Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011244.1 Kokia drynarioides strain JFW-HI SEQ_126222, 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: 289877
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 1 of 2
Found at i:771 original size:29 final size:28
Alignment explanation
Indices: 731--801 Score: 74
Period size: 30 Copynumber: 2.5 Consensus size: 28
721 TTTTTTTGAA
731 AAAAAAAC--TTAACAGTTCAATGACTTT
1 AAAAAAACTTTTAACAGTTCAATGAC-TT
* *
758 AAAAAAACTTTTAAATAGTTCAGTGACTT
1 AAAAAAACTTTT-AACAGTTCAATGACTT
*
787 AAATAAAAATTTTAA
1 AAA-AAAACTTTTAA
802 ATAATTTAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 8 0.22
29 9 0.24
30 20 0.54
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (28 bp):
AAAAAAACTTTTAACAGTTCAATGACTT
Found at i:778 original size:30 final size:30
Alignment explanation
Indices: 744--804 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
734 AAAACTTAAC
*
744 AGTTCAATGACTTTAAA-AAAACTTTTAAAT
1 AGTTCAATGAC-TTAAATAAAAATTTTAAAT
*
774 AGTTCAGTGACTTAAATAAAAATTTTAAAT
1 AGTTCAATGACTTAAATAAAAATTTTAAAT
804 A
1 A
805 ATTTAGTGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (30 bp):
AGTTCAATGACTTAAATAAAAATTTTAAAT
Found at i:813 original size:30 final size:30
Alignment explanation
Indices: 746--813 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 30
736 AACTTAACAG
* * *
746 TTCAATGACTTTAAAAAAACTTTTAAATAG
1 TTCAGTGACTTTAAAAAAAATTTTAAATAA
776 TTCAGTGAC-TTAAATAAAAATTTTAAATAA
1 TTCAGTGACTTTAAA-AAAAATTTTAAATAA
*
806 TTTAGTGA
1 TTCAGTGA
814 TCAAATTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.46, C:0.07, G:0.09, T:0.38
Consensus pattern (30 bp):
TTCAGTGACTTTAAAAAAAATTTTAAATAA
Found at i:6834 original size:23 final size:23
Alignment explanation
Indices: 6803--6914 Score: 134
Period size: 23 Copynumber: 4.8 Consensus size: 23
6793 AAGAGTACCG
* *
6803 AAGTACTAAACAGAGAGCACACA
1 AAGTGCTAAACGGAGAGCACACA
*
6826 AAGTGCTAATAACGGAGAGTACACA
1 AAGTGCT-A-AACGGAGAGCACACA
* * *
6851 AAGTACTAATCGGAGAGCATACA
1 AAGTGCTAAACGGAGAGCACACA
6874 AAGTGCTAAACGGAGAGCACACA
1 AAGTGCTAAACGGAGAGCACACA
* *
6897 CAGTGCTAAATGGAGAGC
1 AAGTGCTAAACGGAGAGC
6915 GCGCTAAGGT
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
23 54 0.72
24 2 0.03
25 19 0.25
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (23 bp):
AAGTGCTAAACGGAGAGCACACA
Found at i:6867 original size:48 final size:46
Alignment explanation
Indices: 6788--6914 Score: 141
Period size: 48 Copynumber: 2.7 Consensus size: 46
6778 ATACGGAACA
* * * *
6788 AAACGAAGAGTAC-CGAAGTACTAAACAGAGAGCACACAAAGTGCT
1 AAACGGAGAGTACACAAAGTACTAATCGGAGAGCACACAAAGTGCT
*
6833 AATAACGGAGAGTACACAAAGTACTAATCGGAGAGCATACAAAGTGCT
1 -A-AACGGAGAGTACACAAAGTACTAATCGGAGAGCACACAAAGTGCT
* * *
6881 AAACGGAGAGCACACACAGTGCTAAAT-GGAGAGC
1 AAACGGAGAGTACACAAAGTACT-AATCGGAGAGC
6915 GCGCTAAGGT
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 27 0.39
47 15 0.21
48 28 0.40
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (46 bp):
AAACGGAGAGTACACAAAGTACTAATCGGAGAGCACACAAAGTGCT
Found at i:13089 original size:19 final size:20
Alignment explanation
Indices: 13051--13089 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
13041 AAGAACACAC
*
13051 AAAGTGCTAATAATGGAGAGT
1 AAAGTGCTAAT-ACGGAGAGT
13072 AAAGTGCTAAT-CGGAGAG
1 AAAGTGCTAATACGGAGAG
13090 CACACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.41, C:0.08, G:0.31, T:0.21
Consensus pattern (20 bp):
AAAGTGCTAATACGGAGAGT
Found at i:13109 original size:23 final size:23
Alignment explanation
Indices: 13076--13136 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
13066 GAGAGTAAAG
*
13076 TGCTAATCGGAGAGCACACAAAA
1 TGCTAAACGGAGAGCACACAAAA
* *
13099 TGCTAAACGGAGAGCACACACAG
1 TGCTAAACGGAGAGCACACAAAA
*
13122 TGCTAAATGGAGAGC
1 TGCTAAACGGAGAGC
13137 GCGCTAAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (23 bp):
TGCTAAACGGAGAGCACACAAAA
Found at i:19292 original size:30 final size:29
Alignment explanation
Indices: 19252--19321 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 29
19242 AAAATGAAAC
* *
19252 TTTGGAAAGTTTGGGGGCCAAAT-TAGAATT
1 TTTGG-AAGTTTGAGGACCAAATCT-GAATT
*
19282 TTTAGGAAGTTTGAGGATCAAATCTGAATT
1 TTT-GGAAGTTTGAGGACCAAATCTGAATT
19312 TTTGGAAGTT
1 TTTGGAAGTT
19322 CGAGTGTCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 7 0.20
30 25 0.71
31 3 0.09
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (29 bp):
TTTGGAAGTTTGAGGACCAAATCTGAATT
Found at i:19331 original size:29 final size:28
Alignment explanation
Indices: 19278--19432 Score: 125
Period size: 30 Copynumber: 5.2 Consensus size: 28
19268 GCCAAATTAG
*
19278 AATTTTTAGGAAGTTTGAGGATCAAATC-T
1 AATTTTT-GGAAGTTCGAGG-TCAAATCAT
*
19307 GAATTTTTGGAAGTTCGAGTGTCAAAACAT
1 -AATTTTTGGAAGTTCGAG-GTCAAATCAT
* * *
19337 AATTTTTGAAAAGTTTAGGGGTCAAATCAT
1 AATTTTTG-GAAG-TTCGAGGTCAAATCAT
* *
19367 AATTTTTGGAAAGTTCGGGGGTCAAAT-TT
1 AATTTTTGG-AAGTTC-GAGGTCAAATCAT
*
19396 AAATTTTTGGATAGTTTTGAGGTCAAATCAT
1 -AATTTTTGGA-AG-TTCGAGGTCAAATCAT
19427 AATTTT
1 AATTTT
19433 AAATAAAATA
Statistics
Matches: 103, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
29 28 0.27
30 68 0.66
31 7 0.07
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (28 bp):
AATTTTTGGAAGTTCGAGGTCAAATCAT
Found at i:19412 original size:60 final size:58
Alignment explanation
Indices: 19252--19432 Score: 179
Period size: 60 Copynumber: 3.0 Consensus size: 58
19242 AAAATGAAAC
* * *
19252 TTTGGAAAGTTTGGGGGCCAAATTAGAATTTTTAGGAAGTTTGAGGATCAAATC-TGAATT
1 TTTGGAAAGTTCGGGGGTCAAATTAGAATTTTT-GGAAGTTTG-GGGTCAAATCAT-AATT
* * ** * *
19312 TTTGG-AAGTTCGAGTGTCAAAACATAATTTTTGAAAAGTTTAGGGGTCAAATCATAATT
1 TTTGGAAAGTTCGGGGGTCAAATTAGAATTTTTG-GAAGTTT-GGGGTCAAATCATAATT
*
19371 TTTGGAAAGTTCGGGGGTCAAATTTA-AATTTTTGGATAGTTTTGAGGTCAAATCATAATT
1 TTTGGAAAGTTCGGGGGTCAAA-TTAGAATTTTTGGA-AG-TTTGGGGTCAAATCATAATT
19431 TT
1 TT
19433 AAATAAAATA
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
58 1 0.01
59 45 0.45
60 49 0.49
61 4 0.04
ACGTcount: A:0.32, C:0.07, G:0.23, T:0.38
Consensus pattern (58 bp):
TTTGGAAAGTTCGGGGGTCAAATTAGAATTTTTGGAAGTTTGGGGTCAAATCATAATT
Found at i:19830 original size:32 final size:33
Alignment explanation
Indices: 19776--19841 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
19766 CTATAAAGAA
19776 AACCTCTTAACCCCCCCTTTTTTTTAAAACCTT
1 AACCTCTTAACCCCCCCTTTTTTTTAAAACCTT
19809 AACCTCTTAACCCCCCC-TTTTTTTAAAACCTT
1 AACCTCTTAACCCCCCCTTTTTTTTAAAACCTT
19841 A
1 A
19842 TCCCCTCCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.26, C:0.36, G:0.00, T:0.38
Consensus pattern (33 bp):
AACCTCTTAACCCCCCCTTTTTTTTAAAACCTT
Found at i:21280 original size:40 final size:40
Alignment explanation
Indices: 21208--21637 Score: 279
Period size: 40 Copynumber: 10.9 Consensus size: 40
21198 AGATTAGATG
21208 CTTCAATCTGCCC-CATGATT-GGAGTAAGAGATTGGTGTGT
1 CTTCAATCTGCCCTC-TGATTAGG-GTAAGAGATTGGTGTGT
* * * *
21248 CTTCAATTTGCCCTCTGAGTAGGGTAAAAGATTGG-ATG-
1 CTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGTGTGT
* * *
21286 CTTTAATCTGCCC-CATGA-TCGAGGTATGAGATTGGAT-TGT
1 CTTCAATCTGCCCTC-TGATTAG-GGTAAGAGATTGG-TGTGT
* * * * *
21326 CATCAATCTACCCTCTGATTAGGGTAAAAGATTGG-AT-A
1 CTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGTGTGT
*
21364 CTTCAATCTGCCC-CATGATT-GGGTTATGAGATTGGTGTGT
1 CTTCAATCTGCCCTC-TGATTAGGG-TAAGAGATTGGTGTGT
* * * *
21404 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATT-G-AT-A
1 CTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGTGTGT
* *
21441 CTTCAATCTGCCC-CATGATTGGGGTATGAGATTGGATGGTGT
1 CTTCAATCTGCCCTC-TGATTAGGGTAAGAGATTGG-T-GTGT
*
21483 CTTCAATCTG-CCTCATGATTGGGGTAAGAGATTGGGTGGTGT
1 CTTCAATCTGCCCTC-TGATTAGGGTAAGAGATT-GGT-GTGT
* * ** *
21525 CTTCAACCTGTCCC-ATGATCGGGGTAAGAGATTGATGTGT
1 CTTCAATCTG-CCCTCTGATTAGGGTAAGAGATTGGTGTGT
* * * * *
21565 TTTCAATCTGCCCTCTAATTAGGATAAAAGATTGG-ATG-
1 CTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGTGTGT
* ** *
21603 ATTCAATCTG-CCTCATGATCGGGGTATGAGATTGG
1 CTTCAATCTGCCCTC-TGATTAGGGTAAGAGATTGG
21638 ATGGTAGCTT
Statistics
Matches: 307, Mismatches: 55, Indels: 58
0.73 0.13 0.14
Matches are distributed among these distances:
37 39 0.13
38 75 0.24
39 12 0.04
40 102 0.33
41 14 0.05
42 61 0.20
43 2 0.01
44 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAGAGATTGGTGTGT
Found at i:21280 original size:78 final size:78
Alignment explanation
Indices: 21166--21637 Score: 554
Period size: 78 Copynumber: 5.9 Consensus size: 78
21156 GAGATGCTAG
* * *
21166 CTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTAGATGCTTCAATCTGCCCCATGATTGGA
1 CTTCAATCTG-CCCT-CTGA-TTA-GGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTGGG
*
21231 GTAAGAGATTGGTGTGT
62 GTATGAGATTGGTGTGT
* * * * *
21248 CTTCAATTTGCCCTCTGAGTAGGGTAAAAGATTGGATGCTTTAATCTGCCCCATGATCGAGGTAT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTGGGGTAT
21313 GAGATTGGAT-TGT
66 GAGATTGG-TGTGT
* * * *
21326 CATCAATCTACCCTCTGATTAGGGTAAAAGATTGGATACTTCAATCTGCCCCATGATTGGGTTAT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTGGGGTAT
21391 GAGATTGGTGTGT
66 GAGATTGGTGTGT
* *
21404 CTTCAATCTGCCCTTTGATTAGGGTAAAAGATT-GATACTTCAATCTGCCCCATGATTGGGGTAT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTGGGGTAT
21468 GAGATTGGATGGTGT
66 GAGATTGG-T-GTGT
* * * * * *
21483 CTTCAATCTG-CCTCATGATTGGGGTAAGAGATTGGGTGGTGTCTTCAACCTGTCCCATGATCGG
1 CTTCAATCTGCCCTC-TGATTAGGGTAAAAGATT--G-GATG-CTTCAATCTGCCCCATGATTGG
* *
21547 GGTAAGAGATTGATGTGT
61 GGTATGAGATTGGTGTGT
* * * * * *
21565 TTTCAATCTGCCCTCTAATTAGGATAAAAGATTGGATGATTCAATCTGCCTCATGATCGGGGTAT
1 CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTGGGGTAT
21630 GAGATTGG
66 GAGATTGG
21638 ATGGTAGCTT
Statistics
Matches: 335, Mismatches: 44, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
77 39 0.12
78 179 0.53
79 36 0.11
80 4 0.01
81 4 0.01
82 36 0.11
83 7 0.02
84 30 0.09
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (78 bp):
CTTCAATCTGCCCTCTGATTAGGGTAAAAGATTGGATGCTTCAATCTGCCCCATGATTGGGGTAT
GAGATTGGTGTGT
Found at i:21595 original size:239 final size:238
Alignment explanation
Indices: 21166--21637 Score: 618
Period size: 239 Copynumber: 2.0 Consensus size: 238
21156 GAGATGCTAG
*
21166 CTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTAGATGCTTCAATCTGCCCCATGATTGGA
1 CTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTAGATACTTCAATCTGCCCCATGATTGGA
* * *
21231 GTAAGAGATTGGTGTGTCTTCAATTTGCCCTCTGAGTAGGGTAAAAGATTGGATGCTTTAATCTG
66 GTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGAGTAGGGTAAAAGATTGGATGCTTCAACCTG
* * *
21296 CCCCATGATCGAGGTATGAGATTGGATTGTCATCAATCTACCCTCTGATTAGGGTAAAAGATTGG
131 CCCCATGATCGAGGTAAGAGATTGGATTGTCATCAATCTACCCTCTAATTAGGATAAAAGATTGG
* *
21361 AT-ACTTCAATCTGCCCCATGATTGGGTTATGAGATTGGTGTGT
196 ATGA-TTCAATCTGCCCCATGATCGGGGTATGAGATTGGTGTGT
*
21404 CTTCAATCTG-CCCT-TTGA-TTA-GGGTAAAAGATT-GATACTTCAATCTGCCCCATGATTGGG
1 CTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTAGATACTTCAATCTGCCCCATGATTGGA
* * * * *
21464 GTATGAGATTGGATGGTGTCTTCAATCTG-CCTCATGATTGGGGTAAGAGATTGGGTGGTGTCTT
66 GTAAGAGATTGG-T-GTGTCTTCAATCTGCCCTC-TGAGTAGGGTAAAAGATT--G-GATG-CTT
* * ** *
21528 CAACCTGTCCCATGATCGGGGTAAGAGATT-GATGTGTTTTCAATCTGCCCTCTAATTAGGATAA
124 CAACCTGCCCCATGATCGAGGTAAGAGATTGGAT-TGTCATCAATCTACCCTCTAATTAGGATAA
*
21592 AAGATTGGATGATTCAATCTGCCTCATGATCGGGGTATGAGATTGG
188 AAGATTGGATGATTCAATCTGCCCCATGATCGGGGTATGAGATTGG
21638 ATGGTAGCTT
Statistics
Matches: 204, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
233 36 0.18
234 17 0.08
235 31 0.15
236 4 0.02
237 5 0.02
238 16 0.08
239 94 0.46
240 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (238 bp):
CTTCAATCTGCCCCTATTGACTTAGGGGTAAAAGATTAGATACTTCAATCTGCCCCATGATTGGA
GTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTGAGTAGGGTAAAAGATTGGATGCTTCAACCTG
CCCCATGATCGAGGTAAGAGATTGGATTGTCATCAATCTACCCTCTAATTAGGATAAAAGATTGG
ATGATTCAATCTGCCCCATGATCGGGGTATGAGATTGGTGTGT
Found at i:21832 original size:21 final size:20
Alignment explanation
Indices: 21780--21875 Score: 70
Period size: 21 Copynumber: 4.6 Consensus size: 20
21770 CAGAGGCGTA
* *
21780 AGATTCGCCTTTACAGCTTC
1 AGATTTGCCTTTACAGCTTG
*
21800 A-ATCTAGCCCTTTACAGCTTTG
1 AGAT-TTG-CCTTTACAGC-TTG
* *
21822 AGATTTGCCTTTGCAGCTTC
1 AGATTTGCCTTTACAGCTTG
*
21842 A-ATTTGCTTTTTTACAGCCTTG
1 AGATTTGC--CTTTACAG-CTTG
21864 AGATTTGCCTTT
1 AGATTTGCCTTT
21876 GTGGCTTCAG
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
19 8 0.14
20 6 0.10
21 28 0.47
22 9 0.15
23 8 0.14
ACGTcount: A:0.19, C:0.24, G:0.16, T:0.42
Consensus pattern (20 bp):
AGATTTGCCTTTACAGCTTG
Found at i:21876 original size:42 final size:42
Alignment explanation
Indices: 21780--21894 Score: 133
Period size: 42 Copynumber: 2.7 Consensus size: 42
21770 CAGAGGCGTA
* * ** *
21780 AGATTCGCCTTTACAGCTTCAATCTAGC-CCTTTACAGCTTTG
1 AGATTTGCCTTTGCAGCTTCAATCT-GCTTTTTTACAGCCTTG
*
21822 AGATTTGCCTTTGCAGCTTCAATTTGCTTTTTTACAGCCTTG
1 AGATTTGCCTTTGCAGCTTCAATCTGCTTTTTTACAGCCTTG
** *
21864 AGATTTGCCTTTGTGGCTTCAGTCTGCTTTT
1 AGATTTGCCTTTGCAGCTTCAATCTGCTTTT
21895 CCTCATCTTC
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
41 2 0.03
42 60 0.97
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (42 bp):
AGATTTGCCTTTGCAGCTTCAATCTGCTTTTTTACAGCCTTG
Found at i:22072 original size:69 final size:69
Alignment explanation
Indices: 21961--22093 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 69
21951 TCTAAGGTAT
* *
21961 AAGGTTCACCGTTGCGGCTTTAACCTTTTCCTCCATATCTCCATGGTACAAGATTCGCCATTGCA
1 AAGGTTCACCGTTGCGGCTTTAACCTTTCCCTCCATATCTCCATGGTACAAGATTCACCATTGCA
22026 GTGC
66 GTGC
* * * *
22030 AAGGTTCACCGTTGTGGCTTTAACCTTTCCCTCTATATCTCCATGGTATAATATTCACCATTGC
1 AAGGTTCACCGTTGCGGCTTTAACCTTTCCCTCCATATCTCCATGGTACAAGATTCACCATTGC
22094 GACTTCAATC
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 58 1.00
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (69 bp):
AAGGTTCACCGTTGCGGCTTTAACCTTTCCCTCCATATCTCCATGGTACAAGATTCACCATTGCA
GTGC
Found at i:22190 original size:49 final size:49
Alignment explanation
Indices: 22137--22280 Score: 139
Period size: 49 Copynumber: 2.9 Consensus size: 49
22127 CAAGGTTCAC
* *
22137 CGTTGGGGCTTCAACCTTTCCTTCCACATCTCCATGGTATAAGATTTGT
1 CGTTGCGGCTTCAACCTTTCCTTCCATATCTCCATGGTATAAGATTTGT
* * * * *
22186 CGTTGCGGCTTCAATCTTTCCCATT--ATTTTTCTATGGTATAAGGTTTGT
1 CGTTGCGGCTTCAACCTTT-CC-TTCCATATCTCCATGGTATAAGATTTGT
* ** * * *
22235 CATTGTTGCTTCAACCTTTCCCTCCATATCTCCATGATATTAGATT
1 CGTTGCGGCTTCAACCTTTCCTTCCATATCTCCATGGTATAAGATT
22281 CACCGTTACT
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.03
49 66 0.90
50 2 0.03
51 2 0.03
ACGTcount: A:0.19, C:0.24, G:0.15, T:0.42
Consensus pattern (49 bp):
CGTTGCGGCTTCAACCTTTCCTTCCATATCTCCATGGTATAAGATTTGT
Found at i:22198 original size:98 final size:98
Alignment explanation
Indices: 22029--22363 Score: 364
Period size: 98 Copynumber: 3.4 Consensus size: 98
22019 CATTGCAGTG
* * * **
22029 CAAGGTTCACCGTTGTGGCTTTAACCTTTCCCTCTATATCTCCATGGTATAATATTCACCATTGC
1 CAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTCCATATCTCCATGGTATAAGATTCGTCATTGC
*
22094 GACTTCAATCTTTCCCATCACGTCTCTAAGGTA
66 GGCTTCAATCTTTCCCATCACGTCTCTAAGGTA
* * * * *
22127 CAAGGTTCACCGTTGGGGCTTCAACCTTTCCTTCCACATCTCCATGGTATAAGATTTGTCGTTGC
1 CAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTCCATATCTCCATGGTATAAGATTCGTCATTGC
* ** * *
22192 GGCTTCAATCTTTCCCATTATTTTTCTATGGTA
66 GGCTTCAATCTTTCCCATCACGTCTCTAAGGTA
* *** * * * *
22225 TAAGGTTTGTCATTGTTGCTTCAACCTTTCCCTCCATATCTCCATGATATTAGATTCACCGTTAC
1 CAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTCCATATCTCCATGGTATAAGATT---CG-T-C
* * *
22290 TTTACAGCTTCAATCTTTCCCATCACGTCTCTAAGGTA
61 ATTGCGGCTTCAATCTTTCCCATCACGTCTCTAAGGTA
* *
22328 CAAGGTTCACCGTTGCGGCTTCAACCTTTCTCTCCA
1 CAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTCCA
22364 AACCTGTGAA
Statistics
Matches: 188, Mismatches: 44, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
98 127 0.68
101 1 0.01
102 1 0.01
103 59 0.31
ACGTcount: A:0.21, C:0.28, G:0.14, T:0.37
Consensus pattern (98 bp):
CAAGGTTCACCGTTGTGGCTTCAACCTTTCCCTCCATATCTCCATGGTATAAGATTCGTCATTGC
GGCTTCAATCTTTCCCATCACGTCTCTAAGGTA
Found at i:22950 original size:111 final size:110
Alignment explanation
Indices: 22766--22968 Score: 291
Period size: 111 Copynumber: 1.8 Consensus size: 110
22756 ACTAATCGTT
* * **
22766 ATTTCAATGCAAAAATGCTTGAACATGTTGTAAGGTGGATGAAATTGAATTTGATTTTAGGCAAA
1 ATTTCAATGCAAAAATGCTTGAACAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGGCAAA
* * *
22831 GCTTGCATGATTAAAAAGGTTAAAAATCATTAGTCCACTAACCTC
66 GCTCGCATGAATAAAAAGATTAAAAATCATTAGTCCACTAACCTC
* *
22876 ATTTCAATGCAAGAATGCTTGAACAGGGTTGTAAGGTGGATAAAATTGAATGTT-ATTGGAGGTA
1 ATTTCAATGCAAAAATGCTTGAACA-GGTTGTAAGGTGGATAAAATTGAAT-TTGATTGGAGGCA
*
22940 AAGCTCGCATGAATGAAAAGATTAAAAAT
64 AAGCTCGCATGAATAAAAAGATTAAAAAT
22969 GACAAACATT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
110 24 0.30
111 55 0.68
112 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.30
Consensus pattern (110 bp):
ATTTCAATGCAAAAATGCTTGAACAGGTTGTAAGGTGGATAAAATTGAATTTGATTGGAGGCAAA
GCTCGCATGAATAAAAAGATTAAAAATCATTAGTCCACTAACCTC
Found at i:27429 original size:30 final size:30
Alignment explanation
Indices: 27358--27430 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
27348 AAAAATGAAA
*
27358 TTTTGGAAAGTTTAGGGGCCAAATTAGAATC
1 TTTTGGAAAGTTTAGGGACCAAATTA-AATC
* * *
27389 GTTTGG-AAGTTTAGGTACCAAATCT-AATT
1 TTTTGGAAAGTTTAGGGACCAAAT-TAAATC
27418 TTTTGGAAAGTTT
1 TTTTGGAAAGTTT
27431 GGGGGTCAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
29 8 0.23
30 21 0.60
31 6 0.17
ACGTcount: A:0.30, C:0.08, G:0.23, T:0.38
Consensus pattern (30 bp):
TTTTGGAAAGTTTAGGGACCAAATTAAATC
Found at i:27451 original size:30 final size:30
Alignment explanation
Indices: 27417--27570 Score: 141
Period size: 30 Copynumber: 5.2 Consensus size: 30
27407 CAAATCTAAT
** *
27417 TTTTTGGAAAGTTTGGGGGTCAAAACTTAA
1 TTTTTGGAAAGTTTAAGGGTCAAAACATAA
** * *
27447 TTTTTCAAAAGGTCAAGGGTCAAAACATAA
1 TTTTTGGAAAGTTTAAGGGTCAAAACATAA
* *
27477 -TTTTAGAAAGTTTAAGGGTCAAATCATAA
1 TTTTTGGAAAGTTTAAGGGTCAAAACATAA
* * *
27506 TTTTTGGAAAGTTTAGGGGTTAAATTCA-AA
1 TTTTTGGAAAGTTTAAGGGTCAAA-ACATAA
* * * *
27536 TTTTTGGATAGTTTATGGGCCAAAACATAT
1 TTTTTGGAAAGTTTAAGGGTCAAAACATAA
27566 TTTTT
1 TTTTT
27571 ATATAAAATA
Statistics
Matches: 100, Mismatches: 21, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
29 26 0.26
30 71 0.71
31 3 0.03
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (30 bp):
TTTTTGGAAAGTTTAAGGGTCAAAACATAA
Found at i:29569 original size:11 final size:11
Alignment explanation
Indices: 29488--29570 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
29478 ATTCCAAAAA
*
29488 TAATATTATTT
1 TAATATTAATT
29499 TAATA-T-ATT
1 TAATATTAATT
29508 TAATATTAAATT
1 TAATATT-AATT
*
29520 TAAT-TTAATC
1 TAATATTAATT
*
29530 TAATATTTATCT
1 TAATATTAAT-T
*
29542 TGATA--AATAT
1 TAATATTAAT-T
29552 T-ATATTAATT
1 TAATATTAATT
29562 TAATATTAA
1 TAATATTAA
29571 AGTGATTAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
9 10 0.18
10 15 0.26
11 21 0.37
12 11 0.19
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.53
Consensus pattern (11 bp):
TAATATTAATT
Found at i:29704 original size:26 final size:24
Alignment explanation
Indices: 29675--29725 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
29665 AGTTGTAGAG
29675 AGAAAATTCTCTGAAGAAATTATTTT
1 AGAAAATT-TCTGAAGAAATT-TTTT
* *
29701 AGAAAATTTCTGGAGATATTTTTT
1 AGAAAATTTCTGAAGAAATTTTTT
29725 A
1 A
29726 TTTATAGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 5 0.22
25 10 0.43
26 8 0.35
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (24 bp):
AGAAAATTTCTGAAGAAATTTTTT
Found at i:39741 original size:51 final size:51
Alignment explanation
Indices: 39679--39777 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
39669 GATGTGCTGT
* * *
39679 GTCACTATTAAAAGACGAAGCTTATAGTTGGTGGACGACTATGCTGGCCGC
1 GTCACTATTAAAAGACGAAGCTTACAATTGGTGGACGACTATGATGGCCGC
*
39730 GTCACTGTTAAAAGACGAAGCTTACAATTGGTGGACGACTATGATGGC
1 GTCACTATTAAAAGACGAAGCTTACAATTGGTGGACGACTATGATGGC
39778 AGTAGTTCTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (51 bp):
GTCACTATTAAAAGACGAAGCTTACAATTGGTGGACGACTATGATGGCCGC
Found at i:43031 original size:3 final size:3
Alignment explanation
Indices: 43023--43086 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
43013 CTAAAACCAA
*
43023 AAT AAT AAT AAC AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
43070 AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AA
43087 AATGATGTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.04
3 55 0.96
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:44275 original size:20 final size:20
Alignment explanation
Indices: 44252--44290 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
44242 TGGGTTAGAC
44252 TTGG-TTTAATAGGGTTTGGT
1 TTGGTTTTAA-AGGGTTTGGT
44272 TTGGTTTTAAAGGGTTTGG
1 TTGGTTTTAAAGGGTTTGG
44291 GTTATTGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.15, C:0.00, G:0.36, T:0.49
Consensus pattern (20 bp):
TTGGTTTTAAAGGGTTTGGT
Found at i:44840 original size:11 final size:11
Alignment explanation
Indices: 44806--44878 Score: 69
Period size: 11 Copynumber: 6.6 Consensus size: 11
44796 GAGATATGCC
44806 AGAAAAGAGAA
1 AGAAAAGAGAA
*
44817 AGAAATG-GAAA
1 AGAAAAGAG-AA
44828 AGAAAAGAGAA
1 AGAAAAGAGAA
44839 AGAAATA-AGAA
1 AGAAA-AGAGAA
* * *
44850 AGGAATGAGAG
1 AGAAAAGAGAA
*
44861 AGAAATGAGAA
1 AGAAAAGAGAA
44872 AGAAAAG
1 AGAAAAG
44879 TGAGAGGCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.02
11 47 0.94
12 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (11 bp):
AGAAAAGAGAA
Found at i:44843 original size:33 final size:33
Alignment explanation
Indices: 44806--44878 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
44796 GAGATATGCC
44806 AGAAAAGAGAAAGAAATG-GAAAAGAAAAGAGAA
1 AGAAAAGAGAAAGAAATGAG-AAAGAAAAGAGAA
* * *
44839 AGAAATA-AGAAAGGAATGAGAGAGAAATGAGAA
1 AGAAA-AGAGAAAGAAATGAGAAAGAAAAGAGAA
44872 AGAAAAG
1 AGAAAAG
44879 TGAGAGGCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.03
33 31 0.91
34 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (33 bp):
AGAAAAGAGAAAGAAATGAGAAAGAAAAGAGAA
Found at i:44884 original size:22 final size:22
Alignment explanation
Indices: 44806--44878 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
44796 GAGATATGCC
44806 AGAAAAGAGAAAGAAATG-GAAA
1 AGAAAAGAGAAAGAAATGAG-AA
*
44828 AGAAAAGAGAAAGAAATAAGAA
1 AGAAAAGAGAAAGAAATGAGAA
* * *
44850 AGGAATGAGAGAGAAATGAGAA
1 AGAAAAGAGAAAGAAATGAGAA
44872 AGAAAAG
1 AGAAAAG
44879 TGAGAGGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (22 bp):
AGAAAAGAGAAAGAAATGAGAA
Found at i:50246 original size:23 final size:24
Alignment explanation
Indices: 50220--50276 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
50210 AATTAATAAT
*
50220 AAAATAAATTAAT-TAAACTCTCCA
1 AAAATAAATTAATCAAAACTC-CCA
* *
50244 AAAATAAAAT-ATCAAAAGTCCC-
1 AAAATAAATTAATCAAAACTCCCA
50266 AAAATAAATTA
1 AAAATAAATTA
50277 TATTTACAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 9 0.33
23 4 0.15
24 14 0.52
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.25
Consensus pattern (24 bp):
AAAATAAATTAATCAAAACTCCCA
Found at i:50305 original size:3 final size:3
Alignment explanation
Indices: 50297--50328 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
50287 CTAAAACCAA
*
50297 AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
50329 AATGACGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:52104 original size:11 final size:11
Alignment explanation
Indices: 52070--52142 Score: 69
Period size: 11 Copynumber: 6.6 Consensus size: 11
52060 GAGATATGTC
52070 AGAAAAGAGAA
1 AGAAAAGAGAA
*
52081 AGAAATG-GAAA
1 AGAAAAGAG-AA
52092 AGAAAAGAGAA
1 AGAAAAGAGAA
52103 AGAAATA-AGAA
1 AGAAA-AGAGAA
* * *
52114 AGGAATGAGAG
1 AGAAAAGAGAA
*
52125 AGAAATGAGAA
1 AGAAAAGAGAA
52136 AGAAAAG
1 AGAAAAG
52143 TGAGAGGCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
10 1 0.02
11 47 0.94
12 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (11 bp):
AGAAAAGAGAA
Found at i:52107 original size:33 final size:33
Alignment explanation
Indices: 52070--52142 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
52060 GAGATATGTC
52070 AGAAAAGAGAAAGAAATG-GAAAAGAAAAGAGAA
1 AGAAAAGAGAAAGAAATGAG-AAAGAAAAGAGAA
* * *
52103 AGAAATA-AGAAAGGAATGAGAGAGAAATGAGAA
1 AGAAA-AGAGAAAGAAATGAGAAAGAAAAGAGAA
52136 AGAAAAG
1 AGAAAAG
52143 TGAGAGGCTT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.03
33 31 0.91
34 2 0.06
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (33 bp):
AGAAAAGAGAAAGAAATGAGAAAGAAAAGAGAA
Found at i:52148 original size:22 final size:22
Alignment explanation
Indices: 52070--52142 Score: 94
Period size: 22 Copynumber: 3.3 Consensus size: 22
52060 GAGATATGTC
52070 AGAAAAGAGAAAGAAATG-GAAA
1 AGAAAAGAGAAAGAAATGAG-AA
*
52092 AGAAAAGAGAAAGAAATAAGAA
1 AGAAAAGAGAAAGAAATGAGAA
* * *
52114 AGGAATGAGAGAGAAATGAGAA
1 AGAAAAGAGAAAGAAATGAGAA
52136 AGAAAAG
1 AGAAAAG
52143 TGAGAGGCTT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (22 bp):
AGAAAAGAGAAAGAAATGAGAA
Found at i:54695 original size:37 final size:37
Alignment explanation
Indices: 54654--54732 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
54644 ACGTCTCTGC
54654 TAGAGCATAACGA-TAAATGATTTGCTTACATCTCGAT
1 TAGAGCATAA-GACTAAATGATTTGCTTACATCTCGAT
** * ** *
54691 TAGAGTGTAATACTATGTGATTTGCTTACATCTCGGT
1 TAGAGCATAAGACTAAATGATTTGCTTACATCTCGAT
54728 TAGAG
1 TAGAG
54733 TGTAATGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 1 0.03
37 34 0.97
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (37 bp):
TAGAGCATAAGACTAAATGATTTGCTTACATCTCGAT
Found at i:54733 original size:37 final size:37
Alignment explanation
Indices: 54671--54819 Score: 201
Period size: 37 Copynumber: 4.0 Consensus size: 37
54661 TAACGATAAA
*
54671 TGATTTGCTTACATCTC-GATTAGAGTGTAATACTATG
1 TGATTTGCTTACATCTCAG-TTAGAGTGTAATGCTATG
*
54708 TGATTTGCTTACATCTCGGTTAGAGTGTAATGCTATG
1 TGATTTGCTTACATCTCAGTTAGAGTGTAATGCTATG
* * * *
54745 TGGTTTGCTTACGTCTCAGTTAGAATGTAATGTTATG
1 TGATTTGCTTACATCTCAGTTAGAGTGTAATGCTATG
* * *
54782 TGATTTGTTTACGTCTCAGTTAGAGTGTAATGCCATG
1 TGATTTGCTTACATCTCAGTTAGAGTGTAATGCTATG
54819 T
1 T
54820 ATGGCTCAGG
Statistics
Matches: 100, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
37 99 0.99
38 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (37 bp):
TGATTTGCTTACATCTCAGTTAGAGTGTAATGCTATG
Found at i:59308 original size:20 final size:20
Alignment explanation
Indices: 59263--59310 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
59253 TTTTTCGACC
*
59263 AAAATTAATTATTTTCTCTA
1 AAAATTAATTATTATCTCTA
* *
59283 ATAATTATTTATTATCAT-TA
1 AAAATTAATTATTATC-TCTA
59303 AAAATTAA
1 AAAATTAA
59311 ATTTTCAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (20 bp):
AAAATTAATTATTATCTCTA
Found at i:61136 original size:38 final size:38
Alignment explanation
Indices: 61085--61164 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
61075 GCTTTCATAG
61085 TTATTTCCCAGAGCTTGAAATTAACACTCTGCATCACT
1 TTATTTCCCAGAGCTTGAAATTAACACTCTGCATCACT
61123 TTATTTCCCAGAGCTTGAAATTAACACTCTGCATCACT
1 TTATTTCCCAGAGCTTGAAATTAACACTCTGCATCACT
61161 TTAT
1 TTAT
61165 CAAATGTGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.29, C:0.25, G:0.10, T:0.36
Consensus pattern (38 bp):
TTATTTCCCAGAGCTTGAAATTAACACTCTGCATCACT
Found at i:61862 original size:15 final size:15
Alignment explanation
Indices: 61842--61879 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
61832 CATGAATGTA
61842 CATCCATAACCACCT
1 CATCCATAACCACCT
*
61857 CATCCAT-CCCACCT
1 CATCCATAACCACCT
61871 CATTCCATA
1 CA-TCCATA
61880 TTTATTAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.29, C:0.47, G:0.00, T:0.24
Consensus pattern (15 bp):
CATCCATAACCACCT
Found at i:66211 original size:67 final size:63
Alignment explanation
Indices: 66069--66218 Score: 237
Period size: 63 Copynumber: 2.4 Consensus size: 63
66059 TTTTATGATT
*
66069 ATAAATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATTTATTATTGTATGAAC
1 ATAAATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATATATTATTGTATGAAC
* * *
66132 ATAAATAAATAAATGTAAAATAATATTAATTTTATTTTATTATTTATATATTATTTTATGAAT
1 ATAAATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATATATTATTGTATGAAC
* *
66195 ATAGATAAATAAATAAATAAATAA
1 ATAAATAAATAAATATA-AAATAA
66219 CAAACCCAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 73 0.92
64 6 0.08
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (63 bp):
ATAAATAAATAAATATAAAATAATATTAATTTTATTTTATTATTTATATATTATTGTATGAAC
Found at i:80386 original size:21 final size:23
Alignment explanation
Indices: 80341--80389 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
80331 AACTCAAAGG
80341 TTTAATATAATATTTGATATTTT
1 TTTAATATAATATTTGATATTTT
* * * *
80364 TTTAATTTGATATTTAATTTTTT
1 TTTAATATAATATTTGATATTTT
80387 TTT
1 TTT
80390 GGTTTATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTAATATAATATTTGATATTTT
Found at i:80471 original size:31 final size:29
Alignment explanation
Indices: 80402--80472 Score: 81
Period size: 31 Copynumber: 2.4 Consensus size: 29
80392 TTTATTTTGT
* *
80402 TACTTATATTTGACATTTTTTTAATTTGA
1 TACTTAAATTTGACATTTTTTTAAGTTGA
*
80431 TA-TCAAAATTTGACCATTTTTTTTAAGTTGA
1 TACT-TAAATTTGA-CA-TTTTTTTAAGTTGA
80462 TACTTAAATTT
1 TACTTAAATTT
80473 TTTGGGATTC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
28 1 0.03
29 9 0.26
30 2 0.06
31 21 0.62
32 1 0.03
ACGTcount: A:0.31, C:0.08, G:0.07, T:0.54
Consensus pattern (29 bp):
TACTTAAATTTGACATTTTTTTAAGTTGA
Found at i:80548 original size:61 final size:59
Alignment explanation
Indices: 80421--80548 Score: 148
Period size: 61 Copynumber: 2.1 Consensus size: 59
80411 TTGACATTTT
* **
80421 TTTAATTTGATATCAAAATTTGACCATTTTTTTTAAGTTGATACTTAAATTTTTTGGGA
1 TTTAATTTGATATCAAAACTTGACCATTTTTTTTAAGTTGATACTTAAATTTTTTAAGA
* * * * * * *
80480 TTCAATTTGATATCAGAACTTGACTCTTTTTTTTTTAATTTGATATTTAATTTTTTTAATA
1 TTTAATTTGATATCAAAACTTGAC-C-ATTTTTTTTAAGTTGATACTTAAATTTTTTAAGA
80541 TTTAATTT
1 TTTAATTT
80549 TAACATGAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 21 0.38
60 1 0.02
61 34 0.61
ACGTcount: A:0.29, C:0.07, G:0.09, T:0.55
Consensus pattern (59 bp):
TTTAATTTGATATCAAAACTTGACCATTTTTTTTAAGTTGATACTTAAATTTTTTAAGA
Found at i:80550 original size:22 final size:22
Alignment explanation
Indices: 80508--80551 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
80498 CTTGACTCTT
* *
80508 TTTTTTTTAATTTGATATTTAA
1 TTTTTTTAAATTTAATATTTAA
80530 TTTTTTTAATATTTAAT-TTTAA
1 TTTTTTTAA-ATTTAATATTTAA
80552 CATGAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
TTTTTTTAAATTTAATATTTAA
Found at i:80699 original size:28 final size:28
Alignment explanation
Indices: 80644--80785 Score: 83
Period size: 28 Copynumber: 5.0 Consensus size: 28
80634 AATATTTAAT
**
80644 AAATTTAGATATCAAATTGAATTTAAAA
1 AAATTTAGATATCAAATTGAATAAAAAA
* *
80672 AAATTTAGGTATCAAATTAGAAAAAAAAATA
1 AAATTTAGATATCAAATT-G-AATAAAAA-A
* * * *
80703 CTAAATTCAGACACCAAATTGAATCAAAAA
1 --AAATTTAGATATCAAATTGAATAAAAAA
* * *
80733 AAA-TTA-ATACCCAATT-AAGAAAAAAA
1 AAATTTAGATATCAAATTGAA-TAAAAAA
* * *
80759 AAATTTAAATATTAAATTAAATAAAAA
1 AAATTTAGATATCAAATTGAATAAAAA
80786 TTTTAAATAT
Statistics
Matches: 86, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
25 2 0.02
26 16 0.19
27 5 0.06
28 32 0.37
29 3 0.03
30 6 0.07
31 7 0.08
32 1 0.01
33 14 0.16
ACGTcount: A:0.60, C:0.08, G:0.06, T:0.27
Consensus pattern (28 bp):
AAATTTAGATATCAAATTGAATAAAAAA
Found at i:80808 original size:24 final size:25
Alignment explanation
Indices: 80752--80822 Score: 99
Period size: 25 Copynumber: 2.9 Consensus size: 25
80742 CCCAATTAAG
* *
80752 AAAAAAAAAATTTAAATATTAAATT
1 AAAAAAAAATTTTAAATATCAAATT
*
80777 AAATAAAAATTTTAAATATCAAATT
1 AAAAAAAAATTTTAAATATCAAATT
*
80802 AAAAAAAAATTTCAAAT-TCAA
1 AAAAAAAAATTTTAAATATCAA
80823 CTACTAAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 4 0.10
25 37 0.90
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAAAAAAATTTTAAATATCAAATT
Found at i:83158 original size:14 final size:14
Alignment explanation
Indices: 83139--83165 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
83129 ACTTGCTACG
83139 GTAATCTTTGCTCA
1 GTAATCTTTGCTCA
83153 GTAATCTTTGCTC
1 GTAATCTTTGCTC
83166 TTAAATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.44
Consensus pattern (14 bp):
GTAATCTTTGCTCA
Found at i:85552 original size:6 final size:6
Alignment explanation
Indices: 85541--85588 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
85531 GGCCCGTTGG
* * *
85541 CTTTGA CTTTGA CTTTGA CTTTGA CTTAGG CTTTTA CTTTGA CTTTGA
1 CTTTGA CTTTGA CTTTGA CTTTGA CTTTGA CTTTGA CTTTGA CTTTGA
85589 TCGTTGACTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
CTTTGA
Found at i:86211 original size:2 final size:2
Alignment explanation
Indices: 86204--86236 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
86194 CTGTGTTTTG
86204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
86237 CACACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:86954 original size:38 final size:39
Alignment explanation
Indices: 86912--87020 Score: 116
Period size: 38 Copynumber: 2.8 Consensus size: 39
86902 GATCTAGCAT
* * *
86912 TTGTTGCAGATTCTTGGGGTAATA-AACGAGAT-TTAGTC
1 TTGTTGCAGATTCTTAGGGTAATATAATGAGATATT-GCC
** *
86950 TTGTTATAGATTCTTAAGGTAATATAATGAGATATTGCC
1 TTGTTGCAGATTCTTAGGGTAATATAATGAGATATTGCC
* *
86989 TTATTGCAGATTC-TCGGGTAATATAATGAGAT
1 TTGTTGCAGATTCTTAGGGTAATATAATGAGAT
87021 CCAACCTTTG
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
38 37 0.64
39 19 0.33
40 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (39 bp):
TTGTTGCAGATTCTTAGGGTAATATAATGAGATATTGCC
Found at i:89324 original size:52 final size:52
Alignment explanation
Indices: 89184--89330 Score: 233
Period size: 52 Copynumber: 2.8 Consensus size: 52
89174 GGCTCAAAGG
* * * *
89184 TAAAGGAATT-ATACACTCACGATGACACATAATCATCGGACCTCATAATCCG
1 TAAAGG-ATTCATATACTCACGATGACACATAGTCATTGGACCTCATAATCCA
89236 TAAAGGATTCATATACTCACGATGACACATAGTCATTGGACCTCATAATCCA
1 TAAAGGATTCATATACTCACGATGACACATAGTCATTGGACCTCATAATCCA
*
89288 TAAAGGATTCATATACTCACGATGACACATAGTCATTAGACCT
1 TAAAGGATTCATATACTCACGATGACACATAGTCATTGGACCT
89331 TTTTCATTTA
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
51 3 0.03
52 86 0.97
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (52 bp):
TAAAGGATTCATATACTCACGATGACACATAGTCATTGGACCTCATAATCCA
Found at i:95597 original size:21 final size:21
Alignment explanation
Indices: 95571--95624 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
95561 TAGTACAAAC
95571 TTCTACTGATACCCTTGAAAA
1 TTCTACTGATACCCTTGAAAA
* *
95592 TTCTACTGATACCCTTGACAG
1 TTCTACTGATACCCTTGAAAA
*
95613 TTTTACTGATAC
1 TTCTACTGATAC
95625 AAGTAAGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.37
Consensus pattern (21 bp):
TTCTACTGATACCCTTGAAAA
Found at i:96454 original size:52 final size:51
Alignment explanation
Indices: 96373--96559 Score: 234
Period size: 52 Copynumber: 3.6 Consensus size: 51
96363 ATTTTATTTA
* **
96373 ATACTCACGATGACACATAGTCATCGGACCTCTTGTTACGTAAAGGAACCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTATTAC-TAAAGGATTCAT
* *
96425 ACACTCACGATGACACATAGTCA-CGGGACCTCATAATCTA-TAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATC-GGACCTC-TTAT-TACTAAAGGATTCAT
* * * *
96477 ATACTCACAATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTATTAC-TAAAGGATTCAT
96529 ATACTCACGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
96560 TTTTCAAATA
Statistics
Matches: 117, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
50 1 0.01
51 2 0.02
52 109 0.93
53 3 0.03
54 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (51 bp):
ATACTCACGATGACACATAGTCATCGGACCTCTTATTACTAAAGGATTCAT
Found at i:99384 original size:42 final size:42
Alignment explanation
Indices: 99254--99474 Score: 234
Period size: 42 Copynumber: 5.3 Consensus size: 42
99244 TGAAGTATAA
* * * *
99254 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGGATT-TG-TAT
1 AAAGGAAGACTAATGTCTCGAGATGAGAATGA-GATTATGAT-T
** * * *
99296 AAATGGAAGACTTGTGACTCGAAATGAGCATGA-ATTATGATT
1 AAA-GGAAGACTAATGTCTCGAGATGAGAATGAGATTATGATT
* *
99338 AAAGGAAGACTAATGTCTCGAGATAAGAATGAGATTATTATT
1 AAAGGAAGACTAATGTCTCGAGATGAGAATGAGATTATGATT
*
99380 AAAGGAAGACTCAA-GTCTTGAGATGAGAATGAGATTATGATT
1 AAAGGAAGACT-AATGTCTCGAGATGAGAATGAGATTATGATT
* * * *
99422 AAAGGAAGACTCATGTCTCGGGATGAGAATTAGAATATGATT
1 AAAGGAAGACTAATGTCTCGAGATGAGAATGAGATTATGATT
99464 AAAGGAAGACT
1 AAAGGAAGACT
99475 TATGACACGT
Statistics
Matches: 152, Mismatches: 21, Indels: 12
0.82 0.11 0.06
Matches are distributed among these distances:
41 27 0.18
42 99 0.65
43 26 0.17
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.27
Consensus pattern (42 bp):
AAAGGAAGACTAATGTCTCGAGATGAGAATGAGATTATGATT
Found at i:106555 original size:42 final size:42
Alignment explanation
Indices: 106422--106609 Score: 211
Period size: 42 Copynumber: 4.5 Consensus size: 42
106412 TGATGTATAA
* *
106422 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAAGATT-TG-TAT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATG-AGATTATGAT-T
* ** * * * *
106464 AAATGGAAAACTTGTGACTCGGAATAAGCATG-GATTATGATT
1 AAA-GGAAGACTCATGTCTCGGGATGAGAATGAGATTATGATT
*
106506 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGATT
*
106548 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATATGATT
1 AAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGATT
* *
106590 AAAGGAAGACTTATGACTCG
1 AAAGGAAGACTCATGTCTCG
106610 TTAGAGCATA
Statistics
Matches: 123, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
41 24 0.20
42 77 0.63
43 22 0.18
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGGGATGAGAATGAGATTATGATT
Found at i:107297 original size:20 final size:22
Alignment explanation
Indices: 107266--107320 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 22
107256 TAGAGTTTTT
* *
107266 AGTATTGGTAGAAGC-ATAACT
1 AGTATCGGTAGAAGCTATAACA
*
107287 A-TATCGGTAGAA-CTATCACA
1 AGTATCGGTAGAAGCTATAACA
107307 AGTATCGGTAGAAG
1 AGTATCGGTAGAAG
107321 TCTGCACTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.04
20 15 0.54
21 12 0.43
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (22 bp):
AGTATCGGTAGAAGCTATAACA
Found at i:110659 original size:27 final size:28
Alignment explanation
Indices: 110629--110687 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
110619 CAAAGGCATT
* * *
110629 TCTTTTCGTA-TTCGCCACAAAGGCTAC
1 TCTTTTCATATTTCACCACAAAGACTAC
*
110656 TC-TTTCATATTTCACCATAAAGACTAC
1 TCTTTTCATATTTCACCACAAAGACTAC
110683 TCTTT
1 TCTTT
110688 CTTGATGTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 6 0.23
27 18 0.69
28 2 0.08
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.39
Consensus pattern (28 bp):
TCTTTTCATATTTCACCACAAAGACTAC
Found at i:111900 original size:21 final size:21
Alignment explanation
Indices: 111871--111927 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
111861 AATGCAGACC
* *
111871 TCTATCGATACATGTGACAGT
1 TCTACCGATACATGTGACACT
* *
111892 TCTACCGATACAAGTGACTCT
1 TCTACCGATACATGTGACACT
*
111913 TCTACCGAAACATGT
1 TCTACCGATACATGT
111928 CTTACTTCTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.30
Consensus pattern (21 bp):
TCTACCGATACATGTGACACT
Found at i:112708 original size:53 final size:53
Alignment explanation
Indices: 112589--112837 Score: 272
Period size: 53 Copynumber: 4.7 Consensus size: 53
112579 TTCGCATTTG
* * * *
112589 ATAACTCACGATGACACAGAGTCATTGGACCTTTAATCCATGAT-GTATTCAT
1 ATAACTCAAGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* * * * ** * *
112641 GTAACTCACGATGACATAAAGTCATTGGACCTTTAATCTGTAATAGAATTCAT
1 ATAACTCAAGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
*
112694 ATAACTCAAGATGACACATAA-TCATCAGACCTTTAATCCATGATAGGATTCAT
1 ATAACTCAAGATGACACA-AAGTCATCGGACCTTTAATCCATGATAGGATTCAT
* * * * *
112747 ATAACTCACA-ATGACATAGAGTCATCGGACATTTAATCCGTGACAGGATTCAT
1 ATAACTCA-AGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
*
112800 ATAACTCACA-AGGACACAAAGTCATCGGACCTTTAATC
1 ATAACTCA-AGATGACACAAAGTCATCGGACCTTTAATC
112838 TTTGGCACAA
Statistics
Matches: 167, Mismatches: 26, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
52 39 0.23
53 125 0.75
54 3 0.02
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (53 bp):
ATAACTCAAGATGACACAAAGTCATCGGACCTTTAATCCATGATAGGATTCAT
Found at i:112783 original size:106 final size:104
Alignment explanation
Indices: 112589--112837 Score: 311
Period size: 106 Copynumber: 2.4 Consensus size: 104
112579 TTCGCATTTG
* * * * * *
112589 ATAACTCACGATGACACAGAGTCATTGGACCTTTAATCCATGATGTATTCATGTAACTCACGATG
1 ATAACTCAAGATGACACA-AATCATCGGACCTTTAATCCATGATGGATTCATATAACTCACAATG
* * * *
112654 ACATAAAGTCATTGGACCTTTAATCTGTAATAGAATTCAT
65 ACATAAAGTCATCGGACATTTAATCCGTAACAGAATTCAT
*
112694 ATAACTCAAGATGACACATAATCATCAGACCTTTAATCCATGATAGGATTCATATAACTCACAAT
1 ATAACTCAAGATGACACA-AATCATCGGACCTTTAATCCATGAT-GGATTCATATAACTCACAAT
* * *
112759 GACATAGAGTCATCGGACATTTAATCCGTGACAGGATTCAT
64 GACATAAAGTCATCGGACATTTAATCCGTAACAGAATTCAT
*
112800 ATAACTCACA-AGGACACAAAGTCATCGGACCTTTAATC
1 ATAACTCA-AGATGACACAAA-TCATCGGACCTTTAATC
112838 TTTGGCACAA
Statistics
Matches: 124, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
105 41 0.33
106 82 0.66
107 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (104 bp):
ATAACTCAAGATGACACAAATCATCGGACCTTTAATCCATGATGGATTCATATAACTCACAATGA
CATAAAGTCATCGGACATTTAATCCGTAACAGAATTCAT
Found at i:112940 original size:10 final size:10
Alignment explanation
Indices: 112925--112949 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
112915 AACCATAAGA
112925 AAGTAGTTAT
1 AAGTAGTTAT
112935 AAGTAGTTAT
1 AAGTAGTTAT
112945 AAGTA
1 AAGTA
112950 AGATTTTAAC
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:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (10 bp):
AAGTAGTTAT
Found at i:113249 original size:20 final size:20
Alignment explanation
Indices: 113224--113263 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
113214 ACAAAATCAA
113224 TACTAGCCGACATAATCATG
1 TACTAGCCGACATAATCATG
113244 TACTAGCCGACATAATCATG
1 TACTAGCCGACATAATCATG
113264 GATCTCCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
TACTAGCCGACATAATCATG
Found at i:115476 original size:55 final size:55
Alignment explanation
Indices: 115407--115583 Score: 223
Period size: 55 Copynumber: 3.2 Consensus size: 55
115397 TTTAATTCAC
* * *
115407 TTATAGCTCGGGTAGGGCTTTGGT-TCGCTTACGTCTTGGTTAGAGCGTAATGCTA
1 TTATAGCTCGGGTAGAGCTTTGGTCT-GCTTACGTCTCGGTTAGAGCGTAAAGCTA
* * *
115462 TTATAGCTCAGGTAGAGCTTTGGACTGCTTACATCTCGGTTAGAGCGTAAAGCTA
1 TTATAGCTCGGGTAGAGCTTTGGTCTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
* * * * *
115517 GTATAGCTCGGGTAGAGCTTTGGTCTGCTTACGTCTCGATTAAAGCGTAAGGTTA
1 TTATAGCTCGGGTAGAGCTTTGGTCTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
115572 TT-TCAGCTCGGG
1 TTAT-AGCTCGGG
115584 AGGAGAGTTA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
54 1 0.01
55 103 0.98
56 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (55 bp):
TTATAGCTCGGGTAGAGCTTTGGTCTGCTTACGTCTCGGTTAGAGCGTAAAGCTA
Found at i:122568 original size:55 final size:55
Alignment explanation
Indices: 122509--122642 Score: 162
Period size: 55 Copynumber: 2.4 Consensus size: 55
122499 AGCTTTGTTT
* *
122509 GCTTACGTCTCGATTAGAGCGTAATGCTATTATAGCTCGA-GTAGAGATTTGGACC
1 GCTTACGTCTCGATTAGAGCGTAAAGCTAGTATAGCT-GAGGTAGAGATTTGGACC
* * * * * * *
122564 GCTTATGTCTCGGTTAGAGTGTAAAGCTAGTATAGCTTAGGTAGAGCTTTGGTCT
1 GCTTACGTCTCGATTAGAGCGTAAAGCTAGTATAGCTGAGGTAGAGATTTGGACC
*
122619 ACTTACGTCTCGATTAGAGCGTAA
1 GCTTACGTCTCGATTAGAGCGTAA
122643 GGTTATTTCA
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 1 0.02
55 64 0.98
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (55 bp):
GCTTACGTCTCGATTAGAGCGTAAAGCTAGTATAGCTGAGGTAGAGATTTGGACC
Found at i:129737 original size:11 final size:11
Alignment explanation
Indices: 129699--129737 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
129689 TTGTGAGCAT
129699 AAAAATAAAAG
1 AAAAATAAAAG
* *
129710 ATAAATAAAAT
1 AAAAATAAAAG
129721 AGAAAATAAAAG
1 A-AAAATAAAAG
129733 AAAAA
1 AAAAA
129738 GTTTAATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (11 bp):
AAAAATAAAAG
Found at i:131450 original size:14 final size:14
Alignment explanation
Indices: 131431--131460 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
131421 CCCTTGTAAG
131431 CCTTTTGACCCAAA
1 CCTTTTGACCCAAA
*
131445 CCTTTTGACCTAAA
1 CCTTTTGACCCAAA
131459 CC
1 CC
131461 AAGTGAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.37, G:0.07, T:0.30
Consensus pattern (14 bp):
CCTTTTGACCCAAA
Found at i:131517 original size:19 final size:19
Alignment explanation
Indices: 131482--131539 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
131472 GCCTGATCGG
*
131482 CTCGACCTGAA-TCCGTTGA
1 CTCGACCCGAACT-CGTTGA
*
131501 CTCGACCCGAACTCGTTTA
1 CTCGACCCGAACTCGTTGA
* *
131520 CCCGACCCAAACTCGTTGA
1 CTCGACCCGAACTCGTTGA
131539 C
1 C
131540 CATTGACTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 32 0.97
20 1 0.03
ACGTcount: A:0.22, C:0.38, G:0.17, T:0.22
Consensus pattern (19 bp):
CTCGACCCGAACTCGTTGA
Found at i:132547 original size:5 final size:5
Alignment explanation
Indices: 132537--132583 Score: 58
Period size: 5 Copynumber: 8.6 Consensus size: 5
132527 TAATTATAGA
132537 TTTAT TTTAT TTTATCT TTTAT TTTAT TTTATCT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTA--T TTTAT TTTAT TTTA--T TTTAT TTTAT TTT
132584 TAGGTTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
5 28 0.74
7 10 0.26
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:132558 original size:12 final size:11
Alignment explanation
Indices: 132537--132585 Score: 64
Period size: 12 Copynumber: 4.4 Consensus size: 11
132527 TAATTATAGA
132537 TTTATTTTATT
1 TTTATTTTATT
*
132548 TTATCTTTTA-T
1 TT-TATTTTATT
132559 TTTATTTTATCT
1 TTTATTTTAT-T
132571 TTTATTTTATT
1 TTTATTTTATT
132582 TTTA
1 TTTA
132586 GGTTTTTATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 6 0.18
11 10 0.30
12 17 0.52
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:132559 original size:17 final size:17
Alignment explanation
Indices: 132537--132583 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
132527 TAATTATAGA
132537 TTTATTTTATTTTATCT
1 TTTATTTTATTTTATCT
132554 TTTATTTTATTTTATCT
1 TTTATTTTATTTTATCT
132571 TTTATTTTATTTT
1 TTTATTTTATTTT
132584 TAGGTTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTTATTTTATCT
Found at i:137710 original size:10 final size:10
Alignment explanation
Indices: 137695--137720 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
137685 TATTTCTAAC
137695 TCATTCCATT
1 TCATTCCATT
137705 TCATTCCATT
1 TCATTCCATT
137715 TCATTC
1 TCATTC
137721 ACTGTATTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (10 bp):
TCATTCCATT
Found at i:140879 original size:32 final size:32
Alignment explanation
Indices: 140825--140887 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
140815 GTGGTTAGGC
*
140825 TGACCTAGGCGTGTTTGTAAGAAAGGATCGCT
1 TGACCTAGGCGTGTTTGCAAGAAAGGATCGCT
* *
140857 TGACTTAGGTGTGTTTGCAAGAAAGGATCGC
1 TGACCTAGGCGTGTTTGCAAGAAAGGATCGC
140888 CTAAGGTCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.32, T:0.29
Consensus pattern (32 bp):
TGACCTAGGCGTGTTTGCAAGAAAGGATCGCT
Found at i:142155 original size:20 final size:21
Alignment explanation
Indices: 142122--142165 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
142112 AAGCCATTTG
142122 ACCCAAACCCTTTTAAACTAA
1 ACCCAAACCCTTTTAAACTAA
* *
142143 ACCCAAA-CCTTTTGACCTAA
1 ACCCAAACCCTTTTAAACTAA
142163 ACC
1 ACC
142166 AAGTGAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.39, C:0.36, G:0.02, T:0.23
Consensus pattern (21 bp):
ACCCAAACCCTTTTAAACTAA
Found at i:144479 original size:19 final size:19
Alignment explanation
Indices: 144431--144479 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
144421 ATTATCCCAA
* *
144431 AAATTACAAGTCTTTAAAAT
1 AAATTA-AAATCTTAAAAAT
**
144451 AAATCCAAATCTTAAAAAT
1 AAATTAAAATCTTAAAAAT
144470 AAATTAAAAT
1 AAATTAAAAT
144480 TCACTCGTCT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATTAAAATCTTAAAAAT
Found at i:153059 original size:11 final size:11
Alignment explanation
Indices: 153043--153067 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
153033 AATATTAGAG
153043 AAATCTTGGAT
1 AAATCTTGGAT
153054 AAATCTTGGAT
1 AAATCTTGGAT
153065 AAA
1 AAA
153068 AACCTACATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (11 bp):
AAATCTTGGAT
Found at i:155512 original size:60 final size:57
Alignment explanation
Indices: 155337--155524 Score: 191
Period size: 61 Copynumber: 3.2 Consensus size: 57
155327 CAGGAAAAAG
* * * *
155337 GGGTCAAAATCAAAATTTTGGAAAGTTTGGAGGTCAAAATGTAATTTTTGAAAGTTTGA
1 GGGTCAAAATCAAAATTTTGGAAAGTTCGG-GATTAAAAT-CAATTTTTGAAAGTTTGA
* * **
155396 -GGTCAAAATGC-AATTTTTAGAAAGTTCGAGCCTTAAAATTCAATTTTTCAGAAAGTTTGA
1 GGGTCAAAAT-CAAAATTTTGGAAAGTTCG-GGATTAAAA-TCAATTTTT--GAAAGTTTGA
*
155456 GGGTCAAAATCAAAATTTTGGAAAGTTCAGGGATTAAAATCAAATTTTTGGAAAGTTTGG
1 GGGTCAAAATCAAAATTTTGGAAAGTTC-GGGATTAAAATC-AATTTTT-GAAAGTTTGA
155516 GGGTCAAAA
1 GGGTCAAAA
155525 CTATATTTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
58 35 0.33
59 3 0.03
60 31 0.29
61 37 0.35
62 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.22, T:0.32
Consensus pattern (57 bp):
GGGTCAAAATCAAAATTTTGGAAAGTTCGGGATTAAAATCAATTTTTGAAAGTTTGA
Found at i:155533 original size:30 final size:29
Alignment explanation
Indices: 155336--155547 Score: 151
Period size: 30 Copynumber: 7.1 Consensus size: 29
155326 TCAGGAAAAA
*
155336 GGGGTCAAAATCAAAATTTTGGAAAGTTTG
1 GGGGTCAAAATC-AATTTTTGGAAAGTTTG
* *
155366 GAGGTCAAAATGTAATTTTT-GAAAGTTT-
1 GGGGTCAAAAT-CAATTTTTGGAAAGTTTG
* * *
155394 GAGGTCAAAATGCAATTTTTAGAAAGTTCG
1 GGGGTCAAAAT-CAATTTTTGGAAAGTTTG
* ** * *
155424 AGCCTTAAAATTCAATTTTTCAGAAAGTTTG
1 GGGGTCAAAA-TCAATTTTT-GGAAAGTTTG
* * **
155455 AGGGTCAAAATCAAAATTTTGGAAAGTTCA
1 GGGGTCAAAATC-AATTTTTGGAAAGTTTG
* *
155485 GGGATTAAAATCAAATTTTTGGAAAGTTTG
1 GGGGTCAAAATC-AATTTTTGGAAAGTTTG
* *
155515 GGGGTCAAAA-CTATATTTTTGAAAAGTTAG
1 GGGGTCAAAATC-A-ATTTTTGGAAAGTTTG
155545 GGG
1 GGG
155548 TCGAATTTGA
Statistics
Matches: 146, Mismatches: 29, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
28 19 0.13
29 17 0.12
30 87 0.60
31 23 0.16
ACGTcount: A:0.37, C:0.08, G:0.23, T:0.33
Consensus pattern (29 bp):
GGGGTCAAAATCAATTTTTGGAAAGTTTG
Found at i:166479 original size:25 final size:25
Alignment explanation
Indices: 166431--166479 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
166421 TCTTAAAACA
* *
166431 AAATGAAAATAACTAAAGCTTAAAG
1 AAATGAAAATAACTAAAACCTAAAG
166456 AAATGAAAATAACTAAAACCTAAA
1 AAATGAAAATAACTAAAACCTAAA
166480 TTACAATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (25 bp):
AAATGAAAATAACTAAAACCTAAAG
Found at i:169941 original size:52 final size:52
Alignment explanation
Indices: 169878--170001 Score: 160
Period size: 52 Copynumber: 2.4 Consensus size: 52
169868 CCCATTTAAT
* * * *
169878 ACTCACAATGACACAAAGTCATCGGACCTTA-AACCCATAATAGGATTCATAA
1 ACTCACGATGACACATAGTCATCGAACCTCATAACCCATAA-AGGATTCATAA
* * *
169930 ACTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATAT
1 ACTCACGATGACACATAGTCATCGAACCTCATAACCCATAAAGGATTCATAA
*
169982 ACTCACGATGATACATAGTC
1 ACTCACGATGACACATAGTC
170002 TCAGATTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
52 56 0.89
53 7 0.11
ACGTcount: A:0.39, C:0.25, G:0.13, T:0.23
Consensus pattern (52 bp):
ACTCACGATGACACATAGTCATCGAACCTCATAACCCATAAAGGATTCATAA
Found at i:173252 original size:50 final size:50
Alignment explanation
Indices: 173155--173321 Score: 192
Period size: 52 Copynumber: 3.3 Consensus size: 50
173145 TTCCCATTTA
* * * * * *
173155 ATACTCACGATGACGCAATGTCATTGGACCTTA-AACCCGTAATAGGATCCAT
1 ATACTCACAATGACAC-A-GTCATCGGACCTCATAATCCGTAA-AGGATTCAT
* *
173207 ATACTCACGATGACACAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACAATGACACAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
173257 ATACTCACAATGATACATAGTCATCGGACCTCGTAATCCGTAAAGGATTCAT
1 ATACTCACAATG--ACACAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
173309 ATACTCACAATGA
1 ATACTCACAATGA
173322 TACATAGTCT
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
50 32 0.31
51 8 0.08
52 62 0.61
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (50 bp):
ATACTCACAATGACACAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:173327 original size:52 final size:52
Alignment explanation
Indices: 173174--173330 Score: 212
Period size: 52 Copynumber: 3.1 Consensus size: 52
173164 ATGACGCAAT
* * * * * *
173174 GTCATTGGACCTTA-AACCCGTAATAGGATCCATATACTCACGATG--ACACA
1 GTCATCGGACCTCATAATCCGTAA-AGGATTCATATACTCACAATGATACATA
*
173224 GTCATCGGACCTCATAATCCATAAAGGATTCATATACTCACAATGATACATA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACAATGATACATA
*
173276 GTCATCGGACCTCGTAATCCGTAAAGGATTCATATACTCACAATGATACATA
1 GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACAATGATACATA
173328 GTC
1 GTC
173331 TCGAATTTAA
Statistics
Matches: 95, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
50 31 0.33
51 7 0.07
52 57 0.60
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
GTCATCGGACCTCATAATCCGTAAAGGATTCATATACTCACAATGATACATA
Found at i:173586 original size:3 final size:3
Alignment explanation
Indices: 173578--173608 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
173568 AGACTTGAAC
173578 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
173609 AGAATAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:174337 original size:62 final size:62
Alignment explanation
Indices: 174238--174362 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
174228 TAAATCTTAA
174238 AACTATGCAAGATAATAGAGCTCGTTAAAGTAATTATGAACCTTCAATTTAATAGGGTTAGG
1 AACTATGCAAGATAATAGAGCTCGTTAAAGTAATTATGAACCTTCAATTTAATAGGGTTAGG
*
174300 AACTATGCAAGATAATAGAGCTCGTTAAAGTAGTTATGAACCTTCAATTTAATAGGGTTAGG
1 AACTATGCAAGATAATAGAGCTCGTTAAAGTAATTATGAACCTTCAATTTAATAGGGTTAGG
174362 A
1 A
174363 TCTAAATTGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (62 bp):
AACTATGCAAGATAATAGAGCTCGTTAAAGTAATTATGAACCTTCAATTTAATAGGGTTAGG
Found at i:176629 original size:52 final size:52
Alignment explanation
Indices: 176551--176728 Score: 216
Period size: 52 Copynumber: 3.4 Consensus size: 52
176541 TTCCCATTTA
* * * * *
176551 ATACTCACAATGACACA-ATGTCATCGGACCTTA-AACCCGTAATAGAATCCAT
1 ATACTCACGATGACACATA-GTCATCGGACCTCACAATCCGTAA-AGGATTCAT
* *
176603 ATACTCATGATGACACATAGTCATCGGACCTCACAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
* * * *
176655 ATACTCACGATGATACATAGTCATCAGACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
*
176707 ATACTCACGATGATACATAGTC
1 ATACTCACGATGACACATAGTC
176729 TCATATTTAA
Statistics
Matches: 111, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
52 103 0.93
53 8 0.07
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCACAATCCGTAAAGGATTCAT
Found at i:179920 original size:52 final size:52
Alignment explanation
Indices: 179856--180026 Score: 161
Period size: 52 Copynumber: 3.3 Consensus size: 52
179846 TTCCCATTTA
* * * *
179856 ATACTCACGATGACACAAATTCATCGGACCTTA-AACTCT-TAATAGGA-TCCAT
1 ATACTCATGATGACACAAATACATCAGACCTCATAA-TCTATAA-AGGAGT-CAT
*
179908 ATACTCATGATGACACATATACATCAGACCTCATAATCTATAAAGGAGTCAT
1 ATACTCATGATGACACAAATACATCAGACCTCATAATCTATAAAGGAGTCAT
* * * * * *
179960 ATACTCATGATGATACATAGT-CATCAAACCTCATAATCCATAACGGATTCAT
1 ATACTCATGATGACACA-AATACATCAGACCTCATAATCTATAAAGGAGTCAT
* *
180012 ATATTCACGATGACA
1 ATACTCATGATGACA
180027 TATAGTCATC
Statistics
Matches: 100, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
52 93 0.93
53 7 0.07
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (52 bp):
ATACTCATGATGACACAAATACATCAGACCTCATAATCTATAAAGGAGTCAT
Found at i:180032 original size:52 final size:52
Alignment explanation
Indices: 179899--180043 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 52
179889 AACTCTTAAT
* * *
179899 AGGATCCATATACTCATGATGACACATA-TACATCAGACCTCATAATCTATAA
1 AGGATTCATATACTCATGATGACACATAGT-CATCAAACCTCATAATCCATAA
* *
179951 AGGAGTCATATACTCATGATGATACATAGTCATCAAACCTCATAATCCATAA
1 AGGATTCATATACTCATGATGACACATAGTCATCAAACCTCATAATCCATAA
* * * * *
180003 CGGATTCATATATTCACGATGACATATAGTCATCGAACCTC
1 AGGATTCATATACTCATGATGACACATAGTCATCAAACCTC
180044 TTTCATTTAC
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
52 79 0.99
53 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (52 bp):
AGGATTCATATACTCATGATGACACATAGTCATCAAACCTCATAATCCATAA
Found at i:180312 original size:16 final size:18
Alignment explanation
Indices: 180291--180326 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
180281 CCTTAATACC
180291 ATTTCA-TT-TCAATTTA
1 ATTTCATTTCTCAATTTA
180307 ATTTCATTTCTCAATTTA
1 ATTTCATTTCTCAATTTA
180325 AT
1 AT
180327 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 2 0.11
18 10 0.56
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTCATTTCTCAATTTA
Found at i:192599 original size:749 final size:748
Alignment explanation
Indices: 191160--192624 Score: 2777
Period size: 749 Copynumber: 2.0 Consensus size: 748
191150 ATAGGTTGCG
* * *
191160 AGTCCTCGACAGCTCATGTGAGCAGCATCGGGTACTGGTAACTGAAAGTTATGAATAGGAAGAGA
1 AGTCCTCGACAACTCATGTGAGCAGCATCAGGTACTGATAACTGAAAGTTATGAATAGGAAGAGA
191225 AGTTGTAAATAACTCAAAGAGCAAAGGAATTATGTTGGCTCGATGGAGTCATTGTTGCTTATTAC
66 AGTTGTAAATAACTCAAAGAGCAAAGGAATTATGTTGGCTCGATGGAGTCATTGTTGCTTATTAC
191290 AATGTTTGGTAACTTCTTAGACTATCGAACTTACTAAGCTATGAAGCTTACCATAGATATTGTTG
131 AATGTTTGGTAACTTCTTAGACTATCGAACTTACTAAGCTATGAAGCTTACCATAGATATTGTTG
191355 TTATTTTGTAGATCGTTTGCTGACTAAAGATCAAATCATCGTCATCTATTTGAAGTCACATTATC
196 TTATTTTGTAGATCGTTTGCTGACTAAAGATCAAATCATCGTCATCTATTTGAAGTCACATTATC
* *
191420 GCGGAGTTTGTCGGTAGATTTTGCATCACTCGGTCTTATGGCATGTACTAGGATGATATTAACCT
261 GCAGAGTTTGTCGGTAGATTTTGCATCACTCAGTCTTATGGCATGTACTAGGATGATATTAACCT
191485 TTGATGTTGAACTAAAGATGTTGAAATCTTACTATTTTGAATGTGTATATGCATGAAGTACAATT
326 TTGATGTTGAACTAAAGATGTTGAAATCTTACTATTTTGAATGTGTATATGCATGAAGTACAATT
191550 TAGATGTTTAAGCTTAAGATGCTTGTAAAGGCTTAGAAGTTATGTATGTTGTGTGATGACCTAAT
391 TAGATGTTTAAGCTTAAGATGCTTGTAAAGGCTTAGAAGTTATGTATGTTGTGTGATGACCTAAT
191615 GCATAACTTGTGTTGGATATGTTTGAGATGTTAAACTTGTGTCTTGACATAAATCTTAAGATTCT
456 GCATAACTTGTGTTGGATATGTTTGAGATGTTAAACTTGTGTCTTGACATAAATCTTAAGATTCT
*
191680 ACATACTTGTTTCAGTAGAACTTTTGCATTTATCAGTAGAAGTACAGGGTAGGAGAGAGGTTGAT
521 ACATACTTGTTTCAGTAGAACTTTTGCATTTATCAATAGAAGTACAGGGTAGGAGAGAGGTTGAT
191745 CTCTGACTTGAGTTGTATCGGTAGTTGAATAACAAGTATCGGTAGTTTTTAGCATTGATGTATCG
586 CTCTGACTTGAGTTGTATCGGTAGTTGAATAACAAGTATCGGTAGTTTTTAGCATTGATGTATCG
* *
191810 GTAGTTTGTATGCATATATCGGTAGAAGTTACAGGGTGAGAATTTTTGCTCTCCAGAGTTTTTGG
651 GTAGTTTGTATGCATATATCAGTAGAAGTTACAAGGTGAGAATTTTT-CTCTCCAGAGTTTTTGG
191875 TAGAGCTAACACAAGTACCGGTAGAAATCTGCAC
715 TAGAGCTAACACAAGTACCGGTAGAAATCTGCAC
* * * *
191909 AGTCCTCGACAACTCGTGTGAGTAGTATCAGGTACTGATAATTGAAAGTTATGAATAGGAAGAGA
1 AGTCCTCGACAACTCATGTGAGCAGCATCAGGTACTGATAACTGAAAGTTATGAATAGGAAGAGA
191974 AGTTGTAAATAACTCAAAGAGCAAAGGAATTATGTTGGCTCGATGGAGTCATTGTTGCTTATTAC
66 AGTTGTAAATAACTCAAAGAGCAAAGGAATTATGTTGGCTCGATGGAGTCATTGTTGCTTATTAC
192039 AATGTTTGGTAACTTCTTAGACTATCGAACTTACTAAGCTATGAAGCTTACCATAGATATTGTTG
131 AATGTTTGGTAACTTCTTAGACTATCGAACTTACTAAGCTATGAAGCTTACCATAGATATTGTTG
192104 TTATTTTGTAGATCGTTTGCTGACTAAAGATCAAATCATCGTCATCTATTTGAAGTCACATTATC
196 TTATTTTGTAGATCGTTTGCTGACTAAAGATCAAATCATCGTCATCTATTTGAAGTCACATTATC
192169 GCAGAGTTTGTCGGTAGATTTTGCATCACTCAGTCTTATGGCATGTACTAGGATGATATTAACCT
261 GCAGAGTTTGTCGGTAGATTTTGCATCACTCAGTCTTATGGCATGTACTAGGATGATATTAACCT
*
192234 TTGATGTTGAACTAAAGATGTTGAAATCTTACTATTTTGAATGTGTATATGTATGAAGTACAATT
326 TTGATGTTGAACTAAAGATGTTGAAATCTTACTATTTTGAATGTGTATATGCATGAAGTACAATT
192299 TAGATGTTTAAGCTTAAGATGCTTGTAAAGGCTTAGAAGTTATGTATGTTGTGTGATGACCTAAT
391 TAGATGTTTAAGCTTAAGATGCTTGTAAAGGCTTAGAAGTTATGTATGTTGTGTGATGACCTAAT
192364 GCATAACTTGTGTTGGATATGTTTGAGATGTTAAACTTGTGTCTTGACATAAATCTTAAGATTCT
456 GCATAACTTGTGTTGGATATGTTTGAGATGTTAAACTTGTGTCTTGACATAAATCTTAAGATTCT
192429 ACATACTTGTTTCAGTAGAACTTTTGCATTTATCAATAGAAGTACAGGGTAGGAGAGAGGTTGAT
521 ACATACTTGTTTCAGTAGAACTTTTGCATTTATCAATAGAAGTACAGGGTAGGAGAGAGGTTGAT
*
192494 CTCTGACTTGAGTTTTATCGGTAGTTGAATAACAAGTATCGGTAGTTTTTAGCATTGATGTATCG
586 CTCTGACTTGAGTTGTATCGGTAGTTGAATAACAAGTATCGGTAGTTTTTAGCATTGATGTATCG
* *
192559 GTAGTTTGTATGCATATATCAGTAGAAGTTGCAAGGTGAGAATTTTTCTCTCTAGAGTTTTTGGT
651 GTAGTTTGTATGCATATATCAGTAGAAGTTACAAGGTGAGAATTTTTCTCTCCAGAGTTTTTGGT
192624 A
716 A
192625 TCGGTAGATG
Statistics
Matches: 700, Mismatches: 16, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
748 18 0.03
749 682 0.97
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.36
Consensus pattern (748 bp):
AGTCCTCGACAACTCATGTGAGCAGCATCAGGTACTGATAACTGAAAGTTATGAATAGGAAGAGA
AGTTGTAAATAACTCAAAGAGCAAAGGAATTATGTTGGCTCGATGGAGTCATTGTTGCTTATTAC
AATGTTTGGTAACTTCTTAGACTATCGAACTTACTAAGCTATGAAGCTTACCATAGATATTGTTG
TTATTTTGTAGATCGTTTGCTGACTAAAGATCAAATCATCGTCATCTATTTGAAGTCACATTATC
GCAGAGTTTGTCGGTAGATTTTGCATCACTCAGTCTTATGGCATGTACTAGGATGATATTAACCT
TTGATGTTGAACTAAAGATGTTGAAATCTTACTATTTTGAATGTGTATATGCATGAAGTACAATT
TAGATGTTTAAGCTTAAGATGCTTGTAAAGGCTTAGAAGTTATGTATGTTGTGTGATGACCTAAT
GCATAACTTGTGTTGGATATGTTTGAGATGTTAAACTTGTGTCTTGACATAAATCTTAAGATTCT
ACATACTTGTTTCAGTAGAACTTTTGCATTTATCAATAGAAGTACAGGGTAGGAGAGAGGTTGAT
CTCTGACTTGAGTTGTATCGGTAGTTGAATAACAAGTATCGGTAGTTTTTAGCATTGATGTATCG
GTAGTTTGTATGCATATATCAGTAGAAGTTACAAGGTGAGAATTTTTCTCTCCAGAGTTTTTGGT
AGAGCTAACACAAGTACCGGTAGAAATCTGCAC
Found at i:201183 original size:3 final size:3
Alignment explanation
Indices: 201104--201169 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
201094 GCTACAACCA
* * * *
201104 AAT ACT AAT ACT AGT AAT AAT AAT AA- AA- AAT ATAT CAACG AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT -AA-T AAT AAT
201150 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
201170 CACGGTAATA
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 5 0.10
5 1 0.02
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:201331 original size:16 final size:16
Alignment explanation
Indices: 201312--201350 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
201302 AAAGTGTTAC
*
201312 AAATAAATACATAAAT
1 AAATAAATACAAAAAT
* *
201328 AAATAAGTATAAAAAT
1 AAATAAATACAAAAAT
201344 AAATAAA
1 AAATAAA
201351 AAATGTAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (16 bp):
AAATAAATACAAAAAT
Found at i:201390 original size:4 final size:4
Alignment explanation
Indices: 201381--201440 Score: 66
Period size: 4 Copynumber: 14.5 Consensus size: 4
201371 AAAATGCTAA
* * *
201381 AAAT AAAT AAAC AAACA AAAT AAAT AAAT AAAT AGAAT AAAC AAAT AAAT
1 AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
*
201431 AAAA AAAT AA
1 AAAT AAAT AA
201441 GGAAAGGACT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
4 40 0.85
5 7 0.15
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:201402 original size:17 final size:17
Alignment explanation
Indices: 201380--201440 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
201370 TAAAATGCTA
* *
201380 AAAATAAATAAACAAAC
1 AAAATAAATAAATAAAT
201397 AAAATAAATAAATAAAT
1 AAAATAAATAAATAAAT
* *
201414 AGAATAAACAAATAAAT
1 AAAATAAATAAATAAAT
201431 AAAA-AAATAA
1 AAAATAAATAA
201441 GGAAAGGACT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
16 5 0.13
17 33 0.87
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:207732 original size:42 final size:42
Alignment explanation
Indices: 207673--207756 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
207663 AATGCTTGCC
207673 TTATTTAATAGACCACCACTACTAATCAAATTTCTATGAAGT
1 TTATTTAATAGACCACCACTACTAATCAAATTTCTATGAAGT
207715 TTATTTAATAGACCACCACTACTAATCAAATTTCTATGAAGT
1 TTATTTAATAGACCACCACTACTAATCAAATTTCTATGAAGT
207757 GCAGGTACAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (42 bp):
TTATTTAATAGACCACCACTACTAATCAAATTTCTATGAAGT
Found at i:210500 original size:21 final size:21
Alignment explanation
Indices: 210461--210507 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
210451 TAGTTCTATT
*
210461 GATACAAGTGAGGCAACTACC
1 GATACAAGTCAGGCAACTACC
* * *
210482 GATACAAGTCATGCTACTATC
1 GATACAAGTCAGGCAACTACC
210503 GATAC
1 GATAC
210508 TAAAAACTCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (21 bp):
GATACAAGTCAGGCAACTACC
Found at i:211181 original size:36 final size:36
Alignment explanation
Indices: 211120--211212 Score: 123
Period size: 36 Copynumber: 2.6 Consensus size: 36
211110 TTGAACAAAA
*
211120 CTGTTGACCCTAAAGGTCATGATGCTCGTTCTACTCC
1 CTGTTGACCC-AAAGGTCATGATGCTCATTCTACTCC
* * *
211157 CTGTTGACCCAAAGGTCATTATGCTCATTTTTCTCC
1 CTGTTGACCCAAAGGTCATGATGCTCATTCTACTCC
* *
211193 CTATTGACCCTAAGGTCATG
1 CTGTTGACCCAAAGGTCATG
211213 CCTGTTACTA
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 39 0.80
37 10 0.20
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.34
Consensus pattern (36 bp):
CTGTTGACCCAAAGGTCATGATGCTCATTCTACTCC
Found at i:214433 original size:5 final size:5
Alignment explanation
Indices: 214418--214456 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
214408 TATAAATATA
214418 TTTCTT TTTCT TTTCT TTTCT TTTCT TCTTCT TTT-T TTT
1 TTTC-T TTTCT TTTCT TTTCT TTTCT T-TTCT TTTCT TTT
214457 ATGTGACTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
5 19 0.59
6 9 0.28
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:214439 original size:16 final size:17
Alignment explanation
Indices: 214418--214456 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
214408 TATAAATATA
214418 TTTCTTTTTCTT-TTCT
1 TTTCTTTTTCTTCTTCT
214434 TTTC-TTTTCTTCTTCT
1 TTTCTTTTTCTTCTTCT
214450 TTT-TTTT
1 TTTCTTTT
214457 ATGTGACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTCTTCTTCT
Found at i:214444 original size:21 final size:20
Alignment explanation
Indices: 214418--214456 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
214408 TATAAATATA
*
214418 TTTCTTTTTCTTTTCTTTTCT
1 TTTCTTCTTCTTTT-TTTTCT
214439 TTTCTTCTTCTTTTTTTT
1 TTTCTTCTTCTTTTTTTT
214457 ATGTGACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (20 bp):
TTTCTTCTTCTTTTTTTTCT
Found at i:217041 original size:16 final size:16
Alignment explanation
Indices: 217020--217050 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
217010 ATAATGTGAA
217020 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
217036 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
217051 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:218233 original size:19 final size:19
Alignment explanation
Indices: 218209--218253 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
218199 ATGAGGGGAG
218209 GCTCCCTATTTATAGTTGA
1 GCTCCCTATTTATAGTTGA
218228 GCTCCCTATTTATAGTTGA
1 GCTCCCTATTTATAGTTGA
218247 GCTCCCT
1 GCTCCCT
218254 CATAAATGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.18, C:0.27, G:0.16, T:0.40
Consensus pattern (19 bp):
GCTCCCTATTTATAGTTGA
Found at i:223887 original size:37 final size:36
Alignment explanation
Indices: 223846--223945 Score: 94
Period size: 38 Copynumber: 2.7 Consensus size: 36
223836 GGATTTGTTC
223846 ATGCAGCGATATTCCTTGGTGCAATTGAAGAATACTT
1 ATGCAGCGATATT-CTTGGTGCAATTGAAGAATACTT
* * * *
223883 ATGCAACAATAGTTC-TGGATACAATTTGAAGAATATTT
1 ATGCAGCGATA-TTCTTGG-TGCAA-TTGAAGAATACTT
* *
223921 ATGCAGTGATAGTCTTGAGTGCAAT
1 ATGCAGCGATATTCTTG-GTGCAAT
223946 CTAAAAGTGC
Statistics
Matches: 49, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
36 3 0.06
37 17 0.35
38 28 0.57
39 1 0.02
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (36 bp):
ATGCAGCGATATTCTTGGTGCAATTGAAGAATACTT
Found at i:229279 original size:36 final size:36
Alignment explanation
Indices: 229191--229291 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
229181 ATCGTTATTT
*
229191 ATTTTACTCCTTATTGACCTCAAAGGTCATGATACTC
1 ATTTTTCTCCTTATTGACC-CAAAGGTCATGATACTC
* * * *
229228 --GTTTCTCCTTGTTGACCCAAAGGTCATTATGCTC
1 ATTTTTCTCCTTATTGACCCAAAGGTCATGATACTC
* *
229262 ATTTTTCTCCTTATTGACCTAAAAGTCATG
1 ATTTTTCTCCTTATTGACCCAAAGGTCATG
229292 CCTGTTACCA
Statistics
Matches: 52, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
34 15 0.29
35 14 0.27
36 23 0.44
ACGTcount: A:0.24, C:0.24, G:0.13, T:0.40
Consensus pattern (36 bp):
ATTTTTCTCCTTATTGACCCAAAGGTCATGATACTC
Found at i:232091 original size:8 final size:9
Alignment explanation
Indices: 232073--232317 Score: 63
Period size: 9 Copynumber: 26.0 Consensus size: 9
232063 TTTTGGTACA
232073 ATAATTTTT
1 ATAATTTTT
232082 ATAA-TTTT
1 ATAATTTTT
*
232090 ATACGAATTTT
1 ATA--ATTTTT
*
232101 ATATTTCTTT
1 ATAATT-TTT
* *
232111 ACATTTTTTT
1 ATA-ATTTTT
*
232121 ATAATTTTC
1 ATAATTTTT
*
232130 ATGACTTTATT
1 AT-AATTT-TT
232141 A-AA-TTTT
1 ATAATTTTT
232148 ATAATTCTTTTT
1 ATAA---TTTTT
* *
232160 CTAAATTTCT
1 AT-AATTTTT
232170 ATACA-TTTT
1 ATA-ATTTTT
*
232179 ATATTTTTT
1 ATAATTTTT
* *
232188 ACAATTTAAT
1 ATAATTT-TT
* *
232198 AAAAGT-TT
1 ATAATTTTT
*
232206 ACAATTTTT
1 ATAATTTTT
* *
232215 TTATTTTTT
1 ATAATTTTT
232224 ATAATTTTT
1 ATAATTTTT
232233 ATAATTTTTTTT
1 ATAA---TTTTT
* *
232245 CTAAATTTT
1 ATAATTTTT
*
232254 GTAATTTTT
1 ATAATTTTT
**
232263 ATTAAAATTT
1 A-TAATTTTT
*
232273 AAAATTTTTT
1 ATAA-TTTTT
*
232283 ATAACTTTT
1 ATAATTTTT
232292 ATTAATTTTT
1 A-TAATTTTT
232302 AT--TTTTT
1 ATAATTTTT
*
232309 ATCATTTTT
1 ATAATTTTT
232318 TGCCACATGT
Statistics
Matches: 171, Mismatches: 40, Indels: 50
0.66 0.15 0.19
Matches are distributed among these distances:
7 10 0.06
8 16 0.09
9 71 0.42
10 47 0.27
11 12 0.07
12 13 0.08
13 2 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:232243 original size:20 final size:19
Alignment explanation
Indices: 232218--232301 Score: 64
Period size: 21 Copynumber: 4.2 Consensus size: 19
232208 AATTTTTTTA
232218 TTTTTTATAATTTTTATAATT
1 TTTTTTATAA-TTTTATAA-T
* *
232239 TTTTTTCTAAATTTTGTAAT
1 TTTTTTAT-AATTTTATAAT
* *
232259 TTTTATTA-AAATTTA-AAA
1 TTTT-TTATAATTTTATAAT
232277 TTTTTTATAACTTTTATTAAT
1 TTTTTTATAA-TTTTA-TAAT
232298 TTTT
1 TTTT
232302 ATTTTTTATC
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
17 3 0.06
18 8 0.16
19 9 0.18
20 5 0.10
21 22 0.45
22 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTTATAATTTTATAAT
Found at i:237235 original size:55 final size:55
Alignment explanation
Indices: 237151--237262 Score: 206
Period size: 55 Copynumber: 2.0 Consensus size: 55
237141 TCAGAGTTTA
*
237151 ATTCTAAACAACCTCATTCTCTTTTGTCAATTATAAGAAAATAGGGACACCCAAG
1 ATTCTAAACAACCTCATTCTCTTTTGTCAATTATAAAAAAATAGGGACACCCAAG
*
237206 ATTCTAAGCAACCTCATTCTCTTTTGTCAATTATAAAAAAATAGGGACACCCAAG
1 ATTCTAAACAACCTCATTCTCTTTTGTCAATTATAAAAAAATAGGGACACCCAAG
237261 AT
1 AT
237263 CACTTTGAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.29
Consensus pattern (55 bp):
ATTCTAAACAACCTCATTCTCTTTTGTCAATTATAAAAAAATAGGGACACCCAAG
Found at i:239062 original size:18 final size:18
Alignment explanation
Indices: 239029--239067 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
239019 GAAATGAGAG
* *
239029 TGAGAGATGAATGATGTT
1 TGAGAGATGAAGGATGAT
*
239047 TGAGAGATGAGGGATGAT
1 TGAGAGATGAAGGATGAT
239065 TGA
1 TGA
239068 AATGAGGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (18 bp):
TGAGAGATGAAGGATGAT
Found at i:241384 original size:50 final size:50
Alignment explanation
Indices: 241309--241408 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
241299 TTTCCTTTGG
241309 GGTATGCTAAAGATCGACCCACTAGTTGAAGTGTCACGATCATTGGTCTT
1 GGTATGCTAAAGATCGACCCACTAGTTGAAGTGTCACGATCATTGGTCTT
241359 GGTATGCTAAAGATCGACCCACTAGTTGAAGTGTCACGATCATTGGTCTT
1 GGTATGCTAAAGATCGACCCACTAGTTGAAGTGTCACGATCATTGGTCTT
241409 ACTTCACCTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (50 bp):
GGTATGCTAAAGATCGACCCACTAGTTGAAGTGTCACGATCATTGGTCTT
Found at i:245209 original size:10 final size:10
Alignment explanation
Indices: 245184--245219 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
245174 TTGGTCTTTA
245184 TAATTAA-CT
1 TAATTAACCT
245193 TAATTAACCT
1 TAATTAACCT
*
245203 TACTTAACCT
1 TAATTAACCT
245213 TAATTAA
1 TAATTAA
245220 ATCCACTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 7 0.29
10 17 0.71
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.42
Consensus pattern (10 bp):
TAATTAACCT
Found at i:246837 original size:50 final size:50
Alignment explanation
Indices: 246778--247051 Score: 168
Period size: 50 Copynumber: 5.5 Consensus size: 50
246768 CAACAATCAT
* * *
246778 CAAAT-CTTATATCCCTGAAGTTACAGTGATCGAATTAAAACTACAAAAG
1 CAAATCCTTATATCCCTGAAGTTGCAGTGATCGGATTAAAGCTACAAAAG
* * * * *
246827 CAAATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGA-TAAAGTTACAAAAC
1 CAAATCCTTATATCCCTGAAGTTGCAGT-GATC-GGATTAAAGCTACAAAAG
* * * **
246878 CAAATCATT-TATCCCTGAAGTTGTAG-GATCGGATTAAAGCTATAGTAG
1 CAAATCCTTATATCCCTGAAGTTGCAGTGATCGGATTAAAGCTACAAAAG
* * * * * * * * *
246926 CAAATCTTTATCTCTCTGAAGTTGTAGTAGAGTCAGA-TGAAGCTACCACAC
1 CAAATCCTTATATCCCTGAAGTTGCAGT-GA-TCGGATTAAAGCTACAAAAG
* * * * **
246977 CAAATCC-TATACCCCTGAAGTTGAAGTGGGTCGGATTGAATTTACGAAAA-
1 CAAATCCTTATATCCCTGAAGTTGCAGT-GATCGGATTAAAGCTAC-AAAAG
* *
247027 CAAATCC-TATCTTCCTGAAGTTGCA
1 CAAATCCTTATATCCCTGAAGTTGCA
247052 ATGAAGCAGA
Statistics
Matches: 171, Mismatches: 44, Indels: 19
0.73 0.19 0.08
Matches are distributed among these distances:
47 3 0.02
48 20 0.12
49 24 0.14
50 78 0.46
51 40 0.23
52 6 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (50 bp):
CAAATCCTTATATCCCTGAAGTTGCAGTGATCGGATTAAAGCTACAAAAG
Found at i:246883 original size:51 final size:51
Alignment explanation
Indices: 246813--246984 Score: 149
Period size: 51 Copynumber: 3.4 Consensus size: 51
246803 GTGATCGAAT
* * *
246813 TAAAACTACAAAAGCAAATCCTTATCTCTCTGAAGTTGCAGTAGAGCAGGA
1 TAAAGCTACAAAACCAAATCCTTATCTCTCTGAAGTTGTAGTAGAGCAGGA
* * *
246864 TAAAGTTACAAAACCAAATCATTTATC-C-CTGAAGTTGTAG--GATC-GGA
1 TAAAGCTACAAAACCAAATC-CTTATCTCTCTGAAGTTGTAGTAGAGCAGGA
* ** * *
246911 TTAAAGCTATAGTAGCAAATCTTTATCTCTCTGAAGTTGTAGTAGAGTCA-GA
1 -TAAAGCTACAAAACCAAATCCTTATCTCTCTGAAGTTGTAGTAGAG-CAGGA
* * *
246963 TGAAGCTACCACACCAAATCCT
1 TAAAGCTACAAAACCAAATCCT
246985 ATACCCCTGA
Statistics
Matches: 94, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
47 9 0.10
48 19 0.20
49 12 0.13
50 11 0.12
51 35 0.37
52 8 0.09
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (51 bp):
TAAAGCTACAAAACCAAATCCTTATCTCTCTGAAGTTGTAGTAGAGCAGGA
Found at i:246955 original size:99 final size:99
Alignment explanation
Indices: 246778--247051 Score: 261
Period size: 99 Copynumber: 2.7 Consensus size: 99
246768 CAACAATCAT
*
246778 CAAATCTTATATCCCTGAAGTTACAGTGATCGAATTAAAACTACAAAAGCAAATCCTTATCTCTC
1 CAAATCTT-TATCCCTGAAGTTGCAGTGATCGAATTAAAACTACAAAAGCAAATCCTTATCTCTC
*
246843 TGAAGTTGCAGTAGAG-CAGGATAAAGTTACAAAAC
65 TGAAGTTGCAGTAGAGTCA-GATAAAGCTACAAAAC
* * * * ** *
246878 CAAATCATTTATCCCTGAAGTTGTAG-GATCGGATTAAAGCTATAGTAGCAAATCTTTATCTCTC
1 CAAATC-TTTATCCCTGAAGTTGCAGTGATCGAATTAAAACTACAAAAGCAAATCCTTATCTCTC
* * * *
246942 TGAAGTTGTAGTAGAGTCAGATGAAGCTACCACAC
65 TGAAGTTGCAGTAGAGTCAGATAAAGCTACAAAAC
* * * * * * **
246977 CAAATCCTATACCCCTGAAGTTGAAGTGGGTCGGATTGAATTTACGAAAA-CAAATCC-TATCT-
1 CAAAT-CTTTATCCCTGAAGTTGCAGT-GATCGAATTAAAACTAC-AAAAGCAAATCCTTATCTC
247039 TCCTGAAGTTGCA
63 T-CTGAAGTTGCA
247052 ATGAAGCAGA
Statistics
Matches: 142, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
99 81 0.57
100 39 0.27
101 20 0.14
102 2 0.01
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (99 bp):
CAAATCTTTATCCCTGAAGTTGCAGTGATCGAATTAAAACTACAAAAGCAAATCCTTATCTCTCT
GAAGTTGCAGTAGAGTCAGATAAAGCTACAAAAC
Found at i:248871 original size:15 final size:15
Alignment explanation
Indices: 248820--248885 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
248810 TTAGACCCTT
248820 TTTA-TTATTTG-TA
1 TTTATTTATTTGTTA
* *
248833 TTTATTCATTTATT-
1 TTTATTTATTTGTTA
248847 TTAGTATTTAATTT-TTA
1 TT--TATTT-ATTTGTTA
248864 TTTATTTATTTGTTA
1 TTTATTTATTTGTTA
248879 TTTATTT
1 TTTATTT
248886 TTATGTCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
13 4 0.09
14 11 0.26
15 16 0.37
16 6 0.14
17 6 0.14
ACGTcount: A:0.23, C:0.02, G:0.05, T:0.71
Consensus pattern (15 bp):
TTTATTTATTTGTTA
Found at i:248896 original size:26 final size:24
Alignment explanation
Indices: 248824--248896 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 24
248814 ACCCTTTTTA
* *
248824 TTATTTGTATTTATTCATTTATTT
1 TTATTTATTTTTATTCATTTATTT
*
248848 TAGTATTTAATTTTTATTTATTTATTT
1 T--TATTT-ATTTTTATTCATTTATTT
248875 GTTATTTATTTTTATGTCATTT
1 -TTATTTATTTTTAT-TCATTT
248897 TATATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
24 1 0.03
25 8 0.20
26 15 0.38
27 15 0.38
28 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (24 bp):
TTATTTATTTTTATTCATTTATTT
Found at i:249051 original size:23 final size:22
Alignment explanation
Indices: 249025--249075 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
249015 TATATTGTCA
249025 TTATTACTAATTATATTGTTATT
1 TTATTACT-ATTATATTGTTATT
* *
249048 TTATTTACTATTATTTTTTTATT
1 TTA-TTACTATTATATTGTTATT
249071 TTATT
1 TTATT
249076 GTGTTATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 2 0.08
23 18 0.72
24 5 0.20
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (22 bp):
TTATTACTATTATATTGTTATT
Found at i:252342 original size:33 final size:33
Alignment explanation
Indices: 252278--252343 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
252268 TCTTTATAAA
* *
252278 TTAAATTGAAAATGATTTTTATATAGTGGGAGC
1 TTAAATTCAAAATGATTTTTATATAGGGGGAGC
252311 TTAAATTCAAAATG-TCTTTTAT-TAAGGGGGAGC
1 TTAAATTCAAAATGAT-TTTTATAT-AGGGGGAGC
252344 AATCTATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.07
33 27 0.93
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (33 bp):
TTAAATTCAAAATGATTTTTATATAGGGGGAGC
Found at i:255423 original size:12 final size:11
Alignment explanation
Indices: 255408--255450 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
255398 CTTCTTTTTT
255408 TTCTTCCTTCTC
1 TTCTT-CTTCTC
255420 TTCTT-TTCT-
1 TTCTTCTTCTC
255429 TTCTTCTTCTC
1 TTCTTCTTCTC
255440 TTGCTTCTTCT
1 TT-CTTCTTCT
255451 TCTACTGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 5 0.18
10 8 0.29
11 2 0.07
12 13 0.46
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (11 bp):
TTCTTCTTCTC
Found at i:255423 original size:21 final size:20
Alignment explanation
Indices: 255397--255451 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
255387 CGAGGCAATA
*
255397 TCTTCTTTTTTTTCTTCCTTC
1 TCTTCTTTTCTTTCTT-CTTC
255418 TCTTCTTTTCTTTCTTCTTC
1 TCTTCTTTTCTTTCTTCTTC
255438 TCTTGCTTCTTCTT
1 TCTT-CTT-TTCTT
255452 CTACTGCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 8 0.26
21 18 0.58
22 5 0.16
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (20 bp):
TCTTCTTTTCTTTCTTCTTC
Found at i:264608 original size:21 final size:21
Alignment explanation
Indices: 264584--264625 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
264574 CATACAATGA
264584 CAAAAAGTACCGATACCTTTT
1 CAAAAAGTACCGATACCTTTT
* *
264605 CAAAAAGTATCGATAGCTTTT
1 CAAAAAGTACCGATACCTTTT
264626 ATCAAGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (21 bp):
CAAAAAGTACCGATACCTTTT
Found at i:273088 original size:57 final size:57
Alignment explanation
Indices: 272995--273117 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 57
272985 AAGTCTTTTT
*
272995 CATTTTCATTTTAATTTTGGAGAAAAGAACATTCATTTCCAAAT-TATTCAATTTCTC
1 CATTTTCATTTTAATTTTGGAGAAAAGAACAATCATTTCCAAATATATTC-ATTTCTC
* * ** * * *
273052 CATTTTTATTTTCATTTTGGAGAAAATCATAATCATTTTCAAATACTTTTCATTTCTC
1 CATTTTCATTTTAATTTTGGAGAAAAGAACAATCATTTCCAAATA-TATTCATTTCTC
273110 CATTTTCA
1 CATTTTCA
273118 CCATTTTTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
57 37 0.67
58 14 0.25
59 4 0.07
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (57 bp):
CATTTTCATTTTAATTTTGGAGAAAAGAACAATCATTTCCAAATATATTCATTTCTC
Done.