Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 101 of 126
Found at i:19856978 original size:20 final size:21
Alignment explanation
Indices: 19856944--19856983 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
19856934 TTTTCTTTTT
19856944 TTTTTTTTTAGCAGGGTTTCAC
1 TTTTTTTTTA-CAGGGTTTCAC
*
19856966 TTTTTTTTT-CAGGTTTTC
1 TTTTTTTTTACAGGGTTTC
19856984 TCTGAAAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.10, C:0.12, G:0.15, T:0.62
Consensus pattern (21 bp):
TTTTTTTTTACAGGGTTTCAC
Found at i:19864765 original size:54 final size:55
Alignment explanation
Indices: 19864681--19864816 Score: 177
Period size: 54 Copynumber: 2.5 Consensus size: 55
19864671 ACCTTCTTAA
* * * *
19864681 AAGGATTATTTAAGTCATTTCTGTATGCCTTAAATGATCCTTTTATTT-T-TTTAT
1 AAGGATCATTTAAGGCATTTCTGTACGCCTTAAATGATCCTTTT-TTTATATATAT
*
19864735 AAGGATCATTTAAGGCATTTTTGTACGCCTTAAATGATCCTTTTTTTATATATAT
1 AAGGATCATTTAAGGCATTTCTGTACGCCTTAAATGATCCTTTTTTTATATATAT
* * *
19864790 AAGGATCATTTAACGTATTTCTATACG
1 AAGGATCATTTAAGGCATTTCTGTACG
19864817 TAGAAAATAA
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
53 3 0.04
54 41 0.58
55 27 0.38
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (55 bp):
AAGGATCATTTAAGGCATTTCTGTACGCCTTAAATGATCCTTTTTTTATATATAT
Found at i:19870743 original size:68 final size:63
Alignment explanation
Indices: 19870611--19870749 Score: 172
Period size: 68 Copynumber: 2.1 Consensus size: 63
19870601 GATGTTCATG
* ** * *
19870611 TTCAATTTTTTTGTACTAGTTAATTAAAGTTATTTATTTTTTTGGTGCTTTTATTGTTATCTT
1 TTCAATTTTTTTGTACTAGTCAATTAAAGTTATTTACCTTTTTGGTGCTTTTAATGTTACCTT
*
19870674 TTCAATTTTTTTGTACTAGTCAATTAAAGCTATGGCATTTACCTTTTTGGTGTTTTTAATGTTAC
1 TTCAATTTTTTTGTACTAGTCAATTAAAG-T-T---ATTTACCTTTTTGGTGCTTTTAATGTTAC
19870739 CTT
61 CTT
19870742 TTC-ATTTT
1 TTCAATTTT
19870750 GGTGACAAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
63 28 0.43
64 1 0.02
65 1 0.02
67 5 0.08
68 30 0.46
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.58
Consensus pattern (63 bp):
TTCAATTTTTTTGTACTAGTCAATTAAAGTTATTTACCTTTTTGGTGCTTTTAATGTTACCTT
Found at i:19873419 original size:12 final size:12
Alignment explanation
Indices: 19873402--19873426 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19873392 ATTTTTGTAA
19873402 GGTGAATAATAT
1 GGTGAATAATAT
19873414 GGTGAATAATAT
1 GGTGAATAATAT
19873426 G
1 G
19873427 TTTGCATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GGTGAATAATAT
Found at i:19873624 original size:42 final size:42
Alignment explanation
Indices: 19873578--19873820 Score: 222
Period size: 42 Copynumber: 5.8 Consensus size: 42
19873568 TCTATTATTA
* * *
19873578 TTCTTAATTGCTCAAATTTATAGTTAAGATTTTTTGTTGTTG
1 TTCTTAATTGCTCAAATTTATAGTTAGGGTTTTCTGTTGTTG
* * * *
19873620 TTCTTAATTGCTCAAATTTATA-TTTGAGATTTTCTATTGTTA
1 TTCTTAATTGCTCAAATTTATAGTTAG-GGTTTTCTGTTGTTG
* *
19873662 TTCTTAATTGCTTGAAA-TAATAGTTAGGGTTTTCTGTTGTTG
1 TTCTTAATTGC-TCAAATTTATAGTTAGGGTTTTCTGTTGTTG
* * * * * * * *
19873704 TCCTTAATTGGTTAAAATTATAGCTAGGGTTTTTTATTATTG
1 TTCTTAATTGCTCAAATTTATAGTTAGGGTTTTCTGTTGTTG
* * *
19873746 TTCTTAATTGCTCGAAA-TTAGAGTTAGGGTTTTCTGCTATTG
1 TTCTTAATTGCTC-AAATTTATAGTTAGGGTTTTCTGTTGTTG
* * *
19873788 TTCTTAATTACTCGAATTGATAGTTAGAGGTTT
1 TTCTTAATTGCTCAAATTTATAGTTAG-GGTTT
19873821 CTGCTATTTA
Statistics
Matches: 163, Mismatches: 31, Indels: 13
0.79 0.15 0.06
Matches are distributed among these distances:
41 8 0.05
42 140 0.86
43 15 0.09
ACGTcount: A:0.24, C:0.09, G:0.17, T:0.50
Consensus pattern (42 bp):
TTCTTAATTGCTCAAATTTATAGTTAGGGTTTTCTGTTGTTG
Found at i:19873651 original size:84 final size:83
Alignment explanation
Indices: 19873563--19873810 Score: 264
Period size: 84 Copynumber: 3.0 Consensus size: 83
19873553 TTTGATTTAT
* * *
19873563 GATTTTCTATTATTATTCTTAATTGCTCAAATTTATAGTTAAGATTTTTTGTTGTTGTTCTTAAT
1 GATTTTCTATTATTATTCTTAATTGCTCAAA-TTATAGTTAGGGTTTTCTGTTGTTGTTCTTAAT
* *
19873628 TGCTCAAATTTATA-TTTG
65 TGCTCAAATTTATAGCTAG
* * * *
19873646 AGATTTTCTATTGTTATTCTTAATTGCTTGAAATAATAGTTAGGGTTTTCTGTTGTTGTCCTTAA
1 -GATTTTCTATTATTATTCTTAATTGC-TCAAATTATAGTTAGGGTTTTCTGTTGTTGTTCTTAA
* * *
19873711 TTGGTTAAAATTATAGCTAG
64 TTGCTCAAATTTATAGCTAG
* * * * * *
19873731 GGTTTTTTATTATTGTTCTTAATTGCTCGAAATTAGAGTTAGGGTTTTCTGCTATTGTTCTTAAT
1 GATTTTCTATTATTATTCTTAATTGCTC-AAATTATAGTTAGGGTTTTCTGTTGTTGTTCTTAAT
* * *
19873796 TACTCGAATTGATAG
65 TGCTCAAATTTATAG
19873811 TTAGAGGTTT
Statistics
Matches: 133, Mismatches: 28, Indels: 6
0.80 0.17 0.04
Matches are distributed among these distances:
83 1 0.01
84 126 0.95
85 6 0.05
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.51
Consensus pattern (83 bp):
GATTTTCTATTATTATTCTTAATTGCTCAAATTATAGTTAGGGTTTTCTGTTGTTGTTCTTAATT
GCTCAAATTTATAGCTAG
Found at i:19884579 original size:40 final size:40
Alignment explanation
Indices: 19884280--19884744 Score: 250
Period size: 40 Copynumber: 11.1 Consensus size: 40
19884270 CAATGAGCAA
* * *
19884280 TTTATTTTTTCAAAGTC-ATGAAGCCTTTGTTTAGAGGAGCTTT
1 TTTA-TTTTTCAAAGTCGTTG-AGCCTCTGATTAGAGGAGC--T
** *
19884323 GTTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAGACAAGCCA
1 -TTTA-TTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAG-CT
* * * * * * *
19884366 TTTA-TTTTCAAAGTTGTGGTGCTTTTGA--AGAGCA-AT
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
* * * *
19884402 TTAATTTTTAAAAGTCGTGGTTA-CCTCTGTTTAGAGGAG-T
1 TTTATTTTTCAAAGTCGT--TGAGCCTCTGATTAGAGGAGCT
*
19884442 AATTTATTGTTTTCAAAGTCGCTGAGCCTCTGATTAGAGGAGCTTT
1 --TTTA-T-TTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC--T
* * * **
19884488 ATTTATTTTCTTTC-AATTCATTAAGCCTCTGATTAGAGGAATT
1 -TTTA--TT-TTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
* * * *
19884531 TTGTTTATTTTCAAAAGTCGTAGTTGCCTCTGTTTAGAGGAGCTTT
1 TT-TAT-TTTTC-AAAGTCGTTG-AGCCTCTGATTAGAGGAGC--T
* *
19884577 ATTTATTTTTCAAAGTC-TTGAGCCTCTGATTGGATGAGCT
1 -TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
*
19884617 ATTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCCA
1 -TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAG-CT
* * *
19884659 TTTA-GTTTCAAAGTCGTGGAGCCTCTGTTTAGAGGAGCTTT
1 TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC--T
19884700 GTTTATTTTACTCAAAGTCGTTGAGCCTCT-ACTTAGAGGAGCT
1 -TTTATTTT--TCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCT
19884743 TT
1 TT
19884745 AACCAAAATT
Statistics
Matches: 325, Mismatches: 61, Indels: 72
0.71 0.13 0.16
Matches are distributed among these distances:
36 3 0.01
37 11 0.03
38 8 0.02
39 1 0.00
40 73 0.22
41 28 0.09
42 34 0.10
43 28 0.09
44 63 0.19
45 64 0.20
46 10 0.03
47 2 0.01
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.42
Consensus pattern (40 bp):
TTTATTTTTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCT
Found at i:19884729 original size:85 final size:85
Alignment explanation
Indices: 19884444--19884742 Score: 263
Period size: 85 Copynumber: 3.5 Consensus size: 85
19884434 AGAGGAGTAA
* * * * *
19884444 TTTATTGTTTTCAAAGTCGCTGAGCCTCTGATTAGAGGAGCTTTATTTAT-TTTCTTTCAATTCA
1 TTTATT-TTCTCAAAGTCGTTGAGCCTCTGATTAGAGGAGC-TCATTTATGTTTC---AAAGTC-
** **
19884508 TTAAGCCTCTGATTAGAGGAATTTTG
60 TGGAGCCTCTGATTAGAGGAGCTTTG
* * * * * * *
19884534 TTTATTTTC-AAAAGTCGTAGTTGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCAAAGTCTTGA
1 TTTATTTTCTCAAAGTCGTTG-AGCCTCTGATTAGAGGAGC-TCATTTATGTTTCAAAGTCTGGA
* * *
19884598 GCCTCTGATTGGATGAGC--TA
64 GCCTCTGATTAGAGGAGCTTTG
19884618 TTTATTTT-TCAAAGTCGTTGAGCCTCTGATTAGAGGAGC-CATTTA-GTTTCAAAGTCGTGGAG
1 TTTATTTTCTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTCATTTATGTTTCAAAGTC-TGGAG
*
19884680 CCTCTGTTTAGAGGAGCTTTG
65 CCTCTGATTAGAGGAGCTTTG
19884701 TTTATTTTACTCAAAGTCGTTGAGCCTCT-ACTTAGAGGAGCT
1 TTTATTTT-CTCAAAGTCGTTGAGCCTCTGA-TTAGAGGAGCT
19884743 TTAACCAAAA
Statistics
Matches: 174, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
80 10 0.06
81 23 0.13
83 26 0.15
84 19 0.11
85 29 0.17
86 17 0.10
87 4 0.02
88 8 0.05
89 28 0.16
90 10 0.06
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (85 bp):
TTTATTTTCTCAAAGTCGTTGAGCCTCTGATTAGAGGAGCTCATTTATGTTTCAAAGTCTGGAGC
CTCTGATTAGAGGAGCTTTG
Found at i:19884970 original size:10 final size:10
Alignment explanation
Indices: 19884932--19884978 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
19884922 CTATGAGTTC
19884932 ATTTT-TTTA
1 ATTTTATTTA
*
19884941 ATTTAATTTA
1 ATTTTATTTA
*
19884951 ATTTGATTTA
1 ATTTTATTTA
*
19884961 ATTTTTTTTA
1 ATTTTATTTA
*
19884971 CTTTTATT
1 ATTTTATT
19884979 ATTATTATGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
9 4 0.13
10 27 0.87
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (10 bp):
ATTTTATTTA
Found at i:19885019 original size:21 final size:22
Alignment explanation
Indices: 19884971--19885054 Score: 79
Period size: 22 Copynumber: 3.9 Consensus size: 22
19884961 ATTTTTTTTA
19884971 CTTTTA-TTAT-TATT-ATGATT
1 CTTTTATTTATCTATTAAT-ATT
*
19884991 ATTATTATTTATCTATTAATATT
1 CTT-TTATTTATCTATTAATATT
*
19885014 -TTTTATTTATCTAATT-ATTTT
1 CTTTTATTTATCT-ATTAATATT
*
19885035 CTTTTAGTTATCTATTAATA
1 CTTTTATTTATCTATTAATA
19885055 AATTATTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.04
21 20 0.38
22 22 0.42
23 7 0.13
24 2 0.04
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.63
Consensus pattern (22 bp):
CTTTTATTTATCTATTAATATT
Found at i:19885039 original size:22 final size:22
Alignment explanation
Indices: 19884995--19885054 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
19884985 ATGATTATTA
19884995 TTATTTATCT-ATTAATATTTT
1 TTATTTATCTAATTAATATTTT
*
19885016 TTATTTATCTAATT-ATTTTCTT
1 TTATTTATCTAATTAATATT-TT
*
19885038 TTAGTTATCT-ATTAATA
1 TTATTTATCTAATTAATA
19885055 AATTATTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTTATCTAATTAATATTTT
Found at i:19885232 original size:14 final size:14
Alignment explanation
Indices: 19885213--19885241 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
19885203 TTAGAAACTG
19885213 TTCTGATCAATCCC
1 TTCTGATCAATCCC
19885227 TTCTGATCAATCCC
1 TTCTGATCAATCCC
19885241 T
1 T
19885242 ATAAATAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.34, G:0.07, T:0.38
Consensus pattern (14 bp):
TTCTGATCAATCCC
Found at i:19885555 original size:18 final size:19
Alignment explanation
Indices: 19885522--19885560 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
19885512 TTTTGTTTAG
19885522 AGAAAAAGAAGAGAAA-AA
1 AGAAAAAGAAGAGAAAGAA
19885540 AGAAAAA-AAGAGGAAAGAA
1 AGAAAAAGAAGA-GAAAGAA
19885559 AG
1 AG
19885561 CAATCTACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.21
18 11 0.58
19 4 0.21
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (19 bp):
AGAAAAAGAAGAGAAAGAA
Found at i:19885832 original size:3 final size:3
Alignment explanation
Indices: 19885826--19885904 Score: 124
Period size: 3 Copynumber: 26.0 Consensus size: 3
19885816 TTTTTCTTAT
*
19885826 TTA TTA TTA TTA TTA TT- TCTT TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
19885871 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
19885905 GGTTAGAATA
Statistics
Matches: 72, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
2 1 0.01
3 67 0.93
4 4 0.06
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:19885945 original size:12 final size:12
Alignment explanation
Indices: 19885929--19885973 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
19885919 GATATTCCTT
19885929 ATTTTATTTTTA
1 ATTTTATTTTTA
* *
19885941 TTTTTATTCTTA
1 ATTTTATTTTTA
19885953 ATTTTA--TTTA
1 ATTTTATTTTTA
19885963 ATTTTATTTTT
1 ATTTTATTTTT
19885974 TTAAATGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTTATTTTTA
Found at i:19886045 original size:57 final size:57
Alignment explanation
Indices: 19885982--19886216 Score: 275
Period size: 58 Copynumber: 4.1 Consensus size: 57
19885972 TTTTAAATGA
*
19885982 TTTTCTT-AAAATAAAATTCTAAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAA
1 TTTTCTTGAAAATAAAATTCT-AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
** *
19886039 TTTTCTTGAAAATAAGTTTTCTAAAAAATATTTTCGAGGAAAAGTTGAAAGTATCAAT
1 TTTTCTTGAAAATAA-AATTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
** * *
19886097 TTTTCTTGAAAATAATTTTCTAAAAAA-ATATTTTAAGGAAAAGTTAAAAGTATCAAT
1 TTTTCTTGAAAATAAAATTCTAAAAAATAT-TTTTGAGGAAAAGTTGAAAGTATCAAT
* * * *
19886154 TTTTCTT-AAAATAGAAACTCT--CAAATGTTTTTGA-GAAAATTTGGAAAGTATCAAT
1 TTTTCTTGAAAATA-AAATTCTAAAAAATATTTTTGAGGAAAAGTT-GAAAGTATCAAT
19886209 TTTTCTTG
1 TTTTCTTG
19886217 TACAAAAGCA
Statistics
Matches: 156, Mismatches: 15, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
54 7 0.04
55 26 0.17
56 9 0.06
57 54 0.35
58 56 0.36
59 4 0.03
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (57 bp):
TTTTCTTGAAAATAAAATTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAAT
Found at i:19886300 original size:16 final size:16
Alignment explanation
Indices: 19886281--19886314 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19886271 ATTATTCTTT
19886281 TTTTTCATTTTATTTC
1 TTTTTCATTTTATTTC
* *
19886297 TTTTTCTTTTTGTTTC
1 TTTTTCATTTTATTTC
19886313 TT
1 TT
19886315 GAATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTTTCATTTTATTTC
Found at i:19886320 original size:25 final size:24
Alignment explanation
Indices: 19886275--19886325 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
19886265 TGAATCATTA
**
19886275 TTCTTTTTTTTCATTTTATTTCTTT
1 TTCTTTTTTTTCATTGAATTT-TTT
19886300 TTCTTTTTGTTTC-TTGAATTTTTT
1 TTCTTTTT-TTTCATTGAATTTTTT
19886324 TT
1 TT
19886326 AATGTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 5 0.22
25 14 0.61
26 4 0.17
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (24 bp):
TTCTTTTTTTTCATTGAATTTTTT
Found at i:19894911 original size:147 final size:147
Alignment explanation
Indices: 19894643--19894914 Score: 372
Period size: 147 Copynumber: 1.9 Consensus size: 147
19894633 ATCCCAGAAT
* *
19894643 GGGGTTTGCCTACCAACCTAAGAAGCCTTTACATCCATGAACCCAATATTAGTAAGGCAGCAATG
1 GGGGTTTGCCTACCAACCTAAGAAGCCTTGACATCCATGAACCAAATATTAGTAAGGCAGCAATG
** *
19894708 GAGTGGGGATTGCATAGACTCACCTCTCTTAAACAACTCCAAATTTCTGGTGGTAATTGTGATGC
66 GAGTGGGGATTGCATAGACTCACCTCTCTTAAACAACTCCAAATTAATGGTAGTAATTGTGATGC
19894773 GGTAACATTTCCAGGAA
131 GGTAACATTTCCAGGAA
* * *
19894790 GGGGTTTGCCTACCAACCTAATAATG-CTTGACATCTC-TGGACCAAATATT-GTTAAGGCAGTA
1 GGGGTTTGCCTACCAACCTAAGAA-GCCTTGACATC-CATGAACCAAATATTAG-TAAGGCAGCA
* ** *
19894852 ATGGAGTGGGGATTGCATAGACTCACCTCTCTTACAA-GACTGGACATTAATGGTAGTAATTGT
63 ATGGAGTGGGGATTGCATAGACTCACCTCTCTTA-AACAACTCCAAATTAATGGTAGTAATTGT
19894915 ATAGATGCGA
Statistics
Matches: 109, Mismatches: 12, Indels: 8
0.84 0.09 0.06
Matches are distributed among these distances:
146 1 0.01
147 104 0.95
148 4 0.04
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (147 bp):
GGGGTTTGCCTACCAACCTAAGAAGCCTTGACATCCATGAACCAAATATTAGTAAGGCAGCAATG
GAGTGGGGATTGCATAGACTCACCTCTCTTAAACAACTCCAAATTAATGGTAGTAATTGTGATGC
GGTAACATTTCCAGGAA
Found at i:19899643 original size:41 final size:41
Alignment explanation
Indices: 19899583--19899666 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
19899573 AAAAGCTATT
*
19899583 AAATTTTAAAAACTCCTCTAAAC-AAATGTTATAAAACTTTA
1 AAATTTTAAAAACTCCTCT-AACTAAAGGTTATAAAACTTTA
* *
19899624 AAATTTTAAGAACTTCTCTAACTAAAGGTTATAAAACTTTA
1 AAATTTTAAAAACTCCTCTAACTAAAGGTTATAAAACTTTA
19899665 AA
1 AA
19899667 CACTCATCTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.35
Consensus pattern (41 bp):
AAATTTTAAAAACTCCTCTAACTAAAGGTTATAAAACTTTA
Found at i:19900124 original size:35 final size:35
Alignment explanation
Indices: 19900063--19900157 Score: 122
Period size: 35 Copynumber: 2.7 Consensus size: 35
19900053 TATTCAAATG
* *
19900063 TCACCACCGAGTGAA-TTTGATAAAAGCTAGGACA
1 TCACCACCAAGTAAATTTTGATAAAAGCTAGGACA
* *
19900097 TCACCACCAAGTAAATTTTGATAAAAGCTCGGATA
1 TCACCACCAAGTAAATTTTGATAAAAGCTAGGACA
*
19900132 TCACCACCAA-TAGAGTTTTGATAAAA
1 TCACCACCAAGTA-AATTTTGATAAAA
19900158 TTCAATCTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
34 15 0.28
35 39 0.72
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.24
Consensus pattern (35 bp):
TCACCACCAAGTAAATTTTGATAAAAGCTAGGACA
Found at i:19900223 original size:35 final size:35
Alignment explanation
Indices: 19900175--19900267 Score: 136
Period size: 35 Copynumber: 2.7 Consensus size: 35
19900165 TTGAATACTT
*
19900175 AGATATCATCACCAAGTGAATTTTGATAAAAGA-TC
1 AGATATCACCACCAAGTGAATTTTGATAAAA-ACTC
19900210 AGATATCACCACCAAGTGAATTTTGATAAAAACTC
1 AGATATCACCACCAAGTGAATTTTGATAAAAACTC
* *
19900245 AGATAGCACCACTAAGT-AATTTT
1 AGATATCACCACCAAGTGAATTTT
19900268 AATCAAATTC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
34 7 0.13
35 47 0.87
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (35 bp):
AGATATCACCACCAAGTGAATTTTGATAAAAACTC
Found at i:19900322 original size:118 final size:118
Alignment explanation
Indices: 19900096--19900323 Score: 275
Period size: 118 Copynumber: 1.9 Consensus size: 118
19900086 AAGCTAGGAC
* * * *
19900096 ATCACCACCAAGTAAATTTTGATAAAAGCTCGGATATCACCACCAATAGAGTTTTGATAAAATTC
1 ATCACCACCAAGTAAATTTTGATAAAAACTCAGATAGCACCACCAATAGAGTTTTAATAAAATTC
* * * * * *
19900161 AATCTTGAATACTTAGATATCATCACCAAGTGAATTTTGATAAAAGATCAGAT
66 AATCTTGAACAATCAAATATCATCACCAAGAGAATTTTAATAAAAGATCAGAT
* * *
19900214 ATCACCACCAAGTGAATTTTGATAAAAACTCAGATAGCACCACTAAGTA-A-TTTTAATCAAATT
1 ATCACCACCAAGTAAATTTTGATAAAAACTCAGATAGCACCACCAA-TAGAGTTTTAATAAAATT
19900277 CAATCTTGAACAATCAAATATCA-CTACCGAA-AGAAGTTTTAATAAAA
65 CAATCTTGAACAATCAAATATCATC-ACC-AAGAGAA-TTTTAATAAAA
19900324 ATCCATATAT
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
116 1 0.01
117 36 0.39
118 54 0.58
119 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.11, T:0.29
Consensus pattern (118 bp):
ATCACCACCAAGTAAATTTTGATAAAAACTCAGATAGCACCACCAATAGAGTTTTAATAAAATTC
AATCTTGAACAATCAAATATCATCACCAAGAGAATTTTAATAAAAGATCAGAT
Found at i:19911681 original size:19 final size:19
Alignment explanation
Indices: 19911657--19911695 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
19911647 AAGATCAGTA
19911657 AAAGCAAGGTCCCTTTTAT
1 AAAGCAAGGTCCCTTTTAT
19911676 AAAGCAAGGTCCCTTTTAT
1 AAAGCAAGGTCCCTTTTAT
19911695 A
1 A
19911696 GTTTCAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (19 bp):
AAAGCAAGGTCCCTTTTAT
Found at i:19920987 original size:21 final size:21
Alignment explanation
Indices: 19920941--19920980 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
19920931 AGTGATTATC
*
19920941 ATATGTACATATAATTAAAAT
1 ATATGTACATATAATCAAAAT
*
19920962 ATATGTACATTTAATCAAA
1 ATATGTACATATAATCAAA
19920981 CAATATGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.05, T:0.38
Consensus pattern (21 bp):
ATATGTACATATAATCAAAAT
Found at i:19924972 original size:66 final size:63
Alignment explanation
Indices: 19924882--19925003 Score: 172
Period size: 66 Copynumber: 1.9 Consensus size: 63
19924872 TGAAATGAAG
* * *
19924882 GCCATCACTAATATTGAATAATAATAGTGTCTCAAAAAAAAGTTGAAAATTATTTTATCTTTTAT
1 GCCATCACTAATATTAAATAATAATAATGTATC--AAAAAAGTTGAAAATTATTTTATCTTTTAT
* *
19924947 GCCATCAACTAATGTTAAATAATAATAATGTATCAAAAAAGTTGATAATTATTTTAT
1 GCCATC-ACTAATATTAAATAATAATAATGTATCAAAAAAGTTGAAAATTATTTTAT
19925004 TTCTTATCTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
64 22 0.43
65 6 0.12
66 23 0.45
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.38
Consensus pattern (63 bp):
GCCATCACTAATATTAAATAATAATAATGTATCAAAAAAGTTGAAAATTATTTTATCTTTTAT
Found at i:19927137 original size:2 final size:2
Alignment explanation
Indices: 19927132--19927165 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
19927122 ACACACACAC
*
19927132 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19927166 GCCGGTGCTA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:19927614 original size:35 final size:35
Alignment explanation
Indices: 19927528--19927614 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
19927518 TTTTTAAAGG
* *
19927528 TTTTCAAAAATGAATATTCAAAAACTTTTTAAAAAT
1 TTTTGAAAAATGAAT-TTCAAAAACTCTTTAAAAAT
* * *
19927564 TTTAG-AACATCAATTTCCAAAAAC-CTTTAAAAAT
1 TTTTGAAAAATGAATTT-CAAAAACTCTTTAAAAAT
19927598 TTTTGAAAAATGAATTT
1 TTTTGAAAAATGAATTT
19927615 TTGAAATAGA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
34 15 0.37
35 23 0.56
36 3 0.07
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (35 bp):
TTTTGAAAAATGAATTTCAAAAACTCTTTAAAAAT
Found at i:19928196 original size:20 final size:21
Alignment explanation
Indices: 19928171--19928221 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
19928161 TTTATTATTT
*
19928171 AATATATATTAC-AACAGTAA
1 AATATATATTACAAAAAGTAA
*
19928191 AATATATATTTCAAAAAGTAA
1 AATATATATTACAAAAAGTAA
19928212 AATAATATAT
1 AAT-ATATAT
19928222 GAACATTCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 11 0.41
21 10 0.37
22 6 0.22
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (21 bp):
AATATATATTACAAAAAGTAA
Found at i:19928197 original size:22 final size:22
Alignment explanation
Indices: 19928172--19928221 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
19928162 TTATTATTTA
*
19928172 ATATATATT-ACAACAGTAAAAT
1 ATATATATTCA-AAAAGTAAAAT
19928194 ATATAT-TTCAAAAAGTAAAAT
1 ATATATATTCAAAAAGTAAAAT
19928215 A-ATATAT
1 ATATATAT
19928222 GAACATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 14 0.56
22 7 0.28
ACGTcount: A:0.56, C:0.06, G:0.04, T:0.34
Consensus pattern (22 bp):
ATATATATTCAAAAAGTAAAAT
Found at i:19932259 original size:22 final size:22
Alignment explanation
Indices: 19932234--19932278 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19932224 CAAATGTCAG
* *
19932234 ATTTGATTGAATGATTAAATTC
1 ATTTGATTGAATAACTAAATTC
19932256 ATTTGATTGAATAACTAAATTC
1 ATTTGATTGAATAACTAAATTC
19932278 A
1 A
19932279 AAGTATCAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (22 bp):
ATTTGATTGAATAACTAAATTC
Found at i:19934818 original size:5 final size:5
Alignment explanation
Indices: 19934806--19934835 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
19934796 TTTGTTTTTC
*
19934806 AAATA AAACA AAATA AAATA AAATA AAATA
1 AAATA AAATA AAATA AAATA AAATA AAATA
19934836 TTCAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:19935615 original size:22 final size:22
Alignment explanation
Indices: 19935572--19935616 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19935562 GATAACTTCA
* ***
19935572 TAAATAAATTATTTTTTTATTT
1 TAAAAAAATTATTTTAAAATTT
19935594 TAAAAAAATTATTTTAAAATTT
1 TAAAAAAATTATTTTAAAATTT
19935616 T
1 T
19935617 TGATTGTATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TAAAAAAATTATTTTAAAATTT
Found at i:19943219 original size:28 final size:28
Alignment explanation
Indices: 19943179--19943236 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
19943169 GCGGGACAAG
19943179 TTAGATTGTGGTGATTGACTGTGGTTTC
1 TTAGATTGTGGTGATTGACTGTGGTTTC
19943207 TTAGATTGTGGTGATTGACTGTGGTTTC
1 TTAGATTGTGGTGATTGACTGTGGTTTC
19943235 TT
1 TT
19943237 GCTCTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.07, G:0.31, T:0.48
Consensus pattern (28 bp):
TTAGATTGTGGTGATTGACTGTGGTTTC
Found at i:19950913 original size:2 final size:2
Alignment explanation
Indices: 19950906--19950935 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
19950896 TAACAATGTC
19950906 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
19950936 CACTATCTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19955867 original size:6 final size:6
Alignment explanation
Indices: 19955837--19955866 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
19955827 GTAATTAAGT
19955837 ATGAAA ATGAAA ATGAAA ATGAAA AT-AAA A
1 ATGAAA ATGAAA ATGAAA ATGAAA ATGAAA A
19955867 AGTTGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (6 bp):
ATGAAA
Found at i:19956203 original size:44 final size:44
Alignment explanation
Indices: 19956140--19956228 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
19956130 ATATATATAT
19956140 ATATGTGACAATAGGATCACTTTAAATAATATTATAATTGATTG
1 ATATGTGACAATAGGATCACTTTAAATAATATTATAATTGATTG
*
19956184 ATATGTGACTATAGGATCACTTTAAATAATATTATAATTGATTG
1 ATATGTGACAATAGGATCACTTTAAATAATATTATAATTGATTG
19956228 A
1 A
19956229 CGTATGAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (44 bp):
ATATGTGACAATAGGATCACTTTAAATAATATTATAATTGATTG
Found at i:19956742 original size:2 final size:2
Alignment explanation
Indices: 19956735--19956761 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19956725 CTATGTGTAC
19956735 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
19956762 GTTAGTCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19957189 original size:29 final size:29
Alignment explanation
Indices: 19957144--19957210 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
19957134 AATTTTATCT
*
19957144 AATTAAAAATTTAATTGATTGAAATAAAA
1 AATTAAAAATTCAATTGATTGAAATAAAA
* *
19957173 AATTAAAAATTCGATTGATTGTAATAAAA
1 AATTAAAAATTCAATTGATTGAAATAAAA
*
19957202 TATTAAAAA
1 AATTAAAAA
19957211 CTTAAACAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.34
Consensus pattern (29 bp):
AATTAAAAATTCAATTGATTGAAATAAAA
Found at i:19968467 original size:19 final size:19
Alignment explanation
Indices: 19968443--19968479 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19968433 ATTGTTTTCA
* *
19968443 TCACCAGTAATCTCACTTC
1 TCACCACTAACCTCACTTC
19968462 TCACCACTAACCTCACTT
1 TCACCACTAACCTCACTT
19968480 TAGGTAGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.41, G:0.03, T:0.30
Consensus pattern (19 bp):
TCACCACTAACCTCACTTC
Found at i:19973326 original size:49 final size:49
Alignment explanation
Indices: 19973260--19973365 Score: 194
Period size: 49 Copynumber: 2.2 Consensus size: 49
19973250 ATTTTAGAAA
*
19973260 AATTTATCCTATACATCACCTCATATCAATTTAAAATCAATTTTAAAGT
1 AATTTATCCTATACATCACCTCATATCAATTTAAAATCAATTTTAAAGC
*
19973309 AATTTATCCTATGCATCACCTCATATCAATTTAAAATCAATTTTAAAGC
1 AATTTATCCTATACATCACCTCATATCAATTTAAAATCAATTTTAAAGC
19973358 AATTTATC
1 AATTTATC
19973366 TTTTAAAAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 55 1.00
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.39
Consensus pattern (49 bp):
AATTTATCCTATACATCACCTCATATCAATTTAAAATCAATTTTAAAGC
Found at i:19973596 original size:284 final size:280
Alignment explanation
Indices: 19973042--19973600 Score: 753
Period size: 284 Copynumber: 2.0 Consensus size: 280
19973032 TTATTATGTA
* * * * **
19973042 CATCACCTCATCTTAATTTAAAATCATTTTTAAAATAATTTATCTTTTTTAATTTATTTGAATTT
1 CATCACCTCATATCAATTTAAAATCAATTTTAAAACAATTTATCTTTTAAAATTTATTTGAATTT
* **
19973107 TATATGAGTATTTAAATTTATCATAACTTTTAAAAATATTATTTAATATCTTTCATATTTTCGAT
66 TATATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATATTTTCGAT
* * * * *
19973172 AAATAATCATTATATTGTCTTCAATTTTTAAATATATTGCACAAAAAAATGTGAATAAAAAATTT
131 AAATAATCATTACATTATCTTCAATTTTAAAATATATTGCACAAAAAAATGTGAAAAAAAAATAT
* * * * *
19973237 AAATACCAGAATAATTTTAGAAAAATTTATCCTATACATCACCTCATATCAATTTAAAATCAATT
196 AAATACCAAAACAACTTCAGAAAAATTTATCCTATACATCACCTCATATCAATTTAAAATCAAGT
19973302 TTAAAGTAATTTATCCTATG
261 TTAAAGTAATTTATCCTATG
*
19973322 CATCACCTCATATCAATTTAAAATCAATTTTAAAGCAATTTATCTTTTAAAAATTTATTTGTAA-
1 CATCACCTCATATCAATTTAAAATCAATTTTAAAACAATTTATCTTTT-AAAATTTATTTG-AAT
*
19973386 TTTATATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATATTTTTT
64 TTTATATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATA-TTTTC
* * * * ** *
19973451 TATAAATAATTATTACATTATCTTTAGCTTTTAAAATATATTTTACAAAAAAAATTTGAAAAAAA
128 GATAAATAATCATTACATTATCTTCA-ATTTTAAAATATATTGCAC-AAAAAAATGTGAAAAAAA
* * * * *
19973516 AATATAAATACGAAAACAACTTCAGGAAAGTTTCTCCTATACATCACCTCATCT-AATTTTAAAA
191 AATATAAATACCAAAACAACTTCAGAAAAATTTATCCTATACATCACCTCATATCAA-TTTAAAA
19973580 TCAAGTTTAAAGTAATTTATC
255 TCAAGTTTAAAGTAATTTATC
19973601 TTTTTTTTAA
Statistics
Matches: 240, Mismatches: 33, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
280 43 0.18
281 66 0.28
282 27 0.11
283 17 0.07
284 87 0.36
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.43
Consensus pattern (280 bp):
CATCACCTCATATCAATTTAAAATCAATTTTAAAACAATTTATCTTTTAAAATTTATTTGAATTT
TATATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATATTTTCGAT
AAATAATCATTACATTATCTTCAATTTTAAAATATATTGCACAAAAAAATGTGAAAAAAAAATAT
AAATACCAAAACAACTTCAGAAAAATTTATCCTATACATCACCTCATATCAATTTAAAATCAAGT
TTAAAGTAATTTATCCTATG
Found at i:19973738 original size:235 final size:232
Alignment explanation
Indices: 19973315--19973772 Score: 634
Period size: 235 Copynumber: 2.0 Consensus size: 232
19973305 AAGTAATTTA
* *
19973315 TCCTATGCATCACCTCATATCAATTTAAAATCAATTTTAAAGCAATTTATCTTTTAAAAATTTAT
1 TCCTATACATCACCTCATATCAATTTAAAATCAAGTTTAAAGCAATTTATCTTTTAAAAATTTAT
* * * * *
19973380 TTGTAATTTATATGAGTATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATA
66 CTGCAATTAACATGAATATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATA
* * *
19973445 TTTTTTTATAAATAATTATTACATTATCTTTAGCTTTTAAAATATATTTTACAAAAAAAATTTGA
131 TATTTTTATAAATAATTATTACATTATCTTCAGCTTTTAAAATATATTTTA-AAAAAAAATGTG-
19973510 AAAAAAAATATAAATACGAAAACAACTTCAGGAAAGTTTC
194 -AAAAAAATATAAATACGAAAACAACTTCAGGAAAGTTTC
* * ***
19973550 TCCTATACATCACCTCATCT-AATTTTAAAATCAAGTTTAAAGTAATTTATCTTTTTTTTAATTT
1 TCCTATACATCACCTCATATCAA-TTTAAAATCAAGTTTAAAGCAATTTATC-TTTTAAAAATTT
* * * *
19973614 ATCTGCAGTTAACATGAATATTTAAATTTATCATAATTTTTAAAAATATTATTTAATATCTTTAA
64 ATCTGCAATTAACATGAATATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAA
* *
19973679 T-TATTTTTATAAATAATTCTTACATTATCTTCAG-TTTTTAAATATATTTTATAAAAAAAATGT
129 TATATTTTTATAAATAATTATTACATTATCTTCAGCTTTTAAAATATATTTTA-AAAAAAAATGT
* *
19973742 GAAAAAAATATAAATACTAAAACAATTTCAG
193 GAAAAAAATATAAATACGAAAACAACTTCAG
19973773 AAAAATCTTC
Statistics
Matches: 197, Mismatches: 24, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
232 28 0.14
234 29 0.15
235 74 0.38
236 66 0.34
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.43
Consensus pattern (232 bp):
TCCTATACATCACCTCATATCAATTTAAAATCAAGTTTAAAGCAATTTATCTTTTAAAAATTTAT
CTGCAATTAACATGAATATTTAAATTTATCACAACTTTTAAAAATATTATTTAATATCTTAAATA
TATTTTTATAAATAATTATTACATTATCTTCAGCTTTTAAAATATATTTTAAAAAAAAATGTGAA
AAAAATATAAATACGAAAACAACTTCAGGAAAGTTTC
Found at i:20001089 original size:195 final size:193
Alignment explanation
Indices: 20000716--20001090 Score: 626
Period size: 195 Copynumber: 1.9 Consensus size: 193
20000706 AAGAGGAGAA
* * *
20000716 GAAGACTGAGAAAATATTATAAAGGATATGTTATGGAAGACAGGAGAAATGCTAGAAAACTGAAT
1 GAAGACTGAGAAAATATTATAAAGGAAATGTTATGGAACACAGGAGAAAGGCTAGAAAACTGAAT
*
20000781 TTCATTTCAGAAATCTAAATTTTGCACAATACAAACTAGAGCAGGCTTTTATAGTAAAGGGTGGA
66 TTCATTTCAGAAATCTAAAATTTGCACAATACAAACTAGAGCAGGCTTTTATAGTAAAGGGTGGA
20000846 CTAGAGACACTTTTCAATTTCCTTGAGAAATCTTGACAACTCAAGAATCCTGCCACAAGATCT
131 CTAGAGACACTTTTCAATTTCCTTGAGAAATCTTGACAACTCAAGAATCCTGCCACAAGATCT
* * *
20000909 GAAGATTGAGAAATTATTATCAAGGAAATGTTATGGAACACAGAGGAGAAAGGCTAGAAAACTGA
1 GAAGACTGAGAAAATATTATAAAGGAAATGTTATGGAACAC--AGGAGAAAGGCTAGAAAACTGA
* *
20000974 ATTTCATTTCAGAAATCTAAAATTTGCACAATACAAACTAGTGCAGGCTTTTATAGTAGAGGGTG
64 ATTTCATTTCAGAAATCTAAAATTTGCACAATACAAACTAGAGCAGGCTTTTATAGTAAAGGGTG
*
20001039 GACTCA-AGACACTTTTCAATTTCCTTGAGAGATCTTGACAACTCAAGAATCC
129 GACT-AGAGACACTTTTCAATTTCCTTGAGAAATCTTGACAACTCAAGAATCC
20001091 CACCAGAAAA
Statistics
Matches: 169, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
193 36 0.21
195 132 0.78
196 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (193 bp):
GAAGACTGAGAAAATATTATAAAGGAAATGTTATGGAACACAGGAGAAAGGCTAGAAAACTGAAT
TTCATTTCAGAAATCTAAAATTTGCACAATACAAACTAGAGCAGGCTTTTATAGTAAAGGGTGGA
CTAGAGACACTTTTCAATTTCCTTGAGAAATCTTGACAACTCAAGAATCCTGCCACAAGATCT
Found at i:20007323 original size:31 final size:30
Alignment explanation
Indices: 20007150--20007325 Score: 116
Period size: 31 Copynumber: 5.8 Consensus size: 30
20007140 AGTATAATTT
*
20007150 TATTTATAAATAATA-TATTATTAATATAATA
1 TATTTATAAATAATATTA-TAATAATA-AATA
* * *
20007181 TATTAATTAATAATATTATATTAATAAATA
1 TATTTATAAATAATATTATAATAATAAATA
* *
20007211 -ATTTA-ATATTAAATATTATTAATTTAATTAATA
1 TATTTATA-AAT-AATATTA-TAA--TAATAAATA
20007244 TATATTAT-AATAATA-TAT--TAATAAATAA
1 TAT-TTATAAATAATATTATAATAATAAAT-A
* * *
20007272 TATACTATTAAT-ATAATATAATAATAAATA
1 TAT-TTATAAATAATATTATAATAATAAATA
20007302 TTATTTATAAATAATATTATAATA
1 -TATTTATAAATAATATTATAATA
20007326 TATTGATAAA
Statistics
Matches: 116, Mismatches: 13, Indels: 32
0.72 0.08 0.20
Matches are distributed among these distances:
27 7 0.06
28 11 0.09
29 12 0.10
30 18 0.16
31 45 0.39
32 4 0.03
33 12 0.10
34 4 0.03
35 3 0.03
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTTATAAATAATATTATAATAATAAATA
Found at i:20007340 original size:23 final size:22
Alignment explanation
Indices: 20007253--20007341 Score: 85
Period size: 20 Copynumber: 4.0 Consensus size: 22
20007243 ATATATTATA
20007253 ATAATATATTAATAAATAATATACT
1 ATAATATATT-ATAAATAATAT--T
* *
20007278 ATTAATATAATAT-AATAATA-A
1 A-TAATATATTATAAATAATATT
*
20007299 ATATTAT-TTATAAATAATATT
1 ATAATATATTATAAATAATATT
20007320 ATAATATATTGATAAATAATAT
1 ATAATATATT-ATAAATAATAT
20007342 AAAGAATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.06
20 12 0.23
21 7 0.13
22 2 0.04
23 11 0.21
24 7 0.13
25 3 0.06
26 8 0.15
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
ATAATATATTATAAATAATATT
Found at i:20007352 original size:109 final size:109
Alignment explanation
Indices: 20007150--20007352 Score: 234
Period size: 109 Copynumber: 1.9 Consensus size: 109
20007140 AGTATAATTT
* * * * * *
20007150 TATTTATAAATAATATATTATTAATATAATATATTAATTAATAATATTATATTAATAAATAATTT
1 TATTAATAAATAATATACTATTAATATAATATAATAATAAATAATATTATAATAATAAATAATAT
* **
20007215 AATATTAAATATTATTAATTTAATTAATATATATTATAATAATA
66 AATATTAAATAATATTAATAGAATTAATATATATTATAATAATA
* *
20007259 TATTAATAAATAATATACTATTAATATAATATAATAATAAATATTATTTATAAATAATATTATAA
1 TATTAATAAATAATATACTATTAATATAATATAATAATAAATAATA-TTAT-AATAATA-AATAA
*
20007324 TATATTGA-TAAATAATA-TAA-AGAA-TAATA
63 TATAAT-ATTAAATAATATTAATAGAATTAATA
20007353 AATAGTTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
109 46 0.59
110 6 0.08
111 9 0.12
112 16 0.21
113 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (109 bp):
TATTAATAAATAATATACTATTAATATAATATAATAATAAATAATATTATAATAATAAATAATAT
AATATTAAATAATATTAATAGAATTAATATATATTATAATAATA
Found at i:20007450 original size:15 final size:15
Alignment explanation
Indices: 20007430--20007469 Score: 62
Period size: 16 Copynumber: 2.6 Consensus size: 15
20007420 ATAATTAGTT
*
20007430 TTTAATATTAATAAA
1 TTTAATATAAATAAA
20007445 TTTAATAATAAATAAA
1 TTTAAT-ATAAATAAA
20007461 TTTAATATA
1 TTTAATATA
20007470 CTTTAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TTTAATATAAATAAA
Found at i:20007513 original size:27 final size:26
Alignment explanation
Indices: 20007437--20007502 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 26
20007427 GTTTTTAATA
* * *
20007437 TTAATAAATTTAATAATAAATAA-AT
1 TTAATATATTTAATATTAAATAATTT
20007462 TTAATATACTTTAATATTAAATAATTT
1 TTAATATA-TTTAATATTAAATAATTT
20007489 TTAATAT-TTTAATA
1 TTAATATATTTAATA
20007503 GTTATATTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
25 14 0.39
26 14 0.39
27 8 0.22
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATATATTTAATATTAAATAATTT
Found at i:20008490 original size:34 final size:34
Alignment explanation
Indices: 20008447--20008523 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
20008437 ATAATATTCG
20008447 AAAATAAATTTTCAAAAAATCATATAAT-TTTTCA
1 AAAATAAATTTTCAAAAAATCATA-AATCTTTTCA
** **
20008481 AAAATAAATTTTCAAAACGTCATAAATCTTTTTG
1 AAAATAAATTTTCAAAAAATCATAAATCTTTTCA
20008515 AAAATAAAT
1 AAAATAAAT
20008524 AAAATTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
33 3 0.08
34 35 0.92
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (34 bp):
AAAATAAATTTTCAAAAAATCATAAATCTTTTCA
Found at i:20010892 original size:2 final size:2
Alignment explanation
Indices: 20010887--20010913 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20010877 ATATATTTAT
20010887 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
20010914 TTTAGGCAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20016733 original size:20 final size:20
Alignment explanation
Indices: 20016708--20016747 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20016698 TAAATCTAAC
20016708 CTTAAATTTTATTTATTTTA
1 CTTAAATTTTATTTATTTTA
20016728 CTTAAATTTTATTTATTTTA
1 CTTAAATTTTATTTATTTTA
20016748 AATTATAATA
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:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTAAATTTTATTTATTTTA
Found at i:20017069 original size:195 final size:194
Alignment explanation
Indices: 20016820--20017275 Score: 552
Period size: 193 Copynumber: 2.3 Consensus size: 194
20016810 ATAATAGTGG
* *
20016820 ATTTTTAAATTTTATTTA-TTTAAATTACAAAACTAGATAAAATATAAAAATATATTATATCTAA
1 ATTTTGAAA-TTTATTTATTTTAAATTATAAAACTAGATAAAATATAAAAATATATTATATCTAA
* * * *
20016884 AAATTAAAAAAAGGGACAAAAACTTAAT-AAAAATAGAAACTTTTAAATTTTATTTATTTTAAAA
65 AAATT--AAAAA--GA-AAAAAATTAATCAAAAATAGAAAATTTGAAAATTTATTTA-TTTAAAA
* *
20016948 -TA-TAAAATTGATAAAAT-T-TATTAAAAACCTATATTATATTTAAAAACGTAAAAAA-AT-TT
124 CTATTAAAATTGATAAAATATATATTAAAAA-ATAAATTATATTTAAAAA--TAAAAAATATATT
*
20017007 AAAAGGAAA
186 AAAAAGAAA
* ** *
20017016 ATTTTGAAATTTGTTTATTTTAAATT-TAAAACTAGATAAAATATACGAATATATTAGATCTAAA
1 ATTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAATATAAAAATATATTATATCTAAA
* * *
20017080 AATTAAAAAGAAAAAAATTTATCAATAATAGAAAATTTGAAAATTTATTTATTTAAAACTATTTA
66 AATTAAAAAGAAAAAAATTAATCAAAAATAGAAAATTTGAAAATTTATTTATTTAAAACTATTAA
** * * * *
20017145 TTTTGATAAAATATATGTTAAAAAATAAATTCTATTTAGAAATAAAAAATTTATTAAAAAGAAA
131 AATTGATAAAATATATATTAAAAAATAAATTATATTTAAAAATAAAAAATATATTAAAAAGAAA
*
20017209 ATTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAATATATTATATCTAAA
1 ATTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAATATAAAAATATATTATATCTAAA
20017274 AA
66 AA
20017276 AAATTCTTAA
Statistics
Matches: 224, Mismatches: 27, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
190 16 0.07
191 35 0.16
192 13 0.06
193 55 0.25
194 44 0.20
195 45 0.20
196 16 0.07
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (194 bp):
ATTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAATATAAAAATATATTATATCTAAA
AATTAAAAAGAAAAAAATTAATCAAAAATAGAAAATTTGAAAATTTATTTATTTAAAACTATTAA
AATTGATAAAATATATATTAAAAAATAAATTATATTTAAAAATAAAAAATATATTAAAAAGAAA
Found at i:20017313 original size:86 final size:85
Alignment explanation
Indices: 20017215--20017441 Score: 241
Period size: 82 Copynumber: 2.7 Consensus size: 85
20017205 GAAAATTTTG
20017215 AAATTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAATATATTATATCTAAAAAAAAT
1 AAATTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAATATATTATATCTAAAAAAAA-
*
20017280 TCTTAA-AGATAGAAA-ACTTC
65 -CTTAATACATAGAAATACTTC
* ** * * *
20017300 AAATTTTATTTATTTTAAACTATAAATTTTGATAAAATATAAAAACTATATTATAT-T---TAAA
1 AAA-TTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAA-TATATTATATCTAAAAAAA
* * ** *
20017361 AGTTAATACATTGAAATTTTTG
64 ACTTAATACATAGAAATACTTC
* * *
20017383 AAATTTATTTATTTTCAATCATAAAACTAGATAACATTTAAAAATATATTATATCTAAA
1 AAATTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAATATATTATATCTAAA
20017442 CATTTTAAAA
Statistics
Matches: 114, Mismatches: 20, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
81 14 0.12
82 41 0.36
83 9 0.08
85 3 0.03
86 37 0.32
87 10 0.09
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (85 bp):
AAATTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAATATATTATATCTAAAAAAAAC
TTAATACATAGAAATACTTC
Found at i:20017512 original size:168 final size:162
Alignment explanation
Indices: 20017205--20017520 Score: 397
Period size: 168 Copynumber: 1.9 Consensus size: 162
20017195 TTATTAAAAA
*
20017205 GAAAATTTTGAAATTTATTTATTTTAAATTATAAAACTAGATAAAATTTAAAAATATATTATATC
1 GAAAATTTTGAAATTTATTTATTTTAAATCATAAAACTAGATAAAATTTAAAAATATATTATATC
**
20017270 TAAAAAAAATTCTTAAAGATAGAAAACTTCAAATTTTATTTATTTTAAACTATAAATTTTGATAA
66 TAAAAAAAATTCTTAAAGATAGAAAACTTCAAAAATTATTTATTTTAAACTATAAATTTTG----
20017335 AATATAAAAACTATATTATATTTAAAAGTTAATACATT
127 AATA-AAAAA-TATATTATATTTAAAAGTTAATACATT
* * *
20017373 GAAATTTTTGAAATTTATTTATTTTCAATCATAAAACTAGATAACATTTAAAAATATATTATATC
1 GAAAATTTTGAAATTTATTTATTTTAAATCATAAAACTAGATAAAATTTAAAAATATATTATATC
*
20017438 TAAACATTTTAAAAATATTCTTAAA-ATTTGAAAA-TT-ATAAAATTATTTATTTTAAACTATAA
66 T--A-A----AAAAA-ATTCTTAAAGA-TAGAAAACTTCA-AAAATTATTTATTTTAAACTATAA
20017500 ATTTTG-ATAAAAAATATATTA
121 ATTTTGAATAAAAAATATATTA
20017521 AAACAATATC
Statistics
Matches: 131, Mismatches: 7, Indels: 20
0.83 0.04 0.13
Matches are distributed among these distances:
168 69 0.53
169 5 0.04
170 4 0.03
171 1 0.01
174 1 0.01
175 36 0.27
176 15 0.11
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (162 bp):
GAAAATTTTGAAATTTATTTATTTTAAATCATAAAACTAGATAAAATTTAAAAATATATTATATC
TAAAAAAAATTCTTAAAGATAGAAAACTTCAAAAATTATTTATTTTAAACTATAAATTTTGAATA
AAAAATATATTATATTTAAAAGTTAATACATT
Found at i:20019114 original size:7 final size:8
Alignment explanation
Indices: 20019088--20019112 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
20019078 TCAAATTTCG
20019088 AATTAAAA
1 AATTAAAA
20019096 AATTAAAA
1 AATTAAAA
20019104 AATTAAAA
1 AATTAAAA
20019112 A
1 A
20019113 TTTGAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATTAAAA
Found at i:20019210 original size:21 final size:25
Alignment explanation
Indices: 20019179--20019235 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 25
20019169 ATAATAAATT
*
20019179 TATATCAAATTTTAT-TT-AAAT-A
1 TATATAAAATTTTATATTAAAATAA
20019201 TAT-TAAAATTTTATATTAAAATAA
1 TATATAAAATTTTATATTAAAATAA
20019225 TATATAAAATT
1 TATATAAAATT
20019236 AAAAAATTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 10 0.33
22 5 0.17
23 4 0.13
24 4 0.13
25 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TATATAAAATTTTATATTAAAATAA
Found at i:20019217 original size:13 final size:13
Alignment explanation
Indices: 20019198--20019236 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
20019188 TTTTATTTAA
20019198 ATATATTAAAATT
1 ATATATTAAAATT
* *
20019211 TTATATTAAAATA
1 ATATATTAAAATT
20019224 ATATA-TAAAATT
1 ATATATTAAAATT
20019236 A
1 A
20019237 AAAAATTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 7 0.32
13 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATTAAAATT
Found at i:20020555 original size:19 final size:20
Alignment explanation
Indices: 20020520--20020557 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
20020510 AGATAATTAC
20020520 AAATTATAATAGTAAAAAAA
1 AAATTATAATAGTAAAAAAA
20020540 AAATT-TAATA-TAAAAAAA
1 AAATTATAATAGTAAAAAAA
20020558 TGATTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (20 bp):
AAATTATAATAGTAAAAAAA
Found at i:20021997 original size:15 final size:15
Alignment explanation
Indices: 20021977--20022029 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
20021967 TAAAAAATTG
*
20021977 ATAAAAATTAATTAA
1 ATAAAATTTAATTAA
20021992 ATAAAATTTAA-T-A
1 ATAAAATTTAATTAA
20022005 A-AAAATTTATATTAA
1 ATAAAATTTA-ATTAA
20022020 ATAAAATTTA
1 ATAAAATTTA
20022030 TTATAGTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
12 8 0.24
13 3 0.09
14 2 0.06
15 12 0.36
16 8 0.24
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATAAAATTTAATTAA
Found at i:20022031 original size:14 final size:14
Alignment explanation
Indices: 20021980--20022032 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
20021970 AAAATTGATA
*
20021980 AAAATTAATTAAAT
1 AAAATTTATTAAAT
*
20021994 AAAATTTAATAAA-
1 AAAATTTATTAAAT
*
20022007 AAATTTATATTAAAT
1 AAAATT-TATTAAAT
20022022 AAAATTTATTA
1 AAAATTTATTA
20022033 TAGTTAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 5 0.16
14 22 0.69
15 5 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AAAATTTATTAAAT
Found at i:20022261 original size:16 final size:17
Alignment explanation
Indices: 20022231--20022266 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20022221 ATATAATATC
20022231 ATAAAATCATAAAAATA
1 ATAAAATCATAAAAATA
*
20022248 ATAAAAT-ATGAAAATA
1 ATAAAATCATAAAAATA
20022264 ATA
1 ATA
20022267 TAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (17 bp):
ATAAAATCATAAAAATA
Found at i:20023180 original size:25 final size:25
Alignment explanation
Indices: 20023134--20023201 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
20023124 TAAATATAAG
*
20023134 AATTATTATATTTAATTATTATATCAA
1 AATTATTA-ATTTATTTATTAT-TCAA
* *
20023161 AA-TATTAATTTATTTTTTATTTAA
1 AATTATTAATTTATTTATTATTCAA
*
20023185 AATTTTTAATTTATTTA
1 AATTATTAATTTATTTA
20023202 ACTCTCATCG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
24 5 0.14
25 23 0.66
26 5 0.14
27 2 0.06
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (25 bp):
AATTATTAATTTATTTATTATTCAA
Found at i:20025030 original size:12 final size:12
Alignment explanation
Indices: 20025013--20025046 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
20025003 GGACCCAAAC
20025013 ACTGCTGCCCAA
1 ACTGCTGCCCAA
20025025 ACTGCTGCCCAA
1 ACTGCTGCCCAA
*
20025037 ACTACTGCCC
1 ACTGCTGCCC
20025047 TTATTGATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.44, G:0.15, T:0.18
Consensus pattern (12 bp):
ACTGCTGCCCAA
Found at i:20025043 original size:15 final size:14
Alignment explanation
Indices: 20025006--20025044 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
20024996 TGGGCATGGA
20025006 CCCAAACACTGCTG
1 CCCAAACACTGCTG
20025020 CCC-AA-ACTGCTG
1 CCCAAACACTGCTG
20025032 CCCAAACTACTGC
1 CCCAAAC-ACTGC
20025045 CCTTATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.45
13 4 0.18
14 3 0.14
15 5 0.23
ACGTcount: A:0.28, C:0.44, G:0.13, T:0.15
Consensus pattern (14 bp):
CCCAAACACTGCTG
Found at i:20026877 original size:115 final size:117
Alignment explanation
Indices: 20026703--20026925 Score: 326
Period size: 115 Copynumber: 1.9 Consensus size: 117
20026693 AATTGTCACG
*
20026703 TTTTTTTATATCATGAAAAAAATTAAAAATGTTCTTTTAATTTATTTATAAAATAATTATTTAAG
1 TTTTTTTATATCATGAAAAAAATTAAAAATGATCTTTT-ATTTATTTATAAAATAATTATTTAAG
* * *
20026768 ATATTTTT-TACATAAAACATCTTAAATAATCATTTTATAAATATATAAAAGTC
65 ATATTTTTGTAAAAAAAAAATCTTAAATAAT-ATTTTATAAATATATAAAAGTC
* ** * *
20026821 TTTTTTTATATTA-GAAAAAAATTTTAAATGATCTTTT-TTTATTTATAAAATGATTATTTAATA
1 TTTTTTTATATCATGAAAAAAATTAAAAATGATCTTTTATTTATTTATAAAATAATTATTTAAGA
20026884 TATTTTTGTAAAAAAAAAATCTTAAATAATATTTTATAAATA
66 TATTTTTGTAAAAAAAAAATCTTAAATAATATTTTATAAATA
20026926 AATTAAAGGA
Statistics
Matches: 95, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
115 43 0.45
116 19 0.20
117 21 0.22
118 12 0.13
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (117 bp):
TTTTTTTATATCATGAAAAAAATTAAAAATGATCTTTTATTTATTTATAAAATAATTATTTAAGA
TATTTTTGTAAAAAAAAAATCTTAAATAATATTTTATAAATATATAAAAGTC
Found at i:20026929 original size:86 final size:83
Alignment explanation
Indices: 20026844--20027009 Score: 192
Period size: 86 Copynumber: 2.0 Consensus size: 83
20026834 GAAAAAAATT
* ** * *
20026844 TTAAATGATCTTTT-TTTATTTATAAAATGATTATTTAATATATTTTTGTAAAAAAAAAATCTTA
1 TTAAAGGAT-TTTTATTT-TTTATAAAAAAATTATTTAAGATATTTCTGT-AAAAAAAAATCTTA
20026908 AATAA-TATTTTATAAATAAA
63 AATAATTATTTTATAAATAAA
* *
20026928 TTAAAGGATTTTTAAAATTTTTTATAAAAAAATTATTTAAGATATTTCTGTATAAAAATATCTTA
1 TTAAAGGATTTTT---ATTTTTTATAAAAAAATTATTTAAGATATTTCTGTAAAAAAAAATCTTA
*
20026993 AATAATTTTTTTATAAA
63 AATAATTATTTTATAAA
20027010 AATAAAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
83 4 0.06
84 8 0.12
85 17 0.25
86 37 0.54
87 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (83 bp):
TTAAAGGATTTTTATTTTTTATAAAAAAATTATTTAAGATATTTCTGTAAAAAAAAATCTTAAAT
AATTATTTTATAAATAAA
Found at i:20026967 original size:25 final size:25
Alignment explanation
Indices: 20026938--20027011 Score: 60
Period size: 27 Copynumber: 2.8 Consensus size: 25
20026928 TTAAAGGATT
20026938 TTTAA-AATTTTTTATAAAAAAATTA
1 TTTAAGAATTTTTTATAAAAAAA-TA
* * *
20026963 TTTAAGATATTTCTGTATAAAAATATC
1 TTTAAGA-ATTT-TTTATAAAAAAATA
* *
20026990 TTAAATAATTTTTTTATAAAAA
1 TTTAAGAA-TTTTTTATAAAAA
20027012 TAAAAAATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
25 5 0.13
26 11 0.28
27 13 0.33
28 10 0.26
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (25 bp):
TTTAAGAATTTTTTATAAAAAAATA
Found at i:20026993 original size:26 final size:25
Alignment explanation
Indices: 20026955--20027013 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
20026945 TTTTTTATAA
20026955 AAAAATTATTTAAGAT-ATTTCTGTAT
1 AAAAA-TATTTAA-ATAATTTCTGTAT
* *
20026981 AAAAATATCTTAAATAATTTTTTTAT
1 AAAAATAT-TTAAATAATTTCTGTAT
20027007 AAAAATA
1 AAAAATA
20027014 AAAAATCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 5 0.17
26 24 0.83
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
AAAAATATTTAAATAATTTCTGTAT
Found at i:20027550 original size:22 final size:25
Alignment explanation
Indices: 20027506--20027556 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 25
20027496 ATTTTTTTAT
20027506 AATAAATATCTTAATTATAATATAAA
1 AATAAATATCTT-ATTATAATATAAA
20027532 AATAAATAT-TT-TTAT-ATATAAA
1 AATAAATATCTTATTATAATATAAA
20027554 AAT
1 AAT
20027557 TTATATTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.40
23 4 0.16
25 2 0.08
26 9 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (25 bp):
AATAAATATCTTATTATAATATAAA
Found at i:20028093 original size:53 final size:53
Alignment explanation
Indices: 20027992--20028094 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 53
20027982 TCATTTTTGG
* * *
20027992 AAAACTTGATATTTCATCTCTATCATACCATGGCACTTGTGATACAAACTGCC
1 AAAACTTGATATTCCATCTCTATCACACCATGGCACTTGTAATACAAACTGCC
*
20028045 AAAACTTGATATTCCATCTCTATCACAGCATGGCACTTGTCAAT-CAAACT
1 AAAACTTGATATTCCATCTCTATCACACCATGGCACTTGT-AATACAAACT
20028095 ACCCAAACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 43 0.96
54 2 0.04
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (53 bp):
AAAACTTGATATTCCATCTCTATCACACCATGGCACTTGTAATACAAACTGCC
Found at i:20028406 original size:17 final size:20
Alignment explanation
Indices: 20028363--20028408 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 20
20028353 TTATTAATTT
20028363 AATT-TTATATTTATATATA
1 AATTATTATATTTATATATA
20028382 AATATATTATA-TTA-ATA-A
1 AAT-TATTATATTTATATATA
20028400 AATTATTAT
1 AATTATTAT
20028409 TTGATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 6 0.24
18 4 0.16
19 6 0.24
20 4 0.16
21 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
AATTATTATATTTATATATA
Found at i:20028436 original size:21 final size:22
Alignment explanation
Indices: 20028407--20028447 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20028397 TAAAATTATT
*
20028407 ATTTGATATTTT-AATTTAAAA
1 ATTTAATATTTTAAATTTAAAA
20028428 ATTTAATATTTTAAATTTAA
1 ATTTAATATTTTAAATTTAA
20028448 TAAGAGTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTAATATTTTAAATTTAAAA
Found at i:20031713 original size:108 final size:107
Alignment explanation
Indices: 20031524--20031733 Score: 316
Period size: 108 Copynumber: 1.9 Consensus size: 107
20031514 ATCAAAGATG
* *
20031524 GAATTAGTAAAAGCAAACATTTTATGGTACTTGAAGCTTCGTTGGACTAGGAACTAGAATCATCC
1 GAATTAATAAAAGCAAACATTTTATGGTA-TTGAAGCTTCATTGGACTAGGAACTAGAATCATCC
20031589 AATCTAGTTGACATATGATTGAAGAACAATTTGAAACAAGGTA
65 AATCTAGTTGACATATGATTGAAGAACAATTTGAAACAAGGTA
*
20031632 GAATTAATAAAAGCAAACATTTTACTGCGT-TT-AGGACTTCATTGGACTAGGAACTAGAATCAT
1 GAATTAATAAAAGCAAACATTTTA-TG-GTATTGAAG-CTTCATTGGACTAGGAACTAGAATCAT
* * *
20031695 CCAATCTAGTTGACATATGTTTGAATAACAGTTTGAAAC
63 CCAATCTAGTTGACATATGATTGAAGAACAATTTGAAAC
20031734 TCTATGCACC
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
107 2 0.02
108 87 0.94
109 2 0.02
110 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (107 bp):
GAATTAATAAAAGCAAACATTTTATGGTATTGAAGCTTCATTGGACTAGGAACTAGAATCATCCA
ATCTAGTTGACATATGATTGAAGAACAATTTGAAACAAGGTA
Found at i:20032064 original size:48 final size:48
Alignment explanation
Indices: 20032004--20032102 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
20031994 TATCTTATAT
* *
20032004 TATGGATATGGTTTGAACTTTGCAGCATGTGCTGATCTTACGAAAACC
1 TATGAATATGGTTTGAACTTTGCAGAATGTGCTGATCTTACGAAAACC
*
20032052 TATGAATATGGTTTGAACTTTGCATAATGTGCTGATCTTACGAAAACC
1 TATGAATATGGTTTGAACTTTGCAGAATGTGCTGATCTTACGAAAACC
20032100 TAT
1 TAT
20032103 CTTTATAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.35
Consensus pattern (48 bp):
TATGAATATGGTTTGAACTTTGCAGAATGTGCTGATCTTACGAAAACC
Found at i:20032563 original size:13 final size:12
Alignment explanation
Indices: 20032540--20032579 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
20032530 TGAAAGTTGA
20032540 TTTAAATTTAAT
1 TTTAAATTTAAT
*
20032552 TTATATATTTAAT
1 TT-TAAATTTAAT
20032565 ATTTAAATTTAAT
1 -TTTAAATTTAAT
20032578 TT
1 TT
20032580 GAATGAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 18 0.75
14 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTAAATTTAAT
Found at i:20033264 original size:11 final size:11
Alignment explanation
Indices: 20033248--20033281 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
20033238 TATTTTATTT
20033248 TTTTAATTTAA
1 TTTTAATTTAA
20033259 TTTTAATTTAA
1 TTTTAATTTAA
20033270 TATTTAAATTTA
1 T-TTT-AATTTA
20033282 GTTCGAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 3 0.14
13 6 0.29
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAATTTAA
Found at i:20033804 original size:32 final size:32
Alignment explanation
Indices: 20033743--20033806 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
20033733 TTGACGATTC
**
20033743 ATGTATTTATATTATATAAAATATTAAAATTT
1 ATGTATTTATATTATATAAAATACAAAAATTT
***
20033775 ATGTATTTATATTATATTTTATACAAAAATTT
1 ATGTATTTATATTATATAAAATACAAAAATTT
20033807 TTAAGTTAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (32 bp):
ATGTATTTATATTATATAAAATACAAAAATTT
Found at i:20041230 original size:18 final size:19
Alignment explanation
Indices: 20041200--20041235 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
20041190 TATTTTAGGA
20041200 TTAAATGTATTTATTTTAT
1 TTAAATGTATTTATTTTAT
20041219 TTAAAT-TATTTATTTTA
1 TTAAATGTATTTATTTTA
20041236 AGAAATATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTAAATGTATTTATTTTAT
Found at i:20051361 original size:417 final size:413
Alignment explanation
Indices: 20050580--20051409 Score: 1135
Period size: 417 Copynumber: 2.0 Consensus size: 413
20050570 ATATAAAAAA
* * * ** *
20050580 AATGTAAAAGAATTACGATTTTATGATATAGATACCTCATAAGATTACTGAAAATTTACTTCTAA
1 AATGTAAAAGAATTACGATTTTATGATATAAACACATCATAAGATTACAAAAAATTTACGTCTAA
* ** * *
20050645 TAAGTGTGAATATTTAAATGAAAGAGTCTATGTATATATGATGCATGAATGCACATGGTATATAT
66 TAAGTATGAATATTTAAATGAAAGAGTCTACATATATATGATGCAAGAATACACATGGTATATAT
* * *
20050710 TTGTTTAAGTTGAGAATATTTTATAAAACTAGAAAAAAATGAAAAATCTATAGATATTAATTGTG
131 TTATTTAAGTTGAGAATATTTCATAAAACTAGAAAAAAATGAAAAATCTATAGATATTAATTATG
* * *
20050775 AGTAAAATTGATTTATTTTGATGTAATTCTCTACAACTAGTAAATTTTTTTTTTTATCTATGGAC
196 AGTAAAATTGATTTATTTTGATGTAATTCTCTACAACTAATAAA--TTTTTTTTTATCAATAGAC
* * * ** *
20050840 TTAGGTCGATTAAGCTGAATCATATTAAATTATTATTTTTGTATAATTGATTGATTGTTTGATTT
259 GTAAGTCGATTAAGCTGAATCATATTAAATTATTATTTTTATATAATTGATTGATCATTTAATTT
* *
20050905 TGTTTCTGCTAGTGTGAATGTTCAATTGATTTTAAGCTTTTTGCCTAACAATTTTTACTTCTCAC
324 TGTTTCTGCTAGTGTGAATGGTCAATTGATTTAAAGCTTTTTGCCTAACAATTTTTACTTCTCA-
* *
20050970 CATTTTTTTTATCATATTTTCTCTTTC
388 C-TATTTTTTATCACATTTTCTCTTTC
* * * * *
20050997 AATGTAAAAGAGTTACGGTTTTATGGTATAAACATATCATAAGATTACAAAAAATTTACGTCTTA
1 AATGTAAAAGAATTACGATTTTATGATATAAACACATCATAAGATTACAAAAAATTTACGTCTAA
* * * *
20051062 TGAGTAT-ATATATTTAAATGAGAGAGTCTACATATATATGGTGCAAGAATACACATATGTATAT
66 TAAGTATGA-ATATTTAAATGAAAGAGTCTACATATATATGATGCAAGAATACACAT-GGTATAT
* * *
20051126 ATTTATTTAAGTTGAGAATATTTCATAAGACTAGAGAAAAATGAGAAAATCTATGGATATTAATT
129 ATTTATTTAAGTTGAGAATATTTCATAAAACTAGAAAAAAATGA-AAAATCTATAGATATTAATT
* * * *
20051191 ATGAGTAAGATTGATTTATTTTGATGTAATTTTTTACAACTAATAGA-TTTTTTTTATCAATAGA
193 ATGAGTAAAATTGATTTATTTTGATGTAATTCTCTACAACTAATAAATTTTTTTTTATCAATAGA
* * *
20051255 CGTAAGTCGATTAAGCTGAATTATGTTAAATTATTATTTTTCATATGATTGATTGATCATTTAAT
258 CGTAAGTCGATTAAGCTGAATCATATTAAATTATTATTTTT-ATATAATTGATTGATCATTTAAT
20051320 TTTGCTTT-TGCTAGTGTGAATGGTCAATTGATTTAAAGCTTTTTGCCTAACAATTTTTACTTCT
322 TTTG-TTTCTGCTAGTGTGAATGGTCAATTGATTTAAAGCTTTTTGCCTAACAATTTTTACTTCT
*
20051384 TACTATTTTTTATCACATTTTCTCTT
386 CACTATTTTTTATCACATTTTCTCTT
20051410 CTAATGTTTT
Statistics
Matches: 361, Mismatches: 47, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
415 21 0.06
416 54 0.15
417 177 0.49
418 49 0.14
419 60 0.17
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.43
Consensus pattern (413 bp):
AATGTAAAAGAATTACGATTTTATGATATAAACACATCATAAGATTACAAAAAATTTACGTCTAA
TAAGTATGAATATTTAAATGAAAGAGTCTACATATATATGATGCAAGAATACACATGGTATATAT
TTATTTAAGTTGAGAATATTTCATAAAACTAGAAAAAAATGAAAAATCTATAGATATTAATTATG
AGTAAAATTGATTTATTTTGATGTAATTCTCTACAACTAATAAATTTTTTTTTATCAATAGACGT
AAGTCGATTAAGCTGAATCATATTAAATTATTATTTTTATATAATTGATTGATCATTTAATTTTG
TTTCTGCTAGTGTGAATGGTCAATTGATTTAAAGCTTTTTGCCTAACAATTTTTACTTCTCACTA
TTTTTTATCACATTTTCTCTTTC
Found at i:20053086 original size:35 final size:38
Alignment explanation
Indices: 20053024--20053097 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 38
20053014 TCAAAAAGAA
* *
20053024 TTTTAAAATTTTTTTTGAATTTATATA-TTGAAAATTT
1 TTTTAAAATGTTTTTAGAATTTATATATTTGAAAATTT
*
20053061 TTTTAAAA-GTTTTTAG-ATTTGTATATTTGAAAATTT
1 TTTTAAAATGTTTTTAGAATTTATATATTTGAAAATTT
20053097 T
1 T
20053098 AAAATTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.24
36 17 0.52
37 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (38 bp):
TTTTAAAATGTTTTTAGAATTTATATATTTGAAAATTT
Found at i:20053548 original size:12 final size:13
Alignment explanation
Indices: 20053490--20053558 Score: 67
Period size: 12 Copynumber: 5.5 Consensus size: 13
20053480 AATATTATTT
20053490 TAAATATAAATATA
1 TAAAT-TAAATATA
20053504 -AAATTAAATATA
1 TAAATTAAATATA
20053516 TATAA--AAATATA
1 TA-AATTAAATATA
20053528 TAAATTTAAATATA
1 TAAA-TTAAATATA
*
20053542 -AAATTAAA-AAA
1 TAAATTAAATATA
20053553 TAAATT
1 TAAATT
20053559 TTTTTATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
11 4 0.08
12 27 0.56
13 8 0.17
14 9 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TAAATTAAATATA
Found at i:20056506 original size:4 final size:4
Alignment explanation
Indices: 20056499--20056527 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
20056489 ACATACACAC
20056499 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
20056528 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:20056532 original size:2 final size:2
Alignment explanation
Indices: 20056525--20056557 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20056515 ACATACATAC
20056525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20056558 GATACACACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20062407 original size:20 final size:20
Alignment explanation
Indices: 20062384--20062436 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
20062374 AAATTAAAAA
*
20062384 TATTAATAGTAAATTTAATC
1 TATTAATGGTAAATTTAATC
20062404 TATTAATGGTAAATTTAATC
1 TATTAATGGTAAATTTAATC
20062424 TATTAATGGTAAA
1 TATTAATGGTAAA
20062437 AAGATTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.43
Consensus pattern (20 bp):
TATTAATGGTAAATTTAATC
Found at i:20062519 original size:209 final size:215
Alignment explanation
Indices: 20062044--20062602 Score: 586
Period size: 209 Copynumber: 2.6 Consensus size: 215
20062034 GAAGAGTTTC
* *
20062044 CAATATATAAATTTAGTATGCGATTAACCCCTTCAAAACAATTGATAATATGAAGTATGAACATT
1 CAATATATAAATTTAGTATGCGATTAATCCCTTC-AAACACTTGATAATATGAAGTATGAACATT
* *
20062109 AAAAAGTCTTGGTCGTCTGATTTGTAGATACATTTGCTTTTAACTGATTTTGAACCAAATTAAAA
65 -AAAAGTCTAGGTCGTCTG--TTGTAGACACATTTGCTTTTAACTGATTTTGAACCAAATTAAAA
* * *
20062174 TATAAATAATAAATTTGATCTATCAGTATAAATTTGATCTATTAATAGTAAAAAAATTTATTAAA
127 TATAAATAATAAATTTAATCTATCAATATAAATTTAATCTATTAATAGTAAAAAAATTTATTAAA
20062239 AATGTCATTTGTAAAAAAAAAAATT
192 AATGTCATTTGT-AAAAAAAAAATT
* * **
20062264 CAATATATTAATTTAGTACGCGATTAATTCCC-TCAAGATGCTTGATAATATGAAGTATG-A-A-
1 CAATATATAAATTTAGTATGCGATTAA-TCCCTTCAA-ACACTTGATAATATGAAGTATGAACAT
* * *
20062325 T-AAA-TCTAGGTCGTCTG-TG-A-ACACCTTTGCTTTTGATTGATTTTGAACCAAATTAAAAAT
64 TAAAAGTCTAGGTCGTCTGTTGTAGACACATTTGCTTTTAACTGATTTTGAACCAAATT-AAAAT
* * * * * *
20062385 ATTAATAGTAAATTTAATCTATTAATGGTAAATTTAATCTATTAATGGTAAAAAGATTTATTAAA
128 ATAAATAATAAATTTAATCTATCAAT-ATAAATTTAATCTATTAATAGTAAAAAAATTTATTAAA
* ** **
20062450 AATGTCGTTTGT-AAAATCATTTT
192 AATGTCATTTGTAAAAAAAAAATT
* * * *
20062473 CAATATATAAATTTAATATGCGATTAATCCCTTCAAACCACTTGATAATATGAAATATAAACATC
1 CAATATATAAATTTAGTATGCGATTAATCCCTTCAAA-CACTTGATAATATGAAGTATGAACATT
* * * *
20062538 AAAATGTCTTGATCGTCTGATTTGT-GTACAC-TTATGC-TTTAGATTGATTTTGAACTAAATTA
65 AAAA-GTCTAGGTCGTCTG--TTGTAG-ACACATT-TGCTTTTA-ACTGATTTTGAACCAAATTA
20062600 AAA
124 AAA
20062603 AATATAATGG
Statistics
Matches: 282, Mismatches: 37, Indels: 41
0.78 0.10 0.11
Matches are distributed among these distances:
208 5 0.02
209 82 0.29
210 28 0.10
211 48 0.17
213 3 0.01
214 12 0.04
215 14 0.05
217 1 0.00
218 3 0.01
219 12 0.04
220 71 0.25
221 3 0.01
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (215 bp):
CAATATATAAATTTAGTATGCGATTAATCCCTTCAAACACTTGATAATATGAAGTATGAACATTA
AAAGTCTAGGTCGTCTGTTGTAGACACATTTGCTTTTAACTGATTTTGAACCAAATTAAAATATA
AATAATAAATTTAATCTATCAATATAAATTTAATCTATTAATAGTAAAAAAATTTATTAAAAATG
TCATTTGTAAAAAAAAAATT
Found at i:20065653 original size:21 final size:22
Alignment explanation
Indices: 20065629--20065675 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
20065619 GAATGTAGAT
*
20065629 ATTACCTTAAATTAA-AAA-AAA
1 ATTACCTT-AATAAATAAATAAA
20065650 ATTA-CTTAATAAATAAATAAA
1 ATTACCTTAATAAATAAATAAA
20065671 ATTAC
1 ATTAC
20065676 TCATGAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 5 0.23
20 6 0.27
21 11 0.50
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.32
Consensus pattern (22 bp):
ATTACCTTAATAAATAAATAAA
Found at i:20068458 original size:43 final size:43
Alignment explanation
Indices: 20068397--20068492 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
20068387 GTTTGAACAG
* * *
20068397 CAAAAGGTCTTGGTCTTCTGCAAGGGGCGGTGGATGAGAAGAT
1 CAAAAGGTCTAGGTCTTCTGCAAGGGCCGGTGGATGAGAAGAC
20068440 CAAAAGGTCTAGGTCTTCTGCAAGGGCCGGTGGATGAGAAGAC
1 CAAAAGGTCTAGGTCTTCTGCAAGGGCCGGTGGATGAGAAGAC
20068483 CAAAAGGTCT
1 CAAAAGGTCT
20068493 TGGCCTTCAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.34, T:0.21
Consensus pattern (43 bp):
CAAAAGGTCTAGGTCTTCTGCAAGGGCCGGTGGATGAGAAGAC
Found at i:20068843 original size:29 final size:29
Alignment explanation
Indices: 20068811--20068875 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
20068801 AATAAATAAA
* *
20068811 TTTATATTTTAAGTACTGTATTAAATATT
1 TTTATATTTGAAGTACTATATTAAATATT
* * *
20068840 TTTAAAATTGAAGTATTATATTAAATATT
1 TTTATATTTGAAGTACTATATTAAATATT
*
20068869 TTAATAT
1 TTTATAT
20068876 AATTTAAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (29 bp):
TTTATATTTGAAGTACTATATTAAATATT
Found at i:20069975 original size:2 final size:2
Alignment explanation
Indices: 20069970--20070002 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20069960 TGTGTGTGCG
20069970 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
20070003 ATATATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:20070007 original size:2 final size:2
Alignment explanation
Indices: 20070002--20070028 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
20069992 TCTCTCTCTC
20070002 TA 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 TA T
20070029 TCTCTTACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20071794 original size:21 final size:21
Alignment explanation
Indices: 20071770--20071809 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
20071760 ATTATATTTT
20071770 AATAATAA-TATTTAATATTAA
1 AATAA-AACTATTTAATATTAA
*
20071791 AATAAAACTATTTATTATT
1 AATAAAACTATTTAATATT
20071810 CTTTATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAAAACTATTTAATATTAA
Found at i:20071825 original size:23 final size:23
Alignment explanation
Indices: 20071814--20072147 Score: 103
Period size: 23 Copynumber: 15.0 Consensus size: 23
20071804 ATTATTCTTT
20071814 ATATTATTTATTAATGTATTATA
1 ATATTATTTATTAATGTATTATA
*
20071837 ATATTATTTATTAATAATATT-T-
1 ATATTATTTATTAAT-GTATTATA
* * *
20071859 AT-TAATATATTACAT-TAATAGT-
1 ATATTATTTATTA-ATGTATTA-TA
* *
20071881 ATATTATTTATTAATATATTATT
1 ATATTATTTATTAATGTATTATA
*
20071904 ATAATATTTATTAAT-TAAATTAATA
1 ATATTATTTATTAATGT--ATT-ATA
* *
20071929 ATTTTATTATTATATAATTTATTAATATA
1 ATATTA-T-TTAT-TAATGTA-T--TATA
*
20071958 ATATTATCTATT-A--TATTATA
1 ATATTATTTATTAATGTATTATA
* *
20071978 ATATTATTTCTTAATATTATTTATTA
1 ATATTATTTATTAAT-GTA-TTA-TA
* *
20072004 ATA-GATTATATTAA--TAGT-T-
1 ATATTATT-TATTAATGTATTATA
* *
20072023 -TATTATTTCTTAATATATTATA
1 ATATTATTTATTAATGTATTATA
20072045 ATATTATTTATT-A---A-TATA
1 ATATTATTTATTAATGTATTATA
* * *
20072063 ATCTGATTTATTTAT-TA-TATA
1 ATATTATTTATTAATGTATTATA
20072084 ATATTATTTATTAA--TA-T-TA
1 ATATTATTTATTAATGTATTATA
* *
20072103 ATA-TATTTGTATAATAT-TTATA
1 ATATTATTTAT-TAATGTATTATA
* **
20072125 ATAATATTTATTAAAATATTATA
1 ATATTATTTATTAATGTATTATA
20072148 TTAAAAGTAT
Statistics
Matches: 241, Mismatches: 30, Indels: 80
0.69 0.09 0.23
Matches are distributed among these distances:
18 27 0.11
19 13 0.05
20 24 0.10
21 28 0.12
22 24 0.10
23 67 0.28
24 9 0.04
25 13 0.05
26 12 0.05
27 8 0.03
28 6 0.02
29 9 0.04
30 1 0.00
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (23 bp):
ATATTATTTATTAATGTATTATA
Found at i:20071841 original size:16 final size:16
Alignment explanation
Indices: 20071822--20072006 Score: 60
Period size: 16 Copynumber: 11.9 Consensus size: 16
20071812 TTATATTATT
20071822 TATTAATGTATT-ATAA
1 TATT-ATGTATTAATAA
*
20071838 TATTATTTATTAATAA
1 TATTATGTATTAATAA
20071854 TA-T-T-TATTAAT-A
1 TATTATGTATTAATAA
*
20071866 TATTA--CATTAATAGTA
1 TATTATGTATTAATA--A
*
20071882 TATTATTTATTAAT-A
1 TATTATGTATTAATAA
*
20071897 TATTAT-TA-TAATATT
1 TATTATGTATTAATA-A
20071912 TATTAAT-TAAATTAATAA
1 TATT-ATGT--ATTAATAA
*
20071930 TTTTAT-TATTATATAA
1 TATTATGTATTA-ATAA
*
20071946 T-TTAT-TAAT-ATAA
1 TATTATGTATTAATAA
* *
20071959 TATTATCTATTATATTA
1 TATTATGTATTA-ATAA
* **
20071976 TAATAT-TATTTCTTAA
1 TATTATGTA-TTAATAA
*
20071992 TATTATTTATTAATA
1 TATTATGTATTAATA
20072007 GATTATATTA
Statistics
Matches: 132, Mismatches: 16, Indels: 42
0.69 0.08 0.22
Matches are distributed among these distances:
12 3 0.02
13 23 0.17
14 7 0.05
15 32 0.24
16 37 0.28
17 15 0.11
18 10 0.08
19 5 0.04
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
TATTATGTATTAATAA
Found at i:20071975 original size:38 final size:37
Alignment explanation
Indices: 20071895--20071994 Score: 107
Period size: 38 Copynumber: 2.7 Consensus size: 37
20071885 TATTTATTAA
20071895 TATATTATTATA-ATATTTATTAAT-TAAATTAATAAT
1 TATATTATTATATA-ATTTATTAATATAAATTAATAAT
* *
20071931 TTTATTATTATATAATTTATTAATATAATATT-ATCTAT
1 TATATTATTATATAATTTATTAATATAA-ATTAAT-AAT
* * *
20071969 TATATTATAATATTATTTCTTAATAT
1 TATATTATTATATAATTTATTAATAT
20071995 TATTTATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
36 21 0.39
37 6 0.11
38 27 0.50
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (37 bp):
TATATTATTATATAATTTATTAATATAAATTAATAAT
Found at i:20071999 original size:141 final size:136
Alignment explanation
Indices: 20071830--20072215 Score: 417
Period size: 141 Copynumber: 2.8 Consensus size: 136
20071820 TTTATTAATG
*
20071830 TATTATAATATTATTTATTAATAATATTTATTAATATATTACATTAATAGTATATTATTTATTAA
1 TATTATAATATTATTT-TTAATAATATTTATTAATATATTATATTAATAGTATATTATTTATTAA
*
20071895 TATATTATTATAATATTTATTAAT-TAAATTAATAATTT-TATTATTATATAAT-TTATTAATAT
65 TATATTATAATAATATTTATTAATAT-AA-T-ATAATTTAT-TTATTATATAATATTATTAAT-T
*
20071957 AATATTATCTATTA
125 AATATTA-ATA-TA
* * * *
20071971 TATTATAATATTATTTCTTAATATTATTTATTAATAGATTATATTAATAGTTTATTATTTCTTAA
1 TATTATAATATTATTT-TTAATAATATTTATTAATATATTATATTAATAGTATATTATTTATTAA
* * * *
20072036 TATATTATAATATTATTTATTAATATAATCTGATTTATTTATTATATAATATTATTTATTAATAT
65 TATATTATAATAATATTTATTAATATAATATAATTTATTTATTATATAATATTATTAATTAATAT
20072101 TAATATA
130 TAATATA
* * * * *
20072108 T-TTGT-ATAATATTTATAATAATATTTATTAAAATATTATATTAAAAGTATATTATTTA-TAAT
1 TATTATAATATTATTTTTAATAATATTTATTAATATATTATATTAATAGTATATTATTTATTAAT
* * *
20072170 ATTTTCTAAT-ATAATATTATTTATTTATTAATATAATATTATTTAT
66 ATATTATAATAAT-AT-TTA-TTA-ATA-TAATATAAT-TTATTTAT
20072216 AAGTAAAATA
Statistics
Matches: 209, Mismatches: 27, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
132 1 0.00
133 14 0.07
134 40 0.19
135 11 0.05
136 5 0.02
137 10 0.05
138 10 0.05
139 25 0.12
140 9 0.04
141 83 0.40
142 1 0.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (136 bp):
TATTATAATATTATTTTTAATAATATTTATTAATATATTATATTAATAGTATATTATTTATTAAT
ATATTATAATAATATTTATTAATATAATATAATTTATTTATTATATAATATTATTAATTAATATT
AATATA
Found at i:20072043 original size:31 final size:30
Alignment explanation
Indices: 20071992--20072057 Score: 87
Period size: 31 Copynumber: 2.2 Consensus size: 30
20071982 TATTTCTTAA
*
20071992 TATTATTTATTAATAGATTATATTAATAGTT
1 TATTATTTATTAATAGATTATAATAATA-TT
* * *
20072023 TATTATTTCTTAATATATTATAATATTATT
1 TATTATTTATTAATAGATTATAATAATATT
20072053 TATTA
1 TATTA
20072058 ATATAATCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (30 bp):
TATTATTTATTAATAGATTATAATAATATT
Found at i:20072186 original size:27 final size:25
Alignment explanation
Indices: 20072156--20072217 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 25
20072146 TATTAAAAGT
*
20072156 ATATTATTTATAATATTTTCTAATATA
1 ATATTATTTATAAT-TTAT-TAATATA
20072183 ATATTA-TT-T-ATTTATTAATATA
1 ATATTATTTATAATTTATTAATATA
20072205 ATATTATTTATAA
1 ATATTATTTATAA
20072218 GTAAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
22 13 0.42
23 5 0.16
24 3 0.10
25 2 0.06
26 2 0.06
27 6 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (25 bp):
ATATTATTTATAATTTATTAATATA
Found at i:20072373 original size:22 final size:22
Alignment explanation
Indices: 20072328--20072377 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
20072318 AAAAATAGTC
**
20072328 TTATTTTTTATTGATTAATAAA
1 TTATTTTTTATTGACCAATAAA
* *
20072350 TTATTTTTTATTTACCAATCAA
1 TTATTTTTTATTGACCAATAAA
20072372 TT-TTTT
1 TTATTTT
20072378 GTCAAACATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (22 bp):
TTATTTTTTATTGACCAATAAA
Found at i:20073062 original size:30 final size:30
Alignment explanation
Indices: 20073028--20073109 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
20073018 CCCAAGATAG
* *
20073028 AATTC-TAAAAAATCTCAAAAAAAGTTAAAA
1 AATTCTTAAAAAAT-TCAAAAAAAATAAAAA
* *
20073058 AATTCTTTAAATATTCAAAAAAAATAAAAA
1 AATTCTTAAAAAATTCAAAAAAAATAAAAA
** * *
20073088 AATGATTAAAAATTTTAAAAAA
1 AATTCTTAAAAAATTCAAAAAA
20073110 TTCTATAGTT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 35 0.85
31 6 0.15
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.28
Consensus pattern (30 bp):
AATTCTTAAAAAATTCAAAAAAAATAAAAA
Found at i:20073149 original size:28 final size:28
Alignment explanation
Indices: 20073093--20073165 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
20073083 AAAAAAATGA
* *
20073093 TTAAAAATTTTAAAAAATTCTATAGTTT
1 TTAAAAATTTTAAAAAATTCTACAATTT
* * *
20073121 TTAAGAATTTTAAAACATTTTACAATTT
1 TTAAAAATTTTAAAAAATTCTACAATTT
*
20073149 TCTAAAAAAATTTAAAA
1 T-T-AAAAATTTTAAAA
20073166 TTTTCAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
28 24 0.67
29 1 0.03
30 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (28 bp):
TTAAAAATTTTAAAAAATTCTACAATTT
Found at i:20073176 original size:19 final size:19
Alignment explanation
Indices: 20073120--20073177 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
20073110 TTCTATAGTT
* *
20073120 TTTAAGAATTTT-AAAACAT
1 TTTAA-AATTTTCAAAAAAA
*
20073139 TTTACAATTTTCTAAAAAAA
1 TTTAAAATTTTC-AAAAAAA
20073159 TTTAAAATTTTCAAAAAAA
1 TTTAAAATTTTCAAAAAAA
20073178 ATCAAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.18
19 11 0.33
20 16 0.48
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.40
Consensus pattern (19 bp):
TTTAAAATTTTCAAAAAAA
Found at i:20073184 original size:19 final size:20
Alignment explanation
Indices: 20073144--20073184 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
20073134 AACATTTTAC
* *
20073144 AATTTTCTAAAAAAATTTAA
1 AATTTTCTAAAAAAAATCAA
20073164 AATTTTC-AAAAAAAATCAA
1 AATTTTCTAAAAAAAATCAA
20073183 AA
1 AA
20073185 CAATTCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTTTCTAAAAAAAATCAA
Found at i:20073227 original size:10 final size:10
Alignment explanation
Indices: 20073212--20073270 Score: 52
Period size: 11 Copynumber: 6.0 Consensus size: 10
20073202 AATTTTCAAA
20073212 AAAAAATTCT
1 AAAAAATTCT
*
20073222 AAAAAATTTTT
1 AAAAAA-TTCT
*
20073233 AAAAAATTATT
1 AAAAAATT-CT
20073244 AAAAAATT-T
1 AAAAAATTCT
*
20073253 --AAAATTCA
1 AAAAAATTCT
20073261 AAAAAATTCT
1 AAAAAATTCT
20073271 CAATAAATAC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
7 6 0.15
9 1 0.02
10 15 0.37
11 19 0.46
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAAATTCT
Found at i:20073236 original size:22 final size:22
Alignment explanation
Indices: 20073212--20073252 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20073202 AATTTTCAAA
20073212 AAAAAATT-CTAAAAAATTTTT
1 AAAAAATTACTAAAAAATTTTT
*
20073233 AAAAAATTATTAAAAAATTT
1 AAAAAATTACTAAAAAATTT
20073253 AAAATTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AAAAAATTACTAAAAAATTTTT
Found at i:20073237 original size:12 final size:11
Alignment explanation
Indices: 20073212--20073251 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
20073202 AATTTTCAAA
*
20073212 AAAAAATT-CT
1 AAAAAATTATT
*
20073222 AAAAAATTTTT
1 AAAAAATTATT
20073233 AAAAAATTATT
1 AAAAAATTATT
20073244 AAAAAATT
1 AAAAAATT
20073252 TAAAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (11 bp):
AAAAAATTATT
Found at i:20073377 original size:19 final size:20
Alignment explanation
Indices: 20073339--20073382 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
20073329 ATAACAATTC
**
20073339 TAAAAAACTCTAAATTTTTT
1 TAAAAAACTCTAAAAGTTTT
20073359 TAAAAAA-TCTAAAAGTTTT
1 TAAAAAACTCTAAAAGTTTT
*
20073378 GAAAA
1 TAAAA
20073383 CTTTTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (20 bp):
TAAAAAACTCTAAAAGTTTT
Found at i:20073377 original size:20 final size:20
Alignment explanation
Indices: 20073339--20073377 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
20073329 ATAACAATTC
*
20073339 TAAAAAACTCTAAATTTTTT
1 TAAAAAACTCTAAAGTTTTT
20073359 TAAAAAA-TCTAAAAGTTTT
1 TAAAAAACTCT-AAAGTTTT
20073378 GAAAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (20 bp):
TAAAAAACTCTAAAGTTTTT
Found at i:20073840 original size:10 final size:10
Alignment explanation
Indices: 20073804--20073863 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
20073794 TTTTCAGATT
20073804 TTTTTTAAAAA
1 TTTTTT-AAAA
*
20073815 TTTGTTTACAA
1 TTT-TTTAAAA
20073826 TTTTTTAAAA
1 TTTTTTAAAA
* * *
20073836 ATTTTCAGAA
1 TTTTTTAAAA
*
20073846 TTTTTTATAA
1 TTTTTTAAAA
20073856 TTTTTTAA
1 TTTTTTAA
20073864 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
10 27 0.69
11 9 0.23
12 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:20073851 original size:22 final size:22
Alignment explanation
Indices: 20073789--20073851 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
20073779 CAAAAAGATG
20073789 AAAAATTTTCAG-ATTTTTTTT
1 AAAAATTTTCAGAATTTTTTTT
* *
20073810 AAAAATTTGTTTACAA--TTTTTT
1 AAAAA-TT-TTCAGAATTTTTTTT
20073832 AAAAATTTTCAGAATTTTTT
1 AAAAATTTTCAGAATTTTTT
20073852 ATAATTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 17 0.52
23 3 0.09
24 1 0.03
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (22 bp):
AAAAATTTTCAGAATTTTTTTT
Found at i:20073882 original size:17 final size:17
Alignment explanation
Indices: 20073856--20073895 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
20073846 TTTTTTATAA
20073856 TTTTTTAATTTA-AAAT
1 TTTTTTAATTTATAAAT
20073872 TTTTTTCAATTTATTAAAT
1 TTTTTT-AATTTA-TAAAT
20073891 TTTTT
1 TTTTT
20073896 ATAGAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.29
17 6 0.29
19 9 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTTTTAATTTATAAAT
Found at i:20074661 original size:11 final size:11
Alignment explanation
Indices: 20074634--20074688 Score: 83
Period size: 11 Copynumber: 4.9 Consensus size: 11
20074624 AAAATTAAAA
20074634 AATATTAATTTT
1 AATA-TAATTTT
* *
20074646 TATATTATTTT
1 AATATAATTTT
20074657 AATATAATTTT
1 AATATAATTTT
20074668 AATATAATTTT
1 AATATAATTTT
20074679 AATATAATTT
1 AATATAATTT
20074689 CTCACCCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
11 36 0.92
12 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
AATATAATTTT
Found at i:20075126 original size:14 final size:14
Alignment explanation
Indices: 20075107--20075139 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20075097 ATATCATTTG
20075107 TAATT-ATTATATTA
1 TAATTAATTA-ATTA
20075121 TAATTAATTAATTA
1 TAATTAATTAATTA
20075135 TAATT
1 TAATT
20075140 TAAAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TAATTAATTAATTA
Found at i:20075135 original size:22 final size:23
Alignment explanation
Indices: 20075107--20075160 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
20075097 ATATCATTTG
*
20075107 TAATTATTATATTATAATTA-AT
1 TAATTATTATATTAAAATTATAT
*
20075129 TAATTATAAT-TTAAAATTATAT
1 TAATTATTATATTAAAATTATAT
*
20075151 AAATT-TTATA
1 TAATTATTATA
20075161 AAAATTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTATTATATTAAAATTATAT
Found at i:20075159 original size:11 final size:11
Alignment explanation
Indices: 20075145--20075175 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
20075135 TAATTTAAAA
20075145 TTATATAAATT
1 TTATATAAATT
*
20075156 TTATAAAAATT
1 TTATATAAATT
20075167 TTATATAAA
1 TTATATAAA
20075176 ATTCATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
TTATATAAATT
Found at i:20077806 original size:31 final size:30
Alignment explanation
Indices: 20077756--20077819 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 30
20077746 TATATACTTT
20077756 AAGATTTTTATCTCTCATGTGTATCATTTG
1 AAGATTTTTATCTCTCATGTGTATCATTTG
* *
20077786 AAGATTGTTTGTCTGTCATGTGTATCATTTG
1 AAGATT-TTTATCTCTCATGTGTATCATTTG
20077817 AAG
1 AAG
20077820 CTAGCAACAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.23, C:0.11, G:0.19, T:0.47
Consensus pattern (30 bp):
AAGATTTTTATCTCTCATGTGTATCATTTG
Found at i:20078883 original size:2 final size:2
Alignment explanation
Indices: 20078878--20078912 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20078868 TGTGTGTGTT
20078878 TA TA TA TA TA 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 TA TA TA TA TA T
20078913 CCGGTTTGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20079262 original size:21 final size:21
Alignment explanation
Indices: 20079221--20079263 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
20079211 TAACTTAAGT
** *
20079221 TCATCTTTTTTTTTTCTTTTC
1 TCATCTTTTTTCCTTCCTTTC
20079242 TCATCTTTTTTCCTTCCTTTC
1 TCATCTTTTTTCCTTCCTTTC
20079263 T
1 T
20079264 ATAGAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.70
Consensus pattern (21 bp):
TCATCTTTTTTCCTTCCTTTC
Found at i:20084189 original size:21 final size:20
Alignment explanation
Indices: 20084134--20084189 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 20
20084124 TAATAATATT
20084134 TTTATAAAATTAATTTATAAAA
1 TTTATAAAA--AATTTATAAAA
* *
20084156 TTCT-TCAATAATTTGATAAAA
1 TT-TATAAAAAATTT-ATAAAA
20084177 TTTATAAAAAATT
1 TTTATAAAAAATT
20084190 ATCCAATAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
20 6 0.22
21 15 0.56
22 5 0.19
23 1 0.04
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.45
Consensus pattern (20 bp):
TTTATAAAAAATTTATAAAA
Found at i:20084197 original size:32 final size:30
Alignment explanation
Indices: 20084145--20084213 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 30
20084135 TTATAAAATT
* *
20084145 AATTTATAAAATTCTTCAATAATTTGATAA
1 AATTTATAAAATTATCCAATAATTTGATAA
*
20084175 AATTTATAAAAAATTATCCAATAGTTTGATAA
1 AATTTAT--AAAATTATCCAATAATTTGATAA
*
20084207 GATTTAT
1 AATTTAT
20084214 GAATTTATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 7 0.21
32 26 0.79
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (30 bp):
AATTTATAAAATTATCCAATAATTTGATAA
Done.