Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 73 of 144
Found at i:15633476 original size:24 final size:24
Alignment explanation
Indices: 15633444--15633499 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
15633434 TGTATAGGTA
15633444 TCTTCTTGTTTTTCATTTTCATTT
1 TCTTCTTGTTTTTCATTTTCATTT
*
15633468 TCTTCTTGTTTTTCATTTTCTTTT
1 TCTTCTTGTTTTTCATTTTCATTT
*
15633492 TCCTCTTG
1 TCTTCTTG
15633500 AGAACTCTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.05, C:0.20, G:0.05, T:0.70
Consensus pattern (24 bp):
TCTTCTTGTTTTTCATTTTCATTT
Found at i:15637350 original size:77 final size:77
Alignment explanation
Indices: 15637255--15637414 Score: 263
Period size: 79 Copynumber: 2.1 Consensus size: 77
15637245 TCATTAAGGA
*
15637255 GAAA-TGCCATGCCTTTTCAACTACATCA-CCTAATGAAGAGACATGACTCATTGGCTTTCC-TA
1 GAAATTGCCATGCCTTTTCAACTACATCAGCCTAATGAAGAGACATGACTCATTAGC-TTCCTTA
15637317 CAAGAGTTAAAAAT
65 CAAGAGTT-AAAAT
15637331 GAAATTGCCATGCCTTTTCAACTACATCAGTCCTAATGAAGAGACATGACTCATTAGCTTCCTTA
1 GAAATTGCCATGCCTTTTCAACTACATCAG-CCTAATGAAGAGACATGACTCATTAGCTTCCTTA
15637396 CAAGAGTTAAAAT
65 CAAGAGTTAAAAT
15637409 GAAATT
1 GAAATT
15637415 AGTGCTTGTA
Statistics
Matches: 79, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
76 4 0.05
77 24 0.30
78 15 0.19
79 36 0.46
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (77 bp):
GAAATTGCCATGCCTTTTCAACTACATCAGCCTAATGAAGAGACATGACTCATTAGCTTCCTTAC
AAGAGTTAAAAT
Found at i:15638707 original size:78 final size:80
Alignment explanation
Indices: 15638544--15638756 Score: 236
Period size: 80 Copynumber: 2.7 Consensus size: 80
15638534 AGTTTAACTT
* * * * *
15638544 ACTAGAGCTGGGCTCACTTTTGTGATTTATCCGCTAGGCACTGGGTGCCATGATTCGACGGGCAT
1 ACTAGAGCTGGGCTCACTTTTATGGTTTATCCGCTAGGCACTAGGTGCCAGGATTCGACGAGCAT
*
15638609 TTGTTGGTTAATCCA
66 TTGTTGGTTAATCAA
**
15638624 ACTAGAGCTGGGCTCACTTTTATGGTTT-TTTGCTAGGCACTAGGTGCCAGGAATT-GAC-AG-A
1 ACTAGAGCTGGGCTCACTTTTATGGTTTATCCGCTAGGCACTAGGTGCCAGG-ATTCGACGAGCA
15638685 TTTTGTTGGTTAATCAA
65 -TTTGTTGGTTAATCAA
* * * * * * *
15638702 ACTAGAGATGGGCTCACTTATTACGGTTTATTCACTAGGCATTGGGTGTCAGGAT
1 ACTAGAGCTGGGCTCACTT-TTATGGTTTATCCGCTAGGCACTAGGTGCCAGGAT
15638757 CATCGACTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 34 0.30
79 32 0.28
80 47 0.41
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.34
Consensus pattern (80 bp):
ACTAGAGCTGGGCTCACTTTTATGGTTTATCCGCTAGGCACTAGGTGCCAGGATTCGACGAGCAT
TTGTTGGTTAATCAA
Found at i:15663449 original size:21 final size:21
Alignment explanation
Indices: 15663423--15663474 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
15663413 TGACACCCAA
15663423 GTATCAATACAAACATGGCAG
1 GTATCAATACAAACATGGCAG
*
15663444 GTATCAATACATACATGGCAG
1 GTATCAATACAAACATGGCAG
15663465 GTATCAATAC
1 GTATCAATAC
15663475 TTGTAGAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (21 bp):
GTATCAATACAAACATGGCAG
Found at i:15666041 original size:102 final size:103
Alignment explanation
Indices: 15665930--15666117 Score: 306
Period size: 102 Copynumber: 1.8 Consensus size: 103
15665920 TTACGAAAAT
* *
15665930 TGTATTGGCCCTTTTGACACAAAATGGAATGACAGCCCAAGCACT-CATCCCGGTTACTCAGCCC
1 TGTATTGGCCCTTTTGACACAAAATGGAATGACAACCCAAGCACTCCATCCCAGTTACTCAGCCC
15665994 AACACACTACTAATTTATTTTCATTTTTTACTTAAGAA
66 AACACACTACTAATTTATTTTCATTTTTTACTTAAGAA
* * *
15666032 TGTATTGGCCCTTTTGACGCGAAATGGAATGACAACCCAAGGACTCCATCCCAGTTACTCAGCCC
1 TGTATTGGCCCTTTTGACACAAAATGGAATGACAACCCAAGCACTCCATCCCAGTTACTCAGCCC
* *
15666097 AACACACTCCTATTTTATTTT
66 AACACACTACTAATTTATTTT
15666118 TTTATTTTTC
Statistics
Matches: 78, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
102 41 0.53
103 37 0.47
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (103 bp):
TGTATTGGCCCTTTTGACACAAAATGGAATGACAACCCAAGCACTCCATCCCAGTTACTCAGCCC
AACACACTACTAATTTATTTTCATTTTTTACTTAAGAA
Found at i:15667888 original size:41 final size:40
Alignment explanation
Indices: 15667838--15667958 Score: 154
Period size: 41 Copynumber: 3.0 Consensus size: 40
15667828 GCATGAAATA
15667838 ATTCAAGCTACGGCTTAGCAGACTATTGAGCCAGTGAAACT
1 ATTCAAGCTACGGCTTAGCAGACT-TTGAGCCAGTGAAACT
* * *
15667879 ATTCAAGCTACAGCTTAGTAGGCTTTAGAGCCAGTGAAACT
1 ATTCAAGCTACGGCTTAGCAGACTTT-GAGCCAGTGAAACT
* *
15667920 ATTCAAGCTACGACTTAGCA-AGCTTTTGAGCCGGTGAAA
1 ATTCAAGCTACGGCTTAGCAGA-C-TTTGAGCCAGTGAAA
15667959 GGGTGATATG
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.03
41 64 0.93
42 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (40 bp):
ATTCAAGCTACGGCTTAGCAGACTTTGAGCCAGTGAAACT
Found at i:15674583 original size:41 final size:40
Alignment explanation
Indices: 15674526--15674651 Score: 148
Period size: 41 Copynumber: 3.1 Consensus size: 40
15674516 CTAAAATAGC
* *
15674526 ATGAAA-TAATTCAAGCTATCTCTTAGTAGGCTATTGAGCCG
1 ATGAAACT-ATTCAAGCTA-CTCTTAGCAGGCTTTTGAGCCG
*
15674567 ATGAAACTATTCAAGCTACGTTTTAGCAGGCTTTTGAGCCTG
1 ATGAAACTATTCAAGCTAC-TCTTAGCAGGCTTTTGAGCC-G
**
15674609 -TGAAACTATTCAAGCTAAGGCTTAGCAGGCTTTTGAGCCG
1 ATGAAACTATTCAAGCT-ACTCTTAGCAGGCTTTTGAGCCG
15674649 ATG
1 ATG
15674652 TAATGATGAA
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
40 2 0.03
41 69 0.93
42 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (40 bp):
ATGAAACTATTCAAGCTACTCTTAGCAGGCTTTTGAGCCG
Found at i:15674739 original size:49 final size:49
Alignment explanation
Indices: 15674629--15674739 Score: 109
Period size: 49 Copynumber: 2.3 Consensus size: 49
15674619 CAAGCTAAGG
* * *
15674629 CTTAGCAGGCTTTTGAGCCGATGTAATGATGAAATAACTCAAGCTACGA
1 CTTAGCAGGCTTTTGAGCCGATGAAAGGATGAAATAACTCAAGCTACAA
* * * * * *
15674678 CTTA-CAAAGCTTTTGAGCCGGTGAAAGGGTGATATGGA-TCAAGTTACAA
1 CTTAGC-AGGCTTTTGAGCCGATGAAAGGATGAAAT-AACTCAAGCTACAA
15674727 CTTAGCAGGCTTT
1 CTTAGCAGGCTTT
15674740 AGGGTCCATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
48 1 0.02
49 46 0.94
50 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (49 bp):
CTTAGCAGGCTTTTGAGCCGATGAAAGGATGAAATAACTCAAGCTACAA
Found at i:15677715 original size:6 final size:6
Alignment explanation
Indices: 15677691--15677731 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
15677681 TCCTATACAT
*
15677691 AAAATG AAAATAA ATAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAAT-A A-AAATA AAAATA AAAATA AAAATA AAA
15677732 TTAGGTTGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 25 0.78
7 3 0.09
8 4 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:15688852 original size:11 final size:12
Alignment explanation
Indices: 15688822--15688854 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
15688812 GTCACAAGTG
15688822 AATTAATTCACA
1 AATTAATTCACA
*
15688834 AATGAATTCA-A
1 AATTAATTCACA
15688845 AATTAATTCA
1 AATTAATTCA
15688855 TTTTGGGTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.52, C:0.12, G:0.03, T:0.33
Consensus pattern (12 bp):
AATTAATTCACA
Found at i:15696613 original size:20 final size:18
Alignment explanation
Indices: 15696561--15696664 Score: 67
Period size: 17 Copynumber: 5.6 Consensus size: 18
15696551 ATGTACAAGA
15696561 TAAATATTAAATTAA-AT
1 TAAATATTAAATTAATAT
15696578 TAAATATTAAGA-TAATCACT
1 TAAATATTAA-ATTAAT-A-T
*
15696598 TTAATATTAAATTAATA-
1 TAAATATTAAATTAATAT
15696615 -AAATATTATTGAGA-TAAGTAT
1 TAAATATTA---A-ATTAA-TAT
*
15696636 TAAAT-TTAATTTAATAT
1 TAAATATTAAATTAATAT
15696653 TAAATTATTAAA
1 TAAA-TATTAAA
15696665 ATATTATTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 28
0.68 0.04 0.28
Matches are distributed among these distances:
16 7 0.10
17 20 0.29
18 6 0.09
19 11 0.16
20 17 0.25
21 3 0.04
22 4 0.06
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (18 bp):
TAAATATTAAATTAATAT
Found at i:15707303 original size:4 final size:4
Alignment explanation
Indices: 15707296--15707328 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
15707286 TATATCAAGC
*
15707296 AAGA AAGA AAGA AAGA AAGA TAGA AAGA AAGA A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA A
15707329 GATGGAATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:15729271 original size:20 final size:20
Alignment explanation
Indices: 15729246--15729283 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15729236 ACCTTTTTTG
*
15729246 TCAAAAAAATTAAAATAAAC
1 TCAAAAAAATAAAAATAAAC
*
15729266 TCAAAAACATAAAAATAA
1 TCAAAAAAATAAAAATAA
15729284 TTAAAAACGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.11, G:0.00, T:0.18
Consensus pattern (20 bp):
TCAAAAAAATAAAAATAAAC
Found at i:15731499 original size:24 final size:24
Alignment explanation
Indices: 15731466--15731516 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
15731456 AGAAATAATC
*
15731466 TTTCAGTTAAACTATGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
*
15731490 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
15731514 TTT
1 TTT
15731517 GAGTCAAACC
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:0.10, G:0.10, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTATTTG
Found at i:15731525 original size:24 final size:24
Alignment explanation
Indices: 15731474--15731525 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
15731464 TCTTTCAGTT
*
15731474 AAACTATGTTTATTTGTTTCAATT
1 AAACTATGTTTATTTGTTTCAATC
* * *
15731498 AAACTCTGTTTATTTGTTTGAGTC
1 AAACTATGTTTATTTGTTTCAATC
15731522 AAAC
1 AAAC
15731526 CCTTATTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.48
Consensus pattern (24 bp):
AAACTATGTTTATTTGTTTCAATC
Found at i:15733626 original size:15 final size:16
Alignment explanation
Indices: 15733602--15733631 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15733592 TAGTGTTTAC
15733602 ATTTTGTGGGTTTTTT
1 ATTTTGTGGGTTTTTT
15733618 ATTTT-TGGGTTTTT
1 ATTTTGTGGGTTTTT
15733632 GGGGTTTAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.07, C:0.00, G:0.23, T:0.70
Consensus pattern (16 bp):
ATTTTGTGGGTTTTTT
Found at i:15737038 original size:17 final size:17
Alignment explanation
Indices: 15737016--15737056 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
15737006 TAATTAACAA
15737016 TCAAATCACTAGAATTT
1 TCAAATCACTAGAATTT
15737033 TCAAATCACTAGAATTT
1 TCAAATCACTAGAATTT
15737050 TCAAATC
1 TCAAATC
15737057 GAATTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.05, T:0.34
Consensus pattern (17 bp):
TCAAATCACTAGAATTT
Found at i:15740959 original size:21 final size:20
Alignment explanation
Indices: 15740921--15740959 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
15740911 TGATCGCGTT
* *
15740921 AATGCATATTTTGTAAAAAC
1 AATGCAGATTTTGAAAAAAC
15740941 AATGCAGATTTTTGAAAAA
1 AATGCAGA-TTTTGAAAAA
15740960 TGGTCCTACC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGCAGATTTTGAAAAAAC
Found at i:15743231 original size:26 final size:26
Alignment explanation
Indices: 15743202--15743260 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 26
15743192 TAGTCAGTCA
*
15743202 CATCTATTTCTCTATCTTCTAGGAGT
1 CATCTATTTCTCTATCTTCTAGAAGT
* *
15743228 CATC--TGT-TCTATCTTTTAGAAGT
1 CATCTATTTCTCTATCTTCTAGAAGT
15743251 CATCTATTTC
1 CATCTATTTC
15743261 GATGCTCAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
23 18 0.69
24 2 0.08
25 2 0.08
26 4 0.15
ACGTcount: A:0.20, C:0.22, G:0.10, T:0.47
Consensus pattern (26 bp):
CATCTATTTCTCTATCTTCTAGAAGT
Found at i:15744278 original size:29 final size:30
Alignment explanation
Indices: 15744246--15744322 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
15744236 AATTCAGCTC
15744246 TTAGTCCTTGTAC-TTT-AATTTGATCAATG
1 TTAGTCCTTGTACTTTTCAATTT-ATCAATG
* * *
15744275 TTAGTTCTTATACTTTTCCAATTTATCAATT
1 TTAGTCCTTGTACTTTT-CAATTTATCAATG
*
15744306 TTAGTCCTTGTAATTTT
1 TTAGTCCTTGTACTTTT
15744323 TTAATTTTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
29 11 0.28
30 3 0.08
31 20 0.51
32 5 0.13
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.53
Consensus pattern (30 bp):
TTAGTCCTTGTACTTTTCAATTTATCAATG
Found at i:15744329 original size:31 final size:31
Alignment explanation
Indices: 15744259--15744337 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
15744249 GTCCTTGTAC
* * *
15744259 TTTAATTTGATCAATGTTAGTTCTTATACTTT
1 TTTAATTT-ATCAATTTTAGTCCTTATAATTT
** *
15744291 TCCAATTTATCAATTTTAGTCCTTGTAATTT
1 TTTAATTTATCAATTTTAGTCCTTATAATTT
*
15744322 TTTAATTT-TGAATTTT
1 TTTAATTTATCAATTTT
15744338 TATTCCTGAC
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 7 0.18
31 25 0.66
32 6 0.16
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (31 bp):
TTTAATTTATCAATTTTAGTCCTTATAATTT
Found at i:15748710 original size:18 final size:18
Alignment explanation
Indices: 15748689--15748730 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
15748679 GTTAATTTTT
*
15748689 TTAATTCGGGTAATTCGA
1 TTAATTCGAGTAATTCGA
15748707 TTAATTCGAGTAATTCGA
1 TTAATTCGAGTAATTCGA
*
15748725 ATAATT
1 TTAATT
15748731 TTTTATACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (18 bp):
TTAATTCGAGTAATTCGA
Found at i:15748724 original size:9 final size:9
Alignment explanation
Indices: 15748690--15748730 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
15748680 TTAATTTTTT
*
15748690 TAATTCGGG
1 TAATTCGAG
*
15748699 TAATTCGAT
1 TAATTCGAG
15748708 TAATTCGAG
1 TAATTCGAG
*
15748717 TAATTCGAA
1 TAATTCGAG
15748726 TAATT
1 TAATT
15748731 TTTTATACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (9 bp):
TAATTCGAG
Found at i:15753956 original size:14 final size:15
Alignment explanation
Indices: 15753937--15753969 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
15753927 TTCCCGGAGT
*
15753937 AAATTCTTGA-AAAA
1 AAATTCGTGATAAAA
15753951 AAATTCGTGATAAAA
1 AAATTCGTGATAAAA
15753966 AAAT
1 AAAT
15753970 ATATATAGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (15 bp):
AAATTCGTGATAAAA
Found at i:15756131 original size:42 final size:40
Alignment explanation
Indices: 15756077--15756154 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
15756067 GAGTGACAAT
*
15756077 GAAAAAGAAAAGAAAATTGAAAA-AAAGAAAGGAAAATGAGA
1 GAAAAAGAAAAG-AAAGTGAAAAGAAAGAAA-GAAAATGAGA
* *
15756118 GAAAATAGCAAAGAAAGTGAAAAGAAAGAGAGAAAAT
1 GAAAA-AGAAAAGAAAGTGAAAAGAAAGAAAGAAAAT
15756155 AAAAAGATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
41 20 0.62
42 12 0.38
ACGTcount: A:0.68, C:0.01, G:0.23, T:0.08
Consensus pattern (40 bp):
GAAAAAGAAAAGAAAGTGAAAAGAAAGAAAGAAAATGAGA
Found at i:15765313 original size:58 final size:57
Alignment explanation
Indices: 15765137--15765318 Score: 201
Period size: 58 Copynumber: 3.1 Consensus size: 57
15765127 TTATTTTTCT
* * *
15765137 AATATTAATTATA-TATTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAA
1 AATA-TAATTAAATTATTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AA
* * * *
15765196 AATGTTATTAAATTATATATTA-TTTTATTATATTGTATTTAATAATAATTATATTAA
1 AATATAATTAAATTAT-TATTATTTTTATTAAATTATATTTAATAATAATTATATTAA
15765253 AATATAATTAAATTAATTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAA
1 AATATAATTAAATT-ATTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAA
*
15765311 AATTTAAT
1 AATATAAT
15765319 AACAATAACC
Statistics
Matches: 105, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
57 19 0.18
58 64 0.61
59 15 0.14
60 7 0.07
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (57 bp):
AATATAATTAAATTATTATTATTTTTATTAAATTATATTTAATAATAATTATATTAA
Found at i:15765493 original size:16 final size:16
Alignment explanation
Indices: 15765472--15765527 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
15765462 TGAATTATTG
*
15765472 ATTACAACCCTATTCC
1 ATTACAACTCTATTCC
*
15765488 ATTACAGCTCTATTCTCC
1 ATTACAACTCTA-T-TCC
15765506 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
15765522 ATTACA
1 ATTACA
15765528 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 19 0.54
17 2 0.06
18 14 0.40
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:15765508 original size:18 final size:16
Alignment explanation
Indices: 15765481--15765529 Score: 71
Period size: 18 Copynumber: 2.9 Consensus size: 16
15765471 GATTACAACC
15765481 CTATTCCATTACAGCT
1 CTATTCCATTACAGCT
*
15765497 CTATTCTCCATTACAACT
1 CTA-T-TCCATTACAGCT
15765515 CTATTCCATTACAGC
1 CTATTCCATTACAGC
15765530 GAACCAAACG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 13 0.45
17 2 0.07
18 14 0.48
ACGTcount: A:0.27, C:0.33, G:0.04, T:0.37
Consensus pattern (16 bp):
CTATTCCATTACAGCT
Found at i:15765606 original size:29 final size:29
Alignment explanation
Indices: 15765574--15765630 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
15765564 CCGTAATTGA
15765574 TTTTCCGAAAAATGTTTTACTTGTTTTAT
1 TTTTCCGAAAAATGTTTTACTTGTTTTAT
**
15765603 TTTTTTGAAAAATGTTTTACTTGTTTTA
1 TTTTCCGAAAAATGTTTTACTTGTTTTA
15765631 CCATGTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.58
Consensus pattern (29 bp):
TTTTCCGAAAAATGTTTTACTTGTTTTAT
Found at i:15771287 original size:14 final size:14
Alignment explanation
Indices: 15771270--15771296 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
15771260 TTTATTTCTT
15771270 TAAAATATATTTAG
1 TAAAATATATTTAG
15771284 TAAAATATATTTA
1 TAAAATATATTTA
15771297 TTTTTAAAAA
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:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (14 bp):
TAAAATATATTTAG
Found at i:15774672 original size:25 final size:25
Alignment explanation
Indices: 15774623--15774672 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
15774613 TTTCGAAAAT
* *
15774623 GAAATGAAAATAACTAAAGCTTAAA
1 GAAATGAAAATAACTAAAACCTAAA
15774648 GAAAT-AATAATAACTAAAACCTAAA
1 GAAATGAA-AATAACTAAAACCTAAA
15774673 TTACAAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 2 0.09
25 20 0.91
ACGTcount: A:0.62, C:0.10, G:0.08, T:0.20
Consensus pattern (25 bp):
GAAATGAAAATAACTAAAACCTAAA
Found at i:15785500 original size:11 final size:11
Alignment explanation
Indices: 15785479--15785551 Score: 78
Period size: 11 Copynumber: 6.4 Consensus size: 11
15785469 GCCTCTCATT
15785479 TTTTCCTTTCTC
1 TTTT-CTTTCTC
15785491 TTTTCTTTCTC
1 TTTTCTTTCTC
*
15785502 TCATTCCTTTCT-
1 T--TTTCTTTCTC
15785514 TATTTCTTTCTC
1 T-TTTCTTTCTC
15785526 TTTTCTTT-TC
1 TTTTCTTTCTC
15785536 TATTTCTTTCTC
1 T-TTTCTTTCTC
15785548 TTTT
1 TTTT
15785552 AATCACTCTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
10 3 0.06
11 34 0.63
12 9 0.17
13 8 0.15
ACGTcount: A:0.04, C:0.26, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTCTTTCTC
Found at i:15785512 original size:24 final size:23
Alignment explanation
Indices: 15785480--15785550 Score: 94
Period size: 22 Copynumber: 3.1 Consensus size: 23
15785470 CCTCTCATTT
15785480 TTTCCTTTCTCT-TTTCTTTCTC
1 TTTCCTTTCTCTATTTCTTTCTC
15785502 TCATTCCTTTCT-TATTTCTTTCTC
1 T--TTCCTTTCTCTATTTCTTTCTC
*
15785526 TTTTCTTT-TCTATTTCTTTCTC
1 TTTCCTTTCTCTATTTCTTTCTC
15785548 TTT
1 TTT
15785551 TAATCACTCT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
21 1 0.02
22 22 0.50
23 1 0.02
24 20 0.45
ACGTcount: A:0.04, C:0.27, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTCCTTTCTCTATTTCTTTCTC
Found at i:15786098 original size:20 final size:20
Alignment explanation
Indices: 15786073--15786115 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
15786063 ACCATTGACC
15786073 GACCGTTGACTTTGATCGTT
1 GACCGTTGACTTTGATCGTT
*
15786093 GACCGTTGACTTTGATTGTT
1 GACCGTTGACTTTGATCGTT
15786113 GAC
1 GAC
15786116 TTTTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.40
Consensus pattern (20 bp):
GACCGTTGACTTTGATCGTT
Found at i:15787188 original size:7 final size:7
Alignment explanation
Indices: 15787176--15787227 Score: 72
Period size: 7 Copynumber: 7.4 Consensus size: 7
15787166 AACATTTTGG
15787176 TTTATTA
1 TTTATTA
15787183 TTTATTA
1 TTTATTA
15787190 TTTATTA
1 TTTATTA
15787197 TTTATTA
1 TTTATTA
15787204 TTT-TTA
1 TTTATTA
15787210 -TTATTAA
1 TTTATT-A
15787217 TATTATTA
1 T-TTATTA
15787225 TTT
1 TTT
15787228 TGGAATTTTA
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
5 2 0.05
6 5 0.12
7 27 0.66
8 2 0.05
9 5 0.12
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTATTA
Found at i:15787190 original size:3 final size:3
Alignment explanation
Indices: 15787177--15787226 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
15787167 ACATTTTGGT
* *
15787177 TTA TTA TTTA TTA TTTA TTA TTTA TTA TTT TTA TTA TTA ATA TTA TTA
1 TTA TTA -TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
15787225 TT
1 TT
15787227 TTGGAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 31 0.77
4 9 0.22
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:15794976 original size:13 final size:14
Alignment explanation
Indices: 15794958--15794992 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
15794948 AAATTATTTT
15794958 TTTTTCTTTTC-TC
1 TTTTTCTTTTCTTC
15794971 TTTTTCTTTTCTTTC
1 TTTTTCTTTTC-TTC
15794986 TTTTTCT
1 TTTTTCT
15794993 CAATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 11 0.55
15 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTTCTTC
Found at i:15806549 original size:21 final size:22
Alignment explanation
Indices: 15806524--15806581 Score: 77
Period size: 21 Copynumber: 2.8 Consensus size: 22
15806514 TCAATCACAT
15806524 AAAGAAAAGAAAAA-AAGATAA
1 AAAGAAAAGAAAAAGAAGATAA
**
15806545 AAAGAAAA-AAAAAGTTGATAA
1 AAAGAAAAGAAAAAGAAGATAA
15806566 AAAG-AAAGAAAAAGAA
1 AAAGAAAAGAAAAAGAA
15806582 AGAATAGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 8 0.26
21 23 0.74
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAGAAAAGAAAAAGAAGATAA
Found at i:15878810 original size:22 final size:23
Alignment explanation
Indices: 15878769--15878814 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 23
15878759 TCAGCAAATG
*
15878769 ATTTTAAAATTATTAAAATTATT
1 ATTTTAAAATTAATAAAATTATT
15878792 ATTTTAAAA-TAATAAAATTATT
1 ATTTTAAAATTAATAAAATTATT
15878814 A
1 A
15878815 AATAATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTAAAATTAATAAAATTATT
Found at i:15879789 original size:31 final size:28
Alignment explanation
Indices: 15879748--15879811 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 28
15879738 ATTAAAGTTA
15879748 TTTAACAATTTTATTATTTCAAAAAACTAAT
1 TTTAACAATTTTA-TATTT-AAAAAA-TAAT
*
15879779 TTTAATAATTTTATATTTAAAAAATAAT
1 TTTAACAATTTTATATTTAAAAAATAAT
15879807 TTTAA
1 TTTAA
15879812 AATCATTTGC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 9 0.28
29 6 0.19
30 5 0.16
31 12 0.38
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAACAATTTTATATTTAAAAAATAAT
Found at i:15879801 original size:28 final size:30
Alignment explanation
Indices: 15879748--15879811 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 30
15879738 ATTAAAGTTA
*
15879748 TTTAACAATTTTATTATTTCAAAAAACTAAT
1 TTTAACAATTTTATTATTT-AAAAAAATAAT
*
15879779 TTTAATAATTTTA-TATTT-AAAAAATAAT
1 TTTAACAATTTTATTATTTAAAAAAATAAT
15879807 TTTAA
1 TTTAA
15879812 AATCATTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 14 0.45
30 5 0.16
31 12 0.39
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (30 bp):
TTTAACAATTTTATTATTTAAAAAAATAAT
Found at i:15887221 original size:40 final size:40
Alignment explanation
Indices: 15887166--15887353 Score: 159
Period size: 40 Copynumber: 4.7 Consensus size: 40
15887156 TGAAAAGAAG
*
15887166 TCAAGCTTCGGCTTAGCAAGCTACGAGTCGGTG-ATAGAAT
1 TCAAGCTTCGGCTTAGCAAGCTACGAGCCGGTGAATA-AAT
* * * * * *
15887206 TCAAGCTTTGACTTAGCAAGTTATGAGCCGATGAATAAGT
1 TCAAGCTTCGGCTTAGCAAGCTACGAGCCGGTGAATAAAT
* *
15887246 TCAAGCTTCGGCTTA-AAAGGCTACGAGCCAGTGAATAAAT
1 TCAAGCTTCGGCTTAGCAA-GCTACGAGCCGGTGAATAAAT
* * ** *
15887286 TCAAGCTAT-GGCTTATCAGGCTACGAGCCATTG-TTAAAAT
1 TCAAGCT-TCGGCTTAGCAAGCTACGAGCCGGTGAAT-AAAT
* * *
15887326 TCAAGCTACGGCTTAGCAGGCTATGAGC
1 TCAAGCTTCGGCTTAGCAAGCTACGAGC
15887354 TGATGAATTG
Statistics
Matches: 120, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
39 3 0.03
40 112 0.93
41 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (40 bp):
TCAAGCTTCGGCTTAGCAAGCTACGAGCCGGTGAATAAAT
Found at i:15887347 original size:80 final size:80
Alignment explanation
Indices: 15887166--15887353 Score: 195
Period size: 80 Copynumber: 2.4 Consensus size: 80
15887156 TGAAAAGAAG
* * * * * *
15887166 TCAAGCTTCGGCTTAGCAAGCTACGAGTCGGTGATAGAATTCAAGCTTTGACTTAGCAAGTTATG
1 TCAAGCTTCGGCTTAGCAGGCTACGAGCCAGTGATAGAATTCAAGCTATGACTTAGCAAGCTACG
15887231 AGCCGATGAATAAGT
66 AGCCGATGAATAAGT
** * * *
15887246 TCAAGCTTCGGCTTAAAAGGCTACGAGCCAGTGAATA-AATTCAAGCTATGGCTTATCAGGCTAC
1 TCAAGCTTCGGCTTAGCAGGCTACGAGCCAGTG-ATAGAATTCAAGCTATGACTTAGCAAGCTAC
15887310 GAGCC-ATTGTTAA-AA-T
65 GAGCCGA-TG--AATAAGT
* *
15887326 TCAAGCTACGGCTTAGCAGGCTATGAGC
1 TCAAGCTTCGGCTTAGCAGGCTACGAGC
15887354 TGATGAATTG
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
79 1 0.01
80 81 0.91
81 5 0.06
82 2 0.02
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (80 bp):
TCAAGCTTCGGCTTAGCAGGCTACGAGCCAGTGATAGAATTCAAGCTATGACTTAGCAAGCTACG
AGCCGATGAATAAGT
Found at i:15892165 original size:42 final size:40
Alignment explanation
Indices: 15892091--15892421 Score: 163
Period size: 42 Copynumber: 7.8 Consensus size: 40
15892081 AAAAGGTAAA
*
15892091 TCATTAGCGGCGCTTACACAAAGCGTCGCTAAAGGTCGGG
1 TCATTAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGG
* * **
15892131 TCTTTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGAC
1 TCATTAGCGGCGC-TTACACA-AAGCGCCGCTAAAGGTCGGG
* * * *
15892173 TCATTAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGG
1 TCATTAGCGGCGCTTACAC-AAAGCGCCGCTAAAGGTCGGG
*
15892214 TCATTAGCGGCTGGATAGCGGCGCTTATC-CAGAAGCGCCGCTAAAAGT-GGAG
1 TC---A-----T---TAGCGGCGCTTA-CACA-AAGCGCCGCTAAAGGTCGG-G
**
15892266 TCATTAGCGGCGCTTACCCACAAA-CGCCGCTAAAGGTCGTA
1 TCATTAGCGGCGCTTA--CACAAAGCGCCGCTAAAGGTCGGG
* * * * * *
15892307 TCATTAGCGACGCTTATATAGAAAGCACCGGTAAAGGTCAGG
1 TCATTAGCGGCGC-T-TACACAAAGCGCCGCTAAAGGTCGGG
* * *
15892349 TTATTAGCGACGCTTTTCTA-ATAAGCGCCGCTAAAGGT---G
1 TCATTAGCGGCGC-TTAC-ACA-AAGCGCCGCTAAAGGTCGGG
** *
15892388 TACATTAGCGGCGCTTTTATATAAGCGCCGCTAA
1 T-CATTAGCGGCGCTTACACA-AAGCGCCGCTAA
15892422 TATATTTAAA
Statistics
Matches: 228, Mismatches: 36, Indels: 55
0.71 0.11 0.17
Matches are distributed among these distances:
38 1 0.00
39 19 0.08
40 22 0.10
41 69 0.30
42 76 0.33
43 4 0.02
44 2 0.01
49 2 0.01
51 2 0.01
52 31 0.14
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (40 bp):
TCATTAGCGGCGCTTACACAAAGCGCCGCTAAAGGTCGGG
Found at i:15892218 original size:41 final size:40
Alignment explanation
Indices: 15892091--15892421 Score: 170
Period size: 41 Copynumber: 7.8 Consensus size: 40
15892081 AAAAGGTAAA
*
15892091 TCATTAGCGGCGCTTACAC-AAAGCGTCGCTAAAGGTCGGG
1 TCATTAGCGGCGCTTACACAAAAGCGCCGCTAAAGGTC-GG
* * * *
15892131 TCTTTAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGAC
1 TCATTAGCGGCGC-TTACACAAAAGCGCCGCTAAAGGTCG-G
* * *
15892173 TCATTAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAGG
1 TCATTAGCGGCGCTTACACAAAAGCGCCGCTAAAGGTC-GG
* * *
15892214 TCATTAGCGGCTGGATAGCGGCGCTTATC-CAGAAGCGCCGCTAAAAGTGGAG
1 TC---A-----T---TAGCGGCGCTTA-CACAAAAGCGCCGCTAAAGGTCG-G
* *
15892266 TCATTAGCGGCGCTTACCCACAAA-CGCCGCTAAAGGTCGTA
1 TCATTAGCGGCGCTTACACA-AAAGCGCCGCTAAAGGTCG-G
* * * * *
15892307 TCATTAGCGACGCTTATATAGAAAGCACCGGTAAAGGTCAGG
1 TCATTAGCGGCGCTTACACA-AAAGCGCCGCTAAAGGTC-GG
* * * *
15892349 TTATTAGCGACGCTTTTCTA-ATAAGCGCCGCTAAAGGT--G
1 TCATTAGCGGCGC-TTAC-ACAAAAGCGCCGCTAAAGGTCGG
** * *
15892388 TACATTAGCGGCGCTTTTATATAAGCGCCGCTAA
1 T-CATTAGCGGCGCTTACACAAAAGCGCCGCTAA
15892422 TATATTTAAA
Statistics
Matches: 228, Mismatches: 38, Indels: 51
0.72 0.12 0.16
Matches are distributed among these distances:
38 1 0.00
39 19 0.08
40 23 0.10
41 74 0.32
42 69 0.30
43 4 0.02
44 3 0.01
49 2 0.01
51 1 0.00
52 32 0.14
ACGTcount: A:0.27, C:0.25, G:0.26, T:0.22
Consensus pattern (40 bp):
TCATTAGCGGCGCTTACACAAAAGCGCCGCTAAAGGTCGG
Found at i:15892258 original size:52 final size:52
Alignment explanation
Indices: 15892177--15892276 Score: 139
Period size: 52 Copynumber: 1.9 Consensus size: 52
15892167 GTCGACTCAT
15892177 TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTCAG-GTCATTAGCGGCTGGA
1 TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGT-AGAGTCATTAGCGGCTGGA
** * * *
15892229 TAGCGGCGCTTATCCAGAAGCGCCGCTAAAAGTGGAGTCATTAGCGGC
1 TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTAGAGTCATTAGCGGC
15892277 GCTTACCCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.02
52 41 0.98
ACGTcount: A:0.28, C:0.24, G:0.30, T:0.18
Consensus pattern (52 bp):
TAGCGGCGCTTAGACAAAAGCGCCACTAAAAGTAGAGTCATTAGCGGCTGGA
Found at i:15892312 original size:93 final size:94
Alignment explanation
Indices: 15892135--15892315 Score: 233
Period size: 93 Copynumber: 1.9 Consensus size: 94
15892125 GTCGGGTCTT
* *
15892135 TAGCGGCGCTTTACCCACAAGCGCCGCTAAAGGTCGACTCATTAGCGGCGCTTAGACAAAAGCGC
1 TAGCGGCGCTTTACCCACAAGCGCCGCTAAAAGTCGACTCATTAGCGGCGCTTACACAAAAGCGC
*
15892200 CACTAAAAGTCAGGTCATTAGCGGCTGGA
66 CACTAAAAGTCAGATCATTAGCGGCTGGA
* * * * *
15892229 TAGCGGCGC-TTATCCAGAAGCGCCGCTAAAAGTGGAGTCATTAGCGGCGCTTACCCACAAA-CG
1 TAGCGGCGCTTTACCCACAAGCGCCGCTAAAAGTCGACTCATTAGCGGCGCTTACACA-AAAGCG
* *
15892292 CCGCTAAAGGTC-GTATCATTAGCG
65 CCACTAAAAGTCAG-ATCATTAGCG
15892316 ACGCTTATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
92 1 0.01
93 62 0.83
94 12 0.16
ACGTcount: A:0.27, C:0.28, G:0.27, T:0.19
Consensus pattern (94 bp):
TAGCGGCGCTTTACCCACAAGCGCCGCTAAAAGTCGACTCATTAGCGGCGCTTACACAAAAGCGC
CACTAAAAGTCAGATCATTAGCGGCTGGA
Found at i:15892565 original size:26 final size:25
Alignment explanation
Indices: 15892514--15892578 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
15892504 TCTGCATGCA
*
15892514 TCACCCCCAAATCACAGAACCCTCT
1 TCACCCCCAAATCGCAGAACCCTCT
15892539 TCACCCCCAAATCGCA-ATACCCTTCT
1 TCACCCCCAAATCGCAGA-ACCC-TCT
15892565 TCACCCCCAAATCG
1 TCACCCCCAAATCG
15892579 TTGAGCCCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
24 1 0.03
25 19 0.51
26 17 0.46
ACGTcount: A:0.29, C:0.48, G:0.05, T:0.18
Consensus pattern (25 bp):
TCACCCCCAAATCGCAGAACCCTCT
Found at i:15892587 original size:26 final size:25
Alignment explanation
Indices: 15892514--15892587 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 25
15892504 TCTGCATGCA
*
15892514 TCACCCCCAAATC-ACAGAACCC-TCT
1 TCACCCCCAAATCGA-TG-ACCCTTCT
15892539 TCACCCCCAAATCGCAAT-ACCCTTCT
1 TCACCCCCAAATCG--ATGACCCTTCT
*
15892565 TCACCCCCAAATCGTTGAGCCCT
1 TCACCCCCAAATCGATGA-CCCT
15892588 CTTTTATTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
24 1 0.02
25 18 0.44
26 21 0.51
28 1 0.02
ACGTcount: A:0.27, C:0.46, G:0.07, T:0.20
Consensus pattern (25 bp):
TCACCCCCAAATCGATGACCCTTCT
Found at i:15892590 original size:25 final size:24
Alignment explanation
Indices: 15892514--15892590 Score: 68
Period size: 25 Copynumber: 3.0 Consensus size: 24
15892504 TCTGCATGCA
*
15892514 TCACCCCCAAATC-ACAGAACCCTCT
1 TCACCCCCAAATCGA-TG-ACCCTCT
15892539 TCACCCCCAAATCGCAAT-ACCCTTCT
1 TCACCCCCAAATCG--ATGACCC-TCT
*
15892565 TCACCCCCAAATCGTTGAGCCCTCT
1 TCACCCCCAAATCGATGA-CCCTCT
15892590 T
1 T
15892591 TTATTTCCCT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
24 1 0.02
25 22 0.50
26 20 0.45
28 1 0.02
ACGTcount: A:0.26, C:0.45, G:0.06, T:0.22
Consensus pattern (24 bp):
TCACCCCCAAATCGATGACCCTCT
Found at i:15892661 original size:44 final size:43
Alignment explanation
Indices: 15892605--15892723 Score: 121
Period size: 44 Copynumber: 2.7 Consensus size: 43
15892595 TTCCCTCAGT
* * *
15892605 CCGTTGCCTCTTCACCTACAAAACCCACTTCTGTTCGCCTCACC
1 CCGTTCCCTCTTCACCT-CAAAACCCACTTCTCTTCCCCTCACC
** *
15892649 CCGTTCCCTCTTCACCCTCAAAACCGGCTTCTCTTCCCCTCACT
1 CCGTTCCCTCTTCA-CCTCAAAACCCACTTCTCTTCCCCTCACC
** * * *
15892693 CCGTTCAGTCTTCACCCCAGAACCCGCTTCT
1 CCGTTCCCTCTTCACCTCAAAACCCACTTCT
15892724 TCAGCCGATC
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
43 14 0.22
44 46 0.73
45 3 0.05
ACGTcount: A:0.16, C:0.47, G:0.09, T:0.28
Consensus pattern (43 bp):
CCGTTCCCTCTTCACCTCAAAACCCACTTCTCTTCCCCTCACC
Found at i:15894645 original size:20 final size:22
Alignment explanation
Indices: 15894606--15894646 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
15894596 TTTTAATAAA
*
15894606 AAATATAAAATTATTAAATATT
1 AAATATAAAATTAATAAATATT
15894628 AAAT-TAAAA-TAATAAATAT
1 AAATATAAAATTAATAAATAT
15894647 ATGTTCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 5 0.28
22 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AAATATAAAATTAATAAATATT
Found at i:15894666 original size:8 final size:9
Alignment explanation
Indices: 15894653--15894963 Score: 83
Period size: 8 Copynumber: 36.3 Consensus size: 9
15894643 ATATATGTTC
15894653 TAATTAT-T
1 TAATTATAT
15894661 TAATTATAT
1 TAATTATAT
* *
15894670 TAAAGTA-AA
1 T-AATTATAT
15894679 TAATTATAT
1 TAATTATAT
15894688 TGAATTAAATATT
1 T-AATT--ATA-T
15894701 TAATTAT-T
1 TAATTATAT
15894709 TAATTATAT
1 TAATTATAT
** * *
15894718 TAAAGAGAA
1 TAATTATAT
15894727 TAATTATAT
1 TAATTATAT
15894736 TAAATTAAATATT
1 T-AATT--ATA-T
15894749 TAATTAT-T
1 TAATTATAT
15894757 TAATTATAT
1 TAATTATAT
* *
15894766 TAAAGTA-AA
1 T-AATTATAT
15894775 TAATTATAT
1 TAATTATAT
15894784 TAAGTTA-A-
1 TAA-TTATAT
*
15894792 -AA-GAT-T
1 TAATTATAT
15894798 TAATTAT-T
1 TAATTATAT
15894806 TAATTATAT
1 TAATTATAT
* *
15894815 TAAAGTA-AA
1 T-AATTATAT
15894824 TAATTATAT
1 TAATTATAT
15894833 TAAGTTA-A-
1 TAA-TTATAT
*
15894841 -AA-GAT-T
1 TAATTATAT
15894847 TAATTAT-T
1 TAATTATAT
*
15894855 TAATTATGT
1 TAATTATAT
* *
15894864 TAAAGTA-AA
1 T-AATTATAT
15894873 TAATTATAT
1 TAATTATAT
15894882 TAATT-TA-
1 TAATTATAT
*
15894889 -AA-GAT-T
1 TAATTATAT
15894895 TAATTAT-T
1 TAATTATAT
15894903 TAATTATAT
1 TAATTATAT
* *
15894912 TAAAGTA-AA
1 T-AATTATAT
15894921 TAATTATAT
1 TAATTATAT
15894930 TAAGTTA-A-
1 TAA-TTATAT
*
15894938 -AA-GAT-T
1 TAATTATAT
15894944 TAATTAT-T
1 TAATTATAT
15894952 TAATTATAT
1 TAATTATAT
15894961 TAA
1 TAA
15894964 AGTAAATAAT
Statistics
Matches: 222, Mismatches: 37, Indels: 87
0.64 0.11 0.25
Matches are distributed among these distances:
5 3 0.01
6 3 0.01
7 14 0.06
8 85 0.38
9 58 0.26
10 41 0.18
12 14 0.06
13 4 0.02
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (9 bp):
TAATTATAT
Found at i:15894818 original size:49 final size:49
Alignment explanation
Indices: 15894653--15895110 Score: 734
Period size: 49 Copynumber: 9.4 Consensus size: 49
15894643 ATATATGTTC
*
15894653 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAA-TT-AAATATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATT-AAGTTAAAAGATT
* *
15894701 TAATTATTTAATTATATTAAAG-AGAATAATTATATTAAATT-AAATATT
1 TAATTATTTAATTATATTAAAGTA-AATAATTATATTAAGTTAAAAGATT
15894749 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
15894798 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
* *
15894847 TAATTATTTAATTATGTTAAAGTAAATAATTATATTAA-TTTAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
15894895 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
*
15894944 TAATTATTTAATTATATTAAAGTAAATAATTATATGAAAG-T-AAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATAT-TAAGTTAAAAGATT
* *
15894992 TAATTACTAAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
*
15895041 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAATATT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
15895090 TAATTATATTTAATTAT-TTAA
1 TAA-T-TATTTAATTATATTAA
15895111 TTAATAAAAA
Statistics
Matches: 387, Mismatches: 13, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
47 6 0.02
48 168 0.43
49 194 0.50
50 8 0.02
51 11 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (49 bp):
TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATT
Found at i:15894880 original size:146 final size:145
Alignment explanation
Indices: 15894653--15895110 Score: 744
Period size: 146 Copynumber: 3.1 Consensus size: 145
15894643 ATATATGTTC
*
15894653 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAA-TTAAATATTTAATTATTTAATTATA
1 TAATTATTTAATTATATTAAAGTAAATAATTATATT-AAGTTAAAGATTTAATTATTTAATTATA
*
15894717 TTAAAG-AGAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAAAGTAAATAATTA
65 TTAAAGTA-AATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTA
15894781 TATTAAGTTAAAAGATT
129 TATTAAGTTAAAAGATT
*
15894798 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATG
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTT-AAAGATTTAATTATTTAATTATA
*
15894863 TTAAAGTAAATAATTATATTAATTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTAT
65 TTAAAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTAT
15894928 ATTAAGTTAAAAGATT
130 ATTAAGTTAAAAGATT
* * *
15894944 TAATTATTTAATTATATTAAAGTAAATAATTATATGAAAG-TAAAGATTTAATTACTAAATTATA
1 TAATTATTTAATTATATTAAAGTAAATAATTATAT-TAAGTTAAAGATTTAATTATTTAATTATA
*
15895008 TTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTA
65 TTAAAGTAAATAATTATATTAAATT-AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTA
*
15895073 TATTAAGTTAAAATATT
129 TATTAAGTTAAAAGATT
15895090 TAATTATATTTAATTAT-TTAA
1 TAA-T-TATTTAATTATATTAA
15895111 TTAATAAAAA
Statistics
Matches: 296, Mismatches: 10, Indels: 12
0.93 0.03 0.04
Matches are distributed among these distances:
144 2 0.01
145 82 0.28
146 192 0.65
147 9 0.03
148 11 0.04
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (145 bp):
TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAGATTTAATTATTTAATTATAT
TAAAGTAAATAATTATATTAAATTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
TTAAGTTAAAAGATT
Found at i:15895095 original size:18 final size:17
Alignment explanation
Indices: 15895064--15895119 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
15895054 ATATTAAAGT
*
15895064 AAATAATTATATTAAGTTA
1 AAATATTTA-ATTAA-TTA
*
15895083 AAATATTTAATTATATTT
1 AAATATTTAATTA-ATTA
*
15895101 AATTATTTAATTAA-TA
1 AAATATTTAATTAATTA
15895117 AAA
1 AAA
15895120 ACAGCCCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 1 0.03
18 18 0.58
19 9 0.29
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AAATATTTAATTAATTA
Found at i:15895117 original size:97 final size:97
Alignment explanation
Indices: 15894653--15895110 Score: 737
Period size: 97 Copynumber: 4.7 Consensus size: 97
15894643 ATATATGTTC
*
15894653 TAATTATTTAATTATATTAAAGTAAATAATTATATTGAA-TTAAATATTTAATTATTTAATTATA
1 TAATTATTTAATTATATTAAAGTAAATAATTATATT-AAGTTAAAGATTTAATTATTTAATTATA
* *
15894717 TTAAAG-AGAATAATTATATTAAATT-AAATATT
65 TTAAAGTA-AATAATTATATTAAGTTAAAAGATT
15894749 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAAGATTTAATTATTTAATTATA
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTT-AAAGATTTAATTATTTAATTATA
15894814 TTAAAGTAAATAATTATATTAAGTTAAAAGATT
65 TTAAAGTAAATAATTATATTAAGTTAAAAGATT
* *
15894847 TAATTATTTAATTATGTTAAAGTAAATAATTATATTAATTTAAAGATTTAATTATTTAATTATAT
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAGATTTAATTATTTAATTATAT
15894912 TAAAGTAAATAATTATATTAAGTTAAAAGATT
66 TAAAGTAAATAATTATATTAAGTTAAAAGATT
* * *
15894944 TAATTATTTAATTATATTAAAGTAAATAATTATATGAAAG-TAAAGATTTAATTACTAAATTATA
1 TAATTATTTAATTATATTAAAGTAAATAATTATAT-TAAGTTAAAGATTTAATTATTTAATTATA
15895008 TTAAAGTAAATAATTATATTAAGTTAAAAGATT
65 TTAAAGTAAATAATTATATTAAGTTAAAAGATT
*
15895041 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAATATTTAATTATATTTAATTA
1 TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTT-AAAGATTTAA-T-TATTTAATTA
15895106 T-TTAA
63 TATTAA
15895111 TTAATAAAAA
Statistics
Matches: 339, Mismatches: 14, Indels: 15
0.92 0.04 0.04
Matches are distributed among these distances:
95 2 0.01
96 41 0.12
97 225 0.66
98 57 0.17
99 5 0.01
100 9 0.03
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (97 bp):
TAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAAGATTTAATTATTTAATTATAT
TAAAGTAAATAATTATATTAAGTTAAAAGATT
Found at i:15900741 original size:66 final size:66
Alignment explanation
Indices: 15900635--15900791 Score: 217
Period size: 66 Copynumber: 2.4 Consensus size: 66
15900625 CAAATTGCTC
*
15900635 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
15900699 AA
65 AA
* ** *
15900701 AACTTAAAGAGGAGGTTGCATTGAGAGAAGCAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
15900766 C
66 A
* * *
15900767 AACTTAAAGTGGAGGCAGCAGCGAG
1 AACTTAAAGAGGAGGCTGCAACGAG
15900792 GCAAGCGGAG
Statistics
Matches: 79, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
65 1 0.01
66 78 0.99
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:15900803 original size:21 final size:21
Alignment explanation
Indices: 15900777--15900829 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
15900767 AACTTAAAGT
15900777 GGAGGCAGCAGCGAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
*
15900798 GGAGGCAGCAGCTAGGCAAGC
1 GGAGGCAGCAGCGAGGCAAGC
* *
15900819 GAAGGAAGCAG
1 GGAGGCAGCAG
15900830 AGGCTACAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.21, G:0.45, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCGAGGCAAGC
Found at i:15901204 original size:43 final size:43
Alignment explanation
Indices: 15901146--15901329 Score: 316
Period size: 43 Copynumber: 4.3 Consensus size: 43
15901136 GCGCTTTATC
*
15901146 AAAAGCGCCGTTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
15901189 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
*
15901232 AAAAGCGCCGCTAAAGTACATGGCCTTCAGCGGCGCTTGTGGA
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
* *
15901275 AAAAGCGCCGCTAAAGTACATGGCCTTCAGCGGCGCTTATGG-
1 AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
*
15901317 GAAAGCGCCGCTA
1 AAAAGCGCCGCTA
15901330 TTTTTTGCGG
Statistics
Matches: 137, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
42 12 0.09
43 125 0.91
ACGTcount: A:0.27, C:0.26, G:0.30, T:0.17
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGA
Found at i:15902937 original size:35 final size:35
Alignment explanation
Indices: 15902891--15902966 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
15902881 AAGATAATAT
*
15902891 ATTTTGTTTAACTTGACTTG-CAAGCAATCTCTTAG
1 ATTTTATTTAACTTGAC-TGACAAGCAATCTCTTAG
15902926 ATTTTATTTAACTTGACTGACAAGCAATCTCTTAG
1 ATTTTATTTAACTTGACTGACAAGCAATCTCTTAG
*
15902961 AATTTA
1 ATTTTA
15902967 GGTCACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 2 0.05
35 36 0.95
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (35 bp):
ATTTTATTTAACTTGACTGACAAGCAATCTCTTAG
Found at i:15906160 original size:24 final size:24
Alignment explanation
Indices: 15906132--15906198 Score: 71
Period size: 24 Copynumber: 2.8 Consensus size: 24
15906122 AGAAATAATC
15906132 TTTCAGTTAAACTTTATTTAATTG
1 TTTCAGTTAAACTTTATTTAATTG
* * *
15906156 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTTTATTTAATTG
* * *
15906180 TCTAAGTCAAACTCTTATT
1 TTTCAGTTAAACT-TTATT
15906199 AGTCTAGATT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTTTATTTAATTG
Found at i:15908137 original size:24 final size:24
Alignment explanation
Indices: 15908109--15908171 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
15908099 AGAAATAATC
*
15908109 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
15908133 TTTCAATTAAACTCTATTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
15908157 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
15908172 TATTAGTCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.10, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:15917377 original size:24 final size:24
Alignment explanation
Indices: 15917345--15917391 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
15917335 TATTTCTTTC
*
15917345 GAGACTTCGAGACATGGCGTTTTT
1 GAGACTTCGAGACATAGCGTTTTT
15917369 GAGACTTCGAGACATAGCGTTTT
1 GAGACTTCGAGACATAGCGTTTT
15917392 CTTCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (24 bp):
GAGACTTCGAGACATAGCGTTTTT
Found at i:15918467 original size:22 final size:22
Alignment explanation
Indices: 15918442--15918484 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
15918432 TGCATGAAAT
15918442 AATTAAT-CAAAATTACACCATA
1 AATTAATCCAAAATT-CACCATA
* *
15918464 AATTCATCCAATATTCACCAT
1 AATTAATCCAAAATTCACCAT
15918485 GCACTTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTAATCCAAAATTCACCATA
Found at i:15920938 original size:95 final size:95
Alignment explanation
Indices: 15920771--15920943 Score: 217
Period size: 95 Copynumber: 1.8 Consensus size: 95
15920761 CTTCCAGGAC
* * * * * **
15920771 GTTAAACATGGGGTTATATTGTGTAAGACCATAGCTTAGTCATAATAACATATTGAGTTCATTGA
1 GTTAAACATGGGATTATACTGTGTAAGACCATAGCTTACTCATAATAACATATGGAGTCCACAGA
15920836 GAAAATAAACACAGGGGAGTTTGCTAAGAT
66 GAAAATAAACACAGGGGAGTTTGCTAAGAT
*
15920866 GTTAAACATGGGATTATACTGTGTAAGACCATAGCTTGACT-ATGGA-AACATATGGAGTCCACC
1 GTTAAACATGGGATTATACTGTGTAAGACCATAGCTT-ACTCAT-AATAACATATGGAGTCCA-C
*
15920929 AG-GATAATAAACACA
63 AGAGAAAATAAACACA
15920944 CGATAGTACC
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
95 62 0.94
96 4 0.06
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (95 bp):
GTTAAACATGGGATTATACTGTGTAAGACCATAGCTTACTCATAATAACATATGGAGTCCACAGA
GAAAATAAACACAGGGGAGTTTGCTAAGAT
Found at i:15924603 original size:24 final size:24
Alignment explanation
Indices: 15924576--15924625 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
15924566 TCATTAATAA
*
15924576 ATAAATGAGTCAATAAACGAGCTT
1 ATAAATGAGCCAATAAACGAGCTT
15924600 ATAAATGAGCCAATAAACGAGCTT
1 ATAAATGAGCCAATAAACGAGCTT
15924624 AT
1 AT
15924626 TTGTGGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.16, T:0.24
Consensus pattern (24 bp):
ATAAATGAGCCAATAAACGAGCTT
Found at i:15934038 original size:22 final size:22
Alignment explanation
Indices: 15934008--15934073 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
15933998 TGAACATGCC
*
15934008 ACCACTGATTTGCAAATAAACT
1 ACCATTGATTTGCAAATAAACT
** *
15934030 GTCATTGATTTGCATATAAACT
1 ACCATTGATTTGCAAATAAACT
* *
15934052 ACCATTGAGTTGTAAATAAACT
1 ACCATTGATTTGCAAATAAACT
15934074 TCCACTAAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (22 bp):
ACCATTGATTTGCAAATAAACT
Found at i:15934238 original size:49 final size:49
Alignment explanation
Indices: 15934105--15934231 Score: 200
Period size: 49 Copynumber: 2.6 Consensus size: 49
15934095 ACTGATATGG
* *
15934105 ACAAGCCACCACTGATATGCAGATTTACTGTTATTGATTTAATATGTGA
1 ACAAGCCACCACTGATATGCAGATTTACTGTCACTGATTTAATATGTGA
*
15934154 ACAAGCCACCATTGATATGCAGATTTACTGTCACTGATTTAATATGTGA
1 ACAAGCCACCACTGATATGCAGATTTACTGTCACTGATTTAATATGTGA
* * *
15934203 ACAAGCCACCACTAATTTGCAGATATACT
1 ACAAGCCACCACTGATATGCAGATTTACT
15934232 ACCACTGCTT
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (49 bp):
ACAAGCCACCACTGATATGCAGATTTACTGTCACTGATTTAATATGTGA
Found at i:15934831 original size:36 final size:36
Alignment explanation
Indices: 15934784--15934853 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
15934774 AATATTATTG
15934784 TCACTAACAAAATTGGTCACTAATAATCTTACTATC
1 TCACTAACAAAATTGGTCACTAATAATCTTACTATC
15934820 TCACTAACAAAATTGGTCACTAATAATCTTACTA
1 TCACTAACAAAATTGGTCACTAATAATCTTACTA
15934854 ACACTTACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (36 bp):
TCACTAACAAAATTGGTCACTAATAATCTTACTATC
Found at i:15935854 original size:24 final size:24
Alignment explanation
Indices: 15935827--15935897 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
15935817 GCACAAAACA
*
15935827 CATGAGCTCGCAATGCATAGCTCG
1 CATGAGCTCGCAATGCATAACTCG
* *
15935851 CATGAGCTGGCAATGCATAACTTG
1 CATGAGCTCGCAATGCATAACTCG
* *
15935875 CAAGAGCTCGCAATGCAAAACTC
1 CATGAGCTCGCAATGCATAACTC
15935898 ATAAGAGATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.31, C:0.27, G:0.23, T:0.20
Consensus pattern (24 bp):
CATGAGCTCGCAATGCATAACTCG
Found at i:15935903 original size:24 final size:24
Alignment explanation
Indices: 15935830--15935917 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
15935820 CAAAACACAT
* *
15935830 GAGCTCGCAATGCATAGCTCGCAT
1 GAGCTCGCAATGCATAACTCGCAA
* *
15935854 GAGCTGGCAATGCATAACTTGCAA
1 GAGCTCGCAATGCATAACTCGCAA
* **
15935878 GAGCTCGCAATGCAAAACTCATAA
1 GAGCTCGCAATGCATAACTCGCAA
* *
15935902 GAGATTGCAATGCATA
1 GAGCTCGCAATGCATA
15935918 GTTTGCAAGA
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (24 bp):
GAGCTCGCAATGCATAACTCGCAA
Found at i:15952298 original size:143 final size:145
Alignment explanation
Indices: 15951977--15952340 Score: 389
Period size: 143 Copynumber: 2.5 Consensus size: 145
15951967 AATAAAAAAT
* * *
15951977 TTTCTTTTGATTAAACAAAAATCACTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTT
1 TTTCTTTT-TTTAAA-AAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAG--
* *
15952042 TTAAAAAAA--AAA--TTGTTTAAAAAATTAAACTTTTTCTTTAAAATCACTAAAAAACAGATTT
62 TTAAAAAAATCAAACTTTGTTTAAAAAATTAAACTTTTTCTTGAAAATAACTAAAAAACAGATTT
15952103 TTATTTTTTAAAAATATAA
127 TTATTTTTTAAAAATATAA
** * *
15952122 -----TTTTTTAATGAAAATCACTACTTCACTTAAAAATTTAAACTTTTATTTCGAAATAGTTAA
1 TTTCTTTTTTTAAAAAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAA
* *
15952182 AAAAATCAGAACTTTGTTT-AAAATTTTAA-TTTTT-TTG-AAATAAACT-AAAAACAGATTTTT
66 AAAAATCA-AACTTTGTTTAAAAAATTAAACTTTTTCTTGAAAAT-AACTAAAAAACAGATTTTT
*
15952242 A-TTTTTAAAAATTTAAA
129 ATTTTTTAAAAATAT-AA
* * * *
15952259 CTTTCTTTTTTTAAAAAAAATCACTATTTTACTTAAAAATCTAAAATTTTATTTTGAAATGGTTA
1 -TTTCTTTTTTTAAAAAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTT-
15952324 AAAAAAATCAAAACTTT
64 AAAAAAATC-AAACTTT
15952341 TTCTTTAAAA
Statistics
Matches: 184, Mismatches: 20, Indels: 31
0.78 0.09 0.13
Matches are distributed among these distances:
136 21 0.11
137 21 0.11
138 48 0.26
139 11 0.06
140 11 0.06
141 6 0.03
143 50 0.27
144 15 0.08
145 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.42
Consensus pattern (145 bp):
TTTCTTTTTTTAAAAAAAATCACTACTTTACTTAAAAATCTAAACTTTTATTTCGAAATAGTTAA
AAAAATCAAACTTTGTTTAAAAAATTAAACTTTTTCTTGAAAATAACTAAAAAACAGATTTTTAT
TTTTTAAAAATATAA
Found at i:15952425 original size:46 final size:45
Alignment explanation
Indices: 15952375--15952535 Score: 119
Period size: 46 Copynumber: 3.4 Consensus size: 45
15952365 TTTTTTATCT
**
15952375 TTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTAG
1 TTAAAAATCCAAACTTTCTCTTTTTTAAAGAAAATCA-TATTTTAG
* * * **
15952421 TTAAAAATCCAAACTTTAT-TTCAAAATAGTTTAAAAAAAATCAAAACTTAG
1 TTAAAAATCCAAACTTTCTCTT-----T--TTTAAAGAAAATCATATTTTAG
* * *
15952472 TTTAAAAA-CTTAAACTTTCTCTTTTTTGAAGAAAATCATTATTTTAC
1 -TTAAAAATC-CAAACTTTCTCTTTTTTAAAGAAAATCA-TATTTTAG
15952519 TTAAAAATCCAAACTTT
1 TTAAAAATCCAAACTTT
15952536 TATTTTGAAA
Statistics
Matches: 87, Mismatches: 16, Indels: 24
0.69 0.13 0.19
Matches are distributed among these distances:
45 2 0.02
46 42 0.48
47 5 0.06
48 1 0.01
50 1 0.01
51 6 0.07
52 28 0.32
53 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (45 bp):
TTAAAAATCCAAACTTTCTCTTTTTTAAAGAAAATCATATTTTAG
Found at i:15952480 original size:129 final size:129
Alignment explanation
Indices: 15952237--15952480 Score: 348
Period size: 130 Copynumber: 1.9 Consensus size: 129
15952227 TAAAAACAGA
* *
15952237 TTTTTATTTTTAAAAATTTAAACTTTCTTTTTTTAAAAAAAATCACTATTTTACTTAAAAATCTA
1 TTTTTATCTTTAAAAATATAAACTTTCTTTTTTTAAAAAAAATCACTATTTTACTTAAAAATCTA
* ** ** *
15952302 AAATTTTATTTTGAAATGGTTAAAAAAAATCAAAACTTTTTCTTTAAAACAACTAAAAAATAAT
66 AAACTTTATTTCAAAATGGTTAAAAAAAATCAAAACTTAGTCTTAAAAACAACTAAAAAATAAT
* *
15952366 TTTTTATCTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTAGTTAAAAATC-
1 TTTTTATCTTTAAAAATATAAACTTTCT-TTTTTTAAAAAAAATCACTATTTTACTTAAAAATCT
* *
15952430 CAAACTTTATTTCAAAATAGTTTAAAAAAAATCAAAACTTAGT-TTAAAAAC
65 AAAACTTTATTTCAAAAT-GGTTAAAAAAAATCAAAACTTAGTCTTAAAAAC
15952481 TTAAACTTTC
Statistics
Matches: 101, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
129 47 0.47
130 54 0.53
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (129 bp):
TTTTTATCTTTAAAAATATAAACTTTCTTTTTTTAAAAAAAATCACTATTTTACTTAAAAATCTA
AAACTTTATTTCAAAATGGTTAAAAAAAATCAAAACTTAGTCTTAAAAACAACTAAAAAATAAT
Found at i:15952486 original size:98 final size:98
Alignment explanation
Indices: 15952374--15952567 Score: 293
Period size: 98 Copynumber: 2.0 Consensus size: 98
15952364 ATTTTTTATC
*
15952374 TTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTAGTTAAAAATCCAAAC-TTT
1 TTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTT
*
15952438 ATTTCAAAATAGTTTAAAAAAAATCAAAACTTAG
66 ATTTCAAAATAG-TTAAAAAAAATAAAAACTTAG
* *
15952472 TTTAAAAACT-TAAACTTTCTCTTTTTTGAAGAAAATCATTATTTTACTTAAAAATCCAAACTTT
1 TTTAAAAA-TATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTT
** *
15952536 TATTTTGAAATTGTTAAAAAAAATAAAAACTT
65 TATTTCAAAATAGTTAAAAAAAATAAAAACTT
15952568 TTCCCAAAAT
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
98 74 0.85
99 13 0.15
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (98 bp):
TTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTT
ATTTCAAAATAGTTAAAAAAAATAAAAACTTAG
Found at i:15953421 original size:42 final size:41
Alignment explanation
Indices: 15953352--15953506 Score: 177
Period size: 42 Copynumber: 3.7 Consensus size: 41
15953342 GAAATGAAAA
* * * *
15953352 AAAAATAAATGGACCTCTACGCTTAGGCCTCTAATTGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCTCTAA-TGCAATG
* * *
15953394 AAAAGTAAATGGAGCTCCACACCTAGGCTTCCGAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGGCCT-CTAATGCAATG
* *
15953436 AAAAGTAAATGGATCTCCACACCT-GGATCTCTAAATGCAATG
1 AAAAGTAAATGGACCTCCACACCTAGG-CCTCT-AATGCAATG
*
15953478 AAAAGTAAACGGACCTCCACACCTAGGCC
1 AAAAGTAAATGGACCTCCACACCTAGGCC
15953507 AAGTAAACGG
Statistics
Matches: 95, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.03
42 87 0.92
43 5 0.05
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAAGTAAATGGACCTCCACACCTAGGCCTCTAATGCAATG
Found at i:15953518 original size:27 final size:27
Alignment explanation
Indices: 15953480--15953533 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
15953470 ATGCAATGAA
15953480 AAGTAAACGGACCTCCACACCTAGGCC
1 AAGTAAACGGACCTCCACACCTAGGCC
15953507 AAGTAAACGGACCTCCACACCTAGGCC
1 AAGTAAACGGACCTCCACACCTAGGCC
15953534 TCTAAATGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.37, G:0.19, T:0.11
Consensus pattern (27 bp):
AAGTAAACGGACCTCCACACCTAGGCC
Found at i:15953549 original size:69 final size:71
Alignment explanation
Indices: 15953438--15953640 Score: 252
Period size: 69 Copynumber: 2.9 Consensus size: 71
15953428 ATGCAATGAA
* * *
15953438 AAGTAAATGGATCTCCACACCT-GGATCTCTAAATGCAATGAAAAGTAAACGGACCTCCACACCT
1 AAGTAAA-GGAACTCCACACCTAGG-CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCT
15953502 AGG-C-C-
64 AGGTCTCT
*
15953507 AAGTAAACGGACCTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
1 AAGTAAA-GGAACTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTA
15953572 GGTCTCT
65 GGTCTCT
* * * * * *
15953579 AAATGCAATGAACTCCACACTTAGGCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACAC
1 AAGT-AAAGGAACTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACAC
15953641 TTGGGCCTCT
Statistics
Matches: 118, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
69 60 0.51
70 3 0.03
71 1 0.01
72 52 0.44
73 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (71 bp):
AAGTAAAGGAACTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAG
GTCTCT
Found at i:15953566 original size:42 final size:42
Alignment explanation
Indices: 15953507--15953788 Score: 336
Period size: 42 Copynumber: 7.0 Consensus size: 42
15953497 CACCTAGGCC
* *
15953507 AAGTAAACGGACCTCCACACCTAGGCCTCTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
* *
15953549 AAGTAAATGGACCTCCACACCTAGGTCTCTAAATGCAAT---
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
* * *
15953588 --G---A---A-CTCCACACTTAGGCCTTTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
* * *
15953621 AAGTAAATGGGCCTCCACACTTGGGCCTCTAAATGTAATGAA
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
*
15953663 AAGTAAATGGGCCTCCACACCTGGGCCTCTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
* * *
15953705 AAGTAAGTGGACCTTCACACCTGGGCCTTTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
* *
15953747 AAGTAAATGAACCTCCATACCTGGGCCTCTAAATGCAATGAA
1 AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
15953789 TGTTTTCCTT
Statistics
Matches: 208, Mismatches: 20, Indels: 24
0.83 0.08 0.10
Matches are distributed among these distances:
30 24 0.12
31 1 0.00
34 1 0.00
35 1 0.00
37 1 0.00
38 1 0.00
42 179 0.86
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.22
Consensus pattern (42 bp):
AAGTAAATGGACCTCCACACCTGGGCCTCTAAATGCAATGAA
Found at i:15953597 original size:30 final size:30
Alignment explanation
Indices: 15953561--15953620 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
15953551 GTAAATGGAC
*
15953561 CTCCACACCTAGGTCTCTAAATGCAATGAA
1 CTCCACACCTAGGCCTCTAAATGCAATGAA
* *
15953591 CTCCACACTTAGGCCTTTAAATGCAATGAA
1 CTCCACACCTAGGCCTCTAAATGCAATGAA
15953621 AAGTAAATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.25
Consensus pattern (30 bp):
CTCCACACCTAGGCCTCTAAATGCAATGAA
Found at i:15953624 original size:72 final size:71
Alignment explanation
Indices: 15953450--15953662 Score: 254
Period size: 72 Copynumber: 3.0 Consensus size: 71
15953440 GTAAATGGAT
* * *
15953450 CTCCACACCT-GGATCTCTAAATGCAATGAAAAGTAAACGGACCTCCACACCTAGGC-C-AAGT-
1 CTCCACACCTAGG-CCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCTCTAAATG
* *
15953511 AAACGGAC
65 AAA-TGAA
15953519 CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGTCTCTAAATG
1 CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGG-CTCTAAATG
*
15953584 CAATGAA
65 AAATGAA
* * * * *
15953591 CTCCACACTTAGGCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACTTGGGCCTCTAAATG
1 CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGG-CTCTAAATG
*
15953656 TAATGAA
65 AAATGAA
15953663 AAGTAAATGG
Statistics
Matches: 126, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
69 50 0.40
70 3 0.02
71 1 0.01
72 70 0.56
73 2 0.02
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (71 bp):
CTCCACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTAGGCTCTAAATGA
AATGAA
Found at i:15962053 original size:17 final size:17
Alignment explanation
Indices: 15962031--15962071 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
15962021 ATATATATGG
15962031 AAATGCAATGACAATAA
1 AAATGCAATGACAATAA
*
15962048 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
*
15962065 TAATGCA
1 AAATGCA
15962072 GAGATACTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:15978048 original size:4 final size:4
Alignment explanation
Indices: 15978032--15978074 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
15978022 ACAAATGAGC
* *
15978032 GAAT GAGT GAAT GAAT GGAT GAAT GAAT GAAT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
15978075 ATTGGGGCAC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:15980165 original size:30 final size:30
Alignment explanation
Indices: 15980131--15980192 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
15980121 TTTTTCCATC
15980131 GTGTTGGTTGTTGTTCATGACTTTGGGTGA
1 GTGTTGGTTGTTGTTCATGACTTTGGGTGA
*
15980161 GTGTTGGTTGTTGTTCGTGACTTTGGGTGA
1 GTGTTGGTTGTTGTTCATGACTTTGGGTGA
15980191 GT
1 GT
15980193 TGTACTCTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.08, C:0.06, G:0.39, T:0.47
Consensus pattern (30 bp):
GTGTTGGTTGTTGTTCATGACTTTGGGTGA
Found at i:15980414 original size:12 final size:13
Alignment explanation
Indices: 15980383--15980420 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
15980373 ATAGCATGCC
*
15980383 TTTTGTGAGCTAA
1 TTTTGTGAGCCAA
15980396 TTTTGTGAGCCAA
1 TTTTGTGAGCCAA
*
15980409 -TTTGTGACCCAA
1 TTTTGTGAGCCAA
15980421 ATCAAGACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 11 0.48
13 12 0.52
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (13 bp):
TTTTGTGAGCCAA
Found at i:15980638 original size:7 final size:7
Alignment explanation
Indices: 15980628--15980703 Score: 80
Period size: 7 Copynumber: 10.9 Consensus size: 7
15980618 TGACCGGACA
15980628 TTGACCG
1 TTGACCG
15980635 TTGACCG
1 TTGACCG
* *
15980642 ATGACAG
1 TTGACCG
15980649 TTGACCG
1 TTGACCG
**
15980656 TTGATAG
1 TTGACCG
*
15980663 TTGACCA
1 TTGACCG
15980670 TTGACCG
1 TTGACCG
15980677 TTGACCG
1 TTGACCG
* *
15980684 ATGACAG
1 TTGACCG
*
15980691 TTGACCA
1 TTGACCG
15980698 TTGACC
1 TTGACC
15980704 TTCCTTTGTT
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 54 1.00
ACGTcount: A:0.24, C:0.24, G:0.25, T:0.28
Consensus pattern (7 bp):
TTGACCG
Found at i:15980654 original size:21 final size:20
Alignment explanation
Indices: 15980611--15980703 Score: 100
Period size: 21 Copynumber: 4.6 Consensus size: 20
15980601 AGCTGTTGAC
*
15980611 TGACTGTTGACCG--GACAT
1 TGACCGTTGACCGATGACAT
15980629 TGACCGTTGACCGATGACAGT
1 TGACCGTTGACCGATGACA-T
** *
15980650 TGACCGTTGATAGTTGACCAT
1 TGACCGTTGACCGATGA-CAT
15980671 TGACCGTTGACCGATGACAGT
1 TGACCGTTGACCGATGACA-T
*
15980692 TGACCATTGACC
1 TGACCGTTGACC
15980704 TTCCTTTGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
18 12 0.19
20 6 0.10
21 42 0.68
22 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.27
Consensus pattern (20 bp):
TGACCGTTGACCGATGACAT
Found at i:15980665 original size:28 final size:28
Alignment explanation
Indices: 15980629--15980702 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
15980619 GACCGGACAT
* *
15980629 TGACCGTTGACCGA-TGACAGTTGACCGT
1 TGACAGTTGACC-ATTGACAGTTGACCGA
* *
15980657 TGATAGTTGACCATTGACCGTTGACCGA
1 TGACAGTTGACCATTGACAGTTGACCGA
15980685 TGACAGTTGACCATTGAC
1 TGACAGTTGACCATTGAC
15980703 CTTCCTTTGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
27 1 0.03
28 39 0.98
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (28 bp):
TGACAGTTGACCATTGACAGTTGACCGA
Found at i:15987496 original size:12 final size:13
Alignment explanation
Indices: 15987465--15987502 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
15987455 ATAGCATGCC
*
15987465 TTTTGTGAGCCAA
1 TTTTGTGACCCAA
15987478 TTTTGTGACCCAA
1 TTTTGTGACCCAA
15987491 -TTTGTGACCCAA
1 TTTTGTGACCCAA
15987503 ATCAAGACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (13 bp):
TTTTGTGACCCAA
Found at i:15987786 original size:7 final size:7
Alignment explanation
Indices: 15987761--15987856 Score: 68
Period size: 7 Copynumber: 13.9 Consensus size: 7
15987751 ATTGATAATA
*
15987761 GTTGGCC
1 GTTGACC
*
15987768 GTTGGCC
1 GTTGACC
15987775 GTTGACC
1 GTTGACC
*
15987782 GTTGACA
1 GTTGACC
**
15987789 GTTGATT
1 GTTGACC
*
15987796 GTTGACT
1 GTTGACC
15987803 GTTGACC
1 GTTGACC
* **
15987810 ATTGATT
1 GTTGACC
**
15987817 GTTGAGA
1 GTTGACC
*
15987824 GTTGATC
1 GTTGACC
15987831 GTTGACC
1 GTTGACC
15987838 GTTGACC
1 GTTGACC
*
15987845 -TTGATC
1 GTTGACC
15987851 GTTGAC
1 GTTGAC
15987857 TTTTTTCGAA
Statistics
Matches: 71, Mismatches: 17, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
6 5 0.07
7 66 0.93
ACGTcount: A:0.16, C:0.18, G:0.30, T:0.36
Consensus pattern (7 bp):
GTTGACC
Found at i:15987835 original size:21 final size:21
Alignment explanation
Indices: 15987712--15987835 Score: 86
Period size: 21 Copynumber: 5.9 Consensus size: 21
15987702 TTGACCGACC
* *
15987712 GTTGACAGTTAACCGTTGACT
1 GTTGACAGTTGACCGTTGATT
* * *
15987733 GTTGGCCGTTGATCGTTGATT
1 GTTGACAGTTGACCGTTGATT
* * * * ***
15987754 GATAATAGTTGGCCGTTGGCC
1 GTTGACAGTTGACCGTTGATT
* *
15987775 GTTGACCGTTGACAGTTGATT
1 GTTGACAGTTGACCGTTGATT
* *
15987796 GTTGACTGTTGACCATTGATT
1 GTTGACAGTTGACCGTTGATT
* *
15987817 GTTGAGAGTTGATCGTTGA
1 GTTGACAGTTGACCGTTGA
15987836 CCGTTGACCT
Statistics
Matches: 72, Mismatches: 31, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 72 1.00
ACGTcount: A:0.19, C:0.15, G:0.30, T:0.37
Consensus pattern (21 bp):
GTTGACAGTTGACCGTTGATT
Found at i:15988530 original size:2 final size:2
Alignment explanation
Indices: 15988523--15988550 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
15988513 AAGATTGAGA
15988523 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15988551 GATAATCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15993348 original size:25 final size:24
Alignment explanation
Indices: 15993310--15993374 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
15993300 ATACCCATTT
15993310 AAAAAATTTATTTTTTATAAATAG
1 AAAAAATTTATTTTTTATAAATAG
*
15993334 AAAAAATTTATTTTTTATAAGTAG
1 AAAAAATTTATTTTTTATAAATAG
15993358 AAAAAATTTTATTTTTT
1 AAAAAA-TTTATTTTTT
15993375 TCTCTCATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
24 29 0.74
25 10 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (24 bp):
AAAAAATTTATTTTTTATAAATAG
Found at i:15993950 original size:51 final size:51
Alignment explanation
Indices: 15993864--15994095 Score: 141
Period size: 51 Copynumber: 4.6 Consensus size: 51
15993854 GAAAATTACT
* ** *
15993864 ATTTTACTTAAAAATCCAAACTTTTAT-TTCGAAATAGTTAAAAAAAATCAAA
1 ATTTTAGTTAAAAATTTAAACTTTT-TCTT-TAAATAGTTAAAAAAAATCAAA
*
15993916 ACTTT-GTTAAAAATTTAAACTTTTTCTTTAAA-A--TAACTAAAAAAT-AGAA
1 ATTTTAGTTAAAAATTTAAACTTTTTCTTTAAATAGTTAA--AAAAAATCA-AA
** * * * * * **
15993965 ATTTATCTTTAAAAATATAAACTTTCTCTTT---T-TTTAGAGAAAATCACT
1 ATTT-TAGTTAAAAATTTAAACTTTTTCTTTAAATAGTTAAAAAAAATCAAA
* *
15994013 ATTTTACTTAAAAATTCAAACTTTTAT-TTCTAAATAGTT-AAAAAAATCAAA
1 ATTTTAGTTAAAAATTTAAACTTTT-TCTT-TAAATAGTTAAAAAAAATCAAA
15994064 ATTTT-GTTTAAAAATTTAAAC-TTTTCTTTAAA
1 ATTTTAG-TTAAAAATTTAAACTTTTTCTTTAAA
15994096 ATTATTTAAA
Statistics
Matches: 137, Mismatches: 25, Indels: 39
0.68 0.12 0.19
Matches are distributed among these distances:
47 21 0.15
48 13 0.09
49 19 0.14
50 12 0.09
51 66 0.48
52 6 0.04
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.41
Consensus pattern (51 bp):
ATTTTAGTTAAAAATTTAAACTTTTTCTTTAAATAGTTAAAAAAAATCAAA
Found at i:15993980 original size:20 final size:21
Alignment explanation
Indices: 15993955--15993995 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
15993945 AAAATAACTA
15993955 AAAAATAGAAA-TTTATCTTT
1 AAAAATAGAAACTTTATCTTT
* *
15993975 AAAAATATAAACTTTCTCTTT
1 AAAAATAGAAACTTTATCTTT
15993996 TTTTAGAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.41
Consensus pattern (21 bp):
AAAAATAGAAACTTTATCTTT
Found at i:15994172 original size:148 final size:148
Alignment explanation
Indices: 15993569--15994218 Score: 846
Period size: 149 Copynumber: 4.4 Consensus size: 148
15993559 TGATTAAACA
*
15993569 AAAATCACT-TCTTTACTTCAAAA-TCAAAACTTTTATTTCGAAATAGTTTTAAAAAAAT-AAAA
1 AAAATCACTAT-TTTACTTAAAAATTC-AAACTTTTATTTCGAAATAG--TTAAAAAAATCAAAA
* *
15993631 ATTTATTTAAAAATTTAAACTTTTTCTTTAAAATCACTAAAAAACAGATTTTTATTTTTAAAAAT
62 CTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAAT
* **
15993696 CTAAACTTT-TTTTAATTAAA-
127 ATAAACTTTCTTTTTTTTAAAG
* * * *
15993716 ATAAT---TATTTTACTTAAAAAATCAAACTTTTATTTCGAAATAGTT-AACAAATCAGAACTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
*
15993777 ATTTAAAAATTTAAACTTTTT-TTT-AAATAACT-AAAAACAGATTTTTATTTTTAAAAATAAAA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
*
15993839 AC--TCTCTTTTTTAAAG
131 ACTTTCTTTTTTTTAAAG
* *
15993855 AAAATTACTATTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
* * ** *
15993920 T-GTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGAAATTTATCTTTAAAAATATA
65 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATA
*
15993984 AACTTTCTCTTTTTTTAGAG
130 AACTTTCT-TTTTTTTAAAG
* *
15994004 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCTAAATAGTTAAAAAAATCAAAATTTT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* ** **
15994069 GTTTAAAAATTTAAAC-TTTTCTTTAAAATTATTTAAAAAGTAGATTTTTATTTTTAAAAATATA
66 ATTTAAAAATTTAAACTTTTTCTTTAAAA-TAACTAAAAAACAGATTTTTATTTTTAAAAATATA
15994133 AACTTTCTTTTTTTTAAAG
130 AACTTTCTTTTTTTTAAAG
* *
15994152 AAAATCACTATTTTATTTAAAAATTTAAACTTTTATTTCGAAATAGTTAAAAAAAATTCAAAACT
1 AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTT-AAAAAAA-TCAAAACT
15994217 TT
64 TT
15994219 CCCAAAATCA
Statistics
Matches: 443, Mismatches: 40, Indels: 37
0.85 0.08 0.07
Matches are distributed among these distances:
137 1 0.00
138 8 0.02
139 34 0.08
140 7 0.02
141 9 0.02
142 67 0.15
143 19 0.04
144 49 0.11
145 11 0.02
146 27 0.06
147 4 0.01
148 86 0.19
149 112 0.25
150 9 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.42
Consensus pattern (148 bp):
AAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAA
ACTTTCTTTTTTTTAAAG
Found at i:15997607 original size:18 final size:17
Alignment explanation
Indices: 15997579--15997625 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
15997569 TTAATTTAAA
*
15997579 TTTTATCATTTTTTATT
1 TTTTATCATTTTATATT
15997596 TTTTATTCATTTTATA-T
1 TTTTA-TCATTTTATATT
15997613 TTTTA-CATTTTAT
1 TTTTATCATTTTAT
15997626 TTAATTACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.29
17 11 0.39
18 9 0.32
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATCATTTTATATT
Found at i:15997608 original size:16 final size:16
Alignment explanation
Indices: 15997541--15997627 Score: 56
Period size: 17 Copynumber: 5.4 Consensus size: 16
15997531 CATTTTATTG
*
15997541 TTATTTATTTATTTA-T
1 TTATTT-TTTATTCATT
* *
15997557 TTATTTTTGTATTTAAT
1 TTATTTTT-TATTCATT
**
15997574 TTAAATTTTA-TCATTTT
1 TTATTTTTTATTCA--TT
15997591 TTATTTTTTATTCATT
1 TTATTTTTTATTCATT
15997607 TTATATTTTTA--CATT
1 TTAT-TTTTTATTCATT
15997622 TTATTT
1 TTATTT
15997628 AATTACATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
14 2 0.03
15 12 0.20
16 20 0.34
17 22 0.37
18 3 0.05
ACGTcount: A:0.24, C:0.03, G:0.01, T:0.71
Consensus pattern (16 bp):
TTATTTTTTATTCATT
Found at i:15997622 original size:33 final size:34
Alignment explanation
Indices: 15997551--15997623 Score: 87
Period size: 33 Copynumber: 2.1 Consensus size: 34
15997541 TTATTTATTT
*
15997551 ATTTATTTATTTTTGTATTTAATTTAAATTTTATC
1 ATTT-TTTATTTTTGTATTCAATTTAAATTTTATC
* *
15997586 ATTTTTTATTTTT-TATTCATTTTATATTTT-TAC
1 ATTTTTTATTTTTGTATTCAATTTAAATTTTAT-C
15997619 ATTTT
1 ATTTT
15997624 ATTTAATTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 1 0.03
33 20 0.59
34 9 0.26
35 4 0.12
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (34 bp):
ATTTTTTATTTTTGTATTCAATTTAAATTTTATC
Found at i:16009393 original size:19 final size:20
Alignment explanation
Indices: 16009358--16009405 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
16009348 GTTAGTTGCA
16009358 TGCATTTATTTTAATTGTCAT-
1 TGCATTT-TTTTAATTGTC-TC
16009379 TGCATTTTTTT-ATTGTCTC
1 TGCATTTTTTTAATTGTCTC
16009398 TGCATTTT
1 TGCATTTT
16009406 ATTTGTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 4 0.15
21 7 0.27
ACGTcount: A:0.17, C:0.12, G:0.10, T:0.60
Consensus pattern (20 bp):
TGCATTTTTTTAATTGTCTC
Found at i:16009428 original size:17 final size:17
Alignment explanation
Indices: 16009408--16009450 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
16009398 TGCATTTTAT
*
16009408 TTGTTTTAGCATTTGCA
1 TTGTTTTAGCATTTCCA
16009425 TTGTTGTT-GCATTTCCA
1 TTGTT-TTAGCATTTCCA
*
16009442 TTTTTTTAG
1 TTGTTTTAG
16009451 TATACTATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.58
Consensus pattern (17 bp):
TTGTTTTAGCATTTCCA
Found at i:16036879 original size:12 final size:12
Alignment explanation
Indices: 16036864--16036901 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
16036854 AAATGAGTCA
16036864 ATAAACGAGCTT
1 ATAAACGAGCTT
**
16036876 ATAAACGAGCCA
1 ATAAACGAGCTT
16036888 ATAAACGAGCTT
1 ATAAACGAGCTT
16036900 AT
1 AT
16036902 TTGTGGACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.16, T:0.21
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:16036879 original size:24 final size:24
Alignment explanation
Indices: 16036852--16036901 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
16036842 TCATTAATAA
* *
16036852 ATAAATGAGTCAATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
16036876 ATAAACGAGCCAATAAACGAGCTT
1 ATAAACGAGCCAATAAACGAGCTT
16036900 AT
1 AT
16036902 TTGTGGACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.16, T:0.22
Consensus pattern (24 bp):
ATAAACGAGCCAATAAACGAGCTT
Found at i:16045483 original size:49 final size:49
Alignment explanation
Indices: 16045415--16045533 Score: 193
Period size: 49 Copynumber: 2.4 Consensus size: 49
16045405 ATCAGTCTCG
*
16045415 CCACTGATATGCAGATTTACTGTCATTGATTTAATATGTGAACAAGCCA
1 CCACTGATATGCAGATTTACTGTCACTGATTTAATATGTGAACAAGCCA
*
16045464 CCATTGATATGCAGATTTACTGTCACTGATTTAATATGTGAACAAGCCA
1 CCACTGATATGCAGATTTACTGTCACTGATTTAATATGTGAACAAGCCA
* * *
16045513 CCACTAATTTGCAGATATACT
1 CCACTGATATGCAGATTTACT
16045534 ACCACTGCTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 64 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (49 bp):
CCACTGATATGCAGATTTACTGTCACTGATTTAATATGTGAACAAGCCA
Found at i:16046176 original size:36 final size:36
Alignment explanation
Indices: 16046135--16046204 Score: 140
Period size: 36 Copynumber: 1.9 Consensus size: 36
16046125 AATACTATTG
16046135 TCACTAACAAAATTGGTCACTAATAATCTTACTATC
1 TCACTAACAAAATTGGTCACTAATAATCTTACTATC
16046171 TCACTAACAAAATTGGTCACTAATAATCTTACTA
1 TCACTAACAAAATTGGTCACTAATAATCTTACTA
16046205 ACACTTACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.40, C:0.21, G:0.06, T:0.33
Consensus pattern (36 bp):
TCACTAACAAAATTGGTCACTAATAATCTTACTATC
Found at i:16047202 original size:24 final size:24
Alignment explanation
Indices: 16047178--16047276 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
16047168 GAAAACACAT
* *
16047178 GAGCTCGCAATGCATAGCTCGCAT
1 GAGCTCGCAATGCATAACTCGCAA
*
16047202 GAGCTGGCAATGCATAACTCGCAA
1 GAGCTCGCAATGCATAACTCGCAA
* *
16047226 GAGCTCGCAATGCAAAACTCACAA
1 GAGCTCGCAATGCATAACTCGCAA
* * **
16047250 GCGATCGCAATGCATAGTTCGCAA
1 GAGCTCGCAATGCATAACTCGCAA
16047274 GAG
1 GAG
16047277 TTCACTATTA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.17
Consensus pattern (24 bp):
GAGCTCGCAATGCATAACTCGCAA
Found at i:16063417 original size:128 final size:128
Alignment explanation
Indices: 16063266--16063497 Score: 344
Period size: 128 Copynumber: 1.8 Consensus size: 128
16063256 CTAAAACGGA
* * *
16063266 TTTTTATTTTTAAAAATTTAAACTTTCTTTTTTTTTAAA-AAAATCACTATTTT-TCTTAAAAAT
1 TTTTTATCTTTAAAAATATAAACTTTC-TCTTTTTTAAAGAAAATCACTATTTTAT-TTAAAAAT
** *
16063329 CCAAAAATTTATTTTGAAATGGTT-AAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAATAA
64 CC-AAAATTTATTTCAAAATAGTTAAAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAATAA
16063393 T
128 T
16063394 TTTTTATCTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTATTTAAAAATCC
1 TTTTTATCTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTATTTAAAAATCC
*
16063459 AAACTTTATTTCAAAATAGTTAAAAAAAATCAAAACTTT
66 AAAATTTATTTCAAAATAGTT-AAAAAAATCAAAACTTT
16063498 GTTTAAAAAT
Statistics
Matches: 93, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
127 27 0.29
128 49 0.53
129 17 0.18
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (128 bp):
TTTTTATCTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTATTTAAAAATCC
AAAATTTATTTCAAAATAGTTAAAAAAATCAAAACTTTTTCTTTAAAATAACTAAAAAATAAT
Found at i:16063524 original size:147 final size:146
Alignment explanation
Indices: 16063362--16063644 Score: 421
Period size: 147 Copynumber: 1.9 Consensus size: 146
16063352 TAAAAAATCA
16063362 AAACTTTTTCTTTAAAATAACTAAAAAATAAT-TTTTTA-TCTTTAAAAATATAAACTTTCTCTT
1 AAACTTTTTCTTTAAAATAACTAAAAAA-AATATTTTTAGT-TTTAAAAATATAAACTTT-TC-T
*
16063425 TTTTAAAGAAAATCACTATTTTATTTAAAAATCCAAAC-TTTATTTCAAAATAGTTAAAAAAAAT
62 TTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTT-AAAAAAAT
16063489 CAAAACTTTGTTTAAAAATTT
126 CAAAACTTTGTTTAAAAATTT
16063510 AAAC-TTTTCTTTAAAATAACTAAAAAAAATAGATTTTTAGTTTTAAAAATATAAACTTTTCTTT
1 AAACTTTTTCTTTAAAATAACTAAAAAAAAT--ATTTTTAGTTTTAAAAATATAAACTTTTCTTT
* * * **
16063574 TTAAAGAAAATTATTATTTTACTTAAAAATTCAAACTTTTATTTTGAAATAGTTAAAAAAATCAA
64 TTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAATCAA
16063639 AACTTT
129 AACTTT
16063645 TCCCAAAATC
Statistics
Matches: 124, Mismatches: 6, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
146 3 0.02
147 75 0.60
148 21 0.17
149 24 0.19
150 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (146 bp):
AAACTTTTTCTTTAAAATAACTAAAAAAAATATTTTTAGTTTTAAAAATATAAACTTTTCTTTTT
AAAGAAAATCACTATTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAATCAAAA
CTTTGTTTAAAAATTT
Found at i:16064076 original size:3 final size:3
Alignment explanation
Indices: 16064068--16064093 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
16064058 CCTAAAAATA
16064068 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
16064094 AATTTGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:16064509 original size:42 final size:42
Alignment explanation
Indices: 16064463--16064774 Score: 462
Period size: 42 Copynumber: 7.4 Consensus size: 42
16064453 CTACGCTTAA
* * *
16064463 GCCTCTAATTGCAATGAAAAGTAAATGGACCTTCACACCTAG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
**
16064505 GCCTCCGAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
* *
16064547 GCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACTTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
* * *
16064589 GCCTTTAAATGCAATGAAAAGTAAATGGGCCTCCACACCGGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
*
16064631 GCCTCTAAATGCAATGAAAAGTAAATGGGCCTCCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
* * *
16064673 GTCTCTAAATGCAATGAAAAGTAAGTGGACCTTCACACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
* * * *
16064715 GCCTTTAAATACAATGAAAAGTAAATGAACCTCCATACCTGG
1 GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
16064757 GCCTCTAAATGCAATGAA
1 GCCTCTAAATGCAATGAA
16064775 TGTTTTCCTT
Statistics
Matches: 243, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 243 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (42 bp):
GCCTCTAAATGCAATGAAAAGTAAATGGACCTCCACACCTGG
Found at i:16065197 original size:21 final size:22
Alignment explanation
Indices: 16065173--16065232 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 22
16065163 TTGCTCTCTC
16065173 TTTCTATTTTTTTCTTC-TTTT
1 TTTCTATTTTTTTCTTCTTTTT
*
16065194 TTTCT-CTTTTTTCTTCTTTTT
1 TTTCTATTTTTTTCTTCTTTTT
16065215 TTTCATTATTTTTTTCTT
1 TTTC--TATTTTTTTCTT
16065233 GATTTAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 10 0.30
21 13 0.39
23 1 0.03
24 9 0.27
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTCTATTTTTTTCTTCTTTTT
Found at i:16065237 original size:12 final size:11
Alignment explanation
Indices: 16065173--16065237 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
16065163 TTGCTCTCTC
16065173 TTTC-TATTTT
1 TTTCTTATTTT
*
16065183 TTTCTTCTTTT
1 TTTCTTATTTT
16065194 TTTCTCT-TTTT
1 TTTCT-TATTTT
16065205 TCTTC-T-TTTT
1 T-TTCTTATTTT
16065215 TTTCATTATTTT
1 TTTC-TTATTTT
16065227 TTTCTTGATTT
1 TTTCTT-ATTT
16065238 AAACAAAATC
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
9 3 0.06
10 10 0.21
11 18 0.38
12 16 0.34
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (11 bp):
TTTCTTATTTT
Found at i:16084246 original size:14 final size:14
Alignment explanation
Indices: 16084227--16084309 Score: 53
Period size: 14 Copynumber: 6.0 Consensus size: 14
16084217 GTTGATCGGA
16084227 TGTTGACCGTTGAC
1 TGTTGACCGTTGAC
** *
16084241 TGTTGACCAAT-AA
1 TGTTGACCGTTGAC
*
16084254 TAGTTGACCATTGAC
1 T-GTTGACCGTTGAC
* * * **
16084269 CGATAATAGTTGAC
1 TGTTGACCGTTGAC
*
16084283 CGTTGACCGTTGAC
1 TGTTGACCGTTGAC
16084297 T-TTGACCGTTGAC
1 TGTTGACCGTTGAC
16084310 CTTAATCTTG
Statistics
Matches: 51, Mismatches: 16, Indels: 5
0.71 0.22 0.07
Matches are distributed among these distances:
13 14 0.27
14 36 0.71
15 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (14 bp):
TGTTGACCGTTGAC
Found at i:16084287 original size:7 final size:7
Alignment explanation
Indices: 16084277--16084310 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
16084267 ACCGATAATA
16084277 GTTGACC
1 GTTGACC
16084284 GTTGACC
1 GTTGACC
16084291 GTTGA-C
1 GTTGACC
*
16084297 TTTGACC
1 GTTGACC
16084304 GTTGACC
1 GTTGACC
16084311 TTAATCTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.15, C:0.26, G:0.26, T:0.32
Consensus pattern (7 bp):
GTTGACC
Found at i:16084291 original size:21 final size:21
Alignment explanation
Indices: 16084235--16084291 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
16084225 GATGTTGACC
* *
16084235 GTTGACTGTTGACCAATAATA
1 GTTGACCGTTGACCGATAATA
*
16084256 GTTGACCATTGACCGATAATA
1 GTTGACCGTTGACCGATAATA
16084277 GTTGACCGTTGACCG
1 GTTGACCGTTGACCG
16084292 TTGACTTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (21 bp):
GTTGACCGTTGACCGATAATA
Found at i:16084303 original size:13 final size:13
Alignment explanation
Indices: 16084285--16084328 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
16084275 TAGTTGACCG
16084285 TTGACCGTTGACT
1 TTGACCGTTGACT
*
16084298 TTGACCGTTGACC
1 TTGACCGTTGACT
* *
16084311 TTAATC-TTGACT
1 TTGACCGTTGACT
16084323 TTGACC
1 TTGACC
16084329 ATTAACTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:16084989 original size:12 final size:12
Alignment explanation
Indices: 16084965--16085000 Score: 63
Period size: 12 Copynumber: 2.9 Consensus size: 12
16084955 ACAGTGATTG
16084965 TGATATATGAGAT
1 TGATAT-TGAGAT
16084978 TGATATTGAGAT
1 TGATATTGAGAT
16084990 TGATATTGAGA
1 TGATATTGAGA
16085001 ATATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.25, T:0.39
Consensus pattern (12 bp):
TGATATTGAGAT
Found at i:16091548 original size:7 final size:7
Alignment explanation
Indices: 16091538--16091682 Score: 60
Period size: 7 Copynumber: 21.0 Consensus size: 7
16091528 GTTGACCGAT
16091538 CGTTGAC
1 CGTTGAC
*
16091545 CGTTGAT
1 CGTTGAC
*
16091552 AGTTGAC
1 CGTTGAC
* *
16091559 CATTGAT
1 CGTTGAC
*
16091566 CGTTGAT
1 CGTTGAC
*
16091573 CGTTGAT
1 CGTTGAC
* *
16091580 CGATAAC
1 CGTTGAC
* *
16091587 AGTTGGC
1 CGTTGAC
16091594 CGTTGAC
1 CGTTGAC
*
16091601 TGTTGAC
1 CGTTGAC
* *
16091608 TGTTGAT
1 CGTTGAC
16091615 CGTTGAC
1 CGTTGAC
*
16091622 TGTTGAC
1 CGTTGAC
* *
16091629 CATTGAT
1 CGTTGAC
* *
16091636 TGTAGAC
1 CGTTGAC
*
16091643 AGTTGAC
1 CGTTGAC
* *
16091650 TGTTGGC
1 CGTTGAC
*
16091657 C-TTGAT
1 CGTTGAC
16091663 CGTTGA-
1 CGTTGAC
* *
16091669 CTTTGAT
1 CGTTGAC
16091676 CGTTGAC
1 CGTTGAC
16091683 TTTTTTCAAA
Statistics
Matches: 98, Mismatches: 38, Indels: 4
0.70 0.27 0.03
Matches are distributed among these distances:
6 9 0.09
7 89 0.91
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (7 bp):
CGTTGAC
Found at i:16091580 original size:14 final size:14
Alignment explanation
Indices: 16091535--16091682 Score: 90
Period size: 14 Copynumber: 10.7 Consensus size: 14
16091525 ACCGTTGACC
16091535 GATCGTTGACCGTT
1 GATCGTTGACCGTT
* *
16091549 GATAGTTGACCATT
1 GATCGTTGACCGTT
*
16091563 GATCGTTGATCGTT
1 GATCGTTGACCGTT
* * *
16091577 GATCGATAACAGTT
1 GATCGTTGACCGTT
** *
16091591 GGCCGTTGACTGTT
1 GATCGTTGACCGTT
*
16091605 GA-CTGTTGATCGTT
1 GATC-GTTGACCGTT
*
16091619 GA-CTGTTGACCATT
1 GATC-GTTGACCGTT
* * *
16091633 GATTGTAGACAGTT
1 GATCGTTGACCGTT
*
16091647 GA-CTGTTGGCC-TT
1 GATC-GTTGACCGTT
*
16091660 GATCGTTGA-CTTT
1 GATCGTTGACCGTT
16091673 GATCGTTGAC
1 GATCGTTGAC
16091683 TTTTTTCAAA
Statistics
Matches: 100, Mismatches: 28, Indels: 12
0.71 0.20 0.09
Matches are distributed among these distances:
12 1 0.01
13 20 0.20
14 79 0.79
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (14 bp):
GATCGTTGACCGTT
Done.