Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008478.1 Hibiscus syriacus cultivar Beakdansim tig00111309_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: 1476524
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:800613 original size:23 final size:24
Alignment explanation
Indices: 800569--800628 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
800559 ATATTTTATA
*
800569 TTTATTTTTTATAAATTAATATTTT
1 TTTAATTTTTAT-AATTAATATTTT
800594 TTTAATTTTTAT-ATTAATATTTT
1 TTTAATTTTTATAATTAATATTTT
* *
800617 CTTAAATTTTAT
1 TTTAATTTTTAT
800629 TTTTATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 21 0.66
25 11 0.34
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTAATTTTTATAATTAATATTTT
Found at i:800639 original size:23 final size:22
Alignment explanation
Indices: 800583--800639 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
800573 TTTTTTATAA
*
800583 ATTAATATTTTTTTAATTTTTAT
1 ATTAAT-TTTTTTTAAATTTTAT
*
800606 ATTAATATTTTCTTAAATTTTAT
1 ATTAAT-TTTTTTTAAATTTTAT
* *
800629 TTTTATTTTTT
1 ATTAATTTTTT
800640 GTAACGTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (22 bp):
ATTAATTTTTTTTAAATTTTAT
Found at i:800725 original size:20 final size:19
Alignment explanation
Indices: 800697--800739 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
800687 AATTATTTCT
800697 TTTTATTTAACAT-TCAATA
1 TTTTATTTAACATCT-AATA
*
800716 TTTTATTTTACCATCTAATA
1 TTTTA-TTTAACATCTAATA
800736 TTTT
1 TTTT
800740 GTTTGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 15 0.71
21 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTATTTAACATCTAATA
Found at i:805303 original size:54 final size:54
Alignment explanation
Indices: 805224--805328 Score: 176
Period size: 54 Copynumber: 1.9 Consensus size: 54
805214 CTATAGATTG
* *
805224 GATTTCAACTTCACAACGAATGATATCCAACTCAAAGCCAATTTGGTGAAATTA
1 GATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAATTA
805278 GATTTCAACTTCACGAA-GAAGGATATCCAACTCAAAACCAATTTGGTGAAA
1 GATTTCAACTTCAC-AACGAAGGATATCCAACTCAAAACCAATTTGGTGAAA
805329 CAACCCTTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
54 46 0.96
55 2 0.04
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (54 bp):
GATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAATTA
Found at i:805621 original size:120 final size:120
Alignment explanation
Indices: 805329--805678 Score: 558
Period size: 120 Copynumber: 2.9 Consensus size: 120
805319 TTTGGTGAAA
* *
805329 CAACCCTTGGATTTTAAC-TCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGG
1 CAACCCTTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGG
* *
805393 ATCCATCCACGATTTCAACTTCACGATGAAGGATATCGTGCCCCACAAGCAGCAATG
66 AGCCATCCACGA-TTCAACTTCACGACGAAGGATATCGTG-CCCACAAGCAGCAATG
* *
805450 CAACCCTTGGATTTCAACTTCACGACAAAAGATATCCAATTCAAAGATCAACTTCACAACGAAGG
1 CAACCCTTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGG
*
805515 AGCCATCCACGATTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGTAATG
66 AGCCATCCACGATTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATG
* * * * *
805570 CAACTCTTGGATTTCAACTTCACGACGAAGGATATCCAACTCCAAGCTCAACTTCACAAGGAAGG
1 CAACCCTTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGG
805635 AGCCATCCACGATTCCAACTTCACGACGAAGGATATCGTGCCCA
66 AGCCATCCACGATT-CAACTTCACGACGAAGGATATCGTGCCCA
805679 ACATATTGAC
Statistics
Matches: 213, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
120 87 0.41
121 72 0.34
122 54 0.25
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.21
Consensus pattern (120 bp):
CAACCCTTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAAGG
AGCCATCCACGATTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATG
Found at i:805876 original size:81 final size:83
Alignment explanation
Indices: 805783--806001 Score: 259
Period size: 81 Copynumber: 2.7 Consensus size: 83
805773 TGTCAACAAA
* * *
805783 CTTCGAGTTCGATTATACTCAACTCAAAGTCACATCATTTGCA-CATAGCTCAAGCAATAAGGGT
1 CTTCGAGTTCGATTACACTCAACTCAAAGTCACATCATTTGCAGCATAGCTCAAGCAAGAAGGGC
* *
805847 TATATGTCATC-AAAGAC
66 TATATGCCAACAAAAGAC
* * *
805864 CTTCGAGTTCGATTACA-TACAACTC-AAGGCATATCATTTGCAGCTTAGCTCAAGGCAAGAAGG
1 CTTCGAGTTCGATTACACT-CAACTCAAAGTCACATCATTTGCAGCATAGCTCAA-GCAAGAAGG
*
805927 GCTATCTGCCAACAAAAGAC
64 GCTATATGCCAACAAAAGAC
* * * *
805947 CTTCGAGTTCAATTACACTCAGCTCAAA-TGCACGTCATTTGCAGCATAACTCAAG
1 CTTCGAGTTCGATTACACTCAACTCAAAGT-CACATCATTTGCAGCATAGCTCAAG
806002 GCGAGAAGAG
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
80 16 0.14
81 31 0.27
82 17 0.15
83 28 0.24
84 23 0.20
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (83 bp):
CTTCGAGTTCGATTACACTCAACTCAAAGTCACATCATTTGCAGCATAGCTCAAGCAAGAAGGGC
TATATGCCAACAAAAGAC
Found at i:806024 original size:84 final size:82
Alignment explanation
Indices: 805747--806024 Score: 291
Period size: 84 Copynumber: 3.4 Consensus size: 82
805737 TCAAGTATAA
* *
805747 CATAACTCAAAGGCGAG-AGGGTTATCTGTCAAC-AA-A-CTTCGAGTTCGATTATACTCAACTC
1 CATAACTC-AAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAACTC
805808 AAAGTCACATCATTTGCA-
65 AAAG-CACATCATTTGCAG
* * * *
805826 CATAGCTCAA-GCAATAAGGGTTATATGTCATCAAAGACCTTCGAGTTCGATTACA-TACAACTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACT-CAACTC
* *
805889 AAGGCATATCATTTGCAG
65 AAAGCACATCATTTGCAG
* * * * * *
805907 CTTAGCTCAAGGCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCAATTACACTCAGCTC
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACACTCAACTC
*
805972 AAATGCACGTCATTTGCAG
65 AAA-GCACATCATTTGCAG
* * * *
805991 CATAACTCAAGGCGAGAAGAGATATCTATCAACA
1 CATAACTCAAGGCAAGAAGGGTTATCTGTCAACA
806025 GGAAACTATC
Statistics
Matches: 163, Mismatches: 26, Indels: 16
0.80 0.13 0.08
Matches are distributed among these distances:
77 3 0.02
78 16 0.10
79 9 0.06
80 14 0.09
81 34 0.21
82 17 0.10
83 30 0.18
84 40 0.25
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (82 bp):
CATAACTCAAGGCAAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACACTCAACTCA
AAGCACATCATTTGCAG
Found at i:807461 original size:7 final size:7
Alignment explanation
Indices: 807449--807499 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
807439 TATTATTTCC
807449 TATATTT
1 TATATTT
807456 TATATTT
1 TATATTT
807463 TATA-TT
1 TATATTT
*
807469 TATTTTT
1 TATATTT
*
807476 TATAAATT
1 TAT-ATTT
*
807484 AATATTT
1 TATATTT
807491 TATTATTT
1 TA-TATTT
807499 T
1 T
807500 TTATATTAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
6 5 0.14
7 20 0.57
8 10 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:807494 original size:61 final size:64
Alignment explanation
Indices: 807429--807571 Score: 147
Period size: 61 Copynumber: 2.3 Consensus size: 64
807419 TATTTTGAAA
*
807429 TTATTATTATTATTATTT-CCTATATT-TTATA-TTTTATATTTATTTTTTAT-AAATTA-ATAT
1 TTATTATTATTATTATTTAAC-ATATTCTTA-ACTTTTATATTTATTTTTTATGAAATTATATAT
807489 T
64 T
* * * *
807490 TTATTATT-TT-TTATATTAACATTTTCTTAACTTTTATTTTTATTTTTTATGACATTATTTTAT
1 TTATTATTATTATTAT-TTAACATATTCTTAACTTTTATATTTATTTTTTATGAAATTA-TATAT
807553 T
64 T
*
807554 GTATTATTATTATTATTT
1 TTATTATTATTATTATTT
807572 TTAATTTAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
59 4 0.06
60 9 0.13
61 30 0.45
62 5 0.07
64 11 0.16
65 4 0.06
66 4 0.06
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (64 bp):
TTATTATTATTATTATTTAACATATTCTTAACTTTTATATTTATTTTTTATGAAATTATATATT
Found at i:807524 original size:25 final size:24
Alignment explanation
Indices: 807468--807514 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
807458 TATTTTATAT
*
807468 TTATTTTTTATAAATTAATATTTTA
1 TTATTTTTTAT-AATTAACATTTTA
807493 TTATTTTTTAT-ATTAACATTTT
1 TTATTTTTTATAATTAACATTTT
807515 CTTAACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
25 11 0.52
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (24 bp):
TTATTTTTTATAATTAACATTTTA
Found at i:807621 original size:20 final size:20
Alignment explanation
Indices: 807604--807645 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
807594 TTTCTTTTTG
807604 TTTAACATTCAATATTTTAT
1 TTTAACATTCAATATTTTAT
* *
807624 TTTACCATTTAATATTTTAT
1 TTTAACATTCAATATTTTAT
807644 TT
1 TT
807646 GATTTTTTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTAACATTCAATATTTTAT
Found at i:815283 original size:20 final size:20
Alignment explanation
Indices: 815245--815293 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
815235 CTCTAAATCA
* **
815245 TTTTTCAAAATTTTCTTTTG
1 TTTTTCAAAATCTAATTTTG
815265 TTTTTCAAAATCTAATTTTG
1 TTTTTCAAAATCTAATTTTG
*
815285 -CTTTCAAAA
1 TTTTTCAAAA
815294 GAAAATTGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:816643 original size:21 final size:20
Alignment explanation
Indices: 816598--816655 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
816588 TTCTAGGTGC
**
816598 AAAGTTTTGAAACT-TTTGT
1 AAAGTTTTGAAACTCTTAAT
816617 AAAGTTTTGAAACTCTTAAT
1 AAAGTTTTGAAACTCTTAAT
816637 AAAAGTTTTTG-AACTCTTA
1 -AAAG-TTTTGAAACTCTTA
816656 CAAAGTTTCC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.41
20 3 0.09
21 12 0.35
22 5 0.15
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.43
Consensus pattern (20 bp):
AAAGTTTTGAAACTCTTAAT
Found at i:822916 original size:43 final size:43
Alignment explanation
Indices: 822861--822953 Score: 159
Period size: 43 Copynumber: 2.2 Consensus size: 43
822851 TCTTTTCCTT
* * *
822861 TTAGTTTTCCATCATATGGTACTTGTGCAATTCCATTTCCGTC
1 TTAGTTTCCCATCATATGGTACTTATGCAATTCCATTTCCCTC
822904 TTAGTTTCCCATCATATGGTACTTATGCAATTCCATTTCCCTC
1 TTAGTTTCCCATCATATGGTACTTATGCAATTCCATTTCCCTC
822947 TTAGTTT
1 TTAGTTT
822954 TCATTTCTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (43 bp):
TTAGTTTCCCATCATATGGTACTTATGCAATTCCATTTCCCTC
Found at i:834951 original size:23 final size:23
Alignment explanation
Indices: 834925--834997 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
834915 CAGCTCATAT
834925 AAATGCACCGAAGTGCCATGTAG
1 AAATGCACCGAAGTGCCATGTAG
* * **
834948 AAATGCATCGATGTGCCGCGTAG
1 AAATGCACCGAAGTGCCATGTAG
* *
834971 AAATGCACCAAAGTGCCATATA-
1 AAATGCACCGAAGTGCCATGTAG
834993 AAATG
1 AAATG
834998 TCTATAATGA
Statistics
Matches: 40, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 5 0.12
23 35 0.88
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCATGTAG
Found at i:835011 original size:22 final size:22
Alignment explanation
Indices: 834986--835036 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
834976 CACCAAAGTG
*
834986 CCATATAAAATGTCTATAATG-A
1 CCATATAAAATCTCTATAA-GAA
* *
835008 CCATATATAATCTCTTTAAGAA
1 CCATATAAAATCTCTATAAGAA
835030 CCATATA
1 CCATATA
835037 CATATTGCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.43, C:0.18, G:0.06, T:0.33
Consensus pattern (22 bp):
CCATATAAAATCTCTATAAGAA
Found at i:841878 original size:23 final size:23
Alignment explanation
Indices: 841851--841911 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
841841 TAGCTCGTAT
841851 AAATGCACCAGAGTGCCACATAG
1 AAATGCACCAGAGTGCCACATAG
* *
841874 AAATGCACC-GAAGTGCCGCGTAG
1 AAATGCACCAG-AGTGCCACATAG
* *
841897 AAATACACCAAAGTG
1 AAATGCACCAGAGTG
841912 TCATATAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.13
Consensus pattern (23 bp):
AAATGCACCAGAGTGCCACATAG
Found at i:841938 original size:22 final size:22
Alignment explanation
Indices: 841913--841962 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
841903 ACCAAAGTGT
*
841913 CATATAAAATGTCCATAATG-AC
1 CATATAAAATCTCCATAA-GAAC
* *
841935 CATATAGAATCTCCTTAAGAAC
1 CATATAAAATCTCCATAAGAAC
841957 CATATA
1 CATATA
841963 CATATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.28
Consensus pattern (22 bp):
CATATAAAATCTCCATAAGAAC
Found at i:842651 original size:15 final size:15
Alignment explanation
Indices: 842631--842670 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
842621 TTTAAAAATA
*
842631 GTATCGATACCTATG
1 GTATCGATACCCATG
*
842646 GTATCGGTACCCATG
1 GTATCGATACCCATG
*
842661 GTACCGATAC
1 GTATCGATAC
842671 TACCCCTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (15 bp):
GTATCGATACCCATG
Found at i:850436 original size:20 final size:19
Alignment explanation
Indices: 850394--850438 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
850384 CGATATAGCA
*
850394 GGTAAAAATATGATAAACT
1 GGTAAAAATATGATAAACC
850413 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGAT-AAACC
850433 GGTAAA
1 GGTAAA
850439 GTGCTACCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.20
Consensus pattern (19 bp):
GGTAAAAATATGATAAACC
Found at i:851057 original size:5 final size:5
Alignment explanation
Indices: 851047--851071 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
851037 TGTAACAAGT
851047 ATTTG ATTTG ATTTG ATTTG ATTTG
1 ATTTG ATTTG ATTTG ATTTG ATTTG
851072 CGTAAACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
ATTTG
Found at i:852792 original size:33 final size:33
Alignment explanation
Indices: 852755--852820 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
852745 AAATAGATGG
*
852755 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
852788 AGTGGTGAAAGTAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
852821 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:855138 original size:201 final size:201
Alignment explanation
Indices: 854904--855641 Score: 1144
Period size: 200 Copynumber: 3.7 Consensus size: 201
854894 GTAAAATTTA
*
854904 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACTGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
854969 TAAATATACCGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTGTGT
66 TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTAATTTTGTGT
* *
855034 CGATACTTTTGGTCCAGAATGAATGTCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
855099 AAAGTG
196 AAAGTG
855105 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* *
855170 TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTTTTTAATTTTTTGT
66 TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTAATTTTGTGT
* *
855235 CGATACTTTTGGTCCATAATGGATGCCAAAAAGGGTGAA-GCATAAAGTGTCGATACATTTTTAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
855299 AAAGTG
196 AAAGTG
* * * * *
855305 TCAATCGCATAAACATATGCATCCATAAGTACAATGTAATAGGTAAATTTAGAATGTAACCGGTA
1 TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
* * *
855370 TAAATATACCGATTTTATGAGATAATAGGTCTACAAC-TGTATTGACACGCTTTTAATTTTGTGT
66 TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTAATTTTGTGT
*
855434 CGATACTTTTAGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
131 CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
855499 AAAGTG
196 AAAGTG
* * * * * * *
855505 T-GAATCCCAAAAACAT-CGAAACCCATAATTATAATGCAATAGGTAAAATTT-CAATGTAACTG
1 TCG-ATCCCAGAAACATATG-CATCCATAAGTATAATGTAATAGGT-AAATTTACAATGTAACCG
* * * *
855567 GTATAAATATATCGGTTTTATGAAAGAATAAGTCTACAACATGTATCGACACGTTTTTAATTTTG
63 GTATAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTAATTTTG
*
855632 TGTCAATACT
128 TGTCGATACT
855642 AATTTAAATA
Statistics
Matches: 493, Mismatches: 39, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
199 61 0.12
200 232 0.47
201 200 0.41
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (201 bp):
TCGATCCCAGAAACATATGCATCCATAAGTATAATGTAATAGGTAAATTTACAATGTAACCGGTA
TAAATATACCGATTTTATGAGAGAATAGGTCTACAACATGTATCGACACGTTTTTAATTTTGTGT
CGATACTTTTGGTCCAGAATGGATGCCAAAAAGGGTGAACGCATAAAGTGTCGATACATTTTCAA
AAAGTG
Found at i:857122 original size:3 final size:3
Alignment explanation
Indices: 857103--857161 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
857093 CAAGCGGTCA
* * * **
857103 ATG AAG ATG AAG ATG ATG ATG AAG ATG GCG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
857151 ATG ATG ATG AT
1 ATG ATG ATG AT
857162 CCAAACAAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.37, C:0.02, G:0.34, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:858513 original size:21 final size:21
Alignment explanation
Indices: 858440--858510 Score: 133
Period size: 21 Copynumber: 3.4 Consensus size: 21
858430 TATTAGTATT
858440 GTGTCGATACATTTTCATAGA
1 GTGTCGATACATTTTCATAGA
858461 GTGTCGATACATTTTCATAGA
1 GTGTCGATACATTTTCATAGA
*
858482 GTGTCGATCCATTTTCATAGA
1 GTGTCGATACATTTTCATAGA
858503 GTGTCGAT
1 GTGTCGAT
858511 CCAAAAGGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.38
Consensus pattern (21 bp):
GTGTCGATACATTTTCATAGA
Found at i:861698 original size:73 final size:73
Alignment explanation
Indices: 861529--861686 Score: 180
Period size: 73 Copynumber: 2.2 Consensus size: 73
861519 AACATGTCAA
* * * * * **
861529 CATAATGTATCGACACTTG-TGTAATTTGTGTCGATACTTATTATCCAGGATGAATGCACAAACG
1 CATAAAGTGTCGACACTTGAT-AAATTTGTGTCGATACTTATTATCCAGAATGAATACACAAAAA
*
861593 AGGTGCACG
65 AGGTGAACG
*
861602 CATAAAGTGTCGACACTTGATAAATTTGTGTCGATACTT-TTGGTCCAGAATGAATAC-CAAAAA
1 CATAAAGTGTCGACACTTGATAAATTTGTGTCGATACTTATT-ATCCAGAATGAATACACAAAAA
861665 AGGTGTAAC-
65 AGGTG-AACG
861674 CATAAAGTGTCGA
1 CATAAAGTGTCGA
861687 TACATTTATA
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
72 24 0.33
73 48 0.66
74 1 0.01
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (73 bp):
CATAAAGTGTCGACACTTGATAAATTTGTGTCGATACTTATTATCCAGAATGAATACACAAAAAA
GGTGAACG
Found at i:862113 original size:83 final size:84
Alignment explanation
Indices: 862013--862168 Score: 278
Period size: 84 Copynumber: 1.9 Consensus size: 84
862003 TAGGTCAATA
*
862013 TAAGCGCTACCTATTACATT-TATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTTCG
1 TAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCG
862077 GTTAAATGCCTATTTTTAT
66 GTTAAATGCCTATTTTTAT
* *
862096 TAAGCGCTACCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTTCCG
1 TAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCG
862161 GTTAAATG
66 GTTAAATG
862169 ATATAACATT
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
83 20 0.29
84 49 0.71
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.42
Consensus pattern (84 bp):
TAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATATTTCCG
GTTAAATGCCTATTTTTAT
Found at i:862140 original size:23 final size:22
Alignment explanation
Indices: 862092--862134 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
862082 ATGCCTATTT
*
862092 TTATTAAGCGCTACCTATTACA
1 TTATTAAGCGCTACCTAATACA
*
862114 TTATATAAGCGTTACCTAATA
1 TTAT-TAAGCGCTACCTAATA
862135 TGTTATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (22 bp):
TTATTAAGCGCTACCTAATACA
Found at i:863907 original size:13 final size:13
Alignment explanation
Indices: 863889--863914 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
863879 TTAAAACAAT
863889 AAGAAATTTTTTA
1 AAGAAATTTTTTA
863902 AAGAAATTTTTTA
1 AAGAAATTTTTTA
863915 GTGAGATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AAGAAATTTTTTA
Found at i:864850 original size:217 final size:216
Alignment explanation
Indices: 864475--864903 Score: 732
Period size: 217 Copynumber: 2.0 Consensus size: 216
864465 GATACATACA
* **
864475 TTGTCATTACTATGAGTGATTTGGCACATATCACATCGTCATGATAGATAATTTGACACATGTCA
1 TTGTCATTACTATAAGTGACGTGGCACATATCACATCGTCATGATAGATAATTTGACACATGTCA
* *
864540 CATTATAATTTTAAGTTATGTAATAATTTTATATTAACAATTAAATACATATAAAAATCTCATGT
66 CATCATAATTTTAAGTTATGTAACAATTTTATATTAACAATTAAATACATATAAAAATCTCATGT
864605 CAGCAACATATGTTATATGTTGATCATTAACTAATTAATGATTTTTGAAAGCTAAAATATTCTAA
131 CAGCAACATATGTTATATGTTGATCATTAACTAATTAATGATTTTTGAAAGCTAAAATATTCTAA
864670 AAACTAACGGTAAAATGAATCC
196 AAA-TAACGGTAAAATGAATCC
* *
864692 TTGTCATTACTATAAGTGACGTGGCACATATCACATCGTCATTATAGATAGTTTGACACATGTCA
1 TTGTCATTACTATAAGTGACGTGGCACATATCACATCGTCATGATAGATAATTTGACACATGTCA
** * *
864757 CATCATAATTTTAAGTTATGTAACAATTTTATATTAGTAATTAAATACATATGAAAATCTTATGT
66 CATCATAATTTTAAGTTATGTAACAATTTTATATTAACAATTAAATACATATAAAAATCTCATGT
* *
864822 TAGCAACATGTGTTATATGTTGATCATTAACTAATTAATGATTTTTGAAAGCTAAAATATTCTAA
131 CAGCAACATATGTTATATGTTGATCATTAACTAATTAATGATTTTTGAAAGCTAAAATATTCTAA
864887 AAATAACGGTAAAATGA
196 AAATAACGGTAAAATGA
864904 TCAAATGTTA
Statistics
Matches: 199, Mismatches: 13, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
216 14 0.07
217 185 0.93
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (216 bp):
TTGTCATTACTATAAGTGACGTGGCACATATCACATCGTCATGATAGATAATTTGACACATGTCA
CATCATAATTTTAAGTTATGTAACAATTTTATATTAACAATTAAATACATATAAAAATCTCATGT
CAGCAACATATGTTATATGTTGATCATTAACTAATTAATGATTTTTGAAAGCTAAAATATTCTAA
AAATAACGGTAAAATGAATCC
Found at i:864985 original size:11 final size:10
Alignment explanation
Indices: 864963--865014 Score: 52
Period size: 11 Copynumber: 5.1 Consensus size: 10
864953 TGACACCCCA
*
864963 AAATTAAAAT
1 AAATTAATAT
864973 AAATTTAATAT
1 AAA-TTAATAT
* *
864984 AAAATAATTAA
1 AAATTAA-TAT
864995 AAATTAATA-
1 AAATTAATAT
865004 AAATTAATAT
1 AAATTAATAT
865014 A
1 A
865015 TTTTAAAAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 9 0.26
10 9 0.26
11 17 0.49
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAATTAATAT
Found at i:866853 original size:2 final size:2
Alignment explanation
Indices: 866846--866872 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
866836 CGCACTTGCT
866846 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 T
866873 GGATATTTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:869352 original size:31 final size:32
Alignment explanation
Indices: 869307--869380 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
869297 TATTTTTTTA
869307 ATATTAT-AAATAATTATT-AAAGTTATCCA-
1 ATATTATAAAATAATTATTAAAAGTTATCCAT
* *
869336 ATTTTTATAAAATAATTATTAAAATTTATCCAT
1 A-TATTATAAAATAATTATTAAAAGTTATCCAT
869369 ATATTATAAAAT
1 ATATTATAAAAT
869381 GGTCATGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
29 1 0.03
30 5 0.13
31 11 0.29
32 20 0.53
33 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (32 bp):
ATATTATAAAATAATTATTAAAAGTTATCCAT
Found at i:873355 original size:22 final size:22
Alignment explanation
Indices: 873327--873396 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
873317 TAATTTCTCT
873327 TATGTATGTAAATGACTAACTA
1 TATGTATGTAAATGACTAACTA
* *
873349 TATGTATG--CAT-A-T-A-TG
1 TATGTATGTAAATGACTAACTA
*
873365 TACGTATGTAAATGACTAACTA
1 TATGTATGTAAATGACTAACTA
873387 TATGTATGTA
1 TATGTATGTA
873397 TGTATGTATG
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 8 0.22
17 1 0.03
18 3 0.08
19 2 0.06
20 3 0.08
21 1 0.03
22 18 0.50
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
TATGTATGTAAATGACTAACTA
Found at i:873435 original size:34 final size:34
Alignment explanation
Indices: 873327--873442 Score: 169
Period size: 34 Copynumber: 3.3 Consensus size: 34
873317 TAATTTCTCT
873327 TATGTATGTAAATGACTAACTATATGTATGCATATATG
1 TATGTATGTAAATGACTAACTATATGTATGC----ATG
* *
873365 TACGTATGTAAATGACTAACTATATGTATGTATG
1 TATGTATGTAAATGACTAACTATATGTATGCATG
873399 TATGTATGTAAATGACTAACTATATGTATGCATG
1 TATGTATGTAAATGACTAACTATATGTATGCATG
*
873433 TATGTCTGTA
1 TATGTATGTA
873443 TAGGAAGAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
34 44 0.60
38 29 0.40
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (34 bp):
TATGTATGTAAATGACTAACTATATGTATGCATG
Found at i:873443 original size:38 final size:38
Alignment explanation
Indices: 873329--873443 Score: 168
Period size: 38 Copynumber: 3.1 Consensus size: 38
873319 ATTTCTCTTA
*
873329 TGTATGTAAATGACTAACTATATGTATGCATATATGTAC
1 TGTATGTAAATGACTAACTATATGTATGCATGTATGT-C
*
873368 -GTATGTAAATGACTAACTATATG--T--ATGTATGTA
1 TGTATGTAAATGACTAACTATATGTATGCATGTATGTC
873401 TGTATGTAAATGACTAACTATATGTATGCATGTATGTC
1 TGTATGTAAATGACTAACTATATGTATGCATGTATGTC
873439 TGTAT
1 TGTAT
873444 AGGAAGAGTG
Statistics
Matches: 68, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
34 30 0.44
36 2 0.03
38 36 0.53
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.40
Consensus pattern (38 bp):
TGTATGTAAATGACTAACTATATGTATGCATGTATGTC
Found at i:877959 original size:21 final size:25
Alignment explanation
Indices: 877907--877963 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
877897 AATTTAAAGA
877907 ATAAAATTAAATATAATTAAACAGTG
1 ATAAAATT-AATATAATTAAACAGTG
877933 ACTAAAATTAA-ATAATTAAA-A-T-
1 A-TAAAATTAATATAATTAAACAGTG
877955 ATAAAATTA
1 ATAAAATTA
877964 TAAATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 8 0.27
22 1 0.03
23 1 0.03
24 1 0.03
25 9 0.30
26 3 0.10
27 7 0.23
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.32
Consensus pattern (25 bp):
ATAAAATTAATATAATTAAACAGTG
Found at i:879230 original size:3 final size:3
Alignment explanation
Indices: 879222--879279 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
879212 TATATTTATT
* * *
879222 TAA TAA TAA TAA TAAA TAT TAA TAT TAA TAA TAA -AG TAA TAA -ATA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
879267 TAA TAA TAA TAA T
1 TAA TAA TAA TAA T
879280 TTTAGAATGG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 2 0.04
3 39 0.87
4 4 0.09
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:879245 original size:19 final size:20
Alignment explanation
Indices: 879221--879275 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
879211 TTATATTTAT
879221 TTAATAATAATAATAAA-TA
1 TTAATAATAATAATAAAGTA
*
879240 TTAATATTAATAATAAAGTA
1 TTAATAATAATAATAAAGTA
*
879260 ATAA-ATATAATAATAA
1 TTAATA-ATAATAATAA
879276 TAATTTTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.55
20 14 0.45
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (20 bp):
TTAATAATAATAATAAAGTA
Found at i:879696 original size:45 final size:45
Alignment explanation
Indices: 879586--879949 Score: 570
Period size: 45 Copynumber: 8.1 Consensus size: 45
879576 GAGGTCTTAT
* * * * *
879586 CATCTTGCACTGTAGGTCTTACAGATGACACTG-AGGCTTT-AAAA
1 CATCATGCACTGAAGGGCTTACAGATGAC-CCGAAGGTTTTGAAAA
* * *
879630 AATCATGCACTGAAGGTCTTACAGATGACCCGAATGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
*
879675 CATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
879720 CATCATGCACTGAAAGGCTTACAGATGACCTGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
879765 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
**
879810 CATCATTTACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
879855 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
* *
879900 CATCATGCACTTAAGGGCTTACAGATGACTCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
879945 CATCA
1 CATCA
879950 AAAAGCTCCC
Statistics
Matches: 297, Mismatches: 21, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
43 2 0.01
44 31 0.10
45 264 0.89
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (45 bp):
CATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAA
Found at i:880010 original size:76 final size:76
Alignment explanation
Indices: 879883--880101 Score: 300
Period size: 76 Copynumber: 2.9 Consensus size: 76
879873 TTACAGATGA
* * * ** *
879883 CCCGAAGG-TTTT-GAAAACATCATGCACT-TAAGGGCTTACAGATGACTCGAAGGTTTTGAAAA
1 CCCGAAGGCTTTTGGAAAACAACCTGCACTAT-AGGTCTTATGGATGACCCGAAGGTTTTGAAAA
879945 CATCAAAAAGCT
65 CATCAAAAAGCT
* *
879957 CCCGAAGGCTTTTGGAAAACAACCTGCACTGTATGTCTTATGGATGACCCGAAGGTTTTGAAAAC
1 CCCGAAGGCTTTTGGAAAACAACCTGCACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
880022 ATCAAAAAGCT
66 ATCAAAAAGCT
* * * *
880033 CCCGAAGGCTTTTTGAAAACATCTTGCACTATAGGTCTTATGGATGACCCGAAGGTTTTAAAAAC
1 CCCGAAGGCTTTTGGAAAACAACCTGCACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
880098 ATCA
66 ATCA
880102 TGCACTGAAG
Statistics
Matches: 129, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.06
75 4 0.03
76 116 0.90
77 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (76 bp):
CCCGAAGGCTTTTGGAAAACAACCTGCACTATAGGTCTTATGGATGACCCGAAGGTTTTGAAAAC
ATCAAAAAGCT
Found at i:880807 original size:22 final size:22
Alignment explanation
Indices: 880779--880855 Score: 100
Period size: 22 Copynumber: 3.5 Consensus size: 22
880769 AATAAGGCTT
880779 TCATCTTTAAAAAAAGAATCTA
1 TCATCTTTAAAAAAAGAATCTA
* *
880801 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAAAGAATCTA
* * * *
880823 TCATCTTTGAAGAATGTATCTA
1 TCATCTTTAAAAAAAGAATCTA
880845 TCATCTTTAAA
1 TCATCTTTAAA
880856 GAATGTAGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (22 bp):
TCATCTTTAAAAAAAGAATCTA
Found at i:881339 original size:54 final size:54
Alignment explanation
Indices: 881226--881380 Score: 177
Period size: 54 Copynumber: 2.9 Consensus size: 54
881216 ATAATCACTG
* * * * * * *
881226 GTTCTTAAAACATGTGACAATACATTCATCCTTTCTCGTGGCTTATGCCCGGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
* * * *
881280 TTTCGTAAAGCTTTTGATAACACATTCATCCTTTCTTGTGGCTTCTGGCCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
* *
881334 GTTCGTAAAGCATTTGACAACACATTCATTCTTT-TATGTGGTTTCTG
1 GTTCGTAAAGCATTTGACAACACATTCATCCTTTCT-TGTGGCTTCTG
881381 TACAGATTTC
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 1 0.01
54 83 0.99
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (54 bp):
GTTCGTAAAGCATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCCAGAT
Found at i:884800 original size:76 final size:75
Alignment explanation
Indices: 884709--884873 Score: 242
Period size: 76 Copynumber: 2.2 Consensus size: 75
884699 TTAAACTCAA
*
884709 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
884773 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
884785 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
884850 TTTAATTAGG
66 TTTAATTAAG
*
884860 ATTTAGAATATTAT
1 ATTTAGGATATTAT
884874 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:885547 original size:21 final size:22
Alignment explanation
Indices: 885522--885562 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
885512 CTTTAATTTG
885522 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
885543 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
885563 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:891104 original size:10 final size:11
Alignment explanation
Indices: 891072--891112 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
891062 ACCCATTTCG
891072 TTATATTTTTGT
1 TTATATTTTT-T
*
891084 TTTTA-TTTTT
1 TTATATTTTTT
891094 TTA-ATTTTTT
1 TTATATTTTTT
891104 TTATATTTT
1 TTATATTTT
891113 AGCGAACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
9 1 0.04
10 11 0.44
11 9 0.36
12 4 0.16
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTATATTTTTT
Found at i:893043 original size:76 final size:75
Alignment explanation
Indices: 892952--893116 Score: 233
Period size: 76 Copynumber: 2.2 Consensus size: 75
892942 TTAAACTCAA
* *
892952 ATTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 ATTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAAT-GGGTTTTAGT
893016 ATTTTAATTAAG
64 ATTTTAATTAAG
* * * *
893028 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATGGGTTTTAGTAT
1 ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATGGGTTTTAGTAT
*
893093 TTTAATTAGG
66 TTTAATTAAG
*
893103 ATTTAGAATATTAT
1 ATTTAGGATATTAT
893117 ATTATTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
75 39 0.49
76 40 0.51
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.56
Consensus pattern (75 bp):
ATTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATGGGTTTTAGTAT
TTTAATTAAG
Found at i:893199 original size:64 final size:64
Alignment explanation
Indices: 893065--893199 Score: 159
Period size: 64 Copynumber: 2.1 Consensus size: 64
893055 CTTTATCTTT
* * **
893065 GTATTTTAGTTTAAATGGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTATTTTTTAG
1 GTATTTTAGTTTAAATGAGTTTTAGCATTTTAATTAGGATTTAGAATATTATAGCATTTTTTAG
* * *
893129 GTATTTTAGTTTAAAT-AGTTTTAAGCGTTTTAATTAGGATTTA-AGATGTTTTAGCATGTTTTT
1 GTATTTTAGTTTAAATGAGTTTT-AGCATTTTAATTAGGATTTAGA-ATATTATAGCAT-TTTTT
893192 AG
63 AG
893194 G-ATTTT
1 GTATTTT
893200 GAAGGCTATA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
63 6 0.10
64 47 0.77
65 8 0.13
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.53
Consensus pattern (64 bp):
GTATTTTAGTTTAAATGAGTTTTAGCATTTTAATTAGGATTTAGAATATTATAGCATTTTTTAG
Found at i:893789 original size:21 final size:22
Alignment explanation
Indices: 893764--893804 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
893754 CTTTAATTTG
893764 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
893785 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
893805 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:897916 original size:6 final size:7
Alignment explanation
Indices: 897899--897939 Score: 50
Period size: 6 Copynumber: 6.0 Consensus size: 7
897889 ATAAAAGTAT
897899 AAATGCA
1 AAATGCA
897906 AAATG-A
1 AAATGCA
897912 AAATGCA
1 AAATGCA
*
897919 AAGATACA
1 AA-ATGCA
897927 AAATGC-
1 AAATGCA
897933 AAATGCA
1 AAATGCA
897940 TGTATGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
6 12 0.41
7 11 0.38
8 6 0.21
ACGTcount: A:0.59, C:0.12, G:0.15, T:0.15
Consensus pattern (7 bp):
AAATGCA
Found at i:898600 original size:36 final size:36
Alignment explanation
Indices: 898555--898626 Score: 108
Period size: 36 Copynumber: 2.0 Consensus size: 36
898545 TCTTGTCGTA
* *
898555 GAATGCTTTTGGTATCAATCTAACAGGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
* *
898591 GAATACTTTTGGTATTAATATAACATGATCTTTGTG
1 GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
898627 TGCATAGCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (36 bp):
GAATACTTTTGGTATCAATATAACAGGATCTTTGTG
Found at i:900307 original size:14 final size:13
Alignment explanation
Indices: 900267--900309 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
900257 TTAATATGAC
* *
900267 TGAAATAAAATAA
1 TGAATTAAAATAT
900280 T-AATTAAAATAT
1 TGAATTAAAATAT
900292 TGAATTAAACATAT
1 TGAATTAAA-ATAT
900306 TGAA
1 TGAA
900310 ATTTAAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 10 0.38
13 8 0.31
14 8 0.31
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (13 bp):
TGAATTAAAATAT
Found at i:901200 original size:16 final size:16
Alignment explanation
Indices: 901179--901209 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
901169 TGGCTTTTAT
901179 AGCCACCATCGAGGAA
1 AGCCACCATCGAGGAA
901195 AGCCACCATCGAGGA
1 AGCCACCATCGAGGA
901210 TGCTCTCGGA
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:0.35, C:0.32, G:0.26, T:0.06
Consensus pattern (16 bp):
AGCCACCATCGAGGAA
Found at i:901656 original size:3 final size:3
Alignment explanation
Indices: 901648--901735 Score: 99
Period size: 3 Copynumber: 29.3 Consensus size: 3
901638 TATATTTATT
* * *
901648 TAA TAA TAA TAA TAAA TAG TAA TAA TAT TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
901694 -ATT TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA T-A TAA TAA T
1 TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
901736 TTTAGAATGG
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 3 0.04
3 64 0.90
4 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:908213 original size:18 final size:18
Alignment explanation
Indices: 908190--908224 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
908180 CAACTAACCC
*
908190 TTAACATCCTAACAACAT
1 TTAACAGCCTAACAACAT
908208 TTAACAGCCTAACAACA
1 TTAACAGCCTAACAACA
908225 CATGGAGGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (18 bp):
TTAACAGCCTAACAACAT
Found at i:909216 original size:12 final size:12
Alignment explanation
Indices: 909199--909223 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
909189 TTGCGCCAAT
909199 GTGGCTTCCGAG
1 GTGGCTTCCGAG
909211 GTGGCTTCCGAG
1 GTGGCTTCCGAG
909223 G
1 G
909224 GAGTGTTGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.24, G:0.44, T:0.24
Consensus pattern (12 bp):
GTGGCTTCCGAG
Found at i:913218 original size:33 final size:33
Alignment explanation
Indices: 913176--913265 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 33
913166 ATTATGAAAG
*
913176 AATATTATTTGTCACAATTTTTTATAATAA-GA
1 AATAATATTTGTCACAATTTTTTATAATAATGA
* * * * ** *
913208 AATTAATATTTGTTATAAATTGTTATTTTAATTA
1 AA-TAATATTTGTCACAATTTTTTATAATAATGA
913242 AATAA-ATTTGTCACAATTTTTTAT
1 AATAATATTTGTCACAATTTTTTAT
913266 TTTGACAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
32 17 0.39
33 24 0.55
34 3 0.07
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (33 bp):
AATAATATTTGTCACAATTTTTTATAATAATGA
Found at i:914712 original size:15 final size:16
Alignment explanation
Indices: 914694--914727 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
914684 CCCAAATTTA
914694 TTTAAAAA-ATTTAAT
1 TTTAAAAACATTTAAT
*
914709 TTTAAAAACATTTCAT
1 TTTAAAAACATTTAAT
914725 TTT
1 TTT
914728 GTCACTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTAAAAACATTTAAT
Found at i:916147 original size:183 final size:183
Alignment explanation
Indices: 915838--916190 Score: 426
Period size: 183 Copynumber: 1.9 Consensus size: 183
915828 TAATTTGTCA
* * * *
915838 TAAAAACGTGAATATCATTATTTTTTGTGATAATTTTTCTGTAATAATTATTAACACTTATAGTT
1 TAAAAACGTGAATATCATTATTTGTTGTGAGAATTTTTCTGTAACAATAATTAACACTTATAGTT
** *
915903 ACAAAATTTGTTAATATATGATTTTTTTGGCGCAAAAAAAATATGGAAGAAAATCTTTGTGACAA
66 ACAAAACATGTCAATATATGATTTTTTTGGCGCAAAAAAAATATGGAAGAAAATCTTTGTGACAA
* *
915968 TATATTTTGTCAGTATAATTAAAATATATAATGACAAACACTATTTTTTTTAC
131 TAAATTTTGTCACTATAATTAAAATATATAATGACAAACACTATTTTTTTTAC
* * * *
916021 TAAAAACTTGAATTTCATTATTTGTTGTGAGAATTTTTTTTGTAACAATAATTATA-GCTTATAG
1 TAAAAACGTGAATATCATTATTTGTTGTGAGAA-TTTTTCTGTAACAATAATTA-ACACTTATAG
* **** ** *
916085 TTACAAAACATGTCACTATATGATTTTGTTT-TTTTACCAAAAAT-TGG-AGATAATCATTTGTG
64 TTACAAAACATGTCAATATATGATTTT-TTTGGCGCAAAAAAAATATGGAAGAAAATC-TTTGTG
* * *
916147 ACTATAAATTTTGTCACTATAATTTAAATATATAATTACAAACA
127 ACAATAAATTTTGTCACTATAATTAAAATATATAATGACAAACA
916191 AAATTTGTCA
Statistics
Matches: 142, Mismatches: 24, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
182 7 0.05
183 77 0.54
184 54 0.38
185 4 0.03
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (183 bp):
TAAAAACGTGAATATCATTATTTGTTGTGAGAATTTTTCTGTAACAATAATTAACACTTATAGTT
ACAAAACATGTCAATATATGATTTTTTTGGCGCAAAAAAAATATGGAAGAAAATCTTTGTGACAA
TAAATTTTGTCACTATAATTAAAATATATAATGACAAACACTATTTTTTTTAC
Found at i:921498 original size:15 final size:15
Alignment explanation
Indices: 921472--921514 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
921462 TTTAGTCGTT
* *
921472 TATTTTAATTTTTAT
1 TATTTTTATTTTTAC
921487 TATTCTTT-TTTTTAC
1 TATT-TTTATTTTTAC
921502 TATTTTTATTTTT
1 TATTTTTATTTTT
921515 GGTTTGTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 3 0.12
15 19 0.79
16 2 0.08
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (15 bp):
TATTTTTATTTTTAC
Found at i:921620 original size:3 final size:3
Alignment explanation
Indices: 921612--921670 Score: 57
Period size: 3 Copynumber: 19.7 Consensus size: 3
921602 TTTACCTCTC
* * * *
921612 ATT ATT ATT ATC ATT ATT ATT GTT ATAT ATT -CT ATT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
*
921657 ATT AAT ATT ATT AT
1 ATT ATT ATT ATT AT
921671 ATATCTTATT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
2 1 0.02
3 40 0.91
4 3 0.07
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:921653 original size:33 final size:33
Alignment explanation
Indices: 921612--921674 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
921602 TTTACCTCTC
* *
921612 ATTATTATTATCATTATTATTGTTATATATTCT
1 ATTATTATTATCATTAATATTATTATATATTCT
* *
921645 ATTATTATTTTTATTAATATTATTATATAT
1 ATTATTATTATCATTAATATTATTATATAT
921675 CTTATTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (33 bp):
ATTATTATTATCATTAATATTATTATATATTCT
Found at i:921735 original size:15 final size:14
Alignment explanation
Indices: 921715--921808 Score: 57
Period size: 13 Copynumber: 6.4 Consensus size: 14
921705 TTCCATTTTC
921715 TTTATTTTATTTTAT
1 TTTATTTT-TTTTAT
*
921730 TTTATTCACTTTTT-T
1 TTTATT--TTTTTTAT
*
921745 TTTATCTTTTTT-T
1 TTTATTTTTTTTAT
* **
921758 TTTATTTTCTTTGG
1 TTTATTTTTTTTAT
*
921772 TTTATTTCATTTGTTGT
1 TTTATTT--TTT-TTAT
*
921789 TTTATTTTCTTTAT
1 TTTATTTTTTTTAT
921803 TTTATT
1 TTTATT
921809 AATTTTCATT
Statistics
Matches: 63, Mismatches: 10, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
13 16 0.25
14 16 0.25
15 14 0.22
16 6 0.10
17 11 0.17
ACGTcount: A:0.13, C:0.06, G:0.04, T:0.77
Consensus pattern (14 bp):
TTTATTTTTTTTAT
Found at i:921758 original size:52 final size:53
Alignment explanation
Indices: 921684--921783 Score: 123
Period size: 52 Copynumber: 1.9 Consensus size: 53
921674 TCTTATTTTT
* *
921684 ACTTTTTTATTTCACTTCTTTTTCCATTTTCTTTATTTTATTTTATTTTATTC
1 ACTTTTTTATTTCACTTCTTTTTCCATTTTCTTTAGTTTATTTCATTTTATTC
* ** *
921737 ACTTTTTT-TTT-ATCTTTTTTTTTTATTTTCTTTGGTTTATTTCATTT
1 ACTTTTTTATTTCA-CTTCTTTTTCCATTTTCTTTAGTTTATTTCATTT
921784 GTTGTTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
51 1 0.03
52 31 0.77
53 8 0.20
ACGTcount: A:0.13, C:0.12, G:0.02, T:0.73
Consensus pattern (53 bp):
ACTTTTTTATTTCACTTCTTTTTCCATTTTCTTTAGTTTATTTCATTTTATTC
Found at i:921807 original size:14 final size:13
Alignment explanation
Indices: 921680--921808 Score: 59
Period size: 14 Copynumber: 9.5 Consensus size: 13
921670 TATATCTTAT
*
921680 TTTTACTTTTTTA
1 TTTTATTTTTTTA
*
921693 TTTCACTTCTTTTTCCA
1 TTTTA-TT-TTTTT--A
*
921710 TTTTCTTTATTTTA
1 TTTTATTT-TTTTA
*
921724 TTTTATTTTATTCA
1 TTTTATTTT-TTTA
*
921738 -CTT-TTTTTTTA
1 TTTTATTTTTTTA
921749 TCTTT-TTTTTTTA
1 T-TTTATTTTTTTA
* *
921762 TTTTCTTTGGTTTA
1 TTTTATTT-TTTTA
* * *
921776 TTTCA-TTTGTTG
1 TTTTATTTTTTTA
921788 TTTTATTTTCTTTA
1 TTTTATTTT-TTTA
921802 TTTTATT
1 TTTTATT
921809 AATTTTCATT
Statistics
Matches: 86, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
11 3 0.03
12 13 0.15
13 26 0.30
14 28 0.33
15 6 0.07
16 6 0.07
17 4 0.05
ACGTcount: A:0.12, C:0.10, G:0.03, T:0.74
Consensus pattern (13 bp):
TTTTATTTTTTTA
Found at i:934146 original size:24 final size:24
Alignment explanation
Indices: 934114--934167 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
934104 ACGTCCATCA
934114 CCTCAGGTCCAAACAACTCCTCGC
1 CCTCAGGTCCAAACAACTCCTCGC
* *
934138 CCTCGGGTCCAAACGACTCCTCGC
1 CCTCAGGTCCAAACAACTCCTCGC
934162 CCTCAG
1 CCTCAG
934168 CTGGAAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.20, C:0.46, G:0.17, T:0.17
Consensus pattern (24 bp):
CCTCAGGTCCAAACAACTCCTCGC
Found at i:944212 original size:15 final size:14
Alignment explanation
Indices: 944185--944233 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
944175 CGCCATAAAT
944185 TGAAAAAAGAAAAAA
1 TGAAAAAA-AAAAAA
*
944200 TG-AACAAAAAAAA
1 TGAAAAAAAAAAAA
*
944213 -GAGAAAAAAAAAA
1 TGAAAAAAAAAAAA
944226 -GAAAAAAA
1 TGAAAAAAA
944234 TAAGGTGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 22 0.76
14 4 0.14
15 2 0.07
ACGTcount: A:0.82, C:0.02, G:0.12, T:0.04
Consensus pattern (14 bp):
TGAAAAAAAAAAAA
Found at i:944219 original size:11 final size:11
Alignment explanation
Indices: 944187--944233 Score: 58
Period size: 11 Copynumber: 4.3 Consensus size: 11
944177 CCATAAATTG
944187 AAAAAAGAAAA
1 AAAAAAGAAAA
** *
944198 AATGAACAAAA
1 AAAAAAGAAAA
*
944209 AAAAGAGAAAA
1 AAAAAAGAAAA
944220 AAAAAAGAAAA
1 AAAAAAGAAAA
944231 AAA
1 AAA
944234 TAAGGTGGGT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:945133 original size:55 final size:55
Alignment explanation
Indices: 945061--945373 Score: 170
Period size: 55 Copynumber: 5.6 Consensus size: 55
945051 AATTTGCTCG
* *
945061 AGATTGGATTTCAACTTCACGATGGAGGATATCCAACTCAAAGC-CAACTTACACA
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTT-CACA
* *
945116 AGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACA
1 AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCACA
* * *
945171 ACGAAGGGGTCATCCACGATTTCAACTTCACGACGAAGGATAT-C--GT----GCTC-AC--AAG
1 A-G-A----T--T---GGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCA-
945226 C-
54 CA
* * *
945227 AGCATTGGATTTTAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACA
1 AG-ATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCACA
* * ** * ***
945283 GCGA--AGATTTCAACTTCACGGTGGAGGATATTGGACTCGAAA-CAATACAACTTACACA
1 -AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTC-AAAGC--T-CAACTT-CACA
*
945341 AGATTGGATTTCAACTTCATGACGAAGGATATC
1 AGATTGGATTTCAACTTCACGACGAAGGATATC
945374 GTGCTCACAA
Statistics
Matches: 195, Mismatches: 31, Indels: 60
0.68 0.11 0.21
Matches are distributed among these distances:
46 24 0.12
47 1 0.01
49 2 0.01
51 1 0.01
53 4 0.02
54 27 0.14
55 51 0.26
56 12 0.06
57 11 0.06
58 6 0.03
59 26 0.13
61 1 0.01
63 2 0.01
65 1 0.01
66 26 0.13
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (55 bp):
AGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAGCTCAACTTCACA
Found at i:947219 original size:26 final size:25
Alignment explanation
Indices: 947177--947251 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 25
947167 TTTCATATTT
947177 TTATTATTCTT-TGTTTTTGTTTGTTA
1 TTATTATTCTTAT-TTTTTGTTT-TTA
* *
947203 TTATTATTCTTATTTTTTCTATTTA
1 TTATTATTCTTATTTTTTGTTTTTA
947228 TTATT-TAT-TTATTTGTTTGTTTTT
1 TTATTAT-TCTTATTT-TTTGTTTTT
947252 TCTTCACATG
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
24 7 0.17
25 16 0.38
26 18 0.43
27 1 0.02
ACGTcount: A:0.15, C:0.04, G:0.07, T:0.75
Consensus pattern (25 bp):
TTATTATTCTTATTTTTTGTTTTTA
Found at i:947315 original size:3 final size:3
Alignment explanation
Indices: 947307--947365 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
947297 TTTACCTCTC
* *
947307 ATT ATT ATT ATC ATT ATT ATT ATT ATAT ATT -CT ATT ATT ATGT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT AT-T ATT
*
947352 ATT AAT ATT ATT AT
1 ATT ATT ATT ATT AT
947366 ATATCTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 2 0.04
3 40 0.87
4 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:947342 original size:12 final size:11
Alignment explanation
Indices: 947326--947375 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
947316 ATCATTATTA
947326 TTATTATATAT
1 TTATTATATAT
*
947337 TCTATTATTATGT
1 T-TATTA-TATAT
947350 TTATTA-ATA-
1 TTATTATATAT
947359 TTATTATATAT
1 TTATTATATAT
947370 CTTATT
1 -TTATT
947376 TTTACTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
9 6 0.19
10 5 0.16
11 1 0.03
12 15 0.47
13 5 0.16
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (11 bp):
TTATTATATAT
Found at i:947493 original size:9 final size:9
Alignment explanation
Indices: 947403--947504 Score: 50
Period size: 9 Copynumber: 11.1 Consensus size: 9
947393 CTTCTTTTTC
*
947403 TATTTTCTT
1 TATTTTATT
947412 TATTTTATTT
1 TATTTTA-TT
947422 TATTTTATT
1 TATTTTATT
* *
947431 CACTTTTTATC
1 TA--TTTTATT
947442 T-TTTTATT
1 TATTTTATT
*
947450 T-TCTTTGCTT
1 TAT-TTT-ATT
*
947460 TATTTCATT
1 TATTTTATT
* *
947469 TGTTGT-TT
1 TATTTTATT
947477 TA-TTTATT
1 TATTTTATT
947485 TATTTTATT
1 TATTTTATT
*
947494 AATTTTCATT
1 TATTTT-ATT
947504 T
1 T
947505 TTTATCTAAC
Statistics
Matches: 69, Mismatches: 15, Indels: 17
0.68 0.15 0.17
Matches are distributed among these distances:
7 2 0.03
8 15 0.22
9 28 0.41
10 17 0.25
11 7 0.10
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.73
Consensus pattern (9 bp):
TATTTTATT
Found at i:949386 original size:17 final size:17
Alignment explanation
Indices: 949337--949387 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
949327 TTTTTTAGAC
949337 TAGAAATTAATAG-CC-
1 TAGAAATTAATAGACCA
* *
949352 TAGATATGTTATTAGACCA
1 TAGA-A-ATTAATAGACCA
949371 TAGAAATTAATAGACCA
1 TAGAAATTAATAGACCA
949388 ATGGATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
15 4 0.14
16 1 0.04
17 16 0.57
18 3 0.11
19 4 0.14
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (17 bp):
TAGAAATTAATAGACCA
Found at i:950612 original size:20 final size:18
Alignment explanation
Indices: 950561--950618 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
950551 ATAATGTGTA
* *
950561 TTTTGGATTAGAAATACG
1 TTTTAGATTAGAAATACT
*
950579 TTTTAGAGTAGAAATACT
1 TTTTAGATTAGAAATACT
950597 TTTTGATGATTAGAAATACT
1 TTTT-A-GATTAGAAATACT
950617 TT
1 TT
950619 GGATTAGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 19 0.56
19 1 0.03
20 14 0.41
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.43
Consensus pattern (18 bp):
TTTTAGATTAGAAATACT
Found at i:950619 original size:18 final size:18
Alignment explanation
Indices: 950561--950627 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
950551 ATAATGTGTA
950561 TTTTG-GATTAGAAATAC
1 TTTTGAGATTAGAAATAC
*
950578 GTTTT-AGAGTAGAAATAC
1 -TTTTGAGATTAGAAATAC
950596 TTTTTGATGATTAGAAATAC
1 -TTTTGA-GATTAGAAATAC
950616 -TTTG-GATTAGAA
1 TTTTGAGATTAGAA
950628 CAAAAGAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
16 8 0.19
18 23 0.53
19 1 0.02
20 11 0.26
ACGTcount: A:0.36, C:0.04, G:0.19, T:0.40
Consensus pattern (18 bp):
TTTTGAGATTAGAAATAC
Found at i:951067 original size:15 final size:15
Alignment explanation
Indices: 951032--951074 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
951022 ACAACCTCTT
*
951032 AATCATTCAGACTGTTA
1 AATCATTCAG--TGCTA
951049 AATCATTCAGTGCTA
1 AATCATTCAGTGCTA
951064 AATCATTCAGT
1 AATCATTCAGT
951075 TTTAACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 15 0.60
17 10 0.40
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (15 bp):
AATCATTCAGTGCTA
Found at i:951144 original size:19 final size:21
Alignment explanation
Indices: 951106--951148 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
951096 CTCTATTTTG
*
951106 TTTTCTGTTTAGGTCTCTCTT
1 TTTTCTGTGTAGGTCTCTCTT
*
951127 TTTTCTGTGTAGGCCTCTCTT
1 TTTTCTGTGTAGGTCTCTCTT
951148 T
1 T
951149 AGAGGTCTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.21, G:0.16, T:0.58
Consensus pattern (21 bp):
TTTTCTGTGTAGGTCTCTCTT
Found at i:952005 original size:31 final size:30
Alignment explanation
Indices: 951959--952038 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
951949 TTCGATAATA
*
951959 TAATAATTATTTTATAGT-ATTTAGATAAATT
1 TAATAA-TATTTTATAATCATTTA-ATAAATT
* *
951990 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATCATTTAATAAATT
952021 TAATAAGTATTTTATAAT
1 TAATAA-TATTTTATAAT
952039 TTTTAAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
30 1 0.02
31 36 0.86
32 5 0.12
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (30 bp):
TAATAATATTTTATAATCATTTAATAAATT
Found at i:952016 original size:19 final size:20
Alignment explanation
Indices: 951992--952041 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
951982 GATAAATTTA
*
951992 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
952011 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
952032 TT-ATAATTTT
1 TTAATAATTTT
952042 TAAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:952688 original size:11 final size:11
Alignment explanation
Indices: 952672--952731 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
952662 TCAATAAAGT
952672 TTAAAAAATTA
1 TTAAAAAATTA
952683 TTAAAAAATTA
1 TTAAAAAATTA
*
952694 TT--AAATTTA
1 TTAAAAAATTA
952703 TT--AAAA-TA
1 TTAAAAAATTA
*
952711 TTATAAAATTA
1 TTAAAAAATTA
*
952722 TTAATAAATT
1 TTAAAAAATT
952732 TATCTAAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
8 4 0.10
9 11 0.26
10 4 0.10
11 23 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:952705 original size:20 final size:19
Alignment explanation
Indices: 952676--952731 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
952666 TAAAGTTTAA
952676 AAAATTATTAAAAAATTATT
1 AAAATTATTAAAAAATTA-T
* *
952696 AAATTTATTAAAATATTAT
1 AAAATTATTAAAAAATTAT
*
952715 AAAATTATTAATAAATT
1 AAAATTATTAAAAAATT
952732 TATCTAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAATTATTAAAAAATTAT
Found at i:952707 original size:31 final size:31
Alignment explanation
Indices: 952672--952755 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 31
952662 TCAATAAAGT
*
952672 TTAAAAAATTATTAAAA-AATTATTAAATTTA
1 TTAAAAAATTA-TAAAATAATTAATAAATTTA
* *
952703 TTAAAATATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAATAATTAATAAATTTA
* *
952734 TCT-AAATACTATAAAATAATTA
1 T-TAAAAAATTATAAAATAATTA
952756 TTGTATTATC
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 5 0.11
31 40 0.87
32 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
TTAAAAAATTATAAAATAATTAATAAATTTA
Found at i:952734 original size:20 final size:19
Alignment explanation
Indices: 952671--952734 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
952661 GTCAATAAAG
*
952671 TTTAAAAAATTATTAAAAA
1 TTTATAAAATTATTAAAAA
* *
952690 ATTATTAAATTTATT-AAAA
1 TTTA-TAAAATTATTAAAAA
952709 TATTATAAAATTATTAATAAA
1 T-TTATAAAATTATTAA-AAA
952730 TTTAT
1 TTTAT
952735 CTAAATACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
19 16 0.44
20 16 0.44
21 4 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTATAAAATTATTAAAAA
Found at i:953337 original size:31 final size:30
Alignment explanation
Indices: 953299--953383 Score: 109
Period size: 29 Copynumber: 2.8 Consensus size: 30
953289 ATTAATGGTT
953299 ATTGAACTTTTGTAAATGTTACAAAATAGTC
1 ATTGAACTTTT-TAAATGTTACAAAATAGTC
* * *
953330 ATTGAACTTTATAAA-ATTACAAAATAGTT
1 ATTGAACTTTTTAAATGTTACAAAATAGTC
* *
953359 ATTGAACTATTTAATTGTTACAAAA
1 ATTGAACTTTTTAAATGTTACAAAA
953384 ATGTTGGTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 24 0.52
30 12 0.26
31 10 0.22
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (30 bp):
ATTGAACTTTTTAAATGTTACAAAATAGTC
Found at i:955662 original size:21 final size:21
Alignment explanation
Indices: 955636--955683 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
955626 ATGAGAGGGT
955636 GATCATTAGAAAGATGAAAGG
1 GATCATTAGAAAGATGAAAGG
955657 GATCATTAGAAAGATGAAAGG
1 GATCATTAGAAAGATGAAAGG
955678 GATCAT
1 GATCAT
955684 CTCTAGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.46, C:0.06, G:0.27, T:0.21
Consensus pattern (21 bp):
GATCATTAGAAAGATGAAAGG
Found at i:957644 original size:22 final size:23
Alignment explanation
Indices: 957619--957671 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
957609 TAGGAAGTGC
*
957619 ATAATTTTTTAAATT-AAATAAA
1 ATAATATTTTAAATTAAAATAAA
*
957641 ATAATATTTTAAGTTAAAATAAA
1 ATAATATTTTAAATTAAAATAAA
*
957664 AAAATATT
1 ATAATATT
957672 AAATTATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 13 0.48
23 14 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAATATTTTAAATTAAAATAAA
Found at i:967999 original size:29 final size:27
Alignment explanation
Indices: 967931--967991 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
967921 TTATATCTGC
*
967931 AAAAATAATTAATTAAATAAAATATTA
1 AAAAATAAATAATTAAATAAAATATTA
* * *
967958 AGCAATTAAAATAATTAAATAAATTATTA
1 A-AAAAT-AAATAATTAAATAAAATATTA
967987 AAAAA
1 AAAAA
967992 ACTAAATATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
27 1 0.04
28 5 0.19
29 20 0.77
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (27 bp):
AAAAATAAATAATTAAATAAAATATTA
Found at i:969056 original size:21 final size:21
Alignment explanation
Indices: 969031--969083 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
969021 GTTTCCAGAT
*
969031 TCGCAACGCGAACATCGATTA
1 TCGCAACGCGAACATCGACTA
*
969052 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
969073 TCGCAATGCGA
1 TCGCAACGCGA
969084 TTTTCCAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:969115 original size:19 final size:19
Alignment explanation
Indices: 969087--969172 Score: 91
Period size: 19 Copynumber: 4.3 Consensus size: 19
969077 AATGCGATTT
*
969087 TCCAAATTCGTTGTGATAG
1 TCCAAATTCGTTGCGATAG
*
969106 TCCAAGTTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
** *
969125 TCCATGTTCGCATTGCGATTTAT
1 TCCAAATTCG--TTGCGA--TAG
969148 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
969167 TCCAAA
1 TCCAAA
969173 ATCGCAACGA
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 34 0.61
21 12 0.21
23 10 0.18
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:970933 original size:2 final size:2
Alignment explanation
Indices: 970926--970967 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
970916 AAAAATTTTA
970926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
970968 TACAAAATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:971754 original size:35 final size:35
Alignment explanation
Indices: 971703--971782 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
971693 AACACAATCA
971703 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* ** *
971738 TCAATTACATTTTAAACCTTAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
971773 TCAATTACAT
1 TCAATTACAT
971783 ACCCAACCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:971797 original size:35 final size:35
Alignment explanation
Indices: 971703--971798 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
971693 AACACAATCA
* *
971703 TCAATTACATTCTAAACCCCAAAA-TCCAAAATACT
1 TCAATTACATACCAAA-CCCAAAATTCCAAAATACT
*** **
971738 TCAATTACATTTTAAACCTTAAATTCCAAAATACT
1 TCAATTACATACCAAACCCAAAATTCCAAAATACT
*
971773 TCAATTACATACCCAACCCAAAATTC
1 TCAATTACATACCAAACCCAAAATTC
971799 ATAATCCATT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 5 0.10
35 46 0.90
ACGTcount: A:0.44, C:0.27, G:0.00, T:0.29
Consensus pattern (35 bp):
TCAATTACATACCAAACCCAAAATTCCAAAATACT
Found at i:972173 original size:148 final size:148
Alignment explanation
Indices: 971951--972243 Score: 462
Period size: 148 Copynumber: 2.0 Consensus size: 148
971941 AAATACTCAA
971951 TTCAGTTTATAAAATAGTTGACTCAAAATATTTTCGACTTGAGTTTATAAAATTTAAATCAAGTC
1 TTCAGTTTATAAAATAGTTGACTCAAAATATTTTCGACTTGAGTTTATAAAATTTAAATCAAGTC
* * * *
972016 GAATTGAATTGAATTTTCGAGTTTTTGTTTAAATTTAATTATAAATATTTATCATATTATAATAT
66 GAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
* *
972081 T-TTTTATTTTAATTCAG
131 TATTTGATTCTAATTCAG
* * * *
972098 TTCAGTTTATAAAATAGTTGACTCAAATTTTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGT
1 TTCAGTTTATAAAATAGTTGACTCAAA-ATATTTTCGACTTGAGTTTATAAAATTTAAATCAAGT
**
972163 CGAATTGAATTGAATTTTTTAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATA
65 CGAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATA
972228 TTATTTGATTCTAATT
130 TTATTTGATTCTAATT
972244 TAAATAGTTT
Statistics
Matches: 132, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
147 27 0.20
148 94 0.71
149 11 0.08
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (148 bp):
TTCAGTTTATAAAATAGTTGACTCAAAATATTTTCGACTTGAGTTTATAAAATTTAAATCAAGTC
GAATTGAATTGAATTTTCGAGTTTCTATTTAAATTTAATTATAAATATTTATAATACTATAATAT
TATTTGATTCTAATTCAG
Found at i:972663 original size:36 final size:35
Alignment explanation
Indices: 972623--972701 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
972613 GGTGTTGGGC
* * *
972623 ATGTAATTAAAGTATTTTTGGAATTT-GAGGTTTAGA
1 ATGTAATTAAAGCA-TTTTGAAATTTGGA-GTTTAAA
**
972659 ATGTAATCGAAGCATTTTGAAATTTGGAGTTTAAA
1 ATGTAATTAAAGCATTTTGAAATTTGGAGTTTAAA
972694 ATGTAATT
1 ATGTAATT
972702 GATGATTGTG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
35 23 0.64
36 13 0.36
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (35 bp):
ATGTAATTAAAGCATTTTGAAATTTGGAGTTTAAA
Found at i:976417 original size:16 final size:17
Alignment explanation
Indices: 976382--976418 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
976372 TTTGCACGGT
976382 GTACGTTAAATTAGAAA
1 GTACGTTAAATTAGAAA
976399 GTACGTTAAATTA-AAA
1 GTACGTTAAATTAGAAA
976415 GTAC
1 GTAC
976419 TATATATGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (17 bp):
GTACGTTAAATTAGAAA
Found at i:976811 original size:81 final size:81
Alignment explanation
Indices: 976675--977248 Score: 744
Period size: 81 Copynumber: 7.1 Consensus size: 81
976665 TTTCCTTTAG
* * ** * ** * * *
976675 TCTTTTACCCAAAGACATTTTGCCTTTCATCTAACTTTCATGATTGAAACCTTTCTTCCAAATGC
1 TCTTTTACTCAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* *
976740 TCAGCTAGGCTATTAA
66 ACAGCTAGGCCATTAA
** * * * **
976756 TCTTTTACGAAAAGATATTTAACCTTTCATCTAACTGGCATAATTGAGACATTTCTATCAAAT-C
1 TCTTTTACTCAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
976820 ACAGCTAGGCTATTAA
66 ACAGCTAGGCCATTAA
* ** * *
976836 TCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
976901 ACAGCTAGGCTATTAA
66 ACAGCTAGGCCATTAA
*
976917 TCTCTTACTCAACA-ATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATG
1 TCTTTTACTCAA-AGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATG
*
976981 CACAGTTAGGCCATTAA
65 CACAGCTAGGCCATTAA
* * *
976998 TATTTTACTCAACGATATTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
977063 ACAGCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
* * * *
977079 TCTTTTACTCGACA-ATATTTAACCGTTCATCTAACTGGCATAATTGACACATTT-TGCGAAATA
1 TCTTTTACTC-AAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATG
*
977142 CACAACTAGTG-CATTAA
65 CACAGCTAG-GCCATTAA
*
977159 TCTTTTACTCAACGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
977224 ACATCTAGGCCATTAA
66 ACAGCTAGGCCATTAA
977240 TCTTTTACT
1 TCTTTTACT
977249 TTTGGAATAA
Statistics
Matches: 439, Mismatches: 46, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.00
80 144 0.33
81 292 0.67
82 2 0.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAGCTAGGCCATTAA
Found at i:976940 original size:161 final size:160
Alignment explanation
Indices: 976700--977248 Score: 753
Period size: 161 Copynumber: 3.4 Consensus size: 160
976690 CATTTTGCCT
** * * * * *
976700 TTCATCTAACTTTCATGATTGAAACCTTTCTTCCAAATGCTCAGCTAGGCTATTAATCTTTTAC-
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * * * *
976764 GAAAAGATATTTAACCTTTCATCTAACTGGCATAATTGAGACATTTCTATCAAAT-CACAGCTAG
66 CAACA-ATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCT-CCAAATACACAGCTAG
* * **
976828 GCTATTAATCTTTTACTCAAAGGTATTTAACAT
129 GC-ATTAATCTTTTACTCAACGATATTTAACCG
* * * *
976861 TTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGGCTATTAATCTCTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * *
976926 CAACAATATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGG
66 CAACAATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCT-CCAAATACACAGCTAGG
*
976991 CCATTAATATTTTACTCAACGATATTTAACCG
130 -CATTAATCTTTTACTCAACGATATTTAACCG
*
977023 TTCATCTAATTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
* * *
977088 CGACAATATTTAACCGTTCATCTAACTGGCATAATTGACACATTT-TGCGAAATACACAACTAGT
66 CAACAATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCT-CCAAATACACAGCTAG-
977152 GCATTAATCTTTTACTCAACGATATTTAACCG
129 GCATTAATCTTTTACTCAACGATATTTAACCG
*
977184 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACATCTAGGCCATTAATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
977249 TTTGGAATAA
Statistics
Matches: 348, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
161 206 0.59
162 141 0.41
163 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (160 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGGCCATTAATCTTTTACT
CAACAATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTCCAAATACACAGCTAGGC
ATTAATCTTTTACTCAACGATATTTAACCG
Found at i:977160 original size:242 final size:241
Alignment explanation
Indices: 976700--977248 Score: 775
Period size: 242 Copynumber: 2.3 Consensus size: 241
976690 CATTTTGCCT
** * * * * * * *
976700 TTCATCTAACTTTCATGATTGAAACCTTTCTTCCAAATGCTCAGCTAGGCTATTAATCTTTTACG
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATTAATCTTTTACT
* * *
976765 AAAAGATATTTAACCTTTCATCTAACTGGCATAATTGAGACATTTCTATCAAATCACAGCTAGGC
66 AAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAATCACAGCTAGGC
* *
976830 TATTAATCTTTTACTCAAAGGTATTTAACATTTCATCTAACTGGCATAATTGACACATTTCTGTC
131 CATTAATCTTTTACTCAAA-GTATTTAACAGTTCATCTAACTGGCATAATTGACACATTTCTGTC
* *
976895 AAATGCACAGCTAGGCTATTAATCTCTTACTCAACAATATTTAACCG
195 AAATACACAACTAGGCTATTAATCTCTTACTCAACAATATTTAACCG
*
976942 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATTAATATTTTACT
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATTAATCTTTTACT
* * * * *
977007 CAACGATATTTAACCGTTCATCTAATTGGCATAATTGACACCTTTCTGCCAAATGCACAGCTAGG
66 AAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAAT-CACAGCTAGG
*
977072 CCATTAATCTTTTACTCGACAA-TATTTAACCGTTCATCTAACTGGCATAATTGACACATTT-TG
130 CCATTAATCTTTTACTC-A-AAGTATTTAACAGTTCATCTAACTGGCATAATTGACACATTTCTG
* *
977135 -CGAAATACACAACTAGTGC-ATTAATCTTTTACTCAACGATATTTAACCG
193 TC-AAATACACAACTAG-GCTATTAATCTCTTACTCAACAATATTTAACCG
977184 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACA-TCTAGGCCATTAATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGT-TAGGCCATTAATCTTTTAC
977248 T
65 T
977249 TTTGGAATAA
Statistics
Matches: 275, Mismatches: 26, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
241 2 0.01
242 205 0.75
243 65 0.24
244 1 0.00
245 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (241 bp):
TTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGCACAGTTAGGCCATTAATCTTTTACT
AAAAGATATTTAACCGTTCATCTAACTGGCATAATTGACACATTTCTACCAAATCACAGCTAGGC
CATTAATCTTTTACTCAAAGTATTTAACAGTTCATCTAACTGGCATAATTGACACATTTCTGTCA
AATACACAACTAGGCTATTAATCTCTTACTCAACAATATTTAACCG
Found at i:977499 original size:57 final size:57
Alignment explanation
Indices: 977409--977543 Score: 209
Period size: 57 Copynumber: 2.4 Consensus size: 57
977399 AAATTTATAT
* * * * *
977409 AATTTCTTAG-TTTTCGCACATAAGGTGCTCATACAGAAATTCATAAACTTATTATG
1 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAAAAATTCATAAACTTATTATG
977465 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAAAAATTCATAAACTTATTATG
1 AATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAAAAATTCATAAACTTATTATG
*
977522 AATTTCTTAACTTTTTGCACAC
1 AATTTCTTAGCTTTTTGCACAC
977544 TTAGTGCCAT
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
56 10 0.14
57 62 0.86
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.38
Consensus pattern (57 bp):
AATTTCTTAGCTTTTTGCACACAAAGTGCCCATACAAAAATTCATAAACTTATTATG
Found at i:977990 original size:20 final size:20
Alignment explanation
Indices: 977965--978020 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
977955 TCTGTGATCA
*
977965 ATGGTATCGATACCATCCTC
1 ATGGTATCGATACCACCCTC
977985 ATGGTATCGATACTC-CCCTC
1 ATGGTATCGATAC-CACCCTC
*
978005 TTGGTATCGATACCAC
1 ATGGTATCGATACCAC
978021 TTGAATCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.30
Consensus pattern (20 bp):
ATGGTATCGATACCACCCTC
Found at i:980505 original size:21 final size:21
Alignment explanation
Indices: 980479--980518 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
980469 CAAGACTTGC
980479 GGTTGAAGAACAATAGAAGGT
1 GGTTGAAGAACAATAGAAGGT
980500 GGTTGAAGAACAATAGAAG
1 GGTTGAAGAACAATAGAAG
980519 TTTGACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.05, G:0.33, T:0.17
Consensus pattern (21 bp):
GGTTGAAGAACAATAGAAGGT
Found at i:983462 original size:32 final size:32
Alignment explanation
Indices: 983426--983589 Score: 166
Period size: 32 Copynumber: 5.1 Consensus size: 32
983416 GTGCTAACCA
* * *
983426 AAGGGAGTATCTTGGGGCCTGAGAGCCTACCC
1 AAGGAAGTACCTTGGGGCCTTAGAGCCTACCC
* ** *
983458 AAGGGAGTACCTTATGGCCTAAGAGCCTACCC
1 AAGGAAGTACCTTGGGGCCTTAGAGCCTACCC
* * *
983490 AAGGAAGTACCTTGAGACCTTAAAGCCTACCC
1 AAGGAAGTACCTTGGGGCCTTAGAGCCTACCC
* * * *
983522 GATGAAGTACCTTGGGACCTTAGAGCCTAGCC
1 AAGGAAGTACCTTGGGGCCTTAGAGCCTACCC
* * * *
983554 AAGGAAATACCTTGGGGCCTCAAAGCCAACCC
1 AAGGAAGTACCTTGGGGCCTTAGAGCCTACCC
983586 AAGG
1 AAGG
983590 TCACCTTAGG
Statistics
Matches: 109, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 109 1.00
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (32 bp):
AAGGAAGTACCTTGGGGCCTTAGAGCCTACCC
Found at i:989006 original size:2 final size:2
Alignment explanation
Indices: 989001--989044 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
988991 TTCTTTTTTA
989001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
989042 AT A
1 AT A
989045 AAAATTTTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:993447 original size:18 final size:18
Alignment explanation
Indices: 993424--993458 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
993414 GCTCCCCATT
*
993424 TACCTAGTCCATTTCATC
1 TACCTAGTCCAATTCATC
993442 TACCTAGTCCAATTCAT
1 TACCTAGTCCAATTCAT
993459 AATGACTCCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.06, T:0.37
Consensus pattern (18 bp):
TACCTAGTCCAATTCATC
Found at i:996665 original size:11 final size:11
Alignment explanation
Indices: 996651--996726 Score: 59
Period size: 11 Copynumber: 6.5 Consensus size: 11
996641 ATAACTTAAT
996651 AATAATAATAA
1 AATAATAATAA
*
996662 AATAATCATAA
1 AATAATAATAA
996673 AGATAATAATTTAA
1 A-ATAATAA--TAA
996687 ACAT-AT-ATCAA
1 A-ATAATAAT-AA
996698 AAGTAATAATAA
1 AA-TAATAATAA
996710 AATAA-AATAA
1 AATAATAATAA
996720 TAATAAT
1 -AATAAT
996727 TAAAATGAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
10 7 0.13
11 23 0.43
12 13 0.25
13 4 0.08
14 6 0.11
ACGTcount: A:0.64, C:0.04, G:0.03, T:0.29
Consensus pattern (11 bp):
AATAATAATAA
Found at i:998144 original size:14 final size:16
Alignment explanation
Indices: 998111--998180 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 16
998101 TTTGGGCTTG
998111 TAATATATATATATATA
1 TAATA-ATATATATATA
998128 TAATAATATA-ATA-A
1 TAATAATATATATATA
*
998142 TAATAATA-ATATTTA
1 TAATAATATATATATA
* * *
998157 GTGATAATAAATTTA-A
1 -TAATAATATATATATA
998173 TAATAATA
1 TAATAATA
998181 ATAAAATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
13 1 0.02
14 11 0.25
15 11 0.25
16 13 0.30
17 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TAATAATATATATATA
Found at i:998174 original size:34 final size:33
Alignment explanation
Indices: 998127--998190 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
998117 ATATATATAT
*
998127 ATAATAATATAATAATAATAATAATATTTAGTG
1 ATAATAATATAATAATAATAATAAAATTTAGTG
*
998160 ATAATAAATTTAATAATAATAATAAAATTTA
1 ATAAT-AATATAATAATAATAATAAAATTTA
998191 AATGAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (33 bp):
ATAATAATATAATAATAATAATAAAATTTAGTG
Found at i:998981 original size:76 final size:76
Alignment explanation
Indices: 998312--998955 Score: 1144
Period size: 76 Copynumber: 8.5 Consensus size: 76
998302 GATGGAAATG
* * *
998312 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
998377 CCTGAAGGCTT
66 CCCGAAGGCTT
998388 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
998453 CCCGAAGGCTT
66 CCCGAAGGCTT
*
998464 TTTGGAAACATCATGCACTCAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
998529 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
998540 TTTGGAAATATCATGCACTGAAGGACTTATAGATGACCTTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
998605 CCCGAAGGCTT
66 CCCGAAGGCTT
*
998616 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
998681 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
998692 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
998757 CTCGAAGGCTT
66 CCCGAAGGCTT
*
998768 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTGAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
998833 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
998844 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
998909 CCCGAAGGCTTT
66 CCCGAAGGC-TT
998921 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
998956 TGGGAAATAG
Statistics
Matches: 543, Mismatches: 24, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
76 506 0.93
77 37 0.07
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:999246 original size:166 final size:166
Alignment explanation
Indices: 998959--999282 Score: 490
Period size: 166 Copynumber: 2.0 Consensus size: 166
998949 ACAGATGTGG
* *
998959 GAAATAGTTTACTAAGTAAAAAACTAAGGAAATTGTTTTCTTACTTTTCAACAATTTCATTTTTA
1 GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
** *
999024 GAAAAGATTGAATGAGAAACTAATGGAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
66 GAAAAGATAAAATGAGAAACTAATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
* *
999089 TGGGTAACATGCCCCAATCTCAAGATAAGGCTGTTA
131 TGGGTAACATGACCCAATCTAAAGATAAGGCTGTTA
*
999125 GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAAGAATTTCA-TTTTA
1 GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
* * * **
999189 GAAAAGATAAAATGAGAAA-TTATGAAAATCGTTTTCTCATTCTGTTTTTTGAAATAACATGTTG
66 GAAAAGATAAAATGAGAAACTAATGAAAATCATTTTCTCA-T-TATTTTTCAAAATAACATGTTG
*
999253 ATTGGGTAACATGACCTAATCTAAAGATAA
129 ATTGGGTAACATGACCCAATCTAAAGATAA
999283 TGCTCATTTT
Statistics
Matches: 142, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
164 17 0.12
165 23 0.16
166 102 0.72
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (166 bp):
GAAATAGTTTACTAAGTAAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTA
GAAAAGATAAAATGAGAAACTAATGAAAATCATTTTCTCATTATTTTTCAAAATAACATGTTGAT
TGGGTAACATGACCCAATCTAAAGATAAGGCTGTTA
Found at i:999822 original size:22 final size:22
Alignment explanation
Indices: 999797--999851 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
999787 AATAAAGCTT
*
999797 TCATCTTTGAAAATAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
999819 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
999841 TCATCTTTGAA
1 TCATCTTTGAA
999852 GAAGTAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1000346 original size:54 final size:53
Alignment explanation
Indices: 1000222--1000422 Score: 232
Period size: 54 Copynumber: 3.8 Consensus size: 53
1000212 CACTGGTTCA
* * * *
1000222 TAAAACATTTGACAATATATTCAT-CTTTTCCTGTGGTTTCTG-TC-GAG-ATG
1 TAAAACATTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGAGTTTG
*
1000272 TAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA-GTTTG
* * **
1000326 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGA-GTTTG
* *
1000380 TAAAGCGTTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
1000423 CAAGATTTCT
Statistics
Matches: 129, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
50 32 0.25
51 7 0.05
52 2 0.02
53 5 0.04
54 79 0.61
55 4 0.03
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAGTTTG
Found at i:1000417 original size:108 final size:104
Alignment explanation
Indices: 1000222--1000422 Score: 278
Period size: 104 Copynumber: 1.9 Consensus size: 104
1000212 CACTGGTTCA
* * * *
1000222 TAAAACATTTGACAATATATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTTGACAA
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
1000287 CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
66 CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
* * **
1000326 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTC-AGACGTTCATAAAGCGTTT
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG-TCGAGACG-T-A-AAA-CACTT
1000390 GACAACACATTCATCCTTTTCTGTGGCTTCTGC
61 GACAACACATTCATCCTTTTCTGTGGCTTCTGC
1000423 CAAGATTTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
104 41 0.49
105 3 0.04
106 1 0.01
107 3 0.04
108 36 0.43
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (104 bp):
TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
Found at i:1000842 original size:35 final size:34
Alignment explanation
Indices: 1000803--1000875 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
1000793 CATTACTTCT
1000803 TATTGAGATGAACCTTCAAAATG-CCCAAATATTC
1 TATTGAGATGAACCTTCAAAATGACCC-AATATTC
** *
1000837 ATATTGTTATGAGCCTTCAAAATGACCCAATATTC
1 -TATTGAGATGAACCTTCAAAATGACCCAATATTC
1000872 TATT
1 TATT
1000876 TCTGGTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
34 4 0.12
35 27 0.79
36 3 0.09
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (34 bp):
TATTGAGATGAACCTTCAAAATGACCCAATATTC
Found at i:1001294 original size:221 final size:221
Alignment explanation
Indices: 1000911--1001352 Score: 866
Period size: 221 Copynumber: 2.0 Consensus size: 221
1000901 GTCCCACATG
1000911 AAACATTTCTGTCTGAAATGGGCTTTCGAGATGCCCCAATATTCTGCTTCTGGTTGACTCTCAAT
1 AAACATTTCTGTCTGAAATGGGCTTTCGAGATGCCCCAATATTCTGCTTCTGGTTGACTCTCAAT
1000976 GTATGTTTGACTTGAATATCATGATTCCCACGAGGTCTAATTTTGACAATATACTATTGTACTTG
66 GTATGTTTGACTTGAATATCATGATTCCCACGAGGTCTAATTTTGACAATATACTATTGTACTTG
1001041 TGGCTTTATTCATGCCCCAAATCTGTTTATCTTGAATACTCTCATTCTGGTGTTACTGAACAGCA
131 TGGCTTTATTCATGCCCCAAATCTGTTTATCTTGAATACTCTCATTCTGGTGTTACTGAACAGCA
1001106 ATGTTGTCAAGTAACTGGAGAAATTC
196 ATGTTGTCAAGTAACTGGAGAAATTC
1001132 AAACATTTCTGTCTGAAATGGGCTTTCGAGATGCCCCAATATTCTGCTTCTGGTTGACTCTCAAT
1 AAACATTTCTGTCTGAAATGGGCTTTCGAGATGCCCCAATATTCTGCTTCTGGTTGACTCTCAAT
*
1001197 GTCTGTTTGACTTGAATATCATGATTCCCACGAGGTCTAATTTTGACAATATACTATTGTACTTG
66 GTATGTTTGACTTGAATATCATGATTCCCACGAGGTCTAATTTTGACAATATACTATTGTACTTG
*
1001262 TGGCTTTTTTCATGCCCCAAATCTGTTTATCTTGAATACTCTCATTCTGGTGTTACTGAACAGCA
131 TGGCTTTATTCATGCCCCAAATCTGTTTATCTTGAATACTCTCATTCTGGTGTTACTGAACAGCA
1001327 ATGTTGTCAAGTAACTGGAGAAATTC
196 ATGTTGTCAAGTAACTGGAGAAATTC
1001353 TCTTTATGTT
Statistics
Matches: 219, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
221 219 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (221 bp):
AAACATTTCTGTCTGAAATGGGCTTTCGAGATGCCCCAATATTCTGCTTCTGGTTGACTCTCAAT
GTATGTTTGACTTGAATATCATGATTCCCACGAGGTCTAATTTTGACAATATACTATTGTACTTG
TGGCTTTATTCATGCCCCAAATCTGTTTATCTTGAATACTCTCATTCTGGTGTTACTGAACAGCA
ATGTTGTCAAGTAACTGGAGAAATTC
Found at i:1002110 original size:114 final size:114
Alignment explanation
Indices: 1001948--1002175 Score: 375
Period size: 114 Copynumber: 2.0 Consensus size: 114
1001938 CATGCAGTTC
* * * * * *
1001948 ATCTTTTAATTCCAATGATTGGTTCTGTGGTTCGTACCGAACCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
*
1002013 CTTCCAGAAGATGCTATTGGGCTTCCTTATTTCTACTATGAGCACATGG
66 CTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCACATGG
* *
1002062 ATCTTTCAAATCCAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGAACA
1 ATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
1002127 CTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCACATGG
66 CTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCACATGG
1002176 CACTTGCTCC
Statistics
Matches: 105, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (114 bp):
ATCTTTCAAATCCAATGATTGATTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTGGGCCTCCTTATTTCTACTATGAGCACATGG
Found at i:1006997 original size:14 final size:15
Alignment explanation
Indices: 1006980--1007020 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1006970 TAAAAGTATG
1006980 AATGCAAAAATG-AA
1 AATGCAAAAATGCAA
*
1006994 AATGCAAAGATGCAA
1 AATGCAAAAATGCAA
1007009 AATG--AAAATGCA
1 AATGCAAAAATGCA
1007021 TATATGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.29
14 11 0.46
15 6 0.25
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (15 bp):
AATGCAAAAATGCAA
Found at i:1007006 original size:8 final size:7
Alignment explanation
Indices: 1006980--1007020 Score: 50
Period size: 6 Copynumber: 5.9 Consensus size: 7
1006970 TAAAAGTATG
1006980 AATGCAAA
1 AATGC-AA
1006988 AATG-AA
1 AATGCAA
1006994 AATGCAA
1 AATGCAA
1007001 AGATGCAA
1 A-ATGCAA
1007009 AATG-AA
1 AATGCAA
1007015 AATGCA
1 AATGCA
1007021 TATATGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 12 0.40
7 7 0.23
8 11 0.37
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:1009383 original size:18 final size:18
Alignment explanation
Indices: 1009362--1009411 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 18
1009352 ATAATAAATA
1009362 AATAAAATAAAAAATAAT
1 AATAAAATAAAAAATAAT
*
1009380 AAT-ATAT-AAAAA-AAT
1 AATAAAATAAAAAATAAT
1009395 AATAAGTAATAAAAAAT
1 AATAA--AATAAAAAAT
1009412 TTGAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
15 6 0.24
16 6 0.24
17 3 0.12
18 5 0.20
19 5 0.20
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATAAAAAATAAT
Found at i:1009408 original size:15 final size:15
Alignment explanation
Indices: 1009349--1009398 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
1009339 TTAATTCTTG
*
1009349 AATATAATAAATAAAT
1 AATAT-ATAAAAAAAT
*
1009365 AAAATA-AAAAATAAT
1 AATATATAAAAA-AAT
1009380 AATATATAAAAAAAT
1 AATATATAAAAAAAT
1009395 AATA
1 AATA
1009399 AGTAATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 4 0.14
15 16 0.55
16 9 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATATATAAAAAAAT
Done.