Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014740.1 Corchorus olitorius cultivar O-4 contig14773, 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: 289335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:3566 original size:104 final size:104
Alignment explanation
Indices: 3386--3593 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
3376 TGCGAAACGT
3386 TGGATTTATCTTGATGCACTCGTTTTTCATCAAAAATGATCTTGATTTGTTAAATCATACAAAGA
1 TGGATTTATCTTGATGCACTCGTTTTTCATCAAAAATGATCTTGATTTGTTAAATCATACAAAGA
3451 CTTAGGGCTAGTTTGATATTGAGGTTGCATTTTGAAAAA
66 CTTAGGGCTAGTTTGATATTGAGGTTGCATTTTGAAAAA
3490 TGGATTTATCTTGATGCACTCGTTTTTCATCAAAAATGATCTTGATTTGTTAAATCATACAAAGA
1 TGGATTTATCTTGATGCACTCGTTTTTCATCAAAAATGATCTTGATTTGTTAAATCATACAAAGA
3555 CTTAGGGCTAGTTTGATATTGAGGTTGCATTTTGAAAAA
66 CTTAGGGCTAGTTTGATATTGAGGTTGCATTTTGAAAAA
3594 GCTTGGTTTG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (104 bp):
TGGATTTATCTTGATGCACTCGTTTTTCATCAAAAATGATCTTGATTTGTTAAATCATACAAAGA
CTTAGGGCTAGTTTGATATTGAGGTTGCATTTTGAAAAA
Found at i:15842 original size:21 final size:21
Alignment explanation
Indices: 15818--15938 Score: 98
Period size: 21 Copynumber: 6.2 Consensus size: 21
15808 TTTTCTGGAA
*
15818 CATCTTCTTCTCCTTCTTGTT
1 CATCTTCTTCTTCTTCTTGTT
* *
15839 CATC-T-TT-TTCTTCATCTT
1 CATCTTCTTCTTCTTCTTGTT
15857 C-TC--CTTCTTCTTCTTGTT
1 CATCTTCTTCTTCTTCTTGTT
*
15875 CATCTTTTTCTTCTTCTTGTT
1 CATCTTCTTCTTCTTCTTGTT
* *
15896 C-TC--CTTCTCCTTCTTGTA
1 CATCTTCTTCTTCTTCTTGTT
* * *
15914 CATCTTTTTCTTTTTCTTCTT
1 CATCTTCTTCTTCTTCTTGTT
15935 CATC
1 CATC
15939 CTCCTCCTCC
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
17 4 0.05
18 32 0.41
19 6 0.08
20 3 0.04
21 33 0.42
ACGTcount: A:0.06, C:0.31, G:0.03, T:0.60
Consensus pattern (21 bp):
CATCTTCTTCTTCTTCTTGTT
Found at i:15864 original size:39 final size:39
Alignment explanation
Indices: 15821--15925 Score: 144
Period size: 36 Copynumber: 2.8 Consensus size: 39
15811 TCTGGAACAT
15821 CTTCTTCTCCTTCTTGTTCATCTTTTTCTTCATCTTCTC
1 CTTCTTCTCCTTCTTGTTCATCTTTTTCTTCATCTTCTC
* * *
15860 CTTC-T-T-CTTCTTGTTCATCTTTTTCTTCTTCTTGTT
1 CTTCTTCTCCTTCTTGTTCATCTTTTTCTTCATCTTCTC
* *
15896 CTCCTTCTCCTTCTTGTACATCTTTTTCTT
1 CTTCTTCTCCTTCTTGTTCATCTTTTTCTT
15926 TTTCTTCTTC
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
36 30 0.52
37 2 0.03
38 2 0.03
39 24 0.41
ACGTcount: A:0.05, C:0.30, G:0.04, T:0.61
Consensus pattern (39 bp):
CTTCTTCTCCTTCTTGTTCATCTTTTTCTTCATCTTCTC
Found at i:15886 original size:6 final size:6
Alignment explanation
Indices: 15820--15935 Score: 79
Period size: 6 Copynumber: 19.3 Consensus size: 6
15810 TTCTGGAACA
* * * * * *
15820 TCTTCT TCTCCT TCTTGT TCATCT TTTTCT TCATCT TCTCCT TCTTCT
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* * * * * * * * *
15868 TCTTGT TCATCT TTTTCT TCTTCT TGTTCT CCTTCT CCTTCT TGTACA
1 TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT TCTTCT
* *
15916 TCTTTT TCTTTT TCTTCT TC
1 TCTTCT TCTTCT TCTTCT TC
15936 ATCCTCCTCC
Statistics
Matches: 80, Mismatches: 30, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
6 80 1.00
ACGTcount: A:0.04, C:0.30, G:0.03, T:0.62
Consensus pattern (6 bp):
TCTTCT
Found at i:15931 original size:39 final size:38
Alignment explanation
Indices: 15824--15946 Score: 160
Period size: 39 Copynumber: 3.2 Consensus size: 38
15814 GGAACATCTT
*
15824 CTTCTCCTTCTTGTTCATCTTTTTC--TTCATCTTCTC
1 CTTCTCCTTCTTGTTCATCTTTTTCTTTTCTTCTTCTC
* *
15860 CTTCTTCTTCTTGTTCATCTTTTTCTTCTTCTTGTTCTC
1 CTTCTCCTTCTTGTTCATCTTTTTCTT-TTCTTCTTCTC
*
15899 CTTCTCCTTCTTGTACATCTTTTTCTTTTTCTTCTTCATC
1 CTTCTCCTTCTTGTTCATCTTTTTC-TTTTCTTCTTC-TC
*
15939 CTCCTCCT
1 CTTCTCCT
15947 CCTCCTCCCT
Statistics
Matches: 75, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
36 24 0.32
39 40 0.53
40 11 0.15
ACGTcount: A:0.05, C:0.33, G:0.03, T:0.59
Consensus pattern (38 bp):
CTTCTCCTTCTTGTTCATCTTTTTCTTTTCTTCTTCTC
Found at i:24118 original size:37 final size:37
Alignment explanation
Indices: 24068--24141 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
24058 CAAAGTCTCG
24068 AACCTAAGACCTGTTTATAAGCTTGAACAAAAACCGC
1 AACCTAAGACCTGTTTATAAGCTTGAACAAAAACCGC
24105 AACCTAAGACCTGTTTATAAGCTTGAACAAAAACCGC
1 AACCTAAGACCTGTTTATAAGCTTGAACAAAAACCGC
24142 TTACCAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.24, G:0.14, T:0.22
Consensus pattern (37 bp):
AACCTAAGACCTGTTTATAAGCTTGAACAAAAACCGC
Found at i:35866 original size:33 final size:33
Alignment explanation
Indices: 35829--35908 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 33
35819 GATATGCAGC
*
35829 AAGATACAGAAAC-TGTGGTTAAAAATGTGCGTG
1 AAGATACA-AAACAGGTGGTTAAAAATGTGCGTG
*
35862 AAGATAGAAAACAAGGTGGTTAAAAATGTGCGTG
1 AAGATACAAAAC-AGGTGGTTAAAAATGTGCGTG
*
35896 AAGATAGAAAACA
1 AAGATACAAAACA
35909 AGAGAGAGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 4 0.09
33 8 0.19
34 31 0.72
ACGTcount: A:0.46, C:0.07, G:0.26, T:0.20
Consensus pattern (33 bp):
AAGATACAAAACAGGTGGTTAAAAATGTGCGTG
Found at i:35882 original size:34 final size:34
Alignment explanation
Indices: 35843--35910 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
35833 TACAGAAACT
35843 GTGGTTAAAAATGTGCGTGAAGATAGAAAACAAG
1 GTGGTTAAAAATGTGCGTGAAGATAGAAAACAAG
35877 GTGGTTAAAAATGTGCGTGAAGATAGAAAACAAG
1 GTGGTTAAAAATGTGCGTGAAGATAGAAAACAAG
35911 AGAGAGCCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.06, G:0.29, T:0.21
Consensus pattern (34 bp):
GTGGTTAAAAATGTGCGTGAAGATAGAAAACAAG
Found at i:48620 original size:2 final size:2
Alignment explanation
Indices: 48613--48637 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48603 GAGTCCATTA
48613 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
48638 ACACCATTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53581 original size:40 final size:40
Alignment explanation
Indices: 53537--53617 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
53527 AATAATTTAT
53537 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAAG
1 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAAG
*
53577 GGAAGGAAAGAAAATAAAGTTATTGAAATTTATAAAGAAG
1 GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAAG
53617 G
1 G
53618 ACCTATTGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (40 bp):
GGAAGGAAAAAAAATAAAGTTATTGAAATTTATAAAGAAG
Found at i:54191 original size:31 final size:31
Alignment explanation
Indices: 54156--54226 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
54146 ACAAAATGAA
54156 AAATGATGGAGCAAAATGAAATTTCAAACAT
1 AAATGATGGAGCAAAATGAAATTTCAAACAT
54187 AAATGATGGAGCAAAATGAAATTTCAAACAT
1 AAATGATGGAGCAAAATGAAATTTCAAACAT
54218 AAATGATGG
1 AAATGATGG
54227 GGTTATTTGC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.51, C:0.08, G:0.18, T:0.23
Consensus pattern (31 bp):
AAATGATGGAGCAAAATGAAATTTCAAACAT
Found at i:60876 original size:11 final size:11
Alignment explanation
Indices: 60860--60889 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
60850 GTATGAAAAA
60860 GGAATATTTTT
1 GGAATATTTTT
60871 GGAATATTTTT
1 GGAATATTTTT
*
60882 AGAATATT
1 GGAATATT
60890 CTTATACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (11 bp):
GGAATATTTTT
Found at i:64501 original size:30 final size:29
Alignment explanation
Indices: 64430--64507 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
64420 GAACTAATAC
* *
64430 AAAACGGCCAAATAAGCCCCTGAACTCTA
1 AAAAAGGCCAAATAAGCCCCTAAACTCTA
***
64459 ATTGCA-GCCAAATAAGCCCCTAAACTCTTA
1 A-AAAAGGCCAAATAAGCCCCTAAACTC-TA
*
64489 AAAAAGGCCAAATATGCCC
1 AAAAAGGCCAAATAAGCCC
64508 TTTTTTGATG
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.41, C:0.29, G:0.13, T:0.17
Consensus pattern (29 bp):
AAAAAGGCCAAATAAGCCCCTAAACTCTA
Found at i:67992 original size:120 final size:120
Alignment explanation
Indices: 67774--68014 Score: 464
Period size: 120 Copynumber: 2.0 Consensus size: 120
67764 AAGACTTAGA
*
67774 GCGCCAAGTTTTCTCAAATACAATATTGCTTGAGAAATCAAACAAGTTGTATTTGGGATACAACT
1 GCGCCAAGTTTTCTCAAATACAATATTGCTTCAGAAATCAAACAAGTTGTATTTGGGATACAACT
*
67839 AAGCCACTTAAGAACATCCAAGGAAGAAGTAGAAGAATTGATTGTGATTTCAGGG
66 AAGCCACTTAAGAACATCCAAGGAAGAAATAGAAGAATTGATTGTGATTTCAGGG
67894 GCGCCAAGTTTTCTCAAATACAATATTGCTTCAGAAATCAAACAAGTTGTATTTGGGATACAACT
1 GCGCCAAGTTTTCTCAAATACAATATTGCTTCAGAAATCAAACAAGTTGTATTTGGGATACAACT
67959 AAGCCACTTAAGAACATCCAAGGAAGAAATAGAAGAATTGATTGTGATTTCAGGG
66 AAGCCACTTAAGAACATCCAAGGAAGAAATAGAAGAATTGATTGTGATTTCAGGG
68014 G
1 G
68015 AAAATCACGT
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 119 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (120 bp):
GCGCCAAGTTTTCTCAAATACAATATTGCTTCAGAAATCAAACAAGTTGTATTTGGGATACAACT
AAGCCACTTAAGAACATCCAAGGAAGAAATAGAAGAATTGATTGTGATTTCAGGG
Found at i:73071 original size:18 final size:18
Alignment explanation
Indices: 73045--73085 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
73035 AAGCCCACCT
* *
73045 AACTTATGTATTAAGCCC
1 AACTAATGTATTAAGCAC
73063 AACTAATGTATTAAGCAC
1 AACTAATGTATTAAGCAC
73081 AACTA
1 AACTA
73086 GTAACCAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (18 bp):
AACTAATGTATTAAGCAC
Found at i:75359 original size:27 final size:27
Alignment explanation
Indices: 75329--75394 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 27
75319 AAGGTTTGCC
* **
75329 CAAAATGCAATTTGGGATATAACGTTA
1 CAAAAAGCAATTAAGGATATAACGTTA
75356 CAAAACAAGCAATTAAGGATATAACGTTA
1 C-AAA-AAGCAATTAAGGATATAACGTTA
*
75385 CGAAAAGCAA
1 CAAAAAGCAA
75395 ACAATTAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.21
28 5 0.15
29 21 0.64
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (27 bp):
CAAAAAGCAATTAAGGATATAACGTTA
Found at i:75375 original size:29 final size:31
Alignment explanation
Indices: 75343--75409 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
75333 ATGCAATTTG
*
75343 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAACAATTAA
75372 GGATATAACGTTACGAAAAGCAAACAATTAA
1 GGATATAACGTTACGAAAAGCAAACAATTAA
75403 GGATATA
1 GGATATA
75410 GTCTGTTAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAACAATTAA
Found at i:75597 original size:31 final size:31
Alignment explanation
Indices: 75517--75597 Score: 117
Period size: 31 Copynumber: 2.6 Consensus size: 31
75507 CCCTAACTGA
* **
75517 TTATATCCTTAATTGCTTAAAATCGAAAACC
1 TTATATCCTTAATTGCTTGAAATAAAAAACC
* *
75548 TCATATCCTTAATTGCTTGAAATAAAAAACG
1 TTATATCCTTAATTGCTTGAAATAAAAAACC
75579 TTATATCCTTAATTGCTTG
1 TTATATCCTTAATTGCTTG
75598 TTTTGTAACG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (31 bp):
TTATATCCTTAATTGCTTGAAATAAAAAACC
Found at i:75646 original size:31 final size:29
Alignment explanation
Indices: 75574--75653 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
75564 TTGAAATAAA
***
75574 AAACGTTATATCCTTAATTGCTTGTTTTG
1 AAACGTTATATCCTTAATTGCTTGTGCAG
*
75603 TAACGTTATATCCTTAATTGCTTGTGGCAG
1 AAACGTTATATCCTTAATTGCTTGT-GCAG
* *
75633 CAAACATTATATCCTAAATTG
1 -AAACGTTATATCCTTAATTG
75654 ATTATTTGGC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 24 0.57
30 1 0.02
31 17 0.40
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (29 bp):
AAACGTTATATCCTTAATTGCTTGTGCAG
Found at i:76491 original size:16 final size:16
Alignment explanation
Indices: 76472--76502 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
76462 ATATTCTAAG
76472 AATACATTTTTCTACT
1 AATACATTTTTCTACT
76488 AATACATTTTTCTAC
1 AATACATTTTTCTAC
76503 CAAGCAATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (16 bp):
AATACATTTTTCTACT
Found at i:76604 original size:19 final size:19
Alignment explanation
Indices: 76580--76616 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
76570 AAAAAGATTA
*
76580 TTTAAATAAAAATATTTTT
1 TTTAAAAAAAAATATTTTT
76599 TTTAAAAAAAAATATTTT
1 TTTAAAAAAAAATATTTT
76617 CTTCCGAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAAAAAAATATTTTT
Found at i:76616 original size:17 final size:18
Alignment explanation
Indices: 76570--76616 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
76560 ATAATACAAT
* *
76570 AAAAAGATTATTTAAATA
1 AAAAATATTTTTTAAATA
*
76588 AAAATATTTTTTTTAAA-A
1 AAAA-ATATTTTTTAAATA
76606 AAAAATATTTT
1 AAAAATATTTT
76617 CTTCCGAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.25
18 9 0.38
19 9 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAAAATATTTTTTAAATA
Found at i:76714 original size:30 final size:31
Alignment explanation
Indices: 76647--76757 Score: 152
Period size: 31 Copynumber: 3.6 Consensus size: 31
76637 AGATGATAAG
* ****
76647 CAAGCAATTTAGGATATAACGTTTTCTGCCG
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
76678 CAAGCAATTAAGGATATAACGTTTT-TATTT
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
* *
76708 CAAGCAATTAAGGATATGACGTTTTCGATTT
1 CAAGCAATTAAGGATATAACGTTTTCTATTT
76739 CAAGCAATTAAGGATATAA
1 CAAGCAATTAAGGATATAA
76758 TCAGTTAGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 25 0.35
31 46 0.65
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (31 bp):
CAAGCAATTAAGGATATAACGTTTTCTATTT
Found at i:76950 original size:29 final size:31
Alignment explanation
Indices: 76876--76942 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
76866 CCTAACGGAC
76876 TATATCCTTAATTGCTCGCTTTTCGTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
*
76907 TATATCCTTAATTGCTTG-TTTT-GTAACGT
1 TATATCCTTAATTGCTCGCTTTTCGTAACGT
76936 TATATCC
1 TATATCC
76943 CAAATTGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
TATATCCTTAATTGCTCGCTTTTCGTAACGT
Found at i:110033 original size:31 final size:32
Alignment explanation
Indices: 109995--110057 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
109985 TGTTAGACTT
109995 GTGTTGGTGGGTCAGCCCAAAG-AAAAAGAAA
1 GTGTTGGTGGGTCAGCCCAAAGAAAAAAGAAA
110026 GTGTTGGTGGGTCAGCCCAAAGAAAAAAGAAA
1 GTGTTGGTGGGTCAGCCCAAAGAAAAAAGAAA
110058 AGGGAAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 22 0.71
32 9 0.29
ACGTcount: A:0.40, C:0.13, G:0.32, T:0.16
Consensus pattern (32 bp):
GTGTTGGTGGGTCAGCCCAAAGAAAAAAGAAA
Found at i:110311 original size:21 final size:20
Alignment explanation
Indices: 110260--110323 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 20
110250 TTGACACTGT
*
110260 TTAGCAACTGTAAAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
*
110281 TTA-CACTGTACAGATTAGA
1 TTAGCACTGTACAGATGAGA
110300 TTAGCTACTGTACAGATGAGA
1 TTAGC-ACTGTACAGATGAGA
110321 TTA
1 TTA
110324 TTAGAGCAGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.42
20 2 0.05
21 20 0.53
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TTAGCACTGTACAGATGAGA
Found at i:116472 original size:80 final size:79
Alignment explanation
Indices: 116310--116473 Score: 278
Period size: 79 Copynumber: 2.1 Consensus size: 79
116300 AAAAATTAGT
116310 AAAAAATTTAAGAAAAAAAAAAGACATTGGGTTTTTTTTGGCAGAAGAAAGGGAATCTAGGCAGT
1 AAAAAATTTAAGAAAAAAAAAAGACATTGGGTTTTTTTTGGCAGAAGAAAGGGAATCTAGGCAGT
116375 AAGCAGTGAGTACA
66 AAGCAGTGAGTACA
*
116389 AAAAAATTTAA-AGAAAAAAAA-ACATTGGGGTTTTTTTTTGGCAGAAGAAAGGGAATCTAGGCA
1 AAAAAATTTAAGAAAAAAAAAAGACATT-GGG-TTTTTTTTGGCAGAAGAAAGGGAATCTAGGCA
*
116452 GTAAGCAGTGGGTACA
64 GTAAGCAGTGAGTACA
116468 AAAAAA
1 AAAAAA
116474 AAAAAAAAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
77 5 0.06
78 12 0.15
79 64 0.79
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (79 bp):
AAAAAATTTAAGAAAAAAAAAAGACATTGGGTTTTTTTTGGCAGAAGAAAGGGAATCTAGGCAGT
AAGCAGTGAGTACA
Found at i:129060 original size:5 final size:6
Alignment explanation
Indices: 129044--129068 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
129034 AAGAAAATGG
129044 CTTTTT CTTTTT CTTTTT CTTTTT C
1 CTTTTT CTTTTT CTTTTT CTTTTT C
129069 AATTTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (6 bp):
CTTTTT
Found at i:131455 original size:14 final size:14
Alignment explanation
Indices: 131436--131464 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
131426 CACTATTTCA
131436 TTAAGACAAAACTG
1 TTAAGACAAAACTG
131450 TTAAGACAAAACTG
1 TTAAGACAAAACTG
131464 T
1 T
131465 GTGCTTAATC
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:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (14 bp):
TTAAGACAAAACTG
Found at i:137538 original size:328 final size:328
Alignment explanation
Indices: 136660--137576 Score: 996
Period size: 332 Copynumber: 2.8 Consensus size: 328
136650 AAAATCATGC
* *
136660 AAAACTGACCCGAAAAAGTTTTT-CT-AATT-TTTTGGCACAGTACTCAGAAAAAATATATAATT
1 AAAACTGACCCG-AAAAGTTTTTCCTCAATTATTTTGCCACAATACTCAGAAAAAATATATAATT
* * * * * *
136722 TAACGGCAAAAAAATTGATGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTGAACT
65 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCCGAATT
* * * * *
136787 AATTTCTAATTGAATCGAAACAAGATTCAGAAGCTCGTAAAAGCAAATCCTTATATCCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-C-ATATGG
* * * * ** * *
136852 CTGAGATTTGCTTCGATGAATATAGATATTTGAAGGAGTCTTTGCGCCAAAAAAT-ACTCTAAAT
192 ATGAGATTTGGTTCGATGAATATAGATA-TTCAAGGAGTCTTTACGCC-AAAAATCAAGCAAAAC
* ** * * *
136916 TGAGTCGGGGCTCCAGAACGCATTTTTAGCAAAAATTTGTGATACGTAGTACACGATTTCTGATA
255 TGAGTCGGGGCTCCAGAACGCAGTTTTAGCAAAAATCCGTGATA-GTAGTAAACAATTTCGGATA
*
136981 AAATTTTGCA
319 AAATTTAGCA
* * *
136991 AAAACTGACCCGAAAAGTTTTTCTTCAATTTTTTTTCCACAATACTCAGAAAAAATATATAATTC
1 AAAACTGACCCGAAAAGTTTTTCCTCAATTATTTTGCCACAATACTCAGAAAAAATATATAATTC
* * * * * *
137056 AACGCAAAAAAAAAATGAAGGGTTTATCACGTTTCAAATAT-TTTTTTCCCA-TTTTTCCGAATT
66 AACGC-CAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CCATTTTTTCCGAATT
* * * **
137119 TATTT-TAAATTAAATCAAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCGATGTG
129 AATTTCT-AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCATATG-G
* * *
137183 ACTGGGATTTGGTTCGATGAATATAGATACTTCATGGAGTCTTTACACCAAAAATCAAGCAAAAC
192 A-TGAGATTTGGTTCGATGAATATAGATA-TTCAAGGAGTCTTTACGCCAAAAATCAAGCAAAAC
* ** * * *
137248 TGAGTTGGGGCTCTGGAACGCGGTTTTAGCTATAAA-CCGTGAT-G-AGTAAACAATTTCGGCTT
255 TGAGTCGGGGCTCCAGAACGCAGTTTTAGC-AAAAATCCGTGATAGTAGTAAACAATTTCGG-AT
137310 AAAA-TTAGCA
318 AAAATTTAGCA
* ** *
137320 AAAACTGATCCGAAATTTTTTTCCTCAA-TATTTTGCCACAATACTCAG-AAAAATATAAAATTC
1 AAAACTGACCCGAAAAGTTTTTCCTCAATTATTTTGCCACAATACTCAGAAAAAATATATAATTC
*
137383 AATGCCAAAAGAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTGTTTCCGAATT
66 AACGCCAAAA-AAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT-TTTCCGAATT
* * * *
137448 AATTTCTAACTAAATCGAAATAAGATACTGATGCTCGTAAAAACAAATCCTTAAATGCATATGGA
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT-CATATGGA
* * * *
137513 TGAGATTTGGTTAGATGAATATAGATATCTCAAGGAGTCTTTATGCCAAATATCATGCAAAACT
193 TGAGATTTGGTTCGATGAATATAGATAT-TCAAGGAGTCTTTACGCCAAAAATCAAGCAAAACT
137577 AAATCGTTTT
Statistics
Matches: 487, Mismatches: 81, Indels: 39
0.80 0.13 0.06
Matches are distributed among these distances:
326 4 0.01
327 48 0.10
328 80 0.16
329 100 0.21
330 23 0.05
331 22 0.05
332 136 0.28
333 43 0.09
334 31 0.06
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (328 bp):
AAAACTGACCCGAAAAGTTTTTCCTCAATTATTTTGCCACAATACTCAGAAAAAATATATAATTC
AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCATATGGATGA
GATTTGGTTCGATGAATATAGATATTCAAGGAGTCTTTACGCCAAAAATCAAGCAAAACTGAGTC
GGGGCTCCAGAACGCAGTTTTAGCAAAAATCCGTGATAGTAGTAAACAATTTCGGATAAAATTTA
GCA
Found at i:138321 original size:491 final size:493
Alignment explanation
Indices: 137694--138681 Score: 1732
Period size: 492 Copynumber: 2.0 Consensus size: 493
137684 AAGAATATAA
*
137694 ATATTTCAAGGGGTTTTTGCGTAAAAAATCATGCGAAATTGAGTCGGGGCTCCGGAACGCGTTTT
1 ATATTTCAAGGGGTTTTTGCGTAAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTT
*
137759 TAGCAAAAAACTGTGATGGCTAGTACATGATTTCTGTTAAATTTTTGCAAAAGTAACCCAGAAAG
66 TAGCAAAAAACTGTGATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAAGTAACCCAGAAAG
*
137824 CTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTGAACGC-AAAAAAAATTGA
131 CTTTTCCCCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTGAACGCGAAAAAAAATTGA
*
137888 AGGATTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGA
196 AGGATTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGA
*
137953 AACAAGATTCAGATGCTCGTAAAGACAAATCCGTAAATTTAATGTGGTTGATATTTTGTTAGATG
261 AAAAAGATTCAGATGCTCGTAAAGACAAATCCGTAAATTTAATGTGGTTGATATTTTGTTAGATG
* **
138018 AATATAGATATTTCAAGGAGTCTCTCTGCCAAAATCATGCAAAACT-ATGTCGGCGTCCCGGAAC
326 AATATACATATTTCAAGGAGTCTCTCTGCCAAAATCATGCAAAACTGA-GTCGGCACCCCGGAAC
* * **
138082 GCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCC-GAAAAA
390 ACGTTTTTAGCCCAAAAATAGTGATGGGAAGTACACGATTTCGGCTAAAAACTGACCCGGAAAAA
138146 TATTTTTCTAAAATTTTTGCCACAATACTCAGAAAAAAT
455 TATTTTTCTAAAATTTTTGCCACAATACTCAGAAAAAAT
138185 ATATTTCAAGGGGTTTTTGCGTAAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTT
1 ATATTTCAAGGGGTTTTTGCGTAAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTT
*
138250 TAGCAAAAAACTGTTATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAAGTAACCC-GAAAA
66 TAGCAAAAAACTGTGATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAAGTAACCCAG-AAA
138314 GCTTTTCCCCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTGAACGCGAAAAAAAATTG
130 GCTTTTCCCCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTGAACGCGAAAAAAAATTG
*
138379 GAGGATTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCG
195 AAGGATTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCG
* *
138444 AAAAAAGATTCAGATGCTCGTAAAGACAAATCCTTAAATTTAATGTGGTTGATATTTTGTTTGAT
260 AAAAAAGATTCAGATGCTCGTAAAGACAAATCCGTAAATTTAATGTGGTTGATATTTTGTTAGAT
* *
138509 GAATATACATATTTCATGGAGTCTTTCTGCCAAAATCATGCAAAACTGAGTCGGCACCCCGGAAC
325 GAATATACATATTTCAAGGAGTCTCTCTGCCAAAATCATGCAAAACTGAGTCGGCACCCCGGAAC
* *
138574 ACGTTTTTTGCCCAAAAATAGTGATGGGAAGTACACGATTTCGGCTAAAAACTGACCCGGAAAAT
390 ACGTTTTTAGCCCAAAAATAGTGATGGGAAGTACACGATTTCGGCTAAAAACTGACCCGGAAAAA
* *
138639 TATTTTTCTAAAATTTTTGTCAGAATACTCAGAAAAAAT
455 TATTTTTCTAAAATTTTTGCCACAATACTCAGAAAAAAT
138678 ATAT
1 ATAT
138682 AATTCAATGC
Statistics
Matches: 471, Mismatches: 22, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
490 1 0.00
491 176 0.37
492 247 0.52
493 47 0.10
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (493 bp):
ATATTTCAAGGGGTTTTTGCGTAAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTT
TAGCAAAAAACTGTGATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAAGTAACCCAGAAAG
CTTTTCCCCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTGAACGCGAAAAAAAATTGA
AGGATTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGA
AAAAAGATTCAGATGCTCGTAAAGACAAATCCGTAAATTTAATGTGGTTGATATTTTGTTAGATG
AATATACATATTTCAAGGAGTCTCTCTGCCAAAATCATGCAAAACTGAGTCGGCACCCCGGAACA
CGTTTTTAGCCCAAAAATAGTGATGGGAAGTACACGATTTCGGCTAAAAACTGACCCGGAAAAAT
ATTTTTCTAAAATTTTTGCCACAATACTCAGAAAAAAT
Found at i:139170 original size:333 final size:333
Alignment explanation
Indices: 138208--139279 Score: 1250
Period size: 333 Copynumber: 3.2 Consensus size: 333
138198 TTTTTGCGTA
* * * * * *
138208 AAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAG-CAAAAAACT-GTTATGGCT
1 AAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCAAAAAA-TAGTGATGGCT
* * * * *
138271 AGTACATGATTTCTGCTAAATTTTTGCAAAAGTAACCCGAAAAGCTTTTCCCCAAAATTTTGCCA
65 AGTACACGATTTCGGCTATATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCA
* * *
138336 CAATAGTCAGAAAAAATATATAATTGAACGCGAAAAAAAATTGGAGGATTTTTCACGCTTCTAAT
130 CAATAGCCAGAAAAAATATATAATTCAACGC-AAAAAAAATTGAAGGATTTTTCACGCTTCTAAT
138401 ATCATTTTTCCA-TTTTTTTCCGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGT
194 ATCATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGT
* * * * * *
138465 AAAGACAAATCCTTAAATTTAATGTGGTTGATATTTTGTTTGATGAATATACATATTTCATGGAG
259 AAAAACAAATCCTTATATTCAATGTGGTTGAGATTTTGTTTGATGAATATAGATATTTCAAGGAG
138530 TCTTTCTGCC
324 TCTTTCTGCC
* * * * **
138540 -AAAATCATGCAAAACTGAGTCGGCACCCCGGAACACGTTTTTTGCCCAAAAATAGTGATGGGAA
1 AAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCAAAAAATAGTGATGGCTA
* ** * *
138604 GTACACGATTTCGGC--TA-------AAAACTGACCCGGAAAATTATTTTTCT-AAAATTTTTGT
66 GTACACGATTTCGGCTATATTTTTGCAAAACTAACCC-GAAAA-GCTTTTCCTCAAAA-TTTTGC
* * * * * *
138659 CAGAATA-CTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCACGCTTCTA
128 CACAATAGC-CAGAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCACGCTTCTA
* * * * * * * *
138723 ATATCGTTTTTCAATTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAAATTCAGA-GATA
192 ATATCATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATGCTC
* * ** *
138787 TTCATAAAACAAATCC-TATTATCCAATGTGACTAAGA-TTTGTTTGATGAATATAGATATTTCA
257 GT-A-AAAACAAATCCTTA-TATTCAATGTGGTTGAGATTTTGTTTGATGAATATAGATATTTCA
*
138850 AGGGGT-TTT-TGCGTC
319 AGGAGTCTTTCTGC--C
* * * * *
138865 AAAAATCATGCGAAATTTAGTCGGGGCTCCGGAACGCGTTTTTAG-CAAAAAATAGTGATGGCTA
1 AAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCAAAAAATAGTGATGGCTA
* * * *
138929 GTACATGATTTCTGCTATATTTTTGCAAAACTAACCCGAAAAGCTTTTGCTCGAAATTTTGCCAC
66 GTACACGATTTCGGCTATATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCAC
* * *
138994 AATAGCCAGAAAAAATATATAATTCAACGCAAAAAAAAATTGAAGGATTTTTCGCTCTTCTACTA
131 AATAGCCAGAAAAAATATATAATTCAACGC-AAAAAAAATTGAAGGATTTTTCACGCTTCTAATA
* *
139059 TCATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTA
195 TCATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGTA
*
139124 AAAACAAATCCTTATATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAGT
260 AAAACAAATCCTTATATTCAATGTGGTTGAGATTTTGTTTGATGAATATAGATATTTCAAGGAGT
139189 CTTTCTGCC
325 CTTTCTGCC
* * * *
139198 AAAAATCATGCAAAACTGAGTCGGCTCCCCGGAACGCGTTTTTAGCCCAAAAATCGTGATGGTTA
1 AAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCAAAAAATAGTGATGGCTA
*
139263 GCACACGATTTCGGCTA
66 GTACACGATTTCGGCTA
139280 AAAACTGACC
Statistics
Matches: 601, Mismatches: 108, Indels: 60
0.78 0.14 0.08
Matches are distributed among these distances:
323 12 0.02
324 53 0.09
325 141 0.23
326 57 0.09
327 2 0.00
330 1 0.00
331 37 0.06
332 91 0.15
333 158 0.26
334 46 0.08
335 3 0.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (333 bp):
AAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCAAAAAATAGTGATGGCTA
GTACACGATTTCGGCTATATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCAC
AATAGCCAGAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCACGCTTCTAATAT
CATTTTTCCATTTTTTTTCCGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATGCTCGTAA
AAACAAATCCTTATATTCAATGTGGTTGAGATTTTGTTTGATGAATATAGATATTTCAAGGAGTC
TTTCTGCC
Found at i:140076 original size:332 final size:331
Alignment explanation
Indices: 139358--141717 Score: 2597
Period size: 332 Copynumber: 7.2 Consensus size: 331
139348 GTTTTTGCGT
* *
139358 TCATGCGAAATTGAGCCGG-GCTCCGGAACGCGTTTTTAG-CAATAAA-CTGTGATGGTTAGTAC
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAGCCAA-AAATC-GTGATGGCTAGTAC
* *
139420 ATGATTTCTGCTAAATTTTTGCAGAAGTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATA
64 ATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATA
* * *
139485 GTCAG-AAAAATATATAATTGAACGCCAAAAAGATTGAAGAATTTTTCACGCTTCTAATATCGTT
129 GTCAGAAAAAATATATAATTCAACGCAAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCG-T
* **
139549 TTTTCAATTTTTTTCCCTAGATTAATTTCTAA-T-AATCGAAAAAAGATTCAGA-GATATTCATA
193 TTTTCAATTTTTTT-CCGA-ATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGT-A-A
*
139611 AAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGGGT-
254 AAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGTC
139675 TTTTGCGTCAAAAA
319 TTTTGCG-CAAAAA
* * *
139689 TCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTTTAG-CAAAAAACTGTGATGGCTAGTACA
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAGCCAAAAATC-GTGATGGCTAGTACA
139753 TGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATAG
65 TGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATAG
* *
139818 TCAGAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCGCGCTTCTAATATCGTTT
130 TCAGAAAAAATATATAATTCAACGCAAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTT
* * * * *
139883 TTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACGA
195 TTCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGTAAAAACAA
* * ** *
139948 ATCCT-TAAATTCAATGTGGTTGAGATTT-TGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
260 ATCCTAT-TATCCAATGTGACTGAGATTTGT-TTCGATGAATATAGATATTTCAAGGAGTCTTT-
140011 TGC-CAAAAA
322 TGCGCAAAAA
* * * *
140020 TCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACA
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAG-CCAAAAATCGTGATGGCTAGTACA
* * * ** *
140085 CGATTTCGGCT--A-------AAAACTGACCCGAAATAATATTTTTCT-AAAATTTTTGCCACAA
65 TGATTTCTGCTAAATTTTTGCAAAACTAACCCG-AA-AAGCTTTTCCTCAAAA-TTTTGCCACAA
* * * * *
140140 TACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCG
127 TAGTCAGAAAAAATATATAATTCAACGCAAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCG
* **
140205 TTTTTCAATTTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGATTCAGA-GATATTCAT
192 TTTTTCAA-TTTTTTT-CCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGT-A-
*
140269 AAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGGGT
253 AAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGT
140334 -TTTTGCGTCAAAAA
318 CTTTTGCG-CAAAAA
* * *
140348 TCATGCGAAATTGAGTCGGGGCTCCGGAACGCGTTTTTAGCAAAAAATAGTGATGGCTAGTACAT
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATGGCTAGTACAT
*
140413 GATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCGAAATTTTGCCACAATAGT
66 GATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATAGT
* * *
140478 CAGAAAAAATATATAATTCAACGCAAAAAAAAATTGAAGGATTTTTCGCGCTTCTAATATCATTT
131 CAGAAAAAATATATAATTCAACGC-AAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTT
* * * * *
140543 TTCCATTATTTTT-CGAATTTATTTCTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACA
195 TTCAATT-TTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGTAAAAACA
* * ** *
140607 AATCCT-TAAATTCAATGTGGTTGAGATTT-TGTTAGATGAATATAGATATTTCAAGGAGTCTTT
259 AATCCTAT-TATCCAATGTGACTGAGATTTGT-TTCGATGAATATAGATATTTCAAGGAGTCTTT
140670 CTGC-CAAAAA
322 -TGCGCAAAAA
* * *
140680 TCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCCAAAAATCGTGATGG-T-GTACA
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAG-CCAAAAATCGTGATGGCTAGTACA
* * * * ** *
140743 CGATTTCGGCT--A-------AAAACTGACCCAAAAAATATTTTTCT-AAAATTTTTGCCACAAT
65 TGATTTCTGCTAAATTTTTGCAAAACTAACCC-GAAAAGCTTTTCCTCAAAA-TTTTGCCACAAT
* * * * *
140798 ACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAATATCGT
128 AGTCAGAAAAAATATATAATTCAACGCAAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGT
* **
140863 TTTTCAAATTTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGATTCAGA-GATATTCAT
193 TTTTC-AA-TTTTTTT-CCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGT-A-
* *
140927 AAAACAAATCCTATTATCCTATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGG-GG
253 AAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGT
140991 CTTTTGCGTCAAAAA
318 CTTTTGCG-CAAAAA
* * * * *
141006 TCATGCGAAATTTAGCCGGGGCTCCGGAACGCGTTTTTAG-CAAAAAACTGTAATGGCTAGTACA
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAGCCAAAAATC-GTGATGGCTAGTACA
141070 TGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATAG
65 TGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATAG
* **
141135 TCAGAAAAAATATATAATTCAACGCAAAAAAAAAATTGAAGGATTTTTCGTGCTTCTAATATCGT
130 TCAGAAAAAATATATAATTCAACGC--AAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGT
* * * *
141200 TTTTCCATTTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
193 TTTTCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGTAAAAAC
* * ** *
141264 AAATCCT-TAAATTCAATGTGGTTGAGATTT-TGTTAGATGAATATAGATATTTCAAGGAGTC-T
258 AAATCCTAT-TATCCAATGTGACTGAGATTTGT-TTCGATGAATATAGATATTTCAAGGAGTCTT
141326 TT-CTG-----A
321 TTGC-GCAAAAA
* * * * * *
141332 CCATGCAAAACTAAGTCGGCG-TCCCGGAACGCGTTTTTAGCCCAAAATCGTGATGGTTAGTACA
1 TCATGCGAAATTGAGTCGGCGCT-CCGGAACGCGTTTTTAGCCAAAAATCGTGATGGCTAGTACA
* * *** * * * *
141396 CGATTTCGGCTAAA-AACTGTCCAAA--AA----AATA--TTTTTC-CAAAATTTTTGGCACAAT
65 TGATTTCTGCTAAATTTTTG-CAAAACTAACCCGAAAAGCTTTTCCTCAAAA-TTTTGCCACAAT
* * * * *
141451 ACTCAGAAAAAATATATAATTCAATGGC-AAAAAGATTGAAGGGTTTTTTACACTTCTAATATCG
128 AGTCAGAAAAAATATATAATTCAA-CGCAAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCG
* * * *
141515 TTTTTCAATTTCTTTCCCGAGTTAATTTCTAAATAAATCGAAAAAAGATTCAGA-GATATTCCT-
192 TTTTTCAATTT-TTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATG--A-TCGTA
* * * *
141578 AAAACAAATCCTATTATCCTATGTGACAGAGATTTGTTTCGATGAATATAGAGATTTCAAGGAAT
253 AAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGT
141643 -TTTTGCGTCAAAAA
318 CTTTTGCG-CAAAAA
* * * * * *
141657 TCATGCGAAATTTAGTCGGTGCTCCGGAACGCGTTTTTAACAAAAAATAGTAATGGCTAGT
1 TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATGGCTAGT
141718 TGATCGGTCG
Statistics
Matches: 1714, Mismatches: 221, Indels: 194
0.81 0.10 0.09
Matches are distributed among these distances:
316 40 0.02
317 9 0.01
318 72 0.04
319 58 0.03
320 9 0.01
322 50 0.03
323 64 0.04
324 23 0.01
325 181 0.11
326 169 0.10
327 91 0.05
328 96 0.06
329 5 0.00
330 14 0.01
331 140 0.08
332 319 0.19
333 153 0.09
334 56 0.03
335 102 0.06
336 26 0.02
337 37 0.02
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (331 bp):
TCATGCGAAATTGAGTCGGCGCTCCGGAACGCGTTTTTAGCCAAAAATCGTGATGGCTAGTACAT
GATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTGCCACAATAGT
CAGAAAAAATATATAATTCAACGCAAAAAAGATTGAAGGATTTTTCACGCTTCTAATATCGTTTT
TCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAAAAGATTCAGATGATCGTAAAAACAAA
TCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGAGTCTTTTGCG
CAAAAA
Found at i:141070 original size:658 final size:657
Alignment explanation
Indices: 139468--141717 Score: 3911
Period size: 658 Copynumber: 3.4 Consensus size: 657
139458 GCTTTTCCTC
* * * **
139468 AAAA-TTTTGCCACAATAGTCAG-AAAAATATATAATTGAACGCCAAAAAGATTGAAGAATTTTT
1 AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTT
*
139531 CACGCTTCTAATATCGTTTTTTCAATTTTTTTCCCTAGATTAATTTCTAA-T-AATCGAAAAAAG
66 CACGCTTCTAATATCG-TTTTTCAATTTTTTTCCCGAG-TTAATTTCTAATTAAATCGAAAAAAG
139594 ATTCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATAT
129 ATTCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATAT
139659 AGATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTT
194 AGATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTT
*
139724 TTTAGCAAAAAACT-GTGATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAA
259 TTTAGCAAAAAA-TAGTAATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAA
139788 AAGCTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGC-AAAAAAAAT
323 AAGCTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAAAT
139852 TGAAGGATTTTTCGCGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAAT
388 TGAAGGATTTTTCGCGCTTCTAATATCGTTTTTCCATTTTTTT-CGAATTTATTTCTAATTAAAT
*
139917 CGAAACAAGATTCAGATGCTCGTAAAAACGAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAG
452 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAG
139982 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGG
517 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGG
140047 AACGCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
582 AACGCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCC-AAA
*
140112 TAATATTTTTCT
646 AAATATTTTTCT
*
140124 AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTT
1 AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTT
140189 CACGCTTCTAATATCGTTTTTCAATTTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGA
66 CACGCTTCTAATATCGTTTTTCAA-TTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGA
140254 TTCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATA
130 TTCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATA
*
140319 GATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGTCGGGGCTCCGGAACGCGTTT
195 GATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTT
*
140384 TTAGCAAAAAATAGTGATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAA
260 TTAGCAAAAAATAGTAATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAA
*
140449 GCTTTTCCTCGAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAAATTG
325 GCTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAAATTG
* *
140514 AAGGATTTTTCGCGCTTCTAATATCATTTTTCCATTATTTTTCGAATTTATTTCTAATTAAATTG
390 AAGGATTTTTCGCGCTTCTAATATCGTTTTTCCATT-TTTTTCGAATTTATTTCTAATTAAATCG
140579 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGAT
454 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGAT
140644 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGGAA
519 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGGAA
140709 CGCGTTTTTAGCCCAAAAATCGTGATGG-T-GTACACGATTTCGGCTAAAAACTGACCCAAAAAA
584 CGCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCAAAAAA
140772 TATTTTTCT
649 TATTTTTCT
*
140781 AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTT
1 AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTT
140846 CACGCTTCTAATATCGTTTTTCAAATTTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAG
66 CACGCTTCTAATATCGTTTTTC-AA-TTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAG
*
140911 ATTCAGAGATATTCATAAAACAAATCCTATTATCCTATGTGACTGAGATTTGTTTCGATGAATAT
129 ATTCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATAT
* *
140976 AGATATTTCAAGGGGCTTTTGCGTCAAAAATCATGCGAAATTTAGCCGGGGCTCCGGAACGCGTT
194 AGATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTT
141041 TTTAGCAAAAAACT-GTAATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAA
259 TTTAGCAAAAAA-TAGTAATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAA
141105 AAGCTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAAAA
323 AAGCTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGC-AAAAAAAAA
*
141170 TTGAAGGATTTTTCGTGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAAT
387 TTGAAGGATTTTTCGCGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAAT
141235 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAG
452 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAG
* * *
141300 ATGAATATAGATATTTCAAGGAGTCTTTCTG------ACCATGCAAAACTAAGTCGGCGTCCCGG
517 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGG
* *
141359 AACGCGTTTTTAGCCC-AAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGTCCAAAAA
582 AACGCGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCAAAA
*
141423 AATATTTTTCC
647 AATATTTTTCT
* *
141434 AAAATTTTTGGCACAATACTCAGAAAAAATATATAATTCAATGGCAAAAAGATTGAAGGGTTTTT
1 AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTT
* * * *
141499 TACACTTCTAATATCGTTTTTCAATTTCTTTCCCGAGTTAATTTCTAAATAAATCGAAAAAAGAT
66 CACGCTTCTAATATCGTTTTTCAATTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGAT
* * *
141564 TCAGAGATATTCCTAAAACAAATCCTATTATCCTATGTGACAGAGATTTGTTTCGATGAATATAG
131 TCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAG
* ** * * *
141629 AGATTTCAAGGAATTTTTGCGTCAAAAATCATGCGAAATTTAGTCGGTGCTCCGGAACGCGTTTT
196 ATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTT
*
141694 TAACAAAAAATAGTAATGGCTAGT
261 TAGCAAAAAATAGTAATGGCTAGT
141718 TGATCGGTCG
Statistics
Matches: 1536, Mismatches: 44, Indels: 33
0.95 0.03 0.02
Matches are distributed among these distances:
650 1 0.00
651 195 0.13
652 44 0.03
653 122 0.08
656 4 0.00
657 137 0.09
658 498 0.32
659 305 0.20
660 225 0.15
661 5 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (657 bp):
AAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTT
CACGCTTCTAATATCGTTTTTCAATTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGAT
TCAGAGATATTCATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAG
ATATTTCAAGGGGTTTTTGCGTCAAAAATCATGCGAAATTGAGCCGGGGCTCCGGAACGCGTTTT
TAGCAAAAAATAGTAATGGCTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAG
CTTTTCCTCAAAATTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAAATTGA
AGGATTTTTCGCGCTTCTAATATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAA
ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGA
ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACG
CGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCAAAAAATA
TTTTTCT
Found at i:145039 original size:657 final size:657
Alignment explanation
Indices: 143481--145092 Score: 2774
Period size: 656 Copynumber: 2.5 Consensus size: 657
143471 GGCTCGATCA
** *
143481 CTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATAGTGC
1 CTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTTC
* * *
143546 CACAATAGTTAGAAAGAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCGCGCTTCTGA
66 CACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCGCGCTTCTAA
*
143611 TATCGTTTTTCTA-TTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
131 TATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
**
143675 --AAATGAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAG
196 AAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAG
* * *
143738 TCTCTCTGCCAAAAATCATGCAAAACTGAATTGGCGCCCCGGAACGCGTTTTTAGCCCAAAAATC
261 TCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCCAAAAATC
*
143803 GTGATGGTTAGTACACGATTTTGGCTAAAAACTGACCAAAAAAATATTTTTCTAAAATTTTTGCC
326 GTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAAAAAAATATTTTTCTAAAATTTTTGCC
*
143868 ACAATACTCAGAAAAAATATAAAATTCATTGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAAT
391 ACAATACTCAGAAAAAATATAAAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAAT
143933 ATCGTTTTTCAATTTTTTTCACGAATTAATTTCTAACTAAATCGAAAAAAGATTCAAAGATATTC
456 ATCGTTTTTCAATTTTTTTCACGAATTAATTTCTAACTAAATCGAAAAAAGATTCAAAGATATTC
*
143998 CTAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGG
521 ATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGG
* * *
144063 GTTTTTGCGTCAAAAATCATGTGAAATTTAGTCGGGGCTCCGGAACGCGTTTTTAGCAAAAAATA
586 GTTTTTGCGTCAAAAATCATGTGAAATTTAGCCGGGACTCCGAAACGCGTTTTTAGCAAAAAATA
144128 GTGATGG
651 GTGATGG
* *
144135 CTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTGCTCGAAATTTTTG
1 CTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTT-
* *
144200 CCACAATAGCCAGAAAAAATATATAATTCAACGC-AAAAAAATTGAAGGATTTTTCGCTCTTCTA
65 CCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCGCGCTTCTA
*
144264 ATATCATTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
130 ATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
144329 TAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGGA
195 TAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGGA
*
144394 GTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCTGGAACGCGTTTTTAGCCCAAAAAT
260 GTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCCAAAAAT
144459 CGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAAAAAAATATTTTTCTAAAATTTTTGC
325 CGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAAAAAAATATTTTTCTAAAATTTTTGC
* *
144524 CACAATACTCAG-AAAAATATATAATTCAATGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAA
390 CACAATACTCAGAAAAAATATAAAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAA
* * * *
144588 TATCGTTTTTCAATTTTTTTCCCGAGTTAATTTCTAATTAAATCGAAAAAAGATTCAGAGATATT
455 TATCGTTTTTCAATTTTTTTCACGAATTAATTTCTAACTAAATCGAAAAAAGATTCAAAGATATT
144653 CATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGG
520 CATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGG
144718 GGTTTTTGCGTCAAAAATCATGCT-AAATTTAGCCGGGACTCCGAAACGCGTTTTTAGCAAAAAA
585 GGTTTTTGCGTCAAAAATCATG-TGAAATTTAGCCGGGACTCCGAAACGCGTTTTTAGCAAAAAA
144782 CT-GTGATGG
649 -TAGTGATGG
* * * *
144791 CTAGAACATGATTTCTGCTAAATTTTTTCAAAACTAACCTGAAATAACTTTTCCTCAAAATTTTT
1 CTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAA-AGCTTTTCCTCAAAATTTTT
144856 CCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAAATTGAAGGATTTTTCGCGCTTCT
65 CCACAATAGTCAGAAAAAATATATAATTCAACGC-AAAAAAAATTGAAGGATTTTTCGCGCTTCT
*
144921 AATATCGTTTTTCCATTTTTTTCCGAATTTATGTCTAATTAAATCGAAACAAGATTCAGATGCTC
129 AATATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
*
144986 GTAAAAACAAATCCTTAAATTCAA-GTGGTTGAGATTTTGTTAAATGAATATAGATATTTCAAGG
194 GTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGG
*
145050 AGTCTTTCTGCCAAAAA-CTATGCAAAACTGAGTCTGCGCCCCG
259 AGTCTTTCTGCCAAAAATC-ATGCAAAACTGAGTCGGCGCCCCG
145093 AAAAATAATT
Statistics
Matches: 905, Mismatches: 43, Indels: 17
0.94 0.04 0.02
Matches are distributed among these distances:
654 99 0.11
655 82 0.09
656 315 0.35
657 294 0.32
658 115 0.13
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (657 bp):
CTAGTACATGATTTCTGCTAAATTTTTGCAAAACTAACCCGAAAAGCTTTTCCTCAAAATTTTTC
CACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAAAATTGAAGGATTTTTCGCGCTTCTAA
TATCGTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
AAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAG
TCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGCGCCCCGGAACGCGTTTTTAGCCCAAAAATC
GTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAAAAAAATATTTTTCTAAAATTTTTGCC
ACAATACTCAGAAAAAATATAAAATTCAATGCCAAAAAGATTGACGGGTTTTTCAAGCTTCTAAT
ATCGTTTTTCAATTTTTTTCACGAATTAATTTCTAACTAAATCGAAAAAAGATTCAAAGATATTC
ATAAAACAAATCCTATTATCCAATGTGACTGAGATTTGTTTCGATGAATATAGATATTTCAAGGG
GTTTTTGCGTCAAAAATCATGTGAAATTTAGCCGGGACTCCGAAACGCGTTTTTAGCAAAAAATA
GTGATGG
Found at i:148541 original size:17 final size:17
Alignment explanation
Indices: 148519--148557 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
148509 CTAAACTTAA
*
148519 AACTTCGTCAATAAAAT
1 AACTTCGTCAATAAAAC
148536 AACTTCGTCAATAAAAC
1 AACTTCGTCAATAAAAC
148553 AACTT
1 AACTT
148558 ACCATACTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.21, G:0.05, T:0.28
Consensus pattern (17 bp):
AACTTCGTCAATAAAAC
Found at i:152669 original size:19 final size:21
Alignment explanation
Indices: 152633--152672 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
152623 ACAGGAGTTT
152633 CCAACACAAAACAACAATTAA
1 CCAACACAAAACAACAATTAA
152654 CCAACAC-AAA-AACAATTAA
1 CCAACACAAAACAACAATTAA
152673 AAAAAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 3 0.16
21 7 0.37
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (21 bp):
CCAACACAAAACAACAATTAA
Found at i:155327 original size:43 final size:43
Alignment explanation
Indices: 155266--155352 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
155256 TACCCTTGGA
155266 GGAAGGGTTTCTCGTTGCTAATATCATTCATTCGGCTGGTGAG
1 GGAAGGGTTTCTCGTTGCTAATATCATTCATTCGGCTGGTGAG
155309 GGAAGGGTTTCTCGTTGCTAATATCATTCATTCGGCTGGTGAG
1 GGAAGGGTTTCTCGTTGCTAATATCATTCATTCGGCTGGTGAG
155352 G
1 G
155353 TAATGCATAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.34
Consensus pattern (43 bp):
GGAAGGGTTTCTCGTTGCTAATATCATTCATTCGGCTGGTGAG
Found at i:155673 original size:102 final size:102
Alignment explanation
Indices: 155497--155702 Score: 412
Period size: 102 Copynumber: 2.0 Consensus size: 102
155487 GGGAGTCTAA
155497 TTCGGTCGATGATGAGATCATGGCTAATGGGCTTCAAACTACACTTGGGAATTTGCTCAAATGTT
1 TTCGGTCGATGATGAGATCATGGCTAATGGGCTTCAAACTACACTTGGGAATTTGCTCAAATGTT
155562 GAAGCAAAATTGTGTGCAATTCGAAAAGGATTACAAG
66 GAAGCAAAATTGTGTGCAATTCGAAAAGGATTACAAG
155599 TTCGGTCGATGATGAGATCATGGCTAATGGGCTTCAAACTACACTTGGGAATTTGCTCAAATGTT
1 TTCGGTCGATGATGAGATCATGGCTAATGGGCTTCAAACTACACTTGGGAATTTGCTCAAATGTT
155664 GAAGCAAAATTGTGTGCAATTCGAAAAGGATTACAAG
66 GAAGCAAAATTGTGTGCAATTCGAAAAGGATTACAAG
155701 TT
1 TT
155703 GCTTCGGACT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (102 bp):
TTCGGTCGATGATGAGATCATGGCTAATGGGCTTCAAACTACACTTGGGAATTTGCTCAAATGTT
GAAGCAAAATTGTGTGCAATTCGAAAAGGATTACAAG
Found at i:156509 original size:24 final size:25
Alignment explanation
Indices: 156460--156508 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
156450 GAACAATATA
156460 TATATGGTAAATATATCTTTCTTTT
1 TATATGGTAAATATATCTTTCTTTT
*
156485 TATAT-GTAAATATA-GTTTCTTTT
1 TATATGGTAAATATATCTTTCTTTT
156508 T
1 T
156509 TTCCAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 9 0.39
25 5 0.22
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (25 bp):
TATATGGTAAATATATCTTTCTTTT
Found at i:157214 original size:24 final size:25
Alignment explanation
Indices: 157165--157213 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
157155 GAACAATATA
157165 TATATGGTAAATATATCTTTCTTTT
1 TATATGGTAAATATATCTTTCTTTT
*
157190 TATAT-GTAAATATA-GTTTCTTTT
1 TATATGGTAAATATATCTTTCTTTT
157213 T
1 T
157214 TTCCAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.39
24 9 0.39
25 5 0.22
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (25 bp):
TATATGGTAAATATATCTTTCTTTT
Found at i:157602 original size:667 final size:669
Alignment explanation
Indices: 156043--158056 Score: 3101
Period size: 705 Copynumber: 2.9 Consensus size: 669
156033 TAGTTGTTAT
* *
156043 TTTTTGCTTATTTTTCACAAAAAAAAAGATGCTTAATCAATTAATTGATAACTTAAAAGTTGTTT
1 TTTTTGCTTGTTTTT-ACAAAAAAAAAGATGCTTAATCAATTAATTGATAGCTTAAAAGTTGTTT
* * *
156108 GGTCAATTTGGACTTGCAATGCGCAATAAAAATTTGTGAAAATTTACGTGGGAAAATTATATATT
65 GGTCAATTTGGACTTGCAATGCGCAATAATAATTTGTGTAAATTTACGCGGGAAAATTATATATT
156173 CAAAGTGAAATTGGCACGCGCGGCAATTATTTAAATGAAGATAAGAAAGGAGTTAAAAGTTCGTT
130 CAAAGTGAAATTGGCACGCGCGGCAATTATTTAAATGAAGATAAGAAAGGAGTTAAAAGTTCGTT
*
156238 GGGAGTTAGAAACAATATATGGTAACTATATCTTTCCAAACTAAACATACTAATTAATTATGGCA
195 GGGAGTTAGAAACAATATATGGTAACTATATCTTTCCAAACTAAACATATTAATTAATTATGGC-
*
156303 AAAAAAAAACACATATTAATTAATTAGTAGTTTATAATATATTGTGTAAACTTGCACGGGACGTC
259 -AAAAAAAACACATATTAATTAATTAGTAGTTTATGATATATTGTGTAAACTTGCACGGGACGTC
156368 ACCATATTTAAAGTAAATTTGGCGCGCACGGTAATTATTCAAAAGAAGATAAGAAAGAAGTTAAA
323 ACCATATTTAAAGTAAATTTGGCGCGCACGGTAATTATTCAAAAGAAGATAAGAAAGAAGTTAAA
156433 CGTTCGTTGGGAGTTGAGAACAATATATATATGGTAAATATATCTTTCTTTTTATATGTAAATAT
388 CGTTCGTTGGGAGTTGAGAACAATATATATATGGTAAATATATCTTTCTTTTTATATGTAAATAT
*
156498 AGTTTCTTTTTTTCCAAAATACGTAAATATAGTTAAAATTGCAGTTTTTCAATTCAATGATAATT
453 AGTTTCTTTTTTTCCAAAATACGTAAATATAGTTAAGATTGCAGTTTTTCAATTCAATGATAATT
* * *
156563 TGCCAAAATCTCACAAATTAAACAGTTCAATTATAAAGTTTAGGATATAAGTACTCAATTTGGTG
518 TGCCAAAATCTCACAAATTAAACATTTCAATTATATAGTTTAGGATACAAGTACTCAATTTGGTG
*
156628 ACCAGATTTGTAACGCAATATAAGTTTGTAACTTTGTATGCAAGGTACATTCAATGGTAACTTTG
583 ACTAGATTTGTAACGC-------------AA-----TAT--AA-G----TT---T-GTAACTTTG
*
156693 TATGCAAGGTACATTTTAATAGTAATAATTTTATTTGACCAAACATTTTAA
619 TATGCAAGGTACATTTTAATAGTAATAATTTTAATTGACCAAACATTTTAA
156744 TTTTTGCTTGTTTTTCACAAAAAAGAAAAAAAAGATGCTTAATCAATTAATTGATAGCTTAAAAG
1 TTTTTGCTTGTTTTT-AC-----A-AAAAAAAAGATGCTTAATCAATTAATTGATAGCTTAAAAG
*
156809 TTGTTCGGTCAATTTGGACTTGCAATGCGCAATAATAATTTGTGTAAATTTACGCGGGAAAATTA
59 TTGTTTGGTCAATTTGGACTTGCAATGCGCAATAATAATTTGTGTAAATTTACGCGGGAAAATTA
*
156874 TATATTCAAAGTGAAATTGGCACGCACGGCAATTATTTAAATGAAGATAAGAAAGGAGTTAAAAG
124 TATATTCAAAGTGAAATTGGCACGCGCGGCAATTATTTAAATGAAGATAAGAAAGGAGTTAAAAG
156939 TTCGTTGGGAGTTAGAAACAATATATGGTAACTATATCTTTCCAAACTAAACATATTAATTAATT
189 TTCGTTGGGAGTTAGAAACAATATATGGTAACTATATCTTTCCAAACTAAACATATTAATTAATT
*
157004 ATGGCAAAAAAAACACATATTAATTAATTAGTAGTTTATGATATATTATGTAAACTTGCACGGGA
254 ATGGCAAAAAAAACACATATTAATTAATTAGTAGTTTATGATATATTGTGTAAACTTGCACGGGA
* *
157069 CGTCACCATATTTAAAGTAAATTTGGTGCGCACGGCAATTATTCAAAAGAAGATAAGAAAGAAGT
319 CGTCACCATATTTAAAGTAAATTTGGCGCGCACGGTAATTATTCAAAAGAAGATAAGAAAGAAGT
157134 TAAACGTTCGTTGGGAGTTGAGAACAATATATATATGGTAAATATATCTTTCTTTTTATATGTAA
384 TAAACGTTCGTTGGGAGTTGAGAACAATATATATATGGTAAATATATCTTTCTTTTTATATGTAA
* * *
157199 ATATAGTTTCTTTTTTTCCAAAATACGTAAATATGGTTAAGATTACAGTTTTCCAATTCAATGAT
449 ATATAGTTTCTTTTTTTCCAAAATACGTAAATATAGTTAAGATTGCAGTTTTTCAATTCAATGAT
* *
157264 AATTTGTCAAAATCTCACAAATCAAACATTTCAATTATATAGTTTAGGATACAAGTACTCAATTT
514 AATTTGCCAAAATCTCACAAATTAAACATTTCAATTATATAGTTTAGGATACAAGTACTCAATTT
157329 GGTGACTAGATTTGTAACGCAATATAAGTTTGTAACTTTGTATGCAAGGTACATTTTAATAGTAA
579 GGTGACTAGATTTGTAACGCAATATAAGTTTGTAACTTTGTATGCAAGGTACATTTTAATAGTAA
*
157394 TAATTTTAATTGACCAAATATTTTAA
644 TAATTTTAATTGACCAAACATTTTAA
*
157420 TTTTTGCTTGTTTTT-CAAAAAAAAA-ATGTTTAATCAATTAATTGATAGCTTAAAAGTTGTTTG
1 TTTTTGCTTGTTTTTACAAAAAAAAAGATGCTTAATCAATTAATTGATAGCTTAAAAGTTGTTTG
* *
157483 GTCAATTTGGACTTGCAATGGGCAATAATAATTTGTGTAAATTTATGCGGGAAAATTATATATTC
66 GTCAATTTGGACTTGCAATGCGCAATAATAATTTGTGTAAATTTACGCGGGAAAATTATATATTC
* * * *
157548 AAAGTGAAATTGGCACGCGCGGCAATTATTCAAATGAAAATAAGAAATGAGTTAAAAGTTTGTTG
131 AAAGTGAAATTGGCACGCGCGGCAATTATTTAAATGAAGATAAGAAAGGAGTTAAAAGTTCGTTG
*
157613 GGAGTTAGAAACAATATATGGTAACCATATCTTTCCAAACTAAACATATTAATTAATTATGGCAA
196 GGAGTTAGAAACAATATATGGTAACTATATCTTTCCAAACTAAACATATTAATTAATTATGGCAA
* * * *
157678 AAGAAACACATATTAATTAA-T--TAGTTTATGATATATTGTGTAAATTTGCACGGAACGTCACA
261 AAAAAACACATATTAATTAATTAGTAGTTTATGATATATTGTGTAAACTTGCACGGGACGTCACC
* *
157740 ATATTTAAAGTAAATTTGGCGCGCACTGTAATTATTCAAAAGAAGATAAGAAAGAAGTTAAAAGT
326 ATATTTAAAGTAAATTTGGCGCGCACGGTAATTATTCAAAAGAAGATAAGAAAGAAGTTAAACGT
** *
157805 TCGTTGGGAGTTGAGAACAATATATATATATATATATATATGAATGATAAATGTTTCTTTTTATA
391 TCGTTGGGAGTTGAGAAC-----A-ATATATATAT-GGTA--AAT-AT--ATCTTTCTTTTTATA
*
157870 TGTAAATATAGTTT-TTTTTTGT-CAAAATACGTAAATATAATTAAGATTGCAGTTTTTCAATTC
444 TGTAAATATAGTTTCTTTTTT-TCCAAAATACGTAAATATAGTTAAGATTGCAGTTTTTCAATTC
* *
157933 AATGATAATTTGCCAAAATCTCCCAAATTAAACATTTTAA-TATATAGTTTAGGATACAAGTACT
508 AATGATAATTTGCCAAAATCTCACAAATTAAACATTTCAATTATATAGTTTAGGATACAAGTACT
157997 CAA-TTGGTGACTAGATTTGTAACGCAATATAAGTTTGTAACTTTGTATGCAAGGTACATT
573 CAATTTGGTGACTAGATTTGTAACGCAATATAAGTTTGTAACTTTGTATGCAAGGTACATT
158057 CAATGGTAAC
Statistics
Matches: 1240, Mismatches: 54, Indels: 66
0.91 0.04 0.05
Matches are distributed among these distances:
664 116 0.09
666 1 0.00
667 242 0.20
668 8 0.01
669 2 0.00
670 10 0.01
671 2 0.00
673 60 0.05
674 30 0.02
675 79 0.06
676 102 0.08
677 1 0.00
680 2 0.00
684 1 0.00
685 2 0.00
687 3 0.00
692 2 0.00
701 17 0.01
705 326 0.26
706 1 0.00
707 233 0.19
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (669 bp):
TTTTTGCTTGTTTTTACAAAAAAAAAGATGCTTAATCAATTAATTGATAGCTTAAAAGTTGTTTG
GTCAATTTGGACTTGCAATGCGCAATAATAATTTGTGTAAATTTACGCGGGAAAATTATATATTC
AAAGTGAAATTGGCACGCGCGGCAATTATTTAAATGAAGATAAGAAAGGAGTTAAAAGTTCGTTG
GGAGTTAGAAACAATATATGGTAACTATATCTTTCCAAACTAAACATATTAATTAATTATGGCAA
AAAAAACACATATTAATTAATTAGTAGTTTATGATATATTGTGTAAACTTGCACGGGACGTCACC
ATATTTAAAGTAAATTTGGCGCGCACGGTAATTATTCAAAAGAAGATAAGAAAGAAGTTAAACGT
TCGTTGGGAGTTGAGAACAATATATATATGGTAAATATATCTTTCTTTTTATATGTAAATATAGT
TTCTTTTTTTCCAAAATACGTAAATATAGTTAAGATTGCAGTTTTTCAATTCAATGATAATTTGC
CAAAATCTCACAAATTAAACATTTCAATTATATAGTTTAGGATACAAGTACTCAATTTGGTGACT
AGATTTGTAACGCAATATAAGTTTGTAACTTTGTATGCAAGGTACATTTTAATAGTAATAATTTT
AATTGACCAAACATTTTAA
Found at i:158956 original size:131 final size:133
Alignment explanation
Indices: 158805--159060 Score: 401
Period size: 132 Copynumber: 1.9 Consensus size: 133
158795 CATTGTTTAA
* * *
158805 ACTTTTATAGTTTTAGTCAACTAAAAGCTCTATT-TTTATTTAATTAAATCTAATATCCTTATAA
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTCCTTATTTAATTAAATCTAATATCCTTATAA
* *
158869 CTATTTAATTTTTA-CTATTTTAATATTTTAATT-AAAAACGTATATATATTAGAATTTTTTTAA
66 CTATTTAATTTTTATC-ATTTTAATAATTTAATTAAAAAACGTAGATATATTAGAATTTTTTTAA
158932 ATAC
130 ATAC
*
158936 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTCCTTATTTAATTAAATCTAATATCCTTATAC
1 ACTTTTATAGTTTTACTCAACTAAAAACTCTATTCCTTATTTAATTAAATCTAATATCCTTATAA
* * *
159001 CTATTTTATTTTTATCATTTTACTAATTTAATTAAAAAACTTAGATATATTAGAATTTTT
66 CTATTTAATTTTTATCATTTTAATAATTTAATTAAAAAACGTAGATATATTAGAATTTTT
159061 AAAATATATT
Statistics
Matches: 113, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
131 32 0.28
132 56 0.50
133 25 0.22
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (133 bp):
ACTTTTATAGTTTTACTCAACTAAAAACTCTATTCCTTATTTAATTAAATCTAATATCCTTATAA
CTATTTAATTTTTATCATTTTAATAATTTAATTAAAAAACGTAGATATATTAGAATTTTTTTAAA
TAC
Found at i:172913 original size:36 final size:36
Alignment explanation
Indices: 172866--172938 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
172856 CCTTGCTTAA
**
172866 ATAATATGATGATTGCCAATTGAGGTTGGTTGAGTT
1 ATAATATGATGATCACCAATTGAGGTTGGTTGAGTT
172902 ATAATATGATGATCACCAATTGAGGTTGGTTGAGTT
1 ATAATATGATGATCACCAATTGAGGTTGGTTGAGTT
172938 A
1 A
172939 GTAAGGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (36 bp):
ATAATATGATGATCACCAATTGAGGTTGGTTGAGTT
Found at i:188341 original size:29 final size:28
Alignment explanation
Indices: 188308--188384 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 28
188298 AAGTAGTATT
* *
188308 AATTAGTGCAAATTTTGTGGTGC-TAAAAA
1 AATTATTGCAAATTTTGT-GT-CAAAAAAA
188337 AATTATTGCAAATTTTGCTGTCAAAAAAA
1 AATTATTGCAAATTTTG-TGTCAAAAAAA
188366 AATTTATTGCAAATTTTGT
1 AA-TTATTGCAAATTTTGT
188385 ATAGAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 1 0.02
29 26 0.60
30 16 0.37
ACGTcount: A:0.39, C:0.08, G:0.14, T:0.39
Consensus pattern (28 bp):
AATTATTGCAAATTTTGTGTCAAAAAAA
Found at i:192954 original size:7 final size:7
Alignment explanation
Indices: 192938--192967 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
192928 AAAAGAAAAG
192938 AAAAAC-
1 AAAAACA
192944 AAAAACA
1 AAAAACA
192951 AAAAACA
1 AAAAACA
192958 AAAAACA
1 AAAAACA
192965 AAA
1 AAA
192968 CATACTGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:203100 original size:36 final size:36
Alignment explanation
Indices: 202826--203102 Score: 270
Period size: 36 Copynumber: 7.7 Consensus size: 36
202816 GCCCAGATGT
** * * * *
202826 AGGATTTGGTCCTTGCCCATAACTCTGTCCAAAGGC
1 AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
* * * **
202862 AGGATTTGCTCCTTGCCCAAAATCCTGGGCATAGCC
1 AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
* **
202898 AGGATTTGCCCCTTG-CC-TGAAGTTCTGACTGTAGCC
1 AGGATTTGCCCCTTGCCCAT-AA-TTCTGCCCATAGCC
* ** *
202934 AGGATTTTCCTGTTGCCCATAATTCTGCCCATGGCC
1 AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
**
202970 AGGATTTGCCTGTTGCCCATAATTCTGCCCATAGCC
1 AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
* ** * *
203006 TGGATTTGCCTGTTGCCCATATTTCTGCCCAAAGCC
1 AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
*
203042 AGGATTTGTCCCTTGCCCATAATTCTGCCCATAGCC
1 AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
* *
203078 TGGATTTGCCCCTTGCCGATAATTC
1 AGGATTTGCCCCTTGCCCATAATTC
203103 CCACCTTCTG
Statistics
Matches: 201, Mismatches: 36, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
35 4 0.02
36 192 0.96
37 4 0.02
38 1 0.00
ACGTcount: A:0.19, C:0.30, G:0.21, T:0.31
Consensus pattern (36 bp):
AGGATTTGCCCCTTGCCCATAATTCTGCCCATAGCC
Found at i:203347 original size:24 final size:24
Alignment explanation
Indices: 203333--203461 Score: 135
Period size: 24 Copynumber: 5.5 Consensus size: 24
203323 GGTTGTATGA
203333 TGGATTCCCTTGCTGGTTTTGCAT
1 TGGATTCCCTTGCTGGTTTTGCAT
* *
203357 TGGATTTCCTTGCTGG--TTGTA-
1 TGGATTCCCTTGCTGGTTTTGCAT
*
203378 TGGACTCCC-TGACTGGTTTTGCAT
1 TGGATTCCCTTG-CTGGTTTTGCAT
* *
203402 TGGATTTCCTTGCTGGGTGTATG-A-
1 TGGATTCCCTTGCT-GGT-TTTGCAT
*
203426 TGGATTGCCTTGCTGGTTTTGCAT
1 TGGATTCCCTTGCTGGTTTTGCAT
203450 TGGATTCCCTTG
1 TGGATTCCCTTG
203462 TCGTTCATAC
Statistics
Matches: 85, Mismatches: 11, Indels: 18
0.75 0.10 0.16
Matches are distributed among these distances:
20 2 0.02
21 11 0.13
22 7 0.08
23 8 0.09
24 48 0.56
25 6 0.07
26 3 0.04
ACGTcount: A:0.10, C:0.19, G:0.28, T:0.43
Consensus pattern (24 bp):
TGGATTCCCTTGCTGGTTTTGCAT
Found at i:203394 original size:45 final size:47
Alignment explanation
Indices: 203319--203461 Score: 193
Period size: 45 Copynumber: 3.0 Consensus size: 47
203309 TGCAAACCCC
*
203319 TGCTGGTTGTATGATGGATTCCCTTGCTGGTTTTGCATTGGATTTCCT
1 TGCTGGGTGTATGATGGATTCCC-TGCTGGTTTTGCATTGGATTTCCT
* *
203367 TGCT-GGT-TGT-ATGGACTCCCTGACTGGTTTTGCATTGGATTTCCT
1 TGCTGGGTGTATGATGGATTCCCTG-CTGGTTTTGCATTGGATTTCCT
* *
203412 TGCTGGGTGTATGATGGATTGCCTTGCTGGTTTTGCATTGGATTCCCT
1 TGCTGGGTGTATGATGGATT-CCCTGCTGGTTTTGCATTGGATTTCCT
203460 TG
1 TG
203462 TCGTTCATAC
Statistics
Matches: 83, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
44 2 0.02
45 35 0.42
46 5 0.06
47 4 0.05
48 33 0.40
49 4 0.05
ACGTcount: A:0.10, C:0.17, G:0.29, T:0.43
Consensus pattern (47 bp):
TGCTGGGTGTATGATGGATTCCCTGCTGGTTTTGCATTGGATTTCCT
Found at i:209828 original size:51 final size:51
Alignment explanation
Indices: 209752--209859 Score: 180
Period size: 51 Copynumber: 2.1 Consensus size: 51
209742 CTTCTTCCTT
* *
209752 CTTCATTTCCCATTCTCCATTTGTTTAGAGGGTACTTAAGTAGAGGTCATG
1 CTTCATTTCCCATTCTCCATTTGTTTAGAGGGGACTTAAGCAGAGGTCATG
* *
209803 CTTCATTTGCCATTCTCCATTTGTTTAGTGGGGACTTAAGCAGAGGTCATG
1 CTTCATTTCCCATTCTCCATTTGTTTAGAGGGGACTTAAGCAGAGGTCATG
209854 CTTCAT
1 CTTCAT
209860 GAAAAATTCT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (51 bp):
CTTCATTTCCCATTCTCCATTTGTTTAGAGGGGACTTAAGCAGAGGTCATG
Found at i:213358 original size:15 final size:16
Alignment explanation
Indices: 213338--213371 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
213328 ACAGCCGGGT
*
213338 AAGAAGAAGAAA-AAA
1 AAGAAGAAAAAAGAAA
213353 AAGAAGAAAAAAGAAA
1 AAGAAGAAAAAAGAAA
213369 AAG
1 AAG
213372 GCAAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAGAAGAAAAAAGAAA
Found at i:221752 original size:12 final size:12
Alignment explanation
Indices: 221735--221765 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
221725 TTGGGTTATT
221735 TGAGTTTTTTAG
1 TGAGTTTTTTAG
221747 TGAGTTTTTTAG
1 TGAGTTTTTTAG
*
221759 TCAGTTT
1 TGAGTTT
221766 ATTAAACACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.16, C:0.03, G:0.23, T:0.58
Consensus pattern (12 bp):
TGAGTTTTTTAG
Found at i:246961 original size:10 final size:10
Alignment explanation
Indices: 246946--246970 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
246936 TATGAGATCT
246946 GAGAAAAAGA
1 GAGAAAAAGA
246956 GAGAAAAAGA
1 GAGAAAAAGA
246966 GAGAA
1 GAGAA
246971 GGAGAAGACG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
GAGAAAAAGA
Found at i:247104 original size:2 final size:2
Alignment explanation
Indices: 247099--247156 Score: 51
Period size: 2 Copynumber: 32.5 Consensus size: 2
247089 ATATAAACGG
247099 AT AT AT CAT AT AT AT AT AT A- AT AT AT AT -T A- AT A- AT AT A-
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
247137 AT A- AT AT -T AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
247157 AAGGGTCGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
1 8 0.17
2 37 0.79
3 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:247115 original size:11 final size:11
Alignment explanation
Indices: 247099--247156 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
247089 ATATAAACGG
*
247099 ATATATCATAT
1 ATATATTATAT
247110 ATATA-TATAAT
1 ATATATTAT-AT
247121 ATATATTA-AT
1 ATATATTATAT
*
247131 A-ATATAATA-
1 ATATATTATAT
247140 ATATTATTATAT
1 ATA-TATTATAT
247152 ATATA
1 ATATA
247157 AAGGGTCGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
9 6 0.16
10 7 0.18
11 20 0.53
12 5 0.13
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATATTATAT
Found at i:247117 original size:13 final size:13
Alignment explanation
Indices: 247099--247157 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
247089 ATATAAACGG
*
247099 ATATATCATATAT
1 ATATATAATATAT
247112 ATATATAATATAT
1 ATATATAATATAT
247125 AT-TAATAATATA-
1 ATAT-ATAATATAT
*
247137 ATA-ATATTATTAT
1 ATATATAATA-TAT
247150 ATATATAA
1 ATATATAA
247158 AGGGTCGGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
13 25 0.66
14 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (13 bp):
ATATATAATATAT
Found at i:271871 original size:14 final size:14
Alignment explanation
Indices: 271849--271881 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
271839 AGTATTTTGC
271849 AAAAA-AAAAAGAA
1 AAAAAGAAAAAGAA
271862 AAAAAGAAAAAGAA
1 AAAAAGAAAAAGAA
*
271876 TAAAAG
1 AAAAAG
271882 TGAACTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAGAA
Found at i:276263 original size:49 final size:49
Alignment explanation
Indices: 276206--276299 Score: 188
Period size: 49 Copynumber: 1.9 Consensus size: 49
276196 ATCATTTTTC
276206 TACCTTCAAGCATAAGAAATTTACTTGAATTAGGATTGACACTTTTGTA
1 TACCTTCAAGCATAAGAAATTTACTTGAATTAGGATTGACACTTTTGTA
276255 TACCTTCAAGCATAAGAAATTTACTTGAATTAGGATTGACACTTT
1 TACCTTCAAGCATAAGAAATTTACTTGAATTAGGATTGACACTTT
276300 GTAAACGTAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (49 bp):
TACCTTCAAGCATAAGAAATTTACTTGAATTAGGATTGACACTTTTGTA
Found at i:286443 original size:21 final size:21
Alignment explanation
Indices: 286419--286459 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
286409 GAAATATTGA
286419 GATTAAACACTGTACATATGG
1 GATTAAACACTGTACATATGG
* *
286440 GATTAGATACTGTACATATG
1 GATTAAACACTGTACATATG
286460 ATAATATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (21 bp):
GATTAAACACTGTACATATGG
Found at i:287921 original size:22 final size:22
Alignment explanation
Indices: 287893--288125 Score: 170
Period size: 22 Copynumber: 10.5 Consensus size: 22
287883 TGTCTCTTTG
*
287893 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAGGA
* *
287915 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGGA
*
287938 -GGTTATCAAAATTCCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
*
287959 TGGTTATCAAAACTTCATATGGA
1 TGGTTATCAAAATTTCATA-GGA
* *
287982 -AGTTATCAAAAATTTCATGGGA
1 TGGTTATC-AAAATTTCATAGGA
*
288004 AGGTTATCAAAATTTCATAGTG-
1 TGGTTATCAAAATTTCATAG-GA
* *
288026 TGG-TACCAAAATTTTATAGGA
1 TGGTTATCAAAATTTCATAGGA
** *
288047 TCAGGTTATTGAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAGGA
* ** *
288071 AGGTTATTGAAATTTCATAGTA
1 TGGTTATCAAAATTTCATAGGA
* * * *
288093 TGATTATCACAATTTTATAGAA
1 TGGTTATCAAAATTTCATAGGA
*
288115 AGGTTATCAAA
1 TGGTTATCAAA
288126 GAGATTATCA
Statistics
Matches: 165, Mismatches: 34, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.01
21 17 0.10
22 112 0.68
23 22 0.13
24 13 0.08
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGGA
Found at i:288062 original size:67 final size:66
Alignment explanation
Indices: 287891--288121 Score: 222
Period size: 67 Copynumber: 3.5 Consensus size: 66
287881 CTTGTCTCTT
* *
287891 TGTGGTTATCAAAATTTCATAAGAT-GGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 TGTGGTTATCAAAATTTCATAGGATAGGTTATTA-AATTTCATG-GGAAGGTTATCAAAATTTCA
287954 TAG
64 TAG
* *
287957 TGTGGTTATCAAAACTTCATATGGA-A-GTTATCAAAAATTTCATGGGAAGGTTATCAAAATTTC
1 TGTGGTTATCAAAATTTCATA-GGATAGGTTAT--TAAATTTCATGGGAAGGTTATCAAAATTTC
288020 ATAG
63 ATAG
* * * * **
288024 TGTGG-TACCAAAATTTTATAGGATCAGGTTATTGAAATTTCTTAGGAAGGTTATTGAAATTTCA
1 TGTGGTTATCAAAATTTCATAGGAT-AGGTTATT-AAATTTCATGGGAAGGTTATCAAAATTTCA
288088 TAG
64 TAG
* * * * *
288091 TATGATTATCACAATTTTATA-GAAAGGTTAT
1 TGTGGTTATCAAAATTTCATAGGATAGGTTAT
288122 CAAAGAGATT
Statistics
Matches: 138, Mismatches: 17, Indels: 20
0.79 0.10 0.11
Matches are distributed among these distances:
65 3 0.02
66 46 0.33
67 70 0.51
68 19 0.14
ACGTcount: A:0.35, C:0.09, G:0.18, T:0.38
Consensus pattern (66 bp):
TGTGGTTATCAAAATTTCATAGGATAGGTTATTAAATTTCATGGGAAGGTTATCAAAATTTCATA
G
Found at i:288155 original size:22 final size:21
Alignment explanation
Indices: 288130--288543 Score: 153
Period size: 22 Copynumber: 18.7 Consensus size: 21
288120 ATCAAAGAGA
*
288130 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* *
288152 TTAT-AAGAATTTCATAGTGTGA
1 TTATCAA-AATTTCATAG-GAGG
*
288174 TTAACAAAATTTCATAAGGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
288196 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* *
288218 TTATCAAAATTTTATAGTATGG
1 TTATCAAAATTTCATAGGA-GG
** *
288240 TTATCAAAATTTTTTAGTGTGG
1 TTATCAAAATTTCATAG-GAGG
* **
288262 TTAACAAAATTTCATATAAAGG
1 TTATCAAAATTTCATA-GGAGG
*
288284 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * * *
288309 AGTACCAACATTTGATAGAAGG
1 -TTATCAAAATTTCATAGGAGG
* * *
288331 TTATC-AAATCTCATAGAATGA
1 TTATCAAAATTTCATAGGA-GG
*
288352 TTATCGAAATTTCATAGAGATCGG
1 TTATCAAAATTTCATAG-GA--GG
* *
288376 ATTATGAAAATTT-ATAGGA-A
1 -TTATCAAAATTTCATAGGAGG
**
288396 TATGATCAAAATTTCATAGTGCTG
1 T-T-ATCAAAATTTCATAG-GAGG
*
288420 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
* * *
288442 TTATCAAAATTACATAATGTA-A
1 TTATCAAAATTTCAT-A-GGAGG
*
288464 TTATCAAAAATTT-ATAGAGGGG
1 TTATC-AAAATTTCATAG-GAGG
* * *
288486 TCAACAAAATTTTATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
288508 TTATCAAAATTTCATAGAGAGG
1 TTATCAAAATTTCATAG-GAGG
*
288530 TTATCAAATTTTCA
1 TTATCAAAATTTCA
288544 AAATGTGATT
Statistics
Matches: 294, Mismatches: 65, Indels: 66
0.69 0.15 0.16
Matches are distributed among these distances:
19 1 0.00
20 19 0.06
21 31 0.11
22 190 0.65
23 20 0.07
24 7 0.02
25 15 0.05
26 2 0.01
28 9 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:288378 original size:25 final size:22
Alignment explanation
Indices: 288318--288414 Score: 69
Period size: 21 Copynumber: 4.4 Consensus size: 22
288308 GAGTACCAAC
* *
288318 ATTTGATAGAA-GGTTATC-AA
1 ATTTCATAGAATGATTATCGAA
*
288338 ATCTCATAGAATGATTATCGAA
1 ATTTCATAGAATGATTATCGAA
288360 ATTTCATAGAGATCGGATTAT-GAAA
1 ATTTCATAGA-AT--GATTATCG-AA
* *
288385 ATTT-ATAGGAAT-ATGATCAAA
1 ATTTCATA-GAATGATTATCGAA
288406 ATTTCATAG
1 ATTTCATAG
288415 TGCTGTTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
20 9 0.15
21 17 0.27
22 14 0.23
23 2 0.03
24 6 0.10
25 14 0.23
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.34
Consensus pattern (22 bp):
ATTTCATAGAATGATTATCGAA
Found at i:288468 original size:44 final size:44
Alignment explanation
Indices: 288400--288568 Score: 148
Period size: 44 Copynumber: 3.8 Consensus size: 44
288390 TAGGAATATG
* * * *
288400 ATCAAAATTTCATAGTGCT-GTTATCAAAATTTCAAAGCGAGGTT
1 ATCAAAATTTCATAATG-TAATTATCAAAATTTCATAGAGAGGTT
* * *
288444 ATCAAAATTACATAATGTAATTATCAAAAATTT-ATAGAGGGGTC
1 ATCAAAATTTCATAATGTAATTATC-AAAATTTCATAGAGAGGTT
* * *
288488 AACAAAATTTTATAGA-G-AGGTTATCAAAATTTCATAGAGAGGTT
1 ATCAAAATTTCATA-ATGTA-ATTATCAAAATTTCATAGAGAGGTT
* * * *
288532 ATCAAATTTTCAAAATGTGATTACCAAAATTTCATAG
1 ATCAAAATTTCATAATGTAATTATCAAAATTTCATAG
288569 TGGTATTTCT
Statistics
Matches: 98, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
43 10 0.10
44 80 0.82
45 8 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (44 bp):
ATCAAAATTTCATAATGTAATTATCAAAATTTCATAGAGAGGTT
Found at i:288480 original size:88 final size:88
Alignment explanation
Indices: 288382--288568 Score: 198
Period size: 88 Copynumber: 2.1 Consensus size: 88
288372 TCGGATTATG
* * * * ** *
288382 AAAATTTATAGGA-ATATGATCAAAATTTCATAGTGCTGTTATCAAAATTTCAAAGCGAGGTTAT
1 AAAATTTATAGGAGAGATCAACAAAATTTCATAGAGAGGTTATCAAAATTTCAAAGAGAGGTTAT
*
288446 CAAAATTACATAATGTAATTATCA
66 CAAAATTACAAAATGTAATTA-CA
* * * *
288470 AAAATTTATA-GAGGGGTCAACAAAATTTTATAGAGAGGTTATCAAAATTTCATAGAGAGGTTAT
1 AAAATTTATAGGAGAGATCAACAAAATTTCATAGAGAGGTTATCAAAATTTCAAAGAGAGGTTAT
* * * *
288534 CAAATTTTCAAAATGTGATTACC
66 CAAAATTACAAAATGTAATTACA
288557 AAAATTTCATAG
1 AAAATTT-ATAG
288569 TGGTATTTCT
Statistics
Matches: 80, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
87 10 0.12
88 70 0.88
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (88 bp):
AAAATTTATAGGAGAGATCAACAAAATTTCATAGAGAGGTTATCAAAATTTCAAAGAGAGGTTAT
CAAAATTACAAAATGTAATTACA
Found at i:289212 original size:22 final size:22
Alignment explanation
Indices: 288649--289212 Score: 215
Period size: 22 Copynumber: 26.0 Consensus size: 22
288639 TTATGGAGTA
* *
288649 ATCAAAATTTC--AGGGAGGAT
1 ATCAAAATTTCATAAGGAGGTT
* *
288669 ATCAAAATTTCATATGAAGGTT
1 ATCAAAATTTCATAAGGAGGTT
*
288691 ATCAAAATTTCAT-AGTTTA-GTT
1 ATCAAAATTTCATAAG--GAGGTT
*
288713 TTCAAAATTTCATAA-GAGGGTT
1 ATCAAAATTTCATAAGGA-GGTT
* ***
288735 ATCAAAATTTCAT-AGTATGCAG
1 ATCAAAATTTCATAAGGA-GGTT
* * *
288757 ATCAAAGTTTCATAGGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* * *
288779 AACAAAATTTCAGAATGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* **
288801 ATAAAAAAAATCAT-AGGAAGGTT
1 AT-CAAAATTTCATAAGG-AGGTT
*
288824 ATCAAAA-TT--T--GTA-GTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
288840 ATCAAGATTTCATCAGGAGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
288862 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATAAGGAGG-TT
288885 ATCAAAATTTCAT-AGCGAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
* * *
288907 ATCACAATTTCAT-AGTGTGATT
1 ATCAAAATTTCATAAG-GAGGTT
* * * *
288929 ATCAAAATTTCAGAATGTGATT
1 ATCAAAATTTCATAAGGAGGTT
* *
288951 A-CTAACAA-TTCATATGAAGGTT
1 ATC-AA-AATTTCATAAGGAGGTT
* * * * *
288973 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
288995 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* *
289017 ATCAACATTTCAT-AGTGTTGGTT
1 ATCAAAATTTCATAAG-G-AGGTT
* ** *
289040 TTCAAAATTTCATTGGGAAGTT
1 ATCAAAATTTCATAAGGAGGTT
289062 ATCAAAATTTCAT-AGTGAGGTCT
1 ATCAAAATTTCATAAG-GAGGT-T
* *
289085 -TCAAAATTCCTTAAGGAGGTT
1 ATCAAAATTTCATAAGGAGGTT
* * *
289106 AACAAAATTTCATAAGAAGATT
1 ATCAAAATTTCATAAGGAGGTT
** * ** *
289128 AAAAAAAATT-ATAAAAAGGCT
1 ATCAAAATTTCATAAGGAGGTT
* * *
289149 CTC-AAATTCCAT--GGTATTGTT
1 ATCAAAATTTCATAAGG-A-GGTT
* *
289170 ATTAAAATTTCAT-AGAAAGGTT
1 ATCAAAATTTCATAAG-GAGGTT
289192 ATCAAAATTTCATAAGGAGGT
1 ATCAAAATTTCATAAGGAGGT
289213 CATAAAAAAT
Statistics
Matches: 394, Mismatches: 112, Indels: 74
0.68 0.19 0.13
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 2 0.01
20 17 0.04
21 23 0.06
22 276 0.70
23 62 0.16
24 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
ATCAAAATTTCATAAGGAGGTT
Found at i:289220 original size:22 final size:22
Alignment explanation
Indices: 289173--289220 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
289163 TATTGTTATT
* *
289173 AAAATTTCATAGAAAGGTTATC
1 AAAATTTCATAGAAAGGTCATA
*
289195 AAAATTTCATA-AGGAGGTCATA
1 AAAATTTCATAGA-AAGGTCATA
289217 AAAA
1 AAAA
289221 ATAATGTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (22 bp):
AAAATTTCATAGAAAGGTCATA
Done.