Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003437.1 Hibiscus syriacus cultivar Beakdansim tig00007244_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 63176
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:97 original size:19 final size:19
Alignment explanation
Indices: 75--139 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
65 AGTTGACTCA
* * *
75 ACTGGACCCGATTGATCTG
1 ACTGGACCGGTTTGGTCTG
*
94 ACTGGACTGGTTTGGTCTG
1 ACTGGACCGGTTTGGTCTG
*
113 AATGGACCGGTTTGGTCTG
1 ACTGGACCGGTTTGGTCTG
132 ACTGGACC
1 ACTGGACC
140 AGTTCTAGAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.17, C:0.22, G:0.32, T:0.29
Consensus pattern (19 bp):
ACTGGACCGGTTTGGTCTG
Found at i:5829 original size:39 final size:37
Alignment explanation
Indices: 5781--5879 Score: 119
Period size: 37 Copynumber: 2.6 Consensus size: 37
5771 TCCCAACAAT
*
5781 GAGGA-CCTGCAGTAAGGACTTACCCTGAGCACAAAATA
1 GAGGAGCCTGCAGTAAGGACTTACCC--AGCACAAAACA
* *
5819 GAGGAGCCTGCTGTAAGGACTTACCCAGCACAAAGCA
1 GAGGAGCCTGCAGTAAGGACTTACCCAGCACAAAACA
* * *
5856 TAGGAGCCTGTAGTAAGGTCTTAC
1 GAGGAGCCTGCAGTAAGGACTTAC
5880 AAGTCATAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 29 0.55
38 5 0.09
39 19 0.36
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.18
Consensus pattern (37 bp):
GAGGAGCCTGCAGTAAGGACTTACCCAGCACAAAACA
Found at i:7758 original size:20 final size:20
Alignment explanation
Indices: 7715--7812 Score: 133
Period size: 20 Copynumber: 4.8 Consensus size: 20
7705 GTAGTATGAA
*
7715 TATTGTTCTTGCAATATTTTTG
1 TATTGTTCTTGTAATA--TTTG
7737 TATTGTTCTTGTAATATTTG
1 TATTGTTCTTGTAATATTTG
*
7757 TATTGTTCTTGCAATATTTG
1 TATTGTTCTTGTAATATTTG
* *
7777 TATTGTTTTTGTAATATATG
1 TATTGTTCTTGTAATATTTG
*
7797 TATTGTTCATGTAATA
1 TATTGTTCTTGTAATA
7813 CCTATACTAT
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 54 0.78
22 15 0.22
ACGTcount: A:0.22, C:0.06, G:0.14, T:0.57
Consensus pattern (20 bp):
TATTGTTCTTGTAATATTTG
Found at i:12278 original size:27 final size:27
Alignment explanation
Indices: 12238--12292 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
12228 AAAATTCTTT
* *
12238 TAAAAATTATGAATCGAATTAATTTAAA
1 TAAAAAATATGAATCAAATT-ATTTAAA
*
12266 TAAAAAAT-TGAATCAAATTTTTTAAA
1 TAAAAAATATGAATCAAATTATTTAAA
12292 T
1 T
12293 CAAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 7 0.29
27 10 0.42
28 7 0.29
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (27 bp):
TAAAAAATATGAATCAAATTATTTAAA
Found at i:14580 original size:37 final size:35
Alignment explanation
Indices: 14523--14694 Score: 130
Period size: 36 Copynumber: 5.0 Consensus size: 35
14513 ATATATATTG
*
14523 TATATAG-TTTGAAAACATTTAAAAAAACATATATA
1 TATATAGTTTTTAAAACATTTAAAAAAA-ATATATA
*
14558 TAATATAGTTTTGAAAACATTT-------ATATAT-
1 T-ATATAGTTTTTAAAACATTTAAAAAAAATATATA
14586 TATATAGTTTTTAAAACATTTTAAAAATAAATATA-A
1 TATATAGTTTTTAAAACA-TTTAAAAA-AAATATATA
* ** *
14622 TATATATTTTTTAAAACATTTTTGAAAATATATATA
1 TATATAGTTTTTAAAACA-TTTAAAAAAAATATATA
** *
14658 TTATATAGTTTTTTAAAACATTTTGAAAATATATATA
1 -TATATAG-TTTTTAAAACATTTAAAAAAAATATATA
14695 GTTAAAAAAT
Statistics
Matches: 116, Mismatches: 6, Indels: 28
0.77 0.04 0.19
Matches are distributed among these distances:
27 16 0.14
28 4 0.03
29 6 0.05
35 7 0.06
36 36 0.31
37 36 0.31
38 11 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATAGTTTTTAAAACATTTAAAAAAAATATATA
Found at i:14591 original size:36 final size:38
Alignment explanation
Indices: 14504--14591 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 38
14494 ATCATATATA
*
14504 AATATATATATATATATTGTATATAGTTTGAAAACATTT
1 AATATAT-TATATATATTGAATATAGTTTGAAAACATTT
* * **
14543 AAAAAAACATATATA-T-AATATAGTTTTGAAAACATTT
1 AATATATTATATATATTGAATATAG-TTTGAAAACATTT
14580 -ATATATTATATA
1 AATATATTATATA
14592 GTTTTTAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
36 14 0.36
37 14 0.36
38 7 0.18
39 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (38 bp):
AATATATTATATATATTGAATATAGTTTGAAAACATTT
Found at i:14591 original size:63 final size:65
Alignment explanation
Indices: 14514--14842 Score: 189
Period size: 65 Copynumber: 4.9 Consensus size: 65
14504 AATATATATA
14514 TATATATTGTATATAG-TTTGAAAACA-TTTAAAAA-AACATATATATAATATAGTTTTGAAAAC
1 TATATATTGTATATAGTTTTGAAAACATTTTAAAAATAA-ATATA-AT-ATATAGTTTTGAAAAC
14576 ATT
63 ATT
* * *
14579 TATATA-T-TATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATATTTTTTAAAACATT
1 TATATATTGTATATAGTTTTGAAAACATTTTAAAAATAAATATAATATATAGTTTTGAAAACA--
14642 TT
64 TT
* * * * *
14644 TGAAAATATATATATTATATAGTTTTTTAAAACATTTTGAAAATATATATAGTTAAAAAATCA-T
1 T----ATATAT-T-GTATATAG-TTTTGAAAACATTTT-AAAA-ATAAATA--TAATATAT-AGT
*
14708 TTTGAAAACATA
54 TTTGAAAACATT
* * * * * *
14720 TATATA-T-TATATAATTTTGAAATCATTTTGAAAAAT-TATATAGTATATAGTTTTAAAAATAT
1 TATATATTGTATATAGTTTTGAAAACATTTT-AAAAATAAATATAATATATAGTTTTGAAAACAT
14782 T
65 T
* *** * *
14783 TTTGA-AAACTATATAATTTTGAAAACATTTTTTAAAAAT--ATATAATATATAATTTT-AAAA
1 TAT-ATATTGTATATAGTTTTGAAAACA--TTTTAAAAATAAATATAATATATAGTTTTGAAAA
14843 TACTTTTGAA
Statistics
Matches: 217, Mismatches: 22, Indels: 51
0.75 0.08 0.18
Matches are distributed among these distances:
62 1 0.00
63 40 0.18
64 17 0.08
65 58 0.27
66 10 0.05
67 22 0.10
68 6 0.03
69 5 0.02
70 1 0.00
71 1 0.00
72 5 0.02
73 7 0.03
74 15 0.07
75 4 0.02
76 8 0.04
78 16 0.07
79 1 0.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (65 bp):
TATATATTGTATATAGTTTTGAAAACATTTTAAAAATAAATATAATATATAGTTTTGAAAACATT
Found at i:14602 original size:27 final size:27
Alignment explanation
Indices: 14552--14606 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
14542 TAAAAAAACA
14552 TATATATAATATAGTTTTGAAAACATT
1 TATATATAATATAGTTTTGAAAACATT
* *
14579 TATATATTATATAGTTTTTAAAACATT
1 TATATATAATATAGTTTTGAAAACATT
14606 T
1 T
14607 TAAAAATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (27 bp):
TATATATAATATAGTTTTGAAAACATT
Found at i:14679 original size:38 final size:35
Alignment explanation
Indices: 14579--14797 Score: 184
Period size: 37 Copynumber: 6.1 Consensus size: 35
14569 TGAAAACATT
*
14579 TATATATTATATAGTTTTTAAAACATTTTAAAAATA
1 TATATATTATATA-TTTTTAAAACATTTTGAAAATA
* *
14615 AATATAATATATATTTTTTAAAACATTTTTGAAAATA
1 TATATATTATATA-TTTTTAAAACA-TTTTGAAAATA
14652 TATATATTATATAGTTTTTTAAAACATTTTGAAAATA
1 TATATATTATATA--TTTTTAAAACATTTTGAAAATA
*
14689 TATATAGTTA-A-A-----AAATCATTTTGAAAACATA
1 TATATA-TTATATATTTTTAAAACATTTTG-AAA-ATA
* *
14720 TATATATTATATAATTTTGAAATCATTTTGAAAA-A
1 TATATATTATAT-ATTTTTAAAACATTTTGAAAATA
* * *
14755 TTATATAGTATATAGTTTTAAAAATATTTTTGAAAACTA
1 -TATATATTATATA-TTTTTAAAACA-TTTTGAAAA-TA
14794 TATA
1 TATA
14798 ATTTTGAAAA
Statistics
Matches: 154, Mismatches: 11, Indels: 34
0.77 0.06 0.17
Matches are distributed among these distances:
29 10 0.06
30 6 0.04
31 10 0.06
33 1 0.01
35 2 0.01
36 43 0.28
37 51 0.33
38 30 0.19
39 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (35 bp):
TATATATTATATATTTTTAAAACATTTTGAAAATA
Found at i:14807 original size:29 final size:29
Alignment explanation
Indices: 14763--14828 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 29
14753 AATTATATAG
* * *
14763 TATATAGTTTTAAAAATATTTTTGAAAAC
1 TATATAATTTTAAAAACATTTTTGAAAAA
* *
14792 TATATAATTTTGAAAACATTTTTTAAAAA
1 TATATAATTTTAAAAACATTTTTGAAAAA
14821 TATATAAT
1 TATATAAT
14829 ATATAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
TATATAATTTTAAAAACATTTTTGAAAAA
Found at i:14812 original size:65 final size:63
Alignment explanation
Indices: 14727--14860 Score: 189
Period size: 65 Copynumber: 2.1 Consensus size: 63
14717 ATATATATAT
* * * *
14727 TATATAATTTTGAAATCA-TTTTGAAAAATTATATAGTATATAGTTTTAAAAATATTTTTGAAAA
1 TATATAATTTTGAAAACATTTTTGAAAAA-TATATAATATATAATTTT-AAAATACTTTTGAAAA
*
14791 CTATATAATTTTGAAAACATTTTTTAAAAATATATAATATATAATTTTAAAATACTTTTGAAAA
1 -TATATAATTTTGAAAACATTTTTGAAAAATATATAATATATAATTTTAAAATACTTTTGAAAA
14855 TATATA
1 TATATA
14861 TTATATATAC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
63 6 0.10
64 15 0.24
65 33 0.52
66 9 0.14
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (63 bp):
TATATAATTTTGAAAACATTTTTGAAAAATATATAATATATAATTTTAAAATACTTTTGAAAA
Found at i:14830 original size:141 final size:139
Alignment explanation
Indices: 14566--14885 Score: 332
Period size: 141 Copynumber: 2.3 Consensus size: 139
14556 TATAATATAG
* * * *
14566 TTTTGAAAACATTTATATATTATATAGTTTTTAAAACATTTTAAAAATAAATATAATATATATTT
1 TTTTGAAAACATATATATATTATATAATTTTGAAAACATTTTAAAAATAAATATAATATATAGTT
* * * *
14631 TTTAAAACATTTTTGAAAATATATATATTATATAGTTTTTTAAAACATTTTGAAAATATATATAG
66 TTAAAAACATTTTTGAAAATATATATATTATAAAATTTTTTAAAACATTATGAAAATATATA-A-
14696 TTAAAAAAT-C
129 TTAAAAAATAC
* * *
14706 ATTTTGAAAACATATATATATTATATAATTTTGAAATCATTTTGAAAAAT-TATATAGTATATAG
1 -TTTTGAAAACATATATATATTATATAATTTTGAAAACATTTT-AAAAATAAATATAATATATAG
* * *
14770 TTTTAAAAATATTTTTGAAAACTATATA-ATTTTGAAAACATTTTTTAAAA-A-TAT-ATAATAT
64 TTTTAAAAACATTTTTGAAAA-TATATATATTAT--AAA-ATTTTTTAAAACATTATGAAAATAT
**
14831 ATAATTTTAAAATAC
125 ATAATTAAAAAATAC
* * *
14846 TTTTGAAAATATATAT-TA-TATATACTTTTGGAAAATATTT
1 TTTTGAAAACATATATATATTATATAATTTT-GAAAACATTT
14886 ATATATATAT
Statistics
Matches: 152, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
137 10 0.07
138 10 0.07
139 22 0.14
140 2 0.01
141 81 0.53
142 14 0.09
143 3 0.02
144 10 0.07
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (139 bp):
TTTTGAAAACATATATATATTATATAATTTTGAAAACATTTTAAAAATAAATATAATATATAGTT
TTAAAAACATTTTTGAAAATATATATATTATAAAATTTTTTAAAACATTATGAAAATATATAATT
AAAAAATAC
Found at i:14832 original size:36 final size:37
Alignment explanation
Indices: 14792--14885 Score: 120
Period size: 36 Copynumber: 2.6 Consensus size: 37
14782 TTTTGAAAAC
* *
14792 TATATAATTTTGAAAACATTTTTTAAAA-ATATATAA
1 TATATAATTTTGAAAATATTTTTGAAAATATATATAA
* *
14828 TATATAATTTT-AAAATACTTTTGAAAATATATATTA
1 TATATAATTTTGAAAATATTTTTGAAAATATATATAA
*
14864 TATATACTTTTGGAAAATATTT
1 TATATAATTTT-GAAAATATTT
14886 ATATATATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 13 0.27
36 28 0.57
38 8 0.16
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATAATTTTGAAAATATTTTTGAAAATATATATAA
Found at i:14857 original size:25 final size:26
Alignment explanation
Indices: 14826--14892 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
14816 AAAAATATAT
*
14826 AATATATAATTTTAAAATACTTTT-GAA
1 AATATAT-ATTAT-AAATACTTTTGGAA
*
14853 AATATATATTATATATACTTTTGGAA
1 AATATATATTATAAATACTTTTGGAA
*
14879 AATATTTATATATA
1 AATATATAT-TATA
14893 TATTATTGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.26
26 15 0.43
27 11 0.31
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (26 bp):
AATATATATTATAAATACTTTTGGAA
Found at i:14893 original size:25 final size:25
Alignment explanation
Indices: 14842--14895 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 25
14832 TAATTTTAAA
14842 ATACTTTTGAAAATATATATTATAT
1 ATACTTTTGAAAATATATATTATAT
*
14867 ATACTTTTGGAAAATATTTATATATAT
1 ATACTTTT-GAAAATATATAT-TATAT
14894 AT
1 AT
14896 TATTGTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 8 0.31
26 11 0.42
27 7 0.27
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (25 bp):
ATACTTTTGAAAATATATATTATAT
Found at i:17349 original size:15 final size:16
Alignment explanation
Indices: 17307--17346 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
17297 TTGAAATAAG
17307 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
17323 CATGTGGGGTAGATAT
1 CATGTGGGGTAGATAT
17339 CATGTGGG
1 CATGTGGG
17347 TAGGATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.23, C:0.07, G:0.40, T:0.30
Consensus pattern (16 bp):
CATGTGGGGTAGATAT
Found at i:21669 original size:84 final size:83
Alignment explanation
Indices: 21379--22097 Score: 663
Period size: 84 Copynumber: 8.7 Consensus size: 83
21369 TTAAAGATAA
* * *** *
21379 CATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* *
21444 GCTCAGTTCCAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
21463 CATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCT---ACCAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* *
21525 CTCAGCTTCGAGGGCACAT
66 CTCAGC-TCCAAGGCACAT
* * * * * * *
21544 CATTTGTAGTATAACTTAAGTCGAGAAGGGTTATATACCAAACAAAGACCTTTGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC-AACAAAGACCTTCGAGTTCGACTAC
* * *
21609 GGTCAGCTCTAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* *
21628 CATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGATCC-TCGAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGA-CCTTCGAGTTCGACTAC
* * *
21689 ACTCAGCTTCGAGGGCACAT
65 GCTCAGC-TCCAAGGCACAT
* * * * * * * *
21709 CATTTACAGCATAACTCAAGACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAC-AAAGACCTTCGAGTTCGACTAC
* *
21774 GCTCAGCTCTAAGGCATAT
65 GCTCAGCTCCAAGGCACAT
* * * *
21793 TATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAA-CAAAGACCTTCGAGTTCGACTAC
21858 GCTCAGCTCCAAGGCACAT
65 GCTCAGCTCCAAGGCACAT
* * * * * *
21877 CATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAGCTG-C--CAAATACTTTTGAGTTCAACTACG
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
21939 CTCAGCTCCAAGGCACAT
66 CTCAGCTCCAAGGCACAT
* * *
21957 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C--CAAAGACCCTCGAGTTCGATTACA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
* * *
22019 CTCAGCTTCGAGGGCATAT
66 CTCAGC-TCCAAGGCACAT
* * * *** * * * * *
22038 CATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACCGAAGACCTCCGAGTTCGA
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGA
22098 TTACATTCAG
Statistics
Matches: 522, Mismatches: 96, Indels: 34
0.80 0.15 0.05
Matches are distributed among these distances:
80 145 0.28
81 123 0.24
82 2 0.00
83 2 0.00
84 199 0.38
85 51 0.10
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (83 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACAT
Found at i:21679 original size:165 final size:162
Alignment explanation
Indices: 21422--22097 Score: 816
Period size: 165 Copynumber: 4.1 Consensus size: 162
21412 TTTGCCAACA
*
21422 AAAGACCTTCGAGTTCGACTACGCTCAGTTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGA
* * *
21487 GAAGGGTTATCTACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGTA
66 GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
*
21552 GTATAACTTAAGTCGAGAAGGGTTATATACCAAAC
131 GTATAACTTAAGTCGAGAAGGGTTATCT-CC--AC
* * *
21587 AAAGACCTTTGAGTTCGACTACGGTCAGCTCTAAGGCATATCATTTGCAGAATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGA
* *
21652 GAAGGGCTATCTGCCAAAGATCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
66 GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
* * * * *
21717 GCATAACTCAAGACTAGAAGGGTTATCTGTCACC
131 GTATAACTTAAGTCGAGAAGGGTTATCT-CCA-C
* * * * *
21751 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCATATTATTTGTAGCATAACTTAAGTCG
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCG
* * * * * *
21816 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
65 AGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
* * * *
21880 TTGCAGTATAGCTTAAGTCGAGAAGGGCTAGCTGC-C
126 TTGCAGTATAACTTAAGTCGAGAAGGGTTATCTCCAC
* * * * * *
21916 AAATACTTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGA
* *
21981 GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACA
66 GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
* * *** *
22046 GCATAACTCAAGGATAGAAGGGTTATCTGTCACC
131 GTATAACTTAAGTCGAGAAGGGTTATCT-CCA-C
* *
22080 GAAGACCTCCGAGTTCGA
1 AAAGACCTTCGAGTTCGA
22098 TTACATTCAG
Statistics
Matches: 431, Mismatches: 70, Indels: 21
0.83 0.13 0.04
Matches are distributed among these distances:
160 28 0.06
161 36 0.08
162 1 0.00
163 1 0.00
164 82 0.19
165 217 0.50
167 1 0.00
168 38 0.09
169 27 0.06
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (162 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGA
GAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCA
GTATAACTTAAGTCGAGAAGGGTTATCTCCAC
Found at i:21817 original size:249 final size:247
Alignment explanation
Indices: 21422--22071 Score: 855
Period size: 249 Copynumber: 2.6 Consensus size: 247
21412 TTTGCCAACA
* *
21422 AAAGACCTTCGAGTTCGACTACGCTCAG-TTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCG
1 AAAGACC-TCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
*
21486 AGAAGGGTTATC--TACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
65 AGAAGGGTTATCTGTACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTT
* * *
21549 GTAGTATAACTTAAGTCGAGAAGGGTTATATACCAAACAAAGACCTTTGAGTTCGACTACGGTCA
130 GTAGCATAACTTAAGTCGAGAAGGGTTATATACCAAACAAAGACCTTCGAGTTCGACTACGCTCA
* * *
21614 GCTCTAAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCC
195 GCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAGCTGCC
* * * * * * * * *
21667 AAAGATCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGACT
1 AAAGA-CCTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
* * * * * *
21732 AGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCATATTAT
65 AGAAGGGTTATCTGT-ACC-AAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCAT
* * *
21796 TTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
128 TTGTAGCATAACTTAAGTCGAGAAGGGTTATATACCAAACAAAGACCTTCGAGTTCGACTACGCT
*
21861 CAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAGCTGCC
193 CAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAGCTGCC
* * * *
21916 AAATACTTTTGAGTTCAACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
1 AAAGAC-CTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCG
*
21980 AGAAGGGCTATCTG--CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTT
65 AGAAGGGTTATCTGTACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTT
** * ***
22043 ACAGCATAACTCAAGGATAGAAGGGTTAT
130 GTAGCATAACTTAAGTCGAGAAGGGTTAT
22072 CTGTCACCGA
Statistics
Matches: 343, Mismatches: 54, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
244 26 0.08
245 62 0.18
246 41 0.12
248 43 0.13
249 145 0.42
250 26 0.08
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (247 bp):
AAAGACCTCGAGTTCGACTACGCTCAGCTTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGA
GAAGGGTTATCTGTACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTG
TAGCATAACTTAAGTCGAGAAGGGTTATATACCAAACAAAGACCTTCGAGTTCGACTACGCTCAG
CTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTAGCTGCC
Found at i:22008 original size:329 final size:328
Alignment explanation
Indices: 21379--22097 Score: 1016
Period size: 329 Copynumber: 2.2 Consensus size: 328
21369 TTAAAGATAA
* * * * * * * *
21379 CATTTGCAACATAGCTCAAGGAAAGAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
* *
21444 GCTCAGTTCCAAGGCATATCATTTGCAGAATAGCTTAAGTCGAGAAGGGTTATCTACCAAAGACC
66 GCTCAGCTCCAAGGCATATCATTTGCAGAATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACC
* * * *
21509 CTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGTAGTATAACTTAAGTCGAGAAGGG
131 CTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGG
* * * * * *
21574 TTATATACCAAACAAAGACCTTTGAGTTCGACTACGGTCAGCTCTAAGGCATATCATTTGCAGAA
196 CTAGATACC--ACAAAGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGAA
*
21639 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGATCCTCGAGTTCGATTACACTCAGCTTCGAGGG
259 TAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGG
21704 CACAT
324 CACAT
21709 CATTTACAGCATAACTCAA-GACTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTA
1 CATTTACAGCATAACTCAAGGA-TAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTA
* * * *
21773 CGCTCAGCTCTAAGGCATATTATTTGTAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAA
65 CGCTCAGCTCCAAGGCATATCATTTGCAGAATAACTTAAGTCGAGAAGGGTTATCT----ACCAA
* * *
21838 AGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAG
126 AGACCCTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAG
* * * *
21902 AAGGGCTAGCT-GC-CAAATACTTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCA
191 AAGGGCTAGATACCACAAAGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCA
*
21965 GCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGA
256 GAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGA
*
22030 GGGCATAT
321 GGGCACAT
* *
22038 CATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACC-GAAGACCTCCGAGTTCGA
1 CATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGA
22098 TTACATTCAG
Statistics
Matches: 347, Mismatches: 36, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
328 16 0.05
329 155 0.45
330 105 0.30
332 1 0.00
333 41 0.12
334 29 0.08
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (328 bp):
CATTTACAGCATAACTCAAGGATAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCATATCATTTGCAGAATAACTTAAGTCGAGAAGGGTTATCTACCAAAGACC
CTCGAGTTCGACTACACTCAGCTTCCAAGGCACATCATTTGCAGTATAACTTAAGTCGAGAAGGG
CTAGATACCACAAAGACCTTTGAGTTCAACTACGCTCAGCTCCAAGGCACATCATTTGCAGAATA
GCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCA
CAT
Found at i:22889 original size:38 final size:37
Alignment explanation
Indices: 22795--23040 Score: 212
Period size: 36 Copynumber: 6.8 Consensus size: 37
22785 TTTTTAAAAA
* * *
22795 AAAACATATATA-ATATATAGTTTTGAAAATATGTTTG
1 AAAATATATATATATATATAGTTTTTAAAACAT-TTTG
* * *
22832 AAAACATTTAAATATTATATAGTTTTTAAAACATTTTG
1 AAAATATATATATA-TATATAGTTTTTAAAACATTTTG
*
22870 AAAATAAATATA-ATATATA-TTTTTAAAACATTTTTG
1 AAAATATATATATATATATAGTTTTTAAAACA-TTTTG
*
22906 AAAATATATATAT-TATATAGTTTTTTTAAACATTTTG
1 AAAATATATATATATATATAG-TTTTTAAAACATTTTG
**
22943 AAAATATATATAGT-T-TA-A----AAAAAACATTTTG
1 AAAATATATATA-TATATATAGTTTTTAAAACATTTTG
* * * *
22974 AAAACATATATATATTATATAATTTTGAAATCATTTTG
1 AAAATATATATATA-TATATAGTTTTTAAAACATTTTG
23012 AAAA-AT-TATATAGTATATAGTTTTTAAAA
1 AAAATATATATATA-TATATAGTTTTTAAAA
23041 ATATTTTTGA
Statistics
Matches: 173, Mismatches: 21, Indels: 31
0.77 0.09 0.14
Matches are distributed among these distances:
30 1 0.01
31 21 0.12
32 1 0.01
33 2 0.01
34 1 0.01
35 11 0.06
36 48 0.28
37 32 0.18
38 39 0.23
39 17 0.10
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (37 bp):
AAAATATATATATATATATAGTTTTTAAAACATTTTG
Found at i:23009 original size:69 final size:68
Alignment explanation
Indices: 22894--23025 Score: 180
Period size: 69 Copynumber: 1.9 Consensus size: 68
22884 ATATATTTTT
* *
22894 AAAACATTTTTGAAAATATATATATTATATAGTTTTTTTAAACATTTTG-AAAATATATATAGTT
1 AAAACATTTTTGAAAATATATATATTATATAG-ATTTTGAAACATTTTGAAAAAT-TATATAGTT
22958 TAAAA
64 TAAAA
22963 AAAACA-TTTTGAAAACATATATATATTATATA-ATTTTGAAATCATTTTGAAAAATTATATAGT
1 AAAACATTTTTG-AAA-ATATATATATTATATAGATTTTGAAA-CATTTTGAAAAATTATATAGT
23026 ATATAGTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
68 12 0.21
69 24 0.42
70 21 0.37
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (68 bp):
AAAACATTTTTGAAAATATATATATTATATAGATTTTGAAACATTTTGAAAAATTATATAGTTTA
AAA
Found at i:23022 original size:106 final size:103
Alignment explanation
Indices: 22859--23131 Score: 310
Period size: 106 Copynumber: 2.7 Consensus size: 103
22849 TATAGTTTTT
* * *
22859 AAAACATTTTG-AAAATAAATATAATATATATTTTTAAAA-CATTTTTGAAAATATATATATTAT
1 AAAACATTTTGAAAAATATATATAATATATAATTTTAAAATCACTTTTGAAAAT-TATATATTAT
** *
22922 ATAGTTTTTTTAAACA-TTTTGAAAA-TATATATAGTTTAAAA
65 ATAGTTTTTAAAAACATTTTTGAAAACGATATA-A-TTT--AA
* * *
22963 AAAACATTTTGAAAACATATATATATTATATAATTTTGAAATCA-TTTTGAAAAATTATATAGTA
1 AAAACATTTTGAAAA-ATATATATAATATATAATTTTAAAATCACTTTTG-AAAATTATATATTA
* **
23027 TATAGTTTTTAAAAATATTTTTGAAAACGATATAATTTTG
64 TATAGTTTTTAAAAACATTTTTGAAAACGATATAATTTAA
*
23067 AAAACATTTT-AAAAAAATATATAATATATAATTTTAAAAT-ACTTTTGAAAA-TATATATTATA
1 AAAACATTTTGAAAAATATATATAATATATAATTTTAAAATCACTTTTGAAAATTATATATTATA
23129 TAG
66 TAG
23132 AATTTTGGAA
Statistics
Matches: 147, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
100 13 0.09
101 5 0.03
102 28 0.19
103 4 0.03
104 21 0.14
105 3 0.02
106 51 0.35
107 17 0.12
108 5 0.03
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (103 bp):
AAAACATTTTGAAAAATATATATAATATATAATTTTAAAATCACTTTTGAAAATTATATATTATA
TAGTTTTTAAAAACATTTTTGAAAACGATATAATTTAA
Found at i:23049 original size:38 final size:38
Alignment explanation
Indices: 22962--23060 Score: 105
Period size: 38 Copynumber: 2.6 Consensus size: 38
22952 ATAGTTTAAA
* *
22962 AAAAACATTTTGAAAACATATATATATTATATAATTTT
1 AAAATCATTTTGAAAACATATATATAGTATATAATTTT
* *
23000 GAAATCATTTTGAAAA-AT-TATATAGTATATAGTTTTT
1 AAAATCATTTTGAAAACATATATATAGTATATA-ATTTT
23037 AAAAAT-ATTTTTGAAAACGATATA
1 -AAAATCA-TTTTGAAAAC-ATATA
23061 ATTTTGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
36 12 0.24
37 7 0.14
38 27 0.54
40 2 0.04
41 2 0.04
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.41
Consensus pattern (38 bp):
AAAATCATTTTGAAAACATATATATAGTATATAATTTT
Found at i:23075 original size:66 final size:64
Alignment explanation
Indices: 22990--23117 Score: 184
Period size: 66 Copynumber: 2.0 Consensus size: 64
22980 TATATATATT
* * * * * *
22990 ATATAATTTTGAAATCATTTTGAAAAATTATATAGTATATAGTTTTTAAAAATATTTTTGAAAAC
1 ATATAATTTTGAAAACATTTTAAAAAAATATATAATATATA-ATTTT-AAAATACTTTTGAAAAC
23055 G
64 G
23056 ATATAATTTTGAAAACATTTTAAAAAAATATATAATATATAATTTTAAAATACTTTTGAAAA
1 ATATAATTTTGAAAACATTTTAAAAAAATATATAATATATAATTTTAAAATACTTTTGAAAA
23118 TATATATTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
64 15 0.27
65 4 0.07
66 37 0.66
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (64 bp):
ATATAATTTTGAAAACATTTTAAAAAAATATATAATATATAATTTTAAAATACTTTTGAAAACG
Found at i:23100 original size:36 final size:36
Alignment explanation
Indices: 23056--23148 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
23046 TTTGAAAACG
*
23056 ATATAATTTTGAAAACATTTTAAAAAAATATATAAT
1 ATATAATTTTGAAAATATTTTAAAAAAATATATAAT
* * *
23092 ATATAATTTT-AAAATACTTTTGAAAATATATATTAT
1 ATATAATTTTGAAAATA-TTTTAAAAAAATATATAAT
*
23128 ATAGAATTTTGGAAAATATTT
1 ATATAATTTT-GAAAATATTT
23149 ATATATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
35 5 0.10
36 35 0.71
37 3 0.06
38 6 0.12
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.43
Consensus pattern (36 bp):
ATATAATTTTGAAAATATTTTAAAAAAATATATAAT
Found at i:24740 original size:6 final size:6
Alignment explanation
Indices: 24728--24764 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
24718 TCGAATCGGG
* *
24728 TAATTT AAATTT AAATTT TAATTT TAATTT TAATTT T
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T
24765 CGCTATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TAATTT
Found at i:26491 original size:15 final size:15
Alignment explanation
Indices: 26467--26500 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
26457 TGAAAATAAT
*
26467 TAGTAGTATATTATA
1 TAGTAATATATTATA
*
26482 TAGTAATATATTTTA
1 TAGTAATATATTATA
26497 TAGT
1 TAGT
26501 TTTGGAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
TAGTAATATATTATA
Found at i:26523 original size:31 final size:32
Alignment explanation
Indices: 26481--26541 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
26471 AGTATATTAT
*
26481 ATAGTAATATAT-TTTATAGTTTTGGAAATAAA
1 ATAGTAATATATATTTA-AGTTTTGAAAATAAA
*
26513 ATAGT-ATATATATTTAATTTTTGAAAATA
1 ATAGTAATATATATTTAAGTTTTGAAAATA
26542 TATATGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (32 bp):
ATAGTAATATATATTTAAGTTTTGAAAATAAA
Found at i:26523 original size:46 final size:45
Alignment explanation
Indices: 26428--26523 Score: 113
Period size: 46 Copynumber: 2.1 Consensus size: 45
26418 ATATATAGAT
* * * *
26428 TATATTATATAGAGTACGTTTTTTAGTTTTGAAAATAATTAGTAG
1 TATATTATATAGAATACATTTTATAGTTTTGAAAATAAATAGTAG
* *
26473 TATATTATATAGTAATATATTTTATAGTTTTGGAAATAAAATAGTA-
1 TATATTATATAG-AATACATTTTATAGTTTTGAAAAT-AAATAGTAG
26519 TATAT
1 TATAT
26524 ATTTAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
45 12 0.28
46 24 0.56
47 7 0.16
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (45 bp):
TATATTATATAGAATACATTTTATAGTTTTGAAAATAAATAGTAG
Found at i:27737 original size:16 final size:16
Alignment explanation
Indices: 27716--27746 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27706 CCAAAAACCA
27716 GAGAAAGGGAAGAAAC
1 GAGAAAGGGAAGAAAC
*
27732 GAGAAAGGGGAGAAA
1 GAGAAAGGGAAGAAA
27747 AACAAAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.42, T:0.00
Consensus pattern (16 bp):
GAGAAAGGGAAGAAAC
Found at i:36622 original size:30 final size:30
Alignment explanation
Indices: 36565--36632 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
36555 ATGCATAAGT
* **
36565 AAATTCATCATTTATAATGCATCACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
* *
36595 AAATGCATCATTTATAGCACATTACCAATA
1 AAATGCATCATTTATAACACATCACCAATA
*
36625 ATATGCAT
1 AAATGCAT
36633 TCGAATTTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATGCATCATTTATAACACATCACCAATA
Found at i:42514 original size:23 final size:23
Alignment explanation
Indices: 42486--42529 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
42476 ATATGATGGA
42486 AAAATGAAAAAAGAA-GAAAAAGG
1 AAAATGAAAAAA-AATGAAAAAGG
42509 AAAATGAAAAAAAATGAAAAA
1 AAAATGAAAAAAAATGAAAAA
42530 ATAAATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (23 bp):
AAAATGAAAAAAAATGAAAAAGG
Found at i:49127 original size:29 final size:29
Alignment explanation
Indices: 49094--49160 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
49084 GTCTTGTTGA
*
49094 ATCTCTTGACTATTAAAAATTATAAAATG
1 ATCTCTCGACTATTAAAAATTATAAAATG
*
49123 ATCTCTCGACTATTAGAAATTATAAAATG
1 ATCTCTCGACTATTAAAAATTATAAAATG
*
49152 GTCTCTCGA
1 ATCTCTCGA
49161 TTATAAGACA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (29 bp):
ATCTCTCGACTATTAAAAATTATAAAATG
Found at i:52120 original size:21 final size:21
Alignment explanation
Indices: 52076--52125 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
52066 AACATTTTTA
**
52076 AAAATATATAATATTTTAGGTT
1 AAAATA-ATAATATTTTAAATT
*
52098 AACATAATAATATTTTAAATT
1 AAAATAATAATATTTTAAATT
52119 AAAATAA
1 AAAATAA
52126 AAACATTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 19 0.79
22 5 0.21
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
AAAATAATAATATTTTAAATT
Found at i:52344 original size:25 final size:24
Alignment explanation
Indices: 52316--52417 Score: 82
Period size: 25 Copynumber: 4.2 Consensus size: 24
52306 TTATAATTAT
52316 ATATATAAAATATATAATTTGAAAA
1 ATATATAAAATATATAATTT-AAAA
* * *
52341 ATATATATAATATATAGTTTAAAT
1 ATATATAAAATATATAATTTAAAA
* * * *
52365 ATATAT-ATATATAT-ATATATAT
1 ATATATAAAATATATAATTTAAAA
* *
52387 ATATATATATATATATATATATAAAA
1 ATATATA-AAATATATA-ATTTAAAA
52413 ATATA
1 ATATA
52418 ATTTATGGTT
Statistics
Matches: 63, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.17
23 6 0.10
24 17 0.27
25 18 0.29
26 11 0.17
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATATATAAAATATATAATTTAAAA
Found at i:52346 original size:2 final size:2
Alignment explanation
Indices: 52341--52409 Score: 104
Period size: 2 Copynumber: 34.5 Consensus size: 2
52331 AATTTGAAAA
* *
52341 AT AT AT AT A- AT AT AT AGT TT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
52383 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
52410 AAAATATAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.02
2 59 0.97
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52416 original size:18 final size:18
Alignment explanation
Indices: 52313--52417 Score: 85
Period size: 18 Copynumber: 6.0 Consensus size: 18
52303 ATATTATAAT
52313 TATATATAT-AAAATATA
1 TATATATATAAAAATATA
52330 TA-AT-T-TGAAAAATATA
1 TATATATAT-AAAAATATA
*** *
52346 TATA-ATATATAGTTTAAA
1 TATATATATA-AAAATATA
* *
52364 TATATATATATATATATA
1 TATATATATAAAAATATA
* *
52382 TATATATATATATATATA
1 TATATATATAAAAATATA
52400 TATATATATAAAAATATA
1 TATATATATAAAAATATA
52418 ATTTATGGTT
Statistics
Matches: 71, Mismatches: 10, Indels: 13
0.76 0.11 0.14
Matches are distributed among these distances:
14 1 0.01
15 1 0.01
16 12 0.17
17 5 0.07
18 47 0.66
19 5 0.07
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TATATATATAAAAATATA
Found at i:52464 original size:31 final size:33
Alignment explanation
Indices: 52404--52464 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 33
52394 TATATATATA
* *
52404 TATATAAAAATATAATTTATGGTTTTGAAAGTT
1 TATATAAAAATATAATTTATGATTATGAAAGTT
*
52437 TATATATAAATAT-A-TTATGATTATGAAA
1 TATATAAAAATATAATTTATGATTATGAAA
52465 TATGAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 12 0.48
32 1 0.04
33 12 0.48
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (33 bp):
TATATAAAAATATAATTTATGATTATGAAAGTT
Found at i:52495 original size:3 final size:3
Alignment explanation
Indices: 52487--52522 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
52477 TATGTTTTCA
52487 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52523 ATTGCAGGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52579 original size:21 final size:20
Alignment explanation
Indices: 52547--52585 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
52537 GTTCAGGTCA
52547 TCCAAGTCCAAGTCCAATGG
1 TCCAAGTCCAAGTCCAATGG
52567 TCCAAGATCCAAGTCCAAT
1 TCCAAG-TCCAAGTCCAAT
52586 TCGGGTCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.31, G:0.15, T:0.21
Consensus pattern (20 bp):
TCCAAGTCCAAGTCCAATGG
Found at i:52597 original size:27 final size:23
Alignment explanation
Indices: 52542--52585 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
52532 CCAGGGTTCA
52542 GGTCATCCAAGTCCAAGTCCAAT
1 GGTCATCCAAGTCCAAGTCCAAT
52565 GG---TCCAAGATCCAAGTCCAAT
1 GGTCATCCAAG-TCCAAGTCCAAT
52586 TCGGGTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 6 0.30
21 12 0.60
23 2 0.10
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (23 bp):
GGTCATCCAAGTCCAAGTCCAAT
Found at i:53790 original size:2 final size:2
Alignment explanation
Indices: 53783--53845 Score: 78
Period size: 2 Copynumber: 32.0 Consensus size: 2
53773 ATTTATACAA
53783 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
53824 -T GAT AT AT GAT AT GT -T AT AT AT
1 AT -AT AT AT -AT AT AT AT AT AT AT
53846 TATTATCTTT
Statistics
Matches: 55, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
1 3 0.05
2 49 0.89
3 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (2 bp):
AT
Done.