Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 59 of 198
Found at i:18105163 original size:127 final size:127
Alignment explanation
Indices: 18104937--18105193 Score: 401
Period size: 127 Copynumber: 2.0 Consensus size: 127
18104927 AGAAGTAAAC
* * *
18104937 TAGAGCAGGTGATGATGTGATTTCCAGAGCTTGAATTGTTTGGAAAGTAGCTCGATTGGGTTGGA
1 TAGAGCAGGTGATGATGTGAGTTCCAGAACTTGAATAGTTTGGAAAGTAGCTCGATTGGGTTGGA
**
18105002 TCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTATGAGCTAAAGAACCT
66 TCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTAACAGCTAAAGAACCT
* *
18105064 TAGAGCAGGTGATGATGTGAGTTCTC-GAATTTGAATAGTTTGGGAAA-TAGCTCGATTGGGTTT
1 TAGAGCAGGTGATGATGTGAGTTC-CAGAACTTGAATAGTTT-GGAAAGTAGCTCGATTGGGTTG
* *
18105127 GATCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTGTAGTAGTAACAGCTAAAGAACCT
64 GATCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTAACAGCTAAAGAACCT
18105191 TAG
1 TAG
18105194 CTATATTAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
127 113 0.95
128 6 0.05
ACGTcount: A:0.29, C:0.13, G:0.28, T:0.30
Consensus pattern (127 bp):
TAGAGCAGGTGATGATGTGAGTTCCAGAACTTGAATAGTTTGGAAAGTAGCTCGATTGGGTTGGA
TCGTCTTGAAATGGTTCAACGGATGGAAACCTTGACCTATAATAGTAACAGCTAAAGAACCT
Found at i:18113715 original size:50 final size:50
Alignment explanation
Indices: 18113656--18113756 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
18113646 ATTTCTTGGG
18113656 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
1 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
18113706 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
1 TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
18113756 T
1 T
18113757 CTAGCATCAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.27
Consensus pattern (50 bp):
TACACATTGAACAGGGCTTACAACAAACTATCAAAAATAGGGTATATTAT
Found at i:18115878 original size:33 final size:33
Alignment explanation
Indices: 18115809--18115990 Score: 129
Period size: 27 Copynumber: 5.6 Consensus size: 33
18115799 ATAAAAAGGG
*
18115809 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
*
18115836 GGTTGCTAAGTGTTGATTCCCCTATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
* *
18115869 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-TA--TT-CAT-T---GGT
*
18115911 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
*
18115938 GGTTGCTAAGTGCTGATT-CCCTGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCT-ATTCATTGGT
18115971 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
18115991 ACCGTATCTT
Statistics
Matches: 124, Mismatches: 8, Indels: 39
0.73 0.05 0.23
Matches are distributed among these distances:
26 3 0.02
27 39 0.31
28 2 0.02
31 4 0.03
32 4 0.03
33 38 0.31
34 3 0.02
35 2 0.02
37 2 0.02
38 2 0.02
39 1 0.01
41 2 0.02
42 22 0.18
ACGTcount: A:0.18, C:0.21, G:0.28, T:0.33
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCTATTCATTGGT
Found at i:18115931 original size:102 final size:102
Alignment explanation
Indices: 18115804--18116034 Score: 412
Period size: 102 Copynumber: 2.3 Consensus size: 102
18115794 ATTGAATAAA
* *
18115804 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGTTGATTCCCCT-ATTCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATT-CCCTGACTCATTGG
18115868 TGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
65 TGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
18115906 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCATTGGT
18115971 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
66 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
*
18116008 AAAGGGGTTGCTAAGTGCTGA-TCCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCCC
18116035 GACTCATTGG
Statistics
Matches: 125, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
101 10 0.08
102 115 0.92
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (102 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCTGACTCATTGGT
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
Found at i:18120856 original size:18 final size:19
Alignment explanation
Indices: 18120833--18120869 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
18120823 ATTATCACAT
*
18120833 ATGTAACACATAAT-TATG
1 ATGTAAAACATAATCTATG
18120851 ATGTAAAACATAATCTATG
1 ATGTAAAACATAATCTATG
18120870 GAATAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (19 bp):
ATGTAAAACATAATCTATG
Found at i:18121837 original size:25 final size:25
Alignment explanation
Indices: 18121809--18121858 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
18121799 TTTATAGGAA
*
18121809 CCTTTAAGCAAATTACCTTTTTTTT
1 CCTTTAAGCAAATTAACTTTTTTTT
* * *
18121834 CCTTTTATCAAATTAATTTTTTTTT
1 CCTTTAAGCAAATTAACTTTTTTTT
18121859 TAAAAAAGCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.02, T:0.58
Consensus pattern (25 bp):
CCTTTAAGCAAATTAACTTTTTTTT
Found at i:18129077 original size:49 final size:49
Alignment explanation
Indices: 18129010--18129206 Score: 205
Period size: 49 Copynumber: 4.0 Consensus size: 49
18129000 CCATATAGGC
* *
18129010 TTCCCAAATGACTCGCCACAAAGGCTTTACAGATGATCCACCACAAAGG
1 TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
* * * * *** *
18129059 TTCCTAGATGTCTTGCCACAAAGGTTTTACAAATGATTTGCCACAAAGC
1 TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
** * * *
18129108 TTCCCAGATGACTCATCACAAAGGCTTTACAGACGATCCACCAAAAAGG
1 TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
* * * **
18129157 CTTCCCAAATGACTCGCCATAAAGGCTTTACAAATTATCTGCCACAAAGG
1 -TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
18129207 CTTTACAGAT
Statistics
Matches: 114, Mismatches: 33, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
49 75 0.66
50 39 0.34
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (49 bp):
TTCCCAGATGACTCGCCACAAAGGCTTTACAAATGATCCACCACAAAGG
Found at i:18129129 original size:98 final size:99
Alignment explanation
Indices: 18129008--18129205 Score: 272
Period size: 98 Copynumber: 2.0 Consensus size: 99
18128998 CACCATATAG
* * * * * *
18129008 GCTTCCCAAATGACTCGCCACAAAGGCTTTACAGATGATCCACCACAAAGG-TTCCTAGATGTCT
1 GCTTCCCAAATGACTCACCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
* * *
18129072 TGCCACAAAGGTTTTACAAATGATTTGCCACAAA
66 CGCCACAAAGGCTTTACAAATGATCTGCCACAAA
* *
18129106 GCTTCCCAGATGACTCATCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
1 GCTTCCCAAATGACTCACCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
* *
18129171 CGCCATAAAGGCTTTACAAATTATCTGCCACAAA
66 CGCCACAAAGGCTTTACAAATGATCTGCCACAAA
18129205 G
1 G
18129206 GCTTTACAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
98 46 0.53
99 40 0.47
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.23
Consensus pattern (99 bp):
GCTTCCCAAATGACTCACCACAAAGGCTTTACAGACGATCCACCAAAAAGGCTTCCCAAATGACT
CGCCACAAAGGCTTTACAAATGATCTGCCACAAA
Found at i:18129225 original size:50 final size:49
Alignment explanation
Indices: 18129171--18129360 Score: 170
Period size: 50 Copynumber: 3.8 Consensus size: 49
18129161 CCAAATGACT
* *
18129171 CGCCATAAAGGCTTTACAAATTATCTGCCACAAAGGCTTTACAGATTATC
1 CGCCATAAAGGCTTT-CAGATTATCTGCCACAAAGGCTTTACAGATGATC
* * *
18129221 CGCCATAAAGGCTTCTGAGA-TATCTTCTCACAAAGGCTTTACAGATGATT
1 CGCCATAAAGGCTT-TCAGATTATCTGC-CACAAAGGCTTTACAGATGATC
* * ** * *
18129271 CACCACAAAGGCATCGCAGATGA-CTCGTCACAAAGGCTTTACAGATGATC
1 CGCCATAAAGGC-TTTCAGATTATCT-GCCACAAAGGCTTTACAGATGATC
* * *
18129321 CGCCATAAAGGCTTCCTAGA-TGTCATACCACAAAGGCTTT
1 CGCCATAAAGGCTTTC-AGATTATC-TGCCACAAAGGCTTT
18129361 TCAAATCAAT
Statistics
Matches: 110, Mismatches: 22, Indels: 16
0.74 0.15 0.11
Matches are distributed among these distances:
49 8 0.07
50 98 0.89
51 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (49 bp):
CGCCATAAAGGCTTTCAGATTATCTGCCACAAAGGCTTTACAGATGATC
Found at i:18129342 original size:25 final size:25
Alignment explanation
Indices: 18129023--18129334 Score: 201
Period size: 25 Copynumber: 12.6 Consensus size: 25
18129013 CCAAATGACT
18129023 CGCCACAAAGGCTTTACAGATGATC
1 CGCCACAAAGGCTTTACAGATGATC
* *
18129048 CACCACAAAGG--TTCCTAGATG-TC
1 CGCCACAAAGGCTTTAC-AGATGATC
* * * *
18129071 TTGCCACAAAGGTTTTACAAATGATT
1 -CGCCACAAAGGCTTTACAGATGATC
* **
18129097 TGCCACAAA-GCTTCCCAGATGA-C
1 CGCCACAAAGGCTTTACAGATGATC
** *
18129120 TCATCACAAAGGCTTTACAGACGATC
1 -CGCCACAAAGGCTTTACAGATGATC
* * ** *
18129146 CACCAAAAAGGCTTCCCAAATGA-C
1 CGCCACAAAGGCTTTACAGATGATC
* * *
18129170 TCGCCATAAAGGCTTTACAAATTATC
1 -CGCCACAAAGGCTTTACAGATGATC
* *
18129196 TGCCACAAAGGCTTTACAGATTATC
1 CGCCACAAAGGCTTTACAGATGATC
* *
18129221 CGCCATAAAGGCTTCT-GAGAT-ATC
1 CGCCACAAAGGCTT-TACAGATGATC
** *
18129245 TTCTCACAAAGGCTTTACAGATGATT
1 CGC-CACAAAGGCTTTACAGATGATC
* * **
18129271 CACCACAAAGGCATCGCAGATGA-C
1 CGCCACAAAGGCTTTACAGATGATC
*
18129295 TCGTCACAAAGGCTTTACAGATGATC
1 -CGCCACAAAGGCTTTACAGATGATC
*
18129321 CGCCATAAAGGCTT
1 CGCCACAAAGGCTT
18129335 CCTAGATGTC
Statistics
Matches: 218, Mismatches: 53, Indels: 32
0.72 0.17 0.11
Matches are distributed among these distances:
23 5 0.02
24 35 0.16
25 167 0.77
26 11 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (25 bp):
CGCCACAAAGGCTTTACAGATGATC
Found at i:18129377 original size:100 final size:100
Alignment explanation
Indices: 18129199--18129382 Score: 257
Period size: 100 Copynumber: 1.8 Consensus size: 100
18129189 AATTATCTGC
* *
18129199 CACAAAGGCTTTACAGATTATCCGCCATAAAGGCTTCTGAGATATCTTCTCACAAAGGCTTTACA
1 CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTTCTGAGATATCTACTCACAAAGGCTTTACA
* *
18129264 GATGATTCACCACAAAGGCATCGCAGATGACTCGT
66 AATAATTCACCACAAAGGCATCGCAGATGACTCGT
* *
18129299 CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTTCCT-AGATGTCATAC-CACAAAGGCTTTT
1 CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTT-CTGAGATATC-TACTCACAAAGGCTTTA
*
18129362 CAAATCAATT-GCCACAAAGGC
64 CAAAT-AATTCACCACAAAGGC
18129383 TTGGTTTGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
100 67 0.91
101 7 0.09
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (100 bp):
CACAAAGGCTTTACAGATGATCCGCCATAAAGGCTTCTGAGATATCTACTCACAAAGGCTTTACA
AATAATTCACCACAAAGGCATCGCAGATGACTCGT
Found at i:18130675 original size:41 final size:41
Alignment explanation
Indices: 18130625--18130710 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
18130615 AAATCCTTAG
*
18130625 ATACTGCTCATGGGAAGATACTTTAACACTAATATACACCA
1 ATACCGCTCATGGGAAGATACTTTAACACTAATATACACCA
*
18130666 ATACCGCTCATGGGAAGATACTTTAACGCTAATATACACCA
1 ATACCGCTCATGGGAAGATACTTTAACACTAATATACACCA
18130707 ATAC
1 ATAC
18130711 TTTAATGCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (41 bp):
ATACCGCTCATGGGAAGATACTTTAACACTAATATACACCA
Found at i:18135866 original size:12 final size:13
Alignment explanation
Indices: 18135841--18135866 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18135831 TAAACAACAT
18135841 ACAAATTAAAAAA
1 ACAAATTAAAAAA
18135854 ACAAATTAAAAAA
1 ACAAATTAAAAAA
18135867 GTAACAATAA
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
ACAAATTAAAAAA
Found at i:18140481 original size:33 final size:36
Alignment explanation
Indices: 18140434--18140612 Score: 163
Period size: 42 Copynumber: 4.8 Consensus size: 36
18140424 GTTATCCGTT
*
18140434 ATCGGTGGATTCAGCACTTAGCAACCACCA-A-TGA
1 ATCGGTGGAATCAGCACTTAGCAACCACCACATTGA
* *
18140468 ATCGG-GGAATCAGCACTTAGCAACCCCTTTCACATTTAA
1 ATCGGTGGAATCAGCACTTAGCAACCAC---CACA-TTGA
18140507 GATACGGTGGAATCAGCACTTAGCAACCACCA-A-TGA
1 -AT-CGGTGGAATCAGCACTTAGCAACCACCACATTGA
* *
18140543 TTCGG-GGAATCAGCACTTAGCAACCCCCTTTACATTTAGA
1 ATCGGTGGAATCAGCACTTAGCAACCACC---ACA-TT-GA
18140583 ATACGGTGGAATCAGCACTTAGCAACCACC
1 AT-CGGTGGAATCAGCACTTAGCAACCACC
18140613 TTTATAGTCA
Statistics
Matches: 118, Mismatches: 9, Indels: 28
0.76 0.06 0.18
Matches are distributed among these distances:
33 42 0.36
34 8 0.07
35 1 0.01
36 5 0.04
37 2 0.02
38 1 0.01
39 5 0.04
40 5 0.04
41 6 0.05
42 43 0.36
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (36 bp):
ATCGGTGGAATCAGCACTTAGCAACCACCACATTGA
Found at i:18140532 original size:42 final size:41
Alignment explanation
Indices: 18140473--18140615 Score: 169
Period size: 42 Copynumber: 3.6 Consensus size: 41
18140463 AATGAATCGG
18140473 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGGT
1 GGAATCAGCACTTAGCAACCCCTTTCACATTT-AGATACGGT
* *
18140515 GGAATCAGCACTTAGCAACCAC---CA-A--T-GATTCGG-
1 GGAATCAGCACTTAGCAACCCCTTTCACATTTAGATACGGT
18140548 GGAATCAGCACTTAGCAACCCCCTTT-ACATTTAGAATACGGT
1 GGAATCAGCACTTAGCAA-CCCCTTTCACATTTAG-ATACGGT
18140590 GGAATCAGCACTTAGCAACCACCTTT
1 GGAATCAGCACTTAGCAACC-CCTTT
18140616 ATAGTCAATG
Statistics
Matches: 86, Mismatches: 4, Indels: 22
0.77 0.04 0.20
Matches are distributed among these distances:
33 18 0.21
34 9 0.10
36 2 0.02
37 1 0.01
38 1 0.01
39 3 0.03
40 1 0.01
41 7 0.08
42 44 0.51
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.24
Consensus pattern (41 bp):
GGAATCAGCACTTAGCAACCCCTTTCACATTTAGATACGGT
Found at i:18140559 original size:75 final size:75
Alignment explanation
Indices: 18140436--18140612 Score: 304
Period size: 75 Copynumber: 2.4 Consensus size: 75
18140426 TATCCGTTAT
*
18140436 CGGTGGATTCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAA-CCCCTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTT-A
18140500 CATTTA-AGATA
65 CATTTAGA-ATA
*
18140511 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCCTTTAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
18140576 ATTTAGAATA
66 ATTTAGAATA
18140586 CGGTGGAATCAGCACTTAGCAACCACC
1 CGGTGGAATCAGCACTTAGCAACCACC
18140613 TTTATAGTCA
Statistics
Matches: 98, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
75 90 0.92
76 8 0.08
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCCTTTAC
ATTTAGAATA
Found at i:18140716 original size:51 final size:51
Alignment explanation
Indices: 18140640--18140818 Score: 200
Period size: 51 Copynumber: 3.5 Consensus size: 51
18140630 CCGGTTCACA
* *
18140640 TAGTAGCCTGCACGTAGTACTACACATGTGACCATTTCCATC-CGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTT-CTTCTCGATACACG
* *** *
18140691 TAGTAGCCTGCACATAGTACTACACATGTGATCAAAGCTTCTCGATACACA
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTTCTTCTCGATACACG
* * * * *
18140742 TAGTAGCCTTCACTTAGTACTACACATTTGACCATTAT-TTCTCGGTACATG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATT-TCTTCTCGATACACG
* *
18140793 TAGTAGCCTTCACACAGTACTACACA
1 TAGTAGCCTGCACATAGTACTACACA
18140819 CGTGTTCATC
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
50 3 0.03
51 104 0.97
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTTCTTCTCGATACACG
Found at i:18145965 original size:13 final size:13
Alignment explanation
Indices: 18145949--18145984 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
18145939 ATTTTGTACT
*
18145949 ACCATTTGATATA
1 ACCATTTCATATA
*
18145962 ACCATTACATATA
1 ACCATTTCATATA
18145975 ACCATTTCAT
1 ACCATTTCAT
18145985 TTTATGCATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (13 bp):
ACCATTTCATATA
Found at i:18169825 original size:41 final size:41
Alignment explanation
Indices: 18169780--18169887 Score: 198
Period size: 41 Copynumber: 2.6 Consensus size: 41
18169770 AATTCGGCCA
* *
18169780 AACATGTAGTAGCAGCATTAAATTCGTCCAGACATATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
18169821 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
1 AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
18169862 AACATGTAGTGGCAGCATTAAATTCG
1 AACATGTAGTGGCAGCATTAAATTCG
18169888 ACATATTAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (41 bp):
AACATGTAGTGGCAGCATTAAATTCGTCCAGACACATTTAT
Found at i:18171722 original size:16 final size:16
Alignment explanation
Indices: 18171701--18171736 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
18171691 CAGCAATGAT
18171701 AGCTTAATTTTATTTA
1 AGCTTAATTTTATTTA
18171717 AGCTTAATTTTATTTA
1 AGCTTAATTTTATTTA
18171733 AGCT
1 AGCT
18171737 AGGATGATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.53
Consensus pattern (16 bp):
AGCTTAATTTTATTTA
Found at i:18173775 original size:13 final size:13
Alignment explanation
Indices: 18173759--18173784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18173749 AGTATTATGT
18173759 TTTATTTATTTAA
1 TTTATTTATTTAA
18173772 TTTATTTATTTAA
1 TTTATTTATTTAA
18173785 ATTTCAGCAC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATTTATTTAA
Found at i:18177211 original size:12 final size:12
Alignment explanation
Indices: 18177194--18177221 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18177184 ATGAGTTATT
18177194 TAAGTAAACAAG
1 TAAGTAAACAAG
18177206 TAAGTAAACAAG
1 TAAGTAAACAAG
18177218 TAAG
1 TAAG
18177222 AGAGTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.18, T:0.18
Consensus pattern (12 bp):
TAAGTAAACAAG
Found at i:18182078 original size:41 final size:41
Alignment explanation
Indices: 18182027--18182120 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
18182017 ATCATTCTGA
18182027 CATTGTCTTACAAAATCTATTATATCTCATGATTTACAATAC
1 CATTG-CTTACAAAATCTATTATATCTCATGATTTACAATAC
*
18182069 CATTGCTTACAAAATCTATTATATCTCATGGTTTACAATAC
1 CATTGCTTACAAAATCTATTATATCTCATGATTTACAATAC
18182110 CATTGCTTACA
1 CATTGCTTACA
18182121 CCGTTTCTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 46 0.90
42 5 0.10
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.39
Consensus pattern (41 bp):
CATTGCTTACAAAATCTATTATATCTCATGATTTACAATAC
Found at i:18187336 original size:36 final size:37
Alignment explanation
Indices: 18187288--18187364 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
18187278 CATGTCTAGG
18187288 ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
1 ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
18187325 ACAT-GCATTGGCATTATTGAGGTTATGAGAGGTCCC
1 ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
18187361 ACAT
1 ACAT
18187365 AAGACCATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.90
37 4 0.10
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (37 bp):
ACATGGCATTGGCATTATTGAGGTTATGAGAGGTCCC
Found at i:18193897 original size:17 final size:17
Alignment explanation
Indices: 18193875--18193912 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
18193865 AAGCTTCCGC
18193875 AAACGAATAATGTTTTG
1 AAACGAATAATGTTTTG
18193892 AAACGAATAATGTTTTG
1 AAACGAATAATGTTTTG
18193909 AAAC
1 AAAC
18193913 TATCACTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (17 bp):
AAACGAATAATGTTTTG
Found at i:18197407 original size:22 final size:22
Alignment explanation
Indices: 18197382--18197430 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
18197372 AAGGTCGCCT
18197382 TAACTACTTTAGCTTTCTGAAC
1 TAACTACTTTAGCTTTCTGAAC
18197404 TAACTACTTTAGCTTTCTGAAC
1 TAACTACTTTAGCTTTCTGAAC
18197426 TAACT
1 TAACT
18197431 CATCGAACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (22 bp):
TAACTACTTTAGCTTTCTGAAC
Found at i:18203614 original size:19 final size:20
Alignment explanation
Indices: 18203572--18203615 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
18203562 TATGTTTCAC
18203572 TTTAATTTCTATTTTTAATG
1 TTTAATTTCTATTTTTAATG
18203592 -TTAATTT-TATTTGTT-ATG
1 TTTAATTTCTATTT-TTAATG
18203610 TTTAAT
1 TTTAAT
18203616 AAGGGGGTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.66
Consensus pattern (20 bp):
TTTAATTTCTATTTTTAATG
Found at i:18204084 original size:17 final size:17
Alignment explanation
Indices: 18204064--18204123 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
18204054 CGCCTATCGT
18204064 TGCCACAAACCCGTCGC
1 TGCCACAAACCCGTCGC
** * ** *
18204081 TGCCGTAAGCCTATTGC
1 TGCCACAAACCCGTCGC
18204098 TGCCACAAACCCGTCGC
1 TGCCACAAACCCGTCGC
*
18204115 TGCCGCAAA
1 TGCCACAAA
18204124 ATCCCTTACT
Statistics
Matches: 30, Mismatches: 13, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.23, C:0.40, G:0.20, T:0.17
Consensus pattern (17 bp):
TGCCACAAACCCGTCGC
Found at i:18204094 original size:34 final size:34
Alignment explanation
Indices: 18204055--18204119 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
18204045 GTTGCTGCAC
*
18204055 GCCTATCGTTGCCACAAACCCGTCGCTGCCGTAA
1 GCCTATCGCTGCCACAAACCCGTCGCTGCCGTAA
*
18204089 GCCTATTGCTGCCACAAACCCGTCGCTGCCG
1 GCCTATCGCTGCCACAAACCCGTCGCTGCCG
18204120 CAAAATCCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.40, G:0.22, T:0.20
Consensus pattern (34 bp):
GCCTATCGCTGCCACAAACCCGTCGCTGCCGTAA
Found at i:18205836 original size:35 final size:35
Alignment explanation
Indices: 18205769--18205895 Score: 175
Period size: 35 Copynumber: 3.6 Consensus size: 35
18205759 ACTCTCTATT
** *
18205769 TTGGTGTGTTTTGGATGGA-TAGCTCTTTTGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
18205803 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
* *
18205838 TTGGTGTGTTTCAGATGGATTAACTCTTATAAGCA
1 TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
* *
18205873 TCTGGTGTGTTTCGGTTGGATTA
1 T-TGGTGTGTTTCAGATGGATTA
18205896 ATCAATGTAC
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
34 17 0.20
35 48 0.57
36 19 0.23
ACGTcount: A:0.18, C:0.10, G:0.29, T:0.43
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGATTAGCTCTTATGAGCA
Found at i:18209662 original size:29 final size:29
Alignment explanation
Indices: 18209625--18209912 Score: 265
Period size: 29 Copynumber: 9.9 Consensus size: 29
18209615 AGTGTGCTAA
*
18209625 TGATGGTCGAAACCATCCCTTTTCATATT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* **
18209654 TGACGGTCGTCACCATCCCTTTTCATA-T
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* * *
18209682 TCGATGGCCGAAACCATCCATTTTCATTAAT
1 T-GATGGTCGAAACCATCCCTTTTCA-TAGT
* * * *
18209713 CGGTGGTCGTAACCATCCTTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* **
18209742 TGATGGTTGTCACCATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* * *
18209771 TGATAGTCGAAACTATCCCTTTTCATAAT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* ** * *
18209800 CGATAATTGAAACTATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
* **
18209829 CGATGGTCGTCACCATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
** *
18209858 TGATGGTCGTCACGATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGT
**
18209887 TGATGGTC-ATCGCCATCCCTTTTCAT
1 TGATGGTCGA-AACCATCCCTTTTCAT
18209913 TGATCGATGA
Statistics
Matches: 215, Mismatches: 40, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
28 2 0.01
29 190 0.88
30 22 0.10
31 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (29 bp):
TGATGGTCGAAACCATCCCTTTTCATAGT
Found at i:18209782 original size:88 final size:87
Alignment explanation
Indices: 18209622--18209912 Score: 327
Period size: 87 Copynumber: 3.3 Consensus size: 87
18209612 CGAAGTGTGC
* *
18209622 TAAT-GATGGTCGAAACCATCCCTTTTCATATTTGACGGTCGTCACCATCCCTTTTCATA-TTCG
1 TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTT-G
*
18209685 ATGGCCGAAACCATCCATTTTCA
65 ATGGTCGAAACCATCCATTTTCA
* * * *
18209708 TTAATCGGTGGTCGTAACCATCCTTTTTCATAGTTGATGGTTGTCACCATCCCTTTTCATAGTTG
1 -TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTG
* * *
18209773 ATAGTCGAAACTATCCCTTTTCA
65 ATGGTCGAAACCATCCATTTTCA
** * * *
18209796 TAATCGATAATTGAAACTATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGTTGA
1 TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTGA
** * *
18209861 TGGTCGTCACGATCCCTTTTCA
66 TGGTCGAAACCATCCATTTTCA
* * **
18209883 TAGTTGATGGTC-ATCGCCATCCCTTTTCAT
1 TAATCGATGGTCGA-AACCATCCCTTTTCAT
18209913 TGATCGATGA
Statistics
Matches: 170, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
86 1 0.01
87 98 0.58
88 69 0.41
89 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.37
Consensus pattern (87 bp):
TAATCGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTTGA
TGGTCGAAACCATCCATTTTCA
Found at i:18209876 original size:58 final size:58
Alignment explanation
Indices: 18209625--18209912 Score: 299
Period size: 58 Copynumber: 4.9 Consensus size: 58
18209615 AGTGTGCTAA
* *
18209625 TGATGGTCGAAACCATCCCTTTTCATATTTGACGGTCGTCACCATCCCTTTTCATA-T
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
* * * * * * *
18209682 TCGATGGCCGAAACCATCCATTTTCATTAATCGGTGGTCGTAACCATCCTTTTTCATAGT
1 T-GATGGTCGAAACCATCCCTTTTCA-TAGTTGATGGTCGTCACCATCCCTTTTCATAGT
* ** * ** * *
18209742 TGATGGTTGTCACCATCCCTTTTCATAGTTGATAGTCGAAACTATCCCTTTTCATAAT
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
* ** * * *
18209800 CGATAATTGAAACTATCCCTTTTCATAGTCGATGGTCGTCACCATCCCTTTTCATAGT
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
** * * *
18209858 TGATGGTCGTCACGATCCCTTTTCATAGTTGATGGTCATCGCCATCCCTTTTCAT
1 TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCAT
18209913 TGATCGATGA
Statistics
Matches: 185, Mismatches: 43, Indels: 5
0.79 0.18 0.02
Matches are distributed among these distances:
57 1 0.01
58 138 0.75
59 44 0.24
60 2 0.01
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (58 bp):
TGATGGTCGAAACCATCCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGT
Found at i:18213083 original size:19 final size:19
Alignment explanation
Indices: 18213059--18213104 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18213049 TCCCTCAACA
18213059 CTCATTTCTCATTCAT-TCT
1 CTCATTTCTCATTC-TCTCT
*
18213078 CTCATTTGTCATTCTCTCT
1 CTCATTTCTCATTCTCTCT
*
18213097 TTCATTTC
1 CTCATTTC
18213105 CCTTTTCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 1 0.04
19 22 0.96
ACGTcount: A:0.13, C:0.30, G:0.02, T:0.54
Consensus pattern (19 bp):
CTCATTTCTCATTCTCTCT
Found at i:18222578 original size:18 final size:16
Alignment explanation
Indices: 18222555--18222590 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
18222545 TGATTTAAAA
18222555 AATAAAAAGTAAATAAGT
1 AATAAAAA-TAAA-AAGT
18222573 AATAAAAATAAAAAGT
1 AATAAAAATAAAAAGT
18222589 AA
1 AA
18222591 AAATTCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (16 bp):
AATAAAAATAAAAAGT
Found at i:18224757 original size:3 final size:3
Alignment explanation
Indices: 18224749--18224780 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
18224739 ACATATGCTT
18224749 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
18224781 TTTTGAGCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:18228435 original size:14 final size:14
Alignment explanation
Indices: 18228418--18228445 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18228408 AATTGAATAA
18228418 AGTAAAATATTGGG
1 AGTAAAATATTGGG
18228432 AGTAAAATATTGGG
1 AGTAAAATATTGGG
18228446 GGCAATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.29, T:0.29
Consensus pattern (14 bp):
AGTAAAATATTGGG
Found at i:18229665 original size:20 final size:20
Alignment explanation
Indices: 18229640--18229688 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
18229630 AAGTTTATAT
18229640 TAAGTAAATGGAATCA-AAAG
1 TAAGTAAATGGAAT-AGAAAG
18229660 TAAGTAAATGGAATAGAAAG
1 TAAGTAAATGGAATAGAAAG
18229680 TAAGTAAAT
1 TAAGTAAAT
18229689 AGAGTGGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.55, C:0.02, G:0.20, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGGAATAGAAAG
Found at i:18233966 original size:12 final size:12
Alignment explanation
Indices: 18233940--18233978 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
18233930 CGCTGCTTCT
* *
18233940 TTACTTACTTTC
1 TTACTTGCTTAC
*
18233952 TTACTTGGTTAC
1 TTACTTGCTTAC
18233964 TTACTTGCTTAC
1 TTACTTGCTTAC
18233976 TTA
1 TTA
18233979 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.21, G:0.08, T:0.54
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:18234290 original size:50 final size:49
Alignment explanation
Indices: 18234170--18234341 Score: 145
Period size: 50 Copynumber: 3.5 Consensus size: 49
18234160 CATGCCAAAA
* * * *
18234170 CCATGTCCCAGACATGGTCTTACATGGGATGTTTTCGGTA--CTGCCAATG
1 CCATGTCCTAGACATGGTCTTACATGGGA-GTTCTC-ATATGGTGCCAATG
* * *
18234219 CCATAT-CTCAGATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATG
1 CCATGTCCT-AGACATGGTCTTACATGGGAGTTCTCATA-TGGTGCCAATG
** * *
18234269 CCATGTCCTAGACATGGTCTTACGA-GGGACCTCTCATCTCGGTGCCAACG
1 CCATGTCCTAGACATGGTCTTAC-ATGGGAGTTCTCATAT-GGTGCCAATG
* *
18234319 CCATGTCCAAGACAAGGTCTTAC
1 CCATGTCCTAGACATGGTCTTAC
18234342 GTGTGACCTC
Statistics
Matches: 100, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
47 2 0.02
48 6 0.06
49 25 0.25
50 64 0.64
51 3 0.03
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (49 bp):
CCATGTCCTAGACATGGTCTTACATGGGAGTTCTCATATGGTGCCAATG
Found at i:18234342 original size:50 final size:50
Alignment explanation
Indices: 18234250--18234356 Score: 142
Period size: 50 Copynumber: 2.1 Consensus size: 50
18234240 ACATGGGAGT
* * * * *
18234250 TCTCATATTGGTGCCCATGCCATGTCCTAGACATGGTCTTACGAGGGACC
1 TCTCATATCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGAGGGACC
* * *
18234300 TCTCATCTCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGTGTGACC
1 TCTCATATCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGAGGGACC
18234350 TCTCATA
1 TCTCATA
18234357 ACCTCAATAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (50 bp):
TCTCATATCGGTGCCAACGCCATGTCCAAGACAAGGTCTTACGAGGGACC
Found at i:18242879 original size:16 final size:18
Alignment explanation
Indices: 18242846--18242879 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
18242836 GTTTAAAAAC
18242846 TAAAAATAGAATAAGTAA
1 TAAAAATAGAATAAGTAA
18242864 TAAAAATA-AA-AAGTAA
1 TAAAAATAGAATAAGTAA
18242880 AAATTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
TAAAAATAGAATAAGTAA
Found at i:18245857 original size:14 final size:15
Alignment explanation
Indices: 18245833--18245861 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
18245823 AAAGAGGCAA
18245833 GAAGAAGGAAAAGAG
1 GAAGAAGGAAAAGAG
18245848 GAAG-AGGAAAAGAG
1 GAAGAAGGAAAAGAG
18245862 AACAAAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (15 bp):
GAAGAAGGAAAAGAG
Found at i:18252373 original size:12 final size:12
Alignment explanation
Indices: 18252356--18252381 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18252346 CTCTGTGGGA
18252356 TCTTTTTCTTCT
1 TCTTTTTCTTCT
18252368 TCTTTTTCTTCT
1 TCTTTTTCTTCT
18252380 TC
1 TC
18252382 GGGATCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
TCTTTTTCTTCT
Found at i:18277442 original size:23 final size:23
Alignment explanation
Indices: 18277413--18277462 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
18277403 CTATTCTCAT
18277413 TTCTTCATACGTTTATAGTTTCC
1 TTCTTCATACGTTTATAGTTTCC
**
18277436 TTCTTCATATTTTTATAGTTTCC
1 TTCTTCATACGTTTATAGTTTCC
18277459 TTCT
1 TTCT
18277463 ATTTCAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.16, C:0.20, G:0.06, T:0.58
Consensus pattern (23 bp):
TTCTTCATACGTTTATAGTTTCC
Found at i:18278065 original size:13 final size:13
Alignment explanation
Indices: 18278047--18278071 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18278037 ATTATTAATA
18278047 TTATTTTGTGTGT
1 TTATTTTGTGTGT
18278060 TTATTTTGTGTG
1 TTATTTTGTGTG
18278072 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:18279075 original size:21 final size:21
Alignment explanation
Indices: 18279049--18279090 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18279039 AATATATATA
*
18279049 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTAAATTT
18279070 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTAAATTT
18279091 GATTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTAAATTT
Found at i:18279800 original size:41 final size:41
Alignment explanation
Indices: 18279717--18279803 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 41
18279707 TGTGTCTAGT
* *
18279717 AGGCTTAATGCCGGTGAAATAATTCAGACCTTACGTCTAGC
1 AGGCTTAATGCCGGTGAAACAATTCAGACCTTACGTCCAGC
* * * *
18279758 AGGCTTAATGCCGGTGATACATTTCGGA-CTATAGGTCCAGC
1 AGGCTTAATGCCGGTGAAACAATTCAGACCT-TACGTCCAGC
18279799 AGGCT
1 AGGCT
18279804 AAGAGCTGGT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
40 2 0.05
41 37 0.95
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (41 bp):
AGGCTTAATGCCGGTGAAACAATTCAGACCTTACGTCCAGC
Found at i:18287498 original size:41 final size:41
Alignment explanation
Indices: 18287453--18287555 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
18287443 GGCTATGTGC
* * *
18287453 CTAGCAGGCTTGATGCCGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* * * *
18287494 CTAGCAGGCTTAATGCCGGTGATACATTTCGGACTATAGGT
1 CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
* *
18287535 CTAGCAGGCTAAAAGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
18287556 TACTGAATCA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCCGGTGAAACAATTCAGACTATACGT
Found at i:18294390 original size:21 final size:21
Alignment explanation
Indices: 18294366--18294407 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
18294356 TATATATATA
*
18294366 TATGTTCTATAAGCTGAATTT
1 TATGTTCTATAAGCTAAATTT
18294387 TATGTTCTATAAGCTAAATTT
1 TATGTTCTATAAGCTAAATTT
18294408 GATTTTATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (21 bp):
TATGTTCTATAAGCTAAATTT
Found at i:18295079 original size:41 final size:41
Alignment explanation
Indices: 18295034--18295125 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
18295024 GGCTATGTGC
* * *
18295034 CTAGCAGGCTTGATGCAGGTGAAATAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCAGGTGAAACAATTCAGACTATACGT
* * * *
18295075 CTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAGGT
1 CTAGCAGGCTTAATGCAGGTGAAACAATTCAGACTATACGT
18295116 CTAGCAGGCT
1 CTAGCAGGCT
18295126 AAAAGCCGGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (41 bp):
CTAGCAGGCTTAATGCAGGTGAAACAATTCAGACTATACGT
Found at i:18303827 original size:22 final size:22
Alignment explanation
Indices: 18303799--18303845 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
18303789 ACAAATCCTA
18303799 TCTCAATTTCCTTCCAAAATCC
1 TCTCAATTTCCTTCCAAAATCC
*
18303821 TCTCAATTTCCTTCCAAAATTC
1 TCTCAATTTCCTTCCAAAATCC
18303843 TCT
1 TCT
18303846 TAAACTCTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.34, G:0.00, T:0.40
Consensus pattern (22 bp):
TCTCAATTTCCTTCCAAAATCC
Found at i:18303877 original size:52 final size:52
Alignment explanation
Indices: 18303799--18303897 Score: 180
Period size: 52 Copynumber: 1.9 Consensus size: 52
18303789 ACAAATCCTA
* *
18303799 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCCTTCCAAAATTCTCTTAAAC
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
18303851 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
1 TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCT
18303898 CAAATCCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.38
Consensus pattern (52 bp):
TCTCAATTTCCTTCCAAAATCCTCTCAATTTCATTCCAAAAATCTCTTAAAC
Found at i:18303878 original size:22 final size:22
Alignment explanation
Indices: 18303850--18303900 Score: 77
Period size: 22 Copynumber: 2.3 Consensus size: 22
18303840 TTCTCTTAAA
*
18303850 CTCTCAATTTCCTTCC-AAAAT
1 CTCTCAATTTCATTCCAAAAAT
18303871 CCTCTCAATTTCATTCCAAAAAT
1 -CTCTCAATTTCATTCCAAAAAT
18303894 CTCTCAA
1 CTCTCAA
18303901 ATCCATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.35
Consensus pattern (22 bp):
CTCTCAATTTCATTCCAAAAAT
Found at i:18304892 original size:20 final size:20
Alignment explanation
Indices: 18304867--18304905 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
18304857 TAACGAGGTA
18304867 AATTTTATAT-TACATTTTGG
1 AATTTT-TATGTACATTTTGG
*
18304887 AATTTTTATGTAGATTTTG
1 AATTTTTATGTACATTTTG
18304906 TAAGAATAAA
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:0.28, C:0.03, G:0.13, T:0.56
Consensus pattern (20 bp):
AATTTTTATGTACATTTTGG
Found at i:18306071 original size:21 final size:21
Alignment explanation
Indices: 18306045--18306086 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18306035 CAGACGCCGA
*
18306045 ACCGGAAGAACAACAATCACC
1 ACCGGAAGAACAACAACCACC
*
18306066 ACCGGAAGAAGAACAACCACC
1 ACCGGAAGAACAACAACCACC
18306087 GCCAGAAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.33, G:0.17, T:0.02
Consensus pattern (21 bp):
ACCGGAAGAACAACAACCACC
Found at i:18306094 original size:21 final size:21
Alignment explanation
Indices: 18306049--18306094 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
18306039 CGCCGAACCG
* *
18306049 GAAGAACAACAATCACCACCG
1 GAAGAACAACAACCACCACCA
* *
18306070 GAAGAAGAACAACCACCGCCA
1 GAAGAACAACAACCACCACCA
18306091 GAAG
1 GAAG
18306095 CTAGAGGAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.30, G:0.20, T:0.02
Consensus pattern (21 bp):
GAAGAACAACAACCACCACCA
Found at i:18306353 original size:23 final size:23
Alignment explanation
Indices: 18306327--18306645 Score: 224
Period size: 23 Copynumber: 12.3 Consensus size: 23
18306317 TTCATACCCT
18306327 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
18306350 AACCCTAACCTAATTTAATTAAAA
1 AACCCTAACCTAATTTAATT-AAA
*
18306374 CCCTAACCTTAACCTAATTTAATTAAAA
1 ----AACCCTAACCTAATTTAATT-AAA
18306402 ACACTAACCTTAACCTAATTTAATTAAA
1 A-AC---CC-TAACCTAATTTAATTAAA
18306430 AACCCTAACCCTACCCTAATTTAATTAAAA
1 AACCCT-A----A-CCTAATTTAATT-AAA
* *
18306460 CCCTAACCTTAACCTAATTTATTTAAA
1 ----AACCCTAACCTAATTTAATTAAA
*
18306487 AACCCTAACCCTAATCTAATTTATTTAAA
1 AACCCTAA--C----CTAATTTAATTAAA
18306516 AACCCTAACCCTAACATAATTTAATTAAA
1 AACCCTAA--C---C-TAATTTAATTAAA
18306545 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
18306568 AACCCTAACCTAATTTATTTAAA
1 AACCCTAACCTAATTTAATTAAA
* * *
18306591 AACACTAACATAATTTATTTAAA
1 AACCCTAACCTAATTTAATTAAA
** *
18306614 AACCCTAACCCTAACCTAATTTAA
1 AACCCTAA-CCTAATTTAATTAAA
18306638 AACCCTAA
1 AACCCTAA
18306646 ACCCTAACCT
Statistics
Matches: 250, Mismatches: 17, Indels: 57
0.77 0.05 0.18
Matches are distributed among these distances:
23 91 0.36
24 26 0.10
25 3 0.01
27 6 0.02
28 42 0.17
29 73 0.29
30 3 0.01
33 1 0.00
34 5 0.02
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:18306465 original size:86 final size:85
Alignment explanation
Indices: 18306325--18306713 Score: 419
Period size: 86 Copynumber: 4.7 Consensus size: 85
18306315 ATTTCATACC
18306325 CTAACCCTAACCTAATTTAATTAAAAACCCT-A----ACCTAATTTAATTAAAACCCTAACCTTA
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTACCTAATTTAATTAAAACCCTAACCTTA
18306385 ACCTAATTTAATTAAAAACA
66 ACCTAATTTAATTAAAAACA
*
18306405 CTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAATTTAATTAAAACCCTAACCTT
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA-CCTAATTTAATTAAAACCCTAACCTT
* *
18306470 AACCTAATTTATTTAAAAACC
65 AACCTAATTTAATTAAAAACA
* * * *
18306491 CTAACCCTAATCTAATTTATTTAAAAACCCTAACCCTAACATAATTTAATT-AAA----AACCCT
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCT-ACCTAATTTAATTAAAACCCTAACCTT
18306551 AACCTAATTTAATT---AA-A
65 AACCTAATTTAATTAAAAACA
* * * *
18306568 --AACCCTAACCTAATTTATTTAAAAACACTAA--C-A--TAATTTATTTAAAAACCCTAACCCT
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTACCTAATTTAATT-AAAACCCTAACCTT
*
18306626 AACCTAATTTAA--AACCCTAAACC
65 AACCTAATTTAATTAA----AAACA
*
18306649 CTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAATTTAATTAAAAACCCTAACCT
1 CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTA-CCTAATTTAATT-AAAACCCTAACCT
18306714 AATTTATTTA
Statistics
Matches: 261, Mismatches: 19, Indels: 49
0.79 0.06 0.15
Matches are distributed among these distances:
69 9 0.03
71 4 0.02
73 1 0.00
75 47 0.18
78 2 0.01
80 32 0.12
81 19 0.07
83 28 0.11
85 5 0.02
86 91 0.35
87 1 0.00
89 22 0.08
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.30
Consensus pattern (85 bp):
CTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTACCTAATTTAATTAAAACCCTAACCTTA
ACCTAATTTAATTAAAAACA
Found at i:18306682 original size:23 final size:23
Alignment explanation
Indices: 18306680--18306787 Score: 171
Period size: 23 Copynumber: 4.7 Consensus size: 23
18306670 TAAAAACCCT
* *
18306680 AACCCTACCCTAATTTAATTAAA
1 AACCCTAACCTAATTTATTTAAA
18306703 AACCCTAACCTAATTTATTTAAA
1 AACCCTAACCTAATTTATTTAAA
*
18306726 AACCCAAACCTAATTTATTTAAA
1 AACCCTAACCTAATTTATTTAAA
18306749 AACCCTAACCTAATTTATTTAAA
1 AACCCTAACCTAATTTATTTAAA
* *
18306772 AACCATAACATAATTT
1 AACCCTAACCTAATTT
18306788 TACCTAATTT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 79 1.00
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.32
Consensus pattern (23 bp):
AACCCTAACCTAATTTATTTAAA
Found at i:18306683 original size:158 final size:155
Alignment explanation
Indices: 18306322--18306780 Score: 537
Period size: 158 Copynumber: 2.9 Consensus size: 155
18306312 TTTATTTCAT
** * ***** *
18306322 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAA-CCTAATTTAATTAAAACCCTAACCTTAA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAAACCCTAA
*
18306386 CCTAATTTAATTAAAAACACTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAATT
66 CCTAATTTAATT-AAAA-AC---CC-TAACCTAATTTATTTAAAAACCCTAA--C-A---TAATT
* * *
18306451 TAATT-AAAACCCTAACCTTAACCTAATTTATTTAAAA
119 TATTTAAAAACCCTAACCCTAACCTAATTTA-TAAAAA
* *
18306488 ACCCTAACCCTAATCTAATTTATTTAAAAACCCTAACCCTAACATAATTTAATTAAAAACCCTAA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAAACCCTAA
*
18306553 CCTAATTTAATTAAAAACCCTAACCTAATTTATTTAAAAACACTAACATAATTTATTTAAAAACC
66 CCTAATTTAATTAAAAACCCTAACCTAATTTATTTAAAAACCCTAACATAATTTATTTAAAAACC
18306618 CTAACCCTAACCTAATTTA-AAACCCTAA
131 CTAACCCTAACCTAATTTATAAA----AA
* * *
18306646 ACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAATTTAATTAAAAACCCTAA
1 ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAAACCCTAA
* * *
18306711 CCTAATTTATTTAAAAACCCAAACCTAATTTATTTAAAAACCCTAACCTAATTTATTTAAAAACC
66 CCTAATTTAATTAAAAACCCTAACCTAATTTATTTAAAAACCCTAACATAATTTATTTAAAAACC
*
18306776 ATAAC
131 CTAAC
18306781 ATAATTTTAC
Statistics
Matches: 261, Mismatches: 26, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
154 2 0.01
155 9 0.03
156 24 0.09
158 128 0.49
159 1 0.00
161 24 0.09
162 2 0.01
165 2 0.01
166 38 0.15
167 31 0.12
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.31
Consensus pattern (155 bp):
ACCCTAACCCTAACCTAATTTAATTAAAAACCCTAACCCTAACATAATTTAATTAAAAACCCTAA
CCTAATTTAATTAAAAACCCTAACCTAATTTATTTAAAAACCCTAACATAATTTATTTAAAAACC
CTAACCCTAACCTAATTTATAAAAA
Found at i:18306758 original size:29 final size:29
Alignment explanation
Indices: 18306322--18306712 Score: 424
Period size: 29 Copynumber: 14.3 Consensus size: 29
18306312 TTTATTTCAT
18306322 ACCCTAACCCTAACCTAATTTAATT--AA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
18306349 A----AACCCTAACCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
18306373 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
18306402 ACACTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
18306431 ACCCTAACCCTACCCTAATTTAATT-AAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
18306459 ACCCTAACCTTAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
18306488 ACCCTAACCCTAATCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
18306517 ACCCTAACCCTAACATAATTTAATT--AA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
18306544 A----AACCCTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
18306569 A-CC---C--TAACCTAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
* *
18306592 ACACTAA--C--A--TAATTTATTTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
18306615 ACCCTAACCCTAACCTAATTTAA--AACCCTAA
1 ACCCTAACCCTAACCTAATTTAATTAA----AA
*
18306646 ACCCTAACCTTAACCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
*
18306675 ACCCTAACCCTACCCTAATTTAATTAAAA
1 ACCCTAACCCTAACCTAATTTAATTAAAA
18306704 ACCCTAACC
1 ACCCTAACC
18306713 TAATTTATTT
Statistics
Matches: 315, Mismatches: 21, Indels: 54
0.81 0.05 0.14
Matches are distributed among these distances:
23 78 0.25
24 4 0.01
25 6 0.02
27 7 0.02
28 44 0.14
29 150 0.48
31 24 0.08
33 2 0.01
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (29 bp):
ACCCTAACCCTAACCTAATTTAATTAAAA
Found at i:18306786 original size:46 final size:46
Alignment explanation
Indices: 18306493--18306787 Score: 205
Period size: 46 Copynumber: 5.8 Consensus size: 46
18306483 TAAAAACCCT
* *
18306493 AACCCTAATCTAATTTATTTAAAAACCCTAACCCTAACATAATTTAATTAAA
1 AACCCTAACCTAATTTATTTAAAAA-CC--A---TAACATAATTTATTTAAA
* * *
18306545 AACCCTAACCTAATTTAATTAAAAACCCTAACCTAATTTATTTAAA
1 AACCCTAACCTAATTTATTTAAAAACCATAACATAATTTATTTAAA
* * * * * *
18306591 AACACTAACATAATTTATTTAAAAACCCTAACCCTAACCTAATTTAAAACCCTA
1 AACCCTAACCTAATTTATTTAAAAACCATAA-CATAA-TTTATTT--AA----A
* * *
18306645 AACCCTAACCTTAACCTAATTTAATTAAAAACCCTAACCCTACCCTAATTTAATTAAA
1 AA--C---CC-TAACCTAATTTATTTAAAAACCATAA--C-A---TAATTTATTTAAA
*
18306703 AACCCTAACCTAATTTATTTAAAAACCCA-AACCTAATTTATTTAAA
1 AACCCTAACCTAATTTATTTAAAAA-CCATAACATAATTTATTTAAA
18306749 AACCCTAACCTAATTTATTTAAAAACCATAACATAATTT
1 AACCCTAACCTAATTTATTTAAAAACCATAACATAATTT
18306788 TACCTAATTT
Statistics
Matches: 200, Mismatches: 22, Indels: 48
0.74 0.08 0.18
Matches are distributed among these distances:
45 3 0.01
46 90 0.45
47 5 0.03
48 5 0.03
50 3 0.01
51 2 0.01
52 44 0.22
53 4 0.02
54 3 0.01
56 2 0.01
58 3 0.01
59 1 0.00
60 24 0.12
61 2 0.01
62 2 0.01
64 4 0.02
65 3 0.01
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.31
Consensus pattern (46 bp):
AACCCTAACCTAATTTATTTAAAAACCATAACATAATTTATTTAAA
Found at i:18306841 original size:56 final size:56
Alignment explanation
Indices: 18306781--18306905 Score: 180
Period size: 56 Copynumber: 2.2 Consensus size: 56
18306771 AAACCATAAC
* * * * *
18306781 ATAATTTTACCTAATTTGGT-AATCTTACTAACCATTAACACACCTTTTTGGGCTTA
1 ATAATTTTACATAATTTGATAAAT-TTACTAACCATTAACAAAACTTATTGGGCTTA
*
18306837 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAAGTTATTGGGCTTA
1 ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAACTTATTGGGCTTA
18306893 ATAATTTTACATA
1 ATAATTTTACATA
18306906 GTTTTACATA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
56 59 0.95
57 3 0.05
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (56 bp):
ATAATTTTACATAATTTGATAAATTTACTAACCATTAACAAAACTTATTGGGCTTA
Found at i:18312480 original size:3 final size:3
Alignment explanation
Indices: 18312474--18312513 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
18312464 CATCATCATC
18312474 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
18312514 GTCTTTTATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:18319952 original size:45 final size:45
Alignment explanation
Indices: 18319879--18320042 Score: 122
Period size: 45 Copynumber: 3.7 Consensus size: 45
18319869 AGACACCAAC
* * *
18319879 CTTGCCTTCTTATACTGACAGCGGAGCAGATTGAAGATAGTAGAT
1 CTTGCCTTCCTATACTGACGGCGAAGCAGATTGAAGATAGTAGAT
* * * * *
18319924 CTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACA-TA-AGC
1 CTTGCCTTCCTATACTGACGGCGAAGCAGATTGAAGATAGTAGA-T
* * * ** * **
18319968 CATGCCTCCCTCTGTTGTA-GTG-G-AGTAGGCTGAAGATAGTAGAT
1 CTTGCCTTCCTATACTG-ACG-GCGAAGCAGATTGAAGATAGTAGAT
18320012 CTTGCCTTCCTATACTGACGGCGAAGCAGAT
1 CTTGCCTTCCTATACTGACGGCGAAGCAGAT
18320043 CAAAGACACA
Statistics
Matches: 84, Mismatches: 27, Indels: 16
0.66 0.21 0.13
Matches are distributed among these distances:
43 13 0.15
44 32 0.38
45 39 0.46
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (45 bp):
CTTGCCTTCCTATACTGACGGCGAAGCAGATTGAAGATAGTAGAT
Found at i:18320029 original size:88 final size:87
Alignment explanation
Indices: 18319901--18320311 Score: 534
Period size: 88 Copynumber: 4.7 Consensus size: 87
18319891 TACTGACAGC
* * * *
18319901 GGAGCAGATTGAAGATAGTAGATCTTGCCTTCCTGTACTGACGGTGAAGCAGATCGAAGACATAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTA-TGACAGTGAAGCAGATCGAAGACACAA
* *
18319966 GCCATGCCTCCCTCTGTTGTAGT
65 GCCTTGCCTCCCTCGGTTGTAGT
* * * * * * *
18319989 GGAGTAGGCTGAAGATAGTAGATCTTGCCTTCCTATACTGACGGCGAAGCAGATCAAAGACACAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTA-TGACAGTGAAGCAGATCGAAGACACAA
*
18320054 GCCTTGCCTCCCTCGATTGTAGT
65 GCCTTGCCTCCCTCGGTTGTAGT
* ** *
18320077 GGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTACATCGACAGTGAAGCAAATCGAAGACACAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTAT-GACAGTGAAGCAGATCGAAGACACAA
* * *
18320142 GTCTTGCCTCCTTCGGTTGTAAT
65 GCCTTGCCTCCCTCGGTTGTAGT
*
18320165 GGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGTATCGACAGTGAAGCAGATCGAAGACACAA
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTAT-GACAGTGAAGCAGATCGAAGACACAA
*
18320230 ACCTTGCCTCCCTCGGTTGTAGT
65 GCCTTGCCTCCCTCGGTTGTAGT
* * * *
18320253 GGAGTAGGTTAAAGATAGTAGGTCTTGCCTTCCTGCATTGACAGTGAAACAGATCGAAG
1 GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTA-TGACAGTGAAGCAGATCGAAG
18320312 CGAATGGTCC
Statistics
Matches: 286, Mismatches: 35, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
87 1 0.00
88 284 0.99
89 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.26, T:0.25
Consensus pattern (87 bp):
GGAGCAGGTTGAAGATAGTAGGTCTTGCCTTCCTGTATGACAGTGAAGCAGATCGAAGACACAAG
CCTTGCCTCCCTCGGTTGTAGT
Found at i:18320104 original size:44 final size:44
Alignment explanation
Indices: 18320056--18320282 Score: 156
Period size: 44 Copynumber: 5.2 Consensus size: 44
18320046 AGACACAAGC
18320056 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
1 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
* * * * ** * * *
18320100 CTTGCCTTCCTAC-ATCGACAGTGAAGCAAATCGAAGACA-CAAGT
1 CTTGCCTCCCT-CGATTG-TAGTGGAGCAGGTTGAAGATAGCAGGT
* * *
18320144 CTTGCCTCCTTCGGTTGTAATGGAGCAGGTTGAAGATAGCAGGT
1 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
* * * * * * * ***
18320188 CTTGCCTTCCT-GTATCGACAGTGAAGCAGATCGAAGACA-CAAAC
1 CTTGCCTCCCTCG-ATTG-TAGTGGAGCAGGTTGAAGATAGCAGGT
* * * *
18320232 CTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTAAAGATAGTAGGT
1 CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
18320276 CTTGCCT
1 CTTGCCT
18320283 TCCTGCATTG
Statistics
Matches: 127, Mismatches: 48, Indels: 16
0.66 0.25 0.08
Matches are distributed among these distances:
43 30 0.24
44 65 0.51
45 32 0.25
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.26
Consensus pattern (44 bp):
CTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGATAGCAGGT
Found at i:18320152 original size:176 final size:175
Alignment explanation
Indices: 18319851--18320311 Score: 539
Period size: 176 Copynumber: 2.6 Consensus size: 175
18319841 TTCCTGTACT
* * * * * ** * * * *
18319851 GACAGCGAAACAGATCGAAGACACCAACCTTGCCTTCTTATACTGACAGCGGAGCAGATTGAAGA
1 GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTG-TAGTGGAGCAGGTTGAAGA
* * *
18319916 TAGTAGATCTTGCCTTCCTGTAC-TGACGGTGAAGCAGATCGAAGACATAAGCCATGCCTCCCTC
65 TAGTAGGTCTTGCCTTCC--TACATGACAGTGAAGCAGATCGAAGACACAAGCCATGCCTCCCTC
* * * *
18319980 TGTTGTAGTGGAGTAGGCTGAAGATAGTAGATCTTGCCTTCCTATA-C
128 GGTTGTAATGGAGCAGGCTGAAGATAGCAGATCTTGCCTTCCTATATC
* *
18320027 TGACGGCGAAGCAGATCAAAGACACAAGCCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGA
1 -GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGA
* * * * *
18320092 TAGCAGGTCTTGCCTTCCTACATCGACAGTGAAGCAAATCGAAGACACAAGTCTTGCCTCCTTCG
65 TAGTAGGTCTTGCCTTCCTACAT-GACAGTGAAGCAGATCGAAGACACAAGCCATGCCTCCCTCG
* * *
18320157 GTTGTAATGGAGCAGGTTGAAGATAGCAGGTCTTGCCTTCCTGTATC
129 GTTGTAATGGAGCAGGCTGAAGATAGCAGATCTTGCCTTCCTATATC
* * * * *
18320204 GACAGTGAAGCAGATCGAAGACACAAACCTTGCCTCCCTCGGTTGTAGTGGAGTAGGTTAAAGAT
1 GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGAT
* *
18320269 AGTAGGTCTTGCCTTCCTGCATTGACAGTGAAACAGATCGAAG
66 AGTAGGTCTTGCCTTCCTACA-TGACAGTGAAGCAGATCGAAG
18320312 CGAATGGTCC
Statistics
Matches: 241, Mismatches: 39, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
174 3 0.01
175 1 0.00
176 200 0.83
177 37 0.15
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (175 bp):
GACAGCGAAGCAGATCAAAGACACAAACCTTGCCTCCCTCGATTGTAGTGGAGCAGGTTGAAGAT
AGTAGGTCTTGCCTTCCTACATGACAGTGAAGCAGATCGAAGACACAAGCCATGCCTCCCTCGGT
TGTAATGGAGCAGGCTGAAGATAGCAGATCTTGCCTTCCTATATC
Found at i:18321758 original size:3 final size:3
Alignment explanation
Indices: 18321728--18321802 Score: 105
Period size: 3 Copynumber: 24.7 Consensus size: 3
18321718 ATTAATTGAT
* * * *
18321728 TTA TTG TTA TTA TTT TTA TTGG TCA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
18321774 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
18321803 GTTAGTCTTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 62 0.98
4 1 0.02
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18321832 original size:17 final size:18
Alignment explanation
Indices: 18321756--18321832 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 18
18321746 TTGGTCATTA
* * *
18321756 TTATTATTATTATTATTA
1 TTATTATTATTGTTAGTC
* * *
18321774 TTATTATTATTATTATTA
1 TTATTATTATTGTTAGTC
18321792 TTATTATTATTGTTAGTC
1 TTATTATTATTGTTAGTC
* *
18321810 TT-TTATTTTTTTTA-TC
1 TTATTATTATTGTTAGTC
18321826 TTATTAT
1 TTATTAT
18321833 ATAGATCCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
16 4 0.08
17 14 0.26
18 35 0.66
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATTATTATTGTTAGTC
Found at i:18321844 original size:22 final size:21
Alignment explanation
Indices: 18321819--18321859 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18321809 CTTTTATTTT
18321819 TTTTATCTTATTATATAGATCC
1 TTTTATCTTATTATA-AGATCC
*
18321841 TTTTATTTTATTATAAGAT
1 TTTTATCTTATTATAAGAT
18321860 ATTATTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTTATCTTATTATAAGATCC
Found at i:18322239 original size:9 final size:9
Alignment explanation
Indices: 18322215--18322244 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
18322205 AGTTATTCAC
18322215 TTTTATTTT
1 TTTTATTTT
18322224 ATTTTATTTT
1 -TTTTATTTT
18322234 TTTTATTTT
1 TTTTATTTT
18322243 TT
1 TT
18322245 ATATAAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTATTTT
Found at i:18325217 original size:2 final size:2
Alignment explanation
Indices: 18325210--18325285 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
18325200 CTCACCGCCT
* *
18325210 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
18325252 TC TC TA TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18325286 CATGTAGGAA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.01, C:0.51, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:18330009 original size:16 final size:16
Alignment explanation
Indices: 18329988--18330018 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18329978 CACCCAAGAC
18329988 ACACCTCAACCTTATA
1 ACACCTCAACCTTATA
*
18330004 ACACCTCAATCTTAT
1 ACACCTCAACCTTAT
18330019 CTGATTAGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.29
Consensus pattern (16 bp):
ACACCTCAACCTTATA
Found at i:18343429 original size:21 final size:19
Alignment explanation
Indices: 18343383--18343457 Score: 132
Period size: 19 Copynumber: 3.8 Consensus size: 19
18343373 AATCTTCAAG
18343383 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18343402 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
18343421 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
18343442 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
18343458 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 35 0.65
21 19 0.35
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:18343479 original size:23 final size:22
Alignment explanation
Indices: 18343383--18343480 Score: 95
Period size: 19 Copynumber: 4.7 Consensus size: 22
18343373 AATCTTCAAG
18343383 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
18343402 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
18343424 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
18343442 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
18343464 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
18343481 GATTTAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.03
19 28 0.42
21 15 0.22
22 10 0.15
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:18343728 original size:23 final size:23
Alignment explanation
Indices: 18343680--18343728 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
18343670 TTGTTCTTAT
* *
18343680 TTTGTTGATTTGTGTATAATTTA
1 TTTGTTGATTTGTATATAATTGA
**
18343703 TTTGTTGATTTGTATATTGTTGA
1 TTTGTTGATTTGTATATAATTGA
18343726 TTT
1 TTT
18343729 CAAATCTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (23 bp):
TTTGTTGATTTGTATATAATTGA
Found at i:18344283 original size:23 final size:22
Alignment explanation
Indices: 18344255--18344298 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
18344245 ATAATTCATA
*
18344255 TACATATATATTTTTCTTATATG
1 TACATATATATATTT-TTATATG
18344278 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
18344299 TTATAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.57
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:18353870 original size:2 final size:2
Alignment explanation
Indices: 18353863--18353896 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
18353853 AACTAGGATT
18353863 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
18353897 AGTGTACAGT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:18356287 original size:24 final size:24
Alignment explanation
Indices: 18356251--18356297 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
18356241 AGTTGAATCA
*
18356251 TCTTTTTATTTTTGTATTTTTCTC
1 TCTTTTTATTTTTATATTTTTCTC
18356275 TCTTGTTTA-TTTTATATTTTTCT
1 TCTT-TTTATTTTTATATTTTTCT
18356298 TTGTTTTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (24 bp):
TCTTTTTATTTTTATATTTTTCTC
Found at i:18361210 original size:37 final size:37
Alignment explanation
Indices: 18361169--18361244 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
18361159 CTCCAAAACC
*
18361169 ATCTCCACTCCAATTCCCCATAACACGCCAAATTACA
1 ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
18361206 ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
1 ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
18361243 AT
1 AT
18361245 TGTACTCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.37, C:0.38, G:0.03, T:0.22
Consensus pattern (37 bp):
ATCTCCACTCCAATTCCACATAACACGCCAAATTACA
Found at i:18364120 original size:2 final size:2
Alignment explanation
Indices: 18364113--18364153 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
18364103 NNNNNNNNNN
18364113 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18364154 AAGAAAACAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:18365496 original size:2 final size:2
Alignment explanation
Indices: 18365480--18365515 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
18365470 AATATAACAA
*
18365480 AT AT CT AT A- 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 AT AT A
18365516 AAAGCTTGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:18366541 original size:20 final size:21
Alignment explanation
Indices: 18366516--18366562 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
18366506 AAATCTGCCA
* *
18366516 TCAAATCT-CCTTCCAGCTTC
1 TCAAATCTGCCATCCAACTTC
18366536 TCAAATCTGCCATCCAACTTC
1 TCAAATCTGCCATCCAACTTC
18366557 TCAAAT
1 TCAAAT
18366563 AGCTACTCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.28, C:0.36, G:0.04, T:0.32
Consensus pattern (21 bp):
TCAAATCTGCCATCCAACTTC
Found at i:18366547 original size:32 final size:34
Alignment explanation
Indices: 18366482--18366549 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 34
18366472 ATCTATTTCC
18366482 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
1 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
* *
18366516 TCAAATCT-CCTTCCAGC-TTCTCAAATCTGCCA
1 TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
18366548 TC
1 TC
18366550 CAACTTCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
32 16 0.50
33 8 0.25
34 8 0.25
ACGTcount: A:0.26, C:0.37, G:0.04, T:0.32
Consensus pattern (34 bp):
TCAAATCTCCCTTCCAACTTTCTAAAATCTGCCA
Found at i:18367327 original size:84 final size:84
Alignment explanation
Indices: 18367221--18367378 Score: 289
Period size: 84 Copynumber: 1.9 Consensus size: 84
18367211 TTATGTATGT
*
18367221 GCCGTTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
*
18367286 GCGGCGTTTCTATCCTAGC
66 GCAGCGTTTCTATCCTAGC
*
18367305 GCCGCTATTGGTTGGGGTTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
18367370 GCAGCGTTT
66 GCAGCGTTT
18367379 GGTTTTAAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 71 1.00
ACGTcount: A:0.17, C:0.16, G:0.31, T:0.36
Consensus pattern (84 bp):
GCCGCTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
GCAGCGTTTCTATCCTAGC
Found at i:18367402 original size:84 final size:84
Alignment explanation
Indices: 18367221--18367404 Score: 262
Period size: 84 Copynumber: 2.2 Consensus size: 84
18367211 TTATGTATGT
* *
18367221 GCCGTTATTGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
* **
18367286 GCGGCGTTTCTATCCTAGC
66 GCAGCGTTTCTATCAAAGC
* *
18367305 GCCGCTATTGGTTGGGGTTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
1 GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
* * *
18367370 GCAGCGTTTGGTTTTAAAGC
66 GCAGCGTTT-CTATCAAAGC
18367390 GCCGCTA-AGGTTGGG
1 GCCGCTATAGGTTGGG
18367405 TTTTTTGCGG
Statistics
Matches: 90, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 78 0.87
85 12 0.13
ACGTcount: A:0.17, C:0.16, G:0.32, T:0.35
Consensus pattern (84 bp):
GCCGCTATAGGTTGGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCACTAATGTTAAGGTATTTA
GCAGCGTTTCTATCAAAGC
Found at i:18368242 original size:21 final size:21
Alignment explanation
Indices: 18368200--18368243 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
18368190 GTATGGATTA
* *
18368200 GGGTTTGGGATTAAGGTTTAG
1 GGGTTGGGGATTAAGGTCTAG
* *
18368221 GGGTTGGGGGTTAGGGTCTAG
1 GGGTTGGGGATTAAGGTCTAG
18368242 GG
1 GG
18368244 TTACGGTCTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.02, G:0.52, T:0.32
Consensus pattern (21 bp):
GGGTTGGGGATTAAGGTCTAG
Found at i:18368244 original size:13 final size:13
Alignment explanation
Indices: 18368228--18368262 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
18368218 TAGGGGTTGG
18368228 GGGTTAGGGTCTA
1 GGGTTAGGGTCTA
*
18368241 GGGTTACGGTCTA
1 GGGTTAGGGTCTA
18368254 GGGTTAGGG
1 GGGTTAGGG
18368263 GTTAGGGGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.14, C:0.09, G:0.49, T:0.29
Consensus pattern (13 bp):
GGGTTAGGGTCTA
Found at i:18368268 original size:13 final size:13
Alignment explanation
Indices: 18368197--18368269 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
18368187 CAGGTATGGA
* *
18368197 TTAGGGTTTGGGA
1 TTAGGGTTAGGGG
*
18368210 TTAAGGTTTAGGGG
1 TT-AGGGTTAGGGG
*
18368224 TTGGGGGTTA-GGG
1 TT-AGGGTTAGGGG
*
18368237 TCTAGGGTTA-CGG
1 T-TAGGGTTAGGGG
18368250 TCTAGGGTTAGGGG
1 T-TAGGGTTAGGGG
18368264 TTAGGG
1 TTAGGG
18368270 GTCAAGGATT
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
13 29 0.60
14 19 0.40
ACGTcount: A:0.15, C:0.04, G:0.48, T:0.33
Consensus pattern (13 bp):
TTAGGGTTAGGGG
Found at i:18368315 original size:14 final size:14
Alignment explanation
Indices: 18368214--18368343 Score: 54
Period size: 14 Copynumber: 9.4 Consensus size: 14
18368204 TTGGGATTAA
*
18368214 GGTTTAGGGGTTGG
1 GGTTTAGGGTTTGG
* * *
18368228 GGGTTAGGGTCTAG
1 GGTTTAGGGTTTGG
* * *
18368242 GG-TTACGGTCTAG
1 GGTTTAGGGTTTGG
*
18368255 GG-TTAGGGGTTAGG
1 GGTTTA-GGGTTTGG
** *
18368269 GGTCAAGGATTTGG
1 GGTTTAGGGTTTGG
* *
18368283 GATTT-GGGGTTGG
1 GGTTTAGGGTTTGG
*
18368296 TAGTTTAGGGTTTGG
1 -GGTTTAGGGTTTGG
18368311 GGTTT-GTGAG-TTGG
1 GGTTTAG-G-GTTTGG
*
18368325 GGTTTGGGGTTTGG
1 GGTTTAGGGTTTGG
18368339 GGTTT
1 GGTTT
18368344 GGGATTAAGG
Statistics
Matches: 86, Mismatches: 22, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
13 23 0.27
14 53 0.62
15 10 0.12
ACGTcount: A:0.11, C:0.03, G:0.49, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGTTTGG
Found at i:18368336 original size:21 final size:21
Alignment explanation
Indices: 18368278--18368346 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
18368268 GGGTCAAGGA
* *
18368278 TTTGGGATTTGGGGTTGGTAG
1 TTTGGGGTTTGGGGTTTGTAG
*
18368299 TTTAGGGTTTGGGGTTTGTGAG
1 TTTGGGGTTTGGGGTTTGT-AG
**
18368321 -TTGGGGTTTGGGGTTTGGGG
1 TTTGGGGTTTGGGGTTTGTAG
18368341 TTTGGG
1 TTTGGG
18368347 ATTAAGGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 1 0.03
21 37 0.93
22 2 0.05
ACGTcount: A:0.06, C:0.00, G:0.51, T:0.43
Consensus pattern (21 bp):
TTTGGGGTTTGGGGTTTGTAG
Found at i:18368344 original size:14 final size:14
Alignment explanation
Indices: 18368278--18368346 Score: 70
Period size: 14 Copynumber: 4.9 Consensus size: 14
18368268 GGGTCAAGGA
*
18368278 TTTGGGATTTGGGG
1 TTTGGGGTTTGGGG
* *
18368292 -TTGGTAGTTTAGGG
1 TTTGG-GGTTTGGGG
*
18368306 TTTGGGGTTTGTGAG
1 TTTGGGGTTTG-GGG
18368321 -TTGGGGTTTGGGG
1 TTTGGGGTTTGGGG
18368334 TTTGGGGTTTGGG
1 TTTGGGGTTTGGG
18368347 ATTAAGGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 6 0.14
14 32 0.73
15 6 0.14
ACGTcount: A:0.06, C:0.00, G:0.51, T:0.43
Consensus pattern (14 bp):
TTTGGGGTTTGGGG
Found at i:18368388 original size:15 final size:15
Alignment explanation
Indices: 18368348--18368390 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
18368338 GGGTTTGGGA
18368348 TTAAGG-TTTAGGGG
1 TTAAGGATTTAGGGG
*
18368362 TTAAGGACTTAGGGG
1 TTAAGGATTTAGGGG
* *
18368377 TTATGTATTTAGGG
1 TTAAGGATTTAGGG
18368391 TTTGAGGTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 6 0.25
15 18 0.75
ACGTcount: A:0.23, C:0.02, G:0.37, T:0.37
Consensus pattern (15 bp):
TTAAGGATTTAGGGG
Found at i:18369259 original size:23 final size:24
Alignment explanation
Indices: 18369233--18369289 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
18369223 CACTTAGCCG
18369233 AAATTCCCCCCAAATTAT-CCCAA
1 AAATTCCCCCCAAATTATCCCCAA
* *
18369256 AAATTCCCCCCGAATTTTCCCCCAA
1 AAATTCCCCCCAAATTAT-CCCCAA
18369281 AAA-TCCCCC
1 AAATTCCCCC
18369290 AATTCTAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 16 0.53
24 6 0.20
25 8 0.27
ACGTcount: A:0.33, C:0.44, G:0.02, T:0.21
Consensus pattern (24 bp):
AAATTCCCCCCAAATTATCCCCAA
Found at i:18369770 original size:12 final size:12
Alignment explanation
Indices: 18369755--18369794 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
18369745 TGTAATGCTA
18369755 TTTGTTCATAAT
1 TTTGTTCATAAT
18369767 TTTGTT-ACTAAT
1 TTTGTTCA-TAAT
*
18369779 TTTGTTCATAAG
1 TTTGTTCATAAT
18369791 TTTG
1 TTTG
18369795 AAACTGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (12 bp):
TTTGTTCATAAT
Found at i:18370002 original size:14 final size:14
Alignment explanation
Indices: 18369970--18369996 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18369960 TTGAAACTTT
18369970 AAATTTAAATTTTA
1 AAATTTAAATTTTA
18369984 AAATTTAAATTTT
1 AAATTTAAATTTT
18369997 GTAATTATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATTTAAATTTTA
Found at i:18371708 original size:16 final size:16
Alignment explanation
Indices: 18371685--18372026 Score: 107
Period size: 16 Copynumber: 21.3 Consensus size: 16
18371675 GTCGGACTTG
*
18371685 CATAACTTATATAATA
1 CATAACTTACATAATA
*
18371701 CTTAACTTACATAATA
1 CATAACTTACATAATA
18371717 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
18371734 CATAA--TA-AGT--TA
1 CATAACTTACA-TAATA
*
18371746 CATAA--T--ATTATA
1 CATAACTTACATAATA
*
18371758 CATAACTCACATAACTA
1 CATAACTTACATAA-TA
*
18371775 AATGAA-TTA-ATATTATA
1 CAT-AACTTACATA--ATA
* ** * *
18371792 CATTAACTTGTCGGACTTG
1 CA-TAACTT-ACATA-ATA
**
18371811 CATAACTTATTTAATA
1 CATAACTTACATAATA
*
18371827 CTTAACTTACATAACTTA
1 CATAACTTACATAA--TA
*
18371845 CTTAACTTACATAATA
1 CATAACTTACATAATA
18371861 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
18371878 CATAA--TA-AGT--TA
1 CATAACTTACA-TAATA
*
18371890 CATAA--T--ATTATA
1 CATAACTTACATAATA
*
18371902 CATAACTCACATAACTA
1 CATAACTTACATAA-TA
*
18371919 AATGAA-TTA-ATATTATA
1 CAT-AACTTACATA--ATA
* ** * *
18371936 CATTAACTTGTCGGACTTG
1 CA-TAACTT-ACATA-ATA
*
18371955 CATAACTTATATAATA
1 CATAACTTACATAATA
*
18371971 CTTAACTTACATAACTTA
1 CATAACTTACATAA--TA
18371989 CATAACTTACATAATA
1 CATAACTTACATAATA
18372005 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
18372022 CATAA
1 CATAA
18372027 TAAGTTACAT
Statistics
Matches: 245, Mismatches: 44, Indels: 73
0.68 0.12 0.20
Matches are distributed among these distances:
10 2 0.01
11 2 0.01
12 28 0.11
13 2 0.01
14 2 0.01
15 6 0.02
16 98 0.40
17 42 0.17
18 55 0.22
19 6 0.02
20 2 0.01
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:18371843 original size:9 final size:9
Alignment explanation
Indices: 18371829--18372018 Score: 89
Period size: 9 Copynumber: 21.3 Consensus size: 9
18371819 ATTTAATACT
18371829 TAACTTACA
1 TAACTTACA
*
18371838 TAACTTACT
1 TAACTTACA
18371847 TAACTTACA
1 TAACTTACA
18371856 TAA--TACA
1 TAACTTACA
18371863 TAACTTACA
1 TAACTTACA
*
18371872 TAA-TAACATAA
1 TAACTTAC---A
*
18371883 TAAGTTACA
1 TAACTTACA
*
18371892 TAATATTATACA
1 T-A-ACT-TACA
*
18371904 TAACTCACA
1 TAACTTACA
*
18371913 TAAC-TAAA
1 TAACTTACA
18371921 TGAA-TTA-A
1 T-AACTTACA
*
18371929 T-ATTATACA
1 TAACT-TACA
*
18371938 TTAACTTGTC-
1 -TAACTT-ACA
** *
18371948 GGACTTGCA
1 TAACTTACA
*
18371957 TAACTTATA
1 TAACTTACA
*
18371966 TAA--TACT
1 TAACTTACA
18371973 TAACTTACA
1 TAACTTACA
18371982 TAACTTACA
1 TAACTTACA
18371991 TAACTTACA
1 TAACTTACA
18372000 TAA--TACA
1 TAACTTACA
18372007 TAACTTACA
1 TAACTTACA
18372016 TAA
1 TAA
18372019 TAACATAATA
Statistics
Matches: 138, Mismatches: 21, Indels: 44
0.68 0.10 0.22
Matches are distributed among these distances:
6 1 0.01
7 20 0.14
8 11 0.08
9 83 0.60
10 5 0.04
11 10 0.07
12 8 0.06
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.35
Consensus pattern (9 bp):
TAACTTACA
Found at i:18371862 original size:25 final size:24
Alignment explanation
Indices: 18371834--18371884 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
18371824 ATACTTAACT
* *
18371834 TACATAACTTACTTAACTTACATAA
1 TACATAACTTACATAA-TAACATAA
18371859 TACATAACTTACATAATAACATAA
1 TACATAACTTACATAATAACATAA
18371883 TA
1 TA
18371885 AGTTACATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (24 bp):
TACATAACTTACATAATAACATAA
Found at i:18371984 original size:25 final size:25
Alignment explanation
Indices: 18371950--18372026 Score: 86
Period size: 25 Copynumber: 3.0 Consensus size: 25
18371940 AACTTGTCGG
* * *
18371950 ACTTGCATAACTTATATAATACTTA
1 ACTTACATAACTTACATAATACATA
18371975 ACTTACATAACTTACATAACTTACATA
1 ACTTACATAACTTACATAA--TACATA
18372002 A--TACATAACTTACATAATAACATA
1 ACTTACATAACTTACATAAT-ACATA
18372026 A
1 A
18372027 TAAGTTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
23 1 0.02
24 6 0.13
25 33 0.72
27 6 0.13
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACATA
Found at i:18371993 original size:34 final size:34
Alignment explanation
Indices: 18371950--18372026 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 34
18371940 AACTTGTCGG
* * *
18371950 ACTTGCATAACTTATATAATACTTAACTTACATA
1 ACTTACATAACTTACATAATACATAACTTACATA
18371984 ACTTACATAACTTACATAATACATAACTTACATA
1 ACTTACATAACTTACATAATACATAACTTACATA
*
18372018 A-TAACATAA
1 ACTTACATAA
18372027 TAAGTTACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 7 0.18
34 32 0.82
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (34 bp):
ACTTACATAACTTACATAATACATAACTTACATA
Found at i:18372993 original size:10 final size:9
Alignment explanation
Indices: 18372974--18373008 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
18372964 TAATATGAAT
18372974 TTTATTATA
1 TTTATTATA
18372983 TTTATTGATA
1 TTTATT-ATA
18372993 TTTATTATA
1 TTTATTATA
18373002 TATTATT
1 T-TTATT
18373009 CATTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 10 0.42
10 14 0.58
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTATTATA
Found at i:18373020 original size:24 final size:21
Alignment explanation
Indices: 18372971--18373020 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 21
18372961 GAATAATATG
*
18372971 AATTTTATTATATTTATTGAT
1 AATTTTATTATATTTATTCAT
18372992 -A-TTTATTATATATTATTCATTT
1 AATTTTATTATAT-TTATTCA--T
18373014 AATTTTA
1 AATTTTA
18373021 AATATTATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
22 1 0.04
23 1 0.04
24 4 0.17
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
AATTTTATTATATTTATTCAT
Found at i:18373307 original size:43 final size:42
Alignment explanation
Indices: 18373194--18373397 Score: 146
Period size: 43 Copynumber: 4.8 Consensus size: 42
18373184 TTTTTATGAA
* * * *
18373194 AAGCGTCGCTAAAAGTCAAGGTCTTTTTGCGGCGTTTGCA-AG
1 AAGCGCCGCTAAAAGTCAAGGTC-TTTAGCGGCGTTTGTATTG
* * *
18373236 AAATCGCCGCTAAAAGT-TAGGGCATTTAGCGGCGTTTGTGATTG
1 -AAGCGCCGCTAAAAGTCAAGGTC-TTTAGCGGCGTTTGT-ATTG
* * * * *
18373280 AAGCGTCGCTAAAGGTCAAGGTCTTTAGTGGCGTTTGTAAATC
1 AAGCGCCGCTAAAAGTCAAGGTCTTTAGCGGCGTTTGT-ATTG
* * * * * *
18373323 AAGCGCCGCT-ATAGGCTAATGTATTTTGCGGCGTTTGTAGTGG
1 AAGCGCCGCTAAAAGTC-AAGGTCTTTAGCGGCGTTTGTA-TTG
*
18373366 AAGCGCCGCTAAAAGTCAAGCT-TTTAGCGGCG
1 AAGCGCCGCTAAAAGTCAAGGTCTTTAGCGGCG
18373398 CTCAAGTCAC
Statistics
Matches: 122, Mismatches: 33, Indels: 13
0.73 0.20 0.08
Matches are distributed among these distances:
42 30 0.25
43 83 0.68
44 9 0.07
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (42 bp):
AAGCGCCGCTAAAAGTCAAGGTCTTTAGCGGCGTTTGTATTG
Found at i:18373536 original size:22 final size:22
Alignment explanation
Indices: 18373493--18373536 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
18373483 TTGCGACGCT
*
18373493 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAGCCCTA
*
18373515 AAAAAGCGCCGCTAAATCCCTA
1 AAAAAGCGCCGCTAAAGCCCTA
18373537 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.30, G:0.18, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAGCCCTA
Found at i:18374750 original size:22 final size:22
Alignment explanation
Indices: 18374702--18374752 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 22
18374692 ATTTAATATA
*
18374702 AATATAATT-ATATATATAATT
1 AATATAATTAACATATATAATT
18374723 -AT-TAATTAACATATATAATT
1 AATATAATTAACATATATAATT
18374743 AATATAATTA
1 AATATAATTA
18374753 TTTTTTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 13 0.50
21 2 0.08
22 6 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATAATTAACATATATAATT
Found at i:18374765 original size:29 final size:32
Alignment explanation
Indices: 18374694--18374766 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 32
18374684 GGTTAGTGAT
18374694 TTAA-TATAA-ATATAATTATATATATAATTA
1 TTAATTATAATATATAATTATATATATAATTA
18374724 TTAATTA-ACATATATAA-T-TA-ATATAATTA
1 TTAATTATA-ATATATAATTATATATATAATTA
**
18374753 TTTTTTATAATATA
1 TTAATTATAATATA
18374767 ATATATTCGG
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
29 19 0.51
30 8 0.22
31 4 0.11
32 6 0.16
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
TTAATTATAATATATAATTATATATATAATTA
Found at i:18378853 original size:3 final size:3
Alignment explanation
Indices: 18378845--18378890 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
18378835 ATATGATACT
18378845 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
18378891 AACAGAAGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:18380474 original size:2 final size:2
Alignment explanation
Indices: 18380467--18380492 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
18380457 GCAATATGGC
18380467 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
18380493 CTTTTATCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18385831 original size:37 final size:37
Alignment explanation
Indices: 18385778--18385852 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
18385768 GAGACTCAAA
*
18385778 TGATTTATAATAAATTTTCGACTTTTCACCTATTAAT
1 TGATTTATAATAAATTTTCGAATTTTCACCTATTAAT
* * **
18385815 TGATTTATAATTAATTTTTGAATTTTCGTCTATTAAT
1 TGATTTATAATAAATTTTCGAATTTTCACCTATTAAT
18385852 T
1 T
18385853 ATAAACCTAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.53
Consensus pattern (37 bp):
TGATTTATAATAAATTTTCGAATTTTCACCTATTAAT
Found at i:18394554 original size:36 final size:36
Alignment explanation
Indices: 18394507--18394656 Score: 138
Period size: 36 Copynumber: 3.9 Consensus size: 36
18394497 GCTAAGCTAC
*
18394507 CACTTATCACTTTTTCACTTGATCAGATAAGTATAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
*
18394543 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCT
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--A--T
* * * *
18394587 ACCACTTATCACTTTGCCTCTTGATCAGATAAGTGTAG
1 --CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
* *
18394625 CTCTTATTACTTTGTCACTTGATCAGATAAGT
1 CACTTATCACTTTGTCACTTGATCAGATAAGT
18394657 GTAGCTAAAG
Statistics
Matches: 95, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
36 58 0.61
38 3 0.03
40 2 0.02
42 2 0.02
44 3 0.03
46 27 0.28
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAT
Found at i:18394594 original size:46 final size:46
Alignment explanation
Indices: 18394543--18394683 Score: 167
Period size: 46 Copynumber: 3.3 Consensus size: 46
18394533 ATAAGTATAT
*
18394543 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
18394589 CACTTATCACTTTGCCTCTTGATCAGATAA--GT-G-T--AGCT--
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
18394627 --CTTATTACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
18394671 TACTTATCACTTT
1 CACTTATCACTTT
18394684 ATTTGTTGAT
Statistics
Matches: 78, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
36 25 0.32
38 2 0.03
39 1 0.01
40 5 0.06
42 5 0.06
43 1 0.01
44 2 0.03
46 37 0.47
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:18394610 original size:82 final size:82
Alignment explanation
Indices: 18394463--18394683 Score: 331
Period size: 82 Copynumber: 2.7 Consensus size: 82
18394453 TTATGTATGG
* **
18394463 TCACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTTTCAC
1 TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCAC
18394525 TTGATCAGATAAGTATA
66 TTGATCAGATAAGTATA
* *
18394542 TCACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCTC
1 TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCAC
*
18394607 TTGATCAGATAAGTGTA
66 TTGATCAGATAAGTATA
* * * *
18394624 GCTCTTATTACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACTACTTATCACTTT
1 TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
18394684 ATTTGTTGAT
Statistics
Matches: 128, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
79 10 0.08
80 5 0.04
81 20 0.16
82 93 0.73
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (82 bp):
TCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGCCAC
TTGATCAGATAAGTATA
Found at i:18399112 original size:16 final size:15
Alignment explanation
Indices: 18399091--18399125 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
18399081 TATATATCAT
18399091 TATTAATTATATTTAA
1 TATTAATTAT-TTTAA
18399107 TATTAATTATTTTAA
1 TATTAATTATTTTAA
18399122 -ATTA
1 TATTA
18399126 TATAAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.21
15 5 0.26
16 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTAATTATTTTAA
Found at i:18399175 original size:90 final size:91
Alignment explanation
Indices: 18399068--18399243 Score: 300
Period size: 91 Copynumber: 1.9 Consensus size: 91
18399058 GGAGAGAATC
* * *
18399068 AATTTTATGAAATTATATATCATTATT-AATTATATTTAATATTAATTATTTTAAATTATATAAA
1 AATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAATTATACAAA
18399132 TTCATATAAGAAAATTTATTATCAAG
66 TTCATATAAGAAAATTTATTATCAAG
*
18399158 AATTTTATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATTTTAAATTATACAAA
1 AATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAATTATACAAA
*
18399223 TTCATATAAGATAATTTATTA
66 TTCATATAAGAAAATTTATTA
18399244 GTTATAATTA
Statistics
Matches: 80, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 26 0.32
91 54 0.68
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (91 bp):
AATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAATTATACAAA
TTCATATAAGAAAATTTATTATCAAG
Found at i:18399212 original size:26 final size:28
Alignment explanation
Indices: 18399158--18399218 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
18399148 TATTATCAAG
* *
18399158 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
18399186 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
18399212 AATTATA
1 AATTATA
18399219 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:18399403 original size:15 final size:15
Alignment explanation
Indices: 18399368--18399419 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
18399358 ATAAGAATTT
*
18399368 TATTAAATTAT-ATA
1 TATTTAATTATAATA
18399382 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
18399396 TATTTAATAATAAT-
1 TATTTAATTATAATA
18399410 TATGTTAATT
1 TAT-TTAATT
18399420 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:18399794 original size:45 final size:44
Alignment explanation
Indices: 18399713--18399803 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
18399703 ATCTCTATTC
*
18399713 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
18399757 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
18399802 CA
1 CA
18399804 CCTCTATTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Done.