Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 150 of 198
Found at i:47575868 original size:82 final size:82
Alignment explanation
Indices: 47575731--47575899 Score: 329
Period size: 82 Copynumber: 2.1 Consensus size: 82
47575721 GGTTGATGAA
47575731 TTTGTGAGTTTCCATTGATGATAGCTTGATGTTTTTGAATGTTGATGATGTAAAATGAATAATTA
1 TTTGTGAGTTTCCATTGATGATAGCTTGATGTTTTTGAATGTTGATGATGTAAAATGAATAATTA
47575796 TTGATAGATTAAAATGT
66 TTGATAGATTAAAATGT
47575813 TTTGTGAGTTTCCATTGATGATAGCTTGATGTTTTTGAATGTTGATGATGTAAAATGAATAATTA
1 TTTGTGAGTTTCCATTGATGATAGCTTGATGTTTTTGAATGTTGATGATGTAAAATGAATAATTA
*
47575878 TTGATAGATTAATATGT
66 TTGATAGATTAAAATGT
47575895 TTTGT
1 TTTGT
47575900 AAAGTGACTT
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 86 1.00
ACGTcount: A:0.30, C:0.04, G:0.21, T:0.46
Consensus pattern (82 bp):
TTTGTGAGTTTCCATTGATGATAGCTTGATGTTTTTGAATGTTGATGATGTAAAATGAATAATTA
TTGATAGATTAAAATGT
Found at i:47576399 original size:34 final size:32
Alignment explanation
Indices: 47576320--47576408 Score: 99
Period size: 32 Copynumber: 2.7 Consensus size: 32
47576310 GTATATGTTT
*
47576320 TATATATTGCTGAATTGATTTAAATATAGATA
1 TATATATTGCCGAATTGATTTAAATATAGATA
* * **
47576352 TATACATTTCCGAATTGATTTGTATAT-GTATACA
1 TATATATTGCCGAATTGATTTAAATATAG-AT--A
47576386 TATATATTGCCGAATTGATTTAA
1 TATATATTGCCGAATTGATTTAA
47576409 GCATTGGATG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
31 1 0.02
32 24 0.53
34 20 0.44
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (32 bp):
TATATATTGCCGAATTGATTTAAATATAGATA
Found at i:47578908 original size:33 final size:33
Alignment explanation
Indices: 47578871--47578933 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
47578861 CAATAAGCAA
* *
47578871 TATTTAACTATCTTAATTTCATTGGATTTTCCT
1 TATTTAACTATCTCAATTCCATTGGATTTTCCT
*
47578904 TATTTCACTATCTCAATTCCATTGGATTTT
1 TATTTAACTATCTCAATTCCATTGGATTTT
47578934 TCACATCTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.06, T:0.52
Consensus pattern (33 bp):
TATTTAACTATCTCAATTCCATTGGATTTTCCT
Found at i:47579588 original size:41 final size:41
Alignment explanation
Indices: 47579523--47579602 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
47579513 CGATTCAATC
* *
47579523 ACAATTCAATTCAAATTCACTTTCCAC-TTTCTAATCAATAT
1 ACAATTCAATACAAATACACTTTCCACTTTTC-AATCAATAT
* *
47579564 ACAATTCAATACCAATACATTTTCCACTTTTCAATCAAT
1 ACAATTCAATACAAATACACTTTCCACTTTTCAATCAAT
47579603 GTACCATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.38
Consensus pattern (41 bp):
ACAATTCAATACAAATACACTTTCCACTTTTCAATCAATAT
Found at i:47580675 original size:5 final size:5
Alignment explanation
Indices: 47580656--47580716 Score: 90
Period size: 5 Copynumber: 12.4 Consensus size: 5
47580646 TTATTTAAGT
47580656 TATACA TAT-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*
47580706 T-TAA AATAA TA
1 TATAA TATAA TA
47580717 CTTGTTTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
4 7 0.14
5 41 0.80
6 3 0.06
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:47582861 original size:21 final size:21
Alignment explanation
Indices: 47582835--47582882 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
47582825 CGACACATAA
*
47582835 GTGCCTGAAACGACACACGAT
1 GTGCCTGAAACGACACACGAG
* *
47582856 GTGCCTGATATGACACACGAG
1 GTGCCTGAAACGACACACGAG
47582877 GTGCCT
1 GTGCCT
47582883 AAAATACGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (21 bp):
GTGCCTGAAACGACACACGAG
Found at i:47582893 original size:23 final size:21
Alignment explanation
Indices: 47582835--47582895 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
47582825 CGACACATAA
*
47582835 GTGCCTGAA-ACGACACACGAT
1 GTGCCT-AATACGACACACGAG
* *
47582856 GTGCCTGATATGACACACGAG
1 GTGCCTAATACGACACACGAG
47582877 GTGCCTAAAATACGACACA
1 GTGCCT--AATACGACACA
47582896 TAAAGTGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.03
21 22 0.69
23 9 0.28
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.16
Consensus pattern (21 bp):
GTGCCTAATACGACACACGAG
Found at i:47584050 original size:17 final size:16
Alignment explanation
Indices: 47584025--47584060 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
47584015 AACCCTAATT
* *
47584025 TTTCCCTTTTCTTTTC
1 TTTCCCCTTTCCTTTC
47584041 TTTCCCCTTTCCTTTC
1 TTTCCCCTTTCCTTTC
47584057 TTTC
1 TTTC
47584061 TTTTTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (16 bp):
TTTCCCCTTTCCTTTC
Found at i:47587020 original size:69 final size:69
Alignment explanation
Indices: 47586922--47587066 Score: 209
Period size: 69 Copynumber: 2.1 Consensus size: 69
47586912 ATTCACAAAT
*
47586922 ATTTGGACAACAGTAAAAACATTTGGACAACATTGACTTGTACCAAAAAGGGACAGCATTAAAGC
1 ATTTGGACAACAGTAAAAACATTTGGACAACATAGACTTGTACCAAAAAGGGACAGCATTAAAGC
47586987 ACTA
66 ACTA
* * * * * * *
47586991 ATTTGGACAGCATTAATAATATTTGGACAACATAGATTTGTACCAAAAATGGACAGCATTTAAGC
1 ATTTGGACAACAGTAAAAACATTTGGACAACATAGACTTGTACCAAAAAGGGACAGCATTAAAGC
*
47587056 GCTA
66 ACTA
47587060 ATTTGGA
1 ATTTGGA
47587067 TAGCCTTATT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (69 bp):
ATTTGGACAACAGTAAAAACATTTGGACAACATAGACTTGTACCAAAAAGGGACAGCATTAAAGC
ACTA
Found at i:47587716 original size:43 final size:43
Alignment explanation
Indices: 47587666--47587760 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 43
47587656 CTAAGATATA
* * *
47587666 GTCTTACATGTTATCACATCTCGATGCCACTGTCCCAGACAA-G
1 GTCTTACATGTAATCACATATCGATGCCAATGTCCCAGA-AATG
* **
47587709 GTCTTACAAGTAATGTCATATCGATGCCAATGTCCCAGAAATG
1 GTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAAATG
47587752 GTCTTACAT
1 GTCTTACAT
47587761 AAAATTATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 2 0.05
43 42 0.95
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (43 bp):
GTCTTACATGTAATCACATATCGATGCCAATGTCCCAGAAATG
Found at i:47590470 original size:41 final size:41
Alignment explanation
Indices: 47590415--47590614 Score: 303
Period size: 41 Copynumber: 4.9 Consensus size: 41
47590405 TACTGAAGTA
* *
47590415 CACCAGCATGAAGCCTGCTAGACA-ATAAGTCTGAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATA-AAGTCTGAAATAATT
* *
47590456 CACCGGCATCAAGCCTACTAGACATAAAGTCTGAAGTAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
* * *
47590497 CACTGGCATCAAGCCTGCTACACATAAAGTCTGAAGTAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
47590538 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
* *
47590579 CACCGGCATCAAGCCTGCTAGACATTAAGCCTGAAA
1 CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAA
47590615 ACCAATTATA
Statistics
Matches: 146, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
41 145 0.99
42 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.21
Consensus pattern (41 bp):
CACCGGCATCAAGCCTGCTAGACATAAAGTCTGAAATAATT
Found at i:47591570 original size:13 final size:13
Alignment explanation
Indices: 47591554--47591585 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
47591544 TTGAGCCTTC
47591554 AAATTTTCACACG
1 AAATTTTCACACG
47591567 AAATTTTCACACG
1 AAATTTTCACACG
47591580 AAATTT
1 AAATTT
47591586 AAACACATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:47597821 original size:3 final size:3
Alignment explanation
Indices: 47597806--47597842 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
47597796 GAGAGAAAGG
47597806 AGA AGA A-A A-A AGA AGA AG- AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
47597843 AGAAAGAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 6 0.19
3 26 0.81
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:47597834 original size:14 final size:14
Alignment explanation
Indices: 47597793--47597838 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
47597783 ACCCCATCCG
*
47597793 GAAGAG-AGAAAGGA
1 GAAGAGAAG-AAGAA
*
47597807 GAAGA-AAAAAGAA
1 GAAGAGAAGAAGAA
47597820 GAAGAGAAGAAGAA
1 GAAGAGAAGAAGAA
47597834 GAAGA
1 GAAGA
47597839 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 9 0.33
14 18 0.67
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
GAAGAGAAGAAGAA
Found at i:47597836 original size:27 final size:27
Alignment explanation
Indices: 47597793--47597846 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
47597783 ACCCCATCCG
*
47597793 GAAGAGAGAAAGGAGAAGAAAAAAGAA
1 GAAGAGAGAAAGAAGAAGAAAAAAGAA
*
47597820 GAAGAGA-AGAAGAAGAAGAAGAAAGAA
1 GAAGAGAGA-AAGAAGAAGAAAAAAGAA
47597847 AGAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (27 bp):
GAAGAGAGAAAGAAGAAGAAAAAAGAA
Found at i:47597845 original size:24 final size:22
Alignment explanation
Indices: 47597793--47597857 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 22
47597783 ACCCCATCCG
* *
47597793 GAAGAGAGAAAGGAGAAGAAAA
1 GAAGAAAGAAAGAAGAAGAAAA
47597815 -AAG-AAGAAGAGAAGAAGAAGAA
1 GAAGAAAGAA-AGAAGAAGAA-AA
47597837 GAAGAAAGAAAGAA-AA-AAAA
1 GAAGAAAGAAAGAAGAAGAAAA
47597857 G
1 G
47597858 TAATGTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 7 0.19
21 14 0.38
22 4 0.11
23 7 0.19
24 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (22 bp):
GAAGAAAGAAAGAAGAAGAAAA
Found at i:47597849 original size:17 final size:17
Alignment explanation
Indices: 47597806--47597850 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 17
47597796 GAGAGAAAGG
47597806 AGAAGAAA-AAAGAAGA
1 AGAAGAAAGAAAGAAGA
47597822 AG-AG-AAG-AAGAAGA
1 AGAAGAAAGAAAGAAGA
47597836 AGAAGAAAGAAAGAA
1 AGAAGAAAGAAAGAA
47597851 AAAAAAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 11 0.44
15 4 0.16
16 5 0.20
17 5 0.20
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAAGAAAGAAAGAAGA
Found at i:47598022 original size:60 final size:60
Alignment explanation
Indices: 47597950--47598068 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
47597940 TTAATTTTTA
* * *
47597950 TAATTATTTTAAAATTAATTTGTTAGTAATTTAGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
47598010 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
1 TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTT
47598069 AGTTTAGTAT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.54
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGTAATTTAGGATTAAGTTATAAATTGTTGTGTTTG
Found at i:47600696 original size:17 final size:18
Alignment explanation
Indices: 47600664--47600699 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
47600654 TTTTTTTGGT
47600664 ATTTTATTTATCAATTTA
1 ATTTTATTTATCAATTTA
47600682 ATTTTATTT-TCAATTTA
1 ATTTTATTTATCAATTTA
47600699 A
1 A
47600700 ATAGTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (18 bp):
ATTTTATTTATCAATTTA
Found at i:47603952 original size:27 final size:27
Alignment explanation
Indices: 47603922--47603983 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
47603912 GCTCCACCAT
47603922 TCGCGCCTCTGAGATAGGCTCAACTAG
1 TCGCGCCTCTGAGATAGGCTCAACTAG
47603949 TCGCGCCTCTGAGATAGGCTCAACTAG
1 TCGCGCCTCTGAGATAGGCTCAACTAG
47603976 TCGCGCCT
1 TCGCGCCT
47603984 ATCAAATAGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.19, C:0.32, G:0.26, T:0.23
Consensus pattern (27 bp):
TCGCGCCTCTGAGATAGGCTCAACTAG
Found at i:47603992 original size:27 final size:27
Alignment explanation
Indices: 47603935--47603992 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
47603925 CGCCTCTGAG
* * *
47603935 ATAGGCTCAACTAGTCGCGCCTCTGAG
1 ATAGGCTCAACTAGTCGCGCCTATCAA
47603962 ATAGGCTCAACTAGTCGCGCCTATCAA
1 ATAGGCTCAACTAGTCGCGCCTATCAA
47603989 ATAG
1 ATAG
47603993 CCGCAACCTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (27 bp):
ATAGGCTCAACTAGTCGCGCCTATCAA
Found at i:47603999 original size:27 final size:27
Alignment explanation
Indices: 47603942--47603999 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
47603932 GAGATAGGCT
* * * * *
47603942 CAACTAGTCGCGCCTCTGAGATAGGCT
1 CAACTAGTCGCGCCTATCAAATAGCCG
47603969 CAACTAGTCGCGCCTATCAAATAGCCG
1 CAACTAGTCGCGCCTATCAAATAGCCG
47603996 CAAC
1 CAAC
47604000 CTGTATTTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.19
Consensus pattern (27 bp):
CAACTAGTCGCGCCTATCAAATAGCCG
Found at i:47609547 original size:16 final size:15
Alignment explanation
Indices: 47609521--47609550 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
47609511 CTTTTTCATC
47609521 TAAATTTTATTTTGT
1 TAAATTTTATTTTGT
47609536 TAAATCTTTATTTTG
1 TAAAT-TTTATTTTG
47609551 AGTTAGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (15 bp):
TAAATTTTATTTTGT
Found at i:47609814 original size:29 final size:30
Alignment explanation
Indices: 47609778--47609874 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 30
47609768 TTTTAAAATA
47609778 TTTTAAAA-TTAAAAAAATTAAAAAAGTAT
1 TTTTAAAATTTAAAAAAATTAAAAAAGTAT
47609807 TTTTAAAATATTTTAAAATTAAAAAATTTAAAAAAGTA-
1 TTTT-AAA-A-TTT---A--AAAAAA-TTAAAAAAGTAT
47609845 TTTTAAAATTTAAAAAAATTAAAAAAGTAT
1 TTTTAAAATTTAAAAAAATTAAAAAAGTAT
47609875 GTAAAAAATA
Statistics
Matches: 57, Mismatches: 0, Indels: 21
0.73 0.00 0.27
Matches are distributed among these distances:
29 15 0.26
30 9 0.16
31 1 0.02
32 1 0.02
33 2 0.04
35 3 0.05
36 2 0.04
37 3 0.05
38 10 0.18
39 11 0.19
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (30 bp):
TTTTAAAATTTAAAAAAATTAAAAAAGTAT
Found at i:47609818 original size:39 final size:38
Alignment explanation
Indices: 47609768--47609893 Score: 166
Period size: 39 Copynumber: 3.2 Consensus size: 38
47609758 TTTAATATAT
47609768 TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAGTA
1 TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAGTA
*
47609806 TTTTTAAAATATTTTAAAATTAAAAAATTTAAAAAAGTA
1 -TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAGTA
**
47609845 TTTTAAAAT-TTAAAAAAATTAAAAAAGTATGTAAAAAA-TA
1 TTTTAAAATATT-TTAAAATTAAAAAA--AT-TAAAAAAGTA
47609885 TTTTAAAAT
1 TTTTAAAAT
47609894 TAAAAAATAT
Statistics
Matches: 79, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
37 2 0.03
38 21 0.27
39 37 0.47
40 12 0.15
41 7 0.09
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (38 bp):
TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAAGTA
Found at i:47609830 original size:28 final size:29
Alignment explanation
Indices: 47609811--47609874 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
47609801 AAGTATTTTT
47609811 AAAA-TATTTTAAAA-TTAAAAAATTTAA
1 AAAAGTATTTTAAAATTTAAAAAATTTAA
*
47609838 AAAAGTATTTTAAAATTTAAAAAAATTAA
1 AAAAGTATTTTAAAATTTAAAAAATTTAA
47609867 AAAAGTAT
1 AAAAGTAT
47609875 GTAAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 4 0.12
28 10 0.29
29 20 0.59
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAGTATTTTAAAATTTAAAAAATTTAA
Found at i:47609858 original size:68 final size:66
Alignment explanation
Indices: 47609772--47609901 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 66
47609762 ATATATTTTT
* **
47609772 AAAATATTTTAAAATTAAAAAAATTAAAAAAGTATTTTTAAAATATTTTAAAATTAAAAAATTTA
1 AAAATATTTTAAAATTAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAATTTA
47609837 A
66 A
47609838 AAAAGTATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAT
1 AAAA-TATTTTAAAA-TTAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAAT
47609902 ATATATTTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 4 0.07
67 10 0.17
68 45 0.76
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (66 bp):
AAAATATTTTAAAATTAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAATTAAAAAATTTA
A
Found at i:47609881 original size:29 final size:28
Alignment explanation
Indices: 47609821--47609881 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 28
47609811 AAAATATTTT
* *
47609821 AAAATTAAAAAATTTAAAAAAGTATTTTA
1 AAAATTAAAAAAATTAAAAAAGTA-TGTA
*
47609850 AAATTTAAAAAAATTAAAAAAGTATGTA
1 AAAATTAAAAAAATTAAAAAAGTATGTA
47609878 AAAA
1 AAAA
47609882 ATATTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (28 bp):
AAAATTAAAAAAATTAAAAAAGTATGTA
Found at i:47609883 original size:30 final size:29
Alignment explanation
Indices: 47609821--47609900 Score: 83
Period size: 29 Copynumber: 2.8 Consensus size: 29
47609811 AAAATATTTT
* **
47609821 AAAA-TTAAAAAATTTAAAAAAGTATTTT
1 AAAATTTAAAAAAATTAAAAAAGTATTAA
47609849 AAAATTTAAAAAAATTAAAAAAGTATGTAA
1 AAAATTTAAAAAAATTAAAAAAGTAT-TAA
**
47609879 AAAATATT-TTAAAATTAAAAAA
1 AAAAT-TTAAAAAAATTAAAAAA
47609901 TATATATTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 4 0.09
29 20 0.45
30 18 0.41
31 2 0.05
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAATTTAAAAAAATTAAAAAAGTATTAA
Found at i:47609892 original size:11 final size:11
Alignment explanation
Indices: 47609723--47609785 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
47609713 GGCCCATTTT
47609723 TATTTT-AAAA
1 TATTTTAAAAA
47609733 -ATTTTAAAAA
1 TATTTTAAAAA
**
47609743 -ATTAAAAAAA
1 TATTTTAAAAA
* *
47609753 GTATTTTTAATA
1 -TATTTTAAAAA
*
47609765 TATTTTTAAAA
1 TATTTTAAAAA
47609776 TATTTTAAAA
1 TATTTTAAAA
47609786 TTAAAAAAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
9 5 0.12
10 12 0.29
11 19 0.45
12 6 0.14
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:47610333 original size:5 final size:5
Alignment explanation
Indices: 47610323--47610351 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
47610313 AAACCTCACT
47610323 CCAAC CCAAC CCAAC CCAAC CCAAC CCAA
1 CCAAC CCAAC CCAAC CCAAC CCAAC CCAA
47610352 TCCATCAGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.59, G:0.00, T:0.00
Consensus pattern (5 bp):
CCAAC
Found at i:47615449 original size:21 final size:21
Alignment explanation
Indices: 47615424--47615468 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
47615414 GATTCTTTAG
47615424 TATTATCT-TTATCGTTATTGT
1 TATTAT-TGTTATCGTTATTGT
*
47615445 TATTATTGTTATTGTTATTGT
1 TATTATTGTTATCGTTATTGT
47615466 TAT
1 TAT
47615469 ATGGTTACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.64
Consensus pattern (21 bp):
TATTATTGTTATCGTTATTGT
Found at i:47615450 original size:15 final size:15
Alignment explanation
Indices: 47615432--47615463 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
47615422 AGTATTATCT
47615432 TTATCGTTATTGTTA
1 TTATCGTTATTGTTA
*
47615447 TTATTGTTATTGTTA
1 TTATCGTTATTGTTA
47615462 TT
1 TT
47615464 GTTATATGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.12, T:0.66
Consensus pattern (15 bp):
TTATCGTTATTGTTA
Found at i:47616930 original size:24 final size:24
Alignment explanation
Indices: 47616900--47616945 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
47616890 AATTTGAATT
*
47616900 TTAAAATTTGAAAAAA-TAGAAAAA
1 TTAAAA-TTAAAAAAAGTAGAAAAA
47616924 TTAAAATTAAAAAAAGTAGAAA
1 TTAAAATTAAAAAAAGTAGAAA
47616946 TATAGAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (24 bp):
TTAAAATTAAAAAAAGTAGAAAAA
Found at i:47618979 original size:2 final size:2
Alignment explanation
Indices: 47618972--47618996 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
47618962 TAGTTGATTG
47618972 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 A
47618997 CACACTCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47625268 original size:11 final size:12
Alignment explanation
Indices: 47625241--47625269 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
47625231 ACTATAGGAA
47625241 CATTCAAATATT
1 CATTCAAATATT
47625253 CATTCAAATA-T
1 CATTCAAATATT
47625264 CATTCA
1 CATTCA
47625270 CCATTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (12 bp):
CATTCAAATATT
Found at i:47631516 original size:12 final size:12
Alignment explanation
Indices: 47631490--47631532 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
47631480 AATATAATAT
*
47631490 AAAGAAAA-TAA
1 AAAGAAAACAAA
47631501 AAAGAAAACAAA
1 AAAGAAAACAAA
*
47631513 AAAGAAAACGAA
1 AAAGAAAACAAA
47631525 AAAGAAAA
1 AAAGAAAA
47631533 AGTGTCAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 8 0.28
12 21 0.72
ACGTcount: A:0.81, C:0.05, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAGAAAACAAA
Found at i:47631753 original size:19 final size:19
Alignment explanation
Indices: 47631725--47631775 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
47631715 GAAAAAAAAC
* *
47631725 TAAAACTAAATAATATTAA
1 TAAAAATAAATAATATGAA
47631744 TAAAAATAAAATAA-ATGAA
1 TAAAAAT-AAATAATATGAA
47631763 T-AAAAT-AATAATA
1 TAAAAATAAATAATA
47631776 ACTAACAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
16 5 0.18
17 1 0.04
18 5 0.18
19 11 0.39
20 6 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATAAATAATATGAA
Found at i:47631769 original size:24 final size:25
Alignment explanation
Indices: 47631719--47631776 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
47631709 TACTGTGAAA
*
47631719 AAAAACTAAAACTAAATAATATTAAT
1 AAAAA-TAAAACTAAATAATATAAAT
47631745 AAAAATAAAA-TAAATGAATA-AAAT
1 AAAAATAAAACTAAAT-AATATAAAT
*
47631769 AATAATAA
1 AAAAATAA
47631777 CTAACAGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 15 0.52
25 9 0.31
26 5 0.17
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAATAAAACTAAATAATATAAAT
Found at i:47633655 original size:12 final size:12
Alignment explanation
Indices: 47633638--47633669 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
47633628 AATTGATTCT
47633638 AATATTTACACA
1 AATATTTACACA
47633650 AATATTTACACA
1 AATATTTACACA
47633662 AATATTTA
1 AATATTTA
47633670 ATTAGACAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (12 bp):
AATATTTACACA
Found at i:47637259 original size:18 final size:19
Alignment explanation
Indices: 47637238--47637275 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
47637228 TTAAATTCTA
47637238 ATTTAACCCAA-AAT-ATTT
1 ATTT-ACCCAAGAATCATTT
47637256 ATTTACCCAAGAATCATTT
1 ATTTACCCAAGAATCATTT
47637275 A
1 A
47637276 AAACTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.42, C:0.18, G:0.03, T:0.37
Consensus pattern (19 bp):
ATTTACCCAAGAATCATTT
Found at i:47639009 original size:56 final size:59
Alignment explanation
Indices: 47638935--47639060 Score: 179
Period size: 56 Copynumber: 2.1 Consensus size: 59
47638925 TCCAGGCTAA
47638935 ATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A-GATCACCCGTCCGGGATAG
1 ATCC-TTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGATAG
*
47638992 AT-CTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATAGGATCACCCGTCCGGGCTAG
1 ATCCTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATAGGATCACCCGTCCGGGATAG
47639053 ATCCTTTT
1 ATCCTTTT
47639061 TACCGTCAAT
Statistics
Matches: 61, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
55 5 0.08
56 27 0.44
57 2 0.03
59 1 0.02
60 1 0.02
61 20 0.33
62 5 0.08
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.30
Consensus pattern (59 bp):
ATCCTTTTCCACATATTCTTCGGGAGGGCTATATCGATAGGATCACCCGTCCGGGATAG
Found at i:47640585 original size:2 final size:2
Alignment explanation
Indices: 47640578--47640610 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
47640568 TTCTTTCCAC
47640578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47640611 CACTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47641597 original size:30 final size:30
Alignment explanation
Indices: 47641556--47641636 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
47641546 GGCCCATTTT
47641556 TATTTTAAAAAT-TTTAAAAAATTAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAG
* *
47641586 TATTTTTAAAATATTTTAAAATTAAAAAA-
1 TATTTTAAAAATATTTAAAAATTAAAAAAG
**
47641615 T-TTAAAAAAATATTTTAAAAAT
1 TATTTTAAAAATA-TTTAAAAAT
47641637 ATTTTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.19
29 9 0.21
30 23 0.53
31 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (30 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAG
Found at i:47641602 original size:11 final size:10
Alignment explanation
Indices: 47641556--47641646 Score: 57
Period size: 10 Copynumber: 9.1 Consensus size: 10
47641546 GGCCCATTTT
47641556 TATTTTAAAA
1 TATTTTAAAA
47641566 -ATTTTAAAA
1 TATTTTAAAA
* **
47641575 AATTAAAAAA
1 TATTTTAAAA
47641585 GTATTTTTAAAA
1 -TA-TTTTAAAA
47641597 TATTTT-AAA
1 TATTTTAAAA
47641606 -A--TTAAAA
1 TATTTTAAAA
* *
47641613 AATTTAAAAAAA
1 TATTT--TAAAA
47641625 TATTTTAAAAA
1 TATTTT-AAAA
47641636 TATTTTAAAA
1 TATTTTAAAA
47641646 T
1 T
47641647 TAAAAAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
8 2 0.03
9 12 0.19
10 17 0.27
11 13 0.21
12 14 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:47641660 original size:11 final size:12
Alignment explanation
Indices: 47641577--47641687 Score: 62
Period size: 12 Copynumber: 9.5 Consensus size: 12
47641567 TTTTAAAAAA
47641577 TTAAAAAAGTATT
1 TTAAAAAA-TATT
*
47641590 TT-TAAAATATT
1 TTAAAAAATATT
*
47641601 TTAAAATTAAAAAATT
1 TT--AA--AAAATATT
*
47641617 TAAAAAAATATT
1 TTAAAAAATATT
47641629 TT-AAAAATATT
1 TTAAAAAATATT
47641640 TT---AAA-A--
1 TTAAAAAATATT
47641646 TTAAAAAAT-TT
1 TTAAAAAATATT
47641657 TTAAAAAAAGTATT
1 TT-AAAAAA-TATT
47641671 TT-AAAAATATT
1 TTAAAAAATATT
47641682 TTAAAA
1 TTAAAA
47641688 TTTAAAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 31
0.68 0.05 0.27
Matches are distributed among these distances:
6 2 0.03
8 1 0.01
9 6 0.08
11 25 0.32
12 26 0.34
13 3 0.04
14 6 0.08
16 8 0.10
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
TTAAAAAATATT
Found at i:47641721 original size:82 final size:81
Alignment explanation
Indices: 47641579--47641735 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 81
47641569 TTAAAAAATT
* * * *
47641579 AAAAAAGTATTTTTAAAATATTTTAAAATTAAAAAATTTAAAAAAATATTTTAAAAATATTTTAA
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAATATGTAAAAAATATTTTAA
47641644 AATTAAAAAATTTTTA
66 AATTAAAAAATTTTTA
*
47641660 AAAAAAGTATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAATATTTTA
1 AAAAAAGTATTTTAAAAATATTTTAAAA-TTAAAAAAATTAAAAAAATATGTAAAAAATATTTTA
47641725 AAATTAAAAAA
65 AAATTAAAAAA
47641736 ATAAATATAT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 27 0.39
82 43 0.61
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (81 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATTAAAAAAATATGTAAAAAATATTTTAA
AATTAAAAAATTTTTA
Found at i:47641727 original size:11 final size:11
Alignment explanation
Indices: 47641556--47641687 Score: 78
Period size: 11 Copynumber: 12.9 Consensus size: 11
47641546 GGCCCATTTT
47641556 TATTTT-AAAA
1 TATTTTAAAAA
47641566 -ATTTTAAAAA
1 TATTTTAAAAA
*
47641576 -A-TTAAAAAA
1 TATTTTAAAAA
*
47641585 GTATTTTTAAAA
1 -TATTTTAAAAA
47641597 TATTTT--AAA
1 TATTTTAAAAA
47641606 -A--TTAAAAA
1 TATTTTAAAAA
*
47641614 -ATTTAAAAAAA
1 TATTT-TAAAAA
47641625 TATTTTAAAAA
1 TATTTTAAAAA
47641636 TATTTT--AAA
1 TATTTTAAAAA
*
47641645 -A-TTAAAAAA
1 TATTTTAAAAA
47641654 T-TTTTAAAAAAA
1 TATTTT--AAAAA
47641666 GTATTTTAAAAA
1 -TATTTTAAAAA
47641678 TATTTTAAAA
1 TATTTTAAAA
47641688 TTTAAAAAAA
Statistics
Matches: 97, Mismatches: 7, Indels: 35
0.70 0.05 0.25
Matches are distributed among these distances:
6 2 0.02
7 2 0.02
8 6 0.06
9 21 0.22
10 8 0.08
11 33 0.34
12 20 0.21
13 1 0.01
14 4 0.04
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:47641736 original size:39 final size:39
Alignment explanation
Indices: 47641556--47641737 Score: 247
Period size: 39 Copynumber: 4.5 Consensus size: 39
47641546 GGCCCATTTT
* *
47641556 TATTTTAAAAATTTTAAAAAATTAAAAAAGTATTTTTAAAA
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
47641597 TATTTTAAAATTAAAAAATTTAAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
*
47641636 TATTTTAAAATTAAAAAATTTTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAA--ATT-AAAAAAGTATTTTAAAAA
* *
47641678 TATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAA-TTAAAAAAATTAAAAAAGTATTTTAAAAA
47641718 TATTTTAAAATTAAAAAAAT
1 TATTTTAAAATTAAAAAAAT
47641738 AAATATATTT
Statistics
Matches: 129, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
39 53 0.41
40 30 0.23
41 11 0.09
42 27 0.21
43 8 0.06
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:47641736 original size:40 final size:40
Alignment explanation
Indices: 47641556--47641736 Score: 238
Period size: 40 Copynumber: 4.5 Consensus size: 40
47641546 GGCCCATTTT
** *
47641556 TATTTTAAAAATTTTAAAAAATTAAAAAAGTATTTTTAAAA
1 TATTTT-AAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* *
47641597 TATTTTAAAATT-AAAAAATTTAAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
**
47641636 TATTTTAAAATTAAAAAATTTTTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAA-AATT-AAAAAAGTATTTTAAAAA
* * *
47641678 TATTTTAAAATTTAAAAAAATTAAAAAAGTATGTAAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
47641718 TATTTTAAAATTAAAAAAA
1 TATTTTAAAATTAAAAAAA
47641737 TAAATATATT
Statistics
Matches: 125, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
39 35 0.28
40 45 0.36
41 11 0.09
42 34 0.27
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:47653002 original size:12 final size:13
Alignment explanation
Indices: 47652974--47653002 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
47652964 TTCATTTTCA
47652974 ATAAAATTCATAT
1 ATAAAATTCATAT
47652987 ATAAAATTCA-AT
1 ATAAAATTCATAT
47652999 ATAA
1 ATAA
47653003 TCAAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAAATTCATAT
Found at i:47657972 original size:48 final size:50
Alignment explanation
Indices: 47657910--47658055 Score: 183
Period size: 54 Copynumber: 2.9 Consensus size: 50
47657900 TAAATTATGG
*
47657910 AGTTAGTTAAATATACAATAATTTACAAAAAAATCATGTAGCAATTCACA-T
1 AGTTA-TTAAATATACAATAATTTAC-AAAAAATCATGTAGCAATTCAAATT
*
47657961 A-TT-TTAAATATACAATAATTTACAAAAAATCATGTAG-AATTTAAATT
1 AGTTATTAAATATACAATAATTTACAAAAAATCATGTAGCAATTCAAATT
47658008 ATGGGGTTAGTTAAATATACAATAATTTACAAAAAATCATGTAGCAAT
1 A----GTTA-TTAAATATACAATAATTTACAAAAAATCATGTAGCAAT
47658056 AATCGACAAT
Statistics
Matches: 84, Mismatches: 2, Indels: 14
0.84 0.02 0.14
Matches are distributed among these distances:
46 6 0.07
47 16 0.19
48 20 0.24
50 2 0.02
51 1 0.01
52 2 0.02
54 34 0.40
55 3 0.04
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (50 bp):
AGTTATTAAATATACAATAATTTACAAAAAATCATGTAGCAATTCAAATT
Found at i:47662804 original size:42 final size:42
Alignment explanation
Indices: 47662729--47662839 Score: 143
Period size: 42 Copynumber: 2.6 Consensus size: 42
47662719 GTACATAAAT
* *
47662729 GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCATAGGA
1 GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCAGAAGA
* * * *
47662771 GCTGAACGGAAACCCGTAAGGGTTAATTTGAAGCTCAGAAGA
1 GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCAGAAGA
*
47662813 GCTAAACTAAAACCCAG-AAGGGTTAAA
1 GCTAAACGAAAACCC-GTAAGGGTTAAA
47662840 CTGAAACTCA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
42 57 0.98
43 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (42 bp):
GCTAAACGAAAACCCGTAAGGGTTAAATGGAAGCTCAGAAGA
Found at i:47662832 original size:21 final size:21
Alignment explanation
Indices: 47662806--47662846 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
47662796 ATTTGAAGCT
47662806 CAGAAGAGCTAAACTAAAACC
1 CAGAAGAGCTAAACTAAAACC
* * *
47662827 CAGAAGGGTTAAACTGAAAC
1 CAGAAGAGCTAAACTAAAAC
47662847 TCATATGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.12
Consensus pattern (21 bp):
CAGAAGAGCTAAACTAAAACC
Found at i:47664134 original size:20 final size:21
Alignment explanation
Indices: 47664077--47664144 Score: 111
Period size: 21 Copynumber: 3.3 Consensus size: 21
47664067 ATATTTACAA
*
47664077 CTCGATTTATAAAATTAAGGT
1 CTCGATTTATAAAATTGAGGT
*
47664098 CTCAATTTATAAAATTGAGGT
1 CTCGATTTATAAAATTGAGGT
47664119 CTCGATTTAT-AAATTGAGGT
1 CTCGATTTATAAAATTGAGGT
47664139 CTCGAT
1 CTCGAT
47664145 ACCCCGTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (21 bp):
CTCGATTTATAAAATTGAGGT
Found at i:47667123 original size:17 final size:18
Alignment explanation
Indices: 47667101--47667134 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47667091 AAAATTGTAA
47667101 TTTAAAT-TCTAATTATT
1 TTTAAATGTCTAATTATT
*
47667118 TTTAAATGTGTAATTAT
1 TTTAAATGTCTAATTAT
47667135 CTCAACTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTAAATGTCTAATTATT
Found at i:47669862 original size:28 final size:28
Alignment explanation
Indices: 47669824--47669883 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
47669814 ATTAATAAAT
*
47669824 ATATTATTTAA-AAAAATTATTTTTAATTC
1 ATATTATTTAATAAAAATT-CTTTT-ATTC
47669853 ATATT-TTTAATTAAAAATTCTTTTATTC
1 ATATTATTTAA-TAAAAATTCTTTTATTC
47669881 ATA
1 ATA
47669884 AAATCAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
28 12 0.43
29 9 0.32
30 7 0.25
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (28 bp):
ATATTATTTAATAAAAATTCTTTTATTC
Found at i:47670165 original size:18 final size:18
Alignment explanation
Indices: 47670142--47670176 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47670132 TTACATATAA
47670142 AAATAATAATTATATTTG
1 AAATAATAATTATATTTG
* *
47670160 AAATAATTATTTTATTT
1 AAATAATAATTATATTT
47670177 TATAATATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AAATAATAATTATATTTG
Found at i:47674931 original size:21 final size:22
Alignment explanation
Indices: 47674907--47674949 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
47674897 AACAAATTTA
*
47674907 AGTA-TGTTGCATTGCAAAAGC
1 AGTATTGTTGCACTGCAAAAGC
*
47674928 AGTATTGTTGTACTGCAAAAGC
1 AGTATTGTTGCACTGCAAAAGC
47674950 TGATTCTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (22 bp):
AGTATTGTTGCACTGCAAAAGC
Found at i:47678248 original size:39 final size:39
Alignment explanation
Indices: 47678190--47678269 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
47678180 ATCTGTGCCT
47678190 AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
1 AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
* *
47678229 AAATCTGATGGAGAGGTTAATGTGGCAACTGATTCTTCA
1 AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
47678268 AA
1 AA
47678270 GGCTGCTGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (39 bp):
AAATCTGAGGGAGAAGTTAATGTGGCAACTGATTCTTCA
Found at i:47688471 original size:30 final size:30
Alignment explanation
Indices: 47688399--47688484 Score: 86
Period size: 31 Copynumber: 2.9 Consensus size: 30
47688389 GATTAAATTA
*
47688399 AAATTAAAGTTTCAAGTATACATTTGAACC
1 AAATTAAAGTTTCAAGTATACAATTGAACC
* * * *
47688429 ACAATTAGAGTTTCACGTATATAATT-ACATC
1 A-AATTAAAGTTTCAAGTATACAATTGA-ACC
*
47688460 AAATTAAAGTTT-ATGTATACAATTG
1 AAATTAAAGTTTCAAGTATACAATTG
47688485 CACATTAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 10 0.22
30 12 0.27
31 23 0.51
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (30 bp):
AAATTAAAGTTTCAAGTATACAATTGAACC
Found at i:47689008 original size:3 final size:3
Alignment explanation
Indices: 47689000--47689053 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
47688990 CATAGTGAGA
*
47689000 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
47689048 AAT AAT
1 AAT AAT
47689054 CTCTAGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47695497 original size:25 final size:24
Alignment explanation
Indices: 47695469--47695521 Score: 88
Period size: 25 Copynumber: 2.2 Consensus size: 24
47695459 ACATATCGCA
47695469 GCTCTTTATGAGCGTCCTGATATAG
1 GCTCTTTATGAGCGTCCTGATAT-G
*
47695494 GCTCTTTATGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTGATATG
47695518 GCTC
1 GCTC
47695522 GCTTGAACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
24 5 0.19
25 22 0.81
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTGATATG
Found at i:47702480 original size:7 final size:7
Alignment explanation
Indices: 47702470--47702501 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
47702460 TGTTTCAAGT
*
47702470 TTCATTC
1 TTCAATC
47702477 TTCAATC
1 TTCAATC
47702484 TTCAATC
1 TTCAATC
47702491 TTCAATC
1 TTCAATC
47702498 TTCA
1 TTCA
47702502 TATTTAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.25, C:0.28, G:0.00, T:0.47
Consensus pattern (7 bp):
TTCAATC
Found at i:47705288 original size:2 final size:2
Alignment explanation
Indices: 47705281--47705308 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
47705271 ATCTTTCTTA
47705281 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
47705309 TATGTGCTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47710721 original size:2 final size:2
Alignment explanation
Indices: 47710710--47710755 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
47710700 TGGTGTCGGC
47710710 AT AT -T 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
47710751 AT AT A
1 AT AT A
47710756 AGTTTGGCCC
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47714437 original size:31 final size:31
Alignment explanation
Indices: 47714400--47714465 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 31
47714390 TTTTTATTAG
47714400 TATATGAATATTATGTTTGTTGATA-TATGA-A
1 TATATGAATATTATGTTTG--GATATTATGACA
47714431 TATATGAATATTATGTTTGGATATTATGACA
1 TATATGAATATTATGTTTGGATATTATGACA
47714462 TATA
1 TATA
47714466 ACCTAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 4 0.12
30 5 0.15
31 24 0.73
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (31 bp):
TATATGAATATTATGTTTGGATATTATGACA
Found at i:47717461 original size:21 final size:21
Alignment explanation
Indices: 47717416--47717462 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
47717406 AAATAATAAA
*
47717416 ATAG-ATTATATATTATTTTT
1 ATAGTATTATATATTATATTT
47717436 ATAGTATTATATATTATGATTT
1 ATAGTATTATATATTAT-ATTT
47717458 -TAGTA
1 ATAGTA
47717463 AATTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 17 0.71
22 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATAGTATTATATATTATATTT
Found at i:47717775 original size:45 final size:44
Alignment explanation
Indices: 47717685--47717776 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
47717675 TTACAATATT
* **
47717685 ATTCCATTCAACCAAACACAAGAATATTATTACAGTTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATACTATTACACCTCTATTCC
* *
47717729 ATTCCATTTAACCAAACA-ATTGAATTACTATTACACCTCTATTCC
1 ATTCCATTCAACCAAACACA-AGAA-TACTATTACACCTCTATTCC
47717774 ATT
1 ATT
47717777 ACAGCTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
43 1 0.02
44 20 0.49
45 20 0.49
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (44 bp):
ATTCCATTCAACCAAACACAAGAATACTATTACACCTCTATTCC
Found at i:47717779 original size:16 final size:16
Alignment explanation
Indices: 47717758--47717809 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
47717748 TTGAATTACT
*
47717758 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
47717774 ATTACAGCTCTATT-C
1 ATTACAGCTCTATTCC
*
47717789 AGTTACAGCTCTATTCT
1 A-TTACAGCTCTATTCC
47717806 ATTA
1 ATTA
47717810 TAGCGAACCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 2 0.06
16 29 0.91
17 1 0.03
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:47727546 original size:30 final size:30
Alignment explanation
Indices: 47727506--47727564 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
47727496 TTAACAATCA
47727506 AAATGACTCTAAAATAATAACAAAATTAAT
1 AAATGACTCTAAAATAATAACAAAATTAAT
*
47727536 AAATGCCTCTAAAATAATAACAAAATTAA
1 AAATGACTCTAAAATAATAACAAAATTAA
47727565 CAATAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.25
Consensus pattern (30 bp):
AAATGACTCTAAAATAATAACAAAATTAAT
Found at i:47727610 original size:11 final size:11
Alignment explanation
Indices: 47727596--47727643 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
47727586 ATATCCAAAC
*
47727596 AATAATAACAA
1 AATAATAGCAA
*
47727607 AATAGTAGCAA
1 AATAATAGCAA
* *
47727618 CATAATAGTAA
1 AATAATAGCAA
*
47727629 AATAGTAGCAA
1 AATAATAGCAA
47727640 AATA
1 AATA
47727644 GGGAGAAAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.60, C:0.08, G:0.10, T:0.21
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:47727622 original size:22 final size:22
Alignment explanation
Indices: 47727597--47727639 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
47727587 TATCCAAACA
47727597 ATAATAACAAAATAGTAGCAAC
1 ATAATAACAAAATAGTAGCAAC
**
47727619 ATAATAGTAAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
47727640 AATAGGGAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.09, G:0.12, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAC
Found at i:47727644 original size:11 final size:11
Alignment explanation
Indices: 47727604--47727644 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
47727594 ACAATAATAA
47727604 CAAAATAGTAG
1 CAAAATAGTAG
* *
47727615 CAACATAATAG
1 CAAAATAGTAG
*
47727626 TAAAATAGTAG
1 CAAAATAGTAG
47727637 CAAAATAG
1 CAAAATAG
47727645 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:47736278 original size:32 final size:32
Alignment explanation
Indices: 47736242--47736316 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 32
47736232 ATATTATACC
47736242 AGCCCAAACCCTTTTAC-CT-TATTTCCCTCCAA
1 AGCCCAAACCCTTTTACTCTAT-TTTCCC-CCAA
*
47736274 AGCCCAAACCTTTTTACTCTATTTTCCCCCAA
1 AGCCCAAACCCTTTTACTCTATTTTCCCCCAA
47736306 AGCCCAAACCC
1 AGCCCAAACCC
47736317 CATCCCCCTC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
32 30 0.77
33 8 0.21
34 1 0.03
ACGTcount: A:0.27, C:0.41, G:0.04, T:0.28
Consensus pattern (32 bp):
AGCCCAAACCCTTTTACTCTATTTTCCCCCAA
Found at i:47736443 original size:42 final size:42
Alignment explanation
Indices: 47736397--47736486 Score: 135
Period size: 42 Copynumber: 2.1 Consensus size: 42
47736387 TTGTCTATCC
* ** *
47736397 AAACCCCTAAATTTATGTTTCTTCTTCAAAAATCCTTAAATT
1 AAACCCCCAAATCCATGTTTCTTCTTCAAAAATCCCTAAATT
*
47736439 AAACCCCCAAATCCATTTTTCTTCTTCAAAAATCCCTAAATT
1 AAACCCCCAAATCCATGTTTCTTCTTCAAAAATCCCTAAATT
47736481 AAACCC
1 AAACCC
47736487 TCTATTCTTC
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.28, G:0.01, T:0.34
Consensus pattern (42 bp):
AAACCCCCAAATCCATGTTTCTTCTTCAAAAATCCCTAAATT
Found at i:47739550 original size:64 final size:66
Alignment explanation
Indices: 47739417--47739554 Score: 165
Period size: 64 Copynumber: 2.1 Consensus size: 66
47739407 AGATGTCTCC
* * *
47739417 TTCCCCTGCATAAAGATGACATAAAGATGACAAAGCAACATTTACACCTATGTTACCAAAAACTG
1 TTCCCCTGCATAAAGAT-AC--AAAGATGACAAAGCAACACTTACACCTATATTACCAAAAACTA
47739482 CTAT
63 CTAT
* * *
47739486 TTCCCCTGCATAAAGAT-C-AAGATGACAAAGCAACACTTACACTTCTATTACCATAAA-TCACT
1 TTCCCCTGCATAAAGATACAAAGATGACAAAGCAACACTTACACCTATATTACCAAAAACT-ACT
47739548 AT
65 AT
47739550 TTCCC
1 TTCCC
47739555 TATCAATTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.02
64 43 0.69
67 1 0.02
69 17 0.27
ACGTcount: A:0.38, C:0.26, G:0.09, T:0.26
Consensus pattern (66 bp):
TTCCCCTGCATAAAGATACAAAGATGACAAAGCAACACTTACACCTATATTACCAAAAACTACTA
T
Found at i:47744406 original size:31 final size:30
Alignment explanation
Indices: 47744357--47744442 Score: 75
Period size: 31 Copynumber: 2.8 Consensus size: 30
47744347 AATATGTATG
* *
47744357 ATTGAATCAAAATTAAAGTTTCATGTATACA
1 ATTGAA-CCAAATCAAAGTTTCATGTATACA
* * ** *
47744388 TTTGAACCACAATCAAAGTTCCACATATATA
1 ATTGAACCA-AATCAAAGTTTCATGTATACA
*
47744419 ATTGTACCAAATCAAAG-TTCATGT
1 ATTGAACCAAATCAAAGTTTCATGT
47744443 GTAACACCCC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
29 4 0.10
30 10 0.24
31 28 0.67
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (30 bp):
ATTGAACCAAATCAAAGTTTCATGTATACA
Found at i:47747191 original size:45 final size:45
Alignment explanation
Indices: 47747128--47747216 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
47747118 GAATGATATT
*
47747128 ATGTATTTAGTATATTGTTGAAAAATAGAACATTGTTAAATTATC
1 ATGTATTTAGCATATTGTTGAAAAATAGAACATTGTTAAATTATC
* * *
47747173 ATGTATTTAGCATGTTGTTGAAAAATGGAATATTGTTAAATTAT
1 ATGTATTTAGCATATTGTTGAAAAATAGAACATTGTTAAATTAT
47747217 GAAATTGAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (45 bp):
ATGTATTTAGCATATTGTTGAAAAATAGAACATTGTTAAATTATC
Found at i:47747395 original size:24 final size:24
Alignment explanation
Indices: 47747276--47747385 Score: 166
Period size: 24 Copynumber: 4.6 Consensus size: 24
47747266 TCGTTCTGTG
*
47747276 GCAAAGGATGAATTGATGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
* *
47747300 TCAAAGGATGAATTAACGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
*
47747324 GCAAAGGATGAATTGACAGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
* *
47747348 GCAAAGGAAGAATTGGCGGTAAAT
1 GCAAAGGATGAATTGACGGTAAAT
47747372 GCAAAGGATGAATT
1 GCAAAGGATGAATT
47747386 AATGGCAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 76 1.00
ACGTcount: A:0.44, C:0.07, G:0.27, T:0.22
Consensus pattern (24 bp):
GCAAAGGATGAATTGACGGTAAAT
Found at i:47747509 original size:21 final size:21
Alignment explanation
Indices: 47747480--47747670 Score: 89
Period size: 21 Copynumber: 9.1 Consensus size: 21
47747470 CATTAACTCA
47747480 TATGAGTTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
* **
47747501 TATGGGTTTCCGTT-AAGCTTT
1 TATGAGTTTCCGTTCAA-CCCT
* * * ** *
47747522 TTTAAGCTTCAATTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * *
47747543 TATGGGTTTCCGTTCAGCTCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
47747564 TTTGAGCTTCAGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * * *
47747585 TATGGGTTTCCATTCAGCTCT
1 TATGAGTTTCCGTTCAACCCT
* * * * *
47747606 TTTCAGCTTCAGTTTAACCCT
1 TATGAGTTTCCGTTCAACCCT
* * *
47747627 TATGGGTTTTCGTTCATCTCC-
1 TATGAGTTTCCGTTCAAC-CCT
*
47747648 TATGAGCTTCCGTTCAACCCT
1 TATGAGTTTCCGTTCAACCCT
47747669 TA
1 TA
47747671 CGGGTTTCTA
Statistics
Matches: 110, Mismatches: 56, Indels: 8
0.63 0.32 0.05
Matches are distributed among these distances:
20 4 0.04
21 102 0.93
22 4 0.04
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (21 bp):
TATGAGTTTCCGTTCAACCCT
Found at i:47747554 original size:42 final size:42
Alignment explanation
Indices: 47747495--47747678 Score: 242
Period size: 42 Copynumber: 4.4 Consensus size: 42
47747485 GTTTCCGTTC
* * *
47747495 AACCCTTATGGGTTTCCGTTAAGCTTTTTTAAGCTTCAATTT
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
*
47747537 AACCCTTATGGGTTTCCGTTCAGCTCTTTTGAGCTTCAGTTT
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
* *
47747579 AACCCTTATGGGTTTCCATTCAGCTCTTTTCAGCTTCAGTTT
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
* * * * * * *
47747621 AACCCTTATGGGTTTTCGTTCATCTCCTATGAGCTTCCGTTC
1 AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
*
47747663 AACCCTTACGGGTTTC
1 AACCCTTATGGGTTTC
47747679 TAATTAGCAC
Statistics
Matches: 126, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.42
Consensus pattern (42 bp):
AACCCTTATGGGTTTCCGTTCAGCTCTTTTAAGCTTCAGTTT
Found at i:47747641 original size:84 final size:84
Alignment explanation
Indices: 47747480--47747678 Score: 272
Period size: 84 Copynumber: 2.4 Consensus size: 84
47747470 CATTAACTCA
* * * *
47747480 TATGAGTTTCCGTTCAACCCTTATGGGTTTCCGTTAAGCTTTTTTAAGCTTCAATTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCCATTAAGCTCTTTTAAGCTTCAATTTAACCCTTA
*
47747545 TGGGTTTCCGTTCAGCTCT
66 TGGGTTTCCGTTCAGCTCC
* * * * *
47747564 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAGCTCTTTTCAGCTTCAGTTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTCCATTAAGCTCTTTTAAGCTTCAATTTAACCCTTA
* *
47747629 TGGGTTTTCGTTCATCTCC
66 TGGGTTTCCGTTCAGCTCC
* *
47747648 TATGAGCTTCCGTTCAACCCTTACGGGTTTC
1 TATGAGCTTCAGTTCAACCCTTATGGGTTTC
47747679 TAATTAGCAC
Statistics
Matches: 99, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 99 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (84 bp):
TATGAGCTTCAGTTCAACCCTTATGGGTTTCCATTAAGCTCTTTTAAGCTTCAATTTAACCCTTA
TGGGTTTCCGTTCAGCTCC
Found at i:47747699 original size:84 final size:84
Alignment explanation
Indices: 47747480--47747705 Score: 229
Period size: 84 Copynumber: 2.7 Consensus size: 84
47747470 CATTAACTCA
* * * ** * ** * * *
47747480 TATGAGTTTCCGTTCAACCCTTATGGGTTTCCGTTAAGCTTTTTTAAGCTTCAATTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTACGGGTTTCAATTCAGCACTTATCAGCTTCAGTTTAACCCTTA
*
47747545 TGGGTTTCCGTTCAGCTCT
66 TGGGTTTCCGTTCAGCTCC
* * * * * *
47747564 TTTGAGCTTCAGTTTAACCCTTATGGGTTTCCATTCAGCTCTTTTCAGCTTCAGTTTAACCCTTA
1 TATGAGCTTCAGTTCAACCCTTACGGGTTTCAATTCAGCACTTATCAGCTTCAGTTTAACCCTTA
* *
47747629 TGGGTTTTCGTTCATCTCC
66 TGGGTTTCCGTTCAGCTCC
* **
47747648 TATGAGCTTCCGTTCAACCCTTACGGGTTTCTAATT-AGCACTTATGTGCTTCAGTTTA
1 TATGAGCTTCAGTTCAACCCTTACGGGTTTC-AATTCAGCACTTATCAGCTTCAGTTTA
47747706 GCCTTCAGGC
Statistics
Matches: 120, Mismatches: 21, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
84 117 0.98
85 3 0.03
ACGTcount: A:0.18, C:0.23, G:0.16, T:0.42
Consensus pattern (84 bp):
TATGAGCTTCAGTTCAACCCTTACGGGTTTCAATTCAGCACTTATCAGCTTCAGTTTAACCCTTA
TGGGTTTCCGTTCAGCTCC
Found at i:47749881 original size:22 final size:22
Alignment explanation
Indices: 47749846--47749915 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
47749836 TATGCACAAG
*
47749846 TAAACGGAGAGCACCAAGGTGC
1 TAAACAGAGAGCACCAAGGTGC
*
47749868 TATAC-GAAGAGCA-CAAGCGTGC
1 TAAACAG-AGAGCACCAAG-GTGC
* *
47749890 TAAACAGAGAGCACTAATGTGC
1 TAAACAGAGAGCACCAAGGTGC
47749912 TAAA
1 TAAA
47749916 AAATAAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 5 0.12
22 32 0.80
23 3 0.08
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (22 bp):
TAAACAGAGAGCACCAAGGTGC
Found at i:47751481 original size:25 final size:25
Alignment explanation
Indices: 47751453--47751562 Score: 82
Period size: 25 Copynumber: 4.4 Consensus size: 25
47751443 TAGCTCTCTT
*
47751453 GAGCTTCCCGATACT-TGGCTCGCAA
1 GAGCTTCCCGATA-TATAGCTCGCAA
* * * *
47751478 GAGCTTTCTGATATATAGCTCGTAT
1 GAGCTTCCCGATATATAGCTCGCAA
* * *
47751503 GAGCTTCCCGTTACT-TAGCTCACAT
1 GAGCTTCCCGATA-TATAGCTCGCAA
* *
47751528 GAGCTTCCC-ATTATATGGCTCGGAA
1 GAGCTTCCCGA-TATATAGCTCGCAA
47751553 GAGCTTCCCG
1 GAGCTTCCCG
47751563 TTTACATGCT
Statistics
Matches: 65, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
24 2 0.03
25 62 0.95
26 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.22, T:0.30
Consensus pattern (25 bp):
GAGCTTCCCGATATATAGCTCGCAA
Found at i:47751518 original size:50 final size:50
Alignment explanation
Indices: 47751452--47751564 Score: 129
Period size: 50 Copynumber: 2.3 Consensus size: 50
47751442 ATAGCTCTCT
* * * ** *
47751452 TGAGCTTCCCGATACTTGGCTCGCAAGAGCTTTCTGA-TATATAGCTCGTA
1 TGAGCTTCCCGTTACTTAGCTCACAAGAGC-TTCCCATTATATAGCTCGGA
* *
47751502 TGAGCTTCCCGTTACTTAGCTCACATGAGCTTCCCATTATATGGCTCGGA
1 TGAGCTTCCCGTTACTTAGCTCACAAGAGCTTCCCATTATATAGCTCGGA
*
47751552 AGAGCTTCCCGTT
1 TGAGCTTCCCGTT
47751565 TACATGCTTG
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
49 4 0.08
50 49 0.92
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (50 bp):
TGAGCTTCCCGTTACTTAGCTCACAAGAGCTTCCCATTATATAGCTCGGA
Found at i:47756385 original size:67 final size:67
Alignment explanation
Indices: 47756277--47756404 Score: 229
Period size: 67 Copynumber: 1.9 Consensus size: 67
47756267 TTATATTACT
47756277 GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCTCTTG
1 GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCTCTTG
47756342 CA
66 CA
* * *
47756344 GGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTTGCGGGAGTGTGCTCT
1 GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCT
47756405 TTGAATTGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (67 bp):
GGGGATTTAGCCTGGACTGGAAATCCCGCTGTAAGAAATGAGATTCGCGGGAGTGTGCTCTCTTG
CA
Found at i:47756597 original size:26 final size:27
Alignment explanation
Indices: 47756530--47756597 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 27
47756520 AAATGATAAG
47756530 TACATAAAATCATGAAATTAAACTTGAAA
1 TACATAAAAT-ATGAAATT-AACTTGAAA
* *
47756559 TACATAGAA-ATGATAATT-ACTTGATA
1 TACATAAAATATGA-AATTAACTTGAAA
47756585 TAC-TAAAATATGA
1 TACATAAAATATGA
47756598 CATGGAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
25 4 0.12
26 14 0.41
27 4 0.12
28 4 0.12
29 8 0.24
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (27 bp):
TACATAAAATATGAAATTAACTTGAAA
Found at i:47757693 original size:32 final size:32
Alignment explanation
Indices: 47757616--47757702 Score: 81
Period size: 32 Copynumber: 2.7 Consensus size: 32
47757606 TTTAAAAAAT
* *
47757616 AAAAAGTTATGAAAGACTAAAAAATTTAAACTTC
1 AAAAA-TTATAAAAAACTAAAAAATTT-AACTTC
*
47757650 AAAAA-TA-AAAAAACTAAACAAATTT-ATTTC
1 AAAAATTATAAAAAACTAAA-AAATTTAACTTC
**
47757680 AAAAATTATAAAAATTTAAAAAA
1 AAAAATTATAAAAAACTAAAAAA
47757703 GTTTTAAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
30 9 0.20
31 14 0.31
32 17 0.38
34 5 0.11
ACGTcount: A:0.63, C:0.07, G:0.03, T:0.26
Consensus pattern (32 bp):
AAAAATTATAAAAAACTAAAAAATTTAACTTC
Found at i:47762767 original size:50 final size:50
Alignment explanation
Indices: 47762643--47762885 Score: 252
Period size: 50 Copynumber: 4.7 Consensus size: 50
47762633 GGGAATGAGA
* * *
47762643 TCCCATGTAAGACCGTGTCTGGGACATGGCATTGGCATCAATAAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-GATGAGAGG
* * *
47762699 TCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGT
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
47762749 TCCCATGTAAGACTATGTCTGGGACATGGCGTTGGCACCGAGATAAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*** * * * * **
47762799 TCCCCCATAAGACCATGTCTGAGACATGGCATGGGCACCAATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* *
47762849 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
47762886 GTACAGAAAA
Statistics
Matches: 158, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
50 121 0.77
51 2 0.01
55 1 0.01
56 34 0.22
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:47771884 original size:6 final size:6
Alignment explanation
Indices: 47771873--47771902 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
47771863 CAATCTGGGA
47771873 CTGATT CTGATT CTGATT CTGATT CTGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT
47771903 GGGAGTAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
CTGATT
Found at i:47773201 original size:16 final size:16
Alignment explanation
Indices: 47773176--47773206 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47773166 TAACAAATGG
47773176 ATAAGATTGGGGTGTT
1 ATAAGATTGGGGTGTT
*
47773192 ATAAGGTTGGGGTGT
1 ATAAGATTGGGGTGT
47773207 GTCTTGGGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.42, T:0.35
Consensus pattern (16 bp):
ATAAGATTGGGGTGTT
Found at i:47777248 original size:3 final size:3
Alignment explanation
Indices: 47777242--47777294 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
47777232 TATCATTATT
*
47777242 ATC ATC ATC ACC 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 ATC ATC ATC ATC
47777290 ATC AT
1 ATC AT
47777295 TGGCTCATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:47779917 original size:15 final size:15
Alignment explanation
Indices: 47779897--47779925 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
47779887 TGAGTATCAT
47779897 CAAAACATGATATAA
1 CAAAACATGATATAA
47779912 CAAAACATGATATA
1 CAAAACATGATATA
47779926 GCCTCTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (15 bp):
CAAAACATGATATAA
Found at i:47780420 original size:14 final size:14
Alignment explanation
Indices: 47780401--47780432 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
47780391 CTTTACTTTC
47780401 CACAGTATCACTTG
1 CACAGTATCACTTG
47780415 CACAGTATCACTTG
1 CACAGTATCACTTG
47780429 CACA
1 CACA
47780433 TATTACATAT
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:0.31, C:0.31, G:0.12, T:0.25
Consensus pattern (14 bp):
CACAGTATCACTTG
Found at i:47780455 original size:13 final size:13
Alignment explanation
Indices: 47780437--47780467 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
47780427 TGCACATATT
47780437 ACATATAAATTCA
1 ACATATAAATTCA
47780450 ACATATAAATTCA
1 ACATATAAATTCA
47780463 ACATA
1 ACATA
47780468 GATAAACTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (13 bp):
ACATATAAATTCA
Found at i:47781223 original size:26 final size:25
Alignment explanation
Indices: 47781144--47781225 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 25
47781134 AAGTTAAAGC
*
47781144 AAGCCA-T-ATCGGGAAGCTCCGGA
1 AAGCCATTAATCGGGAAGCTCCGAA
* * *
47781167 GAGCCATTAATCAGGAAGC-CCACAA
1 AAGCCATTAATCGGGAAGCTCC-GAA
*
47781192 AGAGCCTTTAATCGGGAAGCTCGCGAA
1 A-AGCCATTAATCGGGAAGCTC-CGAA
47781219 AAGCCAT
1 AAGCCAT
47781226 ATAACGAGAC
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
23 5 0.11
24 3 0.07
25 10 0.23
26 21 0.48
27 4 0.09
28 1 0.02
ACGTcount: A:0.34, C:0.26, G:0.26, T:0.15
Consensus pattern (25 bp):
AAGCCATTAATCGGGAAGCTCCGAA
Found at i:47785428 original size:7 final size:7
Alignment explanation
Indices: 47785416--47785450 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
47785406 GTATGCCTAC
47785416 ATTTTTT
1 ATTTTTT
47785423 ATTTTTT
1 ATTTTTT
47785430 ATTTTTT
1 ATTTTTT
47785437 ATTTTTT
1 ATTTTTT
47785444 ATTTTTT
1 ATTTTTT
47785451 TTTAAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
ATTTTTT
Found at i:47788044 original size:17 final size:16
Alignment explanation
Indices: 47788022--47788124 Score: 53
Period size: 17 Copynumber: 6.6 Consensus size: 16
47788012 AGTGGTTATC
47788022 TTAATATTAAATTTAAT
1 TTAATATT-AATTTAAT
*
47788039 TTAATA-T-ATTTTA-
1 TTAATATTAATTTAAT
47788052 TTAAT-TTAA--TAGAT
1 TTAATATTAATTTA-AT
47788066 TTAATATTAAATTTAAT
1 TTAATATT-AATTTAAT
* * *
47788083 CTAATATTTATCTTGA-
1 TTAATATTAAT-TTAAT
47788099 -TAAGTATT-ATATTAAT
1 TTAA-TATTAAT-TTAAT
47788115 TTAATATTAA
1 TTAATATTAA
47788125 AGTGATGAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 26
0.67 0.07 0.26
Matches are distributed among these distances:
12 1 0.02
13 7 0.11
14 11 0.17
15 10 0.15
16 13 0.20
17 22 0.33
18 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (16 bp):
TTAATATTAATTTAAT
Found at i:47788057 original size:18 final size:19
Alignment explanation
Indices: 47788034--47788082 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 19
47788024 AATATTAAAT
*
47788034 TTAATTTAATATATTT-TA
1 TTAATTTAATAGATTTATA
47788052 TTAATTTAATAGATTTAATA
1 TTAATTTAATAGATTT-ATA
47788072 TTAAATTTAAT
1 TT-AATTTAAT
47788083 CTAATATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 15 0.56
20 4 0.15
21 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAATTTAATAGATTTATA
Found at i:47789060 original size:36 final size:36
Alignment explanation
Indices: 47789020--47789107 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
47789010 TGAGCCTCCC
* * *
47789020 CCCATGTGTGGGAGTAGGACCTCCCGTAAGCCTCAA
1 CCCATGTGAGGGAGCAGGACCTCCCGCAAGCCTCAA
* * **
47789056 CCCATATGAGGGAGCAGGACCTCCTGCAAGCCTCTC
1 CCCATGTGAGGGAGCAGGACCTCCCGCAAGCCTCAA
*
47789092 CCCATGTGCGGGAGCA
1 CCCATGTGAGGGAGCA
47789108 ACACATTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (36 bp):
CCCATGTGAGGGAGCAGGACCTCCCGCAAGCCTCAA
Found at i:47789940 original size:8 final size:8
Alignment explanation
Indices: 47789927--47789951 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47789917 TATATTATAT
47789927 TATAATAA
1 TATAATAA
47789935 TATAATAA
1 TATAATAA
47789943 TATAATAA
1 TATAATAA
47789951 T
1 T
47789952 GTATAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TATAATAA
Found at i:47789949 original size:5 final size:5
Alignment explanation
Indices: 47789863--47789930 Score: 129
Period size: 5 Copynumber: 13.8 Consensus size: 5
47789853 AAGTATTAAG
47789863 TATA- TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
47789912 TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATA
47789931 ATAATATAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.06
5 59 0.94
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:47790735 original size:15 final size:15
Alignment explanation
Indices: 47790715--47790764 Score: 66
Period size: 15 Copynumber: 3.2 Consensus size: 15
47790705 TGATAAATTT
47790715 ATTGAATTTATATTG
1 ATTGAATTTATATTG
47790730 ATTGAATTGGTATATAT-
1 ATTGAATT--TATAT-TG
47790747 ATTGAATTTATATTG
1 ATTGAATTTATATTG
47790762 ATT
1 ATT
47790765 ATTTGAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 16 0.52
17 13 0.42
18 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:47790768 original size:13 final size:11
Alignment explanation
Indices: 47790714--47790782 Score: 51
Period size: 11 Copynumber: 6.7 Consensus size: 11
47790704 GTGATAAATT
47790714 TATTGAATTTA
1 TATTGAATTTA
*
47790725 TATTG-ATTGA
1 TATTGAATTTA
* *
47790735 -ATTGGTATATA
1 TATT-GAATTTA
47790746 TATTGAATTTA
1 TATTGAATTTA
47790757 TATTG-A-TTA
1 TATTGAATTTA
*
47790766 T-TTGAATTGA
1 TATTGAATTTA
47790776 -ATTGAAT
1 TATTGAAT
47790783 ATTGGTTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 13
0.71 0.09 0.20
Matches are distributed among these distances:
8 3 0.07
9 8 0.17
10 14 0.30
11 18 0.39
12 3 0.07
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (11 bp):
TATTGAATTTA
Found at i:47790779 original size:18 final size:19
Alignment explanation
Indices: 47790743--47790785 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
47790733 GAATTGGTAT
*
47790743 ATATATTGAATTTATATTGA
1 ATAT-TTGAATTGATATTGA
*
47790763 TTATTTGAATTGA-ATTGA
1 ATATTTGAATTGATATTGA
47790781 ATATT
1 ATATT
47790786 GGTTGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.45
19 8 0.40
20 3 0.15
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
ATATTTGAATTGATATTGA
Found at i:47790941 original size:41 final size:40
Alignment explanation
Indices: 47790897--47791028 Score: 135
Period size: 41 Copynumber: 3.4 Consensus size: 40
47790887 GACTTCGATT
*
47790897 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATT-ATC
* * * * *
47790938 CGATGAGTCACTAGGTGCCAATTTAC-A--TCGGTTTAGC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTATC
* * * *
47790975 CGATGAGACACTGGGAGTCAATTTATTACTTTGAATTATC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTATC
*
47791015 CGATGAGGCACTGG
1 CGATGAGACACTGG
47791029 ATGCCAAATT
Statistics
Matches: 72, Mismatches: 16, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 22 0.31
38 7 0.10
40 20 0.28
41 23 0.32
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTATC
Found at i:47790997 original size:37 final size:40
Alignment explanation
Indices: 47790897--47791004 Score: 114
Period size: 37 Copynumber: 2.8 Consensus size: 40
47790887 GACTTCGATT
**
47790897 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTAC-TCGGATTAAGC
* * * *
47790938 CGATGAGTCACTAGGTGCCAATTTAC-A-TCGG-TTTAGC
1 CGATGAGACACTGGGTGTCAATTTACTACTCGGATTAAGC
* *
47790975 CGATGAGACACTGGGAGTCAATTTATTACT
1 CGATGAGACACTGGGTGTCAATTTACTACT
47791005 TTGAATTATC
Statistics
Matches: 54, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
37 24 0.44
38 5 0.09
39 1 0.02
40 1 0.02
41 23 0.43
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAATTTACTACTCGGATTAAGC
Found at i:47793198 original size:27 final size:29
Alignment explanation
Indices: 47793145--47793198 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 29
47793135 AAATTATAAA
* *
47793145 TTTTATAAAAATTCAAAAAATTGAAAACT
1 TTTTATAAAAAATCAAAAAATTCAAAACT
*
47793174 TTTTA-AAAAAATC-AAAATTTCAAAA
1 TTTTATAAAAAATCAAAAAATTCAAAA
47793199 AATAACATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 10 0.45
28 7 0.32
29 5 0.23
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (29 bp):
TTTTATAAAAAATCAAAAAATTCAAAACT
Found at i:47801824 original size:23 final size:22
Alignment explanation
Indices: 47801784--47801827 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
47801774 AAATTATAAA
*
47801784 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
47801806 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
47801828 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:47802576 original size:22 final size:21
Alignment explanation
Indices: 47802541--47802617 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
47802531 AACGGGTATC
* *
47802541 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
47802562 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
47802585 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
47802604 TGCATATCATATCT
1 TACAAATCATATCT
47802618 AAGATTGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
19 19 0.40
21 4 0.08
22 15 0.31
23 10 0.21
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Found at i:47802584 original size:23 final size:22
Alignment explanation
Indices: 47802541--47802598 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
47802531 AACGGGTATC
* *
47802541 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
47802562 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
47802585 TGCATATCATATCT
1 TACAAATCATATCT
47802599 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:47802601 original size:19 final size:19
Alignment explanation
Indices: 47802577--47802630 Score: 108
Period size: 19 Copynumber: 2.8 Consensus size: 19
47802567 AATCATATCT
47802577 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
47802596 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
47802615 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
47802631 CTTGAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:47807902 original size:16 final size:16
Alignment explanation
Indices: 47807881--47807914 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
47807871 AAACATTTTT
47807881 TTATAAATGTTATATA
1 TTATAAATGTTATATA
*
47807897 TTATAAATTTTATATA
1 TTATAAATGTTATATA
47807913 TT
1 TT
47807915 TTTGGCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
TTATAAATGTTATATA
Found at i:47808653 original size:19 final size:21
Alignment explanation
Indices: 47808629--47808682 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
47808619 TTTTAGTATT
*
47808629 TTGTAGCTCAAATT-AT-GTA
1 TTGTAGCTCAAATTCATAATA
*
47808648 TTGTAG-TTAATATTCATAATA
1 TTGTAGCTCAA-ATTCATAATA
47808669 TTGTAGCTCAAATT
1 TTGTAGCTCAAATT
47808683 GTCAATCCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.11
19 9 0.32
20 2 0.07
21 11 0.39
22 3 0.11
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.44
Consensus pattern (21 bp):
TTGTAGCTCAAATTCATAATA
Found at i:47810632 original size:12 final size:12
Alignment explanation
Indices: 47810615--47810639 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
47810605 CCACTTTATA
47810615 AAAAAATCATTT
1 AAAAAATCATTT
47810627 AAAAAATCATTT
1 AAAAAATCATTT
47810639 A
1 A
47810640 TGATAAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAATCATTT
Found at i:47810682 original size:20 final size:20
Alignment explanation
Indices: 47810644--47810689 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
47810634 CATTTATGAT
*
47810644 AAAATACATAAGATTTTATA
1 AAAATACATAAGATATTATA
47810664 AAAATACATACA-ATATTATA
1 AAAATACATA-AGATATTATA
47810684 ATAAAT
1 A-AAAT
47810690 GAATACCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 18 0.78
21 5 0.22
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATACATAAGATATTATA
Found at i:47811278 original size:20 final size:20
Alignment explanation
Indices: 47811255--47811292 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
47811245 GGGTTTTCCT
* *
47811255 TTTTTTTTATAAGATTATTA
1 TTTTATTTATAAAATTATTA
47811275 TTTTATTTATAAAATTAT
1 TTTTATTTATAAAATTAT
47811293 CATTATAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTATTTATAAAATTATTA
Found at i:47811396 original size:22 final size:22
Alignment explanation
Indices: 47811349--47811406 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
47811339 ATCCATTTAT
* * *
47811349 TTATAAATATTTTTA-ATAATTT
1 TTAT-AATATTTTTATAAAAATA
47811371 TTATAATATTTTTATAAAAATA
1 TTATAATATTTTTATAAAAATA
*
47811393 TTAT-GTATTTTTAT
1 TTATAATATTTTTAT
47811407 TGAAAAATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 19 0.61
22 12 0.39
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
TTATAATATTTTTATAAAAATA
Done.