Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015199.1 Kokia drynarioides strain JFW-HI SEQ_130243, 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: 887795
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 743 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:618923 original size:29 final size:29
Alignment explanation
Indices: 618861--618926 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
618851 ATCAAATTTG
*
618861 TTTTAAATTTAAATTTAAATTTAATTTGA
1 TTTTAAATTTAAATTTAAATTTAAATTGA
* **
618890 GTTTAAATTTATTTTTAAATTTAAAATT-A
1 TTTTAAATTTAAATTTAAATTT-AAATTGA
618919 TTTTAAAT
1 TTTTAAAT
618927 AAAGTCCAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 27 0.87
30 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (29 bp):
TTTTAAATTTAAATTTAAATTTAAATTGA
Found at i:619598 original size:16 final size:15
Alignment explanation
Indices: 619573--619609 Score: 65
Period size: 16 Copynumber: 2.4 Consensus size: 15
619563 AAATTAAGGA
619573 TAATAAAAATAATAT
1 TAATAAAAATAATAT
619588 TAATAATAAATAATAT
1 TAATAA-AAATAATAT
619604 TAATAA
1 TAATAA
619610 CAGTAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
TAATAAAAATAATAT
Found at i:619608 original size:9 final size:9
Alignment explanation
Indices: 619580--619647 Score: 56
Period size: 9 Copynumber: 7.8 Consensus size: 9
619570 GGATAATAAA
619580 AATAATATT
1 AATAATATT
619589 AATAATA--
1 AATAATATT
619596 AATAATATT
1 AATAATATT
* *
619605 AATAACAGT
1 AATAATATT
619614 AATAATA--
1 AATAATATT
619621 AAT-ATGCCATT
1 AATAAT---ATT
619632 AATAATATT
1 AATAATATT
619641 AATAATA
1 AATAATA
619648 AATAAAAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
6 2 0.04
7 10 0.21
9 31 0.65
11 3 0.06
12 2 0.04
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.35
Consensus pattern (9 bp):
AATAATATT
Found at i:620344 original size:5 final size:5
Alignment explanation
Indices: 620334--620358 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
620324 ACCTGAATCT
620334 GACCC GACCC GACCC GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC
620359 AAGATTCGTG
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:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
GACCC
Found at i:620806 original size:29 final size:28
Alignment explanation
Indices: 620771--621080 Score: 131
Period size: 29 Copynumber: 10.7 Consensus size: 28
620761 CAAACTTTTT
*
620771 AAAAATTACATTTTTACCCTTGAACTTCC
1 AAAAATTACATTTTTACCC-CGAACTTCC
* * * *
620800 CAAAATTCCATTTTTGA-CCCTAATTTTTCC
1 AAAAATTACATTTTT-ACCCCGAA--CTTCC
*
620830 -AAAATTACCA-TTTTACCCCCGAACTTCA
1 AAAAATTA-CATTTTTA-CCCCGAACTTCC
* * * *
620858 AAAAATTCCATTTTTTA-TCCTAATTTTTCC
1 AAAAATTACA-TTTTTACCCCGAA--CTTCC
*
620888 AAAAATTAC-TATTTTACCGCCAAACTTCC
1 AAAAATTACAT-TTTTACC-CCGAACTTCC
* * * * *
620917 AAAAATTCCATTTTGACCCCAAATTTTC
1 AAAAATTACATTTTTACCCCGAACTTCC
**
620945 AAAAATTACCA-TTTTATCCTTGAACTTCC
1 AAAAATTA-CATTTTTA-CCCCGAACTTCC
* *
620974 -AAAATT-CTATTTTTGA-CCCTAATTTTTCC
1 AAAAATTAC-ATTTTT-ACCCCGAA--CTTCC
621003 AAAAATTACCA-TTTTACCCTCGAACTTCC
1 AAAAATTA-CATTTTTACCC-CGAACTTCC
* * *
621032 AAAAATTCCATTTTGACCTCGAACTTTTCC
1 AAAAATTACATTTTTACCCCGAAC--TTCC
621062 -AAAATTACCA-TTTTACCCC
1 AAAAATTA-CATTTTTACCCC
621081 CGAGTGTCCA
Statistics
Matches: 209, Mismatches: 41, Indels: 62
0.67 0.13 0.20
Matches are distributed among these distances:
26 1 0.00
27 4 0.02
28 49 0.23
29 99 0.47
30 47 0.22
31 8 0.04
32 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAAATTACATTTTTACCCCGAACTTCC
Found at i:620844 original size:58 final size:58
Alignment explanation
Indices: 620772--621079 Score: 392
Period size: 58 Copynumber: 5.3 Consensus size: 58
620762 AAACTTTTTA
* *
620772 AAAATTA-CATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCCTAATTTTTCC
1 AAAATTACCA-TTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
* * * *
620830 AAAATTACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTTATCCTAATTTTTCC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
* * * * *
620888 AAAAATTACTATTTTACCGC-CAAACTTCCAAAAATTCCA-TTTTGACCCCAAATTTTCA
1 -AAAATTACCATTTTACC-CTCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
* * *
620946 AAAATTACCATTTTATCCTTGAACTTCC-AAAATTCTATTTTTGACCCTAATTTTTCC
1 AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
* *
621003 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGACCTCGAACTTTTCC
1 -AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACC-CTAATTTTTCC
621062 AAAATTACCATTTTACCC
1 AAAATTACCATTTTACCC
621080 CCGAGTGTCC
Statistics
Matches: 215, Mismatches: 27, Indels: 16
0.83 0.10 0.06
Matches are distributed among these distances:
56 9 0.04
57 38 0.18
58 115 0.53
59 52 0.24
60 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (58 bp):
AAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCTAATTTTTCC
Found at i:621017 original size:115 final size:116
Alignment explanation
Indices: 620771--621083 Score: 416
Period size: 115 Copynumber: 2.7 Consensus size: 116
620761 CAAACTTTTT
** * * *
620771 AAAAATTA-CATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCCTAATTTTTCCAAAAT
1 AAAAATTACCA-TTTTACCCTCAAACTTCCAAAAATTCCA-TTTTGACCCCAAATTTTCCAAAAT
* *
620835 TACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTTATCCTAATTTTTCC
64 TACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGACCCTAATTTTTCC
* *
620888 AAAAATTACTATTTTACCGC-CAAACTTCCAAAAATTCCATTTTGACCCCAAATTTTCAAAAATT
1 AAAAATTACCATTTTACC-CTCAAACTTCCAAAAATTCCATTTTGACCCCAAATTTTCCAAAATT
* ** * *
620952 ACCATTTTATCCTTGAACTTC-CAAAATTCTATTTTTGACCCTAATTTTTCC
65 ACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGACCCTAATTTTTCC
* * *
621003 AAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTGACCTCGAACTTTTCCAAAATT
1 AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTGACC-CCAAATTTTCCAAAATT
621068 ACCATTTTACCCCCGA
65 ACCATTTTACCCCCGA
621084 GTGTCCAAAA
Statistics
Matches: 170, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
114 1 0.01
115 69 0.41
116 67 0.39
117 31 0.18
118 2 0.01
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTGACCCCAAATTTTCCAAAATTA
CCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGACCCTAATTTTTCC
Found at i:621062 original size:174 final size:174
Alignment explanation
Indices: 620758--621078 Score: 490
Period size: 174 Copynumber: 1.8 Consensus size: 174
620748 ATATTTCGAC
*
620758 CCCCAAACTTTTTAAAAATTACATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCCTAA
1 CCCCAAACTTTTCAAAAATTACATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCCTAA
* *
620823 TTTTTCCAAAATTACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTTATCCTAATTTTTCC
66 TTTTTCCAAAATTACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGATCCTAACTTTTCC
*
620888 AAAAATTACTATTTTACCGCCAAACTTCCAAAAATTCCATTTTGA
131 -AAAATTACCATTTTACCGCCAAACTTCCAAAAATTCCATTTTGA
* *
620933 CCCCAAA-TTTTCAAAAATTACCA-TTTTATCCTTGAACTT-CCAAAATTCTATTTTTGACCCTA
1 CCCCAAACTTTTCAAAAATTA-CATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCCTA
* *
620995 ATTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCA-TTTTGA-CCTCGAACTT
65 ATTTTTCC-AAAATTACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGATCCT--AACTT
621058 TTCCAAAATTACCATTTTACC
127 TTCCAAAATTACCATTTTACC
621079 CCCGAGTGTC
Statistics
Matches: 134, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
172 3 0.02
173 51 0.38
174 71 0.53
175 9 0.07
ACGTcount: A:0.33, C:0.26, G:0.03, T:0.38
Consensus pattern (174 bp):
CCCCAAACTTTTCAAAAATTACATTTTTACCCTTGAACTTCCCAAAATTCCATTTTTGACCCTAA
TTTTTCCAAAATTACCATTTTACCCCCGAACTTCAAAAAATTCCATTTTTGATCCTAACTTTTCC
AAAATTACCATTTTACCGCCAAACTTCCAAAAATTCCATTTTGA
Found at i:621095 original size:28 final size:28
Alignment explanation
Indices: 621059--621121 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
621049 CTCGAACTTT
*
621059 TCCAAAATTACCATTTTACCCCCGAGTG
1 TCCAAAATTACCATTTTACCCCCGAGTA
* *
621087 TCCAAAATTACCATTTTACCCTCGGGTA
1 TCCAAAATTACCATTTTACCCCCGAGTA
621115 TCCAAAA
1 TCCAAAA
621122 ATCATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.10, T:0.29
Consensus pattern (28 bp):
TCCAAAATTACCATTTTACCCCCGAGTA
Found at i:630756 original size:16 final size:16
Alignment explanation
Indices: 630735--630767 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
630725 ATGATATAAG
630735 GACATTGAGAATGCTC
1 GACATTGAGAATGCTC
630751 GACATTGAGAATGCTC
1 GACATTGAGAATGCTC
630767 G
1 G
630768 CATACGAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (16 bp):
GACATTGAGAATGCTC
Found at i:632911 original size:99 final size:100
Alignment explanation
Indices: 632796--632991 Score: 270
Period size: 99 Copynumber: 2.0 Consensus size: 100
632786 AGTACCGCAA
* * * * *
632796 AGACATGAAGGGAAAGATTTAAGCCGCAGCGGCGAATCCTGTACCACGAAGACACGA-GGAAAAG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAGGGAAAAG
* *
632860 GTTTAAGTCGCAATGGCGAACC-TAGTACCTCACAG
66 GTTTAAGTCACAATAGCGAACCTTA-TACCTCACAG
* * *
632895 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCGCAAAGACACAAGGGGAAAG
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAGGGAAAAG
*
632960 GTTTAAGTCATAATAGCGAACCTTATACCTCA
66 GTTTAAGTCACAATAGCGAACCTTATACCTCA
632992 GAAAGCAGGA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
99 50 0.60
100 32 0.38
101 2 0.02
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (100 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACGGCGAATCCAGTACCACAAAGACACAAGGGAAAAG
GTTTAAGTCACAATAGCGAACCTTATACCTCACAG
Found at i:632918 original size:148 final size:148
Alignment explanation
Indices: 632650--632966 Score: 503
Period size: 148 Copynumber: 2.1 Consensus size: 148
632640 GCACCATGAA
* *
632650 ACATGAAGGGAAAGATCTAAGCCGTAACGGCGAATCCAGTACCACGAAGACACGAGAAAAAGGTT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAGAAAAAGGTT
* *
632715 TAAGTCGCAATGGCGAACTTAGTACCTCACAGAGACATGAAGAGAAAGATCTAAGCCGTAACGG-
66 TAAGTCGCAATGGCGAACCTAGTACCTCACAGAGACATGAAGAGAAAGATCTAAGCCGCAACGGC
*
632779 TGACTCCAGTACCGCAAAG
131 GGA-TCCAGTACCGCAAAG
* * *
632798 ACATGAAGGGAAAGATTTAAGCCGCAGCGGCGAATCCTGTACCACGAAGACACGAGGAAAAGGTT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAGAAAAAGGTT
*
632863 TAAGTCGCAATGGCGAACCTAGTACCTCACAGAGACATGAAGGGAAAGATCTAAGCCGCAACGGC
66 TAAGTCGCAATGGCGAACCTAGTACCTCACAGAGACATGAAGAGAAAGATCTAAGCCGCAACGGC
632928 GGATCCAGTACCGCAAAG
131 GGATCCAGTACCGCAAAG
* *
632946 ACA-CAAGGGGAAAGGTTTAAG
1 ACATGAA-GGGAAAGATTTAAG
632967 TCATAATAGC
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
147 2 0.01
148 152 0.97
149 2 0.01
ACGTcount: A:0.38, C:0.21, G:0.27, T:0.14
Consensus pattern (148 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGACACGAGAAAAAGGTT
TAAGTCGCAATGGCGAACCTAGTACCTCACAGAGACATGAAGAGAAAGATCTAAGCCGCAACGGC
GGATCCAGTACCGCAAAG
Found at i:634177 original size:16 final size:15
Alignment explanation
Indices: 634152--634184 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
634142 AAATTAATGA
634152 TAATAAAAATAATAT
1 TAATAAAAATAATAT
634167 TAATAATAAATAATAT
1 TAATAA-AAATAATAT
634183 TA
1 TA
634185 GCATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAAAAATAATAT
Found at i:634234 original size:9 final size:9
Alignment explanation
Indices: 634159--634238 Score: 51
Period size: 9 Copynumber: 8.8 Consensus size: 9
634149 TGATAATAAA
634159 AATAATATT
1 AATAATATT
634168 AATAATA--
1 AATAATATT
634175 AATAATATT
1 AATAATATT
*
634184 AGCATTAAAATT
1 A--A-TAATATT
* *
634196 AATAACAGT
1 AATAATATT
634205 AATAATA--
1 AATAATATT
*
634212 AATATGACATT
1 AATA--ATATT
634223 AATAATATT
1 AATAATATT
634232 AATAATA
1 AATAATA
634239 AATAAAAGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 18
0.70 0.08 0.22
Matches are distributed among these distances:
7 11 0.20
9 32 0.57
10 1 0.02
11 5 0.09
12 7 0.12
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (9 bp):
AATAATATT
Found at i:635498 original size:57 final size:58
Alignment explanation
Indices: 635353--635724 Score: 372
Period size: 57 Copynumber: 6.5 Consensus size: 58
635343 ACCCCTATAC
* * *
635353 TTTT-CAAAAATTACTTTTTTACCCTCGAACTTCCTAAAATTCCATTTTTACCCCT--
1 TTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAA
*
635408 TTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAA
1 TTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAA
** * * *
635466 TTTTCC-AAAATTACTATTTTACCCTTAAACTTCCAAAAATTTCATTTTTGA-CCTCGA
1 TTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCT-AA
* *
635523 TTTTCCAAAAATTACTATTTTACCCTC-AGATTTCC-AAAATTCCATTTTTGACCCTAA
1 TTTTCCAAAAATTACTATTTTACCCTCGA-ACTTCCAAAAATTCCATTTTTAACCCTAA
* * * * *
635580 TTTTCCAAAAATTACCATTTTACCCTCGGACTTCCAAAAATTCTA-TTTTGA-CCTCGA
1 TTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCT-AA
* * * * *
635637 TTTTCTCGAAAATTA-TCATTTTACCC-CG-ACTTCTAAAAATTCTATTTTTGACCCCGAA
1 TTTTC-CAAAAATTACT-ATTTTACCCTCGAACTTCCAAAAATTCCATTTTT-AACCCTAA
* * * *
635695 CTTTCCCAAAATTACCATTTTGCCCCTCGA
1 TTTTCCAAAAATTACTATTTT-ACCCTCGA
635725 GTGTCCAAAA
Statistics
Matches: 268, Mismatches: 30, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
55 4 0.01
56 68 0.25
57 126 0.47
58 66 0.25
59 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (58 bp):
TTTTCCAAAAATTACTATTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCTAA
Found at i:635502 original size:86 final size:86
Alignment explanation
Indices: 635357--635628 Score: 251
Period size: 86 Copynumber: 3.2 Consensus size: 86
635347 CTATACTTTT
* * * **
635357 CAAAAATTACTTTTTTACCCTC-GAACTTCCTAAAATTCCATTTTT-ACCCCT--TTTTCCAAAA
1 CAAAAATTCCATTTTTACCCTCAG-ATTTCC-AAAATTCCATTTTTGA-CCCTAAACTTCCAAAA
635418 ATTACCATTTTACCCTCGAACTTC
63 ATTACCATTTTACCCTCGAACTTC
*
635442 CAAAAATTCCATTTTTAACCCT-A-ATTTTCCAAAATTAC-TATTTT-ACCCTTAAACTTCCAAA
1 CAAAAATTCCATTTTT-ACCCTCAGA-TTTCCAAAATTCCAT-TTTTGACCC-TAAACTTCCAAA
* **
635503 AATT-TCATTTTTGA-CCTCGATTTTC
62 AATTACCA-TTTT-ACCCTCGAACTTC
* **
635528 CAAAAATTAC-TATTTTACCCTCAGATTTCCAAAATTCCATTTTTGACCCTAATTTTCCAAAAAT
1 CAAAAATTCCAT-TTTTACCCTCAGATTTCCAAAATTCCATTTTTGACCCTAAACTTCCAAAAAT
*
635592 TACCATTTTACCCTCGGACTTC
65 TACCATTTTACCCTCGAACTTC
*
635614 CAAAAATTCTATTTT
1 CAAAAATTCCATTTT
635629 GACCTCGATT
Statistics
Matches: 151, Mismatches: 19, Indels: 33
0.74 0.09 0.16
Matches are distributed among these distances:
83 4 0.03
84 14 0.09
85 27 0.18
86 96 0.64
87 10 0.07
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (86 bp):
CAAAAATTCCATTTTTACCCTCAGATTTCCAAAATTCCATTTTTGACCCTAAACTTCCAAAAATT
ACCATTTTACCCTCGAACTTC
Found at i:635614 original size:29 final size:28
Alignment explanation
Indices: 635357--635751 Score: 219
Period size: 29 Copynumber: 13.8 Consensus size: 28
635347 CTATACTTTT
**
635357 CAAAAATTACTTTTTTACCCTCGAACTTC
1 CAAAAATTACCATTTTACCCTCG-ACTTC
* ***
635386 CTAAAATT-CCATTTTTACCC-CTTTTTC
1 CAAAAATTACCA-TTTTACCCTCGACTTC
635413 CAAAAATTACCATTTTACCCTCGAACTTC
1 CAAAAATTACCATTTTACCCTCG-ACTTC
* *
635442 CAAAAATT-CCATTTTTAACCCT-AATTTTC
1 CAAAAATTACCA-TTTT-ACCCTCGA-CTTC
* **
635471 C-AAAATTACTATTTTACCCTTAAACTTC
1 CAAAAATTACCATTTTACCC-TCGACTTC
* *
635499 CAAAAATT-TCATTTTTGA-CCTCGATTTTC
1 CAAAAATTACCA-TTTT-ACCCTCGA-CTTC
* *
635528 CAAAAATTACTATTTTACCCTCAGATTTC
1 CAAAAATTACCATTTTACCCTC-GACTTC
* *
635557 C-AAAATT-CCATTTTTGACCCT-AATTTTC
1 CAAAAATTACCA-TTTT-ACCCTCGA-CTTC
635585 CAAAAATTACCATTTTACCCTCGGACTTC
1 CAAAAATTACCATTTTACCCTC-GACTTC
* *
635614 CAAAAATT-CTATTTTGA-CCTCGATTTTC
1 CAAAAATTACCATTTT-ACCCTCGA-CTTC
* *
635642 TCGAAAATTATCATTTTACCC-CGACTTC
1 -CAAAAATTACCATTTTACCCTCGACTTC
* *
635670 TAAAAATT-CTATTTTTGACCC-CGAACTTTC
1 CAAAAATTACCA-TTTT-ACCCTCG-AC-TTC
* * *
635700 CCAAAATTACCATTTTGCCCCTCGAGTGTC
1 CAAAAATTACCATTTT-ACCCTCGACT-TC
*
635730 C-AAAATGACCATTTTACCCTCG
1 CAAAAATTACCATTTTACCCTCG
635752 GGTATCCAAA
Statistics
Matches: 288, Mismatches: 42, Indels: 73
0.71 0.10 0.18
Matches are distributed among these distances:
26 1 0.00
27 37 0.13
28 77 0.27
29 128 0.44
30 41 0.14
31 4 0.01
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCTCGACTTC
Found at i:635700 original size:115 final size:113
Alignment explanation
Indices: 635338--635724 Score: 426
Period size: 115 Copynumber: 3.4 Consensus size: 113
635328 AAAAAATATA
* ** * * *
635338 TTTTGACCCCTATACTTTTCAAAAATTACTTTTTTACCCTCGAACTTCCTAAAATTCCATTTTTA
1 TTTTGACCCCTA-ACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCTATTTTGA
**
635403 CC-CCTTTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCAT
65 CCTCGATTTTCCAAAAATTA-CATTTTACCCTCG-ACTT-CAAAAATTCCAT
* * * **
635454 TTTT-AACCCTAATTTTCC-AAAATTACTATTTTACCCTTAAACTTCCAAAAATT-TCATTTTTG
1 TTTTGACCCCTAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCT-A-TTTTG
* *
635516 ACCTCGATTTTCCAAAAATTACTATTTTACCCTCAGATTTCCAAAATTCCAT
64 ACCTCGATTTTCCAAAAATTAC-ATTTTACCCTC-GACTTCAAAAATTCCAT
* *
635568 TTTTGA-CCCTAATTTTCCAAAAATTACCATTTTACCCTCGGACTTCCAAAAATTCTATTTTGAC
1 TTTTGACCCCTAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCTATTTTGAC
* *
635632 CTCGATTTTCTCGAAAATTATCATTTTACCC-CGACTTCTAAAAATTCTAT
66 CTCGATTTTC-CAAAAATTA-CATTTTACCCTCGACTTC-AAAAATTCCAT
* * *
635682 TTTTGACCCCGAACTTTCCCAAAATTACCATTTTGCCCCTCGA
1 TTTTGACCCCTAACTTTCCAAAAATTACCATTTT-ACCCTCGA
635725 GTGTCCAAAA
Statistics
Matches: 232, Mismatches: 26, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
113 37 0.16
114 73 0.31
115 109 0.47
116 13 0.06
ACGTcount: A:0.30, C:0.27, G:0.04, T:0.39
Consensus pattern (113 bp):
TTTTGACCCCTAACTTTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCTATTTTGAC
CTCGATTTTCCAAAAATTACATTTTACCCTCGACTTCAAAAATTCCAT
Found at i:635759 original size:28 final size:29
Alignment explanation
Indices: 635700--635762 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 29
635690 CCGAACTTTC
* * *
635700 CCAAAATTACCATTTTGCCCCTCGAGTGT
1 CCAAAATGACCATTTTGACCCTCGAGTAT
*
635729 CCAAAATGACCATTTT-ACCCTCGGGTAT
1 CCAAAATGACCATTTTGACCCTCGAGTAT
635757 CCAAAA
1 CCAAAA
635763 ATCACATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 15 0.50
29 15 0.50
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.27
Consensus pattern (29 bp):
CCAAAATGACCATTTTGACCCTCGAGTAT
Found at i:635763 original size:29 final size:29
Alignment explanation
Indices: 635700--635772 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
635690 CCGAACTTTC
* * *
635700 CCAAAATTACCATTTTGCCCCTCGAGTGT
1 CCAAAATCACCATTTTGACCCTCGAGTAT
* *
635729 CCAAAATGACCATTTT-ACCCTCGGGTAT
1 CCAAAATCACCATTTTGACCCTCGAGTAT
635757 CCAAAAATCA-CATTTT
1 CC-AAAATCACCATTTT
635773 CAAACCCCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.30, C:0.29, G:0.11, T:0.30
Consensus pattern (29 bp):
CCAAAATCACCATTTTGACCCTCGAGTAT
Found at i:637155 original size:15 final size:14
Alignment explanation
Indices: 637121--637155 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
637111 TTACATTTGA
637121 AATTTAATTTTTAT
1 AATTTAATTTTTAT
*
637135 ATTTTAATTTATTAT
1 AATTTAATTT-TTAT
637150 AATTTA
1 AATTTA
637156 GTTCTCTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AATTTAATTTTTAT
Found at i:640158 original size:11 final size:11
Alignment explanation
Indices: 640142--640171 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
640132 ATGCCAAATT
640142 ATCAAGAATAA
1 ATCAAGAATAA
640153 ATCAAGAATAA
1 ATCAAGAATAA
640164 ATCAAGAA
1 ATCAAGAA
640172 CAAAACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.63, C:0.10, G:0.10, T:0.17
Consensus pattern (11 bp):
ATCAAGAATAA
Found at i:640958 original size:24 final size:24
Alignment explanation
Indices: 640918--640976 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
640908 CTTTTAATAT
*
640918 TTTATTTTTT-ATTAATTT-GATC-
1 TTTATTTTTTAATAAATTTAGA-CA
640940 TTTATTTTTTAACTAAATTTAGACA
1 TTTATTTTTTAA-TAAATTTAGACA
*
640965 TTAATTTTTTAA
1 TTTATTTTTTAA
640977 AAAAGTCATG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 10 0.32
23 1 0.03
24 7 0.23
25 13 0.42
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (24 bp):
TTTATTTTTTAATAAATTTAGACA
Found at i:641282 original size:30 final size:30
Alignment explanation
Indices: 641246--641306 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
641236 ATTCATCTCT
* *
641246 TTTTTAAAAGATTGATGA-TCAAATTTGACTA
1 TTTTAAAAAG-TTGA-GAGTCAAATTTAACTA
641277 TTTTAAAAAGTTGAGAGTCAAATTTAACTA
1 TTTTAAAAAGTTGAGAGTCAAATTTAACTA
641307 AATAAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 16 0.59
31 9 0.33
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (30 bp):
TTTTAAAAAGTTGAGAGTCAAATTTAACTA
Found at i:649565 original size:17 final size:17
Alignment explanation
Indices: 649540--649578 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
649530 AAAATGAGTA
*
649540 TTTTATTTTTTCAAAAG
1 TTTTTTTTTTTCAAAAG
* *
649557 TTTTTTTTTTTGAAAGG
1 TTTTTTTTTTTCAAAAG
649574 TTTTT
1 TTTTT
649579 AGAGTATACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.67
Consensus pattern (17 bp):
TTTTTTTTTTTCAAAAG
Found at i:650217 original size:25 final size:23
Alignment explanation
Indices: 650189--650235 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
650179 TTTTTCATTT
* *
650189 AATTTAATATTTGTTCTTTTTTTAC
1 AATTCAAT-TTTGTT-TTCTTTTAC
650214 AATTCAATTTTGTTTTCTTTTA
1 AATTCAATTTTGTTTTCTTTTA
650236 TTATTTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (23 bp):
AATTCAATTTTGTTTTCTTTTAC
Found at i:653506 original size:21 final size:21
Alignment explanation
Indices: 653466--653507 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
653456 AAAATCTGAT
653466 TCTTCCATGCTGCTGATAAGC
1 TCTTCCATGCTGCTGATAAGC
*
653487 TCTT-CATGCTGCATGCTAAGC
1 TCTTCCATGCTGC-TGATAAGC
653508 CATCAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (21 bp):
TCTTCCATGCTGCTGATAAGC
Found at i:657954 original size:21 final size:21
Alignment explanation
Indices: 657914--657955 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
657904 TAAATCTGAT
657914 TCTTCCATGCTGCTGATAAGC
1 TCTTCCATGCTGCTGATAAGC
*
657935 TCTT-CATGCTGCATGCTAAGC
1 TCTTCCATGCTGC-TGATAAGC
657956 CATCAGTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (21 bp):
TCTTCCATGCTGCTGATAAGC
Found at i:661445 original size:28 final size:28
Alignment explanation
Indices: 661405--661462 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
661395 TAGGACTATA
661405 CTTACACTTGCATCTATCTTTAATTGGC
1 CTTACACTTGCATCTATCTTTAATTGGC
661433 CTTACACTTGCATCTATCTTTAATTGGC
1 CTTACACTTGCATCTATCTTTAATTGGC
661461 CT
1 CT
661463 CTGCATCAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (28 bp):
CTTACACTTGCATCTATCTTTAATTGGC
Found at i:668577 original size:15 final size:16
Alignment explanation
Indices: 668557--668589 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
668547 ATGCCCAACC
668557 AAAATTA-ATATATTA
1 AAAATTAGATATATTA
*
668572 AAAATTAGATATTTTA
1 AAAATTAGATATATTA
668588 AA
1 AA
668590 CCAATCGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATTAGATATATTA
Found at i:671113 original size:17 final size:17
Alignment explanation
Indices: 671093--671128 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
671083 TAATGTTTAT
671093 CGTCGATTAATAGAGAC
1 CGTCGATTAATAGAGAC
671110 CGTCGATTAATAGAGAC
1 CGTCGATTAATAGAGAC
671127 CG
1 CG
671129 AAAAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (17 bp):
CGTCGATTAATAGAGAC
Found at i:671572 original size:33 final size:31
Alignment explanation
Indices: 671519--671581 Score: 90
Period size: 33 Copynumber: 2.0 Consensus size: 31
671509 CCAAGTTAGT
**
671519 AAAAAAAATTTAACTTTTAAAAATTAAAAAA
1 AAAAAAAATTTAACCCTTAAAAATTAAAAAA
671550 AAAAAAAAGTTTAGACCCTTAAAAATTAAAAA
1 AAAAAAAA-TTTA-ACCCTTAAAAATTAAAAA
671582 CACACAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 8 0.29
32 4 0.14
33 16 0.57
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.25
Consensus pattern (31 bp):
AAAAAAAATTTAACCCTTAAAAATTAAAAAA
Found at i:673605 original size:6 final size:6
Alignment explanation
Indices: 673583--673637 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
673573 CGGCCTTGAC
* * * *
673583 GAGGTT GAGATT GAGGTT TAGGTT GAGGTT GAGGTT GTGGTT GGGGTT
1 GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT GAGGTT
*
673631 GGGGTT G
1 GAGGTT G
673638 TTGGTCCTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.13, C:0.00, G:0.51, T:0.36
Consensus pattern (6 bp):
GAGGTT
Found at i:682171 original size:23 final size:23
Alignment explanation
Indices: 682051--682171 Score: 145
Period size: 23 Copynumber: 5.3 Consensus size: 23
682041 GCTGGGGAAA
682051 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
682074 TAGT-AGCCACATACAGTGCAAAT
1 CAGTAAG-CACACACAGTGCAAAT
* * *
682097 TAGTAGGCACACACAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
*
682120 CAGTAAGCACACGCAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* * *
682143 CAGTAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
682166 CAGTAA
1 CAGTAA
682172 ACACCAGTAA
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 2 0.02
23 80 0.96
24 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:682192 original size:69 final size:68
Alignment explanation
Indices: 682048--682179 Score: 171
Period size: 69 Copynumber: 2.0 Consensus size: 68
682038 AGTGCTGGGG
* * *
682048 AAACAGTAAGCACACACAGTGCAAATTAGTAGCCACATACAGTGCAAATTAGTAGGCACACACAG
1 AAACAGTAAGCACACACAGTGCAAATCAGTAGCCACATACAGTGCAAATCAGTA-GAACACACAG
682113 TGCA
65 TGCA
* * *
682117 AAACAGTAAGCACACGCAGTGCAAATCAGTAAG-CACATATAGTGCGAATCAGTA-AACAC-CAG
1 AAACAGTAAGCACACACAGTGCAAATCAGT-AGCCACATACAGTGCAAATCAGTAGAACACACAG
682179 T
65 T
682180 AAGCACACAC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
66 4 0.07
67 4 0.07
69 46 0.82
70 2 0.04
ACGTcount: A:0.42, C:0.23, G:0.19, T:0.16
Consensus pattern (68 bp):
AAACAGTAAGCACACACAGTGCAAATCAGTAGCCACATACAGTGCAAATCAGTAGAACACACAGT
GCA
Found at i:684686 original size:24 final size:23
Alignment explanation
Indices: 684642--684707 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
684632 AATTAATAAA
684642 AATTTGATTTAAACAAA-TAAACAG
1 AATTT-ATTTAAA-AAATTAAACAG
684666 AATTTATTTAAAATAATTAAACAG
1 AATTTATTTAAAA-AATTAAACAG
* *
684690 AGTTTAATTAAAAAATTA
1 AATTTATTTAAAAAATTA
684708 TTTTTTAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 1 0.03
23 14 0.37
24 23 0.61
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.35
Consensus pattern (23 bp):
AATTTATTTAAAAAATTAAACAG
Found at i:689082 original size:20 final size:20
Alignment explanation
Indices: 689044--689082 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
689034 TATATATATA
* * *
689044 TTTAAATTTTTAGATAATTT
1 TTTAAATTTTAAAAAAATTT
689064 TTTAAATTTTAAAAAAATT
1 TTTAAATTTTAAAAAAATT
689083 AATTAATTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
TTTAAATTTTAAAAAAATTT
Found at i:694397 original size:30 final size:30
Alignment explanation
Indices: 694352--694412 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
694342 GTGACATCAA
* * *
694352 CTCAGTTAAAAAATTATAAAAATATCTTTT
1 CTCAATTAAAAAATTACAAAAATATCGTTT
*
694382 CTCAATTAAATAATTACAAAAATATCGTTT
1 CTCAATTAAAAAATTACAAAAATATCGTTT
694412 C
1 C
694413 GTATTTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (30 bp):
CTCAATTAAAAAATTACAAAAATATCGTTT
Found at i:704894 original size:169 final size:164
Alignment explanation
Indices: 704599--704918 Score: 428
Period size: 169 Copynumber: 1.9 Consensus size: 164
704589 ATATGATACG
*
704599 TATACTTTGAAAATGTTCAAGGTGGTACTTAAACTATCAATAATTATAATGATAATTGGAGTAAA
1 TATACTTTGAAAATGTTCAAGGTGATACTTAAACTATCAATAATTATAATGATAATTGGAGTAAA
* * * * *
704664 CACCCATAGTAAATGTTAAACCACCAATGAAAATTCAACCTGTGGATTTTTTCTCCAAATCATTA
66 CACCAATAGTAAATGCTAAACCACCAATGAAAATTCAACATGTGAATTTTTTCTACAAATCATTA
* *
704729 ATTTCACTTGGGTGATATAATCCAATGTGGTGCT
131 ATCTCACATGGGTGATATAATCCAATGTGGTGCT
* * * * *
704763 TATACTTTGAAAATGTTCAAGGTGATACTTAAGCTATTGATTTGTGTATTATTATGATAATTGGA
1 TATACTTTGAAAATGTTCAAGGTGATACTTAAACTA-TCA---AT-AATTATAATGATAATTGGA
* *
704828 GTAAACACCAATTGTAAATGCTAAACCAATCAATGAAAATTCGAA-ATGTGAATTTTTT-TACAA
61 GTAAACACCAATAGTAAATGCTAAACC-ACCAATGAAAATTC-AACATGTGAATTTTTTCTACAA
704891 ATCATTAATCTCACATGGGTGATATAAT
124 ATCATTAATCTCACATGGGTGATATAAT
704919 ATTATGTGAA
Statistics
Matches: 134, Mismatches: 15, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
164 34 0.25
165 2 0.01
168 1 0.01
169 71 0.53
170 24 0.18
171 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (164 bp):
TATACTTTGAAAATGTTCAAGGTGATACTTAAACTATCAATAATTATAATGATAATTGGAGTAAA
CACCAATAGTAAATGCTAAACCACCAATGAAAATTCAACATGTGAATTTTTTCTACAAATCATTA
ATCTCACATGGGTGATATAATCCAATGTGGTGCT
Found at i:709113 original size:12 final size:12
Alignment explanation
Indices: 709096--709120 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
709086 GATGACCGAA
709096 GAGGATTTCAGG
1 GAGGATTTCAGG
709108 GAGGATTTCAGG
1 GAGGATTTCAGG
709120 G
1 G
709121 TGGCAGGGAT
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:0.24, C:0.08, G:0.44, T:0.24
Consensus pattern (12 bp):
GAGGATTTCAGG
Found at i:716903 original size:19 final size:20
Alignment explanation
Indices: 716860--716897 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
716850 TACTTCAAAA
716860 AAAATATTTTAAAATTCAAC
1 AAAATATTTTAAAATTCAAC
716880 AAAAT-TTTTAAAAATTCA
1 AAAATATTTT-AAAATTCA
716898 TAAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
AAAATATTTTAAAATTCAAC
Found at i:721965 original size:17 final size:19
Alignment explanation
Indices: 721943--721979 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
721933 GATATAATTT
*
721943 AAAAA-TAA-ATTTTAAAA
1 AAAAATTAATATTGTAAAA
721960 AAAAATTAATATTGTAAAA
1 AAAAATTAATATTGTAAAA
721979 A
1 A
721980 TAGATGTCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 5 0.29
18 3 0.18
19 9 0.53
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (19 bp):
AAAAATTAATATTGTAAAA
Found at i:729607 original size:56 final size:57
Alignment explanation
Indices: 729541--729655 Score: 205
Period size: 56 Copynumber: 2.0 Consensus size: 57
729531 AAATCAAATC
*
729541 TAAATAAAATTATTGATGTGATATAAATTATTGAAAAA-AAAAATATCACTGTTTTA
1 TAAATAAAATTATTGATGTGACATAAATTATTGAAAAATAAAAATATCACTGTTTTA
*
729597 TAAATAAAATTATTGATGTGACATAAATTATTGAAAAATAATAATATCACTGTTTTA
1 TAAATAAAATTATTGATGTGACATAAATTATTGAAAAATAAAAATATCACTGTTTTA
729654 TA
1 TA
729656 TAATCTTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 37 0.66
57 19 0.34
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (57 bp):
TAAATAAAATTATTGATGTGACATAAATTATTGAAAAATAAAAATATCACTGTTTTA
Found at i:736642 original size:20 final size:20
Alignment explanation
Indices: 736617--736657 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
736607 TTTCCATATG
736617 AAAGTCTGTAATATTCATGA
1 AAAGTCTGTAATATTCATGA
736637 AAAGTCTGTAATATTCATGA
1 AAAGTCTGTAATATTCATGA
736657 A
1 A
736658 TCTTCTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (20 bp):
AAAGTCTGTAATATTCATGA
Found at i:742816 original size:5 final size:5
Alignment explanation
Indices: 742792--742828 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
742782 TTTGTTGTTA
*
742792 TCCA- TCCA- TCCAG TCTAG TCCAG TCCAG TCCAG TCCA
1 TCCAG TCCAG TCCAG TCCAG TCCAG TCCAG TCCAG TCCA
742829 CACTTACGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
4 8 0.27
5 22 0.73
ACGTcount: A:0.22, C:0.41, G:0.14, T:0.24
Consensus pattern (5 bp):
TCCAG
Found at i:746694 original size:22 final size:21
Alignment explanation
Indices: 746682--746723 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 21
746672 AGTTGAAATC
746682 TAAATTTAAATTATTCAAACAA
1 TAAATTTAAATTATTCAAAC-A
746704 TAAATTTAAATTAATTCAAA
1 TAAATTTAAATT-ATTCAAA
746724 ATTTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAAATTATTCAAACA
Found at i:746797 original size:7 final size:7
Alignment explanation
Indices: 746787--746818 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
746777 TATAAATCAT
746787 AAATTCC
1 AAATTCC
746794 AAATTCC
1 AAATTCC
746801 AAATTCC
1 AAATTCC
746808 AAATTCC
1 AAATTCC
746815 AAAT
1 AAAT
746819 ATAGATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.28
Consensus pattern (7 bp):
AAATTCC
Found at i:749530 original size:43 final size:43
Alignment explanation
Indices: 749476--749562 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
749466 TCTGAATGTC
749476 AACACGCAGCCTAAATTTATTCTTTTAAAAGATTAATTTTATA
1 AACACGCAGCCTAAATTTATTCTTTTAAAAGATTAATTTTATA
749519 AACACGCAGCCTAAATTTATTCTTTTAAAAGATTAATTTTATA
1 AACACGCAGCCTAAATTTATTCTTTTAAAAGATTAATTTTATA
749562 A
1 A
749563 GTACACGTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (43 bp):
AACACGCAGCCTAAATTTATTCTTTTAAAAGATTAATTTTATA
Found at i:753427 original size:10 final size:10
Alignment explanation
Indices: 753414--753488 Score: 66
Period size: 10 Copynumber: 7.8 Consensus size: 10
753404 AATGATAAAA
753414 AATAAAAATT
1 AATAAAAATT
*
753424 AATAAAAGTT
1 AATAAAAATT
753434 -ATAAAAATT
1 AATAAAAATT
* **
753443 ATTAAATTTT
1 AATAAAAATT
753453 AATAAAAA-T
1 AATAAAAATT
*
753462 -ATAAAAAAT
1 AATAAAAATT
*
753471 ATTAAAAATT
1 AATAAAAATT
*
753481 TATAAAAA
1 AATAAAAA
753489 AATTACAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
8 7 0.14
9 10 0.20
10 33 0.66
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
AATAAAAATT
Found at i:753465 original size:8 final size:8
Alignment explanation
Indices: 753454--753532 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 8
753444 TTAAATTTTA
753454 ATAAAAAT
1 ATAAAAAT
753462 ATAAAAAAT
1 AT-AAAAAT
753471 ATTAAAAATTT
1 A-TAAAAA--T
753482 ATAAAAAAATT
1 AT--AAAAA-T
*
753493 ACAAAAAT
1 ATAAAAAT
*
753501 CGTAAAAAAAT
1 -AT-AAA-AAT
753512 ATAAAAAT
1 ATAAAAAT
753520 ATAAAAAT
1 ATAAAAAT
753528 ATAAA
1 ATAAA
753533 TTTTTATAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
8 19 0.33
9 20 0.34
10 6 0.10
11 8 0.14
12 5 0.09
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (8 bp):
ATAAAAAT
Found at i:753486 original size:20 final size:19
Alignment explanation
Indices: 753410--753570 Score: 72
Period size: 21 Copynumber: 8.6 Consensus size: 19
753400 CAAAAATGAT
*
753410 AAAAA-ATAAAAATTAATA
1 AAAAATATAAAAATTTATA
**
753428 AAAGTTATAAAAA-TTATTA
1 AAAAATATAAAAATTTA-TA
***
753447 AATTTTAATAAAAA--TATA
1 AAAAAT-ATAAAAATTTATA
753465 AAAAATATTAAAAATTTATAA
1 AAAAATA-TAAAAATTTAT-A
* *
753486 AAAAATTACAAAAATCGTA-A
1 AAAAA-TATAAAAAT-TTATA
753506 AAAAATATAAAAA--TAT-
1 AAAAATATAAAAATTTATA
*
753522 AAAAATAT--AAATTTTTA
1 AAAAATATAAAAATTTATA
* * *
753539 TAAAATCATAAGAAAATTGTA
1 AAAAAT-ATAA-AAATTTATA
753560 AAAAATATAAA
1 AAAAATATAAA
753571 TAAATATAAA
Statistics
Matches: 110, Mismatches: 16, Indels: 33
0.69 0.10 0.21
Matches are distributed among these distances:
14 3 0.03
16 12 0.11
17 6 0.05
18 18 0.16
19 23 0.21
20 20 0.18
21 24 0.22
22 4 0.04
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATAAAAATTTATA
Found at i:753488 original size:11 final size:10
Alignment explanation
Indices: 753417--753581 Score: 52
Period size: 10 Copynumber: 17.3 Consensus size: 10
753407 GATAAAAAAT
753417 AAAAATTA-A
1 AAAAATTATA
*
753426 TAAAAGTTAT-
1 -AAAAATTATA
753436 AAAAATTAT-
1 AAAAATTATA
* *
753445 -TAAATTTTA
1 AAAAATTATA
*
753454 ATAAAAATATA
1 A-AAAATTATA
753465 AAAAA-TATTA
1 AAAAATTA-TA
*
753475 AAAATTTATAA
1 AAAAATTAT-A
*
753486 AAAAATTA-C
1 AAAAATTATA
**
753495 AAAAATCGTA
1 AAAAATTATA
*
753505 AAAAAATAT-
1 AAAAATTATA
753514 AAAAA-TAT-
1 AAAAATTATA
753522 AAAAA-TAT-
1 AAAAATTATA
* *
753530 -AAATTTTTA
1 AAAAATTATA
* *
753539 TAAAATCATA
1 AAAAATTATA
*
753549 AGAAAATTGTA
1 A-AAAATTATA
753560 AAAAA-TATA
1 AAAAATTATA
753569 AATAAA-TATA
1 AA-AAATTATA
753579 AAA
1 AAA
753582 TTCGTAAAAA
Statistics
Matches: 117, Mismatches: 25, Indels: 27
0.69 0.15 0.16
Matches are distributed among these distances:
7 3 0.03
8 19 0.16
9 27 0.23
10 43 0.37
11 25 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAATTATA
Found at i:753498 original size:21 final size:20
Alignment explanation
Indices: 753461--753543 Score: 63
Period size: 16 Copynumber: 4.3 Consensus size: 20
753451 TTAATAAAAA
753461 TATAAAAAATATTAAAAATT
1 TATAAAAAATATTAAAAATT
*
753481 TATAAAAAA-ATTACAAAAATCG
1 TATAAAAAATATT--AAAAAT-T
753503 TA-AAAAAATA-TAAAAA--
1 TATAAAAAATATTAAAAATT
**
753519 TAT-AAAAATA-TAAATTTT
1 TATAAAAAATATTAAAAATT
753537 TATAAAA
1 TATAAAA
753544 TCATAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
16 13 0.25
18 3 0.06
19 11 0.21
20 9 0.17
21 13 0.25
22 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.30
Consensus pattern (20 bp):
TATAAAAAATATTAAAAATT
Found at i:753516 original size:10 final size:10
Alignment explanation
Indices: 753456--753526 Score: 60
Period size: 9 Copynumber: 7.3 Consensus size: 10
753446 AAATTTTAAT
753456 AAAAATAT-A
1 AAAAATATAA
753465 AAAAATATTAA
1 AAAAATA-TAA
**
753476 AAATTTATAA
1 AAAAATATAA
*
753486 AAAAAT-TAC
1 AAAAATATAA
*
753495 AAAAATCGTAA
1 AAAAAT-ATAA
753506 AAAAATAT--
1 AAAAATATAA
753514 AAAAATATAA
1 AAAAATATAA
753524 AAA
1 AAA
753527 TATAAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
8 8 0.16
9 15 0.31
10 12 0.24
11 14 0.29
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (10 bp):
AAAAATATAA
Found at i:753575 original size:10 final size:9
Alignment explanation
Indices: 753456--753581 Score: 71
Period size: 10 Copynumber: 13.3 Consensus size: 9
753446 AAATTTTAAT
753456 AAAAATATA
1 AAAAATATA
753465 AAAAATATTA
1 AAAAATA-TA
*
753475 AAAATTTATA
1 AAAA-ATATA
753485 AAAAA-ATTA
1 AAAAATA-TA
*
753494 CAAAAATCGTA
1 -AAAAAT-ATA
753505 AAAAA-ATA
1 AAAAATATA
753513 TAAAAATAT-
1 -AAAAATATA
753522 AAAAATAT-
1 AAAAATATA
** *
753530 AAATTTTTA
1 AAAAATATA
*
753539 TAAAATCATA
1 AAAAAT-ATA
*
753549 AGAAAATTGTA
1 A-AAAA-TATA
753560 AAAAATATA
1 AAAAATATA
753569 AATAAATATA
1 AA-AAATATA
753579 AAA
1 AAA
753582 TTCGTAAAAA
Statistics
Matches: 90, Mismatches: 14, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
8 16 0.18
9 23 0.26
10 39 0.43
11 11 0.12
12 1 0.01
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (9 bp):
AAAAATATA
Found at i:753799 original size:10 final size:10
Alignment explanation
Indices: 753786--753854 Score: 72
Period size: 10 Copynumber: 6.9 Consensus size: 10
753776 TTTTGATGCA
753786 TTTT-ATAAT
1 TTTTAATAAT
*
753795 TTTTTATGAAT
1 TTTTAAT-AAT
753806 TTTATAA-AA-
1 TTT-TAATAAT
753815 TTTTAATAAT
1 TTTTAATAAT
*
753825 TTTTAATAAAA
1 TTTTAAT-AAT
753836 TTTTAATAAT
1 TTTTAATAAT
753846 TTTTAATAA
1 TTTTAATAA
753855 AATTTCAATA
Statistics
Matches: 51, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
8 3 0.06
9 9 0.18
10 22 0.43
11 15 0.29
12 2 0.04
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:753807 original size:19 final size:20
Alignment explanation
Indices: 753774--753812 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
753764 GTAAAAAAAT
*
753774 TTTTTTGATGCATTTTATAA
1 TTTTTTGATGAATTTTATAA
753794 TTTTTT-ATGAATTTTATAA
1 TTTTTTGATGAATTTTATAA
753813 AATTTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (20 bp):
TTTTTTGATGAATTTTATAA
Found at i:753816 original size:21 final size:21
Alignment explanation
Indices: 753769--753839 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 21
753759 TAATAGTAAA
*
753769 AAAATTTTTTTGATGCATTTTAT
1 AAAA-TTTTTT-ATGAATTTTAT
753792 --AATTTTTTATGAATTTTAT
1 AAAATTTTTTATGAATTTTAT
*
753811 AAAA-TTTTAAT-AATTTTTAAT
1 AAAATTTTTTATGAA-TTTT-AT
753832 AAAATTTT
1 AAAATTTT
753840 AATAATTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
19 12 0.29
20 16 0.39
21 10 0.24
22 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (21 bp):
AAAATTTTTTATGAATTTTAT
Found at i:753840 original size:21 final size:21
Alignment explanation
Indices: 753805--753871 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
753795 TTTTTATGAA
753805 TTTT-ATAAAATTTTAATAAT
1 TTTTAATAAAATTTTAATAAT
753825 TTTTAATAAAATTTTAATAAT
1 TTTTAATAAAATTTTAATAAT
* *
753846 TTTTAATAAAATTTCAATATT
1 TTTTAATAAAATTTTAATAAT
753867 TTTTA
1 TTTTA
753872 TATTTTAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
20 4 0.09
21 40 0.91
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTAATAAAATTTTAATAAT
Found at i:753878 original size:28 final size:28
Alignment explanation
Indices: 753846--753901 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
753836 TTTTAATAAT
753846 TTTTAA-TAAAATTTCAATATTTTTTATA
1 TTTTAATTAAAATTT-AATATTTTTTATA
753874 TTTTAATTAAAATTTAATATTTTTTATA
1 TTTTAATTAAAATTTAATATTTTTTATA
753902 GCTTTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTAATTAAAATTTAATATTTTTTATA
Found at i:761413 original size:10 final size:10
Alignment explanation
Indices: 761398--761466 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
761388 TGTTTATTTA
761398 TATTTTATAT
1 TATTTTATAT
*
761408 TATTTTATTT
1 TATTTTATAT
761418 TATTTTATAAT
1 TATTTTAT-AT
* *
761429 TGTTTGAATAT
1 TATTT-TATAT
761440 GTA-TTTATAAT
1 -TATTTTAT-AT
*
761451 TATATTATAT
1 TATTTTATAT
761461 T-TTTTA
1 TATTTTA
761467 AACTTAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
9 4 0.09
10 24 0.52
11 15 0.33
12 3 0.07
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TATTTTATAT
Found at i:761415 original size:5 final size:5
Alignment explanation
Indices: 761372--761425 Score: 56
Period size: 5 Copynumber: 10.4 Consensus size: 5
761362 GAGTTTTATC
* *
761372 ATTTT -TTTT AATTTT TTGTTT ATTTAT ATTTT ATATT ATTTT ATTTT
1 ATTTT ATTTT -ATTTT AT-TTT ATTT-T ATTTT ATTTT ATTTT ATTTT
761419 ATTTT AT
1 ATTTT AT
761426 AATTGTTTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
4 4 0.10
5 24 0.59
6 13 0.32
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (5 bp):
ATTTT
Found at i:769683 original size:5 final size:5
Alignment explanation
Indices: 769673--769697 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
769663 AAAGAAAGCA
769673 AGAGG AGAGG AGAGG AGAGG AGAGG
1 AGAGG AGAGG AGAGG AGAGG AGAGG
769698 GAATGAATAC
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:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (5 bp):
AGAGG
Found at i:770823 original size:13 final size:13
Alignment explanation
Indices: 770788--770830 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
770778 GACTTAATAT
770788 TTTATTA-TTATA
1 TTTATTATTTATA
*
770800 TTTAGTTATTTTTA
1 TTTA-TTATTTATA
770814 TTTATTATTTA-A
1 TTTATTATTTATA
770826 TTTAT
1 TTTAT
770831 AAATATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 10 0.37
13 9 0.33
14 8 0.30
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TTTATTATTTATA
Found at i:772055 original size:17 final size:17
Alignment explanation
Indices: 772035--772073 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
772025 TTTATTATAA
*
772035 ATTATATTTTAAATATT
1 ATTATATATTAAATATT
*
772052 ATTATATATTAATTATT
1 ATTATATATTAAATATT
*
772069 TTTAT
1 ATTAT
772074 TAATTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTATATATTAAATATT
Found at i:776375 original size:26 final size:27
Alignment explanation
Indices: 776336--776389 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
776326 TATGTCAGCC
*
776336 AATTGTTCCCTAACAAAATGACAATAA
1 AATTGTTCCATAACAAAATGACAATAA
776363 AATT-TTCCATAACAAAATGACAATAA
1 AATTGTTCCATAACAAAATGACAATAA
776389 A
1 A
776390 TTTCTATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 22 0.85
27 4 0.15
ACGTcount: A:0.52, C:0.17, G:0.06, T:0.26
Consensus pattern (27 bp):
AATTGTTCCATAACAAAATGACAATAA
Found at i:777061 original size:26 final size:26
Alignment explanation
Indices: 777025--777077 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
777015 CCCCCTACCC
777025 TTGTATCCTCAATCAATTCCAAGGCA
1 TTGTATCCTCAATCAATTCCAAGGCA
777051 TTGTATCCTCAATCAATTCCAAGGCA
1 TTGTATCCTCAATCAATTCCAAGGCA
777077 T
1 T
777078 ACTTTCGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.32
Consensus pattern (26 bp):
TTGTATCCTCAATCAATTCCAAGGCA
Found at i:791050 original size:94 final size:93
Alignment explanation
Indices: 790943--791130 Score: 340
Period size: 94 Copynumber: 2.0 Consensus size: 93
790933 AATTTAATGA
790943 TTTTTACGGATTAAGATACTAAGTGAAGAAATTATTTAATTTAGATTGATAATGACAGATGAAAT
1 TTTTTACGGATTAAGATACTAAGTGAAGAAATTATTTAATTTAGATTGATAATGACAGATGAAAT
*
791008 CGAGGTGGATTCTTTTTTGGATATTGTT
66 CGAGGTGGATTCTTTCTTGGATATTGTT
*
791036 TTTTCTACGGATTAAGGTACTAAGTGAAGAAATTATTTAATTTAGATTGATAATGACAGATGAAA
1 TTTT-TACGGATTAAGATACTAAGTGAAGAAATTATTTAATTTAGATTGATAATGACAGATGAAA
*
791101 TCGAGGTGGATTCTTTCTTGGATGTTGTT
65 TCGAGGTGGATTCTTTCTTGGATATTGTT
791130 T
1 T
791131 CGCTTATTAG
Statistics
Matches: 91, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
93 4 0.04
94 87 0.96
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.40
Consensus pattern (93 bp):
TTTTTACGGATTAAGATACTAAGTGAAGAAATTATTTAATTTAGATTGATAATGACAGATGAAAT
CGAGGTGGATTCTTTCTTGGATATTGTT
Found at i:794715 original size:20 final size:20
Alignment explanation
Indices: 794683--794723 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
794673 AGTTTTTTAT
794683 AAAACTCAATTAAAATATTA
1 AAAACTCAATTAAAATATTA
*
794703 AAAAC-CAACTTAAAATTTTA
1 AAAACTCAA-TTAAAATATTA
794723 A
1 A
794724 GCAATAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAACTCAATTAAAATATTA
Found at i:795236 original size:82 final size:82
Alignment explanation
Indices: 794996--795239 Score: 337
Period size: 82 Copynumber: 3.0 Consensus size: 82
794986 ATCATACCCT
* * * *
794996 ATGTGATGGTCTGATAGTTAAAGGT-ATTCTCAGTCTCAAATATGATCTGAATTTGAGTCGTGCT
1 ATGTGATGGTCTGATGGTTAAAGGTGTTTTTCA-TCTCAGATATGATCTGAATTTGAGTCGTGCT
*
795060 AGTCATGTTTGTCATTCC
65 AGTCATGTTTGTTATTCC
* * * *
795078 ATGTGATGGTATGATGGTTAAAGGTGTTTTCCGTCTCAGATATGATCTGAATTTGAGTCATGCTA
1 ATGTGATGGTCTGATGGTTAAAGGTGTTTTTCATCTCAGATATGATCTGAATTTGAGTCGTGCTA
* * *
795143 ATCATGTTTGTTGTTTC
66 GTCATGTTTGTTATTCC
* * *
795160 ATGTGATGGTCTAATGGTTAAAGGTGTTTTTCATCTCAGATATGATCTGAATTTGAATCGTTCTA
1 ATGTGATGGTCTGATGGTTAAAGGTGTTTTTCATCTCAGATATGATCTGAATTTGAGTCGTGCTA
795225 GTCATGTTTGTTATT
66 GTCATGTTTGTTATT
795240 TGAATTTTAT
Statistics
Matches: 140, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
82 137 0.98
83 3 0.02
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (82 bp):
ATGTGATGGTCTGATGGTTAAAGGTGTTTTTCATCTCAGATATGATCTGAATTTGAGTCGTGCTA
GTCATGTTTGTTATTCC
Found at i:795880 original size:30 final size:30
Alignment explanation
Indices: 795825--795887 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
795815 TTTTTTAATG
795825 ACATTACTAAATTTTTAAAAAAT-AAAAAT
1 ACATTACTAAATTTTTAAAAAATAAAAAAT
**
795854 ACATATACTAAA-TTTTAAATTTATAAAAAAT
1 ACAT-TACTAAATTTTTAAA-AAATAAAAAAT
795885 ACA
1 ACA
795888 AAGACTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 11 0.38
30 9 0.31
31 9 0.31
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (30 bp):
ACATTACTAAATTTTTAAAAAATAAAAAAT
Found at i:795882 original size:37 final size:37
Alignment explanation
Indices: 795832--795908 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
795822 ATGACATTAC
* * *
795832 TAAATTTTTAAAAAATAAAAATACATATACTAAATTT
1 TAAATTTATAAAAAATAAAAAGACATATAATAAATTT
* * *
795869 TAAATTTATAAAAAATACAAAGACTTATAATATATTT
1 TAAATTTATAAAAAATAAAAAGACATATAATAAATTT
795906 TAA
1 TAA
795909 CTTCATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.38
Consensus pattern (37 bp):
TAAATTTATAAAAAATAAAAAGACATATAATAAATTT
Found at i:800611 original size:29 final size:29
Alignment explanation
Indices: 800579--800661 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 29
800569 ACTATCAATA
* *
800579 TTTTTAATTTGATCACTCAACTATTGTTTTT
1 TTTTTAATTTGATCAC-CAACTATT-ATATT
** *
800610 TTTTCTTTTTTGGTCACCAACTATTA-ATT
1 TTTT-TAATTTGATCACCAACTATTATATT
800639 TTTTTAATTTGATCACCCAACTA
1 TTTTTAATTTGATCA-CCAACTA
800662 ATCAAGATTG
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
28 8 0.19
29 13 0.31
31 12 0.29
32 9 0.21
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.53
Consensus pattern (29 bp):
TTTTTAATTTGATCACCAACTATTATATT
Found at i:807991 original size:6 final size:6
Alignment explanation
Indices: 807980--808009 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
807970 GTAAATGACC
807980 GGAGAG GGAGAG GGAGAG GGAGAAG GGAGA
1 GGAGAG GGAGAG GGAGAG GGAG-AG GGAGA
808010 TGAGGCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.37, C:0.00, G:0.63, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:808988 original size:29 final size:31
Alignment explanation
Indices: 808927--808999 Score: 96
Period size: 30 Copynumber: 2.4 Consensus size: 31
808917 TATAATCTCA
* *
808927 AAAAATCAATTAAGTTCTCTAAAAAAAAATT
1 AAAAATCAATTAAATCCTCTAAAAAAAAATT
*
808958 AAAAA-CAATTAAATCCTC-AAAAAATAATT
1 AAAAATCAATTAAATCCTCTAAAAAAAAATT
*
808987 AAAAATTAATTAA
1 AAAAATCAATTAA
809000 CCTTTCACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 15 0.41
30 17 0.46
31 5 0.14
ACGTcount: A:0.62, C:0.10, G:0.01, T:0.27
Consensus pattern (31 bp):
AAAAATCAATTAAATCCTCTAAAAAAAAATT
Found at i:811889 original size:21 final size:21
Alignment explanation
Indices: 811865--811919 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
811855 CCTGTGCTAG
*
811865 TTCTACCAATACAAGTATAAT
1 TTCTACCAATACAAATATAAT
811886 TTCTACCAATACAAATATAAT
1 TTCTACCAATACAAATATAAT
*
811907 TTCTACCGATACA
1 TTCTACCAATACA
811920 TGTCATGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.42, C:0.22, G:0.04, T:0.33
Consensus pattern (21 bp):
TTCTACCAATACAAATATAAT
Found at i:812718 original size:52 final size:51
Alignment explanation
Indices: 812635--812778 Score: 191
Period size: 52 Copynumber: 2.8 Consensus size: 51
812625 CTTTCACTTC
* * *
812635 ATTCATATACTCACGAGGACACATAACCATCGGACCT-TATAATCCGCAAGGG
1 ATTCATATACTCACGATGACACA-AATCATCGGACCTCT-TAATCCGCAAAGG
*
812687 ATTCATATACTCACGATGACACAAAGTCATCGGACCTCTTAATCCGTAAAGG
1 ATTCATATACTCACGATGACACAAA-TCATCGGACCTCTTAATCCGCAAAGG
* *
812739 ATTCATATACTCACAATGACACTTAATCATCGGACCTCTT
1 ATTCATATACTCACGATGACAC-AAATCATCGGACCTCTT
812779 CGTTTATGGC
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
51 2 0.02
52 78 0.94
53 3 0.04
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (51 bp):
ATTCATATACTCACGATGACACAAATCATCGGACCTCTTAATCCGCAAAGG
Found at i:815906 original size:15 final size:17
Alignment explanation
Indices: 815886--815922 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
815876 AATTAACATT
815886 TTATTTAA-AA-TAATA
1 TTATTTAATAAGTAATA
815901 TTATTTTAATAAGTAATA
1 TTA-TTTAATAAGTAATA
815919 TTAT
1 TTAT
815923 AATATATATG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.16
16 5 0.26
17 3 0.16
18 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATTTAATAAGTAATA
Found at i:816578 original size:13 final size:13
Alignment explanation
Indices: 816554--816588 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
816544 TAGCTAAAAA
816554 TGAAGCGAGCATCT
1 TGAAG-GAGCATCT
816568 TGAAGGAGCATCT
1 TGAAGGAGCATCT
816581 TGAAGGAG
1 TGAAGGAG
816589 AAAAGTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.76
14 5 0.24
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.20
Consensus pattern (13 bp):
TGAAGGAGCATCT
Found at i:817609 original size:21 final size:21
Alignment explanation
Indices: 817540--817619 Score: 67
Period size: 21 Copynumber: 3.7 Consensus size: 21
817530 TTATATATTT
817540 TTTTAGATTTTTTT-TGAAAT-
1 TTTTAGATTTTTTTAT-AAATA
* *
817560 TTTTATAATTTTTTTAAAAATAAAAA
1 TTTTA-GATTTTTTT----ATAAATA
817586 TTTTAGATTTTTTTATAAATA
1 TTTTAGATTTTTTTATAAATA
817607 TTTT-GATTTTTTT
1 TTTTAGATTTTTTT
817620 TTTTGTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
20 14 0.29
21 18 0.37
25 11 0.22
26 6 0.12
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (21 bp):
TTTTAGATTTTTTTATAAATA
Found at i:818063 original size:24 final size:24
Alignment explanation
Indices: 818036--818083 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
818026 AAAATAATTA
818036 TAATTTAATTTACAAATATTACTT
1 TAATTTAATTTACAAATATTACTT
818060 TAATTTAATTTACAAATATTACTT
1 TAATTTAATTTACAAATATTACTT
818084 AAAAAGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
TAATTTAATTTACAAATATTACTT
Found at i:819525 original size:5 final size:5
Alignment explanation
Indices: 819518--819553 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
819508 ACAGCATATG
*
819518 GCCAG GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT G
1 GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT G
819554 GATGGATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.19, C:0.39, G:0.25, T:0.17
Consensus pattern (5 bp):
GCCAT
Found at i:823080 original size:3 final size:3
Alignment explanation
Indices: 823072--823103 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
823062 TCTCATCAAG
*
823072 TGC TGC TGC CGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
823104 GGGTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.34, G:0.34, T:0.31
Consensus pattern (3 bp):
TGC
Found at i:835290 original size:23 final size:22
Alignment explanation
Indices: 835264--835316 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
835254 TTATGTATCC
*
835264 ATACTATATATTATAAAAATAAT
1 ATACTATAT-TAATAAAAATAAT
*
835287 ATACT-TATTAATAAAAATGAT
1 ATACTATATTAATAAAAATAAT
835308 ATA-TATATT
1 ATACTATATT
835317 TTTATCATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 18 0.67
22 3 0.11
23 5 0.19
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (22 bp):
ATACTATATTAATAAAAATAAT
Found at i:837555 original size:17 final size:17
Alignment explanation
Indices: 837533--837565 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
837523 ATTTGGGATG
837533 ATGACATGCGATATAAA
1 ATGACATGCGATATAAA
837550 ATGACATGCGATATAA
1 ATGACATGCGATATAA
837566 CAGTTGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
ATGACATGCGATATAAA
Found at i:838028 original size:41 final size:42
Alignment explanation
Indices: 837964--838072 Score: 141
Period size: 41 Copynumber: 2.6 Consensus size: 42
837954 TTAATGGCGT
* *
837964 TTATA-AAAAAACATCGCTAAAGGTCAGAACATTAGTAGCGC
1 TTATAGAAAAAACGTCGCTAAAGGTCAGAACATTAGCAGCGC
* * * *
838005 TTAT-GAGAAAACGTCGCTAAAGGTCAGAGCATTAGCGGCGT
1 TTATAGAAAAAACGTCGCTAAAGGTCAGAACATTAGCAGCGC
*
838046 TTATAGAAAAAACGTCGCTAAAAGTCA
1 TTATAGAAAAAACGTCGCTAAAGGTCA
838073 AAGAGTAATA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 38 0.66
42 20 0.34
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (42 bp):
TTATAGAAAAAACGTCGCTAAAGGTCAGAACATTAGCAGCGC
Found at i:838153 original size:42 final size:41
Alignment explanation
Indices: 837961--838155 Score: 132
Period size: 41 Copynumber: 4.7 Consensus size: 41
837951 TTTTTAATGG
* * *
837961 CGTTTAT-AAAAAAACATCGCTAAAGGTCAGAA-CATTAGTA
1 CGTTTATGAGAAAAACGTCGCTAAAGGTCA-AAGCATTAGGA
* * *
838001 GCGCTTATGAG-AAAACGTCGCTAAAGGTCAGAGCATTAGCGG
1 -CGTTTATGAGAAAAACGTCGCTAAAGGTCAAAGCATTAG-GA
* *
838043 CGTTTAT-AGAAAAAACGTCGCTAAAAGTCAAAGAGTAATATAGG-
1 CGTTTATGAG-AAAAACGTCGCTAAAGGTC-AA-AG-CAT-TAGGA
** * *
838087 CGTCAATGAG-AAAACGCCACTAAAGGTCAAAGCATTAGCGA
1 CGTTTATGAGAAAAACGTCGCTAAAGGTCAAAGCATTAG-GA
* **
838128 CGTTTATGGGAAAAACACCGCTAAAGGT
1 CGTTTATGAGAAAAACGTCGCTAAAGGT
838156 TAAACAATAG
Statistics
Matches: 120, Mismatches: 21, Indels: 25
0.72 0.13 0.15
Matches are distributed among these distances:
39 3 0.03
40 6 0.05
41 45 0.38
42 35 0.29
43 16 0.13
44 7 0.06
45 5 0.04
46 3 0.03
ACGTcount: A:0.40, C:0.17, G:0.23, T:0.21
Consensus pattern (41 bp):
CGTTTATGAGAAAAACGTCGCTAAAGGTCAAAGCATTAGGA
Found at i:840536 original size:43 final size:43
Alignment explanation
Indices: 840470--840577 Score: 153
Period size: 43 Copynumber: 2.5 Consensus size: 43
840460 ATAAAAAAAT
* *
840470 ACCATGTTCTTTAGAGGCATTTGTAAGAAAAGTGCCGCTAAAG
1 ACCATGTTCTTTAGCGGCGTTTGTAAGAAAAGTGCCGCTAAAG
** *
840513 ACCATGTTCTTTAGCGGCGTTTGTGGGAGAAGTGCCGCTAAAG
1 ACCATGTTCTTTAGCGGCGTTTGTAAGAAAAGTGCCGCTAAAG
* *
840556 ACCATGTTCTTTAACGGTGTTT
1 ACCATGTTCTTTAGCGGCGTTT
840578 TCCCTTAAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
ACCATGTTCTTTAGCGGCGTTTGTAAGAAAAGTGCCGCTAAAG
Found at i:847143 original size:41 final size:40
Alignment explanation
Indices: 847096--847175 Score: 117
Period size: 41 Copynumber: 1.9 Consensus size: 40
847086 ACACTTAAAA
847096 ATATTAAAACAGATAT-TAAAACAACAAACAAATTAAAAACG
1 ATATTAAAACA-AT-TCTAAAACAACAAACAAATTAAAAACG
*
847137 ATATTAAAACAATTCGTAAAACAACAAACAAATTGAAAA
1 ATATTAAAACAATTC-TAAAACAACAAACAAATTAAAAA
847176 TACAATAAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
39 1 0.03
40 2 0.06
41 33 0.92
ACGTcount: A:0.62, C:0.12, G:0.05, T:0.20
Consensus pattern (40 bp):
ATATTAAAACAATTCTAAAACAACAAACAAATTAAAAACG
Found at i:856934 original size:16 final size:16
Alignment explanation
Indices: 856894--856938 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
856884 AGTTTAGGGT
*
856894 TTAAAAATTCTAATTAA
1 TTAAAAATT-TATTTAA
856911 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
856925 TTAAAAATTTATTT
1 TTAAAAATTTATTT
856939 TCATTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 10 0.40
17 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:874658 original size:95 final size:95
Alignment explanation
Indices: 874495--874686 Score: 384
Period size: 95 Copynumber: 2.0 Consensus size: 95
874485 TTATAATTCA
874495 CCAAAAAGAATCGGTAGTTGACACATTAACGGAGTAAATGTGAAACTAACCTTAAGGCCCAACCC
1 CCAAAAAGAATCGGTAGTTGACACATTAACGGAGTAAATGTGAAACTAACCTTAAGGCCCAACCC
874560 CAATCAAAATAAATCCAATCCATATATTTT
66 CAATCAAAATAAATCCAATCCATATATTTT
874590 CCAAAAAGAATCGGTAGTTGACACATTAACGGAGTAAATGTGAAACTAACCTTAAGGCCCAACCC
1 CCAAAAAGAATCGGTAGTTGACACATTAACGGAGTAAATGTGAAACTAACCTTAAGGCCCAACCC
874655 CAATCAAAATAAATCCAATCCATATATTTT
66 CAATCAAAATAAATCCAATCCATATATTTT
874685 CC
1 CC
874687 CAAATATGAA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 97 1.00
ACGTcount: A:0.42, C:0.23, G:0.12, T:0.23
Consensus pattern (95 bp):
CCAAAAAGAATCGGTAGTTGACACATTAACGGAGTAAATGTGAAACTAACCTTAAGGCCCAACCC
CAATCAAAATAAATCCAATCCATATATTTT
Found at i:881146 original size:17 final size:17
Alignment explanation
Indices: 881090--881150 Score: 70
Period size: 17 Copynumber: 3.5 Consensus size: 17
881080 ATTTATATCT
881090 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
* *
881107 ATTAAATTTCACATT-TTGT
1 ATT--ATTT-ATATTATTGA
881126 ATTATTTATATTATTGA
1 ATTATTTATATTATTGA
881143 ATTATTTA
1 ATTATTTA
881151 ATAATGCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.11
17 18 0.50
19 10 0.28
20 4 0.11
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTATTTATATTATTGA
Found at i:884529 original size:16 final size:16
Alignment explanation
Indices: 884508--884555 Score: 66
Period size: 13 Copynumber: 3.1 Consensus size: 16
884498 AAATTTTTAA
884508 TTTTAAAATATTATTT
1 TTTTAAAATATTATTT
884524 TTTT--AAT-TTATTT
1 TTTTAAAATATTATTT
884537 TTATTAAAATATTATTT
1 TT-TTAAAATATTATTT
884554 TT
1 TT
884556 ATAACTGGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.29
14 5 0.18
16 7 0.25
17 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAAATATTATTT
Found at i:887653 original size:27 final size:27
Alignment explanation
Indices: 887615--887670 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
887605 ATACCTGACA
*
887615 ACCAGTGGAGGAACA-CAAAGTGGCGGC
1 ACCAATGGAGGAACATC-AAGTGGCGGC
**
887642 ACCAATGGAGGAGTATCAAGTGGCGGC
1 ACCAATGGAGGAACATCAAGTGGCGGC
887669 AC
1 AC
887671 TCAGGGGTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.96
28 1 0.04
ACGTcount: A:0.32, C:0.21, G:0.36, T:0.11
Consensus pattern (27 bp):
ACCAATGGAGGAACATCAAGTGGCGGC
Done.