Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 113 of 235
Found at i:38788140 original size:17 final size:18
Alignment explanation
Indices: 38788114--38788152 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
38788104 GTATTATATA
*
38788114 ATAATGATAATAGTTA-T
1 ATAATAATAATAGTTAGT
38788131 ATAATAATAATAGTTAGT
1 ATAATAATAATAGTTAGT
38788149 ATAA
1 ATAA
38788153 AAGAAAGGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (18 bp):
ATAATAATAATAGTTAGT
Found at i:38789282 original size:71 final size:71
Alignment explanation
Indices: 38789161--38789307 Score: 276
Period size: 71 Copynumber: 2.1 Consensus size: 71
38789151 ACAATTGTAG
*
38789161 TTTATAGATTTAATTTGCTTATTAATTAAGCATAAAATATTTATTATCTATTATTATTAAATTAA
1 TTTAAAGATTTAATTTGCTTATTAATTAAGCATAAAATATTTATTATCTATTATTATTAAATTAA
38789226 AAGATA
66 AAGATA
*
38789232 TTTAAAGATTTAATTTGCTTATTAATTAAGCATAAAATATTTATTATCTATTATTGTTAAATTAA
1 TTTAAAGATTTAATTTGCTTATTAATTAAGCATAAAATATTTATTATCTATTATTATTAAATTAA
38789297 AAGATA
66 AAGATA
38789303 TTTAA
1 TTTAA
38789308 TAATTAAATA
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (71 bp):
TTTAAAGATTTAATTTGCTTATTAATTAAGCATAAAATATTTATTATCTATTATTATTAAATTAA
AAGATA
Found at i:38789453 original size:21 final size:21
Alignment explanation
Indices: 38789429--38789469 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
38789419 TTTTTATTTA
* *
38789429 ATTAGTAAATAGATATTTATT
1 ATTAGTAAAAAAATATTTATT
*
38789450 ATTATTAAAAAAATATTTAT
1 ATTAGTAAAAAAATATTTAT
38789470 GAGATAAATA
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:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
ATTAGTAAAAAAATATTTATT
Found at i:38791013 original size:38 final size:39
Alignment explanation
Indices: 38790913--38791022 Score: 100
Period size: 39 Copynumber: 2.8 Consensus size: 39
38790903 ACTCTAAGTT
* * *
38790913 GATGAGACACTGGGTGTCATACTGTTACTTCGGATAGATTC
1 GATGAGACA-TGGGTGTCA-AATATTACTTCGGATAGATCC
** *
38790954 GATGAGGTACA-GGGTACCAAAT-TTACTTCGGCTAGA-CC
1 GATGA-G-ACATGGGTGTCAAATATTACTTCGGATAGATCC
38790992 GATGAGACATTGGGTGTCAAATATTACTTCG
1 GATGAGACA-TGGGTGTCAAATATTACTTCG
38791023 AACTATCCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
36 3 0.05
37 1 0.02
38 15 0.26
39 21 0.37
40 2 0.04
41 11 0.19
42 1 0.02
43 3 0.05
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (39 bp):
GATGAGACATGGGTGTCAAATATTACTTCGGATAGATCC
Found at i:38802694 original size:22 final size:21
Alignment explanation
Indices: 38802665--38802705 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
38802655 AAAAATCTAC
38802665 ATATTAATTAGAATATTTTAA
1 ATATTAATTAGAATATTTTAA
* *
38802686 ATATATAATTTGAATTTTTT
1 ATAT-TAATTAGAATATTTT
38802706 TTTAAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (21 bp):
ATATTAATTAGAATATTTTAA
Found at i:38803067 original size:44 final size:44
Alignment explanation
Indices: 38803003--38803389 Score: 465
Period size: 44 Copynumber: 8.9 Consensus size: 44
38802993 ATAAATAGAG
* * *
38803003 AGGATAGATACATAGAAAAAACTGAAGCAAGATAACTTTTAATC
1 AGGATAGACACATAGCAAAAACTGAAGCAAGATAGCTTTTAATC
* *
38803047 AGGATAGACACA-AGGCAAAAACTGGAGCAAGATAGCTATTAATC
1 AGGATAGACACATA-GCAAAAACTGAAGCAAGATAGCTTTTAATC
* *
38803091 AGGATAGATACATAGCAAAAACTGGAA-CAAGATTGCTTTTAATC
1 AGGATAGACACATAGCAAAAACT-GAAGCAAGATAGCTTTTAATC
* *
38803135 AGGATAGACACA-AGGCAAAAACTGGAGCAAGATAGCTATTAATC
1 AGGATAGACACATA-GCAAAAACTGAAGCAAGATAGCTTTTAATC
* *
38803179 AGGATAGATACATAGCAAAAACTGGAA-CAAGATTGCTTTTAATC
1 AGGATAGACACATAGCAAAAACT-GAAGCAAGATAGCTTTTAATC
*
38803223 AGGATAGACACA-AGGC--AAACTGGAGCAAGATAGCTTTTAATC
1 AGGATAGACACATA-GCAAAAACTGAAGCAAGATAGCTTTTAATC
* *
38803265 AGGATAGATACATAGCAAAAACTGGAA-CAAGATTGCTTTTAATC
1 AGGATAGACACATAGCAAAAACT-GAAGCAAGATAGCTTTTAATC
*
38803309 AGGATAGACACA-AGGC--AAACTGGAGCAAGATAGCTTTTAATC
1 AGGATAGACACATA-GCAAAAACTGAAGCAAGATAGCTTTTAATC
* *
38803351 AGGATAGATACATAGCAAAAACT-AGAGCAAGATTGCTTT
1 AGGATAGACACATAGCAAAAACTGA-AGCAAGATAGCTTT
38803390 AAACCAAAGG
Statistics
Matches: 295, Mismatches: 29, Indels: 38
0.81 0.08 0.10
Matches are distributed among these distances:
41 4 0.01
42 68 0.23
43 8 0.03
44 207 0.70
45 8 0.03
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.21
Consensus pattern (44 bp):
AGGATAGACACATAGCAAAAACTGAAGCAAGATAGCTTTTAATC
Found at i:38803298 original size:86 final size:87
Alignment explanation
Indices: 38803003--38803389 Score: 663
Period size: 86 Copynumber: 4.4 Consensus size: 87
38802993 ATAAATAGAG
* **
38803003 AGGATAGATACATAGAAAAAACT-GAAGCAAGATAACTTTTAATCAGGATAGACACAAGGCAAAA
1 AGGATAGATACATAGCAAAAACTGGAA-CAAGATTGCTTTTAATCAGGATAGACACAAGGC-AAA
38803067 ACTGGAGCAAGATAGCTATTAATC
64 ACTGGAGCAAGATAGCTATTAATC
38803091 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGCAAAAA
1 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGC-AAAA
38803156 CTGGAGCAAGATAGCTATTAATC
65 CTGGAGCAAGATAGCTATTAATC
38803179 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGC-AAAC
1 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGCAAAAC
*
38803243 TGGAGCAAGATAGCTTTTAATC
66 TGGAGCAAGATAGCTATTAATC
38803265 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGC-AAAC
1 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGCAAAAC
*
38803329 TGGAGCAAGATAGCTTTTAATC
66 TGGAGCAAGATAGCTATTAATC
* *
38803351 AGGATAGATACATAGCAAAAACTAGAGCAAGATTGCTTT
1 AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTT
38803390 AAACCAAAGG
Statistics
Matches: 292, Mismatches: 6, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
86 148 0.51
88 141 0.48
89 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.20, T:0.21
Consensus pattern (87 bp):
AGGATAGATACATAGCAAAAACTGGAACAAGATTGCTTTTAATCAGGATAGACACAAGGCAAAAC
TGGAGCAAGATAGCTATTAATC
Found at i:38806198 original size:17 final size:17
Alignment explanation
Indices: 38806176--38806209 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
38806166 AAATGTAATA
38806176 CTGCAAAATGAAATTCT
1 CTGCAAAATGAAATTCT
38806193 CTGCAAAATGAAATTCT
1 CTGCAAAATGAAATTCT
38806210 TAGTACTGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (17 bp):
CTGCAAAATGAAATTCT
Found at i:38807506 original size:54 final size:53
Alignment explanation
Indices: 38807442--38807706 Score: 218
Period size: 54 Copynumber: 5.4 Consensus size: 53
38807432 CCTCAAGAAC
*
38807442 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTCCTTGAAGAG
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAG
*
38807495 TTTTGTGGTTTTAAGGGAAATTG------A----T--GGTCCTTTTTTGAAGAG
1 TTTT-TGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAG
* * **
38807537 ATTTTTGGTTTTAAGGGAATTTGATAAAAAGTTTTGAGATTTTTTCTTGAAGAG
1 -TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAG
*
38807591 TTTTGTGGTTTTAAGGGAAATTG------A----T--GGTCCTTTTTTGAAGAG
1 TTTT-TGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAG
* * **
38807633 ATTTTTGGTTTTAAGGGAATTTGATAAAAAGTTTTGAGATTTTTTCTTGAAGAG
1 -TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAG
38807687 TTTTGTGGTTTTAAGGGAAA
1 TTTT-TGGTTTTAAGGGAAA
38807707 CTTATGGTCC
Statistics
Matches: 165, Mismatches: 18, Indels: 57
0.69 0.08 0.24
Matches are distributed among these distances:
42 62 0.38
43 8 0.05
44 2 0.01
48 4 0.02
52 2 0.01
53 12 0.07
54 75 0.45
ACGTcount: A:0.26, C:0.04, G:0.25, T:0.45
Consensus pattern (53 bp):
TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAG
Found at i:38807525 original size:42 final size:42
Alignment explanation
Indices: 38807474--38807561 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
38807464 ATAAAAAGTT
38807474 TTGA-GGTCCTTCCTTGAAGAG-TTTTGTGGTTTTAAGGGAAA
1 TTGATGGTCCTTCCTTGAAGAGATTTT-TGGTTTTAAGGGAAA
** *
38807515 TTGATGGTCCTTTTTTGAAGAGATTTTTGGTTTTAAGGGAAT
1 TTGATGGTCCTTCCTTGAAGAGATTTTTGGTTTTAAGGGAAA
38807557 TTGAT
1 TTGAT
38807562 AAAAAGTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 4 0.10
42 34 0.81
43 4 0.10
ACGTcount: A:0.22, C:0.07, G:0.27, T:0.44
Consensus pattern (42 bp):
TTGATGGTCCTTCCTTGAAGAGATTTTTGGTTTTAAGGGAAA
Found at i:38807586 original size:96 final size:95
Alignment explanation
Indices: 38807260--38807753 Score: 699
Period size: 96 Copynumber: 5.3 Consensus size: 95
38807250 TCAAGAAAGG
*
38807260 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTGTTT-TAGTTT
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGT-TTTGTGGTTT
*
38807324 TAAGGGAAATTGATGGTCC----TCAAGA-A
65 TAAGGGAAATTGATGGTCCTTTTTGAAGAGA
*
38807350 CTTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTGTTT-TAGTT
1 -TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGT-TTTGTGGTT
*
38807414 TTAAGGGAAATTGATGGTCC----TCAAGA-A
64 TTAAGGGAAATTGATGGTCCTTTTTGAAGAGA
*
38807441 CTTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTCCTTGAAGAGTTTTGTGGTTT
1 -TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTT
38807506 TAAGGGAAATTGATGGTCCTTTTTTGAAGAGA
65 TAAGGGAAATTGATGGTCC-TTTTTGAAGAGA
* * **
38807538 TTTTTGGTTTTAAGGGAATTTGATAAAAAGTTTTGAGATTTTTTCTTGAAGAGTTTTGTGGTTTT
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
38807603 AAGGGAAATTGATGGTCCTTTTTTGAAGAGA
66 AAGGGAAATTGATGGTCC-TTTTTGAAGAGA
* * **
38807634 TTTTTGGTTTTAAGGGAATTTGATAAAAAGTTTTGAGATTTTTTCTTGAAGAGTTTTGTGGTTTT
1 TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
*
38807699 AAGGGAAACTT-ATGGTCCTTTCTTGAAGAGC
66 AAGGGAAA-TTGATGGTCCTTT-TTGAAGAGA
38807730 TTTTTGGTTTTAAGGGAAATTGAT
1 TTTTTGGTTTTAAGGGAAATTGAT
38807754 GGTGCTTTCT
Statistics
Matches: 384, Mismatches: 10, Indels: 13
0.94 0.02 0.03
Matches are distributed among these distances:
90 3 0.01
91 168 0.44
95 3 0.01
96 207 0.54
97 3 0.01
ACGTcount: A:0.27, C:0.06, G:0.25, T:0.43
Consensus pattern (95 bp):
TTTTTGGTTTTAAGGGAAATTGATAAAAAGTTTTGAGGTCCTTTCTTGAAGAGTTTTGTGGTTTT
AAGGGAAATTGATGGTCCTTTTTGAAGAGA
Found at i:38807722 original size:42 final size:42
Alignment explanation
Indices: 38807675--38807772 Score: 155
Period size: 42 Copynumber: 2.3 Consensus size: 42
38807665 TTTGAGATTT
38807675 TTTCTTGAAGAG-TTTTGTGGTTTTAAGGGAAACTT-ATGGTCC
1 TTTCTTGAAGAGCTTTT-TGGTTTTAAGGGAAA-TTGATGGTCC
*
38807717 TTTCTTGAAGAGCTTTTTGGTTTTAAGGGAAATTGATGGTGC
1 TTTCTTGAAGAGCTTTTTGGTTTTAAGGGAAATTGATGGTCC
38807759 TTTCTTGAAGAGCT
1 TTTCTTGAAGAGCT
38807773 CTTCTGTTTT
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
41 2 0.04
42 47 0.89
43 4 0.08
ACGTcount: A:0.21, C:0.09, G:0.27, T:0.43
Consensus pattern (42 bp):
TTTCTTGAAGAGCTTTTTGGTTTTAAGGGAAATTGATGGTCC
Found at i:38809260 original size:24 final size:24
Alignment explanation
Indices: 38809232--38809326 Score: 138
Period size: 24 Copynumber: 4.0 Consensus size: 24
38809222 TCTTTCTAGA
* *
38809232 ATATTTAGTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
38809256 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
38809280 ATATTTAACATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
38809304 ATATTT-GACATTTATTAGTATAA
1 ATATTTAG-CATTTATTAGCATAA
38809327 AATCTTTGTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.48
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:38818931 original size:25 final size:26
Alignment explanation
Indices: 38818889--38818946 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
38818879 TTTCTTTTCA
** * *
38818889 TTTTTTAGATTAGGTTTTCCTTTT-T
1 TTTTTTAGAAAAGATTTTACTTTTGT
38818914 TTTTTTAGAAAAGATTTTACTTTTGT
1 TTTTTTAGAAAAGATTTTACTTTTGT
*
38818940 TGTTTTA
1 TTTTTTA
38818947 TTTCTTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.19, C:0.05, G:0.12, T:0.64
Consensus pattern (26 bp):
TTTTTTAGAAAAGATTTTACTTTTGT
Found at i:38824529 original size:75 final size:74
Alignment explanation
Indices: 38824406--38824552 Score: 276
Period size: 75 Copynumber: 2.0 Consensus size: 74
38824396 GAATCAAAGT
38824406 AAACATTTTAATAATCAGCAGATATAATGTTCTGATTATGTTGAATTAATGTTGGATTTTCTGAC
1 AAACATTTTAATAATCAGCAGATATAATGTTCTGATTATGTTGAATTAATGTTGGATTTTCTGAC
*
38824471 ATTCCCCNTG
66 A-TCCCCCTG
38824481 AAACATTTTAATAATCAGCAGATATAATGTTCTGATTATGTTGAATTAATGTTGGATTTTCTGAC
1 AAACATTTTAATAATCAGCAGATATAATGTTCTGATTATGTTGAATTAATGTTGGATTTTCTGAC
38824546 ATCCCCC
66 ATCCCCC
38824553 CCCTTTGTAC
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
74 5 0.07
75 66 0.93
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.39
Consensus pattern (74 bp):
AAACATTTTAATAATCAGCAGATATAATGTTCTGATTATGTTGAATTAATGTTGGATTTTCTGAC
ATCCCCCTG
Found at i:38825874 original size:16 final size:16
Alignment explanation
Indices: 38825853--38825920 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
38825843 TTTGGTTCGC
38825853 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38825869 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
38825885 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
38825901 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
38825917 TGTA
1 TGTA
38825921 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:38826176 original size:16 final size:16
Alignment explanation
Indices: 38826136--38826190 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
38826126 TTAATCATAT
*
38826136 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
38826152 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
38826167 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
38826185 -TAAAAT
1 TTAAAAT
38826191 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:38826183 original size:18 final size:17
Alignment explanation
Indices: 38826156--38826190 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38826146 TTTTTATTAA
*
38826156 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38826174 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38826191 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38826303 original size:18 final size:17
Alignment explanation
Indices: 38826276--38826310 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38826266 TTACTATTAA
*
38826276 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
38826294 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
38826311 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:38826356 original size:61 final size:60
Alignment explanation
Indices: 38826171--38826361 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
38826161 TTTTAATTAA
* *
38826171 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
38826232 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
38826290 A
60 T
*
38826291 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
38826352 AATATATAAT
1 AATATATAAT
38826362 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:38826439 original size:120 final size:120
Alignment explanation
Indices: 38826134--38826417 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
38826124 ATTTAATCAT
*
38826134 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
38826199 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
38826255 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
38826320 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
38826375 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
38826418 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:38828363 original size:19 final size:19
Alignment explanation
Indices: 38828339--38828375 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
38828329 ATAAAATATT
38828339 ATCGTTCAGGTACATATAC
1 ATCGTTCAGGTACATATAC
*
38828358 ATCGTTCAGGTGCATATA
1 ATCGTTCAGGTACATATA
38828376 GAGGTCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
ATCGTTCAGGTACATATAC
Found at i:38853372 original size:71 final size:71
Alignment explanation
Indices: 38853256--38853402 Score: 242
Period size: 71 Copynumber: 2.1 Consensus size: 71
38853246 CGAAGACCTA
* * *
38853256 GGTGTGGTAGATGGATGTGTTTTCATGTGTATATGTATTTTCTACCTAC-GAGCTTTGTACTCAT
1 GGTGTCGTAGATGGATGTGTTTGCATGTGTATATGTATTTTCTACCTACAG-GCTTTGCACTCAT
38853320 GTGCTTT
65 GTGCTTT
*
38853327 GGTGTCGTGGATGGATGTGTTTGCATGTGTATATGTATTTTCTACCTACAGGCTTTGCACTCATG
1 GGTGTCGTAGATGGATGTGTTTGCATGTGTATATGTATTTTCTACCTACAGGCTTTGCACTCATG
38853392 TGCTTT
66 TGCTTT
38853398 GGTGT
1 GGTGT
38853403 GGTGTAGTTA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 70 0.99
72 1 0.01
ACGTcount: A:0.16, C:0.14, G:0.27, T:0.44
Consensus pattern (71 bp):
GGTGTCGTAGATGGATGTGTTTGCATGTGTATATGTATTTTCTACCTACAGGCTTTGCACTCATG
TGCTTT
Found at i:38854533 original size:23 final size:22
Alignment explanation
Indices: 38854503--38854546 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
38854493 TCTCAATTCA
*
38854503 TAAATAAATTCATACCAAAACT
1 TAAATAAAATCATACCAAAACT
*
38854525 TAAACTAAAATCATACCTAAAC
1 TAAA-TAAAATCATACCAAAAC
38854547 ATACGATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.55, C:0.20, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAATAAAATCATACCAAAACT
Found at i:38861073 original size:23 final size:22
Alignment explanation
Indices: 38861047--38861102 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
38861037 TCACAATTGG
38861047 GCATTCAAACTCATACCAAATAT
1 GCATTCAAACTCATACCAAA-AT
* * *
38861070 GCATCCAAAGT-ATACCTAAAT
1 GCATTCAAACTCATACCAAAAT
38861091 G-A-TCAAACTCAT
1 GCATTCAAACTCAT
38861103 TTAATAGACT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
19 5 0.19
20 3 0.11
21 3 0.11
22 7 0.26
23 9 0.33
ACGTcount: A:0.43, C:0.25, G:0.07, T:0.25
Consensus pattern (22 bp):
GCATTCAAACTCATACCAAAAT
Found at i:38864248 original size:13 final size:13
Alignment explanation
Indices: 38864232--38864273 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
38864222 AGGTTTGCAT
*
38864232 ATAGTGTTCACAC
1 ATAGGGTTCACAC
*
38864245 ATAGGGTCCAC-C
1 ATAGGGTTCACAC
38864257 TATAGGGTTCACAC
1 -ATAGGGTTCACAC
38864271 ATA
1 ATA
38864274 CAGGGTTCCA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (13 bp):
ATAGGGTTCACAC
Found at i:38864513 original size:45 final size:45
Alignment explanation
Indices: 38864433--38864547 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 45
38864423 TAAAGTCTGA
* * *
38864433 CACTGGACTGTGGATACACAACAAAAATTCGCAGATGAAACCTGC
1 CACTGGACTGTGGGTACACAACAAAAATTCACAGATAAAACCTGC
* **
38864478 CACTGGATTGTGGGTACACAAC-AAAATATCACAGATAAAATTTGC
1 CACTGGACTGTGGGTACACAACAAAAAT-TCACAGATAAAACCTGC
* * *
38864523 CACTAGACTGTAGGTACACTACAAA
1 CACTGGACTGTGGGTACACAACAAA
38864548 CTATTGCAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 5 0.09
45 51 0.88
46 2 0.03
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (45 bp):
CACTGGACTGTGGGTACACAACAAAAATTCACAGATAAAACCTGC
Found at i:38864561 original size:45 final size:45
Alignment explanation
Indices: 38864475--38864563 Score: 106
Period size: 45 Copynumber: 2.0 Consensus size: 45
38864465 AGATGAAACC
* * * *
38864475 TGCCACTGGATTGTGGGTACACAACAAAATATCACAGATAAAATT
1 TGCCACTAGACTGTAGGTACACAACAAAATATCACAAATAAAATT
* * **
38864520 TGCCACTAGACTGTAGGTACACTACAAACTATTGCAAATAAAAT
1 TGCCACTAGACTGTAGGTACACAACAAAATATCACAAATAAAAT
38864564 CTGTCACTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (45 bp):
TGCCACTAGACTGTAGGTACACAACAAAATATCACAAATAAAATT
Found at i:38865320 original size:29 final size:28
Alignment explanation
Indices: 38865164--38865641 Score: 342
Period size: 28 Copynumber: 17.0 Consensus size: 28
38865154 TTGGTAAAGC
*
38865164 AGGGGACAAAA-TAGTAAAATCT-AAAAAA
1 AGGGG-CAAAACTA-TAAAATCTGAAAAAT
** *
38865192 ATGGGATAAAACTATAAAATCTAAAAAAAT
1 A-GGGGCAAAACTATAAAATCT-GAAAAAT
* * *
38865222 A-GGGAAAAATTGTAAAAT-TGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* ** * *
38865248 ATGGGCAAAGTTGTAAAA-CATAAAAAAT
1 AGGGGCAAAACTATAAAATC-TGAAAAAT
* * ** *
38865276 A-AGGCTAAGTTGTAAAATCTGAAAACAT
1 AGGGGCAAAACTATAAAATCTGAAAA-AT
*
38865304 AGGGGCAAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
38865332 AGTGGAAAAACTATAAAATTTGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * * *
38865360 AGGAGACAAAATTATAAAATTTGACAAAT
1 AGG-GGCAAAACTATAAAATCTGAAAAAT
* *
38865389 AGGGGCTAAACTATAAAATATGAGAAAAT
1 AGGGGCAAAACTATAAAATCTGA-AAAAT
*
38865418 AGGGGCAAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
38865446 AAGGGCTAAACTATAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
38865474 AAGGG-AAAATTATAAAATTTGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * * **
38865501 ATGAGCAAAACTGTAAAATCTTTAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * * * *
38865529 AGAGGAAAAATTGTAAAATCTAAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* *
38865557 A-GGGCAAAAGTGTAAAATCTAGAAAAAT
1 AGGGGCAAAACTATAAAATCT-GAAAAAT
* * * *
38865585 AGGGGCAAAAGTGTAAAATATGGAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
* * *
38865613 ATGGGAAAAACTATAAAATTTGAAAAAT
1 AGGGGCAAAACTATAAAATCTGAAAAAT
38865641 A
1 A
38865642 AGGGACACAA
Statistics
Matches: 366, Mismatches: 69, Indels: 30
0.79 0.15 0.06
Matches are distributed among these distances:
26 7 0.02
27 71 0.19
28 193 0.53
29 89 0.24
30 6 0.02
ACGTcount: A:0.56, C:0.06, G:0.16, T:0.22
Consensus pattern (28 bp):
AGGGGCAAAACTATAAAATCTGAAAAAT
Found at i:38865370 original size:57 final size:55
Alignment explanation
Indices: 38865199--38865641 Score: 363
Period size: 57 Copynumber: 7.9 Consensus size: 55
38865189 AAAATGGGAT
* * * * *
38865199 AAAACTATAAAATCTAAAAAAATAGGGAAAAATTGTAAAA-TTGAAAAATATGGGC
1 AAAATTATAAAATCT-AAAAAATAGGGCAAAACTATAAAATTTGAAAAATAGGGGC
* * * * ** * *
38865254 AAAGTTGTAAAA-CATAAAAAATAAGGCTAAGTTGTAAAATCTGAAAACATAGGGGC
1 AAAATTATAAAATC-TAAAAAATAGGGCAAAACTATAAAATTTGAAAA-ATAGGGGC
* * *
38865310 AAAACTATAAAATCTAAAAAATAGTGGAAAAACTATAAAATTTGAAAAATAGGAGAC
1 AAAATTATAAAATCTAAAAAATAG-GGCAAAACTATAAAATTTGAAAAATAGG-GGC
* * * * *
38865367 AAAATTATAAAATTTGACAAATAGGGGCTAAACTATAAAATATGAGAAAATAGGGGC
1 AAAATTATAAAATCTAAAAAATA-GGGCAAAACTATAAAATTTGA-AAAATAGGGGC
* * * * *
38865424 AAAACTATAAAATCTAAAAAATAAGGGCTAAACTATAAAATCTAAAAAATAAGGG-
1 AAAATTATAAAATCTAAAAAAT-AGGGCAAAACTATAAAATTTGAAAAATAGGGGC
* * * * * * *
38865479 AAAATTATAAAATTTGAAAAATATGAGCAAAACTGTAAAATCTT-TAAAATAGAGGA
1 AAAATTATAAAATCTAAAAAATA-GGGCAAAACTATAAAAT-TTGAAAAATAGGGGC
* * * *
38865535 AAAATTGTAAAATCTAAAAAATAGGGCAAAAGTGTAAAATCTAGAAAAATAGGGGC
1 AAAATTATAAAATCTAAAAAATAGGGCAAAACTATAAAAT-TTGAAAAATAGGGGC
* * * ** *
38865591 AAAAGTGTAAAATATGGAAAATATGGGAAAAACTATAAAATTTGAAAAATA
1 AAAATTATAAAATCTAAAAAATA-GGGCAAAACTATAAAATTTGAAAAATA
38865642 AGGGACACAA
Statistics
Matches: 312, Mismatches: 62, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
54 22 0.07
55 74 0.24
56 97 0.31
57 109 0.35
58 10 0.03
ACGTcount: A:0.56, C:0.07, G:0.16, T:0.22
Consensus pattern (55 bp):
AAAATTATAAAATCTAAAAAATAGGGCAAAACTATAAAATTTGAAAAATAGGGGC
Found at i:38867488 original size:16 final size:17
Alignment explanation
Indices: 38867451--38867488 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
38867441 TATTACATTC
38867451 AAAA-TTAAAAATATTT
1 AAAATTTAAAAATATTT
*
38867467 ATAATTTAAAAATA-TT
1 AAAATTTAAAAATATTT
38867483 AAAATT
1 AAAATT
38867489 ATTTGAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTTAAAAATATTT
Found at i:38870428 original size:18 final size:20
Alignment explanation
Indices: 38870405--38870457 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 20
38870395 TTTTGTTGGC
*
38870405 ATAGGTGAATTGGT-TTAT-
1 ATAGGTGAATTGGTAATATG
38870423 ATAGGTGAATTGGTAATATG
1 ATAGGTGAATTGGTAATATG
*
38870443 ATAAGTGAATTGGTA
1 ATAGGTGAATTGGTA
38870458 TGAGACCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 14 0.45
19 3 0.10
20 14 0.45
ACGTcount: A:0.34, C:0.00, G:0.28, T:0.38
Consensus pattern (20 bp):
ATAGGTGAATTGGTAATATG
Found at i:38870452 original size:20 final size:19
Alignment explanation
Indices: 38870409--38870457 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
38870399 GTTGGCATAG
* *
38870409 GTGAATTGGT-TTATATAG
1 GTGAATTGGTAATATATAA
38870427 GTGAATTGGTAATATGATAA
1 GTGAATTGGTAATAT-ATAA
38870447 GTGAATTGGTA
1 GTGAATTGGTA
38870458 TGAGACCATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 10 0.37
19 3 0.11
20 14 0.52
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.39
Consensus pattern (19 bp):
GTGAATTGGTAATATATAA
Found at i:38879641 original size:176 final size:176
Alignment explanation
Indices: 38879203--38879880 Score: 878
Period size: 176 Copynumber: 3.8 Consensus size: 176
38879193 ATCTTCGCAG
* *
38879203 ATGGTGAATCTTATCTCCATGTATCGACAATGGAACAGATTTTATCACCAGTCTCATCTCTCTGA
1 ATGGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGA
* * *
38879268 GGTAGCAAGAAAGCAAGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTGAG
66 GGTAGCAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAG
* ****
38879333 ATTTGAAGATCTTATTTCTCTGAG-TTGCACCAAAGCAGATCTTCGCAG-
131 ATTTGAAGATCTTATTTCACTGAGATTGCAGTGGAGCAGA---TCG-AGA
* *
38879381 ATGGTGAATCTTATCTTCATGTATCGATAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGA
1 ATGGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGA
* * *
38879446 GGTAGGAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGAAAGTAGATTGAG
66 GGTAGCAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAG
*
38879511 ATTTAAAGATCTTATTTCACTGAGATTGCAGTGGAGCAGATCGAGA
131 ATTTGAAGATCTTATTTCACTGAGATTGCAGTGGAGCAGATCGAGA
* * * * * * *
38879557 ATGGTGGATATTATCTTCATGTATTGGCAATGGAGCAGATTTTATCACCGGCCTCATCCCTCTGA
1 ATGGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGA
** * * * *
38879622 TATAGTAAGAGAGCAGGTTGAATAATAAATCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAG
66 GGTAGCAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAG
* *
38879687 TTTTGAATATCTTATTTCACTGAGATTGCAGTGGAGCAGATCGAGA
131 ATTTGAAGATCTTATTTCACTGAGATTGCAGTGGAGCAGATCGAGA
* * * * * * *
38879733 ATGGTGAATCCTATCTCCATGTATCGGCAATGGAGTAGATTTTACCACTAGCCTTATTTCTCTGA
1 ATGGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGA
* * * **
38879798 GGTGGCAAGAGAGCGGGTTAAAG-ATGGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGACTAA
66 GGTAGCAAGAGAGCAGGTTGAAGAAT-GAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGA-TTG
*
38879862 AGA-CTGAAGATCTTATTTC
129 AGATTTGAAGATCTTATTTC
38879881 CTCAAGTAAT
Statistics
Matches: 436, Mismatches: 60, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
175 4 0.01
176 276 0.63
177 3 0.01
178 142 0.33
179 11 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (176 bp):
ATGGTGAATCTTATCTCCATGTATCGACAATGGAGCAGATTTTATCACCAGCCTCATCTCTCTGA
GGTAGCAAGAGAGCAGGTTGAAGAATGAGTCTTATCTTCCTGAGGTAGCAAGGAAGCAGATTGAG
ATTTGAAGATCTTATTTCACTGAGATTGCAGTGGAGCAGATCGAGA
Found at i:38880148 original size:22 final size:24
Alignment explanation
Indices: 38880100--38880148 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
38880090 AATAGAAATT
*
38880100 TAAA-AAACCAAAACCAAAAATAA
1 TAAATAAACCAAAAACAAAAATAA
38880123 -AAATAAA-CAAAAACAAAAA-AA
1 TAAATAAACCAAAAACAAAAATAA
38880144 TAAAT
1 TAAAT
38880149 TAAGATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 2 0.09
22 18 0.78
23 3 0.13
ACGTcount: A:0.78, C:0.12, G:0.00, T:0.10
Consensus pattern (24 bp):
TAAATAAACCAAAAACAAAAATAA
Found at i:38881605 original size:18 final size:18
Alignment explanation
Indices: 38881557--38881606 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
38881547 ATTTTTATTA
*
38881557 TATCATTTATATTATTTG
1 TATCATTTATATTAATTG
*
38881575 TAAT-GTTTATATTAATTG
1 T-ATCATTTATATTAATTG
*
38881593 TATCATTTGTATTA
1 TATCATTTATATTA
38881607 TTAGTTTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.30, C:0.04, G:0.08, T:0.58
Consensus pattern (18 bp):
TATCATTTATATTAATTG
Found at i:38885344 original size:12 final size:12
Alignment explanation
Indices: 38885327--38885358 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
38885317 GGACACATAG
38885327 TCGTGTCCCAGC
1 TCGTGTCCCAGC
38885339 TCGTGTCCCAGC
1 TCGTGTCCCAGC
38885351 TCGTGTCC
1 TCGTGTCC
38885359 TCACTAGTGT
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:0.06, C:0.41, G:0.25, T:0.28
Consensus pattern (12 bp):
TCGTGTCCCAGC
Found at i:38885402 original size:13 final size:13
Alignment explanation
Indices: 38885384--38885417 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
38885374 TCTGAGTAGG
38885384 GTCACACGGCCGT
1 GTCACACGGCCGT
38885397 GTCACACGGCCGT
1 GTCACACGGCCGT
38885410 GTCACACG
1 GTCACACG
38885418 CTTGTATGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (13 bp):
GTCACACGGCCGT
Found at i:38886482 original size:130 final size:132
Alignment explanation
Indices: 38886273--38886642 Score: 374
Period size: 130 Copynumber: 2.8 Consensus size: 132
38886263 GTGAGAATGT
* * * * * ** * * *
38886273 AAAGGAATGTTCGATCATTTTGAGCAAACGAGAAATCACAACCCAGCACGATAGGGCATGATT-C
1 AAAGG-ATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCC
* * * * *
38886337 TCGAATTGTCAAATATCGAATATTGCCTTCGTTTTAAATAATTTTTAGAAGATATGAATGAAATC
65 ACGAATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAATC
38886402 TT-
130 TTG
* *
38886404 AAAGGGATATTTGATTATTTTAAAC-AA-TCGAAATTGCAACCCAACACGTTAGGGCACGATTCC
1 AAA-GGATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCC
* * ** * * * * *
38886467 ACAAATTGCCAAATATCGCGTATCGCCTTCG-TTCAAGGGA-TTTTAAAAGACATGAGTGAAATT
65 ACGAATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAATC
38886530 TTG
130 TTG
* * * *
38886533 AAATGATATTCGATTATTTTGAGCAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCG
1 AAAGGATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCA
** * *
38886598 CGAATTGTCAAATATTAAATCTCGTCTTCGTTTTAAAGAATTTTT
66 CGAATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTT
38886643 GAATGAATGA
Statistics
Matches: 189, Mismatches: 43, Indels: 13
0.77 0.18 0.05
Matches are distributed among these distances:
128 38 0.20
129 37 0.20
130 85 0.45
131 23 0.12
132 6 0.03
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (132 bp):
AAAGGATATTCGATTATTTTAAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACGATTCCA
CGAATTGTCAAATATCGAATATCGCCTTCGTTTTAAAGAATTTTTAAAAGACATGAATGAAATCT
TG
Found at i:38887842 original size:5 final size:5
Alignment explanation
Indices: 38887832--38887863 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
38887822 CATTATGTGA
38887832 AAAAT AAAAT AAAAT AAAAT -AAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
38887864 GAACACACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:38887857 original size:9 final size:9
Alignment explanation
Indices: 38887833--38887863 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
38887823 ATTATGTGAA
38887833 AAATAAAAT
1 AAATAAAAT
38887842 AAAATAAAAT
1 -AAATAAAAT
38887852 AAATAAAAT
1 AAATAAAAT
38887861 AAA
1 AAA
38887864 GAACACACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (9 bp):
AAATAAAAT
Found at i:38892886 original size:149 final size:149
Alignment explanation
Indices: 38892702--38892985 Score: 342
Period size: 148 Copynumber: 1.9 Consensus size: 149
38892692 TAAAATACAT
* *
38892702 ATAATAATAAACTAAAAGATATGTTATATAAGATTATAT-ATTTAAAAGACGAGAATAAATTTAA
1 ATAATAATAAACTAAAAGATATATTATATAAGATTATATAATATAAAAGA--AGAATAAATTTAA
* *
38892766 AAGAAACTATATGCGTAAAATAATAT-AGAATTAATAATATGCAT-AGAATAAAA-TAATCTTAC
64 AAGAAACTACATGCATAAAATAATATAAG-ATTAATAATATGCATGA-AATAAAATTAATCTTAC
38892828 TATAAAGTACGTATATATATATA
127 TATAAAGTACGTATATATATATA
** * * * * * * *
38892851 ATAATAATAATTTAAAAGATGTATTATGTAGGATTATGTAATATAATATAAGAATAAATTTAAAG
1 ATAATAATAAACTAAAAGATATATTATATAAGATTATATAATATAAAAGAAGAATAAATTTAAAA
* * * * *
38892916 GGAATTACATGTATAAAATAATATAAGATTAATAATATGCATGAAATAAAATTAATTTTATTATA
66 GAAACTACATGCATAAAATAATATAAGATTAATAATATGCATGAAATAAAATTAATCTTACTATA
38892981 AAGTA
131 AAGTA
38892986 TATGTATATA
Statistics
Matches: 113, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
148 55 0.49
149 51 0.45
150 7 0.06
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (149 bp):
ATAATAATAAACTAAAAGATATATTATATAAGATTATATAATATAAAAGAAGAATAAATTTAAAA
GAAACTACATGCATAAAATAATATAAGATTAATAATATGCATGAAATAAAATTAATCTTACTATA
AAGTACGTATATATATATA
Found at i:38896782 original size:20 final size:20
Alignment explanation
Indices: 38896757--38896796 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38896747 TTGTCAAATC
38896757 CCTACTGAAGCAACTTGGCT
1 CCTACTGAAGCAACTTGGCT
38896777 CCTACTGAAGCAACTTGGCT
1 CCTACTGAAGCAACTTGGCT
38896797 AAGAGTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (20 bp):
CCTACTGAAGCAACTTGGCT
Found at i:38897665 original size:18 final size:18
Alignment explanation
Indices: 38897641--38897680 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
38897631 GTCTCTCTCA
38897641 ATAAAAATTCAAAATATTT
1 ATAAAAATTCAAAA-ATTT
*
38897660 ATAAAAATTCTAAAATTT
1 ATAAAAATTCAAAAATTT
38897678 ATA
1 ATA
38897681 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAAAATTCAAAAATTT
Found at i:38901229 original size:75 final size:76
Alignment explanation
Indices: 38901141--38901287 Score: 269
Period size: 75 Copynumber: 1.9 Consensus size: 76
38901131 TTTTTATATG
*
38901141 TAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAGTGTTTCCAA
1 TAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCAA
38901206 A-AAATTTGAA
66 ATAAATTTGAA
*
38901216 TAAAAATAAATTTAAAAAATATAATATATCAAATACAGTAAAAATATTAAAATAAATGTTTCCAA
1 TAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCAA
38901281 ATAAATT
66 ATAAATT
38901288 GAAAATACAT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 64 0.93
76 5 0.07
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (76 bp):
TAAAAATAAATTTAAAAAATATAATATATCAAATACACTAAAAATATTAAAATAAATGTTTCCAA
ATAAATTTGAA
Found at i:38915433 original size:18 final size:18
Alignment explanation
Indices: 38915407--38915591 Score: 128
Period size: 18 Copynumber: 10.3 Consensus size: 18
38915397 AATTGATCGG
*
38915407 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
*
38915425 TTATTCAGTAA-AATCAGA
1 TTATTCAGTAACAGTCA-A
* * *
38915443 -TATTCAGTAAAAATTAA
1 TTATTCAGTAACAGTCAA
*
38915460 GTTATTCAGTAAGAGTC-A
1 -TTATTCAGTAACAGTCAA
* * *
38915478 TTCATTCAGTGACAATCCA
1 TT-ATTCAGTAACAGTCAA
* *
38915497 TTATTCAATAA-TGATCAA
1 TTATTCAGTAACAG-TCAA
* * *
38915515 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
38915533 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
* *
38915552 -TATCCAGTAACAGTTAA
1 TTATTCAGTAACAGTCAA
* *
38915569 TTATTCAGTAATAATCAA
1 TTATTCAGTAACAGTCAA
38915587 TTATT
1 TTATT
38915592 TTATACTTTT
Statistics
Matches: 130, Mismatches: 27, Indels: 20
0.73 0.15 0.11
Matches are distributed among these distances:
17 19 0.15
18 95 0.73
19 16 0.12
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:38915467 original size:19 final size:18
Alignment explanation
Indices: 38915425--38915471 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
38915415 TAACAGTCAA
*
38915425 TTATTCAGT-AAAATCAG
1 TTATTCAGTAAAAATAAG
*
38915442 ATATTCAGTAAAAATTAAG
1 TTATTCAGTAAAAA-TAAG
38915461 TTATTCAGTAA
1 TTATTCAGTAA
38915472 GAGTCATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 8 0.32
18 4 0.16
19 13 0.52
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (18 bp):
TTATTCAGTAAAAATAAG
Found at i:38915471 original size:54 final size:52
Alignment explanation
Indices: 38915407--38915591 Score: 156
Period size: 54 Copynumber: 3.4 Consensus size: 52
38915397 AATTGATCGG
* *
38915407 TTATCCAGTAACAGTCAATTATTCAGTAAAATCAGATATTCAGTAAAAATTAA
1 TTATTCAGTAATAGTCAATTATTCAGTAAAATCA-ATATTCAGTAAAAATTAA
* * * * ** *
38915460 GTTATTCAGTAAGAGTC-ATTCATTCAGTGACAATCCATTATTCAATAATGATCAA
1 -TTATTCAGTAATAGTCAATT-ATTCAGT-AAAAT-CAATATTCAGTAAAAATTAA
* * * * * *
38915515 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAATATCCAGTAACAGTTAA
1 TTATTCAGTAATAGTCAATTATTCAGTAA-AATC-AATATTCAGTAAAAATTAA
*
38915569 TTATTCAGTAATAATCAATTATT
1 TTATTCAGTAATAGTCAATTATT
38915592 TTATACTTTT
Statistics
Matches: 103, Mismatches: 22, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
53 5 0.05
54 77 0.75
55 19 0.18
56 2 0.02
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.36
Consensus pattern (52 bp):
TTATTCAGTAATAGTCAATTATTCAGTAAAATCAATATTCAGTAAAAATTAA
Found at i:38915572 original size:72 final size:72
Alignment explanation
Indices: 38915408--38915591 Score: 221
Period size: 72 Copynumber: 2.6 Consensus size: 72
38915398 ATTGATCGGT
38915408 TATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA-TATTCAGTAAAAATTAAGTTATTCAGTA
1 TATCCAGTAACAGTCAATTATTCAGTAATAATCA-ATTATTCAGTAAAAATTAAGTTATTCAGTA
* *
38915471 AGAGTCAT
65 ACAGTCAA
* * * * * * * *
38915479 TCATTCAGTGACAATCCATTATTCAATAATGATCAATTATTCAGT-AATATTCAGTTATTCAGTA
1 T-ATCCAGTAACAGTCAATTATTCAGTAATAATCAATTATTCAGTAAAAATTAAGTTATTCAGTA
38915543 ACAGTCTAA
65 ACAGTC-AA
*
38915552 TATCCAGTAACAGTTAATTATTCAGTAATAATCAATTATT
1 TATCCAGTAACAGTCAATTATTCAGTAATAATCAATTATT
38915592 TTATACTTTT
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
71 1 0.01
72 77 0.84
73 14 0.15
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (72 bp):
TATCCAGTAACAGTCAATTATTCAGTAATAATCAATTATTCAGTAAAAATTAAGTTATTCAGTAA
CAGTCAA
Found at i:38915842 original size:51 final size:45
Alignment explanation
Indices: 38915749--38915847 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
38915739 ACAAATCCAG
* *
38915749 AACAGTAACAGTATTCAACACACAAAGTGCTGAATCGATAACGGT
1 AACAGTAACAGTATTCGACACACAAAGTGCCGAATCGATAACGGT
* *
38915794 AACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAACAGT
1 AACAGTAACAGTATTCGACACACAAAGTGCCGAATCGATAACGGT
*
38915839 AACGGTAAC
1 AACAGTAAC
38915848 GGTAACAGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.41, C:0.21, G:0.19, T:0.18
Consensus pattern (45 bp):
AACAGTAACAGTATTCGACACACAAAGTGCCGAATCGATAACGGT
Found at i:38916217 original size:9 final size:9
Alignment explanation
Indices: 38916203--38916236 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
38916193 ATAAATCAAT
38916203 TCAATATAA
1 TCAATATAA
38916212 TCAATATAA
1 TCAATATAA
38916221 TCAATATAA
1 TCAATATAA
38916230 TCAATAT
1 TCAATAT
38916237 TCAATCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (9 bp):
TCAATATAA
Found at i:38916219 original size:30 final size:32
Alignment explanation
Indices: 38916168--38916234 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 32
38916158 AATATTCATT
* *
38916168 TCAATTCAAACATTCACATATATTC-ATA-AA
1 TCAATTCAAACAATCACATATAATCAATATAA
*
38916198 TCAATTCAATATAATCA-ATATAATCAATATAA
1 TCAATTCAA-ACAATCACATATAATCAATATAA
38916230 TCAAT
1 TCAAT
38916235 ATTCAATCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 16 0.52
31 8 0.26
32 7 0.23
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.34
Consensus pattern (32 bp):
TCAATTCAAACAATCACATATAATCAATATAA
Found at i:38916223 original size:23 final size:22
Alignment explanation
Indices: 38916179--38916225 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
38916169 CAATTCAAAC
*
38916179 ATTCACATATATTCATAAATCA
1 ATTCACATATAATCATAAATCA
38916201 ATTCA-ATATAATCAATATAATCA
1 ATTCACATATAATC-ATA-AATCA
38916224 AT
1 AT
38916226 ATAATCAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTCACATATAATCATAAATCA
Found at i:38921295 original size:33 final size:33
Alignment explanation
Indices: 38921231--38921294 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
38921221 AAAGGGTAAA
38921231 ATTTAAAAATTTTATAAAAATTAGTAAAAAATC
1 ATTTAAAAATTTTATAAAAATTAGTAAAAAATC
38921264 ATTTAGAAAATTTTA-AAATTAATTA-TAAAAA
1 ATTTA-AAAATTTTATAAA--AATTAGTAAAAA
38921295 TAAAAAAGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
33 8 0.29
34 15 0.54
35 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (33 bp):
ATTTAAAAATTTTATAAAAATTAGTAAAAAATC
Found at i:38921634 original size:19 final size:20
Alignment explanation
Indices: 38921610--38921660 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
38921600 AAATATTATG
* *
38921610 ATTTTTACAATT-TATAATT
1 ATTTTTAAAATTGCATAATT
38921629 ATTTTTTAAAATTGCATAATT
1 A-TTTTTAAAATTGCATAATT
*
38921650 ATTTTCAAAAT
1 ATTTTTAAAAT
38921661 AATTTAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 19 0.70
21 7 0.26
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTTTTAAAATTGCATAATT
Found at i:38921757 original size:19 final size:18
Alignment explanation
Indices: 38921663--38921776 Score: 76
Period size: 19 Copynumber: 6.2 Consensus size: 18
38921653 TTCAAAATAA
38921663 TTTA-AATTATTTAATAGTT
1 TTTACAATT-TTTAATA-TT
* *
38921682 TTTAC-A-TTTTAAAAAT
1 TTTACAATTTTTAATATT
*
38921698 TTAACAATTTTT-ATACTTT
1 TTTACAATTTTTAATA--TT
* *
38921717 TTTACAATTTTTAAGAACT
1 TTTACAATTTTTAA-TATT
38921736 TTTACAACTTTTTAATATT
1 TTTACAA-TTTTTAATATT
*
38921755 TTTA-AATTATTTTATATT
1 TTTACAATT-TTTAATATT
38921773 TTTA
1 TTTA
38921777 AAATAAATTT
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
16 5 0.07
17 11 0.15
18 19 0.25
19 31 0.41
20 8 0.11
21 1 0.01
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTACAATTTTTAATATT
Found at i:38931359 original size:25 final size:24
Alignment explanation
Indices: 38931305--38931366 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 24
38931295 TTTACTCTAC
*
38931305 TTTAAAAAT-TGAATGTAATTAAT
1 TTTAAAAATATAAATGTAATTAAT
* *
38931328 TTGAAAAATATAAATTTAATTTAAT
1 TTTAAAAATATAAATGTAA-TTAAT
*
38931353 TTTAAAATTATAAA
1 TTTAAAAATATAAA
38931367 CTATTGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (24 bp):
TTTAAAAATATAAATGTAATTAAT
Found at i:38936213 original size:13 final size:13
Alignment explanation
Indices: 38936197--38936221 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38936187 ATGTATATAA
38936197 TATATATATAAAC
1 TATATATATAAAC
38936210 TATATATATAAA
1 TATATATATAAA
38936222 AAAAATATGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:38936344 original size:3 final size:3
Alignment explanation
Indices: 38936329--38936386 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
38936319 GTATGCAAGT
*
38936329 ATA ATA A-A A-A ATA ATA ATA ATA GTA ATA ATA ATA ATA ATA ACT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
*
38936372 ATA TTA ATA A-A ATA A
1 ATA ATA ATA ATA ATA A
38936387 ACTAAAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 7 0.15
3 39 0.83
4 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:38937831 original size:44 final size:43
Alignment explanation
Indices: 38937711--38937927 Score: 204
Period size: 44 Copynumber: 4.9 Consensus size: 43
38937701 CGCCATCGTC
* * *
38937711 GATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAA
* * * * *
38937756 GATCTG-TATCTTGGATCCACTTCCTATCAATATAGGAAGATAG
1 GATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGACAA
* * *
38937799 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAA
1 GATCTGCTATCTTCGATCTACTTC-CACCAATATAGGAAGACAA
* * *
38937843 GATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAA
1 GATCTGCTATCTTCGATCTACTT--CCACCAATATAGGAAGACAA
* * *
38937888 GATTTGC-ATCTTTGATCCACTTCCTACCAATATAGGAAGA
1 GATCTGCTATCTTCGATCTACTTCC-ACCAATATAGGAAGA
38937928 TAGGACCTAT
Statistics
Matches: 138, Mismatches: 28, Indels: 14
0.77 0.16 0.08
Matches are distributed among these distances:
42 4 0.03
43 33 0.24
44 72 0.52
45 28 0.20
46 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (43 bp):
GATCTGCTATCTTCGATCTACTTCCACCAATATAGGAAGACAA
Found at i:38950005 original size:339 final size:338
Alignment explanation
Indices: 38949386--38950061 Score: 1289
Period size: 339 Copynumber: 2.0 Consensus size: 338
38949376 ATTAAACATT
38949386 GAATATTGCATTTATTTCGAAAAATCCTTGTCTCGAGAAAGCAACGTGTCACATCCAATGCGTTA
1 GAATATTGCATTTATTTCGAAAAATCCTTGTCTCGAGAAAGCAACGTGTCACATCCAATGCGTTA
38949451 GGACACAACATATTAAATTCTTGATAACGAGCTTTTTATCATTTTTTTAAAGAGTAATCTCGATT
66 GGACACAACATATTAAATTCTTGATAACGAGCTTTTTATCATTTTTTTAAAGAGTAATCTCGATT
* *
38949516 ATTTAAATTCAACGAAGAAAGTCGGAACCCAATGCATTAGGGCTCGATTCTCTCGAAGATCTAAA
131 ATTTAAATTCAACGAAGAAAGTCGAAACCCAATGCATTAGGGCTCGATTCTCTCGAAGATCAAAA
*
38949581 TATCGAATATTACTTTTATTTTGAAATTTCATTTTTGGCCAATCCGATTGAAAAGATACGATTTG
196 TATCGAATATTACTTTTATTTTGAAATTTCATTTTTGGCCAATCCGATTGAAAAGATACGATGTG
38949646 ACAACAATGATGATAATGTAAGTAAAATAACACGAGCAAAACATAAGATAAATAAATAATAAAAC
261 ACAACAATGATGATAATGTAAGTAAAATAACACGAGCAAAACATAAGATAAATAAATAATAAAAC
38949711 GAAGAAAACAATA
326 GAAGAAAACAATA
*
38949724 GAATATTGCATTTATTTCGAAAAATCCTTGTCTCGAGAAAGCAACGTGTCACATCCAATGTGTTA
1 GAATATTGCATTTATTTCGAAAAATCCTTGTCTCGAGAAAGCAACGTGTCACATCCAATGCGTTA
*
38949789 GGACACAACATATTAAATTCTTGATAACGAGTTTTTTATCATTTTTTTTAAAGAGTAATCTCGAT
66 GGACACAACATATTAAATTCTTGATAACGAGCTTTTTATCA-TTTTTTTAAAGAGTAATCTCGAT
38949854 TATTTAAATTCAACGAAGAAAGTCGAAACCCAATGCATTAGGGCTCGATTCTCTCGAAGATCAAA
130 TATTTAAATTCAACGAAGAAAGTCGAAACCCAATGCATTAGGGCTCGATTCTCTCGAAGATCAAA
*
38949919 ATATCGAATATTACTTTTATTTTGAAATTTCATTTTTGGCGAATCCGATTGAAAAGATACGATGT
195 ATATCGAATATTACTTTTATTTTGAAATTTCATTTTTGGCCAATCCGATTGAAAAGATACGATGT
38949984 GACAACAATGATGATAATGTAAGTAAAATAACACGAGCAAAACATAAGATAAATAAATAATAAAA
260 GACAACAATGATGATAATGTAAGTAAAATAACACGAGCAAAACATAAGATAAATAAATAATAAAA
38950049 CGAAGAAAACAAT
325 CGAAGAAAACAAT
38950062 CAAAAAGGCA
Statistics
Matches: 331, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
338 104 0.31
339 227 0.69
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (338 bp):
GAATATTGCATTTATTTCGAAAAATCCTTGTCTCGAGAAAGCAACGTGTCACATCCAATGCGTTA
GGACACAACATATTAAATTCTTGATAACGAGCTTTTTATCATTTTTTTAAAGAGTAATCTCGATT
ATTTAAATTCAACGAAGAAAGTCGAAACCCAATGCATTAGGGCTCGATTCTCTCGAAGATCAAAA
TATCGAATATTACTTTTATTTTGAAATTTCATTTTTGGCCAATCCGATTGAAAAGATACGATGTG
ACAACAATGATGATAATGTAAGTAAAATAACACGAGCAAAACATAAGATAAATAAATAATAAAAC
GAAGAAAACAATA
Found at i:38950483 original size:13 final size:14
Alignment explanation
Indices: 38950465--38950499 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
38950455 CATATGAATG
38950465 TATATAA-TATATA
1 TATATAACTATATA
38950478 TATATAAACTATATA
1 TATAT-AACTATATA
38950493 TATATAA
1 TATATAA
38950500 AAAATATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 5 0.25
14 4 0.20
15 11 0.55
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TATATAACTATATA
Found at i:38950483 original size:15 final size:15
Alignment explanation
Indices: 38950472--38950500 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
38950462 ATGTATATAA
38950472 TATATATATATAAAC
1 TATATATATATAAAC
38950487 TATATATATATAAA
1 TATATATATATAAA
38950501 AAATATGGTA
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:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:38950506 original size:15 final size:15
Alignment explanation
Indices: 38950473--38950506 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
38950463 TGTATATAAT
**
38950473 ATATATATATAAACT
1 ATATATATATAAAAA
38950488 ATATATATATAAAAA
1 ATATATATATAAAAA
38950503 ATAT
1 ATAT
38950507 GGTAATGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATATATAAAAA
Found at i:38950622 original size:3 final size:3
Alignment explanation
Indices: 38950606--38950664 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
38950596 GTATGTAAGT
* *
38950606 ATA ATA A-A AAA ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ACT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
*
38950650 ATA TTA ATA A-A ATA A
1 ATA ATA ATA ATA ATA A
38950665 ACTAAAAACT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
2 5 0.11
3 41 0.87
4 1 0.02
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:38958109 original size:27 final size:25
Alignment explanation
Indices: 38958055--38958109 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 25
38958045 TTTTGAGTAA
38958055 TTTAATTTTTTTTCTTTTATATTCT
1 TTTAATTTTTTTTCTTTTATATTCT
*
38958080 TTTAACTTTTCTTTT-TTTTTTCATTCT
1 TTTAA-TTTT-TTTTCTTTTAT-ATTCT
38958107 TTT
1 TTT
38958110 TTGCTTCTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.19
26 9 0.35
27 12 0.46
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTAATTTTTTTTCTTTTATATTCT
Found at i:38960657 original size:27 final size:27
Alignment explanation
Indices: 38960597--38960683 Score: 120
Period size: 27 Copynumber: 3.2 Consensus size: 27
38960587 GTAATGCAAA
* * *
38960597 AATCTAACCGTTACAATATGATTGTTGG
1 AATCTGACCGTTACAATATG-CTATTGG
*
38960625 AATCTGACCATTACAATATGCTATTGG
1 AATCTGACCGTTACAATATGCTATTGG
*
38960652 AATCTGACCGTTACAATATGCCATTGG
1 AATCTGACCGTTACAATATGCTATTGG
38960679 AATCT
1 AATCT
38960684 AGTCGTTGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 35 0.66
28 18 0.34
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (27 bp):
AATCTGACCGTTACAATATGCTATTGG
Found at i:38971489 original size:26 final size:27
Alignment explanation
Indices: 38971460--38971516 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
38971450 CCTGAATTTG
* *
38971460 ATTTTTTTTACT-AATTTGATACTTAA
1 ATTTTTTTAACTCAATTAGATACTTAA
* *
38971486 ATTTTTTTAATTCAATTAGATATTTAA
1 ATTTTTTTAACTCAATTAGATACTTAA
38971513 ATTT
1 ATTT
38971517 GACACTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTTTTTTAACTCAATTAGATACTTAA
Found at i:38973501 original size:49 final size:49
Alignment explanation
Indices: 38973387--38973501 Score: 135
Period size: 49 Copynumber: 2.4 Consensus size: 49
38973377 GGACATGTGG
* * * *
38973387 GGGA-ACACGAGCGTGTACGATTACACGGTCAAATTAGGTAGGCCGTGT
1 GGGACACACGAGCGTGTGCAATTACACGGGCAAATCAGGTAGGCCGTGT
* * *
38973435 -GGAGCACACGGGTGTGTGCAATTACACGGGCAAATCAGGTAGGTCGTGT
1 GGGA-CACACGAGCGTGTGCAATTACACGGGCAAATCAGGTAGGCCGTGT
*
38973484 GGGACACACAAGCGTGTG
1 GGGACACACGAGCGTGTG
38973502 AAATCACATA
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
47 3 0.06
49 48 0.89
50 3 0.06
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (49 bp):
GGGACACACGAGCGTGTGCAATTACACGGGCAAATCAGGTAGGCCGTGT
Found at i:38974900 original size:31 final size:31
Alignment explanation
Indices: 38974859--38974917 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
38974849 AAGGTCACTA
*
38974859 AACTATTTGAAAGTTTTCATTTAAGTCATTG
1 AACTAGTTGAAAGTTTTCATTTAAGTCATTG
*
38974890 AACTAGTTGAAAGTTTTTATTTAAGTCA
1 AACTAGTTGAAAGTTTTCATTTAAGTCA
38974918 CTGGACTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (31 bp):
AACTAGTTGAAAGTTTTCATTTAAGTCATTG
Found at i:38976615 original size:243 final size:243
Alignment explanation
Indices: 38976183--38976674 Score: 921
Period size: 243 Copynumber: 2.0 Consensus size: 243
38976173 TTCCTCATCC
38976183 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
1 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
38976248 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
66 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
* *
38976313 AAGGATCTCCCCGAAACATTTTAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
131 AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
*
38976378 TTTTTGATAGGAATGTTGTTGGTGTTTATTCCATTGTCTCCATCCACT
196 TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTGTCTCCATCCACT
*
38976426 GGAATGTCCAAATCCCATACCCTGAAGATATCCGCTGTTGATGAATTCATCTCTTCTGCAGATAA
1 GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
38976491 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
66 GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
* *
38976556 AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCTGCTGGGTACCAGTCCTC
131 AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
*
38976621 TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTTTCTCCATCCACT
196 TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTGTCTCCATCCACT
38976669 GGAATG
1 GGAATG
38976675 ACAAGAAGAT
Statistics
Matches: 242, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
243 242 1.00
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.34
Consensus pattern (243 bp):
GGAATGTCCAAATCCCATACCCTGAAGATATCCACTGTTGATGAATTCATCTCTTCTGCAGATAA
GCTTGATTTAACTCCTGAATCAACAGCACTATCCTTTCTTTCATTCTCCTTGTAGGTGGGTCGGA
AAGGATCTCCCCAAAACATTTCAGTGGAATCTTCCTGAAGAAATTGCAGCTGAGTACCAGTCCTC
TTTTTGATAGGAATGTTGTTGGTGTTCATTCCATTGTCTCCATCCACT
Found at i:38980839 original size:18 final size:18
Alignment explanation
Indices: 38980796--38980839 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
38980786 TTAGTAGTGC
38980796 TAAAAAAAATATTTCTGA
1 TAAAAAAAATATTTCTGA
*** *
38980814 TTTCAAAAATATTTTTGA
1 TAAAAAAAATATTTCTGA
38980832 TAAAAAAA
1 TAAAAAAA
38980840 GTTGTACTAA
Statistics
Matches: 19, Mismatches: 7, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.36
Consensus pattern (18 bp):
TAAAAAAAATATTTCTGA
Found at i:38981444 original size:16 final size:16
Alignment explanation
Indices: 38981423--38981463 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
38981413 TTACAAAAAG
38981423 AATACAAGAGAAATAT
1 AATACAAGAGAAATAT
38981439 AATACAAGAGAAATAT
1 AATACAAGAGAAATAT
*
38981455 AATATAAGA
1 AATACAAGA
38981464 TACACACGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.20
Consensus pattern (16 bp):
AATACAAGAGAAATAT
Found at i:38982395 original size:21 final size:21
Alignment explanation
Indices: 38982369--38982444 Score: 64
Period size: 24 Copynumber: 3.5 Consensus size: 21
38982359 TTAGATATTA
38982369 TTATTATCATTACTATTTTTG
1 TTATTATCATTACTATTTTTG
* *
38982390 TTATTATTTTTATTACTATTTCTG
1 TTATTA---TCATTACTATTTTTG
** *
38982414 TTATTATTTTTACTATTATT-
1 TTATTATCATTACTATTTTTG
*
38982434 TTACTATCATT
1 TTATTATCATT
38982445 TTTTTTATAT
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
20 8 0.18
21 17 0.39
24 19 0.43
ACGTcount: A:0.24, C:0.09, G:0.03, T:0.64
Consensus pattern (21 bp):
TTATTATCATTACTATTTTTG
Found at i:38982397 original size:12 final size:12
Alignment explanation
Indices: 38982364--38982435 Score: 72
Period size: 12 Copynumber: 6.0 Consensus size: 12
38982354 TACTATTAGA
*
38982364 TATTATTATTAT
1 TATTATTATTTT
* *
38982376 CATTACTATTTT
1 TATTATTATTTT
*
38982388 TGTTATTATTTT
1 TATTATTATTTT
* *
38982400 TATTACTATTTC
1 TATTATTATTTT
*
38982412 TGTTATTATTTT
1 TATTATTATTTT
*
38982424 TACTATTATTTT
1 TATTATTATTTT
38982436 ACTATCATTT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.67
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:38982404 original size:24 final size:24
Alignment explanation
Indices: 38982366--38982435 Score: 95
Period size: 24 Copynumber: 2.9 Consensus size: 24
38982356 CTATTAGATA
* *
38982366 TTATTATTATCATTACTATTTTTG
1 TTATTATTTTTATTACTATTTTTG
*
38982390 TTATTATTTTTATTACTATTTCTG
1 TTATTATTTTTATTACTATTTTTG
* *
38982414 TTATTATTTTTACTATTATTTT
1 TTATTATTTTTATTACTATTTT
38982436 ACTATCATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.23, C:0.07, G:0.03, T:0.67
Consensus pattern (24 bp):
TTATTATTTTTATTACTATTTTTG
Found at i:38983149 original size:35 final size:34
Alignment explanation
Indices: 38983103--38983326 Score: 263
Period size: 35 Copynumber: 6.5 Consensus size: 34
38983093 TTTCCTTATT
* *
38983103 GAAATACCATACCTACATTTCACAACTCGGTATGG
1 GAAATACCATACCTACGTTTCACAACTCAGTAT-G
* ** *
38983138 GAAATGCCATACCTACG-TTCTTAACTTAGTATG
1 GAAATACCATACCTACGTTTCACAACTCAGTATG
*
38983171 GATAATATCATACCTACGTTTCACAACTCAGTATG
1 GA-AATACCATACCTACGTTTCACAACTCAGTATG
*
38983206 GATGATACCATACCTACGTTTCACAACTCAGTATG
1 GA-AATACCATACCTACGTTTCACAACTCAGTATG
* *
38983241 GTTAATACCATATCTAC-TTTCACAACTCAGTATG
1 G-AAATACCATACCTACGTTTCACAACTCAGTATG
* *
38983275 GATGATACCATACCTACGTTTCACAACTCGGTATG
1 GA-AATACCATACCTACGTTTCACAACTCAGTATG
*
38983310 GTTAATACCATACCTAC
1 G-AAATACCATACCTAC
38983327 TGTTAGAATT
Statistics
Matches: 161, Mismatches: 22, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
33 3 0.02
34 54 0.34
35 104 0.65
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (34 bp):
GAAATACCATACCTACGTTTCACAACTCAGTATG
Found at i:38983221 original size:69 final size:69
Alignment explanation
Indices: 38983105--38983327 Score: 315
Period size: 69 Copynumber: 3.2 Consensus size: 69
38983095 TCCTTATTGA
* * * ** *
38983105 AATACCATACCTACATTTCACAACTCGGTATGGGA-AATGCCATACCTACG-TTCTTAACTTAGT
1 AATACCATACCTAC-TTTCACAACTCAGTAT-GGATGATACCATACCTACGTTTCACAACTCAGT
*
38983168 ATGGAT
64 ATGGTT
*
38983174 AATATCATACCTACGTTTCACAACTCAGTATGGATGATACCATACCTACGTTTCACAACTCAGTA
1 AATACCATACCTAC-TTTCACAACTCAGTATGGATGATACCATACCTACGTTTCACAACTCAGTA
38983239 TGGTT
65 TGGTT
* *
38983244 AATACCATATCTACTTTCACAACTCAGTATGGATGATACCATACCTACGTTTCACAACTCGGTAT
1 AATACCATACCTACTTTCACAACTCAGTATGGATGATACCATACCTACGTTTCACAACTCAGTAT
38983309 GGTT
66 GGTT
38983313 AATACCATACCTACT
1 AATACCATACCTACT
38983328 GTTAGAATTA
Statistics
Matches: 139, Mismatches: 13, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
68 3 0.02
69 109 0.78
70 27 0.19
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.31
Consensus pattern (69 bp):
AATACCATACCTACTTTCACAACTCAGTATGGATGATACCATACCTACGTTTCACAACTCAGTAT
GGTT
Found at i:38983240 original size:104 final size:104
Alignment explanation
Indices: 38983105--38983326 Score: 309
Period size: 104 Copynumber: 2.1 Consensus size: 104
38983095 TCCTTATTGA
* * ** *
38983105 AATACCATACCTACATTTCACAACTCGGTATGGGAAATGCCATACCTACGTTCTTAACTTAGTAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
*
38983170 GGATAATATCATACCTACGTTTCACAACTCAGTATGGAT
66 GGATAATACCATACCTACGTTTCACAACTCAGTATGGAT
* * ** * *
38983209 GATACCATACCTACGTTTCACAACTCAGTATGGTTAATACCATATCTACTTTCACAACTCAGTAT
1 AATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
* * *
38983274 GGATGATACCATACCTACGTTTCACAACTCGGTATGGTT
66 GGATAATACCATACCTACGTTTCACAACTCAGTATGGAT
38983313 AATACCATACCTAC
1 AATACCATACCTAC
38983327 TGTTAGAATT
Statistics
Matches: 102, Mismatches: 16, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
104 102 1.00
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.31
Consensus pattern (104 bp):
AATACCATACCTACATTTCACAACTCAGTATGGGAAATACCATACCTACGTTCACAACTCAGTAT
GGATAATACCATACCTACGTTTCACAACTCAGTATGGAT
Found at i:38987679 original size:535 final size:535
Alignment explanation
Indices: 38986660--38987737 Score: 2052
Period size: 535 Copynumber: 2.0 Consensus size: 535
38986650 CACAAAATTA
* * * * * * *
38986660 TTTA-TATCTTGAGCTACGTAACTCCAAATTGATATCTGTTAATTTTATATGAAACTATACTCGC
1 TTTATTATCTGGAGCTACGTAACTCCAAATTAAGATCTGATAATTTTACATGAAACTAGACTCAC
38986724 ATATATTCTTACTATAAAATTTTCATAATTTTTGGTTTAACCAATAAGTACAGTTTATTCTTTAA
66 ATATATTCTTACTATAAAATTTTCATAATTTTTGGTTTAACCAATAAGTACAGTTTATTCTTTAA
38986789 ATTCACCCCTGTTCTGCTGTCTGACAGTTCTGACCCTTCTTCACTAAAAATTAATTATCTCCTCG
131 ATTCACCCCTGTTCTGCTGTCTGACAGTTCTGACCCTTCTTCACTAAAAATTAATTATCTCCTCG
38986854 TACAAGATTCTAATGATGTTCATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAA
196 TACAAGATTCTAATGATGTTCATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAA
38986919 TATAAATTTAAGCCCTTAATTATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGG
261 TATAAATTTAAGCCCTTAATTATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGG
38986984 AACCCGAATTCATTCTGACCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTG
326 AACCCGAATTCATTCTGACCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTG
38987049 CTTACATTGTTTCTTCTATGATAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTC
391 CTTACATTGTTTCTTCTATGATAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTC
38987114 CTAATTCGATTTATACAATTTATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTA
456 CTAATTCGATTTATACAATTTATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTA
38987179 TTTTAGTGCAAGCTG
521 TTTTAGTGCAAGCTG
* *
38987194 TTTATTATCTGGAGCTACAG-AACTCCAAATTAAGATCTGATAATTTTCCCTGAAACTAGACTCA
1 TTTATTATCTGGAGCTAC-GTAACTCCAAATTAAGATCTGATAATTTTACATGAAACTAGACTCA
38987258 CATATATTCTTACTATAAAATTTTCATAATTTTTGGTTTAACCAATAAGTACAGTTTATTCTTTA
65 CATATATTCTTACTATAAAATTTTCATAATTTTTGGTTTAACCAATAAGTACAGTTTATTCTTTA
38987323 AATTCACCCCTGTTCTGCTGTCTGACAGTTCTGACCCTTCTTCACTAAAAATTAATTATCTCCTC
130 AATTCACCCCTGTTCTGCTGTCTGACAGTTCTGACCCTTCTTCACTAAAAATTAATTATCTCCTC
38987388 GTACAAGATTCTAATGATGTTCATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAA
195 GTACAAGATTCTAATGATGTTCATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAA
38987453 ATATAAATTTAAGCCCTTAATTATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGG
260 ATATAAATTTAAGCCCTTAATTATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGG
38987518 GAACCCGAATTCATTCTGACCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATT
325 GAACCCGAATTCATTCTGACCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATT
38987583 GCTTACATTGTTTCTTCTATGATAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACT
390 GCTTACATTGTTTCTTCTATGATAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACT
38987648 CCTAATTCGATTTATACAATTTATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATT
455 CCTAATTCGATTTATACAATTTATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATT
38987713 ATTTTAGTGCAAGCTG
520 ATTTTAGTGCAAGCTG
38987729 TTTATTATC
1 TTTATTATC
38987738 ATTTTTCCCC
Statistics
Matches: 533, Mismatches: 9, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
534 4 0.01
535 528 0.99
536 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.10, T:0.42
Consensus pattern (535 bp):
TTTATTATCTGGAGCTACGTAACTCCAAATTAAGATCTGATAATTTTACATGAAACTAGACTCAC
ATATATTCTTACTATAAAATTTTCATAATTTTTGGTTTAACCAATAAGTACAGTTTATTCTTTAA
ATTCACCCCTGTTCTGCTGTCTGACAGTTCTGACCCTTCTTCACTAAAAATTAATTATCTCCTCG
TACAAGATTCTAATGATGTTCATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAA
TATAAATTTAAGCCCTTAATTATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGG
AACCCGAATTCATTCTGACCTTGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTG
CTTACATTGTTTCTTCTATGATAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTC
CTAATTCGATTTATACAATTTATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTA
TTTTAGTGCAAGCTG
Found at i:38988506 original size:645 final size:645
Alignment explanation
Indices: 38987410--38988700 Score: 2582
Period size: 645 Copynumber: 2.0 Consensus size: 645
38987400 AATGATGTTC
38987410 ATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAATATAAATTTAAGCCCTTAATT
1 ATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAATATAAATTTAAGCCCTTAATT
38987475 ATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGGAACCCGAATTCATTCTGACCT
66 ATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGGAACCCGAATTCATTCTGACCT
38987540 TGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTGCTTACATTGTTTCTTCTATGA
131 TGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTGCTTACATTGTTTCTTCTATGA
38987605 TAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTCCTAATTCGATTTATACAATTT
196 TAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTCCTAATTCGATTTATACAATTT
38987670 ATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTATTTTAGTGCAAGCTGTTTATT
261 ATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTATTTTAGTGCAAGCTGTTTATT
38987735 ATCATTTTTCCCCTAAGCTTTTAATAAATAACAATTTCATCCCTACTCAATTAGCCTCTCAATTG
326 ATCATTTTTCCCCTAAGCTTTTAATAAATAACAATTTCATCCCTACTCAATTAGCCTCTCAATTG
38987800 AGCTGATTTTTCTCAATTAACACTTTATTATATTACTTTAAACTACTTTACAACCTTTGGAAATC
391 AGCTGATTTTTCTCAATTAACACTTTATTATATTACTTTAAACTACTTTACAACCTTTGGAAATC
38987865 ATAATTTCAGCACTAGACTTTAATTCCAAACATTTTCACAATTAGGTCCTAAAATCAATTTTCAT
456 ATAATTTCAGCACTAGACTTTAATTCCAAACATTTTCACAATTAGGTCCTAAAATCAATTTTCAT
38987930 CAATTTTACTTGATAAAATTATCATATATCTAAATTAAAGCTTCAATTATATGTTTATTCATCAT
521 CAATTTTACTTGATAAAATTATCATATATCTAAATTAAAGCTTCAATTATATGTTTATTCATCAT
38987995 ATTATTCCAGCACTCATCCATATCAACTTTAAAAATTAACCATGAAATCAAAAACTAATA
586 ATTATTCCAGCACTCATCCATATCAACTTTAAAAATTAACCATGAAATCAAAAACTAATA
38988055 ATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAATATAAATTTAAGCCCTTAATT
1 ATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAATATAAATTTAAGCCCTTAATT
38988120 ATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGGAACCCGAATTCATTCTGACCT
66 ATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGGAACCCGAATTCATTCTGACCT
38988185 TGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTGCTTACATTGTTTCTTCTATGA
131 TGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTGCTTACATTGTTTCTTCTATGA
38988250 TAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTCCTAATTCGATTTATACAATTT
196 TAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTCCTAATTCGATTTATACAATTT
38988315 ATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTATTTTAGTGCAAGCTGTTTATT
261 ATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTATTTTAGTGCAAGCTGTTTATT
38988380 ATCATTTTTCCCCTAAGCTTTTAATAAATAACAATTTCATCCCTACTCAATTAGCCTCTCAATTG
326 ATCATTTTTCCCCTAAGCTTTTAATAAATAACAATTTCATCCCTACTCAATTAGCCTCTCAATTG
38988445 AGCTGATTTTTCTCAATTAACACTTTATTATATTACTTTAAACTACTTTACAACCTTTGGAAATC
391 AGCTGATTTTTCTCAATTAACACTTTATTATATTACTTTAAACTACTTTACAACCTTTGGAAATC
38988510 ATAATTTCAGCACTAGACTTTAATTCCAAACATTTTCACAATTAGGTCCTAAAATCAATTTTCAT
456 ATAATTTCAGCACTAGACTTTAATTCCAAACATTTTCACAATTAGGTCCTAAAATCAATTTTCAT
38988575 CAATTTTACTTGATAAAATTATCATATATCTAAATTAAAGCTTCAATTATATGTTTATTCATCAT
521 CAATTTTACTTGATAAAATTATCATATATCTAAATTAAAGCTTCAATTATATGTTTATTCATCAT
38988640 ATTATTCCAGCACTCATCCATATCAACTTTAAAAATTAACCATGAAATCAAAAACTAATA
586 ATTATTCCAGCACTCATCCATATCAACTTTAAAAATTAACCATGAAATCAAAAACTAATA
38988700 A
1 A
38988701 AATAGTAAGT
Statistics
Matches: 646, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
645 646 1.00
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.41
Consensus pattern (645 bp):
ATGTTTGTTTCTATTGAAAATAGACTCATTCAGGATTCTATAAATATAAATTTAAGCCCTTAATT
ATTTTTAATTAATTTTTTATGAATTTTCAAATTCATAACAGGGGAACCCGAATTCATTCTGACCT
TGTCTCACAAAATTTATTATATCTCATGATTTACAAATCCATTGCTTACATTGTTTCTTCTATGA
TAAACTAGACTCAATAAGCTTTAATTTCATATTTTTTTCAACTCCTAATTCGATTTATACAATTT
ATGGTGATTTTTCAAAGTTAGTCTACTGCTGCTGTCCAAAATTATTTTAGTGCAAGCTGTTTATT
ATCATTTTTCCCCTAAGCTTTTAATAAATAACAATTTCATCCCTACTCAATTAGCCTCTCAATTG
AGCTGATTTTTCTCAATTAACACTTTATTATATTACTTTAAACTACTTTACAACCTTTGGAAATC
ATAATTTCAGCACTAGACTTTAATTCCAAACATTTTCACAATTAGGTCCTAAAATCAATTTTCAT
CAATTTTACTTGATAAAATTATCATATATCTAAATTAAAGCTTCAATTATATGTTTATTCATCAT
ATTATTCCAGCACTCATCCATATCAACTTTAAAAATTAACCATGAAATCAAAAACTAATA
Found at i:38989662 original size:125 final size:126
Alignment explanation
Indices: 38989396--38989682 Score: 310
Period size: 125 Copynumber: 2.3 Consensus size: 126
38989386 TTGGAAGTTT
* * **
38989396 GAGAGATCGTGCCCAATCGTGCTGGGTTTCGATTTTTTACATTCAACTGAAATATGGAATACCTT
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTCGA-TTTTTACATTCAACTAAAATACAGAATACCTT
* * * * ** *
38989461 TGTGAAATTTCGTCCACGTTTTCTTAAATTAAAACGAGGCAATATTTTGTGTTCGGGAGTTT
65 TGTGAAATTTCATCCACGTTTTCTTAAATTAAAACGAGGCAATATTCTGTATTCGGAAAATC
* ** *
38989523 GAGAGATCAAGCCCAATCGTGCTGGGTTTCGATTTTT-CATTCGAC-AAAAGTACAGAATATCCT
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTACATTCAACTAAAA-TACAGAATA-CCT
** * * * *
38989586 TT-TGAAATTTCATTTATGTTTTCTTAAATTAAAATGAGGCAATATTCTGTATTTGTAAAATC
64 TTGTGAAATTTCATCCACGTTTTCTTAAATTAAAACGAGGCAATATTCTGTATTCGGAAAATC
* * *
38989648 GATAAATCGTGCCCAATCGTGCTAGGTTGCGATTT
1 GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTT
38989683 ATCGTTTGGC
Statistics
Matches: 133, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
124 3 0.02
125 90 0.68
126 10 0.08
127 30 0.23
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (126 bp):
GAGAAATCGTGCCCAATCGTGCTGGGTTTCGATTTTTACATTCAACTAAAATACAGAATACCTTT
GTGAAATTTCATCCACGTTTTCTTAAATTAAAACGAGGCAATATTCTGTATTCGGAAAATC
Found at i:38997264 original size:30 final size:31
Alignment explanation
Indices: 38997224--38997281 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
38997214 ACTTATAAAT
*
38997224 ATTATTAAAAAATC-TAATAAA-ATTTAATAA
1 ATTATAAAAAAATCATAA-AAATATTTAATAA
*
38997254 ATTATAAAAAATTCATAAAAATATTTAA
1 ATTATAAAAAAATCATAAAAATATTTAA
38997282 AATGTCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.36
Consensus pattern (31 bp):
ATTATAAAAAAATCATAAAAATATTTAATAA
Found at i:38997283 original size:20 final size:19
Alignment explanation
Indices: 38997261--38997312 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
38997251 TAAATTATAA
38997261 AAAATTCATAAAAA-TATTT
1 AAAATTCATAAAAACT-TTT
38997280 AAAATGTCATAAAAACTTTT
1 AAAAT-TCATAAAAACTTTT
*
38997300 AAAATTCTTAAAA
1 AAAATTCATAAAA
38997313 CAATTATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 12 0.40
20 17 0.57
21 1 0.03
ACGTcount: A:0.56, C:0.08, G:0.02, T:0.35
Consensus pattern (19 bp):
AAAATTCATAAAAACTTTT
Found at i:38997284 original size:29 final size:27
Alignment explanation
Indices: 38997219--38997294 Score: 64
Period size: 31 Copynumber: 2.5 Consensus size: 27
38997209 TATATACTTA
38997219 TAAATATTATTAAAAAATCTAATAAAATT
1 TAAA-ATTA-TAAAAAATCTAATAAAATT
38997248 TAATAAATTATAAAAAATTCATAA-AAATATT
1 T-A-AAATTATAAAAAA-TC-TAATAAA-ATT
38997279 TAAAATGTCATAAAAA
1 TAAAAT-T-ATAAAAA
38997295 CTTTTAAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
29 12 0.30
30 12 0.30
31 16 0.40
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (27 bp):
TAAAATTATAAAAAATCTAATAAAATT
Found at i:38997989 original size:9 final size:9
Alignment explanation
Indices: 38997972--38998169 Score: 57
Period size: 10 Copynumber: 20.4 Consensus size: 9
38997962 ATTTTAAGTT
38997972 TTTTAATAA
1 TTTTAATAA
38997981 CTTTT-ATAA
1 -TTTTAATAA
38997990 TTTTCAATAA
1 TTTT-AATAA
* *
38998000 TTTCTTATGAT
1 TTT-TAAT-AA
*
38998011 TTTTTATAA
1 TTTTAATAA
*
38998020 GTTTTTAAGAA
1 --TTTTAATAA
* *
38998031 TTTTTATATG
1 TTTTAATA-A
*
38998041 TTTTTATAAGA
1 TTTTAAT-A-A
38998052 TTTTAA-ATA
1 TTTTAATA-A
38998061 TTTTAAATACA
1 TTTT-AATA-A
*
38998072 TTTTATTAA
1 TTTTAATAA
*
38998081 TTTTATAAAA
1 TTTTA-ATAA
38998091 TTTT-ATAA
1 TTTTAATAA
*
38998099 TTTATTAA-CA
1 -TT-TTAATAA
*
38998109 TTTTTATAA
1 TTTTAATAA
*
38998118 TATTATATTAA
1 T-TT-TAATAA
38998129 TTTTGAATAA
1 TTTT-AATAA
38998139 TATTT--TAA
1 T-TTTAATAA
38998147 TATTTAATAA
1 T-TTTAATAA
*
38998157 TTTTCATAA
1 TTTTAATAA
38998166 TTTT
1 TTTT
38998170 GTCCTGATAT
Statistics
Matches: 143, Mismatches: 24, Indels: 43
0.68 0.11 0.20
Matches are distributed among these distances:
8 18 0.13
9 41 0.29
10 51 0.36
11 33 0.23
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (9 bp):
TTTTAATAA
Found at i:38998016 original size:30 final size:30
Alignment explanation
Indices: 38997982--38998055 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
38997972 TTTTAATAAC
*
38997982 TTTTATAA-TTTTCAATAATTTCTTATGAT-T
1 TTTTATAAGTTTTCAAGAATTT-TTAT-ATGT
*
38998012 TTTTATAAGTTTTTAAGAATTTTTATATGT
1 TTTTATAAGTTTTCAAGAATTTTTATATGT
38998042 TTTTATAAGATTTT
1 TTTTATAAG-TTTT
38998056 AAATATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
29 2 0.05
30 22 0.56
31 15 0.38
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.61
Consensus pattern (30 bp):
TTTTATAAGTTTTCAAGAATTTTTATATGT
Found at i:38998064 original size:30 final size:30
Alignment explanation
Indices: 38997982--38998064 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
38997972 TTTTAATAAC
*
38997982 TTTTAT-A-ATTTTCAATAATTTCTTATGATT
1 TTTTATAAGATTTTAAAT-ATTT-TTATGATT
*
38998012 TTTTATAAGTTTTTAAGA-ATTTTTAT-ATGT
1 TTTTATAAGATTTTAA-ATATTTTTATGAT-T
38998042 TTTTATAAGATTTTAAATATTTT
1 TTTTATAAGATTTTAAATATTTT
38998065 AAATACATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
29 3 0.07
30 31 0.69
31 5 0.11
32 5 0.11
33 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.60
Consensus pattern (30 bp):
TTTTATAAGATTTTAAATATTTTTATGATT
Found at i:38998101 original size:18 final size:18
Alignment explanation
Indices: 38998042--38998165 Score: 65
Period size: 19 Copynumber: 6.4 Consensus size: 18
38998032 TTTTATATGT
* *
38998042 TTTTATAAGATTTTAAATA
1 TTTTATAAAATTTTATA-A
38998061 TTTTA-AATACATTTTATTAA
1 TTTTATAA-A-ATTTTA-TAA
38998081 TTTTATAAAATTTTATAA
1 TTTTATAAAATTTTATAA
*
38998099 -TTTATTAACATTTTTATAA
1 TTTTA-TAA-AATTTTATAA
* *
38998118 TATTATATTAATTTTGAATAA
1 TTTTATA-AAATTTT--ATAA
* *
38998139 TATTT-TAATATTTAATAA
1 T-TTTATAAAATTTTATAA
38998157 TTTTCATAA
1 TTTT-ATAA
38998166 TTTTGTCCTG
Statistics
Matches: 82, Mismatches: 10, Indels: 26
0.69 0.08 0.22
Matches are distributed among these distances:
17 7 0.09
18 13 0.16
19 30 0.37
20 20 0.24
21 10 0.12
22 2 0.02
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTTTATAAAATTTTATAA
Found at i:38998160 original size:48 final size:48
Alignment explanation
Indices: 38998075--38998166 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 48
38998065 AAATACATTT
* *
38998075 TATTAATTTTATAAAATTTTATAATTTATTAACATTTTTATAATATTA
1 TATTAATTTTATAAAATTTTATAATTTAATAACATTTTCATAATATTA
*
38998123 TATTAATTTTGAATAATATTTTA-ATATTTAAT-A-ATTTTCATAAT
1 TATTAATTTT--ATAAAATTTTATA-ATTTAATAACATTTTCATAAT
38998167 TTTGTCCTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
48 20 0.53
49 2 0.05
50 16 0.42
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (48 bp):
TATTAATTTTATAAAATTTTATAATTTAATAACATTTTCATAATATTA
Found at i:39002117 original size:24 final size:23
Alignment explanation
Indices: 39002090--39002149 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
39002080 TGAAAAAAAT
*
39002090 TTTAAATTAAAATTTTGAGTTGAG
1 TTTAAATTAAAAATTTG-GTTGAG
*
39002114 TTT-AATTAAATAAATTTGTTTGAG
1 TTTAAATT-AA-AAATTTGGTTGAG
39002138 -TTAAATTAAAAA
1 TTTAAATTAAAAA
39002150 AATTAATGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 3 0.10
23 8 0.26
24 14 0.45
25 6 0.19
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (23 bp):
TTTAAATTAAAAATTTGGTTGAG
Found at i:39003949 original size:16 final size:16
Alignment explanation
Indices: 39003928--39003959 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
39003918 ATATATTTTC
*
39003928 TTTTAAACAGTAATTA
1 TTTTAAACAATAATTA
39003944 TTTTAAACAATAATTA
1 TTTTAAACAATAATTA
39003960 GCCCAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (16 bp):
TTTTAAACAATAATTA
Found at i:39011612 original size:39 final size:39
Alignment explanation
Indices: 39011564--39011641 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
39011554 TGTGCCTTTT
*
39011564 ATCCCATTTATATAAGCATTCTCATTACATTAAAGAGGG
1 ATCCCATTTATATAAGCATTCTCATTACACTAAAGAGGG
* *
39011603 ATCCTATTTATATAAGCATTCTCCTTACACTAAAGAGGG
1 ATCCCATTTATATAAGCATTCTCATTACACTAAAGAGGG
39011642 GGATAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (39 bp):
ATCCCATTTATATAAGCATTCTCATTACACTAAAGAGGG
Found at i:39012073 original size:21 final size:22
Alignment explanation
Indices: 39012035--39012075 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
39012025 GCTAATGTGG
*
39012035 GATTCAAATTTAAGTTTTAACA
1 GATTCAAAATTAAGTTTTAACA
*
39012057 GATT-AAAATTAATTTTTAA
1 GATTCAAAATTAAGTTTTAA
39012076 TAATGAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (22 bp):
GATTCAAAATTAAGTTTTAACA
Found at i:39012220 original size:69 final size:69
Alignment explanation
Indices: 39012074--39012222 Score: 185
Period size: 69 Copynumber: 2.2 Consensus size: 69
39012064 ATTAATTTTT
* * * * *
39012074 AATAATGAA-AAGTGAGTTATGGGAGTATTCTCTAGTCAATTTGGGATTAAAATTGACTTTTTAA
1 AATAATGAAGAAGTGAGTTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTAA
* *
39012138 TGAC
66 TAAA
* * *
39012142 TATAGTGAAGAAGTTA-TCTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTA
1 AATAATGAAGAAGTGAGT-TATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTA
39012206 ATAAA
65 ATAAA
39012211 AATAATGAAGAA
1 AATAATGAAGAA
39012223 ATTGTCACTT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
68 8 0.12
69 59 0.88
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (69 bp):
AATAATGAAGAAGTGAGTTATGAGAGTATTCTCTAGTCAATGTAGGATTAAAATTAAATTTTTAA
TAAA
Found at i:39015475 original size:70 final size:68
Alignment explanation
Indices: 39015340--39015536 Score: 227
Period size: 70 Copynumber: 2.9 Consensus size: 68
39015330 GTGAGATATT
* * * * * * *
39015340 GGAGTGTTGTCTAGCCAATGTAGGATTAAAATTAATTTTTAATGAAAACAGTGAATACGCGAGCT
1 GGAGTATTCTCTAGTCAATGTGGGATTAAAATTAATTTTTAATGAAAATAGTGAAGAAGCGAGCT
39015405 AT-
66 ATA
* * **
39015407 GAGAGTATAT-TTTAGTTAATGTGGGATTAAAATTAACTTTTTTAATGAAAATAGTGAAGAAGTT
1 G-GAGTAT-TCTCTAGTCAATGTGGGATTAAAATTAA--TTTTTAATGAAAATAGTGAAGAAGCG
39015471 AGCTATA
62 AGCTATA
*
39015478 GGAGTATTCTCTAGTCAATGTGGGATTAAAATTAAATTTTTAATAAAAATAGTGAAGAA
1 GGAGTATTCTCTAGTCAATGTGGGATTAAAATT-AATTTTTAATGAAAATAGTGAAGAA
39015537 ATTATCATTT
Statistics
Matches: 110, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
67 1 0.01
68 27 0.25
69 24 0.22
70 55 0.50
71 3 0.03
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (68 bp):
GGAGTATTCTCTAGTCAATGTGGGATTAAAATTAATTTTTAATGAAAATAGTGAAGAAGCGAGCT
ATA
Found at i:39019047 original size:11 final size:11
Alignment explanation
Indices: 39019014--39019047 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
39019004 GGCAAACAGT
39019014 AAAGAAATTTA
1 AAAGAAATTTA
*
39019025 AAA-AAGTTTA
1 AAAGAAATTTA
39019035 AAAGAAATTTA
1 AAAGAAATTTA
39019046 AA
1 AA
39019048 CATGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (11 bp):
AAAGAAATTTA
Found at i:39019219 original size:16 final size:16
Alignment explanation
Indices: 39019200--39019232 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39019190 AAATAATCAG
39019200 TTTTAAAAAAACATAT
1 TTTTAAAAAAACATAT
*
39019216 TTTTAAAAAAATATAT
1 TTTTAAAAAAACATAT
39019232 T
1 T
39019233 ATTAGCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTTAAAAAAACATAT
Found at i:39026344 original size:6 final size:6
Alignment explanation
Indices: 39026333--39026364 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
39026323 GAAAAACCAA
39026333 AGGCAC AGGCAC AGGCAC AGGCAC AGGCAC AG
1 AGGCAC AGGCAC AGGCAC AGGCAC AGGCAC AG
39026365 CTTCCTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (6 bp):
AGGCAC
Found at i:39036401 original size:43 final size:43
Alignment explanation
Indices: 39036349--39036449 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 43
39036339 TTCTAGGCTT
* * *
39036349 GAAGGCCGATATCA-T-TTCACCGGCATTATAGCCTGCTAGGCCC
1 GAAGCCCGATATCATTATTCACCAGC-TTAAAGCCTGCTAGG-CC
*
39036392 GAAGCCCGATAAT-ATTATTCACCAGCTTAAAGCTTGCTAGGCC
1 GAAGCCCGAT-ATCATTATTCACCAGCTTAAAGCCTGCTAGGCC
*
39036435 GAGGCCCGAATATCA
1 GAAGCCCG-ATATCA
39036450 CATTTCGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
43 21 0.44
44 19 0.40
45 8 0.17
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (43 bp):
GAAGCCCGATATCATTATTCACCAGCTTAAAGCCTGCTAGGCC
Found at i:39039674 original size:43 final size:43
Alignment explanation
Indices: 39039626--39039751 Score: 180
Period size: 43 Copynumber: 2.9 Consensus size: 43
39039616 GTTATCGATA
* * *
39039626 TGTGATTACATGTAAGACCATGTCTAGGACATTGGCATTGTAT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
*
39039669 TGTGATTACGTGTAAGACCATGTCTGGGACATTGACATCGTAT
1 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * *
39039712 TATGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG
1 TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCG
39039752 ACATGTGATA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 74 1.00
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.33
Consensus pattern (43 bp):
TGTGATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:39044533 original size:43 final size:40
Alignment explanation
Indices: 39044467--39044580 Score: 111
Period size: 43 Copynumber: 2.7 Consensus size: 40
39044457 AGCTCGTACA
** * * *
39044467 ATGCCAATGTCCCAGATGTGGTCTTACATGTAATCAAATATC
1 ATGCC-ATGTCCCAGACATGGTCTTACACGAAATAAAATA-C
*
39044509 GATGCCATTGTCCCAGACAAGGTCTTACACGAAATAAAATAC
1 -ATGCCA-TGTCCCAGACATGGTCTTACACGAAATAAAATAC
*
39044551 AGTACCGATGTCCCAGACATGGTCTTACAC
1 A-TGCC-ATGTCCCAGACATGGTCTTACAC
39044581 ATAAATCTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 1 0.02
42 26 0.43
43 33 0.55
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (40 bp):
ATGCCATGTCCCAGACATGGTCTTACACGAAATAAAATAC
Found at i:39046427 original size:35 final size:33
Alignment explanation
Indices: 39046309--39046437 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 33
39046299 GACAAAATTA
**
39046309 TTTTAAAAAAACTAAACCCTAATTTAATTAATTT
1 TTTTAAAAACTCTAAACCCTAATTTAATT-ATTT
*
39046343 TCTTT-AAAACTTTAAACCCTAATTTAACTTATTT
1 T-TTTAAAAACTCTAAACCCTAATTTAA-TTATTT
* * * *
39046377 ATTTAAAACCCCTAAAACCTAATTTAATTATTT
1 TTTTAAAAACTCTAAACCCTAATTTAATTATTT
*
39046410 TTTTAAAAAAACTCTAAATCCTAATTTA
1 TTTT--AAAAACTCTAAACCCTAATTTA
39046438 TTTTTTAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
33 12 0.15
34 42 0.54
35 24 0.31
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.42
Consensus pattern (33 bp):
TTTTAAAAACTCTAAACCCTAATTTAATTATTT
Found at i:39046497 original size:34 final size:33
Alignment explanation
Indices: 39046452--39046552 Score: 150
Period size: 34 Copynumber: 3.0 Consensus size: 33
39046442 TTAAAATTCT
39046452 ACCCTACACCTAAATTATTTTAACAAAACTTTAA
1 ACCCTA-ACCTAAATTATTTTAACAAAACTTTAA
**
39046486 ACCCTGAACCTAAATTATTTTAACAAAACCCT-A
1 ACCCT-AACCTAAATTATTTTAACAAAACTTTAA
39046519 ACCCTAACCCTAAATTATTTTAACAAAACTTTAA
1 ACCCTAA-CCTAAATTATTTTAACAAAACTTTAA
39046553 CCTTAAACCT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
32 2 0.03
33 28 0.47
34 29 0.48
35 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.31
Consensus pattern (33 bp):
ACCCTAACCTAAATTATTTTAACAAAACTTTAA
Found at i:39046554 original size:33 final size:33
Alignment explanation
Indices: 39046452--39046554 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
39046442 TTAAAATTCT
39046452 ACCCT-ACACCTAAATTATTTTAACAAAACTTTAA
1 ACCCTAAC-CCTAAATTATTTTAACAAAACTTT-A
**
39046486 ACCCTGAA-CCTAAATTATTTTAACAAAACCCTA
1 ACCCT-AACCCTAAATTATTTTAACAAAACTTTA
39046519 ACCCTAACCCTAAATTATTTTAACAAAACTTTA
1 ACCCTAACCCTAAATTATTTTAACAAAACTTTA
39046552 ACC
1 ACC
39046555 TTAAACCTTG
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
32 2 0.03
33 32 0.52
34 27 0.44
36 1 0.02
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.30
Consensus pattern (33 bp):
ACCCTAACCCTAAATTATTTTAACAAAACTTTA
Found at i:39050826 original size:22 final size:22
Alignment explanation
Indices: 39050783--39050827 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
39050773 CACATTTGGG
* *
39050783 AAAATCTTATAATATTTTTAAA
1 AAAATCTTATAATAATTCTAAA
39050805 AAAATCTCTATAA-AATTCTAAA
1 AAAATCT-TATAATAATTCTAAA
39050827 A
1 A
39050828 CTTTAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATCTTATAATAATTCTAAA
Found at i:39052967 original size:13 final size:13
Alignment explanation
Indices: 39052949--39052975 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39052939 GCTCGGCAGG
39052949 GACACGCCCGTGT
1 GACACGCCCGTGT
39052962 GACACGCCCGTGT
1 GACACGCCCGTGT
39052975 G
1 G
39052976 CGATTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:39053887 original size:9 final size:9
Alignment explanation
Indices: 39053873--39053902 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
39053863 TATACATAGT
39053873 TTTTATTTC
1 TTTTATTTC
39053882 TTTTATTTC
1 TTTTATTTC
*
39053891 TTTTTTTTC
1 TTTTATTTC
39053900 TTT
1 TTT
39053903 AAGAACAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (9 bp):
TTTTATTTC
Found at i:39056612 original size:230 final size:230
Alignment explanation
Indices: 39056209--39056672 Score: 802
Period size: 230 Copynumber: 2.0 Consensus size: 230
39056199 GTCAACTGCT
* * *
39056209 ACTAAGATGTATTTATTCCCAAATGAACTGGGGAATGGGCCCATGAAATCGATACCCCAGACGTT
1 ACTAAGATGTATTTATTCCCAAATGAACTGGGGAATAGGCCCATGAAATCGATACCCCAAACGTC
* *
39056274 AAATATTTCACATGAAATCATATAGTTTTGAGGCATTTCATCACGTTTAGATATGTTACCTGTCC
66 AAATATTTCACATGAAAGCATATAGTTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
* *
39056339 GTTGGCATTTGTCACATAAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAATAAGAA
131 GTTGGCATTTGTCACATAAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
*
39056404 CCTGATTCAAGTACTTTGTGTGTGGTCTTAGTTCC
196 CCTGATTCAAGTACTTTGTGTGCGGTCTTAGTTCC
*
39056439 ACTAAGATGTATTTATTCCCAAATGAACTGGGGAATAGGCCTATGAAATCGATACCCCAAACGTC
1 ACTAAGATGTATTTATTCCCAAATGAACTGGGGAATAGGCCCATGAAATCGATACCCCAAACGTC
*
39056504 AAATATTTTACATGAAAGCATATAGTTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
66 AAATATTTCACATGAAAGCATATAGTTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
* * *
39056569 GTTGGCATTTGTCACATGAAGTAATATACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
131 GTTGGCATTTGTCACATAAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
*
39056634 CCTGATTCAAGTATTTTGTGTGCGGTCTTAGTTCC
196 CCTGATTCAAGTACTTTGTGTGCGGTCTTAGTTCC
39056669 ACTA
1 ACTA
39056673 TAGTGTCCTC
Statistics
Matches: 220, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
230 220 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (230 bp):
ACTAAGATGTATTTATTCCCAAATGAACTGGGGAATAGGCCCATGAAATCGATACCCCAAACGTC
AAATATTTCACATGAAAGCATATAGTTTTGAGGCATTTCATCACGTTTAGATATGTTACCTATCC
GTTGGCATTTGTCACATAAAGTAACACACCTGATAGCGTCTTTGAATAACGAAGGCCAAAAAAAA
CCTGATTCAAGTACTTTGTGTGCGGTCTTAGTTCC
Found at i:39066630 original size:24 final size:24
Alignment explanation
Indices: 39066603--39066654 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
39066593 TTTCTAGCAG
*
39066603 ATTTAGCATTTATCAGTATAATAT
1 ATTTAGCATTTATCAGCATAATAT
* *
39066627 ATTTAGCATTTGTTAGCATAATAT
1 ATTTAGCATTTATCAGCATAATAT
39066651 ATTT
1 ATTT
39066655 GACTTTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTTATCAGCATAATAT
Found at i:39068369 original size:24 final size:19
Alignment explanation
Indices: 39068320--39068364 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
39068310 CAATCAAATT
39068320 ATAAAATTTAATATTTTTA
1 ATAAAATTTAATATTTTTA
39068339 ATAAAATTTAATATTTTTA
1 ATAAAATTTAATATTTTTA
*
39068358 ATTAAAT
1 ATAAAAT
39068365 AAAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAAATTTAATATTTTTA
Found at i:39068389 original size:19 final size:19
Alignment explanation
Indices: 39068323--39068389 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
39068313 TCAAATTATA
*
39068323 AAATTTAATATTTTTAATA
1 AAATTTAATATTTTTAATT
39068342 AAATTTAATATTTTTAATT
1 AAATTTAATATTTTTAATT
** **
39068361 AAATAAAATATTTAAAATT
1 AAATTTAATATTTTTAATT
*
39068380 AAGTTTAATA
1 AAATTTAATA
39068390 AAATTTAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (19 bp):
AAATTTAATATTTTTAATT
Found at i:39069602 original size:8 final size:8
Alignment explanation
Indices: 39069589--39069617 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39069579 TTTGGATATA
39069589 TATATAGT
1 TATATAGT
39069597 TATATAGT
1 TATATAGT
39069605 TATATAGT
1 TATATAGT
39069613 TATAT
1 TATAT
39069618 GGTACATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (8 bp):
TATATAGT
Found at i:39073699 original size:29 final size:29
Alignment explanation
Indices: 39073666--39073753 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
39073656 AATGTATTTC
39073666 AATATTTTCAATAAATTTTATTATTAACA
1 AATATTTTCAATAAATTTTATTATTAACA
* *
39073695 AATA-TTTGAATTAAA---TA-T-TTAA-T
1 AATATTTTCAA-TAAATTTTATTATTAACA
*
39073718 AATATTTTCAA-CAATCTTTATTATTAACA
1 AATATTTTCAATAAAT-TTTATTATTAACA
39073747 AATATTT
1 AATATTT
39073754 GAATTAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 18
0.66 0.07 0.26
Matches are distributed among these distances:
22 2 0.04
23 4 0.09
24 9 0.20
25 1 0.02
26 4 0.09
27 1 0.02
28 9 0.20
29 15 0.33
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.48
Consensus pattern (29 bp):
AATATTTTCAATAAATTTTATTATTAACA
Found at i:39074185 original size:19 final size:19
Alignment explanation
Indices: 39074161--39074229 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
39074151 ATTATATTTT
39074161 ATCATAAAAATTGTTAAAA
1 ATCATAAAAATTGTTAAAA
* *
39074180 ATCATAAAAAATATTAAAA
1 ATCATAAAAATTGTTAAAA
* *
39074199 TTGATAAAAATTCG-TAAAA
1 ATCATAAAAATT-GTTAAAA
* *
39074218 CTTATAAAAATT
1 ATCATAAAAATT
39074230 ATAAAATTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 41 1.00
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (19 bp):
ATCATAAAAATTGTTAAAA
Found at i:39074208 original size:10 final size:9
Alignment explanation
Indices: 39074164--39074240 Score: 64
Period size: 9 Copynumber: 8.2 Consensus size: 9
39074154 ATATTTTATC
39074164 ATAAAAATT
1 ATAAAAATT
* *
39074173 GTTAAAAATC
1 -ATAAAAATT
*
39074183 ATAAAAAAT
1 ATAAAAATT
*
39074192 ATTAAAATT
1 ATAAAAATT
39074201 GATAAAAATT
1 -ATAAAAATT
* *
39074211 CGTAAAACTT
1 -ATAAAAATT
39074221 ATAAAAATT
1 ATAAAAATT
*
39074230 ATAAAATTT
1 ATAAAAATT
39074239 AT
1 AT
39074241 TATAAAGTTA
Statistics
Matches: 52, Mismatches: 14, Indels: 3
0.75 0.20 0.04
Matches are distributed among these distances:
9 30 0.58
10 22 0.42
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (9 bp):
ATAAAAATT
Found at i:39075245 original size:22 final size:21
Alignment explanation
Indices: 39075199--39075252 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
39075189 ATTAATCATA
*
39075199 TTTAT-ACTTTTTTTATGTATC
1 TTTATAAC-TTTTTTATGAATC
39075220 -TTATAACTTTTTTATGAATC
1 TTTATAACTTTTTTATGAATC
39075240 TTTTATAA-TTTTT
1 -TTTATAACTTTTT
39075253 AAAAGTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 16 0.55
21 7 0.24
22 6 0.21
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (21 bp):
TTTATAACTTTTTTATGAATC
Found at i:39075301 original size:18 final size:16
Alignment explanation
Indices: 39075269--39075339 Score: 54
Period size: 18 Copynumber: 4.1 Consensus size: 16
39075259 TTATAGAAAG
39075269 TTTTTAATATTTTTTA
1 TTTTTAATATTTTTTA
39075285 TTTTTAATATATCTTTTAA
1 TTTTTAATAT-T-TTTT-A
*
39075304 GTTTTT-ATGATTTTTAA
1 -TTTTTAAT-ATTTTTTA
*
39075321 TTTTTTTATAGTTTTTTA
1 -TTTTTAATA-TTTTTTA
39075339 T
1 T
39075340 GAGAAATAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 10 0.22
17 9 0.20
18 15 0.33
19 4 0.09
20 7 0.16
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.70
Consensus pattern (16 bp):
TTTTTAATATTTTTTA
Found at i:39085716 original size:19 final size:19
Alignment explanation
Indices: 39085692--39085728 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
39085682 GGCAAAAATT
*
39085692 AAATACTATTAAATTAATA
1 AAATACTATTAAAATAATA
39085711 AAATACTATTAAAATAAT
1 AAATACTATTAAAATAAT
39085729 TATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATACTATTAAAATAATA
Found at i:39095490 original size:16 final size:16
Alignment explanation
Indices: 39095466--39095504 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
39095456 TTTCATTAAG
*
39095466 AAAACCAGTTAAACCA
1 AAAATCAGTTAAACCA
39095482 AAAATCAGTTAAACCA
1 AAAATCAGTTAAACCA
39095498 AAAATCA
1 AAAATCA
39095505 TGCTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (16 bp):
AAAATCAGTTAAACCA
Done.