Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2839
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: 75960
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:345 original size:175 final size:174
Alignment explanation
Indices: 1--349 Score: 664
Period size: 175 Copynumber: 2.0 Consensus size: 174
*
1 GGACAATTCCAATCGGGTCGGTGTAAAGCTTTTTAAAAAATATTCATACATTTAAAATAACTAAA
1 GGACAATTCCAATCGGGTCGGTGTAAAGCTTTTTAAAAAATATTCATACATTGAAAATAACTAAA
66 ATTATTTATATTATAAATGTTTTTATTTTTATAAATCTAAAATGCATCAAGAATTAAATTATTGT
66 ATTATTTATATTATAAATGTTTTTATTTTTATAAATCTAAAATGCATCAAGAATTAAATTATTGT
131 CTTGAATGAATTTGGAGTTGTACTGAATTAAATAATTATTTGTC
131 CTTGAATGAATTTGGAGTTGTACTGAATTAAATAATTATTTGTC
175 GGACAATTCCAATCGGGTCGGTGTAAAGCTTTTTAAAAAATATTCATACATTGAAAATAACTAAA
1 GGACAATTCCAATCGGGTCGGTGTAAAGCTTTTTAAAAAATATTCATACATTGAAAATAACTAAA
240 ATTATTTATA-TATTAAATGTTTTTTATTTTTATAAATCTAAAATGCATCAAGAATTAAATTATT
66 ATTATTTATATTA-TAAATG-TTTTTATTTTTATAAATCTAAAATGCATCAAGAATTAAATTATT
304 GTCTTGAATGAATTTGGAGTTGTACTGAATTAAATAATTATTTGTC
129 GTCTTGAATGAATTTGGAGTTGTACTGAATTAAATAATTATTTGTC
350 TTAACCGCTA
Statistics
Matches: 172, Mismatches: 1, Indels: 3
0.98 0.01 0.02
Matches are distributed among these distances:
173 2 0.01
174 80 0.47
175 90 0.52
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (174 bp):
GGACAATTCCAATCGGGTCGGTGTAAAGCTTTTTAAAAAATATTCATACATTGAAAATAACTAAA
ATTATTTATATTATAAATGTTTTTATTTTTATAAATCTAAAATGCATCAAGAATTAAATTATTGT
CTTGAATGAATTTGGAGTTGTACTGAATTAAATAATTATTTGTC
Found at i:20017 original size:19 final size:19
Alignment explanation
Indices: 19993--20032 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
19983 GAAAACGAAA
*
19993 GTTAGCTTATTTAGGTCAT
1 GTTAGCGTATTTAGGTCAT
20012 GTTAGCGTATTTAGGTCAT
1 GTTAGCGTATTTAGGTCAT
20031 GT
1 GT
20033 CTTGGTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.45
Consensus pattern (19 bp):
GTTAGCGTATTTAGGTCAT
Found at i:23879 original size:24 final size:26
Alignment explanation
Indices: 23852--23907 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 26
23842 AACTTAATCT
*
23852 ATTTATTTGTAAA-TAATAA-TAATA-
1 ATTTATTT-TAAATTAAAAAGTAATAC
23876 ATTTATTTTAAATTAAAAAGTAATAC
1 ATTTATTTTAAATTAAAAAGTAATAC
23902 ATTTAT
1 ATTTAT
23908 CTCAATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 13 0.46
25 5 0.18
26 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
ATTTATTTTAAATTAAAAAGTAATAC
Found at i:24014 original size:26 final size:26
Alignment explanation
Indices: 23928--24014 Score: 77
Period size: 26 Copynumber: 3.2 Consensus size: 26
23918 ATATGATTAA
23928 ATTTAAAATAAAATTTAAAATTTTAATACAT
1 ATTTAAAAT-AAATTTAAAA--TTAA-AC-T
* * *
23959 ATTTAAATTAAATTT-AAATTGATAGT
1 ATTTAAAATAAATTTAAAATT-AAACT
*
23985 ATTTAAAATAAATTTAAAATTAAACC
1 ATTTAAAATAAATTTAAAATTAAACT
24011 ATTT
1 ATTT
24015 TTCATGATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
26 21 0.45
27 8 0.17
28 1 0.02
29 3 0.06
30 6 0.13
31 8 0.17
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTTAAAATAAATTTAAAATTAAACT
Found at i:31848 original size:16 final size:16
Alignment explanation
Indices: 31812--31855 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
31802 GACTTTTATT
*
31812 AATAATATAAAGAAAC
1 AATAATAAAAAGAAAC
* *
31828 CATAATAAAAAGAATC
1 AATAATAAAAAGAAAC
31844 AATAACTAAAAA
1 AATAA-TAAAAA
31856 AGTCATAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.68, C:0.09, G:0.05, T:0.18
Consensus pattern (16 bp):
AATAATAAAAAGAAAC
Found at i:32576 original size:29 final size:29
Alignment explanation
Indices: 32535--32591 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
32525 TAAATGTCTA
32535 TTTTCGTAATTAATT-TATTTTTCATATTT
1 TTTTCGTAATTAATTGT-TTTTTCATATTT
* *
32564 TTTTTGTAGTTAATTGTTTTTTCATATT
1 TTTTCGTAATTAATTGTTTTTTCATATT
32592 ATTTAGGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 24 0.96
30 1 0.04
ACGTcount: A:0.21, C:0.05, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTTCGTAATTAATTGTTTTTTCATATTT
Found at i:34803 original size:13 final size:13
Alignment explanation
Indices: 34770--34807 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
34760 TTATGTGTAA
34770 TTTATATTATTTT
1 TTTATATTATTTT
**
34783 GGTA-ATTATTTT
1 TTTATATTATTTT
34795 TTTATATTATTTT
1 TTTATATTATTTT
34808 ATTTCATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
12 10 0.50
13 10 0.50
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (13 bp):
TTTATATTATTTT
Found at i:37596 original size:183 final size:183
Alignment explanation
Indices: 37279--37832 Score: 925
Period size: 183 Copynumber: 3.0 Consensus size: 183
37269 CTTTAATGGT
* * * * *
37279 ACAAATGCCGGTAATGAGACGGTTCACGATGATGAGATCTTCGAAGGGAAAGACATAGATACTGA
1 ACAAA-GCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGA
*
37344 TGTTATAACAGAAGCAGATGTGGGGTTGAATAAATCTTCTACATTCGATGAAGGTACAAAAGC-T
65 TGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACAAAA-CTT
*
37408 TGGAAGGAGTCTTCTACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
129 TGGAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
37463 ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
1 ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
*
37528 GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACCAAACTTTG
66 GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACAAAACTTTG
37593 GAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
131 GAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
37646 ACAACA-CCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGA
1 ACAA-AGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGA
* * *
37710 TGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACTGAAGCTC
65 TGTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTAC-AAAACTT
* * *
37775 T-GAAGGAGTCTTCAACTGCTGAACTGGTAGAGTTAAATAAGAATTCGACAGTGA
129 TGGAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
37829 ACAA
1 ACAA
37833 TGCTGAAAGT
Statistics
Matches: 353, Mismatches: 14, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
182 1 0.00
183 341 0.97
184 11 0.03
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (183 bp):
ACAAAGCCGGTAATGAGACAGCTCATGATGATGAGATCTTTGAAGGGAGAGACATAGATACTGAT
GTTATAACAGAAGCAGATGTGGGCTTGAATAAATCTTCTACATTCGATGAAGGTACAAAACTTTG
GAAGGAGTCTTCAACTGCTGAACCGGTAGAGTTAAATAAGAATTCAACAGTGG
Found at i:40805 original size:32 final size:32
Alignment explanation
Indices: 40759--40824 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
40749 GGGTCTTTTT
40759 ACGCCCTTTTTTAGTTTACTAAATACAAATTA
1 ACGCCCTTTTTTAGTTTACTAAATACAAATTA
*
40791 ACGCTCTTTTTTAGTTTACTAAATACAAATTA
1 ACGCCCTTTTTTAGTTTACTAAATACAAATTA
40823 AC
1 AC
40825 TAAATTAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (32 bp):
ACGCCCTTTTTTAGTTTACTAAATACAAATTA
Found at i:41043 original size:22 final size:22
Alignment explanation
Indices: 41015--41059 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
41005 TAAGATTATC
41015 TAAATTAAGAAAATATCTTTAA
1 TAAATTAAGAAAATATCTTTAA
41037 TAAATTAAGAAAATATCTTTAA
1 TAAATTAAGAAAATATCTTTAA
41059 T
1 T
41060 TTATCTTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
TAAATTAAGAAAATATCTTTAA
Found at i:41617 original size:10 final size:11
Alignment explanation
Indices: 41585--41619 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
41575 CGGCCAGCCC
41585 ATATTAATTTTT
1 ATATT-ATTTTT
41597 ATATTATTTTT
1 ATATTATTTTT
41608 ATATTATTTTT
1 ATATTATTTTT
41619 A
1 A
41620 AATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATATTATTTTT
Found at i:44235 original size:3 final size:3
Alignment explanation
Indices: 44229--44253 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
44219 ATCCCAAAAA
44229 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
44254 GCTGTCGCCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:45133 original size:118 final size:119
Alignment explanation
Indices: 44895--45127 Score: 288
Period size: 118 Copynumber: 1.9 Consensus size: 119
44885 TAAATCGAAT
* *
44895 AAAAAACAAAGCCCAGTACAGTAGGGCACGTTTCTTAAAATGATTAAGTATAGAAAATTGCCCTT
1 AAAAAACAAAGCCCAATACAGTAGGGCACGTTTCTTAAAACGATTAAGTATAGAAAATTGCCCTT
* * * * * * * *
44960 ATTAAAAACTATTTGGGAATAAAATGTTGAATAAAATACTTAAATCGAATATAA
66 ATTAAAAACAAGTTGAGAATAAAATATGGAATAAAAGAATTAAAACGAATATAA
* * * * *
45014 AAAAAATAAA-CCCAATACGGTAGGGCACGTTTTTTAAAACGATTAAGTATAGAAAATTGTCTTT
1 AAAAAACAAAGCCCAATACAGTAGGGCACGTTTCTTAAAACGATTAAGTATAGAAAATTGCCCTT
* *
45078 ATGTTAAAAACAAGTTGAGAATACATTATGGAATAAAAGAATTAAAACGA
66 A--TTAAAAACAAGTTGAGAATAAAATATGGAATAAAAGAATTAAAACGA
45128 TTAAAATTTG
Statistics
Matches: 95, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
118 49 0.52
119 9 0.09
120 37 0.39
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (119 bp):
AAAAAACAAAGCCCAATACAGTAGGGCACGTTTCTTAAAACGATTAAGTATAGAAAATTGCCCTT
ATTAAAAACAAGTTGAGAATAAAATATGGAATAAAAGAATTAAAACGAATATAA
Found at i:45543 original size:21 final size:22
Alignment explanation
Indices: 45513--45557 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
45503 TAATAAAAAT
*
45513 ATAATGAATAT-ATAATATTAA
1 ATAATGAATATAATAATATGAA
*
45534 ATAATTAATATAATAATATGAA
1 ATAATGAATATAATAATATGAA
45556 AT
1 AT
45558 CAAAACTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATGAATATAATAATATGAA
Found at i:47253 original size:44 final size:44
Alignment explanation
Indices: 47205--47352 Score: 118
Period size: 44 Copynumber: 3.3 Consensus size: 44
47195 ATTTCAGAGG
* *
47205 GATAAGGTTTGTTGTCTTCGATCTGCTCCACTACTGCTTAAGAA
1 GATAAGATTTGTTGTCTTCGATCTGCTCCACTACTGCTTAGGAA
* ** ** * *
47249 GATAAGATCTGTAATCTTCGGCCTGTTACC-CTACTGCTTAGGGA
1 GATAAGATTTGTTGTCTTCGATCTGCT-CCACTACTGCTTAGGAA
* * * * *
47293 GTTAAAGCCTGTTCATTGTCTTCGATCTGCTCCATTACAGCTTAGGAA
1 GAT-AAG-AT-TT-GTTGTCTTCGATCTGCTCCACTACTGCTTAGGAA
47341 GATAAGATTTGT
1 GATAAGATTTGT
47353 AATTTTTTAG
Statistics
Matches: 74, Mismatches: 24, Indels: 12
0.67 0.22 0.11
Matches are distributed among these distances:
44 35 0.47
45 7 0.09
46 2 0.03
47 6 0.08
48 24 0.32
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (44 bp):
GATAAGATTTGTTGTCTTCGATCTGCTCCACTACTGCTTAGGAA
Found at i:47326 original size:92 final size:93
Alignment explanation
Indices: 47216--47393 Score: 252
Period size: 92 Copynumber: 1.9 Consensus size: 93
47206 ATAAGGTTTG
* * *
47216 TTGTCTTCGATCTGCTCCACTACTGCTTAAGAAGATAAGATCTGTAA-TCTTCGGCCTGTTACCC
1 TTGTCTTCGATCTGCTCCACTACAGCTTAAGAAGATAAGATCTGTAATTCTTCAGCCTATTACCC
47280 TACTGCTTA-GGGAGTTAAAGCCTGTTCA
66 TACTGCTTAGGGGA-TTAAAGCCTGTTCA
* * * * *
47308 TTGTCTTCGATCTGCTCCATTACAGCTTAGGAAGATAAGATTTGTAATTTTTTAGCCTATTACCC
1 TTGTCTTCGATCTGCTCCACTACAGCTTAAGAAGATAAGATCTGTAATTCTTCAGCCTATTACCC
*
47373 TAGTGCTTAGGGGATTAAAGC
66 TACTGCTTAGGGGATTAAAGC
47394 TAGTGGCTTG
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
92 43 0.57
93 28 0.37
94 4 0.05
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (93 bp):
TTGTCTTCGATCTGCTCCACTACAGCTTAAGAAGATAAGATCTGTAATTCTTCAGCCTATTACCC
TACTGCTTAGGGGATTAAAGCCTGTTCA
Found at i:55705 original size:19 final size:20
Alignment explanation
Indices: 55663--55709 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
55653 TACGAAATTT
* *
55663 AATGCATATGATATGATATA
1 AATGCAAATGATATGAGATA
*
55683 AATGCAAATG-TATGAGATG
1 AATGCAAATGATATGAGATA
55702 AATGCAAA
1 AATGCAAA
55710 AAAGAAGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (20 bp):
AATGCAAATGATATGAGATA
Found at i:57670 original size:15 final size:15
Alignment explanation
Indices: 57650--57707 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
57640 CGATGAATTT
57650 ATTGAATTTATATTG
1 ATTGAATTTATATTG
* *
57665 ATTGAAATTATTTTG
1 ATTGAATTTATATTG
57680 ATTGAATTTATATTG
1 ATTGAATTTATATTG
57695 ATTGAATTGTATA
1 ATTGAATT-TATA
57708 ATATATATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:58116 original size:23 final size:22
Alignment explanation
Indices: 58090--58164 Score: 91
Period size: 21 Copynumber: 3.5 Consensus size: 22
58080 AGGCACTTTA
58090 TGTGTCGTATTTGAGGCACCTCG
1 TGTGTCGTATTT-AGGCACCTCG
*
58113 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTTAGGCACCTCG
* **
58134 TGTGTCGT-TTTAGGCACTTTA
1 TGTGTCGTATTTAGGCACCTCG
58155 TGTGTCGTAT
1 TGTGTCGTAT
58165 ACTGATCAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
21 34 0.76
22 2 0.04
23 9 0.20
ACGTcount: A:0.13, C:0.20, G:0.28, T:0.39
Consensus pattern (22 bp):
TGTGTCGTATTTAGGCACCTCG
Found at i:62700 original size:120 final size:121
Alignment explanation
Indices: 62460--62694 Score: 303
Period size: 120 Copynumber: 1.9 Consensus size: 121
62450 TAAATCGAAT
* * *
62460 AAAAAACGAAGCCCAGTACGGTAGGGCACGTTTTTTAAAATGATTAAGTATAGAAAATTGCCCTT
1 AAAAAACGAAGCCCAATACGGTAGGGCACGTTTTTAAAAACGATTAAGTATAGAAAATTGCCCTT
* * * * * *
62525 ATTAAAAACTATTTGGGAATAAAATGTTGAATAAAAAACTTAAATCGAATATAAAA
66 ATTAAAAACAAATTGAGAATAAAATATGGAATAAAAAACTTAAAACGAATATAAAA
* * *
62581 AAAAAATGAA-CCCAATACGGTAGGGCACGTTTTTAAAAACGATTAAGTATAGAAAATTGTCTTT
1 AAAAAACGAAGCCCAATACGGTAGGGCACGTTTTTAAAAACGATTAAGTATAGAAAATTGCCCTT
* *
62645 ATGTTAAAAACAAATTGAGAATACATTATGGAATAAAAGAA-TTAAAACGA
66 A--TTAAAAACAAATTGAGAATAAAATATGGAATAAAA-AACTTAAAACGA
62695 TTAAAATTTG
Statistics
Matches: 97, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
120 50 0.52
121 9 0.09
122 36 0.37
123 2 0.02
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.27
Consensus pattern (121 bp):
AAAAAACGAAGCCCAATACGGTAGGGCACGTTTTTAAAAACGATTAAGTATAGAAAATTGCCCTT
ATTAAAAACAAATTGAGAATAAAATATGGAATAAAAAACTTAAAACGAATATAAAA
Found at i:62829 original size:20 final size:21
Alignment explanation
Indices: 62798--62852 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
62788 GAAAATTAGC
*
62798 AATAGCAATAATAATGGTAAA
1 AATAGCAATAATAATGATAAA
*
62819 AATA-TAATAAT-ATGATAAA
1 AATAGCAATAATAATGATAAA
*
62838 TATAGCAATAATAAT
1 AATAGCAATAATAAT
62853 ATTAATAGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 10 0.36
20 12 0.43
21 6 0.21
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (21 bp):
AATAGCAATAATAATGATAAA
Found at i:62962 original size:22 final size:22
Alignment explanation
Indices: 62927--62968 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
62917 GATAAAAGTG
62927 AAAATTAAAATAATAACTATACT
1 AAAATTAAAATAATAA-TATACT
*
62950 AAAA-TAACATAATAATATA
1 AAAATTAAAATAATAATATA
62969 GTATGTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAATTAAAATAATAATATACT
Found at i:63339 original size:18 final size:17
Alignment explanation
Indices: 63316--63358 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
63306 AATAACAAAT
*
63316 AATAATAATAATAATGTG
1 AATAATAATAAT-AGGTG
63334 AATAAT-ATAATAGGTG
1 AATAATAATAATAGGTG
63350 AAT-ATAATA
1 AATAATAATA
63359 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 2 0.09
16 10 0.43
17 5 0.22
18 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.33
Consensus pattern (17 bp):
AATAATAATAATAGGTG
Found at i:73681 original size:87 final size:88
Alignment explanation
Indices: 73539--73746 Score: 316
Period size: 87 Copynumber: 2.4 Consensus size: 88
73529 CGTTTATTGG
* * *
73539 AAAAACGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAACGTCAA
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAACGTCAA
73603 CGCTTTTAGCGGCGTTTGTG-GT
66 CGCTTTTAGCGGCGTTTGTGTGT
* * * *
73625 AAAAGCGCCGCTAAACGTCAACGCTTTTTATCGGCGTTTGTGGTAAAAGCGACGCTAAAGGTCAA
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAACGTCAA
*
73690 GGCTTTTAGCGGCGTTTGTGTGT
66 CGCTTTTAGCGGCGTTTGTGTGT
73713 -AAAGCGCCGCTAAACGTCAAGGC-TTTTAGCGGCG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCG
73747 CTTTTTTTAC
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 31 0.28
87 77 0.70
88 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (88 bp):
AAAAGCGCCGCTAAACGTCAAGGCTTTTTAGCGGCGTTTGTGGGAAAAGCGACGCTAAACGTCAA
CGCTTTTAGCGGCGTTTGTGTGT
Found at i:73769 original size:43 final size:43
Alignment explanation
Indices: 73539--73746 Score: 319
Period size: 43 Copynumber: 4.8 Consensus size: 43
73529 CGTTTATTGG
* * *
73539 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
*
73582 AAAAGCGCCGCTAAACGTCAACGCTTTTAGCGGCGTTTGTGGT
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
* *
73625 AAAAGCGCCGCTAAACGTCAACGCTTTTTATCGGCGTTTGTGGT
1 AAAAGCGCCGCTAAACGTCAAGGC-TTTTAGCGGCGTTTGTGGT
* *
73669 AAAAGCGACGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGTGTGT
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTG-GT
73713 -AAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCG
1 AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCG
73747 CTTTTTTTAC
Statistics
Matches: 152, Mismatches: 11, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
43 111 0.73
44 41 0.27
ACGTcount: A:0.25, C:0.21, G:0.29, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAACGTCAAGGCTTTTAGCGGCGTTTGTGGT
Done.