Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold23
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: 3824748
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 177433 characters in sequence are not A, C, G, or T
File 4 of 14
Found at i:877392 original size:31 final size:33
Alignment explanation
Indices: 877357--877421 Score: 82
Period size: 32 Copynumber: 2.0 Consensus size: 33
877347 AAAATTTGAA
*
877357 TTTT-ATTAAAATTTGCCAC-CAAT-TTAGATTT
1 TTTTAATTAAAATTTACCACTCAATATTA-ATTT
*
877388 TTTTAATTAAATTTTACCACTCAATATTAATTT
1 TTTTAATTAAAATTTACCACTCAATATTAATTT
877421 T
1 T
877422 ATGATTTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 9 0.31
34 3 0.10
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (33 bp):
TTTTAATTAAAATTTACCACTCAATATTAATTT
Found at i:877977 original size:54 final size:54
Alignment explanation
Indices: 877913--878021 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
877903 AAAAATCTAA
877913 GTATAAAACTTCACTAATAGATAAAATTCAGCCGAACTATATGAATGGGCTATT
1 GTATAAAACTTCACTAATAGATAAAATTCAGCCGAACTATATGAATGGGCTATT
877967 GTATAAAACTTCACTAATAGATAAAATTCAGCCGAACTATATGAATGGGCTATT
1 GTATAAAACTTCACTAATAGATAAAATTCAGCCGAACTATATGAATGGGCTATT
878021 G
1 G
878022 GACCAAACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (54 bp):
GTATAAAACTTCACTAATAGATAAAATTCAGCCGAACTATATGAATGGGCTATT
Found at i:884481 original size:2 final size:2
Alignment explanation
Indices: 884474--884502 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
884464 NNNAAACATA
884474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
884503 AGAATATGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:884678 original size:19 final size:18
Alignment explanation
Indices: 884652--884696 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
884642 GTTGATTAAC
**
884652 AACTAATTAATTATAATT
1 AACTAATTAAACATAATT
884670 AACCTAATTAAACATAATT
1 AA-CTAATTAAACATAATT
884689 AACTAATT
1 AACTAATT
884697 TTAAGCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (18 bp):
AACTAATTAAACATAATT
Found at i:886056 original size:31 final size:30
Alignment explanation
Indices: 886018--886092 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
886008 GATTTGACGC
* *
886018 TTGGGTGACTAAAATGAAAGTAC-CCTAAAAG
1 TTGGGTGACCAAAAT-AAA-AACGCCTAAAAG
*
886049 TTGGGTGACCAAAATAAAAACGTCCTAAAAT
1 TTGGGTGACCAAAATAAAAACG-CCTAAAAG
886080 TTGGGTGACCAAA
1 TTGGGTGACCAAA
886093 TTTTCTAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
29 2 0.05
30 3 0.08
31 34 0.87
ACGTcount: A:0.41, C:0.15, G:0.21, T:0.23
Consensus pattern (30 bp):
TTGGGTGACCAAAATAAAAACGCCTAAAAG
Found at i:891820 original size:13 final size:13
Alignment explanation
Indices: 891802--891826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
891792 TAATATATTT
891802 ATTAATTAAAAAC
1 ATTAATTAAAAAC
891815 ATTAATTAAAAA
1 ATTAATTAAAAA
891827 AATTGAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAC
Found at i:891878 original size:13 final size:12
Alignment explanation
Indices: 891860--891897 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
891850 TAAAATATTT
891860 ATTAATTAAAAA
1 ATTAATTAAAAA
891872 CATTAATTAAAAA
1 -ATTAATTAAAAA
891885 ATTAA--AAAAA
1 ATTAATTAAAAA
891895 ATT
1 ATT
891898 GAACAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.32
12 5 0.20
13 12 0.48
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (12 bp):
ATTAATTAAAAA
Found at i:892818 original size:16 final size:18
Alignment explanation
Indices: 892799--892836 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
892789 TTACTAAAAT
892799 AAAAACCTTA-TG-AGAA
1 AAAAACCTTAGTGAAGAA
*
892815 AAAAATCTTAGTGAAGAA
1 AAAAACCTTAGTGAAGAA
892833 AAAA
1 AAAA
892837 GAATATGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 2 0.11
18 8 0.42
ACGTcount: A:0.61, C:0.08, G:0.13, T:0.18
Consensus pattern (18 bp):
AAAAACCTTAGTGAAGAA
Found at i:893800 original size:11 final size:11
Alignment explanation
Indices: 893786--893829 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
893776 AGATAAATAT
893786 TATTTTATTAA
1 TATTTTATTAA
*
893797 TATTTTAATGAGA
1 TATTTT-ATTA-A
*
893810 TATTTTATTAT
1 TATTTTATTAA
893821 TATTTTATT
1 TATTTTATT
893830 TAGTATAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:895826 original size:33 final size:32
Alignment explanation
Indices: 895783--895943 Score: 142
Period size: 33 Copynumber: 4.8 Consensus size: 32
895773 CAGTGTTTAT
895783 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* * * *
895815 ATGATAAGACCATAACTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGCTGGGCTATGGCATTCTG
* * * * * * *
895848 AACGTAAGACCATGGTTGGACCATGGCAATGTTTAT
1 -ATGTAAGACCATAGCTGGGCTATGGC-AT-TCT-G
895884 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
* * *
895916 ATGATAAGACCATAACTGAGTTATGGCA
1 ATG-TAAGACCATAGCTGGGCTATGGCA
895944 CTACGAATGT
Statistics
Matches: 99, Mismatches: 24, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
32 6 0.06
33 65 0.66
34 5 0.05
35 23 0.23
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.27
Consensus pattern (32 bp):
ATGTAAGACCATAGCTGGGCTATGGCATTCTG
Found at i:895891 original size:101 final size:101
Alignment explanation
Indices: 895716--895955 Score: 426
Period size: 101 Copynumber: 2.4 Consensus size: 101
895706 TGAATTGACG
* * *
895716 GATAAGACCATAACTGGGTTATGGCACTGTGAACGTAAGACTATGGTTGGACCATGGCAGTGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
895781 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
895817 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
895882 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
66 ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
* * *
895918 GATAAGACCATAACTGAGTTATGGCACTACGAATGTAA
1 GATAAGACCATAACTGGGTTATGGCACTATGAACGTAA
895956 AGGATGAATT
Statistics
Matches: 133, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
101 133 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (101 bp):
GATAAGACCATAACTGGGTTATGGCACTATGAACGTAAGACCATGGTTGGACCATGGCAATGTTT
ATATGTAAGACCATAGCTGGGCTATGGCATTCTGAT
Found at i:895981 original size:24 final size:24
Alignment explanation
Indices: 895949--895999 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
895939 TGGCACTACG
895949 AATGTAAAGGATGAATTAATGGAA
1 AATGTAAAGGATGAATTAATGGAA
* *
895973 AATGTAAAGGATGAATTGATGGCA
1 AATGTAAAGGATGAATTAATGGAA
895997 AAT
1 AAT
896000 TACCCAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.25, T:0.25
Consensus pattern (24 bp):
AATGTAAAGGATGAATTAATGGAA
Found at i:899536 original size:20 final size:21
Alignment explanation
Indices: 899494--899550 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
899484 AATATTTTAA
*
899494 ATATAAATATTTATTTTATTTT
1 ATATAAATATTT-GTTTATTTT
899516 ATATAAATATTTGTTTA-TTT
1 ATATAAATATTTGTTTATTTT
**
899536 ATATTCATATTTGTT
1 ATATAAATATTTGTT
899551 CGCTAAGGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 16 0.50
21 4 0.12
22 12 0.38
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (21 bp):
ATATAAATATTTGTTTATTTT
Found at i:900888 original size:9 final size:9
Alignment explanation
Indices: 900876--900928 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
900866 TTTTATACTT
900876 TTTTAATAA
1 TTTTAATAA
*
900885 TTTTAAAAA
1 TTTTAATAA
900894 TTTTAAATAA
1 TTTT-AATAA
*
900904 TTTTTATAGA
1 TTTTAATA-A
**
900914 TTTTTTTAA
1 TTTTAATAA
900923 TTTTAA
1 TTTTAA
900929 ATCTTAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 20 0.56
10 16 0.44
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
TTTTAATAA
Found at i:900897 original size:19 final size:19
Alignment explanation
Indices: 900875--900929 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
900865 CTTTTATACT
900875 TTTTTAATAATTTTAAAAA
1 TTTTTAATAATTTTAAAAA
* * *
900894 TTTTAAATAATTTTTATAGA
1 TTTTTAATAA-TTTTAAAAA
*
900914 TTTTT-TTAATTTTAAA
1 TTTTTAATAATTTTAAA
900930 TCTTAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
18 6 0.21
19 12 0.41
20 11 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTAATAATTTTAAAAA
Found at i:901259 original size:22 final size:22
Alignment explanation
Indices: 901234--901289 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
901224 GACATTTTCC
*
901234 CGTTCTCCCTTCTCTACACTTT
1 CGTTCTCCCTTCTCTACACTCT
*
901256 CGTTCTCCTTTCTCTACACTCT
1 CGTTCTCCCTTCTCTACACTCT
901278 CGTTCTCCCTTC
1 CGTTCTCCCTTC
901290 CTCTCTACGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.07, C:0.43, G:0.05, T:0.45
Consensus pattern (22 bp):
CGTTCTCCCTTCTCTACACTCT
Found at i:901762 original size:14 final size:14
Alignment explanation
Indices: 901745--901773 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
901735 GTTTGTTCTC
901745 TTAAGAGGAAATGG
1 TTAAGAGGAAATGG
901759 TTAAGAGGAAATGG
1 TTAAGAGGAAATGG
901773 T
1 T
901774 GGTGAGGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.24
Consensus pattern (14 bp):
TTAAGAGGAAATGG
Found at i:903127 original size:3 final size:3
Alignment explanation
Indices: 903119--903154 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
903109 TTAAATATTT
903119 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
903155 TCTTTTTGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:905408 original size:27 final size:27
Alignment explanation
Indices: 905378--905450 Score: 74
Period size: 32 Copynumber: 2.5 Consensus size: 27
905368 TGTATTGAAT
905378 TTGTTACATATTGATTATGTTTTAAGC
1 TTGTTACATATTGATTATGTTTTAAGC
*
905405 TTGTTATATATTGAATTTATTATGTTTTAAGC
1 TTGTTACATATTG-----ATTATGTTTTAAGC
**
905437 TTGTTGGATATTGA
1 TTGTTACATATTGA
905451 AATGATTGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
27 13 0.34
32 25 0.66
ACGTcount: A:0.26, C:0.04, G:0.16, T:0.53
Consensus pattern (27 bp):
TTGTTACATATTGATTATGTTTTAAGC
Found at i:905430 original size:32 final size:32
Alignment explanation
Indices: 905391--905451 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
905381 TTACATATTG
*
905391 ATTATGTTTTAAGCTTGTTATATATTGAATTT
1 ATTATGTTTTAAGCTTGTTAGATATTGAATTT
*
905423 ATTATGTTTTAAGCTTGTTGGATATTGAA
1 ATTATGTTTTAAGCTTGTTAGATATTGAA
905452 ATGATTGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.03, G:0.16, T:0.52
Consensus pattern (32 bp):
ATTATGTTTTAAGCTTGTTAGATATTGAATTT
Found at i:906737 original size:32 final size:34
Alignment explanation
Indices: 906701--906785 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 34
906691 ATATTTTTCG
*
906701 GAAAATATTTTCAGGAAATCT-A-CCAAACAACA
1 GAAAATATTTTCAGCAAATCTCATCCAAACAACA
* *
906733 GAAAATATTTTACA-CAGAT-TCATCCAAACACCA
1 GAAAATATTTT-CAGCAAATCTCATCCAAACAACA
*
906766 GAAAATATTTTCAGTAAATC
1 GAAAATATTTTCAGCAAATC
906786 ATTTTCCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 1 0.02
32 17 0.40
33 25 0.58
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (34 bp):
GAAAATATTTTCAGCAAATCTCATCCAAACAACA
Found at i:906820 original size:14 final size:14
Alignment explanation
Indices: 906801--906838 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
906791 CCAAAAAAGT
906801 AAATCATTTTCC-A
1 AAATCATTTTCCGA
*
906814 GAAATCATTTTTCGA
1 -AAATCATTTTCCGA
906829 AAATCATTTT
1 AAATCATTTT
906839 ATTGGCAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.42
Consensus pattern (14 bp):
AAATCATTTTCCGA
Found at i:907259 original size:11 final size:11
Alignment explanation
Indices: 907243--907269 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
907233 ATTCAAATAA
907243 TTTTTTTGAAT
1 TTTTTTTGAAT
907254 TTTTTTTGAAT
1 TTTTTTTGAAT
907265 TTTTT
1 TTTTT
907270 CCATTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (11 bp):
TTTTTTTGAAT
Found at i:907296 original size:95 final size:95
Alignment explanation
Indices: 907098--907390 Score: 496
Period size: 95 Copynumber: 3.0 Consensus size: 95
907088 AATATCTCGT
* * * * *
907098 ATTTCCATCCTTACTTTTACTTCCACTATCATATAAAAAATTCAAAAAAATTATTTGATTTTTTT
1 ATTTCCATCCTTACTTTTATTTCCACTATCATATAAAAAATTCAAATAATTTTTTTGA-ATTTTT
907163 TTTGAATTTTTTCCATTAAAATTTTTAATAA
65 TTTGAATTTTTTCCATTAAAATTTTTAATAA
907194 ATTTCCATCCTTACTTTTATTTCCACTATCATATAAAAAATTCAAATAATTTTTTTGAATTTTTT
1 ATTTCCATCCTTACTTTTATTTCCACTATCATATAAAAAATTCAAATAATTTTTTTGAATTTTTT
907259 TTGAATTTTTTCCATTAAAATTTTTAATAA
66 TTGAATTTTTTCCATTAAAATTTTTAATAA
*
907289 ATTTCCATCCTTACTTTTATTTCCACTATCATATAAAAAAATTTAAATAATTTTTTTTGAATTTT
1 ATTTCCATCCTTACTTTTATTTCCACTATCATAT-AAAAAATTCAAATAA-TTTTTTTGAA-TTT
907354 TTTTTGAATTTTTTCCATTAAAATTTTTAATAA
63 TTTTTGAATTTTTTCCATTAAAATTTTTAATAA
907387 ATTT
1 ATTT
907391 TTATAATTAT
Statistics
Matches: 188, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
95 70 0.37
96 68 0.36
97 10 0.05
98 40 0.21
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (95 bp):
ATTTCCATCCTTACTTTTATTTCCACTATCATATAAAAAATTCAAATAATTTTTTTGAATTTTTT
TTGAATTTTTTCCATTAAAATTTTTAATAA
Found at i:907356 original size:12 final size:12
Alignment explanation
Indices: 907339--907367 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
907329 ATTTAAATAA
907339 TTTTTTTTGAAT
1 TTTTTTTTGAAT
907351 TTTTTTTTGAAT
1 TTTTTTTTGAAT
907363 TTTTT
1 TTTTT
907368 CCATTAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:907930 original size:22 final size:22
Alignment explanation
Indices: 907902--907959 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 22
907892 AAGTAAATAT
*
907902 ATATAATATAATAATA-AAGTAA
1 ATATAATAAAATAA-ACAAGTAA
907924 ATATAATAAAATAAACAAGTAA
1 ATATAATAAAATAAACAAGTAA
907946 ATGA-AAT-AAATAAA
1 AT-ATAATAAAATAAA
907960 GAAAATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
21 8 0.24
22 24 0.73
23 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (22 bp):
ATATAATAAAATAAACAAGTAA
Found at i:908019 original size:13 final size:13
Alignment explanation
Indices: 908001--908029 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
907991 AAAACGAAAT
908001 AGGGAGAAAAGAA
1 AGGGAGAAAAGAA
908014 AGGGAGAAAAGAA
1 AGGGAGAAAAGAA
908027 AGG
1 AGG
908030 AAAGAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (13 bp):
AGGGAGAAAAGAA
Found at i:908032 original size:18 final size:18
Alignment explanation
Indices: 908018--908053 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
908008 AAAGAAAGGG
908018 AGAAAAGAAAGGAAAGAA
1 AGAAAAGAAAGGAAAGAA
908036 AGAAAAGAAAGG-AAGAA
1 AGAAAAGAAAGGAAAGAA
908053 A
1 A
908054 TGAGAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAAGAAAGGAAAGAA
Found at i:908033 original size:9 final size:9
Alignment explanation
Indices: 908021--908053 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
908011 GAAAGGGAGA
908021 AAAGAAAGG
1 AAAGAAAGG
*
908030 AAAGAAAGA
1 AAAGAAAGG
908039 AAAGAAAGG
1 AAAGAAAGG
908048 -AAGAAA
1 AAAGAAA
908054 TGAGAAACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 6 0.27
9 16 0.73
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (9 bp):
AAAGAAAGG
Found at i:909043 original size:40 final size:40
Alignment explanation
Indices: 908927--909061 Score: 114
Period size: 40 Copynumber: 3.4 Consensus size: 40
908917 CGAGTTGATA
* * **
908927 AGACACTAAGTGTCAATTTATTACTTCAGATATATTTGATG
1 AGACACTAGGTGTCAAATTATTACTTCAGAT-TATCCGATG
* * * * * *
908968 AGGCACTGGGTG-CGAA-T-TTACTTCGGTTTAGCCGATG
1 AGACACTAGGTGTCAAATTATTACTTCAGATTATCCGATG
*
909005 AGACACTAGGTGTCAAATTATTACTTCAAATTATCCGATG
1 AGACACTAGGTGTCAAATTATTACTTCAGATTATCCGATG
* * *
909045 AGGCACTGGGTGCCAAA
1 AGACACTAGGTGTCAAA
909062 CTTGTGTGTT
Statistics
Matches: 71, Mismatches: 20, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
37 16 0.23
38 12 0.17
39 2 0.03
40 32 0.45
41 9 0.13
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (40 bp):
AGACACTAGGTGTCAAATTATTACTTCAGATTATCCGATG
Found at i:915024 original size:22 final size:22
Alignment explanation
Indices: 914996--915041 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
914986 GTAAATATAT
*
914996 ATATAATATAATAATA-AAGTAA
1 ATATAATAAAATAA-ACAAGTAA
915018 ATATAATAAAATAAACAAGTAA
1 ATATAATAAAATAAACAAGTAA
915040 AT
1 AT
915042 GAAACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (22 bp):
ATATAATAAAATAAACAAGTAA
Found at i:915260 original size:4 final size:4
Alignment explanation
Indices: 915251--915282 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
915241 AACAGGGAGA
915251 AAAG AAAG AAAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG -AAAG AAAG AAAG AAAG AAAG AAA
915283 TGAGAAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:916193 original size:41 final size:39
Alignment explanation
Indices: 916146--916255 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 39
916136 TTTGGCTTCG
*
916146 AGTCGATGAGACACTGAGTGTCAATTTATTACTTCGGATAT
1 AGTCGATGAGACACTGGGTGTCAA-TTATTACTTCGG-TAT
* * * *
916187 ATTCGATGAGGCATTGGGTG-CGAA-T-TTACTTCGGTTT
1 AGTCGATGAGACACTGGGTGTC-AATTATTACTTCGGTAT
*
916224 AGCCGATGAGACACTGGGTGTCAAATTATTAC
1 AGTCGATGAGACACTGGGTGTC-AATTATTAC
916256 CTCGAATTAT
Statistics
Matches: 55, Mismatches: 10, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
37 18 0.33
38 12 0.22
39 2 0.04
40 5 0.09
41 18 0.33
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.33
Consensus pattern (39 bp):
AGTCGATGAGACACTGGGTGTCAATTATTACTTCGGTAT
Found at i:916273 original size:40 final size:40
Alignment explanation
Indices: 916150--916288 Score: 115
Period size: 40 Copynumber: 3.5 Consensus size: 40
916140 GCTTCGAGTC
* *
916150 GATGAGACACTGAGTGTCAATTTATTACTTCGGATATAT-T
1 GATGAGACACTGGGTGTCAAATTATTACTTCGGAT-TATCT
* * * * * *
916190 CGATGAGGCATTGGGTG-CGAA-T-TTACTTCGGTTTAGCC
1 -GATGAGACACTGGGTGTCAAATTATTACTTCGGATTATCT
* *
916228 GATGAGACACTGGGTGTCAAATTATTACCTCGAATTATCT
1 GATGAGACACTGGGTGTCAAATTATTACTTCGGATTATCT
* * *
916268 GATGAGGCAATGGGTGCCAAA
1 GATGAGACACTGGGTGTCAAA
916289 CTAATGTGTT
Statistics
Matches: 75, Mismatches: 19, Indels: 9
0.73 0.18 0.09
Matches are distributed among these distances:
37 16 0.21
38 13 0.17
39 2 0.03
40 31 0.41
41 13 0.17
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (40 bp):
GATGAGACACTGGGTGTCAAATTATTACTTCGGATTATCT
Found at i:922833 original size:6 final size:6
Alignment explanation
Indices: 922822--922848 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
922812 GTTGTCATTA
922822 TTTAAT TTTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT TTTAAT TTTAAT TTT
922849 TTCTCTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTAAT
Found at i:927815 original size:26 final size:26
Alignment explanation
Indices: 927786--927835 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
927776 ATGATATGCT
*
927786 AGCTCGATACGCGAGCCCAATGTGCA
1 AGCTCGATACGCAAGCCCAATGTGCA
* *
927812 AGCTCGATATGCAAGCTCAATGTG
1 AGCTCGATACGCAAGCCCAATGTG
927836 TGAACCATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (26 bp):
AGCTCGATACGCAAGCCCAATGTGCA
Found at i:927826 original size:13 final size:13
Alignment explanation
Indices: 927750--927829 Score: 54
Period size: 13 Copynumber: 6.2 Consensus size: 13
927740 CCATGCGAGT
* *
927750 TCGATATACGAGC
1 TCGATATGCAAGC
* *
927763 TCAATGTGCAAGC
1 TCGATATGCAAGC
*
927776 AT-GATATGCTAGC
1 -TCGATATGCAAGC
* *
927789 TCGATACGCGAGC
1 TCGATATGCAAGC
* * *
927802 CCAATGTGCAAGC
1 TCGATATGCAAGC
927815 TCGATATGCAAGC
1 TCGATATGCAAGC
927828 TC
1 TC
927830 AATGTGTGAA
Statistics
Matches: 48, Mismatches: 17, Indels: 4
0.70 0.25 0.06
Matches are distributed among these distances:
12 1 0.02
13 46 0.96
14 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.23
Consensus pattern (13 bp):
TCGATATGCAAGC
Found at i:930655 original size:47 final size:47
Alignment explanation
Indices: 930603--930695 Score: 168
Period size: 47 Copynumber: 2.0 Consensus size: 47
930593 GCAACGATAC
* *
930603 TATTTGTATAAAAAGTAAGCAAAAGCATTGATTTTTCTTGTTAATTT
1 TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATTT
930650 TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATT
1 TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATT
930696 ATTTTTTACA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (47 bp):
TATTTGTATAAAAAGTAAGCAAAAACATTAATTTTTCTTGTTAATTT
Found at i:933008 original size:32 final size:32
Alignment explanation
Indices: 932967--933049 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 32
932957 AAACATGTGG
* *
932967 TTTTATGAAATGATAACAAA-TATCAGCTTTC-A
1 TTTTGTGAAATGATAACAAATTA-CAAC-TTCAA
932999 TTTTGTGAAATGATAACAAATTACAACTTCAA
1 TTTTGTGAAATGATAACAAATTACAACTTCAA
933031 TTTTGTGAAATGATAACAA
1 TTTTGTGAAATGATAACAA
933050 TGGGAAACCC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
31 3 0.06
32 42 0.89
33 2 0.04
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (32 bp):
TTTTGTGAAATGATAACAAATTACAACTTCAA
Found at i:933114 original size:17 final size:18
Alignment explanation
Indices: 933088--933128 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
933078 CATTAACCAT
*
933088 AAACCTTAAC-ACACTAA
1 AAACCCTAACAACACTAA
*
933105 AAACCCTAACAACCCTAA
1 AAACCCTAACAACACTAA
933123 AAACCC
1 AAACCC
933129 ATAAATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.51, C:0.37, G:0.00, T:0.12
Consensus pattern (18 bp):
AAACCCTAACAACACTAA
Found at i:933584 original size:22 final size:21
Alignment explanation
Indices: 933553--933595 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 21
933543 TTATTTTAAT
*
933553 TAAAATGGTTAAAGTAAAATA
1 TAAAATGGTTAAAATAAAATA
933574 TAAAAGTGGTTAAAATAAAATA
1 TAAAA-TGGTTAAAATAAAATA
933596 AATCTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (21 bp):
TAAAATGGTTAAAATAAAATA
Found at i:945419 original size:93 final size:87
Alignment explanation
Indices: 945226--945429 Score: 214
Period size: 87 Copynumber: 2.3 Consensus size: 87
945216 ATACCGCATG
* * * *
945226 TACGTCAGCTTTGCTGTGTGCTATTATCTGATCTGGTAACTTAACTACAACTTATTAGTACAGCG
1 TACGTCAGCTTTGCTGCGTGTTATTATCTGATCTGGCAACTTAACTACAACATATTAGTACAGCG
945291 GTTTACTGCACTGTACTACATA
66 GTTTACTGCACTGTACTACATA
* * ** *
945313 TACGTCAGTTTTGCTACGTGTTATTATCTGATCTGGCAGTTTAAACTACAACATGTCT-GTACAG
1 TACGTCAGCTTTGCTGCGTGTTATTATCTGATCTGGCAACTT-AACTACAACATAT-TAGTACAG
*
945377 CGGTTTATCGCAATGCACTGTCCTACATA
64 CGGTTTA---C--TGCACTGTACTACATA
* *
945406 TATG-CTAGCTTTGCTGCGTATTAT
1 TACGTC-AGCTTTGCTGCGTGTTAT
945430 CATCGAGTGG
Statistics
Matches: 95, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
87 35 0.37
88 24 0.25
89 1 0.01
91 1 0.01
92 1 0.01
93 33 0.35
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (87 bp):
TACGTCAGCTTTGCTGCGTGTTATTATCTGATCTGGCAACTTAACTACAACATATTAGTACAGCG
GTTTACTGCACTGTACTACATA
Found at i:946854 original size:16 final size:14
Alignment explanation
Indices: 946826--946873 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
946816 ATACATGTGG
*
946826 AATAAACTAAAATT
1 AATAAATTAAAATT
946840 AACTAAATATAAAATAT
1 AA-TAAAT-TAAAAT-T
946857 AATAAATTAAAAATT
1 AATAAATT-AAAATT
946872 AA
1 AA
946874 AATATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 16 0.55
17 3 0.10
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (14 bp):
AATAAATTAAAATT
Found at i:946877 original size:22 final size:24
Alignment explanation
Indices: 946835--946879 Score: 67
Period size: 22 Copynumber: 1.9 Consensus size: 24
946825 GAATAAACTA
946835 AAATTAACTAAATATAAAATATAAT
1 AAATTAAC-AAATATAAAATATAAT
946860 AAATTAA-AAAT-TAAAATATA
1 AAATTAACAAATATAAAATATA
946880 TTTAAACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
25 7 0.35
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATTAACAAATATAAAATATAAT
Found at i:954054 original size:26 final size:24
Alignment explanation
Indices: 954023--954072 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
954013 CAATTCAAAA
*
954023 TATCTACAATTTTTTTAATCTTATAT
1 TATCTACAATCTTTTT--TCTTATAT
*
954049 TATCTATAATCTTTTTTCTTATAT
1 TATCTACAATCTTTTTTCTTATAT
954073 AATATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
26 14 0.64
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (24 bp):
TATCTACAATCTTTTTTCTTATAT
Found at i:959602 original size:51 final size:51
Alignment explanation
Indices: 959484--959613 Score: 127
Period size: 51 Copynumber: 2.5 Consensus size: 51
959474 GTTTAGCCCT
* * * ** *
959484 CAAAGTATACACATTTTGTCAAATTGGTCTTAATTTAACAAATTTAGCTCG
1 CAAAATATACACATTCTGTCAACTTTATCTTAATTTAACAAATTTACCTCG
* * * * * *
959535 CAACATTTATATATTCTGTCAACTTTATTTTGATTTAACAAATTTAACCT-G
1 CAAAATATACACATTCTGTCAACTTTATCTTAATTTAACAAATTT-ACCTCG
959586 CAAAATATACACATTCTGTCAACATTTA
1 CAAAATATACACATTCTGTCAAC-TTTA
959614 CACAAGATAT
Statistics
Matches: 61, Mismatches: 16, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
51 54 0.89
52 7 0.11
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (51 bp):
CAAAATATACACATTCTGTCAACTTTATCTTAATTTAACAAATTTACCTCG
Found at i:959927 original size:12 final size:12
Alignment explanation
Indices: 959900--959932 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
959890 ACAATAATAA
959900 AATATTTA-ATT
1 AATATTTATATT
*
959911 TATATTTATATT
1 AATATTTATATT
959923 AATATTTATA
1 AATATTTATA
959933 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AATATTTATATT
Found at i:968505 original size:25 final size:25
Alignment explanation
Indices: 968460--968521 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
968450 ACGAGTTATA
* *
968460 AACGGTAAGCTCTTCCGAGCTGAA-T
1 AACGGTAAGCTCTTACAAGCT-AAGT
968485 AACGGTAAGCT-TGTACAAGCTAAGT
1 AACGGTAAGCTCT-TACAAGCTAAGT
*
968510 ATCGGTAAGCTC
1 AACGGTAAGCTC
968522 ATAAGAGCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 3 0.10
25 28 0.90
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (25 bp):
AACGGTAAGCTCTTACAAGCTAAGT
Found at i:980767 original size:189 final size:189
Alignment explanation
Indices: 980437--980815 Score: 740
Period size: 189 Copynumber: 2.0 Consensus size: 189
980427 TAATAGGAAA
980437 TTAATAATAAATTTCTAAATAAGAAAAATAAAGAAAACAGAATAATAAAGGGATTAAATCATAAA
1 TTAATAATAAATTTCTAAATAAGAAAAATAAAGAAAACAGAATAATAAAGGGATTAAATCATAAA
980502 CAAAATCGAATTAACAGGGCGCAATTGGAATTAAAGAAAAGCGAAGGACCATGCTGCAACACGCA
66 CAAAATCGAATTAACAGGGCGCAATTGGAATTAAAGAAAAGCGAAGGACCATGCTGCAACACGCA
980567 CATTACATGGGGAGCCCGATTGGGAAATATCTCGCCCCCCAAAACGTAGCGTTGCGAGC
131 CATTACATGGGGAGCCCGATTGGGAAATATCTCGCCCCCCAAAACGTAGCGTTGCGAGC
* *
980626 TTAATAGTAGATTTCTAAATAAGAAAAATAAAGAAAACAGAATAATAAAGGGATTAAATCATAAA
1 TTAATAATAAATTTCTAAATAAGAAAAATAAAGAAAACAGAATAATAAAGGGATTAAATCATAAA
980691 CAAAATCGAATTAACAGGGCGCAATTGGAATTAAAGAAAAGCGAAGGACCATGCTGCAACACGCA
66 CAAAATCGAATTAACAGGGCGCAATTGGAATTAAAGAAAAGCGAAGGACCATGCTGCAACACGCA
980756 CATTACATGGGGAGCCCGATTGGGAAATATCTCGCCCCCCAAAACGTAGCGTTGCGAGC
131 CATTACATGGGGAGCCCGATTGGGAAATATCTCGCCCCCCAAAACGTAGCGTTGCGAGC
980815 T
1 T
980816 GGACCGAAAC
Statistics
Matches: 188, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
189 188 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.19
Consensus pattern (189 bp):
TTAATAATAAATTTCTAAATAAGAAAAATAAAGAAAACAGAATAATAAAGGGATTAAATCATAAA
CAAAATCGAATTAACAGGGCGCAATTGGAATTAAAGAAAAGCGAAGGACCATGCTGCAACACGCA
CATTACATGGGGAGCCCGATTGGGAAATATCTCGCCCCCCAAAACGTAGCGTTGCGAGC
Found at i:981435 original size:12 final size:12
Alignment explanation
Indices: 981418--981454 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
981408 GCCCTTTTAC
*
981418 AGAAAAATGAAA
1 AGAAAAAAGAAA
981430 AGAAAAAAGAAA
1 AGAAAAAAGAAA
*
981442 AGAAAAAATAAA
1 AGAAAAAAGAAA
981454 A
1 A
981455 TCCCTCCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (12 bp):
AGAAAAAAGAAA
Found at i:982178 original size:87 final size:87
Alignment explanation
Indices: 982031--982355 Score: 425
Period size: 87 Copynumber: 3.7 Consensus size: 87
982021 GTTGTATTTG
* * * * * * * * * * *
982031 TGGCTTAAATATGTTTCCTTATTCTTGGGAAAGATAAGGTTCGCCATTTTGGATCTGCTCCACTA
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA
** *
982096 TTGCTTAGGGAGATAGAACCAG
66 TTGCTTAGGGAGATAGAATTAA
* * *
982118 TGGCTTAAATCAGTTTCGCTACTCCTGGGGAAGATGGGATTCGCCGTCTTCGATCCGCTCCACTA
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA
982183 TTGCTTAGGGAGATAGAATTAA
66 TTGCTTAGGGAGATAGAATTAA
* *
982205 TGGCTTAAATTTGTTTCCCTACTCCTGGGGAAAATGAGATTCGCCGTCTTCGATCCGCTCCACTA
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA
*
982270 TTGCTTAGGGAGATAGGATTAA
66 TTGCTTAGGGAGATAGAATTAA
* * ** *
982292 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATAAGATTTGTTGTCTTCGATCTGCTCCACT
1 TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACT
982356 GTTAACGCAG
Statistics
Matches: 208, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 208 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (87 bp):
TGGCTTAAATCTGTTTCCCTACTCCTGGGGAAGATGAGATTCGCCGTCTTCGATCCGCTCCACTA
TTGCTTAGGGAGATAGAATTAA
Found at i:995843 original size:12 final size:12
Alignment explanation
Indices: 995826--995856 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
995816 GCCCTTTTAC
*
995826 AGAAAAATGAAA
1 AGAAAAACGAAA
995838 AGAAAAACGAAA
1 AGAAAAACGAAA
995850 AGAAAAA
1 AGAAAAA
995857 ATAAAATCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.03
Consensus pattern (12 bp):
AGAAAAACGAAA
Found at i:997824 original size:25 final size:26
Alignment explanation
Indices: 997796--997854 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
997786 ATGCTATTCA
997796 TGAATT-TTAAATGTAGGGATGCAAC
1 TGAATTATTAAATGTAGGGATGCAAC
**
997821 TGAATTAATTATTTGTAGGGATGCAAC
1 TGAATT-ATTAAATGTAGGGATGCAAC
997848 TGAATTA
1 TGAATTA
997855 ATTATTTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 6 0.20
26 1 0.03
27 23 0.77
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.36
Consensus pattern (26 bp):
TGAATTATTAAATGTAGGGATGCAAC
Found at i:997839 original size:27 final size:27
Alignment explanation
Indices: 997807--997861 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
997797 GAATTTTAAA
997807 TGTAGGGATGCAACTGAATTAATTATT
1 TGTAGGGATGCAACTGAATTAATTATT
997834 TGTAGGGATGCAACTGAATTAATTATT
1 TGTAGGGATGCAACTGAATTAATTATT
997861 T
1 T
997862 AATCCTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (27 bp):
TGTAGGGATGCAACTGAATTAATTATT
Found at i:1001289 original size:23 final size:22
Alignment explanation
Indices: 1001251--1001295 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
1001241 TTTTGGTTTG
1001251 TAATAATTTTTTAAAAT-AAAC
1 TAATAATTTTTTAAAATGAAAC
1001272 TAATAATATTTTTAAAAATGAAAC
1 TAATAAT-TTTTT-AAAATGAAAC
1001296 AGTTCCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 5 0.24
24 4 0.19
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (22 bp):
TAATAATTTTTTAAAATGAAAC
Found at i:1001640 original size:19 final size:19
Alignment explanation
Indices: 1001616--1001683 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
1001606 AATCTTCAAG
1001616 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1001635 GATATGTC-ATCTTAGATAT
1 GATATG-CAATCTTAGATAT
1001654 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
1001673 GATATGCAATC
1 GATATGCAATC
1001684 NNNNNNNNNN
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
18 1 0.02
19 45 0.96
20 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:1001927 original size:23 final size:23
Alignment explanation
Indices: 1001883--1001927 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1001873 TCTTATTTTG
* *
1001883 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
*
1001906 TTGATTTGTATATTATTGATTT
1 TTGATTTGTATATAATTGATTT
1001928 CAAATCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:1008676 original size:88 final size:88
Alignment explanation
Indices: 1008513--1008913 Score: 500
Period size: 88 Copynumber: 4.6 Consensus size: 88
1008503 GTGAAGATAA
* * * * *
1008513 CAGATCTTGTCTTCCTGCTCCGACAACGAAGCAGATTGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
1008578 GTAGCAGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* ** * * * *
1008601 CAGATCTTGCCTTACTGCACCGACAGTGAAGCAGATCGAAGACACTAGCCTTTCATCCCTGCGTT
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
1008666 GCAGCGGAGCATGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
1008689 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
1008754 GCAGTGGAGCAGGTTAAAAATTA-
66 GCAGCGGAGCAGGTTAAAAA-TAG
* * * * *
1008777 CAGATCTTGCCTTCCTGCACCGATAGCGAAGCAGATTGAAGACACTAGCCTTGCCTCCC-AGGTT
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
1008841 GTAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *** * * *
1008864 CAGATCTTGCCTTCCTGTACCGATGGCGAAGCAGCTCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCC
1008914 CTATCTCCCT
Statistics
Matches: 272, Mismatches: 39, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
86 2 0.01
87 66 0.24
88 202 0.74
89 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.22
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:1008979 original size:44 final size:44
Alignment explanation
Indices: 1008915--1009207 Score: 154
Period size: 44 Copynumber: 6.7 Consensus size: 44
1008905 ACCCCAGCCC
* * *
1008915 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCA
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCT
* *
1008959 TATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTATGAA-TCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCT
* * * * * *
1009003 TATCTCCCTGAG-CAACAGTGGAGTAGGTTAAAAATAG-CAGATCT
1 TATCTCCCTG-GTCAGCAGTGGAATAGGTTGAAGATTGTAAG-TCT
** * * * * * * **** * *
1009047 TGCCTTCCT-GT-A-CCGATGGCGAAGCAGATCGATGA-CCCCAGCCC
1 TATCTCCCTGGTCAGCAG-T-G-GAA-TAGGTTGAAGATTGTAAGTCT
* * *
1009091 TATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCA
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCT
* *
1009135 TATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTATGAA-TCT
1 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCT
* *
1009179 TATCTCCCTGAG-CAACAGTGGAGTAGGTT
1 TATCTCCCTG-GTCAGCAGTGGAATAGGTT
1009208 AAAAATAGCA
Statistics
Matches: 181, Mismatches: 52, Indels: 32
0.68 0.20 0.12
Matches are distributed among these distances:
41 2 0.01
42 4 0.02
43 8 0.04
44 148 0.82
45 16 0.09
46 2 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCT
Found at i:1009023 original size:88 final size:88
Alignment explanation
Indices: 1008931--1009207 Score: 235
Period size: 88 Copynumber: 3.1 Consensus size: 88
1008921 CCTGGACAGT
1008931 AGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTA
1 AGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTA
1008996 TGAATCTTATCTCCCTGAGCAAC
66 TGAATCTTATCTCCCTGAGCAAC
* * * * * * ** * * * *
1009019 AGTGGAGTAGGTTAAAAATAG-CAGATCTTGCCTTCCT-GT-A-CCGATGGCGAAGCA-GATCGA
1 AGTGGAATAGGTTGAAGATTGTAAG-TCATATCTCCCTGGTCAGCAG-T-G-GAA-TATG-TTGA
* **** ** * **
1009079 TGA-CCCCAGCCCTATCTCCCTG-GACAGT
60 AGATTATGAATCTTATCTCCCTGAG-CAAC
1009107 AGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTA
1 AGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTA
1009172 TGAATCTTATCTCCCTGAGCAAC
66 TGAATCTTATCTCCCTGAGCAAC
*
1009195 AGTGGAGTAGGTT
1 AGTGGAATAGGTT
1009208 AAAAATAGCA
Statistics
Matches: 130, Mismatches: 45, Indels: 28
0.64 0.22 0.14
Matches are distributed among these distances:
85 2 0.02
86 2 0.02
87 12 0.09
88 98 0.75
89 12 0.09
90 2 0.02
91 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (88 bp):
AGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCAGCAGTGGAATATGTTGAAGATTA
TGAATCTTATCTCCCTGAGCAAC
Found at i:1009273 original size:176 final size:176
Alignment explanation
Indices: 1008843--1009235 Score: 759
Period size: 176 Copynumber: 2.2 Consensus size: 176
1008833 CCCAGGTTGT
* *
1008843 AGTGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACCGATGGCGAAGCAGCTCGATGACC
1 AGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACCGATGGCGAAGCAGATCGATGACC
1008908 CCAGCCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCA
66 CCAGCCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCA
1008973 GCAGTGGAATATGTTGAAGATTATGAATCTTATCTCCCTGAGCAAC
131 GCAGTGGAATATGTTGAAGATTATGAATCTTATCTCCCTGAGCAAC
1009019 AGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACCGATGGCGAAGCAGATCGATGACC
1 AGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACCGATGGCGAAGCAGATCGATGACC
1009084 CCAGCCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCA
66 CCAGCCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCA
1009149 GCAGTGGAATATGTTGAAGATTATGAATCTTATCTCCCTGAGCAAC
131 GCAGTGGAATATGTTGAAGATTATGAATCTTATCTCCCTGAGCAAC
*
1009195 AGTGGAGTAGGTTAAAAATAGCAGATCTTGCATTCCTGTAC
1 AGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTAC
1009236 TGGCAGTGAA
Statistics
Matches: 214, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
176 214 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (176 bp):
AGTGGAGTAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACCGATGGCGAAGCAGATCGATGACC
CCAGCCCTATCTCCCTGGACAGTAGTGGAATAGGTTGAAGATTGTAAGTCATATCTCCCTGGTCA
GCAGTGGAATATGTTGAAGATTATGAATCTTATCTCCCTGAGCAAC
Found at i:1009346 original size:50 final size:50
Alignment explanation
Indices: 1009292--1009431 Score: 208
Period size: 50 Copynumber: 2.8 Consensus size: 50
1009282 GCAATGGAAA
* * * *
1009292 AGATTGAAGCCACAACAGCGAATCTTATTTCCCTAGCGTTGTAACAGAGC
1 AGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTGTAACAGAGC
* *
1009342 AGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCATTGTAGCAGAGC
1 AGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTGTAACAGAGC
* *
1009392 AGATTGAAGCCACGATGGAGAATCTTATCTCCCTGGCGTT
1 AGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTT
1009432 AAGGCTTGGA
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 81 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (50 bp):
AGATTGAAGCCACGACGGCGAATCTTATCTCCCTGGCGTTGTAACAGAGC
Found at i:1009986 original size:173 final size:172
Alignment explanation
Indices: 1009799--1010172 Score: 500
Period size: 173 Copynumber: 2.2 Consensus size: 172
1009789 GTAAGCAAGC
* * * **
1009799 CTTATCCTCCTGAAGTTGTTGT-GAGGCAAACTAAATATGGCGAATCTTATCTCCCTGAAGTTAC
1 CTTAT-CTCCTGAAGTTGTAGTGGA-GCAAACCAAAGAAAGCGAATCTTATCTCCCTGAAGTTAC
* * * *
1009863 AGTGGAGTAGATTAAAGCCAATAATCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTAAAATCAC
64 AGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCAC
*
1009928 AGATCTTATCTCTCTGAAGTTATAGAGAGCAAATCGCATC-AGGT
129 AGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCTA-GT
* * * * * * *
1009972 CTTATCTACCTGAAGATGTAGTGGAGTAGACCCAAGAAAGCGAGTCTTATCTCTCTGAAGTTGCA
1 CTTATCT-CCTGAAGTTGTAGTGGAGCAAACCAAAGAAAGCGAATCTTATCTCCCTGAAGTTACA
1010037 GTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCACA
65 GTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCACA
* *
1010102 GATTTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTAGT
130 GATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCTAGT
**
1010145 CTTATCTCCCTGAAGTTACAGTGGAGCA
1 CTTATCT-CCTGAAGTTGTAGTGGAGCA
1010173 GACTAAGTAA
Statistics
Matches: 174, Mismatches: 24, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
172 2 0.01
173 169 0.97
174 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (172 bp):
CTTATCTCCTGAAGTTGTAGTGGAGCAAACCAAAGAAAGCGAATCTTATCTCCCTGAAGTTACAG
TGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCACAG
ATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCTAGT
Found at i:1009997 original size:217 final size:218
Alignment explanation
Indices: 1009618--1010034 Score: 597
Period size: 217 Copynumber: 1.9 Consensus size: 218
1009608 AAGACTGAAG
* * *
1009618 ATGGCGAATCTTATCTCCTTGAAGTTGCAGTGGGGCAGATTAAAGCCAATAATCCTATCTCCCTA
1 ATGGCGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTA
* *
1009683 AAGTCACAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGC
66 AAGTCACAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTAAAGTTACAGAGAGCAAATCGC
* * * *
1009748 ATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGTAAGCAAGCCTTATC-CTCCTG
131 ATCTAGTCTTATCTACCTGAAGATGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTATCTCT-CTG
1009811 AAGTTGTTGTGAGGCAAACTAAAT
195 AAGTTGTTGTGAGGCAAACTAAAT
* * *
1009835 ATGGCGAATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCTTG
1 ATGGCGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTA
** ** * *
1009900 AAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTATAGAGAGCAAATCGC
66 AAGTCACAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTAAAGTTACAGAGAGCAAATCGC
* * * *
1009965 ATC-AGGTCTTATCTACCTGAAGATGTAGTGGAGTAGACCCAAGAAAGCGAGTCTTATCTCTCTG
131 ATCTA-GTCTTATCTACCTGAAGATGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTATCTCTCTG
1010029 AAGTTG
195 AAGTTG
1010035 CAGTGGAGCA
Statistics
Matches: 175, Mismatches: 22, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
216 1 0.01
217 147 0.84
218 25 0.14
219 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (218 bp):
ATGGCGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTA
AAGTCACAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTAAAGTTACAGAGAGCAAATCGC
ATCTAGTCTTATCTACCTGAAGATGCAGTGGAGCAGACCCAAGAAAGCAAGCCTTATCTCTCTGA
AGTTGTTGTGAGGCAAACTAAAT
Found at i:1010076 original size:44 final size:43
Alignment explanation
Indices: 1010019--1010291 Score: 152
Period size: 44 Copynumber: 6.3 Consensus size: 43
1010009 AAGCGAGTCT
*
1010019 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAATCC
* * * * **
1010063 TATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCACA-GATTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-ATAATCC
* * * * * * *
1010107 TATCTCTCTGAAGTTACAG-AGAGCAGA-T--CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-ATAATCC
* * * * *
1010147 TATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGTAAGCAAGCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-TAATCC
* * * *
1010190 TTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGC--GAATCT
1 -TATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A--GCAATAATCC
1010236 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAATCC
1010280 TATCTCCCTGAA
1 TATCTCCCTGAA
1010292 NNNNNNNNNN
Statistics
Matches: 169, Mismatches: 40, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
39 2 0.01
40 20 0.12
41 8 0.05
42 3 0.02
43 14 0.08
44 87 0.51
45 26 0.15
46 7 0.04
47 1 0.01
49 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAATCC
Found at i:1010121 original size:217 final size:215
Alignment explanation
Indices: 1009624--1010291 Score: 577
Period size: 217 Copynumber: 3.1 Consensus size: 215
1009614 GAAGATGGCG
* * ** * * * * *
1009624 AATCTTATCTCCTTGAAGTTGCAGTGGGGCAGATTAAAGCCAATAATCCTATCTCCCTAAAGTCA
1 AATCCTATCTCCCTGAAGTCACAGTGGAGCAGATTAAAACCAATAATCCTATCTCCTTGAAGTTA
* * *
1009689 CAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTAAAGTTGCAGAGAGCAGATCGCATCTAG
66 CAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATC-AG
* * * * *
1009754 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGTAAGCAAGCCTTATC-CTCCTGAAGTTG
130 TCTTATCT-CCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAGTCTTATCTCT-CTGAAGTTG
** * * * *
1009817 TTGT-GAGGCAAACTAAATATGGC--G
193 CAGTGGA-GCAGA-TTAA-A-GCCAAT
* * * * *
1009841 AATCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCTTGAAGTTG
1 AATCCTATCTCCCTGAAGTCACAGTGGAGCAGATTAAAACCAATAATCCTATCTCCTTGAAGTTA
** *
1009906 CAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTATAGAGAGCAAATCGCATCAGG
66 CAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCA-G
* *
1009971 TCTTATCTACCTGAAGATGTAGTGGAGTAGACCCAAGAAAGCGAGTCTTATCTCTCTGAAGTTGC
130 TCTTATCT-CCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAGTCTTATCTCTCTGAAGTTGC
1010036 AGTGGAGCAGATTAAAGCCAAT
194 AGTGGAGCAGATTAAAGCCAAT
* * * * **
1010058 AATCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCACA-GATTTTATCT-CTCTGAAGT
1 AATCCTATCTCCCTGAAGTCACAGTGGAGCAGATTAAAACCA-ATAATCCTATCTCCT-TGAAGT
* *** * * * * * *
1010121 TACAG-AGAGCAGA-TCGCATC-TAG-TCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTA
64 TACAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAG-AGAGCA-AAT-CG-C
* * ** ** * *
1010182 AGCAAGCCTTATCCTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCGAATCTTATCTCCCTG
125 ATC-AGTCTTAT-CTCCTGAAGTTGTAGTGGA-GCAGACCCAAGAAAGCGAGTCTTATCTCTCTG
1010246 AAGTTGCAGTGGAGCAGATTAAAGCCAAT
187 AAGTTGCAGTGGAGCAGATTAAAGCCAAT
1010275 AATCCTATCTCCCTGAA
1 AATCCTATCTCCCTGAA
1010292 NNNNNNNNNN
Statistics
Matches: 374, Mismatches: 62, Indels: 30
0.80 0.13 0.06
Matches are distributed among these distances:
213 20 0.05
214 7 0.02
215 8 0.02
216 12 0.03
217 288 0.77
218 35 0.09
219 4 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.27
Consensus pattern (215 bp):
AATCCTATCTCCCTGAAGTCACAGTGGAGCAGATTAAAACCAATAATCCTATCTCCTTGAAGTTA
CAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCAGT
CTTATCTCCTGAAGTTGTAGTGGAGCAGACCCAAGAAAGCGAGTCTTATCTCTCTGAAGTTGCAG
TGGAGCAGATTAAAGCCAAT
Found at i:1010160 original size:84 final size:84
Alignment explanation
Indices: 1009890--1010171 Score: 259
Period size: 84 Copynumber: 3.3 Consensus size: 84
1009880 CCAATAATCC
* * *
1009890 TATCTCCTTGAAGTTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTATAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAG
*
1009955 AGCAAATCGCATC-AGGTCT
66 AGCAGATCGCATCTA-GTCT
* * * ** ** *
1009974 TATCTACCTGAAGATGTAGTGGAGTAGACCCAAGAA--AGC-GAGTCTTATCTCTCTGAAGTTGC
1 TATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AATCA-CAGA-TCTTATCTCTCTGAAGTTAC
* * * * *
1010036 AGTGGAGCAGATTAAAGCCA-ATAATCC
62 AG-AGAGCAGA-T--CG-CATCTAGTCT
* *
1010063 TATCTCCCTGAAGTCGCAGTGGAGCGGATTAAAATCACAGATTTTATCTCTCTGAAGTTACAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAG
1010128 AGCAGATCGCATCTAGTCT
66 AGCAGATCGCATCTAGTCT
*
1010147 TATCTCCCTGAAGTTACAGTGGAGC
1 TATCTCCCTGAAGTTGCAGTGGAGC
1010172 AGACTAAGTA
Statistics
Matches: 152, Mismatches: 32, Indels: 28
0.72 0.15 0.13
Matches are distributed among these distances:
83 2 0.01
84 54 0.36
85 23 0.15
86 9 0.06
87 10 0.07
88 23 0.15
89 28 0.18
90 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (84 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAG
AGCAGATCGCATCTAGTCT
Found at i:1010242 original size:173 final size:172
Alignment explanation
Indices: 1009844--1010268 Score: 509
Period size: 173 Copynumber: 2.5 Consensus size: 172
1009834 TATGGCGAAT
* * * * * *
1009844 CTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCAATAATCCTATCTCCTTGAAGTTGCAG
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATGAAAGCC-AGAATCCTATCTCCCTGAAGTTGCAG
* *
1009909 TGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTATAGAGAGCAAATCGCATCAGGTCT
65 TGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCAGGTCT
** * * *
1009974 TATCTACCTGAAGATGTAGTGGAGTAGACCCAAGAAAGCGAGT
130 TATCTACCTGAAGATACAGTGGAGCAGACCCAAGAAAGCAAGC
* * *
1010017 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTCGCAG
1 CTTATCTCTCTGAAGTTGCAGTGGAGCAGATGAAAGCC-AGAATCCTATCTCCCTGAAGTTGCAG
* *
1010082 TGGAGCGGATTAAAATCACAGATTTTATCTCTCTGAAGTTACAGAGAGCAGATCGCATCTA-GTC
65 TGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATC-AGGTC
* * * *
1010146 TTATCTCCCTGAAGTTACAGTGGAGCAGA-CTAAGTAAGCAAGC
129 TTATCTACCTGAAGATACAGTGGAGCAGACCCAAGAAAGCAAGC
* * *
1010189 CTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGC-GAATCTTATCTCCCTGAAGTT
1 CTTATCTCT-CTGAAGTTGCAGTGGA-GCAGA-TGAA-A-GCCAGAATCCTATCTCCCTGAAGTT
*
1010251 GCAGTGGAGCAGATTAAA
61 GCAGTGGAGCGGATTAAA
1010269 GCCAATAATC
Statistics
Matches: 221, Mismatches: 25, Indels: 12
0.86 0.10 0.05
Matches are distributed among these distances:
171 4 0.02
172 33 0.15
173 180 0.81
174 2 0.01
175 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (172 bp):
CTTATCTCTCTGAAGTTGCAGTGGAGCAGATGAAAGCCAGAATCCTATCTCCCTGAAGTTGCAGT
GGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACAGAGAGCAAATCGCATCAGGTCTT
ATCTACCTGAAGATACAGTGGAGCAGACCCAAGAAAGCAAGC
Found at i:1010263 original size:45 final size:44
Alignment explanation
Indices: 1009752--1010263 Score: 215
Period size: 44 Copynumber: 11.8 Consensus size: 44
1009742 GATCGCATCT
1009752 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* ** * * *
1009796 AGCCTTATC-CTCCTGAAGTTGTTGT-GAGGCAAACTAAATATGGCGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTAAGTA-AGC-A
* * * * *
1009842 A-TCTTATCTCCCTGAAGTTACAGTGGAGTAGATTAAAGCCAA-TA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
* * ** * *
1009886 A-TCCTATCTCCTTGAAGTTGCAGTGGAGTGGATTAA--AATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* ** * * * * *
1009927 CAGATCTTATCTCTCTGAAGTTATAG-AGAGCA-AAT-CG-CATCA
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * * * * * * *
1009969 GGTCTTATCTACCTGAAGATGTAGTGGAGTAGACCCAAGAAAGCG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGTAAGCA
* * * *
1010014 AGTCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-TA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-TAAGCA
* * * * *
1010059 A-TCCTATCTCCCTGAAGTCGCAGTGGAGCGGATTAA--AATCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * * * * * * *
1010100 CAGATTTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CG-CATCT
1 -AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
*
1010142 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * *
1010186 AGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAG-ATGGCGA
1 AGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGTA-AGC-A
1010232 A-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
1010264 TTAAAGCCAA
Statistics
Matches: 347, Mismatches: 85, Indels: 71
0.69 0.17 0.14
Matches are distributed among these distances:
40 42 0.12
41 16 0.05
42 14 0.04
43 20 0.06
44 155 0.45
45 85 0.24
46 14 0.04
47 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
Found at i:1027535 original size:1 final size:1
Alignment explanation
Indices: 1027531--1027596 Score: 60
Period size: 1 Copynumber: 66.0 Consensus size: 1
1027521 AAAAAAGGAC
* * * * * * * *
1027531 AAAAAAAACAAAAACAAAAACAAAAAAAACAAAAACAAAAAAACAAAAAAAAAAGAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1027596 A
1 A
1027597 TCAAGATGAA
Statistics
Matches: 49, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.88, C:0.09, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:1027547 original size:15 final size:14
Alignment explanation
Indices: 1027519--1027584 Score: 87
Period size: 14 Copynumber: 4.6 Consensus size: 14
1027509 TATTATGCTT
**
1027519 AAAAAAAAGGACAA
1 AAAAAAAAAAACAA
1027533 AAAAAACAAAAACAA
1 AAAAAA-AAAAACAA
1027548 AAACAAAAAAAACAA
1 AAA-AAAAAAAACAA
*
1027563 AAACAAAAAAACAA
1 AAAAAAAAAAACAA
1027577 AAAAAAAA
1 AAAAAAAA
1027585 GAAAAAGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
14 23 0.50
15 20 0.43
16 3 0.07
ACGTcount: A:0.86, C:0.11, G:0.03, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAACAA
Found at i:1027553 original size:21 final size:21
Alignment explanation
Indices: 1027529--1027596 Score: 95
Period size: 21 Copynumber: 3.3 Consensus size: 21
1027519 AAAAAAAAGG
1027529 ACAAAAAAAACAAAAACAAAA
1 ACAAAAAAAACAAAAACAAAA
1027550 ACAAAAAAAACAAAAACAAAA
1 ACAAAAAAAACAAAAACAAAA
* *
1027571 A-AACAAAAA-AAAAAGAAAA
1 ACAAAAAAAACAAAAACAAAA
*
1027590 AGAAAAA
1 ACAAAAA
1027597 TCAAGATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 10 0.23
20 11 0.26
21 22 0.51
ACGTcount: A:0.87, C:0.10, G:0.03, T:0.00
Consensus pattern (21 bp):
ACAAAAAAAACAAAAACAAAA
Found at i:1027596 original size:15 final size:15
Alignment explanation
Indices: 1027529--1027584 Score: 82
Period size: 15 Copynumber: 3.9 Consensus size: 15
1027519 AAAAAAAAGG
1027529 ACAAAAA-AAACAAAA
1 ACAAAAACAAA-AAAA
1027544 ACAAAAACAAAAAAA
1 ACAAAAACAAAAAAA
1027559 ACAAAAAC-AAAAAA
1 ACAAAAACAAAAAAA
1027573 ACAAAAA-AAAAA
1 ACAAAAACAAAAA
1027585 GAAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
14 17 0.44
15 19 0.49
16 3 0.08
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (15 bp):
ACAAAAACAAAAAAA
Found at i:1031342 original size:78 final size:79
Alignment explanation
Indices: 1031185--1031531 Score: 333
Period size: 74 Copynumber: 4.5 Consensus size: 79
1031175 NNNNNNNNNN
* * *
1031185 AGAGGTGAGTTGAGCCTCGGGT--CACGCTGAGGTA--T-TTTTCAATTTCTATTTTTCAAAAAT
1 AGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTATTTTAAATTTCTATTTTTAAAAAAT
*
1031245 CAACTCATATTGCG
66 CAACTCATAATGCG
* *
1031259 AGAGGTGAGTTGAGCCTCAGGTCACACGCCGAGGTATTTATTTTAAATTTCTATTTTT-TAAAAT
1 AGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTATTTTAAATTTCTATTTTTAAAAAAT
1031323 CAACTCATAATGCG
66 CAACTCATAATGCG
* * * * ***
1031337 AGAGGTGAGTTGAGCCTCGGGT--CACTCTGAGG----TATTTTCAATTTCTGTTTTTTTTTAAA
1 AGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTATTTTAAATTTCT-ATTTTTAAAAAA
*
1031396 TCAACTCATATTGCG
65 TCAACTCATAATGCG
* * * * * * *
1031411 AGAAGTGAGTTGAGCCT-TGGACACATGCCGAGGTATTTCTTTTATATTTCTGTTTTTCAAAAAA
1 AGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTATTTTAAATTTCTATTTTT----AAA
* *
1031475 AAATCAACTCTTAATGCT
62 AAATCAACTCATAATGCG
* *
1031493 AGAGGTGAGTTGAGCCTCGGGCCACACGGCGAGGTATTT
1 AGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTT
1031532 TCAATTTCTG
Statistics
Matches: 222, Mismatches: 33, Indels: 27
0.79 0.12 0.10
Matches are distributed among these distances:
72 13 0.06
73 7 0.03
74 55 0.25
75 7 0.03
76 19 0.09
78 45 0.20
79 28 0.13
82 31 0.14
83 17 0.08
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (79 bp):
AGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTATTTTAAATTTCTATTTTTAAAAAAT
CAACTCATAATGCG
Found at i:1031697 original size:10 final size:9
Alignment explanation
Indices: 1031680--1031708 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
1031670 TAATTTTGTG
1031680 TTAAAAAAA
1 TTAAAAAAA
1031689 TTAAAAAAA
1 TTAAAAAAA
1031698 TTAAAAAAA
1 TTAAAAAAA
1031707 TT
1 TT
1031709 GCATTTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:1031773 original size:29 final size:30
Alignment explanation
Indices: 1031734--1031828 Score: 156
Period size: 30 Copynumber: 3.2 Consensus size: 30
1031724 TACTTTCTTG
1031734 AAATTACATTTCAACCCCTAAAATTT-TCT
1 AAATTACATTTCAACCCCTAAAATTTCTCT
* *
1031763 AAATTACATTTTAACCCCTAAAATTTCTCA
1 AAATTACATTTCAACCCCTAAAATTTCTCT
*
1031793 AAATTACATTTCAACCCCTAAACTTTCTCT
1 AAATTACATTTCAACCCCTAAAATTTCTCT
1031823 AAATTA
1 AAATTA
1031829 TGTTTTGGCC
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
29 25 0.42
30 35 0.58
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (30 bp):
AAATTACATTTCAACCCCTAAAATTTCTCT
Found at i:1032309 original size:4 final size:4
Alignment explanation
Indices: 1032295--1032373 Score: 60
Period size: 4 Copynumber: 19.5 Consensus size: 4
1032285 AGTCGAAGGG
*
1032295 AAGA AAG- AAGA AAGA AAGA AAGA AA-A AGAGAA AAAA AAGA AAGA AA-A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA A-AG-A AAGA AAGA AAGA AAGA
1032342 AAGA GAA-A AATGA AAGAA AAGGA AA-A AAGA AA
1 AAGA -AAGA AA-GA AAG-A AA-GA AAGA AAGA AA
1032374 AATATAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
3 13 0.21
4 34 0.55
5 12 0.19
6 3 0.05
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (4 bp):
AAGA
Found at i:1032311 original size:11 final size:11
Alignment explanation
Indices: 1032294--1032372 Score: 51
Period size: 11 Copynumber: 7.3 Consensus size: 11
1032284 AAGTCGAAGG
1032294 GAAGAAAG-AA
1 GAAGAAAGAAA
1032304 GAAAGAAAGAAA
1 G-AAGAAAGAAA
1032316 GAA-AAAGAGAA
1 GAAGAAAGA-AA
*
1032327 -AAAAAAGAAA
1 GAAGAAAGAAA
*
1032337 GAAAAAAGAGAA
1 GAAGAAAGA-AA
*
1032349 AAATGAAAGAAA
1 GAA-GAAAGAAA
*
1032361 -AGGAAA-AAA
1 GAAGAAAGAAA
1032370 GAA
1 GAA
1032373 AAATATAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
9 3 0.05
10 15 0.26
11 25 0.44
12 9 0.16
13 5 0.09
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (11 bp):
GAAGAAAGAAA
Found at i:1032335 original size:29 final size:31
Alignment explanation
Indices: 1032295--1032373 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 31
1032285 AGTCGAAGGG
1032295 AAGAAAGAAGAAAGAAAGAAAGA-AAAAGA-GA
1 AAGAAA-AAGAAAGAAAGAAAGAGAAAA-ATGA
1032326 AA-AAAAAGAAAGAAA-AAAGAGAAAAATGA
1 AAGAAAAAGAAAGAAAGAAAGAGAAAAATGA
*
1032355 AAGAAAAGGAAA-AAAGAAA
1 AAGAAAAAGAAAGAAAGAAA
1032374 AATATAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 6 0.14
29 21 0.49
30 14 0.33
31 2 0.05
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (31 bp):
AAGAAAAAGAAAGAAAGAAAGAGAAAAATGA
Found at i:1032341 original size:20 final size:20
Alignment explanation
Indices: 1032309--1032369 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
1032299 AAGAAGAAAG
1032309 AAAGAAAGAAAAAGAGAAAAA
1 AAAGAAAG-AAAAGAGAAAAA
* *
1032330 AAAGAAAGAAAAAAGAGAAA
1 AAAGAAAGAAAAGAGAAAAA
*
1032350 AATGAAAGAAAAG-GAAAAA
1 AAAGAAAGAAAAGAGAAAAA
1032369 A
1 A
1032370 GAAAAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
19 6 0.17
20 21 0.60
21 8 0.23
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAAAAGAGAAAAA
Found at i:1032367 original size:24 final size:22
Alignment explanation
Indices: 1032300--1032375 Score: 93
Period size: 22 Copynumber: 3.3 Consensus size: 22
1032290 AAGGGAAGAA
1032300 AGAAGAAAGAAAGAAAGAAAAAG
1 AGAA-AAAGAAAGAAAGAAAAAG
1032323 AGAAAAA-AAAGAAAGAAAAAAG
1 AGAAAAAGAAAGAAAG-AAAAAG
1032345 AGAAAAATGAAAGAAAAGGAAAAA-
1 AGAAAAA-GAAAG-AAA-GAAAAAG
1032369 AGAAAAA
1 AGAAAAA
1032376 TATAAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
21 8 0.17
22 16 0.33
23 4 0.08
24 11 0.23
25 8 0.17
26 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
AGAAAAAGAAAGAAAGAAAAAG
Found at i:1032368 original size:17 final size:18
Alignment explanation
Indices: 1032295--1032373 Score: 74
Period size: 17 Copynumber: 4.3 Consensus size: 18
1032285 AGTCGAAGGG
1032295 AAGAAAGAAGAA-AGAAAGA
1 AAGAAAGAA-AAGAGAAA-A
* *
1032314 AAGAAA-AAGAGAAAAAA
1 AAGAAAGAAAAGAGAAAA
1032331 AAGAAAGAAAAAAGAGAAAA
1 AAGAAAG--AAAAGAGAAAA
*
1032351 ATGAAAGAAAAG-GAAAA
1 AAGAAAGAAAAGAGAAAA
1032368 AAGAAA
1 AAGAAA
1032374 AATATAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
17 18 0.36
18 11 0.22
19 6 0.12
20 15 0.30
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (18 bp):
AAGAAAGAAAAGAGAAAA
Found at i:1032433 original size:19 final size:18
Alignment explanation
Indices: 1032409--1032462 Score: 90
Period size: 19 Copynumber: 2.9 Consensus size: 18
1032399 TCGGGTCTAT
1032409 TTGACCCGACCCGTTCGAA
1 TTGACCCGACCCGTT-GAA
1032428 TTGACCCGACCCGTGTGAA
1 TTGACCCGACCCGT-TGAA
1032447 TTGACCCGACCCGTTG
1 TTGACCCGACCCGTTG
1032463 CAGCAGCCCC
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
18 2 0.06
19 31 0.91
20 1 0.03
ACGTcount: A:0.19, C:0.35, G:0.24, T:0.22
Consensus pattern (18 bp):
TTGACCCGACCCGTTGAA
Found at i:1038921 original size:21 final size:22
Alignment explanation
Indices: 1038895--1038937 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1038885 GAATTGAATT
1038895 TAAAGTTATGAAT-TAT-ATATA
1 TAAAGTT-TGAATGTATGATATA
1038916 TAAAGTTTGAATGTATGATATA
1 TAAAGTTTGAATGTATGATATA
1038938 AGTTCTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.14, T:0.42
Consensus pattern (22 bp):
TAAAGTTTGAATGTATGATATA
Found at i:1038936 original size:20 final size:21
Alignment explanation
Indices: 1038895--1038938 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1038885 GAATTGAATT
*
1038895 TAAAGTTATGAATTATATATA
1 TAAAGTTATGAATTATAGATA
1038916 TAAAGTT-TGAATGTAT-GATA
1 TAAAGTTATGAAT-TATAGATA
1038936 TAA
1 TAA
1038939 GTTCTTTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.45, C:0.00, G:0.14, T:0.41
Consensus pattern (21 bp):
TAAAGTTATGAATTATAGATA
Found at i:1039288 original size:41 final size:41
Alignment explanation
Indices: 1039231--1039387 Score: 165
Period size: 41 Copynumber: 3.8 Consensus size: 41
1039221 TTTGAGATTT
* * * *
1039231 TCAGGCTTAATGCCTAGCAGACTTGATGTCGGTGGATTACA
1 TCAGGCTTTATGCCTAGCAGACTTGATGCCGGTGAATTATA
* *
1039272 TCAGGCTTTATGCCTAGCAGGC-TCAGTGCCGGTGAATTATA
1 TCAGGCTTTATGCCTAGCAGACTTGA-TGCCGGTGAATTATA
* * * *
1039313 TCAGACTTTATGTCTAGCAGACTTTG-TGCCGGTGAAATGTA
1 TCAGGCTTTATGCCTAGCAGAC-TTGATGCCGGTGAATTATA
* * *
1039354 TCAGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TCAGGCTTTATGCCTAGCAGACTTGATGCCGGTG
1039388 TTTTATACAA
Statistics
Matches: 95, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
40 4 0.04
41 90 0.95
43 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (41 bp):
TCAGGCTTTATGCCTAGCAGACTTGATGCCGGTGAATTATA
Found at i:1039401 original size:41 final size:40
Alignment explanation
Indices: 1039232--1039406 Score: 131
Period size: 41 Copynumber: 4.3 Consensus size: 40
1039222 TTGAGATTTT
* * * * *
1039232 CAGGCTTAATGCCTAGCAGACTTGATGTCGGTGGA-TTACA
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGT-GATTTATA
* *
1039272 TCAGGCTTTATGCCTAGCAGGC-TCAGTGCCGGTGAATTATA
1 -CAGGCTTTATGCCTAGCAGGCTTTA-TGCCGGTGATTTATA
* * * * *
1039313 TCAGACTTTATGTCTAGCAGACTTTGTGCCGGTGAAATGTAT-
1 -CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG--ATTTATA
* *
1039355 CAGGCTTTGTGCCTAGCAGGCTTTATGCCGGTGTTTTATA
1 CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGATTTATA
*
1039395 CAAGGCTCTATG
1 C-AGGCTTTATG
1039407 TTCTATAAAT
Statistics
Matches: 106, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
39 4 0.04
40 5 0.05
41 92 0.87
42 1 0.01
43 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (40 bp):
CAGGCTTTATGCCTAGCAGGCTTTATGCCGGTGATTTATA
Found at i:1049504 original size:2 final size:2
Alignment explanation
Indices: 1049497--1049533 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
1049487 AATAATTAGA
1049497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
1049534 GGATAAAANN
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1050198 original size:39 final size:39
Alignment explanation
Indices: 1050142--1050368 Score: 185
Period size: 39 Copynumber: 5.8 Consensus size: 39
1050132 AAGCATTTGA
* *
1050142 TTACAAAGTT-GTGTTTCCAATAAGAATTTTAGTATTTTG
1 TTACAAAATTGGT-TTTCCAATAAGAATTTTAGTATTTAG
* * *
1050181 TTACAAAATTGGTTTTCCAATAGGAATTATAGTA-ATAG
1 TTACAAAATTGGTTTTCCAATAAGAATTTTAGTATTTAG
* * * *
1050219 TTGAGAGACTATGG-TTTCCAATTAAGAATTTTAGTATTTGG
1 TT-ACAAAAT-TGGTTTTCCAA-TAAGAATTTTAGTATTTAG
* * *
1050260 TTACAAAATTGATTTTCCAATAAGAATTTTATTA-GTAG
1 TTACAAAATTGGTTTTCCAATAAGAATTTTAGTATTTAG
* * * *
1050298 TTGAGAGATTATGG-TTTCCATTAAGAATTTTAGTATTTAG
1 TT-ACAAAAT-TGGTTTTCCAATAAGAATTTTAGTATTTAG
* * * *
1050338 TTACAAAATTGATTTCCCTATAGGAATTTTA
1 TTACAAAATTGGTTTTCCAATAAGAATTTTA
1050369 TTAATAGTTG
Statistics
Matches: 144, Mismatches: 34, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
38 10 0.07
39 95 0.66
40 35 0.24
41 4 0.03
ACGTcount: A:0.34, C:0.08, G:0.16, T:0.42
Consensus pattern (39 bp):
TTACAAAATTGGTTTTCCAATAAGAATTTTAGTATTTAG
Found at i:1050248 original size:40 final size:39
Alignment explanation
Indices: 1050154--1050410 Score: 157
Period size: 39 Copynumber: 6.6 Consensus size: 39
1050144 ACAAAGTTGT
* * * *
1050154 GTTTCCAATAAGAATTTTAGTATTTTGTT-ACAAAAT-TG
1 GTTTCCAATAAGAATTTTAGTA-ATAGTTGAGAGAATATG
* * *
1050192 GTTTTCCAATAGGAATTATAGTAATAGTTGAGAGACTATG
1 G-TTTCCAATAAGAATTTTAGTAATAGTTGAGAGAATATG
* * * *
1050232 GTTTCCAATTAAGAATTTTAGTATTTGGTT-ACAAAAT-TG
1 GTTTCCAA-TAAGAATTTTAGTA-ATAGTTGAGAGAATATG
* * * *
1050271 ATTTTCCAATAAGAATTTTATTAGTAGTTGAGAGATTATG
1 -GTTTCCAATAAGAATTTTAGTAATAGTTGAGAGAATATG
* * * *
1050311 GTTTCCATTAAGAATTTTAGTATTTAGTT-ACAAAAT-TG
1 GTTTCCAATAAGAATTTTAGTA-ATAGTTGAGAGAATATG
* * * * * * *
1050349 ATTTCCCTATAGGAATTTTATTAATAGTTGAGATATTATA
1 GTTT-CCAATAAGAATTTTAGTAATAGTTGAGAGAATATG
**
1050389 GTTTATAATAAGAATTTTAGTA
1 GTTTCCAATAAGAATTTTAGTA
1050411 TTTGGGTTTT
Statistics
Matches: 163, Mismatches: 44, Indels: 23
0.71 0.19 0.10
Matches are distributed among these distances:
38 19 0.12
39 103 0.63
40 37 0.23
41 4 0.02
ACGTcount: A:0.35, C:0.07, G:0.16, T:0.43
Consensus pattern (39 bp):
GTTTCCAATAAGAATTTTAGTAATAGTTGAGAGAATATG
Found at i:1050365 original size:78 final size:78
Alignment explanation
Indices: 1050154--1050413 Score: 376
Period size: 78 Copynumber: 3.3 Consensus size: 78
1050144 ACAAAGTTGT
* * * *
1050154 GTTTCCAATAAGAATTTTAGTATTTTGTTACAAAATTGGTTTTCCAATAGGAATTATAGTAATAG
1 GTTTCCAATAAGAATTTTAGTATTTAGTTACAAAATTGATTTTCCAATAGGAATTTTATTAATAG
*
1050219 TTGAGAGACTATG
66 TTGAGAGATTATG
* * *
1050232 GTTTCCAATTAAGAATTTTAGTATTTGGTTACAAAATTGATTTTCCAATAAGAATTTTATTAGTA
1 GTTTCCAA-TAAGAATTTTAGTATTTAGTTACAAAATTGATTTTCCAATAGGAATTTTATTAATA
1050297 GTTGAGAGATTATG
65 GTTGAGAGATTATG
* * *
1050311 GTTTCCATTAAGAATTTTAGTATTTAGTTACAAAATTGATTTCCCTATAGGAATTTTATTAATAG
1 GTTTCCAATAAGAATTTTAGTATTTAGTTACAAAATTGATTTTCCAATAGGAATTTTATTAATAG
* *
1050376 TTGAGATATTATA
66 TTGAGAGATTATG
**
1050389 GTTTATAATAAGAATTTTAGTATTT
1 GTTTCCAATAAGAATTTTAGTATTT
1050414 GGGTTTTTTT
Statistics
Matches: 163, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
78 93 0.57
79 70 0.43
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (78 bp):
GTTTCCAATAAGAATTTTAGTATTTAGTTACAAAATTGATTTTCCAATAGGAATTTTATTAATAG
TTGAGAGATTATG
Found at i:1050445 original size:157 final size:157
Alignment explanation
Indices: 1050154--1050450 Score: 337
Period size: 157 Copynumber: 1.9 Consensus size: 157
1050144 ACAAAGTTGT
* * *
1050154 GTTTCCAATAAGAATTTTAGTATTTTGTTACAAAATTGGTTTTCCAATAGGAATTATAGTAATAG
1 GTTTCCAATAAGAATTTTAGTATTTAGTTACAAAATTGATTTCCCAATAGGAATTATAGTAATAG
* * * *** ** *
1050219 TTGAGAGACTATGGTTTCCAATTAAGAATTTTAGTATTTGGTTACAAAATTGATTTTCCAATAAG
66 TTGAGAGACTATAGTTTACAATTAAGAATTTTAGTATTTGGTTACAAAATTAAAAATAAAATAAA
*
1050284 AATTTTATTAGTAGTTGAGAGATTATG
131 AATTTAATTAGTAGTTGAGAGATTATG
* * * *
1050311 GTTTCCATTAAGAATTTTAGTATTTAGTTACAAAATTGATTTCCCTATAGGAATTTTATTAATAG
1 GTTTCCAATAAGAATTTTAGTATTTAGTTACAAAATTGATTTCCCAATAGGAATTATAGTAATAG
* * * *****
1050376 TTGAGATATTATAGTTTATAA-TAAGAATTTTAGTATTTGGGTTTTTTTA-TAAAAATAAAATTA
66 TTGAGAGACTATAGTTTACAATTAAGAATTTTAGTATTT-GGTTACAAAATTAAAAATAAAA-TA
1050439 AAAATTTAATTA
129 AAAATTTAATTA
1050451 TTTACAAAAA
Statistics
Matches: 113, Mismatches: 25, Indels: 4
0.80 0.18 0.03
Matches are distributed among these distances:
156 22 0.19
157 91 0.81
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.43
Consensus pattern (157 bp):
GTTTCCAATAAGAATTTTAGTATTTAGTTACAAAATTGATTTCCCAATAGGAATTATAGTAATAG
TTGAGAGACTATAGTTTACAATTAAGAATTTTAGTATTTGGTTACAAAATTAAAAATAAAATAAA
AATTTAATTAGTAGTTGAGAGATTATG
Found at i:1054943 original size:51 final size:51
Alignment explanation
Indices: 1054883--1055044 Score: 306
Period size: 51 Copynumber: 3.2 Consensus size: 51
1054873 CACATATCAC
* *
1054883 ATCACTTGTCACTTGTCATTGATCAGATAAGTGTAACTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1054934 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1054985 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1 ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
1055036 ATCACTTGT
1 ATCACTTGT
1055045 TATTGATCAG
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 109 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
ATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTT
Found at i:1055338 original size:24 final size:24
Alignment explanation
Indices: 1055310--1055358 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1055300 ATTATAATCG
1055310 GGCATATGACCAATTTATACACAA
1 GGCATATGACCAATTTATACACAA
1055334 GGCATATGACCAATTTATACACAA
1 GGCATATGACCAATTTATACACAA
1055358 G
1 G
1055359 TCATTCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
GGCATATGACCAATTTATACACAA
Found at i:1059160 original size:39 final size:39
Alignment explanation
Indices: 1059118--1059321 Score: 148
Period size: 39 Copynumber: 5.2 Consensus size: 39
1059108 TTTCAAAAAT
*
1059118 AATTTTAGTATTTTGTTACAAAATTGGTTTTCCAAT-AG
1 AATTTTAGTATTTAGTTACAAAATTGGTTTTCCAATAAG
* * * * *
1059156 TAATTATAGTA-ATAGTTGAGAGATTATGG-TTTCCAATTAAG
1 -AATTTTAGTATTTAGTT-ACAAAAT-TGGTTTTCCAA-TAAG
* * *
1059197 AATTTTAGTATTTGGTTAAAAAATTGATTTTCCAATAAG
1 AATTTTAGTATTTAGTTACAAAATTGGTTTTCCAATAAG
* * * * * *
1059236 AATTTTATTA-GTAGTTGAGAGATTATGG-TTTCCTATTAAG
1 AATTTTAGTATTTAGTT-ACAAAAT-TGGTTTTCC-AATAAG
* * *
1059276 AATTTTAGTATTTAGTTACAAAATTGATTTCCCAATAGG
1 AATTTTAGTATTTAGTTACAAAATTGGTTTTCCAATAAG
1059315 AATTTTA
1 AATTTTA
1059322 TTAATATTTG
Statistics
Matches: 124, Mismatches: 30, Indels: 22
0.70 0.17 0.12
Matches are distributed among these distances:
38 8 0.06
39 57 0.46
40 48 0.39
41 11 0.09
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (39 bp):
AATTTTAGTATTTAGTTACAAAATTGGTTTTCCAATAAG
Found at i:1059206 original size:40 final size:40
Alignment explanation
Indices: 1059157--1059285 Score: 138
Period size: 40 Copynumber: 3.2 Consensus size: 40
1059147 TTCCAATAGT
*
1059157 AATTATAGTAATAGTTGAGAGATTATGGTTTCCAATTAAG
1 AATTTTAGTAATAGTTGAGAGATTATGGTTTCCAATTAAG
* * * * *
1059197 AATTTTAGTATTTGGTTAAAAAATTGAT--TTTCCAA-TAAG
1 AATTTTAGTA-ATAGTTGAGAGATT-ATGGTTTCCAATTAAG
* * *
1059236 AATTTTATTAGTAGTTGAGAGATTATGGTTTCCTATTAAG
1 AATTTTAGTAATAGTTGAGAGATTATGGTTTCCAATTAAG
1059276 AATTTTAGTA
1 AATTTTAGTA
1059286 TTTAGTTACA
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
37 2 0.03
38 9 0.13
39 19 0.27
40 29 0.41
41 9 0.13
42 2 0.03
ACGTcount: A:0.36, C:0.05, G:0.17, T:0.43
Consensus pattern (40 bp):
AATTTTAGTAATAGTTGAGAGATTATGGTTTCCAATTAAG
Found at i:1059209 original size:79 final size:78
Alignment explanation
Indices: 1059118--1059371 Score: 330
Period size: 79 Copynumber: 3.2 Consensus size: 78
1059108 TTTCAAAAAT
* * * *
1059118 AATTTTAGTATTTTGTTACAAAATTGGTTTTCCAATAGTAATTATAGTAATAGTTGAGAGATTAT
1 AATTTTAGTATTTAGTTACAAAATTGATTTTCCAATAG-AATTTTATTAATAGTTGAGAGATTAT
1059183 GGTTTCCAATTAAG
65 GGTTTCCAATTAAG
* * *
1059197 AATTTTAGTATTTGGTTAAAAAATTGATTTTCCAATAAGAATTTTATTAGTAGTTGAGAGATTAT
1 AATTTTAGTATTTAGTTACAAAATTGATTTTCCAAT-AGAATTTTATTAATAGTTGAGAGATTAT
*
1059262 GGTTTCCTATTAAG
65 GGTTTCCAATTAAG
* * *
1059276 AATTTTAGTATTTAGTTACAAAATTGATTTCCCAATAGGAATTTTATTAATATTTGAGACATTAT
1 AATTTTAGTATTTAGTTACAAAATTGATTTTCCAATA-GAATTTTATTAATAGTTGAGAGATTAT
** **
1059341 ATTTTATAA-TAAG
65 GGTTTCCAATTAAG
1059354 AATTTTAGTATTTGAGTT
1 AATTTTAGTATTT-AGTT
1059372 TTTTTATAAA
Statistics
Matches: 154, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
78 18 0.12
79 134 0.87
80 2 0.01
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.45
Consensus pattern (78 bp):
AATTTTAGTATTTAGTTACAAAATTGATTTTCCAATAGAATTTTATTAATAGTTGAGAGATTATG
GTTTCCAATTAAG
Found at i:1061821 original size:21 final size:21
Alignment explanation
Indices: 1061796--1061834 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1061786 GTTTATGATT
*
1061796 TTTTTTAGC-TTTTTATTTTG
1 TTTTTTAGCATTTTCATTTTG
1061816 TTTTTTAGCATTTTCATTT
1 TTTTTTAGCATTTTCATTT
1061835 GGGGTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.72
Consensus pattern (21 bp):
TTTTTTAGCATTTTCATTTTG
Found at i:1063597 original size:21 final size:23
Alignment explanation
Indices: 1063564--1063606 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
1063554 TTATGAGTTT
1063564 CTAATGTTATTTAGTCT-TTAAAA
1 CTAATGTTATTTAG-CTATTAAAA
1063587 CTAA-GTT-TTTAGCTATTAAA
1 CTAATGTTATTTAGCTATTAAA
1063607 TCACTTGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 2 0.11
21 10 0.53
22 3 0.16
23 4 0.21
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.47
Consensus pattern (23 bp):
CTAATGTTATTTAGCTATTAAAA
Found at i:1065678 original size:14 final size:14
Alignment explanation
Indices: 1065661--1065690 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1065651 AAGAAAAACA
1065661 AACAAAAAAAAAAG
1 AACAAAAAAAAAAG
*
1065675 AACAAAAGAAAAAG
1 AACAAAAAAAAAAG
1065689 AA
1 AA
1065691 GCGAGATAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (14 bp):
AACAAAAAAAAAAG
Found at i:1066087 original size:10 final size:10
Alignment explanation
Indices: 1066072--1066102 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
1066062 AACCAAATAC
1066072 TTTGTAAAAA
1 TTTGTAAAAA
1066082 TTTGTAAAAAA
1 TTTGT-AAAAA
1066093 TTTGTAAAAA
1 TTTGTAAAAA
1066103 ATTATTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.39
Consensus pattern (10 bp):
TTTGTAAAAA
Found at i:1066093 original size:11 final size:11
Alignment explanation
Indices: 1066072--1066105 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1066062 AACCAAATAC
1066072 TTTGT-AAAAA
1 TTTGTAAAAAA
1066082 TTTGTAAAAAA
1 TTTGTAAAAAA
1066093 TTTGTAAAAAA
1 TTTGTAAAAAA
1066104 TT
1 TT
1066106 ATTAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (11 bp):
TTTGTAAAAAA
Found at i:1070860 original size:34 final size:34
Alignment explanation
Indices: 1070800--1070864 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
1070790 TCAAAGTTGT
* *
1070800 CTTGTCTCGAGACAAAGGGGCTTATGTCTTGAGA
1 CTTGTCTCGAGACAAAGGGCCATATGTCTTGAGA
*
1070834 CTTGTCTCGAGACAAA-GTCCAATATGTCTTG
1 CTTGTCTCGAGACAAAGGGCC-ATATGTCTTG
1070865 GTTTGTCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (34 bp):
CTTGTCTCGAGACAAAGGGCCATATGTCTTGAGA
Found at i:1076078 original size:63 final size:63
Alignment explanation
Indices: 1075979--1076103 Score: 232
Period size: 63 Copynumber: 2.0 Consensus size: 63
1075969 ATACTATAAG
*
1075979 TCCATTCAACCAATATGCCATTTAGGCACCTCAATCACAACCAAGCATTCATACTTAGATTTA
1 TCCATTCAACCAATATGCCATTTAGGCACCTCAATCACAACCAAGCATTCATACTTACATTTA
*
1076042 TCCATTCAACCAATATGTCATTTAGGCACCTCAATCACAACCAAGCATTCATACTTACATTT
1 TCCATTCAACCAATATGCCATTTAGGCACCTCAATCACAACCAAGCATTCATACTTACATTT
1076104 GCATCAAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (63 bp):
TCCATTCAACCAATATGCCATTTAGGCACCTCAATCACAACCAAGCATTCATACTTACATTTA
Found at i:1076085 original size:31 final size:31
Alignment explanation
Indices: 1075985--1076085 Score: 80
Period size: 31 Copynumber: 3.2 Consensus size: 31
1075975 TAAGTCCATT
*
1075985 CAACCAATATGCCATTTAGGCACCTCAATCA
1 CAACCAATATGTCATTTAGGCACCTCAATCA
* ***** * *
1076016 CAACCAAGCAT-TCATACTTAGATTTATCCAT-T
1 CAACCAA-TATGTCAT--TTAGGCACCTCAATCA
1076048 CAACCAATATGTCATTTAGGCACCTCAATCA
1 CAACCAATATGTCATTTAGGCACCTCAATCA
1076079 CAACCAA
1 CAACCAA
1076086 GCATTCATAC
Statistics
Matches: 48, Mismatches: 17, Indels: 10
0.64 0.23 0.13
Matches are distributed among these distances:
30 8 0.17
31 19 0.40
32 13 0.27
33 8 0.17
ACGTcount: A:0.37, C:0.30, G:0.08, T:0.26
Consensus pattern (31 bp):
CAACCAATATGTCATTTAGGCACCTCAATCA
Found at i:1077702 original size:79 final size:79
Alignment explanation
Indices: 1077566--1077749 Score: 210
Period size: 79 Copynumber: 2.3 Consensus size: 79
1077556 AACACACCAG
* * * * *
1077566 ACAGAAGCTCATAAGAGCTAATCTAATCGAAACACGCCAAACAGAAGCTCATAAGAGCTAATCCA
1 ACAGAACCTCATAAGAGCTGATCCACTAGAAACACGCCAAACAGAAGCTCATAAGAGCTAATCC-
*
1077631 AC-CAAAATACGCCAA
65 ACTCAAAAAACGCC-A
* * * * **
1077646 ATAGAACCTCATAAGAGCTGTTCCACTAGAAACATGCC-AACAGAAGCTTATAAGAGCTGGTCCA
1 ACAGAACCTCATAAGAGCTGATCCACTAGAAACACGCCAAACAGAAGCTCATAAGAGCTAATCCA
*
1077710 CTCAAAAAATGCCA
66 CTCAAAAAACGCCA
*
1077724 ACAGAAGCTCATAAGAGCTGATCCAC
1 ACAGAACCTCATAAGAGCTGATCCAC
1077750 CTGAATCATG
Statistics
Matches: 87, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
78 26 0.30
79 31 0.36
80 30 0.34
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (79 bp):
ACAGAACCTCATAAGAGCTGATCCACTAGAAACACGCCAAACAGAAGCTCATAAGAGCTAATCCA
CTCAAAAAACGCCA
Found at i:1077761 original size:39 final size:40
Alignment explanation
Indices: 1077566--1077749 Score: 194
Period size: 40 Copynumber: 4.7 Consensus size: 40
1077556 AACACACCAG
* * * *
1077566 ACAGAAGCTCATAAGAGCTAATCTAATCGAAACACGCCAA
1 ACAGAAGCTCATAAGAGCTGATCCACTCGAAACATGCCAA
* * * *
1077606 ACAGAAGCTCATAAGAGCTAATCCAAC-CAAAATACGCCAA
1 ACAGAAGCTCATAAGAGCTGATCC-ACTCGAAACATGCCAA
* * * *
1077646 ATAGAACCTCATAAGAGCTGTTCCACTAGAAACATGCC-A
1 ACAGAAGCTCATAAGAGCTGATCCACTCGAAACATGCCAA
* * * *
1077685 ACAGAAGCTTATAAGAGCTGGTCCACTCAAAAAATGCC-A
1 ACAGAAGCTCATAAGAGCTGATCCACTCGAAACATGCCAA
1077724 ACAGAAGCTCATAAGAGCTGATCCAC
1 ACAGAAGCTCATAAGAGCTGATCCAC
1077750 CTGAATCATG
Statistics
Matches: 121, Mismatches: 21, Indels: 5
0.82 0.14 0.03
Matches are distributed among these distances:
39 59 0.49
40 61 0.50
41 1 0.01
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (40 bp):
ACAGAAGCTCATAAGAGCTGATCCACTCGAAACATGCCAA
Found at i:1081536 original size:19 final size:21
Alignment explanation
Indices: 1081498--1081540 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
1081488 CCAAAAACCG
*
1081498 TAATTAGGTTATATAATTAAA
1 TAATTAGGTAATATAATTAAA
1081519 TAATTAGG-AATA-AATTAAA
1 TAATTAGGTAATATAATTAAA
1081538 TAA
1 TAA
1081541 AATATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.37
Consensus pattern (21 bp):
TAATTAGGTAATATAATTAAA
Found at i:1090302 original size:27 final size:27
Alignment explanation
Indices: 1090263--1090557 Score: 200
Period size: 27 Copynumber: 10.7 Consensus size: 27
1090253 CTTCGGTCAA
1090263 AAAATGACCGAATTACCCCCGAAGGAT
1 AAAATGACCGAATTACCCCCGAAGGAT
** *
1090290 AAAATGATAGAATTACCCTCGAAGGAT
1 AAAATGACCGAATTACCCCCGAAGGAT
* *
1090317 AAAATGACTGAAATTAGTATTACCCCCAAAAGGA-
1 AAAATGACCG-----A--ATTACCCCC-GAAGGAT
* *** *
1090351 AAAATGACCGAATTACTCTTAAAGGGT
1 AAAATGACCGAATTACCCCCGAAGGAT
*
1090378 AAAATGACCGAATTACCCCCGAAGGGT
1 AAAATGACCGAATTACCCCCGAAGGAT
* * *
1090405 -AAATGATCGAATTAGCCCCGAAGGGT
1 AAAATGACCGAATTACCCCCGAAGGAT
* * *
1090431 AAAATGACCGAATTACACCTGAAGGGT
1 AAAATGACCGAATTACCCCCGAAGGAT
* * **
1090458 AAAATGACCAAATTACACCTAAAGGAT
1 AAAATGACCGAATTACCCCCGAAGGAT
* * **
1090485 AAAATGACTGAAATACCCCAAAAGAGA-
1 AAAATGACCGAATTACCCCCGAAG-GAT
* * * * *
1090512 AAAATGACCAAAATATCACCGAAGGGT
1 AAAATGACCGAATTACCCCCGAAGGAT
* *
1090539 AAAATGACTGAAATACCCC
1 AAAATGACCGAATTACCCC
1090558 TATAGGGTAA
Statistics
Matches: 215, Mismatches: 41, Indels: 24
0.77 0.15 0.09
Matches are distributed among these distances:
26 30 0.14
27 159 0.74
28 2 0.01
29 1 0.00
32 1 0.00
34 17 0.08
35 5 0.02
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (27 bp):
AAAATGACCGAATTACCCCCGAAGGAT
Found at i:1090537 original size:81 final size:81
Alignment explanation
Indices: 1090431--1090583 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 81
1090421 CCCGAAGGGT
* *
1090431 AAAATGACCGAATTACACCTGAAGGGTAAAATGAC-CAAATTACACCTAAAGGATAAAATGACTG
1 AAAATGACCAAAATACACCTGAAGGGTAAAATGACTCAAA-TACACCTAAAGGATAAAATGACT-
1090495 AA-ATACCCCAAAAGAGA
64 AATATACCCCAAAAGAGA
* * * *
1090512 AAAATGACCAAAATATCACC-GAAGGGTAAAATGACTGAAATACCCCTATAGGGTAAAATGACTA
1 AAAATGACCAAAATA-CACCTGAAGGGTAAAATGACTCAAATACACCTAAAGGATAAAATGACTA
1090576 ATATACCC
65 ATATACCC
1090584 TTAGGAGTCG
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
80 2 0.03
81 54 0.86
82 7 0.11
ACGTcount: A:0.48, C:0.19, G:0.16, T:0.18
Consensus pattern (81 bp):
AAAATGACCAAAATACACCTGAAGGGTAAAATGACTCAAATACACCTAAAGGATAAAATGACTAA
TATACCCCAAAAGAGA
Found at i:1090564 original size:27 final size:26
Alignment explanation
Indices: 1090372--1090583 Score: 153
Period size: 27 Copynumber: 7.9 Consensus size: 26
1090362 ATTACTCTTA
* *
1090372 AAGGGTAAAATGACCGAATTACCCCCG
1 AAGGGTAAAATGACTGAAATA-CCCCG
*
1090399 AAGGGT-AAATGA-TCGAATTAGCCCCG
1 AAGGGTAAAATGACT-GAAATA-CCCCG
* * *
1090425 AAGGGTAAAATGACCGAATTACACCTG
1 AAGGGTAAAATGACTGAAATAC-CCCG
* **
1090452 AAGGGTAAAATGAC-CAAATTACACCTA
1 AAGGGTAAAATGACTGAAA-TAC-CCCG
* *
1090479 AAGGATAAAATGACTGAAATACCCCAA
1 AAGGGTAAAATGACTGAAATACCCC-G
* * ** *
1090506 AAGAGAAAAATGACCAAAATATCACCG
1 AAGGGTAAAATGACTGAAATA-CCCCG
*
1090533 AAGGGTAAAATGACTGAAATACCCCT
1 AAGGGTAAAATGACTGAAATACCCCG
1090559 ATAGGGTAAAATGACT-AATATACCC
1 A-AGGGTAAAATGACTGAA-ATACCC
1090584 TTAGGAGTCG
Statistics
Matches: 152, Mismatches: 23, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
26 34 0.22
27 112 0.74
28 6 0.04
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (26 bp):
AAGGGTAAAATGACTGAAATACCCCG
Found at i:1091040 original size:28 final size:27
Alignment explanation
Indices: 1091000--1091065 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 27
1090990 ACTACACTGT
*
1091000 ACTGCTACTGTATTGGGCTAAGGCCTAC
1 ACTG-TACTGTATTGGGCTAAGGCCCAC
*
1091028 ACTGTTACTGTATTGGGCTAAGGCCCGC
1 ACTG-TACTGTATTGGGCTAAGGCCCAC
1091056 ACTGTACTGT
1 ACTGTACTGT
1091066 CACTGAATAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
27 6 0.17
28 29 0.83
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (27 bp):
ACTGTACTGTATTGGGCTAAGGCCCAC
Found at i:1091065 original size:33 final size:31
Alignment explanation
Indices: 1090994--1091070 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 31
1090984 TGCATCACTA
*
1090994 CACTGTACTGCTACTGTATTGGGCTAAGGCC
1 CACTGTACTGTTACTGTATTGGGCTAAGGCC
*
1091025 TAC---ACTGTTACTGTATTGGGCTAAGGCCC
1 CACTGTACTGTTACTGTATTGGGCTAAGG-CC
*
1091054 GCACTGTACTGTCACTG
1 -CACTGTACTGTTACTG
1091071 AATAGGGCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 22 0.59
29 2 0.05
30 2 0.05
31 2 0.05
33 9 0.24
ACGTcount: A:0.19, C:0.26, G:0.25, T:0.30
Consensus pattern (31 bp):
CACTGTACTGTTACTGTATTGGGCTAAGGCC
Found at i:1091638 original size:21 final size:22
Alignment explanation
Indices: 1091613--1091658 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1091603 GGTTTTCAAA
*
1091613 AAACACTTCAATGTGACACG-C
1 AAACACTTCAACGTGACACGTC
1091634 AAACACTTCAACGTGACACGTC
1 AAACACTTCAACGTGACACGTC
1091656 AAA
1 AAA
1091659 TTCGGGCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.41, C:0.28, G:0.13, T:0.17
Consensus pattern (22 bp):
AAACACTTCAACGTGACACGTC
Found at i:1093743 original size:55 final size:53
Alignment explanation
Indices: 1093624--1093784 Score: 146
Period size: 55 Copynumber: 3.0 Consensus size: 53
1093614 AATTACCTCC
* ** * * * *
1093624 GAAGGGTAAAATGACTGAATTACCACCAAAGGGTAAAATGACTGAATTACCCTT
1 GAAGTGTAAAATGACCAAAATACC-CCGAAGGGTAAAATGACCGAAATACCCTT
*
1093678 GAATTGTAAAATGACCAAAATAACCCCCGAAGGGTAAAATGACCGAAATACACC-T
1 GAAGTGTAAAATGACCAAAAT-A-CCCCGAAGGGTAAAATGACCGAAATAC-CCTT
* * * *
1093733 GTAAGT-TAAAATGATCAAAATACCCCTATAGGGTAAAATGACTGATATACCC
1 G-AAGTGTAAAATGACCAAAATACCCCGA-AGGGTAAAATGACCGAAATACCC
1093785 CTAGGAGTTG
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
53 7 0.08
54 36 0.40
55 39 0.44
56 7 0.08
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (53 bp):
GAAGTGTAAAATGACCAAAATACCCCGAAGGGTAAAATGACCGAAATACCCTT
Found at i:1093786 original size:27 final size:26
Alignment explanation
Indices: 1093604--1093787 Score: 120
Period size: 27 Copynumber: 6.8 Consensus size: 26
1093594 CTTGGGCCAA
* * *
1093604 AAAATAACTGAATTACCTCCGAAGGGT
1 AAAATGACTGAAATACC-CCTAAGGGT
* *
1093631 AAAATGACTGAATTACCACCAAAGGGT
1 AAAATGACTGAAATACC-CCTAAGGGT
* * **
1093658 AAAATGACTGAATTACCCTTGAATTGT
1 AAAATGACTGAAATACCCCT-AAGGGT
** *
1093685 AAAATGACCAAAATAACCCCCGAAGGGT
1 AAAATGACTGAAAT-A-CCCCTAAGGGT
* * *
1093713 AAAATGACCGAAATACACCTGTAA-GTT
1 AAAATGACTGAAATAC-CC-CTAAGGGT
*
1093740 AAAATGA-TCAAAATACCCCTATAGGGT
1 AAAATGACT-GAAATACCCCTA-AGGGT
*
1093767 AAAATGACTGATATACCCCTA
1 AAAATGACTGAAATACCCCTA
1093788 GGAGTTGAAA
Statistics
Matches: 124, Mismatches: 24, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
25 2 0.02
26 5 0.04
27 93 0.75
28 21 0.17
29 3 0.02
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (26 bp):
AAAATGACTGAAATACCCCTAAGGGT
Found at i:1094239 original size:28 final size:28
Alignment explanation
Indices: 1094199--1094292 Score: 127
Period size: 28 Copynumber: 3.4 Consensus size: 28
1094189 AGTGCACTGT
* * *
1094199 ACTGTTAATGTATTGGGTTGAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
1094227 ACTGTTACTGTATTGGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
* * *
1094255 ACTATTATTGTATTGGCCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
1094283 ACTG-TACTGT
1 ACTGTTACTGT
1094293 CACTAAATAG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
27 5 0.09
28 53 0.91
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:1094864 original size:21 final size:21
Alignment explanation
Indices: 1094840--1094881 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1094830 GTTGTTCGAA
*
1094840 AAACACTTCAATGTGACACGC
1 AAACACTTCAACGTGACACGC
1094861 AAACACTTCAACGTGACACGC
1 AAACACTTCAACGTGACACGC
1094882 CAAATTCAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.31, G:0.14, T:0.17
Consensus pattern (21 bp):
AAACACTTCAACGTGACACGC
Found at i:1098103 original size:21 final size:20
Alignment explanation
Indices: 1098056--1098096 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1098046 CCCTTATTAT
* * *
1098056 ACACGTTTTTAACCCTAAAA
1 ACACATTTTTAAACATAAAA
1098076 ACACATTTTTAAACATAAAA
1 ACACATTTTTAAACATAAAA
1098096 A
1 A
1098097 TACCATTCTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.20, G:0.02, T:0.29
Consensus pattern (20 bp):
ACACATTTTTAAACATAAAA
Found at i:1110876 original size:19 final size:18
Alignment explanation
Indices: 1110840--1110874 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1110830 AAGCAAATTA
1110840 AACATAATTAATCTAAAT
1 AACATAATTAATCTAAAT
1110858 AACATAAATTAA-CTAAA
1 AACAT-AATTAATCTAAA
1110875 ATTAAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
AACATAATTAATCTAAAT
Done.