Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 56 of 135
Found at i:15913147 original size:21 final size:21
Alignment explanation
Indices: 15913123--15913165 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
15913113 AATATTTATT
*
15913123 TCGGTAGAAGAGTCACTTGTA
1 TCGGTAGAACAGTCACTTGTA
* *
15913144 TCGGTAGACCTGTCACTTGTA
1 TCGGTAGAACAGTCACTTGTA
15913165 T
1 T
15913166 TAGTATAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (21 bp):
TCGGTAGAACAGTCACTTGTA
Found at i:15918011 original size:50 final size:50
Alignment explanation
Indices: 15917951--15918218 Score: 188
Period size: 50 Copynumber: 5.3 Consensus size: 50
15917941 CTTTATCTCA
* * * *
15917951 CTGAAGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCTTATATCC
1 CTGAAGTTGCAGTGGAGCAGGATGAAGCTACAAAAGCAAATCTTATATCC
* * * * * *
15918001 CTGAAGTTGCAATGGATC-GGATTAAAGCTACGAAAGCAAATTCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGGA-TGAAGCTACAAAAGCAAA-TCTTATATCC
* * * **
15918052 CTGAAGTTGCAGTAGAGTAGGATGAAGCTACAAAACCAAATCCAATA-CTC
1 CTGAAGTTGCAGTGGAGCAGGATGAAGCTACAAAAGCAAATCTTATATC-C
* * * * *
15918102 TTGAAGTTGCAGTGG-GTC-GGTTTAAAG-T-CATGAAAGCAAATTTTTATCTCC
1 CTGAAGTTGCAGTGGAG-CAGG-ATGAAGCTACA--AAAGCAAA-TCTTATATCC
* * * * *
15918153 CTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCC
1 CTGAAGTTGCAGTGGAGCAGGATGAAGCTACAAAAGCAAATCTTATATCC
*
15918203 TTGAAGTTGCAGTGGA
1 CTGAAGTTGCAGTGGA
15918219 TTAGATTGAG
Statistics
Matches: 163, Mismatches: 41, Indels: 28
0.70 0.18 0.12
Matches are distributed among these distances:
48 2 0.01
49 7 0.04
50 80 0.49
51 65 0.40
52 7 0.04
53 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (50 bp):
CTGAAGTTGCAGTGGAGCAGGATGAAGCTACAAAAGCAAATCTTATATCC
Found at i:15918079 original size:101 final size:101
Alignment explanation
Indices: 15917943--15918219 Score: 369
Period size: 101 Copynumber: 2.7 Consensus size: 101
15917933 TAACATACCT
* * *
15917943 TTATCTCACTGAAGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCTTATATCCCTGAAGT
1 TTATCTCACTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
*
15918008 TGCAATGGATCGGATTAAAG-CTACGAAAGCAAATTC
66 TGCAGTGGATCGGATTAAAGTC-ACGAAAGCAAATTC
* * * * * * *
15918044 TTATCTCTCTGAAGTTGCAGTAGAGTAGGATGAAGCTACAAAACCAAATCCAATA-CTCTTGAAG
1 TTATCTCACTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATC-CTTGAAG
* * * *
15918108 TTGCAGTGGGTCGGTTTAAAGTCATGAAAGCAAATTT
65 TTGCAGTGGATCGGATTAAAGTCACGAAAGCAAATTC
* *
15918145 TTATCTCCCTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
1 TTATCTCACTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
15918210 TGCAGTGGAT
66 TGCAGTGGAT
15918220 TAGATTGAGG
Statistics
Matches: 149, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
100 1 0.01
101 146 0.98
102 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (101 bp):
TTATCTCACTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
TGCAGTGGATCGGATTAAAGTCACGAAAGCAAATTC
Found at i:15918241 original size:101 final size:101
Alignment explanation
Indices: 15917943--15918298 Score: 362
Period size: 101 Copynumber: 3.5 Consensus size: 101
15917933 TAACATACCT
* * * *
15917943 TTATCTCACTGAAGTTGCAATGGAGCAAGATGAAGCTACAACATCAAATCTTATATCCCTGAAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
*
15918008 TGCAATGGATCGGATTAAAGCTACGA-AAGCAAATTC
66 TGCAGTGGATCGGATTAAAGCTAC-ATAAGCAAATTC
* * * * * * *
15918044 TTATCTCTCTGAAGTTGCAGTAGAGTAGGATGAAGCTACAAAACCAAATCCAATA-CTCTTGAAG
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATC-CTTGAAG
* * *
15918108 TTGCAGTGGGTCGGTTTAAAG-T-CATGAAAGCAAATTT
65 TTGCAGTGGATCGGATTAAAGCTACAT--AAGCAAATTC
*
15918145 TTATCTCCCTGAAGTTGTAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
** * * * *
15918210 TGCAGTGGATTAGATTGAGGCTACATTAGC-AAGTC
66 TGCAGTGGATCGGATTAAAGCTACATAAGCAAATTC
* * * ** * * * *
15918245 CTATCTCCCTAAAGATATAGTGGAGCAAGATAAAGCTATAATATCGAATCCTAT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTAT
15918299 CTTTCTGAGG
Statistics
Matches: 209, Mismatches: 39, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
98 1 0.00
99 1 0.00
100 51 0.24
101 151 0.72
102 2 0.01
103 3 0.01
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.28
Consensus pattern (101 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAACATCAAATCCTATATCCTTGAAGT
TGCAGTGGATCGGATTAAAGCTACATAAGCAAATTC
Found at i:15920148 original size:24 final size:24
Alignment explanation
Indices: 15920111--15920175 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
15920101 TCCCTCTTAT
15920111 ATTTT-ATTTATTTATTTTGCATG
1 ATTTTAATTTATTTATTTTGCATG
* *
15920134 ATTTTAATTTGTTTAATTTGCATG
1 ATTTTAATTTATTTATTTTGCATG
15920158 ATTTTAA-TTATTTATTTT
1 ATTTTAATTTATTTATTTT
15920176 ATTTATTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.38
24 23 0.62
ACGTcount: A:0.25, C:0.03, G:0.08, T:0.65
Consensus pattern (24 bp):
ATTTTAATTTATTTATTTTGCATG
Found at i:15920393 original size:4 final size:4
Alignment explanation
Indices: 15920365--15920433 Score: 61
Period size: 4 Copynumber: 16.8 Consensus size: 4
15920355 CCATTATTAT
* * *
15920365 TTTA -TTA TGTTA TTAA TTGTA TTTA TTTAA TTTA TCTTA TTCA TGT-
1 TTTA TTTA T-TTA TTTA TT-TA TTTA TTT-A TTTA T-TTA TTTA TTTA
15920411 TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTT
15920434 TGTTATTATT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
3 5 0.09
4 33 0.62
5 15 0.28
ACGTcount: A:0.25, C:0.03, G:0.04, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:15921208 original size:22 final size:23
Alignment explanation
Indices: 15921161--15921208 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
15921151 AATTTATTGT
* *
15921161 TTTATTTTTCATTATTTCGTGGA
1 TTTATTTTTAATTATTTCGTGAA
15921184 TTTATTTTTGAATT-TTT-GTGAA
1 TTTATTTTT-AATTATTTCGTGAA
15921206 TTT
1 TTT
15921209 GAATATGTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 7 0.32
23 12 0.55
24 3 0.14
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (23 bp):
TTTATTTTTAATTATTTCGTGAA
Found at i:15933832 original size:8 final size:8
Alignment explanation
Indices: 15933819--15933843 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
15933809 GACACAAGAG
15933819 GAGAGTAA
1 GAGAGTAA
15933827 GAGAGTAA
1 GAGAGTAA
15933835 GAGAGTAA
1 GAGAGTAA
15933843 G
1 G
15933844 TCGAGTAGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.40, T:0.12
Consensus pattern (8 bp):
GAGAGTAA
Found at i:15935120 original size:21 final size:21
Alignment explanation
Indices: 15935096--15935156 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
15935086 ATGACATGTT
*
15935096 TCGGTAGAAGTCTCACTTGTA
1 TCGGTAGAAGTCTCACTAGTA
* * * *
15935117 TCGGTAGAATTTTCCCAAGTA
1 TCGGTAGAAGTCTCACTAGTA
15935138 TCGGTAGAAGTCTGCACTA
1 TCGGTAGAAGTCT-CACTA
15935157 TTTCTAAATT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (21 bp):
TCGGTAGAAGTCTCACTAGTA
Found at i:15935822 original size:19 final size:18
Alignment explanation
Indices: 15935798--15935837 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
15935788 TTTGGAATTA
* *
15935798 AAATAAAGCAATAAGAAAG
1 AAATAAAGAAAGAA-AAAG
15935817 AAATAAAGAAAGAAAAAG
1 AAATAAAGAAAGAAAAAG
15935835 AAA
1 AAA
15935838 AGTGGCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.75, C:0.03, G:0.15, T:0.07
Consensus pattern (18 bp):
AAATAAAGAAAGAAAAAG
Found at i:15936475 original size:26 final size:28
Alignment explanation
Indices: 15936424--15936480 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
15936414 TCACTCTTCA
15936424 TTTGTTTCCTCACTCATGATTTTTTTCT
1 TTTGTTTCCTCACTCATGATTTTTTTCT
*
15936452 TTTGTTT-CT-ACTCAT-TTTTCTTTTCT
1 TTTGTTTCCTCACTCATGATTT-TTTTCT
15936478 TTT
1 TTT
15936481 TGATTTGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 3 0.11
26 15 0.56
27 2 0.07
28 7 0.26
ACGTcount: A:0.09, C:0.19, G:0.05, T:0.67
Consensus pattern (28 bp):
TTTGTTTCCTCACTCATGATTTTTTTCT
Found at i:15944186 original size:13 final size:13
Alignment explanation
Indices: 15944170--15944195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
15944160 TTTTAGCATA
15944170 TAGTTTTCATTTT
1 TAGTTTTCATTTT
15944183 TAGTTTTCATTTT
1 TAGTTTTCATTTT
15944196 CCTTTTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (13 bp):
TAGTTTTCATTTT
Found at i:15954448 original size:20 final size:20
Alignment explanation
Indices: 15954423--15954463 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
15954413 ATGTGGAAAC
*
15954423 AGAGGAAGGAAA-AGAGGAAG
1 AGAGGAA-GAAAGAAAGGAAG
15954443 AGAGGAAGAAAGAAAGGAAG
1 AGAGGAAGAAAGAAAGGAAG
15954463 A
1 A
15954464 AAAAGATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (20 bp):
AGAGGAAGAAAGAAAGGAAG
Found at i:15954843 original size:12 final size:13
Alignment explanation
Indices: 15954826--15954858 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
15954816 ACCAATTGAG
15954826 TTAGTTTTTA-TT
1 TTAGTTTTTAGTT
15954838 TTAGTTTTTAGTT
1 TTAGTTTTTAGTT
15954851 TTAGTTTT
1 TTAGTTTT
15954859 CATGCATATC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (13 bp):
TTAGTTTTTAGTT
Found at i:15954915 original size:17 final size:17
Alignment explanation
Indices: 15954895--15954963 Score: 84
Period size: 17 Copynumber: 4.0 Consensus size: 17
15954885 ACTGTCACCA
*
15954895 CATTTCCTTTGTCATTG
1 CATTTCCATTGTCATTG
**
15954912 CATTTTAATTGTCATTG
1 CATTTCCATTGTCATTG
* *
15954929 CATTTGCATTATCATTG
1 CATTTCCATTGTCATTG
15954946 CATTTCCATTCGTCATTG
1 CATTTCCATT-GTCATTG
15954964 TAAATTAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
17 37 0.86
18 6 0.14
ACGTcount: A:0.19, C:0.20, G:0.12, T:0.49
Consensus pattern (17 bp):
CATTTCCATTGTCATTG
Found at i:15956286 original size:107 final size:107
Alignment explanation
Indices: 15956100--15956317 Score: 427
Period size: 107 Copynumber: 2.0 Consensus size: 107
15956090 TTGCTGCATA
*
15956100 AGAGGATCCAGAATTGCATCCAGAACTGTCGCAGCACCTAACAGCTGTCTGTTTAACACACCAAA
1 AGAGGATCCAGAATTGCATCCAGAACTGTCGCAGCACCTAAAAGCTGTCTGTTTAACACACCAAA
15956165 AATGTTTGAGTTGTACAGCTGGTATAACCAACTAGTATGGCC
66 AATGTTTGAGTTGTACAGCTGGTATAACCAACTAGTATGGCC
15956207 AGAGGATCCAGAATTGCATCCAGAACTGTCGCAGCACCTAAAAGCTGTCTGTTTAACACACCAAA
1 AGAGGATCCAGAATTGCATCCAGAACTGTCGCAGCACCTAAAAGCTGTCTGTTTAACACACCAAA
15956272 AATGTTTGAGTTGTACAGCTGGTATAACCAACTAGTATGGCC
66 AATGTTTGAGTTGTACAGCTGGTATAACCAACTAGTATGGCC
15956314 AGAG
1 AGAG
15956318 AATGCTAGAT
Statistics
Matches: 110, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 110 1.00
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (107 bp):
AGAGGATCCAGAATTGCATCCAGAACTGTCGCAGCACCTAAAAGCTGTCTGTTTAACACACCAAA
AATGTTTGAGTTGTACAGCTGGTATAACCAACTAGTATGGCC
Found at i:15964665 original size:12 final size:12
Alignment explanation
Indices: 15964648--15964673 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15964638 TGAGTGGGTA
15964648 GAAATCTTAAGT
1 GAAATCTTAAGT
15964660 GAAATCTTAAGT
1 GAAATCTTAAGT
15964672 GA
1 GA
15964674 TTGTAAGGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.19, T:0.31
Consensus pattern (12 bp):
GAAATCTTAAGT
Found at i:15973900 original size:27 final size:28
Alignment explanation
Indices: 15973862--15973914 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
15973852 AATGTGGAAG
15973862 CCTTTGAGGCTATTCT-TGATACATGAT
1 CCTTTGAGGCTATTCTCTGATACATGAT
* *
15973889 CCTTTGTGGCTATTCTCTGTTACATG
1 CCTTTGAGGCTATTCTCTGATACATG
15973915 TGAGCCCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (28 bp):
CCTTTGAGGCTATTCTCTGATACATGAT
Found at i:15974637 original size:30 final size:30
Alignment explanation
Indices: 15974603--15974659 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
15974593 TAAATGTAGT
* * *
15974603 TGGATGCTTTTGTGGCTTTCTAATGATGTG
1 TGGATGCCTTTATGGCTATCTAATGATGTG
*
15974633 TGGATGCCTTTATGGCTATCTATTGAT
1 TGGATGCCTTTATGGCTATCTAATGAT
15974660 TAAGCGTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (30 bp):
TGGATGCCTTTATGGCTATCTAATGATGTG
Found at i:15976977 original size:29 final size:29
Alignment explanation
Indices: 15976911--15977075 Score: 195
Period size: 29 Copynumber: 5.7 Consensus size: 29
15976901 TATTTCAGAT
* * * *
15976911 TCAGTCACAAAGACTCTCATATAACATAA
1 TCAGCCACAAAGGCTCTCATATAATAGAA
* ** *
15976940 TTAATCACAGAGGCTCTCATATAATAGAA
1 TCAGCCACAAAGGCTCTCATATAATAGAA
*
15976969 TCAGCCACAAATGCTCTCATATAATAGAA
1 TCAGCCACAAAGGCTCTCATATAATAGAA
* ** * *
15976998 TCAACCACAAAGGCTCAAATATAACAAAA
1 TCAGCCACAAAGGCTCTCATATAATAGAA
*
15977027 TCAGCCACAAAGGCTCGCATATAATAGAA
1 TCAGCCACAAAGGCTCTCATATAATAGAA
15977056 TCAGCCACAAAGGCTCTCAT
1 TCAGCCACAAAGGCTCTCAT
15977076 TTCGGTAAAT
Statistics
Matches: 113, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 113 1.00
ACGTcount: A:0.43, C:0.24, G:0.12, T:0.21
Consensus pattern (29 bp):
TCAGCCACAAAGGCTCTCATATAATAGAA
Found at i:15981890 original size:18 final size:18
Alignment explanation
Indices: 15981867--15981906 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
15981857 GTAGATAATC
* * *
15981867 ATCTTATTGGAAGTGTAA
1 ATCTTAATGAAAGTGCAA
15981885 ATCTTAATGAAAGTGCAA
1 ATCTTAATGAAAGTGCAA
15981903 ATCT
1 ATCT
15981907 ATCCGGTTGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (18 bp):
ATCTTAATGAAAGTGCAA
Found at i:15986128 original size:16 final size:16
Alignment explanation
Indices: 15986101--15986140 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
15986091 CCAATTATAT
*
15986101 TTAATGATTTTATAAA
1 TTAATAATTTTATAAA
* *
15986117 TTTATAATTTTATTAA
1 TTAATAATTTTATAAA
15986133 TTAATAAT
1 TTAATAAT
15986141 ATATTATGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAATAATTTTATAAA
Found at i:15988860 original size:1 final size:1
Alignment explanation
Indices: 15988854--15988878 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
15988844 TATAAGAGGG
15988854 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
15988879 GCGTGTGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:15992139 original size:28 final size:28
Alignment explanation
Indices: 15992095--15992158 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
15992085 AGAAAATAAT
* * * *
15992095 AGCCAATTAGAATTAGTGGTGTTGGCAC
1 AGCCAACTAGAACTAGTGGTATTAGCAC
15992123 AGCCAACTAGAACTAGTGGTATTAGCAC
1 AGCCAACTAGAACTAGTGGTATTAGCAC
*
15992151 AGGCAACT
1 AGCCAACT
15992159 TAGGGGATAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (28 bp):
AGCCAACTAGAACTAGTGGTATTAGCAC
Found at i:16001372 original size:24 final size:23
Alignment explanation
Indices: 16001345--16001394 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
16001335 AATATTTATA
16001345 ATTTTA-ATTATATCTATATTGAAT
1 ATTTTATATTAT-T-TATATTGAAT
*
16001369 ATTTTTATATTATTTATATTTAAT
1 A-TTTTATATTATTTATATTGAAT
16001393 AT
1 AT
16001395 CATTATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
23 1 0.04
24 11 0.48
25 6 0.26
26 5 0.22
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
ATTTTATATTATTTATATTGAAT
Found at i:16003889 original size:154 final size:155
Alignment explanation
Indices: 16003608--16003915 Score: 476
Period size: 154 Copynumber: 2.0 Consensus size: 155
16003598 AATTGAACAC
* *
16003608 ATAGCTACAAATTATGAAAACAATACCAAATTGCAGATTTTGGCACAGAAAGCCCCTAGTTTGTA
1 ATAGCTACAAATTATGAAAACAATACCAAATTGCAAATTTTGGCACAGAAAGCCCCTAGTTTATA
*
16003673 GAGAAAATCAATCATATTAATTGTTACTCTAATTATCACAACTTTGCTAATATGACAAAGAATAT
66 GAGAAAATCAATCATATTAACTGTTACTCTAATTATCACAACTTTGCTAATATGACAAAGAATAT
16003738 AATAAGC-AGGAAAAAAGCAAGGACA
131 AATAAGCTA-GAAAAAAGCAAGGACA
* * *
16003763 ATAGCTACAGATTATGAAGACAATACCAGATTGCAAATTTTGGCACAGAAAGCCCC-AGTTTATA
1 ATAGCTACAAATTATGAAAACAATACCAAATTGCAAATTTTGGCACAGAAAGCCCCTAGTTTATA
* * * * * *
16003827 GAGAAAATCATTCATGTTAACTGTTACTCTAATTGTCATAACTTTGGTAATATGACCAAGAATAT
66 GAGAAAATCAATCATATTAACTGTTACTCTAATTATCACAACTTTGCTAATATGACAAAGAATAT
*
16003892 AATACGCTAGAAAAAAGCAAGGAC
131 AATAAGCTAGAAAAAAGCAAGGAC
16003916 GACTGCTCAT
Statistics
Matches: 139, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
154 86 0.62
155 53 0.38
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (155 bp):
ATAGCTACAAATTATGAAAACAATACCAAATTGCAAATTTTGGCACAGAAAGCCCCTAGTTTATA
GAGAAAATCAATCATATTAACTGTTACTCTAATTATCACAACTTTGCTAATATGACAAAGAATAT
AATAAGCTAGAAAAAAGCAAGGACA
Found at i:16038112 original size:23 final size:25
Alignment explanation
Indices: 16038071--16038129 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 25
16038061 GTTAATAGGG
16038071 ATTTTCAA-TTTACAATTCA-TATC
1 ATTTTCAATTTTACAATTCACTATC
* *
16038094 ATTTTCAATTTTA-ATTTCACTTTC
1 ATTTTCAATTTTACAATTCACTATC
*
16038118 ACTTTCAATTTT
1 ATTTTCAATTTT
16038130 GATCACAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTTCAATTTTACAATTCACTATC
Found at i:16039852 original size:42 final size:42
Alignment explanation
Indices: 16039800--16039884 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
16039790 CAATTGTACT
* **
16039800 CTATCACTGTTTCAAATCCGATTCAAGCACACGGATGTTACA
1 CTATCACTGTTCCAAATCCGATTCAAAAACACGGATGTTACA
* * * *
16039842 CTATTACTGTTCCAACTCCGGTTCAAAAACGCGGATGTTACA
1 CTATCACTGTTCCAAATCCGATTCAAAAACACGGATGTTACA
16039884 C
1 C
16039885 GTTCTGATCC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (42 bp):
CTATCACTGTTCCAAATCCGATTCAAAAACACGGATGTTACA
Found at i:16043933 original size:22 final size:22
Alignment explanation
Indices: 16043902--16043958 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
16043892 ATGTAATATG
*
16043902 CCAATATAATTGATTGATTGCA
1 CCAATTTAATTGATTGATTGCA
* *
16043924 CCAATTTAATTGTTTGATTGCG
1 CCAATTTAATTGATTGATTGCA
16043946 CCAATTTAATTGA
1 CCAATTTAATTGA
16043959 ATATTTTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (22 bp):
CCAATTTAATTGATTGATTGCA
Found at i:16048718 original size:13 final size:13
Alignment explanation
Indices: 16048696--16048731 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
16048686 AAACTTTAAG
16048696 AAAT-AAAATTTT
1 AAATCAAAATTTT
16048708 AAATCAAAATTTT
1 AAATCAAAATTTT
*
16048721 AAATCAGAATT
1 AAATCAAAATT
16048732 CACCAGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.36
Consensus pattern (13 bp):
AAATCAAAATTTT
Found at i:16051402 original size:53 final size:53
Alignment explanation
Indices: 16051319--16051544 Score: 371
Period size: 53 Copynumber: 4.3 Consensus size: 53
16051309 CAGGAGCTCC
*
16051319 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAAA
1 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
** * *
16051372 GTCATCGGACCTTTAATCTATAATAAGATTCATATAACTCTCGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
16051425 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
** *
16051478 GTCATCACACTTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
1 GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
*
16051531 GTCATTGGACCTTT
1 GTCATCGGACCTTT
16051545 TTACATTTAT
Statistics
Matches: 157, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 157 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (53 bp):
GTCATCGGACCTTTAATCCGTAATAGGATTCATATAACTCACGATGACACAGA
Found at i:16054903 original size:18 final size:20
Alignment explanation
Indices: 16054860--16054904 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
16054850 AATATATTTA
*
16054860 AAAAAAATGATAGAAAAACT
1 AAAAAAATGAAAGAAAAACT
16054880 -AAAAAAT-AAAGAAAAA-T
1 AAAAAAATGAAAGAAAAACT
16054897 AAAAAAAT
1 AAAAAAAT
16054905 TATGGGTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 1 0.04
18 15 0.65
19 7 0.30
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (20 bp):
AAAAAAATGAAAGAAAAACT
Found at i:16066950 original size:80 final size:79
Alignment explanation
Indices: 16066807--16066955 Score: 253
Period size: 80 Copynumber: 1.9 Consensus size: 79
16066797 ACTAATTTCA
* * *
16066807 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGCTCTTCATTAGGATCTGATGTAGTTGAAAAGG
1 TTTTAACTATTGTAGGGAAGCCAATGAGTCATGCTCTTCATTAGGATCCGATGTAGTTGAAAAGA
16066872 CATGGCAATTTCGT
66 CATGGCAATTTCGT
*
16066886 TTTTAATTATTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCCGATGTAGTTGAAAAG
1 TTTTAACTATTGTAGGGAAGCCAATGAGTCATG-CTCTTCATTAGGATCCGATGTAGTTGAAAAG
16066951 ACATG
65 ACATG
16066956 ACATTTCTCC
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
79 31 0.48
80 34 0.52
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.34
Consensus pattern (79 bp):
TTTTAACTATTGTAGGGAAGCCAATGAGTCATGCTCTTCATTAGGATCCGATGTAGTTGAAAAGA
CATGGCAATTTCGT
Found at i:16066962 original size:79 final size:79
Alignment explanation
Indices: 16066807--16066962 Score: 251
Period size: 79 Copynumber: 2.0 Consensus size: 79
16066797 ACTAATTTCA
* * *
16066807 TTTTAACTCTTGTAGGGAAGCCAATGAGTCATGCTCTTCATTAGGATCTGATGTAGTTGAAAAGG
1 TTTTAACTATTGTAGGGAAGCCAATGAGTCATGCTCTTCATTAGGATCCGATGTAGTTGAAAAGA
*
16066872 CATGGCAATTTCGT
66 CATGACAATTTCGT
*
16066886 TTTTAATTATTGTAGGGAAGCCAATGAGTCATGTCTCTTCATTAGGATCCGATGTAGTTGAAAAG
1 TTTTAACTATTGTAGGGAAGCCAATGAGTCATG-CTCTTCATTAGGATCCGATGTAGTTGAAAAG
16066951 ACATGAC-ATTTC
65 ACATGACAATTTC
16066963 TCCTTAAATG
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 36 0.51
80 35 0.49
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (79 bp):
TTTTAACTATTGTAGGGAAGCCAATGAGTCATGCTCTTCATTAGGATCCGATGTAGTTGAAAAGA
CATGACAATTTCGT
Found at i:16067001 original size:80 final size:78
Alignment explanation
Indices: 16066917--16067073 Score: 251
Period size: 80 Copynumber: 2.0 Consensus size: 78
16066907 CAATGAGTCA
*
16066917 TGTCTCTTCATTAGGATCCGATGTAGTTGAAAAGACATGACATTTCTCCTTAAATGAAAACTTAT
1 TGTCTCTTCATTAGGATCCGATGTAGCTGAAAAGACATGACATTTCTCCTT-AATGAAAACTTA-
*
16066982 TGTATCCTTAATGTG
64 TGTAACCTTAATGTG
** *
16066997 TGTCTCTTCATTAGGATTTGATGTAGCTGAAAAGACATGACATTTCTCCTTAATGAAGACTTATG
1 TGTCTCTTCATTAGGATCCGATGTAGCTGAAAAGACATGACATTTCTCCTTAATGAAAACTTATG
16067062 TAACCTTAATGT
66 TAACCTTAATGT
16067074 TTTTATTGGT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 13 0.18
79 11 0.15
80 48 0.67
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (78 bp):
TGTCTCTTCATTAGGATCCGATGTAGCTGAAAAGACATGACATTTCTCCTTAATGAAAACTTATG
TAACCTTAATGTG
Found at i:16067529 original size:48 final size:46
Alignment explanation
Indices: 16067477--16067621 Score: 141
Period size: 48 Copynumber: 3.0 Consensus size: 46
16067467 GCTGATGCGT
* *
16067477 TAATGCAAGGCATTTAACAGAGATGCATTTAACAAACAAAACATTTAA
1 TAATGCAA-G-ATTTAACAAAGATGCATTTAACAAACAAAACACTTAA
* *
16067525 TAATGC-AGATTAATAAGCAAAAATGCATTTAACAAACAGAACACTTAA
1 TAATGCAAGATT--TAA-CAAAGATGCATTTAACAAACAAAACACTTAA
* * *
16067573 TGATGCAA-ATTATTAAACAAAGATGCATTTAGCAAATAAAACACTTAA
1 TAATGCAAGA-T-TT-AACAAAGATGCATTTAACAAACAAAACACTTAA
16067621 T
1 T
16067622 GAAGCATAAT
Statistics
Matches: 81, Mismatches: 9, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
45 3 0.04
46 1 0.01
47 4 0.05
48 68 0.84
49 4 0.05
50 1 0.01
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.26
Consensus pattern (46 bp):
TAATGCAAGATTTAACAAAGATGCATTTAACAAACAAAACACTTAA
Found at i:16067622 original size:48 final size:48
Alignment explanation
Indices: 16067492--16067623 Score: 174
Period size: 48 Copynumber: 2.8 Consensus size: 48
16067482 CAAGGCATTT
* * * *
16067492 AACAGAGATGCATTTAACAAACAAAACATTTAATAATGCAGATTAATA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAAATTAATA
* * * *
16067540 AGCAAAAATGCATTTAACAAACAGAACACTTAATGATGCAAATTATTA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAAATTAATA
* *
16067588 AACAAAGATGCATTTAGCAAATAAAACACTTAATGA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGA
16067624 AGCATAATAA
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 71 1.00
ACGTcount: A:0.52, C:0.14, G:0.11, T:0.24
Consensus pattern (48 bp):
AACAAAGATGCATTTAACAAACAAAACACTTAATGATGCAAATTAATA
Found at i:16073795 original size:10 final size:10
Alignment explanation
Indices: 16073780--16073818 Score: 71
Period size: 10 Copynumber: 4.0 Consensus size: 10
16073770 AAACAGTCCT
16073780 TAAACTTTCC
1 TAAACTTTCC
16073790 TAAACTTTCC
1 TAAACTTTCC
16073800 TAAACTTTCC
1 TAAACTTTCC
16073810 TAAA-TTTCC
1 TAAACTTTCC
16073819 ATTCCAACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
9 5 0.17
10 24 0.83
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (10 bp):
TAAACTTTCC
Found at i:16074294 original size:12 final size:12
Alignment explanation
Indices: 16074277--16074301 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16074267 TGTTATCATG
16074277 ATGAATGCTATT
1 ATGAATGCTATT
16074289 ATGAATGCTATT
1 ATGAATGCTATT
16074301 A
1 A
16074302 ATTCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:16077224 original size:7 final size:7
Alignment explanation
Indices: 16077212--16077265 Score: 108
Period size: 7 Copynumber: 7.7 Consensus size: 7
16077202 CTTCAAACGC
16077212 AAAAAAT
1 AAAAAAT
16077219 AAAAAAT
1 AAAAAAT
16077226 AAAAAAT
1 AAAAAAT
16077233 AAAAAAT
1 AAAAAAT
16077240 AAAAAAT
1 AAAAAAT
16077247 AAAAAAT
1 AAAAAAT
16077254 AAAAAAT
1 AAAAAAT
16077261 AAAAA
1 AAAAA
16077266 GGAGTTCTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 47 1.00
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAAAT
Found at i:16082797 original size:108 final size:109
Alignment explanation
Indices: 16082587--16082787 Score: 287
Period size: 108 Copynumber: 1.9 Consensus size: 109
16082577 CAACGCAATA
* * * *
16082587 TTCTTTTATTTTAGGGAATTCGAGAAATTGTGCCCTAACGTATTGAGAATGGTTTTTCTTTGAAC
1 TTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCAAACGTACTGAGAATGATTTTTCTTTGAAC
** *
16082652 CTAAATAATCGAGTATCCTATTTAAAATCATTAAATGTTCGATG
66 CTAAATAATCGAACACCCTATTTAAAATCATTAAATGTTCGATG
* * *
16082696 TTCTTTTA-TTTAGGGAACTCGAGAAATTGTGTCCAAACGTACTGGGTATGATTTTTCTTTGAAC
1 TTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCAAACGTACTGAGAATGATTTTTCTTTGAAC
* *
16082760 CTAAGTAATTGAACACCCTATTTAAAAT
66 CTAAATAATCGAACACCCTATTTAAAAT
16082788 TGATAAATGT
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
108 72 0.90
109 8 0.10
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (109 bp):
TTCTTTTATTTTAGGGAACTCGAGAAATTGTGCCCAAACGTACTGAGAATGATTTTTCTTTGAAC
CTAAATAATCGAACACCCTATTTAAAATCATTAAATGTTCGATG
Found at i:16087508 original size:74 final size:75
Alignment explanation
Indices: 16087429--16087575 Score: 224
Period size: 74 Copynumber: 2.0 Consensus size: 75
16087419 GGAAAATCAA
* * *
16087429 GATTATTCCCTTATTAATAAAGAAGGCAAATAGAAAGTTAG-AAAAGGAATTATATTCTTTCAAA
1 GATTATTCCCCTATTAATAAAGAAGACAAATAGAAAATTAGAAAAAGGAATTATATTCTTTCAAA
16087493 AAGAATATAT
66 AAGAATATAT
* * * *
16087503 GATTATTCCCCTATTAATAGATAATACAAATAGAAAATTAGAAAAAGGAATTATATTCTTTCCAA
1 GATTATTCCCCTATTAATAAAGAAGACAAATAGAAAATTAGAAAAAGGAATTATATTCTTTCAAA
16087568 AAGAATAT
66 AAGAATAT
16087576 TAATTTCCAT
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
74 35 0.54
75 30 0.46
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.31
Consensus pattern (75 bp):
GATTATTCCCCTATTAATAAAGAAGACAAATAGAAAATTAGAAAAAGGAATTATATTCTTTCAAA
AAGAATATAT
Found at i:16101950 original size:36 final size:36
Alignment explanation
Indices: 16101910--16102025 Score: 133
Period size: 36 Copynumber: 3.2 Consensus size: 36
16101900 TGTGATTGCA
* * *
16101910 TACGTCTCGATTAAAGCGTATTACTATGGAAGTGCT
1 TACGTCTCGATTAAAGCGTAATGCTAAGGAAGTGCT
* * * *
16101946 TACGTCTTGGTTAGAGCGTAATGCTAAGGAACTGCT
1 TACGTCTCGATTAAAGCGTAATGCTAAGGAAGTGCT
* * *
16101982 TATGTCTCGATTAAGGCGTAATGCTAAGGAAGAGCT
1 TACGTCTCGATTAAAGCGTAATGCTAAGGAAGTGCT
*
16102018 TATGTCTC
1 TACGTCTC
16102026 AGTTAGAGCA
Statistics
Matches: 66, Mismatches: 14, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (36 bp):
TACGTCTCGATTAAAGCGTAATGCTAAGGAAGTGCT
Found at i:16104484 original size:72 final size:72
Alignment explanation
Indices: 16104376--16104556 Score: 186
Period size: 72 Copynumber: 2.5 Consensus size: 72
16104366 CGGGCTGGAA
* * * * * * *
16104376 ACACGGGTGTGTGCCATACCGTGTATATATATTGTTTTGTAAAAT-AGGTTACAGAGG-ACATAT
1 ACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTTTGTAAAATAAGG-TACAG-GGAACACAC
*
16104439 GGGCTAGGC
64 GAGCTAGGC
* * * **
16104448 ACACGGGCGTGTGCCAGACCGTTTGTGCATACTGTTTTGTGAGTTAAGGTACAGGGAACACACGA
1 ACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTTTGTAAAATAAGGTACAGGGAACACACGA
*
16104513 GCTATGC
66 GCTAGGC
* *
16104520 ACATGGACGTGTGCCAGACCGTGTGTGTATACTGTTT
1 ACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTT
16104557 AGGGATACAC
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
71 2 0.02
72 84 0.94
73 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (72 bp):
ACACGGGCGTGTGCCAGACCGTGTGTGTATACTGTTTTGTAAAATAAGGTACAGGGAACACACGA
GCTAGGC
Found at i:16107143 original size:21 final size:21
Alignment explanation
Indices: 16107099--16107147 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
16107089 AACTAAGACA
* *
16107099 TCTACCGATACAACTCTAGGT
1 TCTATCGATACAACTCAAGGT
16107120 TCTATCGATACAA-TCAAGGCT
1 TCTATCGATACAACTCAAGG-T
16107141 TCTATCG
1 TCTATCG
16107148 GTAGAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.31
Consensus pattern (21 bp):
TCTATCGATACAACTCAAGGT
Found at i:16116557 original size:3 final size:3
Alignment explanation
Indices: 16116549--16116573 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
16116539 GACTACACTC
16116549 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
16116574 ATCGTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16118122 original size:12 final size:12
Alignment explanation
Indices: 16118105--16118130 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16118095 TGTTATCATG
16118105 ATGAATGCTATT
1 ATGAATGCTATT
16118117 ATGAATGCTATT
1 ATGAATGCTATT
16118129 AT
1 AT
16118131 TTCTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:16127985 original size:18 final size:17
Alignment explanation
Indices: 16127959--16127993 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16127949 AAAGAAAACC
*
16127959 CTGAGGAAGAGAAAGGAA
1 CTGAAGAAGAG-AAGGAA
16127977 CTGAAGAAGAGAAGGAA
1 CTGAAGAAGAGAAGGAA
16127994 GAAGAGAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.51, C:0.06, G:0.37, T:0.06
Consensus pattern (17 bp):
CTGAAGAAGAGAAGGAA
Found at i:16128002 original size:8 final size:8
Alignment explanation
Indices: 16127986--16128014 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16127976 ACTGAAGAAG
16127986 AGAAG-GA
1 AGAAGAGA
16127993 AGAAGAGA
1 AGAAGAGA
16128001 AGAAGAGA
1 AGAAGAGA
16128009 AGAAGA
1 AGAAGA
16128015 ATGAAAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 5 0.24
8 16 0.76
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AGAAGAGA
Found at i:16140675 original size:17 final size:18
Alignment explanation
Indices: 16140655--16140694 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
16140645 TTAGTTTTAA
16140655 TGCATTTT-TATTATCAC
1 TGCATTTTATATTATCAC
* *
16140672 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTATCAC
16140690 TGCAT
1 TGCAT
16140695 CATTTTGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.20, C:0.17, G:0.10, T:0.53
Consensus pattern (18 bp):
TGCATTTTATATTATCAC
Found at i:16143350 original size:26 final size:24
Alignment explanation
Indices: 16143292--16143351 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 24
16143282 AATTATTTTC
16143292 TAATTTTTAATTTATTTAATTGAT
1 TAATTTTTAATTTATTTAATTGAT
16143316 TAACTTTTTAATTTATTTTAATTTG-T
1 TAA-TTTTTAATTTA-TTTAA-TTGAT
16143342 TAATATTTTA
1 TAAT-TTTTA
16143352 TACTAATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
24 3 0.09
25 12 0.38
26 14 0.44
27 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (24 bp):
TAATTTTTAATTTATTTAATTGAT
Found at i:16147058 original size:12 final size:12
Alignment explanation
Indices: 16147041--16147066 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
16147031 TGTTATCATG
16147041 ATGAATGCTATT
1 ATGAATGCTATT
16147053 ATGAATGCTATT
1 ATGAATGCTATT
16147065 AT
1 AT
16147067 TTCTTTAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:16152458 original size:16 final size:17
Alignment explanation
Indices: 16152437--16152484 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
16152427 TTATAAAAAA
16152437 TTTCTTTCTTTTTCT-T
1 TTTCTTTCTTTTTCTAT
*
16152453 TTTCTTCCTTTTTCTCAT
1 TTTCTTTCTTTTTCT-AT
*
16152471 TTTGTTTCTTTTTC
1 TTTCTTTCTTTTTC
16152485 AAATGATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTAT
Found at i:16161445 original size:13 final size:14
Alignment explanation
Indices: 16161427--16161456 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
16161417 GTCAACGCAA
16161427 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
16161440 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
16161454 TCA
1 TCA
16161457 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:16164851 original size:100 final size:99
Alignment explanation
Indices: 16164715--16164894 Score: 245
Period size: 100 Copynumber: 1.8 Consensus size: 99
16164705 GCAAAACACC
* ** *
16164715 AAATCCTATCTTCCTGAAGTTGAAGTGAAGCGAATTAAAACAAGTTGCAGATCTCAATCTCCACT
1 AAATCCTATCATCCTGAAGTTGAAGTGAAGCGAATTAAAACAAGTAACAGACCTCAATCTCC-CT
*
16164780 AAAGTTGCAGTGGAATAGAGTGAAGCCATAACCTT
65 AAAGTTCCAGTGGAATAGAGTGAAGCCATAACCTT
* * * * *
16164815 AAATCCTAT-ATCCTTGAAGTTGCAGTGGATCGAATTAAAATAAGTAATAGACCTCAATCTCCCT
1 AAATCCTATCATCC-TGAAGTTGAAGTGAAGCGAATTAAAACAAGTAACAGACCTCAATCTCCCT
16164879 AAAGTTCCAGTGGAAT
65 AAAGTTCCAGTGGAAT
16164895 GGAGCAAAGT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
99 20 0.29
100 49 0.71
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.27
Consensus pattern (99 bp):
AAATCCTATCATCCTGAAGTTGAAGTGAAGCGAATTAAAACAAGTAACAGACCTCAATCTCCCTA
AAGTTCCAGTGGAATAGAGTGAAGCCATAACCTT
Found at i:16165135 original size:99 final size:99
Alignment explanation
Indices: 16164850--16165120 Score: 409
Period size: 99 Copynumber: 2.7 Consensus size: 99
16164840 TGGATCGAAT
* * ** * *
16164850 TAAAATAAGTAAT-AGACCTCAATCTCCCTAAAGTTCCAGTGGAATGGAGCAAAGTTACCACACC
1 TAAAACAAGTAATGA-ATCTCAATCTCCCTAAAGTTGTAGTGGAGTGGAGCGAAGTTACCACACC
*
16164914 AACTCCTATACCTTTAAAATTGCAGAAGGGCGGAG
65 AACTCCTATACCTTTAAAATTGCAAAAGGGCGGAG
* *
16164949 TAAAACAAGTAACGAATCTCAATCTCCCTTAAGTTGTAGTGGAGTGGAGCGAAGTTACCACACCA
1 TAAAACAAGTAATGAATCTCAATCTCCCTAAAGTTGTAGTGGAGTGGAGCGAAGTTACCACACCA
*
16165014 ACTCCTATACCTTTAAAATTGCAAAAGGGTGGAG
66 ACTCCTATACCTTTAAAATTGCAAAAGGGCGGAG
* *
16165048 TAAAACAAGTAATGAATCTCAATCTCCCTGAAGTTGTAGTGGAGTGGAGTGAAGTTACCACACCA
1 TAAAACAAGTAATGAATCTCAATCTCCCTAAAGTTGTAGTGGAGTGGAGCGAAGTTACCACACCA
*
16165113 AATCCTAT
66 ACTCCTAT
16165121 CTTCTTGAAG
Statistics
Matches: 157, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
99 156 0.99
100 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (99 bp):
TAAAACAAGTAATGAATCTCAATCTCCCTAAAGTTGTAGTGGAGTGGAGCGAAGTTACCACACCA
ACTCCTATACCTTTAAAATTGCAAAAGGGCGGAG
Found at i:16165151 original size:99 final size:98
Alignment explanation
Indices: 16164710--16165206 Score: 321
Period size: 99 Copynumber: 5.0 Consensus size: 98
16164700 AACCAGCAAA
* * *
16164710 ACACCAAATCCTATCTTCCTGAAGTTGAAGTGAAGCGAATTAAAACAAGT--TGCAGATCTCAAT
1 ACACCAAATCCTATCTTCTTGAAGTTGCAGTGAAACG-ATTAAAACAAGTAATG-A-ATCTCAAT
* *
16164773 CTCCACTAAAGTTGCAGTGGAATAGAGTGAAG---CC
63 CTCC-CTAAAGTTGCAGTGGAATGGAGCGAAGTTACC
* * * * * * *
16164807 ATAACCTTAAATCCTATATCCTTGAAGTTGCAGTGGATCGAATTAAAATAAGTAAT-AGACCTCA
1 A-CACC--AAATCCTATCTTCTTGAAGTTGCAGTGAAACG-ATTAAAACAAGTAATGA-ATCTCA
* *
16164871 ATCTCCCTAAAGTTCCAGTGGAATGGAGCAAAGTTACC
61 ATCTCCCTAAAGTTGCAGTGGAATGGAGCGAAGTTACC
* * * * * * *
16164909 ACACCAACTCCTATACCT-TTAAAATTGCA--GAAGGGCGGAGTAAAACAAGTAACGAATCTCAA
1 ACACCAAATCCTAT-CTTCTTGAAGTTGCAGTGAA--AC-GATTAAAACAAGTAATGAATCTCAA
* * *
16164971 TCTCCCTTAAGTTGTAGTGGAGTGGAGCGAAGTTACC
62 TCTCCCTAAAGTTGCAGTGGAATGGAGCGAAGTTACC
* * * * ** **** *
16165008 ACACCAACTCCTATACCT-TTAAAATTGCAAAAGGGTGGAGTAAAACAAGTAATGAATCTCAATC
1 ACACCAAATCCTAT-CTTCTTGAAGTTGC-AGTGAAACGATTAAAACAAGTAATGAATCTCAATC
* * * *
16165072 TCCCTGAAGTTGTAGTGGAGTGGAGTGAAGTTACC
64 TCCCTAAAGTTGCAGTGGAATGGAGCGAAGTTACC
* ** *
16165107 ACACCAAATCCTATCTTCTTGAAGTTGCAGTGAAACAGATTAAAACTACGGTAGCGGATCTCAAT
1 ACACCAAATCCTATCTTCTTGAAGTTGCAGTGAAAC-GATTAAAAC-A-AGTAATGAATCTCAAT
* * * * * *
16165172 CTCCCTGATGTTGCACTAGAATAGAGTGAAGTTAC
63 CTCCCTAAAGTTGCAGTGGAATGGAGCGAAGTTAC
16165207 ATCACCATCC
Statistics
Matches: 321, Mismatches: 59, Indels: 36
0.77 0.14 0.09
Matches are distributed among these distances:
97 3 0.01
98 7 0.02
99 207 0.64
100 55 0.17
101 44 0.14
102 5 0.02
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (98 bp):
ACACCAAATCCTATCTTCTTGAAGTTGCAGTGAAACGATTAAAACAAGTAATGAATCTCAATCTC
CCTAAAGTTGCAGTGGAATGGAGCGAAGTTACC
Found at i:16165265 original size:46 final size:46
Alignment explanation
Indices: 16165209--16165990 Score: 990
Period size: 46 Copynumber: 17.0 Consensus size: 46
16165199 GAAGTTACAT
* * *
16165209 CACCATCCAATCTTTTACACCTAAATCTAGAGGGGCAAATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * *
16165255 CACCATCCAATCTTTTATCCCTAAATCCAAAGGGGCAAATTGAAAC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * *
16165301 CACCATCCAATCTTTTACTCCTAAATCTAGAGGGGCAGATTGAAGT
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* *
16165347 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGTAGATTGAAGT
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * * * *
16165393 CACCATCCAATCTTTTACCCTTAAATCCAAAAGGGCAAATTAAAGA
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
*
16165439 CACCATCCAATCTTTTACCCCTAAATCCAGAGGTGCAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * *
16165485 CACCATCCAATCTTTTACCACTAAATCCAGAGGGGCATATTAAAGA
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * *
16165531 CACAATCCAATTTTTTACCACTAAATCCAGAGGGGCAGATTTAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * *
16165577 CACTATCAAATCTTTTACCCCTAAAT-CATAGGGACAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * * *
16165622 CACCATCCAATCTTTTACACCTAAATTCATAGGGGCAAATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * * ** * * *
16165668 CACCATCAAATCTTCTACCCTTAAATATAGAGGGGAAAATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* *
16165714 CAACATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAAC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* *
16165760 CACCATCCAATCTTTTACCCTCTAAATCTAGAGGGACAGATTGAAGC
1 CACCATCCAATCTTTTACCC-CTAAATCCAGAGGGGCAGATTGAAGC
* * * * *
16165807 CACCATCTAATCTTTTACCCCTAAATCTAGAAGGGAAGATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * *
16165853 CAACATCCAATCTTTTACTCCTAAATCCAGAGGGGTAGATTGAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * *
16165899 CACCATTCAATCTTTTACCCCTAAATCCAGAGGGGAAGATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
* * *
16165945 CACCATCCAATCTTTTACCCTTAAATCAAGAGGGGCAGATTAAAGC
1 CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
16165991 TACATAATCA
Statistics
Matches: 639, Mismatches: 95, Indels: 4
0.87 0.13 0.01
Matches are distributed among these distances:
45 39 0.06
46 558 0.87
47 42 0.07
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (46 bp):
CACCATCCAATCTTTTACCCCTAAATCCAGAGGGGCAGATTGAAGC
Found at i:16166100 original size:50 final size:50
Alignment explanation
Indices: 16165953--16166101 Score: 135
Period size: 50 Copynumber: 3.0 Consensus size: 50
16165943 GCCACCATCC
* * * * * * *
16165953 AATCTTTTACCCTTAAATC-A-AGAGGGGCAGATTAAAGCTACATAATCA
1 AATCTTATACCCTTAAAGCTATAGAGAGGCAAATTGAAGCTACAAAAGCA
* * ** *
16166001 AATCTTATA-CCTCTAAAG-TCGTAGAGAGGCATATTGAAGCTGTAGAAGCA
1 AATCTTATACCCT-TAAAGCT-ATAGAGAGGCAAATTGAAGCTACAAAAGCA
*
16166051 AATCTTATACCCTTAAAGCTATAGAGAGGCAAATTGTAGCTACAAAAGCA
1 AATCTTATACCCTTAAAGCTATAGAGAGGCAAATTGAAGCTACAAAAGCA
16166101 A
1 A
16166102 TTTTTAATCT
Statistics
Matches: 79, Mismatches: 16, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
47 3 0.04
48 12 0.15
50 60 0.76
51 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (50 bp):
AATCTTATACCCTTAAAGCTATAGAGAGGCAAATTGAAGCTACAAAAGCA
Found at i:16167764 original size:15 final size:14
Alignment explanation
Indices: 16167737--16167787 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 14
16167727 TTGGTCCCTC
*
16167737 ATTTTTCTTATTTT
1 ATTTTTATTATTTT
16167751 ATTTTGTATTATTTTT
1 ATTTT-TATTA-TTTT
16167767 ATTCATTTATT-TTTT
1 ATT--TTTATTATTTT
16167782 ATTTTT
1 ATTTTT
16167788 TTTTTCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 3 0.09
14 5 0.16
15 11 0.34
16 7 0.22
17 4 0.12
18 2 0.06
ACGTcount: A:0.18, C:0.04, G:0.02, T:0.76
Consensus pattern (14 bp):
ATTTTTATTATTTT
Found at i:16167801 original size:25 final size:26
Alignment explanation
Indices: 16167738--16167806 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 26
16167728 TGGTCCCTCA
*
16167738 TTTTTCTTATTTTATTTTGTATTATTT
1 TTTTTCTTA-TTTATTTTTTATTATTT
*
16167765 TTATTC--ATTTATTTTTTATT-TTT
1 TTTTTCTTATTTATTTTTTATTATTT
* *
16167788 TTTTTCTTACTTATCTTTT
1 TTTTTCTTATTTATTTTTT
16167807 CATGTTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 8 0.23
24 12 0.34
25 10 0.29
27 5 0.14
ACGTcount: A:0.14, C:0.07, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTTCTTATTTATTTTTTATTATTT
Found at i:16193964 original size:17 final size:17
Alignment explanation
Indices: 16193942--16193975 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16193932 TCTTCATCAT
16193942 TTTTTTTCAAACGTGTA
1 TTTTTTTCAAACGTGTA
* *
16193959 TTTTTTTGAATCGTGTA
1 TTTTTTTCAAACGTGTA
16193976 AAACCTTATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.56
Consensus pattern (17 bp):
TTTTTTTCAAACGTGTA
Found at i:16194706 original size:23 final size:23
Alignment explanation
Indices: 16194677--16195280 Score: 762
Period size: 23 Copynumber: 26.3 Consensus size: 23
16194667 ATTATATCTA
*
16194677 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
** *
16194700 TAATTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* * *
16194723 TGATTAAATATTAATGTTATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
16194746 TGCTTAAGTATTAATATGATATA
1 TGCTTAAATATTAATATGATTTG
*
16194769 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* *
16194792 TGATTAAATGTTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
16194815 TGCTTAAGTATTAATATGATCTA
1 TGCTTAAATATTAATATGATTTG
16194838 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
16194861 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
16194884 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * **
16194907 TGCTCAAATATTAATGTGATTCA
1 TGCTTAAATATTAATATGATTTG
* *
16194930 TGCTTAAATAATAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
16194953 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
* * *
16194976 TGATTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
* * *
16194999 TGCTTAAGTATTAATGTGATTTA
1 TGCTTAAATATTAATATGATTTG
16195022 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
16195045 TACTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
16195068 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
16195091 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
*
16195114 TGCTTAAATATT-A-ATGACTTG
1 TGCTTAAATATTAATATGATTTG
* *
16195135 TGCTCAAATATTAATATGTTTTG
1 TGCTTAAATATTAATATGATTTG
16195158 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* * *
16195181 TGCTCAAATATTAATGTTATTTG
1 TGCTTAAATATTAATATGATTTG
*
16195204 TACTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATATGATTTG
* *
16195227 TGATTAAATATTAATATGATTTA
1 TGCTTAAATATTAATATGATTTG
** *
16195250 TAATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATATGATTTG
16195273 TGCTTAAA
1 TGCTTAAA
16195281 GAATCAAGCT
Statistics
Matches: 505, Mismatches: 74, Indels: 4
0.87 0.13 0.01
Matches are distributed among these distances:
21 17 0.03
22 2 0.00
23 486 0.96
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATATGATTTG
Found at i:16200130 original size:10 final size:10
Alignment explanation
Indices: 16200117--16200175 Score: 52
Period size: 10 Copynumber: 6.0 Consensus size: 10
16200107 TATAAAGATA
16200117 TTCTTTCTTT
1 TTCTTTCTTT
16200127 TTCTTTCTTT
1 TTCTTTCTTT
* **
16200137 TTATCAAC-TT
1 TTCT-TTCTTT
16200147 TTCTTTCTTT
1 TTCTTTCTTT
16200157 TTC--TCTTT
1 TTCTTTCTTT
16200165 TTCTTTTCTTT
1 TTC-TTTCTTT
16200176 ATGCGACTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
8 8 0.21
9 1 0.03
10 23 0.61
11 6 0.16
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:16200779 original size:18 final size:19
Alignment explanation
Indices: 16200756--16200794 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
16200746 TAAAACAAAT
16200756 AAAATGCAGA-GACAA-TAA
1 AAAATGCA-ATGACAATTAA
16200774 AAAATGCAATGACAATTAA
1 AAAATGCAATGACAATTAA
16200793 AA
1 AA
16200795 TAAATGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.05
18 13 0.68
19 5 0.26
ACGTcount: A:0.62, C:0.10, G:0.13, T:0.15
Consensus pattern (19 bp):
AAAATGCAATGACAATTAA
Found at i:16206909 original size:17 final size:18
Alignment explanation
Indices: 16206884--16206918 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
16206874 AGTTAAGGAG
*
16206884 CAAGCTTAAGGC-CGATA
1 CAAGATTAAGGCTCGATA
16206901 CAAGATTAAGGCTCGATA
1 CAAGATTAAGGCTCGATA
16206919 GTAGCCTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (18 bp):
CAAGATTAAGGCTCGATA
Found at i:16210192 original size:22 final size:22
Alignment explanation
Indices: 16210164--16210242 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 22
16210154 ATATAAAAAC
16210164 AATAAATAAAAATTAAATACTA
1 AATAAATAAAAATTAAATACTA
16210186 AATAAAT-AAAA-T-AATAC-A
1 AATAAATAAAAATTAAATACTA
* *
16210204 AATAAATAAAAAGATAAAAGGACTA
1 AATAAAT-AAAA-ATTAAA-TACTA
16210229 AATTAAATAAAAAT
1 AA-TAAATAAAAAT
16210243 AAAAACAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
18 8 0.17
19 5 0.11
20 4 0.09
21 5 0.11
22 7 0.15
23 2 0.04
24 4 0.09
25 7 0.15
26 5 0.11
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.23
Consensus pattern (22 bp):
AATAAATAAAAATTAAATACTA
Found at i:16210206 original size:18 final size:19
Alignment explanation
Indices: 16210133--16210215 Score: 75
Period size: 19 Copynumber: 4.4 Consensus size: 19
16210123 TATAAATGGC
16210133 ATAAAAAT-A-ACAAATAA
1 ATAAAAATAATACAAATAA
* * *
16210150 ATGAATATAA-AAACAATAA
1 ATAAAAATAATACA-AATAA
16210169 ATAAAAATTAAATACTAAATAA
1 ATAAAAA-T-AATAC-AAATAA
16210191 AT-AAAATAATACAAATAA
1 ATAAAAATAATACAAATAA
16210209 ATAAAAA
1 ATAAAAA
16210216 GATAAAAGGA
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
17 6 0.11
18 11 0.21
19 19 0.36
20 2 0.04
21 6 0.11
22 8 0.15
23 1 0.02
ACGTcount: A:0.72, C:0.05, G:0.01, T:0.22
Consensus pattern (19 bp):
ATAAAAATAATACAAATAA
Found at i:16210315 original size:30 final size:30
Alignment explanation
Indices: 16210272--16210335 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
16210262 CAAAATTAAG
* *
16210272 TAAAGGACTAAATTGAAAACACAAATAAAT
1 TAAAGGACTAAATTAAAAACACAAATAAAA
*
16210302 TAAAGGTAC-AAATTAAAAACAGAAATAAAA
1 TAAAGG-ACTAAATTAAAAACACAAATAAAA
16210332 TAAA
1 TAAA
16210336 ATATAATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.64, C:0.08, G:0.09, T:0.19
Consensus pattern (30 bp):
TAAAGGACTAAATTAAAAACACAAATAAAA
Found at i:16210505 original size:30 final size:31
Alignment explanation
Indices: 16210471--16210535 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 31
16210461 CAAAATTAAG
*
16210471 TAAAGG-ACTAAATTGAAAAT-GCAAAT-AAAT
1 TAAAGGTAC-AAATTAAAAATAG-AAATAAAAT
16210501 TAAAGGTACAAATTAAAAATAGAAATAAAAT
1 TAAAGGTACAAATTAAAAATAGAAATAAAAT
16210532 TAAA
1 TAAA
16210536 CTAAACTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.23
Consensus pattern (31 bp):
TAAAGGTACAAATTAAAAATAGAAATAAAAT
Found at i:16211640 original size:19 final size:20
Alignment explanation
Indices: 16211602--16211642 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
16211592 TTAGGTTATT
*
16211602 ATTTGGGTTAATTTTATTTGG
1 ATTTGGGTT-ATTGTATTTGG
16211623 ATTTGGGTT-TTGTATTTGG
1 ATTTGGGTTATTGTATTTGG
16211642 A
1 A
16211643 CCTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
21 9 0.47
ACGTcount: A:0.17, C:0.00, G:0.27, T:0.56
Consensus pattern (20 bp):
ATTTGGGTTATTGTATTTGG
Found at i:16211657 original size:21 final size:21
Alignment explanation
Indices: 16211631--16211672 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16211621 GGATTTGGGT
*
16211631 TTTGTATTTGGACCTTAATTA
1 TTTGTAATTGGACCTTAATTA
*
16211652 TTTGTAATTGGACTTTAATTA
1 TTTGTAATTGGACCTTAATTA
16211673 AAAAATGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTGTAATTGGACCTTAATTA
Found at i:16212378 original size:100 final size:100
Alignment explanation
Indices: 16212196--16212719 Score: 665
Period size: 100 Copynumber: 5.2 Consensus size: 100
16212186 CGATCCCTAC
* * * * * *
16212196 AACTTTAGGGATATAGGATTCGGGGTTATGGATTCACTCCATTCAATTGCAACTTC--TGAGAGA
1 AACTTTAGGGGTATAGGATT--TGG-TGTGGCTTCACTCCATTCCACTGCAACTTCAGTG-GAGA
* * *
16212259 TTGAGATTTGCTACGGTTAGTTTTAATCTGCCCCTCTGT
62 TTGAGATCTGCTACTGTTAGTTTTAATCCGCCCCTCTGT
** * * *
16212298 AACTTTAGCAGTATTGGATTTGGTGTGGCTTCACTCCATTCCACTACAACTTTAGTGGAGATTGA
1 AACTTTAGGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGA
*
16212363 GATCTGCTACTGTTAGTTTTAATCCGCCCCTTTGT
66 GATCTGCTACTGTTAGTTTTAATCCGCCCCTCTGT
* **
16212398 AACTTTAGGGGTATAGGATTTGGTGTTGCTTCACTCCATTCCACTGCAACTTCAGCAGAGATTGA
1 AACTTTAGGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGA
* * * *
16212463 GATCTACTACTGTTAGTTTTAATGCACCCCTCCGT
66 GATCTGCTACTGTTAGTTTTAATCCGCCCCTCTGT
* * *
16212498 AACTTTAAGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCGCTGTAACTTCAGTGGAGATTGA
1 AACTTTAGGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGA
* * * **
16212563 GATCTACAACTGTTAGTTTTAATTCGCCCCTCTAC
66 GATCTGCTACTGTTAGTTTTAATCCGCCCCTCTGT
*
16212598 AACTTTAGGGGTATAGGATTTGGTGTGACTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGA
1 AACTTTAGGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGA
* * * *
16212663 GATCTGTTACTGTTAGTTTTAATCCACCTCTCTGC
66 GATCTGCTACTGTTAGTTTTAATCCGCCCCTCTGT
* *
16212698 AACTTTAAGGGTATAAGATTTG
1 AACTTTAGGGGTATAGGATTTG
16212720 TTGTTTTGCA
Statistics
Matches: 367, Mismatches: 53, Indels: 6
0.86 0.12 0.01
Matches are distributed among these distances:
99 24 0.07
100 325 0.89
101 2 0.01
102 16 0.04
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (100 bp):
AACTTTAGGGGTATAGGATTTGGTGTGGCTTCACTCCATTCCACTGCAACTTCAGTGGAGATTGA
GATCTGCTACTGTTAGTTTTAATCCGCCCCTCTGT
Found at i:16213331 original size:21 final size:21
Alignment explanation
Indices: 16213306--16213350 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16213296 AACAATGGCC
*
16213306 AAAAATTGCAAATATTGGTAA
1 AAAAATGGCAAATATTGGTAA
* *
16213327 AAAAATGGCAAATGTTGGTCA
1 AAAAATGGCAAATATTGGTAA
16213348 AAA
1 AAA
16213351 TAAAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (21 bp):
AAAAATGGCAAATATTGGTAA
Found at i:16218996 original size:21 final size:22
Alignment explanation
Indices: 16218958--16219034 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 22
16218948 CTTGAAACTT
* *
16218958 CTACCGATATAAGC-ATACAAA
1 CTACCGATACATGCAATACAAA
16218979 CTACCGATACAT-CAATACTAAAAA
1 CTACCGATACATGCAATAC---AAA
* * *
16219003 CTATCGATACATGTAATTC-AA
1 CTACCGATACATGCAATACAAA
16219024 CTACCGATACA
1 CTACCGATACA
16219035 ACTCAAGTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 1 0.02
21 26 0.58
24 14 0.31
25 4 0.09
ACGTcount: A:0.44, C:0.25, G:0.08, T:0.23
Consensus pattern (22 bp):
CTACCGATACATGCAATACAAA
Found at i:16221783 original size:22 final size:23
Alignment explanation
Indices: 16221742--16221785 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
16221732 TTTTAGGTCC
16221742 TTAGGAATTTATTTCTTTCATAG
1 TTAGGAATTTATTTCTTTCATAG
*
16221765 TTAGGATTTTATTTC-TTCATA
1 TTAGGAATTTATTTCTTTCATA
16221786 ATAAAACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.25, C:0.09, G:0.11, T:0.55
Consensus pattern (23 bp):
TTAGGAATTTATTTCTTTCATAG
Found at i:16226560 original size:17 final size:17
Alignment explanation
Indices: 16226540--16226596 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
16226530 TAATTGTCCC
*
16226540 TGCATTATTAATGTCAT
1 TGCATTATTATTGTCAT
* *
16226557 TGCATTTTTATTGTCAC
1 TGCATTATTATTGTCAT
*
16226574 TGCATCTA-CATTGTCAT
1 TGCAT-TATTATTGTCAT
16226591 TGCATT
1 TGCATT
16226597 TCCATATATA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.94
18 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (17 bp):
TGCATTATTATTGTCAT
Found at i:16226570 original size:34 final size:34
Alignment explanation
Indices: 16226532--16226597 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
16226522 TTGTAGTATA
* *
16226532 ATTGTCCCTGCAT-TATTAATGTCATTGCATTTTT
1 ATTGTCACTGCATCTA-CAATGTCATTGCATTTTT
*
16226566 ATTGTCACTGCATCTACATTGTCATTGCATTT
1 ATTGTCACTGCATCTACAATGTCATTGCATTT
16226598 CCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 26 0.93
35 2 0.07
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.47
Consensus pattern (34 bp):
ATTGTCACTGCATCTACAATGTCATTGCATTTTT
Found at i:16231513 original size:24 final size:24
Alignment explanation
Indices: 16231481--16231570 Score: 153
Period size: 24 Copynumber: 3.8 Consensus size: 24
16231471 ATATATTGGT
*
16231481 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTAGGCTCGTAAGAGC
*
16231505 TAACCATTCTGGGCTCGTAAGAGC
1 TAACCATTCTAGGCTCGTAAGAGC
*
16231529 TAACCATTCTAGGTTCGTAAGAGC
1 TAACCATTCTAGGCTCGTAAGAGC
16231553 TAACCATTCTAGGCTCGT
1 TAACCATTCTAGGCTCGT
16231571 GTGAGTTAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
TAACCATTCTAGGCTCGTAAGAGC
Found at i:16242330 original size:207 final size:206
Alignment explanation
Indices: 16241968--16242386 Score: 759
Period size: 207 Copynumber: 2.0 Consensus size: 206
16241958 ATTTGCTATT
*
16241968 GATTTTAAGTAAAAAGGTGGTAAATTATATAGGAAAAAACCTATATATTTTTTAGTTTACATTTC
1 GATTTTAAGTAAAAAGGTGATAAATTATATAGGAAAAAACCTATATATTTTTTAGTTTACATTTC
* *
16242033 CCCTCTCCTCTCCCTTCTTCGGATATGGTTTTAACGCTCAAAACTTTTTCAACATTCCTCATTAT
66 CCCTCTCCGCTCCCTTCTTCGGATATGGTTTTAACGCTCAAAACTTTTTCAACATTCCCCATTAT
* *
16242098 CTTGATTATCTTATTTTCTCTTAGTTTTCGTTTAGAGTTGATAACACCCACCGTGACATGAATGT
131 CTTGATTATCTTATTTTCTCTTAGTTTTCATTCAGAGTT-ATAACACCCACCGTGACATGAATG-
16242163 TTTAGATATATGG
194 TTTAGATATATGG
16242176 GATTTT-AGTAAAAAGGTGATAAATTATATAGGAAAAAACCTATATATTTTTTAGTTTACATTTC
1 GATTTTAAGTAAAAAGGTGATAAATTATATAGGAAAAAACCTATATATTTTTTAGTTTACATTTC
*
16242240 CCCTCTCCGCTCCCTTCTTCGGATATGGTTTTAACGCTCAAGACTTTTTCAACATTCCCCATTAT
66 CCCTCTCCGCTCCCTTCTTCGGATATGGTTTTAACGCTCAAAACTTTTTCAACATTCCCCATTAT
16242305 CTTGATTATCTTATTTTCTCTTAGTTTTCATTCAGAGTTATAACACCCACCGTGACATGAATGTT
131 CTTGATTATCTTATTTTCTCTTAGTTTTCATTCAGAGTTATAACACCCACCGTGACATGAATGTT
16242370 TAGATATATGG
196 TAGATATATGG
16242381 GATTTT
1 GATTTT
16242387 TTAATTAATT
Statistics
Matches: 205, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
205 19 0.09
206 24 0.12
207 156 0.76
208 6 0.03
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (206 bp):
GATTTTAAGTAAAAAGGTGATAAATTATATAGGAAAAAACCTATATATTTTTTAGTTTACATTTC
CCCTCTCCGCTCCCTTCTTCGGATATGGTTTTAACGCTCAAAACTTTTTCAACATTCCCCATTAT
CTTGATTATCTTATTTTCTCTTAGTTTTCATTCAGAGTTATAACACCCACCGTGACATGAATGTT
TAGATATATGG
Found at i:16246368 original size:11 final size:10
Alignment explanation
Indices: 16246352--16246392 Score: 57
Period size: 11 Copynumber: 4.0 Consensus size: 10
16246342 GGTACAAATT
16246352 TAAAATAGAAA
1 TAAAATA-AAA
16246363 TAAAATAAAA
1 TAAAATAAAA
16246373 TAAAACTAAAA
1 TAAAA-TAAAA
16246384 TAAAA-AAAA
1 TAAAATAAAA
16246393 CAGGGACCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.14
10 8 0.28
11 17 0.59
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (10 bp):
TAAAATAAAA
Found at i:16246370 original size:5 final size:5
Alignment explanation
Indices: 16246352--16246392 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
16246342 GGTACAAATT
16246352 TAAAA TAGAAA TAAAA TAAAA TAAAA CTAAAA TAAAA -AAAA
1 TAAAA TA-AAA TAAAA TAAAA TAAAA -TAAAA TAAAA TAAAA
16246393 CAGGGACCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.12
5 20 0.59
6 10 0.29
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:16246373 original size:16 final size:16
Alignment explanation
Indices: 16246352--16246393 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
16246342 GGTACAAATT
16246352 TAAAATAGAAA-TAAAA
1 TAAAATA-AAACTAAAA
16246368 TAAAATAAAACTAAAA
1 TAAAATAAAACTAAAA
16246384 TAAAA-AAAAC
1 TAAAATAAAAC
16246394 AGGGACCAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (16 bp):
TAAAATAAAACTAAAA
Found at i:16247299 original size:34 final size:32
Alignment explanation
Indices: 16247237--16247301 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 32
16247227 GGCTTTATAA
*
16247237 TTTGGGTTTGTATTTGGGTTAATTTTATTTGGT
1 TTTGGGTTTGTATTTGGCTTAA-TTTATTTGGT
16247270 TTTGGGTTTTGTATTTGGACCTTAA-TTATTTG
1 TTTGGG-TTTGTATTTGG--CTTAATTTATTTG
16247302 TAATTGGACT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 6 0.21
34 18 0.64
36 4 0.14
ACGTcount: A:0.14, C:0.03, G:0.25, T:0.58
Consensus pattern (32 bp):
TTTGGGTTTGTATTTGGCTTAATTTATTTGGT
Found at i:16247303 original size:21 final size:21
Alignment explanation
Indices: 16247277--16247318 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16247267 GGTTTTGGGT
*
16247277 TTTGTATTTGGACCTTAATTA
1 TTTGTAATTGGACCTTAATTA
*
16247298 TTTGTAATTGGACTTTAATTA
1 TTTGTAATTGGACCTTAATTA
16247319 AAAAAAATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.07, G:0.14, T:0.52
Consensus pattern (21 bp):
TTTGTAATTGGACCTTAATTA
Found at i:16253731 original size:15 final size:15
Alignment explanation
Indices: 16253713--16253742 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16253703 TAATCTATAA
16253713 TATAATAATACTTAT
1 TATAATAATACTTAT
*
16253728 TATATTAATACTTAT
1 TATAATAATACTTAT
16253743 AAAATATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATAATACTTAT
Found at i:16254047 original size:17 final size:17
Alignment explanation
Indices: 16254025--16254061 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
16254015 ATAGTAGTAC
16254025 ATTATATATTACATATT
1 ATTATATATTACATATT
*
16254042 ATTATATATTATATATT
1 ATTATATATTACATATT
16254059 ATT
1 ATT
16254062 GTTTATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATATATTACATATT
Found at i:16257239 original size:13 final size:13
Alignment explanation
Indices: 16257213--16257248 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
16257203 TAGCACACAT
*
16257213 AAAACATAGCTTTA
1 AAAACATA-ATTTA
16257227 AAAACATAATTTA
1 AAAACATAATTTA
16257240 AAAACATAA
1 AAAACATAA
16257249 CTGGAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.25
Consensus pattern (13 bp):
AAAACATAATTTA
Found at i:16267743 original size:40 final size:42
Alignment explanation
Indices: 16267699--16267776 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
16267689 GCTTAAGATG
*
16267699 TTAAC-TTCGGTAGTTGG-TTAATTATATTAGGAACTAATGT
1 TTAACTTTCGGTAGTTGGATTAATTATAGTAGGAACTAATGT
* * *
16267739 TTAACTTTGGGTTGTTGGATTAATTATGGTAGGAACTA
1 TTAACTTTCGGTAGTTGGATTAATTATAGTAGGAACTA
16267777 GTACTCATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 5 0.16
41 10 0.31
42 17 0.53
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.42
Consensus pattern (42 bp):
TTAACTTTCGGTAGTTGGATTAATTATAGTAGGAACTAATGT
Found at i:16269679 original size:18 final size:17
Alignment explanation
Indices: 16269629--16269680 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 17
16269619 AAACTTTATT
16269629 CATAATGGGGTTCACATA
1 CATAATGGGG-TCACATA
* *
16269647 CATACATGAGTTCACATA
1 CATA-ATGGGGTCACATA
16269665 CATATATGGGGTCACA
1 CATA-ATGGGGTCACA
16269681 CTCATGTGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (17 bp):
CATAATGGGGTCACATA
Found at i:16272312 original size:14 final size:13
Alignment explanation
Indices: 16272263--16272306 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
16272253 GCACAGGTGC
16272263 ACTTATAAAACATA
1 ACTTA-AAAACATA
16272277 ACTTTAAAAACATA
1 AC-TTAAAAACATA
*
16272291 GCTTAAAAACATA
1 ACTTAAAAACATA
16272304 ACT
1 ACT
16272307 GGAAAACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 13 0.48
14 11 0.41
15 3 0.11
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.27
Consensus pattern (13 bp):
ACTTAAAAACATA
Found at i:16273108 original size:30 final size:30
Alignment explanation
Indices: 16273072--16273142 Score: 88
Period size: 30 Copynumber: 2.4 Consensus size: 30
16273062 CATAAACTAC
16273072 TGCATTTACACGAACTAAAGTCGCACAAGA
1 TGCATTTACACGAACTAAAGTCGCACAAGA
* * ** * *
16273102 TGCATTTACACGGATTGCAGTCGCACGAGC
1 TGCATTTACACGAACTAAAGTCGCACAAGA
16273132 TGCATTTACAC
1 TGCATTTACAC
16273143 AAATTACAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.24
Consensus pattern (30 bp):
TGCATTTACACGAACTAAAGTCGCACAAGA
Found at i:16273362 original size:6 final size:6
Alignment explanation
Indices: 16273351--16273389 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
16273341 GACGCAATGA
16273351 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AA-GGG AAGG
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG AAGG
16273390 ACAAAACGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:16279371 original size:59 final size:60
Alignment explanation
Indices: 16279306--16279420 Score: 142
Period size: 59 Copynumber: 1.9 Consensus size: 60
16279296 ATACTTTGTC
* * * *
16279306 CTAATTTGGTACCTAAATTTGACACTTTTTTT-TAAGTTGGTATTTAAACTTTTTTAGAT
1 CTAATTTGATACCTAAACTTAACACTTTTTTTCTAAGTTGGTATCTAAACTTTTTTAGAT
* ** * *
16279365 CTAATTTGATACCTGAACTTAACTTTTTTTTTCTAATTTGGTATCTAATCTTTTTT
1 CTAATTTGATACCTAAACTTAACACTTTTTTTCTAAGTTGGTATCTAAACTTTTTT
16279421 TAATATTAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
59 26 0.57
60 20 0.43
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (60 bp):
CTAATTTGATACCTAAACTTAACACTTTTTTTCTAAGTTGGTATCTAAACTTTTTTAGAT
Found at i:16279636 original size:34 final size:33
Alignment explanation
Indices: 16279598--16279667 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
16279588 CTTAGATAGC
* *
16279598 AAATT-AGGGAAAAAAAATGCTAAGTTTAGGTACT
1 AAATTAAGGCAAAAAAAAT--TAAATTTAGGTACT
* *
16279632 AAATTAAGTCAAAAAAAATTAAATTTAGGTATT
1 AAATTAAGGCAAAAAAAATTAAATTTAGGTACT
16279665 AAA
1 AAA
16279668 CTAAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 15 0.48
34 5 0.16
35 11 0.35
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (33 bp):
AAATTAAGGCAAAAAAAATTAAATTTAGGTACT
Found at i:16279679 original size:33 final size:34
Alignment explanation
Indices: 16279607--16279679 Score: 85
Period size: 33 Copynumber: 2.1 Consensus size: 34
16279597 CAAATTAGGG
* * * *
16279607 AAAAAAAATGCTAAGTTTAGGTACTAAATTAAGTC
1 AAAAAAAAT-CTAAATTTAGGTACTAAACTAAATA
*
16279642 AAAAAAAAT-TAAATTTAGGTATTAAACTAAATA
1 AAAAAAAATCTAAATTTAGGTACTAAACTAAATA
16279675 AAAAA
1 AAAAA
16279680 TTTAAATACC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 24 0.73
35 9 0.27
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (34 bp):
AAAAAAAATCTAAATTTAGGTACTAAACTAAATA
Found at i:16281059 original size:43 final size:43
Alignment explanation
Indices: 16280993--16281076 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
16280983 GCTATGTGAC
* *
16280993 CTTCATAATTTCGTCCATGCATGCTT-AGCGATTAAGCAAACAG
1 CTTCATAAATTCGTCCATACATGCTTAAG-GATTAAGCAAACAG
*
16281036 CTTCATAAATTCGTCCATACATGCTTAAGGATTATGCAAAC
1 CTTCATAAATTCGTCCATACATGCTTAAGGATTAAGCAAAC
16281077 TCCAATAGTC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (43 bp):
CTTCATAAATTCGTCCATACATGCTTAAGGATTAAGCAAACAG
Found at i:16283980 original size:3 final size:3
Alignment explanation
Indices: 16283972--16284067 Score: 93
Period size: 3 Copynumber: 32.0 Consensus size: 3
16283962 AAATCAAAAT
* * * ** * *
16283972 AAC AAC AAC AAC AAC AAT AGC AGC AAC AAC AGT AAC AAC AGC AAC AGC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* * * *
16284020 AGC AAC AAC AGC AAC AGC AGC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
16284068 TTTGACTTGG
Statistics
Matches: 77, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.57, C:0.31, G:0.09, T:0.02
Consensus pattern (3 bp):
AAC
Found at i:16284067 original size:9 final size:9
Alignment explanation
Indices: 16283972--16284065 Score: 107
Period size: 9 Copynumber: 10.4 Consensus size: 9
16283962 AAATCAAAAT
*
16283972 AACAACAAC
1 AACAGCAAC
* *
16283981 AACAACAAT
1 AACAGCAAC
*
16283990 AGCAGCAAC
1 AACAGCAAC
*
16283999 AACAGTAAC
1 AACAGCAAC
16284008 AACAGCAAC
1 AACAGCAAC
*
16284017 AGCAGCAAC
1 AACAGCAAC
16284026 AACAGCAAC
1 AACAGCAAC
*
16284035 AGCAGCAAC
1 AACAGCAAC
*
16284044 AACAACAAC
1 AACAGCAAC
*
16284053 AACAACAAC
1 AACAGCAAC
16284062 AACA
1 AACA
16284066 ACTTTGACTT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 73 1.00
ACGTcount: A:0.57, C:0.31, G:0.10, T:0.02
Consensus pattern (9 bp):
AACAGCAAC
Found at i:16285451 original size:66 final size:66
Alignment explanation
Indices: 16285345--16285472 Score: 256
Period size: 66 Copynumber: 1.9 Consensus size: 66
16285335 TCTTACTTAT
16285345 GTACTTTTAATCTATTATGCAATTTAACTGAGTAATCTAATAAGTTTCCCTTAAAAAATAATCAA
1 GTACTTTTAATCTATTATGCAATTTAACTGAGTAATCTAATAAGTTTCCCTTAAAAAATAATCAA
16285410 A
66 A
16285411 GTACTTTTAATCTATTATGCAATTTAACTGAGTAATCTAATAAGTTTCCCTTAAAAAATAAT
1 GTACTTTTAATCTATTATGCAATTTAACTGAGTAATCTAATAAGTTTCCCTTAAAAAATAAT
16285473 TGAATTCTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.39
Consensus pattern (66 bp):
GTACTTTTAATCTATTATGCAATTTAACTGAGTAATCTAATAAGTTTCCCTTAAAAAATAATCAA
A
Found at i:16285840 original size:11 final size:11
Alignment explanation
Indices: 16285824--16285858 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
16285814 CTACGAAAAG
*
16285824 AATATAAATAT
1 AATATAAATAA
16285835 AATATAAATAA
1 AATATAAATAA
*
16285846 AATAAAAATAA
1 AATATAAATAA
16285857 AA
1 AA
16285859 AAAGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATATAAATAA
Found at i:16288276 original size:26 final size:25
Alignment explanation
Indices: 16288214--16288277 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
16288204 AAAGAAAGAC
*
16288214 AAAATGAAAATAAACTTAAACCTAAG
1 AAAATGAGAA-AAACTTAAACCTAAG
* *
16288240 AAAAAGAGAAAAACTTAAA-CTGAACT
1 AAAATGAGAAAAACTTAAACCT-AA-G
16288266 AAAATGAGAAAA
1 AAAATGAGAAAA
16288278 TTTAATCTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.06
25 11 0.34
26 19 0.59
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (25 bp):
AAAATGAGAAAAACTTAAACCTAAG
Found at i:16291297 original size:23 final size:24
Alignment explanation
Indices: 16291263--16291312 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
16291253 AAAGATTGTT
16291263 AAAACAACTTC-TAAAAAAAACTC
1 AAAACAACTTCTTAAAAAAAACTC
* *
16291286 AAAAGCAA-TTCTTGAGAAAAACTC
1 AAAA-CAACTTCTTAAAAAAAACTC
16291310 AAA
1 AAA
16291313 GAGAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (24 bp):
AAAACAACTTCTTAAAAAAAACTC
Found at i:16305344 original size:23 final size:24
Alignment explanation
Indices: 16305301--16305345 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
16305291 TTTCCTAAGT
16305301 GGAGAGAAAAGGAAGGTGAGAGAA
1 GGAGAGAAAAGGAAGGTGAGAGAA
16305325 GGAGA-AATAAGG-AGGTGAGAG
1 GGAGAGAA-AAGGAAGGTGAGAG
16305346 GGAATGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.47, T:0.07
Consensus pattern (24 bp):
GGAGAGAAAAGGAAGGTGAGAGAA
Found at i:16329659 original size:19 final size:18
Alignment explanation
Indices: 16329635--16329680 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
16329625 CAAATTTTGA
16329635 ATAATTAATGTTAAAAAAT
1 ATAATTAAT-TTAAAAAAT
* *
16329654 ATAATTTATTT-ATAAA-
1 ATAATTAATTTAAAAAAT
16329670 ATAATTAATTT
1 ATAATTAATTT
16329681 GTGTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 10 0.42
17 4 0.17
18 2 0.08
19 8 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
ATAATTAATTTAAAAAAT
Found at i:16329672 original size:18 final size:19
Alignment explanation
Indices: 16329635--16329672 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
16329625 CAAATTTTGA
16329635 ATAATTAATGTTAAAAAAT
1 ATAATTAATGTTAAAAAAT
* *
16329654 ATAATTTAT-TTATAAAAT
1 ATAATTAATGTTAAAAAAT
16329672 A
1 A
16329673 ATTAATTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATAATTAATGTTAAAAAAT
Found at i:16338189 original size:18 final size:16
Alignment explanation
Indices: 16338155--16338193 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
16338145 TTTAATTTAT
*
16338155 TTAATTTATTAACTTG
1 TTAATTTATTAAATTG
16338171 TTAATTTATTTTAAATTG
1 TTAATTTA--TTAAATTG
16338189 TTAAT
1 TTAAT
16338194 ATTTTTACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
18 12 0.60
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TTAATTTATTAAATTG
Found at i:16346720 original size:12 final size:12
Alignment explanation
Indices: 16346703--16346727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16346693 TTCTGAAGGA
16346703 ATAAAATAAAAC
1 ATAAAATAAAAC
16346715 ATAAAATAAAAC
1 ATAAAATAAAAC
16346727 A
1 A
16346728 AAGTTTGAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAAATAAAAC
Found at i:16357235 original size:22 final size:23
Alignment explanation
Indices: 16357210--16357266 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
16357200 TGTGTCTCAA
16357210 ACACAAT-CCCGTGTATCCACTC
1 ACACAATGCCCGTGTATCCACTC
*
16357232 ACAC-ATGCTCGTGTATCCACTC
1 ACACAATGCCCGTGTATCCACTC
*
16357254 ACAC-ACGCCCGTG
1 ACACAATGCCCGTG
16357267 CCCTTGCCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.25, C:0.40, G:0.14, T:0.21
Consensus pattern (23 bp):
ACACAATGCCCGTGTATCCACTC
Found at i:16357600 original size:23 final size:23
Alignment explanation
Indices: 16357573--16357677 Score: 113
Period size: 23 Copynumber: 4.6 Consensus size: 23
16357563 CGTTTGTTTA
16357573 ATGTTCACGAACATTAATCGAAC
1 ATGTTCACGAACATTAATCGAAC
* *
16357596 ATGTTCACAAACTTTAATCGAAC
1 ATGTTCACGAACATTAATCGAAC
* *
16357619 ATGTTCACGAACATTAAACAAAC
1 ATGTTCACGAACATTAATCGAAC
* * *
16357642 AT-TTCATGAACATATAATTGAAT
1 ATGTTCACGAACAT-TAATCGAAC
* *
16357665 ACGTTCATGAACA
1 ATGTTCACGAACA
16357678 ATGTTAATGA
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 10 0.15
23 48 0.71
24 10 0.15
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (23 bp):
ATGTTCACGAACATTAATCGAAC
Found at i:16357806 original size:12 final size:12
Alignment explanation
Indices: 16357768--16357838 Score: 65
Period size: 12 Copynumber: 6.0 Consensus size: 12
16357758 TCATTAATAA
*
16357768 ATAAACGAAC-T
1 ATAAACGAGCTT
16357779 ATAAACGAG-TT
1 ATAAACGAGCTT
*
16357790 AATAAATGAGCTT
1 -ATAAACGAGCTT
**
16357803 ATAAACGAGCCA
1 ATAAACGAGCTT
*
16357815 ATAAACAAGCTT
1 ATAAACGAGCTT
*
16357827 TTAAACGAGCTT
1 ATAAACGAGCTT
16357839 GTTCGTGAAC
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
11 9 0.19
12 36 0.77
13 2 0.04
ACGTcount: A:0.46, C:0.15, G:0.14, T:0.24
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:16357810 original size:24 final size:24
Alignment explanation
Indices: 16357778--16357836 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
16357768 ATAAACGAAC
** **
16357778 TATAAACGAGTTAATAAATGAGCT
1 TATAAACGAGCCAATAAACAAGCT
16357802 TATAAACGAGCCAATAAACAAGCT
1 TATAAACGAGCCAATAAACAAGCT
*
16357826 TTTAAACGAGC
1 TATAAACGAGC
16357837 TTGTTCGTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (24 bp):
TATAAACGAGCCAATAAACAAGCT
Found at i:16358894 original size:79 final size:81
Alignment explanation
Indices: 16358716--16358982 Score: 242
Period size: 79 Copynumber: 3.4 Consensus size: 81
16358706 CGAGTATGAC
* ** ** * * * *
16358716 ACCCAGTGTCTAGCGGATAAACTGCAAATATGAGCCTAGCTCTAGTTGGATTAACGAAC-AAT-G
1 ACCCAGTGCCTAGCAAATAAACCACAAATGTGAGCCTAGTTCTAGTTGGATTAACCAACGAATAA
* * * * * *
16358779 TCCATGAAATCCTAGC
66 CCCGTCAATTCCTGGA
* * *
16358795 ACCCAATGCCTAGCAGATAAACCACAAATGTGAG-CTCAGCTT-TGGTTGGATTAACCAACGAAT
1 ACCCAGTGCCTAGCAAATAAACCACAAATGTGAGCCT-AG-TTCTAGTTGGATTAACCAACGAAT
* *
16358858 AA-CTGTCAATTCTTGGA
64 AACCCGTCAATTCCTGGA
* * *
16358875 ACCCAGTGCC-AGCAAATAAACCGCAATTGTGAGCCTAGTTCTAGTTGGATTAACCAATGAATAA
1 ACCCAGTGCCTAGCAAATAAACCACAAATGTGAGCCTAGTTCTAGTTGGATTAACCAACGAATAA
*
16358939 CCCGTCAATTCCTGGC
66 CCCGTCAATTCCTGGA
*
16358955 ACCCAGTGCCTAGCGAATAAACCA-AAAT
1 ACCCAGTGCCTAGCAAATAAACCACAAAT
16358983 TGTCAACCCA
Statistics
Matches: 151, Mismatches: 29, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
78 4 0.03
79 88 0.58
80 48 0.32
81 11 0.07
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (81 bp):
ACCCAGTGCCTAGCAAATAAACCACAAATGTGAGCCTAGTTCTAGTTGGATTAACCAACGAATAA
CCCGTCAATTCCTGGA
Found at i:16361215 original size:18 final size:18
Alignment explanation
Indices: 16361181--16361215 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16361171 AGAGAGCAGT
*
16361181 TTTGGTATCGATTTTGAC
1 TTTGGTATCGATATTGAC
*
16361199 TTTGGTATTGATATTGA
1 TTTGGTATCGATATTGA
16361216 AGGCCAAGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.06, G:0.23, T:0.51
Consensus pattern (18 bp):
TTTGGTATCGATATTGAC
Found at i:16369515 original size:28 final size:28
Alignment explanation
Indices: 16369450--16369515 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 28
16369440 ATATTAACGC
*
16369450 GCTTATCG-TATTATTTCGCACTACGGT
1 GCTTATCGTTACTATTTCGCACTACGGT
* * **
16369477 GGTTAAT-GTTACTATTTTGCACTTTGGT
1 GCTT-ATCGTTACTATTTCGCACTACGGT
16369505 GCTTATCGTTA
1 GCTTATCGTTA
16369516 TTTGCACTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.18, C:0.17, G:0.20, T:0.45
Consensus pattern (28 bp):
GCTTATCGTTACTATTTCGCACTACGGT
Found at i:16372437 original size:80 final size:79
Alignment explanation
Indices: 16372302--16372528 Score: 276
Period size: 80 Copynumber: 2.8 Consensus size: 79
16372292 ATATTGATGT
* * * * * *
16372302 AAGGACCCTCCGATGGCTAAGATCCTGCTTATGTTACAGTTTTTTGATAGCTTGTGTGAGCAGCA
1 AAGGACCCTCCGATGGCTAAGATCCAGCATATGTTGCAGATTCTTGACAGCTTGTGTGAGCAGCA
16372367 TCGTGAGTGGGA-AA
66 TCGTGAGT-GGATAA
* *
16372381 TATGGACCCTCCGATGGCTAAGATCCAGCATATGTTGCAGATTCTTGACAGCTTGTGTGAGTAGC
1 -AAGGACCCTCCGATGGCTAAGATCCAGCATATGTTGCAGATTCTTGACAGCTTGTGTGAGCAGC
16372446 ATCGTGAGTGGATAA
65 ATCGTGAGTGGATAA
* * * * * ** *
16372461 AAGGACCGTATCGATGGTTGAGGTCCAGCATATGTTGTGGATTCTTGACAGCCTGTGTGAGCAGC
1 AAGGACCCT-CCGATGGCTAAGATCCAGCATATGTTGCAGATTCTTGACAGCTTGTGTGAGCAGC
16372526 ATC
65 ATC
16372529 ATGTACTGGT
Statistics
Matches: 127, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
79 10 0.08
80 117 0.92
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (79 bp):
AAGGACCCTCCGATGGCTAAGATCCAGCATATGTTGCAGATTCTTGACAGCTTGTGTGAGCAGCA
TCGTGAGTGGATAA
Found at i:16377251 original size:61 final size:61
Alignment explanation
Indices: 16377154--16377365 Score: 293
Period size: 61 Copynumber: 3.5 Consensus size: 61
16377144 GTAAATGCAG
* * * *
16377154 AAAGGTCCAATGACTCTGTGTCATCGTGAGTGTTAAATGAAATGAATCCTATTACGGATTA
1 AAAGGTCCGATGACTTTGTGTCATCATGAGTGTTAAATGAAATGAATCCTATTACGAATTA
* *
16377215 AAAGGTCTGATGACTTTGTGTCATCATGAGTATTAAATGAAATGAATCCTATTACGAATTA
1 AAAGGTCCGATGACTTTGTGTCATCATGAGTGTTAAATGAAATGAATCCTATTACGAATTA
* * *
16377276 CAAGGTCCGATGACTTTGTGTCATCATGAGTGTTAAATGAAATGAATCCTATTATG-ACTA
1 AAAGGTCCGATGACTTTGTGTCATCATGAGTGTTAAATGAAATGAATCCTATTACGAATTA
* * * *
16377336 TAA-GTCCGATGACTCTATGTCATCGTGAGT
1 AAAGGTCCGATGACTTTGTGTCATCATGAGT
16377366 TCAAATGCAA
Statistics
Matches: 136, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
59 24 0.18
60 5 0.04
61 107 0.79
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (61 bp):
AAAGGTCCGATGACTTTGTGTCATCATGAGTGTTAAATGAAATGAATCCTATTACGAATTA
Found at i:16387989 original size:10 final size:10
Alignment explanation
Indices: 16387974--16388008 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
16387964 TTATGTATTC
16387974 TAATTAAATT
1 TAATTAAATT
16387984 TAATTAAATAT
1 TAATTAAAT-T
*
16387995 TAAATAAATT
1 TAATTAAATT
16388005 TAAT
1 TAAT
16388009 CTTAAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TAATTAAATT
Found at i:16395578 original size:7 final size:7
Alignment explanation
Indices: 16395566--16395677 Score: 127
Period size: 7 Copynumber: 15.7 Consensus size: 7
16395556 TTTCATCCCA
*
16395566 AAAAAAT
1 AAAAAAG
*
16395573 AAAAAAT
1 AAAAAAG
*
16395580 AAAGAA-
1 AAAAAAG
*
16395586 AAGAAAG
1 AAAAAAG
16395593 AAAGAAAG
1 AAA-AAAG
16395601 AAAAAAG
1 AAAAAAG
*
16395608 AAAAAAA
1 AAAAAAG
16395615 AAAAAAG
1 AAAAAAG
16395622 AAAAAAG
1 AAAAAAG
16395629 AAAAAAG
1 AAAAAAG
16395636 AAAAAAG
1 AAAAAAG
16395643 AAAAAAAG
1 -AAAAAAG
*
16395651 AAAAAGG
1 AAAAAAG
*
16395658 AAAAAGG
1 AAAAAAG
16395665 AAAAAGAG
1 AAAAA-AG
16395673 AAAAA
1 AAAAA
16395678 GGTGAGGTCA
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
6 4 0.04
7 69 0.74
8 20 0.22
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:16395606 original size:28 final size:26
Alignment explanation
Indices: 16395573--16395655 Score: 93
Period size: 25 Copynumber: 3.2 Consensus size: 26
16395563 CCAAAAAAAT
16395573 AAAAAATAAAGAAAAGAAAGAAAGAAAG
1 AAAAAA-AAAGAAAA-AAAGAAAGAAAG
16395601 AAAAAAGAAA-AAAAAAA-AAAGAAA-
1 AAAAAA-AAAGAAAAAAAGAAAGAAAG
*
16395625 AAAGAAAAAAG-AAAAAAGAAAAAAAG
1 AAA-AAAAAAGAAAAAAAGAAAGAAAG
16395651 AAAAA
1 AAAAA
16395656 GGAAAAAGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
24 12 0.24
25 18 0.37
26 6 0.12
27 4 0.08
28 9 0.18
ACGTcount: A:0.86, C:0.00, G:0.13, T:0.01
Consensus pattern (26 bp):
AAAAAAAAAGAAAAAAAGAAAGAAAG
Done.