Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 56 of 193
Found at i:17402245 original size:6 final size:6
Alignment explanation
Indices: 17402234--17402277 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
17402224 TTTGCTTTTA
*
17402234 AAATTT AAATTT AAA-TT AAGTTT AAA-TT AAATTT AAA-TT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
17402278 AAAGAGATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 14 0.42
6 19 0.58
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (6 bp):
AAATTT
Found at i:17402257 original size:11 final size:11
Alignment explanation
Indices: 17402238--17402277 Score: 71
Period size: 11 Copynumber: 3.6 Consensus size: 11
17402228 CTTTTAAAAT
17402238 TTAAATTTAAA
1 TTAAATTTAAA
*
17402249 TTAAGTTTAAA
1 TTAAATTTAAA
17402260 TTAAATTTAAA
1 TTAAATTTAAA
17402271 TTAAATT
1 TTAAATT
17402278 AAAGAGATCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:17402263 original size:5 final size:5
Alignment explanation
Indices: 17402238--17402280 Score: 50
Period size: 5 Copynumber: 8.0 Consensus size: 5
17402228 CTTTTAAAAT
*
17402238 TTAAA TTTAAA TTAAGT TTAAA TTAAA TTTAAA TTAAA TTAAA
1 TTAAA -TTAAA TTAA-A TTAAA TTAAA -TTAAA TTAAA TTAAA
17402281 GAGATCCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
5 19 0.58
6 14 0.42
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (5 bp):
TTAAA
Found at i:17402384 original size:43 final size:43
Alignment explanation
Indices: 17402331--17402426 Score: 147
Period size: 43 Copynumber: 2.2 Consensus size: 43
17402321 ATTACAATCT
*
17402331 TTGACCCAATTGGGCCCAACTCAGACAACTCAATTGCAAACGC
1 TTGACCCAATTGGGCCCAACTCAGACAACTCAATTGCAAACCC
* * *
17402374 TTGACCCAATTGGGCCCAACTCAGATAACTTAATTGCAAGCCC
1 TTGACCCAATTGGGCCCAACTCAGACAACTCAATTGCAAACCC
*
17402417 TTAACCCAAT
1 TTGACCCAAT
17402427 ACATAATCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.32, C:0.31, G:0.15, T:0.22
Consensus pattern (43 bp):
TTGACCCAATTGGGCCCAACTCAGACAACTCAATTGCAAACCC
Found at i:17404210 original size:29 final size:28
Alignment explanation
Indices: 17404178--17404409 Score: 145
Period size: 29 Copynumber: 7.9 Consensus size: 28
17404168 TGAACTTTCT
17404178 AAAATTCCATTTTTGACCCCGATTTCACC
1 AAAATTCCATTTTT-ACCCCGATTTCACC
* *
17404207 AAAAACTACCA-TTTTACCCTCGAACTTTCA-A
1 -AAAA-TTCCATTTTTACCC-CG-A-TTTCACC
* **
17404238 AAAATTCCATTTTTACCCCTAATTTTTCC
1 AAAATTCCATTTTTACCCC-GATTTCACC
* *
17404267 AAAATTCCATTTTTGAACCCAATTTCACC
1 AAAATTCCATTTTT-ACCCCGATTTCACC
17404296 AAAAATTACCA-TTTTACCCCTGAACTTT--CC
1 -AAAATT-CCATTTTTACCCC-G-A-TTTCACC
*
17404326 AAAATTCCATTTTTGACCCCAATTTCACC
1 AAAATTCCATTTTT-ACCCCGATTTCACC
*
17404355 AAAAATTACCA-TTTTACCCCCGAATTTC-CT
1 -AAAATT-CCATTTTTA-CCCCG-ATTTCACC
* *
17404385 AAAATTCTATTTTTGACCCTGATTT
1 AAAATTCCATTTTT-ACCCCGATTT
17404410 TTCTCAAAAT
Statistics
Matches: 162, Mismatches: 17, Indels: 48
0.71 0.07 0.21
Matches are distributed among these distances:
27 3 0.02
28 13 0.08
29 62 0.38
30 59 0.36
31 17 0.10
32 8 0.05
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGATTTCACC
Found at i:17404308 original size:89 final size:88
Alignment explanation
Indices: 17404173--17404369 Score: 272
Period size: 89 Copynumber: 2.2 Consensus size: 88
17404163 ACCCATGAAC
* * *
17404173 TTTCTAAAATTCCATTTTTGACCCCGATTTCACCAAAAACTACCATTTTA-CCCTCGAACTTTCA
1 TTTCCAAAATTCCATTTTTGAACCCAATTTCACCAAAAACTACCATTTTACCCCT-GAACTTTC-
17404237 AAAAATTCCATTTTT-ACCCCTAATT
64 AAAAATTCCATTTTTGACCCC-AATT
* *
17404262 TTTCCAAAATTCCATTTTTGAACCCAATTTCACCAAAAATTACCATTTTACCCCTGAACTTTCCA
1 TTTCCAAAATTCCATTTTTGAACCCAATTTCACCAAAAACTACCATTTTACCCCTGAACTTTCAA
17404327 AAATTCCATTTTTGACCCCAATT
66 AAATTCCATTTTTGACCCCAATT
**
17404350 TCACCAAAAATTACCATTTT
1 TTTCC-AAAATT-CCATTTT
17404370 ACCCCCGAAT
Statistics
Matches: 97, Mismatches: 7, Indels: 7
0.87 0.06 0.06
Matches are distributed among these distances:
88 21 0.22
89 65 0.67
90 11 0.11
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (88 bp):
TTTCCAAAATTCCATTTTTGAACCCAATTTCACCAAAAACTACCATTTTACCCCTGAACTTTCAA
AAATTCCATTTTTGACCCCAATT
Found at i:17404428 original size:59 final size:59
Alignment explanation
Indices: 17404237--17404403 Score: 241
Period size: 59 Copynumber: 2.8 Consensus size: 59
17404227 CGAACTTTCA
* * *
17404237 AAAAATT-CCATTTTTA-CCCCTAATTTTTCCAAAATTCCATTTTTGAACCCAATTTCACC
1 AAAAATTACCA-TTTTACCCCCGAA-CTTTCCAAAATTCCATTTTTGACCCCAATTTCACC
*
17404296 AAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTGACCCCAATTTCACC
1 AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCAATTTCACC
*
17404355 AAAAATTACCATTTTACCCCCGAA-TTTCCTAAAATTCTATTTTTGACCC
1 AAAAATTACCATTTTACCCCCGAACTTTCC-AAAATTCCATTTTTGACCC
17404404 TGATTTTTCT
Statistics
Matches: 99, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
58 5 0.05
59 86 0.87
60 8 0.08
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.37
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCCCAATTTCACC
Found at i:17404456 original size:59 final size:58
Alignment explanation
Indices: 17404264--17404456 Score: 219
Period size: 59 Copynumber: 3.3 Consensus size: 58
17404254 CCCTAATTTT
* * *
17404264 TCCAAAATTCCATTTTTGAACCCAATTTCACCAAAAATTACCATTTTACCCCTGAACTT
1 TCCAAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAA-TG
*
17404323 TCCAAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAATT
1 TCCAAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAATG
* ** ** * * *
17404381 TCCTAAAATTCTATTTTTGACCCTGATTTTTCTC-AAAATTATCATTTTGCCCTC-AAGTG
1 TCC-AAAATTCCATTTTTGACCCCAATTTCAC-CAAAAATTACCATTTTACCCCCGAA-TG
17404440 TCCAAAATTACCATTTT
1 TCCAAAATT-CCATTTT
17404457 GCCCCCGAGT
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
58 13 0.11
59 104 0.88
60 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.05, T:0.37
Consensus pattern (58 bp):
TCCAAAATTCCATTTTTGACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAATG
Found at i:17404474 original size:28 final size:28
Alignment explanation
Indices: 17404356--17404474 Score: 87
Period size: 28 Copynumber: 4.1 Consensus size: 28
17404346 AATTTCACCA
* *
17404356 AAAATTACCATTTTACCCCCGAATTTCCT
1 AAAATTACCATTTTGCCCCCGAGTTT-CT
* * * *
17404385 AAAATT-CTATTTTTGACCCTGATTTTTCT
1 AAAATTACCA-TTTTGCCCCCGA-GTTTCT
* * * * *
17404414 CAAAATTATCATTTTGCCCTCAAGTGTCC
1 -AAAATTACCATTTTGCCCCCGAGTTTCT
*
17404443 AAAATTACCATTTTGCCCCCGAGTATCT
1 AAAATTACCATTTTGCCCCCGAGTTTCT
17404471 AAAA
1 AAAA
17404475 AGTCTCATTT
Statistics
Matches: 67, Mismatches: 19, Indels: 9
0.71 0.20 0.09
Matches are distributed among these distances:
28 29 0.43
29 20 0.30
30 17 0.25
31 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCGAGTTTCT
Found at i:17409002 original size:3 final size:3
Alignment explanation
Indices: 17408996--17409023 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17408986 TAAAAAAACT
17408996 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17409024 GAAAAGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17411050 original size:17 final size:19
Alignment explanation
Indices: 17411028--17411092 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
17411018 TCTCAATAAT
17411028 ATTATTTTT-TTT-AATCA
1 ATTATTTTTATTTAAATCA
17411045 ATTATTTTTATATTTAAATCA
1 ATTA-TTTT-TATTTAAATCA
*
17411066 ATTATTTTTATATTTAAATTA
1 ATTA-TTTT-TATTTAAATCA
17411087 ATTATT
1 ATTATT
17411093 ACGTAATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
17 4 0.09
18 4 0.09
19 1 0.02
20 5 0.12
21 29 0.67
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTATTTTTATTTAAATCA
Found at i:17411066 original size:21 final size:21
Alignment explanation
Indices: 17411040--17411092 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
17411030 TATTTTTTTT
17411040 AATCAATTATTTTTATATTTA
1 AATCAATTATTTTTATATTTA
17411061 AATCAATTATTTTTATATTTA
1 AATCAATTATTTTTATATTTA
*
17411082 AATTAATTATT
1 AATCAATTATT
17411093 ACGTAATATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (21 bp):
AATCAATTATTTTTATATTTA
Found at i:17414159 original size:62 final size:59
Alignment explanation
Indices: 17414087--17414206 Score: 152
Period size: 62 Copynumber: 2.0 Consensus size: 59
17414077 GTATTTTATT
* * * *
17414087 TATTTAATATTAAA-TTAATTTTAATGTTTATTTTGTAGATAAATATTCTATTAATTTAATAA
1 TATTTAATATTAAATTTAA-TATAATATTTA-TCT-T-GATAAATATTATATTAATTTAATAA
*
17414149 TATTTAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TATTTAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATA
17414207 TTAAAGTGAT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 22 0.42
60 1 0.02
61 2 0.04
62 23 0.44
63 4 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (59 bp):
TATTTAATATTAAATTTAATATAATATTTATCTTGATAAATATTATATTAATTTAATAA
Found at i:17414177 original size:12 final size:12
Alignment explanation
Indices: 17414145--17414178 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
17414135 TATTAATTTA
17414145 ATAATATTTAAT
1 ATAATATTTAAT
17414157 ATTAA-ATTTAAT
1 A-TAATATTTAAT
17414169 ATAATATTTA
1 ATAATATTTA
17414179 TCTTGATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 3 0.15
12 14 0.70
13 3 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAATATTTAAT
Found at i:17416311 original size:21 final size:20
Alignment explanation
Indices: 17416262--17416311 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
17416252 TGAGTTAAAC
* * *
17416262 TAAGTATAAATAGGTTTAAT
1 TAAGTTTAAAAAGGGTTAAT
*
17416282 TAAGATTAAAAAGGGTTAAT
1 TAAGTTTAAAAAGGGTTAAT
17416302 TAAAGTTTAA
1 T-AAGTTTAA
17416312 TGATGAAAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
TAAGTTTAAAAAGGGTTAAT
Found at i:17417255 original size:53 final size:53
Alignment explanation
Indices: 17417155--17417502 Score: 444
Period size: 53 Copynumber: 6.7 Consensus size: 53
17417145 TTGTGCCAAA
17417155 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * ** * *
17417208 GCTTAGAGGTTTGATTACTTTGTGTCATCGTGAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* *
17417261 AATTAGAGGTCCGA-GACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * *
17417313 GATTAAAGGTCTGATGACTCTGTGTCATCGTGAGCTATATGAATCCTATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * *
17417366 GATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
* * * ** *
17417419 GATT-----T-CGATGACTTTGTGTCATCGTGAGATACACAAATCC-ATCATG
1 GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
17417465 TG-TTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 -GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
17417503 CAAATGCGAA
Statistics
Matches: 257, Mismatches: 30, Indels: 17
0.85 0.10 0.06
Matches are distributed among these distances:
46 7 0.03
47 31 0.12
48 1 0.00
51 1 0.00
52 71 0.28
53 146 0.57
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (53 bp):
GATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACG
Found at i:17417352 original size:105 final size:105
Alignment explanation
Indices: 17417156--17417502 Score: 474
Period size: 105 Copynumber: 3.4 Consensus size: 105
17417146 TGTGCCAAAG
* *
17417156 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGGCTTAGAGGTTTG
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTA-AGGTCTG
* * *
17417221 ATTACTTTGTGTCATCGTGAGTTATATGAATCCTATCACGA
65 ATGACTTTGTGTCATCGTGAGATATATGAATCCTATCATGA
*
17417262 ATTAGAGGTCCGA-GACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAAAGGTCTG
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGGATT-AAGGTCTG
* * *
17417326 ATGACTCTGTGTCATCGTGAGCTATATGAATCCTATCATGG
65 ATGACTTTGTGTCATCGTGAGATATATGAATCCTATCATGA
* * *
17417367 ATTAAAGGTCCGATGACTATGTGTCATCGTGAGTTATATGAATCCTATTATGGATT----TC-GA
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAAGGTCTGA
* ** *
17417427 TGACTTTGTGTCATCGTGAGATACACAAATCC-ATCATGT
66 TGACTTTGTGTCATCGTGAGATATATGAATCCTATCATGA
*
17417466 GTTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
1 ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTAT
17417503 CAAATGCGAA
Statistics
Matches: 219, Mismatches: 20, Indels: 11
0.88 0.08 0.04
Matches are distributed among these distances:
99 41 0.19
100 29 0.13
101 2 0.01
105 95 0.43
106 52 0.24
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (105 bp):
ATTAAAGGTCCGATGACTCTGTGTCATCGTGAGTTATATGAATCCTATCACGGATTAAGGTCTGA
TGACTTTGTGTCATCGTGAGATATATGAATCCTATCATGA
Found at i:17418209 original size:21 final size:21
Alignment explanation
Indices: 17418185--17418241 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
17418175 TAGAATTAAG
* *
17418185 ACTTGTTTCGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
17418206 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
17418227 ACTTGTATCGGTAGA
1 ACTTGTATCGGTAGA
17418242 GGTCTGCACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:17419939 original size:18 final size:18
Alignment explanation
Indices: 17419913--17419949 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17419903 TTTTTTAAAA
* *
17419913 ATTATAATAATATAAATT
1 ATTAAAATAATAAAAATT
17419931 ATTAAAATAATAAAAATT
1 ATTAAAATAATAAAAATT
17419949 A
1 A
17419950 ACTTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTAAAATAATAAAAATT
Found at i:17419949 original size:15 final size:15
Alignment explanation
Indices: 17419908--17419950 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 15
17419898 TTTAATTTTT
*
17419908 TAAAAATTATAATAA
1 TAAAAATTAAAATAA
17419923 TATAAATTATTAAAATAA
1 TA-AAA--ATTAAAATAA
17419941 TAAAAATTAA
1 TAAAAATTAA
17419951 CTTTTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
15 7 0.29
16 3 0.12
17 3 0.12
18 11 0.46
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAAAATTAAAATAA
Found at i:17420269 original size:7 final size:7
Alignment explanation
Indices: 17420257--17420292 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
17420247 TTCAGTCCTA
17420257 GTGCAGT
1 GTGCAGT
17420264 GTGCAGT
1 GTGCAGT
17420271 GTGCAGT
1 GTGCAGT
17420278 GTGCAGT
1 GTGCAGT
17420285 GTGCAGT
1 GTGCAGT
17420292 G
1 G
17420293 CGCACCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.14, C:0.14, G:0.44, T:0.28
Consensus pattern (7 bp):
GTGCAGT
Found at i:17420616 original size:25 final size:25
Alignment explanation
Indices: 17420588--17420651 Score: 98
Period size: 25 Copynumber: 2.6 Consensus size: 25
17420578 AATAATCAAT
17420588 ATATAATTAAAAATATATTATATTA
1 ATATAATTAAAAATATATTATATTA
17420613 ATATTAATTAAAAATA-ATTATATTA
1 ATA-TAATTAAAAATATATTATATTA
17420638 ATAT--TTAAAAATAT
1 ATATAATTAAAAATAT
17420652 TTCCTTCTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.24
24 1 0.03
25 15 0.41
26 12 0.32
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
ATATAATTAAAAATATATTATATTA
Found at i:17431159 original size:4 final size:4
Alignment explanation
Indices: 17431150--17431199 Score: 66
Period size: 4 Copynumber: 12.2 Consensus size: 4
17431140 GAGAAGGGAG
*
17431150 AAGA AAGA AAGA AAGA AAGA AAG- AAGA AGGAGA AAGA AAGA AAAA AAGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A--AGA AAGA AAGA AAGA AAGA
17431199 A
1 A
17431200 GAAGGAGAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
3 3 0.07
4 34 0.83
6 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:17431208 original size:21 final size:22
Alignment explanation
Indices: 17431159--17431200 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
17431149 GAAGAAAGAA
*
17431159 AGAAAGAAAG-AAAGAAGAAGG
1 AGAAAGAAAGAAAAAAAGAAGG
17431180 AGAAAGAAAGAAAAAAAGAAG
1 AGAAAGAAAGAAAAAAAGAAG
17431201 AAGGAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (22 bp):
AGAAAGAAAGAAAAAAAGAAGG
Found at i:17431246 original size:28 final size:26
Alignment explanation
Indices: 17431214--17431275 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 26
17431204 GAGAAGAAGG
*
17431214 TTAATTTT-TTTTATTTTGTAAGATTATT
1 TTAATTTTAATTTATTTT-TAA-ATTA-T
17431242 TTAATTTTAAATTTATTTTTAAATTAT
1 TTAATTTT-AATTTATTTTTAAATTAT
17431269 TTAATTT
1 TTAATTT
17431276 GTTAGTAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 8 0.26
28 12 0.39
29 3 0.10
30 8 0.26
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (26 bp):
TTAATTTTAATTTATTTTTAAATTAT
Found at i:17442527 original size:506 final size:507
Alignment explanation
Indices: 17441052--17442574 Score: 2440
Period size: 509 Copynumber: 3.0 Consensus size: 507
17441042 TTGAGTCGAT
* * *
17441052 TGAATTCGATGTGTAAGTCACAAACCCATTGGGTCATATTATCATTGTTAACCTGGTATGTCGTA
1 TGAATTCGATGTGCAAGTCACAAACCCATTGGGTCATATTGTCATTGTTAACCTAGTATGTCGTA
* * * * *
17441117 AATGTCCACTGAAAGTCCAGGGTTATGAATTTTCTACTAATCTGATGTTATTACTATTCTCCGAG
66 AATGTCCACTGAAAGTCCAGGGCTGTGAATTTTCTGCTGATCTAATGTTATTACTATTC-CCGAG
* * *
17441182 TTTGATGTAATATTAGGCATGGATTGGCTAACTGAGCACGACGCAATAGTAAATTGCAAGTAAAG
130 TTTGATGTAATATTAGGCATAGATTGGCTAACTGAGCACGACGCAGTAGTAAATTGCAAGCAAAG
* * *
17441247 ACAGATTAGTTTGAAATGCCTCACATGTGAAGTGATTACTGTTGAGTTTGGTAGGTTGAACAGTG
195 ACAGATTAGTTTGAAATGCCCCACATGTGAAGTGATTACTGTTGAGTCTGGTAGGTTGAATAGTG
* * * *
17441312 AAATAGGGTAATTTAAGCTATTTCAACATAGAAGATGGTTCGCAGAGGCTGTAAAGCATTCCTGG
260 AAACAGGGTAATTTAAGCTATTTCAACACAGAAGATGGTTCGTAGAGGCTGTAAAGCATTCTTGG
* * *
17441377 CATACATACTCGATACACGGGGTTCGGGAATAGAGTTGAAACAAGTACCAGTTGTCAATGAGTAT
325 CATACATACTCGATACACGGGGTTTGGGAACAAAGTTGAAACAAGTACCAGTTGTCAATGAGTAT
** * * * * *
17441442 GCAGATGTGTTTCTGGAAGAATTACCGAGTTTGCCACTGACCAGAGAGGTGGAGTTTGGTATTGA
390 GCAGATGTGTTTCCAGAAGAATTACCGGGTTTGCCACTAACTAGAGAGGTAGAGTTTGATATTGA
* * * * *
17441507 TTTGTTACCTGATACCGCTCCGATCTCAATTCCACCATATAGAATGACACCGAC
455 TTTGTTACCTGGTACCGTTTCGA-CTCAATTCCACCGTATAGAATGGCACCGAC
17441561 TGAATTCGATGTGCAAGTCACAAACCCATTGGGTCATATTGTCATTGTTAACCTAGTATGTCGTA
1 TGAATTCGATGTGCAAGTCACAAACCCATTGGGTCATATTGTCATTGTTAACCTAGTATGTCGTA
*
17441626 AATGTCCACTAAAAGTCCAGGGCTGTGAATTTTCTGCTGATCTAATGTTATTACTATTCCTCGAG
66 AATGTCCACTGAAAGTCCAGGGCTGTGAATTTTCTGCTGATCTAATGTTATTACTATTCC-CGAG
* *
17441691 TTTGATGTAATATTGGGCATAGATTGGCTAACTAAGCACGACGCAGTAGTAAATTGCAAGCAAAG
130 TTTGATGTAATATTAGGCATAGATTGGCTAACTGAGCACGACGCAGTAGTAAATTGCAAGCAAAG
17441756 ACAGATTAGTTTGAAATGCCCCACATGTGAAGTGATTACTGTTGAGTCTGGTAGGTTGAATAGTG
195 ACAGATTAGTTTGAAATGCCCCACATGTGAAGTGATTACTGTTGAGTCTGGTAGGTTGAATAGTG
* *
17441821 AAACAGGGTAATTTCAGCTATTTTAACACAGAAGATGGTTCGTAGAGGCTGTAAAGCATTCTTGG
260 AAACAGGGTAATTTAAGCTATTTCAACACAGAAGATGGTTCGTAGAGGCTGTAAAGCATTCTTGG
17441886 CATACATACTCGATACACGGGGTTTGGGAACAAAGTTGAAACAAGTACCAGTTGTCAATGAGTAT
325 CATACATACTCGATACACGGGGTTTGGGAACAAAGTTGAAACAAGTACCAGTTGTCAATGAGTAT
* * *
17441951 GCAGATGTTTTTCCAGAAGAATTATCGGGTTTGCCACTTACTAGAGAGGTAGAGTTTGATATTGA
390 GCAGATGTGTTTCCAGAAGAATTACCGGGTTTGCCACTAACTAGAGAGGTAGAGTTTGATATTGA
* * *
17442016 TTTGTTACTTGGTACCGTTTCGA-TCAATTCTACCGTATAGAATGGCACCGGC
455 TTTGTTACCTGGTACCGTTTCGACTCAATTCCACCGTATAGAATGGCACCGAC
* *
17442068 TGAATTTGATGTGCAAGTCACAAACCCATTGGGTCATATTGTCATTGTTAACTTAGTATGTCGTA
1 TGAATTCGATGTGCAAGTCACAAACCCATTGGGTCATATTGTCATTGTTAACCTAGTATGTCGTA
* * * *
17442133 AATGTCCACTGAAAGTCCAAGGCTGTGAATTTTTTGCTGATCTAATATTATTACTATTCACCAAG
66 AATGTCCACTGAAAGTCCAGGGCTGTGAATTTTCTGCTGATCTAATGTTATTACTATTC-CCGAG
17442198 TTTGATGTAATATTAGGCATAGATTGGCTAACTGAGCACGACGCAGTAGTAAATTGCAAGCAAAG
130 TTTGATGTAATATTAGGCATAGATTGGCTAACTGAGCACGACGCAGTAGTAAATTGCAAGCAAAG
*
17442263 ACA-AGTTAGTTTGAAATGCCCCACA-GTGAAGTGATTACTTTTGAGTCTGGTAGGTTGAATAGT
195 ACAGA-TTAGTTTGAAATGCCCCACATGTGAAGTGATTACTGTTGAGTCTGGTAGGTTGAATAGT
*
17442326 GAAACAGGGTAATTTTAGCTATTTCAACACAGAAGATGGTTCGTAGAGGCTGTAAAGCATTCTTG
259 GAAACAGGGTAATTTAAGCTATTTCAACACAGAAGATGGTTCGTAGAGGCTGTAAAGCATTCTTG
* * *
17442391 GCATACATACTTGATACACGGGGTTTGGGAACAAAGTTGAAACAAGTACTAGTTGTCAATAAGTA
324 GCATACATACTCGATACACGGGGTTTGGGAACAAAGTTGAAACAAGTACCAGTTGTCAATGAGTA
* *
17442456 TGCAGATGTGTTTCCAAAAGAATTACCGGGTTTGCCACTAACTAGAGTGGTAGAGTTTGATATTG
389 TGCAGATGTGTTTCCAGAAGAATTACCGGGTTTGCCACTAACTAGAGAGGTAGAGTTTGATATTG
* *
17442521 ATTTGTTACCTAGTACCGTTTCTATCTCAATTCCACCGTATAGAATGGCACCGA
454 ATTTGTTACCTGGTACCGTTTCGA-CTCAATTCCACCGTATAGAATGGCACCGA
17442575 TCAAATTGAA
Statistics
Matches: 941, Mismatches: 68, Indels: 11
0.92 0.07 0.01
Matches are distributed among these distances:
506 244 0.26
507 232 0.25
508 28 0.03
509 437 0.46
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (507 bp):
TGAATTCGATGTGCAAGTCACAAACCCATTGGGTCATATTGTCATTGTTAACCTAGTATGTCGTA
AATGTCCACTGAAAGTCCAGGGCTGTGAATTTTCTGCTGATCTAATGTTATTACTATTCCCGAGT
TTGATGTAATATTAGGCATAGATTGGCTAACTGAGCACGACGCAGTAGTAAATTGCAAGCAAAGA
CAGATTAGTTTGAAATGCCCCACATGTGAAGTGATTACTGTTGAGTCTGGTAGGTTGAATAGTGA
AACAGGGTAATTTAAGCTATTTCAACACAGAAGATGGTTCGTAGAGGCTGTAAAGCATTCTTGGC
ATACATACTCGATACACGGGGTTTGGGAACAAAGTTGAAACAAGTACCAGTTGTCAATGAGTATG
CAGATGTGTTTCCAGAAGAATTACCGGGTTTGCCACTAACTAGAGAGGTAGAGTTTGATATTGAT
TTGTTACCTGGTACCGTTTCGACTCAATTCCACCGTATAGAATGGCACCGAC
Found at i:17448260 original size:18 final size:18
Alignment explanation
Indices: 17448224--17448272 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
17448214 AAAATAACTA
** *
17448224 CATTTGAATCAATATTTG
1 CATTTGAATCTGTACTTG
17448242 CATTTGAATCTGTACTTG
1 CATTTGAATCTGTACTTG
*
17448260 CACTTGAATCTGT
1 CATTTGAATCTGT
17448273 TCCTGTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (18 bp):
CATTTGAATCTGTACTTG
Found at i:17449624 original size:11 final size:11
Alignment explanation
Indices: 17449608--17449632 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17449598 ATAAATACAA
17449608 TAAATAAAAAT
1 TAAATAAAAAT
17449619 TAAATAAAAAT
1 TAAATAAAAAT
17449630 TAA
1 TAA
17449633 TTGCTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAATAAAAAT
Found at i:17451255 original size:50 final size:50
Alignment explanation
Indices: 17451209--17451497 Score: 260
Period size: 50 Copynumber: 5.8 Consensus size: 50
17451199 ACAAGATTTG
* * * *
17451209 CTGTTACGGCTTTGATTTGTCTCTCTTCGATTTTAAGGGTGTAAGATTCAC
1 CTGTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGTGTAAGATT-AA
** * * * *
17451260 CT-TTACAACTTTAATTTGTCCCTCTTCAGTTTTAGGGGTATAAGATTTA
1 CTGTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGTGTAAGATTAA
* ** * *
17451309 CCGTTGTGGCTTTAATCTGTCCCTTTTCAATTTTAAGGGTGTAAGATT-A
1 CTGTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGTGTAAGATTAA
* ** * ** * * *
17451358 GTCGTTATTGCTTTAATCTGTCCCTCTTTGATTTTAGGGGTATAAGATTCA
1 CT-GTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGTGTAAGATTAA
* * * *
17451409 CTGTTGCAGCTTTAATTTGTCCTTCTTCAATTTTAAGGGTGTAAGATTCA
1 CTGTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGTGTAAGATTAA
* * *
17451459 CTGTTACGGCTTTAATCTGACCCTCTTCAACTTT-AGGGT
1 CTGTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGT
17451498 ATACGATTCG
Statistics
Matches: 190, Mismatches: 45, Indels: 8
0.78 0.19 0.03
Matches are distributed among these distances:
49 7 0.04
50 179 0.94
51 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (50 bp):
CTGTTACGGCTTTAATTTGTCCCTCTTCAATTTTAAGGGTGTAAGATTAA
Found at i:17451342 original size:100 final size:99
Alignment explanation
Indices: 17451190--17451542 Score: 352
Period size: 100 Copynumber: 3.5 Consensus size: 99
17451180 CCTCTATAAC
* ** * * * * * *
17451190 TTTAGGGGTACAAGATTTGCTGTTACGGCTTTGATTTGTCTCTCTTCGATTTTAAGGGTGTAAGA
1 TTTAGGGGTATAAGATTCACCGTTGCGGCTTTAATCTGTCCCTCTTCAATTTTAAGGGTGTAAGA
* *
17451255 TTCACCTTTACAACTTTAATTTGTCCCTCTTCAGT
66 TTCA-CTTTACAGCTTTAATCTGTCCCTCTTCAGT
* * *
17451290 TTTAGGGGTATAAGATTTACCGTTGTGGCTTTAATCTGTCCCTTTTCAATTTTAAGGGTGTAAGA
1 TTTAGGGGTATAAGATTCACCGTTGCGGCTTTAATCTGTCCCTCTTCAATTTTAAGGGTGTAAGA
* ** *
17451355 TT-AGTCGTTATTGCTTTAATCTGTCCCTCTT-TGAT
66 TTCA--CTTTACAGCTTTAATCTGTCCCTCTTCAG-T
* * * *
17451390 TTTAGGGGTATAAGATTCACTGTTGCAGCTTTAATTTGTCCTTCTTCAATTTTAAGGGTGTAAGA
1 TTTAGGGGTATAAGATTCACCGTTGCGGCTTTAATCTGTCCCTCTTCAATTTTAAGGGTGTAAGA
* * **
17451455 TTCACTGTTACGGCTTTAATCTGACCCTCTTCAAC
66 TTCACT-TTACAGCTTTAATCTGTCCCTCTTCAGT
* * * * * *
17451490 TTTA-GGGTATACGATTCGCCTTTGCGGCTTCAATCTGCCCCTCTTCAACTTTA
1 TTTAGGGGTATAAGATTCACCGTTGCGGCTTTAATCTGTCCCTCTTCAATTTTA
17451543 GGATTTGGTG
Statistics
Matches: 207, Mismatches: 41, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
99 42 0.20
100 164 0.79
101 1 0.00
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.42
Consensus pattern (99 bp):
TTTAGGGGTATAAGATTCACCGTTGCGGCTTTAATCTGTCCCTCTTCAATTTTAAGGGTGTAAGA
TTCACTTTACAGCTTTAATCTGTCCCTCTTCAGT
Found at i:17451423 original size:150 final size:149
Alignment explanation
Indices: 17451217--17451497 Score: 366
Period size: 150 Copynumber: 1.9 Consensus size: 149
17451207 TGCTGTTACG
* * * *
17451217 GCTTTGATTTGTCTCTCTTCGATTTTAAGGGTGTAAGATTCACCTTTACAACTTTAATTTGTCCC
1 GCTTTAATCTGTCCCTCTTCGATTTTAAGGGTATAAGATTCACCTTTACAACTTTAATTTGTCCC
* * * ** * * *
17451282 TCTTCAGTTTTAGGGGTATAAGATTTACCGTTGTGGCTTTAATCTGTCCCTTTTCAATTTTAAGG
66 TCTTCAATTTTAAGGGTATAAGATTCACCGTTACGGCTTTAATCTGACCCTCTTCAACTTT-AGG
17451347 GTGTAAGATTAGTCGTTATT
130 GTGTAAGATTAGTCGTTATT
* * * *
17451367 GCTTTAATCTGTCCCTCTTTGATTTTAGGGGTATAAGATTCA-CTGTTGCAGCTTTAATTTGTCC
1 GCTTTAATCTGTCCCTCTTCGATTTTAAGGGTATAAGATTCACCT-TTACAACTTTAATTTGTCC
* * *
17451431 TTCTTCAATTTTAAGGGTGTAAGATTCACTGTTACGGCTTTAATCTGACCCTCTTCAACTTTAGG
65 CTCTTCAATTTTAAGGGTATAAGATTCACCGTTACGGCTTTAATCTGACCCTCTTCAACTTTAGG
17451496 GT
130 GT
17451498 ATACGATTCG
Statistics
Matches: 111, Mismatches: 19, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
149 7 0.06
150 104 0.94
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (149 bp):
GCTTTAATCTGTCCCTCTTCGATTTTAAGGGTATAAGATTCACCTTTACAACTTTAATTTGTCCC
TCTTCAATTTTAAGGGTATAAGATTCACCGTTACGGCTTTAATCTGACCCTCTTCAACTTTAGGG
TGTAAGATTAGTCGTTATT
Found at i:17454969 original size:82 final size:82
Alignment explanation
Indices: 17454832--17454993 Score: 236
Period size: 82 Copynumber: 2.0 Consensus size: 82
17454822 ACACTCTCGA
* * *
17454832 GTTATGCTTATTGAGAAGACGAAAGATAGGATCACATTTCTCATTTAGTTGTGAGATGAACCGAG
1 GTTATGCTTATTAAGAAGACGAAAGATAAGATCACATTTCTCATTTAGTTGTGAGACGAACCGAG
*
17454897 CGATGTAATTCAGTCGG
66 CGATATAATTCAGTCGG
* * *
17454914 GTTATGCTTCTTAAGAAGAAGGAAA-ATAAGATCACATTTCTCGTTTAGTTGTGAGACGAACCGA
1 GTTATGCTTATTAAGAAG-ACGAAAGATAAGATCACATTTCTCATTTAGTTGTGAGACGAACCGA
*
17454978 GCGATATAATTTAGTC
65 GCGATATAATTCAGTC
17454994 TCCCTAGGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
82 66 0.93
83 5 0.07
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (82 bp):
GTTATGCTTATTAAGAAGACGAAAGATAAGATCACATTTCTCATTTAGTTGTGAGACGAACCGAG
CGATATAATTCAGTCGG
Found at i:17457226 original size:14 final size:15
Alignment explanation
Indices: 17457203--17457234 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
17457193 AGAGTTGTTT
17457203 AAAAGCATAAAAATA
1 AAAAGCATAAAAATA
17457218 AAAAG-ATAAAAATA
1 AAAAGCATAAAAATA
17457232 AAA
1 AAA
17457235 TAAAGTAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.78, C:0.03, G:0.06, T:0.12
Consensus pattern (15 bp):
AAAAGCATAAAAATA
Found at i:17463550 original size:21 final size:21
Alignment explanation
Indices: 17463526--17463574 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
17463516 ACTTGTTTCA
*
17463526 GTAGAAGAGT-ATCTTGTATTG
1 GTAGAAGAGTCA-CTTGTATAG
**
17463547 GTAGAACTGTCACTTGTATAG
1 GTAGAAGAGTCACTTGTATAG
17463568 GTAGAAG
1 GTAGAAG
17463575 TTTGCACTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 22 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.33
Consensus pattern (21 bp):
GTAGAAGAGTCACTTGTATAG
Found at i:17470171 original size:19 final size:19
Alignment explanation
Indices: 17470115--17470172 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
17470105 TATGATGTTT
17470115 TTATTTTTTA-TTTTATTTA
1 TTATTTTTTATTTTTA-TTA
* *
17470134 TTCTTGTTTTTATGATTTATTA
1 TT-AT-TTTTTAT-TTTTATTA
17470156 TTATTTTTTATTTTTAT
1 TTATTTTTTATTTTTAT
17470173 GAAATTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
19 7 0.23
20 8 0.26
21 7 0.23
22 5 0.16
23 4 0.13
ACGTcount: A:0.19, C:0.02, G:0.03, T:0.76
Consensus pattern (19 bp):
TTATTTTTTATTTTTATTA
Found at i:17473470 original size:4 final size:4
Alignment explanation
Indices: 17473449--17473510 Score: 56
Period size: 4 Copynumber: 15.2 Consensus size: 4
17473439 AAAATACATG
* **
17473449 AATA TAATA AATA CAATA AATA AAAA AATA AATA AA-A AATA AAT- GCTA
1 AATA -AATA AATA -AATA AATA AATA AATA AATA AATA AATA AATA AATA
17473497 AATAA AATA AATA A
1 AAT-A AATA AATA A
17473511 TATGAAGAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
3 4 0.09
4 31 0.66
5 12 0.26
ACGTcount: A:0.73, C:0.03, G:0.02, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:17473478 original size:12 final size:12
Alignment explanation
Indices: 17473449--17473492 Score: 54
Period size: 11 Copynumber: 3.6 Consensus size: 12
17473439 AAAATACATG
*
17473449 AATATAATAAATAC
1 AATA-AATAAA-AA
17473463 AATAAATAAAAA
1 AATAAATAAAAA
17473475 AATAAAT-AAAA
1 AATAAATAAAAA
17473486 AATAAAT
1 AATAAAT
17473493 GCTAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 11 0.38
12 8 0.28
13 6 0.21
14 4 0.14
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAAATAAAAA
Found at i:17484778 original size:13 final size:13
Alignment explanation
Indices: 17484760--17484784 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17484750 CCTATTATAT
17484760 CATTTTTAGCATG
1 CATTTTTAGCATG
17484773 CATTTTTAGCAT
1 CATTTTTAGCAT
17484785 TTTATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:17487276 original size:16 final size:17
Alignment explanation
Indices: 17487246--17487287 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
17487236 TGCATGTGGA
17487246 AAATAATAAAATAAA-T
1 AAATAATAAAATAAACT
* *
17487262 AAATAATACATTAAACT
1 AAATAATAAAATAAACT
*
17487279 AAAAAATAA
1 AAATAATAA
17487288 CTCTTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAATAAAATAAACT
Found at i:17489337 original size:21 final size:21
Alignment explanation
Indices: 17489298--17489347 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
17489288 GTTTACTTCT
*
17489298 GATGAGATTAGCTACTGTAGC
1 GATGAGATTAGCTACTGTAAC
* * *
17489319 GATGAGATTGGGTATTGTAAC
1 GATGAGATTAGCTACTGTAAC
*
17489340 AATGAGAT
1 GATGAGAT
17489348 AAAAAATAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (21 bp):
GATGAGATTAGCTACTGTAAC
Found at i:17490353 original size:23 final size:23
Alignment explanation
Indices: 17490327--17490399 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
17490317 TATTTGACTA
17490327 AATTGTAGGCATTTGTCTTCCAC
1 AATTGTAGGCATTTGTCTTCCAC
*
17490350 AATTGTAGAG-ATTTGT-TTGGCTA-
1 AATTGTAG-GCATTTGTCTT--CCAC
*
17490373 ATTTGTAGGCATTTGTCTTCCAC
1 AATTGTAGGCATTTGTCTTCCAC
17490396 AATT
1 AATT
17490400 TCAAGGATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
22 5 0.12
23 30 0.75
24 5 0.12
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (23 bp):
AATTGTAGGCATTTGTCTTCCAC
Found at i:17490362 original size:46 final size:46
Alignment explanation
Indices: 17490293--17490399 Score: 169
Period size: 46 Copynumber: 2.3 Consensus size: 46
17490283 GTCTAGTCAA
*
17490293 TTGTCTTCCACAATTTTAAAGATTTATTTGACTAAATTGTAGGCAT
1 TTGTCTTCCACAATTGTAAAGATTTATTTGACTAAATTGTAGGCAT
* * * *
17490339 TTGTCTTCCACAATTGTAGAGATTTGTTTGGCTAATTTGTAGGCAT
1 TTGTCTTCCACAATTGTAAAGATTTATTTGACTAAATTGTAGGCAT
17490385 TTGTCTTCCACAATT
1 TTGTCTTCCACAATT
17490400 TCAAGGATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 56 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (46 bp):
TTGTCTTCCACAATTGTAAAGATTTATTTGACTAAATTGTAGGCAT
Found at i:17490409 original size:46 final size:45
Alignment explanation
Indices: 17490293--17490413 Score: 163
Period size: 46 Copynumber: 2.6 Consensus size: 45
17490283 GTCTAGTCAA
* *
17490293 TTGTCTTCCACAATTTTAAAGATTTATTTGACTAAATTGTAGGCAT
1 TTGTCTTCCACAA-TTTAAGGATTTGTTTGACTAAATTGTAGGCAT
* *
17490339 TTGTCTTCCACAATTGT-AGAGATTTGTTTGGCTAATTTGTAGGCAT
1 TTGTCTTCCACAATT-TAAG-GATTTGTTTGACTAAATTGTAGGCAT
17490385 TTGTCTTCCACAATTTCAAGGATTTGTTT
1 TTGTCTTCCACAATTT-AAGGATTTGTTT
17490414 CTCTTTTATC
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
45 4 0.06
46 61 0.91
47 2 0.03
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.45
Consensus pattern (45 bp):
TTGTCTTCCACAATTTAAGGATTTGTTTGACTAAATTGTAGGCAT
Found at i:17491054 original size:6 final size:6
Alignment explanation
Indices: 17491043--17491068 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
17491033 GAAGCCTAAG
17491043 AAGGAA AAGGAA AAGGAA AAGGAA AA
1 AAGGAA AAGGAA AAGGAA AAGGAA AA
17491069 AAGAGGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (6 bp):
AAGGAA
Found at i:17497199 original size:24 final size:24
Alignment explanation
Indices: 17497163--17497693 Score: 616
Period size: 24 Copynumber: 22.2 Consensus size: 24
17497153 ACAAGTTGAT
* *
17497163 TACGTTTATGCTCGTCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497187 TACGTTTAAGCTCGTCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
17497211 TACGTTTACGCTCACCA-CATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497234 TACATTCACGCTCGTCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
** *
17497258 TACGTTTACGCTTACTAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
**
17497282 TACGTTTACGCTTACCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
17497306 TACGTTTATGCTCGCCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
17497330 TACGTTTACGCTCACCAGCATGAT
1 TACGTTTACGCTCGCCAGCATGAA
*
17497354 TACGTTTACGCTCGCCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
** *
17497378 TACAATTACGCTCGTCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
17497402 TACGTTTACACTCGCCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497426 TACATTTATGCTCACCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * **
17497450 TACGTTTATGCTCGTCAAAATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* *
17497474 TATGTTTACGCTCGCCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497498 TACGCTTACGCTCACCAGTA-GAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497521 TACGTTTGCACTCGCCTGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497545 TACGTTTATGCTCGACGGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
17497569 TACGTTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
*
17497593 TACATTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497617 TATGTTTACGCTCGTCAACATGAA
1 TACGTTTACGCTCGCCAGCATGAA
* * *
17497641 TATGTTTACGCTTGCCAGCATAAA
1 TACGTTTACGCTCGCCAGCATGAA
*
17497665 TACGTTTACGCTCGCTAGCATGAA
1 TACGTTTACGCTCGCCAGCATGAA
17497689 TACGT
1 TACGT
17497694 GAAACATTGT
Statistics
Matches: 427, Mismatches: 78, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
23 36 0.08
24 391 0.92
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (24 bp):
TACGTTTACGCTCGCCAGCATGAA
Found at i:17503166 original size:23 final size:24
Alignment explanation
Indices: 17503122--17503171 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
17503112 GGAACAGAAT
17503122 AGAACACCATCCAAGAAAAT-AAC
1 AGAACACCATCCAAGAAAATAAAC
* *
17503145 AGAACACCA-CCGAAGCAGATAAAC
1 AGAACACCATCC-AAGAAAATAAAC
17503169 AGA
1 AGA
17503172 GAGCGTAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 2 0.09
23 15 0.65
24 6 0.26
ACGTcount: A:0.54, C:0.26, G:0.14, T:0.06
Consensus pattern (24 bp):
AGAACACCATCCAAGAAAATAAAC
Found at i:17505843 original size:24 final size:24
Alignment explanation
Indices: 17505816--17506087 Score: 278
Period size: 24 Copynumber: 11.2 Consensus size: 24
17505806 GCAAGTTCAT
* * *
17505816 TACGTTTACACTTGTCATCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* *
17505840 TACGTTTATGCTCGCCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* * *
17505864 TACATTTACGGTCGTAAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
*
17505888 TACGTTTACGCACGCTCGCCAGCATGAA
1 TACGTTT----ACGCTCGTCAGCATGAA
*
17505916 TATGTTTACGCTCGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* *
17505940 TACGGTTACGCTCGCCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* *
17505964 TACATTTACACTCGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* * *
17505988 TATGTTTATGCTCGCCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
*
17506012 TAC-TTTATGCTCGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
*
17506035 TATGTTTACGCTC-TCCAGCATGAA
1 TACGTTTACGCTCGT-CAGCATGAA
* * * *
17506059 AACGTTTATGCTCGCCAACATGAA
1 TACGTTTACGCTCGTCAGCATGAA
17506083 TACGT
1 TACGT
17506088 AAAACATTAT
Statistics
Matches: 203, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
23 22 0.11
24 161 0.79
28 20 0.10
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCATGAA
Found at i:17505924 original size:52 final size:48
Alignment explanation
Indices: 17505820--17506087 Score: 313
Period size: 48 Copynumber: 5.5 Consensus size: 48
17505810 GTTCATTACG
* * * *
17505820 TTTACACTTGTCATCATGAATACGTTTATGCTCGCCAGCATGAATACA
1 TTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACA
* * **
17505868 TTTACGGTCGTAAGCATGAATACGTTTACGCACGCTCGCCAGCATGAATATG
1 TTTACGCTCGTCAGCATGAATACGTTT----ACGCTCGCCAGCATGAATACA
*
17505920 TTTACGCTCGTCAGCATGAATACGGTTACGCTCGCCAGCATGAATACA
1 TTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACA
* * *
17505968 TTTACACTCGTCAGCATGAATATGTTTATGCTCGCCAGCATGAATAC-
1 TTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACA
* * * * *
17506015 TTTATGCTCGTCAGCATGAATATGTTTACGCTCTCCAGCATGAAAACG
1 TTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACA
* * *
17506063 TTTATGCTCGCCAACATGAATACGT
1 TTTACGCTCGTCAGCATGAATACGT
17506088 AAAACATTAT
Statistics
Matches: 190, Mismatches: 25, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
47 42 0.22
48 106 0.56
52 42 0.22
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (48 bp):
TTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACA
Found at i:17505995 original size:100 final size:95
Alignment explanation
Indices: 17505819--17506058 Score: 309
Period size: 100 Copynumber: 2.5 Consensus size: 95
17505809 AGTTCATTAC
* * * * **
17505819 GTTTACACTTGTCATCATGAATACGTTTATGCTCGCCAGCATGAATACATTTACGGTCGTAAGCA
1 GTTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACATTTACACTCGTAAGCA
17505884 TGAATACGTTTACGCACGCTCGCCAGCATGAATA
66 TGAATACGTTT----ACGCTCGCCAGCATGAATA
* *
17505918 TGTTTACGCTCGTCAGCATGAATACGGTTACGCTCGCCAGCATGAATACATTTACACTCGTCAGC
1 -GTTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACATTTACACTCGTAAGC
* *
17505983 ATGAATATGTTTATGCTCGCCAGCATGAATA
65 ATGAATACGTTTACGCTCGCCAGCATGAATA
* * * *
17506014 CTTTATGCTCGTCAGCATGAATATGTTTACGCTCTCCAGCATGAA
1 GTTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAA
17506059 AACGTTTATG
Statistics
Matches: 125, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
95 40 0.32
96 18 0.14
100 67 0.54
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (95 bp):
GTTTACGCTCGTCAGCATGAATACGTTTACGCTCGCCAGCATGAATACATTTACACTCGTAAGCA
TGAATACGTTTACGCTCGCCAGCATGAATA
Found at i:17507371 original size:80 final size:80
Alignment explanation
Indices: 17507237--17507547 Score: 372
Period size: 80 Copynumber: 3.9 Consensus size: 80
17507227 AGATATTGAC
*
17507237 TATAAGGACCCTCTGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCA
1 TATAAGGACCCTCCGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCA
*
17507302 ACATCGTGAGTGGAT
66 ACATCATGAGTGGAT
*
17507317 TATAAGGACCCTCCGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGCCAGCTTGTGTGAGCA
1 TATAAGGACCCTCCGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCA
**
17507382 GTATCATGAGTGGAT
66 ACATCATGAGTGGAT
** * ** * * *
17507397 TATTTGGACCCTTCGATAACTAAGATTTTACATATGTTGCGGATTCTTGACAGCTTGTGTGAG-A
1 TATAAGGACCCTCCGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCA
17507461 AGCATCATGAGTGGAT
66 A-CATCATGAGTGGAT
* * * * * * * * * * *
17507477 TATATGGACCGTATCGATGGTTGGGATCCTGCATATATTGCAGTTTCCTGACAGCTTTTGTGAGC
1 TATAAGGACCCT-CCGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGC
*
17507542 AGCATC
65 AACATC
17507548 GTATAGTGGT
Statistics
Matches: 196, Mismatches: 32, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
79 1 0.01
80 152 0.78
81 42 0.21
82 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (80 bp):
TATAAGGACCCTCCGATGGCTGAGATTCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCA
ACATCATGAGTGGAT
Found at i:17507639 original size:25 final size:25
Alignment explanation
Indices: 17507571--17507631 Score: 104
Period size: 25 Copynumber: 2.4 Consensus size: 25
17507561 ATTCTGTTTG
* *
17507571 GGCTCGTAAGAGCGATATGCTGTCT
1 GGCTCGTAAGAGCGATATTCTATCT
17507596 GGCTCGTAAGAGCGATATTCTATCT
1 GGCTCGTAAGAGCGATATTCTATCT
17507621 GGCTCGTAAGA
1 GGCTCGTAAGA
17507632 CCATTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (25 bp):
GGCTCGTAAGAGCGATATTCTATCT
Found at i:17512186 original size:21 final size:21
Alignment explanation
Indices: 17512162--17512213 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
17512152 TTTCTTCTTT
17512162 TCCTTTTGTTTGCACCTATTC
1 TCCTTTTGTTTGCACCTATTC
*
17512183 TCCTTTTGTTTGCACCTCTTC
1 TCCTTTTGTTTGCACCTATTC
*
17512204 TCTTTTTGTT
1 TCCTTTTGTT
17512214 CAACTGGTGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.06, C:0.27, G:0.10, T:0.58
Consensus pattern (21 bp):
TCCTTTTGTTTGCACCTATTC
Found at i:17512467 original size:3 final size:3
Alignment explanation
Indices: 17512459--17512518 Score: 52
Period size: 3 Copynumber: 20.0 Consensus size: 3
17512449 CGGGGCAACA
* * *
17512459 TCT TCT TCT TCT TTT TCT TCCT TC- TCT TCT TTT TCT TCA TCT T-T
1 TCT TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT
*
17512503 TCTT TCT TTT TCT TCT
1 TC-T TCT TCT TCT TCT
17512519 GCCTTAATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
2 4 0.09
3 35 0.78
4 6 0.13
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:17512476 original size:9 final size:9
Alignment explanation
Indices: 17512459--17512518 Score: 66
Period size: 9 Copynumber: 6.3 Consensus size: 9
17512449 CGGGGCAACA
*
17512459 TCTTCTTCT
1 TCTTTTTCT
17512468 TCTTTTTCT
1 TCTTTTTCT
* *
17512477 TCCTTCTCT
1 TCTTTTTCT
17512486 TCTTTTTCT
1 TCTTTTTCT
17512495 TCATCTTTTCTT
1 TC-T-TTTTC-T
17512507 TCTTTTTCT
1 TCTTTTTCT
17512516 TCT
1 TCT
17512519 GCCTTAATAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
9 28 0.65
10 6 0.14
11 6 0.14
12 3 0.07
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (9 bp):
TCTTTTTCT
Found at i:17512487 original size:21 final size:19
Alignment explanation
Indices: 17512460--17512517 Score: 75
Period size: 18 Copynumber: 3.0 Consensus size: 19
17512450 GGGGCAACAT
17512460 CTTCTTCTTCTTTTTCTTC
1 CTTCTTCTTCTTTTTCTTC
17512479 CTTC-TCTTCTTTTTCTTC
1 CTTCTTCTTCTTTTTCTTC
17512497 ATCTT-TTCTTTCTTTTTCTTC
1 --CTTCTTC-TTCTTTTTCTTC
17512518 TGCCTTAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
18 14 0.40
19 4 0.11
20 5 0.14
21 12 0.34
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (19 bp):
CTTCTTCTTCTTTTTCTTC
Found at i:17518655 original size:18 final size:19
Alignment explanation
Indices: 17518615--17518656 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
17518605 ACCTGTGGCT
17518615 GCATCTGAGTATGTGACTA
1 GCATCTGAGTATGTGACTA
* *
17518634 -CATCTGATTCTGTGA-TA
1 GCATCTGAGTATGTGACTA
17518651 GCATCT
1 GCATCT
17518657 AGTCAGGTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (19 bp):
GCATCTGAGTATGTGACTA
Found at i:17520261 original size:24 final size:24
Alignment explanation
Indices: 17520228--17520274 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
17520218 GTTAAGAGTA
17520228 AAAATTGTCAGTA-CAAATGTAATAC
1 AAAATTGTCAG-AGCAAAT-TAATAC
17520253 AAAA-TGTCAGAGCAAATTAATA
1 AAAATTGTCAGAGCAAATTAATA
17520275 AAGATGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 6 0.29
24 11 0.52
25 4 0.19
ACGTcount: A:0.51, C:0.11, G:0.13, T:0.26
Consensus pattern (24 bp):
AAAATTGTCAGAGCAAATTAATAC
Found at i:17528138 original size:9 final size:9
Alignment explanation
Indices: 17528126--17528152 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
17528116 GGAAGAGTTT
17528126 AAAGAAGGA
1 AAAGAAGGA
17528135 AAAGAAGGA
1 AAAGAAGGA
17528144 AAAGAAGGA
1 AAAGAAGGA
17528153 GATAGAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (9 bp):
AAAGAAGGA
Found at i:17534631 original size:15 final size:15
Alignment explanation
Indices: 17534603--17534644 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
17534593 TATTTAATAT
*
17534603 TTATTTTTTGTAGCAC
1 TTATTTTTT-TAGCAA
17534619 TTATTTTTTTAGCAA
1 TTATTTTTTTAGCAA
*
17534634 TTAATTTTTTA
1 TTATTTTTTTA
17534645 ATTTATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
TTATTTTTTTAGCAA
Found at i:17534963 original size:21 final size:19
Alignment explanation
Indices: 17534930--17534976 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
17534920 TAAAAAACTT
*
17534930 TTAAAAAGATATTTAAA-AA
1 TTAAAAAAATA-TTAAATAA
17534949 TATAAAAAAACTATTAAATAA
1 T-TAAAAAAA-TATTAAATAA
17534970 TTAAAAA
1 TTAAAAA
17534977 TTATTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 1 0.04
20 18 0.75
21 5 0.21
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TTAAAAAAATATTAAATAA
Found at i:17535000 original size:15 final size:15
Alignment explanation
Indices: 17534971--17534999 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17534961 ATTAAATAAT
17534971 TAAAAATTATTAAAA
1 TAAAAATTATTAAAA
17534986 TAAAAATT-TTAAAA
1 TAAAAATTATTAAAA
17535000 AAATATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAAATTATTAAAA
Found at i:17535021 original size:44 final size:43
Alignment explanation
Indices: 17534943--17535030 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 43
17534933 AAAAGATATT
* *
17534943 TAAAAATATAAAAAAACTATTAAATAATTAAAAATTATTAAAA
1 TAAAAATATAAAAAAACTATTAAATAATTAAAAATAATAAAAA
* *
17534986 TAAAAATTTTAAAAAAA-TA-TAAATAATATTCAAAATAATAAAAA
1 TAAAAA-TATAAAAAAACTATTAAAT-A-ATTAAAAATAATAAAAA
17535030 T
1 T
17535031 TCCAAAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
42 5 0.13
43 9 0.24
44 24 0.63
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (43 bp):
TAAAAATATAAAAAAACTATTAAATAATTAAAAATAATAAAAA
Found at i:17538400 original size:16 final size:15
Alignment explanation
Indices: 17538355--17538437 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 15
17538345 ACATAAAATG
*
17538355 AAAATAAAATTAA-A
1 AAAATAAAAATAATA
* *
17538369 AGAATGAAAATAAATA
1 AAAATAAAAAT-AATA
17538385 AATAATAAAAATAATA
1 AA-AATAAAAATAATA
* *
17538401 AAAA-AGAAA-AA-G
1 AAAATAAAAATAATA
*
17538413 AAAATAAATAAAAATA
1 AAAATAAA-AATAATA
17538429 AAAATAAAA
1 AAAATAAAA
17538438 TTGGGTTGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
12 4 0.08
13 4 0.08
14 14 0.26
15 7 0.13
16 16 0.30
17 8 0.15
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (15 bp):
AAAATAAAAATAATA
Found at i:17538427 original size:6 final size:6
Alignment explanation
Indices: 17538349--17538437 Score: 53
Period size: 6 Copynumber: 14.5 Consensus size: 6
17538339 CCCAGGACAT
* * *
17538349 AAAATG AAAATA AAATTAA AAGAATG AAAAT- -AAATA AATAATA AAAATA
1 AAAATA AAAATA AAAAT-A AA-AATA AAAATA AAAATA AA-AATA AAAATA
17538398 ATAAA-A AAGAA-A AAGAA-A ATAAATA AAAATA AAAATA AAA
1 A-AAATA AA-AATA AA-AATA A-AAATA AAAATA AAAATA AAA
17538438 TTGGGTTGCT
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
4 4 0.06
5 1 0.01
6 46 0.66
7 17 0.24
8 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:17543792 original size:18 final size:18
Alignment explanation
Indices: 17543757--17543796 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17543747 GTCGGCAGGC
* * *
17543757 TCTTCTTTTTCCTTTTCT
1 TCTTCCTTTCCCTATTCT
17543775 TCTTCCTTTCCCTATTCT
1 TCTTCCTTTCCCTATTCT
17543793 TCTT
1 TCTT
17543797 TATCGTGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.65
Consensus pattern (18 bp):
TCTTCCTTTCCCTATTCT
Found at i:17551330 original size:17 final size:19
Alignment explanation
Indices: 17551308--17551344 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
17551298 GTAAAAATCT
17551308 GAAAAAGAA-AACA-ATTA
1 GAAAAAGAACAACAGATTA
*
17551325 GAAAAATAACAACAGATTA
1 GAAAAAGAACAACAGATTA
17551344 G
1 G
17551345 TAAAGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 4 0.24
19 5 0.29
ACGTcount: A:0.65, C:0.08, G:0.14, T:0.14
Consensus pattern (19 bp):
GAAAAAGAACAACAGATTA
Found at i:17567125 original size:11 final size:11
Alignment explanation
Indices: 17567109--17567159 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
17567099 GATAGTATTT
17567109 TATTAATTTAA
1 TATTAATTTAA
17567120 TATTAAATTTATTA
1 TATT-AATTTA--A
*
17567134 TCTTAATATTAA
1 TATTAAT-TTAA
17567146 -ATTAATTTAA
1 TATTAATTTAA
17567156 TATT
1 TATT
17567160 TATCTTGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
10 4 0.12
11 12 0.36
12 7 0.21
13 3 0.09
14 7 0.21
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TATTAATTTAA
Found at i:17567132 original size:20 final size:20
Alignment explanation
Indices: 17567107--17567148 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17567097 TTGATAGTAT
17567107 TTTATTAAT-TTAATATTAAA
1 TTTATT-ATCTTAATATTAAA
17567127 TTTATTATCTTAATATTAAA
1 TTTATTATCTTAATATTAAA
17567147 TT
1 TT
17567149 AATTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATTATCTTAATATTAAA
Found at i:17567184 original size:60 final size:59
Alignment explanation
Indices: 17567136--17567248 Score: 140
Period size: 61 Copynumber: 1.9 Consensus size: 59
17567126 ATTTATTATC
** * *
17567136 TTAATATTAAA-TTAATTTAATATTTATCTTGAAGTTAAATATTTTATT-AATTGAATAGAT
1 TTAATATTAAATTTAACCTAATACTTATCTT-AA--TAAATATTATATTAAATTGAATAGAT
*
17567196 TTAATATTAAATTTAACCTAATACTTATCTTAATAAATATTATATTAATTTGA
1 TTAATATTAAATTTAACCTAATACTTATCTTAATAAATATTATATTAAATTGA
17567249 TATTAAAGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
58 12 0.26
59 5 0.11
60 13 0.28
61 16 0.35
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (59 bp):
TTAATATTAAATTTAACCTAATACTTATCTTAATAAATATTATATTAAATTGAATAGAT
Found at i:17572432 original size:31 final size:31
Alignment explanation
Indices: 17572391--17572474 Score: 132
Period size: 31 Copynumber: 2.7 Consensus size: 31
17572381 CATTTCACAG
17572391 CTCATGTGAGCATACATGATTACAATTACAA
1 CTCATGTGAGCATACATGATTACAATTACAA
* * *
17572422 CTTATGTGAGCATACATGATTACAATTATAG
1 CTCATGTGAGCATACATGATTACAATTACAA
*
17572453 CTCGTGTGAGCATACATGATTA
1 CTCATGTGAGCATACATGATTA
17572475 TGTATATGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (31 bp):
CTCATGTGAGCATACATGATTACAATTACAA
Found at i:17573294 original size:21 final size:21
Alignment explanation
Indices: 17573265--17573306 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
17573255 TTATTTAAAC
* *
17573265 AAATAATTAGATTCAAGTGGT
1 AAATAATTAAAGTCAAGTGGT
*
17573286 AAATCATTAAAGTCAAGTGGT
1 AAATAATTAAAGTCAAGTGGT
17573307 TTTCAAAAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.19, T:0.31
Consensus pattern (21 bp):
AAATAATTAAAGTCAAGTGGT
Found at i:17574337 original size:22 final size:22
Alignment explanation
Indices: 17574293--17574337 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
17574283 TAGTTATACA
* **
17574293 CGGTGTTTATCGGGCTTTGTGC
1 CGGTGTTTATCGAGCTTAATGC
17574315 CGGTGTTTATCGAGCTTAATGC
1 CGGTGTTTATCGAGCTTAATGC
17574337 C
1 C
17574338 TAGCAGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.20, G:0.31, T:0.38
Consensus pattern (22 bp):
CGGTGTTTATCGAGCTTAATGC
Found at i:17574356 original size:38 final size:38
Alignment explanation
Indices: 17574306--17574476 Score: 234
Period size: 38 Copynumber: 4.5 Consensus size: 38
17574296 TGTTTATCGG
* * *
17574306 GCTTTGTGCCGGTGTTTATCGAGCTTAATGCCTAGCAG
1 GCTTCGTGCCGGTGTTTATCGAGCTTAGTGCCTAGCAA
* *
17574344 GCTTCATGCCGGTATTTATCGAGCTTAGTGCCTAGCAA
1 GCTTCGTGCCGGTGTTTATCGAGCTTAGTGCCTAGCAA
* * *
17574382 GCTTCGTGCCGGTGATTATCGGGCTTAGTTCCTAGCAA
1 GCTTCGTGCCGGTGTTTATCGAGCTTAGTGCCTAGCAA
* *
17574420 GCTTCGTGTCGGTGTTTATCGGGCTTAGTGCCTAGCAA
1 GCTTCGTGCCGGTGTTTATCGAGCTTAGTGCCTAGCAA
* *
17574458 ACTTCGTGTCGGTGTTTAT
1 GCTTCGTGCCGGTGTTTAT
17574477 TATCAGGCTT
Statistics
Matches: 119, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 119 1.00
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.35
Consensus pattern (38 bp):
GCTTCGTGCCGGTGTTTATCGAGCTTAGTGCCTAGCAA
Found at i:17574494 original size:41 final size:39
Alignment explanation
Indices: 17574306--17574516 Score: 232
Period size: 38 Copynumber: 5.5 Consensus size: 39
17574296 TGTTTATCGG
* * * * *
17574306 GCTTTGTGCCGGTGT-TTATCGAGCTTAATGCCTAGCAG
1 GCTTCGTGTCGGTGTATTATCGGGCTTAGTGCCTAGCAA
* * * *
17574344 GCTTCATGCCGGTAT-TTATCGAGCTTAGTGCCTAGCAA
1 GCTTCGTGTCGGTGTATTATCGGGCTTAGTGCCTAGCAA
* *
17574382 GCTTCGTGCCGGTG-ATTATCGGGCTTAGTTCCTAGCAA
1 GCTTCGTGTCGGTGTATTATCGGGCTTAGTGCCTAGCAA
17574420 GCTTCGTGTCGGTGT-TTATCGGGCTTAGTGCCTAGCAA
1 GCTTCGTGTCGGTGTATTATCGGGCTTAGTGCCTAGCAA
* * * *
17574458 ACTTCGTGTCGGTGTTTATTATCAGGCTTTGAGCCTAGCAA
1 GCTTCGTGTCGGTG--TATTATCGGGCTTAGTGCCTAGCAA
*
17574499 GTTTCGTGTCGGTGTATT
1 GCTTCGTGTCGGTGTATT
17574517 GTATTAGGTA
Statistics
Matches: 151, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
38 114 0.75
39 4 0.03
40 1 0.01
41 32 0.21
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.35
Consensus pattern (39 bp):
GCTTCGTGTCGGTGTATTATCGGGCTTAGTGCCTAGCAA
Found at i:17577084 original size:20 final size:20
Alignment explanation
Indices: 17577059--17577099 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17577049 ATTGCTCTAA
17577059 CAACAACTCTCACAATTTAT
1 CAACAACTCTCACAATTTAT
17577079 CAACAACTCTCACAATTTAT
1 CAACAACTCTCACAATTTAT
17577099 C
1 C
17577100 TTGTTTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (20 bp):
CAACAACTCTCACAATTTAT
Found at i:17582899 original size:6 final size:6
Alignment explanation
Indices: 17582884--17582934 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
17582874 CAAAATTTTC
*
17582884 TTTC-T TTTCTT TTTCTT TTTCTT ATTACTT TGTT-TT TTTCTT TTT-TT
1 TTTCTT TTTCTT TTTCTT TTTCTT -TTTCTT T-TTCTT TTTCTT TTTCTT
17582931 TTTC
1 TTTC
17582935 AAATGACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
5 11 0.28
6 22 0.56
7 6 0.15
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (6 bp):
TTTCTT
Found at i:17582921 original size:19 final size:16
Alignment explanation
Indices: 17582879--17582933 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 16
17582869 TTTATCAAAA
*
17582879 TTTTCTTTCTTTTCTT
1 TTTTTTTTCTTTTCTT
17582895 TTTCTTTTTCTTATTACTT
1 TTT-TTTTTCTT-TT-CTT
17582914 TGTTTTTTTCTTTT-TT
1 T-TTTTTTTCTTTTCTT
17582930 TTTT
1 TTTT
17582934 CAAATGACTG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 3 0.09
16 6 0.18
17 7 0.21
18 4 0.12
19 12 0.35
20 2 0.06
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.82
Consensus pattern (16 bp):
TTTTTTTTCTTTTCTT
Found at i:17615409 original size:37 final size:38
Alignment explanation
Indices: 17615359--17615517 Score: 128
Period size: 38 Copynumber: 4.2 Consensus size: 38
17615349 GCTTATGGGG
* *
17615359 CTTAGTGCATAGTAGACTTTGTTC-GGTGTTTATCAGT
1 CTTAGTGCATAGTAGACTTCGTACAGGTGTTTATCAGT
* * *
17615396 CTTAGTGCGTAGTAGGCTTCGTACAGGTGTTTATCGGT
1 CTTAGTGCATAGTAGACTTCGTACAGGTGTTTATCAGT
* * * *
17615434 CTTAGTGCCTAGCA-AGCTTCGTGCCGGTGTTTATCAAG-
1 CTTAGTGCATAGTAGA-CTTCGTACAGGTGTTTATC-AGT
* * * * * *
17615472 CTTAGTGCCTAGCAGGCTTCATGCCGGTGTTTATCGAG-
1 CTTAGTGCATAGTAGACTTCGTACAGGTGTTTATC-AGT
17615510 CTTAGTGC
1 CTTAGTGC
17615518 TTAGCAGGTT
Statistics
Matches: 104, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
37 20 0.19
38 83 0.80
39 1 0.01
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (38 bp):
CTTAGTGCATAGTAGACTTCGTACAGGTGTTTATCAGT
Found at i:17615531 original size:38 final size:39
Alignment explanation
Indices: 17615382--17615533 Score: 186
Period size: 38 Copynumber: 4.0 Consensus size: 39
17615372 AGACTTTGTT
* * * *
17615382 CGGTGTTTATC-AGTCTTAGTGCGTAGTAGGCTTCGTAC
1 CGGTGTTTATCGAGTCTTAGTGCCTAGCAGGCTTCATGC
* * *
17615420 AGGTGTTTATCG-GTCTTAGTGCCTAGCAAGCTTCGTGC
1 CGGTGTTTATCGAGTCTTAGTGCCTAGCAGGCTTCATGC
*
17615458 CGGTGTTTATCAAG-CTTAGTGCCTAGCAGGCTTCATGC
1 CGGTGTTTATCGAGTCTTAGTGCCTAGCAGGCTTCATGC
* *
17615496 CGGTGTTTATCGAG-CTTAGTGCTTAGCAGGTTTCATGC
1 CGGTGTTTATCGAGTCTTAGTGCCTAGCAGGCTTCATGC
17615534 TGTGTATTTA
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
38 99 0.99
39 1 0.01
ACGTcount: A:0.16, C:0.20, G:0.28, T:0.35
Consensus pattern (39 bp):
CGGTGTTTATCGAGTCTTAGTGCCTAGCAGGCTTCATGC
Found at i:17615579 original size:77 final size:76
Alignment explanation
Indices: 17615421--17615582 Score: 175
Period size: 77 Copynumber: 2.1 Consensus size: 76
17615411 GCTTCGTACA
* *
17615421 GGTGTTTATCGGTCTTAGTGCCTAGCAAGCTTCGTGCCGGTGTTTATCAAGCTTAGTGCCTAGCA
1 GGTGTTTATCGGTCTTAGTGCCTAGCAAGCTTCATGCCGGTATTTATCAAGCTTAGTGCCTAGCA
*
17615486 GGCTTCATGCC
66 GACTTCATGCC
* * * * * * *
17615497 GGTGTTTATCGAG-CTTAGTGCTTAGCAGGTTTCATGCTGTGTATTTATTAGGTTTAGTGCCTAG
1 GGTGTTTATCG-GTCTTAGTGCCTAGCAAGCTTCATGCCG-GTATTTATCAAGCTTAGTGCCTAG
* *
17615561 TAGACTTTC-TTCC
64 CAGAC-TTCATGCC
17615574 GGTGTTTAT
1 GGTGTTTAT
17615583 TATCAAGCTT
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
76 32 0.45
77 36 0.51
78 3 0.04
ACGTcount: A:0.16, C:0.19, G:0.27, T:0.39
Consensus pattern (76 bp):
GGTGTTTATCGGTCTTAGTGCCTAGCAAGCTTCATGCCGGTATTTATCAAGCTTAGTGCCTAGCA
GACTTCATGCC
Found at i:17615584 original size:38 final size:38
Alignment explanation
Indices: 17615421--17615584 Score: 120
Period size: 38 Copynumber: 4.3 Consensus size: 38
17615411 GCTTCGTACA
* *
17615421 GGTGTTTA-TCGGTCTTAGTGCCTAGCA-AGCTTCGTGCC
1 GGTGTTTATTAGGT-TTAGTGCCTAGCAGA-CTTCATGCC
* * * *
17615459 GGTGTTTATCAAGCTTAGTGCCTAGCAGGCTTCATGCC
1 GGTGTTTATTAGGTTTAGTGCCTAGCAGACTTCATGCC
* * * ** *
17615497 GGTGTTTA-TCGAGCTTAGTGCTTAGCAGGTTTCATGCT
1 GGTGTTTATTAG-GTTTAGTGCCTAGCAGACTTCATGCC
* * *
17615535 GTGTATTTATTAGGTTTAGTGCCTAGTAGACTTTC-TTCC
1 G-GTGTTTATTAGGTTTAGTGCCTAGCAGAC-TTCATGCC
17615574 GGTGTTTATTA
1 GGTGTTTATTA
17615585 TCAAGCTTTG
Statistics
Matches: 98, Mismatches: 22, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
38 70 0.71
39 23 0.23
40 5 0.05
ACGTcount: A:0.16, C:0.18, G:0.26, T:0.39
Consensus pattern (38 bp):
GGTGTTTATTAGGTTTAGTGCCTAGCAGACTTCATGCC
Found at i:17621038 original size:21 final size:21
Alignment explanation
Indices: 17621014--17621065 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
17621004 GTGCAGACTT
*
17621014 CTACCGATACTTGAGGCAGTA
1 CTACCGATACTTGAGACAGTA
*
17621035 CTACCGATACTTGAGATAGTA
1 CTACCGATACTTGAGACAGTA
17621056 CTACCGATAC
1 CTACCGATAC
17621066 AAGTGAGACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
CTACCGATACTTGAGACAGTA
Found at i:17624224 original size:4 final size:4
Alignment explanation
Indices: 17624217--17624243 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17624207 TATAACATAA
17624217 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
17624244 AGTGAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:17625365 original size:31 final size:31
Alignment explanation
Indices: 17625315--17625389 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
17625305 CCCATTTCAC
* *
17625315 AGCTCATG--AGCATATATGATTACAGTTAT
1 AGCTCATGTAAGCATACATGATTACAGTCAT
17625344 AGCTCATGTAAGCATACATGATTACAGTCAT
1 AGCTCATGTAAGCATACATGATTACAGTCAT
*
17625375 AGCTCGTGTAAGCAT
1 AGCTCATGTAAGCAT
17625390 TTTCTCGGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 8 0.20
31 33 0.80
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (31 bp):
AGCTCATGTAAGCATACATGATTACAGTCAT
Found at i:17627012 original size:21 final size:21
Alignment explanation
Indices: 17626974--17627053 Score: 58
Period size: 21 Copynumber: 3.7 Consensus size: 21
17626964 CCTACAACTT
*
17626974 CTACCGATACAAGC-ATGCAAA
1 CTACCGATAC-ATCTATGCAAA
17626995 CTACCGATACATCTATGCATATAA
1 CTACCGATACATCTATGC--A-AA
* *
17627019 CTACCGATAC-TCACAATTC-AA
1 CTACCGATACAT--CTATGCAAA
17627040 CTACCGATACATCT
1 CTACCGATACATCT
17627054 CAAGTCAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
20 3 0.06
21 26 0.54
22 1 0.02
23 2 0.04
24 12 0.25
25 4 0.08
ACGTcount: A:0.38, C:0.30, G:0.09, T:0.24
Consensus pattern (21 bp):
CTACCGATACATCTATGCAAA
Found at i:17627754 original size:52 final size:52
Alignment explanation
Indices: 17627650--17628026 Score: 542
Period size: 52 Copynumber: 7.2 Consensus size: 52
17627640 CAACGACATA
* * * * *
17627650 TAGTCGTCGGACTTCCTATTCCGTAAAGGAATTCATGTACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGG-ATTCATTTACTCACGATGACACT
** *
17627703 TAGTCATCGGACCTCACCATCCGTAAAGGATTCATATACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* *
17627755 TAGCCATCGGACCTTATAATCCGTAAAGGATTCATTTACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* *
17627807 TAGTCATCGGACCTCATAATCTGTAAAGGATTCATTT-CTCACGATGACATT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* *
17627858 TAGTCATCGGACCTCATAATCCCTAAAGGATTCAATTACTCACGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* *
17627910 TAGTCATCAGACCTCATAATCCGTAAAGGATTCATTTACTCATGATGACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
* * *
17627962 TAGTCATTGGACCTCATAATACGTAAAGGATTTC-TTTACTCACGATAACACT
1 TAGTCATCGGACCTCATAATCCGTAAAGGA-TTCATTTACTCACGATGACACT
*
17628014 TAATCATCGGACC
1 TAGTCATCGGACC
17628027 CTTTTCATTT
Statistics
Matches: 291, Mismatches: 31, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
51 47 0.16
52 218 0.75
53 26 0.09
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (52 bp):
TAGTCATCGGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGACACT
Found at i:17627869 original size:155 final size:155
Alignment explanation
Indices: 17627671--17628026 Score: 529
Period size: 155 Copynumber: 2.3 Consensus size: 155
17627661 CTTCCTATTC
* * *
17627671 CGTAAAGGAATTCATGTACTCACGATGACACTTAGTCATCGGACCTCACCATCCGTAAAGGATTC
1 CGTAAAGG-ATTCAT-TTCTCACGATGACACTTAGTCATCGGACCTCACAATCCCTAAAGGATTC
* *
17627736 -ATATACTCACGATGACACTTAGCCATCGGACCTTATAATCCGTAAAGGATTCATTTACTCACGA
64 AAT-TACTCACGATGACACTTAGCCATCAGACCTCATAATCCGTAAAGGATTCATTTACTCACGA
17627800 TGACACTTAGTCATCGGACCTCATAAT-
128 TGACACTTAGTCATCGGACCTCATAATA
* *
17627827 CTGTAAAGGATTCATTTCTCACGATGACATTTAGTCATCGGACCTCATAATCCCTAAAGGATTCA
1 C-GTAAAGGATTCATTTCTCACGATGACACTTAGTCATCGGACCTCACAATCCCTAAAGGATTCA
* *
17627892 ATTACTCACGATGACACTTAGTCATCAGACCTCATAATCCGTAAAGGATTCATTTACTCATGATG
65 ATTACTCACGATGACACTTAGCCATCAGACCTCATAATCCGTAAAGGATTCATTTACTCACGATG
*
17627957 ACACTTAGTCATTGGACCTCATAATA
130 ACACTTAGTCATCGGACCTCATAATA
* *
17627983 CGTAAAGGATTTC-TTTACTCACGATAACACTTAATCATCGGACC
1 CGTAAAGGA-TTCATTT-CTCACGATGACACTTAGTCATCGGACC
17628027 CTTTTCATTT
Statistics
Matches: 182, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
155 138 0.76
156 37 0.20
157 7 0.04
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (155 bp):
CGTAAAGGATTCATTTCTCACGATGACACTTAGTCATCGGACCTCACAATCCCTAAAGGATTCAA
TTACTCACGATGACACTTAGCCATCAGACCTCATAATCCGTAAAGGATTCATTTACTCACGATGA
CACTTAGTCATCGGACCTCATAATA
Found at i:17627939 original size:207 final size:208
Alignment explanation
Indices: 17627644--17628026 Score: 574
Period size: 207 Copynumber: 1.8 Consensus size: 208
17627634 AACTCACAAC
* * * * *
17627644 GACATATAGTCGTCGGACTTCCTATTCCGTAAAGGAATTCATGTACTCACGATGACACTTAGTCA
1 GACATATAGTCATCGGACCTCATAATCCCTAAAGGAATTCATGTACTCACGATGACACTTAGTCA
* * *
17627709 TCGGACCTCACCATCCGTAAAGGATTCATATACTCACGATGACACTTAGCCATCGGACCTTATAA
66 TCAGACCTCACAATCCGTAAAGGATTCATATACTCACGATGACACTTAGCCATCGGACCTCATAA
* * *
17627774 TCCGTAAAGGA-TTCATTTACTCACGATGACACTTAGTCATCGGACCTCATAATCTGTAAAGGAT
131 TACGTAAAGGATTTC-TTTACTCACGATAACACTTAATCATCGGACCTCATAATCTGTAAAGGAT
17627838 TCATTTCTCACGAT
195 TCATTTCTCACGAT
*
17627852 GACATTTAGTCATCGGACCTCATAATCCCTAAAGG-ATTCAAT-TACTCACGATGACACTTAGTC
1 GACATATAGTCATCGGACCTCATAATCCCTAAAGGAATTC-ATGTACTCACGATGACACTTAGTC
* * * * *
17627915 ATCAGACCTCATAATCCGTAAAGGATTCATTTACTCATGATGACACTTAGTCATTGGACCTCATA
65 ATCAGACCTCACAATCCGTAAAGGATTCATATACTCACGATGACACTTAGCCATCGGACCTCATA
17627980 ATACGTAAAGGATTTCTTTACTCACGATAACACTTAATCATCGGACC
130 ATACGTAAAGGATTTCTTTACTCACGATAACACTTAATCATCGGACC
17628027 CTTTTCATTT
Statistics
Matches: 156, Mismatches: 17, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
207 122 0.78
208 34 0.22
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (208 bp):
GACATATAGTCATCGGACCTCATAATCCCTAAAGGAATTCATGTACTCACGATGACACTTAGTCA
TCAGACCTCACAATCCGTAAAGGATTCATATACTCACGATGACACTTAGCCATCGGACCTCATAA
TACGTAAAGGATTTCTTTACTCACGATAACACTTAATCATCGGACCTCATAATCTGTAAAGGATT
CATTTCTCACGAT
Found at i:17628932 original size:24 final size:20
Alignment explanation
Indices: 17628880--17628921 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17628870 GCTTTTATAA
17628880 TTAACC-TAATTAATCCACT
1 TTAACCTTAATTAATCCACT
17628899 TTAACCTTAATTAATCTCACT
1 TTAACCTTAATTAATC-CACT
17628920 TT
1 TT
17628922 TAAGCACTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 6 0.29
20 9 0.43
21 6 0.29
ACGTcount: A:0.33, C:0.24, G:0.00, T:0.43
Consensus pattern (20 bp):
TTAACCTTAATTAATCCACT
Found at i:17636328 original size:59 final size:58
Alignment explanation
Indices: 17636268--17636698 Score: 580
Period size: 58 Copynumber: 7.4 Consensus size: 58
17636258 AGATTGTCCA
* * *
17636268 AAAATTACCATTTTACCCTCGAATTTTCCAAAATCCCATTTTTAACCCCGATTTTACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * *
17636326 AAAAATTACCATTTTACCCTCGAACTTTCCAAAATCCCACTTTTAACCTCGATTTCACCC
1 -AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA-CC
* *
17636386 AAAATTACCATTTTACCCCCGAACTTTCCTAAATCCCATTTTTAACCCCAATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * ***
17636444 AAAATTACCATTTTACCCCCAAACTTTCCAAAA-CCTCACTTTTAACCTTAATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCC-CATTTTTAACCCCGATTTCACC
* *
17636502 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCACTTTTAACCTCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * *
17636560 AAAATTACCATTTTACACTCGAACTTTCCAAAATCCTATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
* * ** * *
17636618 AAAATTACCATTTTACCCCC-AAATATCCTAAAATCCCATTTTCGACACCGATTTCACA
1 AAAATTACCATTTTACCCCCGAACTTTCC-AAAATCCCATTTTTAACCCCGATTTCACC
17636676 AAAATTA-CATTTTTACCCCCGAA
1 AAAATTACCA-TTTTACCCCCGAA
17636699 AGTTAAAAAT
Statistics
Matches: 335, Mismatches: 31, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
57 10 0.03
58 216 0.64
59 107 0.32
60 2 0.01
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.32
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCCATTTTTAACCCCGATTTCACC
Found at i:17636637 original size:29 final size:29
Alignment explanation
Indices: 17636268--17636697 Score: 195
Period size: 29 Copynumber: 14.8 Consensus size: 29
17636258 AGATTGTCCA
* *
17636268 AAAATTACCATTTTACCCTCGAATTT-TCC
1 AAAATTACCATTTTACCCCCG-ATTTCACC
* * *
17636297 AAAA-TCCCATTTTTAACCCCGATTTTACC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
*
17636326 AAAAATTACCATTTTACCCTCGAACTTT--CC
1 -AAAATTACCATTTTACCCCCG-A-TTTCACC
* * *
17636356 AAAA-TCCCACTTTTAACCTCGATTTCACCC
1 AAAATTACCA-TTTTACCCCCGATTTCA-CC
17636386 AAAATTACCATTTTACCCCCGAACTTT--CC
1 AAAATTACCATTTTACCCCCG-A-TTTCACC
* * * *
17636415 TAAA-TCCCATTTTTAACCCCAATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
*
17636444 AAAATTACCATTTTACCCCCAAACTTT--CC
1 AAAATTACCATTTTACCCCC-GA-TTTCACC
* * ***
17636473 AAAA--CCTCACTTTTAACCTTAATTTCACC
1 AAAATTAC-CA-TTTTACCCCCGATTTCACC
17636502 AAAATTACCATTTTACCCCCGAACTTT--CC
1 AAAATTACCATTTTACCCCCG-A-TTTCACC
* * *
17636531 AAAA-TCCCACTTTTAACCTCGATTTCACC
1 AAAATTACCA-TTTTACCCCCGATTTCACC
* *
17636560 AAAATTACCATTTTACACTCGAACTTT--CC
1 AAAATTACCATTTTACCCCCG-A-TTTCACC
*
17636589 AAAA-T-CCTATTTTTAACCCCGATTTCACC
1 AAAATTACC-A-TTTTACCCCCGATTTCACC
* * *
17636618 AAAATTACCATTTTACCCCCAAATATC-CT
1 AAAATTACCATTTTACCCCC-GATTTCACC
* * *
17636647 AAAA-TCCCATTTT-CGACACCGATTTCACA
1 AAAATTACCATTTTAC--CCCCGATTTCACC
17636676 AAAATTA-CATTTTTACCCCCGA
1 AAAATTACCA-TTTTACCCCCGA
17636698 AAGTTAAAAA
Statistics
Matches: 307, Mismatches: 48, Indels: 92
0.69 0.11 0.21
Matches are distributed among these distances:
27 19 0.06
28 42 0.14
29 162 0.53
30 55 0.18
31 23 0.07
32 6 0.02
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTACCATTTTACCCCCGATTTCACC
Found at i:17643430 original size:30 final size:30
Alignment explanation
Indices: 17643375--17643439 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17643365 TTTTATAGTT
17643375 TATAATTTCTTTTATTTCTTAAAATATTTA
1 TATAATTTCTTTTATTTCTTAAAATATTTA
* *
17643405 TATATTTTCTTTTAAATTT-TT-AAATATTTT
1 TATAATTTCTTTT--ATTTCTTAAAATATTTA
17643435 TATAA
1 TATAA
17643440 AAAAGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
30 24 0.80
31 2 0.07
32 4 0.13
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.62
Consensus pattern (30 bp):
TATAATTTCTTTTATTTCTTAAAATATTTA
Found at i:17646891 original size:2 final size:2
Alignment explanation
Indices: 17646884--17646909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17646874 TTAGATATTT
17646884 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
17646910 AACCCATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17649790 original size:3 final size:3
Alignment explanation
Indices: 17649782--17649809 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17649772 TTTTTGTTAC
17649782 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17649810 TAGTGTTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17652648 original size:44 final size:43
Alignment explanation
Indices: 17652582--17652719 Score: 147
Period size: 43 Copynumber: 3.2 Consensus size: 43
17652572 CTGAATTAAC
* * **
17652582 CTTATGCTCTA-TCCGAGTCATAAGTTCTTCTATTTACAAATGAT
1 CTTATGCTCTAGT-CGAGACATAAG-TCTTCCATTTACAAACAAT
*
17652626 CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTATAAACAAT
1 CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTACAAACAAT
* * *
17652669 CTTATACTCTAGCCGAGACATAAGTCTTCC-TTTA-AACATAAT
1 CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTACAA-ACAAT
*
17652711 CTCATGCTC
1 CTTATGCTC
17652720 ATCCCGAGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 2 0.02
42 15 0.18
43 43 0.52
44 21 0.26
45 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (43 bp):
CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTACAAACAAT
Found at i:17652671 original size:43 final size:42
Alignment explanation
Indices: 17652582--17652871 Score: 185
Period size: 42 Copynumber: 6.8 Consensus size: 42
17652572 CTGAATTAAC
* * *
17652582 CTTATGCTCTA-TCCGAGTCATAAGTTCTTCTATTTACAAATGAT
1 CTTATGCTCTAGT-CGAGACATAAG-TCTTCCATTTA-AAATAAT
*
17652626 CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTATAAACAAT
1 CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTA-AAATAAT
* *
17652669 CTTATACTCTAGCCGAGACATAAGTCTTCC-TTTAAACATAAT
1 CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTAAA-ATAAT
* **
17652711 CTCATGCTC-A-TCCCGAGTA-ACGAGTCTTCC-TTTAAACATAAT
1 CTTATGCTCTAGT--CGAG-ACATAAGTCTTCCATTTAAA-ATAAT
* * *
17652753 CTCATGCTC-A-TCCCGAGTCACAAGTCTTCC-TTTAAACATAAT
1 CTTATGCTCTAGT--CGAGACATAAGTCTTCCATTTAAA-ATAAT
* *
17652795 CTCATGCTC-A-TCCCGAGACATGAGTCTTCC-TTTAAACATAAT
1 CTTATGCTCTAGT--CGAGACATAAGTCTTCCATTTAAA-ATAAT
* *
17652837 CTCATGCT-TA-TCCCGAGACATGAGTCTTCCATTTA
1 CTTATGCTCTAGT--CGAGACATAAGTCTTCCATTTA
17652872 TACATCAAGT
Statistics
Matches: 220, Mismatches: 18, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
41 3 0.01
42 147 0.67
43 48 0.22
44 21 0.10
45 1 0.00
ACGTcount: A:0.29, C:0.26, G:0.11, T:0.34
Consensus pattern (42 bp):
CTTATGCTCTAGTCGAGACATAAGTCTTCCATTTAAAATAAT
Found at i:17652737 original size:42 final size:42
Alignment explanation
Indices: 17652681--17652876 Score: 295
Period size: 42 Copynumber: 4.6 Consensus size: 42
17652671 TATACTCTAG
**
17652681 CCGAGACATAAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
17652723 CCGAGTA-ACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAG-ACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* *
17652765 CCGAGTCACAAGTCTTCCTTTAAACATAATCTCATGCTCATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* *
17652807 CCGAGACATGAGTCTTCCTTTAAACATAATCTCATGCTTATC
1 CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
* *
17652849 CCGAGACATGAGTCTTCCATTTATACAT
1 CCGAGACACGAGTCTTCC-TTTAAACAT
17652877 CAAGTGATTC
Statistics
Matches: 142, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
42 133 0.94
43 9 0.06
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (42 bp):
CCGAGACACGAGTCTTCCTTTAAACATAATCTCATGCTCATC
Found at i:17661744 original size:16 final size:17
Alignment explanation
Indices: 17661699--17661744 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
17661689 AGAGCAAAAA
17661699 AGAGAGAAAAGAAAGAGG
1 AGAGA-AAAAGAAAGAGG
*
17661717 A-AGGAGAAAGAAAG-GG
1 AGA-GAAAAAGAAAGAGG
17661733 AGAGAAAAAGAA
1 AGAGAAAAAGAA
17661745 GGAAATCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
16 11 0.46
17 10 0.42
18 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (17 bp):
AGAGAAAAAGAAAGAGG
Found at i:17663236 original size:52 final size:52
Alignment explanation
Indices: 17663150--17663423 Score: 401
Period size: 52 Copynumber: 5.2 Consensus size: 52
17663140 GTTGGCATAT
* *
17663150 AATCCTTTACGGATTATGAGGTCTGATGACTAAGTGTCATCATGAGTACATG
1 AATCCTTTACGGATTATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATG
*
17663202 AAT-CTTTCACGGATTATGAGGTCTGATGACTAAGTATCATCGTGAGTAAATG
1 AATCCTTT-ACGGATTATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATG
17663254 AATCCTTTACGGATTATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATG
1 AATCCTTTACGGATTATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATG
* * * *
17663306 AATCCTTTACAGATTATAAGGTCCGAT-AGCTAAGTGTCATCGTGAGTATATG
1 AATCCTTTACGGATTATGAGGTCTGATGA-CTAAGTGTCATCGTGAGTAAATG
* * *
17663358 AATCCTTTACAGATGT-TGAGGTCCGATGACTAAGTGTCATCGTGAGTACATG
1 AATCCTTTACGGAT-TATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATG
17663410 AATTCCTTTACGGA
1 AA-TCCTTTACGGA
17663424 ACAAGAGGTC
Statistics
Matches: 205, Mismatches: 11, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
51 5 0.02
52 184 0.90
53 16 0.08
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.32
Consensus pattern (52 bp):
AATCCTTTACGGATTATGAGGTCTGATGACTAAGTGTCATCGTGAGTAAATG
Found at i:17671426 original size:28 final size:28
Alignment explanation
Indices: 17671358--17671481 Score: 97
Period size: 28 Copynumber: 4.5 Consensus size: 28
17671348 GCCAAAGTCC
* * * * *
17671358 CTTTCAAACCAGAGTTCAGAGTAATGCT
1 CTTTCAAGCCAAAGTCCAGAATAACGCT
* * * *
17671386 CTTACGAGTCAAAGTCCAAAATAACGCT
1 CTTTCAAGCCAAAGTCCAGAATAACGCT
** ** * *
17671414 CTTTTGAGCCAAA-AACAGAGTAATGCT
1 CTTTCAAGCCAAAGTCCAGAATAACGCT
*
17671441 CTTACAAGCCAAAGTCCAGAATAACGCT
1 CTTTCAAGCCAAAGTCCAGAATAACGCT
17671469 CTTTCAAGCCAAA
1 CTTTCAAGCCAAA
17671482 AATAGAGTAT
Statistics
Matches: 70, Mismatches: 25, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
27 19 0.27
28 51 0.73
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.23
Consensus pattern (28 bp):
CTTTCAAGCCAAAGTCCAGAATAACGCT
Found at i:17671440 original size:55 final size:55
Alignment explanation
Indices: 17671374--17671490 Score: 180
Period size: 55 Copynumber: 2.1 Consensus size: 55
17671364 AACCAGAGTT
* * **
17671374 CAGAGTAATGCTCTTACGAGTCAAAGTCCAAAATAACGCTCTTTTGAGCCAAAAA
1 CAGAGTAATGCTCTTACAAGCCAAAGTCCAAAATAACGCTCTTTCAAGCCAAAAA
*
17671429 CAGAGTAATGCTCTTACAAGCCAAAGTCCAGAATAACGCTCTTTCAAGCCAAAAA
1 CAGAGTAATGCTCTTACAAGCCAAAGTCCAAAATAACGCTCTTTCAAGCCAAAAA
*
17671484 TAGAGTA
1 CAGAGTA
17671491 TCACTCTTTC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (55 bp):
CAGAGTAATGCTCTTACAAGCCAAAGTCCAAAATAACGCTCTTTCAAGCCAAAAA
Found at i:17671450 original size:27 final size:27
Alignment explanation
Indices: 17671420--17671490 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 27
17671410 CGCTCTTTTG
*
17671420 AGCCAAAAACAGAGTAATGCTCTTACA
1 AGCCAAAAACAGAGTAACGCTCTTACA
** * *
17671447 AGCCAAAGTCCAGAATAACGCTCTTTCA
1 AGCCAAA-AACAGAGTAACGCTCTTACA
*
17671475 AGCCAAAAATAGAGTA
1 AGCCAAAAACAGAGTA
17671491 TCACTCTTTC
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 12 0.35
28 22 0.65
ACGTcount: A:0.44, C:0.23, G:0.15, T:0.18
Consensus pattern (27 bp):
AGCCAAAAACAGAGTAACGCTCTTACA
Found at i:17673472 original size:21 final size:23
Alignment explanation
Indices: 17673435--17673477 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
17673425 TATTTGTTCA
17673435 TTAAATAAATATAA-TTTCATGC
1 TTAAATAAATATAATTTTCATGC
*
17673457 TTAATTAAAT-TAATTTTCATG
1 TTAAATAAATATAATTTTCATG
17673478 GCCCACTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (23 bp):
TTAAATAAATATAATTTTCATGC
Found at i:17676934 original size:16 final size:16
Alignment explanation
Indices: 17676883--17676934 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
17676873 TAATTTTCTT
17676883 GAAAATTTAATTTTG-
1 GAAAATTTAATTTTGA
17676898 GAAAATCTTAGTGATTTTTGA
1 GAAAAT-TTA---A-TTTTGA
17676919 GAAAATTTAATTTTGA
1 GAAAATTTAATTTTGA
17676935 TAAAGTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
15 6 0.19
16 9 0.29
17 1 0.03
19 1 0.03
20 8 0.26
21 6 0.19
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.44
Consensus pattern (16 bp):
GAAAATTTAATTTTGA
Found at i:17677524 original size:17 final size:16
Alignment explanation
Indices: 17677498--17677532 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
17677488 ATAAATATTT
17677498 TATTAATTTAATAGAA
1 TATTAATTTAATAGAA
*
17677514 TATTAAATTTAATATAA
1 TATT-AATTTAATAGAA
17677531 TA
1 TA
17677533 CTTATCAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TATTAATTTAATAGAA
Found at i:17679022 original size:17 final size:17
Alignment explanation
Indices: 17678987--17679028 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
17678977 AGAAAAAGTA
*
17678987 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
*
17679005 GTTAAAGAAGATGGAAG
1 GTTAAAGAAGATGAAAG
17679022 GTTAAAG
1 GTTAAAG
17679029 GTCAAGGGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.48, C:0.02, G:0.29, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:17679028 original size:24 final size:24
Alignment explanation
Indices: 17679001--17679048 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
17678991 CAAGAATATG
* *
17679001 AAAGGTTAAAGAAGATGGAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
* *
17679025 AAAGGTCAAGGGAGATGAAAGGTT
1 AAAGGTCAAAGAAGATGAAAGGTT
17679049 GAACATCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.44, C:0.02, G:0.35, T:0.19
Consensus pattern (24 bp):
AAAGGTCAAAGAAGATGAAAGGTT
Found at i:17684414 original size:17 final size:17
Alignment explanation
Indices: 17684383--17684424 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
17684373 GGAAAATGTA
*
17684383 GTTACAAGAATATGAAAG
1 GTTA-AAGAAGATGAAAG
17684401 GTTAAAGAAGATGAAAG
1 GTTAAAGAAGATGAAAG
17684418 GTTAAAG
1 GTTAAAG
17684425 GTCAAGGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.26, T:0.21
Consensus pattern (17 bp):
GTTAAAGAAGATGAAAG
Found at i:17685176 original size:60 final size:60
Alignment explanation
Indices: 17685111--17685224 Score: 147
Period size: 61 Copynumber: 1.9 Consensus size: 60
17685101 AATCGAACAA
* * * *
17685111 AAAAAAAATTAGGTATCAAATTAGGAAAAAAAAGTCAAGTTGAGGTACCAAATTGGATTCC
1 AAAAAAGATTAAGTACCAAATTAAGAAAAAAAA-TCAAGTTGAGGTACCAAATTGGATTCC
* * * *
17685172 AAAAAAGATTAAGTACCAACTTAAGAAAAAATATCAAGTTTAGGTATCAAATT
1 AAAAAAGATTAAGTACCAAATTAAGAAAAAAAATCAAGTTGAGGTACCAAATT
17685225 AAGAAAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
60 18 0.40
61 27 0.60
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (60 bp):
AAAAAAGATTAAGTACCAAATTAAGAAAAAAAATCAAGTTGAGGTACCAAATTGGATTCC
Found at i:17685254 original size:31 final size:31
Alignment explanation
Indices: 17685185--17685312 Score: 99
Period size: 31 Copynumber: 4.3 Consensus size: 31
17685175 AAAGATTAAG
* *
17685185 TACCAACTTAAGAAAAAATATCAAGTTTAGG
1 TACCAAATTAAGAAAAAATATCAAGTTTAGA
* *
17685216 TATCAAATTAAGAAAAAATGTCAAGTTT-GCA
1 TACCAAATTAAGAAAAAATATCAAGTTTAG-A
*
17685247 TACCAAATTAA-ACCCAAAA-A--AA--TTAGA
1 TACCAAATTAAGA--AAAAATATCAAGTTTAGA
* * * *
17685274 AATCAAATTAATAAAAAATATCAAGTTAAGA
1 TACCAAATTAAGAAAAAATATCAAGTTTAGA
17685305 TACCAAAT
1 TACCAAAT
17685313 GAAGTGTAAG
Statistics
Matches: 74, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
26 4 0.05
27 13 0.18
28 2 0.03
29 4 0.05
30 2 0.03
31 45 0.61
32 4 0.05
ACGTcount: A:0.54, C:0.12, G:0.09, T:0.25
Consensus pattern (31 bp):
TACCAAATTAAGAAAAAATATCAAGTTTAGA
Found at i:17685625 original size:23 final size:22
Alignment explanation
Indices: 17685594--17685637 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17685584 TTAATCTCAA
17685594 TTTTTTATTTTTAAGAATTTAG
1 TTTTTTATTTTTAAGAATTTAG
**
17685616 TTTTTCTATTTTTTTGAATTTA
1 TTTTT-TATTTTTAAGAATTTA
17685638 AAAATTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.23, C:0.02, G:0.07, T:0.68
Consensus pattern (22 bp):
TTTTTTATTTTTAAGAATTTAG
Found at i:17689417 original size:97 final size:97
Alignment explanation
Indices: 17689226--17689417 Score: 267
Period size: 97 Copynumber: 2.0 Consensus size: 97
17689216 CCTTGAAAAG
* * * *
17689226 GGGTATTCGATTATCCCGATTTGAAGAAAAGTCGCCCCTAGTAAGTTAAGGCACAAATTTTCGAA
1 GGGTATTCGATTATCCCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAA
* ** * *
17689291 ACCCGAGATAAAGGAATATTACCTTGATTTAA
66 ACCCGAAATAAAAAAACATTACCTCGATTTAA
* * *
17689323 GGGTATTCGATTATTCTGATTTAAAGAAAAATCGCACCTAGTAAGTTAATGCACAAATTTTCAAA
1 GGGTATTCGATTATCCCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAA
*
17689388 ACCCGAAATAAAAAAACATTGCCTCGATTT
66 ACCCGAAATAAAAAAACATTACCTCGATTT
17689418 TAAATATTTT
Statistics
Matches: 82, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 82 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (97 bp):
GGGTATTCGATTATCCCGATTTAAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAA
ACCCGAAATAAAAAAACATTACCTCGATTTAA
Found at i:17689725 original size:29 final size:31
Alignment explanation
Indices: 17689691--17689769 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 31
17689681 TTCGGAGAGT
*
17689691 TTAA-GGTTAAAATG-CAATTTT-GGAAAATA
1 TTAAGGGTAAAAATGTC-ATTTTAGGAAAATA
17689720 TTAAGGGTAAAAATGTCATTTTAGGAAAAT-
1 TTAAGGGTAAAAATGTCATTTTAGGAAAATA
* *
17689750 TT-GGGGT-AAAATGTGATTTT
1 TTAAGGGTAAAAATGTCATTTT
17689770 TGAAAGTATG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
28 12 0.27
29 8 0.18
30 16 0.36
31 8 0.18
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.37
Consensus pattern (31 bp):
TTAAGGGTAAAAATGTCATTTTAGGAAAATA
Found at i:17689848 original size:29 final size:28
Alignment explanation
Indices: 17689688--17689953 Score: 176
Period size: 28 Copynumber: 9.2 Consensus size: 28
17689678 AGTTTCGGAG
* * *
17689688 AGTTTAAGGTTAAAATGCAATTTTGGAA
1 AGTTTAAGGGTAAAATGTAATTTTTGAA
* * *
17689716 AATATTAAGGGTAAAAATGTCATTTTAGGAA
1 AGT-TTAAGGGT-AAAATGTAATTTT-TGAA
* * *
17689747 AATTT-GGGGTAAAATGTGATTTTTGAA
1 AGTTTAAGGGTAAAATGTAATTTTTGAA
* * * ** *
17689774 AGTATGAGGGCAAAATAAAATTTTTGGA
1 AGTTTAAGGGTAAAATGTAATTTTTGAA
*
17689802 AGTTTAAGGGCAAAATGTAATTTTTGAA
1 AGTTTAAGGGTAAAATGTAATTTTTGAA
*
17689830 AGTTTAAGGGTAAGAATGTAATTTTTGGA
1 AGTTTAAGGGTAA-AATGTAATTTTTGAA
* * *
17689859 AGTTCAAGGATAAAAATATAATTTTTAAGAA
1 AGTTTAAGGGT-AAAATGTAATTTTT--GAA
* * **
17689890 A-TTTAGGGGTCAAAATGTGATTTTAAAA
1 AGTTTAAGGGT-AAAATGTAATTTTTGAA
* * * *
17689918 AGTATAAGGGTCAAAATATGATTTTTAGAC
1 AGTTTAAGGGT-AAAATGTAATTTTT-GAA
17689948 AGTTTA
1 AGTTTA
17689954 GGGACCTTCT
Statistics
Matches: 187, Mismatches: 41, Indels: 18
0.76 0.17 0.07
Matches are distributed among these distances:
27 6 0.03
28 68 0.36
29 65 0.35
30 38 0.20
31 10 0.05
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (28 bp):
AGTTTAAGGGTAAAATGTAATTTTTGAA
Found at i:17689942 original size:88 final size:86
Alignment explanation
Indices: 17689785--17689943 Score: 194
Period size: 88 Copynumber: 1.8 Consensus size: 86
17689775 GTATGAGGGC
* * ** * *
17689785 AAAATAAAATTTTTGGAAGTTTAAGGGCAAAATGTAATTTTTGAAAGTTTAAGGGTAAGAATGTA
1 AAAATAAAATTTTTAGAAATTTAAGGGCAAAATGTAATTTTAAAAAGTATAAGGGTAAGAATATA
17689850 ATTTTTGGAAGTTCAAGGATA
66 ATTTTTGGAAGTTCAAGGATA
* * *
17689871 AAAATATAATTTTTAAGAAATTTAGGGGTCAAAATGTGATTTTAAAAAGTATAAGGGTCAA-AAT
1 AAAATAAAATTTTT-AGAAATTTAAGGG-CAAAATGTAATTTTAAAAAGTATAAGGGT-AAGAAT
*
17689935 ATGATTTTT
63 ATAATTTTT
17689944 AGACAGTTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
86 13 0.22
87 10 0.17
88 35 0.58
89 2 0.03
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (86 bp):
AAAATAAAATTTTTAGAAATTTAAGGGCAAAATGTAATTTTAAAAAGTATAAGGGTAAGAATATA
ATTTTTGGAAGTTCAAGGATA
Found at i:17689956 original size:29 final size:28
Alignment explanation
Indices: 17689753--17689956 Score: 114
Period size: 29 Copynumber: 7.1 Consensus size: 28
17689743 GGAAAATTTG
* *
17689753 GGGT-AAAATGTGATTTTT-GAAAGTATGA
1 GGGTCAAAATGTAATTTTTAG-AAGT-TTA
** *
17689781 GGG-CAAAATAAAATTTTTGGAAGTTTAA
1 GGGTCAAAATGTAATTTTTAGAAGTTT-A
17689809 GGG-CAAAATGTAATTTTT-GAAAGTTTAA
1 GGGTCAAAATGTAATTTTTAG-AAGTTT-A
* *
17689837 GGGT-AAGAATGTAATTTTTGGAAGTTCAA
1 GGGTCAA-AATGTAATTTTTAGAAGTT-TA
* * * *
17689866 GGATAAAAATATAATTTTTAAGAAATTTA
1 GGGTCAAAATGTAATTTTT-AGAAGTTTA
* * * *
17689895 GGGGTCAAAATGTGATTTTAAAAAGTATAA
1 -GGGTCAAAATGTAATTTTTAGAAGT-TTA
* *
17689925 GGGTCAAAATATGATTTTTAGACAGTTTA
1 GGGTCAAAATGTAATTTTTAGA-AGTTTA
17689954 GGG
1 GGG
17689957 ACCTTCTGGG
Statistics
Matches: 139, Mismatches: 24, Indels: 25
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.01
28 48 0.35
29 62 0.45
30 27 0.19
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (28 bp):
GGGTCAAAATGTAATTTTTAGAAGTTTA
Found at i:17691008 original size:20 final size:20
Alignment explanation
Indices: 17690983--17691032 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
17690973 AATTTCTCTT
17690983 TATTATTAATTAT-TATTTAA
1 TATTA-TAATTATGTATTTAA
*
17691003 TATTATAATTATGTATTTAT
1 TATTATAATTATGTATTTAA
17691023 TATT-TAATTA
1 TATTATAATTA
17691033 AATCGTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TATTATAATTATGTATTTAA
Found at i:17691700 original size:17 final size:17
Alignment explanation
Indices: 17691678--17691726 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
17691668 GAACATTATT
* *
17691678 AATTTAAATTTAGAATA
1 AATTTAAACTTAAAATA
17691695 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
* *
17691712 AATCTAAAATTAAAA
1 AATTTAAACTTAAAA
17691727 ATTGGGTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:17692258 original size:59 final size:59
Alignment explanation
Indices: 17692166--17692279 Score: 183
Period size: 59 Copynumber: 1.9 Consensus size: 59
17692156 CCCAAGCTCG
*
17692166 AGGTAAGAGATTGGTTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAATAGTA
1 AGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAATAGTA
* * **
17692225 AGGTAAGAGATTTGCTGATGGTGATCTGCCCCAAGCTTGGGGTAAGAGATCGAAT
1 AGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAAT
17692280 GGCTACAATC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 50 1.00
ACGTcount: A:0.30, C:0.13, G:0.32, T:0.25
Consensus pattern (59 bp):
AGGTAAGAGATTGGCTGATGGTGATATGCCCCAAGCTCAGGGTAAGAGATCGAATAGTA
Found at i:17692419 original size:76 final size:78
Alignment explanation
Indices: 17692265--17692425 Score: 177
Period size: 76 Copynumber: 2.1 Consensus size: 78
17692255 CCAAGCTTGG
* * * * * *
17692265 GGTAAGAGATCGAATGGCTACAATCTGCCTCAGGCTCGAGGTAAGAGATTTACTAATGATGATCT
1 GGTAAGAGATCGAATGGATACAAACTGCCGCAGGCTCGAGGTAAGAGATCTACTAATGATAATCC
17692330 GCCTTAAACTCGA
66 GCCTTAAACTCGA
* * *
17692343 -GTAAGAGATCGAATGGATGCAAACTG-CGCAGGCTC-AGGGTGAGAGATCTACTGATGATAATC
1 GGTAAGAGATCGAATGGATACAAACTGCCGCAGGCTCGA-GGTAAGAGATCTACTAATGATAATC
**
17692405 CG-CTCTAAGGTCGA
65 CGCCT-TAAACTCGA
17692419 GGTAAGA
1 GGTAAGA
17692426 TATCAAATAA
Statistics
Matches: 69, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
75 3 0.04
76 37 0.54
77 29 0.42
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (78 bp):
GGTAAGAGATCGAATGGATACAAACTGCCGCAGGCTCGAGGTAAGAGATCTACTAATGATAATCC
GCCTTAAACTCGA
Done.