Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008143.1 Hibiscus syriacus cultivar Beakdansim tig00110705_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: 1142845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 5
Found at i:906277 original size:102 final size:104
Alignment explanation
Indices: 906021--906297 Score: 305
Period size: 102 Copynumber: 2.6 Consensus size: 104
906011 AGACTCAAAC
* ** * *
906021 AATCTTCATAAAATGTTTATGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAAT
1 AATCTTCATAAAATGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAAT
* *
906086 AAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG
62 AAAACAGGTCCGCTCCCTATTCCGTCAGAGAGTATAGAACTCG
* *
906129 AAAAATCTTCAATAAACA-G-GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTTAA
1 ---AATCTTC-ATAAA-ATGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAA
* *
906192 -CAAAC-GTGTCCGCTCCCTATTCCGTCAGAGAGTATAGGACTCG
61 TAAAACAG-GTCCGCTCCCTATTCCGTCAGAGAGTATAGAACTCG
* *
906235 -ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCGATCTTC-ATAAAA
1 AATCTTCATAAAATGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATAAAA
906298 TGAGTTTGCT
Statistics
Matches: 145, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
100 1 0.01
101 7 0.05
102 48 0.33
105 1 0.01
106 37 0.26
107 9 0.06
110 1 0.01
111 34 0.23
112 6 0.04
113 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (104 bp):
AATCTTCATAAAATGTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAATAAAA
CAGGTCCGCTCCCTATTCCGTCAGAGAGTATAGAACTCG
Found at i:906298 original size:51 final size:51
Alignment explanation
Indices: 906022--906299 Score: 276
Period size: 51 Copynumber: 5.3 Consensus size: 51
906012 GACTCAAACA
* ** * * * *
906022 ATCTTCATAAAATGTTTATGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACA
1 ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGAC-T---CG
* * *
906077 ATCTTCAATAAAACAG-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG
1 ATCTTC-ATAAAA-TGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* *
906129 AAAAATCTTCAATAAACA-G-GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCA
1 ----ATCTTC-ATAAA-ATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
* * *
906184 ATCTTTA-ACAAACGTGTCCGCTCCCTATTCCGTCAGAGAGTATAGGACTCG
1 ATCTTCATA-AAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
906235 ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
1 ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
906286 ATCTTCATAAAATG
1 ATCTTCATAAAATG
906300 AGTTTGCTTC
Statistics
Matches: 193, Mismatches: 19, Indels: 26
0.81 0.08 0.11
Matches are distributed among these distances:
49 2 0.01
50 4 0.02
51 98 0.51
52 2 0.01
55 40 0.21
56 45 0.23
57 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (51 bp):
ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCG
Found at i:906342 original size:37 final size:36
Alignment explanation
Indices: 906301--906372 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
906291 CATAAAATGA
906301 GTTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATG
* *
906338 GTTTGCTTCACTACTCTTCCTTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
906373 TGACCTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATG
Found at i:907671 original size:7 final size:7
Alignment explanation
Indices: 907651--907847 Score: 121
Period size: 7 Copynumber: 26.4 Consensus size: 7
907641 CCTCCTTTTA
907651 TTTC-TT
1 TTTCTTT
907657 TTTCTTT
1 TTTCTTT
*
907664 TTCTTTTT
1 TT-TCTTT
907672 TCTTCTTT
1 T-TTCTTT
*
907680 TTTCATT
1 TTTCTTT
907687 TTTCATTT
1 TTTC-TTT
*
907695 TTTTTATT
1 TTTCT-TT
907703 TTTCATTTT
1 TTTC--TTT
907712 TTTCATTTT
1 TTTC--TTT
*
907721 TTTCATT
1 TTTCTTT
*
907728 TTTCATT
1 TTTCTTT
*
907735 TTTCATT
1 TTTCTTT
*
907742 TTTCATT
1 TTTCTTT
*
907749 TTTCATT
1 TTTCTTT
*
907756 TTTCATT
1 TTTCTTT
*
907763 TTTCATT
1 TTTCTTT
907770 TTTCATTT
1 TTTC-TTT
*
907778 TTTTTTCT
1 TTTCTT-T
907786 TTTCTTCAT
1 TTTCTT--T
907795 TTT-TTT
1 TTTCTTT
*
907801 CTTTATTCT
1 -TTTCTT-T
907810 TTTCTTT
1 TTTCTTT
907817 TCTT-TTT
1 T-TTCTTT
907824 TTTCTTT
1 TTTCTTT
907831 TTTCTTT
1 TTTCTTT
*
907838 TCTCTTT
1 TTTCTTT
907845 TTT
1 TTT
907848 TTCATTATTT
Statistics
Matches: 162, Mismatches: 14, Indels: 29
0.79 0.07 0.14
Matches are distributed among these distances:
6 7 0.04
7 91 0.56
8 42 0.26
9 21 0.13
10 1 0.01
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (7 bp):
TTTCTTT
Found at i:907788 original size:5 final size:5
Alignment explanation
Indices: 907769--907850 Score: 58
Period size: 5 Copynumber: 15.0 Consensus size: 5
907759 CATTTTTCAT
* *
907769 TTTTC ATTTTT TTTTC TTTTC TTCATTT TTTTC TTTATTC TTTTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TT--TTC TTTTC -TT-TTC TTTTC TTTTC
*
907819 TTTT- TTTTC TTTTTTC TTTTC TCTTTT TTTTC
1 TTTTC TTTTC --TTTTC TTTTC T-TTTC TTTTC
907851 ATTATTTTTC
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.06
5 34 0.55
6 12 0.19
7 12 0.19
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:907871 original size:10 final size:9
Alignment explanation
Indices: 907667--907871 Score: 109
Period size: 7 Copynumber: 24.9 Consensus size: 9
907657 TTTCTTTTTC
*
907667 TTTTTTCTT
1 TTTTTTCAT
907676 CTTTTTTCA-
1 -TTTTTTCAT
907685 -TTTTTCAT
1 TTTTTTCAT
907693 TTTTTT--T
1 TTTTTTCAT
*
907700 ATTTTTCAT
1 TTTTTTCAT
907709 TTTTTTCAT
1 TTTTTTCAT
907718 TTTTTTCA-
1 TTTTTTCAT
907726 -TTTTTCA-
1 TTTTTTCAT
907733 -TTTTTCA-
1 TTTTTTCAT
907740 -TTTTTCA-
1 TTTTTTCAT
907747 -TTTTTCA-
1 TTTTTTCAT
907754 -TTTTTCA-
1 TTTTTTCAT
907761 -TTTTTCA-
1 TTTTTTCAT
907768 -TTTTTCATTT
1 TTTTTTCA--T
907778 TTTTTTC-T
1 TTTTTTCAT
*
907786 TTTCTTCAT
1 TTTTTTCAT
907795 TTTTTTC--
1 TTTTTTCAT
* *
907802 TTTATTCTT
1 TTTTTTCAT
*
907811 TTCTTTTCTT
1 TT-TTTTCAT
907821 TTTTTTC--
1 TTTTTTCAT
907828 TTTTTTC--
1 TTTTTTCAT
* *
907835 TTTTCTCTT
1 TTTTTTCAT
907844 TTTTTTCAT
1 TTTTTTCAT
907853 TATTTTTCAT
1 T-TTTTTCAT
907863 TTTTCTTCA
1 TTTT-TTCA
907872 AGCGAAATAT
Statistics
Matches: 169, Mismatches: 10, Indels: 32
0.80 0.05 0.15
Matches are distributed among these distances:
7 81 0.48
8 7 0.04
9 47 0.28
10 28 0.17
11 6 0.04
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:915870 original size:25 final size:25
Alignment explanation
Indices: 915837--915892 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
915827 TTTCAATTCG
*
915837 ATCTGCTCTACTCTTCTGAATGTCA
1 ATCTCCTCTACTCTTCTGAATGTCA
915862 ATCTCCTCTACTCTTCTGAATGTCA
1 ATCTCCTCTACTCTTCTGAATGTCA
915887 ATCTCC
1 ATCTCC
915893 AATCCCTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.20, C:0.32, G:0.09, T:0.39
Consensus pattern (25 bp):
ATCTCCTCTACTCTTCTGAATGTCA
Found at i:929586 original size:108 final size:109
Alignment explanation
Indices: 929391--929590 Score: 273
Period size: 108 Copynumber: 1.8 Consensus size: 109
929381 TCAAATACTA
* *
929391 ATGTCTTAAGAGCGAATAATAAGTCTATTAACTACAAAGTCGTCGTAGTATAATGGTGAGTATTC
1 ATGTCTTAAGAGCGAATAATAAATCTATTAACTACAAAGTCGTCGCAGTATAATGGTGAGTATTC
*
929456 CCGCCTGTCACGCGAGTAACCTGGGTTCGATACCATTAACTAAT
66 CCACCTGTCACGCGAGTAACCTGGGTTCGATACCATTAACTAAT
* * *
929500 ATGTC-TAAGAGCGAATAATAAATCTATTAA-TAACAAAGTTGTTGCAGTATATTGGTGAGTATT
1 ATGTCTTAAGAGCGAATAATAAATCTATTAACT-ACAAAGTCGTCGCAGTATAATGGTGAGTATT
* *
929563 CCTA-CTCGTCACGC-AGGTGACCTGGGTT
65 CCCACCT-GTCACGCGA-GTAACCTGGGTT
929591 TGAACCCCGA
Statistics
Matches: 80, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
107 4 0.05
108 71 0.89
109 5 0.06
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.30
Consensus pattern (109 bp):
ATGTCTTAAGAGCGAATAATAAATCTATTAACTACAAAGTCGTCGCAGTATAATGGTGAGTATTC
CCACCTGTCACGCGAGTAACCTGGGTTCGATACCATTAACTAAT
Found at i:936987 original size:23 final size:23
Alignment explanation
Indices: 936969--937028 Score: 111
Period size: 23 Copynumber: 2.6 Consensus size: 23
936959 CTCGTATAAA
936969 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
936992 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTGCCCCGTAGAAT
*
937015 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
937029 ATATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.32, G:0.27, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCCCGTAGAAT
Found at i:943800 original size:23 final size:23
Alignment explanation
Indices: 943774--943818 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
943764 CACCACAGCT
*
943774 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
943797 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
943819 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:946927 original size:72 final size:71
Alignment explanation
Indices: 946843--946975 Score: 212
Period size: 72 Copynumber: 1.9 Consensus size: 71
946833 CGTTTTTCCA
* *
946843 ATAAAAGCCATTATAGATGGACCTATTGCAGCGTTTTTCAAAAAAACGCCACTATTATTGCGGCT
1 ATAAAAGCCATTATAGATGGACCTATCGCAGCGTTTGTCAAAAAAACGCCACTATTATTGCGGCT
946908 TTATTG
66 TTATTG
* * *
946914 ATAAAACGCCATTATAGATGGATCTATCGCGGCGTTTGTCAAAAAAACGCCACTATTGTTGC
1 ATAAAA-GCCATTATAGATGGACCTATCGCAGCGTTTGTCAAAAAAACGCCACTATTATTGC
946976 CCCGAAATCG
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
71 6 0.11
72 50 0.89
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (71 bp):
ATAAAAGCCATTATAGATGGACCTATCGCAGCGTTTGTCAAAAAAACGCCACTATTATTGCGGCT
TTATTG
Found at i:947016 original size:13 final size:14
Alignment explanation
Indices: 946986--947014 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
946976 CCCGAAATCG
946986 AATATATCTAGAAA
1 AATATATCTAGAAA
947000 AATATATCTAGAAA
1 AATATATCTAGAAA
947014 A
1 A
947015 TAGGGCCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.28
Consensus pattern (14 bp):
AATATATCTAGAAA
Found at i:949009 original size:34 final size:33
Alignment explanation
Indices: 948966--949033 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
948956 TTCATTTTAG
*
948966 TCATTATTTATTTATAGTTGCCCATTATTTTATT
1 TCATTATTTATTTATAATTGCCCATTA-TTTATT
*
949000 TCATTATTTATTTATAATTGGCCATTATTTATT
1 TCATTATTTATTTATAATTGCCCATTATTTATT
949033 T
1 T
949034 ATATTACTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.22
34 25 0.78
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.59
Consensus pattern (33 bp):
TCATTATTTATTTATAATTGCCCATTATTTATT
Found at i:952538 original size:17 final size:18
Alignment explanation
Indices: 952512--952545 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
952502 CGCGGTCGCG
952512 GAAGAAAGAA-AGAAGCA
1 GAAGAAAGAAGAGAAGCA
*
952529 GAAGAGAGAAGAGAAGC
1 GAAGAAAGAAGAGAAGC
952546 GAAAAGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.06, G:0.35, T:0.00
Consensus pattern (18 bp):
GAAGAAAGAAGAGAAGCA
Found at i:952706 original size:2 final size:2
Alignment explanation
Indices: 952699--952724 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
952689 CAATAAAATA
952699 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
952725 TAAGATGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:954968 original size:39 final size:39
Alignment explanation
Indices: 954914--954998 Score: 170
Period size: 39 Copynumber: 2.2 Consensus size: 39
954904 CTCCTGAAGA
954914 GAAAGATTCCCATCTATGGTTTTCAGAACCTGTGCACTT
1 GAAAGATTCCCATCTATGGTTTTCAGAACCTGTGCACTT
954953 GAAAGATTCCCATCTATGGTTTTCAGAACCTGTGCACTT
1 GAAAGATTCCCATCTATGGTTTTCAGAACCTGTGCACTT
954992 GAAAGAT
1 GAAAGAT
954999 CCACATTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (39 bp):
GAAAGATTCCCATCTATGGTTTTCAGAACCTGTGCACTT
Found at i:959108 original size:41 final size:41
Alignment explanation
Indices: 959051--959212 Score: 173
Period size: 41 Copynumber: 3.7 Consensus size: 41
959041 ATAATAGATA
*
959051 ATATTAATTTAAATATTTATCAAAATTAAATTTACTTTTAC
1 ATATTAATTTAAATATTTATAAAAATTAAATTTACTTTTAC
* **
959092 ATATTAACTTAAATATTTATAAAAATGGATAATAATAGGATTGGTTTTGA-
1 ATATTAATTTAAATATTTATAAAAAT---T-A-AAT----TTACTTTT-AC
*
959142 ATATTAATTTAAATATTTATCAAAATTAAATTTACTTTTAC
1 ATATTAATTTAAATATTTATAAAAATTAAATTTACTTTTAC
*
959183 ATATCAATTTAAATATTTATAAAAATTAAA
1 ATATTAATTTAAATATTTATAAAAATTAAA
959213 ATTATTAAAA
Statistics
Matches: 100, Mismatches: 10, Indels: 22
0.76 0.08 0.17
Matches are distributed among these distances:
40 1 0.01
41 58 0.58
44 1 0.01
45 4 0.04
46 4 0.04
47 1 0.01
50 30 0.30
51 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (41 bp):
ATATTAATTTAAATATTTATAAAAATTAAATTTACTTTTAC
Found at i:959917 original size:34 final size:35
Alignment explanation
Indices: 959850--959926 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
959840 AAAGGAGAAT
* *
959850 GGGAGGGGGGGACTATGGATGAGAATGAGGGGGA-A
1 GGGA-GGGGGGACAATGGATGAGAAGGAGGGGGAGA
*
959885 GAGGAGGGGGGACAATGGGTGAGAAGGA-GGGGAGA
1 G-GGAGGGGGGACAATGGATGAGAAGGAGGGGGAGA
959920 GGGAGGG
1 GGGAGGG
959927 AGAAGGGATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
34 11 0.30
35 23 0.62
36 3 0.08
ACGTcount: A:0.29, C:0.03, G:0.61, T:0.08
Consensus pattern (35 bp):
GGGAGGGGGGACAATGGATGAGAAGGAGGGGGAGA
Found at i:961572 original size:32 final size:31
Alignment explanation
Indices: 961467--961607 Score: 144
Period size: 31 Copynumber: 4.5 Consensus size: 31
961457 TAATGGTAAA
* *
961467 ATTTTGAATAAATTTAATTGTTATTTTGTAAT
1 ATTTT-AATAAATTTAATTATTATTTTATAAT
* * * * *
961499 ATTTTGATAAGTCT-ATTGATTGTTTTGTAAT
1 ATTTTAATAAATTTAATT-ATTATTTTATAAT
*
961530 ATTTTGATAAATATTAATTATTATTTTATAAT
1 ATTTTAATAAAT-TTAATTATTATTTTATAAT
* *
961562 ATTTTAATAAATATAATTATTTTTTTATAAT
1 ATTTTAATAAATTTAATTATTATTTTATAAT
961593 A-TTTAA-AAATTTAAT
1 ATTTTAATAAATTTAAT
961608 GACCAAAATG
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.09
30 8 0.09
31 46 0.49
32 28 0.30
33 3 0.03
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (31 bp):
ATTTTAATAAATTTAATTATTATTTTATAAT
Found at i:961593 original size:63 final size:63
Alignment explanation
Indices: 961467--961607 Score: 166
Period size: 63 Copynumber: 2.3 Consensus size: 63
961457 TAATGGTAAA
* * * * * *
961467 ATTTTGAATAAATTTAATTGTTATTTTGTAATATTTTGATAAGTCTATTGATTGTTTTGTAAT
1 ATTTTGAATAAATTTAATTATTATTTTATAATATTTTAATAAATATATTGATTGTTTTATAAT
*
961530 ATTTTG-ATAAATATTAATTATTATTTTATAATATTTTAATAAATATAATT-ATTTTTTTATAAT
1 ATTTTGAATAAAT-TTAATTATTATTTTATAATATTTTAATAAATAT-ATTGATTGTTTTATAAT
961593 A-TTT-AA-AAATTTAAT
1 ATTTTGAATAAATTTAAT
961608 GACCAAAATG
Statistics
Matches: 68, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
60 5 0.07
61 4 0.06
62 10 0.15
63 46 0.68
64 3 0.04
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (63 bp):
ATTTTGAATAAATTTAATTATTATTTTATAATATTTTAATAAATATATTGATTGTTTTATAAT
Found at i:961807 original size:12 final size:11
Alignment explanation
Indices: 961788--961822 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
961778 CTAAATATTC
961788 ATTATTTTTAA
1 ATTATTTTTAA
961799 ATCTATTTTTAA
1 AT-TATTTTTAA
*
961811 ATTTTTTTTAA
1 ATTATTTTTAA
961822 A
1 A
961823 AAAATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTTTTAA
Found at i:961818 original size:11 final size:12
Alignment explanation
Indices: 961790--961822 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
961780 AAATATTCAT
961790 TATTTTTAAATC
1 TATTTTTAAATC
961802 TATTTTTAAAT-
1 TATTTTTAAATC
*
961813 TTTTTTTAAA
1 TATTTTTAAA
961823 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (12 bp):
TATTTTTAAATC
Found at i:962618 original size:23 final size:23
Alignment explanation
Indices: 962601--962716 Score: 160
Period size: 23 Copynumber: 5.0 Consensus size: 23
962591 CTAAATAAAT
962601 ATGTTCACGAATGTTAAACGAAC
1 ATGTTCACGAATGTTAAACGAAC
962624 ATGTTCACGAATGTTAAACGAAC
1 ATGTTCACGAATGTTAAACGAAC
* *
962647 ATGTTCATGGATGTTAAACGAAC
1 ATGTTCACGAATGTTAAACGAAC
* *
962670 ATGTTCACGAACGTTAAATGAAC
1 ATGTTCACGAATGTTAAACGAAC
** * *
962693 ATGTTCGTGAATGCTAAATGAAC
1 ATGTTCACGAATGTTAAACGAAC
962716 A
1 A
962717 AACACGAACA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (23 bp):
ATGTTCACGAATGTTAAACGAAC
Found at i:964804 original size:27 final size:27
Alignment explanation
Indices: 964774--964856 Score: 114
Period size: 29 Copynumber: 3.0 Consensus size: 27
964764 TTTAGAGTCC
964774 GGATTTTTTGTGATTTTTAGAAATTTA
1 GGATTTTTTGTGATTTTTAGAAATTTA
964801 GGATTTTTTTTGTGATTTTTAGAAATTTA
1 GGA--TTTTTTGTGATTTTTAGAAATTTA
* *
964830 GGATTTATT-TGAATTTTATGAAATTTA
1 GGATTTTTTGTGATTTTTA-GAAATTTA
964857 AGGTGTTTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.16
27 16 0.31
29 27 0.53
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (27 bp):
GGATTTTTTGTGATTTTTAGAAATTTA
Found at i:964809 original size:29 final size:29
Alignment explanation
Indices: 964777--964835 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
964767 AGAGTCCGGA
964777 TTTTTTGTGATTTTTAGAAATTTAGGATT
1 TTTTTTGTGATTTTTAGAAATTTAGGATT
964806 TTTTTTGTGATTTTTAGAAATTTAGGATT
1 TTTTTTGTGATTTTTAGAAATTTAGGATT
964835 T
1 T
964836 ATTTGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.17, T:0.59
Consensus pattern (29 bp):
TTTTTTGTGATTTTTAGAAATTTAGGATT
Found at i:966020 original size:23 final size:23
Alignment explanation
Indices: 965977--966020 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
965967 TTTAATTTAA
* *
965977 TAAAAAGATAAAAATTCAATAGT
1 TAAAAAGAGAAAAATTAAATAGT
966000 TAAAAAGAGATAAAA-TAAATA
1 TAAAAAGAGA-AAAATTAAATA
966021 AATTTAATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.66, C:0.02, G:0.09, T:0.23
Consensus pattern (23 bp):
TAAAAAGAGAAAAATTAAATAGT
Found at i:966843 original size:3 final size:3
Alignment explanation
Indices: 966835--966879 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
966825 TTTAGATATA
966835 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
966880 TTAAAAGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:967526 original size:15 final size:15
Alignment explanation
Indices: 967506--967545 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
967496 CCTTTGCCCC
*
967506 AAACCCTAAACTTCT
1 AAACCCTAAACTCCT
967521 AAACCCCTAAACTCCT
1 AAA-CCCTAAACTCCT
967537 -AACCCTAAA
1 AAACCCTAAA
967546 TTTAATGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 7 0.30
15 5 0.22
16 11 0.48
ACGTcount: A:0.42, C:0.38, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTAAACTCCT
Found at i:967706 original size:19 final size:20
Alignment explanation
Indices: 967660--967707 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
967650 GGGGAGGAGA
*
967660 ATTTTTTTTTATAAAAAAAT
1 ATTTTTTTTCATAAAAAAAT
** *
967680 ATAATTTTTCA-ATAAAAAT
1 ATTTTTTTTCATAAAAAAAT
967699 ATTTTTTTT
1 ATTTTTTTT
967708 TTAAAGAAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTTTTTCATAAAAAAAT
Found at i:967736 original size:19 final size:18
Alignment explanation
Indices: 967674--967743 Score: 52
Period size: 19 Copynumber: 3.7 Consensus size: 18
967664 TTTTTTATAA
967674 AAAAATATAATTTTTCAAT
1 AAAAATATAATTTTT-AAT
**
967693 AAAAATATTTTTTTTTTAA-
1 AAAAATA--TAATTTTTAAT
* *
967712 AGAAATATAGGTTTTTAAT
1 AAAAATATA-ATTTTTAAT
*
967731 AAAAATATTATTT
1 AAAAATATAATTT
967744 ATATTTTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 10 0.26
19 20 0.51
20 2 0.05
21 6 0.15
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (18 bp):
AAAAATATAATTTTTAAT
Found at i:968541 original size:7 final size:7
Alignment explanation
Indices: 968531--968555 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
968521 ATCAAAACTG
968531 AAAATTT
1 AAAATTT
968538 AAAATTT
1 AAAATTT
968545 AAAATTT
1 AAAATTT
968552 AAAA
1 AAAA
968556 AATAAATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (7 bp):
AAAATTT
Found at i:980489 original size:36 final size:36
Alignment explanation
Indices: 980448--980523 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
980438 ATTTTCGGGA
*
980448 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
980484 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
980520 TTTT
1 TTTT
980524 TTTAGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:980967 original size:15 final size:15
Alignment explanation
Indices: 980947--980976 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
980937 TATCACAATC
980947 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
980962 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
980977 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:985494 original size:36 final size:36
Alignment explanation
Indices: 985453--985528 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
985443 ATTTTCGGGA
*
985453 TTTTGCTATTTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
985489 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
985525 TTTT
1 TTTT
985529 TTTAGCTATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTTGCTATTTTTGGCAAAATTCGAATAAAGACGAT
Found at i:985975 original size:24 final size:23
Alignment explanation
Indices: 985938--986005 Score: 70
Period size: 22 Copynumber: 2.9 Consensus size: 23
985928 CATTTTCATC
985938 AAAATATTAATTATTAAAATATTTA-
1 AAAATA-TAATTATT--AATATTTAT
*
985963 AAAATATATTTATTAATATTTAT
1 AAAATATAATTATTAATATTTAT
985986 AATAATATAA-TATT-ATATTT
1 AA-AATATAATTATTAATATTT
986006 TTAATATTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
22 14 0.36
23 6 0.15
24 13 0.33
25 6 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATAATTATTAATATTTAT
Found at i:986003 original size:22 final size:24
Alignment explanation
Indices: 985955--986018 Score: 73
Period size: 22 Copynumber: 2.8 Consensus size: 24
985945 TAATTATTAA
*
985955 AATATTTA-AA-AATATATTTATT
1 AATATTTATAATAATATATATATT
985977 AATATTTATAATAATATA-ATATT
1 AATATTTATAATAATATATATATT
* *
986000 -ATATTTTTAATATTATATA
1 AATATTTATAATAATATATA
986019 AAATAATCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 23 0.64
23 7 0.19
24 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTTATAATAATATATATATT
Found at i:986012 original size:31 final size:31
Alignment explanation
Indices: 985967--986115 Score: 94
Period size: 31 Copynumber: 5.1 Consensus size: 31
985957 TATTTAAAAA
985967 TATATTTATTAATATTTATAATAATATAATAT
1 TATATTT-TTAATATTTATAATAATATAATAT
*
985999 TATATTTTTAATA-TTAT-ATAAAAT-A-AT
1 TATATTTTTAATATTTATAATAATATAATAT
*
986026 CA-A---TT-ATA-TTATAATAATATAAGATAT
1 TATATTTTTAATATTTATAATAATAT-A-ATAT
986053 TATATTTTT-AT-TTTAATAAT-ATATAATA-
1 TATATTTTTAATATTT-ATAATAATATAATAT
* * *
986081 AATTTTTTTATATATTTAATAATGA-ATAATAT
1 TATATTTTTA-ATATTT-ATAATAATATAATAT
986113 TAT
1 TAT
986116 TTATATATTT
Statistics
Matches: 94, Mismatches: 7, Indels: 32
0.71 0.05 0.24
Matches are distributed among these distances:
22 7 0.07
23 8 0.09
26 2 0.02
27 6 0.06
28 9 0.10
29 9 0.10
30 7 0.07
31 31 0.33
32 15 0.16
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
TATATTTTTAATATTTATAATAATATAATAT
Found at i:986079 original size:54 final size:52
Alignment explanation
Indices: 985982--986084 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 52
985972 TTATTAATAT
*
985982 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
*
986034 TTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATT
1 TTATAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATAAATT
986085 TTTTTATATA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
52 16 0.36
53 7 0.16
54 22 0.49
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.50
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTTAATATTATATAAAATAATAAATTATA
Found at i:986368 original size:20 final size:20
Alignment explanation
Indices: 986290--986359 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
986280 TTTCCAGATG
986290 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
986310 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
986330 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
986350 TTTTCCAGAA
1 TTTTCCAGAA
986360 TTCAAATTCC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:986368 original size:40 final size:40
Alignment explanation
Indices: 986290--986368 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
986280 TTTCCAGATG
* **
986290 TTTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
*
986330 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTC
986369 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAGAAATCAAATTCA
Found at i:986378 original size:15 final size:15
Alignment explanation
Indices: 986342--986423 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
986332 TTACAGAAAT
**
986342 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
986357 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
986371 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
986386 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
986401 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
986416 GTAATTCA
1 GTAATTCA
986424 TTTTCTGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:986394 original size:30 final size:30
Alignment explanation
Indices: 986342--986423 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
986332 TTACAGAAAT
986342 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
986371 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
986401 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
986424 TTTTCTGGAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:986416 original size:45 final size:44
Alignment explanation
Indices: 986342--986428 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
986332 TTACAGAAAT
**
986342 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
986386 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTCATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
986429 TGGAAAACCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:997141 original size:4 final size:4
Alignment explanation
Indices: 997134--997158 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
997124 AAAAAAAAAA
997134 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
997159 TGTTCTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:1005040 original size:20 final size:20
Alignment explanation
Indices: 1005015--1005054 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1005005 AAAAGATATG
* *
1005015 GAATACATACGCCAAGCTCT
1 GAATACACACACCAAGCTCT
1005035 GAATACACACACCAAGCTCT
1 GAATACACACACCAAGCTCT
1005055 TCCTTGCTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.33, G:0.12, T:0.17
Consensus pattern (20 bp):
GAATACACACACCAAGCTCT
Found at i:1007514 original size:20 final size:21
Alignment explanation
Indices: 1007475--1007514 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
1007465 ACGGAGTTCT
*
1007475 ATTTTATATAAATGTTTTATA
1 ATTTTATATAAATGTCTTATA
*
1007496 ATTTT-TATTAATGTCTTAT
1 ATTTTATATAAATGTCTTAT
1007515 TTTGATAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTTTATATAAATGTCTTATA
Found at i:1011216 original size:13 final size:13
Alignment explanation
Indices: 1011198--1011223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1011188 ACCAAATAAG
1011198 ATATATATATATA
1 ATATATATATATA
1011211 ATATATATATATA
1 ATATATATATATA
1011224 TAGTTCTTCA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATATATATA
Found at i:1011216 original size:15 final size:15
Alignment explanation
Indices: 1011193--1011225 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1011183 CTCTAACCAA
1011193 ATAAGATATATATAT
1 ATAAGATATATATAT
*
1011208 ATAATATATATATAT
1 ATAAGATATATATAT
1011223 ATA
1 ATA
1011226 GTTCTTCATA
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:0.00, G:0.03, T:0.42
Consensus pattern (15 bp):
ATAAGATATATATAT
Found at i:1017616 original size:28 final size:27
Alignment explanation
Indices: 1017574--1017630 Score: 96
Period size: 28 Copynumber: 2.1 Consensus size: 27
1017564 GAATAGTAGT
1017574 TTAGACTCTTAATTTTTATATTTATAA
1 TTAGACTCTTAATTTTTATATTTATAA
*
1017601 TTAGACTCCTTAATTTTTATGTTTATAA
1 TTAGACT-CTTAATTTTTATATTTATAA
1017629 TT
1 TT
1017631 GGGATTTCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (27 bp):
TTAGACTCTTAATTTTTATATTTATAA
Found at i:1019108 original size:64 final size:64
Alignment explanation
Indices: 1018992--1019132 Score: 164
Period size: 64 Copynumber: 2.2 Consensus size: 64
1018982 CACATTGAAT
* * *
1018992 GTGCATCGATGCA-CTCTTTAAAGAAGAATCATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCATCCCTTAAAAGAAGAATCATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * *
1019055 GTGCATCGATGCATCCCCTTAAAATGAA-AA-CATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 GTGCATCGATGCAT-CCCTTAAAA-GAAGAATCATCGAAGGCAATTGGTGCATCGATGCATAGGT
1019118 A
64 A
1019119 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1019133 TATTCAATGC
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
63 15 0.22
64 40 0.60
65 9 0.13
66 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (64 bp):
GTGCATCGATGCATCCCTTAAAAGAAGAATCATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:1019195 original size:19 final size:19
Alignment explanation
Indices: 1019152--1019266 Score: 221
Period size: 19 Copynumber: 6.0 Consensus size: 19
1019142 CACATGTTAA
1019152 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACT-T
1019172 AGAATGCATCGATGCACTT
1 AGAATGCATCGATGCACTT
1019191 AGAATGCATCGATGCACTT
1 AGAATGCATCGATGCACTT
1019210 AGAATGCATCGATGCACTT
1 AGAATGCATCGATGCACTT
1019229 AGAATGCATCGATGCACTT
1 AGAATGCATCGATGCACTT
1019248 AGAATGCATCGATGCACTT
1 AGAATGCATCGATGCACTT
1019267 CAAGGGGAAA
Statistics
Matches: 95, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
19 77 0.81
20 18 0.19
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (19 bp):
AGAATGCATCGATGCACTT
Found at i:1020340 original size:64 final size:63
Alignment explanation
Indices: 1020255--1020395 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 63
1020245 TTGTTTAAGG
* * *
1020255 TGCATCGATGCACATGCAGTGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * *
1020319 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
1020383 TGCATCGATGCAT
1 TGCATCGATGCAT
1020396 GGTGTAGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 61 0.90
65 6 0.09
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:1020768 original size:18 final size:18
Alignment explanation
Indices: 1020733--1020768 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1020723 AAAATGGGTA
* *
1020733 CATATGTTATATGTATTG
1 CATATGTTACATGAATTG
1020751 CATATGTTACATGAATTG
1 CATATGTTACATGAATTG
1020769 AATGAATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (18 bp):
CATATGTTACATGAATTG
Found at i:1021781 original size:22 final size:18
Alignment explanation
Indices: 1021745--1021807 Score: 81
Period size: 18 Copynumber: 3.3 Consensus size: 18
1021735 AGTAGTCATT
1021745 CGGGACATAGTGGTCCTA
1 CGGGACATAGTGGTCCTA
*
1021763 CGGGACGTATACAGTGGTCCTT
1 CGGGAC--AT--AGTGGTCCTA
1021785 CGGGACATAGTGGTCCTA
1 CGGGACATAGTGGTCCTA
1021803 CGGGA
1 CGGGA
1021808 TGAATACTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
18 20 0.51
20 4 0.10
22 15 0.38
ACGTcount: A:0.21, C:0.22, G:0.35, T:0.22
Consensus pattern (18 bp):
CGGGACATAGTGGTCCTA
Found at i:1023065 original size:18 final size:18
Alignment explanation
Indices: 1023021--1023114 Score: 107
Period size: 18 Copynumber: 5.0 Consensus size: 18
1023011 GAGGGATTTT
*
1023021 CAGTGGTCCTTCGGGATAAA
1 CAGTGGTCCTTCGGG--ACA
1023041 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
* * *
1023059 TAGTGGTTCTTCGGAACAA
1 CAGTGGTCCTTCGGGAC-A
1023078 CCAGTGGTCCTTCGGGACA
1 -CAGTGGTCCTTCGGGACA
*
1023097 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
1023115 AATATTCAGT
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
18 33 0.52
19 2 0.03
20 29 0.45
ACGTcount: A:0.20, C:0.23, G:0.31, T:0.26
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:1023083 original size:38 final size:38
Alignment explanation
Indices: 1023022--1023116 Score: 154
Period size: 38 Copynumber: 2.5 Consensus size: 38
1023012 AGGGATTTTC
*
1023022 AGTGGTCCTTCGGGATAAACAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
* * *
1023060 AGTGGTTCTTCGGAACAACCAGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
1023098 AGTGGTCCTTCGGGACAAA
1 AGTGGTCCTTCGGGACAAA
1023117 TATTCAGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 50 1.00
ACGTcount: A:0.22, C:0.22, G:0.31, T:0.25
Consensus pattern (38 bp):
AGTGGTCCTTCGGGACAAACAGTGGTCCTTCGGGACAT
Found at i:1024676 original size:11 final size:11
Alignment explanation
Indices: 1024660--1024686 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1024650 CATCCGTCTC
1024660 AAAAAAATAAT
1 AAAAAAATAAT
1024671 AAAAAAATAAT
1 AAAAAAATAAT
1024682 AAAAA
1 AAAAA
1024687 GAATTAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:1025439 original size:21 final size:21
Alignment explanation
Indices: 1025324--1025439 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
1025314 GCGAAATAAA
**
1025324 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
1025344 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
1025364 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
1025385 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
1025405 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
1025427 AATCGCAACGCGA
1 AATCGCAACGCGA
1025440 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:1025452 original size:20 final size:20
Alignment explanation
Indices: 1025427--1025579 Score: 200
Period size: 20 Copynumber: 7.6 Consensus size: 20
1025417 GATTTTCCAG
* ** *
1025427 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
1025447 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1025467 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1025487 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1025507 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1025527 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1025547 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
1025568 AATCGCAACGCG
1 AATCGCAACGCG
1025580 ATTTTTAAAG
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
20 106 0.90
21 12 0.10
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1025993 original size:33 final size:33
Alignment explanation
Indices: 1025954--1026024 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1025944 TTCACTTAGA
1025954 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1025987 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1026020 TTTCA
1 TTTCA
1026025 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1026151 original size:21 final size:20
Alignment explanation
Indices: 1026104--1026175 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
1026094 TGTAGAAGAG
* **
1026104 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
1026124 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
*
1026146 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1026165 TCGCAACGAGA
1 TCGCAACGAGA
1026176 GAATCGCAAC
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 18 0.41
20 2 0.05
21 14 0.32
22 10 0.23
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1026220 original size:19 final size:19
Alignment explanation
Indices: 1026198--1026325 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
1026188 GAAACCAAAA
*
1026198 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1026217 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1026231 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1026250 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1026264 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1026284 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
1026304 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1026324 TC
1 TC
1026326 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1026239 original size:14 final size:14
Alignment explanation
Indices: 1026220--1026276 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1026210 TTTCATTTCG
1026220 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1026234 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1026253 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1026267 CGTTGCGATT
1 CGTTGCGATT
1026277 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1026245 original size:33 final size:33
Alignment explanation
Indices: 1026203--1026325 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
1026193 CAAAATCGCA
1026203 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1026236 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1026269 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
1026310 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1026326 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1026287 original size:21 final size:21
Alignment explanation
Indices: 1026261--1026325 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
1026251 CGCGTTGCGA
1026261 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1026282 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1026302 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
1026323 TTC
1 TTC
1026326 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1028169 original size:93 final size:93
Alignment explanation
Indices: 1028010--1028325 Score: 614
Period size: 93 Copynumber: 3.4 Consensus size: 93
1028000 TAGATTGCTT
*
1028010 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1028075 TTTGTCTTTGTTTTATCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1028103 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1028168 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1028196 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1028261 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1028289 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1028326 AATACCATGA
Statistics
Matches: 221, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 221 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.45
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1028460 original size:14 final size:14
Alignment explanation
Indices: 1028441--1028497 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1028431 CGAAACTTAA
1028441 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1028455 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
1028474 AATCGCAACGACAG
1 AATCGCAACGAGAG
1028488 AATCGCAACG
1 AATCGCAACG
1028498 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1028479 original size:19 final size:18
Alignment explanation
Indices: 1028455--1028516 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
1028445 GCAACGAGAG
1028455 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAA-GAA
*
1028474 AATCGCAA--CGACAG--
1 AATCGCAACGCGAAAGAA
*
1028488 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAA-GAA
1028507 AATCGCAACG
1 AATCGCAACG
1028517 ACAAAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.23
16 5 0.14
17 4 0.11
19 18 0.51
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.08
Consensus pattern (18 bp):
AATCGCAACGCGAAAGAA
Found at i:1028481 original size:33 final size:33
Alignment explanation
Indices: 1028423--1028530 Score: 153
Period size: 33 Copynumber: 3.2 Consensus size: 33
1028413 TAGTTTACTT
* * *
1028423 TCGCAACACGAAACTTAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAA-TCAAAATCGCAACGACAGAA
*
1028457 TCGCAACGCGAAATGAAAATCGCAACGACAGAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
* *
1028490 TCGCAACGCGAAACCAAAATCGCAACGACAAAA
1 TCGCAACGCGAAATCAAAATCGCAACGACAGAA
1028523 TCGCAACG
1 TCGCAACG
1028531 ACAAAATCGC
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 56 0.82
34 12 0.18
ACGTcount: A:0.45, C:0.27, G:0.19, T:0.09
Consensus pattern (33 bp):
TCGCAACGCGAAATCAAAATCGCAACGACAGAA
Found at i:1028523 original size:14 final size:14
Alignment explanation
Indices: 1028472--1028544 Score: 92
Period size: 14 Copynumber: 4.9 Consensus size: 14
1028462 ACGCGAAATG
1028472 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1028486 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
1028505 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1028519 AAAATCGCAACGAC
1 AAAATCGCAACGAC
1028533 AAAATCGCAACG
1 AAAATCGCAACG
1028545 CGAAACCAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
14 36 0.69
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 10 0.19
ACGTcount: A:0.48, C:0.29, G:0.16, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1028578 original size:19 final size:19
Alignment explanation
Indices: 1028556--1028728 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
1028546 GAAACCAAAA
* *
1028556 TCGCATTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
1028575 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1028589 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1028608 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1028624 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1028641 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
1028660 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
1028679 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
1028698 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1028718 TCGTGTTGCGA
1 TCGCGTTGCGA
1028729 AAGTAAACTA
Statistics
Matches: 125, Mismatches: 18, Indels: 21
0.76 0.11 0.13
Matches are distributed among these distances:
14 17 0.14
16 8 0.06
17 7 0.06
19 81 0.65
20 12 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1028597 original size:14 final size:14
Alignment explanation
Indices: 1028578--1028634 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1028568 TTTTATTTCG
1028578 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1028592 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TCT
*
1028609 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTCT
1028625 CGTTGCGATT
1 CGTTGCGATT
1028635 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1028686 original size:38 final size:38
Alignment explanation
Indices: 1028556--1028728 Score: 159
Period size: 33 Copynumber: 4.8 Consensus size: 38
1028546 GAAACCAAAA
* *
1028556 TCGCATTGCGATTTTTATTTCGCGTTGCGATTCTC---
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1028591 T--CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TG
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* **
1028624 T--CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
** *
1028660 TCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
* *
1028698 TCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCGTTGCGATTTTCA-TTTCGCGTTGCGA
1028729 AAGTAAACTA
Statistics
Matches: 114, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
31 2 0.02
32 1 0.01
33 51 0.45
34 1 0.01
35 2 0.02
36 2 0.02
38 44 0.39
39 11 0.10
ACGTcount: A:0.10, C:0.20, G:0.24, T:0.46
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCATT
Found at i:1030671 original size:14 final size:14
Alignment explanation
Indices: 1030652--1030687 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1030642 ATTGTTTAAT
1030652 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1030666 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1030680 TGATTTGT
1 TGATTTGT
1030688 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1030870 original size:20 final size:19
Alignment explanation
Indices: 1030794--1030892 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
1030784 AAAAATGACT
1030794 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1030813 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1030832 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1030846 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1030866 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1030886 ATCGCAA
1 ATCGCAA
1030893 CGAGAGAATC
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 3 0.04
19 27 0.38
20 30 0.42
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1030896 original size:54 final size:53
Alignment explanation
Indices: 1030794--1030910 Score: 218
Period size: 54 Copynumber: 2.2 Consensus size: 53
1030784 AAAAATGACT
1030794 ATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1030846 ATCGCAATGCGGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1030900 ATCGCAATGCG
1 ATCGCAATGCG
1030911 ATTTTCATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 10 0.16
53 19 0.30
54 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1031072 original size:105 final size:109
Alignment explanation
Indices: 1030907--1031176 Score: 425
Period size: 105 Copynumber: 2.6 Consensus size: 109
1030897 AGAATCGCAA
*
1030907 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGTGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1030972 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
1031012 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
1031077 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
1031123 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
1031177 GTAATTTCCG
Statistics
Matches: 156, Mismatches: 3, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 121 0.78
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:1031144 original size:72 final size:72
Alignment explanation
Indices: 1030929--1031162 Score: 288
Period size: 72 Copynumber: 3.3 Consensus size: 72
1030919 TTCGCATTGC
* *
1030929 GATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGTGATTTTCATTT-CGCATTGCGATTTT
1 GATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTT
*
1030988 CAT-TTCG
65 CATGTTGG
* * * * *
1030995 CA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 GATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTT
*
1031059 TC-TCGTTGC
64 TCAT-GTTGG
1031068 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1031133 ATGTTGG
66 ATGTTGG
1031140 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
1031163 CTCTCGTTGC
Statistics
Matches: 141, Mismatches: 15, Indels: 18
0.81 0.09 0.10
Matches are distributed among these distances:
65 3 0.02
66 12 0.09
67 1 0.01
68 3 0.02
69 4 0.03
71 15 0.11
72 93 0.66
73 7 0.05
74 3 0.02
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (72 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
ATGTTGG
Found at i:1031191 original size:53 final size:52
Alignment explanation
Indices: 1030907--1031176 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
1030897 AGAATCGCAA
1030907 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1030960 TGTGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1031012 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
1031065 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
1031123 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1031170 TGCGATT
1 TGCGATT
1031177 GTAATTTCCG
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 61 0.30
53 108 0.53
54 3 0.01
55 3 0.01
56 3 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1033478 original size:12 final size:12
Alignment explanation
Indices: 1033461--1033485 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1033451 TCTTCGGGGA
1033461 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1033473 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1033485 C
1 C
1033486 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:1034427 original size:20 final size:20
Alignment explanation
Indices: 1034399--1034490 Score: 130
Period size: 20 Copynumber: 4.6 Consensus size: 20
1034389 AAATTTCAGT
* * *
1034399 GTTGTGATTTACAAATTCTC
1 GTTGCGATTTACAGATTATC
*
1034419 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
*
1034439 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
*
1034459 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
1034479 GTTGCGATTTAC
1 GTTGCGATTTAC
1034491 GGATACGCGT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:1034491 original size:20 final size:20
Alignment explanation
Indices: 1034416--1034589 Score: 217
Period size: 20 Copynumber: 8.7 Consensus size: 20
1034406 TTTACAAATT
1034416 CTCGTTGCGATTTACGGATTA
1 CTCGTTGCGATTTACGGA-TA
* *
1034437 -TCGTTGCGATTTACAGATT
1 CTCGTTGCGATTTACGGATA
1034456 CTCGTTGCGATTTACGGATTA
1 CTCGTTGCGATTTACGGA-TA
1034477 -TCGTTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* *
1034496 CGCGTTGCGATATACGGATA
1 CTCGTTGCGATTTACGGATA
* *
1034516 CGCATTGCGATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* *
1034536 CGCGTTGCTATTTACGGATA
1 CTCGTTGCGATTTACGGATA
* *
1034556 CACGTTGCGGTTTACGGATA
1 CTCGTTGCGATTTACGGATA
*
1034576 CGCGTTGCGATTTA
1 CTCGTTGCGATTTA
1034590 TGTGTTCGCG
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
19 3 0.02
20 131 0.97
21 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
CTCGTTGCGATTTACGGATA
Found at i:1034502 original size:60 final size:60
Alignment explanation
Indices: 1034418--1034667 Score: 229
Period size: 60 Copynumber: 4.2 Consensus size: 60
1034408 TACAAATTCT
* * * *
1034418 CGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTAT
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATTAG
* * *
1034478 CGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACGGA-TACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATTA-G
* * * * * *
1034538 CGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACAGATACGCGTTGCGATTTACG-GATTAG
* * * * * * * ** *
1034598 CGTTGCGATTTATGTG-TTCGCGTTGCGATTTTCATATTCGTGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACG-GATACGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATTAG
1034658 CGTTGCGATT
1 CGTTGCGATT
1034668 CTTGAAAATC
Statistics
Matches: 156, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
59 4 0.03
60 149 0.96
61 3 0.02
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACAGATACGCGTTGCGATTTACGGATTAG
Found at i:1034599 original size:20 final size:20
Alignment explanation
Indices: 1034576--1034667 Score: 107
Period size: 20 Copynumber: 4.6 Consensus size: 20
1034566 TTTACGGATA
* *
1034576 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
* *
1034596 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
1034616 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
*
1034636 CGTGTTGCGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
1034656 CGCGTTGCGATT
1 CGCGTTGCGATT
1034668 CTTGAAAATC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 1 0.01
20 66 0.99
ACGTcount: A:0.12, C:0.17, G:0.26, T:0.45
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:1034602 original size:40 final size:40
Alignment explanation
Indices: 1034418--1034628 Score: 232
Period size: 40 Copynumber: 5.3 Consensus size: 40
1034408 TACAAATTCT
* * * *
1034418 CGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
*
1034458 CGTTGCGATTTACGGATTA-TCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACG
* *
1034498 CGTTGCGATATACGGATACGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
* * *
1034538 CGTTGCTATTTACGGATACACGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
* * * *
1034578 CGTTGCGATTTATGTG-TTCGCGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACGCGTTGCGATTTACG-GATACG
1034618 CGTTGCGATTT
1 CGTTGCGATTT
1034629 TCATATTCGT
Statistics
Matches: 150, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
39 2 0.01
40 146 0.97
41 2 0.01
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACG
Found at i:1035047 original size:23 final size:21
Alignment explanation
Indices: 1034990--1035051 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 21
1034980 ATTCAAAACC
* *
1034990 TAATATTAAATAATTACTGTTAT
1 TAATATAAAATAA-TAAT-TTAT
1035013 TAATATAAAATAATAATTTAT
1 TAATATAAAATAATAATTTAT
*
1035034 TTATGATAAGAATAATAA
1 TAAT-ATAA-AATAATAA
1035052 GAATACAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.21
22 7 0.21
23 20 0.59
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (21 bp):
TAATATAAAATAATAATTTAT
Found at i:1035808 original size:2 final size:2
Alignment explanation
Indices: 1035740--1035789 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1035730 ACTTGACAGC
1035740 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1035782 AT AT AT AT
1 AT AT AT AT
1035790 GTTAATGTAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1047964 original size:2 final size:2
Alignment explanation
Indices: 1047957--1047982 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1047947 AAATGGAATG
1047957 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1047983 TAGTTTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1052222 original size:30 final size:28
Alignment explanation
Indices: 1052160--1052235 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
1052150 CACTGCTAAG
1052160 GGTGTTAGATCGGGAAATATAGTCTGACC
1 GGTGTTAGATCGGGAAATATAGTC-GACC
*
1052189 GGTGTTAGATCGGTAAATATACCGGTC-ACC
1 GGTGTTAGATCGGGAAATATA---GTCGACC
* *
1052219 GGTGATATATCGGGAAA
1 GGTGTTAGATCGGGAAA
1052236 AACACCTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.50
30 17 0.43
32 3 0.08
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.26
Consensus pattern (28 bp):
GGTGTTAGATCGGGAAATATAGTCGACC
Found at i:1054534 original size:21 final size:20
Alignment explanation
Indices: 1054502--1054541 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1054492 TACATAATAA
1054502 TTTTTAAAAAATGATCGATT
1 TTTTTAAAAAATGATCGATT
*
1054522 TTTTTATATAAATGATCGAT
1 TTTTTA-AAAAATGATCGAT
1054542 CCCTAATAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (20 bp):
TTTTTAAAAAATGATCGATT
Found at i:1055148 original size:2 final size:2
Alignment explanation
Indices: 1055141--1055209 Score: 138
Period size: 2 Copynumber: 34.5 Consensus size: 2
1055131 GAACTAGTTT
1055141 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1055183 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1055210 TGAATTCTAT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1056337 original size:60 final size:60
Alignment explanation
Indices: 1056271--1056388 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
1056261 ATAGTCAGAT
* * *
1056271 GACCATTTTGTAACTTTTAATAGTTGATG-GACTCAATAAAGCAACACCCTATAGTCGGGG
1 GACCATTTTGTAACTTTTAATAGTTGA-GAGAATCAATAAAACAACACCCTATAATCGGGG
* *
1056331 GACCATTTTGTAACTTTTAATAGTTGAGAGAATCAATAAAACAATATCCTATAATCGG
1 GACCATTTTGTAACTTTTAATAGTTGAGAGAATCAATAAAACAACACCCTATAATCGG
1056389 AAGATCATTT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
59 1 0.02
60 51 0.98
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTTGAGAGAATCAATAAAACAACACCCTATAATCGGGG
Found at i:1056398 original size:60 final size:60
Alignment explanation
Indices: 1056271--1056407 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 60
1056261 ATAGTCAGAT
* * * **
1056271 GACCATTTTGTAACTTTTAATAGTTGATGGACTCAATAAAGCAACACCCTATAGTCGGGG
1 GACCATTTTGTAACTTTTAATAGTTGATGGAATCAATAAAACAACACCCTATAATCGGAA
* *
1056331 GACCATTTTGTAACTTTTAATAGTTGA-GAGAATCAATAAAACAATATCCTATAATCGGAA
1 GACCATTTTGTAACTTTTAATAGTTGATG-GAATCAATAAAACAACACCCTATAATCGGAA
*
1056391 GATCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
1056408 ACCCTAAAAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 1 0.01
60 63 0.94
61 3 0.04
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTTGATGGAATCAATAAAACAACACCCTATAATCGGAA
Found at i:1058770 original size:5 final size:5
Alignment explanation
Indices: 1058760--1058841 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
1058750 AACGGTCAAC
* *
1058760 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
1058809 GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
1058842 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:1058781 original size:22 final size:22
Alignment explanation
Indices: 1058753--1058841 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
1058743 AACGGTCAAC
1058753 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1058775 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1058797 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
1058819 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1058841 G
1 G
1058842 ACCGGTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1058854 original size:9 final size:9
Alignment explanation
Indices: 1058842--1058934 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
1058832 GTCGGGTCGG
1058842 ACCGGTCAA
1 ACCGGTCAA
* *
1058851 ACCGATTCAG
1 ACCG-GTCAA
1058861 ACCGGTCAA
1 ACCGGTCAA
*
1058870 ACCGGTTCGA
1 ACCGG-TCAA
*
1058880 ACCGGTTGAA
1 ACCGG-TCAA
1058890 ACCGGTCAA
1 ACCGGTCAA
1058899 ACCGGTCAGA
1 ACCGGTCA-A
*
1058909 ACCGGTTGAAA
1 ACCGG-T-CAA
*
1058920 ACCGGTTAA
1 ACCGGTCAA
1058929 ACCGGT
1 ACCGGT
1058935 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
9 31 0.45
10 30 0.43
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1058893 original size:29 final size:31
Alignment explanation
Indices: 1058861--1058935 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
1058851 ACCGATTCAG
1058861 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1058890 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
1058920 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1058936 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1058913 original size:19 final size:19
Alignment explanation
Indices: 1058842--1058934 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
1058832 GTCGGGTCGG
*
1058842 ACCGGTCAAACCGATTCAG-
1 ACCGGTCAAACCG-GTCAGA
1058861 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGG-TCAGA
*
1058880 ACCGGTTGAAACCGGTCA-A
1 ACCGG-TCAAACCGGTCAGA
* *
1058899 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGG-TCAGA
*
1058920 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
1058935 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAGA
Found at i:1067376 original size:5 final size:5
Alignment explanation
Indices: 1067366--1067447 Score: 83
Period size: 5 Copynumber: 15.2 Consensus size: 5
1067356 AACGGTCAAC
* *
1067366 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
1067415 GGTCG GGTCG GGTCAAA GGTCG GGTCG GGTCG G
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG G
1067448 ACCGGTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
5 53 0.82
7 12 0.18
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:1067387 original size:22 final size:22
Alignment explanation
Indices: 1067359--1067447 Score: 169
Period size: 22 Copynumber: 4.0 Consensus size: 22
1067349 AACGGTCAAC
1067359 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1067381 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1067403 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
1067425 GGTCAAAGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
1067447 G
1 G
1067448 ACCGGTCAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 66 1.00
ACGTcount: A:0.10, C:0.21, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:1067460 original size:9 final size:9
Alignment explanation
Indices: 1067448--1067540 Score: 78
Period size: 9 Copynumber: 9.7 Consensus size: 9
1067438 GTCGGGTCGG
1067448 ACCGGTCAA
1 ACCGGTCAA
* *
1067457 ACCGATTCAG
1 ACCG-GTCAA
1067467 ACCGGTCAA
1 ACCGGTCAA
*
1067476 ACCGGTTCGA
1 ACCGG-TCAA
*
1067486 ACCGGTTGAA
1 ACCGG-TCAA
1067496 ACCGGTCAA
1 ACCGGTCAA
1067505 ACCGGTCAGA
1 ACCGGTCA-A
*
1067515 ACCGGTTGAAA
1 ACCGG-T-CAA
*
1067526 ACCGGTTAA
1 ACCGGTCAA
1067535 ACCGGT
1 ACCGGT
1067541 TTCCAGCAGC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
9 31 0.45
10 30 0.43
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:1067499 original size:29 final size:31
Alignment explanation
Indices: 1067467--1067541 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
1067457 ACCGATTCAG
1067467 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
1067496 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
1067526 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
1067542 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:1067519 original size:19 final size:19
Alignment explanation
Indices: 1067448--1067540 Score: 75
Period size: 19 Copynumber: 4.8 Consensus size: 19
1067438 GTCGGGTCGG
*
1067448 ACCGGTCAAACCGATTCAG-
1 ACCGGTCAAACCG-GTCAGA
1067467 ACCGGTCAAACCGGTTC-GA
1 ACCGGTCAAACCGG-TCAGA
*
1067486 ACCGGTTGAAACCGGTCA-A
1 ACCGG-TCAAACCGGTCAGA
* *
1067505 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTCA-AACCGG-TCAGA
*
1067526 ACCGGTTAAACCGGT
1 ACCGGTCAAACCGGT
1067541 TTCCAGCAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
18 3 0.05
19 35 0.56
20 16 0.26
21 8 0.13
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTCAGA
Found at i:1083743 original size:23 final size:24
Alignment explanation
Indices: 1083701--1083756 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
1083691 ACTATTTTTC
*
1083701 ATTTTAAATTAAAACAATATATT-T
1 ATTTTAATTTAAAACAATAT-TTAT
* *
1083725 GTTTTAATTTAAAA-TATATTTAT
1 ATTTTAATTTAAAACAATATTTAT
1083748 ATTTTAATT
1 ATTTTAATT
1083757 AATTTGAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 2 0.07
23 13 0.48
24 12 0.44
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (24 bp):
ATTTTAATTTAAAACAATATTTAT
Found at i:1087087 original size:23 final size:22
Alignment explanation
Indices: 1087044--1087087 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
1087034 TAACCATGCA
*
1087044 AACAAAAACAAGAAATTCAAAT
1 AACAAAAACAAGAAATACAAAT
**
1087066 AACAATAAACAAGGTATACAAA
1 AACAA-AAACAAGAAATACAAA
1087088 GCTCTTAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.66, C:0.14, G:0.07, T:0.14
Consensus pattern (22 bp):
AACAAAAACAAGAAATACAAAT
Found at i:1093166 original size:21 final size:21
Alignment explanation
Indices: 1093142--1093202 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1093132 AACTTTGAAA
1093142 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1093163 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1093177 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1093198 AAATG
1 AAATG
1093203 TTTCATTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1093233 original size:37 final size:36
Alignment explanation
Indices: 1093140--1093242 Score: 163
Period size: 35 Copynumber: 2.9 Consensus size: 36
1093130 CCAACTTTGA
*
1093140 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCATTG
1093176 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCATTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCATTG
* *
1093211 AAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 AAAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1093243 GTTAAAAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
35 34 0.55
36 5 0.08
37 23 0.37
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.44
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCATTG
Found at i:1097789 original size:21 final size:21
Alignment explanation
Indices: 1097765--1097825 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
1097755 AACTTTGAAA
1097765 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
1097786 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
1097800 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
1097821 AAATG
1 AAATG
1097826 TTTCTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:1097856 original size:37 final size:37
Alignment explanation
Indices: 1097757--1097875 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
1097747 TGGTAACCAA
1097757 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
1097794 CTTTG-AAAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
1097829 CTTTGAAAAATAGTTTTTCAAAGTTTGGTATATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
*
1097866 -GTTGAAAAAT
1 CTTTGAAAAAT
1097876 GATAATAGGA
Statistics
Matches: 76, Mismatches: 3, Indels: 7
0.88 0.03 0.08
Matches are distributed among these distances:
35 30 0.39
36 18 0.24
37 28 0.37
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:1099374 original size:41 final size:41
Alignment explanation
Indices: 1099329--1099772 Score: 273
Period size: 41 Copynumber: 10.7 Consensus size: 41
1099319 GGTTCATCGA
* *
1099329 TAGTGGCGGTTTTCA-ACAAACGCCGCAAAAGAGTAGTACTT
1 TAGTGGC-GTTTTTATACAAACGCCGCAAAAGAATAGTACTT
* * * *
1099370 TAGTGGCGTTTTTATACAAATGCCGCTATAGAATTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
* *** * * *
1099411 TAGTGGCGTTTTTATACAAACGTCATTATACACAT-GTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGA-ATAGTACTT
* * *
1099452 TAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCA-TACTT
1 TAGTGGCGTTT-T-TATACAAACGCCGCAAAAGAAT-AGTACTT
* * ***
1099495 TAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
* * ** * * * * *
1099536 TAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
* * * * * * *
1099577 TAGTGGCATTTGTGTTTACAAACGTCGCTAAAGACTCGTAATT
1 TAGTGGCGTTT-T-TATACAAACGCCGCAAAAGAATAGTACTT
* * * *
1099620 TAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
* * * * * *
1099661 TATTGACATTTTTATACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
* * * * * * * * *
1099702 TAGTGGTGTTTTTATTCAAACGCTGCTATACACTTGTACTA
1 TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
*
1099743 TAGTGGCGTTTGTGTTTACAAACGCCGCAA
1 TAGTGGCGTTT-T-TATACAAACGCCGCAA
1099773 GTTTACAAAT
Statistics
Matches: 330, Mismatches: 62, Indels: 20
0.80 0.15 0.05
Matches are distributed among these distances:
40 6 0.02
41 244 0.74
42 8 0.02
43 72 0.22
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCAAAAGAATAGTACTT
Found at i:1099500 original size:84 final size:82
Alignment explanation
Indices: 1099364--1099682 Score: 237
Period size: 84 Copynumber: 3.8 Consensus size: 82
1099354 CAAAAGAGTA
* * * **
1099364 GTACTTTAGTGGCGTTTTTATACAAATGCCGCTATAGAATTGTACTTTAGTGGCGTTTTTATACA
1 GTACTATAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGTGGCGTTTTTATACA
1099429 AACGTCATTATACACAT
66 AACGTCATTATACACAT
* *
1099446 GTACTATAGTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATA
1 GTACTATAGTGGCGTTT-T-TATACAAACGCCGCTAAAGAATCATACTTTAGTGGCGTTTTTATA
** * * **
1099511 CAAAC-TCCGCTAAAGACGC
64 CAAACGT-CATTATACACAT
* * * * * * * ** * * *
1099530 GTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCATTTGTGTTTA
1 GTACTATAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGTGGCGTTT-T-TATA
** * *
1099595 CAAACGTCGCTAAAGAC-T
64 CAAACGTCATTATACACAT
* * * * * * * *
1099613 CGTAATTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTACTTTATTGACATTTTTATAC
1 -GTACTATAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGTGGCGTTTTTATAC
1099678 AAACG
65 AAACG
1099683 CCGCTAAAGA
Statistics
Matches: 194, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
82 56 0.29
83 5 0.03
84 132 0.68
85 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (82 bp):
GTACTATAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCATACTTTAGTGGCGTTTTTATACA
AACGTCATTATACACAT
Found at i:1099542 original size:166 final size:166
Alignment explanation
Indices: 1099329--1099766 Score: 535
Period size: 166 Copynumber: 2.6 Consensus size: 166
1099319 GGTTCATCGA
* * * * *
1099329 TAGTGGCGGTTTTCA-ACAAACGCCGCAAAAGA-GTAGTACTTTAGTGGCGTTTTTATACAAATG
1 TAGTGGC-GTTTTTATACAAACGCCGCTAAAGACG-CGTACTTTAGTGGCGTTTTTATTCAAACG
* * * * * *
1099392 CCGCTATAGAATTGTACTTTAGTGGCGTTT-T-TATACAAACGTCATTATACACAT-GTACTATA
64 CCGCTATACACTTGTACTATAGTGGCGTTTGTGTATACAAACGTCACTAAACAC-TCGTAATATA
* *
1099454 GTGGCGTTTGTGTTTACAAACGCCGCTAAAGACTCATACTT
128 GTGGCATTT-T-TATACAAACGCCGCTAAAGACTCATACTT
* *
1099495 TAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACGCC
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGGCGTTTTTATTCAAACGCC
* * * * * *
1099560 GTTATACACTTGTACTATAGTGGCATTTGTGTTTACAAACGTCGCTAAAGACTCGTAATTTAGTG
66 GCTATACACTTGTACTATAGTGGCGTTTGTGTATACAAACGTCACTAAACACTCGTAATATAGTG
*
1099625 GCATTTTTATACAAACGCCGCTAAAGACTCGTACTT
131 GCATTTTTATACAAACGCCGCTAAAGACTCATACTT
* * * * * *
1099661 TATTGACATTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGTGTTTTTATTCAAACGCT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGGCGTTTTTATTCAAACGCC
*
1099726 GCTATACACTTGTACTATAGTGGCGTTTGTGTTTACAAACG
66 GCTATACACTTGTACTATAGTGGCGTTTGTGTATACAAACG
1099767 CCGCAAGTTT
Statistics
Matches: 235, Mismatches: 32, Indels: 10
0.85 0.12 0.04
Matches are distributed among these distances:
165 6 0.03
166 195 0.83
167 4 0.02
168 30 0.13
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (166 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACGCGTACTTTAGTGGCGTTTTTATTCAAACGCC
GCTATACACTTGTACTATAGTGGCGTTTGTGTATACAAACGTCACTAAACACTCGTAATATAGTG
GCATTTTTATACAAACGCCGCTAAAGACTCATACTT
Found at i:1099685 original size:125 final size:125
Alignment explanation
Indices: 1099344--1099685 Score: 495
Period size: 125 Copynumber: 2.7 Consensus size: 125
1099334 GCGGTTTTCA
* * * * * * *
1099344 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCCGCTATAGAATTGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
1099409 TTTAGTGGCGTTTTTATACAAACGTCATTATACACATGTACTATAGTGGCGTTTGTGTTT
66 TTTAGTGGCATTTTTATACAAACGCCGTTATACACATGTACTATAGTGGCATTTGTGTTT
* * *
1099469 ACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
1099534 TTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCATTTGTGTTT
66 TTTAGTGGCATTTTTATACAAACGCCGTTATACACATGTACTATAGTGGCATTTGTGTTT
* * *
1099594 ACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* *
1099659 TTTATTGACATTTTTATACAAACGCCG
66 TTTAGTGGCATTTTTATACAAACGCCG
1099686 CTAAAGACTC
Statistics
Matches: 192, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
125 192 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (125 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
TTTAGTGGCATTTTTATACAAACGCCGTTATACACATGTACTATAGTGGCATTTGTGTTT
Found at i:1099700 original size:125 final size:124
Alignment explanation
Indices: 1099344--1099770 Score: 491
Period size: 125 Copynumber: 3.4 Consensus size: 124
1099334 GCGGTTTTCA
* * * * * * *
1099344 ACAAACGCCGCAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAATGCCGCTATAGAATTGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * *
1099409 TTTAGTGGCGTTTTTATACAAACGTCATTATACACATGTACTATAGTGGCGTTTGTGTTT
66 TTTAGTGGCATTTTTATACAAACGCCGTTATACAC-TGTACTATAGTGGCATTTGTGTTT
* * *
1099469 ACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
*
1099534 TTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCATTTGTGTTT
66 TTTAGTGGCATTTTTATACAAACGCCGTTATACAC-TGTACTATAGTGGCATTTGTGTTT
* * *
1099594 ACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAACGCCGCTAAAGACTCGTAC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
* * * * * * **
1099659 TTTATTGACATTTTTATACAAACGCCGCTAAAGACTCGTACTTTAGTGGTGTTT-T-TATT
66 TTTAGTGGCATTTTTATACAAACGCCGTTATACACT-GTACTATAGTGGCATTTGTGT-TT
* * * * * *
1099718 -CAAACGCTGCTATACACTTGTACTATAGTGGCGTTTGTGTTTACAAACGCCGC
1 ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTT-T-TATACAAACGCCGC
1099771 AAGTTTACAA
Statistics
Matches: 258, Mismatches: 40, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
123 29 0.11
124 5 0.02
125 224 0.87
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (124 bp):
ACAAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTAC
TTTAGTGGCATTTTTATACAAACGCCGTTATACACTGTACTATAGTGGCATTTGTGTTT
Found at i:1099884 original size:21 final size:20
Alignment explanation
Indices: 1099855--1099898 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
1099845 CGCCGTTTAC
*
1099855 CCAAACCATCT-TCTTCACTA
1 CCAAACCATATAT-TTCACTA
1099875 CCAAACCCATATATTTCACTA
1 CCAAA-CCATATATTTCACTA
1099896 CCA
1 CCA
1099899 TTTTTATGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 15 0.71
22 1 0.05
ACGTcount: A:0.34, C:0.39, G:0.00, T:0.27
Consensus pattern (20 bp):
CCAAACCATATATTTCACTA
Found at i:1103594 original size:43 final size:43
Alignment explanation
Indices: 1103532--1103813 Score: 286
Period size: 43 Copynumber: 6.6 Consensus size: 43
1103522 AAGGTAATTA
*
1103532 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACTTTTT
* * * *
1103575 ACGGCGTTTGTGTTCAAAAACGCCGTTATAGGTCTGACATTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACTTTTT
* * *
1103618 GCGGCGTTTGTGTACAAAAACGCCACTATAGGTCTGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACTTTTT
* * * * *
1103661 ACGACGTTTGT-TCTAAAAACGCCAG-TATAAGTCTTA-TCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCC-GCTATAGGTCTGACT-TTTT
* ** *
1103703 GCGGCGTTTGTATCCAAAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTC-TGACTTTTT
* * * * *
1103747 GCAGTGTTTAT-TCCAAAAACGCCGCTATAGGTATCGACCTTTT
1 GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCT-GACTTTTT
*
1103790 GCGGCGTTTGT-TCAAAAAACGCCG
1 GCGGCGTTTGTGTCCAAAAACGCCG
1103814 TAATAGATAT
Statistics
Matches: 196, Mismatches: 36, Indels: 14
0.80 0.15 0.06
Matches are distributed among these distances:
42 34 0.17
43 147 0.75
44 14 0.07
45 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (43 bp):
GCGGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACTTTTT
Found at i:1103732 original size:85 final size:86
Alignment explanation
Indices: 1103532--1103732 Score: 284
Period size: 85 Copynumber: 2.3 Consensus size: 86
1103522 AAGGTAATTA
* *
1103532 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTACGGCGTTTGTGTTCAAAAACG
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTACGACGTTTGTGTTCAAAAACG
*
1103597 CCGTTATAGGTCTGACATTTT
66 CCGTTATAAGTCTGACATTTT
* * *
1103618 GCGGCGTTTGTGTACAAAAACGCCACTATAGGTCTGACCTTTTACGACG-TT-TGTTCTAAAAAC
1 GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTACGACGTTTGTGTTC-AAAAAC
*
1103681 GCCAG-TATAAGTCTTATC-TTTT
65 GCC-GTTATAAGTCTGA-CATTTT
1103703 GCGGCGTTTGTATCCAAAAACGCCGCTATA
1 GCGGCGTTTGTATCCAAAAACGCCGCTATA
1103733 TATCATAACT
Statistics
Matches: 102, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
84 5 0.05
85 51 0.50
86 46 0.45
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (86 bp):
GCGGCGTTTGTATCCAAAAACGCCGCTATAGGTCTGACCTTTTACGACGTTTGTGTTCAAAAACG
CCGTTATAAGTCTGACATTTT
Found at i:1103765 original size:128 final size:129
Alignment explanation
Indices: 1103536--1103813 Score: 312
Period size: 128 Copynumber: 2.2 Consensus size: 129
1103526 TAATTAGCGG
* * * * *
1103536 CGTTTGTATCCAAAAACGCCGCTATAGGTCTGACTTTTTACGGCGTTTGTGTTCAAAAACGCCGT
1 CGTTTGT-TCAAAAAACGCCGCTATAAGTCTGACTTTTTACGGCGTTTGTATCCAAAAACGCCGC
* * * * *
1103601 TATAGGTCTGACATTTTGCGGCGTTTGTGTACAAAAACGCCACTATAGGTCT-GACCTTTTACGA
65 TATAGATCTAACATTTTGCAGCGTTTATGTACAAAAACGCCACTATAGGTATCGACCTTTTACGA
* * *
1103665 CGTTTGTTCTAAAAACGCCAG-TATAAGTCTTA-TCTTTTGCGGCGTTTGTATCCAAAAACGCCG
1 CGTTTGTTCAAAAAACGCC-GCTATAAGTCTGACT-TTTTACGGCGTTTGTATCCAAAAACGCCG
* * * * * *
1103728 CTATATATCATAACTTTTTGCAGTGTTTAT-TCCAAAAACGCCGCTATAGGTATCGACCTTTTGC
64 CTATAGATC-TAACATTTTGCAGCGTTTATGTACAAAAACGCCACTATAGGTATCGACCTTTTAC
*
1103792 GG
128 GA
1103794 CGTTTGTTCAAAAAACGCCG
1 CGTTTGTTCAAAAAACGCCG
1103814 TAATAGATAT
Statistics
Matches: 125, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
127 1 0.01
128 73 0.58
129 51 0.41
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (129 bp):
CGTTTGTTCAAAAAACGCCGCTATAAGTCTGACTTTTTACGGCGTTTGTATCCAAAAACGCCGCT
ATAGATCTAACATTTTGCAGCGTTTATGTACAAAAACGCCACTATAGGTATCGACCTTTTACGA
Found at i:1104333 original size:21 final size:21
Alignment explanation
Indices: 1104307--1104360 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
1104297 ATTTTCAGAT
*
1104307 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
1104328 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
1104349 TCGCAATGCGAA
1 TCGCAATGCGAA
1104361 TATGTAAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:1104645 original size:21 final size:19
Alignment explanation
Indices: 1104621--1104675 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
1104611 TAAATCGCAA
1104621 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTT--CGT
*
1104642 TGCGATTTATTCCAAGTTCGT
1 TGCGA--TAGTCCAAGTTCGT
1104663 TGCGATAGTCCAA
1 TGCGATAGTCCAA
1104676 AATAGCAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 7 0.23
21 13 0.43
23 10 0.33
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.33
Consensus pattern (19 bp):
TGCGATAGTCCAAGTTCGT
Done.