Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 91 of 132
Found at i:28011104 original size:17 final size:17
Alignment explanation
Indices: 28011072--28011114 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
28011062 CTAAACTAAA
28011072 AAGAATGCAGTGACAATT
1 AAGAATGCAGTGACAA-T
28011090 AA-AATGCAG-GCACAAT
1 AAGAATGCAGTG-ACAAT
28011106 AAGAATGCA
1 AAGAATGCA
28011115 TGAAAACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.49, C:0.14, G:0.21, T:0.16
Consensus pattern (17 bp):
AAGAATGCAGTGACAAT
Found at i:28033508 original size:18 final size:18
Alignment explanation
Indices: 28033468--28033508 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
28033458 CTCATTTTCT
28033468 TTACTTTTAATTTTGTTTA
1 TTAC-TTTAATTTTGTTTA
28033487 -TACTTTAA-TTTGTTTAA
1 TTACTTTAATTTTGTTT-A
28033504 TTACT
1 TTACT
28033509 CTTTTACCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 7 0.35
17 6 0.30
18 7 0.35
ACGTcount: A:0.24, C:0.07, G:0.05, T:0.63
Consensus pattern (18 bp):
TTACTTTAATTTTGTTTA
Found at i:28038377 original size:26 final size:26
Alignment explanation
Indices: 28038357--28038424 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 26
28038347 GGACATGCTT
28038357 ATGCAGCGACAATTCTAGACATATTC
1 ATGCAGCGACAATTCTAGACATATTC
* * **
28038383 ATGCAGCGATAATTCTATACAGGTTC
1 ATGCAGCGACAATTCTAGACATATTC
* *
28038409 TTGCAGTGACAATTCT
1 ATGCAGCGACAATTCT
28038425 GGGCGCAATG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (26 bp):
ATGCAGCGACAATTCTAGACATATTC
Found at i:28039970 original size:40 final size:40
Alignment explanation
Indices: 28039871--28039970 Score: 91
Period size: 40 Copynumber: 2.5 Consensus size: 40
28039861 TTTGAAACAA
*
28039871 TTTTCAAATCAAGTTAAAATGATTTTAAACATGTCAAAATG
1 TTTTCAAA-CAAGTTAAAATCATTTTAAACATGTCAAAATG
* * *
28039912 CTTGC--ACTAAGTCAAAAATCATTTT-AACACT-TCAAAATG
1 TTTTCAAAC-AAGT-TAAAATCATTTTAAACA-TGTCAAAATG
28039951 TTTTTCAAACAAGTTAAAAT
1 -TTTTCAAACAAGTTAAAAT
28039971 AGCTCCAGGC
Statistics
Matches: 46, Mismatches: 7, Indels: 13
0.70 0.11 0.20
Matches are distributed among these distances:
38 1 0.02
39 17 0.37
40 19 0.41
41 7 0.15
42 2 0.04
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (40 bp):
TTTTCAAACAAGTTAAAATCATTTTAAACATGTCAAAATG
Found at i:28061252 original size:30 final size:30
Alignment explanation
Indices: 28061178--28061272 Score: 118
Period size: 30 Copynumber: 3.2 Consensus size: 30
28061168 AAACTTAACA
*
28061178 AACAAATGCTTTTAAAATAGTAACAAAATT
1 AACAAATGCTTCTAAAATAGTAACAAAATT
* **
28061208 AATAAAAACTTCTAAAATAGTAACAAAATT
1 AACAAATGCTTCTAAAATAGTAACAAAATT
* * * *
28061238 AACAAATGCCTCTAAAATAATAACGAATTT
1 AACAAATGCTTCTAAAATAGTAACAAAATT
28061268 AACAA
1 AACAA
28061273 TAAAATAAGT
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AACAAATGCTTCTAAAATAGTAACAAAATT
Found at i:28067876 original size:3 final size:3
Alignment explanation
Indices: 28067868--28067909 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
28067858 TTTAATGCTT
28067868 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
28067910 AAATCAAGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:28070138 original size:51 final size:51
Alignment explanation
Indices: 28070057--28070191 Score: 191
Period size: 51 Copynumber: 2.6 Consensus size: 51
28070047 GCTATAAACG
* * *
28070057 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
*
28070109 AAAGGTCCGATGACTAAGTGTTATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
* *
28070160 AAAGGTCCGACGAC-AATATGTCATCGTGAGTA
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGTA
28070192 TTAAATGAAA
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 2 0.03
51 69 0.92
52 4 0.05
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGAATT
Found at i:28077250 original size:51 final size:51
Alignment explanation
Indices: 28077163--28077449 Score: 418
Period size: 51 Copynumber: 5.6 Consensus size: 51
28077153 GCTATAAACG
28077163 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
28077215 AAAGGTTCGGTGACTAAGTGTCATCGTGAGTAAATGAATCATTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
28077266 AAAGGTCTGA-GACTAAATGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* *
28077316 AAAGGTCCGATGACTAAGTGTTATTGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * *
28077367 AAAGGTCCGATGACTGAGTGTCATCGTGAGTAAATGAAT-CTATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCT-TTACGGATT
*
28077418 AAAGGTCCGATGAC-AATATGTCATCGTGAGTA
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGTA
28077450 TTAAATCAAA
Statistics
Matches: 211, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 49 0.23
51 158 0.75
52 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:28077350 original size:101 final size:102
Alignment explanation
Indices: 28077163--28077449 Score: 418
Period size: 101 Copynumber: 2.8 Consensus size: 102
28077153 GCTATAAACG
* *
28077163 AAAGAGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTTCGGTGA
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGA
*
28077228 CTAAGTGTCATCGTGAGTAAATGAATCATTTATGGATT
65 CTAAGTGTCATCGTGAGTAAATGAATCATTTACGGATT
* *
28077266 AAAGGTCTGA-GACTAAATGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
* * *
28077330 TAAGTGTTATTGTGAGTAAATGAATCCTTTACGGATT
66 TAAGTGTCATCGTGAGTAAATGAATCATTTACGGATT
* * *
28077367 AAAGGTCCGATGACTGAGTGTCATCGTGAGTAAATGAAT-CTATGACGAATTAAAGGTCCGATGA
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCT-TTACGGATTAAAGGTCCGATGA
*
28077431 C-AATATGTCATCGTGAGTA
65 CTAA-GTGTCATCGTGAGTA
28077450 TTAAATCAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
101 97 0.59
102 64 0.39
103 4 0.02
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.30
Consensus pattern (102 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAGGTCCGATGAC
TAAGTGTCATCGTGAGTAAATGAATCATTTACGGATT
Found at i:28078169 original size:21 final size:21
Alignment explanation
Indices: 28078145--28078218 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
28078135 AGAGTTTTTA
28078145 GTATCGGTAGATGTATGACTT
1 GTATCGGTAGATGTATGACTT
** * *
28078166 GTATCGGTAGAAATTTCACTT
1 GTATCGGTAGATGTATGACTT
* *
28078187 CTATCGGTAGATGCATGACTT
1 GTATCGGTAGATGTATGACTT
28078208 GTATCGGTAGA
1 GTATCGGTAGA
28078219 ACTAGTACAG
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.35
Consensus pattern (21 bp):
GTATCGGTAGATGTATGACTT
Found at i:28084355 original size:15 final size:15
Alignment explanation
Indices: 28084337--28084367 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28084327 ATACAATGAC
*
28084337 AACATCAACAACAAT
1 AACAACAACAACAAT
28084352 AACAACAACAACAAT
1 AACAACAACAACAAT
28084367 A
1 A
28084368 TTCTCAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.65, C:0.26, G:0.00, T:0.10
Consensus pattern (15 bp):
AACAACAACAACAAT
Found at i:28091551 original size:24 final size:23
Alignment explanation
Indices: 28091515--28091561 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
28091505 ACAATTCAAT
*
28091515 TTTATCTTAATTTCCTTTGACAA
1 TTTATCTTAATTTCCATTGACAA
* *
28091538 TTTATTTTATATTTGCATTGACAA
1 TTTATCTTA-ATTTCCATTGACAA
28091562 ATTAACTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.28, C:0.13, G:0.06, T:0.53
Consensus pattern (23 bp):
TTTATCTTAATTTCCATTGACAA
Found at i:28093983 original size:27 final size:27
Alignment explanation
Indices: 28093915--28094029 Score: 110
Period size: 27 Copynumber: 4.3 Consensus size: 27
28093905 CCACACTTCT
* *
28093915 TTTAGAGTATGCCACAAAGGCAATTCA
1 TTTAGATTATGCCACAAAGGCTATTCA
*
28093942 CTTAG-TGTATGCCACAAAGGCTATTCA
1 TTTAGAT-TATGCCACAAAGGCTATTCA
** *
28093969 TTTAGATTACACCACAAGGGCTATTC-
1 TTTAGATTATGCCACAAAGGCTATTCA
* *
28093995 TTTCAGAGTT-TGGCACAAAGGCTATTCT
1 TTT-AGA-TTATGCCACAAAGGCTATTCA
28094023 TTTAGAT
1 TTTAGAT
28094030 AGTATTGTGG
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
26 4 0.06
27 62 0.86
28 6 0.08
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (27 bp):
TTTAGATTATGCCACAAAGGCTATTCA
Found at i:28107169 original size:29 final size:29
Alignment explanation
Indices: 28107127--28107182 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
28107117 CTTTGACCTG
*
28107127 TAAAACGCGTCCAAGTCAACGCGCTTTAC
1 TAAAACGCGTCCAAGTCAACGCACTTTAC
* * *
28107156 TAAAGCGCTTCCAAGTCAGCGCACTTT
1 TAAAACGCGTCCAAGTCAACGCACTTT
28107183 TGCTCGTGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (29 bp):
TAAAACGCGTCCAAGTCAACGCACTTTAC
Found at i:28107278 original size:21 final size:21
Alignment explanation
Indices: 28107222--28107281 Score: 66
Period size: 22 Copynumber: 2.8 Consensus size: 21
28107212 TAAATAGGGT
* *
28107222 TTAGGGTTTATAAAATTAAGG
1 TTAGGGTTTTTTAAATTAAGG
* **
28107243 TTGTGGGAATTTTAAATTAAGG
1 TT-AGGGTTTTTTAAATTAAGG
28107265 TTAGGGTTTTTTAAATT
1 TTAGGGTTTTTTAAATT
28107282 TTGAAGGGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (21 bp):
TTAGGGTTTTTTAAATTAAGG
Found at i:28109991 original size:38 final size:38
Alignment explanation
Indices: 28109957--28110241 Score: 288
Period size: 38 Copynumber: 7.5 Consensus size: 38
28109947 GATGTTTTTT
* *
28109957 GGGCTTTGTGCCTAGTAGACTTTATACCGGTGTTTATC
1 GGGCTTTGTGCCTAGCAGACTTTATGCCGGTGTTTATC
* * **
28109995 GGGCTTTGTGCTTAGCA-AGTTTTATGCTAGTGTTTATC
1 GGGCTTTGTGCCTAGCAGA-CTTTATGCCGGTGTTTATC
* * * * *
28110033 AGGCTTTATGCCTAACAGGCTTTATGCCAGTGTTTATC
1 GGGCTTTGTGCCTAGCAGACTTTATGCCGGTGTTTATC
** * * * *
28110071 GAACTTTATGCCTAGTAGGCTTTATGCCGATGTTTTATC
1 GGGCTTTGTGCCTAGCAGACTTTATGCCGGTG-TTTATC
* *
28110110 GGGCTTTGTGCCTAGTAGGA-TTTATCCCGGTGTTTATC
1 GGGCTTTGTGCCTAGCA-GACTTTATGCCGGTGTTTATC
*
28110148 GGGCTTTGTGCCTAGCATG-CTTTATGCCGATGTTTATC
1 GGGCTTTGTGCCTAGCA-GACTTTATGCCGGTGTTTATC
* * *
28110186 GGGCTTTGTGCCTAGCAGGCTATATGCCGATGTTTATC
1 GGGCTTTGTGCCTAGCAGACTTTATGCCGGTGTTTATC
* *
28110224 GTGCTTAGTGCCTAGCAG
1 GGGCTTTGTGCCTAGCAG
28110242 GCTTCGTGCT
Statistics
Matches: 208, Mismatches: 33, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
37 2 0.01
38 175 0.84
39 30 0.14
40 1 0.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (38 bp):
GGGCTTTGTGCCTAGCAGACTTTATGCCGGTGTTTATC
Found at i:28110235 original size:76 final size:76
Alignment explanation
Indices: 28109946--28110245 Score: 318
Period size: 76 Copynumber: 3.9 Consensus size: 76
28109936 AGTGATTTAA
* * * * * * * *
28109946 CGATGTTTTTTGGGCTTTGTGCCTAGTAGACTTTATACCGGTGTTTATCGGGCTTTGTGCTTAGC
1 CGATGTTTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGATGTTTATCGGGCTTAGTGCCTAGC
* *
28110011 AAGTTTTATG-
66 AGGCTTTATGC
* * * * **
28110021 CTAGTGTTTATCAGGCTTTATGCCTAACAGGCTTTATGCC-AGTGTTTATCGAACTTTA-TGCCT
1 CGA-TGTTTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGA-TGTTTATCGGGC-TTAGTGCCT
*
28110084 AGTAGGCTTTATGC
63 AGCAGGCTTTATGC
* * * * *
28110098 CGATGTTTTATCGGGCTTTGTGCCTAGTAGGATTTATCCCGGTGTTTATCGGGCTTTGTGCCTAG
1 CGATG-TTTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGATGTTTATCGGGCTTAGTGCCTAG
*
28110163 CATGCTTTATGC
65 CAGGCTTTATGC
* *
28110175 CGATGTTTATCGGGCTTTGTGCCTAGCAGGCTATATGCCGATGTTTATCGTGCTTAGTGCCTAGC
1 CGATGTTTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGATGTTTATCGGGCTTAGTGCCTAGC
28110240 AGGCTT
66 AGGCTT
28110246 CGTGCTGTGG
Statistics
Matches: 180, Mismatches: 38, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
75 2 0.01
76 114 0.63
77 64 0.36
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.40
Consensus pattern (76 bp):
CGATGTTTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGATGTTTATCGGGCTTAGTGCCTAGC
AGGCTTTATGC
Found at i:28110236 original size:153 final size:152
Alignment explanation
Indices: 28109946--28110245 Score: 410
Period size: 153 Copynumber: 2.0 Consensus size: 152
28109936 AGTGATTTAA
* *
28109946 CGATGTTTTTTGGGCTTTGTGCCTAGTAGACTTTATACCGGTGTTTATCGGGCTTTGTGCTTAGC
1 CGATGTTTTTCGGGCTTTGTGCCTAGTAGACTTTATACCGGTGTTTATCGGGCTTTGTGCCTAGC
* * *
28110011 AAGTTTTATGCTAGTGTTTATCAGGCTTTATGCCTAACAGGCTTTATGCCAGTGTTTATCGAACT
66 AAGCTTTATGCGAGTGTTTATCAGGCTTTATGCCTAACAGGCTATATGCCAGTGTTTATCGAACT
*
28110076 TTATGCCTAGTAGGCTTTATGC
131 TTATGCCTAGCAGGCTTTATGC
*
28110098 CGATGTTTTATCGGGCTTTGTGCCTAGTAGGA-TTTATCCCGGTGTTTATCGGGCTTTGTGCCTA
1 CGATGTTTT-TCGGGCTTTGTGCCTAGTA-GACTTTATACCGGTGTTTATCGGGCTTTGTGCCTA
* * * *
28110162 GCATGCTTTATGCCGA-TGTTTATCGGGCTTTGTGCCTAGCAGGCTATATGCC-GATGTTTATCG
64 GCAAGCTTTATG-CGAGTGTTTATCAGGCTTTATGCCTAACAGGCTATATGCCAG-TGTTTATCG
**
28110225 TGC-TTAGTGCCTAGCAGGCTT
127 AACTTTA-TGCCTAGCAGGCTT
28110246 CGTGCTGTGG
Statistics
Matches: 130, Mismatches: 13, Indels: 9
0.86 0.09 0.06
Matches are distributed among these distances:
152 13 0.10
153 113 0.87
154 4 0.03
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.40
Consensus pattern (152 bp):
CGATGTTTTTCGGGCTTTGTGCCTAGTAGACTTTATACCGGTGTTTATCGGGCTTTGTGCCTAGC
AAGCTTTATGCGAGTGTTTATCAGGCTTTATGCCTAACAGGCTATATGCCAGTGTTTATCGAACT
TTATGCCTAGCAGGCTTTATGC
Found at i:28115318 original size:38 final size:38
Alignment explanation
Indices: 28115266--28115519 Score: 242
Period size: 38 Copynumber: 6.7 Consensus size: 38
28115256 TATTGTACGA
*
28115266 TGTTTATC-AGGCTTTGTGCCTAGCAGACTTTATACCGG
1 TGTTTATCGA-GCTTTGTGCCTAGCAGACTTTATGCCGG
* * *
28115304 TGTTTATCGAGCTTTGTGCCTAGCAGGCTATGTGCCGG
1 TGTTTATCGAGCTTTGTGCCTAGCAGACTTTATGCCGG
* * * *
28115342 TGTTTATCGGGCTTTATGCCTAGTAGGCTTTATGCCGG
1 TGTTTATCGAGCTTTGTGCCTAGCAGACTTTATGCCGG
* * **
28115380 TGTTTATTGGGCTTTGTGCCTAGCA-AGCTTTATGTTGG
1 TGTTTATCGAGCTTTGTGCCTAGCAGA-CTTTATGCCGG
* ** *
28115418 TGTTTATCGAGCTTTGTGCCTAACAGACTTTATGTTGA
1 TGTTTATCGAGCTTTGTGCCTAGCAGACTTTATGCCGG
* * * * * * * *
28115456 TGTTTATTGGGCTTTATGCCTAGTAGGCTATGTGCCAG
1 TGTTTATCGAGCTTTGTGCCTAGCAGACTTTATGCCGG
* *
28115494 TATTTATCGAGCTTAGTGCCTAGCAG
1 TGTTTATCGAGCTTTGTGCCTAGCAG
28115520 GCTTCGTGCT
Statistics
Matches: 176, Mismatches: 37, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
38 174 0.99
39 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.39
Consensus pattern (38 bp):
TGTTTATCGAGCTTTGTGCCTAGCAGACTTTATGCCGG
Found at i:28115394 original size:76 final size:76
Alignment explanation
Indices: 28115266--28115519 Score: 287
Period size: 76 Copynumber: 3.3 Consensus size: 76
28115256 TATTGTACGA
* * * *
28115266 TGTTTATC-AGGCTTTGTGCCTAGCAGACTTTATACCGGTGTTTATCGAGCTTTGTGCCTAGCAG
1 TGTTTATCGA-GCTTTATGCCTAGCAGACTTTATGCCGGTGTTTATTGGGCTTTGTGCCTAGCAG
28115330 GCTATGTGCCGG
65 GCTATGTGCCGG
* * * *
28115342 TGTTTATCGGGCTTTATGCCTAGTAGGCTTTATGCCGGTGTTTATTGGGCTTTGTGCCTAGCAAG
1 TGTTTATCGAGCTTTATGCCTAGCAGACTTTATGCCGGTGTTTATTGGGCTTTGTGCCTAGCAGG
* * **
28115407 CTTTATGTTGG
66 CTATGTGCCGG
* * ** * * *
28115418 TGTTTATCGAGCTTTGTGCCTAACAGACTTTATGTTGATGTTTATTGGGCTTTATGCCTAGTAGG
1 TGTTTATCGAGCTTTATGCCTAGCAGACTTTATGCCGGTGTTTATTGGGCTTTGTGCCTAGCAGG
*
28115483 CTATGTGCCAG
66 CTATGTGCCGG
*
28115494 TATTTATCGAGC-TTAGTGCCTAGCAG
1 TGTTTATCGAGCTTTA-TGCCTAGCAG
28115520 GCTTCGTGCT
Statistics
Matches: 145, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
75 2 0.01
76 143 0.99
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.39
Consensus pattern (76 bp):
TGTTTATCGAGCTTTATGCCTAGCAGACTTTATGCCGGTGTTTATTGGGCTTTGTGCCTAGCAGG
CTATGTGCCGG
Found at i:28115468 original size:114 final size:114
Alignment explanation
Indices: 28115266--28115556 Score: 332
Period size: 114 Copynumber: 2.6 Consensus size: 114
28115256 TATTGTACGA
* * * *
28115266 TGTTTATCAGGCTTTGTGCCTAGC-AGACTTTATACCGGTGTTTATCGAGCTTTGTGCCTAGCAG
1 TGTTTATCGGGCTTTGTGCCTAGCAAG-CTTTATGCTGGTGTTTATCGAGCTTTGTGCCTAACAG
* * * * *
28115330 GCTATGTGCCGGTGTTTATCGGGCTTTATGCCTAGTAGGCTTTATGCCGG
65 ACTATATGCCGATGTTTATCGGGCTTTATGCCTAGTAGGCTATATGCCAG
* *
28115380 TGTTTATTGGGCTTTGTGCCTAGCAAGCTTTATGTTGGTGTTTATCGAGCTTTGTGCCTAACAGA
1 TGTTTATCGGGCTTTGTGCCTAGCAAGCTTTATGCTGGTGTTTATCGAGCTTTGTGCCTAACAGA
* ** * *
28115445 CTTTATGTTGATGTTTATTGGGCTTTATGCCTAGTAGGCTATGTGCCAG
66 CTATATGCCGATGTTTATCGGGCTTTATGCCTAGTAGGCTATATGCCAG
* * * * ** * * **
28115494 TATTTATCGAGCTTAGTGCCTAGCAGGCTTCGTGCTGGTGGTTATCAAGCTTAATGCCTAACA
1 TGTTTATCGGGCTTTGTGCCTAGCAAGCTTTATGCTGGTGTTTATCGAGCTTTGTGCCTAACA
28115557 AGCTCCTTGC
Statistics
Matches: 148, Mismatches: 28, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
114 146 0.99
115 2 0.01
ACGTcount: A:0.17, C:0.18, G:0.26, T:0.38
Consensus pattern (114 bp):
TGTTTATCGGGCTTTGTGCCTAGCAAGCTTTATGCTGGTGTTTATCGAGCTTTGTGCCTAACAGA
CTATATGCCGATGTTTATCGGGCTTTATGCCTAGTAGGCTATATGCCAG
Found at i:28115522 original size:38 final size:38
Alignment explanation
Indices: 28115266--28115553 Score: 197
Period size: 38 Copynumber: 7.6 Consensus size: 38
28115256 TATTGTACGA
* * * * *
28115266 TGTTTATC-AGGCTTTGTGCCTAGCAGACTTTATACCGG
1 TGTTTATCGA-GCTTAGTGCCTAGCAGGCTATGTGCCGG
*
28115304 TGTTTATCGAGCTTTGTGCCTAGCAGGCTATGTGCCGG
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTATGTGCCGG
* * * *
28115342 TGTTTATCGGGCTTTA-TGCCTAGTAGGCTTTATGCCGG
1 TGTTTATCGAGC-TTAGTGCCTAGCAGGCTATGTGCCGG
* * * * * * **
28115380 TGTTTATTGGGCTTTGTGCCTAGCAAGCTTTATGTTGG
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTATGTGCCGG
* * * * * ** *
28115418 TGTTTATCGAGCTTTGTGCCTAACAGACTTTATGTTGA
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTATGTGCCGG
* * * *
28115456 TGTTTATTGGGCTTTA-TGCCTAGTAGGCTATGTGCCAG
1 TGTTTATCGAGC-TTAGTGCCTAGCAGGCTATGTGCCGG
* *
28115494 TATTTATCGAGCTTAGTGCCTAGCAGGCT-TCGTGCTGG
1 TGTTTATCGAGCTTAGTGCCTAGCAGGCTAT-GTGCCGG
* * *
28115532 TGGTTATCAAGCTTAATGCCTA
1 TGTTTATCGAGCTTAGTGCCTA
28115554 ACAAGCTCCT
Statistics
Matches: 201, Mismatches: 43, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
37 6 0.03
38 190 0.95
39 5 0.02
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.39
Consensus pattern (38 bp):
TGTTTATCGAGCTTAGTGCCTAGCAGGCTATGTGCCGG
Found at i:28120352 original size:12 final size:12
Alignment explanation
Indices: 28120335--28120375 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
28120325 TTTTGAGAGC
28120335 ATAAAATAAAAG
1 ATAAAATAAAAG
*
28120347 ATAAAATAAAAT
1 ATAAAATAAAAG
*
28120359 AGAAAATAAAAG
1 ATAAAATAAAAG
28120371 -TAAAA
1 ATAAAA
28120376 GTTTGAGATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:28120357 original size:17 final size:17
Alignment explanation
Indices: 28120335--28120375 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
28120325 TTTTGAGAGC
28120335 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
28120352 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
28120369 AGTAAAA
1 A-TAAAA
28120376 GTTTGAGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:28126002 original size:25 final size:25
Alignment explanation
Indices: 28125972--28126021 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
28125962 ATCTAATTTG
28125972 ATTTCTGCTCAATTTTCTCTTATCT
1 ATTTCTGCTCAATTTTCTCTTATCT
28125997 ATTTCTGCTCAATTTTCTCTTATCT
1 ATTTCTGCTCAATTTTCTCTTATCT
28126022 GTTTGTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.16, C:0.24, G:0.04, T:0.56
Consensus pattern (25 bp):
ATTTCTGCTCAATTTTCTCTTATCT
Found at i:28126768 original size:21 final size:21
Alignment explanation
Indices: 28126744--28126790 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
28126734 ATTAACTTTT
28126744 ATTTGTTATTGA-T-TTGTTTCA
1 ATTT-TTATTGACTCTT-TTTCA
*
28126765 ATTTTTGTTGACTCTTTTTCA
1 ATTTTTATTGACTCTTTTTCA
28126786 ATTTT
1 ATTTT
28126791 CTTTTAGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 6 0.26
21 15 0.65
22 2 0.09
ACGTcount: A:0.17, C:0.09, G:0.11, T:0.64
Consensus pattern (21 bp):
ATTTTTATTGACTCTTTTTCA
Found at i:28140861 original size:17 final size:17
Alignment explanation
Indices: 28140839--28140877 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
28140829 CTCCACCTTG
* *
28140839 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
28140856 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
28140873 ACAAG
1 ACAAG
28140878 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:28145687 original size:17 final size:17
Alignment explanation
Indices: 28145665--28145697 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
28145655 TTTGAAAGCA
28145665 TAAAATA-AAAGATAAAC
1 TAAAATAGAAA-ATAAAC
28145682 TAAAATAGAAAATAAA
1 TAAAATAGAAAATAAA
28145698 GGAAAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.73, C:0.03, G:0.06, T:0.18
Consensus pattern (17 bp):
TAAAATAGAAAATAAAC
Found at i:28154230 original size:30 final size:31
Alignment explanation
Indices: 28154177--28154236 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
28154167 CTAATTGAGT
* * *
28154177 TTTAAAATTTTTACGTTTCATTTTTTTGTTG
1 TTTAAAATTTTTAAGTTTAATTTTTATGTTG
*
28154208 TTTAAAA-TTTTAATTTTAATTTTTATGTT
1 TTTAAAATTTTTAAGTTTAATTTTTATGTT
28154237 AATAAAAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (31 bp):
TTTAAAATTTTTAAGTTTAATTTTTATGTTG
Found at i:28164552 original size:11 final size:12
Alignment explanation
Indices: 28164525--28164562 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
28164515 GGGTTTAATC
28164525 AAACTAAAAATT
1 AAACTAAAAATT
28164537 AAACTAAAAATT
1 AAACTAAAAATT
*
28164549 -AACTAAAAAAT
1 AAACTAAAAATT
28164560 AAA
1 AAA
28164563 AATAAATTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (12 bp):
AAACTAAAAATT
Found at i:28166148 original size:17 final size:18
Alignment explanation
Indices: 28166126--28166169 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
28166116 AAACAGAAAC
*
28166126 TATTTTGTTAT-CACATT
1 TATTTTGTTATGCACAAT
28166143 TATTTTG-TATGCACAAT
1 TATTTTGTTATGCACAAT
*
28166160 TCTTTTGTTA
1 TATTTTGTTA
28166170 ACAGTCTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 3 0.13
17 18 0.78
18 2 0.09
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (18 bp):
TATTTTGTTATGCACAAT
Found at i:28195977 original size:16 final size:16
Alignment explanation
Indices: 28195956--28195997 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 16
28195946 AGCAACCGTT
28195956 TCTTTTCTTCTCTT-TC
1 TCTTTTCTTCT-TTCTC
28195972 TCTTTT-TT-TTTCTC
1 TCTTTTCTTCTTTCTC
28195986 TCTTTTCTTCTT
1 TCTTTTCTTCTT
28195998 AAATTAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 9 0.39
15 4 0.17
16 8 0.35
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTTTCTTCTTTCTC
Found at i:28200177 original size:5 final size:5
Alignment explanation
Indices: 28200169--28200193 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28200159 TGAGTTGAAT
28200169 GAAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA
28200194 ACACCATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:28201638 original size:19 final size:19
Alignment explanation
Indices: 28201578--28201644 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
28201568 TGCTATGTTT
28201578 CATTTAATTTTTTTATTTG
1 CATTTAATTTTTTTATTTG
* ** *
28201597 AAGCTATATTTTTGTTA-CT-
1 CATTTA-ATTTTT-TTATTTG
28201616 CATTTAATTTTTTTATTTG
1 CATTTAATTTTTTTATTTG
*
28201635 CATTTCATTT
1 CATTTAATTT
28201645 AATTTTTTAG
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
17 3 0.09
18 7 0.20
19 15 0.43
20 7 0.20
21 3 0.09
ACGTcount: A:0.22, C:0.09, G:0.06, T:0.63
Consensus pattern (19 bp):
CATTTAATTTTTTTATTTG
Found at i:28202728 original size:74 final size:73
Alignment explanation
Indices: 28202585--28202729 Score: 204
Period size: 74 Copynumber: 2.0 Consensus size: 73
28202575 CGATTATTCT
** * *
28202585 TTATTAATGGAGAAGGTAAATGGAAAGTTAGAAAAGAAATTATATTTTTTCCAAAAGAATATAGG
1 TTATTAAAAGAGAAGGCAAATGGAAAGTTAGAAAAGAAATTATATTCTTTCCAAAAGAATATA-G
28202650 ATTTTTCCC
65 ATTTTTCCC
28202659 TTATTAAAAGAGAAGGCAAATGGAAAGTTAGAAAA-ATGAATTATATTCTTTCCAAAAGAATATT
1 TTATTAAAAGAGAAGGCAAATGGAAAGTTAGAAAAGA--AATTATATTCTTTCCAAAAGAATA-T
28202723 A-ATTTTT
63 AGATTTTT
28202730 ATGTCTTTTA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
73 1 0.02
74 38 0.59
75 23 0.36
76 2 0.03
ACGTcount: A:0.44, C:0.06, G:0.16, T:0.34
Consensus pattern (73 bp):
TTATTAAAAGAGAAGGCAAATGGAAAGTTAGAAAAGAAATTATATTCTTTCCAAAAGAATATAGA
TTTTTCCC
Found at i:28203015 original size:138 final size:138
Alignment explanation
Indices: 28202697--28203116 Score: 633
Period size: 138 Copynumber: 3.0 Consensus size: 138
28202687 TAGAAAAATG
* *
28202697 AATTATATTCTTTCCAAAAGAATATTAATTTTTATGTCTTTTATATTTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * *
28202762 TATAACTGTTTATATTAATAAATTCGGTAAAACACATATACAATTAATACTTTGTATGGATCAAA
66 TATAACTATTTATATTAATAAATTCGGT-AAA-ATATATACAATTAATAATTTGTATGAATTAAA
*
28202827 TTAATATATT
129 TTCATATATT
* *
28202837 AATTATATTCTTTACAAAAGAATATTATTTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* *
28202902 TATAACTATTTATATTAATAAATTCAGTAAAATATATACAATTAATAATTTGTATGAATTAAGTT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTGTATGAATTAAATT
28202967 CATATATT
131 CATATATT
* * * *
28202975 AATTATATTCTTTCCAAAAGAATATTAATTTCCACGTCTTTTATATTCTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * *
28203040 TATAATTTTTTATATTAATAAATTCGGTAAAATATATAAAATTAATATTTTGCATGAATTAAATT
66 TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTGTATGAATTAAATT
28203105 CATATATT
131 CATATATT
28203113 AATT
1 AATT
28203117 TTATCTATGT
Statistics
Matches: 255, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
138 165 0.65
139 3 0.01
140 87 0.34
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTATTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTGTATGAATTAAATT
CATATATT
Found at i:28203222 original size:21 final size:21
Alignment explanation
Indices: 28203183--28203222 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
28203173 TTAACTATCA
*
28203183 AATTTAATTAATTTAACAATT
1 AATTTAATTAATGTAACAATT
* *
28203204 AATTTAATTCATGTGACAA
1 AATTTAATTAATGTAACAA
28203223 CAAAATACAA
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:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
AATTTAATTAATGTAACAATT
Found at i:28204858 original size:66 final size:66
Alignment explanation
Indices: 28204780--28204982 Score: 170
Period size: 66 Copynumber: 3.1 Consensus size: 66
28204770 TAATGGTCAA
*
28204780 CAATTTTCCATTTAATCCTTTAATTAATCTTATCAATATCCTATAACATGCAAGCTAACATATCA
1 CAATTTTCCATTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCAAGCTAACATATCA
28204845 T
66 T
* * * * ** * *
28204846 CAATTTTTCATTTAAT-ATTTTATTGAAGGGT-TTTTAAAT-T-AAATTAATC-T-C-ACCATTA
1 CAATTTTCCATTTAATCCTTTAATT-AA---TCTTATAAATATCCTA-TAA-CATGCAAGC-TAA
* *
28204904 -ATGGTCAA
59 CAT-ATCAT
*
28204912 CAATTTTCCATTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCATGCTAACATATCA
1 CAATTTTCCATTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCAAGCTAACATATCA
28204977 T
66 T
28204978 CAATT
1 CAATT
28204983 GTATCATATA
Statistics
Matches: 99, Mismatches: 22, Indels: 32
0.65 0.14 0.21
Matches are distributed among these distances:
63 1 0.01
64 8 0.08
65 15 0.15
66 53 0.54
67 14 0.14
68 7 0.07
69 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.05, T:0.42
Consensus pattern (66 bp):
CAATTTTCCATTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCAAGCTAACATATCA
T
Found at i:28204962 original size:132 final size:132
Alignment explanation
Indices: 28204725--28204982 Score: 498
Period size: 132 Copynumber: 2.0 Consensus size: 132
28204715 CAATCTTAAA
28204725 TTAATATTTTATTGAAGGGTTTTTAAATTAAATTAATCTCACCATTAATGGTCAACAATTTTCCA
1 TTAATATTTTATTGAAGGGTTTTTAAATTAAATTAATCTCACCATTAATGGTCAACAATTTTCCA
*
28204790 TTTAATCCTTTAATTAATCTTATCAATATCCTATAACATGCAAGCTAACATATCATCAATTTTTC
66 TTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCAAGCTAACATATCATCAATTTTTC
28204855 AT
131 AT
28204857 TTAATATTTTATTGAAGGGTTTTTAAATTAAATTAATCTCACCATTAATGGTCAACAATTTTCCA
1 TTAATATTTTATTGAAGGGTTTTTAAATTAAATTAATCTCACCATTAATGGTCAACAATTTTCCA
*
28204922 TTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCATGCTAACATATCATCAATT
66 TTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCAAGCTAACATATCATCAATT
28204983 GTATCATATA
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.36, C:0.16, G:0.06, T:0.42
Consensus pattern (132 bp):
TTAATATTTTATTGAAGGGTTTTTAAATTAAATTAATCTCACCATTAATGGTCAACAATTTTCCA
TTTAATCCTTTAATTAATCTTATAAATATCCTATAACATGCAAGCTAACATATCATCAATTTTTC
AT
Found at i:28206582 original size:19 final size:19
Alignment explanation
Indices: 28206516--28206588 Score: 69
Period size: 19 Copynumber: 3.8 Consensus size: 19
28206506 ACTTGTTTGA
28206516 AAAAT-ATTTTGAAC-TGTT
1 AAAATCATTTT-AACTTGTT
* *
28206534 AAAATGATTTTGACTTAGTT
1 AAAATCATTTTAACTT-GTT
* * *
28206554 CAAATTATTTTCACTTGTT
1 AAAATCATTTTAACTTGTT
28206573 AAAATCATTTTAACTT
1 AAAATCATTTTAACTT
28206589 AATTTTAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
18 7 0.16
19 22 0.49
20 16 0.36
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.47
Consensus pattern (19 bp):
AAAATCATTTTAACTTGTT
Found at i:28207383 original size:140 final size:139
Alignment explanation
Indices: 28207108--28207527 Score: 605
Period size: 138 Copynumber: 3.0 Consensus size: 139
28207098 TAGAAAAATG
* * *
28207108 AATTATATTATTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTAACTGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * **
28207173 TATAATTGTTTATATTAATAAATTTGAAAAAATATGTATACAATTAATATTTTGTATGAATCAAA
66 TATAACTGTTTATATTAATAAATTCGGTAAAATA--TATACAATTAATATTTTGTATGAATCAAA
28207238 TT-TATATATT
129 TTCTATATATT
*
28207248 AATTATATTCTTTTTAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
28207313 TCTAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
28207378 CT-TATATT
131 CTATATATT
* ** * *
28207386 AATTATATTCTTTCCAAAAGAATACCAATTTTCAGGCCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * * *
28207451 TAT-ACTTATTTATATTAATAAATTCAGTAATATATATAAAATTAATATTTTGAATGAATAAAAT
66 TATAAC-TGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
28207515 TC-ATATATT
130 TCTATATATT
28207524 AATT
1 AATT
28207528 TTATCTATGT
Statistics
Matches: 255, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
137 2 0.01
138 162 0.64
139 1 0.00
140 90 0.35
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (139 bp):
AATTATATTCTTTTCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CTATATATT
Found at i:28210415 original size:28 final size:28
Alignment explanation
Indices: 28210378--28210501 Score: 121
Period size: 28 Copynumber: 4.4 Consensus size: 28
28210368 TTATTCGACC
*
28210378 AAATCCAGAATAATGCTCTTTTGAGCCA
1 AAATACAGAATAATGCTCTTTTGAGCCA
* *
28210406 AAATACAGAATAACGTTCTTTCT-AGCCA
1 AAATACAGAATAATGCTCTTT-TGAGCCA
* *
28210434 GAATACAGAATAATGCTCTTTCGAGCCA
1 AAATACAGAATAATGCTCTTTTGAGCCA
*
28210462 GAATAC-GAA-ATAT-CTCTCTTTCGAGCCA
1 AAATACAGAATA-ATGCTCT-TTT-GAGCCA
*
28210490 AAATACAAAATA
1 AAATACAGAATA
28210502 TTTCTTAAGC
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
26 5 0.06
27 7 0.09
28 63 0.80
29 3 0.04
30 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.27
Consensus pattern (28 bp):
AAATACAGAATAATGCTCTTTTGAGCCA
Found at i:28210446 original size:56 final size:56
Alignment explanation
Indices: 28210371--28210501 Score: 153
Period size: 56 Copynumber: 2.4 Consensus size: 56
28210361 AAATGGCTTA
* *
28210371 TTCGA-CC-AAATCCAGAATAATGCTCTTTTGAGCCAAAATAC-AGAATAACGT-TCT
1 TTCGAGCCAAAATACAGAATAATGCTCTTTCGAGCCAAAATACGA-AATAAC-TCTCT
* * * *
28210425 TTCTAGCCAGAATACAGAATAATGCTCTTTCGAGCCAGAATACGAAATATCTCTCT
1 TTCGAGCCAAAATACAGAATAATGCTCTTTCGAGCCAAAATACGAAATAACTCTCT
*
28210481 TTCGAGCCAAAATACAAAATA
1 TTCGAGCCAAAATACAGAATA
28210502 TTTCTTAAGC
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
54 4 0.06
55 3 0.05
56 56 0.88
57 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.27
Consensus pattern (56 bp):
TTCGAGCCAAAATACAGAATAATGCTCTTTCGAGCCAAAATACGAAATAACTCTCT
Found at i:28221155 original size:21 final size:21
Alignment explanation
Indices: 28221131--28221172 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
28221121 TCAGTAAACA
28221131 ATTCAAAAATTGAGCGAAATT
1 ATTCAAAAATTGAGCGAAATT
28221152 ATTCAAAAATTGAGCGAAATT
1 ATTCAAAAATTGAGCGAAATT
28221173 CTATCGATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.29
Consensus pattern (21 bp):
ATTCAAAAATTGAGCGAAATT
Found at i:28226355 original size:158 final size:157
Alignment explanation
Indices: 28226068--28226372 Score: 412
Period size: 158 Copynumber: 1.9 Consensus size: 157
28226058 CTCCATAACC
* *
28226068 TGTAATGCTCACACGAGCTATGAAATGGCCTGCTCACACGAGCTGTGGGTTGAGATGTTGGGCTA
1 TGTAATGCTCACACGAGCTATGAAATGGCCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTA
* ** * * ** * * * *
28226133 CATGATGCTGCTCACACGAGCTGTGGAGAATCCGCAATAAATGTTGGGTCTCATCCGTTAGTAGG
66 CACGATGCAACTCACACGAGCTATAGAGAATCCGCAATAAATGTCAGATCTCAGCCATAAGTAGG
*
28226198 ACATCTAGGACCAGCACCCATAGAACT
131 ACATCTAAGACCAGCACCCATAGAACT
* * *
28226225 TGTAATGGTCACACGAGCTATGAAATGAGCCTGCTCACATGAGTTGTGGGTCGAGATGTTAGGCT
1 TGTAATGCTCACACGAGCTATGAAATG-GCCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCT
** * *
28226290 ACACGATGCAACTCACACGAGCTATAGAGAATCCGTGATAAATGTCAGATCTTAGCTATAAGTAG
65 ACACGATGCAACTCACACGAGCTATAGAGAATCCGCAATAAATGTCAGATCTCAGCCATAAGTAG
28226355 GACATCTAAGACCAGCAC
130 GACATCTAAGACCAGCAC
28226373 TCGTATAACA
Statistics
Matches: 126, Mismatches: 21, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
157 26 0.21
158 100 0.79
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.24
Consensus pattern (157 bp):
TGTAATGCTCACACGAGCTATGAAATGGCCTGCTCACACGAGCTGTGGGTCGAGATGTTAGGCTA
CACGATGCAACTCACACGAGCTATAGAGAATCCGCAATAAATGTCAGATCTCAGCCATAAGTAGG
ACATCTAAGACCAGCACCCATAGAACT
Found at i:28229761 original size:52 final size:52
Alignment explanation
Indices: 28229678--28229802 Score: 191
Period size: 52 Copynumber: 2.4 Consensus size: 52
28229668 TGATATTCAT
* * *
28229678 GATGGCACATAGTTATCGGACCTCATAATCCGAAAAGGATTCATATGCTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGAAAAGGATTCATATACTCAC
* *
28229730 GATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATATACTCAC
1 GATGACACATAGTCATCGGACCTCATAATCCGAAAAGGATTCATATACTCAC
28229782 GATGACAC--AGTCATCGGACCT
1 GATGACACATAGTCATCGGACCT
28229803 TTTGCATTTA
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 12 0.18
52 55 0.82
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (52 bp):
GATGACACATAGTCATCGGACCTCATAATCCGAAAAGGATTCATATACTCAC
Found at i:28230374 original size:18 final size:16
Alignment explanation
Indices: 28230343--28230378 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
28230333 CCTCAATACC
28230343 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
28230359 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
28230377 AT
1 AT
28230379 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:28231989 original size:14 final size:15
Alignment explanation
Indices: 28231970--28232003 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
28231960 ACCAACTTTT
*
28231970 AATTCAATAATT-AA
1 AATTCAACAATTCAA
28231984 AATTCAACAATTCAA
1 AATTCAACAATTCAA
28231999 AATTC
1 AATTC
28232004 CATATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (15 bp):
AATTCAACAATTCAA
Found at i:28236298 original size:21 final size:21
Alignment explanation
Indices: 28236274--28236317 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
28236264 CTACCAGTAG
* * *
28236274 AAGTGGAAGTTCTATCGATAC
1 AAGTAGAAGTACTATCAATAC
*
28236295 AAGTATAAGTACTATCAATAC
1 AAGTAGAAGTACTATCAATAC
28236316 AA
1 AA
28236318 CCCATACTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (21 bp):
AAGTAGAAGTACTATCAATAC
Found at i:28236408 original size:21 final size:19
Alignment explanation
Indices: 28236382--28236424 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
28236372 AACTTTTACT
*
28236382 GATACTACTGAACAGACTACC
1 GATACTACT-AA-AAACTACC
*
28236403 GATACTTCTAAAAACTACC
1 GATACTACTAAAAACTACC
28236422 GAT
1 GAT
28236425 TCTTGGGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 10 0.50
20 2 0.10
21 8 0.40
ACGTcount: A:0.40, C:0.26, G:0.12, T:0.23
Consensus pattern (19 bp):
GATACTACTAAAAACTACC
Found at i:28239308 original size:15 final size:17
Alignment explanation
Indices: 28239288--28239320 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28239278 GACTCAAAAT
28239288 TTAT-AAATT-TATAAA
1 TTATAAAATTATATAAA
28239303 TTATAAAATTATATAAA
1 TTATAAAATTATATAAA
28239320 T
1 T
28239321 AAAAGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATAAAATTATATAAA
Found at i:28241369 original size:6 final size:6
Alignment explanation
Indices: 28241358--28241387 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
28241348 GTATGTAAAT
28241358 ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA
1 ATGTAA ATGTAA ATGTAA ATGTAA ATGTAA
28241388 TGAACTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATGTAA
Found at i:28255801 original size:31 final size:31
Alignment explanation
Indices: 28255760--28255864 Score: 192
Period size: 31 Copynumber: 3.4 Consensus size: 31
28255750 CTTACCTATG
*
28255760 AAGGAAAAACTTTGAACCAATTCATAAGTAT
1 AAGGAAAAACTTGGAACCAATTCATAAGTAT
*
28255791 AAAGAAAAACTTGGAACCAATTCATAAGTAT
1 AAGGAAAAACTTGGAACCAATTCATAAGTAT
28255822 AAGGAAAAACTTGGAACCAATTCATAAGTAT
1 AAGGAAAAACTTGGAACCAATTCATAAGTAT
28255853 AAGGAAAAACTT
1 AAGGAAAAACTT
28255865 CTACTTATGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 71 1.00
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.23
Consensus pattern (31 bp):
AAGGAAAAACTTGGAACCAATTCATAAGTAT
Found at i:28275488 original size:39 final size:39
Alignment explanation
Indices: 28275445--28275540 Score: 113
Period size: 39 Copynumber: 2.5 Consensus size: 39
28275435 AAACACTGCG
* *
28275445 ATGCAATACT-AAGCTGACGGTAACACTGTAAATATCGTA
1 ATGCAATACTGAA-CTGACGGTAACACTATAAATACCGTA
* * *
28275484 ATGCAATACTGAACTGATGTTAACCCTATAAATACCGTA
1 ATGCAATACTGAACTGACGGTAACACTATAAATACCGTA
* *
28275523 ATGTAGTACTGAACTGAC
1 ATGCAATACTGAACTGAC
28275541 AGTGACATTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 46 0.96
40 2 0.04
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (39 bp):
ATGCAATACTGAACTGACGGTAACACTATAAATACCGTA
Found at i:28280183 original size:15 final size:15
Alignment explanation
Indices: 28280146--28280184 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
28280136 TTATGTGCGC
*
28280146 TTAATTCTTGATTTA
1 TTAATTCTTGATATA
*
28280161 GT-ATTCTTGATATA
1 TTAATTCTTGATATA
28280175 TTAATTCTTG
1 TTAATTCTTG
28280185 TTTGATGTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.56
Consensus pattern (15 bp):
TTAATTCTTGATATA
Found at i:28282548 original size:11 final size:11
Alignment explanation
Indices: 28282532--28282565 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
28282522 TCATGTTTTT
28282532 AAAAAAATTGA
1 AAAAAAATTGA
28282543 AAAAAAA-T-A
1 AAAAAAATTGA
28282552 AAAAAAATTGA
1 AAAAAAATTGA
28282563 AAA
1 AAA
28282566 GTTCAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
9 8 0.38
10 2 0.10
11 11 0.52
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAAAAATTGA
Found at i:28282636 original size:28 final size:28
Alignment explanation
Indices: 28282587--28282647 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
28282577 AATTAGTATA
* ***
28282587 TTTATTTTCATTTTATTTTATTTTTATT
1 TTTATTTTCATTATACACTATTTTTATT
28282615 TTTATTTTCATTATACACTATTTTTATT
1 TTTATTTTCATTATACACTATTTTTATT
*
28282643 CTTAT
1 TTTAT
28282648 GTTTTTTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTATTTTCATTATACACTATTTTTATT
Found at i:28284659 original size:23 final size:25
Alignment explanation
Indices: 28284633--28284678 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28284623 CCAATTAAGG
28284633 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
28284656 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
28284679 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:28287454 original size:52 final size:52
Alignment explanation
Indices: 28287397--28287496 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
28287387 ACAGTTTTAC
*
28287397 AATAGAAAGTTGCACTTCTCTAATTTGATCAACCAACACTGATTTAACTCTT
1 AATAGAAAGTTGCACTTCTCTAATTTGATCAACCAACACTGAGTTAACTCTT
* *
28287449 AATAGAAAGTTGCGCTTCTCTAATTTGATCAACCAATACTGAGTTAAC
1 AATAGAAAGTTGCACTTCTCTAATTTGATCAACCAACACTGAGTTAAC
28287497 CGAATATTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (52 bp):
AATAGAAAGTTGCACTTCTCTAATTTGATCAACCAACACTGAGTTAACTCTT
Found at i:28290061 original size:16 final size:16
Alignment explanation
Indices: 28290039--28290094 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
28290029 CGTTTGGTTC
*
28290039 GCTGTAATAGAATAGA
1 GCTGTAATGGAATAGA
*
28290055 ACTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28290071 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28290087 GCTGTAAT
1 GCTGTAAT
28290095 CAGTAATTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.39, C:0.07, G:0.27, T:0.27
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:28290129 original size:46 final size:44
Alignment explanation
Indices: 28290076--28290169 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
28290066 ATAGAGCTGT
* *
28290076 AATGGAATAGAGCTGTAATCAGTAATTCAAT-TGTTTGGTTGATTGG
1 AATGGAATAGAGCTGTAAT-AAT-ATTC-ATGTGTTTGGTTGAATGG
*
28290122 AATGGAATAGAGCTGTAATAATATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
28290166 AATG
1 AATG
28290170 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 2 0.05
46 19 0.43
ACGTcount: A:0.31, C:0.05, G:0.27, T:0.37
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAATAATATTCATGTGTTTGGTTGAATGG
Found at i:28290333 original size:58 final size:56
Alignment explanation
Indices: 28290264--28290409 Score: 179
Period size: 58 Copynumber: 2.5 Consensus size: 56
28290254 AATTTTAATG
*
28290264 ATTATTATTAAATATAATTTAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
* *
28290322 ATTATTATTAAATAAAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
28290380 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
28290410 TATAATATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
57 3 0.04
58 43 0.55
59 15 0.19
60 10 0.13
61 7 0.09
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.47
Consensus pattern (56 bp):
ATTATTATTAAATATAATTTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:28294396 original size:25 final size:25
Alignment explanation
Indices: 28294364--28294412 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
28294354 TAAAACTTGT
28294364 AGTCTTATTTCTTAATCCTAAACTG
1 AGTCTTATTTCTTAATCCTAAACTG
28294389 AGTCTTATTTCTTAATCCTAAACT
1 AGTCTTATTTCTTAATCCTAAACT
28294413 AATATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (25 bp):
AGTCTTATTTCTTAATCCTAAACTG
Found at i:28295484 original size:139 final size:139
Alignment explanation
Indices: 28295234--28295654 Score: 754
Period size: 139 Copynumber: 3.0 Consensus size: 139
28295224 TAAGCAACAC
*
28295234 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGTAACATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
28295299 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
66 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
28295364 AACAGAATG
131 AACAGAATG
28295373 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
*
28295438 TATTTGTACAACCAGCAACACATTGAACCCCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
66 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
*
28295503 AACAAAATG
131 AACAGAATG
* * * *
28295512 TCAATATTTGGGTCTCAAAACACAGTTTCTACAAACATGGTTGTGCAAAATCGGAAGCAATATAA
1 TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
*
28295577 TATTTGTACAA-TAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
66 TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
28295641 AACAGAATG
131 AACAGAATG
*
28295650 GCAAT
1 TCAAT
28295655 GGATGATGAC
Statistics
Matches: 271, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
138 63 0.23
139 208 0.77
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (139 bp):
TCAATATTTGGGTCTCAAAACACAGTTTCTGCAAACATGGTTGTGCAGAATCAGAAGCAACATAA
TATTTGTACAACCAGCAACACATTGAACCTCCTAGAACAAAATAACAGAATCAACAAAGTATCCT
AACAGAATG
Found at i:28308806 original size:7 final size:7
Alignment explanation
Indices: 28308789--28308833 Score: 56
Period size: 7 Copynumber: 6.1 Consensus size: 7
28308779 GAGAATGAGG
28308789 AGGAA-A
1 AGGAAGA
28308795 AGGAAGA
1 AGGAAGA
28308802 AGGAAGA
1 AGGAAGA
28308809 AGGAAAAGA
1 AGG--AAGA
28308818 AGGAGAGA
1 AGGA-AGA
28308826 AGGAAGA
1 AGGAAGA
28308833 A
1 A
28308834 ATTTTTGTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
6 5 0.14
7 16 0.46
8 7 0.20
9 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AGGAAGA
Found at i:28308817 original size:16 final size:17
Alignment explanation
Indices: 28308798--28308830 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
28308788 GAGGAAAAGG
28308798 AAGAAGGA-AGAAGGAA
1 AAGAAGGAGAGAAGGAA
28308814 AAGAAGGAGAGAAGGAA
1 AAGAAGGAGAGAAGGAA
28308831 GAAATTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (17 bp):
AAGAAGGAGAGAAGGAA
Found at i:28313891 original size:40 final size:41
Alignment explanation
Indices: 28313847--28313937 Score: 94
Period size: 40 Copynumber: 2.2 Consensus size: 41
28313837 GGCTTGACCA
* * ** *
28313847 CATTATTGGTAGTTTATCTGCAATACTGGCAGC-TTATCTG
1 CATTATTGGTAGCTTAACCACAATACTGGCAGCACTATCTG
* * * *
28313887 CATTACTGGTGGCTTAACCACATTACTGGCAGCACTATTTG
1 CATTATTGGTAGCTTAACCACAATACTGGCAGCACTATCTG
28313928 CATTATTGGT
1 CATTATTGGT
28313938 GGCACTGTCC
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
40 26 0.65
41 14 0.35
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.37
Consensus pattern (41 bp):
CATTATTGGTAGCTTAACCACAATACTGGCAGCACTATCTG
Found at i:28313901 original size:20 final size:20
Alignment explanation
Indices: 28313810--28313902 Score: 71
Period size: 20 Copynumber: 4.7 Consensus size: 20
28313800 TTGTCTGTAC
* * *
28313810 TACTGGTAGTTTATTTGCAC
1 TACTGGTAGCTTATCTGCAT
* **
28313830 TACTGGTGGCTTGA-CCACAT
1 TACTGGTAGCTT-ATCTGCAT
* * *
28313850 TATTGGTAGTTTATCTGCAA
1 TACTGGTAGCTTATCTGCAT
*
28313870 TACTGGCAGCTTATCTGCAT
1 TACTGGTAGCTTATCTGCAT
*
28313890 TACTGGTGGCTTA
1 TACTGGTAGCTTA
28313903 ACCACATTAC
Statistics
Matches: 53, Mismatches: 18, Indels: 4
0.71 0.24 0.05
Matches are distributed among these distances:
19 1 0.02
20 51 0.96
21 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (20 bp):
TACTGGTAGCTTATCTGCAT
Found at i:28315947 original size:40 final size:40
Alignment explanation
Indices: 28315903--28315989 Score: 120
Period size: 40 Copynumber: 2.2 Consensus size: 40
28315893 CACCGGCATG
* * *
28315903 AAGCCTACTAGGCACAAAGCTCGATAAATACAATGGCACT
1 AAGCCTACTAGGCACAAAGCTCGATAAACACAACGACACT
* * *
28315943 AAGCCTTCTAGGCACTAAGCTCGATAAACACACCGACACT
1 AAGCCTACTAGGCACAAAGCTCGATAAACACAACGACACT
28315983 AAGCCTA
1 AAGCCTA
28315990 ATAAATACAC
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.38, C:0.29, G:0.16, T:0.17
Consensus pattern (40 bp):
AAGCCTACTAGGCACAAAGCTCGATAAACACAACGACACT
Found at i:28315993 original size:24 final size:24
Alignment explanation
Indices: 28315966--28316013 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28315956 ACTAAGCTCG
28315966 ATAAACACACC-GACACTAAGCCTA
1 ATAAACACACCAG-CACTAAGCCTA
*
28315990 ATAAATACACCAGCACTAAGCCTA
1 ATAAACACACCAGCACTAAGCCTA
28316014 CTAGGCACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 21 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.31, G:0.08, T:0.15
Consensus pattern (24 bp):
ATAAACACACCAGCACTAAGCCTA
Found at i:28318921 original size:18 final size:18
Alignment explanation
Indices: 28318884--28318921 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
28318874 TCACACAAAC
*
28318884 ATCACATCAACGAGTAAT
1 ATCACATCAACGAATAAT
28318902 ATCACA-CAACGAATATAT
1 ATCACATCAACGAATA-AT
28318920 AT
1 AT
28318922 AGCATAGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.47, C:0.21, G:0.08, T:0.24
Consensus pattern (18 bp):
ATCACATCAACGAATAAT
Found at i:28319434 original size:19 final size:20
Alignment explanation
Indices: 28319405--28319445 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
28319395 GTTGGTAAAA
28319405 AAAAGTCAACGATCAAAGTC
1 AAAAGTCAACGATCAAAGTC
28319425 AAAA-TCAACGATCAAAGTC
1 AAAAGTCAACGATCAAAGTC
28319444 AA
1 AA
28319446 CGAGTCGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.54, C:0.20, G:0.12, T:0.15
Consensus pattern (20 bp):
AAAAGTCAACGATCAAAGTC
Found at i:28321783 original size:15 final size:15
Alignment explanation
Indices: 28321763--28321792 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28321753 TTTTTTTTTC
28321763 GAATAGATTGATTTA
1 GAATAGATTGATTTA
*
28321778 GAATAGATTTATTTA
1 GAATAGATTGATTTA
28321793 ATAAAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (15 bp):
GAATAGATTGATTTA
Found at i:28322474 original size:10 final size:10
Alignment explanation
Indices: 28322459--28322493 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
28322449 AACCAACCAA
*
28322459 TAAATGATTC
1 TAAATGATTT
28322469 TAAATGATTTT
1 TAAATGA-TTT
28322480 TAAATGATTT
1 TAAATGATTT
28322490 TAAA
1 TAAA
28322494 GACTTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (10 bp):
TAAATGATTT
Found at i:28330276 original size:21 final size:21
Alignment explanation
Indices: 28330250--28330328 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
28330240 TTTTCATTTG
28330250 TATGTTTAAATCGATTGTTTA
1 TATGTTTAAATCGATTGTTTA
** *
28330271 TATGTTTATGAAT-G-TCCTTTT
1 TATGTTTA--AATCGATTGTTTA
* * *
28330292 TTTTTTTGAATCGATTGTTTA
1 TATGTTTAAATCGATTGTTTA
28330313 TATGTTTAAATCGATT
1 TATGTTTAAATCGATT
28330329 ATTACGTAAT
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
19 3 0.07
20 1 0.02
21 34 0.81
22 1 0.02
23 3 0.07
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.56
Consensus pattern (21 bp):
TATGTTTAAATCGATTGTTTA
Found at i:28331073 original size:18 final size:18
Alignment explanation
Indices: 28331050--28331085 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28331040 ACTTATTCTT
*
28331050 TTAAAGTTTAAATCTAAA
1 TTAAAGATTAAATCTAAA
*
28331068 TTAAAGATTAAATTTAAA
1 TTAAAGATTAAATCTAAA
28331086 ATTGAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (18 bp):
TTAAAGATTAAATCTAAA
Found at i:28331792 original size:22 final size:23
Alignment explanation
Indices: 28331764--28331823 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
28331754 ATTGAATTAA
*
28331764 TAATAATATTAATCATAACCA-T
1 TAATAATATTAATAATAACCATT
* *
28331786 TAATAATAATAATAATAACTATT
1 TAATAATATTAATAATAACCATT
28331809 TAATAATTATTAATA
1 TAATAA-TATTAATA
28331824 TTATTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.56
23 7 0.22
24 7 0.22
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TAATAATATTAATAATAACCATT
Found at i:28333028 original size:30 final size:30
Alignment explanation
Indices: 28332995--28333203 Score: 189
Period size: 30 Copynumber: 7.1 Consensus size: 30
28332985 CAAAATTGTA
*
28332995 TTTTAACCTCGAAAACTTTTAAAAATTACA-
1 TTTTAACCTC-AAAACTTTCAAAAATTACAT
* * *
28333025 TTTT--CCCCCAAACTTTCAAAAATTCCAT
1 TTTTAACCTCAAAACTTTCAAAAATTACAT
* *
28333053 TTTTAACCTTAAAACTTCCAAAAATTACAT
1 TTTTAACCTCAAAACTTTCAAAAATTACAT
* * * *
28333083 TTTTGACC-CTAAACTTCCCAAAATTACAT
1 TTTTAACCTCAAAACTTTCAAAAATTACAT
* *
28333112 TTTTGACCCCAAAACTTTCAAAAATTACA-
1 TTTTAACCTCAAAACTTTCAAAAATTACAT
* ** *
28333141 TTTTACCCT-TGAACTTCCAAAAATTACAT
1 TTTTAACCTCAAAACTTTCAAAAATTACAT
*
28333170 TTTTGA-CTCAAGAACTTTCAAAAATTACCAT
1 TTTTAACCTCAA-AACTTTCAAAAATTA-CAT
28333201 TTT
1 TTT
28333204 ACCCCTCAGA
Statistics
Matches: 144, Mismatches: 27, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
27 16 0.11
28 25 0.17
29 36 0.25
30 61 0.42
31 6 0.04
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (30 bp):
TTTTAACCTCAAAACTTTCAAAAATTACAT
Found at i:28333174 original size:58 final size:57
Alignment explanation
Indices: 28332995--28333207 Score: 257
Period size: 58 Copynumber: 3.6 Consensus size: 57
28332985 CAAAATTGTA
* * * * * *
28332995 TTTTAACCTCGAAAACTTTTAAAAATTACATTTTCCCCCAAACTTTCAAAAATTCCAT
1 TTTTGACCTC-AAAACTTTCAAAAATTACATTTTACCCTAAACTTCCAAAAATTACAT
* * * *
28333053 TTTTAACCTTAAAACTTCCAAAAATTACATTTTTGACCCTAAACTTCCCAAAATTACAT
1 TTTTGACCTCAAAACTTTCAAAAATTACA-TTTT-ACCCTAAACTTCCAAAAATTACAT
* *
28333112 TTTTGACCCCAAAACTTTCAAAAATTACATTTTACCCTTGAACTTCCAAAAATTACAT
1 TTTTGACCTCAAAACTTTCAAAAATTACATTTTACCC-TAAACTTCCAAAAATTACAT
28333170 TTTTGA-CTCAAGAACTTTCAAAAATTACCATTTTACCC
1 TTTTGACCTCAA-AACTTTCAAAAATTA-CATTTTACCC
28333208 CTCAGATGTC
Statistics
Matches: 135, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
57 25 0.19
58 56 0.41
59 54 0.40
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.36
Consensus pattern (57 bp):
TTTTGACCTCAAAACTTTCAAAAATTACATTTTACCCTAAACTTCCAAAAATTACAT
Found at i:28334893 original size:23 final size:22
Alignment explanation
Indices: 28334840--28334893 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
28334830 AAAATTCCAA
*
28334840 ATATATATAAAAACTATAAAAT
1 ATATAAATAAAAACTATAAAAT
* * *
28334862 ACAAAAAATAAAAATTATAAACAT
1 A-TATAAATAAAAACTATAAA-AT
28334886 ATATAAAT
1 ATATAAAT
28334894 TCTAAATATA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
22 1 0.04
23 20 0.83
24 3 0.12
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (22 bp):
ATATAAATAAAAACTATAAAAT
Found at i:28334899 original size:17 final size:17
Alignment explanation
Indices: 28334873--28334907 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
28334863 CAAAAAATAA
28334873 AAATTATAAACATATAT
1 AAATTATAAACATATAT
* *
28334890 AAATTCTAAATATATAT
1 AAATTATAAACATATAT
28334907 A
1 A
28334908 TGAAATAATT
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:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
AAATTATAAACATATAT
Found at i:28340055 original size:119 final size:118
Alignment explanation
Indices: 28339807--28340325 Score: 449
Period size: 119 Copynumber: 4.4 Consensus size: 118
28339797 TTTCAGAGAA
* ** * * ** * * **
28339807 TTTAGGGTTAAAATATAATTTTGGAAAAGTT-TAGGGT-AAAATACGGTTTTGGTAAAGTTTAAG
1 TTTAAGGTTAAAATGCAATTTTAGAAAAGTTAAAGGGTCAAAATGTGATTTTGGAAAAGTTTGGG
* ** * * * *
28339870 GTTAAAGTGTGGTTTTAGGAAAA-TTTA-GGGTCAAAATGTGATTTTAAGAAAG
66 GTTAAAATGTAATTTT-GGAAAAGTTTAGGGGTTAAAATATGATTTTAGGGAAG
* * * * * *
28339922 TGTGAGGGTCAAAATGCAATTTTGGAAAAGTTTAAAGGGTTAAAATGTGATTTTGGAAAAATTTG
1 T-TTAAGGTTAAAATGCAATTTTAGAAAAG-TTAAAGGGTCAAAATGTGATTTTGGAAAAGTTTG
* * *
28339987 GGAGTTAAAAATGTGATTTTGGGAAAGTTT-GGGGTTAAAATATGGTTTT-GGGAAG
64 GG-GTT-AAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATATGATTTTAGGGAAG
* * * *
28340042 TTTAAGGTTAAAATGTAATTTTCA-AAAAGTTTATGGGTCAAAATGTGATTGTGGAAAAGTTTGG
1 TTTAAGGTTAAAATGCAATTTT-AGAAAAGTTAAAGGGTCAAAATGTGATTTTGGAAAAGTTT-G
* * *
28340106 GGGTTTAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTTAAGGAAG
64 GGGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATATGATTTTAGGGAAG
* ** * * * * * *
28340161 TTTGACTTTAAAATGCAATTTTAGAGAAGTTAAAGGGTCAAAATATAATTTAGGAGAAGTTTAAG
1 TTTAAGGTTAAAATGCAATTTTAGAAAAGTTAAAGGGTCAAAATGTGATTTTGGAAAAGTTT-GG
* * *
28340226 GGTTAAAATGCAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTAGAGAAG
65 GGTTAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATATGATTTTAGGGAAG
* * * * *
28340280 TTTATGGGTTAAAATGTAATTTTTGAAAAGTTCAAGGGTTAAAATG
1 TTTA-AGGTTAAAATGCAATTTTAGAAAAGTTAAAGGGTCAAAATG
28340326 AAATTTTGAA
Statistics
Matches: 324, Mismatches: 66, Indels: 23
0.78 0.16 0.06
Matches are distributed among these distances:
115 1 0.00
116 24 0.07
117 22 0.07
118 54 0.17
119 149 0.46
120 45 0.14
121 29 0.09
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (118 bp):
TTTAAGGTTAAAATGCAATTTTAGAAAAGTTAAAGGGTCAAAATGTGATTTTGGAAAAGTTTGGG
GTTAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATATGATTTTAGGGAAG
Found at i:28340124 original size:179 final size:173
Alignment explanation
Indices: 28339823--28340325 Score: 473
Period size: 179 Copynumber: 2.8 Consensus size: 173
28339813 GTTAAAATAT
* * * **
28339823 AATTTTGGAAAAGTTTAGGG-TAAAATACGGTTTTGGTA-AAGTTTAAGGTTAAAGTGTGGTTTT
1 AATTTTGGGAAAGTTTAGGGTTAAAATATGGTTTTGG-AGAAGTTTAAGGTTAAAATGTAATTTT
* * *
28339886 AGGAAAA-TTTAGGGTCAAAATGTGATTTTA-AGAAAGTGTGAGGGTCAAAATGCAATTTTGGAA
65 A--AAAAGTTTAGGGTCAAAATGTGA-TTTAGA-AAAGTTTGAGGGTTAAAATGTAATTTTGGAA
* *
28339949 AAGTTTAAAGGGTTAAAATGTGATTTTGGAA-AAATTTGGGAGTTAAAAATGT
126 AAGTTT-AAGGGTTAAAATGTGATTTT--AAGAAATTT--GACTTAAAAATGC
* *
28340001 GATTTTGGGAAAGTTTGGGGTTAAAATATGGTTTTGG-GAAGTTTAAGGTTAAAATGTAATTTTC
1 AATTTTGGGAAAGTTTAGGGTTAAAATATGGTTTTGGAGAAGTTTAAGGTTAAAATGTAATTTT-
* * *
28340065 AAAAAGTTTATGGGTCAAAATGTGATTGTGGAAAAGTTTGGGGGTTTAAATGTAATTTTGGAAAA
65 AAAAAGTTTA-GGGTCAAAATGTGATT-TAGAAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAA
* * *
28340130 GTTTAGGGGTTAAAATGTGATTTTAAGGAAGTTTGACTTTAAAATGC
128 GTTTAAGGGTTAAAATGTGATTTTAA-GAAATTTGACTTAAAAATGC
* * * ** * *
28340177 AATTTT-AGAGAAGTTAAAGGGTCAAAATATAATTTAGGAGAAGTTTAAGGGTTAAAATGCAATT
1 AATTTTGGGA-AAGTT-TAGGGTTAAAATATGGTTTTGGAGAAGTTTAA-GGTTAAAATGTAATT
* * * * * *
28340241 TTGGAAAAGTTTAGGGGTTAAAATATAATTTTAGAGAAGTTT-ATGGGTTAAAATGTAATTTTTG
63 TT-AAAAAGTTTA-GGGTCAAAATGTGA-TTTAGAAAAGTTTGA-GGGTTAAAATGTAATTTTGG
*
28340305 AAAAGTTCAAGGGTTAAAATG
124 AAAAGTTTAAGGGTTAAAATG
28340326 AAATTTTGAA
Statistics
Matches: 270, Mismatches: 40, Indels: 29
0.80 0.12 0.09
Matches are distributed among these distances:
175 2 0.01
176 22 0.08
177 20 0.07
178 78 0.29
179 145 0.54
180 3 0.01
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.35
Consensus pattern (173 bp):
AATTTTGGGAAAGTTTAGGGTTAAAATATGGTTTTGGAGAAGTTTAAGGTTAAAATGTAATTTTA
AAAAGTTTAGGGTCAAAATGTGATTTAGAAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAAGTT
TAAGGGTTAAAATGTGATTTTAAGAAATTTGACTTAAAAATGC
Found at i:28340131 original size:60 final size:59
Alignment explanation
Indices: 28339807--28340325 Score: 410
Period size: 60 Copynumber: 8.8 Consensus size: 59
28339797 TTTCAGAGAA
* ** * *
28339807 TTTAGGGTTAAAATATAATTTTGGAAAAGTTT-AGGG-TAAAATACGGTTTTGGTAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAAAAG
* * ** * *
28339864 TTTAAGGTTAAAGTGTGGTTTTAGGAAAA-TTT-AGGGTCAAAATGTGATTTT-AAGAAAG
1 TTTAGGGTTAAAATGTAATTTT-GGAAAAGTTTAAGGGTTAAAATGTGATTTTGGA-AAAG
* * * *
28339922 TGTGAGGGTCAAAATGCAATTTTGGAAAAGTTTAAAGGGTTAAAATGTGATTTTGGAAAAA
1 T-TTAGGGTTAAAATGTAATTTTGGAAAAGTTT-AAGGGTTAAAATGTGATTTTGGAAAAG
* * * * * * *
28339983 TTTGGGAGTTAAAAATGTGATTTTGGGAAAGTTT-GGGGTTAAAATATGGTTTTGG-GAAG
1 TTTAGG-GTT-AAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAAAAG
* ** * * *
28340042 TTTAAGGTTAAAATGTAATTTTCAAAAAGTTTATGGGTCAAAATGTGATTGTGGAAAAG
1 TTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAAAAG
* * *
28340101 TTTGGGGGTTTAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTGATTTT--AAGGAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAA--AAG
** * * * * * * * * *
28340161 TTT-GACTTTAAAATGCAATTTTAGAGAAGTTAAAGGGTCAAAATATAATTTAGGAGAAG
1 TTTAG-GGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAAAAG
* * * * * *
28340220 TTTAAGGGTTAAAATGCAATTTTGGAAAAGTTTAGGGGTTAAAATATAATTTTAGAGAAG
1 TTT-AGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAAAAG
* *
28340280 TTTATGGGTTAAAATGTAATTTTTGAAAAGTTCAAGGGTTAAAATG
1 TTTA-GGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATG
28340326 AAATTTTGAA
Statistics
Matches: 362, Mismatches: 79, Indels: 39
0.75 0.16 0.08
Matches are distributed among these distances:
57 43 0.12
58 49 0.14
59 71 0.20
60 152 0.42
61 26 0.07
62 21 0.06
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (59 bp):
TTTAGGGTTAAAATGTAATTTTGGAAAAGTTTAAGGGTTAAAATGTGATTTTGGAAAAG
Found at i:28340162 original size:30 final size:30
Alignment explanation
Indices: 28339807--28340332 Score: 288
Period size: 30 Copynumber: 17.8 Consensus size: 30
28339797 TTTCAGAGAA
*
28339807 TTTA-GGGTTAAAATATAATTTT-GGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGG-AAAG
****
28339836 TTTA-GGG-TAAAATACGGTTTT-GGTAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGG-AAAG
* * ** *
28339864 TTTA-AGGTTAAAGTGTGGTTTTAGGAAAA
1 TTTAGGGGTTAAAATGTAATTTTAGGAAAG
* * *
28339893 TTTA-GGGTCAAAATGTGATTTTAAGAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGGAAAG
* * *
28339922 TGT-GAGGGTCAAAATGCAATTTT-GGAAAAG
1 TTTAG-GGGTTAAAATGTAATTTTAGG-AAAG
* * *
28339952 TTTAAAGGGTTAAAATGTGATTTT-GGAAAAA
1 TTT-AGGGGTTAAAATGTAATTTTAGG-AAAG
* *
28339983 TTT-GGGAGTTAAAAATGTGATTTTGGGAAAG
1 TTTAGGG-GTT-AAAATGTAATTTTAGGAAAG
* ** *
28340014 TTT-GGGGTTAAAATATGGTTTT-GGGAAG
1 TTTAGGGGTTAAAATGTAATTTTAGGAAAG
* *
28340042 TTTA-AGGTTAAAATGTAATTTTCA-AAAAG
1 TTTAGGGGTTAAAATGTAATTTT-AGGAAAG
* * * *
28340071 TTTATGGGTCAAAATGTGATTGT-GGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGG-AAAG
* *
28340101 TTTGGGGGTTTAAATGTAATTTT-GGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGG-AAAG
*
28340131 TTTAGGGGTTAAAATGTGATTTTAAGG-AAG
1 TTTAGGGGTTAAAATGTAATTTT-AGGAAAG
*** *
28340161 TTT-GACTTTAAAATGCAATTTTA-GAGAAG
1 TTTAGGGGTTAAAATGTAATTTTAGGA-AAG
* * * *
28340190 TTAAAGGGTCAAAATATAA-TTTAGGAGAAG
1 TTTAGGGGTTAAAATGTAATTTTAGGA-AAG
* *
28340220 TTTAAGGGTTAAAATGCAATTTT-GGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGG-AAAG
*
28340250 TTTAGGGGTTAAAATATAATTTTA-GAGAAG
1 TTTAGGGGTTAAAATGTAATTTTAGGA-AAG
* * *
28340280 TTTATGGGTTAAAATGTAATTTTTGAAAAG
1 TTTAGGGGTTAAAATGTAATTTTAGGAAAG
* * *
28340310 TTCAAGGGTTAAAATGAAATTTT
1 TTTAGGGGTTAAAATGTAATTTT
28340333 GAAACAAAAT
Statistics
Matches: 393, Mismatches: 77, Indels: 53
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.00
28 46 0.12
29 91 0.23
30 200 0.51
31 51 0.13
32 4 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.36
Consensus pattern (30 bp):
TTTAGGGGTTAAAATGTAATTTTAGGAAAG
Found at i:28341353 original size:86 final size:84
Alignment explanation
Indices: 28341179--28341380 Score: 244
Period size: 86 Copynumber: 2.4 Consensus size: 84
28341169 GCTTCATCTC
* * * *
28341179 TTGGTCTACTTCTTTGTATCTCATCAGGAAGATGATCGCTTCATTACTCTATCCACTTCTCTGTA
1 TTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGCCTCATTACTCTATCCACGTCTCTGTA
* *
28341244 TCTCATTAGGAAGATGGAT
66 TCTCATCAAGAAGATGGAT
* * * ** * *
28341263 TTGGTCTACTTCTCTGTATCTCATCAAGAAGATAACCTCCTCACTTGTTTTAATCCACGTCTTTG
1 TTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGCCTCA-TTACTCT-ATCCACGTCTCTG
28341328 TATCTCATCAAGAAGATGGAT
64 TATCTCATCAAGAAGATGGAT
*
28341349 TTGGTCCACCTT-TTTGTATCTCATCAGGAAGA
1 TTGGTCTA-CTTCTTTGTATCTCATCAGGAAGA
28341381 CTATCGCTTT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
84 37 0.37
85 4 0.04
86 55 0.56
87 3 0.03
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (84 bp):
TTGGTCTACTTCTTTGTATCTCATCAGGAAGATAACCGCCTCATTACTCTATCCACGTCTCTGTA
TCTCATCAAGAAGATGGAT
Found at i:28341561 original size:210 final size:209
Alignment explanation
Indices: 28341260--28341651 Score: 597
Period size: 210 Copynumber: 1.9 Consensus size: 209
28341250 TAGGAAGATG
* *
28341260 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATAACCTCCTCACTTGTTTTAATCCACGTCT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATAACCGCATCACTTGTTTTAATCCACGTCT
* * * * * *
28341325 TTGTATCTCATCAAGAAGATGGATTTGGTCCACCTT-TTTGTATCTCATCAGGAAGACTATCGCT
66 CTGTATCTCATCAAGAAGACGGATTTGGTCCA-CTTCTCTGTATCTCATCAGGAAGACGACCACT
* * *
28341389 TTATTGCTTTGACCTACTTCTTAGTATCTCATCAGGAAGATAGGGGTTTGAAGTTTCACTCACAT
130 TTATTGCTTTGACCCACTTCTCAGTATCTCATAAGGAAGAT-GGGGTTTGAAGTTTCACTCACAT
28341454 TGAGCTTCGCTTCATC
194 TGAGCTTCGCTTCATC
* * * * *
28341470 GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCT
1 GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATAACCGCATCACTTGTTTTAATCCACGTCT
* *
28341535 CTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGACGACCACTT
66 CTGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTT
28341600 TATTGCTTTGACCCACTTCTCAGTATCTCATAAGGAAGATGGGGTTTGAAGT
131 TATTGCTTTGACCCACTTCTCAGTATCTCATAAGGAAGATGGGGTTTGAAGT
28341652 CTCATTCAAC
Statistics
Matches: 163, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
209 15 0.09
210 148 0.91
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.36
Consensus pattern (209 bp):
GATTTGGTCTACTTCTCTGTATCTCATCAAGAAGATAACCGCATCACTTGTTTTAATCCACGTCT
CTGTATCTCATCAAGAAGACGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTT
TATTGCTTTGACCCACTTCTCAGTATCTCATAAGGAAGATGGGGTTTGAAGTTTCACTCACATTG
AGCTTCGCTTCATC
Found at i:28341764 original size:46 final size:46
Alignment explanation
Indices: 28341710--28342038 Score: 369
Period size: 46 Copynumber: 7.4 Consensus size: 46
28341700 ATGACCTAGT
*
28341710 GGTATGAGATCGGATGATGACTTCAATTTGCCCCTCTTGACTTAAG
1 GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
* * * *
28341756 GGTATGAGATTTGGATGATGGCTTCAATCTTCCCCTATTGACTTTTAAG
1 GGTATGAGA-TCGGATGATGACTTCAATCTGCCCCTCTTGAC--TTAAG
* * *
28341805 GGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCTTGACTTAGG
1 GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
28341851 GGTATGAGATCGGATGATGACTTCAATCTG---C-C----CTT---
1 GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
*
28341886 -GTATGAGATCGGATGATGACTTCAATCTGCCCTTCTTGACTTAAG
1 GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
* * * * * * * *
28341931 AGTGTGAGATTGGATGATGGCTTCGATCTGCCTCTTTTGACTCAAG
1 GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
*
28341977 GGTATGAGATCGGATGATGACTTCAAT-TGCCCTTCTTGACTTAAG
1 GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
*
28342022 GGTATGAGATTGGATGA
1 GGTATGAGATCGGATGA
28342039 CTGCAATCTG
Statistics
Matches: 239, Mismatches: 29, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
34 29 0.12
38 4 0.02
42 4 0.02
43 1 0.00
45 30 0.13
46 100 0.42
47 27 0.11
48 30 0.13
49 14 0.06
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.34
Consensus pattern (46 bp):
GGTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAG
Found at i:28341895 original size:34 final size:34
Alignment explanation
Indices: 28341852--28341919 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
28341842 TGACTTAGGG
28341852 GTATGAGATCGGATGATGACTTCAATCTGCCCTT
1 GTATGAGATCGGATGATGACTTCAATCTGCCCTT
28341886 GTATGAGATCGGATGATGACTTCAATCTGCCCTT
1 GTATGAGATCGGATGATGACTTCAATCTGCCCTT
28341920 CTTGACTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (34 bp):
GTATGAGATCGGATGATGACTTCAATCTGCCCTT
Found at i:28341939 original size:80 final size:80
Alignment explanation
Indices: 28341806--28341962 Score: 233
Period size: 80 Copynumber: 2.0 Consensus size: 80
28341796 ACTTTTAAGG
* * * *
28341806 GTATGAGATTGGATGATGGCTTCAATCTGCCCCTCTTGACTTAGGGGTATGAGATCGGATGATGA
1 GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAGAGTATGAGATCGGATGATGA
28341871 CTTCAATCTGCCCTT
66 CTTCAATCTGCCCTT
* * * *
28341886 GTATGAGATCGGATGATGACTTCAATCTGCCCTTCTTGACTTAAGAGTGTGAGATTGGATGATGG
1 GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAGAGTATGAGATCGGATGATGA
*
28341951 CTTCGATCTGCC
66 CTTCAATCTGCC
28341963 TCTTTTGACT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (80 bp):
GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAGAGTATGAGATCGGATGATGA
CTTCAATCTGCCCTT
Found at i:28341995 original size:126 final size:127
Alignment explanation
Indices: 28341757--28342010 Score: 368
Period size: 126 Copynumber: 2.0 Consensus size: 127
28341747 TGACTTAAGG
* * * *
28341757 GTATGAGATTTGGATGATGGCTTCAATCTTCCCCTATTGACTTTTAAGGGTATGAGATTGGATGA
1 GTATGAGATTCGGATGATGACTTCAATCTGCCCCTATTGAC-TTTAAGAGTATGAGATTGGATGA
* *
28341822 TGGCTTCAATCTGCCCCTCTTGACTTAGGGGTATGAGATCGGATGATGACTTCAATCTGCCCTT
65 TGGCTTCAATCTGCCCCTCTTGACTCAAGGGTATGAGATCGGATGATGACTTCAAT-TGCCCTT
* * *
28341886 GTATGAGA-TCGGATGATGACTTCAATCTGCCCTTCTTGAC-TTAAGAGTGTGAGATTGGATGAT
1 GTATGAGATTCGGATGATGACTTCAATCTGCCCCTATTGACTTTAAGAGTATGAGATTGGATGAT
* * *
28341949 GGCTTCGATCTGCCTCTTTTGACTCAAGGGTATGAGATCGGATGATGACTTCAATTGCCCTT
66 GGCTTCAATCTGCCCCTCTTGACTCAAGGGTATGAGATCGGATGATGACTTCAATTGCCCTT
28342011 CTTGACTTAA
Statistics
Matches: 113, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
125 7 0.06
126 71 0.63
128 27 0.24
129 8 0.07
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (127 bp):
GTATGAGATTCGGATGATGACTTCAATCTGCCCCTATTGACTTTAAGAGTATGAGATTGGATGAT
GGCTTCAATCTGCCCCTCTTGACTCAAGGGTATGAGATCGGATGATGACTTCAATTGCCCTT
Found at i:28342070 original size:39 final size:38
Alignment explanation
Indices: 28342021--28342124 Score: 109
Period size: 39 Copynumber: 2.7 Consensus size: 38
28342011 CTTGACTTAA
*
28342021 GGGTATGAGATTGGATGACTGCAATCTGCCCCACGATCG
1 GGGTAAGAGATTGGATG-CTGCAATCTGCCCCACGATCG
* ** * **
28342060 GGGTAAGAGATTGGATGGCTGTAATCTGCTTCATGATTT
1 GGGTAAGAGATTGGAT-GCTGCAATCTGCCCCACGATCG
* *
28342099 AGGTAAGAGATTGGATGCTTCAATCT
1 GGGTAAGAGATTGGATGCTGCAATCT
28342125 TTCCCGTCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 8 0.15
39 45 0.83
40 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (38 bp):
GGGTAAGAGATTGGATGCTGCAATCTGCCCCACGATCG
Found at i:28342213 original size:49 final size:50
Alignment explanation
Indices: 28342153--28342375 Score: 219
Period size: 49 Copynumber: 4.5 Consensus size: 50
28342143 AAGGTACTGG
* *
28342153 GTTCG-CCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTGCCG-
1 GTTCGTCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
* * * * *
28342201 GATTC-TCCGTTGCGGCCTTAATGC-TTCCCATCACATCTTCTAAGGTACCGA
1 G-TTCGTCCGTTGCGGCCTCAA-CCTTTCCCTTCAAATCTTC-ATGGTACCGA
* * * *
28342252 GTTCGT-TGTTACGGCTTCAACCTTTCCCTTCAAATCTTCATGATACCGA
1 GTTCGTCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
* *
28342301 GTTCGT-CGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGG
1 GTTCGTCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
* *
28342350 GTT--TACCGTTACGACCTCAACCTTTC
1 GTTCGT-CCGTTGCGGCCTCAACCTTTC
28342376 TTATCACAAT
Statistics
Matches: 144, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 105 0.73
50 35 0.24
51 2 0.01
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.34
Consensus pattern (50 bp):
GTTCGTCCGTTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
Found at i:28342275 original size:99 final size:98
Alignment explanation
Indices: 28342159--28342873 Score: 462
Period size: 99 Copynumber: 7.4 Consensus size: 98
28342149 CTGGGTTCGC
* * * * * *
28342159 CGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTGCCGGATTCTCCGTTGCGGCCTTAATG
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGGCCTCAA-C
*
28342224 C-TTCCCATCACATCTTCTAAGGTACCGAGTTCGT
65 CTTTCCCATCACATCTTCTAAGGTACCG-GTTCAT
* * * * *
28342258 TGTTACGGCTTCAACCTTTCCCTTCAAATCTTCATGATACC-GAGTTCGTCGTTGCGACCTCAAC
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGA-TTCGCCGTTGCGGCCTCAAC
* * * * *
28342322 CTTTCCCTTCAAATCTTC-ATGGTACCGGGTTTAC
65 CTTTCCCATCACATCTTCTAAGGTACC-GGTTCAT
* * * * * *
28342356 CGTTACGACCTCAACCTTT-CTTATCACAA--TTCATTGTACCGGATTCGCCATTGCGACCTTAA
1 CGTTACGGCCTCAACCTTTCCCT-TCA-AATCTTCATGGTACCGGATTCGCCGTTGCGGCCTCAA
** *
28342418 TCC-TTCCCATCATGTCTTTTAAGGTACCGGGTT--T
64 -CCTTTCCCATCACATCTTCTAAGGTACC-GGTTCAT
** * * * *
28342452 -G-T-C-G--T---TGTTTCCCTTCAAATCTTCATGGTATCGGGTTCGCCATTGTGGCCTCAACC
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGGCCTCAACC
* *
28342508 TTTCTCATCACACCTTCTAAGGTACCGGATTCAT
66 TTTCCCATCACATCTTCTAAGGTACCGG-TTCAT
* * * * * *
28342542 CGTTGCGGCCTCAATCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACC
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGGCCTCAACC
* * **
28342607 TTTCCCATCACATCTTTTAAAGTACCGGGTTCGC
66 TTTCCCATCACATCTTCTAAGGTACC-GGTTCAT
* * * * * * * * * *
28342641 CGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACTGGGTTCGCTGTTGTGGCCTTAAC
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGGATTCGCCGTTGCGGCCTCAAC
* * ** **
28342706 CTTTCCCTTCAAATCTTC-ATTGTACCGGGTTCCC
65 CTTTCCCATCACATCTTCTAAGGTACC-GGTTCAT
* ** * *** * * **
28342740 CGTTGCGGCCTCAACCTTTCCCACCACAT-TTCATGGTACCGGATTTATCGTTTCGGCCTGAATA
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGGCCTCAACC
* * *
28342804 TTTCCCATTACATCTTCTGAGGTACCAGGTTCTT
66 TTTCCCATCACATCTTCTAAGGTACC-GGTTCAT
* *** *
28342838 CGTTGCAATCTCAACCTTTTCCTTCAAATCTTCATG
1 CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATG
28342874 TTTTCTCAGT
Statistics
Matches: 483, Mismatches: 105, Indels: 56
0.75 0.16 0.09
Matches are distributed among these distances:
86 2 0.00
87 10 0.02
88 51 0.11
90 2 0.00
91 1 0.00
92 1 0.00
93 2 0.00
94 2 0.00
95 1 0.00
96 1 0.00
97 73 0.15
98 83 0.17
99 213 0.44
100 41 0.08
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.35
Consensus pattern (98 bp):
CGTTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGATTCGCCGTTGCGGCCTCAACC
TTTCCCATCACATCTTCTAAGGTACCGGTTCAT
Found at i:28342289 original size:50 final size:49
Alignment explanation
Indices: 28342153--28342780 Score: 211
Period size: 49 Copynumber: 13.0 Consensus size: 49
28342143 AAGGTACTGG
* * * * *
28342153 GTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTGCCG-
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
* * * * * * *
28342201 GATTC-TCCGTTGCGGCCTTAATGC-TTCCCATCACATCTTCTAAGGTACCGA
1 G-TTCGT-CGTTACGACCTCAA-CCTTTCCCTTCAAATCTTC-ATGGTACCGA
* * * *
28342252 GTTCGTTGTTACGGCTTCAACCTTTCCCTTCAAATCTTCATGATACCGA
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
* *
28342301 GTTCGTCGTTGCGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGG
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
*** * *
28342350 GTTTACCGTTACGACCTCAACCTTT-CTTATCACAA--TTCATTGTACCG-
1 GTTCGTCGTTACGACCTCAACCTTTCCCT-TCA-AATCTTCATGGTACCGA
* * * * * ** * * *
28342397 GATTCGCCATTGCGACCTTAATCC-TTCCCATCATGTCTTTTAAGGTACCGG
1 G-TTCGTCGTTACGACCTCAA-CCTTTCCCTTCAAATC-TTCATGGTACCGA
* * *
28342448 GTTTGTCGTT--G---------TTTCCCTTCAAATCTTCATGGTATCGG
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
* * ** * * * * * *
28342486 GTTCGCCATTGTGGCCTCAACCTTTCTCATCACACCTTCTAAGGTACCG-
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGA
* * * * * * *
28342535 GATTCATCGTTGCGGCCTCAATCTTTCCCTTCATATCTTCATGGTATCGG
1 G-TTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
** * * * * * ** *
28342585 GTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTAAAGTACCGG
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATC-TTCATGGTACCGA
* * * * * * * * *
28342635 GTTCGCCGTTGCGGCCTCAACCTTTTCCATCACATCTTCTAAGGTACTGG
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTC-ATGGTACCGA
** * * * *
28342685 GTTCG-CTGTTGTGGCCTTAACCTTTCCCTTCAAATCTTCATTGTACCGG
1 GTTCGTC-GTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
** * * ** *
28342734 GTTCCCCGTTGCGGCCTCAACCTTTCCCACCACAT-TTCATGGTACCG
1 GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCG
28342781 GATTTATCGT
Statistics
Matches: 448, Mismatches: 97, Indels: 70
0.73 0.16 0.11
Matches are distributed among these distances:
38 17 0.04
39 10 0.02
40 1 0.00
47 1 0.00
48 45 0.10
49 198 0.44
50 173 0.39
51 3 0.01
ACGTcount: A:0.17, C:0.31, G:0.17, T:0.34
Consensus pattern (49 bp):
GTTCGTCGTTACGACCTCAACCTTTCCCTTCAAATCTTCATGGTACCGA
Found at i:28342753 original size:149 final size:149
Alignment explanation
Indices: 28342483--28342768 Score: 414
Period size: 149 Copynumber: 1.9 Consensus size: 149
28342473 TTCATGGTAT
*
28342483 CGGGTTCGCCATTGTGGCCTCAACCTTTCTCATCACACCTTCTAAGGTACCGGATTCATCGTTGC
1 CGGGTTCGCCATTGCGGCCTCAACCTTTCTCATCACACCTTCTAAGGTACCGGATTCATCGTTGC
* * *
28342548 GGCCTCAATCTTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
66 GGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
*
28342613 ATCACATCTTTTAAAGTAC
131 ACCACATCTTTTAAAGTAC
* * * * *
28342632 CGGGTTCGCCGTTGCGGCCTCAACCTTT-TCCATCACATCTTCTAAGGTACTGGGTTC-GCTGTT
1 CGGGTTCGCCATTGCGGCCTCAACCTTTCT-CATCACACCTTCTAAGGTACCGGATTCATC-GTT
* * * *
28342695 GTGGCCTTAACCTTTCCCTTCAAATCTTCATTGTACCGGGTTCCCCGTTGCGGCCTCAACCTTTC
64 GCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTC
28342760 CCACCACAT
129 CCACCACAT
28342769 TTCATGGTAC
Statistics
Matches: 121, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
148 2 0.02
149 119 0.98
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.33
Consensus pattern (149 bp):
CGGGTTCGCCATTGCGGCCTCAACCTTTCTCATCACACCTTCTAAGGTACCGGATTCATCGTTGC
GGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCC
ACCACATCTTTTAAAGTAC
Found at i:28342865 original size:147 final size:148
Alignment explanation
Indices: 28342498--28342873 Score: 373
Period size: 149 Copynumber: 2.5 Consensus size: 148
28342488 TCGCCATTGT
* * * * ** *
28342498 GGCCTCAACCTTTCTCATCACACCTTCTAAGGTACC-GGATTC-ATCGTTGCGGCCTCAATCTTT
1 GGCCTCAACATTTCCCATCACATCTTCTAAGGTACCAGG-TTCGCT-GTTGCAACCTCAACCTTT
* * * *
28342561 CCCTTCATATCTTCATGGTATCGGGTTCACCGTTGCGGCCTCAACCTTTCCCATCACATCTTTTA
64 CCCTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCACCACA-CTTTCA
* *
28342626 AAGTACCGGGTTCGCCGTTGC
128 AAGTACCGGATTCACCGTTGC
* * ** *** *
28342647 GGCCTCAACCTTTTCCATCACATCTTCTAAGGTACTGGGTTCGCTGTTGTGGCCTTAACCTTTCC
1 GGCCTCAACATTTCCCATCACATCTTCTAAGGTACCAGGTTCGCTGTTGCAACCTCAACCTTTCC
* * **
28342712 CTTCAAATCTTCATTGTACCGGGTTCCCCGTTGCGGCCTCAACCTTTCCCACCACA-TTTCATGG
66 CTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCACCACACTTTCAAAG
* * *
28342776 TACCGGATTTATCGTTTC
131 TACCGGATTCACCGTTGC
* * * * * * *
28342794 GGCCTGAATATTTCCCATTACATCTTCTGAGGTACCAGGTTC-TTCGTTGCAATCTCAACCTTTT
1 GGCCTCAACATTTCCCATCACATCTTCTAAGGTACCAGGTTCGCT-GTTGCAACCTCAACCTTTC
28342858 CCTTCAAATCTTCATG
65 CCTTCAAATCTTCATG
28342874 TTTTCTCAGT
Statistics
Matches: 187, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
146 1 0.01
147 80 0.43
149 103 0.55
150 3 0.02
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.34
Consensus pattern (148 bp):
GGCCTCAACATTTCCCATCACATCTTCTAAGGTACCAGGTTCGCTGTTGCAACCTCAACCTTTCC
CTTCAAATCTTCATGGTACCGGGTTCACCGTTGCGGCCTCAACCTTTCCCACCACACTTTCAAAG
TACCGGATTCACCGTTGC
Found at i:28349053 original size:29 final size:29
Alignment explanation
Indices: 28349021--28349419 Score: 283
Period size: 30 Copynumber: 13.4 Consensus size: 29
28349011 TCAAAACATA
* *
28349021 ATTTTGGAAGAGTTTA-AGGTAAAAATGCG
1 ATTTTGGAA-AGTTTAGAGGTCAAAATGTG
*
28349050 ATTTTGGGAAATTTTA-AGGTCAAAATGTG
1 ATTTT-GGAAAGTTTAGAGGTCAAAATGTG
* *
28349079 GTTTTGGGAAAG-TTCGAGGTCAAAATGTG
1 ATTTT-GGAAAGTTTAGAGGTCAAAATGTG
* * *
28349108 ATTTTGAGAAAGTGTAGGGGTCAAAATGTA
1 ATTTTG-GAAAGTTTAGAGGTCAAAATGTG
* * *
28349138 ATTTTGGAAAAGTTTGAGGGGGTTAAAATGTT
1 ATTTTGG-AAAGTTT-A-GAGGTCAAAATGTG
* * *
28349170 ATTTTGGAAAAGTTTAGGAGTTAAAAATGTT
1 ATTTTGG-AAAGTTTA-GAGGTCAAAATGTG
*
28349201 ATTTTGGGAAAGTTTAG-GGTTAAAATGTG
1 ATTTT-GGAAAGTTTAGAGGTCAAAATGTG
* * *
28349230 GTTTTAAGAAAGTTTA-AGGTTAAAATGTG
1 ATTTT-GGAAAGTTTAGAGGTCAAAATGTG
* *
28349259 ATTTTAAGAAAGTTTAGAGGTCAAAATCTG
1 ATTTT-GGAAAGTTTAGAGGTCAAAATGTG
* *
28349289 ATTTTGGAAAAGTTTAGGGGTAAAAATGTG
1 ATTTTGG-AAAGTTTAGAGGTCAAAATGTG
* * *
28349319 ATTTTAGAAAAGTTTAG-GGT--TAATGTA
1 ATTTT-GGAAAGTTTAGAGGTCAAAATGTG
* * * * *
28349346 AATTTGGAAAATTTTAGGGGTCAAAATATA
1 ATTTTGG-AAAGTTTAGAGGTCAAAATGTG
* * *
28349376 ATTTTGGAGAAGTTTAGGGGTAAAAATATG
1 ATTTTGGA-AAGTTTAGAGGTCAAAATGTG
*
28349406 ATTTTTGTAAAGTT
1 A-TTTTGGAAAGTT
28349420 CGATGGTTAA
Statistics
Matches: 309, Mismatches: 43, Indels: 35
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.00
27 17 0.06
28 6 0.02
29 108 0.35
30 114 0.37
31 34 0.11
32 29 0.09
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (29 bp):
ATTTTGGAAAGTTTAGAGGTCAAAATGTG
Found at i:28349132 original size:30 final size:29
Alignment explanation
Indices: 28349007--28349419 Score: 284
Period size: 29 Copynumber: 13.9 Consensus size: 29
28348997 CAAAGAATTT
** *
28349007 GGGGTCAAAACATAATTTTGGAAGAGTTTA
1 GGGGTCAAAATGTGATTTTGGAA-AGTTTA
* * * *
28349037 -AGGTAAAAATGCGATTTTGGGAAATTTTA
1 GGGGTCAAAATGTGATTTT-GGAAAGTTTA
* * *
28349066 -AGGTCAAAATGTGGTTTTGGGAAAG-TTC
1 GGGGTCAAAATGTGATTTT-GGAAAGTTTA
* *
28349094 GAGGTCAAAATGTGATTTTGAGAAAGTGTA
1 GGGGTCAAAATGTGATTTTG-GAAAGTTTA
*
28349124 GGGGTCAAAATGTAATTTTGGAAAAGTTTGA
1 GGGGTCAAAATGTGATTTTGG-AAAGTTT-A
* *
28349155 GGGGGTTAAAATGTTATTTTGGAAAAGTTTA
1 -GGGGTCAAAATGTGATTTTGG-AAAGTTTA
* * *
28349186 GGAGTTAAAAATGTTATTTTGGGAAAGTTTA
1 GG-GGTCAAAATGTGATTTT-GGAAAGTTTA
* * *
28349217 -GGGTTAAAATGTGGTTTTAAGAAAGTTTA
1 GGGGTCAAAATGTGATTTT-GGAAAGTTTA
* * *
28349246 -AGGTTAAAATGTGATTTTAAGAAAGTTTA
1 GGGGTCAAAATGTGATTTT-GGAAAGTTTA
* *
28349275 GAGGTCAAAATCTGATTTTGGAAAAGTTTA
1 GGGGTCAAAATGTGATTTTGG-AAAGTTTA
* *
28349305 GGGGTAAAAATGTGATTTTAGAAAAGTTTA
1 GGGGTCAAAATGTGATTTT-GGAAAGTTTA
* * * *
28349335 -GGGT--TAATGTAAATTTGGAAAATTTTA
1 GGGGTCAAAATGTGATTTTGG-AAAGTTTA
* *
28349362 GGGGTCAAAATATAATTTTGGAGAAGTTTA
1 GGGGTCAAAATGTGATTTTGGA-AAGTTTA
* * *
28349392 GGGGTAAAAATATGATTTTTGTAAAGTT
1 GGGGTCAAAATGTGA-TTTTGGAAAGTT
28349420 CGATGGTTAA
Statistics
Matches: 316, Mismatches: 49, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.00
27 16 0.05
28 7 0.02
29 116 0.37
30 115 0.36
31 32 0.10
32 29 0.09
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (29 bp):
GGGGTCAAAATGTGATTTTGGAAAGTTTA
Found at i:28349274 original size:89 final size:89
Alignment explanation
Indices: 28349021--28349433 Score: 320
Period size: 87 Copynumber: 4.6 Consensus size: 89
28349011 TCAAAACATA
* * * * * * * * *
28349021 ATTTTGGAAGAGTTTA-AGGTAAAAATGCGATTTTGGGAAATTTTAAGGTCAAAATGTGGTTTTG
1 ATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAGTTTAAGGTTAAAATGTGATTTTA
* * * *
28349085 GGAAAG-TTCGAGGTCAAAATGTG
66 GAAAAGTTTAGAGGTAAAAATCTG
* * * * * *
28349108 ATTTT-GAGAAAGTGTAGGGGTCAAAATGTAATTTTGGAAAAGTTTGAGGGGGTTAAAATGTTAT
1 ATTTTGGA-AAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAGTTT-A--AGGTTAAAATGTGAT
* * * *
28349172 TTTGGAAAAGTTTAGGAGTTAAAAATGTT
62 TTTAGAAAAGTTTA-GAGGTAAAAATCTG
* * *
28349201 ATTTTGGGAAAGTTTA-GGGTTAAAATGTGGTTTTA-AGAAAGTTTAAGGTTAAAATGTGATTTT
1 ATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGA-AAAGTTTAAGGTTAAAATGTGATTTT
*
28349264 A-AGAAAGTTTAGAGGTCAAAATCTG
65 AGA-AAAGTTTAGAGGTAAAAATCTG
* * * *
28349289 ATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAGTTTAGGGTT--AATGTAAATTTG
1 ATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAGTTTAAGGTTAAAATGTGATTTTA
* * * * *
28349352 GAAAATTTTAGGGGTCAAAATATA
66 GAAAAGTTTAGAGGTAAAAATCTG
* * * * * *
28349376 ATTTTGGAGAAGTTTAGGGGTAAAAATATGATTTTTGTAAAGTTCGATGGTTAAAATG
1 ATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAGTT-TAAGGTTAAAATG
28349434 AAATTTTGGA
Statistics
Matches: 263, Mismatches: 47, Indels: 29
0.78 0.14 0.09
Matches are distributed among these distances:
86 2 0.01
87 78 0.30
88 54 0.21
89 54 0.21
90 5 0.02
91 22 0.08
92 24 0.09
93 23 0.09
94 1 0.00
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (89 bp):
ATTTTGGAAAAGTTTAGGGGTAAAAATGTGATTTTAGAAAAGTTTAAGGTTAAAATGTGATTTTA
GAAAAGTTTAGAGGTAAAAATCTG
Found at i:28351358 original size:21 final size:21
Alignment explanation
Indices: 28351332--28351382 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
28351322 TACCCTGTAC
28351332 TTCTACCGATACATGCATAAG
1 TTCTACCGATACATGCATAAG
28351353 TTCTACCGATACATGCATAAG
1 TTCTACCGATACATGCATAAG
28351374 TTCTACCGA
1 TTCTACCGA
28351383 AACAAGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACATGCATAAG
Found at i:28352483 original size:28 final size:28
Alignment explanation
Indices: 28352443--28352498 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28352433 TGATATTATG
28352443 AAAGAAAAATGTCATTTTAATTCTTTAA
1 AAAGAAAAATGTCATTTTAATTCTTTAA
28352471 AAAGAAAAATGTCATTTTAATTCTTTAA
1 AAAGAAAAATGTCATTTTAATTCTTTAA
28352499 TTTCACTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (28 bp):
AAAGAAAAATGTCATTTTAATTCTTTAA
Found at i:28353911 original size:50 final size:49
Alignment explanation
Indices: 28353846--28354122 Score: 195
Period size: 50 Copynumber: 5.5 Consensus size: 49
28353836 CAGTACTGCA
* * * *
28353846 AAAAGACAAAAGGGAAAGGTCTAAGTCGCAATAGCAGACCGTGTACCTC
1 AAAAGACAGACGGGAAAGATCTAAGTCGCAATAGCGGACCGTGTACCTC
* * * *
28353895 AGAAGACACGACGGGAAAGATCTAAGATCGCAATGGCGGATCC-AGTACCGTA
1 AAAAGACA-GACGGGAAAGATCTAAG-TCGCAATAGCGGA-CCGTGTACC-TC
* * * *
28353947 AAAAGACAAAAGGGAAAGGTCTAAGTCGTAA-AGGCGGACCGTGTACCTC
1 AAAAGACAGACGGGAAAGATCTAAGTCGCAATA-GCGGACCGTGTACCTC
* * * * * * *
28353996 AGAAGACATGACGGGAAAGATCTATGACCGCAA-CGACGGATC-TAGCACCGTA
1 AAAAGACA-GACGGGAAAGATCTAAG-TCGCAATAG-CGGACCGT-GTACC-TC
* * * * *
28354048 AAAAGACAAAAGGGAAAGGTTTAAGTCGCAAT-GACAGACCGTGTACCTC
1 AAAAGACAGACGGGAAAGATCTAAGTCGCAATAG-CGGACCGTGTACCTC
28354097 AAAAGACACGACGGGAAAGATCTAAG
1 AAAAGACA-GACGGGAAAGATCTAAG
28354123 ACCGTAATGG
Statistics
Matches: 172, Mismatches: 42, Indels: 27
0.71 0.17 0.11
Matches are distributed among these distances:
49 26 0.15
50 72 0.42
51 56 0.33
52 18 0.10
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.14
Consensus pattern (49 bp):
AAAAGACAGACGGGAAAGATCTAAGTCGCAATAGCGGACCGTGTACCTC
Found at i:28353927 original size:101 final size:101
Alignment explanation
Indices: 28353778--28354159 Score: 527
Period size: 101 Copynumber: 3.8 Consensus size: 101
28353768 AGTTGCAACG
* * * *
28353778 GCAGGCCGTGTACCTCAGAGGACATC-ATGGAAAAGATCTAAGACCGCAACGGCGGATCCAGTAC
1 GCAGACCGTGTACCTCAGAAGACA-CGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC
*
28353842 TGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAATA
65 CGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAATA
* *
28353879 GCAGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGATCGCAATGGCGGATCCAGTACC
1 GCAGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC
* *
28353944 GTAAAAAGACAAAAGGGAAAGGTCTAAGTCGTAA-A
66 GCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAATA
* * * * * *
28353979 GGCGGACCGTGTACCTCAGAAGACATGACGGGAAAGATCTATGACCGCAACGACGGATCTAGCAC
1 -GCAGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC
* *
28354044 CGTAAAAAGACAAAAGGGAAAGGTTTAAGTCGCAAT-
65 CGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAATA
* * *
28354080 GACAGACCGTGTACCTCAAAAGACACGACGGGAAAGATCTAAGACCGTAATGGCGGATCCAGTAC
1 G-CAGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTAC
*
28354145 CGCAAAAAGATAAAA
65 CGCAAAAAGACAAAA
28354160 TGGGCAAGCT
Statistics
Matches: 247, Mismatches: 30, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
100 3 0.01
101 244 0.99
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.14
Consensus pattern (101 bp):
GCAGACCGTGTACCTCAGAAGACACGACGGGAAAGATCTAAGACCGCAACGGCGGATCCAGTACC
GCAAAAAGACAAAAGGGAAAGGTCTAAGTCGCAATA
Found at i:28354134 original size:202 final size:202
Alignment explanation
Indices: 28353783--28354159 Score: 594
Period size: 202 Copynumber: 1.9 Consensus size: 202
28353773 CAACGGCAGG
* * * * *
28353783 CCGTGTACCTCAGAGGACATCATGGAAAAGATCTAAGACCGCAACGGCGGATCCAGTACTGCAAA
1 CCGTGTACCTCAGAAGACATCACGGAAAAGATCTAAGACCGCAACGACGGATCCAGCACCGCAAA
*
28353848 AAGACAAAAGGGAAAGGTCTAAGTCGCAATAGCAGACCGTGTACCTCAGAAGACACGACGGGAAA
66 AAGACAAAAGGGAAAGGTCTAAGTCGCAATAGCAGACCGTGTACCTCAAAAGACACGACGGGAAA
* *
28353913 GATCTAAGATCGCAATGGCGGATCCAGTACCGTAAAAAGACAAAAGGGAAAGGTCTAAGTCGTAA
131 GATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGTAA
28353978 AGGCGGA
196 AGGCGGA
* * * * *
28353985 CCGTGTACCTCAGAAGACATGACGGGAAAGATCTATGACCGCAACGACGGATCTAGCACCGTAAA
1 CCGTGTACCTCAGAAGACATCACGGAAAAGATCTAAGACCGCAACGACGGATCCAGCACCGCAAA
*
28354050 AAGACAAAAGGGAAAGGTTTAAGTCGCAAT-GACAGACCGTGTACCTCAAAAGACACGACGGGAA
66 AAGACAAAAGGGAAAGGTCTAAGTCGCAATAG-CAGACCGTGTACCTCAAAAGACACGACGGGAA
* *
28354114 AGATCTAAGACCGTAATGGCGGATCCAGTACCGCAAAAAGATAAAA
130 AGATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAAAGACAAAA
28354160 TGGGCAAGCT
Statistics
Matches: 158, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
201 1 0.01
202 157 0.99
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.14
Consensus pattern (202 bp):
CCGTGTACCTCAGAAGACATCACGGAAAAGATCTAAGACCGCAACGACGGATCCAGCACCGCAAA
AAGACAAAAGGGAAAGGTCTAAGTCGCAATAGCAGACCGTGTACCTCAAAAGACACGACGGGAAA
GATCTAAGACCGCAATGGCGGATCCAGTACCGCAAAAAGACAAAAGGGAAAGGTCTAAGTCGTAA
AGGCGGA
Found at i:28354752 original size:201 final size:201
Alignment explanation
Indices: 28354390--28355638 Score: 1717
Period size: 201 Copynumber: 6.2 Consensus size: 201
28354380 GCGATTATCC
* * * * * **
28354390 ATAAGTGAGGCAGTCATCTTCCTGATAAGATACAGAGAAGTATACCAACTCAAGGCTCAAAATGA
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCAACGCTCAATGTGA
* * *
28354455 GCAAAGCTTCGAA-CCCAGCTTCCTAATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTT
66 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
28354519 AGCTTCCTGATGAGATAC-AGAGAAGTGAACCAAATTCAGCTTCCTGATGAGATACA-ATGAAGC
131 AGCTTCCTGATGAGATACTA-AGAAGTGAACCAAATTCAGCTTCCTGATGAGATACAGA-GAAGC
*
28354582 GAATTGAA
194 GAATTAAA
*
28354590 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCGACGCTCAATGTGA
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCAACGCTCAATGTGA
* * *
28354655 GCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGTCGAAGCAATAAAATAGTT
66 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* *
28354720 AGCTTCCTGATGAGATACTAAGAGGAGAACCAAATTCAGCTTCCTGATGAGATACAGAGAAGC-A
131 AGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCAGCTTCCTGATGAGATACAGAGAAGCGA
*
28354784 ATTTGAA
196 A-TTAAA
* * * *
28354791 ATAAATGAGGCGATCATCTTCTTGATGAGATACAGAGAAGTATGCCAACTCAATGCTCGATGTGA
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCAACGCTCAATGTGA
*
28354856 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGCAATAAAATGGTT
66 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* * * * *
28354921 AGCTTCCTGAAGAGAAACTAAGAAGTGAACCAAATTC-GTCTTCCTAAGGAGATCCAGAGAAGCG
131 AGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCAG-CTTCCTGATGAGATACAGAGAAGCG
28354985 AATTAAA
195 AATTAAA
* * * * * * * *
28354992 ACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAG-AAGACCAAATCAAACCCAGGCTTA
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATG-CCAACTC-AA--C--GCTCA
* * *
28355056 ATATGAGCAAATCTTCGAA-CCCAGCTTCCTGAAGAGATACTGAGAAGCAGGTCAAAGCAATAAA
60 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAA
*
28355120 ATGGTTAGCTTCCTGATGAGATAC-AGAGAAGTGAACCAAATTCAGCTTCCTGATGAGATACAGT
125 ATGGTTAGCTTCCTGATGAGATACTA-AGAAGTGAACCAAATTCAGCTTCCTGATGAGATACAGA
28355184 GAAGCGAATTAAA
189 GAAGCGAATTAAA
* * * *
28355197 ATAAATGAGGCGATCATCTTCCTGATGAGATATAGAGAAGTATGCCAACTCGACGCTCGATGTGA
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCAACGCTCAATGTGA
* * *
28355262 GCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGAAGGTTGAAGCAATAAAATGGTT
66 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* * *
28355327 AGCTTCCTGATGAGATACTGAGAAGGGAACCAAATTCAGCTTCCTGATGAGATACAGAGAAGTGA
131 AGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCAGCTTCCTGATGAGATACAGAGAAGCGA
*
28355392 TTTGAAA
196 ATT-AAA
* * * *
28355399 A-AAATGAGGCGGTCATCTTCCTGATGAGATACAAAGAAGTATGCCAACTCGAGGCTCGATGTGA
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCAACGCTCAATGTGA
28355463 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
66 GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
* * * * * *
28355528 AGCTTCCTGAAGAGATACTAAGAAGTGGACCAAATTC-GTTTTCCTGAGGAGATCCAAAGAAGCG
131 AGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCAG-CTTCCTGATGAGATACAGAGAAGCG
28355592 AATTAAA
195 AATTAAA
* * * * *
28355599 ACAAGTGATGCGGTCATCTTCCTGATGAGACACTGAGAAG
1 ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAG
28355639 AAGGCCAAGT
Statistics
Matches: 929, Mismatches: 100, Indels: 39
0.87 0.09 0.04
Matches are distributed among these distances:
200 100 0.11
201 644 0.69
202 11 0.01
204 2 0.00
205 148 0.16
206 24 0.03
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (201 bp):
ATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCAACTCAACGCTCAATGTGA
GCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTT
AGCTTCCTGATGAGATACTAAGAAGTGAACCAAATTCAGCTTCCTGATGAGATACAGAGAAGCGA
ATTAAA
Found at i:28355603 original size:607 final size:607
Alignment explanation
Indices: 28354442--28355651 Score: 2109
Period size: 607 Copynumber: 2.0 Consensus size: 607
28354432 TACCAACTCA
*
28354442 AGGCTCAAAATGAGCAAAGCTTCGAACCCAGCTTCCTAATGAGATACTGAGAAGCAAGTCGAAGC
1 AGGCTCAAAATGAGCAAAGCTTCGAACCCAGCTTCCTAATGAGATACTGAGAAGCAAGTCAAAGC
28354507 AATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAGCTTCCTGATGAGAT
66 AATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAGCTTCCTGATGAGAT
* *
28354572 ACAATGAAGCGAATTGAAATAAATGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATGCCA
131 ACAATGAAGCGAATTAAAATAAATGAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATGCCA
* *
28354637 ACTCGACGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACATTGAGAAGCAGGT
196 ACTCGACGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGAAGGT
28354702 CGAAGCAATAAAATAGTTAGCTTCCTGATGAGATACTAAGAGGAGAACCAAATTCAGCTTCCTGA
261 CGAAGCAATAAAATAGTTAGCTTCCTGATGAGATACTAAGAGGAGAACCAAATTCAGCTTCCTGA
* * *
28354767 TGAGATACAGAGAAGCAATTTGAAATAAATGAGGCGATCATCTTCTTGATGAGATACAGAGAAGT
326 TGAGATACAGAGAAGCAATTTGAAAAAAATGAGGCGATCATCTTCCTGATGAGATACAAAGAAGT
*
28354832 ATGCCAACTCAATGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAA
391 ATGCCAACTCAAGGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAA
*
28354897 GCAGGTTGAAGCAATAAAATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGAACCAAATTCGTCT
456 GCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGAACCAAATTCGTCT
*
28354962 TCCTAAGGAGATCCAGAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTG
521 TCCTAAGGAGATCCAAAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTG
28355027 AGAAGAAGACCAAATCAAACCC
586 AGAAGAAGACCAAATCAAACCC
* * * *
28355049 AGGCTTAATATGAGCAAATCTTCGAACCCAGCTTCCTGAA-GAGATACTGAGAAGCAGGTCAAAG
1 AGGCTCAAAATGAGCAAAGCTTCGAACCCAGCTTCCT-AATGAGATACTGAGAAGCAAGTCAAAG
28355113 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAGCTTCCTGATGAGA
65 CAATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAGCTTCCTGATGAGA
* *
28355178 TACAGTGAAGCGAATTAAAATAAATGAGGCGATCATCTTCCTGATGAGATATAGAGAAGTATGCC
130 TACAATGAAGCGAATTAAAATAAATGAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATGCC
*
28355243 AACTCGACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGAAGG
195 AACTCGACGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGAAGG
* * *
28355308 TTGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGG-GAACCAAATTCAGCTTCCT
260 TCGAAGCAATAAAATAGTTAGCTTCCTGATGAGATACTAAG-AGGAGAACCAAATTCAGCTTCCT
** *
28355372 GATGAGATACAGAGAAGTGATTTGAAAAAAATGAGGCGGTCATCTTCCTGATGAGATACAAAGAA
324 GATGAGATACAGAGAAGCAATTTGAAAAAAATGAGGCGATCATCTTCCTGATGAGATACAAAGAA
*
28355437 GTATGCCAACTCGAGGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAG
389 GTATGCCAACTCAAGGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAG
* *
28355502 AAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAAGAGATACTAAGAAGTGGACCAAATTCGT
454 AAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGAACCAAATTCGT
* *
28355567 TTTCCTGAGGAGATCCAAAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACAC
519 CTTCCTAAGGAGATCCAAAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACAC
* *
28355632 TGAGAAGAAGGCCAAGTCAA
584 TGAGAAGAAGACCAAATCAA
28355652 TAAAACCAGA
Statistics
Matches: 570, Mismatches: 31, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
607 565 0.99
608 5 0.01
ACGTcount: A:0.36, C:0.19, G:0.23, T:0.22
Consensus pattern (607 bp):
AGGCTCAAAATGAGCAAAGCTTCGAACCCAGCTTCCTAATGAGATACTGAGAAGCAAGTCAAAGC
AATAAAATGGTTAGCTTCCTGATGAGATACAGAGAAGTGAACCAAATTCAGCTTCCTGATGAGAT
ACAATGAAGCGAATTAAAATAAATGAGGCGATCATCTTCCTGATGAGATACAGAGAAGTATGCCA
ACTCGACGCTCAATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGAAGGT
CGAAGCAATAAAATAGTTAGCTTCCTGATGAGATACTAAGAGGAGAACCAAATTCAGCTTCCTGA
TGAGATACAGAGAAGCAATTTGAAAAAAATGAGGCGATCATCTTCCTGATGAGATACAAAGAAGT
ATGCCAACTCAAGGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAA
GCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAAGAGAAACTAAGAAGTGAACCAAATTCGTCT
TCCTAAGGAGATCCAAAGAAGCGAATTAAAACAAGTGATGCGGTCATCTTCCTGATGAGACACTG
AGAAGAAGACCAAATCAAACCC
Found at i:28356055 original size:18 final size:18
Alignment explanation
Indices: 28356032--28356067 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28356022 ACTTTTTCTT
*
28356032 TTAAAGTTTAAATCTAAA
1 TTAAAGATTAAATCTAAA
*
28356050 TTAAAGATTAAATTTAAA
1 TTAAAGATTAAATCTAAA
28356068 ATTGAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.06, T:0.39
Consensus pattern (18 bp):
TTAAAGATTAAATCTAAA
Found at i:28356780 original size:22 final size:23
Alignment explanation
Indices: 28356752--28356811 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
28356742 ATTGAATTAA
*
28356752 TAATAATATTAATCATAACCA-T
1 TAATAATATTAATAATAACCATT
* *
28356774 TAATAATAATAATAATAACTATT
1 TAATAATATTAATAATAACCATT
28356797 TAATAATTATTAATA
1 TAATAA-TATTAATA
28356812 TTATTAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 18 0.56
23 7 0.22
24 7 0.22
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (23 bp):
TAATAATATTAATAATAACCATT
Found at i:28357976 original size:30 final size:29
Alignment explanation
Indices: 28357942--28358154 Score: 153
Period size: 30 Copynumber: 7.2 Consensus size: 29
28357932 CCAAAATTGT
*
28357942 ATTTTAACCCCAAAAACTTTAAAAAATTAC
1 ATTTTAACCCC-AAAACTTTCAAAAATTAC
** * *
28357972 ATTTTTGCCCCCAAACTTTCAAAAATTCC
1 ATTTTAACCCCAAAACTTTCAAAAATTAC
* * *
28358001 ATTTTTGACCCGAAAACTTCCAAAAATTAC
1 A-TTTTAACCCCAAAACTTTCAAAAATTAC
* * *
28358031 ATTTTTGACTCC-AAACTTTCCAAAATTAC
1 A-TTTTAACCCCAAAACTTTCAAAAATTAC
* * * *
28358060 ATTTTTGACCCTAAAACTTCCAAAAAGTAC
1 A-TTTTAACCCCAAAACTTTCAAAAATTAC
* *
28358090 ATTTCT-ACCCTC-GAACTTCCAAAAATTAC
1 ATTT-TAACCC-CAAAACTTTCAAAAATTAC
* * *
28358119 ATTTTTTACTCCGAAACTTTCAAAAATTACC
1 A-TTTTAACCCCAAAACTTTCAAAAATTA-C
28358150 ATTTT
1 ATTTT
28358155 GCCCCCCAAA
Statistics
Matches: 149, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
29 66 0.44
30 81 0.54
31 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (29 bp):
ATTTTAACCCCAAAACTTTCAAAAATTAC
Found at i:28357988 original size:29 final size:29
Alignment explanation
Indices: 28357955--28358160 Score: 189
Period size: 29 Copynumber: 7.0 Consensus size: 29
28357945 TTAACCCCAA
*
28357955 AAACTTTAAAAAATTACATTTTTGCCCCC
1 AAACTTTCAAAAATTACATTTTTGCCCCC
* **
28357984 AAACTTTCAAAAATTCCATTTTTGACCCGA
1 AAACTTTCAAAAATTACATTTTTG-CCCCC
* * *
28358014 AAACTTCCAAAAATTACATTTTTGACTCC
1 AAACTTTCAAAAATTACATTTTTGCCCCC
* **
28358043 AAACTTTCCAAAATTACATTTTTGACCCTA
1 AAACTTTCAAAAATTACATTTTTG-CCCCC
* * * * *
28358073 AAACTTCCAAAAAGTACATTTCTACCCTC
1 AAACTTTCAAAAATTACATTTTTGCCCCC
* * * * *
28358102 GAACTTCCAAAAATTACATTTTTTACTCCG
1 AAACTTTCAAAAATTACA-TTTTTGCCCCC
28358132 AAACTTTCAAAAATTACCA-TTTTGCCCCC
1 AAACTTTCAAAAATTA-CATTTTTGCCCCC
28358161 CAAATGTCCA
Statistics
Matches: 140, Mismatches: 33, Indels: 8
0.77 0.18 0.04
Matches are distributed among these distances:
29 72 0.51
30 66 0.47
31 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
AAACTTTCAAAAATTACATTTTTGCCCCC
Found at i:28358017 original size:59 final size:59
Alignment explanation
Indices: 28357954--28358160 Score: 247
Period size: 59 Copynumber: 3.5 Consensus size: 59
28357944 TTTAACCCCA
** *
28357954 AAAACTTTAAAAAATTACATTTTTGCCCCCAAACTTTCAAAAATTCCATTTTTGACCCG
1 AAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTTCAAAAATTACATTTTTGACCCG
* * * *
28358013 AAAACTTCCAAAAATTACATTTTTGACTCCAAACTTTCCAAAATTACATTTTTGACCCT
1 AAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTTCAAAAATTACATTTTTGACCCG
* * * * * * *
28358072 AAAACTTCCAAAAAGTACATTTCTACCCTCGAACTTCCAAAAATTACATTTTTTACTCCG
1 AAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTTCAAAAATTACATTTTTGAC-CCG
*
28358132 -AAACTTTCAAAAATTACCA-TTTTGCCCCC
1 AAAACTTCCAAAAATTA-CATTTTTGCCCCC
28358161 CAAATGTCCA
Statistics
Matches: 123, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
59 119 0.97
60 4 0.03
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (59 bp):
AAAACTTCCAAAAATTACATTTTTGCCCCCAAACTTTCAAAAATTACATTTTTGACCCG
Found at i:28361254 original size:210 final size:209
Alignment explanation
Indices: 28360883--28361274 Score: 595
Period size: 210 Copynumber: 1.9 Consensus size: 209
28360873 TAGGAAGATG
* * *
28360883 GATTTGATCTACTTCTCTGTATCTCATCAGGAATATAACCTCCTCACTTGTTTTAATCCGCATCT
1 GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCATCT
* * * * * * *
28360948 TTGTATCTCATCAGGAAGACGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGACTATCGCTT
66 CTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTT
* *
28361013 TATTACTTTGACCTACTTCTTAGTATCTCATCAGGAAGATGGGGGTTTGAAGTTTCACTCACATT
131 TATTACTTTGACCCACTTCTCAGTATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCACATT
28361078 GAGCTTCGCTTCATC
195 GAGCTTCGCTTCATC
* * * * *
28361093 GATTTGGTTTACTTCTTTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCT
1 GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCATCT
* *
28361158 CTGTATCTTATCAGAAAGATGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTT
66 CTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTT
*
28361223 TATTGCTTTGACCCACTTCTCAGTATCTCATCAGGAAGATGGGGTTTGAAGT
131 TATTACTTTGACCCACTTCTCAGTATCTCATCAGGAAGATGGGGTTTGAAGT
28361275 CTCATTCGAC
Statistics
Matches: 162, Mismatches: 20, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
209 12 0.07
210 150 0.93
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (209 bp):
GATTTGATCTACTTCTCTGTATCTCATCAGGAAGATAACCGCATCACTTGTTTTAATCCGCATCT
CTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGACCACTT
TATTACTTTGACCCACTTCTCAGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTG
AGCTTCGCTTCATC
Found at i:28361453 original size:48 final size:46
Alignment explanation
Indices: 28361324--28361662 Score: 344
Period size: 46 Copynumber: 7.6 Consensus size: 46
28361314 ATTTGCCCCA
* * * *
28361324 TGACCTAGGGGTATGAGATCGGATGATGACTTCAATTTGCCCCTCT
1 TGACTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
* *
28361370 TGACTTAAGGGTATGAGATTTGGATGATGGCTTCAATCTTCCCCTCT
1 TGACTTAGGGGTATGAGA-TTGGATGATGGCTTCAATCTGCCCCTCT
28361417 TGACTTTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
1 TGAC--TTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
* *
28361465 TGACTTAGAGGCATGAGATTGGATGATGGCTTCAATCTG--CC-C-
1 TGACTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
* * * *
28361507 ---C-T----GTATGAGATCGGATGATGACTTCAATCTGCTCTTCT
1 TGACTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
* * * * * *
28361545 TGACTTAAGGGTGTGAGATTGGATGATAGCTTCGATCT-CTCTCTTT
1 TGACTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGC-CCCTCT
* * * *
28361591 TGACTCAGGGGTATGAGATCGGATGATGACTTCAATCTGCCCTTCT
1 TGACTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
*
28361637 TGACTTAAGGGTATGAGATTGGATGA
1 TGACTTAGGGGTATGAGATTGGATGA
28361663 CTGTAATCTG
Statistics
Matches: 240, Mismatches: 36, Indels: 34
0.77 0.12 0.11
Matches are distributed among these distances:
34 26 0.11
36 1 0.00
37 1 0.00
38 1 0.00
39 1 0.00
41 1 0.00
42 1 0.00
43 1 0.00
44 2 0.01
45 1 0.00
46 131 0.55
47 29 0.12
48 31 0.13
49 13 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (46 bp):
TGACTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTCT
Found at i:28361562 original size:80 final size:80
Alignment explanation
Indices: 28361429--28361582 Score: 220
Period size: 80 Copynumber: 1.9 Consensus size: 80
28361419 ACTTTTAGGG
* * *
28361429 GTATGAGATTGGATGATGGCTTCAATCTGCCCCTCTTGACTTAGAGGCATGAGATTGGATGATGG
1 GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAGAGGCATGAGATTGGATGATAG
28361494 CTTCAATCTGCCCCT
66 CTTCAATCTGCCCCT
* * **
28361509 GTATGAGATCGGATGATGACTTCAATCTGCTCTTCTTGACTTA-AGGGTGTGAGATTGGATGATA
1 GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAGA-GGCATGAGATTGGATGATA
*
28361573 GCTTCGATCT
65 GCTTCAATCT
28361583 CTCTCTTTTG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
79 1 0.02
80 64 0.98
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (80 bp):
GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAGAGGCATGAGATTGGATGATAG
CTTCAATCTGCCCCT
Found at i:28361618 original size:126 final size:128
Alignment explanation
Indices: 28361380--28361632 Score: 323
Period size: 126 Copynumber: 2.0 Consensus size: 128
28361370 TGACTTAAGG
* * * *
28361380 GTATGAGATTTGGATGATGGCTTCAATCTTCCCCTCTTGACTTTTAGGGGTATGAGATTGGATGA
1 GTATGAGATTCGGATGATGACTTCAATCTGCCCCTCTTGAC-TTTAAGGGTATGAGATTGGATGA
* * * *
28361445 TGGCTTCAATCTGCCCCTCTTGACTTAGAGGCATGAGATTGGATGATGGCTTCAATCTGCCCCT
65 TAGCTTCAATCTGCCCCTCTTGACTCAGAGGCATGAGATCGGATGATGACTTCAATCTGCCCCT
* * *
28361509 GTATGAGA-TCGGATGATGACTTCAATCTGCTCTTCTTGAC-TTAAGGGTGTGAGATTGGATGAT
1 GTATGAGATTCGGATGATGACTTCAATCTGCCCCTCTTGACTTTAAGGGTATGAGATTGGATGAT
* * * * *
28361572 AGCTTCGATCT-CTCTCTTTTGACTCAGGGGTATGAGATCGGATGATGACTTCAATCTGCCC
66 AGCTTCAATCTGC-CCCTCTTGACTCAGAGGCATGAGATCGGATGATGACTTCAATCTGCCC
28361633 TTCTTGACTT
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
125 1 0.01
126 71 0.66
128 27 0.25
129 8 0.07
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (128 bp):
GTATGAGATTCGGATGATGACTTCAATCTGCCCCTCTTGACTTTAAGGGTATGAGATTGGATGAT
AGCTTCAATCTGCCCCTCTTGACTCAGAGGCATGAGATCGGATGATGACTTCAATCTGCCCCT
Found at i:28361655 original size:172 final size:174
Alignment explanation
Indices: 28361334--28361662 Score: 486
Period size: 172 Copynumber: 1.9 Consensus size: 174
28361324 TGACCTAGGG
* *
28361334 GTATGAGATCGGATGATGACTTCAATTTGCCCCTCTTGACTTAAGGGTATGAGATTTGGATGATG
1 GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAGGGTATGAGATTTGGATGATA
* * *
28361399 GCTTCAATCTTCCCCTCTTGACTTTTAGGGGTATGAGATTGGATGATGGCTTCAATCTGCCCCTC
66 GCTTCAATCTTCCCCTCTTGAC-TTCAGGGGTATGAGATCGGATGATGACTTCAATCTGCCCCTC
28361464 TTGACTTAGAGGCATGAGATTGGATGATGGCTTCAATCTGCCCCT
130 TTGACTTAGAGGCATGAGATTGGATGATGGCTTCAATCTGCCCCT
* * *
28361509 GTATGAGATCGGATGATGACTTCAATCTGCTCTTCTTGACTTAAGGGTGTGAGA-TTGGATGATA
1 GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAGGGTATGAGATTTGGATGATA
* * * *
28361573 GCTTCGATC-TCTCTCTTTTGAC-TCAGGGGTATGAGATCGGATGATGACTTCAATCTGCCCTTC
66 GCTTCAATCTTC-CCCTCTTGACTTCAGGGGTATGAGATCGGATGATGACTTCAATCTGCCCCTC
*
28361636 TTGACTTA-AGGGTATGAGATTGGATGA
130 TTGACTTAGA-GGCATGAGATTGGATGA
28361663 CTGTAATCTG
Statistics
Matches: 139, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
171 1 0.01
172 61 0.44
173 2 0.01
174 25 0.18
175 50 0.36
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (174 bp):
GTATGAGATCGGATGATGACTTCAATCTGCCCCTCTTGACTTAAGGGTATGAGATTTGGATGATA
GCTTCAATCTTCCCCTCTTGACTTCAGGGGTATGAGATCGGATGATGACTTCAATCTGCCCCTCT
TGACTTAGAGGCATGAGATTGGATGATGGCTTCAATCTGCCCCT
Found at i:28361699 original size:39 final size:39
Alignment explanation
Indices: 28361645--28361739 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 39
28361635 CTTGACTTAA
* *
28361645 GGGTATGAGATTGGATGACTGTAATCTGCCCCACGACCG
1 GGGTAAGAGATTGGATGACTGTAATCTACCCCACGACCG
** * **
28361684 GGGTAAGAGATTGGATGGTTGTAATCTACCCCATGATTG
1 GGGTAAGAGATTGGATGACTGTAATCTACCCCACGACCG
*
28361723 AGGTAAGAGATTGGATG
1 GGGTAAGAGATTGGATG
28361740 CTTCAATCTT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (39 bp):
GGGTAAGAGATTGGATGACTGTAATCTACCCCACGACCG
Found at i:28361944 original size:49 final size:49
Alignment explanation
Indices: 28361891--28361999 Score: 137
Period size: 49 Copynumber: 2.2 Consensus size: 49
28361881 TTGTTACGGA
* * *
28361891 CTCAACCTTTCCTTTCAAATCTTTACGATACCGGGTTCACCATTGCGAC
1 CTCAACCTTTCCCTTCAAATCTTTACGATACCAGGTTCACCATTACGAC
** * * * *
28361940 CTCAACCTTTCCCTTCAAATCTTTGTGGTATCAGGTTTACCGTTACGAC
1 CTCAACCTTTCCCTTCAAATCTTTACGATACCAGGTTCACCATTACGAC
28361989 CTCAACCTTTC
1 CTCAACCTTTC
28362000 TTATCACAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.21, C:0.32, G:0.12, T:0.35
Consensus pattern (49 bp):
CTCAACCTTTCCCTTCAAATCTTTACGATACCAGGTTCACCATTACGAC
Found at i:28362254 original size:99 final size:98
Alignment explanation
Indices: 28362083--28362451 Score: 359
Period size: 99 Copynumber: 3.7 Consensus size: 98
28362073 GTTGTTGTTG
* * *
28362083 TTTCCCTTCAAATCTTCATGGCACCGGGTTCGCCATTGTGGTCTCAACCTTTCCCATCACATCTT
1 TTTCCCTTCAAATCTTCATGGTA-CGGGTTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCTT
* * *
28362148 TTAAGGTACCGAATTTATCGTTACGGCCTTAATC
65 TTAAGGTACCGAATTCACCGTTACGGCCTTAACC
* *
28362182 TTTCCCTTCATATCTTCATGGTATCGGGTTCACCGTTGTGGCCTCAACCTTTCCCATCACATCTT
1 TTTCCCTTCAAATCTTCATGGTA-CGGGTTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCTT
* *
28362247 TTAAGGTACCGAGTTCACCGTTGCGGCCTTAACC
65 TTAAGGTACCGAATTCACCGTTACGGCCTTAACC
* * * * * *
28362281 TTTCCCATCACATCTTCTAAGGTACTGGGTTCGCCGTTGTGGCCTTAACCTTTCCCTTCAAATC-
1 TTTCCCTTCAAATCTTC-ATGGTAC-GGGTTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCT
* * * * * *
28362345 TTCATGGTACCG-GTTCGCCGTTGCAG-CTTCAACC
64 TTTAAGGTACCGAATTCACCGTTACGGCCTT-AACC
* * * * ** * **
28362379 TTTCCCATCACAT-TTCATAGTACCGGATTTACCGTTGCGGCCTCAATATTTCCCATCACATCTT
1 TTTCCCTTCAAATCTTCATGGTA-CGGGTTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCTT
* *
28362443 CTGAGGTAC
65 TTAAGGTAC
28362452 TAGGTTCTTC
Statistics
Matches: 228, Mismatches: 37, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
96 33 0.14
97 13 0.06
98 29 0.13
99 114 0.50
100 39 0.17
ACGTcount: A:0.19, C:0.31, G:0.16, T:0.34
Consensus pattern (98 bp):
TTTCCCTTCAAATCTTCATGGTACGGGTTCGCCGTTGTGGCCTCAACCTTTCCCATCACATCTTT
TAAGGTACCGAATTCACCGTTACGGCCTTAACC
Done.