Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 53 of 290
Found at i:17618257 original size:27 final size:27
Alignment explanation
Indices: 17618227--17618404 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
17618217 ATATTGAGTC
* * * *
17618227 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
17618254 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17618281 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
17618309 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
17618336 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
17618363 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17618390 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17618405 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:17618366 original size:82 final size:81
Alignment explanation
Indices: 17618248--17618403 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
17618238 TGCTATATAA
* *
17618248 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
17618313 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17618330 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17618394 CACTTAGTGC
65 CACTTAGTGC
17618404 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17627574 original size:28 final size:28
Alignment explanation
Indices: 17627511--17627804 Score: 439
Period size: 28 Copynumber: 10.5 Consensus size: 28
17627501 ATATTAAGTC
* *
17627511 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17627538 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17627566 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
* *
17627594 TGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17627622 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17627650 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17627678 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17627706 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17627734 CGCACACTTAGTGCTACATAATCAAGCT
1 CGCACACTTAGTGCTACATAATCAAACT
* * *
17627762 CGCACACTTAGTGCTGTACA-ATTTAAACC
1 CGCACACTTAGTGC--TACATAATCAAACT
17627791 CGCACACTTAGTGC
1 CGCACACTTAGTGC
17627805 CAATCTCATG
Statistics
Matches: 245, Mismatches: 19, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
27 22 0.09
28 200 0.82
29 19 0.08
30 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:17629732 original size:26 final size:26
Alignment explanation
Indices: 17629702--17629753 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
17629692 CTACAAAGAA
17629702 AGGTTTGCTGATTTGACGAAAGACTT
1 AGGTTTGCTGATTTGACGAAAGACTT
17629728 AGGTTTGCTGATTTGACGAAAGACTT
1 AGGTTTGCTGATTTGACGAAAGACTT
17629754 GACTCTCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (26 bp):
AGGTTTGCTGATTTGACGAAAGACTT
Found at i:17638320 original size:31 final size:31
Alignment explanation
Indices: 17638285--17638381 Score: 149
Period size: 31 Copynumber: 3.1 Consensus size: 31
17638275 AACCCTTCCT
*
17638285 GCATTAAATCCAACCAAAAACAGCAAATATA
1 GCATTGAATCCAACCAAAAACAGCAAATATA
17638316 GCATTGAATCCAACCAAAAACAGCAAATATA
1 GCATTGAATCCAACCAAAAACAGCAAATATA
* * * *
17638347 ACATTGGATCCAACCAAAAACAGTAAATGTA
1 GCATTGAATCCAACCAAAAACAGCAAATATA
17638378 GCAT
1 GCAT
17638382 AAAAAATACA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.51, C:0.22, G:0.10, T:0.18
Consensus pattern (31 bp):
GCATTGAATCCAACCAAAAACAGCAAATATA
Found at i:17638659 original size:21 final size:21
Alignment explanation
Indices: 17638634--17638691 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
17638624 TTTGCTGCCA
*
17638634 TCGCTACTGCCTCTGCCTCTC
1 TCGCTACTGCCTCTGCCTCCC
* *
17638655 TCGCTACTGTCGCTGCCTCCC
1 TCGCTACTGCCTCTGCCTCCC
* *
17638676 TCGCTGCTGCATCTGC
1 TCGCTACTGCCTCTGC
17638692 TCTAAGTTGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.05, C:0.45, G:0.19, T:0.31
Consensus pattern (21 bp):
TCGCTACTGCCTCTGCCTCCC
Found at i:17639123 original size:13 final size:14
Alignment explanation
Indices: 17639097--17639125 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
17639087 ACTAACGACG
17639097 AATTAAATCATTAT
1 AATTAAATCATTAT
17639111 AATTAAA-CATTAT
1 AATTAAATCATTAT
17639124 AA
1 AA
17639126 ATATTTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (14 bp):
AATTAAATCATTAT
Found at i:17644144 original size:9 final size:9
Alignment explanation
Indices: 17644130--17644324 Score: 98
Period size: 9 Copynumber: 21.7 Consensus size: 9
17644120 TAAGTATAAT
17644130 TAAGTTATG
1 TAAGTTATG
17644139 TAAGTTATG
1 TAAGTTATG
* * *
17644148 ATATGATATA
1 -TAAGTTATG
*
17644158 T-ATTTATG
1 TAAGTTATG
17644166 T-A-TTATG
1 TAAGTTATG
17644173 TAAGTTATG
1 TAAGTTATG
*
17644182 TAAATTATG
1 TAAGTTATG
17644191 TAAGTTATG
1 TAAGTTATG
* * *
17644200 AAATTTGAACTT
1 TAAGTT--A-TG
* *
17644212 TAAATTATA
1 TAAGTTATG
*
17644221 TTAGTTATG
1 TAAGTTATG
17644230 T-A-TTATG
1 TAAGTTATG
17644237 TAAGTTATG
1 TAAGTTATG
*
17644246 TAAATTATG
1 TAAGTTATG
17644255 TAAGTTATG
1 TAAGTTATG
* * *
17644264 AAATTTGAACTT
1 TAAGTT--A-TG
*
17644276 TAAATTATG
1 TAAGTTATG
17644285 TAAGTTATG
1 TAAGTTATG
*
17644294 -CA-TTATG
1 TAAGTTATG
*
17644301 TAAATTATG
1 TAAGTTATG
*
17644310 TAAATTATG
1 TAAGTTATG
*
17644319 TGAGTT
1 TAAGTT
17644325 GCTGGTGAAC
Statistics
Matches: 142, Mismatches: 31, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
7 17 0.12
8 10 0.07
9 95 0.67
10 8 0.06
11 2 0.01
12 10 0.07
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:17644199 original size:34 final size:34
Alignment explanation
Indices: 17644134--17644324 Score: 161
Period size: 34 Copynumber: 5.9 Consensus size: 34
17644124 TATAATTAAG
* * * * *
17644134 TTATGTAAGTTATG-ATATGATATATATTTATGTA
1 TTATGTAAGTTATGTAAATTATGTA-AGTTATGAA
17644168 TTATGTAAGTTATGTAAATTATGTAAGTTATGAAA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATG-AA
* * * *
17644203 TT-TG-AA-CT-T-TAAATTATATTAGTTATGTA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGAA
17644232 TTATGTAAGTTATGTAAATTATGTAAGTTATGAAA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATG-AA
* *
17644267 TT-TG-AA-CT-T-TAAATTATGTAAGTTATGCA
1 TTATGTAAGTTATGTAAATTATGTAAGTTATGAA
* *
17644296 TTATGTAAATTATGTAAATTATGTGAGTT
1 TTATGTAAGTTATGTAAATTATGTAAGTT
17644325 GCTGGTGAAC
Statistics
Matches: 127, Mismatches: 17, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
29 6 0.05
30 38 0.30
31 6 0.05
32 4 0.03
33 6 0.05
34 54 0.43
35 13 0.10
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (34 bp):
TTATGTAAGTTATGTAAATTATGTAAGTTATGAA
Found at i:17644216 original size:30 final size:30
Alignment explanation
Indices: 17644182--17644293 Score: 136
Period size: 30 Copynumber: 3.6 Consensus size: 30
17644172 GTAAGTTATG
17644182 TAAATTATGTAAGTTATGAAATTTGAACTT
1 TAAATTATGTAAGTTATGAAATTTGAACTT
* * * *
17644212 TAAATTATATTAGTTATG-TATTATGTAAGTTAT
1 TAAATTATGTAAGTTATGAAATT-TG-AA-CT-T
17644245 GTAAATTATGTAAGTTATGAAATTTGAACTT
1 -TAAATTATGTAAGTTATGAAATTTGAACTT
17644276 TAAATTATGTAAGTTATG
1 TAAATTATGTAAGTTATG
17644294 CATTATGTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
29 3 0.04
30 36 0.53
31 3 0.04
32 2 0.03
33 3 0.04
34 18 0.26
35 3 0.04
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (30 bp):
TAAATTATGTAAGTTATGAAATTTGAACTT
Found at i:17644239 original size:64 final size:64
Alignment explanation
Indices: 17644161--17644324 Score: 283
Period size: 64 Copynumber: 2.6 Consensus size: 64
17644151 TGATATATAT
*
17644161 TTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGAACTTTAAATTATATTAG
1 TTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGAACTTTAAATTATATAAG
*
17644225 TTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGAACTTTAAATTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGAACTTTAAATTATATAAG
* * *
17644289 TTATGCATTATGTAAATTATGTAAATTATGTGAGTT
1 TTATGTATTATGTAAGTTATGTAAATTATGTAAGTT
17644325 GCTGGTGAAC
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 95 1.00
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (64 bp):
TTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATGAAATTTGAACTTTAAATTATATAAG
Found at i:17644648 original size:38 final size:38
Alignment explanation
Indices: 17644606--17644730 Score: 137
Period size: 37 Copynumber: 3.2 Consensus size: 38
17644596 ACAACTTAAT
17644606 TTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
1 TTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
** * *
17644644 TTAATT-T-TCGTGATTCAAATAAAACAAAATATTTGAAATTAA
1 TTAATTATGTAATG-TTAAAATAAAATAAAATA-TTG--A--AA
17644686 TTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
1 -TTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
17644725 TTAATT
1 TTAATT
17644731 TTCGTGATTC
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
36 3 0.04
37 17 0.24
38 15 0.21
39 2 0.03
40 1 0.01
41 1 0.01
42 2 0.03
43 9 0.13
44 17 0.24
45 3 0.04
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (38 bp):
TTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
Found at i:17644648 original size:43 final size:43
Alignment explanation
Indices: 17644601--17644731 Score: 175
Period size: 43 Copynumber: 3.2 Consensus size: 43
17644591 TAAATACAAC
17644601 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
1 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
* * * *
17644644 TTAA-TT--TT-CGTGA--TTCAAATAAAACAAAATATTTGAAA
1 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATA-TTGAAA
17644682 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
1 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
17644725 TTAATTT
1 TTAATTT
17644732 TCGTGATTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 14
0.77 0.08 0.15
Matches are distributed among these distances:
37 16 0.22
38 10 0.14
39 5 0.07
40 2 0.03
41 2 0.03
42 5 0.07
43 17 0.23
44 16 0.22
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.40
Consensus pattern (43 bp):
TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAA
Found at i:17644665 original size:37 final size:38
Alignment explanation
Indices: 17644623--17644763 Score: 169
Period size: 37 Copynumber: 3.6 Consensus size: 38
17644613 TGTAATGTTA
*
17644623 AAATAAAATAAAATA-TTGAAATTAATTTTCGTGATTC
1 AAATAAAACAAAATATTTGAAATTAATTTTCGTGATTC
* * *
17644660 AAATAAAACAAAATATTTGAAATTAATTTAATTATGTAATGTTA
1 AAATAAAACAAAATATTTGAAATTAA-TT--TT-CGTGA--TTC
*
17644704 AAATAAAATAAAATA-TTGAAATTAATTTTCGTGATTC
1 AAATAAAACAAAATATTTGAAATTAATTTTCGTGATTC
17644741 AAATAAAACAAAATATTTGAAAT
1 AAATAAAACAAAATATTTGAAAT
17644764 GAAACTTTAA
Statistics
Matches: 87, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
37 30 0.34
38 17 0.20
39 5 0.06
40 2 0.02
41 2 0.02
42 5 0.06
43 10 0.11
44 16 0.18
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.36
Consensus pattern (38 bp):
AAATAAAACAAAATATTTGAAATTAATTTTCGTGATTC
Found at i:17644687 original size:81 final size:81
Alignment explanation
Indices: 17644601--17644763 Score: 326
Period size: 81 Copynumber: 2.0 Consensus size: 81
17644591 TAAATACAAC
17644601 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAATTAATTTTCGTGATTCAAATAA
1 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAATTAATTTTCGTGATTCAAATAA
17644666 AACAAAATATTTGAAA
66 AACAAAATATTTGAAA
17644682 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAATTAATTTTCGTGATTCAAATAA
1 TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAATTAATTTTCGTGATTCAAATAA
17644747 AACAAAATATTTGAAA
66 AACAAAATATTTGAAA
17644763 T
1 T
17644764 GAAACTTTAA
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 82 1.00
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (81 bp):
TTAATTTAATTATGTAATGTTAAAATAAAATAAAATATTGAAATTAATTTTCGTGATTCAAATAA
AACAAAATATTTGAAA
Found at i:17647332 original size:40 final size:41
Alignment explanation
Indices: 17647259--17647342 Score: 113
Period size: 40 Copynumber: 2.1 Consensus size: 41
17647249 AATCTTAAAC
*
17647259 ATAT-TTGCGGCGTTTTAGCGAAAAACGCCGCTAATGACAG
1 ATATATTGCGGAGTTTTAGCGAAAAACGCCGCTAATGACAG
*
17647299 ATATATTGCGGAGTTTTA-C-AACAAACGCCGCTAATGCCAG
1 ATATATTGCGGAGTTTTAGCGAA-AAACGCCGCTAATGACAG
17647339 -TATA
1 ATATA
17647343 GCTCAACTAC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
39 6 0.15
40 22 0.55
41 12 0.30
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (41 bp):
ATATATTGCGGAGTTTTAGCGAAAAACGCCGCTAATGACAG
Found at i:17648736 original size:17 final size:16
Alignment explanation
Indices: 17648714--17648758 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
17648704 TAATTTTTGG
17648714 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
**
17648730 ATTATTTTATAATATTT
1 -TTATTTTATTTTATTT
17648747 TTAATTTTATTT
1 TT-ATTTTATTT
17648759 AGTTATTTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:17654818 original size:28 final size:28
Alignment explanation
Indices: 17654755--17655636 Score: 1730
Period size: 28 Copynumber: 31.5 Consensus size: 28
17654745 ATATTAAGTC
* *
17654755 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTACATAATCAAACT
*
17654782 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654810 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654838 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654866 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654894 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654922 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654950 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17654978 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655006 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655034 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655062 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655090 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655118 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655146 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655174 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655202 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655230 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655258 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655286 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655314 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655342 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655370 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655398 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655426 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655454 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655482 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655510 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655538 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655566 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655594 CGCACACTTAGTGCTACATAATCAAACT
1 CGCACACTTAGTGCTACATAATCAAACT
17655622 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17655637 GTACAATTTA
Statistics
Matches: 852, Mismatches: 2, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
27 22 0.03
28 830 0.97
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (28 bp):
CGCACACTTAGTGCTACATAATCAAACT
Found at i:17657649 original size:11 final size:11
Alignment explanation
Indices: 17657608--17657650 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
17657598 AAGTAATAAC
17657608 AACAAAATAGT
1 AACAAAATAGT
* * *
17657619 AGCAACATAAT
1 AACAAAATAGT
*
17657630 AATAAAATAGT
1 AACAAAATAGT
17657641 AACAAAATAG
1 AACAAAATAG
17657651 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.63, C:0.09, G:0.09, T:0.19
Consensus pattern (11 bp):
AACAAAATAGT
Found at i:17659917 original size:29 final size:29
Alignment explanation
Indices: 17659852--17659909 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
17659842 TTAAAAAAAA
17659852 AATTGAGAACTAAGTTGAAAAGAATGGAG
1 AATTGAGAACTAAGTTGAAAAGAATGGAG
*
17659881 AATTGAGAACTCAGTTGAAAAGAATGGAG
1 AATTGAGAACTAAGTTGAAAAGAATGGAG
17659910 TTTGGAGAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.21
Consensus pattern (29 bp):
AATTGAGAACTAAGTTGAAAAGAATGGAG
Found at i:17662339 original size:21 final size:21
Alignment explanation
Indices: 17662315--17662384 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
17662305 CTATTTAACG
17662315 TTTAAGATTTAAGGTTTAGTA
1 TTTAAGATTTAAGGTTTAGTA
* *
17662336 TTTAGGGTTTAAGGTTTA-TA
1 TTTAAGATTTAAGGTTTAGTA
* *
17662356 GTTTTAGGATTT-AGGATTTTGTA
1 --TTTAAGATTTAAGG-TTTAGTA
17662379 TTTAAG
1 TTTAAG
17662385 GGCTTAAGGG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
20 2 0.05
21 24 0.60
22 12 0.30
23 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
TTTAAGATTTAAGGTTTAGTA
Found at i:17662744 original size:41 final size:41
Alignment explanation
Indices: 17662689--17662813 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 41
17662679 TTTTGTGGAG
* *
17662689 TTTTTCAAAAAGCGCTGCTAATGGATGACCTATAGCGGCGT
1 TTTTTTAAAAAGCGCTGCTAATGGATGATCTATAGCGGCGT
* ** * *
17662730 TTTTTTAAAAAGCGCCGCTAATGCTTAATCTATAGCAGCG-
1 TTTTTTAAAAAGCGCTGCTAATGGATGATCTATAGCGGCGT
* *
17662770 CTTTTTAGAAAA-CGCTGCTAAT-GCTCGATCTATAGCGGCGT
1 TTTTTTA-AAAAGCGCTGCTAATGGAT-GATCTATAGCGGCGT
17662811 TTT
1 TTT
17662814 CAAAAAGCAT
Statistics
Matches: 67, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
39 1 0.01
40 27 0.40
41 39 0.58
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (41 bp):
TTTTTTAAAAAGCGCTGCTAATGGATGATCTATAGCGGCGT
Found at i:17662790 original size:40 final size:39
Alignment explanation
Indices: 17662731--17662821 Score: 112
Period size: 40 Copynumber: 2.3 Consensus size: 39
17662721 TAGCGGCGTT
*
17662731 TTTTTAAAAAGCGCCGCTAATGCTTAATCTATAGCAGCG
1 TTTTTAAAAAGCGCCGCTAATGCTCAATCTATAGCAGCG
* * *
17662770 CTTTTTAGAAAA-CGCTGCTAATGCTCGATCTATAGCGGCG
1 -TTTTTA-AAAAGCGCCGCTAATGCTCAATCTATAGCAGCG
*
17662810 TTTTCAAAAAGC
1 TTTTTAAAAAGC
17662822 ATCGCCAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
38 4 0.09
39 6 0.14
40 30 0.68
41 4 0.09
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (39 bp):
TTTTTAAAAAGCGCCGCTAATGCTCAATCTATAGCAGCG
Found at i:17663962 original size:70 final size:70
Alignment explanation
Indices: 17663823--17663960 Score: 174
Period size: 70 Copynumber: 2.0 Consensus size: 70
17663813 TTATATCTGC
* * * *
17663823 GGTTAAATGCTCTATTTATGTGGTTGGGATCGATGGTTCGAGTCTTCCTTAATTTTTTTGTTTAT
1 GGTTAAATGCTCTATTTATGTGGTTGAGATCGATGGTTCGAGACTTCCTTAATATTTTTGTATAT
17663888 TTTAT
66 TTTAT
*
17663893 GGTTAAGTGCTCTATTTATGTGGTTGAGATCGA-GGATTCGAGACTTCATTCTTAA-ATTTTT-T
1 GGTTAAATGCTCTATTTATGTGGTTGAGATCGATGG-TTCGAGACTTC---CTTAATATTTTTGT
17663955 ATATTT
62 ATATTT
17663961 ATTTTTTGTT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
69 2 0.03
70 41 0.69
71 6 0.10
72 5 0.08
73 5 0.08
ACGTcount: A:0.20, C:0.10, G:0.21, T:0.49
Consensus pattern (70 bp):
GGTTAAATGCTCTATTTATGTGGTTGAGATCGATGGTTCGAGACTTCCTTAATATTTTTGTATAT
TTTAT
Found at i:17666949 original size:31 final size:31
Alignment explanation
Indices: 17666911--17666975 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
17666901 TTTTTAAGAT
*
17666911 TGAGCAGGTATACTTGCGGTCTAGTTTCGAA
1 TGAGCAGGTATACTTGCAGTCTAGTTTCGAA
* *
17666942 TGAGCAGGTATGCTTGCAGTCTGGTTTCGAA
1 TGAGCAGGTATACTTGCAGTCTAGTTTCGAA
17666973 TGA
1 TGA
17666976 CTCTGAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.32
Consensus pattern (31 bp):
TGAGCAGGTATACTTGCAGTCTAGTTTCGAA
Found at i:17669330 original size:40 final size:40
Alignment explanation
Indices: 17669271--17669411 Score: 183
Period size: 40 Copynumber: 3.5 Consensus size: 40
17669261 AATTATGCCA
* * *
17669271 TGAATTGCACTTACATGCCCCTGTAGTACTTCGATACCCT
1 TGAATTGCACTTACGTGCCCCTGTTGTACTTCGGTACCCT
**
17669311 TGAATCACACTTACGTGCCCCTGTTGTACTTCGGTACCCT
1 TGAATTGCACTTACGTGCCCCTGTTGTACTTCGGTACCCT
* ** *
17669351 TAAATTGCACTTACGTATCCATGTTTGTACTTCGGTACCCT
1 TGAATTGCACTTACGTGCCCCTG-TTGTACTTCGGTACCCT
*
17669392 TGAATTGCACATACGTGCCC
1 TGAATTGCACTTACGTGCCC
17669412 TATTTACACT
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
40 52 0.61
41 33 0.39
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.33
Consensus pattern (40 bp):
TGAATTGCACTTACGTGCCCCTGTTGTACTTCGGTACCCT
Found at i:17681471 original size:15 final size:15
Alignment explanation
Indices: 17681451--17681491 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
17681441 ATTTTAACAC
17681451 TATCCTTTTAAAGTT
1 TATCCTTTTAAAGTT
17681466 TATCCTTTTAAAGTT
1 TATCCTTTTAAAGTT
* *
17681481 AATTCTTTTAA
1 TATCCTTTTAA
17681492 TAGTGTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.29, C:0.12, G:0.05, T:0.54
Consensus pattern (15 bp):
TATCCTTTTAAAGTT
Found at i:17682930 original size:15 final size:16
Alignment explanation
Indices: 17682901--17682930 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17682891 TAACTTTGAC
17682901 AAATTCTATATTTAGA
1 AAATTCTATATTTAGA
17682917 AAATTCTA-ATTTAG
1 AAATTCTATATTTAG
17682931 TGGATGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (16 bp):
AAATTCTATATTTAGA
Found at i:17684959 original size:15 final size:16
Alignment explanation
Indices: 17684925--17684965 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
17684915 CTATATAATA
*
17684925 AAATTTAGTT-TATTC
1 AAATTTAATTCTATTC
*
17684940 AAATTTCATTCTATTC
1 AAATTTAATTCTATTC
17684956 -AATTTAATTC
1 AAATTTAATTC
17684966 AAAATAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.51
Consensus pattern (16 bp):
AAATTTAATTCTATTC
Found at i:17687900 original size:26 final size:26
Alignment explanation
Indices: 17687864--17687913 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
17687854 ACATATTTTC
*
17687864 TCAAAATTTTACCGGGGGTAAAATTA
1 TCAAAAATTTACCGGGGGTAAAATTA
* *
17687890 TCAAAAATTTACTGGTGGTAAAAT
1 TCAAAAATTTACCGGGGGTAAAAT
17687914 AAGGATGAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (26 bp):
TCAAAAATTTACCGGGGGTAAAATTA
Found at i:17689882 original size:3 final size:3
Alignment explanation
Indices: 17689874--17689899 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17689864 CTTTTAAGAG
17689874 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
17689900 CACCGAAGCC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:17693907 original size:30 final size:30
Alignment explanation
Indices: 17693861--17693954 Score: 152
Period size: 30 Copynumber: 3.1 Consensus size: 30
17693851 TTTTATTATG
*
17693861 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
17693892 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* *
17693922 CCATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
17693952 CCA
1 CCA
17693955 TAAATATGCA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
30 53 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:17693916 original size:15 final size:15
Alignment explanation
Indices: 17693871--17693948 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
17693861 CCAATATCTC
17693871 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
17693886 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
17693901 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
17693916 GACTTTCCAT-TATTT
1 GA-TACCCATATCTTT
17693931 GATACCCATATCTTT
1 GATACCCATATCTTT
17693946 GAT
1 GAT
17693949 TTTCCATAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
14 9 0.19
15 29 0.62
16 9 0.19
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:17701919 original size:20 final size:20
Alignment explanation
Indices: 17701894--17701934 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
17701884 CATTTGAATT
*
17701894 AACTTTCTTACGGTTTTGAG
1 AACTTTCTTACGATTTTGAG
17701914 AACTTTCTTACGATTTTGAG
1 AACTTTCTTACGATTTTGAG
17701934 A
1 A
17701935 CACTAACTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (20 bp):
AACTTTCTTACGATTTTGAG
Found at i:17706308 original size:17 final size:17
Alignment explanation
Indices: 17706286--17706319 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
17706276 AAAGATTGAT
*
17706286 GAGTTTTTAAGGATGAA
1 GAGTTTTAAAGGATGAA
17706303 GAGTTTTAAAGGATGAA
1 GAGTTTTAAAGGATGAA
17706320 TAAATTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (17 bp):
GAGTTTTAAAGGATGAA
Found at i:17707445 original size:41 final size:41
Alignment explanation
Indices: 17707388--17707469 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
17707378 TGGTTAGGCA
17707388 TAAGCTTCCAAGAGAGTTTATATATAGACTTATCTCTTTCC
1 TAAGCTTCCAAGAGAGTTTATATATAGACTTATCTCTTTCC
* * *
17707429 TAAGCTTCCAAGAGAGTTTATATATATACTTGTTTCTTTCC
1 TAAGCTTCCAAGAGAGTTTATATATAGACTTATCTCTTTCC
17707470 CTCATTGAGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.41
Consensus pattern (41 bp):
TAAGCTTCCAAGAGAGTTTATATATAGACTTATCTCTTTCC
Found at i:17709442 original size:27 final size:27
Alignment explanation
Indices: 17709412--17709589 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
17709402 ATATTGAGTC
* * * *
17709412 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
17709439 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17709466 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
17709494 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
17709521 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
17709548 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17709575 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17709590 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:17709551 original size:82 final size:81
Alignment explanation
Indices: 17709433--17709588 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
17709423 TGCTATATAA
* *
17709433 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
17709498 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17709515 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17709579 CACTTAGTGC
65 CACTTAGTGC
17709589 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17717569 original size:27 final size:27
Alignment explanation
Indices: 17717539--17717716 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
17717529 ATATTGAGTC
* * * *
17717539 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
17717566 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17717593 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
17717621 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
17717648 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
17717675 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
17717702 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
17717717 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:17717678 original size:82 final size:81
Alignment explanation
Indices: 17717560--17717715 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
17717550 TGCTATATAA
* *
17717560 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
17717625 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17717642 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17717706 CACTTAGTGC
65 CACTTAGTGC
17717716 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17718217 original size:12 final size:12
Alignment explanation
Indices: 17718200--17718226 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17718190 ATGGCATACT
17718200 TATGTATATATA
1 TATGTATATATA
17718212 TATGTATATATA
1 TATGTATATATA
17718224 TAT
1 TAT
17718227 ACTTCGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (12 bp):
TATGTATATATA
Found at i:17723127 original size:43 final size:43
Alignment explanation
Indices: 17723066--17723163 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
17723056 TTATAATACA
* * * *
17723066 TGTAAGACCATAGCTGGGCTATGGGTATCGATATGAGATTTCG
1 TGTAAGACCATAGCTGGGCTATGGGCATCGATATGAAATTACC
*
17723109 TGTAAGACCATAGCTGGGCTATTGGCATCGATATGAAATTACC
1 TGTAAGACCATAGCTGGGCTATGGGCATCGATATGAAATTACC
17723152 TGTAAGACCATA
1 TGTAAGACCATA
17723164 TTTGGGATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.29
Consensus pattern (43 bp):
TGTAAGACCATAGCTGGGCTATGGGCATCGATATGAAATTACC
Found at i:17724245 original size:162 final size:162
Alignment explanation
Indices: 17724071--17724395 Score: 623
Period size: 162 Copynumber: 2.0 Consensus size: 162
17724061 ATGCCAAATT
* *
17724071 GGTTAATAAAGAAGGTTGAAATAGTATATGATTTTTATGTAAATCTTGGCTTAGGAATCTTGTTA
1 GGTTAATAAAGAAGGTTGAAATAGTATATGATATTTATGTAAACCTTGGCTTAGGAATCTTGTTA
17724136 ATTGGTATGTGATTTAGTTAAGTAAATGGTTCTGGTATCAGCTTTGATGAGATTGGTATTGAAAT
66 ATTGGTATGTGATTTAGTTAAGTAAATGGTTCTGGTATCAGCTTTGATGAGATTGGTATTGAAAT
17724201 GGTCTATAAATTGATGATTTGAGATTAGTTTG
131 GGTCTATAAATTGATGATTTGAGATTAGTTTG
*
17724233 GGTTAATAAAGAAGGTTGAAATAGTATATGATATTTATGTAAACCTTGGCTTATGAATCTTGTTA
1 GGTTAATAAAGAAGGTTGAAATAGTATATGATATTTATGTAAACCTTGGCTTAGGAATCTTGTTA
17724298 ATTGGTATGTGATTTAGTTAAGTAAATGGTTCTGGTATCAGCTTTGATGAGATTGGTATTGAAAT
66 ATTGGTATGTGATTTAGTTAAGTAAATGGTTCTGGTATCAGCTTTGATGAGATTGGTATTGAAAT
17724363 GGTCTATAAATTGATGATTTGAGATTAGTTTG
131 GGTCTATAAATTGATGATTTGAGATTAGTTTG
17724395 G
1 G
17724396 CTGATTAATT
Statistics
Matches: 160, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 160 1.00
ACGTcount: A:0.30, C:0.05, G:0.24, T:0.41
Consensus pattern (162 bp):
GGTTAATAAAGAAGGTTGAAATAGTATATGATATTTATGTAAACCTTGGCTTAGGAATCTTGTTA
ATTGGTATGTGATTTAGTTAAGTAAATGGTTCTGGTATCAGCTTTGATGAGATTGGTATTGAAAT
GGTCTATAAATTGATGATTTGAGATTAGTTTG
Found at i:17727217 original size:13 final size:13
Alignment explanation
Indices: 17727199--17727225 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17727189 GGTTGCTTAT
17727199 TAAACTAATTAAC
1 TAAACTAATTAAC
17727212 TAAACTAATTAAC
1 TAAACTAATTAAC
17727225 T
1 T
17727226 TATTAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:17747740 original size:39 final size:39
Alignment explanation
Indices: 17747695--17747776 Score: 137
Period size: 39 Copynumber: 2.1 Consensus size: 39
17747685 ATGCAAGACA
*
17747695 CTGGAAATGTATCCGGGCTAAAGTCCCGCAAGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTTCGTG
* *
17747734 CTGGAAATGTGTCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTTCGTG
17747773 CTGG
1 CTGG
17747777 TGTTGGTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.22
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTTCGTG
Found at i:17752515 original size:46 final size:47
Alignment explanation
Indices: 17752396--17752518 Score: 149
Period size: 48 Copynumber: 2.6 Consensus size: 47
17752386 TCACAATGCT
** *
17752396 GCCAATGCATGTCCTAGACATGTCTTACACTAGCACGCATATCTTGAG
1 GCCAATGCATGTCCTAGACATGTCTTACACTAGCACGCA-ATCTCAAA
* * * * *
17752444 GTCGATGCATGTCCTAGACATGTCTTACACTAGCTCTC-GTCTCAAA
1 GCCAATGCATGTCCTAGACATGTCTTACACTAGCACGCAATCTCAAA
*
17752490 GCCAATGCATGTCATAGACATGTCTTACA
1 GCCAATGCATGTCCTAGACATGTCTTACA
17752519 TTGGCTCACA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 30 0.47
48 34 0.53
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (47 bp):
GCCAATGCATGTCCTAGACATGTCTTACACTAGCACGCAATCTCAAA
Found at i:17752829 original size:17 final size:17
Alignment explanation
Indices: 17752807--17752861 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
17752797 GTTACGCATG
17752807 TAACATAGTATGAATAC
1 TAACATAGTATGAATAC
* * * *
17752824 TAACAT-TTAGGCACA-
1 TAACATAGTATGAATAC
17752839 TAACATAGTATGAATAC
1 TAACATAGTATGAATAC
17752856 TAACAT
1 TAACAT
17752862 GCATGAAAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
15 6 0.21
16 10 0.36
17 12 0.43
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (17 bp):
TAACATAGTATGAATAC
Found at i:17753803 original size:24 final size:24
Alignment explanation
Indices: 17753776--17753824 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
17753766 TTCACAACTC
17753776 ATGCATACACACATATTCAATGGA
1 ATGCATACACACATATTCAATGGA
17753800 ATGCATACACACATATTCAATGGA
1 ATGCATACACACATATTCAATGGA
17753824 A
1 A
17753825 ATTTCAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.24
Consensus pattern (24 bp):
ATGCATACACACATATTCAATGGA
Found at i:17756025 original size:40 final size:40
Alignment explanation
Indices: 17755981--17756925 Score: 1718
Period size: 40 Copynumber: 23.6 Consensus size: 40
17755971 GCTCCTCGTT
* *
17755981 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
17756021 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756061 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756101 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756141 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756181 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756221 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756261 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756301 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756341 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756381 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756421 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756461 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756501 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756541 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756581 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756621 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756661 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756701 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756741 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
17756781 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
17756821 CCAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
17756860 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
17756901 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
17756926 CATCATTCAA
Statistics
Matches: 885, Mismatches: 15, Indels: 10
0.97 0.02 0.01
Matches are distributed among these distances:
38 2 0.00
39 32 0.04
40 838 0.95
41 13 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:17765393 original size:28 final size:27
Alignment explanation
Indices: 17765352--17765406 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 27
17765342 CTATATTTTG
* *
17765352 GAGTGTAAGGATGGGTGGGTAAGAATT
1 GAGTGTAAGGATGGATGAGTAAGAATT
17765379 GAGTGTAGAGGATGGATGAGTAAGAATT
1 GAGTGTA-AGGATGGATGAGTAAGAATT
17765407 CTAATTGCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.33, C:0.00, G:0.42, T:0.25
Consensus pattern (27 bp):
GAGTGTAAGGATGGATGAGTAAGAATT
Found at i:17769982 original size:28 final size:28
Alignment explanation
Indices: 17769950--17770019 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
17769940 TATTGAACTC
* * *
17769950 AGTGTACGAAATATTGAGAATGGCACTT
1 AGTGTGCGAAATATTGAGAACGACACTT
17769978 AGTGTGC-AAGATATTGAGAACGACACTT
1 AGTGTGCGAA-ATATTGAGAACGACACTT
17770006 AGTGTGCGAAATAT
1 AGTGTGCGAAATAT
17770020 CGAATGATTC
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 2 0.05
28 33 0.89
29 2 0.05
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAACGACACTT
Found at i:17770460 original size:21 final size:22
Alignment explanation
Indices: 17770429--17770469 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
17770419 GAATGTATTG
*
17770429 TGATGTATGTGGAAATGAAATA
1 TGATGTATGTGCAAATGAAATA
*
17770451 TGAT-TATGTGCCAATGAAA
1 TGATGTATGTGCAAATGAAA
17770470 CATAAACGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (22 bp):
TGATGTATGTGCAAATGAAATA
Found at i:17772167 original size:23 final size:23
Alignment explanation
Indices: 17772137--17772187 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
17772127 CTGACCTAGC
17772137 TTACTAATTTGGGGAATAAAAAT
1 TTACTAATTTGGGGAATAAAAAT
*
17772160 TTACTAATTTGGGGCATAAAAAT
1 TTACTAATTTGGGGAATAAAAAT
17772183 TTACT
1 TTACT
17772188 TTGAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (23 bp):
TTACTAATTTGGGGAATAAAAAT
Found at i:17773750 original size:108 final size:110
Alignment explanation
Indices: 17773598--17773798 Score: 309
Period size: 108 Copynumber: 1.8 Consensus size: 110
17773588 ATCCTTTTGA
* *
17773598 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
17773661 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATGGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATGGT
* * * *
17773706 AACTTATCAATGCCATGTCTTGACATGGTCTTACATTATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
*
17773771 TGTCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
17773799 TATCCTTAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
107 1 0.01
108 48 0.58
109 7 0.08
110 27 0.33
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTTCCTTATGGT
Found at i:17773756 original size:55 final size:53
Alignment explanation
Indices: 17773598--17773805 Score: 213
Period size: 55 Copynumber: 3.8 Consensus size: 53
17773588 ATCCTTTTGA
* * *
17773598 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATTGTATCCTTGCCTTATG
* * * * *
17773651 AACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTTCCTTATGG
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATTGTATCC-TTGCCTTAT-G
* * * *
17773705 TAACTTATCAATGCCATGTCTTGACATGGTCTTACATTATTTCCTTGCCTTA-G
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATTGTATCCTTGCCTTATG
* * *
17773758 AAACCTTACCAATTGTCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -AA-CTTACCAA-TGCCATGCCTTGACATGGTCTTACATTGTATCCTT
17773806 AAACCCTAAT
Statistics
Matches: 126, Mismatches: 23, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
52 2 0.02
53 46 0.37
54 8 0.06
55 68 0.54
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.37
Consensus pattern (53 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATTGTATCCTTGCCTTATG
Found at i:17781381 original size:53 final size:54
Alignment explanation
Indices: 17781252--17781506 Score: 274
Period size: 55 Copynumber: 4.8 Consensus size: 54
17781242 ACACAGGTAC
* * * * *
17781252 CTTACCATTGCCATGACTTGTCATGGTCTTACTTGGTAT-CAT---TT-TGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* *
17781301 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
* * * *
17781354 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATGGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTAT-GAAA
* * * *
17781409 CTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA-GAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
*
17781462 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTATCCTT
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTATCCTT
17781507 AAACCCTAAC
Statistics
Matches: 173, Mismatches: 22, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
49 36 0.21
50 2 0.01
52 2 0.01
53 49 0.28
54 10 0.06
55 72 0.42
56 2 0.01
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (54 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAAA
Found at i:17781443 original size:108 final size:110
Alignment explanation
Indices: 17781299--17781499 Score: 327
Period size: 108 Copynumber: 1.8 Consensus size: 110
17781289 ATCATTTTGA
* *
17781299 AACTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATG-AA-CTCACCAA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTA-GAAACCTCACCAA
17781362 -TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
65 TTGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
* * *
17781407 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
17781472 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTTACATGG
17781500 TATCCTTAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
107 1 0.01
108 49 0.58
109 7 0.08
110 28 0.33
ACGTcount: A:0.22, C:0.25, G:0.18, T:0.34
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGATATCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATGGT
Found at i:17783015 original size:43 final size:43
Alignment explanation
Indices: 17782968--17783081 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
17782958 TATCACATAT
* * *
17782968 CGATGCCACTGTCCTAGACAGGGTCTTACACGAAATTG-ATTAA
1 CGATGCCAATGTCCAAGACATGGTCTTACACGAAATTGTA-TAA
* *
17783011 CGATGCCAATG-CTCAAGGCATGGTCTTACACGTAATTGTATAA
1 CGATGCCAATGTC-CAAGACATGGTCTTACACGAAATTGTATAA
* *
17783054 TGATGCCAATGTCCCAGACATGGTCTTA
1 CGATGCCAATGTCCAAGACATGGTCTTA
17783082 TATATAATCA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
42 1 0.02
43 57 0.95
44 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (43 bp):
CGATGCCAATGTCCAAGACATGGTCTTACACGAAATTGTATAA
Found at i:17801195 original size:13 final size:12
Alignment explanation
Indices: 17801171--17801200 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
17801161 GGGGATCATT
17801171 TTAACTAACTAA
1 TTAACTAACTAA
17801183 TTAACTAAACTAA
1 TTAACT-AACTAA
17801196 TTAAC
1 TTAAC
17801201 CCCTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
TTAACTAACTAA
Found at i:17808988 original size:88 final size:88
Alignment explanation
Indices: 17808879--17809111 Score: 322
Period size: 88 Copynumber: 2.6 Consensus size: 88
17808869 TTCTATTATA
* * * * *
17808879 ATTTCAGGGAGAAGAGATTTGTAGCTTTGATTTACTCCACTGAAACTTCAATGAGATAAGAATTG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATGG
* *
17808944 TGGCTTCGAGCTGCTTCAATGCC
66 TGGCTTCGAGCCGCTCCAATGCC
* * * * *
17808967 ATTTCAAGGAGAAGAGGTTTGTAGCTTCGATCTACTCTGCTAAAACTTCAAGGAGATACGAATGG
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATGG
17809032 TGGCTTCGAGCCGCTCCAATGCC
66 TGGCTTCGAGCCGCTCCAATGCC
* * * *
17809055 ATTCCGGGGAGAGGAGATTTGTAGCCTCGATCTACTCCGCTGAAACTTCAAGGAGAT
1 ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGAT
17809112 CTGCTATTGA
Statistics
Matches: 125, Mismatches: 20, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
88 125 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (88 bp):
ATTTCAGGGAGAAGAGATTTGTAGCTTCGATCTACTCCGCTGAAACTTCAAGGAGATAAGAATGG
TGGCTTCGAGCCGCTCCAATGCC
Found at i:17809393 original size:87 final size:87
Alignment explanation
Indices: 17809137--17809786 Score: 806
Period size: 87 Copynumber: 7.5 Consensus size: 87
17809127 ACCTGGTCCA
* * * ** * ** *
17809137 CTACTGCTTAGGGGGTTAAGG-TTGACAATCTTTGATCCGCTCAACTACTACTTAGGGAGATAAG
1 CTACTACTTAGGGGGTTAAGGCTTG-C-TTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAG
* * *
17809201 ATCAATAA--TTCAGCCT-TGTACC
64 ATCTACAATCTTTAGCCTGT-TACC
* * ** * * * * * * *
17809223 CTACTGCTTAGGGGGTCAAGGCTCACCGTCTTTGATCTGTTCCACTTCAGCTTCAGGGAGACAAG
1 CTACTACTTAGGGGGTTAAGGCT-TGCTTCTTCGATTTGCTCCACTACTG-TTTAGGGAGACAAG
* * *
17809288 ATTTGCAATCTTTAGCCTGTTACA
64 ATCTACAATCTTTAGCCTGTTACC
* * *
17809312 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTATTGATTAGGGAGAGAAGAT
1 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
17809377 CTACAATCTTTAGCCTGTTACC
66 CTACAATCTTTAGCCTGTTACC
* * *
17809399 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCTATTACTGTTTAGGAAGACAAGAT
1 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
17809464 CTACAATCTTTAGCCTGTTACC
66 CTACAATCTTTAGCCTGTTACC
* * *
17809486 CTATTATTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTATTTAGGGAGACAAGAT
1 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
*
17809551 CTACAATCTTTAGCCTGTTACG
66 CTACAATCTTTAGCCTGTTACC
*
17809573 CTACTACTTAGGGGGTTAAGGCTTCCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
1 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
*
17809638 CTACAATCTTCAGCCTGTTACC
66 CTACAATCTTTAGCCTGTTACC
* * * * * *
17809660 CTACTATTTAGGGGGTTAAGGCCTGTTTCTTCGATTTGCTCAACTATTGTTTAGGAAGACAAGAT
1 CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
17809725 CTACAATCTTTAG-CTGTTACC
66 CTACAATCTTTAGCCTGTTACC
*
17809746 CTACTACTTAGGGGGTTAAGGCTTGCTTTCTTCGATCTGCT
1 CTACTACTTAGGGGGTTAAGGCTTGC-TTCTTCGATTTGCT
17809787 ACTGTTTTGG
Statistics
Matches: 490, Mismatches: 67, Indels: 13
0.86 0.12 0.02
Matches are distributed among these distances:
86 67 0.14
87 374 0.76
88 17 0.03
89 31 0.06
90 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.35
Consensus pattern (87 bp):
CTACTACTTAGGGGGTTAAGGCTTGCTTCTTCGATTTGCTCCACTACTGTTTAGGGAGACAAGAT
CTACAATCTTTAGCCTGTTACC
Found at i:17809664 original size:44 final size:44
Alignment explanation
Indices: 17809443--17809672 Score: 123
Period size: 44 Copynumber: 5.3 Consensus size: 44
17809433 TTTGCTCTAT
* * *
17809443 TACTGTTTAGGAAGACAAGATCTACAATCTTTAGCCTGTTACCC
1 TACTATTTAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCC
* * ** * * * ** *
17809487 TATTATTTAGGGGGTTAAG-GCTTGC-TTCTTC-GATTTGCT-CCAC
1 TACTATTTAGGGAGACAAGATC-TACAATCTTCAG-CCTGTTACC-C
* *
17809530 TACTATTTAGGGAGACAAGATCTACAATCTTTAGCCTGTTACGC
1 TACTATTTAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCC
* * ** * * ** ** *
17809574 TACTACTTAGGGGGTTAAG-GCTTCCTTCTTC-GATTTGCT-CCAC
1 TACTATTTAGGGAGACAAGATCTACAATCTTCAG-CCTGTTACC-C
*
17809617 TACTGTTTAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCC
1 TACTATTTAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCC
17809661 TACTATTTAGGG
1 TACTATTTAGGG
17809673 GGTTAAGGCC
Statistics
Matches: 123, Mismatches: 51, Indels: 24
0.62 0.26 0.12
Matches are distributed among these distances:
42 5 0.04
43 51 0.41
44 62 0.50
45 5 0.04
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (44 bp):
TACTATTTAGGGAGACAAGATCTACAATCTTCAGCCTGTTACCC
Found at i:17809952 original size:22 final size:24
Alignment explanation
Indices: 17809924--17809969 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 24
17809914 TAACTAGATG
17809924 TGATGCTTATG-TC-AAAT-AATTA
1 TGATGC-TATGATCGAAATGAATTA
17809946 TGATGCTATGATCGAAATGAATTA
1 TGATGCTATGATCGAAATGAATTA
17809970 AATGCTCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.19
22 8 0.38
23 4 0.19
24 5 0.24
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (24 bp):
TGATGCTATGATCGAAATGAATTA
Found at i:17809967 original size:64 final size:64
Alignment explanation
Indices: 17809866--17810052 Score: 302
Period size: 64 Copynumber: 2.9 Consensus size: 64
17809856 ATGCTTATGT
* * * *
17809866 TTATGCCAAATGACTAGGATGCTATGATCAAAATGAATTAAATGCTCCTAACTAGATGTGATGC
1 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGC
* * *
17809930 TTATGTCAAATAATTATGATGCTATGATCGAAATGAATTAAATGCTCTTACCTAGATGTGATGC
1 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGC
*
17809994 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGT
1 TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGT
17810053 ATTATGAATG
Statistics
Matches: 112, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 112 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (64 bp):
TTATGTCAAATAATTAGGATGCTATGATCGAAATGAATTAAATGCTCCTAACTAGATGTGATGC
Found at i:17816616 original size:11 final size:11
Alignment explanation
Indices: 17816600--17816625 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17816590 TACAAATAGA
17816600 AAAACTAAATT
1 AAAACTAAATT
17816611 AAAACTAAATT
1 AAAACTAAATT
17816622 AAAA
1 AAAA
17816626 TAAGAGGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAACTAAATT
Found at i:17818400 original size:25 final size:26
Alignment explanation
Indices: 17818365--17818422 Score: 77
Period size: 25 Copynumber: 2.3 Consensus size: 26
17818355 CACTTTTATC
17818365 TTTA-TTTATCTT-CTTTGAATACT-T
1 TTTATTTTATCTTCCTTT-AATACTAT
17818389 TTTATTTTATCTTCCTTTAATACTAT
1 TTTATTTTATCTTCCTTTAATACTAT
*
17818415 TTCATTTT
1 TTTATTTT
17818423 TAGGTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 14 0.47
26 12 0.40
ACGTcount: A:0.21, C:0.14, G:0.02, T:0.64
Consensus pattern (26 bp):
TTTATTTTATCTTCCTTTAATACTAT
Found at i:17823824 original size:46 final size:45
Alignment explanation
Indices: 17823771--17823907 Score: 186
Period size: 46 Copynumber: 3.0 Consensus size: 45
17823761 TATATATACA
* *
17823771 CATCTCATACGTATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACGTAT-TCGCATTAGCCATTCGGCTTTACCACATATC
*
17823817 CATCTCATACACGT-TTCGCATTAGCCATTCGGCTTTACCTCATATC
1 CATCTCAT--ACGTATTCGCATTAGCCATTCGGCTTTACCACATATC
**
17823863 CATCTCATACACATTTCGCATTAGCCATTCGGCTTTACCACATAT
1 CATCTCATACGTA-TTCGCATTAGCCATTCGGCTTTACCACATAT
17823908 ATACACTTCC
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
44 2 0.02
46 74 0.91
47 1 0.01
48 4 0.05
ACGTcount: A:0.25, C:0.31, G:0.09, T:0.34
Consensus pattern (45 bp):
CATCTCATACGTATTCGCATTAGCCATTCGGCTTTACCACATATC
Found at i:17823955 original size:47 final size:47
Alignment explanation
Indices: 17823881--17824261 Score: 566
Period size: 47 Copynumber: 8.1 Consensus size: 47
17823871 ACACATTTCG
* * * * * *
17823881 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCA-TGTTCACATTCATCA
* *
17823928 CATTGGCCATTCTGCCTTATCATATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
17823975 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
17824022 CATTGGTCATTCGGCCTTATCACACATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* *
17824069 CATTGGCCATTTGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
17824116 CATTGGCCATTCGGCCTTATCACACATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTAT--CACATATATGCATGTTCACATTCATCA
* *
17824165 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCATATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
* * **
17824212 CATTGGCCATTCGGCCTTATCTCATATATACACATTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
17824259 CAT
1 CAT
17824262 AAAATCCTAA
Statistics
Matches: 305, Mismatches: 26, Indels: 6
0.91 0.08 0.02
Matches are distributed among these distances:
46 1 0.00
47 258 0.85
49 46 0.15
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACATATATGCATGTTCACATTCATCA
Found at i:17824183 original size:143 final size:141
Alignment explanation
Indices: 17823881--17824261 Score: 579
Period size: 143 Copynumber: 2.7 Consensus size: 141
17823871 ACACATTTCG
* * * * * * *
17823881 CATTAGCCATTCGGCTTTACCACATATATACACT-TCCACGTTCATCACATTGGCCATTCT-GCC
1 CATTGGCCATTCGGCCTTATCACACATATGCA-TGTTCACATTCATCACATTGGCCATT-TGGCC
17823944 TTATCAT-ATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
64 TTATC-TCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCAT
17824008 GTTCACATTCATCA
128 GTTCACATTCATCA
*
17824022 CATTGGTCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTTGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTTGGCCTT
17824087 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATATATGCATG
66 ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTAT--CACATATATGCATG
17824152 TTCACATTCATCA
129 TTCACATTCATCA
* *
17824165 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCATATTCATCACATTGGCCATTCGGCCTT
1 CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTTGGCCTT
* **
17824230 ATCTCATATATACACATTCACATTCATCACAT
66 ATCTCATATATGCATGTTCACATTCATCACAT
17824262 AAAATCCTAA
Statistics
Matches: 221, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
140 3 0.01
141 100 0.45
143 118 0.53
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.35
Consensus pattern (141 bp):
CATTGGCCATTCGGCCTTATCACACATATGCATGTTCACATTCATCACATTGGCCATTTGGCCTT
ATCTCATATATGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCATGTT
CACATTCATCA
Found at i:17828421 original size:40 final size:40
Alignment explanation
Indices: 17828343--17828566 Score: 294
Period size: 40 Copynumber: 5.5 Consensus size: 40
17828333 ACCCAAGTAT
* *
17828343 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
17828382 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
17828422 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
17828462 CTTCGGGACTTAGCCCAGG-TATAG-CAACTACTCGGACAAATGC
1 CTTCGGGACTTAGCCC-GGATATAGTC-ACTA---GCACAAATGC
* *
17828505 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
17828545 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
17828567 CATCCGAATA
Statistics
Matches: 164, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
39 12 0.07
40 114 0.70
41 3 0.02
42 2 0.01
43 33 0.20
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17828529 original size:83 final size:80
Alignment explanation
Indices: 17828343--17828566 Score: 294
Period size: 83 Copynumber: 2.8 Consensus size: 80
17828333 ACCCAAGTAT
* * *
17828343 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAG
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
**
17828406 TCACTAGCATGAATGC
65 TCACTAGCACAAATGC
17828422 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCAGG-TATAG
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCC-GGATATAG
*
17828486 -CAACTACTCGGACAAATGC
65 TC-ACTA---GCACAAATGC
* *
17828505 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
17828567 CATCCGAATA
Statistics
Matches: 129, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
79 13 0.10
80 47 0.36
81 3 0.02
82 2 0.02
83 64 0.50
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:17838939 original size:40 final size:40
Alignment explanation
Indices: 17838895--17839158 Score: 360
Period size: 40 Copynumber: 6.7 Consensus size: 40
17838885 GCTCCTCGTT
* *
17838895 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
17838935 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
17838975 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
17839015 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
17839055 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
17839094 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
17839135 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17839159 CATCATTCAA
Statistics
Matches: 206, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
38 2 0.01
39 49 0.24
40 146 0.71
41 9 0.04
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:17847255 original size:87 final size:87
Alignment explanation
Indices: 17847127--17847291 Score: 224
Period size: 87 Copynumber: 1.9 Consensus size: 87
17847117 AATAGACATT
* *
17847127 AAAAACAGAAATTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACTTCTCGCAATTTGAG
1 AAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
* *
17847192 TTGGTTTTTGAAACTTAATTTG
66 TTGATTTTCGAAACTTAATTTG
* * * * * *
17847214 AAAAGCAGAATTTGAAAATACCTC-GACTTGTGATCCGAGGCTCCACTCACTTCTCGCAATATGA
1 AAAAACAGAAATTGAAAATACCTCAG-CGTGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGA
17847278 GTTGATTTTCGAAA
65 GTTGATTTTCGAAA
17847292 ACGGAGATCA
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
86 1 0.01
87 66 0.99
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (87 bp):
AAAAACAGAAATTGAAAATACCTCAGCGTGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
TTGATTTTCGAAACTTAATTTG
Found at i:17847555 original size:78 final size:76
Alignment explanation
Indices: 17847210--17847724 Score: 442
Period size: 76 Copynumber: 6.9 Consensus size: 76
17847200 TGAAACTTAA
* * * * * *
17847210 TTTGAAA-AGCAGAATTTGAAAATACCTCGACTTGTGATCC-GAGGCTCCACTCACTTCTCGCAA
1 TTTGAAAGA-CAGAAATTGAAAATACCTCAAC--GTG-TCCTAAGGCTCAACTCACTTCTTGCAG
17847273 TATGAGTTG-A--TT
62 TATGAGTTGAATTTT
* * * * * * * * *
17847285 TTCGAAA-ACGGAGA-TCAAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATAT
1 TTTGAAAGACAGAAATTGAAAA-TACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTAT
17847348 GAGTTG-A-TTT
65 GAGTTGAATTTT
* * *
17847358 TTTGAAAGACAGGAATTGAAAATACCTCAACGTGTCTTAAGGCTTAACTCACTTCTTGCAGTATG
1 TTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTATG
17847423 AGTTGAATTTT
66 AGTTGAATTTT
17847434 TTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTATG
1 TTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTATG
17847499 AGTTGAATTTTTT
66 AGTTGAA--TTTT
* * * * *
17847512 TTTGAAAGACAGAAATTGAAATTACTTCAACGTGTCTTGAGGCTCAACTCACTTCTTGTAGTATG
1 TTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTATG
17847577 AG-TG------
66 AGTTGAATTTT
* * * * * * * * *
17847581 --T--AATACAGAAA-TAAAAATTATCTCAGCATGTCCCAAGGCTCAACTCACCTCTCGCAATAT
1 TTTGAAAGACAGAAATTGAAAA-TACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTAT
*
17847641 GAGTTGATTTTTT
65 GAGTTGA-ATTTT
* * * * * * *
17847654 TTTGAAAGACAGAAATTGAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATG
1 TTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTATG
17847719 AGTTGA
66 AGTTGA
17847725 TTTAAAAAAA
Statistics
Matches: 366, Mismatches: 51, Indels: 44
0.79 0.11 0.10
Matches are distributed among these distances:
64 4 0.01
65 43 0.12
66 2 0.01
67 1 0.00
71 3 0.01
72 34 0.09
73 13 0.04
74 55 0.15
75 14 0.04
76 72 0.20
77 55 0.15
78 70 0.19
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (76 bp):
TTTGAAAGACAGAAATTGAAAATACCTCAACGTGTCCTAAGGCTCAACTCACTTCTTGCAGTATG
AGTTGAATTTT
Found at i:17847907 original size:74 final size:73
Alignment explanation
Indices: 17847779--17847961 Score: 242
Period size: 74 Copynumber: 2.5 Consensus size: 73
17847769 ACGTGAGCCA
* * ** * *
17847779 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAGTAGAATTTGAAAATACCTCGG
1 AGGCTCAACTCACCTCCCGCAAAATGAGTTGA-TTTTTTGAAAACAGAAATTGAAAATACCTCAG
17847844 CATGCCCCG
65 CATGCCCCG
* * *
17847853 AGGCTCAACTCACCTCCCGTAACATGAGTTTATTTTTTGACAAACA-ACAATTGAAAATACCTCA
1 AGGCTCAACTCACCTCCCGCAAAATGAGTTGATTTTTTGA-AAACAGA-AATTGAAAATACCTCA
*
17847917 GCGTGCCCCG
64 GCATGCCCCG
17847927 AGGCTCAACTCACCTCCCGCAAAATGAGTTGATTT
1 AGGCTCAACTCACCTCCCGCAAAATGAGTTGATTT
17847962 AAAAAACAGA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
73 9 0.09
74 86 0.91
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (73 bp):
AGGCTCAACTCACCTCCCGCAAAATGAGTTGATTTTTTGAAAACAGAAATTGAAAATACCTCAGC
ATGCCCCG
Found at i:17848013 original size:233 final size:236
Alignment explanation
Indices: 17847606--17848054 Score: 719
Period size: 233 Copynumber: 1.9 Consensus size: 236
17847596 AATTATCTCA
* * * *
17847606 GCATGTCCCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGACAGAAATT
1 GCATGCCCCAAGGCTCAACTCACCTCCCGCAACATGAGTT-ATTATTTTTTGAAAGACAGAAATT
* * * * * *
17847671 GAAATTACCTTAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTAAAAAAAC
65 GAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAAAATGAGTTGATTTAAAAAAAC
17847736 AGACATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAA
130 AGACATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAA
17847801 TATGAGTTGATTTTTTTGAAAGTAGAATTTGAAAATACCTCG
195 TATGAGTTGATTTTTTTGAAAGTAGAATTTGAAAATACCTCG
* *
17847843 GCATGCCCCGAGGCTCAACTCACCTCCCGTAACATGAG-T-TTATTTTTTGACAA-ACA-ACAAT
1 GCATGCCCCAAGGCTCAACTCACCTCCCGCAACATGAGTTATTATTTTTTGA-AAGACAGA-AAT
17847904 TGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAAAATGAGTTGATTT-AAAAAA
64 TGAAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAAAATGAGTTGATTTAAAAAAA
*
17847968 CAGACATAAAAACCGAAATTGAAAGTGACTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCA
129 CAGACATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCA
17848033 ATATGAGTTGATTTTTTTGAAA
194 ATATGAGTTGATTTTTTTGAAA
17848055 ACAGAAATGA
Statistics
Matches: 197, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
233 93 0.47
234 68 0.35
235 2 0.01
236 1 0.01
237 33 0.17
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (236 bp):
GCATGCCCCAAGGCTCAACTCACCTCCCGCAACATGAGTTATTATTTTTTGAAAGACAGAAATTG
AAAATACCTCAGCGTGCCCCGAGGCTCAACTCACCTCCCGCAAAATGAGTTGATTTAAAAAAACA
GACATAAAAACAGAAATTGAAAGTGACTCAACACGTGAGCCAAGGCTCAACTCACCTCTCGCAAT
ATGAGTTGATTTTTTTGAAAGTAGAATTTGAAAATACCTCG
Found at i:17849798 original size:47 final size:47
Alignment explanation
Indices: 17849720--17850723 Score: 1866
Period size: 47 Copynumber: 21.3 Consensus size: 47
17849710 CCCTTCGGGA
* * * * * * *
17849720 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
* *
17849766 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17849814 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17849861 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17849908 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17849955 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850002 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850049 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850096 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850143 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850190 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850237 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850284 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850331 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850378 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850425 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850472 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850519 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850566 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850613 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
** *
17850660 CTTATCACATATATATACATTTTCACATTCATCACATCGGTCATTAGGC
1 CTTATCAC--ATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
17850709 CTTATCACATATATA
1 CTTATCACATATATA
17850724 TACATTCACA
Statistics
Matches: 942, Mismatches: 12, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
46 2 0.00
47 894 0.95
48 2 0.00
49 44 0.05
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACCCTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17854449 original size:30 final size:30
Alignment explanation
Indices: 17854413--17854472 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17854403 ATTCTCTTGG
*
17854413 CCGTACCTTCTTATCATGAGCGGCGATCAT
1 CCGTACCTTCTTATCATGAGCGACGATCAT
17854443 CCGTACCTTCTTATCATGAGCGACGATCAT
1 CCGTACCTTCTTATCATGAGCGACGATCAT
17854473 TCTCTTCTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (30 bp):
CCGTACCTTCTTATCATGAGCGACGATCAT
Found at i:17857739 original size:26 final size:26
Alignment explanation
Indices: 17857710--17857817 Score: 162
Period size: 26 Copynumber: 4.2 Consensus size: 26
17857700 TGGTACAAAT
17857710 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
17857736 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
17857762 TAATAATGGGTTATGTAAATGTTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17857788 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17857814 TGAT
1 TGAT
17857818 GGGCATTTCA
Statistics
Matches: 71, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 71 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.38
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:17859650 original size:13 final size:13
Alignment explanation
Indices: 17859592--17859655 Score: 58
Period size: 13 Copynumber: 4.9 Consensus size: 13
17859582 TAAACCAAAT
17859592 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
17859605 TTCTT-AAAAGTAC
1 TT-TTCAAAAGCAC
* * *
17859618 ATTTCCACAGCAC
1 TTTTCAAAAGCAC
* *
17859631 TTCTCAAAAGTAC
1 TTTTCAAAAGCAC
17859644 TTTTCAAAAGCA
1 TTTTCAAAAGCA
17859656 TTGCCAAACT
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
12 2 0.05
13 33 0.89
14 2 0.05
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:17859655 original size:26 final size:26
Alignment explanation
Indices: 17859592--17859655 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
17859582 TAAACCAAAT
*
17859592 TTTTCAAAAGCACTTCTTAAAAGTAC
1 TTTTCAAAAGCACTTCTCAAAAGTAC
* * *
17859618 ATTTCCACAGCACTTCTCAAAAGTAC
1 TTTTCAAAAGCACTTCTCAAAAGTAC
17859644 TTTTCAAAAGCA
1 TTTTCAAAAGCA
17859656 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAGTAC
Found at i:17866915 original size:27 final size:27
Alignment explanation
Indices: 17866885--17867059 Score: 181
Period size: 27 Copynumber: 6.4 Consensus size: 27
17866875 ATATTGAGTC
* *
17866885 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
17866912 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
17866939 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
17866967 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
17866994 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
17867021 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
17867048 CGCACACTTAGT
1 CGCACACTTAGT
17867060 ACTGTACAAT
Statistics
Matches: 127, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:17867024 original size:82 final size:81
Alignment explanation
Indices: 17866906--17867059 Score: 229
Period size: 82 Copynumber: 1.9 Consensus size: 81
17866896 TGCTATATAA
* *
17866906 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
17866971 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
17866988 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
17867052 CACTTAGT
65 CACTTAGT
17867060 ACTGTACAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 14 0.22
82 51 0.78
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:17867045 original size:54 final size:54
Alignment explanation
Indices: 17866885--17867059 Score: 201
Period size: 54 Copynumber: 3.2 Consensus size: 54
17866875 ATATTGAGTC
* * * *
17866885 CGCACACTCAGTGCTAT-ATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGC-ATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
17866939 CGCACACTTAGTGC-TACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCAT-CATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
17866994 CGCACACTTAGTGCATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
17867048 CGCACACTTAGT
1 CGCACACTTAGT
17867060 ACTGTACAAT
Statistics
Matches: 102, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
54 55 0.54
55 45 0.44
56 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCATCATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:17875635 original size:29 final size:29
Alignment explanation
Indices: 17875595--17875753 Score: 169
Period size: 29 Copynumber: 5.6 Consensus size: 29
17875585 CTGTAACCGA
*
17875595 GCACTGTGTGTGCGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTATTGAG
* ** *** *
17875624 GCACTGTGTGTGCGAGTTC-CATAACCAA
1 GCACTGTGTGTGCGAGATCGGTTATTGAG
17875652 GCACTGTGTGTGCGAGATCGGTTATTGAG
1 GCACTGTGTGTGCGAGATCGGTTATTGAG
* * * **
17875681 GCACTGTGTGTGCGAGTTCCGTAACCGA-
1 GCACTGTGTGTGCGAGATCGGTTATTGAG
* *
17875709 GCACTGTGTGTGTGAGATCGGTTGTTGAG
1 GCACTGTGTGTGCGAGATCGGTTATTGAG
17875738 GCACTGTGTGTGCGAG
1 GCACTGTGTGTGCGAG
17875754 TTCCGTAACC
Statistics
Matches: 100, Mismatches: 28, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
28 41 0.41
29 59 0.59
ACGTcount: A:0.17, C:0.18, G:0.36, T:0.29
Consensus pattern (29 bp):
GCACTGTGTGTGCGAGATCGGTTATTGAG
Found at i:17875642 original size:57 final size:57
Alignment explanation
Indices: 17875571--17875808 Score: 352
Period size: 57 Copynumber: 4.1 Consensus size: 57
17875561 ATAGGCACTG
* * *
17875571 TGTGTGTGTGAGTTCTGTAACCGAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCAC
* *
17875628 TGTGTGTGCGAGTTCCATAACCAAGCACTGTGTGTGCGAGATCGGTTATTGAGGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCAC
* *
17875685 TGTGTGTGCGAGTTCCGTAACCGAGCACTGTGTGTGTGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCAC
** *
17875742 TGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGTAAGATCGATTGTT-AGGGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCGAGATCGGTTGTTGA-GGCAC
17875799 TAAGTGTGTG
1 T--GTGTGTG
17875809 AAATGAGATC
Statistics
Matches: 166, Mismatches: 12, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
56 1 0.01
57 158 0.95
59 7 0.04
ACGTcount: A:0.18, C:0.17, G:0.34, T:0.30
Consensus pattern (57 bp):
TGTGTGTGCGAGTTCCGTAACCAAGCACTGTGTGTGCGAGATCGGTTGTTGAGGCAC
Found at i:17875664 original size:28 final size:28
Alignment explanation
Indices: 17875571--17875777 Score: 153
Period size: 28 Copynumber: 7.3 Consensus size: 28
17875561 ATAGGCACTG
* * *
17875571 TGTGTGTGTGAGTTCTGTAACCGAGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCAC
* * **** *
17875599 TGTGTGTGCGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGTTCCG-TAACCAAGCAC
*
17875628 TGTGTGTGCGAGTTCCATAACCAAGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCAC
* * *** *
17875656 TGTGTGTGCGAGATCGGTTATTGAGGCAC
1 TGTGTGTGCGAGTTCCG-TAACCAAGCAC
*
17875685 TGTGTGTGCGAGTTCCGTAACCGAGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCAC
* * * **** *
17875713 TGTGTGTGTGAGATCGGTTGTTGAGGCAC
1 TGTGTGTGCGAGTTCCG-TAACCAAGCAC
17875742 TGTGTGTGCGAGTTCCGTAACCAAGCAC
1 TGTGTGTGCGAGTTCCGTAACCAAGCAC
17875770 TGTGTGTG
1 TGTGTGTG
17875778 TAAGATCGAT
Statistics
Matches: 128, Mismatches: 48, Indels: 6
0.70 0.26 0.03
Matches are distributed among these distances:
28 68 0.53
29 60 0.47
ACGTcount: A:0.17, C:0.18, G:0.35, T:0.30
Consensus pattern (28 bp):
TGTGTGTGCGAGTTCCGTAACCAAGCAC
Found at i:17880783 original size:28 final size:28
Alignment explanation
Indices: 17880751--17880820 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
17880741 TATGGTACTC
*
17880751 AGTGTACGAAATATTGAGAATGTCACTT
1 AGTGTGCGAAATATTGAGAATGTCACTT
*
17880779 AGTGTGCGAGATATTGAGAATGTCACTT
1 AGTGTGCGAAATATTGAGAATGTCACTT
*
17880807 AGTGTGCAAAATAT
1 AGTGTGCGAAATAT
17880821 CGAATGATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.31
Consensus pattern (28 bp):
AGTGTGCGAAATATTGAGAATGTCACTT
Found at i:17883601 original size:30 final size:29
Alignment explanation
Indices: 17883556--17883627 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 29
17883546 TTTGAATATG
*
17883556 TTTAGATC--AAGAACTAAAGAAATCGGA
1 TTTAGATCGGAAGAACTAAAGAAATCGAA
*
17883583 TTTGGATCGGAAGNAACTAAAGAAATCGAA
1 TTTAGATCGGAAG-AACTAAAGAAATCGAA
17883613 TTTAGATCGGAAGAA
1 TTTAGATCGGAAGAA
17883628 AACCAAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
27 7 0.18
29 5 0.13
30 27 0.69
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.22
Consensus pattern (29 bp):
TTTAGATCGGAAGAACTAAAGAAATCGAA
Found at i:17885623 original size:14 final size:14
Alignment explanation
Indices: 17885604--17885631 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17885594 GGATGTATGA
17885604 ATCAAATGATGTAT
1 ATCAAATGATGTAT
17885618 ATCAAATGATGTAT
1 ATCAAATGATGTAT
17885632 TTTCATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (14 bp):
ATCAAATGATGTAT
Found at i:17889687 original size:37 final size:37
Alignment explanation
Indices: 17889625--17889704 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
17889615 CTTATTACGA
* * * *
17889625 AGTCTTACCCGGACATAATCTCCACACGAAGTTATCG
1 AGTCTTACCCAGACAAAATCCCCACACGAAGTCATCG
* *
17889662 GGTCTTACCCAGACAAAATCCCCACACGTAGTCATCG
1 AGTCTTACCCAGACAAAATCCCCACACGAAGTCATCG
17889699 AGTCTT
1 AGTCTT
17889705 TAGAGCTCGG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (37 bp):
AGTCTTACCCAGACAAAATCCCCACACGAAGTCATCG
Found at i:17889901 original size:47 final size:47
Alignment explanation
Indices: 17889823--17890327 Score: 913
Period size: 47 Copynumber: 10.7 Consensus size: 47
17889813 CCCTTCGGGA
* * * * * *
17889823 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
17889870 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17889917 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17889964 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17890011 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17890058 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17890105 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17890152 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17890199 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
17890246 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
17890293 CTTATCACATATATACA-TGTTCACATCCATCACAT
1 CTTATCACATATATACACT-TTCACATTCATCACAT
17890328 AGAATCCTAA
Statistics
Matches: 446, Mismatches: 11, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
46 1 0.00
47 445 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:17893711 original size:40 final size:40
Alignment explanation
Indices: 17893681--17893910 Score: 352
Period size: 40 Copynumber: 5.8 Consensus size: 40
17893671 AGCATGATTA
* * *
17893681 CTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* ** * *
17893721 CTCTTTGGGGTTTAGCACGGATATATCACTACCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
17893761 CTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
17893801 CTCCTCAGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
17893841 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
17893881 CTCTTCGGGACTTAGCCCGGATATATCACT
1 CTCTTCGGGACTTAGCCCGGATATATCACT
17893911 CTCAATTCTC
Statistics
Matches: 169, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 169 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:17914173 original size:104 final size:104
Alignment explanation
Indices: 17914051--17914274 Score: 369
Period size: 104 Copynumber: 2.2 Consensus size: 104
17914041 AATGGATATC
17914051 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* * *
17914116 GGAT-ATCGCACTTAGCACCACCAATGAACCGGGGAATCA
66 GGATCA-CGCACATAGCACCACCAATAAACCGGGAAATCA
17914155 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
1 GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
* *
17914220 GGATCACGCACATAGCACCACCCATAAATCGGGAAATCA
66 GGATCACGCACATAGCACCACCAATAAACCGGGAAATCA
**
17914259 GCACACAGCAACCCCT
1 GCACTTAGCAACCCCT
17914275 TTTATATACA
Statistics
Matches: 112, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
104 111 0.99
105 1 0.01
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCCCTCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGT
GGATCACGCACATAGCACCACCAATAAACCGGGAAATCA
Found at i:17914637 original size:30 final size:29
Alignment explanation
Indices: 17914603--17914667 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
17914593 TAATCCACCA
*
17914603 CCCAACTTTTTTGAAAATTACAATTTTGCC
1 CCCAAC-TTTTTCAAAATTACAATTTTGCC
* * *
17914633 CCCAAACTTTTTCATAATTACACTTTTGTC
1 CCC-AACTTTTTCAAAATTACAATTTTGCC
17914663 CCCAA
1 CCCAA
17914668 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.29, C:0.28, G:0.05, T:0.38
Consensus pattern (29 bp):
CCCAACTTTTTCAAAATTACAATTTTGCC
Found at i:17914641 original size:31 final size:30
Alignment explanation
Indices: 17914610--17914667 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17914600 CCACCCAACT
*
17914610 TTTTTGAAAATTACAATTTTGCCCCCAAAC
1 TTTTTCAAAATTACAATTTTGCCCCCAAAC
* * *
17914640 TTTTTCATAATTACACTTTTGTCCCCAA
1 TTTTTCAAAATTACAATTTTGCCCCCAA
17914668 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTTTCAAAATTACAATTTTGCCCCCAAAC
Found at i:17920190 original size:29 final size:29
Alignment explanation
Indices: 17920144--17920256 Score: 165
Period size: 29 Copynumber: 3.9 Consensus size: 29
17920134 ATGTATGTGC
*
17920144 ATGTGATTTGGGCTTAATGGGCCATATGA
1 ATGTGATTTGGGCCTAATGGGCCATATGA
*
17920173 ATGTGATTTGGGCCTAATGGGCCATACGA
1 ATGTGATTTGGGCCTAATGGGCCATATGA
*
17920202 ATATGATTTGGGCCTAATGGGCCATATGA
1 ATGTGATTTGGGCCTAATGGGCCATATGA
* * *
17920231 ATGAGA-TTGGGCCTAGTGGGCTATAT
1 ATGTGATTTGGGCCTAATGGGCCATAT
17920257 CCATGTATGT
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
28 18 0.24
29 58 0.76
ACGTcount: A:0.25, C:0.13, G:0.31, T:0.31
Consensus pattern (29 bp):
ATGTGATTTGGGCCTAATGGGCCATATGA
Found at i:17922838 original size:40 final size:40
Alignment explanation
Indices: 17922794--17922941 Score: 251
Period size: 40 Copynumber: 3.7 Consensus size: 40
17922784 CAACTCGTAC
*
17922794 AAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAT
* * *
17922834 AAATGCCTTCGGGACTTAGCCCGGATATGGTCGCTAGCAC
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAT
17922874 AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAT
1 AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAT
*
17922914 AAATGCCTTTGGGACTTAGCCCGGATAT
1 AAATGCCTTCGGGACTTAGCCCGGATAT
17922942 CATCCGAATA
Statistics
Matches: 100, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 100 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (40 bp):
AAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCAT
Found at i:17922877 original size:80 final size:80
Alignment explanation
Indices: 17922792--17922941 Score: 282
Period size: 80 Copynumber: 1.9 Consensus size: 80
17922782 AGCAACTCGT
*
17922792 ACAAATGCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCG
1 ACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCG
17922857 GATATGGTCGCTAGC
66 GATATGGTCGCTAGC
*
17922872 ACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTTGGGACTTAGCCCG
1 ACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCG
17922937 GATAT
66 GATAT
17922942 CATCCGAATA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
80 68 1.00
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.25
Consensus pattern (80 bp):
ACAAATGCCTTCGGGACTTAGCCCGGATATAGTCACTAGCATAAATGCCTTCGGGACTTAGCCCG
GATATGGTCGCTAGC
Found at i:17926211 original size:22 final size:23
Alignment explanation
Indices: 17926174--17926226 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
17926164 AATCAAGAGA
17926174 TAATTATAAGAAAACACTCCAAT
1 TAATTATAAGAAAACACTCCAAT
*
17926197 TAATTAT-TGAAAACACTCCAAT
1 TAATTATAAGAAAACACTCCAAT
*
17926219 TAACTATA
1 TAATTATA
17926227 TGGACCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 20 0.74
23 7 0.26
ACGTcount: A:0.49, C:0.17, G:0.04, T:0.30
Consensus pattern (23 bp):
TAATTATAAGAAAACACTCCAAT
Found at i:17926917 original size:56 final size:53
Alignment explanation
Indices: 17926794--17926900 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 53
17926784 CATGACATAG
* *
17926794 CACGCCTCTCAACAGGGCTATATATGAGCATTCGGACCTAGCATGCATCACATTAC
1 CACGCCTCTCAACAGGGCTACATA--AGC-TTCGGACCTAGCATGCACCACATTAC
* *
17926850 CACGCCTCTCAACAGGGCTACATAAGCTCTCGGACCTAGCGTGTACCACAT
1 CACGCCTCTCAACAGGGCTACATAAGCT-TCGGACCTAGCATGCACCACAT
17926901 AATTACATGC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 1 0.02
54 22 0.48
56 23 0.50
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (53 bp):
CACGCCTCTCAACAGGGCTACATAAGCTTCGGACCTAGCATGCACCACATTAC
Found at i:17928650 original size:50 final size:49
Alignment explanation
Indices: 17928405--17928719 Score: 160
Period size: 46 Copynumber: 6.7 Consensus size: 49
17928395 TTTATGTGCT
* * *
17928405 AGTGTAAGA-CATGTGTGGGACAT-GCATCGGC-CATATTAT-GA-GAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-T-TGATGGATGAGTC
* * *
17928451 AATGTAAAACCATGTCTGGGACATGGCATTGGCA-TTGA-GACGA-GAG-C
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATG--GATGAGTC
* * * * *
17928498 TAGTGTAAGA-CATGTCTTGGAAAT-GCATCGAC-CTCGA-GG-TGTAAGCC
1 -AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATGGATG--AGTC
* * ** *
17928545 AGTGTAAGA-CGTGTCTGGGACAT-GCATCAGCTAC---A-AAATGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-ACTTGATGGATGAGTC
* *
17928589 AATGTAAGACCATGTCTAGGACATGGCATCGGCACTAAT-ATGTGA-GAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACT--TGATG-GATGAGTC
* **
17928639 AGTGTAAGACCATATCTGGGACATGGCAT--TAACTTGATGGATGA-T-
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATGGATGAGTC
17928684 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCACT
17928720 CTACCCTGTG
Statistics
Matches: 206, Mismatches: 36, Indels: 53
0.70 0.12 0.18
Matches are distributed among these distances:
44 12 0.06
45 43 0.21
46 60 0.29
47 36 0.17
48 23 0.11
49 1 0.00
50 30 0.15
51 1 0.00
ACGTcount: A:0.30, C:0.18, G:0.28, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCACTTGATGGATGAGTC
Found at i:17931698 original size:8 final size:8
Alignment explanation
Indices: 17931655--17931697 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
17931645 GTGTAATAGC
*
17931655 AAAAGCCA
1 AAAAGCCG
17931663 AAAAGCCG
1 AAAAGCCG
*
17931671 AAAAGTCG
1 AAAAGCCG
*
17931679 AAAAGTCG
1 AAAAGCCG
17931687 AAAAGCC-
1 AAAAGCCG
17931694 AAAA
1 AAAA
17931698 ATTGGGATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
7 4 0.12
8 28 0.88
ACGTcount: A:0.58, C:0.19, G:0.19, T:0.05
Consensus pattern (8 bp):
AAAAGCCG
Found at i:17931698 original size:16 final size:16
Alignment explanation
Indices: 17931655--17931698 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
17931645 GTGTAATAGC
17931655 AAAAGCCAAAAAGCCG
1 AAAAGCCAAAAAGCCG
* * *
17931671 AAAAGTCGAAAAGTCG
1 AAAAGCCAAAAAGCCG
17931687 AAAAGCCAAAAA
1 AAAAGCCAAAAA
17931699 TTGGGATGTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.59, C:0.18, G:0.18, T:0.05
Consensus pattern (16 bp):
AAAAGCCAAAAAGCCG
Found at i:17938169 original size:43 final size:43
Alignment explanation
Indices: 17938013--17938170 Score: 151
Period size: 43 Copynumber: 3.7 Consensus size: 43
17938003 ATGTGTTATT
* * * * *
17938013 GTGTAAGACTACATCTGGGATGTTGGCATTGACT-TATGATTTAC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGA-TATTTGA-TTAC
* * *
17938057 GTGTAAGGCCATGTCTGGGACGTTGGCATC-ATATTTGATTTC
1 GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
* * **
17938099 ATGTAGGACC-CTGTCTGGGACAATGGCATCGATATTTGATTAC
1 GTGTAAGACCAC-GTCTGGGACGTTGGCATCGATATTTGATTAC
*
17938142 GTGTAAGACCACGTCTAGGACGTTGGCAT
1 GTGTAAGACCACGTCTGGGACGTTGGCAT
17938171 TAAACAAGCT
Statistics
Matches: 90, Mismatches: 20, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
42 27 0.30
43 38 0.42
44 25 0.28
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
GTGTAAGACCACGTCTGGGACGTTGGCATCGATATTTGATTAC
Found at i:17951243 original size:31 final size:31
Alignment explanation
Indices: 17951182--17951258 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
17951172 TCCTGAGCTA
* *
17951182 CTCGACAACGATGACCGGCCACCCTAGGTTG
1 CTCGACAACGATGACCCGCCACCCCAGGTTG
* *
17951213 CTCGACAGCGATGACCCGCCACCCCGGGTTG
1 CTCGACAACGATGACCCGCCACCCCAGGTTG
* *
17951244 CCCGGCAACGATGAC
1 CTCGACAACGATGAC
17951259 TTATTATATT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.21, C:0.39, G:0.27, T:0.13
Consensus pattern (31 bp):
CTCGACAACGATGACCCGCCACCCCAGGTTG
Found at i:17951686 original size:17 final size:17
Alignment explanation
Indices: 17951664--17951697 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
17951654 CATGCATATA
17951664 TAATGTA-ATCATTCTTT
1 TAATGTATA-CATTCTTT
17951681 TAATGTATACATTCTTT
1 TAATGTATACATTCTTT
17951698 CAATCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (17 bp):
TAATGTATACATTCTTT
Found at i:17953108 original size:40 final size:40
Alignment explanation
Indices: 17953071--17953255 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
17953061 GCTACTCGTT
*
17953071 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
17953111 CAATTGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
17953151 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
17953190 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
17953231 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
17953256 CATCATTCAA
Statistics
Matches: 125, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
38 2 0.02
39 32 0.26
40 76 0.61
41 15 0.12
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:17953182 original size:79 final size:82
Alignment explanation
Indices: 17953038--17953255 Score: 220
Period size: 79 Copynumber: 2.7 Consensus size: 82
17953028 AAATCACGTA
* * ** * *
17953038 CCTTCGGAAT-TTAA-CCGGATATAG-CTACTCGTTCAAATGCCTTCGGGACATAGCCCGG-TTA
1 CCTTCGG-ATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATA
*
17953099 TAGTAACTCGCACAATTG
65 TAGTAACTCGCACAAATG
* *
17953117 CCTTCGGGA-CTTAACCCGGATTTAGT-AACTCGCACAAATGCCTTCGGG-CTTAGCCCGGAAT-
1 CCTTC-GGATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATA
* *
17953178 TAGTATCTTGCACAAATG
65 TAGTAACTCGCACAAATG
** * *
17953196 CCTTCGGATCTTAGTCCGGATATGGTCACCTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 CCTTCGGATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGA
17953256 CATCATTCAA
Statistics
Matches: 116, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
78 3 0.03
79 61 0.53
80 52 0.45
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CCTTCGGATCTTAACCCGGATATAGTCAACTAGCACAAATGCCTTCGGGACTTAGCCCGGAATAT
AGTAACTCGCACAAATG
Found at i:17959452 original size:38 final size:38
Alignment explanation
Indices: 17959409--17959483 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
17959399 GACAGTGAAC
17959409 TCTTTCCCTAACCCTAGCTGTATCAAGACAGGGGCCTT
1 TCTTTCCCTAACCCTAGCTGTATCAAGACAGGGGCCTT
* * *
17959447 TCTTTCCCTGACTCTAGCTGTATCAAGATAGGGGCCT
1 TCTTTCCCTAACCCTAGCTGTATCAAGACAGGGGCCT
17959484 CAGTTAGTAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.31
Consensus pattern (38 bp):
TCTTTCCCTAACCCTAGCTGTATCAAGACAGGGGCCTT
Found at i:17965341 original size:48 final size:48
Alignment explanation
Indices: 17965265--17965490 Score: 196
Period size: 48 Copynumber: 4.8 Consensus size: 48
17965255 CATGGTAGGG
*
17965265 TGCCAATGCCATTTCCCAGATA-GAGTCTTACATGGGATCACATACCAA
1 TGCCAATGCCATGTCCCAGATATG-GTCTTACATGGGATCACATACCAA
* * * * *
17965313 TTCCAATGCCATGTCCTAGACATGGTCTTACATGGGATCACATATCGA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATACCAA
* * * * *
17965361 TGCCAATGCCATGTCCCAAATATGGTTTTACATGGGATCACACATCGA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATACCAA
* * * * ** * * *
17965409 TGCCGAT---A-G-CCCAGCTATGGTCTAACACGATATTACATATCGA
1 TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATACCAA
*
17965452 TGCCAAAT-CCATGTCCCAGACATGGTCTTACATGGGATC
1 TGCC-AATGCCATGTCCCAGATATGGTCTTACATGGGATC
17965491 GTACATAACC
Statistics
Matches: 142, Mismatches: 30, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
43 29 0.20
44 3 0.02
45 1 0.01
46 1 0.01
47 1 0.01
48 106 0.75
49 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGATATGGTCTTACATGGGATCACATACCAA
Found at i:17965843 original size:14 final size:13
Alignment explanation
Indices: 17965819--17965848 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
17965809 GGTTGTTTAT
17965819 TAAACTAATTAAC
1 TAAACTAATTAAC
17965832 TAAACTTAATTAAC
1 TAAAC-TAATTAAC
17965846 TAA
1 TAA
17965849 TTAAAATAAA
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:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:17970797 original size:20 final size:20
Alignment explanation
Indices: 17970772--17970811 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
17970762 TCTCCTACGC
*
17970772 CCGTGTGTTAGGGTCCACGG
1 CCGTGTATTAGGGTCCACGG
**
17970792 CCGTGTATTATTGTCCACGG
1 CCGTGTATTAGGGTCCACGG
17970812 TTTAACGGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.12, C:0.25, G:0.33, T:0.30
Consensus pattern (20 bp):
CCGTGTATTAGGGTCCACGG
Found at i:17971306 original size:39 final size:39
Alignment explanation
Indices: 17971252--17971327 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
17971242 CGTACTCCTC
*
17971252 ATTCCTACTATCAATCTCATCAAAATAAGGTTTTAAACG
1 ATTCCTACTATCAATCTCATCAAAATAAGCTTTTAAACG
*
17971291 ATTCCTGCTATCAATCTCATCAAAATAAGCTTTTAAA
1 ATTCCTACTATCAATCTCATCAAAATAAGCTTTTAAA
17971328 TGGGTCTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (39 bp):
ATTCCTACTATCAATCTCATCAAAATAAGCTTTTAAACG
Found at i:17978210 original size:28 final size:28
Alignment explanation
Indices: 17978168--17978263 Score: 147
Period size: 28 Copynumber: 3.4 Consensus size: 28
17978158 TAGGTGGGAA
17978168 GTGATTGGGCCTGATGGGCCATATGAAT
1 GTGATTGGGCCTGATGGGCCATATGAAT
* *
17978196 TTGATTGGGCTTGATGGGCCATATGAAT
1 GTGATTGGGCCTGATGGGCCATATGAAT
*
17978224 GTGATTGGGCCTGATGGGCCATGTGAAT
1 GTGATTGGGCCTGATGGGCCATATGAAT
* *
17978252 GAGATTAGGCCT
1 GTGATTGGGCCT
17978264 AAAGGGGCCA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.21, C:0.14, G:0.35, T:0.30
Consensus pattern (28 bp):
GTGATTGGGCCTGATGGGCCATATGAAT
Found at i:17978618 original size:27 final size:27
Alignment explanation
Indices: 17978580--17978866 Score: 312
Period size: 27 Copynumber: 10.7 Consensus size: 27
17978570 TAATAAAGAG
*
17978580 AAATTACTGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
17978607 AAATTACCGAAATACCCTTGATTATG--
1 AAATTACCGAAATACCCTCGATT-TGTA
* *
17978633 AAATTACCGAAATACCCCCAATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
17978660 AAATTATCAAAACACTCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * * *
17978687 AAATTACTGAAACACCATTGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
17978714 AAATTACCGAAACACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
*
17978741 AAATTATCGAAATACCCTCGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* * *
17978768 AAATTACAGAAATACCTTTGATTTGTA
1 AAATTACCGAAATACCCTCGATTTGTA
* *
17978795 AAATTACCGAAACACCC-CTAATTTGTA
1 AAATTACCGAAATACCCTC-GATTTGTA
* * *
17978822 AAATTATCGAAATACCCTTG-TAGTGTA
1 AAATTACCGAAATACCCTCGAT-TTGTA
*
17978849 AAATTACTGAAATACCCT
1 AAATTACCGAAATACCCT
17978867 TGTAGTGTAA
Statistics
Matches: 216, Mismatches: 38, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
25 2 0.01
26 21 0.10
27 191 0.88
28 2 0.01
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATTACCGAAATACCCTCGATTTGTA
Found at i:17978877 original size:81 final size:81
Alignment explanation
Indices: 17978580--17978868 Score: 390
Period size: 81 Copynumber: 3.6 Consensus size: 81
17978570 TAATAAAGAG
*
17978580 AAATTA-CTGAAATACCCTCGATTTGTAAAATTACCGAAATACCCTTGATTATG--AAATTACCG
1 AAATTATC-GAAATACCCTCGATTTGTAAAATTACTGAAATACCCTTGATT-TGTAAAATTACCG
* *
17978642 AAATACCCCCAATTTGTA
64 AAACACCCCTAATTTGTA
* * * * *
17978660 AAATTATCAAAACACTCTCGATTTGTAAAATTACTGAAACACCATTGATTTGTAAAATTACCGAA
1 AAATTATCGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTTGATTTGTAAAATTACCGAA
*
17978725 ACA-CCCTCGATTTGTA
66 ACACCCCT-AATTTGTA
* *
17978741 AAATTATCGAAATACCCTCGATTTGTAAAATTACAGAAATACCTTTGATTTGTAAAATTACCGAA
1 AAATTATCGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTTGATTTGTAAAATTACCGAA
17978806 ACACCCCTAATTTGTA
66 ACACCCCTAATTTGTA
* *
17978822 AAATTATCGAAATACCCTTG-TAGTGTAAAATTACTGAAATACCCTTG
1 AAATTATCGAAATACCCTCGAT-TTGTAAAATTACTGAAATACCCTTG
17978869 TAGTGTAAAG
Statistics
Matches: 183, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
79 2 0.01
80 46 0.25
81 131 0.72
82 4 0.02
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.31
Consensus pattern (81 bp):
AAATTATCGAAATACCCTCGATTTGTAAAATTACTGAAATACCCTTGATTTGTAAAATTACCGAA
ACACCCCTAATTTGTA
Found at i:17978890 original size:27 final size:27
Alignment explanation
Indices: 17978710--17978906 Score: 145
Period size: 27 Copynumber: 7.3 Consensus size: 27
17978700 ACCATTGATT
* * * *
17978710 TGTAAAATTACCGAAACACCCTCG-ATT
1 TGTAAAATTATCGAAATACCCTTGTA-G
* *
17978737 TGTAAAATTATCGAAATACCCTCG-ATT
1 TGTAAAATTATCGAAATACCCTTGTA-G
* *
17978764 TGTAAAATTA-CAGAAATACCTTTG-ATT
1 TGTAAAATTATC-GAAATACCCTTGTA-G
* * * * *
17978791 TGTAAAATTACCGAAACACCCCT-AATT
1 TGTAAAATTATCGAAATACCCTTGTA-G
17978818 TGTAAAATTATCGAAATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
17978845 TGTAAAATTA-CTGAAATACCCTTGTAG
1 TGTAAAATTATC-GAAATACCCTTGTAG
* * *
17978872 TGTAAAGTGATCGACATACCCTTGTAG
1 TGTAAAATTATCGAAATACCCTTGTAG
*
17978899 GGTAAAAT
1 TGTAAAAT
17978907 GACTGTTTTG
Statistics
Matches: 147, Mismatches: 17, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
26 2 0.01
27 142 0.97
28 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.31
Consensus pattern (27 bp):
TGTAAAATTATCGAAATACCCTTGTAG
Found at i:17979986 original size:17 final size:18
Alignment explanation
Indices: 17979964--17979998 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17979954 TTTTGAGTAG
17979964 TAAGAA-AGGGTTTTCAA
1 TAAGAACAGGGTTTTCAA
*
17979981 TAAGAACATGGTTTTCAA
1 TAAGAACAGGGTTTTCAA
17979999 AAAACACTTT
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:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (18 bp):
TAAGAACAGGGTTTTCAA
Found at i:17997598 original size:17 final size:17
Alignment explanation
Indices: 17997576--17997610 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17997566 CAATCTCGAA
17997576 TAACCTTTACTTTTTCT
1 TAACCTTTACTTTTTCT
17997593 TAACCTTTACTTTTTCT
1 TAACCTTTACTTTTTCT
17997610 T
1 T
17997611 CGGTTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (17 bp):
TAACCTTTACTTTTTCT
Done.