Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 54 of 222
Found at i:16318505 original size:54 final size:54
Alignment explanation
Indices: 16318375--16318547 Score: 188
Period size: 54 Copynumber: 3.2 Consensus size: 54
16318365 GGTATAATAG
* * * *
16318375 TCATTTTATCCTATGGGGGTATTTTGGTTATTTTACCCTATGGGGGGTATTTTGG
1 TCATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCTAT-GGGGGTATTTCGA
* * * *
16318430 TCACTCTACCCTAT-CAGGGTATTTTGGTCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGA-GGTATTTTGGTTATTTTACCCTATGGGGGTATTTCGA
* * * * *
16318484 TTATTTTACCCTATGGAGGTATTTCGATTATTTTACACTATGGGGGTATTT-TA
1 TCATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCTATGGGGGTATTTCGA
16318537 GTCATTTTACC
1 -TCATTTTACC
16318548 TATTTTGGGG
Statistics
Matches: 97, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
53 1 0.01
54 61 0.63
55 35 0.36
ACGTcount: A:0.18, C:0.16, G:0.21, T:0.45
Consensus pattern (54 bp):
TCATTTTACCCTATGGAGGTATTTTGGTTATTTTACCCTATGGGGGTATTTCGA
Found at i:16320668 original size:33 final size:33
Alignment explanation
Indices: 16320626--16320707 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
16320616 GGCCTACATG
* *
16320626 CCCGTGTGGCCTCACCCACCCAAATTCACCTTA
1 CCCGTGTGGCCCCACACACCCAAATTCACCTTA
* * *
16320659 CCCGTGTGGCCCCACACGCCCAAATTGACCTTG
1 CCCGTGTGGCCCCACACACCCAAATTCACCTTA
* *
16320692 CTCGTGT-GACCCACAC
1 CCCGTGTGGCCCCACAC
16320708 GGCCTTGCCC
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 8 0.19
33 34 0.81
ACGTcount: A:0.20, C:0.44, G:0.17, T:0.20
Consensus pattern (33 bp):
CCCGTGTGGCCCCACACACCCAAATTCACCTTA
Found at i:16324365 original size:25 final size:25
Alignment explanation
Indices: 16324336--16324385 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
16324326 ATATCTATCA
*
16324336 ACCAGAAGTACTCTCAATCAAAATC
1 ACCAGAAGTACTCTCAACCAAAATC
*
16324361 ACCAGAAGTATTCTCAACCAAAATC
1 ACCAGAAGTACTCTCAACCAAAATC
16324386 CTCAAGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.28, G:0.08, T:0.20
Consensus pattern (25 bp):
ACCAGAAGTACTCTCAACCAAAATC
Found at i:16325330 original size:29 final size:29
Alignment explanation
Indices: 16325297--16325352 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
16325287 TCGTCGCGAA
*
16325297 GCAAAGAAACTACACCCTTTAGTTTCTAC
1 GCAAAGAAACTACACCCTTCAGTTTCTAC
16325326 GCAAAGAAACTACACCCTTCAGTTTCT
1 GCAAAGAAACTACACCCTTCAGTTTCT
16325353 GCTTAGGTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.34, C:0.29, G:0.11, T:0.27
Consensus pattern (29 bp):
GCAAAGAAACTACACCCTTCAGTTTCTAC
Found at i:16326073 original size:14 final size:14
Alignment explanation
Indices: 16326054--16326085 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
16326044 TGATACCACT
16326054 AAATAACACACCCC
1 AAATAACACACCCC
16326068 AAATAACACACCCC
1 AAATAACACACCCC
16326082 AAAT
1 AAAT
16326086 CTGAGAGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.38, G:0.00, T:0.09
Consensus pattern (14 bp):
AAATAACACACCCC
Found at i:16329597 original size:57 final size:57
Alignment explanation
Indices: 16329522--16329697 Score: 280
Period size: 57 Copynumber: 3.1 Consensus size: 57
16329512 CATTTTCAGA
* *
16329522 TCATTTTCATTTTTGAGAAAACTACATTCATTTCCAAATGTTTTCATTTCTCCATTT
1 TCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGTTTTCATTTCTCCATTT
* *
16329579 TCATTTTCATTTTGGAGAAAACCAAATTCATTTCCAAATGTTTTCATTTCTCTATTT
1 TCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGTTTTCATTTCTCCATTT
* *
16329636 TCATTTTCATTTTGGAGAAAACCACAGTTCATTTCCAAATGTTTCCCATTTCTTCATTT
1 TCATTTTCATTTTGGAGAAAACCACA-TTCATTTCCAAATGTTT-TCATTTCTCCATTT
16329695 TCA
1 TCA
16329698 CTATTTCTAT
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
57 78 0.72
58 17 0.16
59 14 0.13
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.47
Consensus pattern (57 bp):
TCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGTTTTCATTTCTCCATTT
Found at i:16330824 original size:37 final size:36
Alignment explanation
Indices: 16330783--16330874 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 36
16330773 GTGTCGTGGC
* *
16330783 GTGTTATTGGTTGGATTAGATCTTATGAGAGTTTGG
1 GTGTTATCGGTTGGATTAGATCTTATAAGAGTTTGG
* *
16330819 TGTGTTATCGGTTGGATTAGCTCTTATAAGTGTTTGG
1 -GTGTTATCGGTTGGATTAGATCTTATAAGAGTTTGG
*
16330856 GATGTTATCGGGTGGATTA
1 G-TGTTATCGGTTGGATTA
16330875 ACTATTATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
36 1 0.02
37 48 0.98
ACGTcount: A:0.18, C:0.05, G:0.33, T:0.43
Consensus pattern (36 bp):
GTGTTATCGGTTGGATTAGATCTTATAAGAGTTTGG
Found at i:16330898 original size:37 final size:37
Alignment explanation
Indices: 16330821--16330910 Score: 110
Period size: 37 Copynumber: 2.5 Consensus size: 37
16330811 GAGTTTGGTG
* * * * *
16330821 TGTTATCGGTTGGATTAGCTCTTATAAGTGTTTGGGA
1 TGTTATCGGTTGGATTAACTATTATAAGCGATTGGCA
* *
16330858 TGTTATCGGGTGGATTAACTATTATGAGCGATTGGCA
1 TGTTATCGGTTGGATTAACTATTATAAGCGATTGGCA
16330895 TGTT-TCGGTTGGATTA
1 TGTTATCGGTTGGATTA
16330911 CTTGTGTACT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
36 11 0.24
37 34 0.76
ACGTcount: A:0.20, C:0.09, G:0.30, T:0.41
Consensus pattern (37 bp):
TGTTATCGGTTGGATTAACTATTATAAGCGATTGGCA
Found at i:16343890 original size:15 final size:15
Alignment explanation
Indices: 16343870--16343902 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
16343860 AATTTTGTAA
*
16343870 AAGTTAAATATAACT
1 AAGTTAAATACAACT
16343885 AAGTTAAATACAACT
1 AAGTTAAATACAACT
16343900 AAG
1 AAG
16343903 AAAACTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (15 bp):
AAGTTAAATACAACT
Found at i:16345134 original size:42 final size:43
Alignment explanation
Indices: 16345087--16345174 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 43
16345077 AGGGTAAATC
* *
16345087 CAACAACCCAAG-TATATCTTCTCCT-TTTTTAATTTCTTTTTT
1 CAACAACCCAAGAT-TATCTTCTCCTCTTTTTAAATTATTTTTT
16345129 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTATTTTTT
1 CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTATTTTTT
16345172 CAA
1 CAA
16345175 TGATAAAAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
42 23 0.55
43 19 0.45
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (43 bp):
CAACAACCCAAGATTATCTTCTCCTCTTTTTAAATTATTTTTT
Found at i:16354674 original size:105 final size:105
Alignment explanation
Indices: 16354548--16354747 Score: 287
Period size: 105 Copynumber: 1.9 Consensus size: 105
16354538 CCGCTTATTG
* * * ** *
16354548 TTCAGAGTTGTGAGCTTAACTTAGCTAACTTAAATATCTAGAGGCTGCAATTTTAAACTGGAAAG
1 TTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGCAATTTTAAA-TCAAAAA
16354613 CC-TTTATAATATCAGCTAGG-AGCGTAGGTCCACAAGTTGT
65 CCTTTTATAATATCAG-TAGGAAGCGTAGGTCCACAAGTTGT
* *
16354653 TTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGTTGCGATTTTAAATCAAAAAC
1 TTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGCAATTTTAAATCAAAAAC
*
16354718 CTTTTATAATATCAGTTGGAAGCGTAGGTC
66 CTTTTATAATATCAGTAGGAAGCGTAGGTC
16354748 TGTGAGCTAT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
104 9 0.11
105 75 0.89
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.32
Consensus pattern (105 bp):
TTCAGAGTTGCGAGCTTAACTTAACTAACTCAAATATCTAGAGGCTGCAATTTTAAATCAAAAAC
CTTTTATAATATCAGTAGGAAGCGTAGGTCCACAAGTTGT
Found at i:16354833 original size:69 final size:69
Alignment explanation
Indices: 16354735--16355619 Score: 550
Period size: 69 Copynumber: 12.8 Consensus size: 69
16354725 AATATCAGTT
* * * *
16354735 GGAAGCGTAGGTCTG-TGAGCTATTTTGGAGGCTACGATCTTAAACTGGCAAGCTTTTGTAATAT
1 GGAA-CGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATAT
* *
16354799 TAGCTG
64 CAACTG
* * ** * ** *
16354805 GGAACGTAAGTCCGCTAGCTATGCTGGAGGCTGTGATCATAAATTGGTGAGCCTTTGTAATATTA
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATCA
*
16354870 GCTG
66 ACTG
* * ** * * * * *
16354874 GGAACATAGGTCC-ATGAGCGGTGTTGAAGGCTACAATCATAAACTGGAAAACCTTTGTAATATT
1 GGAACGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATC
16354938 AACTG
65 AACTG
* * * * * ** *
16354943 GGAACGTAGGTCCACTAGATATGTTGGAGGCTGCAATCATAAACTAGTGAGCCTTTATAATATCA
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATCA
*
16355008 ATTG
66 ACTG
* * * *
16355012 GGAACGTAGGTCTG-TGAGC-A-GCTTTGAAGGCTACGATCATAAA-TCGACAAGCCTTTATAAT
1 GGAACGTAGGTCCGCT-AGCTATG--TTGGAGGCTACGATCATAAACT-GGCAAGCCTTTGTAAT
16355073 ATCAACTG
62 ATCAACTG
* * * ** * * * * * * *
16355081 GAAACTTAGGTCCGCTAGTTGCGTTAGAGGCTGCGATCATAAACCGACTAGCTTTTATAATATCA
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATCA
* *
16355146 ATTA
66 ACTG
* * * * * * ** *
16355150 AGAACGTAGGTCCGCAAGTTCTGTTGGATGCTACAATCATAAACCAGCAAG-CTTCTGTAATGTC
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTT-TGTAATATC
16355214 AACTG
65 AACTG
* * ** * *
16355219 GGAACGTAGGTCCGCTAGCTGTGTTGGAGACTGTGATCATAAA-TCGACAAGCCTTTGTAATACC
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACT-GGCAAGCCTTTGTAATATC
*
16355283 AGCTG
65 AACTG
* * * * * * * * * *
16355288 GGAACGTAGGTTCGCTAGCTATGTTGGATGTTGCAATCATAAACTAGTACGCCTTTGTATTACCA
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATCA
**
16355353 GTTG
66 ACTG
** * * * *
16355357 GGAACAAAGGTCCG-TGAGTTATGTTAGAGGCTACGATCATAAACTGGTAAGCCTTTTTAATATC
1 GGAACGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATC
* *
16355421 AGCTA
65 AACTG
* ** * * * ** * * *
16355426 GGAACATAGGTATGTTAGCTTTGTTGGAGGTTGTGATCATAAACCGTCGAGCCTTTGTAATATCA
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATCA
*
16355491 ATTG
66 ACTG
* * * ** *
16355495 GGAACGTAGGTCCG-TGAGCTGTGTTGGAGGCTGCAATCATAAA-TCAACAAGCCTTTTTAATAT
1 GGAACGTAGGTCCGCT-AGCTATGTTGGAGGCTACGATCATAAACT-GGCAAGCCTTTGTAATAT
* * *
16355558 CTATTA
64 CAACTG
* * * * ** *
16355564 GGAATGTAGGTTCGCTAGCTATATTGGGGGCTGTGATCATAAATTGGCAAGCCTTT
1 GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTT
16355620 CAAAATGACA
Statistics
Matches: 628, Mismatches: 166, Indels: 43
0.75 0.20 0.05
Matches are distributed among these distances:
67 1 0.00
68 8 0.01
69 604 0.96
70 14 0.02
71 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (69 bp):
GGAACGTAGGTCCGCTAGCTATGTTGGAGGCTACGATCATAAACTGGCAAGCCTTTGTAATATCA
ACTG
Found at i:16366984 original size:44 final size:45
Alignment explanation
Indices: 16366904--16366994 Score: 139
Period size: 44 Copynumber: 2.0 Consensus size: 45
16366894 TATACGATAG
*
16366904 ATTTTTTGCATTTATGATATACAATGGTTTTTACCACATTGAACTTTT
1 ATTTTTTGCATTTATG--A-ACAATGGTTTTTACCACATCGAACTTTT
16366952 ATTTTTTGCATTTATG-ACAATGGTTTTTACCACATCGAACTTT
1 ATTTTTTGCATTTATGAACAATGGTTTTTACCACATCGAACTTT
16366995 GTTCGGATTC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
44 26 0.62
48 16 0.38
ACGTcount: A:0.26, C:0.14, G:0.11, T:0.48
Consensus pattern (45 bp):
ATTTTTTGCATTTATGAACAATGGTTTTTACCACATCGAACTTTT
Found at i:16368443 original size:91 final size:91
Alignment explanation
Indices: 16368257--16368445 Score: 249
Period size: 91 Copynumber: 2.1 Consensus size: 91
16368247 AGTGGTGTAT
*
16368257 TTATGTTGCTTTAAGGACTATTGTTTGGTGTATTAATGCAGCAGAAAAATTCTTGTTTAGTCGTC
1 TTATGTTGCTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGTCGTC
* * *
16368322 AATTAATGTTGTCTAAGTGACTATAT
66 AATAAATGTGGTCTAAGTGACTATAA
* * *
16368348 TTATGTTGTTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAG-TAAATTGTTGTTTAGAT-GT
1 TTATGTTGCTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAG-TCGT
* *
16368411 CAATAAATGTGGTTTGAA-TGACTTTAAA
65 CAATAAATGTGGTCT-AAGTGACTAT-AA
16368439 TTATGTT
1 TTATGTT
16368446 AATAATGGTC
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
90 33 0.38
91 53 0.62
ACGTcount: A:0.28, C:0.07, G:0.21, T:0.44
Consensus pattern (91 bp):
TTATGTTGCTTTAAGGACTATTGTTTGGTGTATTAAAGCAGCAGAAAAATTCTTGTTTAGTCGTC
AATAAATGTGGTCTAAGTGACTATAA
Found at i:16375308 original size:20 final size:20
Alignment explanation
Indices: 16375285--16375352 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
16375275 GGGTTATCGT
* *
16375285 AGTGCGAACAAGGACACCGA
1 AGTGCAAACAAGGACACCAA
* * **
16375305 AGTGTATACAAGGGTACCAA
1 AGTGCAAACAAGGACACCAA
* *
16375325 AGTGCAAACAGGGACACCTA
1 AGTGCAAACAAGGACACCAA
16375345 AGTGCAAA
1 AGTGCAAA
16375353 TCCCATACAA
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.41, C:0.21, G:0.26, T:0.12
Consensus pattern (20 bp):
AGTGCAAACAAGGACACCAA
Found at i:16377792 original size:32 final size:34
Alignment explanation
Indices: 16377737--16377802 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 34
16377727 ACACAACAAG
* *
16377737 CAGTAACAGTCTGGGCTTGAACCCTATTCAGTAA
1 CAGTAACAGTCTGGGCTTGAACCCAATACAGTAA
*
16377771 CAGT-ACAGTCT-GGCTTTAACCCAATACAGTAA
1 CAGTAACAGTCTGGGCTTGAACCCAATACAGTAA
16377803 TAGTGTGGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 18 0.62
33 7 0.24
34 4 0.14
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (34 bp):
CAGTAACAGTCTGGGCTTGAACCCAATACAGTAA
Found at i:16377990 original size:26 final size:26
Alignment explanation
Indices: 16377940--16378015 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 26
16377930 ACACCAATAT
* *
16377940 CGCAGTAAAGTTGCCAGTAAT-AGTAA
1 CGCAGCAAAGCTGCCAGT-ATCAGTAA
*
16377966 CGCAGCAAAGCTGCCAGTATCAGTAT
1 CGCAGCAAAGCTGCCAGTATCAGTAA
* *
16377992 CGCATCAAACCTGCCAGTA-CAGTA
1 CGCAGCAAAGCTGCCAGTATCAGTA
16378016 TACTTCCTCC
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
25 7 0.16
26 37 0.84
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (26 bp):
CGCAGCAAAGCTGCCAGTATCAGTAA
Found at i:16386546 original size:22 final size:23
Alignment explanation
Indices: 16386520--16386565 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
16386510 TTAAATTATC
*
16386520 ATTTTTATTTTCT-TATATA-TTT
1 ATTTTCATTTT-TGTATATACTTT
16386542 ATTTTCATTTTTGTATATACTTT
1 ATTTTCATTTTTGTATATACTTT
16386565 A
1 A
16386566 ATATTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 1 0.05
22 16 0.76
23 4 0.19
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (23 bp):
ATTTTCATTTTTGTATATACTTT
Found at i:16386906 original size:18 final size:18
Alignment explanation
Indices: 16386862--16386918 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
16386852 TACTCAAATC
* *
16386862 CAACTCTCTCAATCCTTT
1 CAACTCTCTCAATTCTCT
*
16386880 CTAAC-CTCTCAGTTCTCT
1 C-AACTCTCTCAATTCTCT
*
16386898 CAACTCTCTTAATTCTCT
1 CAACTCTCTCAATTCTCT
16386916 CAA
1 CAA
16386919 TTTTCTCAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 3 0.09
18 26 0.81
19 3 0.09
ACGTcount: A:0.23, C:0.37, G:0.02, T:0.39
Consensus pattern (18 bp):
CAACTCTCTCAATTCTCT
Found at i:16386920 original size:9 final size:9
Alignment explanation
Indices: 16386885--16386927 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
16386875 CCTTTCTAAC
*
16386885 CTCTCAGTT
1 CTCTCAATT
*
16386894 CTCTCAACT
1 CTCTCAATT
*
16386903 CTCTTAATT
1 CTCTCAATT
16386912 CTCTCAATT
1 CTCTCAATT
*
16386921 TTCTCAA
1 CTCTCAA
16386928 GTTTTGTTCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.21, C:0.33, G:0.02, T:0.44
Consensus pattern (9 bp):
CTCTCAATT
Found at i:16389722 original size:43 final size:43
Alignment explanation
Indices: 16389656--16389780 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 43
16389646 AGCTTGTACA
* *
16389656 ATGCCAATGTCCCAGACGTGGTCTTACATGTAATCACATA-TCG
1 ATGCCAATGTCCCAGACGTGGTCTTACACGTAAACACA-AGTCG
* *
16389699 ATGCCACTGTCCCAAACAG-GGTCTTACACGTAAACACAAGTCG
1 ATGCCAATGTCCCAGAC-GTGGTCTTACACGTAAACACAAGTCG
*
16389742 ATGCCAATGTCCCAGACGTGGTCTTACACGAAAAACACA
1 ATGCCAATGTCCCAGACGTGGTCTTACACG-TAAACACA
16389781 TATCAGAGGT
Statistics
Matches: 71, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
42 2 0.03
43 61 0.86
44 8 0.11
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACGTGGTCTTACACGTAAACACAAGTCG
Found at i:16392910 original size:22 final size:21
Alignment explanation
Indices: 16392885--16392928 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
16392875 TTTTGAACAA
* *
16392885 TTTAATTTTTTCTTTTATGTTT
1 TTTAACTTTTTATTTTAT-TTT
16392907 TTTAACTTTTTATTTTATTTT
1 TTTAACTTTTTATTTTATTTT
16392928 T
1 T
16392929 CATTCTCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTAACTTTTTATTTTATTTT
Found at i:16394033 original size:14 final size:14
Alignment explanation
Indices: 16394014--16394041 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16394004 ATAGTGGTAT
16394014 AGTTGGAAGGCTTA
1 AGTTGGAAGGCTTA
16394028 AGTTGGAAGGCTTA
1 AGTTGGAAGGCTTA
16394042 GGCCTATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.36, T:0.29
Consensus pattern (14 bp):
AGTTGGAAGGCTTA
Found at i:16399099 original size:19 final size:20
Alignment explanation
Indices: 16399071--16399117 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
16399061 TGAGTATTGG
* *
16399071 TTTTGATTATGTGATGG-CT
1 TTTTGTTTATGTGATGGCCA
16399090 TTTTGTTTATGTGATGGCCA
1 TTTTGTTTATGTGATGGCCA
16399110 TTTTGTTT
1 TTTTGTTT
16399118 GTATCTGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.13, C:0.06, G:0.23, T:0.57
Consensus pattern (20 bp):
TTTTGTTTATGTGATGGCCA
Found at i:16403083 original size:185 final size:184
Alignment explanation
Indices: 16402767--16403115 Score: 565
Period size: 185 Copynumber: 1.9 Consensus size: 184
16402757 ATGCCATAGC
16402767 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
1 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
* * *
16402832 GTTCAACTTAATTCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATTACTGCAGTCCTTTTG
66 GTTCAACTAAATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTTG
16402897 TCTTGTGTAATATTTGCACTCAAACTCTTATTGTGTTATATTTTTCTGTTTTAGT
131 TCTTGTGTAATATTTGCACTCAAACT-TTATTGTGTTATATTTTTCTGTTTTAGT
* * * * **
16402952 ACATGAGAACACTAAAAAACTTTGTAGCTGGTGTTGGTATGGCTTTTCTGAAAATGTAGCTTAAT
1 ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
* *
16403017 GTTCAAC-AACATGCATGTTTATCTCAGGAAGGCAGTGTCCGGTTTGCATGACTGCAGTCTTTTT
66 GTTCAACTAA-ATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTT
*
16403081 GTCTTGTGTGATATTTGCACTCAAACTTTATTGTG
130 GTCTTGTGTAATATTTGCACTCAAACTTTATTGTG
16403116 AAATTAATAT
Statistics
Matches: 151, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
184 9 0.06
185 142 0.94
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (184 bp):
ACATGAGAACACCAAAAAACTTAGTAGCTGGTGTTGGTATGACTTTTCCGAAAACATAGCTTAAT
GTTCAACTAAATGCATGTTTATCTCAGGAAGGCAGTGTCCAGTTTGCATGACTGCAGTCCTTTTG
TCTTGTGTAATATTTGCACTCAAACTTTATTGTGTTATATTTTTCTGTTTTAGT
Found at i:16433967 original size:2 final size:2
Alignment explanation
Indices: 16433962--16433990 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16433952 TTGGTGTGTT
16433962 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16433991 TATGAGTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16442090 original size:9 final size:9
Alignment explanation
Indices: 16442073--16442109 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16442063 TGAGTTTCCA
16442073 AATTCGAAT
1 AATTCGAAT
*
16442082 AACTCGAAT
1 AATTCGAAT
16442091 AATTCGAAT
1 AATTCGAAT
16442100 AATTCGAAT
1 AATTCGAAT
16442109 A
1 A
16442110 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16442660 original size:9 final size:9
Alignment explanation
Indices: 16442646--16442674 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
16442636 AATTTCACAT
16442646 TTTATATTA
1 TTTATATTA
16442655 TTTATATTA
1 TTTATATTA
16442664 TTTATATTA
1 TTTATATTA
16442673 TT
1 TT
16442675 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:16443054 original size:5 final size:5
Alignment explanation
Indices: 16443044--16443069 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16443034 GAACAAATAT
16443044 ATTCG ATTCG ATTCG ATTCG ATTCG A
1 ATTCG ATTCG ATTCG ATTCG ATTCG A
16443070 ATTCCATCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (5 bp):
ATTCG
Found at i:16444660 original size:251 final size:251
Alignment explanation
Indices: 16444217--16444723 Score: 1005
Period size: 251 Copynumber: 2.0 Consensus size: 251
16444207 TGATTTTGAA
16444217 TTAATGGAAGGAGATGTGAATACGTCCATGGGATTCCGGCAATCGCCTTCTCGGATTGTATTAAG
1 TTAATGGAAGGAGATGTGAATACGTCCATGGGATTCCGGCAATCGCCTTCTCGGATTGTATTAAG
16444282 GACATACTGTTTAAAGAGATGGAGTTGACGGTCATTCACAAGCTGTTAGGGCGCAACATTGGCTA
66 GACATACTGTTTAAAGAGATGGAGTTGACGGTCATTCACAAGCTGTTAGGGCGCAACATTGGCTA
16444347 CAACGTGCTTCACAACTGTATCCTTAATCTCTAGAAACCTGCAAAATCTTTTCATCTAATGGATA
131 CAACGTGCTTCACAACTGTATCCTTAATCTCTAGAAACCTGCAAAATCTTTTCATCTAATGGATA
16444412 TCATTAATGGATATTTTTTGGTTAAGTTTCAGGACATTGACGATTATAACAAAGTC
196 TCATTAATGGATATTTTTTGGTTAAGTTTCAGGACATTGACGATTATAACAAAGTC
16444468 TTAATGGAAGGAGATGTGAATACGTCCATGGGATTCCGGCAATCGCCTTCTCGGATTGTATTAAG
1 TTAATGGAAGGAGATGTGAATACGTCCATGGGATTCCGGCAATCGCCTTCTCGGATTGTATTAAG
16444533 GACATACTGTTTAAAGAGATGGAGTTGACGGTCATTCACAAGCTGTTAGGGCGCAACATTGGCTA
66 GACATACTGTTTAAAGAGATGGAGTTGACGGTCATTCACAAGCTGTTAGGGCGCAACATTGGCTA
16444598 CAACGTGCTTCACAACTGTATCCTTAATCTCTAGAAACCTGCAAAATCTTTTCATCTAATGGATA
131 CAACGTGCTTCACAACTGTATCCTTAATCTCTAGAAACCTGCAAAATCTTTTCATCTAATGGATA
*
16444663 TCATTAATGGATATTTTTTGGTTAAGTTTTAGGACATTGACGATTATAACAAAGTC
196 TCATTAATGGATATTTTTTGGTTAAGTTTCAGGACATTGACGATTATAACAAAGTC
16444719 TTAAT
1 TTAAT
16444724 CTAGGTCCAT
Statistics
Matches: 255, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 255 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (251 bp):
TTAATGGAAGGAGATGTGAATACGTCCATGGGATTCCGGCAATCGCCTTCTCGGATTGTATTAAG
GACATACTGTTTAAAGAGATGGAGTTGACGGTCATTCACAAGCTGTTAGGGCGCAACATTGGCTA
CAACGTGCTTCACAACTGTATCCTTAATCTCTAGAAACCTGCAAAATCTTTTCATCTAATGGATA
TCATTAATGGATATTTTTTGGTTAAGTTTCAGGACATTGACGATTATAACAAAGTC
Found at i:16445417 original size:5 final size:5
Alignment explanation
Indices: 16445407--16445432 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
16445397 TGAGCATTCG
16445407 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
16445433 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:16446214 original size:31 final size:30
Alignment explanation
Indices: 16446179--16446238 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16446169 GGAGGTGGGA
*
16446179 TGGGAAGGGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGGGAATAAAAATTTTAGGGGAAAAG
* * *
16446210 TGGGAGTGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGGGAATAAAAATTTTAGGGGAAAA
16446239 TAAAATGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (30 bp):
TGGGAGGGAATAAAAATTTTAGGGGAAAAG
Found at i:16446465 original size:9 final size:9
Alignment explanation
Indices: 16446451--16446487 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16446441 TATAGTTTGA
16446451 TATTCGAAT
1 TATTCGAAT
16446460 TATTCGAAT
1 TATTCGAAT
*
16446469 TATTCGAGT
1 TATTCGAAT
16446478 TATTCGAAT
1 TATTCGAAT
16446487 T
1 T
16446488 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:16448077 original size:9 final size:9
Alignment explanation
Indices: 16448063--16448129 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
16448053 TTTGGTTAAA
16448063 AATTAACCG
1 AATTAACCG
16448072 AATTAACCG
1 AATTAACCG
*
16448081 AATTACCCG
1 AATTAACCG
*
16448090 AATTAATCG
1 AATTAACCG
* * *
16448099 GATTACCCA
1 AATTAACCG
*
16448108 AATTAACTG
1 AATTAACCG
16448117 AATTAACCG
1 AATTAACCG
16448126 AATT
1 AATT
16448130 GAATCACTAC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:16448248 original size:13 final size:13
Alignment explanation
Indices: 16448232--16448256 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16448222 AATTTTTATG
16448232 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
16448245 ATTGGGTTGGGT
1 ATTGGGTTGGGT
16448257 TGAATACTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.48, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:16450154 original size:37 final size:37
Alignment explanation
Indices: 16450093--16450238 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
16450083 TACGTATGAT
* *
16450093 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
16450128 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
16450165 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
16450202 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
16450239 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:16450255 original size:46 final size:46
Alignment explanation
Indices: 16450202--16450470 Score: 331
Period size: 46 Copynumber: 5.6 Consensus size: 46
16450192 TAAGTGTAGC
* **
16450202 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
16450248 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
16450294 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
16450346 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** *
16450392 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
16450444 CACTTATCACTTTGTCATTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
16450471 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 111 0.56
48 1 0.01
49 2 0.01
50 1 0.01
52 83 0.42
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:16450321 original size:52 final size:52
Alignment explanation
Indices: 16450245--16450456 Score: 292
Period size: 52 Copynumber: 4.2 Consensus size: 52
16450235 TAGCTAAAGC
* *
16450245 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
16450298 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
16450350 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** *
16450396 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
16450448 TATCACTTT
1 TATCACTTT
16450457 GTCATTTGAT
Statistics
Matches: 142, Mismatches: 11, Indels: 13
0.86 0.07 0.08
Matches are distributed among these distances:
46 43 0.30
49 1 0.01
52 86 0.61
53 12 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:16450367 original size:98 final size:98
Alignment explanation
Indices: 16450202--16450470 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
16450192 TAAGTGTAGC
* * *
16450202 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
16450267 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
16450301 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
16450366 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
16450399 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCATTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
16450464 GATCAGA
66 GATCAGA
16450471 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 150 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:16455356 original size:23 final size:23
Alignment explanation
Indices: 16455307--16455360 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
16455297 CAGCTTGTAT
** * *
16455307 GAGCTTACCGTTTCAGCTCTACG
1 GAGCTTACCGGCTCAGCTCAACA
*
16455330 GAGCTTACCGGCTCAGCTCAATA
1 GAGCTTACCGGCTCAGCTCAACA
16455353 GAGCTTAC
1 GAGCTTAC
16455361 TGTTTATCAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (23 bp):
GAGCTTACCGGCTCAGCTCAACA
Found at i:16471258 original size:34 final size:34
Alignment explanation
Indices: 16471220--16471290 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
16471210 TTTATGTTTC
*
16471220 CAAATCAAAATCAACTCAAATAAATAATCTTTAA
1 CAAATCAAAATCAACTCAAAAAAATAATCTTTAA
16471254 CAAATCAAAATCAACTCAAAAAAATAATCTTTAA
1 CAAATCAAAATCAACTCAAAAAAATAATCTTTAA
16471288 CAA
1 CAA
16471291 TTATACATGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (34 bp):
CAAATCAAAATCAACTCAAAAAAATAATCTTTAA
Found at i:16473591 original size:11 final size:11
Alignment explanation
Indices: 16473577--16473624 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
16473567 TTTTTATAAC
16473577 TTTTTAATATAT
1 TTTTTAATAT-T
*
16473589 TTTGTTCATACTT
1 TTT-TTAATA-TT
16473602 TTTTTAATATT
1 TTTTTAATATT
*
16473613 TTTTTAAAATT
1 TTTTTAATATT
16473624 T
1 T
16473625 AAAATGACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
11 13 0.42
12 8 0.26
13 9 0.29
14 1 0.03
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (11 bp):
TTTTTAATATT
Found at i:16479441 original size:16 final size:16
Alignment explanation
Indices: 16479420--16479459 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
16479410 TTTGGTTCGT
*
16479420 TGTAATGGAATAGAGC
1 TGTAATAGAATAGAGC
16479436 TGTAATAGAATAGAGGC
1 TGTAATAGAATAGA-GC
16479453 -GTAATAG
1 TGTAATAG
16479460 TAATTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (16 bp):
TGTAATAGAATAGAGC
Found at i:16479712 original size:18 final size:18
Alignment explanation
Indices: 16479689--16479735 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
16479679 TTATTATTAA
16479689 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
16479707 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
16479725 AT-TAATATTAA
1 ATATAAT-TTAA
16479736 ATATTCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:16479783 original size:61 final size:61
Alignment explanation
Indices: 16479704--16479903 Score: 214
Period size: 61 Copynumber: 3.3 Consensus size: 61
16479694 ATTTAATAAA
*
16479704 AATATATAATTTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
* * ** * ** * *
16479765 AATATATAATACT-ATAAAA-TA-TAAT-TTAAAATAATTATTAT-TAAACATAATTTAATAAA
1 AATATATAAT-CTAATAAAATTATTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
* *
16479824 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATCTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
16479885 AATATATAATACT-ATAAAA
1 AATATATAAT-CTAATAAAA
16479904 ATAATTTTTT
Statistics
Matches: 108, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
58 3 0.03
59 34 0.31
60 17 0.16
61 50 0.46
62 4 0.04
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (61 bp):
AATATATAATCTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:16479816 original size:120 final size:119
Alignment explanation
Indices: 16479677--16479910 Score: 441
Period size: 120 Copynumber: 2.0 Consensus size: 119
16479667 AGTTTAACAG
*
16479677 AATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTC
1 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTC
16479742 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAAAAT
66 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAATTTAAAAT
*
16479797 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTC
1 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTC
16479862 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAATTT
66 TTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAATTT
16479911 TTTTATTTCA
Statistics
Matches: 112, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 7 0.06
120 105 0.94
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (119 bp):
AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTATTAATATTAAATATTC
TTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAATTTAAAAT
Found at i:16479841 original size:59 final size:60
Alignment explanation
Indices: 16479677--16479858 Score: 192
Period size: 61 Copynumber: 3.0 Consensus size: 60
16479667 AGTTTAACAG
16479677 AATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTAATATTAAAT
1 AATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAA-TATTAATATTAAAT
* * * * ** * * *
16479738 -ATTCTTATATGAATTTACTAAAATCATAATATATAATACT-ATAAAATA-TAAT-TTAAAAT
1 AATTATTAT-TAAATATAATTTAATAAAAATATATAAT-TTAATAAAATATTAATATT-AAAT
* *
16479797 AATTATTATTAAACATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAAT
1 AATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAA-TATTAATATTAAAT
16479858 A
1 A
16479859 TTCTTATATG
Statistics
Matches: 93, Mismatches: 20, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 3 0.03
59 34 0.37
60 17 0.18
61 36 0.39
62 3 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (60 bp):
AATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATATTAATATTAAAT
Found at i:16479890 original size:59 final size:59
Alignment explanation
Indices: 16479707--16479890 Score: 191
Period size: 59 Copynumber: 3.1 Consensus size: 59
16479697 TAATAAAAAT
16479707 ATATAATTTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
* * * * * *
16479766 ATAT-ATAATACTATAAAATATAATTTAA-AATAATTATTATTAAACAT-AATTTAATAAAA--A
1 ATATAAT-TTA--ATAAAAT-T-A-TTAATATTAAATATTCTT--ATATGAATTTACTAAAATCA
16479826 T-
58 TA
*
16479827 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
16479886 ATATA
1 ATATA
16479891 TAATACTATA
Statistics
Matches: 98, Mismatches: 13, Indels: 28
0.71 0.09 0.20
Matches are distributed among these distances:
55 3 0.03
56 15 0.15
57 10 0.10
58 5 0.05
59 18 0.18
61 13 0.13
62 5 0.05
63 11 0.11
64 15 0.15
65 3 0.03
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTATTAATATTAAATATTCTTATATGAATTTACTAAAATCATA
Found at i:16480127 original size:34 final size:34
Alignment explanation
Indices: 16480088--16480160 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
16480078 TCAAAATGTT
16480088 AACATAATCATATTTGAAAACCCAATCTAATAAC
1 AACATAATCATATTTGAAAACCCAATCTAATAAC
16480122 AACATAATCATATTTGAAAACCCAATCTAATAAC
1 AACATAATCATATTTGAAAACCCAATCTAATAAC
*
16480156 CACAT
1 AACAT
16480161 TACATACTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.26
Consensus pattern (34 bp):
AACATAATCATATTTGAAAACCCAATCTAATAAC
Found at i:16483593 original size:14 final size:14
Alignment explanation
Indices: 16483574--16483613 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
16483564 TTGATTGGCA
16483574 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
16483588 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
16483602 GGAAAATGTTTT
1 GTAAAATGTTTT
16483614 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:16483626 original size:34 final size:35
Alignment explanation
Indices: 16483582--16483648 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
16483572 CAGTAAAATG
* *
16483582 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
16483616 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
16483649 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:16483635 original size:20 final size:20
Alignment explanation
Indices: 16483597--16483636 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16483587 CGTAAAATGA
**
16483597 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
16483617 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
16483637 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:16493012 original size:200 final size:202
Alignment explanation
Indices: 16492669--16493048 Score: 470
Period size: 202 Copynumber: 1.9 Consensus size: 202
16492659 TCATTGGTCT
* *
16492669 TACTTGTGAAGTGTAAAAACTGCACTGGCAATGTACCAAATGATTTCCCTTATTTAAAACATATA
1 TACTTGTGAAGTCTAAAAACTGCACTGGCAATGTACCAAATGATTTCCCTTATTT-AAACACATA
* * *
16492734 TTATTTATGGGGTTAGTATTTGGTATACTGGTAATGTATTTTTATTCTACAAGCAGCGCCTTAAA
65 TTATTTATGGAGTTAGTATTTGGTACACTGATAATGTATTTTTATTCTACAAGCA-CGCCTTAAA
*
16492799 AATTGTTATTTG-TCTC-TTTTTTTTAAAAATATATTTTTT-ATACTTTTATAAGGCACTTATTA
129 AATTGCTATTTGCTCTCTTTTTTTTTAAAAATAT-TTTTTTAATA-TTTTATAAGGCACTTATTA
16492861 ACCTCTAACTC
192 ACCTCTAACTC
* * * * * * *
16492872 TACTTGTGGAGTCT-AAAACTTCATTGGCAGTGTACTAAAT-ATTTTCCCTTGTTT-AACGCATA
1 TACTTGTGAAGTCTAAAAACTGCACTGGCAATGTACCAAATGA-TTTCCCTTATTTAAACACATA
* * *
16492934 TTATTTAT-GAGTTAGTATTTGGTACACTGATAGTGTATTTTTTTATTCTACAAGTA-GCTTTAA
65 TTATTTATGGAGTTAGTATTTGGTACACTGATAATGTA--TTTTTATTCTACAAGCACGCCTT-A
*
16492997 AAAATTGCTATTTGTCTCTCTTTTTTTTTCAAAATATTTTTTTAATATTTTA
127 AAAATTGCTATTTG-CTCTCTTTTTTTTTAAAAATATTTTTTTAATATTTTA
16493049 ATATACTCTT
Statistics
Matches: 152, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
199 29 0.19
200 28 0.18
201 17 0.11
202 48 0.32
203 30 0.20
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (202 bp):
TACTTGTGAAGTCTAAAAACTGCACTGGCAATGTACCAAATGATTTCCCTTATTTAAACACATAT
TATTTATGGAGTTAGTATTTGGTACACTGATAATGTATTTTTATTCTACAAGCACGCCTTAAAAA
TTGCTATTTGCTCTCTTTTTTTTTAAAAATATTTTTTTAATATTTTATAAGGCACTTATTAACCT
CTAACTC
Found at i:16493516 original size:12 final size:12
Alignment explanation
Indices: 16493499--16493523 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16493489 AAGTTTCTGC
16493499 AGTTAATAAAAA
1 AGTTAATAAAAA
16493511 AGTTAATAAAAA
1 AGTTAATAAAAA
16493523 A
1 A
16493524 ATTTATTAAG
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
AGTTAATAAAAA
Found at i:16493691 original size:26 final size:25
Alignment explanation
Indices: 16493656--16493732 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 25
16493646 AAATTATTAA
*
16493656 AAATAATTATAAAATTATAAAAAAT
1 AAATATTTATAAAATTATAAAAAAT
16493681 ATAATATTTATTAAACATTA-AAAATAAT
1 A-AATATTTA-TAAA-ATTATAAAA-AAT
*
16493709 AAA-ATTCATATAAACTTATAAAAA
1 AAATATT--TATAAAATTATAAAAA
16493733 TTTTAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
25 1 0.02
26 14 0.33
27 18 0.42
28 10 0.23
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (25 bp):
AAATATTTATAAAATTATAAAAAAT
Found at i:16493739 original size:28 final size:28
Alignment explanation
Indices: 16493642--16493740 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 28
16493632 ATATTTTCTC
* *
16493642 ATAAAAATTATTAAAAATAATTATAAAATT
1 ATAAAAATTA-TAAAATTAA-TATAAACTT
* * * *
16493672 ATAAAAAATATAATATTTAT-TAAACAT
1 ATAAAAATTATAAAATTAATATAAACTT
* *
16493699 -TAAAAATAATAAAATTCATATAAACTT
1 ATAAAAATTATAAAATTAATATAAACTT
*
16493726 ATAAAAATTTTAAAA
1 ATAAAAATTATAAAA
16493741 AACCTATAAA
Statistics
Matches: 54, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
26 15 0.28
27 11 0.20
28 13 0.24
29 6 0.11
30 9 0.17
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (28 bp):
ATAAAAATTATAAAATTAATATAAACTT
Found at i:16493792 original size:10 final size:10
Alignment explanation
Indices: 16493768--16493820 Score: 51
Period size: 9 Copynumber: 5.7 Consensus size: 10
16493758 AAAAAACATA
*
16493768 TAATAAA-TC
1 TAATAAATTT
16493777 TAATAAATTT
1 TAATAAATTT
*
16493787 TAATAAATTA
1 TAATAAATTT
16493797 TAA-AAATTT
1 TAATAAATTT
*
16493806 T-ATAAA-AT
1 TAATAAATTT
16493814 TAATAAA
1 TAATAAA
16493821 ACACATTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 3 0.08
9 21 0.57
10 13 0.35
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (10 bp):
TAATAAATTT
Found at i:16493792 original size:19 final size:18
Alignment explanation
Indices: 16493768--16493820 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
16493758 AAAAAACATA
16493768 TAATAAATCTAATAAATTT
1 TAATAAAT-TAATAAATTT
*
16493787 TAATAAATTATAAAAATTT
1 TAATAAATTA-ATAAATTT
16493806 T-ATAAAATTAATAAA
1 TAAT-AAATTAATAAA
16493821 ACACATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAAATTAATAAATTT
Found at i:16493803 original size:9 final size:9
Alignment explanation
Indices: 16493642--16493821 Score: 62
Period size: 10 Copynumber: 18.7 Consensus size: 9
16493632 ATATTTTCTC
16493642 ATAAAAATT
1 ATAAAAATT
*
16493651 ATTAAAAATA
1 A-TAAAAATT
16493661 ATTATAAAATT
1 A-TA-AAAATT
*
16493672 ATAAAAAAT
1 ATAAAAATT
* *
16493681 ATAATATTT
1 ATAAAAATT
*
16493690 ATTAAACA-T
1 A-TAAAAATT
*
16493699 -TAAAAATA
1 ATAAAAATT
16493707 AT-AAAATT
1 ATAAAAATT
*
16493715 CATATAAACTT
1 -ATA-AAAATT
16493726 ATAAAAATT
1 ATAAAAATT
* *
16493735 TTAAAAAACCT
1 AT-AAAAA-TT
*
16493746 ATAAATATT
1 ATAAAAATT
*
16493755 ATAAAAAAACAT
1 AT--AAAAA-TT
16493767 ATAATAAATCT
1 ATAA-AAAT-T
*
16493778 A-ATAAATT
1 ATAAAAATT
*
16493786 TTAATAAATT
1 ATAA-AAATT
16493796 ATAAAAATT
1 ATAAAAATT
*
16493805 TTATAAAATT
1 ATA-AAAATT
16493815 AATAAAA
1 -ATAAAA
16493822 CACATTTAAA
Statistics
Matches: 124, Mismatches: 28, Indels: 37
0.66 0.15 0.20
Matches are distributed among these distances:
7 5 0.04
8 6 0.05
9 38 0.31
10 48 0.39
11 24 0.19
12 3 0.02
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (9 bp):
ATAAAAATT
Found at i:16493871 original size:23 final size:21
Alignment explanation
Indices: 16493845--16493899 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
16493835 TTCAAAATTT
*
16493845 TTATAAAAAAATTTCTTAAAAA
1 TTATAAAAAAA-ATCTTAAAAA
16493867 CTTATAAAATAAAATCTTAAAAA
1 -TTATAAAA-AAAATCTTAAAAA
*
16493890 TTATTAAAAA
1 TTATAAAAAA
16493900 TTAGATAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 7 0.24
23 17 0.59
24 3 0.10
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TTATAAAAAAAATCTTAAAAA
Found at i:16494471 original size:9 final size:9
Alignment explanation
Indices: 16494459--16494529 Score: 54
Period size: 9 Copynumber: 7.6 Consensus size: 9
16494449 GTTTTATGGT
16494459 TTTTTATAA
1 TTTTTATAA
16494468 TTTTTATAA
1 TTTTTATAA
* *
16494477 GTATATATCAA
1 -TTTTTAT-AA
*
16494488 TTTTAAT-A
1 TTTTTATAA
*
16494496 TATTTAATAA
1 T-TTTTATAA
*
16494506 TTTTTTTAA
1 TTTTTATAA
16494515 TTTTTTATAA
1 -TTTTTATAA
16494525 TTTTT
1 TTTTT
16494530 CATAGGTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
8 2 0.04
9 26 0.53
10 19 0.39
11 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:16494471 original size:10 final size:10
Alignment explanation
Indices: 16494458--16494554 Score: 58
Period size: 10 Copynumber: 9.9 Consensus size: 10
16494448 GGTTTTATGG
16494458 TTTTTTATAA
1 TTTTTTATAA
16494468 -TTTTTATAA
1 TTTTTTATAA
* * *
16494477 GTATATATCAA
1 TTTTTTAT-AA
*
16494488 -TTTTAAT-A
1 TTTTTTATAA
* *
16494496 TATTTAATAA
1 TTTTTTATAA
16494506 TTTTTT-TAA
1 TTTTTTATAA
16494515 TTTTTTATAA
1 TTTTTTATAA
* *
16494525 TTTTTCATAGG
1 TTTTTTATA-A
* *
16494536 TTTTTAAGAA
1 TTTTTTATAA
16494546 TTTTTTATA
1 TTTTTTATA
16494555 TGTTTTTCCT
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
8 1 0.02
9 24 0.36
10 32 0.48
11 9 0.14
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:16494524 original size:19 final size:21
Alignment explanation
Indices: 16494488--16494529 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
16494478 TATATATCAA
16494488 TTTTAATATATTTAATAATTT
1 TTTTAATATATTTAATAATTT
*
16494509 TTTTAAT-T-TTTTATAATTT
1 TTTTAATATATTTAATAATTT
16494528 TT
1 TT
16494530 CATAGGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 1 0.05
21 7 0.35
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTAATATATTTAATAATTT
Found at i:16494671 original size:31 final size:31
Alignment explanation
Indices: 16494625--16494699 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
16494615 ACTATTAGAA
*
16494625 TTTATTAGATTTTTTTAT-GATATTTATAAGTT
1 TTTATTA-ATTTTTTTATAAAT-TTTATAAGTT
*
16494657 TTTATTAATTTTTTTATAAATTTTGTAAGTT
1 TTTATTAATTTTTTTATAAATTTTATAAGTT
*
16494688 TATATTAATTTT
1 TTTATTAATTTT
16494700 AATAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 30 0.77
32 9 0.23
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (31 bp):
TTTATTAATTTTTTTATAAATTTTATAAGTT
Found at i:16494754 original size:17 final size:17
Alignment explanation
Indices: 16494732--16494764 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16494722 ATTTTTATAA
16494732 ATTTTTT-TCTATTTTTT
1 ATTTTTTATC-ATTTTTT
16494749 ATTTTTTATCATTTTT
1 ATTTTTTATCATTTTT
16494765 ATGGGAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTTATCATTTTTT
Found at i:16500610 original size:24 final size:25
Alignment explanation
Indices: 16500582--16500634 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
16500572 TTAACAAATT
16500582 AAATAAA-AAGGATA-TTTTCACTTA
1 AAATAAATAAGGATAGTTTTC-CTTA
* *
16500606 AAATAAATCAGGATAGTTTTCGTTA
1 AAATAAATAAGGATAGTTTTCCTTA
16500631 AAAT
1 AAAT
16500635 CTGGCATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 7 0.28
25 13 0.52
26 5 0.20
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (25 bp):
AAATAAATAAGGATAGTTTTCCTTA
Found at i:16507409 original size:16 final size:16
Alignment explanation
Indices: 16507384--16507419 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
16507374 AAAAACAAAT
16507384 AAAATTACATT-ATAA
1 AAAATTACATTAATAA
16507399 AAAATTTACATTAATAA
1 AAAA-TTACATTAATAA
16507416 AAAA
1 AAAA
16507420 ATCACAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.21
16 7 0.37
17 8 0.42
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATTACATTAATAA
Found at i:16507470 original size:96 final size:92
Alignment explanation
Indices: 16507370--16507663 Score: 262
Period size: 103 Copynumber: 3.1 Consensus size: 92
16507360 TGTCAAATAA
*
16507370 ATAAA-AAAACAAATAAAATTACATTATAAAAAATTTACATTAATAAAAAAATCACAAAATACTA
1 ATAAATAAAACAAATAAAATTACATTA-AAAAAA-TTACATTACT-AAAAAATCACAAAATACTA
16507434 AACTGAACACTAACAATTTATATAACCTAATC
63 AACT-AACACTAACAA-TTATATAACCTAATC
* *
16507466 ATAAATTACTAACAAAAACTATAAAATTATCTTTAAAAAAAATTACATTACTAAAAAATCACAAA
1 AT-AA--A-TAA-AACAA--ATAAAATTA-CATT-AAAAAAATTACATTACTAAAAAATCACAAA
** *
16507531 ACCCTAAACTAAACAGTAACAAATTATA-AA-CTAATC
57 ATACTAAACT-AACACTAAC-AATTATATAACCTAATC
* * * *
16507567 ATAAATTACTAACAAAATAACTATAACATTAAAAAAATTACATTACTAATAAATCACAAAATAC-
1 ATAAA-TA-AAAC-AAATAA-AATTACATTAAAAAAATTACATTACTAAAAAATCACAAAATACT
16507631 -AA--AACACTAACAATT-TATAACCTAATC
62 AAACTAACACTAACAATTATATAACCTAATC
16507658 ATAAAT
1 ATAAAT
16507664 TACTAATAAA
Statistics
Matches: 165, Mismatches: 17, Indels: 38
0.75 0.08 0.17
Matches are distributed among these distances:
89 2 0.01
90 7 0.04
91 19 0.12
94 2 0.01
96 33 0.20
97 9 0.05
98 8 0.05
99 3 0.02
100 2 0.01
101 10 0.06
102 6 0.04
103 34 0.21
104 20 0.12
105 9 0.05
106 1 0.01
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (92 bp):
ATAAATAAAACAAATAAAATTACATTAAAAAAATTACATTACTAAAAAATCACAAAATACTAAAC
TAACACTAACAATTATATAACCTAATC
Found at i:16507552 original size:103 final size:101
Alignment explanation
Indices: 16507382--16507864 Score: 433
Period size: 98 Copynumber: 5.0 Consensus size: 101
16507372 AAAAAAACAA
* * * *
16507382 ATAAAATTA-CATTATAAAAAATTTACATTAATAAAAAAATCACAAAATACTAAACTGAACACTA
1 ATAAAATTATCATTA-AAAAAAATTACATTACT-AAAAAATCACAAAACACTAAACTAAACACTA
16507446 ACAATTTATATAACCTAATCATAAATTACTAACAAAAACT
64 ACAA-TT-TATAACCTAATCATAAATTACTAACAAAAACT
* * *
16507486 ATAAAATTATCTTTAAAAAAAATTACATTACTAAAAAATCACAAAACCCTAAACTAAACAGTAAC
1 ATAAAATTATCATTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAAC
* *
16507551 AAATTATAAACTAATCATAAATTACTAAC-AAAA-T
66 AATTTATAACCTAATCATAAATTACTAACAAAAACT
** * * *
16507585 A-ACTA-TAACATT-AAAAAAATTACATTACTAATAAATCAC-AAA-A-T--ACAAAACACTAAC
1 ATAAAATTATCATTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAAC
*
16507642 AATTTATAACCTAATCATAAATTACTAATAAAATAACT
66 AATTTATAACCTAATCATAAATTACTAA-CAAA-AACT
** ** * * * *
16507680 ATAAAATTATTTTTTTAAAAAATTATATTACTAAAATATCATAAAACAC---A--AAATACTAAC
1 ATAAAATTATCATTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAAC
16507740 AATTTATAACCTAATCATAAATTACTAAC--AAA--
66 AATTTATAACCTAATCATAAATTACTAACAAAAACT
* ** * * * *
16507772 AT--AATTCA-CA--AAATAATTTTACATTAATAAGAAATCACAAAATACTAAACTAAACAC-AG
1 ATAAAATT-ATCATTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAA
* *
16507831 CAATTTATAACATAATCCTAAATTACTAACAAAA
65 CAATTTATAACCTAATCATAAATTACTAACAAAA
16507865 TAATTATAAA
Statistics
Matches: 311, Mismatches: 49, Indels: 48
0.76 0.12 0.12
Matches are distributed among these distances:
88 24 0.08
90 4 0.01
91 39 0.13
92 31 0.10
93 8 0.03
94 6 0.02
95 6 0.02
96 28 0.09
97 9 0.03
98 61 0.20
99 5 0.02
100 6 0.02
101 24 0.08
102 1 0.00
103 31 0.10
104 24 0.08
105 4 0.01
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (101 bp):
ATAAAATTATCATTAAAAAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAAC
AATTTATAACCTAATCATAAATTACTAACAAAAACT
Found at i:16507933 original size:190 final size:188
Alignment explanation
Indices: 16507395--16507937 Score: 448
Period size: 190 Copynumber: 2.8 Consensus size: 188
16507385 AAATTACATT
* *
16507395 ATAAAAAATTTACATTAATAAAAAAATCACAAAATACTAAACTGAACACTAACAATTTATATAAC
1 ATAAAAAAATTACATTAAT-AAGAAATCACAAAATAC--AA---AACACTAACAA-TT-TATAAC
* ** * * * *
16507460 CTAATCATAAATTACTAAC-AAA-AACTATAAAATTAT-CTTTAAAAAAAATTACATTACTAAAA
58 ATAATCATAAATTACTAACAAAATAACTATAAAAAAATGCATT-CAAAAAATTATATAACTAAAA
* * * *
16507522 AATCACAAAACCCTAAACTAAACAGT-AACAAATTATAAACTAATCATAAATTACTAACAAAATA
122 TACCATAAAA--C---ACTAAACA-TAAACAATTTATAAACTAATCATAAATTACTAACAAAATA
16507586 ACTATAAC
181 ACTATAAC
* * *
16507594 ATTAAAAAAATTACATTACTAATAAATCACAAAATACAAAACACTAACAATTTATAACCTAATCA
1 A-TAAAAAAATTACATTAATAAGAAATCACAAAATACAAAACACTAACAATTTATAACATAATCA
* ** *** * * *
16507659 TAAATTACTAATAAAATAACTATAAAATTATTTTTTTAAAAAATTATATTACTAAAATATCATAA
65 TAAATTACTAACAAAATAACTATAAAAAAATGCATTCAAAAAATTATATAACTAAAATACCATAA
* *
16507724 AACAC-AAA-ATACTAACAATTTATAACCTAATCATAAATTACTAACAAAATAA-T-TCAC
130 AACACTAAACATA--AACAATTTATAAACTAATCATAAATTACTAACAAAATAACTATAAC
** *
16507781 A-AAATAATTTTACATTAATAAGAAATCACAAAATACTAAACTAAACAC-AGCAATTTATAACAT
1 ATAAA-AAAATTACATTAATAAGAAATCACAAAATAC---A--AAACACTAACAATTTATAACAT
* *
16507844 AATCCTAAATTACTAACAAAATAATTATAAAAAAAACTGCATTCATAAAAATTAT-TAAACT-AA
60 AATCATAAATTACTAACAAAATAACTAT-AAAAAAA-TGCATTCA-AAAAATTATAT-AACTAAA
16507907 A-ACCAT-AAACACTAAACATAAACAATTTATA
121 ATACCATAAAACACTAAACATAAACAATTTATA
16507938 GATAATAATT
Statistics
Matches: 296, Mismatches: 29, Indels: 47
0.80 0.08 0.13
Matches are distributed among these distances:
185 3 0.01
186 28 0.09
187 5 0.02
188 4 0.01
189 40 0.14
190 55 0.19
191 18 0.06
192 36 0.12
193 17 0.06
194 52 0.18
195 3 0.01
197 2 0.01
199 17 0.06
200 16 0.05
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (188 bp):
ATAAAAAAATTACATTAATAAGAAATCACAAAATACAAAACACTAACAATTTATAACATAATCAT
AAATTACTAACAAAATAACTATAAAAAAATGCATTCAAAAAATTATATAACTAAAATACCATAAA
ACACTAAACATAAACAATTTATAAACTAATCATAAATTACTAACAAAATAACTATAAC
Found at i:16508285 original size:28 final size:28
Alignment explanation
Indices: 16508243--16508318 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
16508233 ATGGGACTAG
* *
16508243 TGTAATTTTATAAAATTAAATTCTTTGA
1 TGTAATTTAATAAAATTAAATGCTTTGA
*
16508271 TGTAATTTAACAAAATTAAATGCTTTGA
1 TGTAATTTAATAAAATTAAATGCTTTGA
16508299 TGTAATTTAATAAAATTAAA
1 TGTAATTTAATAAAATTAAA
16508319 AGCATGGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (28 bp):
TGTAATTTAATAAAATTAAATGCTTTGA
Found at i:16514319 original size:48 final size:48
Alignment explanation
Indices: 16514228--16514319 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
16514218 GTAAAAAATC
* * * * ** *
16514228 TTTGAGTTAGTTAAGTTGATAAGTTTTATTTTATTGTCTTAACTTAGT
1 TTTGAGTTAGTCAAGTTCACAAGTCTTATTTTATCATCCTAACTTAGT
16514276 TTTGAGTTAGTCAAGTTCACAAGTCTTATTTTATCATCCTAACT
1 TTTGAGTTAGTCAAGTTCACAAGTCTTATTTTATCATCCTAACT
16514320 CGATGTGAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (48 bp):
TTTGAGTTAGTCAAGTTCACAAGTCTTATTTTATCATCCTAACTTAGT
Found at i:16517361 original size:44 final size:44
Alignment explanation
Indices: 16517308--16517408 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
16517298 CTGCAAACCA
16517308 CTGTGAATCCACAACCAGA-GGCAGATTCCATCTACAGGGTA-TTG
1 CTGTGAATCCACAACCA-ATGGCAGATTCCATCTAC-GGGTACTTG
* * * *
16517352 CTGTGAATCCACAGCCAATGGTAGATTCCATTTGCGGGTACTTG
1 CTGTGAATCCACAACCAATGGCAGATTCCATCTACGGGTACTTG
* *
16517396 TTGTGTATCCACA
1 CTGTGAATCCACA
16517409 GCTGAAAGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 6 0.12
44 43 0.88
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (44 bp):
CTGTGAATCCACAACCAATGGCAGATTCCATCTACGGGTACTTG
Found at i:16521476 original size:60 final size:60
Alignment explanation
Indices: 16521402--16521517 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
16521392 AGATAAGCCC
* ** * *
16521402 TGAACTTGGCAATTGTTTTCACATTGAGG-CTTGAACTTTTTTTTAGTCTAAGTTAGGTCT
1 TGAACTTAGCAATTGTTCCCACATTG-GGTCATGAACTTTTTTTTAGTCCAAGTTAGGTCT
*
16521462 TGAACTTAGCAATTGTTCCCACATTGGGTCATGAACTTTTTTTTGGTCCAAGTTAG
1 TGAACTTAGCAATTGTTCCCACATTGGGTCATGAACTTTTTTTTAGTCCAAGTTAG
16521518 ACCTTGAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 2 0.04
60 47 0.96
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (60 bp):
TGAACTTAGCAATTGTTCCCACATTGGGTCATGAACTTTTTTTTAGTCCAAGTTAGGTCT
Found at i:16521524 original size:60 final size:60
Alignment explanation
Indices: 16521402--16521576 Score: 160
Period size: 60 Copynumber: 2.9 Consensus size: 60
16521392 AGATAAGCCC
* ** * * **
16521402 TGAACTTGGCAATTGTTTTCACATTGAGGCTTGAACTTTTTTTTAGTCTAAGTTAGGTCT
1 TGAACTTAGCAATTGTTCCCACATTGAGGCATGAACTTTTTTTTAGTCCAAGTTAGACCT
*
16521462 TGAACTTAGCAATTGTTCCCACATTG-GGTCATGAACTTTTTTTTGGTCCAAGTTAGACCT
1 TGAACTTAGCAATTGTTCCCACATTGAGG-CATGAACTTTTTTTTAGTCCAAGTTAGACCT
* * * ** * *
16521522 TGAA-TTTGACAATTCTTCACGTATT-ATGACTTGAACTTTTTTTT-GTCCAAGTTAG
1 TGAACTTAG-CAATTGTTCCCACATTGA-GGCATGAACTTTTTTTTAGTCCAAGTTAG
16521577 TCATTGAAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
59 16 0.17
60 79 0.82
61 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (60 bp):
TGAACTTAGCAATTGTTCCCACATTGAGGCATGAACTTTTTTTTAGTCCAAGTTAGACCT
Found at i:16522231 original size:18 final size:18
Alignment explanation
Indices: 16522204--16522250 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
16522194 GAGAAAAAGA
* *
16522204 AGAAGAAGAATAAGAAGG
1 AGAAGGAGAAGAAGAAGG
*
16522222 AGAAGGAGAAGGAGAAGG
1 AGAAGGAGAAGAAGAAGG
16522240 AGAAGGAGAAG
1 AGAAGGAGAAG
16522251 GTATGTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (18 bp):
AGAAGGAGAAGAAGAAGG
Found at i:16522251 original size:6 final size:6
Alignment explanation
Indices: 16522216--16522251 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
16522206 AAGAAGAATA
16522216 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
1 AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG AGAAGG
16522252 TATGTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
AGAAGG
Found at i:16522632 original size:16 final size:16
Alignment explanation
Indices: 16522611--16522643 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16522601 TTCGCTATAT
16522611 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
16522627 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
16522643 T
1 T
16522644 AACAAATCAA
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:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:16522905 original size:14 final size:15
Alignment explanation
Indices: 16522866--16522907 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16522856 TTTTAACATA
*
16522866 ATTATTATTAAATAT
1 ATTATAATTAAATAT
16522881 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
16522895 A-TATAATTTAATA
1 ATTATAATTAAATA
16522908 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:16522957 original size:61 final size:61
Alignment explanation
Indices: 16522892--16523079 Score: 181
Period size: 61 Copynumber: 3.1 Consensus size: 61
16522882 TTATAATTAA
*
16522892 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * * ** * *
16522953 AATATATGATACT-ATAAAA-T-ATAATTTAA-C-ATAATTATTAT-TAAATATATTTTAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA--TAATCAAT-ATTCTTATATGAATTTACTAAAATCAT
*
16523012 AAAATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
16523073 AATATAT
1 AATATAT
16523080 GATACTATAA
Statistics
Matches: 93, Mismatches: 24, Indels: 20
0.68 0.18 0.15
Matches are distributed among these distances:
58 1 0.01
59 33 0.35
60 18 0.19
61 40 0.43
62 1 0.01
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
Found at i:16523030 original size:16 final size:18
Alignment explanation
Indices: 16522995--16523030 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16522985 AATTATTATT
*
16522995 AAATATATTTTAATTAAA
1 AAATATAATTTAATTAAA
16523013 AAATATAATTTAA-TAAA
1 AAATATAATTTAATTAAA
16523030 A
1 A
16523031 TTCTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATATAATTTAATTAAA
Found at i:16523077 original size:59 final size:59
Alignment explanation
Indices: 16522895--16523078 Score: 166
Period size: 59 Copynumber: 3.1 Consensus size: 59
16522885 TAATTAAAAT
*
16522895 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
* * * * * * *
16522954 ATAT-ATGATACTATAAAATATAATTTAA-CAT-AATTATTATTAAATAT-ATTTTAATTAAA--
1 ATATAAT-TTA--ATAAAAT-T--CTTAATAATCAA-TATTCTT--ATATGAATTTACTAAAATC
16523013 A-A
57 ATA
16523015 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
16523074 ATATA
1 ATATA
16523079 TGATACTATA
Statistics
Matches: 95, Mismatches: 14, Indels: 32
0.67 0.10 0.23
Matches are distributed among these distances:
55 4 0.04
56 13 0.14
57 8 0.08
58 6 0.06
59 19 0.20
61 14 0.15
62 6 0.06
63 8 0.08
64 13 0.14
65 4 0.04
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCATA
Found at i:16523124 original size:16 final size:16
Alignment explanation
Indices: 16523115--16523165 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
16523105 AATTAATATT
16523115 AAATATAATTTAATTA
1 AAATATAATTTAATTA
16523131 AAATATATGATTTAA-TA
1 AAATATA--ATTTAATTA
* **
16523148 AAATTTAAAATAATTA
1 AAATATAATTTAATTA
16523164 AA
1 AA
16523166 CTAATAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 11 0.38
17 8 0.28
18 6 0.21
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AAATATAATTTAATTA
Found at i:16523143 original size:18 final size:17
Alignment explanation
Indices: 16523117--16523151 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
16523107 TTAATATTAA
16523117 ATATAATTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
*
16523135 ATATGATTTAATAAAAT
1 ATATAATTTAATAAAAT
16523152 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:16523161 original size:120 final size:120
Alignment explanation
Indices: 16522857--16523152 Score: 506
Period size: 120 Copynumber: 2.5 Consensus size: 120
16522847 TTAATCATAT
16522857 TTTAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA
1 TTTAACATAATTATTATTAAATATAATT-TAATTAAAATATATAATTTAATAAAATTCTTAATAA
*
16522921 TCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAA
65 TCAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
* *
16522977 TTTAACATAATTATTATTAAATATATTTTAATTAAAAAATATAATTTAATAAAATTCTTAATAAT
1 TTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
16523042 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
66 CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
* * *
16523097 TTTGGA-ATAATTAATATTAAATATAATTTAATTAAAATATATGATTTAATAAAATT
1 TTT-AACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATT
16523153 TAAAATAATT
Statistics
Matches: 166, Mismatches: 8, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
120 163 0.98
121 3 0.02
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAACATAATTATTATTAAATATAATTTAATTAAAATATATAATTTAATAAAATTCTTAATAAT
CAATATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAATATAA
Found at i:16523461 original size:92 final size:91
Alignment explanation
Indices: 16523167--16523465 Score: 528
Period size: 91 Copynumber: 3.3 Consensus size: 91
16523157 ATAATTAAAC
*
16523167 TAATAAATTTTCTTATATGAATTTGTATAATTTAAAATAATT-ATTATTAAATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATT-TTAAATATAATTTAATAA
*
16523231 TAATATATAATTTCATAAAATTCTTGA
65 TGATATATAATTTCATAAAATTCTTGA
*
16523258 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATTTTAAATATAATTTAATAAT
16523323 GATATATAATTTCATAAAATTCTTGA
66 GATATATAATTTCATAAAATTCTTGA
16523349 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAAATTTTAAATATAATTTAATAA
1 TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATT-AATTTTAAATATAATTTAATAA
*
16523414 TGATATATAATTTCATAAAATTCTTAA
65 TGATATATAATTTCATAAAATTCTTGA
*
16523441 TAATAAATGTTCTTATATGAATTTA
1 TAATAAATTTTCTTATATGAATTTA
16523466 CTAAAATCAT
Statistics
Matches: 200, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
91 127 0.63
92 73 0.37
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (91 bp):
TAATAAATTTTCTTATATGAATTTATATAATTTAAAATAATTAATTTTAAATATAATTTAATAAT
GATATATAATTTCATAAAATTCTTGA
Found at i:16524945 original size:23 final size:21
Alignment explanation
Indices: 16524885--16524947 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 21
16524875 TCTACTCACT
16524885 AACAAATCAAGAACAATTTCC
1 AACAAATCAAGAACAATTTCC
16524906 AACAGACTATCAA-AACAATTTCC
1 AACA-A--ATCAAGAACAATTTCC
16524929 AGAACAAATCAAGAACAAT
1 --AACAAATCAAGAACAAT
16524948 ATCAAAACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
21 4 0.11
22 6 0.17
23 16 0.44
24 6 0.17
25 4 0.11
ACGTcount: A:0.54, C:0.22, G:0.06, T:0.17
Consensus pattern (21 bp):
AACAAATCAAGAACAATTTCC
Found at i:16526574 original size:23 final size:21
Alignment explanation
Indices: 16526548--16526590 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
16526538 GTTATATAAA
*
16526548 TTGTTATTGTTTAGTTTAATGTT
1 TTGTGATTGTTTA--TTAATGTT
*
16526571 TTGTGATTTTTTATTAATGT
1 TTGTGATTGTTTATTAATGT
16526591 AATTTTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.19, C:0.00, G:0.16, T:0.65
Consensus pattern (21 bp):
TTGTGATTGTTTATTAATGTT
Found at i:16526599 original size:17 final size:16
Alignment explanation
Indices: 16526577--16526612 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
16526567 TGTTTTGTGA
16526577 TTTTTTATTAATGTAAT
1 TTTTTTA-TAATGTAAT
16526594 TTTTTTATAATGTAAT
1 TTTTTTATAATGTAAT
16526610 TTT
1 TTT
16526613 ATTTGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TTTTTTATAATGTAAT
Found at i:16528728 original size:33 final size:33
Alignment explanation
Indices: 16528647--16528738 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
16528637 TCCTAACTCG
* * *
16528647 TATCCACCTCAGTACTCTACTCCTCCCGGCCCA
1 TATCCACCGCCGTACTCCACTCCTCCCGGCCCA
* * *
16528680 TATCTACCGCCGTACTCCACTCCTCTCGGCCCG
1 TATCCACCGCCGTACTCCACTCCTCCCGGCCCA
* * * *
16528713 TATCCGCTGCTGTACTCCATTCCTCC
1 TATCCACCGCCGTACTCCACTCCTCC
16528739 TAGCTCAAGT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.14, C:0.47, G:0.12, T:0.27
Consensus pattern (33 bp):
TATCCACCGCCGTACTCCACTCCTCCCGGCCCA
Found at i:16529075 original size:76 final size:77
Alignment explanation
Indices: 16528925--16529089 Score: 260
Period size: 77 Copynumber: 2.2 Consensus size: 77
16528915 GTAATTTAAA
* * * * * *
16528925 TAACTTTATATTTATGTAATGACTTTTTTTCCATTTTAGTTATTAATTTTAGGGGTTTTTTTTTC
1 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGGTTTTTTTTAC
16528990 AATTTAAATAAT
66 AATTTAAATAAT
16529002 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTA-GGGTTTTTTTTAC
1 TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGGTTTTTTTTAC
16529066 AATTTAAATAAT
66 AATTTAAATAAT
*
16529078 AAACTTTGTATT
1 TAACTTTGTATT
16529090 ATTTACTTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 35 0.43
77 46 0.57
ACGTcount: A:0.28, C:0.08, G:0.09, T:0.55
Consensus pattern (77 bp):
TAACTTTGTATTTATGTAATGACTTTTTTGCCACTTCAATTATTAATTTTAGGGGTTTTTTTTAC
AATTTAAATAAT
Found at i:16532438 original size:27 final size:27
Alignment explanation
Indices: 16532344--16532431 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 27
16532334 GCCGCTTATG
* *
16532344 AGATAGGTGTCACCAGTGGTGCCTACC
1 AGATAGGAGTCACCAGTGGCGCCTACC
* * *
16532371 AGATAAGAGTCACCAGTGGCACCTAGC
1 AGATAGGAGTCACCAGTGGCGCCTACC
*
16532398 AGATAGGAGTCACCAGTGACGCCTACC
1 AGATAGGAGTCACCAGTGGCGCCTACC
16532425 AGATAGG
1 AGATAGG
16532432 CACCACCTCT
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 52 1.00
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (27 bp):
AGATAGGAGTCACCAGTGGCGCCTACC
Found at i:16535606 original size:9 final size:9
Alignment explanation
Indices: 16535592--16535647 Score: 58
Period size: 9 Copynumber: 5.8 Consensus size: 9
16535582 GTAAATATAC
16535592 ATTAAAAAT
1 ATTAAAAAT
16535601 ATTAAAAAT
1 ATTAAAAAT
16535610 ATTAAAAATT
1 ATTAAAAA-T
*
16535620 ACTAAAAAAT
1 A-TTAAAAAT
*
16535630 CTTTAAAAAT
1 -ATTAAAAAT
16535640 ATATAAAA
1 AT-TAAAA
16535648 TGCTAAATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
9 18 0.46
10 15 0.38
11 6 0.15
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (9 bp):
ATTAAAAAT
Found at i:16535617 original size:10 final size:10
Alignment explanation
Indices: 16535595--16535647 Score: 54
Period size: 10 Copynumber: 5.3 Consensus size: 10
16535585 AATATACATT
16535595 AAAAATATT-
1 AAAAATATTA
16535604 AAAAATATTA
1 AAAAATATTA
* *
16535614 AAAATTACTA
1 AAAAATATTA
* *
16535624 AAAAATCTTT
1 AAAAATATTA
16535634 AAAAATATATA
1 AAAAATAT-TA
16535645 AAA
1 AAA
16535648 TGCTAAATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
9 9 0.26
10 21 0.62
11 4 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATATTA
Found at i:16537696 original size:14 final size:15
Alignment explanation
Indices: 16537672--16537700 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16537662 TTTTTCTATG
16537672 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
16537687 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
16537701 AGTTTTGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:16538915 original size:43 final size:42
Alignment explanation
Indices: 16538854--16538969 Score: 162
Period size: 43 Copynumber: 2.7 Consensus size: 42
16538844 TATGTGTTTT
16538854 CGTGTAAGACCACGTCTGGGACGTCGGCATCAATATCTGATTA
1 CGTGTAAGACCACGTCTGGGACGT-GGCATCAATATCTGATTA
* *
16538897 CGTGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTGGCATCAATATCTGATTA
*
16538940 CATGTAAGACCACGTCTGGGACGATGGCAT
1 CGTGTAAGACCACGTCTGGGACG-TGGCAT
16538970 TGTACGAACT
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
42 2 0.03
43 61 0.92
44 3 0.05
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTGGCATCAATATCTGATTA
Found at i:16546945 original size:34 final size:34
Alignment explanation
Indices: 16546907--16546980 Score: 121
Period size: 34 Copynumber: 2.2 Consensus size: 34
16546897 TTTAGTGCTC
* *
16546907 TTTGGTTGTGTGGGATGGATACACTTATGTGCAA
1 TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
*
16546941 TTTGGTTGTGAGGGATGAATGCACTTATGTGCAA
1 TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
16546975 TTTGGT
1 TTTGGT
16546981 GTATTTAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.20, C:0.08, G:0.32, T:0.39
Consensus pattern (34 bp):
TTTGGTTGTGAGGGATGAATACACTTATGTGCAA
Found at i:16548259 original size:94 final size:94
Alignment explanation
Indices: 16548098--16548283 Score: 372
Period size: 94 Copynumber: 2.0 Consensus size: 94
16548088 TAATACTTAA
16548098 GTAACTCATCATTGACATCTAAAAATACACTTCCATTTATAGTTCATATTATATATTCACTTTAC
1 GTAACTCATCATTGACATCTAAAAATACACTTCCATTTATAGTTCATATTATATATTCACTTTAC
16548163 TACTATTCCAACATGTCACATATAACTAG
66 TACTATTCCAACATGTCACATATAACTAG
16548192 GTAACTCATCATTGACATCTAAAAATACACTTCCATTTATAGTTCATATTATATATTCACTTTAC
1 GTAACTCATCATTGACATCTAAAAATACACTTCCATTTATAGTTCATATTATATATTCACTTTAC
16548257 TACTATTCCAACATGTCACATATAACT
66 TACTATTCCAACATGTCACATATAACT
16548284 TCCACACATA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (94 bp):
GTAACTCATCATTGACATCTAAAAATACACTTCCATTTATAGTTCATATTATATATTCACTTTAC
TACTATTCCAACATGTCACATATAACTAG
Found at i:16548976 original size:41 final size:38
Alignment explanation
Indices: 16548931--16549062 Score: 93
Period size: 41 Copynumber: 3.2 Consensus size: 38
16548921 ATAGAAATCA
*
16548931 CTAGGCACATATCTTGAAATGATACACCGGCACAAAGCCTG
1 CTAGGCACAAATC-TGAAAT-ATACACCGGCAC-AAGCCTG
** * ** *
16548972 CTAGGCTTAAAGCCTGATTTAATACACCGGCATGAAGCCTG
1 CTAGGCACAAA-TCTGAAAT-ATACACCGGCA-CAAGCCTG
* * *
16549013 CTAGACATAAAGTCTGAAATATTTCACCGGCATCAAGCCTG
1 CTAGGCACAAA-TCTGAAATA-TACACCGGCA-CAAGCCTG
16549054 CTAGGCACA
1 CTAGGCACA
16549063 TAGAGCCTGA
Statistics
Matches: 71, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
40 1 0.01
41 69 0.97
42 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (38 bp):
CTAGGCACAAATCTGAAATATACACCGGCACAAGCCTG
Found at i:16550904 original size:13 final size:13
Alignment explanation
Indices: 16550886--16550911 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16550876 CATTTCCAGG
16550886 TCATTTTCATTTT
1 TCATTTTCATTTT
16550899 TCATTTTCATTTT
1 TCATTTTCATTTT
16550912 GGAGAAAATT
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:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (13 bp):
TCATTTTCATTTT
Found at i:16550966 original size:57 final size:57
Alignment explanation
Indices: 16550896--16551016 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 57
16550886 TCATTTTCAT
*
16550896 TTTTCATTTTCATTTTGGAGAAAA-TTACATTCATTTCCAAATATTTCCC-TTTCTCCC
1 TTTTCATTTTCATTTTGGAGAAAACTT--ATTCATTTCCAAATATTTCCCATTTCTCCA
*
16550953 TTTTCATTTTCATTTTGGAGAAAACCTTATTCATTTCCAAATGTTTCCCATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAA-CTTATTCATTTCCAAATATTTCCCATTTCTCCA
16551011 TTTTCA
1 TTTTCA
16551017 CCATTTCTGC
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
57 44 0.75
58 13 0.22
59 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (57 bp):
TTTTCATTTTCATTTTGGAGAAAACTTATTCATTTCCAAATATTTCCCATTTCTCCA
Found at i:16561586 original size:69 final size:69
Alignment explanation
Indices: 16561418--16561586 Score: 239
Period size: 69 Copynumber: 2.4 Consensus size: 69
16561408 GATCGAGTAG
* * *
16561418 TTTTAGGAGTTACGATATTAAATCAGCTAACCTTTATAATATCAGCTGTGAACGTAGGTCATCGA
1 TTTTAGGAGTTGCGATCTTAAATCAGCTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGA
** *
16561483 GTTG
66 ACTA
** * *
16561487 TTTTACAAGTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGA
1 TTTTAGGAGTTGCGATCTTAAATCAGCTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGA
16561552 ACTA
66 ACTA
*
16561556 TTTTAGGAGTTGCGATCTTAAATTAGCTAAC
1 TTTTAGGAGTTGCGATCTTAAATCAGCTAAC
16561587 TCAAAGAAAC
Statistics
Matches: 85, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 85 1.00
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.35
Consensus pattern (69 bp):
TTTTAGGAGTTGCGATCTTAAATCAGCTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGA
ACTA
Found at i:16561683 original size:106 final size:106
Alignment explanation
Indices: 16561495--16561744 Score: 392
Period size: 106 Copynumber: 2.4 Consensus size: 106
16561485 TGTTTTACAA
* * ** * *
16561495 GTTGCAATCTTAAATCAACTAACCTTTATAATATCAACTGTGAACGTAGGTCATCGAACTATTTT
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
* * *
16561560 AGGAGTTGCGATCTTAAATTAGCTAACTCAAAGAAACTTAG
66 AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTAG
* * *
16561601 GTTGCGATCTTAAATCGGCTAACCCTTATAATACCAGTTGTGAACGTAGGTCATCAAACTATTTC
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
16561666 AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTAG
66 AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTAG
16561707 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
1 GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGT
16561745 ACTTGTATAG
Statistics
Matches: 129, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 129 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (106 bp):
GTTGCGATCTTAAATCAGCTAACCTTTATAATATCAGTTGTGAACGTAGGTCATCAAACTATTTC
AAGAGTTGCGATATTAAATCAGCTAACTCAAAGAAACTTAG
Found at i:16576194 original size:26 final size:26
Alignment explanation
Indices: 16576162--16576215 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
16576152 CCTCCTCTAC
16576162 CACTAGTTTTTAACAATGAAAAATAT
1 CACTAGTTTTTAACAATGAAAAATAT
*
16576188 CACTAGTTTTTAACAATGAAAACTAT
1 CACTAGTTTTTAACAATGAAAAATAT
16576214 CA
1 CA
16576216 TATTTGGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.33
Consensus pattern (26 bp):
CACTAGTTTTTAACAATGAAAAATAT
Found at i:16579115 original size:26 final size:26
Alignment explanation
Indices: 16579047--16579118 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 26
16579037 TATTTTCTAG
*
16579047 AAATTTTACTAGAG-GTAAAGTCATCA
1 AAATTTTACTAG-GTGTAAAATCATCA
* *
16579073 AAA-TTTACT-GATGGTAAAATCGTCA
1 AAATTTTACTAGGT-GTAAAATCATCA
16579098 AAATTTTACTAGGTGTAAAAT
1 AAATTTTACTAGGTGTAAAAT
16579119 AGGGTTGAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
24 1 0.03
25 19 0.50
26 16 0.42
27 2 0.05
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (26 bp):
AAATTTTACTAGGTGTAAAATCATCA
Found at i:16580007 original size:12 final size:12
Alignment explanation
Indices: 16579990--16580019 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
16579980 CCTTACACGT
16579990 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
16580002 CCGTGTGCTAGG
1 CCGTGTGCCAGG
16580014 CCGTGT
1 CCGTGT
16580020 AATAGCTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:16581284 original size:25 final size:25
Alignment explanation
Indices: 16581246--16581315 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
16581236 TCCTGTACAT
*
16581246 GTATGCTCGTACGAGCTATGAATCG
1 GTATGCTCATACGAGCTATGAATCG
* *
16581271 GTATGCTC-TCACGAGCTGTAAATCG
1 GTATGCTCAT-ACGAGCTATGAATCG
*
16581296 GTAAGCTCATACGAGCTATG
1 GTATGCTCATACGAGCTATG
16581316 GTGTGTCCGC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 1 0.03
25 36 0.95
26 1 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (25 bp):
GTATGCTCATACGAGCTATGAATCG
Found at i:16582806 original size:21 final size:20
Alignment explanation
Indices: 16582778--16582820 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
16582768 AGCCAAACCC
16582778 CTATCTTTCAACTCTTGTAA
1 CTATCTTTCAACTCTTGTAA
* *
16582798 CTATGCTTTTAACTCTTTTAA
1 CTAT-CTTTCAACTCTTGTAA
16582819 CT
1 CT
16582821 CGGTAGGAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.49
Consensus pattern (20 bp):
CTATCTTTCAACTCTTGTAA
Found at i:16585463 original size:23 final size:22
Alignment explanation
Indices: 16585437--16585493 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
16585427 CTCAACATTG
* *
16585437 TGCATGTAAACAAGCCATATTAA
1 TGCAT-TAAACAAGCAAAATTAA
16585460 TGCATCTAAAACAAGCAAAATTAA
1 TGCAT-T-AAACAAGCAAAATTAA
16585484 -GCATTAAACA
1 TGCATTAAACA
16585494 TGTAGTATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 10 0.33
24 14 0.47
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.23
Consensus pattern (22 bp):
TGCATTAAACAAGCAAAATTAA
Found at i:16586602 original size:25 final size:25
Alignment explanation
Indices: 16586541--16586622 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
16586531 ATGCTCTCAT
* *
16586541 GAGCTATAAATCGATAAGCTCATAC
1 GAGCTGTAAATCGATAAGCTCGTAC
* *
16586566 AAG-TCG-AGAATCGGTAAGCTC-TAGC
1 GAGCT-GTA-AATCGATAAGCTCGTA-C
16586591 GAGCTGTAAATCGATAAGCTCGTAC
1 GAGCTGTAAATCGATAAGCTCGTAC
16586616 GAGCTGT
1 GAGCTGT
16586623 GGTGTGTCTG
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.09
25 38 0.83
26 4 0.09
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (25 bp):
GAGCTGTAAATCGATAAGCTCGTAC
Found at i:16598171 original size:26 final size:26
Alignment explanation
Indices: 16598135--16598204 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
16598125 ACATATTTTC
16598135 TCAAAATTTTACAAGGGGTAAAA-CT
1 TCAAAATTTTACAAGGGGTAAAATCT
*
16598160 GTCAAAATTTTACAAGAGGTAAAATCT
1 -TCAAAATTTTACAAGGGGTAAAATCT
16598187 TCAAAATTTTACTAAGGG
1 TCAAAATTTTAC-AAGGG
16598205 TAACATAGGT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 34 0.85
27 6 0.15
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (26 bp):
TCAAAATTTTACAAGGGGTAAAATCT
Found at i:16603867 original size:15 final size:15
Alignment explanation
Indices: 16603849--16603890 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
16603839 TTAACCCAGT
16603849 TAAATTAAATAAATA
1 TAAATTAAATAAATA
*
16603864 TAAATTAAATAACTA
1 TAAATTAAATAAATA
16603879 -AATATTAAATAA
1 TAA-ATTAAATAA
16603891 TCTTACCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATTAAATAAATA
Found at i:16603873 original size:20 final size:20
Alignment explanation
Indices: 16603848--16603888 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
16603838 TTTAACCCAG
16603848 TTAAATTAAATAAATA-TAAA
1 TTAAA-TAAATAAATATTAAA
*
16603868 TTAAATAACTAAATATTAAA
1 TTAAATAAATAAATATTAAA
16603888 T
1 T
16603889 AATCTTACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAATAAATAAATATTAAA
Found at i:16608856 original size:26 final size:27
Alignment explanation
Indices: 16608805--16608859 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
16608795 CAAAAACAAA
16608805 AAATTATGAAAAAATAAAAATGATTTAG
1 AAATTATGAAAAAATAAAAA-GATTTAG
*
16608833 AAATATATG-AAATATAAAAA-ATTTAG
1 AAAT-TATGAAAAAATAAAAAGATTTAG
16608859 A
1 A
16608860 GATAAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 7 0.28
28 14 0.56
29 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (27 bp):
AAATTATGAAAAAATAAAAAGATTTAG
Found at i:16609022 original size:7 final size:7
Alignment explanation
Indices: 16609010--16609057 Score: 51
Period size: 8 Copynumber: 6.3 Consensus size: 7
16609000 AAATAGATTG
16609010 TTAAAAA
1 TTAAAAA
16609017 TTAAAAA
1 TTAAAAA
*
16609024 TAGAAAATA
1 T-TAAAA-A
16609033 TTAAAAA
1 TTAAAAA
16609040 TTATAAAA
1 TTA-AAAA
16609048 TTATAAAA
1 TTA-AAAA
16609056 TT
1 TT
16609058 TTGTTCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
7 12 0.33
8 22 0.61
9 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (7 bp):
TTAAAAA
Found at i:16609339 original size:19 final size:17
Alignment explanation
Indices: 16609317--16609357 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
16609307 AATTCAAAAA
16609317 TAAAAATAAAAATATTTTT
1 TAAAAATAAAAA-A-TTTT
*
16609336 TAAAAATATAAAATTTT
1 TAAAAATAAAAAATTTT
16609353 TAAAA
1 TAAAA
16609358 TTCAATGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.43
18 1 0.05
19 11 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAATAAAAAATTTT
Found at i:16614383 original size:27 final size:26
Alignment explanation
Indices: 16614350--16614454 Score: 115
Period size: 27 Copynumber: 3.9 Consensus size: 26
16614340 TCCAATGTTT
*
16614350 CATTTCATATATCTATTTCCATATAAC
1 CATTTCATATAACTATTT-CATATAAC
*
16614377 CGA-TTCATATAACTATTTCATATATC
1 C-ATTTCATATAACTATTTCATATAAC
*
16614403 TATTTTCATATAACTGA-TTCATATAAC
1 CA-TTTCATATAACT-ATTTCATATAAC
*
16614430 CATTTCATATATCTATTTTCATATA
1 CATTTCATATAACTA-TTTCATATA
16614455 TTCATTTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
25 2 0.03
26 18 0.27
27 44 0.67
28 2 0.03
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.46
Consensus pattern (26 bp):
CATTTCATATAACTATTTCATATAAC
Found at i:16614396 original size:40 final size:40
Alignment explanation
Indices: 16614350--16614454 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
16614340 TCCAATGTTT
*
16614350 CATTTCATATATCTATTTCCATATAACCGATTCATATAAC
1 CATTTCATATATCTATTTTCATATAACCGATTCATATAAC
* *
16614390 TATTTCATATATCTATTTTCATATAACTGATTCATATAAC
1 CATTTCATATATCTATTTTCATATAACCGATTCATATAAC
16614430 CATTTCATATATCTATTTTCATATA
1 CATTTCATATATCTATTTTCATATA
16614455 TTCATTTTCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 61 1.00
ACGTcount: A:0.34, C:0.18, G:0.02, T:0.46
Consensus pattern (40 bp):
CATTTCATATATCTATTTTCATATAACCGATTCATATAAC
Found at i:16614447 original size:13 final size:13
Alignment explanation
Indices: 16614351--16614455 Score: 97
Period size: 13 Copynumber: 7.8 Consensus size: 13
16614341 CCAATGTTTC
16614351 ATTTCATATATCT
1 ATTTCATATATCT
* *
16614364 ATTTCCATATAACCG
1 ATTT-CATAT-ATCT
*
16614379 A-TTCATATAACT
1 ATTTCATATATCT
16614391 ATTTCATATATCT
1 ATTTCATATATCT
*
16614404 ATTTTCATATAACT
1 A-TTTCATATATCT
* *
16614418 GA-TTCATATAACC
1 -ATTTCATATATCT
16614431 ATTTCATATATCT
1 ATTTCATATATCT
16614444 ATTTTCATATAT
1 A-TTTCATATAT
16614456 TCATTTTCAC
Statistics
Matches: 76, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
12 4 0.05
13 40 0.53
14 28 0.37
15 4 0.05
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (13 bp):
ATTTCATATATCT
Found at i:16617118 original size:18 final size:19
Alignment explanation
Indices: 16617085--16617121 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16617075 ACTTTATATT
*
16617085 TTTTATATATACATATACA
1 TTTTATATACACATATACA
16617104 TTTTATA-ACACATATACA
1 TTTTATATACACATATACA
16617122 CTTTCCACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTATATACACATATACA
Done.