Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007993.1 Hibiscus syriacus cultivar Beakdansim tig00110443_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2245901
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 12
Found at i:1090827 original size:28 final size:27
Alignment explanation
Indices: 1090796--1090851 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
1090786 GAAAATATAG
*
1090796 AAAATGAAAATGA-AAACGAAGAAGAAAA
1 AAAATGAAAACGAGAAA-GAA-AAGAAAA
1090824 AAAATGAAAACGAGAAAGAAAAGAAAA
1 AAAATGAAAACGAGAAAGAAAAGAAAA
1090851 A
1 A
1090852 GAGAAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.31
28 15 0.58
29 3 0.12
ACGTcount: A:0.73, C:0.04, G:0.18, T:0.05
Consensus pattern (27 bp):
AAAATGAAAACGAGAAAGAAAAGAAAA
Found at i:1090830 original size:22 final size:23
Alignment explanation
Indices: 1090794--1090850 Score: 82
Period size: 22 Copynumber: 2.5 Consensus size: 23
1090784 AAGAAAATAT
1090794 AGAAAATGAAAATGAAAACGA-AGA
1 AGAAAA-GAAAATGAAAACGAGA-A
1090818 AGAAAA-AAAATGAAAACGAGAA
1 AGAAAAGAAAATGAAAACGAGAA
1090840 AGAAAAGAAAA
1 AGAAAAGAAAA
1090851 AGAGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 20 0.65
23 5 0.16
24 6 0.19
ACGTcount: A:0.72, C:0.04, G:0.19, T:0.05
Consensus pattern (23 bp):
AGAAAAGAAAATGAAAACGAGAA
Found at i:1090855 original size:17 final size:17
Alignment explanation
Indices: 1090769--1090864 Score: 67
Period size: 17 Copynumber: 5.7 Consensus size: 17
1090759 AAACAGAAGA
1090769 AGAAAAAAATAGAAAAAG
1 AGAAAAAAAT-GAAAAAG
* * *
1090787 A-AAATATA-GAAAATG
1 AGAAAAAAATGAAAAAG
* *
1090802 A-AAATGAAAACGAAGAAG
1 AGAAA--AAAATGAAAAAG
*
1090820 A-AAAAAAATGAAAACG
1 AGAAAAAAATGAAAAAG
1090836 AGAAAGAAAA-GAAAAAG
1 AGAAA-AAAATGAAAAAG
1090853 AGAAAAAAATGA
1 AGAAAAAAATGA
1090865 GAGATGAAAA
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
15 10 0.16
16 14 0.23
17 23 0.38
18 14 0.23
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (17 bp):
AGAAAAAAATGAAAAAG
Found at i:1094715 original size:40 final size:40
Alignment explanation
Indices: 1094660--1094781 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
1094650 TGCAGGTTTA
*
1094660 TAATACACTTCGGTGTATATGGTGGGCATGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1094700 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1094740 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1094780 TA
1 TA
1094782 GCACTACGGT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1094979 original size:47 final size:44
Alignment explanation
Indices: 1094885--1095002 Score: 146
Period size: 47 Copynumber: 2.6 Consensus size: 44
1094875 GTAACCATGC
* *
1094885 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGAAA
* * * *
1094929 AAATAAGCTTACGAGCTTATGTAATTTAAATGGTAAGTATTTTGATA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATTGAAA
*
1094976 AAATAAGCTTACGAGCTTATGGGATAA
1 AAATAAGCTTACGAGCTTATGGAATAA
1095003 ATGGTAAGAG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
44 23 0.37
45 1 0.02
46 1 0.02
47 38 0.60
ACGTcount: A:0.41, C:0.08, G:0.19, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGAAA
Found at i:1096689 original size:28 final size:29
Alignment explanation
Indices: 1096649--1096703 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1096639 TTTTATTTTC
1096649 TTCCATTTTTTTA-ATTTGAGAACCTTAG
1 TTCCATTTTTTTACATTTGAGAACCTTAG
*
1096677 TTCC-TTTTATTTACATTTGAGTACCTT
1 TTCCATTTT-TTTACATTTGAGAACCTT
1096704 TTATTTATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 4 0.17
28 8 0.33
29 12 0.50
ACGTcount: A:0.22, C:0.16, G:0.09, T:0.53
Consensus pattern (29 bp):
TTCCATTTTTTTACATTTGAGAACCTTAG
Found at i:1097001 original size:2 final size:2
Alignment explanation
Indices: 1096984--1097020 Score: 51
Period size: 2 Copynumber: 19.0 Consensus size: 2
1096974 TTGCATTACC
1096984 AT AT AT -T AT A- AGT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1097021 GTTCCATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 2 0.06
2 29 0.91
3 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1100829 original size:60 final size:60
Alignment explanation
Indices: 1100751--1100868 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
1100741 ATTCATTTGC
* * *
1100751 TAATTATAAGTTGATATTTTGTTGAG-TCATTTAATTTTTAAAAATTATAAAATAATCATT
1 TAATTATAAGTTGATATTTTATTGAGTTCATTT-ATTATTAAAAATTACAAAATAATCATT
* * *
1100811 TAATTAT-AGTATGTTATTTTATTGAGTTCATTTATTATTAAAAGTTACAAAATGATCA
1 TAATTATAAGT-TGATATTTTATTGAGTTCATTTATTATTAAAAATTACAAAATAATCA
1100869 CCTGATTATT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 3 0.06
60 41 0.82
61 6 0.12
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (60 bp):
TAATTATAAGTTGATATTTTATTGAGTTCATTTATTATTAAAAATTACAAAATAATCATT
Found at i:1101616 original size:12 final size:12
Alignment explanation
Indices: 1101599--1101626 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1101589 AATGGTTTTA
1101599 AGCGGCGGATGT
1 AGCGGCGGATGT
1101611 AGCGGCGGATGT
1 AGCGGCGGATGT
1101623 AGCG
1 AGCG
1101627 ACGTTTTTAC
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:0.18, C:0.18, G:0.50, T:0.14
Consensus pattern (12 bp):
AGCGGCGGATGT
Found at i:1101714 original size:40 final size:39
Alignment explanation
Indices: 1101680--1101810 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 39
1101670 GTTTTTGAAC
1101680 AAACGCCGCAAAATACTATAATTTAGTGGCGTTTTTATAA
1 AAACGCCGCAAAA-ACTATAATTTAGTGGCGTTTTTATAA
* *
1101720 AAACGCCGCTAAAGAA-TCGTAATGTAGTGGCGTTTTTATAA
1 AAACGCCGC-AAA-AACT-ATAATTTAGTGGCGTTTTTATAA
* * *
1101761 AAACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTTATAC
1 AAACGCCGC-AAAAACTA-TAATTTAGTGGCGTTTTTATAA
1101802 AAACGCCGC
1 AAACGCCGC
1101811 TATAGACACG
Statistics
Matches: 79, Mismatches: 7, Indels: 9
0.83 0.07 0.09
Matches are distributed among these distances:
40 12 0.15
41 66 0.84
42 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (39 bp):
AAACGCCGCAAAAACTATAATTTAGTGGCGTTTTTATAA
Found at i:1101855 original size:42 final size:42
Alignment explanation
Indices: 1101705--1102102 Score: 447
Period size: 42 Copynumber: 9.6 Consensus size: 42
1101695 CTATAATTTA
* * * * * *
1101705 GTGGCGTTTTTATA-AAAACGCCGCTAAAGA-ATCGTAATGTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACA-CGTACTTTT
* * *
1101746 GTGGCGTTTTTATA-AAAACGCCGCTATAAACTA-GTA-TTTT
1 GTGGCGTTTTAATACCAAACGCCGCTATAGAC-ACGTACTTTT
*
1101786 AGTGGCGTTTTTATA-CAAACGCCGCTATAGACACGTACTTTT
1 -GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
* * * *
1101828 GTGGCGTTTGAATACCAAACGCCGCTATAGACTCCTACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
* *
1101870 GTGGCATTTT--TACACAAACGCCGCTATAGACACGTACGTTT
1 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACTTTT
1101911 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
* * ** *
1101953 GTGGCGTTTTAATACCAAACGTCGTTATAGATTCGTACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
1101995 GTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTT
1 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACTTTT
** * * *
1102036 GTGGCGTTTTAATACCAAACATCGCTATAGACTCATACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
1102078 GTGGCGTTTTAATACCAAACGCCGC
1 GTGGCGTTTTAATACCAAACGCCGC
1102103 AATTGTCATA
Statistics
Matches: 309, Mismatches: 36, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
40 9 0.03
41 139 0.45
42 154 0.50
43 7 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (42 bp):
GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
Found at i:1101887 original size:83 final size:83
Alignment explanation
Indices: 1101701--1102102 Score: 451
Period size: 83 Copynumber: 4.8 Consensus size: 83
1101691 AATACTATAA
* * * * * * *
1101701 TTTAGTGGCGTTTTTATAAAAACGCCGCTAAAGA-ATCGTAATGTAGTGGCGTTTTTATA-AAAA
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACA-CGTACTTTAGTGGCGTTTTAATACCAAA
* *
1101764 CGCCGCTATAAACTA-GTAT
65 CGCCGCTATAGAC-ACGTAC
* * *
1101783 TTTAGTGGCGTTTTTATACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTGAATACCAAAC
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACCAAAC
* *
1101848 GCCGCTATAGACTCCTAC
66 GCCGCTATAGACACGTAC
*
1101866 TTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACGTTT-GTGGCGTTTTAATACCAAA
1 TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTAC-TTTAGTGGCGTTTTAATACCAAA
1101930 CGCCGCTATAGACACGTAC
65 CGCCGCTATAGACACGTAC
* * * **
1101949 TTTTGTGGCGTTTTAATAC-CAAACGTCGTTATAGATTCGTACTTTAGTGGCGTTTT--TACACA
1 TTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATAC-CA
1102011 AACGCCGCTATAGACACGTAC
63 AACGCCGCTATAGACACGTAC
* ** * *
1102032 TTTTGTGGCGTTTTAATAC-CAAACATCGCTATAGACTCATACTTTAGTGGCGTTTTAATACCAA
1 TTTAGTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACCAA
1102096 ACGCCGC
64 ACGCCGC
1102103 AATTGTCATA
Statistics
Matches: 283, Mismatches: 27, Indels: 18
0.86 0.08 0.05
Matches are distributed among these distances:
82 53 0.19
83 182 0.64
84 42 0.15
85 6 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (83 bp):
TTTAGTGGCGTTTTTACACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACCAAAC
GCCGCTATAGACACGTAC
Found at i:1101973 original size:125 final size:125
Alignment explanation
Indices: 1101705--1102102 Score: 552
Period size: 125 Copynumber: 3.2 Consensus size: 125
1101695 CTATAATTTA
* * * * * * *
1101705 GTGGCGTTTTTATA-AAAACGCCGCTAAAGAATCGTAATGTAGTGGCGTTTTTATAAAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACAAACGCCG
* *
1101769 CTATAAACTA-GTA-TTTTAGTGGCGTTTTTATA-CAAACGCCGCTATAGACACGTACTTTT
66 CTATAGAC-ACGTACTTTT-GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
* * * *
1101828 GTGGCGTTTGAATACCAAACGCCGCTATAGACTCCTACTTTAGTGGCATTTTTACACAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACAAACGCCG
*
1101893 CTATAGACACGTACGTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
66 CTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
* * *
1101953 GTGGCGTTTTAATACCAAACGTCGTTATAGATTCGTACTTTAGTGGCGTTTTTACACAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACAAACGCCG
** * * *
1102018 CTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACATCGCTATAGACTCATACTTTA
66 CTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
1102078 GTGGCGTTTTAATACCAAACGCCGC
1 GTGGCGTTTTAATACCAAACGCCGC
1102103 AATTGTCATA
Statistics
Matches: 243, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
123 13 0.05
124 64 0.26
125 166 0.68
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (125 bp):
GTGGCGTTTTAATACCAAACGCCGCTATAGAATCGTACTTTAGTGGCGTTTTTACACAAACGCCG
CTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
Found at i:1106182 original size:85 final size:85
Alignment explanation
Indices: 1105992--1106311 Score: 362
Period size: 85 Copynumber: 3.7 Consensus size: 85
1105982 AAGGTAATTA
* *
1105992 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTTGCAGCGTTTGTGT-TCAAAAAC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGT-TCT-AAAAAC
* *
1106056 GCTGTTATAGGTCTGAC-CTTTT
64 GCCGCTATAGGTCTG-CTCTTTT
* * *
1106078 GCAGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
1106143 CAG-TATAGGTCTGCTCTTTT
66 C-GCTATAGGTCTGCTCTTTT
* * * *
1106163 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACATTTTGCGGCGTTTTTTCTAGAAACGC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
** *
1106228 CGCTATATATCATAACT-TTTT
66 CGCTATAGGTC-T-GCTCTTTT
* * * * * *
1106249 GCGGCGTTTAT-TCCAAAAATGCCGCTATAGATTTTGACCTTTTGCGGCGTTTGTTCAAAAAAC
1 GCGGCGTTTGTATCAAAAAACGCCGCTATAG-GTCTGACCTTTTGCGGCGTTTGTTCTAAAAAC
1106312 ACTGTAATAG
Statistics
Matches: 202, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
84 2 0.01
85 106 0.52
86 92 0.46
87 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (85 bp):
GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACCTTTTGCGGCGTTTGTTCTAAAAACGC
CGCTATAGGTCTGCTCTTTT
Found at i:1106323 original size:43 final size:42
Alignment explanation
Indices: 1105992--1106311 Score: 349
Period size: 43 Copynumber: 7.5 Consensus size: 42
1105982 AAGGTAATTA
*
1105992 GCGGCGTTTGTATCAAAAAACGCCGCTATAGGTCTGACTTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGGTCTGACCTTTT
* * *
1106035 GCAGCGTTTGTGTTC-AAAAACGCTGTTATAGGTCTGACCTTTT
1 GCGGCG-TT-TGTTCAAAAAACGCCGCTATAGGTCTGACCTTTT
* *
1106078 GCAGCGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGGTCTGACCTTTT
*
1106121 GCGGCGTTTGTTCTAAAAACGCCAG-TATAGGTCTG-CTCTTTT
1 GCGGCGTTTGTTCAAAAAACGCC-GCTATAGGTCTGAC-CTTTT
* *
1106163 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCTGACATTTT
1 GCGGCGTTTGT-TCAAAAAACGCCGCTATAGGTCTGACCTTTT
* * * ** * *
1106206 GCGGCGTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGGTC-TGACCTTTT
* * * * *
1106249 GCGGCGTTTATTCCAAAAATGCCGCTATAGATTTTGACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAG-GTCTGACCTTTT
1106292 GCGGCGTTTGTTCAAAAAAC
1 GCGGCGTTTGTTCAAAAAAC
1106312 ACTGTAATAG
Statistics
Matches: 237, Mismatches: 29, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.02
42 61 0.26
43 163 0.69
44 6 0.03
45 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGGTCTGACCTTTT
Found at i:1107338 original size:20 final size:20
Alignment explanation
Indices: 1107318--1107355 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1107308 AAATTATAAT
1107318 TTTA-TCATTATAAATTGAA
1 TTTATTCATTATAAATTGAA
*
1107337 TTTATTTATTATAAATTGA
1 TTTATTCATTATAAATTGA
1107356 TCTTGATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TTTATTCATTATAAATTGAA
Found at i:1110579 original size:21 final size:21
Alignment explanation
Indices: 1110553--1110604 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
1110543 TCTCAAAGTG
1110553 GTATGAAAAACAACATGATCC
1 GTATGAAAAACAACATGATCC
1110574 GTATGAAAAACAACATGATCC
1 GTATGAAAAACAACATGATCC
*
1110595 GTAAGAAAAA
1 GTATGAAAAA
1110605 AGATCAGGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.17
Consensus pattern (21 bp):
GTATGAAAAACAACATGATCC
Found at i:1111881 original size:24 final size:24
Alignment explanation
Indices: 1111827--1111889 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
1111817 TCATGTCATT
* * * *
1111827 ATTTTGGACAGTGTATGATATTATC
1 ATTTTGGACA-TATATAATATCAAC
*
1111852 ACTTTGGACATATATAATATCAAC
1 ATTTTGGACATATATAATATCAAC
1111876 ATTTTGGACATATA
1 ATTTTGGACATATA
1111890 AGACTTATCA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (24 bp):
ATTTTGGACATATATAATATCAAC
Found at i:1115905 original size:105 final size:105
Alignment explanation
Indices: 1115775--1116339 Score: 1076
Period size: 105 Copynumber: 5.4 Consensus size: 105
1115765 GTGTTGTTTC
*
1115775 GAGTCCAATACCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
1115840 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
1115880 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
1115945 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGCCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
1115985 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1116050 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
1116090 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
*
1116155 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
*
1116195 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAATGTTCGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
1116260 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
1116300 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1116340 GGTAAAACCT
Statistics
Matches: 450, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 450 1.00
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTCGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
Found at i:1117136 original size:50 final size:50
Alignment explanation
Indices: 1117082--1117178 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
1117072 CTTTTTTCTC
* ** *
1117082 TTTTTCCTTTTTTCAATTTAGGGTGCCCTTTCGGGTTTTCACCCTAAACG
1 TTTTTCCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
** *
1117132 TTTTTTTTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTTTTCCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1117179 GCGAAGTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.47
Consensus pattern (50 bp):
TTTTTCCTTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:1126578 original size:10 final size:10
Alignment explanation
Indices: 1126553--1126586 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1126543 AACGTTAGTA
*
1126553 AAATAGAAAT
1 AAATAAAAAT
*
1126563 AGATAAAAAT
1 AAATAAAAAT
1126573 AAATAAAAAT
1 AAATAAAAAT
1126583 AAAT
1 AAAT
1126587 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1127941 original size:19 final size:21
Alignment explanation
Indices: 1127907--1127946 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1127897 GAGAGAGGGA
1127907 AAAAATATATAATAATAATAG
1 AAAAATATATAATAATAATAG
*
1127928 AAAAAT-TA-AATAATTATAG
1 AAAAATATATAATAATAATAG
1127947 TAATACAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
AAAAATATATAATAATAATAG
Found at i:1131851 original size:46 final size:46
Alignment explanation
Indices: 1131797--1131902 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
1131787 CCGTTAATAT
* * * *
1131797 ACCGTTATGTATTTTCATTTATGGCATCATTTCATGCCGATTATGC
1 ACCGTTATGCATTTTCATTTATGACATCATTTCATGCCAATAATGC
*
1131843 ATCGTTATGCATTTTCATTTATGACATCATTTCATGCCAATAATGC
1 ACCGTTATGCATTTTCATTTATGACATCATTTCATGCCAATAATGC
1131889 ACCGTTATGCATTT
1 ACCGTTATGCATTT
1131903 AGTCTGTAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (46 bp):
ACCGTTATGCATTTTCATTTATGACATCATTTCATGCCAATAATGC
Found at i:1132908 original size:31 final size:31
Alignment explanation
Indices: 1132857--1132921 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1132847 GAACCTCGAC
* *
1132857 AACTGTCCATAGGTCCCGAAAAACCTAGGTA
1 AACTATCCATAGGTCCCGAAAAACATAGGTA
* * *
1132888 AACTATCCATATGTCTCGAAAGACATAGGTA
1 AACTATCCATAGGTCCCGAAAAACATAGGTA
1132919 AAC
1 AAC
1132922 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (31 bp):
AACTATCCATAGGTCCCGAAAAACATAGGTA
Found at i:1135623 original size:14 final size:14
Alignment explanation
Indices: 1135585--1135616 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1135575 TTACTCTAAT
1135585 ATCTAGTCAATAAC
1 ATCTAGTCAATAAC
1135599 ATCTAGTCAATAAC
1 ATCTAGTCAATAAC
1135613 ATCT
1 ATCT
1135617 GTTCAATCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (14 bp):
ATCTAGTCAATAAC
Found at i:1137626 original size:31 final size:31
Alignment explanation
Indices: 1137588--1137652 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1137578 AAACCTCGAT
*
1137588 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAG-ACATAGGTA
* *
1137619 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
1137650 AAC
1 AAC
1137653 CCTCGAATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:1138967 original size:20 final size:22
Alignment explanation
Indices: 1138942--1138999 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1138932 TTCCCCTTGA
1138942 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
1138962 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
1138985 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1139000 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:1139012 original size:19 final size:19
Alignment explanation
Indices: 1138988--1139038 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
1138978 CTTTAACATG
*
1138988 TGCATCGATGCACTACCCA
1 TGCATCGATACACTACCCA
*
1139007 TGCATCGATACATTACCCA
1 TGCATCGATACACTACCCA
1139026 TGCATCGATACAC
1 TGCATCGATACAC
1139039 AAATTACCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.29, C:0.33, G:0.14, T:0.24
Consensus pattern (19 bp):
TGCATCGATACACTACCCA
Found at i:1139115 original size:18 final size:19
Alignment explanation
Indices: 1139070--1139117 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
1139060 TTTTAAAGGG
*
1139070 ATGCATCTATGCACTCATT
1 ATGCATCGATGCACTCATT
1139089 ATGCATCGATGCAC-CATT
1 ATGCATCGATGCACTCATT
1139107 -TGCATTCGATG
1 ATGCA-TCGATG
1139118 TTTCTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 4 0.15
18 10 0.37
19 13 0.48
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (19 bp):
ATGCATCGATGCACTCATT
Found at i:1140020 original size:81 final size:81
Alignment explanation
Indices: 1139882--1140376 Score: 794
Period size: 81 Copynumber: 6.1 Consensus size: 81
1139872 TGTTACATAG
* * *
1139882 TCTTTTACTCGAAGGTAATTTAACCTTTAATCTAACTAGCATGATTGACACCTTTCTGTCAAATG
1 TCTTTTACTCAAAGGT-ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATG
*
1139947 CACAACTAGGCAATTAA
65 CACAGCTAGGCAATTAA
* *
1139964 TATTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGAATGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1140029 ACAGCTAGACAATTAA
66 ACAGCTAGGCAATTAA
1140045 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCT-TCCAAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGT-CAAATG
*
1140109 CACAGCTGGGCAATTAA
65 CACAGCTAGGCAATTAA
* * *
1140126 TCTTTTACTCAAAAGTATTTAACCTTTCATCTAACTGGCACGATTGACACCTTTCTATCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
1140191 ACAGCTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * *
1140207 TCTTTTACTCAAAGGTATTTAACCTTTCATCTATCTGGTACGATTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
*
1140272 ACAACTAGGCAATTAA
66 ACAGCTAGGCAATTAA
* * *
1140288 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTCCTGTCCAATG
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTT-CTGTCAAATG
1140353 CACAGCTAGGCAATTAA
65 CACAGCTAGGCAATTAA
1140370 TCTTTTA
1 TCTTTTA
1140377 TTTTAAAACA
Statistics
Matches: 384, Mismatches: 26, Indels: 6
0.92 0.06 0.01
Matches are distributed among these distances:
80 1 0.00
81 336 0.88
82 47 0.12
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGC
ACAGCTAGGCAATTAA
Found at i:1149136 original size:257 final size:254
Alignment explanation
Indices: 1148641--1149206 Score: 707
Period size: 257 Copynumber: 2.2 Consensus size: 254
1148631 GAAAAAAATG
* * * *
1148641 AGAAAGCGATTTCCAAAGTTCCTTACTCAGTAGACTATTTCCAAAATTTGTAAGTCCTTCAGGCC
1 AGAAAGCGATTTCCAAAGTT-CTTACACAGTAAACTATTTCCAAAATTGGAAAGTCCTTCAGGCC
* * *
1148706 ATCAGTAAGCATTTCGAGCATGATGATTAAATCCTTCGGGTCATCTGTCAGTCTTTCGAGAAAGA
65 ATCAATAAGCATTTCGAGCATGATAATTAAATCCTTCGGGACATCTGTCAG--TTTCGAGAAAGA
* * **
1148771 TGATAAGTCTATCGGGACATCTATAATACCTTTGGACAGAATGTTTTAACATGATTTAAAAAAAT
128 GGATAAGTCTATCGGGACATCTATAAGACCTTTCAACAGAATGTTTTAACATGATTTAAAAAAAT
* ** *
1148836 GAGAAAGCGATTTTCAAAGTTTCTCGTTTAGTATTTTCAGAAAAT-GAAACTTTT-AAAGAGTA
193 GAGAAAGCGATTTTCAAAGTTTCTCATTTAG-ATTGACAGAAAATAAAAACTTTTGAAA-AGTA
* * * *
1148898 AGAATGTGATTTCCAAAGCTTCTTACCCAGTAAACTATTTCCAAAATTGGAAAGTCCTTCGGGCC
1 AGAAAGCGATTTCCAAAG-TTCTTACACAGTAAACTATTTCCAAAATTGGAAAGTCCTTCAGGCC
* *
1148963 ATCAATAAGTC-TTTCGAGCATGATAATTAAATCCTTCGGGACATTTGTCAG-TTCGAGCAAGAG
65 ATCAATAAG-CATTTCGAGCATGATAATTAAATCCTTCGGGACATCTGTCAGTTTCGAGAAAGAG
* *
1149026 GATAAGTCGT-TCGGG-CTATCTATAAGACC-TTCAATCAGGATGTTTTCACATGATTTTAAAAA
129 GATAAGTC-TATCGGGAC-ATCTATAAGACCTTTCAA-CAGAATGTTTTAACATGA-TTT--AAA
*
1149088 AAAGATGAGAAAGCGATTTTCAAAGTTTCTCATTTA-ATGTGACAGAAAATAAAAATTTTTGAAA
188 AAA-ATGAGAAAGCGATTTTCAAAGTTTCTCATTTAGAT-TGACAGAAAATAAAAACTTTTGAAA
1149152 AGTA
251 AGTA
*
1149156 AGAAAGCGATTTCCAAAGTTTCTTACATAGTAAACTATTTCCAAAATTGGA
1 AGAAAGCGATTTCCAAAG-TTCTTACACAGTAAACTATTTCCAAAATTGGA
1149207 CCATCAGATG
Statistics
Matches: 269, Mismatches: 28, Indels: 23
0.84 0.09 0.07
Matches are distributed among these distances:
253 4 0.01
254 50 0.19
255 4 0.01
256 2 0.01
257 115 0.43
258 91 0.34
259 3 0.01
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (254 bp):
AGAAAGCGATTTCCAAAGTTCTTACACAGTAAACTATTTCCAAAATTGGAAAGTCCTTCAGGCCA
TCAATAAGCATTTCGAGCATGATAATTAAATCCTTCGGGACATCTGTCAGTTTCGAGAAAGAGGA
TAAGTCTATCGGGACATCTATAAGACCTTTCAACAGAATGTTTTAACATGATTTAAAAAAATGAG
AAAGCGATTTTCAAAGTTTCTCATTTAGATTGACAGAAAATAAAAACTTTTGAAAAGTA
Found at i:1149425 original size:44 final size:44
Alignment explanation
Indices: 1149362--1149865 Score: 463
Period size: 44 Copynumber: 11.6 Consensus size: 44
1149352 AACAAATTGA
*
1149362 AAGATGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * *
1149406 AAGATGAGTTAATCTTTAGTGTTGTTATTCTTGACTTTCTT-GTG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTT-TTCGTG
* * *
1149450 AAGAGGAGTCAATCTTTAGTGATGTCATTCTTAACTTTCTCGTG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * * * * * *
1149494 GAGAGAAGTCAACCTTTTAGTGATATCATTCTTGACTTTCTCATG
1 AAGAGGAGTCAATC-TTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * *
1149539 AAGAGGAGTTAATCTTTAGTGTTGCCATTCTTGACTTTTTTGTG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * * * *
1149583 AAGATGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCATG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
* *
1149627 AAGAGGAGTCAATCTTTAGTGATGTCATTCTTGAC--TTTC-TC
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * * **
1149668 ACGAAGAG---A--TTTAGTGGTGTTGTTCTTGACTTTCTT-GTG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTT-TTCGTG
* * * * * * *
1149707 GAGAGAAGTCAACCTTTTTGTGATGTCATTCTTGACTTTATAGTG
1 AAGAGGAGTCAATC-TTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * *
1149752 AAGAGGAGTCAATCTTTAGTGTTGTTATTCTTAACTTTTTCATG
1 AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
* * * * * *
1149796 AAGAGAAGTCGATATTTCAGTATTGTCA-ACTTGACTTTCTCGTG
1 AAGAGGAGTCAATCTTT-AGTGTTGTCATTCTTGACTTTTTCGTG
*
1149840 AAGAGGAATCAATCTTTTAGTGTTGT
1 AAGAGGAGTCAATC-TTTAGTGTTGT
1149866 TGTCGAAACA
Statistics
Matches: 367, Mismatches: 77, Indels: 32
0.77 0.16 0.07
Matches are distributed among these distances:
36 18 0.05
38 2 0.01
39 7 0.02
41 7 0.02
42 4 0.01
43 1 0.00
44 244 0.66
45 84 0.23
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (44 bp):
AAGAGGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTG
Found at i:1149614 original size:133 final size:132
Alignment explanation
Indices: 1149368--1149861 Score: 495
Period size: 133 Copynumber: 3.8 Consensus size: 132
1149358 TTGAAAGATG
* * * * **
1149368 AGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTGAAGATGAGTTAATCTTTAGTGTTGTTA
1 AGTCAATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTAGTGTTGCCA
* * *
1149433 TTCTTGACTTTCTTGTGAAGAGGAGTCAATCTTTAGTGATGTCATTCTTAACTTTCTCGTGGAGA
66 TTCTTGACTTTCTTGTGAAGAGGAGTCAATCTTTAGTGATATCATTCTTAACTTTCTCATGAAGA
1149498 GA
131 GA
* *
1149500 AGTCAACCTTTTAGTGATATCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTAGTGTTGCC
1 AGTCAATC-TTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTAGTGTTGCC
* * * * *
1149565 ATTCTTGACTTTTTTGTGAAGATGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCATGAAG
65 ATTCTTGACTTTCTTGTGAAGAGGAGTCAATCTTTAGTGATATCATTCTTAACTTTCTCATGAAG
*
1149630 AGG
130 AGA
* ** *
1149633 AGTCAATCTTTAGTGATGTCATTCTTGACTTTCTCACGAAGA-GA-TT--T-AGTGGTGTTG---
1 AGTCAATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTAGTGTTGCCA
* * * * * * *
1149690 TTCTTGACTTTCTTGTGGAGAGAAGTCAACCTTTTTGTGATGTCATTCTTGACTTTAT-AGTGAA
66 TTCTTGACTTTCTTGTGAAGAGGAGTCAATC-TTTAGTGATATCATTCTTAACTTTCTCA-TGAA
*
1149754 GAGG
129 GAGA
* * * * * ** * * *
1149758 AGTCAATCTTTAGTGTTGTTATTCTTAACTTTTTCATGAAGAGAAGTCGATATTTCAGTATTGTC
1 AGTCAATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTT-AGTGTTGCC
* * *
1149823 A-ACTTGACTTTCTCGTGAAGAGGAATCAATCTTTTAGTG
65 ATTCTTGACTTTCTTGTGAAGAGGAGTCAATC-TTTAGTG
1149862 TTGTTGTCGA
Statistics
Matches: 299, Mismatches: 51, Indels: 23
0.80 0.14 0.06
Matches are distributed among these distances:
124 27 0.09
125 66 0.22
126 1 0.00
127 8 0.03
128 1 0.00
129 1 0.00
130 3 0.01
131 7 0.02
132 39 0.13
133 146 0.49
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (132 bp):
AGTCAATCTTTAGTGATGTCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTAGTGTTGCCA
TTCTTGACTTTCTTGTGAAGAGGAGTCAATCTTTAGTGATATCATTCTTAACTTTCTCATGAAGA
GA
Found at i:1149760 original size:213 final size:216
Alignment explanation
Indices: 1149362--1149861 Score: 607
Period size: 213 Copynumber: 2.3 Consensus size: 216
1149352 AACAAATTGA
* * *
1149362 AAGATGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTTTCGTGAAGATGAGTTAATCTTTAGTG
1 AAGATGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTAGTG
* * * *
1149427 TTGTTATTCTTGACTTTCTTGTGAAGAGGAGTCAATCTTTAGTGATGTCATTCTTAACTTTCTCG
66 ATGTCATTCTTGACTTTC-T-TCAAGAAGAG--AA-CTTTAGTGATGTCATTCTTAACTTTCTCG
* *
1149492 TGGAGAGAAGTCAACCTTTTAGTGATATCATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTA
126 TGGAGAGAAGTCAACCTTTTAGTGATATCATTCTTGACTTTATCATGAAGAGGAGTCAATCTTTA
* **
1149557 GTGTTGCCATTCTTGACTTTTTTGTG
191 GTGTTGCCATTCTTAACTTTTTCATG
* * *
1149583 AAGATGAGTCAATCTTTAGTGTTATTATTCTTGACTTTCTCATGAAGAGGAGTCAATCTTTAGTG
1 AAGATGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTAGTG
* * ** * *
1149648 ATGTCATTCTTGACTTTC-TCACGAAGAG-A-TTTAGTGGTGTTGTTCTTGACTTTCTTGTGGAG
66 ATGTCATTCTTGACTTTCTTCAAGAAGAGAACTTTAGTGATGTCATTCTTAACTTTCTCGTGGAG
* *
1149710 AGAAGTCAACCTTTTTGTGATGTCATTCTTGACTTTAT-AGTGAAGAGGAGTCAATCTTTAGTGT
131 AGAAGTCAACCTTTTAGTGATATCATTCTTGACTTTATCA-TGAAGAGGAGTCAATCTTTAGTGT
**
1149774 TGTTATTCTTAACTTTTTCATG
195 TGCCATTCTTAACTTTTTCATG
* * * * *
1149796 AAGA-GAAGTCGATATTTCAGTATTGTCA-ACTTGACTTTCTCGTGAAGAGGAATCAATCTTTTA
1 AAGATG-AGTCAATCTTT-AGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATC-TTTA
1149859 GTG
63 GTG
1149862 TTGTTGTCGA
Statistics
Matches: 242, Mismatches: 33, Indels: 15
0.83 0.11 0.05
Matches are distributed among these distances:
212 2 0.01
213 143 0.59
214 14 0.06
215 1 0.00
218 7 0.03
221 75 0.31
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (216 bp):
AAGATGAGTCAATCTTTAGTGTTGTCATTCTTGACTTTCTCGTGAAGAGGAGTCAATCTTTAGTG
ATGTCATTCTTGACTTTCTTCAAGAAGAGAACTTTAGTGATGTCATTCTTAACTTTCTCGTGGAG
AGAAGTCAACCTTTTAGTGATATCATTCTTGACTTTATCATGAAGAGGAGTCAATCTTTAGTGTT
GCCATTCTTAACTTTTTCATG
Found at i:1153379 original size:42 final size:41
Alignment explanation
Indices: 1153286--1153387 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 41
1153276 AAGGTTTTAT
* * * * *
1153286 AGATGGCCTGAAGGACTTATCATCTTGCTCTAAAGGCTTAC
1 AGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTAC
* *
1153327 AGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTAC
1 AGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGACTTAC
*
1153369 TGATGGCCCGAAGGACTTA
1 AGATGGCCCGAAGGACTTA
1153388 TAAATTGTGA
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 16 0.32
42 34 0.68
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (41 bp):
AGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGACTTAC
Found at i:1153672 original size:80 final size:81
Alignment explanation
Indices: 1153531--1153706 Score: 284
Period size: 80 Copynumber: 2.2 Consensus size: 81
1153521 CATCTTGCTC
*
1153531 TAAAGGCTTACAAATGACCCGAAGGATATTAAGCATCATACTCAAAAGACTTATTGATGGATTTG
1 TAAAGGCTTACAAATTACCCGAAGGATATTAAGCATCATACTCAAAAGACTTATTGATGGATTTG
1153596 CTTCACTACTCTTAGG
66 CTTCACTACTCTTAGG
* * * *
1153612 TGAAGGCTTACAAATTACCCGAAGGAT-TTAATCATCATGCTCGAAAGACTTATTGATGGATTTG
1 TAAAGGCTTACAAATTACCCGAAGGATATTAAGCATCATACTCAAAAGACTTATTGATGGATTTG
*
1153676 CTTCACTACTCTTCGG
66 CTTCACTACTCTTAGG
1153692 TAAAGGCTTA-AAATT
1 TAAAGGCTTACAAATT
1153707 GATTTGCTTC
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
79 5 0.06
80 58 0.66
81 25 0.28
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (81 bp):
TAAAGGCTTACAAATTACCCGAAGGATATTAAGCATCATACTCAAAAGACTTATTGATGGATTTG
CTTCACTACTCTTAGG
Found at i:1153717 original size:37 final size:37
Alignment explanation
Indices: 1153666--1153816 Score: 205
Period size: 37 Copynumber: 4.1 Consensus size: 37
1153656 AAGACTTATT
*
1153666 GATGGATTTGCTTCACTACTCTTC-GGTAAAGGCTTAA
1 GATGGATTTGCTTCACTACTC-TCAGGTGAAGGCTTAA
* * *
1153703 AATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCAGGTGAAGGCTTAA
* *
1153740 GATGGATTTGCTTCACTATTCTCAGATGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCAGGTGAAGGCTTAA
* * *
1153777 GATGGAATTGCTTCACTACTTTCCGGTGAAGGCTTAA
1 GATGGATTTGCTTCACTACTCTCAGGTGAAGGCTTAA
1153814 GAT
1 GAT
1153817 TGCCCTGAGG
Statistics
Matches: 101, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 2 0.02
37 99 0.98
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (37 bp):
GATGGATTTGCTTCACTACTCTCAGGTGAAGGCTTAA
Found at i:1153917 original size:37 final size:37
Alignment explanation
Indices: 1153876--1155458 Score: 1150
Period size: 37 Copynumber: 42.5 Consensus size: 37
1153866 CTTCACTACT
* * **
1153876 GCTTAAGATTGAGTTGCTTCACTACTCTTTGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1153913 GCTTAAGATTGATTTGCTTCACTATTCTCAGGAGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
** * *
1153950 GCTTTAAGACGGA-TTGCTTCACTACTCTTCGGTGAAG
1 GC-TTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * **
1153987 GCTTAAGATGGA-TTGCTTCACTAATCTCTAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1154023 GCTTAAGATTGATTTTCTTCACTATTCTCAGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
**
1154060 GCTTAAGA-TGATTTGCTTCACTATTCTCAAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
** * ** * * *
1154096 GCTTACCATTGCCCTGAGGACTTAATCATCATGCT-CGGATGACTG
1 GCTTAAGATTG--AT-TTG-CTTCA-C-T-ATTCTCCGG-TGA-AG
* * * * * *
1154141 AC-T-A-ATGGATTTGTTTTACTACTCTTCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1154175 GCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
** * *
1154212 GCTTTAAGACGGA-TTGCTTCACTACTCTTCGGTGAAG
1 GC-TTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * ** *
1154249 GCTTAAGATGGA-TTGCTTCACTAATCTCTAGTGAAA
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
*
1154285 GCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* **
1154322 GCTTAAGATGGATTTGCTTCACTATTCTCATGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * * *
1154359 GCTTAAGATTGCCTTGAGGACTTAATCATCATGCT-C-G-GAAG
1 GCTTAAGATTG-ATT--TG-CTTCA-C-T-ATTCTCCGGTGAAG
* * * *
1154400 GCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAG
1 GCTTA-AGATTGATTTGCTTCACTATTCTCCGGTGAAG
* **
1154438 GCTTAAAATTGATTTGCTTCACTATTCTCAAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * * *
1154475 GCTTTAGATGGTTTTGCTTCACTATTCTCCAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * *
1154512 GCTTTAGATTGA-TTGCTTCACTACTCTTCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * * ** **
1154548 GCTTCATATTGATATGCTTCACTCCTCTTTGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
** * *
1154585 GCTTAAGATT-ACCCTGAGGACTTAATCATCATGCT-C-G-GAAG
1 GCTTAAGATTGA---T-TTG-CTTCA-C-T-ATTCTCCGGTGAAG
** * * * *
1154626 GCTTGCTGATGGATTTGCTTCACTACTCTTCGGTAAAG
1 GCTT-AAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1154664 GCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1154701 GCTTAAGATGGATTTGCTTCACTATTCTCAGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
*** ** * * *
1154738 GCTTAAGATTGCCCTGAGT-ACTTAATCATCATGCTCGGAAG
1 GCTTAAGATTGATTTGCTTCAC-TATTC-TC-CGGT--GAAG
* *
1154779 TCTTACTA-ATGGA-TTGCTTCACTATTCTCCGGTGAAG
1 GCTTA--AGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * *
1154816 GCTTAGGA-TGGTTTGCTTCACTATTCTCCAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * * * **
1154852 GCTTAGGA-TGGTTTACTTCACTACTCTTTGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
*
1154888 GATTAAGATTGA-TTGCTTCACTATTCTCCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1154924 GCTTAAGATGGTTTTGCTTCACTATTCTCCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * * * *
1154961 GCTTTAGATGGTTTTGCTTCACTATTCTCTGATGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
** * *
1154998 GCTTAAGATTGCACTGAGGACTTAATCATCATGCT-C-G-GAAG
1 GCTTAAGATTG-A-T-TTG-CTTCA-C-T-ATTCTCCGGTGAAG
* **
1155039 GCTTACTA-ATGGATTTGCTTCACTATTCTATGGTGAAG
1 GCTTA--AGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1155077 GCTTAAGA-TGGTTTGCTTCACTATTCTCCAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * *
1155113 GCTTAAGA-TGGTTTGCTTCACTACTCTTCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * *
1155149 GCTTAAGATTGA-TTGCTTCATTATTCTCCAGTAAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1155185 GCTTCAGATTG-TTTGCTTCACTACTC-CTCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTC-CGGTGAAG
1155221 GCTTAAGATTGA-TTGCTTCACTATTCAT-CGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTC-TCCGGTGAAG
* * *
1155257 GCTTAAGATGGTTTTGCTTCACTATTCTCCAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
** * * *
1155294 ATTTTAGATGGTTTTGCTTCACTATTCTCCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * * *
1155331 GCTTTAGATTGA-TTGCTTCACTACTCTTCGATGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* *
1155367 GCTGAAGATTG-TTTGCTTCACTATTCTCCAGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
* * ** *
1155403 GCTTCAGATTGATCTGCTTCACTCCTCTTCGGTGAAG
1 GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
1155440 GCTTAAGATTGACTTTGCT
1 GCTTAAGATTGA-TTTGCT
1155459 CCAATCTCAT
Statistics
Matches: 1229, Mismatches: 238, Indels: 157
0.76 0.15 0.10
Matches are distributed among these distances:
34 2 0.00
35 19 0.02
36 458 0.37
37 553 0.45
38 64 0.05
39 11 0.01
40 10 0.01
41 60 0.05
42 24 0.02
43 8 0.01
44 18 0.01
45 2 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (37 bp):
GCTTAAGATTGATTTGCTTCACTATTCTCCGGTGAAG
Found at i:1154417 original size:226 final size:216
Alignment explanation
Indices: 1153876--1155448 Score: 1020
Period size: 226 Copynumber: 7.0 Consensus size: 216
1153866 CTTCACTACT
* * * *
1153876 GCTTAAGATTGAGTTGCTTCACTACTCT-TTGGTGAAGGCTTAAGATTGATTTGCTTCAC-T-AT
1 GCTTAAGATGGA-TTGCTTCACTATTCTCAT-GTGAAGGCTTAAGA-TGCTTTGCTTCACATCAT
* * * *
1153938 TCTCAGGAGAAGGCTTTAAGACGGA-TTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTG
63 GCTC--G-GAAGGC-TTATGATGGATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGATTGATTG
* * * *
1154002 CTTCACTAATC-TCTAGTGAAGGCTTAAGATTGATTTTCTTCACTATTCT-CAGGTGAAGGCTTA
123 CTTCACTACTCTTC-GGTGAAGGCTTAAGATGGA-TTGCTTCACTATTCTCCA-GTGAAGGCTTA
*
1154065 AGA-TGATTTGCTTCACTATTC-TCAAGTGAAG
185 AGATTGATTTGCTTCACTATTCTTC-GGTGAAG
** *** *** * * * * * * *
1154096 GCTTACCATTGCCCTG-AGGACTTAATCATCATGCTCGGATGACTGACTA-ATGGATTTGTTTTA
1 GCTTAAGA-TGGATTGCTTCAC-TATTC-TCATG-T--GAAGGCTTA--AGAT-GCTTTGCTTCA
** * *
1154159 C-T-ACT-CTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGA
57 CATCA-TGC-TC-G-GAAGGCTTATGATGGATTTGCTTCACTACTCTC-GGTGAAGGC-TTAAGA
** * * *
1154221 CGGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCTAGTGAAAG
116 TTGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTATTCTCCAGTGAAGG
1154286 CTTAAGATTGATTTGCTTCACTATTC-TCAGGTGAAG
181 CTTAAGATTGATTTGCTTCACTATTCTTC-GGTGAAG
* *
1154322 GCTTAAGATGGATTTGCTTCACTATTCTCATGTGAAGGCTTAAGATTGCCTTGAGGACTTAATCA
1 GCTTAAGATGGA-TTGCTTCACTATTCTCATGTGAAGGCTTAAGA-TG-CTT--TG-CTTCA-CA
*
1154387 TCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATT
59 TCATGCTCGGAAGGCTTA-TGATGGATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGATTGA-T
* * * *
1154452 TGCTTCACTATTC-TCAAGTGAAGGCTTTAGATGGTTTTGCTTCACTATTCTCCAGTGAAGGCTT
121 TGCTTCACTACTCTTC-GGTGAAGGCTTAAGATGG-ATTGCTTCACTATTCTCCAGTGAAGGCTT
* *
1154516 TAGATTGA-TTGCTTCACTACTCTTCGGTGAAG
184 AAGATTGATTTGCTTCACTATTCTTCGGTGAAG
* * * ** * * ** *
1154548 GCTTCATATTGATATGCTTCACTCCTCT-TTGGTGAAGGCTTAAGATTACCCTGAGGACTTAATC
1 GCTTAAGATGGAT-TGCTTCACTATTCTCAT-GTGAAGGCTTAAGA-T--GCT-TTG-CTTCA-C
* * *
1154612 ATCATGCTCGGAAGGCTTGCTGATGGATTTGCTTCACTACTCTTCGGTAAAGGCTTAAAATTGAT
58 ATCATGCTCGGAAGGCTT-ATGATGGATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGATTGA-
*
1154677 TTGCTTCACTATTC-TCAGGTGAAGGCTTAAGATGGATTTGCTTCACTATTCT-CAGGTGAAGGC
120 TTGCTTCACTACTCTTC-GGTGAAGGCTTAAGATGGA-TTGCTTCACTATTCTCCA-GTGAAGGC
*** ** * * *
1154740 TTAAGATTGCCCTGAGT-ACTTAATCATCATGCTCGGAAG
182 TTAAGATTGATTTGCTTCAC-TATTCTTC--GGT--GAAG
* ** * * *
1154779 TCTTACTA-ATGGATTGCTTCACTATTCTCCGGTGAAGGCTTAGGATGGTTTGCTTCAC-T-ATT
1 GCTTA--AGATGGATTGCTTCACTATTCTCATGTGAAGGCTTAAGATGCTTTGCTTCACATCATG
* * * *
1154841 CTCCAGTGAAGGCTTAGGATGG-TTTACTTCACTACTCTTTGGTGAAGGATTAAGATTGATTGCT
64 CT-C-G-GAAGGCTTATGATGGATTTGCTTCACTACTC-TCGGTGAAGGCTTAAGATTGATTGCT
* * * * *
1154905 TCACTATTCTCCGGTGAAGGCTTAAGATGGTTTTGCTTCACTATTCTCCGGTGAAGGCTTTAGAT
125 TCACTACTCTTCGGTGAAGGCTTAAGATGG-ATTGCTTCACTATTCTCCAGTGAAGGCTTAAGAT
* * *
1154970 GGTTTTGCTTCACTATTC-TCTGATGAAG
189 TGATTTGCTTCACTATTCTTC-GGTGAAG
* * *** * *
1154998 GCTTAAGATTGCACTG-AGGACTTAATCATCATGCTCGGAAGGCTTACTA-ATGGATTTGCTTCA
1 GCTTAAGA-TGGATTGCTTCAC-TATTC-TCATG-T--GAAGGCTTA--AGAT-GCTTTGCTTCA
* * * * *
1155061 CTATTCTATGGT--GAAGGCTTAAGATGG-TTTGCTTCACTATTCTCCAGTGAAGGCTTAAGATG
57 C-A-TC-ATGCTCGGAAGGCTTATGATGGATTTGCTTCACTACTCT-CGGTGAAGGCTTAAGATT
* * * *
1155123 GTTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTGCTTCATTATTCTCCAGTAAAGGCT
118 GATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTATTCTCCAGTGAAGGCT
* * *
1155188 TCAGATTG-TTTGCTTCACTACTCCTCGGTGAAG
183 TAAGATTGATTTGCTTCACTATTCTTCGGTGAAG
* * * *
1155221 GCTTAAGATTGATTGCTTCACTATTCATC-GGTGAAGGCTTAAGATGGTTTTGCTTCAC-T-ATT
1 GCTTAAGATGGATTGCTTCACTATTC-TCATGTGAAGGCTTAAGAT-GCTTTGCTTCACATCATG
* * * * *
1155283 CTCCAGTGAA-GATTTTAGATGGTTTTGCTTCACTATTCTCCGGTGAAGGCTTTAGATTGATTGC
64 CT-C-G-GAAGGCTTAT-GATGGATTTGCTTCACTACTCT-CGGTGAAGGCTTAAGATTGATTGC
* * * * *
1155347 TTCACTACTCTTCGATGAAGGCTGAAGATTGTTTGCTTCACTATTCTCCAGTGAAGGCTTCAGAT
124 TTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTATTCTCCAGTGAAGGCTTAAGAT
* **
1155412 TGATCTGCTTCACTCCTCTTCGGTGAAG
189 TGATTTGCTTCACTATTCTTCGGTGAAG
1155440 GCTTAAGAT
1 GCTTAAGAT
1155449 TGACTTTGCT
Statistics
Matches: 1092, Mismatches: 174, Indels: 175
0.76 0.12 0.12
Matches are distributed among these distances:
212 3 0.00
214 1 0.00
216 4 0.00
217 23 0.02
218 111 0.10
219 50 0.05
220 17 0.02
221 10 0.01
222 24 0.02
223 112 0.10
224 91 0.08
225 194 0.18
226 348 0.32
227 56 0.05
228 4 0.00
229 2 0.00
230 4 0.00
231 32 0.03
232 5 0.00
233 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (216 bp):
GCTTAAGATGGATTGCTTCACTATTCTCATGTGAAGGCTTAAGATGCTTTGCTTCACATCATGCT
CGGAAGGCTTATGATGGATTTGCTTCACTACTCTCGGTGAAGGCTTAAGATTGATTGCTTCACTA
CTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTATTCTCCAGTGAAGGCTTAAGATTGATTTG
CTTCACTATTCTTCGGTGAAG
Found at i:1154478 original size:263 final size:262
Alignment explanation
Indices: 1153889--1154593 Score: 1081
Period size: 263 Copynumber: 2.7 Consensus size: 262
1153879 TAAGATTGAG
* * *
1153889 TTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGAGAAGGCTT
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTT
1153954 TAAGACGGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCTAGT
66 TAAGACGGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCTAGT
*
1154019 GAAGGCTTAAGATTGATTTTCTTCACTATTCTCAGGTGAAGGCTTAAGATGATTTGCTTCACTAT
131 GAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATGATTTGCTTCACTAT
* *
1154084 TCTCAAGTGAAGGCTTACCATTGCCCTGAGGACTTAATCATCATGCTCGGATGACTGACTAATGG
196 TCTCAAGTGAAGGCTTAACATTGCCCTGAGGACTTAATCATCATGCTCGGAAGACTGACTAATGG
1154149 AT
261 AT
* *
1154151 TTGTTTTACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTT
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTT
1154216 TAAGACGGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCTAGT
66 TAAGACGGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCTAGT
*
1154281 GAAAGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATGGATTTGCTTCACTA
131 GAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGAT-GATTTGCTTCACTA
* * * * * *
1154346 TTCTCATGTGAAGGCTTAAGATTGCCTTGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATG
195 TTCTCAAGTGAAGGCTTAACATTGCCCTGAGGACTTAATCATCATGCTCGGAAGACTGACTAATG
1154411 GAT
260 GAT
*
1154414 TTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAAGTGAAGGCTT
1 TTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTT
* * * * * * * * *
1154479 T-AGATGGTTTTGCTTCACTATTCTCCAGTGAAGGCTTTAGATTGATTGCTTCACTACTCT-TCG
66 TAAGACGG-ATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCT-A
* * * ** **
1154542 GTGAAGGCTTCATATTGATATGCTTCACTCCTCTTTGGTGAAGGCTTAAGAT
129 GTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGAT
1154594 TACCCTGAGG
Statistics
Matches: 405, Mismatches: 35, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
262 179 0.44
263 226 0.56
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (262 bp):
TTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGGCTT
TAAGACGGATTGCTTCACTACTCTTCGGTGAAGGCTTAAGATGGATTGCTTCACTAATCTCTAGT
GAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATGATTTGCTTCACTAT
TCTCAAGTGAAGGCTTAACATTGCCCTGAGGACTTAATCATCATGCTCGGAAGACTGACTAATGG
AT
Found at i:1154680 original size:263 final size:256
Alignment explanation
Indices: 1153670--1155375 Score: 967
Period size: 263 Copynumber: 6.6 Consensus size: 256
1153660 CTTATTGATG
* * * ** *
1153670 GATTTGCTTCACTACTCTTC-GGTAAAGGC-TTAAAATTGATTTGCTTCACTATTC-TCAGGTGA
1 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTTAAGACGGA-TTGCTTCACTACTCTTCA-GTGA
* *
1153732 AGGCTTAAGATGGATTTGCTTCACTATTCTC-AGATGAAGGCTTAAGATGGA-ATTGCTTCACTA
63 AGGCTTAAGATGGA-TTGCTTCACTAATCTCTAG-TGAAGGCTTAAGATTGATA-TGCTTCACTA
* * * *
1153795 CTTTCCGGTGAAGGCTTAAGATTGCCCTG-AGGACTTAATCATCATGCTCGGAAGGCTTGCTGAT
125 CTCTCAGGTGAAGGCTTAAGA-TGACCTGCAGCAC-TAATC-TCATG-T--GAAGGCTTGCTGAT
* * * *
1153859 GGATTTGCTTCACT-A-CT------GCTTA-AGATTGAGTTGCTTCACTACTCTTTGGTGAAGGC
184 GGATTTGCTTCACTCATCTCGGAAGGCTTACAAATGGATTTGCTTCACTACTCTTCGGTGAAGGC
*
1153915 TTAAGATT
249 TTAAAATT
* *
1153923 GATTTGCTTCACTATTCTCAGGAGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCGGTGAAGG
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCAGTGAAGG
* * *
1153988 CTTAAGATGGATTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATTTTCTTCACTATTCTCA
66 CTTAAGATGGATTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATATGCTTCACTACTCTCA
** ** * * *
1154053 GGTGAAGGCTTAAGATGATTTGCTTCACTATTCTCAAGTGAAGGCTTACCATTGCCCTGA-GGAC
131 GGTGAAGGCTTAAGATGACCTGCAGCACTAATCTCATGTGAAGG-----C-TTG--CTGATGGAT
** * * * * * *
1154117 TT-AATCA-TCATGCTCGGATGACTGACTAATGGATTTGTTTTACTACTCTTCGGTGAAGGCTTA
188 TTGCTTCACTCAT-CTCGGAAGGCTTACAAATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1154180 AAATT
252 AAATT
*
1154185 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCGGTGAAGG
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCAGTGAAGG
* * *
1154250 CTTAAGATGGATTGCTTCACTAATCTCTAGTGAAAGCTTAAGATTGATTTGCTTCACTATTCTCA
66 CTTAAGATGGATTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATATGCTTCACTACTCTCA
** ** * ** ** *
1154315 GGTGAAGGCTTAAGATGGATTTGCTTCACTATTCTCATGTGAAGGCTT-AAGATTGCCTTGAGGA
131 GGTGAAGGCTTAAGAT-GACCTGCAGCACTAATCTCATGTGAAGGCTTGCTGA-TGGATT--TG-
* **
1154379 CTTAATCATCATGCTCGGAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
191 CTTCA-C-TCAT-CTCGGAAGGCTTACAAATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAA
1154444 AATT
253 AATT
* * * * *
1154448 GATTTGCTTCACTATTCTCAAGTGAAGGCTTT-AGATGGTTTTGCTTCACTATTCTCCAGTGAAG
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGG-ATTGCTTCACTACTCTTCAGTGAAG
* * * * * * *
1154512 GCTTTAGATTGATTGCTTCACTACTCT-TCGGTGAAGGCTTCATATTGATATGCTTCACTCCTCT
65 GCTTAAGATGGATTGCTTCACTAATCTCT-AGTGAAGGCTTAAGATTGATATGCTTCACTACTCT
** * *
1154576 TTGGTGAAGGCTTAAGATTACCCTG-AGGACTTAATCATCATGCTCGGAAGGCTTGCTGATGGAT
129 CAGGTGAAGGCTTAAGATGA-CCTGCAGCAC-TAATC-TCATG-T--GAAGGCTTGCTGATGGAT
* *
1154640 TTGCTTCACT-ACTCTTCGGTAAAGGCTTA-AAATTGATTTGCTTCACTATTC-TCAGGTGAAGG
188 TTGCTTCACTCA-TC-TCGG--AAGGCTTACAAATGGATTTGCTTCACTACTCTTC-GGTGAAGG
* *
1154702 CTTAAGATG
248 CTTAAAATT
* *** ** * *
1154711 GATTTGCTTCACTATTCTCAGGTGAAGGC-TTAAGATTGCCCTGAGT-ACTTAATCATCATGCTC
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGA-CGGATTGCTTCAC-TACTCTTCA-G-T-
* * ** * * *
1154774 GGAAGTCTTACTA-ATGGATTGCTTCACTATTCTCCGGTGAAGGCTTAGGA-TGGTTTGCTTCAC
61 -GAAGGCTTA--AGATGGATTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATATGCTTCAC
* * *** * ** * * * ** *
1154837 TATTCTCCA-GTGAAGGCTTAGGATGGTTTACTTCACTACTCT-TTGGTGAAGGATT-AAGATTG
123 TACTCT-CAGGTGAAGGCTTAAGATGACCTGCAGCACTAATCTCAT-GTGAAGGCTTGCTGATGG
* * * *
1154899 A-TTGCTTCACT-ATTCTCCGGTGAAGGCTTA-AGATGGTTTTGCTTCACTATTCTCCGGTGAAG
186 ATTTGCTTCACTCA-TCT-C-G-GAAGGCTTACAAATGGATTTGCTTCACTACTCTTCGGTGAAG
* * *
1154961 GCTTTAGATG
247 GCTTAAAATT
* * * * * * *** * *
1154971 GTTTTGCTTCACTATTCTCTGATGAAGGC-TTAAGATTGCACTG-AGGACTTAATCATCATGCTC
1 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGA-CGGATTGCTTCAC-TACTCTTCA-G-T-
* * * * *
1155034 GGAAGGCTTACTA-ATGGATTTGCTTCACTATTCTATGGTGAAGGCTTAAGA-TGGTTTGCTTCA
61 -GAAGGCTTA--AGATGGA-TTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATATGCTTCA
* *** ** * * ** *
1155097 CTATTCTCCA-GTGAAGGCTTAAGATGGTTTGCTTCACTACTCTTC-GGTGAAGGCTT-AAGATT
122 CTACTCT-CAGGTGAAGGCTTAAGATGACCTGCAGCACTAATC-TCATGTGAAGGCTTGCTGATG
* * * * *
1155159 GA-TTGCTTCA-TTATTCTCCAGTAAAGGCTT-CAGATTG-TTTGCTTCACTACTCCTCGGTGAA
185 GATTTGCTTCACTCA-TCT-C-G-GAAGGCTTACAAATGGATTTGCTTCACTACTCTTCGGTGAA
*
1155220 GGCTTAAGATT
246 GGCTTAAAATT
* * * *
1155231 GA-TTGCTTCACTATTCATC-GGTGAAGGC-TTAAGATGGTTTTGCTTCACTATTCTCCAGTGAA
1 GATTTGCTTCACTATTC-TCAGGTGAAGGCTTTAAGACGG-ATTGCTTCACTACTCTTCAGTGAA
** * * * ** *
1155293 GATTTTAGATGGTTTTGCTTCACTATTCTCCGGTGAAGGCTTTAGATTGAT-TGCTTCACTACTC
64 GGCTTAAGATGG-ATTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATATGCTTCACTACTC
* *
1155357 TTC-GATGAAGGCTGAAGAT
128 -TCAGGTGAAGGCTTAAGAT
1155376 TGTTTGCTTC
Statistics
Matches: 1194, Mismatches: 180, Indels: 157
0.78 0.12 0.10
Matches are distributed among these distances:
247 5 0.00
249 1 0.00
250 4 0.00
251 8 0.01
252 64 0.05
253 64 0.05
254 75 0.06
255 16 0.01
256 2 0.00
257 3 0.00
258 4 0.00
259 37 0.03
260 168 0.14
261 139 0.12
262 207 0.17
263 282 0.24
264 22 0.02
265 5 0.00
266 5 0.00
267 50 0.04
268 32 0.03
269 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.36
Consensus pattern (256 bp):
GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGGATTGCTTCACTACTCTTCAGTGAAGG
CTTAAGATGGATTGCTTCACTAATCTCTAGTGAAGGCTTAAGATTGATATGCTTCACTACTCTCA
GGTGAAGGCTTAAGATGACCTGCAGCACTAATCTCATGTGAAGGCTTGCTGATGGATTTGCTTCA
CTCATCTCGGAAGGCTTACAAATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATT
Found at i:1154761 original size:153 final size:153
Alignment explanation
Indices: 1154185--1155006 Score: 610
Period size: 153 Copynumber: 5.5 Consensus size: 153
1154175 GCTTAAAATT
* ** *
1154185 GATTTGCTTCACTATTCTCAGGTGAAGGCTTTAAGACGGA-TTGCTTCACTACTCTTC-GGTGAA
1 GATTTGCTTCACTATTCTCCGGTGAAGGC-TTAAGATTGATTTGCTTCACTATTC-TCAGGTGAA
* * * * *** *** *
1154248 GGCTTAAGATGGA-TTGCTTCACTAATCTCTAGTGAAAGCTTAAGATTGATTTGCTTCAC-TATT
64 GGCTTAAGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGCCCTG-AGGACTTAAT
* *
1154311 C-TCA-GGT--GAAGGCTTA-AGATG
128 CATCATGCTCGGAAGGCTTACTGATG
** ** *** * *
1154332 GATTTGCTTCACTATTCTCATGTGAAGGCTTAAGATTGCCTTG-AGGACTTAATCATCATGCTCG
1 GATTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATTGATTTGCTTCAC-TATTC-TCA-GGT--
* * * *** ***
1154396 GAAGGCTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAAATTGATTTGCTTCAC-
61 GAAGGCTTA-AGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGCCCTG-AGGACT
* *
1154460 TATTC-TCAAG-T--GAAGGCTT--TAGATG
124 TAATCATCATGCTCGGAAGGCTTACT-GATG
* * * *
1154485 GTTTTGCTTCACTATTCTCCAGTGAAGGCTTTAGATTGA-TTGCTTCACTACTCTTC-GGTGAAG
1 GATTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATTGATTTGCTTCACTATTC-TCAGGTGAAG
* * * * * *
1154548 GCTTCATATTGATATGCTTCACTCCTCTTTGGTGAAGGCTTAAGATTACCCTGAGGACTTAATCA
65 GCTTAAGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGCCCTGAGGACTTAATCA
*
1154613 TCATGCTCGGAAGGCTTGCTGATG
130 TCATGCTCGGAAGGCTTACTGATG
* * * *
1154637 GATTTGCTTCACTACTCTTCGGTAAAGGCTTAAAATTGATTTGCTTCACTATTCTCAGGTGAAGG
1 GATTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGG
* ** *
1154702 CTTAAGATGGATTTGCTTCACTATTCTCAGGTGAAGGCTTAAGATTGCCCTGAGTACTTAATCAT
66 CTTAAGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGCCCTGAGGACTTAATCAT
* *
1154767 CATGCTCGGAAGTCTTACTAATG
131 CATGCTCGGAAGGCTTACTGATG
* *
1154790 GA-TTGCTTCACTATTCTCCGGTGAAGGCTTAGGA-TGGTTTGCTTCACTATTCTCCA-GTGAAG
1 GATTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCT-CAGGTGAAG
* * * * * *
1154852 GCTTAGGATGG-TTTACTTCACTACTCTTTGGTGAAGGATTAAGATTG--AT--TG-CTTCA-C-
65 GCTTAAGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGCCCTGAGGACTTAATCA
* *
1154909 T-ATTCTCCGGTGAAGGCTTA-AGATG
130 TCATGCT-C-G-GAAGGCTTACTGATG
* * * * * *
1154934 GTTTTGCTTCACTATTCTCCGGTGAAGGCTTTAGATGGTTTTGCTTCACTATTCTCTGATGAAGG
1 GATTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGG
1154999 CTTAAGAT
66 CTTAAGAT
1155007 TGCACTGAGG
Statistics
Matches: 553, Mismatches: 95, Indels: 55
0.79 0.14 0.08
Matches are distributed among these distances:
142 4 0.01
143 2 0.00
144 6 0.01
145 43 0.08
146 41 0.07
147 78 0.14
148 13 0.02
149 3 0.01
150 33 0.06
151 51 0.09
152 82 0.15
153 196 0.35
154 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (153 bp):
GATTTGCTTCACTATTCTCCGGTGAAGGCTTAAGATTGATTTGCTTCACTATTCTCAGGTGAAGG
CTTAAGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATTGCCCTGAGGACTTAATCAT
CATGCTCGGAAGGCTTACTGATG
Found at i:1159581 original size:7 final size:7
Alignment explanation
Indices: 1159569--1159607 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
1159559 AACTACATGC
1159569 AATGCAA
1 AATGCAA
1159576 AATGCAA
1 AATGCAA
1159583 AATGCAA
1 AATGCAA
*
1159590 AATAC-A
1 AATGCAA
1159596 AATGC-A
1 AATGCAA
1159602 AATGCA
1 AATGCA
1159608 CGAGGTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 11 0.38
7 18 0.62
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.15
Consensus pattern (7 bp):
AATGCAA
Found at i:1159916 original size:21 final size:21
Alignment explanation
Indices: 1159875--1160013 Score: 151
Period size: 21 Copynumber: 6.8 Consensus size: 21
1159865 TCTTTATGAT
1159875 TGGTCTTCTCGT-CTT-TGAA
1 TGGTCTTCTCGTCCTTGTGAA
* *
1159894 TGATCATCTCGTCCTTGTGAA
1 TGGTCTTCTCGTCCTTGTGAA
* *
1159915 TGGCCTTCTCAT-CTT-TGAA
1 TGGTCTTCTCGTCCTTGTGAA
*
1159934 TGATCTTCTCGTCCTTGTGAA
1 TGGTCTTCTCGTCCTTGTGAA
* * *
1159955 TGGTCTTCTCATCTTTTTGAA
1 TGGTCTTCTCGTCCTTGTGAA
* * *
1159976 TGGTCTTTTCGTCTTTATGAA
1 TGGTCTTCTCGTCCTTGTGAA
1159997 TGGTCTTCTCGTCCTTG
1 TGGTCTTCTCGTCCTTG
1160014 GTATGACTAT
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
19 23 0.24
20 9 0.09
21 65 0.67
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (21 bp):
TGGTCTTCTCGTCCTTGTGAA
Found at i:1159988 original size:42 final size:40
Alignment explanation
Indices: 1159875--1160006 Score: 183
Period size: 40 Copynumber: 3.2 Consensus size: 40
1159865 TCTTTATGAT
* *
1159875 TGGTCTTCTCGTCTTTGAATGATCATCTCGTCCTTGTGAA
1 TGGTCTTCTCATCTTTGAATGATCTTCTCGTCCTTGTGAA
*
1159915 TGGCCTTCTCATCTTTGAATGATCTTCTCGTCCTTGTGAA
1 TGGTCTTCTCATCTTTGAATGATCTTCTCGTCCTTGTGAA
* * * *
1159955 TGGTCTTCTCATCTTTTTGAATGGTCTTTTCGTCTTTATGAA
1 TGGTCTTCTCATC--TTTGAATGATCTTCTCGTCCTTGTGAA
1159997 TGGTCTTCTC
1 TGGTCTTCTC
1160007 GTCCTTGGTA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
40 49 0.60
42 33 0.40
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (40 bp):
TGGTCTTCTCATCTTTGAATGATCTTCTCGTCCTTGTGAA
Found at i:1161799 original size:14 final size:14
Alignment explanation
Indices: 1161780--1161823 Score: 88
Period size: 14 Copynumber: 3.1 Consensus size: 14
1161770 TACAATGATA
1161780 TATCCAAATTTAAT
1 TATCCAAATTTAAT
1161794 TATCCAAATTTAAT
1 TATCCAAATTTAAT
1161808 TATCCAAATTTAAT
1 TATCCAAATTTAAT
1161822 TA
1 TA
1161824 GGCGTTATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TATCCAAATTTAAT
Found at i:1164374 original size:45 final size:45
Alignment explanation
Indices: 1164324--1164514 Score: 185
Period size: 45 Copynumber: 4.2 Consensus size: 45
1164314 GGGTATTACA
* * ** *
1164324 GTTGTCTTTTTTGACTTTCTCGCGAAGATGAGTTAATCTTTTAGT
1 GTTGTCATTCTTGACTTTCTCGTAAAGATGAGTCAATCTTTTAGT
* * *
1164369 GTTGTC-TTCCTTGACTTTCTCGTAAAAAGGAGTCAATCTTTCAGT
1 GTTGTCATT-CTTGACTTTCTCGTAAAGATGAGTCAATCTTTTAGT
* *
1164414 ATTGTCATTCTTGACTTTCTCGTGAAGA-GAAGTCAAT-TTTTCAGT
1 GTTGTCATTCTTGACTTTCTCGTAAAGATG-AGTCAATCTTTT-AGT
*
1164459 GTTGTGATTCTTGACTTTCTCAG-AAAGATGAGTC-ATCATTTTAGT
1 GTTGTCATTCTTGACTTTCTC-GTAAAGATGAGTCAATC-TTTTAGT
* *
1164504 GATGACATTCT
1 GTTGTCATTCT
1164515 CAACTTGACT
Statistics
Matches: 121, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
44 8 0.07
45 105 0.87
46 8 0.07
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.43
Consensus pattern (45 bp):
GTTGTCATTCTTGACTTTCTCGTAAAGATGAGTCAATCTTTTAGT
Found at i:1164579 original size:51 final size:51
Alignment explanation
Indices: 1164511--1164630 Score: 170
Period size: 51 Copynumber: 2.4 Consensus size: 51
1164501 AGTGATGACA
** *
1164511 TTCTCAACTTGACTTTCTTGCAGAGAGGAGTCAACTTTTCAG-TAGTATCCT
1 TTCTCAACTTGACTTTCTCACAGAGAGGAGTCAACTTTTCAGAT-GTATCAT
*
1164562 TTCTCAACTTGATTTTCTCACAGAGAGGAGTCAACTTTTCAGATGTATCAT
1 TTCTCAACTTGACTTTCTCACAGAGAGGAGTCAACTTTTCAGATGTATCAT
* *
1164613 TCCTCAAGTTGACTTTCT
1 TTCTCAACTTGACTTTCT
1164631 AGTGTAGAGA
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 60 0.98
52 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (51 bp):
TTCTCAACTTGACTTTCTCACAGAGAGGAGTCAACTTTTCAGATGTATCAT
Found at i:1164645 original size:51 final size:48
Alignment explanation
Indices: 1164509--1164651 Score: 128
Period size: 51 Copynumber: 2.8 Consensus size: 48
1164499 TTAGTGATGA
1164509 CATTCTCAACTTGACTTTCT-TGCAGAGAGGAGTCAACTTTTCAGTAGTAT
1 CATTCTCAACTTGACTTTCTATG-AGAGA--AGTCAACTTTTCAGTAGTAT
* * * *
1164559 CCTTTCTCAACTTGATTTTCTCACAGAGAGGAGTCAACTTTTCAG-ATGTAT
1 -CATTCTCAACTTGACTTTCT-A-TGAGAGAAGTCAACTTTTCAGTA-GTAT
*
1164610 CATTCCTCAAGTTGACTTTCTAGTGTAGAGAAGTCAAACTTT
1 CATT-CTCAACTTGACTTTCTA-TG-AGAGAAGTC-AACTTT
1164652 CTGTAATGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
50 6 0.08
51 58 0.77
52 6 0.08
53 4 0.05
54 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (48 bp):
CATTCTCAACTTGACTTTCTATGAGAGAAGTCAACTTTTCAGTAGTAT
Found at i:1165489 original size:134 final size:134
Alignment explanation
Indices: 1165262--1165852 Score: 726
Period size: 134 Copynumber: 4.4 Consensus size: 134
1165252 AGATAAGAGG
* * * * * * **
1165262 AGCAAATCATGTACGACTCAATCTTCCCTAAAGAACAAAGAAGTGGATCAAAATTTTCTCGAGTC
1 AGCAAATCAAGTTCGATTCAATCTTCGCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTC
* *
1165327 TGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTATTCTTTTAGATTTGGTCTTCCTGAAGAGCA
66 TGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCA
1165392 GTGA
131 GTGA
*
1165396 AGCAAATCAAGTTTGATTCAATCTTTC-CTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGT
1 AGCAAATCAAGTTCGATTCAATC-TTCGCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGT
* * *
1165460 CTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTCTCCTTTCAGATTTGGTCTTCTTGAAGAGC
65 CTGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGC
*
1165525 AGAGA
130 AGTGA
* * * * * *
1165530 AGCAAATCAAGATCGATTCGATCTTCGCTGAAGAGCAGCGAAATGAATCAAAATTTTATCGTGTC
1 AGCAAATCAAGTTCGATTCAATCTTCGCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTC
*
1165595 TGATCTCCCCTAAAGAGTAGTGGAGCATATT-TTCTTTCTTTCAGATTTGGTCTTCCTGAAGAGC
66 TGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTT-TTTCTTTCAGATTTGGTCTTCCTGAAGAGC
*
1165659 AGCGA
130 AGTGA
* * * * * * **
1165664 AGCAAATCACGTCCGATTCAATCTTCTCTAAAGAGCAGTGAAGTGGATTAATTTTTTCTCGAGTC
1 AGCAAATCAAGTTCGATTCAATCTTCGCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTC
* * * * **
1165729 TGATCT-CCCTAAAGAGTAGTTGG-GGAGATTCTTTTTCTTTCATATTTGGTATTCTTGAAGATT
66 TGATCTCCCCTAAAGAGTAG-TGGAGCAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGC
*
1165792 AGTGC
130 AGTGA
* * * *
1165797 AGTAAATCAAATTTGATTCAATCTTC-CTTGAAGAGCAGC-AAGTGGATCAAATTTTT
1 AGCAAATCAAGTTCGATTCAATCTTCGC-TGAAGAGCAGCGAAGTGGATCAAAATTTT
1165853 TTCCAGATCT
Statistics
Matches: 394, Mismatches: 57, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
132 16 0.04
133 81 0.21
134 294 0.75
135 3 0.01
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.32
Consensus pattern (134 bp):
AGCAAATCAAGTTCGATTCAATCTTCGCTGAAGAGCAGCGAAGTGGATCAAAATTTTCTCGAGTC
TGATCTCCCCTAAAGAGTAGTGGAGCAGATTCTTTTTCTTTCAGATTTGGTCTTCCTGAAGAGCA
GTGA
Found at i:1168036 original size:3 final size:3
Alignment explanation
Indices: 1168028--1168074 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
1168018 TGTCCAAAAT
* *
1168028 TTA TTA TTA TTA TTA TTA TTA TTT TTA GTTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
1168074 T
1 T
1168075 AAGTAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 37 0.95
4 2 0.05
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1170188 original size:26 final size:26
Alignment explanation
Indices: 1170153--1170213 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
1170143 TAGTAATATT
1170153 TTTATTTTATTTTTATAATATTCTAA
1 TTTATTTTATTTTTATAATATTCTAA
1170179 TTTATTTTATTTTTATAATATTCTAA
1 TTTATTTTATTTTTATAATATTCTAA
1170205 TTTATTTTA
1 TTTATTTTA
1170214 GAGAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATTTTATTTTTATAATATTCTAA
Found at i:1170399 original size:20 final size:20
Alignment explanation
Indices: 1170376--1170500 Score: 171
Period size: 20 Copynumber: 6.2 Consensus size: 20
1170366 TGCGATTTTC
* *
1170376 CAAATTCACAACGCGATAGT
1 CAAATTCGCAACACGATAGT
*
1170396 CAAATTCGCAACACGAAAGT
1 CAAATTCGCAACACGATAGT
1170416 CAAATTCGCAACAC-ATAAGT
1 CAAATTCGCAACACGAT-AGT
*
1170436 CAAATTCGCAACACTATAGT
1 CAAATTCGCAACACGATAGT
*
1170456 CAAATTCGTAACACGATAGT
1 CAAATTCGCAACACGATAGT
* *
1170476 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACACGATAGT
1170496 CAAAT
1 CAAAT
1170501 GTTTTTACGC
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 91 0.97
21 2 0.02
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACACGATAGT
Found at i:1170653 original size:22 final size:22
Alignment explanation
Indices: 1170628--1170674 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
1170618 CTACGGCGAC
1170628 ATCCGTCCACATCTCCGACGAA
1 ATCCGTCCACATCTCCGACGAA
* *
1170650 ATCCGTCCCCATTTCCGACGAA
1 ATCCGTCCACATCTCCGACGAA
1170672 ATC
1 ATC
1170675 AGTTTATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.40, G:0.13, T:0.21
Consensus pattern (22 bp):
ATCCGTCCACATCTCCGACGAA
Found at i:1170910 original size:13 final size:13
Alignment explanation
Indices: 1170892--1170923 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1170882 AGTATTTGTC
*
1170892 TTTGTTTTGTCTT
1 TTTGTTTTATCTT
1170905 TTTGTTTTATCTT
1 TTTGTTTTATCTT
1170918 TTTGTT
1 TTTGTT
1170924 GAAGAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.03, C:0.06, G:0.12, T:0.78
Consensus pattern (13 bp):
TTTGTTTTATCTT
Found at i:1170992 original size:19 final size:20
Alignment explanation
Indices: 1170952--1170994 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1170942 AACACCAAAT
1170952 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
*
1170972 TCGCAACGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
1170991 TCGC
1 TCGC
1170995 GTTGCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.44, C:0.26, G:0.19, T:0.12
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:1172748 original size:21 final size:21
Alignment explanation
Indices: 1172724--1172773 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
1172714 GTTAGGGGAA
*
1172724 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTACT
*
1172745 TTACGTCATGAGGTCGGTACT
1 TTACGTGATGAGGTCGGTACT
1172766 TTACGTGA
1 TTACGTGA
1172774 AGATAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.18, C:0.16, G:0.32, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTACT
Found at i:1173005 original size:4 final size:4
Alignment explanation
Indices: 1172996--1173037 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
1172986 TTTTTCGGCA
* *
1172996 TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1173038 TCAGCGGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:1173228 original size:21 final size:21
Alignment explanation
Indices: 1173181--1173276 Score: 61
Period size: 21 Copynumber: 4.6 Consensus size: 21
1173171 GATGCACCTA
**
1173181 TCATCATTCAAGAGGCATC-T
1 TCATCATTCAAGAGGCCCCTT
*
1173201 CCTATCATTCAAGAGGCCCCTT
1 TC-ATCATTCAAGAGGCCCCTT
** *
1173223 TCATCA-TCAAAGAATCCCCTC
1 TCATCATTC-AAGAGGCCCCTT
* * * *
1173244 CCACCGTTCAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTT
*
1173265 TCATCGTTCAAG
1 TCATCATTCAAG
1173277 TGATCCCGAC
Statistics
Matches: 57, Mismatches: 15, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
20 3 0.05
21 50 0.88
22 4 0.07
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.25
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTT
Found at i:1174674 original size:61 final size:65
Alignment explanation
Indices: 1174606--1174743 Score: 169
Period size: 66 Copynumber: 2.2 Consensus size: 65
1174596 TTATACATTG
1174606 AAAGTTGATTTG-TTACAATTGATGAGGAAATAAG-A-T-TTATTTT-TTGATTAATTGATTTGT
1 AAAGTTGATTTGTTTA-AATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGT
1174666 A
65 A
* ** * * *
1174667 AAAGTTGATTTGTTTAATTTGATTTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAAATTGATGAGGAAATAAGAATTATTATTTT-CTTGATTAATTGATTTGT
1174732 A
65 A
1174733 AAAGTTGATTT
1 AAAGTTGATTT
1174744 ATTGTTTCTA
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
61 26 0.40
62 4 0.06
63 1 0.02
64 6 0.09
66 28 0.43
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAAATTGATGAGGAAATAAGAATTATTATTTTCTTGATTAATTGATTTGTA
Found at i:1174676 original size:14 final size:14
Alignment explanation
Indices: 1174657--1174696 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1174647 TTTTGATTAA
1174657 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
1174671 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
1174685 TTGATTTGTAAA
1 TTGATTTGTAAA
1174697 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1174876 original size:20 final size:20
Alignment explanation
Indices: 1174853--1174891 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1174843 TTCGGTTTAT
1174853 GAATTTGACTTTCGCGTTGC
1 GAATTTGACTTTCGCGTTGC
1174873 GAATTTGACTTTCGCGTTG
1 GAATTTGACTTTCGCGTTG
1174892 ATCGCAACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.18, G:0.26, T:0.41
Consensus pattern (20 bp):
GAATTTGACTTTCGCGTTGC
Found at i:1175119 original size:39 final size:39
Alignment explanation
Indices: 1175065--1175151 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1175055 TCAAGTTATA
*
1175065 GATTTTGATTTCCTTTTGCTTGGCACTATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
1175104 GATTTTGATTTCCTTTTTCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1175143 GATTTTGAT
1 GATTTTGAT
1175152 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1175484 original size:18 final size:18
Alignment explanation
Indices: 1175461--1175497 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1175451 TGAAATTTAT
1175461 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
1175479 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
1175497 A
1 A
1175498 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:1175918 original size:25 final size:25
Alignment explanation
Indices: 1175884--1175933 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1175874 ATTATTTTTG
*
1175884 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1175909 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
1175934 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:1176386 original size:18 final size:18
Alignment explanation
Indices: 1176363--1176398 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1176353 AAGCCGGTTG
*
1176363 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
1176381 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
1176399 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1179604 original size:19 final size:20
Alignment explanation
Indices: 1179580--1179690 Score: 95
Period size: 20 Copynumber: 5.7 Consensus size: 20
1179570 ACTAAAACCT
1179580 GTTGCGAAATT-AAATTCGC
1 GTTGCGAAATTGAAATTCGC
* *
1179599 GTTGCGAATTTGAAATTC-A
1 GTTGCGAAATTGAAATTCGC
* *
1179618 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAAATT-GAAATTCGC
* *
1179638 GTTGCGAAATTGGAAACT-GG
1 GTTGCGAAATT-GAAATTCGC
* *
1179658 GTTGCAAAATTGGAATTCGC
1 GTTGCGAAATTGAAATTCGC
*
1179678 GTTGCGAATTTGA
1 GTTGCGAAATTGA
1179691 GATCGTGTTG
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
18 4 0.06
19 26 0.37
20 34 0.48
21 7 0.10
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (20 bp):
GTTGCGAAATTGAAATTCGC
Found at i:1179616 original size:20 final size:20
Alignment explanation
Indices: 1179580--1179708 Score: 97
Period size: 19 Copynumber: 6.6 Consensus size: 20
1179570 ACTAAAACCT
*
1179580 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
1179599 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
*
1179618 GTTGCG-ATTTACAAATTCGC
1 GTTGCGAATTT-GAAATTCGC
* * *
1179638 GTTGCGAAATTGGAAACT-GG
1 GTTGCG-AATTTGAAATTCGC
* * *
1179658 GTTGCAAAATTGGAATTCGC
1 GTTGCGAATTTGAAATTCGC
* *
1179678 GTTGCGAATTTGAGA-TCGT
1 GTTGCGAATTTGAAATTCGC
*
1179697 GTTGCAAATTTG
1 GTTGCGAATTTG
1179709 TTGGTCATTT
Statistics
Matches: 84, Mismatches: 20, Indels: 12
0.72 0.17 0.10
Matches are distributed among these distances:
18 4 0.05
19 43 0.51
20 30 0.36
21 4 0.05
22 3 0.04
ACGTcount: A:0.28, C:0.13, G:0.26, T:0.33
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:1193395 original size:20 final size:20
Alignment explanation
Indices: 1193355--1193393 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1193345 CATTGCAGGA
*
1193355 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCCACAAAAG
1193375 ATTTCATGGCCTCCACAAA
1 ATTT-ATGGCCTCCACAAA
1193394 GACCTTGATG
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:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
ATTTATGGCCTCCACAAAAG
Found at i:1201466 original size:16 final size:17
Alignment explanation
Indices: 1201445--1201478 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1201435 GTTTCAATCG
1201445 ACTAAA-AAGGATAGAC
1 ACTAAAGAAGGATAGAC
*
1201461 ACTAAAGTAGGATAGAC
1 ACTAAAGAAGGATAGAC
1201478 A
1 A
1201479 ACGCCTATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.12, G:0.21, T:0.15
Consensus pattern (17 bp):
ACTAAAGAAGGATAGAC
Found at i:1204398 original size:3 final size:3
Alignment explanation
Indices: 1204390--1204483 Score: 116
Period size: 3 Copynumber: 30.3 Consensus size: 3
1204380 TGTCCAAAAT
*
1204390 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
1204438 TTA GTTA TTA TTA TTAA TAA TAA TAA TTA TTAA CTA TTA TTA TTA T
1 TTA -TTA TTA TTA TT-A TTA TTA TTA TTA TT-A TTA TTA TTA TTA T
1204484 AAGTATAATA
Statistics
Matches: 82, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
3 75 0.91
4 7 0.09
ACGTcount: A:0.36, C:0.01, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:1206539 original size:28 final size:28
Alignment explanation
Indices: 1206508--1206582 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
1206498 AAAATGATAG
*
1206508 TAATATTTTTATTTTA-TTTTATTTTTTA
1 TAATA-TTCTATTTTATTTTTATTTTTTA
1206536 TAATATTCTATTTTATTTTTATTTTTTA
1 TAATATTCTATTTTATTTTTATTTTTTA
** * *
1206564 TTCTATTATATTTAATTTT
1 TAATATTCTATTTTATTTT
1206583 AGTATTGATG
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
27 9 0.22
28 32 0.78
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (28 bp):
TAATATTCTATTTTATTTTTATTTTTTA
Found at i:1206575 original size:33 final size:32
Alignment explanation
Indices: 1206514--1206583 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
1206504 ATAGTAATAT
*
1206514 TTTTATTTTATTTTATTTTTTATAATATTCT-A
1 TTTTATTTTATTTTATTTTCTATAATATT-TAA
*
1206546 TTTTATTTTTATTTT-TTATTCTATTATATTTAA
1 TTTTA-TTTTATTTTATT-TTCTATAATATTTAA
1206579 TTTTA
1 TTTTA
1206584 GTATTGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
32 8 0.24
33 25 0.76
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTATTTTATTTTATTTTCTATAATATTTAA
Found at i:1206588 original size:23 final size:23
Alignment explanation
Indices: 1206539--1206588 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1206529 TTTTTTATAA
* * *
1206539 TATTCTATTTTATTTTTATTTTT
1 TATTCTATTATATTTTAATTTTG
1206562 TATTCTATTATA-TTTAATTTTAG
1 TATTCTATTATATTTTAATTTT-G
1206585 TATT
1 TATT
1206589 GATGATGTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (23 bp):
TATTCTATTATATTTTAATTTTG
Found at i:1209589 original size:51 final size:51
Alignment explanation
Indices: 1209517--1209828 Score: 365
Period size: 51 Copynumber: 6.0 Consensus size: 51
1209507 AAAACTCAAA
** * *
1209517 CAATCTTCATA-AAACAAGTCCGTTCTCTATTCCTTCAGAGAGTATAGGACT
1 CAATCTTCA-ACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
* * *
1209568 AAATCTTCAACAAACGTGTCCGTTCCCTATTCCTTCAGAGAGTATATGACT
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
* * *
1209619 CAATCTTCAATCAAACGTGTCCGCTCCCTATTTCTTCAGAGAGTATATGAATT
1 CAATCTTCAA-CAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATA-GGACT
* ** * *
1209672 GAACAACCTTCAACAAACGTGTATGCTCCCTATTCCTCCAGAAAGTATAGGACT
1 ---CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
* * *
1209726 CAATCTTCAACAAATGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACT
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
* * * *
1209777 CAATCTTCAACAAACGTGTCTGCTCCATATTCTTTCAGAGAGTATAGAACT
1 CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
1209828 C
1 C
1209829 GAACAATAAT
Statistics
Matches: 225, Mismatches: 30, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
50 1 0.00
51 145 0.64
52 34 0.15
53 2 0.01
54 3 0.01
55 31 0.14
56 9 0.04
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (51 bp):
CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACT
Found at i:1209887 original size:52 final size:52
Alignment explanation
Indices: 1209821--1210256 Score: 737
Period size: 52 Copynumber: 8.4 Consensus size: 52
1209811 TCAGAGAGTA
1209821 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
*
1209873 TAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
* * *
1209925 TAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
* *
1209977 TAGAACTCGAACAATAATCTTCCTACGAGACTGTCCAATTTTCTTTAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
* * * * *
1210029 TAGAACTCGAAAAATAATCTTCCTACGGGTCTGCCCAATTTTCTTTAAGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
* *
1210081 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
1210133 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
* *
1210185 TAGAACTCGAACAATAATCTTCCTACGGGTCTGCCCAATTTTCTTCAGGGAC
1 TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
1210237 TAGAACTCGAACAATAATCT
1 TAGAACTCGAACAATAATCT
1210257 CCAACGATCG
Statistics
Matches: 362, Mismatches: 22, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 362 1.00
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.29
Consensus pattern (52 bp):
TAGAACTCGAACAATAATCTTCCTACGAGACTGCCCAATTTTCTTCAGGGAC
Found at i:1210367 original size:55 final size:55
Alignment explanation
Indices: 1210252--1210368 Score: 198
Period size: 55 Copynumber: 2.1 Consensus size: 55
1210242 CTCGAACAAT
* * * *
1210252 AATCTCCAACGATCGCGTCTGCCCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1210307 AATCTTCAACAATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
1210362 AATCTTC
1 AATCTTC
1210369 TTTTGCTTCA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 58 1.00
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (55 bp):
AATCTTCAACAATCACGTCTGCCCCCTATTTATTCAGAGAGTATAAGACTCGAAC
Found at i:1211680 original size:15 final size:14
Alignment explanation
Indices: 1211662--1211695 Score: 59
Period size: 15 Copynumber: 2.4 Consensus size: 14
1211652 TTTTTTTTTG
1211662 TTTTTTTCTTCTTCT
1 TTTTTTTCTTCTT-T
1211677 TTTTTTTCTTCTTT
1 TTTTTTTCTTCTTT
1211691 TTTTT
1 TTTTT
1211696 ATTTTTTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTCTTT
Found at i:1211685 original size:9 final size:9
Alignment explanation
Indices: 1211646--1211775 Score: 63
Period size: 9 Copynumber: 13.7 Consensus size: 9
1211636 CTTGAACCCC
1211646 CTTTTATTTT
1 CTTTT-TTTT
1211656 -TTTTTGTTT
1 CTTTTT-TTT
1211665 -TTTTCTTCTT
1 CTTTT-TT-TT
1211675 CTTTTTTTT
1 CTTTTTTTT
1211684 CTTCTTTTTT
1 CTT-TTTTTT
1211694 -TTATTTTTT
1 CTT-TTTTTT
**
1211703 CCATTTTTT
1 CTTTTTTTT
1211712 CTATTTTTCTAT
1 CT-TTTTT-T-T
1211724 -TTCATTTTTT
1 CTT--TTTTTT
*
1211734 C-ATTTTTT
1 CTTTTTTTT
*
1211742 CATTTTTTT
1 CTTTTTTTT
*
1211751 CATTTTTTT
1 CTTTTTTTT
*
1211760 CATTTTTTT
1 CTTTTTTTT
1211769 CATTTTT
1 C-TTTTT
1211776 CATTTTTCAT
Statistics
Matches: 98, Mismatches: 8, Indels: 28
0.73 0.06 0.21
Matches are distributed among these distances:
8 8 0.08
9 57 0.58
10 21 0.21
11 7 0.07
12 5 0.05
ACGTcount: A:0.08, C:0.12, G:0.01, T:0.78
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:1211693 original size:12 final size:12
Alignment explanation
Indices: 1211653--1211695 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
1211643 CCCCTTTTAT
*
1211653 TTTTTTTTGTT-
1 TTTTTTTTCTTC
*
1211664 TTTTTCTTCTTC
1 TTTTTTTTCTTC
1211676 TTTTTTTTCTTC
1 TTTTTTTTCTTC
1211688 TTTTTTTT
1 TTTTTTTT
1211696 ATTTTTTCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (12 bp):
TTTTTTTTCTTC
Found at i:1211741 original size:22 final size:21
Alignment explanation
Indices: 1211704--1211746 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1211694 TTATTTTTTC
1211704 CATTTTTTCTATTTTTCTATTT
1 CATTTTTTCTATTTTTC-ATTT
1211726 CATTTTTTC-ATTTTTTCATTT
1 CATTTTTTCTA-TTTTTCATTT
1211747 TTTTCATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (21 bp):
CATTTTTTCTATTTTTCATTT
Found at i:1211764 original size:56 final size:57
Alignment explanation
Indices: 1211680--1211790 Score: 156
Period size: 56 Copynumber: 2.0 Consensus size: 57
1211670 TTCTTCTTTT
*
1211680 TTTTCTTCTTTTTTTTATTTTTTCCA-TTTTTTCTATTTTTC-TATTTCATTTTTTCA
1 TTTTCTTCTTTTTTTCATTTTTTCCATTTTTTTC-ATTTTTCATATTTCATTTTTTCA
* *
1211736 TTTT-TTCATTTTTTTCATTTTTTTCATTTTTTTCATTTTTCATTTTTCATTTTTT
1 TTTTCTTC-TTTTTTTCATTTTTTCCATTTTTTTCATTTTTCATATTTCATTTTTT
1211791 TTTATCTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
55 3 0.06
56 27 0.55
57 19 0.39
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.77
Consensus pattern (57 bp):
TTTTCTTCTTTTTTTCATTTTTTCCATTTTTTTCATTTTTCATATTTCATTTTTTCA
Found at i:1211782 original size:8 final size:8
Alignment explanation
Indices: 1211689--1211790 Score: 106
Period size: 9 Copynumber: 12.8 Consensus size: 8
1211679 TTTTTCTTCT
*
1211689 TTTTTTTA
1 TTTTTTCA
1211697 TTTTTTCCA
1 TTTTTT-CA
1211706 TTTTTTC-
1 TTTTTTCA
1211713 TATTTTTC-
1 T-TTTTTCA
*
1211721 -TATTTCA
1 TTTTTTCA
1211728 TTTTTTCA
1 TTTTTTCA
1211736 TTTTTTCA
1 TTTTTTCA
1211744 TTTTTTTCA
1 -TTTTTTCA
1211753 TTTTTTTCA
1 -TTTTTTCA
1211762 TTTTTTTCA
1 -TTTTTTCA
1211771 -TTTTTCA
1 TTTTTTCA
1211778 -TTTTTCA
1 TTTTTTCA
1211785 TTTTTT
1 TTTTTT
1211791 TTTATCTTTA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
6 5 0.06
7 15 0.18
8 32 0.38
9 33 0.39
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTTCA
Found at i:1211792 original size:18 final size:18
Alignment explanation
Indices: 1211662--1211793 Score: 68
Period size: 16 Copynumber: 7.4 Consensus size: 18
1211652 TTTTTTTTTG
* *
1211662 TTTTTTTC-TTCTTCTTT
1 TTTTTTTCATTTTTCATT
1211679 TTTTTCTTC-TTTTT--TT
1 TTTTT-TTCATTTTTCATT
1211695 TATTTTTTCCATTTTTTCTATT
1 T-TTTTTT-CA-TTTTTC-ATT
1211717 TTTCTATTTCATTTTTTCATT
1 TTT-T-TTTCA-TTTTTCATT
*
1211738 TTTTCATT--TTTTTCA--
1 TTTT-TTTCATTTTTCATT
1211753 TTTTTTTCATTTTT--TT
1 TTTTTTTCATTTTTCATT
**
1211769 CATTTTTCATTTTTCATT
1 TTTTTTTCATTTTTCATT
1211787 TTTTTTT
1 TTTTTTT
1211794 ATCTTTAAGC
Statistics
Matches: 91, Mismatches: 8, Indels: 31
0.70 0.06 0.24
Matches are distributed among these distances:
14 2 0.02
15 4 0.04
16 22 0.24
17 17 0.19
18 14 0.15
19 5 0.05
20 3 0.03
21 8 0.09
22 13 0.14
23 3 0.03
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTTTTCATTTTTCATT
Found at i:1212929 original size:3 final size:3
Alignment explanation
Indices: 1212915--1212952 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1212905 ATACCAAGGC
1212915 CTT CTAT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CT-T CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1212953 AATACTAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:1220369 original size:3 final size:3
Alignment explanation
Indices: 1220361--1220401 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
1220351 TAATTTGTAT
1220361 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TTAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TA
1220402 TTTTTAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 2 0.06
3 31 0.86
4 3 0.08
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1222324 original size:22 final size:22
Alignment explanation
Indices: 1222296--1222425 Score: 233
Period size: 22 Copynumber: 5.9 Consensus size: 22
1222286 TTTGTTTACT
1222296 GCTGAATGCGGAACCGTTCAAC
1 GCTGAATGCGGAACCGTTCAAC
*
1222318 GCTGAATGCGAAACCGTTCAAC
1 GCTGAATGCGGAACCGTTCAAC
1222340 GCTGAATGCGGAACCGTTCAAC
1 GCTGAATGCGGAACCGTTCAAC
1222362 GCTGAATGCGGAACCGTTCAAC
1 GCTGAATGCGGAACCGTTCAAC
1222384 GCTGAATGCGGAACCGTTCAAC
1 GCTGAATGCGGAACCGTTCAAC
* *
1222406 GCTGAATGCGAAATCGTTCA
1 GCTGAATGCGGAACCGTTCA
1222426 GCATTCAGTG
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 104 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.19
Consensus pattern (22 bp):
GCTGAATGCGGAACCGTTCAAC
Found at i:1227569 original size:59 final size:60
Alignment explanation
Indices: 1227474--1227629 Score: 174
Period size: 59 Copynumber: 2.6 Consensus size: 60
1227464 AGGGTAGTAT
* * * * * *
1227474 TTTGTTAAGTCTATCGGCTATTAAAAGTTATAAAATGATTATTTGACTATAGA-GTGTTAC
1 TTTGTTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCATTCGACTACA-ATGTGTTAC
* *
1227534 TTTGTTAAGTCTCT-GACTATTAAAAGTTACAAAATGATCATTCGTCTACAATGTGTTAT
1 TTTGTTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCATTCGACTACAATGTGTTAC
* * *
1227593 TTTATTGAGTTTCTCGACTATTAAATA-TTACAAAATG
1 TTTGTTAAGTCTCTCGACTATTAAA-AGTTACAAAATG
1227630 GTCAACTGAC
Statistics
Matches: 82, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.01
59 47 0.57
60 33 0.40
61 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.14, T:0.42
Consensus pattern (60 bp):
TTTGTTAAGTCTCTCGACTATTAAAAGTTACAAAATGATCATTCGACTACAATGTGTTAC
Found at i:1228027 original size:61 final size:61
Alignment explanation
Indices: 1227980--1228096 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
1227970 GCGAATTGGG
* * * *
1227980 AAAATCGCAATGCA-ATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACG-AGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
1228041 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
1228097 TTACATAGCG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 1 0.02
61 47 0.98
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:1228033 original size:20 final size:20
Alignment explanation
Indices: 1227983--1228096 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
1227973 AATTGGGAAA
*
1227983 ATCGCAATGCAATACTGACT
1 ATCGCAATGCGATACTGACT
*
1228003 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
1228023 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
1228044 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
1228064 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* *
1228084 TTCGCAACGCGAT
1 ATCGCAATGCGAT
1228097 TTACATAGCG
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.79
21 13 0.16
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:1228774 original size:52 final size:52
Alignment explanation
Indices: 1228691--1228807 Score: 189
Period size: 52 Copynumber: 2.2 Consensus size: 52
1228681 GAAACCAAAA
* *
1228691 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAAT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAAT
* *
1228743 TCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAAT
*
1228795 TCGCATTGTGATT
1 TCGCATTGCGATT
1228808 CTCTCGTTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCAAT
Found at i:1228783 original size:33 final size:33
Alignment explanation
Indices: 1228746--1228839 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1228736 TTTCAATTCG
1228746 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
* *
1228779 CGTTGCGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1228812 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1228840 AGTAATTTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
Found at i:1228848 original size:85 final size:86
Alignment explanation
Indices: 1228696--1228859 Score: 249
Period size: 85 Copynumber: 1.9 Consensus size: 86
1228686 CAAAATCGCA
* * ** *
1228696 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCAATTCGCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAATTCGCATTGCGATAGTAAT
1228761 TT-CGCATTGCGATTCCCTCG
66 TTCCGCATTGCGATTCCCTCG
* *
1228781 TTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATAGTAAT
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAATTCGCATTGCGATAGTAAT
*
1228846 TTCCGCGTTGCGAT
66 TTCCGCATTGCGAT
1228860 AGACATTAAG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 60 0.86
86 10 0.14
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (86 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAATTCGCATTGCGATAGTAAT
TTCCGCATTGCGATTCCCTCG
Found at i:1231147 original size:14 final size:14
Alignment explanation
Indices: 1231130--1231156 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1231120 TCTTCGGGGA
1231130 CTTTTTCTTCTTCT
1 CTTTTTCTTCTTCT
1231144 CTTTTTCTTCTTC
1 CTTTTTCTTCTTC
1231157 AGGATTATAT
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:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
CTTTTTCTTCTTCT
Found at i:1231365 original size:24 final size:24
Alignment explanation
Indices: 1231331--1231384 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1231321 CTGAAACATC
*
1231331 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
*
1231355 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1231379 ATCAAA
1 ATCAAA
1231385 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1231398 original size:24 final size:24
Alignment explanation
Indices: 1231331--1231398 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1231321 CTGAAACATC
* * * *
1231331 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAGTCCGAATACTGACCAAG
* *
1231355 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1231379 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1231399 TAGTACTCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1232158 original size:20 final size:20
Alignment explanation
Indices: 1232129--1232179 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1232119 TGTATTATCT
1232129 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
1232149 CGTTGTGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
1232169 CGTTGCGAAAG
1 CGTTGCGAAAG
1232180 GCAATCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:1232417 original size:20 final size:20
Alignment explanation
Indices: 1232392--1232481 Score: 164
Period size: 20 Copynumber: 4.5 Consensus size: 20
1232382 ATTCATTTGA
1232392 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1232412 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
1232432 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
1232452 CTATCTCAACGCG-AAATGG
1 CTATCGCAACGCGAAAATGG
1232471 CTATCGCAACG
1 CTATCGCAACG
1232482 ACAAAATCGC
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
19 16 0.24
20 52 0.76
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1232548 original size:19 final size:19
Alignment explanation
Indices: 1232507--1232571 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 19
1232497 GAAATGAAAA
1232507 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
*
1232523 TCG--TTGCGGTTTTCATT
1 TCGCATTGCGATTTTCATT
1232540 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1232559 TCGCATTGCGATT
1 TCGCATTGCGATT
1232572 CTCTCGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.24
16 3 0.07
17 3 0.07
19 26 0.62
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1232602 original size:20 final size:20
Alignment explanation
Indices: 1232577--1232615 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1232567 CGATTCTCTC
1232577 GTTGCGATAGTCAGTTTTGT
1 GTTGCGATAGTCAGTTTTGT
*
1232597 GTTGCGATAGTCTGTTTTG
1 GTTGCGATAGTCAGTTTTG
1232616 CCTTCAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.31, T:0.46
Consensus pattern (20 bp):
GTTGCGATAGTCAGTTTTGT
Found at i:1234626 original size:20 final size:20
Alignment explanation
Indices: 1234603--1234656 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1234593 GAAACTTAAA
1234603 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
1234623 ATCGCAACG-AAGAAATGGCT
1 ATCGCAACGCGA-AAATGACT
*
1234643 ATCGCAATGCGAAA
1 ATCGCAACGCGAAA
1234657 TAAAAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1234678 original size:14 final size:14
Alignment explanation
Indices: 1234659--1234716 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1234649 ATGCGAAATA
1234659 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1234673 AAAATCGCACTGCGAA
1 AAAATCGCA--ACGAC
1234689 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1234705 AAAATCGCAACG
1 AAAATCGCAACG
1234717 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1234701 original size:32 final size:33
Alignment explanation
Indices: 1234643--1234732 Score: 121
Period size: 32 Copynumber: 2.8 Consensus size: 33
1234633 AGAAATGGCT
*
1234643 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCACTGCGAAATAAAAATCGCAACGACAAA
*
1234676 ATCGCACTGCGAAAT-GAAATCGCAACGACAAA
1 ATCGCACTGCGAAATAAAAATCGCAACGACAAA
* *
1234708 ATCGCAAC-GCGAAACACAAATCGCA
1 ATCGC-ACTGCGAAATAAAAATCGCA
1234733 TTGCGATTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 27 0.53
33 24 0.47
ACGTcount: A:0.47, C:0.26, G:0.17, T:0.11
Consensus pattern (33 bp):
ATCGCACTGCGAAATAAAAATCGCAACGACAAA
Found at i:1234769 original size:14 final size:14
Alignment explanation
Indices: 1234750--1234807 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1234740 TTTCATTTCG
*
1234750 CGTTGCGATTTTGT
1 CGTTGCGATTTTTT
1234764 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
*
1234780 CGCATTGTGATTTTTT
1 CG--TTGCGATTTTTT
1234796 CGTTGCGATTTT
1 CGTTGCGATTTT
1234808 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 9 0.24
18 8 0.22
ACGTcount: A:0.10, C:0.16, G:0.22, T:0.52
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1234814 original size:33 final size:33
Alignment explanation
Indices: 1234733--1234823 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
1234723 ACAAATCGCA
*
1234733 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
* *
1234766 TTGCGA-TTTCATTTCGCATTGTGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1234798 TTGCGATTTTCATTTCGCATTACGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1234824 AGCCATTTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
32 29 0.56
33 23 0.44
ACGTcount: A:0.13, C:0.18, G:0.20, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1234835 original size:20 final size:20
Alignment explanation
Indices: 1234810--1234854 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1234800 GCGATTTTCA
*
1234810 TTTCGCATTACGATAGCCAT
1 TTTCGCATTACGATAACCAT
* * *
1234830 TTTCGCGTTGCGATAATCAT
1 TTTCGCATTACGATAACCAT
1234850 TTTCG
1 TTTCG
1234855 TGTTGCGAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
TTTCGCATTACGATAACCAT
Found at i:1235370 original size:18 final size:18
Alignment explanation
Indices: 1235344--1235388 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1235334 GTCGATCAGA
*
1235344 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
1235362 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
1235380 TGATGGCTC
1 TGATGGCTC
1235389 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:1237010 original size:11 final size:11
Alignment explanation
Indices: 1236996--1237028 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1236986 AAATTAAAGT
1236996 TAAATAAATAA
1 TAAATAAATAA
*
1237007 TAAATAAATAT
1 TAAATAAATAA
1237018 TAAATAAATAA
1 TAAATAAATAA
1237029 GAAAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:1238292 original size:3 final size:3
Alignment explanation
Indices: 1238284--1238349 Score: 71
Period size: 3 Copynumber: 21.3 Consensus size: 3
1238274 TTAAATAAGA
* * *
1238284 AAT AAT AAT AAT AAAT AA- AAT AAT TAC AAT AAT AAT AAAT GAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
1238330 AAT AAAT AAT AAT AAT AAT A
1 AAT -AAT AAT AAT AAT AAT A
1238350 GTATAATATA
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 2 0.04
3 42 0.79
4 9 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1238299 original size:13 final size:13
Alignment explanation
Indices: 1238277--1238347 Score: 92
Period size: 13 Copynumber: 5.6 Consensus size: 13
1238267 AAAATAATTA
*
1238277 AATAAGAAATAAT
1 AATAATAAATAAT
1238290 AATAATAAATAA-
1 AATAATAAATAAT
* *
1238302 AATAAT-TACAAT
1 AATAATAAATAAT
*
1238314 AATAATAAATGAT
1 AATAATAAATAAT
1238327 AATAATAAATAAT
1 AATAATAAATAAT
1238340 AATAATAA
1 AATAATAA
1238348 TAGTATAATA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
11 3 0.06
12 12 0.24
13 34 0.69
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (13 bp):
AATAATAAATAAT
Found at i:1238496 original size:39 final size:39
Alignment explanation
Indices: 1238370--1238512 Score: 128
Period size: 40 Copynumber: 3.6 Consensus size: 39
1238360 TATATAAATA
* ** *
1238370 TTTTAAAAAA-CATATAATATATAATTTCCAAAATGTTTT
1 TTTTAAAAAATTATATAATATAT-ATTTTTAAAATATTTT
* * * **
1238409 TTTT-TAAAATTATATAATATATATATTTTTAAAAAAATGC
1 TTTTAAAAAATTATAT-A-ATATATATTTTTAAAATATTTT
* *
1238449 TTTAAAAAAATTATATATTATATATTTTTAAAATATTTT
1 TTTTAAAAAATTATATAATATATATTTTTAAAATATTTT
*
1238488 TTTTAAAAAAACTATATAATATATA
1 TTTT-AAAAAATTATATAATATATA
1238513 AATGTTTTCA
Statistics
Matches: 80, Mismatches: 19, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
38 4 0.05
39 28 0.35
40 32 0.40
41 16 0.20
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (39 bp):
TTTTAAAAAATTATATAATATATATTTTTAAAATATTTT
Found at i:1238528 original size:11 final size:11
Alignment explanation
Indices: 1238512--1238536 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1238502 TATAATATAT
1238512 AAATGTTTTCA
1 AAATGTTTTCA
1238523 AAATGTTTTCA
1 AAATGTTTTCA
1238534 AAA
1 AAA
1238537 CTATATATCA
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:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:1238544 original size:40 final size:40
Alignment explanation
Indices: 1238495--1238628 Score: 158
Period size: 38 Copynumber: 3.5 Consensus size: 40
1238485 TTTTTTTAAA
1238495 AAAACTATATA-ATATATAAATGTTTTC-AAAATG-TTTTC
1 AAAACTATATATATATATAAA-GTTTTCAAAAATGCTTTTC
* *
1238533 AAAACTATATAT-CATATAAA-TTTTCAAAAATGTTTTTC
1 AAAACTATATATATATATAAAGTTTTCAAAAATGCTTTTC
*
1238571 AAAACTATATATAT-TATATACGTTTTCAAAAATGCTTTT-
1 AAAACTATATATATATATA-AAGTTTTCAAAAATGCTTTTC
1238610 AAATA-TATATATATATATA
1 AAA-ACTATATATATATATA
1238629 TATATATATA
Statistics
Matches: 84, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
36 5 0.06
37 6 0.07
38 39 0.46
39 13 0.15
40 21 0.25
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.43
Consensus pattern (40 bp):
AAAACTATATATATATATAAAGTTTTCAAAAATGCTTTTC
Found at i:1238619 original size:2 final size:2
Alignment explanation
Indices: 1238612--1238676 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1238602 ATGCTTTTAA
1238612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1238654 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
1238677 CATTTTCAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1238749 original size:37 final size:36
Alignment explanation
Indices: 1238668--1238751 Score: 98
Period size: 35 Copynumber: 2.3 Consensus size: 36
1238658 ATATATATAT
* * ** *
1238668 ATATATATACATTTTCAAAATGTTTTCAAAGACTAT
1 ATATATATATATTTTCAAAATGTTTTCAAAAAAAAC
*
1238704 ATAT-TATATATTTTTAAAATGTTTTCGAAAAAAAAC
1 ATATATATATATTTTCAAAATGTTTTC-AAAAAAAAC
1238740 ATATATATATAT
1 ATATATATATAT
1238752 ATATATATAC
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
35 20 0.50
36 13 0.32
37 7 0.17
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (36 bp):
ATATATATATATTTTCAAAATGTTTTCAAAAAAAAC
Found at i:1239593 original size:84 final size:81
Alignment explanation
Indices: 1239453--1240210 Score: 783
Period size: 84 Copynumber: 9.2 Consensus size: 81
1239443 TTGAATATAA
* * * *
1239453 TCGAACTCAAAGGTCTTTAG-CAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
*
1239517 TTGGAGCTGAGCGGAG
66 TTGGAGCTGAGCGTAG
* * *
1239533 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
1 TCGAACTCGAAGGTC-TTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
1239598 GCCGTT-GAGCTGAGCGTAG
63 GCC-TTGGAGCTGAGCGTAG
* * * * * *
1239617 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTC-TTTG--GTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
1239682 GCCTTGGAGCTGAGCGTAG
63 GCCTTGGAGCTGAGCGTAG
*
1239701 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGG-T--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
* * * *
1239766 GCCCTCGAAGCTGAGTGTAA
63 G-CCTTGGAGCTGAGCGTAG
* ** * * * * *
1239786 TCGAACTTGGGGGTCTTTTG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
1239850 TTGGAGCTGAGCGTAG
66 TTGGAGCTGAGCGTAG
* * * * * * *
1239866 TCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
1239931 CCCTTGAAGCTGAGTGTAA
64 -CCTTGGAGCTGAGCGTAG
* * * * *
1239950 TCGAACT-TAAGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGC
1 TCGAACTCGAA-GGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
1240013 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
* * * * * * *
1240030 TCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATG
1 TCGAACTCGAAGGTCTTTGGT--CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* * *
1240095 CCCTTGAAGCTGAGTGTAA
64 -CCTTGGAGCTGAGCGTAG
* * * * *
1240114 TCGAACT-TAAGGGTCTTTGG-CAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGC
1 TCGAACTCGAA-GGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGC
1240177 CTTGGAGCTGAGCGTAG
65 CTTGGAGCTGAGCGTAG
1240194 TCGAACTCGAAGGTCTT
1 TCGAACTCGAAGGTCTT
1240211 GGTGGCAGGT
Statistics
Matches: 554, Mismatches: 100, Indels: 48
0.79 0.14 0.07
Matches are distributed among these distances:
80 100 0.18
81 114 0.21
83 76 0.14
84 231 0.42
85 32 0.06
86 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.25, T:0.30
Consensus pattern (81 bp):
TCGAACTCGAAGGTCTTTGGTCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC
TTGGAGCTGAGCGTAG
Found at i:1239627 original size:164 final size:164
Alignment explanation
Indices: 1239390--1240210 Score: 1117
Period size: 164 Copynumber: 5.0 Consensus size: 164
1239380 AATTTTATTG
* * * * * * * *
1239390 ACAGATAACCCTTCTTGCCTTGAGCTATTCTGTAAGCTTGATTTG-CCTCT-AAGTTGAATATAA
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAA--ATGATATGCCCT-TGAAGCTGAGTGTAA
* * * * * *
1239453 TCGAACTCAAAGGTCTTTAGCAGATAACCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCT
63 TCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCT
* * *
1239518 TGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTC
128 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGCTA
* * * *
1239556 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCGTTG-AGCTGAGCGTAGTCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
* * * * * * * * * *
1239620 AACTCAAAGGTCTTTTGTTGGCAGACAACCCTTGTAGACTTAAGTTGTGCTGCAAATGATATGCC
66 AACTTAAGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
* *
1239685 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
127 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GCTA
* * * * * * *
1239724 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
** *
1239789 AACTTGGGGGTCTTTTGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
1239854 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
*
1239888 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
1239953 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
1240018 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
*
1240052 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
1240117 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
1240182 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
1240211 GGTGGCAGGT
Statistics
Matches: 589, Mismatches: 58, Indels: 18
0.89 0.09 0.03
Matches are distributed among these distances:
164 342 0.58
165 74 0.13
166 33 0.06
167 4 0.01
168 115 0.20
169 21 0.04
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (164 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTTGAAGCTGAGTGTAATCG
AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
Found at i:1243649 original size:18 final size:19
Alignment explanation
Indices: 1243608--1243652 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1243598 AGTTAATGTG
1243608 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
1243627 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
1243645 AATGCAAA
1 AATGCAAA
1243653 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:1244299 original size:17 final size:17
Alignment explanation
Indices: 1244273--1244305 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1244263 TGCAAACGAT
*
1244273 GAACACAAAATAAAAGA
1 GAACAAAAAATAAAAGA
1244290 GAACAAAAAATAAAAG
1 GAACAAAAAATAAAAG
1244306 GGTTAGTGAG
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:0.73, C:0.09, G:0.12, T:0.06
Consensus pattern (17 bp):
GAACAAAAAATAAAAGA
Found at i:1246720 original size:3 final size:3
Alignment explanation
Indices: 1246712--1246770 Score: 55
Period size: 3 Copynumber: 18.3 Consensus size: 3
1246702 TTAAATAAGA
* * *
1246712 AAT AAT AAT AAT AAAT AAAT TAC AAT AAT AAT AAAT GAT AAT AAT AAAT
1 AAT AAT AAT AAT -AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT -AAT
1246761 AAT AAT AAT A
1 AAT AAT AAT A
1246771 TATATATATA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 34 0.72
4 13 0.28
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Done.