Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 14 of 14
Found at i:4256727 original size:29 final size:28
Alignment explanation
Indices: 4256688--4256801 Score: 117
Period size: 28 Copynumber: 3.9 Consensus size: 28
4256678 ATTTCTATAT
4256688 ATTTTATAATTTTTA-ACGATTTTTATAAA
1 ATTTTA-AATTTTTATA-GATTTTTATAAA
*
4256717 ATTTTACAATTTTTATAAATTTTTAT-AA
1 ATTTTA-AATTTTTATAGATTTTTATAAA
*
4256745 ATTTTAATATTTTTATAGTTTTTTATTAAA
1 ATTTTAA-ATTTTTATAGATTTTTA-TAAA
4256775 ATTTAATAAATTTTTTATA-ATTTTTAT
1 ATTT--TAAA-TTTTTATAGATTTTTAT
4256802 TGATTTTTAA
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
27 1 0.01
28 23 0.32
29 23 0.32
30 8 0.11
31 7 0.10
32 11 0.15
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATTTTAAATTTTTATAGATTTTTATAAA
Found at i:4256798 original size:41 final size:38
Alignment explanation
Indices: 4256725--4256810 Score: 100
Period size: 41 Copynumber: 2.2 Consensus size: 38
4256715 AAATTTTACA
* *
4256725 ATTTTTATAAATTTTTATAAATTTTAATATTTTTATAG
1 ATTTTTATAAAATTTAATAAATTTTAATATTTTTATAG
* * *
4256763 TTTTTTATTAAAATTTAATAAATTTTTTATAATTTTTATTG
1 ATTTTTA-TAAAATTTAATAAA-TTTTAAT-ATTTTTATAG
4256804 ATTTTTA
1 ATTTTTA
4256811 ATATTTATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 6 0.15
39 12 0.31
40 6 0.15
41 15 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (38 bp):
ATTTTTATAAAATTTAATAAATTTTAATATTTTTATAG
Found at i:4256799 original size:10 final size:10
Alignment explanation
Indices: 4256663--4256801 Score: 89
Period size: 10 Copynumber: 14.5 Consensus size: 10
4256653 TTCTTACGAC
*
4256663 TTTATAAAAT
1 TTTATAAATT
4256673 TTTAT--ATT
1 TTTATAAATT
* *
4256681 TCTATATA-T
1 TTTATAAATT
4256690 TTTAT-AATT
1 TTTATAAATT
*
4256699 TTTA-ACGATT
1 TTTATA-AATT
*
4256709 TTTATAAAAT
1 TTTATAAATT
*
4256719 TTTA-CAATT
1 TTTATAAATT
4256728 TTTATAAATT
1 TTTATAAATT
4256738 TTTATAAA-T
1 TTTATAAATT
*
4256747 TTTA-ATATT
1 TTTATAAATT
**
4256756 TTTATAGTTT
1 TTTATAAATT
*
4256766 TTTATTAAAAT
1 TTTA-TAAATT
*
4256777 TTAATAAATT
1 TTTATAAATT
4256787 TTT-TATAATT
1 TTTATA-AATT
4256797 TTTAT
1 TTTAT
4256802 TGATTTTTAA
Statistics
Matches: 98, Mismatches: 19, Indels: 23
0.70 0.14 0.16
Matches are distributed among these distances:
8 9 0.09
9 29 0.30
10 52 0.53
11 8 0.08
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (10 bp):
TTTATAAATT
Found at i:4256807 original size:20 final size:20
Alignment explanation
Indices: 4256784--4256822 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
4256774 AATTTAATAA
*
4256784 ATTTTTTATAATTT-TTATTG
1 ATTTTTAAT-ATTTATTATTG
4256804 ATTTTTAATATTTATTATT
1 ATTTTTAATATTTATTATT
4256823 TTTTGGTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (20 bp):
ATTTTTAATATTTATTATTG
Found at i:4256810 original size:19 final size:20
Alignment explanation
Indices: 4256663--4256801 Score: 89
Period size: 19 Copynumber: 7.2 Consensus size: 20
4256653 TTCTTACGAC
*
4256663 TTTATAAAATTTTAT--ATT
1 TTTATAAATTTTTATAAATT
* *
4256681 TCTATATA-TTTTAT-AATT
1 TTTATAAATTTTTATAAATT
* *
4256699 TTTA-ACGATTTTTATAAAAT
1 TTTATA-AATTTTTATAAATT
*
4256719 TTTA-CAATTTTTATAAATT
1 TTTATAAATTTTTATAAATT
*
4256738 TTTATAAA-TTTTA-ATATT
1 TTTATAAATTTTTATAAATT
** *
4256756 TTTATAGTTTTTTATTAAAAT
1 TTTATAAATTTTTA-TAAATT
*
4256777 TTAATAAATTTTT-TATAATT
1 TTTATAAATTTTTATA-AATT
4256797 TTTAT
1 TTTAT
4256802 TGATTTTTAA
Statistics
Matches: 93, Mismatches: 19, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
17 7 0.08
18 23 0.25
19 34 0.37
20 16 0.17
21 13 0.14
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (20 bp):
TTTATAAATTTTTATAAATT
Found at i:4256817 original size:17 final size:16
Alignment explanation
Indices: 4256787--4256825 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
4256777 TTAATAAATT
*
4256787 TTTTATAATTTTTATTGA
1 TTTT-TAATATTTATT-A
4256805 TTTTTAATATTTATTA
1 TTTTTAATATTTATTA
4256821 TTTTT
1 TTTTT
4256826 TGGTGACACG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTAATATTTATTA
Found at i:4257669 original size:17 final size:18
Alignment explanation
Indices: 4257637--4257670 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4257627 TTTTTTTTTT
*
4257637 CTTTTACCTTCCCCAAAA
1 CTTTTACCTACCCCAAAA
4257655 CTTTTA-CTACCCCAAA
1 CTTTTACCTACCCCAAA
4257671 CCTCCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.38, G:0.00, T:0.32
Consensus pattern (18 bp):
CTTTTACCTACCCCAAAA
Found at i:4257713 original size:56 final size:56
Alignment explanation
Indices: 4257620--4257747 Score: 163
Period size: 57 Copynumber: 2.3 Consensus size: 56
4257610 CCCCCCCCCC
*
4257620 CCCAAAA-TTTTTTTTTTCTTTTACCTTCCCCAAAACTTTTACTACC-CC-AAACCT
1 CCCAAAACTTTTTTTTTCCTTTTACCTTCCCCAAAACTTTTACTACCTCCTAAA-CT
* * * *
4257674 CCCAAAACTTTGTTTTTCCTTTTGCTTTCCCCCAAAACTTTTACTTCCTCCTAAACT
1 CCCAAAACTTTTTTTTTCCTTTTACCTT-CCCCAAAACTTTTACTACCTCCTAAACT
*
4257731 CTCAAAACTTTTTTTTT
1 CCCAAAACTTTTTTTTT
4257748 TCGAATTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
54 7 0.11
55 16 0.25
56 18 0.29
57 19 0.30
58 3 0.05
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (56 bp):
CCCAAAACTTTTTTTTTCCTTTTACCTTCCCCAAAACTTTTACTACCTCCTAAACT
Found at i:4258121 original size:19 final size:19
Alignment explanation
Indices: 4258097--4258134 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
4258087 AAGTTAATAA
*
4258097 CAAATTTGATGACGGTGGG
1 CAAATTTCATGACGGTGGG
4258116 CAAATTTCATGACGGTGGG
1 CAAATTTCATGACGGTGGG
4258135 TGACAATGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.13, G:0.34, T:0.26
Consensus pattern (19 bp):
CAAATTTCATGACGGTGGG
Found at i:4266369 original size:1 final size:1
Alignment explanation
Indices: 4266363--4266425 Score: 99
Period size: 1 Copynumber: 63.0 Consensus size: 1
4266353 AATGAAATGC
** *
4266363 AAAAAAAAAAAAAAAAAAAAAACCACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4266426 CCCAGCAGAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.95, C:0.05, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4278723 original size:19 final size:20
Alignment explanation
Indices: 4278695--4278738 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
4278685 TTTATAGTTT
*
4278695 TAAATAATTTTTGGG-TAAAA
1 TAAATAA-TTTTGGGCCAAAA
4278715 TAAAT-ATTTTGGGCCAAAA
1 TAAATAATTTTGGGCCAAAA
4278734 TAAAT
1 TAAAT
4278739 TTAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 7 0.32
19 10 0.45
20 5 0.23
ACGTcount: A:0.45, C:0.05, G:0.14, T:0.36
Consensus pattern (20 bp):
TAAATAATTTTGGGCCAAAA
Found at i:4281770 original size:9 final size:9
Alignment explanation
Indices: 4281756--4281793 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
4281746 TCTGTCTAAA
4281756 TTAATGAAT
1 TTAATGAAT
*
4281765 TTAATGAAA
1 TTAATGAAT
*
4281774 TT-ATTAAT
1 TTAATGAAT
4281782 TTAATGAAT
1 TTAATGAAT
4281791 TTA
1 TTA
4281794 TTAATTTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (9 bp):
TTAATGAAT
Found at i:4281784 original size:17 final size:17
Alignment explanation
Indices: 4281762--4281800 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
4281752 TAAATTAATG
4281762 AATTTAATGAAATTATT
1 AATTTAATGAAATTATT
*
4281779 AATTTAATGAATTTATT
1 AATTTAATGAAATTATT
4281796 AATTT
1 AATTT
4281801 GGATTAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
AATTTAATGAAATTATT
Found at i:4282928 original size:20 final size:20
Alignment explanation
Indices: 4282903--4282951 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
4282893 AAGTTTATCT
4282903 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
4282923 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
*
4282943 AAAGTAAAT
1 TAAGTAAAT
4282952 AGAGTGGTAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:4288601 original size:6 final size:6
Alignment explanation
Indices: 4288592--4288674 Score: 64
Period size: 6 Copynumber: 13.5 Consensus size: 6
4288582 TAAGTCTAAG
*
4288592 AAAATA AAAATA AAAATA ACACAACT- -AAA-A AAAATA AACATA AAAATA
1 AAAATA AAAATA AAAATA A-A-AA-TA AAAATA AAAATA AAAATA AAAATA
* * *
4288640 AACATAA AAAATA AAACTA AAAGAAA AAAATA AAA
1 AAAAT-A AAAATA AAAATA AAA-ATA AAAATA AAA
4288675 TCAAGGATCC
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
5 5 0.08
6 43 0.70
7 10 0.16
8 2 0.03
9 1 0.02
ACGTcount: A:0.78, C:0.07, G:0.01, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:4288655 original size:19 final size:18
Alignment explanation
Indices: 4288592--4288674 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 18
4288582 TAAGTCTAAG
4288592 AAAATAAAAATAAAAATAA
1 AAAATAAAAAT-AAAATAA
*
4288611 CACAACT-AAAA-AAAAT-A
1 -A-AAATAAAAATAAAATAA
*
4288628 AACATAAAAATAAACATAA
1 AAAATAAAAATAAA-ATAA
* *
4288647 AAAATAAAACTAAAAGAAA
1 AAAATAAAAATAAAA-TAA
4288666 AAAATAAAA
1 AAAATAAAA
4288675 TCAAGGATCC
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
15 2 0.04
16 5 0.10
17 4 0.08
18 8 0.16
19 24 0.47
20 5 0.10
21 3 0.06
ACGTcount: A:0.78, C:0.07, G:0.01, T:0.13
Consensus pattern (18 bp):
AAAATAAAAATAAAATAA
Found at i:4288700 original size:3 final size:3
Alignment explanation
Indices: 4288685--4288867 Score: 64
Period size: 3 Copynumber: 62.0 Consensus size: 3
4288675 TCAAGGATCC
* * * * * *
4288685 TAA TAA GAA TAA TAA TAC TAA TAA TAC TAA -AA CTCA TAC TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
* * * * *
4288730 TAA TAA TAA CAG TAA -AA TAAA TAA TAA TTAA CTGA TGA TAA TGAA -AC
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA -TAA -TAA TAA TAA T-AA TAA
* * * * * *
4288777 GAA GAA TAA TAA GAA -AA TTA -AA TAA TAA TAA CAA TAAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
4288821 TAA CTAA -AA -AA TAA -AA TAA T-A TAA -AA -AA TAA TAA TAA TTAA
1 TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
4288862 TAA TAA
1 TAA TAA
4288868 ACAAATAAAT
Statistics
Matches: 136, Mismatches: 28, Indels: 32
0.69 0.14 0.16
Matches are distributed among these distances:
2 20 0.15
3 96 0.71
4 20 0.15
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:4288802 original size:16 final size:16
Alignment explanation
Indices: 4288781--4288895 Score: 53
Period size: 16 Copynumber: 7.3 Consensus size: 16
4288771 TGAAACGAAG
4288781 AATAATAAGAA-AATTA
1 AATAATAAGAACAA-TA
*
4288797 AATAATAATAACAATA
1 AATAATAAGAACAATA
* * *
4288813 AATAATTATAACTAAAA
1 AATAATAAGAAC-AATA
* *
4288830 AATAA-AATAA-TATA
1 AATAATAAGAACAATA
* * * *
4288844 AAAAATAATAATAATT
1 AATAATAAGAACAATA
4288860 AATAAT-A-AACAAATA
1 AATAATAAGAAC-AATA
*
4288875 AATAATTAGATA-AATA
1 AATAATAAGA-ACAATA
4288891 AATAA
1 AATAA
4288896 AAAATAAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
14 8 0.10
15 15 0.19
16 44 0.56
17 11 0.14
18 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.27
Consensus pattern (16 bp):
AATAATAAGAACAATA
Found at i:4288877 original size:4 final size:4
Alignment explanation
Indices: 4288809--4288908 Score: 61
Period size: 4 Copynumber: 25.5 Consensus size: 4
4288799 TAATAATAAC
*
4288809 AATA AATA ATTATA ACTA AA-A AATAA AATA ATATA AA-A AAT- AAT-
1 AATA AATA A--ATA AATA AATA AAT-A AATA A-ATA AATA AATA AATA
* * * *
4288853 AAT- AATT AAT- AATA AACA AATA AATA ATTA GATA AATA AATA AA-A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA
4288898 AATAA AATA AA
1 AAT-A AATA AA
4288909 GAACAAGGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
3 21 0.27
4 41 0.53
5 12 0.15
6 4 0.05
ACGTcount: A:0.71, C:0.02, G:0.01, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:4288894 original size:28 final size:25
Alignment explanation
Indices: 4288784--4288903 Score: 86
Period size: 27 Copynumber: 4.5 Consensus size: 25
4288774 AACGAAGAAT
4288784 AATAAGAAAATTAAATAATAATAACAATA
1 AATAA-AAAA-TAAATAATAAT-A-AATA
* *
4288813 AATAATTATAACTAAAAAAT-A-AAATA
1 AATAA--A-AAATAAATAATAATAAATA
*
4288839 ATATAAAAAAT-AATAATAATTAAT-
1 A-ATAAAAAATAAATAATAATAAATA
4288863 AATAAACAAATAAATAATTAGATAAATA
1 AATAAA-AAATAAATAA-TA-ATAAATA
4288891 AATAAAAAATAAA
1 AATAAAAAATAAA
4288904 ATAAAGAACA
Statistics
Matches: 74, Mismatches: 7, Indels: 22
0.72 0.07 0.21
Matches are distributed among these distances:
23 10 0.14
24 9 0.12
25 9 0.12
26 7 0.09
27 17 0.23
28 6 0.08
29 6 0.08
30 8 0.11
31 2 0.03
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (25 bp):
AATAAAAAATAAATAATAATAAATA
Found at i:4288905 original size:16 final size:16
Alignment explanation
Indices: 4288820--4288908 Score: 74
Period size: 16 Copynumber: 5.3 Consensus size: 16
4288810 ATAAATAATT
*
4288820 ATAACTAAAAAATAAA
1 ATAAATAAAAAATAAA
4288836 ATAATATAAAAAATAATA
1 ATAA-ATAAAAAATAA-A
*
4288854 ATAATTAATAATAA-ACAA
1 ATAAATAA-AA-AATA-AA
* *
4288872 ATAAATAATTAGAT-AA
1 ATAAATAA-AAAATAAA
4288888 ATAAATAAAAAATAAA
1 ATAAATAAAAAATAAA
4288904 ATAAA
1 ATAAA
4288909 GAACAAGGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
15 3 0.05
16 21 0.36
17 14 0.24
18 18 0.31
19 3 0.05
ACGTcount: A:0.72, C:0.02, G:0.01, T:0.25
Consensus pattern (16 bp):
ATAAATAAAAAATAAA
Found at i:4288905 original size:28 final size:27
Alignment explanation
Indices: 4288834--4288907 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 27
4288824 CTAAAAAATA
4288834 AAATAATATAAAAAATAATAATAATTAAT
1 AAATAA-ATAAAAAATAA-AATAATTAAT
*
4288863 -AAT--A-AACAAAT-AAATAATTAGAT
1 AAATAAATAAAAAATAAAATAATTA-AT
4288886 AAATAAATAAAAAATAAAATAA
1 AAATAAATAAAAAATAAAATAA
4288908 AGAACAAGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
22 8 0.22
23 3 0.08
24 9 0.24
25 1 0.03
26 1 0.03
27 6 0.16
28 9 0.24
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.26
Consensus pattern (27 bp):
AAATAAATAAAAAATAAAATAATTAAT
Found at i:4309326 original size:46 final size:46
Alignment explanation
Indices: 4309270--4309361 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
4309260 AAACGCCACT
4309270 AAGGATAACGTCGCTAACTTTTGTGGAGCTTACAGAAAAAAACGCC
1 AAGGATAACGTCGCTAACTTTTGTGGAGCTTACAGAAAAAAACGCC
4309316 AAGGATAACGTCGCTAACTTTTGTGGAGCTTACAGAAAAAAACGCC
1 AAGGATAACGTCGCTAACTTTTGTGGAGCTTACAGAAAAAAACGCC
4309362 TTCTTTAGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (46 bp):
AAGGATAACGTCGCTAACTTTTGTGGAGCTTACAGAAAAAAACGCC
Found at i:4309429 original size:43 final size:42
Alignment explanation
Indices: 4309362--4309629 Score: 213
Period size: 43 Copynumber: 6.2 Consensus size: 42
4309352 AAAAAACGCC
* * * * *
4309362 TTCTTTAGCAGCGCTTAGGGAAAAAACGCCGCT-AATGATCATG
1 TTCTTTAGCGGCGCTT-TGGAAAAAACGCCACTAAAAG-TAATG
*
4309405 TTCTTTAGCGGCGCTTTGGAAAAAACGCCACT-AAAGAACATG
1 TTCTTTAGCGGCGCTTTGGAAAAAACGCCACTAAAAGTA-ATG
* *
4309447 ATCTTTAGCGGCG-TTTAGGAAAAAAACGCCGCTAAAAGTAAATG
1 TTCTTTAGCGGCGCTTT-GG-AAAAAACGCCACTAAAAGT-AATG
*
4309491 TTCTATAGCGGCGC-TTGGTAAAAAACGCCACTAAAAGTAATG
1 TTCTTTAGCGGCGCTTTGG-AAAAAACGCCACTAAAAGTAATG
** * ** * *
4309533 TTCTTTAGCGGCGCTTCAT-CTACAAACGCTGCTAAATGTAGTG
1 TTCTTTAGCGGCGCTT--TGGAAAAAACGCCACTAAAAGTAATG
** * * *
4309576 TTCTTTAGCGGCGCTTATTTCATAAAACGCCGCTAAAAGTAGTG
1 TTCTTTAGCGGCGC-T-TTGGAAAAAACGCCACTAAAAGTAATG
4309620 TTCTTTAGCG
1 TTCTTTAGCG
4309630 TTAGCAGCGC
Statistics
Matches: 187, Mismatches: 26, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
41 3 0.02
42 51 0.27
43 80 0.43
44 50 0.27
45 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
TTCTTTAGCGGCGCTTTGGAAAAAACGCCACTAAAAGTAATG
Found at i:4309452 original size:42 final size:43
Alignment explanation
Indices: 4309362--4309548 Score: 204
Period size: 42 Copynumber: 4.4 Consensus size: 43
4309352 AAAAAACGCC
* * * * * *
4309362 TTCTTTAGCAGCGCTTAGGGAAAAAACGCCGCT-AATGATCATG
1 TTCTTTAGCGGCGCTTTGGAAAAAAACGCCACTAAAAGA-AATG
4309405 TTCTTTAGCGGCGCTTTGG-AAAAAACGCCACT-AAAGAACATG
1 TTCTTTAGCGGCGCTTTGGAAAAAAACGCCACTAAAAGAA-ATG
* *
4309447 ATCTTTAGCGGCG-TTTAGGAAAAAAACGCCGCTAAAAGTAAATG
1 TTCTTTAGCGGCGCTTT-GGAAAAAAACGCCACTAAAAG-AAATG
* * *
4309491 TTCTATAGCGGCGC-TTGGTAAAAAACGCCACTAAAAGTAATG
1 TTCTTTAGCGGCGCTTTGGAAAAAAACGCCACTAAAAGAAATG
4309533 TTCTTTAGCGGCGCTT
1 TTCTTTAGCGGCGCTT
4309549 CATCTACAAA
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
41 3 0.02
42 50 0.40
43 49 0.40
44 20 0.16
45 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (43 bp):
TTCTTTAGCGGCGCTTTGGAAAAAAACGCCACTAAAAGAAATG
Found at i:4309560 original size:86 final size:85
Alignment explanation
Indices: 4309362--4309629 Score: 249
Period size: 86 Copynumber: 3.1 Consensus size: 85
4309352 AAAAAACGCC
* * * *
4309362 TTCTTTAGCAGCGCTT-AGGGAAAAAACGCCGCT-AATGATCATGTTCTTTAGCGGCGCTTTGG-
1 TTCTTTAGCGGCG-TTCAGGAAAAAAACGCCGCTAAAAG-TAATGTTCTTTAGCGGCGC-TTGGT
*
4309424 AAAAAACGCCACT-AAAGAACATG
63 AAAAAACGCCACTAAAAGTA-ATG
* * *
4309447 ATCTTTAGCGGCGTTTAGGAAAAAAACGCCGCTAAAAGTAAATGTTCTATAGCGGCGCTTGGTAA
1 TTCTTTAGCGGCGTTCAGGAAAAAAACGCCGCTAAAAGT-AATGTTCTTTAGCGGCGCTTGGTAA
4309512 AAAACGCCACTAAAAGTAATG
65 AAAACGCCACTAAAAGTAATG
*** * * * * **
4309533 TTCTTTAGCGGCGCTTCA-TCTACAAACGCTGCTAAATGTAGTGTTCTTTAGCGGCGCTTATTTC
1 TTCTTTAGCGGCG-TTCAGGAAAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTT-GGT-
* * *
4309597 ATAAAACGCCGCTAAAAGTAGTG
63 AAAAAACGCCACTAAAAGTAATG
4309620 TTCTTTAGCG
1 TTCTTTAGCG
4309630 TTAGCAGCGC
Statistics
Matches: 153, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
84 2 0.01
85 50 0.33
86 63 0.41
87 38 0.25
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (85 bp):
TTCTTTAGCGGCGTTCAGGAAAAAAACGCCGCTAAAAGTAATGTTCTTTAGCGGCGCTTGGTAAA
AAACGCCACTAAAAGTAATG
Found at i:4310071 original size:21 final size:21
Alignment explanation
Indices: 4310047--4310112 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
4310037 ACTTCTCTTG
4310047 CTGCTTCTCTCGCTGCAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
4310068 CTGCTTCTCTCACTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
4310089 CTGCTTC-CTTCGCTGCCGCCT
1 CTGCTTCTC-TCGCTGCAGCCT
4310110 CTG
1 CTG
4310113 TTTTAAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.03, C:0.44, G:0.20, T:0.33
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Done.