Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 146 of 160
Found at i:27933478 original size:22 final size:22
Alignment explanation
Indices: 27933450--27933493 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
27933440 CATTTTTCTT
27933450 CTTCTATCTATATATTACCTCA
1 CTTCTATCTATATATTACCTCA
27933472 CTTCTATCTATATATTACCTCA
1 CTTCTATCTATATATTACCTCA
27933494 ATGTGGGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (22 bp):
CTTCTATCTATATATTACCTCA
Found at i:27948697 original size:9 final size:9
Alignment explanation
Indices: 27948685--27948709 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
27948675 TCTCAGTCAG
27948685 GAAATCATT
1 GAAATCATT
27948694 GAAATCATT
1 GAAATCATT
27948703 GAAATCA
1 GAAATCA
27948710 AAGCCATGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.28
Consensus pattern (9 bp):
GAAATCATT
Found at i:27949160 original size:26 final size:25
Alignment explanation
Indices: 27949130--27949187 Score: 98
Period size: 26 Copynumber: 2.3 Consensus size: 25
27949120 AAATAATAAT
*
27949130 AAAAATTATTATAATTATGATTGAAA
1 AAAAATTATTATAATTACGATT-AAA
27949156 AAAAATTATTATAATTACGATTAAA
1 AAAAATTATTATAATTACGATTAAA
27949181 AAAAATT
1 AAAAATT
27949188 TAATAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (25 bp):
AAAAATTATTATAATTACGATTAAA
Found at i:27950153 original size:2 final size:2
Alignment explanation
Indices: 27950146--27950170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27950136 TAATTAGGAC
27950146 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
27950171 GCATGAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:27955284 original size:3 final size:3
Alignment explanation
Indices: 27955276--27955322 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
27955266 TTATAACTGT
27955276 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
27955323 GTACGGTACG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27960940 original size:9 final size:9
Alignment explanation
Indices: 27960926--27960959 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
27960916 TTTGGTATTT
27960926 TTTATTTTA
1 TTTATTTTA
27960935 TTTA-TTTA
1 TTTATTTTA
27960943 TTTATTTTA
1 TTTATTTTA
*
27960952 TGTATTTT
1 TTTATTTT
27960960 TTTTGCATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (9 bp):
TTTATTTTA
Found at i:27960948 original size:17 final size:16
Alignment explanation
Indices: 27960920--27960961 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
27960910 CCGTTCTTTG
27960920 GTATTTTTTATTTTAT
1 GTATTTTTTATTTTAT
*
27960936 TTATTTATTTATTTTAT
1 GTATTT-TTTATTTTAT
27960953 GTATTTTTT
1 GTATTTTTT
27960962 TTGCATGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (16 bp):
GTATTTTTTATTTTAT
Found at i:27961175 original size:7 final size:7
Alignment explanation
Indices: 27961159--27961196 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
27961149 ATTTATTTTC
*
27961159 AAATAAA
1 AAATATA
27961166 AAATATA
1 AAATATA
27961173 AAATATA
1 AAATATA
27961180 AAAT-TA
1 AAATATA
27961186 AAATATA
1 AAATATA
27961193 AAAT
1 AAAT
27961197 TTTGGAATTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATATA
Found at i:27961189 original size:13 final size:13
Alignment explanation
Indices: 27961159--27961197 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
27961149 ATTTATTTTC
*
27961159 AAATAAAAAATATA
1 AAATATAAAAT-TA
27961173 AAATATAAAATTA
1 AAATATAAAATTA
27961186 AAATATAAAATT
1 AAATATAAAATT
27961198 TTGGAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATAAAATTA
Found at i:27973365 original size:42 final size:42
Alignment explanation
Indices: 27973256--27973593 Score: 361
Period size: 42 Copynumber: 8.0 Consensus size: 42
27973246 ATTGTCGAGG
* * *
27973256 AGCAATTTATTATTTCAAAGTTTTGTTACCTCTATTTAGATG-
1 AGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGA-GA
*
27973298 AGC-ATTTA-TTTTTCAAAGTTTTGTTGCCTCTATTTAGAGA
1 AGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGA
* *
27973338 AGTAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGG
1 AGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGA
* *
27973380 AGCATTTTA-TTTTTCAAAGTTTTGTTGCCTCTATTTAGA-A
1 AGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGA
27973420 GAGCAATTTATTTTCTT-AAAGTTCTGTTGCCTCTATTTAGA-A
1 -AGCAATTTATTTT-TTCAAAGTTCTGTTGCCTCTATTTAGAGA
** * * ** *
27973462 GAGCAATCCATTTTTCCCAAAATAATGTTGCCTTTATTTAGATG-
1 -AGCAATTTATTTTT-TCAAAGTTCTGTTGCCTCTATTTAGA-GA
* *
27973506 AGCAATTTATTTTTCTCTAAAGTTGTGTTGTCTCTATTTAGA-A
1 AGCAATTTATTTTT-TC-AAAGTTCTGTTGCCTCTATTTAGAGA
*
27973549 GAGCAATTTATTTTTTTCAAAATTCTGTTGCCTCTATTTAGAGA
1 -AGCAATTTA-TTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGA
27973593 A
1 A
27973594 AGATTGCCTC
Statistics
Matches: 252, Mismatches: 29, Indels: 29
0.81 0.09 0.09
Matches are distributed among these distances:
39 1 0.00
40 30 0.12
41 48 0.19
42 79 0.31
43 58 0.23
44 31 0.12
45 5 0.02
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (42 bp):
AGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGA
Found at i:27973554 original size:87 final size:82
Alignment explanation
Indices: 27973255--27973592 Score: 419
Period size: 83 Copynumber: 4.0 Consensus size: 82
27973245 GATTGTCGAG
* * * * *
27973255 GAGCAATTTATTATTTCAAAGTTTTGTTACCTCTATTTAGATGAGC-ATTTATTTTTCAAAGTTT
1 GAGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAAGAGCAATTTATTTTTCAAAATTT
27973319 TGTTGCCTCTATTTAGA
66 TGTTGCCTCTATTTAGA
* * * *
27973336 GAAGTAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAGGAGCATTTTATTTTTCAAAGTT
1 G-AGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAAGAGCAATTTATTTTTCAAAATT
27973401 TTGTTGCCTCTATTTAGAA
65 TTGTTGCCTCTATTTAG-A
**
27973420 GAGCAATTTATTTTCTT-AAAGTTCTGTTGCCTCTATTTAGAAGAGCAATCCATTTTTCCCAAAA
1 GAGCAATTTATTTT-TTCAAAGTTCTGTTGCCTCTATTTAGAAGAGCAATTTATTTTT--CAAAA
** *
27973484 TAATGTTGCCTTTATTTAGA
63 TTTTGTTGCCTCTATTTAGA
* *
27973504 TGAGCAATTTATTTTTCTCTAAAGTTGTGTTGTCTCTATTTAGAAGAGCAATTTATTTTTTTCAA
1 -GAGCAATTTATTTTT-TC-AAAGTTCTGTTGCCTCTATTTAGAAGAGCAATTTA--TTTTTCAA
*
27973569 AATTCTGTTGCCTCTATTTAGA
61 AATTTTGTTGCCTCTATTTAGA
27973591 GA
1 GA
27973593 AAGATTGCCT
Statistics
Matches: 223, Mismatches: 22, Indels: 19
0.84 0.08 0.07
Matches are distributed among these distances:
81 1 0.00
82 40 0.18
83 81 0.36
84 6 0.03
85 35 0.16
86 2 0.01
87 53 0.24
89 5 0.02
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (82 bp):
GAGCAATTTATTTTTTCAAAGTTCTGTTGCCTCTATTTAGAAGAGCAATTTATTTTTCAAAATTT
TGTTGCCTCTATTTAGA
Found at i:27973854 original size:6 final size:6
Alignment explanation
Indices: 27973843--27973901 Score: 102
Period size: 6 Copynumber: 10.0 Consensus size: 6
27973833 TAGAATGATC
*
27973843 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT ATTTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
27973891 AATTTT -ATTTT
1 AATTTT AATTTT
27973902 CTTGGTTTCT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
AATTTT
Found at i:27974395 original size:17 final size:16
Alignment explanation
Indices: 27974373--27974411 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
27974363 TAGAGAGAGA
27974373 AAGAGAGAAAAGAAGGG
1 AAGAGAGAAAAGAA-GG
* *
27974390 AAGAGAGAGAAGGAGG
1 AAGAGAGAAAAGAAGG
27974406 AAGAGA
1 AAGAGA
27974412 ATTCTAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (16 bp):
AAGAGAGAAAAGAAGG
Found at i:27974688 original size:4 final size:4
Alignment explanation
Indices: 27974674--27974705 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
27974664 CTTTGGTATT
27974674 TTTA TTTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT
27974706 TATGTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:27974828 original size:24 final size:27
Alignment explanation
Indices: 27974781--27974835 Score: 89
Period size: 25 Copynumber: 2.1 Consensus size: 27
27974771 AATGAATATT
27974781 AATTATCAAATGATGAAATTTATA-AA
1 AATTATCAAATGATGAAATTTATATAA
27974807 AATT-TCAAATGAT-AAATTTATATAA
1 AATTATCAAATGATGAAATTTATATAA
27974832 AATT
1 AATT
27974836 CTTAGGTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
24 9 0.32
25 15 0.54
26 4 0.14
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (27 bp):
AATTATCAAATGATGAAATTTATATAA
Found at i:27983222 original size:19 final size:18
Alignment explanation
Indices: 27983188--27983223 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
27983178 AATTTTAACT
*
27983188 TCAAACTTTAAGTCCAAC
1 TCAAACTTTAAATCCAAC
27983206 TCAAACTTTACAATCCAA
1 TCAAACTTTA-AATCCAA
27983224 ACAAACAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.28, G:0.03, T:0.28
Consensus pattern (18 bp):
TCAAACTTTAAATCCAAC
Found at i:27990161 original size:50 final size:51
Alignment explanation
Indices: 27990095--27990292 Score: 199
Period size: 50 Copynumber: 4.0 Consensus size: 51
27990085 GTTTCGAGAA
**
27990095 AAGATTAAGATTTTTAAAGTCATTGAGCCTCTGCTTAGAAG-AGTTTTTTTT
1 AAGATTAA-ATTTTTAAAGTCATTGAGCCTCTGCTTAGAAGAAGCCTTTTTT
* ** *
27990146 TAGATTAAATTTTTAAAGTTGTTGAGCCTCTACTTAG-AGAAGCCTTTTTT
1 AAGATTAAATTTTTAAAGTCATTGAGCCTCTGCTTAGAAGAAGCCTTTTTT
* * * *
27990196 AAGATTAAATTTTTAAAGCCATTGAACCTCTGCTTAG-AGAA-ACTTTTTC
1 AAGATTAAATTTTTAAAGTCATTGAGCCTCTGCTTAGAAGAAGCCTTTTTT
* * ** * * *
27990245 AAGATAAAATTTTTAAAATTTTTGAGCTTCTG-TTTGAAGAAGTCTTTT
1 AAGATTAAATTTTTAAAGTCATTGAGCCTCTGCTTAGAAGAAGCCTTTT
27990293 AAATTTGCAA
Statistics
Matches: 121, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
48 3 0.02
49 37 0.31
50 74 0.61
51 7 0.06
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.42
Consensus pattern (51 bp):
AAGATTAAATTTTTAAAGTCATTGAGCCTCTGCTTAGAAGAAGCCTTTTTT
Found at i:27990916 original size:27 final size:25
Alignment explanation
Indices: 27990873--27990928 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
27990863 AAAGCTTTTT
*
27990873 ATCAAAAAACCCAAAACCTAAAAAAAA
1 ATCAAAAAACACAAAA-C-AAAAAAAA
*
27990900 ATCAAACAAACAC-AAACAAAATAAA
1 ATCAAA-AAACACAAAACAAAAAAAA
27990925 ATCA
1 ATCA
27990929 CAGTCCCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 11 0.42
26 1 0.04
27 9 0.35
28 5 0.19
ACGTcount: A:0.70, C:0.21, G:0.00, T:0.09
Consensus pattern (25 bp):
ATCAAAAAACACAAAACAAAAAAAA
Found at i:27991787 original size:31 final size:32
Alignment explanation
Indices: 27991750--27991816 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
27991740 TGTAATGAAA
*
27991750 AAAGAATAAAGAAAATAT-TAAAA-AAAATAAT
1 AAAGAATAAACAAAATATATAAAATAAAA-AAT
*
27991781 AAAGAATAAACAGAATATGATAAAATAAAAAAT
1 AAAGAATAAACAAAATAT-ATAAAATAAAAAAT
27991814 AAA
1 AAA
27991817 ATCATAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 16 0.52
33 11 0.35
34 4 0.13
ACGTcount: A:0.73, C:0.01, G:0.07, T:0.18
Consensus pattern (32 bp):
AAAGAATAAACAAAATATATAAAATAAAAAAT
Found at i:28005990 original size:27 final size:26
Alignment explanation
Indices: 28005960--28006012 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
28005950 CTTAAAAATT
28005960 ATATTAAATAAAAAATTTATAATTTAA
1 ATATTAAATAAAAAATTT-TAATTTAA
* * *
28005987 ATATTATATTAAAAATTTTACTTTAA
1 ATATTAAATAAAAAATTTTAATTTAA
28006013 CAATCATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
ATATTAAATAAAAAATTTTAATTTAA
Found at i:28006966 original size:123 final size:124
Alignment explanation
Indices: 28006743--28006982 Score: 294
Period size: 123 Copynumber: 1.9 Consensus size: 124
28006733 GAGAATAGGG
* *
28006743 TTATTTAAGGTATTTCTTGCTAAAAATACCTTTAATAATCTCTTAGTAAAAAAATTTAATGGGAT
1 TTATTTAAGGTATTTCTTGCTAAAAATACCTTGAATAATCTC-TAGTAAAAAAATTTAAGGGGAT
** **
28006808 TATTGAAGGCCTTTTTGTCATAAATGCCTTCAATAA-CCCTATTCAATTTGTTGTATAAGA
65 TATTGAAAACCTTTTTGTCATAAAAACCTTCAATAATCCC-ATTCAATTTGTTGTATAAGA
* *
28006868 TTATTTAAGGTATTTTTTGATTAAAAATACCTTGAATAATC-C-A-TAAAAAAA-TTACGAGGGG
1 TTATTTAAGGTATTTCTTG-CTAAAAATACCTTGAATAATCTCTAGTAAAAAAATTTA--AGGGG
* *
28006929 ATTATTGAAAACATTTTTTGTCA-AAAAACCTTGAATAATCCCATTCAATTTGTT
63 ATTATTGAAAAC-CTTTTTGTCATAAAAACCTTCAATAATCCCATTCAATTTGTT
28006983 TTCTGGCCAA
Statistics
Matches: 100, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
121 3 0.03
122 8 0.08
123 39 0.39
124 12 0.12
125 19 0.19
126 19 0.19
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (124 bp):
TTATTTAAGGTATTTCTTGCTAAAAATACCTTGAATAATCTCTAGTAAAAAAATTTAAGGGGATT
ATTGAAAACCTTTTTGTCATAAAAACCTTCAATAATCCCATTCAATTTGTTGTATAAGA
Found at i:28010720 original size:19 final size:18
Alignment explanation
Indices: 28010682--28010717 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
28010672 TAACAGTTAA
28010682 AAAATAGATTAAATATTT
1 AAAATAGATTAAATATTT
* *
28010700 AAAATATATTTAATATTT
1 AAAATAGATTAAATATTT
28010718 TAATTAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
AAAATAGATTAAATATTT
Found at i:28011064 original size:20 final size:20
Alignment explanation
Indices: 28011041--28011087 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
28011031 AAATATTATA
* *
28011041 TTAATTAATAAATTTATAAT
1 TTAAATAATAAATTTAAAAT
* *
28011061 TTAAATATTAATTTTAAAAT
1 TTAAATAATAAATTTAAAAT
28011081 TTAAATA
1 TTAAATA
28011088 TCATATTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAAATAATAAATTTAAAAT
Found at i:28011102 original size:21 final size:20
Alignment explanation
Indices: 28011058--28011102 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
28011048 ATAAATTTAT
* **
28011058 AATTTAAATATTAATTTTAA
1 AATTTAAATATCAATTACAA
28011078 AATTTAAATATCATATTACAA
1 AATTTAAATATCA-ATTACAA
28011099 AATT
1 AATT
28011103 GTATTATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (20 bp):
AATTTAAATATCAATTACAA
Found at i:28012312 original size:68 final size:69
Alignment explanation
Indices: 28012240--28012371 Score: 174
Period size: 69 Copynumber: 1.9 Consensus size: 69
28012230 TGATGTTTCA
* **
28012240 TTTTTTACACCAACCAAAACTTTACTGCAAATATGACAAATTACCCACTTTACCTAAAAGAAATC
1 TTTTTTACACCAACAAAAACTTTAAAGCAAATATGACAAATTACCCACTTTACCTAAAAGAAATC
28012305 ATTT
66 ATTT
* * * ** * *
28012309 TTTTTTCCACTAACAAAAAGTTTAAAGCAAATATGACCCATTACCCACTTTGCTTAAAAGAAA
1 TTTTTTACACCAACAAAAACTTTAAAGCAAATATGACAAATTACCCACTTTACCTAAAAGAAA
28012372 AATTATTCAA
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
69 53 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.31
Consensus pattern (69 bp):
TTTTTTACACCAACAAAAACTTTAAAGCAAATATGACAAATTACCCACTTTACCTAAAAGAAATC
ATTT
Found at i:28013657 original size:18 final size:17
Alignment explanation
Indices: 28013616--28013657 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28013606 AATATGATAT
* *
28013616 AAAGATAAAATATTAAA
1 AAAGATAAAAAATAAAA
28013633 AAA-ATAAAAAATAAAA
1 AAAGATAAAAAATAAAA
28013649 ATAAGATAA
1 A-AAGATAA
28013658 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 12 0.57
17 5 0.24
18 4 0.19
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (17 bp):
AAAGATAAAAAATAAAA
Found at i:28013759 original size:18 final size:18
Alignment explanation
Indices: 28013738--28013788 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
28013728 TAATATGAAT
28013738 TATAATATATAATTTTTA
1 TATAATATATAATTTTTA
*
28013756 TATAA-ATTATTAATATTTTT
1 TATAATA-TA-TAAT-TTTTA
28013776 TATAATAT-TAATT
1 TATAATATATAATT
28013789 CATGAATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
17 2 0.07
18 11 0.39
19 4 0.14
20 10 0.36
21 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TATAATATATAATTTTTA
Found at i:28018309 original size:17 final size:17
Alignment explanation
Indices: 28018277--28018310 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28018267 GTCTTTGTTC
* *
28018277 TTTAATTTTTTTTTTTT
1 TTTAATTTCTTCTTTTT
28018294 TTTAATTTCTTCTTTTT
1 TTTAATTTCTTCTTTTT
28018311 CTTCTTCAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTAATTTCTTCTTTTT
Found at i:28030670 original size:3 final size:3
Alignment explanation
Indices: 28030656--28030685 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
28030646 AACTTTTTTA
28030656 ATT ATAT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT AT
28030686 CATAATCACG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:28032990 original size:48 final size:48
Alignment explanation
Indices: 28032934--28033029 Score: 156
Period size: 48 Copynumber: 2.0 Consensus size: 48
28032924 CTACTATCAC
* * *
28032934 ATTTTTACACAGCTTCTGGGAAGAAGAAGTTTGATTTGGATTTGATTA
1 ATTTTTACACAGCTTCTAGAAAGAAGAACTTTGATTTGGATTTGATTA
*
28032982 ATTTTTACACAGCTTCTAGAAAGATGAACTTTGATTTGGATTTGATTA
1 ATTTTTACACAGCTTCTAGAAAGAAGAACTTTGATTTGGATTTGATTA
28033030 TTTGGATTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (48 bp):
ATTTTTACACAGCTTCTAGAAAGAAGAACTTTGATTTGGATTTGATTA
Found at i:28033434 original size:24 final size:23
Alignment explanation
Indices: 28033403--28033447 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
28033393 ATATCATATT
28033403 AAATATTTAATTTAAAAATAATA
1 AAATATTTAATTTAAAAATAATA
* *
28033426 AAATAATTTTATTTAAATATAA
1 AAAT-ATTTAATTTAAAAATAA
28033448 AATTATAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATTTAATTTAAAAATAATA
Found at i:28033968 original size:8 final size:8
Alignment explanation
Indices: 28033957--28034016 Score: 57
Period size: 8 Copynumber: 7.0 Consensus size: 8
28033947 TTTATTTAAG
28033957 AATAATTT
1 AATAATTT
28033965 AATAATTTT
1 AATAA-TTT
28033974 AATAATTT
1 AATAATTT
*
28033982 ATTAATTT
1 AATAATTT
*
28033990 TATAAATATT
1 AAT-AAT-TT
28034000 AAATAATTT
1 -AATAATTT
*
28034009 AAAAATTT
1 AATAATTT
28034017 TTGTAAATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 23 0.53
9 13 0.30
10 5 0.12
11 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AATAATTT
Found at i:28033979 original size:17 final size:17
Alignment explanation
Indices: 28033957--28033991 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
28033947 TTTATTTAAG
28033957 AATAATTTAATAATTTT
1 AATAATTTAATAATTTT
*
28033974 AATAATTTATTAATTTT
1 AATAATTTAATAATTTT
28033991 A
1 A
28033992 TAAATATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
AATAATTTAATAATTTT
Found at i:28034015 original size:27 final size:28
Alignment explanation
Indices: 28033974--28034026 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
28033964 TAATAATTTT
**
28033974 AATAATTTATTAA-TTTTATAAATATTA
1 AATAATTTAAAAATTTTTATAAATATTA
*
28034001 AATAATTTAAAAATTTTTGTAAATAT
1 AATAATTTAAAAATTTTTATAAATAT
28034027 AATTTTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (28 bp):
AATAATTTAAAAATTTTTATAAATATTA
Found at i:28035079 original size:2 final size:2
Alignment explanation
Indices: 28035072--28035105 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28035062 TGTGAGCTCT
*
28035072 TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28035106 ACTAAAGGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28035320 original size:28 final size:28
Alignment explanation
Indices: 28035278--28035334 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
28035268 AGAAGCACCT
*
28035278 TCACTATTTTGATATTTGCCATGTACCC
1 TCACTATTTTCATATTTGCCATGTACCC
*
28035306 TCACTATTTTCATATTTTCCATGTACCC
1 TCACTATTTTCATATTTGCCATGTACCC
28035334 T
1 T
28035335 AGGGAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.07, T:0.46
Consensus pattern (28 bp):
TCACTATTTTCATATTTGCCATGTACCC
Found at i:28047815 original size:2 final size:2
Alignment explanation
Indices: 28047808--28047832 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28047798 ATTTACTCGT
28047808 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
28047833 TTAGGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28057940 original size:3 final size:3
Alignment explanation
Indices: 28057932--28057956 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28057922 AAGGCTTAGT
28057932 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
28057957 ATTAAGTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:28060357 original size:29 final size:29
Alignment explanation
Indices: 28060313--28060385 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
28060303 TTTTTTTCAG
*
28060313 TAAGGTTTTATGTTTTT-ATCCTAT-TTAAA
1 TAAGTTTTTAT-TTTTTGAT-CTATATTAAA
*
28060342 TAAGTTTTTATTTTTTGATTTATAATTAAA
1 TAAGTTTTTATTTTTTGATCTAT-ATTAAA
*
28060372 TGAGTTTTTATTTT
1 TAAGTTTTTATTTT
28060386 AAACAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 8 0.21
29 12 0.32
30 18 0.47
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.60
Consensus pattern (29 bp):
TAAGTTTTTATTTTTTGATCTATATTAAA
Found at i:28072080 original size:20 final size:22
Alignment explanation
Indices: 28072030--28072081 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 22
28072020 TGTTTTATTG
28072030 TTATATATTATTTTAATAAAAAT
1 TTATATA-TATTTTAATAAAAAT
*
28072053 TT-TA-ATATATTTAA-ATAAAT
1 TTATATATAT-TTTAATAAAAAT
28072073 TTATATATA
1 TTATATATA
28072082 AAATAATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 10 0.40
21 8 0.32
22 5 0.20
23 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTATATATATTTTAATAAAAAT
Found at i:28074547 original size:2 final size:2
Alignment explanation
Indices: 28074540--28074573 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28074530 AAACATTAGA
28074540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28074574 CAAACACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28079480 original size:17 final size:18
Alignment explanation
Indices: 28079458--28079499 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
28079448 TTTAAAGTCT
28079458 TTAAATATATATAATTG-
1 TTAAATATATATAATTGA
*
28079475 TTAAAT-TTTATAATTGA
1 TTAAATATATATAATTGA
28079492 TTAAATAT
1 TTAAATAT
28079500 GAGTATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 9 0.41
17 12 0.55
18 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTAAATATATATAATTGA
Found at i:28079530 original size:17 final size:17
Alignment explanation
Indices: 28079458--28079530 Score: 53
Period size: 17 Copynumber: 4.3 Consensus size: 17
28079448 TTTAAAGTCT
*
28079458 TTAAATATATATAA-TTG
1 TTAAAT-TATATAATTTA
* *
28079475 TTAAATTTTATAATTGA
1 TTAAATTATATAATTTA
*
28079492 TTAAA-TATGAGT-ATTCA
1 TTAAATTAT-A-TAATTTA
*
28079509 ATAAATTATATAATTTA
1 TTAAATTATATAATTTA
28079526 TTAAA
1 TTAAA
28079531 CTTTTACGTC
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
16 9 0.21
17 30 0.70
18 4 0.09
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (17 bp):
TTAAATTATATAATTTA
Found at i:28080008 original size:22 final size:22
Alignment explanation
Indices: 28079964--28080008 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
28079954 GGAAAAGAGT
* * **
28079964 TAATTTTAAAAAAATAATTAAA
1 TAATTTGAAAAAAAAAAAAAAA
28079986 TAATTTGAAAAAAAAAAAAAAA
1 TAATTTGAAAAAAAAAAAAAAA
28080008 T
1 T
28080009 CCCATACAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
TAATTTGAAAAAAAAAAAAAAA
Found at i:28081157 original size:26 final size:26
Alignment explanation
Indices: 28081115--28081176 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
28081105 ATATGATAAA
28081115 ATAATATTATTTAATTTAATCATATT
1 ATAATATTATTTAATTTAATCATATT
* * *
28081141 ATTATATTATATT-ATTTTATCTTATT
1 ATAATATTAT-TTAATTTAATCATATT
28081167 ATAATATTAT
1 ATAATATTAT
28081177 GTACCAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 29 0.94
27 2 0.06
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (26 bp):
ATAATATTATTTAATTTAATCATATT
Found at i:28089622 original size:70 final size:70
Alignment explanation
Indices: 28089509--28089645 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 70
28089499 CATACATGTG
* * * *
28089509 TGTTTATAATGTTACAATTTATGACTTACTCATGGGTATTTGTTTGGTTTTGGAACAATCTAGAT
1 TGTTTATAATATTACAATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTAGAT
28089574 GAGTT
66 GAGTT
* * *
28089579 TGTTTATGATATTACGATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTGGAT
1 TGTTTATAATATTACAATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTAGAT
28089644 GA
66 GA
28089646 ACTTTTCATG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (70 bp):
TGTTTATAATATTACAATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTAGAT
GAGTT
Found at i:28101848 original size:21 final size:21
Alignment explanation
Indices: 28101805--28101851 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
28101795 TTTGTTTAGT
28101805 AAAAAATTGATTGGTCAACTA
1 AAAAAATTGATTGGTCAACTA
* *
28101826 AAAATAATTTATTGTTCAA-TA
1 AAAA-AATTGATTGGTCAACTA
28101847 AAAAA
1 AAAAA
28101852 TGAGACTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 10 0.43
22 12 0.52
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (21 bp):
AAAAAATTGATTGGTCAACTA
Found at i:28101990 original size:18 final size:18
Alignment explanation
Indices: 28101967--28102130 Score: 82
Period size: 18 Copynumber: 9.2 Consensus size: 18
28101957 AATTTTACTT
28101967 ATAAATTATATTATATTA
1 ATAAATTATATTATATTA
28101985 AT-AA--ATA--ATATT-
1 ATAAATTATATTATATTA
*
28101997 AT--ATTATAGTATATTA
1 ATAAATTATATTATATTA
* *
28102013 ATAAA-AATATTA-ATAA
1 ATAAATTATATTATATTA
* *
28102029 ATAATGTTATAATATATTA
1 ATAA-ATTATATTATATTA
28102048 ATAAATAATATTATAATATATTA
1 ATAAAT--TA-TAT--TATATTA
* *
28102071 ATAAATCATATAATATTA
1 ATAAATTATATTATATTA
28102089 ATAAATCATATATTA-A-TA
1 ATAAAT--TATATTATATTA
*
28102107 AGTAATATTATAATATATTA
1 A-TAA-ATTATATTATATTA
28102127 ATAA
1 ATAA
28102131 TAATATAAAG
Statistics
Matches: 111, Mismatches: 14, Indels: 41
0.67 0.08 0.25
Matches are distributed among these distances:
11 1 0.01
12 2 0.02
13 8 0.07
15 8 0.07
16 9 0.08
17 7 0.06
18 30 0.27
19 15 0.14
20 15 0.14
21 3 0.03
23 13 0.12
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (18 bp):
ATAAATTATATTATATTA
Found at i:28101997 original size:23 final size:23
Alignment explanation
Indices: 28101967--28102088 Score: 123
Period size: 23 Copynumber: 5.6 Consensus size: 23
28101957 AATTTTACTT
28101967 ATAA-ATTATATTATATTAATAA
1 ATAATATTATATTATATTAATAA
*
28101989 ATAATATTATATTATAGT-AT-A
1 ATAATATTATATTATATTAATAA
* *
28102010 TTAATA--A-A-AATATTAATAA
1 ATAATATTATATTATATTAATAA
* *
28102029 ATAATGTTATAATATATTAATAA
1 ATAATATTATATTATATTAATAA
*
28102052 ATAATATTATAATATATTAATAA
1 ATAATATTATATTATATTAATAA
* *
28102075 ATCATATAATATTA
1 ATAATATTATATTA
28102089 ATAAATCATA
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
17 4 0.05
18 3 0.04
19 6 0.07
21 7 0.09
22 7 0.09
23 55 0.67
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAATATTATATTATATTAATAA
Found at i:28102046 original size:63 final size:64
Alignment explanation
Indices: 28101972--28102094 Score: 178
Period size: 63 Copynumber: 1.9 Consensus size: 64
28101962 TACTTATAAA
* * *
28101972 TTATATTATATTAATAAATAATATTATATTATAGTATATTAAT-A-AAAATATTAATAAATAATG
1 TTATAATATATTAATAAATAATATTATAATATAGTA-ATAAATCATAAAATATTAATAAATAATG
* *
28102035 TTATAATATATTAATAAATAATATTATAATATATTAATAAATCATATAATATTAATAAAT
1 TTATAATATATTAATAAATAATATTATAATATAGTAATAAATCATAAAATATTAATAAAT
28102095 CATATATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 5 0.09
63 34 0.64
64 14 0.26
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (64 bp):
TTATAATATATTAATAAATAATATTATAATATAGTAATAAATCATAAAATATTAATAAATAATG
Found at i:28102055 original size:15 final size:15
Alignment explanation
Indices: 28101978--28102114 Score: 83
Period size: 15 Copynumber: 9.2 Consensus size: 15
28101968 TAAATTATAT
28101978 TATATTAATAAAT-A
1 TATATTAATAAATAA
* *
28101992 -ATATT-ATATTATAG
1 TATATTAATA-AATAA
28102006 TATATTAAT-AA-AA
1 TATATTAATAAATAA
28102019 -ATATTAATAAATAA
1 TATATTAATAAATAA
* *
28102033 TGT-TATAATATATTAA
1 TATAT-TAATA-AATAA
* *
28102049 TA-AATAATATTATAA
1 TATATTAATA-AATAA
28102064 TATATTAATAAATCATA
1 TATATTAATAAAT-A-A
*
28102081 TAATATTAATAAATCA
1 T-ATATTAATAAATAA
*
28102097 TATATTAATAAGTAA
1 TATATTAATAAATAA
28102112 TAT
1 TAT
28102115 TATAATATAT
Statistics
Matches: 94, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
12 11 0.12
13 10 0.11
14 4 0.04
15 39 0.41
16 16 0.17
17 2 0.02
18 12 0.13
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (15 bp):
TATATTAATAAATAA
Found at i:28102144 original size:23 final size:23
Alignment explanation
Indices: 28102096--28102144 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
28102086 TTAATAAATC
* *
28102096 ATATATTAATAAGTAATATTATA
1 ATATATTAATAAGTAATATAAGA
28102119 ATATATTAATAA-TAATATAAAGA
1 ATATATTAATAAGTAATAT-AAGA
28102142 ATA
1 ATA
28102145 ATAAATAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 6 0.26
23 17 0.74
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
ATATATTAATAAGTAATATAAGA
Found at i:28102147 original size:56 final size:55
Alignment explanation
Indices: 28101978--28102151 Score: 186
Period size: 56 Copynumber: 3.0 Consensus size: 55
28101968 TAAATTATAT
* **
28101978 TATATTAATAAATAATATTATATTATAGTATATTAATAAAAATATTAATAAATAATGTTATAA
1 TATATTAATAAATAATA-T-TA-TA-A-TATATTAATAATAATA-TAA-AAATAAT-AAATAA
* * * *
28102041 TATATTAATAAATAATATTATAATATATTAATAAATCATATAATATTAATAAATCA
1 TATATTAATAAATAATATTATAATATATTAAT-AATAATATAAAAATAATAAATAA
*
28102097 TATATTAATAAGTAATATTATAATATATTAATAATAATATAAAGAATAATAAATA
1 TATATTAATAAATAATATTATAATATATTAATAATAATATAAA-AATAATAAATA
28102152 GTTTTATTTT
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
55 9 0.09
56 43 0.44
57 5 0.05
58 12 0.12
59 6 0.06
60 2 0.02
61 2 0.02
62 1 0.01
63 17 0.18
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (55 bp):
TATATTAATAAATAATATTATAATATATTAATAATAATATAAAAATAATAAATAA
Found at i:28102243 original size:15 final size:16
Alignment explanation
Indices: 28102223--28102257 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28102213 TATAATTATT
*
28102223 TTTTAAT-ATTAATAA
1 TTTTAATAATAAATAA
28102238 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
28102254 TTTT
1 TTTT
28102258 TACTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:28103342 original size:23 final size:23
Alignment explanation
Indices: 28103315--28103368 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
28103305 TTAATTCCTT
28103315 TTAAATTACAATAAT-ACAAAAAA
1 TTAAATTACAA-AATCACAAAAAA
*
28103338 TTAAAATT-TAAAATCACAAAAAA
1 TT-AAATTACAAAATCACAAAAAA
*
28103361 ATAAATTA
1 TTAAATTA
28103369 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
22 8 0.31
23 13 0.50
24 5 0.19
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (23 bp):
TTAAATTACAAAATCACAAAAAA
Found at i:28111954 original size:70 final size:70
Alignment explanation
Indices: 28111841--28111977 Score: 211
Period size: 70 Copynumber: 2.0 Consensus size: 70
28111831 CATACATGTG
* * * *
28111841 TGTTTATAATGTTACAATTTATGACTTACTCATGGGTATTTGTTTGGTTTTGGAACAATCTAGAT
1 TGTTTATAATATTACAATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTAGAT
28111906 GAGTT
66 GAGTT
* * *
28111911 TGTTTATGATATTACGATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTGGAT
1 TGTTTATAATATTACAATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTAGAT
28111976 GA
66 GA
28111978 ACTTTTCATG
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.45
Consensus pattern (70 bp):
TGTTTATAATATTACAATTTATGACTTACTCATCGGCATTTGTTTGGTTTTAGAACAATCTAGAT
GAGTT
Found at i:28124339 original size:23 final size:23
Alignment explanation
Indices: 28124309--28124430 Score: 123
Period size: 23 Copynumber: 5.6 Consensus size: 23
28124299 AATTTTACTT
28124309 ATAA-ATTATATTATATTAATAA
1 ATAATATTATATTATATTAATAA
*
28124331 ATAATATTATATTATAGT-AT-A
1 ATAATATTATATTATATTAATAA
* *
28124352 TTAATA--A-A-AATATTAATAA
1 ATAATATTATATTATATTAATAA
* *
28124371 ATAATGTTATAATATATTAATAA
1 ATAATATTATATTATATTAATAA
*
28124394 ATAATATTATAATATATTAATAA
1 ATAATATTATATTATATTAATAA
* *
28124417 ATCATATAATATTA
1 ATAATATTATATTA
28124431 ATAAATCATA
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
17 4 0.05
18 3 0.04
19 6 0.07
21 7 0.09
22 7 0.09
23 55 0.67
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (23 bp):
ATAATATTATATTATATTAATAA
Found at i:28124388 original size:63 final size:64
Alignment explanation
Indices: 28124314--28124436 Score: 178
Period size: 63 Copynumber: 1.9 Consensus size: 64
28124304 TACTTATAAA
* * *
28124314 TTATATTATATTAATAAATAATATTATATTATAGTATATTAAT-A-AAAATATTAATAAATAATG
1 TTATAATATATTAATAAATAATATTATAATATAGTA-ATAAATCATAAAATATTAATAAATAATG
* *
28124377 TTATAATATATTAATAAATAATATTATAATATATTAATAAATCATATAATATTAATAAAT
1 TTATAATATATTAATAAATAATATTATAATATAGTAATAAATCATAAAATATTAATAAAT
28124437 CATATATTAA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 5 0.09
63 34 0.64
64 14 0.26
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.44
Consensus pattern (64 bp):
TTATAATATATTAATAAATAATATTATAATATAGTAATAAATCATAAAATATTAATAAATAATG
Found at i:28124480 original size:15 final size:15
Alignment explanation
Indices: 28124320--28124456 Score: 83
Period size: 15 Copynumber: 9.2 Consensus size: 15
28124310 TAAATTATAT
28124320 TATATTAATAAAT-A
1 TATATTAATAAATAA
* *
28124334 -ATATT-ATATTATAG
1 TATATTAATA-AATAA
28124348 TATATTAAT-AA-AA
1 TATATTAATAAATAA
28124361 -ATATTAATAAATAA
1 TATATTAATAAATAA
* *
28124375 TGT-TATAATATATTAA
1 TATAT-TAATA-AATAA
* *
28124391 TA-AATAATATTATAA
1 TATATTAATA-AATAA
28124406 TATATTAATAAATCATA
1 TATATTAATAAAT-A-A
*
28124423 TAATATTAATAAATCA
1 T-ATATTAATAAATAA
*
28124439 TATATTAATAAGTAA
1 TATATTAATAAATAA
28124454 TAT
1 TAT
28124457 TATAATATAT
Statistics
Matches: 94, Mismatches: 15, Indels: 27
0.69 0.11 0.20
Matches are distributed among these distances:
12 11 0.12
13 10 0.11
14 4 0.04
15 39 0.41
16 16 0.17
17 2 0.02
18 12 0.13
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.42
Consensus pattern (15 bp):
TATATTAATAAATAA
Found at i:28124579 original size:17 final size:17
Alignment explanation
Indices: 28124503--28124585 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 17
28124493 TAGTTTTATT
*
28124503 TTAAGTATTTTTT-ATA
1 TTAATTATTTTTTAATA
* *
28124519 TTAACGTAATATTTTAATA
1 TTAA--TTATTTTTTAATA
* *
28124538 TTAAATATTATTATTAAAA
1 TTAATTATT-TT-TTAATA
28124557 TATAATTATTTTTTAATA
1 T-TAATTATTTTTTAATA
*
28124575 TTAATAATTTT
1 TTAATTATTTT
28124586 AATAATAAAT
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
16 4 0.08
17 11 0.22
18 14 0.27
19 15 0.29
20 7 0.14
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAATTATTTTTTAATA
Found at i:28124587 original size:15 final size:16
Alignment explanation
Indices: 28124567--28124601 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28124557 TATAATTATT
*
28124567 TTTTAAT-ATTAATAA
1 TTTTAATAATAAATAA
28124582 TTTTAATAATAAATAA
1 TTTTAATAATAAATAA
28124598 TTTT
1 TTTT
28124602 TACTATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAATAATAAATAA
Found at i:28141347 original size:30 final size:30
Alignment explanation
Indices: 28141311--28141369 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
28141301 ATTTGAGCTA
*
28141311 GTTTTGTACAATTTATTTGTTATTTAATTG
1 GTTTTGTACAATTTATTTATTATTTAATTG
*
28141341 GTTTTGTATAATTTATTTATTATTTAATT
1 GTTTTGTACAATTTATTTATTATTTAATT
28141370 AATTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (30 bp):
GTTTTGTACAATTTATTTATTATTTAATTG
Found at i:28144908 original size:6 final size:6
Alignment explanation
Indices: 28144886--28144919 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
28144876 GGGTAAGAAG
28144886 TTGGAC TTGGAGC -TGGAC TTGGAC TTGGAC TTGG
1 TTGGAC TTGGA-C TTGGAC TTGGAC TTGGAC TTGG
28144920 CAGGTAGGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.04
6 24 0.92
7 1 0.04
ACGTcount: A:0.15, C:0.15, G:0.38, T:0.32
Consensus pattern (6 bp):
TTGGAC
Found at i:28145536 original size:12 final size:12
Alignment explanation
Indices: 28145519--28145568 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
28145509 AATTTATTAT
28145519 ATTTAAAAATAA
1 ATTTAAAAATAA
**
28145531 ATTTAAATTTAA
1 ATTTAAAAATAA
28145543 A-TTAAAAAT--
1 ATTTAAAAATAA
28145552 ATTTAAATAATAA
1 ATTTAAA-AATAA
28145565 ATTT
1 ATTT
28145569 TAGTCTATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
9 1 0.03
10 5 0.17
11 9 0.30
12 11 0.37
13 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTAAAAATAA
Found at i:28146887 original size:7 final size:7
Alignment explanation
Indices: 28146888--28146931 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
28146878 AAAACATAAA
*
28146888 AAAACAT
1 AAAATAT
28146895 AA-ATA-
1 AAAATAT
28146900 AAAATAT
1 AAAATAT
28146907 AAAATAT
1 AAAATAT
28146914 AAAATAT
1 AAAATAT
28146921 AAAATAT
1 AAAATAT
28146928 AAAA
1 AAAA
28146932 AAAATGCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
5 2 0.06
6 5 0.15
7 27 0.79
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATAT
Found at i:28147124 original size:8 final size:8
Alignment explanation
Indices: 28147113--28147142 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
28147103 AAAAACATAA
28147113 ATAAAAAT
1 ATAAAAAT
28147121 ATAAAAAT
1 ATAAAAAT
28147129 AT-AAAAT
1 ATAAAAAT
28147136 ATAAAAA
1 ATAAAAA
28147143 AGAAATGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (8 bp):
ATAAAAAT
Found at i:28147125 original size:29 final size:28
Alignment explanation
Indices: 28147080--28147134 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
28147070 TTTAAATCAG
28147080 ATAAATAAAAAACTAAAACATAAAAAAAC
1 ATAAATAAAAAACTAAAA-ATAAAAAAAC
*
28147109 ATAAATAAAAATA-TAAAAATATAAAA
1 ATAAATAAAAA-ACTAAAAATAAAAAA
28147135 TATAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 7 0.29
29 16 0.67
30 1 0.04
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.18
Consensus pattern (28 bp):
ATAAATAAAAAACTAAAAATAAAAAAAC
Found at i:28147134 original size:15 final size:14
Alignment explanation
Indices: 28147082--28147142 Score: 61
Period size: 15 Copynumber: 4.2 Consensus size: 14
28147072 TAAATCAGAT
28147082 AAATAAAAA-ACTAA
1 AAATAAAAATA-TAA
* * *
28147096 AACATAAAAAAACAT
1 AA-ATAAAAATATAA
28147111 AAATAAAAATATAA
1 AAATAAAAATATAA
28147125 AAATATAAAATATAA
1 AAATA-AAAATATAA
28147140 AAA
1 AAA
28147143 AGAAATGCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 16 0.41
15 22 0.56
16 1 0.03
ACGTcount: A:0.77, C:0.05, G:0.00, T:0.18
Consensus pattern (14 bp):
AAATAAAAATATAA
Found at i:28147242 original size:220 final size:214
Alignment explanation
Indices: 28146839--28147261 Score: 629
Period size: 220 Copynumber: 1.9 Consensus size: 214
28146829 TTCATTGACA
28146839 TGATTTATGATAAAAATTTAAATCAGATAAATAAAAACTAAAACATAAAAAAACATAAATAAAAA
1 TGATTTATGATAAAAATTTAAATCAGATAAATAAAAACTAAAACATAAAAAAACATAAATAAAAA
* *
28146904 TATAAAATATAAAATATAAAATATAAAAAAAATGCAAGAAATTTGACAATTAGGCTTAGAAATTT
66 TATAAAATATAAAATAT--AATATAAAAAAAATGCAAGAAATTGGACAATTAGGCTTAGAAATCT
28146969 GACAAAAAAAAATGCTCAAACTAAATAGGATGTTTACAACTGTCCCTCTTTGCACAGTTTTTGTG
129 GACAAAAAAAAATGCTCAAACTAAATAGGATGTTTACAACTGTCCCTCTTTGCACAGTTTTTGTG
28147034 -AACAAGATATGGATAACTAT
194 AAACAAGATATGGATAACTAT
28147054 TGATTTATGATAAAAATTTAAATCAGATAAATAAAAAACTAAAACATAAAAAAACATAAATAAAA
1 TGATTTATGATAAAAATTTAAATCAGATAAAT-AAAAACTAAAACATAAAAAAACATAAATAAAA
* *
28147119 ATATAAAAATATAAAATAT-A-A-AAAAGAAATGCAGGAAATTGGACAATTAGGCTTAGATCAAA
65 ATAT-AAAATATAAAATATAATATAAAAAAAATGCAAGAAATTGGACAATTAGGCTTAG---AAA
*** **
28147181 TCTGAGCACAATTGATTTGAGTCTCAAACTAAATAGGATGTTTACAACTGTCCCTCTTTGCACAG
126 TCTGA-CA-AAAAAAAAT--G-CTCAAACTAAATAGGATGTTTACAACTGTCCCTCTTTGCACAG
28147246 TTTTTGTGAAACAAGA
186 TTTTTGTGAAACAAGA
28147262 ATTGTGTAAA
Statistics
Matches: 188, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
212 32 0.17
213 1 0.01
214 1 0.01
215 39 0.21
216 38 0.20
217 18 0.10
219 1 0.01
220 51 0.27
221 7 0.04
ACGTcount: A:0.51, C:0.10, G:0.11, T:0.28
Consensus pattern (214 bp):
TGATTTATGATAAAAATTTAAATCAGATAAATAAAAACTAAAACATAAAAAAACATAAATAAAAA
TATAAAATATAAAATATAATATAAAAAAAATGCAAGAAATTGGACAATTAGGCTTAGAAATCTGA
CAAAAAAAAATGCTCAAACTAAATAGGATGTTTACAACTGTCCCTCTTTGCACAGTTTTTGTGAA
ACAAGATATGGATAACTAT
Found at i:28152951 original size:250 final size:251
Alignment explanation
Indices: 28152457--28152961 Score: 924
Period size: 250 Copynumber: 2.0 Consensus size: 251
28152447 AAGTTGGTTA
*
28152457 CACATAGGAAAATATTAGCACACTCACAGCACCTATAAATTGATACCAATTAATCATGCGTTATT
1 CACATAGGAAAAGATTAGCACACTCACAGCACCTATAAATTGATACCAATTAATCATGCGTTATT
28152522 CTTGGTATTAGATGAAATGGTTCTGATTTGAAATTTAATATTAATTCCTTTCATTTTTTGAAAAA
66 CTTGGTATTAGATGAAATGGTTCTGATTTGAAATTTAATATTAATTCCTTTCATTTTTTGAAAAA
28152587 AATAATTTTATTAAAACTCTTTATTTAAGAATATCGAAAAAATCTTTAAGTTAAAGAATTATCTT
131 AATAATTTTATTAAAACTCTTTATTTAAGAATATCGAAAAAATCTTTAAGTTAAAGAATTATCTT
28152652 AATATTTTTAATGTTTAGGCAGAACTTCAAAGATAACTTTTTTTACTAATATTCAC
196 AATATTTTTAATGTTTAGGCAGAACTTCAAAGATAACTTTTTTTACTAATATTCAC
* * *
28152708 CACATAGGAAAAGATTAGCGCCCTCACAGTACCTATAAATTGATACCAATTAATCATGCGTTATT
1 CACATAGGAAAAGATTAGCACACTCACAGCACCTATAAATTGATACCAATTAATCATGCGTTATT
*
28152773 CTTGGTATTGGATGAAATGGTT-TCGATTTGAAATTTAATATTAATTCCTTTCATTTTTTG-AAA
66 CTTGGTATTAGATGAAATGGTTCT-GATTTGAAATTTAATATTAATTCCTTTCATTTTTTGAAAA
* *
28152836 AAATAATTTTATTAAAATTCTTTATTTAAGAATATCGAGAAAATCTTTAAGTTAAAGAATTATCT
130 AAATAATTTTATTAAAACTCTTTATTTAAGAATATCGAAAAAATCTTTAAGTTAAAGAATTATCT
28152901 TAATATTTTTAATGTTTAGGCAGAACTTCAAAGATAACTTTTTTTACTAATATTCAC
195 TAATATTTTTAATGTTTAGGCAGAACTTCAAAGATAACTTTTTTTACTAATATTCAC
28152958 CACA
1 CACA
28152962 ATATTCCTTG
Statistics
Matches: 246, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
250 128 0.52
251 118 0.48
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.39
Consensus pattern (251 bp):
CACATAGGAAAAGATTAGCACACTCACAGCACCTATAAATTGATACCAATTAATCATGCGTTATT
CTTGGTATTAGATGAAATGGTTCTGATTTGAAATTTAATATTAATTCCTTTCATTTTTTGAAAAA
AATAATTTTATTAAAACTCTTTATTTAAGAATATCGAAAAAATCTTTAAGTTAAAGAATTATCTT
AATATTTTTAATGTTTAGGCAGAACTTCAAAGATAACTTTTTTTACTAATATTCAC
Found at i:28153145 original size:11 final size:11
Alignment explanation
Indices: 28153129--28153153 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
28153119 ATGTTTGTTA
28153129 TTTTATTTTAT
1 TTTTATTTTAT
28153140 TTTTATTTTAT
1 TTTTATTTTAT
28153151 TTT
1 TTT
28153154 AAGATAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:28154046 original size:10 final size:10
Alignment explanation
Indices: 28154028--28154056 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
28154018 GAATAAATTT
28154028 TAAAA-AATA
1 TAAAATAATA
28154037 TAAAATAATA
1 TAAAATAATA
28154047 TAAAATAATA
1 TAAAATAATA
28154057 AATTTTGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
TAAAATAATA
Found at i:28156073 original size:5 final size:5
Alignment explanation
Indices: 28156063--28156087 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
28156053 ATATGAAATT
28156063 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
28156088 CAACCAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:28156223 original size:14 final size:13
Alignment explanation
Indices: 28156204--28156266 Score: 54
Period size: 14 Copynumber: 4.6 Consensus size: 13
28156194 TTTGTAAAGG
28156204 AAAATTTTCTTTTT
1 AAAATTTT-TTTTT
28156218 AAAATTTTTTTTAT
1 AAAATTTTTTTT-T
** **
28156232 TTAATTTTTTTAG
1 AAAATTTTTTTTT
*
28156245 AAAATATATTTTTT
1 AAAAT-TTTTTTTT
28156259 AAAATTTT
1 AAAATTTT
28156267 AATTCTCCAA
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
13 9 0.24
14 28 0.76
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
AAAATTTTTTTTT
Found at i:28159323 original size:27 final size:27
Alignment explanation
Indices: 28159249--28159323 Score: 62
Period size: 27 Copynumber: 2.7 Consensus size: 27
28159239 TTACATAAAG
* * *
28159249 ATTAATTATTATATGTTAATAAATAATA
1 ATTATTTATTATTTATT-ATAAATAATA
* * * *
28159277 TTTATATT-TTAATAAATATAAATAATA
1 ATTAT-TTATTATTTATTATAAATAATA
28159304 ATTATTTATTATTTATTATA
1 ATTATTTATTATTTATTATA
28159324 CTTATTAAAA
Statistics
Matches: 34, Mismatches: 11, Indels: 5
0.68 0.22 0.10
Matches are distributed among these distances:
26 2 0.06
27 23 0.68
28 7 0.21
29 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
ATTATTTATTATTTATTATAAATAATA
Found at i:28160136 original size:20 final size:20
Alignment explanation
Indices: 28160111--28160151 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28160101 CAATCAATTC
28160111 TTCACATAAATCATTATCTT
1 TTCACATAAATCATTATCTT
28160131 TTCACATAAATCATTATCTT
1 TTCACATAAATCATTATCTT
28160151 T
1 T
28160152 AGTCTACTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (20 bp):
TTCACATAAATCATTATCTT
Found at i:28170071 original size:17 final size:18
Alignment explanation
Indices: 28170034--28170074 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28170024 TAATATGATA
* *
28170034 TAAAATTTATGAATAAAT
1 TAAAAATTAAGAATAAAT
28170052 TAAAAATTAAGAAT-AAT
1 TAAAAATTAAGAATAAAT
28170069 TAAAAA
1 TAAAAA
28170075 AAAAGTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (18 bp):
TAAAAATTAAGAATAAAT
Found at i:28172186 original size:13 final size:13
Alignment explanation
Indices: 28172170--28172195 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
28172160 TATTGACGTG
28172170 ATATAATTATTTT
1 ATATAATTATTTT
28172183 ATATAATTATTTT
1 ATATAATTATTTT
28172196 TTAACAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATAATTATTTT
Found at i:28172236 original size:27 final size:28
Alignment explanation
Indices: 28172191--28172246 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
28172181 TTATATAATT
28172191 ATTTTTTAACAATAATTAA-ATTCTTTTA
1 ATTTTTTAACAATAATTAATATT-TTTTA
* *
28172219 ATTTTTTCACAAT-TTTAATATTTTTTA
1 ATTTTTTAACAATAATTAATATTTTTTA
28172246 A
1 A
28172247 CAGGGACGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (28 bp):
ATTTTTTAACAATAATTAATATTTTTTA
Found at i:28173570 original size:2 final size:2
Alignment explanation
Indices: 28173563--28173596 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
28173553 GACATTCCTT
28173563 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28173597 CGGCAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28190581 original size:15 final size:15
Alignment explanation
Indices: 28190563--28190592 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28190553 ATGAGATTCT
28190563 ATACACCATGATTGG
1 ATACACCATGATTGG
28190578 ATACACCATGATTGG
1 ATACACCATGATTGG
28190593 TTTTGACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
ATACACCATGATTGG
Found at i:28201330 original size:18 final size:18
Alignment explanation
Indices: 28201309--28201351 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
28201299 TTGATTTGAG
28201309 ATTTGATTT-GAATTTAA
1 ATTTGATTTAGAATTTAA
*
28201326 TATTT-ATTTAGTATTTAA
1 -ATTTGATTTAGAATTTAA
28201344 ATTTGATT
1 ATTTGATT
28201352 ACAATTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
ATTTGATTTAGAATTTAA
Found at i:28213232 original size:16 final size:15
Alignment explanation
Indices: 28213209--28213252 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
28213199 TATATTATAT
28213209 TTTATATAAAAATTA
1 TTTATATAAAAATTA
*
28213224 TTTAT-TATAAATTA
1 TTTATATAAAAATTA
28213238 TATTAATATAAAAAT
1 T-TT-ATATAAAAAT
28213253 ATAAAATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 9 0.38
15 7 0.29
16 2 0.08
17 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTTATATAAAAATTA
Found at i:28218699 original size:1 final size:1
Alignment explanation
Indices: 28218695--28218729 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
28218685 TTGATATCTG
28218695 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
28218730 GAGGAACCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28224944 original size:17 final size:18
Alignment explanation
Indices: 28224899--28224945 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
28224889 AATAAATATG
28224899 CAAATGAAAAAAAATTTT
1 CAAATGAAAAAAAATTTT
*
28224917 CAAA-CAAAAAAAA-TTT
1 CAAATGAAAAAAAATTTT
*
28224933 CAAATGAGAAAAA
1 CAAATGAAAAAAA
28224946 TTGTAGTGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 7 0.28
17 14 0.56
18 4 0.16
ACGTcount: A:0.66, C:0.09, G:0.06, T:0.19
Consensus pattern (18 bp):
CAAATGAAAAAAAATTTT
Found at i:28225241 original size:14 final size:16
Alignment explanation
Indices: 28225211--28225244 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
28225201 TTTAAAAATT
28225211 AAATTAATTTATTTTA
1 AAATTAATTTATTTTA
28225227 AAATTAA-TT-TTTTA
1 AAATTAATTTATTTTA
28225241 AAAT
1 AAAT
28225245 CATTTGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 2 0.11
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATTAATTTATTTTA
Found at i:28227773 original size:9 final size:9
Alignment explanation
Indices: 28227754--28227784 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
28227744 GGTCCTCCCC
28227754 TCCCTTCCCT
1 TCCCTT-CCT
28227764 TCCCTTCCT
1 TCCCTTCCT
28227773 TCCCTTCCT
1 TCCCTTCCT
28227782 TCC
1 TCC
28227785 ATCGCTATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (9 bp):
TCCCTTCCT
Found at i:28227773 original size:14 final size:14
Alignment explanation
Indices: 28227751--28227784 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
28227741 GTGGGTCCTC
*
28227751 CCCTCCCTTCCCTT
1 CCCTTCCTTCCCTT
28227765 CCCTTCCTTCCCTT
1 CCCTTCCTTCCCTT
28227779 -CCTTCC
1 CCCTTCC
28227785 ATCGCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (14 bp):
CCCTTCCTTCCCTT
Found at i:28237523 original size:2 final size:2
Alignment explanation
Indices: 28237516--28237540 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28237506 GTGTTTCACC
28237516 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28237541 TAACAGCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28239159 original size:21 final size:21
Alignment explanation
Indices: 28239135--28239174 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28239125 TATATAAAAA
*
28239135 AAATTCTAA-ATGTTTAAATTC
1 AAATTCAAACATG-TTAAATTC
28239156 AAATTCAAACATGTTAAAT
1 AAATTCAAACATGTTAAAT
28239175 GTCACTCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
AAATTCAAACATGTTAAATTC
Found at i:28242110 original size:15 final size:18
Alignment explanation
Indices: 28242090--28242128 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
28242080 ACTTTTGGCA
28242090 ACAAAAG-A-AGACA-AG
1 ACAAAAGAACAGACACAG
28242105 ACAAAAGAACAGACACAG
1 ACAAAAGAACAGACACAG
28242123 ACAAAA
1 ACAAAA
28242129 CTTACATTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.33
16 1 0.05
17 5 0.24
18 8 0.38
ACGTcount: A:0.67, C:0.18, G:0.15, T:0.00
Consensus pattern (18 bp):
ACAAAAGAACAGACACAG
Found at i:28244118 original size:14 final size:14
Alignment explanation
Indices: 28244085--28244122 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
28244075 TGTAACAAAT
28244085 TATAATAAATTGATA
1 TATAAT-AATTGATA
28244100 TATAATAATT-ATA
1 TATAATAATTGATA
28244113 TAATAATAAT
1 T-ATAATAAT
28244123 GCATCAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 12 0.55
15 6 0.27
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
TATAATAATTGATA
Found at i:28245727 original size:24 final size:25
Alignment explanation
Indices: 28245700--28245752 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
28245690 TCCTAAAATT
28245700 ATATTTTTTAATATT-TAA-TATTTA
1 ATATTTTTT-ATATTATAATTATTTA
*
28245724 ATA-TTTTTATATTATAATTTTTTA
1 ATATTTTTTATATTATAATTATTTA
28245748 ATATT
1 ATATT
28245753 AAAAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.20
23 8 0.32
24 11 0.44
25 1 0.04
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (25 bp):
ATATTTTTTATATTATAATTATTTA
Found at i:28245741 original size:16 final size:16
Alignment explanation
Indices: 28245708--28245753 Score: 53
Period size: 15 Copynumber: 3.0 Consensus size: 16
28245698 TTATATTTTT
*
28245708 TAATA-TTTAATATT-
1 TAATATTTTTATATTA
28245722 TAATATTTTTATATTA
1 TAATATTTTTATATTA
28245738 TAAT-TTTTTAATATTA
1 TAATATTTTT-ATATTA
28245754 AAAATTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.18
15 13 0.46
16 10 0.36
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATATTTTTATATTA
Found at i:28245768 original size:38 final size:37
Alignment explanation
Indices: 28245697--28245768 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 37
28245687 ATATCCTAAA
* *
28245697 ATTATATTTTTTAATATTTAATATTTAATATTTTTAT
1 ATTATATTTTTTAATATTAAAAATTTAATATTTTTAT
28245734 ATTATAATTTTTTAATATTAAAAATTATAA-ATTTT
1 ATTAT-ATTTTTTAATATTAAAAATT-TAATATTTT
28245769 AAAATATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
37 5 0.16
38 23 0.74
39 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (37 bp):
ATTATATTTTTTAATATTAAAAATTTAATATTTTTAT
Found at i:28245980 original size:19 final size:20
Alignment explanation
Indices: 28245956--28246002 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
28245946 TACAGTACCT
*
28245956 TTCCTTTTGTGGGCCCC-AC
1 TTCCTTTTGTGGACCCCAAC
28245975 TTCC-TTTGTGGACCCCAAC
1 TTCCTTTTGTGGACCCCAAC
28245994 TTCTCTTTT
1 TTC-CTTTT
28246003 CTTCGTCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 11 0.46
19 9 0.38
20 1 0.04
21 3 0.12
ACGTcount: A:0.09, C:0.34, G:0.15, T:0.43
Consensus pattern (20 bp):
TTCCTTTTGTGGACCCCAAC
Found at i:28246579 original size:16 final size:15
Alignment explanation
Indices: 28246533--28246579 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
28246523 TGTTAATTTA
28246533 TTAAAATATAATCTATT
1 TTAAAATATAA--TATT
*
28246550 TTAAAA-ACAATATT
1 TTAAAATATAATATT
28246564 TTACAAATATAATATT
1 TTA-AAATATAATATT
28246580 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.27
15 3 0.12
16 10 0.38
17 6 0.23
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (15 bp):
TTAAAATATAATATT
Found at i:28249177 original size:18 final size:18
Alignment explanation
Indices: 28249139--28249178 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28249129 CGACCAACAG
*
28249139 CAACAACAACAAACGAAC
1 CAACAACAACAAACCAAC
* *
28249157 CAACAGCAACAAACCAGC
1 CAACAACAACAAACCAAC
28249175 CAAC
1 CAAC
28249179 TACAGGAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.38, G:0.07, T:0.00
Consensus pattern (18 bp):
CAACAACAACAAACCAAC
Found at i:28253633 original size:13 final size:13
Alignment explanation
Indices: 28253603--28253634 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
28253593 AATTTCGATT
28253603 AAATTTTAAATTA
1 AAATTTTAAATTA
*
28253616 TAATTTTAAATTA
1 AAATTTTAAATTA
28253629 AAATTT
1 AAATTT
28253635 GATTTTTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATTTTAAATTA
Found at i:28259120 original size:22 final size:20
Alignment explanation
Indices: 28259094--28259143 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
28259084 ATATATTAAT
28259094 ATTTATAAATTATTTAAATTTA
1 ATTTATAAA--ATTTAAATTTA
*
28259116 ATTTAAATAAAATTTAAATTTG
1 ATTT--ATAAAATTTAAATTTA
28259138 ATTTAT
1 ATTTAT
28259144 TTATTATTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 2 0.08
22 18 0.72
24 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTATAAAATTTAAATTTA
Found at i:28259173 original size:27 final size:26
Alignment explanation
Indices: 28259132--28259187 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
28259122 ATAAAATTTA
*
28259132 AATTTGATTTATTTA-TTATTGAATTG
1 AATTTGAATTATTTATTTATT-AATTG
28259158 AATTTGAATTATTTTATTTATTAATTG
1 AATTTGAATTA-TTTATTTATTAATTG
28259185 AAT
1 AAT
28259188 CAAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 10 0.37
27 12 0.44
28 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (26 bp):
AATTTGAATTATTTATTTATTAATTG
Found at i:28259202 original size:31 final size:30
Alignment explanation
Indices: 28259125--28259203 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
28259115 AATTTAAATA
* *
28259125 AAATTTAAATTTGATTTATTTATTATTGAATT
1 AAATTTAAATAT--TTTATTTATTATTGAATC
* *
28259157 GAATTTGAATTATTTTATTTATTAATTGAATC
1 AAATTT-AAATATTTTATTTATT-ATTGAATC
28259189 AAATTTAAATATTTT
1 AAATTTAAATATTTT
28259204 TTATATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 18 0.46
32 17 0.44
33 4 0.10
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (30 bp):
AAATTTAAATATTTTATTTATTATTGAATC
Found at i:28259251 original size:18 final size:19
Alignment explanation
Indices: 28259230--28259277 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
28259220 TAATTTATGA
28259230 ATTTAATTAAATTTTTA-T
1 ATTTAATTAAATTTTTATT
* *
28259248 ATTTAAATATATTTTTATT
1 ATTTAATTAAATTTTTATT
28259267 ATTTTAATTAA
1 A-TTTAATTAA
28259278 TAAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.62
19 2 0.08
20 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTAATTAAATTTTTATT
Found at i:28260845 original size:2 final size:2
Alignment explanation
Indices: 28260838--28260873 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28260828 TTCTTAGTTT
28260838 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28260874 GTTGAATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:28262206 original size:322 final size:322
Alignment explanation
Indices: 28261621--28262250 Score: 1098
Period size: 322 Copynumber: 2.0 Consensus size: 322
28261611 TTGGTTAATT
* *
28261621 CTTAATAACCTTCTTAATTATTCACATTGTCTTAAATTATATATGATTCAGTTTCACTAAAATAT
1 CTTAATAACCTTCTTAAATATTCACATCGTCTTAAATTATATATGATTCAGTTTCACTAAAATAT
* *
28261686 TGGGCATATTTATCTATTAAGTTATGCCTGACACAGGAACTCTTTTTGACGTTATCTGTCTTGGA
66 TGGGCACATTTATCTATTAAGTTATGCCTGACACAGAAACTCTTTTTGACGTTATCTGTCTTGGA
*
28261751 TTTTGTTTTGAAAATGTGGAAATTATTTTTAAAAATATTCCGAGTCAGTTCTTAAGAAATATTCT
131 TTTTGTTTTGAAAATGTGGAAATTATTTTTAAAAATATTCCAAGTCAGTTCTTAAGAAATATTCT
* * * *
28261816 CAGTAATTGGAATGTTGGACACTTCTTATAGTCTGAACAATGAATATCTTTCTTGCATCTGGAAA
196 CAATAATTGGAATGTTGGACACTTCTTATAGTCTGAACAATAAATATCTCTCTTGCAACTGGAAA
* *
28261881 TACATCTTCATTGAATTCTTTAACTTTTGCCTGCCATGTTCTTTTCCCTTTTGTGCTTTATG
261 TACATCTTCATTGAATTCTTTAACTTTTGCATGCCATGTTATTTTCCCTTTTGTGCTTTATG
* * * *
28261943 CTTAATAATCTTCTTAAATATTCAGATCGTTTTAAATTATATATGATTCAGTTTCACTAAAGTAT
1 CTTAATAACCTTCTTAAATATTCACATCGTCTTAAATTATATATGATTCAGTTTCACTAAAATAT
* * *
28262008 TGGGCACATTTATCTATTAAGTTATGCCTGACACTGAAACTCTTTTTGATGTTATGTGTCTTGGA
66 TGGGCACATTTATCTATTAAGTTATGCCTGACACAGAAACTCTTTTTGACGTTATCTGTCTTGGA
28262073 TTTTGTTTTGAAAATGTGGAAATTATTTTTAAAAATATTCCAAGTCAGTTCTTAAGAAATATTCT
131 TTTTGTTTTGAAAATGTGGAAATTATTTTTAAAAATATTCCAAGTCAGTTCTTAAGAAATATTCT
28262138 CAATAATTGGAATGTTGGACACTTCTTATAGTCTGAACAATAAATATCTCTCTTGCAACTGGAAA
196 CAATAATTGGAATGTTGGACACTTCTTATAGTCTGAACAATAAATATCTCTCTTGCAACTGGAAA
28262203 TACATCTTCATTGAATTCTTTAACTTTTGCATGCCATGTTATTTTCCC
261 TACATCTTCATTGAATTCTTTAACTTTTGCATGCCATGTTATTTTCCC
28262251 GCTTGTTCAA
Statistics
Matches: 290, Mismatches: 18, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
322 290 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (322 bp):
CTTAATAACCTTCTTAAATATTCACATCGTCTTAAATTATATATGATTCAGTTTCACTAAAATAT
TGGGCACATTTATCTATTAAGTTATGCCTGACACAGAAACTCTTTTTGACGTTATCTGTCTTGGA
TTTTGTTTTGAAAATGTGGAAATTATTTTTAAAAATATTCCAAGTCAGTTCTTAAGAAATATTCT
CAATAATTGGAATGTTGGACACTTCTTATAGTCTGAACAATAAATATCTCTCTTGCAACTGGAAA
TACATCTTCATTGAATTCTTTAACTTTTGCATGCCATGTTATTTTCCCTTTTGTGCTTTATG
Found at i:28266026 original size:25 final size:25
Alignment explanation
Indices: 28265998--28266049 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
28265988 GGGCAGTGGA
*
28265998 TTGTAAGCATAGCAAGTGATTTTCT
1 TTGTAAGCATAGCAAGTGATTGTCT
*
28266023 TTGTAATCATAGCAAGTGATTGTCT
1 TTGTAAGCATAGCAAGTGATTGTCT
28266048 TT
1 TT
28266050 ATTTAGTCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (25 bp):
TTGTAAGCATAGCAAGTGATTGTCT
Found at i:28273584 original size:13 final size:13
Alignment explanation
Indices: 28273568--28273592 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28273558 AAGTTTATTA
28273568 AAATAGTTAGTCC
1 AAATAGTTAGTCC
28273581 AAATAGTTAGTC
1 AAATAGTTAGTC
28273593 ATAGATTATA
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:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (13 bp):
AAATAGTTAGTCC
Found at i:28287013 original size:15 final size:15
Alignment explanation
Indices: 28286993--28287032 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28286983 TCGTTATGAT
28286993 TATTTATTTTTCACA
1 TATTTATTTTTCACA
* *
28287008 TATTTATTTATCTCA
1 TATTTATTTTTCACA
28287023 T-TTTATTTTT
1 TATTTATTTTT
28287033 TAATTATCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTATTTTTCACA
Found at i:28288955 original size:14 final size:14
Alignment explanation
Indices: 28288933--28288970 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
28288923 TAGTTTTATT
*
28288933 ATAATATTATAATTA
1 ATAA-ATTATAATAA
28288948 ATAAATTATAATAA
1 ATAAATTATAATAA
28288962 AT-AATTATA
1 ATAAATTATA
28288971 TAAGAATCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 11 0.50
15 4 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAAATTATAATAA
Found at i:28288956 original size:22 final size:22
Alignment explanation
Indices: 28288930--28288973 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28288920 AATTAGTTTT
*
28288930 ATTATAATATTATAATTA-ATAA
1 ATTATAATA-AATAATTATATAA
28288952 ATTATAATAAATAATTATATAA
1 ATTATAATAAATAATTATATAA
28288974 GAATCTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTATAATAAATAATTATATAA
Found at i:28290119 original size:11 final size:12
Alignment explanation
Indices: 28290103--28290145 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
28290093 ATCATATAAA
28290103 ATATTAT-ATTT
1 ATATTATAATTT
28290114 ATATTATAATTT
1 ATATTATAATTT
* *
28290126 ATATAAAAATTAT
1 ATATTATAATT-T
28290139 ATATTAT
1 ATATTAT
28290146 TTATTGATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
11 7 0.27
12 13 0.50
13 6 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATTATAATTT
Found at i:28290119 original size:31 final size:30
Alignment explanation
Indices: 28290079--28290155 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
28290069 AGAACTAATA
*
28290079 ATTTGTATTATTATATCATATAAAATATTAT
1 ATTTATATTATTATATCATATAAAA-ATTAT
* *
28290110 ATTTATATTATAAT-TTATATAAAAATTAT
1 ATTTATATTATTATATCATATAAAAATTAT
28290139 ATATTAT-TTATTGATAT
1 AT-TTATATTATT-ATAT
28290156 AAAAATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 11 0.28
30 15 0.38
31 13 0.33
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (30 bp):
ATTTATATTATTATATCATATAAAAATTAT
Found at i:28290159 original size:25 final size:25
Alignment explanation
Indices: 28290113--28290164 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
28290103 ATATTATATT
* *
28290113 TATATTATAATTTATATAAAAATTA
1 TATATTATAATTGATATAAAAAATA
*
28290138 TATATTATTTATTGATAT-AAAAATA
1 TATATTA-TAATTGATATAAAAAATA
28290163 TA
1 TA
28290165 AAAAATAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TATATTATAATTGATATAAAAAATA
Found at i:28290222 original size:16 final size:15
Alignment explanation
Indices: 28290190--28290224 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
28290180 TTTTTGTTAA
28290190 TATTTTAAATCATAT
1 TATTTTAAATCATAT
*
28290205 TATTTTAATATTATAT
1 TATTTTAA-ATCATAT
28290221 TATT
1 TATT
28290225 ATATCATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTTAAATCATAT
Found at i:28300891 original size:14 final size:15
Alignment explanation
Indices: 28300862--28300892 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28300852 AATTATTTCG
28300862 TAAAATAATATTTAT
1 TAAAATAATATTTAT
28300877 TAAAATAAT-TTTAT
1 TAAAATAATATTTAT
28300891 TA
1 TA
28300893 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATAATATTTAT
Found at i:28313549 original size:9 final size:9
Alignment explanation
Indices: 28313535--28313561 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28313525 CTGTTGAGCA
28313535 AAGCCAAAC
1 AAGCCAAAC
28313544 AAGCCAAAC
1 AAGCCAAAC
28313553 AAGCCAAAC
1 AAGCCAAAC
28313562 TCAACAACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.33, G:0.11, T:0.00
Consensus pattern (9 bp):
AAGCCAAAC
Found at i:28314943 original size:53 final size:53
Alignment explanation
Indices: 28314859--28314964 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
28314849 TTTACAAAAC
* *
28314859 TAGCTATTTTAAAGTTTTTAAATCTTGGTTTAAACTCCATATAGAAAAAGTAT
1 TAGCTATTTTAAAGTTTTTAAATCTTAGTTTAAACGCCATATAGAAAAAGTAT
28314912 TAGCTATTTTAAAGTTTTTAAATCTTAGTTTAAACGCCATATAGAAAAAGTAT
1 TAGCTATTTTAAAGTTTTTAAATCTTAGTTTAAACGCCATATAGAAAAAGTAT
28314965 CTAGAGATAC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.39, C:0.09, G:0.11, T:0.41
Consensus pattern (53 bp):
TAGCTATTTTAAAGTTTTTAAATCTTAGTTTAAACGCCATATAGAAAAAGTAT
Found at i:28335978 original size:32 final size:32
Alignment explanation
Indices: 28335937--28336000 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
28335927 AGATAGTAAG
28335937 ATAGTTTTTTAAGGTTTCAGGTATGTATTCCA
1 ATAGTTTTTTAAGGTTTCAGGTATGTATTCCA
*
28335969 ATAGTTTTTTAAGGTTTCATGTATGTATTCCA
1 ATAGTTTTTTAAGGTTTCAGGTATGTATTCCA
28336001 TAAAATATCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.17, T:0.48
Consensus pattern (32 bp):
ATAGTTTTTTAAGGTTTCAGGTATGTATTCCA
Found at i:28336556 original size:21 final size:21
Alignment explanation
Indices: 28336532--28336580 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
28336522 TGTACTGAAT
28336532 GGAAAATTTCAATGTTGGTAA
1 GGAAAATTTCAATGTTGGTAA
*
28336553 GGAAAATTTCAATTTTGGTAA
1 GGAAAATTTCAATGTTGGTAA
*
28336574 GTAAAAT
1 GGAAAAT
28336581 ATTATTCATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (21 bp):
GGAAAATTTCAATGTTGGTAA
Found at i:28352680 original size:3 final size:3
Alignment explanation
Indices: 28352653--28352701 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
28352643 TGGCAGTGGA
* * * * *
28352653 GAT GAG GAT GAT GAG GAC GAG GAT GAT GAC GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
28352701 G
1 G
28352702 GTGACGAAGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.04, G:0.41, T:0.22
Consensus pattern (3 bp):
GAT
Done.