Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014632.1 Kokia drynarioides strain JFW-HI SEQ_129671, 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: 298865
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 573 characters in sequence are not A, C, G, or T
Found at i:1661 original size:22 final size:22
Alignment explanation
Indices: 1636--1678 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1626 ATGTTAATTA
1636 GTGTG-TTAATGATGTCCTAAGG
1 GTGTGTTTAATG-TGTCCTAAGG
*
1658 GTGTGTTTAATGTGTCTTAAG
1 GTGTGTTTAATGTGTCCTAAG
1679 AAATCTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.21, C:0.07, G:0.30, T:0.42
Consensus pattern (22 bp):
GTGTGTTTAATGTGTCCTAAGG
Found at i:3567 original size:36 final size:36
Alignment explanation
Indices: 3472--3620 Score: 192
Period size: 36 Copynumber: 4.2 Consensus size: 36
3462 GTGAAAGTGG
* * * *
3472 ATATATGAGTACGTTAATCATGCCATGTGACAGTAA
1 ATATATGGGTATGTTATTCATGCCATGAGACAGTAA
* *
3508 ATATGTGGGTAT-TTATTCATGCCATGAGACAATAA
1 ATATATGGGTATGTTATTCATGCCATGAGACAGTAA
*
3543 ATATATGCGTATGTTATTCATGCCATGAGACAGTAA
1 ATATATGGGTATGTTATTCATGCCATGAGACAGTAA
* * * *
3579 ATATGTGGGTATGTTATTCATGTCATGTGACAGTGA
1 ATATATGGGTATGTTATTCATGCCATGAGACAGTAA
3615 ATATAT
1 ATATAT
3621 TGTGCTAATG
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
35 30 0.31
36 67 0.69
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (36 bp):
ATATATGGGTATGTTATTCATGCCATGAGACAGTAA
Found at i:3588 original size:71 final size:72
Alignment explanation
Indices: 3472--3620 Score: 219
Period size: 71 Copynumber: 2.1 Consensus size: 72
3462 GTGAAAGTGG
*
3472 ATATATGAGTACGTTAATCATGCCATGTGACAGTAAATATGTGGGTAT-TTATTCATGCCATGAG
1 ATATATGAGTACGTTAATCATGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGCCATGAG
3536 ACAATAA
66 ACAATAA
* * * * *
3543 ATATATGCGTATGTTATTCATGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGTCATGTG
1 ATATATGAGTACGTTAATCATGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGCCATGAG
* *
3608 ACAGTGA
66 ACAATAA
3615 ATATAT
1 ATATAT
3621 TGTGCTAATG
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
71 44 0.64
72 25 0.36
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (72 bp):
ATATATGAGTACGTTAATCATGCCATGAGACAGTAAATATGTGGGTATGTTATTCATGCCATGAG
ACAATAA
Found at i:4038 original size:23 final size:23
Alignment explanation
Indices: 4014--4244 Score: 356
Period size: 23 Copynumber: 10.1 Consensus size: 23
4004 AGTAATGCAT
4014 TTTATG-TTAAAAGTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
*
4036 TTTATACTTAAAAGTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
*
4059 TTTATGCTTAAATGTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
4082 TTTATGCTTAAAAGTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
*
4105 TTTATGCTTAAAAGATAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
* *
4128 TTTATGCTTGAAATTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
*
4151 TTTACGCTTAAAAGTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
*
4174 TTTACGCTTAAAAGTTAATGTGA
1 TTTATGCTTAAAAGTTAATGTGA
*
4197 TTTATGCTTAAAAGTTAATATGA
1 TTTATGCTTAAAAGTTAATGTGA
** *
4220 TTTATGCTTAGTAGTTAATATGA
1 TTTATGCTTAAAAGTTAATGTGA
4243 TT
1 TT
4245 AATTTGTAAA
Statistics
Matches: 193, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
22 5 0.03
23 188 0.97
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (23 bp):
TTTATGCTTAAAAGTTAATGTGA
Found at i:6472 original size:21 final size:21
Alignment explanation
Indices: 6448--6502 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
6438 AGGTGAAACC
* *
6448 TGTATCGGTAGAAGAATCTCT
1 TGTATCGGTAGAACAATCACT
* *
6469 TGTATCAGTAGAACTATCACT
1 TGTATCGGTAGAACAATCACT
*
6490 TGTATCGATAGAA
1 TGTATCGGTAGAA
6503 ATCTATACTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (21 bp):
TGTATCGGTAGAACAATCACT
Found at i:12746 original size:52 final size:52
Alignment explanation
Indices: 12670--13103 Score: 597
Period size: 52 Copynumber: 8.4 Consensus size: 52
12660 GTTCGATAAT
* * ** * *
12670 TATGTGTCATCATGAGTATATGAATCCTCTATAGATTATGAGGTCCAATGAT
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
*
12722 TATGTGTCATCATGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* *
12774 TATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTTCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
*
12826 TATGTGTCATCGTGAGTATATAAATCCTTTACGGATTATGAGGTCTC-ATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTC-CGATGAC
**
12878 TATGTGTCATCGTGAGTATAT-AAGTCCTTTACGGATTATGAGGTTTGATGAC
1 TATGTGTCATCGTGAGTATATGAA-TCCTTTACGGATTATGAGGTCCGATGAC
* * * *
12930 TATGTGTCATCGTGAGTGTATAAATCCTTTACGAATTATGAGGTCCAATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
12982 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
1 TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
* * *** * *
13034 TATGTGTCATAGTGAGTATATGATTTCCAACATGGATTA-G-GGTTCGATGAC
1 TATGTGTCATCGTGAGTATATGA-ATCCTTTACGGATTATGAGGTCCGATGAC
*
13085 TCTGTGTCATCGTGAGTAT
1 TATGTGTCATCGTGAGTAT
13104 CAAAAGTGCA
Statistics
Matches: 348, Mismatches: 29, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
51 29 0.08
52 306 0.88
53 13 0.04
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (52 bp):
TATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGGTCCGATGAC
Found at i:15046 original size:12 final size:12
Alignment explanation
Indices: 15029--15068 Score: 71
Period size: 12 Copynumber: 3.3 Consensus size: 12
15019 ATTCTATCTA
15029 TTTTTTCTTCAT
1 TTTTTTCTTCAT
*
15041 TTTTTTCTCCAT
1 TTTTTTCTTCAT
15053 TTTTTTCTTCAT
1 TTTTTTCTTCAT
15065 TTTT
1 TTTT
15069 CATTCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTTCTTCAT
Found at i:16435 original size:22 final size:20
Alignment explanation
Indices: 16400--16441 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
16390 CCATTGTTGA
*
16400 GAAATTGAAGAATTAGGCTT
1 GAAATTGAAGAATTAAGCTT
16420 GAAATTGATAGAAATTAAGCTT
1 GAAATTGA-AG-AATTAAGCTT
16442 AGATTATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (20 bp):
GAAATTGAAGAATTAAGCTT
Found at i:17351 original size:48 final size:49
Alignment explanation
Indices: 17221--17383 Score: 122
Period size: 48 Copynumber: 3.3 Consensus size: 49
17211 TAATGAATTT
* * * *
17221 CATCATTGTCGGGCTATTCGAGATAGTAGAATA-AGTAAATTGTGAGAAC
1 CATCATTGTCGAGCCATTCGGGATAGTAGAATATAG-AAATAGTGAGAAC
* *
17270 CATCTTTGTCGAGCCA--CGTGAGATAGTAAAATATA-AAATAGTGA-AATC
1 CATCATTGTCGAGCCATTCG-G-GATAGTAGAATATAGAAATAGTGAGAA-C
* * * *
17318 CATCGTTGTCGAGCCATTCGGGATGGTAGAATATTGAAATTGTGCAG-AC
1 CATCATTGTCGAGCCATTCGGGATAGTAGAATATAGAAATAGTG-AGAAC
**
17367 CAGTCATTACCGAGCCA
1 CA-TCATTGTCGAGCCA
17384 CCTAGAATGG
Statistics
Matches: 90, Mismatches: 14, Indels: 19
0.73 0.11 0.15
Matches are distributed among these distances:
47 4 0.04
48 35 0.39
49 35 0.39
50 16 0.18
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (49 bp):
CATCATTGTCGAGCCATTCGGGATAGTAGAATATAGAAATAGTGAGAAC
Found at i:18582 original size:36 final size:36
Alignment explanation
Indices: 18524--18611 Score: 126
Period size: 36 Copynumber: 2.5 Consensus size: 36
18514 ACTTCGTAAT
*
18524 TTAA-TTCTTTTACTTTTTAAAGATAGCAAAGATAC
1 TTAACTTCTTTTACTTTTAAAAGATAGCAAAGATAC
18559 TTAACTTCTTTTA-TATTTAAAAGATAGCAAAGATAC
1 TTAACTTCTTTTACT-TTTAAAAGATAGCAAAGATAC
* *
18595 TCAACTTCCTTTACTTT
1 TTAACTTCTTTTACTTT
18612 CCCTAACCTA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
35 5 0.11
36 41 0.87
37 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (36 bp):
TTAACTTCTTTTACTTTTAAAAGATAGCAAAGATAC
Found at i:24020 original size:24 final size:23
Alignment explanation
Indices: 23985--24029 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
23975 AAGGTGAGTG
*
23985 TTCGATTGAA-TTAAATAAAATTA
1 TTCGATTAAATTTAAA-AAAATTA
24008 TTCGAGTTAAATTTAAAAAAAT
1 TTCGA-TTAAATTTAAAAAAAT
24030 AATAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 9 0.47
25 5 0.26
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (23 bp):
TTCGATTAAATTTAAAAAAATTA
Found at i:29932 original size:15 final size:15
Alignment explanation
Indices: 29903--29931 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29893 TTTTTATATT
29903 TTTAGATTTTAAAAA
1 TTTAGATTTTAAAAA
29918 TTTA-ATTTTAAAAA
1 TTTAGATTTTAAAAA
29932 AAAATACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTTAGATTTTAAAAA
Found at i:29998 original size:20 final size:20
Alignment explanation
Indices: 29951--30004 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
29941 ATTTTAGAAT
* *
29951 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTCAA
29970 -TTTTAAAAATTATTTTCAA
1 TTTTTAAAAATTATTTTCAA
*
29989 TTTTTGAAAATTATTT
1 TTTTTAAAAATTATTT
30005 GATTTTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 8 0.27
20 14 0.47
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTCAA
Found at i:30557 original size:30 final size:32
Alignment explanation
Indices: 30517--30581 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
30507 CCACTTTGTG
* *
30517 ATTTAGAAT-AATTTTTTTTAAT-AGTTTAATA
1 ATTTAGAATAAATTTGTTTT-ATCAATTTAATA
30548 ATTTA-AATAAATTTGTTTTATCAATTTAATA
1 ATTTAGAATAAATTTGTTTTATCAATTTAATA
30579 ATT
1 ATT
30582 ATTTTACCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (32 bp):
ATTTAGAATAAATTTGTTTTATCAATTTAATA
Found at i:32100 original size:18 final size:18
Alignment explanation
Indices: 32077--32121 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
32067 AAAAACCTGG
*
32077 TTCTTTCTTTTCTTCTTC
1 TTCTTTCTTTTCATCTTC
32095 TTCTTTCTTTTCATCTTC
1 TTCTTTCTTTTCATCTTC
32113 TTC-TTCTTT
1 TTCTTTCTTT
32122 CTATCTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCTTTCTTTTCATCTTC
Found at i:33759 original size:23 final size:24
Alignment explanation
Indices: 33715--33759 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
33705 TTGTTTATTA
* * *
33715 TTCATTAACATTGTTGGTTTAATG
1 TTCATAAACATTGTTAGATTAATG
33739 TTCATAAACA-TGTTAGATTAA
1 TTCATAAACATTGTTAGATTAA
33760 GTTAAATGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (24 bp):
TTCATAAACATTGTTAGATTAATG
Found at i:34909 original size:35 final size:35
Alignment explanation
Indices: 34858--34928 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
34848 ACAATGATAT
*
34858 TTACTTTCGCCTCTAAATTTGTTTTAACATTGAGA
1 TTACTTTCGCCCCTAAATTTGTTTTAACATTGAGA
* *
34893 TTACTTTTGCCCCTAAATTTGTTTTAACTTTGAGA
1 TTACTTTCGCCCCTAAATTTGTTTTAACATTGAGA
34928 T
1 T
34929 GACACATAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (35 bp):
TTACTTTCGCCCCTAAATTTGTTTTAACATTGAGA
Found at i:36358 original size:2 final size:2
Alignment explanation
Indices: 36353--36382 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36343 ACTCTCTACT
36353 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36383 ATTTAAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36461 original size:18 final size:17
Alignment explanation
Indices: 36434--36467 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
36424 TTATATATAA
36434 TATCTATTATAAAATAT
1 TATCTATTATAAAATAT
36451 TATCTTATTATAAAATA
1 TATC-TATTATAAAATA
36468 AATTTTGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TATCTATTATAAAATAT
Found at i:36571 original size:15 final size:15
Alignment explanation
Indices: 36534--36575 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
36524 GTTGTATTTG
* *
36534 TTTCATTAAAAACAA
1 TTTCATAAAAAATAA
*
36549 TTT-TTAAAAAATAA
1 TTTCATAAAAAATAA
36563 TTTCATAAAAAAT
1 TTTCATAAAAAAT
36576 TGCAAACAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTCATAAAAAATAA
Found at i:36723 original size:18 final size:18
Alignment explanation
Indices: 36702--36736 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
36692 TAAATAGAAT
36702 AATAAAATATTA-AAAATA
1 AATAAAAT-TTATAAAATA
36720 AATAAAATTTATAAAAT
1 AATAAAATTTATAAAAT
36737 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATAAAATTTATAAAATA
Found at i:36733 original size:27 final size:28
Alignment explanation
Indices: 36679--36745 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 28
36669 AACGGAACTT
*
36679 AAATT-TAAAAAATTAAATAGAATAATA
1 AAATTATAAAAAATTAAATAAAATAATA
* *
36706 AAA-TATTAAAAA-TAAATAAAATTTATA
1 AAATTATAAAAAATTAAATAAAA-TAATA
36733 AAATTATAAAAAA
1 AAATTATAAAAAA
36746 AAAAATCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
26 9 0.27
27 16 0.48
28 8 0.24
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (28 bp):
AAATTATAAAAAATTAAATAAAATAATA
Found at i:44648 original size:23 final size:21
Alignment explanation
Indices: 44601--44649 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
44591 GTGTTCGTAG
44601 GAGAGATACTTACATTCTCTT
1 GAGAGATACTTACATTCTCTT
44622 GAGAGATACTTACATTCTCTT
1 GAGAGATACTTACATTCTCTT
*
44643 GCGAGAT
1 GAGAGAT
44650 CACATGTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (21 bp):
GAGAGATACTTACATTCTCTT
Found at i:49798 original size:45 final size:45
Alignment explanation
Indices: 49729--49820 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
49719 CAGTAAACCT
* *
49729 GACTGACCATGCATCCCTCGTAACAAATAGGCACCAAGAAAACTC
1 GACTGACCATGCATCCCTCATAACAAATACGCACCAAGAAAACTC
49774 GACTGACCATGCATCCCTCATAACAAATACGCACCAAGAAAACTC
1 GACTGACCATGCATCCCTCATAACAAATACGCACCAAGAAAACTC
49819 GA
1 GA
49821 GGAAGCAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.39, C:0.32, G:0.14, T:0.15
Consensus pattern (45 bp):
GACTGACCATGCATCCCTCATAACAAATACGCACCAAGAAAACTC
Found at i:58803 original size:18 final size:18
Alignment explanation
Indices: 58780--58830 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
58770 CACATCACGA
58780 TCAGATGCAGTCACATAC
1 TCAGATGCAGTCACATAC
*
58798 TCAGATGCAGTCACATGC
1 TCAGATGCAGTCACATAC
* *
58816 TCATATGCAGCCACA
1 TCAGATGCAGTCACA
58831 GCAGACTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (18 bp):
TCAGATGCAGTCACATAC
Found at i:64104 original size:12 final size:12
Alignment explanation
Indices: 64083--64122 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
64073 GGAGGAGAAC
64083 GAAGAAGAAAAA
1 GAAGAAGAAAAA
* *
64095 GAAGACGAAAGA
1 GAAGAAGAAAAA
64107 GAAGAAGAAAAA
1 GAAGAAGAAAAA
64119 GAAG
1 GAAG
64123 TTCCTATCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.68, C:0.03, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:74044 original size:2 final size:2
Alignment explanation
Indices: 74037--74066 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
74027 CATTTATTGA
74037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74067 TATTTCTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84138 original size:25 final size:25
Alignment explanation
Indices: 84110--84159 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
84100 AAGAGATAAA
84110 ATGAAAGAAATTAAGATCAAAACAT
1 ATGAAAGAAATTAAGATCAAAACAT
84135 ATGAAAGAAATTAAGATCAAAACAT
1 ATGAAAGAAATTAAGATCAAAACAT
84160 CATTGAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (25 bp):
ATGAAAGAAATTAAGATCAAAACAT
Found at i:85321 original size:24 final size:24
Alignment explanation
Indices: 85290--85336 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
85280 AACACCAAAA
85290 CCCATGCATATATA-TATAATAAAG
1 CCCATGCATATATATTAT-ATAAAG
85314 CCCATGCATATATATTATATAAA
1 CCCATGCATATATATTATATAAA
85337 ATAAAGCGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (24 bp):
CCCATGCATATATATTATATAAAG
Found at i:85371 original size:31 final size:29
Alignment explanation
Indices: 85300--85373 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
85290 CCCATGCATA
**
85300 TATATATAATAAAGCCCATGCATATATAT
1 TATATATAATAAAGCCCACACATATATAT
* *
85329 TATATAAAATAAAGCGCACACATATATAT
1 TATATATAATAAAGCCCACACATATATAT
85358 TATCTATATAATAAAG
1 TA--TATATAATAAAG
85374 TTACGTCTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
29 27 0.71
31 11 0.29
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (29 bp):
TATATATAATAAAGCCCACACATATATAT
Found at i:91701 original size:17 final size:17
Alignment explanation
Indices: 91679--91718 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
91669 CTGTAGTATA
* *
91679 ATTGTCCCTGCATTTTT
1 ATTGTCACTACATTTTT
91696 ATTGTCACTACATTTTT
1 ATTGTCACTACATTTTT
91713 ATTGTC
1 ATTGTC
91719 GGTGCATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.17, C:0.20, G:0.10, T:0.53
Consensus pattern (17 bp):
ATTGTCACTACATTTTT
Found at i:96386 original size:25 final size:25
Alignment explanation
Indices: 96349--96414 Score: 87
Period size: 25 Copynumber: 2.6 Consensus size: 25
96339 ATTTATTGAG
* *
96349 GACTAGCTCGTAAGAGCGATATTCT
1 GACTGGCTCGTAAGAGCAATATTCT
* * *
96374 GTCTGGCTTGTAAGAGCAATGTTCT
1 GACTGGCTCGTAAGAGCAATATTCT
96399 GACTGGCTCGTAAGAG
1 GACTGGCTCGTAAGAG
96415 TGTTATTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (25 bp):
GACTGGCTCGTAAGAGCAATATTCT
Found at i:96719 original size:28 final size:28
Alignment explanation
Indices: 96655--96727 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
96645 TCTTGAGGAG
96655 TAATCTGTTT-TTGGCTCGGGTAGAACAA
1 TAATCTGTTTCTT-GCTCGGGTAGAACAA
* * * *
96683 TATTATGTTTCTTGCTCGGGTAGAGCAT
1 TAATCTGTTTCTTGCTCGGGTAGAACAA
*
96711 TAATCTGTTTCTAGCTC
1 TAATCTGTTTCTTGCTC
96728 ATAAAGGAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
28 35 0.95
29 2 0.05
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (28 bp):
TAATCTGTTTCTTGCTCGGGTAGAACAA
Found at i:100565 original size:127 final size:127
Alignment explanation
Indices: 100339--100594 Score: 512
Period size: 127 Copynumber: 2.0 Consensus size: 127
100329 AGTTATTTCA
100339 AGGCTTTTTAAATGTTTATTTTGTCCAACACTTTGAAAATAATTTTTAGGACTTATAAACAATAT
1 AGGCTTTTTAAATGTTTATTTTGTCCAACACTTTGAAAATAATTTTTAGGACTTATAAACAATAT
100404 TTGCAAATTTAAGTAAGGGATTTTTAATATACTTTTTGTTATATCAAAATACTTGAAAAACT
66 TTGCAAATTTAAGTAAGGGATTTTTAATATACTTTTTGTTATATCAAAATACTTGAAAAACT
100466 AGGCTTTTTAAATGTTTATTTTGTCCAACACTTTGAAAATAATTTTTAGGACTTATAAACAATAT
1 AGGCTTTTTAAATGTTTATTTTGTCCAACACTTTGAAAATAATTTTTAGGACTTATAAACAATAT
100531 TTGCAAATTTAAGTAAGGGATTTTTAATATACTTTTTGTTATATCAAAATACTTGAAAAACT
66 TTGCAAATTTAAGTAAGGGATTTTTAATATACTTTTTGTTATATCAAAATACTTGAAAAACT
100593 AG
1 AG
100595 AGCTAATAAG
Statistics
Matches: 129, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
127 129 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.42
Consensus pattern (127 bp):
AGGCTTTTTAAATGTTTATTTTGTCCAACACTTTGAAAATAATTTTTAGGACTTATAAACAATAT
TTGCAAATTTAAGTAAGGGATTTTTAATATACTTTTTGTTATATCAAAATACTTGAAAAACT
Found at i:109974 original size:18 final size:17
Alignment explanation
Indices: 109930--109980 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
109920 TGATATATTC
*
109930 ATTAATAATAGTATTAT
1 ATTAATAATAATATTAT
* *
109947 AATAAATAATAATATTTT
1 -ATTAATAATAATATTAT
109965 ATTAAT--TAATATTAT
1 ATTAATAATAATATTAT
109980 A
1 A
109981 AAATATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 9 0.32
17 5 0.18
18 14 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTAATAATAATATTAT
Found at i:124534 original size:18 final size:17
Alignment explanation
Indices: 124490--124540 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
124480 TGATATATTC
*
124490 ATTAATAATAGTATTAT
1 ATTAATAATAATATTAT
* *
124507 AGTAAATAATAATATTTT
1 A-TTAATAATAATATTAT
124525 ATTAAT--TAATATTAT
1 ATTAATAATAATATTAT
124540 A
1 A
124541 AAATATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 9 0.32
17 5 0.18
18 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (17 bp):
ATTAATAATAATATTAT
Found at i:128168 original size:3 final size:3
Alignment explanation
Indices: 128160--128207 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
128150 TTCCATCTCC
128160 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
128208 TTCTCTCTTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:128867 original size:14 final size:14
Alignment explanation
Indices: 128850--128892 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
128840 CCGTTGATTG
*
128850 TTGACAATTGACTT
1 TTGACCATTGACTT
*
128864 TTGACCGTTGAC-T
1 TTGACCATTGACTT
*
128877 TTGACCATTAACTT
1 TTGACCATTGACTT
128891 TT
1 TT
128893 TTCGAAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.44
Consensus pattern (14 bp):
TTGACCATTGACTT
Found at i:128893 original size:28 final size:28
Alignment explanation
Indices: 128839--128892 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
128829 CTGTTGACCA
* *
128839 ACCGTTGATTGTTGACAATTGACTTTTG
1 ACCGTTGACTGTTGACAATTAACTTTTG
*
128867 ACCGTTGACT-TTGACCATTAACTTTT
1 ACCGTTGACTGTTGACAATTAACTTTT
128893 TTCGAAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (28 bp):
ACCGTTGACTGTTGACAATTAACTTTTG
Found at i:129787 original size:2 final size:2
Alignment explanation
Indices: 129780--129809 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
129770 ACTTTTGAGT
129780 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
129810 ATTGCTGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:135427 original size:3 final size:3
Alignment explanation
Indices: 135419--135451 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
135409 TTCCATCTCC
135419 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
135452 TTCTCTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:135769 original size:7 final size:7
Alignment explanation
Indices: 135753--135798 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
135743 AACTGTTGAC
*
135753 TGACCTT
1 TGACCGT
135760 TGACCGT
1 TGACCGT
*
135767 TGATCGT
1 TGACCGT
135774 TGACCGT
1 TGACCGT
*
135781 TGACTGT
1 TGACCGT
*
135788 TGACTGT
1 TGACCGT
135795 TGAC
1 TGAC
135799 TTTGATCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (7 bp):
TGACCGT
Found at i:135778 original size:14 final size:13
Alignment explanation
Indices: 135759--135818 Score: 57
Period size: 14 Copynumber: 4.4 Consensus size: 13
135749 TGACTGACCT
135759 TTGACCGTTGATCG
1 TTGACCGTTGA-CG
135773 TTGACCGTTGACTG
1 TTGACCGTTGAC-G
* *
135787 TTGACTGTTGACT
1 TTGACCGTTGACG
* *
135800 TTGATCTTTGATCG
1 TTGACCGTTGA-CG
135814 TTGAC
1 TTGAC
135819 TCTGACCATT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
13 9 0.24
14 28 0.76
ACGTcount: A:0.15, C:0.18, G:0.25, T:0.42
Consensus pattern (13 bp):
TTGACCGTTGACG
Found at i:135783 original size:21 final size:21
Alignment explanation
Indices: 135753--135818 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
135743 AACTGTTGAC
135753 TGACCTTTGACCGTTGATCGT
1 TGACCTTTGACCGTTGATCGT
* *
135774 TGACCGTTGACTGTTGA-CTGT
1 TGACCTTTGACCGTTGATC-GT
* *
135795 TGA-CTTTGATCTTTGATCGT
1 TGACCTTTGACCGTTGATCGT
135815 TGAC
1 TGAC
135819 TCTGACCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
20 15 0.42
21 21 0.58
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (21 bp):
TGACCTTTGACCGTTGATCGT
Found at i:137201 original size:36 final size:36
Alignment explanation
Indices: 137151--137306 Score: 193
Period size: 36 Copynumber: 4.6 Consensus size: 36
137141 GGGGGTTACA
*
137151 CTGTTGACCTAAAGGTCATGATGCTCATTTTACTCC
1 CTGTTGACCCAAAGGTCATGATGCTCATTTTACTCC
137187 CTGTTGACCCAAAGGTC---ATG--C---TTACTCC
1 CTGTTGACCCAAAGGTCATGATGCTCATTTTACTCC
* * * *
137215 CTGTTGACCCAAAAGTCATGATGTTTATTTTACTCT
1 CTGTTGACCCAAAGGTCATGATGCTCATTTTACTCC
*
137251 CTGTTGACCCAAAGGTCATGATGCTCATTTTATTCC
1 CTGTTGACCCAAAGGTCATGATGCTCATTTTACTCC
*
137287 CTGTTGACCCAAAGATCATG
1 CTGTTGACCCAAAGGTCATG
137307 CCTATTACCA
Statistics
Matches: 102, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
28 23 0.23
31 4 0.04
33 3 0.03
36 72 0.71
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.35
Consensus pattern (36 bp):
CTGTTGACCCAAAGGTCATGATGCTCATTTTACTCC
Found at i:137214 original size:28 final size:28
Alignment explanation
Indices: 137180--137234 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
137170 GATGCTCATT
*
137180 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTGACCCAAAAGTCATGC
137208 TTACTCCCTGTTGACCCAAAAGTCATG
1 TTACTCCCTGTTGACCCAAAAGTCATG
137235 ATGTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (28 bp):
TTACTCCCTGTTGACCCAAAAGTCATGC
Found at i:137235 original size:64 final size:64
Alignment explanation
Indices: 137151--137270 Score: 195
Period size: 64 Copynumber: 1.9 Consensus size: 64
137141 GGGGGTTACA
* *
137151 CTGTTGACCTAAAGGTCATGATGCTCATTTTACTCCCTGTTGACCCAAAGGTCATGCTTACTCC
1 CTGTTGACCCAAAAGTCATGATGCTCATTTTACTCCCTGTTGACCCAAAGGTCATGCTTACTCC
* * *
137215 CTGTTGACCCAAAAGTCATGATGTTTATTTTACTCTCTGTTGACCCAAAGGTCATG
1 CTGTTGACCCAAAAGTCATGATGCTCATTTTACTCCCTGTTGACCCAAAGGTCATG
137271 ATGCTCATTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.34
Consensus pattern (64 bp):
CTGTTGACCCAAAAGTCATGATGCTCATTTTACTCCCTGTTGACCCAAAGGTCATGCTTACTCC
Found at i:141946 original size:51 final size:52
Alignment explanation
Indices: 141867--141972 Score: 137
Period size: 51 Copynumber: 2.1 Consensus size: 52
141857 AACTAATGGA
*
141867 TTACTAAATGCATGACTTGATTTAATGATGCAAACTTTAACTAA-CATGGGAG
1 TTACTAAATGCATGACTTGATTTAATGATGCAAAC-TTAACTAATCATGAGAG
* * *
141919 TTACTTAATGCATGTCATT-ATTT-ATGATGCAAACTTAATTAATCATGAGAG
1 TTACTAAATGCATGAC-TTGATTTAATGATGCAAACTTAACTAATCATGAGAG
141970 TTA
1 TTA
141973 ATGGATGTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
50 7 0.15
51 21 0.44
52 18 0.38
53 2 0.04
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (52 bp):
TTACTAAATGCATGACTTGATTTAATGATGCAAACTTAACTAATCATGAGAG
Found at i:142183 original size:11 final size:11
Alignment explanation
Indices: 142169--142198 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
142159 AACACTTATT
142169 AAACTTAAATA
1 AAACTTAAATA
142180 AAACTTAAATA
1 AAACTTAAATA
142191 AAA-TTAAA
1 AAACTTAAA
142199 AAGTCCTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (11 bp):
AAACTTAAATA
Found at i:142771 original size:2 final size:2
Alignment explanation
Indices: 142757--142802 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
142747 TATAAAAAAC
142757 TA TA -A TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
142797 TA TA TA
1 TA TA TA
142803 AACATTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:143032 original size:21 final size:22
Alignment explanation
Indices: 142991--143034 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
142981 TAGTGATATG
* *
142991 ATAGTAAAATAGTGGGAAAACA
1 ATAGCAAAATAGTGAGAAAACA
143013 ATAGCAAAATAGT-AGAAAACA
1 ATAGCAAAATAGTGAGAAAACA
143034 A
1 A
143035 CAACAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.59, C:0.07, G:0.18, T:0.16
Consensus pattern (22 bp):
ATAGCAAAATAGTGAGAAAACA
Found at i:143041 original size:21 final size:22
Alignment explanation
Indices: 142996--143042 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
142986 ATATGATAGT
* * *
142996 AAAATAGTGGGAAAACAATAGC
1 AAAATAGTGAGAAAACAACAAC
143018 AAAATAGT-AGAAAACAACAAC
1 AAAATAGTGAGAAAACAACAAC
143039 AAAA
1 AAAA
143043 CATTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.64, C:0.11, G:0.15, T:0.11
Consensus pattern (22 bp):
AAAATAGTGAGAAAACAACAAC
Found at i:173818 original size:24 final size:24
Alignment explanation
Indices: 173791--173867 Score: 109
Period size: 24 Copynumber: 3.2 Consensus size: 24
173781 TAGCCCATAT
* *
173791 GAGCCTAGAATGATTAGCTTTTAC
1 GAGCCCAGAATGATTAGCTCTTAC
*
173815 GAGCCCAGAATGGTTAGCTCTTAC
1 GAGCCCAGAATGATTAGCTCTTAC
* *
173839 AAGCCCAGAATGATTAGATCTTAC
1 GAGCCCAGAATGATTAGCTCTTAC
173863 GAGCC
1 GAGCC
173868 AAGACATAGT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
GAGCCCAGAATGATTAGCTCTTAC
Found at i:181767 original size:12 final size:12
Alignment explanation
Indices: 181750--181788 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
181740 TAACGTGATT
181750 GTTGCTGTTTCA
1 GTTGCTGTTTCA
181762 GTTGCTGTTTCA
1 GTTGCTGTTTCA
*
181774 GTTACTGTTTCA
1 GTTGCTGTTTCA
181786 GTT
1 GTT
181789 TGAAGTGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.51
Consensus pattern (12 bp):
GTTGCTGTTTCA
Found at i:191758 original size:10 final size:10
Alignment explanation
Indices: 191728--191781 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
191718 TTTTAAAAAA
191728 TTTATTATATT
1 TTTATTA-ATT
191739 ATTT-TTAATT
1 -TTTATTAATT
191749 TTTATTAA-T
1 TTTATTAATT
191758 TTTA-TATATT
1 TTTATTA-ATT
191768 TTTATTTAATT
1 TTTA-TTAATT
191779 TTT
1 TTT
191782 TTATATAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
8 2 0.05
9 9 0.24
10 12 0.32
11 9 0.24
12 5 0.14
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTATTAATT
Found at i:191785 original size:32 final size:32
Alignment explanation
Indices: 191701--191786 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 32
191691 AACCCCGTTA
*
191701 ATATTATTTTTAAATTTTTTTAAAAAATTTATT
1 ATATTATTTTT-AATTTTTTTATAAAATTTATT
* *
191734 ATATTATTTTTAA--TTTTTATTAATTTTA-T
1 ATATTATTTTTAATTTTTTTATAAAATTTATT
*
191763 ATATTTTTATTTAATTTTTTTATA
1 ATATTATT-TTTAATTTTTTTATA
191787 TAGTCATTTT
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
29 8 0.18
30 17 0.38
32 9 0.20
33 11 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (32 bp):
ATATTATTTTTAATTTTTTTATAAAATTTATT
Found at i:192185 original size:183 final size:183
Alignment explanation
Indices: 191875--192241 Score: 538
Period size: 183 Copynumber: 2.0 Consensus size: 183
191865 AGTATTATTA
* * * *
191875 ACTTAAAAACGGGTCAAGTCGGGCCAAGCTCGAGCCTTGAATGTTTAAGCTCGAGTTCGGCCCAT
1 ACTTAAAAACGGGTCAAGTCGGGCCAAGCTCGAGACTTGAATGTTCAAGCTCAAGTTCGACCCAT
** * * *
191940 ATTTTAAACAAGCTTAATTTTTTGCCCAAGCCTATTTTTCGGGATTAATATTTTTTCTCAAACCC
66 ATTTTAAACAAGCCAAAATTTTTGCCCAAGCCCATTTTTCGGGATTAATATTTTTACTCAAACCC
* * * * *
192005 TCCCAAATTTCTGGTGAACTTTCATGCCTGGGCGATTAGCCCGACCCATGAAC
131 TCCCAAATTTCAGGCGAACTTTCAGGCCTGGGCGAGTAGCCCAACCCATGAAC
* * *
192058 ACTTAAAAACGGGTTAGGTTGGGCCAAGCTCGAGACTTGAATGTTCAAGC-CTAAGTTCGACCCA
1 ACTTAAAAACGGGTCAAGTCGGGCCAAGCTCGAGACTTGAATGTTCAAGCTC-AAGTTCGACCCA
*
192122 TATTTTAAACAAGCCAAAATTTTTGCCCAAGCCCATTTTTCGGGGTTAATATTTTTACTCAAACC
65 TATTTTAAACAAGCCAAAATTTTTGCCCAAGCCCATTTTTCGGGATTAATATTTTTACTCAAACC
* *
192187 CTCCTAAATTTCAGGCGAACTTTCAGGCCTGGGCGAGTAGCCCAACTCATGAAC
130 CTCCCAAATTTCAGGCGAACTTTCAGGCCTGGGCGAGTAGCCCAACCCATGAAC
192241 A
1 A
192242 GGTCTAGTCA
Statistics
Matches: 163, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
182 1 0.01
183 162 0.99
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (183 bp):
ACTTAAAAACGGGTCAAGTCGGGCCAAGCTCGAGACTTGAATGTTCAAGCTCAAGTTCGACCCAT
ATTTTAAACAAGCCAAAATTTTTGCCCAAGCCCATTTTTCGGGATTAATATTTTTACTCAAACCC
TCCCAAATTTCAGGCGAACTTTCAGGCCTGGGCGAGTAGCCCAACCCATGAAC
Found at i:193745 original size:24 final size:24
Alignment explanation
Indices: 193690--193736 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
193680 GTCACCGTAG
193690 ATACA-AAACATTCAGTGGGGTTT
1 ATACATAAACATTCAGTGGGGTTT
*
193713 ATACATAAACATTCAGTGGTGTTT
1 ATACATAAACATTCAGTGGGGTTT
193737 CTCCTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (24 bp):
ATACATAAACATTCAGTGGGGTTT
Found at i:197201 original size:30 final size:30
Alignment explanation
Indices: 197158--197439 Score: 304
Period size: 30 Copynumber: 9.4 Consensus size: 30
197148 GAACTCATCC
*
197158 AAAATTATATTTTAACCCCTAAA-TTTCTCT
1 AAAATTACATTTTAACCCCTAAACTTTC-CT
*** *
197188 AAAATTTTGTTTTAACCCCTAAAACTTTTCT
1 AAAATTACATTTTAACCCCT-AAACTTTCCT
* * *
197219 AAAATTATA-TTTAACCCTTAAACTTTTC-
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* *
197247 AAAATTACATTTTAACTCCTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* *
197277 AAAATTACATTTTAACCACTAAACTTTCCC
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* *
197307 AAAATTAAATTTTAACCACTAAACTTTCCT
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* * *
197337 AAAATTAAATTTTAACCCTTAAAC-TTCCC
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* *
197366 AAAATTACATTTTGACCCCTAAACTTTCCA
1 AAAATTACATTTTAACCCCTAAACTTTCCT
**
197396 AAAATTACATTTTAACCCCTTAATTTTTCC-
1 AAAATTACATTTTAACCCC-TAAACTTTCCT
197426 ATAAATTACATTTT
1 A-AAATTACATTTT
197440 GACCGCAAAT
Statistics
Matches: 218, Mismatches: 27, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
28 8 0.04
29 49 0.22
30 126 0.58
31 32 0.15
32 3 0.01
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTCCT
Found at i:197262 original size:89 final size:89
Alignment explanation
Indices: 197157--197460 Score: 307
Period size: 89 Copynumber: 3.4 Consensus size: 89
197147 TGAACTCATC
* * *** * *
197157 CAAAATTATATTTTAACCCCTAAATTTCTCTAAAATTTTGTTTTAACCCCTAAAACTTTTCTAAA
1 CAAAATTACATTTTAACCCCTAAATTTCTCCAAAATTACATTTTAACCCCT-AAACTTTCCAAAA
*
197222 ATTATA-TTTAACCCTTAAACTTTT
65 ATTAAATTTTAACCCTTAAACTTTT
* * * *
197246 CAAAATTACATTTTAACTCCTAAACTTTCT-TAAAATTACATTTTAACCACTAAACTTTCCCAAA
1 CAAAATTACATTTTAACCCCTAAA-TTTCTCCAAAATTACATTTTAACCCCTAAACTTTCCAAAA
*
197310 ATTAAATTTTAACCAC-TAAACTTTC
65 ATTAAATTTTAACC-CTTAAACTTTT
* * * *
197335 CTAAAATTAAATTTTAACCCTTAAACTTC-CCAAAATTACATTTTGACCCCTAAACTTTCCAAAA
1 C-AAAATTACATTTTAACCCCTAAATTTCTCCAAAATTACATTTTAACCCCTAAACTTTCCAAAA
* *
197399 ATTACATTTTAACCCCTT-AATTTTT
65 ATTAAATTTTAA-CCCTTAAACTTTT
* *
197424 CCATAAATTACATTTTGACCGC-AAA-TTCTCCAAAATT
1 -CA-AAATTACATTTTAACCCCTAAATTTCTCCAAAATT
197461 TCTTTTTTCG
Statistics
Matches: 180, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
88 19 0.11
89 117 0.65
90 44 0.24
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.39
Consensus pattern (89 bp):
CAAAATTACATTTTAACCCCTAAATTTCTCCAAAATTACATTTTAACCCCTAAACTTTCCAAAAA
TTAAATTTTAACCCTTAAACTTTT
Found at i:197299 original size:119 final size:118
Alignment explanation
Indices: 197158--197439 Score: 350
Period size: 119 Copynumber: 2.4 Consensus size: 118
197148 GAACTCATCC
* * *** * *
197158 AAAATTATATTTTAACCCCTAAATTTCTCTAAAATTTTGTTTTAACCCCTAAAACTTTTCTAAAA
1 AAAATTACATTTTAACCCCTAAATTTC-CCAAAATTAAATTTTAACCACT-AAACTTTCCTAAAA
* ** * **
197223 TTATA-TTTAACCCTTAAACTTTTCAAAATTACATTTTAACTCCTAAACTTTCTT
64 TTAAATTTTAACCCTTAAACTTCCCAAAATTACATTTTAACCCCTAAACTTTCCA
*
197277 AAAATTACATTTTAACCACTAAACTTTCCCAAAATTAAATTTTAACCACTAAACTTTCCTAAAAT
1 AAAATTACATTTTAACCCCTAAA-TTTCCCAAAATTAAATTTTAACCACTAAACTTTCCTAAAAT
*
197342 TAAATTTTAACCCTTAAACTTCCCAAAATTACATTTTGACCCCTAAACTTTCCA
65 TAAATTTTAACCCTTAAACTTCCCAAAATTACATTTTAACCCCTAAACTTTCCA
* * *
197396 AAAATTACATTTTAACCCCTTAATTTTTCCATAAATTACATTTT
1 AAAATTACATTTTAACCCC-TAAATTTCCCA-AAATTAAATTTT
197440 GACCGCAAAT
Statistics
Matches: 140, Mismatches: 19, Indels: 7
0.84 0.11 0.04
Matches are distributed among these distances:
118 17 0.12
119 105 0.75
120 18 0.13
ACGTcount: A:0.38, C:0.21, G:0.01, T:0.40
Consensus pattern (118 bp):
AAAATTACATTTTAACCCCTAAATTTCCCAAAATTAAATTTTAACCACTAAACTTTCCTAAAATT
AAATTTTAACCCTTAAACTTCCCAAAATTACATTTTAACCCCTAAACTTTCCA
Found at i:197460 original size:59 final size:60
Alignment explanation
Indices: 197158--197443 Score: 262
Period size: 59 Copynumber: 4.8 Consensus size: 60
197148 GAACTCATCC
* * *** * * * *
197158 AAAATTATATTTTAACCCC-TAAATTTCTCTAAAATTTTGTTTTAACCCCTAAAACTTTTCT
1 AAAATTACATTTTAACCCCTTAAATTTC-CCAAAATTACATTTTGACCACT-AAACTTTCCA
* * * **
197219 AAAATTATA-TTTAA-CCCTTAAACTTT-TCAAAATTACATTTTAACTC-CTAAACTTTCTT
1 AAAATTACATTTTAACCCCTTAAA-TTTCCCAAAATTACATTTTGAC-CACTAAACTTTCCA
* * * *
197277 AAAATTACATTTTAACCAC-TAAACTTTCCCAAAATTAAATTTTAACCACTAAACTTTCCT
1 AAAATTACATTTTAACCCCTTAAA-TTTCCCAAAATTACATTTTGACCACTAAACTTTCCA
* * *
197337 AAAATTAAATTTTAA-CCCTTAAACTTCCCAAAATTACATTTTGACCCCTAAACTTTCCA
1 AAAATTACATTTTAACCCCTTAAATTTCCCAAAATTACATTTTGACCACTAAACTTTCCA
* *
197396 AAAATTACATTTTAACCCCTTAATTTTTCCATAAATTACATTTTGACC
1 AAAATTACATTTTAACCCCTTAAATTTCCCA-AAATTACATTTTGACC
197444 GCAAATTCTC
Statistics
Matches: 192, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
58 16 0.08
59 79 0.41
60 69 0.36
61 28 0.15
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.40
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTTAAATTTCCCAAAATTACATTTTGACCACTAAACTTTCCA
Found at i:209486 original size:78 final size:78
Alignment explanation
Indices: 209357--209813 Score: 530
Period size: 78 Copynumber: 5.9 Consensus size: 78
209347 TCACAACCAT
* * * * * *
209357 CCAATCTCTTACCCCGTGACAGAGGCAGATTGAAACCATCCGATCTTTTACCCCTATCATAGGGT
1 CCAATCTCTTACCCCGCGACAGGGGAAGATTGCAACCATCCGATCTTTTACCCCGATCATAGGGC
*
209422 AGATTACCGTCAG
66 AGATCACCGTCAG
* * * *
209435 CCAATCTCTTACCCCGCAACAGGGGAAGATAGTAACCATCCGATCTTTTACCCCGATCATGGGGC
1 CCAATCTCTTACCCCGCGACAGGGGAAGATTGCAACCATCCGATCTTTTACCCCGATCATAGGGC
* *
209500 AAATCACCATCAG
66 AGATCACCGTCAG
* * * *
209513 CCAA--TCTTACCCCGCGATAGGGGTAGATTGTAACCATCCTATCTTTTACCCCGATCATAGGGC
1 CCAATCTCTTACCCCGCGACAGGGGAAGATTGCAACCATCCGATCTTTTACCCCGATCATAGGGC
*
209576 AGATCACCGTTAG
66 AGATCACCGTCAG
* * * * *
209589 CCAATCTCTTACCTCGCGACA-AGGACATATTGCAACCATTCGATCTTTTACCTCGATCAT-GGG
1 CCAATCTCTTACCCCGCGACAGGGGA-AGATTGCAACCATCCGATCTTTTACCCCGATCATAGGG
* *
209652 CCAGATCACCATTAG
65 -CAGATCACCGTCAG
* * * *
209667 CCAATCTCTTACCCTGCGACAGGGGCAA-ATTGCAACCATTCGATCTTTTACCCTGATCATGGGG
1 CCAATCTCTTACCCCGCGACAGGGG-AAGATTGCAACCATCCGATCTTTTACCCCGATCATAGGG
*
209731 TAGATCACCGTCAG
65 CAGATCACCGTCAG
* * ** *
209745 CCAATCTCTTACCCCACGACAGGAGAAGATTGCAACCATCTAATCTTTTACCCTGATCATA-GGC
1 CCAATCTCTTACCCCGCGACAGGGGAAGATTGCAACCATCCGATCTTTTACCCCGATCATAGGGC
209809 AGATC
66 AGATC
209814 CAAACTACAC
Statistics
Matches: 324, Mismatches: 47, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
76 67 0.21
77 14 0.04
78 236 0.73
79 6 0.02
80 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (78 bp):
CCAATCTCTTACCCCGCGACAGGGGAAGATTGCAACCATCCGATCTTTTACCCCGATCATAGGGC
AGATCACCGTCAG
Found at i:209646 original size:154 final size:153
Alignment explanation
Indices: 209357--209804 Score: 540
Period size: 154 Copynumber: 2.9 Consensus size: 153
209347 TCACAACCAT
* * *
209357 CCAATCTCTTACCCCGTGACAGAGGCAGATTGAAACCATCCGATCTTTTACCCCTATCATAGGGT
1 CCAA-CTCTTACCCCGCGACAGGGGCAGATTGAAACCATCCGATCTTTTACCCCGATCATAGGGT
* * * * * *
209422 AGATTACCGTCAGCCAATCTCTTACCCCGCAACAGGGGAAGATAGTAACCATCCGATCTTTTACC
65 AGATCACCGTCAGCCAATCTCTTACCCCGCGACA-AGGAAGATTGCAACCATTCGATCTTTTA-C
*
209487 CCGATCATGGGGCAAATCACCATCAG
128 CCGATCATGGGCCAAATCACCATCAG
* * * * *
209513 CCAA-TCTTACCCCGCGATAGGGGTAGATTGTAACCATCCTATCTTTTACCCCGATCATAGGGCA
1 CCAACTCTTACCCCGCGACAGGGGCAGATTGAAACCATCCGATCTTTTACCCCGATCATAGGGTA
* * *
209577 GATCACCGTTAGCCAATCTCTTACCTCGCGACAAGGACATATTGCAACCATTCGATCTTTTACCT
66 GATCACCGTCAGCCAATCTCTTACCCCGCGACAAGGA-AGATTGCAACCATTCGATCTTTTACC-
* *
209642 CGATCATGGGCCAGATCACCATTAG
129 CGATCATGGGCCAAATCACCATCAG
* * * * * *
209667 CCAATCTCTTACCCTGCGACAGGGGCAAATTGCAACCATTCGATCTTTTACCCTGATCATGGGGT
1 CCAA-CTCTTACCCCGCGACAGGGGCAGATTGAAACCATCCGATCTTTTACCCCGATCATAGGGT
* * *
209732 AGATCACCGTCAGCCAATCTCTTACCCCACGACAGGAGAAGATTGCAACCA-TCTAATCTTTTAC
65 AGATCACCGTCAGCCAATCTCTTACCCCGCGACAAG-GAAGATTGCAACCATTC-GATCTTTTAC
209796 CCTGATCAT
128 CC-GATCAT
209805 AGGCAGATCC
Statistics
Matches: 249, Mismatches: 36, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
153 5 0.02
154 127 0.51
155 3 0.01
156 112 0.45
157 2 0.01
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (153 bp):
CCAACTCTTACCCCGCGACAGGGGCAGATTGAAACCATCCGATCTTTTACCCCGATCATAGGGTA
GATCACCGTCAGCCAATCTCTTACCCCGCGACAAGGAAGATTGCAACCATTCGATCTTTTACCCG
ATCATGGGCCAAATCACCATCAG
Found at i:209866 original size:39 final size:39
Alignment explanation
Indices: 209346--209968 Score: 210
Period size: 39 Copynumber: 16.1 Consensus size: 39
209336 GTGAAGTTAC
*
209346 ATCACAACCATCCAATCTCTTACCCCG-TGACA-GAGGCAG
1 ATCACAACCATCCGATCTCTTACCCCGAT--CATGAGGCAG
* * * *
209385 ATTGA-AACCATCCGATCTTTTACCCCTATCAT-AGGGTAG
1 A-TCACAACCATCCGATCTCTTACCCCGATCATGA-GGCAG
* *** * * * * *
209424 ATTACCGTCAGCCAATCTCTTACCCCGCAACA-GGGGAAG
1 ATCACAACCATCCGATCTCTTACCCCG-ATCATGAGGCAG
* * * *
209463 AT-AGTAACCATCCGATCTTTTACCCCGATCATGGGGCAA
1 ATCA-CAACCATCCGATCTCTTACCCCGATCATGAGGCAG
* * * * * *
209502 ATCACCATCAGCC-A-ATCTTACCCCG--CGATAGGGGTAG
1 ATCACAACCATCCGATCTCTTACCCCGATC-AT-GAGGCAG
*** * *
209539 ATTGTAACCATCCTATCTTTTACCCCGATCAT-AGGGCAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGA-GGCAG
**** * * *
209578 ATCACCGTTAGCCAATCTCTTACCTCGCGA-CA--AGGACAT
1 ATCACAACCATCCGATCTCTTACC-C-CGATCATGAGG-CAG
** * * *
209617 ATTGCAACCATTCGATCTTTTACCTCGATCATG-GGCCAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGAGG-CAG
* ** * * * *
209656 ATCACCATTAGCCAATCTCTTACCCTGCGA-CA-GGGGCAA
1 ATCACAACCATCCGATCTCTTACCC--CGATCATGAGGCAG
** * * * * *
209695 ATTGCAACCATTCGATCTTTTACCCTGATCATGGGGTAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGAGGCAG
*** * * * *
209734 ATCACCGTCAGCCAATCTCTTACCCCACGA-CAGGA-GAAG
1 ATCACAACCATCCGATCTCTTA-CCC-CGATCATGAGGCAG
** ** * *
209773 ATTGCAACCATCTAATCTTTTACCCTGATCAT-AGGCAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGAGGCAG
* *
209811 ATC-CAAAC-TACACGATCTCTTACCCTGATCATGAGGCAG
1 ATCACAACCAT-C-CGATCTCTTACCCCGATCATGAGGCAG
*
209850 ATCACAACCATCCGATCTCTTACCCCGATCATAAGGCAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGAGGCAG
* * *
209889 ATTACAGCCATCCGATCTCTTACCCCGACCATGAGGCAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGAGGCAG
* * * * *
209928 ATCATAGCCATCCAATCTCTTACCCCAATCATGGGGCAG
1 ATCACAACCATCCGATCTCTTACCCCGATCATGAGGCAG
209967 AT
1 AT
209969 TGCAGTTATC
Statistics
Matches: 414, Mismatches: 133, Indels: 74
0.67 0.21 0.12
Matches are distributed among these distances:
35 1 0.00
36 3 0.01
37 34 0.08
38 44 0.11
39 295 0.71
40 27 0.07
41 10 0.02
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (39 bp):
ATCACAACCATCCGATCTCTTACCCCGATCATGAGGCAG
Found at i:210998 original size:7 final size:7
Alignment explanation
Indices: 210986--211010 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
210976 AAGTTTATCC
210986 ATTTATT
1 ATTTATT
210993 ATTTATT
1 ATTTATT
211000 ATTTATT
1 ATTTATT
211007 ATTT
1 ATTT
211011 TGTATTTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTATT
Found at i:211209 original size:26 final size:26
Alignment explanation
Indices: 211152--211209 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
211142 TAAAAACCCT
* *
211152 AAATAAAAAACCTAACAAATTAAAAA
1 AAATAAAAAAACTAACAAATCAAAAA
* *
211178 AGATAAAAAAACTAA-AACTCAAAGAA
1 AAATAAAAAAACTAACAAATCAAA-AA
211204 AAATAA
1 AAATAA
211210 TGTTTTTCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.14
Consensus pattern (26 bp):
AAATAAAAAAACTAACAAATCAAAAA
Found at i:211851 original size:30 final size:30
Alignment explanation
Indices: 211807--212057 Score: 207
Period size: 30 Copynumber: 8.4 Consensus size: 30
211797 AAGATTTTGC
*
211807 TTTAA-CCTCTAAACTTTTCTAAAATTATAT
1 TTTAACCCTC-AAACTTTTCTAAAATTACAT
* * *
211837 TTTTACCCTCAAACTTTTCCAAAATTATAT
1 TTTAACCCTCAAACTTTTCTAAAATTACAT
* *
211867 TTTGACCCTTAAAC---T-T-AAATTACAT
1 TTTAACCCTCAAACTTTTCTAAAATTACAT
* *
211892 TTTAACCACT-AAACTTTCCCAAAATTACAT
1 TTTAACC-CTCAAACTTTTCTAAAATTACAT
* * *
211922 TTTAACCCTCAAACTTTCCTAAAGTTGCAT
1 TTTAACCCTCAAACTTTTCTAAAATTACAT
* *
211952 TTTAACCCTTAAACTTTACTAAAATTACAT
1 TTTAACCCTCAAACTTTTCTAAAATTACAT
* *
211982 TTTGACCCTCAAACCTTTCTAAAAAAAATTACA-
1 TTTAACCCTCAAACTTTTCT----AAAATTACAT
* *
212015 TTTCACCCTCTAAA-TTTTCCATAAATTACAT
1 TTTAACCCTC-AAACTTTTCTA-AAATTACAT
212046 TTTAA-CCTCAAA
1 TTTAACCCTCAAA
212058 TTCTCCAAAA
Statistics
Matches: 182, Mismatches: 24, Indels: 31
0.77 0.10 0.13
Matches are distributed among these distances:
25 18 0.10
26 2 0.01
27 1 0.01
29 6 0.03
30 122 0.67
31 8 0.04
33 13 0.07
34 12 0.07
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.39
Consensus pattern (30 bp):
TTTAACCCTCAAACTTTTCTAAAATTACAT
Found at i:211893 original size:25 final size:25
Alignment explanation
Indices: 211858--211907 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
211848 AACTTTTCCA
* *
211858 AAATTATATTTTGACC-CTTAAACTT
1 AAATTACATTTTAACCAC-TAAACTT
211883 AAATTACATTTTAACCACTAAACTT
1 AAATTACATTTTAACCACTAAACTT
211908 TCCCAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 21 0.95
26 1 0.05
ACGTcount: A:0.40, C:0.18, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATTACATTTTAACCACTAAACTT
Found at i:211924 original size:85 final size:85
Alignment explanation
Indices: 211807--211967 Score: 225
Period size: 85 Copynumber: 1.9 Consensus size: 85
211797 AAGATTTTGC
* * * * * * *
211807 TTTAACCTCTAAACTTTTCTAAAATTATATTTTTACCCTCAAACTTTTCC-AAAATTATATTTTG
1 TTTAACCACTAAACTTTCCCAAAATTACATTTTAACCCTCAAAC-TTTCCTAAAATTACATTTTA
211871 ACCCTTAAACTTAAATTACAT
65 ACCCTTAAACTTAAATTACAT
* *
211892 TTTAACCACTAAACTTTCCCAAAATTACATTTTAACCCTCAAACTTTCCTAAAGTTGCATTTTAA
1 TTTAACCACTAAACTTTCCCAAAATTACATTTTAACCCTCAAACTTTCCTAAAATTACATTTTAA
211957 CCCTTAAACTT
66 CCCTTAAACTT
211968 TACTAAAATT
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
84 5 0.08
85 61 0.92
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (85 bp):
TTTAACCACTAAACTTTCCCAAAATTACATTTTAACCCTCAAACTTTCCTAAAATTACATTTTAA
CCCTTAAACTTAAATTACAT
Found at i:213930 original size:68 final size:68
Alignment explanation
Indices: 213721--213975 Score: 318
Period size: 68 Copynumber: 3.8 Consensus size: 68
213711 CCTCAAAAGA
* * * * * * *
213721 GGTTACAAAGTGTAAGGCTATAGCTCGGCTATGACAACCAATAGAGTCTGTCAGGACATTAAACA
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCTGCCAAGACATTAAACA
213786 TGG
66 TGG
* * * * *
213789 GGTTACAAGGTGTAAGACCATAGCTTGGCGAT---AACCAATAGAGTCCGTCAAGACATTAAACA
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCTGCCAAGACATTAAACA
213851 TGG
66 TGG
* * * *
213854 GGTTACAAGGTGCAAGACCATAGCTCGATTATGGCACCCAATAGAGTCTGCCAAGACATTAAATA
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCTGCCAAGACATTAAACA
213919 TGG
66 TGG
* *
213922 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACAAATAAAAGTCTGCCA
1 GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAAT-AGAGTCTGCCA
213976 GTATAGAGAA
Statistics
Matches: 162, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
65 58 0.36
68 94 0.58
69 10 0.06
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (68 bp):
GGTTACAAGGTGTAAGACCATAGCTCGACTATGGCAACCAATAGAGTCTGCCAAGACATTAAACA
TGG
Found at i:217148 original size:338 final size:339
Alignment explanation
Indices: 216651--217262 Score: 951
Period size: 338 Copynumber: 1.8 Consensus size: 339
216641 ACCCAAATGC
* * *
216651 TTCTAAAAGTATAAGATGCATTAGTTTTTAAAGTAGACTCCAAAAAGAATAATTTAGAAATTATT
1 TTCTAAAAGTATAAGATGCATTAGTTTTTAAAGTAGACTCCAAAAAGAACAATTTAAAAAATATT
* * *
216716 TTTCTTTTAGAACTTGAGGTAATAAAGAAAGTTAGATTAAAAATAAGTCTAAAACCTTGTTTTGC
66 TATCTCTTAGAACTTAAGGTAATAAAGAAAGTTAGATTAAAAATAAGTCTAAAACCTTGTTTTGC
** *** * *
216781 TAAAAGAGCCATATTAAATTTTGCCAAATTCCAAGTACAAAAACCATTGTTGTACTTATTTTTAC
131 TAAAAGAGCCATATTAAATTTAACCAAATTCCAAGTACAAAAACCACCATTATACTTATTTTCAC
* *
216846 CAATCTAGCTTTTTGTACACCAATGTAATCCTTGTT-ACACGTGGTTTTGGCCACCAAAACTCTT
196 CAATCTAGCTCTTTGTACACCAATGTAATCCTTGTTCACACGTGGTTTTGGCCA-CAAAACTCCT
216910 TTTATA-AGTACTTCACGCTTGGGGATAAAATGTTTAAGTTTTTTAAGTGGACTCCAAAAAGAAT
260 TTTATAGA-TACTTCACGCTTGGGGATAAAATGTTTAAGTTTTTTAAGTGGACTCCAAAAAGAAT
216974 AATTTAGAAAATATTT
324 AATTTAGAAAATATTT
*
216990 TTCTAAGAGTATAAGATGCATTAGTTTTTAAAGTAGACTCCAAAAAGAACAATTTAAAAAATATT
1 TTCTAAAAGTATAAGATGCATTAGTTTTTAAAGTAGACTCCAAAAAGAACAATTTAAAAAATATT
* * * **
217055 TATCTCTTAGAACTTAAGGTAAT-AATAAAGTTAGATTAGAAATAGGTCTCCAACCTTGTTTTGC
66 TATCTCTTAGAACTTAAGGTAATAAAGAAAGTTAGATTAAAAATAAGTCTAAAACCTTGTTTTGC
*
217119 TAAAAGAGCCATATTAAATTTAACCAAATTCCAAGTACCAAAACCACCATTATACTTATTTTCAC
131 TAAAAGAGCCATATTAAATTTAACCAAATTCCAAGTACAAAAACCACCATTATACTTATTTTCAC
* * *
217184 CAATCTTGCTCTTTGTACACCAATGTTATCCTTGTTGCACATGTGGTTTTGGCCACAAAACTCCT
196 CAATCTAGCTCTTTGTACACCAATGTAATCCTTGTT-CACACGTGGTTTTGGCCACAAAACTCCT
217249 TTTATAGATACTTC
260 TTTATAGATACTTC
217263 CTTCACACCT
Statistics
Matches: 245, Mismatches: 25, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
338 126 0.51
339 102 0.42
340 17 0.07
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (339 bp):
TTCTAAAAGTATAAGATGCATTAGTTTTTAAAGTAGACTCCAAAAAGAACAATTTAAAAAATATT
TATCTCTTAGAACTTAAGGTAATAAAGAAAGTTAGATTAAAAATAAGTCTAAAACCTTGTTTTGC
TAAAAGAGCCATATTAAATTTAACCAAATTCCAAGTACAAAAACCACCATTATACTTATTTTCAC
CAATCTAGCTCTTTGTACACCAATGTAATCCTTGTTCACACGTGGTTTTGGCCACAAAACTCCTT
TTATAGATACTTCACGCTTGGGGATAAAATGTTTAAGTTTTTTAAGTGGACTCCAAAAAGAATAA
TTTAGAAAATATTT
Found at i:218824 original size:27 final size:27
Alignment explanation
Indices: 218786--218837 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
218776 CCAAATGCTT
*
218786 CATAACATAACCATTAGTTAAACCTTA
1 CATAACATAACCATTAGTCAAACCTTA
218813 CATAACATAACCATTAGTCAAACCT
1 CATAACATAACCATTAGTCAAACCT
218838 CAAAAGGTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.27
Consensus pattern (27 bp):
CATAACATAACCATTAGTCAAACCTTA
Found at i:219440 original size:12 final size:12
Alignment explanation
Indices: 219423--219450 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
219413 TCCCACAAAT
219423 ACCATTATTGAA
1 ACCATTATTGAA
219435 ACCATTATTGAA
1 ACCATTATTGAA
219447 ACCA
1 ACCA
219451 ATCGTTGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (12 bp):
ACCATTATTGAA
Found at i:222992 original size:105 final size:105
Alignment explanation
Indices: 222810--223024 Score: 340
Period size: 105 Copynumber: 2.0 Consensus size: 105
222800 AAGAAAACAT
* * * *
222810 TAAATTCTCGTCAGTGCACAGTTATATTCTAACCAACTTTGACAGTGGCAAAATTTAGATCTGGA
1 TAAATTCTCGTCAGTGCACAGTTATACTCTAACCAACTTTGACAGTGACAAAATCTAGATCTAGA
* *
222875 TCTAAGAATGGGAGGTTGAAACCTGCGACTTTTGAAGGTA
66 GCTAAGAATGGGAGGTTGAAACCTGCAACTTTTGAAGGTA
* *
222915 TAAATTCTCGTCAGTGCACAGTTATACTCTAATCAACTTTGACAGTTACAAAATCTAGATCTAGA
1 TAAATTCTCGTCAGTGCACAGTTATACTCTAACCAACTTTGACAGTGACAAAATCTAGATCTAGA
* *
222980 GCTAAGAATGGGAGGTTGAAACCTGTAATTTTTGAAGGTA
66 GCTAAGAATGGGAGGTTGAAACCTGCAACTTTTGAAGGTA
223020 TAAAT
1 TAAAT
223025 AGAAGAATGA
Statistics
Matches: 100, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
105 100 1.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.31
Consensus pattern (105 bp):
TAAATTCTCGTCAGTGCACAGTTATACTCTAACCAACTTTGACAGTGACAAAATCTAGATCTAGA
GCTAAGAATGGGAGGTTGAAACCTGCAACTTTTGAAGGTA
Found at i:228797 original size:23 final size:22
Alignment explanation
Indices: 228761--228804 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
228751 TAAATATTTC
*
228761 ATTAAATAATTTGGGTTGAATTA
1 ATTAAATAAATTGGGTT-AATTA
*
228784 ATTAATTAAATTGGGTTAATT
1 ATTAAATAAATTGGGTTAATT
228805 TTATTTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (22 bp):
ATTAAATAAATTGGGTTAATTA
Found at i:238316 original size:17 final size:17
Alignment explanation
Indices: 238295--238340 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
238285 TTGTTTGAAG
*
238295 AATTTTAAAATTTTTAA
1 AATTTTAAAATTGTTAA
* *
238312 GATTTTAAAAATGTTAA
1 AATTTTAAAATTGTTAA
238329 AATTTTAGAAAT
1 AATTTTA-AAAT
238341 CAACTATTGT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
17 20 0.87
18 3 0.13
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
AATTTTAAAATTGTTAA
Found at i:240396 original size:13 final size:14
Alignment explanation
Indices: 240380--240413 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
240370 GATTTATTCC
240380 ATTAATTTAATT-A
1 ATTAATTTAATTAA
240393 ATTAA-TTAATTAA
1 ATTAATTTAATTAA
240406 ATTAATTT
1 ATTAATTT
240414 CTCAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 11 0.58
14 2 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATTAATTTAATTAA
Found at i:240402 original size:17 final size:17
Alignment explanation
Indices: 240380--240412 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
240370 GATTTATTCC
*
240380 ATTAATTTAATTAATTA
1 ATTAATTAAATTAATTA
240397 ATTAATTAAATTAATT
1 ATTAATTAAATTAATT
240413 TCTCAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTAATTAAATTAATTA
Found at i:241576 original size:2 final size:2
Alignment explanation
Indices: 241569--241598 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
241559 TATTTCTTTA
241569 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
241599 TTGATATTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:249344 original size:11 final size:11
Alignment explanation
Indices: 249330--249370 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
249320 TTAAGCAATT
249330 TTTTTTTTATA
1 TTTTTTTTATA
249341 TTTTTTTTA-A
1 TTTTTTTTATA
*
249351 CTTTTTTTT-TT
1 -TTTTTTTTATA
249362 TTTTTTTTA
1 TTTTTTTTA
249371 CATTCTCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTTTTTATA
Found at i:252494 original size:24 final size:24
Alignment explanation
Indices: 252409--252483 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
252399 TAGACTAATT
* *
252409 AGAGTTTGATTCAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
*
252433 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAATTGAAACAAATAAAC
252457 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAATTGAAACAAATAAAC
252481 AGA
1 AGA
252484 TCTTAACTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.53, C:0.08, G:0.13, T:0.25
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAC
Found at i:254431 original size:24 final size:24
Alignment explanation
Indices: 254403--254461 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
254393 TAGACTAATA
* *
254403 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTAAAACAAATAAAC
*
254427 AGAGTTTAATTAAAACAAATAAAC
1 AGAGTTTAACTAAAACAAATAAAC
*
254451 AAAGTTTAACT
1 AGAGTTTAACT
254462 GAAAGATTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTAAAACAAATAAAC
Found at i:258067 original size:17 final size:17
Alignment explanation
Indices: 258045--258099 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 17
258035 GTGTGGTGTA
258045 ACCGTGTGTGGCACACG
1 ACCGTGTGTGGCACACG
* *
258062 ACC--GTGTGGTATA--
1 ACCGTGTGTGGCACACG
*
258075 ACTGTGTGTGGCACACG
1 ACCGTGTGTGGCACACG
258092 ACCGTGTG
1 ACCGTGTG
258100 GCAACCTGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
13 2 0.07
15 16 0.57
17 10 0.36
ACGTcount: A:0.18, C:0.24, G:0.35, T:0.24
Consensus pattern (17 bp):
ACCGTGTGTGGCACACG
Found at i:258067 original size:30 final size:30
Alignment explanation
Indices: 258033--258100 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
258023 GCACGTAAGG
*
258033 CCGTGTGGTGTAACCGTGTGTGGCACACGA
1 CCGTGTGGTATAACCGTGTGTGGCACACGA
*
258063 CCGTGTGGTATAACTGTGTGTGGCACACGA
1 CCGTGTGGTATAACCGTGTGTGGCACACGA
258093 CCGTGTGG
1 CCGTGTGG
258101 CAACCTGTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.16, C:0.22, G:0.37, T:0.25
Consensus pattern (30 bp):
CCGTGTGGTATAACCGTGTGTGGCACACGA
Found at i:258905 original size:20 final size:20
Alignment explanation
Indices: 258882--258933 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
258872 AAATAGGGGT
*
258882 ACCGAAATGTAAACAGAGGC
1 ACCGAAATGCAAACAGAGGC
* *
258902 ACCGTAATGCAAACAGGGGC
1 ACCGAAATGCAAACAGAGGC
258922 ACC-AAAGTGCAA
1 ACCGAAA-TGCAA
258934 GCATATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (20 bp):
ACCGAAATGCAAACAGAGGC
Found at i:260997 original size:43 final size:43
Alignment explanation
Indices: 260921--261092 Score: 129
Period size: 41 Copynumber: 4.1 Consensus size: 43
260911 GAATCACCTG
* * *
260921 ATGTATAAATGGAAGACTCATGTCTCGGGATGAG-AGTGAGATT
1 ATGTATAAATGAAAGACTCATGACTCGGAATGAGCA-TGAGATT
** *
260964 ATGTATAAATGAAAGACTTGTGACTTGGAATGAGCATGAGATT
1 ATGTATAAATGAAAGACTCATGACTCGGAATGAGCATGAGATT
* * * * * * * *
261007 AT-TTTCAA-GGAAGCCTCATGTCTTGGAAAGAGCATGAGACT
1 ATGTATAAATGAAAGACTCATGACTCGGAATGAGCATGAGATT
* * * * *
261048 ATGT-TAAAGGAAA-ACTAATGTCTCAGAAAGAGCATGAGATT
1 ATGTATAAATGAAAGACTCATGACTCGGAATGAGCATGAGATT
261089 ATGT
1 ATGT
261093 TCAAGGAAAG
Statistics
Matches: 104, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 58 0.56
42 8 0.08
43 37 0.36
44 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.28
Consensus pattern (43 bp):
ATGTATAAATGAAAGACTCATGACTCGGAATGAGCATGAGATT
Found at i:261040 original size:41 final size:41
Alignment explanation
Indices: 260987--261101 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
260977 AGACTTGTGA
* * ** *
260987 CTTGGAATGAGCATGAGATTATTTTCAAGGAAGCCTCATGT
1 CTTGGAAAGAGCATGAGATTATGTTCAAGGAAAACTAATGT
* *
261028 CTTGGAAAGAGCATGAGACTATGTTAAAGGAAAACTAATGT
1 CTTGGAAAGAGCATGAGATTATGTTCAAGGAAAACTAATGT
**
261069 CTCAGAAAGAGCATGAGATTATGTTCAAGGAAA
1 CTTGGAAAGAGCATGAGATTATGTTCAAGGAAA
261102 GACCTATGTC
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 63 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.26
Consensus pattern (41 bp):
CTTGGAAAGAGCATGAGATTATGTTCAAGGAAAACTAATGT
Found at i:261121 original size:41 final size:41
Alignment explanation
Indices: 260995--261129 Score: 127
Period size: 41 Copynumber: 3.3 Consensus size: 41
260985 GACTTGGAAT
* * *
260995 GAGCATGAGATTATTTTCAAGG-AAG-CCTCATGTCTTGGAAA
1 GAGCATGAGATTATGTTCAAGGAAAGACCTAATGTC-T-CAAA
* *
261036 GAGCATGAGACTATGTTAAAGGAAA-A-CTAATGTCTCAGAAA
1 GAGCATGAGATTATGTTCAAGGAAAGACCTAATGTCTC--AAA
*
261077 GAGCATGAGATTATGTTCAAGGAAAGACCT-ATGTCTCATTA
1 GAGCATGAGATTATGTTCAAGGAAAGACCTAATGTCTCA-AA
*
261118 GAGCATAAGATT
1 GAGCATGAGATT
261130 GTTTGAAAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 14
0.77 0.09 0.14
Matches are distributed among these distances:
40 2 0.03
41 64 0.82
42 10 0.13
43 2 0.03
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (41 bp):
GAGCATGAGATTATGTTCAAGGAAAGACCTAATGTCTCAAA
Found at i:261145 original size:41 final size:40
Alignment explanation
Indices: 261095--261185 Score: 94
Period size: 41 Copynumber: 2.2 Consensus size: 40
261085 GATTATGTTC
* * *
261095 AAGGAAAGACCTATGTCTCA-TTAGAGCATAAGATTGTTTGAA
1 AAGG-AAGACCTATGACTCAGTGA-AGCATAAGATCGTTT-AA
* *
261137 AAGGAAGACTTATGACTCGGTGAAGCATAAGATCGTTTAA
1 AAGGAAGACCTATGACTCAGTGAAGCATAAGATCGTTTAA
261177 AGAGGAAGA
1 A-AGGAAGA
261186 TTTACGACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
40 3 0.07
41 33 0.79
42 6 0.14
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (40 bp):
AAGGAAGACCTATGACTCAGTGAAGCATAAGATCGTTTAA
Found at i:270134 original size:28 final size:28
Alignment explanation
Indices: 270090--270146 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
270080 ACTACAGAGT
* *
270090 AAAAATCAAGGCATTGATTGCAAAGAAG
1 AAAAATCAAAGCATTGATTGCAAACAAG
* *
270118 AAAAATCAAAGCTTTGATTTCAAACAAG
1 AAAAATCAAAGCATTGATTGCAAACAAG
270146 A
1 A
270147 GGTGTCAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (28 bp):
AAAAATCAAAGCATTGATTGCAAACAAG
Found at i:275896 original size:16 final size:15
Alignment explanation
Indices: 275875--275904 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
275865 AAAAGCAAAA
275875 AAAATTTGTGTGAAAG
1 AAAATTTGT-TGAAAG
275891 AAAATTTGTTGAAA
1 AAAATTTGTTGAAA
275905 ACATAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (15 bp):
AAAATTTGTTGAAAG
Found at i:278855 original size:20 final size:21
Alignment explanation
Indices: 278830--278868 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
278820 GCAAGGAATT
278830 TGAAACAAA-AAAACTAAAAG
1 TGAAACAAATAAAACTAAAAG
*
278850 TGAAACAAATAAAAGTAAA
1 TGAAACAAATAAAACTAAA
278869 TAGAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.69, C:0.08, G:0.10, T:0.13
Consensus pattern (21 bp):
TGAAACAAATAAAACTAAAAG
Found at i:283754 original size:87 final size:87
Alignment explanation
Indices: 283603--283779 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 87
283593 CTTCATTATA
283603 GGTAAAATCCAACAAAAGACCATTAGCCAATGCGTCGACAAGATTCCTTGTCTGAGCATTCAAAC
1 GGTAAAATCCAACAAAAGACCATTAGCCAATGCGTCGACAAGATTCCTTGTCTGAGCATTCAAAC
283668 CATTATAAAAAATTTCTATTTG
66 CATTATAAAAAATTTCTATTTG
*
283690 GGTACAATCCAACAAAAGACCATTAGCCAATGCGTCGACAAGATTCCTTGTCTGAGCATTCAAAC
1 GGTAAAATCCAACAAAAGACCATTAGCCAATGCGTCGACAAGATTCCTTGTCTGAGCATTCAAAC
283755 CATTATAAAAAATTTCTATTTG
66 CATTATAAAAAATTTCTATTTG
283777 GGT
1 GGT
283780 CTCTTGCTGA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.28
Consensus pattern (87 bp):
GGTAAAATCCAACAAAAGACCATTAGCCAATGCGTCGACAAGATTCCTTGTCTGAGCATTCAAAC
CATTATAAAAAATTTCTATTTG
Found at i:284984 original size:48 final size:48
Alignment explanation
Indices: 284909--285010 Score: 159
Period size: 48 Copynumber: 2.1 Consensus size: 48
284899 AGCCCACACG
* * *
284909 AGCCCAAAATGGTTAGCTCTTATGAGCCCAGATTGGTTAACTCTTACA
1 AGCCCAAAATGGTTAACTCTTACGAGCCCAGATTAGTTAACTCTTACA
* *
284957 AGCCCAAAATGGTTAACTCTTACGAGCCCAGATTAGTTAGCTCTTACG
1 AGCCCAAAATGGTTAACTCTTACGAGCCCAGATTAGTTAACTCTTACA
285005 AGCCCA
1 AGCCCA
285011 GACAGAGTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (48 bp):
AGCCCAAAATGGTTAACTCTTACGAGCCCAGATTAGTTAACTCTTACA
Found at i:285011 original size:24 final size:24
Alignment explanation
Indices: 284906--285012 Score: 133
Period size: 24 Copynumber: 4.5 Consensus size: 24
284896 TTTAGCCCAC
* *
284906 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAACTCTT
* *
284930 ATGAGCCCAGATTGGTTAACTCTT
1 ACGAGCCCAGAATGGTTAACTCTT
* *
284954 ACAAGCCCAAAATGGTTAACTCTT
1 ACGAGCCCAGAATGGTTAACTCTT
* * *
284978 ACGAGCCCAGATTAGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAACTCTT
285002 ACGAGCCCAGA
1 ACGAGCCCAGA
285013 CAGAGTTTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 70 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAACTCTT
Found at i:298303 original size:24 final size:26
Alignment explanation
Indices: 298265--298312 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
298255 TCTACATGGG
298265 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
298291 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
298313 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Done.