:12876 original size:23 final size:22
Alignment explanation
Indices: 12829--12886 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 22
12819 AAGTTCGCTG
*
12829 AAAATAAAATG-AAATAAAACG
1 AAAATAAAATGAAAATAAAACA
12850 AAAATAAAATGAAAATAAAAACA
1 AAAATAAAATGAAAAT-AAAACA
*
12873 AAAATATAATGAAA
1 AAAATAAAATGAAA
12887 TGGGTTGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
21 11 0.33
22 4 0.12
23 18 0.55
ACGTcount: A:0.74, C:0.03, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAATAAAATGAAAATAAAACA
Found at i:18363 original size:15 final size:15
Alignment explanation
Indices: 18343--18371 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
18333 AAAAGATAAG
18343 AATTAAATAAACAAT
1 AATTAAATAAACAAT
18358 AATTAAATAAACAA
1 AATTAAATAAACAA
18372 ATTAAAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTAAATAAACAAT
Found at i:20000 original size:26 final size:27
Alignment explanation
Indices: 19940--20000 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 27
19930 CTTGTATGTT
19940 TATATT-TA-TTATATAACATATAACC
1 TATATTATATTTATATAACATATAACC
* * * *
19965 TATGTCATATTTATA-AACATATATCG
1 TATATTATATTTATATAACATATAACC
19991 TATATTATAT
1 TATATTATAT
20001 GTACATATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
25 4 0.14
26 19 0.68
27 5 0.18
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (27 bp):
TATATTATATTTATATAACATATAACC
Found at i:20376 original size:22 final size:22
Alignment explanation
Indices: 20328--20370 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20318 ACTATACGGT
*
20328 ATGAATAGTACCGTGAACAGTG
1 ATGAACAGTACCGTGAACAGTG
*
20350 ATGAACAGTATCGTGAACAGT
1 ATGAACAGTACCGTGAACAGT
20371 ATTGAATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
ATGAACAGTACCGTGAACAGTG
Found at i:22447 original size:76 final size:75
Alignment explanation
Indices: 22349--22536 Score: 322
Period size: 76 Copynumber: 2.5 Consensus size: 75
22339 TCTTAAATCC
* * *
22349 TAATTAAAACACTTAAAACTATTTAAACTAAAATACTTAAAATAAAGATAAAATATAAAAATAAT
1 TAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
22414 ATCCTAAAACT
65 ATCCTAAAACT
22425 TAATTAAAATACTAAAATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
22490 ATCCTAAAACT
65 ATCCTAAAACT
22501 TAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATAC
22537 AAAGATAAAA
Statistics
Matches: 107, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
75 5 0.05
76 102 0.95
ACGTcount: A:0.59, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
TAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATA
TCCTAAAACT
Found at i:22560 original size:76 final size:74
Alignment explanation
Indices: 22349--22572 Score: 317
Period size: 76 Copynumber: 3.0 Consensus size: 74
22339 TCTTAAATCC
*
22349 TAATTAAAACACTTAAAACTATTTAAACTAAAATACTTAAAATAAAGATAAAATATAAAAATAAT
1 TAATTAAAATAC-TAAAACTATTTAAACTAAAATAC-TAAAATAAAGATAAAATATAAAAATAAT
22414 ATCCTAAAACT
64 ATCCTAAAACT
*
22425 TAATTAAAATACTAAAATCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATA-CTAAAATAAAGATAAAATATAAAAATAAT
22490 ATCCTAAAACT
64 ATCCTAAAACT
* * * *
22501 TAATTAAAATACTAAAACCTATTTAAACTAAAATAC-AAAGATAAA-ATATAATGTTTAAAATAT
1 TAATTAAAATACTAAAA-CTATTTAAACTAAAATACTAAA-ATAAAGATAAAAT-ATAAAAATAA
22564 TATCCTAAA
63 TATCCTAAA
22573 TTTGAGTTTA
Statistics
Matches: 136, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
74 9 0.07
75 26 0.19
76 100 0.74
77 1 0.01
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (74 bp):
TAATTAAAATACTAAAACTATTTAAACTAAAATACTAAAATAAAGATAAAATATAAAAATAATAT
CCTAAAACT
Found at i:41749 original size:30 final size:30
Alignment explanation
Indices: 41695--41753 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41685 AACATTATCA
*
41695 ATTTCATAATCCAACAAACTTAAAACATAAC
1 ATTTCATAATCCAACAAACCTAAAA-ATAAC
41726 ATTT-ATAATACCAAC-AACCTAAAAATAA
1 ATTTCATAAT-CCAACAAACCTAAAAATAA
41754 AAATGTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 13 0.50
31 9 0.35
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.25
Consensus pattern (30 bp):
ATTTCATAATCCAACAAACCTAAAAATAAC
Found at i:45245 original size:29 final size:27
Alignment explanation
Indices: 45166--45259 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 27
45156 AATGTAGTGA
45166 TTGTAAAAATATAGGTTGTTATTGTAAT
1 TTGTAAAAATATA-GTTGTTATTGTAAT
*
45194 ATGTAAAAATATGAGTTGTTATTGTAAT
1 TTGTAAAAATAT-AGTTGTTATTGTAAT
**
45222 TTGTAAAAAGTATATGTCATTATTGTAAT
1 TTGTAAAAA-TATA-GTTGTTATTGTAAT
*
45251 TTATAAAAA
1 TTGTAAAAA
45260 GATTTGTTCT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
28 34 0.59
29 24 0.41
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (27 bp):
TTGTAAAAATATAGTTGTTATTGTAAT
Found at i:45258 original size:57 final size:58
Alignment explanation
Indices: 45165--45318 Score: 143
Period size: 58 Copynumber: 2.7 Consensus size: 58
45155 AAATGTAGTG
* ** * * *
45165 ATTGTAAAAA-TATAGGTTGTTATTGTAATATGTAAAAATATGAGTTGT-TATTGTAA
1 ATTGTAAAAAGTATATGTCATTATTGTAATTTATAAAAATATGAGTTCTCTATTGTAA
* * ** *
45221 TTTGTAAAAAGTATATGTCATTATTGTAATTTATAAAAAGATTTGTTCTCTATTTTAA
1 ATTGTAAAAAGTATATGTCATTATTGTAATTTATAAAAATATGAGTTCTCTATTGTAA
* * * *
45279 ATTATAAAAAG-ATTTGTCCTTTATTGTAGTTTATAAAAAT
1 ATTGTAAAAAGTATATGT-CATTATTGTAATTTATAAAAAT
45319 CTTTGTCCTT
Statistics
Matches: 78, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
56 9 0.12
57 34 0.44
58 35 0.45
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.45
Consensus pattern (58 bp):
ATTGTAAAAAGTATATGTCATTATTGTAATTTATAAAAATATGAGTTCTCTATTGTAA
Found at i:45260 original size:29 final size:27
Alignment explanation
Indices: 45212--45346 Score: 126
Period size: 29 Copynumber: 4.7 Consensus size: 27
45202 ATATGAGTTG
* *
45212 TTATTGTAATTTGTAAAAAGTATATGTC
1 TTATTGTAATTTATAAAAAG-ATTTGTC
45240 ATTATTGTAATTTATAAAAAGATTTGTTC
1 -TTATTGTAATTTATAAAAAGATTTG-TC
* *
45269 TCTATTTTAAATTATAAAAAGATTTGTCC
1 T-TATTGTAATTTATAAAAAGATTTGT-C
* **
45298 TTTATTGTAGTTTATAAAAATCTTTGTCC
1 -TTATTGTAATTTATAAAAAGATTTGT-C
*
45327 TTAAATGTAATTTATAAAAA
1 TT-ATTGTAATTTATAAAAA
45347 AATTAATTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
28 8 0.09
29 81 0.90
30 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.47
Consensus pattern (27 bp):
TTATTGTAATTTATAAAAAGATTTGTC
Found at i:45342 original size:58 final size:58
Alignment explanation
Indices: 45216--45346 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
45206 GAGTTGTTAT
* * *
45216 TGTAATTTGTAAAAAGTATATGTCATTATTGTAATTTATAAAAAGATTTGTTCTCTAT
1 TGTAATTTATAAAAAGTATATGTCATTATTGTAATTTATAAAAAGATTTGTCCTCTAA
* * * * * **
45274 TTTAAATTATAAAAAG-ATTTGTCCTTTATTGTAGTTTATAAAAATCTTTGTCCT-TAAA
1 TGTAATTTATAAAAAGTATATGT-CATTATTGTAATTTATAAAAAGATTTGTCCTCT-AA
45332 TGTAATTTATAAAAA
1 TGTAATTTATAAAAA
45347 AATTAATTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
57 6 0.10
58 53 0.90
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (58 bp):
TGTAATTTATAAAAAGTATATGTCATTATTGTAATTTATAAAAAGATTTGTCCTCTAA
Found at i:46851 original size:40 final size:40
Alignment explanation
Indices: 46807--46899 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 40
46797 GGGTAAAACC
* *
46807 CGACCTCGGCATTACGGTGCATTATTAGGTGAGCAATGCT
1 CGACCTCGGCACTACGGTGCATTATTAGGTGACCAATGCT
46847 CGACCTCGGCACTACGGTGCATTATTAGGTGACCAATGCT
1 CGACCTCGGCACTACGGTGCATTATTAGGTGACCAATGCT
*
46887 CGACCTCAGCACT
1 CGACCTCGGCACT
46900 TTGATGCAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CGACCTCGGCACTACGGTGCATTATTAGGTGACCAATGCT
Found at i:47039 original size:46 final size:46
Alignment explanation
Indices: 46987--47172 Score: 270
Period size: 46 Copynumber: 4.1 Consensus size: 46
46977 GTAAGCATGC
*
46987 AAATAAGCTTACGAGCTTATGGGACTAAATGATAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGGACTAAATGGTAAGTATATTGGTA
* * * *
47033 AAATAAGCTTATGAGCTTATGGTATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGACTAAATGGTAAGTATATTGGTA
* *
47079 AAATAAGCTTACGAGCTTATGGAAC-AAATGGTAAGTATATTGTTA
1 AAATAAGCTTACGAGCTTATGGGACTAAATGGTAAGTATATTGGTA
* *
47124 GAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATA-TGGTA
1 AAATAAGCTTACGAGCTTATGGGACTAAATGGTAAGTATATTGGTA
47168 AAATA
1 AAATA
47173 TTGGATATGC
Statistics
Matches: 124, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
44 10 0.08
45 51 0.41
46 63 0.51
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGGACTAAATGGTAAGTATATTGGTA
Found at i:47130 original size:91 final size:90
Alignment explanation
Indices: 46987--47172 Score: 284
Period size: 91 Copynumber: 2.1 Consensus size: 90
46977 GTAAGCATGC
* *
46987 AAATAAGCTTACGAGCTTATGGGACTAAATGATAAGTATATTGGTAAAATAAGCTTATGAGCTTA
1 AAATAAGCTTACGAGCTTATGGAACTAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
47052 TGGTATTAAATGGTAAGTATTTTGGTA
66 TGG-AATAAATGGTAAGTA-TATGGTA
* * *
47079 AAATAAGCTTACGAGCTTATGGAAC-AAATGGTAAGTATATTGTTAGAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGAACTAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTA
47143 TGGAATAAATGGTAAGTATATGGTA
66 TGGAATAAATGGTAAGTATATGGTA
47168 AAATA
1 AAATA
47173 TTGGATATGC
Statistics
Matches: 87, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
89 11 0.13
90 14 0.16
91 38 0.44
92 24 0.28
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.32
Consensus pattern (90 bp):
AAATAAGCTTACGAGCTTATGGAACTAAATGATAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGGAATAAATGGTAAGTATATGGTA
Found at i:49931 original size:10 final size:10
Alignment explanation
Indices: 49916--49976 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
49906 AATATTTTAT
49916 AAGAAAAAAA
1 AAGAAAAAAA
49926 AAGAAACAGAAA
1 AAGAAA-A-AAA
49938 AA-AAAAGAAA
1 AAGAAAA-AAA
*
49948 AAGAAAGAAA
1 AAGAAAAAAA
*
49958 AAG-AAAAGA
1 AAGAAAAAAA
49967 AAGAAAAAAA
1 AAGAAAAAAA
49977 TGAGACTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 7 0.16
10 24 0.56
11 7 0.16
12 5 0.12
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:49936 original size:16 final size:15
Alignment explanation
Indices: 49916--49975 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 15
49906 AATATTTTAT
49916 AAGAAAAAAAAAGAA
1 AAGAAAAAAAAAGAA
49931 ACAGAAAAAAAAAGAAA
1 A-AGAAAAAAAAAG-AA
*
49948 AAGAAAGAAAAAGAA
1 AAGAAAAAAAAAGAA
49963 AAGAAAGAAAAAA
1 AAGAAA-AAAAAA
49976 ATGAGACTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
15 9 0.22
16 28 0.70
17 3 0.08
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:49954 original size:26 final size:25
Alignment explanation
Indices: 49916--49976 Score: 86
Period size: 26 Copynumber: 2.4 Consensus size: 25
49906 AATATTTTAT
*
49916 AAGAAAAAAAAAGAAACAGAAAAAAA
1 AAGAAAAAAAAAGAAAAAG-AAAAAA
* *
49942 AAGAAAAAGAAAGAAAAAGAAAAGA
1 AAGAAAAAAAAAGAAAAAGAAAAAA
49967 AAGAAAAAAA
1 AAGAAAAAAA
49977 TGAGACTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 14 0.45
26 17 0.55
ACGTcount: A:0.84, C:0.02, G:0.15, T:0.00
Consensus pattern (25 bp):
AAGAAAAAAAAAGAAAAAGAAAAAA
Found at i:54161 original size:45 final size:45
Alignment explanation
Indices: 54019--54204 Score: 268
Period size: 46 Copynumber: 4.1 Consensus size: 45
54009 GTAAGCATGC
* *
54019 AAATAAGCGTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
* *
54065 AAATAAGCTTACGAGCTTATGGTATTAAATGG-ATAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGG-AATAAATGGTA-AGTATATTGGTA
* *
54111 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATATTGTTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
54156 GAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATA-TGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
54200 AAATA
1 AAATA
54205 TTGGATATGC
Statistics
Matches: 127, Mismatches: 10, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
44 8 0.06
45 57 0.45
46 62 0.49
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:54161 original size:91 final size:90
Alignment explanation
Indices: 54019--54204 Score: 268
Period size: 91 Copynumber: 2.1 Consensus size: 90
54009 GTAAGCATGC
**
54019 AAATAAGCGTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCGTACGAGCTTATGGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
54084 TGGTATTAAATGG-ATAGTATTTTGGTA
66 TGG-AATAAATGGTA-AGTA-TATGGTA
* * *
54111 AAATAAGCTTACGAGCTTAT-GGAACAAATGGTAAGTATATTGTTAGAATAAGCTTACGAGCTTA
1 AAATAAGCGTACGAGCTTATGGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
54175 TGGAATAAATGGTAAGTATATGGTA
66 TGGAATAAATGGTAAGTATATGGTA
54200 AAATA
1 AAATA
54205 TTGGATATGC
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
89 11 0.13
90 12 0.14
91 44 0.51
92 19 0.22
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.32
Consensus pattern (90 bp):
AAATAAGCGTACGAGCTTATGGGAACAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGGAATAAATGGTAAGTATATGGTA
Found at i:55279 original size:14 final size:14
Alignment explanation
Indices: 55260--55296 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
55250 CATTGATGAT
55260 TTGAGTAAGAGGAA
1 TTGAGTAAGAGGAA
55274 TTGAGTAAGAGGAA
1 TTGAGTAAGAGGAA
55288 TTGAGTAAG
1 TTGAGTAAG
55297 CGGTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (14 bp):
TTGAGTAAGAGGAA
Found at i:61969 original size:11 final size:11
Alignment explanation
Indices: 61955--61981 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
61945 ATTAAATTAG
61955 AATTAGAATCA
1 AATTAGAATCA
61966 AATTAGAATCA
1 AATTAGAATCA
61977 AATTA
1 AATTA
61982 ATAGGATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (11 bp):
AATTAGAATCA
Found at i:62668 original size:35 final size:35
Alignment explanation
Indices: 62617--62684 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 35
62607 CTTTGATTTA
*
62617 GGGTTTAGAATGTAATT-AAAGTATTTTGGAATTCG
1 GGGTATAGAATGTAATTGAAA-TATTTTGGAATTCG
*
62652 GGGTATAGAATGTAATTGAAATGTTTTGGAATT
1 GGGTATAGAATGTAATTGAAATATTTTGGAATT
62685 TTGAATATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 27 0.90
36 3 0.10
ACGTcount: A:0.32, C:0.01, G:0.26, T:0.40
Consensus pattern (35 bp):
GGGTATAGAATGTAATTGAAATATTTTGGAATTCG
Found at i:67582 original size:28 final size:28
Alignment explanation
Indices: 67549--67602 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
67539 AAAATAATTA
67549 TTGCTTTGTTGGAACATAATCATAAATG
1 TTGCTTTGTTGGAACATAATCATAAATG
67577 TTGCTTTGTTGGAACATAATCATAAA
1 TTGCTTTGTTGGAACATAATCATAAA
67603 AGGAATACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (28 bp):
TTGCTTTGTTGGAACATAATCATAAATG
Found at i:69710 original size:85 final size:85
Alignment explanation
Indices: 69621--70188 Score: 636
Period size: 85 Copynumber: 6.7 Consensus size: 85
69611 AGCTTAATGG
* * ** * * * *
69621 AATCGAACTCGAAGGTATTTGTTGACAGATAGTCCTTTTAGCCTTAAACTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
69686 TATGCCTTTGAGTTG-GATGT
66 TATGCCTTTGAGTTGAG-TGT
* * * *
69706 AATCGGACTCGAAGGTCTTGGTTGATAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTAA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
69771 TGTGCCTTTGAGTTAAGTGT
66 TATGCCTTTGAGTTGAGTGT
* * * * * *
69791 AATCAAACTCGAAGGTCTTAGTTGACAGATAACCCTTCTAGCCTTGAGTTACGCTGTGAATTTGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* * *
69856 TGTGCCTTTGAGCTGTGTGT
66 TATGCCTTTGAGTTGAGTGT
* * * * * *
69876 AATCGAACTAGAAGGCCTTGGTTGACAGATAACCCTTCTCGTCTTGAGCTATGTTATCAATTTGA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
*
69941 TGTGCCTTTGAGTTGAGTGT
66 TATGCCTTTGAGTTGAGTGT
* * * * * * *
69961 AATCGAACTTGAAGGTCTTTTGTTGACATATAGCCCTTATCGCCTTGAGCTATGTTGTAAATTCG
1 AATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
*
70026 ATATGCCTTTGAGCTGAGTGT
65 ATATGCCTTTGAGTTGAGTGT
* * * * *
70047 AATCGAACTCGAAGGTCTTGGTTGACATATAACCTTTCCCGCCTTGAGTTATGCTGTAAATTTAA
1 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
*
70112 TATTCCTTTGAGTTGAGTGT
66 TATGCCTTTGAGTTGAGTGT
* * * * * *
70132 AATCAAACTCGAAGGACTTTTGG-TGACAGATAGCCCTTCTCACTTTGAGTTATGCTG
1 AATCGAACTCGAAGG--TCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTG
70189 CCAATAGTTC
Statistics
Matches: 409, Mismatches: 70, Indels: 7
0.84 0.14 0.01
Matches are distributed among these distances:
85 301 0.74
86 103 0.25
87 5 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (85 bp):
AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
TATGCCTTTGAGTTGAGTGT
Found at i:69864 original size:170 final size:171
Alignment explanation
Indices: 69621--70188 Score: 714
Period size: 171 Copynumber: 3.3 Consensus size: 171
69611 AGCTTAATGG
* * * * * *
69621 AATCGAACTCGAAGGT-ATTTGTTGACAGATAGTCCTTTTAGCCTTAAACTATGCTGTAAATTTG
1 AATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATTTG
* * *
69685 ATATGCCTTTGAGTTGGATGTAATCGGACTCGAAGGTCTTGGTTGATAGATAACCCTTCTCGCCT
66 ATATGCCTTTGAGCTGGATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCT
*
69750 TGAGTTATGCTGTAAATTTAATGTGCCTTTGAGTTAAGTGT
131 TGAGTTATGCTGTAAATTTAATGTGCCTTTGAGTTGAGTGT
* * * * *
69791 AATCAAACTCGAAGGTC-TTAGTTGACAGATAACCCTTCTAGCCTTGAGTTACGCTGTGAATTTG
1 AATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATTTG
* * * *
69855 ATGTGCCTTTGAGCTGTG-TGTAATCGAACTAGAAGGCCTTGGTTGACAGATAACCCTTCTCGTC
66 ATATGCCTTTGAGCTG-GATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCC
* * * * *
69919 TTGAGCTATGTTATCAATTTGATGTGCCTTTGAGTTGAGTGT
130 TTGAGTTATGCTGTAAATTTAATGTGCCTTTGAGTTGAGTGT
* * * * * * *
69961 AATCGAACTTGAAGGTCTTTTGTTGACATATAGCCCTTATCGCCTTGAGCTATGTTGTAAATTCG
1 AATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATTTG
* * *
70026 ATATGCCTTTGAGCT-GAGTGTAATCGAACTCGAAGGTCTTGGTTGACATATAACCTTTCCCGCC
66 ATATGCCTTTGAGCTGGA-TGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCC
* *
70090 TTGAGTTATGCTGTAAATTTAATATTCCTTTGAGTTGAGTGT
130 TTGAGTTATGCTGTAAATTTAATGTGCCTTTGAGTTGAGTGT
* * * *
70132 AATCAAACTCGAAGGACTTTTGGTGACAGATAGCCCTTCTCA-CTTTGAGTTATGCTG
1 AATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCT-AGCCTTGAGCTATGCTG
70189 CCAATAGTTC
Statistics
Matches: 333, Mismatches: 59, Indels: 11
0.83 0.15 0.03
Matches are distributed among these distances:
169 1 0.00
170 159 0.48
171 173 0.52
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (171 bp):
AATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTCTAGCCTTGAGCTATGCTGTAAATTTG
ATATGCCTTTGAGCTGGATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCGCCT
TGAGTTATGCTGTAAATTTAATGTGCCTTTGAGTTGAGTGT
Found at i:70095 original size:256 final size:256
Alignment explanation
Indices: 69679--70172 Score: 652
Period size: 256 Copynumber: 1.9 Consensus size: 256
69669 CTATGCTGTA
* * *
69679 AATTTGATATGCCTTTGAGTTGGATGTAATCGGACTCGAAGGTCTTGGTTGATAGATAACCCTTC
1 AATTTGATATGCCTTTGAGTTGGATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTA
* * * *
69744 TCGCCTTGAGTTATGCTGTAAATTTAATGTGCCTTTGAGTTAAGTGTAATCAAACTCGAAGGTCT
66 TCGCCTTGAGCTATGCTGTAAATTCAATATGCCTTTGAGCTAAGTGTAATCAAACTCGAAGGTCT
* * * * *
69809 TAGTTGACAGATAACCCTTCTAGCCTTGAGTTACGCTGTGAATTTGATGTGCCTTTGAGCTGTGT
131 TAGTTGACAGATAACCCTTCCAGCCTTGAGTTACGCTGTAAATTTAATATGCCTTTGAGCTGAGT
*
69874 GTAATCGAACTAGAAGG-C-CTTGGTTGACAGATAACCCTTCTCGTCTTGAGCTATGTTATC
196 GTAATCAAACTAGAAGGACTCTTGG-TGACAGATAACCCTTCTCGTCTTGAGCTATGTTATC
* * * * *
69934 AATTTGATGTGCCTTTGAGTT-GAGTGTAATCGAACTTGAAGGTCTTTTGTTGACATATAGCCCT
1 AATTTGATATGCCTTTGAGTTGGA-TGTAATCGAACTCGAAGGTC-TTGGTTGACAGATAACCCT
* * * *
69998 TATCGCCTTGAGCTATGTTGTAAATTCGATATGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
64 TATCGCCTTGAGCTATGCTGTAAATTCAATATGCCTTTGAGCTAAGTGTAATCAAACTCGAAGGT
* * * * * * *
70063 CTTGGTTGACATATAACCTTTCCCGCCTTGAGTTATGCTGTAAATTTAATATTCCTTTGAGTTGA
129 CTTAGTTGACAGATAACCCTTCCAGCCTTGAGTTACGCTGTAAATTTAATATGCCTTTGAGCTGA
* * *
70128 GTGTAATCAAACTCGAAGGACTTTTGGTGACAGATAGCCCTTCTC
194 GTGTAATCAAACTAGAAGGACTCTTGGTGACAGATAACCCTTCTC
70173 ACTTTGAGTT
Statistics
Matches: 203, Mismatches: 32, Indels: 6
0.84 0.13 0.02
Matches are distributed among these distances:
254 2 0.01
255 38 0.19
256 141 0.69
257 18 0.09
258 4 0.02
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (256 bp):
AATTTGATATGCCTTTGAGTTGGATGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTA
TCGCCTTGAGCTATGCTGTAAATTCAATATGCCTTTGAGCTAAGTGTAATCAAACTCGAAGGTCT
TAGTTGACAGATAACCCTTCCAGCCTTGAGTTACGCTGTAAATTTAATATGCCTTTGAGCTGAGT
GTAATCAAACTAGAAGGACTCTTGGTGACAGATAACCCTTCTCGTCTTGAGCTATGTTATC
Found at i:75633 original size:28 final size:28
Alignment explanation
Indices: 75597--75657 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
75587 GAAAGAAAAA
*
75597 ATAATTGTTGCTTTGTTGGAACATAATC
1 ATAAATGTTGCTTTGTTGGAACATAATC
75625 ATAAATGTTGCTTTGTTGGAACATAATC
1 ATAAATGTTGCTTTGTTGGAACATAATC
75653 ATAAA
1 ATAAA
75658 AGGAATACAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.39
Consensus pattern (28 bp):
ATAAATGTTGCTTTGTTGGAACATAATC
Found at i:77145 original size:137 final size:137
Alignment explanation
Indices: 76899--77258 Score: 463
Period size: 137 Copynumber: 2.6 Consensus size: 137
76889 AGTGTTCACA
** * *
76899 TGTGTCATTTACCGACCAGATCTCTTTATCACGTAGGAGCCACATCACCCTTAGATAGTCAGACT
1 TGTGTCATCCACCGACCAGATCTCCTTATCACGTAGGAGCCACATCACCCTTAGATAATCAGACT
* *
76964 TCCTCATCACGTAGGAACCGTGTTATCTCCATTATCCCTAAAGATGGCCAGTCATCCTTATCACG
66 TCCTCATCACGTAGGAACCATGTTATCTCCATTATCCCTAAAGATGGCCAGTCATCCTCATCACG
77029 TAGGAAC
131 TAGGAAC
* * *** * *
77036 TGTGTCATCCACCGACCAGATCTCCTCATCACGTAGGTGTTGCATCACCTTTTGA-AATCCAGAC
1 TGTGTCATCCACCGACCAGATCTCCTTATCACGTAGGAGCCACATCACCCTTAGATAAT-CAGAC
* * *
77100 TTTCTTATCACGTAGGAACCATGTTATCTCCATTATCCCTAAAGATGGCCAGTCGTCCTCATCAC
65 TTCCTCATCACGTAGGAACCATGTTATCTCCATTATCCCTAAAGATGGCCAGTCATCCTCATCAC
77165 GTAGGAAC
130 GTAGGAAC
** * * ** * *
77173 AATGTCATCCACTGACCAGATCTCCTTATCATGTAGGAG-CAGTGTCATCCTTAGACAATCAGAC
1 TGTGTCATCCACCGACCAGATCTCCTTATCACGTAGGAGCCA-CATCACCCTTAGATAATCAGAC
*
77237 TTCCTCATCAAGTAGGAACCAT
65 TTCCTCATCACGTAGGAACCAT
77259 ATTGTCACCA
Statistics
Matches: 188, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
136 2 0.01
137 183 0.97
138 3 0.02
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (137 bp):
TGTGTCATCCACCGACCAGATCTCCTTATCACGTAGGAGCCACATCACCCTTAGATAATCAGACT
TCCTCATCACGTAGGAACCATGTTATCTCCATTATCCCTAAAGATGGCCAGTCATCCTCATCACG
TAGGAAC
Found at i:78199 original size:29 final size:29
Alignment explanation
Indices: 78161--78236 Score: 127
Period size: 29 Copynumber: 2.6 Consensus size: 29
78151 TGCTATATTA
*
78161 TTTATTGCATATTAACCACTAACTTTTAT
1 TTTATTGCATATTAACCACTAACTTTTAC
78190 TTTATTGCATATTAACCACTAACTTTTAC
1 TTTATTGCATATTAACCACTAACTTTTAC
78219 TTTATTGCACTA-TAACCA
1 TTTATTGCA-TATTAACCA
78237 TTGTTTATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
29 43 0.96
30 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.45
Consensus pattern (29 bp):
TTTATTGCATATTAACCACTAACTTTTAC
Found at i:78447 original size:131 final size:131
Alignment explanation
Indices: 78213--78467 Score: 447
Period size: 131 Copynumber: 1.9 Consensus size: 131
78203 AACCACTAAC
*
78213 TTTTACTTTATTGCACTATAACCATTGTTTATTTATTTATTTATTGTTTCTATTATTCAATTTGA
1 TTTTACTTTATTGCACTATAACCATTGTTTATTTATTTATTTATTGTTTCTATTATTCAATTCGA
78278 CCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCTGCTAACTACTGG
66 CCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCTGCTAACTACTGG
78343 T
131 T
* * * *
78344 TTTTATTTTATTGCACTCTAACCATTGTTTATTTGTTTATTTATTGTTTCTATTATTCGATTCGA
1 TTTTACTTTATTGCACTATAACCATTGTTTATTTATTTATTTATTGTTTCTATTATTCAATTCGA
* *
78409 CTTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTGCTAAC
66 CCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCTGCTAAC
78468 CACTAACTTT
Statistics
Matches: 117, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
131 117 1.00
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (131 bp):
TTTTACTTTATTGCACTATAACCATTGTTTATTTATTTATTTATTGTTTCTATTATTCAATTCGA
CCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCAGACTCTGCTAACTACTGG
T
Found at i:78595 original size:16 final size:16
Alignment explanation
Indices: 78574--78622 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
78564 TATGGTTAGG
78574 ACTCTGCTAACCGCTA
1 ACTCTGCTAACCGCTA
78590 ACTCTGCTAACCGCTA
1 ACTCTGCTAACCGCTA
*
78606 AC-CTTTCTAACCGCTA
1 ACTC-TGCTAACCGCTA
78622 A
1 A
78623 TTACTAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 1 0.03
16 30 0.97
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (16 bp):
ACTCTGCTAACCGCTA
Found at i:78704 original size:16 final size:15
Alignment explanation
Indices: 78659--78702 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
78649 ATTTCATTTT
*
78659 ATTTATGCTATTTAA
1 ATTTATGCTTTTTAA
* *
78674 CTTTATGCACTTTTAA
1 ATTTATGC-TTTTTAA
78690 ATTTATGCTTTTT
1 ATTTATGCTTTTT
78703 TATTTTCTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.25, C:0.11, G:0.07, T:0.57
Consensus pattern (15 bp):
ATTTATGCTTTTTAA
Found at i:97294 original size:17 final size:17
Alignment explanation
Indices: 97268--97308 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
97258 ACGATCGACT
*
97268 GTTGACCGTTGACCTGC
1 GTTGACCGTTGACCGGC
*
97285 GTTGATCGTTGACCGGC
1 GTTGACCGTTGACCGGC
97302 GTTGACC
1 GTTGACC
97309 ACTGTTGACC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.12, C:0.27, G:0.32, T:0.29
Consensus pattern (17 bp):
GTTGACCGTTGACCGGC
Found at i:100071 original size:80 final size:80
Alignment explanation
Indices: 99933--100211 Score: 373
Period size: 80 Copynumber: 3.5 Consensus size: 80
99923 TGTAAGTCCT
* * * *
99933 TACGGACCTAATGATAT-CTTGGGTAGGGCCCAAGGCATATCCTTAGGTTGGTTTCCTTTGCTTT
1 TACGGATCTAAGGATATCCTTGGGTA-GGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTCT
*
99997 GTGCATAAGGTAACCC
65 GTGCTTAAGGTAACCC
* *
100013 TACGGATATAAGGATACCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGC-CGT
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTC-T
*
100077 GTGCTTAAGGTAGCCC
65 GTGCTTAAGGTAACCC
* * * * *
100093 TACGGATCTAAGGATGTCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCCTTTTTACTC
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGG-TTCC-CTTTGCTC
100158 TGTGCTTAAGGTAACCC
64 TGTGCTTAAGGTAACCC
*
100175 TACGGATCTAAGGATATCCTTAGGTAGGCCCATAGGC
1 TACGGATCTAAGGATATCCTTGGGTAGGCCCA-AGGC
100212 CCCAAGGTAT
Statistics
Matches: 173, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
80 108 0.62
81 12 0.07
82 49 0.28
83 4 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (80 bp):
TACGGATCTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTCTG
TGCTTAAGGTAACCC
Found at i:104694 original size:82 final size:80
Alignment explanation
Indices: 104439--104710 Score: 388
Period size: 80 Copynumber: 3.4 Consensus size: 80
104429 CTTTATGGAC
* *
104439 CTAAGGATAT-CTTGGGTAGGGCCCAAGGCATATCCTTAGGTTAGTTTCCTTTG-TTGTGTGCGT
1 CTAAGGATATCCTTGGGTA-GGCCCAAGGCATATCCTTAGGTTGGTTTCCTTTGCTT-TGTGCTT
104502 AAGGTAACCCTACAGAT
64 AAGGTAACCCTACAGAT
* *
104519 CTAAGGATA-CTCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCTTA
1 CTAAGGATATC-CTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTTCCTTTGCTTTGTGCTTA
104583 AGGTAACCCTACAGAT
65 AGGTAACCCTACAGAT
* * *
104599 CTAAGGATGTCCTTGGGTAGACCCAAGGTATATCCTTAGGTTGGTTTCCTTTTTGCTTTGTGCTT
1 CTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTTCC--TTTGCTTTGTGCTT
* *
104664 AAGATAACCCTACGGAT
64 AAGGTAACCCTACAGAT
104681 CTAAGGATATCCTTGGGTAGGCCCATAGGC
1 CTAAGGATATCCTTGGGTAGGCCCA-AGGC
104711 CCCAAGGTAT
Statistics
Matches: 171, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
80 107 0.63
81 10 0.06
82 51 0.30
83 3 0.02
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (80 bp):
CTAAGGATATCCTTGGGTAGGCCCAAGGCATATCCTTAGGTTGGTTTCCTTTGCTTTGTGCTTAA
GGTAACCCTACAGAT
Found at i:106505 original size:20 final size:19
Alignment explanation
Indices: 106446--106506 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
106436 AAATAGAATG
*
106446 TTTA-AAAGTATCGATACG
1 TTTATAAAGTATCGATACT
* * *
106464 TATATAAAGTATCGAAATT
1 TTTATAAAGTATCGATACT
106483 TTTATAAGAGTATCGATACT
1 TTTATAA-AGTATCGATACT
106503 TTTA
1 TTTA
106507 GTCTGTTTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
18 3 0.09
19 17 0.50
20 14 0.41
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
TTTATAAAGTATCGATACT
Found at i:111102 original size:21 final size:20
Alignment explanation
Indices: 111078--111222 Score: 101
Period size: 21 Copynumber: 6.8 Consensus size: 20
111068 GTCCTTCGGG
*
111078 ACATATATGTGATCCTTTAGA
1 ACATATATGTGGTCCTTT-GA
*
111099 ACATATATGAGGTCCTTTGA
1 ACATATATGTGGTCCTTTGA
*
111119 GACATATATTTGGTCCTTTGGA
1 -ACATATATGTGGTCCTTT-GA
* * *
111141 ACATATATATGGTCCTTAGGG
1 ACATATATGTGGTCCTT-TGA
* * *
111162 ACAATTATATATGGTCCTTCGGG
1 AC-A-TATATGTGGTCCTT-TGA
* *
111185 ACATATATGTGGTCATTTAGG
1 ACATATATGTGGTCCTTT-GA
* *
111206 ACGTATATGAGGTCCTT
1 ACATATATGTGGTCCTT
111223 GGAATAATTT
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.02
21 79 0.76
22 4 0.04
23 19 0.18
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.37
Consensus pattern (20 bp):
ACATATATGTGGTCCTTTGA
Found at i:111171 original size:44 final size:42
Alignment explanation
Indices: 111065--111198 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
111055 AGGGTTCTAC
* * * *
111065 ATGGTCCTTCGGGACATATATGTGATCCTTTAGAACATATAT
1 ATGGTCCTTAGGGACATATATATGGTCCTTTGGAACATATAT
* * *
111107 GA-GGTCCTTTGAGACATATATTTGGTCCTTTGGAACATATAT
1 -ATGGTCCTTAGGGACATATATATGGTCCTTTGGAACATATAT
* *
111149 ATGGTCCTTAGGGACAATTATATATGGTCCTTCGGGACATATAT
1 ATGGTCCTTAGGGAC-A-TATATATGGTCCTTTGGAACATATAT
*
111193 GTGGTC
1 ATGGTC
111199 ATTTAGGACG
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 46 0.60
43 2 0.03
44 28 0.36
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (42 bp):
ATGGTCCTTAGGGACATATATATGGTCCTTTGGAACATATAT
Found at i:118197 original size:21 final size:21
Alignment explanation
Indices: 118134--118299 Score: 116
Period size: 21 Copynumber: 7.8 Consensus size: 21
118124 TCGAGGATTC
* *
118134 TATGTAGTCCTTCAGGACATA
1 TATGTGGTCCTTCGGGACATA
* * * * *
118155 TATGTGATCATTTGGAATATA
1 TATGTGGTCCTTCGGGACATA
*
118176 TATGAGGTCCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
* * * *
118197 TATTTGGTCTTTTGGAACATA
1 TATGTGGTCCTTCGGGACATA
* * *
118218 TATGTGGTCCTTAGGGAAACTTT
1 TATGTGGTCCTTCGGG--ACATA
*
118241 TATGTGGTTCTTCGGGACATA
1 TATGTGGTCCTTCGGGACATA
* ***
118262 TATGTGGTACTTTATGACATA
1 TATGTGGTCCTTCGGGACATA
* *
118283 TATGAGGTCATTCGGGA
1 TATGTGGTCCTTCGGGA
118300 TAATTTTATA
Statistics
Matches: 105, Mismatches: 38, Indels: 4
0.71 0.26 0.03
Matches are distributed among these distances:
21 88 0.84
23 17 0.16
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACATA
Found at i:118260 original size:65 final size:65
Alignment explanation
Indices: 118176--118308 Score: 164
Period size: 65 Copynumber: 2.0 Consensus size: 65
118166 TTGGAATATA
* * *
118176 TATGAGGTCCTTCGGGACATATATTTGGT-CTTT-TGGAACATATATGTGGTCCTTAGGGA-AAC
1 TATGAGGTCCTTCGGGACATATATGTGGTACTTTAT-G-ACATATATGAGGTCATTAGGGATAA-
118238 TTT
63 TTT
* * *
118241 TATGTGGTTCTTCGGGACATATATGTGGTACTTTATGACATATATGAGGTCATTCGGGATAATTT
1 TATGAGGTCCTTCGGGACATATATGTGGTACTTTATGACATATATGAGGTCATTAGGGATAATTT
118306 TAT
1 TAT
118309 ATAGCACTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
65 51 0.86
66 7 0.12
67 1 0.02
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (65 bp):
TATGAGGTCCTTCGGGACATATATGTGGTACTTTATGACATATATGAGGTCATTAGGGATAATTT
Found at i:124570 original size:30 final size:31
Alignment explanation
Indices: 124514--124593 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
124504 GTGATATGAG
124514 CTATGTGATAAAAGTATGGAAAATGATAAGT
1 CTATGTGATAAAAGTATGGAAAATGATAAGT
* *
124545 CTATGTGATAAAGGTATGG-AAATGATATGT
1 CTATGTGATAAAAGTATGGAAAATGATAAGT
* *
124575 CTATGCGATATAAACTATG
1 CTATGTGATA-AAAGTATG
124594 TGAATTGTGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 19 0.44
31 24 0.56
ACGTcount: A:0.40, C:0.06, G:0.23, T:0.31
Consensus pattern (31 bp):
CTATGTGATAAAAGTATGGAAAATGATAAGT
Found at i:124953 original size:9 final size:9
Alignment explanation
Indices: 124939--124972 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
124929 TATCATGGGC
124939 TATTGAATT
1 TATTGAATT
*
124948 TATTGAACT
1 TATTGAATT
*
124957 TATTGAATC
1 TATTGAATT
124966 TATTGAA
1 TATTGAA
124973 ACTATTGAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (9 bp):
TATTGAATT
Found at i:124962 original size:18 final size:18
Alignment explanation
Indices: 124938--124987 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
124928 GTATCATGGG
*
124938 CTATTGAATTTATTG-AA
1 CTATTGAATCTATTGAAA
124955 CTTATTGAATCTATTGAAA
1 C-TATTGAATCTATTGAAA
*
124974 CTATTGAACCTATT
1 CTATTGAATCTATT
124988 ATATGAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 1 0.03
18 25 0.86
19 3 0.10
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (18 bp):
CTATTGAATCTATTGAAA
Found at i:131203 original size:30 final size:31
Alignment explanation
Indices: 131147--131217 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
131137 GTGATATGAG
131147 CTATGTGATAAAAATATGGAAAATGATAAGT
1 CTATGTGATAAAAATATGGAAAATGATAAGT
* ** *
131178 CTATGTGGTAAAGGTATGG-AAATGATATGT
1 CTATGTGATAAAAATATGGAAAATGATAAGT
*
131208 CTATGCGATA
1 CTATGTGATA
131218 TAACTATGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (31 bp):
CTATGTGATAAAAATATGGAAAATGATAAGT
Found at i:131606 original size:17 final size:17
Alignment explanation
Indices: 131567--131615 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
131557 GTATCATGGG
*
131567 CTATTGAATTTATTGAA
1 CTATTGAATCTATTGAA
131584 CTTATTGAATCT-TTGAAA
1 C-TATTGAATCTATTG-AA
*
131602 CTATTGAACCTATT
1 CTATTGAATCTATT
131616 ATATGAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (17 bp):
CTATTGAATCTATTGAA
Found at i:132136 original size:12 final size:11
Alignment explanation
Indices: 132092--132144 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
132082 TTCATGACGA
132092 TGTTCAT-TAC
1 TGTTCATATAC
* *
132102 TGCTCATGACAC
1 TGTTCAT-ATAC
132114 TGTTCAT-TAC
1 TGTTCATATAC
132124 TGTTCATAGTAC
1 TGTTCATA-TAC
132136 TGTTCATAT
1 TGTTCATAT
132145 CGTATTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 15 0.43
11 1 0.03
12 19 0.54
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (11 bp):
TGTTCATATAC
Found at i:132142 original size:22 final size:22
Alignment explanation
Indices: 132083--132130 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
132073 GTAGAACTAT
132083 TCATGACGA-TGTTCATTACTGC
1 TCATGAC-ACTGTTCATTACTGC
*
132105 TCATGACACTGTTCATTACTGT
1 TCATGACACTGTTCATTACTGC
132127 TCAT
1 TCAT
132131 AGTACTGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (22 bp):
TCATGACACTGTTCATTACTGC
Found at i:138030 original size:13 final size:13
Alignment explanation
Indices: 138012--138040 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
138002 CCTTTAGTAG
138012 TTTGAGGACAAAA
1 TTTGAGGACAAAA
138025 TTTGAGGACAAAA
1 TTTGAGGACAAAA
138038 TTT
1 TTT
138041 CTTTTTAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (13 bp):
TTTGAGGACAAAA
Found at i:138872 original size:19 final size:19
Alignment explanation
Indices: 138848--138901 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
138838 AGAATGTTTA
*
138848 AAAGTATCGATACTTATAT
1 AAAGTATCGATACTTATAC
* * *
138867 AAAGTATCGAAACTTTTGC
1 AAAGTATCGATACTTATAC
138886 AATAGTATCGATACTT
1 AA-AGTATCGATACTT
138902 TTGGGCTAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (19 bp):
AAAGTATCGATACTTATAC
Found at i:141569 original size:355 final size:347
Alignment explanation
Indices: 140872--141577 Score: 1299
Period size: 355 Copynumber: 2.0 Consensus size: 347
140862 TACCCAGTTG
140872 AATATGTCATATAAAGGTTGAAGAATCAATCAATTTGTATAAAAACTTTTCAATTTTAGAAAAGG
1 AATATGTCATATAAAGGTTGAAGAATCAATCAATTTGTATAAAAACTTTTCAATTTTAGAAAAGG
140937 TTTTTTGTCAATAATAAAAAATTTCCTCTTTTGTTTTCCCCCTCATTTTTTCCTTTTAATTTATT
66 TTTTTTGTCAATAATAAAAAATTTCCTCTTTTGTTTTCCCCCTCATTTTTTCCTTTTAATTTATT
141002 TCTTTTCCTTAAGCGAAGAGAAGGATATGGGCAAGCAAGGTCCTTGCTATCACTGTGGAGTTACA
131 TCTTTTCCTTAAGCGAAGAGAAGGATATGGGCAAGCAAGGTCCTTGCTATCACTGTGGAGTTACA
141067 AGTGAGTTATTGTTTCTCCGTTAACTTTTTCTTTATAAGCTTTAGGGGAAAAAAAAACCTGAATT
196 AGTGAGTTATTGTTTCTCCGTTAACTTTTTCTTTATAAGCTTTAGGGG-AAAAAAAACCTGAATT
141132 TGAGTTCTAGGATGTGTGTAAATGTAAACTTTTTCTTTAAGTCAGTAAATTCGGTGTATGATTTT
260 TGAGTTCTAGGATGTGTGTAAATGTAAACTTTTTCTTTAAGTCAGTAAATTCGGTGTATGATTTT
141197 ATATTTGCCTGGGATAAATGCAT
325 ATATTTGCCTGGGATAAATGCAT
141220 AATATGTCATATAAAGGTTGAAGAAATCAATCAATTTGTATAAAAACTTTTCAATTTTTAGAAAA
1 AATATGTCATATAAAGGTTGAAG-AATCAATCAATTTGTATAAAAACTTTTCAA-TTTTAGAAAA
141285 GGTTTTTTGTCAATAAATAAAAAAATTTCCTCTTTTGTTTTTCCCCCTCATTTTTTCCTTTTAAT
64 GGTTTTTTGTCAAT-AAT-AAAAAATTTCCTCTTTTG-TTTTCCCCCTCATTTTTTCCTTTTAAT
141350 TTATTTCTTTTCCCTTAAGCGAAAGAGAAGGATATGGGCAAGCAAGGTCCTTGCTATCACTGTGG
126 TTATTTCTTTT-CCTTAAGCG-AAGAGAAGGATATGGGCAAGCAAGGTCCTTGCTATCACTGTGG
141415 AGTTACAAGTGAGTTATTGTTTCTCCGTTAACTTTTTCTTTATAAAGCTTTAGGGG-AAAAAAAC
189 AGTTACAAGTGAGTTATTGTTTCTCCGTTAACTTTTTCTTTAT-AAGCTTTAGGGGAAAAAAAAC
141479 CTGAATTTTGAGTTCTAGGATGTGTGTAAATGTAAACCTTTTTCTTTAAGTCAGTAAATTCGGTG
253 CTGAA-TTTGAGTTCTAGGATGTGTGTAAATGTAAA-CTTTTTCTTTAAGTCAGTAAATTCGGTG
141544 TATGATTTTATATTTGCCT-GGATAAATGCAT
316 TATGATTTTATATTTGCCTGGGATAAATGCAT
141575 AAT
1 AAT
141578 TATATCATTG
Statistics
Matches: 348, Mismatches: 0, Indels: 13
0.96 0.00 0.04
Matches are distributed among these distances:
348 23 0.07
349 30 0.09
350 24 0.07
351 3 0.01
352 18 0.05
353 38 0.11
354 22 0.06
355 131 0.38
356 59 0.17
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (347 bp):
AATATGTCATATAAAGGTTGAAGAATCAATCAATTTGTATAAAAACTTTTCAATTTTAGAAAAGG
TTTTTTGTCAATAATAAAAAATTTCCTCTTTTGTTTTCCCCCTCATTTTTTCCTTTTAATTTATT
TCTTTTCCTTAAGCGAAGAGAAGGATATGGGCAAGCAAGGTCCTTGCTATCACTGTGGAGTTACA
AGTGAGTTATTGTTTCTCCGTTAACTTTTTCTTTATAAGCTTTAGGGGAAAAAAAACCTGAATTT
GAGTTCTAGGATGTGTGTAAATGTAAACTTTTTCTTTAAGTCAGTAAATTCGGTGTATGATTTTA
TATTTGCCTGGGATAAATGCAT
Found at i:150544 original size:17 final size:17
Alignment explanation
Indices: 150522--150592 Score: 58
Period size: 17 Copynumber: 4.2 Consensus size: 17
150512 CAATAAGAGT
150522 TAGTTT-ATTAAATGAAC
1 TAGTTTAATT-AATGAAC
* *
150539 TAGTTTGATGAATG-AC
1 TAGTTTAATTAATGAAC
*
150555 TACTTTAATTAATGAAC
1 TAGTTTAATTAATGAAC
*
150572 TAACTTT-ATTCAATGAAC
1 T-AGTTTAATT-AATGAAC
150590 TAG
1 TAG
150593 ATGCATGAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
16 13 0.29
17 17 0.38
18 15 0.33
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (17 bp):
TAGTTTAATTAATGAAC
Found at i:150579 original size:18 final size:18
Alignment explanation
Indices: 150556--150591 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
150546 ATGAATGACT
150556 ACTTTAATT-AATGAACTA
1 ACTTT-ATTCAATGAACTA
150574 ACTTTATTCAATGAACTA
1 ACTTTATTCAATGAACTA
150592 GATGCATGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.39
Consensus pattern (18 bp):
ACTTTATTCAATGAACTA
Found at i:153570 original size:14 final size:15
Alignment explanation
Indices: 153547--153575 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
153537 CCCATTATCT
153547 GTTTTACTTTATTTA
1 GTTTTACTTTATTTA
153562 GTTTT-CTTTATTTA
1 GTTTTACTTTATTTA
153576 TTGTAGGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.17, C:0.07, G:0.07, T:0.69
Consensus pattern (15 bp):
GTTTTACTTTATTTA
Found at i:160569 original size:14 final size:15
Alignment explanation
Indices: 160550--160579 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
160540 AAGCAAGTAT
160550 GTGT-AACATGTTGC
1 GTGTAAACATGTTGC
160564 GTGTAAACATGTTGC
1 GTGTAAACATGTTGC
160579 G
1 G
160580 AGATAAGCAT
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:0.23, C:0.13, G:0.30, T:0.33
Consensus pattern (15 bp):
GTGTAAACATGTTGC
Found at i:166451 original size:14 final size:14
Alignment explanation
Indices: 166432--166461 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
166422 CTGAAAGTTG
166432 ATGAGCCAGAACAT
1 ATGAGCCAGAACAT
166446 ATGAGCCAGAACAT
1 ATGAGCCAGAACAT
166460 AT
1 AT
166462 TGAAAAGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (14 bp):
ATGAGCCAGAACAT
Found at i:192355 original size:21 final size:21
Alignment explanation
Indices: 192326--192381 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
192316 GATACCAAGG
*
192326 TAAGAGTATCGATACTCCCTA
1 TAAGGGTATCGATACTCCCTA
*
192347 TAAGGGTATCAATACTCCCTA
1 TAAGGGTATCGATACTCCCTA
*
192368 TAGGGGTATCGATA
1 TAAGGGTATCGATA
192382 TTGGGGTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
TAAGGGTATCGATACTCCCTA
Found at i:196058 original size:31 final size:31
Alignment explanation
Indices: 196020--196175 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
196010 CCCGAAGGAC
* *
196020 CAGTCCATA-GATTCCGAAGAACATAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
196051 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
196082 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
196113 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
196144 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
196175 C
1 C
196176 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:197129 original size:21 final size:21
Alignment explanation
Indices: 197105--197149 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
197095 TGTTGTTCGT
* *
197105 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
197126 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
197147 TTG
1 TTG
197150 CCCAGAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:200334 original size:31 final size:31
Alignment explanation
Indices: 200296--200420 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
200286 CCCGAAGGAC
* * *
200296 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
200327 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
200358 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
200389 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
200420 C
1 C
200421 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:201374 original size:21 final size:21
Alignment explanation
Indices: 201350--201394 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
201340 TGTTGTTCGT
* *
201350 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
201371 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
201392 TTG
1 TTG
201395 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:203533 original size:11 final size:12
Alignment explanation
Indices: 203502--203533 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
203492 ACTCCTTCAA
203502 ATGTTCAT-CAT
1 ATGTTCATCCAT
203513 ATGTTCATCCAT
1 ATGTTCATCCAT
203525 A-GTTCATCC
1 ATGTTCATCC
203534 CAAAACACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 16 0.80
12 4 0.20
ACGTcount: A:0.25, C:0.25, G:0.09, T:0.41
Consensus pattern (12 bp):
ATGTTCATCCAT
Found at i:219076 original size:42 final size:42
Alignment explanation
Indices: 218942--219076 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 42
218932 AAATGATTTC
*
218942 ATTGAAGGCCCCTACATTTTTTTTGAATCTCACATTTTACATTTATA
1 ATTGAAGGCCCCT--A--TTTTTTCAATCTCAC-TTTTACATTTATA
* * *
218989 ACT-AAGGCCCCTAATTTTTCAATCTAACTTTTACATTTATA
1 ATTGAAGGCCCCTATTTTTTCAATCTCACTTTTACATTTATA
*
219030 ATTGAA-GCCCCTATTTTTTCAATCCCACTTTTTACATTTATA
1 ATTGAAGGCCCCTATTTTTTCAATCTCAC-TTTTACATTTATA
219072 ATTGA
1 ATTGA
219077 GACTACTAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
41 34 0.44
42 32 0.41
44 1 0.01
46 9 0.12
47 2 0.03
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.44
Consensus pattern (42 bp):
ATTGAAGGCCCCTATTTTTTCAATCTCACTTTTACATTTATA
Found at i:219090 original size:42 final size:42
Alignment explanation
Indices: 218961--219121 Score: 157
Period size: 41 Copynumber: 3.8 Consensus size: 42
218951 CCCTACATTT
* * * * *
218961 TTTTTGAATCTCACATTTTACATTTATAACTAAGGCCCCTAA
1 TTTTTCAATCTCACTTTTTACATTTATAATTGAGACCCCTAA
* *
219003 TTTTTCAATCTAAC-TTTTACATTTATAATTGA-AGCCCCTAT
1 TTTTTCAATCTCACTTTTTACATTTATAATTGAGA-CCCCTAA
* **
219044 TTTTTCAATCCCACTTTTTACATTTATAATTGAGACTACTAA
1 TTTTTCAATCTCACTTTTTACATTTATAATTGAGACCCCTAA
* *
219086 TTTTTTTTATTCTCACTTTTTATC-TTTATAATTGAG
1 --TTTTTCAATCTCACTTTTTA-CATTTATAATTGAG
219122 GTCCTTTACT
Statistics
Matches: 99, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
41 34 0.34
42 34 0.34
43 1 0.01
44 29 0.29
45 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.06, T:0.48
Consensus pattern (42 bp):
TTTTTCAATCTCACTTTTTACATTTATAATTGAGACCCCTAA
Found at i:220405 original size:172 final size:173
Alignment explanation
Indices: 220153--220467 Score: 490
Period size: 172 Copynumber: 1.8 Consensus size: 173
220143 CTGCAACAAG
*
220153 GTGATTGAATGTTCATTGTCAAATGAGTGATAGTAATTAGAACAAACAATACTTTGTAATCACCT
1 GTGATTGAATGTTCATTGTCAAATGAGTAATAGTAATTAGAACAAAC-ATACTTTGTAATCACCT
* * * * * *
220218 TATCTTAATAAAAAAT-ATATAAAAAGATACTTCTTAAATATGATCCGAATCTAAAATCTCTAAT
65 TAGCTTAATAAAAAATCAGAT-AAAAGATAATACTTAAATATGATCCGAATCTAAAATATCTAAA
220282 TTGATTTCAAACGATTCCAAGAAGCATAGGAAATTTGACAGCAAT
129 TTGATTTCAAACGATTCCAAGAAGCATAGGAAATTTGACAGCAAT
* * * * *
220327 GTGATTGAGTGTTCATTGTCAAATGAGTAATAGTATTTAGAATAGAC-TACTTTGTAATCACTTT
1 GTGATTGAATGTTCATTGTCAAATGAGTAATAGTAATTAGAACAAACATACTTTGTAATCACCTT
220391 AGCTTAATAAAAAATCAGATAAAAGATAATACTTAAATATGATCCGAATCTAAAATATCTAAATT
66 AGCTTAATAAAAAATCAGATAAAAGATAATACTTAAATATGATCCGAATCTAAAATATCTAAATT
220456 GATTTCAAACGA
131 GATTTCAAACGA
220468 GGAATAAAAA
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
172 83 0.65
173 3 0.02
174 42 0.33
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (173 bp):
GTGATTGAATGTTCATTGTCAAATGAGTAATAGTAATTAGAACAAACATACTTTGTAATCACCTT
AGCTTAATAAAAAATCAGATAAAAGATAATACTTAAATATGATCCGAATCTAAAATATCTAAATT
GATTTCAAACGATTCCAAGAAGCATAGGAAATTTGACAGCAAT
Found at i:222624 original size:21 final size:21
Alignment explanation
Indices: 222598--222642 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
222588 GATTTCTGGG
* *
222598 CAAGGGCAATCGGTACCCATT
1 CAAGGGCAACCGATACCCATT
* *
222619 CAAGGGGAACCGATACCCCTT
1 CAAGGGCAACCGATACCCATT
222640 CAA
1 CAA
222643 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGCAACCGATACCCATT
Found at i:223629 original size:31 final size:31
Alignment explanation
Indices: 223591--223684 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
223581 AGGGTCGAGG
223591 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
223622 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
223653 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
223684 G
1 G
223685 GTTCTTCGGG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:227382 original size:32 final size:31
Alignment explanation
Indices: 227330--227411 Score: 119
Period size: 32 Copynumber: 2.6 Consensus size: 31
227320 AGGATCGAGG
*
227330 GTTTATCTATGTTCTTCGGGACATATGAACT
1 GTTTACCTATGTTCTTCGGGACATATGAACT
*
227361 GTTTACCTATGTTTCTTCGGGACATATGGACT
1 GTTTACCTATG-TTCTTCGGGACATATGAACT
* *
227393 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
227412 AATCTATGGT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 18 0.39
32 28 0.61
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGAACT
Found at i:231810 original size:31 final size:30
Alignment explanation
Indices: 231750--231840 Score: 123
Period size: 30 Copynumber: 3.0 Consensus size: 30
231740 AGGGTCGAGG
231750 GTTTACCTATGTTCTTCGGGACTATGGACT
1 GTTTACCTATGTTCTTCGGGACTATGGACT
231780 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGAC-TATGGACT
* * *
231811 GATTA-CTAGGTTCTTC-GAATCTATGGACT
1 GTTTACCTATGTTCTTCGGGA-CTATGGACT
231840 G
1 G
231841 GTCCTTCGGG
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
29 11 0.20
30 33 0.59
31 12 0.21
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (30 bp):
GTTTACCTATGTTCTTCGGGACTATGGACT
Found at i:234928 original size:21 final size:21
Alignment explanation
Indices: 234902--234946 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
234892 GATTTCTGGG
* *
234902 CAAGGGCAATCGGTACCCATT
1 CAAGGGCAACCGATACCCATT
* *
234923 CAAGGGGAACCGATACCCCTT
1 CAAGGGCAACCGATACCCATT
234944 CAA
1 CAA
234947 ACGAACAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGCAACCGATACCCATT
Found at i:235938 original size:31 final size:31
Alignment explanation
Indices: 235900--235992 Score: 136
Period size: 30 Copynumber: 3.0 Consensus size: 31
235890 AGGGTCGAGG
235900 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
235931 GTTTACCTATGTTCTTC-GGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
235961 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
235992 G
1 G
235993 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 28 0.49
31 28 0.49
32 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:239561 original size:21 final size:21
Alignment explanation
Indices: 239516--239561 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
239506 GTTACATCCG
* * *
239516 CAATAGCGCCCGCGATGGCCG
1 CAATAGCGCCCGCGACGACCA
239537 CAATAGCGCCCGCGACGACCA
1 CAATAGCGCCCGCGACGACCA
239558 CAAT
1 CAAT
239562 CACGGTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.39, G:0.26, T:0.09
Consensus pattern (21 bp):
CAATAGCGCCCGCGACGACCA
Found at i:242103 original size:45 final size:45
Alignment explanation
Indices: 242048--242155 Score: 207
Period size: 45 Copynumber: 2.4 Consensus size: 45
242038 GTCTTTACTC
*
242048 TAATTTCTAATAAAATAAACTAAGAATAATGTTTTAACTCAACCT
1 TAATTCCTAATAAAATAAACTAAGAATAATGTTTTAACTCAACCT
242093 TAATTCCTAATAAAATAAACTAAGAATAATGTTTTAACTCAACCT
1 TAATTCCTAATAAAATAAACTAAGAATAATGTTTTAACTCAACCT
242138 TAATTCCTAATAAAATAA
1 TAATTCCTAATAAAATAA
242156 TAAATCCAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.48, C:0.14, G:0.04, T:0.34
Consensus pattern (45 bp):
TAATTCCTAATAAAATAAACTAAGAATAATGTTTTAACTCAACCT
Found at i:246714 original size:15 final size:15
Alignment explanation
Indices: 246680--246720 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
246670 TTCTTATTGG
246680 TCATAAATAATTAAA
1 TCATAAATAATTAAA
246695 T-ATAAATACATT-AA
1 TCATAAATA-ATTAAA
246709 TCAT-AATAATTA
1 TCATAAATAATTA
246721 TTTATTTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.13
14 14 0.61
15 6 0.26
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (15 bp):
TCATAAATAATTAAA
Found at i:247029 original size:26 final size:26
Alignment explanation
Indices: 246993--247045 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
246983 ATTAAATATG
*
246993 CACTCACCTTTGTCACACTGTTGAAC
1 CACTCACCTTTGCCACACTGTTGAAC
247019 CACTCACCTTTGCCACACTGTTGAAC
1 CACTCACCTTTGCCACACTGTTGAAC
247045 C
1 C
247046 TTCTCTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.28
Consensus pattern (26 bp):
CACTCACCTTTGCCACACTGTTGAAC
Found at i:248498 original size:12 final size:12
Alignment explanation
Indices: 248481--248506 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
248471 ACCATTCTAA
248481 TAAAATTCAATT
1 TAAAATTCAATT
248493 TAAAATTCAATT
1 TAAAATTCAATT
248505 TA
1 TA
248507 TGAAAAAATC
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:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (12 bp):
TAAAATTCAATT
Found at i:258348 original size:6 final size:6
Alignment explanation
Indices: 258339--258405 Score: 64
Period size: 6 Copynumber: 10.8 Consensus size: 6
258329 TTCGATTCGA
* * * *
258339 GGGAGG GGGAGG GGGAGG GGG-GG GAGGAGG GAGAGA GGGAGA GGGAGA
1 GGGAGG GGGAGG GGGAGG GGGAGG G-GGAGG GGGAGG GGGAGG GGGAGG
258387 GGGAGG GAGAGAGG GGGAG
1 GGGAGG G-G-GAGG GGGAG
258406 AGAGAGAATA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
5 3 0.06
6 40 0.75
7 5 0.09
8 5 0.09
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (6 bp):
GGGAGG
Found at i:258384 original size:14 final size:14
Alignment explanation
Indices: 258360--258412 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
258350 GGGGAGGGGG
258360 GGGAGGAGGGAGAGA
1 GGGA-GAGGGAGAGA
258375 GGGAGA-GG-GAGA
1 GGGAGAGGGAGAGA
258387 -GG-GAGGGAGAGA
1 GGGAGAGGGAGAGA
* *
258399 GGGGGAGAGAGAGA
1 GGGAGAGGGAGAGA
258413 ATAGTTGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 8 0.24
13 4 0.12
14 11 0.33
15 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.66, T:0.00
Consensus pattern (14 bp):
GGGAGAGGGAGAGA
Found at i:258408 original size:12 final size:11
Alignment explanation
Indices: 258353--258411 Score: 52
Period size: 12 Copynumber: 5.3 Consensus size: 11
258343 GGGGGAGGGG
258353 GAGGGGGG-G-
1 GAGGGGGGAGA
*
258362 GAGGAGGGAGA
1 GAGGGGGGAGA
258373 GAGGGAGAGG-GA
1 GAGGG-G-GGAGA
258385 GAGGGAGGGAGA
1 GAGGG-GGGAGA
258397 GAGGGGGAGAGA
1 GAGGGGG-GAGA
258409 GAG
1 GAG
258412 AATAGTTGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
9 7 0.17
10 1 0.02
11 8 0.19
12 24 0.57
13 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (11 bp):
GAGGGGGGAGA
Found at i:260319 original size:3 final size:3
Alignment explanation
Indices: 260311--260338 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
260301 TGGTCTACCC
260311 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
260339 TTTGACCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:268974 original size:87 final size:87
Alignment explanation
Indices: 268827--269010 Score: 314
Period size: 87 Copynumber: 2.1 Consensus size: 87
268817 TAATTCAAAC
268827 CTCAACTTCACAACGAATGAGCCATCAACGATTTCAACTTCACGACGAAGGATATAGTGCCCACA
1 CTCAACTTCACAACGAATGAGCCATCAACGATTTCAACTTCACGACGAAGGATATAGTGCCCACA
*
268892 AGTAGCAATGCAACCCTTGGAT
66 AGAAGCAATGCAACCCTTGGAT
* * * *
268914 CTCAACTTCACAATGAATGAGCCATCCACTATTTCAACTTCACGACGAAGGATATCGTGCCCACA
1 CTCAACTTCACAACGAATGAGCCATCAACGATTTCAACTTCACGACGAAGGATATAGTGCCCACA
268979 AGAAGCAATGCAACCCTTGGAT
66 AGAAGCAATGCAACCCTTGGAT
*
269001 TTCAACTTCA
1 CTCAACTTCA
269011 TGACGAAGGA
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 91 1.00
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (87 bp):
CTCAACTTCACAACGAATGAGCCATCAACGATTTCAACTTCACGACGAAGGATATAGTGCCCACA
AGAAGCAATGCAACCCTTGGAT
Found at i:269072 original size:121 final size:121
Alignment explanation
Indices: 268914--269208 Score: 445
Period size: 118 Copynumber: 2.5 Consensus size: 121
268904 ACCCTTGGAT
* * * *
268914 CTCAACTTCACAATGAATGAGCCATCCACTATTTCAACTTCACGACGAAGGATATCGTGCCCACA
1 CTCAACTTCACAACGAAAGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCCACA
*
268979 AGAAGCAATGCAACCCTTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAAG
66 AGAAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAG
269035 CAT-AACTTCACAACGAAAGAGCCATCCACGATTTCAACTT--C-ACGAAGGATATCATGCCCAC
1 C-TCAACTTCACAACGAAAGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCCAC
* * *
269096 AAGCAGCAATGCAACCCTTGGATTTTAACTTCACGATGAAGGATATCCAATTCAAAG
65 AAGAAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAG
* * * *
269153 CTCAACTTCACAACGAAGGAGCCATCCATGATTTCAACTTCACGACAAAAGATATC
1 CTCAACTTCACAACGAAAGAGCCATCCACGATTTCAACTTCACGACGAAGGATATC
269209 CAACTCCAAG
Statistics
Matches: 157, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
117 1 0.01
118 108 0.69
119 1 0.01
120 1 0.01
121 45 0.29
122 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (121 bp):
CTCAACTTCACAACGAAAGAGCCATCCACGATTTCAACTTCACGACGAAGGATATCATGCCCACA
AGAAGCAATGCAACCCTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAG
Found at i:269171 original size:34 final size:34
Alignment explanation
Indices: 269122--269235 Score: 90
Period size: 34 Copynumber: 3.4 Consensus size: 34
269112 CTTGGATTTT
* *
269122 AACTTCACGATGAAGGATATCCAATTCAAAGCTC
1 AACTTCACAACGAAGGATATCCAATTCAAAGCTC
* * * **
269156 AACTTCACAACGAAGG--AGCC-ATCCATGATTTC
1 AACTTCACAACGAAGGATATCCAATTCA-AAGCTC
* * * * *
269188 AACTTCACGACAAAAGATATCCAACTCCAAGCTC
1 AACTTCACAACGAAGGATATCCAATTCAAAGCTC
269222 AACTTCACAACGAA
1 AACTTCACAACGAA
269236 TGAGCCATCC
Statistics
Matches: 57, Mismatches: 19, Indels: 8
0.68 0.23 0.10
Matches are distributed among these distances:
31 4 0.07
32 19 0.33
34 32 0.56
35 2 0.04
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.20
Consensus pattern (34 bp):
AACTTCACAACGAAGGATATCCAATTCAAAGCTC
Found at i:269193 original size:66 final size:66
Alignment explanation
Indices: 269116--269274 Score: 237
Period size: 66 Copynumber: 2.4 Consensus size: 66
269106 GCAACCCTTG
* * *
269116 GATTTTAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
*
269181 T
66 C
* * * *
269182 GATTTCAACTTCACGACAAAAGATATCCAACTCCAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
269247 C
66 C
*
269248 GATTTCAACTTCATGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
269275 GTGCCCAACA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 82 1.00
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.23
Consensus pattern (66 bp):
GATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCACAACGAAGGAGCCATCCA
C
Found at i:269195 original size:32 final size:31
Alignment explanation
Indices: 269154--269270 Score: 92
Period size: 32 Copynumber: 3.6 Consensus size: 31
269144 AATTCAAAGC
269154 TCAACTTCACAACGAAGGAGCCATCCATGATT
1 TCAACTTCACAACGAAGGAGCCATCCA-GATT
* * * * **
269186 TCAACTTCACGACAAAAGATATCCAACTCCA-AGC
1 TCAACTTCACAAC-GAAG-GAGCC-A-TCCAGATT
*
269220 TCAACTTCACAACGAATGAGCCATCCACGATT
1 TCAACTTCACAACGAAGGAGCCATCCA-GATT
**
269252 TCAACTTCATGACGAAGGA
1 TCAACTTCACAACGAAGGA
269271 TATCGTGCCC
Statistics
Matches: 63, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
30 4 0.06
31 1 0.02
32 32 0.51
33 5 0.08
34 16 0.25
35 1 0.02
36 4 0.06
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.21
Consensus pattern (31 bp):
TCAACTTCACAACGAAGGAGCCATCCAGATT
Found at i:270070 original size:14 final size:13
Alignment explanation
Indices: 270051--270101 Score: 59
Period size: 14 Copynumber: 3.8 Consensus size: 13
270041 TATATGATAA
270051 TAATTACTTATTAT
1 TAATTA-TTATTAT
270065 TAATTATTATTAT
1 TAATTATTATTAT
* *
270078 TATATTAATACTAT
1 TA-ATTATTATTAT
270092 TAATT-TTATT
1 TAATTATTATT
270102 TTTGTAGGCC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 3 0.09
13 12 0.38
14 17 0.53
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATTATTATTAT
Found at i:272727 original size:14 final size:14
Alignment explanation
Indices: 272702--272747 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
272692 TGTTGATAAA
272702 TATTAA-TATTAAC
1 TATTAATTATTAAC
272715 TATTAATTATTAAC
1 TATTAATTATTAAC
* * *
272729 CATTATTTTTTAA-
1 TATTAATTATTAAC
272742 TATTAA
1 TATTAA
272748 GATTGATGTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
13 10 0.37
14 17 0.63
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTAATTATTAAC
Found at i:272805 original size:75 final size:75
Alignment explanation
Indices: 272726--272875 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
272716 ATTAATTATT
272726 AACCATTATTTTTTAATATTAAGATTGATGTGCTAATTTTTATTTTTCCTACGCATGCCCTTTTA
1 AACCATTATTTTTTAATATTAAGATTGATGTGCTAATTTTTATTTTTCCTACGCATGCCCTTTTA
272791 TGCCTTTTTA
66 TGCCTTTTTA
*
272801 AACCATTATTTTTTAATATTAAGATTGATGTGCTAATTTTTATTTTTCGTACGCATGCCCTTTTA
1 AACCATTATTTTTTAATATTAAGATTGATGTGCTAATTTTTATTTTTCCTACGCATGCCCTTTTA
272866 TGCCTTTTTA
66 TGCCTTTTTA
272876 TATAAATTTA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (75 bp):
AACCATTATTTTTTAATATTAAGATTGATGTGCTAATTTTTATTTTTCCTACGCATGCCCTTTTA
TGCCTTTTTA
Found at i:275687 original size:49 final size:49
Alignment explanation
Indices: 275614--275945 Score: 520
Period size: 49 Copynumber: 6.8 Consensus size: 49
275604 TGCACCGAAG
* * *
275614 TGCCGAAATGCACCGTTATACATTTAACTTTCAATAGTGACACATTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
* *
275663 TGCCGAAATGCACCGTTATGCATTTAACTTTAAGTAGTGACACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
* * *
275712 TGCCGAAATACACCGTTATGCATTTAACTTTCATTAGTGGCACCTTCTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
* * *
275761 TGTCGAAATGCACAGTTATGCATTTAACTTTCATTAGTGGCACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
*
275810 TGCCGAAATGCATCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
* * *
275859 TGTCAAAATGCACCATTATGCATTTAACTTTCATTAGTGACACCTTTTA
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
*
275908 TGTCGAAATGCACCGTTATGCATTTAACTTTCATTAGT
1 TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGT
275946 TCATTTTAGA
Statistics
Matches: 260, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 260 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (49 bp):
TGCCGAAATGCACCGTTATGCATTTAACTTTCATTAGTGACACCTTTTA
Found at i:277366 original size:14 final size:13
Alignment explanation
Indices: 277349--277408 Score: 52
Period size: 14 Copynumber: 4.5 Consensus size: 13
277339 TATATTTATC
277349 TTATTCTATTTTGT
1 TTATT-TATTTTGT
*
277363 TTATTT-TTGT-T
1 TTATTTATTTTGT
*
277374 TTATTTATTTGTTT
1 TTATTTATTT-TGT
277388 TTATTTATTTTAGTT
1 TTATTTATTTT-G-T
277403 TTATTT
1 TTATTT
277409 TTCTTCTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 7 0.18
12 5 0.13
13 3 0.08
14 16 0.42
15 7 0.18
ACGTcount: A:0.15, C:0.02, G:0.07, T:0.77
Consensus pattern (13 bp):
TTATTTATTTTGT
Found at i:277380 original size:15 final size:15
Alignment explanation
Indices: 277357--277408 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
277347 TCTTATTCTA
*
277357 TTTTGTTTATTTTTG
1 TTTTATTTATTTTTG
*
277372 TTTTATTTATTTGT-
1 TTTTATTTATTTTTG
*
277386 TTTTATTTATTTTAG
1 TTTTATTTATTTTTG
277401 TTTTATTT
1 TTTTATTT
277409 TTCTTCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.13, C:0.00, G:0.08, T:0.79
Consensus pattern (15 bp):
TTTTATTTATTTTTG
Found at i:277389 original size:29 final size:29
Alignment explanation
Indices: 277331--277412 Score: 87
Period size: 29 Copynumber: 2.8 Consensus size: 29
277321 TTCCCTTATT
* *
277331 TTTATTTTTATATTTATCTTATTCTATTTTG
1 TTTATTTTTGT-TTTAT-TTATTCTATTTTA
*
277362 TTTATTTTTGTTTTATTTATT-TGTTTTTA
1 TTTATTTTTGTTTTATTTATTCT-ATTTTA
*
277391 TTTATTTTAGTTTTATTT-TTCT
1 TTTATTTTTGTTTTATTTATTCT
277413 TCTTTTTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 3 0.07
29 27 0.60
30 5 0.11
31 10 0.22
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.76
Consensus pattern (29 bp):
TTTATTTTTGTTTTATTTATTCTATTTTA
Found at i:277409 original size:5 final size:5
Alignment explanation
Indices: 277330--277409 Score: 51
Period size: 5 Copynumber: 15.8 Consensus size: 5
277320 TTTCCCTTAT
* * * *
277330 TTTTA TTTTTA TATTTA TCTTA TTCTA TTTT- GTTTA TTTTTG TTTTA
1 TTTTA -TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA
277377 -TTTA TTTGT- TTTTA -TTTA TTTTA GTTTTA TTTT
1 TTTTA TTT-TA TTTTA TTTTA TTTTA -TTTTA TTTT
277410 TCTTCTTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
4 12 0.21
5 27 0.47
6 19 0.33
ACGTcount: A:0.16, C:0.03, G:0.05, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:277480 original size:24 final size:21
Alignment explanation
Indices: 277437--277478 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
277427 TAGTCTATTA
*
277437 TTATTATTTTTTGTATTTTAT
1 TTATTATTTTTAGTATTTTAT
277458 TTATTATTATTTAGCTATTTT
1 TTATTATT-TTTAG-TATTTT
277479 TAGGGCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.71
Consensus pattern (21 bp):
TTATTATTTTTAGTATTTTAT
Found at i:279442 original size:25 final size:23
Alignment explanation
Indices: 279414--279473 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
279404 AATTTTAGCA
279414 TTTTTTATTATTATT-TATTTTAT
1 TTTTTTATTATTATTAT-TTTTAT
*
279437 GTTTTTTACTTCTTATTATTTTTAT
1 -TTTTTTA-TTATTATTATTTTTAT
*
279462 TTTATT-TTATTA
1 TTTTTTATTATTA
279474 CTTTTAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.16
24 12 0.39
25 13 0.42
26 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTTATTATTATTATTTTTAT
Found at i:283701 original size:124 final size:124
Alignment explanation
Indices: 283518--284432 Score: 1319
Period size: 124 Copynumber: 7.4 Consensus size: 124
283508 GAACTCAAAG
*
283518 CAACATTCATATTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
* * * * *
283583 CACAACGAAGGGGCCATCCACGATTTCAACTTCACGGCAAAGGATATCATGTCCACCAA
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
* * * * *
283642 TAATAGTCATCTTTAGATTGGATTTCAACTTCACGATGAATGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
* * * *
283707 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACAAAGGATATTGTTCCCACCAG
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
* *
283766 CAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGATATCCAATTAAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
** *
283831 CACAACGAAAGGGTTATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCACCAA
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
* * * * ** *
283890 CAAAATTAATCTCTAGATTGGATTTTAACTTCAAAATGAAGGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
* * * * *
283955 CACAACGAATGGGCCATTCACAATTTCAACTTCACGACGAAGGATATCGTACCCACCAT
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
* *
284014 CAACATTCATCTTTAGATTGGATTTCAACTTTACGACGAAAGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
* * * *
284079 CAAAACGAAGGGGTCATCCACGATTTCAACTTCACGACGAAGGATATTGTGCCCACCAGA
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCA-A
* *
284139 -AACATTCATCTTTAGATTGGATTTCAACTTCATGACGAAGGATATCCAATTCAAGGATCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
* * * * ** *
284203 CACAACGAAAGTGCCATCCACGATTTCAATTTCACGATGAAGGATATTGTTACCACCAG
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
*
284262 CAACATTCATATTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
* * * * * *
284327 CACAACGAAGGGGTCATCCACAATTTCAACTTCATGATGAAGGATATCGTGCCCACCAG
66 CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
*
284386 CAACATTCATCTTTAGATTGGATTTCAACTTCACGAAGAAGGATATC
1 CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATC
284433 GTGCCCATCA
Statistics
Matches: 705, Mismatches: 84, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
124 705 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.27
Consensus pattern (124 bp):
CAACATTCATCTTTAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTT
CACAACGAAAGGGCCATCCACGATTTCAACTTCACGACGAAGGATATCGTGCCCACCAA
Found at i:284439 original size:58 final size:58
Alignment explanation
Indices: 284349--284490 Score: 214
Period size: 58 Copynumber: 2.4 Consensus size: 58
284339 GTCATCCACA
* * * *
284349 ATTTCAACTTCATGATGAAGGATATCGTGCCCACCAGCAACATTCATCTTTAGATTGG
1 ATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATCCATCTTTAGATTGG
*
284407 ATTTCAACTTCACGAAGAAGGATATCGTGCCCATCAACAACATCCATCTTTAGATTGG
1 ATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATCCATCTTTAGATTGG
*
284465 ATTTCAACTTCAC-AACGAATGATATC
1 ATTTCAACTTCACGAA-GAAGGATATC
284491 CAATCCAAAG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
57 2 0.03
58 75 0.97
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (58 bp):
ATTTCAACTTCACGAAGAAGGATATCGTGCCCACCAACAACATCCATCTTTAGATTGG
Found at i:286227 original size:30 final size:30
Alignment explanation
Indices: 286191--286256 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
286181 AAGGAACATA
*
286191 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
286221 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
286251 TGGATA
1 TGGATA
286257 AGTCCTTCGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:289254 original size:3 final size:3
Alignment explanation
Indices: 289246--289276 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
289236 TGAGGAAGAA
289246 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
289277 CCAAGTACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:291121 original size:30 final size:30
Alignment explanation
Indices: 291085--291151 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
291075 AAGGAACATA
*
291085 TGGATAGTTGCCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
291115 TGGATAGTTACCGAGGATCTTTATGACCTC
1 TGGATAGTTACCGAGGATCTTTATGACCTC
291145 TGGATAG
1 TGGATAG
291152 GTCCTTCGGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (30 bp):
TGGATAGTTACCGAGGATCTTTATGACCTC
Found at i:292765 original size:3 final size:3
Alignment explanation
Indices: 292759--292816 Score: 55
Period size: 3 Copynumber: 17.7 Consensus size: 3
292749 CAAAAAAAAT
292759 TTA TTA -TA TTA TTAA TTA TTTA TTTA TTTA TTA TTA TTAA TTA TTTA
1 TTA TTA TTA TTA TT-A TTA -TTA -TTA -TTA TTA TTA TT-A TTA -TTA
292806 TTA TTA TTA TT
1 TTA TTA TTA TT
292817 TTTGTAGGCC
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 2 0.04
3 28 0.56
4 20 0.40
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:292778 original size:7 final size:7
Alignment explanation
Indices: 292759--292816 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
292749 CAAAAAAAAT
292759 TTATTATA
1 TTATTA-A
292767 TTATTAA
1 TTATTAA
*
292774 TTATTTA
1 TTATTAA
*
292781 -T-TTAT
1 TTATTAA
292786 TTATT-A
1 TTATTAA
292792 TTATTAA
1 TTATTAA
*
292799 TTATTTA
1 TTATTAA
292806 TTATT-A
1 TTATTAA
292812 TTATT
1 TTATT
292817 TTTGTAGGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
5 2 0.05
6 13 0.31
7 21 0.50
8 6 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (7 bp):
TTATTAA
Found at i:293501 original size:25 final size:23
Alignment explanation
Indices: 293473--293532 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 23
293463 AATTTTAGCA
293473 TTTTTTATTATTATT-TATTTTAT
1 TTTTTTATTATTATTAT-TTTTAT
*
293496 GTTTTTTACTTCTTATTATTTTTAT
1 -TTTTTTA-TTATTATTATTTTTAT
*
293521 TTTATT-TTATTA
1 TTTTTTATTATTA
293533 CTTTTAGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 5 0.16
24 12 0.39
25 13 0.42
26 1 0.03
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.75
Consensus pattern (23 bp):
TTTTTTATTATTATTATTTTTAT
Found at i:295610 original size:16 final size:16
Alignment explanation
Indices: 295591--295626 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
295581 AACGTTTAAA
295591 ACAAATCCAGTTTTAG
1 ACAAATCCAGTTTTAG
295607 ACAAATCCAGTTTTAG
1 ACAAATCCAGTTTTAG
295623 ACAA
1 ACAA
295627 TAATTAGACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (16 bp):
ACAAATCCAGTTTTAG
Found at i:296068 original size:19 final size:18
Alignment explanation
Indices: 296044--296080 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
296034 AATATCATAA
296044 TGTAATATAAACATAAAAC
1 TGTAATATAAACA-AAAAC
*
296063 TGTAATTTAAACAAAAAC
1 TGTAATATAAACAAAAAC
296081 ATTAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.57, C:0.11, G:0.05, T:0.27
Consensus pattern (18 bp):
TGTAATATAAACAAAAAC
Found at i:297153 original size:29 final size:31
Alignment explanation
Indices: 297097--297156 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 31
297087 CAATTTAAGG
*
297097 CAAAATGGTTTTTGGACTTAAATTGAATTTA
1 CAAAATGGTTTTTGGACTTAAAGTGAATTTA
297128 CAAAAT-GTTTTTGGACTT-AAGTGAATTTA
1 CAAAATGGTTTTTGGACTTAAAGTGAATTTA
297157 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTAAAGTGAATTTA
Found at i:297262 original size:21 final size:20
Alignment explanation
Indices: 297236--297297 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 20
297226 AGGGTGTCAA
297236 AGTGCATCCATGCACCCTTGC
1 AGTGCATCCATGCACCC-TGC
*
297257 AGTGCATCCATGTATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
*
297278 AGTGCACCCATGCA-CCTGC
1 AGTGCATCCATGCACCCTGC
297297 A
1 A
297298 CTAGTGCATC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 6 0.16
21 28 0.76
22 3 0.08
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:297326 original size:20 final size:19
Alignment explanation
Indices: 297301--297374 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
297291 ACCTGCACTA
297301 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTT-T
**
297321 GTGCATCGATGCATCAAGGTT
1 GTGCATCGATGCATC--CTTT
297342 GTGCATCGATGCATCCTGTT
1 GTGCATCGATGCATCCT-TT
*
297362 GTGCATCCATGCA
1 GTGCATCGATGCA
297375 CGAAGGCTGC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
20 29 0.63
21 16 0.35
22 1 0.02
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATCCTTT
Found at i:300643 original size:34 final size:30
Alignment explanation
Indices: 300605--300673 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
300595 TTGATATAAC
300605 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
300639 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
300668 AATTTA
1 AATTTA
300674 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:300684 original size:29 final size:30
Alignment explanation
Indices: 300614--300673 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
300604 CAATTTAAGG
300614 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
300645 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
300674 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:300778 original size:20 final size:21
Alignment explanation
Indices: 300753--300809 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
300743 AGGGTGTCAA
*
300753 AGTGCATCCATGTACCCCT-G
1 AGTGCATCCATGCACCCCTGG
* *
300773 AGTGCATCCATACATCCCTGG
1 AGTGCATCCATGCACCCCTGG
300794 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
300810 TGCACTAGTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.23, C:0.35, G:0.19, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGG
Found at i:300822 original size:22 final size:21
Alignment explanation
Indices: 300794--300869 Score: 88
Period size: 20 Copynumber: 3.7 Consensus size: 21
300784 ACATCCCTGG
*
300794 AGTGCATCCATGCACC-TGCA
1 AGTGCATCGATGCACCATGCA
300814 CTAGTGCATCGATGCACCATGCA
1 --AGTGCATCGATGCACCATGCA
300837 A-TGCATCGATGCACCATGC-
1 AGTGCATCGATGCACCATGCA
*
300856 AGTGCGTC-ATGCAC
1 AGTGCATCGATGCAC
300870 TCAAACACCG
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
19 7 0.14
20 23 0.46
21 1 0.02
22 15 0.30
23 4 0.08
ACGTcount: A:0.25, C:0.32, G:0.22, T:0.21
Consensus pattern (21 bp):
AGTGCATCGATGCACCATGCA
Found at i:300916 original size:20 final size:20
Alignment explanation
Indices: 300890--300957 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
300880 AATGTACTTA
*
300890 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTACT
* **
300910 TTGCATCGATGCATCAAGACT
1 GTGCATCGATGCATC-CTACT
*
300931 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTACT
300951 GTGCATC
1 GTGCATC
300958 CATTCACGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 23 0.59
21 16 0.41
ACGTcount: A:0.19, C:0.28, G:0.22, T:0.31
Consensus pattern (20 bp):
GTGCATCGATGCATCCTACT
Found at i:302845 original size:24 final size:24
Alignment explanation
Indices: 302794--302847 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
302784 AAATGGAGAT
* *
302794 ATCAGATATCAAAATAGAATTCAT
1 ATCAGATATCAAAATAGAATCCAG
* * *
302818 ATCATATATCAGAATAGAGTCCAG
1 ATCAGATATCAAAATAGAATCCAG
302842 ATCAGA
1 ATCAGA
302848 AATTAGAGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (24 bp):
ATCAGATATCAAAATAGAATCCAG
Found at i:305067 original size:15 final size:16
Alignment explanation
Indices: 305043--305072 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
305033 CAAAAAACAT
305043 AAAATATGACTTTTCA
1 AAAATATGACTTTTCA
305059 AAAAT-TGACTTTTC
1 AAAATATGACTTTTC
305073 GGTTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (16 bp):
AAAATATGACTTTTCA
Done.