Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008022.1 Hibiscus syriacus cultivar Beakdansim tig00110495_pilon, whole genome shotgun sequence
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: 1039607
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:341418 original size:24 final size:21
Alignment explanation
Indices: 341383--341425 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
341373 GGCTCATTCT
*
341383 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
341406 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
341426 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:343909 original size:26 final size:24
Alignment explanation
Indices: 343880--343934 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
343870 GTTATCCATT
*
343880 TATA-TATGAGATACAAGTTATTATCA
1 TATACTAT-AGATACAA--TATTATAA
*
343906 TATACTATAGTTACAATATTATAA
1 TATACTATAGATACAATATTATAA
343930 TATAC
1 TATAC
343935 ACATTATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 12 0.46
26 11 0.42
27 3 0.12
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (24 bp):
TATACTATAGATACAATATTATAA
Found at i:350270 original size:14 final size:15
Alignment explanation
Indices: 350236--350282 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
350226 AATTTGGAGT
350236 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
350251 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
350265 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
350282 G
1 G
350283 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:357227 original size:17 final size:17
Alignment explanation
Indices: 357205--357247 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
357195 GAGTTGCAAA
357205 ATTTACCAAGAGGCACC
1 ATTTACCAAGAGGCACC
357222 ATTTACCAAGAGGCACC
1 ATTTACCAAGAGGCACC
*
357239 ATTTGCCAA
1 ATTTACCAA
357248 AAGGAAGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.21
Consensus pattern (17 bp):
ATTTACCAAGAGGCACC
Found at i:358877 original size:13 final size:12
Alignment explanation
Indices: 358836--358937 Score: 56
Period size: 13 Copynumber: 8.7 Consensus size: 12
358826 ACAATCTGTC
*
358836 CATCACCATTAT
1 CATCACCATAAT
*
358848 CA-CGCC-TATAT
1 CATCACCATA-AT
358859 CATCACCATAAT
1 CATCACCATAAT
*
358871 CCATCACCATTAT
1 -CATCACCATAAT
*
358884 CA-CGCC-TATAT
1 CATCACCATA-AT
*
358895 CATCACCATATT
1 CATCACCATAAT
358907 CCATCACCAT-AT
1 -CATCACCATAAT
358919 CA-CACC-TATAT
1 CATCACCATA-AT
*
358930 TATCACCA
1 CATCACCA
358938 ACTTATAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 23
0.67 0.10 0.23
Matches are distributed among these distances:
9 1 0.01
10 6 0.09
11 19 0.28
12 18 0.26
13 24 0.35
ACGTcount: A:0.33, C:0.36, G:0.02, T:0.28
Consensus pattern (12 bp):
CATCACCATAAT
Found at i:358881 original size:36 final size:36
Alignment explanation
Indices: 358834--358937 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
358824 ATACAATCTG
358834 TCCATCACCATTATCACGCCTATATCATCACCATAA
1 TCCATCACCATTATCACGCCTATATCATCACCATAA
*
358870 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAA
* *
358906 TCCATCACCA-TATCACACCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
358938 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAA
Found at i:361889 original size:19 final size:19
Alignment explanation
Indices: 361853--361908 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
361843 AAATAAGGGG
361853 ATAATAATATAAGTAATGAA
1 ATAA-AATATAAGTAATGAA
*
361873 ATGAAATATTAAG-AATGAA
1 ATAAAATA-TAAGTAATGAA
*
361892 ATAAAATA-AAGAAATGA
1 ATAAAATATAAGTAATGA
361909 TAGAGATGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.09
18 5 0.16
19 17 0.53
20 7 0.22
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (19 bp):
ATAAAATATAAGTAATGAA
Found at i:362352 original size:19 final size:20
Alignment explanation
Indices: 362311--362361 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
362301 GAAACACCTT
362311 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
362331 TGAAAATACATGATTTTT-A
1 TGAAAATACATGATTTTTGA
*
362350 TGAAGATACATG
1 TGAAAATACATG
362362 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTGA
Found at i:363315 original size:30 final size:31
Alignment explanation
Indices: 363275--363334 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
363265 ACATGCTGCC
**
363275 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
363306 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
363335 TACAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:366017 original size:19 final size:20
Alignment explanation
Indices: 365976--366026 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
365966 GAAACCCCTT
*
365976 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
365996 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
366015 TGAAGATACATG
1 TGAAAATACATG
366027 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:369294 original size:12 final size:11
Alignment explanation
Indices: 369268--369306 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
369258 CCTTGGCTTG
369268 CTTTATCTTTTT
1 CTTT-TCTTTTT
369280 CTTTTCTTTTGT
1 CTTTTCTTTT-T
369292 CTTTTCTTTTT
1 CTTTTCTTTTT
369303 -TTTT
1 CTTTT
369307 TTTGCACTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 7 0.27
12 15 0.58
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:370042 original size:19 final size:20
Alignment explanation
Indices: 370001--370051 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
369991 GAAACCCCTT
*
370001 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
370021 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
370040 TGAAGATACATG
1 TGAAAATACATG
370052 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:371001 original size:30 final size:31
Alignment explanation
Indices: 370961--371020 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
370951 ACATGCTGCC
**
370961 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
370992 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
371021 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:372261 original size:13 final size:12
Alignment explanation
Indices: 372242--372327 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 12
372232 ATATAGGCGT
372242 GATATGGTGATG
1 GATATGGTGATG
372254 GAATATGGTGAT-
1 G-ATATGGTGATG
*
372266 GATATAGGCG-T-
1 GATAT-GGTGATG
372277 GATAATGGTGATG
1 GAT-ATGGTGATG
372290 GAATATGGTGAT-
1 G-ATATGGTGATG
*
372302 GATATAGGCG-T-
1 GATAT-GGTGATG
372313 GATAATGGTGATG
1 GAT-ATGGTGATG
372326 GA
1 GA
372328 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 22 0.37
12 15 0.25
13 21 0.35
14 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:372292 original size:36 final size:36
Alignment explanation
Indices: 372224--372327 Score: 192
Period size: 36 Copynumber: 2.9 Consensus size: 36
372214 ATTTAGAAGT
*
372224 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
372259 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
372295 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
372328 CAGATTGTAT
Statistics
Matches: 67, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.30, C:0.03, G:0.37, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:377878 original size:13 final size:12
Alignment explanation
Indices: 377858--377943 Score: 67
Period size: 11 Copynumber: 7.2 Consensus size: 12
377848 ATATAGGCGT
377858 GATATGGTGATG
1 GATATGGTGATG
377870 GACTATGGTGAT-
1 GA-TATGGTGATG
*
377882 GATATAGGCG-T-
1 GATAT-GGTGATG
377893 GATAATGGTGATG
1 GAT-ATGGTGATG
377906 GAATATGGTGAT-
1 G-ATATGGTGATG
377918 GATATAGGTG-T-
1 GATAT-GGTGATG
377929 GATAATGGTGATG
1 GAT-ATGGTGATG
377942 GA
1 GA
377944 CAGATTGAAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
11 22 0.35
12 18 0.29
13 20 0.32
14 2 0.03
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:377913 original size:36 final size:36
Alignment explanation
Indices: 377840--377943 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
377830 ATTTAGAAGT
* *
377840 TGGTGATAATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
377875 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
377911 TGGTGATGATATAGGTGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
377944 CAGATTGAAT
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.31
36 45 0.69
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.32
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:377931 original size:11 final size:12
Alignment explanation
Indices: 377841--377941 Score: 65
Period size: 11 Copynumber: 8.6 Consensus size: 12
377831 TTTAGAAGTT
*
377841 GGTGATAATATA
1 GGTGATGATATA
*
377853 GGCG-TGATAT-
1 GGTGATGATATA
377863 GGTGATGGACTAT-
1 GGTGAT-GA-TATA
377876 GGTGATGATATA
1 GGTGATGATATA
*
377888 GGCG-TGATA-A
1 GGTGATGATATA
377898 TGGTGATGGA-ATA
1 -GGTGAT-GATATA
377911 TGGTGATGATATA
1 -GGTGATGATATA
377924 GGTG-TGATA-A
1 GGTGATGATATA
377934 TGGTGATG
1 -GGTGATG
377942 GACAGATTGA
Statistics
Matches: 73, Mismatches: 5, Indels: 22
0.73 0.05 0.22
Matches are distributed among these distances:
10 5 0.07
11 26 0.36
12 20 0.27
13 22 0.30
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:379558 original size:14 final size:15
Alignment explanation
Indices: 379540--379580 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
379530 TCCAACAGTC
379540 AAAAGAAGAA-AAAG
1 AAAAGAAGAAGAAAG
*
379554 CAAAGAA-AAGAAAG
1 AAAAGAAGAAGAAAG
*
379568 AAAAGAAGTAGAA
1 AAAAGAAGAAGAA
379581 GCACTCATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 2 0.09
14 16 0.73
15 4 0.18
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (15 bp):
AAAAGAAGAAGAAAG
Found at i:384879 original size:19 final size:20
Alignment explanation
Indices: 384855--384905 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
384845 TGGCCAAGAG
* *
384855 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
384874 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
384894 CATGTATTTTCA
1 CATGTATTTTCA
384906 AAAGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:385655 original size:34 final size:31
Alignment explanation
Indices: 385613--385684 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
385603 ATACAAAAAG
*
385613 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGAA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTC--AA
385647 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
385678 AAAGAAA
1 AAAGAAA
385685 GCAAGCCAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
31 9 0.25
33 7 0.19
34 20 0.56
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.06
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:388692 original size:19 final size:20
Alignment explanation
Indices: 388668--388718 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
388658 CGGCCAAGAG
* *
388668 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
388687 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
388707 CATGTATTTTCA
1 CATGTATTTTCA
388719 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:391850 original size:19 final size:21
Alignment explanation
Indices: 391826--391869 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
391816 CGACCAAGAG
391826 CATGTATCTTCA-TT-AAAAT
1 CATGTATCTTCATTTAAAAAT
*
391845 CATGTATTTTCATTTAAAAAT
1 CATGTATCTTCATTTAAAAAT
391866 CATG
1 CATG
391870 CATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 9 0.41
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (21 bp):
CATGTATCTTCATTTAAAAAT
Found at i:391866 original size:21 final size:19
Alignment explanation
Indices: 391826--391877 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
391816 CGACCAAGAG
*
391826 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
391845 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
391866 CATGCATTTTCA
1 CATGTATTTTCA
391878 AAGGGATGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:395137 original size:19 final size:21
Alignment explanation
Indices: 395113--395156 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 21
395103 CGGCAAAGAG
395113 CATGTATATTCA-TT-AAAAT
1 CATGTATATTCATTTAAAAAT
*
395132 CATGTATTTTCATTTAAAAAT
1 CATGTATATTCATTTAAAAAT
395153 CATG
1 CATG
395157 CATTTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 9 0.41
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (21 bp):
CATGTATATTCATTTAAAAAT
Found at i:395153 original size:21 final size:19
Alignment explanation
Indices: 395113--395164 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
395103 CGGCAAAGAG
*
395113 CATGTATATTCATTAAAAT
1 CATGTATTTTCATTAAAAT
395132 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
395153 CATGCATTTTCA
1 CATGTATTTTCA
395165 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.44
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:397403 original size:5 final size:5
Alignment explanation
Indices: 397388--397434 Score: 51
Period size: 5 Copynumber: 9.0 Consensus size: 5
397378 TTTAGAGTGC
*
397388 AAAAG -AAAG AAAAG AAAAA AAAAG CAAAAG CAAAAG CAAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG -AAAAG -AAAAG AAAAG
397435 TGAAGCAAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 4 0.11
5 17 0.45
6 17 0.45
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:397424 original size:12 final size:11
Alignment explanation
Indices: 397393--397434 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 11
397383 AGTGCAAAAG
397393 AAAGAAAAG-A
1 AAAGAAAAGCA
*
397403 AAAAAAAAGCA
1 AAAGAAAAGCA
397414 AAAGCAAAAGCA
1 AAAG-AAAAGCA
397426 AAAGAAAAG
1 AAAGAAAAG
397435 TGAAGCAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 8 0.29
11 9 0.32
12 11 0.39
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGCA
Found at i:403053 original size:91 final size:91
Alignment explanation
Indices: 402896--403078 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 91
402886 AATAGAACAC
*
402896 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAAATG
*
402961 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
** * * * *
402987 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGTATGTGGTTCATTTAGGCACCAAAATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAAATG
403052 AAGAGTTCTCTCCCTATTCGACCAAG
66 AAGAGTTCTCTCCCTATTCGACCAAG
403078 C
1 C
403079 ATCAACTACC
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAAATG
AAGAGTTCTCTCCCTATTCGACCAAG
Found at i:403907 original size:15 final size:15
Alignment explanation
Indices: 403896--403924 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
403886 ACTCAAAAAG
403896 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
403911 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
403925 GTTGAAGCAC
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:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:407866 original size:22 final size:23
Alignment explanation
Indices: 407841--407890 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
407831 AATGGAAGGA
* *
407841 TGATGTTATTGGCGTGAT-ATGG
1 TGATGATATAGGCGTGATAATGG
407863 TGATGATATAGGCGTGATAATGG
1 TGATGATATAGGCGTGATAATGG
407886 TGATG
1 TGATG
407891 GAATATGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.24, C:0.04, G:0.36, T:0.36
Consensus pattern (23 bp):
TGATGATATAGGCGTGATAATGG
Found at i:407904 original size:36 final size:36
Alignment explanation
Indices: 407857--407940 Score: 150
Period size: 36 Copynumber: 2.3 Consensus size: 36
407847 TATTGGCGTG
*
407857 ATATGGTGATGATATAGGCGTGATAATGGTGATGGA
1 ATATGGTGATGATATAGGCGTGATAATGGAGATGGA
407893 ATATGGTGATGATATAGGCGTGATAATGGAGATGGA
1 ATATGGTGATGATATAGGCGTGATAATGGAGATGGA
*
407929 TTATGGTGATGA
1 ATATGGTGATGA
407941 AAATAGTATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (36 bp):
ATATGGTGATGATATAGGCGTGATAATGGAGATGGA
Found at i:412947 original size:22 final size:23
Alignment explanation
Indices: 412922--412971 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
412912 AATGGAAGGA
* *
412922 TGATGTTATTGGCGTGAT-ATGG
1 TGATGATATAGGCGTGATAATGG
412944 TGATGATATAGGCGTGATAATGG
1 TGATGATATAGGCGTGATAATGG
412967 TGATG
1 TGATG
412972 GACTATGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.24, C:0.04, G:0.36, T:0.36
Consensus pattern (23 bp):
TGATGATATAGGCGTGATAATGG
Found at i:412986 original size:36 final size:36
Alignment explanation
Indices: 412939--413021 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
412929 ATTGGCGTGA
*
412939 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
*
412975 TATGGTGATGATATAGGCGTGATAATGGAGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
413011 TATGGTGATGA
1 TATGGTGATGA
413022 AAATAGTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
Found at i:413393 original size:18 final size:18
Alignment explanation
Indices: 413370--413409 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
413360 AGAAATAAAT
413370 GATGCTTGGATGAGGGGA
1 GATGCTTGGATGAGGGGA
413388 GATGCTTGGATGAGGGGA
1 GATGCTTGGATGAGGGGA
413406 GATG
1 GATG
413410 TCTTTGGCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.05, G:0.50, T:0.23
Consensus pattern (18 bp):
GATGCTTGGATGAGGGGA
Found at i:415201 original size:23 final size:24
Alignment explanation
Indices: 415173--415231 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
415163 AAAATCAGCA
415173 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
415196 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
415220 AAGAAAA-AAAAG
1 AAGAAAATAAAAG
415232 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.64, C:0.10, G:0.17, T:0.08
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:420264 original size:36 final size:36
Alignment explanation
Indices: 420216--420320 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
420206 GATACAATCT
*
420216 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
420252 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
420288 GTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
420321 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:420957 original size:16 final size:15
Alignment explanation
Indices: 420924--420975 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
420914 GTAAGTTATC
420924 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
420939 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
420955 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
420970 TTCATT
1 TTCATT
420976 ACCATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:424111 original size:14 final size:15
Alignment explanation
Indices: 424088--424131 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
424078 TTTGGAGTGC
424088 AAAAGAAAGAAAATA
1 AAAAGAAAGAAAATA
*
424103 AAAAG-AAGAAAATC
1 AAAAGAAAGAAAATA
424117 AAAAGCAAAAGAAAA
1 AAAAG--AAAGAAAA
424132 GTGAAGCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 13 0.52
15 5 0.20
17 7 0.28
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (15 bp):
AAAAGAAAGAAAATA
Found at i:428063 original size:35 final size:37
Alignment explanation
Indices: 427994--428073 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
427984 ATACTATTTC
*
427994 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
428031 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
428066 CATCACCA
1 CATCACCA
428074 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:429654 original size:21 final size:19
Alignment explanation
Indices: 429621--429664 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
429611 TGTAGGAGTC
* *
429621 TTTTTCTTTTCTTTTTGTT
1 TTTTTCTTTTCTTGTTGCT
429640 TTTTTCTTCTTTCTTGTTGCT
1 TTTTTC-T-TTTCTTGTTGCT
429661 TTTT
1 TTTT
429665 GTTGTAGCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 1 0.05
21 14 0.67
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTGTTGCT
Found at i:430049 original size:33 final size:33
Alignment explanation
Indices: 430007--430075 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
429997 GTTGATGAAT
*
430007 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
430040 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
430073 GAA
1 GAA
430076 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:430080 original size:13 final size:12
Alignment explanation
Indices: 430061--430125 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
430051 TTATTGGCGT
430061 GATATGGTGATG
1 GATATGGTGATG
430073 GAATATGGTGAT-
1 G-ATATGGTGATG
*
430085 GATATAGGCG-T-
1 GATAT-GGTGATG
430096 GATAATGGTGATG
1 GAT-ATGGTGATG
430109 GACTATGGTGAT-
1 GA-TATGGTGATG
430121 GATAT
1 GATAT
430126 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:430116 original size:36 final size:36
Alignment explanation
Indices: 430046--430158 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
430036 AATGGAAGGA
* *
430046 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
430081 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
430117 TGATGATATAGGCGTGATAATAGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
430153 TGATGA
1 TGATGA
430159 AAATAGTATC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 55 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:436147 original size:28 final size:25
Alignment explanation
Indices: 436092--436147 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
436082 TTCTTTGCTT
**
436092 TTTCTTCTTTTGAGTGCTGGATTTC
1 TTTCTTCTTTTGAGTGCTCAATTTC
436117 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGC-TCAATTTC
436145 TTT
1 TTT
436148 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 6 0.23
28 9 0.35
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (25 bp):
TTTCTTCTTTTGAGTGCTCAATTTC
Found at i:452222 original size:16 final size:16
Alignment explanation
Indices: 452201--452232 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
452191 TAGTTAGCTC
*
452201 ATTTGCATTTTAACAT
1 ATTTGCATTCTAACAT
452217 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
452233 TGGTGGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:453372 original size:19 final size:20
Alignment explanation
Indices: 453348--453387 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
453338 ATCTTTTTAT
453348 TTATTTAATTTCATT-CTTA
1 TTATTTAATTTCATTACTTA
*
453367 TTATTTATTTTCATTACTTA
1 TTATTTAATTTCATTACTTA
453387 T
1 T
453388 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTAATTTCATTACTTA
Found at i:456256 original size:19 final size:20
Alignment explanation
Indices: 456240--456284 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
456230 ATTTATTTCA
456240 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
456259 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
456277 TATTCATT
1 T-TTCATT
456285 TTTTAAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Found at i:464561 original size:24 final size:23
Alignment explanation
Indices: 464533--464594 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
464523 ACTTTTCTTT
*
464533 CTTTCTTTTTCTTTTTTTCGATTG
1 CTTTCTTTTTCTTTTTTT-GAGTG
** *
464557 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCTTTTTCTTTTTTTGAGTG
*
464580 CTTTTATTTTTCTTT
1 C-TTTCTTTTTCTTT
464595 GCTGATTTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 5 0.17
24 24 0.83
ACGTcount: A:0.08, C:0.16, G:0.08, T:0.68
Consensus pattern (23 bp):
CTTTCTTTTTCTTTTTTTGAGTG
Found at i:466991 original size:25 final size:25
Alignment explanation
Indices: 466963--467018 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
466953 AATATTTTAT
466963 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
466988 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
*
467013 AAATAA
1 ATATAA
467019 AAAAATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:466991 original size:34 final size:33
Alignment explanation
Indices: 466951--467040 Score: 153
Period size: 34 Copynumber: 2.7 Consensus size: 33
466941 CCCGAACCCG
*
466951 AAAATATTTTATATATAATTAATATAAAAAATA
1 AAAATATTATATATATAATTAATATAAAAAATA
466984 TAAAATATTATATATATAATTAATATAAAAAATA
1 -AAAATATTATATATATAATTAATATAAAAAATA
*
467018 AAAAAATTATATATATAATTAAT
1 AAAATATTATATATATAATTAAT
467041 CGAGGCAGGT
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
33 22 0.41
34 32 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AAAATATTATATATATAATTAATATAAAAAATA
Found at i:469174 original size:17 final size:17
Alignment explanation
Indices: 469152--469192 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
469142 TCATTTTAAG
* *
469152 CATGTTATTATCTCATA
1 CATGTTAATATATCATA
*
469169 CATGTTAATATATCATG
1 CATGTTAATATATCATA
469186 CATGTTA
1 CATGTTA
469193 GATCCTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (17 bp):
CATGTTAATATATCATA
Found at i:471968 original size:19 final size:20
Alignment explanation
Indices: 471913--471971 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
471903 GAGTGCAAAA
471913 AGAAAGAAAAAGACAAAAGAAG
1 AGAAAG-AAAAGA-AAAAGAAG
*
471935 AGAAA-AATCAG-AAAAGAAG
1 AGAAAGAA-AAGAAAAAGAAG
471954 A-AAAGAAAAGAAAAAGAA
1 AGAAAGAAAAGAAAAAGAA
471972 AAATTCAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 18 0.56
20 2 0.06
21 2 0.06
22 5 0.16
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (20 bp):
AGAAAGAAAAGAAAAAGAAG
Found at i:473255 original size:24 final size:24
Alignment explanation
Indices: 473240--473292 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
473230 AAAATCATGG
*
473240 CTTTTGAAAAACCAAAAGATGTGA
1 CTTTTGAAAAACCAAAAGATATGA
* * **
473264 CTTTTGAAGAACCAATAGCCATGA
1 CTTTTGAAAAACCAAAAGATATGA
473288 CTTTT
1 CTTTT
473293 AGTGATTCAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (24 bp):
CTTTTGAAAAACCAAAAGATATGA
Found at i:474416 original size:30 final size:31
Alignment explanation
Indices: 474382--474441 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
474372 CTTAGCTTTA
**
474382 TATTATGCTTACATATGTTTTAGAT-TCATT
1 TATTATGCTTACATATCATTTAGATATCATT
* *
474412 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGCTTACATATCATTTAGATATCAT
474442 GGCAGTATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (31 bp):
TATTATGCTTACATATCATTTAGATATCATT
Found at i:475363 original size:19 final size:20
Alignment explanation
Indices: 475339--475389 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
475329 CGGCCAAGAG
* *
475339 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
475358 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
475378 CATGTATTTTCA
1 CATGTATTTTCA
475390 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:475823 original size:18 final size:20
Alignment explanation
Indices: 475800--475838 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
475790 ATTTATTTAT
475800 TTATTTA-TTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
475818 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
475838 T
1 T
475839 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 7 0.37
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:475841 original size:22 final size:20
Alignment explanation
Indices: 475796--475844 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
475786 TATCATTTAT
475796 TTAT-TTATTTATTTCATTC
1 TTATATTATTTATTTCATTC
475815 -T-TATTATTTATTTTCATTAC
1 TTATATTATTTA-TTTCATT-C
475835 TTATATTATT
1 TTATATTATT
475845 ATCCCCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
17 1 0.04
18 8 0.32
19 7 0.28
20 1 0.04
21 1 0.04
22 7 0.28
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATATTATTTATTTCATTC
Found at i:480342 original size:18 final size:17
Alignment explanation
Indices: 480293--480342 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
480283 AATTGGAGTG
480293 CAAAAAGAAAGAAAAAGA
1 CAAAAAGAAA-AAAAAGA
**
480311 CAAAAAGAAGAAAAAATT
1 CAAAAAGAA-AAAAAAGA
480329 CAGAAAAGAAAAAA
1 CA-AAAAGAAAAAA
480343 GAAATTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (17 bp):
CAAAAAGAAAAAAAAGA
Found at i:486374 original size:23 final size:23
Alignment explanation
Indices: 486329--486374 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
486319 TTATACCTAT
*
486329 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
486352 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
486375 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:488004 original size:8 final size:8
Alignment explanation
Indices: 487976--488023 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
487966 TTGGAGTGCA
487976 AAAAGAAAG
1 AAAAG-AAG
487985 AAAAGACA-
1 AAAAGA-AG
487993 AAAAGAAG
1 AAAAGAAG
488001 AAAAGAAG
1 AAAAGAAG
488009 AAAAGAAG
1 AAAAGAAG
488017 AAAAGAA
1 AAAAGAA
488024 AAGAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 30 0.81
9 6 0.16
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:488006 original size:5 final size:5
Alignment explanation
Indices: 487976--488030 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
487966 TTGGAGTGCA
487976 AAAAG -AAAG AAAAG ACAAA- AAGAAG AAAAG AAGAA- AAGAAG AAAAG
1 AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AA-AAG AA-AAG AAAAG
488022 AAAAG AAAA
1 AAAAG AAAA
488031 AGAGAAGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:488033 original size:16 final size:15
Alignment explanation
Indices: 487975--488033 Score: 64
Period size: 16 Copynumber: 3.7 Consensus size: 15
487965 ATTGGAGTGC
*
487975 AAAAAGAAAGAAAAG
1 AAAAAAAAAGAAAAG
*
487990 ACAAAAAGAAGAAAAG
1 A-AAAAAAAAGAAAAG
*
488006 AAGAAAAGAAGAAAAG
1 AA-AAAAAAAGAAAAG
488022 AAAAGAAAAAGA
1 AAAA-AAAAAGA
488034 GAAGTTCAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
15 4 0.11
16 34 0.89
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:490958 original size:23 final size:23
Alignment explanation
Indices: 490913--490958 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
490903 TTATACCTAT
*
490913 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
490936 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
490959 TATATATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:493544 original size:24 final size:21
Alignment explanation
Indices: 493510--493552 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
493500 TCCACAAGAC
*
493510 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
493532 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
493553 AGAATGTGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:497257 original size:36 final size:36
Alignment explanation
Indices: 497209--497349 Score: 239
Period size: 36 Copynumber: 3.9 Consensus size: 36
497199 GATACAATCT
*
497209 GTCCATCACCATTATCATGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
497245 GTCCATCTCCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
497281 GTCCATCACCATTATCACGCCTATTTCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
497317 GTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
497350 ACTTATAAAT
Statistics
Matches: 99, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.20
36 79 0.80
ACGTcount: A:0.29, C:0.35, G:0.06, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:497289 original size:13 final size:11
Alignment explanation
Indices: 497212--497332 Score: 68
Period size: 11 Copynumber: 10.2 Consensus size: 11
497202 ACAATCTGTC
497212 CATCACCATTAT
1 CATCACCA-TAT
*
497224 CATGC-CTATAT
1 CAT-CACCATAT
497235 CATCACCATAGT
1 CATCACCATA-T
*
497247 CCATCTCCATTAT
1 -CATCACCA-TAT
*
497260 CA-CGCCTATAT
1 CATCACC-ATAT
497271 CATCACCATAGT
1 CATCACCATA-T
497283 CCATCACCATTAT
1 -CATCACCA-TAT
* *
497296 CA-CGCCTATTT
1 CATCACC-ATAT
497307 CATCACCATAGT
1 CATCACCATA-T
497319 CCATCACCATAT
1 -CATCACCATAT
497331 CA
1 CA
497333 CGCCTATATT
Statistics
Matches: 86, Mismatches: 9, Indels: 29
0.69 0.07 0.23
Matches are distributed among these distances:
10 1 0.01
11 32 0.37
12 21 0.24
13 28 0.33
14 4 0.05
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (11 bp):
CATCACCATAT
Found at i:497829 original size:14 final size:15
Alignment explanation
Indices: 497795--497841 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
497785 AATTTGGAGT
497795 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
497810 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
497824 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
497841 G
1 G
497842 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:505810 original size:24 final size:24
Alignment explanation
Indices: 505778--505824 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
505768 GATGTAGGAG
505778 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
505801 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
505825 GTAGCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:507748 original size:13 final size:11
Alignment explanation
Indices: 507726--507791 Score: 62
Period size: 13 Copynumber: 5.5 Consensus size: 11
507716 TATCACGCCT
507726 ATATCATCACC
1 ATATCATCACC
507737 ATAGTCCATCACC
1 ATA-T-CATCACC
*
507750 ATTATCA-CGCC
1 A-TATCATCACC
507761 TATATCATCACC
1 -ATATCATCACC
507773 ATATTCCATCACC
1 ATA-T-CATCACC
507786 ATATCA
1 ATATCA
507792 CGCCTATATT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
11 16 0.35
12 9 0.20
13 19 0.41
14 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.29
Consensus pattern (11 bp):
ATATCATCACC
Found at i:507798 original size:35 final size:36
Alignment explanation
Indices: 507708--507808 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
507698 GACAGGATCA
507708 CATCA-CATTATCACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
507743 CATCACCATTATCACGCCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
507779 CATCACCA-TATCACGCCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
507809 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
35 26 0.41
36 37 0.59
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.29
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTC
Found at i:510192 original size:19 final size:21
Alignment explanation
Indices: 510149--510200 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
510139 GAAATCCCTT
510149 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
510170 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
510189 TGAAGATACATG
1 TGAAAATACATG
510201 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:513365 original size:8 final size:8
Alignment explanation
Indices: 513354--513378 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
513344 TCTTTTTCTT
513354 TTCTTTTC
1 TTCTTTTC
513362 TTCTTTTC
1 TTCTTTTC
513370 TTCTTTTC
1 TTCTTTTC
513378 T
1 T
513379 GATTTTTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:513702 original size:19 final size:20
Alignment explanation
Indices: 513656--513704 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
513646 TAATAAAGGG
513656 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
513676 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
513695 AATAAAATAA
1 AATAAAATAA
513705 AGAAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:515186 original size:36 final size:36
Alignment explanation
Indices: 515127--515239 Score: 149
Period size: 36 Copynumber: 3.2 Consensus size: 36
515117 GATACTATTT
*
515127 TCATCACCATAATCCAT-ATCCATTGTCACGCCTATA
1 TCATCACCATAATCCATCA-CCATTATCACGCCTATA
* *
515163 TCATCACCATAGTCTATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
515199 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
515234 ACATCA
1 TCATCA
515240 TCCTTCCATT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
35 17 0.25
36 51 0.74
37 1 0.01
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.28
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:515908 original size:19 final size:21
Alignment explanation
Indices: 515865--515916 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
515855 GAAACCCCTT
515865 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
515886 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
515905 TGAAGATACATG
1 TGAAAATACATG
515917 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:522911 original size:36 final size:36
Alignment explanation
Indices: 522866--522934 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
522856 CTTCAAAAAG
* *
522866 CTTTTCTTCATTTGAATTTTCCTCTAAACGTTCAAT
1 CTTTTCTTCATTTGAAATTTCCTCCAAACGTTCAAT
*
522902 CTTTTCTTCATTTGAAATTTCCTCCAAATGTTC
1 CTTTTCTTCATTTGAAATTTCCTCCAAACGTTC
522935 TTCATTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.22, C:0.23, G:0.06, T:0.49
Consensus pattern (36 bp):
CTTTTCTTCATTTGAAATTTCCTCCAAACGTTCAAT
Found at i:522943 original size:27 final size:27
Alignment explanation
Indices: 522905--522962 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
522895 GTTCAATCTT
522905 TTCTTCATTTGAAATTTCCTCCAAATG
1 TTCTTCATTTGAAATTTCCTCCAAATG
522932 TTCTTCATTTGAAATTTCCTCCAAATG
1 TTCTTCATTTGAAATTTCCTCCAAATG
522959 TTCT
1 TTCT
522963 CCTCTAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (27 bp):
TTCTTCATTTGAAATTTCCTCCAAATG
Found at i:522977 original size:16 final size:16
Alignment explanation
Indices: 522956--522986 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
522946 TTTCCTCCAA
522956 ATGTTCTCCTCTAAAC
1 ATGTTCTCCTCTAAAC
522972 ATGTTCTCCTCTAAA
1 ATGTTCTCCTCTAAA
522987 TTTGTGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (16 bp):
ATGTTCTCCTCTAAAC
Found at i:524931 original size:17 final size:17
Alignment explanation
Indices: 524901--524941 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
524891 GTGTTGCAAT
524901 AAAAG-AAA-AAAAGA-
1 AAAAGAAAACAAAAGAG
524915 AAGAAGAAAACAAAAGAG
1 AA-AAGAAAACAAAAGAG
524933 AAAAGAAAA
1 AAAAGAAAA
524942 AGACTCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 2 0.09
15 3 0.13
16 3 0.13
17 13 0.57
18 2 0.09
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAGAAAACAAAAGAG
Found at i:527064 original size:19 final size:20
Alignment explanation
Indices: 527025--527064 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
527015 GAATAATAAT
527025 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
527045 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
527064 A
1 A
527065 ATAAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:533381 original size:10 final size:10
Alignment explanation
Indices: 533346--533371 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
533336 AATTTTTTTT
533346 AAAAAAGGCA
1 AAAAAAGGCA
533356 AAAAAAGGCA
1 AAAAAAGGCA
533366 AAAAAA
1 AAAAAA
533372 AAAGCCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGGCA
Found at i:542604 original size:19 final size:18
Alignment explanation
Indices: 542582--542628 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
542572 AGTGAATAAT
542582 AATATAAGTAATGAAAAGA
1 AATATAAG-AATGAAAAGA
*
542601 AATAATAAGAATGAAATGA
1 AAT-ATAAGAATGAAAAGA
542620 AATA-AAGAA
1 AATATAAGAA
542629 GAGATAGAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 5 0.19
18 1 0.04
19 15 0.58
20 5 0.19
ACGTcount: A:0.66, C:0.00, G:0.15, T:0.19
Consensus pattern (18 bp):
AATATAAGAATGAAAAGA
Found at i:546045 original size:19 final size:18
Alignment explanation
Indices: 546023--546068 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
546013 TTTTCTTTTA
546023 TTCTTTTATG-ATTTTTCT
1 TTCTTTT-TGTATTTTTCT
*
546041 CTTCTTTTTGTCTTTTTCT
1 -TTCTTTTTGTATTTTTCT
546060 TTCTTTTTG
1 TTCTTTTTG
546069 CACTCCAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.04, C:0.15, G:0.07, T:0.74
Consensus pattern (18 bp):
TTCTTTTTGTATTTTTCT
Found at i:550300 original size:35 final size:36
Alignment explanation
Indices: 550209--550300 Score: 125
Period size: 35 Copynumber: 2.6 Consensus size: 36
550199 AAGATACAAT
* * *
550209 CTAT-TCATCACCATCTTCTATCACCATTATCATGC
1 CTATATCATCACCATATTCCATCACCATTATCACGC
*
550244 CTATATCATCACCATAGTCCATCACCA-TATCACGC
1 CTATATCATCACCATATTCCATCACCATTATCACGC
*
550279 CTATATCATCACCAAATTCCAT
1 CTATATCATCACCATATTCCAT
550301 TTCCATTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 31 0.62
36 19 0.38
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (36 bp):
CTATATCATCACCATATTCCATCACCATTATCACGC
Found at i:550469 original size:15 final size:16
Alignment explanation
Indices: 550432--550469 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
550422 TCTTTGATAA
550432 CTTTTC-TATCCATTT
1 CTTTTCTTATCCATTT
550447 CTTTTCTTAT-CATTT
1 CTTTTCTTATCCATTT
*
550462 GTTTTCTT
1 CTTTTCTT
550470 CTTCTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.11, C:0.21, G:0.03, T:0.66
Consensus pattern (16 bp):
CTTTTCTTATCCATTT
Found at i:550669 original size:9 final size:9
Alignment explanation
Indices: 550644--550684 Score: 64
Period size: 9 Copynumber: 4.4 Consensus size: 9
550634 CTTGGAGTGC
*
550644 AAAAAGAAA
1 AAAAAGAAG
550653 AGAAAAGAAG
1 A-AAAAGAAG
550663 AAAAAGAAG
1 AAAAAGAAG
550672 AAAAAGAAG
1 AAAAAGAAG
550681 AAAA
1 AAAA
550685 GAAAAAGAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAAAGAAG
Found at i:550676 original size:18 final size:19
Alignment explanation
Indices: 550644--550694 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
550634 CTTGGAGTGC
550644 AAAAAGAAAAGAAAAGAAG
1 AAAAAGAAAAGAAAAGAAG
*
550663 AAAAAGAAGA-AAAAGAAG
1 AAAAAGAAAAGAAAAGAAG
550681 -AAAAGAAAAAGAAA
1 AAAAAG-AAAAGAAA
550695 TTCATAACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.18
18 11 0.39
19 12 0.43
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAGAAG
Found at i:550679 original size:23 final size:23
Alignment explanation
Indices: 550650--550693 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
550640 GTGCAAAAAG
550650 AAAAGAA-AAGAAGAAAAAGAAGA
1 AAAAGAAGAA-AAGAAAAAGAAGA
550673 AAAAGAAGAAAAGAAAAAGAA
1 AAAAGAAGAAAAGAAAAAGAA
550694 ATTCATAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (23 bp):
AAAAGAAGAAAAGAAAAAGAAGA
Found at i:552859 original size:2 final size:2
Alignment explanation
Indices: 552852--552890 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
552842 ATCACCAACT
552852 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
552891 TCTGCTACCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:555264 original size:15 final size:15
Alignment explanation
Indices: 555244--555276 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
555234 TTGATAACAT
555244 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
*
555259 TTCTTTCCATTTCTA
1 TTCTTTCCATTTCAA
555274 TTC
1 TTC
555277 CCTTTCTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (15 bp):
TTCTTTCCATTTCAA
Found at i:555493 original size:6 final size:6
Alignment explanation
Indices: 555482--555516 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
555472 CAAAAGCAAC
*
555482 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAA
555517 GACTCCTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.83, C:0.03, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:555503 original size:13 final size:12
Alignment explanation
Indices: 555479--555516 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
555469 CAACAAAAGC
555479 AACAAAAAGAAA
1 AACAAAAAGAAA
*
555491 AAGAAAGAAGAAA
1 AACAAA-AAGAAA
555504 AACAAAAAGAAA
1 AACAAAAAGAAA
555516 A
1 A
555517 GACTCCTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 12 0.52
13 11 0.48
ACGTcount: A:0.82, C:0.05, G:0.13, T:0.00
Consensus pattern (12 bp):
AACAAAAAGAAA
Found at i:560375 original size:19 final size:18
Alignment explanation
Indices: 560353--560389 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
560343 CCAGGACTCA
*
560353 AAAAGAAGAAAAAGCAAAG
1 AAAAGAAAAAAAAG-AAAG
560372 AAAAGAAAAAAAAGAAAG
1 AAAAGAAAAAAAAGAAAG
560390 TTGAAGCACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAAGAAAG
Found at i:561222 original size:23 final size:23
Alignment explanation
Indices: 561177--561222 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
561167 TTATACCTAT
*
561177 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
561200 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
561223 TATATTATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:563275 original size:24 final size:21
Alignment explanation
Indices: 563241--563283 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
563231 TCCACAAGAT
*
563241 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
563263 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
563284 AGAATGAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:571384 original size:22 final size:21
Alignment explanation
Indices: 571352--571392 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
571342 CCATTTCCAT
571352 TTCATCATCAACACCATCAAC
1 TTCATCATCAACACCATCAAC
*
571373 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
571393 TTTCTGTAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.37, C:0.37, G:0.02, T:0.24
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:573819 original size:16 final size:16
Alignment explanation
Indices: 573789--573822 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
573779 GAAAGCACTC
573789 AAAAAAAGAAGAAGAA
1 AAAAAAAGAAGAAGAA
573805 AAAACAAAGAA-AAGAA
1 AAAA-AAAGAAGAAGAA
573821 AA
1 AA
573823 GAAAGAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAGAAGAA
Found at i:575955 original size:19 final size:21
Alignment explanation
Indices: 575931--575982 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
575921 CGGCCAAGAG
*
575931 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
575950 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
575971 CATGTATTTTCA
1 CATGTATTTTCA
575983 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:581133 original size:24 final size:21
Alignment explanation
Indices: 581098--581140 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
581088 GGCTCATTCT
*
581098 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
581121 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
581141 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:590147 original size:19 final size:20
Alignment explanation
Indices: 590118--590171 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
590108 CCATTCGGCC
590118 AAGAG-CATGTATTTTAATT
1 AAGAGTCATGTATTTTAATT
*
590137 -AGAGTCATGTATTTTCATT
1 AAGAGTCATGTATTTTAATT
* *
590156 AAAAATCATGTATTTT
1 AAGAGTCATGTATTTT
590172 CAAAGGGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 4 0.13
19 13 0.43
20 13 0.43
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.44
Consensus pattern (20 bp):
AAGAGTCATGTATTTTAATT
Found at i:590166 original size:20 final size:19
Alignment explanation
Indices: 590123--590173 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
590113 CGGCCAAGAG
* * *
590123 CATGTATTTTAATTAGAGT
1 CATGTATTTTCATTAAAAT
590142 CATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
590162 CATGTATTTTCA
1 CATGTATTTTCA
590174 AAGGGATTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:593133 original size:33 final size:33
Alignment explanation
Indices: 593089--593157 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
593079 CATCACCATA
*
593089 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
593122 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
593155 TTC
1 TTC
593158 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:597562 original size:36 final size:36
Alignment explanation
Indices: 597510--597622 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 36
597500 GATACTATTT
* *
597510 TCATCATCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
597546 TCATCACCATAGTCCATAACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* * *
597582 TCATCACCATATTCCATCACCA-TATCATGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
597617 ACATCA
1 TCATCA
597623 TCCTTCCATT
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
35 16 0.24
36 52 0.76
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.29
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:597637 original size:33 final size:33
Alignment explanation
Indices: 597593--597661 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
597583 CATCACCATA
*
597593 TTCCATCACCATATCAT-GCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
597626 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
597659 TTC
1 TTC
597662 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.81
34 6 0.19
ACGTcount: A:0.30, C:0.35, G:0.01, T:0.33
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:606625 original size:21 final size:22
Alignment explanation
Indices: 606589--606630 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
606579 AAATGGTTAT
606589 AGTATAGAAATGAATATAGTAAA
1 AGTATAGAAATGAATAT-GTAAA
606612 AGTA-AGAAA-GAATATGTAA
1 AGTATAGAAATGAATATGTAA
606631 GAAGAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 5 0.26
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (22 bp):
AGTATAGAAATGAATATGTAAA
Found at i:607736 original size:19 final size:20
Alignment explanation
Indices: 607697--607748 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
607687 GAAACCCCTT
607697 TGAAAATACATGATGTTTTAA
1 TGAAAATACATGA-GTTTTAA
607718 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGAGTTTTAA
*
607737 TGAAGATACATG
1 TGAAAATACATG
607749 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGAGTTTTAA
Found at i:609114 original size:16 final size:17
Alignment explanation
Indices: 609089--609134 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 17
609079 GTTGAAAAGG
609089 CATC-TTCATG-GGCAA
1 CATCATTCATGAGGCAA
*
609104 CATCATTCATGAAAGGTAA
1 CATCATTCATG--AGGCAA
609123 CATCATTCATGA
1 CATCATTCATGA
609135 AAGGTCACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.15
16 6 0.23
17 1 0.04
19 15 0.58
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (17 bp):
CATCATTCATGAGGCAA
Found at i:609126 original size:19 final size:19
Alignment explanation
Indices: 609102--609139 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
609092 CTTCATGGGC
609102 AACATCATTCATGAAAGGT
1 AACATCATTCATGAAAGGT
609121 AACATCATTCATGAAAGGT
1 AACATCATTCATGAAAGGT
609140 CACAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (19 bp):
AACATCATTCATGAAAGGT
Found at i:612680 original size:1 final size:1
Alignment explanation
Indices: 612676--612702 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
612666 TTTGAATTTG
612676 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
612703 GCACGCCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:617069 original size:19 final size:20
Alignment explanation
Indices: 617023--617071 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
617013 TAATAAAGGG
617023 AATAATAAT-ATAAGTAATGA
1 AATAA-AATAATAAGTAATGA
617043 AA-ATAAATAATAAG-AATGA
1 AATA-AAATAATAAGTAATGA
617062 AATAAAATAA
1 AATAAAATAA
617072 AGAAAGGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.24
Consensus pattern (20 bp):
AATAAAATAATAAGTAATGA
Found at i:617526 original size:19 final size:21
Alignment explanation
Indices: 617483--617534 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
617473 GAAACCCCTT
617483 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
617504 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
617523 TGAAGATACATG
1 TGAAAATACATG
617535 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:619645 original size:23 final size:23
Alignment explanation
Indices: 619615--619662 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
619605 CTAGGAAAGC
619615 AACAAGGATCCTGCTCAAATAAG
1 AACAAGGATCCTGCTCAAATAAG
619638 AACAAGGATCCTGCTCAAATAAG
1 AACAAGGATCCTGCTCAAATAAG
619661 AA
1 AA
619663 AGCTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (23 bp):
AACAAGGATCCTGCTCAAATAAG
Found at i:623197 original size:19 final size:20
Alignment explanation
Indices: 623136--623197 Score: 60
Period size: 19 Copynumber: 3.2 Consensus size: 20
623126 ATTGGAGTGC
* * *
623136 AAAAAGAAGACAAAAATCA-
1 AAAAACAAGAGAAAAATAAG
623155 AAAAACAAGAGAAAAATAAG
1 AAAAACAAGAGAAAAATAAG
623175 -AAAACAAGA-AAAGAA-AAG
1 AAAAACAAGAGAAA-AATAAG
623193 AAAAA
1 AAAAA
623198 GAGAAGTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 6 0.16
19 31 0.84
ACGTcount: A:0.77, C:0.06, G:0.13, T:0.03
Consensus pattern (20 bp):
AAAAACAAGAGAAAAATAAG
Found at i:628608 original size:19 final size:20
Alignment explanation
Indices: 628584--628626 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
628574 AGCATTTATC
628584 TTCATT-AAAAT-TATGTGTT
1 TTCATTAAAAATCT-TGTGTT
628603 TTCATTAAAAATCTTGTGTT
1 TTCATTAAAAATCTTGTGTT
628623 TTCA
1 TTCA
628627 AATGGGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.27
20 15 0.68
21 1 0.05
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.51
Consensus pattern (20 bp):
TTCATTAAAAATCTTGTGTT
Found at i:629097 original size:71 final size:71
Alignment explanation
Indices: 628964--629100 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
628954 TAAGATACTA
* * * *
628964 CCTAAACATCACCATCTTCCATCACCATTTTCACGCCTATAACATCATCATCTTCCCTCACCATT
1 CCTAAACATCACCATATTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCATT
629029 TTCACG
66 TTCACG
* * * *
629035 CCTATAACATCACCATATTCCATTACCA-TTGCACGCCTATATCATTACCATCTTCTATCACCAT
1 CCTA-AACATCACCATATTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCAT
629099 TT
65 TT
629101 AACACCTATA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 36 0.63
72 21 0.37
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (71 bp):
CCTAAACATCACCATATTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCATT
TTCACG
Found at i:629111 original size:35 final size:36
Alignment explanation
Indices: 628964--629100 Score: 188
Period size: 36 Copynumber: 3.9 Consensus size: 36
628954 TAAGATACTA
628964 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* *
628999 CCTATAACATCATCATCTTCCCTCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* * *
629035 CCTATAACATCACCATATTCCATTACCA-TTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTTCACG
* * *
629070 CCTATATCATTACCATCTTCTATCACCATTT
1 CCTATAACATCACCATCTTCCATCACCATTT
629101 AACACCTATA
Statistics
Matches: 88, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
35 33 0.38
36 55 0.62
ACGTcount: A:0.28, C:0.36, G:0.03, T:0.33
Consensus pattern (36 bp):
CCTATAACATCACCATCTTCCATCACCATTTTCACG
Found at i:629113 original size:72 final size:72
Alignment explanation
Indices: 628968--629115 Score: 174
Period size: 71 Copynumber: 2.1 Consensus size: 72
628958 ATACTACCTA
* * * * *
628968 AACATCACCATCTTCCATCACCATTTTCACGCCTATAACATCATCATCTTCCCTCACCATTTTCA
1 AACATCACCATATTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCATTTACA
*
629033 CGCCTAT
66 CGCATAT
* * * *
629040 AACATCACCATATTCCATTACCA-TTGCACGCCTATATCATTACCATCTTCTATCACCATTTAAC
1 AACATCACCATATTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCATTT-AC
629104 AC-CTATAT
65 ACGC-ATAT
629112 AACA
1 AACA
629116 ACCAATCCCT
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
71 33 0.52
72 31 0.48
ACGTcount: A:0.30, C:0.35, G:0.03, T:0.32
Consensus pattern (72 bp):
AACATCACCATATTCCATCACCATTTGCACGCCTATAACATCACCATCTTCCATCACCATTTACA
CGCATAT
Found at i:646733 original size:23 final size:24
Alignment explanation
Indices: 646707--646752 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
646697 TCTTTTCTTT
646707 GATTTTTC-TTCTTTTGAGTGCTG
1 GATTTTTCTTTCTTTTGAGTGCTG
646730 GATTTTTCTTTCTTTTGAGTGCT
1 GATTTTTCTTTCTTTTGAGTGCT
646753 TCACTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.09, C:0.13, G:0.20, T:0.59
Consensus pattern (24 bp):
GATTTTTCTTTCTTTTGAGTGCTG
Found at i:646760 original size:23 final size:24
Alignment explanation
Indices: 646711--646763 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
646701 TTCTTTGATT
* *
646711 TTTC-TTCTTTTGAGTGCTGGATT
1 TTTCTTTCTTTTGAGTGCTGCATC
*
646734 TTTCTTTCTTTTGAGTGCTTCA-C
1 TTTCTTTCTTTTGAGTGCTGCATC
646757 TTTCTTT
1 TTTCTTT
646764 TATGATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 11 0.42
24 15 0.58
ACGTcount: A:0.08, C:0.17, G:0.15, T:0.60
Consensus pattern (24 bp):
TTTCTTTCTTTTGAGTGCTGCATC
Done.