Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 134 of 218
Found at i:40808838 original size:49 final size:44
Alignment explanation
Indices: 40808779--40808955 Score: 167
Period size: 49 Copynumber: 3.9 Consensus size: 44
40808769 TTAAAAATAA
* *
40808779 ACAAATCTTATCTCCCTAAAATTGCAGTGGAGTAGATTAAAGACAGAC
1 ACAAATCTTATCTCCTTAAAATTGCAGTGGAGCAGATTAAAG-C---C
* *
40808827 TACAAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 -ACAAATCTTATCTCCTTAAAATTGCAGTGGAGCAGATTAAAGCC
* ***
40808872 ACAAACCTTATCTCCTTAAAATTGCAGTGGAGCA-AGTTAAAAAT
1 ACAAATCTTATCTCCTTAAAATTGCAGTGGAGCAGA-TTAAAGCC
** * *
40808916 AGCAAATCTTATCTTTTTAAAGTTTACAGTGGAGCAGATT
1 A-CAAATCTTATCTCCTTAAA-ATTGCAGTGGAGCAGATT
40808956 GAAATGATAA
Statistics
Matches: 109, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
43 1 0.01
44 37 0.34
45 17 0.16
46 14 0.13
47 1 0.01
48 1 0.01
49 38 0.35
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (44 bp):
ACAAATCTTATCTCCTTAAAATTGCAGTGGAGCAGATTAAAGCC
Found at i:40808946 original size:139 final size:139
Alignment explanation
Indices: 40808689--40808955 Score: 340
Period size: 139 Copynumber: 1.9 Consensus size: 139
40808679 ATCAGAGATA
* * * * *
40808689 ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCTATAAACTTTAACTCCTTGAAG
1 ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTAACTCCTTAAAA
* * * * *
40808754 TTGTAGTAGAGTAGGTTAAAAATAAACAAATCTTATCTCCCTAAAATTGCAGTGGAGTAGATTAA
66 TTGCAGTAGAGCAAGTTAAAAATAAACAAATCTTATCTCCCTAAAATTACAGTGGAGCAGATTAA
40808819 AGACAGACT
131 AGACAGACT
* *
40808828 ACAAATCTTATCTC-CTTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAACCTTATCTCCTTAAA
1 ACAAATCTTATCTCTC-TGAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTAACTCCTTAAA
* * *** *
40808892 ATTGCAGTGGAGCAAGTTAAAAAT-AGCAAATCTTATCTTTTTAAAGTTTACAGTGGAGCAGATT
65 ATTGCAGTAGAGCAAGTTAAAAATAAACAAATCTTATCTCCCTAAA-ATTACAGTGGAGCAGATT
40808956 GAAATGATAA
Statistics
Matches: 108, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
138 18 0.17
139 90 0.83
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (139 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATTAAAGCCACAAACCTTAACTCCTTAAAA
TTGCAGTAGAGCAAGTTAAAAATAAACAAATCTTATCTCCCTAAAATTACAGTGGAGCAGATTAA
AGACAGACT
Found at i:40809245 original size:89 final size:89
Alignment explanation
Indices: 40809064--40809271 Score: 238
Period size: 89 Copynumber: 2.3 Consensus size: 89
40809054 CTACAAGCTT
* * * * * *
40809064 CAAATCTTATATCCTTGAAGTTGCAGTAGAGCAGATTGAAGATAGCAAATCTTATCTCTCTGAAG
1 CAAATCTTATATCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTCATCGCCCTGAAG
* * ** *
40809129 TTATAGTGGATTAGATTGAAGTTA
66 TTACAATGGAGCAGATTGAAGTAA
* * * * *
40809153 CAAATCTTATCTCCCTGAAGTTGCAATGGAGTAGATTGAAGATA-CGAGTCTCGTCGCCCTGAAG
1 CAAATCTTATATCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTCATCGCCCTGAAG
*
40809217 TTGCAATGGAGCAGATTGAAGATAA
66 TTACAATGGAGCAGATTGAAG-TAA
*
40809242 CAAATCTTATTTCCCTGAAGTTGCAATGGA
1 CAAATCTTATATCCCTGAAGTTGCAATGGA
40809272 AGAAATTAAA
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
88 30 0.30
89 70 0.70
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (89 bp):
CAAATCTTATATCCCTGAAGTTGCAATGGAGCAGATTGAAGATAGCAAATCTCATCGCCCTGAAG
TTACAATGGAGCAGATTGAAGTAA
Found at i:40809329 original size:51 final size:51
Alignment explanation
Indices: 40809244--40809410 Score: 161
Period size: 51 Copynumber: 3.4 Consensus size: 51
40809234 GAAGATAACA
*
40809244 AATCTTATTTCCCTGAAGTTGCAATGGAAGAAATTAAAGCTACAAATTACG
1 AATCTTATCTCCCTGAAGTTGCAATGGAAGAAATTAAAGCTACAAATTACG
* * *
40809295 AATCTTATCTCCTTGAAGTTTCAATTG-AGCAAATTAAAGCTAC-----A--
1 AATCTTATCTCCCTGAAGTTGCAATGGAAG-AAATTAAAGCTACAAATTACG
* * * * * *
40809339 AATCTTATTTCCCTAAAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACA
1 AATCTTATCTCCCT-GAAGTTGCAATGGAAGAAATTAAAGCTACAAATTACG
*
40809391 AATCTTATCTCCCTAAAGTT
1 AATCTTATCTCCCTGAAGTT
40809411 ACAGTAGAGC
Statistics
Matches: 94, Mismatches: 12, Indels: 20
0.75 0.10 0.16
Matches are distributed among these distances:
44 12 0.13
45 22 0.23
46 2 0.02
50 3 0.03
51 42 0.45
52 13 0.14
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.32
Consensus pattern (51 bp):
AATCTTATCTCCCTGAAGTTGCAATGGAAGAAATTAAAGCTACAAATTACG
Found at i:40809410 original size:96 final size:96
Alignment explanation
Indices: 40809209--40809410 Score: 280
Period size: 96 Copynumber: 2.1 Consensus size: 96
40809199 AGTCTCGTCG
* * * *
40809209 CCCTGAAGTTGCAATGGAGCAGATTGAAGATAACAAATCTTATTTCCCTGAAGTTGCAATGGAAG
1 CCCTGAAGTTGCAATGGAGCAAATTAAAGATAACAAATCTTATTTCCCTAAAGTTGCAATGGAAC
*
40809274 AAATTAAAGCTACAAATTACGAATCTTATCT
66 AAATTAAAGCTACAAATTACAAATCTTATCT
* * * *
40809305 CCTTGAAGTTTCAATTGAGCAAATTAAAGCT-ACAAATCTTATTTCCCTAAAAGTTGCAATGGAA
1 CCCTGAAGTTGCAATGGAGCAAATTAAAGATAACAAATCTTATTTCCCT-AAAGTTGCAATGGAA
* *
40809369 CAGATTAAAGCTACAAGTTACAAATCTTATCT
65 CAAATTAAAGCTACAAATTACAAATCTTATCT
*
40809401 CCCTAAAGTT
1 CCCTGAAGTT
40809411 ACAGTAGAGC
Statistics
Matches: 92, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 17 0.18
96 75 0.82
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.30
Consensus pattern (96 bp):
CCCTGAAGTTGCAATGGAGCAAATTAAAGATAACAAATCTTATTTCCCTAAAGTTGCAATGGAAC
AAATTAAAGCTACAAATTACAAATCTTATCT
Found at i:40809421 original size:96 final size:95
Alignment explanation
Indices: 40809240--40809461 Score: 275
Period size: 96 Copynumber: 2.3 Consensus size: 95
40809230 GATTGAAGAT
* * *
40809240 AACAAATCTTATTTCCCTGAAGTTGCAATGGAAGAAATTAAAGCTACAAATTACGAATCTTATCT
1 AACAAATCTTATTTCCCTAAAGTTGCAATGGAACAAATTAAAGCTACAAATTACAAATCTTATCT
* * * *
40809305 CCTTGAAGTTTCAATTGAGCAAATTAAAGC
66 CCCTAAAGTTACAATAGAGCAAATTAAAGC
* * *
40809335 TACAAATCTTATTTCCCTAAAAGTTGCAATGGAACAGATTAAAGCTACAAGTTACAAATCTTATC
1 AACAAATCTTATTTCCCT-AAAGTTGCAATGGAACAAATTAAAGCTACAAATTACAAATCTTATC
* * *
40809400 TCCCTAAAGTTACAGTAGAGCAGATTGAAGC
65 TCCCTAAAGTTACAATAGAGCAAATTAAAGC
* * *
40809431 AACAAGTCCTA-TACCTCTAAAGTTGCAATGG
1 AACAAATCTTATTTCC-CTAAAGTTGCAATGG
40809462 GTTGGATTAA
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
95 33 0.31
96 75 0.69
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.29
Consensus pattern (95 bp):
AACAAATCTTATTTCCCTAAAGTTGCAATGGAACAAATTAAAGCTACAAATTACAAATCTTATCT
CCCTAAAGTTACAATAGAGCAAATTAAAGC
Found at i:40809436 original size:51 final size:52
Alignment explanation
Indices: 40809335--40809437 Score: 136
Period size: 51 Copynumber: 2.0 Consensus size: 52
40809325 AAATTAAAGC
* * * *
40809335 TACAAATCTTATTTCCCTAAAAGTTGCAATGGAACAGATTAAAGCTACAAGT
1 TACAAATCTTATCTCCCTAAAAGTTACAATAGAACAGATTAAAGCAACAAGT
* * *
40809387 TACAAATCTTATCTCCCT-AAAGTTACAGTAGAGCAGATTGAAGCAACAAGT
1 TACAAATCTTATCTCCCTAAAAGTTACAATAGAACAGATTAAAGCAACAAGT
40809438 CCTATACCTC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
51 27 0.61
52 17 0.39
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.27
Consensus pattern (52 bp):
TACAAATCTTATCTCCCTAAAAGTTACAATAGAACAGATTAAAGCAACAAGT
Found at i:40811263 original size:17 final size:17
Alignment explanation
Indices: 40811223--40811283 Score: 65
Period size: 17 Copynumber: 3.8 Consensus size: 17
40811213 ATTATTATTG
* *
40811223 TTATTATTTATTTTTAA
1 TTATTAATTATTTTTTA
40811240 TTATTAATTATTTTTTA
1 TTATTAATTATTTTTTA
* *
40811257 TTTTTAA-AATTTTTTA
1 TTATTAATTATTTTTTA
40811273 -TATT-ATTATTT
1 TTATTAATTATTT
40811284 AATTAGTATT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 1 0.03
15 7 0.19
16 8 0.22
17 21 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTAATTATTTTTTA
Found at i:40812337 original size:17 final size:17
Alignment explanation
Indices: 40812317--40812350 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
40812307 AAATTTAATC
*
40812317 TTAAAAAATAATTAAAA
1 TTAAAAAAAAATTAAAA
40812334 TTAAAAAAAAATTAAAA
1 TTAAAAAAAAATTAAAA
40812351 CCTCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TTAAAAAAAAATTAAAA
Found at i:40813037 original size:122 final size:115
Alignment explanation
Indices: 40812817--40813037 Score: 307
Period size: 122 Copynumber: 1.9 Consensus size: 115
40812807 TAGTCACTGT
* *
40812817 ATATTTAGCCAATTTGTTTTAGGGTTCATAAGAAATTGTATAATTTTTTTTTTATTTTTTAATTG
1 ATATTTAGCCAATTTATTTTAGGGTTCATAAGAAATTGGATAATTTTTTTTTTATTTTTTAATTG
* * *
40812882 GATATTGATGAAACATTTCTTTTCTATGTGTGAAATGTATTCGGGTAAGC
66 GATATTGATGAAACATTTCTTTCCCATGCGTGAAATGTATTCGGGTAAGC
* **
40812932 ATATTTAGCCGATTTATTTTAGGGTTCATAAGAAATTAGGGATTTTTTTATTTCTTTGATTTTTT
1 ATATTTAGCCAATTTATTTTAGGGTTCATAAGAAATT--GGATAATTTT-TTT-TTT-A--TTTT
40812997 TTAATTGGATATTGATGAAACATTTCTTTCCCATGCGTGAA
59 TTAATTGGATATTGATGAAACATTTCTTTCCCATGCGTGAA
40813038 TATTAGAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
115 35 0.38
117 7 0.08
118 3 0.03
119 3 0.03
120 1 0.01
122 42 0.46
ACGTcount: A:0.27, C:0.08, G:0.16, T:0.48
Consensus pattern (115 bp):
ATATTTAGCCAATTTATTTTAGGGTTCATAAGAAATTGGATAATTTTTTTTTTATTTTTTAATTG
GATATTGATGAAACATTTCTTTCCCATGCGTGAAATGTATTCGGGTAAGC
Found at i:40814547 original size:82 final size:82
Alignment explanation
Indices: 40814393--40814591 Score: 310
Period size: 82 Copynumber: 2.4 Consensus size: 82
40814383 TACATCTTTC
* * *
40814393 AACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCTTATAACAGTAAGA
1 AACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAACAATAAAA
*
40814458 TGTTAACCAACCATTTT
66 TGCTAACCAACCATTTT
* *
40814475 AACAAATCATTTAAAAAAATAAACAAAATATGTTATGCTAACAAAATGATCCTAT-ACAAATAAA
1 AACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAAC-AATAAA
40814539 ATGCTAACCAACCATTTT
65 ATGCTAACCAACCATTTT
* *
40814557 AACAAATCATTTCAAAAAACAAATAAAATATGTTA
1 AACAAATCATTTAAAAAAACAAACAAAATATGTTA
40814592 ACCATCTCAA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
81 2 0.02
82 105 0.98
ACGTcount: A:0.53, C:0.15, G:0.05, T:0.27
Consensus pattern (82 bp):
AACAAATCATTTAAAAAAACAAACAAAATATGTTATACTAACAAAATGATCCTATAACAATAAAA
TGCTAACCAACCATTTT
Found at i:40818652 original size:50 final size:50
Alignment explanation
Indices: 40818575--40818806 Score: 241
Period size: 50 Copynumber: 4.5 Consensus size: 50
40818565 TGCCATATCT
* ** * *
40818575 CAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCAATGTCC
1 CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCAATGTCC
*** * *
40818625 CAGACATGGTCTTATGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCC
1 CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCAATGTCC
* * *
40818675 CAAACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCAATGTCC
1 CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCAATGTCC
* * *
40818725 CAGATATGGTCTTACATGGGACCTCTCATAATATCAATGATGCCAATGTC-ATGTCC
1 CAGACATGGTCTTACATGGGACCTCTC---ATATC---GGTGCCAACG-CAATGTCC
*
40818781 CAGACATGGTCTTACATGGGATCTCT
1 CAGACATGGTCTTACATGGGACCTCT
40818807 TTACCCAAAT
Statistics
Matches: 151, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
50 109 0.72
53 4 0.03
56 37 0.25
57 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.28
Consensus pattern (50 bp):
CAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCAATGTCC
Found at i:40820183 original size:18 final size:18
Alignment explanation
Indices: 40820160--40820197 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
40820150 TCACGACCCT
*
40820160 CTCCCTCGCCCTTACCAC
1 CTCCCTCACCCTTACCAC
40820178 CTCCCTCACCCTTACCAC
1 CTCCCTCACCCTTACCAC
40820196 CT
1 CT
40820198 TTATTGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.61, G:0.03, T:0.24
Consensus pattern (18 bp):
CTCCCTCACCCTTACCAC
Found at i:40820268 original size:24 final size:24
Alignment explanation
Indices: 40820224--40820269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40820214 CACCACCCTC
*
40820224 AACCTCACCAAATTTACTACCAAA
1 AACCTCACCAAATTCACTACCAAA
* *
40820248 AACCTCACCACATTCATTACCA
1 AACCTCACCAAATTCACTACCA
40820270 TCACCACCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (24 bp):
AACCTCACCAAATTCACTACCAAA
Found at i:40822734 original size:18 final size:17
Alignment explanation
Indices: 40822702--40822739 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
40822692 TAAATGTTTT
40822702 TTTTTTAATTTAATT-A
1 TTTTTTAATTTAATTCA
40822718 TTTTTTAAGTTTAAATTCA
1 TTTTTTAA-TTT-AATTCA
40822737 TTT
1 TTT
40822740 GCTGATGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 4 0.21
19 4 0.21
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TTTTTTAATTTAATTCA
Found at i:40825007 original size:21 final size:22
Alignment explanation
Indices: 40824975--40825017 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
40824965 CTTTCTCTTC
*
40824975 TTCTTTTGTTTTTCTCC-CCTT
1 TTCTTTTGTTTTCCTCCTCCTT
40824996 TTCTTTCT-TTTTCCTCCTCCTT
1 TTCTTT-TGTTTTCCTCCTCCTT
40825018 CATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTGTTTTCCTCCTCCTT
Found at i:40826952 original size:25 final size:25
Alignment explanation
Indices: 40826897--40826949 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
40826887 GCCAATTTTG
*
40826897 AAATTTATTAAACATGACCAATATC
1 AAATTTATTAAACATGACCAAAATC
* *
40826922 AAATTTATTAAATATGATCAAGAATC
1 AAATTTATTAAACATGACCAA-AATC
40826948 AA
1 AA
40826950 TTTCATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (25 bp):
AAATTTATTAAACATGACCAAAATC
Found at i:40834550 original size:14 final size:15
Alignment explanation
Indices: 40834533--40834561 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40834523 TCTTTCCATT
40834533 TCTTTCT-TCTTCCC
1 TCTTTCTCTCTTCCC
40834547 TCTTTCTCTCTTCCC
1 TCTTTCTCTCTTCCC
40834562 CTCTATTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTCTCTCTTCCC
Found at i:40838406 original size:26 final size:27
Alignment explanation
Indices: 40838377--40838441 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
40838367 GGGCACCTTT
*
40838377 TAAAAAAAATATAAAAT-GTAATACAA
1 TAAAAAAAATATAAAATAGTAATAAAA
* *
40838403 TAAAATAAAAATATATACTAGTAATAAAA
1 T-AAA-AAAAATATAAAATAGTAATAAAA
*
40838432 TTAAAAAAAT
1 TAAAAAAAAT
40838442 TGAAGCCCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
26 1 0.03
27 9 0.28
28 13 0.41
29 9 0.28
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (27 bp):
TAAAAAAAATATAAAATAGTAATAAAA
Found at i:40838426 original size:29 final size:29
Alignment explanation
Indices: 40838381--40838437 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
40838371 ACCTTTTAAA
*
40838381 AAAAATATAAAATGTAATACAA-TAAAAT
1 AAAAATATAAAATGTAATAAAATTAAAAT
* *
40838409 AAAAATATATACTAGTAATAAAATTAAAA
1 AAAAATATAAAAT-GTAATAAAATTAAAA
40838438 AAATTGAAGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.46
29 8 0.33
30 5 0.21
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (29 bp):
AAAAATATAAAATGTAATAAAATTAAAAT
Found at i:40845106 original size:35 final size:35
Alignment explanation
Indices: 40845050--40845118 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
40845040 TAGACATTAC
40845050 GGCCGAATCTAGAAGAGTTACATTAGTTTATTTAT
1 GGCCGAATCTAGAAGAGTTACATTAGTTTATTTAT
* * * *
40845085 GGCCGAATCTGGAATATTTACATTAGTTTGTTTA
1 GGCCGAATCTAGAAGAGTTACATTAGTTTATTTA
40845119 AAAACTCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (35 bp):
GGCCGAATCTAGAAGAGTTACATTAGTTTATTTAT
Found at i:40845873 original size:17 final size:17
Alignment explanation
Indices: 40845851--40845895 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
40845841 TCTTATACAG
**
40845851 AATCAGATGTATTTCAT
1 AATCAGATACATTTCAT
40845868 AATCAGATACATTTCAT
1 AATCAGATACATTTCAT
40845885 AATCAGATACA
1 AATCAGATACA
40845896 AATGCAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (17 bp):
AATCAGATACATTTCAT
Found at i:40851944 original size:20 final size:20
Alignment explanation
Indices: 40851919--40851958 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
40851909 TTTGTAACTT
40851919 TTTAAAGTTGAGTGACCAAA
1 TTTAAAGTTGAGTGACCAAA
40851939 TTTAAAGTTGAGTGACCAAA
1 TTTAAAGTTGAGTGACCAAA
40851959 ACGCGACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (20 bp):
TTTAAAGTTGAGTGACCAAA
Found at i:40866106 original size:17 final size:17
Alignment explanation
Indices: 40866070--40866117 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
40866060 CATTATCCGC
* *
40866070 AATGCACTAAC-ATGAA
1 AATGCAATAACAATAAA
* *
40866086 AATGTAATGACAATAAA
1 AATGCAATAACAATAAA
40866103 AATGCAATAACAATA
1 AATGCAATAACAATA
40866118 TTTACTTATC
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.21
Consensus pattern (17 bp):
AATGCAATAACAATAAA
Found at i:40870734 original size:21 final size:21
Alignment explanation
Indices: 40870708--40870754 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
40870698 TTGTACATAG
*
40870708 AATAGCTGTCTAAAAAGAAAT
1 AATAGCCGTCTAAAAAGAAAT
40870729 AATAGCCGTCTAAAAAGAAAT
1 AATAGCCGTCTAAAAAGAAAT
40870750 AATAG
1 AATAG
40870755 GCCTTGTCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (21 bp):
AATAGCCGTCTAAAAAGAAAT
Found at i:40874822 original size:27 final size:27
Alignment explanation
Indices: 40874771--40875005 Score: 303
Period size: 27 Copynumber: 8.7 Consensus size: 27
40874761 GTAATGGGCC
* * *
40874771 TAAAATAATTGAAATACCCTTGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* * *
40874798 TAGAATGATCGAAATACTCTCGAAGAG
1 TAAAATGATCGAAATACCCTCGAAGGG
40874825 TAAAATGATCGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
40874852 TAAAATGA-CTGAAATACCCTCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
*
40874879 TAAAATGATCGATATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
40874906 TAAAATGATAGAACTACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
40874933 TAAAATGA-CTGAACTACCCTTGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAGGG
* *
40874960 TAAAATGACCGAAATACCCCCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAGGG
* *
40874987 TAAAATGAGCAAAATACCC
1 TAAAATGATCGAAATACCC
40875006 CTATAAGGTA
Statistics
Matches: 184, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
26 1 0.01
27 181 0.98
28 2 0.01
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.20
Consensus pattern (27 bp):
TAAAATGATCGAAATACCCTCGAAGGG
Found at i:40874877 original size:81 final size:81
Alignment explanation
Indices: 40874771--40875023 Score: 346
Period size: 81 Copynumber: 3.1 Consensus size: 81
40874761 GTAATGGGCC
* * * * *
40874771 TAAAATAATTGAAATACCCTTGAAGGGTAGAATGATCGAAATACTCTCGAAGAGTAAAATGATCG
1 TAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCG
40874836 AAATACCCTCGAAGGG
66 AAATACCCTCGAAGGG
* * *
40874852 TAAAATGACTGAAATACCCTCGAAGGGTAAAATGATCGATATACCCTCGAAGGGTAAAATGATAG
1 TAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCG
*
40874917 AACTACCCTCGAAGGG
66 AAATACCCTCGAAGGG
* * * * *
40874933 TAAAATGACTGAACTACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGGTAAAATGAGCA
1 TAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCG
* *
40874998 AAATACCC-CTATAAGG
66 AAATACCCTCGA-AGGG
40875014 TAAAATGACT
1 TAAAATGACT
40875024 ATTATACCCC
Statistics
Matches: 151, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
80 2 0.01
81 149 0.99
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.20
Consensus pattern (81 bp):
TAAAATGACTGAAATACCCTTGAAGGGTAAAATGATCGAAATACCCTCGAAGGGTAAAATGATCG
AAATACCCTCGAAGGG
Found at i:40875031 original size:54 final size:53
Alignment explanation
Indices: 40874771--40875033 Score: 235
Period size: 54 Copynumber: 4.9 Consensus size: 53
40874761 GTAATGGGCC
* * * * * * * * *
40874771 TAAAATAATTGAAATACCCTTGAAGGGTAGAATGATCGAAATACTCTCGAAGAG
1 TAAAATGATCGAAATACCCTCGAAAGGTAAAATGA-CTAAATACCCCCGAAGGG
* *
40874825 TAAAATGATCGAAATACCCTCGAAGGGTAAAATGACTGAAATACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGGTAAAATGACT-AAATACCCCCGAAGGG
* * *
40874879 TAAAATGATCGATATACCCTCGAAGGGTAAAATGA-TAGAACTACCCTCGAAGGG
1 TAAAATGATCGAAATACCCTCGAAAGGTAAAATGACTA-AA-TACCCCCGAAGGG
* * * *
40874933 TAAAATGA-CTGAACTACCCTTGAAGGGTAAAATGACCGAAATACCCCCGAAGGG
1 TAAAATGATC-GAAATACCCTCGAAAGGTAAAATGA-CTAAATACCCCCGAAGGG
* * * *
40874987 TAAAATGAGCAAAATACCC-CTATAAGGTAAAATGACTATTATACCCC
1 TAAAATGATCGAAATACCCTCGA-AAGGTAAAATGACTA-AATACCCC
40875034 TAGGAGTTGA
Statistics
Matches: 180, Mismatches: 20, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
52 1 0.01
53 8 0.04
54 167 0.93
55 3 0.02
56 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (53 bp):
TAAAATGATCGAAATACCCTCGAAAGGTAAAATGACTAAATACCCCCGAAGGG
Found at i:40875239 original size:26 final size:26
Alignment explanation
Indices: 40875199--40875249 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
40875189 GCCATATATA
* *
40875199 CTATTACTGGTAGCTTCGCTGCAATT
1 CTATTACTGGCAGCTTCACTGCAATT
* *
40875225 CTATTATTGGCAGCTTTACTGCAAT
1 CTATTACTGGCAGCTTCACTGCAAT
40875250 ATTGGTGTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.39
Consensus pattern (26 bp):
CTATTACTGGCAGCTTCACTGCAATT
Found at i:40875397 original size:28 final size:28
Alignment explanation
Indices: 40875365--40875445 Score: 90
Period size: 28 Copynumber: 2.9 Consensus size: 28
40875355 TGTTTCTATA
*
40875365 TTGGGCTAAGGCCCACATTGTTACTGCT
1 TTGGGCTAAGGCCCAGATTGTTACTGCT
** * *
40875393 TTGGGCTAAGGCTTAGACTGTTATTGCT
1 TTGGGCTAAGGCCCAGATTGTTACTGCT
* * *
40875421 TAGGGCTCAGGCCCAGATTATTACT
1 TTGGGCTAAGGCCCAGATTGTTACT
40875446 ACATGTCGTA
Statistics
Matches: 41, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.33
Consensus pattern (28 bp):
TTGGGCTAAGGCCCAGATTGTTACTGCT
Found at i:40875900 original size:37 final size:31
Alignment explanation
Indices: 40875829--40875892 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
40875819 ATAACAAGAC
*
40875829 AAACATTTTTTATTTTAATAACAAAGAAGTT
1 AAACAATTTTTATTTTAATAACAAAGAAGTT
40875860 AAACAATTTTTATTTTAATAACAAAGAAGTT
1 AAACAATTTTTATTTTAATAACAAAGAAGTT
40875891 AA
1 AA
40875893 TGTTAAACTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (31 bp):
AAACAATTTTTATTTTAATAACAAAGAAGTT
Found at i:40885346 original size:11 final size:11
Alignment explanation
Indices: 40885330--40885380 Score: 66
Period size: 11 Copynumber: 4.5 Consensus size: 11
40885320 GTAAAGTTAG
40885330 AAATAAAATAA
1 AAATAAAATAA
40885341 AAATAAAATAA
1 AAATAAAATAA
*
40885352 AAAGAAAATAA
1 AAATAAAATAA
* *
40885363 AAACTAAATTGA
1 AAA-TAAAATAA
40885375 AAATAA
1 AAATAA
40885381 TAATTTCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 27 0.77
12 8 0.23
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:40885351 original size:16 final size:16
Alignment explanation
Indices: 40885330--40885364 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40885320 GTAAAGTTAG
40885330 AAATAAAATA-AAAATA
1 AAATAAAA-AGAAAATA
40885346 AAATAAAAAGAAAATA
1 AAATAAAAAGAAAATA
40885362 AAA
1 AAA
40885365 ACTAAATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:40894929 original size:50 final size:50
Alignment explanation
Indices: 40894787--40895028 Score: 182
Period size: 50 Copynumber: 4.7 Consensus size: 50
40894777 GAATATAACA
* * * * ** * * * *
40894787 TGCCAAAGCTATGTCCCAGACATAGTCTTACGTGGGATGTTTCTTGTA-C
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * * **
40894836 TGCCAATGCCATATCCCAGATATGGTCTTACATTGGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
** * *
40894886 TGCGC-ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGC-CAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
* * *
40894936 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAATCTTAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A---T-A-GG
* * *
40894992 TGCCAATGTCATGTTCCAAACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
40895029 TCTCATCACC
Statistics
Matches: 150, Mismatches: 34, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
49 37 0.25
50 78 0.52
51 1 0.01
54 1 0.01
56 33 0.22
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGG
Found at i:40896425 original size:21 final size:21
Alignment explanation
Indices: 40896382--40896430 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
40896372 CAGCACAATC
*
40896382 AGATGTATCCACAACAAGACT
1 AGATGCATCCACAACAAGACT
* *
40896403 AGTTGCATCCAC-ACCAGACCT
1 AGATGCATCCACAACAAGA-CT
40896424 AGATGCA
1 AGATGCA
40896431 ACTAGAACAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (21 bp):
AGATGCATCCACAACAAGACT
Found at i:40900305 original size:16 final size:17
Alignment explanation
Indices: 40900276--40900308 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
40900266 TTCTTATGAA
40900276 ATTTATTATGTAATTTT
1 ATTTATTATGTAATTTT
*
40900293 ATTT-TTATTTAATTTT
1 ATTTATTATGTAATTTT
40900309 TTTGTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTATTATGTAATTTT
Found at i:40900311 original size:19 final size:19
Alignment explanation
Indices: 40900289--40900340 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
40900279 TATTATGTAA
*
40900289 TTTTATTTTTATTTAA-TT
1 TTTTTTTTTTATTTAAGTT
* *
40900307 TTTTTGTTTCTATTCAAGTT
1 TTTTT-TTTTTATTTAAGTT
*
40900327 TGTTTTTTTTATTT
1 TTTTTTTTTTATTT
40900341 TTTTATTTCC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 4 0.15
19 16 0.62
20 6 0.23
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.75
Consensus pattern (19 bp):
TTTTTTTTTTATTTAAGTT
Found at i:40903531 original size:21 final size:21
Alignment explanation
Indices: 40903507--40903549 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40903497 TTAGTTATCC
*
40903507 TTAGACC-ATATTTTAGTATTT
1 TTAGACCAATAATTTAG-ATTT
*
40903528 TTAGTCCAATAATTTAGATTT
1 TTAGACCAATAATTTAGATTT
40903549 T
1 T
40903550 ATGACTCAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (21 bp):
TTAGACCAATAATTTAGATTT
Found at i:40907574 original size:33 final size:33
Alignment explanation
Indices: 40907537--40907608 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
40907527 GATTACTCTC
40907537 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* *
40907570 TTCACTCGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
40907603 TCCACT
1 TTCACT
40907609 TTCGTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:40907721 original size:23 final size:24
Alignment explanation
Indices: 40907689--40907739 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
40907679 GAAATCTCAT
* *
40907689 TTTCATCTTTTTCTTTTCCAT-TTC
1 TTTCATCTTTCT-TTTTCAATGTTC
40907713 TTTCA-CTTTCTTTTTCAATGTTC
1 TTTCATCTTTCTTTTTCAATGTTC
40907736 TTTC
1 TTTC
40907740 CTCGCTCACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.29
23 12 0.50
24 5 0.21
ACGTcount: A:0.10, C:0.24, G:0.02, T:0.65
Consensus pattern (24 bp):
TTTCATCTTTCTTTTTCAATGTTC
Found at i:40910862 original size:51 final size:50
Alignment explanation
Indices: 40910804--40910939 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 50
40910794 ATCAGTTCAT
* *
40910804 ATAGTAGCCTGCACATAGTACTACACATGTGATCGAAGCTATTC-GGTACGC
1 ATAGTAGCCTGCACATAGTACTACACATGTGA-CCAAGC-ATTCTGGTACAC
* * * *
40910855 ATAGTAGCCTGCACATAGTGCTACACATGCGACCTATCATTCTGGTACAC
1 ATAGTAGCCTGCACATAGTACTACACATGTGACCAAGCATTCTGGTACAC
* * *
40910905 GTAGTAGACTGCACATAGTACTACACACGTGACCA
1 ATAGTAGCCTGCACATAGTACTACACATGTGACCA
40910940 TCACTTTCAG
Statistics
Matches: 72, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
49 4 0.06
50 38 0.53
51 30 0.42
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (50 bp):
ATAGTAGCCTGCACATAGTACTACACATGTGACCAAGCATTCTGGTACAC
Found at i:40916169 original size:90 final size:90
Alignment explanation
Indices: 40916012--40916189 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
40916002 CAAAGATGTC
* * *
40916012 TAGTCGAGTTACAGTCACTAAATTATTTTTATTCAGAGCTACGGAGCTCTAAATTAAGTTCCGTC
1 TAGTCGAGTTACAGTCACTAAATTATTTTTATTCAGAGCTACGGAGCTCCAAAATAAGTTCCATC
*
40916077 AATTTTCCACAAAACTAGACTCATA
66 AATTTTCCACAAAACTAAACTCATA
*
40916102 TAGTCGTGTTACAGTCACTAAATTATTTTTATTCAGAGCTACGGAGCTCCAAAATAAGTTCCATC
1 TAGTCGAGTTACAGTCACTAAATTATTTTTATTCAGAGCTACGGAGCTCCAAAATAAGTTCCATC
*
40916167 AATTTTCCACGAAACTAAACTCA
66 AATTTTCCACAAAACTAAACTCA
40916190 CATATCTTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (90 bp):
TAGTCGAGTTACAGTCACTAAATTATTTTTATTCAGAGCTACGGAGCTCCAAAATAAGTTCCATC
AATTTTCCACAAAACTAAACTCATA
Found at i:40916676 original size:16 final size:16
Alignment explanation
Indices: 40916655--40916686 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40916645 GTTTTGCTGC
*
40916655 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
40916671 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
40916687 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:40930228 original size:29 final size:31
Alignment explanation
Indices: 40930171--40930230 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 31
40930161 AATATTAGTC
*
40930171 ATGCAGTGAACAGTATGTAATATCATTAATCG
1 ATGCAGTGAACAGTA-GTAAAATCATTAATCG
40930203 ATGCAGT-AACAGTA-TAAAATCATTAATC
1 ATGCAGTGAACAGTAGTAAAATCATTAATC
40930231 AGTACACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.48
31 7 0.26
32 7 0.26
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (31 bp):
ATGCAGTGAACAGTAGTAAAATCATTAATCG
Found at i:40930662 original size:27 final size:27
Alignment explanation
Indices: 40930632--40930777 Score: 141
Period size: 27 Copynumber: 5.4 Consensus size: 27
40930622 GGTATAACAG
*
40930632 TCATTTTACCCTATAGAGATATTTCGA
1 TCATTTTACCCTATAGGGATATTTCGA
* *
40930659 TCATTTTATCCTAT-GAGGATATTTCCA
1 TCATTTTACCCTATAG-GGATATTTCGA
* * * *
40930686 TCACTCTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATAGGGATATTTCGA
* * *
40930713 TCATTTTACCCTATGGGGGTATTTCGG
1 TCATTTTACCCTATAGGGATATTTCGA
* * * *
40930740 TCATTCTACCCTAGAGGGCTATTTCGG
1 TCATTTTACCCTATAGGGATATTTCGA
*
40930767 TTATTTTACCC
1 TCATTTTACCC
40930778 CAGGTTGGAT
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
26 1 0.01
27 98 0.98
28 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.17, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGATATTTCGA
Found at i:40932317 original size:26 final size:26
Alignment explanation
Indices: 40932288--40932379 Score: 87
Period size: 26 Copynumber: 3.5 Consensus size: 26
40932278 GCCAACACAC
* * *
40932288 CAGTATCGCAGCAAATCTGCTAGTAT
1 CAGTATCACAGCAAAGCTGCCAGTAT
* * *
40932314 CAGTAACGCAACAAAGCTGCCAGTAAT
1 CAGTATCACAGCAAAGCTGCCAGT-AT
* * *
40932341 -AGTATCACAGTAGAGCTTCCAGTAT
1 CAGTATCACAGCAAAGCTGCCAGTAT
40932366 CAGTATCACAGCAA
1 CAGTATCACAGCAA
40932380 TGTTACCAGT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
25 2 0.04
26 48 0.92
27 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (26 bp):
CAGTATCACAGCAAAGCTGCCAGTAT
Found at i:40932622 original size:27 final size:27
Alignment explanation
Indices: 40932606--40933026 Score: 376
Period size: 27 Copynumber: 15.6 Consensus size: 27
40932596 TACCTATTGG
* *
40932606 GGGTATTTCGATAATTTTACCCTTTGG
1 GGGTATTTCGATAATTTTACCCTTCGA
* * * *
40932633 GGGCATTTTGGTAATTTTACCCTTCGG
1 GGGTATTTCGATAATTTTACCCTTCGA
* * *
40932660 GGGTATTTCGATAGTTTTATCCTTCAA
1 GGGTATTTCGATAATTTTACCCTTCGA
* *
40932687 GGGTATTTCAATAATTTTACCAATT-GA
1 GGGTATTTCGATAATTTTACC-CTTCGA
*
40932714 GGGTATTT-TAGTAATTTTACCCTTCGA
1 GGGTATTTCGA-TAATTTTACCCTTCGA
* *
40932741 GAGTATTTC-AGTAAATTTACCCTTCGA
1 GGGTATTTCGA-TAATTTTACCCTTCGA
**
40932768 GGGTATTTCGATAA-TTTACACAAT-GA
1 GGGTATTTCGATAATTTTAC-CCTTCGA
* **
40932794 GGGTATTTC-AGTTATTTTACCCAACGA
1 GGGTATTTCGA-TAATTTTACCCTTCGA
* * * *
40932821 AGGTATTTTGGTAATTTTACTCTTCGA
1 GGGTATTTCGATAATTTTACCCTTCGA
* *
40932848 GGGTA-TGCTGATAATTTTACCCTTCGC
1 GGGTATTTC-GATAATTTTACCCTTCGA
* *
40932875 GGGTATTTTGATAATTTTACCCTTCAA
1 GGGTATTTCGATAATTTTACCCTTCGA
* * *
40932902 GGGTATTTCGGTAAATTTACCCTTCGG
1 GGGTATTTCGATAATTTTACCCTTCGA
*
40932929 GGGTATTTTGGA-AATTTTACCCTTCGA
1 GGGTA-TTTCGATAATTTTACCCTTCGA
40932956 GGGTATTTTCG-TAATTTTACCTCTT-GA
1 GGGTA-TTTCGATAATTTTACC-CTTCGA
* * *
40932983 GGATATTTCGATCATTTTACCCTTCGG
1 GGGTATTTCGATAATTTTACCCTTCGA
*
40933010 GGGTATTTCGATCATTT
1 GGGTATTTCGATAATTT
40933027 GCCCACGACT
Statistics
Matches: 320, Mismatches: 57, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
25 1 0.00
26 32 0.10
27 276 0.86
28 11 0.03
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.42
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACCCTTCGA
Found at i:40938440 original size:17 final size:17
Alignment explanation
Indices: 40938418--40938453 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40938408 AATTAATTTT
*
40938418 AATTAATTAATTTTCTC
1 AATTAAATAATTTTCTC
*
40938435 AATTAAATGATTTTCTC
1 AATTAAATAATTTTCTC
40938452 AA
1 AA
40938454 CCCGATTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:40940930 original size:50 final size:50
Alignment explanation
Indices: 40940866--40940989 Score: 149
Period size: 50 Copynumber: 2.5 Consensus size: 50
40940856 AACGGTCACA
** *
40940866 CGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCTG
1 CGTAAGACCATGTCTAAGACATGGCATTGGCACCAAGATGAGAGGTCCTG
* * * **
40940916 CGTAAGGCCGTGTCTAAGACATGGCGTTGGCACCAAGATGAGAGGTCCCC
1 CGTAAGACCATGTCTAAGACATGGCATTGGCACCAAGATGAGAGGTCCTG
* * *
40940966 CATTAGACCATGTCTAGGACATGG
1 CGTAAGACCATGTCTAAGACATGG
40940990 GACGGGCACC
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
CGTAAGACCATGTCTAAGACATGGCATTGGCACCAAGATGAGAGGTCCTG
Found at i:40940998 original size:50 final size:50
Alignment explanation
Indices: 40940868--40941008 Score: 133
Period size: 50 Copynumber: 2.8 Consensus size: 50
40940858 CGGTCACACG
* * ** ** *
40940868 TAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCTGCG
1 TAAGACCATGTCTAGGACATGGGACGGGCACCGAGATGAGAGGTCCCCCA
* * * *
40940918 TAAGGCCGTGTCTAAGACAT-GG-CGTTGGCACCAAGATGAGAGGTCCCCCA
1 TAAGACCATGTCTAGGACATGGGACG--GGCACCGAGATGAGAGGTCCCCCA
* *
40940968 TTAGACCATGTCTAGGACATGGGACGGGCACCGATATGAGA
1 TAAGACCATGTCTAGGACATGGGACGGGCACCGAGATGAGA
40941009 ACTCTCAAGT
Statistics
Matches: 70, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
49 1 0.01
50 65 0.93
51 2 0.03
52 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (50 bp):
TAAGACCATGTCTAGGACATGGGACGGGCACCGAGATGAGAGGTCCCCCA
Found at i:40941323 original size:20 final size:20
Alignment explanation
Indices: 40941298--40941336 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40941288 TGAGTTATTT
40941298 AAGTAAGAAAGTAAGTAAAC
1 AAGTAAGAAAGTAAGTAAAC
*
40941318 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAAAGTAAGTAAA
40941337 GAAGAAGCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAAAGTAAGTAAAC
Found at i:40941590 original size:24 final size:24
Alignment explanation
Indices: 40941558--40941608 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
40941548 TCGAAACGTT
40941558 TTAACTTCTGGCATGTATAGGGAC
1 TTAACTTCTGGCATGTATAGGGAC
* *
40941582 TTAAGTTCTGGCTTGTATAGGGAC
1 TTAACTTCTGGCATGTATAGGGAC
40941606 TTA
1 TTA
40941609 GTCATTGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (24 bp):
TTAACTTCTGGCATGTATAGGGAC
Found at i:40945447 original size:9 final size:9
Alignment explanation
Indices: 40945433--40945466 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
40945423 AATTAAGGTT
40945433 TGCTTTAAA
1 TGCTTTAAA
40945442 TGCTTTAAA
1 TGCTTTAAA
40945451 TGCTTTAAA
1 TGCTTTAAA
40945460 TGCTTTA
1 TGCTTTA
40945467 TTTTGGTGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (9 bp):
TGCTTTAAA
Found at i:40952723 original size:27 final size:28
Alignment explanation
Indices: 40952642--40952736 Score: 129
Period size: 27 Copynumber: 3.4 Consensus size: 28
40952632 GAGATTGGCG
* * * *
40952642 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
40952671 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
40952699 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
40952726 CTGAGTGTGCG
1 CTAAGTGTGCG
40952737 GACTTAATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.39
28 22 0.36
29 15 0.25
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:40952750 original size:29 final size:27
Alignment explanation
Indices: 40952667--40952750 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
40952657 TAAATTGTAC
* *
40952667 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTAATTATAT
* *
40952695 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTAATTATAT
*
40952722 AGCACTGAGTGTGCGGACTTAATATATAT
1 AGCACTAAGTGTGC-GACTTAAT-TATAT
40952751 TTTTGAATCA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 23 0.46
28 22 0.44
29 5 0.10
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTAATTATAT
Found at i:40958704 original size:50 final size:49
Alignment explanation
Indices: 40958635--40958814 Score: 180
Period size: 50 Copynumber: 3.6 Consensus size: 49
40958625 TATTGAGGTT
* * *
40958635 ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCGTTGGCACTGAG
1 ATGAGAGCTCCCACGTAAGACCATGTCTGG-ACATGGCGTTGGCACCGAG
*
40958685 ATGAGAGCTCTCACGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGCTCCCACGTAAGACCATGTCT-GGACATGGCGTTGGCACCGAG
* ** * * * * * *
40958735 ATGAGAGGTCCCTTGTAAGACTATGTCTAGGACATGGCATGGGTACCAAT
1 ATGAGAGCTCCCACGTAAGACCATGTCT-GGACATGGCGTTGGCACCGAG
* * * *
40958785 ATGAGAACTCTCATGTAAGACCATATCTGG
1 ATGAGAGCTCCCACGTAAGACCATGTCTGG
40958815 GATATGACAT
Statistics
Matches: 108, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
49 2 0.02
50 104 0.96
51 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (49 bp):
ATGAGAGCTCCCACGTAAGACCATGTCTGGACATGGCGTTGGCACCGAG
Found at i:40958772 original size:100 final size:100
Alignment explanation
Indices: 40958635--40958816 Score: 231
Period size: 100 Copynumber: 1.8 Consensus size: 100
40958625 TATTGAGGTT
* * ** *
40958635 ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCGTTGGCACTGAGATGAGAGCTCTCACG
1 ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCATGGGCACCAAGATGAGAACTCTCACG
*
40958700 TAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
66 TAAGACCATATCTGGGACATGGCGTTGGCACCGAG
*** * * * *
40958735 ATGAGAGGTCCCTTGTAAGACTATGTCTAGG-ACATGGCATGGGTACCAATATGAGAACTCTCAT
1 ATGAGAGGTCCCACATAAGACCATGTCT-GGAACATGGCATGGGCACCAAGATGAGAACTCTCAC
40958799 GTAAGACCATATCTGGGA
65 GTAAGACCATATCTGGGA
40958817 TATGACATTT
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
100 66 0.97
101 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (100 bp):
ATGAGAGGTCCCACATAAGACCATGTCTGGAACATGGCATGGGCACCAAGATGAGAACTCTCACG
TAAGACCATATCTGGGACATGGCGTTGGCACCGAG
Found at i:40959105 original size:20 final size:20
Alignment explanation
Indices: 40959080--40959128 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
40959070 TGAGTTATTT
40959080 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
* *
40959100 AAGTAAG-AGAGTAAGTGAAG
1 AAGTAAGCA-AGTAAGTAAAC
40959120 AAG-AAGCAA
1 AAGTAAGCAA
40959129 AGACCATGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.55, C:0.06, G:0.27, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:40961767 original size:21 final size:21
Alignment explanation
Indices: 40961742--40961781 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
40961732 TATTCTTCAT
*
40961742 AATAATTAA-TAATATTGATTA
1 AATAA-TAAGTAATAGTGATTA
40961763 AATAATAAGTAATAGTGAT
1 AATAATAAGTAATAGTGAT
40961782 ATTTTAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
AATAATAAGTAATAGTGATTA
Found at i:40967634 original size:46 final size:46
Alignment explanation
Indices: 40967567--40967659 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
40967557 AACTTATTTC
40967567 AAATAAGTTTTAAATATTACACATTCTCAACAAAATAACAGAAGTA
1 AAATAAGTTTTAAATATTACACATTCTCAACAAAATAACAGAAGTA
40967613 AAATAAGTTTTAAATATTACACATTCTCAACAAAATAACAGAAGTA
1 AAATAAGTTTTAAATATTACACATTCTCAACAAAATAACAGAAGTA
40967659 A
1 A
40967660 CAGAAATAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (46 bp):
AAATAAGTTTTAAATATTACACATTCTCAACAAAATAACAGAAGTA
Found at i:40967662 original size:9 final size:9
Alignment explanation
Indices: 40967641--40967673 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
40967631 ACACATTCTC
40967641 AACA-AAAT
1 AACAGAAAT
*
40967649 AACAGAAGT
1 AACAGAAAT
40967658 AACAGAAAT
1 AACAGAAAT
40967667 AACAGAA
1 AACAGAA
40967674 TACTAAGTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.67, C:0.12, G:0.12, T:0.09
Consensus pattern (9 bp):
AACAGAAAT
Found at i:40970620 original size:32 final size:32
Alignment explanation
Indices: 40970584--40970647 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
40970574 AATTATATTA
*
40970584 AAAATTT-TAAACATTAAATTATAAATAAAAAT
1 AAAATTTCAAAACATT-AATTATAAATAAAAAT
*
40970616 AAAATTTCAAAACATTAATTATAAATATAAAT
1 AAAATTTCAAAACATTAATTATAAATAAAAAT
40970648 TGTTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 22 0.76
33 7 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (32 bp):
AAAATTTCAAAACATTAATTATAAATAAAAAT
Found at i:40983267 original size:11 final size:11
Alignment explanation
Indices: 40983251--40983275 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40983241 TAATTAACTC
40983251 AATTATCATCA
1 AATTATCATCA
40983262 AATTATCATCA
1 AATTATCATCA
40983273 AAT
1 AAT
40983276 GTAAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (11 bp):
AATTATCATCA
Found at i:41005491 original size:81 final size:80
Alignment explanation
Indices: 41005356--41005583 Score: 291
Period size: 81 Copynumber: 2.8 Consensus size: 80
41005346 ATGGGCCACC
* * * * * **
41005356 AATTATCGAAATACCCCCATAGGGTAAAATTATCGAAATAACCTCGAAAGGTAAAATTATTTAAA
1 AATTATCAAAATACCCCCATA-GGTAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAA
**
41005421 TACCCTTTAAGGGTAA
65 TACCCTCAAAGGGTAA
41005437 AATTA-CTAAAATACCCCCATAGGCTAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAA
1 AATTATC-AAAATACCCCCATAGG-TAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAA
41005501 ATACCCTCAAAGGGTAA
64 ATACCCTCAAAGGGTAA
* * *
41005518 AATTATCGAAATACCCTCATAAGGTAAAATTACCAAAATACCCTC--AGGGTAAAATTATCAAAA
1 AATTATCAAAATACCCCCAT-AGGTAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAA
41005581 TAC
65 TAC
41005584 TCTCGAAATG
Statistics
Matches: 131, Mismatches: 12, Indels: 10
0.86 0.08 0.07
Matches are distributed among these distances:
79 20 0.15
80 3 0.02
81 104 0.79
82 4 0.03
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.24
Consensus pattern (80 bp):
AATTATCAAAATACCCCCATAGGTAAAATTACCAAAATACCCTCGAAGGGTAAAATTATCGAAAT
ACCCTCAAAGGGTAA
Found at i:41005623 original size:27 final size:27
Alignment explanation
Indices: 41005364--41005624 Score: 209
Period size: 27 Copynumber: 9.7 Consensus size: 27
41005354 CCAATTATCG
* * *
41005364 AAATACCCCCATAGGGTAAAATTA-TCG
1 AAATACCCTCAAAGGGTAAAATTACT-A
* * *
41005391 AAATAACCTCGAAA-GGTAAAATTATTT
1 AAATACCCTC-AAAGGGTAAAATTACTA
**
41005418 AAATACCCTTTAAGGGTAAAATTACTA
1 AAATACCCTCAAAGGGTAAAATTACTA
* * * *
41005445 AAATACCCCCATAGGCTAAAATTACCA
1 AAATACCCTCAAAGGGTAAAATTACTA
* *
41005472 AAATACCCTCGAAGGGTAAAATTA-TCG
1 AAATACCCTCAAAGGGTAAAATTACT-A
*
41005499 AAATACCCTCAAAGGGTAAAATTA-TCG
1 AAATACCCTCAAAGGGTAAAATTACT-A
*
41005526 AAATACCCTCATAA-GGTAAAATTACCA
1 AAATACCCTCA-AAGGGTAAAATTACTA
41005553 AAATACCCTC--AGGGTAAAATTA-TCA
1 AAATACCCTCAAAGGGTAAAATTACT-A
* * *
41005578 AAATACTCTCGAAA-TGTAAAATGACTA
1 AAATACCCTC-AAAGGGTAAAATTACTA
41005605 AAATACTCC-CAAAGGGTAAA
1 AAATAC-CCTCAAAGGGTAAA
41005625 GTGACAGTTA
Statistics
Matches: 190, Mismatches: 30, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
24 1 0.01
25 20 0.11
26 5 0.03
27 156 0.82
28 8 0.04
ACGTcount: A:0.45, C:0.19, G:0.12, T:0.23
Consensus pattern (27 bp):
AAATACCCTCAAAGGGTAAAATTACTA
Found at i:41005874 original size:26 final size:26
Alignment explanation
Indices: 41005820--41005894 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
41005810 ATGCCATATA
* ***
41005820 TACTGTTATTGGTAGTTTTGCTATGT
1 TACTGTTATTGGTAGCTTTGCTGCAT
41005846 TACTGTTATTGGTAGCTTTGCTGCAT
1 TACTGTTATTGGTAGCTTTGCTGCAT
* * *
41005872 TACTATTACTGGCAGCTTTGCTG
1 TACTGTTATTGGTAGCTTTGCTG
41005895 TAATATTGGT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.47
Consensus pattern (26 bp):
TACTGTTATTGGTAGCTTTGCTGCAT
Found at i:41006050 original size:28 final size:28
Alignment explanation
Indices: 41006007--41006144 Score: 197
Period size: 28 Copynumber: 5.0 Consensus size: 28
41005997 ATTGTAATGT
41006007 TTACTGTAATGGGCTAAGGCCCACACTA
1 TTACTGTAATGGGCTAAGGCCCACACTA
* *
41006035 TTTCTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTAATGGGCTAAGGCCCACACTA
*
41006063 TTACTGTAATGGGCTAAGGCCCACAATA
1 TTACTGTAATGGGCTAAGGCCCACACTA
* * * * *
41006091 TTTCTGTATTGGGCTAAGGCCTATACTG
1 TTACTGTAATGGGCTAAGGCCCACACTA
41006119 TTACTGTAATGGGCTAAGG-CCACACT
1 TTACTGTAATGGGCTAAGGCCCACACT
41006145 GTACTGATAC
Statistics
Matches: 95, Mismatches: 15, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
27 5 0.05
28 90 0.95
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.30
Consensus pattern (28 bp):
TTACTGTAATGGGCTAAGGCCCACACTA
Found at i:41006093 original size:56 final size:56
Alignment explanation
Indices: 41006007--41006139 Score: 230
Period size: 56 Copynumber: 2.4 Consensus size: 56
41005997 ATTGTAATGT
*
41006007 TTACTGTAATGGGCTAAGGCCCACACTATTTCTGTATTGGGCTAAGGCCCACACTA
1 TTACTGTAATGGGCTAAGGCCCACAATATTTCTGTATTGGGCTAAGGCCCACACTA
* * *
41006063 TTACTGTAATGGGCTAAGGCCCACAATATTTCTGTATTGGGCTAAGGCCTATACTG
1 TTACTGTAATGGGCTAAGGCCCACAATATTTCTGTATTGGGCTAAGGCCCACACTA
41006119 TTACTGTAATGGGCTAAGGCC
1 TTACTGTAATGGGCTAAGGCC
41006140 ACACTGTACT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (56 bp):
TTACTGTAATGGGCTAAGGCCCACAATATTTCTGTATTGGGCTAAGGCCCACACTA
Found at i:41012933 original size:81 final size:80
Alignment explanation
Indices: 41012773--41013100 Score: 355
Period size: 81 Copynumber: 4.1 Consensus size: 80
41012763 ACTCCCGTAA
* *
41012773 GGTAAAATTACTGAAATACCCGT--AAGGTAAAATTACCGAAATA-CCCTATAGGGTAAAATTAC
1 GGTAAAATTATTGAAATACCC-TCAAAGGTAAAATTATCGAAATACCCCTATAGGGTAAAATTAC
*
41012835 CAAAATAACCTCAAAG
65 CAAAATACCCTCAAAG
* *
41012851 GGTAAAATTATTGACATACCCTCAAAGGGTAAAATTATCGAAATACCCCCGAT-GGGTAAAATTA
1 GGTAAAATTATTGAAATACCCTCAAA-GGTAAAATTATCGAAATA-CCCCTATAGGGTAAAATTA
** **
41012915 CCAAAGCACCCTTGAAG
64 CCAAAATACCCTCAAAG
* * *
41012932 GGTAAAATTATCGAAATACCCTCAAAAGGTAAAATTATTGAAATACCCCTATAGGGTAAAATTAT
1 GGTAAAATTATTGAAATACCCTC-AAAGGTAAAATTATCGAAATACCCCTATAGGGTAAAATTAC
*
41012997 CGAAATACCCTCAAAG
65 CAAAATACCCTCAAAG
* * * * * *
41013013 AGTAAATTTAATGAAATACCCCTGAAAGGTAAAATTA-CTTAAATA-CCCTCAAAGGGTAAAATT
1 GGTAAAATTATTGAAATA-CCCTCAAAGGTAAAATTATC-GAAATACCCCT-ATAGGGTAAAATT
*
41013076 ACCAAAATACCCCTGAAA-
63 ACCAAAATA-CCCTCAAAG
41013094 GGTAAAA
1 GGTAAAA
41013101 AGACCAAAAT
Statistics
Matches: 207, Mismatches: 32, Indels: 19
0.80 0.12 0.07
Matches are distributed among these distances:
77 1 0.00
78 19 0.09
79 2 0.01
80 27 0.13
81 139 0.67
82 19 0.09
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (80 bp):
GGTAAAATTATTGAAATACCCTCAAAGGTAAAATTATCGAAATACCCCTATAGGGTAAAATTACC
AAAATACCCTCAAAG
Found at i:41013084 original size:54 final size:54
Alignment explanation
Indices: 41012750--41013128 Score: 305
Period size: 54 Copynumber: 7.1 Consensus size: 54
41012740 AATAGGCCAC
* *
41012750 AAATTATCGAAATACTCCC-GTAAGGTAAAATTACTGAAATACCCGT--AA-GGTA
1 AAATTACCGAAATAC-CCCTGAAAGGTAAAATTACTGAAATACCC-TCAAAGGGTA
* ** *
41012802 AAATTACCGAAATA-CCCT-ATAGGGTAAAATTACCAAAATAACCTCAAAGGGTA
1 AAATTACCGAAATACCCCTGA-AAGGTAAAATTACTGAAATACCCTCAAAGGGTA
** * * * * *
41012855 AAATTATTGACATA-CCCTCAAAGGGTAAAATTA-TCGAAATACCCCCGATGGGTA
1 AAATTACCGAAATACCCCTGAAA-GGTAAAATTACT-GAAATACCCTCAAAGGGTA
* * * *
41012909 AAATTACC-AAAGCACCCTTGAAGGGTAAAATTA-TCGAAATACCCTCAAAAGGTA
1 AAATTACCGAAA-TACCCCTGAAAGGTAAAATTACT-GAAATACCCTCAAAGGGTA
** * *
41012963 AAATTATTGAAATACCCCT-ATAGGGTAAAATTA-TCGAAATACCCTCAAAGAGTA
1 AAATTACCGAAATACCCCTGA-AAGGTAAAATTACT-GAAATACCCTCAAAGGGTA
* ** *
41013017 AATTTAATGAAATACCCCTGAAAGGTAAAATTACTTAAATACCCTCAAAGGGTA
1 AAATTACCGAAATACCCCTGAAAGGTAAAATTACTGAAATACCCTCAAAGGGTA
* ** ** * *
41013071 AAATTACCAAAATACCCCTGAAAGGTAAAAAGACCAAAATACCCCCGAAGGGTA
1 AAATTACCGAAATACCCCTGAAAGGTAAAATTACTGAAATACCCTCAAAGGGTA
41013125 AAAT
1 AAAT
41013129 GACTGTTATA
Statistics
Matches: 265, Mismatches: 48, Indels: 26
0.78 0.14 0.08
Matches are distributed among these distances:
50 4 0.02
51 19 0.07
52 15 0.06
53 23 0.09
54 194 0.73
55 10 0.04
ACGTcount: A:0.45, C:0.19, G:0.14, T:0.22
Consensus pattern (54 bp):
AAATTACCGAAATACCCCTGAAAGGTAAAATTACTGAAATACCCTCAAAGGGTA
Found at i:41013106 original size:27 final size:27
Alignment explanation
Indices: 41012771--41013128 Score: 205
Period size: 27 Copynumber: 13.4 Consensus size: 27
41012761 ATACTCCCGT
** *
41012771 AAGGTAAAATTACTGAAATA-CCC-GT
1 AAGGTAAAATTACCAAAATACCCCTGA
*
41012796 AAGGTAAAATTACCGAAATA-CCCT-A
1 AAGGTAAAATTACCAAAATACCCCTGA
* * *
41012821 TAGGGTAAAATTACCAAAATA-ACCTCA
1 -AAGGTAAAATTACCAAAATACCCCTGA
*** * *
41012848 AAGGGTAAAATTATTGACATA-CCCTCA
1 AA-GGTAAAATTACCAAAATACCCCTGA
* * *
41012875 AAGGGTAAAATTATCGAAATACCCCCGA
1 AA-GGTAAAATTACCAAAATACCCCTGA
** ** *
41012903 TGGGTAAAATTACCAAAGCACCCTTGA
1 AAGGTAAAATTACCAAAATACCCCTGA
* * * *
41012930 AGGGTAAAATTATCGAAATA-CCCTCAA
1 AAGGTAAAATTACCAAAATACCCCT-GA
***
41012957 AAGGTAAAATTATTGAAATACCCCT-A
1 AAGGTAAAATTACCAAAATACCCCTGA
* * * *
41012983 TAGGGTAAAATTATCGAAATA-CCCTCA
1 -AAGGTAAAATTACCAAAATACCCCTGA
* ***
41013010 AAGAGTAAATTTAATGAAATACCCCTGA
1 AAG-GTAAAATTACCAAAATACCCCTGA
** *
41013038 AAGGTAAAATTACTTAAATA-CCCTCA
1 AAGGTAAAATTACCAAAATACCCCTGA
41013064 AAGGGTAAAATTACCAAAATACCCCTGA
1 AA-GGTAAAATTACCAAAATACCCCTGA
** *
41013092 AAGGTAAAAAGACCAAAATACCCCCGA
1 AAGGTAAAATTACCAAAATACCCCTGA
*
41013119 AGGGTAAAAT
1 AAGGTAAAAT
41013129 GACTGTTATA
Statistics
Matches: 269, Mismatches: 51, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
25 22 0.08
26 39 0.14
27 185 0.69
28 23 0.09
ACGTcount: A:0.45, C:0.19, G:0.15, T:0.22
Consensus pattern (27 bp):
AAGGTAAAATTACCAAAATACCCCTGA
Found at i:41013351 original size:26 final size:26
Alignment explanation
Indices: 41013322--41013449 Score: 150
Period size: 26 Copynumber: 4.9 Consensus size: 26
41013312 ATGCCACTTA
*
41013322 TACTGTTACTGGCATCTTTGTTGCGT
1 TACTGTTACTGGCAGCTTTGTTGCGT
*
41013348 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTGTTACTGGCAGCTTTGTTGCGT
* * *
41013374 TACTATTACTGGAAGCTTTGTTGCAT
1 TACTGTTACTGGCAGCTTTGTTGCGT
* * *
41013400 TATTGTTACTGGCAGTTTTGCTT-TGT
1 TACTGTTACTGGCAGCTTTG-TTGCGT
* *
41013426 TACTATTACTGGCAACTTTGTTGC
1 TACTGTTACTGGCAGCTTTGTTGC
41013450 AATATTAGTC
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
25 2 0.02
26 79 0.95
27 2 0.02
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.45
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTGTTGCGT
Found at i:41013393 original size:52 final size:51
Alignment explanation
Indices: 41013322--41013450 Score: 168
Period size: 52 Copynumber: 2.5 Consensus size: 51
41013312 ATGCCACTTA
* * *
41013322 TACTGTTACTGGCATCTTTGTTGCGTTACTGTTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGG-AACTTTGTTGCATTACTGTTACTGGCAGCTTTGCTGCGT
* * **
41013374 TACTATTACTGGAAGCTTTGTTGCATTATTGTTACTGGCAGTTTTGCTTTGT
1 TACTATTACTGGAA-CTTTGTTGCATTACTGTTACTGGCAGCTTTGCTGCGT
41013426 TACTATTACTGGCAACTTTGTTGCA
1 TACTATTACTGG-AACTTTGTTGCA
41013451 ATATTAGTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
51 1 0.01
52 65 0.96
53 2 0.03
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (51 bp):
TACTATTACTGGAACTTTGTTGCATTACTGTTACTGGCAGCTTTGCTGCGT
Found at i:41013608 original size:28 final size:28
Alignment explanation
Indices: 41013556--41013637 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
41013546 TACTGCATTG
41013556 TACTGTTTACTGTAATGGGCT-AGGCCCA
1 TACTGTTT-CTGTAATGGGCTAAGGCCCA
*
41013584 TACTGTTTCTGTATTGGGCTAAGGCCCA
1 TACTGTTTCTGTAATGGGCTAAGGCCCA
* * *
41013612 CATTATTTCTGTAATGGGCTAAGGCC
1 TACTGTTTCTGTAATGGGCTAAGGCC
41013638 ACACCGTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 11 0.23
28 37 0.77
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (28 bp):
TACTGTTTCTGTAATGGGCTAAGGCCCA
Found at i:41016905 original size:14 final size:14
Alignment explanation
Indices: 41016886--41016914 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41016876 AATCACTTAG
41016886 TCTGTATGTATAGT
1 TCTGTATGTATAGT
41016900 TCTGTATGTATAGT
1 TCTGTATGTATAGT
41016914 T
1 T
41016915 TCTTGCGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.21, T:0.52
Consensus pattern (14 bp):
TCTGTATGTATAGT
Found at i:41023023 original size:45 final size:45
Alignment explanation
Indices: 41022925--41023040 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 45
41022915 TTTGAGTACT
41022925 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
* *
41022971 TATGATCAAGTGACAAAGTGATAAGTGGTAGGC-TAGCTACATTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTA-GCTTAGCTACACTTA
*
41023016 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
41023041 ATCATACGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
43 12 0.18
44 5 0.08
45 17 0.26
46 29 0.45
47 2 0.03
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:41028971 original size:40 final size:40
Alignment explanation
Indices: 41028820--41029042 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
41028810 TTGAATGATG
* * * *
41028820 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
41028860 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACT-AA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41028899 TTCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41028937 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41028977 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41029018 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41029043 AACGAGGAGC
Statistics
Matches: 163, Mismatches: 13, Indels: 14
0.86 0.07 0.07
Matches are distributed among these distances:
37 13 0.08
38 20 0.12
39 20 0.12
40 100 0.61
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41036803 original size:39 final size:40
Alignment explanation
Indices: 41036702--41036924 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
41036692 TTGAATGATG
* * *
41036702 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
41036741 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
41036782 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41036821 TCCGGGTTAAGT-CCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
41036859 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
41036898 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
41036925 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
38 29 0.18
39 54 0.33
40 69 0.43
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:41036879 original size:78 final size:78
Alignment explanation
Indices: 41036702--41036922 Score: 286
Period size: 78 Copynumber: 2.8 Consensus size: 78
41036692 TTGAATGATG
* * * * *
41036702 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCA-T
*
41036766 TGTGCGAGATACTAAT
63 TGTGCGAGATACTAAA
*
41036782 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTGT
*
41036846 GCGAGTTACTAAA
66 GCGAGATACTAAA
* *
41036859 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
41036923 TGAACGAGGA
Statistics
Matches: 126, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
77 25 0.20
78 45 0.36
79 38 0.30
80 18 0.14
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTGT
GCGAGATACTAAA
Found at i:41040817 original size:29 final size:29
Alignment explanation
Indices: 41040774--41040929 Score: 169
Period size: 29 Copynumber: 5.4 Consensus size: 29
41040764 ATAATCGACC
41040774 AATGAAAAGGGATAGCTTCTGCTATTGAAT
1 AATGAAAAGGGATAGCTTCTGCTA-TGAAT
* *
41040804 -ATGAAAAGGGATAGCTTCGGCTAAAGAAT
1 AATGAAAAGGGATAGCTTCTGCT-ATGAAT
* * *
41040833 -ATGAAAAAGGATAGCTTCGGCTATCAAT
1 AATGAAAAGGGATAGCTTCTGCTATGAAT
*
41040861 AATGAAAAGGGATAGATT-TAGCTATCG-AT
1 AATGAAAAGGGATAGCTTCT-GCTAT-GAAT
*
41040890 AATGAAAAGGGATAGCTT-TGGCTATCAAT
1 AATGAAAAGGGATAGCTTCT-GCTATGAAT
41040919 AATGAAAAGGG
1 AATGAAAAGGG
41040930 TTGTTGACGA
Statistics
Matches: 109, Mismatches: 12, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
28 4 0.04
29 104 0.95
30 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (29 bp):
AATGAAAAGGGATAGCTTCTGCTATGAAT
Found at i:41040866 original size:58 final size:58
Alignment explanation
Indices: 41040774--41040929 Score: 199
Period size: 58 Copynumber: 2.7 Consensus size: 58
41040764 ATAATCGACC
* * * *
41040774 AATGAAAAGGGATAGCTTCTGCTATTGAAT-ATGAAAAGGGATAGCTTCGGCTAAAGA-
1 AATGAAAAGGGATAGCTTCGGCTA-TCAATAATGAAAAGGGATAGATTCAGCTAAAGAT
* * **
41040831 ATATGAAAAAGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTTAGCTATCGAT
1 A-ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTCAGCTAAAGAT
*
41040890 AATGAAAAGGGATAGCTTTGGCTATCAATAATGAAAAGGG
1 AATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGG
41040930 TTGTTGACGA
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
57 5 0.06
58 80 0.93
59 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.25, T:0.25
Consensus pattern (58 bp):
AATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTCAGCTAAAGAT
Found at i:41040946 original size:87 final size:88
Alignment explanation
Indices: 41040774--41040960 Score: 199
Period size: 87 Copynumber: 2.1 Consensus size: 88
41040764 ATAATCGACC
* * *
41040774 AATGAAAAGGGATAGCTTCTGCTATTGAATATGAAAAGGGATAGCTTCGGCTAAAGAATATGAAA
1 AATGAAAAGGGATAGATTCTGCTATCGAATATGAAAAGGGATAGCTTCGGCTAAACAATATGAAA
* *
41040839 AAGGATAGCTTCGGCTATCAA-T
66 AAGGATAGCTTCGACCATCAACT
* *
41040861 AATGAAAAGGGATAGATT-TAGCTATCG-ATAATGAAAAGGGATAGCTTTGGCT-ATCAATAATG
1 AATGAAAAGGGATAGATTCT-GCTATCGAAT-ATGAAAAGGGATAGCTTCGGCTAAACAAT-ATG
* *
41040923 -AAAAGGGTTG-TTGACGACCATCAACT
63 AAAAAGGATAGCTT--CGACCATCAACT
41040949 -ATGAAAAGGGAT
1 AATGAAAAGGGAT
41040961 GGTGACAACC
Statistics
Matches: 85, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
85 2 0.02
86 15 0.18
87 67 0.79
88 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.25
Consensus pattern (88 bp):
AATGAAAAGGGATAGATTCTGCTATCGAATATGAAAAGGGATAGCTTCGGCTAAACAATATGAAA
AAGGATAGCTTCGACCATCAACT
Found at i:41040953 original size:58 final size:57
Alignment explanation
Indices: 41040775--41040960 Score: 173
Period size: 58 Copynumber: 3.2 Consensus size: 57
41040765 TAATCGACCA
* * * * **
41040775 ATGAAAAGGGATAGCTTCTGCTATTGAAT-ATGAAAAGGGATAGCTTCG-GCTAAAGAAT
1 ATGAAAAGGGATAGCTTCGGCTA-TCAATAATGAAAAGGGATAGATT-GAGC-CATCAAT
* * * *
41040833 ATGAAAAAGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTTAGCTATCGAT
1 ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTGAGCCATCAAT
* *
41040890 AATGAAAAGGGATAGCTTTGGCTATCAATAATGAAAAGGG-TTG-TTGACGACCATCAACT
1 -ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTGA-G-CCATCAA-T
41040949 ATGAAAAGGGAT
1 ATGAAAAGGGAT
41040961 GGTGACAACC
Statistics
Matches: 107, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
56 3 0.03
57 10 0.09
58 93 0.87
59 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (57 bp):
ATGAAAAGGGATAGCTTCGGCTATCAATAATGAAAAGGGATAGATTGAGCCATCAAT
Found at i:41040985 original size:30 final size:30
Alignment explanation
Indices: 41040918--41041023 Score: 160
Period size: 30 Copynumber: 3.6 Consensus size: 30
41040908 TGGCTATCAA
* * * * *
41040918 TAATGAAAAGGGTTGTTGACGACCATCAAC
1 TAATGAAAAGGGATGGTGACAACCATCGAT
41040948 T-ATGAAAAGGGATGGTGACAACCATCGAT
1 TAATGAAAAGGGATGGTGACAACCATCGAT
41040977 TAATGAAAAGGGATGGTGACAACCATCGAT
1 TAATGAAAAGGGATGGTGACAACCATCGAT
41041007 TAATGAAAAGGGATGGT
1 TAATGAAAAGGGATGGT
41041024 TTTGACCATC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 24 0.34
30 46 0.66
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (30 bp):
TAATGAAAAGGGATGGTGACAACCATCGAT
Found at i:41041032 original size:30 final size:30
Alignment explanation
Indices: 41040858--41041054 Score: 133
Period size: 29 Copynumber: 6.7 Consensus size: 30
41040848 TTCGGCTATC
* *
41040858 AATAATGAAAAGGGATAGATTTA-G-CTATCG
1 AATAATGAAAAGGGAT-G-GTTACGACCATCG
* * * *
41040888 -ATAATGAAAAGGGATAGCTT-TGGCTATC-
1 AATAATGAAAAGGGAT-GGTTACGACCATCG
*
41040916 AATAATGAAAAGGG-TTGTTGACGACCATC-
1 AATAATGAAAAGGGATGGTT-ACGACCATCG
* *
41040945 AACT-ATGAAAAGGGATGGTGACAACCATCG
1 AA-TAATGAAAAGGGATGGTTACGACCATCG
* * *
41040975 ATTAATGAAAAGGGATGGTGACAACCATCG
1 AATAATGAAAAGGGATGGTTACGACCATCG
* **
41041005 ATTAATGAAAAGGGATGGTTTTGACCATCG
1 AATAATGAAAAGGGATGGTTACGACCATCG
* *
41041035 AAT-AGGAAAAGGGACGGTTA
1 AATAATGAAAAGGGATGGTTA
41041055 TGGAAAGGTA
Statistics
Matches: 140, Mismatches: 18, Indels: 19
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.01
28 4 0.03
29 75 0.54
30 59 0.42
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.23
Consensus pattern (30 bp):
AATAATGAAAAGGGATGGTTACGACCATCG
Found at i:41041044 original size:59 final size:59
Alignment explanation
Indices: 41040884--41041048 Score: 165
Period size: 59 Copynumber: 2.8 Consensus size: 59
41040874 AGATTTAGCT
* * * * * * *
41040884 ATCGATAATGAAAAGGGATAGCTTTGGCTATC-AATAATGAAAAGGGTTGTTGACGACC
1 ATCGATAATGAAAAGGGATGGTTTTGACCATCGAATAATGAAAAGGGATGGTGACAACC
* **** *
41040942 ATCAACT-ATGAAAAGGGATGGTGACAACCATCGATTAATGAAAAGGGATGGTGACAACC
1 ATCGA-TAATGAAAAGGGATGGTTTTGACCATCGAATAATGAAAAGGGATGGTGACAACC
*
41041001 ATCGATTAATGAAAAGGGATGGTTTTGACCATCGAAT-AGGAAAAGGGA
1 ATCGA-TAATGAAAAGGGATGGTTTTGACCATCGAATAATGAAAAGGGA
41041049 CGGTTATGGA
Statistics
Matches: 83, Mismatches: 21, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
58 21 0.25
59 38 0.46
60 24 0.29
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (59 bp):
ATCGATAATGAAAAGGGATGGTTTTGACCATCGAATAATGAAAAGGGATGGTGACAACC
Found at i:41047019 original size:59 final size:58
Alignment explanation
Indices: 41046931--41047079 Score: 149
Period size: 59 Copynumber: 2.6 Consensus size: 58
41046921 AGCTTTGGCT
* * * * * * *
41046931 ATCGATAATGTAAAGGAATGGTGAT-GACCATTAATTATGAAAAGGGGTGGTGACAACC
1 ATCGATAATGAAAAGGGATGGT-TTCGACCATCAAATATGAAAACGGATGGTGACAACC
** *
41046989 ATCGATTAATGAAAAGGGATGGTTTCGACCATCAAATATGAAAACGGATGGTTCCAATC
1 ATCGA-TAATGAAAAGGGATGGTTTCGACCATCAAATATGAAAACGGATGGTGACAACC
* *
41047048 ATCGA-ATATGAAAAGGGACGGTTACGACCATC
1 ATCGATA-ATGAAAAGGGATGGTTTCGACCATC
41047080 GTTTAGCACA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
57 1 0.01
58 29 0.38
59 46 0.61
ACGTcount: A:0.38, C:0.14, G:0.25, T:0.23
Consensus pattern (58 bp):
ATCGATAATGAAAAGGGATGGTTTCGACCATCAAATATGAAAACGGATGGTGACAACC
Found at i:41047079 original size:58 final size:59
Alignment explanation
Indices: 41046956--41047079 Score: 151
Period size: 59 Copynumber: 2.1 Consensus size: 59
41046946 GAATGGTGAT
* * * * * * *
41046956 GACCATTAATTATGAAAAGGGGTGGTGACAACCATCGATTAATGAAAAGGGATGGTTTC
1 GACCATCAAATATGAAAACGGATGGTGACAACCATCGAATAATGAAAAGGGACGGTTAC
** *
41047015 GACCATCAAATATGAAAACGGATGGTTCCAATCATCGAAT-ATGAAAAGGGACGGTTAC
1 GACCATCAAATATGAAAACGGATGGTGACAACCATCGAATAATGAAAAGGGACGGTTAC
41047073 GACCATC
1 GACCATC
41047080 GTTTAGCACA
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
58 23 0.42
59 32 0.58
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (59 bp):
GACCATCAAATATGAAAACGGATGGTGACAACCATCGAATAATGAAAAGGGACGGTTAC
Found at i:41047080 original size:29 final size:29
Alignment explanation
Indices: 41046880--41047080 Score: 138
Period size: 29 Copynumber: 6.9 Consensus size: 29
41046870 TCATTGAACA
*
41046880 ATGAAAAGGGATGGTGACAACCATCGAAT
1 ATGAAAAGGGATGGTTACAACCATCGAAT
* *** *
41046909 ATGAAAAGGGATAGCTT-TGGCTATCG-AT
1 ATGAAAAGGGAT-GGTTACAACCATCGAAT
* * * ** *
41046937 AATGTAAAGGAATGGTGATGACCAT-TAATT
1 -ATGAAAAGGGATGGTTACAACCATCGAA-T
* * *
41046967 ATGAAAAGGGGTGGTGACAACCATCGATT
1 ATGAAAAGGGATGGTTACAACCATCGAAT
* * *
41046996 AATGAAAAGGGATGGTTTCGACCATCAAAT
1 -ATGAAAAGGGATGGTTACAACCATCGAAT
* * *
41047026 ATGAAAACGGATGGTTCCAATCATCGAAT
1 ATGAAAAGGGATGGTTACAACCATCGAAT
* *
41047055 ATGAAAAGGGACGGTTACGACCATCG
1 ATGAAAAGGGATGGTTACAACCATCG
41047081 TTTAGCACAT
Statistics
Matches: 129, Mismatches: 36, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
28 4 0.03
29 98 0.76
30 27 0.21
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.23
Consensus pattern (29 bp):
ATGAAAAGGGATGGTTACAACCATCGAAT
Found at i:41053920 original size:50 final size:49
Alignment explanation
Indices: 41053866--41053991 Score: 141
Period size: 49 Copynumber: 2.6 Consensus size: 49
41053856 TCCTCCATAG
* *
41053866 GACCATGTCTGGGACATGGCA-TGAGAATCGATACAA-TAAC-TCCCATGTAA
1 GACCATGTCTGGGACATGGCATTG-G---CAATACAAGAAACATCCCATGTAA
* * *
41053916 GACCATATCTGGGATATGACATTGGCAATACAAGAAACATCCCATGTAA
1 GACCATGTCTGGGACATGGCATTGGCAATACAAGAAACATCCCATGTAA
*
41053965 GACCATGTCTGGGACATGGCTTTGGCA
1 GACCATGTCTGGGACATGGCATTGGCA
41053992 TGTTATTATC
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
47 7 0.11
48 3 0.05
49 33 0.52
50 19 0.30
51 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (49 bp):
GACCATGTCTGGGACATGGCATTGGCAATACAAGAAACATCCCATGTAA
Found at i:41057176 original size:27 final size:27
Alignment explanation
Indices: 41057162--41057222 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
41057152 CCCTCGTATT
41057162 ATAAAATGAACGAAATACCCCCATAAG
1 ATAAAATGAACGAAATACCCCCATAAG
* * *
41057189 GTAAAATGACCGAAATACCCCCATAGG
1 ATAAAATGAACGAAATACCCCCATAAG
41057216 ATAAAAT
1 ATAAAAT
41057223 AACTGTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.49, C:0.21, G:0.13, T:0.16
Consensus pattern (27 bp):
ATAAAATGAACGAAATACCCCCATAAG
Found at i:41057435 original size:26 final size:26
Alignment explanation
Indices: 41057381--41057435 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
41057371 TGGAGTAAGT
* * *
41057381 ATACTGTTACTGCCATATTTGTTGTG
1 ATACTGTTACTGCCAGATTTGCTGCG
* *
41057407 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGCCAGATTTGCTGCG
41057433 ATA
1 ATA
41057436 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.40
Consensus pattern (26 bp):
ATACTGTTACTGCCAGATTTGCTGCG
Found at i:41062116 original size:14 final size:14
Alignment explanation
Indices: 41062097--41062126 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
41062087 TTGTGCTTTT
41062097 ACATGCCCTTTTAA
1 ACATGCCCTTTTAA
41062111 ACATGCCCTTTTAA
1 ACATGCCCTTTTAA
41062125 AC
1 AC
41062127 TTAAAATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (14 bp):
ACATGCCCTTTTAA
Found at i:41069880 original size:22 final size:21
Alignment explanation
Indices: 41069855--41069898 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
41069845 TGATAAACTT
41069855 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
41069877 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
41069898 T
1 T
41069899 CAACTTAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:41075282 original size:27 final size:27
Alignment explanation
Indices: 41075219--41075288 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
41075209 AATATAATAT
* *
41075219 AATTATAAAATAATTAAATTGTACTTA
1 AATTATAACATAATTAAATTGTAATTA
*
41075246 AATTATTAACAT-ATTAAATTTTAATTA
1 AATTA-TAACATAATTAAATTGTAATTA
* *
41075273 ATTTTATAACAAAATT
1 A-ATTATAACATAATT
41075289 TCATAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
27 24 0.69
28 11 0.31
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.44
Consensus pattern (27 bp):
AATTATAACATAATTAAATTGTAATTA
Found at i:41075850 original size:16 final size:16
Alignment explanation
Indices: 41075829--41075863 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41075819 CTTTCACCTA
41075829 TTCATTCAACACACTT
1 TTCATTCAACACACTT
* *
41075845 TTCATTCCACACATTT
1 TTCATTCAACACACTT
41075861 TTC
1 TTC
41075864 TTTTTTACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.31, G:0.00, T:0.43
Consensus pattern (16 bp):
TTCATTCAACACACTT
Found at i:41080249 original size:10 final size:10
Alignment explanation
Indices: 41080216--41080240 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
41080206 TATCATACAC
41080216 TGTGACTAAA
1 TGTGACTAAA
41080226 TGTGACTAAA
1 TGTGACTAAA
41080236 TGTGA
1 TGTGA
41080241 TTACATGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.32
Consensus pattern (10 bp):
TGTGACTAAA
Found at i:41083923 original size:14 final size:14
Alignment explanation
Indices: 41083904--41083930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41083894 TTGCAATACT
41083904 ATAAAAGAAGTAAA
1 ATAAAAGAAGTAAA
41083918 ATAAAAGAAGTAA
1 ATAAAAGAAGTAA
41083931 GCATAAATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
ATAAAAGAAGTAAA
Found at i:41084501 original size:50 final size:49
Alignment explanation
Indices: 41084263--41084552 Score: 206
Period size: 50 Copynumber: 5.7 Consensus size: 49
41084253 GATAATAACA
* * ** * * *
41084263 TGCCAAAGCCATGTCCCAGACATGGTTTTACATAGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGACCTCTCATCT-CGG
* * * * ** *
41084312 TGCCAATGCCATATCCCATATATTGTCTTACATGAGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GACCTCTCATCTCGG
* * * *** *
41084362 TGCCCATGCCATATCCTAGACATGGTCTTATGGGGGGCCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTA-CATGGACCTCTCATCTCGG
* * *
41084412 TGCCAACGCCATGTCCAAGACATGGTCTTCCATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG-GACCTCTCATCTCGG
* * *
41084462 TGCCAATGCCATGTCCCAGACATGGTCTTACATAGGACCTATGATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGACC--T-CTCATCTC---GG
*
41084518 TGCCAATGCCATGTCCCAAACATGGTCTTACATGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGG
41084553 GATCTCTTTA
Statistics
Matches: 190, Mismatches: 39, Indels: 18
0.77 0.16 0.07
Matches are distributed among these distances:
48 2 0.01
49 35 0.18
50 109 0.57
51 2 0.01
52 1 0.01
53 6 0.03
55 2 0.01
56 33 0.17
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGACCTCTCATCTCGG
Found at i:41084927 original size:29 final size:30
Alignment explanation
Indices: 41084895--41084954 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
41084885 ACCCTCGACT
*
41084895 CTAAGTTTTGA-AAAATTACGA-TTTTGCCC
1 CTAAATTTTGACAAAATTAC-ACTTTTGCCC
* *
41084924 CTAAATTTTTACAGAATTACACTTTTGCCC
1 CTAAATTTTGACAAAATTACACTTTTGCCC
41084954 C
1 C
41084955 AAAGCTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (30 bp):
CTAAATTTTGACAAAATTACACTTTTGCCC
Found at i:41091658 original size:29 final size:29
Alignment explanation
Indices: 41091624--41091697 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
41091614 TAATCAACCA
*
41091624 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
41091653 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
41091682 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
41091698 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:41099743 original size:29 final size:29
Alignment explanation
Indices: 41099709--41099782 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
41099699 TAATCAACCA
*
41099709 CGCACACTTAGTGCCATGTACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAACT
**
41099738 CGCACACTTAGTGCCATGCATTTCAAGTT
1 CGCACACTTAGTGCCATGCATTTCAAACT
*
41099767 CGCACACCTAGTGCCA
1 CGCACACTTAGTGCCA
41099783 ATCTCACAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 3 0.08
29 37 0.93
ACGTcount: A:0.26, C:0.31, G:0.16, T:0.27
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAACT
Found at i:41110172 original size:15 final size:15
Alignment explanation
Indices: 41110152--41110259 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
41110142 TTTATGGAAA
41110152 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
41110167 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
41110181 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41110197 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41110211 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41110227 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41110241 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
41110257 ATC
1 ATC
41110260 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41110189 original size:30 final size:30
Alignment explanation
Indices: 41110146--41110269 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
41110136 TCCATATTTA
* *
41110146 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
41110176 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
41110206 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
41110236 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
41110267 TGG
1 TGG
41110270 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:41114847 original size:15 final size:15
Alignment explanation
Indices: 41114827--41114934 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
41114817 TTTATGGAAA
41114827 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
41114842 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
41114856 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41114872 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41114886 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
41114902 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
41114916 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
41114932 ATC
1 ATC
41114935 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:41114864 original size:30 final size:30
Alignment explanation
Indices: 41114821--41114944 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
41114811 TCCATATTTA
* *
41114821 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
41114851 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
41114881 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
41114911 TGGAAAGTCAAAGATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
41114942 TGG
1 TGG
41114945 CATAATAAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 80 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:41117152 original size:37 final size:37
Alignment explanation
Indices: 41117102--41117180 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
41117092 TTATTACGAA
* *
41117102 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTC-CCACACGAAGTCATCGG
*
41117139 GTCTTACCCGGACAAAATTCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
41117176 GTCTT
1 GTCTT
41117181 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.95
38 2 0.05
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCCCACACGAAGTCATCGG
Found at i:41117416 original size:47 final size:47
Alignment explanation
Indices: 41117299--41117867 Score: 946
Period size: 47 Copynumber: 12.1 Consensus size: 47
41117289 CCCTTCGGGA
* * * * * * *
41117299 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
**
41117346 C-CGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41117392 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41117439 CTTAT--CATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41117484 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41117531 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41117578 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41117627 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41117674 CTTATCACACATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41117721 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41117768 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41117815 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41117864 CTTA
1 CTTA
41117868 CTATCATTTC
Statistics
Matches: 498, Mismatches: 17, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
45 45 0.09
46 37 0.07
47 328 0.66
49 88 0.18
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41117777 original size:237 final size:235
Alignment explanation
Indices: 41117353--41117867 Score: 976
Period size: 237 Copynumber: 2.2 Consensus size: 235
41117343 GGCCCGTCAC
41117353 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
*
41117418 TCATCACATCGGCCATTAGGCCTTATCATATATACACTTTCACATTCATCACATCGGCCATTAGG
66 TCATCACATCGGCCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCCATTAGG
*
41117483 CCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
131 CCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
41117548 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
196 CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
41117588 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
* *
41117653 TCATCACATCGGCTATTAGGCCTTATCACACATATACACTTTCACATTCATCACATCGGCTATTA
66 TCATCACATCGGCCATTAGGCCTTAT--CACATATACACTTTCACATTCATCACATCGGCCATTA
41117718 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATA
129 GGCCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATA
41117783 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
194 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
41117825 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTA
41117868 CTATCATTTC
Statistics
Matches: 274, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
235 90 0.33
237 184 0.67
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.32
Consensus pattern (235 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACATATACACTTTCACATTCATCACATCGGCCATTAGG
CCTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACA
CTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT
Found at i:41122857 original size:19 final size:20
Alignment explanation
Indices: 41122820--41122857 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
41122810 AGTCCATCCC
*
41122820 AAAAATGATATCAAAATCAT
1 AAAAATGATAACAAAATCAT
*
41122840 AAAAATG-TAACAACATCA
1 AAAAATGATAACAAAATCA
41122858 AACTAGCGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 9 0.56
20 7 0.44
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (20 bp):
AAAAATGATAACAAAATCAT
Found at i:41130533 original size:24 final size:24
Alignment explanation
Indices: 41130481--41130539 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
41130471 AATAGTGTTG
* *
41130481 ATTTTGGTACGATATGGTAATGGG
1 ATTTTGGTACGAAATGGTAATGGA
*
41130505 GTTTTGGTACGAAATGGT-ATGGAA
1 ATTTTGGTACGAAATGGTAATGG-A
41130529 ATTTTGGTACG
1 ATTTTGGTACG
41130540 TAATAGACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.13
24 26 0.87
ACGTcount: A:0.25, C:0.05, G:0.32, T:0.37
Consensus pattern (24 bp):
ATTTTGGTACGAAATGGTAATGGA
Found at i:41134815 original size:16 final size:15
Alignment explanation
Indices: 41134779--41134814 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
41134769 TTTTCACTCG
41134779 CTTTTTCTTTTTCAT
1 CTTTTTCTTTTTCAT
41134794 CTTTTTCTTTTCTCA-
1 CTTTTTCTTTT-TCAT
41134809 CTTTTT
1 CTTTTT
41134815 TTCACTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.85
16 3 0.15
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (15 bp):
CTTTTTCTTTTTCAT
Found at i:41137027 original size:18 final size:18
Alignment explanation
Indices: 41136988--41137030 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
41136978 TCACAACACT
*
41136988 TTTTTTTTAAATTCACGA
1 TTTTTTTTAAATTCACCA
* *
41137006 TTTTTTTTCAATTCACCC
1 TTTTTTTTAAATTCACCA
41137024 TTTTTTT
1 TTTTTTT
41137031 ATAATTTCGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.16, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTTTTTAAATTCACCA
Found at i:41137036 original size:18 final size:18
Alignment explanation
Indices: 41136989--41137036 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
41136979 CACAACACTT
*
41136989 TTTTTTTA-AATTCACGA
1 TTTTTTTATAATTCACCA
*
41137006 TTTTTTT-TCAATTCACCC
1 TTTTTTTAT-AATTCACCA
41137024 TTTTTTTATAATT
1 TTTTTTTATAATT
41137037 TCGTATGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 7 0.27
18 18 0.69
19 1 0.04
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTTTATAATTCACCA
Found at i:41140742 original size:28 final size:28
Alignment explanation
Indices: 41140694--41140842 Score: 176
Period size: 28 Copynumber: 5.4 Consensus size: 28
41140684 TATACAGTAT
*
41140694 CAGT-ACAGTGT-GGCCATAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
*
41140720 CAGTAACAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* *
41140748 CAGAAATAGTGTGGGCCTTAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* * * *
41140776 CACTAACAATATGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* * *
41140804 TAGAAATAGTGTGGGCCTTAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
41140832 CAGTAAACAGT
1 CAGT-AACAGT
41140843 ACAATGTAGT
Statistics
Matches: 99, Mismatches: 21, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
26 4 0.04
27 7 0.07
28 83 0.84
29 5 0.05
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.23
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCATTA
Found at i:41140791 original size:56 final size:56
Alignment explanation
Indices: 41140700--41140833 Score: 216
Period size: 56 Copynumber: 2.4 Consensus size: 56
41140690 GTATCAGTAC
* * * *
41140700 AGTGT-GGCCATAGCCCATTACAGTAACAGTGTGGGCCTTAGCCCAATACAGAAAT
1 AGTGTGGGCCTTAGCCCATTACACTAACAATATGGGCCTTAGCCCAATACAGAAAT
*
41140755 AGTGTGGGCCTTAGCCCATTACACTAACAATATGGGCCTTAGCCCAATATAGAAAT
1 AGTGTGGGCCTTAGCCCATTACACTAACAATATGGGCCTTAGCCCAATACAGAAAT
41140811 AGTGTGGGCCTTAGCCCATTACA
1 AGTGTGGGCCTTAGCCCATTACA
41140834 GTAAACAGTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
55 5 0.07
56 68 0.93
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (56 bp):
AGTGTGGGCCTTAGCCCATTACACTAACAATATGGGCCTTAGCCCAATACAGAAAT
Found at i:41140977 original size:26 final size:26
Alignment explanation
Indices: 41140948--41141050 Score: 179
Period size: 26 Copynumber: 4.0 Consensus size: 26
41140938 ACACCAATAT
*
41140948 CGCAACAAAGCTGCCAGTAATAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
*
41140974 CGCAGCAAAGCTGCCAGTAACAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
41141000 CGCAACAAAGCTGCCAGTAACAGTAA
1 CGCAACAAAGCTGCCAGTAACAGTAA
*
41141026 CGCAACAAAGCTGCCAGTAAGAGTA
1 CGCAACAAAGCTGCCAGTAACAGTA
41141051 TATGTGGCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.41, C:0.25, G:0.21, T:0.13
Consensus pattern (26 bp):
CGCAACAAAGCTGCCAGTAACAGTAA
Found at i:41141259 original size:27 final size:27
Alignment explanation
Indices: 41141229--41141730 Score: 434
Period size: 27 Copynumber: 18.7 Consensus size: 27
41141219 TCCATTTCCT
**
41141229 AGGGGTATAACGGTAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
41141256 AGGGGTATTTCGATCATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * **
41141283 GGGGGTATTTTGGTCCTTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * *
41141310 GGGGGTATTTCAGTAATTTTACCCTTT
1 AGGGGTATTTCGGTAATTTTACCCTTC
** *
41141337 ATTGGTATTTCGATAATTTTACCCTT-
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * *
41141363 TGAGGGTATTTCGATAATTTTACTCTAT-
1 AG-GGGTATTTCGGTAATTTTACCCT-TC
*
41141391 AGGGGTATTTTGGTAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
*
41141418 AAGGGTATTTCGGTAATTTTACCCTT-
1 AGGGGTATTTCGGTAATTTTACCCTTC
* * * * *
41141444 TGAGGGTATTTTGATAATTTTACGCTTT
1 AG-GGGTATTTCGGTAATTTTACCCTTC
* * *
41141472 GGGGGTATTTCAGTAATTTTACCCATC
1 AGGGGTATTTCGGTAATTTTACCCTTC
** ***
41141499 AATGGTATTTTAATAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
41141526 -GAGGGTACTTCAGTAATTTTACCCTT-
1 AG-GGGTATTTCGGTAATTTTACCCTTC
* *
41141552 AGGGGTATTTTGTTAATTTTACCCTT-
1 AGGGGTATTTCGGTAATTTTACCCTTC
* *
41141578 TGTGGGTATTTTGGTAATTTTACCCTAT-
1 AG-GGGTATTTCGGTAATTTTACCCT-TC
*
41141606 AGGGGTATTTCTGTAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
*
41141633 -GAGGGTATTTCGATAATTTTACCCTTC
1 AG-GGGTATTTCGGTAATTTTACCCTTC
* * **
41141660 AAGAG--TTTCAATAATTTTACCCTTC
1 AGGGGTATTTCGGTAATTTTACCCTTC
41141685 -GAGGGTATTTCGGTAATTTTACCCTAT-
1 AG-GGGTATTTCGGTAATTTTACCCT-TC
*
41141712 AGAGGTATTTCGGTAATTT
1 AGGGGTATTTCGGTAATTT
41141731 GTGGCCCATT
Statistics
Matches: 388, Mismatches: 70, Indels: 34
0.79 0.14 0.07
Matches are distributed among these distances:
25 21 0.05
26 24 0.06
27 336 0.87
28 7 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.44
Consensus pattern (27 bp):
AGGGGTATTTCGGTAATTTTACCCTTC
Found at i:41141303 original size:54 final size:53
Alignment explanation
Indices: 41141242--41141730 Score: 488
Period size: 54 Copynumber: 9.1 Consensus size: 53
41141232 GGTATAACGG
* * *
41141242 TAATTTTACCCTTC-AGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTTGG
1 TAATTTTACCCTTCGA-GGGTATTTCGATAATTTTACCCTT-AGGGGTATTTTGA
** * ** *
41141296 TCCTTTTACCCTTCGGGGGTATTTC-AGTAATTTTACCCTTTATTGGTATTTCGA
1 TAATTTTACCCTTCGAGGGTATTTCGA-TAATTTTACCC-TTAGGGGTATTTTGA
* * *
41141350 TAATTTTACCCTTTGAGGGTATTTCGATAATTTTACTCTATAGGGGTATTTTGG
1 TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCT-TAGGGGTATTTTGA
* * *
41141404 TAATTTTACCCTTCAAGGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTTGA
1 TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTAG-GGGTATTTTGA
* * * * ** *
41141458 TAATTTTACGCTTTGGGGGTATTTC-AGTAATTTTACCCATCAATGGTATTTTAA
1 TAATTTTACCCTTCGAGGGTATTTCGA-TAATTTTACCC-TTAGGGGTATTTTGA
* *
41141512 TAATTTTACCCTTCGAGGGTACTTC-AGTAATTTTACCCTTAGGGGTATTTTGT
1 TAATTTTACCCTTCGAGGGTATTTCGA-TAATTTTACCCTTAGGGGTATTTTGA
* * * *
41141565 TAATTTTACCCTTTGTGGGTATTTTGGTAATTTTACCCTATAGGGGTATTTCTG-
1 TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCT-TAGGGGTATTT-TGA
* * **
41141619 TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTCAAGAG--TTTCAA
1 TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTT-AGGGGTATTTTGA
* * * *
41141671 TAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACCCTATAGAGGTATTTCGG
1 TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCT-TAGGGGTATTTTGA
41141725 TAATTT
1 TAATTT
41141731 GTGGCCCATT
Statistics
Matches: 357, Mismatches: 62, Indels: 32
0.79 0.14 0.07
Matches are distributed among these distances:
52 43 0.12
53 49 0.14
54 259 0.73
55 6 0.02
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.44
Consensus pattern (53 bp):
TAATTTTACCCTTCGAGGGTATTTCGATAATTTTACCCTTAGGGGTATTTTGA
Found at i:41141335 original size:81 final size:80
Alignment explanation
Indices: 41141241--41141730 Score: 504
Period size: 81 Copynumber: 6.1 Consensus size: 80
41141231 GGGTATAACG
* * * * **
41141241 GTAATTTTACCCTTCAGGGGTATTTCGATCATTTTACCCTTCGGGGGTATTTTGGTCCTTTTACC
1 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACC
41141306 CTTCGGGGGTATTTCA
66 CTT-GGGGGTATTTCA
* ** * * *
41141322 GTAATTTTACCCTTTATTGGTATTTCGATAATTTTACCCTTTGAGGGTATTTCGATAATTTTACT
1 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACC
* **
41141387 CTATAGGGGTATTTTG
66 CT-TGGGGGTATTTCA
* * * *
41141403 GTAATTTTACCCTTCAAGGGTATTTCGGTAATTTTACCCTTTGAGGGTATTTTGATAATTTTACG
1 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTAC-
*
41141468 CTTTGGGGGTATTTCA
65 CCTTGGGGGTATTTCA
* * ** * *
41141484 GTAATTTTACCCATCAATGGTATTTTAATAATTTTACCCTTCGAGGGTACTTCAGTAATTTTACC
1 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACC
* *
41141549 CTTAGGGGTATTT-T
66 CTTGGGGGTATTTCA
*** * * * *
41141563 GTTAATTTTACCCTTTGTGGGTATTTTGGTAATTTTACCCTATAG-GGGTATTTCTGTAATTTTA
1 G-TAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCT-TCGAGGGTATTTCGGTAATTTTA
*
41141627 CCCTTCGAGGGTATTTC-
64 CCCTT-GGGGGTATTTCA
* *
41141644 GATAATTTTACCCTTCAAGAG--TTTCAATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTAC
1 G-TAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTAC
* * *
41141707 CCTATAGAGGTATTTCG
65 CCT-TGGGGGTATTTCA
41141724 GTAATTT
1 GTAATTT
41141731 GTGGCCCATT
Statistics
Matches: 338, Mismatches: 62, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
78 2 0.01
79 52 0.15
80 68 0.20
81 214 0.63
82 2 0.01
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (80 bp):
GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCGGTAATTTTACC
CTTGGGGGTATTTCA
Done.